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1168 Commits

Author SHA1 Message Date
Gregory L. Lee
08aaecd1e2 adding py-pyspy package 2023-11-14 08:03:39 -08:00
Gregory L. Lee
b237d303df adding py-pyspy package 2023-11-13 17:26:52 -08:00
Gregory L. Lee
c3015d2a1b adding py-pyspy package 2023-11-13 17:09:38 -08:00
Adam J. Stewart
ab60bfe36a py-numpy: add v1.26.2 (#41046) 2023-11-13 16:41:05 -07:00
John W. Parent
8bcc3e2820 CMake Package: support building ~ownlibs on Windows (#38758) 2023-11-13 14:26:33 -08:00
Hariharan Devarajan
388f141a92 Release Brahma v0.0.2 (#40994) 2023-11-13 14:25:12 -08:00
Todd Gamblin
f74b083a15 info: improve coverage (#41001)
Tests didn't cover the new `--variants-by-name` parameter in #40998.
Add some parameterization to hit that.

This changeset makes me think that the main section-printing loop in `spack info` isn't
factored so well. It makes it difficult to pass different arguments to different helper
functions.  I could break it out into if statements if folks think that would be cleaner.
2023-11-13 13:45:18 -08:00
heatherkellyucl
5b9d260054 gzip: deprecate <1.13 for vulnerability (#41044) 2023-11-13 13:38:16 -07:00
Greg Becker
4bd47d89db spack diff: allow hashes from mirrors (#41043) 2023-11-13 12:27:52 -08:00
Daniel Arndt
96f3c76052 dealii: add v9.5.0, v9.5.1 (#40747)
* dealii: 9.5.0

* kokkos+cuda_lambda

* dealii ^kokkos@3.7: require +cuda +cuda_lambda +wrapper

* Added 9.5.1, try ~cgal when +cuda

* Forward Cuda architecture request

* Remove workaround

* Try not enforcing the Kokkos compiler

* Enforce using nvcc_wrapper with Trilinos+Cuda

* Don't define CMAKE_*_COMPILER to point to MPI wrappers

* Use the same compiler as Trilinos/Kokkos

* Only check for Trilinos compiler

* Disable Trilinos+Cuda

* Disable Cuda support

* Try CUDA build without ninja

* Combined examples and examples_compile

* Use f-string for cuda_arch

* p -> _package

* Indentation

* Fix up f-string

---------

Co-authored-by: Luca Heltai <luca.heltai@sissa.it>
Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
2023-11-13 12:29:55 -06:00
H. Joe Lee
9c74eda61f hdf5: add a new variant for enabling sub-filing VFD (#40804) 2023-11-13 11:18:02 -07:00
dependabot[bot]
d9de93a0fc build(deps): bump black from 23.10.1 to 23.11.0 in /lib/spack/docs (#40967)
Bumps [black](https://github.com/psf/black) from 23.10.1 to 23.11.0.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](https://github.com/psf/black/compare/23.10.1...23.11.0)

---
updated-dependencies:
- dependency-name: black
  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>
2023-11-13 08:18:06 -07:00
Wouter Deconinck
3892fadbf6 qwt: conflict with qt-base (Qt6) (#40883) 2023-11-13 12:42:37 +01:00
Glenn Horton-Smith
62b32080a8 epics-base: patch to avoid failure on "perl xsubpp" when "xsubpp" otherwise works fine. (#40849) 2023-11-13 12:29:51 +01:00
Wanlin Wang
09d66168c4 riscv-gnu-toolchain: add v2023.09.13 -> v2023.10.18 (#40854) 2023-11-13 12:19:09 +01:00
Tuomas Koskela
d7869da36b conquest: add build system changes and library paths (#40718) 2023-11-13 12:13:53 +01:00
Mikael Simberg
b6864fb1c3 Add license directives to various packages (#41039) 2023-11-13 04:03:48 -07:00
Harmen Stoppels
e6125061e1 Compiler.debug_flags: drop -gz (#40900)
That enables compression of the debug symbols, it doesn't toggle them on
or off.
2023-11-13 11:33:40 +01:00
dependabot[bot]
491bd48897 build(deps): bump black in /.github/workflows/style (#40968)
Bumps [black](https://github.com/psf/black) from 23.10.1 to 23.11.0.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](https://github.com/psf/black/compare/23.10.1...23.11.0)

---
updated-dependencies:
- dependency-name: black
  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>
2023-11-13 11:18:52 +01:00
Victoria Cherkas
ad4878f770 metkit: add v1.10.2 and v1.10.17 (#40668) 2023-11-13 10:56:52 +01:00
Satish Balay
420eff11b7 superlu-dist: add v8.2.0 (#41004) 2023-11-13 10:55:05 +01:00
Adam J. Stewart
15e7aaf94d py-mypy: add v1.4:v1.7 (#41015) 2023-11-13 10:33:33 +01:00
Adam J. Stewart
bd6c5ec82d py-pandas: add v2.1.3 (#41017) 2023-11-13 10:26:56 +01:00
dependabot[bot]
4e171453c0 build(deps): bump mypy from 1.6.1 to 1.7.0 in /lib/spack/docs (#41020)
Bumps [mypy](https://github.com/python/mypy) from 1.6.1 to 1.7.0.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](https://github.com/python/mypy/compare/v1.6.1...v1.7.0)

---
updated-dependencies:
- dependency-name: mypy
  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>
2023-11-13 10:13:26 +01:00
Adam J. Stewart
420bce5cd2 GEOS: add new versions (#41030) 2023-11-13 10:09:58 +01:00
Thomas Gruber
b4f6c49bc0 likwid: add 5.3.0 version (#41008) 2023-11-13 10:09:39 +01:00
David Gardner
da4f2776d2 sundials: add license directive (#41028) 2023-11-13 10:08:28 +01:00
Adam J. Stewart
e2f274a634 PyTorch: allow +openmp on macOS (#41025) 2023-11-13 10:07:18 +01:00
Christian Glusa
15dcd3c65c py-pynucleus: Add variant, modify dependencies (#41006) 2023-11-11 16:24:12 -06:00
Matthew Archer
49c2894def update to latest version (#40905) 2023-11-11 16:16:45 -06:00
Stephen Hudson
1ae37f6720 libEnsemble: add v1.1.0 (#40969) 2023-11-11 16:15:43 -06:00
Adrien Berchet
15f6368c7f Add geomdl package (#40933) 2023-11-11 15:55:08 -06:00
Terry Cojean
57b63228ce Ginkgo: 1.7.0, change compatibility, update option oneapi->sycl (#40874)
Signed-off-by: Terry Cojean <terry.cojean@kit.edu>
2023-11-11 09:00:52 -06:00
Greg Becker
13abfb7013 spack deconcretize command (#38803)
We have two ways to concretize now:
* `spack concretize` concretizes only the root specs that are not concrete in the environment.
* `spack concretize -f` eliminates all cached concretization data and reconcretizes the *entire* environment.

This PR adds `spack deconcretize`, which eliminates cached concretization data for a spec.  This allows
users greater control over what is preserved from their `spack.lock` file and what is reused when not
using `spack concretize -f`.  If you want to update a spec installed in your environment, you can call
`spack deconcretize` on it, and that spec and any relevant dependents will be removed from the lock file.

`spack concretize` has two options:
* `--root`: limits deconcretized specs to *specific* roots in the environment. You can use this to
  deconcretize exactly one root in a `unify: false` environment.  i.e., if `foo` root is a dependent
  of `bar`, both roots, `spack deconcretize bar` will *not* deconcretize `foo`.
* `--all`: deconcretize *all* specs that match the input spec. By default `spack deconcretize`
  will complain about multiple matches, like `spack uninstall`.
2023-11-10 14:55:35 -08:00
Nils Lehmann
b41fc1ec79 new release (#41010) 2023-11-10 11:52:59 -07:00
Henri Menke
124e41da23 libpspio 0.3.0 (#40953)
Co-authored-by: Alec Scott <alec@bcs.sh>
2023-11-10 09:48:50 -08:00
Massimiliano Culpo
f6039d1d45 builtin.repo: fix ^mkl pattern in minor packages (#41003)
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2023-11-10 17:18:24 +01:00
Victoria Cherkas
8871bd5ba5 fdb: add dependency on eckit later release (#40737)
* depends_on("eckit@1.24.4:", when="@5.11.22:")

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

Co-authored-by: Alec Scott <alec@bcs.sh>

* make latest tagged release the default install

* revert f258f46660

---------

Co-authored-by: Alec Scott <alec@bcs.sh>
2023-11-10 07:54:25 -08:00
Cody Balos
efe85755d8 alquimia: apply patch for iso_c_binding to latest version (#40989) 2023-11-10 08:31:38 -06:00
Cody Balos
7aaa17856d pflotran: tweak for building with xsdk rocm/hip (#40990) 2023-11-10 08:30:35 -06:00
Massimiliano Culpo
fbf02b561a gromacs et al: fix ^mkl pattern (#41002)
The ^mkl pattern was used to refer to three packages
even though none of software using it was depending
on "mkl".

This pattern, which follows Hyrum's law, is now being
removed in favor of a more explicit one.

In this PR gromacs, abinit, lammps, and quantum-espresso
are modified.

Intel packages are also modified to provide "lapack"
and "blas" together.
2023-11-10 13:56:04 +00:00
Harmen Stoppels
4027a2139b env: compute env mods only for installed roots (#40997)
And improve the error message (load vs unload).

Of course you could have some uninstalled dependency too, but as long as
it doesn't implement `setup_run_environment` etc, I don't think it hurts
to attempt to load the root anyways, given that failure to do so is a
warning, not a fatal error.
2023-11-10 12:32:48 +01:00
Todd Gamblin
f0ced1af42 info: rework spack info command to display variants better (#40998)
This changes variant display to use a much more legible format, and to use screen space
much better (particularly on narrow terminals). It also adds color the variant display
to match other parts of `spack info`.

Descriptions and variant value lists that were frequently squished into a tiny column
before now have closer to the full terminal width.

This change also preserves any whitespace formatting present in `package.py`, so package
maintainers can make easer-to-read descriptions of variant values if they want. For
example, `gasnet` has had a nice description of the `conduits` variant for a while, but
it was wrapped and made illegible by `spack info`. That is now fixed and the original
newlines are kept.

Conditional variants are grouped by their when clauses by default, but if you do not
like the grouping, you can display all the variants in order with `--variants-by-name`.
I'm not sure when people will prefer this, but it makes it easier to tell that a
particular variant is/isn't there. I do think grouping by `when` is the better default.
2023-11-10 12:31:28 +01:00
David Boehme
2e45edf4e3 Add adiak v0.4.0 (#40993)
* Add adiak v0.4.0
* Fix style checks
2023-11-09 21:23:00 -07:00
Adam J. Stewart
4bcfb01566 py-black: add v23.10: (#40959) 2023-11-10 00:10:28 +01:00
Adam J. Stewart
b8bb8a70ce PyTorch: specify CUDA root directory (#40855) 2023-11-09 14:25:54 -08:00
Hariharan Devarajan
dd2b436b5a new release cpp-logger v0.0.2 (#40972) 2023-11-09 13:08:04 -08:00
Hariharan Devarajan
da2cc2351c Release Gotcha v1.0.5 (#40973) 2023-11-09 13:06:56 -08:00
eugeneswalker
383ec19a0c Revert "Deactivate Cray sles, due to unavailable runner (#40291)" (#40910)
This reverts commit 4b06862a7f.
2023-11-09 12:24:18 -08:00
Todd Gamblin
45f8a0e42c docs: tweak formatting of +: and -: operators (#40988)
Just trying to make these stand out a bit more in the docs.
2023-11-09 19:55:29 +00:00
Dom Heinzeller
4636a7f14f Add symlinks for hdf5 library names when built in debug mode (#40965)
* Add symlinks for hdf5 library names when built in debug mode
* Only apply bug fix for debug libs when build type is Debug
2023-11-09 11:40:53 -08:00
Kelly (KT) Thompson
38f3f57a54 [lcov] Add build and runtime deps necessary for lcov@2.0.0: (#40974)
* [lcov] Add build and runtime deps necessary for lcov@2.0.0:
   + Many additional Perl package dependecies are required for the new version of lcov.
   + Some of the new dependencies were not known to spack until now.
* Style fix
2023-11-09 11:37:38 -08:00
Satish Balay
b17d7cd0e6 mfem: add hipblas dependency for superlu-dist (#40981) 2023-11-09 11:19:48 -08:00
Satish Balay
b5e2f23b6c hypre: add in hipblas dependency due to superlu-dist (#40980) 2023-11-09 11:03:03 -08:00
Brian Van Essen
7a4df732e1 DiHydrogen, Hydrogen, and Aluminum CachedCMakePackage (#39714) 2023-11-09 19:08:37 +01:00
George Young
7e6aaf9458 py-macs3: adding zlib dependency (#40979) 2023-11-09 16:44:24 +01:00
Cody Balos
2d35d29e0f sundials: add v6.6.2 (#40920) 2023-11-09 07:38:40 -06:00
Scott Wittenburg
1baed0d833 buildcache: skip unrecognized metadata files (#40941)
This commit improves forward compatibility of Spack with newer build cache metadata formats.

Before this commit, invalid or unrecognized metadata would be fatal errors, now they just cause
a mirror to be skipped.

Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
2023-11-09 13:30:41 +00:00
Harmen Stoppels
cadc2a1aa5 Set version to 0.22.0.dev0 (#40975) 2023-11-09 10:02:29 +01:00
Satish Balay
78449ba92b intel-oneapi-mkl: do not set __INTEL_POST_CFLAGS env variable (#40947)
This triggers warnings from icx compiler - that breaks petsc configure

$ I_MPI_CC=icx /opt/intel/oneapi/mpi/2021.7.0/bin/mpiicc -E a.c > /dev/null
$ __INTEL_POST_CFLAGS=-Wl,-rpath,/opt/intel/oneapi/mkl/2022.2.0/lib/intel64 I_MPI_CC=icx /opt/intel/oneapi/mpi/2021.7.0/bin/mpiicc -E a.c > /dev/null
icx: warning: -Wl,-rpath,/opt/intel/oneapi/mkl/2022.2.0/lib/intel64: 'linker' input unused [-Wunused-command-line-argument]
2023-11-09 08:40:12 +01:00
Massimiliano Culpo
26d6bfbb7f modules: remove deprecated code and test data (#40966)
This removes a few deprecated attributes from the
schema of the "modules" section. Test data for
deprecated options is removed as well.
2023-11-09 08:15:46 +01:00
Sergio Sánchez Ramírez
3405fe60f1 libgit2: add python as test dependency (#40863)
Libgit2 requires python as build dependency. I was getting an error because it was falling back to system Python which is compiled with Intel compilers and thus, `libgit2` was failing because it couldn't find `libimf.so` (which doesn't make sense).

Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2023-11-08 23:20:55 +01:00
Harmen Stoppels
53c266b161 modules: restore exclude_implicits (#40958) 2023-11-08 22:56:55 +01:00
Thomas Madlener
ed8ecc469e podio: Add the latest tag (0.17.2) (#40956)
* podio: Add myself as maintainer
* podio: Add 0.17.2 tag
2023-11-08 14:53:23 -07:00
Harmen Stoppels
b2840acd52 Revert "defaults/modules.yaml: hide implicits (#40906)" (#40955)
This reverts commit a2f00886e9.
2023-11-08 14:33:50 -07:00
Tom Vander Aa
c35250b313 libevent: always autogen.sh (#40945)
The libevent release tarballs ship with a `configure` script generated by an old `libtool`. The `libtool` generated by `configure` is not compatible with `MACOSX_DEPLOYMENT_VERSION` > 10. Regeneration of the `configure` scripts fixes build on macOS. 

Original configure contains:
```
    case $host_os in
    rhapsody* | darwin1.[012])
      _lt_dar_allow_undefined='$wl-undefined ${wl}suppress' ;;
    darwin1.*)
      _lt_dar_allow_undefined='$wl-flat_namespace $wl-undefined ${wl}suppress' ;;
    darwin*) # darwin 5.x on
      # if running on 10.5 or later, the deployment target defaults
      # to the OS version, if on x86, and 10.4, the deployment
      # target defaults to 10.4. Don't you love it?
      case ${MACOSX_DEPLOYMENT_TARGET-10.0},$host in
        10.0,*86*-darwin8*|10.0,*-darwin[91]*)
          _lt_dar_allow_undefined='$wl-undefined ${wl}dynamic_lookup' ;;
        10.[012][,.]*)
          _lt_dar_allow_undefined='$wl-flat_namespace $wl-undefined ${wl}suppress' ;;
        10.*)
          _lt_dar_allow_undefined='$wl-undefined ${wl}dynamic_lookup' ;;
      esac
```

After re-running `autogen.sh`:
```
    case $host_os in
    rhapsody* | darwin1.[012])
      _lt_dar_allow_undefined='$wl-undefined ${wl}suppress' ;;
    darwin1.*)
      _lt_dar_allow_undefined='$wl-flat_namespace $wl-undefined ${wl}suppress' ;;
    darwin*)
      case $MACOSX_DEPLOYMENT_TARGET,$host in
        10.[012],*|,*powerpc*-darwin[5-8]*)
          _lt_dar_allow_undefined='$wl-flat_namespace $wl-undefined ${wl}suppress' ;;
        *)
          _lt_dar_allow_undefined='$wl-undefined ${wl}dynamic_lookup' ;;
      esac
```
2023-11-08 22:33:09 +01:00
Adam J. Stewart
e114853115 py-lightning: add v2.1.1 (#40957) 2023-11-08 13:15:23 -08:00
Cameron Smith
89fc9a9d47 lcov: add version2, embed perl path in binaries (#39342)
* lcov: add version2, perl dep at build and runtime
* lcov: add runtime deps
* namespace-autoclean: new perl package
* datetime: dep on autoclean
* formatting
2023-11-08 11:23:23 -08:00
Massimiliano Culpo
afc693645a tcl: filter compiler wrappers to avoid pointing to Spack (#40946) 2023-11-08 19:38:41 +01:00
downloadico
4ac0e511ad abinit: add v9.10.3 (#40919)
* abinit:	add v9.10.3
Changed	configure arguments for specfying how to use Wannier90 for versions
after 9.8.
When the mpi variant is requested, set the F90 environment variable to point
to the MPI Fortran wrapper when building versions after 9.8 instead of FC.
---------

Co-authored-by: Alec Scott <hi@alecbcs.com>
2023-11-08 10:15:49 -08:00
Henri Menke
b0355d6cc0 ScaFaCoS 1.0.4 (#40948) 2023-11-08 10:17:58 -07:00
Konstantinos Parasyris
300d53d6f8 Add new tag on AMS (#40949) 2023-11-08 08:52:53 -08:00
Greg Becker
0b344e0fd3 tutorial stack: update for changes to the basics section for SC23 (#40942) 2023-11-07 23:46:57 -08:00
Peter Scheibel
15adb308bf RAJA package: find libs (#40885) 2023-11-08 08:33:04 +01:00
Michael Kuhn
050d565375 julia: constrain patchelf version (#40938)
* julia: constrain patchelf version

patchelf@0.18 breaks (at least) `libjulea-internal.so`, leading to
errors like:
```
$ julia --version
ERROR: Unable to load dependent library $SPACK/opt/spack/linux-centos8-x86_64_v3/gcc-12.3.0/julia-1.9.2-6hf5qx2q27jth2fkm6kgqmfdlhzzw6pl/bin/../lib/julia/libjulia-internal.so.1
Message:$SPACK/opt/spack/linux-centos8-x86_64_v3/gcc-12.3.0/julia-1.9.2-6hf5qx2q27jth2fkm6kgqmfdlhzzw6pl/bin/../lib/julia/libjulia-internal.so.1: ELF load command address/offset not properly aligned
```

* patchelf: prefer v0.17.x since v0.18 breaks libraries
2023-11-08 08:13:54 +01:00
Matthew Thompson
f6ef2c254e mapl: add v2.41 and v2.42 (#40870)
* mapl: add 2.41 and 2.42

* Conflict MPICH 3
2023-11-07 17:36:11 -08:00
Freifrau von Bleifrei
62c27b1924 discotec: add compression variant (#40925) 2023-11-07 14:58:48 -08:00
SWAT Team (JSC)
2ff0766aa4 adds cubew 4.8.1, cubelib 4.8.1 and cubegui 4.8.1, 4.8.2 (#40612)
* exago: fix v1.5.1 tag; only allow python up to 3.10 for for @:1.5 (#40676)
* exago: fix v1.5.1 tag; only allow python up to 3.10 for for @:1.5 due to pybind error with py 3.11
* hiop@:1.0 +cuda: constrain to cuda@:11.9
* fixes syntax of maintainers

---------

Co-authored-by: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com>
2023-11-07 14:40:36 -08:00
Mark W. Krentel
dc245e87f9 intel-xed: fix git hash for mbuild, add version 2023.10.11 (#40922)
* intel-xed: fix git hash for mbuild, add version 2023.10.11
   Fixes #40912
* Fix the git commit hash for mbuild 2022.04.17.  This was broken in
   commit eef9939c21 by mixing up the hashes for xed versus mbuild.
* Add versions 2023.08.21 and 2023.10.11.
* fix style
2023-11-07 14:36:42 -08:00
Harmen Stoppels
c1f134e2a0 tutorial: use lmod@8.7.18 because @8.7.19: has bugs (#40939) 2023-11-07 23:04:45 +01:00
Mosè Giordano
391940d2eb julia: Add v1.9.3 (#40911) 2023-11-07 22:06:12 +01:00
Adam J. Stewart
8c061e51e3 sleef: build shared libs (#40893) 2023-11-07 21:48:59 +01:00
Richarda Butler
5774df6b7a Propagate variant across nodes that don't have that variant (#38512)
Before this PR, variant were not propagated to leaf nodes that could accept 
the propagated value, if some intermediate node couldn't accept it.

This PR fixes that issue by marking nodes as "candidate" for propagation
and by setting the variant only if it can be accepted by the node.

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-11-07 21:04:41 +01:00
Harmen Stoppels
3a5c1eb5f3 tutorial pipeline: force gcc@12.3.0 (#40937) 2023-11-07 20:53:44 +01:00
Harmen Stoppels
3a2ec729f7 Ensure global command line arguments end up in args like before (#40929) 2023-11-07 20:35:56 +01:00
Jacob King
a093f4a8ce superlu-dist: add +parmetis variant. (#40746)
* Expose ability to make parmetis an optional superlu-dist dependency to
spack package management.

* rename parmetis variant: Enable ParMETIS library

---------

Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
2023-11-07 10:21:38 -08:00
Scott Wittenburg
b8302a8277 ci: do not retry timed out build jobs (#40936) 2023-11-07 17:44:28 +00:00
Massimiliano Culpo
32f319157d Update the branch for the tutorial command (#40934) 2023-11-07 16:59:48 +00:00
Harmen Stoppels
75dfad8788 catch exceptions in which_string (#40935) 2023-11-07 17:17:31 +01:00
Vanessasaurus
f3ba20db26 fix configure args for darshan-runtime (#40873)
Problem: the current configure arguments are added lists to a list,
and this needs to be adding strings to the same list.
Solution: ensure we add each item (string) separately.

Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2023-11-07 07:00:28 -08:00
Rob Falgout
6301edbd5d Update package.py for new release 2.30.0 (#40907) 2023-11-07 07:58:00 -07:00
Massimiliano Culpo
c232bf435a Change container labeling so that "latest" is the latest tag (#40593)
* Use `major.minor.patch`, `major.minor`, `major` in tags

* Ensure `latest` is the semver largest version, and not "latest in time"

* Remove Ubuntu 18.04 from the list of images
2023-11-07 11:53:36 +01:00
Massimiliano Culpo
f3537bc66b ASP: targets, compilers and providers soft-preferences are only global (#31261)
Modify the packages.yaml schema so that soft-preferences on targets,
compilers and providers can only be specified under the "all" attribute.
This makes them effectively global preferences.

Version preferences instead can only be specified under a package
specific section.

If a preference attribute is found in a section where it should
not be, it will be ignored and a warning is printed to screen.
2023-11-07 07:46:06 +01:00
Massimiliano Culpo
4004f27bc0 archspec: update to v0.2.2 (#40917)
Adds support for Neoverse V2
2023-11-07 07:44:52 +01:00
Todd Gamblin
910190f55b database: optimize query() by skipping unnecessary virtual checks (#40898)
Most queries will end up calling `spec.satisfies(query)` on everything in the DB, which
will cause Spack to ask whether the query spec is virtual if its name doesn't match the
target spec's. This can be expensive, because it can cause Spack to check if any new
virtuals showed up in *all* the packages it knows about. That can currently trigger
thousands of `stat()` calls.

We can avoid the virtual check for most successful queries if we consider that if there
*is* a match by name, the query spec *can't* be virtual. This PR adds an optimization to
the query loop to save any comparisons that would trigger a virtual check for last.

- [x] Add a `deferred` list to the `query()` loop.
- [x] First run through the `query()` loop *only* checks for name matches.
- [x] Query loop now returns early if there's a name match, skipping most `satisfies()` calls.
- [x] Second run through the `deferred()` list only runs if query spec is virtual.
- [x] Fix up handling of concrete specs.
- [x] Add test for querying virtuals in DB.
- [x] Avoid allocating deferred if not necessary.

---------

Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
2023-11-07 01:00:37 +00:00
Harmen Stoppels
4ce80b95f3 spack compiler find --[no]-mixed-toolchain (#40902)
Currently there's some hacky logic in the AppleClang compiler that makes
it also accept `gfortran` as a fortran compiler if `flang` is not found.

This is guarded by `if sys.platform` checks s.t. it only applies to
Darwin.

But on Linux the feature of detecting mixed toolchains is highly
requested too, cause it's rather annoying to run into a failed build of
`openblas` after dozens of minutes of compiling its dependencies, just
because clang doesn't have a fortran compiler.

In particular in CI where the system compilers may change during system
updates, it's typically impossible to fix compilers in a hand-written
compilers.yaml config file: the config will almost certainly be outdated
sooner or later, and maintaining one config file per target machine and
writing logic to select the correct config is rather undesirable too.

---

This PR introduces a flag `spack compiler find --mixed-toolchain` that
fills out missing `fc` and `f77` entries in `clang` / `apple-clang` by
picking the best matching `gcc`.

It is enabled by default on macOS, but not on Linux, matching current
behavior of `spack compiler find`.

The "best matching gcc" logic and compiler path updates are identical to
how compiler path dictionaries are currently flattened "horizontally"
(per compiler id). This just adds logic to do the same "vertically"
(across different compiler ids).

So, with this change on Ubuntu 22.04:

```
$ spack compiler find --mixed-toolchain
==> Added 6 new compilers to /home/harmen/.spack/linux/compilers.yaml
    gcc@13.1.0  gcc@12.3.0  gcc@11.4.0  gcc@10.5.0  clang@16.0.0  clang@15.0.7
==> Compilers are defined in the following files:
    /home/harmen/.spack/linux/compilers.yaml

```

you finally get:

```
compilers:
- compiler:
    spec: clang@=15.0.7
    paths:
      cc: /usr/bin/clang
      cxx: /usr/bin/clang++
      f77: /usr/bin/gfortran
      fc: /usr/bin/gfortran
    flags: {}
    operating_system: ubuntu23.04
    target: x86_64
    modules: []
    environment: {}
    extra_rpaths: []
- compiler:
    spec: clang@=16.0.0
    paths:
      cc: /usr/bin/clang-16
      cxx: /usr/bin/clang++-16
      f77: /usr/bin/gfortran
      fc: /usr/bin/gfortran
    flags: {}
    operating_system: ubuntu23.04
    target: x86_64
    modules: []
    environment: {}
    extra_rpaths: []
```

The "best gcc" is automatically default system gcc, since it has no
suffixes / prefixes.
2023-11-06 15:17:31 -08:00
Sinan
8f1f9048ec package/qgis: add latest ltr (#40752)
* package/qgis: add latest ltr

* fix bug

* [@spackbot] updating style on behalf of Sinan81

* make flake happy

---------

Co-authored-by: sbulut <sbulut@3vgeomatics.com>
Co-authored-by: Sinan81 <Sinan81@users.noreply.github.com>
2023-11-06 15:55:20 -07:00
Harmen Stoppels
e7372a54a1 docs: expand section about relocation, suggest padding (#40909) 2023-11-06 14:49:54 -08:00
Michael Kuhn
5074b7e922 Add support for aliases (#17229)
Add a new config section: `config:aliases`, which is a dictionary mapping aliases
to commands.

For instance:


```yaml
config:
    aliases:
        sp: spec -I
```

will define a new command `sp` that will execute `spec` with the `-I`
argument. 

Aliases cannot override existing commands, and this is ensured with a test.

We cannot currently alias subcommands. Spack will warn about any aliases
containing a space, but will not error, which leaves room for subcommand
aliases in the future.

---------

Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2023-11-06 14:37:46 -08:00
Harmen Stoppels
461eb944bd Don't let runtime env variables of compiler like deps leak into the build environment (#40916)
* Test that setup_run_environment changes to CC/CXX/FC/F77 are dropped in build env

* compilers set in run env shouldn't impact build

Adds `drop` to EnvironmentModifications courtesy of @haampie, and uses
it to clear modifications of CC, CXX, F77 and FC made by
`setup_{,dependent_}run_environment` routines when producing an
environment in BUILD context.

* comment / style

* comment

---------

Co-authored-by: Tom Scogland <scogland1@llnl.gov>
2023-11-06 14:30:27 -08:00
Harmen Stoppels
4700108b5b fix prefix_inspections keys in example (#40904) 2023-11-06 13:22:13 -08:00
Harmen Stoppels
3384181868 docs: mention public build cache for GHA (#40908) 2023-11-06 13:21:16 -08:00
Vicente Bolea
f0f6e54b29 adios2: add v2.9.2 release (#40832) 2023-11-06 12:15:29 -08:00
Harmen Stoppels
a2f00886e9 defaults/modules.yaml: hide implicits (#40906) 2023-11-06 10:37:29 -08:00
Harmen Stoppels
1235084c20 Introduce default_args context manager (#39964)
This adds a rather trivial context manager that lets you deduplicate repeated
arguments in directives, e.g.

```python
depends_on("py-x@1", when="@1", type=("build", "run"))
depends_on("py-x@2", when="@2", type=("build", "run"))
depends_on("py-x@3", when="@3", type=("build", "run"))
depends_on("py-x@4", when="@4", type=("build", "run"))
```

can be condensed to

```python
with default_args(type=("build", "run")):
    depends_on("py-x@1", when="@1")
    depends_on("py-x@2", when="@2")
    depends_on("py-x@3", when="@3")
    depends_on("py-x@4", when="@4")
```

The advantage is it's clear for humans, the downside it's less clear for type checkers due to type erasure.
2023-11-06 10:22:29 -08:00
Greg Becker
b5538960c3 error messages: condition chaining (#40173)
Create chains of causation for error messages.

The current implementation is only completed for some of the many errors presented by the concretizer. The rest will need to be filled out over time, but this demonstrates the capability.

The basic idea is to associate conditions in the solver with one another in causal relationships, and to associate errors with the proximate causes of their facts in the condition graph. Then we can construct causal trees to explain errors, which will hopefully present users with useful information to avoid the error or report issues.

Technically, this is implemented as a secondary solve. The concretizer computes the optimal model, and if the optimal model contains an error, then a secondary solve computes causation information about the error(s) in the concretizer output.

Examples:

$ spack solve hdf5 ^cmake@3.0.1
==> Error: concretization failed for the following reasons:

   1. Cannot satisfy 'cmake@3.0.1'
   2. Cannot satisfy 'cmake@3.0.1'
        required because hdf5 ^cmake@3.0.1 requested from CLI 
   3. Cannot satisfy 'cmake@3.18:' and 'cmake@3.0.1
        required because hdf5 ^cmake@3.0.1 requested from CLI 
        required because hdf5 depends on cmake@3.18: when @1.13: 
          required because hdf5 ^cmake@3.0.1 requested from CLI 
   4. Cannot satisfy 'cmake@3.12:' and 'cmake@3.0.1
        required because hdf5 depends on cmake@3.12: 
          required because hdf5 ^cmake@3.0.1 requested from CLI 
        required because hdf5 ^cmake@3.0.1 requested from CLI

$ spack spec cmake ^curl~ldap   # <-- with curl configured non-buildable and an external with `+ldap`
==> Error: concretization failed for the following reasons:

   1. Attempted to use external for 'curl' which does not satisfy any configured external spec
   2. Attempted to build package curl which is not buildable and does not have a satisfying external
        attr('variant_value', 'curl', 'ldap', 'True') is an external constraint for curl which was not satisfied
   3. Attempted to build package curl which is not buildable and does not have a satisfying external
        attr('variant_value', 'curl', 'gssapi', 'True') is an external constraint for curl which was not satisfied
   4. Attempted to build package curl which is not buildable and does not have a satisfying external
        'curl+ldap' is an external constraint for curl which was not satisfied
        'curl~ldap' required
        required because cmake ^curl~ldap requested from CLI 

$ spack solve yambo+mpi ^hdf5~mpi
==> Error: concretization failed for the following reasons:

   1. 'hdf5' required multiple values for single-valued variant 'mpi'
   2. 'hdf5' required multiple values for single-valued variant 'mpi'
    Requested '~mpi' and '+mpi'
        required because yambo depends on hdf5+mpi when +mpi 
          required because yambo+mpi ^hdf5~mpi requested from CLI 
        required because yambo+mpi ^hdf5~mpi requested from CLI 
   3. 'hdf5' required multiple values for single-valued variant 'mpi'
    Requested '~mpi' and '+mpi'
        required because netcdf-c depends on hdf5+mpi when +mpi 
          required because netcdf-fortran depends on netcdf-c 
            required because yambo depends on netcdf-fortran 
              required because yambo+mpi ^hdf5~mpi requested from CLI 
          required because netcdf-fortran depends on netcdf-c@4.7.4: when @4.5.3: 
            required because yambo depends on netcdf-fortran 
              required because yambo+mpi ^hdf5~mpi requested from CLI 
          required because yambo depends on netcdf-c 
            required because yambo+mpi ^hdf5~mpi requested from CLI 
          required because yambo depends on netcdf-c+mpi when +mpi 
            required because yambo+mpi ^hdf5~mpi requested from CLI 
        required because yambo+mpi ^hdf5~mpi requested from CLI 

Future work:

In addition to fleshing out the causes of other errors, I would like to find a way to associate different components of the error messages with different causes. In this example it's pretty easy to infer which part is which, but I'm not confident that will always be the case. 

See the previous PR #34500 for discussion of how the condition chains are incomplete. In the future, we may need custom logic for individual attributes to associate some important choice rules with conditions such that clingo choices or other derivations can be part of the explanation.

---------

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-11-06 09:55:21 -08:00
Michael Kuhn
d3d82e8d6b c-blosc2: add v2.11.1 (#40889) 2023-11-06 09:48:42 -08:00
Tamara Dahlgren
17a9198c78 Environments: remove environments created with SpackYAMLErrors (#40878) 2023-11-06 18:48:28 +01:00
Juan Miguel Carceller
c6c689be28 pythia8: fix configure args (#40644)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-11-06 09:33:23 -08:00
AMD Toolchain Support
ab563c09d2 enable threading in amdlibflame (#40852)
Co-authored-by: vkallesh <Vijay-teekinavar.Kallesh@amd.com>
2023-11-06 09:20:19 -08:00
Sergio Sánchez Ramírez
abdac36fd5 Add Python as build dependency of Julia (#40903) 2023-11-06 09:03:38 -07:00
Harmen Stoppels
b8a18f0a78 mpich: remove unnecessary tuples and upperbounds (#40899)
* mpich: remove unnecessary tuples

* remove redundant :3.3.99 upperbound
2023-11-06 07:58:50 -07:00
Wouter Deconinck
17656b2ea0 qt: new version 5.15.11 (#40884)
* qt: new version 5.15.11

* qt: open end patch for qtlocation when gcc-10:
2023-11-06 06:08:19 -07:00
Harmen Stoppels
3c641c8509 spack env activate: create & activate default environment without args (#40756)
This PR implements the concept of "default environment", which doesn't have to be
created explicitly. The aim is to lower the barrier for adopting environments.

To (create and) activate the default environment, run

```
$ spack env activate
```

This mimics the behavior of

```
$ cd
```

which brings you to your home directory.

This is not a breaking change, since `spack env activate` without arguments
currently errors. It is similar to the already existing `spack env activate --temp`
command which always creates an env in a temporary directory, the difference
is that the default environment is a managed / named environment named `default`.

The name `default` is not a reserved name, it's just that `spack env activate`
creates it for you if you don't have it already.

With this change, you can get started with environments faster:

```
$ spack env activate [--prompt]
$ spack install --add x y z
```

instead of

```
$ spack env create default
==> Created environment 'default in /Users/harmenstoppels/spack/var/spack/environments/default
==> You can activate this environment with:
==>   spack env activate default
$ spack env activate [--prompt] default 
$ spack install --add x y z
```

Notice that Spack supports switching (but not stacking) environments, so the
parallel with `cd` is pretty clear:

```
$ spack env activate named_env
$ spack env status
==> In environment named_env
$ spack env activate
$ spack env status
==> In environment default
```
2023-11-05 22:53:26 -08:00
Michael Kuhn
141c7de5d8 Add command and package suggestions (#40895)
* Add command suggestions

This adds suggestions of similar commands in case users mistype a
command. Before:
```
$ spack spack
==> Error: spack is not a recognized Spack command or extension command; check with `spack commands`.
```
After:
```
$ spack spack
==> Error: spack is not a recognized Spack command or extension command; check with `spack commands`.

Did you mean one of the following commands?
  spec
  patch
```

* Add package name suggestions

* Remove suggestion to run spack clean -m
2023-11-05 14:32:09 -08:00
Todd Gamblin
f6b23b4653 bugfix: compress aliases for first command in completion (#40890)
This completes to `spack concretize`:

```
spack conc<tab>
```

but this still gets hung up on the difference between `concretize` and `concretise`:

```
spack -e . conc<tab>
```

We were checking `"$COMP_CWORD" = 1`, which tracks the word on the command line
including any flags and their args, but we should track `"$COMP_CWORD_NO_FLAGS" = 1` to
figure out if the arg we're completing is the first real command.
2023-11-05 10:15:37 +00:00
Harmen Stoppels
4755b28398 Hidden modules: always append hash (#40868) 2023-11-05 08:56:11 +01:00
Tamara Dahlgren
c9dfb9b0fd Environments: Add support for including definitions files (#33960)
This PR adds support for including separate definitions from `spack.yaml`.

Supporting the inclusion of files with definitions enables user to make
curated/standardized collections of packages that can re-used by others.
2023-11-05 00:47:06 -07:00
Veselin Dobrev
5a67c578b7 mfem: allow cuda/rocm builds with superlu-dist built without cuda/rocm (#40847) 2023-11-04 20:15:56 -05:00
Michael Kuhn
e47be18acb c-blosc: add v1.21.5 (#40888) 2023-11-04 16:51:37 -07:00
Harmen Stoppels
6593d22c4e spack.modules.commmon: pass spec to SetupContext (#40886)
Currently module globals aren't set before running
`setup_[dependent_]run_environment` to compute environment modifications
for module files. This commit fixes that.
2023-11-04 20:42:47 +00:00
Massimiliano Culpo
f51dad976e hdf5-vol-async: better specify dependency condition (#40882) 2023-11-04 20:31:52 +01:00
Cameron Rutherford
ff8cd597e0 hiop: fix cuda constraints (#40875) 2023-11-04 13:09:59 -05:00
eugeneswalker
fd22d109a6 sundials +sycl: add cxxflags=-fsycl via flag_handler (#40845) 2023-11-04 08:55:19 -05:00
zv-io
88ee3a0fba linux-headers: support multiple versions (#40877)
The download URL for linux-headers was hardcoded to 4.x;
we need to derive the correct URL from the version number.
2023-11-04 12:21:12 +01:00
Massimiliano Culpo
f50377de7f environment: solve one spec per child process (#40876)
Looking at the memory profiles of concurrent solves
for environment with unify:false, it seems memory
is only ramping up.

This exchange in the potassco mailing list:
 https://sourceforge.net/p/potassco/mailman/potassco-users/thread/b55b5b8c2e8945409abb3fa3c935c27e%40lohn.at/#msg36517698

Seems to suggest that clingo doesn't release memory
until end of the application.

Since when unify:false we distribute work to processes,
here we give a maxtaskperchild=1, so we clean memory
after each solve.
2023-11-03 23:10:42 +00:00
Adam J. Stewart
8e96d3a051 GDAL: add v3.7.3 (#40865) 2023-11-03 22:59:52 +01:00
Richarda Butler
8fc1ba2d7a Bugfix: propagation of multivalued variants (#39833)
Don't encourage use of default value if propagating a multivalued variant.
2023-11-03 12:09:39 -07:00
Massimiliano Culpo
668a5b45e5 clingo-bootstrap: force setuptools through variant (#40866) 2023-11-03 16:53:45 +01:00
Andrew W Elble
70171d6caf squashfuse: remove url_for_version (#40862)
0.5.0 tarball now has the 'v' removed from the name
2023-11-03 10:34:25 -04:00
Thomas-Ulrich
0f1898c82a xdmf3: fix compilation with hdf5@1.10 and above (#37551) 2023-11-03 14:23:49 +01:00
Massimiliano Culpo
db16335aec ASP-based solver: fix for unsplittable providers (#40859)
Some providers must provide virtuals "together", i.e.
if they provide one virtual of a set, they must be the
providers also of the others.

There was a bug though, where we were not checking if
the other virtuals in the set were needed at all in
the DAG.

This commit fixes the bug.
2023-11-03 12:56:37 +01:00
Harmen Stoppels
3082ce6a22 oci parsing: make image name case insensitive (#40858) 2023-11-03 12:50:30 +01:00
George Young
fe0cf80e05 py-spython: updating to @0.3.1 (#40839)
* py-spython: updating to @0.3.1

* Adding `when=` for py-semver

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-11-03 05:07:58 -06:00
Thomas-Ulrich
a5e6097af7 fix typo in packaging guide (#40853) 2023-11-03 09:56:13 +01:00
eugeneswalker
d4a1618e07 tau: update 2.33 hash, add syscall variant (#40851)
Co-authored-by: wspear <wjspear@gmail.com>
2023-11-03 07:58:00 +01:00
Veselin Dobrev
48a21970d1 MFEM: add logic to find CUDA math-libs when using HPC SDK installation (#40815)
* mfem: add logic to find CUDA math-libs when using HPC SDK installation

* [@spackbot] updating style on behalf of v-dobrev
2023-11-02 20:19:11 -07:00
Martin Aumüller
864d47043c qt-svg: new package for Qt6 SVG module (#40834)
enables loading of SVG icons by providing plugin used by qt-base
2023-11-02 17:05:54 -07:00
Martin Aumüller
c2af2bcac3 qt-*: add v6.5.3 & v6.6.0 (#40833) 2023-11-02 19:52:15 -04:00
Martin Aumüller
7c79c744b6 libtheora: fix build on macos (#40840)
* libtheora: regenerate Makefile.in during autoreconf

The patch to inhibit running of configure would exit autogen.sh so early
that it did not yet run autoconf/automake/...
Instead of patching autogen.sh, just pass -V as argument, as this is
passed on to configure and lets it just print its version instead of
configuring the build tree.

Also drop arguments from autogen.sh, as they are unused when configure
does not run.

* libtheora: fix build on macos

Apply upstream patches in order to avoid unresolved symbols during building of libtheoraenc.
These patches require re-running automake/autoconf/...

Error messages:
libtool: link: /Users/ma/git/spack/lib/spack/env/clang/clang -dynamiclib  -o .libs/libtheoraenc.1.dylib  .libs/apiwrapper.o .libs/fragment.o .libs/idct.o .libs/internal.o .libs/state.o .libs/quant.o .l
ibs/analyze.o .libs/fdct.o .libs/encfrag.o .libs/encapiwrapper.o .libs/encinfo.o .libs/encode.o .libs/enquant.o .libs/huffenc.o .libs/mathops.o .libs/mcenc.o .libs/rate.o .libs/tokenize.o   -L/opt/spac
k/darwin-sonoma-m1/apple-clang-15.0.0/libtheora-1.1.1-uflq3jvysewnrmlj5x5tvltst65ho3v4/lib -logg -lm  -Wl,-exported_symbols_list -Wl,/var/folders/zv/qr55pmd9065glf0mcltpx5bm000102/T/ma/spack-stage/spac
k-stage-libtheora-1.1.1-uflq3jvysewnrmlj5x5tvltst65ho3v4/spack-src/lib/theoraenc.exp   -install_name  /opt/spack/darwin-sonoma-m1/apple-clang-15.0.0/libtheora-1.1.1-uflq3jvysewnrmlj5x5tvltst65ho3v4/lib
/libtheoraenc.1.dylib -compatibility_version 3 -current_version 3.2
ld: warning: search path '/opt/spack/darwin-sonoma-m1/apple-clang-15.0.0/libtheora-1.1.1-uflq3jvysewnrmlj5x5tvltst65ho3v4/lib' not found
ld: Undefined symbols:
  _th_comment_add, referenced from:
      _theora_comment_add in apiwrapper.o
  _th_comment_add_tag, referenced from:
      _theora_comment_add_tag in apiwrapper.o
  _th_comment_clear, referenced from:
      _theora_comment_clear in apiwrapper.o
  _th_comment_init, referenced from:
      _theora_comment_init in apiwrapper.o
  _th_comment_query, referenced from:
      _theora_comment_query in apiwrapper.o
  _th_comment_query_count, referenced from:
      _theora_comment_query_count in apiwrapper.o

* libtheora: add git versions

stable as version name for theora-1.1 branch was chosen so that it sorts between 1.1.x and master

* libtheora: remove unused patch

thanks to @michaelkuhn for noticing
2023-11-03 00:08:22 +01:00
garylawson
94d143763e Update Anaconda3 -- add version 2023.09-0 for x86_64, aarch64, and ppc64le (#40622)
* Add 2023.09-0 for x86_64, aarch64, and ppc64le
   extend the anaconda3 package.py to support aarch64 and ppc64le. 
   add the latest version of anaconda3 to each new platform, including the existing x86_64
* formatting
2023-11-02 16:42:44 -06:00
Vanessasaurus
6f9425c593 Automated deployment to update package flux-sched 2023-10-18 (#40596)
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
Co-authored-by: Tom Scogland <scogland1@llnl.gov>
2023-11-02 13:16:39 -07:00
Nicolas Cornu
05953e4491 highfive: 2.8.0 (#40837)
Co-authored-by: Nicolas Cornu <me@alkino.fr>
2023-11-02 14:03:44 -06:00
Sergey Kosukhin
6b236f130c eccodes: rename variant 'definitions' to 'extra_definitions' (#36186) 2023-11-02 13:28:31 -06:00
Greg Becker
fa08de669e bugfix: computing NodeID2 in requirement node_flag_source (#40846) 2023-11-02 20:17:54 +01:00
Seth R. Johnson
c2193b5470 py-pint: new versions 0.21, 0.22 (#40745)
* py-pint: new versions 0.21, 0.22

* Address feedback

* Fix dumb typo

* Add typing extension requirement
2023-11-02 14:13:19 -05:00
Chris Richardson
b5b94d89d3 Update to latest version (#40778) 2023-11-02 14:07:44 -05:00
vucoda
dd57b58c2f py-pyside2: fix to build with newer llvm and to use spack install headers (#40544)
* Fix py-pyside2 to build with newer llvm and to use spack libglx and libxcb headers where system headers are missing

pyside2 needs LLVM_INSTALL_DIR to be set when using llvm 11: and expects system headers for libglx and libxcb and won't build otherwise.

* Fix styling

* remove raw string type

* Update var/spack/repos/builtin/packages/py-pyside2/package.py

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-11-02 14:03:18 -05:00
Chris Richardson
29a30963b3 Fixes to ffcx @0.6.0 (#40787) 2023-11-02 14:02:07 -05:00
Jordan Ogas
3447e425f0 add charliecloud 0.35 (#40842)
* add charliecloud 0.35
* fix linter rage
* fix linter rage?
2023-11-02 11:23:49 -07:00
Juan Miguel Carceller
518da16833 Gaudi: Add a few versions and a dependency on tbb after 37.1 (#40802)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-11-02 11:15:27 -07:00
Paul R. C. Kent
4633327e60 llvm: add 17.0.2-4 (#40820) 2023-11-02 17:00:35 +01:00
Harmen Stoppels
6930176ac6 clingo ^pyhton@3.12: revisit distutils fix (#40844) 2023-11-02 16:48:21 +01:00
Adam J. Stewart
bb64b22066 PyTorch: build with external sleef (#40763)
Co-authored-by: adamjstewart <adamjstewart@users.noreply.github.com>
2023-11-02 16:09:49 +01:00
Harmen Stoppels
8b0ab67de4 depfile: deal with empty / non-concrete env (#40816) 2023-11-02 16:04:35 +01:00
Satish Balay
dbf21bf843 exago: update petsc dependency (#40831) 2023-11-02 07:29:37 -07:00
Harmen Stoppels
af3a29596e go/rust bootstrap: no versions if unsupported arch (#40841)
The lookup in a dictionary causes KeyError on package load for
unsupported architectures such as i386 and ppc big endian.
2023-11-02 08:13:13 -06:00
Harmen Stoppels
80944d22f7 spack external find: fix multi-arch troubles (#33973) 2023-11-02 09:45:31 +01:00
Tamara Dahlgren
f56efaff3e env remove: add a unit test removing two environments (#40814) 2023-11-02 08:51:08 +01:00
Martin Aumüller
83bb2002b4 openscenegraph: support more file formats (#39897) 2023-11-02 08:41:03 +01:00
Massimiliano Culpo
16fa3b9f07 Cherry-picking virtual dependencies (#35322)
This PR makes it possible to select only a subset of virtual dependencies from a spec that _may_ provide more. To select providers, a syntax to specify edge attributes is introduced:
```
hdf5 ^[virtuals=mpi] mpich
```
With that syntax we can concretize specs like:
```console
$ spack spec strumpack ^[virtuals=mpi] intel-parallel-studio+mkl ^[virtuals=lapack] openblas
```

On `develop` this would currently fail with:
```console
$ spack spec strumpack ^intel-parallel-studio+mkl ^openblas
==> Error: Spec cannot include multiple providers for virtual 'blas'
    Requested 'intel-parallel-studio' and 'openblas'
```

In package recipes, virtual specs that are declared in the same `provides` directive need to be provided _together_. This means that e.g. `openblas`, which has:
```python
provides("blas", "lapack")
```
needs to provide both `lapack` and `blas` when requested to provide at least one of them.

## Additional notes

This capability is needed to model compilers. Assuming that languages are treated like virtual dependencies, we might want e.g. to use LLVM to compile C/C++ and Gnu GCC to compile Fortran. This can be accomplished by the following[^1]:
```
hdf5 ^[virtuals=c,cxx] llvm ^[virtuals=fortran] gcc
```

[^1]: We plan to add some syntactic sugar around this syntax, and reuse the `%` sigil to avoid having a lot of boilerplate around compilers.

Modifications:
- [x] Add syntax to interact with edge attributes from spec literals
- [x] Add concretization logic to be able to cherry-pick virtual dependencies
- [x] Extend semantic of the `provides` directive to express when virtuals need to be provided together
- [x] Add unit-tests and documentation
2023-11-01 23:35:23 -07:00
Thomas Madlener
6cd2241e49 edm4hep: Add 0.10.1 tag and update maintainers (#40829)
* edm4hep: add latest tag
* edm4hep: Add myself as maintainer
2023-11-01 23:04:00 -06:00
snehring
6af45230b4 ceres-solver: adding version 2.2.0 (#40824)
* ceres-solver: adding version 2.2.0
* ceres-solver: adding suite-sparse dep
2023-11-01 17:47:55 -07:00
snehring
a8285f0eec vcftools: add v0.1.16 (#40805)
* vcftools: adding new version 0.1.16

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

Co-authored-by: Alec Scott <alec@bcs.sh>

---------

Co-authored-by: Alec Scott <alec@bcs.sh>
2023-11-01 16:33:12 -07:00
Adam J. Stewart
e7456e1aab py-matplotlib: add v3.8.1 (#40819) 2023-11-01 16:33:00 -07:00
Jeremy L Thompson
dd636dd3fb libCEED v0.12.0, Ratel v0.3.0 (#40822)
* ratel - add v0.3.0
* libceed - add version 0.12.0
2023-11-01 16:29:18 -07:00
Mikael Simberg
a73c95b734 pika: Add 0.20.0 (#40817) 2023-11-01 17:19:56 -06:00
Miroslav Stoyanov
33b355a085 heffte: add v2.4.0 (#40741)
* update the heffte versions

* remove obsolete patch files

* update testing

* style

* restore version (unknown reason)

* restore old patch

* change the syntax

* [@spackbot] updating style on behalf of mkstoyanov

* missed one

* style
2023-11-01 16:54:11 -06:00
Satish Balay
f7630f265b pflotran: add version 5.0.0 (#40828)
alquimia: add version 1.1.0
And fix alquimia@master
2023-11-01 15:16:04 -07:00
dependabot[bot]
9744e86d02 build(deps): bump black in /.github/workflows/style (#40681)
Bumps [black](https://github.com/psf/black) from 23.9.1 to 23.10.1.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](https://github.com/psf/black/compare/23.9.1...23.10.1)

---
updated-dependencies:
- dependency-name: black
  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>
2023-11-01 14:20:29 -07:00
Harmen Stoppels
ff6bbf03a1 changelog: add 0.20.2 and 0.20.3 changes (#40818) 2023-11-01 22:09:11 +01:00
Cameron Rutherford
0767c8673e hiop: fix cuda constraints and add tag to versions (#40721)
* hiop: fix cuda constraints and add tag to versions

* hiop: fix styling
2023-11-01 13:21:14 -07:00
Satish Balay
9aa75eaf65 superlu-dist: -std=c99 prevents usage of putenv() (#40729) 2023-11-01 12:44:13 -07:00
Weiqun Zhang
73f012b999 amrex: add v23.11 (#40821) 2023-11-01 12:38:02 -07:00
Satish Balay
c7a8a83cbf petsc, py-petsc4py: add v3.20.1 (#40794) 2023-11-01 12:37:53 -07:00
Satish Balay
5f87db98ea butterflypack: add version 2.4.0 (#40826) 2023-11-01 12:20:13 -07:00
Brian Van Essen
d05dc8a468 LBANN: add explicit variant for shared builds (#40808) 2023-11-01 13:18:57 -06:00
wspear
afa2a2566e Add 2.33 to tau (#40810) 2023-11-01 12:10:35 -07:00
Thomas Madlener
581f45b639 podio: Add latest tags and variants and update dependencies accordingly (#40182)
* Make sure sio is in dependent build env for podio

* podio: Fix likely(?) typo in root dependency

* podio: Add latest tag and new variants + dependencies

* podio: Add v00-16-07 tag

* podio: Fix dependencies flagged by package audit

* podio: Simplify root dependency

* podio: Add 0.17.1 tag
2023-11-01 13:44:11 -05:00
Bilal Mirza
92780a9af6 fix: sentence framing (#40809) 2023-11-01 11:41:37 +01:00
Harmen Stoppels
2ea8e6c820 Executable.add_default_arg: multiple (#40801) 2023-11-01 09:14:37 +01:00
Harmen Stoppels
ac976a4bf4 Parser: fix ambiguity with whitespace in version ranges (#40344)
Allowing white space around `:` in version ranges introduces an ambiguity:

```
a@1: b
```

parses as `a@1:b` but should really be parsed as two separate specs `a@1:` and `b`.

With white space disallowed around `:` in ranges, the ambiguity is resolved.
2023-11-01 09:08:57 +01:00
Harmen Stoppels
e5f3ffc04f SetupContext.get_env_modifications fixes and documentation (#40683)
Call setup_dependent_run_environment on both link and run edges,
instead of only run edges, which restores old behavior.

Move setup_build_environment into get_env_modifications

Also call setup_run_environment on direct build deps, since their run
environment has to be set up.
2023-11-01 08:47:15 +01:00
Harmen Stoppels
7aaed4d6f3 Revert python build isolation & setuptools source install (#40796)
* Revert "Improve build isolation in PythonPipBuilder (#40224)"

This reverts commit 0f43074f3e.

* Revert "py-setuptools: sdist + rpath patch backport (#40205)"

This reverts commit 512e41a84a.
2023-11-01 07:10:34 +01:00
Tamara Dahlgren
f5d717cd5a Fix env remove indentation (#40811) 2023-11-01 00:08:46 -06:00
Sreenivasa Murthy Kolam
cb018fd7eb Enable address sanitizer in rocm's llvm-amdgpu package. (#40570)
* enable address sanitizer in rocm's llvm-amdgpu package
* remove references to 5.7.0 for now
* fix style error
* address review comments
2023-10-31 19:09:40 -06:00
Luisa Burini
e5cebb6b6f fix create/remove env with invalid spack.yaml (#39898)
* fix create/remove env with invalid spack.yaml
* fix isort error
* fix env ident unittests
* Fix pull request points
2023-10-31 15:39:42 -07:00
Patrick Bridges
4738b45fb1 beatnik: mall changes for v1.0 (#40726)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-10-31 22:28:48 +01:00
Harmen Stoppels
343ed8a3fa force color in subshell if not SPACK_COLOR (#40782) 2023-10-31 22:27:00 +01:00
Adam J. Stewart
58e5315089 PyTorch: build with external gloo (#40759)
* PyTorch: build with external gloo

* Fix gloo compilation with GCC 11

* undeprecate

* py-torch+cuda+gloo requires gloo+cuda
2023-10-31 16:25:24 -05:00
Samuel Li
26649e71f9 Update sperr (#40626)
* update SPERR package
* remove blank line
* update SPERR to be version 0.7.1
* a little clean up
* bound versions that require zstd
* add USE_ZSTD
* add libpressio-sperr version upbound
* update libpressio-sperr
* address review comments
* improve format

---------

Co-authored-by: Samuel Li <Sam@Navada>
Co-authored-by: Samuel Li <sam@cisl-m121a>
2023-10-31 13:53:09 -07:00
Peter Scheibel
2f2d9ae30d Fix cflags requirements (#40639) 2023-10-31 21:19:12 +01:00
jalcaraz
f9c0a15ba0 TAU: Added dyninst variant (#40790)
* Added dyninst variant

* Added dyninst variant and fixed some issues

* Update package.py

* Removed whitespace

* Update package.py

* Update package.py

* Fixed conflicting version

---------

Co-authored-by: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com>
2023-10-31 13:28:16 -06:00
Sreenivasa Murthy Kolam
14cb923dd8 add new recipe for rocm packages- amdsmi (#39270)
* add new recipe for rocm packages- amdsmilib
* update tags,maintainers list
2023-10-31 10:18:32 -07:00
Massimiliano Culpo
544a121248 Fix interaction of spec literals that propagate variants with unify:false (#40789)
* Add tests to ensure variant propagation syntax can round-trip to/from string

* Add a regression test for the bug in 35298

* Reconstruct the spec constraints in the worker process

Specs do not preserve any information on propagation of variants
when round-tripping to/from JSON (which we use to pickle), but
preserve it when round-tripping to/from strings.

Therefore, we pass a spec literal to the worker and reconstruct
the Spec objects there.
2023-10-31 17:50:13 +01:00
Harmen Stoppels
cd6bb9e159 spack checksum: improve signature (#40800) 2023-10-31 16:52:53 +01:00
Greg Sjaardema
e420a685a9 Seacas: Update for latest seacas releaes version (#40698) 2023-10-31 09:38:20 -06:00
Harmen Stoppels
40a5c1ff2d spack checksum: fix error when initial filter yields empty list (#40799) 2023-10-31 15:08:41 +01:00
Harmen Stoppels
6933e1c3cb ci: bump tutorial image and toolchain (#40795) 2023-10-31 12:58:33 +01:00
Harmen Stoppels
160bfd881d tutorial: replace zlib -> gmake to avoid deprecated versions (#40769) 2023-10-31 10:04:53 +01:00
G-Ragghianti
81997ae6d6 Added NVML and cgroup support to the slurm package (#40638)
* Added NVML support to the slurm package
* dbus package is required for cgroup support
* Fixing formatting
* Style fix
* Added PAM support
* Added ROCm SMI support
2023-10-30 19:12:09 -07:00
Todd Gamblin
702a2250fa docs: update license() docs with examples and links (#40598)
- [x] Add links to information people are going to want to know when adding license
      information to their packages (namely OSI licenses and SPDX identifiers).
- [x] Update the packaging docs for `license()` with Spack as an example for `when=`.
      After all, it's a dual-licensed package that changed once in the past.
- [x] Add link to https://spdx.org/licenses/ in the `spack create` boilerplate as well.
2023-10-30 18:54:31 -07:00
Freifrau von Bleifrei
3a0f9ce226 selalib: add (sca)lapack dependency (#40667)
* selalib: add (sca)lapack dependency
* selalib: change when "-mpi" to "~mpi"
2023-10-30 18:28:52 -07:00
Thomas Madlener
a095c8113d dd4hep: Add tag for version 1.27 (#40776) 2023-10-30 17:55:33 -07:00
Larry Knox
4ef433b64d Add hdf5 version 1.14.3. (#40786)
Add hdf5 version 1.10.11.
Update version condition for adding h5pfc->h5fc symlink.  File h5pfc
exists in versions 1.10.10 and 1.10.22.
2023-10-30 17:22:55 -06:00
dependabot[bot]
f228c7cbcc build(deps): bump black from 23.9.1 to 23.10.1 in /lib/spack/docs (#40680)
Bumps [black](https://github.com/psf/black) from 23.9.1 to 23.10.1.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](https://github.com/psf/black/compare/23.9.1...23.10.1)

---
updated-dependencies:
- dependency-name: black
  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>
2023-10-31 00:11:53 +01:00
MatthewLieber
e9ca16ab07 adding sha for OMB 7.3 release (#40784)
Co-authored-by: Matt Lieber <lieber.31@osu.edu>
2023-10-30 16:01:48 -07:00
Andrew W Elble
47ac2b8d09 squashfuse: add version 0.5.0 (#40775) 2023-10-30 11:33:22 -06:00
Harmen Stoppels
b1b8500eba ci: print colored specs in concretization progress (#40711) 2023-10-30 15:29:27 +01:00
Harmen Stoppels
060a1ff2f3 tty: flush immediately (#40774) 2023-10-30 15:07:30 +01:00
marcost2
9ed9a541c9 freesurfer: fix support for linux (#39864)
* Load the script file during enviroment setup so that all the enviroment variables are set properly
* Patch csh/tcsh so that it uses spacks via env
* Update SHA for latest version
* Extend shebang to perl and fix up the regex
2023-10-30 14:19:42 +01:00
Alec Scott
1ebf1c8d1c must: remove release candidates (#40476) 2023-10-30 14:08:23 +01:00
SXS Bot
c2f3943e9e spectre: add v2023.10.11 (#40463)
Co-authored-by: nilsvu <nilsvu@users.noreply.github.com>
2023-10-30 13:56:05 +01:00
Brian Vanderwende
1ba530bff5 Get utilities necessary for successful PIO build (#40502) 2023-10-30 13:53:57 +01:00
RichardBuntLinaro
cc09e88a4a linaro-forge: add v23.0.4 (#40772) 2023-10-30 06:43:07 -06:00
Harmen Stoppels
2f3801196d binary_distribution.py: fix type annotation singleton (#40572)
Convince the language server it's really just a BinaryCacheIndex,
otherwise it defaults to thinking it's Singleton, and can't autocomplete
etc.
2023-10-30 12:52:47 +01:00
Juan Miguel Carceller
d03289c38b Fetch recola from gitlab and add a new version of collier (#40651)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-10-30 12:22:31 +01:00
kwryankrattiger
e720d8640a ISPC: Drop ncurses workaround in favor of patch (#39662)
ISPC had a bug in their lookup for NCurses, this was fixed upstream and
backported here.
2023-10-30 12:16:25 +01:00
Federico Ficarelli
00602cda4f pegtl: add v3.2.7 (#35687) 2023-10-30 12:12:20 +01:00
Alberto Sartori
35882130ce justbuild: add version 1.2.2 (#40701) 2023-10-30 12:09:42 +01:00
Brian Van Essen
1586c8c786 aluminum: make network variants "sticky" (#40715) 2023-10-30 11:26:24 +01:00
Wouter Deconinck
a9e78dc7d8 acts: new variant +binaries when +examples (#40738)
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
2023-10-30 10:40:31 +01:00
wspear
b53b235cff RAJA: add "plugins" variant (#40750) 2023-10-30 09:40:08 +01:00
Veselin Dobrev
33cb8c988f Fix an issue with using the environment variable MACHTYPE which is not always defined (#40733)
* Fix an issue reported here:
   https://github.com/spack/spack/pull/36154#issuecomment-1781854894

* [@spackbot] updating style on behalf of v-dobrev
2023-10-30 09:36:02 +01:00
Adam J. Stewart
6511d3dfff py-pandas: add v2.1.2 (#40734) 2023-10-30 03:32:48 -05:00
Adam J. Stewart
272ca0fc24 PyTorch: build with external fp16 (#40760) 2023-10-30 09:28:52 +01:00
Martin Aumüller
a8f42b865f pcl: checksum new versions (#39039) 2023-10-30 08:54:36 +01:00
Cameron Rutherford
7739c54eb5 exago: fix exago missing on PYTHONPATH when +python (#40748) 2023-10-30 08:35:36 +01:00
Veselin Dobrev
bd1bb7d1ba mfem: support petsc+rocm with spack-installed rocm (#40768) 2023-10-30 01:17:51 -06:00
Massimiliano Culpo
6983db1392 ASP-based solver: avoid cycles in clingo using hidden directive (#40720)
The code should be functonally equivalent to what it was before,
but now to avoid cycles by design we are using a "hidden"
feature of clingo
2023-10-30 07:38:53 +01:00
Wouter Deconinck
2a797f90b4 acts: add v28.1.0:30.3.2 (#40723)
* acts: new version from 28.1.0 to 30.3.1

* acts: new version 30.3.2

* acts: new variant +podio
2023-10-29 18:01:27 -07:00
Harmen Stoppels
2e097b4cbd py-numcodecs: fix broken sse / avx2 variables (#40754) 2023-10-29 13:45:23 -05:00
Aoba
a1282337c0 Add liggght patched for newer compiler (#38685)
* Add liggght patched for newer compiler

Add C++ 17 support
Add Clang and Oneapi support

* Add maintainers

* Fix format in liggghts

* Fix maintainers before versions

Co-authored-by: Alec Scott <alec@bcs.sh>

* Fix style and user to usr

* Update package.py

---------

Co-authored-by: Alec Scott <alec@bcs.sh>
2023-10-29 09:56:27 -07:00
Jerome Soumagne
361d973f97 mercury: add v2.3.1 (#40749) 2023-10-28 10:05:50 -07:00
Lydéric Debusschère
64ec6e7d8e py-moarchiving: new package (#40558)
* [add] py-moarchiving: new package

* py-moarchiving: update from review: description, variant default value is False, switch when and type

---------

Co-authored-by: LydDeb <lyderic.debusschere@eolen.com>
2023-10-28 08:06:48 -05:00
Lydéric Debusschère
9f95945cb5 py-generateds: new package (#40555)
* [add] py-generateds: new package

* py-generateds: Update from review

Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>

* py-generateds: add versions 2.41.5, 2.42.1, 2.42.2, 2.43.1 and 2.43.2

---------

Co-authored-by: LydDeb <lyderic.debusschere@eolen.com>
Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
2023-10-28 08:05:37 -05:00
Rémi Lacroix
21f3240e08 NCCL: Add version 2.19.3-1 (#40704) 2023-10-28 08:03:02 -05:00
Jen Herting
28d617c1c8 New version of py-langsmith (#40674)
Co-authored-by: Benjamin Meyers <bsmits@rit.edu>
2023-10-28 08:02:19 -05:00
Erik Heeren
7da4b3569f py-bluepyemodel: opensourcing with dependencies (#40592)
* py-bluepyemodel: new package with dependencies

* py-morphio: add MPI as dependency to avoid failing builds

* Formatting

* py-bluepyefe: no need to set NEURON_INIT_MPI

* py-morphio: unifurcation branch is ancient history

* py-bluepyopt: only set NEURON_INIT_MPI with +neuron

* py-efel: get rid of old version

* py-morph{-tool,io}: rename develop to master to match branch

* py-bluepyefe: unset PMI_RANK is also neuron-related

* py-bluepyopt: PMI_RANK is also neuron-related

* Implement review remarks

* py-morph-tool, py-neurom: small fixes

* py-morphio: reword dependencies
2023-10-28 07:55:49 -05:00
Manuela Kuhn
f8aa66b62e py-comm: add 0.1.4 (#40669) 2023-10-28 07:51:55 -05:00
Adam J. Stewart
a1d3e0002c py-numpy: add v1.26 (#40057) 2023-10-28 13:17:32 +02:00
John W. Parent
148dce96ed MSVC: detection from registry (#38500)
Typically MSVC is detected via the VSWhere program. However, this may
not be available, or may be installed in an unpredictable location.
This PR adds an additional approach via Windows Registry queries to
determine VS install location root.

Additionally:

* Construct vs_install_paths after class-definition time (move it to
  variable-access time).
* Skip over keys for which a user does not have read permissions
  when performing searches (previously the presence of these keys
  would have caused an error, regardless of whether they were
  needed).
* Extend helper functionality with option for regex matching on
  registry keys vs. exact string matching.
* Some internal refactoring: remove boolean parameters in some cases
  where the function was always called with the same value
  (e.g. `find_subkey`)
2023-10-27 16:58:50 -07:00
Mosè Giordano
9e01199e13 hipsycl: restrict compatibility with llvm for v0.8.0 (#40736) 2023-10-27 21:33:48 +02:00
eugeneswalker
ed7274a4d0 e4s ci stacks: add exago specs (#40712)
* e4s ci: add exago +cuda, +rocm builds

* exago: rename 5-18-2022-snapshot to snapshot.5-18-2022

* disable exago +rocm for non-external rocm ci install

* note that hiop +rocm fails to find hip libraries when they are spack-installed
2023-10-27 11:15:11 -07:00
eugeneswalker
f2963e41ba mgard@2020-10-01 %oneapi@2023: turn of c++11-narrowing via cxxflags (#40743) 2023-10-27 12:08:33 -06:00
John W. Parent
069762cd37 External finding: update default paths; treat .bat as executable on Windows (#39850)
.bat or .exe files can be considered executable on Windows. This PR
expands the regex for detectable packages to allow for the detection
of packages that vendor .bat wrappers (intel mpi for example).

Additional changes:

* Outside of Windows, when searching for executables `path_hints=None`
  was used to indicate that default path hints should be provided,
  and `[]` was taken to mean that no defaults should be chosen
  (in that case, nothing is searched); behavior on Windows has
  now been updated to match.
* Above logic for handling of `path_hints=[]`  has also been extended
  to library search (for both Linux and Windows).
* All exceptions for external packages were documented as timeout
  errors: this commit adds a distinction for other types of errors
  in warning messages to the user.
2023-10-27 10:40:44 -07:00
Harmen Stoppels
195f965076 OCI buildcache (#38358)
Credits to @ChristianKniep for advocating the idea of OCI image layers
being identical to spack buildcache tarballs.

With this you can configure an OCI registry as a buildcache:

```console 
$ spack mirror add my_registry oci://user/image # Dockerhub

$ spack mirror add my_registry oci://ghcr.io/haampie/spack-test # GHCR

$ spack mirror set --push --oci-username ... --oci-password ... my_registry  # set login credentials
```

which should result in this config:

```yaml
mirrors:
  my_registry:
    url: oci://ghcr.io/haampie/spack-test
    push:
      access_pair: [<username>, <password>]
```

It can be used like any other registry

```
spack buildcache push my_registry [specs...]
```

It will upload the Spack tarballs in parallel, as well as manifest + config
files s.t. the binaries are compatible with `docker pull` or `skopeo copy`.

In fact, a base image can be added to get a _runnable_ image:

```console
$ spack buildcache push --base-image ubuntu:23.04 my_registry python
Pushed ... as [image]:python-3.11.2-65txfcpqbmpawclvtasuog4yzmxwaoia.spack

$ docker run --rm -it [image]:python-3.11.2-65txfcpqbmpawclvtasuog4yzmxwaoia.spack
```

which should really be a game changer for sharing binaries.

Further, all content-addressable blobs that are downloaded and verified
will be cached in Spack's download cache. This should make repeated
`push` commands faster, as well as `push` followed by a separate
`update-index` command.

An end to end example of how to use this in Github Actions is here:

**https://github.com/haampie/spack-oci-buildcache-example**


TODO:

- [x] Generate environment modifications in config so PATH is set up
- [x] Enrich config with Spack's `spec` json (this is allowed in the OCI specification)
- [x] When ^ is done, add logic to create an index in say `<image>:index` by fetching all config files (using OCI distribution discovery API)
- [x] Add logic to use object storage in an OCI registry in `spack install`.
- [x] Make the user pick the base image for generated OCI images.
- [x] Update buildcache install logic to deal with absolute paths in tarballs
- [x] Merge with `spack buildcache` command
- [x] Merge #37441 (included here)
- [x] Merge #39077 (included here)
- [x] #39187 + #39285
- [x] #39341
- [x] Not a blocker: #35737 fixes correctness run env for the generated container images

NOTE:

1. `oci://` is unfortunately taken, so it's being abused in this PR to mean "oci type mirror". `skopeo` uses `docker://` which I'd like to avoid, given that classical docker v1 registries are not supported.
2. this is currently `https`-only, given that basic auth is used to login. I _could_ be convinced to allow http, but I'd prefer not to, given that for a `spack buildcache push` command multiple domains can be involved (auth server, source of base image, destination registry). Right now, no urllib http handler is added, so redirects to https and auth servers with http urls will simply result in a hard failure.

CAVEATS:

1. Signing is not implemented in this PR. `gpg --clearsign` is not the nicest solution, since (a) the spec.json is merged into the image config, which must be valid json, and (b) it would be better to sign the manifest (referencing both config/spec file and tarball) using more conventional image signing tools
2. `spack.binary_distribution.push` is not yet implemented for the OCI buildcache, only `spack buildcache push` is. This is because I'd like to always push images + deps to the registry, so that it's `docker pull`-able, whereas in `spack ci` we really wanna push an individual package without its deps to say `pr-xyz`, while its deps reside in some `develop` buildcache.
3. The `push -j ...` flag only works for OCI buildcache, not for others
2023-10-27 15:30:04 +02:00
Ashwin Kumar Karnad
3fff8be929 octopus: split netcdf-c and netcdf-fortran dependency (#40685) 2023-10-27 14:24:44 +02:00
Satish Balay
1bf758a784 strumpack: add version 7.2.0 (#40732) 2023-10-27 04:29:15 -07:00
Harmen Stoppels
9b8fb413c3 gromacs: default to external blas & lapack (#40490)
* gromacs: default to external blas & lapack

* drop vendored lapack/blas altogether
2023-10-27 09:51:12 +02:00
Harmen Stoppels
51275df0b1 ci: spack compiler find should list extra config scopes (#40727)
otherwise it detected pre-configured compilers in an potentially different way.
2023-10-27 09:43:01 +02:00
dmt4
af13d16c2c Fixes and options for package spglib (#40684)
* Fix cmake_args for spglib v2.1.0+

* Add option to build fortran interface in package spglib

* fix style as sugested by ci/prechecks/style

* Enable fortran variant from v1.16.4 as suggested

Co-authored-by: Rocco Meli <r.meli@bluemail.ch>

---------

Co-authored-by: Rocco Meli <r.meli@bluemail.ch>
2023-10-27 08:55:57 +02:00
Harmen Stoppels
37f48aff8b gromacs: fix version branch in intel fftw (#40489) 2023-10-27 08:29:02 +02:00
Alec Scott
feda52f800 akantu: use f-strings (#40466)
Co-authored-by: Nicolas Richart <nrichart@users.noreply.github.com>
2023-10-27 08:12:20 +02:00
Satish Balay
8959d65577 plasma: add version 23.8.2 (#40728) 2023-10-26 16:48:20 -06:00
Carlos Bederián
546695f193 itk: misc fixes (#39832)
* itk: patch missing include for newer compilers

* itk: The package doesn't use MPI

* itk: package requires the high-level hdf5 api

* itk: patch url with ?full_index=1

* itk: point to 4041 commit in master

* itk: don't constrain hdf5 with ~mpi
2023-10-26 15:13:27 -07:00
snehring
c3f5ee54d4 ldak: add v5.2 & add maintainer (#40710)
* ldak: update to 5.2, add maintainer

* ldak: use compiler.openmp_flag
2023-10-26 15:12:10 -07:00
Daniel Arndt
d64f312726 dataTransferKit: add v3.1.1, v3.1.0 (#40556)
* Update DataTransferKit for 3.1.1 release

* Require Trilinos-14 for 3.1.0 and higher
2023-10-26 15:10:16 -07:00
Adam J. Stewart
b4b25dec64 PythonPackage: allow archive_files to be overridden (#40694) 2023-10-26 15:25:56 -05:00
Torbjörn Lönnemark
81172f9251 curl: Fix librtmp variant (#40713)
* rtmpdump: New package

* curl: Fix librtmp variant

Add the previously missing dependency required for rtmp support.

