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...

341 Commits

Author SHA1 Message Date
Gregory Becker
79e821a43e docs: consistently use 'managed environment' over 'named ...' 2023-02-21 15:53:34 -08:00
psakievich
c16f166dcc Update lib/spack/docs/environments.rst 2023-02-21 16:33:45 -07:00
psakiev
4ae9730ffe remove env's 2023-02-21 12:57:13 -07:00
psakiev
9debeaf4e7 Try to resolve uninstall failure 2023-02-21 12:01:10 -07:00
psakiev
47cdefcbe8 Try setting mutable_mock_env in each func 2023-02-21 11:18:26 -07:00
psakiev
2acc356ed4 Style 2023-02-21 10:09:22 -07:00
psakiev
36bf6c9009 Add unit-tests back 2023-02-21 10:00:50 -07:00
psakiev
29fbad20a2 Undo hoops for avoiding env include 2023-02-21 09:18:44 -07:00
psakiev
5f78703af8 Fixture function scope 2023-02-21 08:53:07 -07:00
psakiev
9b390bdc2c Add back mutable-config 2023-02-15 16:55:33 -07:00
psakiev
bc427e8435 Adjust vars in mutable_mock_env_path 2023-02-15 14:46:54 -07:00
psakiev
3c6e6e22be Undo all unit-tests to see if CI will pass 2023-02-15 13:08:19 -07:00
psakievich
4a8f755632 [@spackbot] updating style on behalf of psakievich 2023-02-13 18:52:06 +00:00
psakievich
51de7ed7ee Merge branch 'develop' into f/env-location 2023-02-13 10:50:53 -07:00
Larry Knox
c5d7ea04d0 Add hdf5-vol-log version 1.4.0. (#35453) 2023-02-13 11:27:22 -06:00
Rocco Meli
1bc425ddad Add chemfiles and py-chemfiles (#35410) 2023-02-13 06:53:10 -07:00
Adam J. Stewart
471684add4 py-pip: add v23.0 (#35369) 2023-02-11 07:47:15 -08:00
Vanessasaurus
973d33a8f1 Automated deployment to update package flux-sched 2023-02-09 (#35415)
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2023-02-10 22:34:06 -08:00
Adam J. Stewart
d0387cbbaf py-pytorch-lightning: add v1.9.1 (#35445)
* py-pytorch-lightning: add v1.9.1
* flake8
2023-02-10 18:37:42 -08:00
renjithravindrankannath
97d59c2efb Adding checksum for 5.3.3 of RVS (#35446)
Co-authored-by: sreenivasa murthy kolam <sreenivasamurthy.kolam@amd.com>
2023-02-10 18:12:56 -08:00
Chris Green
b69378c8cb Maintainer username update chissg -> greenc-FNAL (#35444) 2023-02-10 18:02:46 -08:00
H. Joe Lee
f1b004a0d3 pmdk: add the latest release 1.12.1 (#35440)
* pmdk: add the latest release 1.12.1
  Both master and 1.12.1 require CMake.
* pmdk: fix style
2023-02-10 14:44:22 -08:00
Sangu Mbekelu
1f7c59eb06 new py-amplpy package (#35359)
* new py-amplpy package
* [@spackbot] updating style on behalf of sm2939
* Update package.py
* Rename var/spack/repos/builtin/py-amplpy/package.py to var/spack/repos/builtin/packages/py-amplpy/package.py
* Edited file to change copyright year/dependencies and changed the directory of the file

---------

Co-authored-by: Sangu Mbekelu <s.mbekelu9@gmail.com>
2023-02-10 11:23:19 -08:00
John W. Parent
e1341d70ce MSBuilder/MSVC: correct toolchain ver (#35424)
#35098 added the correct extraction of toolset version for the MSVC
compiler. This updates the associated method in MSBuilder to retrieve
the (now correct) property.
2023-02-10 10:53:16 -08:00
SXS Bot
38c321abb3 spectre: add v2023.02.09 (#35426)
Co-authored-by: sxs-bot <sxs-bot@users.noreply.github.com>
2023-02-10 10:05:14 -08:00
Zack Galbreath
82041ac5a3 Restore our ability to submit build/test results to CDash from GitLab CI (#35328)
* Restore our ability to submit build/test results to CDash from GitLab CI

* Don't use CDash upload URL as report filename
2023-02-10 12:01:05 -06:00
Adam J. Stewart
ecf93c77ae py-fiona: add v1.9.1 (#35433) 2023-02-10 09:32:25 -08:00
Teo
34e42d5540 bug fix: halide -> Halide or something. (#35431) 2023-02-10 08:33:04 -08:00
Alex Richert
cdcbf7dc46 Add AlexanderRichert-NOAA as ESMF maintainer (#35430) 2023-02-10 08:23:06 -08:00
Richard Berger
e25501f76c singularity-eos: add v1.7.0, cleanup package (#35163)
* singularity-eos: add v1.7.0, cleanup package
* Update var/spack/repos/builtin/packages/singularity-eos/package.py
---------

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Co-authored-by: rbberger <rbberger@users.noreply.github.com>
2023-02-10 07:58:08 -08:00
Vanessasaurus
7fec7cd013 Automated deployment to update package flux-core 2023-02-09 (#35414)
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2023-02-10 02:03:50 -08:00
simonleary-umass-edu
3d881dbad7 meme add perl-xml-simple dependency (#35408)
Meme 4.5.0 has the first occurrence of the string
```
use XML::Simple
```
I found this by doing a binary search manually extracting tarballs until `grep` came up empty.
2023-02-10 01:21:40 -08:00
Sébastien Valat
c818e36d79 malt: new package (versions : 1.2.1) (#35272)
* malt: new package (versions : 1.2.1)
* malt: Fix remarks on new package (versions : 1.2.1)
* malt: Fix PR remarks by removing un-needed functions overriding
* malt: Fix NodeJs => NodeJS
* Use new maintainers syntax.
2023-02-09 19:58:28 -08:00
Sangu Mbekelu
4fbbb23933 new ampltools package (#35357)
* new ampltools package

* [@spackbot] updating style on behalf of sm2939

* Update and rename var/spack/repos/builtin/py-ampltools/package.py to var/spack/repos/builtin/packages/py-ampltools/package.py

Edited file to change copyright year/dependencies and edited directory

---------

Co-authored-by: Sangu Mbekelu <s.mbekelu9@gmail.com>
2023-02-09 19:57:42 -08:00
H. Joe Lee
b35af7d9e7 protobuf: add 3.21.12. (#35396)
* protobuf: add 3.21.12.
* protobuf: add maintainer and fix checksum
2023-02-09 16:11:24 -08:00
eugeneswalker
f7de22eb14 gpu test stack: add test w/ ^cuda@12 builds on A100 w/ newer driver (#35375)
* gpu test stack: test cuda@12 builds on A100 w/ newer driver

* get gpu info via nvidia-smi;

* kokkos+cuda^cuda@12 has genuine failure
2023-02-09 12:18:03 -07:00
Bill Williams
72f57ffede Score-P updates for version 8.0 (#35256)
* Add Score-P 8.0 and Cube 4.7/4.8 packages.
* Score-P 8.0 requires 4.8, not 4.7, Cube packages
* Add maintainer
* Add CUDA and HIP variants. Add version checks for CUDA (Score-P 8 requires CUDA 7), ROCm (variant only valid as of Score-P 8), and MPI (Score-P 7 requires at least version 2.2 of the MPI standard).
* Deprecate everything pre-7.0.
* Fix HIP dependencies and enable CUDA and HIP variants for configure.
* Deprecate OTF2 pre-2.3 and Cube pre-4.6
2023-02-09 10:50:50 -08:00
Loïc Pottier
12f43380b9 rabbitmq-c: fix bug when POLT < 1.14 compilation failed (POPT_ARG_ARGV undeclared) (#35403)
Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
2023-02-09 10:24:48 -08:00
Frank Willmore
ffdc85e8ce Update package.py (#35402)
adding explicit dependency on X11 (needed when there is not a system install)
2023-02-09 10:04:15 -08:00
John W. Parent
259a32e5e4 Windows: MSMPI package fixes (#35112)
* Add "fake" mpi compiler wrappers to msmpi: msmpi doesn't actually
  provide wrappers, so this just assigns the wrappers to be whatever
  compiler that a dependent is using. Packages referencing the
  wrappers would otherwise break. This is assumed to be workable
  because build scripts will need to assemble appropriate information
  to pass to the compiler anyway
* Fix msmpi detection stanza ('executable' is not the correct name of
  the property)
* Fix compiler pkg dereference
2023-02-09 09:53:59 -08:00
Teo
8c0b8c785f tiramisu: new package (#35364)
* add initial package.

* Update package.py

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

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

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

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

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

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

* Update package.py

* Hopefully this will be fine.

* Update package.py

* Update package.py

* Update package.py

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

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-02-09 09:09:30 -08:00
snehring
02d3bd782d py-netcdf4: adding version 1.6.2 (#35393)
* py-netcdf4: adding version 1.6.2

* py-netcdf4: updating setuptools dep.
2023-02-08 18:10:28 -08:00
Erik Heeren
b6906be846 cvise: new package (#35366)
* cvise: new package
* cvise: colordiff as optional dependency
* cvise: remove old versions and correctly name master version
* cvise: update license date
* cvise: use maintainers directive
* Remove @olupton as maintainer

After live discussion: it's been too long since he did anything with this package.
2023-02-08 16:13:32 -08:00
H. Joe Lee
a0ce6f7890 protobuf-c: add 1.4.1 version (#35397)
* protobuf-c: add 1.4.1 version
* protobuf-c: add maintainers
2023-02-08 15:49:59 -08:00
Rocco Meli
09cf265ff4 Add new versions of spglib (#35332)
* add spglib versions
* add maintainer
* fmt
* maintainer
* url
2023-02-08 15:37:47 -08:00
Adam J. Stewart
0d72b29193 wrf: fix v4.4.2 checksum (#35401) 2023-02-08 14:24:24 -08:00
Wouter Deconinck
7f1467e795 dd4hep: new version 1.24, depends_on podio@0.16: (#35384)
* dd4hep: new version 1.24, depends_on podio@0.16:
* Update var/spack/repos/builtin/packages/dd4hep/package.py

Co-authored-by: Valentin Volkl <valentin.volkl@cern.ch>
2023-02-08 10:51:22 -08:00
Mikael Simberg
f89cd29054 Add whip 0.2.0 (#35390) 2023-02-08 10:36:05 -08:00
Matthieu Dorier
89720583c3 [mochi-margo] Added version 0.12.1 (#35392) 2023-02-08 10:33:51 -08:00
Adam J. Stewart
7e78efcc44 spack help --spec: fix indentation (#35383) 2023-02-08 08:46:56 -08:00
Dan Lipsa
126accfce1 Fix external freetype that provides freetype-config.cmake (#35363)
* Fix external freetype that provides freetype-config.cmake

---------

Co-authored-by: Dan Lipsa <dan.lipsa@khq.kitware.com>
2023-02-08 10:00:14 -06:00
Massimiliano Culpo
27c2ff6c64 Ensure we print the correct branch number for tutorials (#35371) 2023-02-08 09:46:21 +01:00
Scott Wittenburg
9bde77199c bindist: use append as a method, not assignable attr (#35379) 2023-02-08 09:42:28 +01:00
Adam J. Stewart
f5ed18f6a3 py-installer: bootstrap without pip (#35341)
* py-installer: bootstrap without pip

* [@spackbot] updating style on behalf of adamjstewart

---------

Co-authored-by: adamjstewart <adamjstewart@users.noreply.github.com>
2023-02-07 22:30:06 -06:00
Christian Glusa
ccd11666c6 py-gmsh-interop: Fix PyPI link (#35381) 2023-02-07 20:23:41 -08:00
Christian Glusa
df80cffafa New package: PyNucleus & dependencies (#35327)
* Add py-scikit-sparse package

* Add py-gmsh-interop package

* Add py-modepy package

* Add py-pymbolic package

* Add py-meshpy package

* Add py-pynucleus package

* Add new version of py-pytools
2023-02-07 14:12:15 -08:00
Adam J. Stewart
b52d4b8abf py-symengine: setuptools 61+ not yet working (#35368)
* py-symengine: setuptools 61+ not yet working
* symengine still required for master
2023-02-07 11:49:07 -08:00
Teo
96624d1490 halide: new package (#35254)
* add halide package.

* some style changes.

* small fix

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

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>

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

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

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

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

* Update package.py

add comment to requirements.txt

* Update package.py

Fix version order.

* Update package.py

style

* Update package.py

Removed unneeded vars.

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

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

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

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

* Update package.py

Fix some deps

* Update package.py

* Fix finding llvm cmake info

* Update package.py

---------

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-02-07 13:12:29 -06:00
Dan Lipsa
1648968514 Windows: Fix spack.bat handling of env commands (#35143)
This PR enables the successful execution of the spack binary cache
tutorial on Windows. It assumes gnupg and file are available (they
can be installed with choco).

