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2276 Commits

Author SHA1 Message Date
eugeneswalker
a260bf038d boost: fix v1.78 build with oneapi (#30463) 2022-05-04 10:41:58 -07:00
Sergey Kosukhin
e0045a9daa cray platform: unload cray-mpich (#29898) 2022-04-12 08:50:20 -07:00
Tom Vander Aa
783615cacf intel-oneapi-mpi: set I_MPI_ROOT in setup_dependent_build_environment (#28890)
* setting I_MPI_ROOT is sometimes needed for find_package(MPI) in cmake to work
2022-02-15 08:23:04 -08:00
Thomas Madlener
a91621c6e1 fastjet add v3.3.4, fjcontrib add v1.045 (#22667) 2022-02-15 08:23:00 -08:00
estewart08
fe35ce1843 AMD rocm-openmp-extras: add v4.5.2 (#28790) 2022-02-14 10:14:44 -07:00
Toyohisa Kameyama
5353032eef Python: fix build with Fujitsu compiler (#28744) 2022-02-14 08:06:34 -06:00
Olli Lupton
dc57f987a7 py-{mizani,plotnine}: add packages. (#28841)
* py-{mizani,plotnine}: add packages.

* Add missing python dependency.
2022-02-14 03:20:29 -07:00
G-Ragghianti
aa6e725633 magma: move the execution of stand-alone tests to preferred directory (#28895) 2022-02-14 11:19:45 +01:00
John Wohlbier
9649246764 palisade-development: change fppe-logreg variant to point to a stable tag instead of a branch (#28717)
Co-authored-by: John Wohlbier <jgwohlbier@sei.cmu.edu>
2022-02-14 11:18:38 +01:00
Adam J. Stewart
b0658b8b03 py-pandas: add v1.4.1 (#28904) 2022-02-14 11:01:13 +01:00
Adam J. Stewart
e0a0f41ff9 py-mypy: add new versions (#28905) 2022-02-14 11:01:00 +01:00
Seth R. Johnson
3a4ab5f96f trilinos: disable UVM for 13.2+ (#28879) 2022-02-14 10:54:15 +01:00
Jen Herting
2c56cbd2bc [py-ctgan] fixed py-torchvision version range (#28892) 2022-02-13 22:26:10 -07:00
Harmen Stoppels
bece9fd823 Bump libtree (#28908) 2022-02-13 15:50:15 -08:00
Seth R. Johnson
97e4b43ddc go: mark conflict for ancient compilers (#28888) 2022-02-13 14:20:27 -07:00
Adam J. Stewart
cab0e4cb24 py-grpcio: add v1.43.0 (#28784) 2022-02-12 20:13:21 +01:00
Sarah Osborn
8c943261a2 hypre: add v2.24.0 (#28896) 2022-02-12 12:47:55 +01:00
Steve Leak
9f1db4e3a5 cray: add NVIDIA to the list of canonical names (#28246) 2022-02-12 10:45:46 +01:00
Adam Moody
0a25370e78 lwgrp/dtcmp packages: add version 1.0.5 and 1.1.4, respectively(#28817) 2022-02-11 18:52:51 -08:00
Olli Lupton
b840557d64 ffmpeg package: add libx264 variant; fix license variants. (#28808)
Prior to this patch, setting +gpl did not pass --enable-gpl and
did not allow GPL-only codecs to be enabled.
2022-02-11 18:40:35 -08:00
Brian Van Essen
fc7b7cfeab LBANN SW stack packages: gcc-toolchain and clang support (#28769)
* Added support to LBANN, Hydrogen, DiHydrogen, and Aluminum to capture
  a gcc-toolchain cxxflags argument and pass it to a CMAKE_CUDA_FLAG
  argument when set.  This helps deal with compiling with clang on
  systems with old base gcc installations.
* Added a dependency on py-scipy when enabling tests on LBANN.
* Updated the C++ standard for Hydrogen to C++17.
* Added a new variant +apps to enable (or disable) python packages that
  are used by applications in the LBANN repo, but are not strictly
  required for building and using LBANN.
* Added a run time dependency for both py-pytest and py-scipy so that
  they are activated in any environment.
* Added support for building LBANN, Hydrogen, and DiHydrogen with the
  IBM ESSL BLAS library.  This requires explicit identification of
  additional LAPACK libraries, since ESSL does not implement LAPACK, but
  is found by CMake.
* Fixed a bug in the LBANN dependency on OpenCV for Power architectures.
  The +powerpc variant is only required for GCC toolchains and causes
  Clang to break. Switched to only enabling when using %gcc on power.
2022-02-11 17:33:15 -08:00
Richarda Butler
af4d555c20 Update/caliper stand alone test compiler (#28526) 2022-02-11 15:02:40 -08:00
Simon Frasch
dc949a5bda spfft: fix missing hipFFT dependency with latest ROCm versions (#28880) 2022-02-11 14:17:40 -07:00
Teodor Nikolov
7ec9958b48 [rocm-smi-lib] Disable pdf generation with a patch (#28842)
- Installation often hangs building the documentation. This happens when
  doxygen and latex are found. To avoid the issue, comment-out that part
  of the code until an explicit cmake variable to disable documentation
  generation is available.
2022-02-11 13:47:50 -07:00
Cody Balos
853200c42d sundials: add new version and fix smoke tests (#28894)
* sundials: fix smoke tests

* sundials: add new version

* use cmake+make instead of make for tests, fix style

* use cmake_bin workaround from https://github.com/spack/spack/pull/28622
2022-02-11 12:23:58 -08:00
Dom Heinzeller
ef030ed0ee Bug fix for findutils: apply nonnull.patch only for versions 4.8.0+ (#28857) 2022-02-11 11:47:27 -07:00
haralmha
e365b05821 openloops: remove README from install prefix (#28767) 2022-02-11 11:11:33 -07:00
Glenn Johnson
61528c0b0a swftools package: patches for GCC@10: (#28296) 2022-02-11 09:54:53 -08:00
Danny McClanahan
e8838109d8 move typing_extensions.py back into typing.py =\ (#28549) 2022-02-11 09:52:01 -08:00
Mikael Simberg
389b24c4dc hpx: add conflict for Asio/CUDA (#27947)
* Add missing Asio versions from 1.16.0 to 1.21.0

* Add conflict for Asio/CUDA to HPX package

Co-authored-by: Mikael Simberg <mikael.simberg@iki.if>
2022-02-11 11:03:55 +01:00
Adam Moody
6c47aa06fc libyogrt: add v1.27 (#28835)
Signed-off-by: Adam Moody <moody20@llnl.gov>
2022-02-11 11:02:35 +01:00
haralmha
7c9e015c25 coral: add 3.3.10 and libtirpc dependency (#28802)
Co-authored-by: Harald Minde Hansen <harald.minde.hansen@cern.ch>
2022-02-11 09:58:57 +00:00
Adam J. Stewart
d0e2462908 py-fiona: add v1.8.21 (#28810) 2022-02-11 10:57:42 +01:00
Nils Vu
2d223fb275 spectre: add v2022.02.08 (#28834) 2022-02-11 09:53:16 +00:00
Wouter Deconinck
ba1b203848 assimp: add v5.2.1 (#28818) 2022-02-11 10:47:12 +01:00
ravil-mobile
94826a3f1d pspamm: new package (#28825)
Co-authored-by: ravil <ravil.dorozhinskii@tum.de>
2022-02-11 10:39:24 +01:00
ravil-mobile
73463f61d7 impalajit-llvm: add new package (#28826)
Co-authored-by: ravil <ravil.dorozhinskii@tum.de>
2022-02-11 10:36:46 +01:00
Adam Moody
dff770667e mpifileutils: add v0.11.1 (#28837)
Signed-off-by: Adam Moody <moody20@llnl.gov>
2022-02-11 10:26:56 +01:00
Gilles Grospellier
bb3a1dc7a5 icet: add variants to enable 'opengl' and shared libraries. (#27281) 2022-02-11 09:26:29 +00:00
Gilles Grospellier
a783f92fba dotnet-core-sdk: add v6.0.2. (#28843) 2022-02-11 10:21:03 +01:00
Sergey Kosukhin
b11767de48 eccodes: update package (#28849)
* eccodes: modernize the package

* eccodes: add patch fixing location of NetCDF

* eccodes: add variant 'shared'

* eccodes: enable building with NAG compiler

* eccodes: add property 'libs'

* eccodes: add variant 'definitions'

* eccodes: add variant 'samples'

* eccodes: add variant 'tools'
2022-02-11 10:10:31 +01:00
haralmha
1e494eec2f cool: add v3.3.10 (#28858)
Co-authored-by: Harald Minde Hansen <harald.minde.hansen@cern.ch>
Co-authored-by: Valentin Volkl <valentin.volkl@cern.ch>
2022-02-11 09:41:45 +01:00
Olivier Cessenat
5b71839127 subversion: add the external find feature using svn (#28862) 2022-02-11 09:40:29 +01:00
kwryankrattiger
a45c7c185b Ecp sdk update package contraints (#28693)
* ECP-SDK: Require HDF5 1.12

* ECP-SDK: Require SDK spec for SDK packages
2022-02-11 09:35:30 +01:00
Seth R. Johnson
c16ce9408e qt: patch version 5 on macOS 12 SDK (#28865)
Note that the SDK is not the same as the system version: using
apple-clang@13 is a better match than `os=monterey` since this actually
fails on bigsur as well, as long as xcode 13 is being used.
2022-02-11 09:31:37 +01:00
Ben Darwin
4c396d2cee minc-toolkit: fix perl dependencies (#28868) 2022-02-11 09:30:36 +01:00
Sergey Kosukhin
c80c92aa39 serialbox: add new package (#28872) 2022-02-11 09:23:47 +01:00
kwryankrattiger
cba918c081 Ascent: add dependency on adios2, remove deprecated variant (#28876)
Also update specs to be less complicated for dray/mfem/vtk-h.
Removed deprecated adios variant.
2022-02-11 09:14:06 +01:00
Bryan Herman
37728900e6 PVM package: fix missing install files and runtime env (#28851) 2022-02-10 18:03:11 -08:00
Carlos Bederián
b547819c40 ucx package: add version 1.12.0 (#28752) 2022-02-10 17:53:42 -08:00
Jon Rood
e9b50324cf trilinos: add rocm_rdc variant (#28873)
* Add rocm_rdc variant to trilinos.

* Fix syntax error.
2022-02-10 16:53:22 -07:00
eugeneswalker
8d8822f749 arborx +rocm: use hipcc and depend on rocthrust (#28875) 2022-02-10 15:39:40 -08:00
Seth R. Johnson
2fa6cd6d23 macOS: always set MACOSX_DEPLOYMENT_TARGET (#28797)
* core: Make platform environment an instance not class method

In preparation for accessing data constructed in __init__.

* macos: set consistent macosx deployment target

This should silence numerous warnings from mixed gcc/macos toolchains.

* perl: prevent too-new deployment target version

```
*** Unexpected MACOSX_DEPLOYMENT_TARGET=11
***
*** Please either set it to a valid macOS version number (e.g., 10.15) or to empty.
```

* Stylin'

* Add deployment target overrides to failing autoconf packages

* Move configure workaround to base autoconf package

This reverts commit 3c119eaf8b4fb37c943d503beacf5ad2aa513d4c.

* Stylin'

* macos: add utility functions for SDK

These aren't yet used but should probably be added to spack debug
report.
2022-02-10 23:22:30 +00:00
Adam J. Stewart
e502a264b5 MAGMA: declare cuda_arch support conflicts (#28811) 2022-02-10 16:52:23 -06:00
Harmen Stoppels
93e7efdc42 hsakmt-roct: dont look for libudev or compiler support libs (#28861) 2022-02-10 23:04:54 +01:00
Manuela Kuhn
16d1746fc3 py-llvmlite: add 0.38.0 (#28822) 2022-02-10 15:26:35 -06:00
Massimiliano Culpo
4437ff1fc3 Stabilize the concretization of ecp-data-vis-sdk by preferring conduit@0.7.2 (#28871) 2022-02-10 21:45:07 +01:00
Massimiliano Culpo
e6e109cbc5 ASP-based solver: reduce input facts and add heuristic (#28848)
* Remove node_target_satisfies/3 in favor of target_satisfies/2

When emitting input facts we don't need to couple target with
packages, but we can emit fewer facts independently and let
the grounder combine them.

* Remove compiler_version_satisfies/4 in favor of compiler_version_satisfies/3

When emitting input facts we don't need to couple compilers with
packages, but we can emit fewer facts independently and let
the grounder combine them.

* Introduce heuristic in the ASP-program

With heuristic we can drive clingo to make better
initial guesses, which lead to fewer choices and
conflicts in the overall solve
2022-02-10 11:37:10 -08:00
eugeneswalker
81a6d17f4c e4s: new specs: nccmp, nco, wannier90, lammps (#28833) 2022-02-10 10:47:19 -08:00
eugeneswalker
1e4c08f3a5 llvm-doe: rename @clacc to @develop.clacc for proper version matching (#28859) 2022-02-10 10:08:54 -08:00
Olivier Cessenat
8b39aa1b50 cvs: add the external find feature for cvs (#28863) 2022-02-10 12:35:22 -05:00
Christoph Junghans
5206bca19b lammps: add new versions (#27462)
* lammps: add new versions
2022-02-10 11:37:21 -05:00
Seth R. Johnson
92b26257f4 Fix CMakePackage.define for libs/headers (#28838)
The 'libs' property returned by a spec is not a list nor tuple.

Closes #28836.
2022-02-10 13:43:22 +00:00
luker
fa38af285c Adding support for rocmcc to cray-libsci package (#28601) 2022-02-10 10:50:33 +01:00
Greg Becker
130354b867 spack audit: fix spurious failures for target/platform conflicts (#28860) 2022-02-10 09:10:23 +01:00
Tamara Dahlgren
36ef59bc67 Tests: move has_test_method to spack.package (#28813) 2022-02-09 22:27:48 -08:00
Mark Grondona
634cba930e flux-core: add v0.34, v0.35 and deprecate v0.27.0 and earlier (#28852)
* flux-core: add versions 0.34.0 and 0.35.0

* flux-core: deprecate versions <= 0.27.0
2022-02-09 16:12:39 -08:00
Massimiliano Culpo
549c785227 Detecting "Cray" as "linux" during bootstrap (#28726)
* bootstrap: avoid detecting "Cray" and treat the platform as "linux"

* bootstrap: create a proper context manager to disable cray
2022-02-09 17:41:11 -05:00
Cory Bloor
a582670e15 rocrand: add spack test support and cleanup (#27437) 2022-02-09 14:30:56 -07:00
Robert Cohn
7f1759b52e Remove danvev as maintainer of intel packages (#28806)
* Remove danvev as maintainer of intel packages
* Update hash to trigger gitlab again
2022-02-09 09:51:36 -08:00
Olivier Cessenat
d4ca803fc5 freetype: add 2.11.1 and update Intel conflict (#28606) 2022-02-08 21:34:38 +01:00
Massimiliano Culpo
ffa58a20c6 CI: pin the version of pathlib to v2.3.6 (#28832) 2022-02-08 20:00:20 +00:00
G-Ragghianti
500e05ee50 SLATE package: tests (#28723)
This improves the stand-alone tests for slate by providing most
of the dependencies to the test framework and enabling stand-alone
tests on all versions except the oldest.
2022-02-08 10:30:57 -08:00
Toyohisa Kameyama
c1b51d6e99 fujitsu frontistr: New package (#28514)
* fujitsu-frontistr: new package.

* Add frontistr@5.3
Add fujitsu-frontistr static variant
style fix.

* update copyrigght year.
2022-02-07 18:42:26 -08:00
Michael Bentley
e97bffc3e8 flit: remove dependency from development branch version (#28789) 2022-02-07 18:35:18 -07:00
Adam J. Stewart
457fe842f0 py-scipy: add v1.8.0 (#28798) 2022-02-07 16:35:32 -07:00
Adam J. Stewart
1809a122ef py-pymumps: remove install_options (#28452) 2022-02-07 14:27:17 -08:00
Axel Huebl
8430e28a52 AMReX: +tiny_profile (#28785)
* AMReX: +tiny_profile

The tiny profiler options in AMReX are by default off but needed
by WarpX. Adds a new variant to control it.

* Add Erik Palmer as Co-Maintainer

... so he receives pings on updates of the package for review.
2022-02-07 15:15:25 -07:00
Tim Haines
c791ddc742 libiberty: add versions from v2.34.1 to v2.37 (#28792) 2022-02-07 06:12:08 -07:00
Harmen Stoppels
9a194dd0a9 Bump ca-certificates-mozilla (#28803) 2022-02-07 06:11:50 -07:00
VladimirUspenskii
0ce71b38b0 Add oneAPI packages from the 2022.1.2 release (#28750)
Co-authored-by: Robert Cohn <rscohn2@gmail.com>
Co-authored-by: Robert Cohn <robert.s.cohn@intel.com>
2022-02-07 14:01:50 +01:00
Stephen Sachs
14902a5821 intel-mkl: BLACS with intel-oneapi-mpi (#28476)
Identify the correct BLACS libaries when `intel-oneapi-mpi` is used.
2022-02-07 13:26:20 +01:00
Seth R. Johnson
efc35c2ffc gcc: fix build on apple-clang@13 (#28801) 2022-02-07 13:04:37 +01:00
Jordan Galby
37ae4c0fdb Support config variables in config.yaml extensions paths (#17772) 2022-02-07 11:40:52 +01:00
Adam J. Stewart
f3139555b1 py-torch: update dep constraints (#28743)
The version of the ONNX submodule was updated between the PyTorch
1.9 and 1.10 releases, which fixed builds with newer protobuf but
broke builds with older protobuf.

Also this adds minimum version reqs for numpy/typing-extensions
(which were not present before).
2022-02-06 21:33:12 -08:00
Harmen Stoppels
aa5e1a0723 git: new versions (#28777) 2022-02-06 10:58:17 -08:00
Seth R. Johnson
6e36c71d68 Fix GCC 8 build on macOS bigsur %apple-clang@12.0.5 (#28795)
* gcc: revise patch range on darwin

* gcc: add conflict to work around bootstrap failure

closes #23296 . See https://gcc.gnu.org/bugzilla/show_bug.cgi?id=100340
.

```
Comparing stages 2 and 3
Bootstrap comparison failure!
gcc/tree-ssa-operands.o differs
gcc/tree-ssanames.o differs
gcc/ipa-inline.o differs
gcc/tree-ssa-pre.o differs
gcc/gimple-loop-interchange.o differs
...
```
639 total differences.

* gcc: bump conflict up to correct later version
2022-02-06 07:48:16 -05:00
Axel Huebl
d82dcd35b3 WarpX: add v22.02 (#28742) 2022-02-04 23:53:51 -07:00
Toyohisa Kameyama
797c061743 openfdtd: add version 2.6.3, 2.7.1, 2.7.3 and support Fujitsu Compiler. (#28472) 2022-02-04 11:54:39 -08:00
Toyohisa Kameyama
c29e6dbd20 wrf: Add New version, support fujitsu compiler, refactor and bug fix. (#28567)
* wrf: Add version 4.3, support fujitsu compioler, output build log, and fix to build diffwrf.
2022-02-04 11:53:59 -08:00
Toyohisa Kameyama
cccd1ce376 atompaw: use autotoolsPackage and support Fujitsu compiler. (#28471)
* atompaw: use autotoolsPackage and support Fujitsu compiler.
2022-02-04 11:50:55 -08:00
Harmen Stoppels
73077f3a67 database: fix reindex with uninstalled deps (#28764)
* Fix reindex with uninstalled deps

When a prefix of a dep is removed, and the db is reindexed, it is added
through the dependent, but until now it incorrectly listed the spec as
'installed'.

There was also some questionable behavior in the db when the same spec
was added multiple times, it would always be marked installed.

* Always reserve path

* Only add installed spec's prefixes to install prefixes set

* Improve warning, and ensure ensure only ensures

* test: reindex with every file system remnant removed except for the old index; it should give a database with nothing installed, including records with installed==False,external==False,ref_count==0,explicit=True, and these should be removable from the database
2022-02-04 19:31:39 +00:00
Massimiliano Culpo
5881a03408 Use Spec.constrain to construct spec lists for stacks (#28783)
* stacks: add regression tests for matrix expansion

* Use constrain semantics to construct spec lists for stacks

* Fix semantics for constraining an anonymous spec. Add tests
2022-02-04 19:17:23 +00:00
Axel Huebl
d668dea97d WarpX/HiPACE: noacc PSATD also needs FFTW (#28756)
Forgot to add that `compute=noacc` also needs FFTW3 for PSATD builds.
2022-02-04 10:59:47 -08:00
Valentin Volkl
45a285a751 py-kubernetes: add new versions up to v21.7.0 (#28687)
* py-kubernetes: add new versions up to v21.7.0

* py-kubernetes: update python dependency
2022-02-04 11:25:10 -06:00
Marko Kabic
7af48f4570 Adding new package: COSTA (#28727) 2022-02-04 10:02:32 -07:00
Glenn Johnson
d0019d7049 cntk: fix build and add comments (#28676) 2022-02-04 10:56:21 -06:00
Adam J. Stewart
caa1a5cec7 py-mpi4py: fix install_options (#28759) 2022-02-04 11:22:11 +01:00
Axel Huebl
172ec0e3a1 py-warpx: needs no py-cmake (#28761)
Since in Spack we pull binaries out of the `warpx` package, we don't
need `py-cmake` to build `py-warpx`.
Generally, `py-cmake` in `pyproject.toml` is just a mean for us to
tell `pip` to make a `cmake` CLI tool available.
2022-02-04 11:21:32 +01:00
eugeneswalker
4c04a0c0b7 e4s ci: uncomment variorum following pr #28754 (#28763) 2022-02-04 11:15:35 +01:00
Adam J. Stewart
9ca4c10b34 py-numpy: add v1.22.2 (#28771) 2022-02-04 11:11:41 +01:00
Tim Haines
fda89b3b4c flit: add version for development branch (#28773) 2022-02-04 11:10:11 +01:00
Tim Haines
1ba6e27830 fpchecker: add version for master branch (#28774) 2022-02-04 11:09:22 +01:00
Tim Haines
9c686a12c1 pruners-ninja: Add version for master branch (#28765) 2022-02-03 14:59:42 -08:00
Weiqun Zhang
c7def4121a amrex: add v22.02 (#28757) 2022-02-03 14:37:52 -08:00
Pieter Ghysels
bdf37db9e4 STRUMPACK new versions 6.3.0, 6.2.1, 6.2.0 (#28762)
* Add new versions for STRUMPACK, newer ButterflyPACK dependency

* small fix
2022-02-03 12:42:36 -08:00
liuyangzhuan
f503b3770b Bump butterflypack versions to v.2.1.0 (#28758)
* added package gptune with all its dependencies: adding py-autotune, pygmo, py-pyaml, py-autotune, py-gpy, py-lhsmdu, py-hpbandster, pagmo2, py-opentuner; modifying superlu-dist, py-scikit-optimize

* adding gptune package

* minor fix for macos spack test

* update patch for py-scikit-optimize; update test files for gptune

* fixing gptune package style error

* fixing unit tests

* a few changes reviewed in the PR

* improved gptune package.py with a few newly added/improved dependencies

* fixed a few style errors

* minor fix on package name py-pyro4

* fixing more style errors

* Update var/spack/repos/builtin/packages/py-scikit-optimize/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* resolved a few issues in the PR

* fixing file permissions

* a few minor changes

* style correction

* minor correction to jq package file

* Update var/spack/repos/builtin/packages/py-pyro4/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* fixing a few issues in the PR

* adding py-selectors34 required by py-pyro4

* improved the superlu-dist package

* improved the superlu-dist package

* moree changes to gptune and py-selectors34 based on the PR

* Update var/spack/repos/builtin/packages/py-selectors34/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* improved gptune package: 1. addressing comments of tldahlgren in PR 26936; 2. adding variant openmpi

* fixing style issue of gptune

* changing file mode

* improved gptune package: add variant mpispawn which depends on openmpi; add variant superlu and hypre for installing the drivers; modified hypre package file to add a gptune variant

* fixing style error

* corrected pddrive_spawn path in gptune test; enforcing gcc>7

* fixing style error

* setting environment variables when loading gptune

* removing debug print in hypre/package.py

* adding superlu-dist v7.2.0; fixing an issue with CMAKE_INSTALL_LIBDIR

* changing site_packages_dir to python_platlib

* not using python3.9 for py-gpy, which causes due to dropped support of tp_print

* more replacement of site_packages_dir

* fixing a few dependencies in gptune; added a gptune version

* adding url for gptune

* minor correction of gptune

* updating versions in butterflypack

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-02-03 12:42:21 -08:00
Matthieu Dorier
4a308d0d4b [py-xonsh] added py-xonsh package (#28746)
* [py-xonsh] added py-xonsh package

* [py-xonsh] change dependency to python 3.6

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-02-03 14:09:10 -06:00
eugeneswalker
48b2cf54cf variorum: needs jansson (#28754) 2022-02-03 10:45:19 -08:00
Mosè Giordano
5208fcf1ea libblastrampoline: Add versions 4.1.0, 5.0.0, 5.0.1 (#28732) 2022-02-03 11:55:48 +01:00
Chris White
98fe047671 Sundials: update version sha, add -D to cmake option (#28720) 2022-02-03 11:48:18 +01:00
Satish Balay
95f77dacd6 petsc, py-petsc4py: add versions 3.16.4 (#28729) 2022-02-03 11:47:34 +01:00
Harmen Stoppels
4134b318ac libgit2: add mmap variant, disabling it makes it work on filesystems that do not implement mmap (#28520) 2022-02-03 11:31:53 +01:00
liuyangzhuan
932408ac2b gptune: add v2.1.0 (#28739) 2022-02-03 11:02:46 +01:00
kwryankrattiger
5a640f9063 conduit: convert HDF5 constaint to compile flag (#28735) 2022-02-03 10:43:39 +01:00
Greg Sjaardema
7c5db7678a seacas: add v2022-01-27 (#28738) 2022-02-03 10:41:48 +01:00
Cyrus Harrison
cdf17fdfe5 conduit: add v0.8.2 (#28730) 2022-02-03 10:39:46 +01:00
Harmen Stoppels
2ada0fa5a2 julia: fix gfortran version detection (#28741) 2022-02-03 10:37:14 +01:00
Nils Vu
18b83c3833 Change my name (#28737) 2022-02-02 15:21:45 -08:00
Glenn Johnson
22b7d9cf67 llvm: patch for gcc-11 (#28547)
* llvm: patch for gcc-11

- added llvm-gcc11.patch
- adjusted version constraints on existing missing-includes patch.

* remove unnecessary comment

Co-authored-by: Tom Scogland <scogland1@llnl.gov>
2022-02-02 13:32:16 -07:00
Adam J. Stewart
fa8c9e4939 py-torch: avoid build issue with newer protobuf (#28721) 2022-02-02 12:23:47 -07:00
Adam J. Stewart
3576e5f3d6 Revert "Deprecate Python 2 installations" (#28411)
This reverts commit 7b76e3982f.
2022-02-02 10:12:33 -08:00
Massimiliano Culpo
cd04109e17 Add a "sticky" property to variants (#28630)
* Add sticky variants

* Add unit tests for sticky variants

* Add documentation for sticky variants

* Revert "Revert 19736 because conflicts are avoided by clingo by default (#26721)"

This reverts commit 33ef7d57c1.

* Add stickiness to "allow-unsupported-compiler"
2022-02-02 10:05:24 -08:00
dependabot[bot]
dd7acecf3d build(deps): bump docker/build-push-action from 2.8.0 to 2.9.0 (#28719)
Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 2.8.0 to 2.9.0.
- [Release notes](https://github.com/docker/build-push-action/releases)
- [Commits](1814d3dfb3...7f9d37fa54)

---
updated-dependencies:
- dependency-name: docker/build-push-action
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2022-02-02 11:57:31 +01:00
Carlos Bederián
d3bfdcb566 gromacs: Add versions 2021.4 and 2021.5 (#28722) 2022-02-02 03:44:12 -07:00
Marcus Boden
e1ec08b749 Snakemake: add v6.15.1 (#28724) 2022-02-02 10:32:36 +01:00
Glenn Johnson
3b5afef842 new packages: py-rst2pdf and py-smartypants (#28697)
* new packages: py-rst2pdf and py-smartypants

The py-smartypants package is a dependency of py-rst2pdf.

* add missing dependencies
2022-02-01 23:56:09 -07:00
Sebastian Pipping
b9bb303063 expat: Add latest release 2.4.4 with security fixes (#28692) 2022-02-01 16:29:29 -07:00
Adam J. Stewart
7144af9c3a py-argparse: skip dep for newer Python (#28718) 2022-02-01 15:38:11 -07:00
Rao Garimella
50c6075509 Jali package: add version 1.1.6 (#28545)
Boost dependency is only needed for @:1.1.5
2022-02-01 14:22:24 -08:00
Harmen Stoppels
b93b64ca67 TermStatusLine: fix python 2.7 and add test (#28715)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2022-02-01 21:59:29 +01:00
Massimiliano Culpo
7c31d4d279 CI: macOS try to build latest GCC (#28709) 2022-02-01 21:29:27 +01:00
Nils Leif Fischer
4a29512113 py-rich: fix installation with poetry (#28710) 2022-02-01 14:19:40 -06:00
Teodor Nikolov
9cf20b9d32 Sarus: Add 1.4.1, use commits instead of tarballs, tests (#28705)
- To retrieve the correct spack version we need to get it from the git
  repo.

- Recommend installing the package with root for production

- Add Tomas as maintainer to sarus' spack package

- Add the option to disable unit tests in latest versions
2022-02-01 11:49:58 -07:00
Harmen Stoppels
165f686400 lua: add fetcher for luarocks (#28707) 2022-02-01 10:44:51 -07:00
Jose E. Roman
427d281d15 SLEPc: add v3.16.2 (#28706) 2022-02-01 09:38:28 -07:00
estewart08
0a595d488b rocm-openmp-extras: add v4.3.1 and v4.5.0 (#27653) 2022-02-01 16:39:33 +01:00
kwryankrattiger
099a16ed8f ParaView/VTK: Update hdf5 constraints (#28691)
hdf5@1.10: is required for the new version of vtkHDFReader
2022-02-01 09:50:11 -05:00
kwryankrattiger
eb7bc7fc4b Ascent/Conduit: Update the +fortran build config (#28646)
Do not silently turn off fortran support based on checking if
a fortran compiler exists. Let the build fail if there is no
working fortran compiler.
2022-02-01 07:44:48 -07:00
Adam J. Stewart
bdfcf7c92b py-torchgeo: specify libtiff variants (#28681) 2022-02-01 08:43:54 -06:00
Cyrus Harrison
3f6d045c53 conduit: add new variant and hcfg entry (#27822) 2022-02-01 13:53:30 +01:00
Cyrus Harrison
b300a9d7a5 dray: add new variant and host config entry (#28598) 2022-02-01 13:52:12 +01:00
Torbjörn Lönnemark
218b1c153c p7zip: fix build on gcc 11 (#28376)
Fixes the following build failure when building with gcc 11:

         478    ../../../../CPP/7zip/Archive/Wim/WimHandler.cpp: In member function 'virtual LONG NArchive::NWim::CHandler::GetArchiveProperty(PROPID, PROPVARIANT*)':
      >> 479    ../../../../CPP/7zip/Archive/Wim/WimHandler.cpp:308:11: error: use of an operand of type 'bool' in 'operator++' is forbidden in C++17
         480      308 |           numMethods++;
         481          |           ^~~~~~~~~~
      >> 482    ../../../../CPP/7zip/Archive/Wim/WimHandler.cpp:318:9: error: use of an operand of type 'bool' in 'operator++' is forbidden in C++17
         483      318 |         numMethods++;
         484          |         ^~~~~~~~~~
2022-02-01 12:26:00 +01:00
Nils Leif Fischer
c3bad2a935 gettext: find external (#28610) 2022-02-01 12:25:02 +01:00
Brent Huisman
dedf4a1470 Add version v0.6 to Arbor package. (#28628)
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2022-02-01 12:24:28 +01:00
Sergey Kosukhin
0e28356aba Eccodes: update urls and add new versions (#28614) 2022-02-01 12:20:06 +01:00
Massimiliano Culpo
80a3f01bbb gcc: allow building 11.2.0 on macOS (#28662) 2022-02-01 11:19:24 +00:00
Cyrus Harrison
f5a70dece8 ascent: add patch for gcc 10 + 11 (#28592) 2022-02-01 12:18:48 +01:00
Mikhail Titov
d7e7542486 Update package versions: RADICAL-Cybertools (RE, RP, RS, RU) (#28523)
* rct: update packages (RE, RP, RS, RU) with new versions

* rct: minor version release for RP

* rct: fixed versions for dependencies (RS and RU)
2022-02-01 11:35:14 +01:00
Glenn Johnson
a3f0c3ca93 saga-gis: tweak dependencies and deprecate some versions (#28677)
- deprecate versions 2 and 3
- set needed opencv variants
- adjust proj constraint
- patch header path for opencv
2022-02-01 11:09:50 +01:00
Glenn Johnson
ab2187780b libdc1394: update dependencies and add libraw1394 dependency (#28675) 2022-02-01 11:09:00 +01:00
Adam J. Stewart
7ac66547da py-black: add v22.1.0 (#28680) 2022-02-01 11:06:24 +01:00
Pat Riehecky
4b52f0e4d7 jsonnet: add new package (#28645)
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-02-01 10:22:52 +01:00
Mikael Simberg
d8dcb91297 pika: add v0.1.0 (#28684)
Co-authored-by: Mikael Simberg <mikael.simberg@iki.if>
2022-02-01 10:20:01 +01:00
Valentin Volkl
5e8ef57a82 alpaka: add v0.8.0 (#28689) 2022-02-01 10:19:40 +01:00
Vicente Bolea
c9e135729c vtk-m: add v1.7.1 release (#28690) 2022-02-01 10:19:19 +01:00
Nils Leif Fischer
8ccc4df6ff charmpp: default backend to 'multicore' on macOS (#28443) 2022-02-01 10:17:48 +01:00
Tom Scogland
545a429646 llvm: add llvm_config helper (#28670)
Add a helper as a base to build better libs etc. methods
2022-02-01 09:58:39 +01:00
Paul Kuberry
bff5d253cf xyce: add 'plugin' variant (#28698) 2022-02-01 09:49:57 +01:00
Ryan Marcellino
3456a355ce maven: add v3.8.4 (#28699) 2022-02-01 09:48:52 +01:00
Dylan Jude
aedb106c5f samrai: add "--enable-shared" option as "+shared" (#28695) 2022-02-01 09:48:19 +01:00
Adam J. Stewart
a4a23ff713 py-torch: fix python_platlib reference (#28565) 2022-02-01 09:44:08 +01:00
Adam J. Stewart
728ac61bd8 pygmo: fix build (#28702) 2022-02-01 09:38:06 +01:00
Glenn Johnson
21524f5149 opencv: add new version, variant, and patch (#27374)
* opencv: add new version, variant, and patch

- added version 4.5.4
- added tesseract variant
- added patch to not add system paths

* Add leptonica depends and contrib conflicts

* Add dependencies for 1394 support

- new package: libraw1394
- add sdl dependency to libdc1394
- add conflict for openjpeg and jasper

* Adjust dependencies and conflicts for opencv modules

* rewrite of opencv

- all prebuilt apps are now variants and can be installed
- core is no longer a variant. It was always built anyway so it was not
  really a variant.
- contrib is no longer a variant. All of the contrib modules are now
  available as variants.
- components that can not be built with Spack are no longer variants.
  They are set to 'off' to prevent pulling from system.
- handle the case where a module and a component have the same name
- use `with when` framework
- adjust dependencies and conflicts
- new package: libraw1394
- have libdc1394 depend on libraw1394
- patch to find clp
- patch to find onnx
- patch for cvv to find Qt
- format with black

* Incorporate recommended changes

- fix variants and dependencies on packages that depend on opencv
- remove opencv-3.2 and patches
- add some new patches to handle different versions
- cntk needs further work
- the openvslam package was markde deprecated as it is no longer an
  active project and the repository has no code

* Remove gmake dependency.

* Remove sdl support

SDL is only used in an example case, but the examples are not built.

* remove openvslam

* Remove opencv+flann variant from 3dtk

* Back out cfitsio constraint from py-astropy

* remove opencv+flann variant from dlib

* remove boost constraint from 3dtk

* Remove non-opencv related bohrium changes

* Adjustments for cntk

- protobuf constraint at version 3.10
- need specific variants for opencv
- improve patch

* Deprecate CNTK package

* variant tweaks

- added appropriate conflicts for cublas
- made cuda/cudev relationship explicit
- moved openx to pending components as it needs an openvx package

* fix isort style error

* Use date version from kaldi rather than commit

* Revert changes from a bad rebase

* Add +flann to 3dtk and dlib

* Use compression support with libtiff

* remove `+datasets` from opencv dependency 

The py-torchgeo package does not need opencv+datasets.

* fix typo

zip --> zlib
2022-01-31 21:24:03 -06:00
eugeneswalker
6e99f328b6 e4s ci: add spec: gptune (#28604) 2022-01-31 18:44:25 -08:00
eugeneswalker
d6d29f7c09 mesa18: depends on python@3.8.99 max (#28345) 2022-01-31 13:20:33 -07:00
Pat Riehecky
a5d0687115 Update Packages: py-asgiref, py-h11, py-websockets (#28649) 2022-01-31 14:13:44 -06:00
iarspider
a909f2d910 Add checksum for py-cryptography 3.2.1 (#28685) 2022-01-31 14:11:41 -06:00
liuyangzhuan
3b64ca30c7 changing site_packages_dir to python_platlib for gptune (#28669)
* added package gptune with all its dependencies: adding py-autotune, pygmo, py-pyaml, py-autotune, py-gpy, py-lhsmdu, py-hpbandster, pagmo2, py-opentuner; modifying superlu-dist, py-scikit-optimize

* adding gptune package

* minor fix for macos spack test

* update patch for py-scikit-optimize; update test files for gptune

* fixing gptune package style error

* fixing unit tests

* a few changes reviewed in the PR

* improved gptune package.py with a few newly added/improved dependencies

* fixed a few style errors

* minor fix on package name py-pyro4

* fixing more style errors

* Update var/spack/repos/builtin/packages/py-scikit-optimize/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* resolved a few issues in the PR

* fixing file permissions

* a few minor changes

* style correction

* minor correction to jq package file

* Update var/spack/repos/builtin/packages/py-pyro4/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* fixing a few issues in the PR

* adding py-selectors34 required by py-pyro4

* improved the superlu-dist package

* improved the superlu-dist package

* moree changes to gptune and py-selectors34 based on the PR

* Update var/spack/repos/builtin/packages/py-selectors34/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* improved gptune package: 1. addressing comments of tldahlgren in PR 26936; 2. adding variant openmpi

* fixing style issue of gptune

* changing file mode

* improved gptune package: add variant mpispawn which depends on openmpi; add variant superlu and hypre for installing the drivers; modified hypre package file to add a gptune variant

* fixing style error

* corrected pddrive_spawn path in gptune test; enforcing gcc>7

* fixing style error

* setting environment variables when loading gptune

* removing debug print in hypre/package.py

* adding superlu-dist v7.2.0; fixing an issue with CMAKE_INSTALL_LIBDIR

* changing site_packages_dir to python_platlib

* not using python3.9 for py-gpy, which causes due to dropped support of tp_print

* more replacement of site_packages_dir

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-01-31 11:21:06 -08:00
Massimiliano Culpo
68cf57d0d0 Fix SECURITY.md file by adding v0.17.x to supported versions (#28661) 2022-01-31 10:04:06 -08:00
Harmen Stoppels
f080e593cb julia: add targets constraint to llvm (#28682) 2022-01-31 06:29:23 -07:00
Paul Kuberry
fff9a29401 trilinos: Fix cxxstd effects for Trilinos versions <13 (#28663) 2022-01-31 00:41:21 -07:00
Adam J. Stewart
1679274ac2 py-horovod: add py-tensorflow-estimator dependency (#28674) 2022-01-29 20:22:19 -06:00
Jen Herting
c78a754e5d New package: py-kaldiio (#28643)
* espnet first build with depends

* fixed flake8

* updated to lastest version and removed python dependency

* changed to pypi and version 2.17.2

* [py-kaldiio] depends on py-pytest-runner

* [py-kaldiio] updated copyright

Co-authored-by: Sid Pendelberry <sid@rit.edu>
2022-01-29 12:52:23 -06:00
Valentin Volkl
813a0d9b19 prmon: better testing, fix checksums (#28672)
* prmon: make sure integration tests do not run in parallel

Some integration tests fail if not run on an otherwise idle machine.

* prmon: run unittests based on googletest

* prmon: fix checksums
2022-01-29 14:32:57 +01:00
Seth R. Johnson
aece700e14 superlu: simplify cmake logic and fix cuda conflict (#28658)
* superlu-dist: use CMakePackage helper functions

* Fix #28609

It's OK to have CUDA in the dependency tree as long as it's not being
used for superlu-cuda.
2022-01-29 12:58:09 +00:00
Pat Riehecky
a98a261b74 Update Packages: py-celery py-kombu py-amqp py-pytz py-click-plugins (#28648) 2022-01-28 16:47:10 -07:00
Pat Riehecky
6f3670d1eb New Package: py-python-dotenv (#28651) 2022-01-28 14:23:25 -07:00
Pat Riehecky
f189e5eb1c Update Package: py-pre-commit (#28665) 2022-01-28 14:36:48 -06:00
Massimiliano Culpo
bc06c1206d macholib, altgraph: update vendored dependency (#28664) 2022-01-28 10:55:12 -08:00
Massimiliano Culpo
4bd761d1d5 Update actions/setup-python to latest version (#28634) 2022-01-28 14:17:59 +01:00
Graeme A Stewart
02b48f5206 prmon: add up to v3.0.1, add new maintainers (#28657)
* Update prmon package to latest versions

Add recent versions of the prmon package
Add the spdlog dependency for versions >=3
Add package developers as additional maintainers
Update name of development branch to 'main'

* Correct checksum for v3.0.1
2022-01-28 04:42:02 -07:00
Michele Martone
cce8f3faf5 librsb: added v1.2.0.11/v1.3.0.0 (#28637) 2022-01-28 11:46:54 +01:00
Tim Haines
5519289f1d fpchecker: add v0.3.5 (#28639)
Co-authored-by: Tim Haines <thaines@cs.wisc.edu>
2022-01-28 11:44:18 +01:00
Nils Leif Fischer
d80241a203 spectre: allow disabling debug symbols (#28511)
* spectre: allow disabling debug symbols

* spectre: fix PCH builds

* spectre: support builds with shared libs
2022-01-28 11:40:02 +01:00
Desmond Orton
1e1e3ae80a metabat: switch to CMakePackage, deprecate old versions (#28384) 2022-01-28 11:34:35 +01:00
kwryankrattiger
a3755e5c76 ParaView: Require Ninja for builds (#28650) 2022-01-28 11:30:23 +01:00
Satish Balay
4c3bc0d3dc slepc: switch from using -with-arpack-dir to --with-arpack-include/lib options (#28654)
Also save configure.log, make.log
2022-01-28 11:20:35 +01:00
Adam J. Stewart
46b9911289 py-torch: add v1.10.2 (#28653) 2022-01-28 11:01:17 +01:00
Vasileios Karakasis
e06319a3dc Add more ReFrame versions (#28655) 2022-01-28 02:42:07 -07:00
Desmond Orton
bf80a9f83a at-spi2-core: patch for version 2.40.1 and beyond (#28497)
at-spi2-core is automatically selecting dbus-broker and enabling systemd if it finds dbus-broker-launch which some systems might have even without systemd being part of the actual spack environment. This is not ideal for a spack package.
2022-01-28 10:40:26 +01:00
Tom Vander Aa
f7f7a168e9 ucx backtrace-detail variant (#28625)
ucx has the configure option --[enable|disable]-backtrace detail.
This option is not explicitely set by spack, causing problems on my system, because
./configure does not find the bfd.h header file / libbfd.so library.

Added variant + dependencies (binutils). Disabled by default
2022-01-28 10:35:10 +01:00
liuyangzhuan
80f92cfdde gptune: add variants (mpispawn, hypre) (#27733)
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-01-28 10:31:56 +01:00
Toyohisa Kameyama
693f0958b5 trilinos: version 12 cxxstd flags (#28582)
* trilinos: version 12 requires cxxstd=11

* trilinos: use cmake version 3.21 or old when trilinos version 12

* conflict cxxstd=17 and cmake@3.2.[01]

* trilinos: version 12 requires cxxstd=11.

* Trilinos_CXX11_FLAGS is set to ' ' to avoid inject C++11 flag.

* set Trilinos_CXX11_FLAGS only version 12 or older.
2022-01-28 01:29:18 -07:00
Seth R. Johnson
2fd26be988 Trilinos: minimize E4S CUDA build (#28591)
* trilinos: update dependencies

Use the tribits deps to clarify some dependencies, and group some together
using `with` statements, eliminating some transitive conflict duplication.

* trilinos: Restricit cuda incompatibility

* e4s: vastly reduce number of packages in trilinos-cuda build

Not clear who the customers of cuda-enabled trilinos are, or what options
they need, or which sets of options conflict...

* e4s: remove ~wrapper from trilinos+cuda
2022-01-27 21:08:15 -07:00
Jen Herting
405adce5ae New package: py-wordcloud (#28482)
* [py-wordcloud] created template

* [py-wordcloud]

- added dependencies
- added homepage
- added description
- removed fixmes
- updated copyright
2022-01-27 15:08:57 -07:00
Jen Herting
a2170c9e04 New package: py-spectral (#28481)
* simple build of spectral

* fixed trailing whitespace for style

* [py-spectral] updated copyright

* [py-spectral] runtime imports py-numpy

Co-authored-by: Sid Pendelberry <sid@rit.edu>
2022-01-27 14:57:14 -07:00
Jen Herting
bae2a2660e New package: py-deepecho (#28488)
* [py-deepecho] created template

* [py-deepecho]

- added dependencies
- added homepage
- added description
- removed fixmes
- updated copyright

* [py-deepecho] flake8

* [py-deepecho] removed .999

* [py-deepecho] added dependency on py-pytest-runner
2022-01-27 15:25:28 -06:00
Harmen Stoppels
08fb190264 python: 3.9.10, 3.10.2 (#28635) 2022-01-27 14:03:02 -07:00
Massimiliano Culpo
b9b1665cb2 Pin the version of "coverage" in CI to 6.2 (#28638)
Hotfix for coverage v6.3 blocking our CI workflows
2022-01-27 20:35:05 +01:00
Paul Kuberry
ec9748eaf3 xyce: Add cxxstd variant with only valid value of 11 (#28616) 2022-01-27 11:40:57 -05:00
Max Zeyen
28ea1bab68 gpi-space: add new package (#27989) 2022-01-27 07:35:20 -07:00
Gregory Lee
61ea456f5d conduit: add v0.8.1 and patch to add algorithm for std sort (#28618) 2022-01-27 12:26:18 +01:00
Tim Moon
71c8375862 Update CMake to 3.21 in LBANN-related projects (#28507)
* Update CMake to 3.21 in LBANN-related projects

* Allow CMake 3.17 for older versions of LBANN, Hydrogen, Aluminum
2022-01-27 12:21:45 +01:00
kwryankrattiger
8106983ddb Vtkm kokkos variant (#28363)
* VTK-m: Make vtk-m consistent with ROCmPackage

* VTKm: Add kokkos variant

Specifying +kokkos will enable kokkos backend.
Specifying +kokkos with +rocm will require a kokkos with a ROCm backend.
Specifying +cuda enables VTK-m native CUDA backend. VTK-m native cuda backend
  is not compatible with the kokkos +cuda backend.

* VTK-m: Add cuda_native variant

Required to allow specifying a vtk-m spec the selects a
cuda_arch and predictably propagate that to the underlying kokkos
dependency.

This also makes explicit selecting kokkos with a cuda backend or using
the VTK-m cuda backend.
2022-01-27 01:08:13 -07:00
Nils Leif Fischer
28bda22e52 New packages: py-quaternionic and py-spherical (#28611) 2022-01-26 17:48:43 -05:00
kwryankrattiger
991438a242 Mesa(18): Use libllvm virtual package (#28365)
* Mesa(18): Use libllvm virtual package

* Mesa patch configuration

Patch Mesa to define LLVM_VERSION_SUFFIX if llvm is pre-release

* Patch llvm-config to define LLVM_VERSION_SUFFIX
2022-01-26 15:16:41 -05:00
Harmen Stoppels
92abffa2d4 cmake: new version 3.22.2 (#28608) 2022-01-26 11:28:00 -07:00
Massimiliano Culpo
3cf5df7e3b Ensure "spack unit-test" can bootstrap clingo (#28572) 2022-01-26 14:19:15 +01:00
Valentin Volkl
b700335be7 lhapdfsets: add new package (#25477) 2022-01-26 04:58:58 -07:00
haralmha
b7bb687d17 vbfnlo: use patch method and filter_file instead of patch directive (#28506)
* Patch only for @3.0.0beta5

* Replace version specific patch file with patch function

Co-authored-by: root <root@hahansencs8.cern.ch>
2022-01-26 11:16:02 +01:00
Harmen Stoppels
e3d62b2f7b Print 'Waiting for another process to install x, y, z' in distributed builds (#28535)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2022-01-26 10:42:08 +01:00
Seth R. Johnson
5300cbbb2e trilinos: Enable LAPACK functionality in amesos2 (#28577) 2022-01-25 17:30:40 -08:00
Richarda Butler
38a1036c46 Bugfix: Tasmanian stand alone test (#28496) 2022-01-26 01:10:28 +00:00
Ryan Marcellino
75db515af2 alluxio: new version v2.7.2 (#28589) 2022-01-25 19:46:37 -05:00
Adam J. Stewart
2ace2a750b Fix build of libnetworkit/py-networkit (#28458) 2022-01-25 17:07:43 -06:00
Cyrus Harrison
7134cab8c4 occa: new release 1.2.0 release, and commit refs for prior releases (#28590) 2022-01-25 13:26:32 -07:00
Adam J. Stewart
4c57503e7e py-tensorboard-plugin-wit: install wheel (#28566) 2022-01-25 14:00:17 -06:00
Daniele Cesarini
1f3f1100b3 New packages: BigDFT suite (#26853) 2022-01-25 10:35:09 -08:00
Seth R. Johnson
edb99a2b05 Nalu wind: simplify version dependencies with trilinos (#28588)
* nalu-wind: simplify trilinos variant requirements

* nalu-wind: simplify version dependencies

With spack versioning, 'master' < 'develop' and 'develop' > 2.18.2.
2022-01-25 12:22:21 -05:00
eugeneswalker
fe76d6563a tau: %clang needs cmake for build (#28531)
* tau%clang needs cmake for build

* specify cmake@3.14:
2022-01-25 09:18:56 -08:00
Mark Grondona
4af334fb7e flux-pmix: add new package (#28559)
* pmix: add v4.1.0

* flux-pmix: add flux-pmix package
2022-01-25 09:35:36 -07:00
Daniele Cesarini
bed3a69498 mosquitto, cjson: added new packages (#28550)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2022-01-25 05:08:29 -07:00
Kai Torben Ohlhus
b36920283d octave: add maintainer @siko1056 (#28584) 2022-01-25 04:33:02 -07:00
Mikael Simberg
5cfaead675 Rename hpx-local to pika (#28585) 2022-01-25 04:32:39 -07:00
Wouter Deconinck
79d28db558 geant4: GEANT4_INSTALL_DATA=OFF and depends_on geant4-data type=run (#28581)
* [geant4] set GEANT4_INSTALL_DATA=OFF

* [geant4] downgrade geant4-data dependency to type=run
2022-01-25 11:38:13 +01:00
Jordan Ogas
5cb10f7362 charliecloud: add v0.26 (#28571) 2022-01-25 11:07:43 +01:00
Kai Torben Ohlhus
13eee02b41 octave: add v6.4.0 (#28580) 2022-01-25 09:44:31 +01:00
Andrew Davison
9fd870388c py-lazyarray: add versions from 0.3.3 to 0.5.2 (#28574)
* py-lazyarray: add versions from 0.3.3 to 0.5.2

* Restore py-setuptools dependency since pip replaces distutils with setuptools
2022-01-24 12:26:31 -07:00
Mark Grondona
a40d064030 flux-core: add v0.32.0 and v0.33.0 (#28347)
Additional changes:

 - update documentation of C4.1 link
 - do not set FLUX_PMI_LIBRARY_PATH
 - remove unnecessary ",master" from depends_on()
2022-01-24 09:20:49 -08:00
Wouter Deconinck
520b80fd5d gaudi: add v36.1, v36.2 and v36.3 (#28078) 2022-01-24 09:08:29 -07:00
Daniele Cesarini
ebedf3f83b cassandra: add v4.0.1, changed download url (#28551) 2022-01-24 10:09:38 +01:00
Adam J. Stewart
947c270446 Resource stage: no space before colon (#28560) 2022-01-24 10:01:28 +01:00
Adam J. Stewart
1c12e964ac grep: prevent recursive symlink (#28561) 2022-01-24 10:00:31 +01:00
Adam J. Stewart
471fa04c4b py-pandas: add v1.4.0 (#28563) 2022-01-24 09:59:52 +01:00
Adam J. Stewart
68c23549b0 py-pillow: add v9.0.0 (#28564) 2022-01-24 09:59:32 +01:00
Peter Brady
20f2ee99bc glm: add develop version (#28499)
* Add a new version to track development

The released versions do not properly install via cmake which leads to
errors when linking against the library.  These upstream problems have
been addressed on the glm development branch.

* Move git to class level and remove redundant depends
2022-01-24 09:47:43 +01:00
Sebastian Ehlert
03ba35920d dftd4: add v3.3.0 (#28558) 2022-01-23 08:14:13 -07:00
Timo Heister
8c85f72322 aspect: development branch is called main now (#28512) 2022-01-23 13:37:17 +01:00
Todd Gamblin
ecfc57ea3e m4: move patches hosted at savannah into the repo (#28515)
These URLs were giving 404's to me and to some of our users --
they do not seem to be reliable, so moving them into the tree.
2022-01-23 13:35:05 +01:00
iarspider
7e5afd1e73 libzmq: add variants "docs", "libbsd" (#28503) 2022-01-23 13:27:18 +01:00
Erik Schnetter
03e93345b1 compose: add new package (#28371) 2022-01-23 12:18:29 +01:00
Erik Schnetter
065e445e4d openmpi: declare more build dependencies for @master (#28309) 2022-01-23 11:10:02 +01:00
Jordan Galby
b526eafa45 Fix spack -C command_line_scope with other flags (#28418)
The option `spack -C` was broken if another flag that touched config was
also set (`spack -C ... -d`, `-c config:...` etc...).
2022-01-23 11:02:13 +01:00
Peter Brady
551c44f0fd petaca: add shared library variant (#28543) 2022-01-23 10:44:29 +01:00
John Wohlbier
3893b90cb9 palisade: add a named version for the "fppe-logreg" branch (#28544)
Co-authored-by: John Wohlbier <jgwohlbier@sei.cmu.edu>
2022-01-23 10:43:32 +01:00
Wouter Deconinck
5ff72ca079 acts: add v15.0.1 (#28539)
This is a bugfix version only, for an issue observed in production environments.
2022-01-23 10:32:20 +01:00
Erik Schnetter
4d70e4f281 libfyaml: add v0.7.12 (#28555) 2022-01-23 10:17:12 +01:00
Wouter Deconinck
ffb3f3a20d Python: ensurepip install instead of upgrade (#28553) 2022-01-22 21:55:56 -06:00
Axel Huebl
c38d34223a openPMD-api: add version 0.14.4 (#28546) 2022-01-21 17:35:16 -08:00
Danny McClanahan
0c2de252f1 introduce llnl.util.compat to remove sys.version_info checks (#21720)
- also split typing.py into typing_extensions and add py2 shims
2022-01-21 12:32:52 -08:00
Sebastian Schmitt
796f5a3cbc Bump py-brian2 to 2.5.0.2 (#28533) 2022-01-21 13:34:23 -06:00
Sreenivasa Murthy Kolam
417227e1eb bump up the version for 3.10.5 release (#28536) 2022-01-21 09:53:37 -07:00
Seth R. Johnson
9ac207c901 vecgeom/veccore: fix version interdependency (#28164)
* vecgeom: require exact version of veccore

Fixes configure error from downstream package:
```
CMake Error at /rnsdhpc/code/spack/opt/spack/apple-clang/cmake/7zgbrwt/share/cmake-3.22/Modules/CMakeFindDependencyMacro.cmake:47 (find_package):
  Could not find a configuration file for package "VecCore" that is
  compatible with requested version "0.8.0".

  The following configuration files were considered but not accepted:

    /rnsdhpc/code/spack/var/spack/environments/celeritas/.spack-env/view/lib/cmake/VecCore/VecCoreConfig.cmake, version: 0.6.0
```

* veccore: add new versions
2022-01-21 13:11:12 +00:00
Bram Veenboer
bd43467cbf CUDA: add v11.6.0 (#28439) 2022-01-21 11:08:20 +00:00
Wouter Deconinck
9b803a00b3 [geant4-data] depends_on g4ensdfstate also @11 (#28388)
I guess that one got dropped by mistake in the geant4 upgrade...
2022-01-21 10:54:19 +00:00
Danny McClanahan
645b40b249 add six.raise_from() to preserve exception traceback (#28532)
* add six.raise_from() to preserve exception traceback

* add tests for code coverage
2022-01-21 00:24:12 -08:00
Scott Wittenburg
282fd57114 trilinos: conflict with cuda >= 11.6.0 (#28530) 2022-01-20 21:08:34 -05:00
Patrick Bridges
76b7095445 Add flags to cabana to enable hypre and heffte when they are part of … (#28517)
* Add flags to cabana to enable hypre and heffte when they are part of spec. Also add googletest to build dependencies

* Fixed mixed spaced and tabs

* Update package.py

* Update package.py

* Update package.py

* Modified to request specifically heFFTe version 2.0.0 due to
limitations in heFFTe cmakefiles.

* Update var/spack/repos/builtin/packages/cabana/package.py

Co-authored-by: Christoph Junghans <christoph.junghans@gmail.com>

* Integrated more heffte and hypre versions into cabana requests

Co-authored-by: Christoph Junghans <christoph.junghans@gmail.com>
2022-01-20 15:32:25 -07:00
Anton Kozhevnikov
5719b40ded SIRIUS: add Eigen dependency (#28525)
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2022-01-20 22:10:03 +01:00
Erik Schnetter
de7de9778f hdf5: Add missing "close" statement (#28317)
* hdf5: Add missing "close" statement

* hdf5: Apply fortran-kinds patch only to @1.10.7
2022-01-20 14:11:34 -06:00
Harmen Stoppels
9a23fbbcf0 Julia: build without vendored dependencies (#27280)
* Julia unvendored

* restrict LBT
2022-01-20 11:07:04 -05:00
Mosè Giordano
1a5add3021 libblastrampoline: Add v4.0.0 and co-maintainer (#28521) 2022-01-20 05:08:24 -07:00
Jon Rood
5e699d5354 Remove unnecessary CMAKE_C_COMPILER from nalu-wind. (#28513) 2022-01-19 18:57:31 -08:00
Nils Leif Fischer
c11ce3bd1f New package: SpECTRE numerical relativity code (#28399)
* New package: SpECTRE numerical relativity code
2022-01-19 10:18:07 -08:00
kwryankrattiger
d5297b29be ParaView/VTK: Constrain version for ADIOS2 patch. (#28505)
* ParaView/VTK: Constrain version for ADIOS2 patch.

Older available versions of ParaView/VTK predate
ADIODS2 support.

ParaView lower bound is 5.8 and VTK lower bound is 8.2.0

* ParaView: Gate the ADIOS2 by verison
2022-01-19 13:15:24 -05:00
Adam J. Stewart
5e351ffff4 py-shiboken: fix build with new Python (#28464) 2022-01-19 10:32:29 -07:00
Charles Doutriaux
192f5cf66d Adding Kosh python package v2.0 (#28426) 2022-01-19 09:14:31 -07:00
Adam J. Stewart
22426f17d1 SIPPackage: fix build system (#28447) 2022-01-19 12:35:46 +01:00
Adam J. Stewart
cb95a30be7 py-astropy: remove install_options (#28448) 2022-01-19 12:35:01 +01:00
Adam J. Stewart
5688252a1f py-pygpu: remove install_options (#28449)
* py-pygpu: remove install_options

* Fix dependencies
2022-01-19 12:34:36 +01:00
Adam J. Stewart
cdac2cd4f2 py-pymol: don't install with pip (#28450) 2022-01-19 12:33:59 +01:00
Adam J. Stewart
d12bc3121a py-pyodbc: remove install_options (#28454) 2022-01-19 12:33:08 +01:00
Adam J. Stewart
3b2c7633eb py-numpy: remove install_options (#28459) 2022-01-19 12:31:47 +01:00
Adam J. Stewart
abe77ec8ab py-scipy: remove -j flag (#28460) 2022-01-19 12:31:23 +01:00
Adam J. Stewart
d6c841f67c py-python-meep: remove install_options (#28461)
* py-python-meep: remove install_options

* Remove unused import
2022-01-19 12:27:38 +01:00
Adam J. Stewart
e6ba8eb060 py-scs: fix CUDA build (#28463) 2022-01-19 12:17:22 +01:00
Stephen Sachs
d25e4889ba Remove '==> OpenFOAM bashrc env: ' from module (#28444)
It seems that spack reads the output of `setup_run_environment` to build the actual spack modules and lmod modules. So, any output here will used verbatim on the shell.

This patch fixes https://github.com/spack/spack/issues/26733
2022-01-19 12:00:31 +01:00
Richarda Butler
7fb11ea84f caliper: fix stand alone test (#28390) 2022-01-19 11:59:46 +01:00
Adam J. Stewart
d853e2db57 py-pyside2: fix various build issues (#28455) 2022-01-19 11:57:40 +01:00
Jen Herting
017c6786da py-smac: new package (#28490) 2022-01-19 11:51:53 +01:00
Logan Harbour
9723d918bb spack compiler info exit 1 when no compilers are found (#28493)
fixes #28492
2022-01-19 11:50:15 +01:00
dependabot[bot]
93ebc4f47b build(deps): bump docker/build-push-action from 2.7.0 to 2.8.0 (#28495)
Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 2.7.0 to 2.8.0.
- [Release notes](https://github.com/docker/build-push-action/releases)
- [Commits](a66e35b9cb...1814d3dfb3)

---
updated-dependencies:
- dependency-name: docker/build-push-action
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2022-01-19 11:27:59 +01:00
Cameron Rutherford
4918b7d007 exago: add v1.3.0 (#28498) 2022-01-19 11:15:15 +01:00
Hadrien G
7ae2d2e387 acts: update requirements on autodiff (#28501) 2022-01-19 10:59:04 +01:00
Thomas Helfer
8da204de61 mgis, tfel: add explicit dependency to py-numpy (#28502) 2022-01-19 10:57:13 +01:00
Harmen Stoppels
3dccb913a9 spack: add tcl/lmod as dependencies(#28355) 2022-01-19 10:02:04 +01:00
Jen Herting
97376f4694 New package: py-meldmd (#28479)
* [py-meldmd] created template

* [py-meldmd] added dependencies

* [py-meldmd]

- added homepage
- added description
- removed fixmes

* [py-meldmd] updated copyright
2022-01-18 20:17:24 -07:00
Melven Roehrig-Zoellner
10a0ce8c49 valgrind package: add versions 3.18.0 and 3.18.1 (#28453) 2022-01-18 18:28:05 -08:00
Adam J. Stewart
95fe66cb18 Add xgboost 1.5.2 (#28462)
Also remove obsolete py-dask-xgboost package
2022-01-18 18:11:08 -08:00
Adam J. Stewart
05df2c3371 py-sphinx: add v4.4.0 (#28465) 2022-01-18 18:06:44 -08:00
Adam J. Stewart
c5b1fcf5f9 py-torchmetrics: add v0.7.0 (#28489) 2022-01-18 18:00:09 -08:00
Jen Herting
68c0bdb698 New package: py-pyrfr (#28485)
* [py-pyrfr] create template

* [py-pyrfr]

- added homepage
- added description
- added dependencies
- updated copyright
- removed fixmes
2022-01-18 16:20:42 -07:00
Mathew Cleveland
e7b4a9bfd7 draco: new version 7.13.0 (#28359)
* Add release draco-7.13.0

* fix hash

Co-authored-by: Cleveland <cleveland@lanl.gov>
2022-01-18 17:40:04 -05:00
Jen Herting
24d9d4544e renamed package to align with usage (#28487)
Co-authored-by: Sid Pendelberry <sid@rit.edu>
2022-01-18 16:27:33 -06:00
Jen Herting
cac86345e5 New package: py-fastai (#28151)
* [py-fastai] new package

* [py-fastai] flake8

* [py-fastai] added dependencies from settings.ini

* [py-fastai] py-pillow -> pil

* [py-fastai] set version for py-setuptools

* [py-fastai] removed .999

Co-authored-by: Sid Pendelberry <sid@rit.edu>
2022-01-18 13:44:29 -07:00
Peter Brady
b5bb06cc36 New package: cppcoro (#28467)
A library for c++ coroutine abstractions
2022-01-18 12:03:33 -08:00
Tom Payerle
4d10df3003 petsc: add libspqr.so to list of suite-sparse libraries (#28478)
Should fix  #28477
2022-01-18 11:20:40 -07:00
Harmen Stoppels
e72f87ec64 Switch lmod default all:autoload from none to direct (#28357)
* Switch lmod module all autoload default from none to direct

* Fix the docs
2022-01-18 09:06:41 -08:00
Paul Kuberry
612430859e Xyce: add version 7.4.0 and '+shared' variant (#28469) 2022-01-18 10:05:39 -07:00
Jen Herting
bd987d9278 [py-tpot] fixed dependency and added version 0.11.7 (#28484)
* [py-tpot] fixed py-scipy dependency

* [py-tpot] added version 0.11.7
2022-01-18 10:45:49 -06:00
Joe Kaushal
58c598ffe6 new package: op2-dsl (#28396) 2022-01-18 09:20:33 -07:00
renjithravindrankannath
2f7a32a74d Updated recipes for 4.5.2 and corrected run style errors (#28413) 2022-01-18 14:12:22 +01:00
Jon Rood
7ae8a5d55b Add ROCmPackage to trilinos (#28424)
* Add ROCmPackage to trilinos.

* Simplify Trilinos ROCm support. Add MI200 to Kokkos AMD GPU arch map.
2022-01-18 06:24:32 -05:00
Teodor Nikolov
64913af04a New package: Sarus (#28349)
And tini
2022-01-18 03:59:09 -07:00
Mark W. Krentel
d642a396af hpctoolkit: add version 2022.01.15 (#28473) 2022-01-18 10:41:11 +01:00
Adam J. Stewart
5ca6ba6c8b py-tomopy: add v1.11.0 (#28466) 2022-01-17 21:50:43 -06:00
Hadrien G
f88b40308d ACTS: fix autodiff version requirements (#28440) 2022-01-17 12:14:29 -07:00
Tamara Dahlgren
f238835b65 is_system_path: return False if path is None (#28403) 2022-01-17 08:44:10 -07:00
kwryankrattiger
7e3677db6f Fix issue when propagating cuda with other variant (#28377)
+cuda was hiding propagation of hdf5 and adios2 to paraview
2022-01-17 13:57:43 +01:00
Erik Schnetter
b2f92a1307 mpc: add v1.2.1 (#28307) 2022-01-17 13:49:45 +01:00
Timothy Brown
e17434b9e2 WRF: add the ability to compile with Intel. (#28382) 2022-01-17 13:48:47 +01:00
Luc Berger
6add69d658 Kokkos Kernels: release maintenance (#28409)
1. adding latest release 3.5.0
2. updating cmake requirement to match that of Kokkos
3. adding logic to depend on the right version of Kokkos by default
2022-01-17 12:48:20 +00:00
Eric Brugger
20796b2045 VTK-m: Add testlib variant. (#28324) 2022-01-17 13:43:41 +01:00
Sreenivasa Murthy Kolam
53801f3ebb deprecate rocm-4.1.0 and older rocm releases (#28395) 2022-01-17 13:08:24 +01:00
eugeneswalker
0f3637e332 nalu-wind: depends on trilinos +gtest (#28414) 2022-01-17 12:55:42 +01:00
Adam J. Stewart
6c4e765f40 Open3D: use Spack-installed 3rd party deps when possible (#28422) 2022-01-17 12:54:22 +01:00
Adam J. Stewart
e7c9f05cd9 miniconda: source conda.sh setup script (#28321) 2022-01-17 12:53:41 +01:00
Adam J. Stewart
5d56a3b306 py-numpy: add v1.22.1 (#28423) 2022-01-17 12:52:43 +01:00
Glenn Horton-Smith
58fd0d859a net-snmp: add v5.9.1 (#28268) 2022-01-17 12:51:15 +01:00
Hadrien G
f5a2f693dc acts: add v16.0.0 (#28438) 2022-01-17 04:11:27 -07:00
Mark W. Krentel
905c6973c9 hpcviewer: add v2022.01. (#28425) 2022-01-17 10:15:48 +01:00
Erik Schnetter
350d2da8b9 findutils: ensure __nonnull is defined on macOS (#28316) 2022-01-17 10:14:39 +01:00
Adam J. Stewart
20bccc3843 mesa18: explicitly specify python executable (#28420) 2022-01-17 09:50:44 +01:00
Nils Leif Fischer
624b3a00ff brigand: only build tests when requested (#28228) 2022-01-17 09:45:34 +01:00
Adam J. Stewart
b93ff6fdff PyTorch: specify CUDA version incompatibility (#28432) 2022-01-17 09:41:23 +01:00
Adam J. Stewart
5c4a250bf9 NCCL: specify cuda_arch (#28433) 2022-01-17 09:40:38 +01:00
Adam J. Stewart
5e595586a7 zip: add external detection (#28434) 2022-01-17 09:39:17 +01:00
Vanessasaurus
dbb36ef8b1 Fixing pthread-stack-min-fix.patch patch version range (#28437)
pthread-stack-min-fix.patch should no be applied to 1.73.0
See https://github.com/spack/spack/issues/28436
2022-01-17 01:32:11 -07:00
Sebastian Pipping
425995db3e expat: Add latest release 2.4.3 with security fixes (#28435) 2022-01-16 17:23:02 -07:00
Luc Berger
e093187266 Kokkos: updating package list, maintainers and minimum cmake version (#28410)
* Kokkos: updating package list, maintainers and minimum cmake version
* Kokkos: updating maintainers list

Updating maintainers list to have the correct GitHub handle for Jan.
2022-01-16 11:50:34 -08:00
Christoph Junghans
a817538870 votca: add v2022 (#28431) 2022-01-16 07:50:02 -07:00
Brian Van Essen
b8d159c62d hwloc: added support to find external (#28348) 2022-01-15 16:44:13 -07:00
Peter Brady
415d662ec0 Fix boost build failures on newer glibc 2022-01-15 14:02:30 -08:00
Peter Brady
30b3cd3b44 chaco: new package (#28342)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2022-01-15 14:08:18 -07:00
Peter Brady
1dd9238021 chaparral: add new package (#28343) 2022-01-15 14:05:03 -07:00
Nicholas Knoblauch
a5c0a4dca4 Add libdeflate as variant for htslib (#24141) 2022-01-15 10:07:45 -07:00
Sreenivasa Murthy Kolam
ebdf1cb73e rocm ecosystem: bump version for 4.5.2 release (#28358) 2022-01-15 08:59:15 -07:00
Marcus Boden
9e87a6a4b7 snakemake: add v6.13.1 and new variant (#28393) 2022-01-15 08:56:01 -07:00
Nils Leif Fischer
3f903c49e4 charmpp: use CMake for versions 7.0.0+ (#28401) 2022-01-14 23:56:16 -07:00
Todd Gamblin
93377942d1 Update copyright year to 2022 2022-01-14 22:50:21 -08:00
Todd Gamblin
e3527983ac spack license update-copyright-year now updates the LICENSE-MIT file
`spack license update-copyright-year` was updating license headers but not the MIT
license file. Make it do that and add a test.

Also simplify the way we bump the latest copyright year so that we only need to
update it in one place.
2022-01-14 22:50:21 -08:00
Jen Herting
1422bde25a kaldi: new version 2021-11-16 (#28154)
* [kaldi] Added version 2021-11-16

* [kaldi] Added logic for new version and when cuda 11 is used

* [kaldi] Added patch file when cuda 11 as cub is now built into it

* [kaldi] removed .999 and simplified some logic

Co-authored-by: Doug Heckman <dahdco@rit.edu>
2022-01-14 23:08:15 -07:00
Chris White
ed105fcc76 New Package: ATS (#28013)
* add py-ats package

* add new 7.0.10 tag

* add myself as a maintainer

* add dependencies for python and setuptools

* style

* added todo for flux

* words

* update versions users should use
2022-01-14 22:32:12 -07:00
Brian Spilner
39f19bcc16 CDO package: add version 2.0.3 (#28416) 2022-01-14 18:53:55 -08:00
Adam J. Stewart
a2181e9d25 Python: add ensurepip variant (#28205) 2022-01-14 20:09:42 -06:00
Adam J. Stewart
6235184522 valgrind: default to ~ubsan (#28389) 2022-01-14 16:29:16 -07:00
Satish Balay
9ed32a3c65 gdbm@1.22: fix build on MacOS (#28379) 2022-01-14 14:02:50 -07:00
Peter Brady
2917aad6f9 scorpio: add new package (#28375)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2022-01-14 13:47:36 -07:00
Adam J. Stewart
3540f8200a PythonPackage: install packages with pip (#27798)
* Use pip to bootstrap pip

* Bootstrap wheel from source

* Update PythonPackage to install using pip

* Update several packages

* Add wheel as base class dep

* Build phase no longer exists

* Add py-poetry package, fix py-flit-core bootstrapping

* Fix isort build

* Clean up many more packages

* Remove unused import

* Fix unit tests

* Don't directly run setup.py

* Typo fix

* Remove unused imports

* Fix issues caught by CI

* Remove custom setup.py file handling

* Use PythonPackage for installing wheels

* Remove custom phases in PythonPackages

* Remove <phase>_args methods

* Remove unused import

* Fix various packages

* Try to test Python packages directly in CI

* Actually run the pipeline

* Fix more packages

* Fix mappings, fix packages

* Fix dep version

* Work around bug in concretizer

* Various concretization fixes

* Fix gitlab yaml, packages

* Fix typo in gitlab yaml

* Skip more packages that fail to concretize

* Fix? jupyter ecosystem concretization issues

* Solve Jupyter concretization issues

* Prevent duplicate entries in PYTHONPATH

* Skip fenics-dolfinx

* Build fewer Python packages

* Fix missing npm dep

* Specify image

* More package fixes

* Add backends for every from-source package

* Fix version arg

* Remove GitLab CI stuff, add py-installer package

* Remove test deps, re-add install_options

* Function declaration syntax fix

* More build fixes

* Update spack create template

* Update PythonPackage documentation

* Fix documentation build

* Fix unit tests

* Remove pip flag added only in newer pip

* flux: add explicit dependency on jsonschema

* Update packages that have been added since this was branched off of develop

* Move Python 2 deprecation to a separate PR

* py-neurolab: add build dep on py-setuptools

* Use wheels for pip/wheel

* Allow use of pre-installed pip for external Python

* pip -> python -m pip

* Use python -m pip for all packages

* Fix py-wrapt

* Add both platlib and purelib to PYTHONPATH

* py-pyyaml: setuptools is needed for all versions

* py-pyyaml: link flags aren't needed

* Appease spack audit packages

* Some build backend is required for all versions, distutils -> setuptools

* Correctly handle different setup.py filename

* Use wheels for py-tomli to avoid circular dep on py-flit-core

* Fix busco installation procedure

* Clarify things in spack create template

* Test other Python build backends

* Undo changes to busco

* Various fixes

* Don't test other backends
2022-01-14 12:37:57 -06:00
eugeneswalker
0b2507053e hsakmt-roct@4.5.0: needs pkgconf (#28400) 2022-01-14 08:38:19 -07:00
Adam J. Stewart
e0f044561e Python: improve site_packages_dir handling (#28346)
* Python: improve site_packages_dir handling

* Replace all site_packages_dir with purelib/platlib
2022-01-13 20:11:16 -06:00
Adam J. Stewart
2e238307c7 Python: add maintainers for Python 2 (#28386) 2022-01-13 20:05:42 -06:00
Jim Galarowicz
b7accb6a9d Add new survey package to spack. (#25518)
* Add new package to spack.  survey is a lightweight application performance tool that also gathers system information and stores it as metadata.

* Add maintainer and note about source access.

* Update the man path per spack reviewer suggestion.

* Remove redundant settings for PYTHONPATH, PATH, and MANPATH.

* Move to a one mpi collector approach for cce/tce integration.

* Add pyyaml dependency

* Make further spack reviewer changes to python type specs, mpi args, build type variant.

* Add reviewer requested changes.

* Add reviewer docstring requested changes.

* Add more updates from spack reviewer comments.

* Update the versions to use tags, not branches

* Redo dashes to fix issue with spack testing.

Co-authored-by: Jim Galarowicz <jgalarowicz@newmexicoconsortium.org>
2022-01-13 19:59:05 -06:00
Erik
eda565f3b1 AMReX Smoke Test (#27411) 2022-01-13 17:43:43 +00:00
Andrew W Elble
1ea4497802 musl: set syslibdir correctly, new versions (#28373) 2022-01-13 03:50:11 -07:00
Adam J. Stewart
7d3a696d27 fenics: specify python exe (#28323) 2022-01-12 12:47:21 -07:00
Harmen Stoppels
d74396ad21 Do not initialize config on spack compiler list (#28042)
When `spack compiler list` is run without being restricted to a
particular scope, and no compilers are found, say that none are 
available, and hint that the use should run spack compiler find to 
auto detect compilers.

* Improve docs
* Check if stdin is a tty
* add a test
2022-01-12 16:26:28 +00:00
Massimiliano Culpo
91fc4cf28f bootstrap: fix bootstrapping GnuPG from different macOS versions (#28350) 2022-01-12 08:18:16 -08:00
Nils Leif Fischer
38fee7e0da libogg: patch stdint include, add v1.3.5 (#28332)
Backport a patch for v1.3.4 that fixes an unsigned typedef problem
on macOS: https://github.com/xiph/ogg/pull/64

Also add v1.3.5 that has this issue fixed.
2022-01-12 09:17:52 -07:00
Andrew W Elble
b3043cae8f grace: workaround for buffer overflows (#28232)
spack paths can be long and this overflows (at least) these buffers
inside of the bundled T1lib inside of the grace distribution, leading
to crashes on startup.
2022-01-12 17:14:37 +01:00
kwryankrattiger
6c9b781e6e ECP-DAV: Propagate adios2 variant to paraview (#26747)
Depends on #26728 and #26175
2022-01-12 11:14:12 -05:00
Matthieu Dorier
04b9d87fca gptune: fix build by setting compilers to mpi wrappers (#28235) 2022-01-12 17:13:37 +01:00
Harmen Stoppels
868eaeb70e lmod: add v8.6.5 (#28353) 2022-01-12 08:26:43 -07:00
Nils Leif Fischer
0e1e705e15 charmpp: disable pre-7.0.0 macOS builds with clang@7: (#28221)
Charm++ versions below 7.0.0 have build issues on macOS, mainly due to the
pre-7.0.0 `VERSION` file conflicting with other version files on the
system: https://github.com/UIUC-PPL/charm/issues/2844. Specifically, it
conflicts with LLVM's `<version>` header that was added in llvm@7.0.0 to
comply with the C++20 standard:
https://en.cppreference.com/w/cpp/header/version. The conflict only occurs
on case-insensitive file systems, as typically used on macOS machines.
2022-01-12 15:53:49 +01:00
Adam J. Stewart
faaf38ca7d py-torch: use conditional variants (#28242) 2022-01-12 15:52:16 +01:00
Todd Gamblin
54d741ba54 unparser: handle package-level loops, if statements, and with blocks
Many packages implement logic at the class level to handle complex dependencies and
conflicts. Others have started using `with when("@1.0"):` blocks since we added that
capability. The loops and other control logic can cause some pure directive logic not to
be removed by our package hashing logic -- and in many cases that's a lot of code that
will cause unnecessary rebuilds.

This commit changes the unparser so that it will descend into these blocks. Specifically:

  1. Descend into loops, if statements, and with blocks at the class level.
  2. Don't look inside function definitions (in or outside a class).
  3. Don't look at nested class definitions (they don't have directives)
  4. Add logic to *remove* empty loops/with blocks/if statements if all directives
     in them were removed.

This allows our package hash to ignore a lot of pure metadata that it was not ignoring
before, and makes it less sensitive.

In addition, we add `maintainers` and `tags` to the list of metadata attributes that
Spack should remove from packages when constructing canonoical source for a package
hash.

- [x] Make unparser handle if/for/while/with at class level.
- [x] Add tests for control logic removal.
- [x] Add a test to ensure that all packages are not only unparseable, but also
      that their canonical source is still compilable. This is a test for
      our control logic removal.
- [x] Add another unparse test package that has complex logic.
2022-01-12 06:14:18 -08:00
Todd Gamblin
101f080138 unparser: add unparser unit tests
These are the unit tests from astunparse, converted to pytest, with a few backports from
upstream cpython. These should hopefully keep `unparser.py` well covered as we change it.
2022-01-12 06:14:18 -08:00
Todd Gamblin
4d7226832d unparser: rename t to node to mirror upstream
These refactors have happened in upstream `ast.unparse()`
2022-01-12 06:14:18 -08:00
Todd Gamblin
0370324f1f unparser: rename _Class() methods to visit_Class() to mirror upstream
These are refactors that have happened in upstream `ast.unparse()`
2022-01-12 06:14:18 -08:00
Todd Gamblin
ec16c2d7c2 unparser: do a better job of roundtripping strings
Handle complex f-strings.  Backport of:

    a993e901eb#
2022-01-12 06:14:18 -08:00
Todd Gamblin
e9612696fd unparser: treat print(a, b, c) and print((a, b, c)) the same
We can't tell `print(a, b, c)` and `print((a, b, c))` apart -- both of these expressions
generate different ASTs in Python 2 and Python 3.  However, we can decide that we don't
care.  This commit treats both of them the same when `py_ver_consistent` is set with
`unparse()`.

This means that the package hash won't notice changes from printing a tuple to printing
multiple values, but we don't care, because this is extremely unlikely to affect the build.
More than likely this is just an error message for the user of the package.

- [x] treat `print(a, b, c)` and `print((a, b, c))` the same in py2 and py3
- [x] add another package parsing test -- legion -- that exercises this feature
2022-01-12 06:14:18 -08:00
Todd Gamblin
a18a0e7a47 commands: add spack pkg source and spack pkg hash
To make it easier to see how package hashes change and how they are computed, add two
commands:

* `spack pkg source <spec>`: dumps source code for a package to the terminal

* `spack pkg source --canonical <spec>`: dumps canonicalized source code for a
   package to the terminal. It strips comments, directives, and known-unused
   multimethods from the package. It is used to generate package hashes.

* `spack pkg hash <spec>`: This gives the package hash for a particular spec.
  It is generated from the canonical source code for the spec.

- [x] `add spack pkg source` and `spack pkg hash`
- [x] add tests
- [x] fix bug in multimethod resolution with boolean `@when` values

Co-authored-by: Greg Becker <becker33@llnl.gov>
2022-01-12 06:14:18 -08:00
Todd Gamblin
106ae7abe6 package_hash: switch to using canonical source instead of AST repr
We are planning to switch to using full hashes for Spack specs, which means that the
package hash will be included in the deployment descriptor. This means we need a more
robust package hash than simply dumping the `repr` of the AST.

The AST repr that we previously used for package content is unreliable because it can
vary between python versions (Python's AST actually changes fairly frequently).

- [x] change `package_hash`, `package_ast`, and `canonical_source` to accept a string for
      alternate source instead of a filename.
- [x] consolidate package hash tests in `test/util/package_hash.py`.
- [x] remove old `package_content` method.
- [x] make `package_hash` do what `canonical_source_hash` was doing before.
- [x] modify `content_hash` in `package.py` to use the new `package_hash` function.

Co-authored-by: Danny McClanahan <1305167+cosmicexplorer@users.noreply.github.com>
2022-01-12 06:14:18 -08:00
Todd Gamblin
39afe946a0 unparser: Don't omit parenthesis when unparsing a slice
Backport of
  c102a14825

Includes support for Python 2.
2022-01-12 06:14:18 -08:00
Todd Gamblin
0776c3b4d6 unparser: Don't put unnecessary parentheses on class declarations
Backport of
* 25160cdc47
2022-01-12 06:14:18 -08:00
Todd Gamblin
ff5e73d6eb package_hash: add test to ensure that every package in Spack can be unparsed
- [x] add option to canonical source to *not* filter multimethods
- [x] add test to unparse every package in builtin
2022-01-12 06:14:18 -08:00
Todd Gamblin
b6dde510bd package_hash: add test to ensure consistency across Python versions
Our package hash is supposed to be consistent from python version to python version.
Test this by adding some known unparse inputs and ensuring that they always have the
same canonical hash.  This test relies on the fact that we run Spack's unit tests
across many python versions.  We can't compute for several python versions within the
same test run so we precompute the hashes and check them in CI.
2022-01-12 06:14:18 -08:00
Todd Gamblin
800229a448 package_hash: fix handling of multimethods and add tests
Package hashing was not properly handling multimethods. In particular, it was removing
any functions that had decorators from the output, so we'd miss things like
`@run_after("install")`, etc.

There were also problems with handling multiple `@when`'s in a single file, and with
handling `@when` functions that *had* to be evaluated dynamically.

- [x] Rework static `@when` resolution for package hash
- [x] Ensure that functions with decorators are not removed from output
- [x] Add tests for many different @when scenarios (multiple @when's,
      combining with other decorators, default/no default, etc.)

Co-authored-by: Danny McClanahan <1305167+cosmicexplorer@users.noreply.github.com>
2022-01-12 06:14:18 -08:00
Todd Gamblin
93a6c51d88 package_hash: rework RemoveDirectives and add a test
Previously we used `directives.__all__` to get directive names, but it wasn't
quite right -- it included `DirectiveMeta`, etc.  It's not wrong, but it's also
not the clearest way to do this.

- [x] Refactor `@directive` to track names in `directive_names` global
- [x] Rename `_directive_names` to `_directive_dict_names` in `DirectiveMeta`
- [x] Add a test for `RemoveDirectives`

Co-authored-by: Danny McClanahan <1305167+cosmicexplorer@users.noreply.github.com>
2022-01-12 06:14:18 -08:00
Todd Gamblin
8880a00862 package_hash: remove all unassigned strings, not just docstrings
Some packages use top-level unassigned strings instead of comments, either just after a
docstring on in the body somewhere else. Ignore those strings becasue they have no
effect on package behavior.

- [x] adjust RemoveDocstrings to remove all free-standing strings.
- [x] move tests for util/package_hash.py to test/util/package_hash.py

Co-authored-by: Danny McClanahan <1305167+cosmicexplorer@users.noreply.github.com>
2022-01-12 06:14:18 -08:00
Todd Gamblin
572fbf4f49 unparser: handle unicode string literals consistently across Python versions
Python 2 and 3 represent string literals differently in the AST. Python 2 requires '\x'
literals, and Python 3 source is always unicode, and allows unicode to be written
directly.  These also unparse differently by default.

- [x] modify unparser to write both out the way `repr` would in Python 2 when
  `py_ver_consistent` is provided.
2022-01-12 06:14:18 -08:00
Todd Gamblin
396c37d82f unparser: implement operator precedence algorithm for unparser
Backport operator precedence algorithm from here:
    397b96f6d7

This eliminates unnecessary parentheses from our unparsed output and makes Spack's unparser
consistent with the one in upstream Python 3.9+, with one exception.

Our parser normalizes argument order when `py_ver_consistent` is set, so that star arguments
in function calls come last.  We have to do this because Python 2's AST doesn't have information
about their actual order.

If we ever support only Python 3.9 and higher, we can easily switch over to `ast.unparse`, as
the unparsing is consistent except for this detail (modulo future changes to `ast.unparse`)
2022-01-12 06:14:18 -08:00
Todd Gamblin
afb358313a unparser: refactor delimiting with context managers in ast.unparse
Backport of 4b3b1226e8
2022-01-12 06:14:18 -08:00
Todd Gamblin
5847eb1e65 unparser: add block() context manager for indentation
This is a backport of a refactor from cpython 3.9
2022-01-12 06:14:18 -08:00
Todd Gamblin
2badd6500e unparse: Make unparsing consistent for 2.7 and 3.5-3.10
Previously, there were differences in the unparsed code for Python 2.7 and for 3.5-3.10.
This makes unparsed code the same across these Python versions by:

    1. Ensuring there are no spaces between unary operators and
       their operands.
    2. Ensuring that *args and **kwargs are always the last arguments,
       regardless of the python version.
    3. Always unparsing print as a function.
    4. Not putting an extra comma after Python 2 class definitions.

Without these changes, the same source can generate different code for different
Python versions, depending on subtle AST differences.

One place where single source will generate an inconsistent AST is with
multi-argument print statements, e.g.:

```
    print("foo", "bar", "baz")
```

In Python 2, this prints a tuple; in Python 3, it is the print function with
multiple arguments.  Use `from __future__ import print_function` to avoid
this inconsistency.
2022-01-12 06:14:18 -08:00
Todd Gamblin
b324fe5d95 externals: add astunparse
Add `astunparse` as `spack_astunparse`. This library unparses Python ASTs and we're
adding it under our own name so that we can make modifications to it.

Ultimately this will be used to make `package_hash` consistent across Python versions.
2022-01-12 06:14:18 -08:00
Andrew W Elble
a38cdddd37 perl-tk: add missing dependencies (#28240) 2022-01-12 14:53:25 +01:00
Dylan Simon
2cf22ad5f2 e2fsprogs: fix non-root install (#28255) 2022-01-12 14:52:46 +01:00
Harmen Stoppels
c8e01752a1 Use depends_on over load in lmod module files generated by Spack (#28352) 2022-01-12 13:29:22 +00:00
snehring
640a4f7dcd poamsa: fix build errors for gcc10+ (#28262) 2022-01-12 14:09:55 +01:00
Danny McClanahan
435a241869 yarn: add runtime dependency on node-js@4.0: (#27654) 2022-01-12 13:05:49 +00:00
H. Joe Lee
a5ff3206f9 HDF5 GPU VFD: add new package. (#28272) 2022-01-12 13:59:51 +01:00
Melven Roehrig-Zoellner
5bb5bf3efb ITensor: add v3.1.10 and 'shared' variant (#28370) 2022-01-12 05:20:10 -07:00
Adam J. Stewart
55a62a1ee5 py-async-timeout: fix checksum issue (#28329) 2022-01-12 10:53:12 +01:00
Nils Leif Fischer
7fa81a66af libtheora: disable docs by default (#28330) 2022-01-12 10:24:58 +01:00
Nils Leif Fischer
4e0372b9b7 curl: add support for external detection (#28331) 2022-01-12 10:24:10 +01:00
Massimiliano Culpo
5476e5d035 Remove tut since it requires deprecated Python 3.6 (#28360) 2022-01-12 09:34:50 +01:00
kwryankrattiger
363a565ce3 Packaging: Virtual package for libllvm (#27200)
Add an abstraction around libllvm to allow libllvm
providers to be specified for all packages.