The variant has been broken since its addition in PR #25166.

Fixes one of the two issues reported in #26887.
2023-10-26 21:11:43 +02:00
Alec Scott
cbf9dd0aee unmaintained a* packages: update to use f-strings (#40467) 2023-10-26 21:08:55 +02:00
Ryan Danehy
7ecb9243c1 Update spack package for exago@1.6.0 release (#40614)
* Update spack package for exago:1.6.0

* update style

* Weird spack style env bug fixed

* Update spack package for exago:1.6.0

* update style

* Weird spack style env bug fixed

* changes to allow release 1.6.0

* fix depends, and versioning

* rm cmake variable

* add s

* style fix

---------

Co-authored-by: Ryan Danehy <dane678@deception04.pnl.gov>
Co-authored-by: Ryan Danehy <dane678@deception03.pnl.gov>
Co-authored-by: ryan.danehy@pnnl.gov <dane678@we45149.home>
2023-10-26 11:18:31 -07:00
Harmen Stoppels
e96f31c29d spack checksum pkg@1.2, use as version filter (#39694)
* spack checksum pkg@1.2, use as version filter

Currently pkg@1.2 splits on @ and looks for 1.2 specifically, with this
PR pkg@1.2 is a filter so any matching 1.2, 1.2.1, ..., 1.2.10 version
is displayed.

* fix tests

* fix style
2023-10-26 09:57:55 -07:00
Auriane R
53d5011192 Add conflict between cxxstd > 17 and cuda < 12 in pika (#40717)
* Add conflict with C++ standard > 17 and cuda < 12

* Removing map_cxxstd since boost supports C++20 flag
2023-10-26 16:08:21 +02:00
Xavier Delaruelle
751b64cbcd modules: no --delim option if separator is colon character (#39010)
Update Tcl modulefile template to simplify generated `append-path`,
`prepend-path` and `remove-path` commands and improve their readability.

If path element delimiter is colon character, do not set the `--delim`
option as it is the default delimiter value.
2023-10-26 15:55:49 +02:00
Adam J. Stewart
f57c2501a3 PythonPackage: nested config_settings (#40693)
* PythonPackage: nested config_settings

* flake8
2023-10-26 08:18:02 -05:00
Harmen Stoppels
1c8073c21f spack checksum: show long flags in usage output (#40407) 2023-10-26 14:48:35 +02:00
Xavier Delaruelle
86520abb68 modules: hide implicit modulefiles (#36619)
Renames exclude_implicits to hide_implicits

When hide_implicits option is enabled, generate modulefile of
implicitly installed software and hide them. Even if implicit, those
modulefiles may be referred as dependency in other modulefiles thus they
should be generated to make module properly load dependent module.

A new hidden property is added to BaseConfiguration class.

To hide modulefiles, modulercs are generated along modulefiles. Such rc
files contain specific module command to indicate a module should be
hidden (for instance when using "module avail").

A modulerc property is added to TclFileLayout and LmodFileLayout classes
to get fully qualified path name of the modulerc associated to a given
modulefile.

Modulerc files will be located in each module directory, next to the
version modulefiles. This scheme is supported by both module tool
implementations.

modulerc_header and hide_cmd_format attributes are added to
TclModulefileWriter and LmodModulefileWriter. They help to know how to
generate a modulerc file with hidden commands for each module tool.

Tcl modulerc file requires an header. As we use a command introduced on
Modules 4.7 (module-hide --hidden-loaded), a version requirement is
added to header string.

For lmod, modules that open up a hierarchy are never hidden, even if
they are implicitly installed.

Modulerc is created, updated or removed when associated modulefile is
written or removed. If an implicit modulefile becomes explicit, hidden
command in modulerc for this modulefile is removed. If modulerc becomes
empty, this file is removed. Modulerc file is not rewritten when no
content change is detected.

Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
2023-10-26 11:49:13 +00:00
Alberto Invernizzi
bf88ed45da libluv: require CMake 3 and CMP0042 (#40716) 2023-10-26 03:33:27 -06:00
Harmen Stoppels
b4cf3d9f18 git versions: fix commit shas [automated] (#40703) 2023-10-26 11:26:47 +02:00
Ben Boeckel
8e19576ec5 Paraview 5.12 prep (#40527)
* paraview: rebase the adios2 patch for 5.12-to-be

* paraview: disable fastfloat and token for 5.12-to-be

* paraview: require older protobuf for 5.12 as well

* paraview: require C++11-supporting protobuf for `master` too
2023-10-25 16:26:49 -07:00
Victoria Cherkas
3c590ad071 fdb: add releases v5.11.23 and v5.11.17 (#40571) 2023-10-25 16:24:54 -07:00
afzpatel
3e47f3f05c initial commit to fix mivisionx build for 5.6 (#40579) 2023-10-25 16:24:31 -07:00
Dominic Hofer
d9edc92119 cuda: add NVHPC_CUDA_HOME. (#40507)
* [cuda] Add NVHPC_CUDA_HOME.

* Add CUDA_HOME and NVHC_CUDA_HOME to cuda's dependent build env.

---------

Co-authored-by: Dominic Hofer <dominic.hofer@meteoswiss.ch>
2023-10-25 16:22:22 -07:00
Filippo Barbari
2a245fdd21 Added Highway versions up to 1.0.7 (#40691) 2023-10-25 15:49:46 -07:00
Adam J. Stewart
932d7a65e0 PyTorch: patch breakpad dependency (#40648) 2023-10-25 23:10:48 +02:00
dependabot[bot]
6bd2dd032b build(deps): bump pytest from 7.4.2 to 7.4.3 in /lib/spack/docs (#40697) 2023-10-25 20:58:53 +02:00
Harmen Stoppels
c0a4be156c ci: don't put compilers in config (#40700)
* ci: don't register detectable compilers

Cause they go out of sync...

* remove intel compiler, it can be detected too

* Do not run spack compiler find since compilers are registered in concretize job already

* trilinos: work around +stokhos +cuda +superlu-dist bug due to EMPTY macro
2023-10-25 11:55:04 -07:00
Harmen Stoppels
0c30418732 ci: darwin aarch64 use apple-clang-15 tag (#40706) 2023-10-25 17:35:47 +02:00
Adam J. Stewart
3063093322 py-lightning: py-torch~distributed is broken again (#40696) 2023-10-25 13:06:35 +02:00
Rocco Meli
f4bbc0dbd2 Add dlaf variant to cp2k (#40702) 2023-10-25 04:13:32 -06:00
Taillefumier Mathieu
1ecb100e43 [cp2k] Use fftw3 MKL by default when cp2k is compiled with mkl (#40671) 2023-10-25 09:55:13 +02:00
John W. Parent
e1da9339d9 Windows: search PATH for patch utility (#40513)
Previously, we only searched for `patch` inside of whatever Git
installation was available because the most common installation of Git
available on Windows had `patch`. That's not true for all possible
installations of Git though, so this updates the search to also check
PATH.
2023-10-24 16:37:26 -07:00
Alex Richert
2d203df075 Add ufs-utils@1.11.0 (#40695)
* Add ufs-utils@1.11.0
* Update package.py
2023-10-24 15:46:23 -07:00
renjithravindrankannath
50f25964cf Updating rvs binary path. (#40604)
* Updating rvs binary path
* Updating spec check as per the recommendation
2023-10-24 15:30:02 -07:00
AMD Toolchain Support
95558d67ae openmpi: fix pmi@4.2.3: compat (#40686) 2023-10-24 20:06:32 +02:00
Filippo Barbari
83532b5469 Added new benchmark version up to 1.8.3 (#40689) 2023-10-24 10:26:26 -07:00
Alberto Invernizzi
444c27ca53 neovim: conflict for libluv problem on macOS + add newer versions of neovim and libluv (#40690)
* add conflict with libluv version >=1.44 just on macOS
* minor change
* add libluv versions
* neovim: add newer releases
2023-10-24 10:21:58 -07:00
eugeneswalker
d075732cc5 hiop +cuda: fix issue 40678 (#40688) 2023-10-24 10:28:23 -06:00
eugeneswalker
cf9a32e6db exago: fix v1.5.1 tag; only allow python up to 3.10 for for @:1.5 (#40676)
* exago: fix v1.5.1 tag; only allow python up to 3.10 for for @:1.5 due to pybind error with py 3.11

* hiop@:1.0 +cuda: constrain to cuda@:11.9
2023-10-24 01:08:05 -06:00
Annop Wongwathanarat
bc54aa1e82 armpl-gcc: add version 23.10 and macOS support (#40511) 2023-10-24 00:58:04 -06:00
Nakano Masaki
88622d5129 fix installation error of bear (#40637)
Co-authored-by: Tom Scogland <scogland1@llnl.gov>
2023-10-23 13:02:15 -07:00
Vicente Bolea
d0982115b3 Adios2: add kokkos variant (#40623)
* adios2: update variants and dependencies

* adios2: add kokkos rocm|cuda|sycl variant

* e4s oneapi ci stack: add adios2 +sycl

* e4s ci stack: add adios2 +rocm

* [@spackbot] updating style on behalf of vicentebolea

* Apply suggestions from code review

* adios2: fixed cuda variant

* update ecp-data-vis-sdk

* Update share/spack/gitlab/cloud_pipelines/stacks/e4s-power/spack.yaml

---------

Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
Co-authored-by: vicentebolea <vicentebolea@users.noreply.github.com>
2023-10-23 13:01:57 -07:00
Taillefumier Mathieu
1e4a5791b2 Add rccl and nccl variants to cp2k and cosma (#40451) 2023-10-23 12:37:42 -07:00
Jim Galarowicz
8def7f5583 Update survey package file for survey version 9 changes. (#40619)
* Update survey package file for survey version 9 changes.
* Fix single quote - make double.
* Small change to trigger spack tests
2023-10-23 12:31:20 -07:00
Adam J. Stewart
66f07088cb py-scikit-learn: add v1.3.2 (#40672) 2023-10-23 13:56:27 -05:00
Michael Kuhn
bf6d5df0ec audit: add check for GitLab patches (#40656)
GitLab's .patch URLs only provide abbreviated hashes, while .diff URLs
provide full hashes. There does not seem to be a parameter to force
.patch URLs to also return full hashes, so we should make sure to use
the .diff ones.
2023-10-23 20:22:39 +02:00
Olivier Cessenat
3eac79bba7 ngspice: new version 41 and option osdi (#40664) 2023-10-23 12:56:12 -04:00
Juan Miguel Carceller
47c9760492 geant4: add patch for when using the system expat library (#40650)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-10-23 16:11:51 +01:00
Harmen Stoppels
a452e8379e nghttp2: add v1.57.0 (#40652) 2023-10-23 16:22:41 +02:00
Aiden Grossman
a6466b9ddd 3proxy: respect compiler choice (#39240) 2023-10-23 03:43:54 -06:00
Harmen Stoppels
96548047f8 concretizer verbose: show progress in % too (#40654) 2023-10-23 10:26:20 +02:00
Harmen Stoppels
a675156c70 py-cython: new version, python 3.11 upperbound (#40343) 2023-10-23 09:37:20 +02:00
Tamara Dahlgren
cfc5363053 Docs: Update spec variant checks plus python quotes and string formatting (#40643) 2023-10-23 09:15:03 +02:00
Michael Kuhn
d9167834c4 libtheora: fix GitLab patch (#40657)
GitLab's .patch URLs do not provide stable/full hashes, while .diff URLs
do. See #40656 for more information.
2023-10-23 09:00:22 +02:00
Michael Kuhn
8a4860480a knem: fix GitLab patch (#40662)
GitLab's .patch URLs do not provide stable/full hashes, while .diff URLs
do. See #40656 for more information.
2023-10-23 08:59:58 +02:00
Michael Kuhn
f4c813f74a gobject-introspection: fix GitLab patch (#40661)
GitLab's .patch URLs do not provide stable/full hashes, while .diff URLs
do. See #40656 for more information.
2023-10-23 08:59:38 +02:00
Michael Kuhn
8b4e557fed garfieldpp: fix GitLab patch (#40660)
GitLab's .patch URLs do not provide stable/full hashes, while .diff URLs
do. See #40656 for more information.
2023-10-23 08:59:10 +02:00
Michael Kuhn
c5d0fd42e6 vtk: fix GitLab patch (#40659)
GitLab's .patch URLs do not provide stable/full hashes, while .diff URLs
do. See #40656 for more information.
2023-10-23 08:58:47 +02:00
Michael Kuhn
428202b246 libxml2: fix GitLab patch (#40658)
GitLab's .patch URLs do not provide stable/full hashes, while .diff URLs
do. See #40656 for more information.
2023-10-23 08:58:24 +02:00
Bill Williams
1c0d3bc071 Add Score-P 8.3 and dependencies (#40478)
Includes Score-P 8.3 and Cubew/cubelib 4.8.2.
2023-10-22 22:11:19 +02:00
Juan Miguel Carceller
eea3c07628 glib: add patch with a fix for PTRACE_0_EXITKILL (#40655)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-10-22 11:18:16 -06:00
Harmen Stoppels
7cd5fcb484 zlib-ng: add v2.1.4 (#40647) 2023-10-22 11:17:48 -06:00
Juan Miguel Carceller
bbb4c939da py-kiwisolver: add a new version (#40653)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-10-22 09:07:31 -05:00
Tamara Dahlgren
f915489c62 Docs: Add version range example to conditional dependencies (#40630)
* Docs: Add version range example to conditional dependencies

* Add when context manager example
2023-10-22 10:52:44 +02:00
Martin Aumüller
1527853efd intel-tbb: patch patch for Apple's patch (#40640)
While e.g. GNU patch 2.7.6 (as provided by homebrew) would apply the previous
version of this patch without problems, Apple's patch 2.0-12u11-Apple fails
to find out which file to patch.

Adding two lines to the patch fixes that. Renamed the patch in order to
not require a `spack clean -m`.
2023-10-21 09:26:36 -04:00
Harmen Stoppels
d820cf73e9 py-kombu: fix setuptools bound (#40646) 2023-10-21 13:38:30 +02:00
Scott Wittenburg
8714b24420 py-kombu: pick older version of py-setuptools (#40642) 2023-10-21 08:38:03 +02:00
Lydéric Debusschère
0c18f81b80 [add] py-dict2css: new package (#40552)
Co-authored-by: LydDeb <lyderic.debusschere@eolen.com>
2023-10-20 18:09:13 -06:00
Andrey Alekseenko
d442fac69a gromacs: add 2022.6, 2023.2, 2023.3 versions (#38906)
* gromacs: add 2022.6, 2023.2 versions
* gromacs: add version 2023.3
2023-10-20 17:28:45 -06:00
Garth N. Wells
76c57af021 py-fenics-ffcx: update to v0.7 (#40569) 2023-10-20 12:04:02 -05:00
Harmen Stoppels
27a0425e5d concretize separately: show concretization time per spec as they concretize when verbose (#40634) 2023-10-20 17:09:19 +02:00
Harmen Stoppels
4bade7ef96 gromacs +cp2k: build in CI (#40494)
* gromacs +cp2k: build in CI

* libxsmm: x86 only

* attempt to fix dbcsr + new mpich

* use c11 standard

* gromacs: does not depend on dbcsr

* cp2k: build with cmake in CI, s.t. dbcsr is a separate package

* cp2k: cmake patches for config files and C/C++ std

* cp2k: remove unnecessary constraints due to patch
2023-10-20 16:20:20 +02:00
Lydéric Debusschère
a0e33bf7b0 py-corner: new package (#40546)
* [add] py-corner: new package

* py-corner: remove py-wheel dependence with respect to reviewing commentary

---------

Co-authored-by: LydDeb <lyderic.debusschere@eolen.com>
2023-10-20 07:37:15 -05:00
Massimiliano Culpo
cbc39977ca ASP-based solver: minimize weights over edges (#40632)
With the introduction of multiple build dependencies from the same package in the DAG, we need to minimize a few weights accounting for edges rather than nodes. If we don't do that we might have multiple "optimal" solutions that differ only in how the same nodes are connected together. This commit ensures optimal versions are picked per parent in case of multiple choices for a dependency.
2023-10-20 14:37:07 +02:00
Adam J. Stewart
06fc24df5e TensorFlow/Keras/TensorBoard: add v2.14.0 (#40297)
Co-authored-by: adamjstewart <adamjstewart@users.noreply.github.com>
2023-10-20 14:23:54 +02:00
Claire Guilbaud
9543abd2d9 add recipes for sphinx-book-theme and its dependencies if unknown (#40312)
* add recipes for sphinx-book-theme and its dependencies if unknown

* fix version and mission https

* fix based on reviewers remarks
2023-10-20 07:18:41 -05:00
Lydéric Debusschère
004d3e4cca [add] py-fraction: new package (#40554)
Co-authored-by: LydDeb <lyderic.debusschere@eolen.com>
2023-10-20 07:03:48 -05:00
Lydéric Debusschère
25aff66d34 [add] py-cssutils: new package (#40551)
Co-authored-by: LydDeb <lyderic.debusschere@eolen.com>
2023-10-20 07:01:38 -05:00
Lydéric Debusschère
9bd77b2ed3 [add] py-css-parser: new package (#40550)
Co-authored-by: LydDeb <lyderic.debusschere@eolen.com>
2023-10-20 07:00:46 -05:00
Manuela Kuhn
5de1c1c98f py-statsmodels: add 0.14.0 (#39156)
* py-statsmodels: add 0.14.0

* Fix style

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

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

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

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

* Remove python limits

* Remove comment

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-10-20 06:59:26 -05:00
Manuela Kuhn
5b9b5eaa28 py-dcm2bids: add v3.1.0 (#40447)
* py-dcm2bids: add 3.1.0

* Fix python restriction
2023-10-20 06:56:48 -05:00
Manuela Kuhn
00ee72396f py-bidscoin: add v4.1.1 and py-argparse-manpage: add new package (#40414)
* py-bidscoin: add 4.1.1

* Fix style

* Fix restrictions for dependencies
2023-10-20 06:55:41 -05:00
snehring
aa4d55004c Add package py-macs3 and dependencies (#40498)
* py-cykhash: adding new package py-cykhash

* py-hmmlearn: adding new package py-hmmlearn

* py-macs3: adding new package py-macs3

* py-macs3: adding python version restriction and other changes.
2023-10-20 06:53:41 -05:00
Harmen Stoppels
468f6c757e schema/compilers.py: fix validation of 2+ entries (#40627)
Fix the following syntax which validates only the first array entry:

```python
"compilers": {
    "type": "array",
    "items": [
        {
            "type": ...
        }
    ]
}
```

to

```python
"compilers": {
    "type": "array",
    "items": {
        "type": ...
    }
}
```

which validates the entire array.

Oops...
2023-10-20 09:51:49 +02:00
Adam J. Stewart
0907d43783 Drop support for external PythonX.Y (#40628)
On some systems, multiple pythonx.y are placed in the same prefix as
pythonx (where only one of them is associated with that pythonx).
Spack external detection for Python was willing to register all of
these as external versions. Moreover, the `package.py` for Python
was able to distinguish these.

This can cause an issue for some build systems, which will just look
for python3 for example, so if that python3 is actually python3.6,
and the build system needs 3.7 (which spack may have found in the
same prefix, and offered as a suitable external), it will fail when
invoking python3.

To avoid that issue, we simply avoid treating pythonx.y as external
candidates. In the above case, Spack would only detect a Python 3.6
external, and the build would be forced to use a Spack-built Python
3.7 (which we consider a good thing).
2023-10-20 00:29:38 -06:00
wspear
c9e5173bbd TAU: Respect ~fortran for +mpi (#40617) 2023-10-19 23:24:17 -06:00
Vicente Bolea
0019faaa17 vtk-m: update to latest release (#40624) 2023-10-19 18:02:25 -06:00
Lydéric Debusschère
e30f53f206 perl: change permissions in order to apply patch on version 5.38.0 (#40609)
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2023-10-20 00:00:24 +02:00
dependabot[bot]
f2ba25e09d build(deps): bump actions/checkout from 4.1.0 to 4.1.1 (#40584) 2023-10-19 23:04:40 +02:00
dependabot[bot]
405de56c71 build(deps): bump mypy from 1.6.0 to 1.6.1 in /lib/spack/docs (#40603) 2023-10-19 23:03:48 +02:00
dependabot[bot]
ba571f2404 build(deps): bump mypy from 1.6.0 to 1.6.1 in /.github/workflows/style (#40602) 2023-10-19 23:03:23 +02:00
dependabot[bot]
4c1785d5f6 build(deps): bump urllib3 from 2.0.6 to 2.0.7 in /lib/spack/docs (#40583) 2023-10-19 23:02:51 +02:00
Adam J. Stewart
fa4d5ee929 py-rasterio: add v1.3.9 (#40621) 2023-10-19 12:08:43 -07:00
Cody Balos
8720cec283 add nvechip to sundials components when mfem+rocm (#40512) 2023-10-19 12:08:24 -07:00
Harmen Stoppels
72b36ac144 Improve setup build / run / test environment (#35737)
This adds a `SetupContext` class which is responsible for setting
package.py module globals, and computing the changes to environment
variables for the build, test or run context.

The class uses `effective_deptypes` which takes a list of specs (e.g. single
item of a spec to build, or a list of environment roots) and a context
(build, run, test), and outputs a flat list of specs that affect the
environment together with a flag in what way they do so. This list is
topologically ordered from root to leaf, so that one can be assured that
dependents override variables set by dependencies, not the other way
around.

This is used to replace the logic in `modifications_from_dependencies`,
which has several issues: missing calls to `setup_run_environment`, and
the order in which operations are applied.

Further, it should improve performance a bit in certain cases, since
`effective_deptypes` run in O(v + e) time, whereas `spack env activate`
currently can take up to O(v^2 + e) time due to loops over roots. Each
edge in the DAG is visited once by calling `effective_deptypes` with
`env.concrete_roots()`.

By marking and propagating flags through the DAG, this commit also fixes
a bug where Spack wouldn't call `setup_run_environment` for runtime
dependencies of link dependencies. And this PR ensures that Spack
correctly sets up the runtime environment of direct build dependencies.

Regarding test dependencies: in a build context they are are build-time
test deps, whereas in a test context they are install-time test deps.
Since there are no means to distinguish the build/install type test deps,
they're both.

Further changes:

- all `package.py` module globals are guaranteed to be set before any of the
  `setup_(dependent)_(run|build)_env` functions is called
- traversal order during setup: first the group of externals, then the group
  of non-externals, with specs in each group traversed topological (dependencies
  are setup before dependents)
- modules: only ever call `setup_dependent_run_environment` of *direct* link/run
   type deps
- the marker in `set_module_variables_for_package` is dropped, since we should
  call the method once per spec. This allows us to set only a cheap subset of
  globals on the module: for example it's not necessary to compute the expensive
  `cmake_args` and w/e if the spec under consideration is not the root node to be
  built.
- `spack load`'s `--only` is deprecated (it has no effect now), and `spack load x`
  now means: do everything that's required for `x` to work at runtime, which
  requires runtime deps to be setup -- just like `spack env activate`.
- `spack load` no longer loads build deps (of build deps) ...
- `spack env activate` on partially installed or broken environments: this is all
  or nothing now. If some spec errors during setup of its runtime env, you'll only
  get the unconditional variables + a warning that says the runtime changes for
  specs couldn't be applied.
- Remove traversal in upward direction from `setup_dependent_*` in packages.
  Upward traversal may iterate to specs that aren't children of the roots
  (e.g. zlib / python have hundreds of dependents, only a small fraction is
  reachable from the roots. Packages should only modify the direct dependent
  they receive as an argument)
2023-10-19 20:44:05 +02:00
Harmen Stoppels
79896ee85c spack checksum: restore ability to select top n (#40531)
The ability to select the top N versions got removed in the checksum overhaul,
cause initially numbers were used for commands.

Now that we settled on characters for commands, let's make numbers pick the top
N again.
2023-10-19 11:33:01 -07:00
Vanessasaurus
408ee04014 Automated deployment to update package flux-core 2023-10-19 (#40605)
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2023-10-19 10:16:42 -07:00
Harmen Stoppels
3f594e86a1 libvorbis: drop -force_cpusubtype_ALL flag (#40616)
This flag was only relevant when targeting powerpc from apple-clang,
which we don't do. The flag is removed from apple-clang@15. Let's drop
it unconditionally.
2023-10-19 10:15:18 -07:00
Scott Wittenburg
46c1a8e4c6 gitlab ci: Rework how mirrors are configured (#39939)
Improve how mirrors are used in gitlab ci, where we have until now thought
of them as only a string.

By configuring ci mirrors ahead of time using the proposed mirror templates,
and by taking advantage of the expressiveness that spack now has for mirrors,
this PR will allow us to easily switch the protocol/url we use for fetching
binary dependencies.

This change also deprecates some gitlab functionality and marks it for
removal in Spack 0.23:

    - arguments to "spack ci generate":
        * --buildcache-destination
        * --copy-to
    - gitlab configuration options:
        * enable-artifacts-buildcache
        * temporary-storage-url-prefix
2023-10-19 11:04:59 -05:00
Satish Balay
b2d3e01fe6 petsc: add variant +sycl (#40562)
* petsc: add variant +sycl

* petsc: add in gmake as dependency - so that consistent make gets used between petsc and slepc builds [that can have different env for each of the builds]
2023-10-19 07:31:02 -07:00
Harmen Stoppels
681639985a ci: remove incorrect compilers.yaml (#40610) 2023-10-19 16:11:42 +02:00
Massimiliano Culpo
a1ca1a944a ASP-based solver: single Spec instance per dag hash (#39590)
Reused specs used to be referenced directly into the built spec.

This might cause issues like in issue 39570 where two objects in
memory represent the same node, because two reused specs were
loaded from different sources but referred to the same spec
by DAG hash.

The issue is solved by copying concrete specs to a dictionary keyed
by dag hash.
2023-10-19 16:00:45 +02:00
Tamara Dahlgren
4f49f7b9df Stand-alone test feature deprecation postponed to v0.22 (#40600) 2023-10-19 06:03:54 -06:00
Aiden Grossman
fb584853dd byte-unixbench: respect compiler choice (#39242)
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2023-10-19 02:20:34 -06:00
Aiden Grossman
cc47b06756 connect-proxy: respect compiler choice (#39243) 2023-10-19 09:58:58 +02:00
Aiden Grossman
b68a620fc2 bioawk: respect compiler choice (#39241) 2023-10-19 09:55:57 +02:00
Aiden Grossman
e417ca54a0 busybox: respect compiler choice (#39239) 2023-10-19 09:55:06 +02:00
Michael Kuhn
5bbf8454d0 julia: Fix build for @1.9 (#39045)
julia@1.9 tries to download ittapi, which requires cmake. Disable it
explicitly.
2023-10-19 09:09:45 +02:00
Annop Wongwathanarat
67b8dd0913 acfl: add version 23.10 (#40510) 2023-10-18 17:07:40 -07:00
Harmen Stoppels
a42eb0d2bd unparse: also support generic type aliases (#40328) 2023-10-18 23:16:05 +02:00
Harmen Stoppels
294e659ae8 AutotoolsPackage / MakefilePackage: add gmake build dependency (#40380) 2023-10-18 19:56:54 +02:00
Harmen Stoppels
55198c49e5 llvm: fix ncurses+termlib linking in lldb (#40594) 2023-10-18 19:04:49 +02:00
Harmen Stoppels
dc071a3995 Fix dev-build keep_stage behavior (#40576)
`spack dev-build` would incorrectly set `keep_stage=True` for the
entire DAG, including for non-dev specs, even though the dev specs
have a DIYStage which never deletes sources.
2023-10-18 11:44:26 +00:00
Lydéric Debusschère
db5d0ac6ac [fix] py-werkzeug: add constraint in python dependence (#40590)
py-werkzeug@:0.12 does not work with python@3.10:

Test with py-werkzeug 0.12.2 and python 3.10:
```
$ python3.10 -c 'import werkzeug'
py-werkzeug-0.12.2/lib/python3.11/site-packages/werkzeug/datastructures.py", line 16, in <module>
from collections import Container, Iterable, MutableSet
ImportError: cannot import name 'Container' from 'collections'
```

Test with py-werkzeug 0.12.2 and python 3.9:
```
python3.9 -c "from collections import Container"
<string>:1: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3, and in 3.10 it will stop working
```
2023-10-18 13:04:21 +02:00
Aiden Grossman
2802013dc6 Add license directive (#39346)
This patch adds in a license directive to get the ball rolling on adding in license 
information about packages to spack. I'm primarily interested in just adding
license into spack, but this would also help with other efforts that people are
interested in such as adding license information to the ASP solve for 
concretization to make sure licenses are compatible.

Usage:

Specifying the specific license that a package is released under in a project's
`package.py` is good practice. To specify a license, find the SPDX identifier for
a project and then add it using the license directive:

```python
   license("<SPDX Identifier HERE>")
```

For example, for Apache 2.0, you might write:

```python
   license("Apache-2.0")
```

Note that specifying a license without a when clause makes it apply to all
versions and variants of the package, which might not actually be the case.
For example, a project might have switched licenses at some point or have
certain build configurations that include files that are licensed differently.
To account for this, you can specify when licenses should be applied. For
example, to specify that a specific license identifier should only apply
to versionup to and including 1.5, you could write the following directive:

```python
   license("MIT", when="@:1.5")
```
2023-10-18 03:58:19 -07:00
Greg Becker
37bafce384 abi.py: fix typo, add type-hints (#38216)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-10-18 11:22:55 +02:00
jfavre
da0813b049 paraview: add variant for NVIDIA IndeX (#40577)
* add variant for NVIDIA IndeX
* remove whitespaces
2023-10-17 13:03:41 -06:00
Dennis Klein
e2bb2595b3 xmlto: add more dependencies (#40578)
`xmllint` is called by `xmlto` during generation of `libzmq`'s docs, so
adding `libxml2`.

The docbook deps and the patches are taken from
https://src.fedoraproject.org/rpms/xmlto/blob/rawhide/f/xmlto.spec

There are still many more dependencies missing, but this is out of scope
of this patch (which is only concerned about the use case of `libzmq`).
2023-10-17 11:58:46 -07:00
Mikael Simberg
b7cbcfdcab Add tracy 0.10 (#40573) 2023-10-17 11:35:55 -07:00
Peter Scheibel
9cde25b39e Allow / in GitVersion (#39398)
This commit allows version specifiers to refer to git branches that contain
forward slashes. For example, the following is valid syntax now:

    pkg@git.releases/1.0
   
It also adds a new method `Spec.format_path(fmt)` which is like `Spec.format`,
but also maps unsafe characters to `_` after interpolation. The difference is
as follows:

    >>> Spec("pkg@git.releases/1.0").format("{name}/{version}")
    'pkg/git.releases/1.0'

    >>> Spec("pkg@git.releases/1.0").format_path("{name}/{version}")
    'pkg/git.releases_1.0'

The `format_path` method is used in all projections. Notice that this method
also maps `=` to `_`

    >>> Spec("pkg@git.main=1.0").format_path("{name}/{version}")
    'pkg/git.main_1.0'
   
which should avoid syntax issues when `Spec.prefix` is literally copied into a
Makefile as sometimes happens in AutotoolsPackage or MakefilePackage
2023-10-17 20:33:59 +02:00
Rocco Meli
49ea0a8e2e Add mpi_f08 variant to CP2K (#40574)
* add mpi_f08 variant
* add conflict
* add conflict with released versions of cp2k and +mpi_f08
2023-10-17 11:33:13 -07:00
Adam J. Stewart
d317ddfebe py-rtree: add v1.1.0 (#40575) 2023-10-17 11:25:18 -07:00
Cameron Rutherford
b1eef4c82d hiop: 1.0.1 release (#40580) 2023-10-17 11:14:17 -07:00
Harmen Stoppels
a4ad365de0 patchelf: fix compilation with GCC 7 (#40581) 2023-10-17 11:12:09 -07:00
wspear
8c257d55b4 Support apple-clang in pdt (#40582) 2023-10-17 11:23:15 -06:00
Harmen Stoppels
bd165ebc4d Support spack env activate --with-view <name> <env> (#40549)
Currently `spack env activate --with-view` exists, but is a no-op.

So, it is not too much of a breaking change to make this redundant flag
accept a value `spack env activate --with-view <name>` which activates
a particular view by name.

The view name is stored in `SPACK_ENV_VIEW`.

This also fixes an issue where deactivating a view that was activated
with `--without-view` possibly removes entries from PATH, since now we
keep track of whether the default view was "enabled" or not.
2023-10-17 15:40:48 +02:00
Massimiliano Culpo
348e5cb522 packages: use "requires" to allow only selected compilers (#40567)
A few packages have encoded an idiom that pre-dates the introduction
of the 'requires' directive, and they cycle over all compilers
to conflict with the ones that are not supported.

Here instead we reverse the logic, and require the ones that
are supported.
2023-10-17 08:38:06 +02:00
Patrick Bridges
7cc17f208c Creation of Beatnik package and associated updates to silo and cabana spack package (#40382)
* Added initial package for building Beatnik with spack

* Fixed github ID for Jason as a maintainer.

* Major revision of beatnik spack package to properly support GPU spack builds with CUDA (and ROCm, though that it untested)

* Marked that beatnik 1.0 will require cabana 0.6.0. We will wait for the cabana 0.6.0 release before we release beatnik

* Update to beatnik package spec to compile with hipcc when +rocm

* Updated spack package for cabana for version 0.6.0 and appropriate heffte dependency

* Updated beatnik package to require cabana 0.6.0

* More updates to cabana and beatnik to build with cabana 0.6.0

* Finish removing BLT dependence from beatnik

* More updates to beatnik package for compiling on cray systems

* Updated beatnik package for new cabana package

* Changes to silo package for new silo version

* Fixed version specs for heffte to be able to concretize and build

* Fixed spack style issues for beatnik and silo packages

* More spack formatting fixes to beatnik and silo

* Patrick adopting silo package as maintainer for now

* Should address final style changes to beatnik package spec

* Yet more style fixes.

* Perhaps this is the final style fixes? :)

* Minor fix to cabana package on required versions
2023-10-16 21:13:31 -06:00
Eric Berquist
2913cd936a Add latest versions of rlwrap (#40563)
* Add latest versions of rlwrap
* rlwrap: fix URL for v0.46.1
2023-10-16 20:28:51 -06:00
Stephen Sachs
361a185ddb intel-oneapi-compilers: ifx is located in bin not bin/intel64 (#40561)
This is a fix on top of https://github.com/spack/spack/pull/40557 .
Tagging @rscohn2 for review.
2023-10-16 20:23:46 -06:00
Seth R. Johnson
9d5615620a py-furo: new version (#40559) 2023-10-16 17:10:31 -04:00
Adam J. Stewart
ae185087e7 py-grayskull: add new package (#40293)
* py-grayskull: add new package

* [@spackbot] updating style on behalf of adamjstewart

---------

Co-authored-by: adamjstewart <adamjstewart@users.noreply.github.com>
2023-10-16 15:37:50 -05:00
Massimiliano Culpo
4a96d29e69 Use string representation of deptypes for concrete specs (#40566) 2023-10-16 22:36:22 +02:00
Adam J. Stewart
1e44f33163 py-fiona: add v1.9.5 (#40497) 2023-10-16 15:34:13 -05:00
Adam J. Stewart
348493abcd py-shapely: add v2.0.2 (#40523) 2023-10-16 15:33:56 -05:00
Adam J. Stewart
2bc4bfa877 py-grpcio: cython 3 still not supported (#40537) 2023-10-16 15:33:32 -05:00
Adam J. Stewart
3e3b287761 py-lightning: add v2.1.0 (#40496) 2023-10-16 14:14:46 -05:00
renjithravindrankannath
74bbb1ef1b Updating patch to enable flag mcode-object-version=none (#40367)
* Updating patch to add flag mcode-object-version=none when
   device libs is buils as part of llvm-amdgpu
* Limiting patch to +rocm-device-libs variant and adding
   appropriate comment for the patch
* Updating llvmpatch as per the mailine code
   Updating hsa-rocr patch as per the latest code
   Updating the if elif condition for the hip test src path
* Updating flags for 5.5 relases and above
* Updating build flags and patches
2023-10-16 10:25:10 -07:00
Dom Heinzeller
22405fbb68 Fix version incompatibilities of py-pandas and py-openpyxl (#40472)
* Fix version incompatibilities of py-pandas and py-openpyxl

* Add variant excel for py-pandas

* Add package py-pyxlsb

* Add versios for py-xlsxwriter

* Define excel dependencies for py-pandas 1.4, 1.5, 2.0, 2.1

* Fix variant excel in py-pandas

* Add package py-odfpy, which is also a dependency for py-pandas@2.0:

* Rearrange excel dependencies for py-pandas

* Change url to pypi

* Add missing newline to fix style in py-odfpy
2023-10-16 10:28:38 -06:00
Diego Alvarez S
14d935bd6c Add nextflow 23.10.0 (#40547) 2023-10-16 09:06:36 -07:00
Garth N. Wells
363b9d3c7b fenics-basix: update for v0.7 (#40440)
* Uodate for Basix 0.7

* Version fix for nanobind dependency

* Simplification

* Version update and simplify dependencies

* Add comment on location of pyproject.toml

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

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-10-16 08:53:02 -06:00
Stephen Sachs
8347ae3766 intel-oneapi-compilers: ifx uses --gcc-name & --gxx-name (#40557)
`ifx` uses the older syntax instead of `--gcc-toolchain`. Tested up to version
2023.2.0.
2023-10-16 10:24:21 -04:00
Garth N. Wells
1106f6b9f2 py-fenics-ufl: update version and add test (#40534)
* Update py-ufl vesion

* Syntax fix

* Syntax fix

* Add test

* Updates following comments
2023-10-16 06:52:59 -05:00
Lydéric Debusschère
e22117304e [add] py-cylc-uiserver: new recipe (#39983)
* [add] py-cylc-uiserver: new recipe

* py-cylc-uiserver: remove version constraint on the dependence python

* [fix] py-cylc-uiserver: add forgotten dependence py-graphql-core

---------

Co-authored-by: LydDeb <lyderic.debusschere.tgcc@cea.fr>
2023-10-16 06:51:11 -05:00
Vanessasaurus
10999c0283 fix: flux-core needs libarchive with +iconv (#40541)
Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2023-10-15 17:43:10 -06:00
Todd Gamblin
7adeee0980 README.md: tweak matrix description to indicate bridging (#40540)
This tweaks the matrix description to indicate that it's bridged with Slack. So people
don't think they're missing out (even though the icon says there are only 3 users on
Matrix).
2023-10-15 22:48:05 +00:00
Harmen Stoppels
a9cfa32c34 spack checksum: handle all versions dropped better (#40530)
* spack checksum: fix error when all versions are dropped

* add test
2023-10-15 15:08:11 -07:00
Garth N. Wells
718aa8b82f Version update and simplify dependencies (#40543) 2023-10-15 15:53:03 -06:00
Adam J. Stewart
dbf3bed380 py-torchdata: version rename (#40522) 2023-10-15 13:22:49 -07:00
Adam J. Stewart
ef55c7c916 Python: allow OneAPI 2024 when it's released (#40536) 2023-10-15 11:18:04 -06:00
Adam J. Stewart
2015d3d2bc py-click: fix Python 3.6 support (#40535) 2023-10-15 19:16:51 +02:00
Alec Scott
76bac6d4bf Add matrix space link and badge to README (#40532) 2023-10-15 09:28:08 +00:00
Miroslav Stoyanov
b960d476e3 tasmanian: patch for clang17 (#40515) 2023-10-15 00:07:15 -05:00
Veselin Dobrev
8a311d7746 mfem: add a patch for v4.6 for gcc 13, see mfem PR 3903 (#40495) 2023-10-15 00:01:53 -05:00
Miroslav Stoyanov
39d2baec8a heffte: fix rocm deps (#40514) 2023-10-14 23:55:01 -05:00
Dom Heinzeller
26e063177d Bug fixes in py-awscrt to fix build errors reported in #40386 (#40469)
* Bug fix in var/spack/repos/builtin/packages/py-awscrt/package.py: on Linux, tell aws-crt-python to use libcrypto from spack (openssl)

* Bug fix in var/spack/repos/builtin/packages/py-awscrt/package.py: add missing build dependencies cmake (for all), openssl (for linux)

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

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-10-14 21:02:41 +00:00
Alex Richert
149d1946ee Add static support for proj (#40322)
* Add static-only option for proj

* Update proj

* update proj

* Update package.py

* [@spackbot] updating style on behalf of AlexanderRichert-NOAA

* Update package.py

* proj: Add pic and static variant support for cmake
2023-10-14 13:09:24 -05:00
Manuela Kuhn
3604f6238d py-pydicom: add 2.4.3 (#40487) 2023-10-14 13:06:51 -05:00
Manuela Kuhn
2ad9470670 py-pybids: add 0.16.3 (#40486) 2023-10-14 13:05:36 -05:00
Manuela Kuhn
8dde74854a py-cfgv: add 3.4.0 (#40465) 2023-10-14 13:03:43 -05:00
Manuela Kuhn
fa5aadbbc0 py-charset-normalizer: add 3.3.0 (#40471) 2023-10-14 12:56:59 -05:00
Manuela Kuhn
0989cb8866 py-click: add 8.1.7 (#40473) 2023-10-14 12:56:14 -05:00
Manuela Kuhn
b536260eb5 py-chardet: add 5.2.0 (#40468) 2023-10-14 12:47:01 -05:00
Manuela Kuhn
8f2de4663e py-certifi: add 2023.7.22 (#40445) 2023-10-14 12:41:34 -05:00
Manuela Kuhn
0693892521 py-bidskit: add 2023.9.7 (#40444) 2023-10-14 12:40:40 -05:00
Manuela Kuhn
3be78717d2 py-pyqt6: add 6.5.2 (#40413) 2023-10-14 12:34:45 -05:00
Sam Gillingham
655d123785 py-python-fmask: update to latest versions (#40378)
* tidy and add new version

* add comment about dependencies

* whitespace
2023-10-14 12:28:51 -05:00
Lydéric Debusschère
b8cb36ce50 [add] py-graphene-tornado: new recipe, required by py-cylc-uiserver (#39985)
* [add] py-graphene-tornado: new recipe, required by py-cylc-uiserver

* py-graphene-tornado: Taking reviewing into account

* py-graphene-tornado: add type run in dependences py-jinja, py-tornado and py-werkzeug

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

---------

Co-authored-by: LydDeb <lyderic.debusschere.tgcc@cea.fr>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-10-14 12:25:02 -05:00
Manuela Kuhn
bc3cd02776 py-urllib3: add 2.0.6 (#40207)
* py-urllib3: add 2.0.5

* Add py-brotli package

* Group brotli dependencies and make limits more specific

* Add minimum version limits to variants

* Remove python upper limit for py-brotli

* Fix restrictions for py-brotli dependency

* Fix py-brotli dependency

* py-urllib3: add 2.0.6
2023-10-14 12:23:54 -05:00
Seth R. Johnson
a027adcaa2 cpr: new package (#40509)
* New package: cpr

* Support libcpr version 1.9

* Fix build phase for git

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

Co-authored-by: Alec Scott <alec@bcs.sh>

* [@spackbot] updating style on behalf of sethrj

---------

Co-authored-by: Alec Scott <alec@bcs.sh>
2023-10-14 08:31:53 -07:00
Harmen Stoppels
3783032d28 screen: add v4.9.1 (#40529) 2023-10-14 08:29:55 -07:00
Harmen Stoppels
c0ac5e3f6b git: add 2.42 (#40528) 2023-10-14 08:28:52 -07:00
Michael Kuhn
87371d58d5 libbson, mongo-c-driver: add 1.24.4 (#40518) 2023-10-14 11:38:00 +02:00
Michael Kuhn
ef11fd7f75 libfuse: add 3.16.2 (#40519) 2023-10-14 11:37:07 +02:00
Michael Kuhn
d0f046e788 mariadb-c-client: add 3.3.7 (#40521) 2023-10-14 11:35:46 +02:00
Michael Kuhn
794fb9b252 rocksdb: add 8.6.7 (#40525) 2023-10-14 11:34:32 +02:00
Michael Kuhn
86c7d646c3 Fix pkgconfig dependencies (#40524)
`pkgconfig` is the correct virtual dependency.
2023-10-14 11:33:36 +02:00
Michael Kuhn
7d96077667 glib: add 2.78.0, 2.76.6 (#40517) 2023-10-14 11:33:16 +02:00
Michael Kuhn
a6fbfedc08 sqlite: add 3.43.2 (#40520) 2023-10-14 11:32:25 +02:00
Alex Richert
a6cfeabc10 cairo: add shared and pic variants (#40302) 2023-10-13 14:21:43 -06:00
Martin Aumüller
a3a29006aa wayland: dot is a build dependency (#39854)
* wayland: dot is a build dependency

otherwise this build failure happens:
../spack-src/doc/meson.build:5:6: ERROR: Program 'dot' not found or not executable

* wayland: make building of documentation optional

renders several dependencies optional
2023-10-13 21:57:13 +02:00
Harmen Stoppels
a5cb7a9816 spack checksum: improve interactive filtering (#40403)
* spack checksum: improve interactive filtering

* fix signature of executable

* Fix restart when using editor

* Don't show [x version(s) are new] when no known versions (e.g. in spack create <url>)

* Test ^D in test_checksum_interactive_quit_from_ask_each

* formatting

* colorize / skip header on invalid command

* show original total, not modified total

* use colify for command list

* Warn about possible URL changes

* show possible URL change as comment

* make mypy happy

* drop numbers

* [o]pen editor -> [e]dit
2023-10-13 19:43:22 +00:00
Gabriel Cretin
edf4aa9f52 Fpocket: fix installation (#40499)
* Fpocket: fix edit() positional args + add install()

* Remove comments

* Fix line too long

* Fix line too long

* Remove extension specification in version

Co-authored-by: Alec Scott <alec@bcs.sh>

* Use f-strings

Co-authored-by: Alec Scott <alec@bcs.sh>

* Fix styling

* Use the default MakefilePackage install stage

---------

Co-authored-by: Alec Scott <alec@bcs.sh>
2023-10-13 11:30:20 -07:00
Dom Heinzeller
02c680ec3a texinfo package: fix external detection (#40470)
A complete texinfo install includes both `info` and `makeinfo`. Some
system installations of texinfo may exclude one or the other. This
updates the external finding logic to require both.
2023-10-13 10:39:08 -07:00
David Huber
8248e180ca Add gsi-ncdiag v1.1.2 (#40508) 2023-10-13 08:48:23 -07:00
Harmen Stoppels
c9677b2465 Expand multiple build systems section (#39589)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-10-13 14:59:44 +02:00
Massimiliano Culpo
3752fe9e42 Better error message when wrong platform is used (#40492)
fixes #40299
2023-10-13 11:18:55 +02:00
Matthew Chan
8a0de10f60 containerize: update docs to activate env before using container templates (#40493) 2023-10-13 06:59:44 +00:00
Adam J. Stewart
6aa8d76e32 py-cmocean: add v3.0.3 (#40482) 2023-10-12 20:32:48 -06:00
Nils Vu
fb1d0f60d9 catch2: add +pic and +shared options (#40337)
Also add latest version
2023-10-12 20:13:01 -06:00
Martin Aumüller
728eaa515f ospray: new versions 2.11.0 and 2.12.0 (#40394)
* openimagedenoise: checksum 2.0.1
* ospray: new versions 2.11.0 and 2.12.0
  - both depend on embree@4
  - also update dependency versions for rkcommon, openvkl, openimagedenois and ispc
  - expose that dependency on openvkl is optional since @2.11 with variant "volumes"
* ospray: limit embree to @3 for ospray @:2.10
2023-10-12 14:13:15 -07:00
Julius Plehn
7c354095a9 Updates Variorum to 0.7.0 (#40488) 2023-10-12 11:27:06 -06:00
Harmen Stoppels
64ef33767f modules:prefix_inspections: allow empty dict (#40485)
Currently

```
modules:
  prefix_inspections:: {}
```

gives you the builtin defaults instead of no mapping.
2023-10-12 09:28:16 -07:00
Dennis Klein
265432f7b7 libzmq: Revert "libzmq: make location of libsodium explicit (#34553)" (#40477)
and make variants independent of upstream defaults
2023-10-12 09:15:00 -06:00
dependabot[bot]
aa7dfdb5c7 build(deps): bump python-levenshtein in /lib/spack/docs (#40461)
Bumps [python-levenshtein](https://github.com/maxbachmann/python-Levenshtein) from 0.22.0 to 0.23.0.
- [Release notes](https://github.com/maxbachmann/python-Levenshtein/releases)
- [Changelog](https://github.com/maxbachmann/python-Levenshtein/blob/main/HISTORY.md)
- [Commits](https://github.com/maxbachmann/python-Levenshtein/compare/v0.22.0...v0.23.0)

---
updated-dependencies:
- dependency-name: python-levenshtein
  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>
2023-10-12 14:38:33 +00:00
Alec Scott
bfe37435a4 go: add v1.21.3 and deprecate previous versions due to CVE-2023-39533 (#40454) 2023-10-12 07:40:04 -06:00
Adam J. Stewart
285a50f862 PyTorch: fix build with Xcode 15 (#40460) 2023-10-12 07:27:03 -06:00
Harmen Stoppels
995e82e72b gettext: Add 0.22.3 and fix keyerror: "shared" (#39423)
After the merge of #37957 (Add static and pic variants), if a gettext install
from a build before that merge is present, building any package using gettext
fails with keyerror: "shared" because the use of self.spec.variants["shared"]
does not check for the presence of the new variant in the old installation
but expects that the new key variants["shared"] exists always.

Fix it with a fallback to the default of True and update gettext to v22.3

Co-authored-by: Bernharad Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2023-10-12 04:40:38 -06:00
Massimiliano Culpo
3935e047c6 Remove deprecated "extra_instructions" option for containers (#40365) 2023-10-12 12:12:15 +02:00
Harmen Stoppels
0fd2427d9b clingo: fix build with Python 3.12 (#40154) 2023-10-12 12:11:22 +02:00
Alec Scott
30d29d0201 acfl: use f-strings (#40433) 2023-10-12 11:30:22 +02:00
Tim Haines
3e1f2392d4 must: add versions 1.8.0 and 1.9.0 (#40141) 2023-10-11 22:34:22 -07:00
Lydéric Debusschère
6a12a40208 [add] py-cylc-rose: new recipe (#39980)
* [add] py-cylc-rose: new recipe

* py-cylc-rose: update recipe

---------

Co-authored-by: LydDeb <lyderic.debusschere.tgcc@cea.fr>
2023-10-11 22:31:46 -07:00
Leonhard Reichenbach
90e73391c2 opendatadetector: add version v3.0.0 (#39693) 2023-10-11 22:29:00 -07:00
Alec Scott
deec1b7c2e adios2: use f-strings (#40437) 2023-10-11 21:08:00 -06:00
Scott Wittenburg
d9cb1a1070 buildcache: Tell servers not to cache index or hash (#40339) 2023-10-11 18:13:57 -06:00
afzpatel
01747b50df fix ck build for 5.6.1 (#40304)
* initial commit to fix ck build for 5.6.1
* disable mlir for miopen-hip
* use satisfies for checking specs and add nlohmann-json dependency for 5.4 onwards
2023-10-11 14:43:21 -07:00
Alex Richert
df01a11e07 apr-util: Fix spack install apr-util +crypto ^openssl~shared (#40301) 2023-10-11 23:38:28 +02:00
Victor Brunini
7a4b479724 cmake: drop CMAKE_STATIC_LINKER_FLAGS (#40423)
Because those end up being passed to ar which does not understand linker
arguments. This was making ldflags largely unusuable for statically
linked cmake packages.
2023-10-11 23:30:44 +02:00
Harmen Stoppels
89e34d56a1 curl: add v8.4.0, allow r@8.3: to use it (#40442)
* curl: 8.4.0

* fix r curl upperbound range
2023-10-11 21:04:09 +02:00
Miroslav Stoyanov
a5853ee51a update for the tasmanain versions (#40453) 2023-10-11 12:33:31 -06:00
Alec Scott
537ab48167 acts: use f-strings (#40434) 2023-10-11 11:03:30 -07:00
Alec Scott
e43a090877 abduco: use f-string (#40432) 2023-10-11 19:51:26 +02:00
Alec Scott
275a2f35b5 adiak: use f-strings (#40435) 2023-10-11 10:48:39 -07:00
Alec Scott
dae746bb96 abacus: use f-string (#40431) 2023-10-11 19:48:32 +02:00
Alec Scott
3923b81d87 adios: use f-strings (#40436) 2023-10-11 10:47:42 -07:00
Alec Scott
5d582a5e48 7zip: use f-strings (#40430) 2023-10-11 19:46:23 +02:00
Alec Scott
7dbc712fba 3proxy: use f-strings (#40429) 2023-10-11 19:44:57 +02:00
Alec Scott
639ef9e24a adol-c: use f-strings (#40438) 2023-10-11 10:43:31 -07:00
Alex Richert
86d2200523 krb5: Fix spack install krb5 ^openssl~shared (#40306) 2023-10-11 19:37:48 +02:00
Massimiliano Culpo
fe6860e0d7 cmake: add v3.27.7 (#40441) 2023-10-11 10:20:49 -07:00
Manuela Kuhn
8f2e68aeb8 c-blosc2: add 2.10.5 (#40428) 2023-10-11 19:19:58 +02:00
Laura Weber
bc4c887452 tecplot: Add version 2023r1 (#40425) 2023-10-11 10:05:37 -07:00
Alec Scott
b3534b4435 restic: add v0.16.0 (#40439) 2023-10-11 19:04:26 +02:00
Massimiliano Culpo
861bb4d35a Update bootstrap buildcache to support Python 3.12 (#40404)
* Add support for Python 3.12
* Use optimized build of clingo
2023-10-11 19:03:17 +02:00
Harmen Stoppels
65e7ec0509 spider: respect <base> tag (#40443) 2023-10-11 08:49:50 -07:00
Manuela Kuhn
1ab8886695 qt-base: fix-build without opengl (#40421) 2023-10-11 08:56:59 -04:00
dependabot[bot]
26136c337f build(deps): bump mypy from 1.5.1 to 1.6.0 in /.github/workflows/style (#40422)
Bumps [mypy](https://github.com/python/mypy) from 1.5.1 to 1.6.0.
- [Commits](https://github.com/python/mypy/compare/v1.5.1...v1.6.0)

---
updated-dependencies:
- dependency-name: mypy
  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>
2023-10-11 06:35:51 -06:00
dependabot[bot]
e3b71b32aa build(deps): bump mypy from 1.5.1 to 1.6.0 in /lib/spack/docs (#40424)
Bumps [mypy](https://github.com/python/mypy) from 1.5.1 to 1.6.0.
- [Commits](https://github.com/python/mypy/compare/v1.5.1...v1.6.0)

---
updated-dependencies:
- dependency-name: mypy
  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>
2023-10-11 12:35:41 +00:00
Alec Scott
6d1711f4c2 Update legacy .format() calls to fstrings in installer.py (#40426) 2023-10-11 12:35:37 +00:00
Massimiliano Culpo
26f291ef25 spack buildcache: fix a typo in a function call (#40446)
fixes #40415
2023-10-11 13:09:21 +02:00
Martin Aumüller
da030617a1 botan: checksum 3.2.0 (#40417) 2023-10-10 21:52:51 -06:00
Martin Aumüller
1ebfcd3b18 openvkl: add 1.3.2 (#40392)
* openvkl: add 1.3.2

works with (and requires) embree@4

* openvkl: simplify formatting with f-string

thank you for the suggestion in the review
2023-10-10 21:24:17 -06:00
Edward Hartnett
d385a57da3 w3emc: add v2.11.0 (#40376)
* added version 2.11.0

* more fixes
2023-10-10 15:11:14 -07:00
eugeneswalker
37df8bfc73 e4s arm stack: duplicate and target neoverse v1 (#40369)
* e4s arm stack: duplicate and target both neoverse n1, v1

* remove neoverse_n1 target until issue #40397 is resolved
2023-10-10 14:32:51 -07:00
Adam J. Stewart
b781a530a1 GCC: fix build with Apple Clang 15 (#40318) 2023-10-10 22:35:15 +02:00
Harmen Stoppels
390b0aa25c More helpful error when patch lookup fails (#40379) 2023-10-10 21:09:04 +02:00
Adam J. Stewart
620835e30c py-jupyter-packaging: remove duplicate packages (#38671)
* py-jupyter-packaging: remove duplicate packages

* Allow py-jupyter-packaging to be duplicated in DAG

* Deprecate version of py-jupyterlab that requires py-jupyter-packaging at run-time
2023-10-10 13:50:22 -05:00
Adam J. Stewart
da10487219 Update PyTorch ecosystem (#40321)
* Update PyTorch ecosystem

* py-pybind11: better documentation of supported compilers

* py-torchdata: add v0.7.0

* Black fixes

* py-torchtext: fix Python reqs

* py-horovod: py-torch 2.1.0 not yet supported
2023-10-10 13:45:32 -05:00
Miroslav Stoyanov
4d51810888 find rocm fix (#40388)
* find rocm fix
* format fix
* style fix
* formatting is broken
2023-10-10 10:42:26 -07:00
Harmen Stoppels
6c7b2e1056 git: optimize build by not setting CFLAGS (#40387) 2023-10-10 11:48:06 +02:00
Carlos Bederián
749e99bf11 python: add 3.11.6 (#40384) 2023-10-10 09:53:04 +02:00
Martin Aumüller
6db8e0a61e embree: checksum 4.3.0 (#40395) 2023-10-09 20:44:10 -06:00
Martin Aumüller
6fe914421a rkcommon: checksum 0.11.0 (#40391) 2023-10-09 20:43:56 -06:00
Andrew W Elble
9275f180bb openmm: new version 8.0.0 (#40396) 2023-10-09 20:33:40 -06:00
Tom Epperly
2541b42fc2 Add a new release sha256 hash (#37680) 2023-10-09 20:28:45 -06:00
Auriane R
fb340f130b Add pika 0.19.1 (#40385) 2023-10-09 20:23:54 -06:00
Dennis Klein
d2ddd99ef6 libzmq: add v4.3.5 (#40383) 2023-10-09 17:30:46 -06:00
kenche-linaro
492a8111b9 linaro-forge: added package file for rebranded product (#39587) 2023-10-09 12:14:14 -07:00
George Young
d846664165 paintor: new package @3.0 (#40359)
* paintor: new package @3.0
* Update var/spack/repos/builtin/packages/paintor/package.py
---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-10-09 09:54:44 -07:00
Vanessasaurus
31b3e4898b Add: flux-pmix 0.4.0 (#40323)
* Automated deployment to update package flux-pmix 2023-10-05

* Pin exactly to flux-core 0.49.0 when between 0.3 and 0.4

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

Co-authored-by: Mark Grondona <mark.grondona@gmail.com>

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

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

---------

Co-authored-by: github-actions <github-actions@users.noreply.github.com>
Co-authored-by: Mark Grondona <mark.grondona@gmail.com>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-10-09 09:29:18 -07:00
Harmen Stoppels
82f1267486 unparse: drop python 3.3 remnants (#40331) 2023-10-09 08:22:27 -07:00
Harmen Stoppels
19202b2528 docs: update Spack prerequisites (#40381) 2023-10-09 13:41:36 +00:00
Adam J. Stewart
831cbec71f py-pydevtool: add new package (#40377) 2023-10-09 15:09:59 +02:00
Patrick Broderick
bb2ff802e2 fftx: add v1.1.3 (#40283) 2023-10-09 15:06:59 +02:00
dependabot[bot]
83e9537f57 build(deps): bump python-levenshtein in /lib/spack/docs (#40220)
Bumps [python-levenshtein](https://github.com/maxbachmann/python-Levenshtein) from 0.21.1 to 0.22.0.
- [Release notes](https://github.com/maxbachmann/python-Levenshtein/releases)
- [Changelog](https://github.com/maxbachmann/python-Levenshtein/blob/main/HISTORY.md)
- [Commits](https://github.com/maxbachmann/python-Levenshtein/compare/v0.21.1...v0.22.0)

---
updated-dependencies:
- dependency-name: python-levenshtein
  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>
2023-10-09 15:02:14 +02:00
Gavin John
3488e83deb py-s3cmd: Add new versions (#40212)
* Add new versions of py-s3cmd

* Use correct hashes
2023-10-09 07:46:38 -05:00
Jacob King
c116eee921 nimrod-aai: add v23.9. (#40303) 2023-10-09 14:39:40 +02:00
Adam J. Stewart
9cb291b41b py-jsonargparse: add v4.25.0 (#40185) 2023-10-09 14:33:45 +02:00
Thomas Dickerson
c0f1072dc7 racket packages: fix typo after multiple build systems support (#40088) 2023-10-09 14:21:13 +02:00
Jordan Galby
3108036533 elfutils: fix +debuginfod again with new libarchive versions (#40314) 2023-10-09 14:17:58 +02:00
Mike Renfro
215c699307 velvet: improved variants (#40225) 2023-10-09 12:47:54 +02:00
jmuddnv
f609093c6e Adding NVIDIA HPC SDK 23.9 (#40371) 2023-10-09 12:35:59 +02:00
Joe Schoonover
eb4fd98f09 feq-parse: add v2.0.3 (#40230) 2023-10-09 12:31:23 +02:00
Harmen Stoppels
08da9a854a parser: use non-capturing groups (#40373) 2023-10-09 07:18:27 +02:00
Mark (he/his) C. Miller
3a18fe04cc Update CITATION.cff with conf dates (#40375)
Add `start-date` and `end-date` to citation
2023-10-08 18:04:25 -07:00
Harmen Stoppels
512e41a84a py-setuptools: sdist + rpath patch backport (#40205) 2023-10-08 11:47:36 -06:00
Alex Richert
8089aedde1 gettext: Add static and pic options (#37957) 2023-10-08 17:42:21 +02:00
Manuela Kuhn
6b9e103305 py-tables: add 3.9.0 (#40340)
* py-tables: add 3.9.0

* Add conflict with apple-clang
2023-10-08 10:28:13 -05:00
Jen Herting
00396fbe6c [py-tokenizers] added version 0.13.3 (#40360) 2023-10-08 10:27:18 -05:00
Jen Herting
a3be9cb853 [py-tensorboardx] Added version 2.6.2.2 (#39731)
* [py-tensorboardx] Added version 2.6.2.2

* [py-tensorboardx] flake8

* [py-tensorboardx] requires py-setuptools-scm
2023-10-08 10:21:55 -05:00
Jen Herting
81f58229ab py-torch-sparse: add v0.6.17 (#39495)
* [py-torch-sparse] New version 0.6.17

* [py-torch-sparse] added dependency on parallel-hashmap

* [py-torch-sparse]

- spack only supports python@3.7:
- py-pytest-runner only needed with old versions
2023-10-08 10:20:46 -05:00
Jen Herting
2eb16a8ea2 [py-lvis] New package (#39080)
* [py-lvis] New package

* [py-lvis] flake8

* [py-lvis] os agnostic

* [py-lvis] added comment for imported dependency

* [py-lvis] style fix
2023-10-08 10:18:01 -05:00
Manuela Kuhn
9db782f8d9 py-bids-validator: add 1.13.1 (#40356)
* py-bids-validator: add 1.13.1

* Fix style
2023-10-08 10:16:08 -05:00
Lydéric Debusschère
633df54520 [add] py-cylc-flow: new recipe (#39986)
* [add] py-cylc-flow: new recipe

* py-cylc-flow: fix py-protobuf version

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

* py-cylc-flow: fix py-colorama version

Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>

* py-cylc-flow: Update dependence on py-aiofiles

Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>

* py-cylc-flow: Update dependence on py-pyzmq

Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>

* py-cylcflow: remove useless dependence

* py-cylc-flow: fix indent

* py-cylc-flow: fix argument in depends_on; move lines

* py-cylc-flow: fix the type of the dependence py-setuptools

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
Co-authored-by: LydDeb <lyderic.debusschere.tgcc@cea.fr>
2023-10-08 10:06:13 -05:00
Mark (he/his) C. Miller
e2a7f2ee9a Update CITATION.cff (#40363)
You will note the `Cite this repository` link is not working.

This commit fixes the underlying file...

* `authors` was not indented
* `authors` required by `preferred-citation`
* `authors` list required at top level (I simply duplicated)
* `"USA"` not correct country code
* `month` requires an integer month number
* Added URL to the actual pdf of the cited paper
* Used `identifiers` for doi and LLNL doc number
* added `abstract` copied from paper

Various fixes were confirmed by `cffconvert` using `docker run -v `pwd`:/app citationcff/cffconvert --validate`
2023-10-07 17:44:31 -07:00
Massimiliano Culpo
28c49930e2 Remove warning for custom module configuration, when no module is enabled (#40358)
The warning was added in v0.20 and was slated for removal in v0.21
2023-10-07 09:21:04 +02:00
Ken Raffenetti
6c1868f8ae yaksa: add version 0.3 (#40368) 2023-10-06 22:28:15 -06:00
Massimiliano Culpo
4f992475f4 Python add v3.11.5 (#40330) 2023-10-06 18:03:00 -06:00
Alex Richert
7a358c9005 Change 'exit' to 'return' in setup-env.sh (#36137)
* Change 'exit' to 'return' in `setup-env.sh` to avoid losing shell in some cases when sourcing twice.
2023-10-06 16:19:19 -07:00
Veselin Dobrev
b5079614b0 MFEM: add new version v4.6 (#40170)
* [mfem] Initial changes for v4.6

* [@spackbot] updating style on behalf of v-dobrev

* [mfem] Set the proper download link for v4.6
2023-10-06 15:31:23 -07:00
Alex Richert
482525d0f9 Update bufr recipe (#40033)
* Update bufr recipe
* Add v12.0.1
* style fixes
* remove test-related functionality for bufr
* Re-add testing

---------

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-10-06 15:04:51 -07:00
snehring
599220924d wise2: adding new package wise2 (#40341) 2023-10-06 14:24:44 -07:00
Harmen Stoppels
d341be83e5 VersionRange: improve error message for empty range (#40345) 2023-10-06 14:19:49 -07:00
George Young
b027d7d0de metal: new package @2020-05-05 (#40355)
* metal: new package
* style

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-10-06 14:14:45 -07:00
Howard Pritchard
0357df0c8b openmpi: add 4.1.6 release (#40361)
related to #40232

Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2023-10-06 13:06:37 -07:00
Edward Hartnett
f70ae6e3c4 g2: updated for 3.4.8 release (#40366)
* updated for 3.4.8 release
2023-10-06 13:02:17 -07:00
Manuela Kuhn
921ed1c21b py-expecttest: new package (#40347) 2023-10-06 14:34:47 -05:00
Manuela Kuhn
c95d43771a py-asttokens: add 2.4.0 (#40349) 2023-10-06 14:33:56 -05:00
Manuela Kuhn
db3d816f8b py-argcomplete: add 3.1.2 (#40348) 2023-10-06 14:32:21 -05:00
Manuela Kuhn
1d6a142608 py-anyio: add 4.0.0 (#40346) 2023-10-06 14:27:53 -05:00
George Young
98271c3712 topaz: new package @0.2.5 (#40352)
* topaz: new package @0.2.5

* switching over to pypi

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-10-06 13:00:03 -06:00
Manuela Kuhn
e3f6df884e py-zipp: add 3.17.0 (#40278)
* py-zipp: add 3.17.0

* Re-add python@3.7 dependency
2023-10-06 13:54:25 -05:00
Sam Gillingham
b0f36b2cd9 RIOS: add recent versions (#40243)
* add recent versions of RIOS

* fix depends_on syntax

* fix typo

* fix sha and add parallel variant

* remove self

* try doing in one
2023-10-06 13:52:15 -05:00
Lydéric Debusschère
5524492e25 [add] py-metomi-rose: new recipe, required by py-cylc-rose (#39981)
* [add] py-metomi-rose: new recipe, required by py-cylc-rose

* py-metomi-rose: remove version constraint on python

---------

Co-authored-by: LydDeb <lyderic.debusschere.tgcc@cea.fr>
2023-10-06 13:49:59 -05:00
Sam Gillingham
112f045352 py-tuiview: add recent versions of tuiview (#40244)
* add recent versions of tuiview and remove Qt4 version

* reformat

* fix stray tabs

* add back a deprecated 1.1.7

* tabs

* more tabs

* reformat

* comma
2023-10-06 13:49:06 -05:00
Harmen Stoppels
72ed8711a7 unparse: drop python 2 remnants (#40329) 2023-10-06 09:42:47 -07:00
Harmen Stoppels
55e0c2c900 openssh: 9.5p1 (#40354) 2023-10-06 09:37:42 -07:00
Massimiliano Culpo
e20c05fcdf Make "minimal" the default duplicate strategy (#39621)
* Allow branching out of the "generic build" unification set

For cases like the one in https://github.com/spack/spack/pull/39661
we need to relax rules on unification sets.

The issue is that, right now, nodes in the "generic build" unification
set are unified together with their build dependencies. This was done
out of caution to avoid the risk of circular dependencies, which would
ultimately cause a very slow solve.

For build-tools like Cython, however, the build dependencies is masked
by a long chain of "build, run" dependencies that belong in the
"generic build" unification space.

To allow splitting on cases like this, we relax the rule disallowing
branching out of the "generic build" unification set.

* Fix issue with pure build virtual dependencies

Pure build virtual dependencies were not accounted properly in the
list of possible virtuals. This caused some facts connecting virtuals
to the corresponding providers to not be emitted, and in the end
lead to unsat problems.

* Fixed a few issues in packages

py-gevent: restore dependency on py-cython@3
jsoncpp: fix typo in build dependency
ecp-data-vis-sdk: update spack.yaml and cmake recipe
py-statsmodels: add v0.13.5

* Make dependency on "blt" of type "build"
2023-10-06 10:24:21 +02:00
Harmen Stoppels
36183eac40 python: add 3.12.0 (but keep 3.11 preferred) (#40282) 2023-10-06 09:44:09 +02:00
Alex Richert
7254c76b68 ecFlow update (#40305)
* Support static openssl for ecflow

* Update ecflow/static openssl

* Update ssl settings in ecflow

* add pic variant for ecflow

* style fix

* Update package.py

* Update package.py
2023-10-05 20:04:44 -07:00
eugeneswalker
e0e6ff5a68 Revert "cray rhel: disable due to runner issues (#40324)" (#40335)
This reverts commit bf7f54449b.
2023-10-05 10:32:52 -07:00
snehring
b0d49d4973 pbmpi: adding new version and maintainer (#40319) 2023-10-05 10:13:50 -07:00
Harmen Stoppels
4ce5d14066 unparse: drop python 3.4 remnants (#40333) 2023-10-05 09:52:23 -07:00
Thomas Madlener
9e9653ac58 whizard: Make sure to detect LCIO if requested (#40316) 2023-10-05 08:53:56 -07:00
Auriane R
bec873aec9 Add pika 0.19.0 (#40313) 2023-10-05 09:34:22 +02:00
Harmen Stoppels
bf7f54449b cray rhel: disable due to runner issues (#40324) 2023-10-05 08:45:33 +02:00
Cameron Rutherford
9f0e3c0fed exago: add and logging variant. (#40188) 2023-10-05 06:57:17 +02:00
eugeneswalker
79e7da9420 trilinos: add variant to build tests (#40284)
* trilinos: add variant: testing

* trilinos: rename +testing to +test
2023-10-04 16:32:30 -05:00
Harmen Stoppels
0f43074f3e Improve build isolation in PythonPipBuilder (#40224)
We run pip with `--no-build-isolation` because we don't wanna let pip
install build deps.

As a consequence, when pip runs hooks, it runs hooks of *any* package it
can find in `sys.path`.

For Spack-built Python this includes user site packages -- there
shouldn't be any system site packages. So in this case it suffices to
set the environment variable PYTHONNOUSERSITE=1.

For external Python, more needs to be done, cause there is no env
variable that disables both system and user site packages; setting the
`python -S` flag doesn't work because pip runs subprocesses that don't
inherit this flag (and there is no API to know if -S was passed)

So, for external Python, an empty venv is created before invoking pip in
Spack's build env ensures that pip can no longer see anything but
standard libraries and `PYTHONPATH`.

The downside of this is that pip will generate shebangs that point to
the python executable from the venv. So, for external python an extra
step is necessary where we fix up shebangs post install.
2023-10-04 14:38:50 -05:00
Ken Raffenetti
d297098504 yaksa: Allow unsupported host compiler with CUDA (#40298)
Fixes #40272.
2023-10-04 09:37:58 -07:00
Josh Bowden
284eaf1afe Damaris release v1.9.2 (#40285)
* Update to latest dot versions and improved installation of Damaris python module damaris4py

* fix for visit dependency typo

* whitespace check

* whitespace check

* fix for style issue

* reviewer suggestions for integrating Python added

* suggestion for boost depends statement added
2023-10-04 09:34:43 -06:00
Dom Heinzeller
da637dba84 Add new package awscli-v2 and its missing dependency awscrt (#40288)
* Add new package awscli-v2 and its missing dependency awscrt

* Remove boilerplate comments from awscli-v2 and awscrt packages

* Fix typos in var/spack/repos/builtin/packages/awscli-v2/package.py

* Update var/spack/repos/builtin/packages/awscli-v2/package.py

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

* Update var/spack/repos/builtin/packages/awscli-v2/package.py

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

* Update var/spack/repos/builtin/packages/awscli-v2/package.py

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

* Update var/spack/repos/builtin/packages/awscli-v2/package.py

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

* Update var/spack/repos/builtin/packages/awscli-v2/package.py

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

* Address reviewer comments

* Remove py-pip version dependency from var/spack/repos/builtin/packages/awscli-v2/package.py

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-10-04 09:34:23 -06:00
Harmen Stoppels
931fce2c24 py-isort: needs setuptools build dep before v5 (#40234)
* py-isort: needs setuptools build dep before v5

Detected in #40224.

In the past, system setuptools could be picked up when using an external
python, so py-isort@4 would install fine. With the linked PR, pip can
only consider packages that Spack controls from PYTHONPATH, so the issue
of missing py-setuptools showed up.

* py-importlib-metadata: fix lowerbounds on python

* review

* py-isort unconditionally add optional setuptools dep to prevent picking up user package at runtime

* style

* drop optional py-setuptools run dep
2023-10-04 03:31:46 -06:00
Adam J. Stewart
42fbf17c82 py-einops: add v0.7.0 (#40296) 2023-10-04 04:28:49 -05:00
Harmen Stoppels
d9cacf664c petsc: add conflict on rocm 5.6: for now (#40300)
hipsparse@5.6.0 changed hipsparseSpSV_solve() API, but reverted in 5.6.1
2023-10-04 09:59:59 +02:00
Scott Wittenburg
7bf6780de2 ci: pull E4S images from github instead of dockerhub (#40307) 2023-10-04 09:55:06 +02:00
eugeneswalker
91178d40f3 e4s arm: disable bricks due to target=aarch64 not being respected (#40308) 2023-10-04 09:51:14 +02:00
kwryankrattiger
2817cd2936 ADIOS2: v2.8 is not compatible with HDF5 v1.14: (#40258) 2023-10-03 16:45:24 -05:00
Scott Wittenburg
92a6ddcbc3 ci: Change how job names appear in gitlab (#39963) 2023-10-03 15:16:41 -06:00
Sinan
58017f484c fix_qgis_build_with_pysip5 (#39941)
* fix_qgis_build_with_pysip5

* build fails with newer protobuf

* somehow findgdal can figure this out.