* Fix handling of args with quotes in spack.bat
* `file` utility can be installed on Windows (e.g. with choco): update
  error message accordingly
2023-02-07 11:04:14 -08:00
Paul Kuberry
8358f430a4 xyce: change cmake cxx compiler variable (#35365) 2023-02-07 14:00:15 -05:00
Adam J. Stewart
ec045f993b py-fastrlock: add v0.8.1 (#35370) 2023-02-07 11:23:07 -07:00
Mosè Giordano
7fe2039b01 texinfo: Require ncurses (#35356)
I don't know if this is new in version 7.0, but to build `info`, which is a required executable at the end of the recipe, it is necessary to have a terminal library, otherwise you get
```
[...]
checking for tgetent in -ltinfo... no
checking for tgetent in -lncurses... no
checking for tgetent in -lcurses... no
checking for tgetent in -ltermlib... no
checking for tgetent in -ltermcap... no
checking for tgetent in -lterminfo... no
configure: WARNING: info needs a terminal library, one of: tinfo ncurses curses termlib termcap terminfo
[...]
configure: WARNING: Could not find a terminal library among tinfo ncurses curses termlib termcap terminfo
configure: WARNING: The programs from `info' directory will not be built.
```
then compilation runs, `info` is not built and installation fails according to Spack because the required executable is missing.
2023-02-07 05:27:21 -08:00
dependabot[bot]
25cb55ccd9 build(deps): bump docker/build-push-action from 3.3.0 to 4.0.0 (#35252)
Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 3.3.0 to 4.0.0.
- [Release notes](https://github.com/docker/build-push-action/releases)
- [Commits](37abcedcc1...3b5e8027fc)

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

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-02-07 08:17:53 +01:00
dependabot[bot]
d4e075f667 build(deps): bump docker/setup-buildx-action from 2.2.1 to 2.4.1 (#35354)
Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 2.2.1 to 2.4.1.
- [Release notes](https://github.com/docker/setup-buildx-action/releases)
- [Commits](8c0edbc76e...f03ac48505)

---
updated-dependencies:
- dependency-name: docker/setup-buildx-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>
2023-02-07 08:17:10 +01:00
Wouter Deconinck
ae98d2ba2f Support packages for using scitokens on OSG (#35334)
* Support packages for using scitokens on OSG

The Open Science Grid (OSG)  encourages scitokens to provide
certain services (e.g. writing to xrootd). Spack already
supports this through scitokens-cpp and xrootd +scitokens-cpp.

This adds py-htgettoken, a python utility to get a scitoken
from a vault through web authentication. To support htgettoken,
this also adds py-gssapi.

This also adds the OSG CA cert collection which is typically
at /etc/grid-security but pointed to in user installations by
the X509_CERTS_DIR variable.

This allows userspace through spack for functionality that
otherwise depends on installing the RPMs provided by OSG.

* fine, I'll fix style myself then

* fix maintainers

* py-gssapi: version before depends_on

* remove list_url

* add documentation on reason for git describe version numbers

* Apply suggestions from code review

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

* better BEARER_TOKEN definition

* import os

* remove older version that don't build with setuptools

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-02-06 23:23:03 -06:00
snehring
8e49bf0c5b wps: adding version 4.4 (#35358) 2023-02-06 19:22:41 -08:00
Paul Kuberry
1bb119dbd7 xyce: add version 7.6.0 and RPATH patch for prior (#35360) 2023-02-06 19:17:31 -08:00
Matthias Wolf
a7f39da5db Fix path handling in prefix inspections (#35318)
At least with ZSH, prefix inspections containing `./bin` result in a
`$PREFIX/./bin` and result in strange `$PATH` handling.

I.e., `module load git` will prepend `/path/to/git/./bin`, `which git`
will find the right executable, but `git --version` will print the
system one. Normalize the relative path to avoid this behavior.

See also spack/spack#31867.
2023-02-06 19:12:30 -08:00
Rocco Meli
1d3a74d926 freesasa: add new package (#35192)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-02-06 18:52:45 -08:00
Rocco Meli
0448f18ab2 maeparser: add new package (#35191)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-02-06 18:52:23 -08:00
Daniele Colombo
2516ed181a relion: add patch to repair DoublePrec_CPU=OFF build (#35317)
* relion: add patch to repair DoublePrec_CPU=OFF build
* relion: added maintainer

Co-authored-by: Daniele Colombo <daniele.colombo@fht.org>
2023-02-06 15:32:06 -08:00
Sreenivasa Murthy Kolam
7740b37923 rocm llvm-amdgpu package - Build libcxx and libcxxabi thru LLVM_ENABLE_RUNTIMES flag. (#33610)
* changes to enable LLVM_ENABLE_RUNTIMES for libcxx and libcxxabi
* remove version update for 5.3.0 as it is done thru PR #33320 to enable
ci and reviews
2023-02-06 15:03:08 -08:00
Sreenivasa Murthy Kolam
358cc5ed1a Update the ROCm packages for ROCm-5.4.0 release. (#35071)
* initial commit for rocm-5.4.0 release
* update the versions for more packages for 5.4.0 release
* update the gallium patch for mesa for libllvm-15 for ROCm-5.4.0 release
* update rocm-openmp-extras and rocwmma recipes for 5.4.0 release
* fix build error for rocfft for 5.4.0
* address review comments for rocfft for 5.4.0 change
* undo the removal of the older patch file
* bump up the version for hipfft for 5.4.0
* fix the failure after the merge with develop
* add recipes updates for 5.4.0 for migraphx.miopen-hip,miopen-opencl
* address the review comments on the mesa patch.update the rdc package for
5.4.0 release
* fix style errors
2023-02-06 15:00:10 -08:00
Adam J. Stewart
30b8cfad98 py-mypy: add v1.0.0 (#35362) 2023-02-06 16:59:04 -06:00
Tamara Dahlgren
383a343412 GenericBuilder: facilitate post-install phase test callbacks (#35314) 2023-02-06 12:51:01 -08:00
Wouter Deconinck
3714d3443b acts: new versions 21.1.1, 22.0.1, 23.0.0 (#35227)
* acts: new versions 21.1.1, 22.0.1, 23.0.0

New versions:
- [major 23.0.0](https://github.com/acts-project/acts/compare/v22.0.0...v23.0.0):
  - new option `ACTS_BUILD_PLUGIN_GEANT4` -> enabled with existing variant `geant4`
  - new option `ACTS_BUILD_EXAMPLES_BINARIES`:
    - it is my understanding that the binaries for examples are deprecated (in favor of python examples); warnings to this effect have been printed for a few versions, and now the building of binaries is disabled by default,
    - rather than introducing a variant to enable deprecated behavior for only one or two versions, I propose that we just follow the default and keep this disabled. 
- [bugfix 22.0.1](https://github.com/acts-project/acts/compare/v22.0.0...v22.0.1) (no build system changes)
- [bugfix 21.1.1](https://github.com/acts-project/acts/compare/v21.1.0...v21.1.1) (no build system changes)

* acts: correct 23.0.0 sha

Co-authored-by: Hadrien G. <knights_of_ni@gmx.com>
2023-02-06 12:37:51 -08:00
Wouter Deconinck
42a452d54c estarlight, dpmjet: new packages (#32834)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-02-06 09:09:22 -07:00
Jim Galarowicz
a913ed229d Restore openspeedshop and openspeedshop-utils, update the cbtf components (#35052) 2023-02-06 16:10:41 +01:00
Vanessasaurus
7c122da48b flux-core: add missing dependency(#35312) 2023-02-06 06:29:30 -08:00
Glenn Johnson
fdaa54941d r-cvxr: add new package with dependencies (#35275) 2023-02-06 15:13:37 +01:00
Wouter Deconinck
135832650f qt: new version 5.15.8 (#35352)
No build system changes, just bug fixes.

https://github.com/qt/qtbase/compare/v5.15.7-lts-lgpl...v5.15.8-lts-lgpl

Builds fine on linux-ubuntu22.10-skylake.
2023-02-06 06:12:57 -08:00
Stephen Sachs
29d710fdec wrf: add optional netcdf_classic variant (#35261)
Co-authored-by: Stephen Sachs <stesachs@amazon.com>
2023-02-06 15:12:32 +01:00
Mikael Simberg
13c4f92907 hpx: further constrain version for mimalloc patch (#35257) 2023-02-06 15:10:08 +01:00
Erik Schnetter
7a2c9601e8 reprimand: add v1.5 (#35245)
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-02-06 15:08:08 +01:00
Harmen Stoppels
31959b72b0 bump: nss + dep (#35294) 2023-02-06 15:06:16 +01:00
Erik Heeren
8109877424 amdlibflame: needs modern make (#35297)
See https://github.com/flame/libflame/issues/55
2023-02-06 15:05:16 +01:00
snehring
91243ecb5b tau: updating python version restriction (#35268)
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-02-06 14:58:04 +01:00
William Moses
1fc2bf846d enzyme: add v0.0.48 (#35304) 2023-02-06 14:56:46 +01:00
Vasileios Karakasis
848344d9a5 ReFrame: add versions up to v4.0.4 (#35330) 2023-02-06 14:39:47 +01:00
Cameron Smith
e08da4e2b6 pumi and zoltan: allow building when no fortran compiler is available (#35333) 2023-02-06 14:35:44 +01:00
Wouter Deconinck
75a72766ff assimp: new version 5.2.5 (#35335)
Bugfix release only. No build system changes.
2023-02-06 14:34:15 +01:00
Wileam Y. Phan
797e230498 intel-gtpin: add v3.2.2 (#35342) 2023-02-06 13:51:03 +01:00
Wouter Deconinck
1c6993145e libdrm: new versions 2.4.111-114 (#35343)
As of 2.4.113, the flag for man-pages is now a feature,
so true/false is now enabled/disabled. Other similarly
changed options are not used in the spack recipe (i.e.
experimental kms drivers).
2023-02-06 13:28:18 +01:00
Wouter Deconinck
00573d6ea2 sherpa: new version 2.2.14 (#35344)
"Version 2.2.14 contains a critical bug fix"
2023-02-06 13:12:19 +01:00
Luke Diorio-Toth
4c0116bd64 mash: added patch with limits header (#35209)
Co-authored-by: luke <luke@DESKTOP-E4JNTC1.attlocal.net>
2023-02-06 13:08:31 +01:00
Rémi Lacroix
f0d8355248 libxc 6.0.0: fix a bug affecting CP2K (#35347)
The patch fixes a missing comma at end of line in mgga_xc_b97mv.c.
2023-02-06 13:05:13 +01:00
Rémi Lacroix
01c21d0496 n2p2: add v2.2.0. (#35348) 2023-02-06 13:03:05 +01:00
Adam J. Stewart
43057e2edd py-numpy: add v1.24.2 (#35350) 2023-02-06 12:38:34 +01:00
Mikael Simberg
ba8d9f22ef Add pika 0.12.0 and pika-algorithms 0.1.1 (#35296) 2023-02-06 12:32:57 +01:00
Wouter Deconinck
07d7c32d79 qt: new versions 6.4.0, 6.4.1, 6.4.2 (#34698)
* qt: new versions 6.4.0, 6.4.1

- New libpsl vendored dependency in qt-base.
- New embree and tinyexr dependency in qt-quick3d.

We need to figure out a better way to deal with these vendored
dependencies in src/3rdparty. Removing them was a way to make sure
they are not used unintentionally. Many of these dependencies cannot
be overridden with a QT_FEATURE_system_* flag and are included directly
in cpp files. Many change versions from release to release, so even if
they use system (ie spack managed) versions we need to support this in
the depends_on lines.

What we can rely on?
- src/3rdparty is where vendored stuff is stored
- not much else...

Possible ways to deal with this:
- Change vendor_deps_to_keep to dict with versions, eg
```
vendor_deps_to_keep = {
    "xatlas": "@6:",
    "embree": "@6.4:",
    "tinyexr": "@6.4:",
}
```
- Similarly introduce system_deps_to_use:
```
system_deps_to_use = {
    "assimp@5.2:": "@6:",
}
```
and derive depends_on and QT_FEATURE_system_* from this dict.

* qt-*: new version 6.4.2, invert vendored pkgs logic

* qt-base: fix vendor_deps_to_avoid typo

* qt-*: move lots into QtPackage base layer
2023-02-05 22:38:05 -05:00
Massimiliano Culpo
017a15988c Don't use CDash upload URL as report filename (#35338)
fixes #35337
2023-02-05 12:58:45 +01:00
Cameron Rutherford
1ad290e5a2 Require 0.7.1 for ExaGO 1.5.0+. (#35331) 2023-02-03 22:10:14 -08:00
eugeneswalker
f6fa64f979 ci: add minimal gpu testing stack (#35251)
* ci: add minimal gpu testing stack

* kokkos +cuda requires +wrapper...