This is targeting allowing mesa to build against
llvm-amdgpu or intel-llvm or llvm or any other
custom llvm variant that arises for specific GPU
toolchains
2022-01-11 13:28:13 -08:00
Erik Schnetter
d4a468c160 memkind: add v1.12.0 (#28306) 2022-01-11 11:23:36 -07:00
Erik Schnetter
6690bb7411 openblas: New version 0.3.19 (#28308) 2022-01-11 16:55:23 +01:00
Adam J. Stewart
2ab871dd17 py-aiohttp: switch to PyPI tarball (#28333) 2022-01-11 14:33:02 +01:00
Adam J. Stewart
2ea8abef34 Open3D: add missing LLVM dep (#28334) 2022-01-11 14:32:34 +01:00
Erik Schnetter
67d9abb5f1 ffmpeg: add v4.4.1 (#28300) 2022-01-11 14:21:43 +01:00
Harmen Stoppels
f611eb0283 hdf5: prefer stable over experimental releases (#28340) 2022-01-11 10:32:28 +01:00
Harmen Stoppels
78debc1143 mbedtls: add v2.16.12, v2.28.0 and v3.1.0(#28281) 2022-01-11 10:28:58 +01:00
Adam J. Stewart
7b76e3982f Deprecate Python 2 installations (#28003)
* Deprecate Python 2 installations

* Deprecate py-python-meep

* Deprecate older easybuild backend libs

* Deprecate Python 3.6

* Deprecate miniconda2
2022-01-10 15:45:35 -06:00
Erik Schnetter
675210bd8b automake: New version 1.16.5 (#28299) 2022-01-10 21:33:14 +01:00
Erik Schnetter
0236e88af4 gawk: New version 5.1.1 (#28301) 2022-01-10 21:32:53 +01:00
Erik Schnetter
c939af8185 gdbm: New version 1.22 (#28302) 2022-01-10 21:32:40 +01:00
Erik Schnetter
33d8e8f31c grep: New version 3.7 (#28303) 2022-01-10 21:32:33 +01:00
Erik Schnetter
f678d5818f lorene: Beautify package title in documentation (#28305) 2022-01-10 21:32:20 +01:00
Erik Schnetter
4ef8e15ed3 wi4mpi: New version 3.5.0 (#28313) 2022-01-10 21:31:30 +01:00
Erik Schnetter
09ca7c4d9c wget: New version 1.21.2 (#28312) 2022-01-10 21:31:13 +01:00
Erik Schnetter
76d9adae8c openssl: New version 1.1.1m (#28310) 2022-01-10 21:30:58 +01:00
Peter Scheibel
9f7fb6d01a stage.steal_source: preserve symlinks
This avoids dangling symlink errors. ignore_dangling_symlinks option would be more-targeted but is only available for Python >= 3.2 (#28318)
2022-01-10 10:10:49 -08:00
Adam J. Stewart
cc32b08205 Python: set default config_vars (#28290)
* Python: set default config_vars

* Add missing commas

* dso_suffix not present for some reason

* Remove use of default_site_packages_dir

* Use config_vars during bootstrapping too

* Catch more errors

* Fix unit tests

* Catch more errors

* Update docstring
2022-01-10 12:00:06 -06:00
Marcus Boden
5958306466 New packages: google-crc32c and py-google-crc32c (#28293) 2022-01-10 08:58:02 -06:00
Erik Schnetter
464d294b63 z3: New version 4.8.14 (#28314) 2022-01-10 14:31:52 +01:00
Erik Schnetter
b7f4a421e4 hwloc: New version 2.7.0 (#28298) 2022-01-10 12:00:51 +01:00
Peter Brady
fe64afb479 New package: petaca (#28326)
* Add the petaca fortran/c package

* Adopt date for version name and remove variants
2022-01-09 19:49:49 -05:00
luker
0277067e5f blaspp: set BLA_VENDOR for cray (#28104)
* for Cray's libsci in blaspp, set BLA_VENDOR=all

* Update package.py

* Update package.py

* Update package.py
2022-01-08 15:41:50 -05:00
Adam J. Stewart
334102addd SQLite: add new version/variant (#28204) 2022-01-08 12:57:57 -06:00
Erik Schnetter
52d475e89b openssh: New version 8.8p1 (#28325) 2022-01-08 13:10:28 +01:00
Martin Diehl
2bb844ee0e Damask improvements (#28178) 2022-01-08 06:50:38 -05:00
Jógvan Magnus Haugaard Olsen
897616f073 Dalton package: add versions and variants (#28226)
* Update existing 2020.0 version to use tag
* Add versions 2018.2 and master
* Add patches for GCC/Intel
* Use MPI compiler wrappers when +mpi
* Constrain CMake build dependency (need >= 3.1)
* Add variants for optional components (e.g QFIT library)
2022-01-07 18:59:17 -08:00
Anton Kozhevnikov
34f0222fdd ELPA package: don't check threading support during build (#28227)
./configure tries to execute an MPI test, which is not possible on
most HPC platforms (if you don't build on a compute node), so this
check is disabled to allow the build to proceed. Ideally we could
check this by placing constraints on the MPI that Spack builds (e.g.
require building a version that is guaranteed to have threading
support).
2022-01-07 18:13:46 -08:00
Peter Brady
d125bdfaa0 Catch2 package: add versions 2.13.8 and 3.0.0-preview4 (#28297) 2022-01-07 16:55:49 -08:00
Satish Balay
6a60201e80 petsc, py-petsc4py: add versions 3.16.3 (#28277) 2022-01-07 17:15:27 -06:00
Glenn Johnson
a3f5b712d3 py-pyzmq: adjust constraints for python-3.9 (#28264)
Version 18.1 builds with python-3.9
2022-01-07 15:08:02 -06:00
Filippo Spiga
b2336402a7 NVIDIA HPC SDK package: add version 22.1 (#28288) 2022-01-07 12:02:46 -08:00
Glenn Johnson
5091dc2124 r-kegg-db: mark deprecated, removed from bioconductor-3.13 (#28271) 2022-01-07 11:17:36 -07:00
Robert Cohn
7bed76786d py-matplotlib: fix config for oneapi compiler (#28265)
* py-matplotlib: fix config for oneapi compiler

* Small change to trigger CI restart
2022-01-07 11:17:14 -07:00
Glenn Johnson
0e45ad2d7f r-illuminahumanmethylationepicmanifest: remove invalid homepage (#28269) 2022-01-07 10:59:19 -07:00
Sebastian Pipping
43e064880e uriparser: Add latest release 0.9.6 with security fixes (#28291) 2022-01-07 10:14:11 -07:00
Kyle Gerheiser
04a95e3425 ip package: add v4.0.0 (#28237)
Keep 3.3.3 the preferred version until other packages can be updated
2022-01-06 19:46:31 -08:00
snehring
496b28bb58 viennarna package: add version 2.5.0 (#28261) 2022-01-06 19:44:50 -08:00
Sreenivasa Murthy Kolam
94bd667ba6 Update the rocm recipes for 4.5.0 release (#27535)
* rocm recipes updates for 4.5.0

* update to rocm recipes for 4.5.0 release

* updates to the rocm recipes for rocm-4.5.0 release

* fix style errors

* update to rocm-validation-suite for rocm-4.5.0 release

* bump up rccl recipe for rocm-4.5.0

* bump up version for rdc for rocm-4.5.0

* update miopengemm, miopen-opencl,rocm-opencl recipes for 4.5.0 release

* bump up version for mivisiox for rocm-4.5.0 release

* update the rocm-validation-suite recipe

* no need to change the perl path for 4.5.0

* fix the build failure with the recent change made for hip package

* modify checksum for the llvm-amdgpu for 4.5.0

* fix the build issue aftere recent changes made for enabling test

* fix the build issue with 4.5.0

* add new recipe for hipsolver

* address review comments
2022-01-06 13:24:00 -08:00
Adam J. Stewart
186730a284 bazel: python executable required (#28286)
* bazel: python executable required

* python: add autodetection of +pythoncmd
2022-01-06 15:16:43 -06:00
Adam J. Stewart
6e31094d77 GDAL: add new version (#28238)
* GDAL: add new version

* Use conflicts for PCRE
2022-01-06 12:26:24 -07:00
luker
27cbf46dd6 lapackpp: set BLA_VENDOR for cray (#28125) 2022-01-06 13:44:28 -05:00
Glenn Johnson
83a98c3807 r-genomeinfodbdata: add version 1.2.7 (#28266)
Also adjust formatting.
2022-01-06 11:30:31 -06:00
Glenn Johnson
2262bd1797 r package: add version 4.1.2 (#28244)
Set +libidn2 for the curl dependency. This is necessary after #25166.
2022-01-06 11:28:58 -06:00
Harmen Stoppels
f0b70b7c8e Fix spack install --v[tab] spec (#28278) 2022-01-06 14:47:03 +01:00
Harmen Stoppels
f8d4b4746c Fix double space in prompt after 'spack env activate -p' (#28279) 2022-01-06 04:59:07 -07:00
Glenn Johnson
f33f67ebd3 r-illuminahumanmethylationepicanno-ilm10b4-hg19: remove invalid homepage (#28267) 2022-01-06 11:35:40 +01:00
Axel Huebl
cc866f3c02 WarpX: 22.01 (#28225)
* WarpX: 22.01

Update `warpx` & `py-warpx` to the latest release, `22.01`.

* Python in 22.01+: Relax even further

See: https://github.com/ECP-WarpX/WarpX/pull/2664
2022-01-05 20:50:45 -08:00
Glenn Johnson
a43ed9286f GCC package: allow building gcc-5 on newer Linux (#27386)
Remove cyclades support so gcc-5 can build against newer glibc
versions (e.g. 2.31).
2022-01-05 14:14:28 -08:00
Harmen Stoppels
071778b919 llvm: make targets a multivalued variant (#27735)
* llvm: make targets a multivalued variant

* Fix the targets variant values

1. Make them lowercase and add a mapping to cmake equivalent
2. auto -> all
2. Restore composability by using a multivalued variant, so that
   `targets=all` and `targets=x86` is combined to `targets=all,x86`
   which is then transformed into LLVM_TARGETS_TO_BUILD=all.

* use targets=x86 in iwyu

* Default to nvptx/amdgpu/host arch targets

* default to none

* Update var/spack/repos/builtin/packages/zig/package.py
2022-01-05 14:11:05 -07:00
Andrew W Elble
a4f0fbafbb Add function to determine Linux kernel version (#27855)
This reports the kernel version (vs. the distro version) on Linux and
returns a valid Version (stripping characters like '+' which may be
present for custom-built kernels).
2022-01-05 10:22:43 -08:00
Pat McCormick
52cfd17917 Address legion package build issue on macOS with apple-clang-12 (#28241)
* Added C++ standard variant as a primary work-around for issues with apple-clang 12.x
but could also be helpful for broader uses.
2022-01-05 10:20:24 -08:00
Dylan Simon
f34598214b py-pyzmq: fix deptype of libzmq (#28254) 2022-01-05 10:59:33 -07:00
Severin Strobl
f064c5ee4f py-appdirs: patch for encoding issue (#28253)
Reading appdirs.py without explicitly requesting UTF-8 decoding results
in the build process to fail for Python 3.6.

See https://github.com/ActiveState/appdirs/pull/152 for the upstream
fix.
2022-01-05 10:59:12 -07:00
Marcus Boden
3e992aa283 Snakemake: New Version 6.12.3 (#28252)
* snakemake: New version
The newer versions of snakemake have a lot of new dependencies. The
optional dependencies still have to be added.

* removed comment

* some changes

* added reports variant

* deprecate older version and add me as maintainer

* Added dependency py-ratelimiter
2022-01-05 09:53:30 -07:00
Adam J. Stewart
c226835aa5 py-zipfile-deflate64: add new package (#27971) 2022-01-05 09:29:25 -07:00
kwryankrattiger
9e616ca7b7 VTK: Patch ADIOS2 module to fix cyclic dependency (#27784) 2022-01-05 11:21:08 -05:00
Harmen Stoppels
b23bd81cd9 ccache: add v4.5 and v4.5.1 (#28249) 2022-01-05 15:49:56 +01:00
Harmen Stoppels
39a346bde0 subversion: add v1.14.1, build in parallel (#28250) 2022-01-05 15:48:45 +01:00
Harmen Stoppels
89d3590300 sirius, spfft: make rocm arch variants conditional (#28251) 2022-01-05 15:47:40 +01:00
Massimiliano Culpo
0f74b7ec44 GnuPG: add v2.3.4 and update dependencies (#28248) 2022-01-05 15:42:18 +01:00
Andrew W Elble
422ae20a45 new package: py-lmdb (#28239) 2022-01-04 17:59:16 -07:00
snehring
efc5d0a3b4 snap-korf: version update + fix for compilers newer than gcc5 (#28243) 2022-01-04 17:44:04 -07:00
Marcus Boden
431473ea9b py-smart-open: Adding new version and dependencies (#28220)
* py-smart-open: Adding new version and dependencies

* fix python version and variant description/default
2022-01-04 14:20:15 -07:00
Jen Herting
cbe47f2066 New package: py-fastdownload (#28150)
* [py-fastdownload] created template

* [py-fastdownload]

- added homepage
- added description
- added dependencies
- removed fixmes
2022-01-04 15:14:59 -06:00
Axel Huebl
e43795de28 Fix: py-adios Cython run (#28223)
* Fix: py-adios Cython run

Always run Cython before `py-adios` installs.
This makes sure the `.cpp` files from `.pyx` files are freshly
created and work with newer CPython versions than the one checked
in.

* Cleanup: `rm` -> `os.remove`
2022-01-04 12:05:18 -07:00
Andrew W Elble
dc1b6aa8c6 new package: r-cca and dependencies (#28229)
Co-authored-by: Andrew W Elble <aweits@skl-a-00.rc.rit.edu>
2022-01-04 11:41:21 -07:00
Andrew W Elble
b924a5db14 new package: r-rpsychi (#28231)
Co-authored-by: Andrew W Elble <aweits@skl-a-00.rc.rit.edu>
2022-01-04 12:39:37 -06:00
Andrew W Elble
0264bb8343 new package: r-ccp (#28230)
Co-authored-by: Andrew W Elble <aweits@skl-a-00.rc.rit.edu>
2022-01-04 12:37:40 -06:00
Matthieu Dorier
c24bb64792 [py-gpustat] Added new version (#28135)
* [py-gpustat] Added new version

* [py-gpustat] marking 0.6.0 as preferred

* [py-gpustat] updated dependencies

* [py-gpustat] added dependency on python 3.4+

* [py-gpustat] corrected dependency to py-pytest-runner
2022-01-04 11:20:57 -06:00
Teodor Nikolov
cdb04931ab New version of neovim (#28222) 2022-01-04 07:14:01 -07:00
Harmen Stoppels
dce4f161d4 Drop preferred hdf5 version (#28091)
* Drop preferred hdf5 version

* Fix conduit

* Add compat bound for silo on hdf5

* Update var/spack/repos/builtin/packages/conduit/package.py

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

* hdf5 <= 1.10 for conduit <= 0.7

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-01-04 02:24:37 -08:00
Nils Leif Fischer
ffc3272a2b charmpp: add conflict with +shared on macOS with GCC (#28211) 2022-01-04 10:31:55 +01:00
Stephen McDowell
8d19db8628 cudnn: add v8.3.1 (#28071) 2022-01-04 09:25:13 +01:00
Nils Leif Fischer
1250b77607 doxygen: fix build issue with external Py3 (#28216)
Doxygen's build system uses CMake's deprecated `FindPythonInterp`,
which can get confused by other `python` executables in the PATH.
See issue: https://github.com/spack/spack/issues/28215
2022-01-04 09:10:39 +01:00
Nils Leif Fischer
1b5eaf62de doxygen: add v1.9.3 (#28217) 2022-01-04 09:08:14 +01:00
Weiqun Zhang
dd03a1a91e amrex: add v22.01 (#28214) 2022-01-04 09:06:59 +01:00
Tom Payerle
7cd8bae799 namd: Fix issue when building with interface=python ^python@3.8 (#28218)
Patch to add --embed flag to config-python when interface=python and
using python@3.8:

This is because python@3.8 changed behavior of python-config --ldflags
(and --libs) such that it no longer includes -lpython unless --embed
flag is used.

See e.g. https://github.com/mesonbuild/meson/issues/5629
2022-01-04 09:04:46 +01:00
Wouter Deconinck
ae2509339d qt: depends_on assimp@5.0 when @5.14: +opengl (#28191)
* qt: depends_on assimp@5.0 when @5.14: +opengl

* [qt] patch for assimp@5.14:5

* [qt] depends_on assimp@5.0.0:5.0

* [qt] remove depends_on gmake again
2022-01-03 12:56:11 -07:00
Matthieu Dorier
7a8862e316 [py-aiohttp] added new version (#28210)
* [py-aiohttp] added new version

* [py-aiohttp] changed dependency on setuptools

* [py-aiohttp] fixed some of the dependencies

* [py-aiohttp] updated dependency to py-typing-extensions

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-01-03 12:38:15 -07:00
Marcus Boden
20780ec61c New package: py-azure-storage-blob (#28209)
* New package: py-azure-storage-blob

* fixed typo

* Update var/spack/repos/builtin/packages/py-azure-storage-blob/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-azure-storage-blob/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-azure-storage-blob/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-01-03 12:34:59 -07:00
Matthieu Dorier
98dfe7e7e0 [py-asynctest] Added py-asynctest package (#28194)
* [py-asynctest] Added py-asynctest package

* [py-asynctest] added dependency to py-setuptools
2022-01-03 11:25:11 -06:00
Marcus Boden
94f5d0a3f4 py-azure-core: Added v1.21.1 (#28208) 2022-01-03 11:24:04 -06:00
Marcus Boden
997dba8ffd py-msrest: new version 0.6.21 (#28207) 2022-01-03 11:22:48 -06:00
AMD Toolchain Support
6f95296972 cp2k: fix dependency libraries (#28128)
* fixing build issues in cp2k dependencies

* fixing style issues

* reverting elpa.prefix.lib and grammer correction

* addressing the suggestions
2022-01-03 10:32:26 -05:00
Cyrus Harrison
c85c725b08 apcomp add v0.4.0 and new variant (#27820) 2022-01-03 10:40:18 +00:00
Vicente Bolea
a06d93f6cb VTKm: add v1.7.0 (#27864)
Co-authored-by: Cyrus Harrison <cyrush@llnl.gov>
2022-01-03 11:36:11 +01:00
Seth R. Johnson
8daaee3ed6 ROOT: unset MACOSX_DEPLOYMENT_TARGET for macOS (#28163) 2022-01-03 11:21:15 +01:00
Adam J. Stewart
e40eceba4c py-torchgeo: add v0.2.0 (#28200) 2022-01-03 11:20:07 +01:00
Tiziano Müller
c220abb011 elpa: add version 2021.11.001, add +autotune variant (#28134) 2022-01-02 22:56:03 -07:00
AMD Toolchain Support
71cb9fd9fd openmpi: extend version range for cray flags (#28107)
Co-authored-by: mohan babu <mohbabul@amd.com>
2022-01-02 21:17:24 -05:00
Maciej Wójcik
8fdb6e2b61 gromacs-swaxs: add new versions (#28157)
* Deprecate invalid versions

* Add new gromacs-swaxs releases
2022-01-02 21:02:25 -05:00
Eric Berquist
676d321b28 direnv: new version 2.30.2 (#28179) 2022-01-02 21:00:32 -05:00
Adam J. Stewart
d6d1d33e88 libtiff: fix build on macOS Monterey (#28185)
* libtiff: fix build on macOS Monterey

* patch configure, not configure.ac

* Revert "patch configure, not configure.ac"

This reverts commit 8bf315cb22.

* Force Spack to run autoreconf using new patch
2022-01-02 20:50:26 -05:00
Adam J. Stewart
89830c2117 Revert "[py-aiohttp] added new version (#28132)" (#28192)
This reverts commit fee855030d.
2022-01-02 13:22:28 -05:00
Nils Leif Fischer
4e16948a1f libsharp: add pic option (#28197) 2022-01-02 13:19:03 -05:00
Adam J. Stewart
c530672f0e py-nbsphinx: add v0.8.8 (#28198) 2022-01-02 13:17:40 -05:00
Adam J. Stewart
38af2c6c9b py-numpy: add v1.22.0 (#28199) 2022-01-02 13:17:25 -05:00
Matthieu Dorier
a99d485016 [py-aiosignal] Added new py-aiosignal package (#28138) 2022-01-02 10:31:47 -06:00
Matthieu Dorier
fc9bfe5317 [py-async-timeout] new versions (#28195)
* [py-async-timeout] new versions

* [py-async-timeout] corrected dependency

* [py-async-timeout] more fixes to dependencies
2021-12-31 10:58:57 -07:00
Wouter Deconinck
4e80b18851 [qt] depends_on zstd@1.3 when @5.13: (#28193) 2021-12-30 19:05:00 -07:00
Matthieu Dorier
fee855030d [py-aiohttp] added new version (#28132)
* [py-aiohttp] added new version

* [py-aiohttp] updated py-setuptools version dependency

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-12-30 11:58:04 -06:00
Enrico Usai
c06aaebefd Fix pyyaml dependency conflicts (#28177)
For versions of aws-parallelcluster >= 2.9, the pyyaml dependency had to be >= 5.3.1 and == 5.1.2
at the same time making impossible to install ParallelCluster >= 2.9 from spack repository.
See issue: https://github.com/spack/spack/issues/28172

Fixed by limiting pyyaml 5.1.2 version to aws-parallelcluster < 2.8, according to this commit:
7255d314b7

Tested with a manual installation of aws-parallelcluster@2.11.4
2021-12-30 11:53:28 -06:00
Massimiliano Culpo
c2e1a12cdf Ensure some version known to Spack can satisfy constraints in depends_on (#28131)
Add a new check to `spack audit` to scan and verify that version constraints may be satisfied

Modifications:
 - [x] Add a new check to `spack audit` to scan and verify that version constraints may be satisfied by some version declared in the built-in repository
- [x] Fix issues found by CI

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-12-29 12:16:07 -08:00
Marcus Boden
27202b2240 py-datrie: New package, initial commit (#28126)
* py-datrie: New package, initial commit

* removed boilerplate

* Update var/spack/repos/builtin/packages/py-datrie/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-datrie/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-12-29 10:12:09 -06:00
Marcus Boden
c2015f6a9c new package: py-pulp (#28174) 2021-12-29 10:11:33 -06:00
Marcus Boden
e09ab1a01c new package: py-connectionpool (#28173) 2021-12-29 10:10:43 -06:00
Marcus Boden
2018606c32 new package: py-toposort (#28171)
* new package: py-toposort

* style fix
2021-12-29 10:09:44 -06:00
Tom Payerle
eba3e1a20c trilinos: fix x11 noheaderserror (#27966)
* trilinos: fix define_tpl to handle depspecs w/out headers

This should address #27758 (i.e. errors due to netlib-scalapack not
having headers)

* trilinos: This fixes a mismatch in variant name and spec name for x11/libx11
2021-12-29 15:28:20 +00:00
Brian Spilner
95f2b10b4f ruby: add v3.1.0 (#28159) 2021-12-29 16:16:45 +01:00
Adam J. Stewart
04f298a34f py-scikit-learn: add v1.0.2 (#28160) 2021-12-29 16:15:33 +01:00
Joel Falcou
bcf497a5fa eve: new package (#28169) 2021-12-29 15:41:27 +01:00
Joseph Wang
e0d8964453 geant4: sha256sum has changed (#28158) 2021-12-28 19:01:00 -06:00
Matthieu Dorier
ae15c87bf0 [py-frozenlist] Added py-frozenlist package (#28137) 2021-12-28 14:05:09 -07:00
Matthieu Dorier
cd19782943 [py-minio] Added py-minio package (#28139)
* [py-minio] Added py-minio package

* [py-minio] added missing dependencies for py-minio

* [py-minio] added type=('build', 'run') in dependencies

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-12-28 10:44:03 -07:00
Matthieu Dorier
9d5ce4962d [py-dh-scikit-optimize] Added new versions (#28133)
* [py-dh-scikit-optimize] Added new versions

* [py-dh-scikit-optimize] fixing dependencies

* making py-configspace a required dependency of py-dh-scikit-learn
2021-12-28 09:59:14 -07:00
Matthieu Dorier
b5b54dbd02 [py-blessed] added new versions (#28167) 2021-12-28 10:43:07 -06:00
Martin Diehl
3cd599d6f6 Fixed typos: 'wtih' instead of 'with' (#28166) 2021-12-28 09:45:43 +01:00
Morten Kristensen
2f5c8ee699 py-vermin: add latest version 1.3.3 (#28162) 2021-12-27 10:09:00 -06:00
Jen Herting
e028ee0d59 New package: py-kaggle (#28152)
* new package

* changed py-six dependency

Co-authored-by: Sid Pendelberry <sid@rit.edu>
2021-12-24 10:47:44 -06:00
snehring
7fa31911fe satsuma2: add v2021-03-04 and build error fix (#28120) 2021-12-24 09:41:07 -07:00
Wouter Deconinck
f181b6fef6 root: depends_on fcgi and re-enabled +http support (#28115) 2021-12-24 09:20:13 -07:00
Adam J. Stewart
e2bda65947 py-blessings: fix setuptools version (#28141) 2021-12-24 09:02:09 -07:00
Jen Herting
50a3e3bfd3 New package: py-pyts (#28142)
* [py-pyts] new package

* [py-pyts] removed upperbound for python

Co-authored-by: Sid Pendelberry <sid@rit.edu>
2021-12-24 08:38:09 -07:00
Olivier Cessenat
eda8151fa0 banner: new package (#26743) 2021-12-24 15:12:47 +01:00
Mikael Simberg
edd55bc73d Add HPXLocal package file (#28106)
Co-authored-by: Mikael Simberg <mikael.simberg@iki.if>
2021-12-24 15:00:40 +01:00
Cyrus Harrison
0863148c4f conduit: add v0.8.0 release and change def for parmetis var (#28102) 2021-12-24 14:46:56 +01:00
Glenn Johnson
d098f92c4a r-hdf5r: use pkg-config to find hdf5 (#27847)
* r-hdf5r: use pkg-config to find hdf5

Since hdf5 was switched from autotools to cmake, the hdf5 compiler
wrappers can not be used to find and configure hdf5. This PR switches to
using pkg-config for configuration.

* Add comment about configure patch
2021-12-24 14:43:13 +01:00
albestro
6ed282bb2d ccls: add v0.20210330 (#28111) 2021-12-24 14:13:50 +01:00
Ye Luo
e945d3763b quantum-espresso: add v7.0 (#28144) 2021-12-24 14:13:05 +01:00
albestro
262c680997 neovim: add tree-sitter dependency + add v0.6.0 (#28145) 2021-12-24 13:57:15 +01:00
Jen Herting
054149698b py-fastprogress: new package (#28149) 2021-12-24 13:50:45 +01:00
Wouter Deconinck
a294acfb73 pythia8: bugfix for pythia8 +fastjet (#28153) 2021-12-24 13:47:18 +01:00
Cyrus Harrison
9602d0a03c dray: add v0.1.8 and v0.1.7 (#28147) 2021-12-24 13:43:11 +01:00
snehring
a3048438c3 lordec update and gatb-core (#28119)
* lordec: version update to 0.9 adding gatb-core as dep

* gatb-core: adding new package gatb-core
2021-12-24 13:42:30 +01:00
Vicente Bolea
6331778552 ParaView: add v5.10.0 (#28121) 2021-12-24 13:40:33 +01:00
Cody Balos
1513e57eee sundials: add v6.0.0 (#28032) 2021-12-24 13:38:36 +01:00
AMD Toolchain Support
d52e55d8de vasp: add support for aocc (#27950)
Co-authored-by: mohan babu <mohbabul@amd.com>
2021-12-24 13:36:15 +01:00
kjrstory
9c8a75ff9c npb package: add version 3.4.1 (#28122)
* The Class F problem has been added to seven of the benchmarks
  (BT, SP, LU, CG, MG, FT, and EP).
* The Class E problem has been added to the IS benchmark.
* In version 3.4.1, 'the number of processes' option does not apply.
* MPIFC and FC flags were added.
2021-12-23 18:52:59 -07:00
Glenn Johnson
f3035f98e1 r-htmltools: fix version 0.5.2 (#28124)
The lastest version of r-htmltools needs version 1.1.0 of r-fastmap.
This is not specified in the DESCRIPTION file.
2021-12-23 16:35:09 -07:00
Jen Herting
15951f0e6b New package: py-fastcore (#28148)
* [py-fastcore] created template

* [py-fastcore]

- added dependencies
- added homepage
- added description
- removed fixmes

* [py-fastcore] depends on setuptools
2021-12-23 14:11:17 -07:00
Axel Huebl
1c3881b48a HDF5 package: change 1.10.8/1.13.0 CMake Path (#28103)
These versions change the install location of CMake files used
by dependents, but most dependents don't seem to look in this
new location.

Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
Co-authored-by: Chris White <white238@llnl.gov>
2021-12-23 12:11:50 -08:00
Jen Herting
704c81eda4 amber package: add ambertools21 for @20 (#28064)
* [amber] added 3 more patches for amber20
* [amber] updated dependencies for @20 (cuda, parallel-netcdf)
2021-12-23 11:39:09 -08:00
Massimiliano Culpo
60a5b2a85e Merge tag 'v0.17.1' into develop 2021-12-23 19:48:36 +01:00
Massimiliano Culpo
4381cb5957 New subcommand: spack bootstrap status (#28004)
This command pokes the environment, Python interpreter
and bootstrap store to check if dependencies needed by
Spack are available.

If any are missing, it shows a comprehensible message.
2021-12-23 10:34:04 -08:00
Andrew W Elble
74d64fd61a py-pymol: update package, new version 2.5.0 (#28044)
* py-pymol: update package, new version 2.5.0

* ensure legacy plugins still load/work
2021-12-23 12:33:53 -05:00
Massimiliano Culpo
82bdda9a89 Reduce the unit tests jobs for the original concretizer
Only test Python 2.7, 3.6 and 3.9
2021-12-23 16:45:06 +01:00
Massimiliano Culpo
e974b44e86 Fix execution of style tests 2021-12-23 16:34:31 +01:00
Massimiliano Culpo
69b8cddb1b Bump version and update CHANGELOG.md 2021-12-23 16:02:09 +01:00
Tom Scogland
8e659f512e locks: allow locks to work under high contention (#27846)
* locks: allow locks to work under high contention

This is a bug found by Harshitha Menon.  

The `lock=None` line shouldn't be a release but should be 
```
return (lock_type, None)
``` 
to inform the caller it couldn't get the lock type requested without
disturbing the existing lock object in the database.  There were also a
couple of bugs due to taking write locks at the beginning without any
checking or release, and not releasing read locks before requeueing.
This version no longer gives me read upgrade to write errors, even
running 200 instances on one box.

* Change lock in check_deps_status to read, release if not installed,
  not sure why this was ever write, but read definitely is more
  appropriate here, and the read lock is only held out of the scope if
  the package is installed.

* Release read lock before requeueing to reduce chance of livelock, the
  timeout that caused the original issue now happens in roughly 3 of 200
  workers instead of 199 on average.
2021-12-23 16:02:09 +01:00
Harmen Stoppels
5daf023aec Regenerate views when specs already installed (#28113)
With this commit:
```
$ spack env activate --temp
$ spack install zlib
==> All of the packages are already installed
==> Updating view at /tmp/spack-faiirgmt/.spack-env/view
$ spack install zlib
==> All of the packages are already installed
```

Before this PR:
```
$ spack env activate --temp
$ spack install zlib
==> All of the packages are already installed
$ spack install zlib
==> All of the packages are already installed
```

No view was generated
2021-12-23 16:02:09 +01:00
Massimiliano Culpo
87abda4cdd py-pandas: fix issue reported by vermin 2021-12-23 16:02:09 +01:00
Morten Kristensen
fa5e186d4a py-vermin: add latest version 1.3.2 (#28072)
* py-vermin: add latest version 1.3.2

* [vermin] Fixed usages of super() without arguments (v3+)
2021-12-23 16:02:09 +01:00
Paul Spencer
e1cc28a30a sbang: respect package permissive package permissions for sbang (#25764)
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2021-12-23 16:02:09 +01:00
victorusu
17edf1ae90 Add setdefault option to tcl module (#14686)
This commit introduces the command

spack module tcl setdefault <package>

similar to the one already available for lmod

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-12-23 16:02:09 +01:00
Harmen Stoppels
79fd1c5114 Set backup=False by default in filter_file (#28036) 2021-12-23 16:02:09 +01:00
Harmen Stoppels
13e36c5457 Fix table formatting (#28037) 2021-12-23 16:02:09 +01:00
Harmen Stoppels
b2694013d4 Revert "patches: make re-applied patches idempotent (#26784)" (#27625)
This reverts commit c5ca0db27f.
2021-12-23 16:02:09 +01:00
Andrew W Elble
8f3b025b55 MANPATH needs a trailing ':' to utilize system defaults (#21682)
otherwise spack breaks using system man pages by default.

Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2021-12-23 16:02:09 +01:00
Christian Goll
37fbe30c4a Added opensuse/leap:15 to spack containerize (#27837)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-12-23 16:02:09 +01:00
Tamara Dahlgren
314867e635 Provide meaningful message for empty environment installs (#28031)
* Provide a meaningful failure message for installation of an empty environment

* Allow regenerating view per offline discussion
2021-12-23 16:02:09 +01:00
Greg Becker
9345bf81b9 Add option to minimize full debug cores. include warning message about performance (#27970)
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2021-12-23 16:02:09 +01:00
Dan Bonachea
adf4e91658 upcxx: Update the UPC++ package to 2021.9.0 (#26996)
* upcxx: Update the UPC++ package to 2021.9.0

* Add the new release, and a missing older one.

* Remove the spack package cruft for supporting the obsolete build system that
  was present in older versions that are no longer supported.

* General cleanups.

Support for library versions older than 2020.3.0 is officially retired,
for two reasons:

1. Releases prior to 2020.3.0 had a required dependency on Python 2,
   which is [officially EOL](https://www.python.org/doc/sunset-python-2/)
   as of Jan 1 2020, and is no longer considered secure.
2. (Most importantly) The UPC++ development team is unable/unwilling to
   support releases more than two years old.  UPC++ provides robust
   backwards-compatibility to earlier releases of UPC++ v1.0, with very
   rare well-documented/well-motivated exceptions.  Users are strongly
   encouraged to update to a current version of UPC++.

NOTE: Most of the lines changed in this commit are simply re-indentation,
and thus might be best reviewed in a diff that ignores whitespace.

* upcxx: Detect Cray XC more explicitly

This change is necessary to prevent false matches occuring on new Cray Shasta
systems, which do not use the aries network but were incorrectly being treated
as a Cray XC + aries platform.

UPC++ has not yet deployed official native support for Cray Shasta, but this
change is sufficient to allow building the portable backends there.
2021-12-23 16:02:09 +01:00
Harmen Stoppels
20ad47f9e1 Install dir creation message demoted to "debug" level (#27911) 2021-12-23 16:02:09 +01:00
Greg Becker
7e5de95a30 Improve debug info from concretizer (#27707) 2021-12-23 16:02:09 +01:00
Massimiliano Culpo
e9f7fb03c9 spack audit: fix API calls (#27713)
This broke in #24858
2021-12-23 16:02:09 +01:00
Paul Ferrell
9d4291e590 Handle byte sequences which are not encoded as UTF8 while logging. (#21447)
Fix builds which produce a lines with non-UTF8 output while logging
The alternative is to read in binary mode, and then decode while
ignoring errors.
2021-12-23 16:02:09 +01:00
Harmen Stoppels
8f98f1d182 Use bash in setup_git.sh (#27676) 2021-12-23 16:02:09 +01:00
Harmen Stoppels
654f6839eb ci: run style unit tests only if we target develop (#27472)
Some tests assume the base branch is develop, but this branch may not
have been checked out.
2021-12-23 16:02:09 +01:00
Harmen Stoppels
c8daa7218d Turn some verbose messages into debug messages (#27408) 2021-12-23 16:02:09 +01:00
Harmen Stoppels
d862507bcf Fix overloaded argparse keys (#27379)
Commands should not reuse option names defined in main.
2021-12-23 16:02:09 +01:00
Jordan Galby
7c6b253d89 Fix log-format reporter ignoring install errors (#25961)
When running `spack install --log-format junit|cdash ...`, install
errors were ignored. This made spack continue building dependents of
failed install, ignoring `--fail-fast`, and exit 0 at the end.
2021-12-23 16:02:09 +01:00
Robert Underwood
abd418cc31 openmpi fix external find for 0.17 (#27255) 2021-12-23 16:02:09 +01:00
Dylan Simon
544826c825 make --enable-locks actually enable locks (#24675) 2021-12-23 16:02:09 +01:00
Vinícius
afd65a4cd0 simgrid package: add versions 3.28 and 3.29 (#28118) 2021-12-23 02:53:14 -07:00
Hadrien G
b6da473800 acts: add v15.1 and record incompatibility (#27942)
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
2021-12-22 23:02:16 -07:00
Christoph Junghans
eee0f2b9d5 votca-*: merge packages into one (#28073)
* votca-*: merge packages into one

* Update package.py

* votca-*: make old version as deprecated

* votca-*: mark stable deprecated as well
2021-12-22 21:42:14 -07:00
Jen Herting
cb5d53e5a9 New package: py-qpth (#28047)
Co-authored-by: Doug Heckman <dahdco@rit.edu>
2021-12-22 20:29:08 -07:00
albestro
b5ba20ada4 New package: tree-sitter (#28110) 2021-12-22 19:18:09 -08:00
Bernhard Kaindl
d236b9438d llvm: Fix the llvm versions for using the MicrosoftDemange patch (#28140) 2021-12-22 16:53:10 -07:00
Tom Scogland
b7b6542804 locks: allow locks to work under high contention (#27846)
* locks: allow locks to work under high contention

This is a bug found by Harshitha Menon.  

The `lock=None` line shouldn't be a release but should be 
```
return (lock_type, None)
``` 
to inform the caller it couldn't get the lock type requested without
disturbing the existing lock object in the database.  There were also a
couple of bugs due to taking write locks at the beginning without any
checking or release, and not releasing read locks before requeueing.
This version no longer gives me read upgrade to write errors, even
running 200 instances on one box.

* Change lock in check_deps_status to read, release if not installed,
  not sure why this was ever write, but read definitely is more
  appropriate here, and the read lock is only held out of the scope if
  the package is installed.

* Release read lock before requeueing to reduce chance of livelock, the
  timeout that caused the original issue now happens in roughly 3 of 200
  workers instead of 199 on average.
2021-12-22 16:25:05 +01:00
Joseph Snyder
34873f5fe7 Use consistent method of checking for presence of info in connection (#27694)
Fixes #27652

Ensure that mirror's to_dict function returns a syaml_dict object for all code
paths.

Switch to using the .get function for accessing the potential information from
the S3 mirror objects.  If the key is not there, it will gracefully return
None instead of failing with a KeyError

Additionally, check that the connection object is a dictionary before trying
to "get" from it.

Add a test for the capturing of the new S3 information.
2021-12-22 16:15:49 +01:00
Pat Riehecky
522a7c8ee0 New package: microsocks (#27859) 2021-12-21 16:55:15 -08:00
Mark Olesen
433f743074 openfoam package: add v2112 release and latest patched v2106 (#28108)
Also remove x86_64-only handling for Darwin
2021-12-21 16:47:39 -08:00
Seth R. Johnson
38196894db perl: fix macOS build (#26290)
* perl: fix macOS build

With both 5.34.0 and 5.32.1 the build fails on macos-bigsur-skylake
%clang@12.0.5 and %clang13.0.0 :
```
2 errors found in build log:
     579013    /private/var/folders/fy/x2xtwh1n7fn0_0q2kk29xkv9vvmbqb/T/s3j/spack-stage/spack-stage-perl-5.34.0-tpha2u52qfwaraidpzzbf6u4dbqg7dk5/spack-src/cpan/
               Math-BigInt-FastCalc/../../miniperl "-I../../lib" -MExtUtils::Command::MM -e 'cp_nonempty' -- FastCalc.bs ../../lib/auto/Math/BigInt/FastCalc/Fas
               tCalc.bs 644
     579014
     579015    	Everything is up to date. Type '/Applications/Xcode.app/Contents/Developer/usr/bin/make test' to run test suite.
     579016    DYLD_LIBRARY_PATH=/private/var/folders/fy/x2xtwh1n7fn0_0q2kk29xkv9vvmbqb/T/s3j/spack-stage/spack-stage-perl-5.34.0-tpha2u52qfwaraidpzzbf6u4dbqg7d
               k5/spack-src  ./perl -Ilib -I. installperl --destdir=
     579017    WARNING: You've never run 'make test' or some tests failed! (Installing anyway.)
     579018      /rnsdhpc/code/spack/opt/spack/apple-clang/perl/tpha2u5/bin/perl5.34.0
  >> 579019    install_name_tool: error: sh -c '/Applications/Xcode.app/Contents/Developer/usr/bin/xcodebuild -sdk /Applications/Xcode.app/Contents/Developer/Pl
               atforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -find install_name_tool 2> /dev/null' failed with exit code 256: (null) (errno=Invalid argument
               )
     579020    xcode-select: Failed to locate 'install_name_tool', requesting installation of command line developer tools.
     579021    Cannot update /rnsdhpc/code/spack/opt/spack/apple-clang/perl/tpha2u5/bin/perl5.34.0 dependency paths
  >> 579022    make: *** [install-all] Error 72
```
This is due to SYSTEM_VERSION_COMPAT being set.

* perl: conditionally set SYSTEM_VERSION_COMPAT based on CLT

The version of command line tools is the only difference between
@alalazo and my builds: his (v11) works only when SYSTEM_VERSION_COMPAT
is set to 1, and mine (v12.5 and v13) only work when it is unset.
2021-12-21 22:22:35 +01:00
Harmen Stoppels
db69a291d4 Regenerate views when specs already installed (#28113)
With this commit:
```
$ spack env activate --temp
$ spack install zlib
==> All of the packages are already installed
==> Updating view at /tmp/spack-faiirgmt/.spack-env/view
$ spack install zlib
==> All of the packages are already installed
```

Before this PR:
```
$ spack env activate --temp
$ spack install zlib
==> All of the packages are already installed
$ spack install zlib
==> All of the packages are already installed
```

No view was generated
2021-12-21 18:41:12 +01:00
snehring
389beaef97 structure: fixing build errors with gcc10+ removing unused dep (#28097) 2021-12-21 18:39:26 +01:00
iarspider
8ebad6963b New package: py-onnxmltools and dependencies (#28023)
* New package: py-onnxmltools and dependencies

* Small fix

* Changes from review

* Apply suggestions from code review

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update recipe following review

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-12-21 11:15:13 -06:00
dependabot[bot]
43042c14e0 build(deps): bump docker/login-action from 1.10.0 to 1.12.0 (#28100)
Bumps [docker/login-action](https://github.com/docker/login-action) from 1.10.0 to 1.12.0.
- [Release notes](https://github.com/docker/login-action/releases)
- [Commits](f054a8b539...42d299face)

---
updated-dependencies:
- dependency-name: docker/login-action
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-12-21 11:29:40 +01:00
snehring
6b91d3700b soapdenovo2: fixing compiler errors in gcc10+ (#28098) 2021-12-21 10:51:47 +01:00
Adam J. Stewart
7aa2bdca44 py-build: add virtualenv variant (#28099) 2021-12-21 10:43:42 +01:00
snehring
5005e9a856 pcma: fixing compilation issues with gcc10+ (#28101) 2021-12-21 10:41:44 +01:00
Chris White
0a43dd1019 axom: add v0.6.1, fixed e4s builds (#28067) 2021-12-21 10:40:16 +01:00
Marie Houillon
a6d89853d4 openCARP packages: add version 8.2 (#28087)
Co-authored-by: openCARP consortium <info@opencarp.org>
2021-12-20 19:09:41 -08:00
Brian Spilner
116deb0386 CDO package: add version 2.0.2 (#28086)
Also fix URL for version 2.0.1 (sha256 is not changed)
2021-12-20 19:08:49 -08:00
Jen Herting
6647b2a4ca New package: py-ctgan (#28050)
Co-authored-by: Sid Pendelberry <sid@rit.edu>
2021-12-20 19:07:21 -08:00
Valentin Volkl
6c62fa461e harfbuzz package: add version 2.9.1 (#27927) 2021-12-20 18:29:52 -08:00
Jen Herting
e9edb5c96b New package: py-liac-arff (#28046) 2021-12-20 18:18:09 -08:00
Jen Herting
9869a2d0da New package: py-rdt (#28048)
Co-authored-by: Sid Pendelberry <sid@rit.edu>
2021-12-20 18:10:52 -08:00
Jen Herting
024c2b690a New package: py-faker (#28049)
Co-authored-by: Sid Pendelberry <sid@rit.edu>
2021-12-20 18:08:53 -08:00
Enrico Usai
cd211acd80 aws-parallelcluster: add v2.11.4 (#28094)
Also remove tilne from admins.
2021-12-20 16:49:49 -08:00
Anton Kozhevnikov
494f0053ae add sha256 sum (#28095) 2021-12-20 15:50:18 -07:00
Robert Cohn
d45280369f Intel oneAPI packages: add 2022.1.1 release (#28096)
Co-authored-by: Egorov, Andrey <andrey.egorov@intel.com>
2021-12-20 14:06:32 -08:00
Adam J. Stewart
c68652c88c py-torchgeo: add v0.1.1 (#28082) 2021-12-20 16:18:27 +01:00
Vanessasaurus
a94b4eef79 Fixing spacing of libabigail to : (#28085) 2021-12-20 03:56:03 -07:00
Erik Schnetter
94dd9685cc nsimd: Declare missing py-chardet dependency (#28030)
Found by @stevenrbrandt.
2021-12-20 08:43:31 +01:00
Adam J. Stewart
a0f175f327 py-nbconvert: add v6.3.0 (#28075) 2021-12-20 07:57:27 +01:00
Wouter Deconinck
ea692ca6f7 assimp: add v5.1.4 (#28079) 2021-12-20 07:48:07 +01:00
Adam J. Stewart
02aab770db py-kornia: add v0.6.2 (#28080) 2021-12-20 07:30:34 +01:00
Adam J. Stewart
cdc5c44bb1 py-numpy: add v1.21.5 (#28081) 2021-12-20 07:30:17 +01:00
Vanessasaurus
da9e152ed1 Fix bugs in spack monitor (#27511)
Updates to installer.py did not account for spack monitor, so as currently implemented
there are three cases of failure that spack monitor will not account for. To fix this we add additional
hooks, including an on cancel and also do a custom action on concretization fail.

Signed-off-by: vsoch <vsoch@users.noreply.github.com>

Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2021-12-20 06:54:41 +01:00
Seth R. Johnson
ece1e3905e cmake: new versions 3.22.x (#28077) 2021-12-19 19:59:00 -07:00
Todd Gamblin
bfc69f0e4b jsonschema: use more specific schema identifiers
The latest version of `jsonschema` fails if we're not specific about which schema draft
specification we're using.  Update all of them to use the latest one (draft-07).
2021-12-19 12:55:42 -08:00
Todd Gamblin
7703043195 externals: Upgrade jsonschema to v3.2.0
Our `jsonschema` external won't support Python 3.10, so we need to upgrade it.
It currently generates this warning:

    lib/spack/external/jsonschema/compat.py:6: DeprecationWarning: Using or importing the ABCs
        from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3, and
        in 3.10 it will stop working

This upgrades `jsonschema` to 3.2.0, the latest version with support for Python 2.7.  The next
version after this (4.0.0) drops support for 2.7 and 3.6, so we'll have to wait to upgrade to it.

Dependencies have been added in prior commits.
2021-12-19 12:55:42 -08:00
Todd Gamblin
f83e0fb81a externals: add attrs for new jsonschema
Updating `jsonschema` to 3.2.0 requires `attrs`. Add it to externals.
2021-12-19 12:55:42 -08:00
Todd Gamblin
90592b3cbe externals: add pyrsistent for new jsonschema
Updating `jsonschema` to 3.2.0 requires `pyrsistent`. Adding just the pieces of it
that are needed for `jsonschema`.
2021-12-19 12:55:42 -08:00
Todd Gamblin
04536db387 externals: add functools32 for new jsonschema
Updating `jsonschema` to 3.2.0 requires `functools32`, just for Python 2.
2021-12-19 12:55:42 -08:00
Tamara Dahlgren
e470131a77 Tests: remove test_get_stage_root_in_spack since it writes to the spack directory (#28056) 2021-12-19 11:31:38 -08:00
Wouter Deconinck
1e35d06bf0 geant4: new version 11.0.0 (preferred remains 10.7.3) (#27931)
* [geant4] new version 11.0.0

* [geant4] prefer 10.7.3 for now

* [vecgeom] new version 1.1.18

* [clhep] new version 2.4.5.1

* [g4emlow] new version 8.0

* [g4particlexs] new version 4.p

* [geant4-data] new version 11.0.0

* [geant4] @11.0.0: cxxstd=17: ^clhep@2.4.5.1: ^vecgeom@1.1.18:

* [geant4] depends_on cmake@3.16:

* [geant4-data] remove g4tendl comment

* [g4tendl] new version 1.4

* [geant4] default cxxstd=11 when @10, 17 when @11; use CMAKE_CXX_STANDARD

* [geant4] variant tbb whe @11:, depends_on tbb, sets GEANT4_USE_TBB

* [geant4] new variant vtk when @11:, depends_on vtk@8.2:

* [geant4] simplify GEANT4_USE_VTK with define_from_variant

* [geant4] remove variant cxxstd conditional again

* [geant4] flake8 space after comma
2021-12-19 10:43:59 -05:00
Adam J. Stewart
1a576e732e Python: default to 3.9 (#27997)
Both [Anaconda](https://www.anaconda.com/products/individual) and [Homebrew](https://formulae.brew.sh/formula/python@3.9) now default to Python 3.9, so Spack should follow suit.

I also added Python 3.10 while I was at it. Confirmed that it builds successfully on macOS 10.15.7 with Apple Clang 12.0.0. I'm unable to test the Cray and Fujitsu patches.

Fixes #27921
2021-12-19 00:08:20 -08:00
Paul Spencer
30244c2c40 sbang: respect package permissive package permissions for sbang (#25764)
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2021-12-18 22:07:20 -08:00
Morten Kristensen
9ace418371 py-vermin: add latest version 1.3.2 (#28072)
* py-vermin: add latest version 1.3.2

* [vermin] Fixed usages of super() without arguments (v3+)
2021-12-18 11:17:02 -07:00
Stephen McDowell
87978f7989 skip googletest and googlebenchmark for header only library (#28068) 2021-12-18 10:29:05 -06:00
Larry Knox
e96b91dd37 HDF5 package: add version 1.13.0 (#28010) 2021-12-17 14:47:47 -08:00
AMD Toolchain Support
541ccd6669 What's new in AOCL 3.1 (#27988)
* What's new in AOCL 3.1

1) AMD BLIS:
    1.a) Supports Dynamic Dispatch and AOCL Dynamic feature
    1.b) Improvements in DGEMM, ZGEMM, DTRSM, DSYRK, xGEMV, and DOTV
2) AMD libFLAME:
    2.a) Supports LAPACK 3.10.0 specification
    2.b) Optimized factorization and ZGEEV routines
3) AMD FFTW:
    3.a) Features like 'AMD application optimization layer', 'Fast MPI transpose algorithm' and 'Top N planner' are added
4) AMD LibM:
    4.a) Optimized exp2, log2 (Single and Double precision) scalar and vector
    4.b) Optimized log10f (scalar and vector) and powf vector variants to support WRF4.1.2 benchmark
5) AOCL-Sparse:
    5.a) New API for sparse matrix and dense matrix multiplication
6) AMD ScaLAPACK:
    6.a) ILP64 support has been enabled
7) AOCL enabled MUMPS library:
    7.a) CMake based build system on Windows for AOCL enabled MUMPS sparse solver library will be available shortly on GitHub
        7.a.i)	Refer https://github.com/amd/mumps-build
    7.b) Spack-based recipe on Linux for AOCL enabled MUMPS sparse solver library will be enabled shortly

* Fix invalid version range error

* Incorporated review comments

1) Restore to previous url value
2) Instead of if else statements, used spack's enable_or_disable feature

* Incorporated following review comments:

1. Use of satisfies() for spec checks
2. Seperate conflict statements to check for minimum and maximum GCC versions
3. Used CMakePackage helpers
4. Code rearrangement to have the directives listed before methods
2021-12-17 09:28:41 -08:00
Valentin Volkl
140e8085dd sherpa: add new package (#27592)
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
2021-12-17 18:16:58 +01:00
AMD Toolchain Support
2597fff76b FFTW3 library inclusion (#27936)
Co-authored-by: mohan babu <mohbabul@amd.com>
2021-12-17 18:11:59 +01:00
iarspider
225595235c New package: py-xrootdpyfs (#28058)
* New package: py-xrootdpyfs

* Add old version of py-fs

* Replace 2to3.patch with running 2to3

* Just restriuct setuptools version

* Update var/spack/repos/builtin/packages/py-fs/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-12-17 10:11:20 -07:00
Vanessasaurus
d9c4b91af3 Remove ability to run spack monitor without auth (#27888)
spack monitor now requires authentication as each build must be associated
with a user, so it does not make sense to allow the --monitor-no-auth flag
and this commit will remove it
2021-12-17 18:00:43 +01:00
Max Zeyen
ee2974869c gpi-2: add version 1.3.3 (#27881) 2021-12-17 17:57:48 +01:00
Adeeb Arif Kor
c940e9fc7e dolfinx: add ADIOS2 variant (#27540) 2021-12-17 17:55:30 +01:00
Tom Payerle
c3a929fdfc suite-sparse: fix issues with tbb (#28054)
* suite-sparse: Fix check for +/- tbb variant

Changed
'tbb' in spec
to
'+tbb' in spec

The former would configure suite-sparse to use tbb if any dependency
package (e.g. intel-oneapi-mkl) depends on tbb, even if
suite-sparse~tbb was specified.

* suite-sparse: conflict when trying to use 2021.x versions of tbb

See https://github.com/DrTimothyAldenDavis/SuiteSparse/issues/72

suite-sparse depends on task_schedule_init to control the number
of threads when e.g. interfacing with MATLAB.  However, Intel
dropped task_schedule_init in the 2021.x releases of TBB (it has
been deprecated since TBB 4.3.5).

We just raise a spack conflict when using tbb @2021.x and +tbb

Because tbb is a virtual package and is not versioned, I have
instead checked for either intel-oneapi-tbb@2021: or
intel-tbb@2021:, not the most elegant but should do the job

* suite-sparse: fix style issues
2021-12-17 09:32:59 -07:00
Manuela Kuhn
6313d84d38 r-viridislite: add 0.4.0 (#27872) 2021-12-17 17:19:42 +01:00
snehring
10ccbc9a2c bridger: fixing issues with newer compilers (#28008) 2021-12-17 17:14:44 +01:00
Drew Whitehouse
bbe69aa725 libcxxwrap-julia: fix the git branch name master -> main (#28033) 2021-12-17 17:03:03 +01:00
Adam J. Stewart
8b3858081d py-mypy: add v0.920 (#28034) 2021-12-17 17:02:06 +01:00
Adam J. Stewart
809d0523d9 Add py-pytorch v1.10.1 and py-pytorchvision v0.11.2 (#28055) 2021-12-17 16:14:54 +01:00
haralmha
e1f6a2e6b5 Specify dependencies to py-setuptools@:57.99 for packages using 2to3 (#27777) 2021-12-17 08:08:01 -06:00
Wouter Deconinck
956bb91cfe [autodiff] new package for optional dependency of acts (#28028) 2021-12-17 14:22:46 +01:00
Wouter Deconinck
23cb7d761e [vecmem] new package for optional dependency of acts (#28029) 2021-12-17 14:21:51 +01:00
Wouter Deconinck
1813a809ff [acts] depends_on dd4hep +dddetectors (+ddg4 when +geant4) (#27861) 2021-12-17 14:17:52 +01:00
ravil-mobile
e3f0be41d4 Updated dpcpp package (#27953)
* Added installation of OpenMP as an option
* Added a softlink (dpcpp) to clang++ to
mimic the packaged version of dpcpp

Co-authored-by: ravil <ravil.dorozhinskii@tum.de>
2021-12-17 14:16:13 +01:00
iarspider
618fd04729 py-vector: add new package (#28057) 2021-12-17 14:14:38 +01:00
Harmen Stoppels
04bed42831 libtree: add v3.0.1 (#28040) 2021-12-17 10:34:24 +01:00
Massimiliano Culpo
661fd7bb67 Fix building container images (#28063)
* Fix building container images

Patchelf is bootstrapped from sources, so we cannot
disable that mechanism until a finer selection is
possible in the configuration.

* Build on changes to the Dockerfile

* Don't login to Dockerhub on PRs
2021-12-17 09:19:21 +00:00
victorusu
18615b1485 Add setdefault option to tcl module (#14686)
This commit introduces the command

spack module tcl setdefault <package>

similar to the one already available for lmod

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-12-17 10:05:32 +01:00
AMD Toolchain Support
f754ed9788 Additional flags for ROMS (#27951)
Co-authored-by: mohan babu <mohbabul@amd.com>
2021-12-16 19:47:20 -08:00
iarspider
6443086222 CMake: fix rhash detection (#27944)
* RHash: update version; create symlink librash.so

* Install headers

* Flake-8

* Update package.py

* Update package.py

* Update package.py (#19)

* Update package.py

* Update package.py

* Update var/spack/repos/builtin/packages/rhash/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Fix installation on macOS

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-12-16 18:02:26 -07:00
Larry Knox
556565ca0d hdf5: add version 1.10.8 (#27613)
* Update hdf5/package.py to add HDF5 1.10.8 release and move
  preferred version from 1.10.7 to 1.10.8.
* silo: versions before 4.11 conflict with hdf5 >= 1.10.8.
* Add patch file for silo@4.11 with hdf5 1.10 >=1.10.8 and
  hdf5 1.12 >= 1.12.1.
2021-12-16 16:51:02 -08:00
Satish Balay
40886599ce petsc: enable +rocm+kokkos (#27779)
Also fix kokkos-kernels when kokkos is built with +rocm
2021-12-16 14:47:31 -08:00
eugeneswalker
2310da0070 rocprofiler-dev package: needs numactl as link dep for tests (#27839) 2021-12-16 14:17:05 -08:00
Jen Herting
e76de4138e New package: py-pynisher (#28052)
* [py-pynisher] created template

* [py-pynisher]

- Added homepage
- Added description
- Removed fixmes
- added dependencies
2021-12-16 14:21:45 -06:00
Howard Pritchard
43aeb4e48e OpenMPI Package: add variant for romio (#27897)
Add option to disable the internal romio build.
2021-12-16 10:49:28 -08:00
iarspider
305f1d68d6 New package: py-scinum (#28041)
* New package: py-scinum

* Update var/spack/repos/builtin/packages/py-scinum/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-12-16 11:29:14 -07:00
Tracy-Pantleo
1b273ed5c9 wonton package: fix reference error (#27963) 2021-12-16 09:55:37 -08:00
iarspider
bb1d0d1900 New package: py-schema (#28039) 2021-12-16 11:54:59 -06:00
iarspider
f262693983 New package: py-shellingham (#28043) 2021-12-16 11:43:52 -06:00
iarspider
8c81469f94 New version: py-correctionlib 2.1.0 (#28051) 2021-12-16 10:36:57 -07:00
vijay kallesh
6c250640c4 aocc: add v3.2.0 (#27946)
Co-authored-by: amd-toolchain-support <toolchainsupport@amd.com>
2021-12-16 14:37:59 +01:00
Harmen Stoppels
fb93979b94 Set backup=False by default in filter_file (#28036) 2021-12-16 13:50:20 +01:00
Harmen Stoppels
6357de4e61 Fix table formatting (#28037) 2021-12-16 12:13:12 +00:00
Andrew W Elble
96535cc4f9 MANPATH needs a trailing ':' to utilize system defaults (#21682)
otherwise spack breaks using system man pages by default.

Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2021-12-16 10:54:35 +00:00
Christian Goll
bd0ffa8a3c Added opensuse/leap:15 to spack containerize (#27837)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-12-16 09:47:15 +00:00
Tamara Dahlgren
ac49ce8b3b Provide meaningful message for empty environment installs (#28031)
* Provide a meaningful failure message for installation of an empty environment

* Allow regenerating view per offline discussion
2021-12-15 22:56:54 -08:00
Tamara Dahlgren
9240614928 Bugfix: Simplify preferred-test versions; set checksum defaults (#28026)
* Simplify preferred-test versions; set checksum defaults

* Fix test_preferred failure
2021-12-16 06:55:28 +01:00
snehring
89044ff5d5 delly2: updating to v0.9.1 (#28000) 2021-12-16 06:47:11 +01:00
Thomas Green
315f01fc96 meep: fixed dependencies (#27574)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-12-16 06:44:26 +01:00
snehring
e99aff93e1 samtools: fixing build issue due to change in 1.14 (#28024) 2021-12-16 06:34:22 +01:00
AMD Toolchain Support
42677ded8e Fix for OpenFOAM pthread issue for AOCC 3.2 (#27949)
* Fix for OpenFOAM pthread issue for AOCC 3.2

* addressing the review comments

* updating when command for aocc v3.2.0 and above

Co-authored-by: mohan babu <mohbabul@amd.com>
2021-12-15 21:45:17 -06:00
Dennis R Kennetz
d375a7ea0a pcre package: update download URL (#27867)
* ftp url is dead as stated in the home page. The sha256 is the same in the sourceforge dl.
* added myself as a maintainer per spackbot's rec
2021-12-15 18:58:13 -08:00
Jen Herting
3b4c622661 New package: py-copulas (#27920)
Co-authored-by: Sid Pendelberry <sid@rit.edu>
2021-12-15 18:56:13 -08:00
Erik Schnetter
ba87593afd mpitrampoline package: add versions up to 2.8.0 (#27928) 2021-12-15 18:53:03 -08:00
Adam J. Stewart
af1ec6275d py-matplotlib: add v3.5.1 (#27929) 2021-12-15 18:52:21 -08:00
Adam J. Stewart
3ff2fb43cf py-pandas: add v1.3.5 (#27930) 2021-12-15 18:52:02 -08:00
Wouter Deconinck
a148e37c4c assimp package: add version 5.1.3 (#27934) 2021-12-15 18:51:01 -08:00
Thomas Gruber
4d876bac0c likwid package: add version 5.2.1 (#27935) 2021-12-15 18:49:19 -08:00
Asher Mancinelli
114b35144e ExaGO package: add version 1.2.0; update dependency constraints (#27961)
* PETSc is a core dependency, yet we left a variant for PETSc.
  This was removed, and ExaGO always depends on PETSc. The CMake
  arguments were updated accordingly.
* camp+cuda is only a dependency when we build with RAJA and CUDA.
2021-12-15 18:23:36 -08:00
snehring
69184dc390 opa-psm2 package: add version 11.2.206 (#27968) 2021-12-15 18:13:22 -08:00
Mikhail Titov
70aea4cd82 RADICAL-Cybertools packages: add versions (#28002)
* py-radical-entk: add version 1.9.0
* py-radical-pilot: add version 1.10.1
* py-radical-utils: add version 1.9.1
* py-radical-utils: requires py-pymongo less than version 4
2021-12-15 17:53:05 -08:00
Adam J. Stewart
e091eacde0 New package: py-trojanzoo-sphinx-theme (#27972) 2021-12-15 17:48:43 -08:00
Adam J. Stewart
9447ec9600 py-sphinx package: add version 4.3.1 (#27933) 2021-12-15 16:22:22 -08:00
iarspider
351a1d8d37 New package: py-pysqlite3 (#28020)
* New package: py-pysqlite3

* Apply suggestions from code review

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-12-15 14:35:07 -07:00
iarspider
b0f996c8ef New package: py-prwlock (#28017) 2021-12-15 12:00:28 -06:00
iarspider
4de197f778 New package: py-pybrain (#28019) 2021-12-15 11:59:04 -06:00
iarspider
bd7d3faa10 New package: py-parsimonious (#28015) 2021-12-15 11:29:36 -06:00
iarspider
bc152da68b New version: py-prompt-toolkit 3.0.24 (#28016) 2021-12-15 11:17:25 -06:00
Harmen Stoppels
72ca7d6ee5 Revert "patches: make re-applied patches idempotent (#26784)" (#27625)
This reverts commit c5ca0db27f.
2021-12-15 08:56:03 -08:00
Harmen Stoppels
acc688b5e1 libtree: add v3.0.0 (#28011) 2021-12-15 17:38:10 +01:00
Adam J. Stewart
0cf3176462 open3d: add new package (#27577) 2021-12-15 17:34:22 +01:00
kwryankrattiger
116e1bb6cb mesa: check correct LLVM variant for dylib (#27862) 2021-12-15 16:37:35 +01:00
Wouter Deconinck
9c1be2a510 mesa: add v21.2.6, v21.3.1 (#27796) 2021-12-15 14:13:52 +01:00
Greg Becker
5319b6e3b1 Add option to minimize full debug cores. include warning message about performance (#27970)
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2021-12-15 08:52:53 +01:00
iarspider
ce94a786ae New package: py-neurolab (#27996)
* New package: py-neurolab

* Update package.py

* Update package.py
2021-12-14 15:23:06 -07:00
iarspider
25c29d277f New package: py-lizard (#27994)
* New package: py-lizard

* Update package.py
2021-12-14 14:44:19 -07:00
iarspider
e51337fcd9 New package: py-nbdime (#27995) 2021-12-14 15:22:24 -06:00
Zack Galbreath
3139894794 ci: Catch Exceptions when attempting to register a CDash build (#27883)
This PR also slightly changes the behavior in ci_rebuild().
We now still attempt to submit `spack install` results to CDash
even if the initial registration failed due to connection issues.

This commit follows in the spirit of #24299. We do not want `spack install`
to exit with a non-zero status when something goes wrong while attempting to
report results to CDash.
2021-12-14 14:18:08 -07:00
iarspider
5bbb63ed93 New package: py-law (#27993) 2021-12-14 15:04:46 -06:00
iarspider
bc618c2c6c OpenLDAP package: update dependencies for 2.6.0 (#27830)
Update a number of dependency constraints for @2.6.0: (including
adding new optional dependency package wiredtiger).
2021-12-14 11:27:02 -08:00
downloadico
97a1d48512 Abinit package: add option to install tests (#27842) 2021-12-14 11:04:28 -08:00
Harmen Stoppels
9ec638c7bb Add libtree 3.0.0-rc9 (#27990) 2021-12-14 14:17:38 +01:00
iarspider
c1d51593d1 New packages: py-keras2onnx, py-onnxconverter-common (#27962)
* New packages: py-keras2onnx, py-onnxconverter-common

* Update package.py (#18)

* Update package.py

* Update package.py
2021-12-13 12:47:27 -07:00
Massimiliano Culpo
948bc98fa6 Add a CI job to audit all the packages in the built-in repository (#27945)
* Add a CI job to audit all the packages in the built-in repository

* flecsi: fixed typo for dependency on legion

* py-pythonqwt: fix a typo in variant name

* sollve: removed a conflict with a non-existing variant

* acts: fixed use of wrong variant in dd4hep

Also removed duplicated variant declaration in dd4hep

* aoflagger: update variant of a dependency

Issues introduced indirectly in #22925

* camellia: removed unused variant

Issue introduced indirectly in #26150

* cbtf-*: remove cti variants and dependency on mrnet+cti

Issue introduced in #14178

* flecsale: update variants to match flecsi

Issue introduced in #11679

* grnboost: fixed issue with non-existing variant in a dependency

This package possibly never worked since #8763

* nalu: fixed issue with non-existing variant in a dependency

* open-iscsi: fixed issue with non-existing variant in a dependency

* openspeedshop-*: remove use of non-existing mrnet+cti variant

* percept: fixed issue with non-existing variant in a dependency

* phyluce: fixed issue with non-existing variant in a dependency

Issue introduced in #12952

* phyluce: fixed issue with non-existing variant in a dependency

Issue introduced in #22340
2021-12-13 10:44:15 -08:00
Scot Halverson
28d31316b7 CPU Architecture support (#27924)
* CPU Architecture Support

This commit removes the `native` variant in favor of Spack's built-in support for specifying a target cpu architecture.  It also passes this information to the Legion build system so that it correctly passes the architecture to GASNet when built internally

* fixing whitespace

* Update package.py

based on a conversation with @streichler, this change sets `BUILD_MARCH` to an empty string, which will prevent legion's CMake build system from inserting `-march=native` and allow Spack to provide the correct architecture flags.

* Update package.py

adding a comment on what problem this MR solves.

* Update package.py

formatting
2021-12-13 10:06:57 -08:00
iarspider
f876813531 New package: py-histbook (#27956) 2021-12-13 11:55:57 -06:00
iarspider
ec8ef9d292 New package: py-histogrammar (#27957) 2021-12-13 11:55:09 -06:00
iarspider
7836b60825 New package: py-jupyter-server-mathjax (#27958) 2021-12-13 11:54:01 -06:00
Manuela Kuhn
17367a702e r-packrat: add 0.7.0 (#27901) 2021-12-13 11:19:39 -06:00
Manuela Kuhn
1bd2c40228 r-rsconnect: add 0.8.17 (#27900) 2021-12-13 11:19:18 -06:00
Manuela Kuhn
71e71c0b60 r-vroom: add 1.5.7 (#27874) 2021-12-13 11:18:38 -06:00
Manuela Kuhn
f920976fa6 r-r6: add 2.5.1 (#27871) 2021-12-13 11:16:47 -06:00
eugeneswalker
26dcb0ffc4 vtk-m +cuda: conflicts with cuda_arch=none (#27916) 2021-12-13 08:46:09 -08:00
Harmen Stoppels
f6802b733a Install dir creation message demoted to "debug" level (#27911) 2021-12-13 11:45:31 +01:00
iarspider
7b9ce3a940 New package: py-hep-ml (#27909) 2021-12-11 14:41:08 -07:00
iarspider
dc88538e80 New package: py-grpcio-tools; add new version of py-grpcio (#27907) 2021-12-11 14:35:07 -07:00
Axel Huebl
9875a0e228 PICMI: 0.16 & 0.18 & WarpX 1D (#27876)
* PICMI: 0.16 & 0.18 & WarpX 1D

Update the `py-picmistandard` and the latest WarpX release.
Preparing 1D support (testable inputs coming for 22.01+).

* Fix style: overlong line

* Update pypi example link

* Fix requirement ranges

* WarpX 21.12: Update Patch

Follow-up from
  https://github.com/ECP-WarpX/WarpX/pull/2646

* fix style

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-12-11 14:14:00 -07:00
Sergey Kosukhin
ee46a1077c openjpeg: add missing dependencies and optionally disable them (#27904)
* openjpeg: add missing dependencies and optionally disable them

* openjpeg: remove variant 'ownlibs'

* openjpeg: bugfix

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* openjpeg: do not build CODEC executables by default

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-12-11 11:51:17 -06:00
Manuela Kuhn
5d11bc9a77 r-emmeans: add 1.7.1-1 (#27870) 2021-12-10 22:27:06 -06:00
Manuela Kuhn
a9b2a18880 r-dt: add 0.20 (#27868) 2021-12-10 22:26:10 -06:00
Peter Brady
27ba835236 lua package: fix build with ncurses~termlib (#27863)
Get link flags directly from dependencies rather than hardcoding
2021-12-10 20:24:33 -08:00
Satish Balay
e4da7db567 superlu-dist: superlu-cray-ftn-case.patch patch does not apply for versions older than 7.1.0 (#27913) 2021-12-10 21:58:22 -06:00
Satish Balay
2f35b0487b petsc, py-petsc4py: add versions 3.16.2 (#27841) 2021-12-10 21:58:09 -06:00
Manuela Kuhn
81bb380916 r-cpp11 package: add version 0.4.2 (#27869) 2021-12-10 19:53:16 -08:00
Manuela Kuhn
08573b4cb8 r-htmltools package: add version 0.5.2 (#27899) 2021-12-10 19:03:38 -08:00
eugeneswalker
b9717ca261 vtk-h +cuda: pass cuda_arch to vtk-m dependency (#27923) 2021-12-10 17:32:11 -07:00
Filippo Spiga
5d6a9a70c8 Adding NVIDIA HPC SDK 21.11 (#27910) 2021-12-10 15:04:38 -08:00
Timothy Brown
f3b5704663 [parallelio] add variant to turn off timing messages. (#27590)
* [parallelio] add variant to turn off timing messages.
2021-12-10 14:58:49 -08:00
iarspider
d5773ac5bf New package: py-hist and it's dependencies (#27914)
* New package: py-hist and it's dependencies

* Update var/spack/repos/builtin/packages/py-hist/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-histoprint/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-mplhep/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update py-hist recipe

* Update package.py

* Fix py-iminuit recipe (requires py-cmake now)

* Update package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-12-10 18:31:22 +00:00
Ye Luo
363a263114 Update quantum-espresso package (#27808)
* Override compiler as MPI wrapper in CMake.

* Refine quantum-espresso variant interations.

* Correct formatting.
2021-12-10 10:18:32 -08:00
iarspider
140a2721e6 New package: py-correctionlib (#27882)
* New package: py-correctionlib

* Update var/spack/repos/builtin/packages/py-correctionlib/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-correctionlib/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Add py-make and update py-correctionlib recipe

* Add py-bind11 dependency

* Update package.py

* Update package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-12-10 11:34:31 -06:00
iarspider
8b6bb245db New package: py-flawfinder (#27887)
* New package: py-flawfinder

* Build py-flawfinder from source

* Update package.py
2021-12-10 11:25:21 -06:00
iarspider
059bc53760 New package: py-hepdata-lib (#27912) 2021-12-10 11:24:22 -06:00
Adam J. Stewart
0960c0810c Extends: support spec, not just package name (#27754) 2021-12-10 13:30:21 +01:00
Greg Becker
dc87157e80 Improve debug info from concretizer (#27707) 2021-12-10 10:49:33 +01:00
Massimiliano Culpo
d17511a806 Refactor "spack buildcache" command (#27776)
This PR is meant to move code with "business logic" from `spack.cmd.buildcache` to appropriate core modules[^1]. 

Modifications:
- [x] Add `spack.binary_distribution.push` to create a binary package from a spec and push it to a mirror
- [x] Add `spack.binary_distribution.install_root_node` to install only the root node of a concrete spec from a buildcache (may check the sha256 sum if it is passed in as input)
- [x] Add `spack.binary_distribution.install_single_spec` to install a single concrete spec from a buildcache
- [x] Add `spack.binary_distribution.download_single_spec` to download a single concrete spec from a buildcache to a local destination
- [x] Add `Spec.from_specfile` that construct a spec given the path of a JSON or YAML spec file
- [x] Removed logic from `spack.cmd.buildcache`
- [x] Removed calls to `spack.cmd.buildcache` in `spack.bootstrap`
- [x] Deprecate `spack buildcache copy` with a message that says it will be removed in v0.19.0

[^1]: The rationale is that commands should be lightweight wrappers of the core API, since that helps with both testing and scripting (easier mocking and no need to invoke `SpackCommand`s in a script).
2021-12-10 10:23:14 +01:00
eugeneswalker
e199d7ef6b umpire: needs cmake@:3.20 when +rocm (#27893) 2021-12-09 16:14:56 -08:00
eugeneswalker
b286c62feb raja +rocm: depends on cmake@:3.20 for now (#27895) 2021-12-09 16:14:10 -08:00
iarspider
32c442afdb New package: py-cmsml (#27880)
* New package: py-cmsml

* Update var/spack/repos/builtin/packages/py-cmsml/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-12-09 16:47:12 -07:00
iarspider
75154318af New package: py-cx-oracle (#27884)
* New package: py-cx-oracle

* Add dependencies from pyproject.toml

* Update var/spack/repos/builtin/packages/py-cx-oracle/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-12-09 16:54:29 -06:00
iarspider
74f4c73c24 Add py-climate (#27879)
* fixing bugs in spack monitor

updates to installer.py did not account for spack monitor, so as currently implemented
there are three cases of failure that spack monitor will not account for. To fix this we add additional
hooks, including an on cancel and also do a custom action on concretization fail.

Signed-off-by: vsoch <vsoch@users.noreply.github.com>

* New package: py-climate

* Revert "fixing bugs in spack monitor"

This reverts commit bf7f6bf0e3.

* Flake-8

* Update package.py

* Update package.py

Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2021-12-09 15:26:18 -07:00
eugeneswalker
9445b931ec llvm-doe: update maintainer to vlkale (#27894) 2021-12-09 15:14:12 -07:00
iarspider
621760a8b8 New packages: py-backports-os, py-fs (#27886) 2021-12-09 13:29:39 -06:00
iarspider
065f349813 New package: py-downhill (#27885) 2021-12-09 13:27:14 -06:00
eugeneswalker
48b1531966 boost: add v1.78 (#27889) 2021-12-09 12:14:07 -07:00
Hans Fangohr
262d5e6791 New package: dust (#27845) 2021-12-09 09:44:18 -08:00
Mikael Simberg
361a2ccdf6 Add conflict to HPX package for Boost/HIP noinline issue (#27878) 2021-12-09 13:33:51 +01:00
eugeneswalker
c930f871f3 llvm-doe: incorporate updates to official llvm Spack package (#27866)
* llvm-doe: incorporate select configurations from llvm package

* add newline at end of file
2021-12-08 16:21:11 -08:00
eugeneswalker
b9a2e71a8b e4s ci: expand +cuda specs (#27272) 2021-12-08 16:13:45 -08:00
Massimiliano Culpo
01d077d4bc Make external detection more resilient to individual package errors (#27854)
After this PR an error in a single package while detecting
external software won't abort the entire procedure.

The error is reported to screen as a warning.
2021-12-08 13:58:21 -08:00
iarspider
79a04605d3 New package: py-aiosqlite (#27852)
* New package: py-aiosqlite

* Update package.py
2021-12-08 18:24:44 +00:00
iarspider
a873c7f456 New package: py-boost-histogram (#27853)
* New package: py-boost-histogram

* Update var/spack/repos/builtin/packages/py-boost-histogram/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-12-08 18:19:06 +00:00
Jerome Soumagne
5881ec5389 mercury: add version 2.1.0 (#27825)
Update package recipe to be more idiomatic
2021-12-08 15:16:19 +01:00
Valentin Volkl
50cb742377 libdrm: fix build error with clang (#27848) 2021-12-08 15:05:38 +01:00
Valentin Volkl
4ccfe5108c dd4hep: add version 0.19 and variants for subpackages (#27717)
* dd4hep: add version 0.19 and variants for subpackages

* dd4hep: deprecate old versions, add tbb variant
2021-12-08 14:04:43 +01:00
Dylan Simon
39e6f987bb ncurses: keep ncurses and ncursesw headers (#27372)
- Copy ncursesw headers to include/ (matches prior behavior)
- include/ncurses no-longer keeps a copy of ncursesw headers
2021-12-08 00:04:49 -07:00
Tamara Dahlgren
d458e82286 rocm: add gfx90a (#27823) 2021-12-07 17:19:48 -08:00
Manuela Kuhn
1314273a42 r-rio: add 0.5.29 (#27838) 2021-12-07 17:56:24 -06:00
Manuela Kuhn
0337bb50d9 r-diffobj: 0.3.5 (#27836) 2021-12-07 17:53:28 -06:00
Manuela Kuhn
4227a546a1 r-desc: add 1.4.0 (#27834) 2021-12-07 17:52:54 -06:00
Manuela Kuhn
5f4af3ac8a r-dbi: add 1.1.1 (#27833) 2021-12-07 17:51:20 -06:00
Manuela Kuhn
4a53536464 r-crosstalk: add 1.2.0 (#27832) 2021-12-07 17:50:07 -06:00
Manuela Kuhn
3b491ccbbd r-rmarkdown: add 2.11 (#27831) 2021-12-07 17:48:36 -06:00
Harmen Stoppels
3d1b9e4dbc "spack buildcache install": don't catch exception (#27674)
Remove a try/catch for an error with no handling. If the affected
code doesn't execute successfully, then the associated variable
is undefined and another (more-obscure) error occurs shortly after.
2021-12-07 13:17:17 -08:00
Massimiliano Culpo
f81d84dfc6 Release procedure: add a step to update docs (#27734) 2021-12-07 11:30:14 +00:00
Asher Mancinelli
7254d0fe94 HiOp: add versions, variants for rocm (#27824) 2021-12-07 11:38:10 +01:00
Glenn Johnson
3160ab66db 3dtk: set boost constraint (#27806) 2021-12-07 11:28:41 +01:00
Axel Huebl
941e6505d0 WarpX: 21.12 (#27800)
Update `warpx` & `py-warpx` to the latest release, `21.12`.
2021-12-06 17:16:46 -08:00
iarspider
687bc7d40e py-rich: add version 10.9.0 (#27826) 2021-12-06 15:32:01 -07:00
Manuela Kuhn
949923c03f r-blob: add 1.2.2 (#27797) 2021-12-06 22:00:59 +00:00
Manuela Kuhn
1d8575cd83 r-colorspace: add 2.0-2 (#27815) 2021-12-06 15:43:26 -06:00
Manuela Kuhn
3949cd567d r-jquerylib: add new package (#27716) 2021-12-06 15:42:20 -06:00
Manuela Kuhn
4ece86c64a r-brio: add 1.1.3 (#27801) 2021-12-06 15:25:43 -06:00
Manuela Kuhn
1a2d522eaa r-conquer: add 1.2.1 (#27802) 2021-12-06 15:24:56 -06:00
Manuela Kuhn
c18e91d771 r-crayon: 1.4.2 (#27803) 2021-12-06 15:23:32 -06:00
Manuela Kuhn
451a4f2cfa r-brms: add 2.16.3 (#27809) 2021-12-06 15:22:34 -06:00
Manuela Kuhn
88175417bb r-cli: add 3.1.0 (#27810) 2021-12-06 15:20:26 -06:00
Manuela Kuhn
4de7c6a901 r-car: add 3.0-12 (#27811) 2021-12-06 15:14:21 -06:00
Manuela Kuhn
0d5eb2657a r-colourpicker: add 1.1.1 (#27816) 2021-12-06 14:09:58 -06:00
Manuela Kuhn
9b3ac00c2d r-backports: add 1.4.0 (#27710) 2021-12-06 14:08:31 -06:00
Manuela Kuhn
b4f47cbdec r-bh: add 1.75.0-0 (#27711) 2021-12-06 14:07:01 -06:00
Manuela Kuhn
ccda43673a r-rcpparmadillo: add 0.10.7.3.0 (#27712) 2021-12-06 14:04:55 -06:00
Jen Herting
3b8a34240e [py-pyspellchecker] New package (#27788)
Co-authored-by: Sid Pendelberry <sid@rit.edu>
2021-12-06 10:57:50 -06:00
Jen Herting
d0fffa9212 apktool: new package (#27782) 2021-12-06 17:20:31 +01:00
Hector Barrios
0106e6ec9c mumps: fix problem when using Intel OneAPI mkl static lib (#27725) 2021-12-06 17:14:33 +01:00
Glenn Johnson
37a4c0ff59 r-prettydoc: fix dependency (#27791)
The markdown dependency is `r-rmarkdown` rather than `r-markdown`.
2021-12-06 17:13:44 +01:00
Glenn Johnson
30007f7897 r-affy: set r version constraint (#27792) 2021-12-06 17:00:03 +01:00
Glenn Johnson
caba5c4692 Remove the autotools resources (#27793)
This essentially reverts #18917 as it seems to no longer be necessary
due to recent autotools changes in core spack.
2021-12-06 16:59:25 +01:00
Wouter Deconinck
bc3a3d9249 opencascade: add v7.6.0 (#27799) 2021-12-06 16:44:19 +01:00
Glenn Johnson
599b8c3533 suite-sparse: Add CXSparse and SPQR to targets (#27804) 2021-12-06 16:40:07 +01:00
Michael Kuhn
e6432d2380 glib: add 2.70.2 (#27812) 2021-12-06 16:34:26 +01:00
Glenn Johnson
39ebf9c5a7 Set preferred version of vtk to 9.0.3 (#27817)
There is a library symbol issue with libioss and python with version
9.1.0 so set preferred version to 9.0.3.
2021-12-06 16:28:35 +01:00
Wouter Deconinck
a332c26780 acts: use variants['cuda_arch'] only when +cuda (#27813)
Since #27185, the cuda_arch variant values are conditional on +cuda. This means that for -cuda specs, the installation fails with:
```
==> acts: Executing phase: 'cmake'
==> Error: KeyError: 'cuda_arch'

/home/wdconinc/git/spack/var/spack/repos/builtin/packages/acts/package.py:222, in cmake_args:
        219        log_failure_threshold = spec.variants['log_failure_threshold'].value
        220        args.append("-DACTS_LOG_FAILURE_THRESHOLD={0}".format(log_failure_threshold))
        221
  >>    222        cuda_arch = spec.variants['cuda_arch'].value
        223        if cuda_arch != 'none':
        224            args.append('-DCUDA_FLAGS=-arch=sm_{0}'.format(cuda_arch[0]))
        225
```
2021-12-06 16:25:27 +01:00
Glenn Johnson
a8a226b748 bohrium: missing dependencies (#27807) 2021-12-06 16:23:25 +01:00
Wouter Deconinck
9b1b38d2de librsvg,libcroco: add doc variant to avoid unsolvable constraints due to gtkplus (#27790)
* [libcroco] add variant doc, depends_on gtk-doc when +doc
* [librsvg] add variant doc, depends_on gtk-doc when +doc
2021-12-06 14:08:22 +01:00
Wouter Deconinck
2bb075c850 rivet: hepmc=3: Fix prefix of --with-hepmc3 (#27814) 2021-12-06 10:42:54 +01:00
Glenn Johnson
235edd0742 new package: py-tensorflow-datasets (#27746)
* new package: py-tensorflow-datasets

- includes new dependency package: py-tensorflow-metadata

* Update var/spack/repos/builtin/packages/py-tensorflow-datasets/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-tensorflow-metadata/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-12-05 12:06:43 -06:00
Glenn Johnson
252cd48b9c py-astropy: set version constraint on cfitsio (#27805) 2021-12-05 12:06:09 -06:00
Ben Bergen
c2def5c2f4 cgdb: add depends_on('gdb', type='run') (#27753)
* Added gdb Dependency

When using spack to install cgdb, a spack-built gdb is necessary to
avoid dynamic link errors.

- Added maintainer: tuxfan
- Set preferred to 'master' (best version for spack currently)

* Update: The gdb dependency added by this PR is for runtime

Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2021-12-05 08:02:23 -07:00
Manuela Kuhn
25a9888102 r-v8: add 3.6.0 (#27714)
* r-v8: add 3.6.0

* Add conflict and deprecate version 3.4.0
2021-12-05 00:56:47 -06:00
Manuela Kuhn
1eec99ce1d py-imagesize: add 1.3.0 (#27787) 2021-12-03 21:05:05 -07:00
Manuela Kuhn
c0dab7617f py-jeepney: add 0.7.1 (#27786) 2021-12-03 20:16:56 -07:00
Chung ShinYee
041973d1d5 julia: update versions and add znver3 to Julia's CPU target (#27770)
* julia: new versions.

* julia: Support AMD Milan CPU znver3.
2021-12-03 18:31:47 -07:00
kwryankrattiger
203ccdd976 LLVM: Revert build_llvm_dylib to llvm_dylib (#27761) 2021-12-03 23:47:05 +01:00
Tamara Dahlgren
6f9dc1c926 berkeley-db: Add minimal external detection (#27752) 2021-12-03 23:42:45 +01:00
Manuela Kuhn
324e046f06 r-tictoc: add 1.0.1 (#27715) 2021-12-03 16:14:29 -06:00
Asher Mancinelli
21d1e03e37 ExaGO: add new versions (#27768) 2021-12-03 13:59:16 -08:00
Mark W. Krentel
34c1d196a4 hpctoolkit: add support for smoke tests (#27783)
This adds support in spack for both build/install tests (spack install
--run-tests) and post-install smoke tests (spack test run).

Hpctoolkit itself only recently added tests, so for now, this only
applies to branch master.
2021-12-03 12:52:34 -08:00
Jen Herting
bd2b5cc7aa [libzmq] added version 4.3.4 (#27780) 2021-12-03 13:44:04 -07:00
Simo Tuomisto
cfb8d6f8ac New package: mujoco (#27656) 2021-12-03 11:40:09 -08:00
Weiqun Zhang
0a656de60b amrex: add new release 21.12 (#27781) 2021-12-03 11:00:14 -08:00
Hans Pabst
23bd0f3178 LIBXSMM 1.17 (#27775) 2021-12-03 10:48:40 -08:00
Hans Pabst
0e7220b2f2 Fixed typo (NAMD). (#27774) 2021-12-03 10:40:34 -08:00
Bernhard Kaindl
53eb24af9b singularity, singularityce: Add 3.8.5 and ce-3.9.1 (#27778) 2021-12-03 11:23:08 -07:00
Richarda Butler
86b17193de Parallel-netcdf: Update Spack test dir (#27232)
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2021-12-03 10:03:14 -08:00
Filippo Spiga
96a50db344 CUDA: add v11.5.1 (#27689) 2021-12-03 06:13:51 -07:00
Ethan Stam
4c922ec572 ParaView: add dependencies needed in paraview@master (#27745)
* The proj and nlohmann-json packages are needed in paraview@master
* ParaView: bump master subdir version to 5.10
2021-12-02 17:18:23 -08:00
Terry Cojean
b80b085575 Ginkgo package: add oneAPI support (#26868)
To use this, you can "spack install intel-oneapi-compilers" and then
"spack compiler add" the new compiler. You would need to install with
"spack install ginkgo+oneapi%dpcpp"
2021-12-02 17:13:25 -08:00
Michael Kuhn
fbd67feead nss: add 3.73 (#27767) 2021-12-03 00:55:57 +01:00
Peter Scheibel
edb971a10e Support packages which need to explicitly refer to dpcpp by name (#27168)
* Hack to support packages which need to explicitly refer to dpcpp by name
* cc script needs to know about dpcpp
2021-12-02 15:49:20 -08:00
Michael Kuhn
693a15ea00 nspr: add 4.32 (#27766) 2021-12-03 00:36:50 +01:00
Bernhard Kaindl
4d1a6cd362 libseccomp package: add version 2.5.3 (#27756)
- Use .tar.gz archive
- Update 2.3.3 to use .tar.gz archive (and update checksum)
- autoreconf dependency is no-longer required
- The new version depends on gperf
2021-12-02 14:52:23 -08:00
Bernhard Kaindl
9e1e7fa1d7 lvm2 package: add version 2.03.14 (#27760) 2021-12-02 14:37:59 -08:00
Ben Darwin
07ab4623e6 New package: f3d (add version 1.1.1) (#27755) 2021-12-02 14:35:55 -08:00
Jen Herting
66c5199362 New package: py-fire (#27731)
* dependency for stylegan2

* fixed copyright

* [py-fire]

- fixed some formatting
- url -> pypi

* [py-fire] removed extra https://

* [py-fire]

- removed python version restriction
- enum34 -> py-enum34

* [py-fire] removed .999

Co-authored-by: Sid Pendelberry <sid@rit.edu>
2021-12-02 14:58:25 -06:00
Jen Herting
ca32b08825 New package: py-vector-quantize-pytorch (#27759)
* [py-vector-quantize-pytorch] New package

* [py-vector-quantize-pytorch] flake8

* [py-vector-quantize-pytorch] removed unnecessary dependency

Co-authored-by: Sid Pendelberry <sid@rit.edu>
2021-12-02 14:53:49 -06:00
Ye Luo
1cdb764422 QMCPACK: fix use of MPI wrappers (#27744) 2021-12-01 18:39:06 -08:00
Tiziano Müller
d0beab8012 elpa package: add version 2021.05.002_bugfix (#27748)
* elpa: filter _bugfix in version for include dir
* libxc: add version 5.1.7
2021-12-01 18:29:23 -08:00
Bernhard Kaindl
04519d261d New package: goshimmer (#27339) 2021-12-01 17:05:30 -08:00
Axel Huebl
e590ec6f3f Add: openPMD-viewer (#27516)
* Add: openPMD-viewer

Add the `py-openpmd-viewer` package.