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

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

* fix gdal lib again

* qgis needs QtPositioning provided by qt+location option

* fix FindPyQt5 cmake file

* fix bug

* fix qsci sip issue

* fix bug

* blackify

* improve

* add latest LTR

* add build dep

* revert until bug is fixed

* specify proj version for qgis 3.28

* improve gdal libs search via indicating gdal-config

* make flake happy

* improve deps

* add 3.28.11, improve style

* fix style

* [@spackbot] updating style on behalf of Sinan81

---------

Co-authored-by: Sinan81 <Sinan@world>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Sinan81 <Sinan81@users.noreply.github.com>
2023-10-03 14:21:51 -05:00
George Young
86d2e1af97 falco: new package @1.2.1 (#40289)
* falco: new package @1.2.1
* specifying gmake
* Replacing homepage - readthedocs is empty

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-10-03 11:26:49 -07:00
Adam J. Stewart
bf23be291b py-tables: add v3.8.0 (#40295) 2023-10-03 11:12:55 -07:00
Lydéric Debusschère
3b32a9918c [add] py-graphene: new recipe, required by py-cylc-flow (#39988) 2023-10-03 11:21:36 -06:00
Jordan Galby
f0260c84b4 Fix binutils regression on +gas~ld fix (#40292) 2023-10-03 17:28:55 +02:00
eugeneswalker
8746c75db0 e4s ci stacks: sync with e4s-23.08 (#40263)
* e4s amd64 gcc ci stack: sync with e4s-23.08

* e4s amd64 oneapi ci stack: sync with e4s-23.08

* e4s ppc64 gcc ci stack: sync with e4s-23.08

* add new ci stack: e4s amd64 gcc w/ external rocm

* add new ci stack: e4s arm gcc ci

* updates

* py-scipy: -fvisibility issue is resolved in 2023.1.0: #39464

* paraview oneapi fails

* comment out pkgs that fail to build on power

* fix arm stack name

* fix cabana +cuda specification

* comment out failing spces

* visit fails build on arm

* comment out slepc arm builds due to make issue

* comment out failing dealii arm builds
2023-10-03 08:12:51 -07:00
Gavin John
e8f230199f py-biom-format: Fix package file issues and bring up to date (#39962)
* Fix python versioning issue for py-biom-format

* Update deps according to feedback

* Remove version requirement for py-cython

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

* Only depend on py-six for versions >=2.1.10

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

* Add py-future as non-dependency for 2.1.15

* There we are. Everything anyone could ever want

* Missed cython version change

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-10-03 09:55:15 -05:00
GeorgeJuniorGG
1e3c7abc1c Adding dynaconf module (#39762)
* Adding dynaconf module

* Fixing style

* Adding dependency
2023-10-03 06:23:29 -05:00
Manuela Kuhn
12e51da102 py-yarl: add 1.9.2 (#40277) 2023-10-03 06:22:20 -05:00
Tom Payerle
992291c738 py-dipy: Update version to support python@3.10 (#40229)
* py-dipy: Update version to support python@3.10

py-dipy only adds support to python@3.10 in py-dipy@1.5.0

See #40228

* py-dipy: fix formatting issues

* py-dipy: another formatting fix

* py-dipy: Use depends instead of conflicts

* py-dipy: formatting fix

* py-dipy: Updating for @1.7.0

Added new minimum version requirements for
py-cython
py-numpy
py-scipy
py-h5py
as suggested by @manuelakuhn
(py-nibabel min version unchanged for @1.7.0)
2023-10-03 06:10:14 -05:00
Manuela Kuhn
78e63fa257 py-wcwidth: add 0.2.7 (#40256) 2023-10-03 06:04:30 -05:00
Manuela Kuhn
487ea8b263 py-virtualenv: add 20.24.5 (#40255)
* py-virtualenv: add 20.22.0

* py-platformdirs: add 3.5.3

* py-filelock: add 3.12.4

* py-distlib: add 0.3.7
2023-10-03 06:03:35 -05:00
Manuela Kuhn
0d877b4184 py-websocket-client: add 1.6.3 (#40274) 2023-10-03 05:58:53 -05:00
Manuela Kuhn
994544f208 py-werkzeug: add 2.3.7 and 3.0.0 (#40275) 2023-10-03 05:57:27 -05:00
Manuela Kuhn
36bb2a5d09 py-wrapt: add 1.15.0 (#40276) 2023-10-03 05:55:28 -05:00
Stephen Hudson
071c1c38dc py-libEnsemble: add v1.0.0 (#40203)
* py-libEnsemble: add v1.0.0

* Add version ranges for deps

* Add comments to variants

* Put when before type

* Fix line lengths

* Re-format

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

Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>

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

Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>

---------

Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
2023-10-03 05:48:17 -05:00
Lydéric Debusschère
b480ae2b7d [add] py-graphql-relay: new package (#39807)
* [add] py-graphql-relay: new package

* py-graphql-relay: Update package.py

Remove leftovers from version 3.2.0:
* archive name in pypi
* dependencies

* [fix] py-graphql-relay: remove constraint on python version; add dependence py-rx because of ModuleNotFoundError during spack test

* [fix] py-graphql-relay: remove py-rx dependence; py-graphql-core: add dependencies for version 2.3.2

* py-graphql-core: Update from review; set build backend, py-poetry for version 3: and py-setuptools for version 2

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-10-03 05:45:06 -05:00
Lydéric Debusschère
7a390f503d [add] py-metomi-isodatetime: new recipe, required by py-cylc-flow (#39990)
* [add] py-metomi-isodatetime: new recipe, required by py-cylc-flow

* py-metomi-isodatetime: use sources from pypi instead of github
2023-10-03 05:42:46 -05:00
dependabot[bot]
b7cb3462d4 build(deps): bump actions/setup-python from 4.7.0 to 4.7.1 (#40287)
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.0 to 4.7.1.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](61a6322f88...65d7f2d534)

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

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-10-03 12:28:02 +02:00
dependabot[bot]
f2230100ac build(deps): bump urllib3 from 2.0.5 to 2.0.6 in /lib/spack/docs (#40286)
Bumps [urllib3](https://github.com/urllib3/urllib3) from 2.0.5 to 2.0.6.
- [Release notes](https://github.com/urllib3/urllib3/releases)
- [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst)
- [Commits](https://github.com/urllib3/urllib3/compare/v2.0.5...2.0.6)

---
updated-dependencies:
- dependency-name: urllib3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-10-03 12:27:36 +02:00
Massimiliano Culpo
4b06862a7f Deactivate Cray sles, due to unavailable runner (#40291)
This reverts commit 0274091204.
2023-10-03 11:06:36 +02:00
Harmen Stoppels
06057d6dba Buildcache tarballs with rootfs structure (#39341)
Two changes in this PR:

1. Register absolute paths in tarballs, which makes it easier
   to use them as container image layers, or rootfs in general, outside
   of Spack. Spack supports this already on develop.
2. Assemble the tarfile entries "by hand", which has a few advantages:
   1. Avoid reading `/etc/passwd`, `/etc/groups`, `/etc/nsswitch.conf`
      which `tar.add(dir)` does _for each file it adds_
   2. Reduce the number of stat calls per file added by a factor two,
      compared to `tar.add`, which should help with slow, shared filesystems
      where these calls are expensive
   4. Create normalized `TarInfo` entries from the start, instead of letting
      Python create them and patching them after the fact
   5. Don't recurse into subdirs before processing files, to avoid
      keeping nested directories opened. (this changes the tar entry
      order slightly, it's like sorting by `(not is_dir, name)`.
2023-10-03 09:56:18 +02:00
Sam Reeve
bb03a1768b Add AdditiveFOAM package (#39295)
* Add AdditiveFOAM package
* Add AdditiveFOAM build and install

Co-authored-by: kjrstory <kjrstory@gmail.com>
Co-authored-by: Knapp, Gerry <knappgl@ornl.gov>

---------

Co-authored-by: kjrstory <kjrstory@gmail.com>
Co-authored-by: Knapp, Gerry <knappgl@ornl.gov>
2023-10-02 16:27:13 -07:00
Adam J. Stewart
75ed26258c py-torchgeo: add v0.5.0 (#40267)
* py-torchgeo: add v0.5.0

* Better documentation of dependency quirks
2023-10-02 15:23:49 -05:00
eugeneswalker
1da8477a3c vtk-m@2.0: depend on kokkos@3.7:3.9 per issue #40268 (#40281) 2023-10-02 12:26:55 -07:00
Christoph Weber
4c111554ae Add ipm package (#40069) 2023-10-02 11:46:17 -07:00
renjithravindrankannath
615312fcee Rocm 5.6.0 & 5.6.1 release updates (#39673)
* 5.6.0 updates
* Rocm 5.6.0 updates
* Style and audit corrections for 5.6
* Patching smi path for tests.
* Style correction
* 5.6.1 updates
* Updated hip tests for ci build  failure
   Updated hiprand with the release tag
   Taken care the review comment rocsolver
* Adding rocm-smi path for 5.6
* Adding the patch file
* Setting library directory uniform
* gl depends on mesa but it should not be llvm variant
* Fix for the issue 39520 by setting CMAKE_INSTALL_LIBDIR=lib
* i1 muls can sometimes happen after SCEV. They resulted in
   ISel failures because we were missing the patterns for them.
* 5.6.0 & 5.6.1 updates for migraphx, miopen-hip, mivisionx
* Revert "5.6.0 & 5.6.1 updates for migraphx, miopen-hip, mivisionx"
   This reverts commit f54c9c6c67.
* Revert operator mixup fix
* Splitting compiler-rt-linkage-for-host and operator mixup patch
* Adding missing patch for reverting operator mixup
* 5.6 update for composable-kernel,migraphx,miopen-hip and mivisionx
* Updating rvs, rcd and rccl for 5.6.1. adding comment for llvm patch
2023-10-02 11:36:51 -07:00
Joseph Wang
453625014d fix lhapdf package (#37384)
* fix lhapdf package
* [@spackbot] updating style on behalf of joequant

---------

Co-authored-by: joequant <joequant@users.noreply.github.com>
2023-10-02 11:33:54 -07:00
G-Ragghianti
1b75651af6 Implemented +sycl for slate (#39927)
* Implemented +sycl for slate

* style

* style

* add slate +sycl to ci

* slate +sycl: explicitly specify +mpi

* comment out slate+sycl+mpi in e4s oneapi stack

* removing requirement of intel-oneapi-mpi

* Added slate+sycl to e4s oneapi stack

* Removing obsolete comment

---------

Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
2023-10-02 07:35:00 -07:00
Thomas Madlener
b3e3604f46 libtirpc: Add latest version and allow for builds on macOS (#40189) 2023-10-02 15:02:33 +02:00
Harmen Stoppels
6c4ce379ca buildcache: ignore errors of newer buildcache version (#40279)
Currently buildcaches are forward incompatible in an annoying way: spack
errors out when trying to use them.

With this change, you just get a warning.
2023-10-02 14:51:48 +02:00
Harmen Stoppels
a9dcba76ce py-importlib-metadata: add patch releases (#40249)
importlib_metadata 4.11.4 fixes some nasty issues with
`metadata.entry_points(...)`, so ensure we have those bugfixes.
2023-10-02 10:09:36 +02:00
Harmen Stoppels
32f21f2a01 Spack python 3.12: PEP 695 unparse support (#40155) 2023-10-02 00:25:52 -07:00
Greg Sjaardema
e60bbd1bfc Cgns fix no fortran config (#40241)
* SEACAS: Update package.py to handle new SEACAS project name

The base project name for the SEACAS project has changed from
"SEACASProj" to "SEACAS" as of @2022-10-14, so the package
needed to be updated to use the new project name when needed.

The refactor also changes several:
    "-DSome_CMAKE_Option:BOOL=ON"
to
   define("Some_CMAKE_Option", True)

* CGNS: If fortran not enabled, do not specify parallel fortran compiler

* Update package formatting as suggested by black

* Accept suggested change
2023-10-02 16:03:47 +09:00
Freifrau von Bleifrei
71c5b948d0 discotec package: add selalib variant (#40222) 2023-10-02 07:14:50 +02:00
Tom Payerle
726d6b9881 zoltan: Fixes for #40198 (#40199)
Fix issue in configure_args which resulted in duplicate "--with-ldflags" arguments (with different values) being passed to configure.  And extended the fix to similar arguments.

Also, repeated some flags to "--with-libs" to "--with-ldflags" as when the flags were only in "--with-libs", they did not seem to be picked up everywhere.  I suspect this is a bug in the configure script, but adding to both locations seems to solve it and should not have any adverse effects.

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-10-02 07:11:36 +02:00
Sinan
aff64c02e8 xv: new package (#40032)
Co-authored-by: Sinan81 <Sinan@world>
2023-10-02 07:06:00 +02:00
Matthew Archer
31ae5cba91 add maintainers to py-nanobind (#40235) 2023-10-02 07:03:49 +02:00
Sam Reeve
0a91d2411a cabana: add v0.6 (#40168) 2023-10-02 06:57:55 +02:00
snehring
5f3af3d5e4 perl-dbd-mysql update to 4.050 (#40245)
* perl-devel-checklib: adding new package perl-devel-checklib

* perl-dbd-mysql: adding new version 4.050 and a new build dep
2023-10-02 06:45:11 +02:00
Satish Balay
37158cb913 petsc,py-petsc4py,slepc,py-slepc4py: add version 3.20.0 (#40260) 2023-10-02 06:28:37 +02:00
Wouter Deconinck
a596e16a37 libxkbcommon: new versions 1.4.1, 1.5.0 (#40273) 2023-10-02 05:54:55 +02:00
Weiqun Zhang
4e69f5121f amrex: add v23.10 (#40270) 2023-10-02 05:53:16 +02:00
Wouter Deconinck
2a0f4393c3 assimp: new version 5.3.1 (#40271) 2023-10-02 05:52:30 +02:00
Wouter Deconinck
c9e1e7d90c acts: impose cxxstd variant on geant4 dependency (#39767) 2023-10-02 05:49:51 +02:00
Juan Miguel Carceller
7170f2252c rivet: remove deprecated versions and clean up recipe (#39861)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
2023-10-02 05:48:35 +02:00
eugeneswalker
b09073e01e py-pandas@0.24.2 %oneapi: add cflag=-Wno-error=implicit-function-declaration (#39470) 2023-10-01 14:42:56 -06:00
eugeneswalker
2d509dc3eb py-scipy: -fvisibility issue is resolved in 2023.1.0: (#39464)
* py-scipy: -fvisibility issue is resolved in 2023.1.0:

* e4s oneapi ci: add py-scipy
2023-10-01 17:29:21 +00:00
Martin Aumüller
8a9d45cc29 embree: fix linux build on aarch64 for 3.13.5 (#39749)
- upstream patch does not apply cleanly to older versions, not required
  for newer ones
- also add conflict for older versions, except for 3.13.3 which works by
  chance
2023-10-01 09:04:37 -07:00
Wouter Deconinck
b25f8643ff geant4, vecgeom: support variant cxxstd=20 (#39785) 2023-10-01 21:33:37 +09:00
Juan Miguel Carceller
9120b6644d qt: change version for opengl dependencies (#39718) 2023-10-01 21:31:11 +09:00
eugeneswalker
68dbd25f5f e4s cray sles ci: expand spec list (#40162)
* e4s cray sles stack: expand spec list

* remove unnecessary packages:trilinos:one_of
2023-09-30 21:32:33 -07:00
Todd Gamblin
9e54134daf docs: Replace package list with packages.spack.io (#40251)
For a long time, the docs have generated a huge, static HTML package list. It has some
disadvantages:

* It's slow to load
* It's slow to build
* It's hard to search

We now have a nice website that can tell us about Spack packages, and it's searchable so
users can easily find the one or two packages out of 7400 that they're looking for. We
should link to this instead of including a static package list page in the docs.

- [x] Replace package list link with link to packages.spack.io
- [x] Remove `package_list.html` generation from `conf.py`.
- [x] Add a new section for "Links" to the docs.
- [x] Remove docstring notes from contribution guide (we haven't generated RST
      for package docstrings for a while)
- [x] Remove referencese to `package-list` from docs.
2023-10-01 05:36:22 +02:00
eugeneswalker
08a9345fcc e4s ci: add packages: drishti, dxt-explorer (#39597)
* e4s ci: add packages: drishti, dxt-explorer

* e4s oneapi ci: comment out dxt-explorer until r%oneapi issue #40257 is resolved
2023-09-30 06:15:58 +09:00
John W. Parent
7d072cc16f Windows: detect all available SDK versions (#39823)
Currently, Windows SDK detection will only pick up SDK versions
related to the current version of Windows Spack is running on.
However, in some circumstances, we want to detect other version
of the SDK, for example, for compiling on Windows 11 for Windows
10 to ensure an API is compatible with Win10.
2023-09-29 20:17:10 +00:00
snehring
d81f457e7a modeltest-ng: adding new version, swapping maintainer (#40217)
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2023-09-29 20:19:29 +02:00
Peter Scheibel
3969653f1b Cray manifest: compiler handling fixes (#40061)
* Make use of `prefix` in the Cray manifest schema (prepend it to
  the relative CC etc.) - this was a Spack error.
* Warn people when wrong-looking compilers are found in the manifest
  (i.e. non-existent CC path).
* Bypass compilers that we fail to add (don't allow a single bad
  compiler to terminate the entire read-cray-manifest action).
* Refactor Cray manifest tests: module-level variables have been
  replaced with fixtures, specifically using the `test_platform`
  fixture, which allows the unit tests to run with the new
  concretizer.
* Add unit test to check case where adding a compiler raises an
  exception (check that this doesn't prevent processing the
  rest of the manifest).
2023-09-29 09:47:30 -07:00
Jordan Galby
db37672abf Print error when missing git (#40254)
Like a missing curl.
2023-09-29 15:14:39 +00:00
eugeneswalker
1f75ca96df kokkos-nvcc-wrapper: add v4.1.00 (#40240) 2023-09-29 17:08:42 +02:00
Harmen Stoppels
605835fe42 Don't drop build deps on overwrite install (#40252)
If you `spack install x ^y` where `y` is a pure build dep of `x`, and
then uninstall `y`, and then `spack install --overwrite x ^y`, the build
fails because `y` is not re-installed.

Same can happen when you install a develop spec, run `spack gc`,
modify sources, and install again; develop specs rely on overwrite
install to work correctly.
2023-09-29 16:40:21 +02:00
Abhishek Yenpure
6c2748c37d Adding Catalyst 2.0 smoke test (#40112)
--  Performaing formatting changes
  --  Formatting file to conform with spack style
  --  Adding updates from review
  --  Removing old release candidates from the specification
  --  Adding external conduit support for Catalyst
  --  Adding Catalyst to `CMAKE_PREFIX_PATH` for the test to find
2023-09-29 16:36:24 +02:00
Massimiliano Culpo
210d221357 Test package detection in a systematic way (#18175)
This PR adds a new audit sub-command to check that detection of relevant packages
is performed correctly in a few scenarios mocking real use-cases. The data for each 
package being tested is in a YAML file called detection_test.yaml alongside the 
corresponding package.py file.

This is to allow encoding detection tests for compilers and other widely used tools, 
in preparation for compilers as dependencies.
2023-09-29 10:24:42 +02:00
Mark W. Krentel
c9ef5c8152 hpctoolkit: add version 2023.08.1 (#40248)
Add versions 2020.08.1 and branch 2023.08.stable.  Note: the version
numbers are a little different.  Here, 2023.08.1 means release no. 1
from the release/2023.08 branch.
2023-09-29 00:48:05 -06:00
eugeneswalker
0274091204 Revert "e4s cray sles: suspend ci until machine issues resolved (#40219)" (#40238)
This reverts commit 5165524ca6.
2023-09-29 07:25:50 +02:00
John W. Parent
3f2f0cc146 openblas package: fix lib suffix construction in libs (#40242) 2023-09-28 22:02:37 -06:00
Massimiliano Culpo
a236fce31f Partial removal of circular dependencies between spack and llnl (#40090)
Modifications:
- [x] Move `spack.util.string` to `llnl.string`
- [x] Remove dependency of `llnl` on `spack.error`
- [x] Move path of `spack.util.path` to `llnl.path`
- [x] Move `spack.util.environment.get_host_*` to `spack.spec`
2023-09-28 16:21:52 +00:00
snehring
f77a38a96b mash: fix compilation for aarch64 (#40218) 2023-09-28 10:16:11 -06:00
Harmen Stoppels
6d55066b94 Use st_nlink in hardlink tracking (#39328)
Only add potential hardlinks to a set/dict, instead of each file. This
should be much cheaper, since hardlinks are very rare.
2023-09-28 13:24:56 +00:00
Harmen Stoppels
78132f2d6b glibc: dont link libgcc_eh.a pre 2.17, and backport at_random auxval patch (#40013)
This resolves an interesting circular dependency between gcc and glibc:

1. glibc < 2.17 depends on libgcc.a and libgcc_eh.a
2. libgcc_eh.a is only built when gcc is configured with
   --enable-shared
3. but building shared libraries requires crt*.o and libc.so

Backport AT_RANDOM auxval changes to avoid dealing with wrong inline 
assembly (fallback code fails on ubuntu 23.04)
2023-09-28 13:30:43 +02:00
Brian Vanderwende
fba47e87d7 Support optional vars script arguments (#40064) 2023-09-28 06:52:22 -04:00
Massimiliano Culpo
bf8e8d9f5f cmake: add v3.27.6 (#40037)
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
2023-09-28 11:06:28 +02:00
Sam Gillingham
ebc0e9be19 kealib: add 1.5.1 and 1.5.2 versions (#40202)
* add recent kealib versions
* udpdate depends_on so hl not required for latest version
2023-09-27 19:08:28 -06:00
Vicente Bolea
b6f08f1d4e vtk-m: add VTK-m 2.1.0-rc1 (#39581) 2023-09-27 10:13:18 -06:00
Jared Popelar
d9724597ed Trilinos package: build on Windows (#34622)
Update Trilinos and dependencies to build a limited version of Trilinos
on Windows.

* Support trilinos~mpi~shared on Windows
* superlu: force CMake build on Windows
* boost: update to build on Windows (proper option formatting and
  build tool names)
* pcre, openblas: add CMake-based build (keep prior build system
  as default on platforms other than Windows)
* openblas: add patch when using Intel Fortran compiler (currently
  this is included as part of the hybrid %msvc compiler in Spack)

Co-authored-by: John Parent <john.parent@kitware.com>
2023-09-27 09:58:12 -06:00
kwryankrattiger
c90c946d52 ParaView: Add versio 5.11.2 (#40213) 2023-09-27 10:20:13 -05:00
Martin Aumüller
bb66d15d08 ffmpeg: fix build with XCode 15 (#40187)
As reported in #40159, a shared library build of ffmpeg 6.0 fails with the linker that was added with XCode 15:
ld: building exports trie: duplicate symbol '_av_ac3_parse_header'
clang: error: linker command failed with exit code 1 (use -v to see invocation)

Forcing the old linker with -Wl,-ld_classic works around this.
2023-09-27 16:41:32 +02:00
snehring
1cd2d07f0b last: add new version, fix build on aarch64 (#40216)
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2023-09-27 16:32:18 +02:00
Garth N. Wells
43cb49d87a py-nanonbind: add new versions (#40161) 2023-09-27 16:28:26 +02:00
eugeneswalker
5165524ca6 e4s cray sles: suspend ci until machine issues resolved (#40219) 2023-09-27 04:51:34 +02:00
Martin Aumüller
38dc3a6896 vtk: @9.2 need seacas@2022-10-14, fix macos (#39896)
Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2023-09-26 13:48:44 -06:00
John W. Parent
115e448bd3 Paraview package: update freetype find patch for shared libs (#40085)
VTK's (and therefore Paraview's) FindFreetype module required patching to
handle static import libraries from Freetype. However it did not cover
shared libraries. This adds support for importing shared freetype into the VTK build
2023-09-26 10:41:24 -07:00
Harmen Stoppels
5c25437c9f spack --profile: dump to stderr (#40209) 2023-09-26 16:18:47 +02:00
Christoph Weber
0e72ff4a0d ploticus: new package (#39881)
Co-authored-by: Bernhard Kaindl <contact@bernhard.kaindl.dev>
2023-09-26 08:15:12 -05:00
Matt Fraser
90edd18d1f Add NCCL v2.18.5-1 release to recipe (#40201) 2023-09-26 08:05:23 -05:00
Massimiliano Culpo
40dbadb868 crosstool-ng: add v1.26.0 (#40204) 2023-09-26 11:17:39 +02:00
Martin Aumüller
c16546bd4c libressl: fix package & new versions (#39741) 2023-09-26 10:39:29 +02:00
Dom Heinzeller
143e6a4fbb Always apply Python unixcompilers.py rpath fix, not just on cray (#39929)
* Rename var/spack/repos/builtin/packages/python/cray-rpath-3.1.patch as var/spack/repos/builtin/packages/python/rpath-non-gcc.patch and apply unconditionally

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

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-09-26 02:38:20 -06:00
Martin Aumüller
13816f19fd opencv: add 4.7.0 and 4.8.0 and fix ffmpeg dependency (#39013) 2023-09-26 10:28:29 +02:00
Martin Aumüller
34ff3b408b seacas: correctly limit fmt dependency (#39756)
versions older than 2022-10-14 do not build with fmt@10, either:
fmt/core.h:1579:3: error: static_assert failed due to requirement 'formattable'
2023-09-26 06:35:38 +02:00
Victor A. P. Magri
aec88ef3e6 hypre: add support for magma (#40121) 2023-09-26 06:27:14 +02:00
snehring
9fda22d942 bcl2fastq2: patch for compiling on aarch64 (#40195) 2023-09-26 06:26:19 +02:00
snehring
550613ee3a gmap-gsnap: add v2023-07-20 and aarch64 support (#40200) 2023-09-26 05:59:31 +02:00
Ethan Williams
5341834ebe Elbencho: add elbencho package (#40193)
* add elbencho package
* pep8 compliant
* add description
* depends on boost
* boost options
* dependencies
* fix ncurses not linking properly missing tinfo
* pep8 fix
* fix style of boost variants
* final style fix - spack style is happy
* correct cufile env variable name

---------

Co-authored-by: Ethan W <mail@ethanwilliams.xyz>
2023-09-25 18:53:28 -06:00
Alberto Invernizzi
fc027e34d1 apex: add new version 2.6.3 + deal with ompt build problem (#40073)
* add new version 2.6.3
* add conflict for openmp when using gcc
2023-09-25 16:00:58 -07:00
Harmen Stoppels
aef58776b4 openssl: new versions (#40194)
apparently there was still a 1.1.1 release
2023-09-25 21:54:05 +02:00
Cameron Smith
4e17a40d09 omegah: new version (#40192) 2023-09-25 13:53:36 -06:00
Matthieu Dorier
d97251a4c6 spdlog: add version 1.12.0 (#40186) 2023-09-25 12:23:02 -07:00
snehring
2a66a67132 subread: removing mtune arg to compiler (#40197) 2023-09-25 12:19:25 -07:00
eugeneswalker
10fd69ec74 new package: gsibec (#40137) 2023-09-25 11:28:04 -06:00
Harmen Stoppels
9889a0cac6 py-numcodecs: drop upperbound, add new version, avoid native compilation (#40183)
* py-numcodecs: drop upperbound, add new version, avoid native compilation

* py-numcodecs: add entrypoints

* Remove another upperbound on python

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-09-25 07:28:32 -06:00
Harmen Stoppels
65ffd0dd63 jsoncpp: add meson build system, update package, update cmake ~ownlibs (#39639) 2023-09-25 10:13:30 +02:00
Bernhard Kaindl
3d2c779b87 openssh: add version 9.4p1 and fix compile issue with new zlib-1.3 (#40174)
The fix for the compile issue was improved by Bernhard Kaindl.
He also added to fix two classes of other build fails:
- add missing openssl dependency version limit to older openssh versions
- add missing -fcommon for new compilers building old openssh versions

Co-authored-by: snehring <snehring@iastate.edu>
2023-09-25 08:30:10 +02:00
Harmen Stoppels
b57c2a10d4 phist: remove python 3.10 upperbound (#40175) 2023-09-25 08:28:13 +02:00
Diego Alvarez S
849a0a5eeb Add opendjk 11.0.20.1+1, 17.0.8.1+1 (#40035) 2023-09-25 05:09:30 +02:00
Rocco Meli
7e4a6160b9 namd: Add NAMD 3.0b3 and ARM support (#40134) 2023-09-25 05:04:17 +02:00
dependabot[bot]
646e7b4b00 build(deps): bump black in /.github/workflows/style (#40165)
Bumps [black](https://github.com/psf/black) from 23.1.0 to 23.9.1.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](https://github.com/psf/black/compare/23.1.0...23.9.1)

---
updated-dependencies:
- dependency-name: black
  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>
2023-09-24 17:48:02 +00:00
eugeneswalker
eea86c3981 new package: ecmwf-atlas (#40136) 2023-09-24 10:43:09 -06:00
dependabot[bot]
37c48fc82c build(deps): bump urllib3 from 2.0.4 to 2.0.5 in /lib/spack/docs (#40119)
Bumps [urllib3](https://github.com/urllib3/urllib3) from 2.0.4 to 2.0.5.
- [Release notes](https://github.com/urllib3/urllib3/releases)
- [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst)
- [Commits](https://github.com/urllib3/urllib3/compare/2.0.4...v2.0.5)

---
updated-dependencies:
- dependency-name: urllib3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-09-24 17:35:48 +02:00
George Young
47daba3dc1 blast-plus: add 2.14.1 (#40179)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-09-24 09:33:38 -06:00
Brian Vanderwende
46062d98fd visit: Add NetCDF format support (#40065) 2023-09-24 17:26:34 +02:00
François Trahay
4e37084ed4 EZTrace: add v2.1 (#39748) 2023-09-24 17:12:32 +02:00
Thomas Madlener
e7c229393d garfieldpp: Fix the signature of setup_dependent_build_environment (#40133) 2023-09-24 17:04:41 +02:00
Houjun Tang
87fd9c3e93 sw4: add v3.0 (#40146) 2023-09-24 16:54:32 +02:00
snehring
676f2a3175 hmmer: adding new version 3.4 (#40148) 2023-09-24 16:53:18 +02:00
Adam J. Stewart
5fe7f5329b py-torchvision: minimize dependencies (#40163) 2023-09-24 16:27:09 +02:00
Adam J. Stewart
c6a3dd03ab py-torchmetrics: add v1.2.0 (#40164) 2023-09-24 16:25:34 +02:00
Hartmut Kaiser
ebdd5e28f2 flecsi: bumping HPX requirement to V1.9.1 (#32355) 2023-09-24 16:24:33 +02:00
dependabot[bot]
068abdd105 build(deps): bump mypy from 1.5.0 to 1.5.1 in /.github/workflows/style (#40166)
Bumps [mypy](https://github.com/python/mypy) from 1.5.0 to 1.5.1.
- [Commits](https://github.com/python/mypy/compare/v1.5.0...v1.5.1)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-09-24 16:21:41 +02:00
dependabot[bot]
9ec372a86c build(deps): bump actions/checkout from 4.0.0 to 4.1.0 (#40172)
Bumps [actions/checkout](https://github.com/actions/checkout) from 4.0.0 to 4.1.0.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](3df4ab11eb...8ade135a41)

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

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-09-24 16:08:15 +02:00
Alec Scott
5e05f6b7c6 bfs: add v3.0.2 (#40176) 2023-09-24 15:53:15 +02:00
Alec Scott
7988d8c67d glab: add v1.33.0 (#40177) 2023-09-24 15:53:01 +02:00
Alec Scott
658a3f2fdb hugo: add v0.118.2 (#40178) 2023-09-24 15:52:42 +02:00
Rocco Meli
582f0289af Add mda-xdrlib and update pyedr and panedr (#39912)
* ensure umpire~cuda~rocm when ~cuda~rocm

* Add mda-xdrlib and update pyedr and panedr

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

Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>

* code review

* fix python pin, conflated with py-tomli

---------

Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
2023-09-24 02:07:59 -06:00
eugeneswalker
95b737d923 trilinos +shylu: patch to resolve trilinos issue #12048 (#40169)
* trilinos +shylu: patch to resolve trilinos issue #12048

* e4s ci: build xyce ^trilinos+shylu

---------

Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>
2023-09-24 16:28:03 +09:00
Adam J. Stewart
d7e9a13f53 protobuf: add v4.24.3 (#40152) 2023-09-23 20:04:10 +02:00
Tom Payerle
25e45f9f07 py-tinyarray: add version 1.2.4, needed for python@3.10 (#40171)
* py-tinyarray: add version 1.2.4, needed for python@3.10

Added @1.2.4
Require @1.2.4 when using python@3.10:

* py-tinyarray: format fix
2023-09-23 08:57:46 -05:00
Cameron Smith
38cc51ec36 pumi: add version 2.2.8 (#40143) 2023-09-22 14:38:46 -07:00
Massimiliano Culpo
5c10c29923 Pin the version of tools used in CI, have dependabot manage their version (#40066) 2023-09-22 10:33:01 -07:00
eugeneswalker
daf95227bf e4s cray rhel stack: expand to full spec list (#40111)
* e4s cray rhel stack: expand to full spec list

* comment out gasnet; require %gcc for unzip

* require openblas@0.3.20 to get around %cce error; follow up with issue report

* comment out failing specs;

* comment out axom and xyce due to errors

* improve clarity of failing specs
2023-09-22 16:04:20 +00:00
Adam J. Stewart
480a5e0848 py-pyzmq: fix order of decorators (#40157) 2023-09-22 17:20:56 +02:00
Satish Balay
783e253f7d llvm: add version 17.0.1 (#40108) 2023-09-22 14:41:23 +02:00
Harmen Stoppels
716196930a Remove distutils dependency in Spack (#40153)
* msvc.py: don't import distutils

Introduced in #27021, makes Spack forward incompatible with Python.

The module was already deprecated at the time of the PR.

* update spack package
2023-09-22 13:04:58 +02:00
Adam J. Stewart
f42402129a py-matplotlib: add v3.7.3 (#39961) 2023-09-22 11:23:57 +02:00
Adam J. Stewart
419878f035 Add support for macOS Sonoma (#40115) 2023-09-22 04:21:26 -05:00
Harmen Stoppels
32927fd1c1 py-pyzmq: force recythonize of older versions (#40151) 2023-09-22 03:18:34 -06:00
Harmen Stoppels
092a5a8d75 py-gpy: re-cythonize & drop python upperbound (#40089)
* py-gpy: drop cython induced python upperbound

* py-gpy: bump scipy

* py-fn-py: python bounds for old version, new version w/o

* py-statsmodels: force recythonization

* py-gpy: clarifying comment about cython build type
2023-09-22 04:18:01 -05:00
Adam J. Stewart
f082b19058 py-pyproj: add v3.6.1 (#40128) 2023-09-22 03:29:37 -05:00
Harmen Stoppels
eb7e26006f py-hpbandster: use build/run deps instead of build (#40102) 2023-09-22 02:18:39 -06:00
Adam J. Stewart
2d3d9640dc py-pandas: add v2.1.1 (#40127) 2023-09-22 10:16:01 +02:00
Adam J. Stewart
f95080393a libzmq: fix build with Apple Clang 15.0.0 (#40116) 2023-09-22 10:14:43 +02:00
Adam J. Stewart
0b8203940a OpenBLAS: add v0.3.24 (#40132)
Co-authored-by: adamjstewart <adamjstewart@users.noreply.github.com>
2023-09-22 08:58:23 +02:00
Adam J. Stewart
3bd7859e7f py-scikit-learn: add v1.3.1 (#40126) 2023-09-22 08:39:38 +02:00
eugeneswalker
599b612edf add met v11.1.0 (#40138) 2023-09-22 08:35:10 +02:00
eugeneswalker
6f9126d738 add metplus v5.1.0 (#40139) 2023-09-22 08:30:38 +02:00
eugeneswalker
59399ab1f8 add scotch v7.0.4 (#40140) 2023-09-22 08:30:22 +02:00
Lydéric Debusschère
b67f619448 py-aiofiles: Add version 0.7.0 required by py-cylc-flow (#39987)
* py-aiofiles: Add version 0.7.0 required by py-cylc-flow

* py-aiofiles: update from review

* depends on py-setuptools before 0.6
* depends on py-poetry-core after 0.7

Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>

* py-aiofiles: Taking reviewing into account; add a upper version constraint for Python.

* py-aiofiles: update from review, set lower version of python

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

---------

Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-09-22 00:29:03 -05:00
eugeneswalker
2755706115 Revert "e4s-cray: drop in ci as there are no runners (#40122)" (#40144)
This reverts commit bd8d0324a9.
2023-09-21 22:38:26 -06:00
Thiago Genez
43ed8a12b7 openssh: Fix segfault on x86_64-darwin (#40044)
Import patches from homebrew
2023-09-22 01:41:22 +02:00
Alex Richert
3f5b4a4907 Update grib-util package.py (#40120) 2023-09-21 14:15:06 -07:00
Garth N. Wells
cd16478aba py-fenics-dolfinx: add version upper bound for Python dependency (#40125)
* py-fenics-dolfinx: add upper bound on Python version

* Small fix

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

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-09-21 13:17:45 -06:00
Rocco Meli
aa87c747f9 Add missing platform in Charm++ (#40051)
Add missing `linux` platform in Charm++ when building for `arm8`.
2023-09-21 20:31:17 +02:00
Steven R. Brandt
9210b19398 lorene: add C++ headers to the install (#39909) 2023-09-21 20:27:23 +02:00
George Young
4d156b9e6b relion: add 4.0.1, fix build on Rocky8 (#40074)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-09-21 20:24:03 +02:00
Jonas Thies
56df8b61a2 phist: fix compatibility with python@3.11: (#40082) 2023-09-21 20:21:35 +02:00
Anton Kozhevnikov
170867e38a SIRIUS: remove old versions (#40105) 2023-09-21 20:18:58 +02:00
Wileam Y. Phan
5ca9fd6c82 Fix false detection of llvm-amdgpu as llvm and llvm-doe (#40113) 2023-09-21 20:15:20 +02:00
Robert Underwood
ef165c80b3 py-nanobind add cmake path (#40079)
* py-nanobind add cmake path

* fix style

---------

Co-authored-by: Robert Underwood <runderwood@anl.gov>
2023-09-21 13:15:02 -05:00
Lydéric Debusschère
6859694e8e [add] py-graphql-ws: new recipe, required by py-cylc-uiserver (#39991)
* [add] py-graphql-ws: new recipe, required by py-cylc-uiserver

* py-graphql-ws: remove constraint on version for python
2023-09-21 13:14:11 -05:00
John W. Parent
aeaca77630 Harden compiler detection against errors (#39736)
Fixes #39622

Add a timeout to compiler detection and allow Spack to proceed when
this timeout occurs.

In all cases, the timeout is 120 seconds: it is assumed any compiler
invocation we do for the purposes of verifying it would resolve in
that amount of time.

Also refine executables that are tested as being possible MSVC
instances, and limit where we try to detect MSVC. In more detail:

* Compiler detection should timeout after a certain period of time.
  Because compiler detection executes arbitrary executables on the
  system, we could encounter a program that just hangs, or even a
  compiler that hangs on a license key or similar. A timeout
  prevents this from hanging Spack.
* Prevents things like cl-.* from being detected as potential MSVC
  installs. cl is always just cl in all cases that Spack supports.
  Change the MSVC class to indicate this.
* Prevent compilers unsupported on certain platforms from being
  detected there (i.e. don't look for MSVC on systems other than
  Windows).

The first point alone is sufficient to address #39622, but the
next two reduce the likelihood of timeouts (which is useful since
those slow down the user even if they are survivable).
2023-09-21 10:42:12 -07:00
AMD Toolchain Support
2a9d1d444b aocl-sparse: use .libs instead of hard-coded value for library computation (#39868)
Co-authored-by: matooley <phil.tooley@amd.com>
2023-09-21 18:47:29 +02:00
Massimiliano Culpo
abad16c198 Restore virtuals normalization on edge construction (#40130)
Put back normalization of the "virtuals" input as a sorted tuple. 

Without this we might get edges that differ just for the order of 
virtuals, or that have lists, which are not hashable.

Add unit-tests to prevent regressions.
2023-09-21 17:02:34 +02:00
Massimiliano Culpo
4c0bc39054 Remove Python 3.6 from bootstrap tests on Ubuntu, add 3.11 (#40131) 2023-09-21 15:14:47 +02:00
Harmen Stoppels
501d322264 e4s: drop python 3.8 preference (#40123) 2023-09-21 15:07:21 +02:00
Manuela Kuhn
59fc09e93f py-versioneer: add 0.29 (#40076) 2023-09-21 07:22:20 -05:00
Harmen Stoppels
8bd54e2f8f cython: fix recythonize by default patch (#40096) 2023-09-21 07:09:47 -05:00
Sinan
bd8d121a23 package:pylint fix isort dependency versions (#40094)
Co-authored-by: sbulut <sbulut@3vgeomatics.com>
2023-09-21 06:43:44 -05:00
Lydéric Debusschère
2bd487988f [add] py-ansimarkup: new recipe required by py-cylc-flow (#39989)
* [add] py-ansimarkup: new recipe required by py-cylc-flow

* py-ansimarkup: remove version constraint on python, add version 2.1.0
2023-09-21 06:36:15 -05:00
Manuela Kuhn
452e56f467 py-vcrpy: add 5.1.0 (#40075) 2023-09-21 06:28:25 -05:00
Christian Glusa
62e94b0cb7 py-scikit-sparse: add 0.4.11, 0.4.12 (#40077) 2023-09-21 06:27:04 -05:00
Thomas Dickerson
5d331d4141 Bazel patch specs were too restrictive (#40084)
These patches should always be applied - the existing Bazel code is always wrong, working on some older compilers was a lucky fluke.
2023-09-21 05:27:11 -05:00
Harmen Stoppels
bd8d0324a9 e4s-cray: drop in ci as there are no runners (#40122) 2023-09-21 09:54:06 +00:00
Adam J. Stewart
d79a3ecc28 py-gevent: relax dependency constraints (#40117) 2023-09-21 09:00:28 +02:00
Harmen Stoppels
dac3b45387 gptune: doesnt depend on cython (#40104) 2023-09-20 15:31:45 -07:00
Dom Heinzeller
31fe78e378 ESMF package: fix netcdf static libs and variant combinations (#39738)
Add "snapshot" variant for identifying UFS WM support
2023-09-20 10:28:52 -07:00
Patrick Gartung
e16ca49036 Revert PR 40091 which duplicates PR 38987 (#40107) 2023-09-20 13:03:49 -04:00
Auriane R
a7ee72708a Add support for C++23 in pika and pika-algorithms packages (#40078)
* Add C++23 support for pika

* Add C++23 support for pika-algorithms as well
2023-09-20 09:28:25 -06:00
Auriane R
c4a53cf376 Add 23 and 26 to the cxxstd variant for boost (#40081) 2023-09-20 16:21:06 +02:00
Massimiliano Culpo
e963d02a07 Fix a leftover typo from depflag rework (#40101) 2023-09-20 14:16:53 +00:00
Harmen Stoppels
f89451b4b8 cython: add build-tools tag (#40100) 2023-09-20 15:18:04 +02:00
Raffaele Solcà
9c87506c2c DLA-Future: add v0.2.1 (#40098) 2023-09-20 14:58:23 +02:00
Auriane R
35223543e9 Add 23 to the cxxstd variant of fmt (#40080) 2023-09-20 11:20:41 +02:00
Marc Mengel
e1b22325ea Add details on error messages from requirements (#40092) 2023-09-20 06:16:29 +02:00
Patrick Gartung
2389047072 Fix error in qt5.15 building qtlocation with gcc13 (#40091) 2023-09-19 16:18:34 -06:00
Richard Berger
f49c58708b FleCSI updates (#40087)
* flecsi: update description and flog variant help
* flecsi: use kokkos_cxx when needed
2023-09-19 14:28:13 -06:00
Daryl W. Grunau
d916073397 eospac: expose version 6.5.7 (#40060)
Co-authored-by: Daryl W. Grunau <dwg@lanl.gov>
2023-09-19 11:44:20 -07:00
AMD Toolchain Support
bfa514af98 python version dependency for supporting nwchem-702 build (#40072)
Co-authored-by: viveshar <vivek.sharma2@amd.com>
2023-09-19 11:41:04 -07:00
Harmen Stoppels
c57e2140c2 ci: dont use nightly image tag (#40070) 2023-09-19 17:53:28 +02:00
Tuomas Koskela
9e21d490ea conquest: add new package (#40053) 2023-09-19 09:38:37 -06:00
Massimiliano Culpo
3b4ca0374e Use process pool executors for web-crawling and retrieving archives (#39888)
Fix a race condition when searching urls, and updating a shared
set '_visited'.
2023-09-19 15:32:59 +02:00
Harmen Stoppels
7d33c36a30 ci: drop redundant packages.yaml (#40068) 2023-09-19 11:47:48 +02:00
Massimiliano Culpo
4f14db19c4 ASP-based solver: declare deprecated versions iff config:deprecated:true (#40011)
By default, do not let deprecated versions enter the solve.

Previously you could concretize to something deprecated, only to get errors on install.

With this commit, we get errors on concretization, so the issue is caught earlier.
2023-09-19 09:44:49 +00:00
AMD Toolchain Support
a0dcf9620b Lammps: don't apply AOCC patches to versions containing the backport (#39844)
Co-authored-by: Phil Tooley <phil.tooley@amd.com>
2023-09-19 08:52:15 +02:00
Tim Haines
9a9c3a984b extrae: add versions 4.0.5, 4.0.6 (#40063) 2023-09-19 08:45:59 +02:00
Manuela Kuhn
a3543e2248 py-typing-extensions: add 4.8.0 (#40049) 2023-09-19 01:02:31 -05:00
Adam J. Stewart
4cdbb04b15 py-lightning: add v2.0.8/9 (#40058) 2023-09-18 21:13:24 -06:00
Adam J. Stewart
2594be9459 py-rarfile: add v4.1 (#40054) 2023-09-18 19:58:39 -06:00
Scott Wittenburg
8f07983ab6 adios2: add smoke tests (#39970) 2023-09-18 19:43:46 -06:00
dependabot[bot]
8e34eaaa75 build(deps): bump docker/setup-buildx-action from 2.10.0 to 3.0.0 (#39967)
Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 2.10.0 to 3.0.0.
- [Release notes](https://github.com/docker/setup-buildx-action/releases)
- [Commits](885d1462b8...f95db51fdd)

---
updated-dependencies:
- dependency-name: docker/setup-buildx-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>
2023-09-19 00:48:30 +00:00
Andrew-Dunning-NNL
7e7d373ab3 mdspan: new package (#40024)
* new package mdspan

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

Co-authored-by: Alec Scott <alec@bcs.sh>

* mdspan- fix style

---------

Co-authored-by: Alec Scott <alec@bcs.sh>
2023-09-18 18:44:17 -06:00
Adam J. Stewart
dbd520f851 Better detection of Python libs/headers (#39308) 2023-09-18 15:46:33 -07:00
afzpatel
4fd7fa5fc1 new package composable kernel (#39222)
* initial commit to add composable kernel package
* change dependencies to type build and add amdgpu_target variant
* fix spacing
* fix styling
* remove rocmmlir from miopen-hip recipe
* enable miopen with ck after 5.5.1
* fix typo
2023-09-18 14:24:45 -07:00
Johann Gaebler
84d2097a8c r-wru: Add R package wru (#39935) 2023-09-18 14:15:56 -07:00
Brian Vanderwende
842f19c6e3 grads: add versions and variants (#40017)
* Add grads versions, variants, and dependency
* Bugfix for hdf4 libs and style fixes
* Switch boolean variant checking syntax
2023-09-18 13:34:46 -07:00
eugeneswalker
577ea0a0a8 pmix: new versions (#40055) 2023-09-18 12:47:36 -07:00
Brian Vanderwende
4d8f9ff3e8 xxdiff: add new package (#40021)
* Add new package xxdiff

* style fixes

* Versioning updates to match best practices

* Full hash and flex, bison as build deps
2023-09-18 12:40:22 -07:00
rfeki
60ce6c7302 Add cuda as a variant to opa-psm2 (#39754)
Signed-off-by: Raafat Feki <rfeki@cornelisnetworks.com>
2023-09-18 12:28:37 -07:00
Manuela Kuhn
d111bde69e py-tqdm: add 4.66.1 (#39952) 2023-09-18 13:04:39 -06:00
eugeneswalker
3045ed0e43 Revert "gitlab ci: temporarily disable darwin aarch64 (#39974)" (#40052)
This reverts commit 2c13361b09.
2023-09-18 12:48:32 -06:00
Freifrau von Bleifrei
2de0e30016 SeLaLib: add new package (#39847) 2023-09-18 13:15:10 -05:00
Manuela Kuhn
15085ef6e5 py-tornado: add 6.3.3 (#39949)
* py-tornado: add 6.3.3

* Fix style
2023-09-18 11:18:36 -06:00
Manuela Kuhn
0c2849da4d py-twine: add 4.0.2 (#40026) 2023-09-18 11:50:51 -05:00
Manuela Kuhn
75eeab1297 py-types-psutil: add 5.9.5.16 (#40027) 2023-09-18 11:49:20 -05:00
Dom Heinzeller
b8e32ff6b3 Fix several build errors for hdf-eos2 (not only but in particular on macOS w/ apple-clang) (#39877)
Fix permissions for configure file in var/spack/repos/builtin/packages/hdf-eos2/package.py, fix dependencies to match what hdf provides, update compiler flags for apple-clang
2023-09-18 18:47:25 +02:00
Manuela Kuhn
e7924148af py-types-typed-ast: add 1.5.8.7 (#40047) 2023-09-18 11:47:00 -05:00
Manuela Kuhn
d454cf4711 py-types-urllib3: add 1.26.25.14 (#40048)
* py-types-urllib3: add 1.26.25.14

* Fix style
2023-09-18 11:44:26 -05:00
George Young
ba81ef50f5 cpat: new package @3.0.4 (#40022)
* cpat: new package @3.0.4

* Update package.py

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-09-18 11:37:21 -05:00
Manuela Kuhn
d5dd4b8b5d py-types-python-dateutil: add 2.8.19.14 (#40038) 2023-09-18 11:34:53 -05:00
Manuela Kuhn
0e47548cb6 py-types-requests: add 2.31.0.2 (#40039) 2023-09-18 11:34:01 -05:00
Manuela Kuhn
74974d85f6 py-types-setuptools: add 68.2.0.0 (#40040) 2023-09-18 11:33:01 -05:00
dependabot[bot]
7925bb575e build(deps): bump docker/login-action from 2.2.0 to 3.0.0 (#39966)
Bumps [docker/login-action](https://github.com/docker/login-action) from 2.2.0 to 3.0.0.
- [Release notes](https://github.com/docker/login-action/releases)
- [Commits](465a07811f...343f7c4344)

---
updated-dependencies:
- dependency-name: docker/login-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>
2023-09-18 18:23:37 +02:00
dependabot[bot]
976cb02f78 build(deps): bump docker/setup-qemu-action from 2.2.0 to 3.0.0 (#39968)
Bumps [docker/setup-qemu-action](https://github.com/docker/setup-qemu-action) from 2.2.0 to 3.0.0.
- [Release notes](https://github.com/docker/setup-qemu-action/releases)
- [Commits](2b82ce82d5...68827325e0)

---
updated-dependencies:
- dependency-name: docker/setup-qemu-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>
2023-09-18 18:22:58 +02:00
dependabot[bot]
f1bdc74789 build(deps): bump docker/build-push-action from 4.2.1 to 5.0.0 (#39969)
Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 4.2.1 to 5.0.0.
- [Release notes](https://github.com/docker/build-push-action/releases)
- [Commits](0a97817b6a...0565240e2d)

---
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>
2023-09-18 18:22:41 +02:00
Lydéric Debusschère
920347c21a py-werkzeug: Add version 0.12.2 required by py-graphene-tornado @2.6.1 (#39984) 2023-09-18 11:21:22 -05:00
Ben Cowan
c00ece6cf2 Enabled building GCC 13.1 on darwin/aarch64. (#38667) 2023-09-18 18:20:19 +02:00
Juan Miguel Carceller
7b0157c7e7 python: Don't prefer 3.10 (#40036) 2023-09-18 10:08:49 -06:00
Lydéric Debusschère
1b3a2ba06a [add] py-ldap3: new recipe, required by py-metomi-rose (#39982) 2023-09-18 11:06:23 -05:00
Manuela Kuhn
dc22a80f86 py-traits: add 6.4.2 (#39976) 2023-09-18 10:57:47 -05:00
Manuela Kuhn
27d6a75692 py-trove-classifiers: add 2023.8.7 (#39977) 2023-09-18 10:50:55 -05:00
George Young
70456ce4a7 py-rseqc: add 5.0.1 (#39953)
* py-rseqec: add 5.0.1

* Update package.py

* style ...

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-09-18 10:49:58 -05:00
Lydéric Debusschère
078369ec2b [chore] py-aniso8601: Add version 7.0.0 (#39808)
* [chore] py-aniso8601: Add version 3.0.2 required by py-graphene

* py-aniso8601: Add version 7.0.0 and constraints on python version

* py-aniso8601: fix style

* [fix] py-aniso8601: remove version 3.0.2 which depends on removed version of python; set the minimal version of python to 3.7

* py-aniso8601: remove version constraint on python
2023-09-18 10:46:30 -05:00
Diego Alvarez S
da8e022f6b Nextflow: add 22.04.3 (#40034) 2023-09-18 17:39:27 +02:00
George Young
c8a3f1a8ae chexmix: new package (#38441)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-09-18 17:36:44 +02:00
Michael Kuhn
be3f7b5da3 checksum: use FIXME instead of FIX ME when adding versions (#40050)
The former is highlighted by editors, while the latter is not.
2023-09-18 17:31:11 +02:00
Martin Aumüller
68d7ce3bb6 coin3d: apply upstream patches to fix build on Centos 8 (#39839)
fixes undefined references to dlerror, dlopen, dlsym, dlclose and
XDefaultScreenOfDisplay, XScreenNumberOfScreen, XCreatePixmap, XFree, XFreePixmap, XCloseDisplay, XOpenDisplay
2023-09-18 17:16:56 +02:00
Rémi Lacroix
7a490e95b6 Julia: Fix sha256 for some LLVM patches (#40041) 2023-09-18 10:52:00 +02:00
Joscha Legewie
088e4c6b64 grass: Update spec for gdal dependency (#38396) 2023-09-15 21:36:46 -05:00
Caetano Melone
76816d722a CI: add spec to job vars (#39905)
* CI: add details about built spec to ci job variables

Co-authored-by: Alec Scott <alec@bcs.sh>
Co-authored-by: Alec Scott <hi@alecbcs.com>
2023-09-15 14:40:00 -06:00
Scott Wittenburg
cbabdf283c gitlab ci: submit the correct audience for protected publish jobs (#40046) 2023-09-15 20:09:18 +00:00
John W. Parent
060bc01273 Windows RPATHing: fix symlink error (#39933)
With 349ba83, you cannot symlink() if the link already exists.
Update the simulated RPATHing logic on Windows to account for that.
2023-09-15 12:55:18 -07:00
Harmen Stoppels
0280ac51ed linux-headers: drop rsync dep, add new version (#39867) 2023-09-15 17:23:29 +02:00
David Gardner
bd442fea40 update sha256 after new tarball uploads (#40030) 2023-09-15 17:20:37 +02:00
Massimiliano Culpo
fb9e5fcc4f Group primitive url/path handling functions together (#40028) 2023-09-15 15:43:23 +02:00
Jack Morrison
bc02453f6d Sandia OpenSHMEM: Update to include version 1.5.2 (#40025) 2023-09-15 08:38:47 -04:00
dependabot[bot]
74a6c48d96 build(deps): bump sphinx from 7.2.5 to 7.2.6 in /lib/spack/docs (#40029)
Bumps [sphinx](https://github.com/sphinx-doc/sphinx) from 7.2.5 to 7.2.6.
- [Release notes](https://github.com/sphinx-doc/sphinx/releases)
- [Changelog](https://github.com/sphinx-doc/sphinx/blob/master/CHANGES.rst)
- [Commits](https://github.com/sphinx-doc/sphinx/compare/v7.2.5...v7.2.6)

---
updated-dependencies:
- dependency-name: sphinx
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-09-15 09:51:51 +02:00
Alex Richert
854f169ded Add shared and pic variants to libxml2 (#38094) 2023-09-14 19:57:52 -07:00
Adam Grofe
94c2043b28 Add Scine QCMaquis recipe to builtin packages (#39709)
* Add Scine QCMaquis recipe to builtin packages
* Format scine-qcmaquis recipe using black
* Remove import os from scine-qcmaquis recipe
* Reduce length of symmetries line in scine-qcmaquis
* Add myself as a maintainer of the scine-qcmaquis recipe
* Update Scine-QCMaquis recipe following the review
  PR URL: https://github.com/spack/spack/pull/39709
  Changes:
  - Updated Symmetries variant to us multi feature
  - Added dependency to boost+chrono since it was undocumented
  - Use define_from_variant to setup CMake args
  - Make version 3.1.2 be preferred since 3.1.3 build is broken
* Change build_tests boolean condition

---------

Co-authored-by: Adam Grofe <adamgrofe@microsoft.com>
2023-09-14 17:57:42 -04:00
Scott Wittenburg
579df768ca gitlab ci: Put Cray binaries in public mirrors (#39938) 2023-09-14 15:11:29 -06:00
George Young
e004db8f77 meme: add 5.5.4, correct dependencies (#40014)
* meme: add 5.5.4, correct dependencies
* variant renaming

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-09-14 13:52:40 -05:00
George Young
2d1cca2839 gffread: new package @0.12.7 (#40015)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-09-14 13:34:22 -04:00
Alex Richert
8dae369a69 Set # of ninja procs to 'make_jobs' for scipy (#293) (#38831) 2023-09-14 13:08:59 -04:00
Alex Richert
0d76436780 Add pic option & maintainer to lz4 (#38095)
Co-authored-by: Greg Becker <becker33@llnl.gov>
2023-09-14 09:50:11 -07:00
Massimiliano Culpo
34402beeb7 Ensure PythonExtension is consistent when finding externals (#40012)
PythonExtension is a base class for PythonPackage, and
is meant to be used for any package that is a Python
extension but is not built using "python_pip".

The "update_external_dependency" method in the base
class calls another method that is defined in the derived
class.

Push "get_external_python_for_prefix" up in the hierarchy
to make method calls consistent.
2023-09-14 18:26:40 +02:00
Dan LaManna
6a249944f5 Add OIDC tokens to gitlab-ci jobs (#39813)
* Add OIDC tokens to gitlab-ci jobs

This should allow us to start issuing just-in-time generated
credentials for CI jobs that need to modify binary mirrors. The "aud"
claim of the token describes what the token is allowed to do. The
claim is verified against a set of rules on the IAM role using signed
information from GitLab. See spack-infrastructure for the claim
verification logic.

---------

Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
2023-09-14 09:59:25 -06:00
Harmen Stoppels
6838ee6bb8 Add efficient deptype flag and spack.deptypes module (#39472)
This commit replaces the internal representation of deptypes with `int`, which is more compact
and faster to operate with.

Double loops like:
```
any(x in ys for x in xs)
```
are replaced by constant operations bool(xs & ys), where xs and ys are dependency types. 

Global constants are exposed for convenience in `spack.deptypes`
2023-09-14 12:25:24 +02:00
Massimiliano Culpo
d50f296d4f data-vis-sdk: make llvm~libomptarget the default (#40007)
Currently the configuration of the pipeline is such that
there are multiple "optimal" solutions. This is due to
the pipeline making ~lld the default for LLVM, but leaving
+libomptarget from package.py

Since LLVM recipe has a:

conflicts("~lld", "+libomptarget")

clingo is forced to change one of the two defaults, and
the penalty for doing so is the same for each. Hence, it
is random whether we'll get +libomptarget+lld
or ~libomptarget~lld.

This fixes it by changing also the default for libomptarget.
2023-09-14 09:19:47 +02:00
Alex Richert
e5d227e73d Support static case for find_libraries() in xz (#38100)
* Update xz

* add maintainer to xz

* [@spackbot] updating style on behalf of AlexanderRichert-NOAA
2023-09-13 22:34:11 -04:00
Alex Richert
af7b4c5a2f Add pic variant for libpng (#37964) 2023-09-13 20:43:10 -04:00
Alex Richert
75e9742d71 Allow git to compile against static curl (#37960) 2023-09-13 16:03:06 -07:00
Billae
e2f2559a5a add trompeloeil package (#39944)
* add trompeloeil package
* remove maintainer as he wish not to be
* fix style
2023-09-13 16:02:24 -07:00
Alex Richert
cac7f9774a Add static-only option for udunits (#38099)
* Add static-only option for udunits

* add maintainer to udunits
2023-09-13 15:58:55 -07:00
Alex Richert
6c4f8e62ae Add libs property/find_libraries to libiconv (#37962) 2023-09-13 15:52:30 -07:00
Alex Richert
cb03db3d69 Add pic and shared variants to GSL (#37961)
* Add pic and shared variants for gsl

* fix gsl variant logic

* make +pic default for gsl
2023-09-13 15:49:32 -07:00
Alex Richert
372bbb43a8 ip recipe updates (#39997) 2023-09-13 15:41:45 -07:00
Alex Richert
7b763faa1c Add develop version to g2tmpl (#39994)
* Add develop version to g2tmpl
* Update package.py
2023-09-13 15:39:42 -07:00
Alex Richert
4a79857b5e Add develop version for gfsio (#39995)
* Add develop version for gfsio
* Update package.py
2023-09-13 15:38:13 -07:00
Alex Richert
61df3b9080 Add develop version to landsfcutil (#39998) 2023-09-13 15:36:43 -07:00
Alex Richert
0b134aa711 Add two versions to ncio recipe (#39999) 2023-09-13 15:35:29 -07:00
Alex Richert
ea71477a9d Add develop version for nemsio (#40000) 2023-09-13 15:32:32 -07:00
Alex Richert
bc26848cee Add develop version to nemsiogfs (#40001) 2023-09-13 15:31:19 -07:00
Alex Richert
3e50ee70be Add develop version to sfcio (#40002)
* Add develop version to sfcio
* Update package.py
2023-09-13 15:30:14 -07:00
Alex Richert
0d8a20b05e Add develop version to sigio (#40003) 2023-09-13 15:28:48 -07:00
Alex Richert
74d63c2fd3 Add develop version to wrfio (#40004) 2023-09-13 15:17:42 -07:00
Alex Richert
a0622a2ee0 Add check() to sp recipe (#40005) 2023-09-13 15:14:07 -07:00
Alex Richert
a25a910ba0 Update upp recipe (#40006) 2023-09-13 15:10:05 -07:00
snehring
0e5ce57fd5 interproscan: adding new version and variant to include databases. (#40009) 2023-09-13 18:03:44 -04:00
Jordan Ogas
e86c07547d add charliecloud 0.34, deprecate previous (#40008) 2023-09-13 14:59:24 -07:00
Harmen Stoppels
d7b5a27d1d Revert "ASP-based solver: don't declare deprecated versions unless required (#38181)" (#40010)
This reverts commit babd29da50.
2023-09-13 23:33:55 +02:00
Laura Bellentani
eee8fdc438 scorep: Change in configuration option for nvhpc compiler (#39919)
* scorep version 8.1 added
* configure finds cudart and cupti in the nvhpcsdk suite
* style fixed
* changes to find libcuda.so in cuda directory

---------

Co-authored-by: Laura Bellentani <lbellen1@login01.leonardo.local>
2023-09-13 16:07:32 -04:00
Cameron Rutherford
5a91802807 hiop: Add version 1.0.0 (#39972) 2023-09-13 10:15:30 -07:00
Harmen Stoppels
7fd56da5b7 glibc: add older versions (#39978) 2023-09-13 10:06:42 -07:00
Adam J. Stewart
eefa5d6cb5 GDAL: add v3.7.2 (#39979) 2023-09-13 09:59:51 -07:00
AMD Toolchain Support
845973273a CP2K package: various AOCC compatibility fixes (#39773)
* cp2k: patch several old versions to help newer compilers
* cp2k: use -O2 optimization for AOCC compiler
* cp2k: do not support old AOCC compilers
* cp2k: simplify when clause due to conflicting out old compilers
* cp2k: give a more meaningful message for confilcts

Co-authored-by: Ning Li <ning.li@amd.com>
Co-authored-by: Phil Tooley <phil.tooley@amd.com>
2023-09-13 09:48:45 -07:00
Gurkirat Singh
0696497ffa Add cmake package for v2.1.0 and master (git) versions of libfirefly (#39778)
* libfirefly: Add cmake package for v2.1.0 and master (git) versions

* Separate git URL from version declaration

Co-authored-by: Alec Scott <alec@bcs.sh>
2023-09-13 09:17:33 -07:00
Massimiliano Culpo
babd29da50 ASP-based solver: don't declare deprecated versions unless required (#38181)
Currently, the concretizer emits facts for all versions known to Spack, including deprecated versions, and has a specific optimization objective to minimize their use.

This commit simplifies how deprecated versions are handled by considering possible versions for a spec only if they appear in a spec literal, or if the `config:deprecated:true` is set directly or through the `--deprecated` flag. The optimization objective has also been removed, in favor of just ordering versions and having deprecated ones last.

This results in:

a) no delayed errors on install, but concretization errors when deprecated versions would be the only option. This is in particular relevant for CI where it's better to get errors early
b) a slight concretization speed-up due to fewer facts
c) a simplification of the logic program.

Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
2023-09-13 18:15:57 +02:00
Massimiliano Culpo
c4e2d24ca9 Spec.tree: add type hints (#39948) 2023-09-13 11:53:14 +02:00
Harmen Stoppels
2c13361b09 gitlab ci: temporarily disable darwin aarch64 (#39974)
as there are no or few runners available
2023-09-13 11:11:33 +02:00
Harmen Stoppels
e8740b40da unifyfs: support openssl 3 (#39945)
* unifyfs: drop upperbound on deprecated openssl

The package uses deprecated MD5 functions from OpenSSL, which causes
warnings, but (a) Spack by default disables -Werror, and (b) those
functions will continue to exist in OpenSSL 3.

* unifyfs: enable parallel build, only make check sequential

* unifyfs: order class methods by install phases
2023-09-13 08:59:47 +02:00
Harmen Stoppels
e45fc994aa py-maestrowf: new version, fix artificial py-cryptography dep, support openssl 3 (#39946)
* py-maestrowf: add new version 1.1.9, deprecate development releases

* py-maestrowf: drop py-cryptography in 1.1.9

* py-maestrowf: drop py-cryptography dependency entirely, since it is not a direct dependency

* py-merlin: new version, ensure openssl 3 compat

* py-merlin: drop py-coloredlogs@10: lowerbound

* py-maestrowf: add py-rich, reorder deps

* py-celery: explain why upperbound is in spack but not in requirements.txt
2023-09-13 07:30:52 +02:00
Alex Richert
ed3f5fba1f Update g2c recipe: add develop version and misc. variants (#39965)
* Update g2c recipe: add develop version and misc. variants
* add testing to g2c
* Update package.py
2023-09-12 18:23:48 -04:00
Adam J. Stewart
d0e8a4d26f py-lightly: add v1.4.18 (#39960) 2023-09-12 16:53:41 -04:00
Massimiliano Culpo
60a5f70b80 Fix typo in metaclasses (#39947) 2023-09-12 22:53:21 +02:00
Scott Wittenburg
fa9acb6a98 ci: Tag reindex job to match the image architecture (#39958) 2023-09-12 16:33:56 -04:00
Johann Gaebler
621d42d0c7 r-piggyback: Add R package piggyback (#39932) 2023-09-12 12:53:47 -07:00
Johann Gaebler
cfdaee4725 r-pl94171: Add R package PL94171 (#39926) 2023-09-12 12:51:23 -07:00
Massimiliano Culpo
306ba86709 binutils: add v2.41 (#39483) 2023-09-12 21:15:45 +02:00
George Young
b47fd61f18 bam-readcount: add 1.0.1, correct build flags (#39950)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-09-12 11:26:30 -07:00
Tamara Dahlgren
c10ff27600 CI/Add superlu-dist to broken stand-alone tests due to hang (#38908)
* Add superlu-dist to broken stand-alone CI tests
* Revert "disable superlu test (#38894)"
  This reverts commit e16397b5d8.
2023-09-12 11:09:25 -07:00
Adam Moody
9056f31f11 mpifileutils: switch to main branch (#39525) 2023-09-12 10:57:29 -07:00
Dom Heinzeller
513232cdb3 libjpeg-turbo: Fix Darwin lib install name (#39834)
* Fix Darwin lib install name in var/spack/repos/builtin/packages/libjpeg-turbo/package.py

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

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

---------

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-09-12 10:49:30 -07:00
Dom Heinzeller
30893dd99a Filter spack compiler wrappers for h4cc in var/spack/repos/builtin/packages/hdf/package.py (#39870) 2023-09-12 10:41:04 -07:00
Alex Richert
b7c2411b50 g2 package bugfix (#39923)
* g2 package bugfix

* g2: fix w3emc dep

* fix setup_run_environment

* Update package.py

* Update package.py

* Update package.py

* Update package.py

* Update package.py

* style fix

* Update var/spack/repos/builtin/packages/g2/package.py

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>

* Update var/spack/repos/builtin/packages/g2/package.py

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>

---------

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-09-12 10:40:37 -07:00
Weiqun Zhang
002e833993 amrex: add v23.09 (#39788) 2023-09-12 10:39:56 -07:00
Martin Aumüller
02c9296db4 openexr: add 2.4.3, 2.5.9, 3.1.11 & 3.2.0 (#39863)
* openexr: add 2.4.3, 2.5.9, 3.1.11 & 3.2.0

- 2.5.9 is the latest version compatible with OpenScenGraph
- improved compatibility with GCC 13

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

* openexr: drop unsupported debug variant

--disable/enable-debug is not supported by ./configure in 1.3, 1.7, 2.0, 2.2 and 2.3

* openexr: transform into multi-build system package

simplifies package considerably, as nothing special seems to be required

* openexr: pkg-config is also used by @3

* openexr: use system libdeflate instead of internal

if no libdeflate is found, openexr would download and build its own starting with 3.2.0

* openexr: disable tests

would download lots of data during cmake and make build times noticably longer

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-09-12 10:37:48 -07:00
Vincent Michaud-Rioux
562065c427 Update PennyLane packages to v0.32. (#39688)
* Update PennyLane packages to v0.32.

* Reformat.

* Couple small fixes.

* Fix Lightning cmake_args.

* Couple dep fixes in py-pennylane + plugins.

* Fix scipy condition.

* Add comment on conflicting requirement.
2023-09-12 12:19:29 -05:00
Harmen Stoppels
9d00bcb286 openssl: deprecate 1.1.1 (#39942) 2023-09-12 12:45:51 +02:00
Harmen Stoppels
a009a1a62a asp.py: fix deprecation warning (#39943) 2023-09-12 09:27:03 +00:00
Mikael Simberg
f7692d5699 Add gperftools 2.13 (#39940) 2023-09-12 11:26:19 +02:00
George Young
12e1768fdb filtlong: add v0.2.1, patch for %gcc@13: (#39775)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-09-12 04:03:02 -04:00
dependabot[bot]
28a3be3eca build(deps): bump black from 23.7.0 to 23.9.1 in /lib/spack/docs (#39937)
Bumps [black](https://github.com/psf/black) from 23.7.0 to 23.9.1.
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](https://github.com/psf/black/compare/23.7.0...23.9.1)

---
updated-dependencies:
- dependency-name: black
  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>
2023-09-12 07:44:19 +02:00
Brian Van Essen
33500b5169 lbann: make two variants sticky (#39710)
* Make the state of the Python Front End (PFE) and Python data reader
support sticky so that the concretizer does not arbitrarily disable
them.

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-09-12 01:42:48 -04:00
Stephen Sachs
91011a8c5f [gromacs] Fix 2021.2 build error (#39722)
* [gromacs] Fix 2021.2 build error

See https://gromacs.bioexcel.eu/t/compilation-failure-for-gromacs-2021-1-and-2021-2-with-cmake-3-20-2/2129

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

Co-authored-by: Andrey Alekseenko <al42and@gmail.com>

---------

Co-authored-by: Andrey Alekseenko <al42and@gmail.com>
2023-09-11 19:49:18 -04:00
Caetano Melone
4570c9de5b fish: add 3.6.0, 3.6.1, update cmake requirement (#39899) 2023-09-11 19:34:33 -04:00
Adam J. Stewart
e7507dcd08 py-build: add v1 (#39930) 2023-09-11 19:04:32 -04:00
Dom Heinzeller
4711758593 Add awscli@1.29.41 and its dependency py-botocore@1.31.41 (#39878)
* Add awscli@1.29.41 and its dependency py-botocore@1.31.41

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

Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>

---------

Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
2023-09-11 18:02:46 -04:00
Sinan
b55e9e8248 package_qscintilla_build_with_qt6 (#39544)
* package_qscintilla_build_with_qt6

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

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

* improve

* fix Qsci.abi3.so install

* simplify, fix, tidy

* fix style

* fix style

* fix style

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

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

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

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

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

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

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

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

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

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

* improve

* improve style

* fix style

* make black happy

* add ver 2.14.1

* update

* make black happy

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

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

* improve

---------

Co-authored-by: Sinan81 <Sinan@world>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-09-11 16:58:28 -05:00
Adam J. Stewart
2e62cfea3e py-black: add v23.9 (#39931) 2023-09-11 16:36:16 -05:00
Manuela Kuhn
286e1147d6 py-tifffile: add 2023.8.30 (#39918) 2023-09-11 16:34:20 -05:00
Manuela Kuhn
7e3d228d19 py-tinycss2: add 1.2.1 (#39921) 2023-09-11 16:32:42 -05:00
Manuela Kuhn
a1ab42c8c0 py-tomlkit: add 0.12.1 (#39922) 2023-09-11 16:31:55 -05:00
Rocco Meli
57a2f2ddde tidynamics: add v1.1.2 (#39911)
* ensure umpire~cuda~rocm when ~cuda~rocm

* update tydynamics
2023-09-11 16:17:17 -05:00
Mike Renfro
b7b7b2fac4 correct py-bx-python@0.8.8 python dependency (#39766)
* correct python dependency for 0.8.8

* add missing zlib dependency

* restore missing whitespace

* correct versions for 0.9.0, clarify rules for future releases

* Update package.py

* Remove whitespace for black check
2023-09-11 16:16:28 -05:00
Tim Haines
5ac1167250 fpchecker: add version 0.4.0 (#39924) 2023-09-11 17:16:20 -04:00
Richard Berger
fcc4185132 cuda: add versions 12.2.0 and 12.2.1 (#39684) 2023-09-11 23:13:06 +02:00
sid
943c8091c2 py-fairscale and dependencies py-pgzip libgit2 py-pygit2 (#39220)
* simple build of py-openai

* added variants to py-openai

* py-pandas-stubs is a dependency for py-openai

* fixed format and flake8 errors for py-openai

* black format error for py-pandas-stubs

* [@spackbot] updating style on behalf of sidpbury

* made style and format changes to py-openai

* made style and format changes to py-pandas-stubs

* py-types-pytz is a dependency for py-openai

* [@spackbot] updating style on behalf of sidpbury

* updated py-openpyxl for ver 3.0.7 and 3.1.2

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

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

* ajs requested changes for py-openai

* updated py-openpyxl for supported python

* [@spackbot] updating style on behalf of sidpbury

* updated py-openpyxl

* removed requirement.txt dependencies in  py-openpyxl

* removed python depends on from openpyxl

* updated package to support newer versions

* updated version of py-pygit2

* py-fairscale is a new package in support of torch

* py-pgzip is a dependency for py-fairscale

* switch fairscale pypi, added extra variant for convenience

* removed python dependency

* changed multiple requirement versions

* changes for upstream py-fairscale

* changes for upsteam py-pygit2

* Update package.py

* Update package.py

* sorted out some of the dependency versions

* removed version 1.12.2 because dependency could not be met

* updated py-cached-property dependency

* suggested changes from adamjstewart

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-09-11 16:11:02 -05:00
Nils Vu
a7a6f2aaef spectre: add v2023.08.18 and v2023.09.07 (#39925) 2023-09-11 17:10:28 -04:00
Rocco Meli
5aaa82fb69 Update MDAnalysis (#39787)
* ensure umpire~cuda~rocm when ~cuda~rocm

* update mdanalysis

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

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

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-09-11 16:06:20 -05:00
Simon Pintarelli
bc33d5f421 update q-e-sirius package (#39744) 2023-09-11 22:48:19 +02:00
Juan Miguel Carceller
0e4e232ad1 Add another url for whizard (#37354)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-09-11 22:45:21 +02:00
Scot Halverson
145d44cd97 gdrcopy: inherit from CudaPackage, update dependencies (#39596) 2023-09-11 22:36:20 +02:00
Fábio de Andrade Barboza
e797a89fe1 py-pipdeptree: add new package; py-hatchling: add 1.18.0 (#39697)
* py-hatchling: add 1.18.0

* py-pipdeptree: add new package

* py-hatchling: add Python 3.8 dependency

* Apply suggestion from code review

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

---------

Co-authored-by: Fábio de Andrade Barboza <f168817@dac.unicamp.br>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-09-11 15:14:33 -05:00
Jose E. Roman
254a2bc3ea SLEPc: add v3.19.2 (#39805)
Co-authored-by: Satish Balay <balay@mcs.anl.gov>
2023-09-11 22:13:21 +02:00
Fábio de Andrade Barboza
873652a33e py-enum-tools: add new package and dependencies (#39672)
* Adds package 'enum-tools'

* Fixes syntax

* py-enum-tools: update pypi link and dependencies

* py-whey: add new package

* py-consolekit: add new package

* py-shippinglabel: add new package

* py-project-parser: add new package

* py-handy-archives: add new package

* py-domdf-python-tools: add new package

* py-dom-toml: add new package

* py-dist-meta: add new package

* py-deprecation-alias: add new package

* py-pygments: add versions 2.16.0 and 2.16.1

* py-mistletoe: add new package

* py-apeye: add new package

* py-apeye-core: add new package

* Fix dependencies' names and remove redundancies

* Fix style

* py-enum-tools: fix dependencies

* py-mistletoe: update dependencies

* Apply suggestions from code review

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

* py-whey: fix dependencies

* py-whey: fix style

* py-apeye: fix dependencies

---------

Co-authored-by: Fábio de Andrade Barboza <f168817@dac.unicamp.br>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-09-11 15:12:46 -05:00
Travis
3f686734ab dakota: add v6.18 (#39882)
Co-authored-by: Travis Drayna <tdrayna@loki.local>
2023-09-11 22:06:16 +02:00
Thomas Madlener
e1373d5408 dd4hep: make sure to find libraries correctly (#39516) 2023-09-11 16:04:42 -04:00
dslarm
a2054564d8 ctffind: extend a Power 9 patch to AArch64 (#39137) 2023-09-11 16:04:20 -04:00
Sébastien Valat
ea75dbf7bd MALT: add v1.2.2 (#39890) 2023-09-11 21:57:36 +02:00
Sébastien Valat
63a67e525b NUMAPROF: add v1.1.5 (#39891) 2023-09-11 21:57:04 +02:00
Manuela Kuhn
95aaaeb5af py-dunamai: add 1.18.0 (#39849) 2023-09-11 14:56:34 -05:00
Harmen Stoppels
a0bd53148b glibc: fix deps, drop pre 2.17 (#39806)
* glibc: add missing deps, drop < 2.17

Building glibc 2.17 requires linking libgcc_{s,eh}.a, which themselves
depend on whatever glibc the current gcc uses for its runtime libraries.

