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620 Commits

Author SHA1 Message Date
Gregory Becker
1c6bb8cfc3 add regression number 2023-06-21 11:35:57 -07:00
Gregory Becker
9244ecacf0 bugfix: environments with unify:false can concretize abstract hash without name 2023-06-21 11:34:16 -07:00
markus-ferrell
1df4afb53f Enable build system guess tests on windows (#36971) 2023-06-15 11:40:09 -07:00
Adam J. Stewart
4991f0e484 MXNet: fix flag versions (#38402) 2023-06-15 11:34:21 -07:00
markus-ferrell
09fd7d68eb Windows testing: enable graph, mark, and info cmd tests (#36977) 2023-06-15 11:28:52 -07:00
Jacob King
2ace8a55c1 Create package.py file for NIMROD abstract accelerated infrastructure. (#38405)
Co-authored-by: jacobrking <jacobrking@users.noreply.github.com>
2023-06-15 11:24:55 -07:00
Manuela Kuhn
861acb9467 py-nibabel: add 5.1.0 (#38379) 2023-06-15 13:14:26 -05:00
Thomas Madlener
eea743de46 podio: Add py-tabulate as new run and test dependency (#38409) 2023-06-15 10:56:00 -07:00
George Young
e2b6e5a7ec py-numba: add 0.57.0, update dependency ranges (#38390)
* py-numba: add 0.57.0, update dependency ranges

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

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

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

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

* Update package.py

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
2023-06-15 12:39:12 -05:00
Manuela Kuhn
2f2dc3695c py-datalad: add 0.18.4 (#37936) 2023-06-15 12:22:45 -05:00
Tamara Dahlgren
6eb5e57199 tests/py-horovod: convert to new stand-alone test process (#38366) 2023-06-15 12:17:09 -05:00
Tamara Dahlgren
9a047eb95f tests/py-libensemble: convert to new stand-alone test process (#38344) 2023-06-15 12:09:57 -05:00
Tamara Dahlgren
ef42fd7a2f tests/py-eccodes: convert to new stand-alone test process (#38346) 2023-06-15 11:58:00 -05:00
Manuela Kuhn
e642c2ea28 py-neurora: add 1.1.6.10 (#38378) 2023-06-15 11:14:28 -05:00
Massimiliano Culpo
f27d012e0c Add virtual information on DAG edges (#34821)
* DependencySpec: add virtuals attribute on edges

This works for both the new and the old concretizer. Also,
added type hints to involved functions.

* Improve virtual reconstruction from old format

* Reconstruct virtuals when reading from Cray manifest

* Reconstruct virtual information on test dependencies
2023-06-15 07:16:54 -07:00
Tamara Dahlgren
c638311796 test/dust: convert to new stand-alone test process (#38367) 2023-06-14 20:27:35 -07:00
Manuela Kuhn
2a02bea405 py-nbclient: add 0.8.0 (#38325) 2023-06-14 17:31:03 -05:00
Manuela Kuhn
219b42d991 py-nbconvert: add 7.4.0 (#38326)
* py-nbconvert: add 7.4.0

* Move historical dependencies after variant
2023-06-14 17:28:30 -05:00
Manuela Kuhn
c290ec1f62 py-docutils: re-add python@3.7 (#38336) 2023-06-14 17:19:27 -05:00
Satish Balay
e7ede86733 magma@master: add python dependency (#38341) 2023-06-14 17:15:40 -05:00
Thomas Madlener
e3e7609af4 edm4hep: Add version 0.9 (#38205) 2023-06-14 16:53:31 -04:00
Dennis Klein
49d7ebec36 fairmq: Add v1.6.0 (#38392) 2023-06-14 16:47:59 -04:00
Alec Scott
7c3d82d819 ltp: add v20230516 (#38138) 2023-06-14 16:27:27 -04:00
George Young
1c0fbec9ce subread: add 2.0.6, update download paths (#38200)
* subread: add 2.0.6, update download paths
* Update var/spack/repos/builtin/packages/subread/package.py

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-06-14 13:20:29 -07:00
kjrstory
ca4d60ae25 openradioss-starter,engine: new package (#38291)
* openradioss-starter,engine: new package
* openradioss-engine: change version name develop to main
* openradioss-starter: change version name develop to main
2023-06-14 13:04:03 -07:00
Alec Scott
dc571e20d6 freeipmi: add v1.6.9 (#38349) 2023-06-14 13:02:02 -07:00
Kim Liegeois
1485275d0c Add Binder spackage (#38371)
* Add Binder spackage
* Format binder recipe
* Format binder recipe
2023-06-14 12:41:35 -07:00
pabloaledo
1afbf72037 add bioconductor-ebseq (#38380)
* add buiconductor-ebseq
  Signed-off-by: Pablo <pablo.aledo@seqera.io>

---------

Signed-off-by: Pablo <pablo.aledo@seqera.io>
2023-06-14 12:40:57 -07:00
Rémi Lacroix
407fd80f95 ctffind: Add a patch to fix incorrect return types. (#38085)
Prevent the code from crashing (cf. https://grigoriefflab.umassmed.edu/comment/1696#comment-1696).
2023-06-14 12:29:41 -07:00
Tamara Dahlgren
62525d9076 dsqss: convert to new stand-alone test process (#38372) 2023-06-14 11:54:47 -07:00
Alec Scott
c2371263d1 lastz: add v1.04.22 (#38388)
* lastz: add v1.04.22

* Fix formatting of versions to include extra space
2023-06-14 10:05:45 -07:00
Alec Scott
5a870182ec ipopt: add v3.14.9 (#38387) 2023-06-14 10:04:54 -07:00
Alec Scott
e33ad83256 imath: add v3.1.9 (#38386) 2023-06-14 10:03:41 -07:00
Alec Scott
0352a1df5d imagemagick: add v7.1.1-11 (#38385) 2023-06-14 10:02:36 -07:00
Alec Scott
ade44bce62 cgal: add v5.5.2 (#38384) 2023-06-14 10:01:33 -07:00
Mark W. Krentel
ddb29ebc34 intel-xed: add version 2023.06.07 (#38373)
Add version 2023.06.07, update python to 3.7.
2023-06-14 09:46:53 -07:00
Mark W. Krentel
19a62630e5 hpcviewer: add version 2023.05 (#38374) 2023-06-14 09:45:21 -07:00
Alec Scott
5626802aa0 cloc: add v1.96.1 (#38348) 2023-06-14 12:28:08 -04:00
kwryankrattiger
f68063afbc DaV: Drop propagation of HDF5 to darshan (#38361)
Darshan Runtime does not properly link symols for HDF5 when using shared
libraries.
2023-06-14 11:02:18 -05:00
Alec Scott
8103d019d6 hbase: add v2.5.4 (#38353) 2023-06-14 11:47:53 -04:00
Alec Scott
ce89cdd9d7 fzf: add v0.41.1 (#38351) 2023-06-14 11:38:02 -04:00
Alec Scott
20d9b356f0 hashcat: add v6.2.6 (#38352) 2023-06-14 11:32:56 -04:00
Alec Scott
3401438a3a hyperfine: add v1.17.0 (#38354) 2023-06-14 11:23:20 -04:00
Alec Scott
dcf1999d22 ftxui: add v4.1.1 (#38350) 2023-06-14 11:16:13 -04:00
snehring
9e3c3ae298 Repeatmodeler 2.0.4 (#38337)
* perl-devel-size: adding new package
* repeatmodeler: adding new version 2.0.4
* perl-devel-size: adding proper description
2023-06-14 11:10:50 -04:00
Tamara Dahlgren
40d6b84b4d dssp: convert to new stand-alone test process (#38368) 2023-06-14 07:27:49 -07:00
Xavier Delaruelle
2db09f27af modules: use depends-on to autoload module with Lmod on Tcl (#38347)
Update Tcl modulefile template to use the `depends-on` command to
autoload modules if Lmod is the current module tool.

Autoloading modules with `module load` command in Tcl modulefile does
not work well for Lmod at some extend. An attempt to unload then load
designated module is performed each time such command is encountered. It
may lead to a load storm that may not end correctly with large number of
module dependencies.

`depends-on` command should be used for Lmod instead of `module load`,
as it checks if module is already loaded, and does not attempt to reload
this module.

Lua modulefile template already uses `depends_on` command to autoload
dependencies. Thus it is already considered that to use Lmod with Spack,
it must support `depends_on` command (version 7.6+).

Environment Modules copes well with `module load` command to autoload
dependencies (version 3.2+). `depends-on` command is supported starting
version 5.1 (as an alias of `prereq-all` command) which was relased last
year.

This change introduces a test to determine if current module tool that
evaluates modulefile is Lmod. If so, autoload dependencies are defined
with `depends-on` command. Otherwise `module load` command is used.

Test is based on `LMOD_VERSION_MAJOR` environment variable, which is set
by Lmod starting version 5.1.

Fixes #36764
2023-06-14 15:35:53 +02:00
dependabot[bot]
6979d6a96f build(deps): bump python-levenshtein in /lib/spack/docs (#38339)
Bumps [python-levenshtein](https://github.com/maxbachmann/python-Levenshtein) from 0.21.0 to 0.21.1.
- [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/v0.21.0...v0.21.1)

---
updated-dependencies:
- dependency-name: python-levenshtein
  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>
2023-06-14 13:03:15 +02:00
dependabot[bot]
deffd2acc9 build(deps): bump docker/build-push-action from 4.1.0 to 4.1.1 (#38369)
Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 4.1.0 to 4.1.1.
- [Release notes](https://github.com/docker/build-push-action/releases)
- [Commits](44ea916f6c...2eb1c1961a)

---
updated-dependencies:
- dependency-name: docker/build-push-action
  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>
2023-06-14 09:48:57 +02:00
dependabot[bot]
988f71f434 build(deps): bump docker/setup-buildx-action from 2.6.0 to 2.7.0 (#38370)
Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 2.6.0 to 2.7.0.
- [Release notes](https://github.com/docker/setup-buildx-action/releases)
- [Commits](6a58db7e0d...ecf95283f0)

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

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-06-14 09:36:41 +02:00
kjrstory
4fe76f973a SU2: add versions up to 7.5.1, update dependencies (#37767)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-06-13 18:33:10 -04:00
Raffaele Solcà
8e4e6ad529 add DLA-Future package (#38224) 2023-06-13 18:03:13 -04:00
Edoardo Aprà
3586a2dbe3 NWChem: fix fftw3 variant + patch (#38250) 2023-06-13 22:43:39 +02:00
Dan Lipsa
4648939043 Windows bugfix: path-to-URL conversion (#37827)
When interpreting local paths as relative URL endpoints, they were
formatted as Windows paths on Windows (i.e. with '\'). URLs should
always be POSIX-style.
2023-06-13 10:08:09 -07:00
Xavier Delaruelle
746eaaf01a modules: append trailing delimiter to MANPATH when set (#36678)
Update modulefile templates to append a trailing delimiter to MANPATH
environment variable, if the modulefile sets it.

With a trailing delimiter at ends of MANPATH's value, man will search
the system man pages after searching the specific paths set.

Using append-path/append_path to add this element, the module tool
ensures it is appended only once. When modulefile is unloaded, the
number of append attempt is decreased, thus the trailing delimiter is
removed only if this number equals 0.

Disclaimer: no path element should be appended to MANPATH by generated
modulefiles. It should always be prepended to ensure this variable's
value ends with the trailing delimiter.

Fixes #11355.
2023-06-13 10:29:11 +02:00
Alberto Sartori
bd2f78ae9a justbuild: bump version 1.1.2 (#38320) 2023-06-12 21:34:38 -04:00
Alec Scott
a4ebe01dec curl: add v8.1.2 (#38332) 2023-06-12 19:34:24 -04:00
Alex Richert
94e9e18558 Update sp package (#38208) 2023-06-12 17:51:57 -04:00
Alec Scott
d2e0ac4d1f cpp-httplib: add v0.12.5 (#38331) 2023-06-12 14:51:11 -07:00
Alec Scott
36321fef1c direnv: add v2.32.3 (#38333) 2023-06-12 14:48:06 -07:00
Alec Scott
e879877878 etcd: add v3.5.9 (#38334) 2023-06-12 14:46:43 -07:00
Alec Scott
f0bce3eb25 fastp: add v0.23.4 (#38335) 2023-06-12 14:45:45 -07:00
Wouter Deconinck
316bfd8b7d opencascade: new variants (#35345)
* opencascade: new variants

OpenCascade has several major modules and not every
application needs all of them. This adds variants for
the various modules.

It also uodatws the 3rdparty dependency treatment.

* [@spackbot] updating style on behalf of wdconinc

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

* opencascade: remove variant foundation_classes (always true)

* [@spackbot] updating style on behalf of wdconinc

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

---------

Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
2023-06-12 11:56:55 -05:00
Jerome Soumagne
92593fecd5 mercury: add v2.3.0 (#38279)
* fix Boost dependency

* fix testing and move psm2/sockets as unsupported

* fix style to separate maintainers/tags/version
2023-06-12 08:51:22 -07:00
MatthewLieber
8db5fecdf5 mvapich2: add hwloc_graphics variant (#38028)
Co-authored-by: Matthew Lieber <lieber.31@osu.edu>
2023-06-12 17:25:10 +02:00
Niclas Jansson
eee696f320 neko: add v0.6.0 and fixed rocm package recipe (#38024) 2023-06-12 17:17:12 +02:00
willdunklin
8689cf392f mochi-margo: correct patch versions (#38087) 2023-06-12 17:13:52 +02:00
Bruno Turcksin
15d4cce2eb Add new Kokkos release (#38049) 2023-06-12 17:08:51 +02:00
Peter Scheibel
45fbb82d1a pip is a pythonextension not a pythonpackage, and it turns out we werent doing our external surgery on things that inherited pythonextension (#38186) 2023-06-12 17:07:28 +02:00
Adam J. Stewart
2861c89b89 Deprecate R packages for spatial analysis (#38158)
* Deprecate R packages for spatial analysis

* [@spackbot] updating style on behalf of adamjstewart

---------

Co-authored-by: adamjstewart <adamjstewart@users.noreply.github.com>
2023-06-12 15:55:40 +02:00
Alec Scott
135bfeeb27 libtlx: add v0.6.1 (#38134) 2023-06-12 15:54:50 +02:00
Alec Scott
8fa9c66a7d ccache: add v4.8.1 (#38114) 2023-06-12 15:54:27 +02:00
snehring
5e6174cbe2 cdhit: add missing perl dep, patch shebangs (#38179) 2023-06-12 15:51:59 +02:00
MichaelLaufer
b4ad883b0d wrf: add v4.5.0 (#37618) 2023-06-12 15:48:54 +02:00
Juan Miguel Carceller
a681111a23 whizard: add tirpc/lib to the link flags (#38050)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-06-12 15:24:27 +02:00
Manuela Kuhn
d2436afb66 gdb: fix debuginfod for version 10 (#38058) 2023-06-12 15:20:45 +02:00
Martin Pokorny
e43444cbb6 kokkos: fix c++20 constraint (#37555) 2023-06-12 15:07:03 +02:00
nkgh77
8c0d947114 FrontISTR: relax the requirement on Trillinos (#38321) 2023-06-12 15:02:21 +02:00
Thomas Madlener
5ba4a2b83a podio: bump minimal version of catch2 (#38255) 2023-06-12 08:47:48 -04:00
Harmen Stoppels
da45073ef9 buildcache: remove deprecated api (#37246)
The API was deprecated in v0.20 and is slated for removal in v0.21
2023-06-12 14:33:26 +02:00
kwryankrattiger
61e17fb36d DaV: Use VTKm for all build configurations of ParaView (#38184) 2023-06-12 14:25:50 +02:00
Wouter Deconinck
9f13a90dd2 superlu: new version 6.0.0 (#38262)
No changes to build system required. Changelog: https://github.com/xiaoyeli/superlu/compare/v5.3.0...v6.0.0

Since this new version adds "64-bit indexing support", and since at least one dependent package (`armadillo`) requires "32-bit integers" (faa6cbf895), the previous version remains preferred.

* [@spackbot] updating style on behalf of wdconinc

---------

Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
2023-06-12 14:23:42 +02:00
Juan Miguel Carceller
ef4b35ea63 gaudi: remove the py-qmtest dependency (#38274)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-06-12 14:22:21 +02:00
George Young
66187c8a6e orthofinder: add 2.5.5, add variants (#38298)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-12 14:13:15 +02:00
Massimiliano Culpo
c8d95512fc bootstrap: add minimum versions required for flake8 and pytest (#38322) 2023-06-12 12:29:35 +02:00
George Young
c74fa648b9 fastq-screen: add 0.15.3, add variants (#38288)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-12 10:37:51 +02:00
snehring
4cc5e9cac6 ltr-retriever 2.9.4 (#38300) 2023-06-12 10:05:44 +02:00
snehring
41345d18f9 perl-libwww-perl: adding perl-clone dependency (#38301) 2023-06-12 10:04:29 +02:00
Alec Scott
0dd1316b68 alglib: add v4.00.0 (#38313) 2023-06-12 09:46:24 +02:00
Alec Scott
d8cc185e22 bismark: add v0.24.1 (#38315) 2023-06-12 09:45:53 +02:00
Alec Scott
061051270c blogbench: add v1.2 (#38316) 2023-06-12 09:45:42 +02:00
Alec Scott
61445159db consul: add v1.15.3 (#38317) 2023-06-12 09:45:30 +02:00
Christopher Christofi
7fa3c7f0fa Fix typo in example code block (#38318) 2023-06-11 22:12:36 -04:00
Manuela Kuhn
9c0fe30f42 py-mypy: add 1.3.0 (#38286)
* py-mypy: add 1.3.0

* Remove redundant py-typed-ast dependency

* Read python@3.7 dep
2023-06-11 15:22:55 -04:00
George Young
d00010819f py-deeptools: add 3.5.2, update dependency versions (#38287)
* py-deeptools: add 3.5.2, update dependency versions

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

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

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

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

* Rearranging dependencies to match setup.py

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
2023-06-11 15:17:52 -04:00
Manuela Kuhn
248b05b32a py-jedi: add 0.18.2 (#38177)
* py-jedi: add 0.18.2

* Add setuptools as run dependency
2023-06-11 15:12:56 -04:00
dependabot[bot]
8232e934e9 build(deps): bump docker/login-action from 2.1.0 to 2.2.0 (#38241)
Bumps [docker/login-action](https://github.com/docker/login-action) from 2.1.0 to 2.2.0.
- [Release notes](https://github.com/docker/login-action/releases)
- [Commits](f4ef78c080...465a07811f)

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

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-06-11 13:36:31 -05:00
dependabot[bot]
9d005839af build(deps): bump docker/setup-buildx-action from 2.5.0 to 2.6.0 (#38242)
Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 2.5.0 to 2.6.0.
- [Release notes](https://github.com/docker/setup-buildx-action/releases)
- [Commits](4b4e9c3e2d...6a58db7e0d)

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

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-06-11 13:36:02 -05:00
dependabot[bot]
a7e5c73608 build(deps): bump docker/setup-qemu-action from 2.1.0 to 2.2.0 (#38243)
Bumps [docker/setup-qemu-action](https://github.com/docker/setup-qemu-action) from 2.1.0 to 2.2.0.
- [Release notes](https://github.com/docker/setup-qemu-action/releases)
- [Commits](e81a89b173...2b82ce82d5)

---
updated-dependencies:
- dependency-name: docker/setup-qemu-action
  dependency-type: direct:production
  update-type: version-update:semver-minor
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2023-06-11 13:35:42 -05:00
dependabot[bot]
7896625919 build(deps): bump urllib3 from 2.0.2 to 2.0.3 in /lib/spack/docs (#38244)
Bumps [urllib3](https://github.com/urllib3/urllib3) from 2.0.2 to 2.0.3.
- [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/2.0.2...2.0.3)

---
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>
2023-06-11 13:35:22 -05:00
dependabot[bot]
fb43cb8166 build(deps): bump sphinx-rtd-theme in /lib/spack/docs (#38245)
Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) from 1.2.1 to 1.2.2.
- [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst)
- [Commits](https://github.com/readthedocs/sphinx_rtd_theme/compare/1.2.1...1.2.2)

---
updated-dependencies:
- dependency-name: sphinx-rtd-theme
  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>
2023-06-11 13:35:03 -05:00
dependabot[bot]
28f68e5d11 build(deps): bump docker/build-push-action from 4.0.0 to 4.1.0 (#38306)
Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 4.0.0 to 4.1.0.
- [Release notes](https://github.com/docker/build-push-action/releases)
- [Commits](3b5e8027fc...44ea916f6c)

---
updated-dependencies:
- dependency-name: docker/build-push-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>
2023-06-11 13:34:44 -05:00
dependabot[bot]
1199eeed0b build(deps): bump docker/build-push-action from 4.0.0 to 4.1.0 (#38306)
Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 4.0.0 to 4.1.0.
- [Release notes](https://github.com/docker/build-push-action/releases)
- [Commits](3b5e8027fc...44ea916f6c)

---
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>
2023-06-11 13:34:33 -05:00
Manuela Kuhn
8ffeb4900b py-multidict: add 6.0.4 (#38284) 2023-06-11 12:03:21 -05:00
Manuela Kuhn
456550da3f py-mne: add 1.4.2 (#38228) 2023-06-11 11:52:01 -05:00
Olivier Cessenat
b2676fe2dd Gxsview new version 2023.05.29 (#38310)
* netpbm: new version 10.73.43

* gxsview: new version 2023.05.29
2023-06-11 09:48:04 -07:00
Jen Herting
8561ec6249 [py-spacy-legacy] New package (#38276) 2023-06-11 11:45:23 -05:00
Jen Herting
5b775d82ac [py-spacy-loggers] new package (#38275) 2023-06-11 11:44:19 -05:00
Jen Herting
b43088cc16 [py-langcodes] new package (#38273) 2023-06-11 11:43:16 -05:00
Manuela Kuhn
237eab136a py-nbclassic: add 1.0.0 and py-notebook-shim: add 0.2.3 (#38289) 2023-06-11 11:36:38 -05:00
Marie Houillon
ffffa2794b New version for openCARP packages, v13.0 (#37940)
* New version for openCARP packages

* Update carputils dependencies

* Update types of openCARP dependencies

* Add type "run" to setuptools dependency

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

* Add package py-common as carputils dependency

* Add setuptools dependency for py-common

* Remove spaces on blank line

* Restrict type of dependency setuptools to "build"

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

---------

Co-authored-by: openCARP consortium <info@opencarp.org>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-06-11 11:25:41 -05:00
George Young
433b44403f py-pybktree: new package (#38209)
* py-pykbtree: new package

* py-pybktree: new package

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-11 11:16:33 -05:00
Manuela Kuhn
fa2e1c0653 py-pandas: exchange import_modules with skip_modules (#38227) 2023-06-11 11:14:56 -05:00
Manuela Kuhn
00257f6824 py-more-itertools: add 9.1.0 (#38229) 2023-06-11 11:14:43 -05:00
kjrstory
3b8366f3d3 slurm: add new version(23.02.2, 22.05.9) (#38285) 2023-06-10 18:48:48 -07:00
dependabot[bot]
a73f511404 build(deps): bump actions/checkout from 3.5.2 to 3.5.3 (#38305)
Bumps [actions/checkout](https://github.com/actions/checkout) from 3.5.2 to 3.5.3.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](8e5e7e5ab8...c85c95e3d7)

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

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-06-10 18:45:37 -07:00
Vanessasaurus
c823e01baf Automated deployment to update package flux-core 2023-06-10 (#38308)
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2023-06-10 18:30:10 -07:00
Carson Woods
4188080899 Add new Podman package versions and fix patch (#38234)
* Add new podman versions and correct the versions which patch is applied to
* Replace the existing maintainer with alecbcs at maintainers request
2023-06-10 20:40:58 +02:00
Fabien Bruneval
ef6ea2c93f correct SHA for ABINIT 9.8.3 and add ABINIT 9.8.4 (#38283) 2023-06-09 12:24:28 -07:00
Greg Becker
3c672905d0 install status arg: update to default true and add inverse (#38252)
* install status arg: update to default true and add inverse

* update bash completion

* fix tests broken by output change
2023-06-09 10:38:05 -07:00
Jen Herting
ee106c747f [py-typer] new package (#38270)
* [py-typer] new package

* [py-typer] added version 0.7.0
2023-06-09 12:10:09 -05:00
Jen Herting
295726e6b8 [py-catalogue] added version 2.0.8 (#38266) 2023-06-09 12:01:04 -05:00
afzpatel
2654d64a3c comgr: enable testing (#35605) 2023-06-09 18:04:19 +02:00
Stephen Sachs
d91ec8500f [gromacs] Fix intel (classic) libstdc++ path (#37822)
* [gromacs] Fix intel (classic) libstdc++ path

Gromacs's `cmake` run will look for `--gcc-toolchain` (e.g. LLVM, icpx) or
`--gcc-name` (e.g. icpc) in `CMAKE_CXX_FLAGS`. Only if it does not find a good
g++ candidate there it will look for `GMX_GPLUSPLUS_PATH`:
cb6b311c39/cmake/FindLibStdCpp.cmake (L97)

Spack installed intel compilers already define a g++ for std libs. But in
`icp{c,x}.cfg` instead of the compile line. If we use the pre-defined g++ we not
only have less chance of mixing g++ versions, but also don't need to explicitly
add `gcc` as dependency to `gromacs`.

* Fix format

* Use a variant

As there is no way to check if a file exists at depends_on stage

* Fix format

* New name and fail if variant is used with other compiler

* Line too long.
2023-06-09 09:17:49 -04:00
Jonathon Anderson
c354cc51d0 containerize: use an ENTRYPOINT script (#37769) 2023-06-09 09:25:13 +02:00
Massimiliano Culpo
d5747a61e7 Hotfix to avoid building compilers from sources in pcluster pipelines (#38256)
The pcluster image has am internal buildcache without an index.

Also, we need to force reuse to avoid rebuilding GCC, since the default is 
to only reuse dependencies - and that is subject to changes in the GCC 
recipe.
2023-06-09 07:56:28 +02:00
Chris White
e88c747abc BLT package: add version 0.5.3 (#38247) 2023-06-09 00:36:00 -04:00
Martin Pokorny
cfe9e5bca4 glab: add new versions (#38236)
* glab: add new versions

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

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

---------

Co-authored-by: Alec Scott <alec@bcs.sh>
2023-06-08 20:36:16 -07:00
Manuela Kuhn
48f7655a62 py-mako: add 1.2.4 (#38194) 2023-06-08 19:10:02 -04:00
Manuela Kuhn
a1111a9858 py-lxml: add 4.9.2 (#38191) 2023-06-08 19:09:41 -04:00
Manuela Kuhn
b8b9a798bf py-looseversion: add 1.2.0 (#38190) 2023-06-08 19:03:05 -04:00
Manuela Kuhn
7a1e94c775 py-msgpack: add 1.0.5 (#38230) 2023-06-08 18:02:42 -04:00
Manuela Kuhn
8c4b2173d2 py-mistune: add 2.0.5 (#38214) 2023-06-08 17:43:51 -04:00
George Young
4c4cd7b3ea py-llvmlite: add 0.40.0, update llvm dependency information (#38171)
* py-llvmlite: add 0.40.0, update llvm dependency information

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

Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>

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

Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>

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

Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>

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

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

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-06-08 16:10:48 -05:00
George Young
e92554414b gatk: add 4.4, update to java@17 (#38211)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-08 16:01:56 -04:00
George Young
d165e2c94b bowtie2: add 2.5.1 (#38201)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-08 16:01:34 -04:00
George Young
a97bd31afe trimgalore: add 0.6.10, adding variants (#38206)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-08 15:55:03 -04:00
George Young
d7719b26f9 seqtk: add 1.4 (#38193)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-08 15:48:54 -04:00
Manuela Kuhn
855c0fd9e0 py-markupsafe: add 2.1.3 (#38198) 2023-06-08 15:37:26 -04:00
Daniele Cesarini
4156397027 New packages: eprosima-fastdds and dependencies (#38079) 2023-06-08 12:27:06 -07:00
Juan Miguel Carceller
b4bbe5e305 ocaml: don't use the spack compiler (#38251)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-06-08 12:17:29 -07:00
Adam J. Stewart
f5b595071e py-lightning: add v2.0.3 (#38260) 2023-06-08 15:14:28 -04:00
George Young
b6f2184cce bedtools2: patching to build with gcc@13 (#38254)
* bedtools2: patching to build with gcc@13

* bedtools2: patching to build with gcc@13

* Update var/spack/repos/builtin/packages/bedtools2/package.py

Yep, sure. Makes sense.

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

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Alec Scott <alec@bcs.sh>
2023-06-08 14:59:01 -04:00
Axel Huebl
9288067380 Mold: 1.11.0 (#38235)
* Mold: 1.11.0

Add the latest release of the `mold` linker.

* SHA for 1.7.1: zip to tar
2023-06-08 11:34:57 -07:00
Massimiliano Culpo
ddfc43be96 Forbid using env: as a top level environment attribute (#38199)
* Remove "env" from environment schema

* Remove spack.env.schema.keys

* Remove spack.environment.config_dict
2023-06-08 14:34:17 -04:00
Adam J. Stewart
63cad5d338 py-lightly: add v1.4.7 (#38259) 2023-06-08 14:04:16 -04:00
Ivan Maidanski
436ecdfb19 bdw-gc: add v8.2.4 (#37969)
* bdw-gc: add v8.2.4
* bdw-gc: Fix download URL for old package versions

---------

Co-authored-by: Tamara Dahlgren <dahlgren1@llnl.gov>
2023-06-08 14:03:57 -04:00
John W. Parent
06817600e4 CMake/Windows bugfix: Make CMAKE_INSTALL_PREFIX a posix path (#36842)
CMake gives off a warning when passed Windows style paths as
install prefixes as the resultant path often causes invalid
escape sequences.
2023-06-08 10:05:38 -07:00
Wouter Deconinck
4ae1a73d54 (r-rcpp)ensmallen: new package (#38249)
* ensmallen: new package
  ensmallen is a high-quality C++ library for non-linear numerical optimization.
* r-rcppensmallen: new package

---------

Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
2023-06-08 09:53:02 -07:00
Massimiliano Culpo
f29aab0d03 Fix compiler removal from command line (#38057)
* Improve lib/spack/spack/test/cmd/compiler.py

* Use "tmp_path" in the "mock_executable" fixture

* Return a pathlib.Path from mock_executable

* Fix mock_executable fixture on Windows

"mock_gcc" was very similar to mock_executable, so use the latter to reduce code duplication

* Remove wrong compiler cache, fix compiler removal

fixes #37996

_CACHE_CONFIG_FILES was both unneeded and wrong, if called
subsequently with different scopes.

Here we remove that cache, and we fix an issue with compiler
removal triggered by having the same compiler spec in multiple
scopes.
2023-06-08 09:38:20 -07:00
eugeneswalker
cea1b3123e e4s oneapi ci: use official intel oneapi-derived runner image (#38176)
* e4s oneapi ci: use official intel oneapi-derived runner image

* update oneapi image

* tau builds ok, but only with libdrm - comment out for now, follow up with pr later
2023-06-08 09:17:22 -07:00
Alec Scott
b22ccf279d junit4: add v4.13.2 (#38122) 2023-06-08 11:54:09 -04:00
Wouter Deconinck
81e15ce36e (r-rcpp)armadillo: new version 12.4.0 (#38246)
* armadillo: new version 12.4.0
   No build system changes necessary, https://gitlab.com/conradsnicta/armadillo-code/-/compare/12.2.x...12.4.x
* r-rcpparmadillo: new version 0.12.4.0.0
2023-06-08 11:49:17 -04:00
George Young
8907e52933 bismark: add 0.24.1, add HISAT2 dependency (#38210)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-08 11:49:00 -04:00
Carlos Bederián
80cefedac5 quantum-espresso: add 7.2 (#38223) 2023-06-08 11:23:54 -04:00
Seth R. Johnson
b85a66f77a trilinos: drop preferred version (#38086) 2023-06-08 11:18:44 -04:00
Alec Scott
a0ba3d890a cni-plugins: add v1.3.0 (#38064) 2023-06-08 10:27:20 +02:00
Manuela Kuhn
315873cbd3 py-keyring: add 23.13.1 (#38183)
* py-keyring: add 23.13.1

* [@spackbot] updating style on behalf of manuelakuhn
2023-06-07 23:00:05 -05:00
Thomas Bouvier
e05095af90 py-nvidia-dali: update versions up to v1.26.0 (#38022)
* `py-nvidia-dali`: update versions up to v1.26.0

* Add proper `cuda` dependency version
2023-06-07 22:52:52 -05:00
Thomas Bouvier
e0d6a73f96 py-horovod: add versions v0.27.0 and v0.28.0 (#38016)
* `py-horovod`: add versions v0.27.0 and v0.28.0

* fix: typo

* Add upper version bound for `py-pyarrow`
2023-06-07 22:51:19 -05:00
Manuela Kuhn
6ebfb41ad9 py-json5: add 0.9.14 (#38178) 2023-06-07 22:16:28 -05:00
Manuela Kuhn
d0aa01c807 py-jaraco-classes: add 3.2.3 (#38167) 2023-06-07 21:48:58 -05:00
Manuela Kuhn
1265c7df47 py-jupyter-client: add 8.2.0 (#38180) 2023-06-07 21:48:12 -05:00
Alec Scott
91e3f14959 hbase: add v2.5.3 (#38073) 2023-06-07 18:11:21 -07:00
Alec Scott
5f03eb650d chemfiles: add v0.10.4 (#38063) 2023-06-07 18:05:37 -07:00
Martin Pokorny
e0e6133444 casacore: add v3.5.0 (#37806) 2023-06-07 23:12:08 +02:00
Nate deVelder
ee68baf254 OpenFAST: add v3.3.0, v3.4.0 and v3.4.1 (#37407) 2023-06-07 23:10:39 +02:00
Christopher Kotfila
785c1a2070 Add documentation about package signing model (#30939)
Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-06-07 23:05:44 +02:00
Dan Lipsa
79656655ba Guard for define in netcdf 4.9.0 and later. (#37853)
* Guard for define in netcdf 4.9.0 and later.

This code is already available in ParaView 5.11.0 so no patching
needed there.

* Add latest needed version (even if not in spack).

---------

Co-authored-by: Dan Lipsa <dan.lipsa@khq.kitware.com>
2023-06-07 14:20:27 -05:00
Sajid Ali
74921788a8 llvm: add new versions and set default for libomptarget according to os (#38092)
* llvm: add new versions and set default for libomptarget according to os

	modified:   var/spack/repos/builtin/packages/llvm/package.py

* Incorporate reviewer suggestions

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

---------

Co-authored-by: Sergey Kosukhin <skosukhin@gmail.com>
2023-06-07 10:55:46 -05:00
Carlos Bederián
b313b28e64 nwchem: remove -mtune=native flags (#37892)
Co-authored-by: Edoardo Aprà <edoardo.apra@gmail.com>
2023-06-07 09:02:35 +02:00
eugeneswalker
5f1bc15e80 E4S Cray CI Stack (#37837)
* e4s cray ci stack

* e4s ci: add cray

* add zen4 tag

* WIP: new defintions just for cray

* updates

* remove ci signing job overrride, not necessary

* echo $PATH and show modules loaded

* add mirror

* add external def for cray-libsci

* comment out quantum-espresso

* use /etc/protected-runner as key path

* cray ci stack: do not remove tags: [spack, public]

* make cray stack composable

* generate job should run on public tagged runner, override default config:install_tree:root

* CI: Use relative path in default script

* CI: Use relative includes paths for shell runners

* Use concrete_env_dir for relpath

* ml-darwin-aarch64-mps: jax has bazel codesign issue

---------

Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
Co-authored-by: Ryan Krattiger <ryan.krattiger@kitware.com>
2023-06-06 18:41:32 -07:00
Mikael Simberg
fa9fb60df3 CachedCMakePackage: fix bug where CMAKE_CUDA_ARCHITECTURES=none is set (#38169)
#37592 updated cached cmake packages to set CMAKE_CUDA_ARCHITECTURES.
The condition `if archs != "none"` lead to `CMAKE_CUDA_ARCHITECTURES=none`
when cuda_arch=none (incorrect check on the value of a multi-valued
variant), i.e. CMAKE_CUDA_ARCHITECTURES is always set. This PR udpates
the condition to if archs[0] != "none" to ensure CMAKE_CUDA_ARCHITECTURES
is only set if cuda_arch is not none (which seems to be the pattern used
in other packages).

This does the same for HIP (although in general ROCmPackage disallows
amdgpu_target=none when +rocm).
2023-06-06 14:41:02 -07:00
Mosè Giordano
e759e6c410 julia: Update patch for llvm 14 without binary files (#37959) 2023-06-06 21:53:20 +02:00
Jonathon Anderson
f41446258a containers: don't install epel-release on Fedora (#37766) 2023-06-06 21:50:46 +02:00
Erik Schnetter
268649654d openssl: add versions 1.1.1u, 3.0.9, 3.1.1 (#38023) 2023-06-06 21:49:01 +02:00
Diego Alvarez S
12e249f64e Add nextflow 23.04.1 (#38166) 2023-06-06 12:12:50 -07:00
Tamara Dahlgren
c34cd76f2a perl: convert to new stand-alone test process (#37727) 2023-06-06 12:07:44 -07:00
Tamara Dahlgren
815b210fc8 tests/ginkgo: converted to new stand-alone test process (#35730)
* Ginkgo: converted to new stand-alone test process

* ginkgo: update string formatting, compiler setting
2023-06-06 11:58:53 -07:00
Tamara Dahlgren
e5d5efb4c1 tests/darshan-util: convert to new stand-alone test process (#37836) 2023-06-06 11:56:40 -07:00
Tamara Dahlgren
0aa4b4d990 tests/oommf: convert to new stand-alone test process (#38009)
* oommf: convert to new stand-alone test process

* oommf: Switch build-time tests to documented approach
2023-06-06 11:55:33 -07:00
Tamara Dahlgren
01c1d334ae tests/mfem: convert to new stand-alone test process (#38011)
* mfem: convert to new stand-alone test process
* Restore make target, use config_mk property
2023-06-06 11:42:51 -07:00
Massimiliano Culpo
717fc11a46 Don't build rocky:9 images for ppc64le (#38202)
See https://docs.rockylinux.org/release_notes/9_2/
2023-06-06 17:46:53 +02:00
eugeneswalker
d21c49e329 @develop+stokhos: do not set Stokhos_ENABLE_PCE_Scalar_Type=False (#38187) 2023-06-06 08:32:21 -07:00
Tamara Dahlgren
6937d9dddc eigenexa: convert to new stand-alone test process (#35745) 2023-06-06 15:08:51 +02:00
Thomas Bouvier
4c2531d5fb libraqm: add missing fribidi dependency (#36125)
* `libraqm`: add missing `fribidi` dependency
* `libraqm`: add `sheenbidi` variant
* [@spackbot] updating style on behalf of thomas-bouvier

---------

Co-authored-by: thomas-bouvier <thomas-bouvier@users.noreply.github.com>
2023-06-05 18:13:42 -04:00
Alex Richert
62fd890c52 Rename fpic variant to pic for fms (#38101) 2023-06-05 14:58:52 -07:00
Alex Richert
4772fd7723 Add MADIS package (#38097)
* Add MADIS package
* madis update
* [@spackbot] updating style on behalf of AlexanderRichert-NOAA
* allow arg mismatch for gcc@10: for madis
2023-06-05 14:31:51 -07:00
snehring
7c11faceb0 ninja-phylogeny: adding new package ninja-phylogeny (#38182) 2023-06-05 16:44:51 -04:00
Alec Scott
053550e28a asdcplib: add v2_10_38 (#37971) 2023-06-05 12:46:19 -07:00
Alec Scott
3ed7258447 fjcontrib: add v1.052 (#38116) 2023-06-05 14:25:30 -05:00
Manuela Kuhn
a5cf5baa9e py-jupyterlab: add 4.0.1 incl. new dependencies (#38102) 2023-06-05 13:54:20 -05:00
Alec Scott
ec8039cc74 seal: add v4.1.1 (#38155) 2023-06-05 11:46:40 -07:00
snehring
9bfa840c27 ncbi-rmblastn: adding new version 2.14.0 (#38173)
* ncbi-rmblastn: adding new version 2.14.0
* ncbi-rmblastn: add maintainer
2023-06-05 11:45:15 -07:00
Alec Scott
9865f42335 azcopy: add v10.19.0 (#38106) 2023-06-05 10:56:34 -07:00
Alec Scott
dba2829871 hssp: add v3.1.5 (#38107) 2023-06-05 10:51:30 -07:00
Alec Scott
8c0e1fbed9 diamond: add v2.1.7 (#38115) 2023-06-05 10:46:39 -07:00
Alec Scott
187488b75b optional-lite: add v3.5.0 (#38148) 2023-06-05 10:24:37 -07:00
Alec Scott
2aa35fef3e nccmp: add v1.9.1.0 (#38142) 2023-06-05 10:15:25 -07:00
Nathalie Furmento
d373fc36ae starpu: add release 1.3.11 (#38172) 2023-06-05 09:12:40 -07:00
Massimiliano Culpo
e483762015 Update RtD and Sphinx configuration (#38046) 2023-06-05 17:39:11 +02:00
Houjun Tang
5840a00000 Update package.py require HDF5 1.14+ (#38026) 2023-06-05 11:27:53 -04:00
George Young
110f836927 fastqc: add 0.12.1, update patch files (#37934)
* fastqc: add 0.12.1

* fastqc: add 0.12.1

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

Yeah, had considered doing the same, I'd just opted to maintain the status quo. All good.

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

* Update package.py

Style fiddles to make the bot contented.