* openPMD-viewer: Improve Variant Control

* openPMD-viewer: Update to Source from Pip/PyPA

https://spack.readthedocs.io/en/latest/build_systems/pythonpackage.html#pypi-vs-github

* Fix style: comment

* openPMD-viewer: fix requirements

add reviewer feedback
2021-12-01 16:19:54 -07:00
Tiziano Müller
08b00f8804 cp2k: fix build issues without cuda, and with elpa on openSUSE (#27738) 2021-12-01 17:00:01 -06:00
Vanessasaurus
326acea29d py-tern: new package (#27599)
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2021-12-01 14:41:05 -07:00
Jen Herting
97126cac4b New package: py-yq (#27729)
* pypi build of yq

* [py-yq]

- removed duplicate py-yaml dependency
- fixed py-yaml version number

* [py-yq] fix py-xmltodict version range

* [py-yq] self assign maintainer

* [py-yq] setuptools is runtime dependency

Co-authored-by: Sid Pendelberry <sid@rit.edu>
2021-12-01 13:25:24 -08:00
Jen Herting
2ddc522864 New package: py-retry (#27730)
* package dependency

* [py-retry]

- added homepage
- removed unnecessary depends_on

* [py-retry] added dependencies back

* [py-retry] removed .999

Co-authored-by: Sid Pendelberry <sid@rit.edu>
2021-12-01 14:14:55 -07:00
Joseph Wang
d7b21fc40b madgraph5amc package: use Spack compiler wrapper (#27523)
This fix allows madgraph5amc to build with Clang.
2021-12-01 12:18:07 -08:00
kwryankrattiger
041f91b176 ECP-DAV package: Add sensei to SDK (#27537)
- Add sensei to the SDK with appropriate propagations
- Rework variants to SENSEI package to avoid providing broken builds
- Turn off miniapps by default, these are examples and not critical to using sensei
2021-12-01 12:10:22 -08:00
Thomas Green
ab85e79a91 py-pybind11: add CMake dependency (#27573) 2021-12-01 11:57:27 -08:00
Manuela Kuhn
faa04a03c0 seacas: fix x11 dependency (#27737) 2021-12-01 10:11:14 -08:00
Mark W. Krentel
820d49b84e libmonitor: add version 2021.11.08 (#27740) 2021-12-01 10:09:49 -08:00
Marc Joos
81bdf1a386 wi4mpi: add new package (#27530) 2021-12-01 09:29:08 -07:00
Jen Herting
5a9bc4bfb2 New package: py-gin-config (#27732)
* [py-gin-config] created template

* [py-gin-config]

- depends on setup tools
- added homepage
- added description
- removed fixmes
2021-12-01 09:52:59 -06:00
Severin Strobl
67c8a63a0a adol-c: add variant stdczero (#27721) 2021-12-01 16:24:15 +01:00
Luis Yanes
4859649229 portcullis: add v1.2.3 (#27661)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-12-01 05:34:52 -07:00
Vicente Bolea
6e90a853f4 ParaView: Add 5.10.0-RC2 release (#27696) 2021-12-01 11:53:54 +01:00
Howard Pritchard
aacbc64a23 OPENMPI: add 4.0.7 release (#27697)
add the 4.0.7 release to the OMPI spack package

Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2021-12-01 11:53:16 +01:00
ravil-mobile
658f42ef0f dpcpp: added a new package (#25130)
dpcpp stands for Data Parallel C++
dpcpp is Intel's implementation of SYCL

Co-authored-by: ravil <ravil.dorozhinskii@tum.de>
2021-12-01 11:43:38 +01:00
Ye Luo
787cc535e9 qmcpack: more restriction on openblas variants (#27723) 2021-12-01 11:30:58 +01:00
Vasileios Karakasis
452a693aab Add more ReFrame versions (#27728) 2021-11-30 15:56:03 -07:00
Ye Luo
23206fa4b5 quantum-espresso: add CMake and libxc variants (#27724) 2021-11-30 23:26:39 +01:00
Glenn Johnson
bcaa87574d vtk package: add version 9.1.0; add new dependencies (#27467)
This PR updates the vtk package to use new variable names and adds some
dependencies.

- add version 9.1.0
- add version 1.4.2 to gl2ps package. This is needed to use gl2ps as a
  dependency.
- new package: utf8cpp, used as a dependency for version 9.
- add dependencies when possible
    - pugixml
    - libogg
    - libtheora
    - utf8cpp
    - gl2ps
    - proj
- turn off configuring MPI if ~mpi
- always use the package-provided FindHDF5.cmake for versions up to 8.
  Version @9: already does this so does not need a patch.
- use new CMake variables for version 9
- remove unused CMake variables depending on version
2021-11-30 15:14:05 -07:00
Piotr Luszczek
d57bcc0b85 cpio: reuse patch for %gcc10: for %clang as well (#27589)
and replace patch download with simple filter_file() to fix the duplicate definition.

Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2021-11-30 23:09:00 +01:00
Sebastian Schmitt
c96a6f990e Bump Brian2 (#27700)
* Bump Brian2

* Remove doc variant; the documentation is not build anyways
2021-11-30 11:32:04 -07:00
Marco De La Pierre
88cf4ce865 updated recipe for quantum-espresso 6.8 (#27607) 2021-11-30 10:05:53 -08:00
Manuela Kuhn
5e193618cb gtk-doc: fix source url and add 1.33.2 (#27719) 2021-11-30 09:29:06 -07:00
Davide Mancusi
0e83c0e792 gtkplus: fix generation of configure_args (#27718) 2021-11-30 17:26:39 +01:00
Massimiliano Culpo
645a7dc14c spack audit: fix API calls (#27713)
This broke in #24858
2021-11-30 14:59:55 +01:00
Adam J. Stewart
5044df88ab Add citation information to GitHub (#27518) 2021-11-30 01:37:50 -07:00
Manuela Kuhn
ab2bc933b8 py-idna: add 3.3 (#27708) 2021-11-29 21:28:57 -07:00
Valentin Volkl
b13778c2c6 py-iminuit: add new versions 2.8.4 (#27680)
* py-iminuit: add new versions 2.8.4

* py-iminuit: update python dependency

* py-iminuit: fix typo

* flake8
2021-11-29 20:19:52 -07:00
Manuela Kuhn
54df6d0a56 py-setuptools: add 59.4.0 (#27692) 2021-11-29 19:52:50 -07:00
Manuela Kuhn
44746dfbd6 r-tidyverse: add 1.3.1 (#27291) 2021-11-29 18:24:44 -06:00
Harmen Stoppels
a86d574208 dsfmt package: fix shared libs (#27628)
Also:

* Remove 2.2.3 (doesn't build shared libs)
* Add versions 2.2.4 and 2.2.5
2021-11-29 15:57:32 -08:00
Satish Balay
cb71308d22 petsc: archive configure.log make.log from the build (#27677)
Also enable verbose build
2021-11-29 16:10:50 -07:00
Ben Darwin
02b4a65086 py-intensity-normalization: add package (at version 2.1.1) (#27593)
* py-scikit-fuzzy: new package (at version 0.4.2)

* py-intensity-normalization: new package (at version 2.1.1)
2021-11-29 15:33:16 -06:00
Manuela Kuhn
838294b10d py-gevent: add 21.8.0 (#27699) 2021-11-29 15:29:09 -06:00
Manuela Kuhn
22eebff261 py-pyparsing: add 3.0.6 (#27693)
* py-pyparsing: add 3.0.6

* Add suggestions
2021-11-29 14:02:08 -07:00
Manuela Kuhn
a98e8ad4b5 py-packaging: add 21.3 (#27691)
* py-packaging: add 21.3

* Update var/spack/repos/builtin/packages/py-packaging/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-11-29 13:56:09 -07:00
Bernhard Kaindl
2d34082b0c llvm: Fix building llvm@4:9 using %clang@6: and %gcc@10: (#27233)
Add z3 variant, fix @:9%gcc@9: with glibc2.31, fix no_cyclades range
2021-11-29 12:48:18 -08:00
Manuela Kuhn
1f1da6806c py-tifffile: add 2021.11.2 (#27695) 2021-11-29 12:52:55 -07:00
Manuela Kuhn
647a26bc9e py-httpretty: add 1.1.4 (#27687) 2021-11-29 11:42:58 -06:00
Manuela Kuhn
561b0ca029 py-zope-interface: add 5.4.0 (#27596) 2021-11-29 11:42:00 -06:00
Manuela Kuhn
3c5295ee8a py-gast: add 0.5.3 (#27686) 2021-11-29 11:40:59 -06:00
Manuela Kuhn
914cf5ff87 py-importlib-metadata: add 4.8.2 (#27690) 2021-11-29 11:40:17 -06:00
Thomas Madlener
ecb588740a Speed up install of environments with dev packages (#27167)
* only check file modification times once per dev package
2021-11-29 09:34:23 -08:00
Manuela Kuhn
4858a26400 py-humanize: add 3.12.0 (#27688) 2021-11-29 10:58:09 -06:00
Eric Brugger
995a29d2f3 VisIt: remove upper range restriction on llvm. (#27648) 2021-11-29 17:38:31 +01:00
Adam J. Stewart
fcd5f960f8 py-matplotlib: add v3.5.0 (#27486)
* py-matplotlib: add v3.5.0

* Remove deprecated versions, update setup.cfg filename

* Add additional dependencies, save config file

* Add patch to fix matplotlibrc
2021-11-29 17:19:01 +01:00
Howard Pritchard
54d88f1a1c OpenMPI: add version 4.1.2 (#27645)
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2021-11-29 16:45:20 +01:00
Adam J. Stewart
fee8ac9721 py-scipy: add v1.7.3 (#27649) 2021-11-29 16:44:17 +01:00
Manuela Kuhn
1326e9d538 py-greenlet: add v1.1.2 (#27594) 2021-11-29 16:43:38 +01:00
Bernhard Kaindl
bd0960cda8 gpgme: Add 0.16.0 and address test suite issues (#27604)
A part of the gpgme testsuite by default even runs during normal
make and make install phases, creating a public keyring in ~/.gnupg.
Prevent this and avoid build failures in containers due to another
problem of the test suite and fix a test case of the new 0.16.0 release.
2021-11-29 16:43:12 +01:00
Ethan Stam
cfd2ea0cff ParaView: Build edition strings should be uppercase (#27534) 2021-11-29 16:38:25 +01:00
Adam J. Stewart
e5e9dc2d92 py-pytorch-lightning: add v1.5.3 (#27650) 2021-11-29 16:31:58 +01:00
Derek Ryan Strong
f8d03b1060 pixz: add v1.0.7 (#27651) 2021-11-29 16:29:10 +01:00
Harmen Stoppels
037ece674b distro: don't use deprecated linux_distribution (#27658) 2021-11-29 16:26:19 +01:00
Nicolas Cornu
87cf38a427 Random123: add v1.14.0 from github (#27660) 2021-11-29 16:13:50 +01:00
Massimiliano Culpo
0d10408a25 bootstrap: restrict patchelf to v0.13.x (#27685) 2021-11-29 15:41:25 +01:00
Bernhard Kaindl
48d98b4c9e podman: new package (with dependencies) (#27603)
When the uidmap tools are installed on a system, this allows to run
containers as unprivileged user (rootless and daemonless) slimilar
to singularity, but using a familiar CLI: "alias docker=podman"

This is helpful to run e.g. spack builds in containers to reproduce
build failures from CI without requiring a installation of docker.
The required dependencies of podman are added as well.
2021-11-29 15:39:19 +01:00
Valentin Volkl
64c4fbd220 edm4hep: update hepmc dependency (#27678) 2021-11-29 14:55:07 +01:00
Bernhard Kaindl
af0ba4e3ef gtkplus: fix build of GTK2 versions with gcc-11, skip X tests (#26970)
Fix to not attempt to patch a nonexisting file for old versions
when building with gcc-11. Skip the build-time tests as all access
the X DISPLAY and open many windows on the screen.
2021-11-29 14:46:51 +01:00
Harmen Stoppels
5dce4d79bd patchelf: add v0.13.1, v0.14, v0.14.1 (#27681) 2021-11-29 13:46:15 +01:00
Paul Ferrell
c0edb17b93 Handle byte sequences which are not encoded as UTF8 while logging. (#21447)
Fix builds which produce a lines with non-UTF8 output while logging
The alternative is to read in binary mode, and then decode while
ignoring errors.
2021-11-29 13:27:02 +01:00
Vanessasaurus
bdde70c9d3 "branch" spelling mistake in libbeato (#27682)
I was browsing package metadata, as one does on a Sunday, and stumbled across a new kind of version attribute - brancch! I suspect this is supposed to be "branch."
2021-11-29 13:17:40 +01:00
iarspider
8ff81d4362 Fix py-astroid recipe (#27670) 2021-11-28 11:07:53 -06:00
Mark Grondona
1b71ceb384 add flux-core v0.31.0 and flux-sched v0.20.0 (#27336)
Update flux-core and flux-sched package.py to include latest releases.

For flux-sched:

 - Add patch to disable false-positive-happy valgrind test
 - pin yaml-cpp to 0.6.3 due to issue described at:
   https://github.com/flux-framework/flux-sched/issues/886
2021-11-28 02:18:00 +01:00
Joseph Wang
0ab5828d0d gdk-pixbuf: Fix 2.42.2 and add 2.42.6 (#27254)
Starting with meson 0.60, unknown args produce errors and
the -Dx11 arg is only present in @:2.40
https://gitlab.gnome.org/GNOME/gtk-osx/-/issues/44

Add tiff variant: Default disabled since fails the tests in part.
Only libtiff@:3.9 pass, but these old versions have severe security issues.

Deprecate @:2.41 as they are affected by the high-severity CVE-2021-20240:
https://nvd.nist.gov/vuln/detail/CVE-2021-20240
2021-11-28 01:30:14 +01:00
iarspider
d5b243de14 py-scipy: update pybind11 versions (#27679) 2021-11-27 16:03:43 -06:00
iarspider
1d8d975721 Apply requested fix from #27643 (#27672) 2021-11-26 16:45:38 -06:00
iarspider
96ce0e393d New version: py-send2trash 1.8.0 (#27583) 2021-11-26 14:35:03 -07:00
Jannis Schönleber
cf3762369c dyninst: use spack libiberty path (#25779) 2021-11-26 15:58:53 -05:00
iarspider
8138ebaa32 New version: py-tomlkit 0.7.2 (#27633) 2021-11-26 13:11:20 -07:00
iarspider
eb42514124 New version: py-threadpoolctl 3.0.0 (#27632) 2021-11-26 13:10:58 -07:00
Harmen Stoppels
4d6891162d Use bash in setup_git.sh (#27676) 2021-11-26 18:03:05 +00:00
iarspider
978f091822 Fix py-aiohttp recipe (#27671) 2021-11-26 08:17:01 -07:00
Massimiliano Culpo
a96f2f603b Bootstrap patchelf like GnuPG (#27532)
Remove a custom bootstrapping procedure to
use spack.bootstrap instead

Modifications:
* Reference count the bootstrap context manager
* Avoid SpackCommand to make the bootstrapping
  procedure more transparent
* Put back requirement on patchelf being in PATH for unit tests
* Add an e2e test to check bootstrapping patchelf
2021-11-26 15:32:13 +01:00
iarspider
2cdc758860 Fix version constraint in py-ipykernel (#27665)
* Fix version constrains in py-ipykernel and py-ipython

Before the fix:
```
$ spack spec  py-ipykernel@6.4.1  ^py-jupyter-client@7.0.6
==> Error: py-ipykernel@6.4.1 ^py-jupyter-client@7.0.6 is unsatisfiable, conflicts are:
  no version satisfies the given constraints
```

After the fix:
```
```
(thanks god the old concretizer is still there - it provides sane error messages!)

* Fix py-ipython recipe

* Revert "Fix py-ipython recipe"

This reverts commit d65071665f.
2021-11-25 17:58:43 -07:00
Seth R. Johnson
9904159356 New package: py-sphinx-argparse (#27663) 2021-11-25 13:54:34 -06:00
Maxim Belkin
6e095a9741 module_file_support: update format for configuration (#27598) 2021-11-25 08:41:32 +01:00
iarspider
90b4f55001 New version: py-theano 1.0.5 (#27631) 2021-11-24 18:16:48 -07:00
iarspider
60e683f5d3 New version: py-requests 2.26.0 (redo of #27579) (#27647) 2021-11-24 17:38:01 -07:00
iarspider
a9a6e00d14 New version: py-rsa 4.7.2 (#27581) 2021-11-24 16:52:44 -07:00
iarspider
6fa0feb7de New version: py-rich 10.14.0 (redo of #27580) (#27646) 2021-11-24 16:04:53 -07:00
iarspider
0db93a5dea py-virtualenv package: add version 20.10.0; new dependency py-distlib (#27637)
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-11-24 15:38:03 -07:00
Massimiliano Culpo
270ba10962 spack flake8: remove deprecated command (#27290)
The "spack flake8" command wwas deprecated in favor
of "spack style". The deprecation wwarning is in the
0.17.X series, so removing it for v0.18.x
2021-11-24 14:20:11 -08:00
iarspider
f8025d4f88 New version: py-requests-oauthlib 1.3.0 (#27578) 2021-11-24 16:20:02 -06:00
liuyangzhuan
83f97e8eba Adding packages for gptune and its dependencies (#26936)
* added package gptune with all its dependencies: adding py-autotune, pygmo, py-pyaml, py-autotune, py-gpy, py-lhsmdu, py-hpbandster, pagmo2, py-opentuner; modifying superlu-dist, py-scikit-optimize

* adding gptune package

* minor fix for macos spack test

* update patch for py-scikit-optimize; update test files for gptune

* fixing gptune package style error

* fixing unit tests

* a few changes reviewed in the PR

* improved gptune package.py with a few newly added/improved dependencies

* fixed a few style errors

* minor fix on package name py-pyro4

* fixing more style errors

* Update var/spack/repos/builtin/packages/py-scikit-optimize/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* resolved a few issues in the PR

* fixing file permissions

* a few minor changes

* style correction

* minor correction to jq package file

* Update var/spack/repos/builtin/packages/py-pyro4/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* fixing a few issues in the PR

* adding py-selectors34 required by py-pyro4

* improved the superlu-dist package

* improved the superlu-dist package

* moree changes to gptune and py-selectors34 based on the PR

* Update var/spack/repos/builtin/packages/py-selectors34/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-11-24 16:06:43 -06:00
Brian Spilner
d6b0c838dd cdo package: add version 2.0.1 (#27608) 2021-11-24 13:20:28 -08:00
Paul
94bcd21ccd Go package: add versions 1.17.3 and 1.16.10 (#27614) 2021-11-24 13:10:23 -08:00
Satish Balay
d8ac578ce1 petsc: add variant kokkos (with +cuda) (#27624) 2021-11-24 13:09:14 -08:00
Tim Haines
f9bae91dea Dyninst package: Add versions 12.0.0 and 12.0.1 (#27623) 2021-11-24 12:23:30 -08:00
iarspider
6147b47719 py-terminado package: add version 0.12.1 (#27629) 2021-11-24 12:03:04 -08:00
iarspider
191de76ccb py-testpath package: add version 0.5.0 (#27630) 2021-11-24 12:02:18 -08:00
iarspider
b500d40a25 py-uproot package: add version 4.1.8 (#27635) 2021-11-24 12:01:25 -08:00
iarspider
43c663c5cf py-virtualenv-clone package: add version 0.5.7 (#27636) 2021-11-24 11:58:41 -08:00
iarspider
3fdab96728 py-virtualenvwrapper package: add version 4.8.4 (#27638) 2021-11-24 11:45:36 -08:00
iarspider
fcd51d81d9 py-wcwidth package: add version 0.2.5 (#27639) 2021-11-24 11:44:51 -08:00
iarspider
83a2014ede py-websocket-client package: add version 1.2.1 (#27640) 2021-11-24 11:43:42 -08:00
iarspider
1c38810e11 py-wheel package: add version 0.37.0 (#27641) 2021-11-24 11:42:02 -08:00
Maciej Wójcik
10ca5f1cd2 GROMACS-SWAXS package: add versions including 2021.4-0.1 (#27642) 2021-11-24 11:41:16 -08:00
iarspider
e7eaebebd4 py-yarl package: add version 1.7.2 (#27643) 2021-11-24 11:40:06 -08:00
Robert Cohn
76ad803f25 intel-oneapi-mkl: add cluster libs and option for static linking (#26256) 2021-11-24 11:04:05 -08:00
Harmen Stoppels
dbf67d912c Make patchelf test use the realpath (#27618)
I think this test should be removed, but when it stays, it should at
least follow the symlink, cause it fails for me if I let spack build
patchelf and have a symlink in a view.
2021-11-24 11:17:23 +01:00
Massimiliano Culpo
5c3dfacdc5 Update distro to v1.6.0 (#27263) 2021-11-24 10:10:11 +00:00
albestro
635984f077 umpire: fix gcc@10.3.0 conflict (#27620)
Make sure that `gcc@10.3.0-[number]` also matches the conflict.
2021-11-24 02:49:51 -07:00
Massimiliano Culpo
70d5d234db Update Jinja2 to v2.11.3 and MarkupSafe to v1.1.1 (#27264) 2021-11-24 10:21:35 +01:00
Massimiliano Culpo
12da0a9a69 Update six to v1.16.0 (#27265) 2021-11-24 10:20:04 +01:00
Harmen Stoppels
97ebcb99b4 libblastrampoline: use tarballs and add maintainer (#27619)
* Use tarballs for libblastrampoline

* Add myself as maintainer
2021-11-24 09:45:57 +01:00
Vanessasaurus
a5bd6acd90 Adding oras go package (#27605)
Signed-off-by: vsoch <vsoch@users.noreply.github.com>

Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2021-11-24 07:06:29 +01:00
Sreenivasa Murthy Kolam
d6d78b8457 rocm-tensile: Add new GPUs to tensile-architecture list (#26913) 2021-11-23 18:35:16 -08:00
Thomas Dickerson
c263b64d2e Racket package: disable parallel build; add variants (#27506)
- Prevent `-j` flags to `make`, which has been known to cause problems
  with Racket builds.
- Add variants for various common build flags, including support
  for both versions of the Racket VM environment.

In addition:

- Prefer the minimal release to improve install times. Bells and
  whistles carry their own runtime dependencies and should be
  installed via `raco`. An enterprising user may even create a
  `RacoPackage` class to make spack aware of `raco` installed packages.
- Match the official version numbering scheme.
2021-11-23 16:45:18 -08:00
Harmen Stoppels
dfc95cdf1c llvm: use ninja by default (#27521)
* llvm: use ninja by default

* Use ninja for omp when it's not a runtime
2021-11-23 16:28:17 -08:00
John Wohlbier
0f1c04ed7e Add encryption library packages: helib, palisade-development, and seal (#27495)
Add packages for three common homomorphic encryption libraries.
HElib, Palisade, and Seal. Also add package for number theoretic library NTL.
2021-11-23 15:11:37 -08:00
Harmen Stoppels
cced832cac Fix leaky tests (#27616)
* fix: cc.py should use a function not session scope
* fix: don't let build env vars leak to other tests
* fix: don't leak build env in dev_build test
2021-11-23 14:10:48 -08:00
Manuela Kuhn
2d20e557df py-flask: add 2.0.2 (#27615) 2021-11-23 11:11:12 -07:00
Vanessasaurus
14607b352c adding new package go cosign (#27606)
Signed-off-by: vsoch <vsoch@users.noreply.github.com>

Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2021-11-23 09:56:45 -08:00
Massimiliano Culpo
fa7189b480 Remove support for Python 2.6 (#27256)
Modifications:
- [x] Removed `centos:6` unit test, adjusted vermin checks
- [x] Removed backport of `collections.OrderedDict`
- [x] Removed backport of `functools.total_ordering`
- [x] Removed Python 2.6 specific skip markers in unit tests
- [x] Fixed a few minor Python 2.6 related TODOs in code

Updating the vendored dependencies will be done in separate PRs
2021-11-23 09:06:17 -08:00
Manuela Kuhn
812663de62 py-cython: add 3.0.0a9 (#27609)
* py-cython: add 3.0.0a9

* Update var/spack/repos/builtin/packages/py-cython/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-11-23 16:33:29 +00:00
Larry Knox
f96e3371a0 Update to latest commit hash for vol-log-based. (#27612)
Update minimum hdf5 version to 1.13.0.
2021-11-23 10:09:19 -05:00
Larry Knox
8476a2e4a1 Add hdf5-vol-external-passthrough package. (#27289)
* Add hdf5-vol-external-passthrough package.

* Add version v1.0 for vol-external-passthrough release.

* Remove incorrect comment.

* Add source url and checksum.  Update HDF5 minimum version.
2021-11-23 10:06:48 -05:00
Nathan Hanford
2104f1273a bugfix: Allow legacy tests to be read after hash break (#26078)
* added a test case

Co-authored-by: Nathan Hanford <hanford1@llnl.gov>
2021-11-22 21:49:41 -07:00
iarspider
feb66cba01 New version: py-stevedore 3.5.0 (#27586) 2021-11-22 18:31:31 -06:00
Manuela Kuhn
b961491ad2 py-zope-event: add 4.5.0 (#27595) 2021-11-22 16:05:13 -07:00
iarspider
411b3ecc37 New version: py-singledispatch 3.7.0 (#27584)
* New version: py-singledispatch 3.7.0

* Apply suggestions from code review

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-11-22 15:44:07 -07:00
Robert Blake
3e63bc08ee ncurses: fix external package detection on OS X (#27490) 2021-11-22 14:37:58 -08:00
Piotr Luszczek
e90d5ad6cf Intel packages: add support for LLVM OpenMP (#26517) 2021-11-22 13:41:43 -08:00
Harmen Stoppels
abec10fcd5 suite-sparse package: add support for blas symbol suffix (#27510) 2021-11-22 13:18:39 -08:00
Massimiliano Culpo
6f8fd5b7a7 raja: fix recipe for old versions (#27591)
Raja didn't depend on camp prior to v0.12.0
2021-11-22 22:07:54 +01:00
Massimiliano Culpo
5eba5dc271 Make CUDA and ROCm architecture conditional (#27185)
* Make CUDA and ROCm architecture conditional

fixes #14337

The variant to specify which architecture to use
for CUDA and ROCm are now conditional on +cuda and
+rocm respectively.

* cp2k: make all CUDA related variants conditional on +cuda
2021-11-22 07:54:19 -05:00
Wouter Deconinck
5f10562ad1 [geant4] new version geant4@10.7.3 (#27568)
* [geant4] new version geant4@10.7.3

Release notes: https://geant4-data.web.cern.ch/ReleaseNotes/Patch4.10.7-3.txt, no build system changes.

* [geant4] depends_on geant4-data@10.7.3

* [geant4-data] new version @10.7.3
2021-11-22 12:37:11 +00:00
Hadrien G
596f2e7c4d acts: add v15, embrace conditional variants (#27529) 2021-11-22 10:49:54 +01:00
Mahendra Paipuri
1a95b979d8 Disable rsmi for hwloc when rocm is not enabled (#27547)
Co-authored-by: mahendrapaipuri <mahendra.paipuri@inria.fr>
2021-11-22 10:47:56 +01:00
Harmen Stoppels
0024e5cc9b Make _enable_or_disable(...) return an empty array for conditional variants whose condition is not met (#27504) 2021-11-22 10:47:09 +01:00
Adam J. Stewart
cda9d6d981 py-rapidfuzz: add new package (#27559) 2021-11-22 10:38:33 +01:00
Manuela Kuhn
d3b35c4063 py-itsdangerous: add 2.0.1 (#27556) 2021-11-22 10:38:10 +01:00
Harmen Stoppels
3bfd78e6b8 ccache: speed up builds, don't build tests (#27567) 2021-11-22 10:28:05 +01:00
psakievich
c167b7d532 nalu-wind: remove cxxstd from trilinos dependency to enable testing for cpp17 (#27563) 2021-11-22 10:18:30 +01:00
Wouter Deconinck
6d30d87d7e mesa: add v21.2.4 and v21.2.5 (#27571)
Last bugfix versions before just released version @21.3.0 which will be part of a separate PR.
2021-11-22 10:14:00 +01:00
Thomas Green
e7b97c9473 harminv: update for blas/lapack (#27572) 2021-11-22 09:51:46 +01:00
Sebastian Ehlert
8d1e66a627 fpm: add v0.5.0 (#27575) 2021-11-22 09:48:10 +01:00
Adam J. Stewart
7c14c86ffd py-laspy: add new package (#27576) 2021-11-22 09:45:30 +01:00
Tracy-Pantleo
49b0952371 portage, tangram, wonton: update dependencies (#26886)
* tangram/wonton spack

* portage spack update

* wonton spack updated

* tangram spack updated

* white space removed

* Update package.py

* Update package.py

* Update package.py

* Update package.py

portage spack upstream

* Update package.py

for loop test

* Update package.py

style errors

* Update package.py

* tangram

* Update package.py

* Update package.py

* Update package.py

* Update package.py

* Update package.py

edits

* Update package.py

* Update package.py

remove @master

* Update package.py

remove @master

* Update var/spack/repos/builtin/packages/portage/package.py

Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>

* Update var/spack/repos/builtin/packages/wonton/package.py

Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>

* Update package.py

* Update package.py

* Update package.py

* Update package.py

Co-authored-by: Tracy Nicole Pantleo <tpantleo@varan.lanl.gov>
Co-authored-by: Tracy Nicole Pantleo - 361537 <tpantleo@darwin-fe1.lanl.gov>
Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>
2021-11-19 22:09:56 -05:00
iarspider
e47fa05eb8 New version: py-pyzmq 22.3.0 (#27543)
* New version: py-pyzmq 22.3.0

* Update var/spack/repos/builtin/packages/py-pyzmq/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-11-19 13:53:02 -07:00
Adam J. Stewart
2c5fc14bf9 py-progressbar2: add v3.55.0 (#27558) 2021-11-19 14:35:44 -06:00
Adam J. Stewart
fd0f0e564d py-ruamel-yaml-clib: link to python (#27557) 2021-11-19 14:35:31 -06:00
Manuela Kuhn
aa934d00e3 py-jinja2: add 3.0.3 (#27560) 2021-11-19 14:35:18 -06:00
Raghu Raja
f26d25e24b libfabric: Add v1.14.0 release (#27562)
Signed-off-by: Raghu Raja <raghu@enfabrica.net>
2021-11-19 13:35:00 -07:00
Jen Herting
99f954f1c1 [py-pickle5] New package (#27533)
Co-authored-by: Sid Pendelberry <sid@rit.edu>
2021-11-19 14:31:22 -06:00
Joseph Snyder
d759612523 Add connection specification to mirror creation (#24244)
* Add connection specification to mirror creation

This allows each mirror to contain information about the credentials
used to access it.

Update command and tests based on comments

Switch to only "long form" flags for the s3 connection information.
Use the "any" function instead of checking for an empty list when looking
for s3 connection information.

Split test to use the access token separately from the access id and key.
Use long flag form in test.

Add endpoint_url to available S3 options.

Extend the special parameters for an S3 mirror to accept the
endpoint_url parameter.

Add a test.

* Add connection information per URL not per mirror

Expand the mirror-based connection information to be per-URL.
This will allow a user to specify different S3 connection information
for both the fetch and the push URLs.

Add a parameter for "profile", another way of storing the id/secret pair.

* Switch from "access_profile" to "profile"
2021-11-19 15:28:34 -05:00
Manuela Kuhn
a5c50220db py-werkzeug: add 2.0.2 (#27555) 2021-11-19 12:17:06 -07:00
Manuela Kuhn
cdc5b32240 py-cycler: add 0.11.0 and get sources from pypi (#27550)
* py-cycler: add 0.11.0

* Update var/spack/repos/builtin/packages/py-cycler/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-11-19 11:20:14 -07:00
Manuela Kuhn
efe635a3f8 py-debugpy: add 1.5.1 (#27551) 2021-11-19 11:05:12 -07:00
iarspider
0288ef8733 New version: py-pyaml 6.0 (#27542) 2021-11-19 11:35:50 -06:00
iarspider
e08ebff139 New version: py-qtconsole 5.2.0 (#27554)
* New version: py-qtconsole 5.2.0

* Apply suggestions from code review

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-11-19 10:10:59 -07:00
Jen Herting
af1b61569f New package: py-lws (#27536)
* [py-lws] added package

* added cython support

* updates for upstream

* updated py-lws with cython only option

* changes to py-lws for flake8

* [py-lws]

- update copyright
- url -> pypi

Co-authored-by: Sid Pendelberry <sid@rit.edu>
2021-11-19 11:03:52 -06:00
Manuela Kuhn
7784ff55d6 py-filelock: add 3.4.0 (#27553) 2021-11-19 09:35:07 -07:00
iarspider
7be632b558 New version: openldap 2.6.0; (#27520)
* New version: openldap 2.6.0;
fix recipe for groff (requires pkg-config to find uchardet);
fix recipe for openldap (requires groff to build documentation)

* Restrict openldap versions of py-python-ldap and percona-server

* Update var/spack/repos/builtin/packages/groff/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-11-19 10:31:40 -06:00
iarspider
047062eedf New versopn: py-python-daemon 2.3.0 (#27519)
* New versopn: py-python-daemon 2.3.0

* Update package.py
2021-11-19 10:30:47 -06:00
iarspider
f472716e96 New version: py-pythran 0.10.0 (#27528)
* New version: py-pythran 0.10.0

* Update package.py
2021-11-19 10:21:21 -06:00
Manuela Kuhn
347da5f7b3 py-babel: add 2.9.1 (#27544) 2021-11-19 10:20:58 -06:00
Manuela Kuhn
4a18957093 py-coverage: add 6.1.2 (#27545) 2021-11-19 10:20:07 -06:00
Harmen Stoppels
3fcc6c669f Spack requires Python 2.7: from 0.18.0: (#27505)
* Spack requires Python 2.7: from 0.18.0:

* Better bounds
2021-11-19 10:18:21 -06:00
Manuela Kuhn
33b380937a py-cryptography: add 3.4.8 and 35.0.0 (#27548) 2021-11-19 10:16:21 -06:00
Manuela Kuhn
eb515b87d7 py-click: add 8.0.3 (#27549) 2021-11-19 10:13:24 -06:00
Harmen Stoppels
c5aee4d9b4 define_from_variant: return an empty string for non-existing variants (#27503)
This permits to use conditional variants without a lot of boilerplate.
2021-11-19 14:10:00 +01:00
iarspider
3db918b1cd New version: py-pytools 2021.2.9 (#27531) 2021-11-19 02:23:03 -07:00
Michael Kuhn
eefff81289 otf: specify zlib prefix explicitly (#27491)
This causes `otfconfig` to also list zlib's library directory.
Otherwise, `-lz` cannot be found. Also remove `--with-zlibsymbols`,
which doesn't seem to be supported anymore.
2021-11-19 09:37:27 +01:00
Michael Davis
3375db12a5 Adding --reuse to dev-build command. (#27487) 2021-11-19 09:25:45 +01:00
Diego Alvarez
4d059ead8c nextflow: add v21.10.1 (#27538) 2021-11-19 09:21:14 +01:00
Eric Brugger
4cf71b2c7f VisIt: update for building with 3.2.1. (#27036)
Include several several patches to vtk 8.1 for building on a 
system with no system install X11 libraries or include files.

Specify specific versions of dependent packages that are known to work with 3.2.1.

Tested on spock.olcf.ornl.gov. The GUI came up and rendered images 
and an image was successfully saved using off screen rendering from 
data from curv2d.silo.
2021-11-19 09:05:13 +01:00
Massimiliano Culpo
57d3b02800 Remove spurious debug print (#27541) 2021-11-19 09:02:22 +01:00
haralmha
4d1f09c752 thepeg: fix version condition bug (#27501) 2021-11-19 08:56:00 +01:00
iarspider
c183111a61 py-rapidjson: add version 1.5 (#27527) 2021-11-18 17:52:06 -08:00
Manuela Kuhn
0b6ce17dc4 py-ply: get sources from pypi (#27526)
* py-ply: use pypi

* Add py-setuptools dependency
2021-11-18 16:52:51 -07:00
Massimiliano Culpo
e3cd91af53 Refactor bootstrap of "spack style" dependencies (#27485)
Remove the "get_executable" function from the
spack.bootstrap module. Now "flake8", "isort",
"mypy" and "black" will use the same
bootstrapping method as GnuPG.
2021-11-18 15:23:09 +01:00
iarspider
d0c4aeb0c0 Fix cyrus-sasl recipe: requires groff to build documentation (#27522) 2021-11-18 15:10:37 +01:00
Massimiliano Culpo
f981682bdc Allow recent pytest versions to be used with Spack (#25371)
Currently Spack vendors `pytest` at a version which is three major 
versions behind the latest (3.2.5 vs. 6.2.4). We do that since v3.2.5 
is the latest version supporting Python 2.6. Remaining so much 
behind the currently supported versions though might introduce 
some incompatibilities and is surely a technical debt.

This PR modifies Spack to:
- Use the vendored `pytest@3.2.5` only as a fallback solution, 
  if the Python interpreter used for Spack doesn't provide a newer one
- Be able to parse `pytest --collect-only` in all the different output 
  formats from v3.2.5 to v6.2.4 and use it consistently for `spack unit-test --list-*`
- Updating the unit tests in Github Actions to use a more recent `pytest` version
2021-11-18 15:08:59 +01:00
Harmen Stoppels
8f7640dbef ci: run style unit tests only if we target develop (#27472)
Some tests assume the base branch is develop, but this branch may not
have been checked out.
2021-11-18 13:00:39 +01:00
Alec Scott
7ee736a158 Add Clingo v5.5.1 (#27512) 2021-11-18 06:27:01 +01:00
Glenn Johnson
b260efd9c4 new package: py-scikit-learn-extra (#27439)
* new package: py-scikit-learn-extra

* Remove extra blank line

* Add missing py-cython dependency
2021-11-17 23:13:19 -06:00
Manuela Kuhn
b4fcb4d43c py-envisage: add 6.0.1 (#27517) 2021-11-17 23:12:28 -06:00
haralmha
301a506aa2 py-pygraphviz: Add version 1.7 (#26712)
* Add version 1.7

* Fixup! Add version 1.7
2021-11-17 23:08:56 -06:00
Harmen Stoppels
40a6ac62d3 llvm: introduce [build/link]_llvm_dylib (#27450)
Apart from building a single dylib for LLVM, users should also be able
to link tools against it.
2021-11-17 20:10:59 -07:00
Alec Scott
d24d13559b Add Htslib v1.14, Samtools v1.14, and Bcftools v1.14 (#27515) 2021-11-17 14:30:18 -08:00
Axel Huebl
367c3d8a83 openPMD-validator: 1.1.0.2 (#27514)
Add the latest versions.
2021-11-17 14:26:23 -08:00
Alec Scott
684d9cef23 Add LMOD v8.5.27 (#27513) 2021-11-17 14:21:57 -08:00
Ben Bergen
c459adbf6a Updated Repository Information (#27496) 2021-11-17 10:02:41 -08:00
Jose E. Roman
d9a39d6128 New patch release SLEPc 3.16.1 (#27509) 2021-11-17 09:57:53 -08:00
Manuela Kuhn
26c5001ec4 py-ipykernel: add 5.5.6 (#27498) 2021-11-17 11:06:08 -06:00
Harmen Stoppels
c05746eac2 llvm: use LIBCXX_ENABLE_STATIC_ABI_LIBRARY=ON (#27448)
The previous workaround of using CMAKE_INSTALL_RPATH=ON was used to
avoid CMake trying to write an RPATH into the linker script libcxx.so,
which is nonsensical. See commit f86ed1e.

However, CMAKE_INSTALL_RPATH=ON seems to disable the build RPATH, which
breaks LLVM during the build when it has to locate its build-time shared
libraries (e.g. libLLVM.so). That required yet another workaround, where
some shared libraries were installed "by hand", so that they were picked
up from the install libdir. See commit 8a81229.

This was a dirty workaround, and also makes it impossible to use ninja,
since we explicitly invoked make.

This commit removes the two old workaround, and sets
LIBCXX_ENABLE_STATIC_ABI_LIBRARY=ON, so that libc++abi.a is linked into
libc++.so, which makes it enough to link with -lc++ or invoke clang++
with -stdlib=libc++, so that our install succeeds and linking LLVM's c++
standard lib is still easy.
2021-11-17 09:14:05 -07:00
Harmen Stoppels
d900abe7e1 openblas: add a symbol suffix variant (#27500)
Some packages use a 64_ or _64 symbol suffix for the ilp64 (= 64-bit
integers) intefrace for BLAS. In particular if we want to support shim
libraries like libopenblastrampoline supporting both the 32 and 64 bit
integer version of blas, it must be possible to distinguish between the
two.
2021-11-17 08:52:56 -07:00
Bernhard Kaindl
2765861705 qt+webkit: Build needs Py2, but mesa/Meson needs Py3 (#27466)
mesa inherits MesonPackage (since October 2020) which depends on Py@3.
The conflicts('mesa') enables a regular build of `qt@5.7:5.15+webkit`
without having to specify the exact version by causing the concretizer
to select mesa18 which does not depend on python@3.

Co-authored-by: Bernhard Kaindl <bernhard.kaindl@ait.ac.at>
2021-11-17 07:42:49 -05:00
Harmen Stoppels
ac8993ac38 New version of Spack and new conflicts (#27384) 2021-11-17 11:25:33 +01:00
Harmen Stoppels
cc62689504 Fix overly generic exceptions in log parser (#27413)
This type of error is skipped:

make[1]: *** [Makefile:222: /tmp/user/spack-stage/.../spack-src/usr/lib/julia/libopenblas64_.so.so] Error 1

but it's useful to have it, especially when a package sets a variable
incorrectly in makefiles
2021-11-17 11:24:14 +01:00
Vasileios Karakasis
9260c38408 Add ReFrame 3.9.1 (#27493) 2021-11-17 00:44:59 +00:00
iarspider
b4ac385d70 New version: py-pytest-cov 3.0.0; add 'toml' variant to py-coverage (#27478)
* New version: py-pytest-cov 3.0.0; add 'toml' variant to py-coverage

* Update package.py
2021-11-16 17:16:59 -07:00
iarspider
85a98fc758 New version: py-pylint 2.8.2; new package py-platformdirs (#27473)
* New version: py-pylint 2.8.2; new package py-platformdirs

* Update var/spack/repos/builtin/packages/py-platformdirs/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-pylint/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-11-16 17:10:52 -07:00
Harmen Stoppels
0221639e8a llvm: maintainers (#27482) 2021-11-16 15:41:02 -07:00
Brian Spilner
7ad9fc7fdb cdo: new release cdo-2.0.0 (#27457) 2021-11-16 22:08:43 +01:00
Robert Cohn
67cba372e8 Intel mpi: allow use of external libfabric (#27292)
Intel mpi comes with an installation of libfabric (which it needs as a
dependency). It can use other implementations of libfabric at runtime
though, so if you install a package that depends on `mpi` and
`libfabric`, you can specify `intel-mpi+external-libfabric` and ensure
that the Spack-built instance is used (both by `intel-mpi` and the
root).

Apply analogous change to intel-oneapi-mpi.
2021-11-16 12:55:24 -08:00
iarspider
b194b957ce New versions: py-pyasn1 0.4.8, py-pyasn1-modules 0.2.8 (#27453)
* New versions: py-pyasn1 0.4.8, py-pyasn1-modules 0.2.8

* Update package.py
2021-11-16 13:52:56 -07:00
Thomas Kluyver
df5892ac89 Add py-h5py 3.6.0 (#27476) 2021-11-16 13:28:08 -06:00
iarspider
a432d971b1 New version: py-pyrsistent 0.18.0 (#27477)
* New version: py-pyrsistent 0.18.0

* Update package.py

* Update var/spack/repos/builtin/packages/py-pyrsistent/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-11-16 12:20:04 -07:00
Manuela Kuhn
85cf8af026 py-pyqt-builder: add new package (#27484) 2021-11-16 12:11:30 -07:00
iarspider
a867320021 New version: py-pytest 6.2.5 (#27481)
* New version: py-pytest 6.2.5

* Update var/spack/repos/builtin/packages/py-pytest/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-11-16 12:11:08 -07:00
Harmen Stoppels
a70d917da6 Bump curl (#27471) 2021-11-16 10:30:28 -08:00
iarspider
b9314fd887 New version: py-pu 1.11.0 (#27452) 2021-11-16 11:49:42 -06:00
iarspider
de916bd27b New version: py-pycuda 2021.1 (#27458) 2021-11-16 11:46:23 -06:00
iarspider
9f6dd08e1c New version: py-pycurl 7.44.1 (#27470) 2021-11-16 11:40:43 -06:00
iarspider
db307f9946 New version: py-pymongo 3.12.1 (#27474) 2021-11-16 11:39:28 -06:00
Harmen Stoppels
7c3b146789 llvm: flang implies mlir (#27449) 2021-11-16 10:08:07 -07:00
Harmen Stoppels
54fc26bf34 Add Python 3.9.9 (#27475) 2021-11-16 10:17:23 -06:00
Harmen Stoppels
a780f96a25 Add a symbol suffix option to LLVM (#27445) 2021-11-16 06:06:07 -08:00
Arjun Guha
bb54e9a4be racket: fix URL extrapolation (#27459) 2021-11-16 08:38:47 +01:00
Bernhard Kaindl
ada598668b mesa: Use the llvm-config of spec['llvm'] for '+llvm' (#27235)
Fix builds on hosts where /usr/bin/llvm-config-* is found and provides an
incompatible version: Ensure that the llvm-config of spec['llvm'] is used.
2021-11-16 08:07:48 +01:00
Robert Cohn
8c7fdadeba Add a maintainer for Intel packages (#27465) 2021-11-16 08:03:12 +01:00
Ben Bergen
5a8271d0c6 lanl-cmake-modules: new package (#27447)
Several projects have not yet added modern CMake support. This package
adds find_package support for some of these projects.
2021-11-16 07:31:24 +01:00
Hans Fangohr
35bf91012f oommf: new package (#26933)
Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2021-11-15 15:04:08 +01:00
Erik Schnetter
beddcd6a6d pgplot: Correct build error with shared libraries (#27154)
When building pgplot as shared library, dependencies need to be listed explicitly.
2021-11-15 13:51:43 +01:00
Thomas Madlener
6ce4a5ce8c lcio: add v2.17 (#27238) 2021-11-15 13:49:43 +01:00
Edgar Leon
4a71704ae4 mpibind: add python bindings (#27127) 2021-11-15 13:48:14 +01:00
Kyle Gerheiser
ce9ae3c70d Add module variables for NCEPLIBS (#27162)
Use setup_run_environment to search for libraries and set env variables for module generation.

Libraries are installed with CMAKE_INSTALL_LIBDIR, which can be lib or lib64 depending on the machine, which makes it impossible to hardcode through modules.yaml.
2021-11-15 13:21:53 +01:00
Harmen Stoppels
55e853c160 mbedtls: fix shared libs needed section and add new version (#27285) 2021-11-15 13:10:51 +01:00
Sinan
90a92c4efc libspatialite: add v5.0.1 (#27181)
Co-authored-by: sbulut <sbulut@3vgeomatics.com>
2021-11-15 11:48:08 +01:00
kwryankrattiger
fbfc27d707 ECP-DAV-SDK: remove catalyst (#27204)
Temporarily remove +catalyst, assumes catalyst is on when +paraview
2021-11-15 11:46:14 +01:00
Michael Kuhn
aac505d4ff libfuse: fix build with new glibc (#27376)
glibc 2.34+ breaks libfuse@2 (see https://bugs.gentoo.org/803923). While
we are at it, backport a few patches from upstream.
2021-11-15 11:29:44 +01:00
laestrada
e5a0986433 gchp: add v13.2.1 (#27318)
Co-authored-by: laestrada <lestrada00@gmail.com>
2021-11-15 11:28:25 +01:00
Glenn Johnson
2ea1037369 llvm: remove cyclades code from llvm-10:11 (#27385) 2021-11-15 11:27:00 +01:00
Glenn Johnson
faeea04712 star-ccm-plus: add version and environment setup (#27388)
- add version 16.06.008_01
- set up run environment
2021-11-15 11:26:05 +01:00
Glenn Johnson
cdcde36f51 perl-forks: handle non-threaded perl (#27392)
If the perl that perl-forks is built against is non-threaded the build
system will drop into interactive mode to ask about simulating ithreads.
This causes the build to hang. Set FORKS_SIMULATE_USEITHREADS to avoid
going into interactive mode.
2021-11-15 11:24:36 +01:00
Glenn Johnson
85a33bd2f1 perl-dbd-mysql: depend on mysql-client (#27393) 2021-11-15 11:24:09 +01:00
Glenn Johnson
19493e4932 ncl: add dependencies (#27394)
- zstd
- makedepend
2021-11-15 11:23:50 +01:00
Glenn Johnson
557556bbfd maker: add perl-dbd-mysql dependency (#27395) 2021-11-15 11:23:30 +01:00
Glenn Johnson
d01129e9c8 mariadb-c-client: add krb5 dependency (#27396) 2021-11-15 11:23:08 +01:00
Diego Alvarez
972ae2393a nextflow: add v21.10.0 (#27400) 2021-11-15 11:22:39 +01:00
Harmen Stoppels
21308eb5cc Turn some verbose messages into debug messages (#27408) 2021-11-15 11:21:37 +01:00
Valentin Volkl
4c0f5f85c0 edm4hep: add v0.4 (#27412) 2021-11-15 11:17:17 +01:00
Harmen Stoppels
9573eb5315 dsfmt: new package (#27415) 2021-11-15 11:15:42 +01:00
Glenn Johnson
d1df044b42 asciidoc: add autotools dependencies (#27418) 2021-11-15 11:13:00 +01:00
Glenn Johnson
9171d56146 czmq: use Spack's docbook (#27419) 2021-11-15 11:11:29 +01:00
Glenn Johnson
8dc8282651 dbus: use Spack's docbook (#27420) 2021-11-15 11:11:11 +01:00
Glenn Johnson
6e646e42a5 gpu-burn: set spack compiler (#27421) 2021-11-15 11:10:57 +01:00
Glenn Johnson
91b8a87fc7 interproscan: add missing dependency (#27423) 2021-11-15 11:10:27 +01:00
Glenn Johnson
5aaee953c5 libbeagle: add opencl variant (#27424) 2021-11-15 11:10:02 +01:00
Glenn Johnson
9d9fc522c8 libdrm: use Spack docbook (#27425) 2021-11-15 11:09:04 +01:00
Glenn Johnson
5e8368d0c9 libint: fix build (#27426)
- use project autogen.sh script
- set boost path
- make sure to build the compiler before the library
2021-11-15 11:08:48 +01:00
Glenn Johnson
c91b2b42a8 libzmq: use Spack docbook (#27427) 2021-11-15 11:07:30 +01:00
Desmond Orton
4cc42789db py-mxfold2: new package at v0.1.1 (#27383) 2021-11-15 11:07:02 +01:00
Glenn Johnson
f281b59394 hdf-eos5: use szip virtual (#27422) 2021-11-15 11:05:44 +01:00
Oliver Perks
4bd6a11c25 MEEP: update version and libctl (#27433) 2021-11-15 11:03:49 +01:00
Chris White
7b4c08db21 umpire: disable building docs (#27434) 2021-11-15 11:01:20 +01:00
Brian Van Essen
100b212538 Added support for new version of Cray libsci. (#27435) 2021-11-15 11:00:43 +01:00
Arjun Guha
9877c21c50 racket: add new package at v8.3.0 (#27446) 2021-11-15 10:56:26 +01:00
Adam J. Stewart
54cc7d0f30 py-pytorch-lightning: add v1.5.0 (#27266) 2021-11-15 10:49:35 +01:00
Adam J. Stewart
ee8f46e826 py-build: add new package (#27270) 2021-11-15 10:48:43 +01:00
Manuela Kuhn
d9a687af45 py-sip: add 5.5.0 and 6.4.0 (#27357) 2021-11-14 22:18:08 -06:00
Mark W. Krentel
f92a2d688d elfutils: add version 0.186 (#27345) 2021-11-13 18:49:53 -06:00
iarspider
3706fef9af New version: py-pexpect 4.8.0 (#27401) 2021-11-13 17:31:56 -07:00
iarspider
76fed9c04d New version: py-plac; fix tests (#27405) 2021-11-13 17:28:27 -07:00
Glenn Johnson
7a00cef055 qt: turn off features if not supported by the kernel (#27438)
If building Qt on a system with a recent glibc but an older kernel, it
is possible that Qt configures features based on glibc that are not
supported in the kernel. This PR tests the kernel version and ensures
certain features are disabled if the kernel does not support them.
2021-11-13 15:39:50 -05:00
Manuela Kuhn
9fb9399487 py-pycortex: add new package (#27432) 2021-11-13 12:24:51 -06:00
Manuela Kuhn
94eb175e07 py-lxml: add 4.6.4 (#27440) 2021-11-13 12:19:46 -06:00
Manuela Kuhn
8e9ef0f6f6 py-neurokit2: add 0.1.5 (#27441) 2021-11-13 12:17:14 -06:00
Manuela Kuhn
02355d32bd py-deepdiff: add new package (#27442) 2021-11-13 12:14:46 -06:00
Manuela Kuhn
e3389e9017 py-pytest-runner: add 5.3.1 (#27443) 2021-11-13 12:12:59 -06:00
Manuela Kuhn
984715e859 py-imageio: add 2.10.3 (#27431) 2021-11-13 05:22:27 -07:00
Seth R. Johnson
31fec1f730 py-h5sh: replace github with pypi (#27409) 2021-11-12 19:01:25 -06:00
Satish Balay
446e4ff54b xsdk: add version @0.7.0 (#27250)
- add xsdk_depends_on() that propagates cuda, rocm options
- enable +cuda for hypre, mfem, amrex
- enable +rocm for mfem, sundials, magma, amrex, tasmanian, ginkgo, heffte
- deprecate @0.5.0
- remove 'debug' variant as it doesn't really exist
- heffte: remove binding to openmpi+cuda
- dtk: use 3.1-rc2 on macos (3.1-rc3 elsewhere)
- petsc: disable trilinos

Co-authored-by: Cody Balos <balos1@llnl.gov>
2021-11-12 17:20:35 -06:00
Cody Balos
203a5a0f71 sundials: fix for rocm support (#27295) 2021-11-12 16:13:32 -06:00
Manuela Kuhn
98fbfa2739 py-pybids: add 0.14.0 (#27430) 2021-11-12 15:04:51 -07:00
Cody Balos
c4b52098f3 superlu-dist: fix case for cce fortran compiler (#27296)
* superlu-dist: fix build with cce fortran compiler
2021-11-12 15:27:15 -06:00
iarspider
3f4d0943d7 New version: py-pkgconfig 1.5.5 (#27402)
* New version: py-pkgconfig 1.5.5

* Actually add version 1.5.5; fix dependency
2021-11-12 12:59:00 -07:00
iarspider
67f4e2674f New version: py-prettytable 2.4.0; update homepage (#27407)
* New version: py-prettytable 2.4.0; update homepage

* Update var/spack/repos/builtin/packages/py-prettytable/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-11-12 12:52:48 -07:00
iarspider
441a76b646 New version: py-prometheus-client 0.12.0 ... (#27410)
* New version: py-prometheus-client 0.12.0; new dependency (py-twisted) version 21.7.0 + it's dependencies

* Apply suggestions from code review (1/?)

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Changes from review (2/?)

* Changes from review (3/?)

* Changes from review (4/?)

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-11-12 11:31:47 -07:00
Harmen Stoppels
4b16c6fb0c bump python 3.9.8 (#27381) 2021-11-12 11:17:16 -06:00
Glenn Johnson
8d06abb8ed py-numpy: add support for intel-oneapi-mkl (#27390) 2021-11-12 11:16:09 -06:00
Glenn Johnson
77203c940c py-grpcio: add re2 dependency and set paths (#27391) 2021-11-12 11:14:45 -06:00
iarspider
f9c4cb5f8a New version: py-pathlib2 2.3.6 (#27398) 2021-11-12 11:12:03 -06:00
iarspider
1d166a2151 New version: py-pbr 5.7.0 (#27399) 2021-11-12 11:11:04 -06:00
Jen Herting
79e520957b New package: py-pyscipopt (#27363)
* build of pyscipopt w/ scipoptsuite 7.0.1

* removed type from scipoptsuite"

* removed url

* updated to 3.4.0

* [py-pyscipopt] removed redundant python dependency and fixed dependency types

Co-authored-by: Sid Pendelberry <sid@rit.edu>
2021-11-12 10:07:59 -07:00
iarspider
9c386b181a New version: py-pkginfo 1.7.1 (#27403) 2021-11-12 11:04:36 -06:00
iarspider
c9e96018be New version: py-pluggy 1.0.0 (#27406) 2021-11-12 11:03:25 -06:00
Seth R. Johnson
a04cc4470e Add PyPI docs and warning in auto-generated package (#27404)
* docs: Add cross-references for pypi setup

* create: add warning for missing pypi
2021-11-12 10:58:44 -06:00
Andrew W Elble
407f68a67b new package: py-qiskit-aer and dependencies (#27198)
* new package: py-qiskit-aer and dependencies

+updates for dependencies

* flake8 fix

* forgot homepages

* incorporate feedback

* py-cmake and py-ninja to py-tweedledum, prevent py-cmake from
completely rebuilding cmake

* py-ninja: avoid rebuilding ninja

* other feedback fixes

* additional fixes
2021-11-12 10:45:07 -06:00
Massimiliano Culpo
c5dd3265ed Update the Public key of the tutorial (#27370) 2021-11-12 11:46:02 +01:00
Harmen Stoppels
9637ed05f5 Fix overloaded argparse keys (#27379)
Commands should not reuse option names defined in main.
2021-11-11 23:34:18 -08:00
Desmond Orton
11f6aac1e3 New Package: py-setuptools-cpp (#27382) 2021-11-11 23:30:18 -08:00
Adam J. Stewart
dbad9fd58a py-torchgeo: add version 0.1.0 (#27274) 2021-11-11 23:25:20 -08:00
Harmen Stoppels
62b1c3411c suite-sparse: general fixes (#27283)
- disable graphblas by default (very slow to compile)
- fix patch upperbound for cuda 11
- remove find_system_libs; not sure why it was added in the first place,
but it makes spack rather unusable as it introduces an rpath to /lib/...
2021-11-11 23:21:53 -08:00
Ben Cowan
f5e107e046 gcc package: Mac OS patch not needed for @12: 2021-11-11 23:15:38 -08:00
Robert Cohn
c91074514a intel-oneapi-mkl: define MKLROOT for dependents (#27302)
Fixes #27260
2021-11-11 23:12:48 -08:00
Adam J. Stewart
c8fdce28e6 PyTorch: fix compilation of +distributed~tensorpipe (#27337) 2021-11-11 23:09:10 -08:00
Tiziano Müller
38592b9e4f boost: ensure Spack wrappers are used for %intel (#27348)
Fixes #26117
2021-11-11 23:02:08 -08:00
Manuela Kuhn
f777cc079d py-formulaic: add new package (#27373) 2021-11-11 22:22:51 -07:00
Adam J. Stewart
17025f5354 GDAL: add v3.4.0 (#27288) 2021-11-11 19:31:51 -07:00
Charles Doutriaux
7858a2f05c Adds Sina Python Package to Spack (#27219) 2021-11-11 17:20:23 -08:00
eugeneswalker
a35d3b895b e4s ci: enable tau +mpi +python variants (#27273) 2021-11-11 17:14:31 -08:00
Chris White
1d8c2498ee update exercise build option for 0.14.0 (#27338) 2021-11-11 17:06:08 -08:00
Mark W. Krentel
f548243e9e elfutils: add version 0.186 (#27345) 2021-11-11 17:04:53 -08:00
Timothy Brown
eb9a520adb Adding a new ESMF version and checksum. (#27367) 2021-11-11 17:02:08 -08:00
Adam J. Stewart
89a59b98e7 py-scipy: add v1.7.2 (#27252) 2021-11-12 00:40:29 +01:00
Adam J. Stewart
e3645d666e py-numpy: add v1.21.4 (#27251) 2021-11-12 00:11:26 +01:00
Manuela Kuhn
dcef7b066c py-pillow: add 8.4.0 (#27371) 2021-11-11 16:04:45 -07:00
Seth R. Johnson
c9ed4bce66 py-wurlitzer: new package (#27328)
* py-wurlitzer: new package

* py-wurlitzer: use PyPI repository

* py-wurlitzer: use pypi attribute
2021-11-11 14:34:50 -07:00
Jen Herting
44b5c1e41a New package: py-parmed (#27362)
* [py-parmed] created template

* [py-parmed]

- added homepage
- added description
- removed fixmes
- added dependencies
2021-11-11 13:58:29 -06:00
iarspider
0d06bf6027 New version: py-nbconvert 6.2.0 (#27350)
* New version: py-nbconvert 6.2.0

* Update package.py
2021-11-11 11:58:56 -07:00
iarspider
a2eadbbcdf New version: py-pandocfilters 1.5.0 (#27359) 2021-11-11 11:07:53 -07:00
iarspider
347ad11b68 New version: py-parso 0.8.2 (#27360)
* New version: py-parso 0.8.2

* Update package.py
2021-11-11 10:58:45 -07:00
eugeneswalker
f2920cbf62 tau: add v2.31 (#27342) 2021-11-11 09:53:07 -08:00
Manuela Kuhn
7513a644b9 py-h5py: add v3.5.0 (#27344) 2021-11-11 18:51:52 +01:00
Harmen Stoppels
f097a24253 fuse-overlayfs: add maintainer, add v1.7, v1.7.1 (#27349) 2021-11-11 18:50:32 +01:00
iarspider
53168d4e57 New version: py-notebook 6.4.5 (#27353) 2021-11-11 09:55:44 -07:00
Manuela Kuhn
72f41a6591 py-interface-meta: add new package (#27340) 2021-11-11 10:48:46 -06:00
iarspider
00c84aa54f New version: py-oauthlib 3.1.1 (#27356)
* New version: py-oauthlib 3.1.1

* Update var/spack/repos/builtin/packages/py-oauthlib/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-11-11 09:43:50 -07:00
haralmha
e32dd27eb7 Generalize env var PYTHON to avoid version conflicts (#27334)
* Generalize env var PYTHON to avoid version conflicts

* Use available python executable

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-11-11 10:37:54 -06:00
iarspider
9ce0abf34f New version: py-nbconvert 0.5.5 (#27347) 2021-11-11 10:37:10 -06:00
iarspider
569a9a9dcc New version: py-nest-asyncio 1.5.1 (#27351) 2021-11-11 10:35:33 -06:00
iarspider
945594fa98 New version: py-networkx 2.6.3 (#27352) 2021-11-11 10:29:45 -06:00
Daryl W. Grunau
770bbba676 Trilinos: fix DEP_INCLUDE_DIRS definition (#27341) 2021-11-11 05:30:44 -05:00
Dan Bonachea
8d021a2915 upcxx: Update the UPC++ package to 2021.9.0 (#26996)
* upcxx: Update the UPC++ package to 2021.9.0

* Add the new release, and a missing older one.

* Remove the spack package cruft for supporting the obsolete build system that
  was present in older versions that are no longer supported.

* General cleanups.

Support for library versions older than 2020.3.0 is officially retired,
for two reasons:

1. Releases prior to 2020.3.0 had a required dependency on Python 2,
   which is [officially EOL](https://www.python.org/doc/sunset-python-2/)
   as of Jan 1 2020, and is no longer considered secure.
2. (Most importantly) The UPC++ development team is unable/unwilling to
   support releases more than two years old.  UPC++ provides robust
   backwards-compatibility to earlier releases of UPC++ v1.0, with very
   rare well-documented/well-motivated exceptions.  Users are strongly
   encouraged to update to a current version of UPC++.

NOTE: Most of the lines changed in this commit are simply re-indentation,
and thus might be best reviewed in a diff that ignores whitespace.

* upcxx: Detect Cray XC more explicitly

This change is necessary to prevent false matches occuring on new Cray Shasta
systems, which do not use the aries network but were incorrectly being treated
as a Cray XC + aries platform.

UPC++ has not yet deployed official native support for Cray Shasta, but this
change is sufficient to allow building the portable backends there.
2021-11-10 13:48:02 -08:00
Manuela Kuhn
8411cc934d py-setupmeta: add new package (#27327)
* py-setupmeta: add new package

* Update var/spack/repos/builtin/packages/py-setupmeta/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-11-10 13:43:46 -07:00
iarspider
5e0208a710 New version: py-mpld3 0.5.5 (#27329)
* New version: py-mpld3 0.5.5

* Update package.py

* Update package.py
2021-11-10 11:07:51 -07:00
Manuela Kuhn
335bcdc206 py-traits: add 6.3.1 (#27321) 2021-11-10 11:49:13 -06:00
Manuela Kuhn
89d98a780d py-traitlets: add 5.1.1 (#27322) 2021-11-10 11:48:14 -06:00
iarspider
b5e0ac35c8 New versions: py-more-itertools 8.9.0, 8.11.0 (#27325) 2021-11-10 11:45:27 -06:00
Manuela Kuhn
a31f2be91a py-wrapt: add 1.13.3 (#27326) 2021-11-10 11:42:28 -06:00
iarspider
4633f19971 New verison of py-mpmath: 1.2.1 (#27331) 2021-11-10 11:33:20 -06:00
iarspider
0e5cc0d79b New versions of py-multidict: 5.1.0 and 5.2.0 (#27332) 2021-11-10 10:31:46 -07:00
Veselin Dobrev
ceabb96c89 Add a patch for mfem v4.3 to support cusparse >= 11.4 (#27267) 2021-11-09 20:29:06 -06:00
iarspider
723f2f465b New version: py-markdown 3.3.4 (#27310)
* New version: py-markdown 3.3.4

* Changes from review

* Update package.py
2021-11-09 17:19:41 -07:00
Karen C. Tsai
376e5ffd6e fix typo (#27319) 2021-11-09 17:16:41 -07:00
Massimiliano Culpo
b16bfe4f5f spack tutorial: fix output to screen (#27316)
Spack was checking out v0.17, the output reported v0.16
2021-11-09 15:10:22 -08:00
Maxim Belkin
0ab5d42bd5 Fix typos (ouptut) (#27317) 2021-11-09 16:11:34 -06:00
Harmen Stoppels
0322431c5c libssh2: add new versions and crypto=mbedtls|openssl (#27284) 2021-11-09 22:24:23 +01:00
Karen C. Tsai
81a0f7222c create py-sphinx-multiversion spackage (#27314) 2021-11-09 14:09:13 -07:00
iarspider
d8f4339c18 New version: py-mako 1.1.5 (#27308) 2021-11-09 13:39:34 -06:00
Manuela Kuhn
41d4473df4 py-pooch: add 1.5.2 (#27305) 2021-11-09 13:37:16 -06:00
Olivier Cessenat
31c932eec9 octave: override qtchooser, add bz2 variant (#26802)
* octave: override qtchooser, add bz2 variant

* fix texinfo not found from "spack install --test=root -v"

Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2021-11-09 19:36:42 +01:00
Kyle Gerheiser
86c8c3306b Add variant for the --enable-two-level-namespace option in MPICH (#27230) 2021-11-09 15:48:01 +00:00
Jordan Galby
6e9c0a8155 Fix log-format reporter ignoring install errors (#25961)
When running `spack install --log-format junit|cdash ...`, install
errors were ignored. This made spack continue building dependents of
failed install, ignoring `--fail-fast`, and exit 0 at the end.
2021-11-09 15:47:32 +00:00
Larry Knox
8a836213f7 Add hdf5-vol-async package. (#26874)
* Add hdf5-vol-async package.
Add HDF5 1.13.0-rc6 version for building vol-async.

* Style test required another blank line.

* Change hdf5 dependency to develop-1.13+mpi+threadsafe.

* Update args for hdf5-vol-async.
2021-11-09 10:31:34 -05:00
Harmen Stoppels
6e6847d9c7 openlibm: new package (#27286) 2021-11-09 04:52:12 -08:00
Harmen Stoppels
321604b4e5 utf8proc: add new versions (#27287) 2021-11-09 04:50:34 -08:00
iarspider
a7363af47e New version: py-jsonpickle 2.0.0 (#27145) 2021-11-09 05:46:51 -07:00
eugeneswalker
560abc9c14 flecsi 2.1.0: requires gcc>=9 (#27195) 2021-11-09 12:32:41 +00:00
Martin Pokorny
65b0588e80 Fix usage of CMakePackage.define_from_variant() (#27307)
Added `self` target to method calls
2021-11-09 04:52:46 -07:00
Alec Scott
a193e6a204 Add v1.57.0 to Rclone (#27205) 2021-11-09 04:34:48 -07:00
Andrey Prokopenko
7763c7a1cc Deprecate pre-release ArborX version (#27248) 2021-11-09 12:04:54 +01:00
Mikhail Titov
e272e5039d rct: update packages (RP, RU) with new versions (#27306) 2021-11-09 12:03:35 +01:00
Jean-Paul Pelteret
8f88f34973 SymEngine: Update package to 0.8.1 (#27304) 2021-11-09 12:03:07 +01:00
Jean-Paul Pelteret
b4a2fd1fcd deal.II: Update for 9.3.2 release (#27303) 2021-11-09 12:02:51 +01:00
Massimiliano Culpo
752aa7adde Allow triggering the "Bootstrap" workflow manually (#27298) 2021-11-09 12:02:24 +01:00
Robert Underwood
2153ac5863 openmpi fix external find for 0.17 (#27255) 2021-11-09 11:58:14 +01:00
TZ
808375429d openmpi: does not support "--without-pmix" (#27258)
Open MPI currently fails to build with scheduler=slurm if +pmix is
not given with a fatal error due to ``config_args +=
self.with_or_without('pmix', ...)`` resulting in --without-pmix.
However, Open MPI's configure points out "Note that Open MPI does
not support --without-pmix."

The PR only adds "--with-pmix=PATH" if +pmix is part of the spec.
Otherwise, nothing is added and Open MPI can fall back to its
internal PMIX sources.

(The other alternative would be to depend on +pmix in for
scheduler=slurm as is done for +pmi.)
2021-11-09 11:55:56 +01:00
Dylan Simon
2b990b400e make --enable-locks actually enable locks (#24675) 2021-11-09 10:52:08 +00:00
Desmond Orton
34be8d0670 Rebased develop to fix pipeline issues (#27209) 2021-11-09 11:47:59 +01:00
Desmond Orton
eae2027db7 Build Fix (#27210) 2021-11-09 11:46:51 +01:00
Hanwen
65aadf0332 aws-parallelcluster: add v2.11.3 (#27244) 2021-11-09 11:42:09 +01:00
Glenn Johnson
44bf54edee xrootd: add new version and variant (#27245)
- add version 5.3.2
- add krb variant
- add patch to not look for systemd
2021-11-09 11:41:39 +01:00
estewart08
daa8a2fe87 [AMD][rocm-openmp-extras] Update for ROCm 4.3. (#25482)
- Added new checksums for 4.3.
- Now using llvm-amdgpu ~openmp in order to use the rocm-device-libs
  build as external project in llvm-amdgpu package. We still need
  to pull device-libs in using resource for the build as some headers
  are not installed.
- Updated symlink creation to now remove an existing link if  present
  to avoid issues on partial reinstalls when debugging.
- Adjusted the flang_warning to be a part of Cmake options instead of
  a filter_file for better compatability.
- The dependency on hsa-rocr-dev created some problems as type was changed
  to the default build/link. This issue was because ROCr uses libelf and
  the build of openmp expects elfutils. When link is specified libelf
  was being found in the path first, causing errors. This was
  introduced with the llvm-amdgpu external project build of device-libs.
- On a bare bone installation of sles15 it was noted that libquadmath0 was
  needed as a dependency. On 18.04 gcc-multilib was also needed.

* Workaround for libelf headers being used instead of elfutils.
2021-11-09 10:36:13 +00:00
Cameron Rutherford
b8d6351f80 Remove requiring hiop+shared in ExaGO. (#27141) 2021-11-09 11:35:10 +01:00
Cory Bloor
7cb3e9bf43 hipblas: Add spack test support (#27074) 2021-11-09 11:32:36 +01:00
luker
8ce37d9153 HPCG Fix for the Cray complier (CCE) (#25197)
CCE's c++ compiler (Clang based) does not accept the '-ftree-vectorizer-verbose=0'
flag. That flag is removed and a suitable substitution is made.
2021-11-09 10:26:02 +00:00
Cory Bloor
a9c6881bbc rocsolver: Add spack test support (#26919) 2021-11-09 11:25:03 +01:00
Ben Darwin
7c118ee22b ants: fix build by setting BUILD_TESTING=OFF (#26768)
Due to Kitware API changes, default ANTs builds were failing, presumably for all versions (https://github.com/ANTsX/ANTs/issues/1236).
This commit defaults BUILD_TESTING to OFF, preventing calls against
these APIs and fixing all versions.
Note that the ANTs test suite was not clean anyway (e.g. ANTs/#842).
2021-11-09 11:19:32 +01:00
Valentin Volkl
a3dd0e7861 build_environment: clean *_ROOT variables (#26474)
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2021-11-09 11:16:42 +01:00
Joseph Wang
abdd206f65 add libtirpc for rpc/types.h (#26628)
rpc/types.h has been removed in recent glibc
2021-11-09 11:14:28 +01:00
Sreenivasa Murthy Kolam
1d09474975 fix rvs build issue by using yaml-cpp spack recipe (#26000) 2021-11-09 11:09:15 +01:00
Tsuyoshi Yamaura
3484434fe2 New package: SCALE (#25574) 2021-11-09 00:19:47 -08:00
iarspider
f164bae4a3 Python tests: skip importing weirdly-named modules (#27151)
* Python tests: allow importing weirdly-named modules

e.g. with dashes in name

* SIP tests: allow importing weirdly-named modules

* Skip modules with invalid names

* Changes from review

* Update from review

* Update from review

* Cleanup
2021-11-08 19:22:33 +00:00
Brian Van Essen
db504db9aa Added new hash values for recent versions. (#27294) 2021-11-08 19:02:30 +00:00
iarspider
bff894900e New version: py-lz4 3.1.3; use external lz4 instead of bundled one (#27282)
* New version: py-lz4 3.1.3; use external lz4 instead of bundled one

* Update var/spack/repos/builtin/packages/py-lz4/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Changes from review

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-11-08 18:14:46 +00:00
iarspider
71f8460357 New versions of py-keyring: 23.1.0, 23.2.0, 23.2.1 (#27276) 2021-11-08 10:59:40 -06:00
iarspider
f9d0007546 New version: py-lazy-object-proxy 1.6.0 (#27277) 2021-11-08 10:58:26 -06:00
iarspider
14232b40d9 New version: py-lockfile 0.12.2 (#27279) 2021-11-08 10:56:34 -06:00
Seth R. Johnson
18d506c7fb trilinos: disable optional packages by default (#26815) 2021-11-08 08:29:35 -05:00
Maciej Wójcik
c384ac88a0 gromacs-swaxs: new package (#26902) 2021-11-08 13:51:23 +01:00
Maciej Wójcik
8f59707f04 gromacs-chain-coordinate: inherit from gromacs package (#27246) 2021-11-08 13:50:42 +01:00
Massimiliano Culpo
62f0c70a8c OpenSUSE: try to apply workaround to avoid CI error (#27275) 2021-11-08 11:56:19 +00:00
Ben Bergen
1fc753af66 Updated Versions (#27268)
- Added 7.1 release
- Added master git branch
2021-11-07 19:41:49 -07:00
Brice Videau
f02dec2bbb Update py-ytopt package and add necessary dependencies (#26879)
* Add spack package py-ytopt-team-ytopt and required dependencies.

* Removed old ytop package.

* Added author as maintainer.

* Fix style.

* Update var/spack/repos/builtin/packages/py-config-space/package.py

Update python dependency to 3.7

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-config-space/package.py

Remove run dependency from py-cython.

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-config-space/package.py

Added run dependency type for py-pyparsing.

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Updated description of py-dh-scikit-optimize.

* Source py-dh-scikit-optimize from PyPI.

* Added latest py-dh-scikit-optimize version.

* Made plots option False by default for py-dh-scikit-optimize.

* Removed 0.9.4 as it needs additional dependencies.

* Added version dependencies.

* Added missing py-joblib dependencies.

* Added run dependency type.

* Added python 2.7+ as supported for py-pyaml.

* Change py-config-space to py-configspace.

* Added dependency on python 3.6+.

* Fix py-configspace package naming.

* Changed py-autotune to py-ytopt-autotune.

* Update var/spack/repos/builtin/packages/py-pyaml/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Added debug variant with py-ray dependency.

* Added missing py-mpi4py missing dependency.

* Removed erroneous variant.

* Added debug variant to py-ray.

* Fix indentation.

* Removed debug variant of py-ray.

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-11-06 10:52:30 -05:00
Todd Gamblin
285548588f Update CHANGELOG.md for 0.17.0 2021-11-05 17:22:32 -07:00
Todd Gamblin
0e3d0516e6 bump version number to 0.17.0 2021-11-05 17:11:37 -07:00
Ben Darwin
12429bda35 py-itk: fix dependencies (#27164) 2021-11-05 16:26:18 -05:00
Seth R. Johnson
c5be548046 New package: GNDS (#27176)
Adds a new package for the AMPX/SCALE implementation of the GNDS
interface,
https://www.oecd.org/publications/specifications-for-the-generalised-nuclear-database-structure-gnds-94d5e451-en.htm
.
2021-11-05 14:04:47 -06:00
Bernhard Kaindl
d9d1319442 qt: replace conflicts('%gcc@11:', when='@5.9:5.14') with -include limits (#27241)
Noting that missing numeric_limits was the cause of the compile issues
with gcc-11, I tested adding -include limits fixing @5.9:5.14%gcc@11.
Therefore, we can replace the conflicts('%gcc@11:', when='@5.9:5.14').

Co-authored-by: Bernhard Kaindl <bernhard.kaindl@ait.ac.at>
2021-11-05 14:06:31 -04:00
Theofilos Manitaras
549bd70449 py-mpi4py: Add newer versions (#27239)
* py-mpi4py: Add newer versions

* Address PR comments
2021-11-05 11:07:44 -06:00
Axel Huebl
4f692e4d9f openPMD-api: 0.14.3 (#27211)
Add the latest release.
2021-11-05 10:53:03 -06:00
Massimiliano Culpo
0feb5ec70a Prevent additional properties to be in the answer set when reusing specs (#27240)
* Prevent additional properties to be in the answer set when reusing specs

fixes #27237

The mechanism to reuse concrete specs relies on imposing
the set of constraints stemming from the concrete spec
being reused.

We also need to prevent that other constraints get added
to this set.
2021-11-05 10:52:44 -06:00
Peter Brady
178e15c39d ctags uses custom autogen.sh script (#27229) 2021-11-05 09:46:09 -07:00
Sinan
0b4b731479 package/py-zarr_add_v2.10.2 (#27212)
* package/py-zarr_add_v2.10.2

* improve python dep version constraints

Co-authored-by: sbulut <sbulut@3vgeomatics.com>
2021-11-05 09:23:41 -05:00
Bernhard Kaindl
91c7c24260 hdf5: Skip racy test cases(which loop endless on many cores) (#27068) 2021-11-05 09:59:45 -04:00
Seth R. Johnson
42d8e9eeb5 trilinos: explicitly use variants instead of spec for TPLs (#27221)
Fixes https://github.com/spack/spack/pull/27188#issuecomment-961212214
2021-11-05 09:07:33 -04:00
Manuela Kuhn
d2c26fef46 r-readr: add 2.0.2 (#27177) 2021-11-05 06:34:40 -06:00
Mikhail Titov
d7ae9414c2 exaworks: swift-t package (#27234) 2021-11-05 10:46:35 +01:00
Carlos Bederián
b06198f1d4 gmsh: add dependency on gl and glu providers when +fltk (#27169) 2021-11-05 10:45:53 +01:00
Harmen Stoppels
8bb5ed8464 make version docs reflect reality (#27149)
* make version docs reflect reality

* typo and make things

* 2.6 -> 2.7 in example
2021-11-05 09:39:31 +00:00
Massimiliano Culpo
e93a2db8b7 hpx: simplify instrumentation_args function (#27226) 2021-11-05 02:34:40 -06:00
Todd Gamblin
e13e697067 commands: spack load --list alias for spack find --loaded (#27184)
See #25249 and https://github.com/spack/spack/pull/27159#issuecomment-958163679.
This adds `spack load --list` as an alias for `spack find --loaded`.  The new command is
not as powerful as `spack find --loaded`, as you can't combine it with all the queries or
formats that `spack find` provides.  However, it is more intuitively located in the command
structure in that it appears in the output of `spack load --help`.

The idea here is that people can use `spack load --list`  for simple stuff but fall back to
`spack find --loaded` if they need more.

- add help to `spack load --list` that references `spack find`
- factor some parts of `spack find` out to be called from `spack load`
- add shell tests
- update docs

Co-authored-by: Peter Josef Scheibel <scheibel1@llnl.gov>
Co-authored-by: Richarda Butler <39577672+RikkiButler20@users.noreply.github.com>
2021-11-05 00:58:29 -07:00
Simon Frasch
bfbf9deb74 spfft: add version 1.0.5 (#27223) 2021-11-05 01:52:37 -06:00
Simon Frasch
6bae3cd6bb spla: add version 1.5.2 (#27222) 2021-11-05 08:45:34 +01:00
Todd Gamblin
8e76244266 docs for experimental --reuse argument to spack install
Add docs for `--reuse`, along with a warning that it will likely be
removed and refactored.
2021-11-05 00:15:47 -07:00
Gregory Becker
5efa76a033 error message for reusing multiple hashes for package 2021-11-05 00:15:47 -07:00
Todd Gamblin
ac1e05fe1b concretizer: add error messages and simplify asp.py 2021-11-05 00:15:47 -07:00
Massimiliano Culpo
0186f0f955 Fix logic program for multi-valued variants
Reformulate variant rules so that we minimize both

1. The number of non-default values being used
2. The number of default values not-being used

This is crucial for MV variants where we may have
more than one default value
2021-11-05 00:15:47 -07:00
Todd Gamblin
e0c3d074c0 bugfix: handle hashes that only exist in input specs
In our tests, we use concrete specs generated from mock packages,
which *only* occur as inputs to the solver. This fixes two problems:

1. We weren't previously adding facts to encode the necessary
   `depends_on()` relationships, and specs were unsatisfiable on
   reachability.

2. Our hash lookup for reconstructing the DAG does not
   consider that a hash may have come from the inputs.
2021-11-05 00:15:47 -07:00
Todd Gamblin
a4a2ed3c34 concretizer: exempt already-installed specs from compiler and variant rules
Concrete specs that are already installed or that come from a buildcache
may have compilers and variant settings that we do not recognize, but that
shouldn't prevent reuse (at least not until we have a more detailed compiler
model).

- [x] make sure compiler and variant consistency rules only apply to
      built specs
- [x] don't validate concrete specs on input, either -- they're concrete
      and we shouldn't apply today's rules to yesterday's build
2021-11-05 00:15:47 -07:00
Todd Gamblin
49ed41b028 spack diff: more flexible tests, restore transitive diff with spec_clauses
In switching to hash facts for concrete specs, we lost the transitive facts
from dependencies. This was fine for solves, because they were implied by
the imposed constraints from every hash. However, for `spack diff`, we want
to see what the hashes mean, so we need another mode for `spec_clauses()` to
show that.

This adds a `expand_hashes` argument to `spec_clauses()` that allows us to
output *both* the hashes and their implications on dependencies. We use
this mode in `spack diff`.
2021-11-05 00:15:47 -07:00
Massimiliano Culpo
3e3e84ba30 Add a missing definition in the logic program 2021-11-05 00:15:47 -07:00
Massimiliano Culpo
be2cf16b67 Add buildcache to reusable specs 2021-11-05 00:15:47 -07:00
Massimiliano Culpo
31dfad9c16 spack install: add --reuse argument 2021-11-05 00:15:47 -07:00
Massimiliano Culpo
e2744fafa1 spack concretize: add --reuse argument 2021-11-05 00:15:47 -07:00
Massimiliano Culpo
290f57c779 spack spec: add --reuse argument 2021-11-05 00:15:47 -07:00
Todd Gamblin
652fa663b5 concretizer: get rid of last maximize directive in concretize.lp
- [x] Get rid of forgotten maximize directive.
- [x] Simplify variant handling
- [x] Fix bug in treatment of defaults on externals (don't count
      non-default variants on externals against them)
2021-11-05 00:15:47 -07:00
Massimiliano Culpo
da57b8775f Update command completion 2021-11-05 00:15:47 -07:00
Massimiliano Culpo
0d74a4f46e Trim dependencies on externals 2021-11-05 00:15:47 -07:00
Massimiliano Culpo
0b80035eaa Fix a unit test to match the new OS semantics
CNL, debian6 and Suse are not compatible
2021-11-05 00:15:47 -07:00
Massimiliano Culpo
4d25fc0068 ASP-based solve: if an OS is set, respect the value 2021-11-05 00:15:47 -07:00
Massimiliano Culpo
6e297b9ba1 Fix a type in "variant_not_default" rule 2021-11-05 00:15:47 -07:00
Todd Gamblin
ace4586bf8 concretizer: rework spack solve output to handle reuse better 2021-11-05 00:15:47 -07:00
Todd Gamblin
c537785f6f spec: ensure_valid_variants() should not validate concrete specs
Variants in concrete specs are "always" correct -- or at least we assume
them to be b/c they were concretized before. Their variants need not match
the current version of the package.
2021-11-05 00:15:47 -07:00
Todd Gamblin
b60a95cd5d concretizer: unify handling of single- and multi-valued variants
Multi-valued variants previously maximized default values to handle
cases where the default contained two values, e.g.:

    variant("foo", default="bar,baz")

This is because previously we were minimizing non-default values, and
`foo=bar`, `foo=baz`, and `foo=bar,baz` all had the same score, as
none of them had any "non-default" values.

This commit changes the approach and considers a non-default value
to be either a value set to something not default *or* the absence
of a default value from the set value.  This allows multi- and
single-valued variants to be handled the same way, with the same
minimization criterion.  It alse means that the "best" value for every
optimization criterion is now zero, which allows us to make useful
assumptions about the optimization criteria.
2021-11-05 00:15:47 -07:00
Todd Gamblin
b88da9d73d concretizer: reuse installs, but assign default values for new builds
Minimizing builds is tricky. We want a minimizing criterion because
we want to reuse the avaialble installs, but we also want things that
have to be built to stick to *default preferences* from the package
and from the user. We therefore treat built specs differently and
apply a different set of optimization criteria to them. Spack's *first*
priority is to reuse what it can, but if it builds something, the built
specs will respect defaults and preferences.

This is implemented by bumping the priority of optimization criteria
for built specs -- so that they take precedence over the otherwise
topmost-priority criterion to reuse what is installed.

The scheme relies on all of our optimization criteria being minimizations.
That is, we need the case where all specs are reused to be better than
any built spec could be. Basically, if nothing is built, all the build
criteria are zero (the best possible) and the number of built packages
dominates. If something *has* to be built, it must be strictly worse
than full reuse, because:

  1. it increases the number of built specs
  2. it must have either zero or some positive number for all criteria

Our optimziation criteria effectively sum into two buckets at once to
accomplish this. We use a `build_priority()` number to shift the
priority of optimization criteria for built specs higher.
2021-11-05 00:15:47 -07:00
Todd Gamblin
cfb60ab9e1 tests: make spack diff test more lenient
The constraints in the `spack diff` test were very specific and assumed
a lot about the structure of what was being diffed. Relax them a bit to
make them more resilient to changes.
2021-11-05 00:15:47 -07:00
Todd Gamblin
9eb94be6dd concretizer: only minimize builds when --reuse is enabled.
Make the first minimization conditional on whether `--reuse` is enabled in the solve.
If `--reuse` is not enabled, there will be nothing in the set to minimize and the
objective function (for this criterion) will be 0 for every answer set.
2021-11-05 00:15:47 -07:00
Todd Gamblin
40b914503e concretizer: adjust integrity constraints to only apply to builds.
Many of the integrity constraints in the concretizer are there to restrict how solves are done, but
they ignore that past solves may have had different initial conditions. For example, for things
we're building, we want the allowed variants to be restricted to those currently in Spack packages,
but if we are reusing a concrete spec, we need to be flexible about names that may have existed in
old packages.

Similarly, restrictions around compatibility of OS's, compiler versions, compiler OS support, etc.
are really only about what is supported by the *current* set of compilers/build tools known to
Spack, not about what we may get from concrete specs.

- [x] restrict certain integrity constraints to only apply to packages that we need to build, and
      omit concrete specs from consideration.
2021-11-05 00:15:47 -07:00
Todd Gamblin
2c142f9dd4 concretizer: rework operating system semantics for installed packages
The OS logic in the concretizer is still the way it was in the first version.
Defaults are implemented in a fairly inflexible way using straight logic. Most
of the other sections have been reworked to leave these kinds of decisions to
optimization. This commit does that for OS's as well.