Newer gcc depends on gnu extensions of libdl it seems, so that means you
simply cannot build old glibc with gcc-using-new-glibc.

The relevant fix in glibc is this commit:

commit 95f5a9a866695da4e038aa4e6ccbbfd5d9cf63b7
Author: Joseph Myers <joseph@codesourcery.com>
Date:   Tue Jul 3 19:14:59 2012 +0000

    Avoid use of libgcc_s and libgcc_eh when building glibc.

See also references to that commit in the glibc mailing list.

* update the gmake bound

* add --without-selinux
2023-09-11 10:45:53 -07:00
Massimiliano Culpo
3302b176fd Update archspec to latest commit (#39920)
- [x] Intel flags for old architectures
- [x] Support for Sapphire Rapids
- [x] Cache the "ancestors" computation
2023-09-11 10:03:35 -07:00
Taillefumier Mathieu
4672346d9c Support of versions of cp2k below 7 marked as deprecated (#39652)
SIRIUS was introduced in version 7 of cp2k but could be used
in practice in version 9 (input format and functionalities).
SIRIUS with version 6 and below are marked as a dependency
conflict until CP2K version 9.

Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
2023-09-11 18:46:52 +02:00
Tom Payerle
4182e97761 elpa: Add --enable-scalapack-tests to configure when +autotune (#39728)
When building elpa +autotune, we apparently need to add
the configure option --enable-scalapack-tests
2023-09-11 18:37:56 +02:00
Seth R. Johnson
5598de88ff celeritas: add v0.3.2 (#39879) 2023-09-11 12:18:48 -04:00
Simon Pintarelli
d88ecf0af0 sirius: fix cuda_arch flags (#39889) 2023-09-11 12:13:49 -04:00
Scott Wittenburg
516f0461b8 gitlab ci: Use image with awscli for rebuild-index job (#39636)
Instead of pointing to the image on DockerHub, which rate limits us and
causes pipeline failures durying busy times, use the version at ghcr.

And we might as well use the ghcr version everywhere else too.
2023-09-11 18:03:11 +02:00
Alex Richert
b8cf7c3835 w3emc: add develop version and more variants (#39884)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-09-11 18:02:50 +02:00
Annop Wongwathanarat
707684a7b7 acfl: map rocky9 to RHEL-9 (#39892) 2023-09-11 11:58:45 -04:00
Alex Richert
739aebbd18 sp: add develop version, build precision, and OpenMP support (#39874)
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-09-11 17:41:32 +02:00
Tao Lin
71c053c391 Garfield++: Add the patch to fix the missing headers and Set the environment variable HEED_DATABASE (#39904) 2023-09-11 11:13:22 -04:00
Thomas Gruber
9a0a4eceaf likwid: search library path for compilation with hwloc (#39659) 2023-09-11 11:03:21 -04:00
kjrstory
19f8e9147d openfoam-org: zoltan renumbering and decompsition (#39915) 2023-09-11 16:42:50 +02:00
George Young
e99750fd3c transdecoder: add 5.7.1 (#39916)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-09-11 16:37:36 +02:00
George Young
33cde87775 gffcompare: new package @0.12.6 (#39917)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-09-11 16:13:49 +02:00
Annop Wongwathanarat
e63597bf79 wrf: fix patches for 4.2 to 4.4.2 for aarch64 config (#39900) 2023-09-11 16:02:21 +02:00
Robert Cohn
2f63342677 intel-oneapi-mkl: hpcx-mpi support (#39750) 2023-09-11 15:47:52 +02:00
Freifrau von Bleifrei
04eae7316f DisCoTec: add new package (#35239)
Co-authored-by: Alexander Van Craen <40516079+vancraar@users.noreply.github.com>
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-09-11 04:18:00 -04:00
Adam Fidel
67d6c086d8 singularity: fix package name in comment (#39822) 2023-09-10 12:33:10 -04:00
Mark (he/his) C. Miller
69370c9c8f Update package H5Z-ZFP to 1.1.1 (#39740)
* update to 1.1.1

* add maintainers

* add 1.1.0; set default
2023-09-10 09:27:24 -07:00
Rocco Meli
9948785220 spglib: add v2.1.0 (#39910)
* ensure umpire~cuda~rocm when ~cuda~rocm

* update spglib
2023-09-10 08:48:13 -07:00
dependabot[bot]
4047e025e0 build(deps): bump docker/build-push-action from 4.1.1 to 4.2.1 (#39901)
Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 4.1.1 to 4.2.1.
- [Release notes](https://github.com/docker/build-push-action/releases)
- [Commits](2eb1c1961a...0a97817b6a)

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

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-09-10 09:52:15 +02:00
dependabot[bot]
783bbdf2db build(deps): bump actions/upload-artifact from 3.1.2 to 3.1.3 (#39852)
Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 3.1.2 to 3.1.3.
- [Release notes](https://github.com/actions/upload-artifact/releases)
- [Commits](0b7f8abb15...a8a3f3ad30)

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

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-09-08 22:58:55 +02:00
Thomas Madlener
a65f13f79f root: add latest available tag (#39895) 2023-09-08 14:48:54 -04:00
John W. Parent
fc391d5332 NMake Builder: change property name (#39824)
NMake makefiles are still called makefiles. The corresponding builder
variable was called "nmakefile", which is a bit unintuitive and lead
to a few easy-to-make, hard-to-notice mistakes when creating packages.
This commit renames the builder property to be "makefile"
2023-09-08 11:23:13 -07:00
eugeneswalker
e05f12f18e veloc: add v1.7 (#39465)
* updates for VELOC 1.6

* veloc: add v1.7

---------

Co-authored-by: Bogdan Nicolae <bogdan.nicolae@acm.org>
2023-09-08 12:57:14 -05:00
John W. Parent
14f248652c Spack on Windows: fix shell scripts when root contains a space (#39875)
Enclose variable tracking root in quotes.
2023-09-08 13:49:16 -04:00
AMD Toolchain Support
87f99de3fb Cloverleaf-ref: proposal for a -ref version only (#39894)
* Cloverleaf-ref: proposal for a -ref version only
* Cloverleaf-ref: fixing typo.

---------

Co-authored-by: fpanichi <fpanichi@amd.com>
2023-09-08 10:47:00 -07:00
Dan Lipsa
9e7fe04a77 Windows decompression: fix removal of intermediate file (#38958)
Extensionless archives requiring two-stage decompression and extraction
require intermediate archives to be renamed after decompression/extraction
to prevent collision. Prior behavior attempted to cleanup the intermediate
archive with the original name, this PR ensures the renamed folder is
cleaned instead.

Co-authored-by: Dan Lipsa <dan.lipsa@khq.kitware.com>
Co-authored-by: John Parent <john.parent@kitware.com>
2023-09-08 10:27:43 -07:00
Todd Gamblin
45d149c7d3 bugfix: only complete aliases for potential aliases (#39887)
Smart alias completion introduced in #39499 wasn't as smart as it needed to be, and
would complete any invalid command prefix and some env names with alias names.

- [x] don't complete aliases if there are no potential completions
      e.g., don't convert `spack isnotacommand` -> `spack concretize`

- [x] don't complete with an aliases if we're not looking at a top-level subcommand.
2023-09-08 12:51:26 +02:00
Anton Kozhevnikov
8250a085b0 BUILD_TESTING is a CMake variable and should not be scoped (#39866) 2023-09-08 10:14:06 +02:00
Massimiliano Culpo
39b9f214a8 Speed-up spack external find execution (#39843)
* Perform external spec detection with multiple workers

The logic to perform external spec detection has been refactored
into classes. These classes use the GoF "template" pattern to account
for the small differences between searching for "executables" and
for "libraries", while unifying the larger part of the algorithm.

A ProcessPoolExecutor is used to parallelize the work.

* Speed-up external find by tagging detectable packages automatically

Querying packages by tag is much faster than inspecting the repository,
since tags are cached. This commit adds a "detectable" tag to every
package that implements the detection protocol, and external detection
uses it to search for packages.

* Pass package names instead of package classes to workers

The slowest part of the search is importing the Python modules
associated with candidate packages. The import is done serially
before we distribute the work to the pool of executors.

This commit pushes the import of the Python module to the job
performed by the workers, and passes just the name of the packages
to the executors.

In this way imports can be done in parallel.

* Rework unit-tests for Windows

Some unit tests were doing a full e2e run of a command
just to check a input handling. Make the test more
focused by just stressing a specific function.

Mark as xfailed 2 tests on Windows, that will be fixed
by a PR in the queue. The tests are failing because we
monkeypatch internals in the parent process, but the
monkeypatching is not done in the "spawned" child
process.
2023-09-08 09:25:50 +02:00
Massimiliano Culpo
7631b5ea14 crosstool-ng: add new package (#39865) 2023-09-08 08:16:39 +02:00
dependabot[bot]
a4d2f8332f build(deps): bump pytest from 7.4.1 to 7.4.2 in /lib/spack/docs (#39883)
Bumps [pytest](https://github.com/pytest-dev/pytest) from 7.4.1 to 7.4.2.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/7.4.1...7.4.2)

---
updated-dependencies:
- dependency-name: pytest
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-09-08 08:16:19 +02:00
Tamara Dahlgren
007f02e06a Docs/Packaging guide: Add BundlePackage (#39691)
* Docs/Packaging guide: Add BundlePackage
* Adjusted version ordering note to reflect convention.
2023-09-07 19:45:51 -07:00
kwryankrattiger
8ec1657136 CI Timing Statistics (#38598)
* Write timing information for installs from cache

* CI: aggregate and upload install_times.json to artifacts

* CI: Don't change root directory for artifact generation

* Flat event based timer variation

Event based timer allows for easily starting and stopping timers without
wiping sub-timer data. It also requires less branching logic when
tracking time.

The json output is non-hierarchical in this version and hierarchy is
less rigidly enforced between starting and stopping.

* Add and write timers for top level install

* Update completion

* remove unused subtimer api

* Fix unit tests

* Suppress timing summary option

* Save timers summaries to user_data artifacts

* Remove completion from fish

* Move spack python to script section

* Write timer correctly for non-cache installs

* Re-add hash to timer file

* Fish completion updates

* Fix null timer yield value

* fix type hints

* Remove timer-summary-file option

* Add "." in front of non-package timer name

---------

Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
2023-09-07 15:41:31 -05:00
eflumerf
c5fc794d77 epics-base package: use the Spack compiler wrappers (#39752)
Edit configuration file to use the Spack compiler wrappers.
2023-09-07 16:28:57 -04:00
Sam Reeve
5c409f794a Make Cabana a Cuda/ROCm package (matching ArborX) (#39809) 2023-09-07 13:36:09 -06:00
Rocco Meli
06b30842e4 Allow to build latest released version of CP2K with CMake (#39782)
* allow to build latest version of cp2k with cmake
* apply black
2023-09-07 12:11:30 -07:00
Niclas Jansson
ebbe63013d neko: add v0.6.1 and fix package (#39751)
* neko: add v0.6.1 and fix package
* Change to a conditional variant for gslib
2023-09-07 11:30:52 -07:00
David Gardner
3f7f10ca2b add SUNDIALS v6.6.1 (#39853) 2023-09-07 11:20:54 -07:00
Vanessasaurus
6a5a074150 Automated deployment to update package flux-core 2023-09-07 (#39856)
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2023-09-07 11:18:55 -07:00
Vanessasaurus
c046c61cff Automated deployment to update package flux-security 2023-09-07 (#39855)
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2023-09-07 11:17:56 -07:00
Harmen Stoppels
7bd95f6ad3 move determine_number_of_jobs into spack.util.cpus, use it in concretize (#37620) 2023-09-07 13:16:51 +02:00
Martin Aumüller
4429e17db0 lua: unzip also required during build (#39802)
Unzip required during build otherwise configuration of luarocks fails during installation of lua@5.3.6 on ubuntu 22.04 w/o system unzip.
2023-09-07 01:48:14 -04:00
Johann Gaebler
65dd6e1196 r-furrr: Add furrr R package. (#39814)
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-09-07 01:08:27 -04:00
Johann Gaebler
a43da48d23 r-functional: Add the functional R package. (#39826)
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-09-07 01:03:45 -04:00
Matheus Henrique
f9c06669ca Add Figcone Package (#39804)
* Add Figcone Package
* Fix the style
* add url
* fix style removing whitespace of a blanck line
* remove versions
2023-09-07 01:03:31 -04:00
Geoffrey Lentner
11c6431c9a duckdb: add v0.8.1 (#39851) 2023-09-07 00:58:50 -04:00
Johann Gaebler
1e85a1b227 r-tinytiger: Add tinytiger R package. (#39828)
* r-tinytiger: Add tinytiger R package.
* Fix homepage.

---------

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-09-07 00:58:36 -04:00
Rémi Lacroix
b81aa42179 CUDA 10.1/10.2: Fix conflicts with PGI 19+. (#39747)
The condition probably did not get updated when the behavior of the version specifier changed.
2023-09-07 00:58:19 -04:00
Tom Payerle
c59f68a33d seacas: Set TPL_ENABLE_Pthread=ON when +thread_safe (#39703)
* seacas: Set TPL_ENABLE_Pthread=ON when +thread_safe
  This should fix #39702
  Basically, following suggestion of error message and setting
  TPL_ENABLE_Pthread to the value of the boolean spack variant thread_safe
* seacas: Fix style issue
  Add space after comment #
2023-09-06 16:20:04 -07:00
Tom Payerle
743a93902d cgns: Add -fPIC to Fortan/C compilation flags (#39700)
* cgns: Add -fPIC to Fortan/C compilation flags
  This should fix #39699
* cgns: Add -fPIC compilation flags when +fortran
  Incorporating suggestions of @aumuell with addition of making +pic required when +fortran
2023-09-06 16:18:07 -07:00
Paul Kuberry
5bc5139552 xyce: add version 7.7.0 and specialize patch (#39696) 2023-09-06 16:14:27 -07:00
Brian Vanderwende
3be450c16f Use correct hash for 3.0 (#39743) 2023-09-06 16:12:14 -07:00
Rémi Lacroix
c733fe9c34 Eigen: Fix patch URL (#39746) 2023-09-06 16:05:20 -07:00
Johann Gaebler
e2edb45d2c Add libpostal Package (#39758)
* Add libpostal.
* Add back Spack license.
2023-09-06 15:19:14 -07:00
Johann Gaebler
b2a95fb4b7 r-sets: Add R sets package (#39760)
* r-sets: Add r-sets.
* r-sets: Fix R dependency for first version.
* r-sets: Remove package versions for which a compatible version of R cannot be installed.
2023-09-06 15:07:37 -07:00
Johann Gaebler
7bf7a266ba r-humaniformat: Add R humaniformat package (#39761)
* r-humaniformat: Add r-humaniformat.
* r-humaniformat: Remove blank line at end of file.
* Fix broken link in description.
2023-09-06 15:01:38 -07:00
Josh Bowden
2341074694 new damaris package updated to use Daamris v.1.9.0 and including py-mpi4py dependency when +python specified (#39774) 2023-09-06 14:53:22 -07:00
Simon Pintarelli
1c0dbab821 sirius: simplify hip architectures, fix umpire dependency (#39776) 2023-09-06 14:46:38 -07:00
kjrstory
865c8b606c openfoam-org: add variant scotch (#39841) 2023-09-06 13:47:04 -07:00
Harmen Stoppels
c98afbc44c musl: bump (#39838) 2023-09-06 13:43:49 -07:00
Patrick Broderick
57cd822fb7 FFTX: replace extends with variants (#39701)
The spiral-software package had a number of extensions, but does not
work unless they actually exist in the spiral software prefix (creating
a view is not sufficient). With the removal of "spack activate"
(different from "spack env activate"), a new approach is needed to
support optional components of `spiral-software` . This commit updates
the spiral-software package to copy the dependency installations into
its own prefix.

This commit also adds versions for `fftx` and `spiral-software`, as
well as an optional `spiral-software-jit` package.
2023-09-06 16:35:33 -04:00
SXS Bot
627c2d3bf6 spectre: add v2023.07.29 (#39145)
Co-authored-by: sxs-bot <sxs-bot@users.noreply.github.com>
2023-09-06 13:09:49 -07:00
Dominic Hofer
3b1b261cd8 Handles case of empty craype_dir (#39371)
The craype_dir folder can be empty. It happens to be the case on Arolla and Tsa at CSCS.
2023-09-06 11:54:42 -07:00
John W. Parent
40c4c81c19 "spack config add": support values with ":" (#39831)
This is a fixed version of b72a268

* That commit would discard the final key component (so if you set
  "config:install_tree:root", it would discard "root" and just set
  install tree).
* When setting key:"value", with the quotes, that commit would
  discard the quotes, which would confuse the system if adding a
  value like "{example}" (the "{" character indicates a dictionary).
  This commit retains the quotes.
2023-09-06 18:44:00 +00:00
Jack Morrison
642451e047 libfabric: Add versions 1.18.2, 1.19.0 (#39757) 2023-09-06 13:38:28 -04:00
Auriane R
6630ddb47d Add pika 0.18.0 (#39842) 2023-09-06 19:21:05 +02:00
Sam Reeve
7fd7d0b9fd exaca: add version 1.2 (#39810) 2023-09-06 12:58:13 -04:00
Edward Hartnett
f7d71ec792 g2: add dependencies, build options, and v3.4.6 release (#39717)
* adding bacio to g2 dependencies
* edited documentation
* added version 3.4.6
* starting with 3.4.6, can use any version of jasper
* adding w3emc dependency for versions up to 3.4.5
* removed t-brown as maintainer at his request
2023-09-06 02:46:26 -07:00
Harmen Stoppels
d80bc70481 gitlab: set cache and config dir in top-level file (#39829) 2023-09-06 08:16:35 +02:00
Matheus Henrique
81cfe39ae3 Add cmdlime package (#39835)
* Add cmdlime package
* remove the blank line at the end of file
2023-09-06 00:38:03 -04:00
Sam Reeve
ed058fd212 cabana: fix gtest dependency (#39811) 2023-09-05 22:13:42 -06:00
leonardo araujo
1da12490fa new package: Yade (#39786)
* feat: yade package
* fix: dependencies for Yade
* feat: yade versions
* fix: cmake_args and version_url
* fix: Spack license identifier
* fix: black formatter
* fix: black would be reformatted? yes!
* feat: add maintainer

---------

Co-authored-by: leo magdanello <araujo.leonardo@luizalabs.com>
2023-09-05 17:47:46 -07:00
Adam J. Stewart
8b5b4ade0e CMakePackage: remove -DBUILD_TESTING flag (#37967) 2023-09-05 18:29:34 -05:00
Mikael Simberg
12bc4cf093 umpire: Add 2022.10.0 (#37998)
* Add umpire 2022.10.0
* Add patches to umpire@2022.10.0
* Add axom 0.8.0 and 0.8.1
* Remove Umpire 2023.06.0
2023-09-05 11:54:05 -07:00
Harmen Stoppels
f8676db7f4 Revert ""spack config add": allow values with a ":" (#39279)" (#39825)
This reverts commit b72a268bc5.
2023-09-05 20:07:16 +02:00
Wouter Deconinck
dd747c5c48 xerces-c: support variant cxxstd=20 (#39784) 2023-09-05 17:44:48 +02:00
Wouter Deconinck
cf031e83f0 compilers/gcc.py: support cxx{20,23}_flag (#39777) 2023-09-05 17:09:22 +02:00
Juan Miguel Carceller
f709518916 podio, edm4hep and lcio: add lib and lib64 to LD_LIBRARY_PATH (#37881)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-09-05 17:00:16 +02:00
Wouter Deconinck
aa9eb33108 boost: support variant cxxstd=20 (#39769) 2023-09-05 14:45:12 +02:00
Massimiliano Culpo
818c9aeb5a Add type-hints to the spack.detection package (#39803) 2023-09-05 14:19:57 +02:00
Mikael Simberg
cfdf19ed6b hpx-kokkos: add 0.4.0 and other minor changes (#39723)
* Add hpx-kokkos 0.4.0

* Make git global package property in hpx-kokkos instead of having it version-specific

* Add variant for choosing future type in hpx-kokkos

* Add support for testing hpx-kokkos
2023-09-05 13:41:06 +02:00
pabloaledo
566754440f Add maintainers to some bioconductor packages (#39801)
Signed-off-by: Pablo <pablo.aledo@seqera.io>
2023-09-05 13:29:55 +02:00
Wouter Deconinck
f0658243c0 clhep: support variant cxxstd=20 (#39768) 2023-09-05 12:06:50 +02:00
dependabot[bot]
06b6b05dbd build(deps): bump actions/checkout from 3.6.0 to 4.0.0 (#39789)
Bumps [actions/checkout](https://github.com/actions/checkout) from 3.6.0 to 4.0.0.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](f43a0e5ff2...3df4ab11eb)

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

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2023-09-05 09:52:14 +02:00
dependabot[bot]
189cd59d13 build(deps): bump pytest from 7.4.0 to 7.4.1 in /lib/spack/docs (#39790)
Bumps [pytest](https://github.com/pytest-dev/pytest) from 7.4.0 to 7.4.1.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/7.4.0...7.4.1)

---
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- dependency-name: pytest
  dependency-type: direct:production
  update-type: version-update:semver-patch
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2023-09-05 09:51:41 +02:00
Harmen Stoppels
5a43f4ba55 Set backtrace in ci (#39737) 2023-09-05 09:44:14 +02:00
Harmen Stoppels
29aa7117f4 glibc: add package (#39695) 2023-09-04 07:55:57 +02:00
Jen Herting
d367b4285a py-dataclasses-json: add new package (#39493)
* [py-dataclasses-json] New package

* [py-dataclasses-json] limiting py-poetry-core versions
2023-09-02 16:27:47 -05:00
Jen Herting
260e735425 [py-preshed] added version 3.0.8 (#38969)
* [py-preshed] added version 3.0.8

* [py-preshed] reordered for consistancy
2023-09-02 16:25:41 -05:00
John W. Parent
ca872f9c34 Windows: fix pwsh env activate/deactivate; load/unload (#39118)
These commands are currently broken on powershell (Windows) due to
improper use of the InvokeCommand commandlet and a lack of direct
support for the `--pwsh` argument in `spack load`, `spack unload`,
and `spack env deactivate`.
2023-09-01 11:36:27 -07:00
John W. Parent
b72a268bc5 "spack config add": allow values with a ":" (#39279)
If you wanted to set a configuration option like
`config:install_tree:root` to "C:/path/to/config.yaml", Spack  had
trouble parsing this because of the ":" in the value. This adds
logic to allow using quotes to enclose the value, so you can add
`config:install_tree:root:"C:/path/to/config.yaml"`.

Configuration keys should never contain a quote character, so the
presence of any quote is taken to mean that the rest of the string
is specifying the value.
2023-09-01 11:05:02 -07:00
Adam J. Stewart
818195a3bd py-pandas: add v2.1.0 (#39707) 2023-08-31 11:08:44 -05:00
Anton Kozhevnikov
679d41ea66 [NVHPC] add a possibility to control default CUDA version (#38909)
* add a possibility to control default cuda version

* fix stype

* style fix

* resolve comment

* resolve comment

* Fix style in nvhpc package.py

---------

Co-authored-by: antonk <antonk@cscs.ch>
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
2023-08-31 16:16:31 +02:00
Massimiliano Culpo
86216cc36e environment: improve spack remove matching (#39390)
search for equivalent specs, not for equal strings when selecting a spec to remove.
2023-08-31 09:28:52 +00:00
dependabot[bot]
ecb7ad493f build(deps): bump sphinx from 7.2.4 to 7.2.5 in /lib/spack/docs (#39716)
Bumps [sphinx](https://github.com/sphinx-doc/sphinx) from 7.2.4 to 7.2.5.
- [Release notes](https://github.com/sphinx-doc/sphinx/releases)
- [Changelog](https://github.com/sphinx-doc/sphinx/blob/master/CHANGES)
- [Commits](https://github.com/sphinx-doc/sphinx/compare/v7.2.4...v7.2.5)

---
updated-dependencies:
- dependency-name: sphinx
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-08-31 10:40:33 +02:00
Harmen Stoppels
fb1e81657c Remove a few local imports in tests (#39719) 2023-08-31 10:40:02 +02:00
Raffaele Solcà
34e4c62e8c dla-future: add v0.2.0 (#39705) 2023-08-31 10:39:22 +02:00
Harmen Stoppels
acb02326aa ASP-based solver: add hidden mode to ignore versions that are moving targets, use that in CI (#39611)
Setting the undocumented variable SPACK_CONCRETIZER_REQUIRE_CHECKSUM
now causes the solver to avoid accounting for versions that are not checksummed.

This feature is used in CI to avoid spurious concretization against e.g. develop branches.
2023-08-31 08:09:37 +00:00
Pat McCormick
c1756257c2 llvm: fix for Flang variant due to exception handling (#36171)
* The flang project does not support exceptions enabled in the core llvm
library (and developer guidelines explicitly state they should not be
used).  For this reason, when the flang variant is selected,
LLVM_ENABLE_EH needs to be disabled.  In the current main branch of
llvm (and thus future releases), enabling flang and setting
LLVM_ENABLE_EH will cause the overall build to fail.

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

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

* fix syntax

---------

Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
Co-authored-by: Satish Balay <balay@mcs.anl.gov>
2023-08-30 23:22:33 -05:00
John W. Parent
1ee7c735ec Windows: oneapi/msvc consistency (#39180)
Currently, OneAPI's setvars scripts effectively disregard any arguments
we're passing to the MSVC vcvars env setup script, and additionally,
completely ignore the requested version of OneAPI, defaulting to whatever
the latest installed on the system is.

This leads to a scenario where we have improperly constructed Windows
native development environments, with potentially multiple versions of
MSVC and OneAPI being loaded or called in the same env. Obviously this is
far from ideal and leads to some fairly inscrutable errors such as
overlapping header files between MSVC and OneAPI and a different version
of OneAPI being called than the env was setup for.

This PR solves this issue by creating a structured invocation of each
relevant script in an order that ensures the correct values are set in
the resultant build env.

The order needs to be:

1. MSVC vcvarsall
2. The compiler specific env.bat script for the relevant version of
   the oneapi compiler we're looking for. The root setvars scripts seems
   to respect this as well, although it is less explicit
3. The root oneapi setvars script, which sets up everything else the
   oneapi env needs and seems to respect previous env invocations.
2023-08-30 23:19:38 +00:00
Adam J. Stewart
22deed708e py-llvmlite: add Python version requirements (#39711) 2023-08-30 16:15:44 -07:00
Todd Gamblin
6693dc5eb8 completion: make bash completion work in zsh
`compgen -W` does not behave the same way in zsh as it does in bash; it seems not to
actually generate the completions we want.

- [x] add a zsh equivalent and `_compgen_w` to abstract it away
- [x] use `_compgen_w` instead of `compgen -W`
2023-08-30 12:42:31 -07:00
Todd Gamblin
396f219011 completion: add alias handling
Bash completion is now smarter about handling aliases. In particular, if all completions
for some input command are aliased to the same thing, we'll just complete with that thing.

If you've already *typed* the full alias for a command, we'll complete the alias.

So, for example, here there's more than one real command involved, so all aliases are
shown:

```console
$ spack con
concretise    concretize    config        containerise  containerize
```

Here, there are two possibilities: `concretise` and `concretize`, but both map to
`concretize` so we just complete that:

```console
$ spack conc
concretize
```

And here, the user has already typed `concretis`, so we just go with it as there is only
one option:

```console
 spack concretis
concretise
```
2023-08-30 12:42:31 -07:00
Todd Gamblin
a3ecd7efed Add concretise and containerise aliases for our UK users
From a user:

> Aargh.
> ```
> ==> Error: concretise is not a recognized Spack command or extension command; check with `spack commands`.
> ```

To make things easier for our friends in the UK, this adds `concretise` and
`containerise` aliases for the `spack concretize` and `spack containerize` commands.

- [x] add aliases
- [x] update completions
2023-08-30 12:42:31 -07:00
Chris Green
ae5511afd6 [procps] New versions (#38650)
* [procps] New versions 3.3.14, 3.3.3.15..3.3.17, 4.0.0..4.0.3

* Put upper bound on patch application

* [Patch was
  merged](https://gitlab.com/procps-ng/procps/-/merge_requests/189) for
  upcoming 4.0.4.
2023-08-30 13:09:06 -05:00
Ryan Marcellino
78fe2c63fa py-parsl: add v2023.08.21 (#39642)
* py-parsl: add v2023.08.21

* fix style

* add missing deps
2023-08-29 18:33:00 -05:00
Dewi
f4f396745e amg2023 package: cmake build (#39618)
Switch from makefile to CMake-based build. CMake support is currently
in a specific branch of the amg2023 repo, so add this branch as a
version in the package.
2023-08-29 15:47:36 -07:00
Loïc Pottier
f3c6d892b1 Upgrading py-pika versions (#39670)
* Upgraded py-pika versions

Signed-off-by: Loïc Pottier <pottier1@llnl.gov>

* Upgraded py-pika versions

Signed-off-by: Loïc Pottier <pottier1@llnl.gov>

* added variants and adding setuptools constraint

Signed-off-by: Loïc Pottier <pottier1@llnl.gov>

* missing setuptools for older versions

Signed-off-by: Loïc Pottier <pottier1@llnl.gov>

---------

Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
2023-08-29 17:20:22 -05:00
Adam J. Stewart
2f5988cec7 libpng: add libs property (#39638) 2023-08-29 14:00:28 -07:00
Tom Payerle
44922f734d boxlib: Add BL_USE_PARTICLES cmake var (#39660)
Set BL_USE_PARTICLES to 1, which should case boxlib build to include Particles classes
according to CMakeLists.txt.

This seems to fix #18172
The aforementioned error seems to occur in cmake phase while processing
CMakeLists.txt in Src/C_ParticleLib, and appears to be due to the
variable containing the list of src files for the add_library() call
being empty unless BL_USE_PARTICLES is set to 1.
2023-08-29 13:57:02 -07:00
G-Ragghianti
144e657c58 Added release 2023.08.25 (#39665) 2023-08-29 13:54:31 -07:00
Jen Herting
6f48fe2b6f [mathematica] added version 13.0.1 (#39675) 2023-08-29 13:47:33 -07:00
Jim Edwards
fcd03adc02 Jedwards/parallelio262 (#39676)
* add parallelio@2.6.2
* add comments
2023-08-29 13:44:54 -07:00
Alberto Sartori
0620b954be justbuild: add v1.2.1 (#39679) 2023-08-29 15:23:22 -04:00
Jen Herting
6174b829f7 [py-tiktoken] added verison 0.3.1 (#39677) 2023-08-29 14:28:39 -04:00
Adam J. Stewart
0d4b1c6a73 py-torchmetrics: add v1.1.1 (#39685) 2023-08-29 13:25:29 -05:00
Matthew Thompson
fb9797bd67 mapl: Fix pflogger dependency (#39683) 2023-08-29 14:22:52 -04:00
Jen Herting
4eee3c12c1 [py-gradio] New package (#39304)
* [py-gradio] New package

* [py-gradio] added deps from requirements.txt

* [py-gradio] py-pillow -> pil
2023-08-29 14:08:54 -04:00
Adam J. Stewart
3e5f9a2138 py-lightly: add v1.4.17 (#39686) 2023-08-29 11:05:02 -07:00
LydDeb
8295a45999 py-distributed: use py-jinja2 versions from 2.10.3 (#39658)
In depends_on py-jinja2, use versions from 2.10.3, instead of strict equality, according to the pyproject.toml of py-distributed 2023.4.1
2023-08-29 12:09:48 -05:00
Harmen Stoppels
5138c71d34 Revert "Add style tool to fix fish file formatting (#39155)" (#39680)
This reverts commit 70c71e8f93.
2023-08-29 18:12:19 +02:00
Harmen Stoppels
eef9939c21 Automated git version fixes (#39637)
Use full length commit sha instead of short prefixes, to improve
reproducibility (future clashes) and guard against compromised repos and
man in the middle attacks.

Abbreviated commit shas are expanded to full length, to guard against future
clashes on short hash. It also guards against compromised repos and
man in the middle attacks, where attackers can easily fabricate a malicious
commit with a shasum prefix collision.

Versions with just tags now also get a commit sha, which can later be used to
check for retagged commits.
2023-08-29 16:33:03 +02:00
dependabot[bot]
ffddaabaa0 build(deps): bump sphinx from 7.2.3 to 7.2.4 in /lib/spack/docs (#39668)
Bumps [sphinx](https://github.com/sphinx-doc/sphinx) from 7.2.3 to 7.2.4.
- [Release notes](https://github.com/sphinx-doc/sphinx/releases)
- [Changelog](https://github.com/sphinx-doc/sphinx/blob/master/CHANGES)
- [Commits](https://github.com/sphinx-doc/sphinx/compare/v7.2.3...v7.2.4)

---
updated-dependencies:
- dependency-name: sphinx
  dependency-type: direct:production
  update-type: version-update:semver-patch
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2023-08-29 14:45:06 +02:00
dependabot[bot]
f664d1edaa build(deps): bump docker/setup-buildx-action from 2.9.1 to 2.10.0 (#39669)
Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 2.9.1 to 2.10.0.
- [Release notes](https://github.com/docker/setup-buildx-action/releases)
- [Commits](4c0219f9ac...885d1462b8)

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

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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-08-29 14:44:42 +02:00
Harmen Stoppels
6d5d1562bd fmt: 10.1.1 (#39664) 2023-08-29 10:47:42 +02:00
Adam J. Stewart
70c71e8f93 Add style tool to fix fish file formatting (#39155) 2023-08-28 22:16:44 -05:00
Jonathon Anderson
d9d1eb24f9 modules: copy matched config to prevent bleed (#39421) 2023-08-28 15:03:29 -07:00
kwryankrattiger
cef59ad0bf Patch VTK to enable python 3.8 in VTK 8.2 (#38735)
* VTK: Add patch for python 3.8 support

* CI: Re-enable VisIt in CI

* Configure spec matrix for stack with VisIt

* Add pugixml dep for 8.2.0

* Make VTK and ParaView consistent on proj dep

* OpenMPI 3: provides MP support by default

* Add details on proj dep in ParaView

* Add python 3.8 to test mock repo

* Patches to get VisIt VTK interface

* CI: Disable VisIt with GUI in DAV
2023-08-28 16:56:31 -05:00
Brian Vanderwende
a1e117a98b singularityce: arg handling fix (#39663) 2023-08-28 15:52:57 -04:00
Loris Ercole
cb855d5ffd kokkos: avoid setting multiple cuda_arch (#38723)
The kokkos package does not support building with cuda with multiple
`cuda_arch`. An error is raised if multiple `cuda_arch` are specified.
2023-08-28 14:13:05 -04:00
Matthew Thompson
3866ff0096 mapl: add 2.40, deprecate old versions (#39615)
* Add MAPL 2.40, deprecated old versions
* Undo some variant changes
* style fixes
* Make variants reflect Cmake options
* Remove pnetcdf variant
* Clean up depends_on
2023-08-28 11:11:03 -07:00
Todd Gamblin
6dc167e43d security: change SECURITY.md to recommend GitHub's private reporting (#39651)
GitHub's beta private security issue reporting feature is enabled on the Spack repo now,
so we can change `SECURITY.md` to recommend using it instead of `maintainers@spack.io`.

- [x] Update `SECURITY.md` to direct people to the GitHub security tab.
- [x] Update working in `SECURITY.md` to say "last two major releases" with a link to
      the releases page, instead of explicitly listing release names. This way we don't have
      to update it (which we keep forgetting to do).
2023-08-28 18:06:17 +00:00
Ashwin Kumar Karnad
0fd085be8e octopus: specify the scalapack library not the directory (#39109)
* octopus: specify the scalapack library not the directory
* octopus: use spec.scalapack.libs.ld_flags
2023-08-28 09:57:24 -07:00
Massimiliano Culpo
74fba221f1 GnuPG: add v2.4.3 (#39654)
Also updates a few dependencies
2023-08-28 10:58:16 -04:00
Harmen Stoppels
deeeb86067 Fix a few issues with git versions / moving targets in packages (#39635) 2023-08-28 15:48:13 +02:00
Jen Herting
98daf5b7ec py-scikit-optimize: add v0.9.0 and move gptune patch (#38738)
Co-authored-by: liuyangzhuan <liuyangzhuan@gmail.com>
2023-08-28 07:43:25 -04:00
Harmen Stoppels
8a3d98b632 Remove mxnet from darwin aarch64 since theres no supported release (#39644) 2023-08-28 12:21:10 +02:00
Harmen Stoppels
0cc945b367 libarchive: use openssl by default (#39640) 2023-08-28 09:23:33 +02:00
Stan Tomov
e732155e8c magma: add v2.7.2 (#39645) 2023-08-28 08:57:59 +02:00
Harmen Stoppels
c07fb833a9 libarchive: new versions (#39646) 2023-08-28 08:52:59 +02:00
Harmen Stoppels
7d566b481f libuv: add versions up to v1.46.0 (#39647) 2023-08-28 08:52:13 +02:00
Christopher Christofi
a72e5e762e py-igraph: new package with version 0.10.6 (#39179) 2023-08-27 14:46:21 -05:00
Nichols A. Romero
0eb22ef770 llvm: ensure runtimes set rpaths (#39641)
Ensure that CMAKE_INSTALL_RPATH_USE_LINK_PATH is propagated to sub-make when building runtimes.
2023-08-27 08:41:59 +02:00
Peter Scheibel
95f78440f1 External ROCm: add example configuration (#39602)
* add an example of an external rocm configuration
* include more info
* generalize section to all GPU support
2023-08-26 15:46:25 -07:00
John W. Parent
74a51aba50 CMake: add versions 3.26.4|5 and 3.27.* (#39628)
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
2023-08-26 21:26:41 +02:00
Daryl W. Grunau
b370ecfbda py-scipy: re-apply scipy/scipy#14935 workaround (#39555)
* re-apply scipy/scipy#14935 workaround

* restrict to %intel and eliminate Version() check

---------

Co-authored-by: Daryl W. Grunau <dwg@lanl.gov>
2023-08-26 08:44:57 -05:00
LydDeb
04d55b7600 py-dask: use py-jinja2 versions from 2.10.3 (#39631)
In depends_on py-jinja2, use versions from 2.10.3, instead of strict equality, according to the pyproject.toml of dask 2023.4.1
2023-08-26 00:56:39 -05:00
Tim Gymnich
d695438851 Update package.py (#39619) 2023-08-26 00:55:03 -05:00
Nichols A. Romero
f0447d63ad llvm: fix +lldb optional deps and add lua variant (#39579)
* llvm: fix +lldb optional deps, add lua variant

* use good old conflicts

---------

Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
2023-08-25 17:46:33 -05:00
Mikael Simberg
e8a7a04f14 Add gperftools 2.12 (#39623) 2023-08-25 14:57:00 -07:00
Paul R. C. Kent
23316f0352 QMCPACK: add v3.17.1 (#39626) 2023-08-25 14:55:36 -07:00
Brian Van Essen
b3433cb872 LBANN package: strip hostname on non-LC systems. (#39601) 2023-08-25 14:55:24 -07:00
James Smillie
349ba83bc6 Windows symlinking support (#38599)
This reapplies 66f7540, which adds supports for hardlinks/junctions on
Windows systems where developer mode is not enabled.

The commit was reverted on account of multiple issues:

* Checks added to prevent dangling symlinks were interfering with
  existing CI builds on Linux (i.e. builds that otherwise succeed were
  failing for creating dangling symlinks).
* The logic also updated symlinking to perform redirection of relative
  paths, which lead to malformed symlinks.

This commit fixes these issues.
2023-08-25 12:18:19 -07:00
Thomas-Ulrich
ecfd9ef12b add memalign option to petsc to be used with tandem (#37282) 2023-08-25 09:03:53 -05:00
Loris Ercole
4502351659 intel-oneapi-mkl: add hpcx-mpi to the list of supported MPI libs (#39625)
Co-authored-by: Loris Ercole <a-lercole@microsoft.com>
2023-08-25 08:53:22 -04:00
Adam J. Stewart
8a08f09ac0 py-scipy: add v1.11.2 (#39515) 2023-08-25 06:03:22 -04:00
Erik Heeren
60ecd0374e arrow: explicitly disable RE2 and UTF8PROC flags when not in dependencies (#35353)
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2023-08-25 09:04:06 +02:00
Richard Berger
52ccee79d8 legion: drop cray-pmi dependency (#39620)
There are other ways to enforce cray-pmi being loaded in environments
that use cray-mpich. This avoids breaking environments where this was
already the case and avoids forcing them to declare an external.
2023-08-25 08:51:38 +02:00
dependabot[bot]
7f0f1b63d6 build(deps): bump actions/checkout from 3.5.3 to 3.6.0 (#39617)
Bumps [actions/checkout](https://github.com/actions/checkout) from 3.5.3 to 3.6.0.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](c85c95e3d7...f43a0e5ff2)

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

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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-08-25 08:27:56 +02:00
Adam J. Stewart
b65f1f22ec py-sphinx: add v7.2.3 (#39612) 2023-08-24 18:30:13 -07:00
Richard Berger
e9efa1df75 legion: depend on cray-pmi when using gasnet and cray-mpich (#39614) 2023-08-24 18:17:24 -07:00
Jonas Thies
884a5b8b07 phist: new version 1.12.0 (#39616) 2023-08-24 18:12:42 -07:00
AMD Toolchain Support
91d674f5d0 AOCL spack recipes for 4.1 release w. new AOCL-Utils library (#39489)
* AOCC and AOCL spack recipes for 4.1 release
* Fix broken checksum
* remove blank line
* Add missing `@when` for 4.1 only function

---------

Co-authored-by: vijay kallesh <Vijay-teekinavar.Kallesh@amd.com>
2023-08-24 18:05:39 -07:00
Matt Drozt
76fbb8cd8f [py-smartsim] New Package (#39306)
* Create a smartsim package

* rm ss 0.4.2

* no py upper bound, add build dep

* add setup_build_env

* add comment to find ml deps lower bounds

* Apply suggestions from code review

Correct dep versions, use `python_purelib`

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

* remove the cuda/rocm vars

* point editors to bin deps version constraints

* Apply suggestions from code review

Loosen `py-smartredis` constraint, enforce `setup.cfg` py version

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

* style

* rm rai lower bound

* lower bound setuptools

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-08-24 18:03:52 -04:00
Wouter Deconinck
0f3f2a8024 py-particle: new versions through 0.23.0 (#39547)
* py-particle: new versions through 0.23.0

* py-particle: depends_on py-deprecated
2023-08-24 16:22:33 -05:00
Frédéric Simonis
5a5f774369 preCICE: prepare for version 3 (#39486) 2023-08-24 14:04:36 -04:00
Adam J. Stewart
f5212ae139 py-sphinx: add v7.2 (#39513) 2023-08-24 12:07:24 -04:00
Sajid Ali
4b618704bf add magma variant to strumpack (#39224)
* add magma variant to strumpack
* clarify conflicts to be excuive to rocm/cuda, without it +magma+cuda fails as it is ~rocm
   modified:   var/spack/repos/builtin/packages/strumpack/package.py
* add missing depends_on for magma variant
2023-08-24 08:39:24 -07:00
Harmen Stoppels
46285d9725 zlib-ng: build system patches (#39559) 2023-08-24 12:13:22 +02:00
eugeneswalker
36852fe348 h5bench: add e4s tag (#39595) 2023-08-24 08:58:07 +02:00
Harmen Stoppels
8914d26867 rebuild-index: fix race condition by avoiding parallelism (#39594) 2023-08-24 08:26:56 +02:00
Massimiliano Culpo
fdea5e7624 Remove leftover attributes from parser (#39574)
#35042 introduced lazy hash parsing, but didn't remove a
few attributes from the parser that were needed only for
concrete specs

This commit removes them, since they are effectively
dead code.
2023-08-24 08:04:43 +02:00
dependabot[bot]
ca1e4d54b5 build(deps): bump sphinx from 7.2.2 to 7.2.3 in /lib/spack/docs (#39603)
Bumps [sphinx](https://github.com/sphinx-doc/sphinx) from 7.2.2 to 7.2.3.
- [Release notes](https://github.com/sphinx-doc/sphinx/releases)
- [Changelog](https://github.com/sphinx-doc/sphinx/blob/master/CHANGES)
- [Commits](https://github.com/sphinx-doc/sphinx/compare/v7.2.2...v7.2.3)

---
updated-dependencies:
- dependency-name: sphinx
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

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Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-08-24 07:55:14 +02:00
Ryan Mulhall
656528bbbb fms: add v2023.02 and v2023.01.01 (#39434)
* Add 2023.02 and 2023.01.01 with variant for mpp_io and fms_io deprecation

Co-authored-by: rem1776 <Ryan.Mulhall@noaa.gov>
2023-08-24 03:58:50 +02:00
Alan Orth
4d42e9d1f3 perl-http-message: add dependency on perl-clone (#39567)
Clone is a hard dependency as of HTTP-Message v6.44. This causes
problems in packages like Roary which depend on perl-http-message:

    $ spack load roary
    $ roary
    Use of uninitialized value in require at /var/scratch/spack/opt/spack/linux-centos8-x86_64_v3/gcc-8.5.0/perl-http-message-6.44-lzp5th4jddd3gojkjfli4hljgem2nl26/lib/perl5/HTTP/Headers.pm line 8.
    Can't locate Clone.pm in @INC (you may need to install the Clone module) (@INC contains:  /home/aorth/lib ...

See: https://github.com/libwww-perl/HTTP-Message/blob/master/Changes
2023-08-24 03:33:10 +02:00
Julien Cortial
d058c1d649 Add package mpi-test-suite (#39487) 2023-08-24 03:18:58 +02:00
Martin Aumüller
43854fc2ec ffmpeg: apply upstream fix for build with binutils 2.41 (#39392)
While spack does not yet provide binutils 2.41, they might still be
installed. However, building ffmpeg on x86_64 fails with multiple errors like
this:
./libavcodec/x86/mathops.h:125: Error: operand type mismatch for `shr'

also reported here: https://trac.ffmpeg.org/ticket/10405
2023-08-24 03:11:02 +02:00
Julien Cortial
6a2149df6e Make lcov dependency on perl explicit (#39485) 2023-08-24 03:05:00 +02:00
Brent Huisman
af38d097ac Arbor: version added: v0.9.0 (#39374) 2023-08-24 02:59:53 +02:00
Richard Berger
e67dca73d1 lammps: simplify url_for_version logic (#39554)
Use the stable_versions variable to check stable versions
2023-08-24 02:44:39 +02:00
Richard Berger
2e6ed1e707 slurm: add version 23-02-3-1 and 23-02-4-1 (#39598) 2023-08-23 20:43:21 -04:00
Greg Becker
53d2ffaf83 Add amg2023 package; remove amg package (#39105)
Add amg2023 package

Consolidate existing amg and amg2013 packages (they reference the
same code) under the amg2013 name to minimize confusion between
amg2023 and amg2013.

Co-authored-by: Riyaz Haque <haque1@llnl.gov>
2023-08-23 19:48:44 -04:00
svengoldberg
a95e061fed Include t8code package (#39391)
* t8code: Create new spack package

Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2023-08-23 18:48:21 -04:00
Vicente Bolea
e01b9b38ef adios2: correct c-blosc dependency (#39385)
* adios2: correct c-blosc dependency

* c-blosc2: disable oneapi spec
2023-08-23 14:44:26 -07:00
lorddavidiii
eac15badd3 cfitsio: add new version 4.3.0 (#39588) 2023-08-23 17:32:37 -04:00
Massimiliano Culpo
806b8aa966 Uppercase global constants in spec.py (#39573)
* Uppercase global constants in spec.py

Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2023-08-23 21:26:30 +00:00
Greg Becker
9e5ca525f7 do not warn for invalid package name on repo.yaml if subdirectory: '' (#39439) 2023-08-23 23:23:35 +02:00
Simon Pintarelli
5ea4322f88 elpa 2023.05 (#39585) 2023-08-23 22:39:04 +02:00
Harmen Stoppels
4ca2d8bc19 aws-sdk-cpp: disable flaky tests in build (#39565) 2023-08-23 21:59:22 +02:00
Massimiliano Culpo
e0059ef961 ASP-based solver: split heuristic for duplicate nodes (#39593)
The heuristic for duplicate nodes contains a few typos, and
apparently slows down the solve for specs that have a lot of
sub-optimal choices to be taken.

This is likely because with a lot of sub-optimal choices, the
low priority, flawed heuristic is being used by clingo.

Here I split the heuristic, so complex rules that matter only
if we allow multiple nodes from the same package are used
only in that case.
2023-08-23 19:02:20 +00:00
Cameron Rutherford
7d9fad9576 Add kpp2 branch tag and move to GitHub. (#39503) 2023-08-23 08:55:54 -07:00
Richard Berger
553277a84f FleCSI dependency updates (#39557)
* use full cuda_arch list
* update compiler requirement
* update boost requirements
* propagate +kokkos to legion in non-GPU cases
* add missing graphviz dependency for +doc
2023-08-23 15:40:10 +02:00
Harmen Stoppels
00a3ebd0bb llvm: fix elf dep conditions and cmake bug (#39566) 2023-08-23 07:33:23 -04:00
Julien Cortial
ffc9060e11 Add CDT (Constrained Delaunay Triangulation) library (#39488) 2023-08-23 11:29:25 +02:00
Dom Heinzeller
31d5f56913 Add --fail-fast option for generating build caches (#38496)
Co-authored-by: Harmen Stoppels <me@harmenstoppels.nl>
2023-08-23 11:20:33 +02:00
Adam J. Stewart
bfdebae831 py-nbmake: add v1.4.3 (#39514) 2023-08-23 11:13:10 +02:00
eugeneswalker
aa83fa44e1 libyogrt %oneapi: add cflag=-Wno-error=implicit-function-declaration (#39522) 2023-08-23 11:10:37 +02:00
Martin Aumüller
e56291dd45 embree: new versions and ARM support (#38083) 2023-08-23 11:10:07 +02:00
Paul R. C. Kent
2f52545214 QMCPACK: add v3.17.0 (#39523) 2023-08-23 11:08:40 +02:00
Leopold Talirz
5090023e3a xtb: fix la_backend logic (#38309) 2023-08-23 11:08:13 +02:00
Giuseppe Congiu
d355880110 PAPI misc fixes (#39191)
Spack installs the hsa-rocr-dev and rocprofiler packages into different
directories. However, PAPI typically expects those to be under the same
directory and locates such directory through the PAPI_ROCM_ROOT env
variable.

The PAPI rocm component also allows users to override PAPI_ROCM_ROOT to
locate directly the librocprofiler64.so through the HSA_TOOLS_LIB env
variable that acts directly onto the HSA runtime tools mechanism.

Hence, in order to account for the decoupling of hsa and rocprofiler,
this patch sets HSA_TOOLS_LIB to librocprofiler64.so full path.
2023-08-23 10:09:54 +02:00
snehring
1a0434b808 sentieon-genomics: adding version 202308 (#39572) 2023-08-23 10:05:03 +02:00
Laura Weber
c3eec8a36f sublime-test: add v4.4152 (#39577) 2023-08-23 10:04:24 +02:00
eflumerf
25b8cf93d2 xmlrpc-c: add build of xmlrpc tools directory (#39580) 2023-08-23 09:41:27 +02:00
Adam J. Stewart
34ff7605e6 py-torchmetrics: add v1.1.0 (#39582) 2023-08-23 09:34:53 +02:00
Adam J. Stewart
e026fd3613 py-lightly: add v1.4.16 (#39583) 2023-08-23 09:34:15 +02:00
Tamara Dahlgren
3f5f4cfe26 docs: API, f-string, and path updates to test section (#39584) 2023-08-23 09:22:25 +02:00
Mikael Simberg
74fe9ccef3 Update version constraint for HIP patch (#39578) 2023-08-23 09:09:14 +02:00
Wouter Deconinck
fd5a8b2075 py-boost-histogram: new version 1.3.2 (#39558) 2023-08-22 19:34:09 -05:00
Wouter Deconinck
33793445cf py-uhi: new versions 0.3.2, 0.3.3 (#39548) 2023-08-22 19:23:52 -05:00
Wouter Deconinck
f4a144c8ac py-hepunits: new version 2.3.2 (#39546) 2023-08-22 19:21:51 -05:00
Vincent Michaud-Rioux
6c439ec022 Update/py pennylane lightning (#39466)
* Update pennylane-lightning.

* Update Lightning-Kokkos to v0.31

* Constrain scipy version.

* Update var/spack/repos/builtin/packages/py-pennylane-lightning-kokkos/package.py

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

* Fix PLK kokkos dep versioning.

* Move kokkos ver outised backend loop and reformat.

* Update package.py

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-08-22 19:14:31 -05:00
genric
209409189a py-xarray: add v2023.7.0 (#39418)
* py-xarray: add v2023.7.0

* address review comments
2023-08-22 19:13:19 -05:00
Tim Haines
ff900566e0 libiberty: add version 2.41 (#39569) 2023-08-22 16:29:21 -04:00
eugeneswalker
a954a0bb9f tau: add v2.32.1 (#39504) 2023-08-22 16:24:05 -04:00
Kamil Iskra
c21e00f504 spack.caches: make fetch_cache_location lowercase (#39575)
fetch_cache_location was erroneously renamed to FETCH_cache_location
as part of #39428, breaking "spack module create".
2023-08-22 16:18:51 -04:00
Massimiliano Culpo
9ae1317e79 ASP-based solver: use edge properties for reused specs (#39508)
Since #34821 we are annotating virtual dependencies on
DAG edges, and reconstructing virtuals in memory when
we read a concrete spec from previous formats.

Therefore, we can remove a TODO in asp.py, and rely on
"virtual_on_edge" facts to be imposed.
2023-08-22 12:07:51 -07:00
Wouter Deconinck
9f1a30d3b5 veccore: new variant vc (#39542)
* veccore: new variants umesimd and vc

* veccore: remove variant umesimd again
2023-08-22 11:20:19 -04:00
Harmen Stoppels
1340995249 clingo-bootstrap: pgo, lto, allocator optimizations (#34926)
Add support for PGO and LTO for gcc, clang and apple-clang, and add a
patch to allow mimalloc as an allocator in operator new/delete, give
reduces clingo runtime by about 30%.
2023-08-22 14:44:07 +02:00
dependabot[bot]
afebc11742 Bump sphinx from 6.2.1 to 7.2.2 in /lib/spack/docs (#39502)
Bumps [sphinx](https://github.com/sphinx-doc/sphinx) from 6.2.1 to 7.2.2.
- [Release notes](https://github.com/sphinx-doc/sphinx/releases)
- [Changelog](https://github.com/sphinx-doc/sphinx/blob/master/CHANGES)
- [Commits](https://github.com/sphinx-doc/sphinx/compare/v6.2.1...v7.2.2)

---
updated-dependencies:
- dependency-name: sphinx
  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>
2023-08-22 12:02:58 +02:00
Jim Edwards
34e9fc612c parallelio: add v2.6.1 (#39479) 2023-08-22 09:44:06 +02:00
dependabot[bot]
1d8ff7f742 Bump sphinx-rtd-theme from 1.2.2 to 1.3.0 in /lib/spack/docs (#39562)
Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) from 1.2.2 to 1.3.0.
- [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst)
- [Commits](https://github.com/readthedocs/sphinx_rtd_theme/compare/1.2.2...1.3.0)

---
updated-dependencies:
- dependency-name: sphinx-rtd-theme
  dependency-type: direct:production
  update-type: version-update:semver-minor
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Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-08-22 09:32:39 +02:00
Axel Huebl
0e27f05611 openPMD-api: 0.15.2 (#39528)
Latest patch release.
2023-08-21 18:31:53 -07:00
Axel Huebl
19aaa97ff2 C-Blosc2: v2.10.2 (#39537)
This fixes regressions with external dependencies introduced
in 2.10.1
2023-08-21 18:29:58 -07:00
Kamil Iskra
990309355f [bats] Update to v1.10.0 (#39561)
* [bats] Update to v1.10.0
  Original bats has been abandoned for years; nowadays it's
  community-maintained.
* [bats] Fix style
2023-08-21 18:25:35 -07:00
eugeneswalker
2cb66e6e44 tasmanian@:7.9 +cuda conflicts with cuda@12 (#39541) 2023-08-21 13:08:12 -07:00
David Gardner
cfaade098a add sundials v6.6.0 (#39526) 2023-08-21 10:48:58 -07:00
Wouter Deconinck
ed65532e27 singularityce: fix after no spaces in Executable allowed (#39553) 2023-08-21 13:43:11 -04:00
Dr Marco Claudio De La Pierre
696d4a1b85 amdblis recipe: adding variant for a performance flag (#39549)
* amdblis recipe: adding variant for a performance flag

Signed-off-by: Dr Marco De La Pierre <marco.delapierre@gmail.com>

* typo fix

Signed-off-by: Dr Marco De La Pierre <marco.delapierre@gmail.com>

* style fix

Signed-off-by: Dr Marco De La Pierre <marco.delapierre@gmail.com>

* another typo fix

Signed-off-by: Dr Marco De La Pierre <marco.delapierre@gmail.com>

* one more style fix

Signed-off-by: Dr Marco De La Pierre <marco.delapierre@gmail.com>

---------

Signed-off-by: Dr Marco De La Pierre <marco.delapierre@gmail.com>
2023-08-21 10:16:39 -07:00
Taillefumier Mathieu
8def75b414 Update cp2k recipe (#39128)
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>
Co-authored-by: Rocco Meli <r.meli@bluemail.ch>
2023-08-21 17:09:28 +02:00
Harmen Stoppels
5389db821d aws-sdk-cpp: new versions and greatly reduce install size(#39511) 2023-08-21 14:52:21 +02:00
Wouter Deconinck
0d5ae3a809 cepgen: new version 1.1.0 (#39550) 2023-08-21 08:08:05 +02:00
Wouter Deconinck
b61ad8d2a8 whizard: new versions 3.1.1 and 3.1.2 (#39540) 2023-08-21 08:07:36 +02:00
Wouter Deconinck
b35db020eb zlib: new version 1.3 (#39539) 2023-08-21 08:06:41 +02:00
Wouter Deconinck
ca1d15101e zlib: add git url (#39533) 2023-08-21 08:04:28 +02:00
Brian Spilner
c9ec5fb9ac cdo: add v2.2.2 (#39506)
* update cdo-2.2.2

* add note on hdf5
2023-08-18 15:46:50 -07:00
Todd Gamblin
71abb8c7f0 less: update version, dependencies (#39521) 2023-08-18 15:43:54 -07:00
John W. Parent
4dafae8d17 spack.bat: Fixup CL arg parsing (#39359)
Previous changes to this file stopped directly processing CL args to
stop batch `for` from interpolating batch reserved characters needed in
arguments like URLS. In doing so, we relied on `for` for an easy
"split" operation, however this incorrectly splits paths with spaces in
certain cases. Processing everything ourselves with manual looping via
`goto` statements allows for full control over CL parsing and handling
of both paths with spaces and reserved characters.
2023-08-18 14:29:47 -07:00
Jen Herting
b2b00df5cc [py-gradio-client] New package (#39496) 2023-08-18 12:03:37 -05:00
Jen Herting
114e5d4767 [py-openmim] Beginning work (#39494) 2023-08-18 12:00:48 -05:00
Jen Herting
fd70e7fb31 [py-confection] new package (#39491) 2023-08-18 11:59:47 -05:00
George Young
77760c8ea4 py-multiqc: add 1.15, correct py-matplotlib dependency (#39509)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-08-18 11:56:20 -05:00
Jen Herting
737a6dcc73 py-markdown-it-py: add linkify variant and v2.2.0 (#39492)
* [py-markdown-it-py] added linkify variant

* [py-markdown-it-py] added version 2.2.0
2023-08-18 11:14:15 -05:00
Seth R. Johnson
3826fe3765 fortrilinos: release 2.3.0 compatible with trilinos@14 (#39500)
* fortrilinos: release 2.3.0 compatible with trilinos@14.0
2023-08-18 12:10:00 -04:00
Benjamin Meyers
edb11941b2 New: py-alpaca-farm, py-alpaca-eval, py-tiktoken; Updated: py-accerlate, py-transformers (#39432) 2023-08-18 10:29:12 -05:00
Axel Huebl
1bd58a8026 WarpX 23.08 (#39407)
* WarpX 23.08

Update WarpX and related Python packages to the lastest releases.

* fix style

---------

Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
2023-08-18 10:03:47 -05:00
Jordan Galby
f8e0c8caed Fix Spack freeze on install child process unexpected exit (#39015)
* Fix spack frozen on child process defunct

* Rename parent/child pipe to read/write to emphasize non-duplex mode
2023-08-18 09:41:02 +02:00
Vijay M
d0412c1578 Updating the versions of available tarballs and adding an eigen3 variant as well (#39498) 2023-08-17 22:23:32 -04:00
Harmen Stoppels
ec500adb50 zlib-api: use zlib-ng +compat by default (#39358)
In the HPC package manager, we want the fastest `zlib`  implementation by default.  `zlib-ng` is up to 4x faster than stock `zlib`, and it can do things like take advantage of AVX-512 instructions.  This PR makes `zlib-ng` the default `zlib-api` provider (`zlib-api` was introduced earlier, in #37372).

As far as I can see, the only issues you can encounter are:

1. Build issues with packages that heavily rely on `zlib` internals. In Gitlab CI only one out of hundreds of packages had that issue (it extended zlib with deflate stuff, and used its own copy of zlib sources).
2. Packages that like to detect `zlib-ng` separately and rely on `zlib-ng` internals. The only issue I've found with this among the hundreds of packages built in CI is `perl` trying to report more specific zlib-ng version details, and relied on some internals that got refactored. But yeah... that warrants a patch / conflict and is nothing special.

At runtime, you cannot really have any issues, given that zlib and zlib-ng export the exact same symbols (and zlib-ng tests this in their CI).

You can't really have issues with externals when using zlib-ng either. The only type of issue is when system zlib is rather new, and not marked as external; if another external uses new symbols, and Spack builds an older zlib/zlib-ng, then the external might not find the new symbols. But this is a configuration issue, and it's not an issue caused by zlib-ng, as the same would happen with older Spack zlib.

* zlib-api: use zlib-ng +compat by default
* make a trivial change to zlib-ng to trigger a rebuild
* add `haampie` as maintainer
2023-08-17 14:03:14 -07:00
Harmen Stoppels
30f5c74614 py-flake8: bump including deps (#39426) 2023-08-17 21:02:11 +02:00
Massimiliano Culpo
713eb210ac zig: add v0.11.0 (#39484) 2023-08-17 19:18:00 +02:00
Massimiliano Culpo
a022e45866 ASP-based solver: optimize key to intermediate dicts (#39471)
Computing str(spec) is faster than computing hash(spec), and
since all the abstract specs we deal with come from user configuration
they cannot cover DAG structures that are not captured by str() but
are captured by hash()
2023-08-17 14:11:49 +02:00
eugeneswalker
82685a68d9 boost %oneapi: add cxxflags -Wno-error=enum-constexpr-conversion (#39477) 2023-08-17 07:49:20 -04:00
dependabot[bot]
b19691d503 Bump mypy from 1.5.0 to 1.5.1 in /lib/spack/docs (#39478)
Bumps [mypy](https://github.com/python/mypy) from 1.5.0 to 1.5.1.
- [Commits](https://github.com/python/mypy/compare/v1.5.0...v1.5.1)

---
updated-dependencies:
- dependency-name: mypy
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-08-17 12:35:49 +02:00
eugeneswalker
54ea860b37 gmsh %oneapi: add cflag: -Wno-error=implicit-function-declaration (#39476) 2023-08-17 06:09:07 -04:00
eugeneswalker
fb598baa53 py-ruamel-yaml-clib %oneapi: -Wno-error=incompatible-function-pointer-types (#39480) 2023-08-17 11:59:45 +02:00
1521 changed files with 49051 additions and 14146 deletions

View File

@@ -10,3 +10,8 @@ updates:
directory: "/lib/spack/docs"
schedule:
interval: "daily"
# Requirements to run style checks
- package-ecosystem: "pip"
directory: "/.github/workflows/style"
schedule:
interval: "daily"

View File

@@ -22,8 +22,8 @@ jobs:
matrix:
operating_system: ["ubuntu-latest", "macos-latest"]
steps:
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
- uses: actions/setup-python@61a6322f88396a6271a6ee3565807d608ecaddd1 # @v2
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # @v2
- uses: actions/setup-python@65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236 # @v2
with:
python-version: ${{inputs.python_version}}
- name: Install Python packages
@@ -34,6 +34,7 @@ jobs:
run: |
. share/spack/setup-env.sh
coverage run $(which spack) audit packages
coverage run $(which spack) audit externals
coverage combine
coverage xml
- name: Package audits (without coverage)
@@ -41,6 +42,7 @@ jobs:
run: |
. share/spack/setup-env.sh
$(which spack) audit packages
$(which spack) audit externals
- uses: codecov/codecov-action@eaaf4bedf32dbdc6b720b63067d99c4d77d6047d # @v2.1.0
if: ${{ inputs.with_coverage == 'true' }}
with:

View File

@@ -24,7 +24,7 @@ jobs:
make patch unzip which xz python3 python3-devel tree \
cmake bison bison-devel libstdc++-static
- name: Checkout
uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
with:
fetch-depth: 0
- name: Setup non-root user
@@ -42,8 +42,8 @@ jobs:
shell: runuser -u spack-test -- bash {0}
run: |
source share/spack/setup-env.sh
spack bootstrap disable github-actions-v0.5
spack bootstrap disable github-actions-v0.4
spack bootstrap disable github-actions-v0.3
spack external find cmake bison
spack -d solve zlib
tree ~/.spack/bootstrap/store/
@@ -62,7 +62,7 @@ jobs:
make patch unzip xz-utils python3 python3-dev tree \
cmake bison
- name: Checkout
uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
with:
fetch-depth: 0
- name: Setup non-root user
@@ -80,8 +80,8 @@ jobs:
shell: runuser -u spack-test -- bash {0}
run: |
source share/spack/setup-env.sh
spack bootstrap disable github-actions-v0.5
spack bootstrap disable github-actions-v0.4
spack bootstrap disable github-actions-v0.3
spack external find cmake bison
spack -d solve zlib
tree ~/.spack/bootstrap/store/
@@ -99,7 +99,7 @@ jobs:
bzip2 curl file g++ gcc gfortran git gnupg2 gzip \
make patch unzip xz-utils python3 python3-dev tree
- name: Checkout
uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
with:
fetch-depth: 0
- name: Setup non-root user
@@ -133,7 +133,7 @@ jobs:
make patch unzip which xz python3 python3-devel tree \
cmake bison
- name: Checkout
uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
with:
fetch-depth: 0
- name: Setup repo
@@ -145,8 +145,8 @@ jobs:
- name: Bootstrap clingo
run: |
source share/spack/setup-env.sh
spack bootstrap disable github-actions-v0.5
spack bootstrap disable github-actions-v0.4
spack bootstrap disable github-actions-v0.3
spack external find cmake bison
spack -d solve zlib
tree ~/.spack/bootstrap/store/
@@ -158,13 +158,16 @@ jobs:
run: |
brew install cmake bison@2.7 tree
- name: Checkout
uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
- uses: actions/setup-python@65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236 # @v2
with:
python-version: "3.12"
- name: Bootstrap clingo
run: |
source share/spack/setup-env.sh
export PATH=/usr/local/opt/bison@2.7/bin:$PATH
spack bootstrap disable github-actions-v0.5
spack bootstrap disable github-actions-v0.4
spack bootstrap disable github-actions-v0.3
spack external find --not-buildable cmake bison
spack -d solve zlib
tree ~/.spack/bootstrap/store/
@@ -179,11 +182,11 @@ jobs:
run: |
brew install tree
- name: Checkout
uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
- name: Bootstrap clingo
run: |
set -ex
for ver in '3.6' '3.7' '3.8' '3.9' '3.10' ; do
for ver in '3.7' '3.8' '3.9' '3.10' '3.11' ; do
not_found=1
ver_dir="$(find $RUNNER_TOOL_CACHE/Python -wholename "*/${ver}.*/*/bin" | grep . || true)"
echo "Testing $ver_dir"
@@ -204,7 +207,7 @@ jobs:
runs-on: ubuntu-20.04
steps:
- name: Checkout
uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
with:
fetch-depth: 0
- name: Setup repo
@@ -214,7 +217,7 @@ jobs:
- name: Bootstrap clingo
run: |
set -ex
for ver in '3.6' '3.7' '3.8' '3.9' '3.10' ; do
for ver in '3.7' '3.8' '3.9' '3.10' '3.11' ; do
not_found=1
ver_dir="$(find $RUNNER_TOOL_CACHE/Python -wholename "*/${ver}.*/*/bin" | grep . || true)"
echo "Testing $ver_dir"
@@ -247,7 +250,7 @@ jobs:
bzip2 curl file g++ gcc patchelf gfortran git gzip \
make patch unzip xz-utils python3 python3-dev tree
- name: Checkout
uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
with:
fetch-depth: 0
- name: Setup non-root user
@@ -265,6 +268,7 @@ jobs:
shell: runuser -u spack-test -- bash {0}
run: |
source share/spack/setup-env.sh
spack bootstrap disable github-actions-v0.4
spack bootstrap disable spack-install
spack -d gpg list
tree ~/.spack/bootstrap/store/
@@ -283,7 +287,7 @@ jobs:
make patch unzip xz-utils python3 python3-dev tree \
gawk
- name: Checkout
uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
with:
fetch-depth: 0
- name: Setup non-root user
@@ -302,8 +306,8 @@ jobs:
run: |
source share/spack/setup-env.sh
spack solve zlib
spack bootstrap disable github-actions-v0.5
spack bootstrap disable github-actions-v0.4
spack bootstrap disable github-actions-v0.3
spack -d gpg list
tree ~/.spack/bootstrap/store/
@@ -316,10 +320,11 @@ jobs:
# Remove GnuPG since we want to bootstrap it
sudo rm -rf /usr/local/bin/gpg
- name: Checkout
uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
- name: Bootstrap GnuPG
run: |
source share/spack/setup-env.sh
spack bootstrap disable github-actions-v0.4
spack bootstrap disable spack-install
spack -d gpg list
tree ~/.spack/bootstrap/store/
@@ -333,13 +338,13 @@ jobs:
# Remove GnuPG since we want to bootstrap it
sudo rm -rf /usr/local/bin/gpg
- name: Checkout
uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
- name: Bootstrap GnuPG
run: |
source share/spack/setup-env.sh
spack solve zlib
spack bootstrap disable github-actions-v0.5
spack bootstrap disable github-actions-v0.4
spack bootstrap disable github-actions-v0.3
spack -d gpg list
tree ~/.spack/bootstrap/store/

View File

@@ -38,12 +38,11 @@ jobs:
# Meaning of the various items in the matrix list
# 0: Container name (e.g. ubuntu-bionic)
# 1: Platforms to build for
# 2: Base image (e.g. ubuntu:18.04)
# 2: Base image (e.g. ubuntu:22.04)
dockerfile: [[amazon-linux, 'linux/amd64,linux/arm64', 'amazonlinux:2'],
[centos7, 'linux/amd64,linux/arm64,linux/ppc64le', 'centos:7'],
[centos-stream, 'linux/amd64,linux/arm64,linux/ppc64le', 'centos:stream'],
[leap15, 'linux/amd64,linux/arm64,linux/ppc64le', 'opensuse/leap:15'],
[ubuntu-bionic, 'linux/amd64,linux/arm64,linux/ppc64le', 'ubuntu:18.04'],
[ubuntu-focal, 'linux/amd64,linux/arm64,linux/ppc64le', 'ubuntu:20.04'],
[ubuntu-jammy, 'linux/amd64,linux/arm64,linux/ppc64le', 'ubuntu:22.04'],
[almalinux8, 'linux/amd64,linux/arm64,linux/ppc64le', 'almalinux:8'],
@@ -56,20 +55,22 @@ jobs:
if: github.repository == 'spack/spack'
steps:
- name: Checkout
uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # @v2
- name: Set Container Tag Normal (Nightly)
run: |
container="${{ matrix.dockerfile[0] }}:latest"
echo "container=${container}" >> $GITHUB_ENV
echo "versioned=${container}" >> $GITHUB_ENV
# On a new release create a container with the same tag as the release.
- name: Set Container Tag on Release
if: github.event_name == 'release'
run: |
versioned="${{matrix.dockerfile[0]}}:${GITHUB_REF##*/}"
echo "versioned=${versioned}" >> $GITHUB_ENV
- uses: docker/metadata-action@96383f45573cb7f253c731d3b3ab81c87ef81934
id: docker_meta
with:
images: |
ghcr.io/${{ github.repository_owner }}/${{ matrix.dockerfile[0] }}
${{ github.repository_owner }}/${{ matrix.dockerfile[0] }}
tags: |
type=schedule,pattern=nightly
type=schedule,pattern=develop
type=semver,pattern={{version}}
type=semver,pattern={{major}}.{{minor}}
type=semver,pattern={{major}}
type=ref,event=branch
type=ref,event=pr
- name: Generate the Dockerfile
env:
@@ -86,19 +87,19 @@ jobs:
fi
- name: Upload Dockerfile
uses: actions/upload-artifact@0b7f8abb1508181956e8e162db84b466c27e18ce
uses: actions/upload-artifact@a8a3f3ad30e3422c9c7b888a15615d19a852ae32
with:
name: dockerfiles
path: dockerfiles
- name: Set up QEMU
uses: docker/setup-qemu-action@2b82ce82d56a2a04d2637cd93a637ae1b359c0a7 # @v1
uses: docker/setup-qemu-action@68827325e0b33c7199eb31dd4e31fbe9023e06e3
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@4c0219f9ac95b02789c1075625400b2acbff50b1 # @v1
uses: docker/setup-buildx-action@f95db51fddba0c2d1ec667646a06c2ce06100226
- name: Log in to GitHub Container Registry
uses: docker/login-action@465a07811f14bebb1938fbed4728c6a1ff8901fc # @v1
uses: docker/login-action@343f7c4344506bcbf9b4de18042ae17996df046d
with:
registry: ghcr.io
username: ${{ github.actor }}
@@ -106,21 +107,18 @@ jobs:
- name: Log in to DockerHub
if: github.event_name != 'pull_request'
uses: docker/login-action@465a07811f14bebb1938fbed4728c6a1ff8901fc # @v1
uses: docker/login-action@343f7c4344506bcbf9b4de18042ae17996df046d
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
- name: Build & Deploy ${{ matrix.dockerfile[0] }}
uses: docker/build-push-action@2eb1c1961a95fc15694676618e422e8ba1d63825 # @v2
uses: docker/build-push-action@0565240e2d4ab88bba5387d719585280857ece09
with:
context: dockerfiles/${{ matrix.dockerfile[0] }}
platforms: ${{ matrix.dockerfile[1] }}
push: ${{ github.event_name != 'pull_request' }}
cache-from: type=gha
cache-to: type=gha,mode=max
tags: |
spack/${{ env.container }}
spack/${{ env.versioned }}
ghcr.io/spack/${{ env.container }}
ghcr.io/spack/${{ env.versioned }}
tags: ${{ steps.docker_meta.outputs.tags }}
labels: ${{ steps.docker_meta.outputs.labels }}

View File

@@ -35,7 +35,7 @@ jobs:
core: ${{ steps.filter.outputs.core }}
packages: ${{ steps.filter.outputs.packages }}
steps:
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # @v2
if: ${{ github.event_name == 'push' }}
with:
fetch-depth: 0

View File

@@ -14,10 +14,10 @@ jobs:
build-paraview-deps:
runs-on: windows-latest
steps:
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
with:
fetch-depth: 0
- uses: actions/setup-python@61a6322f88396a6271a6ee3565807d608ecaddd1
- uses: actions/setup-python@65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236
with:
python-version: 3.9
- name: Install Python packages

View File

@@ -0,0 +1,7 @@
black==23.11.0
clingo==5.6.2
flake8==6.1.0
isort==5.12.0
mypy==1.6.1
types-six==1.16.21.9
vermin==1.5.2

View File

@@ -15,7 +15,7 @@ jobs:
strategy:
matrix:
os: [ubuntu-latest]
python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
concretizer: ['clingo']
on_develop:
- ${{ github.ref == 'refs/heads/develop' }}
@@ -45,12 +45,16 @@ jobs:
os: ubuntu-latest
concretizer: 'clingo'
on_develop: false
- python-version: '3.11'
os: ubuntu-latest
concretizer: 'clingo'
on_develop: false
steps:
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # @v2
with:
fetch-depth: 0
- uses: actions/setup-python@61a6322f88396a6271a6ee3565807d608ecaddd1 # @v2
- uses: actions/setup-python@65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236 # @v2
with:
python-version: ${{ matrix.python-version }}
- name: Install System packages
@@ -94,10 +98,10 @@ jobs:
shell:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # @v2
with:
fetch-depth: 0
- uses: actions/setup-python@61a6322f88396a6271a6ee3565807d608ecaddd1 # @v2
- uses: actions/setup-python@65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236 # @v2
with:
python-version: '3.11'
- name: Install System packages
@@ -133,7 +137,7 @@ jobs:
dnf install -y \
bzip2 curl file gcc-c++ gcc gcc-gfortran git gnupg2 gzip \
make patch tcl unzip which xz
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # @v2
- name: Setup repo and non-root user
run: |
git --version
@@ -152,10 +156,10 @@ jobs:
clingo-cffi:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # @v2
with:
fetch-depth: 0
- uses: actions/setup-python@61a6322f88396a6271a6ee3565807d608ecaddd1 # @v2
- uses: actions/setup-python@65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236 # @v2
with:
python-version: '3.11'
- name: Install System packages
@@ -185,12 +189,12 @@ jobs:
runs-on: macos-latest
strategy:
matrix:
python-version: ["3.10"]
python-version: ["3.11"]
steps:
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # @v2
with:
fetch-depth: 0
- uses: actions/setup-python@61a6322f88396a6271a6ee3565807d608ecaddd1 # @v2
- uses: actions/setup-python@65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236 # @v2
with:
python-version: ${{ matrix.python-version }}
- name: Install Python packages

View File

@@ -18,15 +18,15 @@ jobs:
validate:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
- uses: actions/setup-python@61a6322f88396a6271a6ee3565807d608ecaddd1 # @v2
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
- uses: actions/setup-python@65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236
with:
python-version: '3.11'
cache: 'pip'
- name: Install Python Packages
run: |
pip install --upgrade pip
pip install --upgrade vermin
pip install --upgrade pip setuptools
pip install -r .github/workflows/style/requirements.txt
- name: vermin (Spack's Core)
run: vermin --backport importlib --backport argparse --violations --backport typing -t=3.6- -vvv lib/spack/spack/ lib/spack/llnl/ bin/
- name: vermin (Repositories)
@@ -35,16 +35,17 @@ jobs:
style:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
with:
fetch-depth: 0
- uses: actions/setup-python@61a6322f88396a6271a6ee3565807d608ecaddd1 # @v2
- uses: actions/setup-python@65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236
with:
python-version: '3.11'
cache: 'pip'
- name: Install Python packages
run: |
python3 -m pip install --upgrade pip setuptools types-six black==23.1.0 mypy isort clingo flake8
pip install --upgrade pip setuptools
pip install -r .github/workflows/style/requirements.txt
- name: Setup git configuration
run: |
# Need this for the git tests to succeed.
@@ -68,7 +69,7 @@ jobs:
dnf install -y \
bzip2 curl file gcc-c++ gcc gcc-gfortran git gnupg2 gzip \
make patch tcl unzip which xz
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # @v2
- name: Setup repo and non-root user
run: |
git --version

View File

@@ -15,10 +15,10 @@ jobs:
unit-tests:
runs-on: windows-latest
steps:
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
with:
fetch-depth: 0
- uses: actions/setup-python@61a6322f88396a6271a6ee3565807d608ecaddd1
- uses: actions/setup-python@65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236
with:
python-version: 3.9
- name: Install Python packages
@@ -39,10 +39,10 @@ jobs:
unit-tests-cmd:
runs-on: windows-latest
steps:
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
with:
fetch-depth: 0
- uses: actions/setup-python@61a6322f88396a6271a6ee3565807d608ecaddd1
- uses: actions/setup-python@65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236
with:
python-version: 3.9
- name: Install Python packages
@@ -63,10 +63,10 @@ jobs:
build-abseil:
runs-on: windows-latest
steps:
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
with:
fetch-depth: 0
- uses: actions/setup-python@61a6322f88396a6271a6ee3565807d608ecaddd1
- uses: actions/setup-python@65d7f2d534ac1bc67fcd62888c5f4f3d2cb2b236
with:
python-version: 3.9
- name: Install Python packages
@@ -75,6 +75,5 @@ jobs:
- name: Build Test
run: |
spack compiler find
spack external find cmake
spack external find ninja
spack -d external find cmake ninja
spack -d install abseil-cpp

View File

@@ -1,3 +1,33 @@
# v0.20.3 (2023-10-31)
## Bugfixes
- Fix a bug where `spack mirror set-url` would drop configured connection info (reverts #34210)
- Fix a minor issue with package hash computation for Python 3.12 (#40328)
# v0.20.2 (2023-10-03)
## Features in this release
Spack now supports Python 3.12 (#40155)
## Bugfixes
- Improve escaping in Tcl module files (#38375)
- Make repo cache work on repositories with zero mtime (#39214)
- Ignore errors for newer, incompatible buildcache version (#40279)
- Print an error when git is required, but missing (#40254)
- Ensure missing build dependencies get installed when using `spack install --overwrite` (#40252)
- Fix an issue where Spack freezes when the build process unexpectedly exits (#39015)
- Fix a bug where installation failures cause an unrelated `NameError` to be thrown (#39017)
- Fix an issue where Spack package versions would be incorrectly derived from git tags (#39414)
- Fix a bug triggered when file locking fails internally (#39188)
- Prevent "spack external find" to error out when a directory cannot be accessed (#38755)
- Fix multiple performance regressions in environments (#38771)
- Add more ignored modules to `pyproject.toml` for `mypy` (#38769)
# v0.20.1 (2023-07-10)
## Spack Bugfixes

View File

@@ -27,12 +27,53 @@
# And here's the CITATION.cff format:
#
cff-version: 1.2.0
type: software
message: "If you are referencing Spack in a publication, please cite the paper below."
title: "The Spack Package Manager: Bringing Order to HPC Software Chaos"
abstract: >-
Large HPC centers spend considerable time supporting software for thousands of users, but the complexity of HPC software is quickly outpacing the capabilities of existing software management tools.
Scientific applications require specific versions of compilers, MPI, and other dependency libraries, so using a single, standard software stack is infeasible.
However, managing many configurations is difficult because the configuration space is combinatorial in size.
We introduce Spack, a tool used at Lawrence Livermore National Laboratory to manage this complexity.
Spack provides a novel, re- cursive specification syntax to invoke parametric builds of packages and dependencies.
It allows any number of builds to coexist on the same system, and it ensures that installed packages can find their dependencies, regardless of the environment.
We show through real-world use cases that Spack supports diverse and demanding applications, bringing order to HPC software chaos.
preferred-citation:
title: "The Spack Package Manager: Bringing Order to HPC Software Chaos"
type: conference-paper
doi: "10.1145/2807591.2807623"
url: "https://github.com/spack/spack"
url: "https://tgamblin.github.io/pubs/spack-sc15.pdf"
authors:
- family-names: "Gamblin"
given-names: "Todd"
- family-names: "LeGendre"
given-names: "Matthew"
- family-names: "Collette"
given-names: "Michael R."
- family-names: "Lee"
given-names: "Gregory L."
- family-names: "Moody"
given-names: "Adam"
- family-names: "de Supinski"
given-names: "Bronis R."
- family-names: "Futral"
given-names: "Scott"
conference:
name: "Supercomputing 2015 (SC15)"
city: "Austin"
region: "Texas"
country: "US"
date-start: 2015-11-15
date-end: 2015-11-20
month: 11
year: 2015
identifiers:
- description: "The concept DOI of the work."
type: doi
value: 10.1145/2807591.2807623
- description: "The DOE Document Release Number of the work"
type: other
value: "LLNL-CONF-669890"
authors:
- family-names: "Gamblin"
given-names: "Todd"
- family-names: "LeGendre"
@@ -47,12 +88,3 @@ preferred-citation:
given-names: "Bronis R."
- family-names: "Futral"
given-names: "Scott"
title: "The Spack Package Manager: Bringing Order to HPC Software Chaos"
conference:
name: "Supercomputing 2015 (SC15)"
city: "Austin"
region: "Texas"
country: "USA"
month: November 15-20
year: 2015
notes: LLNL-CONF-669890

View File

@@ -7,6 +7,7 @@
[![Read the Docs](https://readthedocs.org/projects/spack/badge/?version=latest)](https://spack.readthedocs.io)
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
[![Slack](https://slack.spack.io/badge.svg)](https://slack.spack.io)
[![Matrix](https://img.shields.io/matrix/spack-space%3Amatrix.org?label=Matrix)](https://matrix.to/#/#spack-space:matrix.org)
Spack is a multi-platform package manager that builds and installs
multiple versions and configurations of software. It works on Linux,
@@ -62,7 +63,10 @@ Resources:
* **Slack workspace**: [spackpm.slack.com](https://spackpm.slack.com).
To get an invitation, visit [slack.spack.io](https://slack.spack.io).
* [**Github Discussions**](https://github.com/spack/spack/discussions): not just for discussions, also Q&A.
* **Matrix space**: [#spack-space:matrix.org](https://matrix.to/#/#spack-space:matrix.org):
[bridged](https://github.com/matrix-org/matrix-appservice-slack#matrix-appservice-slack) to Slack.
* [**Github Discussions**](https://github.com/spack/spack/discussions):
not just for discussions, but also Q&A.
* **Mailing list**: [groups.google.com/d/forum/spack](https://groups.google.com/d/forum/spack)
* **Twitter**: [@spackpm](https://twitter.com/spackpm). Be sure to
`@mention` us!