* require pass

* add raja+cuda
2023-02-03 18:33:34 -08:00
John W. Parent
1826a41cdd MSVC compiler: add platform toolset version (#35098) 2023-02-03 17:53:24 -08:00
Massimiliano Culpo
509a8ea5e2 py-packaging: add constrain on python version (#35325) 2023-02-03 19:00:23 +01:00
Erik Heeren
ca202ba11e py-igor: new package (#35229)
* py-igor: new package

* py-igor: review remarks
2023-02-03 09:02:43 -07:00
Erik Heeren
0b1d51e450 Add py netpyne, meautility, and lfpykit (#35262)
* py-netpyne: new package with dependencies

* py-netpyne, py-meautility, py-lfpykit: license update

* py-netpyne: review remarks

* py-netpyne: style

* py-netpyne: don't limit python version
2023-02-03 09:29:30 -06:00
Manuela Kuhn
2936573fc6 py-glmsingle: add 1.1 (#35311) 2023-02-03 09:28:16 -06:00
Rémi Lacroix
5d4c250354 CMake: Add version 3.25.2 (#35196) 2023-02-02 20:27:56 -08:00
Adam J. Stewart
b0913b1bf8 py-torchmetrics: add v0.11.1 (#35260) 2023-02-02 18:32:46 -08:00
John W. Parent
c49e2e5620 NMake builder: fix incorrect variable reference (#34937) 2023-02-02 16:34:35 -08:00
Adam J. Stewart
60624265f8 py-black: add v23.1.0 (#35279)
* py-black: add v23.1.0
* py-packaging: add v23.1.0
2023-02-02 14:32:37 -08:00
Larry Knox
79aa9e9c87 Update to latest version. (#35309)
Update hdf5-vol-external-passthrough to latest version compatible with HDF5 1.14
2023-02-02 16:16:56 -06:00
Wouter Deconinck
f2b0c1deab py-minkowskiengine: new package (sparse tensor autodiff by Nvidia) (#35302)
* py-minkowskiengine: new package (sparse tensor autodiff by Nvidia)

This python package (with cuda support) provides torch support for sparse
tensors. The `pybind11` headers are not found without the patch to `setup.py`.

* [@spackbot] updating style on behalf of wdconinc

* py-minkowskiengine: depends_on numpy, pybind11 type=link; no patch

* [@spackbot] updating style on behalf of wdconinc

---------

Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
2023-02-02 16:03:01 -06:00
John W. Parent
7d50680d9c zlib package: fix build on Windows (#35103) 2023-02-02 13:53:16 -08:00
snehring
defa4a2340 py-getorganelle: rename to getorganelle and add version 1.7.7.0 (#35270)
* py-getorganelle: rename to getorganelle and add version 1.7.7.0

* py-getorganelle: deprecating package
2023-02-02 13:13:32 -06:00
Manuela Kuhn
1e1d1ec43b py-nilearn: add 0.10.0 (#35303) 2023-02-02 13:02:19 -06:00
Rémi Lacroix
0e41788812 LAMMPS: Package KIM requires CURL after version 20190329 (#35182) 2023-02-02 06:12:27 -08:00
Massimiliano Culpo
ddecf07045 Use the maintainers directive in all packages (#35201) 2023-02-01 21:07:25 -08:00
Weiqun Zhang
9865a42b20 amrex: add v23.02 (#35286) 2023-02-01 15:32:38 -08:00
Jordan Galby
2432be5911 glib: 2.74: needs pcre2@10.34: (#35283) 2023-02-01 12:53:03 -08:00
Timothy Brown
002bd8d20b [WRF] Adding new versions (#35244)
* [WRF] Adding new versions.
* Style fixes.
2023-02-01 12:29:35 -08:00
Glenn Johnson
eac04af0e7 fastqc: Use the spack built perl (#35276)
The fastqc script was using the system perl. This PR sets the script to
use the spack built/provided perl. This PR also removes the code that
adds the java path. That should be handled by module loading as far as I
know.
2023-02-01 09:47:10 -08:00
Larry Knox
448bd31c87 Add hdf5 versions 1.14.0, develop-1.14 and update develop version from develop-1.13 to develop-1.15 (#34734)
* Add HDF5 version 1.13.3.

* Remove maintainers no longer with The HDFGroup.

* Add version hdf5-vol-async@1.4

* Add HDF5 version 1.14.0, develop-1.14, develop-1.15.
Add missing conflicts for api version and develop versions.

* Add conflicts statement to hdf5/package.py to avoid building hdf5 with
MPICH 4.0.x versions with bug that causes testphdf5 test to fail.

* Add patch to call find_package(MPI) for dependent packages not finding
it, not having called it themselves.

* Remove language components from find_package(MPI) in
hdf5_1_14_0_config_find_mpi.patch.

* Add HDF5 version 1.14.0, develop-1.14, develop-1.15.
Add missing conflicts for api version and develop versions.

* Add conflicts statement to hdf5/package.py to avoid building hdf5 with
MPICH 4.0.x versions with bug that causes testphdf5 test to fail.

* Add patch to call find_package(MPI) for dependent packages not finding
it, not having called it themselves.

* Remove language components from find_package(MPI) in
hdf5_1_14_0_config_find_mpi.patch.

* Don't guard ParaView patch on HDF5 variant

ParaView always needsd  HDF5 and ignores the variant.

* py-h5py: Newer versions of HDF5 introduce breaking API changes

---------

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Co-authored-by: Ryan Krattiger <ryan.krattiger@kitware.com>
2023-02-01 09:17:17 -06:00
Massimiliano Culpo
46466302a9 Pin black to 22.12.0 to avoid spurious style changes (#35282)
We need to sync changes on major versions with
spackbot, to avoid the bot saying everything is
allright and have CI failing nonetheless.
2023-02-01 15:45:12 +01:00
Erik Heeren
5e39acea16 py-equation: new package (#35198)
* py-equation: new package

* py-equation: add variants for extra dependencies
2023-02-01 00:02:11 -06:00
Thomas Bouvier
cfdf0b6987 nccl: v2.15.5-1, v2.16.2-1 (#35248)
* `nccl`: v2.15.5-1, v2.16.2-1
* Fix wrong sha256
* Revert checksums (after GitHub has algorithm change reverted)
2023-01-31 19:17:20 -08:00
Erik Schnetter
6be6935671 libffi: New version 3.4.4 (#35087) 2023-01-31 16:46:41 -08:00
eugeneswalker
68233db9f6 Revert "flex%oneapi@2023.0.0: -Wno-error=implicit-function-declaration (#34900)" (#35181)
This reverts commit 62f83dfb6d.
2023-01-31 16:37:10 -08:00
renjithravindrankannath
aea2c73b04 Adding rocm-opencl prefix lib path to LD_LIBRARY_PATH for run_environment (#35011) 2023-01-31 16:26:42 -08:00
Harmen Stoppels
5dc5db6679 Fix awscli and deps (#35158)
* py-docutils/py-pyyaml specify python 3.11 compat

* bump awscli / py-botocore

* fix botocore again

* review fixes

* .
2023-01-31 13:32:53 -08:00
Alan Williams
51702a725b Add trilinos-solvers variant to nalu-wind package. (#35267)
* Add trilinos-solvers variant to nalu-wind package.
   This allows nalu-wind to be built against a trilinos installation
   which doesn't have amesos2, belos, ifpack2, or muelu enabled, if
   the nalu-wind user provides the spec 'nalu-wind@master~trilinos-solvers'
   Support for these solver-packages remains on by default.
* Fixed a style issue reported by CI.
* Incorporate change in wording suggested from review comments.
   ... to clarify that at least one, or both, of hypre and/or
   trilinos-solvers must be enabled. The error condition is if
   both are disabled.
* That style checker is picky...
* It really did want a trailing comma...
2023-01-31 12:42:43 -08:00
Erik Heeren
931c0edaf4 py-munkres: new package (#35259) 2023-01-31 13:41:23 -06:00
eugeneswalker
689bdd6f36 strumpack +rocm: set CMAKE_CXX_COMPILER to hipcc (#35153)
* strumpack +rocm: set CMAKE_CXX_COMPILER to hipcc

* strumpack@7.0.1+rocm^mpich: patch in upstream commit
2023-01-31 10:51:02 -08:00
Erik Heeren
a426db06e7 py-matplotlibscalebar: new package (#35242)
* py-matplotlibscalebar: new package

* py-matplotlibscalebar: style

* py-matplotlib-scalebar: review remarks
2023-01-31 08:27:16 -08:00
Erik Heeren
4b12d015e1 py-jinja2-cli: new package (#35238)
* py-jinja2-cli: new package

* Update var/spack/repos/builtin/packages/py-jinja2-cli/package.py

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-31 08:17:17 -08:00
Jen Herting
ecd4eac184 [py-protoc-gen-swagger] new package (#35241)
* [py-protoc-gen-swagger] new package

* [@spackbot] updating style on behalf of qwertos

---------

Co-authored-by: qwertos <qwertos@users.noreply.github.com>
2023-01-30 15:20:51 -08:00
Jean-Baptiste Skutnik
4d502c8ff7 Update py-docker package (#35217)
* Add py-docker@5:

* [@spackbot] updating style on behalf of spoutn1k

* Ignore `tls` variant

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

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

* `py-docker`: `py-paramiko` version fix

---------

Co-authored-by: spoutn1k <spoutn1k@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-30 15:20:04 -08:00
kent-cheung-arm
227c6061e5 arm-forge: add 22.1.3 (#35200) 2023-01-30 12:36:39 -08:00
Adam J. Stewart
3453f59ba3 py-fiona: add v1.9.0 (#35247) 2023-01-30 13:56:25 -06:00
Alex Richert
3201b4e2a1 HDF5 static (#34577)
* Add HDF5 static support for netcdf-c
* Update var/spack/repos/builtin/packages/hdf5/package.py
   Apply pkgconfig fix for all libraries, not just lz

Co-authored-by: Sergey Kosukhin <skosukhin@gmail.com>

* Update package.py
   Fix pkg config templates
* remove subprocess+2 lines
* Try netcdf-c changes only

Co-authored-by: Sergey Kosukhin <skosukhin@gmail.com>
2023-01-30 11:51:07 -08:00
Adam J. Stewart
80d26168b5 py-torchgeo: add v0.4.0 (#35155)
* py-torchgeo: add v0.4.0
* Add missing java dep
2023-01-30 11:47:10 -08:00
Adam J. Stewart
67040e79c5 py-protobuf: various updates (#35188) 2023-01-30 13:17:31 -06:00
Adam J. Stewart
a116775ff3 py-shapely: add v2.0.1 (#35246) 2023-01-30 11:08:08 -08:00
Erik Heeren
de2aaeb26f py-mariadb: new package (#35240)
* py-mariadb: new package

* py-mariadb: style
2023-01-30 13:07:15 -06:00
Erik Heeren
830e3211e5 py-hjson: fix typo in latest version (#35234) 2023-01-30 12:49:07 -06:00
Tamara Dahlgren
6b3b7f8b7f Bugfix: Update Petsc Python dependency (#35216)
* Bugfix: Update Petsc python dependency for at least 3.18:
* Update var/spack/repos/builtin/packages/petsc/package.py

Co-authored-by: Satish Balay <balay@mcs.anl.gov>
2023-01-30 10:21:50 -08:00
eugeneswalker
99f3716346 e4s: add and prefer boost +python +filesystem +iostreams +system (#35180) 2023-01-30 07:37:35 -08:00
Cory Bloor
4f6ef3b698 rocblas: remove unnecessary conflicts (#35232)
The gfx906:xnack- and gfx908:xnack- targets were introduced in ROCm 4.1
and replaced gfx906 and gfx908 as default build targets, but the library
can still be built for gfx906 and gfx908 if requested.
2023-01-30 16:08:36 +01:00
Ken Raffenetti
2dc020af31 mpich: add 4.0.3 and 4.1 releases (#35218) 2023-01-30 14:01:13 +01:00
snehring
17f2d66285 montage: fixing compilation issues for newer gcc versions (#35220) 2023-01-30 13:57:41 +01:00
simonleary-umass-edu
32f480936a apptainer: update constraint on go dependency (#35230) 2023-01-30 13:56:52 +01:00
Satish Balay
481b598963 hypre: Update URL using citation instructions from https://github.com/hypre-space/hypre/wiki/Citing-hypre (#35225) 2023-01-30 11:29:06 +01:00
John W. Parent
4b186df5b4 adios2: allow building on Windows (#35102) 2023-01-30 11:15:54 +01:00
aleixrocks
f4dac7cd4c OmpSs: add v2022.11 (#35228) 2023-01-30 11:11:36 +01:00
eugeneswalker
48a63719b2 e4s oneapi: use oneapi@2023.0.0 (#34634) 2023-01-29 13:22:14 -08:00
Alec Scott
f576b4b6c5 gmake: Fix too many levels of symbolic links error (#35224)
* gedit: Fix too many levels of symlinks error

* Fix package formatting with black
2023-01-29 15:00:35 -06:00
eugeneswalker
9f5d9266e6 e4s: add power stack (#32710)
* e4s: restore builds builds

* gitlab ci: allow UO to build protected binaries for signing

* use newer image; comment out failing builds

* gitlab-ci: Some tweaks for e4s power builds

- fix tags (no longer require generate jobs to run on aws)
- fix resource requests for generation jobs resource requests
- remove SPACK_SIGNING_KEY from protected power build jobs
- update UO signing key path
- change the CDash build group to reflect stack name
- retry pipeline generation jobs *always*

* correct double packages: section

* gitlab-ci:script: modernize

* remove new gnu make, not for ppc64le

---------

Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
2023-01-29 10:53:02 -06:00
John W. Parent
28c4809a8f freetype: add CMake support (#35107) 2023-01-28 10:32:17 -08:00
Michael Kuhn
57d6b70226 xz: add 5.4.1 and 5.2.10 (#35172) 2023-01-28 08:32:19 -08:00
Ben Cowan
508fcd8240 Added newer versions of PyAMG and added dependencies for 4.2 and later. (#35185)
* Added newer versions of PyAMG and added dependencies for 4.2 and later.