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Alec Scott <alec@bcs.sh>
2023-06-05 11:07:51 -04:00
Weiqun Zhang
d6765f66ae amrex: add version 23.06 (#38056) 2023-06-05 07:44:32 -07:00
Alec Scott
19dac780e8 iozone: add v3_506 (#38118) 2023-06-05 13:00:23 +02:00
Alec Scott
b82b549c59 iqtree2: add v2.2.2 (#38119) 2023-06-05 13:00:06 +02:00
Alec Scott
b376401ece jimtcl: add v0.82 (#38120) 2023-06-05 12:59:48 +02:00
Alec Scott
7d956dbe9e jline3: add v3.22.0 (#38121) 2023-06-05 12:59:32 +02:00
Alec Scott
6db1d84bb0 kubernetes: add v1.27.2 (#38123) 2023-06-05 12:58:47 +02:00
Alec Scott
2094fa3056 simde: add v0.7.6 (#38157) 2023-06-05 06:38:46 -04:00
Alec Scott
3d255bc213 leptonica: add v1.83.1 (#38125) 2023-06-05 12:36:16 +02:00
Alec Scott
5538dda722 libcint: add v5.3.0 (#38127) 2023-06-05 12:36:02 +02:00
Alec Scott
1c0d89bf25 libeatmydata: add v131 (#38128) 2023-06-05 12:35:46 +02:00
Alec Scott
4cc0199fbb libibumad: add v46.0 (#38130) 2023-06-05 12:35:33 +02:00
Alec Scott
edb8226fff librdkafka: add v2.1.1 (#38131) 2023-06-05 12:35:20 +02:00
Alec Scott
ef972cf642 libspiro: add v20221101 (#38132) 2023-06-05 12:35:03 +02:00
Alec Scott
50c13541e4 libgd: add v2.3.3 (#38129) 2023-06-05 06:29:32 -04:00
Alec Scott
fd5d7cea6e perl-math-bigint: add v1.999838 (#38150) 2023-06-05 06:29:15 -04:00
Alec Scott
526314b275 laszip: add v3.4.3 (#38124) 2023-06-05 06:29:00 -04:00
Alec Scott
7b37c30019 libthai: add v0.1.29 (#38133) 2023-06-05 11:28:44 +02:00
Alec Scott
dc03c3ad9e libvori: add v220621 (#38135) 2023-06-05 11:26:58 +02:00
Alec Scott
61b485f75d lsscsi: add v0.32 (#38136) 2023-06-05 11:26:42 +02:00
Alec Scott
e24151783f ltp: add v20230127 (#38137) 2023-06-05 11:25:55 +02:00
Alec Scott
ed9714e5ae mariadb-c-client: add v3.3.5 (#38140) 2023-06-05 11:25:22 +02:00
Alec Scott
ea620a083c nco: add v5.1.6 (#38143) 2023-06-05 11:24:54 +02:00
Alec Scott
504a8be666 nettle: add v3.9.1 (#38144) 2023-06-05 11:24:34 +02:00
Alec Scott
d460870c77 ngmlr: add v0.2.7 (#38145) 2023-06-05 11:24:19 +02:00
Alec Scott
f0f77251b3 nim: add v1.9.3 (#38146) 2023-06-05 11:24:00 +02:00
Alec Scott
bdd454b70b openexr: add v3.1.7 (#38147) 2023-06-05 11:23:26 +02:00
Alec Scott
aea6662774 pgdspider: add v2.1.1.5 (#38151) 2023-06-05 11:22:41 +02:00
Alec Scott
fe6bcb36c7 primer3: add v2.6.1 (#38152) 2023-06-05 11:22:22 +02:00
Alec Scott
2474a2efe1 sbt: add v1.8.3 (#38154) 2023-06-05 11:22:06 +02:00
Alec Scott
4cfd49019c signify: add v31 (#38156) 2023-06-05 11:20:04 +02:00
Alec Scott
7beae8af30 madx: add v5.09.00 (#38139) 2023-06-05 11:19:37 +02:00
Umashankar Sivakumar
22fc5d2039 papi: update git URL (#38042) 2023-06-05 11:13:17 +02:00
Alec Scott
b70fc461a4 at-spi2-core: add v2.48.3 (#38162) 2023-06-05 11:09:57 +02:00
Alec Scott
e756436d7c grep: add v3.11 (#38163) 2023-06-05 11:09:34 +02:00
Alec Scott
8dd87e2572 hugo: add v0.112.7 (#38164) 2023-06-05 11:09:12 +02:00
Manuela Kuhn
853bf95bd2 py-ipython: add 8.14.0 (#38113) 2023-06-04 22:18:00 -04:00
Manuela Kuhn
1c80d07fd2 py-iso8601: add 1.1.0 (#38110) 2023-06-04 22:07:43 -04:00
Manuela Kuhn
6fd8001604 py-ipykernel: add 6.23.1 (#38111) 2023-06-04 21:52:55 -04:00
Pariksheet Nanda
c08f9fd6fc py-jaxlib: patch bazel server cpu limit (#37548) (#38090) 2023-06-04 19:28:41 -04:00
Adam J. Stewart
c3fb998414 GMT: add new versions (#37921)
* GMT: add new versions

* [@spackbot] updating style on behalf of adamjstewart

---------

Co-authored-by: adamjstewart <adamjstewart@users.noreply.github.com>
2023-06-04 18:00:49 -05:00
George Young
3368a98210 py-htseq: add 2.0.3, switch to PyPI (#37935)
* py-htseq: add 0.12.3, switching over to new GitHub repo

* py-htseq: add 0.12.3, switching over to new GitHub repo

Style fixes

* py-htseq: add 2.0.3, switch to PyPI

* py-htseq: add 2.0.3, switch to PyPI

* Update package.py

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

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

* Removing SWIG

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-06-04 17:55:16 -05:00
Manuela Kuhn
606b7c7f16 py-hatch-fancy-pypi-readme: add 23.1.0 (#38075) 2023-06-04 17:30:33 -05:00
Manuela Kuhn
2f4e66be09 py-hatchling: add 1.17.0 (#38076) 2023-06-04 17:29:40 -05:00
Manuela Kuhn
9ce3e8707c py-humanize: add 4.6.0 (#38077) 2023-06-04 17:28:45 -05:00
Manuela Kuhn
d6a96745ee py-identify: add 2.5.24 (#38088) 2023-06-04 17:27:47 -05:00
Manuela Kuhn
a0fcdd092b py-imageio: add 2.30.0 (#38089) 2023-06-04 17:27:08 -05:00
Christoph Junghans
e17d09e607 votca: stable branch was removed (#38043) 2023-06-04 17:26:02 -05:00
Manuela Kuhn
847d67f223 py-gast: add 0.5.4 (#38054)
* py-gast: add 0.5.4

* py-pythran: add 0.12.2 and restict upper bound of py-gast
2023-06-04 17:25:35 -05:00
Alec Scott
7ae0e06a62 libbson: add v1.23.4 (#38126) 2023-06-04 16:33:51 -05:00
Alec Scott
d3df97df8b hyperfine: add v1.16.1 (#38108) 2023-06-04 12:45:51 +02:00
Sergey Kosukhin
7d5d075809 llvm: optionally build compiler-rt, libcxx and libunwind as runtimes (#32476)
* llvm: replace +omp_as_runtime with omp=runtime

* llvm: fetch 'libomp-libflags-as-list.patch' from upstream repo

* llvm: replace 'llvm14-hwloc-ompd.patch' with the official fix from upstream repo

* llvm: fix-up for the black reformatting

* llvm: fetch 'constexpr_longdouble.patch' from upstream repo

* llvm: optionally build libcxx as a runtime

* llvm: fetch 'llvm5-sanitizer-ustat.patch' from upstream repo

* llvm: update 'sanitizer-ipc_perm_mode.patch'

* llvm: refactor compiler conflicts when libcxx=project

* llvm: fetch 'llvm_python_path.patch' from upstream repo

* llvm: update comments and condition for 'xray_buffer_queue-cstddef.patch'

* llvm: optionally build compiler-rt as a runtime

* llvm: fetch 'lldb_external_ncurses-10.patch' from upstream repo

* llvm: fetch 'llvm_py37.patch' from upstream repo

* llvm: rename variant 'internal_unwind' to 'libunwind'

* llvm: optionally build libunwind as a runtime

* llvm: extend the list of maintainers

* llvm: allow for explicit '~clang~flang~libomptarget~lldb~omp_debug~z3'

* llvm: fetch 'llvm5-lld-ELF-Symbols.patch' from FreeBSD port repo

* llvm: fetch most of 'missing-includes.patch' from upstream repo and reuse 'llvm-gcc11.patch'

* llvm: regroup patches for missing include directives and drop compiler constraints for them

* llvm: fetch 'llvm-gcc11.patch' from upstream repo

* llvm: fetch 'no_cyclades.patch' from upstream repo

* llvm: update comments and condition for 'no_cyclades9.patch'

* llvm: rename variant 'omp' to 'openmp'

* llvm: constrain and rename variant 'omp_tsan' to 'libomp_tsan'

* llvm: rename variant 'omp_debug' to 'libomptarget_debug'

* llvm: do not apply same patch twice

* llvm: constrain and document the '*-thread.patch' patches

* llvm: document the '~lld+libomptarget' conflict

* llvm: update comments for the 'D133513.diff' patch
2023-06-03 23:08:10 -05:00
Peter Scheibel
237a0d8999 Add explicit CMake .libs implementation that returns an empty list; same for .headers (#35816) 2023-06-03 18:08:02 -07:00
Alec Scott
6952ed9950 c-blosc: add v1.21.4 (#37973) 2023-06-03 13:52:43 -04:00
Thomas Madlener
3e2d1bd413 lcio: Add latest version 2.20 (#38078) 2023-06-03 10:35:17 -07:00
Martin Aumüller
9dfba4659e botan: checksum new versions and enable external find (#38081)
* botan: checksum new versions, including new major

version 3 breaks API

* botan: support external find
2023-06-03 10:33:59 -07:00
Michael Kuhn
7fca252aa4 sqlite: add 3.42.0 (#38091) 2023-06-03 10:30:25 -07:00
Wouter Deconinck
fa23a0228f py-hatch-fancy-pypi-readme: depends_on when typo (#38103) 2023-06-03 09:57:03 -05:00
Massimiliano Culpo
ed76966a3a gnupg: add v2.4.2 (#38059)
* gnupg: add v2.4.2

* [@spackbot] updating style on behalf of alalazo

---------

Co-authored-by: alalazo <alalazo@users.noreply.github.com>
2023-06-02 09:28:54 -07:00
willdunklin
2015a51d1a sz: add versions v2.1.12.5 and v2.1.12.4 (#38060) 2023-06-02 09:28:05 -05:00
Manuela Kuhn
34b8fe827e py-flask: add 2.3.2, py-blinker: add 1.6.2, py-werkzeug: add 2.3.4 (#38025) 2023-06-02 05:57:22 -04:00
Manuela Kuhn
6f1ed9b2e4 py-exceptiongroup: add 1.1.1 (#38018) 2023-06-02 05:47:49 -04:00
M. Eric Irrgang
dd00f50943 Add py-gmxapi version 0.4.2 (#38053) 2023-06-02 03:07:34 -04:00
Sam Grayson
f0ec625321 singularityce: add v3.11.3 (#38055) 2023-06-02 08:04:39 +02:00
Manuela Kuhn
d406c371a8 py-formulaic: add 0.6.1 (#38035) 2023-06-01 19:23:15 -04:00
Sean Koyama
42d374a34d double-batched-fft-library: patch to add search paths to findOpenCL.cmake (#36355)
* double-batched-fft-library: PATCH: add search paths to find libOpenCL

* Apply patch up to version 0.3.6
2023-06-01 16:17:04 -07:00
Sean Koyama
d90e4fcc3d lua-luafilesystem: update source URL and improve rockspec detection (#36692)
* lua-luafilesystem: updated sources to new URL. Changed versioning to dot-separated versions.

* lua-luafilesystem: override install phase to find correct rockspec

* lua-luafilesystem: improved rockspec detection

* lua-luafilesystem: added lua version constraint for older versions
2023-06-01 16:15:42 -07:00
Manuela Kuhn
a44fde9dc9 py-docutils: add 0.20.1 (#38001) 2023-06-01 18:18:29 -04:00
Manuela Kuhn
9ac8841dab py-fonttools: add 4.39.4 (#38027) 2023-06-01 18:13:20 -04:00
Manuela Kuhn
a1f87638ec py-future: add 0.18.3 (#38041)
* py-future: add 0.18.3

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

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-06-01 17:48:13 -04:00
Manuela Kuhn
3b55e0a65d py-executing: add 1.2.0 (#38019) 2023-06-01 17:38:09 -04:00
Massimiliano Culpo
42667fe7fa Memoize a few hot functions during module file generation (#37739) 2023-06-01 13:36:42 -07:00
Ted Stern
cd27611d2f Adding libpsm3 package (#37444)
* Adding libpsm3 package
* Make changes suggested by flake8
* Make one more flake8-suggested change, blank line after 'import os'
* Change to standard header to pass flake8 tests
* Update doc string, remove unnecessary comments
* Reviewer-recommende changes
* Alphabetize variants
* Use helper functions
* Change quotes to pass spack style check
2023-06-01 13:01:43 -07:00
Massimiliano Culpo
b111d2172e py-archspec: add v0.2.1 (#38014) 2023-06-01 14:58:45 -05:00
Tobias Ribizel
055263fa3c Fix OpenCV detection on Ubuntu (#35336)
* fix OpenCV detection on Ubuntu

* Update package.py

* Simplify version detection

* remove superfluous `return`
2023-06-01 14:38:17 -05:00
Manuela Kuhn
f34f207bdc py-datalad-neuroimaging: add 0.3.3 (#38017) 2023-06-01 14:31:54 -05:00
snehring
0c9f0fd40d openssh: depend on krb5+shared when +gssapi (#38034) 2023-06-01 13:17:44 -04:00
pauleonix
24d5b1e645 asio: Add stable versions up to 1.28.0 (#38007)
Co-authored-by: Mikael Simberg <mikael.simberg@iki.fi>

- Add pkgconfig dependency from 1.23.0 onward.
- Add conflict of old versions with new gcc due to missing includes.
- Deprecate uneven minor versions because they are not regarded as stable.
- Add maintainer
2023-06-01 11:09:27 +02:00
Mikael Simberg
616f7bcaef pika: add 0.16.0 and pika-algorithms 0.1.3 (#38021)
* pika: add 0.16.0

* pika-algorithms: add 0.1.3

---------

Co-authored-by: Alberto Invernizzi <9337627+albestro@users.noreply.github.com>
2023-06-01 04:18:26 -04:00
Greg Becker
dace0316a2 Spec.format: print false attributes if requested (#37932) 2023-06-01 09:08:45 +02:00
Greg Sjaardema
3bb86418b8 seacas: add 2023-05 release, update fmt dependency (#38008)
The fmt dependency for the previous release was incorrect as does not work with latest lib::fmt.  Fixed that specification
2023-06-01 02:48:50 -04:00
Veselin Dobrev
6f6489a2c7 xSDK examples v0.4.0 (#37295)
* [xsdk-examples] Initial commit for v0.4.0

* [xsdk-examples] v0.4.0 depends on xsdk@0.8.0

* add in missing xsdk dependencies

* [xsdk-examples] remove repeated 'depends_on' directive

* [xsdk-examples] simplify and extend a bit the package

[mfem] process more optional dependencies of HiOp

[strumpack, superlu-dist] add a workaround for an issue on Mac

* [mfem] fix the handling of the hiop dependency

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

* [xsdk-examples] enable 'heffte' and 'tasmanian' if enabled in 'xsdk'

* [xsdk-examples] Add PUMI dependency

* [xsdk-examples] Add preCICE dependency

* [xsdk-examples] add +rocm

* heffte: add in a backport fix for building xsdk-examples with cuda

* [xsdk] Remove the explicit requirement for deal.II to be built +hdf5

* ENABLE_ROCM -> ENABLE_HIP

* [hiop] Workaround for CMake not finding Cray's BLAS (libsci)

[xsdk-examples] Set CUDA/HIP architectures; sync cuda/rocm variants with xsdk

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

* [exago] Workaround for CMake not finding Cray's LAPACK/BLAS, libsci

[mfem] Tweaks for running tests under Flux and PBS

* [slate] Pass CUDA/HIP architectures to CMake

* [heffte] For newer CMake versions, set CMAKE_CUDA_ARCHITECTURES

* [hypre] Patch v2.26.0 to fix sequential compilation in 'src/seq_mv'

* [xsdk-examples] Some tweaks in dependencies and compilers used

* [xsdk] Make the 'trilinos' variant sticky

[xsdk-examples] Tweak dependencies

* [slate] Fix copy-paste error

* [xsdk-examples] Workaround for CMakePackage not having the legacy
   property 'build_directory'

* [xsdk-examples] Replace the testing branch used temporarily for v0.4.0 with
                the official release

---------

Co-authored-by: Satish Balay <balay@mcs.anl.gov>
2023-05-31 21:57:53 -04:00
Brian Van Essen
543b697df1 CachedCMakePackage: add CUDA/HIP options and improve independent builds (#37592)
* Add CMake options for building with CUDA/HIP support to
  CachedCMakePackages (intended to reduce duplication across packages
  building with +hip/+cuda and using CachedCMakePackage)
* Define generic variables like CMAKE_PREFIX_PATH for
  CachedCMakePackages (so that a user may invoke "cmake" themselves
  without needing to setthem on the command line).
* Make `lbann` a CachedCMakePackage.

Co-authored-by: Chris White <white238@llnl.gov>
2023-05-31 17:35:11 -07:00
QuellynSnead
042dc2e1d8 libtheora: enforce math library (libm.so) linkage (#37891) 2023-05-31 13:45:11 -07:00
Mosè Giordano
f745e49d9a julia: add patch to fix printing of BigFloat with MPFR v4.2 (#37992) 2023-05-31 15:32:12 -04:00
Michael Kuhn
eda21cdfba gcc: add 11.4.0 (#37988) 2023-05-31 09:15:45 -04:00
Adam J. Stewart
bc8b026072 py-pandas: add v2.0.2 (#38005) 2023-05-30 22:48:51 -04:00
Tiziano Müller
0f84782fcc Bugfix: cray manifest parsing regression (#37909)
fa7719a changed syntax for specifying exact versions, which are
required for some compiler specs (including those read as part
of parsing a Cray manifest). This fixes that and also makes a
couple other improvements to manifest parsing.

* Instantiate compiler specs with exact versions (fixes #37893)
* fix slingshot network detection (CPE 22.10+ has libcxi.so
  in /usr/lib64)
* "spack external find": add arg to ignore default dir for cray
  manifests
2023-05-30 18:03:44 -07:00
AMD Toolchain Support
43b86ce282 HPL: amdalloc with AOCC 4.0 (#37757)
* adding amdalloc when using aocc 4


* adding and libm for aocc3.2
2023-05-30 16:40:41 -07:00
AMD Toolchain Support
d30698d9a8 cp2k fixes for aocc (#37758) 2023-05-30 16:33:00 -07:00
Massimiliano Culpo
8e9efa86c8 Simplify implementation of "get_compiler_config" (#37989) 2023-05-30 15:11:33 -07:00
Jack Morrison
84faf5a6cf intel-mpi-benchmarks: Add MPI implementation check variant (#37363)
* Add MPI implementation check variant to Intel MPI Benchmarks

* [@spackbot] updating style on behalf of jack-morrison
2023-05-30 16:37:58 -05:00
Eric Berquist
9428749a3c Update SST packages to 13.0.0 (#37467)
* add sst-{core,elements,macro} v13.0.0

* Add newest DUMPI versions and remove unavailable ones

* update maintainer lists

* sst-core: tracking and profiling flags

* sst-elements with Pin requires the Pin location

* sst-core: Zoltan integration was removed in version 12

* spack style fixes

* sst-core: ensure Python is in the sst{sim,info}.x rpaths

* sst-macro: update homepage and maintainers

* spack style --fix
2023-05-30 16:35:33 -05:00
Michael Kuhn
efdac68c28 julia: fix build for @1.8.4:1.8.5 (#37990)
julia@1.8.4:1.8.5 fails to build because it does not find libstdc++ (see https://github.com/JuliaLang/julia/issues/47987).
2023-05-30 13:49:15 -07:00
Carlos Bederián
5398c31e82 ucx: add 1.14.1 (#37991) 2023-05-30 13:46:39 -07:00
Thomas Madlener
188168c476 podio: Add 0.16.5 tag (#37994) 2023-05-30 13:39:15 -07:00
Michael Kuhn
4af84ac208 gobject-introspection: add 1.76.1 (#37995) 2023-05-30 13:37:53 -07:00
Manuela Kuhn
deb8b51098 py-dunamai: add 1.17.0 (#38003) 2023-05-30 15:34:15 -04:00
Manuela Kuhn
0d582b2ea9 py-duecredit: add 0.9.2 (#38002) 2023-05-30 15:33:54 -04:00
Manuela Kuhn
f88b01c34b py-datalad-container: add 1.2.0 (#38000) 2023-05-30 15:28:34 -04:00
Manuela Kuhn
0533c6a1b8 py-datalad-metalad: add 0-4-17 and new dep py-datalad-deprecated (#37993)
* py-datalad-metalad: add 0-4-17 and new dep py-datalad-deprecated

* Fix style
2023-05-30 15:18:15 -04:00
Manuela Kuhn
f73d5c2b0e py-cryptography: add 40.0.2 (#37925)
* py-cryptography: add 40.0.2

* Add pkgconfig dependency
2023-05-30 10:26:17 -05:00
Tamara Dahlgren
567d0ee455 tests/hdf5: convert to new stand-alone test process (#35732) 2023-05-29 16:56:17 +02:00
Tamara Dahlgren
577df6f498 sqlite: convert to new stand-alone test process (#37722) 2023-05-29 07:59:23 -04:00
Harmen Stoppels
8790efbcfe Remove patchelf self-relocation (#33834) 2023-05-29 13:14:24 +02:00
Tamara Dahlgren
212b1edb6b tests/biobambam2: convert to new stand-alone test process (#35696) 2023-05-29 12:54:38 +02:00
snehring
d85a27f317 sentieon-genomics: replacing square brackets in help (#37622) 2023-05-29 12:52:36 +02:00
Chris White
5622afbfd1 amgx: add v2.2.0 and v2.3.0 (#37567) 2023-05-29 12:42:36 +02:00
Carlos Bederián
f345038317 nwchem: fix non-fftw fftw-api providers (#37442) 2023-05-29 12:41:41 +02:00
Michael Kuhn
e43d4cfee0 glib: add 2.76.3 and 2.76.2, update build systems (#37226)
This also converts the package to the new way of handling multiple build
systems.

Co-authored-by: michaelkuhn <michaelkuhn@users.noreply.github.com>
2023-05-29 06:38:57 -04:00
Vanessasaurus
7070658e2a Automated deployment to update package flux-core 2023-05-15 (#37684)
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2023-05-29 12:35:22 +02:00
dependabot[bot]
fc4b032fb4 build(deps): bump codecov/codecov-action from 3.1.3 to 3.1.4 (#37688)
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3.1.3 to 3.1.4.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](894ff025c7...eaaf4bedf3)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  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>
2023-05-29 12:34:34 +02:00
Vanessasaurus
8c97d8ad3f add flux-security variant to flux-core (#37689)
This will build flux-security separately to have a flux-imp
that can be defined in a flux broker.toml. Note that the user
that wants a multi-user setup is recommended to create a view,
and then a system/broker.toml in flux config directory that
points to it.

Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2023-05-29 12:34:07 +02:00
Alberto Invernizzi
26107fe6b2 highfive: add newer versions + add git repo (#37635)
* add versions
* add develop pointing to git@master
2023-05-29 06:09:02 -04:00
Tamara Dahlgren
9278c0df21 binutils: convert to new stand-alone test process (#37690) 2023-05-29 11:59:09 +02:00
Tamara Dahlgren
37e95713f4 libsigsegv: convert to new stand-alone test process (#37691) 2023-05-29 11:58:39 +02:00
SXS Bot
3ae8a3a517 spectre: add v2023.05.16 (#37716)
Co-authored-by: sxs-bot <sxs-bot@users.noreply.github.com>
2023-05-29 11:56:21 +02:00
Tamara Dahlgren
031af84e90 m4: convert to new stand-alone test process (#37723) 2023-05-29 11:49:28 +02:00
Annop Wongwathanarat
7d4b65491d armpl-gcc: add version 23.04.1 (#37907) 2023-05-29 05:49:19 -04:00
Harmen Stoppels
3038d1e7cd Use @= in some packages (#37737)
Change the pattern @x.y:x.y.0 -> @=x.y

Co-authored-by: haampie <haampie@users.noreply.github.com>
2023-05-29 11:47:00 +02:00
Lehman Garrison
b2e6ef97ce hdfview: add 3.1.4, 3.2.0, 3.3.0. Update dependencies. (#37745) 2023-05-29 11:41:44 +02:00
Tamara Dahlgren
e55236ce5b tests/arborx: convert to new stand-alone test process (#37778)
Co-authored-by: Andrey Prokopenko <andrey.prok@gmail.com>
2023-05-29 11:33:07 +02:00
Alec Scott
68dfd6ba6e hbase: add v2.5.3 (#37518)
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-05-29 11:29:11 +02:00
Jim Galarowicz
38d2459f94 survey: add v1.0.8 (#37385) 2023-05-29 11:26:56 +02:00
Nicolas Cornu
e309f367af catch2: new versions (#37742) 2023-05-29 11:26:06 +02:00
Harmen Stoppels
3b59c95323 fix InternalConcretizerError msg (#37791) 2023-05-29 11:24:43 +02:00
Howard Pritchard
fddaeadff8 OPENMPI: disable use of sphinx (#37717)
Sphinx is used to build Open MPI manpages, etc. as part of the make dist
process to create release tarballs.  There should be no need/use to do
this within Spack.  Also some sites have older Sphinx installs which
aren't compatible with the needs of the Open MPI documentation.
For example, attempts to install openmpi@main fail at NERSC owing to
such a situation.

Since Spack normally is used to build from release tarballs, in which
the docs have already been installed, this should present no issues.

This configuration option will be ignored for older than 5.0.0 Open MPI releases.

Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2023-05-29 11:23:42 +02:00
Joel Falcou
c85eaf9dc5 Add package for KUMI tuple library (#37795) 2023-05-29 11:23:06 +02:00
Brian Vanderwende
ddec7f8aec bbcp: fix cloning "master" version (#37802) 2023-05-29 11:21:48 +02:00
AMD Toolchain Support
f057d7154b NAMD: add AVXTILES support (#37040) 2023-05-29 11:10:09 +02:00
Tamara Dahlgren
a102950d67 berkeley-db: convert to new stand-alone test process (#35702) 2023-05-29 10:56:42 +02:00
Howard Pritchard
783be9b350 dealii - add platform-introspection variant (#37833)
This option is needed for DFT FE - or more accurately the check needs to
be checked off for a number of platforms or else the code doesn't work.

Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2023-05-29 10:56:03 +02:00
Juan Miguel Carceller
27c8135207 xrootd: add patch for when libraries are installed in lib64 (#37858)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-05-29 10:36:57 +02:00
Tamara Dahlgren
77ce4701b9 Bugfix/tests: add slash to test log message (#37874) 2023-05-29 10:36:36 +02:00
Juan Miguel Carceller
73ad3f729e dd4hep: add patch to fix missing hits when using LCIO (#37854)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-05-29 10:35:14 +02:00
Jim Edwards
1e7a64ad85 parallelio: add v2.6.0 release and ncint variant (#37805) 2023-05-29 10:19:15 +02:00
Tamara Dahlgren
3a5864bcdb tests/sip: convert to new stand-alone test process (#35693) 2023-05-29 10:16:35 +02:00
Alec Scott
7e13a7dccb cbc: add v2.10.9 (#37974) 2023-05-29 04:04:28 -04:00
Alec Scott
e3249fa155 bedops: add v2.4.41 (#37972) 2023-05-29 04:04:06 -04:00
Thomas-Ulrich
0c20760576 pumi: fix simmodsuite base variant, and mpi lib name (#37401) 2023-05-29 09:59:32 +02:00
Alec Scott
7ee7995493 cracklib: add v2.9.9 (#37976) 2023-05-29 03:59:13 -04:00
Alec Scott
ba1fac1c31 cpio: add v2.14 (#37975) 2023-05-29 03:58:53 -04:00
Adam J. Stewart
b05f0ecb6f py-segmentation-models-pytorch: add v0.3.3 (#37970) 2023-05-29 09:48:32 +02:00
Alec Scott
d5c66b75c3 cyrus-sasl: add v2.1.28 (#37978) 2023-05-29 09:31:54 +02:00
Alec Scott
98303d6956 double-conversion: add v3.3.0 (#37979) 2023-05-29 09:31:38 +02:00
Alec Scott
4622d638a6 elfio: add v3.11 (#37980) 2023-05-29 09:31:23 +02:00
Alec Scott
02023265fc erfa: add v2.0.0 (#37981) 2023-05-29 09:31:09 +02:00
Alec Scott
8a075998f8 erlang: add v26.0 (#37982) 2023-05-29 09:30:28 +02:00
Alec Scott
f2f48b1872 fasttransforms: add v0.6.2 (#37983) 2023-05-29 09:30:10 +02:00
Alec Scott
168d63c447 glog: add v0.6.0 (#37985) 2023-05-29 09:29:34 +02:00
Alec Scott
c25d4cbc1d gradle: add v8.1.1 (#37986) 2023-05-29 09:29:07 +02:00
snehring
ccb07538f7 Beast2: add v2.7.4, add javafx (#37419) 2023-05-29 09:28:32 +02:00
Alec Scott
1356b13b2f form: add v4.3.1 (#37984) 2023-05-29 09:24:34 +02:00
Tamara Dahlgren
935f862863 tests/flibcpp: convert to new stand-alone test process (#37782) 2023-05-28 10:47:23 +02:00
Tamara Dahlgren
9f6d9df302 patchelf: convert to new stand-alone test process (#37831) 2023-05-28 10:46:23 +02:00
Tamara Dahlgren
65d33c02a1 gasnet: convert to new stand-alone test process (#35727) 2023-05-28 10:45:11 +02:00
Tamara Dahlgren
40073e7b21 hdf: convert to new stand-alone test process (#37843) 2023-05-28 10:44:42 +02:00
Tamara Dahlgren
752e02e2f2 tests/upcxx: convert to new stand-alone test process (#37832)
Co-authored-by: Dan Bonachea <dobonachea@lbl.gov>
2023-05-28 10:44:04 +02:00
Vanessasaurus
d717b3a33f Automated deployment to update package flux-core 2023-05-04 (#37421)
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2023-05-28 10:42:44 +02:00
Bruno Turcksin
9817f24c9a kokkos-nvcc-wrapper: Remove unnecessary dependencies (#37794) 2023-05-28 10:19:30 +02:00
Bruno Turcksin
1f7c4b0557 Kokkos: remove unused variants (#37800) 2023-05-28 10:18:53 +02:00
Xavier Delaruelle
6c42d2b7f7 modules: improve default naming scheme (#37808)
Change default naming scheme for tcl modules for a more user-friendly
experience. 

Change from flat projection to "per software name" projection.

Flat naming scheme restrains module selection capabilities. The
`{name}/{version}...` scheme make possible to use user-friendly
mechanisms:

* implicit defaults (`module load git`)
* extended default (`module load git/2`)
* advanced version specifiers (`module load git@2:`)
2023-05-28 10:06:30 +02:00
Tamara Dahlgren
8df036a5a5 tests/cmake: convert to new stand-alone test process (#37724) 2023-05-28 09:59:21 +02:00
dependabot[bot]
582ebee74c build(deps): bump actions/setup-python from 4.6.0 to 4.6.1 (#37894)
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.6.0 to 4.6.1.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](57ded4d7d5...bd6b4b6205)

---
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>
2023-05-28 09:58:14 +02:00
Annop Wongwathanarat
1017b9ddde acfl: add version 23.04.1 and fix checksums for 22.1 (#37908)
Checksums for 22.1 need updates due to an IT incident at developer.arm.com. The package tarballs needed to be recreated.
2023-05-28 09:57:31 +02:00
Thomas Madlener
80ae73119d whizard: Fix parallel build race condition (#37890) 2023-05-28 09:55:52 +02:00
Tamara Dahlgren
1d88f690a4 tests/darshan-runtime: convert to new stand-alone test process (#37838) 2023-05-28 09:46:31 +02:00
Filippo Spiga
fbb271d804 Adding NVIDIA HPC SDK 23.5 (#37913) 2023-05-28 09:45:08 +02:00
Hao Lyu
d6aac873b7 copy namelist and xml to ./bin (#37933) 2023-05-28 09:43:27 +02:00
Tamara Dahlgren
ab3ffd9361 archer: convert to new stand-alone test process (#35697) 2023-05-28 09:41:38 +02:00
Tamara Dahlgren
3b9454a5cc tests/bolt: convert to new stand-alone test process (#35695)
* bolt: convert to new stand-alone test process
* Remove redundant test_requires_compiler (so above directives)
2023-05-27 18:46:11 -07:00
Tamara Dahlgren
c8eb0f9361 tests/amrex: convert to new stand-alone test process (#35698)
* amrex: convert to new stand-alone test process
* smoke->stand-alone
2023-05-27 18:44:06 -07:00
George Young
fb0f14eb06 py-macs2: add 2.2.8, updated dependencies (#37944)
* py-macs2: add 2.2.8, updated dependencies

* Update package.py

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-05-27 14:29:12 -05:00
George Young
e489ee4e2e py-cutadapt: add 4.4, 4.3, 4.2 versions (#37929)
* py-cutadapt: add 4.4, 4.3, 4.2 versions

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

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

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

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

* Update package.py

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-05-27 14:27:43 -05:00
Alex Richert
fcd49f2f08 Add shared and pic variants to libtiff (#37965)
* Add static-only option for libtiff

* update libtiff to add pic variant

* fix libtiff pic setting
2023-05-27 11:24:27 -05:00
Alex Richert
b3268c2703 freetype: add pic and shared variants (#37898) 2023-05-27 01:05:10 +02:00
George Young
d1bfcfafe3 py-multiqc: add 1.14, bump dependencies (#37946)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-05-26 17:55:03 -05:00
Manuela Kuhn
490c9f5e16 py-datalad-metadata-model: add 0.3.10 (#37937) 2023-05-26 17:28:36 -05:00
Manuela Kuhn
85628d1474 py-debugpy: add 1.6.7 (#37941) 2023-05-26 17:27:50 -05:00
Manuela Kuhn
720c34d18d py-distro: add 1.8.0 (#37942) 2023-05-26 17:27:06 -05:00
mschouler
cd175377ca Update melissa build (#37609)
* Remove deprecated package

* Add up-to-date melissa builds

* Remove blank lines and FIXME comments

* Use directive syntax for maintainers and remove unnecessary comments

* Remove unused function

* Deprecate former melissa recipe

* Change melissa python package name

* Update setuptools and rapidjson dependencies versions

* Fix mypy error

* Restore rapidjson version

* Variant simplification

* Make variants lower case

* Deprecate former omitted version

* Make torch version consistent with requirement file

* Fix variants definition

* Fix style error

---------

Co-authored-by: Marc Schouler <marc.schouler@inria.fr>
2023-05-26 17:26:29 -05:00
Manuela Kuhn
b91ec05e13 py-coloredlogs: add 15.0.1 and py-humanfriendly: add 10.0 (#37905) 2023-05-26 17:22:02 -05:00
Manuela Kuhn
3bb15f420b py-contourpy: add 1.0.7 (#37914) 2023-05-26 17:19:40 -05:00
Manuela Kuhn
124a81df5b py-coverage: add 5.5 (#37922) 2023-05-26 17:06:39 -05:00
Lee James O'Riordan
d9472c083d Update py-pennylane ecosystem to support v0.30.0 (#37763)
* Update PennyLane ecosystem for 0.30 release

* Update package dep versions

* Fix formatting

* Update dep versions

* Remove PL hard pin and rely on PLQ to define version

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

Co-authored-by: Vincent Michaud-Rioux <vincent.michaud-rioux@xanadu.ai>

* Convert pybind11 from build to link dep, and PL ver limit

---------

Co-authored-by: Vincent Michaud-Rioux <vincent.michaud-rioux@xanadu.ai>
2023-05-26 16:55:21 -05:00
Manuela Kuhn
ac2a5ef4dd py-beautifulsoup4: add 4.12.2 (#37820) 2023-05-26 16:54:43 -05:00
Manuela Kuhn
ea210a6acf py-chardet: add 5.1.0 (#37879)
* py-chardet: add 5.1.0

* Remove py-setuptools as run dependency
2023-05-26 16:51:54 -05:00
kwryankrattiger
afb3bef7af CI: Use relative path in default script (#36649) 2023-05-26 14:28:48 -06:00
George Young
b5b5881426 picard: add 3.0.0, switch to java@17: (#37948)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-05-26 15:38:26 -04:00
George Young
76fc7915a8 minimap2: adding 2.26 (#37945)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-05-26 10:12:14 -07:00
George Young
e7798b619b hyphy: add 2.5.51hf, update dependencies for switch to MPI (#37938)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-05-26 09:48:26 -07:00
Kai Torben Ohlhus
8ecef12a20 Strip inactive maintainer. (#36048) 2023-05-26 10:47:39 -04:00
Brian Spilner
694292ebbf cdo: add 2.2.0 (#37244) 2023-05-26 10:01:49 +02:00
Howard Pritchard
7f18f6f8a1 PMIx and PRRTe: disabled use of sphinx (#37750)
Related to https://github.com/spack/spack/pull/37717

No need to be rebuilding openmpi man pages and other docs in
spack as it almost always is used with release tarballs.

See #37717 for more details.

Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2023-05-26 09:49:02 +02:00
John W. Parent
0b12a480eb Windows MSVC: do not set sdk version if installing sdk (#37930)
Note the win-sdk package is not installable and reports an error
which instructs the user how to add it. Without this fix, a
(more confusing) error occurs before this message can be generated.
2023-05-25 21:38:04 -04:00
George Young
2d91a79af3 fastp: add version 0.23.3, add build dependencies (#37931)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-05-25 21:28:13 -04:00
Leonard-Anderson-NNL
72fcee7227 gradle:add 7.3 (#37928)
Co-authored-by: Cloud User <leonardanderson@leonardander001.hzterscemazurawp3xenxzahla.bx.internal.cloudapp.net>
2023-05-25 20:55:09 -04:00
John W. Parent
d147ef231f Windows: fix "spack build-env" (#37923)
"spack build-env" was not generating proper environment variable
definitions on Windows; this commit updates the generated commands
to succeed with batch/PowerShell.
2023-05-25 17:08:15 -07:00
eugeneswalker
1c7af83d32 update ci ml darwin keypath (#37927) 2023-05-25 16:27:56 -07:00
John W. Parent
b982dfc071 Windows CI: add paraview deps nightly build (#37924)
Add a nightly job to attempt building all Paraview dependencies and
upload the results to cdash. This check doesn't affect the reported
build/test status of Spack. We are using this to monitor the state of
Windows support while working on more-robust checks (eventually the
Windows build will have to succeed to merge PRs to Spack).
2023-05-25 16:13:41 -07:00
H. Joe Lee
c0da8a00fc fix(protobuf-c): set version bound for protobuf dependency (#37917)
Fix #37887 GitLab CI failure.
2023-05-25 19:08:54 -04:00
H. Joe Lee
3f18f689d8 fix(dpdk): add a new version 23.03. (#37919)
Fix E4S GitLab CI issue #37887.
2023-05-25 18:58:41 -04:00
Simon Pintarelli
9dc4553cf3 sirius: add rocsolver/wannier90 (#37900)
* sirius: add rocsolver dependency for 7.5:
* add wannier90
2023-05-25 15:58:04 -07:00
Tim Haines
9a99c94b75 Dyninst: add standalone test (#37876)
* Dyninst: add standalone test
* Add docstring with description
* Don't use join_path for builtin path objects
* Whitespace
* Update format of docstring
2023-05-25 18:48:52 -04:00
John W. Parent
682f0b2a54 Protobuf package: CMake fix for Windows build (#37926)
Qualify reference with namespace. A pending upstream PR will eventually
make this unnecessary, so the patch is only applied for 3.22. versions.
2023-05-25 15:41:16 -07:00
Richard Berger
dbab0c1ff5 flecsi: disable cinch dependency for v1 release (#37857)
* flecsi: disable cinch dependency for v1 releases
* [@spackbot] updating style on behalf of rbberger

---------

Co-authored-by: rbberger <rbberger@users.noreply.github.com>
2023-05-25 14:59:45 -07:00
Xavier Delaruelle
2bf95f5340 environment-modules: fix @main version requirements (#37807)
Some requirements for @main version of environment-modules were missing:

* python (to build ChangeLog documentation file)
* py-sphinx@1.0: (to build man-pages, etc)

Also adding gzip, which is now required to build ChangeLog.gz (which is
now shipped instead of ChangeLog).

Other versions are not requiring these tools (as documentation is
pre-built in dist tarball).
2023-05-25 22:29:26 +02:00
Tamara Dahlgren
55561405b8 Bugfix/tests: write not append stand-alone test status (#37841) 2023-05-25 12:36:24 -07:00
H. Joe Lee
8eef458cea fix(pmdk): add pkconfig as dependency (#37896)
Fix #37887 failure.
2023-05-25 10:35:48 -07:00
Stephen Sachs
64eea9d996 [devito] Move to version 4.8.1 (#37915)
* [devito] Move to version 4.8.1

* Fix: Adding patch file

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

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

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

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

* Addressing @adamjstewart comments

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-05-25 13:33:10 -04:00
Alex Richert
60b4e2128b Add shared variant to geos package (#37899)
Co-authored-by: alexrichert <alexrichert@gmail.com>
2023-05-25 11:42:51 -04:00
Adam J. Stewart
2f8cea2792 Add macOS ML CI stacks (#36586)
* Add macOS ML CI stacks

* torchmeta is no longer maintained and requires ancient PyTorch

* Add MXNet

* update darwin aarch64 stacks

* add darwin-aarch64 scoped config.yaml

* remove unnecessary cleanup job

* fix specifications

* fix labels

* fix labels

* fix indent on tags specification

* no tags for trigger jobs

* try overriding tags in stack spack.yaml

* do not use CI_STACK_CONFIG_SCOPES

* incorporate config:install_tree:root: overrides and compiler defs

* copy relevant ci-scoped config settings directly into stack spack.yaml

* remove build-job-remove

* spack ci generate: add debug flag

* include cdash config directly in stack spack.yaml

* customize build-job script section to avoid absolute paths

* add any-job specification

* tags: use aarch64-macos instead of aarch64

* generate tags: use aarch64-macos instead of aarch64

* do not add morepadding

* use shared mirror; comment out known failures

* remove any-job

* nproc || true

* comment out specs failing due to bazel from cache codesign issue

---------

Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
2023-05-25 01:12:54 -04:00
M. Eric Irrgang
06f9bcf734 Update for py-gmxapi for 0.4.1. (#37834)
* Update for py-gmxapi for 0.4.1.

* Note 0.4.1 hash from PyPI.
* Note relaxed dependencies for future versions.

* Update var/spack/repos/builtin/packages/py-gmxapi/package.py
2023-05-24 22:03:10 -05:00
Manuela Kuhn
ee2725762f py-charset-normalizer: add 3.1.0 (#37880) 2023-05-24 21:57:29 -05:00
Manuela Kuhn
eace0a177c py-bids-validator: add 1.11.0 (#37845) 2023-05-24 21:36:45 -05:00
Manuela Kuhn
80c7d74707 py-bottleneck: add 1.3.7 (#37847) 2023-05-24 21:36:01 -05:00
Manuela Kuhn
a6f5bf821d py-certifi: add 2023.5.7 (#37848) 2023-05-24 21:35:13 -05:00
Manuela Kuhn
b214406253 py-attrs: add 23.1.0 (#37817)
* py-attrs: add 23.1.0

* Add missing dependency
2023-05-24 20:21:31 -05:00
Manuela Kuhn
5b003d80e5 py-babel: add 2.12.1 (#37818)
* py-babel: add 2.12.1

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

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-05-24 20:13:02 -05:00
Adam J. Stewart
185b2d3ee7 py-rasterio: add v1.3.7 (#37886) 2023-05-24 18:48:16 -04:00
Adam J. Stewart
71bb2a1899 py-lightly: add v1.4.6 (#37885) 2023-05-24 16:43:07 -04:00
Nathalie Furmento
785c31b730 starpu: add release 1.4.1 (#37883) 2023-05-24 09:36:56 -07:00
QuellynSnead
175da4a88a paraview (protobuf failure) #37437 (#37440)
When attempting to build paraview@5.10.1 using a recent Intel
compiler (Classic or OneAPI) or the IBM XL compiler, the build
fails if the version of protobuf used is > 3.18
2023-05-24 11:09:48 -05:00
willdunklin
73fc1ef11c sensei: Allow Paraview 5.11 for sensei develop version (#37719) 2023-05-24 11:00:35 -05:00
Stephen Sachs
2d77e44f6f Pcluster local buildcache (#37852)
* [pcluster pipeline] Use local buildcache instead of upstream spack

Spack currently does not relocate compiler references from upstream spack
installations. When using a buildcache we don't need an upstream spack.

* gcc needs to be installed via postinstall to get correct deps

* quantum-espresso@gcc@12.3.0 returns ICE on neoverse_{n,v}1

* Force gitlab to pull the new container

* Revert "Force gitlab to pull the new container"

This reverts commit 3af5f4cd88.