As with targets, we optimize for target matches. We also try to optimize for
OS matches between nodes. Additionally, this commit adds the notion of
"OS compatibility" where we allow for builds to depend on binaries for certain
other OS's. e.g, for macos, a bigsur build can depend on an already installed
(concrete) catalina build. One cool thing about this is that we can declare
additional compatible OS's later, e.g. CentOS and RHEL.
2021-11-05 00:15:47 -07:00
Todd Gamblin
9c70d51a4f concretizer: impose() for concrete specs should use body facts.
The concretizer doesn't get a say in whether constraints from
concrete specs are imposed, so use body facts for them.
2021-11-05 00:15:47 -07:00
Todd Gamblin
3866b3e7d3 include installed hashes in solve and optimize for reuse 2021-11-05 00:15:47 -07:00
Todd Gamblin
7abe4ab309 rename checked_spec_clauses() to spec_clauses() 2021-11-05 00:15:47 -07:00
Todd Gamblin
ad5d632eeb add --reuse option to spack solve 2021-11-05 00:15:47 -07:00
Sinan
288176326c new package: librttopo (#27182)
Co-authored-by: sbulut <sbulut@3vgeomatics.com>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2021-11-04 21:01:42 -06:00
Alec Scott
82b45d112f [New Package] Add Restic v0.12.1 (#27208)
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2021-11-04 17:12:34 -07:00
Massimiliano Culpo
839057e98d Rename the temporary scope for bootstrap buildcache (#27231)
If we don't rename Spack will fail with:
```
ImportError: cannot bootstrap the "clingo" Python module from spec "clingo-bootstrap@spack+python %gcc target=x86_64" due to the following failures:
    'spack-install' raised ValueError: Invalid config scope: 'bootstrap'.  Must be one of odict_keys(['_builtin', 'defaults', 'defaults/cray', 'bootstrap/cray', 'disable_modules', 'overrides-0'])
    Please run `spack -d spec zlib` for more verbose error messages
```
in case bootstrapping from binaries fails and we are
falling back to bootstrapping from sources.
2021-11-04 16:17:00 -07:00
Ben Darwin
f2a42ac4c6 c3d: add new package (#27155) 2021-11-04 15:38:28 -07:00
Tamara Dahlgren
080f1872b8 Add the spack tutorial environment as a cloud pipeline stack (#27137) 2021-11-04 15:14:46 -07:00
Jerome Soumagne
c25a4ecfc2 libfabric: add 1.13.2 (#27202) 2021-11-04 15:04:40 -07:00
Massimiliano Culpo
79f754a968 Sort arguments lexicographically in command's help (#27196) 2021-11-04 12:41:58 -07:00
downloadico
084ce46107 exciting: add "oxygen" version, multiple fixes (#27217)
ensure that none of ^intel-mkl, ^intel-mpi, and ^mkl are used, unless
the compiler is intel.
Fix bad logic in the src/src_xs/m_makespectrum.f90 file in the oxygen version.
Add the -fallow-argument-mismatch for gcc >= 10.
2021-11-04 12:24:27 -07:00
Cameron Smith
7542d8adc8 omega-h: add support for stand-alone testing (#26931)
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2021-11-04 12:02:02 -07:00
Joe Schoonover
4cc2adcbc3 Add new versions for HOHQMesh and switch to tar-ball releases (#27194)
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2021-11-04 11:54:02 -07:00
Jon Rood
ed3d459a83 Add RelWithDebInfo to protobuf build_type list. (#27220) 2021-11-04 10:16:44 -07:00
Andre Merzky
f6ed8b6150 Feature/exaworks spack (#27216)
* add exaworks spack meta package

* add maintainer

* switch to `BundlePackage`

* flake8

* another flake8 fix

* remove incorrect dependency
2021-11-04 06:07:45 -06:00
Massimiliano Culpo
1dcabdbc8d mfem, hpx: fix recipes after conditional variants (#27215) 2021-11-04 03:52:38 -06:00
Seth R. Johnson
503576c017 kokkos: refactor defines to use helper functions (#27189) 2021-11-04 09:31:29 +01:00
Erik Schnetter
6a7b07c60b ssht: New version 1.5.1 (#27173) 2021-11-03 22:10:56 -06:00
Cameron Stanavige
7102e295b9 scr: 3.0rc2 release, variants and deps updates (#27178)
* scr: 3.0rc2 release, variants and deps updates

This adds 3.0rc2 release for end users to aid in testing scr for
upcoming 3.0 release.

Included in this change:
- Require most recent component versions for this release
- Add a variant for PDSH as it is now an optional dependency with
this release
- Add bbapi and datawarp (dw) variants
- bbapi_fallback variant now requires bbapi variant with latest
release
- Add variants to enable/disable examples and tests
- Add shared variant and current conflicts with ~shared
- Update cmake_args to account for added variants where needed

Additional updates:
- Add maintainers
- Use lists and for loops to clean up repetitive code involving all
components
- Use self.define and self.define_from_variant to clean up cmake_args
- Use consistent quoting throughout package

* Un-deprecate v2 and legacy

* Use new conditional variants
2021-11-03 20:06:02 -07:00
Erik Schnetter
b9cdaa5429 simulationio package: add variants asdf, hdf5, rnpl, silo (#27172)
Define new variants asdf, hdf5, rnpl, silo to allow disabling or
enabling dependencies.
2021-11-03 18:07:35 -07:00
Erik Schnetter
0d30799bef hwloc: New version 2.6.0 (#27170) 2021-11-03 15:45:38 -07:00
Erik Schnetter
4045ab45de mpitrampoline: New version 2.2.0 (#27171) 2021-11-03 15:42:14 -07:00
Erik Schnetter
91a6e38404 shtools: disable libtool, add 4.9.1, fix --test=root (#27014)
The Makefile expects the "other" libtool, not the GNU libtool we have in Spack.
Closes https://github.com/spack/spack/issues/26993
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2021-11-03 23:33:52 +01:00
Thomas Helfer
c0a81399bf tfel and mgis: add new versions and fix tests (#27011)
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2021-11-03 23:24:28 +01:00
Andrew W Elble
7b3e02471b new package: telegraf (#27201) 2021-11-03 15:00:33 -07:00
David Boehme
47babb2518 Add Caliper v2.7.0 (#27197) 2021-11-03 13:22:43 -06:00
Seth R. Johnson
12a0738030 trilinos: mark conflicts in @:13.1+tpetra^cuda@11 (#27188)
* trilinos: fix @13.0.1+tpetra^cuda@11
* Mark CUDA conflict with old versions and always define TPL
* trilinos: patch doesn't build so just mark as conflict
2021-11-03 12:38:03 -06:00
Axel Huebl
e5a9beed28 WarpX: 21.11 (#27158)
Update `warpx` & `py-warpx` to the latest release, `21.11`.
2021-11-03 11:18:23 -07:00
Kyle Gerheiser
25f1aad1c8 nemsio package: add version 2.5.4; add option to build without MPI (#27030)
Version 2.5.4 adds an option which allows Nemsio to be built without MPI
2021-11-03 10:18:17 -07:00
Manuela Kuhn
09eb79b571 r-reprex: add 2.0.1 (#27174) 2021-11-03 12:05:28 -05:00
Satish Balay
346f3652c6 petsc, py-petsc4py: add versions 3.16.1 (#27152) 2021-11-03 10:52:35 -05:00
Manuela Kuhn
78b1512966 py-datalad: add 0.15.3 (#27193) 2021-11-03 09:49:46 -06:00
iarspider
dede8c9d6b New version: py-jupyterlab-pygments 0.1.2 (#27186) 2021-11-03 10:27:55 -05:00
Manuela Kuhn
8e4d5a0922 sip: fix python_include_dir (#26953) 2021-11-03 10:27:04 -05:00
Manuela Kuhn
5c13c5892b py-nibetaseries: add new package (#27187) 2021-11-03 10:26:30 -05:00
Greg Becker
67cd92e6a3 Allow conditional variants (#24858)
A common question from users has been how to model variants 
that are new in new versions of a package, or variants that are 
dependent on other variants. Our stock answer so far has been
an unsatisfying combination of "just have it do nothing in the old
version" and "tell Spack it conflicts".

This PR enables conditional variants, on any spec condition. The 
syntax is straightforward, and matches that of previous features.
2021-11-03 08:11:31 +01:00
Massimiliano Culpo
78c08fccd5 Bootstrap GnuPG (#24003)
* GnuPG: allow bootstrapping from buildcache and sources

* Add a test to bootstrap GnuPG from binaries

* Disable bootstrapping in tests

* Add e2e test to bootstrap GnuPG from sources on Ubuntu

* Add e2e test to bootstrap GnuPG on macOS
2021-11-02 23:15:24 -07:00
Richarda Butler
1a3747b2b3 Update docs how to display loaded modules (#27159)
* Update spack load docs
2021-11-02 22:12:08 -07:00
dependabot[bot]
a382a6c0e2 build(deps): bump actions/checkout from 2.3.5 to 2.4.0 (#27179)
Bumps [actions/checkout](https://github.com/actions/checkout) from 2.3.5 to 2.4.0.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](1e204e9a92...ec3a7ce113)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-11-03 02:52:28 +00:00
Manuela Kuhn
61ded65888 r-dtplyr: add new package (#27112) 2021-11-03 00:24:21 +00:00
Dan Lipsa
f1fb816d93 Add build editions for catalyst builds. (#22676)
* Add build editions for catalyst builds.

* Fix style.

* Build edition works only for 5.8:
2021-11-02 17:36:53 -04:00
kwryankrattiger
f1afd5ff27 Add and propagate CUDA variants for DAV SDK (#26476) 2021-11-02 17:31:50 -04:00
Satish Balay
c9f8dd93f3 trilinos: new version 13.2.0 (#27106)
* trilinos: add @13.2.0, and switch default to cxxstd=14

* trilinos: fix python dependency when using +ifpack or +ifpack2

* trilinos: add conflict for ~epetra +ml when @13.2.0:

* trilinos: keep 13.0.1 as the preferred version

* Update var/spack/repos/builtin/packages/trilinos/package.py

Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>

* update

Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>
2021-11-02 13:07:42 -06:00
Greg Becker
b3711c0d9d Improved error messages from clingo (#26719)
This PR adds error message sentinels to the clingo solve, attached to each of the rules that could fail a solve. The unsat core is then restricted to these messages, which makes the minimization problem tractable. Errors that can only be generated by a bug in the logic program or generating code are prefaced with "Internal error" to make clear to users that something has gone wrong on the Spack side of things.

* minimize unsat cores manually

* only errors messages are choices/assumptions for performance

* pre-check for unreachable nodes

* update tests for new error message

* make clingo concretization errors show up in cdash reports fully

* clingo: make import of clingo.ast parsing routines robust to clingo version

Older `clingo` has `parse_string`; newer `clingo` has `parse_files`.  Make the
code work wtih both.

* make AST access functions backward-compatible with clingo 5.4.0

Clingo AST API has changed since 5.4.0; make some functions to help us
handle both versions of the AST.

Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2021-11-02 10:55:50 -07:00
Manuela Kuhn
3187689862 r-googlesheets4: add new package (#27114) 2021-11-02 11:46:48 -06:00
Manuela Kuhn
00b6927c65 r-dbplyr: add 2.1.1 (#27111) 2021-11-02 17:35:56 +00:00
Manuela Kuhn
9dc790bbe2 r-haven: add 2.4.3 (#27115) 2021-11-02 17:07:55 +00:00
Manuela Kuhn
ae76692c2e r-lubridate: add 1.8.0 (#27117) 2021-11-02 16:55:27 +00:00
iarspider
fa63bebf36 New versions of py-jupyter-server; fix tests (#27153)
* New versions of py-jupyter-server; fix tests

* Update package.py
2021-11-02 10:37:53 -06:00
Tom Payerle
eee4522103 trilinos: Additional fix for linking C code when built with PyTrilinos (#19834)
This removes `-lpytrilinos` from Makefile.export.Trilinos so that C code
trying to link against a Trilinos built with PyTrilinos does not fail
due to undefined references to python routines (libpytrilinos is only
used when importing PyTrilinos in python, in which case those references
are already defined by Python).

There was already a bit of code to do something similar for C codes
importing Trilinos via a CMake mechanism, this extends that to a basic
Makefile mechanism as well.  This patch also updates the comments to
remove a stale link discussing this issue, and replacing with links to
the some Trilinos issue reports related to the matter.
2021-11-02 12:31:10 -04:00
Manuela Kuhn
b8a44870a4 r-vroom: add new package (#27118) 2021-11-02 11:28:43 -05:00
Manuela Kuhn
426033bc5b r-brms: add 2.16.1 (#27148) 2021-11-02 11:21:54 -05:00
Manuela Kuhn
c2a7f8c608 r-rvest: add 1.0.2 (#27147) 2021-11-02 11:21:09 -05:00
Manuela Kuhn
429a60c703 r-callr: add 3.7.0 (#27146) 2021-11-02 11:19:09 -05:00
Manuela Kuhn
23f8a7331e r-forcats: add 0.5.1 (#27113) 2021-11-02 11:17:22 -05:00
Manuela Kuhn
6e2de9e41f r-processx-3.5.2 (#27119) 2021-11-02 11:13:13 -05:00
Seth R. Johnson
9cfecec002 relocate: do not change library id to use rpaths on package install (#27139)
After #26608 I got a report about missing rpaths when building a
downstream package independently using a spack-installed toolchain
(@tmdelellis). This occurred because the spack-installed libraries were
being linked into the downstream app, but the rpaths were not being
manually added. Prior to #26608 autotools-installed libs would retain
their hard-coded path and would thus propagate their link information
into the downstream library on mac.

We could solve this problem *if* the mac linker (ld) respected
`LD_RUN_PATH` like it does on GNU systems, i.e. adding `rpath` entries
to each item in the environment variable. However on mac we would have
to manually add rpaths either using spack's compiler wrapper scripts or
manually (e.g. using `CMAKE_BUILD_RPATH` and pointing to the libraries of
all the autotools-installed spack libraries).

The easier and safer thing to do for now is to simply stop changing the
dylib IDs.
2021-11-02 17:04:29 +01:00
Manuela Kuhn
34b2742817 r-hms: add 1.1.1 (#27116) 2021-11-02 11:03:52 -05:00
Manuela Kuhn
9d124bdac6 r-crayon: add 1.4.1 (#27110) 2021-11-02 10:49:56 -05:00
Manuela Kuhn
507f7a94d9 r-broom: add 0.7.9 and 0.7.10 (#27109) 2021-11-02 10:48:32 -05:00
Sinan
5fdf6e5f68 package/qgis_revert_incorrect_constraint (#27140)
* package/qgis_revert_incorrect_constraint

* fix bug

* also update dependency constraints

* also update python version constraints

Co-authored-by: sbulut <sbulut@3vgeomatics.com>
2021-11-02 10:43:29 -05:00
iarspider
669954a71d New version: py-isort 5.9.3 (#27144) 2021-11-02 10:42:34 -05:00
iarspider
6f44bf01e0 New version: py-jupyter-console 6.4.0; download sources from pip (#27150) 2021-11-02 10:37:37 -05:00
Joseph Wang
372fc78e98 yoda: add zlib as a dependency (#26454)
Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-11-02 12:37:23 +01:00
Cameron Smith
ca30940868 pumi: support build/install time and stand-alone testing (#26832) 2021-11-02 12:18:46 +01:00
Bernhard Kaindl
5a4d03060b gtk packages: fix dependencies (#26960)
gconf depends on gettext and libintl (dep: intltool)
glibmm, gtkmm, libcanberra and cups need pkgconfig
glibmm needs libsigc++ < 2.9x(which are 3.x pre-releases)
libsigc++@:2.9 depends on m4 for the build

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-11-02 10:39:25 +00:00
Chien-Chang Feng
bf411c7c55 pgplot: add intel compiler support and add more driver (#26761) 2021-11-02 11:30:28 +01:00
Massimiliano Culpo
3f3048e157 Fix GitHub Action's container build (#27143)
#26538 introduced a typo that causes the Docker image
build to fail.
2021-11-02 04:02:04 -06:00
Jean Luca Bez
85bdf4f74e h5bench: update maintainers and versions (#27083) 2021-11-02 10:52:36 +01:00
Glenn Johnson
cf50905ee9 modifications to docbook-xml (#27131)
- added more versions in case packages request a specific version of
  docbook-xml
- added a "current" alias to handle when packages use that
2021-11-02 10:50:07 +01:00
Glenn Johnson
f972863712 fsl: new version, updated constraints and patches (#27129)
- add version 6.0.5
- add patch to allow fsl to use newer gcc versions
- add patch to allow fsl to use newer cuda versions
- remove constraints on gcc and cuda versions
- add filters to prevent using system headers and libraries
- clean up the installed tree
2021-11-02 10:49:22 +01:00
Michael Kuhn
1e26e25bc8 spack arch: add --generic argument (#27061)
The `--generic` argument allows printing the best generic target for the
current machine. This can be quite handy when wanting to find the
generic architecture to use when building a shared software stack for
multiple machines.
2021-11-02 10:19:23 +01:00
Tamara Dahlgren
9d3d7c68fb Add tag filters to spack test list (#26842) 2021-11-02 10:00:21 +01:00
dependabot[bot]
94e0bf0112 build(deps): bump actions/checkout from 2.3.4 to 2.3.5 (#27135)
Bumps [actions/checkout](https://github.com/actions/checkout) from 2.3.4 to 2.3.5.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](5a4ac9002d...1e204e9a92)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-11-02 08:55:28 +01:00
iarspider
80807e6dd4 Add missing dependency to py-setuptools-scm (#27132) 2021-11-01 20:04:43 -06:00
Weiqun Zhang
840c9b7b4a amrex: add new release 21.11 (#27126) 2021-11-02 02:49:03 +01:00
Vicente Bolea
6a5ea3db99 vtkm: add v1.7.0-rc1 (#26882) 2021-11-02 02:42:10 +01:00
Manuela Kuhn
78a073218f r-tzdb: add new package (#27105) 2021-11-01 17:10:13 -05:00
Manuela Kuhn
881b2dcf05 r-rcpp: add 1.0.7 (#27088) 2021-11-01 17:09:18 -05:00
eugeneswalker
8bc01ff63c py-pylint needs pip for build (#27123)
* py-pylint: needs py-pip for build

* alphabetize py- dependencies

* add comment pointing to issue

* fix style
2021-11-01 21:50:36 +00:00
Andre Merzky
e0a929ba60 New package: exaworks (#27054) 2021-11-01 14:15:41 -07:00
Tamara Dahlgren
d4cecd9ab2 feature: add "spack tags" command (#26136)
This PR adds a "spack tags" command to output package tags or 
(available) packages with those tags. It also ensures each package
is listed in the tag cache ONLY ONCE per tag.
2021-11-01 20:40:29 +00:00
Chuck Atkins
b56f464c29 GCC 11 fixes (#27122)
* adios2: Fix compile errors for gcc 11

* unifyfs: Suppress bogus warnings for gcc 11

* conduit: Fix compile errors for gcc 11
2021-11-01 14:31:39 -06:00
Harmen Stoppels
6845307384 Pin actions to a commit sha instead of tag (#26538) 2021-11-01 10:44:03 -07:00
Bernhard Kaindl
02aa1d5d48 intel-gpu-tools: add v1.20 (#26588)
Add version 1.20, fix including the glib-2.0 header files
and add missing dependencies: libunwind and kmod.
2021-11-01 17:35:14 +01:00
Bernhard Kaindl
8ca411c749 glib: skip tests which we cannot make pass (#26693)
glib has a few tests which have external dependencies or
try to access the X server. We cannot run those.

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-11-01 17:33:35 +01:00
Jon Rood
888de27210 kokkos-nvcc-wrapper: add HPE MPT to MPI environment variables (#27069) 2021-11-01 17:31:33 +01:00
Chuck Atkins
15d407c674 ci: Enable more packages in the DVSDK CI pipeline (#27025)
* ci: Enable more packages in the DVSDK CI pipeline

* doxygen: Add conflicts for gcc bugs

* dray: Add version constraints for api breakage with newer deps
2021-11-01 08:54:50 -07:00
Satish Balay
a1eb5596ec kokkos-kernels: add variant 'shared' (#27097)
* kokkos-kernels: add variant 'shared'

* Update var/spack/repos/builtin/packages/kokkos-kernels/package.py
2021-11-01 11:45:26 -04:00
iarspider
6c4f891b8f New version: py-typing-extensions 3.10.0.2 (#27120) 2021-11-01 10:04:18 -05:00
iarspider
99ee9a826a New version: py-beautifulsoup4 4.10.0 (#27121) 2021-11-01 10:02:57 -05:00
iarspider
8dcbd2ee6f alpgen: fix cms recipe (#26812) 2021-11-01 15:13:25 +01:00
Mahendra Paipuri
be0df5c47a ucx:add rocm variant (#26992)
Co-authored-by: mahendrapaipuri <mahendra.paipuri@inria.fr>
2021-11-01 15:05:56 +01:00
Ben Boeckel
80ba7040f8 python: detect Python from custom Xcode installations (#27023) 2021-11-01 07:55:15 -05:00
Hans Pabst
9094d6bb68 Updated LIBXSMM. (#27108) 2021-11-01 04:34:52 -06:00
Kenny Shen
3253faf01e cpp-argparse: new package (#27107) 2021-11-01 10:54:25 +01:00
Massimiliano Culpo
d73b1b9742 Fix caching of spack.repo.all_package_names() (#26991)
fixes #24522
2021-11-01 02:16:30 -06:00
Manuela Kuhn
b87678c2dd r-tidyr: add 1.1.4 (#27099) 2021-10-31 21:44:33 -05:00
Manuela Kuhn
8b8e7bd8e9 r-cpp11: add 0.4.0 (#27103) 2021-10-31 21:42:52 -05:00
Manuela Kuhn
200a1079d3 r-curl: add 4.3.2 (#27102) 2021-10-31 21:42:25 -05:00
Manuela Kuhn
3cd8381eb2 r-tidyselect: add 1.1.1 (#27101) 2021-10-31 21:41:16 -05:00
Manuela Kuhn
6b76b76d26 r-data-table: add 1.14.2 (#27100) 2021-10-31 21:40:36 -05:00
Manuela Kuhn
3406e8e632 r-dplyr: add 1.0.7 (#27098) 2021-10-31 21:40:07 -05:00
Manuela Kuhn
f363864f7f r-posterior: add new package (#27093) 2021-10-31 21:39:04 -05:00
Manuela Kuhn
543e5480a1 r-googledrive: add new package (#27095) 2021-10-31 21:37:26 -05:00
Manuela Kuhn
f8be56c941 r-withr: add 2.4.2 (#27094) 2021-10-31 21:35:41 -05:00
Manuela Kuhn
b6f6bbe371 r-nlme: add 3.1-153 (#27092) 2021-10-31 21:34:11 -05:00
Manuela Kuhn
ec8dc1830b r-bayesplot-1.8.1 (#27091) 2021-10-31 21:31:29 -05:00
Manuela Kuhn
86d2ab5240 r-mgcv: add 1.8-38 (#27090) 2021-10-31 21:30:34 -05:00
Manuela Kuhn
885e4d50e8 r-matrix: add 1.3-4 (#27089) 2021-10-31 21:29:54 -05:00
Manuela Kuhn
9397ca0a9f r-tibble: add 3.1.5 (#27087) 2021-10-31 21:25:19 -05:00
Manuela Kuhn
2b3207073d r-matrixstats: add 0.61.0 (#27086) 2021-10-31 21:23:10 -05:00
Manuela Kuhn
75a6d50fdc r-ids: add new package (#27104) 2021-10-31 21:21:54 -05:00
Bernhard Kaindl
6344d163b3 qt: @5.8:5.14.2 don't build with gcc@11, fix build of 5.6.3 (#27072)
5.14.2 fails with %gcc@11 with Error: 'numeric_limits' is not a class template
5.8.0 has multiple compile failures as well: Extend the conflict to those too.
- Fix also the confgigure of @5.6.3 (tested with %gcc@11)
2021-10-31 21:22:15 -04:00
Sinan
6c1f952bda package/qgis: fix runtime issue, improve package file, add new versions (#27084)
* package/qgis: fix runtime issue, improve package file, add new versions

* replace conflict with depends_on

* tidy up

Co-authored-by: sbulut <sbulut@3vgeomatics.com>
2021-10-31 18:24:44 -05:00
iarspider
f45ef21e37 New versions of py-gitpython: 3.1.13 - 3.1.24 (#27052)
* New versions of py-gitpython

* Update package.py
2021-10-30 11:19:51 -05:00
iarspider
30573f5e5c New versions: py-gitdb 4.0.7, 4.0.8, 4.0.9 (#27051)
* New versions: py-gitdb 4.0.7, 4.0.8, 4.0.9

* Update var/spack/repos/builtin/packages/py-gitdb/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-10-30 11:19:22 -05:00
iarspider
4262a66f5e New versions of py-google-auth and py-google-auth-oauthlib (#27056)
* New versions of py-google-auth and py-google-auth-oauthlib

* Update var/spack/repos/builtin/packages/py-google-auth/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-10-30 11:18:48 -05:00
iarspider
bdfb281a35 New version: py-deprecation 2.1.0 (#27001)
* New version: py-deprecation 2.1.0

* Update package.py
2021-10-30 07:25:31 -06:00
iarspider
0ef0a27ea0 New version: py-html5lib 1.1 (#27059)
* New verion: py-html5lib 1.1

* Update var/spack/repos/builtin/packages/py-html5lib/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-html5lib/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update package.py

* Update package.py

* Update package.py

* Update package.py

* Update var/spack/repos/builtin/packages/py-html5lib/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-html5lib/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-10-30 06:10:32 -06:00
Glenn Johnson
15e5508fcf r-vctrs: Fix checksums after setting url to CRAN (#27080)
This package had its url set to a github url and was then changed to a
CRAN url. The checksums need to change as a result.
2021-10-30 09:51:20 +02:00
Vasileios Karakasis
b1c4c1b6ca Add more ReFrame versions (#27082) 2021-10-30 09:17:30 +02:00
Jon Rood
c19a4e12c7 trilinos: Avoid Intel compiler segfaults in Trilinos with STK (#27073) 2021-10-29 22:03:46 -04:00
Kyle Gerheiser
c19514e540 w3emc package: add versions 2.9.2 and 2.7.3 (#27031) 2021-10-29 16:39:45 -07:00
Manuela Kuhn
657b9204ca New package: r-distributional (#27048) 2021-10-29 16:37:59 -07:00
Adam J. Stewart
1aaa7bd089 GDAL package: add version 3.3.3 (#27071) 2021-10-29 16:21:28 -07:00
iarspider
9448864c0e New versions: ipython 7.27.0 and 7.28.0 (#27066)
* New versions: ipython 7.27.0 and 7.28.0

* Changes from MR (1/2)

* Fix dep name (2/2)
2021-10-29 17:13:44 -06:00
Scott Wittenburg
f2a36bdf14 pipelines: llvm kills the xlarge, use huge (#27079) 2021-10-29 22:01:35 +00:00
Peter Scheibel
7eddf3ae9b For Spack commands that fail but don't throw exceptions, we were discarding the return code (#27077) 2021-10-29 14:14:41 -07:00
iarspider
b9e63c9f42 New version: py-importlib-resources 5.3.0 (#27064)
* New version: py-importlib-resources 5.3.0

* Update var/spack/repos/builtin/packages/py-importlib-resources/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-10-29 15:07:59 -06:00
Jen Herting
c38d3044fa New package: py-pypulse (#27026)
* python package py-pypulse created - per Andy

* URL fixed

* [py-pypulse]

- removed duplicate dependency
- updated copyright

* [py-pypulse] added version 0.1.1

* [py-pypulse] depends on setuptools

* [py-pypulse] url -> pypi

* [py-pypulse] simplified python dependency

Co-authored-by: Alex C Leute <aclrc@sporcsubmit.rc.rit.edu>
2021-10-29 14:58:58 -06:00
iarspider
ec23ce4176 New version: py-immutables 0.16 (#27060)
* New version: py-immutables 0.16

* Changes from review
2021-10-29 14:53:12 -06:00
Bernhard Kaindl
9a1626e54a py-slurm-pipeline: Add 4.0.4, Fix base.py: import six for @:3 (#26968)
* py-slurm-pipeline: Add 4.0.4, Fix base.py: import six for @:3

Before 4.0.0, slurm_pipeline/base.py has: `from six import string_types`

* Added depends_on('py-pytest@6.2.2:', type='build') as requested by Adam

* remove comment requested to be removed
2021-10-29 14:52:57 -06:00
Jon Rood
91408ef6ad trilinos: add MPICH and HPE MPT MPI environment variables (#27070) 2021-10-29 14:05:10 -06:00
genric
749640faf9 py-ipyparallel: add 7.1.0 (#26984) 2021-10-29 14:10:36 -05:00
Simon Pintarelli
494ba67704 sirius: add mpi datatypes patch for recent cray mpich (#27065) 2021-10-29 12:31:56 -06:00
Baptiste Jonglez
b8bc030a3c py-torch: Add a breakpad variant, disable it for ppc64 and ppc64le (#26990) 2021-10-29 13:00:48 -05:00
Massimiliano Culpo
3eb52b48b8 config add: infer type based on JSON schema validation errors (#27035)
- [x] Allow dding enumerated types and types whose default value is forbidden by the schema
- [x] Add a test for using enumerated types in the tests for `spack config add`
- [x] Make `config add` tests use the `mutable_config` fixture so they do not
      affect other tests

Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2021-10-29 18:44:49 +02:00
Manuela Kuhn
20b7485cd4 r-cli: add 3.0.1 (#27047) 2021-10-29 10:57:14 -05:00
Manuela Kuhn
d36b045e2d r-afex: add 1.0-1 (#27032) 2021-10-29 10:55:46 -05:00
Thomas Madlener
874f06e29c curl: fix mbedtls versions and certs config (#26877)
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2021-10-29 08:55:48 -06:00
Jon Rood
962d06441e m4: set times of m4.texi to fix build on Summit GPFS (#26994)
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2021-10-29 16:05:41 +02:00
Bernhard Kaindl
fd10e54409 libssh2: skip the testsuite when docker is not installed (#26962)
The build-time testsuite which would be run when building
with tests needs docker. Check that it exists before
attempting to execute the tests.

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-10-29 07:04:40 -06:00
Harmen Stoppels
49034abd76 Fix exit codes posix shell wrapper (#27012)
* Correct exit code in sh wrapper

* Fix tests

* SC2069
2021-10-29 08:10:22 +00:00
Harmen Stoppels
f610b506cd elfio: add minimum version requirements to cmake (#27033) 2021-10-29 09:28:19 +02:00
Axel Huebl
5a7496eb82 WarpX & HiPACE++: Constrain FFTW for No-MPI (#27043)
Contrain FFTW for no-MPI to simplify builds and logic to handle.
2021-10-29 09:19:23 +02:00
Valentin Churavy
7a6a232730 add Julia 1.7.0-rc2 (#27016) 2021-10-29 08:24:38 +02:00
Manuela Kuhn
4031ea5e03 r-gargle: add new (#27046) 2021-10-29 05:19:50 +00:00
Manuela Kuhn
852e14a655 r-openssl: add 1.4.5 (#27045) 2021-10-29 04:17:35 +00:00
Manuela Kuhn
5b2d9ae0b0 r-car: add 3.0-11 (#27044) 2021-10-29 04:14:06 +00:00
Manuela Kuhn
dc3b818192 r-future: add 1.22.1 (#27041) 2021-10-29 03:58:00 +00:00
Manuela Kuhn
5c1874c387 r-pillar: add 1.6.4 (#27040) 2021-10-29 03:47:42 +00:00
Manuela Kuhn
fcf6a46aeb r-digest: add 0.6.28 (#27039) 2021-10-29 03:00:10 +00:00
Manuela Kuhn
180bb5003c r-farver: add 2.1.0 (#27038) 2021-10-29 02:46:55 +00:00
Manuela Kuhn
2e880c5513 r-ggplot2: add 3.3.5 (#27037) 2021-10-29 02:36:49 +00:00
Manuela Kuhn
71412f547d r-generics: add 0.1.1 (#27034) 2021-10-29 01:44:13 +00:00
Harmen Stoppels
574395af93 Fix exit codes in fish (#27028) 2021-10-29 01:10:31 +00:00
Manuela Kuhn
c04b2fa26a r-rappdirs: add 0.3.3 (#26989) 2021-10-28 17:55:38 -05:00
Manuela Kuhn
19c77f11b6 r-emmeans: add 1.7.0 (#26987) 2021-10-28 17:54:24 -05:00
Manuela Kuhn
1f4ada6b22 r-fansi: add 0.5.0 (#26986) 2021-10-28 17:51:45 -05:00
Manuela Kuhn
4ff87ea04f r-lifecycle: add 1.0.1 (#26975) 2021-10-28 17:42:56 -05:00
Manuela Kuhn
d5520a264b r-parallelly: add 1.28.1 (#26974) 2021-10-28 17:40:58 -05:00
Manuela Kuhn
999044033b r-vctrs: add 0.3.8 (#26966) 2021-10-28 17:39:09 -05:00
Todd Gamblin
233dabbd4f bugfix: config edit should work with a malformed spack.yaml
If you don't format `spack.yaml` correctly, `spack config edit` still fails and
you have to edit your `spack.yaml` manually.

- [x] Add some code to `_main()` to defer `ConfigFormatError` when loading the
  environment, until we know what command is being run.

- [x] Make `spack config edit` use `SPACK_ENV` instead of the config scope
  object to find `spack.yaml`, so it can work even if the environment is bad.

Co-authored-by: scheibelp <scheibel1@llnl.gov>
2021-10-28 15:37:44 -07:00
Todd Gamblin
374e3465c5 bugfix: spack config get <section> in environments
`spack config get <section>` was erroneously returning just the `spack.yaml`
for the environment.

It should return the combined configuration for that section (including
anything from `spack.yaml`), even in an environment.

- [x] reorder conditions in `cmd/config.py` to fix
2021-10-28 15:37:44 -07:00
Todd Gamblin
2bd513d659 config: ensure that options like --debug are set first
`spack --debug config edit` was not working properly -- it would not do show a
stack trace for configuration errors.

- [x] Rework `_main()` and add some notes for maintainers on where things need
      to go for configuration to work properly.
- [x] Move config setup to *after* command-line parsing is done.

Co-authored-by: scheibelp <scheibel1@llnl.gov>
2021-10-28 15:37:44 -07:00
Todd Gamblin
56ad721eb5 errors: Rework error handling in main()
`main()` has grown, and in some cases code that can generate errors has gotten
outside the top-level try/catch in there. This means that simple errors like
config issues give you large stack traces, which shouldn't happen without
`--debug`.

- [x] Split `main()` into `main()` for the top-level error handling and
      `_main()` with all logic.
2021-10-28 15:37:44 -07:00
Manuela Kuhn
732be7dec6 r-ellipsis: add 0.3.2 (#26965) 2021-10-28 17:36:10 -05:00
Manuela Kuhn
895bd75762 r-rlang: add 0.4.12 (#26963) 2021-10-28 17:34:06 -05:00
Manuela Kuhn
dd1eb7ea18 r-mvtnorm: add 1.1-3 (#26957) 2021-10-28 17:31:43 -05:00
Manuela Kuhn
494dc0bd13 r-lme4: add 1.1-27.1 (#26955)
* r-lme4: add 1.1-27.1

* Use cran instead of explicit url
2021-10-28 17:30:21 -05:00
Manuela Kuhn
4b2564a2d6 llvm: fix gcc11 build for @11 (#27013) 2021-10-28 16:07:56 -06:00
iarspider
eb2d44a57b New versions of py-flake8 and py-pyflakes (#27008)
* New versions of py-flake8 and py-pyflakes

* Changes from review
2021-10-28 21:56:28 +00:00
Todd Gamblin
a1216138f6 config: fix SPACK_DISABLE_LOCAL_CONFIG, remove $user_config_path (#27022)
There were some loose ends left in ##26735 that cause errors when
using `SPACK_DISABLE_LOCAL_CONFIG`.

- [x] Fix hard-coded `~/.spack` references in `install_test.py` and `monitor.py`

Also, if `SPACK_DISABLE_LOCAL_CONFIG` is used, there is the issue that
`$user_config_path`, when used in configuration files, makes no sense,
because there is no user config scope.

Since we already have `$user_cache_path` in configuration files, and since there
really shouldn't be *any* data stored in a configuration scope (which is what
you'd configure in `config.yaml`/`bootstrap.yaml`/etc., this just removes
`$user_config_path`.

There will *always* be a `$user_cache_path`, as Spack needs to write files, but
we shouldn't rely on the existence of a particular configuration scope in the
Spack code, as scopes are configurable, both in number and location.

- [x] Remove `$user_config_path` substitution.
- [x] Fix reference to `$user_config_path` in `etc/spack/deaults/bootstrap.yaml`
      to refer to `$user_cache_path`, which is where it was intended to be.
2021-10-28 21:33:44 +00:00
Daryl W. Grunau
d0e177e711 depend on libevent when +pmix (#27020)
Co-authored-by: Daryl W. Grunau <dwg@lanl.gov>
2021-10-28 23:19:19 +02:00
Phil Carns
7fd1d2b03f mochi-margo: add version 0.9.6 (#26951) 2021-10-28 23:11:30 +02:00
Valentin Churavy
7f8b0d4820 add MPItrampoline 2.0.0 (#27019) 2021-10-28 22:20:38 +02:00
iarspider
612639534a New version: py-distro 1.6.0 (#27003) 2021-10-28 14:38:36 -05:00
iarspider
f512bb1dc1 New versions: docutils 0.17, 0.17.1, 0.18 (#27005) 2021-10-28 13:53:02 -05:00
Harmen Stoppels
6d030ba137 Deactivate previous env before activating new one (#25409)
* Deactivate previous env before activating new one

Currently on develop you can run `spack env activate` multiple times to switch
between environments, but they leave traces, even though Spack only supports
one active environment at a time.

Currently:

```console
$ spack env create a
$ spack env create b
$ spack env activate -p a
[a] $ spack env activate -p b
[b] [a] $ spack env activate -p b
[a] [b] [a] $ spack env activate -p a
[a] [b] [c] $ echo $MANPATH | tr ":" "\n"
/path/to/environments/a/.spack-env/view/share/man
/path/to/environments/a/.spack-env/view/man
/path/to/environments/b/.spack-env/view/share/man
/path/to/environments/b/.spack-env/view/man
```

This PR fixes that:

```console
$ spack env activate -p a
[a] $ spack env activate -p b
[b] $ spack env activate -p a
[a] $ echo $MANPATH | tr ":" "\n"
/path/to/environments/a/.spack-env/view/share/man
/path/to/environments/a/.spack-env/view/man
```
2021-10-28 11:39:25 -07:00
Tom Scogland
87e456d59c spack setup-env.sh: make zsh loading async compatible, and ~10x faster (in some cases) (#26120)
Currently spack is a bit of a bad actor as a zsh plugin, and it was my
fault.  The autoload and compinit should really be handled by the user,
as was made abundantly clear when I found spack was doing completion
initialization for *all* of my plugins due to a deferred setup that was
getting messed up by it.

Making this conditional took spack load time from 1.5 seconds (with
module loading disabled) to 0.029 seconds. I can actually afford to load
spack by default with this change in.

Hopefully someday we'll do proper zsh completion support, but for now
this helps a lot.

* use zsh hist expansion in place of dirname
* only run (bash)compinit if compdef/complete missing
* add zsh compiled files to .gitignore
* move changes to .in file, because spack
2021-10-28 11:32:59 -07:00
iarspider
5faa457a35 New version: py-fasteners 0.16.3 (#27006) 2021-10-28 13:15:50 -05:00
Harmen Stoppels
8ca3a0fdf8 Remove failing macOS test (#27009) 2021-10-28 09:30:51 -07:00
Brent Huisman
63fcb0331b Add Pybind11 v2.8 (#26867)
* Add Pybind11 v2.8

* Add Python dependency

* Update package.py

* Added Pybind v2.8.1
2021-10-28 16:14:49 +00:00
Robert Blackwell
8fd94e3114 YamlFilesystemView: improve file removal performance via batching (#24355)
* Drastically improve YamlFilesystemView file removal via batching

The `remove_file` routine has to check if the file is owned by multiple packages, so it doesn't
remove necessary files. This is done by the `get_all_specs` routine, which walks the entire
package tree. With large numbers of packages on shared file systems, this can take seconds
per file tree traversal, which adds up extremely quickly. For example, a single deactivate
of a largish python package in our software stack on GPFS took approximately 40 minutes.

This patch simply replaces `remove_file` with a batch `remove_files` routine. This routine
removes a list of files rather than a single file, requiring only one traversal per batch. In
practice this means a package can be removed in seconds time, rather than potentially hours,
essentially a ~100x speedup (ignoring initial deactivation logic, which takes about 3 minutes
in our test setup).
2021-10-28 07:39:16 -07:00
Harmen Stoppels
c13f915735 cmake: add v3.21.4, v3.20.6 (#27004) 2021-10-28 13:59:46 +00:00
Cameron Stanavige
afbc67fdd8 dtcmp & lwgrp: add shared variant (#26999) 2021-10-28 15:00:54 +02:00
Michael Kuhn
e9f3ef785d Fix sbang hook for non-writable files (#27007)
* Fix sbang hook for non-writable files

PR #26793 seems to have broken the sbang hook for files with missing
write permissions. Installing perl now breaks with the following error:
```
==> [2021-10-28-12:09:26.832759] Error: PermissionError: [Errno 13] Permission denied: '$SPACK/opt/spack/linux-fedora34-zen2/gcc-11.2.1/perl-5.34.0-afuweplnhphcojcowsc2mb5ngncmczk4/bin/cpanm'
```

Temporarily add write permissions to the original file so it can be
overwritten with the patched one.

And test that file permissions are preserved in sbang even for non-writable files

Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2021-10-28 14:49:23 +02:00
Erik Schnetter
7c886bcac1 nsimd: add v3.0.1, determine SIMD variant automatically by default (#26850) 2021-10-28 14:38:48 +02:00
Paul Ferrell
4ee37c37de buildcaches: fix directory link relocation (#26948)
When relocating a binary distribution, Spack only checks files to see
if they are a link that needs to be relocated. Directories can be
such links as well, however, and need to undergo the same checks
and potential relocation.
2021-10-28 14:34:31 +02:00
Seth R. Johnson
890095e876 llvm: use cmake helper functions (#26988)
* llvm: use cmake helper functipack stns

* llvm: review feedback
2021-10-27 20:26:22 +00:00
iarspider
7416df692a New versions: py-cffi 1.15.0, 1.14.6 (#26979)
* New versions: py-cffi 1.15.0, 1.14.6

* Changes from review
2021-10-27 15:01:15 -05:00
iarspider
dd0770fd64 New versions of py-cachetools (#26976)
* New versions of py-cachetools

* Changes from review
2021-10-27 15:00:48 -05:00
iarspider
704c94429b New version: py-bottle@0.12.19 (#26973)
* New version: py-bottle@0.12.19

* Changes from review
2021-10-27 15:00:19 -05:00
Mark W. Krentel
21d909784c hpcviewer: add support for macosx, add version 2021.10 (#26823) 2021-10-27 19:51:14 +00:00
Kyle Gerheiser
e35eacf87b Add w3emc version 2.9.1 (#26880) 2021-10-27 12:05:06 -06:00
iarspider
dc40405fd6 New version: py-contextlib2 21.6.0 (#26985) 2021-10-27 11:08:25 -06:00
Massimiliano Culpo
3d5444fdd8 Remove documentation tests from GitHub Actions (#26981)
We moved documentation tests to readthedocs since a while,
so remove the one on GitHub.
2021-10-27 19:02:52 +02:00
iarspider
80d4a83636 New versions: py-boken@2.3.3, 2.4.0, 2.4.1 (#26972) 2021-10-27 11:59:42 -05:00
iarspider
39f46b1c3b New version: py-certifi 2021.10.8 (#26978) 2021-10-27 11:54:37 -05:00
H. Joe Lee
1fcc9c6552 hdf5-vol-log: add new package (#26956) 2021-10-27 16:48:44 +00:00
iarspider
1842785eae New version: py-commonmark 0.9.1 (#26983) 2021-10-27 11:47:28 -05:00
Mosè Giordano
acb8ab338d fftw: add v3.3.10 (#26982) 2021-10-27 15:29:53 +00:00
Bernhard Kaindl
d1803af957 fontconfig: add v2.13.94 and fix test with dash (#26961)
Fix install --test=root with /bin/sh -> dash: A test uses
SIGINT SIGTERM SIGABRT EXIT for trap -> use signal numbers
2021-10-27 16:20:57 +02:00
Bernhard Kaindl
f4431851ab perl-extutils-installpaths: depend on perl-extutils-config (#26969) 2021-10-27 16:02:14 +02:00
Pieter Ghysels
1f728ab4ce strumpack: add v6.1.0, remove unused variants (#26971) 2021-10-27 15:58:54 +02:00
Valentin Volkl
9fa20b8a39 recola: fix compilation (#26634)
* recola: fix compilation

* Update var/spack/repos/builtin/packages/recola-sm/package.py

Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>

* flake8

* fixes

* fix typo

* fix typo

Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>
2021-10-27 07:19:35 -06:00
Todd Gamblin
4f124bc9e7 tests: speed up spack list tests (#26958)
`spack list` tests are not using mock packages for some reason, and many
are marked as potentially slow. This isn't really necessary; we don't need
6,000 packages to test the command.

- [x] update tests to use `mock_packages` fixture
- [x] remove `maybeslow` annotations
2021-10-27 05:10:39 -06:00
Harmen Stoppels
e04b172eb0 Allow non-UTF-8 encoding in sbang hook (#26793)
Currently Spack reads full files containing shebangs to memory as
strings, meaning Spack would have to guess their encoding. Currently
Spack has a fixed guess of UTF-8.

This is unnecessary, since e.g. the Linux kernel does not assume an
encoding on paths at all, it's just bytes and some delimiters on the
byte level.

This commit does the following:

1. Shebangs are treated as bytes, so that e.g. latin1 encoded files do
not throw UnicodeEncoding errors, and adds a test for this.
2. No more bytes than necessary are read to memory, we only have to read
until the first newline, and from there on we an copy the file byte by
bytes instead of decoding and re-encoding text.
3. We cap the number of bytes read to 4096, if no newline is found
before that, we don't attempt to patch it.
4. Add support for luajit too.

This should make Spack both more efficient and usable for non-UTF8
files.
2021-10-27 02:59:10 -07:00
Harmen Stoppels
2fd87046cd Fix assumption v.concrete => isinstance(v, Version) (#26537)
* Add test
* Only extend with Git version when using Version
* xfail v.concrete test
2021-10-27 02:58:04 -07:00
Harmen Stoppels
ae6e83b1d5 config: overrides for caches and system and user scopes (#26735)
Spack's `system` and `user` scopes provide ways for administrators and
users to set global defaults for all Spack instances, but for use cases
where one wants a clean Spack installation, these scopes can be undesirable.
For example, users may want to opt out of global system configuration, or
they may want to ignore their own home directory settings when running in
a continuous integration environment.

Spack also, by default, keeps various caches and user data in `~/.spack`,
but users may want to override these locations.

Spack provides three environment variables that allow you to override or
opt out of configuration locations:

 * `SPACK_USER_CONFIG_PATH`: Override the path to use for the
   `user` (`~/.spack`) scope.

 * `SPACK_SYSTEM_CONFIG_PATH`: Override the path to use for the
   `system` (`/etc/spack`) scope.

 * `SPACK_DISABLE_LOCAL_CONFIG`: set this environment variable to completely
   disable *both* the system and user configuration directories. Spack will
   only consider its own defaults and `site` configuration locations.

And one that allows you to move the default cache location:

 * `SPACK_USER_CACHE_PATH`: Override the default path to use for user data
   (misc_cache, tests, reports, etc.)

With these settings, if you want to isolate Spack in a CI environment, you can do this:

   export SPACK_DISABLE_LOCAL_CONFIG=true
   export SPACK_USER_CACHE_PATH=/tmp/spack

This is a stop-gap approach until we have figured out how to deal with
the system and user config scopes more generally, as there are plans to
potentially / eventually get rid of them.

**User config**

Spack is a bit of a pain when you have:

- a shared $HOME folder across different systems.
- multiple Spack versions on the same system.

**System config**

- On shared systems with a versioned programming environment / toolkit,
  system administrators want to provide config for each version (e.g.
  21.09, 21.10) of the programming environment, and the user Spack
  instance should be able to pick this up without a steep learning
  curve.
- On shared systems the user should be able to opt out of the
  hard-coded config scope in /etc/spack, since it may be incompatible
  with their particular instance. Currently Spack can only opt out of all
  config scopes through overrides with `"config:":`, `"packages:":`, but that
  also drops the defaults config, which would have to be repeated, which
  is undesirable, especially the lengthy packages.yaml.

An example use case is: having config in this folder:

```
/path/to/programming/environment/{version}/{compilers,packages}.yaml
```

and have `module load spack-system-config` set the variable

```
SPACK_SYSTEM_CONFIG_PATH=/path/to/programming/environment/{version}
```

where the user no longer has to worry about what `{version}` they are
on.

**Continuous integration**

Finally, there is the use case of continuous integration, which may
clone an arbitrary Spack version, which optimally should not pick up
system or user config from the previous run (like may happen in
classical bare metal non-containerized filesystem side effect ridden
jenkins pipelines). In fact this is very similar to how spack itself
tries to avoid picking up system dependencies during builds...

**But environments solve this?**

- You could do `include`s in environment files to get similar behavior
  to the spack_system_config_path example, but environments require you
  to:
  1) require paths to individual config files, not directories.
  2) fail if the listed config file does not exist
- They allow you to override config scopes, but this is generally too
  rigurous, as it requires you to repeat the default config, in
  particular packages.yaml, and just defies the point of layered config.

Co-authored-by: Tom Scogland <tscogland@llnl.gov>
Co-authored-by: Tim Fuller <tjfulle@sandia.gov>
Co-authored-by: Steve Leak <sleak@lbl.gov>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2021-10-26 18:08:25 -07:00
Ye Luo
7dc94b6683 Build OpenMP in LLVM via LLVM_ENABLE_RUNTIMES. (#26870) 2021-10-26 17:43:28 -06:00
Hao Lyu
02bea6d2d2 fix bug when there is version id in the path of compiler (#26916) 2021-10-26 14:12:58 -07:00
Greg Becker
9a637bbd09 modules: allow user to remove arch dir (#24156)
* allow no arch-dir modules

* add tests for modules with no arch

* document arch-specific module roots
2021-10-26 13:26:09 -07:00
Mark W. Krentel
444e156685 hpctoolkit: add version 2021.10.15 (#26881) 2021-10-26 13:15:09 -07:00
Richarda Butler
bc616a60b7 Py-Libensemble: Add E4S testsuite stand alone test (#26270) 2021-10-26 13:11:53 -07:00
Miroslav Stoyanov
ad03981468 fix the spack test dir (#26816) 2021-10-26 13:07:04 -07:00
Sreenivasa Murthy Kolam
5ee2ab314c ROCm packages: add RelWithDebInfo build_type (#26888)
Also set default build_type to Release for many ROCm packages.
2021-10-26 12:18:38 -07:00
Greg Becker
a8a08f66ad modules: configurable module defaults (#24367)
Any spec satisfying a default will be symlinked to `default`

If multiple specs have modulefiles in the same directory and satisfy
configured module defaults, then whichever was written last will be
default.
2021-10-26 19:34:06 +02:00
Kyle Gerheiser
dee75a4945 upp: Add version 10.0.10 (#26946) 2021-10-26 19:26:34 +02:00
Seth R. Johnson
aacdd5614e htop: add new URL and versions (#26928) 2021-10-26 19:14:06 +02:00
Ben Morgan
a2e5a28892 virtest: prevent out-of-order build/test (#26944)
Use of `-R` flag to CTest command causes "empty-14" test to run,
by matching "empty", before the empty-14 target is built.

Patch CTest command in buildscript to match name exactly.
2021-10-26 18:55:54 +02:00
Asher Mancinelli
94a9733822 hiop: update constraints and add new version (#26905)
* Update hiop package dependencies

* Use single quotes to shrink diff

* add hiop 0.5.1

* apply flake8

* Apply formatting suggestions
2021-10-26 11:43:03 -04:00
iarspider
fb1f3b1a1c Add checksum for py-argon2-cffi 21.1.0 and update python dependency (#26894)
* Add checksum for py-argon2-cffi 21.1.0 and update python dependency

* Update package.py
2021-10-26 09:32:11 -06:00
iarspider
d673e634d0 New versions: py-bleach 4.0.0 and 4.1.0 (#26947) 2021-10-26 09:23:10 -06:00
iarspider
1f1f121e8f New version: py-beniget 0.4.1 (#26945) 2021-10-26 09:02:03 -06:00
Wouter Deconinck
ba2a03e1da geant4: depends_on vecgeom@1.1.8:1.1 range (#26917)
* [geant4] depends_on vecgeom@1.1.8:1.1 range

While previous versions were unclear, the [geant4.10.7 release notes](https://geant4-data.web.cern.ch/ReleaseNotes/ReleaseNotes4.10.7.html) indicate that vecgeom@1.1.8 is a minimum required version, not an exact required version ("Set VecGeom-1.1.8 as minimum required version for optional build with VecGeom."). This will allow some more freedom on the concretizer solutions while allowing geant4 to take advantage of bugfixes and improvements in vecgeom.

* [vecgeom] new version 1.1.17
2021-10-26 10:31:37 -04:00
Seth R. Johnson
dad68e41e0 freetype: explicitly specify dependencies (#26942)
Freetype picked up 'brotli' from homebrew, causing issues downstream.
2021-10-26 04:07:48 -06:00
eugeneswalker
1ae38037ef tau: add version 2.30.2 (#26941) 2021-10-26 05:36:29 -04:00
Chuck Atkins
80d8c93452 unifyfs: Remove the hdf5 variant (examples only) (#26932)
UnifyFS doesn't actually use HDF5 for anything.  Enabling it only enables
a few examples to be built so it's not actually a dependency of the package.
2021-10-26 09:42:52 +02:00
Seth R. Johnson
bdcbc4cefe qt package: versions @:5.13 don't build with gcc@11: (#26922) 2021-10-25 18:20:54 -07:00
Ronak Buch
1d53810d77 charmpp: add version 7.0.0 (#26940) 2021-10-25 18:16:37 -07:00
Adam J. Stewart
4a8c53472d py-kornia: add version 0.6.1 (#26939) 2021-10-25 18:15:57 -07:00
Adam J. Stewart
b05df2cdc7 py-shapely: add version 1.8.0 (#26937) 2021-10-25 18:15:22 -07:00
Adam J. Stewart
92cef8d7ad py-scikit-learn: add version 1.0.1 (#26934) 2021-10-25 18:14:17 -07:00
Adam J. Stewart
912c6ff6e8 PyTorch/torchvision: add version 1.10.0/0.11.1 (#26889)
* For py-torch: Also update dependencies: many version constraints
  with an upper bound of @1.9 are now open (e.g. `@1.8.0:1.9` is
  converted to `@1.8.0:`).
* For py-torchvision: Also add 0.11.0 and update ^pil constraint
  to avoid building with 8.3.0
2021-10-25 15:26:12 -07:00
iarspider
cdcdd71b41 Add new versions of py-autopep8 and py-pycodestyle (#26924)
* Add new versions of py-autopep8 (1.5.7, 1.6.0) and py-pycodestyle (2.7.0, 2.8.0)

* Update package.py

* Restore old versions
2021-10-25 22:08:52 +00:00
Daniel Arndt
e221617386 deal.II package: Update CMake variable for >=9.3.0 (#26909) 2021-10-25 15:00:40 -07:00
Massimiliano Culpo
6063600a7b containerize: pin the Spack version used in a container (#21910)
This PR permits to specify the `url` and `ref` of the Spack instance used in a container recipe simply by expanding the YAML schema as outlined in #20442:
```yaml
container:
  images:
    os: amazonlinux:2
    spack:
      ref: develop
      resolve_sha: true
```
The `resolve_sha` option, if true, verifies the `ref` by cloning the Spack repository in a temporary directory and transforming any tag or branch name to a commit sha. When this new ability is leveraged an additional "bootstrap" stage is added, which builds an image with Spack setup and ready to install software. The Spack repository to be used can be customized with the `url` keyword under `spack`.

Modifications:
- [x] Permit to pin the version of Spack, either by branch or tag or sha
- [x] Added a few new OSes (centos:8, amazonlinux:2, ubuntu:20.04, alpine:3, cuda:11.2.1)
- [x] Permit to print the bootstrap image as a standalone
- [x] Add documentation on the new part of the schema
- [x] Add unit tests for different use cases
2021-10-25 13:09:27 -07:00
iarspider
ff65e6352f py-avro: new version 1.10.2 (#26927)
* Add checksum for py-avro@1.10.2

* Update package.py
2021-10-25 11:45:33 -05:00
Olli Lupton
06c983d38f cuda: add 11.4.1, 11.4.2, 11.5.0. (#26892)
* cuda: add 11.4.1, 11.4.2, 11.5.0.

Note that the curses dependency from cuda-gdb was dropped in 11.4.0.

* Update clang/gcc constraints.

* Address review, assume clang 12 is OK from 11.4.1 onwards.

* superlu-dist@7.1.0 conflicts with cuda@11.5.0.

* Update var/spack/repos/builtin/packages/superlu-dist/package.py

Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>

Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2021-10-25 09:05:21 -07:00
iarspider
b0752bf1b3 Add checksum for py-atomicwrites@1.4.0 (#26923) 2021-10-25 10:54:04 -05:00
Kendra Long!
c9847766e4 draco: new version 7_12_0 (#26907)
* Add draco-7_12_0 to package file

* Update hash to zip version
2021-10-25 11:35:38 -04:00
Kelly (KT) Thompson
86a9c703db eospac: new default version 6.5.0 (#26723)
* [pkg][new version] Provide eospac@6.5.0 and mark it as default.

* Merge in changes found in #21629

* Mark all alpha/beta versions as deprecated.

- Addresses @sethrj's recommendation
- Also add a note indicated why these versions are marked this way.
2021-10-25 11:10:46 -04:00
Harmen Stoppels
276e637522 Reduce verbosity of module files warning
1. Currently it prints not just the spec name, but the dependencies +
their variants + their compilers + their architectures + ...
2. It's clear from the context what spec the message applies to, so,
let's not print the spec at all.
2021-10-25 17:07:56 +02:00
Olivier Cessenat
b51e0b363e silo: new release 4.11 (#26876) 2021-10-25 08:13:54 -06:00
Manuela Kuhn
e9740a9978 py-nipype: add 1.7.0 (#26883) 2021-10-25 06:55:50 -06:00
Harmen Stoppels
cc8d8cc9cb Return early in do_fetch when there is no code or a package is external (#26926)
Co-authored-by: Ryan Krattiger <ryan.krattiger@kitware.com>
2021-10-25 13:51:23 +02:00
Todd Gamblin
de8e795563 virtuals: simplify virtual handling
These three rules in `concretize.lp` are overly complex:

```prolog
:- not provider(Package, Virtual),
   provides_virtual(Package, Virtual),
   virtual_node(Virtual).
```

```prolog
  :- provides_virtual(Package, V1), provides_virtual(Package, V2), V1 != V2,
     provider(Package, V1), not provider(Package, V2),
     virtual_node(V1), virtual_node(V2).
```

```prolog
provider(Package, Virtual) :- root(Package), provides_virtual(Package, Virtual).
```

and they can be simplified to just:

```prolog
provider(Package, Virtual) :- node(Package), provides_virtual(Package, Virtual).
```

- [x] simplify virtual rules to just one implication
- [x] rename `provides_virtual` to `virtual_condition_holds`
2021-10-25 09:11:04 +02:00
Massimiliano Culpo
6d69d23aa5 Add a unit test to prevent regression 2021-10-25 09:11:04 +02:00
Massimiliano Culpo
dd4d7bae1d ASP-based solver: a package eligible to provide a virtual must provide it
fixes #26866

This semantics fits with the way Spack currently treats providers of
virtual dependencies. It needs to be revisited when #15569 is reworked
with a new syntax.
2021-10-25 09:11:04 +02:00
Miguel Dias Costa
1e90160d68 berkeleygw: force openmp propagation on some providers of blas / ffw-api (#26918) 2021-10-25 07:42:05 +02:00
Michael Kuhn
dfcd5d4c81 hyperfine: new package (#26901) 2021-10-24 20:47:56 -04:00
Satish Balay
e3b7eb418f Add new math solver versions (#26903)
* tasmanian: add @7.7
* butterflypack: add @2.0.0
* pflotran: add @3.0.2
* alquimia: add @1.0.9
* superlu-dist: add @7.1.1
2021-10-24 20:45:44 -04:00
Michael Kuhn
fb5d4d9397 meson: add 0.60.0 (#26921) 2021-10-24 20:35:11 -04:00
Scott Wittenburg
2003fa1b35 Mark flaky test_ci_rebuild as xfail (#26911) 2021-10-24 22:46:26 +02:00
Michael Kuhn
b481b5114a Fix pkg-config dependencies (#26912)
pkg-config and pkgconf are implementations of the pkgconfig provider.
2021-10-24 20:39:50 +02:00
Michael Kuhn
d7148a74a0 glib: add 2.70.0 (#26915) 2021-10-24 20:39:30 +02:00
Seth R. Johnson
c255e91bba gcc: support alternate mechanism for providing GCC rpaths (#26590)
* gcc: support runtime ability to not install spack rpaths

Fixes #26582 .

* gcc: Fix malformed specs file and add docs

The updated docs point out that the spack-modified GCC does *not*
follow the usual behavior of LD_RUN_PATH!

* gcc: fix bad rpath on macOS

This bug has been around since the beginning of the GCC package file:
the rpath command it generates for macOS writes a single (invalid)
rpath entry.

* gcc: only write rpaths for directories with shared libraries

The original lib64+lib was just a hack for "in case either has one" but
it's easy to tell whether either has libraries that can be directly
referenced.
2021-10-24 13:46:52 -04:00
Michael Kuhn
5a38165674 python: add 3.9.7, 3.8.12, 3.7.12 and 3.6.15 (#26914) 2021-10-24 11:43:39 -06:00
Morten Kristensen
9e11e62bca py-vermin: add latest version 1.3.1 (#26920)
* py-vermin: add latest version 1.3.1

* Exclude line from Vermin since version is already being checked for

Vermin 1.3.1 finds that `encoding` kwarg of builtin `open()` requires Python 3+.
2021-10-24 16:49:05 +00:00
Mark Grondona
7fee7a7ce1 flux-core, -sched: update to latest versions, fix czmq build error (#26840)
* flux-core: fix compile error with czmq_containers
* Fix build with clang and gcc-11
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2021-10-23 17:37:44 +02:00
Jen Herting
7380161ea6 [py-emcee] added versions 3.0.2 and 3.1.1 (#26910)
* [py-emcee] added version 3.0.2

* [py-emcee] added version 3.1.1
2021-10-22 17:52:45 -06:00
eugeneswalker
0baec34dd7 E4S amd64 CI: add parsec (#26906) 2021-10-22 15:02:47 -06:00
Wouter Deconinck
d04b6e0fb5 acts: fix misspelled variant in depends_on (#26904)
Correct variant is plural `unit_tests`.
2021-10-22 12:19:51 -06:00
Harmen Stoppels
336c60c618 Document backport in py (#26897) 2021-10-22 19:14:35 +02:00
iarspider
0beb2e1ab2 Update py-aiohttp to 3.7.4 and py-chartdet to 4.0 (#26893)
* Update py-aiohttp to 3.7.4 and py-chartdet to 4.0

* Changes from review

* Update package.py

* Update var/spack/repos/builtin/packages/py-chardet/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-10-22 16:36:56 +00:00
iarspider
aa2bcbdc12 Use pypi for astroid; add versions 2.7.3 and 2.8.3; update dependencies (#26900)
* Use pypi for astroid; add versions 2.7.3 and 2.8.3; update dependencies

* py-six is not required for recent versions
2021-10-22 16:21:22 +00:00
Wouter Deconinck
d5880f3e7e acts: add v14.0.0, v14.1.0 added "python" and "analysis" variants (#26657) 2021-10-22 17:43:35 +02:00
Robert Cimrman
2d41d6fc9e py-sfepy: fix version 2021.3 tar.gz hash (#26890) 2021-10-22 10:23:58 -05:00
iarspider
8349a8ac60 Add py-asn1crypto@1.4.0 (#26895) 2021-10-22 10:22:30 -05:00
Manuela Kuhn
edc7341625 py-jupyterlab: add 3.1.18 and 3.2.1 (#26896) 2021-10-22 10:21:00 -05:00
Harmen Stoppels
609a42d63b Shorten long shebangs only if the execute permission is set (#26899)
The OS should only interpret shebangs, if a file is executable. 

Thus, there should be no need to modify files where no execute bit is set. 

This solves issues that are e.g. encountered while packaging software as 
COVISE (https://github.com/hlrs-vis/covise), which includes example data
in Tecplot format. The sbang post-install hook is applied to every installed
file that starts with the two characters #!, but this fails on the binary Tecplot
files, as they happen to start with #!TDV. Decoding them with UTF-8 fails 
and an exception is thrown during post_install.

Co-authored-by: Martin Aumüller <aumuell@reserv.at>
2021-10-22 16:55:19 +02:00
Harmen Stoppels
d274769761 Backport #186 from py-py to fix macOS failures (#26653)
Backports the relevant bits of 0f77b6e66f
2021-10-22 13:52:46 +02:00
Harmen Stoppels
7cec6476c7 Remove hard-coded repository in centos6 unit test (#26885)
This makes it easier to run tests in a fork.
2021-10-22 10:24:03 +02:00
Doug Jacobsen
d1d0021647 Add GCS Bucket Mirrors (#26382)
This commit contains changes to support Google Cloud Storage 
buckets as mirrors, meant for hosting Spack build-caches. This 
feature is beneficial for folks that are running infrastructure on 
Google Cloud Platform. On public cloud systems, resources are
ephemeral and in many cases, installing compilers, MPI flavors,
and user packages from scratch takes up considerable time.

Giving users the ability to host a Spack mirror that can store build
caches in GCS buckets offers a clean solution for reducing
application rebuilds for Google Cloud infrastructure.

Co-authored-by: Joe Schoonover <joe@fluidnumerics.com>
2021-10-22 06:22:38 +02:00
Miroslav Stoyanov
d024faf044 heffte: new version with rocm (#26878) 2021-10-22 01:12:46 +00:00
Cameron Stanavige
8b8bec2179 scr/veloc: component releases (#26716)
* scr/veloc: component releases

Update the ECP-VeloC component packages in preparation for an
upcoming scr@3.0rc2 release.

All
- Add new release versions
- Add new `shared` variant for all components
- Add zlib link dependency to packages that were missing it
- Add maintainers
- Use self.define and self.define_from_variant to clean up cmake_args

axl
- Add independent vendor async support variants

rankstr
- Update older version sha that fails checksum on install

* Fix scr build error

Lock dependencies for scr@3.0rc1 to the versions released at the same
time.
2021-10-21 18:05:59 -07:00
Frank Willmore
a707bf345d Add vacuumms package (#26838) 2021-10-21 17:12:08 -07:00
Robert Cimrman
9b28f99dd2 py-sfepy: add v2021.3 (#26865) 2021-10-21 23:50:38 +00:00
Manuela Kuhn
dbe1060420 py-neurokit2: add 0.1.4.1 (#26871)
* py-neurokit2: add 0.1.4.1

* Update var/spack/repos/builtin/packages/py-neurokit2/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-10-21 21:03:04 +00:00
eugeneswalker
3720d06e26 update E4S CI environments in preparation for 21.11 release (#26826)
* update E4S CI environments in preparation for 21.11 release

* e4s ci env: use clingo
2021-10-21 07:06:02 -07:00
Alexander Jaust
3176c6d860 [py-pyprecice] add v2.3.0.1 and fix hash of v2.2.1.1 (#26846) 2021-10-21 08:36:24 -05:00
Harmen Stoppels
3fa0654d0b Make 'spack location -e' print the current env, and 'spack cd -e' go to the current env (#26654) 2021-10-21 13:19:48 +02:00
Eric Brugger
7f4bf2b2e1 vtk: make use of system GLEW dependent on osmesa being disabled. (#26764) 2021-10-21 09:53:13 +02:00
Vanessasaurus
3fe1785d33 libabigail: support source install (#26807)
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-10-21 09:22:22 +02:00
Wouter Deconinck
b65937e193 kassiopeia: add v3.8.0; new variants log4cxx, boost (#26841) 2021-10-21 07:44:57 +02:00
Alexander Jaust
97d244eb95 Make superlu-dist@7.1.0 request CMake 3.18.1 or newer (#26849) 2021-10-21 07:43:30 +02:00
Edward Hartnett
88591536c8 bacio: add v2.5.0 (#26851) 2021-10-21 07:41:47 +02:00
RichardABunt
f78e5383cc arm-forge: add v21.1 (#26852) 2021-10-21 07:41:06 +02:00
downloadico
34d4091dbc tramonto: add new package (#26858) 2021-10-21 07:18:33 +02:00
Stephen Hudson
afd4a72937 libEnsemble: add v0.8.0 (#26864) 2021-10-21 07:14:31 +02:00
Adam J. Stewart
342f89e277 py-numpy: add v1.21.3 (#26860) 2021-10-21 07:13:43 +02:00
Luc Berger
fc7178da17 Kokkos Kernels: updating maintainers and releases (#26855)
Adding the latests releases of Kokkos Kernels and the official maintainers for the package.
2021-10-20 12:19:56 -07:00
iarspider
594325ae09 Add py-sniffio version 1.2.0 and fix dependencies (#26847)
* Add py-sniffio version 1.2.0 and fix dependencies

* Changes from review
2021-10-20 16:30:26 +00:00
iarspider
fcff01aaaf Update py-anyio to 3.3.4 (#26821)
* Update py-anyio to 3.3.4

* Changes from PR
2021-10-20 10:36:45 -05:00
Manuela Kuhn
b9c633d086 py-bids-validator: add 1.8.4 (#26844) 2021-10-20 10:33:27 -05:00
kwryankrattiger
45bea7cef7 Update ECP dav helper for propagating variants (#26175) 2021-10-20 11:22:07 -04:00
Martin Aumüller
029b47ad72 embree: add checksums for 3.12.2 & 3.13.1 (#26675)
Includes fix for for dependency ispc: fix build if cc -m32 is not possible
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2021-10-20 16:41:18 +02:00
Tamara Dahlgren
cc8b6ca69f Add --preferred and --latest tospack checksum (#25830) 2021-10-20 13:38:55 +00:00
Adam J. Stewart
f184900b1a damask: fix maintainer GitHub handle (#26829) 2021-10-20 14:57:13 +02:00
Wouter Deconinck
abc8cfe8fa cppgsl: branch master is now main (#26834) 2021-10-20 14:56:01 +02:00
Massimiliano Culpo
56209cb114 Reduce verbosity of error messages when concretizing environments (#26843)
With this commit stacktraces of subprocesses are shown only if debug mode is active
2021-10-20 11:30:07 +00:00
Alexander Jaust
26b58701bc Fix typo in repositories.rst (#26845) 2021-10-20 11:11:17 +00:00
Wouter Deconinck
42a6e1fcee root: prepend dependent_spec.prefix.include to ROOT_INCLUDE_PATH (#26379)
Spack is not populating CPATH anymore (e3f97b37e6 (diff-259adc895c0b2e8fca42ffb99d8051eec0712c868d12d8da255d32f1663acdc7)), and downstream packages ([gaudi](1aa7758dbb/var/spack/repos/builtin/packages/gaudi/package.py (L116))) have alrady started to include this in their package.py files. Instead of propagating this to all downstream packages, it tries to address the issue at the source.
2021-10-20 09:15:14 +02:00
Massimiliano Culpo
1983d6d9d0 Pipelines: pin importlib-metadata and setuptools-scm versions (#26831)
This will hopefully be a hotfix for the issue with pipelines
in #26813 and #26820
2021-10-19 16:09:40 -07:00
Chris White
b7d94ebc4f allow camp to use blt package (#26765) 2021-10-19 16:09:15 -07:00
Harmen Stoppels
1b634f05e0 A single process pool is not something to boast about (#26837) 2021-10-19 23:04:52 +00:00
Greg Becker
7dc0ca4ee6 cray architecture detection for zen3/milan (#26827)
* Update cray architecture detection for milan

Update the cray architecture module table with x86-milan -> zen3
Make cray architecture more robust to back off from frontend
architecture to a recent ancestor if necessary. This should make
future cray updates less paingful for users.

Co-authored-by: Gregory Becker <becker33.llnl.gov>
Co-authored-by: Todd Gamblin <gamblin2@llnl.gov>
2021-10-19 21:39:50 +00:00
Kai Germaschewski
501fa6767b adios2: fix unresolved symbols in 2.6.0 when built with gcc10 (#23871) 2021-10-19 21:09:07 +00:00
Harmen Stoppels
e7c7f44bb6 Reduce verbosity of threaded concretization (#26822)
1. Don't use 16 digits of precision for the seconds, round to 2 digits after the comma
2. Don't print if we don't concretize (i.e. `spack concretize` without `-f` doesn't have to tell me it did nothing in `0.00` seconds)
2021-10-19 18:33:17 +00:00
iarspider
bc99d8a2fd Update py-zipp (#26819)
* Update py-zipp

* Fix typo
2021-10-19 13:29:32 -05:00
Garth N. Wells
2bfff5338f py-fenics-ffcx: dependency updates (#26783)
* Update py-fenics-ffcx dependencies

* Relax some version numbering

* Remove stray colon
2021-10-19 13:28:20 -05:00
iarspider
a678a66683 py-setuptools-scm: make py-tomli dependency an open range (#26820) 2021-10-19 16:08:56 +00:00
Massimiliano Culpo
4c082a5357 Relax os constraints in e4s pipelines (#26547) 2021-10-19 10:51:37 -05:00
Massimiliano Culpo
2d45a9d617 Speed-up environment concretization on linux with a process pool (#26264)
* Speed-up environment concretization with a process pool

We can exploit the fact that the environment is concretized
separately and use a pool of processes to concretize it.

* Add module spack.util.parallel

Module includes `pool` and `parallel_map` abstractions,
along with implementation details for both.

* Add a new hash type to pass specs across processes

* Add tty msg with concretization time
2021-10-19 10:09:34 -05:00
Ryan Mast
64a323b22d spdlog: add v1.9.0, v1.9.1 and v1.9.2 (#26777) 2021-10-19 16:55:36 +02:00
Ryan Mast
f7666f0074 asio: Add versions up to 1.20.0 (#26778) 2021-10-19 16:54:55 +02:00
Ryan Mast
b72723d5d9 cli11: added v2.1.1, v2.1.0 (#26780) 2021-10-19 16:54:33 +02:00
Ryan Mast
65d344b2f8 cli11: disable building the examples (#26781) 2021-10-19 16:53:45 +02:00
Adam J. Stewart
9afc5ba198 py-pandas: add v1.3.4 (#26788) 2021-10-19 16:50:42 +02:00
Christopher Kotfila
ad35251860 Fix trigger and child links in pipeline docs (#26814) 2021-10-19 14:44:36 +00:00
Paul
9eaccf3bbf Add Go 1.17.2 and 1.16.9 (#26794) 2021-10-19 16:30:59 +02:00
Mark Grondona
bb1833bc8c flux: update maintainer of flux-core, flux-sched (#26800) 2021-10-19 16:30:33 +02:00
Robert Pavel
c66aa858c2 Made Legion Dependency on Gasnet Tarball Explicit (#26805)
Made legion dependency on a gasnet tarball explicit so as to take
advantage of spack mirrors for the purpose of deploying on machines with
firewalls
2021-10-19 16:28:43 +02:00
Erik Schnetter
4fc8ed10cb nsimd: add v3.0 (#26806) 2021-10-19 16:27:29 +02:00
Adam J. Stewart
0de8c65a2d Libtiff: improve compression support (#26809) 2021-10-19 16:17:37 +02:00
genric
42fb34e903 py-xarray: add v0.18.2 (#26811) 2021-10-19 16:15:56 +02:00
iarspider
d6fc914a9b Update py-importlib-metadata and py-setuptools-scm (#26813) 2021-10-19 16:08:53 +02:00
Massimiliano Culpo
79c92062a8 Gitlab pipelines: use images from the Spack organization (#26796) 2021-10-19 14:38:39 +02:00
Scott Wittenburg
95538de731 Speed up pipeline generation (#26622)
- [x] Stage already concretized specs instead of abstract ones
- [x] Reduce number of network calls by reading naughty list up front
2021-10-18 20:58:02 -07:00
Miguel Dias Costa
d41ddb8a9c new package: berkeleygw (#21455) 2021-10-18 18:17:58 -07:00
Harmen Stoppels
2b54132b9a cosma: add new versions and improve package (#24136)
* cosma: add new versions and improve package

* Move method below depends_on's
2021-10-18 18:06:14 -07:00
Todd Gamblin
c5ca0db27f patches: make re-applied patches idempotent (#26784)
We use POSIX `patch` to apply patches to files when building, but
`patch` by default prompts the user when it looks like a patch
has already been applied. This means that:

1. If a patch lands in upstream and we don't disable it
   in a package, the build will start failing.
2. `spack develop` builds (which keep the stage around) will
   fail the second time you try to use them.

To avoid that, we can run `patch` with `-N` (also called
`--forward`, but the long option is not in POSIX). `-N` causes
`patch` to just ignore patches that have already been applied.
This *almost* makes `patch` idempotent, except that it returns 1
when it detects already applied patches with `-N`, so we have to
look at the output of the command to see if it's safe to ignore
the error.

- [x] Remove non-POSIX `-s` option from `patch` call
- [x] Add `-N` option to `patch`
- [x] Ignore error status when `patch` returns 1 due to `-N`
- [x] Add tests for applying a patch twice and applying a bad patch
- [x] Tweak `spack.util.executable` so that it saves the error that
      *would have been* raised with `fail_on_error=True`. This lets
      us easily re-raise it.

Co-authored-by: Greg Becker <becker33@llnl.gov>
2021-10-18 23:11:42 +00:00
Mickaël Schoentgen
a118e799ae httpie: add v2.6.0 (#26791)
Signed-off-by: Mickaël Schoentgen <contact@tiger-222.fr>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-10-18 21:21:08 +00:00
Seth R. Johnson
bf42d3d49b file and python dependents: add missing dependencies (#26785)
* py-magic: delete redundant package

This package is actually named py-python-magic (since the project itself
is "python-magic").

* New package: libmagic

* Py-python-magic: add required runtime dependency on libmagic and new version

* Py-filemagic: add required runtime dependency

* py-magic: restore and mark as redundant

This reverts commit 4cab7fb69e.

* file: add implicit dependencies and static variant

Replaces redundant libmagic that I added. Compression headers were previously
being picked up from the system.

* Fix py-python-magic dependency

* Update python version requirements
2021-10-18 21:11:16 +00:00
Miroslav Stoyanov
e0ff44a056 tasmanian: add smoke test (#26763) 2021-10-18 16:09:46 -04:00
Seth R. Johnson
c48b733773 Make macOS installed libraries more relocatable (#26608)
* relocate: call install_name_tool less

* zstd: fix race condition

Multiple times on my mac, trying to install in parallel led to failures
from multiple tasks trying to simultaneously create `$PREFIX/lib`.

* PackageMeta: simplify callback flush

* Relocate: use spack.platforms instead of platform

* Relocate: code improvements

* fix zstd

* Automatically fix rpaths for packages on macOS

* Only change library IDs when the path is already in the rpath

This restores the hardcoded library path for GCC.

* Delete nonexistent rpaths and add more testing

* Relocate: Allow @executable_path and @loader_path
2021-10-18 13:34:16 -04:00
Shahzeb Siddiqui
3c013b5be6 docutils > 0.17 issue with rendering list items in sphinx (#26355)
* downgrade_docutils_version

* invalid version

* Update requirements.txt

* Improve spelling and shorten the reference link

* Update spack.yaml

* update version requirement

* update version to maximum of 0.16

Co-authored-by: bernhardkaindl <43588962+bernhardkaindl@users.noreply.github.com>
2021-10-18 16:55:46 +00:00
Harmen Stoppels
30e8dd95b5 Remove unused exist_errors in installer.py (#26650) 2021-10-18 15:53:51 +02:00
Harmen Stoppels
1e5f7b3542 Don't print error output in the test whether gpgconf works (#26682) 2021-10-18 15:52:53 +02:00
Sreenivasa Murthy Kolam
1156c7d0a9 allow multiple values for tensile_architecture and expand the gpu list for rocm-4.3.1 (#26745) 2021-10-18 08:48:07 +02:00
Xavier Delaruelle
cab17c4ac3 environment-modules: add version 5.0.1 (#26786) 2021-10-18 08:46:57 +02:00
Harmen Stoppels
33ef7d57c1 Revert 19736 because conflicts are avoided by clingo by default (#26721) 2021-10-18 08:41:35 +02:00
Valentin Volkl
9c7e71df34 py-jupytext: add new package (#26732)
* py-jupytext: add new package

* Apply suggestions from code review

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* update jupytext dependencies

* Apply suggestions from code review

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* py-jupytext: remove py-jupyerlab dependency

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-10-17 18:51:42 -05:00
Morten Kristensen
03f84fb440 py-vermin: add latest version 1.3.0 (#26787) 2021-10-17 11:46:53 -05:00
Valentin Volkl
d496568ff9 py-gevent: add version 1.5 (#26731)
* py-gevent: add version 1.5

* py-gevent: update dependencies for v1.5.0

* Apply suggestions from code review

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-gevent/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-10-17 11:07:11 -05:00
Sam Reeve
ba62b691a6 Add ECP tags for CoPA and related packages (#26739)
* Add ECP tags for CoPA (and related) packages

* Update CoPA maintainers
2021-10-17 10:00:28 -04:00
Ryan Mast
b794b5bd4d nlohmann-json: update to version 3.10.4 (#26779) 2021-10-17 09:56:20 -04:00
Bernhard Kaindl
64143f970e [Fix for the GitLab CI] phist: prefer @1.9.5 (1.9.6 is not compatible w/ mpich%gcc:9) (#26773)
* phist: Prefer 1.9.5 (1.9.6 uses mpi_f08, but not available in CI)

* phist: remove dupe of 1.9.5, missing preferred=True

Also, for 1.9.6, patch the (most, one does not work) tests to use
2021-10-16 11:18:07 -07:00
Scot Halverson
b2f059e547 Update GASNet package.py to include version 2021.9.0 (#26736) 2021-10-15 21:15:32 +02:00
Mosè Giordano
2cf7d43e62 libblastrampoline: add v3.1.0 (#26769)
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2021-10-15 18:17:26 +00:00
Brice Videau
0bc1bffe50 Fix ruby dependent extensions. (#26729)
* Fix ruby dependent extensions.

* Added Kerilk as maintainer.
2021-10-15 16:59:32 +00:00
Axel Huebl
33da53e325 GCC: Conflict for <12 for M1 (#26318)
aarch64/M1 is only a supported build combination for GCC in
the planned GCC 12+ release.
2021-10-15 12:30:09 -04:00
Mickaël Schoentgen
6686db42ad py-charset-normalizer: add v2.0.7 (#26756)
Signed-off-by: Mickaël Schoentgen <contact@tiger-222.fr>
2021-10-15 15:58:09 +00:00
Manuela Kuhn
ec67bec22a py-rdflib: add 6.0.2 (#26757) 2021-10-15 10:35:59 -05:00
Manuela Kuhn
2a5a576667 py-ipykernel: add 6.4.1 and fix deps (#26758) 2021-10-15 10:34:51 -05:00
Manuela Kuhn
5dc8094f84 py-setuptools: add 58.2.0 (#26759) 2021-10-15 10:31:52 -05:00
Manuela Kuhn
012b4f479f py-jupyter-client: add 6.1.12 (#26760) 2021-10-15 10:30:50 -05:00
Harmen Stoppels
f8e4aa7d70 Revert "Don't run lsb_release on linux (#26707)" (#26754)
This reverts commit fcac95b065.
2021-10-15 09:34:04 +00:00
Harmen Stoppels
e0fbf09239 EnvironmentModifications: allow disabling stack tracing (#26706)
Currently Spack keeps track of the origin in the code of any
modification to the environment variables. This is very slow 
and enabled unconditionally even in code paths where the 
origin of the modification is never queried.

The only place where we inspect the origins of environment 
modifications is before we start a build, If there's an override 
of the type `e.set(...)` after incremental changes like 
`e.append_path(..)`, which is a "suspicious" change.

This is very rare though.

If an override like this ever happens, it might mean a package is
broken. If that leads to build errors, we can just ask the user to run
`spack -d install ...` and check the warnings issued by Spack to find
the origins of the problem.
2021-10-15 10:00:44 +02:00
Vanessasaurus
842e56efb8 libabigail: add v2.0 (#26753)
Signed-off-by: vsoch <vsoch@users.noreply.github.com>

Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2021-10-15 07:53:29 +02:00
Joseph Wang
0749d94ad3 Disable parallel builds in groff and gosam-contrib (#26730)
Work around to #26726 and #26714
2021-10-15 07:20:18 +02:00
Cameron Rutherford
2bc0ea70ed HiOp: add v0.5.0 + small changes in dependencies (#26744) 2021-10-15 07:09:09 +02:00
kwryankrattiger
bf5ef3b6b9 paraview: add adios2 variant (#26728) 2021-10-15 07:07:04 +02:00
Timothy Brown
7ccdae5233 Removing NCEP Post (ncep-post). (#26749)
UPP and ncep-post are the same package, so this PR 
removes the duplication. 

ncep-post was originally named after the upstream repo
that now changed its name to UPP.
2021-10-15 07:04:14 +02:00
Eric Brugger
ea453db674 vtk: modify conflict between osmesa and qt (#26752) 2021-10-15 06:58:43 +02:00
Tamara Dahlgren
41d375f6a4 Stand-alone tests: disallow re-using an alias (#25881)
It can be frustrating to successfully run `spack test run --alias <name>` only to find you cannot get the results because you already use `<name>` in some previous stand-alone test execution.  This PR prevents that from happening.
2021-10-14 15:08:00 -07:00
Tamara Dahlgren
beb8a36792 Remove extra tag assignments (#26692) 2021-10-14 14:50:09 -07:00
Manuela Kuhn
28ebe2f495 py-datalad: add 0.15.2 (#26750) 2021-10-14 21:44:52 +00:00
Harmen Stoppels
4acda0839b cp2k: use variant propagation trick for virtuals (#26737) 2021-10-14 23:11:22 +02:00
Massimiliano Culpo
eded8f48dc ASP-based solver: add a rule for version uniqueness in virtual packages (#26740)
fixes #26718

A virtual package may or may not have a version, but it
never has more than one. Previously we were missing a rule
for that.
2021-10-14 23:06:41 +02:00
Christoph Junghans
d9d0ceb726 add py-pyh5md and update py-espressopp (#26746)
* add  py-pyh5md and update py-espressopp

* Update package.py
2021-10-14 19:17:02 +00:00
Bernhard Kaindl
6ca4d554cd libfive: Add all variants, +qt needs qt@5.15.2:+opengl (#26629)
Refresh of deps to fix the build and add variants from CMakeLists.txt
2021-10-14 11:42:01 -07:00
Mosè Giordano
74c6b7d8c1 sombrero: add version 2021-08-16 (#26741) 2021-10-14 19:41:50 +02:00
Bernhard Kaindl
95030a97b6 vc: Enable the testsuite, excluding tests failing on Zen2 (#26699)
This fixes running the testsuite, it adds the package virtest for it.
2021-10-14 09:02:31 -07:00
Miroslav Stoyanov
b64a7fe1ff switch to the smoke testing included in heffte (#26720) 2021-10-14 08:58:29 -07:00
iarspider
160371f879 alpgen: new package (#26713)
Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2021-10-14 16:58:09 +02:00
Thomas Madlener
49354140be edm4hep: new version, fix tests (depends on catch2) (#26679) 2021-10-14 14:04:45 +00:00
Thomas Madlener
25704ae8e6 podio: new version and fix python unittest env (#26649) 2021-10-14 13:54:02 +00:00
Bernhard Kaindl
a61853816f phist: Fix build of 1.9.6, fix build- and install-tests (#26727)
Primary fix:

Due to a typo in a version range, overlapping PR merges resulted
in a build failure of the latest version:
Don't attempt to remove a non-existing file for version 1.9.6.

Secondary fixes:

update_tpetra_gotypes.patch was mentioned twice, and the version
range has to exclude @1.4.2, to which it cannot be applied.

Add depend_on() py-pytest, py-numpy and pkgconfig with type='test'

@:1.9.0 fail with 'Rank mismatch with gfortran@10:, add a conflicts().

raise InstallError('~mpi not possible with kernel_lib=builtin!')
when applicable.

Fixes for spack install --test=root phist:

mpiexec -n12 puts a lot of stress on a pod and gets stuck in a loop
very often: Reduce the mpiexec procs and the number of threads.

Remove @run_after('build') @on_package_attributes(run_tests=True):
from 'def check()': fixes it from getting called twice

The build script of 'make test_install' for the installcheck expects
the examples to be copied to self.stage.path: Provide them.
2021-10-14 08:14:25 -04:00
AMD Toolchain Support
8c1399ff7c LAMMPS: update recipe for %aocc (#26710)
* updating the recipe for betterment

* addressing the suggesions received from reviewers

* adding package helper macros

Co-authored-by: mohan002 <mohbabul@amd.com>
2021-10-14 12:03:15 +00:00
Eric Brugger
2bc97f62fd Qt: Qt fixes for a Cray AMD system. (#26722)
* Qt fixes for a Cray AMD system.

* Update to latest changes.
2021-10-14 07:41:26 -04:00
Massimiliano Culpo
949094544e Constrain abstract specs rather than concatenating strings in the "when" context manager (#26700)
Using the Spec.constrain method doesn't work since it might
trigger a repository lookup which could break our directives
and triggers a circular import error.

To fix that we introduce a function to merge abstract anonymous
specs, based only on package names, which does not perform any
lookup in the repository.
2021-10-14 12:33:10 +02:00
Bernhard Kaindl
2c3ea68dd1 openslide: Fix missing dependencies: gdk-pixbuf and perl-alien-libxml2 (#26620)
Add missing pkgconfig to openslide and its dep perl-alien-libxml2.

Fix shared-mime-info to be a runtime dependency of gdk-pixbuf,
Otherwise, configure cannot detect use gdk-pixbuf without error.
2021-10-13 19:07:27 -05:00
Bernhard Kaindl
99200f91b7 r-imager: add depends_on('r+X') and bump version (#26697) 2021-10-13 19:02:54 -05:00
Satish Balay
36bd69021d dealii: @9.3.1 has build errors with boost@1.77.0 - so add dependency on boost@1.76.0 [or lower] (#26709) 2021-10-14 01:30:53 +02:00
Harmen Stoppels
fcac95b065 Don't run lsb_release on linux (#26707)
Running `lsb_release` on Linux takes about 50ms because it is written in
Python. We do not use the output, so this change makes use not call it.
2021-10-14 01:27:24 +02:00
Manuela Kuhn
0227fc3ddc py-mne: add full variant (#26702) 2021-10-13 16:59:46 -05:00
Keita Iwabuchi
7c8c29a231 metall: add version 0.17 (#26694)
Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2021-10-13 22:10:16 +02:00
Bernhard Kaindl
5782cb6083 magics: Add v4.9.3 to fix build with gcc@11, skip broken testcase (#26695)
To build with gcc-11, v4.9.3 is needed, conflict added for older revs.
2021-10-13 12:14:37 -07:00
Bernhard Kaindl
f4a132256a qgis: fix build of LTS release with proj>7 (#26696)
Co-authored-by: Sinan <sbulutw@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-10-13 20:42:18 +02:00
David Beckingsale
2864212ae3 Add camp 0.3.0 and 0.2.3 (#26717) 2021-10-13 18:41:35 +00:00
Bernhard Kaindl
87663c6796 vapor: Fix the build and update: Use correct deps and find numpy incdir (#26630)
vapor needs proj@:7 and gives a list of tested dependency versions.
Make it find the numpy include path and add version 3.5.0 as well
2021-10-13 13:25:18 -04:00
Bernhard Kaindl
14a929a651 sfcgal: build fails with cgal@:4.6, works with cgal@4.7: (#26642)
Use depends_on('cgal@4.7: +core') to fix the build
2021-10-13 11:47:09 -05:00
Bernhard Kaindl
bcd1272253 wireshark: Fix install race and skip network capture tests (#26698)
The network capture tests can't pass when built as normal user.
2021-10-13 12:39:19 -04:00
Todd Kordenbrock
6125117b5d SEACAS: add a Faodel variant (#26583)
* SEACAS: add a Faodel variant

* Use safer CMake and variant packages instead of directly adding parameters
Add a "+faodel ~mpi" dependency to balance "+faodel +mpi"
2021-10-13 12:39:11 -04:00
Satish Balay
37278c9fa0 superlu-dist add version 7.1.0 (#26708) 2021-10-13 11:34:43 -05:00
Patrick Gartung
047c95aa8d buildcache: do one less tar file extraction
The buildcache is now extracted in a temporary folder within the current store,
moved to its final place and relocated. 