* Fixed dependencies.
2023-01-27 13:11:21 -08:00
Sebastian Grimberg
bec79d9ee1 New Spack package: Palace (#35189) 2023-01-27 12:47:18 -08:00
Jean-Baptiste Skutnik
27775163ca Added e4s-cl package (#35117)
* Added e4s-cl package

* Version order change

* Added e4s-cl dependencies

* Added python-sotools dependency

* [@spackbot] updating style on behalf of spoutn1k

* Add missing versions to py- packages

* Fix style

* [@spackbot] updating style on behalf of spoutn1k

* Update var/spack/repos/builtin/packages/e4s-cl/package.py

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

* Update var/spack/repos/builtin/packages/e4s-cl/package.py

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

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

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

* Add docker removing patch for e4s-cl

Co-authored-by: spoutn1k <spoutn1k@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-27 10:02:39 -08:00
Erik Heeren
b1cf512d78 py-nexusforge: add with dependencies (#35208)
* py-nexusforge: add with dependencies

* py-pyshacl, py-sseclient: more style

* py-hjson, py-nexus-sdk, py-nexusforge, py-puremagic: more style

* py-pyshacl: license update

* py-nexusforge, py-prettytable, py-pyshacl: review remarks

* py-nexusforge: make the variant mean something

Too hasty to commit...
2023-01-27 09:12:31 -08:00
Erik Heeren
0bfd06d0b6 Py ipyparallel (#35178)
* py-ipyparallel: add 8.4.1, which builds with py-hatchling

* py-ipyparallel: copyright and redundant py-setuptools dependency

* py-ipyparallel: py-packaging was dropped after 8.0.0
2023-01-27 08:52:23 -08:00
Jose E. Roman
367bd4d670 New patch release SLEPc 3.18.2 (#35176) 2023-01-27 07:44:19 -07:00
Mosè Giordano
8f359df2d3 libblastrampoline: Add v5.3.0 and v5.4.0 (#35194) 2023-01-27 09:51:18 +01:00
Massimiliano Culpo
cc2ae9f270 Add a maintainers directive (#35083)
fixes #34879

This commit adds a new maintainer directive,
which by default extend the list of maintainers
for a given package.

The directive is backward compatible with the current
practice of having a "maintainers" list declared at
the class level.
2023-01-27 07:51:24 +01:00
Erik Heeren
75f1077b4b py-nptyping, py-typish: add package (#35126)
* py-typish: add package

* py-typish: style fix

* py-nptyping: new package

* py-nptyping, py-typish: review remarks

* py-nptying: style

* py-nptyping: generic url, avoid pypi for now
2023-01-26 10:21:38 -06:00
Erik Heeren
b1e6507060 py-deap: add 1.3.3 (#35175) 2023-01-26 10:19:03 -06:00
Adam J. Stewart
2981b4e5ee py-rasterio: add v1.3.5 (#35167) 2023-01-26 15:41:05 +01:00
Harmen Stoppels
6847d73504 Cleanup of binary text relocation (#34188)
Move the relocation of binary text in its own class

Drop threaded text replacement, since the current bottleneck 
is decompression. It would be better to parallellize over packages,
instead of over files per package.

A small improvement with separate classes for text replacement is that we
now compile the regex in the constructor; previously it was compiled per
binary to be relocated.
2023-01-26 12:18:53 +01:00
Mosè Giordano
eeba92e788 wrf: Fix patching of config file when using GCC for v3.9.1.1 (#35140)
The regex doesn't actually work because dollar signs and parentheses have to be
escaped.  Also, compiling with OpenMPI requires defining the macro
`MPI2SUPPORT`.
2023-01-26 11:59:54 +01:00
Massimiliano Culpo
84917cfa79 Extract functions to read spec files from different format (#35094)
This commit makes explicit the format version of the spec file
we are reading from.

Before there were different functions capable of reading some
part of the spec file at multiple format versions. The decision
was implicit, since checks were based on the structure of the
JSON without ever checking a format version number.

The refactor makes also explicit which spec file format is used
by which database and lockfile format, since the information is
stored in global mappings.

To ensure we don't change the hash of old specs, JSON representations
of specs have been added as data. A unit tests checks that we read
the correct hash in, and that the hash stays the same when we
re-serialize the spec using the most recent format version.

Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
2023-01-26 10:40:46 +01:00
Wouter Deconinck
14e327be23 opencascade: add v7.7.0 (#35039) 2023-01-26 10:36:49 +01:00
Harmen Stoppels
c329f7de33 binutils: v2.30, 2.39, 2.40 (#35128)
- Add `binutils +pgo`
- Add dejagnu build dep and fix its deps
- Default to -O3 -g0 when using gcc/clang to make binutils faster and
  smaller
2023-01-26 10:28:26 +01:00
Sebastian Ehlert
f686a90779 Add package for serenity and its scine wrapper (#35072) 2023-01-26 02:00:34 -07:00
Harmen Stoppels
918bb63c3a test/config.py: fix import issues (#35076) 2023-01-26 09:53:44 +01:00
renjithravindrankannath
8d0cbb9812 Setting LIBDIR to lib in rocm-smi-lib across all platform (#34805) 2023-01-26 09:38:35 +01:00
mtaylo12
95a76de7d5 py-poetry-core GIT_DIR fix (#35139) 2023-01-26 09:26:53 +01:00
Richard Berger
0b388ff930 ports-of-call: add v1.4.1, deprecate old versions (#35151) 2023-01-26 08:18:55 +01:00
Filippo Spiga
d25ac66a5d NVIDIA HPC SDK: add v23.1 (#35169) 2023-01-25 22:47:38 -08:00
Seth R. Johnson
682ffd30ac p5-h5py: restrict python version based on import bugs (#35166)
```
  File ".../spack/var/spack/environments/scale-mpi/.spack-env/._view/4yiorsdd4pefrnwgrwlwt3yzo5i235il/lib/python3.10/site-packages/h5py/_hl/base.py", line 19, in <module>
     from collections import (Mapping, MutableMapping, KeysView,
ImportError: cannot import name 'Mapping' from 'collections' (.../spack/var/spack/environments/scale-mpi/.spack-env/._view/4yiorsdd4pefrnwgrwlwt3yzo5i235il/lib/python3.10/collections/__init__.py)
```

Fixed in https://github.com/h5py/h5py/pull/1069 which was first merged
in v2.9.
2023-01-26 07:28:39 +01:00
Matthew Thompson
af3dba8db6 Update gftl, gftl-shared, fargparse, pfunit, yafyaml, pflogger (#35119) 2023-01-26 07:06:05 +01:00
eugeneswalker
08a24b5e03 trilinos@14: conflicts with cxxstd=14 (#35164) 2023-01-25 20:33:44 -08:00
Adam J. Stewart
65fbc5a461 py-sphobjinv: add v2.3.1 (#35044) 2023-01-25 14:09:00 -08:00
Adam J. Stewart
80f3888cc8 py-pytorch-lightning: add +extra variant (#35121)
* py-pytorch-lightning: add +extra variant

* Update dependencies

* py-fsspec: add v2023.1.0
2023-01-25 15:58:26 -06:00
Christopher Christofi
5845750a10 perl-math-symbolic: add 0.612 (#35145) 2023-01-25 13:25:49 -08:00
Michael Kuhn
c529a0fddf qperf: add verbs support (#35147) 2023-01-25 13:20:55 -08:00
Adam J. Stewart
d7265d7ddc py-cligj: add v0.7.2 (#35149) 2023-01-25 13:17:20 -08:00
Adam J. Stewart
df0be87ada py-pycocotools: add v2.0.6 (#35150) 2023-01-25 13:14:21 -08:00
Adam J. Stewart
af2aeb275f py-scikit-learn: add v1.2.1 (#35152) 2023-01-25 13:10:57 -08:00
Richard Berger
4fef0bac20 spiner: add v1.6.0 (#35154) 2023-01-25 13:08:16 -08:00
Loïc Pottier
b32a07bbe1 amqp-cpp: added RabbitMQ C++ API (#35156)
Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
2023-01-25 13:05:32 -08:00
Sebastian Ehlert
8709dbc232 Add Orca version 5.0.3-f.1 (#35157) 2023-01-25 12:18:46 -08:00
Christopher Christofi
54b9e3ce07 py-colorlover: new package with version 0.3.0 (#35144) 2023-01-25 11:36:43 -06:00
Sebastian Ehlert
d35c24a3ed Add packages for scine modules (#34969)
* Add packages for scine modules

- lbfgspp (dependency for scine-utilities)
- scine-core
- scine-utilities and py-scine-utilities (virtual)
- scine-readuct and py-scine-readuct (virtual)
- scine-sparrow and py-scine-sparrow (virtual)
- scine-database and py-scine-database (virtual)
- scine-molassembler and py-scine-molassembler (virtual)
- scine-xtb and py-scine-xtb (virtual)
- py-scine-chemoton
- py-scine-puffin

* Fix line-length for flake8

* Remove virtual dependencies

* Update detection of boost, minor fixes in packages / dependencies

* Correctly declare build-only dependencies, add git versions

* Add sparrow dummy packages, fix dependencies

* Rename latest version from develop to master

* Restore original sparrow package

* Also rename latest version for chemoton and puffin
2023-01-25 11:33:37 -06:00
Matthias Wolf
d4d200952e py-flatten-dict: require poetry to build. (#35122)
* py-flatten-dict: require poetry to build.

The sources seem to contain a bundled, auto-generated `setup.py`.
Building with `pip` insist on using Poetry as mentioned in
`pyproject.toml`, so require it as a build dependency.

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

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

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-25 11:33:04 -06:00
Erik Heeren
902a40bf72 py-lazy: add 1.4 and 1.5 (#35124)
* py-lazy: add 1.4 and 1.5

* py-lazy: add url_for_version
2023-01-25 11:24:50 -06:00
Thomas Bouvier
a2d51cd4db Add package py-continuum (#35082)
* Add package `py-continuum`

* `py-continuum`: missing `py-pytest-mock` dependency

* `py-continuum`: add missing python dependency

* [@spackbot] updating style on behalf of thomas-bouvier

* Patch to remove useless `prospector` package

* Link to original PR

Co-authored-by: thomas-bouvier <thomas-bouvier@users.noreply.github.com>
2023-01-25 11:23:35 -06:00
Erik Heeren
f8e433689a py-pyspark: new versions (#35129)
* py-pyspark: new versions

* py-py4j: new versions

* py-py4j: more style

* py-py4j: even more style

* py-spark, py4j: review remarks
2023-01-25 11:22:43 -06:00
Harmen Stoppels
5f8c09fd33 Print file summary on checksum validation failure (#35161)
Currently we print "sha256 checksum failed for [file]. Expected X but
got Y".

This PR extends that message with file size and contents info:

"... but got Y. File size = 123456 bytes. Contents = b'abc...def'"

That way we can immediately see if the file was downloaded only
partially, or if we downloaded a text page instead of a binary, etc.