View File

@@ -2,24 +2,26 @@
## Supported Versions
We provide security updates for the following releases.
We provide security updates for `develop` and for the last two
stable (`0.x`) release series of Spack. Security updates will be
made available as patch (`0.x.1`, `0.x.2`, etc.) releases.
For more on Spack's release structure, see
[`README.md`](https://github.com/spack/spack#releases).
| Version | Supported |
| ------- | ------------------ |
| develop | :white_check_mark: |
| 0.19.x | :white_check_mark: |
| 0.18.x | :white_check_mark: |
## Reporting a Vulnerability
To report a vulnerability or other security
issue, email maintainers@spack.io.
You can report a vulnerability using GitHub's private reporting
feature:
You can expect to hear back within two days.
If your security issue is accepted, we will do
our best to release a fix within a week. If
fixing the issue will take longer than this,
we will discuss timeline options with you.
1. Go to [github.com/spack/spack/security](https://github.com/spack/spack/security).
2. Click "Report a vulnerability" in the upper right corner of that page.
3. Fill out the form and submit your draft security advisory.
More details are available in
[GitHub's docs](https://docs.github.com/en/code-security/security-advisories/guidance-on-reporting-and-writing/privately-reporting-a-security-vulnerability).
You can expect to hear back about security issues within two days.
If your security issue is accepted, we will do our best to release
a fix within a week. If fixing the issue will take longer than
this, we will discuss timeline options with you.

View File

@@ -14,7 +14,7 @@
::
@echo off
set spack=%SPACK_ROOT%\bin\spack
set spack="%SPACK_ROOT%"\bin\spack
::#######################################################################
:: This is a wrapper around the spack command that forwards calls to
@@ -51,65 +51,43 @@ setlocal enabledelayedexpansion
:: subcommands will never start with '-'
:: everything after the subcommand is an arg
:: we cannot allow batch "for" loop to directly process CL args
:: a number of batch reserved characters are commonly passed to
:: spack and allowing batch's "for" method to process the raw inputs
:: results in a large number of formatting issues
:: instead, treat the entire CLI as one string
:: and split by space manually
:: capture cl args in variable named cl_args
set cl_args=%*
:process_cl_args
rem tokens=1* returns the first processed token produced
rem by tokenizing the input string cl_args on spaces into
rem the named variable %%g
rem While this make look like a for loop, it only
rem executes a single time for each of the cl args
rem the actual iterative loop is performed by the
rem goto process_cl_args stanza
rem we are simply leveraging the "for" method's string
rem tokenization
for /f "tokens=1*" %%g in ("%cl_args%") do (
set t=%%~g
rem remainder of string is composed into %%h
rem these are the cl args yet to be processed
rem assign cl_args var to only the args to be processed
rem effectively discarding the current arg %%g
rem this will be nul when we have no further tokens to process
set cl_args=%%h
rem process the first space delineated cl arg
rem of this iteration
if "!t:~0,1!" == "-" (
if defined _sp_subcommand (
rem We already have a subcommand, processing args now
if not defined _sp_args (
set "_sp_args=!t!"
) else (
set "_sp_args=!_sp_args! !t!"
)
) else (
if not defined _sp_flags (
set "_sp_flags=!t!"
shift
) else (
set "_sp_flags=!_sp_flags! !t!"
shift
)
)
) else if not defined _sp_subcommand (
set "_sp_subcommand=!t!"
shift
) else (
rem Set first cl argument (denoted by %1) to be processed
set t=%1
rem shift moves all cl positional arguments left by one
rem meaning %2 is now %1, this allows us to iterate over each
rem argument
shift
rem assign next "first" cl argument to cl_args, will be null when
rem there are now further arguments to process
set cl_args=%1
if "!t:~0,1!" == "-" (
if defined _sp_subcommand (
rem We already have a subcommand, processing args now
if not defined _sp_args (
set "_sp_args=!t!"
shift
) else (
set "_sp_args=!_sp_args! !t!"
shift
)
) else (
if not defined _sp_flags (
set "_sp_flags=!t!"
) else (
set "_sp_flags=!_sp_flags! !t!"
)
)
) else if not defined _sp_subcommand (
set "_sp_subcommand=!t!"
) else (
if not defined _sp_args (
set "_sp_args=!t!"
) else (
set "_sp_args=!_sp_args! !t!"
)
)
rem if this is not nil, we have more tokens to process
rem if this is not nu;ll, we have more tokens to process
rem start above process again with remaining unprocessed cl args
if defined cl_args goto :process_cl_args

View File

@@ -39,12 +39,26 @@ function Read-SpackArgs {
return $SpackCMD_params, $SpackSubCommand, $SpackSubCommandArgs
}
function Set-SpackEnv {
# This method is responsible
# for processing the return from $(spack <command>)
# which are returned as System.Object[]'s containing
# a list of env commands
# Invoke-Expression can only handle one command at a time
# so we iterate over the list to invoke the env modification
# expressions one at a time
foreach($envop in $args[0]){
Invoke-Expression $envop
}
}
function Invoke-SpackCD {
if (Compare-CommonArgs $SpackSubCommandArgs) {
python $Env:SPACK_ROOT/bin/spack cd -h
python "$Env:SPACK_ROOT/bin/spack" cd -h
}
else {
$LOC = $(python $Env:SPACK_ROOT/bin/spack location $SpackSubCommandArgs)
$LOC = $(python "$Env:SPACK_ROOT/bin/spack" location $SpackSubCommandArgs)
if (($NULL -ne $LOC)){
if ( Test-Path -Path $LOC){
Set-Location $LOC
@@ -61,7 +75,7 @@ function Invoke-SpackCD {
function Invoke-SpackEnv {
if (Compare-CommonArgs $SpackSubCommandArgs[0]) {
python $Env:SPACK_ROOT/bin/spack env -h
python "$Env:SPACK_ROOT/bin/spack" env -h
}
else {
$SubCommandSubCommand = $SpackSubCommandArgs[0]
@@ -69,46 +83,46 @@ function Invoke-SpackEnv {
switch ($SubCommandSubCommand) {
"activate" {
if (Compare-CommonArgs $SubCommandSubCommandArgs) {
python $Env:SPACK_ROOT/bin/spack env activate $SubCommandSubCommandArgs
python "$Env:SPACK_ROOT/bin/spack" env activate $SubCommandSubCommandArgs
}
elseif ([bool]($SubCommandSubCommandArgs.Where({$_ -eq "--pwsh"}))) {
python $Env:SPACK_ROOT/bin/spack env activate $SubCommandSubCommandArgs
python "$Env:SPACK_ROOT/bin/spack" env activate $SubCommandSubCommandArgs
}
elseif (!$SubCommandSubCommandArgs) {
python $Env:SPACK_ROOT/bin/spack env activate $SubCommandSubCommandArgs
python "$Env:SPACK_ROOT/bin/spack" env activate $SubCommandSubCommandArgs
}
else {
$SpackEnv = $(python $Env:SPACK_ROOT/bin/spack $SpackCMD_params env activate "--pwsh" $SubCommandSubCommandArgs)
$ExecutionContext.InvokeCommand($SpackEnv)
$SpackEnv = $(python "$Env:SPACK_ROOT/bin/spack" $SpackCMD_params env activate "--pwsh" $SubCommandSubCommandArgs)
Set-SpackEnv $SpackEnv
}
}
"deactivate" {
if ([bool]($SubCommandSubCommandArgs.Where({$_ -eq "--pwsh"}))) {
python $Env:SPACK_ROOT/bin/spack env deactivate $SubCommandSubCommandArgs
python"$Env:SPACK_ROOT/bin/spack" env deactivate $SubCommandSubCommandArgs
}
elseif($SubCommandSubCommandArgs) {
python $Env:SPACK_ROOT/bin/spack env deactivate -h
python "$Env:SPACK_ROOT/bin/spack" env deactivate -h
}
else {
$SpackEnv = $(python $Env:SPACK_ROOT/bin/spack $SpackCMD_params env deactivate --pwsh)
$ExecutionContext.InvokeCommand($SpackEnv)
$SpackEnv = $(python "$Env:SPACK_ROOT/bin/spack" $SpackCMD_params env deactivate "--pwsh")
Set-SpackEnv $SpackEnv
}
}
default {python $Env:SPACK_ROOT/bin/spack $SpackCMD_params $SpackSubCommand $SpackSubCommandArgs}
default {python "$Env:SPACK_ROOT/bin/spack" $SpackCMD_params $SpackSubCommand $SpackSubCommandArgs}
}
}
}
function Invoke-SpackLoad {
if (Compare-CommonArgs $SpackSubCommandArgs) {
python $Env:SPACK_ROOT/bin/spack $SpackCMD_params $SpackSubCommand $SpackSubCommandArgs
python "$Env:SPACK_ROOT/bin/spack" $SpackCMD_params $SpackSubCommand $SpackSubCommandArgs
}
elseif ([bool]($SpackSubCommandArgs.Where({($_ -eq "--pwsh") -or ($_ -eq "--list")}))) {
python $Env:SPACK_ROOT/bin/spack $SpackCMD_params $SpackSubCommand $SpackSubCommandArgs
python "$Env:SPACK_ROOT/bin/spack" $SpackCMD_params $SpackSubCommand $SpackSubCommandArgs
}
else {
$SpackEnv = $(python $Env:SPACK_ROOT/bin/spack $SpackCMD_params $SpackSubCommand "--pwsh" $SpackSubCommandArgs)
$ExecutionContext.InvokeCommand($SpackEnv)
$SpackEnv = $(python "$Env:SPACK_ROOT/bin/spack" $SpackCMD_params $SpackSubCommand "--pwsh" $SpackSubCommandArgs)
Set-SpackEnv $SpackEnv
}
}
@@ -116,7 +130,7 @@ function Invoke-SpackLoad {
$SpackCMD_params, $SpackSubCommand, $SpackSubCommandArgs = Read-SpackArgs $args
if (Compare-CommonArgs $SpackCMD_params) {
python $Env:SPACK_ROOT/bin/spack $SpackCMD_params $SpackSubCommand $SpackSubCommandArgs
python "$Env:SPACK_ROOT/bin/spack" $SpackCMD_params $SpackSubCommand $SpackSubCommandArgs
exit $LASTEXITCODE
}
@@ -128,5 +142,5 @@ switch($SpackSubCommand)
"env" {Invoke-SpackEnv}
"load" {Invoke-SpackLoad}
"unload" {Invoke-SpackLoad}
default {python $Env:SPACK_ROOT/bin/spack $SpackCMD_params $SpackSubCommand $SpackSubCommandArgs}
default {python "$Env:SPACK_ROOT/bin/spack" $SpackCMD_params $SpackSubCommand $SpackSubCommandArgs}
}

View File

@@ -9,15 +9,15 @@ bootstrap:
# may not be able to bootstrap all the software that Spack needs,
# depending on its type.
sources:
- name: 'github-actions-v0.5'
metadata: $spack/share/spack/bootstrap/github-actions-v0.5
- name: 'github-actions-v0.4'
metadata: $spack/share/spack/bootstrap/github-actions-v0.4
- name: 'github-actions-v0.3'
metadata: $spack/share/spack/bootstrap/github-actions-v0.3
- name: 'spack-install'
metadata: $spack/share/spack/bootstrap/spack-install
trusted:
# By default we trust bootstrapping from sources and from binaries
# produced on Github via the workflow
github-actions-v0.5: true
github-actions-v0.4: true
github-actions-v0.3: true
spack-install: true

View File

@@ -41,4 +41,4 @@ concretizer:
# "none": allows a single node for any package in the DAG.
# "minimal": allows the duplication of 'build-tools' nodes only (e.g. py-setuptools, cmake etc.)
# "full" (experimental): allows separation of the entire build-tool stack (e.g. the entire "cmake" subDAG)
strategy: none
strategy: minimal

View File

@@ -229,3 +229,11 @@ config:
flags:
# Whether to keep -Werror flags active in package builds.
keep_werror: 'none'
# A mapping of aliases that can be used to define new commands. For instance,
# `sp: spec -I` will define a new command `sp` that will execute `spec` with
# the `-I` argument. Aliases cannot override existing commands.
aliases:
concretise: concretize
containerise: containerize
rm: remove

View File

@@ -60,7 +60,7 @@ packages:
xxd: [xxd-standalone, vim]
yacc: [bison, byacc]
ziglang: [zig]
zlib-api: [zlib, zlib-ng+compat]
zlib-api: [zlib-ng+compat, zlib]
permissions:
read: world
write: user

View File

@@ -1,4 +1,3 @@
package_list.html
command_index.rst
spack*.rst
llnl*.rst

View File

@@ -45,7 +45,8 @@ Listing available packages
To install software with Spack, you need to know what software is
available. You can see a list of available package names at the
:ref:`package-list` webpage, or using the ``spack list`` command.
`packages.spack.io <https://packages.spack.io>`_ website, or
using the ``spack list`` command.
.. _cmd-spack-list:
@@ -60,7 +61,7 @@ can install:
:ellipsis: 10
There are thousands of them, so we've truncated the output above, but you
can find a :ref:`full list here <package-list>`.
can find a `full list here <https://packages.spack.io>`_.
Packages are listed by name in alphabetical order.
A pattern to match with no wildcards, ``*`` or ``?``,
will be treated as though it started and ended with
@@ -1525,6 +1526,30 @@ any MPI implementation will do. If another package depends on
error. Likewise, if you try to plug in some package that doesn't
provide MPI, Spack will raise an error.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Explicit binding of virtual dependencies
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
There are packages that provide more than just one virtual dependency. When interacting with them, users
might want to utilize just a subset of what they could provide, and use other providers for virtuals they
need.
It is possible to be more explicit and tell Spack which dependency should provide which virtual, using a
special syntax:
.. code-block:: console
$ spack spec strumpack ^[virtuals=mpi] intel-parallel-studio+mkl ^[virtuals=lapack] openblas
Concretizing the spec above produces the following DAG:
.. figure:: images/strumpack_virtuals.svg
:scale: 60 %
:align: center
where ``intel-parallel-studio`` *could* provide ``mpi``, ``lapack``, and ``blas`` but is used only for the former. The ``lapack``
and ``blas`` dependencies are satisfied by ``openblas``.
^^^^^^^^^^^^^^^^^^^^^^^^
Specifying Specs by Hash
^^^^^^^^^^^^^^^^^^^^^^^^

View File

@@ -155,16 +155,182 @@ List of popular build caches
* `Extreme-scale Scientific Software Stack (E4S) <https://e4s-project.github.io/>`_: `build cache <https://oaciss.uoregon.edu/e4s/inventory.html>`_
----------
Relocation
----------
Initial build and later installation do not necessarily happen at the same
location. Spack provides a relocation capability and corrects for RPATHs and
non-relocatable scripts. However, many packages compile paths into binary
artifacts directly. In such cases, the build instructions of this package would
need to be adjusted for better re-locatability.
When using buildcaches across different machines, it is likely that the install
root will be different from the one used to build the binaries.
To address this issue, Spack automatically relocates all paths encoded in binaries
and scripts to their new location upon install.
Note that there are some cases where this is not possible: if binaries are built in
a relatively short path, and then installed to a longer path, there may not be enough
space in the binary to encode the new path. In this case, Spack will fail to install
the package from the build cache, and a source build is required.
To reduce the likelihood of this happening, it is highly recommended to add padding to
the install root during the build, as specified in the :ref:`config <config-yaml>`
section of the configuration:
.. code-block:: yaml
config:
install_tree:
root: /opt/spack
padded_length: 128
-----------------------------------------
OCI / Docker V2 registries as build cache
-----------------------------------------
Spack can also use OCI or Docker V2 registries such as Dockerhub, Quay.io,
Github Packages, GitLab Container Registry, JFrog Artifactory, and others
as build caches. This is a convenient way to share binaries using public
infrastructure, or to cache Spack built binaries in Github Actions and
GitLab CI.
To get started, configure an OCI mirror using ``oci://`` as the scheme,
and optionally specify a username and password (or personal access token):
.. code-block:: console
$ spack mirror add --oci-username username --oci-password password my_registry oci://example.com/my_image
Spack follows the naming conventions of Docker, with Dockerhub as the default
registry. To use Dockerhub, you can omit the registry domain:
.. code-block:: console
$ spack mirror add --oci-username username --oci-password password my_registry oci://username/my_image
From here, you can use the mirror as any other build cache:
.. code-block:: console
$ spack buildcache push my_registry <specs...> # push to the registry
$ spack install <specs...> # install from the registry
A unique feature of buildcaches on top of OCI registries is that it's incredibly
easy to generate get a runnable container image with the binaries installed. This
is a great way to make applications available to users without requiring them to
install Spack -- all you need is Docker, Podman or any other OCI-compatible container
runtime.
To produce container images, all you need to do is add the ``--base-image`` flag
when pushing to the build cache:
.. code-block:: console
$ spack buildcache push --base-image ubuntu:20.04 my_registry ninja
Pushed to example.com/my_image:ninja-1.11.1-yxferyhmrjkosgta5ei6b4lqf6bxbscz.spack
$ docker run -it example.com/my_image:ninja-1.11.1-yxferyhmrjkosgta5ei6b4lqf6bxbscz.spack
root@e4c2b6f6b3f4:/# ninja --version
1.11.1
If ``--base-image`` is not specified, distroless images are produced. In practice,
you won't be able to run these as containers, since they don't come with libc and
other system dependencies. However, they are still compatible with tools like
``skopeo``, ``podman``, and ``docker`` for pulling and pushing.
.. note::
The docker ``overlayfs2`` storage driver is limited to 128 layers, above which a
``max depth exceeded`` error may be produced when pulling the image. There
are `alternative drivers <https://docs.docker.com/storage/storagedriver/>`_.
------------------------------------
Spack build cache for GitHub Actions
------------------------------------
To significantly speed up Spack in GitHub Actions, binaries can be cached in
GitHub Packages. This service is an OCI registry that can be linked to a GitHub
repository.
A typical workflow is to include a ``spack.yaml`` environment in your repository
that specifies the packages to install, the target architecture, and the build
cache to use under ``mirrors``:
.. code-block:: yaml
spack:
specs:
- python@3.11
config:
install_tree:
root: /opt/spack
padded_length: 128
packages:
all:
require: target=x86_64_v2
mirrors:
local-buildcache: oci://ghcr.io/<organization>/<repository>
A GitHub action can then be used to install the packages and push them to the
build cache:
.. code-block:: yaml
name: Install Spack packages
on: push
env:
SPACK_COLOR: always
jobs:
example:
runs-on: ubuntu-22.04
permissions:
packages: write
steps:
- name: Checkout
uses: actions/checkout@v3
- name: Checkout Spack
uses: actions/checkout@v3
with:
repository: spack/spack
path: spack
- name: Setup Spack
run: echo "$PWD/spack/bin" >> "$GITHUB_PATH"
- name: Concretize
run: spack -e . concretize
- name: Install
run: spack -e . install --no-check-signature
- name: Run tests
run: ./my_view/bin/python3 -c 'print("hello world")'
- name: Push to buildcache
run: |
spack -e . mirror set --oci-username ${{ github.actor }} --oci-password "${{ secrets.GITHUB_TOKEN }}" local-buildcache
spack -e . buildcache push --base-image ubuntu:22.04 --unsigned --update-index local-buildcache
if: ${{ !cancelled() }}
The first time this action runs, it will build the packages from source and
push them to the build cache. Subsequent runs will pull the binaries from the
build cache. The concretizer will ensure that prebuilt binaries are favored
over source builds.
The build cache entries appear in the GitHub Packages section of your repository,
and contain instructions for pulling and running them with ``docker`` or ``podman``.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Using Spack's public build cache for GitHub Actions
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Spack offers a public build cache for GitHub Actions with a set of common packages,
which lets you get started quickly. See the following resources for more information:
* `spack/github-actions-buildcache <https://github.com/spack/github-actions-buildcache>`_
.. _cmd-spack-buildcache:

View File

@@ -3,6 +3,103 @@
SPDX-License-Identifier: (Apache-2.0 OR MIT)
.. _concretizer-options:
==========================================
Concretization Settings (concretizer.yaml)
==========================================
The ``concretizer.yaml`` configuration file allows to customize aspects of the
algorithm used to select the dependencies you install. The default configuration
is the following:
.. literalinclude:: _spack_root/etc/spack/defaults/concretizer.yaml
:language: yaml
--------------------------------
Reuse already installed packages
--------------------------------
The ``reuse`` attribute controls whether Spack will prefer to use installed packages (``true``), or
whether it will do a "fresh" installation and prefer the latest settings from
``package.py`` files and ``packages.yaml`` (``false``).
You can use:
.. code-block:: console
% spack install --reuse <spec>
to enable reuse for a single installation, and you can use:
.. code-block:: console
spack install --fresh <spec>
to do a fresh install if ``reuse`` is enabled by default.
``reuse: true`` is the default.
------------------------------------------
Selection of the target microarchitectures
------------------------------------------
The options under the ``targets`` attribute control which targets are considered during a solve.
Currently the options in this section are only configurable from the ``concretizer.yaml`` file
and there are no corresponding command line arguments to enable them for a single solve.
The ``granularity`` option can take two possible values: ``microarchitectures`` and ``generic``.
If set to:
.. code-block:: yaml
concretizer:
targets:
granularity: microarchitectures
Spack will consider all the microarchitectures known to ``archspec`` to label nodes for
compatibility. If instead the option is set to:
.. code-block:: yaml
concretizer:
targets:
granularity: generic
Spack will consider only generic microarchitectures. For instance, when running on an
Haswell node, Spack will consider ``haswell`` as the best target in the former case and
``x86_64_v3`` as the best target in the latter case.
The ``host_compatible`` option is a Boolean option that determines whether or not the
microarchitectures considered during the solve are constrained to be compatible with the
host Spack is currently running on. For instance, if this option is set to ``true``, a
user cannot concretize for ``target=icelake`` while running on an Haswell node.
---------------
Duplicate nodes
---------------
The ``duplicates`` attribute controls whether the DAG can contain multiple configurations of
the same package. This is mainly relevant for build dependencies, which may have their version
pinned by some nodes, and thus be required at different versions by different nodes in the same
DAG.
The ``strategy`` option controls how the solver deals with duplicates. If the value is ``none``,
then a single configuration per package is allowed in the DAG. This means, for instance, that only
a single ``cmake`` or a single ``py-setuptools`` version is allowed. The result would be a slightly
faster concretization, at the expense of making a few specs unsolvable.
If the value is ``minimal`` Spack will allow packages tagged as ``build-tools`` to have duplicates.
This allows, for instance, to concretize specs whose nodes require different, and incompatible, ranges
of some build tool. For instance, in the figure below the latest `py-shapely` requires a newer `py-setuptools`,
while `py-numpy` still needs an older version:
.. figure:: images/shapely_duplicates.svg
:scale: 70 %
:align: center
Up to Spack v0.20 ``duplicates:strategy:none`` was the default (and only) behavior. From Spack v0.21 the
default behavior is ``duplicates:strategy:minimal``.
.. _build-settings:
================================
@@ -232,76 +329,6 @@ Specific limitations include:
then Spack will not add a new external entry (``spack config blame packages``
can help locate all external entries).
.. _concretizer-options:
----------------------
Concretizer options
----------------------
``packages.yaml`` gives the concretizer preferences for specific packages,
but you can also use ``concretizer.yaml`` to customize aspects of the
algorithm it uses to select the dependencies you install:
.. literalinclude:: _spack_root/etc/spack/defaults/concretizer.yaml
:language: yaml
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Reuse already installed packages
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The ``reuse`` attribute controls whether Spack will prefer to use installed packages (``true``), or
whether it will do a "fresh" installation and prefer the latest settings from
``package.py`` files and ``packages.yaml`` (``false``).
You can use:
.. code-block:: console
% spack install --reuse <spec>
to enable reuse for a single installation, and you can use:
.. code-block:: console
spack install --fresh <spec>
to do a fresh install if ``reuse`` is enabled by default.
``reuse: true`` is the default.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Selection of the target microarchitectures
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The options under the ``targets`` attribute control which targets are considered during a solve.
Currently the options in this section are only configurable from the ``concretizer.yaml`` file
and there are no corresponding command line arguments to enable them for a single solve.
The ``granularity`` option can take two possible values: ``microarchitectures`` and ``generic``.
If set to:
.. code-block:: yaml
concretizer:
targets:
granularity: microarchitectures
Spack will consider all the microarchitectures known to ``archspec`` to label nodes for
compatibility. If instead the option is set to:
.. code-block:: yaml
concretizer:
targets:
granularity: generic
Spack will consider only generic microarchitectures. For instance, when running on an
Haswell node, Spack will consider ``haswell`` as the best target in the former case and
``x86_64_v3`` as the best target in the latter case.
The ``host_compatible`` option is a Boolean option that determines whether or not the
microarchitectures considered during the solve are constrained to be compatible with the
host Spack is currently running on. For instance, if this option is set to ``true``, a
user cannot concretize for ``target=icelake`` while running on an Haswell node.
.. _package-requirements:
--------------------
@@ -499,56 +526,52 @@ Package Preferences
In some cases package requirements can be too strong, and package
preferences are the better option. Package preferences do not impose
constraints on packages for particular versions or variants values,
they rather only set defaults -- the concretizer is free to change
them if it must due to other constraints. Also note that package
preferences are of lower priority than reuse of already installed
packages.
they rather only set defaults. The concretizer is free to change
them if it must, due to other constraints, and also prefers reusing
installed packages over building new ones that are a better match for
preferences.
Here's an example ``packages.yaml`` file that sets preferred packages:
Most package preferences (``compilers``, ``target`` and ``providers``)
can only be set globally under the ``all`` section of ``packages.yaml``:
.. code-block:: yaml
packages:
all:
compiler: [gcc@12.2.0, clang@12:, oneapi@2023:]
target: [x86_64_v3]
providers:
mpi: [mvapich2, mpich, openmpi]
These preferences override Spack's default and effectively reorder priorities
when looking for the best compiler, target or virtual package provider. Each
preference takes an ordered list of spec constraints, with earlier entries in
the list being preferred over later entries.
In the example above all packages prefer to be compiled with ``gcc@12.2.0``,
to target the ``x86_64_v3`` microarchitecture and to use ``mvapich2`` if they
depend on ``mpi``.
The ``variants`` and ``version`` preferences can be set under
package specific sections of the ``packages.yaml`` file:
.. code-block:: yaml
packages:
opencv:
compiler: [gcc@4.9]
variants: +debug
gperftools:
version: [2.2, 2.4, 2.3]
all:
compiler: [gcc@4.4.7, 'gcc@4.6:', intel, clang, pgi]
target: [sandybridge]
providers:
mpi: [mvapich2, mpich, openmpi]
At a high level, this example is specifying how packages are preferably
concretized. The opencv package should prefer using GCC 4.9 and
be built with debug options. The gperftools package should prefer version
2.2 over 2.4. Every package on the system should prefer mvapich2 for
its MPI and GCC 4.4.7 (except for opencv, which overrides this by preferring GCC 4.9).
These options are used to fill in implicit defaults. Any of them can be overwritten
on the command line if explicitly requested.
In this case, the preference for ``opencv`` is to build with debug options, while
``gperftools`` prefers version 2.2 over 2.4.
Package preferences accept the follow keys or components under
the specific package (or ``all``) section: ``compiler``, ``variants``,
``version``, ``providers``, and ``target``. Each component has an
ordered list of spec ``constraints``, with earlier entries in the
list being preferred over later entries.
Any preference can be overwritten on the command line if explicitly requested.
Sometimes a package installation may have constraints that forbid
the first concretization rule, in which case Spack will use the first
legal concretization rule. Going back to the example, if a user
requests gperftools 2.3 or later, then Spack will install version 2.4
as the 2.4 version of gperftools is preferred over 2.3.
An explicit concretization rule in the preferred section will always
take preference over unlisted concretizations. In the above example,
xlc isn't listed in the compiler list. Every listed compiler from
gcc to pgi will thus be preferred over the xlc compiler.
The syntax for the ``provider`` section differs slightly from other
concretization rules. A provider lists a value that packages may
``depends_on`` (e.g, MPI) and a list of rules for fulfilling that
dependency.
Preferences cannot overcome explicit constraints, as they only set a preferred
ordering among homogeneous attribute values. Going back to the example, if
``gperftools@2.3:`` was requested, then Spack will install version 2.4
since the most preferred version 2.2 is prohibited by the version constraint.
.. _package_permissions:

View File

@@ -127,9 +127,9 @@ check out a commit from the ``master`` branch, you would want to add:
.. code-block:: python
depends_on('autoconf', type='build', when='@master')
depends_on('automake', type='build', when='@master')
depends_on('libtool', type='build', when='@master')
depends_on("autoconf", type="build", when="@master")
depends_on("automake", type="build", when="@master")
depends_on("libtool", type="build", when="@master")
It is typically redundant to list the ``m4`` macro processor package as a
dependency, since ``autoconf`` already depends on it.
@@ -145,7 +145,7 @@ example, the ``bash`` shell is used to run the ``autogen.sh`` script.
.. code-block:: python
def autoreconf(self, spec, prefix):
which('bash')('autogen.sh')
which("bash")("autogen.sh")
"""""""""""""""""""""""""""""""""""""""
patching configure or Makefile.in files
@@ -186,9 +186,9 @@ To opt out of this feature, use the following setting:
To enable it conditionally on different architectures, define a property and
make the package depend on ``gnuconfig`` as a build dependency:
.. code-block
.. code-block:: python
depends_on('gnuconfig', when='@1.0:')
depends_on("gnuconfig", when="@1.0:")
@property
def patch_config_files(self):
@@ -230,7 +230,7 @@ version, this can be done like so:
@property
def force_autoreconf(self):
return self.version == Version('1.2.3')
return self.version == Version("1.2.3")
^^^^^^^^^^^^^^^^^^^^^^^
Finding configure flags
@@ -278,13 +278,22 @@ function like so:
def configure_args(self):
args = []
if '+mpi' in self.spec:
args.append('--enable-mpi')
if self.spec.satisfies("+mpi"):
args.append("--enable-mpi")
else:
args.append('--disable-mpi')
args.append("--disable-mpi")
return args
Alternatively, you can use the :ref:`enable_or_disable <autotools_enable_or_disable>` helper:
.. code-block:: python
def configure_args(self):
return [self.enable_or_disable("mpi")]
Note that we are explicitly disabling MPI support if it is not
requested. This is important, as many Autotools packages will enable
options by default if the dependencies are found, and disable them
@@ -295,9 +304,11 @@ and `here <https://wiki.gentoo.org/wiki/Project:Quality_Assurance/Automagic_depe
for a rationale as to why these so-called "automagic" dependencies
are a problem.
By default, Autotools installs packages to ``/usr``. We don't want this,
so Spack automatically adds ``--prefix=/path/to/installation/prefix``
to your list of ``configure_args``. You don't need to add this yourself.
.. note::
By default, Autotools installs packages to ``/usr``. We don't want this,
so Spack automatically adds ``--prefix=/path/to/installation/prefix``
to your list of ``configure_args``. You don't need to add this yourself.
^^^^^^^^^^^^^^^^
Helper functions
@@ -308,6 +319,8 @@ You may have noticed that most of the Autotools flags are of the form
``--without-baz``. Since these flags are so common, Spack provides a
couple of helper functions to make your life easier.
.. _autotools_enable_or_disable:
"""""""""""""""""
enable_or_disable
"""""""""""""""""
@@ -319,11 +332,11 @@ typically used to enable or disable some feature within the package.
.. code-block:: python
variant(
'memchecker',
"memchecker",
default=False,
description='Memchecker support for debugging [degrades performance]'
description="Memchecker support for debugging [degrades performance]"
)
config_args.extend(self.enable_or_disable('memchecker'))
config_args.extend(self.enable_or_disable("memchecker"))
In this example, specifying the variant ``+memchecker`` will generate
the following configuration options:
@@ -343,15 +356,15 @@ the ``with_or_without`` method.
.. code-block:: python
variant(
'schedulers',
"schedulers",
values=disjoint_sets(
('auto',), ('alps', 'lsf', 'tm', 'slurm', 'sge', 'loadleveler')
).with_non_feature_values('auto', 'none'),
("auto",), ("alps", "lsf", "tm", "slurm", "sge", "loadleveler")
).with_non_feature_values("auto", "none"),
description="List of schedulers for which support is enabled; "
"'auto' lets openmpi determine",
)
if 'schedulers=auto' not in spec:
config_args.extend(self.with_or_without('schedulers'))
if not spec.satisfies("schedulers=auto"):
config_args.extend(self.with_or_without("schedulers"))
In this example, specifying the variant ``schedulers=slurm,sge`` will
generate the following configuration options:
@@ -376,16 +389,16 @@ generated, using the ``activation_value`` argument to
.. code-block:: python
variant(
'fabrics',
"fabrics",
values=disjoint_sets(
('auto',), ('psm', 'psm2', 'verbs', 'mxm', 'ucx', 'libfabric')
).with_non_feature_values('auto', 'none'),
("auto",), ("psm", "psm2", "verbs", "mxm", "ucx", "libfabric")
).with_non_feature_values("auto", "none"),
description="List of fabrics that are enabled; "
"'auto' lets openmpi determine",
)
if 'fabrics=auto' not in spec:
config_args.extend(self.with_or_without('fabrics',
activation_value='prefix'))
if not spec.satisfies("fabrics=auto"):
config_args.extend(self.with_or_without("fabrics",
activation_value="prefix"))
``activation_value`` accepts a callable that generates the configure
parameter value given the variant value; but the special value
@@ -409,16 +422,16 @@ When Spack variants and configure flags do not correspond one-to-one, the
.. code-block:: python
variant('debug_tools', default=False)
config_args += self.enable_or_disable('debug-tools', variant='debug_tools')
variant("debug_tools", default=False)
config_args += self.enable_or_disable("debug-tools", variant="debug_tools")
Or when one variant controls multiple flags:
.. code-block:: python
variant('debug_tools', default=False)
config_args += self.with_or_without('memchecker', variant='debug_tools')
config_args += self.with_or_without('profiler', variant='debug_tools')
variant("debug_tools", default=False)
config_args += self.with_or_without("memchecker", variant="debug_tools")
config_args += self.with_or_without("profiler", variant="debug_tools")
""""""""""""""""""""
@@ -432,8 +445,8 @@ For example:
.. code-block:: python
variant('profiler', when='@2.0:')
config_args += self.with_or_without('profiler')
variant("profiler", when="@2.0:")
config_args += self.with_or_without("profiler")
will neither add ``--with-profiler`` nor ``--without-profiler`` when the version is
below ``2.0``.
@@ -452,10 +465,10 @@ the variant values require atypical behavior.
def with_or_without_verbs(self, activated):
# Up through version 1.6, this option was named --with-openib.
# In version 1.7, it was renamed to be --with-verbs.
opt = 'verbs' if self.spec.satisfies('@1.7:') else 'openib'
opt = "verbs" if self.spec.satisfies("@1.7:") else "openib"
if not activated:
return '--without-{0}'.format(opt)
return '--with-{0}={1}'.format(opt, self.spec['rdma-core'].prefix)
return f"--without-{opt}"
return f"--with-{opt}={self.spec['rdma-core'].prefix}"
Defining ``with_or_without_verbs`` overrides the behavior of a
``fabrics=verbs`` variant, changing the configure-time option to
@@ -479,7 +492,7 @@ do this like so:
.. code-block:: python
configure_directory = 'src'
configure_directory = "src"
^^^^^^^^^^^^^^^^^^^^^^
Building out of source
@@ -491,7 +504,7 @@ This can be done using the ``build_directory`` variable:
.. code-block:: python
build_directory = 'spack-build'
build_directory = "spack-build"
By default, Spack will build the package in the same directory that
contains the ``configure`` script
@@ -514,8 +527,8 @@ library or build the documentation, you can add these like so:
.. code-block:: python
build_targets = ['all', 'docs']
install_targets = ['install', 'docs']
build_targets = ["all", "docs"]
install_targets = ["install", "docs"]
^^^^^^^
Testing

View File

@@ -9,9 +9,32 @@
Bundle
------
``BundlePackage`` represents a set of packages that are expected to work well
together, such as a collection of commonly used software libraries. The
associated software is specified as bundle dependencies.
``BundlePackage`` represents a set of packages that are expected to work
well together, such as a collection of commonly used software libraries.
The associated software is specified as dependencies.
If it makes sense, variants, conflicts, and requirements can be added to
the package. :ref:`Variants <variants>` ensure that common build options
are consistent across the packages supporting them. :ref:`Conflicts
and requirements <packaging_conflicts>` prevent attempts to build with known
bugs or limitations.
For example, if ``MyBundlePackage`` is known to only build on ``linux``,
it could use the ``require`` directive as follows:
.. code-block:: python
require("platform=linux", msg="MyBundlePackage only builds on linux")
Spack has a number of built-in bundle packages, such as:
* `AmdAocl <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/amd-aocl/package.py>`_
* `EcpProxyApps <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/ecp-proxy-apps/package.py>`_
* `Libc <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/libc/package.py>`_
* `Xsdk <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/xsdk/package.py>`_
where ``Xsdk`` also inherits from ``CudaPackage`` and ``RocmPackage`` and
``Libc`` is a virtual bundle package for the C standard library.
^^^^^^^^

View File

@@ -87,7 +87,7 @@ A typical usage of these methods may look something like this:
.. code-block:: python
def initconfig_mpi_entries(self)
def initconfig_mpi_entries(self):
# Get existing MPI configurations
entries = super(self, Foo).initconfig_mpi_entries()
@@ -95,25 +95,25 @@ A typical usage of these methods may look something like this:
# This spec has an MPI variant, and we need to enable MPI when it is on.
# This hypothetical package controls MPI with the ``FOO_MPI`` option to
# cmake.
if '+mpi' in self.spec:
entries.append(cmake_cache_option('FOO_MPI', True, "enable mpi"))
if self.spec.satisfies("+mpi"):
entries.append(cmake_cache_option("FOO_MPI", True, "enable mpi"))
else:
entries.append(cmake_cache_option('FOO_MPI', False, "disable mpi"))
entries.append(cmake_cache_option("FOO_MPI", False, "disable mpi"))
def initconfig_package_entries(self):
# Package specific options
entries = []
entries.append('#Entries for build options')
entries.append("#Entries for build options")
bar_on = '+bar' in self.spec
entries.append(cmake_cache_option('FOO_BAR', bar_on, 'toggle bar'))
bar_on = self.spec.satisfies("+bar")
entries.append(cmake_cache_option("FOO_BAR", bar_on, "toggle bar"))
entries.append('#Entries for dependencies')
entries.append("#Entries for dependencies")
if self.spec['blas'].name == 'baz': # baz is our blas provider
entries.append(cmake_cache_string('FOO_BLAS', 'baz', 'Use baz'))
entries.append(cmake_cache_path('BAZ_PREFIX', self.spec['baz'].prefix))
if self.spec["blas"].name == "baz": # baz is our blas provider
entries.append(cmake_cache_string("FOO_BLAS", "baz", "Use baz"))
entries.append(cmake_cache_path("BAZ_PREFIX", self.spec["baz"].prefix))
^^^^^^^^^^^^^^^^^^^^^^
External documentation

View File

@@ -54,8 +54,8 @@ to terminate such build attempts with a suitable message:
.. code-block:: python
conflicts('cuda_arch=none', when='+cuda',
msg='CUDA architecture is required')
conflicts("cuda_arch=none", when="+cuda",
msg="CUDA architecture is required")
Similarly, if your software does not support all versions of the property,
you could add ``conflicts`` to your package for those versions. For example,
@@ -66,13 +66,13 @@ custom message should a user attempt such a build:
.. code-block:: python
unsupported_cuda_archs = [
'10', '11', '12', '13',
'20', '21',
'30', '32', '35', '37'
"10", "11", "12", "13",
"20", "21",
"30", "32", "35", "37"
]
for value in unsupported_cuda_archs:
conflicts('cuda_arch={0}'.format(value), when='+cuda',
msg='CUDA architecture {0} is not supported'.format(value))
conflicts(f"cuda_arch={value}", when="+cuda",
msg=f"CUDA architecture {value} is not supported")
^^^^^^^
Methods
@@ -107,16 +107,16 @@ class of your package. For example, you can add it to your
spec = self.spec
args = []
...
if '+cuda' in spec:
if spec.satisfies("+cuda"):
# Set up the cuda macros needed by the build
args.append('-DWITH_CUDA=ON')
cuda_arch_list = spec.variants['cuda_arch'].value
args.append("-DWITH_CUDA=ON")
cuda_arch_list = spec.variants["cuda_arch"].value
cuda_arch = cuda_arch_list[0]
if cuda_arch != 'none':
args.append('-DCUDA_FLAGS=-arch=sm_{0}'.format(cuda_arch))
if cuda_arch != "none":
args.append(f"-DCUDA_FLAGS=-arch=sm_{cuda_arch}")
else:
# Ensure build with cuda is disabled
args.append('-DWITH_CUDA=OFF')
args.append("-DWITH_CUDA=OFF")
...
return args
@@ -125,7 +125,7 @@ You will need to customize options as needed for your build.
This example also illustrates how to check for the ``cuda`` variant using
``self.spec`` and how to retrieve the ``cuda_arch`` variant's value, which
is a list, using ``self.spec.variants['cuda_arch'].value``.
is a list, using ``self.spec.variants["cuda_arch"].value``.
With over 70 packages using ``CudaPackage`` as of January 2021 there are
lots of examples to choose from to get more ideas for using this package.

View File

@@ -57,13 +57,13 @@ If you look at the ``perl`` package, you'll see:
.. code-block:: python
phases = ['configure', 'build', 'install']
phases = ["configure", "build", "install"]
Similarly, ``cmake`` defines:
.. code-block:: python
phases = ['bootstrap', 'build', 'install']
phases = ["bootstrap", "build", "install"]
If we look at the ``cmake`` example, this tells Spack's ``PackageBase``
class to run the ``bootstrap``, ``build``, and ``install`` functions
@@ -78,7 +78,7 @@ If we look at ``perl``, we see that it defines a ``configure`` method:
.. code-block:: python
def configure(self, spec, prefix):
configure = Executable('./Configure')
configure = Executable("./Configure")
configure(*self.configure_args())
There is also a corresponding ``configure_args`` function that handles
@@ -92,7 +92,7 @@ phases are pretty simple:
make()
def install(self, spec, prefix):
make('install')
make("install")
The ``cmake`` package looks very similar, but with a ``bootstrap``
function instead of ``configure``:
@@ -100,14 +100,14 @@ function instead of ``configure``:
.. code-block:: python
def bootstrap(self, spec, prefix):
bootstrap = Executable('./bootstrap')
bootstrap = Executable("./bootstrap")
bootstrap(*self.bootstrap_args())
def build(self, spec, prefix):
make()
def install(self, spec, prefix):
make('install')
make("install")
Again, there is a ``boostrap_args`` function that determines the
correct bootstrap flags to use.
@@ -128,16 +128,16 @@ before or after a particular phase. For example, in ``perl``, we see:
.. code-block:: python
@run_after('install')
@run_after("install")
def install_cpanm(self):
spec = self.spec
if '+cpanm' in spec:
with working_dir(join_path('cpanm', 'cpanm')):
perl = spec['perl'].command
perl('Makefile.PL')
if spec.satisfies("+cpanm"):
with working_dir(join_path("cpanm", "cpanm")):
perl = spec["perl"].command
perl("Makefile.PL")
make()
make('install')
make("install")
This extra step automatically installs ``cpanm`` in addition to the
base Perl installation.
@@ -174,10 +174,10 @@ In the ``perl`` package, we can see:
.. code-block:: python
@run_after('build')
@run_after("build")
@on_package_attributes(run_tests=True)
def test(self):
make('test')
make("test")
As you can guess, this runs ``make test`` *after* building the package,
if and only if testing is requested. Again, this is not specific to
@@ -189,7 +189,7 @@ custom build systems, it can be added to existing build systems as well.
.. code-block:: python
@run_after('install')
@run_after("install")
@on_package_attributes(run_tests=True)
works as expected. However, if you reverse the ordering:
@@ -197,7 +197,7 @@ custom build systems, it can be added to existing build systems as well.
.. code-block:: python
@on_package_attributes(run_tests=True)
@run_after('install')
@run_after("install")
the tests will always be run regardless of whether or not
``--test=root`` is requested. See https://github.com/spack/spack/issues/3833

View File

@@ -25,8 +25,8 @@ use Spack to build packages with the tools.
The Spack Python class ``IntelOneapiPackage`` is a base class that is
used by ``IntelOneapiCompilers``, ``IntelOneapiMkl``,
``IntelOneapiTbb`` and other classes to implement the oneAPI
packages. See the :ref:`package-list` for the full list of available
oneAPI packages or use::
packages. Search for ``oneAPI`` at `<packages.spack.io>`_ for the full
list of available oneAPI packages, or use::
spack list -d oneAPI

View File

@@ -59,7 +59,7 @@ using GNU Make, you should add a dependency on ``gmake``:
.. code-block:: python
depends_on('gmake', type='build')
depends_on("gmake", type="build")
^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -93,8 +93,8 @@ there are any other variables you need to set, you can do this in the
.. code-block:: python
def edit(self, spec, prefix):
env['PREFIX'] = prefix
env['BLASLIB'] = spec['blas'].libs.ld_flags
env["PREFIX"] = prefix
env["BLASLIB"] = spec["blas"].libs.ld_flags
`cbench <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/cbench/package.py>`_
@@ -113,7 +113,7 @@ you can do this like so:
.. code-block:: python
build_targets = ['CC=cc']
build_targets = ["CC=cc"]
If you do need access to the spec, you can create a property like so:
@@ -125,8 +125,8 @@ If you do need access to the spec, you can create a property like so:
spec = self.spec
return [
'CC=cc',
'BLASLIB={0}'.format(spec['blas'].libs.ld_flags),
"CC=cc",
f"BLASLIB={spec['blas'].libs.ld_flags}",
]
@@ -145,12 +145,12 @@ and a ``filter_file`` method to help with this. For example:
.. code-block:: python
def edit(self, spec, prefix):
makefile = FileFilter('Makefile')
makefile = FileFilter("Makefile")
makefile.filter(r'^\s*CC\s*=.*', 'CC = ' + spack_cc)
makefile.filter(r'^\s*CXX\s*=.*', 'CXX = ' + spack_cxx)
makefile.filter(r'^\s*F77\s*=.*', 'F77 = ' + spack_f77)
makefile.filter(r'^\s*FC\s*=.*', 'FC = ' + spack_fc)
makefile.filter(r"^\s*CC\s*=.*", f"CC = {spack_cc}")
makefile.filter(r"^\s*CXX\s*=.*", f"CXX = {spack_cxx}")
makefile.filter(r"^\s*F77\s*=.*", f"F77 = {spack_f77}")
makefile.filter(r"^\s*FC\s*=.*", f"FC = {spack_fc}")
`stream <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/stream/package.py>`_
@@ -181,16 +181,16 @@ well for storing variables:
def edit(self, spec, prefix):
config = {
'CC': 'cc',
'MAKE': 'make',
"CC": "cc",
"MAKE": "make",
}
if '+blas' in spec:
config['BLAS_LIBS'] = spec['blas'].libs.joined()
if spec.satisfies("+blas"):
config["BLAS_LIBS"] = spec["blas"].libs.joined()
with open('make.inc', 'w') as inc:
with open("make.inc", "w") as inc:
for key in config:
inc.write('{0} = {1}\n'.format(key, config[key]))
inc.write(f"{key} = {config[key]}\n")
`elk <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/elk/package.py>`_
@@ -204,14 +204,14 @@ them in a list:
def edit(self, spec, prefix):
config = [
'INSTALL_DIR = {0}'.format(prefix),
'INCLUDE_DIR = $(INSTALL_DIR)/include',
'LIBRARY_DIR = $(INSTALL_DIR)/lib',
f"INSTALL_DIR = {prefix}",
"INCLUDE_DIR = $(INSTALL_DIR)/include",
"LIBRARY_DIR = $(INSTALL_DIR)/lib",
]
with open('make.inc', 'w') as inc:
with open("make.inc", "w") as inc:
for var in config:
inc.write('{0}\n'.format(var))
inc.write(f"{var}\n")
`hpl <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/hpl/package.py>`_
@@ -284,7 +284,7 @@ can tell Spack where to locate it like so:
.. code-block:: python
build_directory = 'src'
build_directory = "src"
^^^^^^^^^^^^^^^^^^^
@@ -299,8 +299,8 @@ install the package:
def install(self, spec, prefix):
mkdir(prefix.bin)
install('foo', prefix.bin)
install_tree('lib', prefix.lib)
install("foo", prefix.bin)
install_tree("lib", prefix.lib)
^^^^^^^^^^^^^^^^^^^^^^

View File

@@ -152,16 +152,16 @@ set. Once set, ``pypi`` will be used to define the ``homepage``,
.. code-block:: python
homepage = 'https://pypi.org/project/setuptools/'
url = 'https://pypi.org/packages/source/s/setuptools/setuptools-49.2.0.zip'
list_url = 'https://pypi.org/simple/setuptools/'
homepage = "https://pypi.org/project/setuptools/"
url = "https://pypi.org/packages/source/s/setuptools/setuptools-49.2.0.zip"
list_url = "https://pypi.org/simple/setuptools/"
is equivalent to:
.. code-block:: python
pypi = 'setuptools/setuptools-49.2.0.zip'
pypi = "setuptools/setuptools-49.2.0.zip"
If a package has a different homepage listed on PyPI, you can
@@ -208,7 +208,7 @@ dependencies to your package:
.. code-block:: python
depends_on('py-setuptools@42:', type='build')
depends_on("py-setuptools@42:", type="build")
Note that ``py-wheel`` is already listed as a build dependency in the
@@ -232,7 +232,7 @@ Look for dependencies under the following keys:
* ``dependencies`` under ``[project]``
These packages are required for building and installation. You can
add them with ``type=('build', 'run')``.
add them with ``type=("build", "run")``.
* ``[project.optional-dependencies]``
@@ -279,12 +279,12 @@ distutils library, and has almost the exact same API. In addition to
* ``setup_requires``
These packages are usually only needed at build-time, so you can
add them with ``type='build'``.
add them with ``type="build"``.
* ``install_requires``
These packages are required for building and installation. You can
add them with ``type=('build', 'run')``.
add them with ``type=("build", "run")``.
* ``extras_require``
@@ -296,7 +296,7 @@ distutils library, and has almost the exact same API. In addition to
These are packages that are required to run the unit tests for the
package. These dependencies can be specified using the
``type='test'`` dependency type. However, the PyPI tarballs rarely
``type="test"`` dependency type. However, the PyPI tarballs rarely
contain unit tests, so there is usually no reason to add these.
See https://setuptools.pypa.io/en/latest/userguide/dependency_management.html
@@ -321,7 +321,7 @@ older versions of flit may use the following keys:
* ``requires`` under ``[tool.flit.metadata]``
These packages are required for building and installation. You can
add them with ``type=('build', 'run')``.
add them with ``type=("build", "run")``.
* ``[tool.flit.metadata.requires-extra]``
@@ -434,12 +434,12 @@ the BLAS/LAPACK library you want pkg-config to search for:
.. code-block:: python
depends_on('py-pip@22.1:', type='build')
depends_on("py-pip@22.1:", type="build")
def config_settings(self, spec, prefix):
return {
'blas': spec['blas'].libs.names[0],
'lapack': spec['lapack'].libs.names[0],
"blas": spec["blas"].libs.names[0],
"lapack": spec["lapack"].libs.names[0],
}
@@ -463,10 +463,10 @@ has an optional dependency on ``libyaml`` that can be enabled like so:
def global_options(self, spec, prefix):
options = []
if '+libyaml' in spec:
options.append('--with-libyaml')
if spec.satisfies("+libyaml"):
options.append("--with-libyaml")
else:
options.append('--without-libyaml')
options.append("--without-libyaml")
return options
@@ -492,10 +492,10 @@ allows you to specify the directories to search for ``libyaml``:
def install_options(self, spec, prefix):
options = []
if '+libyaml' in spec:
if spec.satisfies("+libyaml"):
options.extend([
spec['libyaml'].libs.search_flags,
spec['libyaml'].headers.include_flags,
spec["libyaml"].libs.search_flags,
spec["libyaml"].headers.include_flags,
])
return options
@@ -556,7 +556,7 @@ detected are wrong, you can provide the names yourself by overriding
.. code-block:: python
import_modules = ['six']
import_modules = ["six"]
Sometimes the list of module names to import depends on how the
@@ -571,9 +571,9 @@ This can be expressed like so:
@property
def import_modules(self):
modules = ['yaml']
if '+libyaml' in self.spec:
modules.append('yaml.cyaml')
modules = ["yaml"]
if self.spec.satisfies("+libyaml"):
modules.append("yaml.cyaml")
return modules
@@ -586,14 +586,14 @@ Instead of defining the ``import_modules`` explicitly, only the subset
of module names to be skipped can be defined by using ``skip_modules``.
If a defined module has submodules, they are skipped as well, e.g.,
in case the ``plotting`` modules should be excluded from the
automatically detected ``import_modules`` ``['nilearn', 'nilearn.surface',
'nilearn.plotting', 'nilearn.plotting.data']`` set:
automatically detected ``import_modules`` ``["nilearn", "nilearn.surface",
"nilearn.plotting", "nilearn.plotting.data"]`` set:
.. code-block:: python
skip_modules = ['nilearn.plotting']
skip_modules = ["nilearn.plotting"]
This will set ``import_modules`` to ``['nilearn', 'nilearn.surface']``
This will set ``import_modules`` to ``["nilearn", "nilearn.surface"]``
Import tests can be run during the installation using ``spack install
--test=root`` or at any time after the installation using
@@ -612,11 +612,11 @@ after the ``install`` phase:
.. code-block:: python
@run_after('install')
@run_after("install")
@on_package_attributes(run_tests=True)
def install_test(self):
with working_dir('spack-test', create=True):
python('-c', 'import numpy; numpy.test("full", verbose=2)')
with working_dir("spack-test", create=True):
python("-c", "import numpy; numpy.test('full', verbose=2)")
when testing is enabled during the installation (i.e., ``spack install
@@ -638,7 +638,7 @@ provides Python bindings in a ``python`` directory, you can use:
.. code-block:: python
build_directory = 'python'
build_directory = "python"
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

View File

@@ -81,28 +81,27 @@ class of your package. For example, you can add it to your
class MyRocmPackage(CMakePackage, ROCmPackage):
...
# Ensure +rocm and amdgpu_targets are passed to dependencies
depends_on('mydeppackage', when='+rocm')
depends_on("mydeppackage", when="+rocm")
for val in ROCmPackage.amdgpu_targets:
depends_on('mydeppackage amdgpu_target={0}'.format(val),
when='amdgpu_target={0}'.format(val))
depends_on(f"mydeppackage amdgpu_target={val}",
when=f"amdgpu_target={val}")
...
def cmake_args(self):
spec = self.spec
args = []
...
if '+rocm' in spec:
if spec.satisfies("+rocm"):
# Set up the hip macros needed by the build
args.extend([
'-DENABLE_HIP=ON',
'-DHIP_ROOT_DIR={0}'.format(spec['hip'].prefix)])
rocm_archs = spec.variants['amdgpu_target'].value
if 'none' not in rocm_archs:
args.append('-DHIP_HIPCC_FLAGS=--amdgpu-target={0}'
.format(",".join(rocm_archs)))
"-DENABLE_HIP=ON",
f"-DHIP_ROOT_DIR={spec['hip'].prefix}"])
rocm_archs = spec.variants["amdgpu_target"].value
if "none" not in rocm_archs:
args.append(f"-DHIP_HIPCC_FLAGS=--amdgpu-target={','.join(rocm_archs}")
else:
# Ensure build with hip is disabled
args.append('-DENABLE_HIP=OFF')
args.append("-DENABLE_HIP=OFF")
...
return args
...
@@ -114,7 +113,7 @@ build.
This example also illustrates how to check for the ``rocm`` variant using
``self.spec`` and how to retrieve the ``amdgpu_target`` variant's value
using ``self.spec.variants['amdgpu_target'].value``.
using ``self.spec.variants["amdgpu_target"].value``.
All five packages using ``ROCmPackage`` as of January 2021 also use the
:ref:`CudaPackage <cudapackage>`. So it is worth looking at those packages

View File

@@ -57,7 +57,7 @@ overridden like so:
.. code-block:: python
def test(self):
scons('check')
scons("check")
^^^^^^^^^^^^^^^
@@ -88,7 +88,7 @@ base class already contains:
.. code-block:: python
depends_on('scons', type='build')
depends_on("scons", type="build")
If you want to specify a particular version requirement, you can override
@@ -96,7 +96,7 @@ this in your package:
.. code-block:: python
depends_on('scons@2.3.0:', type='build')
depends_on("scons@2.3.0:", type="build")
^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -238,14 +238,14 @@ the package build phase. This is done by overriding ``build_args`` like so:
def build_args(self, spec, prefix):
args = [
'PREFIX={0}'.format(prefix),
'ZLIB={0}'.format(spec['zlib'].prefix),
f"PREFIX={prefix}",
f"ZLIB={spec['zlib'].prefix}",
]
if '+debug' in spec:
args.append('DEBUG=yes')
if spec.satisfies("+debug"):
args.append("DEBUG=yes")
else:
args.append('DEBUG=no')
args.append("DEBUG=no")
return args
@@ -275,8 +275,8 @@ environment variables. For example, cantera has the following option:
* env_vars: [ string ]
Environment variables to propagate through to SCons. Either the
string "all" or a comma separated list of variable names, e.g.
'LD_LIBRARY_PATH,HOME'.
- default: 'LD_LIBRARY_PATH,PYTHONPATH'
"LD_LIBRARY_PATH,HOME".
- default: "LD_LIBRARY_PATH,PYTHONPATH"
In the case of cantera, using ``env_vars=all`` allows us to use

View File

@@ -48,9 +48,6 @@
os.environ["COLIFY_SIZE"] = "25x120"
os.environ["COLUMNS"] = "120"
# Generate full package list if needed
subprocess.call(["spack", "list", "--format=html", "--update=package_list.html"])
# Generate a command index if an update is needed
subprocess.call(
[
@@ -207,6 +204,7 @@ def setup(sphinx):
("py:class", "clingo.Control"),
("py:class", "six.moves.urllib.parse.ParseResult"),
("py:class", "TextIO"),
("py:class", "hashlib._Hash"),
# Spack classes that are private and we don't want to expose
("py:class", "spack.provider_index._IndexBase"),
("py:class", "spack.repo._PrependFileLoader"),
@@ -214,6 +212,7 @@ def setup(sphinx):
# Spack classes that intersphinx is unable to resolve
("py:class", "spack.version.StandardVersion"),
("py:class", "spack.spec.DependencySpec"),
("py:class", "spack.spec.InstallStatus"),
("py:class", "spack.spec.SpecfileReaderBase"),
("py:class", "spack.install_test.Pb"),
]

View File

@@ -304,3 +304,17 @@ To work properly, this requires your terminal to reset its title after
Spack has finished its work, otherwise Spack's status information will
remain in the terminal's title indefinitely. Most terminals should already
be set up this way and clear Spack's status information.
-----------
``aliases``
-----------
Aliases can be used to define new Spack commands. They can be either shortcuts
for longer commands or include specific arguments for convenience. For instance,
if users want to use ``spack install``'s ``-v`` argument all the time, they can
create a new alias called ``inst`` that will always call ``install -v``:
.. code-block:: yaml
aliases:
inst: install -v

View File

@@ -243,9 +243,11 @@ lower-precedence settings. Completely ignoring higher-level configuration
options is supported with the ``::`` notation for keys (see
:ref:`config-overrides` below).
There are also special notations for string concatenation and precendense override.
Using the ``+:`` notation can be used to force *prepending* strings or lists. For lists, this is identical
to the default behavior. Using the ``-:`` works similarly, but for *appending* values.
There are also special notations for string concatenation and precendense override:
* ``+:`` will force *prepending* strings or lists. For lists, this is the default behavior.
* ``-:`` works similarly, but for *appending* values.
:ref:`config-prepend-append`
^^^^^^^^^^^

View File

@@ -212,18 +212,12 @@ under the ``container`` attribute of environments:
final:
- libgomp
# Extra instructions
extra_instructions:
final: |
RUN echo 'export PS1="\[$(tput bold)\]\[$(tput setaf 1)\][gromacs]\[$(tput setaf 2)\]\u\[$(tput sgr0)\]:\w $ "' >> ~/.bashrc
# Labels for the image
labels:
app: "gromacs"
mpi: "mpich"
A detailed description of the options available can be found in the
:ref:`container_config_options` section.
A detailed description of the options available can be found in the :ref:`container_config_options` section.
-------------------
Setting Base Images
@@ -525,6 +519,13 @@ the example below:
COPY data /share/myapp/data
{% endblock %}
The Dockerfile is generated by running:
.. code-block:: console
$ spack -e /opt/environment containerize
Note that the environment must be active for spack to read the template.
The recipe that gets generated contains the two extra instruction that we added in our template extension:
.. code-block:: Dockerfile

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@@ -310,53 +310,11 @@ Once all of the dependencies are installed, you can try building the documentati
$ make clean
$ make
If you see any warning or error messages, you will have to correct those before
your PR is accepted.
If you are editing the documentation, you should obviously be running the
documentation tests. But even if you are simply adding a new package, your
changes could cause the documentation tests to fail:
.. code-block:: console
package_list.rst:8745: WARNING: Block quote ends without a blank line; unexpected unindent.
At first, this error message will mean nothing to you, since you didn't edit
that file. Until you look at line 8745 of the file in question:
.. code-block:: rst
Description:
NetCDF is a set of software libraries and self-describing, machine-
independent data formats that support the creation, access, and sharing
of array-oriented scientific data.
Our documentation includes :ref:`a list of all Spack packages <package-list>`.
If you add a new package, its docstring is added to this page. The problem in
this case was that the docstring looked like:
.. code-block:: python
class Netcdf(Package):
"""
NetCDF is a set of software libraries and self-describing,
machine-independent data formats that support the creation,
access, and sharing of array-oriented scientific data.
"""
Docstrings cannot start with a newline character, or else Sphinx will complain.
Instead, they should look like:
.. code-block:: python
class Netcdf(Package):
"""NetCDF is a set of software libraries and self-describing,
machine-independent data formats that support the creation,
access, and sharing of array-oriented scientific data."""
Documentation changes can result in much more obfuscated warning messages.
If you don't understand what they mean, feel free to ask when you submit
your PR.
If you see any warning or error messages, you will have to correct those before your PR
is accepted. If you are editing the documentation, you should be running the
documentation tests to make sure there are no errors. Documentation changes can result
in some obfuscated warning messages. If you don't understand what they mean, feel free
to ask when you submit your PR.
--------
Coverage

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@@ -0,0 +1,113 @@
.. 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)
==========================
Using External GPU Support
==========================
Many packages come with a ``+cuda`` or ``+rocm`` variant. With no added
configuration Spack will download and install the needed components.
It may be preferable to use existing system support: the following sections
help with using a system installation of GPU libraries.
-----------------------------------
Using an External ROCm Installation
-----------------------------------
Spack breaks down ROCm into many separate component packages. The following
is an example ``packages.yaml`` that organizes a consistent set of ROCm
components for use by dependent packages:
.. code-block:: yaml
packages:
all:
compiler: [rocmcc@=5.3.0]
variants: amdgpu_target=gfx90a
hip:
buildable: false
externals:
- spec: hip@5.3.0
prefix: /opt/rocm-5.3.0/hip
hsa-rocr-dev:
buildable: false
externals:
- spec: hsa-rocr-dev@5.3.0
prefix: /opt/rocm-5.3.0/
llvm-amdgpu:
buildable: false
externals:
- spec: llvm-amdgpu@5.3.0
prefix: /opt/rocm-5.3.0/llvm/
comgr:
buildable: false
externals:
- spec: comgr@5.3.0
prefix: /opt/rocm-5.3.0/
hipsparse:
buildable: false
externals:
- spec: hipsparse@5.3.0
prefix: /opt/rocm-5.3.0/
hipblas:
buildable: false
externals:
- spec: hipblas@5.3.0
prefix: /opt/rocm-5.3.0/
rocblas:
buildable: false
externals:
- spec: rocblas@5.3.0
prefix: /opt/rocm-5.3.0/
rocprim:
buildable: false
externals:
- spec: rocprim@5.3.0
prefix: /opt/rocm-5.3.0/rocprim/
This is in combination with the following compiler definition:
.. code-block:: yaml
compilers:
- compiler:
spec: rocmcc@=5.3.0
paths:
cc: /opt/rocm-5.3.0/bin/amdclang
cxx: /opt/rocm-5.3.0/bin/amdclang++
f77: null
fc: /opt/rocm-5.3.0/bin/amdflang
operating_system: rhel8
target: x86_64
This includes the following considerations:
- Each of the listed externals specifies ``buildable: false`` to force Spack
to use only the externals we defined.
- ``spack external find`` can automatically locate some of the ``hip``/``rocm``
packages, but not all of them, and furthermore not in a manner that
guarantees a complementary set if multiple ROCm installations are available.
- The ``prefix`` is the same for several components, but note that others
require listing one of the subdirectories as a prefix.
-----------------------------------
Using an External CUDA Installation
-----------------------------------
CUDA is split into fewer components and is simpler to specify:
.. code-block:: yaml
packages:
all:
variants:
- cuda_arch=70
cuda:
buildable: false
externals:
- spec: cuda@11.0.2
prefix: /opt/cuda/cuda-11.0.2/
where ``/opt/cuda/cuda-11.0.2/lib/`` contains ``libcudart.so``.