"spack clean -s" has been extended to also clean the temporary extraction directory.

Add hardlinks with absolute paths for libraries in the corge, garply and quux packages
to detect incorrect handling of hardlinks in tests.
2021-10-13 17:38:29 +02:00
haralmha
e6b76578d2 Add version 4.12.0 (#26532) 2021-10-13 14:07:48 +00:00
iarspider
81c272fcb7 photos-f: new package (Fortran version) (#26703) 2021-10-13 15:56:11 +02:00
Jose E. Roman
c47eb7217e slepc: set up SLEPC_DIR for dependent packages (#26701) 2021-10-13 15:51:08 +02:00
Jen Herting
8ad608a756 py-convokit: new package (#26236)
Co-authored-by: Sid Pendelberry <sid@rit.edu>
2021-10-13 15:50:07 +02:00
Joseph Wang
252784ccf5 cppgsl: disable tests on gcc11 (#26593) 2021-10-13 09:36:45 -04:00
Bernhard Kaindl
b771c4ea01 phist: Fix build: ppc64_sse.patch only applies to 1.9.4 (#26704)
ppc64_sse.patch can only be applied to 1.9.4:
* Older releases don't have the patched file
* All newer releases carry the change of the patch already.
2021-10-13 09:20:50 -04:00
Francis Kloss
53461b7b04 salome-medcoupling: new package (with dependencies) (#25785)
Adds new packages for using MEDCoupling from SALOME platform
2021-10-13 13:50:37 +02:00
Joe Schoonover
4d58661d08 feq-parse: add version 1.1.0 and update maintainer (#26060) 2021-10-13 00:20:21 +00:00
Valentin Volkl
81d157b05e garfieldpp: update dependencies, add variant (#25816) 2021-10-13 02:13:50 +02:00
Jen Herting
0f9080738f [py-spacy] added version 2.3.7 (#25999) 2021-10-12 23:57:04 +00:00
Scott McMillan
b937aa205b Fix Amber patch target specification (#26687)
Co-authored-by: Scott McMillan <smcmillan@nvidia.com>
2021-10-13 00:15:05 +02:00
Jose E. Roman
31b0fe21a2 py-slepc4py: add missing depends_on() (#26688) 2021-10-13 00:09:19 +02:00
Bernhard Kaindl
e7bfaeea52 libical: Add missing deps: pkgconfig, glib and libxml2 (#26618)
Libical needs pkgconfig, glib and libxml2 to build.
2021-10-12 23:22:49 +02:00
Harmen Stoppels
1ed695dca7 Improve error messages for bootstrap download failures (#26599) 2021-10-12 22:11:07 +02:00
Bernhard Kaindl
b6ad9848d2 babelflow, parallelmergetree: fix build with gcc11 (#26681)
gcc-11 does not include the <limits> and <algorithm> as side effect
of including other header, at least not as often as earlier gcc did.
2021-10-12 21:45:00 +02:00
Stephen Herbein
8d04c8d23c flux-core, flux-sched: add 0.29.0, 0.18.0 and cleanup env vars (#26391)
Problem: Flux expects the `FLUX_PMI_LIBRARY_PATH` to point directly at
the `libpmi.so` installed by Flux.  When the env var is unset,
prepending to it results in this behavior.  In the rare case that the
env var is already set, then the spack `libpmi.so` gets prepended with a
`:`, which Flux then attempts to interpret as a single path.

Solution: don't prepend to the path, instead set the path to point to
the `libpmi.so` (which will be undone when Flux is unloaded).

* flux-core: remove deprecated environment variables

The earliest checksummed version in this package is 0.15.0. As of
0.12.0, wreck (and its associated paths) no longer exist in Flux. As of
0.13.0, the `FLUX_RCX_PATH` variables are no longer used. So clean up
these env vars from the `setup_run_environment`.
2021-10-12 21:39:43 +02:00
Adam J. Stewart
47554e1e2f GMT: add conflict for GCC 11 (#26684) 2021-10-12 17:56:17 +00:00
Bernhard Kaindl
862ce517ce gromacs: @2018:2020: add #include <limits> for newer %gcc builds (#26678)
gromacs@2018:2020.6 is fixed to build with gcc@11.2.0
by adding #include <limits> to a few header files.

Thanks to Maciej Wójcik <w8jcik@gmail.com> for testing versions.
2021-10-12 11:39:09 -06:00
Alexander Jaust
50a2316a15 Add missing spack command in basic usage tutorial (#26646)
The `find` command was missing for the examples forcing colorized output. Without this (or another suitable) command, spack produces output that is not using any color. Thus, without the `find` command one does not see any difference between forced colorized and non-colorized output.
2021-10-12 19:23:53 +02:00
Mark W. Krentel
2edfccf61d binutils: fix parallel make for version 2.36 (#26611)
There was a bug in 2.36.* of missing Makefile dependencies.  The
previous workaround was to require 2.36 to be built serially.  This is
now fixed upstream in 2.37 and this PR adds the patch to restore
parallel make to 2.36.
2021-10-12 19:01:46 +02:00
Veselin Dobrev
e2a64bb483 mfem: patch @4.3.0 to support hypre up to v2.23.0 (#26640) 2021-10-12 18:29:56 +02:00
Manuela Kuhn
ff66c237c0 py-niworkflows: add new package (#26639)
* py-niworkflows: add new package

* Update var/spack/repos/builtin/packages/py-niworkflows/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* remove unnecessary comment

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-10-12 11:22:44 -05:00
Manuela Kuhn
f8910c7859 py-nistats: add new package (#26662)
* py-nistats: add new package

* Update var/spack/repos/builtin/packages/py-nistats/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* remove `conflicts`

* remove test dependencies

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-10-12 11:22:00 -05:00
Harmen Stoppels
e168320bb1 spack: Add package (#25979)
* Make python 2 use 'from __future__ import absolute_import' to allow import spack.pkgkit

* Add Spack

* Improve ranges
2021-10-12 11:39:39 -04:00
Sergei Shudler
f58f5f8a0d babelflow, parallelmergetree: add the current versions (#26660) 2021-10-12 17:36:13 +02:00
Vanessasaurus
ce7eebfc1f allowing spack monitor to handle redirect (#26666)
when deployed on kubernetes, the server sends back permanent redirect responses.
This is elegantly handled by the requests library, but not urllib that we have
to use here, so I have to manually handle it by parsing the exception to
get the Location header, and then retrying the request there.

Signed-off-by: vsoch <vsoch@users.noreply.github.com>
2021-10-12 17:29:22 +02:00
Jonas Thies
f66ae104bf phist: force MPI compiler wrappers (#26312)
* packages/phist, re #26002: force phist to use MPI compiler wrappers (copied from trilinos package)

* packages/phist re #26002, use cmake-provded FindMPI module only

* packages/phist source code formatting

* packages/phist: set MPI_HOME rather than MPI_BASE_DIR, thanks @sethri.

* phist: delete own FindMPI.cmake for older versions (rather than patching it away)

* packages/phist: remove blank line

* phist: adjust sorting of imports

* phist: change order of imports
2021-10-12 11:11:00 -04:00
Joseph Wang
1e382d6d20 madgraph5amc: Add changes fixing bugs shown by gcc10 (#26643) 2021-10-12 15:55:48 +02:00
Martin Aumüller
6f8f37ffb1 ispc: update development branch name and limit to llvm@12 (#26676)
1.16 and 1.16.1 are not compatible with LLVM 13
2021-10-12 14:31:24 +02:00
Massimiliano Culpo
551120ee0b ASP-based solver: decrease the priority of multi-valued variant optimization for root (#26677)
The ASP-based solver maximizes the number of values in multi-valued
variants (if other higher order constraints are met), to avoid cases
where only a subset of the values that have been specified on the
command line or imposed by another constraint are selected.

Here we swap the priority of this optimization target with the
selection of the default providers, to avoid unexpected results
like the one in #26598
2021-10-12 14:15:48 +02:00
Harmen Stoppels
c2bf585d17 Fix potentially broken shutil.rmtree in tests (#26665)
Seems like https://bugs.python.org/issue29699 is relevant. Better to
just ignore errors when removing them tmpdir. The OS will remove it
anyways.

Errors are happening randomly from tests that are using this fixture.
2021-10-12 14:01:52 +02:00
Martin Diehl
66b32b337f damask{,-grid,-mesh}: add @3.0.0-alpha5 (#26570) 2021-10-12 13:22:09 +02:00
Maciej Wójcik
4b2cbd3aea gromacs: Add Gromacs 2020.6 and Plumed 2.7.2 (#26663) 2021-10-12 13:01:10 +02:00
Bernhard Kaindl
cb06f91df7 boost: Fix build of 1.53:1.54 with glibc>=2.17 (#26659)
Fix missing declaration of uintptr_t with glibc>=2.17 in 1.53:1.54
See: https://bugs.gentoo.org/482372
2021-10-12 10:59:36 +02:00
Harmen Stoppels
0c0831861c Avoid quadratic complexity in log parser (#26568)
TL;DR: there are matching groups trying to match 1 or more occurrences of
something. We don't use the matching group. Therefore it's sufficient to test
for 1 occurrence. This reduce quadratic complexity to linear time.

---

When parsing logs of an mpich build, I'm getting a 4 minute (!!) wait
with 16 threads for regexes to run:

```
In [1]: %time p.parse("mpich.log")
Wall time: 4min 14s
```

That's really unacceptably slow... 

After some digging, it seems a few regexes tend to have `O(n^2)` scaling
where `n` is the string / log line length. I don't think they *necessarily*
should scale like that, but it seems that way. The common pattern is this

```
([^:]+): error
```

which matches `: error` literally, and then one or more non-colons before that. So
for a log line like this:

```
abcdefghijklmnopqrstuvwxyz: error etc etc
```

Any of these are potential group matches when using `search` in Python:

```
abcdefghijklmnopqrstuvwxyz
 bcdefghijklmnopqrstuvwxyz
  cdefghijklmnopqrstuvwxyz
                         ⋮
                        yz
                         z
```

but clearly the capture group should return the longest match.

My hypothesis is that Python has a very bad implementation of `search`
that somehow considers all of these, even though it can be implemented
in linear time by scanning for `: error` first, and then greedily expanding
the longest possible `[^:]+` match to the left. If Python indeed considers
all possible matches, then with `n` matches of length `1 .. n` you
see the `O(n^2)` slowness (i verified this by replacing + with {1,k}
and doubling `k`, it doubles the execution time indeed).

This PR fixes this by removing the `+`, so effectively changing the 
O(n^2) into a O(n) worst case.

The reason we are fine with dropping `+` is that we don't use the
capture group anywhere, so, we just ensure `:: error` is not a match
but `x: error` is.

After going from O(n^2) to O(n), the 15MB mpich build log is parsed
in `1.288s`, so about 200x faster.

Just to be sure I've also updated `^CMake Error.*:` to `^CMake Error`,
so that it does not match with all the possible `:`'s in the line.
Another option is to use `.*?` there to make it quit scanning as soon as
possible, but what line that starts with `CMake Error` that does not have
a colon is really a false positive...
2021-10-12 00:05:11 -07:00
Manuela Kuhn
580a20c243 py-templateflow: add 0.4.2 (#26471)
* py-templateflow: add 0.4.2

* py-templateflow: fix python dependency for 0.4.2

* py-templateflow: remove wheel dependency for older versions
2021-10-11 21:37:50 -05:00
Manuela Kuhn
eb486371b2 py-pysurfer: add new package (#26638) 2021-10-11 21:36:43 -05:00
Manuela Kuhn
0da892f2dd py-pandas: fix installation and tests for versions @:0.25 (#26668) 2021-10-12 00:44:32 +00:00
Daniele Cesarini
a36a5ab624 fleur: new package (#26631) 2021-10-12 02:31:23 +02:00
Todd Kordenbrock
af2ecf87d4 Faodel: Update for the v1.2108.1 release (#26516) 2021-10-11 23:17:42 +00:00
Valentin Volkl
a0b9face0d frontier-client: add missing openssl dependency (#26636) 2021-10-12 01:02:12 +02:00
Kevin Pedretti
0b62974160 openblas: fix build on riscv64 (#26565)
OpenBLAS now has support for the riscv64 architecture. This commit
extends the spack openblas package.py to handle building on riscv64.
2021-10-12 00:55:45 +02:00
Alan Sill
833f1de24a bcl2fastq2: add boost@1.55 as default boost dependency (#26655)
When PR #26659 is merged, boost version boost@1.54.0 will be available for build too.

Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2021-10-11 22:21:17 +00:00
Bernhard Kaindl
4eb176b070 motif package: fix linking the simple_app demo program (#26574) 2021-10-11 15:00:42 -07:00
Desmond Orton
95e63e0c29 New Package Qualimap:2.2.1 (#26615)
Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2021-10-11 19:28:34 +00:00
Derek Ryan Strong
2644a15ff9 GNU parallel package: add version 20210922 (#26591) 2021-10-11 12:08:06 -07:00
Marie Houillon
c7785b74be openCARP packages: add version 8.1 (#26602) 2021-10-11 12:07:05 -07:00
Bernhard Kaindl
260f4ca190 mapserver: Add missing deps: giflib and postgresql (#26619) 2021-10-11 12:04:18 -07:00
Michael Kuhn
d1f3279607 installer: Support showing status information in terminal title (#16259)
Installing packages with a lot of dependencies does not have an easy way
of judging the current progress (apart from running `spack spec -I pkg`
in another terminal). This change allows Spack to update the terminal's
title with status information, including its current progress as well as
information about the current and total number of packages.
2021-10-11 17:54:59 +02:00
Seth R. Johnson
8f62039d45 llvm: add conflict for newer apple-clang versions (#26633) 2021-10-11 17:49:23 +02:00
Bernhard Kaindl
2e9512fe8b mesa: gallium fails with llvm@13: use 'llvm@6:12', add mesa@21.2.3 (#26627)
The software rasterizer of Mesa's Gallium3D(even @21.2.3) fails to
build with llvm@13.0.0, use: depends_on('llvm@6:12', when='+llvm')
2021-10-11 17:34:33 +02:00
Matthew Archer
e034930775 kahip: update build system to cmake for v3.11, retain scons for older versions (#25645)
* kahip: update to cmake for v3.11, retain scons for older versions

* kahip: update build system to cmake for v3.11, retain SCons for older versions

* address PR comments and add maintainer

* address PR comments - correct version to 2.10, add deprecated and url, and remove scons version
2021-10-11 10:20:43 -05:00
Daniele Cesarini
79aba5942a Update of siesta libs (#26489) 2021-10-11 09:09:39 -05:00
iarspider
78200b6b41 Add new versions of kiwisolver (#26597) 2021-10-11 09:09:01 -05:00
Harmen Stoppels
89220bc0e1 Only install env modifications in <prefix>/.spack (#24081)
- Do not store the full list of environment variables in
  <prefix>/.spack/spack-build-env.txt because it may contain user secrets.

- Only store environment variable modifications upon installation.

- Variables like PATH may still contain user and system paths to make
  spack-build-env.txt sourceable. Variables containing paths are
  modified through prepending/appending, and if we don't apply these
  to the current environment variable, we end up with statements like
  `export PATH=/path/to/spack/bin` with system paths missing, meaning
  no system binaries are in the path, which is a bad user experience.

- Do write the full environment to spack-build-env.txt in the staging dir,
  but ensure it is readonly for the current user, to make it a bit safer
  on shared systems.
2021-10-11 09:07:45 -05:00
Harmen Stoppels
c0c9ab113e Add spack env activate --temp (#25388)
Creates an environment in a temporary directory and activates it, which
is useful for a quick ephemeral environment:

```
$ spack env activate -p --temp
[spack-1a203lyg] $ spack add zlib
==> Adding zlib to environment /tmp/spack-1a203lyg
==> Updating view at /tmp/spack-1a203lyg/.spack-env/view
```
2021-10-11 06:56:03 -04:00
Harmen Stoppels
f28b08bf02 Remove unused --dependencies flag (#25731) 2021-10-11 10:16:11 +02:00
iarspider
ad75f74334 New package: py-cppy (required for py-kiwisolver) (#26645) 2021-10-10 17:14:20 -05:00
Manuela Kuhn
4e1fdfeb18 py-nilearn: add 0.4.2 and 0.6.2 (#26635) 2021-10-09 19:14:13 -05:00
Manuela Kuhn
7f46b9a669 py-pyvistaqt: add new package (#26637) 2021-10-09 21:00:00 +00:00
Michael Kuhn
5deb8a05c4 environment-modules: fix build (#26632)
PR #25904 moved the `--with-tcl` option to only older versions. However,
without this option, the build breaks:
```
checking for Tcl configuration... configure: error: Can't find Tcl configuration definitions. Use --with-tcl to specify a directory containing tclConfig.sh
```
2021-10-09 12:43:54 -05:00
Bernhard Kaindl
9194ca1e2f idna: Add versions 2.9 for sierrapy #23768 and 3.2(current) (#26616)
py-sierrapy was merged accidentally and pins its versions to exact
numbers. Add 2.9 as the version for sierrapy and the current 3.2
2021-10-09 11:31:11 -05:00
Joseph Wang
e6cc92554d py-awkward: add py-yaml as depends (#26626) 2021-10-09 17:35:22 +02:00
Joseph Wang
03ab5dee31 evtgen: fix pythia typo (#26625) 2021-10-09 16:11:58 +02:00
Bernhard Kaindl
93df47f4d5 librsvg: fix build when does not use -pthread for linking (#26592)
librsvg uses pthread_atfork() but does not use -pthread on Ubuntu 18.04 %gcc@8
2021-10-09 13:10:13 +02:00
Derek Ryan Strong
4b5cc8e3bd Add R 4.1.1 (#26589) 2021-10-08 20:02:03 -05:00
Derek Ryan Strong
e89d4b730a Add Julia 1.6.3 (#26624) 2021-10-09 00:58:19 +00:00
Massimiliano Culpo
2386630e10 Remove DB reindex during a read operation (#26601)
The DB should be what is trusted for certain operations.
If it is not present when read we should assume the
corresponding store is empty, rather than trying a
write operation during a read.

* Add a unit test
* Document what needs to be there in tests
2021-10-08 22:35:23 +00:00
Bernhard Kaindl
21ce23816e py-twisted,py-storm: dep on zope.interface, bump storm version (#26610)
* py-twisted,py-storm: dep on zope.interface, bump storm version

py-twisted and py-storm's import tests need zope.interface.
py-storm: Use pypi and add version 0.25. It didn't change reqs.
zope.infterface@4.5.0 imports removed Feature: Use setuptools@:45

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* py-storm: all deps updated with type=('build', 'run')

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-10-08 21:20:39 +00:00
psakievich
8ebb705871 Trilinos: update for CUDA and Nalu-Wind (#26614) 2021-10-08 21:08:54 +00:00
Bernhard Kaindl
7e8f2e0c11 py-hypothesis: Add variants django, dumpy, pandas and fix import tests (#26604) 2021-10-08 21:00:47 +00:00
Manuela Kuhn
654268b065 py-bcrypt, py-bleach, py-decorator, py-pygdal: fix python dependency (#26596)
* py-bcrypt, py-bleach, py-decorator, py-pygdal: fix python dependency

* Update var/spack/repos/builtin/packages/py-bleach/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-10-08 15:56:22 -05:00
Bernhard Kaindl
6d0d8d021a py-pymatgen: fix build of old versions, bump version to 2021.3.9 (#26249)
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-10-08 19:54:40 +00:00
Bernhard Kaindl
f1f614ee9f py-anytree: Add dep py-six@1.9.0 as required by setup.py (#26603)
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-10-08 19:36:12 +00:00
Manuela Kuhn
88c33686fd py-matplotlib: fix 3.4.3 (#26586)
* py-matplotlib: fix 3.4.3

* Update var/spack/repos/builtin/packages/py-matplotlib/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-10-08 13:52:10 -05:00
Bernhard Kaindl
de86726483 py-traceback2: Fix depends_on: add six and py-linecache2 (#26607) 2021-10-08 13:35:36 -05:00
Bernhard Kaindl
a95c1dd615 py-keras-preprocessing: Add missing deps: six@1.9.0: and numpy@1.9.1: (#26605)
* py-keras-preprocessing: Add missing deps: six@1.9.0: and numpy@1.9.1:

Add deps: pip download --no-binary :all: keras-preprocessing==1.1.2
Collecting numpy>=1.9.1
  Installing build dependencies: started
Collecting six>=1.9.0

* Update var/spack/repos/builtin/packages/py-keras-preprocessing/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-10-08 13:34:25 -05:00
Harmen Stoppels
7d89a95028 Fix leaky spack.binary_distribution.binary_index in tests (#26609)
* Fix issues with leaky binary index across tests

* More rigorous binary_index reset as now other tests are failing :(
2021-10-08 13:41:47 -04:00
Manuela Kuhn
32b35e1a78 py-neurora: add new package (#26479) 2021-10-08 13:39:45 +00:00
Tamara Dahlgren
7f2611a960 Allow Version('') and map it to the empty tuple (#25953) 2021-10-08 10:36:54 +02:00
Rodrigo Ceccato de Freitas
169d0a5649 cling: add missing CMake dependency (#26577) 2021-10-08 09:28:37 +02:00
Adam J. Stewart
f390289629 More strict ReadTheDocs tests (#26580) 2021-10-08 09:27:17 +02:00
Daniel G Travieso
10de12c7d0 add hash field to spec on find --json and assert in test its there (#26443)
Co-authored-by: Daniel Travieso <daniel@dgtravieso.com>
2021-10-07 23:50:05 -07:00
Bernhard Kaindl
449a5832c8 llvm: llvm@13+libcxx needs a very recent C++ compiler (#26584)
libc++-13 does not support %gcc@:10, see:
https://bugs.llvm.org/show_bug.cgi?id=51359#c1

https://libcxx.llvm.org/#platform-and-compiler-support says:
- GCC    11     - latest stable release per GCC’s release page
- Clang: 11, 12 - latest two stable releases per LLVM’s release page
- AppleClang 12 - latest stable release per Xcode’s release page
2021-10-08 00:25:51 +00:00
Pedro Demarchi Gomes
28529f9eaf re2 pic support (#26513) 2021-10-08 01:01:40 +02:00
Oliver Perks
da31c7e894 Updatepackage/minigmg (#26467)
* MiniGMG, add support for optimised flags + SIMDe implementation of AVX instrinsics

* Add .gitlab-ci.yml

* NVHPC fast

* remove CI

* Syntax fix
2021-10-07 14:49:14 -05:00
Paul Ferrell
0b9914e2f5 Fix for license symlinking issue. (#26576)
When a symlink to a license file exists but is broken, the license symlink post-install hook fails
because os.path.exists() checks the existence of the target not the symlink itself.
os.path.lexists() is the proper function to use.
2021-10-07 19:18:35 +00:00
Seth R. Johnson
9853fd50e2 itk: use CMakePackage helpers (#26572) 2021-10-07 10:49:51 -05:00
Scott Wittenburg
0561af1975 Pipelines: retry service job on system errors (#26508)
Retry rebuild-index, cleanup, and no-op jobs automatically if they fail
due to infrastructure-related problems.
2021-10-07 08:59:51 -06:00
Kevin Huck
b33a0923e1 apex: support profiling/tracing HIP applications (#26569)
libz is added for compressing google trace events output.
2021-10-07 16:22:40 +02:00
Harmen Stoppels
05834e7c9d Memoize the result of spack.platforms.host() (#26573) 2021-10-07 14:04:05 +02:00
Olivier Cessenat
20ee786d09 visit: add an external find function (determine_version) (#25817)
* visit: add an external find function (determine_version)

* visit: correct too long comment line

* visit: forgot to set executables

* visit: external find uses signgle dash version

* visit: found as external asking visit version
2021-10-07 10:19:58 +00:00
Manuela Kuhn
653d5e1590 py-mayavi: add 4.7.3 (#26566) 2021-10-06 19:15:34 -05:00
Tyler Funnell
60909f7250 fish: adding version 3.3.1 (#26488)
* fish: adding version 3.3.1

* adding maintainer

* Update var/spack/repos/builtin/packages/fish/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-10-06 20:42:45 +00:00
Manuela Kuhn
b787065bdb py-scikit-image: add 0.18.3 and fix dependencies (#26406) 2021-10-06 15:30:27 -05:00
Jen Herting
3945e2ad93 New package: py-clean-text (#26511)
* [py-clean-text] created template

* [py-clean-text]

- added description
- added dependencies
- removed fixmes
2021-10-06 19:44:33 +00:00
Tamara Dahlgren
affd2236e6 Provide more info in SbangPathError to aid CI debugging (#26316) 2021-10-06 21:03:33 +02:00
Kevin Pedretti
cb5b28392e Patch from upstream needed to build numactl on riscv64. (#26541)
The most recent release of numactl (2.0.14) fails to build on riscv64
because of a missing "-latomic". This patch from upstream resolves this
issue. It can be dropped once the next version of numactl is released.
2021-10-06 11:50:21 -07:00
Rodrigo Ceccato de Freitas
b1f7b39a06 ucx: fix typo in config description (#26564) 2021-10-06 18:44:22 +00:00
Manuela Kuhn
770c4fd0b2 py-nipype: add 1.4.2 (#26472) 2021-10-06 20:35:42 +02:00
Massimiliano Culpo
98ee00b977 Restore the correct computation of stores in environments (#26560)
Environments push/pop scopes upon activation. If some lazily
evaluated value depending on the current configuration was
computed and cached before the scopes are pushed / popped
there will be an inconsistency in the current state.

This PR fixes the issue for stores, but it would be better
to move away from global state.
2021-10-06 11:32:26 -07:00
Jose E. Roman
fdf76ecb51 New release slepc4py 3.16.0 (#26468) 2021-10-06 11:18:53 -07:00
Manuela Kuhn
9a75f44846 py-svgutils: add 0.3.1 (#26470) 2021-10-06 11:15:36 -07:00
haralmha
6ce4d26c25 Add 1.4.2 (#26475) 2021-10-06 11:13:55 -07:00
haralmha
8fc04984ba Add 1.9.3 (#26483) 2021-10-06 11:10:58 -07:00
haralmha
cfde432b19 Add 1.1.1 (#26484) 2021-10-06 11:10:05 -07:00
haralmha
ae9428df84 Add 14.16.1 (#26485) 2021-10-06 11:09:06 -07:00
haralmha
533705f4e3 Add 1.0.2 (#26486) 2021-10-06 10:50:28 -07:00
haralmha
2b6d7cc74c Add 4.2.0 (#26498) 2021-10-06 10:35:04 -07:00
g-mathias
9978353057 New package: intel oneapi advisor (#26535)
Co-authored-by: lu64bag3 <gerald.mathias@lrz.de>
2021-10-06 10:28:55 -07:00
Massimiliano Culpo
319ae9254e Remove the spack.architecture module (#25986)
The `spack.architecture` module contains an `Arch` class that is very similar to `spack.spec.ArchSpec` but points to platform, operating system and target objects rather than "names". There's a TODO in the class since 2016:

abb0f6e27c/lib/spack/spack/architecture.py (L70-L75)

and this PR basically addresses that. Since there are just a few places where the `Arch` class was used, here we query the relevant platform objects where they are needed directly from `spack.platforms`. This permits to clean the code from vestigial logic.

Modifications:
- [x] Remove the `spack.architecture` module and replace its use by `spack.platforms`
- [x] Remove unneeded tests
2021-10-06 10:28:12 -07:00
g-mathias
232086c6af new package: intel oneapi inspector (#26549)
Co-authored-by: lu64bag3 <gerald.mathias@lrz.de>
2021-10-06 10:25:18 -07:00
Danny McClanahan
e2e8e5c1e2 use conflicts() instead of referring to SpecError in mesa (#26562)
* mesa: use conflicts() instead of referring to SpecError
2021-10-06 10:07:42 -07:00
Paul R. C. Kent
fefe624141 llvm: new version 13.0.0 (#26563) 2021-10-06 16:53:49 +00:00
Alec Scott
4732c722e7 Add v1.56.2 to Rclone (#26556) 2021-10-06 09:53:34 -07:00
Alec Scott
97407795f6 Add v5.3.0 to Superlu (#26558) 2021-10-06 09:50:12 -07:00
haralmha
fe723b2ad8 py-jupyter-client: add 6.1.12 (#26503) 2021-10-06 09:21:10 -04:00
haralmha
d27bb7984a py-ptyprocess: add 0.7.0 (#26504) 2021-10-06 09:20:30 -04:00
haralmha
a59d6be99b py-setuptools: add 57.1.0 (#26505) 2021-10-06 09:19:49 -04:00
haralmha
ceb962fe17 py-six: add 1.16.0 (#26506) 2021-10-06 09:18:55 -04:00
Manuela Kuhn
11bdd18b1f py-matplotlib: fix qhull dependency (#26553) 2021-10-06 09:18:11 -04:00
Jen Herting
b92fd08028 py-ftfy: added version 6.0.3 (#26509) 2021-10-06 08:51:15 -04:00
Jen Herting
bc152fc6c4 New package: py-emoji (#26510)
* [py-emoji] created template

* [py-emoji]

- removed fixmes
- added homepage
- added description
- added dependencies
2021-10-06 08:50:24 -04:00
Frédéric Simonis
51f77f8af1 precice: add version 2.3.0 (#26551) 2021-10-06 08:44:59 -04:00
haralmha
8366f87cbf gnuplot: add version 5.4.2 (#26529) 2021-10-06 08:41:49 -04:00
haralmha
ab5962e997 hadoop: add version 2.7.5 (#26530) 2021-10-06 08:41:28 -04:00
haralmha
943f1e7a3a Add 7.6.3 (#26502) 2021-10-06 14:04:48 +02:00
Ivan Maidanski
1d258151f3 bdw-gc: add v8.0.6 (#26545) 2021-10-06 07:24:51 -04:00
haralmha
2cdfa33677 Add 6.0.2 (#26501) 2021-10-06 13:19:29 +02:00
haralmha
199bd9f8f8 py-decorator: Add version 5.0.9 and 5.10. (#26500)
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2021-10-06 02:24:47 +00:00
haralmha
0c02f6c36d py-hepdata-validator: Add version 0.2.3 and 0.3.0 (#26496)
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2021-10-06 02:15:06 +00:00
haralmha
c97c135f1d py-heapdict: Add version 1.0.0 (#26495)
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2021-10-06 01:16:18 +00:00
haralmha
d07c366408 Add 1.28.1 (#26494)
py-grpcio: Add version 1.28.1
2021-10-06 02:27:55 +02:00
haralmha
df93becc99 Add 2021.4.1 (#26493)
py-distributed: Add version 2021.4.1
2021-10-06 02:26:05 +02:00
haralmha
5e9497e05a Add 0.7.1 (#26492)
py-defusedxml: add version 0.7.1
2021-10-06 02:25:04 +02:00
haralmha
2e28281f1a py-bleach: Add version 3.3.1 (#26490)
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2021-10-06 00:18:09 +00:00
haralmha
e8b9074300 py-dask: add version 2021.4.1 (#26491) 2021-10-06 02:17:52 +02:00
haralmha
eafa0ff085 py-pygdal: Add versions 3.3.0.10 and 3.3.2.10 (#26528)
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2021-10-05 23:57:59 +00:00
haralmha
b20e7317ab py-backcall: Add version 0.2.0 (#26487) 2021-10-06 01:55:27 +02:00
haralmha
2773178897 Add versions 3.1.6, 3.1.7 and 3.2.0 (#26527) 2021-10-06 01:48:18 +02:00
Bernhard Kaindl
e39866f443 h5utils: Fix build and add new version (#26133)
@1.12.1+png depends_on libpng@:1.5.0 because it needs the old API

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2021-10-05 23:13:02 +00:00
Massimiliano Culpo
d7fc17d5db Set explicitly write permission for packages (#26539) 2021-10-05 23:12:25 +00:00
Olivier Cessenat
cc6508ec09 vtk: gui support for vtk 9 added (#25636) 2021-10-05 22:54:39 +00:00
haralmha
3157a97743 Add version 3.16.1 (#26534) 2021-10-06 00:27:17 +02:00
haralmha
aac7e28ea0 dd4hep: Add version 01-18 (#26525)
* Add 01-18

* Keep master on top and change version name format
2021-10-05 17:37:31 -04:00
Kevin Pedretti
47607dcac5 Use gnuconfig package for config file replacement for RISC-V. (#26364)
* Use gnuconfig package for config file replacement for RISC-V.

This extends the changes in #26035 to handle RISC-V. Before this change,
many packages fail to configure on riscv64 due to config.guess being too
old to know about RISC-V. This is seen out of the box when clingo fails
to build from source due to pkgconfig failing to configure, throwing
error: "configure: error: cannot guess build type; you must specify one".

* Add riscv64 architecture

* Update vendored archspec from upstream project.
These archspec updates include changes needed to support riscv64.

* Update archspec's __init__.py to reflect the commit hash of archspec being used.
2021-10-05 19:22:55 +00:00
Harmen Stoppels
d998ea1bd4 Move shell aware env into spack.environment.shell (#25608)
Cherry-picked from #25564 so this is standalone.

With this PR we can activate an environment in Spack itself, without computing changes to environment variables only necessary for "shell aware" env activation.

1. Activating an environment:
    
    ```python
    spack.environment.activate(Environment(xyz)) -> None
    ```
    this basically just sets `_active_environment` and modifies some config scopes.

2. Activating an environment **and** getting environment variable modifications for the shell:

    ```python
    spack.environment.shell.activate(Environment(xyz)) -> EnvironmentModifications
    ```

This should make it easier/faster to do unit tests and scripting with spack, without the cli interface.
2021-10-05 18:25:43 +00:00
haralmha
713bbdbe7c postgresql: Add versions 14.0 and 12.2 (#26499) 2021-10-05 13:34:46 +02:00
haralmha
789beaffb7 doxygen: Add versions 1.9.2 and 1.8.18 (#26497) 2021-10-05 12:49:48 +02:00
Ricardo Jesus
4ee74c01e3 meme: Fix compilation with arm and nvhpc compilers (#24883)
* Fix compilation with `arm` and `nvhpc` compilers

* Update package.py
2021-10-05 05:55:12 -04:00
Jonas Thies
7f2fd50d20 phist: add a patch for the case +host arch=ppc64le (#26216) 2021-10-05 08:33:41 +00:00
Guilherme Perrotta
7ea9c75494 py-flatbuffers: add new package (#26444)
Python port of the "flatbuffers" package
2021-10-05 10:10:43 +02:00
Ivan Maidanski
1a651f1dca libatomic_ops: add v7.6.12 (#26512) 2021-10-05 10:08:57 +02:00
Manuela Kuhn
4e6f2ede0a py-rsatoolbox: add new package (#26514) 2021-10-05 10:07:03 +02:00
Axel Huebl
e1fb77496c WarpX: 21.10 (#26507) 2021-10-05 10:01:26 +02:00
David Gardner
85de527668 sundials: Add 5.8.0 and sycl variant (#26524) 2021-10-05 10:00:11 +02:00
Heiko Bauke
f6a4f6bda7 mpl: add new package (#26522) 2021-10-05 09:59:14 +02:00
Mihael Hategan
95846ad443 py-parsl: new package (see https://parsl-project.org/) (#26360) 2021-10-05 09:53:02 +02:00
Massimiliano Culpo
337b54fab0 Isolate bootstrap configuration from user configuration (#26071)
* Isolate bootstrap configuration from user configuration

* Search for build dependencies automatically if bootstrapping from sources

The bootstrapping logic will search for build dependencies
automatically if bootstrapping anything form sources. Any
external spec, if found, is written in a scope that is specific
to bootstrapping.

* Don't clean the bootstrap store with "spack clean -a"

* Copy bootstrap.yaml and config.yaml in the bootstrap area
2021-10-05 09:16:09 +02:00
Seth R. Johnson
3cf426df99 zstd: fix install name on macOS (#26518)
Reverting from CMake to Make install caused
`-install_path=/usr/local/lib/libzstd.1.dylib` to be hardcoded into the
zstd. Now we explicitly pass the PREFIX into the build command so that
the correct spack install path is saved.

Fixes #26438 and also the ROOT install issue I had :)
2021-10-05 02:03:48 +00:00
Nisarg Patel
b5673d70de molden: fix build with gcc@10: (#25803) 2021-10-05 01:36:20 +00:00
Todd Gamblin
84c878b66a cc: make error messages more clear
- [x] Our wrapper error messages are sometimes hard to differentiate from other build
      output, so prefix all errors from `die()` with '[spack cc] ERROR:'

- [x] The error we raise when running, say, `fc` without a Fortran compiler was not
      clear enough. Clarify the message and the comment.
2021-10-04 18:30:19 -07:00
Todd Gamblin
052b2e1b08 cc: convert compiler wrapper to posix shell
This converts everything in cc to POSIX sh, except for the parts currently
handled with bash arrays. Tests are still passing.

This version tries to be as straightforward as possible. Specifically, most conversions
are kept simple -- convert ifs to ifs, handle indirect expansion the way we do in
`setup-env.sh`, only mess with the logic in `cc`, and don't mess with the python code at
all.

The big refactor is for arrays. We can't rely on bash's nice arrays and be ignorant of
separators anymore. So:

1. To avoid complicated separator logic, there are three types of lists. They are:

    * `$lsep`-separated lists, which end with `_list`. `lsep` is customizable, but we
      picked `^G` (alarm bell) for `$lsep` because it's ASCII and it's unlikely that it
      would actually appear in any arguments. If we need to get fancier (and I will lose
      faith in the world if we do) then we could consider XON or XOFF.
    * `:`-separated directory lists, which end with `_dirs`, `_DIRS`, `PATH`, or `PATHS`
    * Whitespace-separated lists (like flags), which can have any other name.

    Whitespace and colon-separated lists come with the territory with PATHs from env
    vars and lists of flags. `^G` separated lists are what we use for most internal
    variables, b/c it's more likely to work.

2. To avoid subshells, use a bunch of functions that do dirty `eval` stuff instead. This
   adds 3 functions to deal with lists:

    * `append LISTNAME ELEMENT [SEP]` will put `ELEMENT` at the end of the list called
      `LISTNAME`. You can optionally say what separator you expect to use. Note that we
      are taking advantage of everything being global and passing lists by name.

    * `prepend LISTNAME ELEMENT [SEP]` like append, but puts `ELEMENT` at the start of
      `LISTNAME`

    * `extend LISTNAME1 LISTNAME2 [PREFIX]` appends everything in LISTNAME2 to
       LISTNAME1, and optionally prepends `PREFIX` to every element (this is useful for
       things like `-I`, `-isystem `, etc.

    * `preextend LISTNAME1 LISTNAME2 [PREFIX]` prepends everything in LISTNAME2 to
       LISTNAME1 in order, and optionally prepends `PREFIX` to every element.

The routines determine the separator for each argument by its name, so we don't have to
pass around separators everywhere. Amazingly, as long as you do not expand variables'
values within an `eval` environment, you can do all this and still preserve quoting.
When iterating over lists, the user of this API still has to set and unset `IFS`
properly.

We ended up having to ignore shellcheck SC2034 (unused variable), because using evals
all over the place means that shellcheck doesn't notice that our list variables are
actually used.

So far this is looking pretty good. I took the most complex unit test I could find
(which runs a sample link line) and ran the same command line 200 times in a shell
script.  Times are roughly as follows:

For this invocation:

```console
$ bash -c 'time (for i in `seq 1 200`; do ~/test_cc.sh > /dev/null; done)'
```

I get the following performance numbers (the listed shells are what I put in `cc`'s
shebang):

**Original**
* Old version of `cc` with arrays and `bash v3.2.57` (macOS builtin): `4.462s` (`.022s` / call)
* Old version of `cc` with arrays and `bash v5.1.8` (Homebrew): `3.267s` (`.016s` / call)

**Using many subshells (#26408)**
*  with `bash v3.2.57`: `25.302s` (`.127s` / call)
*  with `bash v5.1.8`: `27.801s` (`.139s` / call)
*  with `dash`: `15.302s` (`.077s` / call)

This version didn't seem to work with zsh.

**This PR (no subshells)**
*  with `bash v3.2.57`: `4.973s` (`.025s` / call)
*  with `bash v5.1.8`: `4.984s` (`.025s` / call)
*  with `zsh`: `2.995s` (`.015s` / call)
*  with `dash`: `1.890s` (`.0095s` / call)

Dash, with the new posix design, is easily the winner.

So there are several interesting things to note here:

1. Running the posix version in `bash` is slower than using `bash` arrays. That is to be
   expected because it's doing a bunch of string processing where it likely did not have
   to before, at least in `bash`.

2. `zsh`, at least on macOS, is significantly faster than the ancient `bash` they ship
   with the system. Using `zsh` with the new version also makes the posix wrappers
   faster than `develop`. So it's worth preferring `zsh` if we have it. I suppose we
   should also try this with newer `bash` on Linux.

3. `bash v5.1.8` seems to be significantly faster than the old system `bash v3.2.57` for
   arrays. For straight POSIX stuff, it's a little slower. It did not seem to matter
   whether `--posix` was used.

4. `dash` is way faster than `bash` or `zsh`, so the real payoff just comes from being
   able to use it. I am not sure if that is mostly startup time, but it's significant.
   `dash` is ~2.4x faster than the original `bash` with arrays.

So, doing a lot of string stuff is slower than arrays, but converting to posix seems
worth it to be able to exploit `dash`.

- [x] Convert all but array-related portions to sh
- [x] Fix basic shellcheck issues.
- [x] Convert arrays to use a few convenience functions: `append` and `extend`
- [x] Get `cc` tests passing.
- [x] Add `cc` tests where needed passing.
- [x] Benchmarking.

Co-authored-by: Tom Scogland <scogland1@llnl.gov>
Co-authored-by: Danny McClanahan <1305167+cosmicexplorer@users.noreply.github.com>
2021-10-04 18:30:19 -07:00
Todd Gamblin
472638f025 .gitignore needs to be below env and ENV for case-insensitive FS 2021-10-04 18:30:19 -07:00
haralmha
8d0025b8af Add 5.2.0 (#26481) 2021-10-04 19:37:34 -05:00
Martin Pokorny
32f8dad0e2 log4cxx: new version and fix for c++11 (#26480)
* Add version 0.12.1

* Add variant to build with C++11 standard

build with c++11 standard requires boost threads, and needs explicit setting of
CMAKE_CXX_STANDARD
2021-10-05 00:34:03 +00:00
KoyamaSohei
c426386f46 intel-tbb: install pkgconfig file (#23977)
* intel-tbb: install pkgconfig file

* intel-tbb: install pkgconfig file when @:2021.2.0

* intel-tbb: add blank line

* intel-tbb: fix library name to refer

* intel-tbb: fix library name to refer again

* intel-tbb: use self.prefix.lib.pkgconfig
2021-10-04 21:38:31 +00:00
Tamara Dahlgren
5a9e5ddb3d Stand-alone tests: distinguish NO-TESTS from PASSED (#25880)
Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>
2021-10-04 19:57:08 +00:00
snehring
675bdada49 esys-particle: add new package esys-particle (#25338)
* esys-particle: add new package esys-particle

* esys-particle: requested changes

* esys-particle: placating isort
2021-10-04 19:41:31 +00:00
Daniel Ahlin
c59223effe gcc: apply nvcc patch to more versions (#24295)
Apply to all known affected versions (10.1.0 to 10.3.0 and 11.1.0)
2021-10-04 21:02:57 +02:00
haralmha
6a6bc3ecbb git: new version 2.29.2 (#26478) 2021-10-04 18:23:38 +00:00
iarspider
b88c80bb1b Add new pythia8 variants and fix url_for_version (#26280)
* Add new pythia8 variants
Add proper description to the existing ones

* Flake-8

* Flake-8

* Style

* Fix Pythia8 recipe

* Fix typo in variant description

* Update package.py
2021-10-04 12:52:51 -05:00
haralmha
b9e8d2d648 cppgsl: new version 3.1.0 (#26477) 2021-10-04 13:25:44 -04:00
Manuela Kuhn
377c781d7e py-scikit-learn: add 0.19.2 and 0.22.2.post1 (#26473) 2021-10-04 18:48:26 +02:00
snehring
9a8712f4cb masurca: Fix build with glibc-2.32+ (#26173)
remove sysctl.h which is not used by the build
2021-10-04 17:59:01 +02:00
Pedro Demarchi Gomes
90fa50d9df Avoid replacing symlinked spack.yaml when concretizing an environment (#26428) 2021-10-04 14:59:03 +00:00
Pedro Demarchi Gomes
4ae71b0297 use umpire version 5.0.1:5 (#26451) 2021-10-04 16:32:47 +02:00
Vicente Bolea
572791006d paraview: add v5.10.0-RC1 release (#26291) 2021-10-04 09:32:03 -04:00
mcuma
fa528c96e6 octave: add support for MKL (#25952) 2021-10-04 14:57:57 +02:00
iarspider
4f1c195bf9 grpc: update recipe (#25261)
1) forward `+shared` to re2
2) add `cxxstd` variant
3) use "more idiomatic" way of setting CMake options
2021-10-04 14:53:17 +02:00
Andreas Baumbach
35dd474473 Improve an error message in stage.py (#23737) 2021-10-04 14:47:14 +02:00
Tiziano Müller
2ca58e91d6 cp2k: bugfix for intel oneapi (#26143) 2021-10-04 14:41:49 +02:00
Oliver Perks
ad98e88173 arm: added download and better detection (#25460) 2021-10-04 14:35:20 +02:00
Harmen Stoppels
e557730c96 gnupg: Add version 1 (#23798)
From the gnupg.org website:

> GnuPG 1.4 is the old, single binary version which still support the
> unsafe PGP-2 keys. However, it lacks many modern features and will
> receive only important updates.

I'm starting to appreciate gpg1 more, because it is relocatable (gng2
has hard-coded paths to gpg-agent and other tools) and it does not
require gpg-agent at all.
2021-10-04 08:29:41 -04:00
iarspider
50b1b654c9 evtgen: fix mac build and version 2.0.0 with pythia >= 8.304. (#25933) 2021-10-04 14:06:49 +02:00
Manuela Kuhn
e9accaaca1 py-duecredit: add v0.6.5 (#26465) 2021-10-04 14:01:12 +02:00
Manuela Kuhn
68648b3ff5 py-nibabel: add v2.4.1 (#26462) 2021-10-04 14:00:49 +02:00
Valentin Volkl
e4d5bcf916 podio: remove build_type variant (provided by base package class already) (#26463) 2021-10-04 14:00:20 +02:00
Bernhard Kaindl
3fff338844 freebayes: Fix running the testsuite and add pkgconfig (#26440)
freebayes needs the tools of the vcflib it includes to run tests
2021-10-04 14:00:08 +02:00
Nikolay Simakov
225927c1c3 graph500: added option -fcommon for gcc@10.2 (#25367)
* graph500: added option -fcommon for gcc@10.2:, otherwise failed to build with "multiple definition of `column'"

* graph500: moved setting cflag to flag_handler
2021-10-04 13:42:33 +02:00
iarspider
bf9cf87d9b libunwind: add variants (#26099) 2021-10-04 13:04:39 +02:00
Manuela Kuhn
f1839c6aae py-pybids: add v0.9.5 (#26461) 2021-10-04 10:35:06 +00:00
Harmen Stoppels
d84d7f0599 Disable tests on hip for cmake 3.21 (#26460) 2021-10-04 10:20:07 +00:00
Manuela Kuhn
e2ee3066cf py-mne: add new package (#26446) 2021-10-04 09:56:58 +00:00
Manuela Kuhn
1f451924b1 py-sphinxcontrib-napoleon: add new package (#26457) 2021-10-04 09:52:56 +00:00
Manuela Kuhn
8bcbead42b py-templateflow: add new package (#26458) 2021-10-04 09:47:37 +00:00
Dylan Simon
9926799aeb Fix NonVirtualInHierarchyError message format (#26008) 2021-10-04 10:38:09 +02:00
Seth R. Johnson
205b414162 hdf5: allow implicit functions on apple-clang (#26409)
Work around issues in older hdf5 build and overzealous build flags:
```
 >> 1420    /var/folders/j4/fznvdyhx4875h6fhkqjn2kdr4jvyqd/T/9te/spack-stage/spack-stage-hdf5-1.10.4-feyl6tz6hpx5kl7m33avpuacwje2ubul/spack-src/src/H5Odeprec.c:141:8: error: implicit decl
             aration of function 'H5CX_set_apl' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
```
2021-10-04 10:19:56 +02:00
Seth R. Johnson
5d431087ab python: correctly disable ~tkinter when @3.8 (#26365)
The older patch does not apply so the build ends up failing:
```
     1539    In file included from /private/var/folders/fy/x2xtwh1n7fn0_0q2kk29xkv9vvmbqb/T/s3j/spack-stage/spack-stage-python-3.8.11
             -6jyb6sxztfs6fw26xdbc3ktmbtut3ypr/spack-src/Modules/_tkinter.c:48:
  >> 1540    /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/tk.h:86:11: f
             atal error: 'X11/Xlib.h' file not found
     1541    #       include <X11/Xlib.h>
     1542                    ^~~~~~~~~~~~
     1543    1 error generated.
```
2021-10-04 10:18:23 +02:00
iarspider
7104b8599e Update byacc (#25837)
Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2021-10-04 09:55:20 +02:00
G-Ragghianti
7009724f0d papi: new variants rocm and rocm_smi (#26214) 2021-10-04 09:53:17 +02:00
Manuela Kuhn
81abbb41bc git-annex: add 8.20210804 for amd64 (#26449) 2021-10-04 09:50:05 +02:00
Manuela Kuhn
d0da7c8440 py-pockets: add new package (#26452) 2021-10-04 09:43:10 +02:00
Massimiliano Culpo
69abc4d860 Build ppc64le docker images (#26442)
* Update archspec
* Add ppc64le to docker images
2021-10-04 09:34:53 +02:00
Massimiliano Culpo
e91815de7c Update Spec.full_hash docstring (#26456)
The docstring is outdated since #21735
when the build hash has been included
in the full hash.
2021-10-04 07:33:22 +00:00
Garth N. Wells
baa50c6679 FEniCSx: fix CMake root directory and dependency versions (#26445) 2021-10-04 09:20:53 +02:00
Manuela Kuhn
44d7218038 py-seaborn: add v0.11.2 (#26447) 2021-10-04 09:17:38 +02:00
Manuela Kuhn
9e0aabdef3 py-transforms3d: add new package (#26448) 2021-10-04 09:17:04 +02:00
Joseph Wang
91598912f7 ocaml: add v4.13.1 (#26453)
This is needed in order to make it work with glibc-2.34
2021-10-04 08:47:30 +02:00
Daniel Arndt
862bcc5059 ArborX: Explicitly set path to Kokkos (#26347)
* Explicitly set path to Kokkos for ArborX testing

* Improve formatting

* Update var/spack/repos/builtin/packages/arborx/package.py

Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>

* Remove blank line

Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>
2021-10-03 23:04:52 -04:00
Hector
2f6590ddd1 source-highlight: add gcc11 patch (#26412) 2021-10-03 16:07:39 +00:00
Lorién López Villellas
c0b383b3e1 PICSAR: added support for GCC >10.0 and arm compiler (#24927)
* -fallow-argument-mismatch flag added when compiling with GCC to avoid a compilation error when using a GCC version > 10.0.

Co-authored-by: Haz99 <jsalamerosanz@gmail.com>

* Filtered every occurrence of "!$OMP SIMD SAFELEN(LVEC2)" when compiling with nvhcp to avoid a compilation error.

Co-authored-by: Haz99 <jsalamerosanz@gmail.com>

* Line with more than 80 characters split into multiple lines.

Co-authored-by: Haz99 <jsalamerosanz@gmail.com>
2021-10-03 10:11:04 -04:00
Jordan Galby
0d6a2381b2 Fix JSONDecodeError when using compiler modules (#25624)
When using modules for compiler (and/or external package), if a
package's `setup_[dependent_]build_environment` sets `PYTHONHOME`, it
can influence the python subprocess executed to gather module
information.

The error seen was:

```
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
```

But the actual hidden error happened in the `python -c 'import
json...'` subprocess, which made it return an empty string as json:

```
ModuleNotFoundError: No module named 'encodings'
```

This fix uses `python -E` to ignore `PYTHONHOME` and
`PYTHONPATH`. Should be safe here because the python subprocess code
only use packages built-in python.

The python subprocess in `environment.py` was also patched to be safe
and consistent.
2021-10-03 16:10:33 +02:00
Harmen Stoppels
b9e72557e8 Remove .99 from version ranges (#26422)
In most cases, .99 can be omitted thanks to #26402 .
2021-10-03 09:09:02 -04:00
Tim Moon
2de116d285 DiHydrogen: Specify required NVSHMEM variants (#26384) 2021-10-03 08:30:27 -04:00
Bernhard Kaindl
f6ce95bfcb chombo: several build fixes: csh, space regex and install (#26424)
See description of the the PR for details on the changes.
2021-10-03 14:28:28 +02:00
Harmen Stoppels
e53bd0eba8 bison: new versions 3.8:3.8.2 (#26439) 2021-10-03 07:57:03 -04:00
Takahiro Ueda
d603f4519d form: use version tarballs, fix and enable gmp and zlib variants (#26425)
Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
Co-authored-by: iarspider <iarspider@gmail.com>
2021-10-03 08:45:33 +00:00
Michael Kuhn
d4b3724557 meson: add 0.59.2 (#26430) 2021-10-03 10:41:08 +02:00
Michael Kuhn
abce326ea3 openblas: add 0.3.18 (#26429) 2021-10-03 10:38:48 +02:00
Manuela Kuhn
4c1285b1c2 py-svgutils: new package (#26437) 2021-10-03 02:38:36 +02:00
Marc Fehling
34a1e4d8b6 p4est: bump/update to 2.8 (#26081) 2021-10-03 01:56:03 +02:00
Manuela Kuhn
ee568cb6a4 py-packaging: bump version to 21.0 (#26436) 2021-10-02 23:31:24 +00:00
Manuela Kuhn
0db072dc4a py-attrs: bump version to 21.2.0 (#26435) 2021-10-02 23:23:02 +00:00
Manuela Kuhn
6a188b2b13 py-nitransforms: new package (#26434) 2021-10-03 01:06:13 +02:00
Wouter Deconinck
846428a661 podio: add supported CMAKE_BUILD_TYPE values (#26432) 2021-10-03 00:38:36 +02:00
Manuela Kuhn
aee1d44edf py-pybids: bump version to 0.13.2 (#26433) 2021-10-03 00:36:02 +02:00
Sreenivasa Murthy Kolam
f1c83b00d4 atmi: replace /usr/bin/rsync with depends_on rsync (#26353) 2021-10-03 00:32:46 +02:00
Manuela Kuhn
8dcd568769 py-ipyvtk-simple: new package (#26431) 2021-10-02 23:18:08 +02:00
Josh Bowden
aaf35fd520 damaris: bump version to 1.5.0, add variant examples (#26220) 2021-10-02 23:06:17 +02:00
Manuela Kuhn
bc6edc7baf py-ipycanvas: new package (#26426) 2021-10-02 22:30:09 +02:00
Olivier Cessenat
2ce3be3a27 fltk: new version 1.3.7, new variant xft (#26423) 2021-10-02 16:27:38 -04:00
Manuela Kuhn
b65360f721 py-ipyevents: add new package (#26427) 2021-10-02 22:23:09 +02:00
Robert Romero
57803887e8 cddlib: use github URLs and bump version (#26315)
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2021-10-02 19:50:32 +00:00
Weiqun Zhang
43e08af7b2 amrex: bump version to 21.10 (#26416) 2021-10-02 18:25:50 +02:00
Massimiliano Culpo
0e469fc01e clingo-bootstrap: add a variant for static libstdc++ (#26421) 2021-10-02 14:53:24 +02:00
Mihael Hategan
b3d3ce1c37 py-pytest-random-order: new package - plugin for py-pytest. (#26413) 2021-10-02 12:38:09 +02:00
Rob Falgout
d9f25f223f Add hypre release 2.23.0 (#26418) 2021-10-02 09:52:50 +02:00
Howard Pritchard
3575c14a6a ucx: add version 1.11.2 (#26417)
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2021-10-02 09:49:48 +02:00
Wouter Deconinck
314f5fdb97 New versions: geant4@10.7.2, geant4-data@10.7.2 (#25449)
* [geant4] new version 10.7.2

* [geant4-data] new version 10.7.2
2021-10-01 17:08:15 -07:00
Mihael Hategan
d8f23c0f6d Added py-typeguard package. (#26411)
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2021-10-01 23:58:39 +00:00
Harmen Stoppels
d0e49ae4bb Simplify setup_package in build environment (#26070)
* Remove redundant preserve environment code in build environment

* Remove fix for a bug in a module

See https://github.com/spack/spack/issues/3153#issuecomment-280460041,
this shouldn't be part of core spack.

* Don't module unload cray-libsci on all platforms
2021-10-01 19:41:30 -04:00
Cory Bloor
b6169c213d Fix error message when test throws AttributeError (#25895)
Narrow the scope of the try/except block, to avoid a misleading
error message if fn() throws an AttributeError.
2021-10-01 19:40:24 -04:00
Mihael Hategan
d19105f761 Added py-sqlalchemy-stubs package. (#26414)
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2021-10-01 21:50:55 +00:00
bernhardkaindl
9893718f78 axel(download manager): fix build, bump version (#26140) 2021-10-01 23:48:33 +02:00
Seth R. Johnson
2f630226e7 trilinos: add conflict and enable gtest for developers (#26150) 2021-10-01 15:53:16 -04:00
Harmen Stoppels
50feaae81c Allow non-empty ranges 1.1.0:1.1 (#26402) 2021-10-01 12:23:26 -07:00
Chris Richardson
bce269df13 Fenicsx update dependency and build for main branch (#25864)
* Updates to make it work again for main
* Use property

Co-authored-by: Chris <cnr12@cam.ac.uk>
2021-10-01 12:05:19 -07:00
Harmen Stoppels
18760de972 Spack install: handle failed restore of backup (#25647)
Spack has logic to preserve an installation prefix when it is being
overwritten: if the new install fails, the old files are restored.
This PR adds error handling for when this backup restoration fails
(i.e. the new install fails, and then some unexpected error prevents
restoration from the backup).
2021-10-01 11:40:48 -07:00
Olivier Cessenat
df590bb6ee hypre: add version 2.22.1; add fortran variant; becomes AutotoolsPackage (#25781) 2021-10-01 11:31:24 -07:00
bernhardkaindl
da171bd561 uftrace(dynamic function graph tracer): bump version (#26224) 2021-10-01 18:28:25 +00:00
Luciano Zago
f878f769a2 gh: add new package (#26405) 2021-10-01 17:58:47 +00:00
bernhardkaindl
ffb6597808 xrootd: Add current version 5.3.1 and restrict to openssl@1 (#26303) 2021-10-01 17:50:35 +00:00
Piotr Luszczek
f75ad02ba2 Add new package: ffte (#26340) 2021-10-01 17:27:38 +00:00
Scott Wittenburg
9f09156923 Retry pipeline generation jobs in certain cases 2021-10-01 10:12:37 -07:00
Scott Wittenburg
d11156f361 Add DAG scheduling to child pipelines 2021-10-01 10:12:37 -07:00
Scott Wittenburg
4637c51c7f Service jobs do not need an active environment 2021-10-01 10:12:37 -07:00
Scott Wittenburg
d233c20725 Activate concrete env dir in all service jobs 2021-10-01 10:12:37 -07:00
Scott Wittenburg
5f527075bf Use same image to build e4s as to generate it 2021-10-01 10:12:37 -07:00
Scott Wittenburg
f6fcfd2acc Use same image to build dvsdk as to generate it 2021-10-01 10:12:37 -07:00
Scott Wittenburg
ae092915ac Use default runner image for radiuss 2021-10-01 10:12:37 -07:00
Victor
98466f9b12 Add pmix variant to openmpi package (#26342)
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2021-10-01 18:43:55 +02:00
Manuela Kuhn
0735419592 py-traitsui: add v7.2.1 (#26392) 2021-10-01 15:57:21 +00:00
Daniel Arndt
7293913e1c DataTransferKit: add v3.1-rc3 (#26269) 2021-10-01 17:33:09 +02:00
Seth R. Johnson
f2ef34638d graphviz: macOS patch not needed on newer version (#26292)
The autoconf file was updated in 2.49.0 but is still needed in older
versions.
2021-10-01 17:30:23 +02:00
bernhardkaindl
6aff4831e3 cmor: bump version and depend on the specific libuuid packages needed by version. (#26149) 2021-10-01 17:29:39 +02:00
Georgiana Mania
7d77f36f83 eigen: add v3.4.0 (#26296) 2021-10-01 17:24:58 +02:00
haralmha
9c8041b8e4 hoppet: add new package (#26297)
Co-authored-by: Harald Minde Hansen <hahansen@office.dyndns.cern.ch>
2021-10-01 17:24:17 +02:00
Manuela Kuhn
eff5bd4005 py-coverage: add v5.5 (#26407) 2021-10-01 15:14:41 +00:00
Axel Huebl
177fe731b1 llvm-openmp: 12.0.1 (#26320)
Add the latest LLVM OpenMP release.
This one compiles for aarch64/M1 on mac.
2021-10-01 17:06:12 +02:00
bernhardkaindl
6b96486d42 py-gsutil: add v5.2 (#26337) 2021-10-01 17:03:54 +02:00
Daniel Arndt
f168d264d1 ArborX: add v1.1 (#26344) 2021-10-01 17:02:05 +02:00
Michael Kuhn
12dc01318e otf: Explicitly disable MPI and ZOIDFS (#26346)
Otherwise, global installations of MPI could be picked up by OTF.
2021-10-01 17:01:31 +02:00
bernhardkaindl
ad8b8b3377 damask-grid, damask-mesh: fix spack install --test=root (#26350) 2021-10-01 16:59:31 +02:00
Edgar Leon
4078c5e537 mpibind: add v0.7.0 and new flux variant (#26359) 2021-10-01 16:56:22 +02:00
Adam Moody
60aa97b25f LWGRP: add v1.0.4 DTCMP: add v1.1.2 and v1.1.3 (#26362) 2021-10-01 16:42:10 +02:00
Satish Balay
6362b3014a petsc,py-petsc4py add versions 3.15.5, 3.16.0 (#26375) 2021-10-01 16:37:28 +02:00
Christoph Conrads
07e91e8afa med: work around "could not find TARGET hdf5" error (#25312)
Fixes #24671, fixes #26051
2021-10-01 10:27:22 -04:00
Ryan Mast
c3c28d510f ns-3-dev: add v3.31, v3.32, v3.33, and v3.34 (#26383) 2021-10-01 16:15:39 +02:00
Pieter Ghysels
d765b4b53d STRUMPACK: add v6.0.0 (#26386)
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2021-10-01 16:12:41 +02:00
Manuela Kuhn
66866e45f2 py-pyface: add v7.3.0 (#26389) 2021-10-01 16:07:27 +02:00
Manuela Kuhn
ef202cbd37 py-ipywidgets: add 7.6.5 and get sources from pypi (#26393) 2021-10-01 16:06:25 +02:00
Mihael Hategan
e9609b62c6 Python Globus SDK (globus.org): add new package (#26395) 2021-10-01 16:05:49 +02:00
bernhardkaindl
da7666a967 py-pyside: restrict version of dependency on v1.2.2 (#26396)
Restrict @:1.2.2 to older sphinx versions to not fail the build
2021-10-01 16:04:36 +02:00
Manuela Kuhn
627c7007ef py-pyvista: add new package (#26398) 2021-10-01 16:00:30 +02:00
Anna Masalskaya
8fc770608d Add oneAPI packages from 2021.4 release (#26401) 2021-10-01 15:58:32 +02:00
Jose E. Roman
91f668a695 SLEPc: add v3.16 (#26403) 2021-10-01 15:55:42 +02:00
Manuela Kuhn
f775e81fca py-fury: add new package (#26404) 2021-10-01 15:53:50 +02:00
Harmen Stoppels
5b9f60f9bb bootstrapping: improve error messages (#26399) 2021-10-01 13:00:14 +02:00
bernhardkaindl
6ca42f0199 boost: @1.77.0: need updated python_jam.patch for +python (#26363)
One hunk changed and the new patch is refreshed using quilt.
2021-10-01 11:09:32 +02:00
Tamara Dahlgren
2d1ebbe0a2 Add info command tests to increase coverage (#26127) 2021-09-30 22:13:45 -04:00
Tamara Dahlgren
3feab42203 py-setuptools-rust: remove checksum url workaround (#25843) 2021-09-30 22:13:26 -04:00
Tamara Dahlgren
7aedeca764 Replace spec-related install_test asserts with exceptions; added unit tests (#25982) 2021-09-30 22:05:06 -04:00
Manuela Kuhn
c58cd83e38 py-shiboken2: add new package (#26390) 2021-10-01 01:19:41 +00:00
Manuela Kuhn
032ce20171 vtk: fix install path to lib (#26387) 2021-10-01 02:52:09 +02:00
Paul Spencer
046ed47b1f New package: slurm-drmaa (#25424)
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2021-10-01 00:07:03 +00:00
Manuela Kuhn
c076aeb192 py-jupyterlab: add new package (#26357) 2021-10-01 01:33:28 +02:00
Massimiliano Culpo
74d36076c2 ArchSpec: minor cleanup of a few methods (#26376)
* Remove vestigial code to be compatible with Spack v0.9.X
* ArchSpec: reworked __repr__ to be more adherent to common Python idioms
* ArchSpec: simplified __init__.py and copy()
2021-09-30 16:03:39 -07:00
Robert Underwood
a75c86f178 GDB: Fix for GMP and Python (#26366)
closes  #26354 and #26358

Previously we did not pass paths for GDB or GMP and ./configure would
get confused about which one to pull from.  Be more specific.

Built with all variants enabled and fixed the fixable versions and variants:
@:8.1 were fixable by limiting python versions for these to @:3.6.
7.10.1 and 7.11(.1) were fixable to build with glibc-2.25 and newer
using two long patches.
gdb 7.8 and 7.9 weren't fixable as there is no backport if the fix
to build these with glibc-2.25 and newer:
http://lists.busybox.net/pipermail/buildroot/2017-March/188055.html

Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2021-09-30 22:40:35 +00:00
Massimiliano Culpo
8ade8a77dd Build container images on Github Actions and push to multiple registries (#26247)
Modifications:
- Modify the workflow to build container images without pushing when the workflow file itself is modified
- Strip the leading ghcr.io/spack/ from env.container env.versioned to prepare pushing to multiple registries
- Fixed CentOS 7 and Amazon Linux builds
- Login and push to Docker Hub as well as Github Action
- Add a badge to README.md with the status of docker images
2021-09-30 23:34:47 +02:00
Jen Herting
7bda430de0 [py-tabulate] added version 0.8.9 (#25974) 2021-09-30 23:02:14 +02:00
Cory Bloor
4238318de2 rocsolver: Tighten rocsolver package dependencies (#25917)
- Specify CMake minimum version more precisely
- Ensure rocBLAS is available at build time
- Limit workaround for missing rocblas include path
  to the only affected version (4.1.0)
- Make hip a build and link dependency
- Remove hip's link dependencies

Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2021-09-30 22:57:28 +02:00
Robert Underwood
7694c58736 sz: fix for external python sitelib (#26067)
fixes #25973
2021-09-30 11:52:20 -07:00
bernhardkaindl
af54f7b15b gromacs-chain-coordinate: Fix calling the test suite (#26367) 2021-09-30 18:18:03 +02:00
Harmen Stoppels
1aa7758dbb match .spack literal, not as a regex (#26374) 2021-09-30 14:54:57 +00:00
Harmen Stoppels
727dcef2f4 Disable __skip_rocmclang again (#26187)
CMake 3.21.3 disables the broken hipcc-as-rocmclang detection again.

From the release notes:

> The AMD ROCm Platform hipcc compiler was identifed by CMake 3.21.0
> through 3.21.2 as a distinct compiler with id ROCMClang. This has been
> removed because it caused regressions. Instead:
> * hipcc may no longer be used as a HIP compiler because it interferes
>   with flags CMake needs to pass to Clang. Use Clang directly.
> * hipcc may once again be used as a CXX compiler, and is treated as
>   whatever compiler it selects underneath, as CMake 3.20 and below
>   did.
2021-09-30 16:01:17 +02:00
Harmen Stoppels
4dee7d2b22 Add a conflict for patchelf to catch errors earlier in bootstrapping (#26373) 2021-09-30 15:18:56 +02:00
Harmen Stoppels
525aa11827 Bump version from v0.16.2 to v0.16.3 (#26372) 2021-09-30 11:54:48 +00:00
Olivier Cessenat
9e70fc630e dos2unix: new version 7.4.2 and enforce link with gettext (#26371) 2021-09-30 12:04:32 +02:00
Harmen Stoppels
b96d836a72 Move gnuconfig under the spack org (#26370) 2021-09-30 11:30:29 +02:00
Diego Alvarez
56eddf2e3c Added OpenJDK 17, 11 for Darwin, and set preferred to 11 (#26368) 2021-09-30 11:29:36 +02:00
Maciej Wójcik
7c3b2c1aa8 gromacs-chain-coordinate: new package (#25426) 2021-09-30 04:12:37 +02:00
Shahzeb Siddiqui
ef9967c7f4 Add e4s tags (#23382)
Add 'e4s' tags for all packages according to https://github.com/E4S-Project/e4s/blob/master/E4S_Products.md
2021-09-29 17:57:52 -07:00
acastanedam
02f356159b linux-pam: include more official (recent) releases (#26065) 2021-09-29 20:51:39 -04:00
David Beckingsale
d31830eaf5 Move new CUDA conflicts inside when('~allow-unsupported-compilers') block (#26132)
* Move new CUDA conflicts inside when('~allow-unsupported-compilers') block

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2021-09-30 00:22:26 +00:00
Valentin Volkl
2ea1bf84ec py-snappy: add patch to fix dependencies (#26352)
* py-snappy: add patch to fix dependencies

* Update var/spack/repos/builtin/packages/py-snappy/req.patch

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-09-29 15:50:42 -05:00
Manuela Kuhn
0a7804f52e py-jupyterlab: add 3.0.14, 3.0.18 and 3.1.14 (#26339) 2021-09-29 14:34:18 -05:00
Valentin Volkl
805d59d47f geos: fix patch versions (#26351) 2021-09-29 18:32:37 +00:00
Manuela Kuhn
10638ea449 py-jupyter-packaging: add 0.7.12 and 0.10.6 (#26338)
* py-jupyter-packaging: add 0.7.12 and 0.10.6

* Update var/spack/repos/builtin/packages/py-jupyter-packaging/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-jupyter-packaging/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-09-29 18:31:32 +00:00
Howard Pritchard
6d613bded0 cray-mvapich2: add a package to support (#26273)
The format of the HPE/Cray supplied module for cray-mvapich2 on HPE apollo systems is
very different from the cray-mpich module supplied on Cray EX and XE
systems.

Recent changes to the cray-mpich package -

https://github.com/spack/spack/pull/23470

broke support for cray-mvapich2 and relies now on the structure of the
cray-mpich module to work properly.

Rather than try to support two very different vendor mpich modules
using the same spack package, just add another one specialized for
the cray-mvapich2 module.

Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
2021-09-29 20:12:13 +02:00
Martin Diehl
f32feeee45 new package(s): DAMASK (damask, damask-grid, damask-mesh) (#25692) 2021-09-29 19:57:01 +02:00
Manuela Kuhn
c75e84e9f3 py-qtpy: add 1.11.2 (#26343) 2021-09-29 11:19:23 -05:00
Harmen Stoppels
7fdb879308 ca-certificates-mozilla for openssl & curl (#26263)
1. Changes the variant of openssl to `certs=mozilla/system/none` so that
   users can pick whether they want Spack or system certs, or if they
   don't want certs at all.
2. Keeps the default behavior of openssl to use certs=systems.
3. Changes the curl configuration to not guess the ca path during
   config, but rather fall back to whatever the tls provider is
   configured with. If we don't do this, curl will still pick up system
   certs if it finds them.

As a minor fix, it also adds the build dep `pkgconfig` to curl, since
that's being used during the configure phase to get openssl compilation
flags.
2021-09-29 09:05:58 -07:00
iarspider
24263c9e92 New package: py-async-lru (#26328) 2021-09-29 18:05:36 +02:00
Manuela Kuhn
7cd3af5d52 py-mffpy: add new package (#26345) 2021-09-29 17:59:50 +02:00
bernhardkaindl
4a31f0fb0f py-mock: fix depends of @:2.0.0 and bump version (#26336)
* py-mock: fix depends of `@:2.0.0` and bump version

fixes the build of `py-gsutil`, it depends on `'py-mock@:2.0.0'`.

* Update var/spack/repos/builtin/packages/py-mock/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/py-mock/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Apply the other requested changes

* Add requested change: Add the python@3.6 for newer versions

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-09-29 15:39:57 +00:00
Greg Sjaardema
5132cfcc63 seacas: new release and fixes for metis/parmetis (#26310)
* seacas: new release and fixes for metis/parmetis

* Update to add sha256 checksum for latest seacas release

* Updated the documentation strings with new applications

* Fixed the metis/parmetis variants and logic depending on whether mpi
  is enabled/disabled. (There is still a zoltan issue I need to fix,
  but this will at least allow seacas to be built without
  metis/parmetis or with +mpi+parmetis.  The ~mpi+metis still needs
  work elsewhere.)

* Enable cpup, slice, zellij in +applications
2021-09-29 16:53:49 +02:00
Harmen Stoppels
9d39a1bf42 Un-unset TERM and DISPLAY (#26326)
For interactive `spack build-env`'s this is undesired behavior
2021-09-29 16:28:32 +02:00
bernhardkaindl
11278dd55a py-monotonic: bump version to 1.6 (#26335)
Fixes `spack solve py-gsutil`: It depends on 'py-monotonic@1.4:'
2021-09-29 09:19:47 -05:00
Pat Riehecky
e45979d39a Added OpenJDK 16.0.2 (#26322) 2021-09-29 14:19:38 +00:00
MichaelLaufer
ed54d6c926 py-netcdf4: adds parallel IO support (#26178) 2021-09-29 08:21:16 -05:00
iarspider
634b0b25c4 Add new package: py-backports-entry-points-selectable (#26329) 2021-09-29 15:09:27 +02:00
Manuela Kuhn
ac29b70d18 py-dipy: add new package (#26331) 2021-09-29 15:05:34 +02:00
Manuela Kuhn
e01947effc py-imageio-ffmpeg: add 0.4.5, fix installation and import (#26330) 2021-09-29 14:56:16 +02:00
Manuela Kuhn
78dbac69e9 py-pyqt5-sip: add new package (#26325) 2021-09-29 14:52:29 +02:00
bernhardkaindl
80c8978691 krb5: bump version and limit depends_on('openssl') to @1 (#26332)
krb5 uses an openssl RSA API which is deprecated in OpenSSL@3.0.0
with an const/non-const mismatch.
2021-09-29 11:24:08 +00:00
Manuela Kuhn
ab6b531e10 py-argcomplete: add 1.12.3 (#26228) 2021-09-29 13:10:03 +02:00
Olli Lupton
cffa1e7f6c Add ccache 4.4.2. (#26327) 2021-09-29 09:41:28 +00:00
Axel Huebl
c5410bd333 FFTW: NEON SIMD is float-only (#26321)
Fix on Apple Mac M1 (aarch64):
```
configure: error: NEON requires single precision
```
2021-09-29 02:40:45 +00:00
Ben Darwin
c578882bb2 itk: add version 5.2.1 (#26307) 2021-09-28 18:15:42 -07:00
Greg Sjaardema
a550416a1f netcdf-c: Update for 4.8.1 and new download site (#26309)
NetCDF-4.8.1 has been released.

    As discussed in https://github.com/Unidata/netcdf-c/issues/2110
    (netcdf-c-4.8.1.tar.gz not on ftp site... #2110), the canonical
    download site for netCDF releases has been changed and the previous
    ftp site is no longer available.

    This PR updates the `url` to point to the new recommended download
    site and updates the sha256 checksums for the new tar files.
2021-09-28 17:21:28 -07:00
Gregory Lee
82d857dced qhull deprecated libqhull.so in 2020.2 (#26304) 2021-09-28 16:54:30 -07:00
Manuela Kuhn
32b5669e8d py-pytz: add 2021.1 (#26289) 2021-09-28 18:07:28 +00:00
iarspider
a2c16356a1 dire: Fix depends for new pythia version scheme (#26294)
Pythia version numbering was changed in #26255 from xyyy to x.yyy
2021-09-28 18:05:52 +02:00
Edward Hartnett
4f4984e313 wrf-io: added NOAA software maintainers, added openmp variant (#26113) 2021-09-28 08:55:09 -07:00
Tamara Dahlgren
5ace5ca7a4 Post 26211 rebase updates (#26246) 2021-09-28 08:53:59 -07:00
Manuela Kuhn
519f75b865 py-scooby: add new package (#26284) 2021-09-28 17:51:37 +02:00
Diego Alvarez
023d9e3b4c Added OpenJDK 11.0.12_7 (#26299) 2021-09-28 17:47:45 +02:00
iarspider
9810a80c6d Update nlohmann-json to 3.10.2 (#26260)
* Update nlohmann-json

* fix testsuite

Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2021-09-28 08:45:34 -07:00
Harmen Stoppels
6c33047514 Squashfs is a makefilepackage (#26300) 2021-09-28 17:45:16 +02:00
bernhardkaindl
3c5a4157b0 py-anuga: add git main version to support build with python@3.5: (#26248)
* py-anuga: add git main version to support build with python@3.5:

py-anuga's main branch has been converted to Python-3 recently.

* py-triangle: use pypi, py-anuga: Fixed depends and test suite works now
2021-09-28 10:37:09 -05:00
bernhardkaindl
d00c9b47f2 py-tomopy: version bump and master, add new deps, make runtest pass (#26252)
Current py-tomopy has many features and dependencies, add them.
2021-09-28 10:33:29 -05:00
Manuela Kuhn
79808f92ae py-numba: add 0.54.0 and restrict old dependencies (#26281)
* py-numba: add 0.54.0 and restrict old dependencies

* Update var/spack/repos/builtin/packages/py-numba/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-09-28 10:32:44 -05:00
Manuela Kuhn
0f5c63b0c3 py-xlrd: add 2.0.1 (#26282) 2021-09-28 10:31:45 -05:00
Manuela Kuhn
b8dd8b07f9 py-appdirs: add 1.4.4 (#26298) 2021-09-28 10:26:23 -05:00
Diego Alvarez
f65a50d9f9 Update Nextflow (#26042) 2021-09-28 07:15:17 -04:00
Harmen Stoppels
4ce9c839ac Add OpenSSL 3 (#26097)
* OpenSSL 3.0.0

* Remove openssl constraint in e4s to test 3.0.0

* Restrict openssl

* Restrict openssl to @:1 in unifyfs

* Revert "Remove openssl constraint in e4s to test 3.0.0"

This reverts commit 0f0355609771764280ab1b6a523c80843a4f85d6.

* Prefer 1.x
2021-09-28 10:36:55 +02:00
Massimiliano Culpo
aa8727f6f9 Move detection logic in its own package (#26119)
The logic to perform detection of already installed
packages has been extracted from cmd/external.py
and put into the spack.detection package.

In this way it can be reused programmatically for
other purposes, like bootstrapping.

The new implementation accounts for cases where the
executables are placed in a subdirectory within <prefix>/bin
2021-09-28 09:05:49 +02:00
bernhardkaindl
499d39f211 libp11: Fix build and add new version (#26135)
The build needs `pkgconfig` and `openssl`, `m4` is already added by `autoconf`.
Also add the current version of `libp11` to the list of versions.

Co-authored-by: Bernhard Kaindl <bernhard.kaindl@ait.ac.at>
2021-09-28 04:01:08 +02:00
Manuela Kuhn
cd8e85d802 py-dataclasses: add 0.8 (#26283) 2021-09-27 20:18:07 -05:00
Manuela Kuhn
c1cfbc5536 py-meshio: add 5.0.1 and 4.4.6 (#26285) 2021-09-27 20:17:22 -05:00
Manuela Kuhn
87b23cc9cd py-deprecated: add 1.2.13 and get sources from pypi (#26286) 2021-09-27 20:15:35 -05:00
Harmen Stoppels
87450f3688 Use gnuconfig package for config file replacement (#26035)
* Use gnuconfig package for config file replacement

Currently the autotools build system tries to pick up config.sub and
config.guess files from the system (in /usr/share) on arm and power.
This is introduces an implicit system dependency which we can avoid by
distributing config.guess and config.sub files in a separate package,
such as the new `gnuconfig` package which is very lightweight/text only
(unlike automake where we previously pulled these files from as a
backup). This PR adds `gnuconfig` as an unconditional build dependency
for arm and power archs.

In case the user needs a system version of config.sub and config.guess,
they are free to mark `gnuconfig` as an external package with the prefix
pointing to the directory containing the config files:

```yaml
    gnuconfig:
      externals:
      - spec: gnuconfig@master
        prefix: /tmp/tmp.ooBlkyAKdw/lol
      buildable: false
```

Apart from that, this PR gives some better instructions for users when
replacing config files goes wrong.

* Mock needs this package too now, because autotools adds a depends_on

* Add documentation

* Make patch_config_files a prop, fix the docs, add integrations tests

* Make macOS happy
2021-09-27 18:38:14 -04:00
Tamara Dahlgren
c0da0d83ff qhull: use secure github URLS instead of www.qhull.org downloads (#26211) 2021-09-27 14:50:43 -07:00
Manuela Kuhn
9b7a8f69fb py-python-picard: add new package (#26268) 2021-09-27 23:39:30 +02:00
Brian Van Essen
acc8673e1a Updated versions for cuDNN and NVSHMEM (#26272) 2021-09-27 13:54:15 -07:00
Adam J. Stewart
5c1e133d23 py-torchvision: add v0.10.1 (#26267) 2021-09-27 13:35:53 -07:00
Manuela Kuhn
1ad8c0d67d py-llvmlite: add 0.37.0 (#26278) 2021-09-27 13:33:28 -07:00
Manuela Kuhn
044e2def4f py-datalad: move datalad wtf test over from py-datalad-metalad (#26274)
* py-datalad: move datalad wtf test over from py-datalad-metalad

* Update var/spack/repos/builtin/packages/py-datalad/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-09-27 15:24:48 -05:00
Manuela Kuhn
44355a4f18 py-numexpr: add 2.7.3 (#26279) 2021-09-27 20:13:59 +00:00
Manuela Kuhn
6b94d7e6a3 py-tqdm: add 4.62.3 (#26277) 2021-09-27 19:55:22 +00:00
Manuela Kuhn
441c602d2d py-nilearn: add 0.8.1 (#26276) 2021-09-27 14:50:13 -05:00
Thomas Madlener
285df128a1 [openloops][vbfnlo] Fix recipes and updated dependencies (#24461)
* [vbfnlo] Add doc variant to toggle building of docs

* [openloops] Add scons to dependencies

Make sure that the build_processes does not accidentally pick up a
non-suitable scons version from the underlying system

* [openloops] Set OLPYTHON to make sure the right scons is picked

* [openloops] Fix Flake8 style complaints
2021-09-27 11:40:33 -07:00
Richarda Butler
c68536e9d3 MPICH: Add E4S testsuite stand alone test (#25634) 2021-09-27 11:36:53 -07:00
Ben Darwin
c07af15946 mrtrix3: add version 3.0.3 (#25943) 2021-09-27 11:33:42 -07:00
iarspider
e256d02963 Update highfive (#26262)
* Add new versions of highfive
* Fix CMake option name
2021-09-27 11:24:37 -07:00
Marie Houillon
87c7a7e103 New packages for openCARP (#25909)
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2021-09-27 11:21:43 -07:00
Melven Roehrig-Zoellner
6b2192ef96 source-highlight: allow to build the git master branch (#25947)
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2021-09-27 11:16:55 -07:00
Miroslav Stoyanov
5130f43eb3 added workaround for rocm/cmake bug in tasmanian (#25949) 2021-09-27 11:14:21 -07:00
Edward Hartnett
c592e17d49 added package g2c from NOAAs NCEPLIBS project (#26190)
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2021-09-27 11:03:54 -07:00
Olivier Cessenat
27c0b4a0f7 sundials package: @:5.7.0 requires hypre@:2.22.0 (#25903)
sundials@:5.7.0 fails to build with hypre@2.22.1
2021-09-27 10:58:54 -07:00
Steven Smith
ee63cfe0fd New Package: EcoSLIM (#25975)
Co-authored-by: Steven Smith <Steven Smith>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2021-09-27 10:38:53 -07:00
psakievich
df9d1dd1cb Correct path comparisons for fs view (#25891)
* Fix path comparisons in copy views

* Get correct permissions

* Set group id though os

Co-authored-by: Philip Sakievich <psakiev@sanida.gov>
2021-09-27 09:51:38 -07:00
jacorvar
33957f2745 add mantainer to bedops (#26141) 2021-09-27 16:23:50 +00:00
bernhardkaindl
0cc80f5118 spindle: It seems it needs mpi.h to compile, adding depends on mpi. (#26151)
Workaround this compile error for gcc by adding -Wno-narrowing for it:
spindle_logd.cc:65:76: error: narrowing conversion of '255' from 'int' to 'char'
spindle_logd.cc:65:76: error: narrowing conversion of '223' from 'int' to 'char'
spindle_logd.cc:65:76: error: narrowing conversion of '191' from 'int' to 'char'

spindle 0.8.1 wants to compile tests with mpi.h, newer versions need mpicc,
thus add: depends_on("mpi"). Spindle supports the --no-mpi to disable MPI.
2021-09-27 08:58:47 -07:00
Edward Hartnett
ffedc3637c added NOAAs UPP package (#26198) 2021-09-27 08:56:05 -07:00
Adam J. Stewart
4d3becdfd9 py-torch: add v1.9.1 (#26159) 2021-09-27 09:30:47 -05:00
bernhardkaindl
4a130b9185 perl: Fix test case bug perl#15544: Don't fail with PATH >1000 chars (#26245)
Fix the perl test case bug Perl/perl5#15544
Variable PATH longer than 1000 characters (as is usual with spack) fails a perl test case
The fix is: Don't test PATH in testcase perlbug.t
Fixes `spack install --test=all` for specs triggering a build and test of perl!
2021-09-27 15:18:36 +02:00
Manuela Kuhn
2acfe55b74 exempi: fix expat dependency (#26221)
* exempi: fix expat dependency and fix test with --test=root

Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2021-09-27 14:52:23 +02:00
iarspider
8710353336 pythia8: update to v8.306, change url, set environment variables for dependents (#26255) 2021-09-27 09:05:51 +00:00
Jen Herting
514d04c8f1 New package: r-klar (#25390) 2021-09-27 02:53:03 +00:00
Jen Herting
87e91178a6 New package: r-questionr (#25395) 2021-09-26 21:35:24 -05:00
Manuela Kuhn
e90534d45e py-python-gitlab: add 2.10.1 (#26229) 2021-09-27 01:24:05 +02:00
Wouter Deconinck
caa33b7b05 [acts] eigen is not only a build dependency (#26257)
The ActsConfig.cmake includes a `find_dependency(Eigen3)` line. Requiring depends_on type='build' does not expose eigen to dependents during their build.

Ref: https://github.com/acts-project/acts/blob/v13.0.0/cmake/ActsConfig.cmake.in#L59
2021-09-27 01:23:44 +02:00
lorddavidiii
8fa6597d43 cfitsio: add version 4.0.0 (#26218) 2021-09-27 01:18:09 +02:00
Seth R. Johnson
7e2fc45354 trilinos: default gotype=long_long (#26253)
"Long long" is the default type when building trilinos on its own, and
many downstream packages (both in and out of spack) rely on it. E4S
already sets this explicitly to long_long.
2021-09-26 16:51:23 +02:00
Desmond Orton
3e7cee27d7 masurca: add versions up to v4.0.5 (#26171)
Co-authored-by: las_djorton <las_djorton@babybuild.las.iastate.edu>
2021-09-26 15:53:59 +02:00
Wouter Deconinck
798ef2bdb0 vtk: depends_on freetype @:2.10.2 through @:9.0.1 only (#26180)
The issues in https://gitlab.kitware.com/vtk/vtk/-/issues/18033 were fixed in:
- dae1718d50
- 31e8e4ebeb

These fixes are in vtk@9.0.2 https://github.com/Kitware/VTK/releases/tag/v9.0.2 and beyond.
2021-09-26 15:52:51 +02:00
Brian Van Essen
cc658c5f1e lbann: add support for building with the ONNX C++ library (#26130) 2021-09-26 15:50:09 +02:00
Valentin Volkl
1f972f90c8 podio, edm4hep: fix tests (#26116)
Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>
2021-09-26 15:49:10 +02:00
Brian Van Essen
123c105771 onnx: fix python version in environments (#26131)
When using the ONNX package inside of an environment that specifies a
python3 executable, it will attempt to use a system installed
version.  This can lead to a failure where the system python and the
environment python don't agree and the system python ends up with an
invalid environment.  Forces ONNX to use the same version of python as
the rest of the spec.

Co-authored-by: Greg Becker <becker33@llnl.gov>
2021-09-26 15:48:45 +02:00
Brian Van Essen
b909560ed5 Added CMake command to export compiler directories to support emacs LSP mode. (#26118) 2021-09-26 15:47:46 +02:00
Paul Spencer
0e6e9c23a1 libsignal-protocol-c: new package (#26121)
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2021-09-26 15:47:15 +02:00
Hadrien G
a99d8463ac diffutils: Add v3.8, fixes an incompatibility with newer glibc (#26237) 2021-09-26 12:30:16 +02:00
Harmen Stoppels
e76462da38 Compiler conflict in umpire as a range (#26161) 2021-09-26 12:28:30 +02:00
Harmen Stoppels
fbda52d1b0 Curl 7.79.0 (#26075) 2021-09-26 12:28:05 +02:00
Manuela Kuhn
ab85961e73 py-datalad-hirni: add new package (#26227) 2021-09-26 09:20:36 +00:00
Nikolay Simakov
72cabcf454 enzo: build extra tools, add optimization variant (#25401)
* added inits and rings tools to be built
* added opt variant
2021-09-26 10:59:06 +02:00
iarspider
344b37730b jemalloc: add more variants (#26144) 2021-09-26 10:56:27 +02:00
bernhardkaindl
5967a10432 candle-benchmarks: depend_on()s: Fix obsoleted and renamed variants (#26250)
Fix solving/concretizing candle-benchmarks:
py-theano: The requested variant +gpu us now named +cuda
opencv: The requested variants +python and +zlib are now fixed deps
2021-09-26 10:37:01 +02:00
bernhardkaindl
6ccda81368 log_parser.py: Find failed test case messages in error logs (#25694)
- Match failed autotest tests show the word "FAILED" near the end
- Match "FAIL: ", "FATAL: ", "failed ", "Failed test" of other suites
- autotest "   ok"$ means the test passed, independend of text before.
- autoconf messages showing missing tools are fatal later, show them.
2021-09-26 10:35:04 +02:00
bernhardkaindl
34415f6878 swiftsim: Fix build with version bump and depends_on('gsl') (#26166)
swiftsim-0.7.0 didn't build because of a configure script issue and
more. Fix the build by a version bump and adding `depends_on('gsl')`.
2021-09-26 10:32:44 +02:00
bernhardkaindl
a947680e37 dropwatch: make check starts a daemon which does not stop: Skip it (#26164)
dropwatch is a network packet drop checker and it's make check starts
a daemon which does not terminate.