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-01-25 15:02:41 +00:00
Harmen Stoppels
8eb4807615 libxc: 6.1.0 (#35159)
Currently 6.0.0 fails on develop about incorrect shasum, but I can't
reproduce; maybe the download was temporarily unavailable.
2023-01-25 14:12:59 +01:00
Rocco Meli
047a481e48 Update COSTA package (#35137) 2023-01-25 12:01:46 +01:00
Gilles Gouaillardet
051abfb894 py-scipy: do not build 1.6 and older with python < 3.10.1 (#35120)
py-scipy 1.6 and older come with pre cython-ized files that
use the _PyGen_Send symbol that was removed from python 3.10.0.161,
so do not build these old versions with python 3.10.1 and later
2023-01-24 18:32:21 -08:00
eugeneswalker
0447ba1213 loki%gcc@11: -std=c++14 to avoid issue #32122 (#35148) 2023-01-24 17:42:33 -08:00
Rémi Lacroix
ff3dbe9394 LAMMPS: Add package ml-hdnnp. (#35133)
First added as user-hdnnp in version 20210527.
2023-01-24 17:15:23 -08:00
Thomas Bouvier
90d00f8a59 Add package py-nvidia-dali (#35058)
* Add package `py-nvidia-dali`

* Add linux check

* Add missing deps
2023-01-24 18:26:04 -06:00
Taillefumier Mathieu
fdc6bd3f1c Fix dbcsr checksums (#35134) 2023-01-24 22:33:12 +01:00
Cory Bloor
d17aaf8729 hip: add cuda variant (#33872) 2023-01-24 22:30:58 +01:00
Jen Herting
ef6699b874 New package: srcml (#35097)
* Initial srcml
* [srcml]
  - Fixed dependencies likely will need some more rework
  - Disabling packaging cmake file (for now)
  - Added patch to fix issue with source code library import
* [srcml] updated copyright
* [srcml] requires antlr complied with -fPIC
* [srcml] cleaned up dependencies
* [srcml] flake8
* [srcml] limiting boost versions

Co-authored-by: Benjamin Meyers <bsmits@rit.edu>
Co-authored-by: qwertos <qwertos@users.noreply.github.com>
2023-01-24 13:13:56 -08:00
Adam J. Stewart
f5418ac344 py-planetary-computer: add new package (#35089) 2023-01-24 10:25:29 -08:00
Mikael Simberg
909a5b1d83 Add whip 0.1.0 and use in pika (#35073)
* Add whip 0.1.0
* Make pika depend on whip@0.1.0

Co-authored-by: msimberg <msimberg@users.noreply.github.com>
2023-01-24 10:20:10 -08:00
Emil Briggs
9a0884bfed rmgdft: Update for version 5.0.1 (#35047)
* Updated for RMG version 5.0.1
* Update var/spack/repos/builtin/packages/rmgdft/package.py

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-01-24 10:18:05 -08:00
Seth R. Johnson
a9d5db572c ForTrilinos: new version 2.2.0 (#35138) 2023-01-24 09:52:45 -08:00
Harmen Stoppels
16dbbb9b26 libgcrypt: make sure flags go through env (#35135)
Parts of libgcrypt should not be optimized with -O1/2/3, so it's best to
let the build system do that; the build system cannot know the compiler
wrapper would inject optimization flags
2023-01-24 09:47:33 -08:00
John W. Parent
3695200a3c hdf5: remove direct dependency on msmpi on Windows (#35111) 2023-01-24 07:57:40 -08:00
Matthieu Dorier
a1b2ba412b mochi-margo: add v0.12 (#35132) 2023-01-24 16:46:27 +01:00
John W. Parent
c81f1235a9 Windows: conflict with Apple-GL (#35114) 2023-01-24 16:41:30 +01:00
Taillefumier Mathieu
eaa16338de Update dbcsr version (#35131) 2023-01-24 15:38:49 +01:00
Massimiliano Culpo
115b6b2a51 Avoid creating help.sh and test.sh in cwd (#35123)
When running unit-test the test/ci.py module is leaving
garbage (help.sh, test.sh files) in the current working
directory.

This commit changes the current working directory to a
temporary path before those files are created.
2023-01-24 03:42:15 -08:00
kwryankrattiger
cd2d6a6397 ParaView/VTK: Patch xdmf2 for HDF5 1.13 (#33930)
* ParaView/VTK: Patch xdmf2 for HDF5 1.13

* Meson: update meson build system for 0.64

* ParaView: Change HDF5 1.13 patch to 1.13.1/2 patchs

* Mesa: Remove legacy mesa option from meson_args

* Use append to assemble meson args
2023-01-23 19:22:21 -08:00
Erik Schnetter
c5086a5d0e curl: New version 7.87.0 (#35088) 2023-01-23 19:02:31 -08:00
downloadico
b5fc217dc2 actually add samtools 1.16.1 and fix Copyright dates on samtools, bcftools, and htslib (#35118)
* samtools: add version 1.16.1 (for real this time!)
also, fix Copyright date

* bcftools and htslib: fix Copyright date
2023-01-23 17:37:40 -08:00
Richarda Butler
a4b8753456 Update: spack help --spec (#35115)
* Update variant & compiler propagation
* Add the info for non boolean variants
* Add example for multi variants
2023-01-24 00:42:08 +00:00
Jean-Luc Fattebert
f3e7669400 Update qmd-progress package.py (#34841) 2023-01-23 14:20:19 -08:00
HELICS-bot
042d305ed0 helics: Add version 3.4.0 (#35096)
Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
2023-01-23 13:56:19 -08:00
Rémi Lacroix
aca4be1fff n2p2: Allow building shared libraries (#35080) 2023-01-23 13:46:19 -08:00
Alex Richert
beba33b2d8 Update parallelio from NOAA-EMC fork (#34837) 2023-01-23 22:29:06 +01:00
Wouter Deconinck
0f2e0a01a9 freeimage: fails to compile with c++17, use c++14 (#35067)
* freeimage: fails to compile with c++17, use c++14
  Only `opencascade` when a (non-default) variant depends on `freeimage`, which seems to have gone unmaintained. There are c++17 standard violations [[1]]( https://en.cppreference.com/w/cpp/language/except_spec) in the code, so we can at most expect c++14. Since some compilers default to c++17 (gcc-12) we need to be explicit.
* freeimage: install directly in prefix
* freeimage: fix inverted patch
2023-01-23 12:14:19 -08:00
downloadico
c2d68975bc update Samtools, bcftools, and htslib versions (#35043)
* samtools: add version 1.6.1
* htslib: update version to 1.6
* bcftools: update version to 1.6
2023-01-23 12:13:05 -08:00
Christopher Christofi
b9e196e40c perl-test-leaktrace: add 0.17 (#35063) 2023-01-23 10:58:08 -08:00
Jen Herting
a7fbe60660 [antlr] added pic variant (#35091)
* [antlr] modernize config arg processing
* [antlr] added pic variant
* [antlr] flake8
2023-01-23 10:52:23 -08:00
Mark W. Krentel
64b373e156 hpcviewer: add version 2023.01 (#35036) 2023-01-23 10:26:54 -08:00
Harmen Stoppels
13739e0783 environments: don't replace relative view path with absolute path on concretize/install (#34958)
* environments: don't rewrite relative view path, expand path on cli ahead of time

Currently if you have a spack.yaml that specifies a view by relative
path, Spack expands it to an absolute path on `spack -e . install` and
persists that to disk.

This is rather annoying when you have a `spack.yaml` file inside a git
repo, cause you want to use relative paths to make it relocatable, but
you constantly have to undo the changes made to spack.yaml by Spack.

So, as an alternative:

1. Always stick to paths as they are provided in spack.yaml, never
   replace them with a canonicalized version
2. Turn relative paths on the command line into absolute paths before
   storing to spack.yaml. This way you can do `spack env create --dir
   ./env --with-view ./view` and both `./env` and `./view` are resolved
   to the current working dir, as expected (not `./env/view`). This
   corresponds to the old behavior of `spack env create`.

* create --with-view always takes a value
2023-01-23 10:03:54 -08:00
Massimiliano Culpo
b8684008d0 apptainer: add v1.1.5 (#35075) 2023-01-23 09:53:10 -08:00
eugeneswalker
a82fe2010f e4s: add cusz +cuda (#35004) 2023-01-23 09:15:39 -08:00
Thomas Bouvier
3bd0d9a3d2 py-pytest-mock: add v3.10.0 (#35074) 2023-01-23 09:33:11 -06:00
Thomas Bouvier
fbc24d7bab py-datasets: add v2.8.0 (#35069)
* `py-datasets`: add v2.8.0

* Add missing +http variant + fix wrong dependency versions
2023-01-22 17:08:40 -06:00
eugeneswalker
4b91a40bdf axom: need to specify +rocm as part of dependency constraints (#35066)
* axom: need to specify +cuda, +rocm as part of dependency constraints

* remove lines 120, 128

* fix line length, spack style issue
2023-01-22 11:23:39 -08:00
Thomas Bouvier
b7a68938c2 arrow: don't use when as a keyword argument to filter_file() (#35065)
Co-authored-by: thomas-bouvier <thomas-bouvier@users.noreply.github.com>
2023-01-22 09:05:37 +01:00
Alex Richert
ce8727cece Add --exclude option to 'spack external find' (#35013)
* Add --exclude option to 'spack external find' to ignore user-specified external packages
* Update bash completion arg order for external find

Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2023-01-21 15:43:20 -08:00
Thomas Bouvier
da1165ffa3 py-wandb: add v0.13.9 (#35059)
* `py-wandb`: add v0.13.9

* `py-wandb`: mark v0.10.1 as deprecated

* Fixes suggested by @adamjstewart

* No platform-specific requirements
2023-01-21 17:21:41 -06:00
Dylan Simon
f593309b4e py-numba: fix py-numpy version dependencies (#35054)
as per #34362 comments
2023-01-21 07:17:53 -08:00
Harmen Stoppels
a15448eae8 gmake: bootstrap without make (#35050) 2023-01-21 02:27:56 -08:00
Matthew Thompson
cc01e33d53 fms: add 32bit variant, add protections (#35010)
The GEOS Earth System Model currently requires the 32-bit variant of FMS. This PR adds that variant.
2023-01-21 10:27:13 +01:00
markus-ferrell
c3e3c392a6 Windows/testing: enable tests for "spack find" (#33588) 2023-01-20 17:54:06 -08:00
John W. Parent
a424f7f173 Identify Windows support with tags (#35027)
All packages with explicit Windows support can be found with
`spack list --tags=windows`.

This also removes the documentation which explicitly lists
supported packages on Windows (which is currently out of date and
is now unnecessary with the added tags).

Note that if a package does not appear in this list, it *may*
still build on Windows, but it likely means that no explicit
attempt has been made to support it.
2023-01-20 13:32:28 -08:00
QuellynSnead
d192dab5a1 netlib-lapack: Fix Fortran detection for XL (#35048)
* PR 30738 introduced changes in how we access compiler info. Looks like the XL case
got missed.
2023-01-20 13:13:39 -08:00
Harmen Stoppels
aa91358cc2 libbsd: bump (#35029) 2023-01-20 11:48:57 -08:00
Thomas Bouvier
bdc0b73b7a Add package py-imagehash (#35015)
* Add package `py-imagehash`

* Use virtual package for `py-pillow`
2023-01-20 10:28:04 -08:00
eugeneswalker
62f83dfb6d flex%oneapi@2023.0.0: -Wno-error=implicit-function-declaration (#34900) 2023-01-20 10:18:13 -08:00
Zack Galbreath
91fd6d5a84 Allocate more memory for generate jobs in all stacks (#35040)
* Allocate more memory for generate jobs in all stacks
* Add a 60 minute timeout on generate jobs
2023-01-20 11:06:49 -07:00
Harmen Stoppels
a14b5de43c ca-certificates-mozilla: 2023-01-10 (#35018) 2023-01-20 09:52:47 -08:00
Harmen Stoppels
5fde84d0cb libiconv: bump (#35035) 2023-01-20 08:37:48 -08:00
Harmen Stoppels
434a3d02ac ncurses: bump (#35033) 2023-01-20 08:07:43 -08:00
Harmen Stoppels
cb213ae9af sqlite: bump (#35032) 2023-01-20 06:52:40 -08:00
eugeneswalker
3e2721ac7f hypre: add option for sycl variant (#34987)
* hypre: add option for sycl variant

* hypre +sycl conflicts with @:2.23

* hypre +sycl: raise InstallError for unsupported compiler
2023-01-20 05:43:05 -08:00
Marco De La Pierre
f2f3d03d00 Add nf-core-tools, and three remainder deps (#34466)
* nextflow recipe: added latest stable version

* tower-cli recipe: added latest release

* recipes tower-agent and tower-cli renamed to nf-tower-agent and nf-tower-cli

* recipes nf-tower-agent and nf-tower-cli: small fix

* nf-core-tools recipe: added most py- dependencies

* nf-core-tools: recipe without galaxy-tool-util (for testing)

* fixed typos in py-yacman recipe

* fixed typos in py-pytest-workflow recipe

* fixed typo in nf-core-tools recipe

* fixed typos in py-yacman recipe

* fixes in recipes for py-questionary and py-url-normalize

* fixes to py-yacman recipe

* style fixes to py- packages that are dependencies to nf-core-tools

* fix in py-requests-cache recipe

* added missing dep in py-requests-cache recipe

* nf-core-tools deps: removed redundant python dep for py packages oyaml and piper

* nf-core-tools recipe: final, incl dep on py-galaxy-tool-util

* nf-core-tools: new version with extra dependency

* added py-galaxy-util, draft: added some required dep versions, still have to add 40+ deps