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After

Width:  |  Height:  |  Size: 58 KiB

View File

@@ -54,9 +54,16 @@ or refer to the full manual below.
features
getting_started
basic_usage
Tutorial: Spack 101 <https://spack-tutorial.readthedocs.io>
replace_conda_homebrew
.. toctree::
:maxdepth: 2
:caption: Links
Tutorial (spack-tutorial.rtfd.io) <https://spack-tutorial.readthedocs.io>
Packages (packages.spack.io) <https://packages.spack.io>
Binaries (binaries.spack.io) <https://cache.spack.io>
.. toctree::
:maxdepth: 2
:caption: Reference
@@ -72,11 +79,11 @@ or refer to the full manual below.
repositories
binary_caches
command_index
package_list
chain
extensions
pipelines
signing
gpu_configuration
.. toctree::
:maxdepth: 2

View File

@@ -519,11 +519,11 @@ inspections and customize them per-module-set.
modules:
prefix_inspections:
bin:
./bin:
- PATH
man:
./man:
- MANPATH
'':
./:
- CMAKE_PREFIX_PATH
Prefix inspections are only applied if the relative path inside the
@@ -579,7 +579,7 @@ the view.
view_relative_modules:
use_view: my_view
prefix_inspections:
bin:
./bin:
- PATH
view:
my_view:

View File

@@ -1,17 +0,0 @@
.. 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)
.. _package-list:
============
Package List
============
This is a list of things you can install using Spack. It is
automatically generated based on the packages in this Spack
version.
.. raw:: html
:file: package_list.html

View File

@@ -363,6 +363,42 @@ one of these::
If Spack finds none of these variables set, it will look for ``vim``, ``vi``, ``emacs``,
``nano``, and ``notepad``, in that order.
^^^^^^^^^^^^^^^^^
Bundling software
^^^^^^^^^^^^^^^^^
If you have a collection of software expected to work well together with
no source code of its own, you can create a :ref:`BundlePackage <bundlepackage>`.
Examples where bundle packages can be useful include defining suites of
applications (e.g, `EcpProxyApps
<https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/ecp-proxy-apps/package.py>`_), commonly used libraries
(e.g., `AmdAocl <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/amd-aocl/package.py>`_),
and software development kits (e.g., `EcpDataVisSdk <https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/ecp-data-vis-sdk/package.py>`_).
These versioned packages primarily consist of dependencies on the associated
software packages. They can include :ref:`variants <variants>` to ensure
common build options are consistently applied to dependencies. Known build
failures, such as not building on a platform or when certain compilers or
variants are used, can be flagged with :ref:`conflicts <packaging_conflicts>`.
Build requirements, such as only building with specific compilers, can similarly
be flagged with :ref:`requires <packaging_conflicts>`.
The ``spack create --template bundle`` command will create a skeleton
``BundlePackage`` ``package.py`` for you:
.. code-block:: console
$ spack create --template bundle --name coolsdk
Now you can fill in the basic package documentation, version(s), and software
package dependencies along with any other relevant customizations.
.. note::
Remember that bundle packages have no software of their own so there
is nothing to download.
^^^^^^^^^^^^^^^^^^^^^^^^^
Non-downloadable software
^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -610,7 +646,16 @@ add a line like this in the package class:
version("8.2.0", md5="1c9f62f0778697a09d36121ead88e08e")
version("8.1.2", md5="d47dd09ed7ae6e7fd6f9a816d7f5fdf6")
Versions should be listed in descending order, from newest to oldest.
.. note::
By convention, we list versions in descending order, from newest to oldest.
.. note::
:ref:`Bundle packages <bundlepackage>` do not have source code so
there is nothing to fetch. Consequently, their version directives
consist solely of the version name (e.g., ``version("202309")``).
^^^^^^^^^^^^^
Date Versions
@@ -1504,7 +1549,7 @@ its value:
def configure_args(self):
...
if "+shared" in self.spec:
if self.spec.satisfies("+shared"):
extra_args.append("--enable-shared")
else:
extra_args.append("--disable-shared")
@@ -1591,7 +1636,7 @@ Within a package recipe a multi-valued variant is tested using a ``key=value`` s
.. code-block:: python
if "languages=jit" in spec:
if spec.satisfies("languages=jit"):
options.append("--enable-host-shared")
"""""""""""""""""""""""""""""""""""""""""""
@@ -2307,7 +2352,7 @@ the following at the command line of a bash shell:
.. code-block:: console
$ for i in {1..12}; do nohup spack install -j 4 mpich@3.3.2 >> mpich_install.txt 2>&1 &; done
$ for i in {1..12}; do nohup spack install -j 4 mpich@3.3.2 >> mpich_install.txt 2>&1 & done
.. note::
@@ -2512,9 +2557,10 @@ Conditional dependencies
^^^^^^^^^^^^^^^^^^^^^^^^
You may have a package that only requires a dependency under certain
conditions. For example, you may have a package that has optional MPI support,
- MPI is only a dependency when you want to enable MPI support for the
package. In that case, you could say something like:
conditions. For example, you may have a package with optional MPI support.
You would then provide a variant to reflect that the feature is optional
and specify the MPI dependency only applies when MPI support is enabled.
In that case, you could say something like:
.. code-block:: python
@@ -2522,13 +2568,39 @@ package. In that case, you could say something like:
depends_on("mpi", when="+mpi")
``when`` can include constraints on the variant, version, compiler, etc. and
the :mod:`syntax<spack.spec>` is the same as for Specs written on the command
line.
If a dependency/feature of a package isn't typically used, you can save time
by making it conditional (since Spack will not build the dependency unless it
is required for the Spec).
Suppose the above package also has, since version 3, optional `Trilinos`
support and you want them both to build either with or without MPI. Further
suppose you require a version of `Trilinos` no older than 12.6. In that case,
the `trilinos` variant and dependency directives would be:
.. code-block:: python
variant("trilinos", default=False, description="Enable Trilinos support")
depends_on("trilinos@12.6:", when="@3: +trilinos")
depends_on("trilinos@12.6: +mpi", when="@3: +trilinos +mpi")
Alternatively, you could use the `when` context manager to equivalently specify
the `trilinos` variant dependencies as follows:
.. code-block:: python
with when("@3: +trilinos"):
depends_on("trilinos@12.6:")
depends_on("trilinos +mpi", when="+mpi")
The argument to ``when`` in either case can include any Spec constraints that
are supported on the command line using the same :ref:`syntax <sec-specs>`.
.. note::
If a dependency isn't typically used, you can save time by making it
conditional since Spack will not build the dependency unless it is
required for the Spec.
.. _dependency_dependency_patching:
@@ -2616,60 +2688,6 @@ appear in the package file (or in this case, in the list).
right version. If two packages depend on ``binutils`` patched *the
same* way, they can both use a single installation of ``binutils``.
.. _setup-dependent-environment:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Influence how dependents are built or run
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Spack provides a mechanism for dependencies to influence the
environment of their dependents by overriding the
:meth:`setup_dependent_run_environment <spack.package_base.PackageBase.setup_dependent_run_environment>`
or the
:meth:`setup_dependent_build_environment <spack.builder.Builder.setup_dependent_build_environment>`
methods.
The Qt package, for instance, uses this call:
.. literalinclude:: _spack_root/var/spack/repos/builtin/packages/qt/package.py
:pyobject: Qt.setup_dependent_build_environment
:linenos:
to set the ``QTDIR`` environment variable so that packages
that depend on a particular Qt installation will find it.
Another good example of how a dependency can influence
the build environment of dependents is the Python package:
.. literalinclude:: _spack_root/var/spack/repos/builtin/packages/python/package.py
:pyobject: Python.setup_dependent_build_environment
:linenos:
In the method above it is ensured that any package that depends on Python
will have the ``PYTHONPATH``, ``PYTHONHOME`` and ``PATH`` environment
variables set appropriately before starting the installation. To make things
even simpler the ``python setup.py`` command is also inserted into the module
scope of dependents by overriding a third method called
:meth:`setup_dependent_package <spack.package_base.PackageBase.setup_dependent_package>`
:
.. literalinclude:: _spack_root/var/spack/repos/builtin/packages/python/package.py
:pyobject: Python.setup_dependent_package
:linenos:
This allows most python packages to have a very simple install procedure,
like the following:
.. code-block:: python
def install(self, spec, prefix):
setup_py("install", "--prefix={0}".format(prefix))
Finally the Python package takes also care of the modifications to ``PYTHONPATH``
to allow dependencies to run correctly:
.. literalinclude:: _spack_root/var/spack/repos/builtin/packages/python/package.py
:pyobject: Python.setup_dependent_run_environment
:linenos:
.. _packaging_conflicts:
@@ -2678,7 +2696,7 @@ Conflicts and requirements
--------------------------
Sometimes packages have known bugs, or limitations, that would prevent them
to build e.g. against other dependencies or with certain compilers. Spack
from building e.g. against other dependencies or with certain compilers. Spack
makes it possible to express such constraints with the ``conflicts`` directive.
Adding the following to a package:
@@ -2814,6 +2832,70 @@ variant(s) are selected. This may be accomplished with conditional
extends("python", when="+python")
...
.. _setup-environment:
--------------------------------------------
Runtime and build time environment variables
--------------------------------------------
Spack provides a few methods to help package authors set up the required environment variables for
their package. Environment variables typically depend on how the package is used: variables that
make sense during the build phase may not be needed at runtime, and vice versa. Further, sometimes
it makes sense to let a dependency set the environment variables for its dependents. To allow all
this, Spack provides four different methods that can be overridden in a package:
1. :meth:`setup_build_environment <spack.builder.Builder.setup_build_environment>`
2. :meth:`setup_run_environment <spack.package_base.PackageBase.setup_run_environment>`
3. :meth:`setup_dependent_build_environment <spack.builder.Builder.setup_dependent_build_environment>`
4. :meth:`setup_dependent_run_environment <spack.package_base.PackageBase.setup_dependent_run_environment>`
The Qt package, for instance, uses this call:
.. literalinclude:: _spack_root/var/spack/repos/builtin/packages/qt/package.py
:pyobject: Qt.setup_dependent_build_environment
:linenos:
to set the ``QTDIR`` environment variable so that packages that depend on a particular Qt
installation will find it.
The following diagram will give you an idea when each of these methods is called in a build
context:
.. image:: images/setup_env.png
:align: center
Notice that ``setup_dependent_run_environment`` can be called multiple times, once for each
dependent package, whereas ``setup_run_environment`` is called only once for the package itself.
This means that the former should only be used if the environment variables depend on the dependent
package, whereas the latter should be used if the environment variables depend only on the package
itself.
--------------------------------
Setting package module variables
--------------------------------
Apart from modifying environment variables of the dependent package, you can also define Python
variables to be used by the dependent. This is done by implementing
:meth:`setup_dependent_package <spack.package_base.PackageBase.setup_dependent_package>`. An
example of this can be found in the ``Python`` package:
.. literalinclude:: _spack_root/var/spack/repos/builtin/packages/python/package.py
:pyobject: Python.setup_dependent_package
:linenos:
This allows Python packages to directly use these variables:
.. code-block:: python
def install(self, spec, prefix):
...
install("script.py", python_platlib)
.. note::
We recommend using ``setup_dependent_package`` sparingly, as it is not always clear where
global variables are coming from when editing a ``package.py`` file.
-----
Views
-----
@@ -2892,6 +2974,33 @@ The ``provides("mpi")`` call tells Spack that the ``mpich`` package
can be used to satisfy the dependency of any package that
``depends_on("mpi")``.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Providing multiple virtuals simultaneously
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Packages can provide more than one virtual dependency. Sometimes, due to implementation details,
there are subsets of those virtuals that need to be provided together by the same package.
A well-known example is ``openblas``, which provides both the ``lapack`` and ``blas`` API in a single ``libopenblas``
library. A package that needs ``lapack`` and ``blas`` must either use ``openblas`` to provide both, or not use
``openblas`` at all. It cannot pick one or the other.
To express this constraint in a package, the two virtual dependencies must be listed in the same ``provides`` directive:
.. code-block:: python
provides('blas', 'lapack')
This makes it impossible to select ``openblas`` as a provider for one of the two
virtual dependencies and not for the other. If you try to, Spack will report an error:
.. code-block:: console
$ spack spec netlib-scalapack ^[virtuals=lapack] openblas ^[virtuals=blas] atlas
==> Error: concretization failed for the following reasons:
1. Package 'openblas' needs to provide both 'lapack' and 'blas' together, but provides only 'lapack'
^^^^^^^^^^^^^^^^^^^^
Versioned Interfaces
^^^^^^^^^^^^^^^^^^^^
@@ -3394,6 +3503,56 @@ is equivalent to:
Constraints from nested context managers are also combined together, but they are rarely
needed or recommended.
.. _default_args:
------------------------
Common default arguments
------------------------
Similarly, if directives have a common set of default arguments, you can
group them together in a ``with default_args()`` block:
.. code-block:: python
class PyExample(PythonPackage):
with default_args(type=("build", "run")):
depends_on("py-foo")
depends_on("py-foo@2:", when="@2:")
depends_on("py-bar")
depends_on("py-bz")
The above is short for:
.. code-block:: python
class PyExample(PythonPackage):
depends_on("py-foo", type=("build", "run"))
depends_on("py-foo@2:", when="@2:", type=("build", "run"))
depends_on("py-bar", type=("build", "run"))
depends_on("py-bz", type=("build", "run"))
.. note::
The ``with when()`` context manager is composable, while ``with default_args()``
merely overrides the default. For example:
.. code-block:: python
with default_args(when="+feature"):
depends_on("foo")
depends_on("bar")
depends_on("baz", when="+baz")
is equivalent to:
.. code-block:: python
depends_on("foo", when="+feature")
depends_on("bar", when="+feature")
depends_on("baz", when="+baz") # Note: not when="+feature+baz"
.. _install-method:
------------------
@@ -3456,7 +3615,7 @@ need to override methods like ``configure_args``:
def configure_args(self):
args = ["--enable-cxx"] + self.enable_or_disable("libs")
if "libs=static" in self.spec:
if self.spec.satisfies("libs=static"):
args.append("--with-pic")
return args
@@ -3590,7 +3749,8 @@ regardless of the build system. The arguments for the phase are:
The arguments ``spec`` and ``prefix`` are passed only for convenience, as they always
correspond to ``self.spec`` and ``self.spec.prefix`` respectively.
If the ``package.py`` encodes builders explicitly, the signature for a phase changes slightly:
If the ``package.py`` has build instructions in a separate
:ref:`builder class <multiple_build_systems>`, the signature for a phase changes slightly:
.. code-block:: python
@@ -3600,56 +3760,6 @@ If the ``package.py`` encodes builders explicitly, the signature for a phase cha
In this case the package is passed as the second argument, and ``self`` is the builder instance.
.. _multiple_build_systems:
^^^^^^^^^^^^^^^^^^^^^^
Multiple build systems
^^^^^^^^^^^^^^^^^^^^^^
There are cases where a software actively supports two build systems, or changes build systems
as it evolves, or needs different build systems on different platforms. Spack allows dealing with
these cases natively, if a recipe is written using builders explicitly.
For instance, software that supports two build systems unconditionally should derive from
both ``*Package`` base classes, and declare the possible use of multiple build systems using
a directive:
.. code-block:: python
class ArpackNg(CMakePackage, AutotoolsPackage):
build_system("cmake", "autotools", default="cmake")
In this case the software can be built with both ``autotools`` and ``cmake``. Since the package
supports multiple build systems, it is necessary to declare which one is the default. The ``package.py``
will likely contain some overriding of default builder methods:
.. code-block:: python
class CMakeBuilder(spack.build_systems.cmake.CMakeBuilder):
def cmake_args(self):
pass
class AutotoolsBuilder(spack.build_systems.autotools.AutotoolsBuilder):
def configure_args(self):
pass
In more complex cases it might happen that the build system changes according to certain conditions,
for instance across versions. That can be expressed with conditional variant values:
.. code-block:: python
class ArpackNg(CMakePackage, AutotoolsPackage):
build_system(
conditional("cmake", when="@0.64:"),
conditional("autotools", when="@:0.63"),
default="cmake",
)
In the example the directive impose a change from ``Autotools`` to ``CMake`` going
from ``v0.63`` to ``v0.64``.
^^^^^^^^^^^^^^^^^^
Mixin base classes
^^^^^^^^^^^^^^^^^^
@@ -3696,6 +3806,106 @@ for instance:
In the example above ``Cp2k`` inherits all the conflicts and variants that ``CudaPackage`` defines.
.. _multiple_build_systems:
----------------------
Multiple build systems
----------------------
There are cases where a package actively supports two build systems, or changes build systems
as it evolves, or needs different build systems on different platforms. Spack allows dealing with
these cases by splitting the build instructions into separate builder classes.
For instance, software that supports two build systems unconditionally should derive from
both ``*Package`` base classes, and declare the possible use of multiple build systems using
a directive:
.. code-block:: python
class Example(CMakePackage, AutotoolsPackage):
variant("my_feature", default=True)
build_system("cmake", "autotools", default="cmake")
In this case the software can be built with both ``autotools`` and ``cmake``. Since the package
supports multiple build systems, it is necessary to declare which one is the default.
Additional build instructions are split into separate builder classes:
.. code-block:: python
class CMakeBuilder(spack.build_systems.cmake.CMakeBuilder):
def cmake_args(self):
return [
self.define_from_variant("MY_FEATURE", "my_feature")
]
class AutotoolsBuilder(spack.build_systems.autotools.AutotoolsBuilder):
def configure_args(self):
return self.with_or_without("my-feature", variant="my_feature")
In this example, ``spack install example +feature build_sytem=cmake`` will
pick the ``CMakeBuilder`` and invoke ``cmake -DMY_FEATURE:BOOL=ON``.
Similarly, ``spack install example +feature build_system=autotools`` will pick
the ``AutotoolsBuilder`` and invoke ``./configure --with-my-feature``.
Dependencies are always specified in the package class. When some dependencies
depend on the choice of the build system, it is possible to use when conditions as
usual:
.. code-block:: python
class Example(CMakePackage, AutotoolsPackage):
build_system("cmake", "autotools", default="cmake")
# Runtime dependencies
depends_on("ncurses")
depends_on("libxml2")
# Lowerbounds for cmake only apply when using cmake as the build system
with when("build_system=cmake"):
depends_on("cmake@3.18:", when="@2.0:", type="build")
depends_on("cmake@3:", type="build")
# Specify extra build dependencies used only in the configure script
with when("build_system=autotools"):
depends_on("perl", type="build")
depends_on("pkgconfig", type="build")
Very often projects switch from one build system to another, or add support
for a new build system from a certain version, which means that the choice
of the build system typically depends on a version range. Those situations can
be handled by using conditional values in the ``build_system`` directive:
.. code-block:: python
class Example(CMakePackage, AutotoolsPackage):
build_system(
conditional("cmake", when="@0.64:"),
conditional("autotools", when="@:0.63"),
default="cmake",
)
In the example the directive impose a change from ``Autotools`` to ``CMake`` going
from ``v0.63`` to ``v0.64``.
The ``build_system`` can be used as an ordinary variant, which also means that it can
be used in ``depends_on`` statements. This can be useful when a package *requires* that
its dependency has a CMake config file, meaning that the dependent can only build when the
dependency is built with CMake, and not Autotools. In that case, you can force the choice
of the build system in the dependent:
.. code-block:: python
class Dependent(CMakePackage):
depends_on("example build_system=cmake")
.. _install-environment:
-----------------------
@@ -4268,7 +4478,7 @@ for supported features, for instance:
.. code-block:: python
if "avx512" in spec.target:
if spec.satisfies("target=avx512"):
args.append("--with-avx512")
The snippet above will append the ``--with-avx512`` item to a list of arguments only if the corresponding
@@ -4773,17 +4983,17 @@ For example, running:
results in spack checking that the installation created the following **file**:
* ``self.prefix/bin/reframe``
* ``self.prefix.bin.reframe``
and the following **directories**:
* ``self.prefix/bin``
* ``self.prefix/config``
* ``self.prefix/docs``
* ``self.prefix/reframe``
* ``self.prefix/tutorials``
* ``self.prefix/unittests``
* ``self.prefix/cscs-checks``
* ``self.prefix.bin``
* ``self.prefix.config``
* ``self.prefix.docs``
* ``self.prefix.reframe``
* ``self.prefix.tutorials``
* ``self.prefix.unittests``
* ``self.prefix.cscs-checks``
If **any** of these paths are missing, then Spack considers the installation
to have failed.
@@ -4927,7 +5137,7 @@ installed executable. The check is implemented as follows:
@on_package_attributes(run_tests=True)
def check_list(self):
with working_dir(self.stage.source_path):
reframe = Executable(join_path(self.prefix, "bin", "reframe"))
reframe = Executable(self.prefix.bin.reframe)
reframe("-l")
.. warning::
@@ -5147,8 +5357,8 @@ embedded test parts.
for example in ["ex1", "ex2"]:
with test_part(
self,
"test_example_{0}".format(example),
purpose="run installed {0}".format(example),
f"test_example_{example}",
purpose=f"run installed {example}",
):
exe = which(join_path(self.prefix.bin, example))
exe()
@@ -5226,11 +5436,10 @@ Below illustrates using this feature to compile an example.
...
cxx = which(os.environ["CXX"])
cxx(
"-L{0}".format(self.prefix.lib),
"-I{0}".format(self.prefix.include),
"{0}.cpp".format(exe),
"-o",
exe
f"-L{self.prefix.lib}",
f"-I{self.prefix.include}",
f"{exe}.cpp",
"-o", exe
)
cxx_example = which(exe)
cxx_example()
@@ -5247,14 +5456,14 @@ Saving build-time files
We highly recommend re-using build-time test sources and pared down
input files for testing installed software. These files are easier
to keep synchronized with software capabilities since they reside
within the software's repository.
within the software's repository.
If that is not possible, you can add test-related files to the package
repository (see :ref:`adding custom files <cache_custom_files>`). It
will be important to maintain them so they work across listed or supported
versions of the package.
You can use the ``cache_extra_test_sources`` method to copy directories
You can use the ``cache_extra_test_sources`` helper to copy directories
and or files from the source build stage directory to the package's
installation directory.
@@ -5262,10 +5471,15 @@ The signature for ``cache_extra_test_sources`` is:
.. code-block:: python
def cache_extra_test_sources(self, srcs):
def cache_extra_test_sources(pkg, srcs):
where each argument has the following meaning:
* ``pkg`` is an instance of the package for the spec under test.
* ``srcs`` is a string *or* a list of strings corresponding to the
paths of subdirectories and or files needed for stand-alone testing.
where ``srcs`` is a string *or* a list of strings corresponding to the
paths of subdirectories and or files needed for stand-alone testing.
The paths must be relative to the staged source directory. Contents of
subdirectories and files are copied to a special test cache subdirectory
of the installation prefix. They are automatically copied to the appropriate
@@ -5286,21 +5500,18 @@ and using ``foo.c`` in a test method is illustrated below.
srcs = ["tests",
join_path("examples", "foo.c"),
join_path("examples", "bar.c")]
self.cache_extra_test_sources(srcs)
cache_extra_test_sources(self, srcs)
def test_foo(self):
exe = "foo"
src_dir = join_path(
self.test_suite.current_test_cache_dir, "examples"
)
src_dir = self.test_suite.current_test_cache_dir.examples
with working_dir(src_dir):
cc = which(os.environ["CC"])
cc(
"-L{0}".format(self.prefix.lib),
"-I{0}".format(self.prefix.include),
"{0}.c".format(exe),
"-o",
exe
f"-L{self.prefix.lib}",
f"-I{self.prefix.include}",
f"{exe}.c",
"-o", exe
)
foo = which(exe)
foo()
@@ -5326,9 +5537,9 @@ the files using the ``self.test_suite.current_test_cache_dir`` property.
In our example above, test methods can use the following paths to reference
the copy of each entry listed in ``srcs``, respectively:
* ``join_path(self.test_suite.current_test_cache_dir, "tests")``
* ``join_path(self.test_suite.current_test_cache_dir, "examples", "foo.c")``
* ``join_path(self.test_suite.current_test_cache_dir, "examples", "bar.c")``
* ``self.test_suite.current_test_cache_dir.tests``
* ``join_path(self.test_suite.current_test_cache_dir.examples, "foo.c")``
* ``join_path(self.test_suite.current_test_cache_dir.examples, "bar.c")``
.. admonition:: Library packages should build stand-alone tests
@@ -5347,7 +5558,7 @@ the copy of each entry listed in ``srcs``, respectively:
If one or more of the copied files needs to be modified to reference
the installed software, it is recommended that those changes be made
to the cached files **once** in the ``copy_test_sources`` method and
***after** the call to ``self.cache_extra_test_sources()``. This will
***after** the call to ``cache_extra_test_sources()``. This will
reduce the amount of unnecessary work in the test method **and** avoid
problems testing in shared instances and facility deployments.
@@ -5394,7 +5605,7 @@ property as shown below.
"""build and run custom-example"""
data_dir = self.test_suite.current_test_data_dir
exe = "custom-example"
src = datadir.join("{0}.cpp".format(exe))
src = datadir.join(f"{exe}.cpp")
...
# TODO: Build custom-example using src and exe
...
@@ -5410,7 +5621,7 @@ Reading expected output from a file
The helper function ``get_escaped_text_output`` is available for packages
to retrieve and properly format the text from a file that contains the
expected output from running an executable that may contain special
expected output from running an executable that may contain special
characters.
The signature for ``get_escaped_text_output`` is:
@@ -5444,7 +5655,7 @@ added to the package's ``test`` subdirectory.
db_filename, ".dump", output=str.split, error=str.split
)
for exp in expected:
assert re.search(exp, out), "Expected '{0}' in output".format(exp)
assert re.search(exp, out), f"Expected '{exp}' in output"
If the file was instead copied from the ``tests`` subdirectory of the staged
source code, the path would be obtained as shown below.
@@ -5457,7 +5668,7 @@ source code, the path would be obtained as shown below.
db_filename = test_cache_dir.join("packages.db")
Alternatively, if the file was copied to the ``share/tests`` subdirectory
as part of the installation process, the test could access the path as
as part of the installation process, the test could access the path as
follows:
.. code-block:: python
@@ -5494,9 +5705,12 @@ Invoking the method is the equivalent of:
.. code-block:: python
errors = []
for check in expected:
if not re.search(check, actual):
raise RuntimeError("Expected '{0}' in output '{1}'".format(check, actual))
errors.append(f"Expected '{check}' in output '{actual}'")
if errors:
raise RuntimeError("\n ".join(errors))
.. _accessing-files:
@@ -5536,7 +5750,7 @@ repository, and installation.
- ``self.test_suite.test_dir_for_spec(self.spec)``
* - Current Spec's Build-time Files
- ``self.test_suite.current_test_cache_dir``
- ``join_path(self.test_suite.current_test_cache_dir, "examples", "foo.c")``
- ``join_path(self.test_suite.current_test_cache_dir.examples, "foo.c")``
* - Current Spec's Custom Test Files
- ``self.test_suite.current_test_data_dir``
- ``join_path(self.test_suite.current_test_data_dir, "hello.f90")``
@@ -5551,7 +5765,7 @@ Inheriting stand-alone tests
Stand-alone tests defined in parent (.e.g., :ref:`build-systems`) and
virtual (e.g., :ref:`virtual-dependencies`) packages are executed by
packages that inherit from or provide interface implementations for those
packages, respectively.
packages, respectively.
The table below summarizes the stand-alone tests that will be executed along
with those implemented in the package itself.
@@ -5621,7 +5835,7 @@ for ``openmpi``:
SKIPPED: test_version_oshcc: oshcc is not installed
...
==> [2023-03-10-16:04:02.215227] Completed testing
==> [2023-03-10-16:04:02.215597]
==> [2023-03-10-16:04:02.215597]
======================== SUMMARY: openmpi-4.1.4-ubmrigj ========================
Openmpi::test_bin_mpirun .. PASSED
Openmpi::test_bin_ompi_info .. PASSED
@@ -6071,7 +6285,7 @@ in the extra attributes can implement this method like this:
@classmethod
def validate_detected_spec(cls, spec, extra_attributes):
"""Check that "compilers" is in the extra attributes."""
msg = ("the extra attribute "compilers" must be set for "
msg = ("the extra attribute 'compilers' must be set for "
"the detected spec '{0}'".format(spec))
assert "compilers" in extra_attributes, msg
@@ -6147,7 +6361,100 @@ follows:
"foo-package@{0}".format(version_str)
)
.. _package-lifecycle:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Add detection tests to packages
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
To ensure that software is detected correctly for multiple configurations
and on different systems users can write a ``detection_test.yaml`` file and
put it in the package directory alongside the ``package.py`` file.
This YAML file contains enough information for Spack to mock an environment
and try to check if the detection logic yields the results that are expected.
As a general rule, attributes at the top-level of ``detection_test.yaml``
represent search mechanisms and they each map to a list of tests that should confirm
the validity of the package's detection logic.
The detection tests can be run with the following command:
.. code-block:: console
$ spack audit externals
Errors that have been detected are reported to screen.
""""""""""""""""""""""""""
Tests for PATH inspections
""""""""""""""""""""""""""
Detection tests insisting on ``PATH`` inspections are listed under
the ``paths`` attribute:
.. code-block:: yaml
paths:
- layout:
- executables:
- "bin/clang-3.9"
- "bin/clang++-3.9"
script: |
echo "clang version 3.9.1-19ubuntu1 (tags/RELEASE_391/rc2)"
echo "Target: x86_64-pc-linux-gnu"
echo "Thread model: posix"
echo "InstalledDir: /usr/bin"
results:
- spec: 'llvm@3.9.1 +clang~lld~lldb'
Each test is performed by first creating a temporary directory structure as
specified in the corresponding ``layout`` and by then running
package detection and checking that the outcome matches the expected
``results``. The exact details on how to specify both the ``layout`` and the
``results`` are reported in the table below:
.. list-table:: Test based on PATH inspections
:header-rows: 1
* - Option Name
- Description
- Allowed Values
- Required Field
* - ``layout``
- Specifies the filesystem tree used for the test
- List of objects
- Yes
* - ``layout:[0]:executables``
- Relative paths for the mock executables to be created
- List of strings
- Yes
* - ``layout:[0]:script``
- Mock logic for the executable
- Any valid shell script
- Yes
* - ``results``
- List of expected results
- List of objects (empty if no result is expected)
- Yes
* - ``results:[0]:spec``
- A spec that is expected from detection
- Any valid spec
- Yes
"""""""""""""""""""""""""""""""
Reuse tests from other packages
"""""""""""""""""""""""""""""""
When using a custom repository, it is possible to customize a package that already exists in ``builtin``
and reuse its external tests. To do so, just write a ``detection_tests.yaml`` alongside the customized
``package.py`` with an ``includes`` attribute. For instance the ``detection_tests.yaml`` for
``myrepo.llvm`` might look like:
.. code-block:: yaml
includes:
- "builtin.llvm"
This YAML file instructs Spack to run the detection tests defined in ``builtin.llvm`` in addition to
those locally defined in the file.
-----------------------------
Style guidelines for packages
@@ -6606,3 +6913,63 @@ To achieve backward compatibility with the single-class format Spack creates in
Overall the role of the adapter is to route access to attributes of methods first through the ``*Package``
hierarchy, and then back to the base class builder. This is schematically shown in the diagram above, where
the adapter role is to "emulate" a method resolution order like the one represented by the red arrows.
------------------------------
Specifying License Information
------------------------------
Most of the software in Spack is open source, and most open source software is released
under one or more `common open source licenses <https://opensource.org/licenses/>`_.
Specifying the license that a package is released under in a project's
`package.py` is good practice. To specify a license, find the `SPDX identifier
<https://spdx.org/licenses/>`_ for a project and then add it using the license
directive:
.. code-block:: python
license("<SPDX Identifier HERE>")
For example, the SPDX ID for the Apache Software License, version 2.0 is ``Apache-2.0``,
so you'd write:
.. code-block:: python
license("Apache-2.0")
Or, for a dual-licensed package like Spack, you would use an `SPDX Expression
<https://spdx.github.io/spdx-spec/v2-draft/SPDX-license-expressions/>`_ with both of its
licenses:
.. code-block:: python
license("Apache-2.0 OR MIT")
Note that specifying a license without a when clause makes it apply to all
versions and variants of the package, which might not actually be the case.
For example, a project might have switched licenses at some point or have
certain build configurations that include files that are licensed differently.
Spack itself used to be under the ``LGPL-2.1`` license, until it was relicensed
in version ``0.12`` in 2018.
You can specify when a ``license()`` directive applies using with a ``when=``
clause, just like other directives. For example, to specify that a specific
license identifier should only apply to versions up to ``0.11``, but another
license should apply for later versions, you could write:
.. code-block:: python
license("LGPL-2.1", when="@:0.11")
license("Apache-2.0 OR MIT", when="@0.12:")
Note that unlike for most other directives, the ``when=`` constraints in the
``license()`` directive can't intersect. Spack needs to be able to resolve
exactly one license identifier expression for any given version. To specify
*multiple* licenses, use SPDX expressions and operators as above. The operators
you probably care most about are:
* ``OR``: user chooses one license to adhere to; and
* ``AND``: user has to adhere to all the licenses.
You may also care about `license exceptions
<https://spdx.org/licenses/exceptions-index.html>`_ that use the ``WITH`` operator,
e.g. ``Apache-2.0 WITH LLVM-exception``.

View File

@@ -213,6 +213,16 @@ pipeline jobs.
``spack ci generate``
^^^^^^^^^^^^^^^^^^^^^
Throughout this documentation, references to the "mirror" mean the target
mirror which is checked for the presence of up-to-date specs, and where
any scheduled jobs should push built binary packages. In the past, this
defaulted to the mirror at index 0 in the mirror configs, and could be
overridden using the ``--buildcache-destination`` argument. Starting with
Spack 0.23, ``spack ci generate`` will require you to identify this mirror
by the name "buildcache-destination". While you can configure any number
of mirrors as sources for your pipelines, you will need to identify the
destination mirror by name.
Concretizes the specs in the active environment, stages them (as described in
:ref:`staging_algorithm`), and writes the resulting ``.gitlab-ci.yml`` to disk.
During concretization of the environment, ``spack ci generate`` also writes a

View File

@@ -4,7 +4,7 @@
SPDX-License-Identifier: (Apache-2.0 OR MIT)
=====================================
Using Spack to Replace Homebrew/Conda
Spack for Homebrew/Conda Users
=====================================
Spack is an incredibly powerful package manager, designed for supercomputers
@@ -191,18 +191,18 @@ The ``--fresh`` flag tells Spack to use the latest version of every package
where possible instead of trying to optimize for reuse of existing installed
packages.
The ``--force`` flag in addition tells Spack to overwrite its previous
concretization decisions, allowing you to choose a new version of Python.
If any of the new packages like Bash are already installed, ``spack install``
The ``--force`` flag in addition tells Spack to overwrite its previous
concretization decisions, allowing you to choose a new version of Python.
If any of the new packages like Bash are already installed, ``spack install``
won't re-install them, it will keep the symlinks in place.
-----------------------------------
Updating & Cleaning Up Old Packages
-----------------------------------
If you're looking to mimic the behavior of Homebrew, you may also want to
clean up out-of-date packages from your environment after an upgrade. To
upgrade your entire software stack within an environment and clean up old
If you're looking to mimic the behavior of Homebrew, you may also want to
clean up out-of-date packages from your environment after an upgrade. To
upgrade your entire software stack within an environment and clean up old
package versions, simply run the following commands:
.. code-block:: console
@@ -212,9 +212,9 @@ package versions, simply run the following commands:
$ spack concretize --fresh --force
$ spack install
$ spack gc
Running ``spack mark -i --all`` tells Spack to mark all of the existing
packages within an environment as "implicitly" installed. This tells
Running ``spack mark -i --all`` tells Spack to mark all of the existing
packages within an environment as "implicitly" installed. This tells
spack's garbage collection system that these packages should be cleaned up.
Don't worry however, this will not remove your entire environment.
@@ -223,8 +223,8 @@ a fresh concretization and will re-mark any packages that should remain
installed as "explicitly" installed.
**Note:** if you use multiple spack environments you should re-run ``spack install``
in each of your environments prior to running ``spack gc`` to prevent spack
from uninstalling any shared packages that are no longer required by the
in each of your environments prior to running ``spack gc`` to prevent spack
from uninstalling any shared packages that are no longer required by the
environment you just upgraded.
--------------

View File

@@ -1,13 +1,13 @@
sphinx==6.2.1
sphinx==7.2.6
sphinxcontrib-programoutput==0.17
sphinx_design==0.5.0
sphinx-rtd-theme==1.2.2
python-levenshtein==0.21.1
sphinx-rtd-theme==1.3.0
python-levenshtein==0.23.0
docutils==0.18.1
pygments==2.16.1
urllib3==2.0.4
pytest==7.4.0
urllib3==2.0.7
pytest==7.4.3
isort==5.12.0
black==23.7.0
black==23.11.0
flake8==6.1.0
mypy==1.5.0
mypy==1.7.0

View File

@@ -1,9 +1,7 @@
Name, Supported Versions, Notes, Requirement Reason
Python, 3.6--3.11, , Interpreter for Spack
Python, 3.6--3.12, , Interpreter for Spack
C/C++ Compilers, , , Building software
make, , , Build software
patch, , , Build software
bash, , , Compiler wrappers
tar, , , Extract/create archives
gzip, , , Compress/Decompress archives
unzip, , , Compress/Decompress archives
1 Name Supported Versions Notes Requirement Reason
2 Python 3.6--3.11 3.6--3.12 Interpreter for Spack
3 C/C++ Compilers Building software
make Build software
4 patch Build software
bash Compiler wrappers
5 tar Extract/create archives
6 gzip Compress/Decompress archives
7 unzip Compress/Decompress archives

View File

@@ -18,7 +18,7 @@
* Homepage: https://pypi.python.org/pypi/archspec
* Usage: Labeling, comparison and detection of microarchitectures
* Version: 0.2.1 (commit 9e1117bd8a2f0581bced161f2a2e8d6294d0300b)
* Version: 0.2.2 (commit 1dc58a5776dd77e6fc6e4ba5626af5b1fb24996e)
astunparse
----------------

View File

@@ -1,2 +1,2 @@
"""Init file to avoid namespace packages"""
__version__ = "0.2.0"
__version__ = "0.2.2"

View File

@@ -79,14 +79,18 @@ def __init__(self, name, parents, vendor, features, compilers, generation=0):
self.features = features
self.compilers = compilers
self.generation = generation
# Cache the ancestor computation
self._ancestors = None
@property
def ancestors(self):
"""All the ancestors of this microarchitecture."""
value = self.parents[:]
for parent in self.parents:
value.extend(a for a in parent.ancestors if a not in value)
return value
if self._ancestors is None:
value = self.parents[:]
for parent in self.parents:
value.extend(a for a in parent.ancestors if a not in value)
self._ancestors = value
return self._ancestors
def _to_set(self):
"""Returns a set of the nodes in this microarchitecture DAG."""

View File

@@ -145,6 +145,13 @@
"flags": "-march={name} -mtune=generic -mcx16 -msahf -mpopcnt -msse3 -msse4.1 -msse4.2 -mssse3"
}
],
"intel": [
{
"versions": "16.0:",
"name": "corei7",
"flags": "-march={name} -mtune=generic -mpopcnt"
}
],
"oneapi": [
{
"versions": "2021.2.0:",
@@ -217,6 +224,13 @@
"flags": "-march={name} -mtune=generic -mcx16 -msahf -mpopcnt -msse3 -msse4.1 -msse4.2 -mssse3 -mavx -mavx2 -mbmi -mbmi2 -mf16c -mfma -mlzcnt -mmovbe -mxsave"
}
],
"intel": [
{
"versions": "16.0:",
"name": "core-avx2",
"flags": "-march={name} -mtune={name} -fma -mf16c"
}
],
"oneapi": [
{
"versions": "2021.2.0:",
@@ -300,6 +314,13 @@
"flags": "-march={name} -mtune=generic -mcx16 -msahf -mpopcnt -msse3 -msse4.1 -msse4.2 -mssse3 -mavx -mavx2 -mbmi -mbmi2 -mf16c -mfma -mlzcnt -mmovbe -mxsave -mavx512f -mavx512bw -mavx512cd -mavx512dq -mavx512vl"
}
],
"intel": [
{
"versions": "16.0:",
"name": "skylake-avx512",
"flags": "-march={name} -mtune={name}"
}
],
"oneapi": [
{
"versions": "2021.2.0:",
@@ -1412,6 +1433,92 @@
]
}
},
"sapphirerapids": {
"from": [
"icelake"
],
"vendor": "GenuineIntel",
"features": [
"mmx",
"sse",
"sse2",
"ssse3",
"sse4_1",
"sse4_2",
"popcnt",
"aes",
"pclmulqdq",
"avx",
"rdrand",
"f16c",
"movbe",
"fma",
"avx2",
"bmi1",
"bmi2",
"rdseed",
"adx",
"clflushopt",
"xsavec",
"xsaveopt",
"avx512f",
"avx512vl",
"avx512bw",
"avx512dq",
"avx512cd",
"avx512vbmi",
"avx512ifma",
"sha_ni",
"clwb",
"rdpid",
"gfni",
"avx512_vbmi2",
"avx512_vpopcntdq",
"avx512_bitalg",
"avx512_vnni",
"vpclmulqdq",
"vaes",
"avx512_bf16",
"cldemote",
"movdir64b",
"movdiri",
"pdcm",
"serialize",
"waitpkg"
],
"compilers": {
"gcc": [
{
"versions": "11.0:",
"flags": "-march={name} -mtune={name}"
}
],
"clang": [
{
"versions": "12.0:",
"flags": "-march={name} -mtune={name}"
}
],
"intel": [
{
"versions": "2021.2:",
"flags": "-march={name} -mtune={name}"
}
],
"oneapi": [
{
"versions": "2021.2:",
"flags": "-march={name} -mtune={name}"
}
],
"dpcpp": [
{
"versions": "2021.2:",
"flags": "-march={name} -mtune={name}"
}
]
}
},
"k10": {
"from": ["x86_64"],
"vendor": "AuthenticAMD",
@@ -2065,8 +2172,6 @@
"pku",
"gfni",
"flush_l1d",
"erms",
"avic",
"avx512f",
"avx512dq",
"avx512ifma",
@@ -2083,12 +2188,12 @@
"compilers": {
"gcc": [
{
"versions": "10.3:13.0",
"versions": "10.3:12.2",
"name": "znver3",
"flags": "-march={name} -mtune={name} -mavx512f -mavx512dq -mavx512ifma -mavx512cd -mavx512bw -mavx512vl -mavx512vbmi -mavx512vbmi2 -mavx512vnni -mavx512bitalg"
},
{
"versions": "13.1:",
"versions": "12.3:",
"name": "znver4",
"flags": "-march={name} -mtune={name}"
}
@@ -2213,6 +2318,26 @@
]
}
},
"power10": {
"from": ["power9"],
"vendor": "IBM",
"generation": 10,
"features": [],
"compilers": {
"gcc": [
{
"versions": "11.1:",
"flags": "-mcpu={name} -mtune={name}"
}
],
"clang": [
{
"versions": "11.0:",
"flags": "-mcpu={name} -mtune={name}"
}
]
}
},
"ppc64le": {
"from": [],
"vendor": "generic",
@@ -2300,6 +2425,29 @@
]
}
},
"power10le": {
"from": ["power9le"],
"vendor": "IBM",
"generation": 10,
"features": [],
"compilers": {
"gcc": [
{
"name": "power10",
"versions": "11.1:",
"flags": "-mcpu={name} -mtune={name}"
}
],
"clang": [
{
"versions": "11.0:",
"family": "ppc64le",
"name": "power10",
"flags": "-mcpu={name} -mtune={name}"
}
]
}
},
"aarch64": {
"from": [],
"vendor": "generic",
@@ -2487,6 +2635,37 @@
]
}
},
"armv9.0a": {
"from": ["armv8.5a"],
"vendor": "generic",
"features": [],
"compilers": {
"gcc": [
{
"versions": "12:",
"flags": "-march=armv9-a -mtune=generic"
}
],
"clang": [
{
"versions": "14:",
"flags": "-march=armv9-a -mtune=generic"
}
],
"apple-clang": [
{
"versions": ":",
"flags": "-march=armv9-a -mtune=generic"
}
],
"arm": [
{
"versions": ":",
"flags": "-march=armv9-a -mtune=generic"
}
]
}
},
"thunderx2": {
"from": ["armv8.1a"],
"vendor": "Cavium",
@@ -2708,8 +2887,12 @@
],
"arm" : [
{
"versions": "20:",
"versions": "20:21.9",
"flags" : "-march=armv8.2-a+fp16+rcpc+dotprod+crypto"
},
{
"versions": "22:",
"flags" : "-mcpu=neoverse-n1"
}
],
"nvhpc" : [
@@ -2837,7 +3020,7 @@
},
{
"versions": "22:",
"flags" : "-march=armv8.4-a+sve+ssbs+fp16+bf16+crypto+i8mm+rng"
"flags" : "-mcpu=neoverse-v1"
}
],
"nvhpc" : [
@@ -2849,6 +3032,126 @@
]
}
},
"neoverse_v2": {
"from": ["neoverse_n1", "armv9.0a"],
"vendor": "ARM",
"features": [
"fp",
"asimd",
"evtstrm",
"aes",
"pmull",
"sha1",
"sha2",
"crc32",
"atomics",
"fphp",
"asimdhp",
"cpuid",
"asimdrdm",
"jscvt",
"fcma",
"lrcpc",
"dcpop",
"sha3",
"sm3",
"sm4",
"asimddp",
"sha512",
"sve",
"asimdfhm",
"dit",
"uscat",
"ilrcpc",
"flagm",
"ssbs",
"sb",
"paca",
"pacg",
"dcpodp",
"sve2",
"sveaes",
"svepmull",
"svebitperm",
"svesha3",
"svesm4",
"flagm2",
"frint",
"svei8mm",
"svebf16",
"i8mm",
"bf16",
"dgh",
"bti"
],
"compilers" : {
"gcc": [
{
"versions": "4.8:5.99",
"flags": "-march=armv8-a"
},
{
"versions": "6:6.99",
"flags" : "-march=armv8.1-a"
},
{
"versions": "7.0:7.99",
"flags" : "-march=armv8.2-a -mtune=cortex-a72"
},
{
"versions": "8.0:8.99",
"flags" : "-march=armv8.4-a+sve -mtune=cortex-a72"
},
{
"versions": "9.0:9.99",
"flags" : "-march=armv8.5-a+sve -mtune=cortex-a76"
},
{
"versions": "10.0:11.99",
"flags" : "-march=armv8.5-a+sve+sve2+i8mm+bf16 -mtune=cortex-a77"
},
{
"versions": "12.0:12.99",
"flags" : "-march=armv9-a+i8mm+bf16 -mtune=cortex-a710"
},
{
"versions": "13.0:",
"flags" : "-mcpu=neoverse-v2"
}
],
"clang" : [
{
"versions": "9.0:10.99",
"flags" : "-march=armv8.5-a+sve"
},
{
"versions": "11.0:13.99",
"flags" : "-march=armv8.5-a+sve+sve2+i8mm+bf16"
},
{
"versions": "14.0:15.99",
"flags" : "-march=armv9-a+i8mm+bf16"
},
{
"versions": "16.0:",
"flags" : "-mcpu=neoverse-v2"
}
],
"arm" : [
{
"versions": "23.04.0:",
"flags" : "-mcpu=neoverse-v2"
}
],
"nvhpc" : [
{
"versions": "23.3:",
"name": "neoverse-v2",
"flags": "-tp {name}"
}
]
}
},
"m1": {
"from": ["armv8.4a"],
"vendor": "Apple",

105
lib/spack/llnl/path.py Normal file
View File

@@ -0,0 +1,105 @@
# 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)
"""Path primitives that just require Python standard library."""
import functools
import sys
from typing import List, Optional
from urllib.parse import urlparse
class Path:
"""Enum to identify the path-style."""
unix: int = 0
windows: int = 1
platform_path: int = windows if sys.platform == "win32" else unix
def format_os_path(path: str, mode: int = Path.unix) -> str:
"""Formats the input path to use consistent, platform specific separators.
Absolute paths are converted between drive letters and a prepended '/' as per platform
requirement.
Parameters:
path: the path to be normalized, must be a string or expose the replace method.
mode: the path file separator style to normalize the passed path to.
Default is unix style, i.e. '/'
"""
if not path:
return path
if mode == Path.windows:
path = path.replace("/", "\\")
else:
path = path.replace("\\", "/")
return path
def convert_to_posix_path(path: str) -> str:
"""Converts the input path to POSIX style."""
return format_os_path(path, mode=Path.unix)
def convert_to_windows_path(path: str) -> str:
"""Converts the input path to Windows style."""
return format_os_path(path, mode=Path.windows)
def convert_to_platform_path(path: str) -> str:
"""Converts the input path to the current platform's native style."""
return format_os_path(path, mode=Path.platform_path)
def path_to_os_path(*parameters: str) -> List[str]:
"""Takes an arbitrary number of positional parameters, converts each argument of type
string to use a normalized filepath separator, and returns a list of all values.
"""
def _is_url(path_or_url: str) -> bool:
if "\\" in path_or_url:
return False
url_tuple = urlparse(path_or_url)
return bool(url_tuple.scheme) and len(url_tuple.scheme) > 1
result = []
for item in parameters:
if isinstance(item, str) and not _is_url(item):
item = convert_to_platform_path(item)
result.append(item)
return result
def system_path_filter(_func=None, arg_slice: Optional[slice] = None):
"""Filters function arguments to account for platform path separators.
Optional slicing range can be specified to select specific arguments
This decorator takes all (or a slice) of a method's positional arguments
and normalizes usage of filepath separators on a per platform basis.
Note: `**kwargs`, urls, and any type that is not a string are ignored
so in such cases where path normalization is required, that should be
handled by calling path_to_os_path directly as needed.
Parameters:
arg_slice: a slice object specifying the slice of arguments
in the decorated method over which filepath separators are
normalized
"""
def holder_func(func):
@functools.wraps(func)
def path_filter_caller(*args, **kwargs):
args = list(args)
if arg_slice:
args[arg_slice] = path_to_os_path(*args[arg_slice])
else:
args = path_to_os_path(*args)
return func(*args, **kwargs)
return path_filter_caller
if _func:
return holder_func(_func)
return holder_func

67
lib/spack/llnl/string.py Normal file
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@@ -0,0 +1,67 @@
# 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)
"""String manipulation functions that do not have other dependencies than Python
standard library
"""
from typing import List, Optional
def comma_list(sequence: List[str], article: str = "") -> str:
if type(sequence) is not list:
sequence = list(sequence)
if not sequence:
return ""
if len(sequence) == 1:
return sequence[0]
out = ", ".join(str(s) for s in sequence[:-1])
if len(sequence) != 2:
out += "," # oxford comma
out += " "
if article:
out += article + " "
out += str(sequence[-1])
return out
def comma_or(sequence: List[str]) -> str:
"""Return a string with all the elements of the input joined by comma, but the last
one (which is joined by 'or').
"""
return comma_list(sequence, "or")
def comma_and(sequence: List[str]) -> str:
"""Return a string with all the elements of the input joined by comma, but the last
one (which is joined by 'and').
"""
return comma_list(sequence, "and")
def quote(sequence: List[str], q: str = "'") -> List[str]:
"""Quotes each item in the input list with the quote character passed as second argument."""
return [f"{q}{e}{q}" for e in sequence]
def plural(n: int, singular: str, plural: Optional[str] = None, show_n: bool = True) -> str:
"""Pluralize <singular> word by adding an s if n != 1.
Arguments:
n: number of things there are
singular: singular form of word
plural: optional plural form, for when it's not just singular + 's'
show_n: whether to include n in the result string (default True)
Returns:
"1 thing" if n == 1 or "n things" if n != 1
"""
number = f"{n} " if show_n else ""
if n == 1:
return f"{number}{singular}"
elif plural is not None:
return f"{number}{plural}"
else:
return f"{number}{singular}s"

459
lib/spack/llnl/url.py Normal file
View File

@@ -0,0 +1,459 @@
# 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)
"""URL primitives that just require Python standard library."""
import itertools
import os.path
import re
from typing import Optional, Set, Tuple
from urllib.parse import urlsplit, urlunsplit
# Archive extensions allowed in Spack
PREFIX_EXTENSIONS = ("tar", "TAR")
EXTENSIONS = ("gz", "bz2", "xz", "Z")
NO_TAR_EXTENSIONS = ("zip", "tgz", "tbz2", "tbz", "txz")
# Add PREFIX_EXTENSIONS and EXTENSIONS last so that .tar.gz is matched *before* .tar or .gz
ALLOWED_ARCHIVE_TYPES = (
tuple(".".join(ext) for ext in itertools.product(PREFIX_EXTENSIONS, EXTENSIONS))
+ PREFIX_EXTENSIONS
+ EXTENSIONS
+ NO_TAR_EXTENSIONS
)
CONTRACTION_MAP = {"tgz": "tar.gz", "txz": "tar.xz", "tbz": "tar.bz2", "tbz2": "tar.bz2"}
def find_list_urls(url: str) -> Set[str]:
r"""Find good list URLs for the supplied URL.
By default, returns the dirname of the archive path.
Provides special treatment for the following websites, which have a
unique list URL different from the dirname of the download URL:
========= =======================================================
GitHub https://github.com/<repo>/<name>/releases
GitLab https://gitlab.\*/<repo>/<name>/tags
BitBucket https://bitbucket.org/<repo>/<name>/downloads/?tab=tags
CRAN https://\*.r-project.org/src/contrib/Archive/<name>
PyPI https://pypi.org/simple/<name>/
LuaRocks https://luarocks.org/modules/<repo>/<name>
========= =======================================================
Note: this function is called by `spack versions`, `spack checksum`,
and `spack create`, but not by `spack fetch` or `spack install`.
Parameters:
url (str): The download URL for the package
Returns:
set: One or more list URLs for the package
"""
url_types = [
# GitHub
# e.g. https://github.com/llnl/callpath/archive/v1.0.1.tar.gz
(r"(.*github\.com/[^/]+/[^/]+)", lambda m: m.group(1) + "/releases"),
# GitLab API endpoint
# e.g. https://gitlab.dkrz.de/api/v4/projects/k202009%2Flibaec/repository/archive.tar.gz?sha=v1.0.2
(
r"(.*gitlab[^/]+)/api/v4/projects/([^/]+)%2F([^/]+)",
lambda m: m.group(1) + "/" + m.group(2) + "/" + m.group(3) + "/tags",
),
# GitLab non-API endpoint
# e.g. https://gitlab.dkrz.de/k202009/libaec/uploads/631e85bcf877c2dcaca9b2e6d6526339/libaec-1.0.0.tar.gz
(r"(.*gitlab[^/]+/(?!api/v4/projects)[^/]+/[^/]+)", lambda m: m.group(1) + "/tags"),
# BitBucket
# e.g. https://bitbucket.org/eigen/eigen/get/3.3.3.tar.bz2
(r"(.*bitbucket.org/[^/]+/[^/]+)", lambda m: m.group(1) + "/downloads/?tab=tags"),
# CRAN
# e.g. https://cran.r-project.org/src/contrib/Rcpp_0.12.9.tar.gz
# e.g. https://cloud.r-project.org/src/contrib/rgl_0.98.1.tar.gz
(
r"(.*\.r-project\.org/src/contrib)/([^_]+)",
lambda m: m.group(1) + "/Archive/" + m.group(2),
),
# PyPI
# e.g. https://pypi.io/packages/source/n/numpy/numpy-1.19.4.zip
# e.g. https://www.pypi.io/packages/source/n/numpy/numpy-1.19.4.zip
# e.g. https://pypi.org/packages/source/n/numpy/numpy-1.19.4.zip
# e.g. https://pypi.python.org/packages/source/n/numpy/numpy-1.19.4.zip
# e.g. https://files.pythonhosted.org/packages/source/n/numpy/numpy-1.19.4.zip
# e.g. https://pypi.io/packages/py2.py3/o/opencensus-context/opencensus_context-0.1.1-py2.py3-none-any.whl
(
r"(?:pypi|pythonhosted)[^/]+/packages/[^/]+/./([^/]+)",
lambda m: "https://pypi.org/simple/" + m.group(1) + "/",
),
# LuaRocks
# e.g. https://luarocks.org/manifests/gvvaughan/lpeg-1.0.2-1.src.rock
# e.g. https://luarocks.org/manifests/openresty/lua-cjson-2.1.0-1.src.rock
(
r"luarocks[^/]+/(?:modules|manifests)/(?P<org>[^/]+)/"
+ r"(?P<name>.+?)-[0-9.-]*\.src\.rock",
lambda m: "https://luarocks.org/modules/"
+ m.group("org")
+ "/"
+ m.group("name")
+ "/",
),
]
list_urls = {os.path.dirname(url)}
for pattern, fun in url_types:
match = re.search(pattern, url)
if match:
list_urls.add(fun(match))
return list_urls
def strip_query_and_fragment(url: str) -> Tuple[str, str]:
"""Strips query and fragment from a url, then returns the base url and the suffix.
Args:
url: URL to be stripped
Raises:
ValueError: when there is any error parsing the URL
"""
components = urlsplit(url)
stripped = components[:3] + (None, None)
query, frag = components[3:5]
suffix = ""
if query:
suffix += "?" + query
if frag:
suffix += "#" + frag
return urlunsplit(stripped), suffix
SOURCEFORGE_RE = re.compile(r"(.*(?:sourceforge\.net|sf\.net)/.*)(/download)$")
def split_url_on_sourceforge_suffix(url: str) -> Tuple[str, ...]:
"""If the input is a sourceforge URL, returns base URL and "/download" suffix. Otherwise,
returns the input URL and an empty string.
"""
match = SOURCEFORGE_RE.search(url)
if match is not None:
return match.groups()
return url, ""
def has_extension(path_or_url: str, ext: str) -> bool:
"""Returns true if the extension in input is present in path, false otherwise."""
prefix, _ = split_url_on_sourceforge_suffix(path_or_url)
if not ext.startswith(r"\."):
ext = rf"\.{ext}$"
if re.search(ext, prefix):
return True
return False
def extension_from_path(path_or_url: Optional[str]) -> Optional[str]:
"""Tries to match an allowed archive extension to the input. Returns the first match,
or None if no match was found.
Raises:
ValueError: if the input is None
"""
if path_or_url is None:
raise ValueError("Can't call extension() on None")
for t in ALLOWED_ARCHIVE_TYPES:
if has_extension(path_or_url, t):
return t
return None
def remove_extension(path_or_url: str, *, extension: str) -> str:
"""Returns the input with the extension removed"""
suffix = rf"\.{extension}$"
return re.sub(suffix, "", path_or_url)
def check_and_remove_ext(path: str, *, extension: str) -> str:
"""Returns the input path with the extension removed, if the extension is present in path.
Otherwise, returns the input unchanged.
"""
if not has_extension(path, extension):
return path
path, _ = split_url_on_sourceforge_suffix(path)
return remove_extension(path, extension=extension)
def strip_extension(path_or_url: str, *, extension: Optional[str] = None) -> str:
"""If a path contains the extension in input, returns the path stripped of the extension.
Otherwise, returns the input path.
If extension is None, attempts to strip any allowed extension from path.
"""
if extension is None:
for t in ALLOWED_ARCHIVE_TYPES:
if has_extension(path_or_url, ext=t):
extension = t
break
else:
return path_or_url
return check_and_remove_ext(path_or_url, extension=extension)
def split_url_extension(url: str) -> Tuple[str, ...]:
"""Some URLs have a query string, e.g.:
1. https://github.com/losalamos/CLAMR/blob/packages/PowerParser_v2.0.7.tgz?raw=true
2. http://www.apache.org/dyn/closer.cgi?path=/cassandra/1.2.0/apache-cassandra-1.2.0-rc2-bin.tar.gz
3. https://gitlab.kitware.com/vtk/vtk/repository/archive.tar.bz2?ref=v7.0.0
In (1), the query string needs to be stripped to get at the
extension, but in (2) & (3), the filename is IN a single final query
argument.
This strips the URL into three pieces: ``prefix``, ``ext``, and ``suffix``.
The suffix contains anything that was stripped off the URL to
get at the file extension. In (1), it will be ``'?raw=true'``, but
in (2), it will be empty. In (3) the suffix is a parameter that follows
after the file extension, e.g.:
1. ``('https://github.com/losalamos/CLAMR/blob/packages/PowerParser_v2.0.7', '.tgz', '?raw=true')``
2. ``('http://www.apache.org/dyn/closer.cgi?path=/cassandra/1.2.0/apache-cassandra-1.2.0-rc2-bin', '.tar.gz', None)``
3. ``('https://gitlab.kitware.com/vtk/vtk/repository/archive', '.tar.bz2', '?ref=v7.0.0')``
"""
# Strip off sourceforge download suffix.
# e.g. https://sourceforge.net/projects/glew/files/glew/2.0.0/glew-2.0.0.tgz/download
prefix, suffix = split_url_on_sourceforge_suffix(url)
ext = extension_from_path(prefix)
if ext is not None:
prefix = strip_extension(prefix)
return prefix, ext, suffix
try:
prefix, suf = strip_query_and_fragment(prefix)
except ValueError:
# FIXME: tty.debug("Got error parsing path %s" % path)
# Ignore URL parse errors here
return url, ""
ext = extension_from_path(prefix)
prefix = strip_extension(prefix)
suffix = suf + suffix
if ext is None:
ext = ""
return prefix, ext, suffix
def strip_version_suffixes(path_or_url: str) -> str:
"""Some tarballs contain extraneous information after the version:
* ``bowtie2-2.2.5-source``
* ``libevent-2.0.21-stable``
* ``cuda_8.0.44_linux.run``
These strings are not part of the version number and should be ignored.
This function strips those suffixes off and returns the remaining string.
The goal is that the version is always the last thing in ``path``:
* ``bowtie2-2.2.5``
* ``libevent-2.0.21``
* ``cuda_8.0.44``
Args:
path_or_url: The filename or URL for the package
Returns:
The ``path`` with any extraneous suffixes removed
"""
# NOTE: This could be done with complicated regexes in parse_version_offset
# NOTE: The problem is that we would have to add these regexes to the end
# NOTE: of every single version regex. Easier to just strip them off
# NOTE: permanently
suffix_regexes = [
# Download type
r"[Ii]nstall",
r"all",
r"code",
r"[Ss]ources?",
r"file",
r"full",
r"single",
r"with[a-zA-Z_-]+",
r"rock",
r"src(_0)?",
r"public",
r"bin",
r"binary",
r"run",
r"[Uu]niversal",
r"jar",
r"complete",
r"dynamic",
r"oss",
r"gem",
r"tar",
r"sh",
# Download version
r"release",
r"bin",
r"stable",
r"[Ff]inal",
r"rel",
r"orig",
r"dist",
r"\+",
# License
r"gpl",
# Arch
# Needs to come before and after OS, appears in both orders
r"ia32",
r"intel",
r"amd64",
r"linux64",
r"x64",
r"64bit",
r"x86[_-]64",
r"i586_64",
r"x86",
r"i[36]86",
r"ppc64(le)?",
r"armv?(7l|6l|64)",
# Other
r"cpp",
r"gtk",
r"incubating",
# OS
r"[Ll]inux(_64)?",
r"LINUX",
r"[Uu]ni?x",
r"[Ss]un[Oo][Ss]",
r"[Mm]ac[Oo][Ss][Xx]?",
r"[Oo][Ss][Xx]",
r"[Dd]arwin(64)?",
r"[Aa]pple",
r"[Ww]indows",
r"[Ww]in(64|32)?",
r"[Cc]ygwin(64|32)?",
r"[Mm]ingw",
r"centos",
# Arch
# Needs to come before and after OS, appears in both orders
r"ia32",
r"intel",
r"amd64",
r"linux64",
r"x64",
r"64bit",
r"x86[_-]64",
r"i586_64",
r"x86",
r"i[36]86",
r"ppc64(le)?",
r"armv?(7l|6l|64)?",
# PyPI
r"[._-]py[23].*\.whl",
r"[._-]cp[23].*\.whl",
r"[._-]win.*\.exe",
]
for regex in suffix_regexes:
# Remove the suffix from the end of the path
# This may be done multiple times
path_or_url = re.sub(r"[._-]?" + regex + "$", "", path_or_url)
return path_or_url
def expand_contracted_extension(extension: str) -> str:
"""Returns the expanded version of a known contracted extension.
This function maps extensions like ".tgz" to ".tar.gz". On unknown extensions,
return the input unmodified.
"""
extension = extension.strip(".")
return CONTRACTION_MAP.get(extension, extension)
def expand_contracted_extension_in_path(
path_or_url: str, *, extension: Optional[str] = None
) -> str:
"""Returns the input path or URL with any contraction extension expanded.
Args:
path_or_url: path or URL to be expanded
extension: if specified, only attempt to expand that extension
"""
extension = extension or extension_from_path(path_or_url)
if extension is None:
return path_or_url
expanded = expand_contracted_extension(extension)
if expanded != extension:
return re.sub(rf"{extension}", rf"{expanded}", path_or_url)
return path_or_url
def compression_ext_from_compressed_archive(extension: str) -> Optional[str]:
"""Returns compression extension for a compressed archive"""
extension = expand_contracted_extension(extension)
for ext in [*EXTENSIONS]:
if ext in extension:
return ext
return None
def strip_compression_extension(path_or_url: str, ext: Optional[str] = None) -> str:
"""Strips the compression extension from the input, and returns it. For instance,
"foo.tgz" becomes "foo.tar".
If no extension is given, try a default list of extensions.
Args:
path_or_url: input to be stripped
ext: if given, extension to be stripped
"""
if not extension_from_path(path_or_url):
return path_or_url
expanded_path = expand_contracted_extension_in_path(path_or_url)
candidates = [ext] if ext is not None else EXTENSIONS
for current_extension in candidates:
modified_path = check_and_remove_ext(expanded_path, extension=current_extension)
if modified_path != expanded_path:
return modified_path
return expanded_path
def allowed_archive(path_or_url: str) -> bool:
"""Returns true if the input is a valid archive, False otherwise."""
return (
False if not path_or_url else any(path_or_url.endswith(t) for t in ALLOWED_ARCHIVE_TYPES)
)
def determine_url_file_extension(path: str) -> str:
"""This returns the type of archive a URL refers to. This is
sometimes confusing because of URLs like:
(1) https://github.com/petdance/ack/tarball/1.93_02
Where the URL doesn't actually contain the filename. We need
to know what type it is so that we can appropriately name files
in mirrors.
"""
match = re.search(r"github.com/.+/(zip|tar)ball/", path)
if match:
if match.group(1) == "zip":
return "zip"
elif match.group(1) == "tar":
return "tar.gz"
prefix, ext, suffix = split_url_extension(path)
return ext

View File

@@ -11,6 +11,7 @@
import itertools
import numbers
import os
import pathlib
import posixpath
import re
import shutil
@@ -18,14 +19,17 @@
import sys
import tempfile
from contextlib import contextmanager
from itertools import accumulate
from typing import Callable, Iterable, List, Match, Optional, Tuple, Union
import llnl.util.symlink
from llnl.util import tty
from llnl.util.lang import dedupe, memoized
from llnl.util.symlink import islink, symlink
from llnl.util.symlink import islink, readlink, resolve_link_target_relative_to_the_link, symlink
from spack.util.executable import Executable, which
from spack.util.path import path_to_os_path, system_path_filter
from ..path import path_to_os_path, system_path_filter
if sys.platform != "win32":
import grp
@@ -101,7 +105,7 @@ def _nop(args, ns=None, follow_symlinks=None):
pass
# follow symlinks (aka don't not follow symlinks)
follow = follow_symlinks or not (os.path.islink(src) and os.path.islink(dst))
follow = follow_symlinks or not (islink(src) and islink(dst))
if follow:
# use the real function if it exists
def lookup(name):
@@ -152,6 +156,37 @@ def lookup(name):
shutil.copystat = copystat
def polite_path(components: Iterable[str]):
"""
Given a list of strings which are intended to be path components,
generate a path, and format each component to avoid generating extra
path entries.
For example all "/", "\", and ":" characters will be replaced with
"_". Other characters like "=" will also be replaced.
"""
return os.path.join(*[polite_filename(x) for x in components])
@memoized
def _polite_antipattern():
# A regex of all the characters we don't want in a filename
return re.compile(r"[^A-Za-z0-9_.-]")
def polite_filename(filename: str) -> str:
"""
Replace generally problematic filename characters with underscores.
This differs from sanitize_filename in that it is more aggressive in
changing characters in the name. For example it removes "=" which can
confuse path parsing in external tools.
"""
# This character set applies for both Windows and Linux. It does not
# account for reserved filenames in Windows.
return _polite_antipattern().sub("_", filename)
def getuid():
if sys.platform == "win32":
import ctypes
@@ -169,7 +204,7 @@ def rename(src, dst):
if sys.platform == "win32":
# Windows path existence checks will sometimes fail on junctions/links/symlinks
# so check for that case
if os.path.exists(dst) or os.path.islink(dst):
if os.path.exists(dst) or islink(dst):
os.remove(dst)
os.rename(src, dst)
@@ -333,8 +368,7 @@ def groupid_to_group(x):
if string:
regex = re.escape(regex)
filenames = path_to_os_path(*filenames)
for filename in filenames:
for filename in path_to_os_path(*filenames):
msg = 'FILTER FILE: {0} [replacing "{1}"]'
tty.debug(msg.format(filename, regex))
@@ -566,7 +600,7 @@ def set_install_permissions(path):
# If this points to a file maintained in a Spack prefix, it is assumed that
# this function will be invoked on the target. If the file is outside a
# Spack-maintained prefix, the permissions should not be modified.
if os.path.islink(path):
if islink(path):
return
if os.path.isdir(path):
os.chmod(path, 0o755)
@@ -635,7 +669,7 @@ def chmod_x(entry, perms):
@system_path_filter
def copy_mode(src, dest):
"""Set the mode of dest to that of src unless it is a link."""
if os.path.islink(dest):
if islink(dest):
return
src_mode = os.stat(src).st_mode
dest_mode = os.stat(dest).st_mode
@@ -721,26 +755,12 @@ def install(src, dest):
copy(src, dest, _permissions=True)
@system_path_filter
def resolve_link_target_relative_to_the_link(link):
"""
os.path.isdir uses os.path.exists, which for links will check
the existence of the link target. If the link target is relative to
the link, we need to construct a pathname that is valid from
our cwd (which may not be the same as the link's directory)
"""
target = os.readlink(link)
if os.path.isabs(target):
return target
link_dir = os.path.dirname(os.path.abspath(link))
return os.path.join(link_dir, target)
@system_path_filter
def copy_tree(
src: str,
dest: str,
symlinks: bool = True,
allow_broken_symlinks: bool = sys.platform != "win32",
ignore: Optional[Callable[[str], bool]] = None,
_permissions: bool = False,
):
@@ -763,6 +783,8 @@ def copy_tree(
src (str): the directory to copy
dest (str): the destination directory
symlinks (bool): whether or not to preserve symlinks
allow_broken_symlinks (bool): whether or not to allow broken (dangling) symlinks,
On Windows, setting this to True will raise an exception. Defaults to true on unix.
ignore (typing.Callable): function indicating which files to ignore
_permissions (bool): for internal use only
@@ -770,6 +792,8 @@ def copy_tree(
IOError: if *src* does not match any files or directories
ValueError: if *src* is a parent directory of *dest*
"""
if allow_broken_symlinks and sys.platform == "win32":
raise llnl.util.symlink.SymlinkError("Cannot allow broken symlinks on Windows!")
if _permissions:
tty.debug("Installing {0} to {1}".format(src, dest))
else:
@@ -783,6 +807,11 @@ def copy_tree(
if not files:
raise IOError("No such file or directory: '{0}'".format(src))
# For Windows hard-links and junctions, the source path must exist to make a symlink. Add
# all symlinks to this list while traversing the tree, then when finished, make all
# symlinks at the end.
links = []
for src in files:
abs_src = os.path.abspath(src)
if not abs_src.endswith(os.path.sep):
@@ -805,7 +834,7 @@ def copy_tree(
ignore=ignore,
follow_nonexisting=True,
):
if os.path.islink(s):
if islink(s):
link_target = resolve_link_target_relative_to_the_link(s)
if symlinks:
target = os.readlink(s)
@@ -819,7 +848,9 @@ def escaped_path(path):
tty.debug("Redirecting link {0} to {1}".format(target, new_target))
target = new_target
symlink(target, d)
links.append((target, d, s))
continue
elif os.path.isdir(link_target):
mkdirp(d)
else:
@@ -834,9 +865,17 @@ def escaped_path(path):
set_install_permissions(d)
copy_mode(s, d)
for target, d, s in links:
symlink(target, d, allow_broken_symlinks=allow_broken_symlinks)
if _permissions:
set_install_permissions(d)
copy_mode(s, d)
@system_path_filter
def install_tree(src, dest, symlinks=True, ignore=None):
def install_tree(
src, dest, symlinks=True, ignore=None, allow_broken_symlinks=sys.platform != "win32"
):
"""Recursively install an entire directory tree rooted at *src*.
Same as :py:func:`copy_tree` with the addition of setting proper
@@ -847,12 +886,21 @@ def install_tree(src, dest, symlinks=True, ignore=None):
dest (str): the destination directory
symlinks (bool): whether or not to preserve symlinks
ignore (typing.Callable): function indicating which files to ignore
allow_broken_symlinks (bool): whether or not to allow broken (dangling) symlinks,
On Windows, setting this to True will raise an exception.
Raises:
IOError: if *src* does not match any files or directories
ValueError: if *src* is a parent directory of *dest*
"""
copy_tree(src, dest, symlinks=symlinks, ignore=ignore, _permissions=True)
copy_tree(
src,
dest,
symlinks=symlinks,
allow_broken_symlinks=allow_broken_symlinks,
ignore=ignore,
_permissions=True,
)
@system_path_filter
@@ -1256,7 +1304,12 @@ def traverse_tree(
Keyword Arguments:
order (str): Whether to do pre- or post-order traversal. Accepted
values are 'pre' and 'post'
ignore (typing.Callable): function indicating which files to ignore
ignore (typing.Callable): function indicating which files to ignore. This will also
ignore symlinks if they point to an ignored file (regardless of whether the symlink
is explicitly ignored); note this only supports one layer of indirection (i.e. if
you have x -> y -> z, and z is ignored but x/y are not, then y would be ignored
but not x). To avoid this, make sure the ignore function also ignores the symlink
paths too.
follow_nonexisting (bool): Whether to descend into directories in
``src`` that do not exit in ``dest``. Default is True
follow_links (bool): Whether to descend into symlinks in ``src``
@@ -1283,11 +1336,24 @@ def traverse_tree(
dest_child = os.path.join(dest_path, f)
rel_child = os.path.join(rel_path, f)
# If the source path is a link and the link's source is ignored, then ignore the link too,
# but only do this if the ignore is defined.
if ignore is not None:
if islink(source_child) and not follow_links:
target = readlink(source_child)
all_parents = accumulate(target.split(os.sep), lambda x, y: os.path.join(x, y))
if any(map(ignore, all_parents)):
tty.warn(
f"Skipping {source_path} because the source or a part of the source's "
f"path is included in the ignores."
)
continue
# Treat as a directory
# TODO: for symlinks, os.path.isdir looks for the link target. If the
# target is relative to the link, then that may not resolve properly
# relative to our cwd - see resolve_link_target_relative_to_the_link
if os.path.isdir(source_child) and (follow_links or not os.path.islink(source_child)):
if os.path.isdir(source_child) and (follow_links or not islink(source_child)):
# When follow_nonexisting isn't set, don't descend into dirs
# in source that do not exist in dest
if follow_nonexisting or os.path.exists(dest_child):
@@ -1313,7 +1379,11 @@ def traverse_tree(
def lexists_islink_isdir(path):
"""Computes the tuple (lexists(path), islink(path), isdir(path)) in a minimal
number of stat calls."""
number of stat calls on unix. Use os.path and symlink.islink methods for windows."""
if sys.platform == "win32":
if not os.path.lexists(path):
return False, False, False
return os.path.lexists(path), islink(path), os.path.isdir(path)
# First try to lstat, so we know if it's a link or not.
try:
lst = os.lstat(path)
@@ -1528,7 +1598,7 @@ def remove_if_dead_link(path):
Parameters:
path (str): The potential dead link
"""
if os.path.islink(path) and not os.path.exists(path):
if islink(path) and not os.path.exists(path):
os.unlink(path)
@@ -1587,7 +1657,7 @@ def remove_linked_tree(path):
kwargs["onerror"] = readonly_file_handler(ignore_errors=True)
if os.path.exists(path):
if os.path.islink(path):
if islink(path):
shutil.rmtree(os.path.realpath(path), **kwargs)
os.unlink(path)
else:
@@ -2388,7 +2458,7 @@ def library_dependents(self):
"""
Set of directories where package binaries/libraries are located.
"""
return set([self.pkg.prefix.bin]) | self._additional_library_dependents
return set([pathlib.Path(self.pkg.prefix.bin)]) | self._additional_library_dependents
def add_library_dependent(self, *dest):
"""
@@ -2401,9 +2471,9 @@ def add_library_dependent(self, *dest):
"""
for pth in dest:
if os.path.isfile(pth):
self._additional_library_dependents.add(os.path.dirname)
self._additional_library_dependents.add(pathlib.Path(pth).parent)
else:
self._additional_library_dependents.add(pth)
self._additional_library_dependents.add(pathlib.Path(pth))
@property
def rpaths(self):
@@ -2416,7 +2486,7 @@ def rpaths(self):
dependent_libs.extend(list(find_all_shared_libraries(path, recursive=True)))
for extra_path in self._addl_rpaths:
dependent_libs.extend(list(find_all_shared_libraries(extra_path, recursive=True)))
return set(dependent_libs)
return set([pathlib.Path(x) for x in dependent_libs])
def add_rpath(self, *paths):
"""
@@ -2432,7 +2502,7 @@ def add_rpath(self, *paths):
"""
self._addl_rpaths = self._addl_rpaths | set(paths)
def _link(self, path, dest_dir):
def _link(self, path: pathlib.Path, dest_dir: pathlib.Path):
"""Perform link step of simulated rpathing, installing
simlinks of file in path to the dest_dir
location. This method deliberately prevents
@@ -2440,27 +2510,35 @@ def _link(self, path, dest_dir):
This is because it is both meaningless from an rpath
perspective, and will cause an error when Developer
mode is not enabled"""
file_name = os.path.basename(path)
dest_file = os.path.join(dest_dir, file_name)
if os.path.exists(dest_dir) and not dest_file == path:
def report_already_linked():
# We have either already symlinked or we are encoutering a naming clash
# either way, we don't want to overwrite existing libraries
already_linked = islink(str(dest_file))
tty.debug(
"Linking library %s to %s failed, " % (str(path), str(dest_file))
+ "already linked."
if already_linked
else "library with name %s already exists at location %s."
% (str(file_name), str(dest_dir))
)
file_name = path.name
dest_file = dest_dir / file_name
if not dest_file.exists() and dest_dir.exists() and not dest_file == path:
try:
symlink(path, dest_file)
symlink(str(path), str(dest_file))
# For py2 compatibility, we have to catch the specific Windows error code
# associate with trying to create a file that already exists (winerror 183)
# Catch OSErrors missed by the SymlinkError checks
except OSError as e:
if sys.platform == "win32" and (e.winerror == 183 or e.errno == errno.EEXIST):
# We have either already symlinked or we are encoutering a naming clash
# either way, we don't want to overwrite existing libraries
already_linked = islink(dest_file)
tty.debug(
"Linking library %s to %s failed, " % (path, dest_file) + "already linked."
if already_linked
else "library with name %s already exists at location %s."
% (file_name, dest_dir)
)
pass
report_already_linked()
else:
raise e
# catch errors we raise ourselves from Spack
except llnl.util.symlink.AlreadyExistsError:
report_already_linked()
def establish_link(self):
"""
@@ -2693,7 +2771,7 @@ def remove_directory_contents(dir):
"""Remove all contents of a directory."""
if os.path.exists(dir):
for entry in [os.path.join(dir, entry) for entry in os.listdir(dir)]:
if os.path.isfile(entry) or os.path.islink(entry):
if os.path.isfile(entry) or islink(entry):
os.unlink(entry)
else:
shutil.rmtree(entry)