- Skip this test to not block builds.
- Add depends_on('pkgconfig', type='build')
  It is needed in case the host does not have pkg-config installed.
- Remove the depends_on('m4', type='build'):
  The depends_on('autoconf', type='build') pulls m4 as it needs it.
2021-09-26 10:32:04 +02:00
bernhardkaindl
2154786b61 dnstop: needs ncurses and it forgot to add -ltinfo (#26163)
dnstop misses a depends('ncurses') and it needs
to link with libtinfo from ncurses as well.
2021-09-26 10:30:42 +02:00
bernhardkaindl
9a64a229a0 xfwp: Fix build using: env.append_flags('CPPFLAGS', '-D_GNU_SOURCE') (#26157)
Without -D_GNU_SOURCE, the build of xfwp has many compilation errors.
Example: io.c:1039:7: error: implicit declaration of function 'swab'
2021-09-26 10:29:43 +02:00
bernhardkaindl
7189a69c70 rivet: Fix of build and tests on Ubuntu 18.04 w/ version bump (#26152)
When using Ubuntu's gcc-8.4.0 on Ubuntu 18.04 to compile rivet-3.1.3,
compilation errors related to UnstableParticles(), "UFS" show up.

Compilation with this compiler is fixed in rivet-3.1.4, adding it.

Adding type='link' to the depends on 'hepmc' and 'hepmc' fixes
the tests to find libHepMC.so.4 in `spack install --tests=all`

Co-authored-by: Valentin Volkl <valentin.volkl@cern.ch>
2021-09-26 10:29:08 +02:00
bernhardkaindl
fee0831b63 acct: skip installcheck: fails checking if all progs have --help (#26093)
Checks if all programs support --help and --version but not all do.
2021-09-26 10:26:21 +02:00
bernhardkaindl
919a893c08 mountpointattr: Fix checksum of 1.1.1 and fix build(patch is only for 1.1) (#26087) 2021-09-26 10:25:50 +02:00
bernhardkaindl
91ce8354a2 cairo: pass tests: devs wrote that other people shouldn't attempt them (#26086)
The cairo test suite is huge, has many backends and the README states
that running and attempting to pass it is not a goal for normal users,
it has so many dependencies into the system, including fonts, that
passing it is not a goal realistically in reach soon:
Skip it, it takes far too long to be practical.
2021-09-26 10:25:26 +02:00
bernhardkaindl
c411779c51 libfuse: Fix build when meson doesn't get host's udev pkg (#26147)
Despite the patch disabling installation of rules, meson's setup
stage looks up the udev package to get `/lib/udev/rules.d`, but as
spack has no `systemd/udev` package, it would fail to build.

Fix such builds by passing `-Dudevrulesdir` and bump version to 3.10.5
2021-09-26 10:24:30 +02:00
Manuela Kuhn
17857083b0 py-datalad-container: add new package (#26222) 2021-09-26 10:18:17 +02:00
Manuela Kuhn
dbbc2879e5 py-datalad-neuroimaging: add new package (#26223) 2021-09-26 10:17:22 +02:00
Manuela Kuhn
d627026910 py-datalad-webapp: add new package (#26226) 2021-09-26 09:50:01 +02:00
Manuela Kuhn
3b323d6c90 py-datalad-metalad: add new package (#26225)
Added py-nose for import and a simple installtest from appveyor.yml

Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2021-09-26 07:44:18 +00:00
bernhardkaindl
7ca657aef6 libidl builds using flex and bison: Add them as build-depends (#26183) 2021-09-26 09:40:18 +02:00
Jen Herting
27e6032f73 New package: py-gpyopt (#26232)
Co-authored-by: Sid Pendelberry <sid@rit.edu>
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2021-09-26 07:34:18 +00:00
Adam J. Stewart
76ca57bb2f py-scikit-learn: add v1.0 (#26243) 2021-09-26 08:33:58 +02:00
Jen Herting
56858eb34e first build of py-doe2 a fork of py-doe (#26235)
Co-authored-by: Sid Pendelberry <sid@rit.edu>
2021-09-26 08:12:40 +02:00
Carlos Bederián
b4b3b256bc ucx: use bfd instead of lld with %aocc (#26254) 2021-09-26 04:47:07 +02:00
Jen Herting
3c14d130ca New package: r-styler (#25399) 2021-09-25 20:50:22 +00:00
Sreenivasa Murthy Kolam
b56e1d1f6d limit the amd_target_sram_ecc to rocm-3.9.0-4.0.0 (#26240) 2021-09-25 19:18:44 +00:00
Sam Reeve
b2376db632 cabana: add 0.4 and new dependency variants (#25847)
Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>
Co-authored-by: Christoph Junghans <junghans@votca.org>
2021-09-25 12:04:24 -06:00
Glenn Johnson
d8dc1f2c80 new package: dicom3tools (#25700) 2021-09-25 08:43:17 -06:00
Jen Herting
348cebfb8f py-sobol-seq: new package (#26234)
Co-authored-by: Sid Pendelberry <sid@rit.edu>
2021-09-25 14:39:36 +02:00
Jen Herting
3f7d6763e0 New package: py-pydoe (#26233)
Co-authored-by: Sid Pendelberry <sid@rit.edu>
2021-09-25 14:34:35 +02:00
bernhardkaindl
ff511e090a autotools doc PR: No depends_on('m4') with depends_on('autoconf') (#26101)
* autotoolspackage.rst: No depends_on('m4') with depends_on('autoconf')
  - Remove `m4` from the example depends_on() lines for the autoreconf phase.
  - Change the branch used as example from develop to master as it is
    far more common in the packages of spack's builtin repo.
- Fix the wrong info that libtoolize and aclocal are run explicitly
  in the autoreconf phase by default. autoreconf calls these internally
  as needed, thus autotools.py also does not call them directly.
- Add that autoreconf() also adds -I<aclocal-prefix>/share/aclocal.
- Add an example how to set autoreconf_extra_args.
- Add an example of a custom autoreconf phase for running autogen.sh.

Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2021-09-25 10:15:03 +02:00
Alec Scott
ef7cf83ea5 Add Go v1.17.1 (#26128) 2021-09-25 01:22:34 -06:00
acastanedam
b67cfc0fd1 gpi-2: improve GPI-2 installation (#25808)
Based on the original script of R. Mijakovic further improvements of
GPI-2 installation, in particular different official versions,
configuration setups and even testing. Importantly, the non-autotools
way of installation for older versions is also considered, which is
relevant for some packages using GPI-2.

Co-authored-by: Arcesio Castaneda Medina <arcesio.castaneda.medina@itwm.fraunhofer.de>
2021-09-25 00:58:46 -06:00
bernhardkaindl
e3dc586064 xload: fix build by disabling gettext and add v1.1.3 (#26142)
xload failed with unresolved referenced to libintl functions:
Disabled it's use of gettext calls and added the last "new" version.

Co-authored-by: Bernhard Kaindl <bernhard.kaindl@ait.ac.at>
2021-09-25 00:58:32 -06:00
AMD Toolchain Support
ed13addf3b Cloverleaf: adding AOCC support (#26148)
Co-authored-by: Mohan Babu <mohbabul@amd.com>
2021-09-25 00:49:43 -06:00
Adam J. Stewart
b8e21f2b0b GDAL: fix build of Java bindings (#26244) 2021-09-25 00:01:45 -06:00
Manuela Kuhn
7e67652983 py-datalad: add 0.15.1 (#26230) 2021-09-24 23:40:48 -06:00
kwryankrattiger
a9cb31ab49 Enable cinema variant in ecp-data-vis-sdk (#26176) 2021-09-25 07:18:34 +02:00
Filippo Spiga
c725ca83ce nvhpc: add v21.9 (#26217) 2021-09-25 07:15:22 +02:00
bernhardkaindl
2eddc60baa tauola: Fix build: The current build wants lhapdf headers by default (#26154)
The hand-written `configure` script of this package does not handle
--without-<feature> at all. The source wants to use `lhapdf` headers
even if support of lhapdf is not indicated using `--with-lhapdf`.

Enable the variant `lhapdf` by default: It fixes the build of the
current package and provides the TauSpinner feature as well.
2021-09-24 20:16:59 -06:00
bernhardkaindl
13d313d3ad scallop: Fix build by bumping the version to 0.10.5 (#26162)
build of 0.10.3 fails with CoinPragma.hpp: No such file or directory
2021-09-24 18:11:06 -06:00
Olivier Cessenat
8ed7f65bc8 pigz: new version 2.6 (#26066) 2021-09-24 17:17:08 -06:00
bernhardkaindl
742bd1f149 nix: bump version, add new depends and make installcheck pass (#26179)
The current version of `nix` has some more features and has more
dependencies. The installcheck is quite involved but passes now.
2021-09-24 17:08:10 -06:00
bernhardkaindl
8d70f94aae cgdcbxd: Fix build: Use DESTDIR=self.prefix to not write to /etc (#26145)
Fix the build for normal non-root/non-system-user builds, as we cannot
know that we'd have to uninstall these files even if installed as root.
Also add `pkgconfig` and remove not explicitly needed `depends_on('m4')`
2021-09-24 16:32:09 -06:00
luker
ab90cd8fc4 Tau rocm fix (#26134)
* update the Tau package to use the correct ROCm dependencies and prefixes

    1st:
    When the rocm variant is selected, tau defaults to look for rocm in /opt/rocm
    which is not guarenteed to be the correct location -- this has been fixed
    to provide the prefix for hsa-rocr-dev (which is now a dependency when +rocm is
    selected).

    2nd:
    the rocprofiler dependency package was not specified correctly, it should
    be called rocprofiler-dev, also rocprofiler-dev is a dependency when
    +rocprofiler is selected.

added roctracer support
2021-09-24 16:29:04 -06:00
bernhardkaindl
cdcecda9d0 sst-dumpi: Correct the wrong checksum of the current version (#26181)
Correct the sha256 of the current version as shown by `spack checksum`
2021-09-24 14:17:16 -06:00
bernhardkaindl
adc7fee12e w3m: Fix build by disabling RAND_egd and japanese messages (#26168)
w3m's build fails with `undefined reference to `RAND_egd'` which
is an deprecated insecure feature and from building japanese messages.

Disabling both makes the build of `w3m` work.
2021-09-24 13:26:14 -06:00
bernhardkaindl
12252f1ca4 iproute2: add v5.10.0 and v5.11.0, add missing deps (#26182)
iproute2 needs libmnl and builds using flex and bison: Add them.
2021-09-24 12:37:52 -06:00
bernhardkaindl
7efb18b502 nginx: Bump version for OpenSSL@3 and restrict @:1.21.2 to openssl@:1 (#26156) 2021-09-24 12:16:51 -06:00
bernhardkaindl
45c84a2b04 xdriinfo: uses glXGetProcAddressARB, add: depends_on('gl') (#26184) 2021-09-24 12:08:07 -06:00
Edward Hartnett
2c9dfcabf8 added NOAA package prod_util (#26197) 2021-09-24 11:44:09 -06:00
Edward Hartnett
1a0e1597c8 nemsio: Add v2.5.3, which includes dependency change, and maintainers (#26188) 2021-09-24 11:41:15 -06:00
Adam J. Stewart
9a17dc0001 py-torchvision: rename master -> main (#26160) 2021-09-24 11:32:23 -06:00
Robert Cohn
3a48f5f931 intel-oneapi-mpi/mkl packages: add ilp64 support (#26045) 2021-09-24 10:32:06 -07:00
Edward Hartnett
73913a5d51 added GFDL FMS package (#26191) 2021-09-24 11:14:16 -06:00
Scott Wittenburg
45b70d9798 Pipelines: Disable ppc builds until we have resources or make it smaller (#26238) 2021-09-24 08:24:36 -07:00
bernhardkaindl
cdbb586a93 autotools.py/autoreconf: Show the depends_on()s to add to the package (#26115)
This commit shows a template for cut-and-paste into the package to fix it:

```py
==> fast-global-file-status: Executing phase: 'autoreconf'
==> Error: RuntimeError: Cannot generate configure: missing dependencies autoconf, automake, libtool.

Please add the following lines to the package:

    depends_on('autoconf', type='build', when='@master')
    depends_on('automake', type='build', when='@master')
    depends_on('libtool', type='build', when='@master')

Update the version (when='@master') as needed.
```
    
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2021-09-24 09:17:07 -06:00
bernhardkaindl
bcf708098d kmod: Add the missing depends on m4 and pkgconfig (#26137)
The build needs pkgconfig and lzma, m4 is already added by autoconf.

Disable generation of kmod manpages as spack does not have xsltproc yet.

Co-authored-by: Bernhard Kaindl <bernhard.kaindl@ait.ac.at>
2021-09-24 08:02:09 -06:00
Edward Hartnett
71378bcf39 landsfcutil: new package (#26193) 2021-09-24 13:48:58 +02:00
Wouter Deconinck
f68b2ea73a acts: add v13.0.0 (#26196) 2021-09-24 13:47:25 +02:00
Edward Hartnett
2d8f06bfa0 ufs-utils: added NOAA maintainers (#26201) 2021-09-24 13:07:18 +02:00
Harmen Stoppels
87e1ed0ef1 Bump cmake 3.21.3 (#26186) 2021-09-24 04:13:52 -06:00
Troy Redfearn
ef6013da9c Added new versions and deprecated vulnerable versions (#26206) 2021-09-24 03:37:44 -06:00
Tamara Dahlgren
c348daf4dc Add 'radiuss' tags to RADIUSS packages (#26212) 2021-09-24 03:20:14 -06:00
Edward Hartnett
21eaf31291 g2tmpl: added NOAA maintainers (#26192) 2021-09-24 02:35:02 -06:00
Edward Hartnett
6d2ce0535f added NOAA package grib-util (#26200)
* added NOAA package grib-util
2021-09-24 02:17:07 -06:00
Ben Bergen
2e4528c55c Added mising '+' for kokkos (#26202) 2021-09-24 02:14:25 -06:00
Edward Hartnett
6f8c9edefc added NOAA ncio package (#26194) 2021-09-24 02:14:11 -06:00
Edward Hartnett
d532f5b40c added NOAA package nemsiogfs (#26195) 2021-09-24 02:08:06 -06:00
Wouter Deconinck
fb2e764f50 assimp: depends_on zlib (#26199)
Assimp searches for zlib (or builds its own version). When it searches, it can find a system install that is not provided by spack. Ref: d286aadbdf/CMakeLists.txt (L451)
2021-09-24 02:05:06 -06:00
Andrew-Dunning-NNL
7bb5dd7a14 gradle: add new versions through 7.2 (#26203) 2021-09-24 02:02:17 -06:00
iarspider
1299c714c4 gosamcontrib: add libs variants (#26030) 2021-09-24 10:00:02 +02:00
Ryan Mast
2bcdb33666 helics: Add versions 2.8.0, 3.0.0, and 3.0.1 (#26046) 2021-09-24 01:52:52 -06:00
Harmen Stoppels
a6bb3a66ea Remove centos:6 image references (#26095)
This was EOL November 30th, 2020. I believe the "builds" are failing on
develop because of it.
2021-09-24 09:47:49 +02:00
Wouter Deconinck
117ea5a239 opencascade: add v7.5.3; added VTK INCLUDE cmake flag (#26209) 2021-09-24 09:27:07 +02:00
Massimiliano Culpo
03c203effa Use Leap instead of Tumbleweed for e2e bootstrapping test (#26205)
Tumbleweed has been broken for a couple of days. The attempt
to fix it in #26170 didn't really work. Let's try to move to
a more stable release series for OpenSuse.
2021-09-24 01:22:40 -06:00
Mikhail Titov
ba452f7645 radical cybertools: add v1.8.0 (#26215) 2021-09-24 09:22:02 +02:00
Edward Hartnett
54ea7caf3f g2: add maintainers and version 3.4.5 (#26105)
* added new release, added noaa software maintainers to maintainer list

* updated comment

* removed trailing whitespace
2021-09-24 00:17:07 -06:00
kjrstory
bdab4c9f1f fontconfig: add dependency python (#25960) 2021-09-23 23:26:05 -06:00
iarspider
72c22696ac gperftools package: add variants (#26032)
* Make libunwind optional
* Add support for sized_delete and debugalloc

Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2021-09-23 22:40:28 -06:00
Thomas Kluyver
fdc9cb0adb h5py: new version 3.4 (#25935)
No changes to dependencies or supported Python versions.

https://docs.h5py.org/en/stable/whatsnew/3.4.html
2021-09-23 12:12:33 -06:00
bernhardkaindl
ea459993db python: Fix regression in python-2.7.17+-distutils-C++.patch (#25821) 2021-09-23 07:38:58 -05:00
Christoph Conrads
45c6fe2b94 SQLite: make variants discoverable (#25885)
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2021-09-23 09:54:02 +02:00
Harmen Stoppels
56a81ec81c Pin opensuse image in bootstrap tests (#26170)
Currently zypper in opensuse containers throws 'not permitted'

Temporarily fix the digest until they fixed their upstream package manager issues
2021-09-23 08:03:43 +02:00
Gregory Becker
1195ac02e5 Merge tag 'v0.16.3' into develop 2021-09-22 16:25:40 -07:00
Brian Van Essen
fa92482675 dihydrogen package: add missing dependency (#25896) 2021-09-22 12:03:15 -07:00
Edward Hartnett
76ad001c56 added NOAA software maintainers to maintainer list (#26112) 2021-09-22 07:24:16 -04:00
bernhardkaindl
4ccd2e8ff0 pango: Fix build: restore autotools-based versions (#26084)
Fix the build of pango and it's 20 dependents: Only provide the versions which
support the build using autotools (conversion to MesonPackage didn't progress)
This only restores the list of versions of August 10, before the build broke.
2021-09-22 05:13:49 -06:00
Alec Scott
2b6a8ccf29 Add Rclone v1.56.1 (#26124) 2021-09-22 04:07:48 -06:00
albestro
7613511718 add conflict (#26028) 2021-09-22 12:07:19 +02:00
Alec Scott
ed3aa9633d Add Picard v2.26.2 (#26125) 2021-09-22 04:04:44 -06:00
kjrstory
24ca007448 su2: add version 7.0.4-7.2.0 (#25956) 2021-09-22 01:07:44 -06:00
Alec Scott
86ddcd0e2d Add Slepc v3.15.2 (#26123) 2021-09-21 23:13:51 -06:00
Edward Hartnett
5097a41675 gfsio: add NOAA software maintainers (#26106)
* added NOAA software maintainers to maintainer list

* added comment about NCEPLIBS
2021-09-21 19:20:47 -06:00
Harmen Stoppels
3b55c2e715 Bump version and update changelog 2021-09-21 16:58:41 -07:00
Harmen Stoppels
7caa844d49 Fix style tests 2021-09-21 16:58:41 -07:00
Harmen Stoppels
4cd6381ed5 Remove centos:6 image references
This was EOL November 30th, 2020. I believe the "builds" are failing on
develop because of it.
2021-09-21 16:58:41 -07:00
Massimiliano Culpo
aebc8f6ce5 docker: remove boto3 from CentOS 6 since it requires and updated pip (#24813) 2021-09-21 16:58:41 -07:00
Massimiliano Culpo
073c92d526 docker: Fix CentOS 6 build on Docker Hub (#24804)
This change make yum usable again on CentOS 6
2021-09-21 16:58:41 -07:00
Greg Becker
0e85d7011e Ensure all roots of an installed environment are marked explicit in db (#24277) 2021-09-21 16:58:41 -07:00
Todd Gamblin
77e633efa1 locks: only open lockfiles once instead of for every lock held (#24794)
This adds lockfile tracking to Spack's lock mechanism, so that we ensure that there
is only one open file descriptor per inode.

The `fcntl` locks that Spack uses are associated with an inode and a process.
This is convenient, because if a process exits, it releases its locks.
Unfortunately, this also means that if you close a file, *all* locks associated
with that file's inode are released, regardless of whether the process has any
other open file descriptors on it.

Because of this, we need to track open lock files so that we only close them when
a process no longer needs them.  We do this by tracking each lockfile by its
inode and process id.  This has several nice properties:

1. Tracking by pid ensures that, if we fork, we don't inadvertently track the parent
   process's lockfiles. `fcntl` locks are not inherited across forks, so we'll
   just track new lockfiles in the child.
2. Tracking by inode ensures that referencs are counted per inode, and that we don't
   inadvertently close a file whose inode still has open locks.
3. Tracking by both pid and inode ensures that we only open lockfiles the minimum
   number of times necessary for the locks we have.

Note: as mentioned elsewhere, these locks aren't thread safe -- they're designed to
work in Python and assume the GIL.

Tasks:
- [x] Introduce an `OpenFileTracker` class to track open file descriptors by inode.
- [x] Reference-count open file descriptors and only close them if they're no longer
      needed (this avoids inadvertently releasing locks that should not be released).
2021-09-21 16:58:41 -07:00
Todd Gamblin
2ae92ebdbb Use AWS CloudFront for source mirror (#23978)
Spack's source mirror was previously in a plain old S3 bucket. That will still
work, but we can do better. This switches to AWS's CloudFront CDN for hosting
the mirror.

CloudFront is 16x faster (or more) than the old bucket.

- [x] change mirror to https://mirror.spack.io
2021-09-21 16:58:41 -07:00
Harmen Stoppels
7f29dd238f Cray: fix extracting paths from module files (#23472)
Co-authored-by: Tiziano Müller <tm@dev-zero.ch>
2021-09-21 16:58:41 -07:00
Adam J. Stewart
0f486080b3 Fix use of quotes in Python build system (#22279) 2021-09-21 16:58:41 -07:00
Michael Kuhn
6b0c775448 clang/llvm: fix version detection (#19978)
This PR fixes two problems with clang/llvm's version detection. clang's
version output looks like this:

```
clang version 11.0.0
Target: x86_64-unknown-linux-gnu
```

This caused clang's version to be misdetected as:

```
clang@11.0.0
Target:
```

This resulted in errors when trying to actually use it as a compiler.

When using `spack external find`, we couldn't determine the compiler
version, resulting in errors like this:

```
==> Warning: "llvm@11.0.0+clang+lld+lldb" has been detected on the system but will not be added to packages.yaml [reason=c compiler not found for llvm@11.0.0+clang+lld+lldb]
```

Changing the regex to only match until the end of the line fixes these
problems.

Fixes: #19473
2021-09-21 16:58:41 -07:00
Adam J. Stewart
9120856c01 Fix fetching for Python 3.9.6 (#24686)
When using Python 3.9.6, Spack is no longer able to fetch anything. Commands like `spack fetch` and `spack install` all break.

Python 3.9.6 includes a [new change](https://github.com/python/cpython/pull/25853/files#diff-b3712475a413ec972134c0260c8f1eb1deefb66184f740ef00c37b4487ef873eR462) that means that `scheme` must be a string, it cannot be None. The solution is to use an empty string like the method default.

Fixes #24644. Also see https://github.com/Homebrew/homebrew-core/pull/80175 where this issue was discovered by CI. Thanks @branchvincent for reporting such a serious issue before any actual users encountered it!

Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2021-09-21 16:58:41 -07:00
Edward Hartnett
90d953d3f6 w3emc: add NOAA software maintainers (#26110) 2021-09-21 17:54:19 -06:00
Tiziano Müller
d34b2638c7 boost: fix for @1.77.0%intel (#25965)
Add patch for build script from boost repo.
2021-09-21 16:07:25 -07:00
bernhardkaindl
979c355c99 spack/build_environment.py: Clean MAKEFLAGS, DISPLAY and TERM (#26092)
clean_environment(): Unset three more environment variables:

MAKEFLAGS: Affects make, can eg indirectly inhibit enabling parallel build
DISPLAY: Tests of GUI widget libraries might try to connect to an X server
TERM: Could make testsuites attempt to color their output
2021-09-22 00:23:10 +02:00
Edward Hartnett
92f199d57b added NOAA software maintainers to the maintainers list (#26102) 2021-09-21 16:16:49 -06:00
Edward Hartnett
fd716ce0c5 sfcio: add NOAA software maintainers (#26108)
* added NOAA software maintainers to maintainer list

* added comment about NCEPLIBS project
2021-09-21 15:28:37 -06:00
Edward Hartnett
d865caa7f7 ip2: add NOAA software maintainers and deprecation note (#26107)
* added NOAA software maintainers to maintainer list, added comment about library being deprecated

* deleted trailing whitespace
2021-09-21 14:49:13 -06:00
bernhardkaindl
981551b47f libtool: fix running the unit-tests with spack install --test root (#25707)
Besides adding autoconf and automake as needed for tests of 2.4.6,
skip Fortran test cases when Fortran compilers are not provided.
2021-09-21 14:18:29 -06:00
Tamara Dahlgren
c3cb863b82 Feature: Add deprecated versions section to spack info output (#25972) 2021-09-21 11:49:36 -07:00
AMD Toolchain Support
8de77bb304 Fix for - Installation issue: amdlibflame #25878 (#25987)
* Fix for - Installation issue: amdlibflame #25878

* Updated with python+pythoncmd - Symlink 'python3' executable to 'python'
2021-09-21 11:15:23 -07:00
Edward Hartnett
a8977f828e w3nco: add NOAA software maintainers (#26111) 2021-09-21 12:08:43 -06:00
Jonas Thies
6c487f4c6d packages/phist new version 1.9.5 (#26114) 2021-09-21 11:57:22 -06:00
Edward Hartnett
24500d4115 added noaa software maintainers to maintainer list (#26103) 2021-09-21 09:58:53 -07:00
iarspider
2741037c69 Fix FORM recipe (#26104) 2021-09-21 09:57:40 -07:00
Edward Hartnett
d278837316 sigio: add NOAA software maintainers (#26109) 2021-09-21 10:39:05 -06:00
bernhardkaindl
22cfc19bcb ddd,debuild,flux-sched: add missing dependencies (#26090) 2021-09-21 18:08:11 +02:00
Melven Roehrig-Zoellner
c24413a530 petsc: fix for enabling openmp (#25942)
* petsc: fix for enabling openmp

* petsc: shorten comment (style guidelines)

* petsc: move flag to make code more clear
2021-09-21 07:13:35 -06:00
natshineman
544b3f447d mvapich2-gdr: add v2.3.6 (#26076)
Co-authored-by: Nick Contini <contini.26@buckeyemail.osu.edu>
2021-09-21 06:19:56 -06:00
Gregory Lee
05ca19d9d7 fgfs: fix missing autotools depends_on (#26005)
* added build deps for fgfs

* added build deps when building master branch
2021-09-21 07:40:59 -04:00
Harmen Stoppels
a326713826 py-abcpy: new package (#25713) 2021-09-21 13:10:16 +02:00
bernhardkaindl
1b95c97bb3 ccfits: add v2.6 (#26089)
ccfits@2.5 doesn't compile on Ubuntu 18.04: Update to version 2.6.
2021-09-21 04:43:48 -06:00
bernhardkaindl
c6a33c28de Fix deps of diffmark,faiss,fgsl,fipcheck,nbdkit,ncbi-magicblast,xcb-util-cursor (#26091)
Fix missing type='build' deps for cpio, m4, pkg-config and python in
diffmark, faiss, fgsl, fipcheck, nbdkit, ncbi-magicblast and xcb-util-cursor
2021-09-21 04:16:43 -06:00
Harmen Stoppels
58663692a4 Rename 'variant_name' to 'variant' and document it in autotools build system (#26064) 2021-09-21 11:27:41 +02:00
Christoph Junghans
45ba4d94bd votca-* packages: add version 2021.2 (#26058) 2021-09-20 16:14:19 -07:00
Adam J. Stewart
3e3b7b1394 New package: py-torchgeo (#26059) 2021-09-20 16:12:55 -07:00
Jordan Ogas
d0fd9e6d5f charliecloud package: add version 0.25 (#26073) 2021-09-20 16:08:41 -07:00
adityakavalur
88880c5369 Include newer versions of UCX (#26072) 2021-09-20 23:41:26 +02:00
Danny McClanahan
aa7e354a3a patch serf and scons to use #!/usr/bin/env python3 (#26062) 2021-09-20 22:12:30 +02:00
iarspider
f3d2f62468 Add variants to FORM recipe (#25963) 2021-09-20 13:53:54 -06:00
Edward Hartnett
65f285831e added NOAA maintainers to ip package (#26055) 2021-09-20 11:36:03 -06:00
Olivier Cessenat
0197b364a2 mfem and petsc: alter hypre dependencies (#25902)
Hypre latest version 2.22.1 breaks MFEM and PETSc.
2021-09-20 09:51:29 -07:00
Edward Hartnett
96eefea9a3 added NOAA software team to maintainers list (#26056) 2021-09-20 09:01:53 -06:00
Olivier Cessenat
1ea58e0cb9 p7zip: resolve gcc 10 conflict (#25676)
Fix credit: Eric Brugger
2021-09-20 07:43:07 -04:00
Tamara Dahlgren
c6f9e9baf6 strumpack: Update stand-alone test to use stage directory (#25751) 2021-09-20 07:36:58 -04:00
kjrstory
430caaf5f6 paraview: patch for version 5.9.1 with gcc 11.1.0 (#25887)
* paraview: patch for version 5.9.1 with gcc 11.1.0

* Fix : blank line contains whitespace
2021-09-20 07:31:54 -04:00
Robert Underwood
6476e0cf02 gdb: new version v11.1 (#25920) 2021-09-20 07:30:37 -04:00
Jen Herting
acd4186a88 New packages: py-imgaug (#25894)
* updates from sid

* [py-imgaug] url -> pypi

* [py-imgaug] added version 0.4.0 and fixed up dependencies

* [py-imgaug] updated copyright

Co-authored-by: Andrew Elble <aweits@rit.edu>
2021-09-20 07:29:43 -04:00
iarspider
ca8d16c9d1 Allow setting variant name in AutotoolsPackage._activate_or_not (#26054) 2021-09-20 10:54:24 +02:00
jacorvar
d20fa421ca Fix R version (#26061)
R version should be `3.0.0` instead of `3.00`.
2021-09-20 10:47:40 +02:00
Edward Hartnett
8fceaf4a33 added NOAA software team to maintainers list (#26057) 2021-09-19 19:02:02 -06:00
Vanessasaurus
534bad0ff7 updating OmegaH to 9.34.1 (#26015) 2021-09-19 08:55:54 -06:00
Todd Gamblin
4f8b643404 Create SECURITY.md 2021-09-19 06:43:14 -07:00
Vanessasaurus
c2f42a6f09 updating kokkos to 3.4.01 (#26013) 2021-09-19 06:10:55 -06:00
Vanessasaurus
148c7aeb06 updating singularity to 3.8.3 (#26020)
Signed-off-by: vsoch <vsoch@users.noreply.github.com>

Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2021-09-19 04:20:15 -06:00
jacorvar
4f79a83dd1 Fix R version (#26047)
R version should be `3.0.0`, in contrast to `3.00`.
2021-09-19 12:14:14 +02:00
Alec Scott
2d4d51eb5e Add v1.6.0 to Benchmark (#25996) 2021-09-18 20:59:02 -06:00
Cameron Smith
b14d6d217e omegah: add version 9.34.1 (#25828) 2021-09-18 19:58:44 -06:00
Alec Scott
5b400a69b7 Add v0.935 to Angsd (#25995) 2021-09-18 18:46:55 -06:00
Adam J. Stewart
c0839b14d5 Python: use platform-specific site packages dir (#25998) 2021-09-19 00:37:50 +00:00
Seth R. Johnson
6ff5795342 cmake: allow gcc on macOS for newer versions (#25994) 2021-09-18 17:34:43 -06:00
Michele Martone
60f0d0ac20 librsb: add v1.2.0.10 (#26044) 2021-09-18 17:43:41 -04:00
Axel Huebl
8f3482b2ce FFTW: Fix OpenMP Build on macOS (#26039) 2021-09-18 15:13:47 -06:00
Vanessasaurus
fc79a5da17 updating siesta to 4.0.2 (#26021) 2021-09-18 08:05:02 -06:00
Vanessasaurus
1880db8457 updating universal ctags to 5.2.0.xxxx (#26024) 2021-09-18 07:13:55 -06:00
Vanessasaurus
6538727fb3 updating sparsehash to 2.0.4 (#26023) 2021-09-18 06:52:59 -06:00
Vanessasaurus
f5275fecc5 updating htslib to 1.13 (#26012) 2021-09-18 06:26:00 -06:00
Vanessasaurus
d499309433 updating nco to 5.0.1 (#26014) 2021-09-18 06:23:05 -06:00
Vanessasaurus
c5e2662dea updating graphviz to 2.49.0 (#26011) 2021-09-18 06:19:56 -06:00
Vanessasaurus
7b0a505795 updating veloc to 1.5 and cleaning up spacing (#26025) 2021-09-18 06:10:56 -06:00
Vanessasaurus
e8b86b7ec6 updating cloc to 1.9.0 (#26009) 2021-09-18 05:44:04 -06:00
Vanessasaurus
608a0b1f8f updating poppler (#26016) 2021-09-18 05:10:56 -06:00
Vanessasaurus
abd11cf042 updating raxml to 8.2.12 (#26018) 2021-09-18 04:58:50 -06:00
Vanessasaurus
8ad910d8f1 updating protobuf (Gooooogle!) to 3.18.0 (#26017) 2021-09-18 04:40:49 -06:00
Vanessasaurus
d5c985b888 updating samtools to 1.13 (#26019) 2021-09-18 04:16:51 -06:00
Vanessasaurus
f0443d0327 updating spades to 3.15.3 (#26022) 2021-09-18 03:46:50 -06:00
Vanessasaurus
9af1858bff updating gatk to 4.2.2.0 (#26010) 2021-09-18 10:07:28 +02:00
David Beckingsale
fa3265ea51 Convert RAJA, CHAI and Umpire to CachedCMakePackages (#25788)
* Switch Umpire to CMakeCachedPackage
* Fix missing import
* Correct tests option in Umpire
* Switch RAJA to CachedCMakePackage
* Convert CHAI to CachedCMakePackage
* Corrections in RAJA
* Patches in Umpire & RAJA for BLT target export
* Fixup style
* Fixup incorrect use of cmake_cache_string
2021-09-17 21:29:41 -07:00
Chris White
79ac572f21 update tutorial version of hdf5 (#25368) 2021-09-17 17:34:56 -07:00
Massimiliano Culpo
b847bb72f0 Bootstrap should search for compilers after switching config scopes (#26029)
fixes #25992

Currently the bootstrapping process may need a compiler.

When bootstrapping from sources the need is obvious, while
when bootstrapping from binaries it's currently needed in
case patchelf is not on the system (since it will be then
bootstrapped from sources).

Before this PR we were searching for compilers as the
first operation, in case they were not declared in
the configuration. This fails in case we start
bootstrapping from within an environment.

The fix is to defer the search until we have swapped
configuration.
2021-09-17 18:28:48 -06:00
Harmen Stoppels
4d36c40cfb Bump reframe (#25970) 2021-09-17 14:23:05 -06:00
Olli Lupton
ae9adba900 Add ccache v4.4.1. (#25957) 2021-09-17 13:37:58 -06:00
Cyrus Harrison
bd415ec841 improve ascent package to use stages and cmake base (#25720)
* improve ascent package to use stages and cmake base

* style

* more style
2021-09-17 10:37:16 -07:00
iarspider
7e7de25aba fmt: add variant for shared library (#25969) 2021-09-17 08:04:55 -06:00
eugeneswalker
730720d50a variant build: openmp_ref should be openmp (#26006) 2021-09-17 06:38:00 -06:00
iarspider
8e486c1e57 gosam: new version 2.1.1 (#25985) 2021-09-17 06:10:41 -06:00
Kurt Sansom
be8e52fbbe GCC: patch for gcc 10.3.0 ICE when using nvcc (#25980)
* fix: patch for gcc 10.3.0 ICE when using nvcc

* fix: use URL reference instead

* fix: add missing sha256sum
2021-09-16 18:43:56 -06:00
Edward Hartnett
f8fae997d3 added package.py for GPTL (#25993) 2021-09-16 17:11:05 -06:00
Massimiliano Culpo
71a3173a32 Filter UserWarning out of test output (#26001) 2021-09-16 14:56:00 -06:00
Miroslav Stoyanov
e027cecff2 workaround a cmake/rocm bug in heffte (#25948) 2021-09-16 13:26:07 -06:00
Alec Scott
bb29c5d674 Add v7.0.2 to Admixtools (#25997) 2021-09-16 12:08:15 -06:00
G-Ragghianti
c4e26ac7c8 Fix for problem with cmake@3.21 (#25989) 2021-09-16 11:52:59 -06:00
AMD Toolchain Support
cf81046bb1 New package: ROMS (#25990)
Co-authored-by: Mohan Babu <mohbabul@amd.com>
2021-09-16 10:34:45 -07:00
Michael Kuhn
2d34acf29e cc: Use parameter expansion instead of basename (#24509)
While debugging #24508, I noticed that we call `basename` in `cc`. The
same can be achieved by using Bash's parameter expansion, saving one
external process per call.

Parameter expansion cannot replace basename for directories in some
cases, but is guaranteed to work for executables.
2021-09-16 16:25:49 +00:00
Michael Kuhn
d73fe19d93 Recommend Git's manyFiles feature (#25977)
Git 2.24 introduced a feature flag for repositories with many files, see:
https://github.blog/2019-11-03-highlights-from-git-2-24/#feature-macros

Since Spack's Git repository contains roughly 8,500 files, it can be
worthwhile to enable this, especially on slow file systems such as NFS:
```
$ hyperfine --warmup 3 'cd spack-default; git status' 'cd spack-manyfiles; git status'
Benchmark #1: cd spack-default; git status
  Time (mean ± σ):      3.388 s ±  0.095 s    [User: 256.2 ms, System: 625.8 ms]
  Range (min … max):    3.168 s …  3.535 s    10 runs

Benchmark #2: cd spack-manyfiles; git status
  Time (mean ± σ):     168.7 ms ±  10.9 ms    [User: 98.6 ms, System: 126.1 ms]
  Range (min … max):   144.8 ms … 188.0 ms    19 runs

Summary
  'cd spack-manyfiles; git status' ran
   20.09 ± 1.42 times faster than 'cd spack-default; git status'
```
2021-09-16 09:41:10 -06:00
Harmen Stoppels
5b211c90f5 Bump sirius 7.2.x (#25939) 2021-09-16 15:00:58 +02:00
Massimiliano Culpo
fa6366a7df Add a deprecation warning when using the old concretizer (#25966) 2021-09-16 13:25:24 +02:00
Mikael Simberg
b09ad2cc8c Update HPX package (#25775)
* Add support for C++20 to HPX package

* Enable unity builds in HPX package when available

* Add support for HIP/ROCm to HPX package

* Rearrange and update required versions for HPX package

* Add C++20 option to asio package
2021-09-16 13:24:17 +02:00
Harmen Stoppels
ccfdac8402 Improve bootstrapping docs a hair (#25962) 2021-09-16 07:02:31 -04:00
Harmen Stoppels
abb0f6e27c Fix NameError in foreground/background test (#25967) 2021-09-16 10:39:07 +02:00
Harmen Stoppels
3fe9b34362 Inform the user about bootstrapping (#25964) 2021-09-16 09:28:24 +02:00
jacorvar
c0122242ee bedops: Fix checksum for 2.4.40 (#25958)
Fixes #25951
2021-09-15 16:17:40 -07:00
Adam J. Stewart
0015f700b7 py-pybind11: use PythonPackage install method (#25650) 2021-09-15 11:57:33 -07:00
dependabot[bot]
5d23638fdc build(deps): bump codecov/codecov-action from 2.0.3 to 2.1.0 (#25925)
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 2.0.3 to 2.1.0.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/master/CHANGELOG.md)
- [Commits](https://github.com/codecov/codecov-action/compare/v2.0.3...v2.1.0)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2021-09-15 16:02:05 +02:00
Tamara Dahlgren
f0b4afe7db Raise exception when 1+ stand-alone tests fail (#25857) 2021-09-15 08:04:59 -04:00
Ben Corbett
75497537a4 Added LvArray 0.2.2 (#25950) 2021-09-15 01:44:07 -06:00
Massimiliano Culpo
c52426ea7a Make clingo the default solver (#25502)
Modifications:
- [x] Change `defaults/config.yaml`
- [x] Add a fix for bootstrapping patchelf from sources if `compilers.yaml` is empty
- [x] Make `SPACK_TEST_SOLVER=clingo` the default for unit-tests
- [x] Fix package failures in the e4s pipeline

Caveats:
1. CentOS 6 still uses the original concretizer as it can't connect to the buildcache due to issues with `ssl` (bootstrapping from sources requires a C++14 capable compiler)
1. I had to update the image tag for GitlabCI in e699f14.  
1. libtool v2.4.2 has been deprecated and other packages received some update
2021-09-14 22:44:16 -07:00
Adam J. Stewart
0d0d438c11 Add a __reduce__ method to Environment (#25678)
* Add a __reduce__ method to Environment
* Add unit test
* Convert Path to str
2021-09-14 22:37:36 -07:00
Vanessasaurus
ef5ad4eb34 Adding ability to compare git references to spack install (#24639)
This will allow a user to (from anywhere a Spec is parsed including both name and version) refer to a git commit in lieu of 
a package version, and be able to make comparisons with releases in the history based on commits (or with other commits). We do this by way of:

 - Adding a property, is_commit, to a version, meaning I can always check if a version is a commit and then change some action.
 - Adding an attribute to the Version object which can lookup commits from a git repo and find the last known version before that commit, and the distance
 - Construct new Version comparators, which are tuples. For normal versions, they are unchanged. For commits with a previous version x.y.z, d commits away, the comparator is (x, y, z, '', d). For commits with no previous version, the comparator is ('', d) where d is the distance from the first commit in the repo.
 - Metadata on git commits is cached in the misc_cache, for quick lookup later.
 - Git repos are cached as bare repos in `~/.spack/git_repos`
 - In both caches, git repo urls are turned into file paths within the cache

If a commit cannot be found in the cached git repo, we fetch from the repo. If a commit is found in the cached metadata, we do not recompare to newly downloaded tags (assuming repo structure does not change). The cached metadata may be thrown out by using the `spack clean -m` option if you know the repo structure has changed in a way that invalidates existing entries. Future work will include automatic updates.

# Finding previous versions
Spack will search the repo for any tags that match the string of a version given by the `version` directive. Spack will also search for any tags that match `v + string` for any version string. Beyond that, Spack will search for tags that match a SEMVER regex (i.e., tags of the form x.y.z) and interpret those tags as valid versions as well. Future work will increase the breadth of tags understood by Spack

For each tag, Spack queries git to determine whether the tag is an ancestor of the commit in question or not. Spack then sorts the tags that are ancestors of the commit by commit-distance in the repo, and takes the nearest ancestor. The version represented by that tag is listed as the previous version for the commit.

Not all commits will find a previous version, depending on the package workflow. Future work may enable more tangential relationships between commits and versions to be discovered, but many commits in real world git repos require human knowledge to associate with a most recent previous version. Future work will also allow packages to specify commit/tag/version relationships manually for such situations.

# Version comparisons.
The empty string is a valid component of a Spack version tuple, and is in fact the lowest-valued component. It cannot be generated as part of any valid version. These two characteristics make it perfect for delineating previous versions from distances. For any version x.y.z, (x, y, z, '', _) will be less than any "real" version beginning x.y.z. This ensures that no distance from a release will cause the commit to be interpreted as "greater than" a version which is not an ancestor of it.

Signed-off-by: vsoch <vsoch@users.noreply.github.com>

Co-authored-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: Gregory Becker <becker33@llnl.gov>
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2021-09-14 22:12:34 -07:00
David Beckingsale
c3bc3e61aa gcc: apply backported fixes to v4.9.3 (#25945) 2021-09-15 07:10:04 +02:00
Satish Balay
148071ac8a dealii: add version 9.3.1 (#25915) 2021-09-14 15:26:08 -06:00
Scott Wittenburg
bf7c12b4df Pipelines: (Re)enable E4S on Power stack (#25921)
Pipelines: (Re)enable E4S on Power stack
2021-09-14 14:55:50 -06:00
Weston Ortiz
56c375743a Add missing mumps TPL commands (#25940) 2021-09-14 20:26:37 +01:00
Vanessasaurus
c6edfa3f31 Update spack monitor to support new spec (#25928)
This PR coincides with tiny changes to spack to support spack monitor using the new spec
the corresponding spack monitor PR is at https://github.com/spack/spack-monitor/pull/31.
Since there are no changes to the database we can actually update the current server
fairly easily, so either someone can test locally or we can just update and then
test from that (and update as needed).

Signed-off-by: vsoch <vsoch@users.noreply.github.com>

Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2021-09-14 08:02:04 -06:00
Harmen Stoppels
fc96c49b0b Add py-pot with patch (#25712) 2021-09-14 15:55:02 +02:00
Harmen Stoppels
ce790a89f2 reframe: set PYTHONPATH at runtime (#25842) 2021-09-14 15:54:14 +02:00
Valentin Volkl
1b633e1ca4 ocaml: add patch for clang@11: (#25886) 2021-09-14 09:34:57 +02:00
Ben Darwin
2ac9dc76c4 dcmtk: add v3.6.4, v3.6.5, v3.6.6 (#25923) 2021-09-14 09:22:48 +02:00
Weston Ortiz
d7c5aa46fe trilinos: variant for libx11 (#25823) 2021-09-14 08:53:53 +02:00
Edward Hartnett
f6eb16982a added new version of parallelio library (#25916) 2021-09-13 18:22:54 -06:00
David Beckingsale
be1c4bc563 Rename camp 'main' version (#25918) 2021-09-13 16:55:55 -06:00
Timothy Brown
998de97091 ESMF, NEMSIO and UFS-UTILS changes. (#25846)
* ESMF and NEMSIO changes.

- Updating ESMF to set the COMM correctly when using Intel oneapi.
- Explicitly setting the CMake MPI Fortran compiler for NEMSIO.

* Update UFS utils CMake to use MPI_<lang>_COMPILER.
2021-09-13 16:13:43 -06:00
Greg Becker
dad69e7d7c Fix environment reading from lockfile to trust written hashes (#25879)
#22845 revealed a long-standing bug that had never been triggered before, because the
hashing algorithm had been stable for multiple years while the bug was in production. The
bug was that when reading a concretized environment, Spack did not properly read in the
build hashes associated with the specs in the environment. Those hashes were recomputed
(and as long as we didn't change the algorithm, were recomputed identically). Spack's
policy, though, is never to recompute a hash. Once something is installed, we respect its
metadata hash forever -- even if internally Spack changes the hashing method. Put
differently, once something is concretized, it has a concrete hash, and that's it -- forever.

When we changed the hashing algorithm for performance in #22845 we exposed the bug.
This PR fixes the bug at its source, but properly reading in the cached build hash attributes
associated with the specs. I've also renamed some variables in the Environment class
methods to make a mistake of this sort more difficult to make in the future.

* ensure environment build hashes are never recomputed
* add comment clarifying reattachment of env build hashes
* bump lockfile version and include specfile version in env meta
* Fix unit-test for v1 to v2 conversion

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2021-09-13 15:25:48 -06:00
Massimiliano Culpo
c699e907fc Update command to setup tutorial (#24488) 2021-06-23 19:38:36 -05:00
7560 changed files with 90866 additions and 31261 deletions

View File

@@ -1,6 +1,8 @@
name: Bootstrapping
on:
# This Workflow can be triggered manually
workflow_dispatch:
pull_request:
branches:
- develop
@@ -19,7 +21,7 @@ on:
jobs:
fedora-sources:
fedora-clingo-sources:
runs-on: ubuntu-latest
container: "fedora:latest"
steps:
@@ -29,7 +31,7 @@ jobs:
bzip2 curl file gcc-c++ gcc gcc-gfortran git gnupg2 gzip \
make patch unzip which xz python3 python3-devel tree \
cmake bison bison-devel libstdc++-static
- uses: actions/checkout@v2
- uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
- name: Setup repo and non-root user
run: |
git --version
@@ -46,7 +48,7 @@ jobs:
spack -d solve zlib
tree ~/.spack/bootstrap/store/
ubuntu-sources:
ubuntu-clingo-sources:
runs-on: ubuntu-latest
container: "ubuntu:latest"
steps:
@@ -59,7 +61,7 @@ jobs:
bzip2 curl file g++ gcc gfortran git gnupg2 gzip \
make patch unzip xz-utils python3 python3-dev tree \
cmake bison
- uses: actions/checkout@v2
- uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
- name: Setup repo and non-root user
run: |
git --version
@@ -76,18 +78,47 @@ jobs:
spack -d solve zlib
tree ~/.spack/bootstrap/store/
opensuse-sources:
ubuntu-clingo-binaries-and-patchelf:
runs-on: ubuntu-latest
container: "opensuse/tumbleweed:latest"
container: "ubuntu:latest"
steps:
- name: Install dependencies
env:
DEBIAN_FRONTEND: noninteractive
run: |
apt-get update -y && apt-get upgrade -y
apt-get install -y \
bzip2 curl file g++ gcc gfortran git gnupg2 gzip \
make patch unzip xz-utils python3 python3-dev tree
- uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
- name: Setup repo and non-root user
run: |
git --version
git fetch --unshallow
. .github/workflows/setup_git.sh
useradd -m spack-test
chown -R spack-test .
- name: Bootstrap clingo
shell: runuser -u spack-test -- bash {0}
run: |
source share/spack/setup-env.sh
spack -d solve zlib
tree ~/.spack/bootstrap/store/
opensuse-clingo-sources:
runs-on: ubuntu-latest
container: "opensuse/leap:latest"
steps:
- name: Install dependencies
run: |
zypper update -y
# Harden CI by applying the workaround described here: https://www.suse.com/support/kb/doc/?id=000019505
zypper update -y || zypper update -y
zypper install -y \
bzip2 curl file gcc-c++ gcc gcc-fortran tar git gpg2 gzip \
make patch unzip which xz python3 python3-devel tree \
cmake bison
- uses: actions/checkout@v2
- uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
- name: Setup repo and non-root user
run: |
git --version
@@ -101,13 +132,13 @@ jobs:
spack -d solve zlib
tree ~/.spack/bootstrap/store/
macos-sources:
macos-clingo-sources:
runs-on: macos-latest
steps:
- name: Install dependencies
run: |
brew install cmake bison@2.7 tree
- uses: actions/checkout@v2
- uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
- name: Bootstrap clingo
run: |
source share/spack/setup-env.sh
@@ -126,8 +157,8 @@ jobs:
- name: Install dependencies
run: |
brew install tree
- uses: actions/checkout@v2
- uses: actions/setup-python@v2
- uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
- uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
with:
python-version: ${{ matrix.python-version }}
- name: Bootstrap clingo
@@ -137,15 +168,14 @@ jobs:
spack -d solve zlib
tree ~/.spack/bootstrap/store/
ubuntu-clingo-binaries:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['2.7', '3.5', '3.6', '3.7', '3.8', '3.9']
steps:
- uses: actions/checkout@v2
- uses: actions/setup-python@v2
- uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
- uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
with:
python-version: ${{ matrix.python-version }}
- name: Setup repo and non-root user
@@ -159,3 +189,94 @@ jobs:
spack bootstrap untrust spack-install
spack -d solve zlib
tree ~/.spack/bootstrap/store/
ubuntu-gnupg-binaries:
runs-on: ubuntu-latest
container: "ubuntu:latest"
steps:
- name: Install dependencies
env:
DEBIAN_FRONTEND: noninteractive
run: |
apt-get update -y && apt-get upgrade -y
apt-get install -y \
bzip2 curl file g++ gcc patchelf gfortran git gzip \
make patch unzip xz-utils python3 python3-dev tree
- uses: actions/checkout@v2
- name: Setup repo and non-root user
run: |
git --version
git fetch --unshallow
. .github/workflows/setup_git.sh
useradd -m spack-test
chown -R spack-test .
- name: Bootstrap GnuPG
shell: runuser -u spack-test -- bash {0}
run: |
source share/spack/setup-env.sh
spack bootstrap untrust spack-install
spack -d gpg list
tree ~/.spack/bootstrap/store/
ubuntu-gnupg-sources:
runs-on: ubuntu-latest
container: "ubuntu:latest"
steps:
- name: Install dependencies
env:
DEBIAN_FRONTEND: noninteractive
run: |
apt-get update -y && apt-get upgrade -y
apt-get install -y \
bzip2 curl file g++ gcc patchelf gfortran git gzip \
make patch unzip xz-utils python3 python3-dev tree \
gawk
- uses: actions/checkout@v2
- name: Setup repo and non-root user
run: |
git --version
git fetch --unshallow
. .github/workflows/setup_git.sh
useradd -m spack-test
chown -R spack-test .
- name: Bootstrap GnuPG
shell: runuser -u spack-test -- bash {0}
run: |
source share/spack/setup-env.sh
spack solve zlib
spack bootstrap untrust github-actions
spack -d gpg list
tree ~/.spack/bootstrap/store/
macos-gnupg-binaries:
runs-on: macos-latest
steps:
- name: Install dependencies
run: |
brew install tree
# Remove GnuPG since we want to bootstrap it
sudo rm -rf /usr/local/bin/gpg
- uses: actions/checkout@v2
- name: Bootstrap GnuPG
run: |
source share/spack/setup-env.sh
spack bootstrap untrust spack-install
spack -d gpg list
tree ~/.spack/bootstrap/store/
macos-gnupg-sources:
runs-on: macos-latest
steps:
- name: Install dependencies
run: |
brew install gawk tree
# Remove GnuPG since we want to bootstrap it
sudo rm -rf /usr/local/bin/gpg
- uses: actions/checkout@v2
- name: Bootstrap GnuPG
run: |
source share/spack/setup-env.sh
spack solve zlib
spack bootstrap untrust github-actions
spack -d gpg list
tree ~/.spack/bootstrap/store/

View File

@@ -1,15 +1,27 @@
name: Build & Deploy Docker Containers
name: Containers
on:
# This Workflow can be triggered manually
workflow_dispatch:
# Build new Spack develop containers nightly.
schedule:
- cron: '34 0 * * *'
# Run on pull requests that modify this file
pull_request:
branches:
- develop
paths:
- '.github/workflows/build-containers.yml'
- 'share/spack/docker/*'
# Let's also build & tag Spack containers on releases.
release:
types: [published]
jobs:
deploy-images:
runs-on: ubuntu-latest
runs-on: ubuntu-latest
permissions:
packages: write
strategy:
# Even if one container fails to build we still want the others
# to continue their builds.
@@ -17,19 +29,19 @@ jobs:
# A matrix of Dockerfile paths, associated tags, and which architectures
# they support.
matrix:
dockerfile: [[amazon-linux, amazonlinux-2.dockerfile, 'linux/amd64,linux/arm64'],
[centos7, centos-7.dockerfile, 'linux/amd64,linux/arm64'],
[leap15, leap-15.dockerfile, 'linux/amd64,linux/arm64'],
[ubuntu-xenial, ubuntu-1604.dockerfile, 'linux/amd64,linux/arm64'],
[ubuntu-bionic, ubuntu-1804.dockerfile, 'linux/amd64,linux/arm64']]
dockerfile: [[amazon-linux, amazonlinux-2.dockerfile, 'linux/amd64,linux/arm64'],
[centos7, centos-7.dockerfile, 'linux/amd64,linux/arm64,linux/ppc64le'],
[leap15, leap-15.dockerfile, 'linux/amd64,linux/arm64,linux/ppc64le'],
[ubuntu-xenial, ubuntu-1604.dockerfile, 'linux/amd64,linux/arm64,linux/ppc64le'],
[ubuntu-bionic, ubuntu-1804.dockerfile, 'linux/amd64,linux/arm64,linux/ppc64le']]
name: Build ${{ matrix.dockerfile[0] }}
steps:
- name: Checkout
uses: actions/checkout@v2
uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
- name: Set Container Tag Normal (Nightly)
run: |
container="ghcr.io/spack/${{ matrix.dockerfile[0]}}:latest"
container="${{ matrix.dockerfile[0] }}:latest"
echo "container=${container}" >> $GITHUB_ENV
echo "versioned=${container}" >> $GITHUB_ENV
@@ -37,7 +49,7 @@ jobs:
- name: Set Container Tag on Release
if: github.event_name == 'release'
run: |
versioned="ghcr.io/spack/${{matrix.dockerfile[0]}}:${GITHUB_REF##*/}"
versioned="${{matrix.dockerfile[0]}}:${GITHUB_REF##*/}"
echo "versioned=${versioned}" >> $GITHUB_ENV
- name: Check ${{ matrix.dockerfile[1] }} Exists
@@ -48,25 +60,34 @@ jobs:
exit 1;
fi
- name: Set up QEMU
uses: docker/setup-qemu-action@27d0a4f181a40b142cce983c5393082c365d1480 # @v1
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@94ab11c41e45d028884a99163086648e898eed25 # @v1
- name: Log in to GitHub Container Registry
uses: docker/login-action@v1
uses: docker/login-action@42d299face0c5c43a0487c477f595ac9cf22f1a7 # @v1
with:
registry: ghcr.io
username: ${{ github.actor }}
password: ${{ secrets.GITHUB_TOKEN }}
- name: Set up QEMU
uses: docker/setup-qemu-action@v1
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v1
- name: Log in to DockerHub
if: ${{ github.event_name != 'pull_request' }}
uses: docker/login-action@42d299face0c5c43a0487c477f595ac9cf22f1a7 # @v1
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
- name: Build & Deploy ${{ matrix.dockerfile[1] }}
uses: docker/build-push-action@v2
uses: docker/build-push-action@7f9d37fa544684fb73bfe4835ed7214c255ce02b # @v2
with:
file: share/spack/docker/${{matrix.dockerfile[1]}}
platforms: ${{ matrix.dockerfile[2] }}
push: true
push: ${{ github.event_name != 'pull_request' }}
tags: |
${{ env.container }}
${{ env.versioned }}
spack/${{ env.container }}
spack/${{ env.versioned }}
ghcr.io/spack/${{ env.container }}
ghcr.io/spack/${{ env.versioned }}

View File

@@ -2,19 +2,7 @@
. share/spack/setup-env.sh
echo -e "config:\n build_jobs: 2" > etc/spack/config.yaml
spack config add "packages:all:target:[x86_64]"
# TODO: remove this explicit setting once apple-clang detection is fixed
cat <<EOF > etc/spack/compilers.yaml
compilers:
- compiler:
spec: apple-clang@11.0.3
paths:
cc: /usr/bin/clang
cxx: /usr/bin/clang++
f77: /usr/local/bin/gfortran-9
fc: /usr/local/bin/gfortran-9
modules: []
operating_system: catalina
target: x86_64
EOF
spack compiler find
spack compiler info apple-clang
spack debug report
spack solve zlib

View File

@@ -24,23 +24,23 @@ jobs:
name: gcc with clang
runs-on: macos-latest
steps:
- uses: actions/checkout@v2
- uses: actions/setup-python@v2
- uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
- uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
with:
python-version: 3.9
- name: spack install
run: |
. .github/workflows/install_spack.sh
# 9.2.0 is the latest version on which we apply homebrew patch
spack install -v --fail-fast gcc@9.2.0 %apple-clang
spack install -v --fail-fast gcc@11.2.0 %apple-clang
install_jupyter_clang:
name: jupyter
runs-on: macos-latest
timeout-minutes: 700
steps:
- uses: actions/checkout@v2
- uses: actions/setup-python@v2
- uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
- uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
with:
python-version: 3.9
- name: spack install
@@ -52,8 +52,8 @@ jobs:
name: scipy, mpl, pd
runs-on: macos-latest
steps:
- uses: actions/checkout@v2
- uses: actions/setup-python@v2
- uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
- uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
with:
python-version: 3.9
- name: spack install
@@ -62,17 +62,3 @@ jobs:
spack install -v --fail-fast py-scipy %apple-clang
spack install -v --fail-fast py-matplotlib %apple-clang
spack install -v --fail-fast py-pandas %apple-clang
install_mpi4py_clang:
name: mpi4py, petsc4py
runs-on: macos-latest
steps:
- uses: actions/checkout@v2
- uses: actions/setup-python@v2
with:
python-version: 3.9
- name: spack install
run: |
. .github/workflows/install_spack.sh
spack install -v --fail-fast py-mpi4py %apple-clang
spack install -v --fail-fast py-petsc4py %apple-clang

View File

@@ -1,9 +1,8 @@
#!/usr/bin/env sh
#!/bin/bash -e
git config --global user.email "spack@example.com"
git config --global user.name "Test User"
# With fetch-depth: 0 we have a remote develop
# but not a local branch. Don't do this on develop
if [ "$(git branch --show-current)" != "develop" ]
then
git branch develop origin/develop
# create a local pr base branch
if [[ -n $GITHUB_BASE_REF ]]; then
git fetch origin "${GITHUB_BASE_REF}:${GITHUB_BASE_REF}"
fi

View File

@@ -15,8 +15,8 @@ jobs:
validate:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/setup-python@v2
- uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
- uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
with:
python-version: 3.9
- name: Install Python Packages
@@ -24,17 +24,17 @@ jobs:
pip install --upgrade pip
pip install --upgrade vermin
- name: vermin (Spack's Core)
run: vermin --backport argparse --violations --backport typing -t=2.6- -t=3.5- -vvv lib/spack/spack/ lib/spack/llnl/ bin/
run: vermin --backport argparse --violations --backport typing -t=2.7- -t=3.5- -vvv lib/spack/spack/ lib/spack/llnl/ bin/
- name: vermin (Repositories)
run: vermin --backport argparse --violations --backport typing -t=2.6- -t=3.5- -vvv var/spack/repos
run: vermin --backport argparse --violations --backport typing -t=2.7- -t=3.5- -vvv var/spack/repos
# Run style checks on the files that have been changed
style:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
with:
fetch-depth: 0
- uses: actions/setup-python@v2
- uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
with:
python-version: 3.9
- name: Install Python packages
@@ -48,26 +48,6 @@ jobs:
- name: Run style tests
run: |
share/spack/qa/run-style-tests
# Build the documentation
documentation:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/setup-python@v2
with:
python-version: 3.9
- name: Install System packages
run: |
sudo apt-get -y update
sudo apt-get install -y coreutils ninja-build graphviz
- name: Install Python packages
run: |
pip install --upgrade pip six setuptools
pip install --upgrade -r lib/spack/docs/requirements.txt
- name: Build documentation
run: |
share/spack/qa/run-doc-tests
# Check which files have been updated by the PR
changes:
runs-on: ubuntu-latest
@@ -77,12 +57,12 @@ jobs:
packages: ${{ steps.filter.outputs.packages }}
with_coverage: ${{ steps.coverage.outputs.with_coverage }}
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
if: ${{ github.event_name == 'push' }}
with:
fetch-depth: 0
# For pull requests it's not necessary to checkout the code
- uses: dorny/paths-filter@v2
- uses: dorny/paths-filter@b2feaf19c27470162a626bd6fa8438ae5b263721
id: filter
with:
# See https://github.com/dorny/paths-filter/issues/56 for the syntax used below
@@ -112,17 +92,24 @@ jobs:
# Run unit tests with different configurations on linux
unittests:
needs: [ validate, style, documentation, changes ]
needs: [ validate, style, changes ]
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [2.7, 3.5, 3.6, 3.7, 3.8, 3.9]
concretizer: ['original', 'clingo']
concretizer: ['clingo']
include:
- python-version: 2.7
concretizer: original
- python-version: 3.6
concretizer: original
- python-version: 3.9
concretizer: original
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
with:
fetch-depth: 0
- uses: actions/setup-python@v2
- uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
with:
python-version: ${{ matrix.python-version }}
- name: Install System packages
@@ -134,12 +121,16 @@ jobs:
patchelf cmake bison libbison-dev kcov
- name: Install Python packages
run: |
pip install --upgrade pip six setuptools codecov coverage[toml]
pip install --upgrade pip six setuptools pytest codecov "coverage[toml]<=6.2"
# ensure style checks are not skipped in unit tests for python >= 3.6
# note that true/false (i.e., 1/0) are opposite in conditions in python and bash
if python -c 'import sys; sys.exit(not sys.version_info >= (3, 6))'; then
pip install --upgrade flake8 isort>=4.3.5 mypy>=0.900 black
fi
- name: Pin pathlib for Python 2.7
if: ${{ matrix.python-version == 2.7 }}
run: |
pip install -U pathlib2==2.3.6
- name: Setup git configuration
run: |
# Need this for the git tests to succeed.
@@ -171,19 +162,19 @@ jobs:
SPACK_TEST_SOLVER: ${{ matrix.concretizer }}
run: |
share/spack/qa/run-unit-tests
- uses: codecov/codecov-action@v2.0.3
- uses: codecov/codecov-action@f32b3a3741e1053eb607407145bc9619351dc93b # @v2.1.0
if: ${{ needs.changes.outputs.with_coverage == 'true' }}
with:
flags: unittests,linux,${{ matrix.concretizer }}
# Test shell integration
shell:
needs: [ validate, style, documentation, changes ]
needs: [ validate, style, changes ]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
with:
fetch-depth: 0
- uses: actions/setup-python@v2
- uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
with:
python-version: 3.9
- name: Install System packages
@@ -193,7 +184,7 @@ jobs:
sudo apt-get install -y coreutils kcov csh zsh tcsh fish dash bash
- name: Install Python packages
run: |
pip install --upgrade pip six setuptools codecov coverage[toml]
pip install --upgrade pip six setuptools pytest codecov coverage[toml]==6.2
- name: Setup git configuration
run: |
# Need this for the git tests to succeed.
@@ -209,44 +200,15 @@ jobs:
COVERAGE: true
run: |
share/spack/qa/run-shell-tests
- uses: codecov/codecov-action@v2.0.3
- uses: codecov/codecov-action@f32b3a3741e1053eb607407145bc9619351dc93b # @v2.1.0
if: ${{ needs.changes.outputs.with_coverage == 'true' }}
with:
flags: shelltests,linux
# Test for Python2.6 run on Centos 6
centos6:
needs: [ validate, style, documentation, changes ]
runs-on: ubuntu-latest
container: spack/github-actions:centos6
steps:
- name: Run unit tests (full test-suite)
# The CentOS 6 container doesn't run with coverage, but
# under the same conditions it runs the full test suite
if: ${{ needs.changes.outputs.with_coverage == 'true' }}
env:
HOME: /home/spack-test
run: |
whoami && echo $HOME && cd $HOME
git clone https://github.com/spack/spack.git && cd spack
git fetch origin ${{ github.ref }}:test-branch
git checkout test-branch
share/spack/qa/run-unit-tests
- name: Run unit tests (only package tests)
if: ${{ needs.changes.outputs.with_coverage == 'false' }}
env:
HOME: /home/spack-test
ONLY_PACKAGES: true
run: |
whoami && echo $HOME && cd $HOME
git clone https://github.com/spack/spack.git && cd spack
git fetch origin ${{ github.ref }}:test-branch
git checkout test-branch
share/spack/qa/run-unit-tests
# Test RHEL8 UBI with platform Python. This job is run
# only on PRs modifying core Spack
rhel8-platform-python:
needs: [ validate, style, documentation, changes ]
needs: [ validate, style, changes ]
runs-on: ubuntu-latest
if: ${{ needs.changes.outputs.with_coverage == 'true' }}
container: registry.access.redhat.com/ubi8/ubi
@@ -256,7 +218,7 @@ jobs:
dnf install -y \
bzip2 curl file gcc-c++ gcc gcc-gfortran git gnupg2 gzip \
make patch tcl unzip which xz
- uses: actions/checkout@v2
- uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
- name: Setup repo and non-root user
run: |
git --version
@@ -268,16 +230,17 @@ jobs:
shell: runuser -u spack-test -- bash {0}
run: |
source share/spack/setup-env.sh
spack -d solve zlib
spack unit-test -k 'not cvs and not svn and not hg' -x --verbose
# Test for the clingo based solver (using clingo-cffi)
clingo-cffi:
needs: [ validate, style, documentation, changes ]
needs: [ validate, style, changes ]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
with:
fetch-depth: 0
- uses: actions/setup-python@v2
- uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
with:
python-version: 3.9
- name: Install System packages
@@ -289,7 +252,7 @@ jobs:
patchelf kcov
- name: Install Python packages
run: |
pip install --upgrade pip six setuptools codecov coverage[toml] clingo
pip install --upgrade pip six setuptools pytest codecov coverage[toml]==6.2 clingo
- name: Setup git configuration
run: |
# Need this for the git tests to succeed.
@@ -311,28 +274,28 @@ jobs:
SPACK_TEST_SOLVER: clingo
run: |
share/spack/qa/run-unit-tests
- uses: codecov/codecov-action@v2.0.3
- uses: codecov/codecov-action@f32b3a3741e1053eb607407145bc9619351dc93b # @v2.1.0
if: ${{ needs.changes.outputs.with_coverage == 'true' }}
with:
flags: unittests,linux,clingo
# Run unit tests on MacOS
build:
needs: [ validate, style, documentation, changes ]
needs: [ validate, style, changes ]
runs-on: macos-latest
strategy:
matrix:
python-version: [3.8]
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
with:
fetch-depth: 0
- uses: actions/setup-python@v2
- uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
with:
python-version: ${{ matrix.python-version }}
- name: Install Python packages
run: |
pip install --upgrade pip six setuptools
pip install --upgrade codecov coverage[toml]
pip install --upgrade pytest codecov coverage[toml]==6.2
- name: Setup Homebrew packages
run: |
brew install dash fish gcc gnupg2 kcov
@@ -357,8 +320,37 @@ jobs:
echo "ONLY PACKAGE RECIPES CHANGED [skipping coverage]"
$(which spack) unit-test -x -m "not maybeslow" -k "package_sanity"
fi
- uses: codecov/codecov-action@v2.0.3
- uses: codecov/codecov-action@f32b3a3741e1053eb607407145bc9619351dc93b # @v2.1.0
if: ${{ needs.changes.outputs.with_coverage == 'true' }}
with:
files: ./coverage.xml
flags: unittests,macos
# Run audits on all the packages in the built-in repository
package-audits:
needs: [ validate, style, changes ]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@ec3a7ce113134d7a93b817d10a8272cb61118579 # @v2
- uses: actions/setup-python@f38219332975fe8f9c04cca981d674bf22aea1d3 # @v2
with:
python-version: 3.9
- name: Install Python packages
run: |
pip install --upgrade pip six setuptools pytest codecov coverage[toml]==6.2
- name: Package audits (with coverage)
if: ${{ needs.changes.outputs.with_coverage == 'true' }}
run: |
. share/spack/setup-env.sh
coverage run $(which spack) audit packages
coverage combine
coverage xml
- name: Package audits (wwithout coverage)
if: ${{ needs.changes.outputs.with_coverage == 'false' }}
run: |
. share/spack/setup-env.sh
$(which spack) audit packages
- uses: codecov/codecov-action@f32b3a3741e1053eb607407145bc9619351dc93b # @v2.1.0
if: ${{ needs.changes.outputs.with_coverage == 'true' }}
with:
flags: unittests,linux,audits

5
.gitignore vendored
View File

@@ -132,11 +132,11 @@ celerybeat.pid
.env
.venv
env/
!/lib/spack/env
venv/
ENV/
env.bak/
venv.bak/
!/lib/spack/env
# Spyder project settings
.spyderproject
@@ -210,6 +210,9 @@ tramp
/eshell/history
/eshell/lastdir
# zsh byte-compiled files
*.zwc
# elpa packages
/elpa/

View File

@@ -2,6 +2,7 @@ version: 2
sphinx:
configuration: lib/spack/docs/conf.py
fail_on_warning: true
python:
version: 3.7

View File

@@ -1,3 +1,212 @@
# v0.17.1 (2021-12-23)
### Spack Bugfixes
* Allow locks to work under high contention (#27846)
* Improve errors messages from clingo (#27707 #27970)
* Respect package permissions for sbang (#25764)
* Fix --enable-locks behavior (#24675)
* Fix log-format reporter ignoring install errors (#25961)
* Fix overloaded argparse keys (#27379)
* Allow style commands to run with targets other than "develop" (#27472)
* Log lock messages to debug level, instead of verbose level (#27408)
* Handle invalid unicode while logging (#21447)
* spack audit: fix API calls to variants (#27713)
* Provide meaningful message for empty environment installs (#28031)
* Added opensuse leap containers to spack containerize (#27837)
* Revert "patches: make re-applied patches idempotent" (#27625)
* MANPATH can use system defaults (#21682)
* Add "setdefault" subcommand to `spack module tcl` (#14686)
* Regenerate views when specs already installed (#28113)
### Package bugfixes
* Fix external package detection for OpenMPI (#27255)
* Update the UPC++ package to 2021.9.0 (#26996)
* Added py-vermin v1.3.2 (#28072)
# v0.17.0 (2021-11-05)
`v0.17.0` is a major feature release.
## Major features in this release
1. **New concretizer is now default**
The new concretizer introduced as an experimental feature in `v0.16.0`
is now the default (#25502). The new concretizer is based on the
[clingo](https://github.com/potassco/clingo) logic programming system,
and it enables us to do much higher quality and faster dependency solving
The old concretizer is still available via the `concretizer: original`
setting, but it is deprecated and will be removed in `v0.18.0`.
2. **Binary Bootstrapping**
To make it easier to use the new concretizer and binary packages,
Spack now bootstraps `clingo` and `GnuPG` from public binaries. If it
is not able to bootstrap them from binaries, it installs them from
source code. With these changes, you should still be able to clone Spack
and start using it almost immediately. (#21446, #22354, #22489, #22606,
#22720, #22720, #23677, #23946, #24003, #25138, #25607, #25964, #26029,
#26399, #26599).
3. **Reuse existing packages (experimental)**
The most wanted feature from our
[2020 user survey](https://spack.io/spack-user-survey-2020/) and
the most wanted Spack feature of all time (#25310). `spack install`,
`spack spec`, and `spack concretize` now have a `--reuse` option, which
causes Spack to minimize the number of rebuilds it does. The `--reuse`
option will try to find existing installations and binary packages locally
and in registered mirrors, and will prefer to use them over building new
versions. This will allow users to build from source *far* less than in
prior versions of Spack. This feature will continue to be improved, with
configuration options and better CLI expected in `v0.17.1`. It will become
the *default* concretization mode in `v0.18.0`.
4. **Better error messages**
We have improved the error messages generated by the new concretizer by
using *unsatisfiable cores*. Spack will now print a summary of the types
of constraints that were violated to make a spec unsatisfiable (#26719).
5. **Conditional variants**
Variants can now have a `when="<spec>"` clause, allowing them to be
conditional based on the version or other attributes of a package (#24858).
6. **Git commit versions**
In an environment and on the command-line, you can now provide a full,
40-character git commit as a version for any package with a top-level
`git` URL. e.g., `spack install hdf5@45bb27f58240a8da7ebb4efc821a1a964d7712a8`.
Spack will compare the commit to tags in the git repository to understand
what versions it is ahead of or behind.
7. **Override local config and cache directories**
You can now set `SPACK_DISABLE_LOCAL_CONFIG` to disable the `~/.spack` and
`/etc/spack` configuration scopes. `SPACK_USER_CACHE_PATH` allows you to
move caches out of `~/.spack`, as well (#27022, #26735). This addresses
common problems where users could not isolate CI environments from local
configuration.
8. **Improvements to Spack Containerize**
For added reproducibility, you can now pin the Spack version used by
`spack containerize` (#21910). The container build will only build
with the Spack version pinned at build recipe creation instead of the
latest Spack version.
9. **New commands for dealing with tags**
The `spack tags` command allows you to list tags on packages (#26136), and you
can list tests and filter tags with `spack test list` (#26842).
## Other new features of note
* Copy and relocate environment views as stand-alone installations (#24832)
* `spack diff` command can diff two installed specs (#22283, #25169)
* `spack -c <config>` can set one-off config parameters on CLI (#22251)
* `spack load --list` is an alias for `spack find --loaded` (#27184)
* `spack gpg` can export private key with `--secret` (#22557)
* `spack style` automatically bootstraps dependencies (#24819)
* `spack style --fix` automatically invokes `isort` (#24071)
* build dependencies can be installed from build caches with `--include-build-deps` (#19955)
* `spack audit` command for checking package constraints (#23053)
* Spack can now fetch from `CVS` repositories (yep, really) (#23212)
* `spack monitor` lets you upload analysis about installations to a
[spack monitor server](https://github.com/spack/spack-monitor) (#23804, #24321,
#23777, #25928))
* `spack python --path` shows which `python` Spack is using (#22006)
* `spack env activate --temp` can create temporary environments (#25388)
* `--preferred` and `--latest` options for `spack checksum` (#25830)
* `cc` is now pure posix and runs on Alpine (#26259)
* `SPACK_PYTHON` environment variable sets which `python` spack uses (#21222)
* `SPACK_SKIP_MODULES` lets you source `setup-env.sh` faster if you don't need modules (#24545)
## Major internal refactors
* `spec.yaml` files are now `spec.json`, yielding a large speed improvement (#22845)
* Splicing allows Spack specs to store mixed build provenance (#20262)
* More extensive hooks API for installations (#21930)
* New internal API for getting the active environment (#25439)
## Performance Improvements
* Parallelize separate concretization in environments; Previously 55 min E4S solve
now takes 2.5 min (#26264)
* Drastically improve YamlFilesystemView file removal performance via batching (#24355)
* Speed up spec comparison (#21618)
* Speed up environment activation (#25633)
## Archspec improvements
* support for new generic `x86_64_v2`, `x86_64_v3`, `x86_64_v4` targets
(see [archspec#31](https://github.com/archspec/archspec-json/pull/31))
* `spack arch --generic` lets you get the best generic architecture for
your node (#27061)
* added support for aocc (#20124), `arm` compiler on `graviton2` (#24904)
and on `a64fx` (#24524),
## Infrastructure, buildcaches, and services
* Add support for GCS Bucket Mirrors (#26382)
* Add `spackbot` to help package maintainers with notifications. See
[spack.github.io/spackbot](https://spack.github.io/spackbot/)
* Reproducible pipeline builds with `spack ci rebuild` (#22887)
* Removed redundant concretizations from GitLab pipeline generation (#26622)
* Spack CI no longer generates jobs for unbuilt specs (#20435)
* Every pull request pipeline has its own buildcache (#25529)
* `--no-add` installs only specified specs and only if already present in… (#22657)
* Add environment-aware `spack buildcache sync` command (#25470)
* Binary cache installation speedups and improvements (#19690, #20768)
## Deprecations and Removals
* `spack setup` was deprecated in v0.16.0, and has now been removed.
Use `spack develop` and `spack dev-build`.
* Remove unused `--dependencies` flag from `spack load` (#25731)
* Remove stubs for `spack module [refresh|find|rm|loads]`, all of which
were deprecated in 2018.
## Notable Bugfixes
* Deactivate previous env before activating new one (#25409)
* Many fixes to error codes from `spack install` (#21319, #27012, #25314)
* config add: infer type based on JSON schema validation errors (#27035)
* `spack config edit` now works even if `spack.yaml` is broken (#24689)
## Packages
* Allow non-empty version ranges like `1.1.0:1.1` (#26402)
* Remove `.99`'s from many version ranges (#26422)
* Python: use platform-specific site packages dir (#25998)
* `CachedCMakePackage` for using *.cmake initial config files (#19316)
* `lua-lang` allows swapping `lua` and `luajit` (#22492)
* Better support for `ld.gold` and `ld.lld` (#25626)
* build times are now stored as metadata in `$prefix/.spack` (#21179)
* post-install tests can be reused in smoke tests (#20298)
* Packages can use `pypi` attribute to infer `homepage`/`url`/`list_url` (#17587)
* Use gnuconfig package for `config.guess` file replacement (#26035)
* patches: make re-applied patches idempotent (#26784)
## Spack community stats
* 5969 total packages, 920 new since `v0.16.0`
* 358 new Python packages, 175 new R packages
* 513 people contributed to this release
* 490 committers to packages
* 105 committers to core
* Lots of GPU updates:
* ~77 CUDA-related commits
* ~66 AMD-related updates
* ~27 OneAPI-related commits
* 30 commits from AMD toolchain support
* `spack test` usage in packages is increasing
* 1669 packages with tests (mostly generic python tests)
* 93 packages with their own tests
# v0.16.3 (2021-09-21)
* clang/llvm: fix version detection (#19978)
* Fix use of quotes in Python build system (#22279)
* Cray: fix extracting paths from module files (#23472)
* Use AWS CloudFront for source mirror (#23978)
* Ensure all roots of an installed environment are marked explicit in db (#24277)
* Fix fetching for Python 3.8 and 3.9 (#24686)
* locks: only open lockfiles once instead of for every lock held (#24794)
* Remove the EOL centos:6 docker image
# v0.16.2 (2021-05-22)
* Major performance improvement for `spack load` and other commands. (#23661)

58
CITATION.cff Normal file
View File

@@ -0,0 +1,58 @@
# If you are referencing Spack in a publication, please cite the SC'15 paper
# described here.
#
# Here's the raw citation:
#
# Todd Gamblin, Matthew P. LeGendre, Michael R. Collette, Gregory L. Lee,
# Adam Moody, Bronis R. de Supinski, and W. Scott Futral.
# The Spack Package Manager: Bringing Order to HPC Software Chaos.
# In Supercomputing 2015 (SC15), Austin, Texas, November 15-20 2015. LLNL-CONF-669890.
#
# Or, in BibTeX:
#
# @inproceedings{Gamblin_The_Spack_Package_2015,
# address = {Austin, Texas, USA},
# author = {Gamblin, Todd and LeGendre, Matthew and
# Collette, Michael R. and Lee, Gregory L. and
# Moody, Adam and de Supinski, Bronis R. and Futral, Scott},
# doi = {10.1145/2807591.2807623},
# month = {November 15-20},
# note = {LLNL-CONF-669890},
# series = {Supercomputing 2015 (SC15)},
# title = {{The Spack Package Manager: Bringing Order to HPC Software Chaos}},
# url = {https://github.com/spack/spack},
# year = {2015}
# }
#
# And here's the CITATION.cff format:
#
cff-version: 1.2.0
message: "If you are referencing Spack in a publication, please cite the paper below."
preferred-citation:
type: conference-paper
doi: "10.1145/2807591.2807623"
url: "https://github.com/spack/spack"
authors:
- family-names: "Gamblin"
given-names: "Todd"
- family-names: "LeGendre"
given-names: "Matthew"
- family-names: "Collette"
given-names: "Michael R."
- family-names: "Lee"
given-names: "Gregory L."
- family-names: "Moody"
given-names: "Adam"
- family-names: "de Supinski"
given-names: "Bronis R."
- family-names: "Futral"
given-names: "Scott"
title: "The Spack Package Manager: Bringing Order to HPC Software Chaos"
conference:
name: "Supercomputing 2015 (SC15)"
city: "Austin"
region: "Texas"
country: "USA"
month: November 15-20
year: 2015
notes: LLNL-CONF-669890

View File

@@ -34,10 +34,22 @@ includes the sbang tool directly in bin/sbang. These packages are covered
by various permissive licenses. A summary listing follows. See the
license included with each package for full details.
PackageName: altgraph
PackageHomePage: https://altgraph.readthedocs.io/en/latest/index.html
PackageLicenseDeclared: MIT
PackageName: argparse
PackageHomePage: https://pypi.python.org/pypi/argparse
PackageLicenseDeclared: Python-2.0
PackageName: astunparse
PackageHomePage: https://github.com/simonpercivall/astunparse
PackageLicenseDeclared: Python-2.0
PackageName: attrs
PackageHomePage: https://github.com/python-attrs/attrs
PackageLicenseDeclared: MIT
PackageName: ctest_log_parser
PackageHomePage: https://github.com/Kitware/CMake
PackageLicenseDeclared: BSD-3-Clause
@@ -46,8 +58,8 @@ PackageName: distro
PackageHomePage: https://pypi.python.org/pypi/distro
PackageLicenseDeclared: Apache-2.0
PackageName: functools
PackageHomePage: https://github.com/python/cpython/blob/2.7/Lib/functools.py
PackageName: functools32
PackageHomePage: https://github.com/MiCHiLU/python-functools32
PackageLicenseDeclared: Python-2.0
PackageName: jinja2
@@ -58,6 +70,10 @@ PackageName: jsonschema
PackageHomePage: https://pypi.python.org/pypi/jsonschema
PackageLicenseDeclared: MIT
PackageName: macholib
PackageHomePage: https://macholib.readthedocs.io/en/latest/index.html
PackageLicenseDeclared: MIT
PackageName: markupsafe
PackageHomePage: https://pypi.python.org/pypi/MarkupSafe
PackageLicenseDeclared: BSD-3-Clause
@@ -70,6 +86,10 @@ PackageName: py
PackageHomePage: https://pypi.python.org/pypi/py
PackageLicenseDeclared: MIT
PackageName: pyrsistent
PackageHomePage: http://github.com/tobgu/pyrsistent
PackageLicenseDeclared: MIT
PackageName: pytest
PackageHomePage: https://pypi.python.org/pypi/pytest
PackageLicenseDeclared: MIT
@@ -85,11 +105,3 @@ PackageLicenseDeclared: Apache-2.0 OR MIT
PackageName: six
PackageHomePage: https://pypi.python.org/pypi/six
PackageLicenseDeclared: MIT
PackageName: macholib
PackageHomePage: https://macholib.readthedocs.io/en/latest/index.html
PackageLicenseDeclared: MIT
PackageName: altgraph
PackageHomePage: https://altgraph.readthedocs.io/en/latest/index.html
PackageLicenseDeclared: MIT

View File

@@ -1,6 +1,6 @@
MIT License
Copyright (c) 2013-2020 LLNS, LLC and other Spack Project Developers.
Copyright (c) 2013-2022 LLNS, LLC and other Spack Project Developers.
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal

View File

@@ -4,6 +4,7 @@
[![Bootstrapping](https://github.com/spack/spack/actions/workflows/bootstrap.yml/badge.svg)](https://github.com/spack/spack/actions/workflows/bootstrap.yml)
[![macOS Builds (nightly)](https://github.com/spack/spack/workflows/macOS%20builds%20nightly/badge.svg?branch=develop)](https://github.com/spack/spack/actions?query=workflow%3A%22macOS+builds+nightly%22)
[![codecov](https://codecov.io/gh/spack/spack/branch/develop/graph/badge.svg)](https://codecov.io/gh/spack/spack)
[![Containers](https://github.com/spack/spack/actions/workflows/build-containers.yml/badge.svg)](https://github.com/spack/spack/actions/workflows/build-containers.yml)
[![Read the Docs](https://readthedocs.org/projects/spack/badge/?version=latest)](https://spack.readthedocs.io)
[![Slack](https://slack.spack.io/badge.svg)](https://slack.spack.io)
@@ -26,7 +27,7 @@ for examples and highlights.
To install spack and your first package, make sure you have Python.
Then:
$ git clone https://github.com/spack/spack.git
$ git clone -c feature.manyFiles=true https://github.com/spack/spack.git
$ cd spack/bin
$ ./spack install zlib
@@ -124,6 +125,9 @@ If you are referencing Spack in a publication, please cite the following paper:
[**The Spack Package Manager: Bringing Order to HPC Software Chaos**](https://www.computer.org/csdl/proceedings/sc/2015/3723/00/2807623.pdf).
In *Supercomputing 2015 (SC15)*, Austin, Texas, November 15-20 2015. LLNL-CONF-669890.
On GitHub, you can copy this citation in APA or BibTeX format via the "Cite this repository"
button. Or, see the comments in `CITATION.cff` for the raw BibTeX.
License
----------------

25
SECURITY.md Normal file
View File

@@ -0,0 +1,25 @@
# Security Policy
## Supported Versions
We provide security updates for the following releases.
For more on Spack's release structure, see
[`README.md`](https://github.com/spack/spack#releases).
| Version | Supported |
| ------- | ------------------ |
| develop | :white_check_mark: |
| 0.17.x | :white_check_mark: |
| 0.16.x | :white_check_mark: |
## Reporting a Vulnerability
To report a vulnerability or other security
issue, email maintainers@spack.io.
You can expect to hear back within two days.
If your security issue is accepted, we will do
our best to release a fix within a week. If
fixing the issue will take longer than this,
we will discuss timeline options with you.