* nextflow and nf-core-tools packages: added my self as maintainer

* style fixes

* style fix for nf-core-tools recipe

* added license to py-logmuse recipe

* audit fixes

* style fix after audit fix

* py-galaxy-tool-util: added deps 1st bunch

* audit/style fixes, including adding missing dep package

* more audit/style fixes

* more more audit/style fixes

* moooore audit fixes

* py-galaxy-tool-util: dependencies 2nd chunk

* silly audit fix

* py-galaxy-util deps: 3rd bunch - first 20 done

* fixes

* style fix

* py-galaxy-tool-util: 4th bunch of deps

* stashing dep recipe backbones for py-galaxy-tool-util

* nf-core-tools: using pre-built wheel for dependency py-galaxy-tool-util

* nf-core-tools: adding also py-galaxy-util, as wheel

* fix

* nextflow: added latest bugfix version

* Update var/spack/repos/builtin/packages/nf-core-tools/package.py

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

* Update var/spack/repos/builtin/packages/nf-core-tools/package.py

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

* nf-core-tools pr: 1st bunch of review edits

* nf-core-tools: 2nd bunch of review edits

* adding back tower-agent and tower-cli as deprecated

* nf-core-tools: 3rd bunch of review edits

* small style fix

* prepping py-galaxy-tool-util for further work

* nf-core-tools: last bunch of deps, except for galaxy-tool-util and pulsar

* audit fixes

* updates to py-galaxy-tool-util and its deps, still 2 to work on

* one style fix

* updated recipe for py-galaxy-util

* updated recipe for py-pulsar-galaxy-lib

* typo fix

* shasum fixes

* updated py-sqlalchemy from develop

* added newest versions (today) for nf-tower-agent and nf-tower-cli

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

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

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

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

* adding 2nd bunch of nf-core deps from update/nextflow-tools

* adding 3rd bunch of nf-core deps from update/nextflow-tools

* 4th chunk of nf-core deps from update/nextflow-tools

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

* py-gxformat2: added comment

* py-lagom: now using github tarballs

* fix for py-lagom

* adding missing deps to py-fastapi-utils

* another fix to py-lagom

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

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

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

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

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

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

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

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

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

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

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

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

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

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

* fixes from PR review

* adding missing deps, from PR review

* py-galaxy2cwl from github tarball, as per PR review

* fix to py-tuswsgi, as per PR review

* nf-tools: edits from PR review

* adding 3x more galaxy deps

* fix

* fixing circular dep of py-poetry-plugin-export with py-poetry

* added newest nf-core-tools version

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

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

* fix in py-poetry-plugin-export

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-01-20 04:05:26 -08:00
Harmen Stoppels
2a55a9ef80 file: zstd support (#35041) 2023-01-20 09:54:19 +01:00
Massimiliano Culpo
8f8394a829 Add type hints to DependencySpec (#35021)
* DependencySpec: add type hints

* DependencySpec: make deptypes a keyword only argument
2023-01-20 09:53:57 +01:00
Harmen Stoppels
fb7c8d1768 libidn2: bump (#35034) 2023-01-20 00:28:45 -08:00
Harmen Stoppels
6a6181f07a libffi: bump (#35030) 2023-01-19 22:58:39 -08:00
Tal Ben-Nun
c6b98cea07 Fix string append in OpenCV package (#35008)
* Fix string append in OpenCV package

* style
2023-01-19 18:36:09 -08:00
Annop Wongwathanarat
a1b0213fcb qmcpack: enable linking with armpl-gcc and acfl for BLAS and FFT (#34496) 2023-01-19 18:09:12 -08:00
eugeneswalker
6713f7feda e4s: ecp-data-vis-sdk +rocm: remove redundant amdgpu_target specification (#35022) 2023-01-20 00:18:41 +00:00
Harmen Stoppels
cdd2010a76 libunistring: bump to 1.1 (#35031) 2023-01-19 14:38:03 -08:00
Adam J. Stewart
a15b77bdf6 py-pandas: add v1.5.3 (#35025) 2023-01-19 13:45:45 -08:00
David Zmick
b40e96b006 nmap: don't depend on py2 (ndiff and zenmap); add 7.93 (#34851)
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-01-19 19:50:53 +01:00
Harmen Stoppels
c97f5ecfee file: bump (#35028) 2023-01-19 11:29:15 -07:00
Matthew Thompson
d35a91f776 pfunit: fix max_array_rank variant (#34952)f 2023-01-19 18:49:42 +01:00
Brian Van Essen
939b749726 HDF5: supports external detection (#34940) 2023-01-19 08:44:00 -08:00
Harmen Stoppels
80db7a8a52 buildcache create: make "file exists" less verbose (#35019)
Currently we print 3 lines of "file exist" warning per tarball, this is
a bit excessive. Instead, it can be a simple single-line tty.warn
message.
2023-01-19 15:35:24 +00:00
Todd Gamblin
d0c1b7a14e python: remove CPATH from setup_run_environment (#34727)
Currently, the `python` package tries to set `CPATH` in `setup_run_environment()`.

We no longer set `CPATH` and other destructive environment variables (like
`LD_LIBRARY_PATH`) in modules, so we shouldn't do something special for Python.

Also, the way `python` sets `CPATH` causes issues. Because it does a header search to
find directories containing headers, if you bootstrap `mypy` or other style tools on a
fresh Ubuntu image with *no* python devel headers installed, you'll get an error like
this when trying to load the thing you just installed:

```console
[root@980de539843d /]# spack -b load py-mypy
==> Error: Unable to locate python headers in any of these locations:
/usr/include/python3.6m
/usr/include/3.6
/usr/Headers
```

The headers and includes aren't needed to get `mypy` in the path or for `mypy` to work,
so we're failing unnecessarily here.

- [x] remove `setup_run_environment()` from `python/package.py`
2023-01-19 07:08:39 -08:00
Stephen Sachs
45ea7c19e5 [py-numpy, py-scipy] Enable MKL & ARMpl (#34979) 2023-01-19 08:01:31 -07:00
Harmen Stoppels
a357a39963 depfile: --make-target-prefix -> --make-prefix (#35009)
Since SPACK_PACKAGE_IDS is now also "namespaced" with <prefix>, it makes
more sense to call the flag `--make-prefix` and alias the old flag
`--make-target-prefix` to it.
2023-01-19 14:58:34 +01:00
Harmen Stoppels
a7613407df git: bump. CVE-2022-41903 / CVE-2022-23521 (#35014)
Co-Authored-By: Alec Scott <scott112@llnl.gov>

Co-authored-by: Alec Scott <scott112@llnl.gov>
2023-01-19 14:57:28 +01:00
Mark W. Krentel
0cdb7ccdd3 hpctoolkit: update cray support (#34995)
1. add variant cray-static, older crays build hpcprof-mpi static,
   newer ones build dynamic.

2. move URL patches from github to gitlab.

3. add workaround for a bug where a file is mistakenly overwritten.

4. add conflict for hpcprof-mpi at 2022.10.01.

* [@spackbot] updating style on behalf of mwkrentel

Co-authored-by: mwkrentel <mwkrentel@users.noreply.github.com>
2023-01-18 23:23:09 -08:00
eugeneswalker
fed4eb2526 e4s ci: clean up unnecessary constraints (#35006) 2023-01-18 21:23:15 -08:00
eugeneswalker
1bf1c7de76 e4s: add sz3 (#35007) 2023-01-18 22:21:30 -06:00
eugeneswalker
ae5408de9a e4s ci: add veloc (#35003) 2023-01-18 16:48:23 -08:00
Adam J. Stewart
d0f5a62a7d VTK: fix 9.1–9.2 builds (#34589)
* VTK: add missing dependencies

* Deal with missing verdict dep

* http -> https

* Add patch to fix failing cmake

* Update netcdf-cxx usage in build recipe

* netcdf-cxx4 doesn't work
2023-01-18 17:29:29 -06:00
Greg Becker
08101639cd Bugfix: External Python Extensions (#34202)
Normally when using external packages in concretization, Spack ignores
all dependencies of the external. #33777 updated this logic to attach
a Python Spec to external Python extensions (most py-* packages), but
as implemented there were a couple issues:

* this did not account for concretization groups and could generate
  multiple different python specs for a single DAG
* in some cases this created a fake Python spec with insufficient
  details to be usable (concretization/installation of the
  extension would fail)

This PR addresses both of these issues: 

* For environment specs that are concretized together, external python
  extensions in those specs will all be assigned the same Python spec
* If Spack needs to "invent" a Python spec, then it will have all the
  needed details (e.g. compiler/architecture)
2023-01-18 15:17:28 -08:00
Harmen Stoppels
fce95e2efb license year bump (#34921)
* license bump year
* fix black issues of modified files
* mypy
* fix 2021 -> 2023
2023-01-18 14:30:17 -08:00
eugeneswalker
e391edf2f5 hdf5@1.8.21 %oneapi@2023.0.0: -Wno-error=int-conversion (#34983) 2023-01-18 12:23:00 -08:00
Todd Gamblin
c9e85ada15 npm: Add latest version, update build (#34947)
* npm: Add latest version, update build

The `npm` package had gotten a bit long in the tooth and only suported the last version
for which running `configure` / `make` / `make install` actually worked.

- [x] Update the package to support npm@9, in which `npm install .` works properly and
  installation is easier.

- [x] Update the package so that `npm@6:8` also install successfullly. The incantation
  that is *supposed* to work on these versions is `node bin/npm-cli.js install $(node
  bin/npm-cli.js pack . | tail -1)`, but depending on the version one of `npm install`
  or `npm pack` will fail when run straight from the install directory. So now we just
  manually copies things over.

This seems to make the `npm` install much more reliable for all of `npm@6:9` (at least
for me).

udpates the `npm` build to support versions 6-9 and fixes the install for all of
them on macos.

* update for review
2023-01-18 14:18:33 -06:00
eugeneswalker
8eb803ab4c e4s: add py-h5py ~mpi variant (#34998) 2023-01-18 19:28:47 +00:00
Annop Wongwathanarat
ee3529fc10 lammps: enable linking with armpl-gcc FFT (#34980) 2023-01-18 11:25:41 -08:00
Harmen Stoppels
f050b1cf78 depfile: variable with all identifiers (#34678)
With the new variable [prefix/]SPACK_PACKAGE_IDS you can conveniently execute
things after each successful install.