Seems the gitlab version does not yet support "pull_policy" in .gitlab-ci.yml

* Gitlab keeps picking up wrong container. Renaming

* Update containers once more after failed build
2023-05-24 06:55:00 -07:00
Greg Becker
033599c4cd bugfix: env concretize after remove (#37877) 2023-05-24 15:41:57 +02:00
Harmen Stoppels
8096ed4b22 spack remove: fix traversal when user specs intersect (#37882)
drop unnecessary double loop over the matching user specs.
2023-05-24 09:23:46 -04:00
Simon Pintarelli
b49bfe25af update nlcglib package (#37578) 2023-05-24 11:17:15 +02:00
Houjun Tang
8b2f34d802 Add async vol v1.6 (#37875) 2023-05-24 01:47:46 -04:00
H. Joe Lee
3daed0d6a7 hdf5-vol-daos: add a new package (#35653)
* hdf5-vol-daos: add a new package
* hdf5-vol-daos: address @soumagne review

---------

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-05-23 23:42:42 -04:00
Glenn Johnson
d6c1f75e8d julia: remove myself from maintainers list (#37868) 2023-05-23 16:22:56 -05:00
Laura Weber
c80a4c1ddc Updated hash for latest maintenance release (2022.2.1) (#37842) 2023-05-23 14:08:55 -07:00
Glenn Johnson
466abcb62d gate: remove myself as maintainer (#37862) 2023-05-23 14:03:52 -07:00
Glenn Johnson
69e99f0c16 Remove myself as maintainer of R packages (#37859)
* Remove myself as maintainer of R packages
  I will no longer have the time to properly maintain these packages.
* fix flake8 test for import
2023-05-23 15:35:32 -05:00
Glenn Johnson
bbee6dfc58 bart: remove myself as maintainer (#37860) 2023-05-23 16:08:07 -04:00
Glenn Johnson
2d60cf120b heasoft: remove myself as maintainer (#37866) 2023-05-23 14:37:57 -05:00
Glenn Johnson
db17fc2f33 opencv: remove myself from maintainers list (#37870) 2023-05-23 14:34:52 -05:00
eugeneswalker
c62080d498 e4s ci: add dealii (#32484) 2023-05-23 21:34:31 +02:00
Glenn Johnson
f9bbe549fa gatetools: remove myself as maintainer (#37863) 2023-05-23 15:32:54 -04:00
H. Joe Lee
55d7fec69c daos: add a new package (#35649) 2023-05-23 21:30:23 +02:00
Glenn Johnson
e938907150 reditools: remove myself as maintainer (#37871) 2023-05-23 15:28:16 -04:00
Glenn Johnson
0c40b86e96 itk: remove myself as maintainer (#37867) 2023-05-23 15:27:55 -04:00
Glenn Johnson
3d4cf0d8eb mumax: remove myself as maintainer (#37869) 2023-05-23 15:23:28 -04:00
Glenn Johnson
966e19d278 gurobi: remove myself as maintainer (#37865) 2023-05-23 15:23:05 -04:00
Glenn Johnson
8f930462bd fplo: remove myself as maintainer (#37861) 2023-05-23 15:17:50 -04:00
kjrstory
bf4fccee15 New package: FDS (#37850) 2023-05-23 11:59:05 -07:00
Manuela Kuhn
784771a008 py-bleach: add 6.0.0 (#37846) 2023-05-23 11:50:53 -07:00
Glenn Johnson
e4a9d9ae5b Bioc updates (#37297)
* add version 1.48.0 to bioconductor package r-a4
* add version 1.48.0 to bioconductor package r-a4base
* add version 1.48.0 to bioconductor package r-a4classif
* add version 1.48.0 to bioconductor package r-a4core
* add version 1.48.0 to bioconductor package r-a4preproc
* add version 1.48.0 to bioconductor package r-a4reporting
* add version 1.54.0 to bioconductor package r-absseq
* add version 1.30.0 to bioconductor package r-acde
* add version 1.78.0 to bioconductor package r-acgh
* add version 2.56.0 to bioconductor package r-acme
* add version 1.70.0 to bioconductor package r-adsplit
* add version 1.72.0 to bioconductor package r-affxparser
* add version 1.78.0 to bioconductor package r-affy
* add version 1.76.0 to bioconductor package r-affycomp
* add version 1.58.0 to bioconductor package r-affycontam
* add version 1.72.0 to bioconductor package r-affycoretools
* add version 1.48.0 to bioconductor package r-affydata
* add version 1.52.0 to bioconductor package r-affyilm
* add version 1.70.0 to bioconductor package r-affyio
* add version 1.76.0 to bioconductor package r-affyplm
* add version 1.46.0 to bioconductor package r-affyrnadegradation
* add version 1.48.0 to bioconductor package r-agdex
* add version 3.32.0 to bioconductor package r-agilp
* add version 2.50.0 to bioconductor package r-agimicrorna
* add version 1.32.0 to bioconductor package r-aims
* add version 1.32.0 to bioconductor package r-aldex2
* add version 1.38.0 to bioconductor package r-allelicimbalance
* add version 1.26.0 to bioconductor package r-alpine
* add version 2.62.0 to bioconductor package r-altcdfenvs
* add version 2.24.0 to bioconductor package r-anaquin
* add version 1.28.0 to bioconductor package r-aneufinder
* add version 1.28.0 to bioconductor package r-aneufinderdata
* add version 1.72.0 to bioconductor package r-annaffy
* add version 1.78.0 to bioconductor package r-annotate
* add version 1.62.0 to bioconductor package r-annotationdbi
* add version 1.24.0 to bioconductor package r-annotationfilter
* add version 1.42.0 to bioconductor package r-annotationforge
* add version 3.8.0 to bioconductor package r-annotationhub
* add version 3.30.0 to bioconductor package r-aroma-light
* add version 1.32.0 to bioconductor package r-bamsignals
* add version 2.16.0 to bioconductor package r-beachmat
* add version 2.60.0 to bioconductor package r-biobase
* add version 2.8.0 to bioconductor package r-biocfilecache
* add version 0.46.0 to bioconductor package r-biocgeneric
* add version 1.10.0 to bioconductor package r-biocio
* add version 1.18.0 to bioconductor package r-biocneighbors
* add version 1.34.0 to bioconductor package r-biocparallel
* add version 1.16.0 to bioconductor package r-biocsingular
* add version 2.28.0 to bioconductor package r-biocstyle
* add version 3.17.1 to bioconductor package r-biocversion
* add version 2.56.0 to bioconductor package r-biomart
* add version 1.28.0 to bioconductor package r-biomformat
* add version 2.68.0 to bioconductor package r-biostrings
* add version 1.48.0 to bioconductor package r-biovizbase
* add version 1.10.0 to bioconductor package r-bluster
* add version 1.68.0 to bioconductor package r-bsgenome
* add version 1.36.0 to bioconductor package r-bsseq
* add version 1.42.0 to bioconductor package r-bumphunter
* add version 2.66.0 to bioconductor package r-category
* add version 2.30.0 to bioconductor package r-champ
* add version 2.32.0 to bioconductor package r-champdata
* add version 1.50.0 to bioconductor package r-chipseq
* add version 4.8.0 to bioconductor package r-clusterprofiler
* add version 1.36.0 to bioconductor package r-cner
* add version 1.32.0 to bioconductor package r-codex
* add version 2.16.0 to bioconductor package r-complexheatmap
* add version 1.74.0 to bioconductor package r-ctc
* add version 2.28.0 to bioconductor package r-decipher
* add version 0.26.0 to bioconductor package r-delayedarray
* add version 1.22.0 to bioconductor package r-delayedmatrixstats
* add version 1.40.0 to bioconductor package r-deseq2
* add version 1.46.0 to bioconductor package r-dexseq
* add version 1.42.0 to bioconductor package r-dirichletmultinomial
* add version 2.14.0 to bioconductor package r-dmrcate
* add version 1.74.0 to bioconductor package r-dnacopy
* add version 3.26.0 to bioconductor package r-dose
* add version 2.48.0 to bioconductor package r-dss
* add version 3.42.0 to bioconductor package r-edger
* add version 1.20.0 to bioconductor package r-enrichplot
* add version 2.24.0 to bioconductor package r-ensembldb
* add version 1.46.0 to bioconductor package r-exomecopy
* add version 2.8.0 to bioconductor package r-experimenthub
* add version 1.26.0 to bioconductor package r-fgsea
* add version 2.72.0 to bioconductor package r-gcrma
* add version 1.36.0 to bioconductor package r-gdsfmt
* add version 1.82.0 to bioconductor package r-genefilter
* add version 1.36.0 to bioconductor package r-genelendatabase
* add version 1.72.0 to bioconductor package r-genemeta
* add version 1.78.0 to bioconductor package r-geneplotter
* add version 1.22.0 to bioconductor package r-genie3
* add version 1.36.0 to bioconductor package r-genomeinfodb
* update r-genomeinfodbdata
* add version 1.36.0 to bioconductor package r-genomicalignments
* add version 1.52.0 to bioconductor package r-genomicfeatures
* add version 1.52.0 to bioconductor package r-genomicranges
* add version 2.68.0 to bioconductor package r-geoquery
* add version 1.48.0 to bioconductor package r-ggbio
* add version 3.8.0 to bioconductor package r-ggtree
* add version 2.10.0 to bioconductor package r-glimma
* add version 1.12.0 to bioconductor package r-glmgampoi
* add version 5.54.0 to bioconductor package r-globaltest
* update r-go-db
* add version 1.20.0 to bioconductor package r-gofuncr
* add version 2.26.0 to bioconductor package r-gosemsim
* add version 1.52.0 to bioconductor package r-goseq
* add version 2.66.0 to bioconductor package r-gostats
* add version 1.78.0 to bioconductor package r-graph
* add version 1.62.0 to bioconductor package r-gseabase
* add version 1.32.0 to bioconductor package r-gtrellis
* add version 1.44.0 to bioconductor package r-gviz
* add version 1.28.0 to bioconductor package r-hdf5array
* add version 1.72.0 to bioconductor package r-hypergraph
* add version 1.36.0 to bioconductor package r-illumina450probevariants-db
* add version 0.42.0 to bioconductor package r-illuminaio
* add version 1.74.0 to bioconductor package r-impute
* add version 1.38.0 to bioconductor package r-interactivedisplaybase
* add version 2.34.0 to bioconductor package r-iranges
* add version 1.60.0 to bioconductor package r-kegggraph
* add version 1.40.0 to bioconductor package r-keggrest
* add version 3.56.0 to bioconductor package r-limma
* add version 2.52.0 to bioconductor package r-lumi
* add version 1.76.0 to bioconductor package r-makecdfenv
* add version 1.78.0 to bioconductor package r-marray
* add version 1.12.0 to bioconductor package r-matrixgenerics
* add version 1.8.0 to bioconductor package r-metapod
* add version 2.46.0 to bioconductor package r-methylumi
* add version 1.46.0 to bioconductor package r-minfi
* add version 1.34.0 to bioconductor package r-missmethyl
* add version 1.80.0 to bioconductor package r-mlinterfaces
* add version 1.12.0 to bioconductor package r-mscoreutils
* add version 2.26.0 to bioconductor package r-msnbase
* add version 2.56.0 to bioconductor package r-multtest
* add version 1.38.0 to bioconductor package r-mzid
* add version 2.34.0 to bioconductor package r-mzr
* add version 1.62.0 to bioconductor package r-oligoclasses
* update r-org-hs-eg-db
* add version 1.42.0 to bioconductor package r-organismdbi
* add version 1.40.0 to bioconductor package r-pathview
* add version 1.92.0 to bioconductor package r-pcamethods
* update r-pfam-db
* add version 1.44.0 to bioconductor package r-phyloseq
* add version 1.62.0 to bioconductor package r-preprocesscore
* add version 1.32.0 to bioconductor package r-protgenerics
* add version 1.34.0 to bioconductor package r-quantro
* add version 2.32.0 to bioconductor package r-qvalue
* add version 1.76.0 to bioconductor package r-rbgl
* add version 2.40.0 to bioconductor package r-reportingtools
* add version 2.44.0 to bioconductor package r-rgraphviz
* add version 2.44.0 to bioconductor package r-rhdf5
* add version 1.12.0 to bioconductor package r-rhdf5filters
* add version 1.22.0 to bioconductor package r-rhdf5lib
* add version 1.76.0 to bioconductor package r-roc
* add version 1.28.0 to bioconductor package r-rots
* add version 2.16.0 to bioconductor package r-rsamtools
* add version 1.60.0 to bioconductor package r-rtracklayer
* add version 0.38.0 to bioconductor package r-s4vectors
* add version 1.8.0 to bioconductor package r-scaledmatrix
* add version 1.28.0 to bioconductor package r-scater
* add version 1.14.0 to bioconductor package r-scdblfinder
* add version 1.28.0 to bioconductor package r-scran
* add version 1.10.0 to bioconductor package r-scuttle
* add version 1.66.0 to bioconductor package r-seqlogo
* add version 1.58.0 to bioconductor package r-shortread
* add version 1.74.0 to bioconductor package r-siggenes
* add version 1.22.0 to bioconductor package r-singlecellexperiment
* add version 1.34.0 to bioconductor package r-snprelate
* add version 1.50.0 to bioconductor package r-snpstats
* add version 2.36.0 to bioconductor package r-somaticsignatures
* add version 1.12.0 to bioconductor package r-sparsematrixstats
* add version 1.40.0 to bioconductor package r-spem
* add version 1.38.0 to bioconductor package r-sseq
* add version 1.30.0 to bioconductor package r-summarizedexperiment
* add version 3.48.0 to bioconductor package r-sva
* add version 1.38.0 to bioconductor package r-tfbstools
* add version 1.22.0 to bioconductor package r-tmixclust
* add version 2.52.0 to bioconductor package r-topgo
* add version 1.24.0 to bioconductor package r-treeio
* add version 1.28.0 to bioconductor package r-tximport
* add version 1.28.0 to bioconductor package r-tximportdata
* add version 1.46.0 to bioconductor package r-variantannotation
* add version 3.68.0 to bioconductor package r-vsn
* add version 2.6.0 to bioconductor package r-watermelon
* add version 2.46.0 to bioconductor package r-xde
* add version 1.58.0 to bioconductor package r-xmapbridge
* add version 0.40.0 to bioconductor package r-xvector
* add version 1.26.0 to bioconductor package r-yapsa
* add version 1.26.0 to bioconductor package r-yarn
* add version 1.46.0 to bioconductor package r-zlibbioc
* Revert "add version 1.82.0 to bioconductor package r-genefilter"
  This reverts commit 1702071c6d.
* Revert "add version 0.38.0 to bioconductor package r-s4vectors"
  This reverts commit 58a7df2387.
* add version 0.38.0 to bioconductor package r-s4vectors
* Revert "add version 1.28.0 to bioconductor package r-aneufinder"
  This reverts commit 0a1f59de6c.
* add version 1.28.0 to bioconductor package r-aneufinder
* Revert "add version 2.16.0 to bioconductor package r-beachmat"
  This reverts commit cd49fb8e4c.
* add version 2.16.0 to bioconductor package r-beachmat
* Revert "add version 4.8.0 to bioconductor package r-clusterprofiler"
  This reverts commit 6e9a951cbe.
* add version 4.8.0 to bioconductor package r-clusterprofiler
* Fix syntax error
* r-genefilter: add version 1.82.0
* new package: r-basilisk-utils
* new package: r-basilisk
* new package: r-densvis
* new package: r-dir-expiry
* r-affyplm: add zlib dependency
* r-cner: add zlib dependency
* r-mzr: add zlib dependency
* r-rhdf5filters: add zstd dependency
* r-shortread: add zlib dependency
* r-snpstats: add zlib dependency

---------

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-05-23 11:40:00 -07:00
snehring
a6886983dc usalign: new package (#37646)
* usalign: adding new package
* usalign: updating shasum, adding note about distribution
2023-05-23 11:30:40 -07:00
Andrey Parfenov
93a34a9635 hpcg: apply patch with openmp pragma changes for intel and oneapi compilers (#37856)
Signed-off-by: Andrey Parfenov <andrey.parfenov@intel.com>
2023-05-23 11:52:45 -04:00
Todd Gamblin
91a54029f9 libgcrypt: patch 1.10.2 on macos (#37844)
macOS doesn't have `getrandom`, and 1.10.2 fails to compile because of this.

There's an upstream fix at https://dev.gnupg.org/T6442 that will be in the next
`libgcrypt` release, but the patch is available now.
2023-05-23 06:03:13 -04:00
Juan Miguel Carceller
5400b49ed6 dd4hep: add LD_LIBRARY_PATH for plugins for Gaudi (#37824)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-05-23 10:28:26 +01:00
Juan Miguel Carceller
c17fc3c0c1 gaudi: add gaudi to LD_LIBRARY_PATH (#37821)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-05-23 10:27:55 +01:00
Juan Miguel Carceller
6f248836ea dd4hep: restrict podio versions (#37699)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-05-23 10:20:31 +01:00
snehring
693c1821b0 py-pastml: adding version for compatibility with py-topiary-asr (#37828) 2023-05-22 14:44:00 -05:00
Manuela Kuhn
62afe3bd5a py-asttokens: add 2.2.1 (#37816) 2023-05-22 14:40:08 -05:00
genric
53a756d045 py-dask: add v2023.4.1 (#37550)
* py-dask: add v2023.4.1

* address review comments
2023-05-22 14:29:23 -05:00
Adam J. Stewart
321b687ae6 py-huggingface-hub: add v0.14.1, cli variant (#37815) 2023-05-22 11:19:41 -07:00
Adam J. Stewart
c8617f0574 py-fiona: add v1.9.4 (#37780) 2023-05-22 13:17:13 -05:00
Adam J. Stewart
7843e2ead0 azcopy: add new package (#37693) 2023-05-22 11:09:06 -07:00
Juan Miguel Carceller
dca3d071d7 gaudi: fix issue with fmt::format (#37810)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-05-22 10:33:05 -07:00
eugeneswalker
436f077482 tau %oneapi: -Wno-error=implicit-function-declaration (#37829) 2023-05-22 13:13:02 -04:00
simonleary-umass-edu
ab3f705019 deleted package.py better error message (#37814)
adds the namespace to the exception object's string representation
2023-05-22 09:59:07 -07:00
Tamara Dahlgren
d739989ec8 swig: convert to new stand-alone test process (#37786) 2023-05-22 09:39:30 -07:00
Jordan Galby
52ee1967d6 llvm: Fix hwloc@1 and hwloc@:2.3 compatibility (#35387) 2023-05-22 10:28:57 -05:00
Andrey Prokopenko
1af7284b5d arborx: new version 1.4 (#37809) 2023-05-21 12:25:53 -07:00
Todd Gamblin
e1bcefd805 Update CHANGELOG.md for v0.20.0 2023-05-21 01:48:34 +02:00
Manuela Kuhn
2159b0183d py-argcomplete: add 3.0.8 (#37797)
* py-argcomplete: add 3.0.8

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

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

* [@spackbot] updating style on behalf of manuelakuhn

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-05-20 11:31:28 -05:00
kwryankrattiger
078fd225a9 Mochi-Margo: Add patch for pthreads detection (#36109) 2023-05-20 07:43:27 -07:00
Manuela Kuhn
83974828c7 libtiff: disable use of sphinx (#37803) 2023-05-19 21:37:19 -05:00
Manuela Kuhn
2412f74557 py-anyio: add 3.6.2 (#37796) 2023-05-19 21:36:39 -05:00
Manuela Kuhn
db06d3621d py-alabaster: add 0.7.13 (#37798) 2023-05-19 21:34:00 -05:00
Jose E. Roman
c25170d2f9 New patch release SLEPc 3.19.1 (#37675)
* New patch release SLEPc 3.19.1

* py-slepc4py: add explicit dependency on py-numpy
2023-05-19 21:33:21 -05:00
Vanessasaurus
b3dfe13670 Automated deployment to update package flux-security 2023-05-16 (#37696)
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2023-05-19 12:07:57 -07:00
Harmen Stoppels
6358e84b48 fix binutils dep of spack itself (#37738) 2023-05-19 12:02:36 -07:00
Swann Perarnau
8e634d8e49 aml: v0.2.1 (#37621)
* aml: v0.2.1

* add version 0.2.1
* fix hip variant bug

* [fix] pkgconf required for all builds

On top of needing pkgconf for autoreconf builds, the release configure
scripts needs pkgconf do detect dependencies if any of the hwloc, ze, or
opencl variants are active.

* Remove deprecation for v0.2.0 based on PR advise.
2023-05-19 11:58:28 -07:00
Mark W. Krentel
1a21376515 intel-xed: add version 2023.04.16 (#37582)
* intel-xed: add version 2023.04.16
 1. add version 2023.04.16
 2. adjust the mbuild resource to better match the xed version at the time
 3. replace three conflicts() with one new requires() for x86_64 target
 4. add patch for libxed-ild for some new avx512 instructions
    * [@spackbot] updating style on behalf of mwkrentel
    * Fix the build for 2023.04.16.  XED requires its source directory to be exactly 'xed', so add a symlink.
 5. move the mbuild resource up one level, xed wants it to be in the same directory as the xed source dir
 6. deprecate 10.2019.03
    * semantic style fix: add OSError to except
    * [@spackbot] updating style on behalf of mwkrentel

---------

Co-authored-by: mwkrentel <mwkrentel@users.noreply.github.com>
2023-05-19 10:28:18 -07:00
Harmen Stoppels
bf45a2b6d3 spack env create: generate a view when newly created env has concrete specs (#37799) 2023-05-19 18:44:54 +02:00
Thomas-Ulrich
475ce955e7 hipsycl: add v0.9.4 (#37247) 2023-05-19 18:29:45 +02:00
Robert Underwood
5e44289787 updates for the libpressio ecosystem (#37764)
* updates for the libpressio ecosystem

* [@spackbot] updating style on behalf of robertu94

* style fix: remove FIXME

---------

Co-authored-by: Robert Underwood <runderwood@anl.gov>
Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
2023-05-19 09:24:31 -07:00
Massimiliano Culpo
e66888511f archspec: fix entry in the JSON file (#37793) 2023-05-19 09:57:57 -04:00
Tamara Dahlgren
e9e5beee1f fortrilinos: convert to new stand-alone test process (#37783) 2023-05-19 08:06:33 -04:00
Tamara Dahlgren
ffd134c09d formetis: converted to new stand-alone test process (#37785) 2023-05-19 08:05:23 -04:00
Massimiliano Culpo
bfadd5c9a5 lmod: allow core compiler to be specified with a version range (#37789)
Use CompilerSpec with satisfies instead of string equality tests

Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2023-05-19 13:21:40 +02:00
Greg Becker
16e9279420 compiler specs: do not print '@=' when clear from context (#37787)
Ensure that spack compiler add/find/list and lists of concrete specs
print the compiler effectively as {compiler.name}{@compiler.version}.

Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2023-05-19 11:31:27 +02:00
Satish Balay
ac0903ef9f llvm: add version 16.0.3 (#37472) 2023-05-19 03:37:57 -04:00
Cyrus Harrison
648839dffd add conduit 0.8.8 release (#37776) 2023-05-19 00:34:19 -04:00
Pieter Ghysels
489a604920 Add STRUMPACK versions 7.1.2 and 7.1.3 (#37779) 2023-05-18 23:18:50 -04:00
eugeneswalker
2ac3435810 legion +rocm: apply patch for --offload-arch (#37775)
* legion +rocm: apply patch for --offload-arch

* constrain to latest version
2023-05-18 23:03:50 -04:00
Alec Scott
69ea180d26 fzf: add v0.40.0 and refactor package (#37569)
* fzf: add v0.40.0 and refactor package
* Remove unused imports
2023-05-18 15:23:20 -07:00
Alec Scott
f52f217df0 roctracer-dev-api: add v5.5.0 (#37484) 2023-05-18 15:11:36 -07:00
Alec Scott
df74aa5d7e amqp-cpp: add v4.3.24 (#37504) 2023-05-18 15:09:30 -07:00
Alec Scott
41932c53ae libjwt: add v1.15.3 (#37521) 2023-05-18 15:05:27 -07:00
Alec Scott
4296db794f rdkit: add v2023_03_1 (#37529) 2023-05-18 15:05:07 -07:00
H. Joe Lee
9ab9302409 py-jarvis-util: add a new package (#37729)
* py-jarvis-util: add a new package

* Apply suggestions from code review

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-05-18 17:28:59 -04:00
Benjamin Meyers
0187376e54 Update py-nltk (#37703)
* Update py-nltk

* [@spackbot] updating style on behalf of meyersbs

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

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-05-18 17:14:20 -04:00
Aditya Bhamidipati
7340d2cb83 update package nccl version 2.17, 2.18 (#37721) 2023-05-18 15:47:01 -05:00
Benjamin Meyers
641d4477d5 New package py-tensorly (#37705) 2023-05-18 15:38:23 -05:00
Benjamin Meyers
3ff2fb69af New package py-scikit-tensor-py3 (#37706) 2023-05-18 15:37:43 -05:00
vucoda
e3024b1bcb Update py-jedi 0.17.2 checksum in package.py (#37700)
Pypi for jedi-0.17.2.tar.gz does not match the package.py file.

https://pypi.org/project/jedi/0.17.2/#copy-hash-modal-60e943e3-1192-4b12-90e2-4d639cb5b4f7
2023-05-18 15:15:47 -05:00
Dom Heinzeller
e733b87865 Remove references to gmake executable, only use make (#37280) 2023-05-18 19:03:03 +00:00
Victor Lopez Herrero
919985dc1b dlb: add v3.3.1 (#37759) 2023-05-18 10:29:41 -07:00
Michael Kuhn
d746f7d427 harfbuzz: add 7.3.0 (#37753)
Do not prefer 5.3.1 anymore since it does not build with newer compilers. Linux distributions have also moved to 6.x and newer.
2023-05-18 10:27:48 -07:00
kaanolgu
b6deab515b [babelstream] FIX: maintainers list missing a comma (#37761) 2023-05-18 10:25:04 -07:00
Glenn Johnson
848220c4ba update R: add version 4.3.0 (#37090) 2023-05-18 10:13:28 -07:00
Glenn Johnson
98462bd27e Cran updates (#37296)
* add version 1.28.3 to r-hexbin
* add version 5.0-1 to r-hmisc
* add version 0.5.5 to r-htmltools
* add version 1.6.2 to r-htmlwidgets
* add version 1.4.2 to r-igraph
* add version 0.42.19 to r-imager
* add version 1.0-5 to r-inum
* add version 0.9-14 to r-ipred
* add version 1.3.2 to r-irkernel
* add version 2.2.0 to r-janitor
* add version 0.1-10 to r-jpeg
* add version 1.2.2 to r-jsonify
* add version 0.9-32 to r-kernlab
* add version 1.7-2 to r-klar
* add version 1.42 to r-knitr
* add version 1.14.0 to r-ks
* add version 2.11.0 to r-labelled
* add version 1.7.2.1 to r-lava
* add version 0.6-15 to r-lavaan
* add version 2.1.2 to r-leaflet
* add version 2.9-0 to r-lfe
* add version 1.1.6 to r-lhs
* add version 1.1-33 to r-lme4
* add version 1.5-9.7 to r-locfit
* add version 0.4.3 to r-log4r
* add version 5.6.18 to r-lpsolve
* add version 0.2-11 to r-lwgeom
* add version 2.7.4 to r-magick
* add version 1.22.1 to r-maldiquant
* add version 1.2.11 to r-mapproj
* add version 1.6 to r-markdown
* add version 7.3-59 to r-mass
* add version 1.5-4 to r-matrix
* add version 0.63.0 to r-matrixstats
* add version 4.2-3 to r-memuse
* add version 4.0-0 to r-metafor
* add version 1.8-42 to r-mgcv
* add version 3.15.0 to r-mice
* add version 0.4-5 to r-mitml
* add version 2.0.0 to r-mixtools
* add version 0.1.11 to r-modelr
* add version 1.4-23 to r-multcomp
* add version 0.1-9 to r-multcompview
* add version 0.1-13 to r-mutoss
* add version 1.18.1 to r-network
* add version 3.3.4 to r-nleqslv
* add version 3.1-162 to r-nlme
* add version 0.26 to r-nmf
* add version 0.60-17 to r-np
* add version 4.2.5.2 to r-openxlsx
* add version 2022.11-16 to r-ordinal
* add version 0.6.0.8 to r-osqp
* add version 0.9.1 to r-packrat
* add version 1.35.0 to r-parallelly
* add version 1.3-13 to r-party
* add version 1.2-20 to r-partykit
* add version 1.7-0 to r-pbapply
* add version 0.3-9 to r-pbdzmq
* add version 1.2 to r-pegas
* add version 1.5-1 to r-phytools
* add version 1.9.0 to r-pillar
* add version 1.4.0 to r-pkgbuild
* add version 2.1.0 to r-pkgcache
* add version 0.5.0 to r-pkgdepends
* add version 2.0.7 to r-pkgdown
* add version 1.3.2 to r-pkgload
* add version 0.1-8 to r-png
* add version 1.1.22 to r-polspline
* add version 1.0.1 to r-pool
* add version 1.4.1 to r-posterior
* add version 3.8.1 to r-processx
* add version 2023.03.31 to r-prodlim
* add version 1.0-12 to r-proj4
* add version 2.5.0 to r-projpred
* add version 0.1.6 to r-pryr
* add version 1.7.5 to r-ps
* add version 1.0.1 to r-purrr
* add version 1.3.2 to r-qqconf
* add version 0.25.5 to r-qs
* add version 1.60 to r-qtl
* add version 0.4.22 to r-quantmod
* add version 5.95 to r-quantreg
* add version 0.7.8 to r-questionr
* add version 1.2.5 to r-ragg
* add version 0.15.1 to r-ranger
* add version 3.6-20 to r-raster
* add version 2.2.13 to r-rbibutils
* add version 1.0.10 to r-rcpp
* add version 0.12.2.0.0 to r-rcpparmadillo
* add version 0.1.7 to r-rcppde
* add version 0.3.13 to r-rcppgsl
* add version 1.98-1.12 to r-rcurl
* add version 1.2-1 to r-rda
* add version 2.1.4 to r-readr
* add version 1.4.2 to r-readxl
* add version 1.0.6 to r-recipes
* add version 1.1.6 to r-repr
* add version 1.2.16 to r-reproducible
* add version 0.3.0 to r-require
* add version 1.28 to r-reticulate
* add version 2.0.7 to r-rfast
* add version 1.6-6 to r-rgdal
* add version 0.6-2 to r-rgeos
* add version 1.1.3 to r-rgl
* add version 0.2.18 to r-rinside
* add version 4-14 to r-rjags
* add version 1.3-1.8 to r-rjsonio
* add version 2.21 to r-rmarkdown
* add version 0.9-2 to r-rmpfr
* add version 0.7-1 to r-rmpi
* add version 6.6-0 to r-rms
* add version 0.10.25 to r-rmysql
* add version 0.8.7 to r-rncl
* add version 2.4.11 to r-rnexml
* add version 0.95-1 to r-robustbase
* add version 1.3-20 to r-rodbc
* add version 7.2.3 to r-roxygen2
* add version 1.4.5 to r-rpostgres
* add version 0.7-5 to r-rpostgresql
* add version 0.8.29 to r-rsconnect
* add version 0.4-15 to r-rsnns
* add version 2.3.1 to r-rsqlite
* add version 0.7.2 to r-rstatix
* add version 1.1.2 to r-s2
* add version 0.4.5 to r-sass
* add version 0.1.9 to r-scatterpie
* add version 0.3-43 to r-scatterplot3d
* add version 3.2.4 to r-scs
* add version 1.6-4 to r-segmented
* add version 4.2-30 to r-seqinr
* add version 0.26 to r-servr
* add version 4.3.0 to r-seurat
* add version 1.0-12 to r-sf
* add version 0.4.2 to r-sfheaders
* add version 1.1-15 to r-sfsmisc
* add version 1.7.4 to r-shiny
* add version 1.9.0 to r-signac
* add version 1.6.0.3 to r-smoof
* add version 0.1.7-1 to r-sourcetools
* add version 1.6-0 to r-sp
* add version 1.3-0 to r-spacetime
* add version 7.3-16 to r-spatial
* add version 2.0-0 to r-spatialeco
* add version 1.2-8 to r-spatialreg
* add version 3.0-5 to r-spatstat
* add version 3.0-1 to r-spatstat-data
* add version 3.1-0 to r-spatstat-explore
* add version 3.1-0 to r-spatstat-geom
* add version 3.1-0 to r-spatstat-linnet
* add version 3.1-4 to r-spatstat-random
* add version 3.0-1 to r-spatstat-sparse
* add version 3.0-2 to r-spatstat-utils
* add version 2.2.2 to r-spdata
* add version 1.2-8 to r-spdep
* add version 0.6-1 to r-stars
* add version 1.5.0 to r-statmod
* add version 4.8.0 to r-statnet-common
* add version 1.7.12 to r-stringi
* add version 1.5.0 to r-stringr
* add version 1.9.1 to r-styler
* add version 3.5-5 to r-survival
* add version 1.5-4 to r-tclust
* add version 1.7-29 to r-terra
* add version 3.1.7 to r-testthat
* add version 1.1-2 to r-th-data
* add version 1.2 to r-tictoc
* add version 1.3.2 to r-tidycensus
* add version 1.2.3 to r-tidygraph
* add version 1.3.0 to r-tidyr
* add version 2.0.0 to r-tidyverse
* add version 0.2.0 to r-timechange
* add version 0.45 to r-tinytex
* add version 0.4.1 to r-triebeard
* add version 1.0-9 to r-truncnorm
* add version 0.10-53 to r-tseries
* add version 0.8-1 to r-units
* add version 4.3.0 to r-v8
* add version 1.4-11 to r-vcd
* add version 1.14.0 to r-vcfr
* add version 0.6.2 to r-vctrs
* add version 1.1-8 to r-vgam
* add version 0.4.0 to r-vioplot
* add version 1.6.1 to r-vroom
* add version 1.72-1 to r-wgcna
* add version 0.4.1 to r-whisker
* add version 0.7.2 to r-wk
* add version 0.39 to r-xfun
* add version 1.7.5.1 to r-xgboost
* add version 1.0.7 to r-xlconnect
* add version 3.99-0.14 to r-xml
* add version 0.13.1 to r-xts
* add version 2.3.7 to r-yaml
* add version 2.3.0 to r-zip
* add version 1.8-12 to r-zoo
* r-bigmem: dependency on uuid
* r-bio3d: dependency on zlib
* r-devtools: dependency cleanup
* r-dose: dependency cleanup
* r-dss: dependency cleanup
* r-enrichplot: dependency cleanup
* r-fgsea: dependency cleanup
* r-geor: dependency cleanup
* r-ggridges: dependency cleanup
* r-lobstr: dependency cleanup
* r-lubridate: dependency cleanup
* r-mnormt: dependency cleanup
* r-sctransform: version format correction
* r-seuratobject: dependency cleanup
* r-tidyselect: dependency cleanup
* r-tweenr: dependency cleanup
* r-uwot: dependency cleanup
* new package: r-clock
* new package: r-conflicted
* new package: r-diagram
* new package: r-doby
* new package: r-httr2
* new package: r-kableextra
* new package: r-mclogit
* new package: r-memisc
* new package: r-spatstat-model
* r-rmysql: use mariadb-client
* r-snpstats: add zlib dependency
* r-qs: add zstd dependency
* r-rcppcnpy: add zlib dependency
* black reformatting
* Revert "r-dose: dependency cleanup"
  This reverts commit 4c8ae8f5615ee124fff01ce43eddd3bb5d06b9bc.
* Revert "r-dss: dependency cleanup"
  This reverts commit a6c5c15c617a9a688fdcfe2b70c501c3520d4706.
* Revert "r-enrichplot: dependency cleanup"
  This reverts commit 65e116c18a94d885bc1a0ae667c1ef07d1fe5231.
* Revert "r-fgsea: dependency cleanup"
  This reverts commit ffe2cdcd1f73f69d66167b941970ede0281b56d7.
* r-rda: this package is back in CRAN
* r-sctransform: fix copyright
* r-seurat: fix copyright
* r-seuratobject: fix copyright
* Revert "add version 6.0-94 to r-caret"
  This reverts commit 236260597de97a800bfc699aec1cd1d0e3d1ac60.
* add version 6.0-94 to r-caret
* Revert "add version 1.8.5 to r-emmeans"
  This reverts commit 64a129beb0bd88d5c88fab564cade16c03b956ec.
* add version 1.8.5 to r-emmeans
* Revert "add version 5.0-1 to r-hmisc"
  This reverts commit 517643f4fd8793747365dfcfc264b894d2f783bd.
* add version 5.0-1 to r-hmisc
* Revert "add version 1.42 to r-knitr"
  This reverts commit 2a0d9a4c1f0ba173f7423fed59ba725bac902c37.
* add version 1.42 to r-knitr
* Revert "add version 1.6 to r-markdown"
  This reverts commit 4b5565844b5704559b819d2e775fe8dec625af99.
* add version 1.6 to r-markdown
* Revert "add version 0.26 to r-nmf"
  This reverts commit 4c44a788b17848f2cda67b32312a342c0261caec.
* add version 0.26 to r-nmf
* Revert "add version 2.3.1 to r-rsqlite"
  This reverts commit 5722ee2297276e4db8beee461d39014b0b17e420.
* add version 2.3.1 to r-rsqlite
* Revert "add version 1.0-12 to r-sf"
  This reverts commit ee1734fd62cc02ca7a9359a87ed734f190575f69.
* add version 1.0-12 to r-sf
* fix syntax error
2023-05-18 09:57:43 -07:00
Cameron Stanavige
2e2515266d unifyfs: new v1.1 release (#37756)
Add v1.1 release
Update mochi-margo dependency compatible versions
Update version range of libfabric conflict
2023-05-18 09:42:27 -07:00
Chris Green
776ab13276 [xrootd] New variants, new version, improve build config (#37682)
* Add FNAL Spack team to maintainers

* New variants and configuration improvements

* Version dependent "no-systemd" patches.

* New variants `client_only`, and `davix`

* Better handling of `cxxstd` for different versions, including
  improved patching and CMake options.

* Version-specific CMake requirements.

* Better version-specific handling of `openssl` dependency.

* `py-setuptools` required for `+python` build.

* Specific enable/disable of CMake options and use of
  `-DFORCE_ENABLED=TRUE` to prevent unwanted/non-portable activation
  of features.

* Better handling of `+python` configuration.

* New version 5.5.5
2023-05-18 10:49:18 -05:00
Massimiliano Culpo
c2ce9a6d93 Bump Spack version on develop to 0.21.0.dev0 (#37760) 2023-05-18 12:47:55 +02:00
Peter Scheibel
4e3ed56dfa Bugfix: allow preferred new versions from externals (#37747) 2023-05-18 09:40:26 +02:00
Tamara Dahlgren
dcfcc03497 maintainers: switch from list to directive (#37752) 2023-05-17 22:25:57 +00:00
Stephen Sachs
125c20bc06 Add aws-plcuster[-aarch64] stacks (#37627)
Add aws-plcuster[-aarch64] stacks.  These stacks build packages defined in
https://github.com/spack/spack-configs/tree/main/AWS/parallelcluster

They use a custom container from https://github.com/spack/gitlab-runners which
includes necessary ParallelCluster software to link and build as well as an
upstream spack installation with current GCC and dependencies.

Intel and ARM software is installed and used during the build stage but removed
from the buildcache before the signing stage.

Files `configs/linux/{arch}/ci.yaml` select the necessary providers in order to
build for specific architectures (icelake, skylake, neoverse_{n,v}1).
2023-05-17 16:21:10 -06:00
Brian Van Essen
f7696a4480 Added version 1.3.1 (#37735) 2023-05-17 14:51:02 -07:00
Harmen Stoppels
a5d7667cb6 lmod: fix build, bump patch version (#37744) 2023-05-17 13:18:02 -04:00
Massimiliano Culpo
d45818ccff Limit deepcopy to just the initial "all" section (#37718)
Modifications:
- [x] Limit the scope of the deepcopy when initializing module file writers
2023-05-17 10:17:41 -07:00
Scott Wittenburg
bcb7af6eb3 gitlab ci: no copy-only pipelines w/ deprecated config (#37720)
Make it clear that copy-only pipelines are not supported while still
using the deprecated ci config format. Also ensure that the deprecated
stack does not fail on spack pipelines for tags.
2023-05-17 09:46:30 -06:00
Juan Miguel Carceller
f438fb6c79 whizard: build newer versions in parallel (#37422) 2023-05-17 17:15:50 +02:00
Harmen Stoppels
371a8a361a libxcb: depend on python, remove releases that need python 2 (#37698) 2023-05-17 17:05:30 +02:00
Tamara Dahlgren
86b9ce1c88 spack test: fix stand-alone test suite status reporting (#37602)
* Fix reporting of packageless specs as having no tests

* Add test_test_output_multiple_specs with update to simple-standalone-test (and tests)

* Refactored test status summary; added more tests or checks
2023-05-17 16:03:21 +02:00
Seth R. Johnson
05232034f5 celeritas: new version 0.2.2 (#37731)
* celeritas: new version 0.2.2

* [@spackbot] updating style on behalf of sethrj
2023-05-17 05:38:09 -04:00
Peter Scheibel
7a3da0f606 Tk/Tcl packages: speed up file search (#35902) 2023-05-17 09:27:05 +02:00
Yoshiaki Senda
d96406a161 Add recently added Spack Docker Images to documentation (#37732)
Signed-off-by: Yoshiaki Senda <yoshiaki@live.it>
2023-05-17 08:48:27 +02:00
Tamara Dahlgren
ffa5962356 emacs: convert to new stand-alone test process (#37725) 2023-05-17 00:25:35 -04:00
Massimiliano Culpo
67e74da3ba Fix spack find not able to display version ranges in compilers (#37715) 2023-05-17 00:24:38 -04:00
Chris Green
9ee2d79de1 libxpm package: fix RHEL8 build with libintl (#37713)
Set LDFLAGS rather than LDLIBS
2023-05-16 13:32:26 -05:00
John W. Parent
79e4a13eee Windows: fix MSVC version handling (#37711)
MSVC compiler logic was using string parsing to extract version
from compiler spec, which was fragile. This broke in #37572, so has
been fixed and made more robust by using attribute access.
2023-05-16 11:00:55 -07:00
kwryankrattiger
4627438373 CI: Expand E4S ROCm stack to include missing DaV packages (#36843)
* CI: Expand E4S ROCm stack to include missing DaV packages

Ascent: Fixup for VTK-m with Kokkos backend

* DaV SDK: Removed duplicated openmp variant for ascent

* Drop visit and add conflict for Kokkos

* E4S: Drop ascent from CUDA builds
2023-05-16 09:34:52 -05:00
Harmen Stoppels
badaaf7092 gha rhel8-platform-python: configure git safe.directory (#37708) 2023-05-16 16:31:13 +02:00
Harmen Stoppels
815ac000cc Revert "hdf5: fix showconfig (#34920)" (#37707)
This reverts commit 192e564e26.
2023-05-16 15:57:15 +02:00
Peter Scheibel
7bc5b26c52 Requirements and preferences should not define (non-git) versions (#37687)
Ensure that requirements `packages:*:require:@x` and preferences `packages:*:version:[x]`
fail concretization when no version defined in the package satisfies `x`. This always holds
except for git versions -- they are defined on the fly.
2023-05-16 15:45:11 +02:00
Harmen Stoppels
a0e7ca94b2 gha bootstrap-dev-rhel8: configure git safe.directory (#37702)
git has been updated to something more recent
2023-05-16 15:21:42 +02:00
Harmen Stoppels
e56c90d839 check_modules_set_name: do not check for "enable" key (#37701) 2023-05-16 11:51:52 +02:00
Ye Luo
54003d4d72 Update llvm recipe regarding libomptarget. (#36675) 2023-05-16 11:20:02 +02:00
QuellynSnead
c47b554fa1 libxcb/xcb-proto: Enable internal Python dependency (#37575)
In the past, Spack did not allow two different versions of the
same package within a DAG. That led to difficulties with packages
that still required Python 2 while other packages had already
switched to Python 3.

The libxcb and xcb-proto packages did not have Python 3 support
for a time. To get around this issue, Spack maintainers disabled
their dependency on an internal (i.e., Spack-provided) Python
(see #4145),forcing these packages to look for a system-provided
Python (see #7646).

This has worked for us all right, but with the arrival of our most
recent platform we seem to be missing the critical xcbgen Python
module on the system. Since most software has largely moved on to
Python 3 now, let's re-enable internal Spack dependencies for the
libxcb and xcb-proto packages.
2023-05-16 10:00:01 +02:00
Mikael Simberg
b027f64a7f Add conflict for pika with fmt@10 and +cuda/rocm (#37679) 2023-05-16 09:24:02 +02:00
Greg Becker
3765a5f7f8 unify: when_possible and unify: true -- Bugfix for error in 37438 (#37681)
Two bugs came in from #37438

1. `unify: when_possible` was broken, because of an incorrect assertion. abstract/concrete
   spec pairs were compared against the results that were in the process of being computed,
   rather than against the previous results.
2. `unify: true` had an ordering bug that could mix the association between abstract and
   concrete specs

- [x] 1 is resolved by creating a lookup from old concrete specs to old abstract specs,
      and we use that to associate the "new" concrete specs that happen to be the old
      ones with their abstract specs (since those are stripped out for concretization
- [x] 2 is resolved by combining the new and old abstract as lists instead of combining
      them as sets. This is important because `set() | set()` does not make any ordering
      promises, even though set ordering is otherwise guaranteed in `python@3.7:`
2023-05-16 01:08:34 -04:00
Robert Blake
690661eadd Upgrading kosh to 3.0 (#37471)
* Upgrading kosh to 3.0.

* Accidentally regressed the package, changing back.

* Updating py-hdbscan versions for kosh.

* Fixing bug in patch.

* Adding 3.0.1

* Removing 3.0.

* Updating package deps for hdbscan to match requirements.txt.

* Version reqs for 3.0.*, need newer numpy and networkx

* spack style

* Reordering to match setup.py, adding "type" to python depends.
2023-05-16 01:08:20 -04:00
eugeneswalker
f7bbc326e4 trilinos: @develop fixes (#37615)
* trilinos@develop fixes

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

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

---------

Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>
2023-05-15 17:25:14 -07:00
Scott Wittenburg
a184bfc1a6 gitlab ci: reduce job name length of build_systems pipeline (#37686) 2023-05-16 00:26:37 +02:00
Alec Scott
81634440fb circos: add v0.69-9 (#37479) 2023-05-15 14:43:44 -07:00
Alec Scott
711d7683ac alluxio: add v2.9.3 (#37488) 2023-05-15 14:42:48 -07:00
Alec Scott
967356bcf5 codec2: add v1.1.0 (#37480) 2023-05-15 14:42:08 -07:00
Alec Scott
c006ed034a coinutils: add v2.11.9 (#37481) 2023-05-15 14:41:25 -07:00
Alec Scott
d065c65d94 g2c: add v1.7.0 (#37482) 2023-05-15 14:40:41 -07:00
Alec Scott
e23c372ff1 shadow: add v4.13 (#37485) 2023-05-15 14:38:32 -07:00
Alec Scott
25d2de5629 yoda: add v1.9.8 (#37487) 2023-05-15 14:37:31 -07:00
Alec Scott
d73a23ce35 cpp-httplib: add v0.12.3 (#37490) 2023-05-15 14:35:32 -07:00
Alec Scott
a62cb3c0f4 entt: add v3.11.1 (#37491) 2023-05-15 14:34:47 -07:00
Alec Scott
177da4595e harfbuzz: add v7.2.0 (#37492) 2023-05-15 14:34:06 -07:00
Alec Scott
e4f05129fe libconfuse: add v3.3 (#37493) 2023-05-15 14:33:19 -07:00
Alec Scott
c25b994917 libnsl: add v2.0.0 (#37494) 2023-05-15 14:32:49 -07:00
Alec Scott
95c4c5270a p11-kit: add v0.24.1 (#37495) 2023-05-15 14:31:43 -07:00
Alec Scott
1cf6a15a08 packmol: add v20.0.0 (#37496)
* packmol: add v20.0.0
* Fix zoltan homepage url
2023-05-15 14:29:01 -07:00
Alec Scott
47d206611a perl-module-build-tiny: add v0.044 (#37497) 2023-05-15 14:25:53 -07:00
Alec Scott
a6789cf653 zoltan: add v3.901 (#37498) 2023-05-15 14:25:00 -07:00
Alec Scott
933cd858e0 bdii: add v6.0.1 (#37499) 2023-05-15 14:24:14 -07:00
Alec Scott
8856361076 audit-userspace: add v3.1.1 (#37505) 2023-05-15 14:15:48 -07:00
Alec Scott
d826df7ef6 babl: add v0.1.106 (#37506) 2023-05-15 14:15:28 -07:00
Alec Scott
d8a9b42da6 actsvg: add v0.4.33 (#37503) 2023-05-15 14:14:45 -07:00
Alec Scott
7d926f86e8 bat: add v0.23.0 (#37507) 2023-05-15 14:09:51 -07:00
Alec Scott
1579544d57 beast-tracer: add v1.7.2 (#37508) 2023-05-15 14:09:18 -07:00
Alec Scott
1cee3fb4a5 cronie: add v1.6.1 (#37509) 2023-05-15 14:08:41 -07:00
Alec Scott
a8e2ad53dd cups: add v2.3.3 (#37510) 2023-05-15 14:08:09 -07:00
Alec Scott
6821fa7246 diamond: add v2.1.6 (#37511) 2023-05-15 14:07:31 -07:00
Alec Scott
09c68da1bd dust: add v0.8.6 (#37513) 2023-05-15 14:06:31 -07:00
Alec Scott
73064d62cf f3d: add v2.0.0 (#37514) 2023-05-15 14:05:37 -07:00
Alec Scott
168ed2a782 fullock: add v1.0.50 (#37515) 2023-05-15 14:02:36 -07:00
Alec Scott
9f60b29495 graphviz: add v8.0.5 (#37517) 2023-05-15 14:00:50 -07:00
Alec Scott
7abcd78426 krakenuniq: add v1.0.4 (#37519) 2023-05-15 13:59:15 -07:00
Alec Scott
d5295301de libfyaml: add v0.8 (#37520) 2023-05-15 13:58:13 -07:00
Alec Scott
beccc49b81 libluv: add v1.44.2-1 (#37522) 2023-05-15 13:55:57 -07:00
Alec Scott
037e7ffe33 libvterm: add v0.3.1 (#37524) 2023-05-15 13:54:15 -07:00
Alec Scott
293da8ed20 lighttpd: add v1.4.69 (#37525) 2023-05-15 13:53:30 -07:00
Alec Scott
2780ab2f6c mrchem: add v1.1.2 (#37526) 2023-05-15 13:51:54 -07:00
Alec Scott
1ed3c81b58 mutationpp: add v1.0.5 (#37527) 2023-05-15 13:50:48 -07:00
Alec Scott
50ce0a25b2 preseq: add v2.0.3 (#37528) 2023-05-15 13:49:47 -07:00
Alec Scott
d784227603 shtools: add v4.10.2 (#37530) 2023-05-15 13:47:15 -07:00
Alec Scott
ab9ed91539 tig: add v2.5.8 (#37531) 2023-05-15 13:46:03 -07:00
Alec Scott
421256063e trimgalore: add v0.6.9 (#37532) 2023-05-15 13:44:44 -07:00
Alec Scott
75459bc70c vdt: add v0.4.4 (#37533) 2023-05-15 13:43:40 -07:00
Carson Woods
33752eabb8 Improve package source code context display on error (#37655)
Spack displays package code context when it shouldn't (e.g., on `FetchError`s)
and doesn't display it when it should (e.g., when errors occur in builder classes.
The line attribution can sometimes be off by one, as well.