View File

@@ -1,7 +1,7 @@
#!/bin/sh
# -*- python -*-
#
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
@@ -33,11 +33,11 @@ import sys
min_python3 = (3, 5)
if sys.version_info[:2] < (2, 6) or (
if sys.version_info[:2] < (2, 7) or (
sys.version_info[:2] >= (3, 0) and sys.version_info[:2] < min_python3
):
v_info = sys.version_info[:3]
msg = "Spack requires Python 2.6, 2.7 or %d.%d or higher " % min_python3
msg = "Spack requires Python 2.7 or %d.%d or higher " % min_python3
msg += "You are running spack with Python %d.%d.%d." % v_info
sys.exit(msg)
@@ -54,8 +54,6 @@ spack_external_libs = os.path.join(spack_lib_path, "external")
if sys.version_info[:2] <= (2, 7):
sys.path.insert(0, os.path.join(spack_external_libs, "py2"))
if sys.version_info[:2] == (2, 6):
sys.path.insert(0, os.path.join(spack_external_libs, "py26"))
sys.path.insert(0, spack_external_libs)

View File

@@ -1,6 +1,6 @@
#!/bin/sh
#
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -4,7 +4,7 @@ bootstrap:
enable: true
# Root directory for bootstrapping work. The software bootstrapped
# by Spack is installed in a "store" subfolder of this root directory
root: ~/.spack/bootstrap
root: $user_cache_path/bootstrap
# Methods that can be used to bootstrap software. Each method may or
# may not be able to bootstrap all of the software that Spack needs,
# depending on its type.
@@ -29,4 +29,4 @@ bootstrap:
# By default we trust bootstrapping from sources and from binaries
# produced on Github via the workflow
github-actions: true
spack-install: true
spack-install: true

View File

@@ -42,8 +42,8 @@ config:
# (i.e., ``$TMP` or ``$TMPDIR``).
#
# Another option that prevents conflicts and potential permission issues is
# to specify `~/.spack/stage`, which ensures each user builds in their home
# directory.
# to specify `$user_cache_path/stage`, which ensures each user builds in their
# home directory.
#
# A more traditional path uses the value of `$spack/var/spack/stage`, which
# builds directly inside Spack's instance without staging them in a
@@ -60,13 +60,13 @@ config:
# identifies Spack staging to avoid accidentally wiping out non-Spack work.
build_stage:
- $tempdir/$user/spack-stage
- ~/.spack/stage
- $user_cache_path/stage
# - $spack/var/spack/stage
# Directory in which to run tests and store test results.
# Tests will be stored in directories named by date/time and package
# name/hash.
test_stage: ~/.spack/test
test_stage: $user_cache_path/test
# Cache directory for already downloaded source tarballs and archived
# repositories. This can be purged with `spack clean --downloads`.
@@ -75,7 +75,7 @@ config:
# Cache directory for miscellaneous files, like the package index.
# This can be purged with `spack clean --misc-cache`
misc_cache: ~/.spack/cache
misc_cache: $user_cache_path/cache
# Timeout in seconds used for downloading sources etc. This only applies
@@ -134,7 +134,7 @@ config:
# enabling locks.
locks: true
# The default url fetch method to use.
# The default url fetch method to use.
# If set to 'curl', Spack will require curl on the user's system
# If set to 'urllib', Spack will use python built-in libs to fetch
url_fetch_method: urllib
@@ -160,11 +160,10 @@ config:
# sufficiently for many specs.
#
# 'clingo': Uses a logic solver under the hood to solve DAGs with full
# backtracking and optimization for user preferences.
# backtracking and optimization for user preferences. Spack will
# try to bootstrap the logic solver, if not already available.
#
# 'clingo' currently requires the clingo ASP solver to be installed and
# built with python bindings. 'original' is built in.
concretizer: original
concretizer: clingo
# How long to wait to lock the Spack installation database. This lock is used
@@ -191,3 +190,8 @@ config:
# Set to 'false' to allow installation on filesystems that doesn't allow setgid bit
# manipulation by unprivileged user (e.g. AFS)
allow_sgid: true
# Whether to set the terminal title to display status information during
# building and installing packages. This gives information about Spack's
# current progress as well as the current and total number of packages.
terminal_title: false

View File

@@ -46,7 +46,13 @@ modules:
enable:
- tcl
tcl:
all:
autoload: none
# Default configurations if lmod is enabled
lmod:
all:
autoload: direct
hierarchy:
- mpi

View File

@@ -34,6 +34,7 @@ packages:
java: [openjdk, jdk, ibm-java]
jpeg: [libjpeg-turbo, libjpeg]
lapack: [openblas, amdlibflame]
libllvm: [llvm, llvm-amdgpu]
lua-lang: [lua, lua-luajit]
mariadb-client: [mariadb-c-client, mariadb]
mkl: [intel-mkl]

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)
@@ -59,7 +59,7 @@ are available:
install_files : install file listing read from install_manifest.json
environment_variables : environment variables parsed from spack-build-env.txt
config_args : config args loaded from spack-configure-args.txt
abigail : Application Binary Interface (ABI) features for objects
libabigail : Application Binary Interface (ABI) features for objects
In the above, the first three are fairly simple - parsing metadata files from

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)
@@ -31,13 +31,13 @@ colorized output with a flag
.. code-block:: console
$ spack --color always | less -R
$ spack --color always find | less -R
or an environment variable
.. code-block:: console
$ SPACK_COLOR=always spack | less -R
$ SPACK_COLOR=always spack find | less -R
--------------------------
Listing available packages
@@ -188,6 +188,34 @@ configuration a **spec**. In the commands above, ``mpileaks`` and
``mpileaks@3.0.4`` are both valid *specs*. We'll talk more about how
you can use them to customize an installation in :ref:`sec-specs`.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Reusing installed dependencies
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. warning::
The ``--reuse`` option described here is experimental, and it will
likely be replaced with a different option and configuration settings
in the next Spack release.
By default, when you run ``spack install``, Spack tries to build a new
version of the package you asked for, along with updated versions of
its dependencies. This gets you the latest versions and configurations,
but it can result in unwanted rebuilds if you update Spack frequently.
If you want Spack to try hard to reuse existing installations as dependencies,
you can add the ``--reuse`` option:
.. code-block:: console
$ spack install --reuse mpich
This will not do anything if ``mpich`` is already installed. If ``mpich``
is not installed, but dependencies like ``hwloc`` and ``libfabric`` are,
the ``mpich`` will be build with the installed versions, if possible.
You can use the :ref:`spack spec -I <cmd-spack-spec>` command to see what
will be reused and what will be built before you install.
.. _cmd-spack-uninstall:
^^^^^^^^^^^^^^^^^^^
@@ -868,8 +896,9 @@ your path:
These commands will add appropriate directories to your ``PATH``,
``MANPATH``, ``CPATH``, and ``LD_LIBRARY_PATH`` according to the
:ref:`prefix inspections <customize-env-modifications>` defined in your
modules configuration. When you no longer want to use a package, you
can type unload or unuse similarly:
modules configuration.
When you no longer want to use a package, you can type unload or
unuse similarly:
.. code-block:: console
@@ -910,6 +939,22 @@ first ``libelf`` above, you would run:
$ spack load /qmm4kso
To see which packages that you have loaded to your enviornment you would
use ``spack find --loaded``.
.. code-block:: console
$ spack find --loaded
==> 2 installed packages
-- linux-debian7 / gcc@4.4.7 ------------------------------------
libelf@0.8.13
-- linux-debian7 / intel@15.0.0 ---------------------------------
libelf@0.8.13
You can also use ``spack load --list`` to get the same output, but it
does not have the full set of query options that ``spack find`` offers.
We'll learn more about Spack's spec syntax in the next section.
@@ -1649,6 +1694,7 @@ and it will be added to the ``PYTHONPATH`` in your current shell:
Now ``import numpy`` will succeed for as long as you keep your current
session open.
The loaded packages can be checked using ``spack find --loaded``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Loading Extensions via Modules

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)
@@ -112,20 +112,44 @@ phase runs:
.. code-block:: console
$ libtoolize
$ aclocal
$ autoreconf --install --verbose --force
$ autoreconf --install --verbose --force -I <aclocal-prefix>/share/aclocal
All you need to do is add a few Autotools dependencies to the package.
Most stable releases will come with a ``configure`` script, but if you
check out a commit from the ``develop`` branch, you would want to add:
In case you need to add more arguments, override ``autoreconf_extra_args``
in your ``package.py`` on class scope like this:
.. code-block:: python
depends_on('autoconf', type='build', when='@develop')
depends_on('automake', type='build', when='@develop')
depends_on('libtool', type='build', when='@develop')
depends_on('m4', type='build', when='@develop')
autoreconf_extra_args = ["-Im4"]
All you need to do is add a few Autotools dependencies to the package.
Most stable releases will come with a ``configure`` script, but if you
check out a commit from the ``master`` branch, you would want to add:
.. code-block:: python
depends_on('autoconf', type='build', when='@master')
depends_on('automake', type='build', when='@master')
depends_on('libtool', type='build', when='@master')
It is typically redundant to list the ``m4`` macro processor package as a
dependency, since ``autoconf`` already depends on it.
"""""""""""""""""""""""""""""""
Using a custom autoreconf phase
"""""""""""""""""""""""""""""""
In some cases, it might be needed to replace the default implementation
of the autoreconf phase with one running a script interpreter. In this
example, the ``bash`` shell is used to run the ``autogen.sh`` script.
.. code-block:: python
def autoreconf(self, spec, prefix):
which('bash')('autogen.sh')
"""""""""""""""""""""""""""""""""""""""
patching configure or Makefile.in files
"""""""""""""""""""""""""""""""""""""""
In some cases, developers might need to distribute a patch that modifies
one of the files used to generate ``configure`` or ``Makefile.in``.
@@ -135,6 +159,57 @@ create a new patch that directly modifies ``configure``. That way,
Spack can use the secondary patch and additional build system
dependencies aren't necessary.
""""""""""""""""""""""""""""
Old Autotools helper scripts
""""""""""""""""""""""""""""
Autotools based tarballs come with helper scripts such as ``config.sub`` and
``config.guess``. It is the responsibility of the developers to keep these files
up to date so that they run on every platform, but for very old software
releases this is impossible. In these cases Spack can help to replace these
files with newer ones, without having to add the heavy dependency on
``automake``.
Automatic helper script replacement is currently enabled by default on
``ppc64le`` and ``aarch64``, as these are the known cases where old scripts fail.
On these targets, ``AutotoolsPackage`` adds a build dependency on ``gnuconfig``,
which is a very light-weight package with newer versions of the helper files.
Spack then tries to run all the helper scripts it can find in the release, and
replaces them on failure with the helper scripts from ``gnuconfig``.
To opt out of this feature, use the following setting:
.. code-block:: python
patch_config_files = False
To enable it conditionally on different architectures, define a property and
make the package depend on ``gnuconfig`` as a build dependency:
.. code-block
depends_on('gnuconfig', when='@1.0:')
@property
def patch_config_files(self):
return self.spec.satisfies("@1.0:")
.. note::
On some exotic architectures it is necessary to use system provided
``config.sub`` and ``config.guess`` files. In this case, the most
transparent solution is to mark the ``gnuconfig`` package as external and
non-buildable, with a prefix set to the directory containing the files:
.. code-block:: yaml
gnuconfig:
buildable: false
externals:
- spec: gnuconfig@master
prefix: /usr/share/configure_files/
""""""""""""""""
force_autoreconf
""""""""""""""""
@@ -324,8 +399,47 @@ options:
--with-libfabric=</path/to/libfabric>
"""""""""""""""""""""""
The ``variant`` keyword
"""""""""""""""""""""""
When Spack variants and configure flags do not correspond one-to-one, the
``variant`` keyword can be passed to ``with_or_without`` and
``enable_or_disable``. For example:
.. code-block:: python
variant('debug_tools', default=False)
config_args += self.enable_or_disable('debug-tools', variant='debug_tools')
Or when one variant controls multiple flags:
.. code-block:: python
variant('debug_tools', default=False)
config_args += self.with_or_without('memchecker', variant='debug_tools')
config_args += self.with_or_without('profiler', variant='debug_tools')
""""""""""""""""""""
activation overrides
Conditional variants
""""""""""""""""""""
When a variant is conditional and its condition is not met on the concrete spec, the
``with_or_without`` and ``enable_or_disable`` methods will simply return an empty list.
For example:
.. code-block:: python
variant('profiler', when='@2.0:')
config_args += self.with_or_without('profiler)
will neither add ``--with-profiler`` nor ``--without-profiler`` when the version is
below ``2.0``.
""""""""""""""""""""
Activation overrides
""""""""""""""""""""
Finally, the behavior of either ``with_or_without`` or

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)
@@ -145,6 +145,20 @@ and without the :meth:`~spack.build_systems.cmake.CMakePackage.define` and
return args
Spack supports CMake defines from conditional variants too. Whenever the condition on
the variant is not met, ``define_from_variant()`` will simply return an empty string,
and CMake simply ignores the empty command line argument. For example the following
.. code-block:: python
variant('example', default=True, when='@2.0:')
def cmake_args(self):
return [self.define_from_variant('EXAMPLE', 'example')]
will generate ``'cmake' '-DEXAMPLE=ON' ...`` when `@2.0: +example` is met, but will
result in ``'cmake' '' ...`` when the spec version is below ``2.0``.
^^^^^^^^^^
Generators

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)
@@ -9,224 +9,94 @@
PythonPackage
-------------
Python packages and modules have their own special build system.
Python packages and modules have their own special build system. This
documentation covers everything you'll need to know in order to write
a Spack build recipe for a Python library.
^^^^^^
Phases
^^^^^^
^^^^^^^^^^^
Terminology
^^^^^^^^^^^
The ``PythonPackage`` base class provides the following phases that
can be overridden:
In the Python ecosystem, there are a number of terms that are
important to understand.
* ``build``
* ``build_py``
* ``build_ext``
* ``build_clib``
* ``build_scripts``
* ``install``
* ``install_lib``
* ``install_headers``
* ``install_scripts``
* ``install_data``
**PyPI**
The `Python Package Index <https://pypi.org/>`_, where most Python
libraries are hosted.
These are all standard ``setup.py`` commands and can be found by running:
**sdist**
Source distributions, distributed as tarballs (.tar.gz) and zip
files (.zip). Contain the source code of the package.
.. code-block:: console
**bdist**
Built distributions, distributed as wheels (.whl). Contain the
pre-built library.
$ python setup.py --help-commands
**wheel**
A binary distribution format common in the Python ecosystem. This
file is actually just a zip file containing specific metadata and
code. See the
`documentation <https://packaging.python.org/en/latest/specifications/binary-distribution-format/>`_
for more details.
**build frontend**
Command-line tools used to build and install wheels. Examples
include `pip <https://pip.pypa.io/>`_,
`build <https://pypa-build.readthedocs.io/>`_, and
`installer <https://installer.readthedocs.io/>`_.
By default, only the ``build`` and ``install`` phases are run:
**build backend**
Libraries used to define how to build a wheel. Examples
include `setuptools <https://setuptools.pypa.io/>`__,
`flit <https://flit.readthedocs.io/>`_, and
`poetry <https://python-poetry.org/>`_.
#. ``build`` - build everything needed to install
#. ``install`` - install everything from build directory
^^^^^^^^^^^
Downloading
^^^^^^^^^^^
If for whatever reason you need to run more phases, simply modify your
``phases`` list like so:
.. code-block:: python
phases = ['build_ext', 'install']
Each phase provides a function ``<phase>`` that runs:
.. code-block:: console
$ python -s setup.py --no-user-cfg <phase>
Each phase also has a ``<phase_args>`` function that can pass arguments to
this call. All of these functions are empty except for the ``install_args``
function, which passes ``--prefix=/path/to/installation/prefix``. There is
also some additional logic specific to setuptools and eggs.
If you need to run a phase that is not a standard ``setup.py`` command,
you'll need to define a function for it like so:
.. code-block:: python
phases = ['configure', 'build', 'install']
def configure(self, spec, prefix):
self.setup_py('configure')
^^^^^^
Wheels
^^^^^^
Some Python packages are closed-source and distributed as wheels.
Instead of using the ``PythonPackage`` base class, you should extend
the ``Package`` base class and implement the following custom installation
procedure:
.. code-block:: python
def install(self, spec, prefix):
pip = which('pip')
pip('install', self.stage.archive_file, '--prefix={0}'.format(prefix))
This will require a dependency on pip, as mentioned below.
^^^^^^^^^^^^^^^
Important files
^^^^^^^^^^^^^^^
Python packages can be identified by the presence of a ``setup.py`` file.
This file is used by package managers like ``pip`` to determine a
package's dependencies and the version of dependencies required, so if
the ``setup.py`` file is not accurate, the package will not build properly.
For this reason, the ``setup.py`` file should be fairly reliable. If the
documentation and ``setup.py`` disagree on something, the ``setup.py``
file should be considered to be the truth. As dependencies are added or
removed, the documentation is much more likely to become outdated than
the ``setup.py``.
The Python ecosystem has evolved significantly over the years. Before
setuptools became popular, most packages listed their dependencies in a
``requirements.txt`` file. Once setuptools took over, these dependencies
were listed directly in the ``setup.py``. Newer PEPs introduced additional
files, like ``setup.cfg`` and ``pyproject.toml``. You should look out for
all of these files, as they may all contain important information about
package dependencies.
Some Python packages are closed-source and are distributed as Python
wheels. For example, ``py-azureml-sdk`` downloads a ``.whl`` file. This
file is simply a zip file, and can be extracted using:
.. code-block:: console
$ unzip *.whl
The zip file will not contain a ``setup.py``, but it will contain a
``METADATA`` file which contains all the information you need to
write a ``package.py`` build recipe.
^^^^
PyPI
^^^^
The vast majority of Python packages are hosted on PyPI - The Python
Package Index. ``pip`` only supports packages hosted on PyPI, making
it the only option for developers who want a simple installation.
Search for "PyPI <package-name>" to find the download page. Note that
some pages are versioned, and the first result may not be the newest
version. Click on the "Latest Version" button to the top right to see
if a newer version is available. The download page is usually at::
The first step in packaging a Python library is to figure out where
to download it from. The vast majority of Python packages are hosted
on `PyPI <https://pypi.org/>`_, which is
:ref:`preferred over GitHub <pypi-vs-github>` for downloading
packages. Search for the package name on PyPI to find the project
page. The project page is usually located at::
https://pypi.org/project/<package-name>
Since PyPI is so common, the ``PythonPackage`` base class has a
``pypi`` attribute that can be set. Once set, ``pypi`` will be used
to define the ``homepage``, ``url``, and ``list_url``. For example,
the following:
.. code-block:: python
homepage = 'https://pypi.org/project/setuptools/'
url = 'https://pypi.org/packages/source/s/setuptools/setuptools-49.2.0.zip'
list_url = 'https://pypi.org/simple/setuptools/'
is equivalent to:
.. code-block:: python
pypi = 'setuptools/setuptools-49.2.0.zip'
^^^^^^^^^^^
Description
^^^^^^^^^^^
The top of the PyPI downloads page contains a description of the
package. The first line is usually a short description, while there
may be a several line "Project Description" that follows. Choose whichever
is more useful. You can also get these descriptions on the command-line
using:
.. code-block:: console
$ python setup.py --description
$ python setup.py --long-description
^^^^^^^^
Homepage
^^^^^^^^
Package developers use ``setup.py`` to upload new versions to PyPI.
The ``setup`` method often passes metadata like ``homepage`` to PyPI.
This metadata is displayed on the left side of the download page.
Search for the text "Homepage" under "Project links" to find it. You
should use this page instead of the PyPI page if they differ. You can
also get the homepage on the command-line by running:
.. code-block:: console
$ python setup.py --url
^^^
URL
^^^
If ``pypi`` is set as mentioned above, ``url`` and ``list_url`` will
be automatically set for you. If both ``.tar.gz`` and ``.zip`` versions
are available, ``.tar.gz`` is preferred. If some releases offer both
``.tar.gz`` and ``.zip`` versions, but some only offer ``.zip`` versions,
use ``.zip``.
Some Python packages are closed-source and do not ship ``.tar.gz`` or ``.zip``
files on either PyPI or GitHub. If this is the case, you can still download
and install a Python wheel. For example, ``py-azureml-sdk`` is closed source
and can be downloaded from::
On the project page, there is a "Download files" tab containing
download URLs. Whenever possible, we prefer to build Spack packages
from source. If PyPI only has wheels, check to see if the project is
hosted on GitHub and see if GitHub has source distributions. The
project page usually has a "Homepage" and/or "Source code" link for
this. If the project is closed-source, it may only have wheels
available. For example, ``py-azureml-sdk`` is closed-source and can
be downloaded from::
https://pypi.io/packages/py3/a/azureml_sdk/azureml_sdk-1.11.0-py3-none-any.whl
Once you've found a URL to download the package from, run:
You may see Python-specific or OS-specific URLs. Note that when you add a
``.whl`` URL, you should add ``expand=False`` to ensure that Spack doesn't
try to extract the wheel:
.. code-block:: console
.. code-block:: python
$ spack create <url>
version('1.11.0', sha256='d8c9d24ea90457214d798b0d922489863dad518adde3638e08ef62de28fb183a', expand=False)
to create a new package template.
.. _pypi-vs-github:
"""""""""""""""
PyPI vs. GitHub
"""""""""""""""
Many packages are hosted on PyPI, but are developed on GitHub or another
version control systems. The tarball can be downloaded from either
location, but PyPI is preferred for the following reasons:
Many packages are hosted on PyPI, but are developed on GitHub or
another version control system hosting service. The source code can
be downloaded from either location, but PyPI is preferred for the
following reasons:
#. PyPI contains the bare minimum number of files needed to install the package.
#. PyPI contains the bare minimum number of files needed to install
the package.
You may notice that the tarball you download from PyPI does not
have the same checksum as the tarball you download from GitHub.
@@ -263,249 +133,124 @@ location, but PyPI is preferred for the following reasons:
PyPI is nice because it makes it physically impossible to
re-release the same version of a package with a different checksum.
^^^^^^^^^^^^^^^^^^^^^^^^^
Build system dependencies
^^^^^^^^^^^^^^^^^^^^^^^^^
The only reason to use GitHub instead of PyPI is if PyPI only has
wheels or if the PyPI sdist is missing a file needed to build the
package. If this is the case, please add a comment above the ``url``
explaining this.
There are a few dependencies common to the ``PythonPackage`` build system.
^^^^
PyPI
^^^^
""""""
Python
""""""
Obviously, every ``PythonPackage`` needs Python at build-time to run
``python setup.py build && python setup.py install``. Python is also
needed at run-time if you want to import the module. Due to backwards
incompatible changes between Python 2 and 3, it is very important to
specify which versions of Python are supported. If the documentation
mentions that Python 3 is required, this can be specified as:
Since PyPI is so commonly used to host Python libraries, the
``PythonPackage`` base class has a ``pypi`` attribute that can be
set. Once set, ``pypi`` will be used to define the ``homepage``,
``url``, and ``list_url``. For example, the following:
.. code-block:: python
depends_on('python@3:', type=('build', 'run'))
homepage = 'https://pypi.org/project/setuptools/'
url = 'https://pypi.org/packages/source/s/setuptools/setuptools-49.2.0.zip'
list_url = 'https://pypi.org/simple/setuptools/'
If Python 2 is required, this would look like:
is equivalent to:
.. code-block:: python
depends_on('python@:2', type=('build', 'run'))
pypi = 'setuptools/setuptools-49.2.0.zip'
If Python 2.7 is the only version that works, you can use:
If a package has a different homepage listed on PyPI, you can
override it by setting your own ``homepage``.
^^^^^^^^^^^
Description
^^^^^^^^^^^
The top of the PyPI project page contains a short description of the
package. The "Project description" tab may also contain a longer
description of the package. Either of these can be used to populate
the package docstring.
^^^^^^^^^^^^^
Build backend
^^^^^^^^^^^^^
Once you've determined the basic metadata for a package, the next
step is to determine the build backend. ``PythonPackage`` uses
`pip <https://pip.pypa.io/>`_ to install the package, but pip
requires a backend to actually build the package.
To determine the build backend, look for a ``pyproject.toml`` file.
If there is no ``pyproject.toml`` file and only a ``setup.py`` or
``setup.cfg`` file, you can assume that the project uses
:ref:`setuptools`. If there is a ``pyproject.toml`` file, see if it
contains a ``[build-system]`` section. For example:
.. code-block:: toml
[build-system]
requires = [
"setuptools>=42",
"wheel",
]
build-backend = "setuptools.build_meta"
This section does two things: the ``requires`` key lists build
dependencies of the project, and the ``build-backend`` key defines
the build backend. All of these build dependencies should be added as
dependencies to your package:
.. code-block:: python
depends_on('python@2.7:2.8', type=('build', 'run'))
depends_on('py-setuptools@42:', type='build')
The documentation may not always specify supported Python versions.
Another place to check is in the ``setup.py`` or ``setup.cfg`` file.
Look for a line containing ``python_requires``. An example from
`py-numpy <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/py-numpy/package.py>`_
looks like:
Note that ``py-wheel`` is already listed as a build dependency in the
``PythonPackage`` base class, so you don't need to add it unless you
need to specify a specific version requirement or change the
dependency type.
.. code-block:: python
See `PEP 517 <https://www.python.org/dev/peps/pep-0517/>`_ and
`PEP 518 <https://www.python.org/dev/peps/pep-0518/>`_ for more
information on the design of ``pyproject.toml``.
python_requires='>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*'
Depending on which build backend a project uses, there are various
places that run-time dependencies can be listed.
"""""""""
distutils
"""""""""
You may also find a version check at the top of the ``setup.py``:
Before the introduction of setuptools and other build backends,
Python packages had to rely on the built-in distutils library.
Distutils is missing many of the features that setuptools and other
build backends offer, and users are encouraged to use setuptools
instead. In fact, distutils was deprecated in Python 3.10 and will be
removed in Python 3.12. Because of this, pip actually replaces all
imports of distutils with setuptools. If a package uses distutils,
you should instead add a build dependency on setuptools. Check for a
``requirements.txt`` file that may list dependencies of the project.
.. code-block:: python
if sys.version_info[:2] < (2, 7) or (3, 0) <= sys.version_info[:2] < (3, 4):
raise RuntimeError("Python version 2.7 or >= 3.4 required.")
This can be converted to Spack's spec notation like so:
.. code-block:: python
depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
If you are writing a recipe for a package that only distributes
wheels, look for a section in the ``METADATA`` file that looks like::
Requires-Python: >=3.5,<4
This would be translated to:
.. code-block:: python
extends('python')
depends_on('python@3.5:3.999', type=('build', 'run'))
Many ``setup.py`` or ``setup.cfg`` files also contain information like::
Programming Language :: Python :: 2
Programming Language :: Python :: 2.6
Programming Language :: Python :: 2.7
Programming Language :: Python :: 3
Programming Language :: Python :: 3.3
Programming Language :: Python :: 3.4
Programming Language :: Python :: 3.5
Programming Language :: Python :: 3.6
This is a list of versions of Python that the developer likely tests.
However, you should not use this to restrict the versions of Python
the package uses unless one of the two former methods (``python_requires``
or ``sys.version_info``) is used. There is no logic in setuptools
that prevents the package from building for Python versions not in
this list, and often new releases like Python 3.7 or 3.8 work just fine.
.. _setuptools:
""""""""""
setuptools
""""""""""
Originally, the Python language had a single build system called
distutils, which is built into Python. Distutils provided a common
framework for package authors to describe their project and how it
should be built. However, distutils was not without limitations.
Most notably, there was no way to list a project's dependencies
with distutils. Along came setuptools, a non-builtin build system
designed to overcome the limitations of distutils. Both projects
use a similar API, making the transition easy while adding much
needed functionality. Today, setuptools is used in around 90% of
the Python packages in Spack.
Since setuptools isn't built-in to Python, you need to add it as a
dependency. To determine whether or not a package uses setuptools,
search the file for an import statement like:
.. code-block:: python
import setuptools
or:
.. code-block:: python
from setuptools import setup
Some packages are designed to work with both setuptools and distutils,
so you may find something like:
.. code-block:: python
try:
from setuptools import setup
except ImportError:
from distutils.core import setup
This uses setuptools if available, and falls back to distutils if not.
In this case, you would still want to add a setuptools dependency, as
it offers us more control over the installation.
Unless specified otherwise, setuptools is usually a build-only dependency.
That is, it is needed to install the software, but is not needed at
run-time. This can be specified as:
.. code-block:: python
depends_on('py-setuptools', type='build')
"""
pip
"""
Packages distributed as Python wheels will require an extra dependency
on pip:
.. code-block:: python
depends_on('py-pip', type='build')
We will use pip to install the actual wheel.
""""""
cython
""""""
Compared to compiled languages, interpreted languages like Python can
be quite a bit slower. To work around this, some Python developers
rewrite computationally demanding sections of code in C, a process
referred to as "cythonizing". In order to build these package, you
need to add a build dependency on cython:
.. code-block:: python
depends_on('py-cython', type='build')
Look for references to "cython" in the ``setup.py`` to determine
whether or not this is necessary. Cython may be optional, but
even then you should list it as a required dependency. Spack is
designed to compile software, and is meant for HPC facilities
where speed is crucial. There is no reason why someone would not
want an optimized version of a library instead of the pure-Python
version.
Note that some release tarballs come pre-cythonized, and cython is
not needed as a dependency. However, this is becoming less common
as Python continues to evolve and developers discover that cythonized
sources are no longer compatible with newer versions of Python and
need to be re-cythonized.
^^^^^^^^^^^^^^^^^^^
Python dependencies
^^^^^^^^^^^^^^^^^^^
When you install a package with ``pip``, it reads the ``setup.py``
file in order to determine the dependencies of the package.
If the dependencies are not yet installed, ``pip`` downloads them
and installs them for you. This may sound convenient, but Spack
cannot rely on this behavior for two reasons:
#. Spack needs to be able to install packages on air-gapped networks.
If there is no internet connection, ``pip`` can't download the
package dependencies. By explicitly listing every dependency in
the ``package.py``, Spack knows what to download ahead of time.
#. Duplicate installations of the same dependency may occur.
Spack supports *activation* of Python extensions, which involves
symlinking the package installation prefix to the Python installation
prefix. If your package is missing a dependency, that dependency
will be installed to the installation directory of the same package.
If you try to activate the package + dependency, it may cause a
problem if that package has already been activated.
For these reasons, you must always explicitly list all dependencies.
Although the documentation may list the package's dependencies,
often the developers assume people will use ``pip`` and won't have to
worry about it. Always check the ``setup.py`` to find the true
dependencies.
If the package relies on ``distutils``, it may not explicitly list its
dependencies. Check for statements like:
.. code-block:: python
try:
import numpy
except ImportError:
raise ImportError("numpy must be installed prior to installation")
Obviously, this means that ``py-numpy`` is a dependency.
If the package uses ``setuptools``, check for the following clues:
If the ``pyproject.toml`` lists ``setuptools.build_meta`` as a
``build-backend``, or if the package has a ``setup.py`` that imports
``setuptools``, or if the package has a ``setup.cfg`` file, then it
uses setuptools to build. Setuptools is a replacement for the
distutils library, and has almost the exact same API. Dependencies
can be listed in the ``setup.py`` or ``setup.cfg`` file. Look for the
following arguments:
* ``python_requires``
As mentioned above, this specifies which versions of Python are
required.
This specifies the version of Python that is required.
* ``setup_requires``
@@ -517,43 +262,88 @@ If the package uses ``setuptools``, check for the following clues:
These packages are required for building and installation. You can
add them with ``type=('build', 'run')``.
* ``extra_requires``
* ``extras_require``
These packages are optional dependencies that enable additional
functionality. You should add a variant that optionally adds these
dependencies. This variant should be False by default.
* ``test_requires``
* ``tests_require``
These are packages that are required to run the unit tests for the
package. These dependencies can be specified using the
``type='test'`` dependency type. However, the PyPI tarballs rarely
contain unit tests, so there is usually no reason to add these.
In the root directory of the package, you may notice a
``requirements.txt`` file. It may look like this file contains a list
of all of the package's dependencies. Don't be fooled. This file is
used by tools like Travis to install the pre-requisites for the
package... and a whole bunch of other things. It often contains
dependencies only needed for unit tests, like:
See https://setuptools.pypa.io/en/latest/userguide/dependency_management.html
for more information on how setuptools handles dependency management.
See `PEP 440 <https://www.python.org/dev/peps/pep-0440/#version-specifiers>`_
for documentation on version specifiers in setuptools.
* mock
* nose
* pytest
""""
flit
""""
It can also contain dependencies for building the documentation, like
sphinx. If you can't find any information about the package's
dependencies, you can take a look in ``requirements.txt``, but be sure
not to add test or documentation dependencies.
There are actually two possible ``build-backend`` for flit, ``flit``
and ``flit_core``. If you see these in the ``pyproject.toml``, add a
build dependency to your package. With flit, all dependencies are
listed directly in the ``pyproject.toml`` file. Older versions of
flit used to store this info in a ``flit.ini`` file, so check for
this too.
Newer PEPs have added alternative ways to specify a package's dependencies.
If you don't see any dependencies listed in the ``setup.py``, look for a
``setup.cfg`` or ``pyproject.toml``. These files can be used to store the
same ``install_requires`` information that ``setup.py`` used to use.
Either of these files may contain keys like:
If you are write a recipe for a package that only distributes wheels,
check the ``METADATA`` file for lines like::
* ``requires-python``
This specifies the version of Python that is required
* ``dependencies`` or ``requires``
These packages are required for building and installation. You can
add them with ``type=('build', 'run')``.
* ``project.optional-dependencies`` or ``requires-extra``
This section includes keys with lists of optional dependencies
needed to enable those features. You should add a variant that
optionally adds these dependencies. This variant should be False
by default.
See https://flit.readthedocs.io/en/latest/pyproject_toml.html for
more information.
""""""
poetry
""""""
Like flit, poetry also has two possible ``build-backend``, ``poetry``
and ``poetry_core``. If you see these in the ``pyproject.toml``, add
a build dependency to your package. With poetry, all dependencies are
listed directly in the ``pyproject.toml`` file. Dependencies are
listed in a ``[tool.poetry.dependencies]`` section, and use a
`custom syntax <https://python-poetry.org/docs/dependency-specification/#version-constraints>`_
for specifying the version requirements. Note that ``~=`` works
differently in poetry than in setuptools and flit for versions that
start with a zero.
""""""
wheels
""""""
Some Python packages are closed-source and are distributed as Python
wheels. For example, ``py-azureml-sdk`` downloads a ``.whl`` file. This
file is simply a zip file, and can be extracted using:
.. code-block:: console
$ unzip *.whl
The zip file will not contain a ``setup.py``, but it will contain a
``METADATA`` file which contains all the information you need to
write a ``package.py`` build recipe. Check for lines like::
Requires-Python: >=3.5,<4
Requires-Dist: azureml-core (~=1.11.0)
Requires-Dist: azureml-dataset-runtime[fuse] (~=1.11.0)
Requires-Dist: azureml-train (~=1.11.0)
@@ -565,62 +355,58 @@ check the ``METADATA`` file for lines like::
Requires-Dist: azureml-train-automl (~=1.11.0); extra == 'automl'
Lines that use ``Requires-Dist`` are similar to ``install_requires``.
Lines that use ``Provides-Extra`` are similar to ``extra_requires``,
and you can add a variant for those dependencies. The ``~=1.11.0``
syntax is equivalent to ``1.11.0:1.11.999``.
""""""""""
setuptools
""""""""""
Setuptools is a bit of a special case. If a package requires setuptools
at run-time, how do they express this? They could add it to
``install_requires``, but setuptools is imported long before this and is
needed to read this line. And since you can't install the package
without setuptools, the developers assume that setuptools will already
be there, so they never mention when it is required. We don't want to
add run-time dependencies if they aren't needed, so you need to
determine whether or not setuptools is needed. Grep the installation
directory for any files containing a reference to ``setuptools`` or
``pkg_resources``. Both modules come from ``py-setuptools``.
``pkg_resources`` is particularly common in scripts found in
``prefix/bin``.
``Requires-Python`` is equivalent to ``python_requires`` and
``Requires-Dist`` is equivalent to ``install_requires``.
``Provides-Extra`` is used to name optional features (variants) and
a ``Requires-Dist`` with ``extra == 'foo'`` will list any
dependencies needed for that feature.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Passing arguments to setup.py
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The default build and install phases should be sufficient to install
most packages. However, you may want to pass additional flags to
either phase.
The default install phase should be sufficient to install most
packages. However, the installation instructions for a package may
suggest passing certain flags to the ``setup.py`` call. The
``PythonPackage`` class has two techniques for doing this.
You can view the available options for a particular phase with:
""""""""""""""
Global options
""""""""""""""
.. code-block:: console
$ python setup.py <phase> --help
Each phase provides a ``<phase_args>`` function that can be used to
pass arguments to that phase. For example,
`py-numpy <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/py-numpy/package.py>`_
adds:
These flags are added directly after ``setup.py`` when pip runs
``python setup.py install``. For example, the ``py-pyyaml`` package
has an optional dependency on ``libyaml`` that can be enabled like so:
.. code-block:: python
def build_args(self, spec, prefix):
args = []
def global_options(self, spec, prefix):
options = []
if '+libyaml' in spec:
options.append('--with-libyaml')
else:
options.append('--without-libyaml')
return options
# From NumPy 1.10.0 on it's possible to do a parallel build.
if self.version >= Version('1.10.0'):
# But Parallel build in Python 3.5+ is broken. See:
# https://github.com/spack/spack/issues/7927
# https://github.com/scipy/scipy/issues/7112
if spec['python'].version < Version('3.5'):
args = ['-j', str(make_jobs)]
return args
"""""""""""""""
Install options
"""""""""""""""
These flags are added directly after ``install`` when pip runs
``python setup.py install``. For example, the ``py-pyyaml`` package
allows you to specify the directories to search for ``libyaml``:
.. code-block:: python
def install_options(self, spec, prefix):
options = []
if '+libyaml' in spec:
options.extend([
spec['libyaml'].libs.search_flags,
spec['libyaml'].headers.include_flags,
])
return options
^^^^^^^
@@ -662,9 +448,9 @@ a "package" is a directory containing files like:
whereas a "module" is a single Python file.
The ``PythonPackage`` base class automatically detects these module
names for you. If, for whatever reason, the module names detected
are wrong, you can provide the names yourself by overriding
The ``PythonPackage`` base class automatically detects these package
and module names for you. If, for whatever reason, the module names
detected are wrong, you can provide the names yourself by overriding
``import_modules`` like so:
.. code-block:: python
@@ -685,10 +471,8 @@ This can be expressed like so:
@property
def import_modules(self):
modules = ['yaml']
if '+libyaml' in self.spec:
modules.append('yaml.cyaml')
return modules
@@ -706,10 +490,10 @@ Unit tests
""""""""""
The package may have its own unit or regression tests. Spack can
run these tests during the installation by adding phase-appropriate
test methods.
run these tests during the installation by adding test methods after
installation.
For example, ``py-numpy`` adds the following as a check to run
For example, ``py-numpy`` adds the following as a check to run
after the ``install`` phase:
.. code-block:: python
@@ -733,34 +517,14 @@ when testing is enabled during the installation (i.e., ``spack install
Setup file in a sub-directory
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
In order to be compatible with package managers like ``pip``, the package
is required to place its ``setup.py`` in the root of the tarball. However,
not every Python package cares about ``pip`` or PyPI. If you are installing
a package that is not hosted on PyPI, you may find that it places its
``setup.py`` in a sub-directory. To handle this, add the directory containing
``setup.py`` to the package like so:
Many C/C++ libraries provide optional Python bindings in a
subdirectory. To tell pip which directory to build from, you can
override the ``build_directory`` attribute. For example, if a package
provides Python bindings in a ``python`` directory, you can use:
.. code-block:: python
build_directory = 'source'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Alternate names for setup.py
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
As previously mentioned, packages need to call their setup script ``setup.py``
in order to be compatible with package managers like ``pip``. However, some
packages like
`py-meep <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/py-meep/package.py>`_ and
`py-adios <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/py-adios/package.py>`_
come with multiple setup scripts, one for a serial build and another for a
parallel build. You can override the default name to use like so:
.. code-block:: python
def setup_file(self):
return 'setup-mpi.py' if '+mpi' in self.spec else 'setup.py'
build_directory = 'python'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -774,10 +538,14 @@ on Python are not necessarily ``PythonPackage``'s.
Choosing a build system
"""""""""""""""""""""""
First of all, you need to select a build system. ``spack create`` usually
does this for you, but if for whatever reason you need to do this manually,
choose ``PythonPackage`` if and only if the package contains a ``setup.py``
file.
First of all, you need to select a build system. ``spack create``
usually does this for you, but if for whatever reason you need to do
this manually, choose ``PythonPackage`` if and only if the package
contains one of the following files:
* ``pyproject.toml``
* ``setup.py``
* ``setup.cfg``
"""""""""""""""""""""""
Choosing a package name
@@ -850,10 +618,9 @@ having to add that module to ``PYTHONPATH``.
When deciding between ``extends`` and ``depends_on``, the best rule of
thumb is to check the installation prefix. If Python libraries are
installed to ``prefix/lib/python2.7/site-packages`` (where 2.7 is the
MAJOR.MINOR version of Python you used to install the package), then
you should use ``extends``. If Python libraries are installed elsewhere
or the only files that get installed reside in ``prefix/bin``, then
installed to ``<prefix>/lib/pythonX.Y/site-packages``, then you
should use ``extends``. If Python libraries are installed elsewhere
or the only files that get installed reside in ``<prefix>/bin``, then
don't use ``extends``, as symlinking the package wouldn't be useful.
^^^^^^^^^^^^^^^^^^^^^
@@ -886,4 +653,17 @@ External documentation
^^^^^^^^^^^^^^^^^^^^^^
For more information on Python packaging, see:
https://packaging.python.org/
* https://packaging.python.org/
For more information on build and installation frontend tools, see:
* pip: https://pip.pypa.io/
* build: https://pypa-build.readthedocs.io/
* installer: https://installer.readthedocs.io/
For more information on build backend tools, see:
* setuptools: https://setuptools.pypa.io/
* flit: https://flit.readthedocs.io/
* poetry: https://python-poetry.org/

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
@@ -30,6 +30,7 @@
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
sys.path.insert(0, os.path.abspath('_spack_root/lib/spack/external'))
sys.path.insert(0, os.path.abspath('_spack_root/lib/spack/external/pytest-fallback'))
if sys.version_info[0] < 3:
sys.path.insert(

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)
@@ -259,3 +259,16 @@ and ld.so will ONLY search for dependencies in the ``RUNPATH`` of
the loading object.
DO NOT MIX the two options within the same install tree.
----------------------
``terminal_title``
----------------------
By setting this option to ``true``, Spack will update the terminal's title to
provide information about its current progress as well as the current and
total package numbers.
To work properly, this requires your terminal to reset its title after
Spack has finished its work, otherwise Spack's status information will
remain in the terminal's title indefinitely. Most terminals should already
be set up this way and clear Spack's status information.

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)
@@ -402,12 +402,15 @@ Spack-specific variables
Spack understands several special variables. These are:
* ``$env``: name of the currently active :ref:`environment <environments>`
* ``$spack``: path to the prefix of this Spack installation
* ``$tempdir``: default system temporary directory (as specified in
Python's `tempfile.tempdir
<https://docs.python.org/2/library/tempfile.html#tempfile.tempdir>`_
variable.
* ``$user``: name of the current user
* ``$user_cache_path``: user cache directory (``~/.spack`` unless
:ref:`overridden <local-config-overrides>`)
Note that, as with shell variables, you can write these as ``$varname``
or with braces to distinguish the variable from surrounding characters:
@@ -562,3 +565,39 @@ built in and are not overridden by a configuration file. The
command line. ``dirty`` and ``install_tree`` come from the custom
scopes ``./my-scope`` and ``./my-scope-2``, and all other configuration
options come from the default configuration files that ship with Spack.
.. _local-config-overrides:
------------------------------
Overriding Local Configuration
------------------------------
Spack's ``system`` and ``user`` scopes provide ways for administrators and users to set
global defaults for all Spack instances, but for use cases where one wants a clean Spack
installation, these scopes can be undesirable. For example, users may want to opt out of
global system configuration, or they may want to ignore their own home directory
settings when running in a continuous integration environment.
Spack also, by default, keeps various caches and user data in ``~/.spack``, but
users may want to override these locations.
Spack provides three environment variables that allow you to override or opt out of
configuration locations:
* ``SPACK_USER_CONFIG_PATH``: Override the path to use for the
``user`` scope (``~/.spack`` by default).
* ``SPACK_SYSTEM_CONFIG_PATH``: Override the path to use for the
``system`` scope (``/etc/spack`` by default).
* ``SPACK_DISABLE_LOCAL_CONFIG``: set this environment variable to completely disable
**both** the system and user configuration directories. Spack will only consider its
own defaults and ``site`` configuration locations.
And one that allows you to move the default cache location:
* ``SPACK_USER_CACHE_PATH``: Override the default path to use for user data
(misc_cache, tests, reports, etc.)
With these settings, if you want to isolate Spack in a CI environment, you can do this::
export SPACK_DISABLE_LOCAL_CONFIG=true
export SPACK_USER_CACHE_PATH=/tmp/spack

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)
@@ -126,12 +126,12 @@ are currently supported are summarized in the table below:
* - Ubuntu 18.04
- ``ubuntu:18.04``
- ``spack/ubuntu-bionic``
* - CentOS 6
- ``centos:6``
- ``spack/centos6``
* - CentOS 7
- ``centos:7``
- ``spack/centos7``
* - openSUSE Leap
- ``opensuse/leap``
- ``spack/leap15``
All the images are tagged with the corresponding release of Spack:
@@ -200,7 +200,7 @@ Setting Base Images
The ``images`` subsection is used to select both the image where
Spack builds the software and the image where the built software
is installed. This attribute can be set in two different ways and
is installed. This attribute can be set in different ways and
which one to use depends on the use case at hand.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -260,10 +260,54 @@ software is respectively built and installed:
ENTRYPOINT ["/bin/bash", "--rcfile", "/etc/profile", "-l"]
This method of selecting base images is the simplest of the two, and we advise
This is the simplest available method of selecting base images, and we advise
to use it whenever possible. There are cases though where using Spack official
images is not enough to fit production needs. In these situations users can manually
select which base image to start from in the recipe, as we'll see next.
images is not enough to fit production needs. In these situations users can
extend the recipe to start with the bootstrapping of Spack at a certain pinned
version or manually select which base image to start from in the recipe,
as we'll see next.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Use a Bootstrap Stage for Spack
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
In some cases users may want to pin the commit sha that is used for Spack, to ensure later
reproducibility, or start from a fork of the official Spack repository to try a bugfix or
a feature in the early stage of development. This is possible by being just a little more
verbose when specifying information about Spack in the ``spack.yaml`` file:
.. code-block:: yaml
images:
os: amazonlinux:2
spack:
# URL of the Spack repository to be used in the container image
url: <to-use-a-fork>
# Either a commit sha, a branch name or a tag
ref: <sha/tag/branch>
# If true turn a branch name or a tag into the corresponding commit
# sha at the time of recipe generation
resolve_sha: <true/false>
``url`` specifies the URL from which to clone Spack and defaults to https://github.com/spack/spack.
The ``ref`` attribute can be either a commit sha, a branch name or a tag. The default value in
this case is to use the ``develop`` branch, but it may change in the future to point to the latest stable
release. Finally ``resolve_sha`` transform branch names or tags into the corresponding commit
shas at the time of recipe generation, to allow for a greater reproducibility of the results
at a later time.
The list of operating systems that can be used to bootstrap Spack can be
obtained with:
.. command-output:: spack containerize --list-os
.. note::
The ``resolve_sha`` option uses ``git rev-parse`` under the hood and thus it requires
to checkout the corresponding Spack repository in a temporary folder before generating
the recipe. Recipe generation may take longer when this option is set to true because
of this additional step.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Use Custom Images Provided by Users
@@ -415,6 +459,18 @@ to customize the generation of container recipes:
- Version of Spack use in the ``build`` stage
- Valid tags for ``base:image``
- Yes, if using constrained selection of base images
* - ``images:spack:url``
- Repository from which Spack is cloned
- Any fork of Spack
- No
* - ``images:spack:ref``
- Reference for the checkout of Spack
- Either a commit sha, a branch name or a tag
- No
* - ``images:spack:resolve_sha``
- Resolve branches and tags in ``spack.yaml`` to commits in the generated recipe
- True or False (default: False)
- No
* - ``images:build``
- Image to be used in the ``build`` stage
- Any valid container image

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)
@@ -71,7 +71,7 @@ locally to speed up the review process.
new release that is causing problems. If this is the case, please file an issue.
We currently test against Python 2.6, 2.7, and 3.5-3.7 on both macOS and Linux and
We currently test against Python 2.7 and 3.5-3.9 on both macOS and Linux and
perform 3 types of tests:
.. _cmd-spack-unit-test:
@@ -338,15 +338,6 @@ Once all of the dependencies are installed, you can try building the documentati
If you see any warning or error messages, you will have to correct those before
your PR is accepted.
.. note::
There is also a ``run-doc-tests`` script in ``share/spack/qa``. The only
difference between running this script and running ``make`` by hand is that
the script will exit immediately if it encounters an error or warning. This
is necessary for CI. If you made a lot of documentation changes, it is
much quicker to run ``make`` by hand so that you can see all of the warnings
at once.
If you are editing the documentation, you should obviously be running the
documentation tests. But even if you are simply adding a new package, your
changes could cause the documentation tests to fail:

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)
@@ -210,15 +210,6 @@ Spec-related modules
but compilers aren't fully integrated with the build process
yet.
:mod:`spack.architecture`
:func:`architecture.default_arch <spack.architecture.default_arch>` is used
to determine the host architecture while building.
.. warning::
Not yet implemented. Should eventually have architecture
descriptions for cross-compiling.
^^^^^^^^^^^^^^^^^
Build environment
^^^^^^^^^^^^^^^^^
@@ -680,6 +671,13 @@ If you need to write a hook that is relevant to a failure within a build
process, you would want to instead use ``on_phase_failure``.
"""""""""""""""""""""""""""
``on_install_cancel(spec)``
"""""""""""""""""""""""""""
The same, but triggered if a spec install is cancelled for any reason.
"""""""""""""""""""""""""""""""""""""""""""""""
``on_phase_success(pkg, phase_name, log_file)``
"""""""""""""""""""""""""""""""""""""""""""""""
@@ -1186,6 +1184,10 @@ completed, the steps to make the major release are:
If CI is not passing, submit pull requests to ``develop`` as normal
and keep rebasing the release branch on ``develop`` until CI passes.
#. Make sure the entire documentation is up to date. If documentation
is outdated submit pull requests to ``develop`` as normal
and keep rebasing the release branch on ``develop``.
#. Follow the steps in :ref:`publishing-releases`.
#. Follow the steps in :ref:`merging-releases`.

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)
@@ -38,8 +38,7 @@ obtained by cloning the corresponding git repository:
.. code-block:: console
$ pwd
/home/user
$ cd ~/
$ mkdir tmp && cd tmp
$ git clone https://github.com/alalazo/spack-scripting.git
Cloning into 'spack-scripting'...
@@ -62,7 +61,7 @@ paths to ``config.yaml``. In the case of our example this means ensuring that:
config:
extensions:
- /home/user/tmp/spack-scripting
- ~/tmp/spack-scripting
is part of your configuration file. Once this is setup any command that the extension provides
will be available from the command line:

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)
@@ -35,7 +35,7 @@ Getting Spack is easy. You can clone it from the `github repository
.. code-block:: console
$ git clone https://github.com/spack/spack.git
$ git clone -c feature.manyFiles=true https://github.com/spack/spack.git
This will create a directory called ``spack``.
@@ -88,74 +88,71 @@ the environment.
Bootstrapping clingo
^^^^^^^^^^^^^^^^^^^^
Spack supports using ``clingo`` as an external solver to compute which software
needs to be installed. The default configuration allows Spack to install
``clingo`` from a public buildcache, created by a Github Action workflow. In this
case the bootstrapping procedure is transparent to the user, except for a
slightly long waiting time on the first concretization of a spec:
Spack uses ``clingo`` under the hood to resolve optimal versions and variants of
dependencies when installing a package. Since ``clingo`` itself is a binary,
Spack has to install it on initial use, which is called bootstrapping.
Spack provides two ways of bootstrapping ``clingo``: from pre-built binaries
(default), or from sources. The fastest way to get started is to bootstrap from
pre-built binaries.
.. note::
When bootstrapping from pre-built binaries, Spack currently requires
``patchelf`` on Linux and ``otool`` on macOS. If ``patchelf`` is not in the
``PATH``, Spack will build it from sources, and a C++ compiler is required.
The first time you concretize a spec, Spack will bootstrap in the background:
.. code-block:: console
$ spack find -b
==> Showing internal bootstrap store at "/home/spack/.spack/bootstrap/store"
==> 0 installed packages
$ time spack spec zlib
Input spec
--------------------------------
zlib
$ time spack solve zlib
==> Best of 2 considered solutions.
==> Optimization Criteria:
Priority Criterion Value
1 deprecated versions used 0
2 version weight 0
3 number of non-default variants (roots) 0
4 multi-valued variants 0
5 preferred providers for roots 0
6 number of non-default variants (non-roots) 0
7 preferred providers (non-roots) 0
8 compiler mismatches 0
9 version badness 0
10 count of non-root multi-valued variants 0
11 non-preferred compilers 0
12 target mismatches 0
13 non-preferred targets 0
Concretized
--------------------------------
zlib@1.2.11%gcc@7.5.0+optimize+pic+shared arch=linux-ubuntu18.04-zen
zlib@1.2.11%gcc@11.1.0+optimize+pic+shared arch=linux-ubuntu18.04-broadwell
real 0m30,618s
user 0m27,278s
sys 0m1,549s
real 0m20.023s
user 0m18.351s
sys 0m0.784s
After this command you'll see that ``clingo`` has been installed for Spack's own use:
.. code-block:: console
$ spack find -b
==> Showing internal bootstrap store at "/home/spack/.spack/bootstrap/store"
==> 2 installed packages
==> Showing internal bootstrap store at "/root/.spack/bootstrap/store"
==> 3 installed packages
-- linux-rhel5-x86_64 / gcc@9.3.0 -------------------------------
clingo-bootstrap@spack python@3.6
-- linux-ubuntu18.04-zen / gcc@7.5.0 ----------------------------
patchelf@0.13
Subsequent calls to the concretizer will then be much faster:
.. code-block:: console
$ time spack solve zlib
$ time spack spec zlib
[ ... ]
real 0m1,222s
user 0m1,146s
sys 0m0,059s
real 0m0.490s
user 0m0.431s
sys 0m0.041s
If for security or for other reasons you don't want to or can't install precompiled
binaries, Spack can fall-back to bootstrap ``clingo`` from source files. To forbid
Spack from retrieving binaries from the bootstrapping buildcache, the following
command must be given:
If for security concerns you cannot bootstrap ``clingo`` from pre-built
binaries, you have to mark this bootstrapping method as untrusted. This makes
Spack fall back to bootstrapping from sources:
.. code-block:: console
$ spack bootstrap untrust github-actions
==> "github-actions" is now untrusted and will not be used for bootstrapping
since an "untrusted" way of bootstrapping software will not be considered
by Spack. You can verify the new settings are effective with:
You can verify that the new settings are effective with:
.. code-block:: console
@@ -181,33 +178,25 @@ by Spack. You can verify the new settings are effective with:
Description:
Specs built from sources by Spack. May take a long time.
When bootstrapping from sources, Spack requires a compiler with support
for C++14 (GCC on ``linux``, Apple Clang on ``darwin``) and static C++
standard libraries on ``linux``. Spack will build the required software
on the first request to concretize a spec:
.. note::
When bootstrapping from sources, Spack requires a full install of Python
including header files (e.g. ``python3-dev`` on Debian), and a compiler
with support for C++14 (GCC on Linux, Apple Clang on macOS) and static C++
standard libraries on Linux.
Spack will build the required software on the first request to concretize a spec:
.. code-block:: console
$ spack solve zlib
$ spack spec zlib
[+] /usr (external bison-3.0.4-wu5pgjchxzemk5ya2l3ddqug2d7jv6eb)
[+] /usr (external cmake-3.19.4-a4kmcfzxxy45mzku4ipmj5kdiiz5a57b)
[+] /usr (external python-3.6.9-x4fou4iqqlh5ydwddx3pvfcwznfrqztv)
==> Installing re2c-1.2.1-e3x6nxtk3ahgd63ykgy44mpuva6jhtdt
[ ... ]
==> Optimization: [0, 0, 0, 0, 0, 1, 0, 0, 0]
zlib@1.2.11%gcc@10.1.0+optimize+pic+shared arch=linux-ubuntu18.04-broadwell
.. tip::
If you want to speed-up bootstrapping ``clingo`` from sources, you may try to
search for ``cmake`` and ``bison`` on your system:
.. code-block:: console
$ spack external find cmake bison
==> The following specs have been detected on this system and added to /home/spack/.spack/packages.yaml
bison@3.0.4 cmake@3.19.4
"""""""""""""""""""
The Bootstrap Store
"""""""""""""""""""
@@ -282,9 +271,10 @@ Compiler configuration
----------------------
Spack has the ability to build packages with multiple compilers and
compiler versions. Spack searches for compilers on your machine
automatically the first time it is run. It does this by inspecting
your ``PATH``.
compiler versions. Compilers can be made available to Spack by
specifying them manually in ``compilers.yaml``, or automatically by
running ``spack compiler find``, but for convenience Spack will
automatically detect compilers the first time it needs them.
.. _cmd-spack-compilers:
@@ -292,7 +282,7 @@ your ``PATH``.
``spack compilers``
^^^^^^^^^^^^^^^^^^^
You can see which compilers spack has found by running ``spack
You can see which compilers are available to Spack by running ``spack
compilers`` or ``spack compiler list``:
.. code-block:: console
@@ -331,9 +321,10 @@ An alias for ``spack compiler find``.
``spack compiler find``
^^^^^^^^^^^^^^^^^^^^^^^
If you do not see a compiler in this list, but you want to use it with
Spack, you can simply run ``spack compiler find`` with the path to
where the compiler is installed. For example:
Lists the compilers currently available to Spack. If you do not see
a compiler in this list, but you want to use it with Spack, you can
simply run ``spack compiler find`` with the path to where the
compiler is installed. For example:
.. code-block:: console

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)
@@ -39,7 +39,7 @@ package:
.. code-block:: console
$ git clone https://github.com/spack/spack.git
$ git clone -c feature.manyFiles=true https://github.com/spack/spack.git
$ cd spack/bin
$ ./spack install libelf

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)
@@ -213,6 +213,18 @@ location). The set ``my_custom_lmod_modules`` will install its lmod
modules to ``/path/to/install/custom/lmod/modules`` (and still install
its tcl modules, if any, to the default location).
By default, an architecture-specific directory is added to the root
directory. A module set may override that behavior by setting the
``arch_folder`` config value to ``False``.
.. code-block:: yaml
modules:
default:
roots:
tcl: /path/to/install/tcl/modules
arch_folder: false
Obviously, having multiple module sets install modules to the default
location could be confusing to users of your modules. In the next
section, we will discuss enabling and disabling module types (module
@@ -261,29 +273,30 @@ of the installed software. For instance, in the snippet below:
.. code-block:: yaml
modules:
tcl:
# The keyword `all` selects every package
all:
environment:
set:
BAR: 'bar'
# This anonymous spec selects any package that
# depends on openmpi. The double colon at the
# end clears the set of rules that matched so far.
^openmpi::
environment:
set:
BAR: 'baz'
# Selects any zlib package
zlib:
environment:
prepend_path:
LD_LIBRARY_PATH: 'foo'
# Selects zlib compiled with gcc@4.8
zlib%gcc@4.8:
environment:
unset:
- FOOBAR
default:
tcl:
# The keyword `all` selects every package
all:
environment:
set:
BAR: 'bar'
# This anonymous spec selects any package that
# depends on openmpi. The double colon at the
# end clears the set of rules that matched so far.
^openmpi::
environment:
set:
BAR: 'baz'
# Selects any zlib package
zlib:
environment:
prepend_path:
LD_LIBRARY_PATH: 'foo'
# Selects zlib compiled with gcc@4.8
zlib%gcc@4.8:
environment:
unset:
- FOOBAR
you are instructing Spack to set the environment variable ``BAR=bar`` for every module,
unless the associated spec satisfies ``^openmpi`` in which case ``BAR=baz``.
@@ -310,9 +323,10 @@ your system. If you write a configuration file like:
.. code-block:: yaml
modules:
tcl:
whitelist: ['gcc', 'llvm'] # Whitelist will have precedence over blacklist
blacklist: ['%gcc@4.4.7'] # Assuming gcc@4.4.7 is the system compiler
default:
tcl:
whitelist: ['gcc', 'llvm'] # Whitelist will have precedence over blacklist
blacklist: ['%gcc@4.4.7'] # Assuming gcc@4.4.7 is the system compiler
you will prevent the generation of module files for any package that
is compiled with ``gcc@4.4.7``, with the only exception of any ``gcc``
@@ -337,8 +351,9 @@ shows how to set hash length in the module file names:
.. code-block:: yaml
modules:
tcl:
hash_length: 7
default:
tcl:
hash_length: 7
To help make module names more readable, and to help alleviate name conflicts
with a short hash, one can use the ``suffixes`` option in the modules
@@ -348,11 +363,12 @@ For instance, the following config options,
.. code-block:: yaml
modules:
tcl:
all:
suffixes:
^python@2.7.12: 'python-2.7.12'
^openblas: 'openblas'
default:
tcl:
all:
suffixes:
^python@2.7.12: 'python-2.7.12'
^openblas: 'openblas'
will add a ``python-2.7.12`` version string to any packages compiled with
python matching the spec, ``python@2.7.12``. This is useful to know which
@@ -367,10 +383,11 @@ covered in :ref:`adding_projections_to_views`.
.. code-block:: yaml
modules:
tcl:
projections:
all: '{name}/{version}-{compiler.name}-{compiler.version}-module'
^mpi: '{name}/{version}-{^mpi.name}-{^mpi.version}-{compiler.name}-{compiler.version}-module'
default:
tcl:
projections:
all: '{name}/{version}-{compiler.name}-{compiler.version}-module'
^mpi: '{name}/{version}-{^mpi.name}-{^mpi.version}-{compiler.name}-{compiler.version}-module'
will create module files that are nested in directories by package
name, contain the version and compiler name and version, and have the
@@ -391,15 +408,16 @@ that are already in the LMod hierarchy.
.. code-block:: yaml
modules:
enable:
- tcl
tcl:
projections:
all: '{name}/{version}-{compiler.name}-{compiler.version}'
all:
conflict:
- '{name}'
- 'intel/14.0.1'
default:
enable:
- tcl
tcl:
projections:
all: '{name}/{version}-{compiler.name}-{compiler.version}'
all:
conflict:
- '{name}'
- 'intel/14.0.1'
will create module files that will conflict with ``intel/14.0.1`` and with the
base directory of the same module, effectively preventing the possibility to
@@ -419,16 +437,17 @@ that are already in the LMod hierarchy.
.. code-block:: yaml
modules:
enable:
- lmod
lmod:
core_compilers:
- 'gcc@4.8'
core_specs:
- 'python'
hierarchy:
- 'mpi'
- 'lapack'
default:
enable:
- lmod
lmod:
core_compilers:
- 'gcc@4.8'
core_specs:
- 'python'
hierarchy:
- 'mpi'
- 'lapack'
that will generate a hierarchy in which the ``lapack`` and ``mpi`` layer can be switched
independently. This allows a site to build the same libraries or applications against different
@@ -449,6 +468,36 @@ that are already in the LMod hierarchy.
For hierarchies that are deeper than three layers ``lmod spider`` may have some issues.
See `this discussion on the LMod project <https://github.com/TACC/Lmod/issues/114>`_.
""""""""""""""""""""""
Select default modules
""""""""""""""""""""""
By default, when multiple modules of the same name share a directory,
the highest version number will be the default module. This behavior
of the ``module`` command can be overridden with a symlink named
``default`` to the desired default module. If you wish to configure
default modules with Spack, add a ``defaults`` key to your modules
configuration:
.. code-block:: yaml
modules:
my-module-set:
tcl:
defaults:
- gcc@10.2.1
- hdf5@1.2.10+mpi+hl%gcc
These defaults may be arbitrarily specific. For any package that
satisfies a default, Spack will generate the module file in the
appropriate path, and will generate a default symlink to the module
file as well.
.. warning::
If Spack is configured to generate multiple default packages in the
same directory, the last modulefile to be generated will be the
default module.
.. _customize-env-modifications:
"""""""""""""""""""""""""""""""""""
@@ -549,11 +598,12 @@ do so by using the environment blacklist:
.. code-block:: yaml
modules:
tcl:
all:
filter:
# Exclude changes to any of these variables
environment_blacklist: ['CPATH', 'LIBRARY_PATH']
default:
tcl:
all:
filter:
# Exclude changes to any of these variables
environment_blacklist: ['CPATH', 'LIBRARY_PATH']
The configuration above will generate module files that will not contain
modifications to either ``CPATH`` or ``LIBRARY_PATH``.
@@ -565,42 +615,39 @@ modifications to either ``CPATH`` or ``LIBRARY_PATH``.
Autoload dependencies
"""""""""""""""""""""
In some cases it can be useful to have module files that automatically load
their dependencies. This may be the case for Python extensions, if not
activated using ``spack activate``:
Often it is required for a module to have its (transient) dependencies loaded as well.
One example where this is useful is when one package needs to use executables provided
by its dependency; when the dependency is autoloaded, the executable will be in the
PATH. Similarly for scripting languages such as Python, packages and their dependencies
have to be loaded together.
Autoloading is enabled by default for LMod, as it has great builtin support for through
the ``depends_on`` function. For Environment Modules it is disabled by default.
Autoloading can also be enabled conditionally:
.. code-block:: yaml
modules:
tcl:
^python:
autoload: 'direct'
modules:
default:
tcl:
all:
autoload: none
^python:
autoload: direct
The configuration file above will produce module files that will
load their direct dependencies if the package installed depends on ``python``.
The allowed values for the ``autoload`` statement are either ``none``,
``direct`` or ``all``. The default is ``none``.
.. tip::
Building external software
Setting ``autoload`` to ``direct`` for all packages can be useful
when building software outside of a Spack installation that depends on
artifacts in that installation. E.g. (adjust ``lmod`` vs ``tcl``
as appropriate):
.. code-block:: yaml
modules:
lmod:
all:
autoload: 'direct'
``direct`` or ``all``.
.. note::
TCL prerequisites
In the ``tcl`` section of the configuration file it is possible to use
the ``prerequisites`` directive that accepts the same values as
``autoload``. It will produce module files that have a ``prereq``
statement instead of automatically loading other modules.
statement, which can be used to autoload dependencies in some versions
of Environment Modules.
------------------------
Maintaining Module Files

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)
@@ -695,20 +695,23 @@ example, ``py-sphinx-rtd-theme@0.1.10a0``. In this case, numbers are
always considered to be "newer" than letters. This is for consistency
with `RPM <https://bugzilla.redhat.com/show_bug.cgi?id=50977>`_.
Spack versions may also be arbitrary non-numeric strings; any string
here will suffice; for example, ``@develop``, ``@master``, ``@local``.
Versions are compared as follows. First, a version string is split into
multiple fields based on delimiters such as ``.``, ``-`` etc. Then
matching fields are compared using the rules below:
Spack versions may also be arbitrary non-numeric strings, for example
``@develop``, ``@master``, ``@local``.
#. The following develop-like strings are greater (newer) than all
numbers and are ordered as ``develop > main > master > head > trunk``.
The order on versions is defined as follows. A version string is split
into a list of components based on delimiters such as ``.``, ``-`` etc.
Lists are then ordered lexicographically, where components are ordered
as follows:
#. Numbers are all less than the chosen develop-like strings above,
and are sorted numerically.
#. The following special strings are considered larger than any other
numeric or non-numeric version component, and satisfy the following
order between themselves: ``develop > main > master > head > trunk``.
#. All other non-numeric versions are less than numeric versions, and
are sorted alphabetically.
#. Numbers are ordered numerically, are less than special strings, and
larger than other non-numeric components.
#. All other non-numeric components are less than numeric components,
and are ordered alphabetically.
The logic behind this sort order is two-fold:
@@ -729,7 +732,7 @@ Version selection
When concretizing, many versions might match a user-supplied spec.
For example, the spec ``python`` matches all available versions of the
package ``python``. Similarly, ``python@3:`` matches all versions of
Python3. Given a set of versions that match a spec, Spack
Python 3 and above. Given a set of versions that match a spec, Spack
concretization uses the following priorities to decide which one to
use:
@@ -1419,6 +1422,86 @@ other similar operations:
).with_default('auto').with_non_feature_values('auto'),
)
^^^^^^^^^^^^^^^^^^^^
Conditional Variants
^^^^^^^^^^^^^^^^^^^^
The variant directive accepts a ``when`` clause. The variant will only
be present on specs that otherwise satisfy the spec listed as the
``when`` clause. For example, the following class has a variant
``bar`` when it is at version 2.0 or higher.
.. code-block:: python
class Foo(Package):
...
variant('bar', default=False, when='@2.0:', description='help message')
The ``when`` clause follows the same syntax and accepts the same
values as the ``when`` argument of
:py:func:`spack.directives.depends_on`
^^^^^^^^^^^^^^^
Sticky Variants
^^^^^^^^^^^^^^^
The variant directive can be marked as ``sticky`` by setting to ``True`` the
corresponding argument:
.. code-block:: python
variant('bar', default=False, sticky=True)
A ``sticky`` variant differs from a regular one in that it is always set
to either:
#. An explicit value appearing in a spec literal or
#. Its default value
The concretizer thus is not free to pick an alternate value to work
around conflicts, but will error out instead.
Setting this property on a variant is useful in cases where the
variant allows some dangerous or controversial options (e.g. using unsupported versions
of a compiler for a library) and the packager wants to ensure that
allowing these options is done on purpose by the user, rather than
automatically by the solver.
^^^^^^^^^^^^^^^^^^^
Overriding Variants
^^^^^^^^^^^^^^^^^^^
Packages may override variants for several reasons, most often to
change the default from a variant defined in a parent class or to
change the conditions under which a variant is present on the spec.
When a variant is defined multiple times, whether in the same package
file or in a subclass and a superclass, the last definition is used
for all attributes **except** for the ``when`` clauses. The ``when``
clauses are accumulated through all invocations, and the variant is
present on the spec if any of the accumulated conditions are
satisfied.
For example, consider the following package:
.. code-block:: python
class Foo(Package):
...
variant('bar', default=False, when='@1.0', description='help1')
variant('bar', default=True, when='platform=darwin', description='help2')
...
This package ``foo`` has a variant ``bar`` when the spec satisfies
either ``@1.0`` or ``platform=darwin``, but not for other platforms at
other versions. The default for this variant, when it is present, is
always ``True``, regardless of which condition of the variant is
satisfied. This allows packages to override variants in packages or
build system classes from which they inherit, by modifying the variant
values without modifying the ``when`` clause. It also allows a package
to implement ``or`` semantics for a variant ``when`` clause by
duplicating the variant definition.
------------------------------------
Resources (expanding extra tarballs)
------------------------------------
@@ -2063,7 +2146,7 @@ Version ranges
^^^^^^^^^^^^^^
Although some packages require a specific version for their dependencies,
most can be built with a range of version. For example, if you are
most can be built with a range of versions. For example, if you are
writing a package for a legacy Python module that only works with Python
2.4 through 2.6, this would look like:
@@ -2072,9 +2155,9 @@ writing a package for a legacy Python module that only works with Python
depends_on('python@2.4:2.6')
Version ranges in Spack are *inclusive*, so ``2.4:2.6`` means any version
greater than or equal to ``2.4`` and up to and including ``2.6``. If you
want to specify that a package works with any version of Python 3, this
would look like:
greater than or equal to ``2.4`` and up to and including any ``2.6.x``. If
you want to specify that a package works with any version of Python 3 (or
higher), this would look like:
.. code-block:: python
@@ -2085,29 +2168,30 @@ requires Python 2, you can similarly leave out the lower bound:
.. code-block:: python
depends_on('python@:2.9')
depends_on('python@:2')
Notice that we didn't use ``@:3``. Version ranges are *inclusive*, so
``@:3`` means "up to and including 3".
``@:3`` means "up to and including any 3.x version".
What if a package can only be built with Python 2.6? You might be
What if a package can only be built with Python 2.7? You might be
inclined to use:
.. code-block:: python
depends_on('python@2.6')
depends_on('python@2.7')
However, this would be wrong. Spack assumes that all version constraints
are absolute, so it would try to install Python at exactly ``2.6``. The
correct way to specify this would be:
are exact, so it would try to install Python not at ``2.7.18``, but
exactly at ``2.7``, which is a non-existent version. The correct way to
specify this would be:
.. code-block:: python
depends_on('python@2.6.0:2.6.999')
depends_on('python@2.7.0:2.7')
A spec can contain multiple version ranges separated by commas.
For example, if you need Boost 1.59.0 or newer, but there are known
issues with 1.64.0, 1.65.0, and 1.66.0, you can say:
A spec can contain a version list of ranges and individual versions
separated by commas. For example, if you need Boost 1.59.0 or newer,
but there are known issues with 1.64.0, 1.65.0, and 1.66.0, you can say:
.. code-block:: python
@@ -2824,7 +2908,7 @@ is equivalent to:
depends_on('elpa+openmp', when='+openmp+elpa')
Constraints from nested context managers are also added together, but they are rarely
Constraints from nested context managers are also combined together, but they are rarely
needed or recommended.
.. _install-method:
@@ -2885,7 +2969,7 @@ The package base class, usually specialized for a given build system, determines
actual set of entities available for overriding.
The classes that are currently provided by Spack are:
+-------------------------=--------------------------------+----------------------------------+
+----------------------------------------------------------+----------------------------------+
| **Base Class** | **Purpose** |
+==========================================================+==================================+
| :class:`~spack.package.Package` | General base class not |

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)
@@ -48,9 +48,9 @@ or Amazon Elastic Kubernetes Service (`EKS <https://aws.amazon.com/eks>`_), thou
topics are outside the scope of this document.
Spack's pipelines are now making use of the
`trigger <https://docs.gitlab.com/12.9/ee/ci/yaml/README.html#trigger>`_ syntax to run
`trigger <https://docs.gitlab.com/ee/ci/yaml/#trigger>`_ syntax to run
dynamically generated
`child pipelines <https://docs.gitlab.com/12.9/ee/ci/parent_child_pipelines.html>`_.
`child pipelines <https://docs.gitlab.com/ee/ci/pipelines/parent_child_pipelines.html>`_.
Note that the use of dynamic child pipelines requires running Gitlab version
``>= 12.9``.

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)
@@ -335,7 +335,7 @@ merged YAML from all configuration files, use ``spack config get repos``:
- ~/myrepo
- $spack/var/spack/repos/builtin
mNote that, unlike ``spack repo list``, this does not include the
Note that, unlike ``spack repo list``, this does not include the
namespace, which is read from each repo's ``repo.yaml``.
^^^^^^^^^^^^^^^^^^^^^

View File

@@ -5,3 +5,6 @@ sphinx>=3.4,!=4.1.2
sphinxcontrib-programoutput
sphinx-rtd-theme
python-levenshtein
# Restrict to docutils <0.17 to workaround a list rendering issue in sphinx.
# https://stackoverflow.com/questions/67542699
docutils <0.17

View File

@@ -1,4 +1,4 @@
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
@@ -17,6 +17,7 @@ spack:
# Sphinx
- "py-sphinx@3.4:4.1.1,4.1.3:"
- py-sphinxcontrib-programoutput
- py-docutils@:0.16
- py-sphinx-rtd-theme
# VCS
- git

View File

@@ -1,5 +1,5 @@
Name, Supported Versions, Notes, Requirement Reason
Python, 2.6/2.7/3.5-3.9, , Interpreter for Spack
Python, 2.7/3.5-3.9, , Interpreter for Spack
C/C++ Compilers, , , Building software
make, , , Build software
patch, , , Build software
@@ -15,3 +15,4 @@ gnupg2, , , Sign/Verify Buildcaches
git, , , Manage Software Repositories
svn, , Optional, Manage Software Repositories
hg, , Optional, Manage Software Repositories
Python header files, , Optional (e.g. ``python3-dev`` on Debian), Bootstrapping from sources
1 Name Supported Versions Notes Requirement Reason
2 Python 2.6/2.7/3.5-3.9 2.7/3.5-3.9 Interpreter for Spack
3 C/C++ Compilers Building software
4 make Build software
5 patch Build software
15 git Manage Software Repositories
16 svn Optional Manage Software Repositories
17 hg Optional Manage Software Repositories
18 Python header files Optional (e.g. ``python3-dev`` on Debian) Bootstrapping from sources

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)

578
lib/spack/env/cc vendored
View File

@@ -1,6 +1,7 @@
#!/bin/bash
#!/bin/sh
# shellcheck disable=SC2034 # evals in this script fool shellcheck
#
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
@@ -20,25 +21,33 @@
# -Wl,-rpath arguments for dependency /lib directories.
#
# Reset IFS to the default: whitespace-separated lists. When we use
# other separators, we set and reset it.
unset IFS
# Separator for lists whose names end with `_list`.
# We pick the alarm bell character, which is highly unlikely to
# conflict with anything. This is a literal bell character (which
# we have to use since POSIX sh does not convert escape sequences
# like '\a' outside of the format argument of `printf`).
# NOTE: Depending on your editor this may look empty, but it is not.
readonly lsep=''
# This is an array of environment variables that need to be set before
# the script runs. They are set by routines in spack.build_environment
# as part of the package installation process.
parameters=(
SPACK_ENV_PATH
SPACK_DEBUG_LOG_DIR
SPACK_DEBUG_LOG_ID
SPACK_COMPILER_SPEC
SPACK_CC_RPATH_ARG
SPACK_CXX_RPATH_ARG
SPACK_F77_RPATH_ARG
SPACK_FC_RPATH_ARG
SPACK_TARGET_ARGS
SPACK_DTAGS_TO_ADD
SPACK_DTAGS_TO_STRIP
SPACK_LINKER_ARG
SPACK_SHORT_SPEC
SPACK_SYSTEM_DIRS
)
readonly params="\
SPACK_ENV_PATH
SPACK_DEBUG_LOG_DIR
SPACK_DEBUG_LOG_ID
SPACK_COMPILER_SPEC
SPACK_CC_RPATH_ARG
SPACK_CXX_RPATH_ARG
SPACK_F77_RPATH_ARG
SPACK_FC_RPATH_ARG
SPACK_LINKER_ARG
SPACK_SHORT_SPEC
SPACK_SYSTEM_DIRS"
# Optional parameters that aren't required to be set
@@ -58,60 +67,157 @@ parameters=(
# Test command is used to unit test the compiler script.
# SPACK_TEST_COMMAND
# die()
# Prints a message and exits with error 1.
function die {
echo "$@"
# die MESSAGE
# Print a message and exit with error code 1.
die() {
echo "[spack cc] ERROR: $*"
exit 1
}
# read input parameters into proper bash arrays.
# SYSTEM_DIRS is delimited by :
IFS=':' read -ra SPACK_SYSTEM_DIRS <<< "${SPACK_SYSTEM_DIRS}"
# empty VARNAME
# Return whether the variable VARNAME is unset or set to the empty string.
empty() {
eval "test -z \"\${$1}\""
}
# SPACK_<LANG>FLAGS and SPACK_LDLIBS are split by ' '
IFS=' ' read -ra SPACK_FFLAGS <<< "$SPACK_FFLAGS"
IFS=' ' read -ra SPACK_CPPFLAGS <<< "$SPACK_CPPFLAGS"
IFS=' ' read -ra SPACK_CFLAGS <<< "$SPACK_CFLAGS"
IFS=' ' read -ra SPACK_CXXFLAGS <<< "$SPACK_CXXFLAGS"
IFS=' ' read -ra SPACK_LDFLAGS <<< "$SPACK_LDFLAGS"
IFS=' ' read -ra SPACK_LDLIBS <<< "$SPACK_LDLIBS"
# setsep LISTNAME
# Set the global variable 'sep' to the separator for a list with name LISTNAME.
# There are three types of lists:
# 1. regular lists end with _list and are separated by $lsep
# 2. directory lists end with _dirs/_DIRS/PATH(S) and are separated by ':'
# 3. any other list is assumed to be separated by spaces: " "
setsep() {
case "$1" in
*_dirs|*_DIRS|*PATH|*PATHS)
sep=':'
;;
*_list)
sep="$lsep"
;;
*)
sep=" "
;;
esac
}
# prepend LISTNAME ELEMENT [SEP]
#
# Prepend ELEMENT to the list stored in the variable LISTNAME,
# assuming the list is separated by SEP.
# Handles empty lists and single-element lists.
prepend() {
varname="$1"
elt="$2"
if empty "$varname"; then
eval "$varname=\"\${elt}\""
else
# Get the appropriate separator for the list we're appending to.
setsep "$varname"
eval "$varname=\"\${elt}${sep}\${$varname}\""
fi
}
# append LISTNAME ELEMENT [SEP]
#
# Append ELEMENT to the list stored in the variable LISTNAME,
# assuming the list is separated by SEP.
# Handles empty lists and single-element lists.
append() {
varname="$1"
elt="$2"
if empty "$varname"; then
eval "$varname=\"\${elt}\""
else
# Get the appropriate separator for the list we're appending to.
setsep "$varname"
eval "$varname=\"\${$varname}${sep}\${elt}\""
fi
}
# extend LISTNAME1 LISTNAME2 [PREFIX]
#
# Append the elements stored in the variable LISTNAME2
# to the list stored in LISTNAME1.
# If PREFIX is provided, prepend it to each element.
extend() {
# Figure out the appropriate IFS for the list we're reading.
setsep "$2"
if [ "$sep" != " " ]; then
IFS="$sep"
fi
eval "for elt in \${$2}; do append $1 \"$3\${elt}\"; done"
unset IFS
}
# preextend LISTNAME1 LISTNAME2 [PREFIX]
#
# Prepend the elements stored in the list at LISTNAME2
# to the list at LISTNAME1, preserving order.
# If PREFIX is provided, prepend it to each element.
preextend() {
# Figure out the appropriate IFS for the list we're reading.
setsep "$2"
if [ "$sep" != " " ]; then
IFS="$sep"
fi
# first, reverse the list to prepend
_reversed_list=""
eval "for elt in \${$2}; do prepend _reversed_list \"$3\${elt}\"; done"
# prepend reversed list to preextend in order
IFS="${lsep}"
for elt in $_reversed_list; do prepend "$1" "$3${elt}"; done
unset IFS
}
# system_dir PATH
# test whether a path is a system directory
function system_dir {
system_dir() {
IFS=':' # SPACK_SYSTEM_DIRS is colon-separated
path="$1"
for sd in "${SPACK_SYSTEM_DIRS[@]}"; do
if [ "${path}" == "${sd}" ] || [ "${path}" == "${sd}/" ]; then
for sd in $SPACK_SYSTEM_DIRS; do
if [ "${path}" = "${sd}" ] || [ "${path}" = "${sd}/" ]; then
# success if path starts with a system prefix
unset IFS
return 0
fi
done
unset IFS
return 1 # fail if path starts no system prefix
}
for param in "${parameters[@]}"; do
if [[ -z ${!param+x} ]]; then
# Fail with a clear message if the input contains any bell characters.
if eval "[ \"\${*#*${lsep}}\" != \"\$*\" ]"; then
die "Compiler command line contains our separator ('${lsep}'). Cannot parse."
fi
# ensure required variables are set
for param in $params; do
if eval "test -z \"\${${param}:-}\""; then
die "Spack compiler must be run from Spack! Input '$param' is missing."
fi
done
# Check if optional parameters are defined
# If we aren't asking for debug flags, don't add them
if [[ -z ${SPACK_ADD_DEBUG_FLAGS+x} ]]; then
if [ -z "${SPACK_ADD_DEBUG_FLAGS:-}" ]; then
SPACK_ADD_DEBUG_FLAGS="false"
fi
# SPACK_ADD_DEBUG_FLAGS must be true/false/custom
is_valid="false"
for param in "true" "false" "custom"; do
if [ "$param" == "$SPACK_ADD_DEBUG_FLAGS" ]; then
if [ "$param" = "$SPACK_ADD_DEBUG_FLAGS" ]; then
is_valid="true"
fi
done
# Exit with error if we are given an incorrect value
if [ "$is_valid" == "false" ]; then
die "SPACK_ADD_DEBUG_FLAGS, if defined, must be one of 'true' 'false' or 'custom'"
if [ "$is_valid" = "false" ]; then
die "SPACK_ADD_DEBUG_FLAGS, if defined, must be one of 'true', 'false', or 'custom'."
fi
# Figure out the type of compiler, the language, and the mode so that
@@ -128,7 +234,7 @@ fi
# ld link
# ccld compile & link
command=$(basename "$0")
command="${0##*/}"
comp="CC"
case "$command" in
cpp)
@@ -142,7 +248,7 @@ case "$command" in
lang_flags=C
debug_flags="-g"
;;
c++|CC|g++|clang++|armclang++|icpc|icpx|pgc++|nvc++|xlc++|xlc++_r|FCC)
c++|CC|g++|clang++|armclang++|icpc|icpx|dpcpp|pgc++|nvc++|xlc++|xlc++_r|FCC)
command="$SPACK_CXX"
language="C++"
comp="CXX"
@@ -174,7 +280,7 @@ esac
# If any of the arguments below are present, then the mode is vcheck.
# In vcheck mode, nothing is added in terms of extra search paths or
# libraries.
if [[ -z $mode ]] || [[ $mode == ld ]]; then
if [ -z "$mode" ] || [ "$mode" = ld ]; then
for arg in "$@"; do
case $arg in
-v|-V|--version|-dumpversion)
@@ -186,16 +292,16 @@ if [[ -z $mode ]] || [[ $mode == ld ]]; then
fi
# Finish setting up the mode.
if [[ -z $mode ]]; then
if [ -z "$mode" ]; then
mode=ccld
for arg in "$@"; do
if [[ $arg == -E ]]; then
if [ "$arg" = "-E" ]; then
mode=cpp
break
elif [[ $arg == -S ]]; then
elif [ "$arg" = "-S" ]; then
mode=as
break
elif [[ $arg == -c ]]; then
elif [ "$arg" = "-c" ]; then
mode=cc
break
fi
@@ -222,42 +328,46 @@ dtags_to_strip="${SPACK_DTAGS_TO_STRIP}"
linker_arg="${SPACK_LINKER_ARG}"
# Set up rpath variable according to language.
eval rpath=\$SPACK_${comp}_RPATH_ARG
rpath="ERROR: RPATH ARG WAS NOT SET"
eval "rpath=\${SPACK_${comp}_RPATH_ARG:?${rpath}}"
# Dump the mode and exit if the command is dump-mode.
if [[ $SPACK_TEST_COMMAND == dump-mode ]]; then
if [ "$SPACK_TEST_COMMAND" = "dump-mode" ]; then
echo "$mode"
exit
fi
# Check that at least one of the real commands was actually selected,
# otherwise we don't know what to execute.
if [[ -z $command ]]; then
die "ERROR: Compiler '$SPACK_COMPILER_SPEC' does not support compiling $language programs."
# If, say, SPACK_CC is set but SPACK_FC is not, we want to know. Compilers do not
# *have* to set up Fortran executables, so we need to tell the user when a build is
# about to attempt to use them unsuccessfully.
if [ -z "$command" ]; then
die "Compiler '$SPACK_COMPILER_SPEC' does not have a $language compiler configured."
fi
#
# Filter '.' and Spack environment directories out of PATH so that
# this script doesn't just call itself
#
IFS=':' read -ra env_path <<< "$PATH"
IFS=':' read -ra spack_env_dirs <<< "$SPACK_ENV_PATH"
spack_env_dirs+=("" ".")
export PATH=""
for dir in "${env_path[@]}"; do
new_dirs=""
IFS=':'
for dir in $PATH; do
addpath=true
for env_dir in "${spack_env_dirs[@]}"; do
if [[ "${dir%%/}" == "$env_dir" ]]; then
addpath=false
break
fi
for spack_env_dir in $SPACK_ENV_PATH; do
case "${dir%%/}" in
"$spack_env_dir"|'.'|'')
addpath=false
break
;;
esac
done
if $addpath; then
export PATH="${PATH:+$PATH:}$dir"
if [ $addpath = true ]; then
append new_dirs "$dir"
fi
done
unset IFS
export PATH="$new_dirs"
if [[ $mode == vcheck ]]; then
if [ "$mode" = vcheck ]; then
exec "${command}" "$@"
fi
@@ -265,16 +375,20 @@ fi
# It doesn't work with -rpath.
# This variable controls whether they are added.
add_rpaths=true
if [[ ($mode == ld || $mode == ccld) && "$SPACK_SHORT_SPEC" =~ "darwin" ]];
then
for arg in "$@"; do
if [[ ($arg == -r && $mode == ld) ||
($arg == -r && $mode == ccld) ||
($arg == -Wl,-r && $mode == ccld) ]]; then
add_rpaths=false
break
fi
done
if [ "$mode" = ld ] || [ "$mode" = ccld ]; then
if [ "${SPACK_SHORT_SPEC#*darwin}" != "${SPACK_SHORT_SPEC}" ]; then
for arg in "$@"; do
if [ "$arg" = "-r" ]; then
if [ "$mode" = ld ] || [ "$mode" = ccld ]; then
add_rpaths=false
break
fi
elif [ "$arg" = "-Wl,-r" ] && [ "$mode" = ccld ]; then
add_rpaths=false
break
fi
done
fi
fi
# Save original command for debug logging
@@ -297,17 +411,22 @@ input_command="$*"
# The libs variable is initialized here for completeness, and it is also
# used later to inject flags supplied via `ldlibs` on the command
# line. These come into the wrappers via SPACK_LDLIBS.
#
includes=()
libdirs=()
rpaths=()
system_includes=()
system_libdirs=()
system_rpaths=()
libs=()
other_args=()
isystem_system_includes=()
isystem_includes=()
# The loop below breaks up the command line into these lists of components.
# The lists are all bell-separated to be as flexible as possible, as their
# contents may come from the command line, from ' '-separated lists,
# ':'-separated lists, etc.
include_dirs_list=""
lib_dirs_list=""
rpath_dirs_list=""
system_include_dirs_list=""
system_lib_dirs_list=""
system_rpath_dirs_list=""
isystem_system_include_dirs_list=""
isystem_include_dirs_list=""
libs_list=""
other_args_list=""
while [ $# -ne 0 ]; do
@@ -327,32 +446,32 @@ while [ $# -ne 0 ]; do
isystem_was_used=true
if [ -z "$arg" ]; then shift; arg="$1"; fi
if system_dir "$arg"; then
isystem_system_includes+=("$arg")
append isystem_system_include_dirs_list "$arg"
else
isystem_includes+=("$arg")
append isystem_include_dirs_list "$arg"
fi
;;
-I*)
arg="${1#-I}"
if [ -z "$arg" ]; then shift; arg="$1"; fi
if system_dir "$arg"; then
system_includes+=("$arg")
append system_include_dirs_list "$arg"
else
includes+=("$arg")
append include_dirs_list "$arg"
fi
;;
-L*)
arg="${1#-L}"
if [ -z "$arg" ]; then shift; arg="$1"; fi
if system_dir "$arg"; then
system_libdirs+=("$arg")
append system_lib_dirs_list "$arg"
else
libdirs+=("$arg")
append lib_dirs_list "$arg"
fi
;;
-l*)
# -loopopt=0 is generated erroneously in autoconf <= 2.69,
# and passed by ifx to the linker, which confuses it with a
# and passed by ifx to the linker, which confuses it with a
# library. Filter it out.
# TODO: generalize filtering of args with an env var, so that
# TODO: we do not have to special case this here.
@@ -363,66 +482,76 @@ while [ $# -ne 0 ]; do
fi
arg="${1#-l}"
if [ -z "$arg" ]; then shift; arg="$1"; fi
other_args+=("-l$arg")
append other_args_list "-l$arg"
;;
-Wl,*)
arg="${1#-Wl,}"
if [ -z "$arg" ]; then shift; arg="$1"; fi
if [[ "$arg" = -rpath=* ]]; then
rp="${arg#-rpath=}"
elif [[ "$arg" = --rpath=* ]]; then
rp="${arg#--rpath=}"
elif [[ "$arg" = -rpath,* ]]; then
rp="${arg#-rpath,}"
elif [[ "$arg" = --rpath,* ]]; then
rp="${arg#--rpath,}"
elif [[ "$arg" =~ ^-?-rpath$ ]]; then
shift; arg="$1"
if [[ "$arg" != -Wl,* ]]; then
die "-Wl,-rpath was not followed by -Wl,*"
fi
rp="${arg#-Wl,}"
elif [[ "$arg" = "$dtags_to_strip" ]] ; then
: # We want to remove explicitly this flag
else
other_args+=("-Wl,$arg")
fi
case "$arg" in
-rpath=*) rp="${arg#-rpath=}" ;;
--rpath=*) rp="${arg#--rpath=}" ;;
-rpath,*) rp="${arg#-rpath,}" ;;
--rpath,*) rp="${arg#--rpath,}" ;;
-rpath|--rpath)
shift; arg="$1"
case "$arg" in
-Wl,*)
rp="${arg#-Wl,}"
;;
*)
die "-Wl,-rpath was not followed by -Wl,*"
;;
esac
;;
"$dtags_to_strip")
: # We want to remove explicitly this flag
;;
*)
append other_args_list "-Wl,$arg"
;;
esac
;;
-Xlinker,*)
arg="${1#-Xlinker,}"
if [ -z "$arg" ]; then shift; arg="$1"; fi
if [[ "$arg" = -rpath=* ]]; then
rp="${arg#-rpath=}"
elif [[ "$arg" = --rpath=* ]]; then
rp="${arg#--rpath=}"
elif [[ "$arg" = -rpath ]] || [[ "$arg" = --rpath ]]; then
shift; arg="$1"
if [[ "$arg" != -Xlinker,* ]]; then
die "-Xlinker,-rpath was not followed by -Xlinker,*"
fi
rp="${arg#-Xlinker,}"
else
other_args+=("-Xlinker,$arg")
fi
case "$arg" in
-rpath=*) rp="${arg#-rpath=}" ;;
--rpath=*) rp="${arg#--rpath=}" ;;
-rpath|--rpath)
shift; arg="$1"
case "$arg" in
-Xlinker,*)
rp="${arg#-Xlinker,}"
;;
*)
die "-Xlinker,-rpath was not followed by -Xlinker,*"
;;
esac
;;
*)
append other_args_list "-Xlinker,$arg"
;;
esac
;;
-Xlinker)
if [[ "$2" == "-rpath" ]]; then
if [[ "$3" != "-Xlinker" ]]; then
if [ "$2" = "-rpath" ]; then
if [ "$3" != "-Xlinker" ]; then
die "-Xlinker,-rpath was not followed by -Xlinker,*"
fi
shift 3;
rp="$1"
elif [[ "$2" = "$dtags_to_strip" ]] ; then
elif [ "$2" = "$dtags_to_strip" ]; then
shift # We want to remove explicitly this flag
else
other_args+=("$1")
append other_args_list "$1"
fi
;;
*)
if [[ "$1" = "$dtags_to_strip" ]] ; then
if [ "$1" = "$dtags_to_strip" ]; then
: # We want to remove explicitly this flag
else
other_args+=("$1")
append other_args_list "$1"
fi
;;
esac
@@ -430,9 +559,9 @@ while [ $# -ne 0 ]; do
# test rpaths against system directories in one place.
if [ -n "$rp" ]; then
if system_dir "$rp"; then
system_rpaths+=("$rp")
append system_rpath_dirs_list "$rp"
else
rpaths+=("$rp")
append rpath_dirs_list "$rp"
fi
fi
shift
@@ -445,16 +574,15 @@ done
# See the gmake manual on implicit rules for details:
# https://www.gnu.org/software/make/manual/html_node/Implicit-Variables.html
#
flags=()
flags_list=""
# Add debug flags
if [ "${SPACK_ADD_DEBUG_FLAGS}" == "true" ]; then
flags=("${flags[@]}" "${debug_flags}")
if [ "${SPACK_ADD_DEBUG_FLAGS}" = "true" ]; then
extend flags_list debug_flags
# If a custom flag is requested, derive from environment
elif [ "$SPACK_ADD_DEBUG_FLAGS" == "custom" ]; then
IFS=' ' read -ra SPACK_DEBUG_FLAGS <<< "$SPACK_DEBUG_FLAGS"
flags=("${flags[@]}" "${SPACK_DEBUG_FLAGS[@]}")
elif [ "$SPACK_ADD_DEBUG_FLAGS" = "custom" ]; then
extend flags_list SPACK_DEBUG_FLAGS
fi
# Fortran flags come before CPPFLAGS
@@ -462,7 +590,8 @@ case "$mode" in
cc|ccld)
case $lang_flags in
F)
flags=("${flags[@]}" "${SPACK_FFLAGS[@]}") ;;
extend flags_list SPACK_FFLAGS
;;
esac
;;
esac
@@ -470,7 +599,8 @@ esac
# C preprocessor flags come before any C/CXX flags
case "$mode" in
cpp|as|cc|ccld)
flags=("${flags[@]}" "${SPACK_CPPFLAGS[@]}") ;;
extend flags_list SPACK_CPPFLAGS
;;
esac
@@ -479,67 +609,67 @@ case "$mode" in
cc|ccld)
case $lang_flags in
C)
flags=("${flags[@]}" "${SPACK_CFLAGS[@]}") ;;
extend flags_list SPACK_CFLAGS
;;
CXX)
flags=("${flags[@]}" "${SPACK_CXXFLAGS[@]}") ;;
extend flags_list SPACK_CXXFLAGS
;;
esac
flags=(${SPACK_TARGET_ARGS[@]} "${flags[@]}")
# prepend target args
preextend flags_list SPACK_TARGET_ARGS
;;
esac
# Linker flags
case "$mode" in
ld|ccld)
flags=("${flags[@]}" "${SPACK_LDFLAGS[@]}") ;;
extend flags_list SPACK_LDFLAGS
;;
esac
# On macOS insert headerpad_max_install_names linker flag
if [[ ($mode == ld || $mode == ccld) && "$SPACK_SHORT_SPEC" =~ "darwin" ]];
then
case "$mode" in
ld)
flags=("${flags[@]}" -headerpad_max_install_names) ;;
ccld)
flags=("${flags[@]}" "-Wl,-headerpad_max_install_names") ;;
esac
if [ "$mode" = ld ] || [ "$mode" = ccld ]; then
if [ "${SPACK_SHORT_SPEC#*darwin}" != "${SPACK_SHORT_SPEC}" ]; then
case "$mode" in
ld)
append flags_list "-headerpad_max_install_names" ;;
ccld)
append flags_list "-Wl,-headerpad_max_install_names" ;;
esac
fi
fi
IFS=':' read -ra rpath_dirs <<< "$SPACK_RPATH_DIRS"
if [[ $mode == ccld || $mode == ld ]]; then
if [[ "$add_rpaths" != "false" ]] ; then
if [ "$mode" = ccld ] || [ "$mode" = ld ]; then
if [ "$add_rpaths" != "false" ]; then
# Append RPATH directories. Note that in the case of the
# top-level package these directories may not exist yet. For dependencies
# it is assumed that paths have already been confirmed.
rpaths=("${rpaths[@]}" "${rpath_dirs[@]}")
extend rpath_dirs_list SPACK_RPATH_DIRS
fi
fi
IFS=':' read -ra link_dirs <<< "$SPACK_LINK_DIRS"
if [[ $mode == ccld || $mode == ld ]]; then
libdirs=("${libdirs[@]}" "${link_dirs[@]}")
if [ "$mode" = ccld ] || [ "$mode" = ld ]; then
extend lib_dirs_list SPACK_LINK_DIRS
fi
# add RPATHs if we're in in any linking mode
case "$mode" in
ld|ccld)
# Set extra RPATHs
IFS=':' read -ra extra_rpaths <<< "$SPACK_COMPILER_EXTRA_RPATHS"
libdirs+=("${extra_rpaths[@]}")
if [[ "$add_rpaths" != "false" ]] ; then
rpaths+=("${extra_rpaths[@]}")
extend lib_dirs_list SPACK_COMPILER_EXTRA_RPATHS
if [ "$add_rpaths" != "false" ]; then
extend rpath_dirs_list SPACK_COMPILER_EXTRA_RPATHS
fi
# Set implicit RPATHs
IFS=':' read -ra implicit_rpaths <<< "$SPACK_COMPILER_IMPLICIT_RPATHS"
if [[ "$add_rpaths" != "false" ]] ; then
rpaths+=("${implicit_rpaths[@]}")
if [ "$add_rpaths" != "false" ]; then
extend rpath_dirs_list SPACK_COMPILER_IMPLICIT_RPATHS
fi
# Add SPACK_LDLIBS to args
for lib in "${SPACK_LDLIBS[@]}"; do
libs+=("${lib#-l}")
for lib in $SPACK_LDLIBS; do
append libs_list "${lib#-l}"
done
;;
esac
@@ -547,63 +677,62 @@ esac
#
# Finally, reassemble the command line.
#
# Includes and system includes first
args=()
# flags assembled earlier
args+=("${flags[@]}")
args_list="$flags_list"
# Insert include directories just prior to any system include directories
# NOTE: adding ${lsep} to the prefix here turns every added element into two
extend args_list include_dirs_list "-I"
extend args_list isystem_include_dirs_list "-isystem${lsep}"
for dir in "${includes[@]}"; do args+=("-I$dir"); done
for dir in "${isystem_includes[@]}"; do args+=("-isystem" "$dir"); done
case "$mode" in
cpp|cc|as|ccld)
if [ "$isystem_was_used" = "true" ]; then
extend args_list SPACK_INCLUDE_DIRS "-isystem${lsep}"
else
extend args_list SPACK_INCLUDE_DIRS "-I"
fi
;;
esac
IFS=':' read -ra spack_include_dirs <<< "$SPACK_INCLUDE_DIRS"
if [[ $mode == cpp || $mode == cc || $mode == as || $mode == ccld ]]; then
if [[ "$isystem_was_used" == "true" ]] ; then
for dir in "${spack_include_dirs[@]}"; do args+=("-isystem" "$dir"); done
else
for dir in "${spack_include_dirs[@]}"; do args+=("-I$dir"); done
fi
fi
for dir in "${system_includes[@]}"; do args+=("-I$dir"); done
for dir in "${isystem_system_includes[@]}"; do args+=("-isystem" "$dir"); done
extend args_list system_include_dirs_list -I
extend args_list isystem_system_include_dirs_list "-isystem${lsep}"
# Library search paths
for dir in "${libdirs[@]}"; do args+=("-L$dir"); done
for dir in "${system_libdirs[@]}"; do args+=("-L$dir"); done
extend args_list lib_dirs_list "-L"
extend args_list system_lib_dirs_list "-L"
# RPATHs arguments
case "$mode" in
ccld)
if [ -n "$dtags_to_add" ] ; then args+=("$linker_arg$dtags_to_add") ; fi
for dir in "${rpaths[@]}"; do args+=("$rpath$dir"); done
for dir in "${system_rpaths[@]}"; do args+=("$rpath$dir"); done
if [ -n "$dtags_to_add" ] ; then
append args_list "$linker_arg$dtags_to_add"
fi
extend args_list rpath_dirs_list "$rpath"
extend args_list system_rpath_dirs_list "$rpath"
;;
ld)
if [ -n "$dtags_to_add" ] ; then args+=("$dtags_to_add") ; fi
for dir in "${rpaths[@]}"; do args+=("-rpath" "$dir"); done
for dir in "${system_rpaths[@]}"; do args+=("-rpath" "$dir"); done
if [ -n "$dtags_to_add" ] ; then
append args_list "$dtags_to_add"
fi
extend args_list rpath_dirs_list "-rpath${lsep}"
extend args_list system_rpath_dirs_list "-rpath${lsep}"
;;
esac
# Other arguments from the input command
args+=("${other_args[@]}")
extend args_list other_args_list
# Inject SPACK_LDLIBS, if supplied
for lib in "${libs[@]}"; do
args+=("-l$lib");
done
extend args_list libs_list "-l"
full_command=("$command" "${args[@]}")
full_command_list="$command"
extend full_command_list args_list
# prepend the ccache binary if we're using ccache
if [ -n "$SPACK_CCACHE_BINARY" ]; then
case "$lang_flags" in
C|CXX) # ccache only supports C languages
full_command=("${SPACK_CCACHE_BINARY}" "${full_command[@]}")
prepend full_command_list "${SPACK_CCACHE_BINARY}"
# workaround for stage being a temp folder
# see #3761#issuecomment-294352232
export CCACHE_NOHASHDIR=yes
@@ -612,25 +741,36 @@ if [ -n "$SPACK_CCACHE_BINARY" ]; then
fi
# dump the full command if the caller supplies SPACK_TEST_COMMAND=dump-args
if [[ $SPACK_TEST_COMMAND == dump-args ]]; then
IFS="
" && echo "${full_command[*]}"
exit
elif [[ $SPACK_TEST_COMMAND =~ dump-env-* ]]; then
var=${SPACK_TEST_COMMAND#dump-env-}
echo "$0: $var: ${!var}"
elif [[ -n $SPACK_TEST_COMMAND ]]; then
die "ERROR: Unknown test command"
if [ -n "${SPACK_TEST_COMMAND=}" ]; then
case "$SPACK_TEST_COMMAND" in
dump-args)
IFS="$lsep"
for arg in $full_command_list; do
echo "$arg"
done
unset IFS
exit
;;
dump-env-*)
var=${SPACK_TEST_COMMAND#dump-env-}
eval "printf '%s\n' \"\$0: \$var: \$$var\""
;;
*)
die "Unknown test command: '$SPACK_TEST_COMMAND'"
;;
esac
fi
#
# Write the input and output commands to debug logs if it's asked for.
#
if [[ $SPACK_DEBUG == TRUE ]]; then
if [ "$SPACK_DEBUG" = TRUE ]; then
input_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_DEBUG_LOG_ID.in.log"
output_log="$SPACK_DEBUG_LOG_DIR/spack-cc-$SPACK_DEBUG_LOG_ID.out.log"
echo "[$mode] $command $input_command" >> "$input_log"
echo "[$mode] ${full_command[*]}" >> "$output_log"
echo "[$mode] ${full_command_list}" >> "$output_log"
fi
exec "${full_command[@]}"
# Execute the full command, preserving spaces with IFS set
# to the alarm bell separator.
IFS="$lsep"; exec $full_command_list