For example push just-built packages to a buildcache

```
SPACK ?= spack
export SPACK_COLOR = always
MAKEFLAGS += -Orecurse
MY_BUILDCACHE := $(CURDIR)/cache

.PHONY: all clean

all: push

ifeq (,$(filter clean,$(MAKECMDGOALS)))
include env.mk
endif

# the relevant part: push has *all* example/push/<pkg identifier> as prereqs
push: $(addprefix example/push/,$(example/SPACK_PACKAGE_IDS))
	$(SPACK) -e . buildcache update-index --directory $(MY_BUILDCACHE)
	$(info Pushed everything, yay!)

# and each example/push/<pkg identifier> has the install target as prereq,
# and the body can use target local $(HASH) and $(SPEC) variables to do
# things, such as pushing to a build cache
example/push/%: example/install/%
	@mkdir -p $(dir $@)
	$(SPACK) -e . buildcache create --allow-root --only=package --unsigned --directory $(MY_BUILDCACHE) /$(HASH) # push $(SPEC)
	@touch $@

spack.lock: spack.yaml
	$(SPACK) -e . concretize -f

env.mk: spack.lock
	$(SPACK) -e . env depfile -o $@ --make-target-prefix example

clean:
	rm -rf spack.lock env.mk example/
``
2023-01-18 19:19:46 +01:00
Stephen Sachs
6cf32110b9 [armpl-gcc] Make pkg-config files available (#34978)
* [armpl-gcc] Make pkg-config files available
  ARMpl pkgconfig files are located in a non-default location and do not have the
  .pc extension. Changing those both helps pkgconfig pick them up correctly, e.g.
  in the meson build of `py-scipy`.
* Address @annop-w comments
* symlink instead of cp.

Co-authored-by: Stephen Sachs <stesachs@amazon.com>
2023-01-18 07:57:55 -08:00
psakiev
047110c086 Debug print statement 2023-01-11 05:37:29 -07:00
psakiev
7fa16089fc Add entry to tmpconfig 2023-01-11 04:46:42 -07:00
Philip Sakievich
065eaa739f Remove accidental bleed over trilinos change 2023-01-10 09:38:51 -07:00
psakiev
8d8e88c177 Try renaming dir 2023-01-09 16:24:14 -07:00
psakiev
8cc69cecfc Add function scope 2023-01-09 15:27:27 -07:00
psakiev
9c690a1ef5 Revert "Try something else"
This reverts commit 3532d6ff16.
2023-01-09 14:20:28 -07:00
psakiev
3532d6ff16 Try something else 2023-01-09 13:22:13 -07:00
psakiev
7494893d3b Drop the hidden dir 2023-01-09 12:46:59 -07:00
psakievich
54e4a72b8e Merge branch 'develop' into f/env-location 2023-01-07 22:23:23 -07:00
psakiev
b86980461f Modify failing test 2023-01-07 20:59:44 -07:00
psakiev
23b5932f73 Make hidden dir for mock env location 2022-12-21 14:56:52 -07:00
psakiev
93760847e8 Use tmpdir for all mutable env paths 2022-12-19 21:18:37 -07:00
psakievich
a35d2f39af Merge branch 'develop' into f/env-location 2022-12-19 17:02:19 -07:00
psakiev
af17cc60a9 Add tmpdir 2022-12-19 16:13:01 -07:00
psakiev
b0528cae3f Improve robustness of env test in parallel 2022-12-19 16:07:34 -07:00
psakiev
372a18392a Add syntax for debugging CI 2022-12-19 13:54:45 -07:00
psakievich
70db49dfed Merge branch 'develop' into f/env-location 2022-12-19 13:50:43 -07:00
psakiev
1d24c196da Use proper import 2022-12-08 12:36:36 -07:00
psakievich
fa3d768947 Update lib/spack/spack/environment/environment.py 2022-12-08 12:34:57 -07:00
psakiev
9b6a109c7e Remove constraint on environments_root creation 2022-12-07 22:24:18 -07:00
psakievich
663967d984 Merge branch 'develop' into f/env-location 2022-12-07 15:03:51 -07:00
psakiev
b47ff2a2de Fix missing function 2022-12-07 14:32:36 -07:00
psakiev
f7b4993810 Address reviewer comments 2022-12-07 14:25:12 -07:00
psakiev
3e07eb8cf0 Fix scope detection issue 2022-12-01 22:21:10 -07:00
psakievich
e773396747 Merge branch 'develop' into f/env-location 2022-12-01 17:00:36 -07:00
psakiev
e19cc2385e Don't automatically create the default env path 2022-12-01 16:50:24 -07:00
psakievich
e867662e1b Merge branch 'develop' into f/env-location 2022-11-09 17:19:41 -07:00
psakiev
6aad926838 Fix unicode error 2022-11-09 15:50:16 -07:00
psakievich
41cf807804 Merge branch 'develop' into f/env-location 2022-11-09 15:09:22 -07:00
psakiev
cf8b919954 Remove accidental changes to bin/sbang 2022-11-09 13:39:56 -07:00
psakiev
47957dccf4 Remove shell driven command from env activation test 2022-11-09 13:19:17 -07:00
Philip Sakievich
38313cadf4 Revert "avoid using realpath, readlink -f is more portable"
This reverts commit 2cae95334c.
2022-11-08 23:40:03 -07:00
Philip Sakievich
730d005a56 Only create default path when used 2022-11-08 23:39:03 -07:00
psakiev
2f7c850a20 style 2022-11-08 23:08:19 -07:00
psakiev
5aa7a564d3 Why do we have mutliple cod paths for env activation? 2022-11-08 22:59:29 -07:00
psakiev
d50c8f1727 Add guard-rail and unit-test (not working) 2022-11-08 22:41:09 -07:00
psakievich
0ac6dfa8f3 Merge branch 'develop' into f/env-location 2022-10-12 08:45:01 -06:00
Philip Sakievich
0b0ffe645d Ugh python 2 🤦‍♂️ 2022-10-11 22:37:57 -06:00
Philip Sakievich
9984c838c8 Fix failing shell tests 2022-10-11 22:18:43 -06:00
psakievich
b1bd61321d Merge branch 'develop' into f/env-location 2022-10-11 21:53:49 -06:00
psakievich
c144558245 Merge branch 'develop' into f/env-location 2022-09-29 11:50:06 -06:00
psakiev
ef43044672 Change name of variable 2022-09-27 22:17:29 -06:00
psakievich
da7294cd90 Update lib/spack/spack/test/config.py
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-09-27 21:08:32 -06:00
psakievich
addb891f42 Update lib/spack/docs/environments.rst
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-09-27 21:08:25 -06:00
psakievich
bce2d38bfc Merge branch 'develop' into f/env-location 2022-09-27 14:40:57 -06:00
Tom Scogland
2cae95334c avoid using realpath, readlink -f is more portable 2022-09-27 18:33:52 +00:00
psakiev
076d60ce35 Add check that env_root dir exists 2022-09-27 12:02:43 -06:00
psakiev
9ecdafd8de Add some documentation 2022-09-27 11:25:31 -06:00
psakievich
76fde639e8 Update lib/spack/spack/environment/environment.py
Co-authored-by: Greg Becker <becker33@llnl.gov>

Add back path canonicalization
2022-09-27 11:17:47 -06:00
psakiev
490b5eef7c Rework path access strategy 2022-09-27 10:57:28 -06:00
psakiev
3f2e77e5fa Allow users to specify root env dir
Environments managed by spack have some advantages over anonymous Environments
but they are tucked away inside spack's directory tree. This PR gives
users the ability to specify where the environments should live.

See #32823
2022-09-26 22:31:29 -06:00
7885 changed files with 19552 additions and 11716 deletions

View File

@@ -89,7 +89,7 @@ jobs:
uses: docker/setup-qemu-action@e81a89b1732b9c48d79cd809d8d81d79c4647a18 # @v1
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@8c0edbc76e98fa90f69d9a2c020dcb50019dc325 # @v1
uses: docker/setup-buildx-action@f03ac48505955848960e80bbb68046aa35c7b9e7 # @v1
- name: Log in to GitHub Container Registry
uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a # @v1
@@ -106,7 +106,7 @@ jobs:
password: ${{ secrets.DOCKERHUB_TOKEN }}
- name: Build & Deploy ${{ matrix.dockerfile[0] }}
uses: docker/build-push-action@37abcedcc1da61a57767b7588cb9d03eb57e28b3 # @v2
uses: docker/build-push-action@3b5e8027fcad23fda98b2e3ac259d8d67585f671 # @v2
with:
context: dockerfiles/${{ matrix.dockerfile[0] }}
platforms: ${{ matrix.dockerfile[1] }}

View File

@@ -44,7 +44,7 @@ jobs:
cache: 'pip'
- name: Install Python packages
run: |
python3 -m pip install --upgrade pip six setuptools types-six black mypy isort clingo flake8
python3 -m pip install --upgrade pip six setuptools types-six black==22.12.0 mypy isort clingo flake8
- name: Setup git configuration
run: |
# Need this for the git tests to succeed.

View File

@@ -1,6 +1,6 @@
MIT License
Copyright (c) 2013-2022 LLNS, LLC and other Spack Project Developers.
Copyright (c) 2013-2023 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

@@ -1,4 +1,4 @@
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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

@@ -1,6 +1,6 @@
#!/bin/sh
#
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
# sbang project developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)

View File

@@ -1,7 +1,7 @@
#!/bin/sh
# -*- python -*-
#
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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

@@ -1,6 +1,6 @@
#!/bin/sh
#
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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

@@ -72,6 +72,7 @@ config:
root: $TMP_DIR/install
misc_cache: $$user_cache_path/cache
source_cache: $$user_cache_path/source
environments_root: $TMP_DIR/envs
EOF
cat >"$SPACK_USER_CONFIG_PATH/bootstrap.yaml" <<EOF
bootstrap:

View File

@@ -1,4 +1,4 @@
:: Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
:: Copyright 2013-2023 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)
@@ -83,6 +83,16 @@ if defined _sp_flags (
exit /B 0
)
)
if not defined _sp_subcommand (
if not defined _sp_args (
if not defined _sp_flags (
python "%spack%" --help
exit /B 0
)
)
)
:: pass parsed variables outside of local scope. Need to do
:: this because delayedexpansion can only be set by setlocal
echo %_sp_flags%>flags
@@ -92,24 +102,24 @@ endlocal
set /p _sp_subcommand=<subcmd
set /p _sp_flags=<flags
set /p _sp_args=<args
set str_subcommand=%_sp_subcommand:"='%
set str_flags=%_sp_flags:"='%
set str_args=%_sp_args:"='%
if "%str_subcommand%"=="ECHO is off." (set "_sp_subcommand=")
if "%str_flags%"=="ECHO is off." (set "_sp_flags=")
if "%str_args%"=="ECHO is off." (set "_sp_args=")
if "%_sp_subcommand%"=="ECHO is off." (set "_sp_subcommand=")
if "%_sp_subcommand%"=="ECHO is on." (set "_sp_subcommand=")
if "%_sp_flags%"=="ECHO is off." (set "_sp_flags=")
if "%_sp_flags%"=="ECHO is on." (set "_sp_flags=")
if "%_sp_args%"=="ECHO is off." (set "_sp_args=")
if "%_sp_args%"=="ECHO is on." (set "_sp_args=")
del subcmd
del flags
del args
:: Filter out some commands. For any others, just run the command.
if "%_sp_subcommand%" == "cd" (
if %_sp_subcommand% == "cd" (
goto :case_cd
) else if "%_sp_subcommand%" == "env" (
) else if %_sp_subcommand% == "env" (
goto :case_env
) else if "%_sp_subcommand%" == "load" (
) else if %_sp_subcommand% == "load" (
goto :case_load
) else if "%_sp_subcommand%" == "unload" (
) else if %_sp_subcommand% == "unload" (
goto :case_load
) else (
goto :default_case
@@ -143,19 +153,21 @@ goto :end_switch
:: If no args or args contain --bat or -h/--help: just execute.
if NOT defined _sp_args (
goto :default_case
)else if NOT "%_sp_args%"=="%_sp_args:--help=%" (
)
set args_no_quote=%_sp_args:"=%
if NOT "%args_no_quote%"=="%args_no_quote:--help=%" (
goto :default_case
) else if NOT "%_sp_args%"=="%_sp_args: -h=%" (
) else if NOT "%args_no_quote%"=="%args_no_quote: -h=%" (
goto :default_case
) else if NOT "%_sp_args%"=="%_sp_args:--bat=%" (
) else if NOT "%args_no_quote%"=="%args_no_quote:--bat=%" (
goto :default_case
) else if NOT "%_sp_args%"=="%_sp_args:deactivate=%" (
) else if NOT "%args_no_quote%"=="%args_no_quote:deactivate=%" (
for /f "tokens=* USEBACKQ" %%I in (
`call python "%spack%" %_sp_flags% env deactivate --bat %_sp_args:deactivate=%`
`call python %spack% %_sp_flags% env deactivate --bat %args_no_quote:deactivate=%`
) do %%I
) else if NOT "%_sp_args%"=="%_sp_args:activate=%" (
) else if NOT "%args_no_quote%"=="%args_no_quote:activate=%" (
for /f "tokens=* USEBACKQ" %%I in (
`call python "%spack%" %_sp_flags% env activate --bat %_sp_args:activate=%`
`python %spack% %_sp_flags% env activate --bat %args_no_quote:activate=%`
) do %%I
) else (
goto :default_case
@@ -220,4 +232,4 @@ for %%I in (%~2) do (
:pathadd "%~1" "%%I\%%Z"
)
)
exit /B %ERRORLEVEL%
exit /B %ERRORLEVEL%

View File

@@ -1,4 +1,4 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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

@@ -81,6 +81,10 @@ config:
source_cache: $spack/var/spack/cache
## Directory where spack managed environments are created and stored
# environments_root: $spack/var/spack/environments
# Cache directory for miscellaneous files, like the package index.
# This can be purged with `spack clean --misc-cache`
misc_cache: $user_cache_path/cache

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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)
@@ -163,7 +163,7 @@ def setup(sphinx):
# General information about the project.
project = "Spack"
copyright = "2013-2021, Lawrence Livermore National Laboratory."
copyright = "2013-2023, Lawrence Livermore National Laboratory."
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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)
@@ -58,9 +58,9 @@ Using Environments
Here we follow a typical use case of creating, concretizing,
installing and loading an environment.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Creating a named Environment
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Creating a managed Environment
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
An environment is created by:
@@ -72,7 +72,8 @@ Spack then creates the directory ``var/spack/environments/myenv``.
.. note::
All named environments are stored in the ``var/spack/environments`` folder.
All managed environments by default are stored in the ``var/spack/environments`` folder.
This location can be changed by setting the ``environments_root`` variable in ``config.yaml``.
In the ``var/spack/environments/myenv`` directory, Spack creates the
file ``spack.yaml`` and the hidden directory ``.spack-env``.
@@ -1039,7 +1040,7 @@ gets installed and is available for use in the ``env`` target.
$(SPACK) -e . concretize -f
env.mk: spack.lock
$(SPACK) -e . env depfile -o $@ --make-target-prefix spack
$(SPACK) -e . env depfile -o $@ --make-prefix spack
env: spack/env
$(info Environment installed!)
@@ -1062,9 +1063,9 @@ the include is conditional.
.. note::
When including generated ``Makefile``\s, it is important to use
the ``--make-target-prefix`` flag and use the non-phony target
``<target-prefix>/env`` as prerequisite, instead of the phony target
``<target-prefix>/all``.
the ``--make-prefix`` flag and use the non-phony target
``<prefix>/env`` as prerequisite, instead of the phony target
``<prefix>/all``.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Building a subset of the environment
@@ -1089,4 +1090,52 @@ output (``spack install --verbose``) while its dependencies are installed silent
$ make -j16 install-deps/python-3.11.0-<hash> SPACK_INSTALL_FLAGS=--show-log-on-error
# Install the root spec with verbose output.
$ make -j16 install/python-3.11.0-<hash> SPACK_INSTALL_FLAGS=--verbose
$ make -j16 install/python-3.11.0-<hash> SPACK_INSTALL_FLAGS=--verbose
^^^^^^^^^^^^^^^^^^^^^^^^^
Adding post-install hooks
^^^^^^^^^^^^^^^^^^^^^^^^^
Another advanced use-case of generated ``Makefile``\s is running a post-install
command for each package. These "hooks" could be anything from printing a
post-install message, running tests, or pushing just-built binaries to a buildcache.
This can be accomplished through the generated ``[<prefix>/]SPACK_PACKAGE_IDS``
variable. Assuming we have an active and concrete environment, we generate the