- [x] Display package context when errors occur in a subclass of `PackageBase`
- [x] Display package context when errors occur in a subclass of `BaseBuilder`
- [x] Do not display package context when errors occur in `PackageBase`,
      `BaseBuilder` or other core code that is not in a `package.py` file.
- [x] Fix off-by-one error for core code (don't subtract one from the line number *unless*
      it's in an actual `package.py` file.

---------

Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2023-05-15 13:38:11 -07:00
Alec Scott
f1d1bb9167 gsl-lite: add v0.41.0 (#37483) 2023-05-15 13:36:03 -07:00
Alec Scott
68eaff24b0 crtm-fix: correct invalid checksum for v2.4.0 (#37500) 2023-05-15 13:34:32 -07:00
Alec Scott
862024cae1 dos2unix: add v7.4.4 (#37512) 2023-05-15 13:31:19 -07:00
Adam J. Stewart
9d6bcd67c3 Update PyTorch ecosystem (#37562) 2023-05-15 13:29:44 -07:00
Chris White
d97ecfe147 SUNDIALS: new version of sundials and guard against examples being install (#37576)
* add new version of sundials and guard against examples not installing
* fix flipping of variant
* fix directory not being there when writing a file
2023-05-15 13:21:37 -07:00
Alec Scott
0d991de50a subversion: add v1.14.2 (#37543) 2023-05-15 13:16:04 -07:00
Alec Scott
4f278a0255 go: add v1.20.4 (#37660)
* go: add v1.20.4
* Deprecate v1.20.2 and v1.19.7 due to CVE-2023-24538
2023-05-15 13:10:02 -07:00
Chris Green
6e72a3cff1 [davix] Enable third party copies with gSOAP (#37648)
* [davix] Enable third party copies with gSOAP

* Add FNAL Spack team to maintainers
2023-05-15 14:46:52 -05:00
snehring
1532c77ce6 micromamba: adding version 1.4.2 (#37594)
* micromamba: adding version 1.4.2
* micromamba: change to micromamba-1.4.2 tag artifacts
2023-05-15 10:40:54 -07:00
Mikael Simberg
5ffbce275c Add ut (#37603) 2023-05-15 10:35:55 -07:00
Carsten Uphoff
0e2ff2dddb Add double-batched FFT library v0.4.0 (#37616)
Signed-off-by: Carsten Uphoff <carsten.uphoff@intel.com>
2023-05-15 10:28:52 -07:00
Mikael Simberg
c0c446a095 stdexec: Add 23.03 (#37638) 2023-05-15 10:20:12 -07:00
snehring
33dbd44449 tmscore: adding new package (#37644) 2023-05-15 10:17:50 -07:00
Sean Koyama
7b0979c1e9 hwloc: explicitly disable building netloc for ~netloc (#35604)
* hwloc: explicitly disable building netloc for ~netloc

* hwloc: update syntax for netloc variant configure argument

---------

Co-authored-by: Sean Koyama <skoyama@anl.gov>
2023-05-15 12:16:21 -05:00
snehring
c9849dd41d tmalign: new version 20220412 (#37645) 2023-05-15 10:14:58 -07:00
Chris Green
d44e97d3f2 [scitokens-cpp] New variant cxxstd, depend on standalone jwt-cpp (#37643)
* Add FNAL Spack team to maintainers
* New variant `cxxstd`
* Depend on `jwt-cpp`
* New versions: 0.7.2, 0.7.3
2023-05-15 13:08:00 -04:00
Adam J. Stewart
8713ab0f67 py-timm: add v0.9 (#37654)
* py-timm: add v0.9
* add v0.9.1 and v0.9.2
* add new package py-safetensors (v0.3.1)
2023-05-15 09:41:58 -07:00
Harmen Stoppels
6a47339bf8 oneapi: before script load modules (#37678) 2023-05-15 18:39:58 +02:00
Alec Scott
1c0fb6d641 amrfinder: add v3.11.8 (#37656) 2023-05-15 09:38:29 -07:00
Alec Scott
b45eee29eb canal: add v1.1.6 (#37657) 2023-05-15 09:36:17 -07:00
Alec Scott
6d26274459 code-server: add v4.12.0 (#37658) 2023-05-15 09:35:17 -07:00
Alec Scott
2fb07de7bc fplll: add v5.4.4 (#37659) 2023-05-15 09:34:13 -07:00
Alec Scott
7678dc6b49 iso-codes: add v4.15.0 (#37661) 2023-05-15 09:27:05 -07:00
Frank Willmore
1944dd55a7 Update package.py for maker (#37662) 2023-05-15 09:25:43 -07:00
Adam J. Stewart
0b6c724743 py-sphinx: add v7.0.1 (#37665) 2023-05-15 09:23:22 -07:00
eugeneswalker
fa98023375 new pkg: py-psana (#37666) 2023-05-15 09:19:54 -07:00
Todd Gamblin
e79a911bac bugfix: allow reuse of packages from foreign namespaces
We currently throw a nasty error if you try to reuse packages from some other namespace
(e.g., OLCF), but we should be able to reuse patched local versions of builtin packages.

Right now the only obstacle to that is that we try to look up virtual info for unknown
namespaces, and we can't get the package from the repo to do that. We *can* assume that
a package with a known namespace is similar, and that its virtual provider information
is reasonably accurate, so we now do that. This isn't 100% accurate, but neither is
relying on the package itself, as it may have gone out of date.

The real solution here is virtual edge information, but this is a stopgap until we have
that.
2023-05-15 09:15:49 -07:00
Todd Gamblin
fd3efc71fd bugfix: don't look up virtual information for unknown packages
`spec_clauses()` attempts to look up package information for concrete specs in order to
determine which virtuals they may provide. This fails for renamed/deleted dependencies
of buildcaches and installed packages.

This will eventually be fixed by #35258, which adds virtual information on edges, but we
need a workaround to make older buildcaches usable.

- [x] make an exception for renamed packages and omit their virtual constraints
- [x] add a note that this will be solved by adding virtuals to edges
2023-05-15 09:15:49 -07:00
Todd Gamblin
0458de18de bugfix: don't look up patches from packages for concrete specs
The concretizer can fail with `reuse:true` if a buildcache or installation contains a
package with a dependency that has been renamed or deleted in the main repo (e.g.,
`netcdf` was refactored to `netcdf-c`, `netcdf-fortran`, etc., but there are still
binary packages with dependencies called `netcdf`).

We should still be able to install things for which we are missing `package.py` files.

`Spec.inject_patches_variant()` was failing this requirement by attempting to look up
the package class for concrete specs.  This isn't needed -- we can skip it.

- [x] swap two conditions in `Spec.inject_patches_variant()`
2023-05-15 09:15:49 -07:00
Vanessasaurus
f94ac8c770 add new package flux-security (#37668)
I will follow this up with a variant to flux-core to add flux-security, and then automation in the flux-framework/spack repository.

Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2023-05-15 09:14:44 -07:00
Andrew W Elble
a03c28a916 routinator: update, deprecate old version (#37676) 2023-05-15 09:10:40 -07:00
Victor Lopez Herrero
7b7fdf27f3 dlb: add v3.3 (#37677) 2023-05-15 09:08:57 -07:00
Sergey Kosukhin
192e564e26 hdf5: fix showconfig (#34920)
Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2023-05-15 11:03:03 -05:00
Chris Green
b8c5099cde [jwt-cpp] New package (#37641)
* [jwt-cpp] New package

* Update homepage

Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>

* [@spackbot] updating style on behalf of greenc-FNAL

---------

Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
Co-authored-by: greenc-FNAL <greenc-FNAL@users.noreply.github.com>
2023-05-15 10:16:11 -05:00
Stephen Sachs
ea5bca9067 palace: add v0.11.1 and explicit BLAS support (#37605) 2023-05-15 16:11:50 +02:00
Harmen Stoppels
e33eafd34f Bump tutorial command (#37674) 2023-05-15 13:54:52 +02:00
Xavier Delaruelle
e1344b5497 environment-modules: add version 5.3.0 (#37671) 2023-05-15 09:32:53 +02:00
1262 changed files with 13508 additions and 5727 deletions

View File

@@ -19,8 +19,8 @@ jobs:
package-audits:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
- uses: actions/setup-python@57ded4d7d5e986d7296eab16560982c6dd7c923b # @v2
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
- uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0 # @v2
with:
python-version: ${{inputs.python_version}}
- name: Install Python packages
@@ -38,7 +38,7 @@ jobs:
run: |
. share/spack/setup-env.sh
$(which spack) audit packages
- uses: codecov/codecov-action@894ff025c7b54547a9a2a1e9f228beae737ad3c2 # @v2.1.0
- uses: codecov/codecov-action@eaaf4bedf32dbdc6b720b63067d99c4d77d6047d # @v2.1.0
if: ${{ inputs.with_coverage == 'true' }}
with:
flags: unittests,linux,audits

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@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
with:
fetch-depth: 0
- name: Setup non-root user
@@ -62,7 +62,7 @@ jobs:
make patch unzip xz-utils python3 python3-dev tree \
cmake bison
- name: Checkout
uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
with:
fetch-depth: 0
- name: Setup non-root user
@@ -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@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
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@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
with:
fetch-depth: 0
- name: Setup repo
@@ -158,7 +158,7 @@ jobs:
run: |
brew install cmake bison@2.7 tree
- name: Checkout
uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
- name: Bootstrap clingo
run: |
source share/spack/setup-env.sh
@@ -179,11 +179,11 @@ jobs:
run: |
brew install tree
- name: Checkout
uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
- name: Bootstrap clingo
run: |
set -ex
for ver in '3.7' '3.8' '3.9' '3.10' '3.11' ; do
for ver in '3.6' '3.7' '3.8' '3.9' '3.10' ; do
not_found=1
ver_dir="$(find $RUNNER_TOOL_CACHE/Python -wholename "*/${ver}.*/*/bin" | grep . || true)"
echo "Testing $ver_dir"
@@ -204,7 +204,7 @@ jobs:
runs-on: ubuntu-20.04
steps:
- name: Checkout
uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
with:
fetch-depth: 0
- name: Setup repo
@@ -214,7 +214,7 @@ jobs:
- name: Bootstrap clingo
run: |
set -ex
for ver in '3.7' '3.8' '3.9' '3.10' '3.11' ; do
for ver in '3.6' '3.7' '3.8' '3.9' '3.10' ; do
not_found=1
ver_dir="$(find $RUNNER_TOOL_CACHE/Python -wholename "*/${ver}.*/*/bin" | grep . || true)"
echo "Testing $ver_dir"
@@ -247,7 +247,7 @@ jobs:
bzip2 curl file g++ gcc patchelf gfortran git gzip \
make patch unzip xz-utils python3 python3-dev tree
- name: Checkout
uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
with:
fetch-depth: 0
- name: Setup non-root user
@@ -283,7 +283,7 @@ jobs:
make patch unzip xz-utils python3 python3-dev tree \
gawk
- name: Checkout
uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
with:
fetch-depth: 0
- name: Setup non-root user
@@ -316,7 +316,7 @@ jobs:
# Remove GnuPG since we want to bootstrap it
sudo rm -rf /usr/local/bin/gpg
- name: Checkout
uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
- name: Bootstrap GnuPG
run: |
source share/spack/setup-env.sh
@@ -333,7 +333,7 @@ jobs:
# Remove GnuPG since we want to bootstrap it
sudo rm -rf /usr/local/bin/gpg
- name: Checkout
uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
- name: Bootstrap GnuPG
run: |
source share/spack/setup-env.sh

View File

@@ -49,14 +49,14 @@ jobs:
[almalinux8, 'linux/amd64,linux/arm64,linux/ppc64le', 'almalinux:8'],
[almalinux9, 'linux/amd64,linux/arm64,linux/ppc64le', 'almalinux:9'],
[rockylinux8, 'linux/amd64,linux/arm64', 'rockylinux:8'],
[rockylinux9, 'linux/amd64,linux/arm64,linux/ppc64le', 'rockylinux:9'],
[rockylinux9, 'linux/amd64,linux/arm64', 'rockylinux:9'],
[fedora37, 'linux/amd64,linux/arm64,linux/ppc64le', 'fedora:37'],
[fedora38, 'linux/amd64,linux/arm64,linux/ppc64le', 'fedora:38']]
name: Build ${{ matrix.dockerfile[0] }}
if: github.repository == 'spack/spack'
steps:
- name: Checkout
uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
- name: Set Container Tag Normal (Nightly)
run: |
@@ -92,13 +92,13 @@ jobs:
path: dockerfiles
- name: Set up QEMU
uses: docker/setup-qemu-action@e81a89b1732b9c48d79cd809d8d81d79c4647a18 # @v1
uses: docker/setup-qemu-action@2b82ce82d56a2a04d2637cd93a637ae1b359c0a7 # @v1
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@4b4e9c3e2d4531116a6f8ba8e71fc6e2cb6e6c8c # @v1
uses: docker/setup-buildx-action@ecf95283f03858871ff00b787d79c419715afc34 # @v1
- name: Log in to GitHub Container Registry
uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a # @v1
uses: docker/login-action@465a07811f14bebb1938fbed4728c6a1ff8901fc # @v1
with:
registry: ghcr.io
username: ${{ github.actor }}
@@ -106,13 +106,13 @@ jobs:
- name: Log in to DockerHub
if: github.event_name != 'pull_request'
uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a # @v1
uses: docker/login-action@465a07811f14bebb1938fbed4728c6a1ff8901fc # @v1
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
- name: Build & Deploy ${{ matrix.dockerfile[0] }}
uses: docker/build-push-action@3b5e8027fcad23fda98b2e3ac259d8d67585f671 # @v2
uses: docker/build-push-action@2eb1c1961a95fc15694676618e422e8ba1d63825 # @v2
with:
context: dockerfiles/${{ matrix.dockerfile[0] }}
platforms: ${{ matrix.dockerfile[1] }}

View File

@@ -35,7 +35,7 @@ jobs:
core: ${{ steps.filter.outputs.core }}
packages: ${{ steps.filter.outputs.packages }}
steps:
- uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
if: ${{ github.event_name == 'push' }}
with:
fetch-depth: 0

View File

@@ -0,0 +1,31 @@
name: Windows Paraview Nightly
on:
schedule:
- cron: '0 2 * * *' # Run at 2 am
defaults:
run:
shell:
powershell Invoke-Expression -Command "./share/spack/qa/windows_test_setup.ps1"; {0}
jobs:
build-paraview-deps:
runs-on: windows-latest
steps:
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
with:
fetch-depth: 0
- uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0
with:
python-version: 3.9
- name: Install Python packages
run: |
python -m pip install --upgrade pip six pywin32 setuptools coverage
- name: Build Test
run: |
spack compiler find
spack external find cmake ninja win-sdk win-wdk wgl msmpi
spack -d install -y --cdash-upload-url https://cdash.spack.io/submit.php?project=Spack+on+Windows --cdash-track Nightly --only dependencies paraview
exit 0

View File

@@ -47,10 +47,10 @@ jobs:
on_develop: false
steps:
- uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
with:
fetch-depth: 0
- uses: actions/setup-python@57ded4d7d5e986d7296eab16560982c6dd7c923b # @v2
- uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0 # @v2
with:
python-version: ${{ matrix.python-version }}
- name: Install System packages
@@ -87,17 +87,17 @@ jobs:
UNIT_TEST_COVERAGE: ${{ matrix.python-version == '3.11' }}
run: |
share/spack/qa/run-unit-tests
- uses: codecov/codecov-action@894ff025c7b54547a9a2a1e9f228beae737ad3c2
- uses: codecov/codecov-action@eaaf4bedf32dbdc6b720b63067d99c4d77d6047d
with:
flags: unittests,linux,${{ matrix.concretizer }}
# Test shell integration
shell:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
with:
fetch-depth: 0
- uses: actions/setup-python@57ded4d7d5e986d7296eab16560982c6dd7c923b # @v2
- uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0 # @v2
with:
python-version: '3.11'
- name: Install System packages
@@ -118,7 +118,7 @@ jobs:
COVERAGE: true
run: |
share/spack/qa/run-shell-tests
- uses: codecov/codecov-action@894ff025c7b54547a9a2a1e9f228beae737ad3c2
- uses: codecov/codecov-action@eaaf4bedf32dbdc6b720b63067d99c4d77d6047d
with:
flags: shelltests,linux
@@ -133,7 +133,7 @@ jobs:
dnf install -y \
bzip2 curl file gcc-c++ gcc gcc-gfortran git gnupg2 gzip \
make patch tcl unzip which xz
- uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
- name: Setup repo and non-root user
run: |
git --version
@@ -152,10 +152,10 @@ jobs:
clingo-cffi:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
with:
fetch-depth: 0
- uses: actions/setup-python@57ded4d7d5e986d7296eab16560982c6dd7c923b # @v2
- uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0 # @v2
with:
python-version: '3.11'
- name: Install System packages
@@ -176,7 +176,7 @@ jobs:
SPACK_TEST_SOLVER: clingo
run: |
share/spack/qa/run-unit-tests
- uses: codecov/codecov-action@894ff025c7b54547a9a2a1e9f228beae737ad3c2 # @v2.1.0
- uses: codecov/codecov-action@eaaf4bedf32dbdc6b720b63067d99c4d77d6047d # @v2.1.0
with:
flags: unittests,linux,clingo
# Run unit tests on MacOS
@@ -186,10 +186,10 @@ jobs:
matrix:
python-version: ["3.10"]
steps:
- uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
with:
fetch-depth: 0
- uses: actions/setup-python@57ded4d7d5e986d7296eab16560982c6dd7c923b # @v2
- uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0 # @v2
with:
python-version: ${{ matrix.python-version }}
- name: Install Python packages
@@ -211,6 +211,6 @@ jobs:
$(which spack) solve zlib
common_args=(--dist loadfile --tx '4*popen//python=./bin/spack-tmpconfig python -u ./bin/spack python' -x)
$(which spack) unit-test --cov --cov-config=pyproject.toml --cov-report=xml:coverage.xml "${common_args[@]}"
- uses: codecov/codecov-action@894ff025c7b54547a9a2a1e9f228beae737ad3c2
- uses: codecov/codecov-action@eaaf4bedf32dbdc6b720b63067d99c4d77d6047d
with:
flags: unittests,macos

View File

@@ -18,8 +18,8 @@ jobs:
validate:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
- uses: actions/setup-python@57ded4d7d5e986d7296eab16560982c6dd7c923b # @v2
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
- uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0 # @v2
with:
python-version: '3.11'
cache: 'pip'
@@ -35,16 +35,16 @@ jobs:
style:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
with:
fetch-depth: 0
- uses: actions/setup-python@57ded4d7d5e986d7296eab16560982c6dd7c923b # @v2
- uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0 # @v2
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==6.0.0
python3 -m pip install --upgrade pip setuptools types-six black==23.1.0 mypy isort clingo flake8
- name: Setup git configuration
run: |
# Need this for the git tests to succeed.
@@ -68,7 +68,7 @@ jobs:
dnf install -y \
bzip2 curl file gcc-c++ gcc gcc-gfortran git gnupg2 gzip \
make patch tcl unzip which xz
- uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # @v2
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9 # @v2
- name: Setup repo and non-root user
run: |
git --version
@@ -81,6 +81,7 @@ jobs:
shell: runuser -u spack-test -- bash {0}
run: |
source share/spack/setup-env.sh
spack debug report
spack -d bootstrap now --dev
spack style -t black
spack unit-test -V

View File

@@ -15,10 +15,10 @@ jobs:
unit-tests:
runs-on: windows-latest
steps:
- uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
with:
fetch-depth: 0
- uses: actions/setup-python@57ded4d7d5e986d7296eab16560982c6dd7c923b
- uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0
with:
python-version: 3.9
- name: Install Python packages
@@ -33,16 +33,16 @@ jobs:
./share/spack/qa/validate_last_exit.ps1
coverage combine -a
coverage xml
- uses: codecov/codecov-action@894ff025c7b54547a9a2a1e9f228beae737ad3c2
- uses: codecov/codecov-action@eaaf4bedf32dbdc6b720b63067d99c4d77d6047d
with:
flags: unittests,windows
unit-tests-cmd:
runs-on: windows-latest
steps:
- uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
with:
fetch-depth: 0
- uses: actions/setup-python@57ded4d7d5e986d7296eab16560982c6dd7c923b
- uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0
with:
python-version: 3.9
- name: Install Python packages
@@ -57,16 +57,16 @@ jobs:
./share/spack/qa/validate_last_exit.ps1
coverage combine -a
coverage xml
- uses: codecov/codecov-action@894ff025c7b54547a9a2a1e9f228beae737ad3c2
- uses: codecov/codecov-action@eaaf4bedf32dbdc6b720b63067d99c4d77d6047d
with:
flags: unittests,windows
build-abseil:
runs-on: windows-latest
steps:
- uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab
- uses: actions/checkout@c85c95e3d7251135ab7dc9ce3241c5835cc595a9
with:
fetch-depth: 0
- uses: actions/setup-python@57ded4d7d5e986d7296eab16560982c6dd7c923b
- uses: actions/setup-python@bd6b4b6205c4dbad673328db7b31b7fab9e241c0
with:
python-version: 3.9
- name: Install Python packages

View File

@@ -1,42 +1,3 @@
# 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
- Spec removed from an environment where not actually removed if `--force` was not given (#37877)
- Speed-up module file generation (#37739)
- Hotfix for a few recipes that treat CMake as a link dependency (#35816)
- Fix re-running stand-alone test a second time, which was getting a trailing spurious failure (#37840)
- Fixed reading JSON manifest on Cray, reporting non-concrete specs (#37909)
- Fixed a few bugs when generating Dockerfiles from Spack (#37766,#37769)
- Fixed a few long-standing bugs when generating module files (#36678,#38347,#38465,#38455)
- Fixed issues with building Python extensions using an external Python (#38186)
- Fixed compiler removal from command line (#38057)
- Show external status as [e] (#33792)
- Backported `archspec` fixes (#37793)
- Improved a few error messages (#37791)
# v0.20.0 (2023-05-21)
`v0.20.0` is a major feature release.

View File

@@ -143,6 +143,26 @@ The OS that are currently supported are summarized in the table below:
* - Amazon Linux 2
- ``amazonlinux:2``
- ``spack/amazon-linux``
* - AlmaLinux 8
- ``almalinux:8``
- ``spack/almalinux8``
* - AlmaLinux 9
- ``almalinux:9``
- ``spack/almalinux9``
* - Rocky Linux 8
- ``rockylinux:8``
- ``spack/rockylinux8``
* - Rocky Linux 9
- ``rockylinux:9``
- ``spack/rockylinux9``
* - Fedora Linux 37
- ``fedora:37``
- ``spack/fedora37``
* - Fedora Linux 38
- ``fedora:38``
- ``spack/fedora38``
All the images are tagged with the corresponding release of Spack:

View File

@@ -916,9 +916,9 @@ function, as shown in the example below:
.. code-block:: yaml
projections:
zlib: "{name}-{version}"
^mpi: "{name}-{version}/{^mpi.name}-{^mpi.version}-{compiler.name}-{compiler.version}"
all: "{name}-{version}/{compiler.name}-{compiler.version}"
zlib: {name}-{version}
^mpi: {name}-{version}/{^mpi.name}-{^mpi.version}-{compiler.name}-{compiler.version}
all: {name}-{version}/{compiler.name}-{compiler.version}
The entries in the projections configuration file must all be either
specs or the keyword ``all``. For each spec, the projection used will
@@ -1132,11 +1132,11 @@ index once every package is pushed. Note how this target uses the generated
example/push/%: example/install/%
@mkdir -p $(dir $@)
$(info About to push $(SPEC) to a buildcache)
$(SPACK) -e . buildcache create --allow-root --only=package --directory $(BUILDCACHE_DIR) /$(HASH)
$(SPACK) -e . buildcache push --allow-root --only=package $(BUILDCACHE_DIR) /$(HASH)
@touch $@
push: $(addprefix example/push/,$(example/SPACK_PACKAGE_IDS))
$(info Updating the buildcache index)
$(SPACK) -e . buildcache update-index --directory $(BUILDCACHE_DIR)
$(SPACK) -e . buildcache update-index $(BUILDCACHE_DIR)
$(info Done!)
@touch $@

View File

@@ -317,7 +317,7 @@ installed, but you know that new compilers have been added to your
.. code-block:: console
$ module load gcc-4.9.0
$ module load gcc/4.9.0
$ spack compiler find
==> Added 1 new compiler to ~/.spack/linux/compilers.yaml
gcc@4.9.0

View File

@@ -76,6 +76,7 @@ or refer to the full manual below.
chain
extensions
pipelines
signing
.. toctree::
:maxdepth: 2

View File

@@ -35,27 +35,27 @@ showing lots of installed packages:
$ module avail
--------------------------------------------------------------- ~/spack/share/spack/modules/linux-ubuntu14-x86_64 ---------------------------------------------------------------
autoconf-2.69-gcc-4.8-qextxkq hwloc-1.11.6-gcc-6.3.0-akcisez m4-1.4.18-gcc-4.8-ev2znoc openblas-0.2.19-gcc-6.3.0-dhkmed6 py-setuptools-34.2.0-gcc-6.3.0-fadur4s
automake-1.15-gcc-4.8-maqvukj isl-0.18-gcc-4.8-afi6taq m4-1.4.18-gcc-6.3.0-uppywnz openmpi-2.1.0-gcc-6.3.0-go2s4z5 py-six-1.10.0-gcc-6.3.0-p4dhkaw
binutils-2.28-gcc-4.8-5s7c6rs libiconv-1.15-gcc-4.8-at46wg3 mawk-1.3.4-gcc-4.8-acjez57 openssl-1.0.2k-gcc-4.8-dkls5tk python-2.7.13-gcc-6.3.0-tyehea7
bison-3.0.4-gcc-4.8-ek4luo5 libpciaccess-0.13.4-gcc-6.3.0-gmufnvh mawk-1.3.4-gcc-6.3.0-ostdoms openssl-1.0.2k-gcc-6.3.0-gxgr5or readline-7.0-gcc-4.8-xhufqhn
bzip2-1.0.6-gcc-4.8-iffrxzn libsigsegv-2.11-gcc-4.8-pp2cvte mpc-1.0.3-gcc-4.8-g5mztc5 pcre-8.40-gcc-4.8-r5pbrxb readline-7.0-gcc-6.3.0-zzcyicg
bzip2-1.0.6-gcc-6.3.0-bequudr libsigsegv-2.11-gcc-6.3.0-7enifnh mpfr-3.1.5-gcc-4.8-o7xm7az perl-5.24.1-gcc-4.8-dg5j65u sqlite-3.8.5-gcc-6.3.0-6zoruzj
cmake-3.7.2-gcc-6.3.0-fowuuby libtool-2.4.6-gcc-4.8-7a523za mpich-3.2-gcc-6.3.0-dmvd3aw perl-5.24.1-gcc-6.3.0-6uzkpt6 tar-1.29-gcc-4.8-wse2ass
curl-7.53.1-gcc-4.8-3fz46n6 libtool-2.4.6-gcc-6.3.0-n7zmbzt ncurses-6.0-gcc-4.8-dcpe7ia pkg-config-0.29.2-gcc-4.8-ib33t75 tcl-8.6.6-gcc-4.8-tfxzqbr
expat-2.2.0-gcc-4.8-mrv6bd4 libxml2-2.9.4-gcc-4.8-ryzxnsu ncurses-6.0-gcc-6.3.0-ucbhcdy pkg-config-0.29.2-gcc-6.3.0-jpgubk3 util-macros-1.19.1-gcc-6.3.0-xorz2x2
flex-2.6.3-gcc-4.8-yf345oo libxml2-2.9.4-gcc-6.3.0-rltzsdh netlib-lapack-3.6.1-gcc-6.3.0-js33dog py-appdirs-1.4.0-gcc-6.3.0-jxawmw7 xz-5.2.3-gcc-4.8-mew4log
gcc-6.3.0-gcc-4.8-24puqve lmod-7.4.1-gcc-4.8-je4srhr netlib-scalapack-2.0.2-gcc-6.3.0-5aidk4l py-numpy-1.12.0-gcc-6.3.0-oemmoeu xz-5.2.3-gcc-6.3.0-3vqeuvb
gettext-0.19.8.1-gcc-4.8-yymghlh lua-5.3.4-gcc-4.8-im75yaz netlib-scalapack-2.0.2-gcc-6.3.0-hjsemcn py-packaging-16.8-gcc-6.3.0-i2n3dtl zip-3.0-gcc-4.8-rwar22d
gmp-6.1.2-gcc-4.8-5ub2wu5 lua-luafilesystem-1_6_3-gcc-4.8-wkey3nl netlib-scalapack-2.0.2-gcc-6.3.0-jva724b py-pyparsing-2.1.10-gcc-6.3.0-tbo6gmw zlib-1.2.11-gcc-4.8-pgxsxv7
help2man-1.47.4-gcc-4.8-kcnqmau lua-luaposix-33.4.0-gcc-4.8-mdod2ry netlib-scalapack-2.0.2-gcc-6.3.0-rgqfr6d py-scipy-0.19.0-gcc-6.3.0-kr7nat4 zlib-1.2.11-gcc-6.3.0-7cqp6cj
autoconf/2.69-gcc-4.8-qextxkq hwloc/1.11.6-gcc-6.3.0-akcisez m4/1.4.18-gcc-4.8-ev2znoc openblas/0.2.19-gcc-6.3.0-dhkmed6 py-setuptools/34.2.0-gcc-6.3.0-fadur4s
automake/1.15-gcc-4.8-maqvukj isl/0.18-gcc-4.8-afi6taq m4/1.4.18-gcc-6.3.0-uppywnz openmpi/2.1.0-gcc-6.3.0-go2s4z5 py-six/1.10.0-gcc-6.3.0-p4dhkaw
binutils/2.28-gcc-4.8-5s7c6rs libiconv/1.15-gcc-4.8-at46wg3 mawk/1.3.4-gcc-4.8-acjez57 openssl/1.0.2k-gcc-4.8-dkls5tk python/2.7.13-gcc-6.3.0-tyehea7
bison/3.0.4-gcc-4.8-ek4luo5 libpciaccess/0.13.4-gcc-6.3.0-gmufnvh mawk/1.3.4-gcc-6.3.0-ostdoms openssl/1.0.2k-gcc-6.3.0-gxgr5or readline/7.0-gcc-4.8-xhufqhn
bzip2/1.0.6-gcc-4.8-iffrxzn libsigsegv/2.11-gcc-4.8-pp2cvte mpc/1.0.3-gcc-4.8-g5mztc5 pcre/8.40-gcc-4.8-r5pbrxb readline/7.0-gcc-6.3.0-zzcyicg
bzip2/1.0.6-gcc-6.3.0-bequudr libsigsegv/2.11-gcc-6.3.0-7enifnh mpfr/3.1.5-gcc-4.8-o7xm7az perl/5.24.1-gcc-4.8-dg5j65u sqlite/3.8.5-gcc-6.3.0-6zoruzj
cmake/3.7.2-gcc-6.3.0-fowuuby libtool/2.4.6-gcc-4.8-7a523za mpich/3.2-gcc-6.3.0-dmvd3aw perl/5.24.1-gcc-6.3.0-6uzkpt6 tar/1.29-gcc-4.8-wse2ass
curl/7.53.1-gcc-4.8-3fz46n6 libtool/2.4.6-gcc-6.3.0-n7zmbzt ncurses/6.0-gcc-4.8-dcpe7ia pkg-config/0.29.2-gcc-4.8-ib33t75 tcl/8.6.6-gcc-4.8-tfxzqbr
expat/2.2.0-gcc-4.8-mrv6bd4 libxml2/2.9.4-gcc-4.8-ryzxnsu ncurses/6.0-gcc-6.3.0-ucbhcdy pkg-config/0.29.2-gcc-6.3.0-jpgubk3 util-macros/1.19.1-gcc-6.3.0-xorz2x2
flex/2.6.3-gcc-4.8-yf345oo libxml2/2.9.4-gcc-6.3.0-rltzsdh netlib-lapack/3.6.1-gcc-6.3.0-js33dog py-appdirs/1.4.0-gcc-6.3.0-jxawmw7 xz/5.2.3-gcc-4.8-mew4log
gcc/6.3.0-gcc-4.8-24puqve lmod/7.4.1-gcc-4.8-je4srhr netlib-scalapack/2.0.2-gcc-6.3.0-5aidk4l py-numpy/1.12.0-gcc-6.3.0-oemmoeu xz/5.2.3-gcc-6.3.0-3vqeuvb
gettext/0.19.8.1-gcc-4.8-yymghlh lua/5.3.4-gcc-4.8-im75yaz netlib-scalapack/2.0.2-gcc-6.3.0-hjsemcn py-packaging/16.8-gcc-6.3.0-i2n3dtl zip/3.0-gcc-4.8-rwar22d
gmp/6.1.2-gcc-4.8-5ub2wu5 lua-luafilesystem/1_6_3-gcc-4.8-wkey3nl netlib-scalapack/2.0.2-gcc-6.3.0-jva724b py-pyparsing/2.1.10-gcc-6.3.0-tbo6gmw zlib/1.2.11-gcc-4.8-pgxsxv7
help2man/1.47.4-gcc-4.8-kcnqmau lua-luaposix/33.4.0-gcc-4.8-mdod2ry netlib-scalapack/2.0.2-gcc-6.3.0-rgqfr6d py-scipy/0.19.0-gcc-6.3.0-kr7nat4 zlib/1.2.11-gcc-6.3.0-7cqp6cj
The names should look familiar, as they resemble the output from ``spack find``.
For example, you could type the following command to load the ``cmake`` module:
.. code-block:: console
$ module load cmake-3.7.2-gcc-6.3.0-fowuuby
$ module load cmake/3.7.2-gcc-6.3.0-fowuuby
Neither of these is particularly pretty, easy to remember, or easy to
type. Luckily, Spack offers many facilities for customizing the module
@@ -779,35 +779,35 @@ cut-and-pasted into a shell script. For example:
$ spack module tcl loads --dependencies py-numpy git
# bzip2@1.0.6%gcc@4.9.3=linux-x86_64
module load bzip2-1.0.6-gcc-4.9.3-ktnrhkrmbbtlvnagfatrarzjojmkvzsx
module load bzip2/1.0.6-gcc-4.9.3-ktnrhkrmbbtlvnagfatrarzjojmkvzsx
# ncurses@6.0%gcc@4.9.3=linux-x86_64
module load ncurses-6.0-gcc-4.9.3-kaazyneh3bjkfnalunchyqtygoe2mncv
module load ncurses/6.0-gcc-4.9.3-kaazyneh3bjkfnalunchyqtygoe2mncv
# zlib@1.2.8%gcc@4.9.3=linux-x86_64
module load zlib-1.2.8-gcc-4.9.3-v3ufwaahjnviyvgjcelo36nywx2ufj7z
module load zlib/1.2.8-gcc-4.9.3-v3ufwaahjnviyvgjcelo36nywx2ufj7z
# sqlite@3.8.5%gcc@4.9.3=linux-x86_64
module load sqlite-3.8.5-gcc-4.9.3-a3eediswgd5f3rmto7g3szoew5nhehbr
module load sqlite/3.8.5-gcc-4.9.3-a3eediswgd5f3rmto7g3szoew5nhehbr
# readline@6.3%gcc@4.9.3=linux-x86_64
module load readline-6.3-gcc-4.9.3-se6r3lsycrwxyhreg4lqirp6xixxejh3
module load readline/6.3-gcc-4.9.3-se6r3lsycrwxyhreg4lqirp6xixxejh3
# python@3.5.1%gcc@4.9.3=linux-x86_64
module load python-3.5.1-gcc-4.9.3-5q5rsrtjld4u6jiicuvtnx52m7tfhegi
module load python/3.5.1-gcc-4.9.3-5q5rsrtjld4u6jiicuvtnx52m7tfhegi
# py-setuptools@20.5%gcc@4.9.3=linux-x86_64
module load py-setuptools-20.5-gcc-4.9.3-4qr2suj6p6glepnedmwhl4f62x64wxw2
module load py-setuptools/20.5-gcc-4.9.3-4qr2suj6p6glepnedmwhl4f62x64wxw2
# py-nose@1.3.7%gcc@4.9.3=linux-x86_64
module load py-nose-1.3.7-gcc-4.9.3-pwhtjw2dvdvfzjwuuztkzr7b4l6zepli
module load py-nose/1.3.7-gcc-4.9.3-pwhtjw2dvdvfzjwuuztkzr7b4l6zepli
# openblas@0.2.17%gcc@4.9.3+shared=linux-x86_64
module load openblas-0.2.17-gcc-4.9.3-pw6rmlom7apfsnjtzfttyayzc7nx5e7y
module load openblas/0.2.17-gcc-4.9.3-pw6rmlom7apfsnjtzfttyayzc7nx5e7y
# py-numpy@1.11.0%gcc@4.9.3+blas+lapack=linux-x86_64
module load py-numpy-1.11.0-gcc-4.9.3-mulodttw5pcyjufva4htsktwty4qd52r
module load py-numpy/1.11.0-gcc-4.9.3-mulodttw5pcyjufva4htsktwty4qd52r
# curl@7.47.1%gcc@4.9.3=linux-x86_64
module load curl-7.47.1-gcc-4.9.3-ohz3fwsepm3b462p5lnaquv7op7naqbi
module load curl/7.47.1-gcc-4.9.3-ohz3fwsepm3b462p5lnaquv7op7naqbi
# autoconf@2.69%gcc@4.9.3=linux-x86_64
module load autoconf-2.69-gcc-4.9.3-bkibjqhgqm5e3o423ogfv2y3o6h2uoq4
module load autoconf/2.69-gcc-4.9.3-bkibjqhgqm5e3o423ogfv2y3o6h2uoq4
# cmake@3.5.0%gcc@4.9.3~doc+ncurses+openssl~qt=linux-x86_64
module load cmake-3.5.0-gcc-4.9.3-x7xnsklmgwla3ubfgzppamtbqk5rwn7t
module load cmake/3.5.0-gcc-4.9.3-x7xnsklmgwla3ubfgzppamtbqk5rwn7t
# expat@2.1.0%gcc@4.9.3=linux-x86_64
module load expat-2.1.0-gcc-4.9.3-6pkz2ucnk2e62imwakejjvbv6egncppd
module load expat/2.1.0-gcc-4.9.3-6pkz2ucnk2e62imwakejjvbv6egncppd
# git@2.8.0-rc2%gcc@4.9.3+curl+expat=linux-x86_64
module load git-2.8.0-rc2-gcc-4.9.3-3bib4hqtnv5xjjoq5ugt3inblt4xrgkd
module load git/2.8.0-rc2-gcc-4.9.3-3bib4hqtnv5xjjoq5ugt3inblt4xrgkd
The script may be further edited by removing unnecessary modules.
@@ -826,12 +826,12 @@ For example, consider the following on one system:
.. code-block:: console
$ module avail
linux-SuSE11-x86_64/antlr-2.7.7-gcc-5.3.0-bdpl46y
linux-SuSE11-x86_64/antlr/2.7.7-gcc-5.3.0-bdpl46y
$ spack module tcl loads antlr # WRONG!
# antlr@2.7.7%gcc@5.3.0~csharp+cxx~java~python arch=linux-SuSE11-x86_64
module load antlr-2.7.7-gcc-5.3.0-bdpl46y
module load antlr/2.7.7-gcc-5.3.0-bdpl46y
$ spack module tcl loads --prefix linux-SuSE11-x86_64/ antlr
# antlr@2.7.7%gcc@5.3.0~csharp+cxx~java~python arch=linux-SuSE11-x86_64
module load linux-SuSE11-x86_64/antlr-2.7.7-gcc-5.3.0-bdpl46y
module load linux-SuSE11-x86_64/antlr/2.7.7-gcc-5.3.0-bdpl46y

View File

@@ -3071,7 +3071,7 @@ follows:
# The library provided by the bar virtual package
@property
def bar_libs(self):
return find_libraries("libFooBar", root=sef.home, recursive=True)
return find_libraries("libFooBar", root=self.home, recursive=True)
# The baz virtual package home
@property

View File

@@ -1,8 +1,8 @@
sphinx==6.2.1
sphinxcontrib-programoutput==0.17
sphinx_design==0.4.1
sphinx-rtd-theme==1.2.1
python-levenshtein==0.21.0
sphinx-rtd-theme==1.2.2
python-levenshtein==0.21.1
docutils==0.18.1
pygments==2.15.1
urllib3==2.0.2
urllib3==2.0.3