1
lib/spack/env/oneapi/dpcpp vendored Symbolic link
View File

@@ -0,0 +1 @@
../cc

View File

@@ -1,4 +1,4 @@
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
@@ -6,24 +6,54 @@
"""This module contains the following external, potentially separately
licensed, packages that are included in Spack:
altgraph
--------
* Homepage: https://altgraph.readthedocs.io/en/latest/index.html
* Usage: dependency of macholib
* Version: 0.17.2
archspec
--------
* Homepage: https://pypi.python.org/pypi/archspec
* Usage: Labeling, comparison and detection of microarchitectures
* Version: 0.1.2 (commit 4dbf253daf37e4a008e4beb6489f347b4a35aed4)
* Version: 0.1.2 (commit 85757b6666422fca86aa882a769bf78b0f992f54)
argparse
--------
* Homepage: https://pypi.python.org/pypi/argparse
* Usage: We include our own version to be Python 2.6 compatible.
* Usage: We include our own version to be Python 3.X compatible.
* Version: 1.4.0
* Note: This package has been slightly modified to improve
error message formatting. See the following commit if the
vendored copy ever needs to be updated again:
https://github.com/spack/spack/pull/6786/commits/dfcef577b77249106ea4e4c69a6cd9e64fa6c418
astunparse
----------------
* Homepage: https://github.com/simonpercivall/astunparse
* Usage: Unparsing Python ASTs for package hashes in Spack
* Version: 1.6.3 (plus modifications)
* Note: This is in ``spack.util.unparse`` because it's very heavily
modified, and we want to track coverage for it.
Specifically, we have modified this library to generate consistent unparsed ASTs
regardless of the Python version. It is based on:
1. The original ``astunparse`` library;
2. Modifications for consistency;
3. Backports from the ``ast.unparse`` function in Python 3.9 and later
The unparsing is now mostly consistent with upstream ``ast.unparse``, so if
we ever require Python 3.9 or higher, we can drop this external package.
attrs
----------------
* Homepage: https://github.com/python-attrs/attrs
* Usage: Needed by jsonschema.
* Version: 21.2.0 (83d3cd70f90a3f4d19ee8b508e58d1c58821c0ad)
ctest_log_parser
----------------
@@ -37,49 +67,43 @@
* Homepage: https://pypi.python.org/pypi/distro
* Usage: Provides a more stable linux distribution detection.
* Version: 1.0.4 (last version supporting Python 2.6)
* Version: 1.6.0 (64946a1e2a9ff529047070657728600e006c99ff)
* Note: Last version supporting Python 2.7
functools
---------
* Homepage: https://github.com/python/cpython/blob/2.7/Lib/functools.py
* Usage: Used for implementation of total_ordering.
* Version: Unversioned
* Note: This is the functools.total_ordering implementation
from Python 2.7 backported so we can run on Python 2.6.
functools32
-----------
* Homepage: https://github.com/MiCHiLU/python-functools32
* Usage: Needed by jsonschema when using Python 2.7.
* Version: 3.2.3-2
jinja2
------
* Homepage: https://pypi.python.org/pypi/Jinja2
* Usage: A modern and designer-friendly templating language for Python.
* Version: 2.10
* Version: 2.11.3 (last version supporting Python 2.7)
jsonschema
----------
* Homepage: https://pypi.python.org/pypi/jsonschema
* Usage: An implementation of JSON Schema for Python.
* Version: 2.4.0 (last version before functools32 dependency was added)
* Note: functools32 doesn't support Python 2.6 or 3.0, so jsonschema
cannot be upgraded any further until we drop 2.6.
Also, jsonschema/validators.py has been modified NOT to try to import
requests (see 7a1dd517b8).
* Version: 3.2.0 (last version before 2.7 and 3.6 support was dropped)
* Note: We don't include tests or benchmarks; just what Spack needs.
macholib
--------
* Homepage: https://macholib.readthedocs.io/en/latest/index.html#
* Usage: Manipulation of Mach-o binaries for relocating macOS buildcaches on Linux
* Version: 1.15.2
markupsafe
----------
* Homepage: https://pypi.python.org/pypi/MarkupSafe
* Usage: Implements a XML/HTML/XHTML Markup safe string for Python.
* Version: 1.0
orderddict
----------
* Homepage: https://pypi.org/project/ordereddict/
* Usage: A drop-in substitute for Py2.7's new collections.OrderedDict
that works in Python 2.4-2.6.
* Version: 1.1
* Version: 1.1.1 (last version supporting Python 2.7)
py
--
@@ -88,6 +112,16 @@
* Usage: Needed by pytest. Library with cross-python path,
ini-parsing, io, code, and log facilities.
* Version: 1.4.34 (last version supporting Python 2.6)
* Note: This packages has been modified:
* https://github.com/pytest-dev/py/pull/186 was backported
pyrsistent
----------
* Homepage: http://github.com/tobgu/pyrsistent/
* Usage: Needed by `jsonschema`
* Version: 0.16.1 (last version supporting Python 2.7)
* Note: We only include the parts needed for `jsonschema`.
pytest
------
@@ -118,20 +152,6 @@
* Homepage: https://pypi.python.org/pypi/six
* Usage: Python 2 and 3 compatibility utilities.
* Version: 1.11.0
macholib
--------
* Homepage: https://macholib.readthedocs.io/en/latest/index.html#
* Usage: Manipulation of Mach-o binaries for relocating macOS buildcaches on Linux
* Version: 1.12
altgraph
--------
* Homepage: https://altgraph.readthedocs.io/en/latest/index.html
* Usage: dependency of macholib
* Version: 0.16.1
* Version: 1.16.0
"""

View File

@@ -1,4 +1,4 @@
'''
"""
altgraph.Dot - Interface to the dot language
============================================
@@ -107,7 +107,7 @@
- for more details on how to control the graph drawing process see the
`graphviz reference
<http://www.research.att.com/sw/tools/graphviz/refs.html>`_.
'''
"""
import os
import warnings
@@ -115,25 +115,34 @@
class Dot(object):
'''
"""
A class providing a **graphviz** (dot language) representation
allowing a fine grained control over how the graph is being
displayed.
If the :command:`dot` and :command:`dotty` programs are not in the current
system path their location needs to be specified in the contructor.
'''
"""
def __init__(
self, graph=None, nodes=None, edgefn=None, nodevisitor=None,
edgevisitor=None, name="G", dot='dot', dotty='dotty',
neato='neato', graphtype="digraph"):
'''
self,
graph=None,
nodes=None,
edgefn=None,
nodevisitor=None,
edgevisitor=None,
name="G",
dot="dot",
dotty="dotty",
neato="neato",
graphtype="digraph",
):
"""
Initialization.
'''
"""
self.name, self.attr = name, {}
assert graphtype in ['graph', 'digraph']
assert graphtype in ["graph", "digraph"]
self.type = graphtype
self.temp_dot = "tmp_dot.dot"
@@ -148,8 +157,10 @@ def __init__(
if graph is not None and nodes is None:
nodes = graph
if graph is not None and edgefn is None:
def edgefn(node, graph=graph):
return graph.out_nbrs(node)
if nodes is None:
nodes = ()
@@ -177,20 +188,19 @@ def edgefn(node, graph=graph):
self.edge_style(head, tail, **edgestyle)
def style(self, **attr):
'''
"""
Changes the overall style
'''
"""
self.attr = attr
def display(self, mode='dot'):
'''
def display(self, mode="dot"):
"""
Displays the current graph via dotty
'''
"""
if mode == 'neato':
if mode == "neato":
self.save_dot(self.temp_neo)
neato_cmd = "%s -o %s %s" % (
self.neato, self.temp_dot, self.temp_neo)
neato_cmd = "%s -o %s %s" % (self.neato, self.temp_dot, self.temp_neo)
os.system(neato_cmd)
else:
self.save_dot(self.temp_dot)
@@ -199,24 +209,24 @@ def display(self, mode='dot'):
os.system(plot_cmd)
def node_style(self, node, **kwargs):
'''
"""
Modifies a node style to the dot representation.
'''
"""
if node not in self.edges:
self.edges[node] = {}
self.nodes[node] = kwargs
def all_node_style(self, **kwargs):
'''
"""
Modifies all node styles
'''
"""
for node in self.nodes:
self.node_style(node, **kwargs)
def edge_style(self, head, tail, **kwargs):
'''
"""
Modifies an edge style to the dot representation.
'''
"""
if tail not in self.nodes:
raise GraphError("invalid node %s" % (tail,))
@@ -229,10 +239,10 @@ def edge_style(self, head, tail, **kwargs):
def iterdot(self):
# write graph title
if self.type == 'digraph':
yield 'digraph %s {\n' % (self.name,)
elif self.type == 'graph':
yield 'graph %s {\n' % (self.name,)
if self.type == "digraph":
yield "digraph %s {\n" % (self.name,)
elif self.type == "graph":
yield "graph %s {\n" % (self.name,)
else:
raise GraphError("unsupported graphtype %s" % (self.type,))
@@ -240,11 +250,11 @@ def iterdot(self):
# write overall graph attributes
for attr_name, attr_value in sorted(self.attr.items()):
yield '%s="%s";' % (attr_name, attr_value)
yield '\n'
yield "\n"
# some reusable patterns
cpatt = '%s="%s",' # to separate attributes
epatt = '];\n' # to end attributes
cpatt = '%s="%s",' # to separate attributes
epatt = "];\n" # to end attributes
# write node attributes
for node_name, node_attr in sorted(self.nodes.items()):
@@ -256,25 +266,24 @@ def iterdot(self):
# write edge attributes
for head in sorted(self.edges):
for tail in sorted(self.edges[head]):
if self.type == 'digraph':
if self.type == "digraph":
yield '\t"%s" -> "%s" [' % (head, tail)
else:
yield '\t"%s" -- "%s" [' % (head, tail)
for attr_name, attr_value in \
sorted(self.edges[head][tail].items()):
for attr_name, attr_value in sorted(self.edges[head][tail].items()):
yield cpatt % (attr_name, attr_value)
yield epatt
# finish file
yield '}\n'
yield "}\n"
def __iter__(self):
return self.iterdot()
def save_dot(self, file_name=None):
'''
"""
Saves the current graph representation into a file
'''
"""
if not file_name:
warnings.warn(DeprecationWarning, "always pass a file_name")
@@ -284,19 +293,18 @@ def save_dot(self, file_name=None):
for chunk in self.iterdot():
fp.write(chunk)
def save_img(self, file_name=None, file_type="gif", mode='dot'):
'''
def save_img(self, file_name=None, file_type="gif", mode="dot"):
"""
Saves the dot file as an image file
'''
"""
if not file_name:
warnings.warn(DeprecationWarning, "always pass a file_name")
file_name = "out"
if mode == 'neato':
if mode == "neato":
self.save_dot(self.temp_neo)
neato_cmd = "%s -o %s %s" % (
self.neato, self.temp_dot, self.temp_neo)
neato_cmd = "%s -o %s %s" % (self.neato, self.temp_dot, self.temp_neo)
os.system(neato_cmd)
plot_cmd = self.dot
else:
@@ -305,5 +313,9 @@ def save_img(self, file_name=None, file_type="gif", mode='dot'):
file_name = "%s.%s" % (file_name, file_type)
create_cmd = "%s -T%s %s -o %s" % (
plot_cmd, file_type, self.temp_dot, file_name)
plot_cmd,
file_type,
self.temp_dot,
file_name,
)
os.system(create_cmd)

View File

@@ -13,9 +13,10 @@
#--Nathan Denny, May 27, 1999
"""
from altgraph import GraphError
from collections import deque
from altgraph import GraphError
class Graph(object):
"""
@@ -58,8 +59,10 @@ def __init__(self, edges=None):
raise GraphError("Cannot create edge from %s" % (item,))
def __repr__(self):
return '<Graph: %d nodes, %d edges>' % (
self.number_of_nodes(), self.number_of_edges())
return "<Graph: %d nodes, %d edges>" % (
self.number_of_nodes(),
self.number_of_edges(),
)
def add_node(self, node, node_data=None):
"""
@@ -111,7 +114,7 @@ def add_edge(self, head_id, tail_id, edge_data=1, create_nodes=True):
self.nodes[tail_id][0].append(edge)
self.nodes[head_id][1].append(edge)
except KeyError:
raise GraphError('Invalid nodes %s -> %s' % (head_id, tail_id))
raise GraphError("Invalid nodes %s -> %s" % (head_id, tail_id))
# store edge information
self.edges[edge] = (head_id, tail_id, edge_data)
@@ -124,13 +127,12 @@ def hide_edge(self, edge):
time.
"""
try:
head_id, tail_id, edge_data = \
self.hidden_edges[edge] = self.edges[edge]
head_id, tail_id, edge_data = self.hidden_edges[edge] = self.edges[edge]
self.nodes[tail_id][0].remove(edge)
self.nodes[head_id][1].remove(edge)
del self.edges[edge]
except KeyError:
raise GraphError('Invalid edge %s' % edge)
raise GraphError("Invalid edge %s" % edge)
def hide_node(self, node):
"""
@@ -144,7 +146,7 @@ def hide_node(self, node):
self.hide_edge(edge)
del self.nodes[node]
except KeyError:
raise GraphError('Invalid node %s' % node)
raise GraphError("Invalid node %s" % node)
def restore_node(self, node):
"""
@@ -157,7 +159,7 @@ def restore_node(self, node):
self.restore_edge(edge)
del self.hidden_nodes[node]
except KeyError:
raise GraphError('Invalid node %s' % node)
raise GraphError("Invalid node %s" % node)
def restore_edge(self, edge):
"""
@@ -170,7 +172,7 @@ def restore_edge(self, edge):
self.edges[edge] = head_id, tail_id, data
del self.hidden_edges[edge]
except KeyError:
raise GraphError('Invalid edge %s' % edge)
raise GraphError("Invalid edge %s" % edge)
def restore_all_edges(self):
"""
@@ -203,7 +205,7 @@ def edge_by_id(self, edge):
head, tail, data = self.edges[edge]
except KeyError:
head, tail = None, None
raise GraphError('Invalid edge %s' % edge)
raise GraphError("Invalid edge %s" % edge)
return (head, tail)
@@ -339,7 +341,7 @@ def out_edges(self, node):
try:
return list(self.nodes[node][1])
except KeyError:
raise GraphError('Invalid node %s' % node)
raise GraphError("Invalid node %s" % node)
def inc_edges(self, node):
"""
@@ -348,7 +350,7 @@ def inc_edges(self, node):
try:
return list(self.nodes[node][0])
except KeyError:
raise GraphError('Invalid node %s' % node)
raise GraphError("Invalid node %s" % node)
def all_edges(self, node):
"""
@@ -488,7 +490,7 @@ def iterdfs(self, start, end=None, forward=True):
The forward parameter specifies whether it is a forward or backward
traversal.
"""
visited, stack = set([start]), deque([start])
visited, stack = {start}, deque([start])
if forward:
get_edges = self.out_edges
@@ -515,7 +517,7 @@ def iterdata(self, start, end=None, forward=True, condition=None):
condition callback is only called when node_data is not None.
"""
visited, stack = set([start]), deque([start])
visited, stack = {start}, deque([start])
if forward:
get_edges = self.out_edges
@@ -547,7 +549,7 @@ def _iterbfs(self, start, end=None, forward=True):
traversal. Returns a list of tuples where the first value is the hop
value the second value is the node id.
"""
queue, visited = deque([(start, 0)]), set([start])
queue, visited = deque([(start, 0)]), {start}
# the direction of the bfs depends on the edges that are sampled
if forward:

View File

@@ -1,7 +1,7 @@
'''
"""
altgraph.GraphAlgo - Graph algorithms
=====================================
'''
"""
from altgraph import GraphError
@@ -28,9 +28,9 @@ def dijkstra(graph, start, end=None):
Adapted to altgraph by Istvan Albert, Pennsylvania State University -
June, 9 2004
"""
D = {} # dictionary of final distances
P = {} # dictionary of predecessors
Q = _priorityDictionary() # estimated distances of non-final vertices
D = {} # dictionary of final distances
P = {} # dictionary of predecessors
Q = _priorityDictionary() # estimated distances of non-final vertices
Q[start] = 0
for v in Q:
@@ -44,7 +44,8 @@ def dijkstra(graph, start, end=None):
if w in D:
if vwLength < D[w]:
raise GraphError(
"Dijkstra: found better path to already-final vertex")
"Dijkstra: found better path to already-final vertex"
)
elif w not in Q or vwLength < Q[w]:
Q[w] = vwLength
P[w] = v
@@ -76,7 +77,7 @@ def shortest_path(graph, start, end):
# Utility classes and functions
#
class _priorityDictionary(dict):
'''
"""
Priority dictionary using binary heaps (internal use only)
David Eppstein, UC Irvine, 8 Mar 2002
@@ -92,22 +93,22 @@ class _priorityDictionary(dict):
order. Each item is not removed until the next item is requested,
so D[x] will still return a useful value until the next iteration
of the for-loop. Each operation takes logarithmic amortized time.
'''
"""
def __init__(self):
'''
"""
Initialize priorityDictionary by creating binary heap of pairs
(value,key). Note that changing or removing a dict entry will not
remove the old pair from the heap until it is found by smallest()
or until the heap is rebuilt.
'''
"""
self.__heap = []
dict.__init__(self)
def smallest(self):
'''
"""
Find smallest item after removing deleted items from front of heap.
'''
"""
if len(self) == 0:
raise IndexError("smallest of empty priorityDictionary")
heap = self.__heap
@@ -115,9 +116,11 @@ def smallest(self):
lastItem = heap.pop()
insertionPoint = 0
while 1:
smallChild = 2*insertionPoint+1
if smallChild+1 < len(heap) and \
heap[smallChild] > heap[smallChild+1]:
smallChild = 2 * insertionPoint + 1
if (
smallChild + 1 < len(heap)
and heap[smallChild] > heap[smallChild + 1]
):
smallChild += 1
if smallChild >= len(heap) or lastItem <= heap[smallChild]:
heap[insertionPoint] = lastItem
@@ -127,22 +130,24 @@ def smallest(self):
return heap[0][1]
def __iter__(self):
'''
"""
Create destructive sorted iterator of priorityDictionary.
'''
"""
def iterfn():
while len(self) > 0:
x = self.smallest()
yield x
del self[x]
return iterfn()
def __setitem__(self, key, val):
'''
"""
Change value stored in dictionary and add corresponding pair to heap.
Rebuilds the heap if the number of deleted items gets large, to avoid
memory leakage.
'''
"""
dict.__setitem__(self, key, val)
heap = self.__heap
if len(heap) > 2 * len(self):
@@ -152,15 +157,15 @@ def __setitem__(self, key, val):
newPair = (val, key)
insertionPoint = len(heap)
heap.append(None)
while insertionPoint > 0 and newPair < heap[(insertionPoint-1)//2]:
heap[insertionPoint] = heap[(insertionPoint-1)//2]
insertionPoint = (insertionPoint-1)//2
while insertionPoint > 0 and newPair < heap[(insertionPoint - 1) // 2]:
heap[insertionPoint] = heap[(insertionPoint - 1) // 2]
insertionPoint = (insertionPoint - 1) // 2
heap[insertionPoint] = newPair
def setdefault(self, key, val):
'''
"""
Reimplement setdefault to pass through our customized __setitem__.
'''
"""
if key not in self:
self[key] = val
return self[key]

View File

@@ -1,11 +1,11 @@
'''
"""
altgraph.GraphStat - Functions providing various graph statistics
=================================================================
'''
"""
def degree_dist(graph, limits=(0, 0), bin_num=10, mode='out'):
'''
def degree_dist(graph, limits=(0, 0), bin_num=10, mode="out"):
"""
Computes the degree distribution for a graph.
Returns a list of tuples where the first element of the tuple is the
@@ -15,10 +15,10 @@ def degree_dist(graph, limits=(0, 0), bin_num=10, mode='out'):
Example::
....
'''
"""
deg = []
if mode == 'inc':
if mode == "inc":
get_deg = graph.inc_degree
else:
get_deg = graph.out_degree
@@ -34,38 +34,38 @@ def degree_dist(graph, limits=(0, 0), bin_num=10, mode='out'):
return results
_EPS = 1.0/(2.0**32)
_EPS = 1.0 / (2.0 ** 32)
def _binning(values, limits=(0, 0), bin_num=10):
'''
"""
Bins data that falls between certain limits, if the limits are (0, 0) the
minimum and maximum values are used.
Returns a list of tuples where the first element of the tuple is the
center of the bin and the second element of the tuple are the counts.
'''
"""
if limits == (0, 0):
min_val, max_val = min(values) - _EPS, max(values) + _EPS
else:
min_val, max_val = limits
# get bin size
bin_size = (max_val - min_val)/float(bin_num)
bin_size = (max_val - min_val) / float(bin_num)
bins = [0] * (bin_num)
# will ignore these outliers for now
for value in values:
try:
if (value - min_val) >= 0:
index = int((value - min_val)/float(bin_size))
index = int((value - min_val) / float(bin_size))
bins[index] += 1
except IndexError:
pass
# make it ready for an x,y plot
result = []
center = (bin_size/2) + min_val
center = (bin_size / 2) + min_val
for i, y in enumerate(bins):
x = center + bin_size * i
result.append((x, y))

View File

@@ -1,31 +1,29 @@
'''
"""
altgraph.GraphUtil - Utility classes and functions
==================================================
'''
"""
import random
from collections import deque
from altgraph import Graph
from altgraph import GraphError
from altgraph import Graph, GraphError
def generate_random_graph(
node_num, edge_num, self_loops=False, multi_edges=False):
'''
def generate_random_graph(node_num, edge_num, self_loops=False, multi_edges=False):
"""
Generates and returns a :py:class:`~altgraph.Graph.Graph` instance with
*node_num* nodes randomly connected by *edge_num* edges.
'''
"""
g = Graph.Graph()
if not multi_edges:
if self_loops:
max_edges = node_num * node_num
else:
max_edges = node_num * (node_num-1)
max_edges = node_num * (node_num - 1)
if edge_num > max_edges:
raise GraphError(
"inconsistent arguments to 'generate_random_graph'")
raise GraphError("inconsistent arguments to 'generate_random_graph'")
nodes = range(node_num)
@@ -52,17 +50,16 @@ def generate_random_graph(
return g
def generate_scale_free_graph(
steps, growth_num, self_loops=False, multi_edges=False):
'''
def generate_scale_free_graph(steps, growth_num, self_loops=False, multi_edges=False):
"""
Generates and returns a :py:class:`~altgraph.Graph.Graph` instance that
will have *steps* \* *growth_num* nodes and a scale free (powerlaw)
will have *steps* \\* *growth_num* nodes and a scale free (powerlaw)
connectivity. Starting with a fully connected graph with *growth_num*
nodes at every step *growth_num* nodes are added to the graph and are
connected to existing nodes with a probability proportional to the degree
of these existing nodes.
'''
# FIXME: The code doesn't seem to do what the documentation claims.
"""
# The code doesn't seem to do what the documentation claims.
graph = Graph.Graph()
# initialize the graph
@@ -113,7 +110,7 @@ def filter_stack(graph, head, filters):
in *removes*.
"""
visited, removes, orphans = set([head]), set(), set()
visited, removes, orphans = {head}, set(), set()
stack = deque([(head, head)])
get_data = graph.node_data
get_edges = graph.out_edges
@@ -137,8 +134,6 @@ def filter_stack(graph, head, filters):
visited.add(tail)
stack.append((last_good, tail))
orphans = [
(lg, tl)
for (lg, tl) in orphans if tl not in removes]
orphans = [(lg, tl) for (lg, tl) in orphans if tl not in removes]
return visited, removes, orphans

View File

@@ -27,7 +27,7 @@ def __init__(self, graph=None, debug=0):
graph.add_node(self, None)
def __repr__(self):
return '<%s>' % (type(self).__name__,)
return "<%s>" % (type(self).__name__,)
def flatten(self, condition=None, start=None):
"""
@@ -58,6 +58,7 @@ def iter_edges(lst, n):
if ident not in seen:
yield self.findNode(ident)
seen.add(ident)
return iter_edges(outraw, 3), iter_edges(incraw, 2)
def edgeData(self, fromNode, toNode):
@@ -87,12 +88,12 @@ def filterStack(self, filters):
visited, removes, orphans = filter_stack(self.graph, self, filters)
for last_good, tail in orphans:
self.graph.add_edge(last_good, tail, edge_data='orphan')
self.graph.add_edge(last_good, tail, edge_data="orphan")
for node in removes:
self.graph.hide_node(node)
return len(visited)-1, len(removes), len(orphans)
return len(visited) - 1, len(removes), len(orphans)
def removeNode(self, node):
"""
@@ -135,7 +136,7 @@ def getRawIdent(self, node):
"""
if node is self:
return node
ident = getattr(node, 'graphident', None)
ident = getattr(node, "graphident", None)
return ident
def __contains__(self, node):
@@ -192,8 +193,7 @@ def msg(self, level, s, *args):
Print a debug message with the given level
"""
if s and level <= self.debug:
print("%s%s %s" % (
" " * self.indent, s, ' '.join(map(repr, args))))
print("%s%s %s" % (" " * self.indent, s, " ".join(map(repr, args))))
def msgin(self, level, s, *args):
"""

View File

@@ -1,4 +1,4 @@
'''
"""
altgraph - a python graph library
=================================
@@ -138,13 +138,11 @@
@newfield contributor: Contributors:
@contributor: U{Reka Albert <http://www.phys.psu.edu/~ralbert/>}
'''
# import pkg_resources
# __version__ = pkg_resources.require('altgraph')[0].version
# pkg_resources is not finding the altgraph import despite the fact that it is in sys.path
# there is no .dist-info or .egg-info for pkg_resources to query the version from
# so it must be set manually
__version__ = '0.16.1'
"""
import pkg_resources
__version__ = pkg_resources.require("altgraph")[0].version
class GraphError(ValueError):
pass

View File

@@ -49,6 +49,19 @@ $ tox
congratulations :)
```
## Citing Archspec
If you are referencing `archspec` in a publication, please cite the following
paper:
* Massimiliano Culpo, Gregory Becker, Carlos Eduardo Arango Gutierrez, Kenneth
Hoste, and Todd Gamblin.
[**`archspec`: A library for detecting, labeling, and reasoning about
microarchitectures**](https://tgamblin.github.io/pubs/archspec-canopie-hpc-2020.pdf).
In *2nd International Workshop on Containers and New Orchestration Paradigms
for Isolated Environments in HPC (CANOPIE-HPC'20)*, Online Event, November
12, 2020.
## License
Archspec is distributed under the terms of both the MIT license and the

View File

@@ -206,11 +206,26 @@ def host():
# Get a list of possible candidates for this micro-architecture
candidates = compatible_microarchitectures(info)
# Sorting criteria for candidates
def sorting_fn(item):
return len(item.ancestors), len(item.features)
# Get the best generic micro-architecture
generic_candidates = [c for c in candidates if c.vendor == "generic"]
best_generic = max(generic_candidates, key=sorting_fn)
# Filter the candidates to be descendant of the best generic candidate.
# This is to avoid that the lack of a niche feature that can be disabled
# from e.g. BIOS prevents detection of a reasonably performant architecture
candidates = [c for c in candidates if c > best_generic]
# If we don't have candidates, return the best generic micro-architecture
if not candidates:
return best_generic
# Reverse sort of the depth for the inheritance tree among only targets we
# can use. This gets the newest target we satisfy.
return sorted(
candidates, key=lambda t: (len(t.ancestors), len(t.features)), reverse=True
)[0]
return max(candidates, key=sorting_fn)
def compatibility_check(architecture_family):
@@ -245,7 +260,13 @@ def compatibility_check_for_power(info, target):
"""Compatibility check for PPC64 and PPC64LE architectures."""
basename = platform.machine()
generation_match = re.search(r"POWER(\d+)", info.get("cpu", ""))
generation = int(generation_match.group(1))
try:
generation = int(generation_match.group(1))
except AttributeError:
# There might be no match under emulated environments. For instance
# emulating a ppc64le with QEMU and Docker still reports the host
# /proc/cpuinfo and not a Power
generation = 0
# We can use a target if it descends from our machine type and our
# generation (9 for POWER9, etc) is at least its generation.
@@ -285,3 +306,22 @@ def compatibility_check_for_aarch64(info, target):
and (target.vendor == vendor or target.vendor == "generic")
and target.features.issubset(features)
)
@compatibility_check(architecture_family="riscv64")
def compatibility_check_for_riscv64(info, target):
"""Compatibility check for riscv64 architectures."""
basename = "riscv64"
uarch = info.get("uarch")
# sifive unmatched board
if uarch == "sifive,u74-mc":
uarch = "u74mc"
# catch-all for unknown uarchs
else:
uarch = "riscv64"
arch_root = TARGETS[basename]
return (target == arch_root or arch_root in target.ancestors) and (
target == uarch or target.vendor == "generic"
)

View File

@@ -173,6 +173,12 @@ def family(self):
return roots.pop()
@property
def generic(self):
"""Returns the best generic architecture that is compatible with self"""
generics = [x for x in [self] + self.ancestors if x.vendor == "generic"]
return max(generics, key=lambda x: len(x.ancestors))
def to_dict(self, return_list_of_items=False):
"""Returns a dictionary representation of this object.

View File

@@ -2017,6 +2017,44 @@
"features": [],
"compilers": {
}
},
"riscv64": {
"from": [],
"vendor": "generic",
"features": [],
"compilers": {
"gcc": [
{
"versions": "7.1:",
"flags" : "-march=rv64gc"
}
],
"clang": [
{
"versions": "9.0:",
"flags" : "-march=rv64gc"
}
]
}
},
"u74mc": {
"from": ["riscv64"],
"vendor": "SiFive",
"features": [],
"compilers": {
"gcc": [
{
"versions": "10.2:",
"flags" : "-march=rv64gc -mtune=sifive-7-series"
}
],
"clang" : [
{
"versions": "12.0:",
"flags" : "-march=rv64gc -mtune=sifive-7-series"
}
]
}
}
},
"feature_aliases": {

21
lib/spack/external/attr/LICENSE vendored Normal file
View File

@@ -0,0 +1,21 @@
The MIT License (MIT)
Copyright (c) 2015 Hynek Schlawack
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

78
lib/spack/external/attr/__init__.py vendored Normal file
View File

@@ -0,0 +1,78 @@
from __future__ import absolute_import, division, print_function
import sys
from functools import partial
from . import converters, exceptions, filters, setters, validators
from ._cmp import cmp_using
from ._config import get_run_validators, set_run_validators
from ._funcs import asdict, assoc, astuple, evolve, has, resolve_types
from ._make import (
NOTHING,
Attribute,
Factory,
attrib,
attrs,
fields,
fields_dict,
make_class,
validate,
)
from ._version_info import VersionInfo
__version__ = "21.2.0"
__version_info__ = VersionInfo._from_version_string(__version__)
__title__ = "attrs"
__description__ = "Classes Without Boilerplate"
__url__ = "https://www.attrs.org/"
__uri__ = __url__
__doc__ = __description__ + " <" + __uri__ + ">"
__author__ = "Hynek Schlawack"
__email__ = "hs@ox.cx"
__license__ = "MIT"
__copyright__ = "Copyright (c) 2015 Hynek Schlawack"
s = attributes = attrs
ib = attr = attrib
dataclass = partial(attrs, auto_attribs=True) # happy Easter ;)
__all__ = [
"Attribute",
"Factory",
"NOTHING",
"asdict",
"assoc",
"astuple",
"attr",
"attrib",
"attributes",
"attrs",
"cmp_using",
"converters",
"evolve",
"exceptions",
"fields",
"fields_dict",
"filters",
"get_run_validators",
"has",
"ib",
"make_class",
"resolve_types",
"s",
"set_run_validators",
"setters",
"validate",
"validators",
]
if sys.version_info[:2] >= (3, 6):
from ._next_gen import define, field, frozen, mutable
__all__.extend((define, field, frozen, mutable))

152
lib/spack/external/attr/_cmp.py vendored Normal file
View File

@@ -0,0 +1,152 @@
from __future__ import absolute_import, division, print_function
import functools
from ._compat import new_class
from ._make import _make_ne
_operation_names = {"eq": "==", "lt": "<", "le": "<=", "gt": ">", "ge": ">="}
def cmp_using(
eq=None,
lt=None,
le=None,
gt=None,
ge=None,
require_same_type=True,
class_name="Comparable",
):
"""
Create a class that can be passed into `attr.ib`'s ``eq``, ``order``, and
``cmp`` arguments to customize field comparison.
The resulting class will have a full set of ordering methods if
at least one of ``{lt, le, gt, ge}`` and ``eq`` are provided.
:param Optional[callable] eq: `callable` used to evaluate equality
of two objects.
:param Optional[callable] lt: `callable` used to evaluate whether
one object is less than another object.
:param Optional[callable] le: `callable` used to evaluate whether
one object is less than or equal to another object.
:param Optional[callable] gt: `callable` used to evaluate whether
one object is greater than another object.
:param Optional[callable] ge: `callable` used to evaluate whether
one object is greater than or equal to another object.
:param bool require_same_type: When `True`, equality and ordering methods
will return `NotImplemented` if objects are not of the same type.
:param Optional[str] class_name: Name of class. Defaults to 'Comparable'.
See `comparison` for more details.
.. versionadded:: 21.1.0
"""
body = {
"__slots__": ["value"],
"__init__": _make_init(),
"_requirements": [],
"_is_comparable_to": _is_comparable_to,
}
# Add operations.
num_order_functions = 0
has_eq_function = False
if eq is not None:
has_eq_function = True
body["__eq__"] = _make_operator("eq", eq)
body["__ne__"] = _make_ne()
if lt is not None:
num_order_functions += 1
body["__lt__"] = _make_operator("lt", lt)
if le is not None:
num_order_functions += 1
body["__le__"] = _make_operator("le", le)
if gt is not None:
num_order_functions += 1
body["__gt__"] = _make_operator("gt", gt)
if ge is not None:
num_order_functions += 1
body["__ge__"] = _make_operator("ge", ge)
type_ = new_class(class_name, (object,), {}, lambda ns: ns.update(body))
# Add same type requirement.
if require_same_type:
type_._requirements.append(_check_same_type)
# Add total ordering if at least one operation was defined.
if 0 < num_order_functions < 4:
if not has_eq_function:
# functools.total_ordering requires __eq__ to be defined,
# so raise early error here to keep a nice stack.
raise ValueError(
"eq must be define is order to complete ordering from "
"lt, le, gt, ge."
)
type_ = functools.total_ordering(type_)
return type_
def _make_init():
"""
Create __init__ method.
"""
def __init__(self, value):
"""
Initialize object with *value*.
"""
self.value = value
return __init__
def _make_operator(name, func):
"""
Create operator method.
"""
def method(self, other):
if not self._is_comparable_to(other):
return NotImplemented
result = func(self.value, other.value)
if result is NotImplemented:
return NotImplemented
return result
method.__name__ = "__%s__" % (name,)
method.__doc__ = "Return a %s b. Computed by attrs." % (
_operation_names[name],
)
return method
def _is_comparable_to(self, other):
"""
Check whether `other` is comparable to `self`.
"""
for func in self._requirements:
if not func(self, other):
return False
return True
def _check_same_type(self, other):
"""
Return True if *self* and *other* are of the same type, False otherwise.
"""
return other.value.__class__ is self.value.__class__

242
lib/spack/external/attr/_compat.py vendored Normal file
View File

@@ -0,0 +1,242 @@
from __future__ import absolute_import, division, print_function
import platform
import sys
import types
import warnings
PY2 = sys.version_info[0] == 2
PYPY = platform.python_implementation() == "PyPy"
if PYPY or sys.version_info[:2] >= (3, 6):
ordered_dict = dict
else:
from collections import OrderedDict
ordered_dict = OrderedDict
if PY2:
from collections import Mapping, Sequence
from UserDict import IterableUserDict
# We 'bundle' isclass instead of using inspect as importing inspect is
# fairly expensive (order of 10-15 ms for a modern machine in 2016)
def isclass(klass):
return isinstance(klass, (type, types.ClassType))
def new_class(name, bases, kwds, exec_body):
"""
A minimal stub of types.new_class that we need for make_class.
"""
ns = {}
exec_body(ns)
return type(name, bases, ns)
# TYPE is used in exceptions, repr(int) is different on Python 2 and 3.
TYPE = "type"
def iteritems(d):
return d.iteritems()
# Python 2 is bereft of a read-only dict proxy, so we make one!
class ReadOnlyDict(IterableUserDict):
"""
Best-effort read-only dict wrapper.
"""
def __setitem__(self, key, val):
# We gently pretend we're a Python 3 mappingproxy.
raise TypeError(
"'mappingproxy' object does not support item assignment"
)
def update(self, _):
# We gently pretend we're a Python 3 mappingproxy.
raise AttributeError(
"'mappingproxy' object has no attribute 'update'"
)
def __delitem__(self, _):
# We gently pretend we're a Python 3 mappingproxy.
raise TypeError(
"'mappingproxy' object does not support item deletion"
)
def clear(self):
# We gently pretend we're a Python 3 mappingproxy.
raise AttributeError(
"'mappingproxy' object has no attribute 'clear'"
)
def pop(self, key, default=None):
# We gently pretend we're a Python 3 mappingproxy.
raise AttributeError(
"'mappingproxy' object has no attribute 'pop'"
)
def popitem(self):
# We gently pretend we're a Python 3 mappingproxy.
raise AttributeError(
"'mappingproxy' object has no attribute 'popitem'"
)
def setdefault(self, key, default=None):
# We gently pretend we're a Python 3 mappingproxy.
raise AttributeError(
"'mappingproxy' object has no attribute 'setdefault'"
)
def __repr__(self):
# Override to be identical to the Python 3 version.
return "mappingproxy(" + repr(self.data) + ")"
def metadata_proxy(d):
res = ReadOnlyDict()
res.data.update(d) # We blocked update, so we have to do it like this.
return res
def just_warn(*args, **kw): # pragma: no cover
"""
We only warn on Python 3 because we are not aware of any concrete
consequences of not setting the cell on Python 2.
"""
else: # Python 3 and later.
from collections.abc import Mapping, Sequence # noqa
def just_warn(*args, **kw):
"""
We only warn on Python 3 because we are not aware of any concrete
consequences of not setting the cell on Python 2.
"""
warnings.warn(
"Running interpreter doesn't sufficiently support code object "
"introspection. Some features like bare super() or accessing "
"__class__ will not work with slotted classes.",
RuntimeWarning,
stacklevel=2,
)
def isclass(klass):
return isinstance(klass, type)
TYPE = "class"
def iteritems(d):
return d.items()
new_class = types.new_class
def metadata_proxy(d):
return types.MappingProxyType(dict(d))
def make_set_closure_cell():
"""Return a function of two arguments (cell, value) which sets
the value stored in the closure cell `cell` to `value`.
"""
# pypy makes this easy. (It also supports the logic below, but
# why not do the easy/fast thing?)
if PYPY:
def set_closure_cell(cell, value):
cell.__setstate__((value,))
return set_closure_cell
# Otherwise gotta do it the hard way.
# Create a function that will set its first cellvar to `value`.
def set_first_cellvar_to(value):
x = value
return
# This function will be eliminated as dead code, but
# not before its reference to `x` forces `x` to be
# represented as a closure cell rather than a local.
def force_x_to_be_a_cell(): # pragma: no cover
return x
try:
# Extract the code object and make sure our assumptions about
# the closure behavior are correct.
if PY2:
co = set_first_cellvar_to.func_code
else:
co = set_first_cellvar_to.__code__
if co.co_cellvars != ("x",) or co.co_freevars != ():
raise AssertionError # pragma: no cover
# Convert this code object to a code object that sets the
# function's first _freevar_ (not cellvar) to the argument.
if sys.version_info >= (3, 8):
# CPython 3.8+ has an incompatible CodeType signature
# (added a posonlyargcount argument) but also added
# CodeType.replace() to do this without counting parameters.
set_first_freevar_code = co.replace(
co_cellvars=co.co_freevars, co_freevars=co.co_cellvars
)
else:
args = [co.co_argcount]
if not PY2:
args.append(co.co_kwonlyargcount)
args.extend(
[
co.co_nlocals,
co.co_stacksize,
co.co_flags,
co.co_code,
co.co_consts,
co.co_names,
co.co_varnames,
co.co_filename,
co.co_name,
co.co_firstlineno,
co.co_lnotab,
# These two arguments are reversed:
co.co_cellvars,
co.co_freevars,
]
)
set_first_freevar_code = types.CodeType(*args)
def set_closure_cell(cell, value):
# Create a function using the set_first_freevar_code,
# whose first closure cell is `cell`. Calling it will
# change the value of that cell.
setter = types.FunctionType(
set_first_freevar_code, {}, "setter", (), (cell,)
)
# And call it to set the cell.
setter(value)
# Make sure it works on this interpreter:
def make_func_with_cell():
x = None
def func():
return x # pragma: no cover
return func
if PY2:
cell = make_func_with_cell().func_closure[0]
else:
cell = make_func_with_cell().__closure__[0]
set_closure_cell(cell, 100)
if cell.cell_contents != 100:
raise AssertionError # pragma: no cover
except Exception:
return just_warn
else:
return set_closure_cell
set_closure_cell = make_set_closure_cell()

23
lib/spack/external/attr/_config.py vendored Normal file
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@@ -0,0 +1,23 @@
from __future__ import absolute_import, division, print_function
__all__ = ["set_run_validators", "get_run_validators"]
_run_validators = True
def set_run_validators(run):
"""
Set whether or not validators are run. By default, they are run.
"""
if not isinstance(run, bool):
raise TypeError("'run' must be bool.")
global _run_validators
_run_validators = run
def get_run_validators():
"""
Return whether or not validators are run.
"""
return _run_validators

395
lib/spack/external/attr/_funcs.py vendored Normal file
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@@ -0,0 +1,395 @@
from __future__ import absolute_import, division, print_function
import copy
from ._compat import iteritems
from ._make import NOTHING, _obj_setattr, fields
from .exceptions import AttrsAttributeNotFoundError
def asdict(
inst,
recurse=True,
filter=None,
dict_factory=dict,
retain_collection_types=False,
value_serializer=None,
):
"""
Return the ``attrs`` attribute values of *inst* as a dict.
Optionally recurse into other ``attrs``-decorated classes.
:param inst: Instance of an ``attrs``-decorated class.
:param bool recurse: Recurse into classes that are also
``attrs``-decorated.
:param callable filter: A callable whose return code determines whether an
attribute or element is included (``True``) or dropped (``False``). Is
called with the `attr.Attribute` as the first argument and the
value as the second argument.
:param callable dict_factory: A callable to produce dictionaries from. For
example, to produce ordered dictionaries instead of normal Python
dictionaries, pass in ``collections.OrderedDict``.
:param bool retain_collection_types: Do not convert to ``list`` when
encountering an attribute whose type is ``tuple`` or ``set``. Only
meaningful if ``recurse`` is ``True``.
:param Optional[callable] value_serializer: A hook that is called for every
attribute or dict key/value. It receives the current instance, field
and value and must return the (updated) value. The hook is run *after*
the optional *filter* has been applied.
:rtype: return type of *dict_factory*
:raise attr.exceptions.NotAnAttrsClassError: If *cls* is not an ``attrs``
class.
.. versionadded:: 16.0.0 *dict_factory*
.. versionadded:: 16.1.0 *retain_collection_types*
.. versionadded:: 20.3.0 *value_serializer*
"""
attrs = fields(inst.__class__)
rv = dict_factory()
for a in attrs:
v = getattr(inst, a.name)
if filter is not None and not filter(a, v):
continue
if value_serializer is not None:
v = value_serializer(inst, a, v)
if recurse is True:
if has(v.__class__):
rv[a.name] = asdict(
v,
True,
filter,
dict_factory,
retain_collection_types,
value_serializer,
)
elif isinstance(v, (tuple, list, set, frozenset)):
cf = v.__class__ if retain_collection_types is True else list
rv[a.name] = cf(
[
_asdict_anything(
i,
filter,
dict_factory,
retain_collection_types,
value_serializer,
)
for i in v
]
)
elif isinstance(v, dict):
df = dict_factory
rv[a.name] = df(
(
_asdict_anything(
kk,
filter,
df,
retain_collection_types,
value_serializer,
),
_asdict_anything(
vv,
filter,
df,
retain_collection_types,
value_serializer,
),
)
for kk, vv in iteritems(v)
)
else:
rv[a.name] = v
else:
rv[a.name] = v
return rv
def _asdict_anything(
val,
filter,
dict_factory,
retain_collection_types,
value_serializer,
):
"""
``asdict`` only works on attrs instances, this works on anything.
"""
if getattr(val.__class__, "__attrs_attrs__", None) is not None:
# Attrs class.
rv = asdict(
val,
True,
filter,
dict_factory,
retain_collection_types,
value_serializer,
)
elif isinstance(val, (tuple, list, set, frozenset)):
cf = val.__class__ if retain_collection_types is True else list
rv = cf(
[
_asdict_anything(
i,
filter,
dict_factory,
retain_collection_types,
value_serializer,
)
for i in val
]
)
elif isinstance(val, dict):
df = dict_factory
rv = df(
(
_asdict_anything(
kk, filter, df, retain_collection_types, value_serializer
),
_asdict_anything(
vv, filter, df, retain_collection_types, value_serializer
),
)
for kk, vv in iteritems(val)
)
else:
rv = val
if value_serializer is not None:
rv = value_serializer(None, None, rv)
return rv
def astuple(
inst,
recurse=True,
filter=None,
tuple_factory=tuple,
retain_collection_types=False,
):
"""
Return the ``attrs`` attribute values of *inst* as a tuple.
Optionally recurse into other ``attrs``-decorated classes.
:param inst: Instance of an ``attrs``-decorated class.
:param bool recurse: Recurse into classes that are also
``attrs``-decorated.
:param callable filter: A callable whose return code determines whether an
attribute or element is included (``True``) or dropped (``False``). Is
called with the `attr.Attribute` as the first argument and the
value as the second argument.
:param callable tuple_factory: A callable to produce tuples from. For
example, to produce lists instead of tuples.
:param bool retain_collection_types: Do not convert to ``list``
or ``dict`` when encountering an attribute which type is
``tuple``, ``dict`` or ``set``. Only meaningful if ``recurse`` is
``True``.
:rtype: return type of *tuple_factory*
:raise attr.exceptions.NotAnAttrsClassError: If *cls* is not an ``attrs``
class.
.. versionadded:: 16.2.0
"""
attrs = fields(inst.__class__)
rv = []
retain = retain_collection_types # Very long. :/
for a in attrs:
v = getattr(inst, a.name)
if filter is not None and not filter(a, v):
continue
if recurse is True:
if has(v.__class__):
rv.append(
astuple(
v,
recurse=True,
filter=filter,
tuple_factory=tuple_factory,
retain_collection_types=retain,
)
)
elif isinstance(v, (tuple, list, set, frozenset)):
cf = v.__class__ if retain is True else list
rv.append(
cf(
[
astuple(
j,
recurse=True,
filter=filter,
tuple_factory=tuple_factory,
retain_collection_types=retain,
)
if has(j.__class__)
else j
for j in v
]
)
)
elif isinstance(v, dict):
df = v.__class__ if retain is True else dict
rv.append(
df(
(
astuple(
kk,
tuple_factory=tuple_factory,
retain_collection_types=retain,
)
if has(kk.__class__)
else kk,
astuple(
vv,
tuple_factory=tuple_factory,
retain_collection_types=retain,
)
if has(vv.__class__)
else vv,
)
for kk, vv in iteritems(v)
)
)
else:
rv.append(v)
else:
rv.append(v)
return rv if tuple_factory is list else tuple_factory(rv)
def has(cls):
"""
Check whether *cls* is a class with ``attrs`` attributes.
:param type cls: Class to introspect.
:raise TypeError: If *cls* is not a class.
:rtype: bool
"""
return getattr(cls, "__attrs_attrs__", None) is not None
def assoc(inst, **changes):
"""
Copy *inst* and apply *changes*.
:param inst: Instance of a class with ``attrs`` attributes.
:param changes: Keyword changes in the new copy.
:return: A copy of inst with *changes* incorporated.
:raise attr.exceptions.AttrsAttributeNotFoundError: If *attr_name* couldn't
be found on *cls*.
:raise attr.exceptions.NotAnAttrsClassError: If *cls* is not an ``attrs``
class.
.. deprecated:: 17.1.0
Use `evolve` instead.
"""
import warnings
warnings.warn(
"assoc is deprecated and will be removed after 2018/01.",
DeprecationWarning,
stacklevel=2,
)
new = copy.copy(inst)
attrs = fields(inst.__class__)
for k, v in iteritems(changes):
a = getattr(attrs, k, NOTHING)
if a is NOTHING:
raise AttrsAttributeNotFoundError(
"{k} is not an attrs attribute on {cl}.".format(
k=k, cl=new.__class__
)
)
_obj_setattr(new, k, v)
return new
def evolve(inst, **changes):
"""
Create a new instance, based on *inst* with *changes* applied.
:param inst: Instance of a class with ``attrs`` attributes.
:param changes: Keyword changes in the new copy.
:return: A copy of inst with *changes* incorporated.
:raise TypeError: If *attr_name* couldn't be found in the class
``__init__``.
:raise attr.exceptions.NotAnAttrsClassError: If *cls* is not an ``attrs``
class.
.. versionadded:: 17.1.0
"""
cls = inst.__class__
attrs = fields(cls)
for a in attrs:
if not a.init:
continue
attr_name = a.name # To deal with private attributes.
init_name = attr_name if attr_name[0] != "_" else attr_name[1:]
if init_name not in changes:
changes[init_name] = getattr(inst, attr_name)
return cls(**changes)
def resolve_types(cls, globalns=None, localns=None, attribs=None):
"""
Resolve any strings and forward annotations in type annotations.
This is only required if you need concrete types in `Attribute`'s *type*
field. In other words, you don't need to resolve your types if you only
use them for static type checking.
With no arguments, names will be looked up in the module in which the class
was created. If this is not what you want, e.g. if the name only exists
inside a method, you may pass *globalns* or *localns* to specify other
dictionaries in which to look up these names. See the docs of
`typing.get_type_hints` for more details.
:param type cls: Class to resolve.
:param Optional[dict] globalns: Dictionary containing global variables.
:param Optional[dict] localns: Dictionary containing local variables.
:param Optional[list] attribs: List of attribs for the given class.
This is necessary when calling from inside a ``field_transformer``
since *cls* is not an ``attrs`` class yet.
:raise TypeError: If *cls* is not a class.
:raise attr.exceptions.NotAnAttrsClassError: If *cls* is not an ``attrs``
class and you didn't pass any attribs.
:raise NameError: If types cannot be resolved because of missing variables.
:returns: *cls* so you can use this function also as a class decorator.
Please note that you have to apply it **after** `attr.s`. That means
the decorator has to come in the line **before** `attr.s`.
.. versionadded:: 20.1.0
.. versionadded:: 21.1.0 *attribs*
"""
try:
# Since calling get_type_hints is expensive we cache whether we've
# done it already.
cls.__attrs_types_resolved__
except AttributeError:
import typing
hints = typing.get_type_hints(cls, globalns=globalns, localns=localns)
for field in fields(cls) if attribs is None else attribs:
if field.name in hints:
# Since fields have been frozen we must work around it.
_obj_setattr(field, "type", hints[field.name])
cls.__attrs_types_resolved__ = True
# Return the class so you can use it as a decorator too.
return cls

3052
lib/spack/external/attr/_make.py vendored Normal file

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158
lib/spack/external/attr/_next_gen.py vendored Normal file
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"""
These are Python 3.6+-only and keyword-only APIs that call `attr.s` and
`attr.ib` with different default values.
"""
from functools import partial
from attr.exceptions import UnannotatedAttributeError
from . import setters
from ._make import NOTHING, _frozen_setattrs, attrib, attrs
def define(
maybe_cls=None,
*,
these=None,
repr=None,
hash=None,
init=None,
slots=True,
frozen=False,
weakref_slot=True,
str=False,
auto_attribs=None,
kw_only=False,
cache_hash=False,
auto_exc=True,
eq=None,
order=False,
auto_detect=True,
getstate_setstate=None,
on_setattr=None,
field_transformer=None,
):
r"""
The only behavioral differences are the handling of the *auto_attribs*
option:
:param Optional[bool] auto_attribs: If set to `True` or `False`, it behaves
exactly like `attr.s`. If left `None`, `attr.s` will try to guess:
1. If any attributes are annotated and no unannotated `attr.ib`\ s
are found, it assumes *auto_attribs=True*.
2. Otherwise it assumes *auto_attribs=False* and tries to collect
`attr.ib`\ s.
and that mutable classes (``frozen=False``) validate on ``__setattr__``.
.. versionadded:: 20.1.0
"""
def do_it(cls, auto_attribs):
return attrs(
maybe_cls=cls,
these=these,
repr=repr,
hash=hash,
init=init,
slots=slots,
frozen=frozen,
weakref_slot=weakref_slot,
str=str,
auto_attribs=auto_attribs,
kw_only=kw_only,
cache_hash=cache_hash,
auto_exc=auto_exc,
eq=eq,
order=order,
auto_detect=auto_detect,
collect_by_mro=True,
getstate_setstate=getstate_setstate,
on_setattr=on_setattr,
field_transformer=field_transformer,
)
def wrap(cls):
"""
Making this a wrapper ensures this code runs during class creation.
We also ensure that frozen-ness of classes is inherited.
"""
nonlocal frozen, on_setattr
had_on_setattr = on_setattr not in (None, setters.NO_OP)
# By default, mutable classes validate on setattr.
if frozen is False and on_setattr is None:
on_setattr = setters.validate
# However, if we subclass a frozen class, we inherit the immutability
# and disable on_setattr.
for base_cls in cls.__bases__:
if base_cls.__setattr__ is _frozen_setattrs:
if had_on_setattr:
raise ValueError(
"Frozen classes can't use on_setattr "
"(frozen-ness was inherited)."
)
on_setattr = setters.NO_OP
break
if auto_attribs is not None:
return do_it(cls, auto_attribs)
try:
return do_it(cls, True)
except UnannotatedAttributeError:
return do_it(cls, False)
# maybe_cls's type depends on the usage of the decorator. It's a class
# if it's used as `@attrs` but ``None`` if used as `@attrs()`.
if maybe_cls is None:
return wrap
else:
return wrap(maybe_cls)
mutable = define
frozen = partial(define, frozen=True, on_setattr=None)
def field(
*,
default=NOTHING,
validator=None,
repr=True,
hash=None,
init=True,
metadata=None,
converter=None,
factory=None,
kw_only=False,
eq=None,
order=None,
on_setattr=None,
):
"""
Identical to `attr.ib`, except keyword-only and with some arguments
removed.
.. versionadded:: 20.1.0
"""
return attrib(
default=default,
validator=validator,
repr=repr,
hash=hash,
init=init,
metadata=metadata,
converter=converter,
factory=factory,
kw_only=kw_only,
eq=eq,
order=order,
on_setattr=on_setattr,
)

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@@ -0,0 +1,85 @@
from __future__ import absolute_import, division, print_function
from functools import total_ordering
from ._funcs import astuple
from ._make import attrib, attrs
@total_ordering
@attrs(eq=False, order=False, slots=True, frozen=True)
class VersionInfo(object):
"""
A version object that can be compared to tuple of length 1--4:
>>> attr.VersionInfo(19, 1, 0, "final") <= (19, 2)
True
>>> attr.VersionInfo(19, 1, 0, "final") < (19, 1, 1)
True
>>> vi = attr.VersionInfo(19, 2, 0, "final")
>>> vi < (19, 1, 1)
False
>>> vi < (19,)
False
>>> vi == (19, 2,)
True
>>> vi == (19, 2, 1)
False
.. versionadded:: 19.2
"""
year = attrib(type=int)
minor = attrib(type=int)
micro = attrib(type=int)
releaselevel = attrib(type=str)
@classmethod
def _from_version_string(cls, s):
"""
Parse *s* and return a _VersionInfo.
"""
v = s.split(".")
if len(v) == 3:
v.append("final")
return cls(
year=int(v[0]), minor=int(v[1]), micro=int(v[2]), releaselevel=v[3]
)
def _ensure_tuple(self, other):
"""
Ensure *other* is a tuple of a valid length.
Returns a possibly transformed *other* and ourselves as a tuple of
the same length as *other*.
"""
if self.__class__ is other.__class__:
other = astuple(other)
if not isinstance(other, tuple):
raise NotImplementedError
if not (1 <= len(other) <= 4):
raise NotImplementedError
return astuple(self)[: len(other)], other
def __eq__(self, other):
try:
us, them = self._ensure_tuple(other)
except NotImplementedError:
return NotImplemented
return us == them
def __lt__(self, other):
try:
us, them = self._ensure_tuple(other)
except NotImplementedError:
return NotImplemented
# Since alphabetically "dev0" < "final" < "post1" < "post2", we don't
# have to do anything special with releaselevel for now.
return us < them

111
lib/spack/external/attr/converters.py vendored Normal file
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"""
Commonly useful converters.
"""
from __future__ import absolute_import, division, print_function
from ._compat import PY2
from ._make import NOTHING, Factory, pipe
if not PY2:
import inspect
import typing
__all__ = [
"pipe",
"optional",
"default_if_none",
]
def optional(converter):
"""
A converter that allows an attribute to be optional. An optional attribute
is one which can be set to ``None``.
Type annotations will be inferred from the wrapped converter's, if it
has any.
:param callable converter: the converter that is used for non-``None``
values.
.. versionadded:: 17.1.0
"""
def optional_converter(val):
if val is None:
return None
return converter(val)
if not PY2:
sig = None
try:
sig = inspect.signature(converter)
except (ValueError, TypeError): # inspect failed
pass
if sig:
params = list(sig.parameters.values())
if params and params[0].annotation is not inspect.Parameter.empty:
optional_converter.__annotations__["val"] = typing.Optional[
params[0].annotation
]
if sig.return_annotation is not inspect.Signature.empty:
optional_converter.__annotations__["return"] = typing.Optional[
sig.return_annotation
]
return optional_converter
def default_if_none(default=NOTHING, factory=None):
"""
A converter that allows to replace ``None`` values by *default* or the
result of *factory*.
:param default: Value to be used if ``None`` is passed. Passing an instance
of `attr.Factory` is supported, however the ``takes_self`` option
is *not*.
:param callable factory: A callable that takes no parameters whose result
is used if ``None`` is passed.
:raises TypeError: If **neither** *default* or *factory* is passed.
:raises TypeError: If **both** *default* and *factory* are passed.
:raises ValueError: If an instance of `attr.Factory` is passed with
``takes_self=True``.
.. versionadded:: 18.2.0
"""
if default is NOTHING and factory is None:
raise TypeError("Must pass either `default` or `factory`.")
if default is not NOTHING and factory is not None:
raise TypeError(
"Must pass either `default` or `factory` but not both."
)
if factory is not None:
default = Factory(factory)
if isinstance(default, Factory):
if default.takes_self:
raise ValueError(
"`takes_self` is not supported by default_if_none."
)
def default_if_none_converter(val):
if val is not None:
return val
return default.factory()
else:
def default_if_none_converter(val):
if val is not None:
return val
return default
return default_if_none_converter

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lib/spack/external/attr/exceptions.py vendored Normal file
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from __future__ import absolute_import, division, print_function
class FrozenError(AttributeError):
"""
A frozen/immutable instance or attribute have been attempted to be
modified.
It mirrors the behavior of ``namedtuples`` by using the same error message
and subclassing `AttributeError`.
.. versionadded:: 20.1.0
"""
msg = "can't set attribute"
args = [msg]
class FrozenInstanceError(FrozenError):
"""
A frozen instance has been attempted to be modified.
.. versionadded:: 16.1.0
"""
class FrozenAttributeError(FrozenError):
"""
A frozen attribute has been attempted to be modified.
.. versionadded:: 20.1.0
"""
class AttrsAttributeNotFoundError(ValueError):
"""
An ``attrs`` function couldn't find an attribute that the user asked for.
.. versionadded:: 16.2.0
"""
class NotAnAttrsClassError(ValueError):
"""
A non-``attrs`` class has been passed into an ``attrs`` function.
.. versionadded:: 16.2.0
"""
class DefaultAlreadySetError(RuntimeError):
"""
A default has been set using ``attr.ib()`` and is attempted to be reset
using the decorator.
.. versionadded:: 17.1.0
"""
class UnannotatedAttributeError(RuntimeError):
"""
A class with ``auto_attribs=True`` has an ``attr.ib()`` without a type
annotation.
.. versionadded:: 17.3.0
"""
class PythonTooOldError(RuntimeError):
"""
It was attempted to use an ``attrs`` feature that requires a newer Python
version.
.. versionadded:: 18.2.0
"""
class NotCallableError(TypeError):
"""
A ``attr.ib()`` requiring a callable has been set with a value
that is not callable.
.. versionadded:: 19.2.0
"""
def __init__(self, msg, value):
super(TypeError, self).__init__(msg, value)
self.msg = msg
self.value = value
def __str__(self):
return str(self.msg)

52
lib/spack/external/attr/filters.py vendored Normal file
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@@ -0,0 +1,52 @@
"""
Commonly useful filters for `attr.asdict`.
"""
from __future__ import absolute_import, division, print_function
from ._compat import isclass
from ._make import Attribute
def _split_what(what):
"""
Returns a tuple of `frozenset`s of classes and attributes.
"""
return (
frozenset(cls for cls in what if isclass(cls)),
frozenset(cls for cls in what if isinstance(cls, Attribute)),
)
def include(*what):
"""
Whitelist *what*.
:param what: What to whitelist.
:type what: `list` of `type` or `attr.Attribute`\\ s
:rtype: `callable`
"""
cls, attrs = _split_what(what)
def include_(attribute, value):
return value.__class__ in cls or attribute in attrs
return include_
def exclude(*what):
"""
Blacklist *what*.
:param what: What to blacklist.
:type what: `list` of classes or `attr.Attribute`\\ s.
:rtype: `callable`
"""
cls, attrs = _split_what(what)
def exclude_(attribute, value):
return value.__class__ not in cls and attribute not in attrs
return exclude_

77
lib/spack/external/attr/setters.py vendored Normal file
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@@ -0,0 +1,77 @@
"""
Commonly used hooks for on_setattr.
"""
from __future__ import absolute_import, division, print_function
from . import _config
from .exceptions import FrozenAttributeError
def pipe(*setters):
"""
Run all *setters* and return the return value of the last one.
.. versionadded:: 20.1.0
"""
def wrapped_pipe(instance, attrib, new_value):
rv = new_value
for setter in setters:
rv = setter(instance, attrib, rv)
return rv
return wrapped_pipe
def frozen(_, __, ___):
"""
Prevent an attribute to be modified.
.. versionadded:: 20.1.0
"""
raise FrozenAttributeError()
def validate(instance, attrib, new_value):
"""
Run *attrib*'s validator on *new_value* if it has one.
.. versionadded:: 20.1.0
"""
if _config._run_validators is False:
return new_value
v = attrib.validator
if not v:
return new_value
v(instance, attrib, new_value)
return new_value
def convert(instance, attrib, new_value):
"""
Run *attrib*'s converter -- if it has one -- on *new_value* and return the
result.
.. versionadded:: 20.1.0
"""
c = attrib.converter
if c:
return c(new_value)
return new_value
NO_OP = object()
"""
Sentinel for disabling class-wide *on_setattr* hooks for certain attributes.
Does not work in `pipe` or within lists.
.. versionadded:: 20.1.0
"""

379
lib/spack/external/attr/validators.py vendored Normal file
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@@ -0,0 +1,379 @@
"""
Commonly useful validators.
"""
from __future__ import absolute_import, division, print_function
import re
from ._make import _AndValidator, and_, attrib, attrs
from .exceptions import NotCallableError
__all__ = [
"and_",
"deep_iterable",
"deep_mapping",
"in_",
"instance_of",
"is_callable",
"matches_re",
"optional",
"provides",
]
@attrs(repr=False, slots=True, hash=True)
class _InstanceOfValidator(object):
type = attrib()
def __call__(self, inst, attr, value):
"""
We use a callable class to be able to change the ``__repr__``.
"""
if not isinstance(value, self.type):
raise TypeError(
"'{name}' must be {type!r} (got {value!r} that is a "
"{actual!r}).".format(
name=attr.name,
type=self.type,
actual=value.__class__,
value=value,
),
attr,
self.type,
value,
)
def __repr__(self):
return "<instance_of validator for type {type!r}>".format(
type=self.type
)
def instance_of(type):
"""
A validator that raises a `TypeError` if the initializer is called
with a wrong type for this particular attribute (checks are performed using
`isinstance` therefore it's also valid to pass a tuple of types).
:param type: The type to check for.
:type type: type or tuple of types
:raises TypeError: With a human readable error message, the attribute
(of type `attr.Attribute`), the expected type, and the value it
got.
"""
return _InstanceOfValidator(type)
@attrs(repr=False, frozen=True, slots=True)
class _MatchesReValidator(object):
regex = attrib()
flags = attrib()
match_func = attrib()
def __call__(self, inst, attr, value):
"""
We use a callable class to be able to change the ``__repr__``.
"""
if not self.match_func(value):
raise ValueError(
"'{name}' must match regex {regex!r}"
" ({value!r} doesn't)".format(
name=attr.name, regex=self.regex.pattern, value=value
),
attr,
self.regex,
value,
)
def __repr__(self):
return "<matches_re validator for pattern {regex!r}>".format(
regex=self.regex
)
def matches_re(regex, flags=0, func=None):
r"""
A validator that raises `ValueError` if the initializer is called
with a string that doesn't match *regex*.
:param str regex: a regex string to match against
:param int flags: flags that will be passed to the underlying re function
(default 0)
:param callable func: which underlying `re` function to call (options
are `re.fullmatch`, `re.search`, `re.match`, default
is ``None`` which means either `re.fullmatch` or an emulation of
it on Python 2). For performance reasons, they won't be used directly
but on a pre-`re.compile`\ ed pattern.
.. versionadded:: 19.2.0
"""
fullmatch = getattr(re, "fullmatch", None)
valid_funcs = (fullmatch, None, re.search, re.match)
if func not in valid_funcs:
raise ValueError(
"'func' must be one of %s."
% (
", ".join(
sorted(
e and e.__name__ or "None" for e in set(valid_funcs)
)
),
)
)
pattern = re.compile(regex, flags)
if func is re.match:
match_func = pattern.match
elif func is re.search:
match_func = pattern.search
else:
if fullmatch:
match_func = pattern.fullmatch
else:
pattern = re.compile(r"(?:{})\Z".format(regex), flags)
match_func = pattern.match
return _MatchesReValidator(pattern, flags, match_func)
@attrs(repr=False, slots=True, hash=True)
class _ProvidesValidator(object):
interface = attrib()
def __call__(self, inst, attr, value):
"""
We use a callable class to be able to change the ``__repr__``.
"""
if not self.interface.providedBy(value):
raise TypeError(
"'{name}' must provide {interface!r} which {value!r} "
"doesn't.".format(
name=attr.name, interface=self.interface, value=value
),
attr,
self.interface,
value,
)
def __repr__(self):
return "<provides validator for interface {interface!r}>".format(
interface=self.interface
)
def provides(interface):
"""
A validator that raises a `TypeError` if the initializer is called
with an object that does not provide the requested *interface* (checks are
performed using ``interface.providedBy(value)`` (see `zope.interface
<https://zopeinterface.readthedocs.io/en/latest/>`_).
:param interface: The interface to check for.
:type interface: ``zope.interface.Interface``
:raises TypeError: With a human readable error message, the attribute
(of type `attr.Attribute`), the expected interface, and the
value it got.
"""
return _ProvidesValidator(interface)
@attrs(repr=False, slots=True, hash=True)
class _OptionalValidator(object):
validator = attrib()
def __call__(self, inst, attr, value):
if value is None:
return
self.validator(inst, attr, value)
def __repr__(self):
return "<optional validator for {what} or None>".format(
what=repr(self.validator)
)
def optional(validator):
"""
A validator that makes an attribute optional. An optional attribute is one
which can be set to ``None`` in addition to satisfying the requirements of
the sub-validator.
:param validator: A validator (or a list of validators) that is used for
non-``None`` values.
:type validator: callable or `list` of callables.
.. versionadded:: 15.1.0
.. versionchanged:: 17.1.0 *validator* can be a list of validators.
"""
if isinstance(validator, list):
return _OptionalValidator(_AndValidator(validator))
return _OptionalValidator(validator)
@attrs(repr=False, slots=True, hash=True)
class _InValidator(object):
options = attrib()
def __call__(self, inst, attr, value):
try:
in_options = value in self.options
except TypeError: # e.g. `1 in "abc"`
in_options = False
if not in_options:
raise ValueError(
"'{name}' must be in {options!r} (got {value!r})".format(
name=attr.name, options=self.options, value=value
)
)
def __repr__(self):
return "<in_ validator with options {options!r}>".format(
options=self.options
)
def in_(options):
"""
A validator that raises a `ValueError` if the initializer is called
with a value that does not belong in the options provided. The check is
performed using ``value in options``.
:param options: Allowed options.
:type options: list, tuple, `enum.Enum`, ...
:raises ValueError: With a human readable error message, the attribute (of
type `attr.Attribute`), the expected options, and the value it
got.
.. versionadded:: 17.1.0
"""
return _InValidator(options)
@attrs(repr=False, slots=False, hash=True)
class _IsCallableValidator(object):
def __call__(self, inst, attr, value):
"""
We use a callable class to be able to change the ``__repr__``.
"""
if not callable(value):
message = (
"'{name}' must be callable "
"(got {value!r} that is a {actual!r})."
)
raise NotCallableError(
msg=message.format(
name=attr.name, value=value, actual=value.__class__
),
value=value,
)
def __repr__(self):
return "<is_callable validator>"
def is_callable():
"""
A validator that raises a `attr.exceptions.NotCallableError` if the
initializer is called with a value for this particular attribute
that is not callable.
.. versionadded:: 19.1.0
:raises `attr.exceptions.NotCallableError`: With a human readable error
message containing the attribute (`attr.Attribute`) name,
and the value it got.
"""
return _IsCallableValidator()
@attrs(repr=False, slots=True, hash=True)
class _DeepIterable(object):
member_validator = attrib(validator=is_callable())
iterable_validator = attrib(
default=None, validator=optional(is_callable())
)
def __call__(self, inst, attr, value):
"""
We use a callable class to be able to change the ``__repr__``.
"""
if self.iterable_validator is not None:
self.iterable_validator(inst, attr, value)
for member in value:
self.member_validator(inst, attr, member)
def __repr__(self):
iterable_identifier = (
""
if self.iterable_validator is None
else " {iterable!r}".format(iterable=self.iterable_validator)
)
return (
"<deep_iterable validator for{iterable_identifier}"
" iterables of {member!r}>"
).format(
iterable_identifier=iterable_identifier,
member=self.member_validator,
)
def deep_iterable(member_validator, iterable_validator=None):
"""
A validator that performs deep validation of an iterable.
:param member_validator: Validator to apply to iterable members
:param iterable_validator: Validator to apply to iterable itself
(optional)
.. versionadded:: 19.1.0
:raises TypeError: if any sub-validators fail
"""
return _DeepIterable(member_validator, iterable_validator)
@attrs(repr=False, slots=True, hash=True)
class _DeepMapping(object):
key_validator = attrib(validator=is_callable())
value_validator = attrib(validator=is_callable())
mapping_validator = attrib(default=None, validator=optional(is_callable()))
def __call__(self, inst, attr, value):
"""
We use a callable class to be able to change the ``__repr__``.
"""
if self.mapping_validator is not None:
self.mapping_validator(inst, attr, value)
for key in value:
self.key_validator(inst, attr, key)
self.value_validator(inst, attr, value[key])
def __repr__(self):
return (
"<deep_mapping validator for objects mapping {key!r} to {value!r}>"
).format(key=self.key_validator, value=self.value_validator)
def deep_mapping(key_validator, value_validator, mapping_validator=None):
"""
A validator that performs deep validation of a dictionary.
:param key_validator: Validator to apply to dictionary keys
:param value_validator: Validator to apply to dictionary values
:param mapping_validator: Validator to apply to top-level mapping
attribute (optional)
.. versionadded:: 19.1.0
:raises TypeError: if any sub-validators fail
"""
return _DeepMapping(key_validator, value_validator, mapping_validator)

View File

@@ -77,52 +77,18 @@
from six import StringIO
from six import string_types
class prefilter(object):
"""Make regular expressions faster with a simple prefiltering predicate.
Some regular expressions seem to be much more costly than others. In
most cases, we can evaluate a simple precondition, e.g.::
lambda x: "error" in x
to avoid evaluating expensive regexes on all lines in a file. This
can reduce parse time for large files by orders of magnitude when
evaluating lots of expressions.
A ``prefilter`` object is designed to act like a regex,, but
``search`` and ``match`` check the precondition before bothering to
evaluate the regular expression.
Note that ``match`` and ``search`` just return ``True`` and ``False``
at the moment. Make them return a ``MatchObject`` or ``None`` if it
becomes necessary.
"""
def __init__(self, precondition, *patterns):
self.patterns = [re.compile(p) for p in patterns]
self.pre = precondition
self.pattern = "\n ".join(
('MERGED:',) + patterns)
def search(self, text):
return self.pre(text) and any(p.search(text) for p in self.patterns)
def match(self, text):
return self.pre(text) and any(p.match(text) for p in self.patterns)
_error_matches = [
prefilter(
lambda x: any(s in x for s in (
'Error:', 'error', 'undefined reference', 'multiply defined')),
"([^:]+): error[ \\t]*[0-9]+[ \\t]*:",
"([^:]+): (Error:|error|undefined reference|multiply defined)",
"([^ :]+) ?: (error|fatal error|catastrophic error)",
"([^:]+)\\(([^\\)]+)\\) ?: (error|fatal error|catastrophic error)"),
"^FAILED",
"^FAIL: ",
"^FATAL: ",
"^failed ",
"FAILED",
"Failed test",
"^[Bb]us [Ee]rror",
"^[Ss]egmentation [Vv]iolation",
"^[Ss]egmentation [Ff]ault",
":.*[Pp]ermission [Dd]enied",
"[^ :]:[0-9]+: [^ \\t]",
"[^:]: error[ \\t]*[0-9]+[ \\t]*:",
"^Error ([0-9]+):",
"^Fatal",
"^[Ee]rror: ",
@@ -132,6 +98,9 @@ def match(self, text):
"^cc[^C]*CC: ERROR File = ([^,]+), Line = ([0-9]+)",
"^ld([^:])*:([ \\t])*ERROR([^:])*:",
"^ild:([ \\t])*\\(undefined symbol\\)",
"[^ :] : (error|fatal error|catastrophic error)",
"[^:]: (Error:|error|undefined reference|multiply defined)",
"[^:]\\([^\\)]+\\) ?: (error|fatal error|catastrophic error)",
"^fatal error C[0-9]+:",
": syntax error ",
"^collect2: ld returned 1 exit status",
@@ -140,7 +109,7 @@ def match(self, text):
"^Unresolved:",
"Undefined symbol",
"^Undefined[ \\t]+first referenced",
"^CMake Error.*:",
"^CMake Error",
":[ \\t]cannot find",
":[ \\t]can't find",
": \\*\\*\\* No rule to make target [`'].*\\'. Stop",
@@ -154,6 +123,7 @@ def match(self, text):
"ld: 0706-006 Cannot find or open library file: -l ",
"ild: \\(argument error\\) can't find library argument ::",
"^could not be found and will not be loaded.",
"^WARNING: '.*' is missing on your system",
"s:616 string too big",
"make: Fatal error: ",
"ld: 0711-993 Error occurred while writing to the output file:",
@@ -175,44 +145,38 @@ def match(self, text):
"instantiated from ",
"candidates are:",
": warning",
": WARNING",
": \\(Warning\\)",
": note",
" ok",
"Note:",
"makefile:",
"Makefile:",
":[ \\t]+Where:",
"([^ :]+):([0-9]+): Warning",
"[^ :]:[0-9]+: Warning",
"------ Build started: .* ------",
]
#: Regexes to match file/line numbers in error/warning messages
_warning_matches = [
prefilter(
lambda x: 'warning' in x,
"([^ :]+):([0-9]+): warning:",
"([^:]+): warning ([0-9]+):",
"([^:]+): warning[ \\t]*[0-9]+[ \\t]*:",
"([^ :]+) : warning",
"([^:]+): warning"),
prefilter(
lambda x: 'note:' in x,
"^([^ :]+):([0-9]+): note:"),
prefilter(
lambda x: any(s in x for s in ('Warning', 'Warnung')),
"^(Warning|Warnung) ([0-9]+):",
"^(Warning|Warnung)[ :]",
"^cxx: Warning:",
"([^ :]+):([0-9]+): (Warning|Warnung)",
"^CMake Warning.*:"),
"file: .* has no symbols",
"[^ :]:[0-9]+: warning:",
"[^ :]:[0-9]+: note:",
"^cc[^C]*CC: WARNING File = ([^,]+), Line = ([0-9]+)",
"^ld([^:])*:([ \\t])*WARNING([^:])*:",
"[^:]: warning [0-9]+:",
"^\"[^\"]+\", line [0-9]+: [Ww](arning|arnung)",
"[^:]: warning[ \\t]*[0-9]+[ \\t]*:",
"^(Warning|Warnung) ([0-9]+):",
"^(Warning|Warnung)[ :]",
"WARNING: ",
"[^ :] : warning",
"[^:]: warning",
"\", line [0-9]+\\.[0-9]+: [0-9]+-[0-9]+ \\([WI]\\)",
"^cxx: Warning:",
"file: .* has no symbols",
"[^ :]:[0-9]+: (Warning|Warnung)",
"\\([0-9]*\\): remark #[0-9]*",
"\".*\", line [0-9]+: remark\\([0-9]*\\):",
"cc-[0-9]* CC: REMARK File = .*, Line = [0-9]*",
"^CMake Warning",
"^\\[WARNING\\]",
]
@@ -223,8 +187,6 @@ def match(self, text):
"/usr/.*/X11/XResource\\.h:[0-9]+: war.*: ANSI C\\+\\+ forbids declaration",
"WARNING 84 :",
"WARNING 47 :",
"makefile:",
"Makefile:",
"warning: Clock skew detected. Your build may be incomplete.",
"/usr/openwin/include/GL/[^:]+:",
"bind_at_load",
@@ -343,8 +305,7 @@ def _profile_match(matches, exceptions, line, match_times, exc_times):
def _parse(lines, offset, profile):
def compile(regex_array):
return [regex if isinstance(regex, prefilter) else re.compile(regex)
for regex in regex_array]
return [re.compile(regex) for regex in regex_array]
error_matches = compile(_error_matches)
error_exceptions = compile(_error_exceptions)

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