associated ``Makefile`` with a prefix ``example``:
.. code:: console
$ spack env depfile -o env.mk --make-prefix example
And we now include it in a different ``Makefile``, in which we create a target
``example/push/%`` with ``%`` referring to a package identifier. This target
depends on the particular package installation. In this target we automatically
have the target-specific ``HASH`` and ``SPEC`` variables at our disposal. They
are respectively the spec hash (excluding leading ``/``), and a human-readable spec.
Finally, we have an entrypoint target ``push`` that will update the buildcache
index once every package is pushed. Note how this target uses the generated
``example/SPACK_PACKAGE_IDS`` variable to define its prerequisites.
.. code:: Makefile
SPACK ?= spack
BUILDCACHE_DIR = $(CURDIR)/tarballs
.PHONY: all
all: push
include env.mk
example/push/%: example/install/%
@mkdir -p $(dir $@)
$(info About to push $(SPEC) to a buildcache)
$(SPACK) -e . buildcache create --allow-root --only=package --directory $(BUILDCACHE_DIR) /$(HASH)
@touch $@
push: $(addprefix example/push/,$(example/SPACK_PACKAGE_IDS))
$(info Updating the buildcache index)
$(SPACK) -e . buildcache update-index --directory $(BUILDCACHE_DIR)
$(info Done!)
@touch $@

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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)
@@ -116,7 +116,7 @@ creates a simple python file:
# FIXME: Add a list of GitHub accounts to
# notify when the package is updated.
# maintainers = ["github_user1", "github_user2"]
# maintainers("github_user1", "github_user2")
version("0.8.13", sha256="591a9b4ec81c1f2042a97aa60564e0cb79d041c52faa7416acb38bc95bd2c76d")

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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)
@@ -1700,29 +1700,15 @@ If in the previous step, you did not have CMake or Ninja installed, running the
Windows Compatible Packages
"""""""""""""""""""""""""""
Many Spack packages are not currently compatible with Windows, due to Unix
dependencies or incompatible build tools like autoconf. Here are several
packages known to work on Windows:
* abseil-cpp
* bzip2
* clingo
* cpuinfo
* cmake
* hdf5
* glm
* nasm
* netlib-lapack (requires Intel Fortran)
* ninja
* openssl
* perl
* python
* ruby
* wrf
* zlib
Not all spack packages currently have Windows support. Some are inherently incompatible with the
platform, and others simply have yet to be ported. To view the current set of packages with Windows
support, the list command should be used via `spack list -t windows`. If there's a package you'd like
to install on Windows but is not in that list, feel free to reach out to request the port or contribute
the port yourself.
.. note::
This is by no means a comprehensive list
This is by no means a comprehensive list, some packages may have ports that were not tagged
while others may just work out of the box on Windows and have not been tagged as such.
^^^^^^^^^^^^^^
For developers
@@ -1734,3 +1720,4 @@ Instructions for creating the installer are at
https://github.com/spack/spack/blob/develop/lib/spack/spack/cmd/installer/README.md
Alternatively a pre-built copy of the Windows installer is available as an artifact of Spack's Windows CI
available at each run of the CI on develop or any PR.

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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)
@@ -234,7 +234,7 @@ generates a boilerplate template for your package, and opens up the new
.. code-block:: python
:linenos:
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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)
@@ -268,7 +268,7 @@ generates a boilerplate template for your package, and opens up the new
# FIXME: Add a list of GitHub accounts to
# notify when the package is updated.
# maintainers = ["github_user1", "github_user2"]
# maintainers("github_user1", "github_user2")
version("6.2.1", sha256="eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c")
@@ -319,14 +319,8 @@ The rest of the tasks you need to do are as follows:
#. Add a comma-separated list of maintainers.
The ``maintainers`` field is a list of GitHub accounts of people
who want to be notified any time the package is modified. When a
pull request is submitted that updates the package, these people
will be requested to review the PR. This is useful for developers
who maintain a Spack package for their own software, as well as
users who rely on a piece of software and want to ensure that the
package doesn't break. It also gives users a list of people to
contact for help when someone reports a build error with the package.
Add a list of Github accounts of people who want to be notified
any time the package is modified. See :ref:`package_maintainers`.
#. Add ``depends_on()`` calls for the package's dependencies.
@@ -497,6 +491,31 @@ some examples:
In general, you won't have to remember this naming convention because
:ref:`cmd-spack-create` and :ref:`cmd-spack-edit` handle the details for you.
.. _package_maintainers:
-----------
Maintainers
-----------
Each package in Spack may have one or more maintainers, i.e. one or more
GitHub accounts of people who want to be notified any time the package is
modified.
When a pull request is submitted that updates the package, these people will
be requested to review the PR. This is useful for developers who maintain a
Spack package for their own software, as well as users who rely on a piece of
software and want to ensure that the package doesn't break. It also gives users
a list of people to contact for help when someone reports a build error with
the package.
To add maintainers to a package, simply declare them with the ``maintainers`` directive:
.. code-block:: python
maintainers("user1", "user2")
The list of maintainers is additive, and includes all the accounts eventually declared in base classes.
-----------------
Trusted Downloads
-----------------

View File

@@ -1,4 +1,4 @@
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
.. Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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)

2
lib/spack/env/cc vendored
View File

@@ -1,7 +1,7 @@
#!/bin/sh -f
# shellcheck disable=SC2034 # evals in this script fool shellcheck
#
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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)
@@ -23,7 +23,7 @@
from llnl.util.lang import dedupe, memoized
from llnl.util.symlink import islink, symlink
from spack.util.executable import CommandNotFoundError, Executable, which
from spack.util.executable import Executable, which
from spack.util.path import path_to_os_path, system_path_filter
is_windows = _platform == "win32"
@@ -117,13 +117,7 @@ def path_contains_subdirectory(path, root):
@memoized
def file_command(*args):
"""Creates entry point to `file` system command with provided arguments"""
try:
file_cmd = which("file", required=True)
except CommandNotFoundError as e:
if is_windows:
raise CommandNotFoundError("`file` utility is not available on Windows")
else:
raise e
file_cmd = which("file", required=True)
for arg in args:
file_cmd.add_default_arg(arg)
return file_cmd
@@ -134,7 +128,11 @@ def _get_mime_type():
"""Generate method to call `file` system command to aquire mime type
for a specified path
"""
return file_command("-b", "-h", "--mime-type")
if is_windows:
# -h option (no-dereference) does not exist in Windows
return file_command("-b", "--mime-type")
else:
return file_command("-b", "-h", "--mime-type")
@memoized

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@@ -1,4 +1,4 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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)

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@@ -1,4 +1,4 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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)

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@@ -1,4 +1,4 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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)

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@@ -1,4 +1,4 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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)

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@@ -1,4 +1,4 @@
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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)

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@@ -1,4 +1,4 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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)

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@@ -1,4 +1,4 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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)

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@@ -1,4 +1,4 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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)

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@@ -1,4 +1,4 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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)

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@@ -1,4 +1,4 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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)

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@@ -1,4 +1,4 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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)

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@@ -1,4 +1,4 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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)

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@@ -1,4 +1,4 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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)
@@ -47,7 +47,7 @@
import spack.util.url as url_util
import spack.util.web as web_util
from spack.caches import misc_cache_location
from spack.relocate import utf8_paths_to_single_binary_regex
from spack.relocate_text import utf8_paths_to_single_binary_regex
from spack.spec import Spec
from spack.stage import Stage
from spack.util.executable import which
@@ -294,10 +294,12 @@ def update_spec(self, spec, found_list):
cur_entry["spec"] = new_entry["spec"]
break
else:
current_list.append = {
"mirror_url": new_entry["mirror_url"],
"spec": new_entry["spec"],
}
current_list.append(
{
"mirror_url": new_entry["mirror_url"],
"spec": new_entry["spec"],
}
)
def update(self, with_cooldown=False):
"""Make sure local cache of buildcache index files is up to date.
@@ -510,9 +512,9 @@ class NoOverwriteException(spack.error.SpackError):
"""
def __init__(self, file_path):
err_msg = "\n%s\nexists\n" % file_path
err_msg += "Use -f option to overwrite."
super(NoOverwriteException, self).__init__(err_msg)
super(NoOverwriteException, self).__init__(
'"{}" exists in buildcache. Use --force flag to overwrite.'.format(file_path)
)
class NoGpgException(spack.error.SpackError):
@@ -1730,16 +1732,16 @@ def is_backup_file(file):
# For all buildcaches
# relocate the install prefixes in text files including dependencies
relocate.unsafe_relocate_text(text_names, prefix_to_prefix_text)
relocate.relocate_text(text_names, prefix_to_prefix_text)
# relocate the install prefixes in binary files including dependencies
relocate.unsafe_relocate_text_bin(files_to_relocate, prefix_to_prefix_bin)
relocate.relocate_text_bin(files_to_relocate, prefix_to_prefix_bin)
# If we are installing back to the same location
# relocate the sbang location if the spack directory changed
else:
if old_spack_prefix != new_spack_prefix:
relocate.unsafe_relocate_text(text_names, prefix_to_prefix_text)
relocate.relocate_text(text_names, prefix_to_prefix_text)
def _extract_inner_tarball(spec, filename, extract_to, unsigned, remote_checksum):

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@@ -1,4 +1,4 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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)

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@@ -1,4 +1,4 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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)

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@@ -1,4 +1,4 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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)
@@ -171,7 +171,7 @@ def mypy_root_spec():
def black_root_spec():
"""Return the root spec used to bootstrap black"""
return _root_spec("py-black")
return _root_spec("py-black@:22.12.0")
def flake8_root_spec():

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@@ -1,4 +1,4 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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)
@@ -8,7 +8,7 @@
import spack.directives
import spack.package_base
from ._checks import BaseBuilder, apply_macos_rpath_fixups
from ._checks import BaseBuilder, apply_macos_rpath_fixups, execute_install_time_tests
class Package(spack.package_base.PackageBase):
@@ -38,7 +38,16 @@ class GenericBuilder(BaseBuilder):
legacy_methods: Tuple[str, ...] = ()
#: Names associated with package attributes in the old build-system format
legacy_attributes: Tuple[str, ...] = ("archive_files",)
legacy_attributes: Tuple[str, ...] = (
"archive_files",
"install_time_test_callbacks",
)
#: Callback names for post-install phase tests
install_time_test_callbacks = []
# On macOS, force rpaths for shared library IDs and remove duplicate rpaths
spack.builder.run_after("install", when="platform=darwin")(apply_macos_rpath_fixups)
# unconditionally perform any post-install phase tests
spack.builder.run_after("install")(execute_install_time_tests)

View File

@@ -1,4 +1,4 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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)
@@ -1101,6 +1101,7 @@ def _setup_dependent_env_callback(self, env, dependent_spec, compilers_of_client
"CMAKE_PREFIX_PATH": self.normalize_path("mkl"),
"CMAKE_LIBRARY_PATH": self.component_lib_dir("mkl"),
"CMAKE_INCLUDE_PATH": self.component_include_dir("mkl"),
"PKG_CONFIG_PATH": os.path.join(self.normalize_path("mkl"), "bin", "pkgconfig"),
}
env.set("MKLROOT", env_mods["MKLROOT"])
@@ -1108,6 +1109,7 @@ def _setup_dependent_env_callback(self, env, dependent_spec, compilers_of_client
env.append_path("CMAKE_PREFIX_PATH", env_mods["CMAKE_PREFIX_PATH"])
env.append_path("CMAKE_LIBRARY_PATH", env_mods["CMAKE_LIBRARY_PATH"])
env.append_path("CMAKE_INCLUDE_PATH", env_mods["CMAKE_INCLUDE_PATH"])
env.append_path("PKG_CONFIG_PATH", env_mods["PKG_CONFIG_PATH"])
debug_print("adding/modifying build env:", env_mods)

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@@ -1,4 +1,4 @@
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2023 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)

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