View File

@@ -14,7 +14,7 @@
from llnl.util import lang, tty
import spack.util.string
from ..string import plural
if sys.platform != "win32":
import fcntl
@@ -169,7 +169,7 @@ def _attempts_str(wait_time, nattempts):
if nattempts <= 1:
return ""
attempts = spack.util.string.plural(nattempts, "attempt")
attempts = plural(nattempts, "attempt")
return " after {} and {}".format(lang.pretty_seconds(wait_time), attempts)

View File

@@ -2,77 +2,189 @@
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import errno
import os
import re
import shutil
import subprocess
import sys
import tempfile
from os.path import exists, join
from llnl.util import lang
from llnl.util import lang, tty
from ..path import system_path_filter
if sys.platform == "win32":
from win32file import CreateHardLink
is_windows = sys.platform == "win32"
def symlink(real_path, link_path):
"""
Create a symbolic link.
On Windows, use junctions if os.symlink fails.
def symlink(source_path: str, link_path: str, allow_broken_symlinks: bool = not is_windows):
"""
if sys.platform != "win32":
os.symlink(real_path, link_path)
elif _win32_can_symlink():
# Windows requires target_is_directory=True when the target is a dir.
os.symlink(real_path, link_path, target_is_directory=os.path.isdir(real_path))
else:
try:
# Try to use junctions
_win32_junction(real_path, link_path)
except OSError as e:
if e.errno == errno.EEXIST:
# EEXIST error indicates that file we're trying to "link"
# is already present, don't bother trying to copy which will also fail
# just raise
raise
Create a link.
On non-Windows and Windows with System Administrator
privleges this will be a normal symbolic link via
os.symlink.
On Windows without privledges the link will be a
junction for a directory and a hardlink for a file.
On Windows the various link types are:
Symbolic Link: A link to a file or directory on the
same or different volume (drive letter) or even to
a remote file or directory (using UNC in its path).
Need System Administrator privileges to make these.
Hard Link: A link to a file on the same volume (drive
letter) only. Every file (file's data) has at least 1
hard link (file's name). But when this method creates
a new hard link there will be 2. Deleting all hard
links effectively deletes the file. Don't need System
Administrator privileges.
Junction: A link to a directory on the same or different
volume (drive letter) but not to a remote directory. Don't
need System Administrator privileges.
Parameters:
source_path (str): The real file or directory that the link points to.
Must be absolute OR relative to the link.
link_path (str): The path where the link will exist.
allow_broken_symlinks (bool): On Linux or Mac, don't raise an exception if the source_path
doesn't exist. This will still raise an exception on Windows.
"""
source_path = os.path.normpath(source_path)
win_source_path = source_path
link_path = os.path.normpath(link_path)
# Never allow broken links on Windows.
if sys.platform == "win32" and allow_broken_symlinks:
raise ValueError("allow_broken_symlinks parameter cannot be True on Windows.")
if not allow_broken_symlinks:
# Perform basic checks to make sure symlinking will succeed
if os.path.lexists(link_path):
raise AlreadyExistsError(
f"Link path ({link_path}) already exists. Cannot create link."
)
if not os.path.exists(source_path):
if os.path.isabs(source_path) and not allow_broken_symlinks:
# An absolute source path that does not exist will result in a broken link.
raise SymlinkError(
f"Source path ({source_path}) is absolute but does not exist. Resulting "
f"link would be broken so not making link."
)
else:
# If all else fails, fall back to copying files
shutil.copyfile(real_path, link_path)
# os.symlink can create a link when the given source path is relative to
# the link path. Emulate this behavior and check to see if the source exists
# relative to the link path ahead of link creation to prevent broken
# links from being made.
link_parent_dir = os.path.dirname(link_path)
relative_path = os.path.join(link_parent_dir, source_path)
if os.path.exists(relative_path):
# In order to work on windows, the source path needs to be modified to be
# relative because hardlink/junction dont resolve relative paths the same
# way as os.symlink. This is ignored on other operating systems.
win_source_path = relative_path
elif not allow_broken_symlinks:
raise SymlinkError(
f"The source path ({source_path}) is not relative to the link path "
f"({link_path}). Resulting link would be broken so not making link."
)
# Create the symlink
if sys.platform == "win32" and not _windows_can_symlink():
_windows_create_link(win_source_path, link_path)
else:
os.symlink(source_path, link_path, target_is_directory=os.path.isdir(source_path))
def islink(path):
return os.path.islink(path) or _win32_is_junction(path)
def islink(path: str) -> bool:
"""Override os.islink to give correct answer for spack logic.
For Non-Windows: a link can be determined with the os.path.islink method.
Windows-only methods will return false for other operating systems.
For Windows: spack considers symlinks, hard links, and junctions to
all be links, so if any of those are True, return True.
Args:
path (str): path to check if it is a link.
Returns:
bool - whether the path is any kind link or not.
"""
return any([os.path.islink(path), _windows_is_junction(path), _windows_is_hardlink(path)])
# '_win32' functions based on
# https://github.com/Erotemic/ubelt/blob/master/ubelt/util_links.py
def _win32_junction(path, link):
# junctions require absolute paths
if not os.path.isabs(link):
link = os.path.abspath(link)
def _windows_is_hardlink(path: str) -> bool:
"""Determines if a path is a windows hard link. This is accomplished
by looking at the number of links using os.stat. A non-hard-linked file
will have a st_nlink value of 1, whereas a hard link will have a value
larger than 1. Note that both the original and hard-linked file will
return True because they share the same inode.
# os.symlink will fail if link exists, emulate the behavior here
if exists(link):
raise OSError(errno.EEXIST, "File exists: %s -> %s" % (link, path))
Args:
path (str): Windows path to check for a hard link
if not os.path.isabs(path):
parent = os.path.join(link, os.pardir)
path = os.path.join(parent, path)
path = os.path.abspath(path)
Returns:
bool - Whether the path is a hard link or not.
"""
if sys.platform != "win32" or os.path.islink(path) or not os.path.exists(path):
return False
CreateHardLink(link, path)
return os.stat(path).st_nlink > 1
def _windows_is_junction(path: str) -> bool:
"""Determines if a path is a windows junction. A junction can be
determined using a bitwise AND operation between the file's
attribute bitmask and the known junction bitmask (0x400).
Args:
path (str): A non-file path
Returns:
bool - whether the path is a junction or not.
"""
if sys.platform != "win32" or os.path.islink(path) or os.path.isfile(path):
return False
import ctypes.wintypes
get_file_attributes = ctypes.windll.kernel32.GetFileAttributesW # type: ignore[attr-defined]
get_file_attributes.argtypes = (ctypes.wintypes.LPWSTR,)
get_file_attributes.restype = ctypes.wintypes.DWORD
invalid_file_attributes = 0xFFFFFFFF
reparse_point = 0x400
file_attr = get_file_attributes(str(path))
if file_attr == invalid_file_attributes:
return False
return file_attr & reparse_point > 0
@lang.memoized
def _win32_can_symlink():
def _windows_can_symlink() -> bool:
"""
Determines if windows is able to make a symlink depending on
the system configuration and the level of the user's permissions.
"""
if sys.platform != "win32":
tty.warn("windows_can_symlink method can't be used on non-Windows OS.")
return False
tempdir = tempfile.mkdtemp()
dpath = join(tempdir, "dpath")
fpath = join(tempdir, "fpath.txt")
dpath = os.path.join(tempdir, "dpath")
fpath = os.path.join(tempdir, "fpath.txt")
dlink = join(tempdir, "dlink")
flink = join(tempdir, "flink.txt")
dlink = os.path.join(tempdir, "dlink")
flink = os.path.join(tempdir, "flink.txt")
import llnl.util.filesystem as fs
@@ -96,24 +208,140 @@ def _win32_can_symlink():
return can_symlink_directories and can_symlink_files
def _win32_is_junction(path):
def _windows_create_link(source: str, link: str):
"""
Determines if a path is a win32 junction
Attempts to create a Hard Link or Junction as an alternative
to a symbolic link. This is called when symbolic links cannot
be created.
"""
if os.path.islink(path):
return False
if sys.platform != "win32":
raise SymlinkError("windows_create_link method can't be used on non-Windows OS.")
elif os.path.isdir(source):
_windows_create_junction(source=source, link=link)
elif os.path.isfile(source):
_windows_create_hard_link(path=source, link=link)
else:
raise SymlinkError(
f"Cannot create link from {source}. It is neither a file nor a directory."
)
if sys.platform == "win32":
import ctypes.wintypes
GetFileAttributes = ctypes.windll.kernel32.GetFileAttributesW
GetFileAttributes.argtypes = (ctypes.wintypes.LPWSTR,)
GetFileAttributes.restype = ctypes.wintypes.DWORD
def _windows_create_junction(source: str, link: str):
"""Duly verify that the path and link are eligible to create a junction,
then create the junction.
"""
if sys.platform != "win32":
raise SymlinkError("windows_create_junction method can't be used on non-Windows OS.")
elif not os.path.exists(source):
raise SymlinkError("Source path does not exist, cannot create a junction.")
elif os.path.lexists(link):
raise AlreadyExistsError("Link path already exists, cannot create a junction.")
elif not os.path.isdir(source):
raise SymlinkError("Source path is not a directory, cannot create a junction.")
INVALID_FILE_ATTRIBUTES = 0xFFFFFFFF
FILE_ATTRIBUTE_REPARSE_POINT = 0x400
import subprocess
res = GetFileAttributes(path)
return res != INVALID_FILE_ATTRIBUTES and bool(res & FILE_ATTRIBUTE_REPARSE_POINT)
cmd = ["cmd", "/C", "mklink", "/J", link, source]
proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
out, err = proc.communicate()
tty.debug(out.decode())
if proc.returncode != 0:
err = err.decode()
tty.error(err)
raise SymlinkError("Make junction command returned a non-zero return code.", err)
return False
def _windows_create_hard_link(path: str, link: str):
"""Duly verify that the path and link are eligible to create a hard
link, then create the hard link.
"""
if sys.platform != "win32":
raise SymlinkError("windows_create_hard_link method can't be used on non-Windows OS.")
elif not os.path.exists(path):
raise SymlinkError(f"File path {path} does not exist. Cannot create hard link.")
elif os.path.lexists(link):
raise AlreadyExistsError(f"Link path ({link}) already exists. Cannot create hard link.")
elif not os.path.isfile(path):
raise SymlinkError(f"File path ({link}) is not a file. Cannot create hard link.")
else:
tty.debug(f"Creating hard link {link} pointing to {path}")
CreateHardLink(link, path)
def readlink(path: str):
"""Spack utility to override of os.readlink method to work cross platform"""
if _windows_is_hardlink(path):
return _windows_read_hard_link(path)
elif _windows_is_junction(path):
return _windows_read_junction(path)
else:
return os.readlink(path)
def _windows_read_hard_link(link: str) -> str:
"""Find all of the files that point to the same inode as the link"""
if sys.platform != "win32":
raise SymlinkError("Can't read hard link on non-Windows OS.")
link = os.path.abspath(link)
fsutil_cmd = ["fsutil", "hardlink", "list", link]
proc = subprocess.Popen(fsutil_cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
out, err = proc.communicate()
if proc.returncode != 0:
raise SymlinkError(f"An error occurred while reading hard link: {err.decode()}")
# fsutil response does not include the drive name, so append it back to each linked file.
drive, link_tail = os.path.splitdrive(os.path.abspath(link))
links = set([os.path.join(drive, p) for p in out.decode().splitlines()])
links.remove(link)
if len(links) == 1:
return links.pop()
elif len(links) > 1:
# TODO: How best to handle the case where 3 or more paths point to a single inode?
raise SymlinkError(f"Found multiple paths pointing to the same inode {links}")
else:
raise SymlinkError("Cannot determine hard link source path.")
def _windows_read_junction(link: str):
"""Find the path that a junction points to."""
if sys.platform != "win32":
raise SymlinkError("Can't read junction on non-Windows OS.")
link = os.path.abspath(link)
link_basename = os.path.basename(link)
link_parent = os.path.dirname(link)
fsutil_cmd = ["dir", "/a:l", link_parent]
proc = subprocess.Popen(fsutil_cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
out, err = proc.communicate()
if proc.returncode != 0:
raise SymlinkError(f"An error occurred while reading junction: {err.decode()}")
matches = re.search(rf"<JUNCTION>\s+{link_basename} \[(.*)]", out.decode())
if matches:
return matches.group(1)
else:
raise SymlinkError("Could not find junction path.")
@system_path_filter
def resolve_link_target_relative_to_the_link(link):
"""
os.path.isdir uses os.path.exists, which for links will check
the existence of the link target. If the link target is relative to
the link, we need to construct a pathname that is valid from
our cwd (which may not be the same as the link's directory)
"""
target = readlink(link)
if os.path.isabs(target):
return target
link_dir = os.path.dirname(os.path.abspath(link))
return os.path.join(link_dir, target)
class SymlinkError(RuntimeError):
"""Exception class for errors raised while creating symlinks,
junctions and hard links
"""
class AlreadyExistsError(SymlinkError):
"""Link path already exists."""

View File

@@ -211,6 +211,7 @@ def info(message, *args, **kwargs):
stream.write(line + "\n")
else:
stream.write(indent + _output_filter(str(arg)) + "\n")
stream.flush()
def verbose(message, *args, **kwargs):

View File

@@ -4,7 +4,7 @@
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
#: PEP440 canonical <major>.<minor>.<micro>.<devN> string
__version__ = "0.21.0.dev0"
__version__ = "0.22.0.dev0"
spack_version = __version__

View File

@@ -8,8 +8,8 @@
from llnl.util.lang import memoized
import spack.spec
import spack.version
from spack.compilers.clang import Clang
from spack.spec import CompilerSpec
from spack.util.executable import Executable, ProcessError
@@ -17,7 +17,9 @@ class ABI:
"""This class provides methods to test ABI compatibility between specs.
The current implementation is rather rough and could be improved."""
def architecture_compatible(self, target, constraint):
def architecture_compatible(
self, target: spack.spec.Spec, constraint: spack.spec.Spec
) -> bool:
"""Return true if architecture of target spec is ABI compatible
to the architecture of constraint spec. If either the target
or constraint specs have no architecture, target is also defined
@@ -34,7 +36,7 @@ def _gcc_get_libstdcxx_version(self, version):
a compiler's libstdc++ or libgcc_s"""
from spack.build_environment import dso_suffix
spec = CompilerSpec("gcc", version)
spec = spack.spec.CompilerSpec("gcc", version)
compilers = spack.compilers.compilers_for_spec(spec)
if not compilers:
return None
@@ -77,16 +79,20 @@ def _gcc_compiler_compare(self, pversion, cversion):
return False
return plib == clib
def _intel_compiler_compare(self, pversion, cversion):
def _intel_compiler_compare(
self, pversion: spack.version.ClosedOpenRange, cversion: spack.version.ClosedOpenRange
) -> bool:
"""Returns true iff the intel version pversion and cversion
are ABI compatible"""
# Test major and minor versions. Ignore build version.
if len(pversion.version) < 2 or len(cversion.version) < 2:
return False
return pversion.version[:2] == cversion.version[:2]
pv = pversion.lo
cv = cversion.lo
return pv.up_to(2) == cv.up_to(2)
def compiler_compatible(self, parent, child, **kwargs):
def compiler_compatible(
self, parent: spack.spec.Spec, child: spack.spec.Spec, loose: bool = False
) -> bool:
"""Return true if compilers for parent and child are ABI compatible."""
if not parent.compiler or not child.compiler:
return True
@@ -95,7 +101,7 @@ def compiler_compatible(self, parent, child, **kwargs):
# Different compiler families are assumed ABI incompatible
return False
if kwargs.get("loose", False):
if loose:
return True
# TODO: Can we move the specialized ABI matching stuff
@@ -116,9 +122,10 @@ def compiler_compatible(self, parent, child, **kwargs):
return True
return False
def compatible(self, target, constraint, **kwargs):
def compatible(
self, target: spack.spec.Spec, constraint: spack.spec.Spec, loose: bool = False
) -> bool:
"""Returns true if target spec is ABI compatible to constraint spec"""
loosematch = kwargs.get("loose", False)
return self.architecture_compatible(target, constraint) and self.compiler_compatible(
target, constraint, loose=loosematch
target, constraint, loose=loose
)

View File

@@ -38,10 +38,13 @@ def _search_duplicate_compilers(error_cls):
import ast
import collections
import collections.abc
import glob
import inspect
import itertools
import pathlib
import pickle
import re
import warnings
from urllib.request import urlopen
import llnl.util.lang
@@ -304,10 +307,17 @@ def _check_build_test_callbacks(pkgs, error_cls):
@package_directives
def _check_patch_urls(pkgs, error_cls):
"""Ensure that patches fetched from GitHub have stable sha256 hashes."""
"""Ensure that patches fetched from GitHub and GitLab have stable sha256
hashes."""
github_patch_url_re = (
r"^https?://(?:patch-diff\.)?github(?:usercontent)?\.com/"
".+/.+/(?:commit|pull)/[a-fA-F0-9]*.(?:patch|diff)"
r".+/.+/(?:commit|pull)/[a-fA-F0-9]+\.(?:patch|diff)"
)
# Only .diff URLs have stable/full hashes:
# https://forum.gitlab.com/t/patches-with-full-index/29313
gitlab_patch_url_re = (
r"^https?://(?:.+)?gitlab(?:.+)/"
r".+/.+/-/(?:commit|merge_requests)/[a-fA-F0-9]+\.(?:patch|diff)"
)
errors = []
@@ -318,19 +328,27 @@ def _check_patch_urls(pkgs, error_cls):
if not isinstance(patch, spack.patch.UrlPatch):
continue
if not re.match(github_patch_url_re, patch.url):
continue
full_index_arg = "?full_index=1"
if not patch.url.endswith(full_index_arg):
errors.append(
error_cls(
"patch URL in package {0} must end with {1}".format(
pkg_cls.name, full_index_arg
),
[patch.url],
if re.match(github_patch_url_re, patch.url):
full_index_arg = "?full_index=1"
if not patch.url.endswith(full_index_arg):
errors.append(
error_cls(
"patch URL in package {0} must end with {1}".format(
pkg_cls.name, full_index_arg
),
[patch.url],
)
)
elif re.match(gitlab_patch_url_re, patch.url):
if not patch.url.endswith(".diff"):
errors.append(
error_cls(
"patch URL in package {0} must end with .diff".format(
pkg_cls.name
),
[patch.url],
)
)
)
return errors
@@ -798,3 +816,76 @@ def _analyze_variants_in_directive(pkg, constraint, directive, error_cls):
errors.append(err)
return errors
#: Sanity checks on package directives
external_detection = AuditClass(
group="externals",
tag="PKG-EXTERNALS",
description="Sanity checks for external software detection",
kwargs=("pkgs",),
)
def packages_with_detection_tests():
"""Return the list of packages with a corresponding detection_test.yaml file."""
import spack.config
import spack.util.path
to_be_tested = []
for current_repo in spack.repo.PATH.repos:
namespace = current_repo.namespace
packages_dir = pathlib.PurePath(current_repo.packages_path)
pattern = packages_dir / "**" / "detection_test.yaml"
pkgs_with_tests = [
f"{namespace}.{str(pathlib.PurePath(x).parent.name)}" for x in glob.glob(str(pattern))
]
to_be_tested.extend(pkgs_with_tests)
return to_be_tested
@external_detection
def _test_detection_by_executable(pkgs, error_cls):
"""Test drive external detection for packages"""
import spack.detection
errors = []
# Filter the packages and retain only the ones with detection tests
pkgs_with_tests = packages_with_detection_tests()
selected_pkgs = []
for current_package in pkgs_with_tests:
_, unqualified_name = spack.repo.partition_package_name(current_package)
# Check for both unqualified name and qualified name
if unqualified_name in pkgs or current_package in pkgs:
selected_pkgs.append(current_package)
selected_pkgs.sort()
if not selected_pkgs:
summary = "No detection test to run"
details = [f' "{p}" has no detection test' for p in pkgs]
warnings.warn("\n".join([summary] + details))
return errors
for pkg_name in selected_pkgs:
for idx, test_runner in enumerate(
spack.detection.detection_tests(pkg_name, spack.repo.PATH)
):
specs = test_runner.execute()
expected_specs = test_runner.expected_specs
not_detected = set(expected_specs) - set(specs)
if not_detected:
summary = pkg_name + ": cannot detect some specs"
details = [f'"{s}" was not detected [test_id={idx}]' for s in sorted(not_detected)]
errors.append(error_cls(summary=summary, details=details))
not_expected = set(specs) - set(expected_specs)
if not_expected:
summary = pkg_name + ": detected unexpected specs"
msg = '"{0}" was detected, but was not expected [test_id={1}]'
details = [msg.format(s, idx) for s in sorted(not_expected)]
errors.append(error_cls(summary=summary, details=details))
return errors

File diff suppressed because it is too large Load Diff

View File

@@ -143,7 +143,9 @@ def _bootstrap_config_scopes() -> Sequence["spack.config.ConfigScope"]:
def _add_compilers_if_missing() -> None:
arch = spack.spec.ArchSpec.frontend_arch()
if not spack.compilers.compilers_for_arch(arch):
new_compilers = spack.compilers.find_new_compilers()
new_compilers = spack.compilers.find_new_compilers(
mixed_toolchain=sys.platform == "darwin"
)
if new_compilers:
spack.compilers.add_compilers_to_config(new_compilers, init_config=False)

View File

@@ -214,7 +214,7 @@ def _install_and_test(
with spack.config.override(self.mirror_scope):
# This index is currently needed to get the compiler used to build some
# specs that we know by dag hash.
spack.binary_distribution.binary_index.regenerate_spec_cache()
spack.binary_distribution.BINARY_INDEX.regenerate_spec_cache()
index = spack.binary_distribution.update_cache_and_get_specs()
if not index:
@@ -228,7 +228,7 @@ def _install_and_test(
if not abstract_spec.intersects(candidate_spec):
continue
if python_spec is not None and python_spec not in abstract_spec:
if python_spec is not None and not abstract_spec.intersects(f"^{python_spec}"):
continue
for _, pkg_hash, pkg_sha256 in item["binaries"]:
@@ -291,6 +291,10 @@ def try_import(self, module: str, abstract_spec_str: str) -> bool:
with spack_python_interpreter():
# Add hint to use frontend operating system on Cray
concrete_spec = spack.spec.Spec(abstract_spec_str + " ^" + spec_for_current_python())
# This is needed to help the old concretizer taking the `setuptools` dependency
# only when bootstrapping from sources on Python 3.12
if spec_for_current_python() == "python@3.12":
concrete_spec.constrain("+force_setuptools")
if module == "clingo":
# TODO: remove when the old concretizer is deprecated # pylint: disable=fixme
@@ -446,16 +450,11 @@ def ensure_executables_in_path_or_raise(
current_bootstrapper.last_search["spec"],
current_bootstrapper.last_search["command"],
)
env_mods = spack.util.environment.EnvironmentModifications()
for dep in concrete_spec.traverse(
root=True, order="post", deptype=("link", "run")
):
env_mods.extend(
spack.user_environment.environment_modifications_for_spec(
dep, set_package_py_globals=False
)
cmd.add_default_envmod(
spack.user_environment.environment_modifications_for_specs(
concrete_spec, set_package_py_globals=False
)
cmd.add_default_envmod(env_mods)
)
return cmd
assert exception_handler, (
@@ -476,16 +475,16 @@ def ensure_executables_in_path_or_raise(
def _add_externals_if_missing() -> None:
search_list = [
# clingo
spack.repo.PATH.get_pkg_class("cmake"),
spack.repo.PATH.get_pkg_class("bison"),
"cmake",
"bison",
# GnuPG
spack.repo.PATH.get_pkg_class("gawk"),
"gawk",
# develop deps
spack.repo.PATH.get_pkg_class("git"),
"git",
]
if IS_WINDOWS:
search_list.append(spack.repo.PATH.get_pkg_class("winbison"))
externals = spack.detection.by_executable(search_list)
search_list.append("winbison")
externals = spack.detection.by_path(search_list)
# System git is typically deprecated, so mark as non-buildable to force it as external
non_buildable_externals = {k: externals.pop(k) for k in ("git",) if k in externals}
spack.detection.update_configuration(externals, scope="bootstrap", buildable=True)

View File

@@ -15,9 +15,9 @@
from llnl.util import tty
import spack.build_environment
import spack.environment
import spack.tengine
import spack.util.cpus
import spack.util.executable
from spack.environment import depfile
@@ -137,7 +137,7 @@ def _install_with_depfile(self) -> None:
"-C",
str(self.environment_root()),
"-j",
str(spack.build_environment.determine_number_of_jobs(parallel=True)),
str(spack.util.cpus.determine_number_of_jobs(parallel=True)),
**kwargs,
)

View File

@@ -40,11 +40,15 @@
import sys
import traceback
import types
from collections import defaultdict
from enum import Flag, auto
from itertools import chain
from typing import List, Tuple
import llnl.util.tty as tty
from llnl.string import plural
from llnl.util.filesystem import join_path
from llnl.util.lang import dedupe
from llnl.util.lang import dedupe, stable_partition
from llnl.util.symlink import symlink
from llnl.util.tty.color import cescape, colorize
from llnl.util.tty.log import MultiProcessFd
@@ -54,35 +58,37 @@
import spack.build_systems.python
import spack.builder
import spack.config
import spack.deptypes as dt
import spack.main
import spack.package_base
import spack.paths
import spack.platforms
import spack.repo
import spack.schema.environment
import spack.spec
import spack.store
import spack.subprocess_context
import spack.user_environment
import spack.util.path
import spack.util.pattern
from spack import traverse
from spack.context import Context
from spack.error import NoHeadersError, NoLibrariesError
from spack.install_test import spack_install_test_log
from spack.installer import InstallError
from spack.util.cpus import cpus_available
from spack.util.cpus import determine_number_of_jobs
from spack.util.environment import (
SYSTEM_DIRS,
EnvironmentModifications,
env_flag,
filter_system_paths,
get_path,
inspect_path,
is_system_path,
validate,
)
from spack.util.executable import Executable
from spack.util.log_parse import make_log_context, parse_log_events
from spack.util.module_cmd import load_module, module, path_from_modules
from spack.util.string import plural
#
# This can be set by the user to globally disable parallel builds.
@@ -109,7 +115,6 @@
SPACK_CCACHE_BINARY = "SPACK_CCACHE_BINARY"
SPACK_SYSTEM_DIRS = "SPACK_SYSTEM_DIRS"
# Platform-specific library suffix.
if sys.platform == "darwin":
dso_suffix = "dylib"
@@ -406,19 +411,13 @@ def set_compiler_environment_variables(pkg, env):
def set_wrapper_variables(pkg, env):
"""Set environment variables used by the Spack compiler wrapper
(which have the prefix `SPACK_`) and also add the compiler wrappers
to PATH.
"""Set environment variables used by the Spack compiler wrapper (which have the prefix
`SPACK_`) and also add the compiler wrappers to PATH.
This determines the injected -L/-I/-rpath options; each
of these specifies a search order and this function computes these
options in a manner that is intended to match the DAG traversal order
in `modifications_from_dependencies`: that method uses a post-order
traversal so that `PrependPath` actions from dependencies take lower
precedence; we use a post-order traversal here to match the visitation
order of `modifications_from_dependencies` (so we are visiting the
lowest priority packages first).
"""
This determines the injected -L/-I/-rpath options; each of these specifies a search order and
this function computes these options in a manner that is intended to match the DAG traversal
order in `SetupContext`. TODO: this is not the case yet, we're using post order, SetupContext
is using topo order."""
# Set environment variables if specified for
# the given compiler
compiler = pkg.compiler
@@ -537,78 +536,42 @@ def update_compiler_args_for_dep(dep):
env.set(SPACK_RPATH_DIRS, ":".join(rpath_dirs))
def determine_number_of_jobs(
parallel=False, command_line=None, config_default=None, max_cpus=None
):
"""
Packages that require sequential builds need 1 job. Otherwise we use the
number of jobs set on the command line. If not set, then we use the config
defaults (which is usually set through the builtin config scope), but we
cap to the number of CPUs available to avoid oversubscription.
Parameters:
parallel (bool or None): true when package supports parallel builds
command_line (int or None): command line override
config_default (int or None): config default number of jobs
max_cpus (int or None): maximum number of CPUs available. When None, this
value is automatically determined.
"""
if not parallel:
return 1
if command_line is None and "command_line" in spack.config.scopes():
command_line = spack.config.get("config:build_jobs", scope="command_line")
if command_line is not None:
return command_line
max_cpus = max_cpus or cpus_available()
# in some rare cases _builtin config may not be set, so default to max 16
config_default = config_default or spack.config.get("config:build_jobs", 16)
return min(max_cpus, config_default)
def set_module_variables_for_package(pkg):
def set_package_py_globals(pkg, context: Context = Context.BUILD):
"""Populate the Python module of a package with some useful global names.
This makes things easier for package writers.
"""
# Put a marker on this module so that it won't execute the body of this
# function again, since it is not needed
marker = "_set_run_already_called"
if getattr(pkg.module, marker, False):
return
module = ModuleChangePropagator(pkg)
jobs = determine_number_of_jobs(parallel=pkg.parallel)
m = module
m.make_jobs = jobs
# TODO: make these build deps that can be installed if not found.
m.make = MakeExecutable("make", jobs)
m.ninja = MakeExecutable("ninja", jobs, supports_jobserver=False)
# TODO: johnwparent: add package or builder support to define these build tools
# for now there is no entrypoint for builders to define these on their
# own
if sys.platform == "win32":
m.nmake = Executable("nmake")
m.msbuild = Executable("msbuild")
# analog to configure for win32
m.cscript = Executable("cscript")
if context == Context.BUILD:
jobs = determine_number_of_jobs(parallel=pkg.parallel)
m.make_jobs = jobs
# Find the configure script in the archive path
# Don't use which for this; we want to find it in the current dir.
m.configure = Executable("./configure")
# TODO: make these build deps that can be installed if not found.
m.make = MakeExecutable("make", jobs)
m.gmake = MakeExecutable("gmake", jobs)
m.ninja = MakeExecutable("ninja", jobs, supports_jobserver=False)
# TODO: johnwparent: add package or builder support to define these build tools
# for now there is no entrypoint for builders to define these on their
# own
if sys.platform == "win32":
m.nmake = Executable("nmake")
m.msbuild = Executable("msbuild")
# analog to configure for win32
m.cscript = Executable("cscript")
# Standard CMake arguments
m.std_cmake_args = spack.build_systems.cmake.CMakeBuilder.std_args(pkg)
m.std_meson_args = spack.build_systems.meson.MesonBuilder.std_args(pkg)
m.std_pip_args = spack.build_systems.python.PythonPipBuilder.std_args(pkg)
# Find the configure script in the archive path
# Don't use which for this; we want to find it in the current dir.
m.configure = Executable("./configure")
# Put spack compiler paths in module scope.
# Standard CMake arguments
m.std_cmake_args = spack.build_systems.cmake.CMakeBuilder.std_args(pkg)
m.std_meson_args = spack.build_systems.meson.MesonBuilder.std_args(pkg)
m.std_pip_args = spack.build_systems.python.PythonPipBuilder.std_args(pkg)
# Put spack compiler paths in module scope. (Some packages use it
# in setup_run_environment etc, so don't put it context == build)
link_dir = spack.paths.build_env_path
m.spack_cc = os.path.join(link_dir, pkg.compiler.link_paths["cc"])
m.spack_cxx = os.path.join(link_dir, pkg.compiler.link_paths["cxx"])
@@ -632,9 +595,6 @@ def static_to_shared_library(static_lib, shared_lib=None, **kwargs):
m.static_to_shared_library = static_to_shared_library
# Put a marker on this module so that it won't execute the body of this
# function again, since it is not needed
setattr(m, marker, True)
module.propagate_changes_to_mro()
@@ -760,12 +720,15 @@ def load_external_modules(pkg):
load_module(external_module)
def setup_package(pkg, dirty, context="build"):
def setup_package(pkg, dirty, context: Context = Context.BUILD):
"""Execute all environment setup routines."""
if context not in ["build", "test"]:
raise ValueError("'context' must be one of ['build', 'test'] - got: {0}".format(context))
if context not in (Context.BUILD, Context.TEST):
raise ValueError(f"'context' must be Context.BUILD or Context.TEST - got {context}")
set_module_variables_for_package(pkg)
# First populate the package.py's module with the relevant globals that could be used in any
# of the setup_* functions.
setup_context = SetupContext(pkg.spec, context=context)
setup_context.set_all_package_py_globals()
# Keep track of env changes from packages separately, since we want to
# issue warnings when packages make "suspicious" modifications.
@@ -773,13 +736,15 @@ def setup_package(pkg, dirty, context="build"):
env_mods = EnvironmentModifications()
# setup compilers for build contexts
need_compiler = context == "build" or (context == "test" and pkg.test_requires_compiler)
need_compiler = context == Context.BUILD or (
context == Context.TEST and pkg.test_requires_compiler
)
if need_compiler:
set_compiler_environment_variables(pkg, env_mods)
set_wrapper_variables(pkg, env_mods)
tty.debug("setup_package: grabbing modifications from dependencies")
env_mods.extend(modifications_from_dependencies(pkg.spec, context, custom_mods_only=False))
env_mods.extend(setup_context.get_env_modifications())
tty.debug("setup_package: collected all modifications from dependencies")
# architecture specific setup
@@ -787,28 +752,13 @@ def setup_package(pkg, dirty, context="build"):
target = platform.target(pkg.spec.architecture.target)
platform.setup_platform_environment(pkg, env_mods)
if context == "build":
tty.debug("setup_package: setup build environment for root")
builder = spack.builder.create(pkg)
builder.setup_build_environment(env_mods)
if (not dirty) and (not env_mods.is_unset("CPATH")):
tty.debug(
"A dependency has updated CPATH, this may lead pkg-"
"config to assume that the package is part of the system"
" includes and omit it when invoked with '--cflags'."
)
elif context == "test":
tty.debug("setup_package: setup test environment for root")
env_mods.extend(
inspect_path(
pkg.spec.prefix,
spack.user_environment.prefix_inspections(pkg.spec.platform),
exclude=is_system_path,
)
)
pkg.setup_run_environment(env_mods)
if context == Context.TEST:
env_mods.prepend_path("PATH", ".")
elif context == Context.BUILD and not dirty and not env_mods.is_unset("CPATH"):
tty.debug(
"A dependency has updated CPATH, this may lead pkg-config to assume that the package "
"is part of the system includes and omit it when invoked with '--cflags'."
)
# First apply the clean environment changes
env_base.apply_modifications()
@@ -846,158 +796,257 @@ def setup_package(pkg, dirty, context="build"):
return env_base
def _make_runnable(pkg, env):
# Helper method which prepends a Package's bin/ prefix to the PATH
# environment variable
prefix = pkg.prefix
class EnvironmentVisitor:
def __init__(self, *roots: spack.spec.Spec, context: Context):
# For the roots (well, marked specs) we follow different edges
# than for their deps, depending on the context.
self.root_hashes = set(s.dag_hash() for s in roots)
for dirname in ["bin", "bin64"]:
bin_dir = os.path.join(prefix, dirname)
if os.path.isdir(bin_dir):
env.prepend_path("PATH", bin_dir)
if context == Context.BUILD:
# Drop direct run deps in build context
# We don't really distinguish between install and build time test deps,
# so we include them here as build-time test deps.
self.root_depflag = dt.BUILD | dt.TEST | dt.LINK
elif context == Context.TEST:
# This is more of an extended run environment
self.root_depflag = dt.TEST | dt.RUN | dt.LINK
elif context == Context.RUN:
self.root_depflag = dt.RUN | dt.LINK
def neighbors(self, item):
spec = item.edge.spec
if spec.dag_hash() in self.root_hashes:
depflag = self.root_depflag
else:
depflag = dt.LINK | dt.RUN
return traverse.sort_edges(spec.edges_to_dependencies(depflag=depflag))
def modifications_from_dependencies(
spec, context, custom_mods_only=True, set_package_py_globals=True
):
"""Returns the environment modifications that are required by
the dependencies of a spec and also applies modifications
to this spec's package at module scope, if need be.
class UseMode(Flag):
#: Entrypoint spec (a spec to be built; an env root, etc)
ROOT = auto()
Environment modifications include:
#: A spec used at runtime, but no executables in PATH
RUNTIME = auto()
- Updating PATH so that executables can be found
- Updating CMAKE_PREFIX_PATH and PKG_CONFIG_PATH so that their respective
tools can find Spack-built dependencies
- Running custom package environment modifications
#: A spec used at runtime, with executables in PATH
RUNTIME_EXECUTABLE = auto()
Custom package modifications can conflict with the default PATH changes
we make (specifically for the PATH, CMAKE_PREFIX_PATH, and PKG_CONFIG_PATH
environment variables), so this applies changes in a fixed order:
#: A spec that's a direct build or test dep
BUILDTIME_DIRECT = auto()
- All modifications (custom and default) from external deps first
- All modifications from non-external deps afterwards
#: A spec that should be visible in search paths in a build env.
BUILDTIME = auto()
With that order, `PrependPath` actions from non-external default
environment modifications will take precedence over custom modifications
from external packages.
#: Flag is set when the (node, mode) is finalized
ADDED = auto()
A secondary constraint is that custom and default modifications are
grouped on a per-package basis: combined with the post-order traversal this
means that default modifications of dependents can override custom
modifications of dependencies (again, this would only occur for PATH,
CMAKE_PREFIX_PATH, or PKG_CONFIG_PATH).
Args:
spec (spack.spec.Spec): spec for which we want the modifications
context (str): either 'build' for build-time modifications or 'run'
for run-time modifications
custom_mods_only (bool): if True returns only custom modifications, if False
returns custom and default modifications
set_package_py_globals (bool): whether or not to set the global variables in the
package.py files (this may be problematic when using buildcaches that have
been built on a different but compatible OS)
"""
if context not in ["build", "run", "test"]:
raise ValueError(
"Expecting context to be one of ['build', 'run', 'test'], " "got: {0}".format(context)
def effective_deptypes(
*specs: spack.spec.Spec, context: Context = Context.BUILD
) -> List[Tuple[spack.spec.Spec, UseMode]]:
"""Given a list of input specs and a context, return a list of tuples of
all specs that contribute to (environment) modifications, together with
a flag specifying in what way they do so. The list is ordered topologically
from root to leaf, meaning that environment modifications should be applied
in reverse so that dependents override dependencies, not the other way around."""
visitor = traverse.TopoVisitor(
EnvironmentVisitor(*specs, context=context),
key=lambda x: x.dag_hash(),
root=True,
all_edges=True,
)
traverse.traverse_depth_first_with_visitor(traverse.with_artificial_edges(specs), visitor)
# Dictionary with "no mode" as default value, so it's easy to write modes[x] |= flag.
use_modes = defaultdict(lambda: UseMode(0))
nodes_with_type = []
for edge in visitor.edges:
parent, child, depflag = edge.parent, edge.spec, edge.depflag
# Mark the starting point
if parent is None:
use_modes[child] = UseMode.ROOT
continue
parent_mode = use_modes[parent]
# Nothing to propagate.
if not parent_mode:
continue
# Dependending on the context, include particular deps from the root.
if UseMode.ROOT & parent_mode:
if context == Context.BUILD:
if (dt.BUILD | dt.TEST) & depflag:
use_modes[child] |= UseMode.BUILDTIME_DIRECT
if dt.LINK & depflag:
use_modes[child] |= UseMode.BUILDTIME
elif context == Context.TEST:
if (dt.RUN | dt.TEST) & depflag:
use_modes[child] |= UseMode.RUNTIME_EXECUTABLE
elif dt.LINK & depflag:
use_modes[child] |= UseMode.RUNTIME
elif context == Context.RUN:
if dt.RUN & depflag:
use_modes[child] |= UseMode.RUNTIME_EXECUTABLE
elif dt.LINK & depflag:
use_modes[child] |= UseMode.RUNTIME
# Propagate RUNTIME and RUNTIME_EXECUTABLE through link and run deps.
if (UseMode.RUNTIME | UseMode.RUNTIME_EXECUTABLE | UseMode.BUILDTIME_DIRECT) & parent_mode:
if dt.LINK & depflag:
use_modes[child] |= UseMode.RUNTIME
if dt.RUN & depflag:
use_modes[child] |= UseMode.RUNTIME_EXECUTABLE
# Propagate BUILDTIME through link deps.
if UseMode.BUILDTIME & parent_mode:
if dt.LINK & depflag:
use_modes[child] |= UseMode.BUILDTIME
# Finalize the spec; the invariant is that all in-edges are processed
# before out-edges, meaning that parent is done.
if not (UseMode.ADDED & parent_mode):
use_modes[parent] |= UseMode.ADDED
nodes_with_type.append((parent, parent_mode))
# Attach the leaf nodes, since we only added nodes with out-edges.
for spec, parent_mode in use_modes.items():
if parent_mode and not (UseMode.ADDED & parent_mode):
nodes_with_type.append((spec, parent_mode))
return nodes_with_type
class SetupContext:
"""This class encapsulates the logic to determine environment modifications, and is used as
well to set globals in modules of package.py."""
def __init__(self, *specs: spack.spec.Spec, context: Context) -> None:
"""Construct a ModificationsFromDag object.
Args:
specs: single root spec for build/test context, possibly more for run context
context: build, run, or test"""
if (context == Context.BUILD or context == Context.TEST) and not len(specs) == 1:
raise ValueError("Cannot setup build environment for multiple specs")
specs_with_type = effective_deptypes(*specs, context=context)
self.specs = specs
self.context = context
self.external: List[Tuple[spack.spec.Spec, UseMode]]
self.nonexternal: List[Tuple[spack.spec.Spec, UseMode]]
# Reverse so we go from leaf to root
self.nodes_in_subdag = set(id(s) for s, _ in specs_with_type)
# Split into non-external and external, maintaining topo order per group.
self.external, self.nonexternal = stable_partition(
reversed(specs_with_type), lambda t: t[0].external
)
self.should_be_runnable = UseMode.BUILDTIME_DIRECT | UseMode.RUNTIME_EXECUTABLE
self.should_setup_run_env = (
UseMode.BUILDTIME_DIRECT | UseMode.RUNTIME | UseMode.RUNTIME_EXECUTABLE
)
self.should_setup_dependent_build_env = UseMode.BUILDTIME | UseMode.BUILDTIME_DIRECT
self.should_setup_build_env = UseMode.ROOT if context == Context.BUILD else UseMode(0)
env = EnvironmentModifications()
if context == Context.RUN or context == Context.TEST:
self.should_be_runnable |= UseMode.ROOT
self.should_setup_run_env |= UseMode.ROOT
# Note: see computation of 'custom_mod_deps' and 'exe_deps' later in this
# function; these sets form the building blocks of those collections.
build_deps = set(spec.dependencies(deptype=("build", "test")))
link_deps = set(spec.traverse(root=False, deptype="link"))
build_link_deps = build_deps | link_deps
build_and_supporting_deps = set()
for build_dep in build_deps:
build_and_supporting_deps.update(build_dep.traverse(deptype="run"))
run_and_supporting_deps = set(spec.traverse(root=False, deptype=("run", "link")))
test_and_supporting_deps = set()
for test_dep in set(spec.dependencies(deptype="test")):
test_and_supporting_deps.update(test_dep.traverse(deptype="run"))
# Everything that calls setup_run_environment and setup_dependent_* needs globals set.
self.should_set_package_py_globals = (
self.should_setup_dependent_build_env | self.should_setup_run_env | UseMode.ROOT
)
# In a build context, the root and direct build deps need build-specific globals set.
self.needs_build_context = UseMode.ROOT | UseMode.BUILDTIME_DIRECT
# All dependencies that might have environment modifications to apply
custom_mod_deps = set()
if context == "build":
custom_mod_deps.update(build_and_supporting_deps)
# Tests may be performed after build
custom_mod_deps.update(test_and_supporting_deps)
else:
# test/run context
custom_mod_deps.update(run_and_supporting_deps)
if context == "test":
custom_mod_deps.update(test_and_supporting_deps)
custom_mod_deps.update(link_deps)
def set_all_package_py_globals(self):
"""Set the globals in modules of package.py files."""
for dspec, flag in chain(self.external, self.nonexternal):
pkg = dspec.package
# Determine 'exe_deps': the set of packages with binaries we want to use
if context == "build":
exe_deps = build_and_supporting_deps | test_and_supporting_deps
elif context == "run":
exe_deps = set(spec.traverse(deptype="run"))
elif context == "test":
exe_deps = test_and_supporting_deps
if self.should_set_package_py_globals & flag:
if self.context == Context.BUILD and self.needs_build_context & flag:
set_package_py_globals(pkg, context=Context.BUILD)
else:
# This includes runtime dependencies, also runtime deps of direct build deps.
set_package_py_globals(pkg, context=Context.RUN)
def default_modifications_for_dep(dep):
if dep in build_link_deps and not is_system_path(dep.prefix) and context == "build":
prefix = dep.prefix
for spec in dspec.dependents():
# Note: some specs have dependents that are unreachable from the root, so avoid
# setting globals for those.
if id(spec) not in self.nodes_in_subdag:
continue
dependent_module = ModuleChangePropagator(spec.package)
pkg.setup_dependent_package(dependent_module, spec)
dependent_module.propagate_changes_to_mro()
env.prepend_path("CMAKE_PREFIX_PATH", prefix)
def get_env_modifications(self) -> EnvironmentModifications:
"""Returns the environment variable modifications for the given input specs and context.
Environment modifications include:
- Updating PATH for packages that are required at runtime
- Updating CMAKE_PREFIX_PATH and PKG_CONFIG_PATH so that their respective
tools can find Spack-built dependencies (when context=build)
- Running custom package environment modifications: setup_run_environment,
setup_dependent_run_environment, setup_build_environment,
setup_dependent_build_environment.
for directory in ("lib", "lib64", "share"):
pcdir = os.path.join(prefix, directory, "pkgconfig")
if os.path.isdir(pcdir):
env.prepend_path("PKG_CONFIG_PATH", pcdir)
The (partial) order imposed on the specs is externals first, then topological
from leaf to root. That way externals cannot contribute search paths that would shadow
Spack's prefixes, and dependents override variables set by dependencies."""
env = EnvironmentModifications()
for dspec, flag in chain(self.external, self.nonexternal):
tty.debug(f"Adding env modifications for {dspec.name}")
pkg = dspec.package
if dep in exe_deps and not is_system_path(dep.prefix):
_make_runnable(dep, env)
if self.should_setup_dependent_build_env & flag:
self._make_buildtime_detectable(dspec, env)
def add_modifications_for_dep(dep):
tty.debug("Adding env modifications for {0}".format(dep.name))
# Some callers of this function only want the custom modifications.
# For callers that want both custom and default modifications, we want
# to perform the default modifications here (this groups custom
# and default modifications together on a per-package basis).
if not custom_mods_only:
default_modifications_for_dep(dep)
for root in self.specs: # there is only one root in build context
spack.builder.create(pkg).setup_dependent_build_environment(env, root)
# Perform custom modifications here (PrependPath actions performed in
# the custom method override the default environment modifications
# we do to help the build, namely for PATH, CMAKE_PREFIX_PATH, and
# PKG_CONFIG_PATH)
if dep in custom_mod_deps:
dpkg = dep.package
if set_package_py_globals:
set_module_variables_for_package(dpkg)
if self.should_setup_build_env & flag:
spack.builder.create(pkg).setup_build_environment(env)
current_module = ModuleChangePropagator(spec.package)
dpkg.setup_dependent_package(current_module, spec)
current_module.propagate_changes_to_mro()
if self.should_be_runnable & flag:
self._make_runnable(dspec, env)
if context == "build":
builder = spack.builder.create(dpkg)
builder.setup_dependent_build_environment(env, spec)
else:
dpkg.setup_dependent_run_environment(env, spec)
tty.debug("Added env modifications for {0}".format(dep.name))
if self.should_setup_run_env & flag:
run_env_mods = EnvironmentModifications()
for spec in dspec.dependents(deptype=dt.LINK | dt.RUN):
if id(spec) in self.nodes_in_subdag:
pkg.setup_dependent_run_environment(run_env_mods, spec)
pkg.setup_run_environment(run_env_mods)
if self.context == Context.BUILD:
# Don't let the runtime environment of comiler like dependencies leak into the
# build env
run_env_mods.drop("CC", "CXX", "F77", "FC")
env.extend(run_env_mods)
# Note that we want to perform environment modifications in a fixed order.
# The Spec.traverse method provides this: i.e. in addition to
# the post-order semantics, it also guarantees a fixed traversal order
# among dependencies which are not constrained by post-order semantics.
for dspec in spec.traverse(root=False, order="post"):
if dspec.external:
add_modifications_for_dep(dspec)
return env
for dspec in spec.traverse(root=False, order="post"):
# Default env modifications for non-external packages can override
# custom modifications of external packages (this can only occur
# for modifications to PATH, CMAKE_PREFIX_PATH, and PKG_CONFIG_PATH)
if not dspec.external:
add_modifications_for_dep(dspec)
def _make_buildtime_detectable(self, dep: spack.spec.Spec, env: EnvironmentModifications):
if is_system_path(dep.prefix):
return
return env
env.prepend_path("CMAKE_PREFIX_PATH", dep.prefix)
for d in ("lib", "lib64", "share"):
pcdir = os.path.join(dep.prefix, d, "pkgconfig")
if os.path.isdir(pcdir):
env.prepend_path("PKG_CONFIG_PATH", pcdir)
def _make_runnable(self, dep: spack.spec.Spec, env: EnvironmentModifications):
if is_system_path(dep.prefix):
return
for d in ("bin", "bin64"):
bin_dir = os.path.join(dep.prefix, d)
if os.path.isdir(bin_dir):
env.prepend_path("PATH", bin_dir)
def get_cmake_prefix_path(pkg):
@@ -1027,9 +1076,9 @@ def get_cmake_prefix_path(pkg):
def _setup_pkg_and_run(
serialized_pkg, function, kwargs, child_pipe, input_multiprocess_fd, jsfd1, jsfd2
serialized_pkg, function, kwargs, write_pipe, input_multiprocess_fd, jsfd1, jsfd2
):
context = kwargs.get("context", "build")
context: str = kwargs.get("context", "build")
try:
# We are in the child process. Python sets sys.stdin to
@@ -1045,15 +1094,15 @@ def _setup_pkg_and_run(
if not kwargs.get("fake", False):
kwargs["unmodified_env"] = os.environ.copy()
kwargs["env_modifications"] = setup_package(
pkg, dirty=kwargs.get("dirty", False), context=context
pkg, dirty=kwargs.get("dirty", False), context=Context.from_string(context)
)
return_value = function(pkg, kwargs)
child_pipe.send(return_value)
write_pipe.send(return_value)
except StopPhase as e:
# Do not create a full ChildError from this, it's not an error
# it's a control statement.
child_pipe.send(e)
write_pipe.send(e)
except BaseException:
# catch ANYTHING that goes wrong in the child process
exc_type, exc, tb = sys.exc_info()
@@ -1102,10 +1151,10 @@ def _setup_pkg_and_run(
context,
package_context,
)
child_pipe.send(ce)
write_pipe.send(ce)
finally:
child_pipe.close()
write_pipe.close()
if input_multiprocess_fd is not None:
input_multiprocess_fd.close()
@@ -1149,7 +1198,7 @@ def child_fun():
For more information on `multiprocessing` child process creation
mechanisms, see https://docs.python.org/3/library/multiprocessing.html#contexts-and-start-methods
"""
parent_pipe, child_pipe = multiprocessing.Pipe()
read_pipe, write_pipe = multiprocessing.Pipe(duplex=False)
input_multiprocess_fd = None
jobserver_fd1 = None
jobserver_fd2 = None
@@ -1174,7 +1223,7 @@ def child_fun():
serialized_pkg,
function,
kwargs,
child_pipe,
write_pipe,
input_multiprocess_fd,
jobserver_fd1,
jobserver_fd2,
@@ -1183,6 +1232,12 @@ def child_fun():
p.start()
# We close the writable end of the pipe now to be sure that p is the
# only process which owns a handle for it. This ensures that when p
# closes its handle for the writable end, read_pipe.recv() will
# promptly report the readable end as being ready.
write_pipe.close()
except InstallError as e:
e.pkg = pkg
raise
@@ -1192,7 +1247,16 @@ def child_fun():
if input_multiprocess_fd is not None:
input_multiprocess_fd.close()
child_result = parent_pipe.recv()
def exitcode_msg(p):
typ = "exit" if p.exitcode >= 0 else "signal"
return f"{typ} {abs(p.exitcode)}"
try:
child_result = read_pipe.recv()
except EOFError:
p.join()
raise InstallError(f"The process has stopped unexpectedly ({exitcode_msg(p)})")
p.join()
# If returns a StopPhase, raise it
@@ -1212,6 +1276,10 @@ def child_fun():
child_result.print_context()
raise child_result
# Fallback. Usually caught beforehand in EOFError above.
if p.exitcode != 0:
raise InstallError(f"The process failed unexpectedly ({exitcode_msg(p)})")
return child_result

View File

@@ -46,6 +46,7 @@ class AutotoolsPackage(spack.package_base.PackageBase):
depends_on("gnuconfig", type="build", when="target=ppc64le:")
depends_on("gnuconfig", type="build", when="target=aarch64:")
depends_on("gnuconfig", type="build", when="target=riscv64:")
depends_on("gmake", type="build")
conflicts("platform=windows")
def flags_to_build_system_args(self, flags):

View File

@@ -34,6 +34,11 @@ def cmake_cache_option(name, boolean_value, comment="", force=False):
return 'set({0} {1} CACHE BOOL "{2}"{3})\n'.format(name, value, comment, force_str)
def cmake_cache_filepath(name, value, comment=""):
"""Generate a string for a cmake cache variable of type FILEPATH"""
return 'set({0} "{1}" CACHE FILEPATH "{2}")\n'.format(name, value, comment)
class CachedCMakeBuilder(CMakeBuilder):
#: Phases of a Cached CMake package
#: Note: the initconfig phase is used for developer builds as a final phase to stop on
@@ -257,6 +262,15 @@ def initconfig_hardware_entries(self):
entries.append(
cmake_cache_path("HIP_CXX_COMPILER", "{0}".format(self.spec["hip"].hipcc))
)
llvm_bin = spec["llvm-amdgpu"].prefix.bin
llvm_prefix = spec["llvm-amdgpu"].prefix
# Some ROCm systems seem to point to /<path>/rocm-<ver>/ and
# others point to /<path>/rocm-<ver>/llvm
if os.path.basename(os.path.normpath(llvm_prefix)) != "llvm":
llvm_bin = os.path.join(llvm_prefix, "llvm/bin/")
entries.append(
cmake_cache_filepath("CMAKE_HIP_COMPILER", os.path.join(llvm_bin, "clang++"))
)
archs = self.spec.variants["amdgpu_target"].value
if archs[0] != "none":
arch_str = ";".join(archs)
@@ -277,7 +291,7 @@ def std_initconfig_entries(self):
"#------------------{0}".format("-" * 60),
"# CMake executable path: {0}".format(self.pkg.spec["cmake"].command.path),
"#------------------{0}\n".format("-" * 60),
cmake_cache_path("CMAKE_PREFIX_PATH", cmake_prefix_path),
cmake_cache_string("CMAKE_PREFIX_PATH", cmake_prefix_path),
self.define_cmake_cache_from_variant("CMAKE_BUILD_TYPE", "build_type"),
]

View File

@@ -142,10 +142,10 @@ def flags_to_build_system_args(self, flags):
# We specify for each of them.
if flags["ldflags"]:
ldflags = " ".join(flags["ldflags"])
ld_string = "-DCMAKE_{0}_LINKER_FLAGS={1}"
# cmake has separate linker arguments for types of builds.
for type in ["EXE", "MODULE", "SHARED", "STATIC"]:
self.cmake_flag_args.append(ld_string.format(type, ldflags))
self.cmake_flag_args.append(f"-DCMAKE_EXE_LINKER_FLAGS={ldflags}")
self.cmake_flag_args.append(f"-DCMAKE_MODULE_LINKER_FLAGS={ldflags}")
self.cmake_flag_args.append(f"-DCMAKE_SHARED_LINKER_FLAGS={ldflags}")
# CMake has libs options separated by language. Apply ours to each.
if flags["ldlibs"]:
@@ -274,7 +274,6 @@ def std_args(pkg, generator=None):
generator,
define("CMAKE_INSTALL_PREFIX", pathlib.Path(pkg.prefix).as_posix()),
define("CMAKE_BUILD_TYPE", build_type),
define("BUILD_TESTING", pkg.run_tests),
]
# CMAKE_INTERPROCEDURAL_OPTIMIZATION only exists for CMake >= 3.9
@@ -451,7 +450,6 @@ def cmake_args(self):
* CMAKE_INSTALL_PREFIX
* CMAKE_BUILD_TYPE
* BUILD_TESTING
which will be set automatically.
"""

View File

@@ -154,7 +154,7 @@ def cuda_flags(arch_list):
conflicts("%pgi@:15.3,15.5:", when="+cuda ^cuda@7.5 target=x86_64:")
conflicts("%pgi@:16.2,16.0:16.3", when="+cuda ^cuda@8 target=x86_64:")
conflicts("%pgi@:15,18:", when="+cuda ^cuda@9.0:9.1 target=x86_64:")
conflicts("%pgi@:16,19:", when="+cuda ^cuda@9.2.88:10 target=x86_64:")
conflicts("%pgi@:16,19:", when="+cuda ^cuda@9.2.88:10.0 target=x86_64:")
conflicts("%pgi@:17,20:", when="+cuda ^cuda@10.1.105:10.2.89 target=x86_64:")
conflicts("%pgi@:17,21:", when="+cuda ^cuda@11.0.2:11.1.0 target=x86_64:")
conflicts("%clang@:3.4", when="+cuda ^cuda@:7.5 target=x86_64:")

View File

@@ -9,7 +9,8 @@
import spack.builder
import spack.package_base
from spack.directives import build_system, conflicts
from spack.directives import build_system, conflicts, depends_on
from spack.multimethod import when
from ._checks import (
BaseBuilder,
@@ -29,7 +30,10 @@ class MakefilePackage(spack.package_base.PackageBase):
legacy_buildsystem = "makefile"
build_system("makefile")
conflicts("platform=windows", when="build_system=makefile")
with when("build_system=makefile"):
conflicts("platform=windows")
depends_on("gmake", type="build")
@spack.builder.builder("makefile")

View File

@@ -10,7 +10,7 @@
import spack.builder
import spack.package_base
from spack.directives import build_system, depends_on, variant
from spack.directives import build_system, conflicts, depends_on, variant
from spack.multimethod import when
from ._checks import BaseBuilder, execute_build_time_tests
@@ -47,6 +47,13 @@ class MesonPackage(spack.package_base.PackageBase):
variant("strip", default=False, description="Strip targets on install")
depends_on("meson", type="build")
depends_on("ninja", type="build")
# Python detection in meson requires distutils to be importable, but distutils no longer
# exists in Python 3.12. In Spack, we can't use setuptools as distutils replacement,
# because the distutils-precedence.pth startup file that setuptools ships with is not run
# when setuptools is in PYTHONPATH; it has to be in system site-packages. In a future meson
# release, the distutils requirement will be dropped, so this conflict can be relaxed.
# We have patches to make it work with meson 1.1 and above.
conflicts("^python@3.12:", when="^meson@:1.0")
def flags_to_build_system_args(self, flags):
"""Produces a list of all command line arguments to pass the specified

View File

@@ -95,7 +95,7 @@ def makefile_root(self):
return self.stage.source_path
@property
def nmakefile_name(self):
def makefile_name(self):
"""Name of the current makefile. This is currently an empty value.
If a project defines this value, it will be used with the /f argument
to provide nmake an explicit makefile. This is usefule in scenarios where
@@ -126,8 +126,8 @@ def build(self, pkg, spec, prefix):
"""Run "nmake" on the build targets specified by the builder."""
opts = self.std_nmake_args
opts += self.nmake_args()
if self.nmakefile_name:
opts.append("/f {}".format(self.nmakefile_name))
if self.makefile_name:
opts.append("/F{}".format(self.makefile_name))
with fs.working_dir(self.build_directory):
inspect.getmodule(self.pkg).nmake(
*opts, *self.build_targets, ignore_quotes=self.ignore_quotes
@@ -139,8 +139,8 @@ def install(self, pkg, spec, prefix):
opts = self.std_nmake_args
opts += self.nmake_args()
opts += self.nmake_install_args()
if self.nmakefile_name:
opts.append("/f {}".format(self.nmakefile_name))
if self.makefile_name:
opts.append("/F{}".format(self.makefile_name))
opts.append(self.define("PREFIX", prefix))
with fs.working_dir(self.build_directory):
inspect.getmodule(self.pkg).nmake(

View File

@@ -9,11 +9,10 @@
import shutil
from os.path import basename, dirname, isdir
from llnl.util.filesystem import find_headers, find_libraries, join_path
from llnl.util.filesystem import find_headers, find_libraries, join_path, mkdirp
from llnl.util.link_tree import LinkTree
from spack.directives import conflicts, variant
from spack.package import mkdirp
from spack.util.environment import EnvironmentModifications
from spack.util.executable import Executable
@@ -61,6 +60,11 @@ def component_prefix(self):
"""Path to component <prefix>/<component>/<version>."""
return self.prefix.join(join_path(self.component_dir, self.spec.version))
@property
def env_script_args(self):
"""Additional arguments to pass to vars.sh script."""
return ()
def install(self, spec, prefix):
self.install_component(basename(self.url_for_version(spec.version)))
@@ -124,7 +128,7 @@ def setup_run_environment(self, env):
if "~envmods" not in self.spec:
env.extend(
EnvironmentModifications.from_sourcing_file(
join_path(self.component_prefix, "env", "vars.sh")
join_path(self.component_prefix, "env", "vars.sh"), *self.env_script_args
)
)
@@ -207,3 +211,7 @@ def link_flags(self):
@property
def ld_flags(self):
return "{0} {1}".format(self.search_flags, self.link_flags)
#: Tuple of Intel math libraries, exported to packages
INTEL_MATH_LIBRARIES = ("intel-mkl", "intel-oneapi-mkl", "intel-parallel-studio")

View File

@@ -16,19 +16,36 @@
import spack.builder
import spack.config
import spack.deptypes as dt
import spack.detection
import spack.multimethod
import spack.package_base
import spack.spec
import spack.store
from spack.directives import build_system, depends_on, extends, maintainers
from spack.error import NoHeadersError, NoLibrariesError, SpecError
from spack.error import NoHeadersError, NoLibrariesError
from spack.install_test import test_part
from spack.version import Version
from ._checks import BaseBuilder, execute_install_time_tests
def _flatten_dict(dictionary):
"""Iterable that yields KEY=VALUE paths through a dictionary.
Args:
dictionary: Possibly nested dictionary of arbitrary keys and values.
Yields:
A single path through the dictionary.
"""
for key, item in dictionary.items():
if isinstance(item, dict):
# Recursive case
for value in _flatten_dict(item):
yield f"{key}={value}"
else:
# Base case
yield f"{key}={item}"
class PythonExtension(spack.package_base.PackageBase):
maintainers("adamjstewart")
@@ -226,7 +243,48 @@ def update_external_dependencies(self, extendee_spec=None):
python.external_path = self.spec.external_path
python._mark_concrete()
self.spec.add_dependency_edge(python, deptypes=("build", "link", "run"), virtuals=())
self.spec.add_dependency_edge(python, depflag=dt.BUILD | dt.LINK | dt.RUN, virtuals=())
def get_external_python_for_prefix(self):
"""
For an external package that extends python, find the most likely spec for the python
it depends on.
First search: an "installed" external that shares a prefix with this package
Second search: a configured external that shares a prefix with this package
Third search: search this prefix for a python package
Returns:
spack.spec.Spec: The external Spec for python most likely to be compatible with self.spec
"""
python_externals_installed = [
s for s in spack.store.STORE.db.query("python") if s.prefix == self.spec.external_path
]
if python_externals_installed:
return python_externals_installed[0]
python_external_config = spack.config.get("packages:python:externals", [])
python_externals_configured = [
spack.spec.parse_with_version_concrete(item["spec"])
for item in python_external_config
if item["prefix"] == self.spec.external_path
]
if python_externals_configured:
return python_externals_configured[0]
python_externals_detection = spack.detection.by_path(
["python"], path_hints=[self.spec.external_path]
)
python_externals_detected = [
d.spec
for d in python_externals_detection.get("python", [])
if d.prefix == self.spec.external_path
]
if python_externals_detected:
return python_externals_detected[0]
raise StopIteration("No external python could be detected for %s to depend on" % self.spec)
class PythonPackage(PythonExtension):
@@ -273,54 +331,16 @@ def list_url(cls):
name = cls.pypi.split("/")[0]
return "https://pypi.org/simple/" + name + "/"
def get_external_python_for_prefix(self):
"""
For an external package that extends python, find the most likely spec for the python
it depends on.
First search: an "installed" external that shares a prefix with this package
Second search: a configured external that shares a prefix with this package
Third search: search this prefix for a python package
Returns:
spack.spec.Spec: The external Spec for python most likely to be compatible with self.spec
"""
python_externals_installed = [
s for s in spack.store.STORE.db.query("python") if s.prefix == self.spec.external_path
]
if python_externals_installed:
return python_externals_installed[0]
python_external_config = spack.config.get("packages:python:externals", [])
python_externals_configured = [
spack.spec.parse_with_version_concrete(item["spec"])
for item in python_external_config
if item["prefix"] == self.spec.external_path
]
if python_externals_configured:
return python_externals_configured[0]
python_externals_detection = spack.detection.by_executable(
[spack.repo.PATH.get_pkg_class("python")], path_hints=[self.spec.external_path]
)
python_externals_detected = [
d.spec
for d in python_externals_detection.get("python", [])
if d.prefix == self.spec.external_path
]
if python_externals_detected:
return python_externals_detected[0]
raise StopIteration("No external python could be detected for %s to depend on" % self.spec)
@property
def headers(self):
"""Discover header files in platlib."""
# Remove py- prefix in package name
name = self.spec.name[3:]
# Headers may be in either location
include = self.prefix.join(self.spec["python"].package.include)
platlib = self.prefix.join(self.spec["python"].package.platlib)
include = self.prefix.join(self.spec["python"].package.include).join(name)
platlib = self.prefix.join(self.spec["python"].package.platlib).join(name)
headers = fs.find_all_headers(include) + fs.find_all_headers(platlib)
if headers:
@@ -334,13 +354,14 @@ def libs(self):
"""Discover libraries in platlib."""
# Remove py- prefix in package name
library = "lib" + self.spec.name[3:].replace("-", "?")
root = self.prefix.join(self.spec["python"].package.platlib)
name = self.spec.name[3:]
for shared in [True, False]:
libs = fs.find_libraries(library, root, shared=shared, recursive=True)
if libs:
return libs
root = self.prefix.join(self.spec["python"].package.platlib).join(name)
libs = fs.find_all_libraries(root, recursive=True)
if libs:
return libs
msg = "Unable to recursively locate {} libraries in {}"
raise NoLibrariesError(msg.format(self.spec.name, root))
@@ -357,7 +378,7 @@ class PythonPipBuilder(BaseBuilder):
legacy_long_methods = ("install_options", "global_options", "config_settings")
#: Names associated with package attributes in the old build-system format
legacy_attributes = ("build_directory", "install_time_test_callbacks")
legacy_attributes = ("archive_files", "build_directory", "install_time_test_callbacks")
#: Callback names for install-time test
install_time_test_callbacks = ["test"]
@@ -402,14 +423,15 @@ def build_directory(self):
def config_settings(self, spec, prefix):
"""Configuration settings to be passed to the PEP 517 build backend.
Requires pip 22.1 or newer.
Requires pip 22.1 or newer for keys that appear only a single time,
or pip 23.1 or newer if the same key appears multiple times.
Args:
spec (spack.spec.Spec): build spec
prefix (spack.util.prefix.Prefix): installation prefix
Returns:
dict: dictionary of KEY, VALUE settings
dict: Possibly nested dictionary of KEY, VALUE settings
"""
return {}
@@ -445,29 +467,28 @@ def global_options(self, spec, prefix):
def install(self, pkg, spec, prefix):
"""Install everything from build directory."""
args = PythonPipBuilder.std_args(pkg) + ["--prefix=" + prefix]
for key, value in self.config_settings(spec, prefix).items():
if spec["py-pip"].version < Version("22.1"):
raise SpecError(
"'{}' package uses 'config_settings' which is only supported by "
"pip 22.1+. Add the following line to the package to fix this:\n\n"
' depends_on("py-pip@22.1:", type="build")'.format(spec.name)
)
args.append("--config-settings={}={}".format(key, value))
args = PythonPipBuilder.std_args(pkg) + [f"--prefix={prefix}"]
for setting in _flatten_dict(self.config_settings(spec, prefix)):
args.append(f"--config-settings={setting}")
for option in self.install_options(spec, prefix):
args.append("--install-option=" + option)
args.append(f"--install-option={option}")
for option in self.global_options(spec, prefix):
args.append("--global-option=" + option)
args.append(f"--global-option={option}")
if pkg.stage.archive_file and pkg.stage.archive_file.endswith(".whl"):
args.append(pkg.stage.archive_file)
else:
args.append(".")
pip = inspect.getmodule(pkg).pip
pip = spec["python"].command
# Hide user packages, since we don't have build isolation. This is
# necessary because pip / setuptools may run hooks from arbitrary
# packages during the build. There is no equivalent variable to hide
# system packages, so this is not reliable for external Python.
pip.add_default_env("PYTHONNOUSERSITE", "1")
pip.add_default_arg("-m")
pip.add_default_arg("pip")
with fs.working_dir(self.build_directory):
pip(*args)

View File

@@ -10,9 +10,10 @@
import llnl.util.tty as tty
import spack.builder
from spack.build_environment import SPACK_NO_PARALLEL_MAKE, determine_number_of_jobs
from spack.build_environment import SPACK_NO_PARALLEL_MAKE
from spack.directives import build_system, extends, maintainers
from spack.package_base import PackageBase
from spack.util.cpus import determine_number_of_jobs
from spack.util.environment import env_flag
from spack.util.executable import Executable, ProcessError
@@ -63,7 +64,7 @@ class RacketBuilder(spack.builder.Builder):
@property
def subdirectory(self):
if self.racket_name:
if self.pkg.racket_name:
return "pkgs/{0}".format(self.pkg.racket_name)
return None
@@ -92,7 +93,7 @@ def install(self, pkg, spec, prefix):
"--copy",
"-i",
"-j",
str(determine_number_of_jobs(parallel)),
str(determine_number_of_jobs(parallel=parallel)),
"--",
os.getcwd(),
]