484
lib/spack/docs/signing.rst Normal file
View File

@@ -0,0 +1,484 @@
.. Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
Spack Project Developers. See the top-level COPYRIGHT file for details.
SPDX-License-Identifier: (Apache-2.0 OR MIT)
.. _signing:
=====================
Spack Package Signing
=====================
The goal of package signing in Spack is to provide data integrity
assurances around official packages produced by the automated Spack CI
pipelines. These assurances directly address the security of Spacks
software supply chain by explaining why a security-conscious user can
be reasonably justified in the belief that packages installed via Spack
have an uninterrupted auditable trail back to change management
decisions judged to be appropriate by the Spack maintainers. This is
achieved through cryptographic signing of packages built by Spack CI
pipelines based on code that has been transparently reviewed and
approved on GitHub. This document describes the signing process for
interested users.
.. _risks:
------------------------------
Risks, Impact and Threat Model
------------------------------
This document addresses the approach taken to safeguard Spacks
reputation with regard to the integrity of the package data produced by
Spacks CI pipelines. It does not address issues of data confidentiality
(Spack is intended to be largely open source) or availability (efforts
are described elsewhere). With that said the main reputational risk can
be broadly categorized as a loss of faith in the data integrity due to a
breach of the private key used to sign packages. Remediation of a
private key breach would require republishing the public key with a
revocation certificate, generating a new signing key, an assessment and
potential rebuild/resigning of all packages since the key was breached,
and finally direct intervention by every spack user to update their copy
of Spacks public keys used for local verification.
The primary threat model used in mitigating the risks of these stated
impacts is one of individual error not malicious intent or insider
threat. The primary objective is to avoid the above impacts by making a
private key breach nearly impossible due to oversight or configuration
error. Obvious and straightforward measures are taken to mitigate issues
of malicious interference in data integrity and insider threats but
these attack vectors are not systematically addressed. It should be hard
to exfiltrate the private key intentionally, and almost impossible to
leak the key by accident.
.. _overview:
-----------------
Pipeline Overview
-----------------
Spack pipelines build software through progressive stages where packages
in later stages nominally depend on packages built in earlier stages.
For both technical and design reasons these dependencies are not
implemented through the default GitLab artifacts mechanism; instead
built packages are uploaded to AWS S3 mirrors (buckets) where they are
retrieved by subsequent stages in the pipeline. Two broad categories of
pipelines exist: Pull Request (PR) pipelines and Develop/Release
pipelines.
- PR pipelines are launched in response to pull requests made by
trusted and untrusted users. Packages built on these pipelines upload
code to quarantined AWS S3 locations which cache the built packages
for the purposes of review and iteration on the changes proposed in
the pull request. Packages built on PR pipelines can come from
untrusted users so signing of these pipelines is not implemented.
Jobs in these pipelines are executed via normal GitLab runners both
within the AWS GitLab infrastructure and at affiliated institutions.
- Develop and Release pipelines **sign** the packages they produce and carry
strong integrity assurances that trace back to auditable change management
decisions. These pipelines only run after members from a trusted group of
reviewers verify that the proposed changes in a pull request are appropriate.
Once the PR is merged, or a release is cut, a pipeline is run on protected
GitLab runners which provide access to the required signing keys within the
job. Intermediary keys are used to sign packages in each stage of the
pipeline as they are built and a final job officially signs each package
external to any specific packages build environment. An intermediate key
exists in the AWS infrastructure and for each affiliated instritution that
maintains protected runners. The runners that execute these pipelines
exclusively accept jobs from protected branches meaning the intermediate keys
are never exposed to unreviewed code and the official keys are never exposed
to any specific build environment.
.. _key_architecture:
----------------
Key Architecture
----------------
Spacks CI process uses public-key infrastructure (PKI) based on GNU Privacy
Guard (gpg) keypairs to sign public releases of spack package metadata, also
called specs. Two classes of GPG keys are involved in the process to reduce the
impact of an individual private key compromise, these key classes are the
*Intermediate CI Key* and *Reputational Key*. Each of these keys has signing
sub-keys that are used exclusively for signing packages. This can be confusing
so for the purpose of this explanation well refer to Root and Signing keys.
Each key has a private and a public component as well as one or more identities
and zero or more signatures.
-------------------
Intermediate CI Key
-------------------
The Intermediate key class is used to sign and verify packages between stages
within a develop or release pipeline. An intermediate key exists for the AWS
infrastructure as well as each affiliated institution that maintains protected
runners. These intermediate keys are made available to the GitLab execution
environment building the package so that the packages dependencies may be
verified by the Signing Intermediate CI Public Key and the final package may be
signed by the Signing Intermediate CI Private Key.
+---------------------------------------------------------------------------------------------------------+
| **Intermediate CI Key (GPG)** |
+==================================================+======================================================+
| Root Intermediate CI Private Key (RSA 4096)# | Root Intermediate CI Public Key (RSA 4096) |
+--------------------------------------------------+------------------------------------------------------+
| Signing Intermediate CI Private Key (RSA 4096) | Signing Intermediate CI Public Key (RSA 4096) |
+--------------------------------------------------+------------------------------------------------------+
| Identity: “Intermediate CI Key <maintainers@spack.io>” |
+---------------------------------------------------------------------------------------------------------+
| Signatures: None |
+---------------------------------------------------------------------------------------------------------+
The *Root intermediate CI Private Key*\ Is stripped out of the GPG key and
stored offline completely separate from Spacks infrastructure. This allows the
core development team to append revocation certificates to the GPG key and
issue new sub-keys for use in the pipeline. It is our expectation that this
will happen on a semi regular basis. A corollary of this is that *this key
should not be used to verify package integrity outside the internal CI process.*
----------------
Reputational Key
----------------
The Reputational Key is the public facing key used to sign complete groups of
development and release packages. Only one key pair exsits in this class of
keys. In contrast to the Intermediate CI Key the Reputational Key *should* be
used to verify package integrity. At the end of develop and release pipeline a
final pipeline job pulls down all signed package metadata built by the pipeline,
verifies they were signed with an Intermediate CI Key, then strips the
Intermediate CI Key signature from the package and re-signs them with the
Signing Reputational Private Key. The officially signed packages are then
uploaded back to the AWS S3 mirror. Please note that separating use of the
reputational key into this final job is done to prevent leakage of the key in a
spack package. Because the Signing Reputational Private Key is never exposed to
a build job it cannot accidentally end up in any built package.
+---------------------------------------------------------------------------------------------------------+
| **Reputational Key (GPG)** |
+==================================================+======================================================+
| Root Reputational Private Key (RSA 4096)# | Root Reputational Public Key (RSA 4096) |
+--------------------------------------------------+------------------------------------------------------+
| Signing Reputational Private Key (RSA 4096) | Signing Reputational Public Key (RSA 4096) |
+--------------------------------------------------+------------------------------------------------------+
| Identity: “Spack Project <maintainers@spack.io>” |
+---------------------------------------------------------------------------------------------------------+
| Signatures: Signed by core development team [#f1]_ |
+---------------------------------------------------------------------------------------------------------+
The Root Reputational Private Key is stripped out of the GPG key and stored
offline completely separate from Spacks infrastructure. This allows the core
development team to append revocation certificates to the GPG key in the
unlikely event that the Signing Reputation Private Key is compromised. In
general it is the expectation that rotating this key will happen infrequently if
at all. This should allow relatively transparent verification for the end-user
community without needing deep familiarity with GnuPG or Public Key
Infrastructure.
.. _build_cache_format:
------------------
Build Cache Format
------------------
A binary package consists of a metadata file unambiguously defining the
built package (and including other details such as how to relocate it)
and the installation directory of the package stored as a compressed
archive file. The metadata files can either be unsigned, in which case
the contents are simply the json-serialized concrete spec plus metadata,
or they can be signed, in which case the json-serialized concrete spec
plus metadata is wrapped in a gpg cleartext signature. Built package
metadata files are named to indicate the operating system and
architecture for which the package was built as well as the compiler
used to build it and the packages name and version. For example::
linux-ubuntu18.04-haswell-gcc-7.5.0-zlib-1.2.12-llv2ysfdxnppzjrt5ldybb5c52qbmoow.spec.json.sig
would contain the concrete spec and binary metadata for a binary package
of ``zlib@1.2.12``, built for the ``ubuntu`` operating system and ``haswell``
architecture. The id of the built package exists in the name of the file
as well (after the package name and version) and in this case begins
with ``llv2ys``. The id distinguishes a particular built package from all
other built packages with the same os/arch, compiler, name, and version.
Below is an example of a signed binary package metadata file. Such a
file would live in the ``build_cache`` directory of a binary mirror::
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
{
"spec": {
<concrete-spec-contents-omitted>
},
"buildcache_layout_version": 1,
"binary_cache_checksum": {
"hash_algorithm": "sha256",
"hash": "4f1e46452c35a5e61bcacca205bae1bfcd60a83a399af201a29c95b7cc3e1423"
},
"buildinfo": {
"relative_prefix":
"linux-ubuntu18.04-haswell/gcc-7.5.0/zlib-1.2.12-llv2ysfdxnppzjrt5ldybb5c52qbmoow",
"relative_rpaths": false
}
}
-----BEGIN PGP SIGNATURE-----
iQGzBAEBCgAdFiEETZn0sLle8jIrdAPLx/P+voVcifMFAmKAGvwACgkQx/P+voVc
ifNoVgv/VrhA+wurVs5GB9PhmMA1m5U/AfXZb4BElDRwpT8ZcTPIv5X8xtv60eyn
4EOneGVbZoMThVxgev/NKARorGmhFXRqhWf+jknJZ1dicpqn/qpv34rELKUpgXU+
QDQ4d1P64AIdTczXe2GI9ZvhOo6+bPvK7LIsTkBbtWmopkomVxF0LcMuxAVIbA6b
887yBvVO0VGlqRnkDW7nXx49r3AG2+wDcoU1f8ep8QtjOcMNaPTPJ0UnjD0VQGW6
4ZFaGZWzdo45MY6tF3o5mqM7zJkVobpoW3iUz6J5tjz7H/nMlGgMkUwY9Kxp2PVH
qoj6Zip3LWplnl2OZyAY+vflPFdFh12Xpk4FG7Sxm/ux0r+l8tCAPvtw+G38a5P7
QEk2JBr8qMGKASmnRlJUkm1vwz0a95IF3S9YDfTAA2vz6HH3PtsNLFhtorfx8eBi
Wn5aPJAGEPOawEOvXGGbsH4cDEKPeN0n6cy1k92uPEmBLDVsdnur8q42jk5c2Qyx
j3DXty57
=3gvm
-----END PGP SIGNATURE-----
If a user has trusted the public key associated with the private key
used to sign the above spec file, the signature can be verified with
gpg, as follows::
$ gpg verify linux-ubuntu18.04-haswell-gcc-7.5.0-zlib-1.2.12-llv2ysfdxnppzjrt5ldybb5c52qbmoow.spec.json.sig
The metadata (regardless whether signed or unsigned) contains the checksum
of the ``.spack`` file containing the actual installation. The checksum should
be compared to a checksum computed locally on the ``.spack`` file to ensure the
contents have not changed since the binary spec plus metadata were signed. The
``.spack`` files are actually tarballs containing the compressed archive of the
install tree. These files, along with the metadata files, live within the
``build_cache`` directory of the mirror, and together are organized as follows::
build_cache/
# unsigned metadata (for indexing, contains sha256 of .spack file)
<arch>-<compiler>-<name>-<ver>-24zvipcqgg2wyjpvdq2ajy5jnm564hen.spec.json
# clearsigned metadata (same as above, but signed)
<arch>-<compiler>-<name>-<ver>-24zvipcqgg2wyjpvdq2ajy5jnm564hen.spec.json.sig
<arch>/
<compiler>/
<name>-<ver>/
# tar.gz-compressed prefix (may support more compression formats later)
<arch>-<compiler>-<name>-<ver>-24zvipcqgg2wyjpvdq2ajy5jnm564hen.spack
Uncompressing and extracting the ``.spack`` file results in the install tree.
This is in contrast to previous versions of spack, where the ``.spack`` file
contained a (duplicated) metadata file, a signature file and a nested tarball
containing the install tree.
.. _internal_implementation:
-----------------------
Internal Implementation
-----------------------
The technical implementation of the pipeline signing process includes components
defined in Amazon Web Services, the Kubernetes cluster, at affilicated
institutions, and the GitLab/GitLab Runner deployment. We present the techincal
implementation in two interdependent sections. The first addresses how secrets
are managed through the lifecycle of a develop or release pipeline. The second
section describes how Gitlab Runner and pipelines are configured and managed to
support secure automated signing.
Secrets Management
^^^^^^^^^^^^^^^^^^
As stated above the Root Private Keys (intermediate and reputational)
are stripped from the GPG keys and stored outside Spacks
infrastructure.
.. warning::
**TODO**
- Explanation here about where and how access is handled for these keys.
- Both Root private keys are protected with strong passwords
- Who has access to these and how?
**Intermediate CI Key**
-----------------------
Multiple intermediate CI signing keys exist, one Intermediate CI Key for jobs
run in AWS, and one key for each affiliated institution (e.g. Univerity of
Oregon). Here we describe how the Intermediate CI Key is managed in AWS:
The Intermediate CI Key (including the Signing Intermediate CI Private Key is
exported as an ASCII armored file and stored in a Kubernetes secret called
``spack-intermediate-ci-signing-key``. For convenience sake, this same secret
contains an ASCII-armored export of just the *public* components of the
Reputational Key. This secret also contains the *public* components of each of
the affiliated institutions' Intermediate CI Key. These are potentially needed
to verify dependent packages which may have been found in the public mirror or
built by a protected job running on an affiliated institution's infrastrcuture
in an earlier stage of the pipeline.
Procedurally the ``spack-intermediate-ci-signing-key`` secret is used in
the following way:
1. A ``large-arm-prot`` or ``large-x86-prot`` protected runner picks up
a job tagged ``protected`` from a protected GitLab branch. (See
`Protected Runners and Reserved Tags <#_8bawjmgykv0b>`__).
2. Based on its configuration, the runner creates a job Pod in the
pipeline namespace and mounts the spack-intermediate-ci-signing-key
Kubernetes secret into the build container
3. The Intermediate CI Key, affiliated institutions' public key and the
Reputational Public Key are imported into a keyring by the ``spack gpg …``
sub-command. This is initiated by the jobs build script which is created by
the generate job at the beginning of the pipeline.
4. Assuming the package has dependencies those specs are verified using
the keyring.
5. The package is built and the spec.json is generated
6. The spec.json is signed by the keyring and uploaded to the mirrors
build cache.
**Reputational Key**
--------------------
Because of the increased impact to end users in the case of a private
key breach, the Reputational Key is managed separately from the
Intermediate CI Keys and has additional controls. First, the Reputational
Key was generated outside of Spacks infrastructure and has been signed
by the core development team. The Reputational Key (along with the
Signing Reputational Private Key) was then ASCII armor exported to a
file. Unlike the Intermediate CI Key this exported file is not stored as
a base64 encoded secret in Kubernetes. Instead\ *the key file
itself*\ is encrypted and stored in Kubernetes as the
``spack-signing-key-encrypted`` secret in the pipeline namespace.
The encryption of the exported Reputational Key (including the Signing
Reputational Private Key) is handled by `AWS Key Management Store (KMS) data
keys
<https://docs.aws.amazon.com/kms/latest/developerguide/concepts.html#data-keys>`__.
The private key material is decrypted and imported at the time of signing into a
memory mounted temporary directory holding the keychain. The signing job uses
the `AWS Encryption SDK
<https://docs.aws.amazon.com/encryption-sdk/latest/developer-guide/crypto-cli.html>`__
(i.e. ``aws-encryption-cli``) to decrypt the Reputational Key. Permission to
decrypt the key is granted to the job Pod through a Kubernetes service account
specifically used for this, and only this, function. Finally, for convenience
sake, this same secret contains an ASCII-armored export of the *public*
components of the Intermediate CI Keys and the Reputational Key. This allows the
signing script to verify that packages were built by the pipeline (both on AWS
or at affiliated institutions), or signed previously as a part of a different
pipeline. This is is done *before* importing decrypting and importing the
Signing Reputational Private Key material and officially signing the packages.
Procedurally the ``spack-singing-key-encrypted`` secret is used in the
following way:
1. The ``spack-package-signing-gitlab-runner`` protected runner picks
up a job tagged ``notary`` from a protected GitLab branch (See
`Protected Runners and Reserved Tags <#_8bawjmgykv0b>`__).
2. Based on its configuration, the runner creates a job pod in the
pipeline namespace. The job is run in a stripped down purpose-built
image ``ghcr.io/spack/notary:latest`` Docker image. The runner is
configured to only allow running jobs with this image.
3. The runner also mounts the ``spack-signing-key-encrypted`` secret to
a path on disk. Note that this becomes several files on disk, the
public components of the Intermediate CI Keys, the public components
of the Reputational CI, and an AWS KMS encrypted file containing the
Singing Reputational Private Key.
4. In addition to the secret, the runner creates a tmpfs memory mounted
directory where the GnuPG keyring will be created to verify, and
then resign the package specs.
5. The job script syncs all spec.json.sig files from the build cache to
a working directory in the jobs execution environment.
6. The job script then runs the ``sign.sh`` script built into the
notary Docker image.
7. The ``sign.sh`` script imports the public components of the
Reputational and Intermediate CI Keys and uses them to verify good
signatures on the spec.json.sig files. If any signed spec does not
verify the job immediately fails.
8. Assuming all specs are verified, the ``sign.sh`` script then unpacks
the spec json data from the signed file in preparation for being
re-signed with the Reputational Key.
9. The private components of the Reputational Key are decrypted to
standard out using ``aws-encryption-cli`` directly into a ``gpg
import …`` statement which imports the key into the
keyring mounted in-memory.
10. The private key is then used to sign each of the json specs and the
keyring is removed from disk.
11. The re-signed json specs are resynced to the AWS S3 Mirror and the
public signing of the packages for the develop or release pipeline
that created them is complete.
Non service-account access to the private components of the Reputational
Key that are managed through access to the symmetric secret in KMS used
to encrypt the data key (which in turn is used to encrypt the GnuPG key
- See:\ `Encryption SDK
Documentation <https://docs.aws.amazon.com/encryption-sdk/latest/developer-guide/crypto-cli-examples.html#cli-example-encrypt-file>`__).
A small trusted subset of the core development team are the only
individuals with access to this symmetric key.
.. _protected_runners:
Protected Runners and Reserved Tags
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Spack has a large number of Gitlab Runners operating in its build farm.
These include runners deployed in the AWS Kubernetes cluster as well as
runners deployed at affiliated institutions. The majority of runners are
shared runners that operate across projects in gitlab.spack.io. These
runners pick up jobs primarily from the spack/spack project and execute
them in PR pipelines.
A small number of runners operating on AWS and at affiliated institutions are
registered as specific *protected* runners on the spack/spack project. In
addition to protected runners there are protected branches on the spack/spack
project. These are the ``develop`` branch, any release branch (i.e. managed with
the ``releases/v*`` wildcard) and any tag branch (managed with the ``v*``
wildcard) Finally Spacks pipeline generation code reserves certain tags to make
sure jobs are routed to the correct runners, these tags are ``public``,
``protected``, and ``notary``. Understanding how all this works together to
protect secrets and provide integrity assurances can be a little confusing so
lets break these down:
- **Protected Branches**- Protected branches in Spack prevent anyone
other than Maintainers in GitLab from pushing code. In the case of
Spack the only Maintainer level entity pushing code to protected
branches is Spack bot. Protecting branches also marks them in such a
way that Protected Runners will only run jobs from those branches
- **Protected Runners**- Protected Runners only run jobs from protected
branches. Because protected runners have access to secrets, it's critical
that they not run Jobs from untrusted code (i.e. PR branches). If they did it
would be possible for a PR branch to tag a job in such a way that a protected
runner executed that job and mounted secrets into a code execution
environment that had not been reviewed by Spack maintainers. Note however
that in the absence of tagging used to route jobs, public runners *could* run
jobs from protected branches. No secrets would be at risk of being breached
because non-protected runners do not have access to those secrets; lack of
secrets would, however, cause the jobs to fail.
- **Reserved Tags**- To mitigate the issue of public runners picking up
protected jobs Spack uses a small set of “reserved” job tags (Note that these
are *job* tags not git tags). These tags are “public”, “private”, and
“notary.” The majority of jobs executed in Spacks GitLab instance are
executed via a ``generate`` job. The generate job code systematically ensures
that no user defined configuration sets these tags. Instead, the ``generate``
job sets these tags based on rules related to the branch where this pipeline
originated. If the job is a part of a pipeline on a PR branch it sets the
``public`` tag. If the job is part of a pipeline on a protected branch it
sets the ``protected`` tag. Finally if the job is the package signing job and
it is running on a pipeline that is part of a protected branch then it sets
the ``notary`` tag.
Protected Runners are configured to only run jobs from protected branches. Only
jobs running in pipelines on protected branches are tagged with ``protected`` or
``notary`` tags. This tightly couples jobs on protected branches to protected
runners that provide access to the secrets required to sign the built packages.
The secrets are can **only** be accessed via:
1. Runners under direct control of the core development team.
2. Runners under direct control of trusted maintainers at affiliated institutions.
3. By code running the automated pipeline that has been reviewed by the
Spack maintainers and judged to be appropriate.
Other attempts (either through malicious intent or incompetence) can at
worst grab jobs intended for protected runners which will cause those
jobs to fail alerting both Spack maintainers and the core development
team.
.. [#f1]
The Reputational Key has also cross signed core development team
keys.

View File

@@ -139,7 +139,7 @@ def get_fh(self, path):
def release_by_stat(self, stat):
key = (stat.st_dev, stat.st_ino, os.getpid())
open_file = self._descriptors.get(key)
assert open_file, "Attempted to close non-existing inode: %s" % stat.st_ino
assert open_file, "Attempted to close non-existing inode: %s" % stat.st_inode
open_file.refs -= 1
if not open_file.refs:

View File

@@ -4,7 +4,7 @@
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
#: PEP440 canonical <major>.<minor>.<micro>.<devN> string
__version__ = "0.20.2"
__version__ = "0.21.0.dev0"
spack_version = __version__

View File

@@ -199,11 +199,11 @@ def _associate_built_specs_with_mirror(self, cache_key, mirror_url):
with self._index_file_cache.read_transaction(cache_key):
db._read_from_file(cache_path)
except spack_db.InvalidDatabaseVersionError as e:
tty.warn(
msg = (
f"you need a newer Spack version to read the buildcache index for the "
f"following mirror: '{mirror_url}'. {e.database_version_message}"
)
return
raise BuildcacheIndexError(msg) from e
spec_list = db.query_local(installed=False, in_buildcache=True)
@@ -760,13 +760,12 @@ def hashes_to_prefixes(spec):
}
def get_buildinfo_dict(spec, rel=False):
def get_buildinfo_dict(spec):
"""Create metadata for a tarball"""
manifest = get_buildfile_manifest(spec)
return {
"sbang_install_path": spack.hooks.sbang.sbang_install_path(),
"relative_rpaths": rel,
"buildpath": spack.store.layout.root,
"spackprefix": spack.paths.prefix,
"relative_prefix": os.path.relpath(spec.prefix, spack.store.layout.root),
@@ -1209,9 +1208,6 @@ class PushOptions(NamedTuple):
#: Overwrite existing tarball/metadata files in buildcache
force: bool = False
#: Whether to use relative RPATHs
relative: bool = False
#: Allow absolute paths to package prefixes when creating a tarball
allow_root: bool = False
@@ -1281,41 +1277,17 @@ def _build_tarball_in_stage_dir(spec: Spec, out_url: str, stage_dir: str, option
raise NoOverwriteException(url_util.format(remote_specfile_path))
pkg_dir = os.path.basename(spec.prefix.rstrip(os.path.sep))
workdir = os.path.join(stage_dir, pkg_dir)
# TODO: We generally don't want to mutate any files, but when using relative
# mode, Spack unfortunately *does* mutate rpaths and links ahead of time.
# For now, we only make a full copy of the spec prefix when in relative mode.
if options.relative:
# tarfile is used because it preserves hardlink etc best.
binaries_dir = workdir
temp_tarfile_name = tarball_name(spec, ".tar")
temp_tarfile_path = os.path.join(tarfile_dir, temp_tarfile_name)
with closing(tarfile.open(temp_tarfile_path, "w")) as tar:
tar.add(name="%s" % spec.prefix, arcname=".")
with closing(tarfile.open(temp_tarfile_path, "r")) as tar:
tar.extractall(workdir)
os.remove(temp_tarfile_path)
else:
binaries_dir = spec.prefix
binaries_dir = spec.prefix
# create info for later relocation and create tar
buildinfo = get_buildinfo_dict(spec, options.relative)
buildinfo = get_buildinfo_dict(spec)
# optionally make the paths in the binaries relative to each other
# in the spack install tree before creating tarball
if options.relative:
make_package_relative(workdir, spec, buildinfo, options.allow_root)
elif not options.allow_root:
if not options.allow_root:
ensure_package_relocatable(buildinfo, binaries_dir)
_do_create_tarball(tarfile_path, binaries_dir, pkg_dir, buildinfo)
# remove copy of install directory
if options.relative:
shutil.rmtree(workdir)
# get the sha256 checksum of the tarball
checksum = checksum_tarball(tarfile_path)
@@ -1336,7 +1308,6 @@ def _build_tarball_in_stage_dir(spec: Spec, out_url: str, stage_dir: str, option
# This will be used to determine is the directory layout has changed.
buildinfo = {}
buildinfo["relative_prefix"] = os.path.relpath(spec.prefix, spack.store.layout.root)
buildinfo["relative_rpaths"] = options.relative
spec_dict["buildinfo"] = buildinfo
with open(specfile_path, "w") as outfile:
@@ -1596,35 +1567,6 @@ def download_tarball(spec, unsigned=False, mirrors_for_spec=None):
return None
def make_package_relative(workdir, spec, buildinfo, allow_root):
"""
Change paths in binaries to relative paths. Change absolute symlinks
to relative symlinks.
"""
prefix = spec.prefix
old_layout_root = buildinfo["buildpath"]
orig_path_names = list()
cur_path_names = list()
for filename in buildinfo["relocate_binaries"]:
orig_path_names.append(os.path.join(prefix, filename))
cur_path_names.append(os.path.join(workdir, filename))
platform = spack.platforms.by_name(spec.platform)
if "macho" in platform.binary_formats:
relocate.make_macho_binaries_relative(cur_path_names, orig_path_names, old_layout_root)
if "elf" in platform.binary_formats:
relocate.make_elf_binaries_relative(cur_path_names, orig_path_names, old_layout_root)
allow_root or relocate.ensure_binaries_are_relocatable(cur_path_names)
orig_path_names = list()
cur_path_names = list()
for linkname in buildinfo.get("relocate_links", []):
orig_path_names.append(os.path.join(prefix, linkname))
cur_path_names.append(os.path.join(workdir, linkname))
relocate.make_link_relative(cur_path_names, orig_path_names)
def ensure_package_relocatable(buildinfo, binaries_dir):
"""Check if package binaries are relocatable."""
binaries = [os.path.join(binaries_dir, f) for f in buildinfo["relocate_binaries"]]

View File

@@ -175,12 +175,12 @@ def black_root_spec() -> str:
def flake8_root_spec() -> str:
"""Return the root spec used to bootstrap flake8"""
return _root_spec("py-flake8")
return _root_spec("py-flake8@3.8.2:")
def pytest_root_spec() -> str:
"""Return the root spec used to bootstrap flake8"""
return _root_spec("py-pytest")
return _root_spec("py-pytest@6.2.4:")
def ensure_environment_dependencies() -> None:

View File

@@ -589,7 +589,6 @@ def set_module_variables_for_package(pkg):
# 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
@@ -1028,7 +1027,7 @@ def get_cmake_prefix_path(pkg):
def _setup_pkg_and_run(
serialized_pkg, function, kwargs, write_pipe, input_multiprocess_fd, jsfd1, jsfd2
serialized_pkg, function, kwargs, child_pipe, input_multiprocess_fd, jsfd1, jsfd2
):
context = kwargs.get("context", "build")
@@ -1049,12 +1048,12 @@ def _setup_pkg_and_run(
pkg, dirty=kwargs.get("dirty", False), context=context
)
return_value = function(pkg, kwargs)
write_pipe.send(return_value)
child_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.
write_pipe.send(e)
child_pipe.send(e)
except BaseException:
# catch ANYTHING that goes wrong in the child process
exc_type, exc, tb = sys.exc_info()
@@ -1103,10 +1102,10 @@ def _setup_pkg_and_run(
context,
package_context,
)
write_pipe.send(ce)
child_pipe.send(ce)
finally:
write_pipe.close()
child_pipe.close()
if input_multiprocess_fd is not None:
input_multiprocess_fd.close()
@@ -1150,7 +1149,7 @@ 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
"""
read_pipe, write_pipe = multiprocessing.Pipe(duplex=False)
parent_pipe, child_pipe = multiprocessing.Pipe()
input_multiprocess_fd = None
jobserver_fd1 = None
jobserver_fd2 = None
@@ -1175,7 +1174,7 @@ def child_fun():
serialized_pkg,
function,
kwargs,
write_pipe,
child_pipe,
input_multiprocess_fd,
jobserver_fd1,
jobserver_fd2,
@@ -1184,12 +1183,6 @@ 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
@@ -1199,16 +1192,7 @@ def child_fun():
if input_multiprocess_fd is not None:
input_multiprocess_fd.close()
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)})")
child_result = parent_pipe.recv()
p.join()
# If returns a StopPhase, raise it
@@ -1228,10 +1212,6 @@ def exitcode_msg(p):
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
@@ -1276,8 +1256,9 @@ def make_stack(tb, stack=None):
func = getattr(obj, tb.tb_frame.f_code.co_name, "")
if func:
typename, *_ = func.__qualname__.partition(".")
if isinstance(obj, CONTEXT_BASES) and typename not in basenames:
break
if isinstance(obj, CONTEXT_BASES) and typename not in basenames:
break
else:
return None

View File

@@ -2,6 +2,7 @@
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import collections.abc
import os
from typing import Tuple
@@ -13,21 +14,24 @@
from .cmake import CMakeBuilder, CMakePackage
def cmake_cache_path(name, value, comment=""):
def cmake_cache_path(name, value, comment="", force=False):
"""Generate a string for a cmake cache variable"""
return 'set({0} "{1}" CACHE PATH "{2}")\n'.format(name, value, comment)
force_str = " FORCE" if force else ""
return 'set({0} "{1}" CACHE PATH "{2}"{3})\n'.format(name, value, comment, force_str)
def cmake_cache_string(name, value, comment=""):
def cmake_cache_string(name, value, comment="", force=False):
"""Generate a string for a cmake cache variable"""
return 'set({0} "{1}" CACHE STRING "{2}")\n'.format(name, value, comment)
force_str = " FORCE" if force else ""
return 'set({0} "{1}" CACHE STRING "{2}"{3})\n'.format(name, value, comment, force_str)
def cmake_cache_option(name, boolean_value, comment=""):
def cmake_cache_option(name, boolean_value, comment="", force=False):
"""Generate a string for a cmake configuration option"""
value = "ON" if boolean_value else "OFF"
return 'set({0} {1} CACHE BOOL "{2}")\n'.format(name, value, comment)
force_str = " FORCE" if force else ""
return 'set({0} {1} CACHE BOOL "{2}"{3})\n'.format(name, value, comment, force_str)
class CachedCMakeBuilder(CMakeBuilder):
@@ -63,6 +67,34 @@ def cache_name(self):
def cache_path(self):
return os.path.join(self.pkg.stage.source_path, self.cache_name)
# Implement a version of the define_from_variant for Cached packages
def define_cmake_cache_from_variant(self, cmake_var, variant=None, comment=""):
"""Return a Cached CMake field from the given variant's value.
See define_from_variant in lib/spack/spack/build_systems/cmake.py package
"""
if variant is None:
variant = cmake_var.lower()
if variant not in self.pkg.variants:
raise KeyError('"{0}" is not a variant of "{1}"'.format(variant, self.pkg.name))
if variant not in self.pkg.spec.variants:
return ""
value = self.pkg.spec.variants[variant].value
field = None
if isinstance(value, bool):
field = cmake_cache_option(cmake_var, value, comment)
else:
if isinstance(value, collections.abc.Sequence) and not isinstance(value, str):
value = ";".join(str(v) for v in value)
else:
value = str(value)
field = cmake_cache_string(cmake_var, value, comment)
return field
def initconfig_compiler_entries(self):
# This will tell cmake to use the Spack compiler wrappers when run
# through Spack, but use the underlying compiler when run outside of
@@ -130,6 +162,17 @@ def initconfig_compiler_entries(self):
libs_string = libs_format_string.format(lang)
entries.append(cmake_cache_string(libs_string, libs_flags))
# Set the generator in the cached config
if self.spec.satisfies("generator=make"):
entries.append(cmake_cache_string("CMAKE_GENERATOR", "Unix Makefiles"))
if self.spec.satisfies("generator=ninja"):
entries.append(cmake_cache_string("CMAKE_GENERATOR", "Ninja"))
entries.append(
cmake_cache_string(
"CMAKE_MAKE_PROGRAM", "{0}/ninja".format(spec["ninja"].prefix.bin)
)
)
return entries
def initconfig_mpi_entries(self):
@@ -195,26 +238,57 @@ def initconfig_hardware_entries(self):
"#------------------{0}\n".format("-" * 60),
]
# Provide standard CMake arguments for dependent CachedCMakePackages
if spec.satisfies("^cuda"):
entries.append("#------------------{0}".format("-" * 30))
entries.append("# Cuda")
entries.append("#------------------{0}\n".format("-" * 30))
cudatoolkitdir = spec["cuda"].prefix
entries.append(cmake_cache_path("CUDA_TOOLKIT_ROOT_DIR", cudatoolkitdir))
cudacompiler = "${CUDA_TOOLKIT_ROOT_DIR}/bin/nvcc"
entries.append(cmake_cache_path("CMAKE_CUDA_COMPILER", cudacompiler))
entries.append(cmake_cache_path("CUDAToolkit_ROOT", cudatoolkitdir))
entries.append(cmake_cache_path("CMAKE_CUDA_COMPILER", "${CUDAToolkit_ROOT}/bin/nvcc"))
entries.append(cmake_cache_path("CMAKE_CUDA_HOST_COMPILER", "${CMAKE_CXX_COMPILER}"))
# Include the deprecated CUDA_TOOLKIT_ROOT_DIR for supporting BLT packages
entries.append(cmake_cache_path("CUDA_TOOLKIT_ROOT_DIR", cudatoolkitdir))
archs = spec.variants["cuda_arch"].value
if archs[0] != "none":
arch_str = ";".join(archs)
entries.append(
cmake_cache_string("CMAKE_CUDA_ARCHITECTURES", "{0}".format(arch_str))
)
if "+rocm" in spec:
entries.append("#------------------{0}".format("-" * 30))
entries.append("# ROCm")
entries.append("#------------------{0}\n".format("-" * 30))
# Explicitly setting HIP_ROOT_DIR may be a patch that is no longer necessary
entries.append(cmake_cache_path("HIP_ROOT_DIR", "{0}".format(spec["hip"].prefix)))
entries.append(
cmake_cache_path("HIP_CXX_COMPILER", "{0}".format(self.spec["hip"].hipcc))
)
archs = self.spec.variants["amdgpu_target"].value
if archs[0] != "none":
arch_str = ";".join(archs)
entries.append(
cmake_cache_string("CMAKE_HIP_ARCHITECTURES", "{0}".format(arch_str))
)
entries.append(cmake_cache_string("AMDGPU_TARGETS", "{0}".format(arch_str)))
entries.append(cmake_cache_string("GPU_TARGETS", "{0}".format(arch_str)))
return entries
def std_initconfig_entries(self):
cmake_prefix_path_env = os.environ["CMAKE_PREFIX_PATH"]
cmake_prefix_path = cmake_prefix_path_env.replace(os.pathsep, ";")
return [
"#------------------{0}".format("-" * 60),
"# !!!! This is a generated file, edit at own risk !!!!",
"#------------------{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),
]
def initconfig_package_entries(self):

View File

@@ -5,6 +5,7 @@
import collections.abc
import inspect
import os
import pathlib
import platform
import re
import sys
@@ -15,7 +16,6 @@
import spack.build_environment
import spack.builder
import spack.package_base
import spack.util.path
from spack.directives import build_system, conflicts, depends_on, variant
from spack.multimethod import when
@@ -271,7 +271,7 @@ def std_args(pkg, generator=None):
args = [
"-G",
generator,
define("CMAKE_INSTALL_PREFIX", pkg.prefix),
define("CMAKE_INSTALL_PREFIX", pathlib.Path(pkg.prefix).as_posix()),
define("CMAKE_BUILD_TYPE", build_type),
define("BUILD_TESTING", pkg.run_tests),
]

View File

@@ -223,7 +223,7 @@ 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"))
self.spec.add_dependency_edge(python, deptypes=("build", "link", "run"), virtuals=())
class PythonPackage(PythonExtension):

View File

@@ -7,7 +7,7 @@
import llnl.util.lang as lang
from spack.directives import extends, maintainers
from spack.directives import extends
from .generic import GenericBuilder, Package
@@ -71,8 +71,6 @@ class RPackage(Package):
GenericBuilder = RBuilder
maintainers("glennpj")
#: This attribute is used in UI queries that need to know the build
#: system base class
build_system_class = "RPackage"

View File

@@ -10,6 +10,7 @@
from llnl.util.filesystem import find, join_path, working_dir
import spack.builder
import spack.install_test
import spack.package_base
from spack.directives import build_system, depends_on, extends
from spack.multimethod import when
@@ -30,8 +31,8 @@ class SIPPackage(spack.package_base.PackageBase):
#: Name of private sip module to install alongside package
sip_module = "sip"
#: Callback names for install-time test
install_time_test_callbacks = ["test"]
#: Callback names for install-time testing
install_time_test_callbacks = ["test_imports"]
#: Legacy buildsystem attribute used to deserialize and install old specs
legacy_buildsystem = "sip"
@@ -87,18 +88,20 @@ def python(self, *args, **kwargs):
"""The python ``Executable``."""
inspect.getmodule(self).python(*args, **kwargs)
def test(self):
def test_imports(self):
"""Attempts to import modules of the installed package."""
# Make sure we are importing the installed modules,
# not the ones in the source directory
python = inspect.getmodule(self).python
for module in self.import_modules:
self.run_test(
inspect.getmodule(self).python.path,
["-c", "import {0}".format(module)],
with spack.install_test.test_part(
self,
"test_imports_{0}".format(module),
purpose="checking import of {0}".format(module),
work_dir="spack-test",
)
):
python("-c", "import {0}".format(module))
@spack.builder.builder("sip")

View File

@@ -751,7 +751,7 @@ def generate_gitlab_ci_yaml(
env.concretize()
env.write()
yaml_root = ev.config_dict(env.manifest)
yaml_root = env.manifest[ev.TOP_LEVEL_KEY]
# Get the joined "ci" config with all of the current scopes resolved
ci_config = cfg.get("ci")
@@ -946,7 +946,7 @@ def generate_gitlab_ci_yaml(
# Add config scopes to environment
env_includes = env_yaml_root["spack"].get("include", [])
cli_scopes = [
os.path.abspath(s.path)
os.path.relpath(s.path, concrete_env_dir)
for s in cfg.scopes().values()
if type(s) == cfg.ImmutableConfigScope
and s.path not in env_includes
@@ -1095,7 +1095,7 @@ def generate_gitlab_ci_yaml(
raise AttributeError
def main_script_replacements(cmd):
return cmd.replace("{env_dir}", concrete_env_dir)
return cmd.replace("{env_dir}", rel_concrete_env_dir)
job_object["script"] = _unpack_script(
job_object["script"], op=main_script_replacements

View File

@@ -43,13 +43,6 @@ def setup_parser(subparser):
subparsers = subparser.add_subparsers(help="buildcache sub-commands")
push = subparsers.add_parser("push", aliases=["create"], help=push_fn.__doc__)
# TODO: remove from Spack 0.21
push.add_argument(
"-r",
"--rel",
action="store_true",
help="make all rpaths relative before creating tarballs. (deprecated)",
)
push.add_argument("-f", "--force", action="store_true", help="overwrite tarball if it exists.")
push.add_argument(
"-u", "--unsigned", action="store_true", help="push unsigned buildcache tarballs"
@@ -63,37 +56,7 @@ def setup_parser(subparser):
push.add_argument(
"-k", "--key", metavar="key", type=str, default=None, help="Key for signing."
)
output = push.add_mutually_exclusive_group(required=False)
# TODO: remove from Spack 0.21
output.add_argument(
"-d",
"--directory",
metavar="directory",
dest="mirror_flag",
type=arguments.mirror_directory,
help="local directory where buildcaches will be written. (deprecated)",
)
# TODO: remove from Spack 0.21
output.add_argument(
"-m",
"--mirror-name",
metavar="mirror-name",
dest="mirror_flag",
type=arguments.mirror_name,
help="name of the mirror where buildcaches will be written. (deprecated)",
)
# TODO: remove from Spack 0.21
output.add_argument(
"--mirror-url",
metavar="mirror-url",
dest="mirror_flag",
type=arguments.mirror_url,
help="URL of the mirror where buildcaches will be written. (deprecated)",
)
# Unfortunately we cannot add this to the mutually exclusive group above,
# because we have further positional arguments.
# TODO: require from Spack 0.21
push.add_argument("mirror", type=str, help="Mirror name, path, or URL.", nargs="?")
push.add_argument("mirror", type=str, help="Mirror name, path, or URL.")
push.add_argument(
"--update-index",
"--rebuild-index",
@@ -127,13 +90,6 @@ def setup_parser(subparser):
install.add_argument(
"-m", "--multiple", action="store_true", help="allow all matching packages "
)
# TODO: remove from Spack 0.21
install.add_argument(
"-a",
"--allow-root",
action="store_true",
help="allow install root string in binary files after RPATH substitution. (deprecated)",
)
install.add_argument(
"-u",
"--unsigned",
@@ -272,71 +228,17 @@ def setup_parser(subparser):
default=None,
help="A quoted glob pattern identifying copy manifest files",
)
source = sync.add_mutually_exclusive_group(required=False)
# TODO: remove in Spack 0.21
source.add_argument(
"--src-directory",
metavar="DIRECTORY",
dest="src_mirror_flag",
type=arguments.mirror_directory,
help="Source mirror as a local file path (deprecated)",
)
# TODO: remove in Spack 0.21
source.add_argument(
"--src-mirror-name",
metavar="MIRROR_NAME",
dest="src_mirror_flag",
type=arguments.mirror_name,
help="Name of the source mirror (deprecated)",
)
# TODO: remove in Spack 0.21
source.add_argument(
"--src-mirror-url",
metavar="MIRROR_URL",
dest="src_mirror_flag",
type=arguments.mirror_url,
help="URL of the source mirror (deprecated)",
)
# TODO: only support this in 0.21
source.add_argument(
sync.add_argument(
"src_mirror",
metavar="source mirror",
type=arguments.mirror_name_or_url,
help="Source mirror name, path, or URL",
nargs="?",
)
dest = sync.add_mutually_exclusive_group(required=False)
# TODO: remove in Spack 0.21
dest.add_argument(
"--dest-directory",
metavar="DIRECTORY",
dest="dest_mirror_flag",
type=arguments.mirror_directory,
help="Destination mirror as a local file path (deprecated)",
)
# TODO: remove in Spack 0.21
dest.add_argument(
"--dest-mirror-name",
metavar="MIRROR_NAME",
type=arguments.mirror_name,
dest="dest_mirror_flag",
help="Name of the destination mirror (deprecated)",
)
# TODO: remove in Spack 0.21
dest.add_argument(
"--dest-mirror-url",
metavar="MIRROR_URL",
dest="dest_mirror_flag",
type=arguments.mirror_url,
help="URL of the destination mirror (deprecated)",
)
# TODO: only support this in 0.21
dest.add_argument(
sync.add_argument(
"dest_mirror",
metavar="destination mirror",
type=arguments.mirror_name_or_url,
help="Destination mirror name, path, or URL",
nargs="?",
)
sync.set_defaults(func=sync_fn)
@@ -344,39 +246,8 @@ def setup_parser(subparser):
update_index = subparsers.add_parser(
"update-index", aliases=["rebuild-index"], help=update_index_fn.__doc__
)
update_index_out = update_index.add_mutually_exclusive_group(required=True)
# TODO: remove in Spack 0.21
update_index_out.add_argument(
"-d",
"--directory",
metavar="directory",
dest="mirror_flag",
type=arguments.mirror_directory,
help="local directory where buildcaches will be written (deprecated)",
)
# TODO: remove in Spack 0.21
update_index_out.add_argument(
"-m",
"--mirror-name",
metavar="mirror-name",
dest="mirror_flag",
type=arguments.mirror_name,
help="name of the mirror where buildcaches will be written (deprecated)",
)
# TODO: remove in Spack 0.21
update_index_out.add_argument(
"--mirror-url",
metavar="mirror-url",
dest="mirror_flag",
type=arguments.mirror_url,
help="URL of the mirror where buildcaches will be written (deprecated)",
)
# TODO: require from Spack 0.21
update_index_out.add_argument(
"mirror",
type=arguments.mirror_name_or_url,
help="Destination mirror name, path, or URL",
nargs="?",
update_index.add_argument(
"mirror", type=arguments.mirror_name_or_url, help="Destination mirror name, path, or URL"
)
update_index.add_argument(
"-k",
@@ -436,32 +307,12 @@ def _concrete_spec_from_args(args):
def push_fn(args):
"""create a binary package and push it to a mirror"""
if args.mirror_flag:
mirror = args.mirror_flag
elif not args.mirror:
raise ValueError("No mirror provided")
else:
mirror = arguments.mirror_name_or_url(args.mirror)
if args.mirror_flag:
tty.warn(
"Using flags to specify mirrors is deprecated and will be removed in "
"Spack 0.21, use positional arguments instead."
)
if args.rel:
tty.warn("The --rel flag is deprecated and will be removed in Spack 0.21")
# TODO: remove this in 0.21. If we have mirror_flag, the first
# spec is in the positional mirror arg due to argparse limitations.
input_specs = args.specs
if args.mirror_flag and args.mirror:
input_specs.insert(0, args.mirror)
mirror = arguments.mirror_name_or_url(args.mirror)
url = mirror.push_url
specs = bindist.specs_to_be_packaged(
_matching_specs(input_specs, args.spec_file),
_matching_specs(args.specs, args.spec_file),
root="package" in args.things_to_install,
dependencies="dependencies" in args.things_to_install,
)
@@ -486,7 +337,6 @@ def push_fn(args):
url,
bindist.PushOptions(
force=args.force,
relative=args.rel,
unsigned=args.unsigned,
allow_root=args.allow_root,
key=args.key,
@@ -524,9 +374,6 @@ def install_fn(args):
if not args.specs:
tty.die("a spec argument is required to install from a buildcache")
if args.allow_root:
tty.warn("The --allow-root flag is deprecated and will be removed in Spack 0.21")
query = bindist.BinaryCacheQuery(all_architectures=args.otherarch)
matches = spack.store.find(args.specs, multiple=args.multiple, query_fn=query)
for match in matches:
@@ -710,21 +557,8 @@ def sync_fn(args):
manifest_copy(glob.glob(args.manifest_glob))
return 0
# If no manifest_glob, require a source and dest mirror.
# TODO: Simplify in Spack 0.21
if not (args.src_mirror_flag or args.src_mirror) or not (
args.dest_mirror_flag or args.dest_mirror
):
raise ValueError("Source and destination mirror are required.")
if args.src_mirror_flag or args.dest_mirror_flag:
tty.warn(
"Using flags to specify mirrors is deprecated and will be removed in "
"Spack 0.21, use positional arguments instead."
)
src_mirror = args.src_mirror_flag if args.src_mirror_flag else args.src_mirror
dest_mirror = args.dest_mirror_flag if args.dest_mirror_flag else args.dest_mirror
src_mirror = args.src_mirror
dest_mirror = args.dest_mirror
src_mirror_url = src_mirror.fetch_url
dest_mirror_url = dest_mirror.push_url
@@ -803,13 +637,7 @@ def update_index(mirror: spack.mirror.Mirror, update_keys=False):
def update_index_fn(args):
"""Update a buildcache index."""
if args.mirror_flag:
tty.warn(
"Using flags to specify mirrors is deprecated and will be removed in "
"Spack 0.21, use positional arguments instead."
)
mirror = args.mirror_flag if args.mirror_flag else args.mirror
update_index(mirror, update_keys=args.keys)
update_index(args.mirror, update_keys=args.keys)
def buildcache(parser, args):

View File

@@ -228,7 +228,7 @@ def ci_reindex(args):
Use the active, gitlab-enabled environment to rebuild the buildcache
index for the associated mirror."""
env = spack.cmd.require_active_env(cmd_name="ci rebuild-index")
yaml_root = ev.config_dict(env.manifest)
yaml_root = env.manifest[ev.TOP_LEVEL_KEY]
if "mirrors" not in yaml_root or len(yaml_root["mirrors"].values()) < 1:
tty.die("spack ci rebuild-index requires an env containing a mirror")

View File

@@ -349,7 +349,7 @@ def install_status():
"-I",
"--install-status",
action="store_true",
default=False,
default=True,
help="show install status of packages. packages can be: "
"installed [+], missing and needed by an installed package [-], "
"installed in and upstream instance [^], "
@@ -357,6 +357,17 @@ def install_status():
)
@arg
def no_install_status():
return Args(
"--no-install-status",
dest="install_status",
action="store_false",
default=True,
help="do not show install status annotations",
)
@arg
def no_checksum():
return Args(

View File

@@ -715,7 +715,7 @@ def __call__(self, stage, url):
output = tar("--exclude=*/*/*", "-tf", stage.archive_file, output=str)
except ProcessError:
output = ""
lines = output.split("\n")
lines = output.splitlines()
# Determine the build system based on the files contained
# in the archive.

View File

@@ -44,7 +44,11 @@ def setup_parser(subparser):
)
# Below are arguments w.r.t. spec display (like spack spec)
arguments.add_common_arguments(subparser, ["long", "very_long", "install_status"])
arguments.add_common_arguments(subparser, ["long", "very_long"])
install_status_group = subparser.add_mutually_exclusive_group()
arguments.add_common_arguments(install_status_group, ["install_status", "no_install_status"])
subparser.add_argument(
"-y",
"--yaml",

View File

@@ -31,7 +31,11 @@ def setup_parser(subparser):
for further documentation regarding the spec syntax, see:
spack help --spec
"""
arguments.add_common_arguments(subparser, ["long", "very_long", "install_status"])
arguments.add_common_arguments(subparser, ["long", "very_long"])
install_status_group = subparser.add_mutually_exclusive_group()
arguments.add_common_arguments(install_status_group, ["install_status", "no_install_status"])
format_group = subparser.add_mutually_exclusive_group()
format_group.add_argument(
"-y",

View File

@@ -151,7 +151,11 @@ def setup_custom_environment(self, pkg, env):
arch = arch.replace("-", "_")
# vcvars can target specific sdk versions, force it to pick up concretized sdk
# version, if needed by spec
sdk_ver = "" if "win-sdk" not in pkg.spec else pkg.spec["win-sdk"].version.string + ".0"
sdk_ver = (
""
if "win-sdk" not in pkg.spec or pkg.name == "win-sdk"
else pkg.spec["win-sdk"].version.string + ".0"
)
# provide vcvars with msvc version selected by concretization,
# not whatever it happens to pick up on the system (highest available version)
out = subprocess.check_output( # novermin

View File

@@ -81,7 +81,7 @@
# Same as above, but including keys for environments
# this allows us to unify config reading between configs and environments
all_schemas = copy.deepcopy(section_schemas)
all_schemas.update(dict((key, spack.schema.env.schema) for key in spack.schema.env.keys))
all_schemas.update({spack.schema.env.TOP_LEVEL_KEY: spack.schema.env.schema})
#: Path to the default configuration
configuration_defaults_path = ("defaults", os.path.join(spack.paths.etc_path, "defaults"))
@@ -111,14 +111,6 @@
overrides_base_name = "overrides-"
def first_existing(dictionary, keys):
"""Get the value of the first key in keys that is in the dictionary."""
try:
return next(k for k in keys if k in dictionary)
except StopIteration:
raise KeyError("None of %s is in dict!" % str(keys))
class ConfigScope(object):
"""This class represents a configuration scope.
@@ -838,12 +830,10 @@ def _config():
def add_from_file(filename, scope=None):
"""Add updates to a config from a filename"""
import spack.environment as ev
# Get file as config dict
# Extract internal attributes, if we are dealing with an environment
data = read_config_file(filename)
if any(k in data for k in spack.schema.env.keys):
data = ev.config_dict(data)
if spack.schema.env.TOP_LEVEL_KEY in data:
data = data[spack.schema.env.TOP_LEVEL_KEY]
# update all sections from config dict
# We have to iterate on keys to keep overrides from the file

View File

@@ -37,7 +37,7 @@ def validate(configuration_file):
config = syaml.load(f)
# Ensure we have a "container" attribute with sensible defaults set
env_dict = ev.config_dict(config)
env_dict = config[ev.TOP_LEVEL_KEY]
env_dict.setdefault(
"container", {"format": "docker", "images": {"os": "ubuntu:22.04", "spack": "develop"}}
)

View File

@@ -50,7 +50,7 @@ def create(configuration, last_phase=None):
configuration (dict): how to generate the current recipe
last_phase (str): last phase to be printed or None to print them all
"""
name = ev.config_dict(configuration)["container"]["format"]
name = configuration[ev.TOP_LEVEL_KEY]["container"]["format"]
return _writer_factory[name](configuration, last_phase)
@@ -138,7 +138,7 @@ class PathContext(tengine.Context):
template_name: Optional[str] = None
def __init__(self, config, last_phase):
self.config = ev.config_dict(config)
self.config = config[ev.TOP_LEVEL_KEY]
self.container_config = self.config["container"]
# Operating system tag as written in the configuration file

View File

@@ -164,7 +164,10 @@ def entries_to_specs(entries):
continue
parent_spec = spec_dict[entry["hash"]]
dep_spec = spec_dict[dep_hash]
parent_spec._add_dependency(dep_spec, deptypes=deptypes)
parent_spec._add_dependency(dep_spec, deptypes=deptypes, virtuals=())
for spec in spec_dict.values():
spack.spec.reconstruct_virtuals_on_edges(spec)
return spec_dict

View File

@@ -60,7 +60,7 @@
# DB version. This is stuck in the DB file to track changes in format.
# Increment by one when the database format changes.
# Versions before 5 were not integers.
_db_version = vn.Version("6")
_db_version = vn.Version("7")
# For any version combinations here, skip reindex when upgrading.
# Reindexing can take considerable time and is not always necessary.
@@ -72,6 +72,7 @@
# version is saved to disk the first time the DB is written.
(vn.Version("0.9.3"), vn.Version("5")),
(vn.Version("5"), vn.Version("6")),
(vn.Version("6"), vn.Version("7")),
]
# Default timeout for spack database locks in seconds or None (no timeout).
@@ -105,7 +106,11 @@
def reader(version):
reader_cls = {vn.Version("5"): spack.spec.SpecfileV1, vn.Version("6"): spack.spec.SpecfileV3}
reader_cls = {
vn.Version("5"): spack.spec.SpecfileV1,
vn.Version("6"): spack.spec.SpecfileV3,
vn.Version("7"): spack.spec.SpecfileV4,
}
return reader_cls[version]
@@ -743,7 +748,9 @@ def _assign_dependencies(self, spec_reader, hash_key, installs, data):
spec_node_dict = spec_node_dict[spec.name]
if "dependencies" in spec_node_dict:
yaml_deps = spec_node_dict["dependencies"]
for dname, dhash, dtypes, _ in spec_reader.read_specfile_dep_specs(yaml_deps):
for dname, dhash, dtypes, _, virtuals in spec_reader.read_specfile_dep_specs(
yaml_deps
):
# It is important that we always check upstream installations
# in the same order, and that we always check the local
# installation first: if a downstream Spack installs a package
@@ -766,7 +773,7 @@ def _assign_dependencies(self, spec_reader, hash_key, installs, data):
tty.warn(msg)
continue
spec._add_dependency(child, deptypes=dtypes)
spec._add_dependency(child, deptypes=dtypes, virtuals=virtuals)
def _read_from_file(self, filename):
"""Fill database from file, do not maintain old data.
@@ -1172,7 +1179,7 @@ def _add(
for dep in spec.edges_to_dependencies(deptype=_tracked_deps):
dkey = dep.spec.dag_hash()
upstream, record = self.query_by_spec_hash(dkey)
new_spec._add_dependency(record.spec, deptypes=dep.deptypes)
new_spec._add_dependency(record.spec, deptypes=dep.deptypes, virtuals=dep.virtuals)
if not upstream:
record.ref_count += 1

View File

@@ -112,15 +112,10 @@ def path_to_dict(search_paths):
# Reverse order of search directories so that a lib in the first
# entry overrides later entries
for search_path in reversed(search_paths):
try:
for lib in os.listdir(search_path):
lib_path = os.path.join(search_path, lib)
if llnl.util.filesystem.is_readable_file(lib_path):
path_to_lib[lib_path] = lib
except OSError as e:
msg = f"cannot scan '{search_path}' for external software: {str(e)}"
llnl.util.tty.debug(msg)
for lib in os.listdir(search_path):
lib_path = os.path.join(search_path, lib)
if llnl.util.filesystem.is_readable_file(lib_path):
path_to_lib[lib_path] = lib
return path_to_lib

View File

@@ -337,6 +337,7 @@
"""
from .environment import (
TOP_LEVEL_KEY,
Environment,
SpackEnvironmentError,
SpackEnvironmentViewError,
@@ -345,7 +346,6 @@
active_environment,
all_environment_names,
all_environments,
config_dict,
create,
create_in_dir,
deactivate,
@@ -369,6 +369,7 @@
)
__all__ = [
"TOP_LEVEL_KEY",
"Environment",
"SpackEnvironmentError",
"SpackEnvironmentViewError",
@@ -377,7 +378,6 @@
"active_environment",
"all_environment_names",
"all_environments",
"config_dict",
"create",
"create_in_dir",
"deactivate",

View File

@@ -39,6 +39,7 @@
import spack.stage
import spack.store
import spack.subprocess_context
import spack.traverse
import spack.user_environment as uenv
import spack.util.cpus
import spack.util.environment
@@ -50,9 +51,9 @@
import spack.util.spack_yaml as syaml
import spack.util.url
import spack.version
from spack import traverse
from spack.filesystem_view import SimpleFilesystemView, inverse_view_func_parser, view_func_parser
from spack.installer import PackageInstaller
from spack.schema.env import TOP_LEVEL_KEY
from spack.spec import Spec
from spack.spec_list import InvalidSpecConstraintError, SpecList
from spack.util.path import substitute_path_variables
@@ -124,7 +125,7 @@ def default_manifest_yaml():
valid_environment_name_re = r"^\w[\w-]*$"
#: version of the lockfile format. Must increase monotonically.
lockfile_format_version = 4
lockfile_format_version = 5
READER_CLS = {
@@ -132,6 +133,7 @@ def default_manifest_yaml():
2: spack.spec.SpecfileV1,
3: spack.spec.SpecfileV2,
4: spack.spec.SpecfileV3,
5: spack.spec.SpecfileV4,
}
@@ -361,19 +363,6 @@ def ensure_env_root_path_exists():
fs.mkdirp(env_root_path())
def config_dict(yaml_data):
"""Get the configuration scope section out of an spack.yaml"""
# TODO (env:): Remove env: as a possible top level keyword in v0.21
key = spack.config.first_existing(yaml_data, spack.schema.env.keys)
if key == "env":
msg = (
"using 'env:' as a top-level attribute of a Spack environment is deprecated and "
"will be removed in Spack v0.21. Please use 'spack:' instead."
)
warnings.warn(msg)
return yaml_data[key]
def all_environment_names():
"""List the names of environments that currently exist."""
# just return empty if the env path does not exist. A read-only
@@ -437,6 +426,32 @@ def _is_dev_spec_and_has_changed(spec):
return mtime > record.installation_time
def _spec_needs_overwrite(spec, changed_dev_specs):
"""Check whether the current spec needs to be overwritten because either it has
changed itself or one of its dependencies have changed
"""
# if it's not installed, we don't need to overwrite it
if not spec.installed:
return False
# If the spec itself has changed this is a trivial decision
if spec in changed_dev_specs:
return True
# if spec and all deps aren't dev builds, we don't need to overwrite it
if not any(spec.satisfies(c) for c in ("dev_path=*", "^dev_path=*")):
return False
# If any dep needs overwrite, or any dep is missing and is a dev build then
# overwrite this package
if any(
((not dep.installed) and dep.satisfies("dev_path=*"))
or _spec_needs_overwrite(dep, changed_dev_specs)
for dep in spec.traverse(root=False)
):
return True
def _error_on_nonempty_view_dir(new_root):
"""Defensively error when the target view path already exists and is not an
empty directory. This usually happens when the view symlink was removed, but
@@ -621,16 +636,18 @@ def specs_for_view(self, concretized_root_specs):
From the list of concretized user specs in the environment, flatten
the dags, and filter selected, installed specs, remove duplicates on dag hash.
"""
dag_hash = lambda spec: spec.dag_hash()
# With deps, requires traversal
if self.link == "all" or self.link == "run":
deptype = ("run") if self.link == "run" else ("link", "run")
specs = list(
traverse.traverse_nodes(
concretized_root_specs, deptype=deptype, key=traverse.by_dag_hash
spack.traverse.traverse_nodes(
concretized_root_specs, deptype=deptype, key=dag_hash
)
)
else:
specs = list(dedupe(concretized_root_specs, key=traverse.by_dag_hash))
specs = list(dedupe(concretized_root_specs, key=dag_hash))
# Filter selected, installed specs
with spack.store.db.read_transaction():
@@ -793,8 +810,8 @@ def write_transaction(self):
def _construct_state_from_manifest(self):
"""Read manifest file and set up user specs."""
self.spec_lists = collections.OrderedDict()
for item in config_dict(self.manifest).get("definitions", []):
env_configuration = self.manifest[TOP_LEVEL_KEY]
for item in env_configuration.get("definitions", []):
entry = copy.deepcopy(item)
when = _eval_conditional(entry.pop("when", "True"))
assert len(entry) == 1
@@ -806,13 +823,13 @@ def _construct_state_from_manifest(self):
else:
self.spec_lists[name] = user_specs
spec_list = config_dict(self.manifest).get(user_speclist_name, [])
spec_list = env_configuration.get(user_speclist_name, [])
user_specs = SpecList(
user_speclist_name, [s for s in spec_list if s], self.spec_lists.copy()
)
self.spec_lists[user_speclist_name] = user_specs
enable_view = config_dict(self.manifest).get("view")
enable_view = env_configuration.get("view")
# enable_view can be boolean, string, or None
if enable_view is True or enable_view is None:
self.views = {default_view_name: ViewDescriptor(self.path, self.view_path_default)}
@@ -827,14 +844,11 @@ def _construct_state_from_manifest(self):
else:
self.views = {}
# Retrieve the current concretization strategy
configuration = config_dict(self.manifest)
# Retrieve unification scheme for the concretizer
self.unify = spack.config.get("concretizer:unify", False)
# Retrieve dev-build packages:
self.dev_specs = copy.deepcopy(configuration.get("develop", {}))
self.dev_specs = copy.deepcopy(env_configuration.get("develop", {}))
for name, entry in self.dev_specs.items():
# spec must include a concrete version
assert Spec(entry["spec"]).versions.concrete_range_as_version
@@ -954,7 +968,7 @@ def included_config_scopes(self):
# load config scopes added via 'include:', in reverse so that
# highest-precedence scopes are last.
includes = config_dict(self.manifest).get("include", [])
includes = self.manifest[TOP_LEVEL_KEY].get("include", [])
missing = []
for i, config_path in enumerate(reversed(includes)):
# allow paths to contain spack config/environment variables, etc.
@@ -1047,10 +1061,7 @@ def env_file_config_scope(self):
"""Get the configuration scope for the environment's manifest file."""
config_name = self.env_file_config_scope_name()
return spack.config.SingleFileScope(
config_name,
self.manifest_path,
spack.schema.env.schema,
[spack.config.first_existing(self.manifest, spack.schema.env.keys)],
config_name, self.manifest_path, spack.schema.env.schema, [TOP_LEVEL_KEY]
)
def config_scopes(self):
@@ -1538,12 +1549,13 @@ def _concretize_separately(self, tests=False):
for h in self.specs_by_hash:
current_spec, computed_spec = self.specs_by_hash[h], by_hash[h]
for node in computed_spec.traverse():
test_deps = node.dependencies(deptype="test")
for test_dependency in test_deps:
test_edges = node.edges_to_dependencies(deptype="test")
for current_edge in test_edges:
test_dependency = current_edge.spec
if test_dependency in current_spec[node.name]:
continue
current_spec[node.name].add_dependency_edge(
test_dependency.copy(), deptypes="test"
test_dependency.copy(), deptypes="test", virtuals=current_edge.virtuals
)
results = [
@@ -1796,29 +1808,17 @@ def _add_concrete_spec(self, spec, concrete, new=True):
self.specs_by_hash[h] = concrete
def _get_overwrite_specs(self):
# Find all dev specs that were modified.
changed_dev_specs = [
s
for s in traverse.traverse_nodes(
self.concrete_roots(), order="breadth", key=traverse.by_dag_hash
)
if _is_dev_spec_and_has_changed(s)
]
# Collect all specs in the environment first before checking which ones
# to rebuild to avoid checking the same specs multiple times
specs_to_check = set()
for dag_hash in self.concretized_order:
root_spec = self.specs_by_hash[dag_hash]
specs_to_check.update(root_spec.traverse(root=True))
changed_dev_specs = set(s for s in specs_to_check if _is_dev_spec_and_has_changed(s))
# Collect their hashes, and the hashes of their installed parents.
# Notice: with order=breadth all changed dev specs are at depth 0,
# even if they occur as parents of one another.
return [
spec.dag_hash()
for depth, spec in traverse.traverse_nodes(
changed_dev_specs,
root=True,
order="breadth",
depth=True,
direction="parents",
key=traverse.by_dag_hash,
)
if depth == 0 or spec.installed
s.dag_hash() for s in specs_to_check if _spec_needs_overwrite(s, changed_dev_specs)
]
def _install_log_links(self, spec):
@@ -1925,7 +1925,7 @@ def install_specs(self, specs=None, **install_args):
def all_specs(self):
"""Return all specs, even those a user spec would shadow."""
roots = [self.specs_by_hash[h] for h in self.concretized_order]
specs = [s for s in traverse.traverse_nodes(roots, key=traverse.by_dag_hash)]
specs = [s for s in spack.traverse.traverse_nodes(roots, lambda s: s.dag_hash())]
specs.sort()
return specs
@@ -1971,18 +1971,13 @@ def concrete_roots(self):
roots *without* associated user spec"""
return [root for _, root in self.concretized_specs()]
def get_by_hash(self, dag_hash: str) -> List[Spec]:
# If it's not a partial hash prefix we can early exit
early_exit = len(dag_hash) == 32
matches = []
for spec in traverse.traverse_nodes(
self.concrete_roots(), key=traverse.by_dag_hash, order="breadth"
):
def get_by_hash(self, dag_hash):
matches = {}
roots = [self.specs_by_hash[h] for h in self.concretized_order]
for spec in spack.traverse.traverse_nodes(roots, key=lambda s: s.dag_hash()):
if spec.dag_hash().startswith(dag_hash):
matches.append(spec)
if early_exit:
break
return matches
matches[spec.dag_hash()] = spec
return list(matches.values())
def get_one_by_hash(self, dag_hash):
"""Returns the single spec from the environment which matches the
@@ -1994,14 +1989,11 @@ def get_one_by_hash(self, dag_hash):
def all_matching_specs(self, *specs: spack.spec.Spec) -> List[Spec]:
"""Returns all concretized specs in the environment satisfying any of the input specs"""
# Look up abstract hashes ahead of time, to avoid O(n^2) traversal.
specs = [s.lookup_hash() for s in specs]
# Avoid double lookup by directly calling _satisfies.
key = lambda s: s.dag_hash()
return [
s
for s in traverse.traverse_nodes(self.concrete_roots(), key=traverse.by_dag_hash)
if any(s._satisfies(t) for t in specs)
for s in spack.traverse.traverse_nodes(self.concrete_roots(), key=key)
if any(s.satisfies(t) for t in specs)
]
@spack.repo.autospec
@@ -2025,9 +2017,9 @@ def matching_spec(self, spec):
env_root_to_user = {root.dag_hash(): user for user, root in self.concretized_specs()}
root_matches, dep_matches = [], []
for env_spec in traverse.traverse_nodes(
for env_spec in spack.traverse.traverse_nodes(
specs=[root for _, root in self.concretized_specs()],
key=traverse.by_dag_hash,
key=lambda s: s.dag_hash(),
order="breadth",
):
if not env_spec.satisfies(spec):
@@ -2101,8 +2093,8 @@ def _get_environment_specs(self, recurse_dependencies=True):
if recurse_dependencies:
specs.extend(
traverse.traverse_nodes(
specs, root=False, deptype=("link", "run"), key=traverse.by_dag_hash
spack.traverse.traverse_nodes(
specs, root=False, deptype=("link", "run"), key=lambda s: s.dag_hash()
)
)
@@ -2111,7 +2103,9 @@ def _get_environment_specs(self, recurse_dependencies=True):
def _to_lockfile_dict(self):
"""Create a dictionary to store a lockfile for this environment."""
concrete_specs = {}
for s in traverse.traverse_nodes(self.specs_by_hash.values(), key=traverse.by_dag_hash):
for s in spack.traverse.traverse_nodes(
self.specs_by_hash.values(), key=lambda s: s.dag_hash()
):
spec_dict = s.node_dict_with_hashes(hash=ht.dag_hash)
# Assumes no legacy formats, since this was just created.
spec_dict[ht.dag_hash.name] = s.dag_hash()
@@ -2192,9 +2186,9 @@ def _read_lockfile_dict(self, d):
# and add them to the spec
for lockfile_key, node_dict in json_specs_by_hash.items():
name, data = reader.name_and_data(node_dict)
for _, dep_hash, deptypes, _ in reader.dependencies_from_node_dict(data):
for _, dep_hash, deptypes, _, virtuals in reader.dependencies_from_node_dict(data):
specs_by_hash[lockfile_key]._add_dependency(
specs_by_hash[dep_hash], deptypes=deptypes
specs_by_hash[dep_hash], deptypes=deptypes, virtuals=virtuals
)
# Traverse the root specs one at a time in the order they appear.
@@ -2268,7 +2262,7 @@ def ensure_env_directory_exists(self, dot_env: bool = False) -> None:
def update_environment_repository(self) -> None:
"""Updates the repository associated with the environment."""
for spec in traverse.traverse_nodes(self.new_specs):
for spec in spack.traverse.traverse_nodes(self.new_specs):
if not spec.concrete:
raise ValueError("specs passed to environment.write() must be concrete!")
@@ -2386,17 +2380,28 @@ def _concretize_from_constraints(spec_constraints, tests=False):
# Accept only valid constraints from list and concretize spec
# Get the named spec even if out of order
root_spec = [s for s in spec_constraints if s.name]
if len(root_spec) != 1:
m = "The constraints %s are not a valid spec " % spec_constraints
m += "concretization target. all specs must have a single name "
m += "constraint for concretization."
raise InvalidSpecConstraintError(m)
spec_constraints.remove(root_spec[0])
hash_spec = [s for s in spec_constraints if s.abstract_hash]
error_message = "The constraints %s are not a valid spec " % spec_constraints
error_message += "concretization target. all specs must have a single name "
error_message += "constraint for concretization."
if len(root_spec) > 1:
raise InvalidSpecConstraintError(error_message)
if len(root_spec) < 1:
if len(hash_spec) < 1:
raise InvalidSpecConstraintError(error_message)
if root_spec:
spec_constraints.remove(root_spec[0])
root_spec = root_spec[0] if root_spec else Spec()
invalid_constraints = []
while True:
# Attach all anonymous constraints to one named spec
s = root_spec[0].copy()
s = root_spec.copy()
for c in spec_constraints:
if c not in invalid_constraints:
s.constrain(c)
@@ -2674,8 +2679,8 @@ def add_user_spec(self, user_spec: str) -> None:
Args:
user_spec: user spec to be appended
"""
config_dict(self.pristine_yaml_content).setdefault("specs", []).append(user_spec)
config_dict(self.yaml_content).setdefault("specs", []).append(user_spec)
self.pristine_configuration.setdefault("specs", []).append(user_spec)
self.configuration.setdefault("specs", []).append(user_spec)
self.changed = True
def remove_user_spec(self, user_spec: str) -> None:
@@ -2688,8 +2693,8 @@ def remove_user_spec(self, user_spec: str) -> None:
SpackEnvironmentError: when the user spec is not in the list
"""
try:
config_dict(self.pristine_yaml_content)["specs"].remove(user_spec)
config_dict(self.yaml_content)["specs"].remove(user_spec)
self.pristine_configuration["specs"].remove(user_spec)
self.configuration["specs"].remove(user_spec)
except ValueError as e:
msg = f"cannot remove {user_spec} from {self}, no such spec exists"
raise SpackEnvironmentError(msg) from e
@@ -2706,8 +2711,8 @@ def override_user_spec(self, user_spec: str, idx: int) -> None:
SpackEnvironmentError: when the user spec cannot be overridden
"""
try:
config_dict(self.pristine_yaml_content)["specs"][idx] = user_spec
config_dict(self.yaml_content)["specs"][idx] = user_spec
self.pristine_configuration["specs"][idx] = user_spec
self.configuration["specs"][idx] = user_spec
except ValueError as e:
msg = f"cannot override {user_spec} from {self}"
raise SpackEnvironmentError(msg) from e
@@ -2723,14 +2728,14 @@ def add_definition(self, user_spec: str, list_name: str) -> None:
Raises:
SpackEnvironmentError: is no valid definition exists already
"""
defs = config_dict(self.pristine_yaml_content).get("definitions", [])
defs = self.pristine_configuration.get("definitions", [])
msg = f"cannot add {user_spec} to the '{list_name}' definition, no valid list exists"
for idx, item in self._iterate_on_definitions(defs, list_name=list_name, err_msg=msg):
item[list_name].append(user_spec)
break
config_dict(self.yaml_content)["definitions"][idx][list_name].append(user_spec)
self.configuration["definitions"][idx][list_name].append(user_spec)
self.changed = True
def remove_definition(self, user_spec: str, list_name: str) -> None:
@@ -2744,7 +2749,7 @@ def remove_definition(self, user_spec: str, list_name: str) -> None:
SpackEnvironmentError: if the user spec cannot be removed from the list,
or the list does not exist
"""
defs = config_dict(self.pristine_yaml_content).get("definitions", [])
defs = self.pristine_configuration.get("definitions", [])
msg = (
f"cannot remove {user_spec} from the '{list_name}' definition, "
f"no valid list exists"
@@ -2757,7 +2762,7 @@ def remove_definition(self, user_spec: str, list_name: str) -> None:
except ValueError:
pass
config_dict(self.yaml_content)["definitions"][idx][list_name].remove(user_spec)
self.configuration["definitions"][idx][list_name].remove(user_spec)
self.changed = True
def override_definition(self, user_spec: str, *, override: str, list_name: str) -> None:
@@ -2772,7 +2777,7 @@ def override_definition(self, user_spec: str, *, override: str, list_name: str)
Raises:
SpackEnvironmentError: if the user spec cannot be overridden
"""
defs = config_dict(self.pristine_yaml_content).get("definitions", [])
defs = self.pristine_configuration.get("definitions", [])
msg = f"cannot override {user_spec} with {override} in the '{list_name}' definition"
for idx, item in self._iterate_on_definitions(defs, list_name=list_name, err_msg=msg):
@@ -2783,7 +2788,7 @@ def override_definition(self, user_spec: str, *, override: str, list_name: str)
except ValueError:
pass
config_dict(self.yaml_content)["definitions"][idx][list_name][sub_index] = override
self.configuration["definitions"][idx][list_name][sub_index] = override
self.changed = True
def _iterate_on_definitions(self, definitions, *, list_name, err_msg):
@@ -2815,24 +2820,24 @@ def set_default_view(self, view: Union[bool, str, pathlib.Path, Dict[str, str]])
True the default view is used for the environment, if False there's no view.
"""
if isinstance(view, dict):
config_dict(self.pristine_yaml_content)["view"][default_view_name].update(view)
config_dict(self.yaml_content)["view"][default_view_name].update(view)
self.pristine_configuration["view"][default_view_name].update(view)
self.configuration["view"][default_view_name].update(view)
self.changed = True
return
if not isinstance(view, bool):
view = str(view)
config_dict(self.pristine_yaml_content)["view"] = view
config_dict(self.yaml_content)["view"] = view
self.pristine_configuration["view"] = view
self.configuration["view"] = view
self.changed = True
def remove_default_view(self) -> None:
"""Removes the default view from the manifest file"""
view_data = config_dict(self.pristine_yaml_content).get("view")
view_data = self.pristine_configuration.get("view")
if isinstance(view_data, collections.abc.Mapping):
config_dict(self.pristine_yaml_content)["view"].pop(default_view_name)
config_dict(self.yaml_content)["view"].pop(default_view_name)
self.pristine_configuration["view"].pop(default_view_name)
self.configuration["view"].pop(default_view_name)
self.changed = True
return
@@ -2849,12 +2854,10 @@ def add_develop_spec(self, pkg_name: str, entry: Dict[str, str]) -> None:
if entry["path"] == pkg_name:
entry.pop("path")
config_dict(self.pristine_yaml_content).setdefault("develop", {}).setdefault(
pkg_name, {}
).update(entry)
config_dict(self.yaml_content).setdefault("develop", {}).setdefault(pkg_name, {}).update(
self.pristine_configuration.setdefault("develop", {}).setdefault(pkg_name, {}).update(
entry
)
self.configuration.setdefault("develop", {}).setdefault(pkg_name, {}).update(entry)
self.changed = True
def remove_develop_spec(self, pkg_name: str) -> None:
@@ -2867,11 +2870,11 @@ def remove_develop_spec(self, pkg_name: str) -> None:
SpackEnvironmentError: if there is nothing to remove
"""
try:
del config_dict(self.pristine_yaml_content)["develop"][pkg_name]
del self.pristine_configuration["develop"][pkg_name]
except KeyError as e:
msg = f"cannot remove '{pkg_name}' from develop specs in {self}, entry does not exist"
raise SpackEnvironmentError(msg) from e
del config_dict(self.yaml_content)["develop"][pkg_name]
del self.configuration["develop"][pkg_name]
self.changed = True
def absolutify_dev_paths(self, init_file_dir: Union[str, pathlib.Path]) -> None:
@@ -2882,11 +2885,11 @@ def absolutify_dev_paths(self, init_file_dir: Union[str, pathlib.Path]) -> None:
init_file_dir: directory with the "spack.yaml" used to initialize the environment.
"""
init_file_dir = pathlib.Path(init_file_dir).absolute()
for _, entry in config_dict(self.pristine_yaml_content).get("develop", {}).items():
for _, entry in self.pristine_configuration.get("develop", {}).items():
expanded_path = os.path.normpath(str(init_file_dir / entry["path"]))
entry["path"] = str(expanded_path)
for _, entry in config_dict(self.yaml_content).get("develop", {}).items():
for _, entry in self.configuration.get("develop", {}).items():
expanded_path = os.path.normpath(str(init_file_dir / entry["path"]))
entry["path"] = str(expanded_path)
self.changed = True
@@ -2900,6 +2903,16 @@ def flush(self) -> None:
_write_yaml(self.pristine_yaml_content, f)
self.changed = False
@property
def pristine_configuration(self):
"""Return the dictionaries in the pristine YAML, without the top level attribute"""
return self.pristine_yaml_content[TOP_LEVEL_KEY]
@property
def configuration(self):
"""Return the dictionaries in the YAML, without the top level attribute"""
return self.yaml_content[TOP_LEVEL_KEY]
def __len__(self):
return len(self.yaml_content)

View File

@@ -763,11 +763,7 @@ def version_from_git(git_exe):
@property
def git(self):
if not self._git:
try:
self._git = spack.util.git.git(required=True)
except CommandNotFoundError as exc:
tty.error(str(exc))
raise
self._git = spack.util.git.git()
# Disable advice for a quieter fetch
# https://github.com/git/git/blob/master/Documentation/RelNotes/1.7.2.txt

View File

@@ -544,6 +544,7 @@ def _static_edges(specs, deptype):
spack.spec.Spec(parent_name),
spack.spec.Spec(dependency_name),
deptypes=deptype,
virtuals=(),
)

View File

@@ -231,7 +231,9 @@ def _packages_needed_to_bootstrap_compiler(compiler, architecture, pkgs):
dep.concretize()
# mark compiler as depended-on by the packages that use it
for pkg in pkgs:
dep._dependents.add(spack.spec.DependencySpec(pkg.spec, dep, deptypes=("build",)))
dep._dependents.add(
spack.spec.DependencySpec(pkg.spec, dep, deptypes=("build",), virtuals=())
)
packages = [(s.package, False) for s in dep.traverse(order="post", root=False)]
packages.append((dep.package, True))
@@ -2436,11 +2438,10 @@ def get_deptypes(self, pkg):
else:
cache_only = self.install_args.get("dependencies_cache_only")
# Include build dependencies if pkg is going to be built from sources, or
# if build deps are explicitly requested.
if include_build_deps or not (
cache_only or pkg.spec.installed and not pkg.spec.dag_hash() in self.overwrite
):
# Include build dependencies if pkg is not installed and cache_only
# is False, or if build depdencies are explicitly called for
# by include_build_deps.
if include_build_deps or not (cache_only or pkg.spec.installed):
deptypes.append("build")
if self.run_tests(pkg):
deptypes.append("test")

View File

@@ -393,7 +393,7 @@ class BaseConfiguration(object):
querying easier. It needs to be sub-classed for specific module types.
"""
default_projections = {"all": "{name}-{version}-{compiler.name}-{compiler.version}"}
default_projections = {"all": "{name}/{version}-{compiler.name}-{compiler.version}"}
def __init__(self, spec, module_set_name, explicit=None):
# Module where type(self) is defined
@@ -671,12 +671,6 @@ def configure_options(self):
# the configure option section
return None
def modification_needs_formatting(self, modification):
"""Returns True if environment modification entry needs to be formatted."""
return (
not isinstance(modification, (spack.util.environment.SetEnv)) or not modification.raw
)
@tengine.context_property
@memoized
def environment_modifications(self):
@@ -740,12 +734,11 @@ def environment_modifications(self):
_check_tokens_are_valid(x.name, message=msg)
# Transform them
x.name = spec.format(x.name, transform=transform)
if self.modification_needs_formatting(x):
try:
# Not every command has a value
x.value = spec.format(x.value)
except AttributeError:
pass
try:
# Not every command has a value
x.value = spec.format(x.value)
except AttributeError:
pass
x.name = str(x.name).replace("-", "_")
return [(type(x).__name__, x) for x in env if x.name not in exclude]

View File

@@ -108,6 +108,5 @@
# These are just here for editor support; they will be replaced when the build env
# is set up.
make = MakeExecutable("make", jobs=1)
gmake = MakeExecutable("gmake", jobs=1)
ninja = MakeExecutable("ninja", jobs=1)
configure = Executable(join_path(".", "configure"))

View File

@@ -291,7 +291,7 @@ def next_spec(
if root_spec.concrete:
raise spack.spec.RedundantSpecError(root_spec, "^" + str(dependency))
root_spec._add_dependency(dependency, deptypes=())
root_spec._add_dependency(dependency, deptypes=(), virtuals=())
else:
break

View File

@@ -292,8 +292,8 @@ def from_json(stream, repository):
index.providers = _transform(
providers,
lambda vpkg, plist: (
spack.spec.SpecfileV3.from_node_dict(vpkg),
set(spack.spec.SpecfileV3.from_node_dict(p) for p in plist),
spack.spec.SpecfileV4.from_node_dict(vpkg),
set(spack.spec.SpecfileV4.from_node_dict(p) for p in plist),
),
)
return index

View File

@@ -6,7 +6,6 @@
import itertools
import os
import re
import shutil
from collections import OrderedDict
import macholib.mach_o
@@ -356,13 +355,7 @@ def _set_elf_rpaths(target, rpaths):
# Join the paths using ':' as a separator
rpaths_str = ":".join(rpaths)
# If we're relocating patchelf itself, make a copy and use it
bak_path = None
if target.endswith("/bin/patchelf"):
bak_path = target + ".bak"
shutil.copy(target, bak_path)
patchelf, output = executable.Executable(bak_path or _patchelf()), None
patchelf, output = executable.Executable(_patchelf()), None
try:
# TODO: revisit the use of --force-rpath as it might be conditional
# TODO: if we want to support setting RUNPATH from binary packages
@@ -371,9 +364,6 @@ def _set_elf_rpaths(target, rpaths):
except executable.ProcessError as e:
msg = "patchelf --force-rpath --set-rpath {0} failed with error {1}"
tty.warn(msg.format(target, e))
finally:
if bak_path and os.path.exists(bak_path):
os.remove(bak_path)
return output
@@ -686,7 +676,7 @@ def is_relocatable(spec):
Raises:
ValueError: if the spec is not installed
"""
if not spec.installed:
if not spec.install_status():
raise ValueError("spec is not installed [{0}]".format(str(spec)))
if spec.external or spec.virtual:

View File

@@ -24,7 +24,7 @@
import traceback
import types
import uuid
from typing import Any, Dict, List, Union
from typing import Dict, Union
import llnl.util.filesystem as fs
import llnl.util.lang
@@ -424,7 +424,7 @@ def _create_new_cache(self) -> Dict[str, os.stat_result]:
def last_mtime(self):
return max(sinfo.st_mtime for sinfo in self._packages_to_stats.values())
def modified_since(self, since: float) -> List[str]:
def modified_since(self, since):
return [name for name, sinfo in self._packages_to_stats.items() if sinfo.st_mtime > since]
def __getitem__(self, item):
@@ -550,34 +550,35 @@ class RepoIndex(object):
when they're needed.
``Indexers`` should be added to the ``RepoIndex`` using
``add_indexer(name, indexer)``, and they should support the interface
``add_index(name, indexer)``, and they should support the interface
defined by ``Indexer``, so that the ``RepoIndex`` can read, generate,
and update stored indices.
Generated indexes are accessed by name via ``__getitem__()``."""
Generated indexes are accessed by name via ``__getitem__()``.
def __init__(
self,
package_checker: FastPackageChecker,
namespace: str,
cache: spack.util.file_cache.FileCache,
):
"""
def __init__(self, package_checker, namespace, cache):
self.checker = package_checker
self.packages_path = self.checker.packages_path
if sys.platform == "win32":
self.packages_path = spack.util.path.convert_to_posix_path(self.packages_path)
self.namespace = namespace
self.indexers: Dict[str, Indexer] = {}
self.indexes: Dict[str, Any] = {}
self.indexers = {}
self.indexes = {}
self.cache = cache
def add_indexer(self, name: str, indexer: Indexer):
def add_indexer(self, name, indexer):
"""Add an indexer to the repo index.
Arguments:
name: name of this indexer
indexer: object implementing the ``Indexer`` interface"""
name (str): name of this indexer
indexer (object): an object that supports create(), read(),
write(), and get_index() operations
"""
self.indexers[name] = indexer
def __getitem__(self, name):
@@ -598,15 +599,17 @@ def _build_all_indexes(self):
because the main bottleneck here is loading all the packages. It
can take tens of seconds to regenerate sequentially, and we'd
rather only pay that cost once rather than on several
invocations."""
invocations.
"""
for name, indexer in self.indexers.items():
self.indexes[name] = self._build_index(name, indexer)
def _build_index(self, name: str, indexer: Indexer):
def _build_index(self, name, indexer):
"""Determine which packages need an update, and update indexes."""
# Filename of the provider index cache (we assume they're all json)
cache_filename = f"{name}/{self.namespace}-index.json"
cache_filename = "{0}/{1}-index.json".format(name, self.namespace)
# Compute which packages needs to be updated in the cache
index_mtime = self.cache.mtime(cache_filename)
@@ -630,7 +633,8 @@ def _build_index(self, name: str, indexer: Indexer):
needs_update = self.checker.modified_since(new_index_mtime)
for pkg_name in needs_update:
indexer.update(f"{self.namespace}.{pkg_name}")
namespaced_name = "%s.%s" % (self.namespace, pkg_name)
indexer.update(namespaced_name)
indexer.write(new)
@@ -1235,7 +1239,7 @@ def get_pkg_class(self, pkg_name):
try:
module = importlib.import_module(fullname)
except ImportError:
raise UnknownPackageError(pkg_name)
raise UnknownPackageError(fullname)
except Exception as e:
msg = f"cannot load package '{pkg_name}' from the '{self.namespace}' repository: {e}"
raise RepoError(msg) from e

View File

@@ -209,7 +209,7 @@ def update(data):
# Warn if deprecated section is still in the environment
ci_env = ev.active_environment()
if ci_env:
env_config = ev.config_dict(ci_env.manifest)
env_config = ci_env.manifest[ev.TOP_LEVEL_KEY]
if "gitlab-ci" in env_config:
tty.die("Error: `gitlab-ci` section detected with `ci`, these are not compatible")

View File

@@ -15,8 +15,8 @@
import spack.schema.packages
import spack.schema.projections
#: legal first keys in the schema
keys = ("spack", "env")
#: Top level key in a manifest file
TOP_LEVEL_KEY = "spack"
spec_list_schema = {
"type": "array",
@@ -47,8 +47,8 @@
"title": "Spack environment file schema",
"type": "object",
"additionalProperties": False,
"patternProperties": {
"^env|spack$": {
"properties": {
"spack": {
"type": "object",
"default": {},
"additionalProperties": False,

View File

@@ -2500,10 +2500,15 @@ def depends_on(self, pkg, dep, type):
assert len(dependencies) < 2, msg
if not dependencies:
self._specs[pkg].add_dependency_edge(self._specs[dep], deptypes=(type,))
self._specs[pkg].add_dependency_edge(self._specs[dep], deptypes=(type,), virtuals=())
else:
# TODO: This assumes that each solve unifies dependencies
dependencies[0].add_type(type)
dependencies[0].update_deptypes(deptypes=(type,))
def virtual_on_edge(self, pkg, provider, virtual):
dependencies = self._specs[pkg].edges_to_dependencies(name=provider)
assert len(dependencies) == 1
dependencies[0].update_virtuals((virtual,))
def reorder_flags(self):
"""Order compiler flags on specs in predefined order.
@@ -2581,6 +2586,8 @@ def sort_fn(function_tuple):
return (-2, 0)
elif name == "external_spec_selected":
return (0, 0) # note out of order so this goes last
elif name == "virtual_on_edge":
return (1, 0)
else:
return (-1, 0)

View File

@@ -300,6 +300,11 @@ attr("depends_on", Package, Provider, Type)
provider(Provider, Virtual),
not external(Package).
attr("virtual_on_edge", Package, Provider, Virtual)
:- dependency_holds(Package, Virtual, Type),
provider(Provider, Virtual),
not external(Package).
% dependencies on virtuals also imply that the virtual is a virtual node
attr("virtual_node", Virtual)
:- dependency_holds(Package, Virtual, Type),