View File

@@ -25,6 +25,7 @@
import llnl.util.filesystem as fs
import llnl.util.tty as tty
from llnl.util.lang import memoized
from llnl.util.tty.color import cescape, colorize
import spack
import spack.binary_distribution as bindist
@@ -45,11 +46,30 @@
from spack.reporters import CDash, CDashConfiguration
from spack.reporters.cdash import build_stamp as cdash_build_stamp
JOB_RETRY_CONDITIONS = ["always"]
# See https://docs.gitlab.com/ee/ci/yaml/#retry for descriptions of conditions
JOB_RETRY_CONDITIONS = [
# "always",
"unknown_failure",
"script_failure",
"api_failure",
"stuck_or_timeout_failure",
"runner_system_failure",
"runner_unsupported",
"stale_schedule",
# "job_execution_timeout",
"archived_failure",
"unmet_prerequisites",
"scheduler_failure",
"data_integrity_failure",
]
TEMP_STORAGE_MIRROR_NAME = "ci_temporary_mirror"
SPACK_RESERVED_TAGS = ["public", "protected", "notary"]
# TODO: Remove this in Spack 0.23
SHARED_PR_MIRROR_URL = "s3://spack-binaries-prs/shared_pr_mirror"
JOB_NAME_FORMAT = (
"{name}{@version} {/hash:7} {%compiler.name}{@compiler.version}{arch=architecture}"
)
spack_gpg = spack.main.SpackCommand("gpg")
spack_compiler = spack.main.SpackCommand("compiler")
@@ -69,48 +89,23 @@ def __exit__(self, exc_type, exc_value, exc_traceback):
return False
def get_job_name(spec, osarch, build_group):
"""Given the necessary parts, format the gitlab job name
def get_job_name(spec: spack.spec.Spec, build_group: str = ""):
"""Given a spec and possibly a build group, return the job name. If the
resulting name is longer than 255 characters, it will be truncated.
Arguments:
spec (spack.spec.Spec): Spec job will build
osarch: Architecture TODO: (this is a spack.spec.ArchSpec,
but sphinx doesn't recognize the type and fails).
build_group (str): Name of build group this job belongs to (a CDash
notion)
Returns: The job name
"""
item_idx = 0
format_str = ""
format_args = []
format_str += "{{{0}}}".format(item_idx)
format_args.append(spec.name)
item_idx += 1
format_str += "/{{{0}}}".format(item_idx)
format_args.append(spec.dag_hash(7))
item_idx += 1
format_str += " {{{0}}}".format(item_idx)
format_args.append(spec.version)
item_idx += 1
format_str += " {{{0}}}".format(item_idx)
format_args.append(spec.compiler)
item_idx += 1
format_str += " {{{0}}}".format(item_idx)
format_args.append(osarch)
item_idx += 1
job_name = spec.format(JOB_NAME_FORMAT)
if build_group:
format_str += " {{{0}}}".format(item_idx)
format_args.append(build_group)
item_idx += 1
job_name = "{0} {1}".format(job_name, build_group)
return format_str.format(*format_args)
return job_name[:255]
def _remove_reserved_tags(tags):
@@ -118,15 +113,6 @@ def _remove_reserved_tags(tags):
return [tag for tag in tags if tag not in SPACK_RESERVED_TAGS]
def _get_spec_string(spec):
format_elements = ["{name}{@version}", "{%compiler}"]
if spec.architecture:
format_elements.append(" {arch=architecture}")
return spec.format("".join(format_elements))
def _spec_deps_key(s):
return "{0}/{1}".format(s.name, s.dag_hash(7))
@@ -231,22 +217,22 @@ def _print_staging_summary(spec_labels, stages, mirrors_to_check, rebuild_decisi
tty.msg("Staging summary ([x] means a job needs rebuilding):")
for stage_index, stage in enumerate(stages):
tty.msg(" stage {0} ({1} jobs):".format(stage_index, len(stage)))
tty.msg(f" stage {stage_index} ({len(stage)} jobs):")
for job in sorted(stage):
for job in sorted(stage, key=lambda j: (not rebuild_decisions[j].rebuild, j)):
s = spec_labels[job]
rebuild = rebuild_decisions[job].rebuild
reason = rebuild_decisions[job].reason
reason_msg = " ({0})".format(reason) if reason else ""
tty.msg(
" [{1}] {0} -> {2}{3}".format(
job, "x" if rebuild else " ", _get_spec_string(s), reason_msg
)
)
if rebuild_decisions[job].mirrors:
tty.msg(" found on the following mirrors:")
for murl in rebuild_decisions[job].mirrors:
tty.msg(" {0}".format(murl))
reason_msg = f" ({reason})" if reason else ""
spec_fmt = "{name}{@version}{%compiler}{/hash:7}"
if rebuild_decisions[job].rebuild:
status = colorize("@*g{[x]} ")
msg = f" {status}{s.cformat(spec_fmt)}{reason_msg}"
else:
msg = f"{s.format(spec_fmt)}{reason_msg}"
if rebuild_decisions[job].mirrors:
msg += f" [{', '.join(rebuild_decisions[job].mirrors)}]"
msg = colorize(f" @K - {cescape(msg)}@.")
tty.msg(msg)
def _compute_spec_deps(spec_list):
@@ -308,7 +294,7 @@ def append_dep(s, d):
dependencies.append({"spec": s, "depends": d})
for spec in spec_list:
for s in spec.traverse(deptype=all):
for s in spec.traverse(deptype="all"):
if s.external:
tty.msg("Will not stage external pkg: {0}".format(s))
continue
@@ -316,7 +302,7 @@ def append_dep(s, d):
skey = _spec_deps_key(s)
spec_labels[skey] = s
for d in s.dependencies(deptype=all):
for d in s.dependencies(deptype="all"):
dkey = _spec_deps_key(d)
if d.external:
tty.msg("Will not stage external dep: {0}".format(d))
@@ -337,7 +323,7 @@ def _spec_matches(spec, match_string):
def _format_job_needs(
dep_jobs, osname, build_group, prune_dag, rebuild_decisions, enable_artifacts_buildcache
dep_jobs, build_group, prune_dag, rebuild_decisions, enable_artifacts_buildcache
):
needs_list = []
for dep_job in dep_jobs:
@@ -347,7 +333,7 @@ def _format_job_needs(
if not prune_dag or rebuild:
needs_list.append(
{
"job": get_job_name(dep_job, dep_job.architecture, build_group),
"job": get_job_name(dep_job, build_group),
"artifacts": enable_artifacts_buildcache,
}
)
@@ -700,7 +686,7 @@ def generate_gitlab_ci_yaml(
remote_mirror_override (str): Typically only needed when one spack.yaml
is used to populate several mirrors with binaries, based on some
criteria. Spack protected pipelines populate different mirrors based
on branch name, facilitated by this option.
on branch name, facilitated by this option. DEPRECATED
"""
with spack.concretize.disable_compiler_existence_check():
with env.write_transaction():
@@ -797,17 +783,39 @@ def generate_gitlab_ci_yaml(
"instead.",
)
if "mirrors" not in yaml_root or len(yaml_root["mirrors"].values()) < 1:
tty.die("spack ci generate requires an env containing a mirror")
pipeline_mirrors = spack.mirror.MirrorCollection(binary=True)
deprecated_mirror_config = False
buildcache_destination = None
if "buildcache-destination" in pipeline_mirrors:
if remote_mirror_override:
tty.die(
"Using the deprecated --buildcache-destination cli option and "
"having a mirror named 'buildcache-destination' at the same time "
"is not allowed"
)
buildcache_destination = pipeline_mirrors["buildcache-destination"]
else:
deprecated_mirror_config = True
# TODO: This will be an error in Spack 0.23
ci_mirrors = yaml_root["mirrors"]
mirror_urls = [url for url in ci_mirrors.values()]
remote_mirror_url = mirror_urls[0]
# TODO: Remove this block in spack 0.23
remote_mirror_url = None
if deprecated_mirror_config:
if "mirrors" not in yaml_root or len(yaml_root["mirrors"].values()) < 1:
tty.die("spack ci generate requires an env containing a mirror")
ci_mirrors = yaml_root["mirrors"]
mirror_urls = [url for url in ci_mirrors.values()]
remote_mirror_url = mirror_urls[0]
spack_buildcache_copy = os.environ.get("SPACK_COPY_BUILDCACHE", None)
if spack_buildcache_copy:
buildcache_copies = {}
buildcache_copy_src_prefix = remote_mirror_override or remote_mirror_url
buildcache_copy_src_prefix = (
buildcache_destination.fetch_url
if buildcache_destination
else remote_mirror_override or remote_mirror_url
)
buildcache_copy_dest_prefix = spack_buildcache_copy
# Check for a list of "known broken" specs that we should not bother
@@ -819,6 +827,7 @@ def generate_gitlab_ci_yaml(
enable_artifacts_buildcache = False
if "enable-artifacts-buildcache" in ci_config:
tty.warn("Support for enable-artifacts-buildcache will be removed in Spack 0.23")
enable_artifacts_buildcache = ci_config["enable-artifacts-buildcache"]
rebuild_index_enabled = True
@@ -827,13 +836,15 @@ def generate_gitlab_ci_yaml(
temp_storage_url_prefix = None
if "temporary-storage-url-prefix" in ci_config:
tty.warn("Support for temporary-storage-url-prefix will be removed in Spack 0.23")
temp_storage_url_prefix = ci_config["temporary-storage-url-prefix"]
# If a remote mirror override (alternate buildcache destination) was
# specified, add it here in case it has already built hashes we might
# generate.
# TODO: Remove this block in Spack 0.23
mirrors_to_check = None
if remote_mirror_override:
if deprecated_mirror_config and remote_mirror_override:
if spack_pipeline_type == "spack_protected_branch":
# Overriding the main mirror in this case might result
# in skipping jobs on a release pipeline because specs are
@@ -853,8 +864,9 @@ def generate_gitlab_ci_yaml(
cfg.default_modify_scope(),
)
# TODO: Remove this block in Spack 0.23
shared_pr_mirror = None
if spack_pipeline_type == "spack_pull_request":
if deprecated_mirror_config and spack_pipeline_type == "spack_pull_request":
stack_name = os.environ.get("SPACK_CI_STACK_NAME", "")
shared_pr_mirror = url_util.join(SHARED_PR_MIRROR_URL, stack_name)
spack.mirror.add(
@@ -906,6 +918,7 @@ def generate_gitlab_ci_yaml(
job_log_dir = os.path.join(pipeline_artifacts_dir, "logs")
job_repro_dir = os.path.join(pipeline_artifacts_dir, "reproduction")
job_test_dir = os.path.join(pipeline_artifacts_dir, "tests")
# TODO: Remove this line in Spack 0.23
local_mirror_dir = os.path.join(pipeline_artifacts_dir, "mirror")
user_artifacts_dir = os.path.join(pipeline_artifacts_dir, "user_data")
@@ -920,13 +933,13 @@ def generate_gitlab_ci_yaml(
rel_job_log_dir = os.path.relpath(job_log_dir, ci_project_dir)
rel_job_repro_dir = os.path.relpath(job_repro_dir, ci_project_dir)
rel_job_test_dir = os.path.relpath(job_test_dir, ci_project_dir)
# TODO: Remove this line in Spack 0.23
rel_local_mirror_dir = os.path.join(local_mirror_dir, ci_project_dir)
rel_user_artifacts_dir = os.path.relpath(user_artifacts_dir, ci_project_dir)
# Speed up staging by first fetching binary indices from all mirrors
# (including the override mirror we may have just added above).
try:
bindist.binary_index.update()
bindist.BINARY_INDEX.update()
except bindist.FetchCacheError as e:
tty.warn(e)
@@ -1023,19 +1036,23 @@ def main_script_replacements(cmd):
if "after_script" in job_object:
job_object["after_script"] = _unpack_script(job_object["after_script"])
osname = str(release_spec.architecture)
job_name = get_job_name(release_spec, osname, build_group)
job_name = get_job_name(release_spec, build_group)
job_vars = job_object.setdefault("variables", {})
job_vars["SPACK_JOB_SPEC_DAG_HASH"] = release_spec_dag_hash
job_vars["SPACK_JOB_SPEC_PKG_NAME"] = release_spec.name
job_vars["SPACK_JOB_SPEC_PKG_VERSION"] = release_spec.format("{version}")
job_vars["SPACK_JOB_SPEC_COMPILER_NAME"] = release_spec.format("{compiler.name}")
job_vars["SPACK_JOB_SPEC_COMPILER_VERSION"] = release_spec.format("{compiler.version}")
job_vars["SPACK_JOB_SPEC_ARCH"] = release_spec.format("{architecture}")
job_vars["SPACK_JOB_SPEC_VARIANTS"] = release_spec.format("{variants}")
job_object["needs"] = []
if spec_label in dependencies:
if enable_artifacts_buildcache:
# Get dependencies transitively, so they're all
# available in the artifacts buildcache.
dep_jobs = [d for d in release_spec.traverse(deptype=all, root=False)]
dep_jobs = [d for d in release_spec.traverse(deptype="all", root=False)]
else:
# In this case, "needs" is only used for scheduling
# purposes, so we only get the direct dependencies.
@@ -1046,7 +1063,6 @@ def main_script_replacements(cmd):
job_object["needs"].extend(
_format_job_needs(
dep_jobs,
osname,
build_group,
prune_dag,
rebuild_decisions,
@@ -1132,6 +1148,7 @@ def main_script_replacements(cmd):
},
)
# TODO: Remove this block in Spack 0.23
if enable_artifacts_buildcache:
bc_root = os.path.join(local_mirror_dir, "build_cache")
job_object["artifacts"]["paths"].extend(
@@ -1161,10 +1178,12 @@ def main_script_replacements(cmd):
_print_staging_summary(spec_labels, stages, mirrors_to_check, rebuild_decisions)
# Clean up remote mirror override if enabled
if remote_mirror_override:
spack.mirror.remove("ci_pr_mirror", cfg.default_modify_scope())
if spack_pipeline_type == "spack_pull_request":
spack.mirror.remove("ci_shared_pr_mirror", cfg.default_modify_scope())
# TODO: Remove this block in Spack 0.23
if deprecated_mirror_config:
if remote_mirror_override:
spack.mirror.remove("ci_pr_mirror", cfg.default_modify_scope())
if spack_pipeline_type == "spack_pull_request":
spack.mirror.remove("ci_shared_pr_mirror", cfg.default_modify_scope())
tty.debug("{0} build jobs generated in {1} stages".format(job_id, stage_id))
@@ -1195,10 +1214,28 @@ def main_script_replacements(cmd):
sync_job["needs"] = [
{"job": generate_job_name, "pipeline": "{0}".format(parent_pipeline_id)}
]
if "variables" not in sync_job:
sync_job["variables"] = {}
sync_job["variables"]["SPACK_COPY_ONLY_DESTINATION"] = (
buildcache_destination.fetch_url
if buildcache_destination
else remote_mirror_override or remote_mirror_url
)
if "buildcache-source" in pipeline_mirrors:
buildcache_source = pipeline_mirrors["buildcache-source"].fetch_url
else:
# TODO: Remove this condition in Spack 0.23
buildcache_source = os.environ.get("SPACK_SOURCE_MIRROR", None)
sync_job["variables"]["SPACK_BUILDCACHE_SOURCE"] = buildcache_source
output_object["copy"] = sync_job
job_id += 1
if job_id > 0:
# TODO: Remove this block in Spack 0.23
if temp_storage_url_prefix:
# There were some rebuild jobs scheduled, so we will need to
# schedule a job to clean up the temporary storage location
@@ -1232,6 +1269,13 @@ def main_script_replacements(cmd):
signing_job["when"] = "always"
signing_job["retry"] = {"max": 2, "when": ["always"]}
signing_job["interruptible"] = True
if "variables" not in signing_job:
signing_job["variables"] = {}
signing_job["variables"]["SPACK_BUILDCACHE_DESTINATION"] = (
buildcache_destination.push_url # need the s3 url for aws s3 sync
if buildcache_destination
else remote_mirror_override or remote_mirror_url
)
output_object["sign-pkgs"] = signing_job
@@ -1240,13 +1284,13 @@ def main_script_replacements(cmd):
stage_names.append("stage-rebuild-index")
final_job = spack_ci_ir["jobs"]["reindex"]["attributes"]
index_target_mirror = mirror_urls[0]
if remote_mirror_override:
index_target_mirror = remote_mirror_override
final_job["stage"] = "stage-rebuild-index"
target_mirror = remote_mirror_override or remote_mirror_url
if buildcache_destination:
target_mirror = buildcache_destination.push_url
final_job["script"] = _unpack_script(
final_job["script"],
op=lambda cmd: cmd.replace("{index_target_mirror}", index_target_mirror),
op=lambda cmd: cmd.replace("{index_target_mirror}", target_mirror),
)
final_job["when"] = "always"
@@ -1268,20 +1312,24 @@ def main_script_replacements(cmd):
"SPACK_CONCRETE_ENV_DIR": rel_concrete_env_dir,
"SPACK_VERSION": spack_version,
"SPACK_CHECKOUT_VERSION": version_to_clone,
# TODO: Remove this line in Spack 0.23
"SPACK_REMOTE_MIRROR_URL": remote_mirror_url,
"SPACK_JOB_LOG_DIR": rel_job_log_dir,
"SPACK_JOB_REPRO_DIR": rel_job_repro_dir,
"SPACK_JOB_TEST_DIR": rel_job_test_dir,
# TODO: Remove this line in Spack 0.23
"SPACK_LOCAL_MIRROR_DIR": rel_local_mirror_dir,
"SPACK_PIPELINE_TYPE": str(spack_pipeline_type),
"SPACK_CI_STACK_NAME": os.environ.get("SPACK_CI_STACK_NAME", "None"),
# TODO: Remove this line in Spack 0.23
"SPACK_CI_SHARED_PR_MIRROR_URL": shared_pr_mirror or "None",
"SPACK_REBUILD_CHECK_UP_TO_DATE": str(prune_dag),
"SPACK_REBUILD_EVERYTHING": str(rebuild_everything),
"SPACK_REQUIRE_SIGNING": os.environ.get("SPACK_REQUIRE_SIGNING", "False"),
}
if remote_mirror_override:
# TODO: Remove this block in Spack 0.23
if deprecated_mirror_config and remote_mirror_override:
(output_object["variables"]["SPACK_REMOTE_MIRROR_OVERRIDE"]) = remote_mirror_override
spack_stack_name = os.environ.get("SPACK_CI_STACK_NAME", None)
@@ -2021,43 +2069,23 @@ def process_command(name, commands, repro_dir, run=True, exit_on_failure=True):
def create_buildcache(
input_spec: spack.spec.Spec,
*,
pipeline_mirror_url: Optional[str] = None,
buildcache_mirror_url: Optional[str] = None,
sign_binaries: bool = False,
input_spec: spack.spec.Spec, *, destination_mirror_urls: List[str], sign_binaries: bool = False
) -> List[PushResult]:
"""Create the buildcache at the provided mirror(s).
Arguments:
input_spec: Installed spec to package and push
buildcache_mirror_url: URL for the buildcache mirror
pipeline_mirror_url: URL for the pipeline mirror
destination_mirror_urls: List of urls to push to
sign_binaries: Whether or not to sign buildcache entry
Returns: A list of PushResults, indicating success or failure.
"""
results = []
# Create buildcache in either the main remote mirror, or in the
# per-PR mirror, if this is a PR pipeline
if buildcache_mirror_url:
for mirror_url in destination_mirror_urls:
results.append(
PushResult(
success=push_mirror_contents(input_spec, buildcache_mirror_url, sign_binaries),
url=buildcache_mirror_url,
)
)
# Create another copy of that buildcache in the per-pipeline
# temporary storage mirror (this is only done if either
# artifacts buildcache is enabled or a temporary storage url
# prefix is set)
if pipeline_mirror_url:
results.append(
PushResult(
success=push_mirror_contents(input_spec, pipeline_mirror_url, sign_binaries),
url=pipeline_mirror_url,
success=push_mirror_contents(input_spec, mirror_url, sign_binaries), url=mirror_url
)
)
@@ -2237,13 +2265,13 @@ def build_name(self):
spec.architecture,
self.build_group,
)
tty.verbose(
tty.debug(
"Generated CDash build name ({0}) from the {1}".format(build_name, spec.name)
)
return build_name
build_name = os.environ.get("SPACK_CDASH_BUILD_NAME")
tty.verbose("Using CDash build name ({0}) from the environment".format(build_name))
tty.debug("Using CDash build name ({0}) from the environment".format(build_name))
return build_name
@property # type: ignore
@@ -2257,11 +2285,11 @@ def build_stamp(self):
Returns: (str) current CDash build stamp"""
build_stamp = os.environ.get("SPACK_CDASH_BUILD_STAMP")
if build_stamp:
tty.verbose("Using build stamp ({0}) from the environment".format(build_stamp))
tty.debug("Using build stamp ({0}) from the environment".format(build_stamp))
return build_stamp
build_stamp = cdash_build_stamp(self.build_group, time.time())
tty.verbose("Generated new build stamp ({0})".format(build_stamp))
tty.debug("Generated new build stamp ({0})".format(build_stamp))
return build_stamp
@property # type: ignore

View File

@@ -11,6 +11,7 @@
from textwrap import dedent
from typing import List, Match, Tuple
import llnl.string
import llnl.util.tty as tty
from llnl.util.filesystem import join_path
from llnl.util.lang import attr_setdefault, index_by
@@ -29,7 +30,6 @@
import spack.user_environment as uenv
import spack.util.spack_json as sjson
import spack.util.spack_yaml as syaml
import spack.util.string
# cmd has a submodule called "list" so preserve the python list module
python_list = list
@@ -342,9 +342,9 @@ def iter_groups(specs, indent, all_headers):
print()
header = "%s{%s} / %s{%s}" % (
spack.spec.architecture_color,
spack.spec.ARCHITECTURE_COLOR,
architecture if architecture else "no arch",
spack.spec.compiler_color,
spack.spec.COMPILER_COLOR,
f"{compiler.display_str}" if compiler else "no compiler",
)
@@ -516,7 +516,7 @@ def print_how_many_pkgs(specs, pkg_type=""):
category, e.g. if pkg_type is "installed" then the message
would be "3 installed packages"
"""
tty.msg("%s" % spack.util.string.plural(len(specs), pkg_type + " package"))
tty.msg("%s" % llnl.string.plural(len(specs), pkg_type + " package"))
def spack_is_git_repo():

View File

@@ -3,6 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import llnl.util.tty as tty
import llnl.util.tty.colify
import llnl.util.tty.color as cl
import spack.audit
@@ -20,6 +21,15 @@ def setup_parser(subparser):
# Audit configuration files
sp.add_parser("configs", help="audit configuration files")
# Audit package recipes
external_parser = sp.add_parser("externals", help="check external detection in packages")
external_parser.add_argument(
"--list",
action="store_true",
dest="list_externals",
help="if passed, list which packages have detection tests",
)
# Https and other linting
https_parser = sp.add_parser("packages-https", help="check https in packages")
https_parser.add_argument(
@@ -29,7 +39,7 @@ def setup_parser(subparser):
# Audit package recipes
pkg_parser = sp.add_parser("packages", help="audit package recipes")
for group in [pkg_parser, https_parser]:
for group in [pkg_parser, https_parser, external_parser]:
group.add_argument(
"name",
metavar="PKG",
@@ -62,6 +72,18 @@ def packages_https(parser, args):
_process_reports(reports)
def externals(parser, args):
if args.list_externals:
msg = "@*{The following packages have detection tests:}"
tty.msg(cl.colorize(msg))
llnl.util.tty.colify.colify(spack.audit.packages_with_detection_tests(), indent=2)
return
pkgs = args.name or spack.repo.PATH.all_package_names()
reports = spack.audit.run_group(args.subcommand, pkgs=pkgs)
_process_reports(reports)
def list(parser, args):
for subcommand, check_tags in spack.audit.GROUPS.items():
print(cl.colorize("@*b{" + subcommand + "}:"))
@@ -78,6 +100,7 @@ def list(parser, args):
def audit(parser, args):
subcommands = {
"configs": configs,
"externals": externals,
"packages": packages,
"packages-https": packages_https,
"list": list,

View File

@@ -3,6 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import spack.cmd.common.env_utility as env_utility
from spack.context import Context
description = (
"run a command in a spec's install environment, or dump its environment to screen or file"
@@ -14,4 +15,4 @@
def build_env(parser, args):
env_utility.emulate_env_utility("build-env", "build", args)
env_utility.emulate_env_utility("build-env", Context.BUILD, args)

View File

@@ -3,16 +3,20 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import argparse
import copy
import glob
import hashlib
import json
import multiprocessing.pool
import os
import shutil
import sys
import tempfile
from typing import List
import urllib.request
from typing import Dict, List, Optional, Tuple
import llnl.util.tty as tty
import llnl.util.tty.color as clr
from llnl.string import plural
from llnl.util.lang import elide_list
import spack.binary_distribution as bindist
@@ -20,18 +24,38 @@
import spack.cmd.common.arguments as arguments
import spack.config
import spack.environment as ev
import spack.error
import spack.hash_types as ht
import spack.mirror
import spack.oci.oci
import spack.oci.opener
import spack.relocate
import spack.repo
import spack.spec
import spack.stage
import spack.store
import spack.user_environment
import spack.util.crypto
import spack.util.url as url_util
import spack.util.web as web_util
from spack.build_environment import determine_number_of_jobs
from spack.cmd import display_specs
from spack.oci.image import (
Digest,
ImageReference,
default_config,
default_index_tag,
default_manifest,
default_tag,
tag_is_spec,
)
from spack.oci.oci import (
copy_missing_layers_with_retry,
get_manifest_and_config_with_retry,
upload_blob_with_retry,
upload_manifest_with_retry,
)
from spack.spec import Spec, save_dependency_specfiles
from spack.stage import Stage
from spack.util.string import plural
description = "create, download and install binary packages"
section = "packaging"
@@ -57,7 +81,9 @@ def setup_parser(subparser: argparse.ArgumentParser):
push_sign.add_argument(
"--key", "-k", metavar="key", type=str, default=None, help="key for signing"
)
push.add_argument("mirror", type=str, help="mirror name, path, or URL")
push.add_argument(
"mirror", type=arguments.mirror_name_or_url, help="mirror name, path, or URL"
)
push.add_argument(
"--update-index",
"--rebuild-index",
@@ -78,7 +104,15 @@ def setup_parser(subparser: argparse.ArgumentParser):
"Alternatively, one can decide to build a cache for only the package or only the "
"dependencies",
)
arguments.add_common_arguments(push, ["specs"])
push.add_argument(
"--fail-fast",
action="store_true",
help="stop pushing on first failure (default is best effort)",
)
push.add_argument(
"--base-image", default=None, help="specify the base image for the buildcache. "
)
arguments.add_common_arguments(push, ["specs", "jobs"])
push.set_defaults(func=push_fn)
install = subparsers.add_parser("install", help=install_fn.__doc__)
@@ -262,6 +296,21 @@ def _matching_specs(specs: List[Spec]) -> List[Spec]:
return [spack.cmd.disambiguate_spec(s, ev.active_environment(), installed=any) for s in specs]
def _format_spec(spec: Spec) -> str:
return spec.cformat("{name}{@version}{/hash:7}")
def _progress(i: int, total: int):
if total > 1:
digits = len(str(total))
return f"[{i+1:{digits}}/{total}] "
return ""
def _make_pool():
return multiprocessing.pool.Pool(determine_number_of_jobs(parallel=True))
def push_fn(args):
"""create a binary package and push it to a mirror"""
if args.spec_file:
@@ -275,62 +324,86 @@ def push_fn(args):
else:
specs = spack.cmd.require_active_env("buildcache push").all_specs()
mirror = arguments.mirror_name_or_url(args.mirror)
if args.allow_root:
tty.warn(
"The flag `--allow-root` is the default in Spack 0.21, will be removed in Spack 0.22"
)
url = mirror.push_url
# Check if this is an OCI image.
try:
image_ref = spack.oci.oci.image_from_mirror(args.mirror)
except ValueError:
image_ref = None
# For OCI images, we require dependencies to be pushed for now.
if image_ref:
if "dependencies" not in args.things_to_install:
tty.die("Dependencies must be pushed for OCI images.")
if not args.unsigned:
tty.warn(
"Code signing is currently not supported for OCI images. "
"Use --unsigned to silence this warning."
)
# This is a list of installed, non-external specs.
specs = bindist.specs_to_be_packaged(
specs,
root="package" in args.things_to_install,
dependencies="dependencies" in args.things_to_install,
)
url = args.mirror.push_url
# When pushing multiple specs, print the url once ahead of time, as well as how
# many specs are being pushed.
if len(specs) > 1:
tty.info(f"Selected {len(specs)} specs to push to {url}")
skipped = []
failed = []
# tty printing
color = clr.get_color_when()
format_spec = lambda s: s.format("{name}{@version}{/hash:7}", color=color)
total_specs = len(specs)
digits = len(str(total_specs))
# TODO: unify this logic in the future.
if image_ref:
with tempfile.TemporaryDirectory(
dir=spack.stage.get_stage_root()
) as tmpdir, _make_pool() as pool:
skipped = _push_oci(args, image_ref, specs, tmpdir, pool)
else:
skipped = []
for i, spec in enumerate(specs):
try:
bindist.push_or_raise(
spec,
url,
bindist.PushOptions(
force=args.force,
unsigned=args.unsigned,
key=args.key,
regenerate_index=args.update_index,
),
)
for i, spec in enumerate(specs):
try:
bindist.push_or_raise(
spec,
url,
bindist.PushOptions(
force=args.force,
unsigned=args.unsigned,
key=args.key,
regenerate_index=args.update_index,
),
)
if total_specs > 1:
msg = f"[{i+1:{digits}}/{total_specs}] Pushed {format_spec(spec)}"
else:
msg = f"Pushed {format_spec(spec)} to {url}"
msg = f"{_progress(i, len(specs))}Pushed {_format_spec(spec)}"
if len(specs) == 1:
msg += f" to {url}"
tty.info(msg)
tty.info(msg)
except bindist.NoOverwriteException:
skipped.append(_format_spec(spec))
except bindist.NoOverwriteException:
skipped.append(format_spec(spec))
# Catch any other exception unless the fail fast option is set
except Exception as e:
if args.fail_fast or isinstance(
e, (bindist.PickKeyException, bindist.NoKeyException)
):
raise
failed.append((_format_spec(spec), e))
if skipped:
if len(specs) == 1:
tty.info("The spec is already in the buildcache. Use --force to overwrite it.")
elif len(skipped) == len(specs):
tty.info("All specs are already in the buildcache. Use --force to overwite them.")
tty.info("All specs are already in the buildcache. Use --force to overwrite them.")
else:
tty.info(
"The following {} specs were skipped as they already exist in the buildcache:\n"
@@ -340,6 +413,352 @@ def push_fn(args):
)
)
if failed:
if len(failed) == 1:
raise failed[0][1]
raise spack.error.SpackError(
f"The following {len(failed)} errors occurred while pushing specs to the buildcache",
"\n".join(
elide_list([f" {spec}: {e.__class__.__name__}: {e}" for spec, e in failed], 5)
),
)
# Update the index if requested
# TODO: remove update index logic out of bindist; should be once after all specs are pushed
# not once per spec.
if image_ref and len(skipped) < len(specs) and args.update_index:
with tempfile.TemporaryDirectory(
dir=spack.stage.get_stage_root()
) as tmpdir, _make_pool() as pool:
_update_index_oci(image_ref, tmpdir, pool)
def _get_spack_binary_blob(image_ref: ImageReference) -> Optional[spack.oci.oci.Blob]:
"""Get the spack tarball layer digests and size if it exists"""
try:
manifest, config = get_manifest_and_config_with_retry(image_ref)
return spack.oci.oci.Blob(
compressed_digest=Digest.from_string(manifest["layers"][-1]["digest"]),
uncompressed_digest=Digest.from_string(config["rootfs"]["diff_ids"][-1]),
size=manifest["layers"][-1]["size"],
)
except Exception:
return None
def _push_single_spack_binary_blob(image_ref: ImageReference, spec: spack.spec.Spec, tmpdir: str):
filename = os.path.join(tmpdir, f"{spec.dag_hash()}.tar.gz")
# Create an oci.image.layer aka tarball of the package
compressed_tarfile_checksum, tarfile_checksum = spack.oci.oci.create_tarball(spec, filename)
blob = spack.oci.oci.Blob(
Digest.from_sha256(compressed_tarfile_checksum),
Digest.from_sha256(tarfile_checksum),
os.path.getsize(filename),
)
# Upload the blob
upload_blob_with_retry(image_ref, file=filename, digest=blob.compressed_digest)
# delete the file
os.unlink(filename)
return blob
def _retrieve_env_dict_from_config(config: dict) -> dict:
"""Retrieve the environment variables from the image config file.
Sets a default value for PATH if it is not present.
Args:
config (dict): The image config file.
Returns:
dict: The environment variables.
"""
env = {"PATH": "/bin:/usr/bin"}
if "Env" in config.get("config", {}):
for entry in config["config"]["Env"]:
key, value = entry.split("=", 1)
env[key] = value
return env
def _archspec_to_gooarch(spec: spack.spec.Spec) -> str:
name = spec.target.family.name
name_map = {"aarch64": "arm64", "x86_64": "amd64"}
return name_map.get(name, name)
def _put_manifest(
base_images: Dict[str, Tuple[dict, dict]],
checksums: Dict[str, spack.oci.oci.Blob],
spec: spack.spec.Spec,
image_ref: ImageReference,
tmpdir: str,
):
architecture = _archspec_to_gooarch(spec)
dependencies = list(
reversed(
list(
s
for s in spec.traverse(order="topo", deptype=("link", "run"), root=True)
if not s.external
)
)
)
base_manifest, base_config = base_images[architecture]
env = _retrieve_env_dict_from_config(base_config)
spack.user_environment.environment_modifications_for_specs(spec).apply_modifications(env)
# Create an oci.image.config file
config = copy.deepcopy(base_config)
# Add the diff ids of the dependencies
for s in dependencies:
config["rootfs"]["diff_ids"].append(str(checksums[s.dag_hash()].uncompressed_digest))
# Set the environment variables
config["config"]["Env"] = [f"{k}={v}" for k, v in env.items()]
# From the OCI v1.0 spec:
# > Any extra fields in the Image JSON struct are considered implementation
# > specific and MUST be ignored by any implementations which are unable to
# > interpret them.
# We use this to store the Spack spec, so we can use it to create an index.
spec_dict = spec.to_dict(hash=ht.dag_hash)
spec_dict["buildcache_layout_version"] = 1
spec_dict["binary_cache_checksum"] = {
"hash_algorithm": "sha256",
"hash": checksums[spec.dag_hash()].compressed_digest.digest,
}
config.update(spec_dict)
config_file = os.path.join(tmpdir, f"{spec.dag_hash()}.config.json")
with open(config_file, "w") as f:
json.dump(config, f, separators=(",", ":"))
config_file_checksum = Digest.from_sha256(
spack.util.crypto.checksum(hashlib.sha256, config_file)
)
# Upload the config file
upload_blob_with_retry(image_ref, file=config_file, digest=config_file_checksum)
oci_manifest = {
"mediaType": "application/vnd.oci.image.manifest.v1+json",
"schemaVersion": 2,
"config": {
"mediaType": base_manifest["config"]["mediaType"],
"digest": str(config_file_checksum),
"size": os.path.getsize(config_file),
},
"layers": [
*(layer for layer in base_manifest["layers"]),
*(
{
"mediaType": "application/vnd.oci.image.layer.v1.tar+gzip",
"digest": str(checksums[s.dag_hash()].compressed_digest),
"size": checksums[s.dag_hash()].size,
}
for s in dependencies
),
],
"annotations": {"org.opencontainers.image.description": spec.format()},
}
image_ref_for_spec = image_ref.with_tag(default_tag(spec))
# Finally upload the manifest
upload_manifest_with_retry(image_ref_for_spec, oci_manifest=oci_manifest)
# delete the config file
os.unlink(config_file)
return image_ref_for_spec
def _push_oci(
args,
image_ref: ImageReference,
installed_specs_with_deps: List[Spec],
tmpdir: str,
pool: multiprocessing.pool.Pool,
) -> List[str]:
"""Push specs to an OCI registry
Args:
args: The command line arguments.
image_ref: The image reference.
installed_specs_with_deps: The installed specs to push, excluding externals,
including deps, ordered from roots to leaves.
Returns:
List[str]: The list of skipped specs (already in the buildcache).
"""
# Reverse the order
installed_specs_with_deps = list(reversed(installed_specs_with_deps))
# The base image to use for the package. When not set, we use
# the OCI registry only for storage, and do not use any base image.
base_image_ref: Optional[ImageReference] = (
ImageReference.from_string(args.base_image) if args.base_image else None
)
# Spec dag hash -> blob
checksums: Dict[str, spack.oci.oci.Blob] = {}
# arch -> (manifest, config)
base_images: Dict[str, Tuple[dict, dict]] = {}
# Specs not uploaded because they already exist
skipped = []
if not args.force:
tty.info("Checking for existing specs in the buildcache")
to_be_uploaded = []
tags_to_check = (image_ref.with_tag(default_tag(s)) for s in installed_specs_with_deps)
available_blobs = pool.map(_get_spack_binary_blob, tags_to_check)
for spec, maybe_blob in zip(installed_specs_with_deps, available_blobs):
if maybe_blob is not None:
checksums[spec.dag_hash()] = maybe_blob
skipped.append(_format_spec(spec))
else:
to_be_uploaded.append(spec)
else:
to_be_uploaded = installed_specs_with_deps
if not to_be_uploaded:
return skipped
tty.info(
f"{len(to_be_uploaded)} specs need to be pushed to {image_ref.domain}/{image_ref.name}"
)
# Upload blobs
new_blobs = pool.starmap(
_push_single_spack_binary_blob, ((image_ref, spec, tmpdir) for spec in to_be_uploaded)
)
# And update the spec to blob mapping
for spec, blob in zip(to_be_uploaded, new_blobs):
checksums[spec.dag_hash()] = blob
# Copy base image layers, probably fine to do sequentially.
for spec in to_be_uploaded:
architecture = _archspec_to_gooarch(spec)
# Get base image details, if we don't have them yet
if architecture in base_images:
continue
if base_image_ref is None:
base_images[architecture] = (default_manifest(), default_config(architecture, "linux"))
else:
base_images[architecture] = copy_missing_layers_with_retry(
base_image_ref, image_ref, architecture
)
# Upload manifests
tty.info("Uploading manifests")
pushed_image_ref = pool.starmap(
_put_manifest,
((base_images, checksums, spec, image_ref, tmpdir) for spec in to_be_uploaded),
)
# Print the image names of the top-level specs
for spec, ref in zip(to_be_uploaded, pushed_image_ref):
tty.info(f"Pushed {_format_spec(spec)} to {ref}")
return skipped
def _config_from_tag(image_ref: ImageReference, tag: str) -> Optional[dict]:
# Don't allow recursion here, since Spack itself always uploads
# vnd.oci.image.manifest.v1+json, not vnd.oci.image.index.v1+json
_, config = get_manifest_and_config_with_retry(image_ref.with_tag(tag), tag, recurse=0)
# Do very basic validation: if "spec" is a key in the config, it
# must be a Spec object too.
return config if "spec" in config else None
def _update_index_oci(
image_ref: ImageReference, tmpdir: str, pool: multiprocessing.pool.Pool
) -> None:
response = spack.oci.opener.urlopen(urllib.request.Request(url=image_ref.tags_url()))
spack.oci.opener.ensure_status(response, 200)
tags = json.load(response)["tags"]
# Fetch all image config files in parallel
spec_dicts = pool.starmap(
_config_from_tag, ((image_ref, tag) for tag in tags if tag_is_spec(tag))
)
# Populate the database
db_root_dir = os.path.join(tmpdir, "db_root")
db = bindist.BuildCacheDatabase(db_root_dir)
for spec_dict in spec_dicts:
spec = Spec.from_dict(spec_dict)
db.add(spec, directory_layout=None)
db.mark(spec, "in_buildcache", True)
# Create the index.json file
index_json_path = os.path.join(tmpdir, "index.json")
with open(index_json_path, "w") as f:
db._write_to_file(f)
# Create an empty config.json file
empty_config_json_path = os.path.join(tmpdir, "config.json")
with open(empty_config_json_path, "wb") as f:
f.write(b"{}")
# Upload the index.json file
index_shasum = Digest.from_sha256(spack.util.crypto.checksum(hashlib.sha256, index_json_path))
upload_blob_with_retry(image_ref, file=index_json_path, digest=index_shasum)
# Upload the config.json file
empty_config_digest = Digest.from_sha256(
spack.util.crypto.checksum(hashlib.sha256, empty_config_json_path)
)
upload_blob_with_retry(image_ref, file=empty_config_json_path, digest=empty_config_digest)
# Push a manifest file that references the index.json file as a layer
# Notice that we push this as if it is an image, which it of course is not.
# When the ORAS spec becomes official, we can use that instead of a fake image.
# For now we just use the OCI image spec, so that we don't run into issues with
# automatic garbage collection of blobs that are not referenced by any image manifest.
oci_manifest = {
"mediaType": "application/vnd.oci.image.manifest.v1+json",
"schemaVersion": 2,
# Config is just an empty {} file for now, and irrelevant
"config": {
"mediaType": "application/vnd.oci.image.config.v1+json",
"digest": str(empty_config_digest),
"size": os.path.getsize(empty_config_json_path),
},
# The buildcache index is the only layer, and is not a tarball, we lie here.
"layers": [
{
"mediaType": "application/vnd.oci.image.layer.v1.tar+gzip",
"digest": str(index_shasum),
"size": os.path.getsize(index_json_path),
}
],
}
upload_manifest_with_retry(image_ref.with_tag(default_index_tag), oci_manifest)
def install_fn(args):
"""install from a binary package"""
@@ -390,7 +809,7 @@ def preview_fn(args):
)
def check_fn(args):
def check_fn(args: argparse.Namespace):
"""check specs against remote binary mirror(s) to see if any need to be rebuilt
this command uses the process exit code to indicate its result, specifically, if the
@@ -405,7 +824,7 @@ def check_fn(args):
specs = spack.cmd.parse_specs(args.spec or args.spec_file)
if specs:
specs = _matching_specs(specs, specs)
specs = _matching_specs(specs)
else:
specs = spack.cmd.require_active_env("buildcache check").all_specs()
@@ -498,12 +917,12 @@ def copy_buildcache_file(src_url, dest_url, local_path=None):
local_path = os.path.join(tmpdir, os.path.basename(src_url))
try:
temp_stage = Stage(src_url, path=os.path.dirname(local_path))
temp_stage = spack.stage.Stage(src_url, path=os.path.dirname(local_path))
try:
temp_stage.create()
temp_stage.fetch()
web_util.push_to_url(local_path, dest_url, keep_original=True)
except web_util.FetchError as e:
except spack.error.FetchError as e:
# Expected, since we have to try all the possible extensions
tty.debug("no such file: {0}".format(src_url))
tty.debug(e)
@@ -592,6 +1011,20 @@ def manifest_copy(manifest_file_list):
def update_index(mirror: spack.mirror.Mirror, update_keys=False):
# Special case OCI images for now.
try:
image_ref = spack.oci.oci.image_from_mirror(mirror)
except ValueError:
image_ref = None
if image_ref:
with tempfile.TemporaryDirectory(
dir=spack.stage.get_stage_root()
) as tmpdir, _make_pool() as pool:
_update_index_oci(image_ref, tmpdir, pool)
return
# Otherwise, assume a normal mirror.
url = mirror.push_url
bindist.generate_package_index(url_util.join(url, bindist.build_cache_relative_path()))

View File

@@ -3,10 +3,10 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import argparse
import re
import sys
import llnl.string
import llnl.util.lang
from llnl.util import tty
@@ -15,11 +15,11 @@
import spack.spec
import spack.stage
import spack.util.crypto
import spack.util.web as web_util
from spack.cmd.common import arguments
from spack.package_base import PackageBase, deprecated_version, preferred_version
from spack.util.editor import editor
from spack.util.format import get_version_lines
from spack.util.naming import valid_fully_qualified_module_name
from spack.version import Version
description = "checksum available versions of a package"
@@ -35,30 +35,30 @@ def setup_parser(subparser):
help="don't clean up staging area when command completes",
)
subparser.add_argument(
"-b",
"--batch",
"-b",
action="store_true",
default=False,
help="don't ask which versions to checksum",
)
subparser.add_argument(
"-l",
"--latest",
"-l",
action="store_true",
default=False,
help="checksum the latest available version",
)
subparser.add_argument(
"-p",
"--preferred",
"-p",
action="store_true",
default=False,
help="checksum the known Spack preferred version",
)
modes_parser = subparser.add_mutually_exclusive_group()
modes_parser.add_argument(
"-a",
"--add-to-package",
"-a",
action="store_true",
default=False,
help="add new versions to package",
@@ -66,27 +66,26 @@ def setup_parser(subparser):
modes_parser.add_argument(
"--verify", action="store_true", default=False, help="verify known package checksums"
)
arguments.add_common_arguments(subparser, ["package"])
subparser.add_argument("package", help="name or spec (e.g. `cmake` or `cmake@3.18`)")
subparser.add_argument(
"versions", nargs=argparse.REMAINDER, help="versions to generate checksums for"
"versions",
nargs="*",
help="checksum these specific versions (if omitted, Spack searches for remote versions)",
)
arguments.add_common_arguments(subparser, ["jobs"])
subparser.epilog = (
"examples:\n"
" `spack checksum zlib@1.2` autodetects versions 1.2.0 to 1.2.13 from the remote\n"
" `spack checksum zlib 1.2.13` checksums exact version 1.2.13 directly without search\n"
)
def checksum(parser, args):
# Did the user pass 'package@version' string?
if len(args.versions) == 0 and "@" in args.package:
args.versions = [args.package.split("@")[1]]
args.package = args.package.split("@")[0]
# Make sure the user provided a package and not a URL
if not valid_fully_qualified_module_name(args.package):
tty.die("`spack checksum` accepts package names, not URLs.")
spec = spack.spec.Spec(args.package)
# Get the package we're going to generate checksums for
pkg_cls = spack.repo.PATH.get_pkg_class(args.package)
pkg = pkg_cls(spack.spec.Spec(args.package))
pkg = spack.repo.PATH.get_pkg_class(spec.name)(spec)
# Build a list of versions to checksum
versions = [Version(v) for v in args.versions]
# Define placeholder for remote versions.
@@ -96,7 +95,7 @@ def checksum(parser, args):
# Add latest version if requested
if args.latest:
remote_versions = pkg.fetch_remote_versions()
remote_versions = pkg.fetch_remote_versions(args.jobs)
if len(remote_versions) > 0:
latest_version = sorted(remote_versions.keys(), reverse=True)[0]
versions.append(latest_version)
@@ -119,27 +118,50 @@ def checksum(parser, args):
# if we get here, it's because no valid url was provided by the package
# do expensive fallback to try to recover
if remote_versions is None:
remote_versions = pkg.fetch_remote_versions()
remote_versions = pkg.fetch_remote_versions(args.jobs)
if version in remote_versions:
url_dict[version] = remote_versions[version]
if len(versions) <= 0:
if remote_versions is None:
remote_versions = pkg.fetch_remote_versions()
remote_versions = pkg.fetch_remote_versions(args.jobs)
url_dict = remote_versions
# A spidered URL can differ from the package.py *computed* URL, pointing to different tarballs.
# For example, GitHub release pages sometimes have multiple tarballs with different shasum:
# - releases/download/1.0/<pkg>-1.0.tar.gz (uploaded tarball)
# - archive/refs/tags/1.0.tar.gz (generated tarball)
# We wanna ensure that `spack checksum` and `spack install` ultimately use the same URL, so
# here we check whether the crawled and computed URLs disagree, and if so, prioritize the
# former if that URL exists (just sending a HEAD request that is).
url_changed_for_version = set()
for version, url in url_dict.items():
possible_urls = pkg.all_urls_for_version(version)
if url not in possible_urls:
for possible_url in possible_urls:
if web_util.url_exists(possible_url):
url_dict[version] = possible_url
break
else:
url_changed_for_version.add(version)
if not url_dict:
tty.die(f"Could not find any remote versions for {pkg.name}")
# print an empty line to create a new output section block
print()
elif len(url_dict) > 1 and not args.batch and sys.stdin.isatty():
filtered_url_dict = spack.stage.interactive_version_filter(
url_dict,
pkg.versions,
url_changes=url_changed_for_version,
initial_verion_filter=spec.versions,
)
if not filtered_url_dict:
exit(0)
url_dict = filtered_url_dict
else:
tty.info(f"Found {llnl.string.plural(len(url_dict), 'version')} of {pkg.name}")
version_hashes = spack.stage.get_checksums_for_versions(
url_dict,
pkg.name,
keep_stage=args.keep_stage,
batch=(args.batch or len(versions) > 0 or len(url_dict) == 1),
fetch_options=pkg.fetch_options,
url_dict, pkg.name, keep_stage=args.keep_stage, fetch_options=pkg.fetch_options
)
if args.verify:
@@ -239,7 +261,7 @@ def add_versions_to_package(pkg: PackageBase, version_lines: str):
parsed_version = Version(contents_version.group(1))
if parsed_version < new_versions[0][0]:
split_contents[i:i] = [new_versions.pop(0)[1], " # FIX ME", "\n"]
split_contents[i:i] = [new_versions.pop(0)[1], " # FIXME", "\n"]
num_versions_added += 1
elif parsed_version == new_versions[0][0]:

View File

@@ -19,6 +19,7 @@
import spack.hash_types as ht
import spack.mirror
import spack.util.gpg as gpg_util
import spack.util.timer as timer
import spack.util.url as url_util
import spack.util.web as web_util
@@ -190,6 +191,14 @@ def ci_generate(args):
"""
env = spack.cmd.require_active_env(cmd_name="ci generate")
if args.copy_to:
tty.warn("The flag --copy-to is deprecated and will be removed in Spack 0.23")
if args.buildcache_destination:
tty.warn(
"The flag --buildcache-destination is deprecated and will be removed in Spack 0.23"
)
output_file = args.output_file
copy_yaml_to = args.copy_to
run_optimizer = args.optimize
@@ -253,6 +262,8 @@ def ci_rebuild(args):
check a single spec against the remote mirror, and rebuild it from source if the mirror does
not contain the hash
"""
rebuild_timer = timer.Timer()
env = spack.cmd.require_active_env(cmd_name="ci rebuild")
# Make sure the environment is "gitlab-enabled", or else there's nothing
@@ -261,12 +272,6 @@ def ci_rebuild(args):
if not ci_config:
tty.die("spack ci rebuild requires an env containing ci cfg")
tty.msg(
"SPACK_BUILDCACHE_DESTINATION={0}".format(
os.environ.get("SPACK_BUILDCACHE_DESTINATION", None)
)
)
# Grab the environment variables we need. These either come from the
# pipeline generation step ("spack ci generate"), where they were written
# out as variables, or else provided by GitLab itself.
@@ -274,6 +279,7 @@ def ci_rebuild(args):
job_log_dir = os.environ.get("SPACK_JOB_LOG_DIR")
job_test_dir = os.environ.get("SPACK_JOB_TEST_DIR")
repro_dir = os.environ.get("SPACK_JOB_REPRO_DIR")
# TODO: Remove this in Spack 0.23
local_mirror_dir = os.environ.get("SPACK_LOCAL_MIRROR_DIR")
concrete_env_dir = os.environ.get("SPACK_CONCRETE_ENV_DIR")
ci_pipeline_id = os.environ.get("CI_PIPELINE_ID")
@@ -282,9 +288,12 @@ def ci_rebuild(args):
job_spec_pkg_name = os.environ.get("SPACK_JOB_SPEC_PKG_NAME")
job_spec_dag_hash = os.environ.get("SPACK_JOB_SPEC_DAG_HASH")
spack_pipeline_type = os.environ.get("SPACK_PIPELINE_TYPE")
# TODO: Remove this in Spack 0.23
remote_mirror_override = os.environ.get("SPACK_REMOTE_MIRROR_OVERRIDE")
# TODO: Remove this in Spack 0.23
remote_mirror_url = os.environ.get("SPACK_REMOTE_MIRROR_URL")
spack_ci_stack_name = os.environ.get("SPACK_CI_STACK_NAME")
# TODO: Remove this in Spack 0.23
shared_pr_mirror_url = os.environ.get("SPACK_CI_SHARED_PR_MIRROR_URL")
rebuild_everything = os.environ.get("SPACK_REBUILD_EVERYTHING")
require_signing = os.environ.get("SPACK_REQUIRE_SIGNING")
@@ -341,21 +350,36 @@ def ci_rebuild(args):
full_rebuild = True if rebuild_everything and rebuild_everything.lower() == "true" else False
pipeline_mirrors = spack.mirror.MirrorCollection(binary=True)
deprecated_mirror_config = False
buildcache_destination = None
if "buildcache-destination" in pipeline_mirrors:
buildcache_destination = pipeline_mirrors["buildcache-destination"]
else:
deprecated_mirror_config = True
# TODO: This will be an error in Spack 0.23
# If no override url exists, then just push binary package to the
# normal remote mirror url.
# TODO: Remove in Spack 0.23
buildcache_mirror_url = remote_mirror_override or remote_mirror_url
if buildcache_destination:
buildcache_mirror_url = buildcache_destination.push_url
# Figure out what is our temporary storage mirror: Is it artifacts
# buildcache? Or temporary-storage-url-prefix? In some cases we need to
# force something or pipelines might not have a way to propagate build
# artifacts from upstream to downstream jobs.
# TODO: Remove this in Spack 0.23
pipeline_mirror_url = None
# TODO: Remove this in Spack 0.23
temp_storage_url_prefix = None
if "temporary-storage-url-prefix" in ci_config:
temp_storage_url_prefix = ci_config["temporary-storage-url-prefix"]
pipeline_mirror_url = url_util.join(temp_storage_url_prefix, ci_pipeline_id)
# TODO: Remove this in Spack 0.23
enable_artifacts_mirror = False
if "enable-artifacts-buildcache" in ci_config:
enable_artifacts_mirror = ci_config["enable-artifacts-buildcache"]
@@ -451,12 +475,14 @@ def ci_rebuild(args):
# If we decided there should be a temporary storage mechanism, add that
# mirror now so it's used when we check for a hash match already
# built for this spec.
# TODO: Remove this block in Spack 0.23
if pipeline_mirror_url:
mirror = spack.mirror.Mirror(pipeline_mirror_url, name=spack_ci.TEMP_STORAGE_MIRROR_NAME)
spack.mirror.add(mirror, cfg.default_modify_scope())
pipeline_mirrors.append(pipeline_mirror_url)
# Check configured mirrors for a built spec with a matching hash
# TODO: Remove this block in Spack 0.23
mirrors_to_check = None
if remote_mirror_override:
if spack_pipeline_type == "spack_protected_branch":
@@ -474,7 +500,8 @@ def ci_rebuild(args):
)
pipeline_mirrors.append(remote_mirror_override)
if spack_pipeline_type == "spack_pull_request":
# TODO: Remove this in Spack 0.23
if deprecated_mirror_config and spack_pipeline_type == "spack_pull_request":
if shared_pr_mirror_url != "None":
pipeline_mirrors.append(shared_pr_mirror_url)
@@ -496,6 +523,7 @@ def ci_rebuild(args):
tty.msg("No need to rebuild {0}, found hash match at: ".format(job_spec_pkg_name))
for match in matches:
tty.msg(" {0}".format(match["mirror_url"]))
# TODO: Remove this block in Spack 0.23
if enable_artifacts_mirror:
matching_mirror = matches[0]["mirror_url"]
build_cache_dir = os.path.join(local_mirror_dir, "build_cache")
@@ -510,7 +538,8 @@ def ci_rebuild(args):
# only want to keep the mirror being used by the current pipeline as it's binary
# package destination. This ensures that the when we rebuild everything, we only
# consume binary dependencies built in this pipeline.
if full_rebuild:
# TODO: Remove this in Spack 0.23
if deprecated_mirror_config and full_rebuild:
spack_ci.remove_other_mirrors(pipeline_mirrors, cfg.default_modify_scope())
# No hash match anywhere means we need to rebuild spec
@@ -576,7 +605,9 @@ def ci_rebuild(args):
"SPACK_COLOR=always",
"SPACK_INSTALL_FLAGS={}".format(args_to_string(deps_install_args)),
"-j$(nproc)",
"install-deps/{}".format(job_spec.format("{name}-{version}-{hash}")),
"install-deps/{}".format(
ev.depfile.MakefileSpec(job_spec).safe_format("{name}-{version}-{hash}")
),
],
spack_cmd + ["install"] + root_install_args,
]
@@ -673,21 +704,25 @@ def ci_rebuild(args):
# print out some instructions on how to reproduce this build failure
# outside of the pipeline environment.
if install_exit_code == 0:
if buildcache_mirror_url or pipeline_mirror_url:
for result in spack_ci.create_buildcache(
input_spec=job_spec,
buildcache_mirror_url=buildcache_mirror_url,
pipeline_mirror_url=pipeline_mirror_url,
sign_binaries=spack_ci.can_sign_binaries(),
):
msg = tty.msg if result.success else tty.warn
msg(
"{} {} to {}".format(
"Pushed" if result.success else "Failed to push",
job_spec.format("{name}{@version}{/hash:7}", color=clr.get_color_when()),
result.url,
)
mirror_urls = [buildcache_mirror_url]
# TODO: Remove this block in Spack 0.23
if pipeline_mirror_url:
mirror_urls.append(pipeline_mirror_url)
for result in spack_ci.create_buildcache(
input_spec=job_spec,
destination_mirror_urls=mirror_urls,
sign_binaries=spack_ci.can_sign_binaries(),
):
msg = tty.msg if result.success else tty.warn
msg(
"{} {} to {}".format(
"Pushed" if result.success else "Failed to push",
job_spec.format("{name}{@version}{/hash:7}", color=clr.get_color_when()),
result.url,
)
)
# If this is a develop pipeline, check if the spec that we just built is
# on the broken-specs list. If so, remove it.
@@ -736,6 +771,14 @@ def ci_rebuild(args):
print(reproduce_msg)
rebuild_timer.stop()
try:
with open("install_timers.json", "w") as timelog:
extra_attributes = {"name": ".ci-rebuild"}
rebuild_timer.write_json(timelog, extra_attributes=extra_attributes)
except Exception as e:
tty.debug(str(e))
# Tie job success/failure to the success/failure of building the spec
return install_exit_code

View File

@@ -796,7 +796,9 @@ def names(args: Namespace, out: IO) -> None:
commands = copy.copy(spack.cmd.all_commands())
if args.aliases:
commands.extend(spack.main.aliases.keys())
aliases = spack.config.get("config:aliases")
if aliases:
commands.extend(aliases.keys())
colify(commands, output=out)
@@ -812,6 +814,11 @@ def bash(args: Namespace, out: IO) -> None:
parser = spack.main.make_argument_parser()
spack.main.add_all_commands(parser)
aliases_config = spack.config.get("config:aliases")
if aliases_config:
aliases = ";".join(f"{key}:{val}" for key, val in aliases_config.items())
out.write(f'SPACK_ALIASES="{aliases}"\n\n')
writer = BashCompletionWriter(parser.prog, out, args.aliases)
writer.write(parser)

View File

@@ -12,7 +12,7 @@
import spack.cmd
import spack.config
import spack.dependency as dep
import spack.deptypes as dt
import spack.environment as ev
import spack.mirror
import spack.modules
@@ -114,16 +114,13 @@ def __call__(self, parser, namespace, jobs, option_string):
class DeptypeAction(argparse.Action):
"""Creates a tuple of valid dependency types from a deptype argument."""
"""Creates a flag of valid dependency types from a deptype argument."""
def __call__(self, parser, namespace, values, option_string=None):
deptype = dep.all_deptypes
if values:
deptype = tuple(x.strip() for x in values.split(","))
if deptype == ("all",):
deptype = "all"
deptype = dep.canonical_deptype(deptype)
if not values or values == "all":
deptype = dt.ALL
else:
deptype = dt.canonicalize(values.split(","))
setattr(namespace, self.dest, deptype)
@@ -285,9 +282,8 @@ def deptype():
return Args(
"--deptype",
action=DeptypeAction,
default=dep.all_deptypes,
help="comma-separated list of deptypes to traverse\n\ndefault=%s"
% ",".join(dep.all_deptypes),
default=dt.ALL,
help="comma-separated list of deptypes to traverse (default=%s)" % ",".join(dt.ALL_TYPES),
)
@@ -547,7 +543,7 @@ def add_concretizer_args(subparser):
)
def add_s3_connection_args(subparser, add_help):
def add_connection_args(subparser, add_help):
subparser.add_argument(
"--s3-access-key-id", help="ID string to use to connect to this S3 mirror"
)
@@ -563,6 +559,8 @@ def add_s3_connection_args(subparser, add_help):
subparser.add_argument(
"--s3-endpoint-url", help="endpoint URL to use to connect to this S3 mirror"
)
subparser.add_argument("--oci-username", help="username to use to connect to this OCI mirror")
subparser.add_argument("--oci-password", help="password to use to connect to this OCI mirror")
def use_buildcache(cli_arg_value):

View File

@@ -0,0 +1,30 @@
# 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)
import sys
from typing import List
import llnl.util.tty as tty
import spack.cmd
display_args = {"long": True, "show_flags": False, "variants": False, "indent": 4}
def confirm_action(specs: List[spack.spec.Spec], participle: str, noun: str):
"""Display the list of specs to be acted on and ask for confirmation.
Args:
specs: specs to be removed
participle: action expressed as a participle, e.g. "uninstalled"
noun: action expressed as a noun, e.g. "uninstallation"
"""
tty.msg(f"The following {len(specs)} packages will be {participle}:\n")
spack.cmd.display_specs(specs, **display_args)
print("")
answer = tty.get_yes_or_no("Do you want to proceed?", default=False)
if not answer:
tty.msg(f"Aborting {noun}")
sys.exit(0)

View File

@@ -7,14 +7,15 @@
import llnl.util.tty as tty
import spack.build_environment as build_environment
import spack.cmd
import spack.cmd.common.arguments as arguments
import spack.deptypes as dt
import spack.error
import spack.paths
import spack.spec
import spack.store
from spack import traverse
from spack import build_environment, traverse
from spack.context import Context
from spack.util.environment import dump_environment, pickle_environment
@@ -41,14 +42,14 @@ def setup_parser(subparser):
class AreDepsInstalledVisitor:
def __init__(self, context="build"):
if context not in ("build", "test"):
raise ValueError("context can only be build or test")
if context == "build":
self.direct_deps = ("build", "link", "run")
def __init__(self, context: Context = Context.BUILD):
if context == Context.BUILD:
# TODO: run deps shouldn't be required for build env.
self.direct_deps = dt.BUILD | dt.LINK | dt.RUN
elif context == Context.TEST:
self.direct_deps = dt.BUILD | dt.TEST | dt.LINK | dt.RUN
else:
self.direct_deps = ("build", "test", "link", "run")
raise ValueError("context can only be Context.BUILD or Context.TEST")
self.has_uninstalled_deps = False
@@ -71,11 +72,11 @@ def accept(self, item):
def neighbors(self, item):
# Direct deps: follow build & test edges.
# Transitive deps: follow link / run.
deptypes = self.direct_deps if item.depth == 0 else ("link", "run")
return item.edge.spec.edges_to_dependencies(deptype=deptypes)
depflag = self.direct_deps if item.depth == 0 else dt.LINK | dt.RUN
return item.edge.spec.edges_to_dependencies(depflag=depflag)
def emulate_env_utility(cmd_name, context, args):
def emulate_env_utility(cmd_name, context: Context, args):
if not args.spec:
tty.die("spack %s requires a spec." % cmd_name)
@@ -119,7 +120,7 @@ def emulate_env_utility(cmd_name, context, args):
hashes=True,
# This shows more than necessary, but we cannot dynamically change deptypes
# in Spec.tree(...).
deptypes="all" if context == "build" else ("build", "test", "link", "run"),
deptypes="all" if context == Context.BUILD else ("build", "test", "link", "run"),
),
)

View File

@@ -31,6 +31,19 @@ def setup_parser(subparser):
aliases=["add"],
help="search the system for compilers to add to Spack configuration",
)
mixed_toolchain_group = find_parser.add_mutually_exclusive_group()
mixed_toolchain_group.add_argument(
"--mixed-toolchain",
action="store_true",
default=sys.platform == "darwin",
help="Allow mixed toolchains (for example: clang, clang++, gfortran)",
)
mixed_toolchain_group.add_argument(
"--no-mixed-toolchain",
action="store_false",
dest="mixed_toolchain",
help="Do not allow mixed toolchains (for example: clang, clang++, gfortran)",
)
find_parser.add_argument("add_paths", nargs=argparse.REMAINDER)
find_parser.add_argument(
"--scope",
@@ -86,7 +99,9 @@ def compiler_find(args):
# Below scope=None because we want new compilers that don't appear
# in any other configuration.
new_compilers = spack.compilers.find_new_compilers(paths, scope=None)
new_compilers = spack.compilers.find_new_compilers(
paths, scope=None, mixed_toolchain=args.mixed_toolchain
)
if new_compilers:
spack.compilers.add_compilers_to_config(new_compilers, scope=args.scope, init_config=False)
n = len(new_compilers)
@@ -185,7 +200,7 @@ def compiler_list(args):
os_str = os
if target:
os_str += "-%s" % target
cname = "%s{%s} %s" % (spack.spec.compiler_color, name, os_str)
cname = "%s{%s} %s" % (spack.spec.COMPILER_COLOR, name, os_str)
tty.hline(colorize(cname), char="-")
colify(reversed(sorted(c.spec.display_str for c in compilers)))

View File

@@ -407,7 +407,9 @@ def config_prefer_upstream(args):
pkgs = {}
for spec in pref_specs:
# Collect all the upstream compilers and versions for this package.
pkg = pkgs.get(spec.name, {"version": [], "compiler": []})
pkg = pkgs.get(spec.name, {"version": []})
all = pkgs.get("all", {"compiler": []})
pkgs["all"] = all
pkgs[spec.name] = pkg
# We have no existing variant if this is our first added version.
@@ -418,8 +420,8 @@ def config_prefer_upstream(args):
pkg["version"].append(version)
compiler = str(spec.compiler)
if compiler not in pkg["compiler"]:
pkg["compiler"].append(compiler)
if compiler not in all["compiler"]:
all["compiler"].append(compiler)
# Get and list all the variants that differ from the default.
variants = []

View File

@@ -5,6 +5,7 @@
import os
import re
import sys
import urllib.parse
import llnl.util.tty as tty
@@ -62,6 +63,10 @@ class {class_name}({base_class_name}):
# notify when the package is updated.
# maintainers("github_user1", "github_user2")
# FIXME: Add the SPDX identifier of the project's license below.
# See https://spdx.org/licenses/ for a list.
license("UNKNOWN")
{versions}
{dependencies}
@@ -822,7 +827,12 @@ def get_versions(args, name):
if args.url is not None and args.template != "bundle" and valid_url:
# Find available versions
try:
url_dict = spack.util.web.find_versions_of_archive(args.url)
url_dict = spack.url.find_versions_of_archive(args.url)
if len(url_dict) > 1 and not args.batch and sys.stdin.isatty():
url_dict_filtered = spack.stage.interactive_version_filter(url_dict)
if url_dict_filtered is None:
exit(0)
url_dict = url_dict_filtered
except UndetectableVersionError:
# Use fake versions
tty.warn("Couldn't detect version in: {0}".format(args.url))
@@ -834,11 +844,7 @@ def get_versions(args, name):
url_dict = {version: args.url}
version_hashes = spack.stage.get_checksums_for_versions(
url_dict,
name,
first_stage_function=guesser,
keep_stage=args.keep_stage,
batch=(args.batch or len(url_dict) == 1),
url_dict, name, first_stage_function=guesser, keep_stage=args.keep_stage
)
versions = get_version_lines(version_hashes, url_dict)

View File

@@ -0,0 +1,103 @@
# 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)
import argparse
import sys
from typing import List
import llnl.util.tty as tty
import spack.cmd
import spack.cmd.common.arguments as arguments
import spack.cmd.common.confirmation as confirmation
import spack.environment as ev
import spack.spec
description = "remove specs from the concretized lockfile of an environment"
section = "environments"
level = "long"
# Arguments for display_specs when we find ambiguity
display_args = {"long": True, "show_flags": False, "variants": False, "indent": 4}
def setup_parser(subparser):
subparser.add_argument(
"--root", action="store_true", help="deconcretize only specific environment roots"
)
arguments.add_common_arguments(subparser, ["yes_to_all", "specs"])
subparser.add_argument(
"-a",
"--all",
action="store_true",
dest="all",
help="deconcretize ALL specs that match each supplied spec",
)
def get_deconcretize_list(
args: argparse.Namespace, specs: List[spack.spec.Spec], env: ev.Environment
) -> List[spack.spec.Spec]:
"""
Get list of environment roots to deconcretize
"""
env_specs = [s for _, s in env.concretized_specs()]
to_deconcretize = []
errors = []
for s in specs:
if args.root:
# find all roots matching given spec
to_deconc = [e for e in env_specs if e.satisfies(s)]
else:
# find all roots matching or depending on a matching spec
to_deconc = [e for e in env_specs if any(d.satisfies(s) for d in e.traverse())]
if len(to_deconc) < 1:
tty.warn(f"No matching specs to deconcretize for {s}")
elif len(to_deconc) > 1 and not args.all:
errors.append((s, to_deconc))
to_deconcretize.extend(to_deconc)
if errors:
for spec, matching in errors:
tty.error(f"{spec} matches multiple concrete specs:")
sys.stderr.write("\n")
spack.cmd.display_specs(matching, output=sys.stderr, **display_args)
sys.stderr.write("\n")
sys.stderr.flush()
tty.die("Use '--all' to deconcretize all matching specs, or be more specific")
return to_deconcretize
def deconcretize_specs(args, specs):
env = spack.cmd.require_active_env(cmd_name="deconcretize")
if args.specs:
deconcretize_list = get_deconcretize_list(args, specs, env)
else:
deconcretize_list = [s for _, s in env.concretized_specs()]
if not args.yes_to_all:
confirmation.confirm_action(deconcretize_list, "deconcretized", "deconcretization")
with env.write_transaction():
for spec in deconcretize_list:
env.deconcretize(spec)
env.write()
def deconcretize(parser, args):
if not args.specs and not args.all:
tty.die(
"deconcretize requires at least one spec argument.",
" Use `spack deconcretize --all` to deconcretize ALL specs.",
)
specs = spack.cmd.parse_specs(args.specs) if args.specs else [any]
deconcretize_specs(args, specs)

View File

@@ -74,7 +74,7 @@ def dependencies(parser, args):
spec,
transitive=args.transitive,
expand_virtuals=args.expand_virtuals,
deptype=args.deptype,
depflag=args.deptype,
)
if spec.name in dependencies:

View File

@@ -99,10 +99,7 @@ def dev_build(self, args):
spec = specs[0]
if not spack.repo.PATH.exists(spec.name):
tty.die(
"No package for '{0}' was found.".format(spec.name),
" Use `spack create` to create a new package",
)
raise spack.repo.UnknownPackageError(spec.name)
if not spec.versions.concrete_range_as_version:
tty.die(

View File

@@ -200,6 +200,8 @@ def diff(parser, args):
specs = []
for spec in spack.cmd.parse_specs(args.specs):
# If the spec has a hash, check it before disambiguating
spec.replace_hash()
if spec.concrete:
specs.append(spec)
else:

View File

@@ -43,10 +43,7 @@ def edit_package(name, repo_path, namespace):
if not os.access(path, os.R_OK):
tty.die("Insufficient permissions on '%s'!" % path)
else:
tty.die(
"No package for '{0}' was found.".format(spec.name),
" Use `spack create` to create a new package",
)
raise spack.repo.UnknownPackageError(spec.name)
editor(path)

View File

@@ -5,10 +5,13 @@
import argparse
import os
import shlex
import shutil
import sys
import tempfile
from typing import Optional
import llnl.string as string
import llnl.util.filesystem as fs
import llnl.util.tty as tty
from llnl.util.tty.colify import colify
@@ -28,7 +31,6 @@
import spack.schema.env
import spack.spec
import spack.tengine
import spack.util.string as string
from spack.util.environment import EnvironmentModifications
description = "manage virtual environments"
@@ -96,22 +98,16 @@ def env_activate_setup_parser(subparser):
view_options = subparser.add_mutually_exclusive_group()
view_options.add_argument(
"-v",
"--with-view",
action="store_const",
dest="with_view",
const=True,
default=True,
help="update PATH, etc., with associated view",
"-v",
metavar="name",
help="set runtime environment variables for specific view",
)
view_options.add_argument(
"-V",
"--without-view",
action="store_const",
dest="with_view",
const=False,
default=True,
help="do not update PATH, etc., with associated view",
"-V",
action="store_true",
help="do not set runtime environment variables for any view",
)
subparser.add_argument(
@@ -149,10 +145,13 @@ def create_temp_env_directory():
return tempfile.mkdtemp(prefix="spack-")
def env_activate(args):
if not args.activate_env and not args.dir and not args.temp:
tty.die("spack env activate requires an environment name, directory, or --temp")
def _tty_info(msg):
"""tty.info like function that prints the equivalent printf statement for eval."""
decorated = f'{colorize("@*b{==>}")} {msg}\n'
print(f"printf {shlex.quote(decorated)};")
def env_activate(args):
if not args.shell:
spack.cmd.common.shell_init_instructions(
"spack env activate", " eval `spack env activate {sh_arg} [...]`"
@@ -165,12 +164,25 @@ def env_activate(args):
env_name_or_dir = args.activate_env or args.dir
# When executing `spack env activate` without further arguments, activate
# the default environment. It's created when it doesn't exist yet.
if not env_name_or_dir and not args.temp:
short_name = "default"
if not ev.exists(short_name):
ev.create(short_name)
action = "Created and activated"
else:
action = "Activated"
env_path = ev.root(short_name)
_tty_info(f"{action} default environment in {env_path}")
# Temporary environment
if args.temp:
elif args.temp:
env = create_temp_env_directory()
env_path = os.path.abspath(env)
short_name = os.path.basename(env_path)
ev.create_in_dir(env).write(regenerate=False)
_tty_info(f"Created and activated temporary environment in {env_path}")
# Managed environment
elif ev.exists(env_name_or_dir) and not args.dir:
@@ -197,10 +209,20 @@ def env_activate(args):
# Activate new environment
active_env = ev.Environment(env_path)
# Check if runtime environment variables are requested, and if so, for what view.
view: Optional[str] = None
if args.with_view:
view = args.with_view
if not active_env.has_view(view):
tty.die(f"The environment does not have a view named '{view}'")
elif not args.without_view and active_env.has_view(ev.default_view_name):
view = ev.default_view_name
cmds += spack.environment.shell.activate_header(
env=active_env, shell=args.shell, prompt=env_prompt if args.prompt else None
env=active_env, shell=args.shell, prompt=env_prompt if args.prompt else None, view=view
)
env_mods.extend(spack.environment.shell.activate(env=active_env, add_view=args.with_view))
env_mods.extend(spack.environment.shell.activate(env=active_env, view=view))
cmds += env_mods.shell_modifications(args.shell)
sys.stdout.write(cmds)
@@ -239,6 +261,13 @@ def env_deactivate_setup_parser(subparser):
const="bat",
help="print bat commands to activate the environment",
)
shells.add_argument(
"--pwsh",
action="store_const",
dest="shell",
const="pwsh",
help="print pwsh commands to activate the environment",
)
def env_deactivate(args):
@@ -368,28 +397,33 @@ def env_remove(args):
and manifests embedded in repositories should be removed manually.
"""
read_envs = []
bad_envs = []
for env_name in args.rm_env:
env = ev.read(env_name)
read_envs.append(env)
try:
env = ev.read(env_name)
read_envs.append(env)
except (spack.config.ConfigFormatError, ev.SpackEnvironmentConfigError):
bad_envs.append(env_name)
if not args.yes_to_all:
answer = tty.get_yes_or_no(
"Really remove %s %s?"
% (
string.plural(len(args.rm_env), "environment", show_n=False),
string.comma_and(args.rm_env),
),
default=False,
)
environments = string.plural(len(args.rm_env), "environment", show_n=False)
envs = string.comma_and(args.rm_env)
answer = tty.get_yes_or_no(f"Really remove {environments} {envs}?", default=False)
if not answer:
tty.die("Will not remove any environments")
for env in read_envs:
name = env.name
if env.active:
tty.die("Environment %s can't be removed while activated." % env.name)
tty.die(f"Environment {name} can't be removed while activated.")
env.destroy()
tty.msg("Successfully removed environment '%s'" % env.name)
tty.msg(f"Successfully removed environment '{name}'")
for bad_env_name in bad_envs:
shutil.rmtree(
spack.environment.environment.environment_dir_from_name(bad_env_name, exists_ok=True)
)
tty.msg(f"Successfully removed environment '{bad_env_name}'")
#
@@ -536,8 +570,8 @@ def env_update_setup_parser(subparser):
def env_update(args):
manifest_file = ev.manifest_file(args.update_env)
backup_file = manifest_file + ".bkp"
needs_update = not ev.is_latest_format(manifest_file)
needs_update = not ev.is_latest_format(manifest_file)
if not needs_update:
tty.msg('No update needed for the environment "{0}"'.format(args.update_env))
return
@@ -655,18 +689,31 @@ def env_depfile(args):
# Currently only make is supported.
spack.cmd.require_active_env(cmd_name="env depfile")
env = ev.active_environment()
# What things do we build when running make? By default, we build the
# root specs. If specific specs are provided as input, we build those.
filter_specs = spack.cmd.parse_specs(args.specs) if args.specs else None
template = spack.tengine.make_environment().get_template(os.path.join("depfile", "Makefile"))
model = depfile.MakefileModel.from_env(
ev.active_environment(),
env,
filter_specs=filter_specs,
pkg_buildcache=depfile.UseBuildCache.from_string(args.use_buildcache[0]),
dep_buildcache=depfile.UseBuildCache.from_string(args.use_buildcache[1]),
make_prefix=args.make_prefix,
jobserver=args.jobserver,
)
# Warn in case we're generating a depfile for an empty environment. We don't automatically
# concretize; the user should do that explicitly. Could be changed in the future if requested.
if model.empty:
if not env.user_specs:
tty.warn("no specs in the environment")
elif filter_specs is not None:
tty.warn("no concrete matching specs found in environment")
else:
tty.warn("environment is not concretized. Run `spack concretize` first")
makefile = template.render(model.to_dict())
# Finally write to stdout/file.

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