View File

@@ -50,7 +50,6 @@
"""
import collections
import collections.abc
import enum
import io
import itertools
import os
@@ -171,17 +170,7 @@
)
#: specfile format version. Must increase monotonically
SPECFILE_FORMAT_VERSION = 3
# InstallStatus is used to map install statuses to symbols for display
# Options are artificially disjoint for dispay purposes
class InstallStatus(enum.Enum):
installed = "@g{[+]} "
upstream = "@g{[^]} "
external = "@g{[e]} "
absent = "@K{ - } "
missing = "@r{[-]} "
SPECFILE_FORMAT_VERSION = 4
def colorize_spec(spec):
@@ -725,47 +714,81 @@ class DependencySpec:
parent: starting node of the edge
spec: ending node of the edge.
deptypes: list of strings, representing dependency relationships.
virtuals: virtual packages provided from child to parent node.
"""
__slots__ = "parent", "spec", "deptypes"
__slots__ = "parent", "spec", "parameters"
def __init__(self, parent: "Spec", spec: "Spec", *, deptypes: dp.DependencyArgument):
def __init__(
self,
parent: "Spec",
spec: "Spec",
*,
deptypes: dp.DependencyArgument,
virtuals: Tuple[str, ...],
):
self.parent = parent
self.spec = spec
self.deptypes = dp.canonical_deptype(deptypes)
self.parameters = {
"deptypes": dp.canonical_deptype(deptypes),
"virtuals": tuple(sorted(set(virtuals))),
}
def update_deptypes(self, deptypes: dp.DependencyArgument) -> bool:
deptypes = set(deptypes)
deptypes.update(self.deptypes)
deptypes = tuple(sorted(deptypes))
changed = self.deptypes != deptypes
@property
def deptypes(self) -> Tuple[str, ...]:
return self.parameters["deptypes"]
self.deptypes = deptypes
return changed
@property
def virtuals(self) -> Tuple[str, ...]:
return self.parameters["virtuals"]
def _update_edge_multivalued_property(
self, property_name: str, value: Tuple[str, ...]
) -> bool:
current = self.parameters[property_name]
update = set(current) | set(value)
update = tuple(sorted(update))
changed = current != update
if not changed:
return False
self.parameters[property_name] = update
return True
def update_deptypes(self, deptypes: Tuple[str, ...]) -> bool:
"""Update the current dependency types"""
return self._update_edge_multivalued_property("deptypes", deptypes)
def update_virtuals(self, virtuals: Tuple[str, ...]) -> bool:
"""Update the list of provided virtuals"""
return self._update_edge_multivalued_property("virtuals", virtuals)
def copy(self) -> "DependencySpec":
return DependencySpec(self.parent, self.spec, deptypes=self.deptypes)
def add_type(self, type: dp.DependencyArgument):
self.deptypes = dp.canonical_deptype(self.deptypes + dp.canonical_deptype(type))
"""Return a copy of this edge"""
return DependencySpec(
self.parent, self.spec, deptypes=self.deptypes, virtuals=self.virtuals
)
def _cmp_iter(self):
yield self.parent.name if self.parent else None
yield self.spec.name if self.spec else None
yield self.deptypes
yield self.virtuals
def __str__(self) -> str:
return "%s %s--> %s" % (
self.parent.name if self.parent else None,
self.deptypes,
self.spec.name if self.spec else None,
)
parent = self.parent.name if self.parent else None
child = self.spec.name if self.spec else None
return f"{parent} {self.deptypes}[virtuals={','.join(self.virtuals)}] --> {child}"
def canonical(self) -> Tuple[str, str, Tuple[str, ...]]:
return self.parent.dag_hash(), self.spec.dag_hash(), self.deptypes
def canonical(self) -> Tuple[str, str, Tuple[str, ...], Tuple[str, ...]]:
return self.parent.dag_hash(), self.spec.dag_hash(), self.deptypes, self.virtuals
def flip(self) -> "DependencySpec":
return DependencySpec(parent=self.spec, spec=self.parent, deptypes=self.deptypes)
"""Flip the dependency, and drop virtual information"""
return DependencySpec(
parent=self.spec, spec=self.parent, deptypes=self.deptypes, virtuals=()
)
class CompilerFlag(str):
@@ -1586,10 +1609,12 @@ def _set_compiler(self, compiler):
)
self.compiler = compiler
def _add_dependency(self, spec: "Spec", *, deptypes: dp.DependencyArgument):
def _add_dependency(
self, spec: "Spec", *, deptypes: dp.DependencyArgument, virtuals: Tuple[str, ...]
):
"""Called by the parser to add another spec as a dependency."""
if spec.name not in self._dependencies or not spec.name:
self.add_dependency_edge(spec, deptypes=deptypes)
self.add_dependency_edge(spec, deptypes=deptypes, virtuals=virtuals)
return
# Keep the intersection of constraints when a dependency is added
@@ -1607,34 +1632,58 @@ def _add_dependency(self, spec: "Spec", *, deptypes: dp.DependencyArgument):
"Cannot depend on incompatible specs '%s' and '%s'" % (dspec.spec, spec)
)
def add_dependency_edge(self, dependency_spec: "Spec", *, deptypes: dp.DependencyArgument):
def add_dependency_edge(
self,
dependency_spec: "Spec",
*,
deptypes: dp.DependencyArgument,
virtuals: Tuple[str, ...],
):
"""Add a dependency edge to this spec.
Args:
dependency_spec: spec of the dependency
deptypes: dependency types for this edge
virtuals: virtuals provided by this edge
"""
deptypes = dp.canonical_deptype(deptypes)
# Check if we need to update edges that are already present
selected = self._dependencies.select(child=dependency_spec.name)
for edge in selected:
has_errors, details = False, []
msg = f"cannot update the edge from {edge.parent.name} to {edge.spec.name}"
if any(d in edge.deptypes for d in deptypes):
msg = (
'cannot add a dependency on "{0.spec}" of {1} type '
'when the "{0.parent}" has the edge {0!s} already'
has_errors = True
details.append(
(
f"{edge.parent.name} has already an edge matching any"
f" of these types {str(deptypes)}"
)
)
raise spack.error.SpecError(msg.format(edge, deptypes))
if any(v in edge.virtuals for v in virtuals):
has_errors = True
details.append(
(
f"{edge.parent.name} has already an edge matching any"
f" of these virtuals {str(virtuals)}"
)
)
if has_errors:
raise spack.error.SpecError(msg, "\n".join(details))
for edge in selected:
if id(dependency_spec) == id(edge.spec):
# If we are here, it means the edge object was previously added to
# both the parent and the child. When we update this object they'll
# both see the deptype modification.
edge.add_type(deptypes)
edge.update_deptypes(deptypes=deptypes)
edge.update_virtuals(virtuals=virtuals)
return
edge = DependencySpec(self, dependency_spec, deptypes=deptypes)
edge = DependencySpec(self, dependency_spec, deptypes=deptypes, virtuals=virtuals)
self._dependencies.add(edge)
dependency_spec._dependents.add(edge)
@@ -1907,12 +1956,12 @@ def lookup_hash(self):
for node in self.traverse(root=False):
if node.abstract_hash:
new = node._lookup_hash()
spec._add_dependency(new, deptypes=())
spec._add_dependency(new, deptypes=(), virtuals=())
# reattach nodes that were not otherwise satisfied by new dependencies
for node in self.traverse(root=False):
if not any(n._satisfies(node) for n in spec.traverse()):
spec._add_dependency(node.copy(), deptypes=())
spec._add_dependency(node.copy(), deptypes=(), virtuals=())
return spec
@@ -2047,8 +2096,14 @@ def to_node_dict(self, hash=ht.dag_hash):
name_tuple = ("name", name)
for dspec in edges_for_name:
hash_tuple = (hash.name, dspec.spec._cached_hash(hash))
type_tuple = ("type", sorted(str(s) for s in dspec.deptypes))
deps_list.append(syaml.syaml_dict([name_tuple, hash_tuple, type_tuple]))
parameters_tuple = (
"parameters",
syaml.syaml_dict(
(key, dspec.parameters[key]) for key in sorted(dspec.parameters)
),
)
ordered_entries = [name_tuple, hash_tuple, parameters_tuple]
deps_list.append(syaml.syaml_dict(ordered_entries))
d["dependencies"] = deps_list
# Name is included in case this is replacing a virtual.
@@ -2372,7 +2427,7 @@ def spec_and_dependency_types(s):
dag_node, dependency_types = spec_and_dependency_types(s)
dependency_spec = spec_builder({dag_node: s_dependencies})
spec._add_dependency(dependency_spec, deptypes=dependency_types)
spec._add_dependency(dependency_spec, deptypes=dependency_types, virtuals=())
return spec
@@ -2390,8 +2445,10 @@ def from_dict(data):
spec = SpecfileV1.load(data)
elif int(data["spec"]["_meta"]["version"]) == 2:
spec = SpecfileV2.load(data)
else:
elif int(data["spec"]["_meta"]["version"]) == 3:
spec = SpecfileV3.load(data)
else:
spec = SpecfileV4.load(data)
# Any git version should
for s in spec.traverse():
@@ -2540,6 +2597,7 @@ def _concretize_helper(self, concretizer, presets=None, visited=None):
def _replace_with(self, concrete):
"""Replace this virtual spec with a concrete spec."""
assert self.virtual
virtuals = (self.name,)
for dep_spec in itertools.chain.from_iterable(self._dependents.values()):
dependent = dep_spec.parent
deptypes = dep_spec.deptypes
@@ -2550,7 +2608,11 @@ def _replace_with(self, concrete):
# add the replacement, unless it is already a dep of dependent.
if concrete.name not in dependent._dependencies:
dependent._add_dependency(concrete, deptypes=deptypes)
dependent._add_dependency(concrete, deptypes=deptypes, virtuals=virtuals)
else:
dependent.edges_to_dependencies(name=concrete.name)[0].update_virtuals(
virtuals=virtuals
)
def _expand_virtual_packages(self, concretizer):
"""Find virtual packages in this spec, replace them with providers,
@@ -3191,7 +3253,9 @@ def _merge_dependency(self, dependency, visited, spec_deps, provider_index, test
# If it's a virtual dependency, try to find an existing
# provider in the spec, and merge that.
virtuals = ()
if spack.repo.path.is_virtual_safe(dep.name):
virtuals = (dep.name,)
visited.add(dep.name)
provider = self._find_provider(dep, provider_index)
if provider:
@@ -3247,7 +3311,7 @@ def _merge_dependency(self, dependency, visited, spec_deps, provider_index, test
# Add merged spec to my deps and recurse
spec_dependency = spec_deps[dep.name]
if dep.name not in self._dependencies:
self._add_dependency(spec_dependency, deptypes=dependency.type)
self._add_dependency(spec_dependency, deptypes=dependency.type, virtuals=virtuals)
changed |= spec_dependency._normalize_helper(visited, spec_deps, provider_index, tests)
return changed
@@ -3584,15 +3648,20 @@ def _constrain_dependencies(self, other):
changed |= edges_from_name[0].update_deptypes(
other._dependencies[name][0].deptypes
)
changed |= edges_from_name[0].update_virtuals(
other._dependencies[name][0].virtuals
)
# Update with additional constraints from other spec
# operate on direct dependencies only, because a concrete dep
# represented by hash may have structure that needs to be preserved
for name in other.direct_dep_difference(self):
dep_spec_copy = other._get_dependency(name)
dep_copy = dep_spec_copy.spec
deptypes = dep_spec_copy.deptypes
self._add_dependency(dep_copy.copy(), deptypes=deptypes)
self._add_dependency(
dep_spec_copy.spec.copy(),
deptypes=dep_spec_copy.deptypes,
virtuals=dep_spec_copy.virtuals,
)
changed = True
return changed
@@ -3976,7 +4045,7 @@ def spid(spec):
new_specs[spid(edge.spec)] = edge.spec.copy(deps=False)
new_specs[spid(edge.parent)].add_dependency_edge(
new_specs[spid(edge.spec)], deptypes=edge.deptypes
new_specs[spid(edge.spec)], deptypes=edge.deptypes, virtuals=edge.virtuals
)
def copy(self, deps=True, **kwargs):
@@ -4344,7 +4413,7 @@ def write_attribute(spec, attribute, color):
if callable(current):
raise SpecFormatStringError("Attempted to format callable object")
if not current:
if current is None:
# We're not printing anything
return
@@ -4412,20 +4481,12 @@ def __str__(self):
def install_status(self):
"""Helper for tree to print DB install status."""
if not self.concrete:
return InstallStatus.absent
if self.external:
return InstallStatus.external
upstream, record = spack.store.db.query_by_spec_hash(self.dag_hash())
if not record:
return InstallStatus.absent
elif upstream and record.installed:
return InstallStatus.upstream
elif record.installed:
return InstallStatus.installed
else:
return InstallStatus.missing
return None
try:
record = spack.store.db.get_record(self)
return record.installed
except KeyError:
return None
def _installed_explicitly(self):
"""Helper for tree to print DB install status."""
@@ -4439,10 +4500,7 @@ def _installed_explicitly(self):
def tree(self, **kwargs):
"""Prints out this spec and its dependencies, tree-formatted
with indentation.
Status function may either output a boolean or an InstallStatus
"""
with indentation."""
color = kwargs.pop("color", clr.get_color_when())
depth = kwargs.pop("depth", False)
hashes = kwargs.pop("hashes", False)
@@ -4474,12 +4532,14 @@ def tree(self, **kwargs):
if status_fn:
status = status_fn(node)
if status in list(InstallStatus):
out += clr.colorize(status.value, color=color)
if node.installed_upstream:
out += clr.colorize("@g{[^]} ", color=color)
elif status is None:
out += clr.colorize("@K{ - } ", color=color) # !installed
elif status:
out += clr.colorize("@g{[+]} ", color=color)
out += clr.colorize("@g{[+]} ", color=color) # installed
else:
out += clr.colorize("@r{[-]} ", color=color)
out += clr.colorize("@r{[-]} ", color=color) # missing
if hashes:
out += clr.colorize("@K{%s} ", color=color) % node.dag_hash(hlen)
@@ -4655,12 +4715,16 @@ def from_self(name, transitive):
if name in self_nodes:
for edge in self[name].edges_to_dependencies():
dep_name = deps_to_replace.get(edge.spec, edge.spec).name
nodes[name].add_dependency_edge(nodes[dep_name], deptypes=edge.deptypes)
nodes[name].add_dependency_edge(
nodes[dep_name], deptypes=edge.deptypes, virtuals=edge.virtuals
)
if any(dep not in self_nodes for dep in self[name]._dependencies):
nodes[name].build_spec = self[name].build_spec
else:
for edge in other[name].edges_to_dependencies():
nodes[name].add_dependency_edge(nodes[edge.spec.name], deptypes=edge.deptypes)
nodes[name].add_dependency_edge(
nodes[edge.spec.name], deptypes=edge.deptypes, virtuals=edge.virtuals
)
if any(dep not in other_nodes for dep in other[name]._dependencies):
nodes[name].build_spec = other[name].build_spec
@@ -4750,11 +4814,40 @@ def merge_abstract_anonymous_specs(*abstract_specs: Spec):
# Update with additional constraints from other spec
for name in current_spec_constraint.direct_dep_difference(merged_spec):
edge = next(iter(current_spec_constraint.edges_to_dependencies(name)))
merged_spec._add_dependency(edge.spec.copy(), deptypes=edge.deptypes)
merged_spec._add_dependency(
edge.spec.copy(), deptypes=edge.deptypes, virtuals=edge.virtuals
)
return merged_spec
def reconstruct_virtuals_on_edges(spec):
"""Reconstruct virtuals on edges. Used to read from old DB and reindex.
Args:
spec: spec on which we want to reconstruct virtuals
"""
# Collect all possible virtuals
possible_virtuals = set()
for node in spec.traverse():
try:
possible_virtuals.update({x for x in node.package.dependencies if Spec(x).virtual})
except Exception as e:
warnings.warn(f"cannot reconstruct virtual dependencies on package {node.name}: {e}")
continue
# Assume all incoming edges to provider are marked with virtuals=
for vspec in possible_virtuals:
try:
provider = spec[vspec]
except KeyError:
# Virtual not in the DAG
continue
for edge in provider.edges_from_dependents():
edge.update_virtuals([vspec])
class SpecfileReaderBase:
@classmethod
def from_node_dict(cls, node):
@@ -4838,7 +4931,7 @@ def _load(cls, data):
# Pass 0: Determine hash type
for node in nodes:
for _, _, _, dhash_type in cls.dependencies_from_node_dict(node):
for _, _, _, dhash_type, _ in cls.dependencies_from_node_dict(node):
any_deps = True
if dhash_type:
hash_type = dhash_type
@@ -4869,8 +4962,10 @@ def _load(cls, data):
# Pass 2: Finish construction of all DAG edges (including build specs)
for node_hash, node in hash_dict.items():
node_spec = node["node_spec"]
for _, dhash, dtypes, _ in cls.dependencies_from_node_dict(node):
node_spec._add_dependency(hash_dict[dhash]["node_spec"], deptypes=dtypes)
for _, dhash, dtypes, _, virtuals in cls.dependencies_from_node_dict(node):
node_spec._add_dependency(
hash_dict[dhash]["node_spec"], deptypes=dtypes, virtuals=virtuals
)
if "build_spec" in node.keys():
_, bhash, _ = cls.build_spec_from_node_dict(node, hash_type=hash_type)
node_spec._build_spec = hash_dict[bhash]["node_spec"]
@@ -4904,9 +4999,10 @@ def load(cls, data):
for node in nodes:
# get dependency dict from the node.
name, data = cls.name_and_data(node)
for dname, _, dtypes, _ in cls.dependencies_from_node_dict(data):
deps[name]._add_dependency(deps[dname], deptypes=dtypes)
for dname, _, dtypes, _, virtuals in cls.dependencies_from_node_dict(data):
deps[name]._add_dependency(deps[dname], deptypes=dtypes, virtuals=virtuals)
reconstruct_virtuals_on_edges(result)
return result
@classmethod
@@ -4935,18 +5031,20 @@ def read_specfile_dep_specs(cls, deps, hash_type=ht.dag_hash.name):
if h.name in elt:
dep_hash, deptypes = elt[h.name], elt["type"]
hash_type = h.name
virtuals = []
break
else: # We never determined a hash type...
raise spack.error.SpecError("Couldn't parse dependency spec.")
else:
raise spack.error.SpecError("Couldn't parse dependency types in spec.")
yield dep_name, dep_hash, list(deptypes), hash_type
yield dep_name, dep_hash, list(deptypes), hash_type, list(virtuals)
class SpecfileV2(SpecfileReaderBase):
@classmethod
def load(cls, data):
result = cls._load(data)
reconstruct_virtuals_on_edges(result)
return result
@classmethod
@@ -4980,7 +5078,7 @@ def read_specfile_dep_specs(cls, deps, hash_type=ht.dag_hash.name):
raise spack.error.SpecError("Couldn't parse dependency spec.")
else:
raise spack.error.SpecError("Couldn't parse dependency types in spec.")
result.append((dep_name, dep_hash, list(deptypes), hash_type))
result.append((dep_name, dep_hash, list(deptypes), hash_type, list(virtuals)))
return result
@classmethod
@@ -5000,6 +5098,20 @@ class SpecfileV3(SpecfileV2):
pass
class SpecfileV4(SpecfileV2):
@classmethod
def extract_info_from_dep(cls, elt, hash):
dep_hash = elt[hash.name]
deptypes = elt["parameters"]["deptypes"]
hash_type = hash.name
virtuals = elt["parameters"]["virtuals"]
return dep_hash, deptypes, hash_type, virtuals
@classmethod
def load(cls, data):
return cls._load(data)
class LazySpecCache(collections.defaultdict):
"""Cache for Specs that uses a spec_like as key, and computes lazily
the corresponding value ``Spec(spec_like``.

View File

@@ -100,15 +100,9 @@ def quote(text):
return ['"{0}"'.format(line) for line in text]
def curly_quote(text):
"""Encloses each line of text in curly braces"""
return ["{{{0}}}".format(line) for line in text]
def _set_filters(env):
"""Sets custom filters to the template engine environment"""
env.filters["textwrap"] = textwrap.wrap
env.filters["prepend_to_line"] = prepend_to_line
env.filters["join"] = "\n".join
env.filters["quote"] = quote
env.filters["curly_quote"] = curly_quote

View File

@@ -201,12 +201,12 @@ def test_default_rpaths_create_install_default_layout(mirror_dir):
install_cmd("--no-cache", sy_spec.name)
# Create a buildache
buildcache_cmd("push", "-au", "-d", mirror_dir, cspec.name, sy_spec.name)
buildcache_cmd("push", "-au", mirror_dir, cspec.name, sy_spec.name)
# Test force overwrite create buildcache (-f option)
buildcache_cmd("push", "-auf", "-d", mirror_dir, cspec.name)
buildcache_cmd("push", "-auf", mirror_dir, cspec.name)
# Create mirror index
buildcache_cmd("update-index", "-d", mirror_dir)
buildcache_cmd("update-index", mirror_dir)
# List the buildcaches in the mirror
buildcache_cmd("list", "-alv")
@@ -214,13 +214,13 @@ def test_default_rpaths_create_install_default_layout(mirror_dir):
uninstall_cmd("-y", "--dependents", gspec.name)
# Test installing from build caches
buildcache_cmd("install", "-au", cspec.name, sy_spec.name)
buildcache_cmd("install", "-u", cspec.name, sy_spec.name)
# This gives warning that spec is already installed
buildcache_cmd("install", "-au", cspec.name)
buildcache_cmd("install", "-u", cspec.name)
# Test overwrite install
buildcache_cmd("install", "-afu", cspec.name)
buildcache_cmd("install", "-fu", cspec.name)
buildcache_cmd("keys", "-f")
buildcache_cmd("list")
@@ -246,35 +246,10 @@ def test_default_rpaths_install_nondefault_layout(mirror_dir):
# Install some packages with dependent packages
# test install in non-default install path scheme
buildcache_cmd("install", "-au", cspec.name, sy_spec.name)
buildcache_cmd("install", "-u", cspec.name, sy_spec.name)
# Test force install in non-default install path scheme
buildcache_cmd("install", "-auf", cspec.name)
@pytest.mark.requires_executables(*args)
@pytest.mark.maybeslow
@pytest.mark.nomockstage
@pytest.mark.usefixtures("default_config", "cache_directory", "install_dir_default_layout")
def test_relative_rpaths_create_default_layout(mirror_dir):
"""
Test the creation and installation of buildcaches with relative
rpaths into the default directory layout scheme.
"""
gspec, cspec = Spec("garply").concretized(), Spec("corge").concretized()
# Install 'corge' without using a cache
install_cmd("--no-cache", cspec.name)
# Create build cache with relative rpaths
buildcache_cmd("push", "-aur", "-d", mirror_dir, cspec.name)
# Create mirror index
buildcache_cmd("update-index", "-d", mirror_dir)
# Uninstall the package and deps
uninstall_cmd("-y", "--dependents", gspec.name)
buildcache_cmd("install", "-uf", cspec.name)
@pytest.mark.requires_executables(*args)
@@ -291,19 +266,19 @@ def test_relative_rpaths_install_default_layout(mirror_dir):
gspec, cspec = Spec("garply").concretized(), Spec("corge").concretized()
# Install buildcache created with relativized rpaths
buildcache_cmd("install", "-auf", cspec.name)
buildcache_cmd("install", "-uf", cspec.name)
# This gives warning that spec is already installed
buildcache_cmd("install", "-auf", cspec.name)
buildcache_cmd("install", "-uf", cspec.name)
# Uninstall the package and deps
uninstall_cmd("-y", "--dependents", gspec.name)
# Install build cache
buildcache_cmd("install", "-auf", cspec.name)
buildcache_cmd("install", "-uf", cspec.name)
# Test overwrite install
buildcache_cmd("install", "-auf", cspec.name)
buildcache_cmd("install", "-uf", cspec.name)
@pytest.mark.requires_executables(*args)
@@ -320,7 +295,7 @@ def test_relative_rpaths_install_nondefault(mirror_dir):
cspec = Spec("corge").concretized()
# Test install in non-default install path scheme and relative path
buildcache_cmd("install", "-auf", cspec.name)
buildcache_cmd("install", "-uf", cspec.name)
def test_push_and_fetch_keys(mock_gnupghome):
@@ -401,7 +376,7 @@ def test_spec_needs_rebuild(monkeypatch, tmpdir):
install_cmd(s.name)
# Put installed package in the buildcache
buildcache_cmd("push", "-u", "-a", "-d", mirror_dir.strpath, s.name)
buildcache_cmd("push", "-u", "-a", mirror_dir.strpath, s.name)
rebuild = bindist.needs_rebuild(s, mirror_url)
@@ -430,8 +405,8 @@ def test_generate_index_missing(monkeypatch, tmpdir, mutable_config):
install_cmd("--no-cache", s.name)
# Create a buildcache and update index
buildcache_cmd("push", "-uad", mirror_dir.strpath, s.name)
buildcache_cmd("update-index", "-d", mirror_dir.strpath)
buildcache_cmd("push", "-ua", mirror_dir.strpath, s.name)
buildcache_cmd("update-index", mirror_dir.strpath)
# Check package and dependency in buildcache
cache_list = buildcache_cmd("list", "--allarch")
@@ -443,7 +418,7 @@ def test_generate_index_missing(monkeypatch, tmpdir, mutable_config):
os.remove(*libelf_files)
# Update index
buildcache_cmd("update-index", "-d", mirror_dir.strpath)
buildcache_cmd("update-index", mirror_dir.strpath)
with spack.config.override("config:binary_index_ttl", 0):
# Check dependency not in buildcache
@@ -519,10 +494,10 @@ def test_update_sbang(tmpdir, test_mirror):
install_cmd("--no-cache", old_spec.name)
# Create a buildcache with the installed spec.
buildcache_cmd("push", "-u", "-a", "-d", mirror_dir, old_spec_hash_str)
buildcache_cmd("push", "-u", "-a", mirror_dir, old_spec_hash_str)
# Need to force an update of the buildcache index
buildcache_cmd("update-index", "-d", mirror_dir)
buildcache_cmd("update-index", mirror_dir)
# Uninstall the original package.
uninstall_cmd("-y", old_spec_hash_str)
@@ -538,7 +513,7 @@ def test_update_sbang(tmpdir, test_mirror):
assert new_spec.dag_hash() == old_spec.dag_hash()
# Install package from buildcache
buildcache_cmd("install", "-a", "-u", "-f", new_spec.name)
buildcache_cmd("install", "-u", "-f", new_spec.name)
# Continue blowing away caches
bindist.clear_spec_cache()

View File

@@ -3,8 +3,6 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import sys
import pytest
import spack.cmd.create
@@ -12,8 +10,6 @@
import spack.util.executable
import spack.util.url as url_util
pytestmark = pytest.mark.skipif(sys.platform == "win32", reason="does not run on windows")
@pytest.fixture(
scope="function",

View File

@@ -291,7 +291,7 @@ def make_build_job(name, deps, stage, use_artifact_buildcache, optimize, use_dep
def make_rebuild_index_job(use_artifact_buildcache, optimize, use_dependencies):
result = {
"stage": "stage-rebuild-index",
"script": "spack buildcache update-index --mirror-url s3://mirror",
"script": "spack buildcache update-index s3://mirror",
"tags": ["tag-0", "tag-1"],
"image": {"name": "spack/centos7", "entrypoint": [""]},
"after_script": ['rm -rf "./spack"'],

View File

@@ -3,6 +3,7 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import pickle
import sys
import pytest
@@ -39,7 +40,10 @@ def test_dump(tmpdir):
with tmpdir.as_cwd():
build_env("--dump", _out_file, "zlib")
with open(_out_file) as f:
assert any(line.startswith("PATH=") for line in f.readlines())
if sys.platform == "win32":
assert any(line.startswith('set "PATH=') for line in f.readlines())
else:
assert any(line.startswith("PATH=") for line in f.readlines())
@pytest.mark.usefixtures("config", "mock_packages", "working_env")

View File

@@ -85,7 +85,7 @@ def tests_buildcache_create(install_mockery, mock_fetch, monkeypatch, tmpdir):
pkg = "trivial-install-test-package"
install(pkg)
buildcache("push", "-d", str(tmpdir), "--unsigned", pkg)
buildcache("push", "--unsigned", str(tmpdir), pkg)
spec = Spec(pkg).concretized()
tarball_path = spack.binary_distribution.tarball_path_name(spec, ".spack")
@@ -105,7 +105,7 @@ def tests_buildcache_create_env(
add(pkg)
install()
buildcache("push", "-d", str(tmpdir), "--unsigned")
buildcache("push", "--unsigned", str(tmpdir))
spec = Spec(pkg).concretized()
tarball_path = spack.binary_distribution.tarball_path_name(spec, ".spack")
@@ -118,7 +118,7 @@ def test_buildcache_create_fails_on_noargs(tmpdir):
"""Ensure that buildcache create fails when given no args or
environment."""
with pytest.raises(spack.main.SpackCommandError):
buildcache("push", "-d", str(tmpdir), "--unsigned")
buildcache("push", "--unsigned", str(tmpdir))
def test_buildcache_create_fail_on_perm_denied(install_mockery, mock_fetch, monkeypatch, tmpdir):
@@ -127,7 +127,7 @@ def test_buildcache_create_fail_on_perm_denied(install_mockery, mock_fetch, monk
tmpdir.chmod(0)
with pytest.raises(OSError) as error:
buildcache("push", "-d", str(tmpdir), "--unsigned", "trivial-install-test-package")
buildcache("push", "--unsigned", str(tmpdir), "trivial-install-test-package")
assert error.value.errno == errno.EACCES
tmpdir.chmod(0o700)
@@ -159,11 +159,11 @@ def test_update_key_index(
# Put installed package in the buildcache, which, because we're signing
# it, should result in the public key getting pushed to the buildcache
# as well.
buildcache("push", "-a", "-d", mirror_dir.strpath, s.name)
buildcache("push", "-a", mirror_dir.strpath, s.name)
# Now make sure that when we pass the "--keys" argument to update-index
# it causes the index to get update.
buildcache("update-index", "--keys", "-d", mirror_dir.strpath)
buildcache("update-index", "--keys", mirror_dir.strpath)
key_dir_list = os.listdir(os.path.join(mirror_dir.strpath, "build_cache", "_pgp"))
@@ -213,27 +213,25 @@ def verify_mirror_contents():
# Install a package and put it in the buildcache
s = Spec(out_env_pkg).concretized()
install(s.name)
buildcache("push", "-u", "-f", "-a", "--mirror-url", src_mirror_url, s.name)
buildcache("push", "-u", "-f", "-a", src_mirror_url, s.name)
env("create", "test")
with ev.read("test"):
add(in_env_pkg)
install()
buildcache("push", "-u", "-f", "-a", "--mirror-url", src_mirror_url, in_env_pkg)
buildcache("push", "-u", "-f", "-a", src_mirror_url, in_env_pkg)
# Now run the spack buildcache sync command with all the various options
# for specifying mirrors
# Use urls to specify mirrors
buildcache(
"sync", "--src-mirror-url", src_mirror_url, "--dest-mirror-url", dest_mirror_url
)
buildcache("sync", src_mirror_url, dest_mirror_url)
verify_mirror_contents()
shutil.rmtree(dest_mirror_dir)
# Use local directory paths to specify fs locations
buildcache("sync", "--src-directory", src_mirror_dir, "--dest-directory", dest_mirror_dir)
buildcache("sync", src_mirror_dir, dest_mirror_dir)
verify_mirror_contents()
shutil.rmtree(dest_mirror_dir)
@@ -242,7 +240,7 @@ def verify_mirror_contents():
mirror("add", "src", src_mirror_url)
mirror("add", "dest", dest_mirror_url)
buildcache("sync", "--src-mirror-name", "src", "--dest-mirror-name", "dest")
buildcache("sync", "src", "dest")
verify_mirror_contents()
@@ -260,7 +258,7 @@ def test_buildcache_create_install(
pkg = "trivial-install-test-package"
install(pkg)
buildcache("push", "-d", str(tmpdir), "--unsigned", pkg)
buildcache("push", "--unsigned", str(tmpdir), pkg)
spec = Spec(pkg).concretized()
tarball_path = spack.binary_distribution.tarball_path_name(spec, ".spack")
@@ -324,12 +322,12 @@ def fake_push(node, push_url, options):
monkeypatch.setattr(spack.binary_distribution, "push_or_raise", fake_push)
buildcache_create_args = ["create", "-d", str(tmpdir), "--unsigned"]
buildcache_create_args = ["create", "--unsigned"]
if things_to_install != "":
buildcache_create_args.extend(["--only", things_to_install])
buildcache_create_args.extend([slash_hash])
buildcache_create_args.extend([str(tmpdir), slash_hash])
buildcache(*buildcache_create_args)

View File

@@ -1055,7 +1055,7 @@ def test_ci_nothing_to_rebuild(
)
install_cmd("archive-files")
buildcache_cmd("push", "-a", "-f", "-u", "--mirror-url", mirror_url, "archive-files")
buildcache_cmd("push", "-a", "-f", "-u", mirror_url, "archive-files")
filename = str(tmpdir.join("spack.yaml"))
with open(filename, "w") as f:
@@ -1155,8 +1155,8 @@ def test_ci_generate_mirror_override(
second_ci_yaml = str(tmpdir.join(".gitlab-ci-2.yml"))
with ev.read("test"):
install_cmd()
buildcache_cmd("push", "-u", "--mirror-url", mirror_url, "patchelf")
buildcache_cmd("update-index", "--mirror-url", mirror_url, output=str)
buildcache_cmd("push", "-u", mirror_url, "patchelf")
buildcache_cmd("update-index", mirror_url, output=str)
# This generate should not trigger a rebuild of patchelf, since it's in
# the main mirror referenced in the environment.
@@ -1297,7 +1297,7 @@ def test_push_mirror_contents(
mirror_cmd("rm", "test-ci")
# Test generating buildcache index while we have bin mirror
buildcache_cmd("update-index", "--mirror-url", mirror_url)
buildcache_cmd("update-index", mirror_url)
index_path = os.path.join(buildcache_path, "index.json")
with open(index_path) as idx_fd:
index_object = json.load(idx_fd)
@@ -1613,7 +1613,7 @@ def test_ci_rebuild_index(
ypfd.write(spec_json)
install_cmd("--add", "--keep-stage", "-f", json_path)
buildcache_cmd("push", "-u", "-a", "-f", "--mirror-url", mirror_url, "callpath")
buildcache_cmd("push", "-u", "-a", "-f", mirror_url, "callpath")
ci_cmd("rebuild-index")
buildcache_path = os.path.join(mirror_dir.strpath, "build_cache")
@@ -1647,7 +1647,7 @@ def test_ci_generate_bootstrap_prune_dag(
install_cmd("gcc@=12.2.0%gcc@10.2.1")
# Put installed compiler in the buildcache
buildcache_cmd("push", "-u", "-a", "-f", "-d", mirror_dir.strpath, "gcc@12.2.0%gcc@10.2.1")
buildcache_cmd("push", "-u", "-a", "-f", mirror_dir.strpath, "gcc@12.2.0%gcc@10.2.1")
# Now uninstall the compiler
uninstall_cmd("-y", "gcc@12.2.0%gcc@10.2.1")
@@ -1662,7 +1662,7 @@ def test_ci_generate_bootstrap_prune_dag(
install_cmd("--no-check-signature", "b%gcc@=12.2.0")
# Put spec built with installed compiler in the buildcache
buildcache_cmd("push", "-u", "-a", "-f", "-d", mirror_dir.strpath, "b%gcc@12.2.0")
buildcache_cmd("push", "-u", "-a", "-f", mirror_dir.strpath, "b%gcc@12.2.0")
# Now uninstall the spec
uninstall_cmd("-y", "b%gcc@12.2.0")

View File

@@ -396,16 +396,17 @@ def reset_string():
with envdir.as_cwd():
with open("spack.yaml", "w") as f:
f.write(
f"""\
"""\
spack:
specs:
- {test_spec}@0.0.0
- %s@0.0.0
develop:
dev-build-test-install:
spec: dev-build-test-install@0.0.0
path: {build_dir}
path: %s
"""
% (test_spec, build_dir)
)
env("create", "test", "./spack.yaml")

View File

@@ -32,7 +32,7 @@ def check_develop(self, env, spec, path=None):
assert dev_specs_entry["spec"] == str(spec)
# check yaml representation
yaml = ev.config_dict(env.manifest)
yaml = env.manifest[ev.TOP_LEVEL_KEY]
assert spec.name in yaml["develop"]
yaml_entry = yaml["develop"][spec.name]
assert yaml_entry["spec"] == str(spec)

View File

@@ -2402,6 +2402,21 @@ def test_env_activate_default_view_root_unconditional(mutable_mock_env_path):
)
@pytest.mark.regression("38510")
def test_concretize_separately_abstract_hash(install_mockery, mock_fetch):
"""Check that a root can have no name if it has a hash."""
s = Spec("trivial-install-test-package").concretized()
install(str(s))
e = ev.create("test")
e.unify = False
e.add(f"/{s.dag_hash()}")
e.concretize()
assert list(e.concretized_specs()) == [(Spec(f"/{s.dag_hash()}"), s)]
def test_concretize_user_specs_together():
e = ev.create("coconcretization")
e.unify = True
@@ -2688,7 +2703,7 @@ def test_modules_relative_to_views(environment_from_manifest, install_mockery, m
spec = e.specs_by_hash[e.concretized_order[0]]
view_prefix = e.default_view.get_projection_for_spec(spec)
modules_glob = "%s/modules/**/*" % e.path
modules_glob = "%s/modules/**/*/*" % e.path
modules = glob.glob(modules_glob)
assert len(modules) == 1
module = modules[0]
@@ -2724,12 +2739,12 @@ def test_multiple_modules_post_env_hook(environment_from_manifest, install_mocke
spec = e.specs_by_hash[e.concretized_order[0]]
view_prefix = e.default_view.get_projection_for_spec(spec)
modules_glob = "%s/modules/**/*" % e.path
modules_glob = "%s/modules/**/*/*" % e.path
modules = glob.glob(modules_glob)
assert len(modules) == 1
module = modules[0]
full_modules_glob = "%s/full_modules/**/*" % e.path
full_modules_glob = "%s/full_modules/**/*/*" % e.path
full_modules = glob.glob(full_modules_glob)
assert len(full_modules) == 1
full_module = full_modules[0]

View File

@@ -396,30 +396,3 @@ def test_use_tags_for_detection(command_args, mock_executable, mutable_config, m
assert "The following specs have been" in output
assert "cmake" in output
assert "openssl" not in output
@pytest.mark.regression("38733")
@pytest.mark.skipif(sys.platform == "win32", reason="the test uses bash scripts")
def test_failures_in_scanning_do_not_result_in_an_error(
mock_executable, monkeypatch, mutable_config
):
"""Tests that scanning paths with wrong permissions, won't cause `external find` to error."""
cmake_exe1 = mock_executable(
"cmake", output="echo cmake version 3.19.1", subdir=("first", "bin")
)
cmake_exe2 = mock_executable(
"cmake", output="echo cmake version 3.23.3", subdir=("second", "bin")
)
# Remove access from the first directory executable
cmake_exe1.parent.chmod(0o600)
value = os.pathsep.join([str(cmake_exe1.parent), str(cmake_exe2.parent)])
monkeypatch.setenv("PATH", value)
output = external("find", "cmake")
assert external.returncode == 0
assert "The following specs have been" in output
assert "cmake" in output
assert "3.23.3" in output
assert "3.19.1" not in output

View File

@@ -3,16 +3,12 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import sys
import pytest
from spack.main import SpackCommand, SpackCommandError
graph = SpackCommand("graph")
pytestmark = pytest.mark.skipif(sys.platform == "win32", reason="does not run on windows")
@pytest.mark.db
@pytest.mark.usefixtures("mock_packages", "database")

View File

@@ -4,7 +4,6 @@
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import argparse
import sys
import pytest
@@ -13,8 +12,6 @@
info = SpackCommand("info")
pytestmark = pytest.mark.skipif(sys.platform == "win32", reason="Not yet implemented on Windows")
@pytest.fixture(scope="module")
def parser():

View File

@@ -966,7 +966,7 @@ def test_compiler_bootstrap_from_binary_mirror(
install("gcc@=10.2.0")
# Put installed compiler in the buildcache
buildcache("push", "-u", "-a", "-f", "-d", mirror_dir.strpath, "gcc@10.2.0")
buildcache("push", "-u", "-a", "-f", mirror_dir.strpath, "gcc@10.2.0")
# Now uninstall the compiler
uninstall("-y", "gcc@10.2.0")
@@ -1138,7 +1138,7 @@ def install_use_buildcache(opt):
# Populate the buildcache
install(package_name)
buildcache("push", "-u", "-a", "-f", "-d", mirror_dir.strpath, package_name, dependency_name)
buildcache("push", "-u", "-a", "-f", mirror_dir.strpath, package_name, dependency_name)
# Uninstall the all of the packages for clean slate
uninstall("-y", "-a")

View File

@@ -3,8 +3,6 @@
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import sys
import pytest
import spack.store
@@ -15,8 +13,6 @@
install = SpackCommand("install")
uninstall = SpackCommand("uninstall")
pytestmark = pytest.mark.skipif(sys.platform == "win32", reason="does not run on windows")
@pytest.mark.db
def test_mark_mode_required(mutable_database):

View File

@@ -235,7 +235,7 @@ def test_mirror_destroy(
# Put a binary package in a buildcache
install("--no-cache", spec_name)
buildcache("push", "-u", "-a", "-f", "-d", mirror_dir.strpath, spec_name)
buildcache("push", "-u", "-a", "-f", mirror_dir.strpath, spec_name)
contents = os.listdir(mirror_dir.strpath)
assert "build_cache" in contents
@@ -245,7 +245,7 @@ def test_mirror_destroy(
assert not os.path.exists(mirror_dir.strpath)
buildcache("push", "-u", "-a", "-f", "-d", mirror_dir.strpath, spec_name)
buildcache("push", "-u", "-a", "-f", mirror_dir.strpath, spec_name)
contents = os.listdir(mirror_dir.strpath)
assert "build_cache" in contents

View File

@@ -157,7 +157,7 @@ def _parse_types(string):
def test_spec_deptypes_nodes():
output = spec("--types", "--cover", "nodes", "dt-diamond")
output = spec("--types", "--cover", "nodes", "--no-install-status", "dt-diamond")
types = _parse_types(output)
assert types["dt-diamond"] == [" "]
@@ -167,7 +167,7 @@ def test_spec_deptypes_nodes():
def test_spec_deptypes_edges():
output = spec("--types", "--cover", "edges", "dt-diamond")
output = spec("--types", "--cover", "edges", "--no-install-status", "dt-diamond")
types = _parse_types(output)
assert types["dt-diamond"] == [" "]

View File

@@ -2170,3 +2170,14 @@ def test_concretization_with_compilers_supporting_target_any(self):
with spack.config.override("compilers", compiler_configuration):
s = spack.spec.Spec("a").concretized()
assert s.satisfies("%gcc@12.1.0")
@pytest.mark.parametrize("spec_str", ["mpileaks", "mpileaks ^mpich"])
def test_virtuals_are_annotated_on_edges(self, spec_str, default_mock_concretization):
"""Tests that information on virtuals is annotated on DAG edges"""
spec = default_mock_concretization(spec_str)
mpi_provider = spec["mpi"].name
edges = spec.edges_to_dependencies(name=mpi_provider)
assert len(edges) == 1 and edges[0].virtuals == ("mpi",)
edges = spec.edges_to_dependencies(name="callpath")
assert len(edges) == 1 and edges[0].virtuals == ()

View File

@@ -1,17 +0,0 @@
#!/usr/bin/env bash
#
# 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)
_module_raw() { return 1; };
module() { return 1; };
ml() { return 1; };
export -f _module_raw;
export -f module;
export -f ml;
export MODULES_AUTO_HANDLING=1
export __MODULES_LMCONFLICT=bar&foo
export NEW_VAR=new

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@@ -31,194 +31,164 @@ class Amdfftw(FftwBase):
Example : spack install amdfftw precision=float
"""
_name = 'amdfftw'
_name = "amdfftw"
homepage = "https://developer.amd.com/amd-aocl/fftw/"
url = "https://github.com/amd/amd-fftw/archive/3.0.tar.gz"
git = "https://github.com/amd/amd-fftw.git"
maintainers = ['amd-toolchain-support']
maintainers("amd-toolchain-support")
version('3.1', sha256='3e777f3acef13fa1910db097e818b1d0d03a6a36ef41186247c6ab1ab0afc132')
version('3.0.1', sha256='87030c6bbb9c710f0a64f4f306ba6aa91dc4b182bb804c9022b35aef274d1a4c')
version('3.0', sha256='a69deaf45478a59a69f77c4f7e9872967f1cfe996592dd12beb6318f18ea0bcd')
version('2.2', sha256='de9d777236fb290c335860b458131678f75aa0799c641490c644c843f0e246f8')
version("3.1", sha256="3e777f3acef13fa1910db097e818b1d0d03a6a36ef41186247c6ab1ab0afc132")
version("3.0.1", sha256="87030c6bbb9c710f0a64f4f306ba6aa91dc4b182bb804c9022b35aef274d1a4c")
version("3.0", sha256="a69deaf45478a59a69f77c4f7e9872967f1cfe996592dd12beb6318f18ea0bcd")
version("2.2", sha256="de9d777236fb290c335860b458131678f75aa0799c641490c644c843f0e246f8")
variant('shared', default=True,
description='Builds a shared version of the library')
variant('openmp', default=True,
description='Enable OpenMP support')
variant('threads', default=False,
description='Enable SMP threads support')
variant('debug', default=False,
description='Builds a debug version of the library')
variant("shared", default=True, description="Builds a shared version of the library")
variant("openmp", default=True, description="Enable OpenMP support")
variant("threads", default=False, description="Enable SMP threads support")
variant("debug", default=False, description="Builds a debug version of the library")
variant(
'amd-fast-planner',
"amd-fast-planner",
default=False,
description='Option to reduce the planning time without much'
'tradeoff in the performance. It is supported for'
'Float and double precisions only.')
description="Option to reduce the planning time without much"
"tradeoff in the performance. It is supported for"
"Float and double precisions only.",
)
variant("amd-top-n-planner", default=False, description="Build with amd-top-n-planner support")
variant(
'amd-top-n-planner',
default=False,
description='Build with amd-top-n-planner support')
variant(
'amd-mpi-vader-limit',
default=False,
description='Build with amd-mpi-vader-limit support')
variant(
'static',
default=False,
description='Build with static suppport')
variant(
'amd-trans',
default=False,
description='Build with amd-trans suppport')
variant(
'amd-app-opt',
default=False,
description='Build with amd-app-opt suppport')
"amd-mpi-vader-limit", default=False, description="Build with amd-mpi-vader-limit support"
)
variant("static", default=False, description="Build with static suppport")
variant("amd-trans", default=False, description="Build with amd-trans suppport")
variant("amd-app-opt", default=False, description="Build with amd-app-opt suppport")
depends_on('texinfo')
depends_on("texinfo")
provides('fftw-api@3', when='@2:')
provides("fftw-api@3", when="@2:")
conflicts(
'precision=quad',
when='@2.2 %aocc',
msg='Quad precision is not supported by AOCC clang version 2.2')
"precision=quad",
when="@2.2 %aocc",
msg="Quad precision is not supported by AOCC clang version 2.2",
)
conflicts(
'+debug',
when='@2.2 %aocc',
msg='debug mode is not supported by AOCC clang version 2.2')
"+debug", when="@2.2 %aocc", msg="debug mode is not supported by AOCC clang version 2.2"
)
conflicts("%gcc@:7.2", when="@2.2:", msg="GCC version above 7.2 is required for AMDFFTW")
conflicts(
'%gcc@:7.2',
when='@2.2:',
msg='GCC version above 7.2 is required for AMDFFTW')
"+amd-fast-planner ", when="+mpi", msg="mpi thread is not supported with amd-fast-planner"
)
conflicts(
'+amd-fast-planner ',
when='+mpi',
msg='mpi thread is not supported with amd-fast-planner')
"+amd-fast-planner", when="@2.2", msg="amd-fast-planner is supported from 3.0 onwards"
)
conflicts(
'+amd-fast-planner',
when='@2.2',
msg='amd-fast-planner is supported from 3.0 onwards')
"+amd-fast-planner",
when="precision=quad",
msg="Quad precision is not supported with amd-fast-planner",
)
conflicts(
'+amd-fast-planner',
when='precision=quad',
msg='Quad precision is not supported with amd-fast-planner')
"+amd-fast-planner",
when="precision=long_double",
msg="long_double precision is not supported with amd-fast-planner",
)
conflicts(
'+amd-fast-planner',
when='precision=long_double',
msg='long_double precision is not supported with amd-fast-planner')
"+amd-top-n-planner",
when="@:3.0.0",
msg="amd-top-n-planner is supported from 3.0.1 onwards",
)
conflicts(
'+amd-top-n-planner',
when='@:3.0.0',
msg='amd-top-n-planner is supported from 3.0.1 onwards')
"+amd-top-n-planner",
when="precision=long_double",
msg="long_double precision is not supported with amd-top-n-planner",
)
conflicts(
'+amd-top-n-planner',
when='precision=long_double',
msg='long_double precision is not supported with amd-top-n-planner')
"+amd-top-n-planner",
when="precision=quad",
msg="Quad precision is not supported with amd-top-n-planner",
)
conflicts(
'+amd-top-n-planner',
when='precision=quad',
msg='Quad precision is not supported with amd-top-n-planner')
"+amd-top-n-planner",
when="+amd-fast-planner",
msg="amd-top-n-planner cannot be used with amd-fast-planner",
)
conflicts(
'+amd-top-n-planner',
when='+amd-fast-planner',
msg='amd-top-n-planner cannot be used with amd-fast-planner')
"+amd-top-n-planner", when="+threads", msg="amd-top-n-planner works only for single thread"
)
conflicts(
'+amd-top-n-planner',
when='+threads',
msg='amd-top-n-planner works only for single thread')
"+amd-top-n-planner", when="+mpi", msg="mpi thread is not supported with amd-top-n-planner"
)
conflicts(
'+amd-top-n-planner',
when='+mpi',
msg='mpi thread is not supported with amd-top-n-planner')
"+amd-top-n-planner",
when="+openmp",
msg="openmp thread is not supported with amd-top-n-planner",
)
conflicts(
'+amd-top-n-planner',
when='+openmp',
msg='openmp thread is not supported with amd-top-n-planner')
"+amd-mpi-vader-limit",
when="@:3.0.0",
msg="amd-mpi-vader-limit is supported from 3.0.1 onwards",
)
conflicts(
'+amd-mpi-vader-limit',
when='@:3.0.0',
msg='amd-mpi-vader-limit is supported from 3.0.1 onwards')
"+amd-mpi-vader-limit",
when="precision=quad",
msg="Quad precision is not supported with amd-mpi-vader-limit",
)
conflicts("+amd-trans", when="+threads", msg="amd-trans works only for single thread")
conflicts("+amd-trans", when="+mpi", msg="mpi thread is not supported with amd-trans")
conflicts("+amd-trans", when="+openmp", msg="openmp thread is not supported with amd-trans")
conflicts(
'+amd-mpi-vader-limit',
when='precision=quad',
msg='Quad precision is not supported with amd-mpi-vader-limit')
"+amd-trans",
when="precision=long_double",
msg="long_double precision is not supported with amd-trans",
)
conflicts(
'+amd-trans',
when='+threads',
msg='amd-trans works only for single thread')
"+amd-trans", when="precision=quad", msg="Quad precision is not supported with amd-trans"
)
conflicts("+amd-app-opt", when="@:3.0.1", msg="amd-app-opt is supported from 3.1 onwards")
conflicts("+amd-app-opt", when="+mpi", msg="mpi thread is not supported with amd-app-opt")
conflicts(
'+amd-trans',
when='+mpi',
msg='mpi thread is not supported with amd-trans')
"+amd-app-opt",
when="precision=long_double",
msg="long_double precision is not supported with amd-app-opt",
)
conflicts(
'+amd-trans',
when='+openmp',
msg='openmp thread is not supported with amd-trans')
conflicts(
'+amd-trans',
when='precision=long_double',
msg='long_double precision is not supported with amd-trans')
conflicts(
'+amd-trans',
when='precision=quad',
msg='Quad precision is not supported with amd-trans')
conflicts(
'+amd-app-opt',
when='@:3.0.1',
msg='amd-app-opt is supported from 3.1 onwards')
conflicts(
'+amd-app-opt',
when='+mpi',
msg='mpi thread is not supported with amd-app-opt')
conflicts(
'+amd-app-opt',
when='precision=long_double',
msg='long_double precision is not supported with amd-app-opt')
conflicts(
'+amd-app-opt',
when='precision=quad',
msg='Quad precision is not supported with amd-app-opt')
"+amd-app-opt",
when="precision=quad",
msg="Quad precision is not supported with amd-app-opt",
)
def configure(self, spec, prefix):
"""Configure function"""
# Base options
options = [
'--prefix={0}'.format(prefix),
'--enable-amd-opt'
]
options = ["--prefix={0}".format(prefix), "--enable-amd-opt"]
# Check if compiler is AOCC
if '%aocc' in spec:
options.append('CC={0}'.format(os.path.basename(spack_cc)))
options.append('FC={0}'.format(os.path.basename(spack_fc)))
options.append('F77={0}'.format(os.path.basename(spack_fc)))
if "%aocc" in spec:
options.append("CC={0}".format(os.path.basename(spack_cc)))
options.append("FC={0}".format(os.path.basename(spack_fc)))
options.append("F77={0}".format(os.path.basename(spack_fc)))
if '+debug' in spec:
options.append('--enable-debug')
if "+debug" in spec:
options.append("--enable-debug")
if '+mpi' in spec:
options.append('--enable-mpi')
options.append('--enable-amd-mpifft')
if "+mpi" in spec:
options.append("--enable-mpi")
options.append("--enable-amd-mpifft")
else:
options.append('--disable-mpi')
options.append('--disable-amd-mpifft')
options.append("--disable-mpi")
options.append("--disable-amd-mpifft")
options.extend(self.enable_or_disable('shared'))
options.extend(self.enable_or_disable('openmp'))
options.extend(self.enable_or_disable('threads'))
options.extend(self.enable_or_disable('amd-fast-planner'))
options.extend(self.enable_or_disable('amd-top-n-planner'))
options.extend(self.enable_or_disable('amd-mpi-vader-limit'))
options.extend(self.enable_or_disable('static'))
options.extend(self.enable_or_disable('amd-trans'))
options.extend(self.enable_or_disable('amd-app-opt'))
options.extend(self.enable_or_disable("shared"))
options.extend(self.enable_or_disable("openmp"))
options.extend(self.enable_or_disable("threads"))
options.extend(self.enable_or_disable("amd-fast-planner"))
options.extend(self.enable_or_disable("amd-top-n-planner"))
options.extend(self.enable_or_disable("amd-mpi-vader-limit"))
options.extend(self.enable_or_disable("static"))
options.extend(self.enable_or_disable("amd-trans"))
options.extend(self.enable_or_disable("amd-app-opt"))
if not self.compiler.f77 or not self.compiler.fc:
options.append('--disable-fortran')
options.append("--disable-fortran")
# Cross compilation is supported in amd-fftw by making use of target
# variable to set AMD_ARCH configure option.
@@ -226,17 +196,16 @@ class Amdfftw(FftwBase):
# use target variable to set appropriate -march option in AMD_ARCH.
arch = spec.architecture
options.append(
'AMD_ARCH={0}'.format(
arch.target.optimization_flags(
spec.compiler).split('=')[-1]))
"AMD_ARCH={0}".format(arch.target.optimization_flags(spec.compiler).split("=")[-1])
)
# Specific SIMD support.
# float and double precisions are supported
simd_features = ['sse2', 'avx', 'avx2']
simd_features = ["sse2", "avx", "avx2"]
simd_options = []
for feature in simd_features:
msg = '--enable-{0}' if feature in spec.target else '--disable-{0}'
msg = "--enable-{0}" if feature in spec.target else "--disable-{0}"
simd_options.append(msg.format(feature))
# When enabling configure option "--enable-amd-opt", do not use the
@@ -246,20 +215,19 @@ class Amdfftw(FftwBase):
# Double is the default precision, for all the others we need
# to enable the corresponding option.
enable_precision = {
'float': ['--enable-float'],
'double': None,
'long_double': ['--enable-long-double'],
'quad': ['--enable-quad-precision']
"float": ["--enable-float"],
"double": None,
"long_double": ["--enable-long-double"],
"quad": ["--enable-quad-precision"],
}
# Different precisions must be configured and compiled one at a time
configure = Executable('../configure')
configure = Executable("../configure")
for precision in self.selected_precisions:
opts = (enable_precision[precision] or []) + options[:]
# SIMD optimizations are available only for float and double
if precision in ('float', 'double'):
if precision in ("float", "double"):
opts += simd_options
with working_dir(precision, create=True):

View File

@@ -16,21 +16,21 @@ from spack.package import *
class Llvm(CMakePackage, CudaPackage):
"""The LLVM Project is a collection of modular and reusable compiler and
toolchain technologies. Despite its name, LLVM has little to do
with traditional virtual machines, though it does provide helpful
libraries that can be used to build them. The name "LLVM" itself
is not an acronym; it is the full name of the project.
toolchain technologies. Despite its name, LLVM has little to do
with traditional virtual machines, though it does provide helpful
libraries that can be used to build them. The name "LLVM" itself
is not an acronym; it is the full name of the project.
"""
homepage = "https://llvm.org/"
url = "https://github.com/llvm/llvm-project/archive/llvmorg-7.1.0.tar.gz"
list_url = "https://releases.llvm.org/download.html"
git = "https://github.com/llvm/llvm-project"
maintainers = ['trws', 'haampie']
maintainers("trws", "haampie")
tags = ['e4s']
tags = ["e4s"]
generator = 'Ninja'
generator = "Ninja"
family = "compiler" # Used by lmod
@@ -80,13 +80,12 @@ class Llvm(CMakePackage, CudaPackage):
# to save space, build with `build_type=Release`.
variant(
"clang",
default=True,
description="Build the LLVM C/C++/Objective-C compiler frontend",
"clang", default=True, description="Build the LLVM C/C++/Objective-C compiler frontend"
)
variant(
"flang",
default=False, when='@11: +clang',
default=False,
when="@11: +clang",
description="Build the LLVM Fortran compiler frontend "
"(experimental - parser only, needs GCC)",
)
@@ -95,27 +94,23 @@ class Llvm(CMakePackage, CudaPackage):
default=False,
description="Include debugging code in OpenMP runtime libraries",
)
variant("lldb", default=True, when='+clang', description="Build the LLVM debugger")
variant("lldb", default=True, when="+clang", description="Build the LLVM debugger")
variant("lld", default=True, description="Build the LLVM linker")
variant("mlir", default=False, when='@10:', description="Build with MLIR support")
variant("mlir", default=False, when="@10:", description="Build with MLIR support")
variant(
"internal_unwind",
default=True, when='+clang',
description="Build the libcxxabi libunwind",
"internal_unwind", default=True, when="+clang", description="Build the libcxxabi libunwind"
)
variant(
"polly",
default=True,
description="Build the LLVM polyhedral optimization plugin, "
"only builds for 3.7.0+",
description="Build the LLVM polyhedral optimization plugin, " "only builds for 3.7.0+",
)
variant(
"libcxx",
default=True, when='+clang',
description="Build the LLVM C++ standard library",
"libcxx", default=True, when="+clang", description="Build the LLVM C++ standard library"
)
variant(
"compiler-rt", when='+clang',
"compiler-rt",
when="+clang",
default=True,
description="Build LLVM compiler runtime, including sanitizers",
)
@@ -124,11 +119,7 @@ class Llvm(CMakePackage, CudaPackage):
default=(sys.platform != "darwin"),
description="Add support for LTO with the gold linker plugin",
)
variant(
"split_dwarf",
default=False,
description="Build with split dwarf information",
)
variant("split_dwarf", default=False, description="Build with split dwarf information")
variant(
"llvm_dylib",
default=True,
@@ -136,18 +127,40 @@ class Llvm(CMakePackage, CudaPackage):
)
variant(
"link_llvm_dylib",
default=False, when='+llvm_dylib',
default=False,
when="+llvm_dylib",
description="Link LLVM tools against the LLVM shared library",
)
variant(
"targets",
default="none",
description=("What targets to build. Spack's target family is always added "
"(e.g. X86 is automatically enabled when targeting znver2)."),
values=("all", "none", "aarch64", "amdgpu", "arm", "avr", "bpf", "cppbackend",
"hexagon", "lanai", "mips", "msp430", "nvptx", "powerpc", "riscv",
"sparc", "systemz", "webassembly", "x86", "xcore"),
multi=True
description=(
"What targets to build. Spack's target family is always added "
"(e.g. X86 is automatically enabled when targeting znver2)."
),
values=(
"all",
"none",
"aarch64",
"amdgpu",
"arm",
"avr",
"bpf",
"cppbackend",
"hexagon",
"lanai",
"mips",
"msp430",
"nvptx",
"powerpc",
"riscv",
"sparc",
"systemz",
"webassembly",
"x86",
"xcore",
),
multi=True,
)
variant(
"build_type",
@@ -157,51 +170,52 @@ class Llvm(CMakePackage, CudaPackage):
)
variant(
"omp_tsan",
default=False, when='@6:',
default=False,
when="@6:",
description="Build with OpenMP capable thread sanitizer",
)
variant(
"omp_as_runtime",
default=True,
when='+clang @12:',
when="+clang @12:",
description="Build OpenMP runtime via ENABLE_RUNTIME by just-built Clang",
)
variant('code_signing', default=False,
when='+lldb platform=darwin',
description="Enable code-signing on macOS")
variant("python", default=False, description="Install python bindings")
variant('version_suffix', default='none', description="Add a symbol suffix")
variant(
'shlib_symbol_version',
default='none',
"code_signing",
default=False,
when="+lldb platform=darwin",
description="Enable code-signing on macOS",
)
variant("python", default=False, description="Install python bindings")
variant("version_suffix", default="none", description="Add a symbol suffix")
variant(
"shlib_symbol_version",
default="none",
description="Add shared library symbol version",
when='@13:'
when="@13:",
)
variant(
'z3',
default=False,
when='+clang @8:',
description='Use Z3 for the clang static analyzer'
"z3", default=False, when="+clang @8:", description="Use Z3 for the clang static analyzer"
)
provides('libllvm@14', when='@14.0.0:14')
provides('libllvm@13', when='@13.0.0:13')
provides('libllvm@12', when='@12.0.0:12')
provides('libllvm@11', when='@11.0.0:11')
provides('libllvm@10', when='@10.0.0:10')
provides('libllvm@9', when='@9.0.0:9')
provides('libllvm@8', when='@8.0.0:8')
provides('libllvm@7', when='@7.0.0:7')
provides('libllvm@6', when='@6.0.0:6')
provides('libllvm@5', when='@5.0.0:5')
provides('libllvm@4', when='@4.0.0:4')
provides('libllvm@3', when='@3.0.0:3')
provides("libllvm@14", when="@14.0.0:14")
provides("libllvm@13", when="@13.0.0:13")
provides("libllvm@12", when="@12.0.0:12")
provides("libllvm@11", when="@11.0.0:11")
provides("libllvm@10", when="@10.0.0:10")
provides("libllvm@9", when="@9.0.0:9")
provides("libllvm@8", when="@8.0.0:8")
provides("libllvm@7", when="@7.0.0:7")
provides("libllvm@6", when="@6.0.0:6")
provides("libllvm@5", when="@5.0.0:5")
provides("libllvm@4", when="@4.0.0:4")
provides("libllvm@3", when="@3.0.0:3")
extends("python", when="+python")
# Build dependency
depends_on("cmake@3.4.3:", type="build")
depends_on('cmake@3.13.4:', type='build', when='@12:')
depends_on("cmake@3.13.4:", type="build", when="@12:")
depends_on("ninja", type="build")
depends_on("python@2.7:2.8", when="@:4 ~python", type="build")
depends_on("python", when="@5: ~python", type="build")
@@ -242,7 +256,7 @@ class Llvm(CMakePackage, CudaPackage):
# clang/lib: a lambda parameter cannot shadow an explicitly captured entity
conflicts("%clang@8:", when="@:4")
# Internal compiler error on gcc 8.4 on aarch64 https://bugzilla.redhat.com/show_bug.cgi?id=1958295
conflicts('%gcc@8.4:8.4.9', when='@12: target=aarch64:')
conflicts("%gcc@8.4:8.4.9", when="@12: target=aarch64:")
# When these versions are concretized, but not explicitly with +libcxx, these
# conflicts will enable clingo to set ~libcxx, making the build successful:
@@ -252,17 +266,17 @@ class Llvm(CMakePackage, CudaPackage):
# GCC 11 - latest stable release per GCC release page
# Clang: 11, 12 - latest two stable releases per LLVM release page
# AppleClang 12 - latest stable release per Xcode release page
conflicts("%gcc@:10", when="@13:+libcxx")
conflicts("%clang@:10", when="@13:+libcxx")
conflicts("%gcc@:10", when="@13:+libcxx")
conflicts("%clang@:10", when="@13:+libcxx")
conflicts("%apple-clang@:11", when="@13:+libcxx")
# libcxx-4 and compiler-rt-4 fail to build with "newer" clang and gcc versions:
conflicts('%gcc@7:', when='@:4+libcxx')
conflicts('%clang@6:', when='@:4+libcxx')
conflicts('%apple-clang@6:', when='@:4+libcxx')
conflicts('%gcc@7:', when='@:4+compiler-rt')
conflicts('%clang@6:', when='@:4+compiler-rt')
conflicts('%apple-clang@6:', when='@:4+compiler-rt')
conflicts("%gcc@7:", when="@:4+libcxx")
conflicts("%clang@6:", when="@:4+libcxx")
conflicts("%apple-clang@6:", when="@:4+libcxx")
conflicts("%gcc@7:", when="@:4+compiler-rt")
conflicts("%clang@6:", when="@:4+compiler-rt")
conflicts("%apple-clang@6:", when="@:4+compiler-rt")
# cuda_arch value must be specified
conflicts("cuda_arch=none", when="+cuda", msg="A value for cuda_arch must be specified.")
@@ -270,27 +284,27 @@ class Llvm(CMakePackage, CudaPackage):
# LLVM bug https://bugs.llvm.org/show_bug.cgi?id=48234
# CMake bug: https://gitlab.kitware.com/cmake/cmake/-/issues/21469
# Fixed in upstream versions of both
conflicts('^cmake@3.19.0', when='@6:11.0.0')
conflicts("^cmake@3.19.0", when="@6:11.0.0")
# Github issue #4986
patch("llvm_gcc7.patch", when="@4.0.0:4.0.1+lldb %gcc@7.0:")
# sys/ustat.h has been removed in favour of statfs from glibc-2.28. Use fixed sizes:
patch('llvm5-sanitizer-ustat.patch', when="@4:6.0.0+compiler-rt")
patch("llvm5-sanitizer-ustat.patch", when="@4:6.0.0+compiler-rt")
# Fix lld templates: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=230463
patch('llvm4-lld-ELF-Symbols.patch', when="@4+lld%clang@6:")
patch('llvm5-lld-ELF-Symbols.patch', when="@5+lld%clang@7:")
patch("llvm4-lld-ELF-Symbols.patch", when="@4+lld%clang@6:")
patch("llvm5-lld-ELF-Symbols.patch", when="@5+lld%clang@7:")
# Fix missing std:size_t in 'llvm@4:5' when built with '%clang@7:'
patch('xray_buffer_queue-cstddef.patch', when="@4:5+compiler-rt%clang@7:")
patch("xray_buffer_queue-cstddef.patch", when="@4:5+compiler-rt%clang@7:")
# https://github.com/llvm/llvm-project/commit/947f9692440836dcb8d88b74b69dd379d85974ce
patch('sanitizer-ipc_perm_mode.patch', when="@5:7+compiler-rt%clang@11:")
patch('sanitizer-ipc_perm_mode.patch', when="@5:9+compiler-rt%gcc@9:")
patch("sanitizer-ipc_perm_mode.patch", when="@5:7+compiler-rt%clang@11:")
patch("sanitizer-ipc_perm_mode.patch", when="@5:9+compiler-rt%gcc@9:")
# github.com/spack/spack/issues/24270: MicrosoftDemangle for %gcc@10: and %clang@13:
patch('missing-includes.patch', when='@8')
patch("missing-includes.patch", when="@8")
# Backport from llvm master + additional fix
# see https://bugs.llvm.org/show_bug.cgi?id=39696
@@ -315,33 +329,33 @@ class Llvm(CMakePackage, CudaPackage):
patch("llvm_python_path.patch", when="@:11")
# Workaround for issue https://github.com/spack/spack/issues/18197
patch('llvm7_intel.patch', when='@7 %intel@18.0.2,19.0.0:19.1.99')
patch("llvm7_intel.patch", when="@7 %intel@18.0.2,19.0.0:19.1.99")
# Remove cyclades support to build against newer kernel headers
# https://reviews.llvm.org/D102059
patch('no_cyclades.patch', when='@10:12.0.0')
patch('no_cyclades9.patch', when='@6:9')
patch("no_cyclades.patch", when="@10:12.0.0")
patch("no_cyclades9.patch", when="@6:9")
patch('llvm-gcc11.patch', when='@9:11%gcc@11:')
patch("llvm-gcc11.patch", when="@9:11%gcc@11:")
# add -lpthread to build OpenMP libraries with Fujitsu compiler
patch('llvm12-thread.patch', when='@12 %fj')
patch('llvm13-thread.patch', when='@13 %fj')
patch("llvm12-thread.patch", when="@12 %fj")
patch("llvm13-thread.patch", when="@13 %fj")
# avoid build failed with Fujitsu compiler
patch('llvm13-fujitsu.patch', when='@13 %fj')
patch("llvm13-fujitsu.patch", when="@13 %fj")
# patch for missing hwloc.h include for libompd
patch('llvm14-hwloc-ompd.patch', when='@14')
patch("llvm14-hwloc-ompd.patch", when="@14")
# make libflags a list in openmp subproject when ~omp_as_runtime
patch('libomp-libflags-as-list.patch', when='@3.7:')
patch("libomp-libflags-as-list.patch", when="@3.7:")
# The functions and attributes below implement external package
# detection for LLVM. See:
#
# https://spack.readthedocs.io/en/latest/packaging_guide.html#making-a-package-discoverable-with-spack-external-find
executables = ['clang', 'flang', 'ld.lld', 'lldb']
executables = ["clang", "flang", "ld.lld", "lldb"]
@classmethod
def filter_detected_exes(cls, prefix, exes_in_prefix):
@@ -351,7 +365,7 @@ class Llvm(CMakePackage, CudaPackage):
# on some port and would hang Spack during detection.
# clang-cl and clang-cpp are dev tools that we don't
# need to test
if any(x in exe for x in ('vscode', 'cpp', '-cl', '-gpu')):
if any(x in exe for x in ("vscode", "cpp", "-cl", "-gpu")):
continue
result.append(exe)
return result
@@ -360,20 +374,20 @@ class Llvm(CMakePackage, CudaPackage):
def determine_version(cls, exe):
version_regex = re.compile(
# Normal clang compiler versions are left as-is
r'clang version ([^ )\n]+)-svn[~.\w\d-]*|'
r"clang version ([^ )\n]+)-svn[~.\w\d-]*|"
# Don't include hyphenated patch numbers in the version
# (see https://github.com/spack/spack/pull/14365 for details)
r'clang version ([^ )\n]+?)-[~.\w\d-]*|'
r'clang version ([^ )\n]+)|'
r"clang version ([^ )\n]+?)-[~.\w\d-]*|"
r"clang version ([^ )\n]+)|"
# LLDB
r'lldb version ([^ )\n]+)|'
r"lldb version ([^ )\n]+)|"
# LLD
r'LLD ([^ )\n]+) \(compatible with GNU linkers\)'
r"LLD ([^ )\n]+) \(compatible with GNU linkers\)"
)
try:
compiler = Executable(exe)
output = compiler('--version', output=str, error=str)
if 'Apple' in output:
output = compiler("--version", output=str, error=str)
if "Apple" in output:
return None
match = version_regex.search(output)
if match:
@@ -387,38 +401,39 @@ class Llvm(CMakePackage, CudaPackage):
@classmethod
def determine_variants(cls, exes, version_str):
variants, compilers = ['+clang'], {}
variants, compilers = ["+clang"], {}
lld_found, lldb_found = False, False
for exe in exes:
if 'clang++' in exe:
compilers['cxx'] = exe
elif 'clang' in exe:
compilers['c'] = exe
elif 'flang' in exe:
variants.append('+flang')
compilers['fc'] = exe
compilers['f77'] = exe
elif 'ld.lld' in exe:
if "clang++" in exe:
compilers["cxx"] = exe
elif "clang" in exe:
compilers["c"] = exe
elif "flang" in exe:
variants.append("+flang")
compilers["fc"] = exe
compilers["f77"] = exe
elif "ld.lld" in exe:
lld_found = True
compilers['ld'] = exe
elif 'lldb' in exe:
compilers["ld"] = exe
elif "lldb" in exe:
lldb_found = True
compilers['lldb'] = exe
compilers["lldb"] = exe
variants.append('+lld' if lld_found else '~lld')
variants.append('+lldb' if lldb_found else '~lldb')
variants.append("+lld" if lld_found else "~lld")
variants.append("+lldb" if lldb_found else "~lldb")
return ''.join(variants), {'compilers': compilers}
return "".join(variants), {"compilers": compilers}
@classmethod
def validate_detected_spec(cls, spec, extra_attributes):
# For LLVM 'compilers' is a mandatory attribute
msg = ('the extra attribute "compilers" must be set for '
'the detected spec "{0}"'.format(spec))
assert 'compilers' in extra_attributes, msg
compilers = extra_attributes['compilers']
for key in ('c', 'cxx'):
msg = '{0} compiler not found for {1}'
msg = 'the extra attribute "compilers" must be set for ' 'the detected spec "{0}"'.format(
spec
)
assert "compilers" in extra_attributes, msg
compilers = extra_attributes["compilers"]
for key in ("c", "cxx"):
msg = "{0} compiler not found for {1}"
assert key in compilers, msg.format(key, spec)
@property
@@ -426,10 +441,10 @@ class Llvm(CMakePackage, CudaPackage):
msg = "cannot retrieve C compiler [spec is not concrete]"
assert self.spec.concrete, msg
if self.spec.external:
return self.spec.extra_attributes['compilers'].get('c', None)
return self.spec.extra_attributes["compilers"].get("c", None)
result = None
if '+clang' in self.spec:
result = os.path.join(self.spec.prefix.bin, 'clang')
if "+clang" in self.spec:
result = os.path.join(self.spec.prefix.bin, "clang")
return result
@property
@@ -437,10 +452,10 @@ class Llvm(CMakePackage, CudaPackage):
msg = "cannot retrieve C++ compiler [spec is not concrete]"
assert self.spec.concrete, msg
if self.spec.external:
return self.spec.extra_attributes['compilers'].get('cxx', None)
return self.spec.extra_attributes["compilers"].get("cxx", None)
result = None
if '+clang' in self.spec:
result = os.path.join(self.spec.prefix.bin, 'clang++')
if "+clang" in self.spec:
result = os.path.join(self.spec.prefix.bin, "clang++")
return result
@property
@@ -448,10 +463,10 @@ class Llvm(CMakePackage, CudaPackage):
msg = "cannot retrieve Fortran compiler [spec is not concrete]"
assert self.spec.concrete, msg
if self.spec.external:
return self.spec.extra_attributes['compilers'].get('fc', None)
return self.spec.extra_attributes["compilers"].get("fc", None)
result = None
if '+flang' in self.spec:
result = os.path.join(self.spec.prefix.bin, 'flang')
if "+flang" in self.spec:
result = os.path.join(self.spec.prefix.bin, "flang")
return result
@property
@@ -459,27 +474,25 @@ class Llvm(CMakePackage, CudaPackage):
msg = "cannot retrieve Fortran 77 compiler [spec is not concrete]"
assert self.spec.concrete, msg
if self.spec.external:
return self.spec.extra_attributes['compilers'].get('f77', None)
return self.spec.extra_attributes["compilers"].get("f77", None)
result = None
if '+flang' in self.spec:
result = os.path.join(self.spec.prefix.bin, 'flang')
if "+flang" in self.spec:
result = os.path.join(self.spec.prefix.bin, "flang")
return result
@property
def libs(self):
return LibraryList(self.llvm_config("--libfiles", "all",
result="list"))
return LibraryList(self.llvm_config("--libfiles", "all", result="list"))
@run_before('cmake')
@run_before("cmake")
def codesign_check(self):
if self.spec.satisfies("+code_signing"):
codesign = which('codesign')
mkdir('tmp')
llvm_check_file = join_path('tmp', 'llvm_check')
copy('/usr/bin/false', llvm_check_file)
codesign = which("codesign")
mkdir("tmp")
llvm_check_file = join_path("tmp", "llvm_check")
copy("/usr/bin/false", llvm_check_file)
try:
codesign('-f', '-s', 'lldb_codesign', '--dryrun',
llvm_check_file)
codesign("-f", "-s", "lldb_codesign", "--dryrun", llvm_check_file)
except ProcessError:
# Newer LLVM versions have a simple script that sets up
@@ -489,32 +502,32 @@ class Llvm(CMakePackage, CudaPackage):
setup()
except Exception:
raise RuntimeError(
'spack was unable to either find or set up'
'code-signing on your system. Please refer to'
'https://lldb.llvm.org/resources/build.html#'
'code-signing-on-macos for details on how to'
'create this identity.'
"spack was unable to either find or set up"
"code-signing on your system. Please refer to"
"https://lldb.llvm.org/resources/build.html#"
"code-signing-on-macos for details on how to"
"create this identity."
)
def flag_handler(self, name, flags):
if name == 'cxxflags':
if name == "cxxflags":
flags.append(self.compiler.cxx11_flag)
return(None, flags, None)
elif name == 'ldflags' and self.spec.satisfies('%intel'):
flags.append('-shared-intel')
return(None, flags, None)
return(flags, None, None)
return (None, flags, None)
elif name == "ldflags" and self.spec.satisfies("%intel"):
flags.append("-shared-intel")
return (None, flags, None)
return (flags, None, None)
def setup_build_environment(self, env):
"""When using %clang, add only its ld.lld-$ver and/or ld.lld to our PATH"""
if self.compiler.name in ['clang', 'apple-clang']:
for lld in 'ld.lld-{0}'.format(self.compiler.version.version[0]), 'ld.lld':
if self.compiler.name in ["clang", "apple-clang"]:
for lld in "ld.lld-{0}".format(self.compiler.version.version[0]), "ld.lld":
bin = os.path.join(os.path.dirname(self.compiler.cc), lld)
sym = os.path.join(self.stage.path, 'ld.lld')
sym = os.path.join(self.stage.path, "ld.lld")
if os.path.exists(bin) and not os.path.exists(sym):
mkdirp(self.stage.path)
os.symlink(bin, sym)
env.prepend_path('PATH', self.stage.path)
env.prepend_path("PATH", self.stage.path)
def setup_run_environment(self, env):
if "+clang" in self.spec:
@@ -531,7 +544,7 @@ class Llvm(CMakePackage, CudaPackage):
define = CMakePackage.define
from_variant = self.define_from_variant
python = spec['python']
python = spec["python"]
cmake_args = [
define("LLVM_REQUIRES_RTTI", True),
define("LLVM_ENABLE_RTTI", True),
@@ -544,14 +557,13 @@ class Llvm(CMakePackage, CudaPackage):
define("LIBOMP_HWLOC_INSTALL_DIR", spec["hwloc"].prefix),
]
version_suffix = spec.variants['version_suffix'].value
if version_suffix != 'none':
cmake_args.append(define('LLVM_VERSION_SUFFIX', version_suffix))
version_suffix = spec.variants["version_suffix"].value
if version_suffix != "none":
cmake_args.append(define("LLVM_VERSION_SUFFIX", version_suffix))
shlib_symbol_version = spec.variants.get('shlib_symbol_version', None)
if shlib_symbol_version is not None and shlib_symbol_version.value != 'none':
cmake_args.append(define('LLVM_SHLIB_SYMBOL_VERSION',
shlib_symbol_version.value))
shlib_symbol_version = spec.variants.get("shlib_symbol_version", None)
if shlib_symbol_version is not None and shlib_symbol_version.value != "none":
cmake_args.append(define("LLVM_SHLIB_SYMBOL_VERSION", shlib_symbol_version.value))
if python.version >= Version("3"):
cmake_args.append(define("Python3_EXECUTABLE", python.command.path))
@@ -562,47 +574,56 @@ class Llvm(CMakePackage, CudaPackage):
runtimes = []
if "+cuda" in spec:
cmake_args.extend([
define("CUDA_TOOLKIT_ROOT_DIR", spec["cuda"].prefix),
define("LIBOMPTARGET_NVPTX_COMPUTE_CAPABILITIES",
",".join(spec.variants["cuda_arch"].value)),
define("CLANG_OPENMP_NVPTX_DEFAULT_ARCH",
"sm_{0}".format(spec.variants["cuda_arch"].value[-1])),
])
cmake_args.extend(
[
define("CUDA_TOOLKIT_ROOT_DIR", spec["cuda"].prefix),
define(
"LIBOMPTARGET_NVPTX_COMPUTE_CAPABILITIES",
",".join(spec.variants["cuda_arch"].value),
),
define(
"CLANG_OPENMP_NVPTX_DEFAULT_ARCH",
"sm_{0}".format(spec.variants["cuda_arch"].value[-1]),
),
]
)
if "+omp_as_runtime" in spec:
cmake_args.extend([
define("LIBOMPTARGET_NVPTX_ENABLE_BCLIB", True),
# work around bad libelf detection in libomptarget
define("LIBOMPTARGET_DEP_LIBELF_INCLUDE_DIR",
spec["libelf"].prefix.include),
])
cmake_args.extend(
[
define("LIBOMPTARGET_NVPTX_ENABLE_BCLIB", True),
# work around bad libelf detection in libomptarget
define(
"LIBOMPTARGET_DEP_LIBELF_INCLUDE_DIR", spec["libelf"].prefix.include
),
]
)
else:
# still build libomptarget but disable cuda
cmake_args.extend([
define("CUDA_TOOLKIT_ROOT_DIR", "IGNORE"),
define("CUDA_SDK_ROOT_DIR", "IGNORE"),
define("CUDA_NVCC_EXECUTABLE", "IGNORE"),
define("LIBOMPTARGET_DEP_CUDA_DRIVER_LIBRARIES", "IGNORE"),
])
cmake_args.extend(
[
define("CUDA_TOOLKIT_ROOT_DIR", "IGNORE"),
define("CUDA_SDK_ROOT_DIR", "IGNORE"),
define("CUDA_NVCC_EXECUTABLE", "IGNORE"),
define("LIBOMPTARGET_DEP_CUDA_DRIVER_LIBRARIES", "IGNORE"),
]
)
cmake_args.append(from_variant("LIBOMPTARGET_ENABLE_DEBUG", "omp_debug"))
if "+lldb" in spec:
projects.append("lldb")
cmake_args.append(define('LLDB_ENABLE_LIBEDIT', True))
cmake_args.append(define('LLDB_ENABLE_NCURSES', True))
cmake_args.append(define('LLDB_ENABLE_LIBXML2', False))
if spec.version >= Version('10'):
cmake_args.append(from_variant("LLDB_ENABLE_PYTHON", 'python'))
cmake_args.append(define("LLDB_ENABLE_LIBEDIT", True))
cmake_args.append(define("LLDB_ENABLE_NCURSES", True))
cmake_args.append(define("LLDB_ENABLE_LIBXML2", False))
if spec.version >= Version("10"):
cmake_args.append(from_variant("LLDB_ENABLE_PYTHON", "python"))
else:
cmake_args.append(define("LLDB_DISABLE_PYTHON", '~python' in spec))
cmake_args.append(define("LLDB_DISABLE_PYTHON", "~python" in spec))
if spec.satisfies("@5.0.0: +python"):
cmake_args.append(define("LLDB_USE_SYSTEM_SIX", True))
if "+gold" in spec:
cmake_args.append(
define("LLVM_BINUTILS_INCDIR", spec["binutils"].prefix.include)
)
cmake_args.append(define("LLVM_BINUTILS_INCDIR", spec["binutils"].prefix.include))
if "+clang" in spec:
projects.append("clang")
@@ -612,10 +633,10 @@ class Llvm(CMakePackage, CudaPackage):
else:
projects.append("openmp")
if '@8' in spec:
cmake_args.append(from_variant('CLANG_ANALYZER_ENABLE_Z3_SOLVER', 'z3'))
elif '@9:' in spec:
cmake_args.append(from_variant('LLVM_ENABLE_Z3_SOLVER', 'z3'))
if "@8" in spec:
cmake_args.append(from_variant("CLANG_ANALYZER_ENABLE_Z3_SOLVER", "z3"))
elif "@9:" in spec:
cmake_args.append(from_variant("LLVM_ENABLE_Z3_SOLVER", "z3"))
if "+flang" in spec:
projects.append("flang")
@@ -634,26 +655,26 @@ class Llvm(CMakePackage, CudaPackage):
projects.append("polly")
cmake_args.append(define("LINK_POLLY_INTO_TOOLS", True))
cmake_args.extend([
define("BUILD_SHARED_LIBS", False),
from_variant("LLVM_BUILD_LLVM_DYLIB", "llvm_dylib"),
from_variant("LLVM_LINK_LLVM_DYLIB", "link_llvm_dylib"),
from_variant("LLVM_USE_SPLIT_DWARF", "split_dwarf"),
# By default on Linux, libc++.so is a ldscript. CMake fails to add
# CMAKE_INSTALL_RPATH to it, which fails. Statically link libc++abi.a
# into libc++.so, linking with -lc++ or -stdlib=libc++ is enough.
define('LIBCXX_ENABLE_STATIC_ABI_LIBRARY', True)
])
cmake_args.extend(
[
define("BUILD_SHARED_LIBS", False),
from_variant("LLVM_BUILD_LLVM_DYLIB", "llvm_dylib"),
from_variant("LLVM_LINK_LLVM_DYLIB", "link_llvm_dylib"),
from_variant("LLVM_USE_SPLIT_DWARF", "split_dwarf"),
# By default on Linux, libc++.so is a ldscript. CMake fails to add
# CMAKE_INSTALL_RPATH to it, which fails. Statically link libc++abi.a
# into libc++.so, linking with -lc++ or -stdlib=libc++ is enough.
define("LIBCXX_ENABLE_STATIC_ABI_LIBRARY", True),
]
)
cmake_args.append(define(
"LLVM_TARGETS_TO_BUILD",
get_llvm_targets_to_build(spec)))
cmake_args.append(define("LLVM_TARGETS_TO_BUILD", get_llvm_targets_to_build(spec)))
cmake_args.append(from_variant("LIBOMP_TSAN_SUPPORT", "omp_tsan"))
if self.compiler.name == "gcc":
compiler = Executable(self.compiler.cc)
gcc_output = compiler('-print-search-dirs', output=str, error=str)
gcc_output = compiler("-print-search-dirs", output=str, error=str)
for line in gcc_output.splitlines():
if line.startswith("install:"):
@@ -665,7 +686,7 @@ class Llvm(CMakePackage, CudaPackage):
cmake_args.append(define("GCC_INSTALL_PREFIX", gcc_prefix))
if self.spec.satisfies("~code_signing platform=darwin"):
cmake_args.append(define('LLDB_USE_SYSTEM_DEBUGSERVER', True))
cmake_args.append(define("LLDB_USE_SYSTEM_DEBUGSERVER", True))
# Semicolon seperated list of projects to enable
cmake_args.append(define("LLVM_ENABLE_PROJECTS", projects))
@@ -689,20 +710,24 @@ class Llvm(CMakePackage, CudaPackage):
# rebuild libomptarget to get bytecode runtime library files
with working_dir(ompdir, create=True):
cmake_args = [
'-G', 'Ninja',
define('CMAKE_BUILD_TYPE', spec.variants['build_type'].value),
"-G",
"Ninja",
define("CMAKE_BUILD_TYPE", spec.variants["build_type"].value),
define("CMAKE_C_COMPILER", spec.prefix.bin + "/clang"),
define("CMAKE_CXX_COMPILER", spec.prefix.bin + "/clang++"),
define("CMAKE_INSTALL_PREFIX", spec.prefix),
define('CMAKE_PREFIX_PATH', prefix_paths)
define("CMAKE_PREFIX_PATH", prefix_paths),
]
cmake_args.extend(self.cmake_args())
cmake_args.extend([
define("LIBOMPTARGET_NVPTX_ENABLE_BCLIB", True),
define("LIBOMPTARGET_DEP_LIBELF_INCLUDE_DIR",
spec["libelf"].prefix.include),
self.stage.source_path + "/openmp",
])
cmake_args.extend(
[
define("LIBOMPTARGET_NVPTX_ENABLE_BCLIB", True),
define(
"LIBOMPTARGET_DEP_LIBELF_INCLUDE_DIR", spec["libelf"].prefix.include
),
self.stage.source_path + "/openmp",
]
)
cmake(*cmake_args)
ninja()
@@ -717,22 +742,22 @@ class Llvm(CMakePackage, CudaPackage):
install_tree("bin", join_path(self.prefix, "libexec", "llvm"))
def llvm_config(self, *args, **kwargs):
lc = Executable(self.prefix.bin.join('llvm-config'))
if not kwargs.get('output'):
kwargs['output'] = str
lc = Executable(self.prefix.bin.join("llvm-config"))
if not kwargs.get("output"):
kwargs["output"] = str
ret = lc(*args, **kwargs)
if kwargs.get('result') == "list":
if kwargs.get("result") == "list":
return ret.split()
else:
return ret
def get_llvm_targets_to_build(spec):
targets = spec.variants['targets'].value
targets = spec.variants["targets"].value
# Build everything?
if 'all' in targets:
return 'all'
if "all" in targets:
return "all"
# Convert targets variant values to CMake LLVM_TARGETS_TO_BUILD array.
spack_to_cmake = {
@@ -753,10 +778,10 @@ def get_llvm_targets_to_build(spec):
"systemz": "SystemZ",
"webassembly": "WebAssembly",
"x86": "X86",
"xcore": "XCore"
"xcore": "XCore",
}
if 'none' in targets:
if "none" in targets:
llvm_targets = set()
else:
llvm_targets = set(spack_to_cmake[target] for target in targets)

View File

@@ -22,127 +22,140 @@ class PyTorch(PythonPackage, CudaPackage):
with strong GPU acceleration."""
homepage = "https://pytorch.org/"
git = "https://github.com/pytorch/pytorch.git"
git = "https://github.com/pytorch/pytorch.git"
maintainers = ['adamjstewart']
maintainers("adamjstewart")
# Exact set of modules is version- and variant-specific, just attempt to import the
# core libraries to ensure that the package was successfully installed.
import_modules = ['torch', 'torch.autograd', 'torch.nn', 'torch.utils']
import_modules = ["torch", "torch.autograd", "torch.nn", "torch.utils"]
version('master', branch='master', submodules=True)
version('1.10.1', tag='v1.10.1', submodules=True)
version('1.10.0', tag='v1.10.0', submodules=True)
version('1.9.1', tag='v1.9.1', submodules=True)
version('1.9.0', tag='v1.9.0', submodules=True)
version('1.8.2', tag='v1.8.2', submodules=True)
version('1.8.1', tag='v1.8.1', submodules=True)
version('1.8.0', tag='v1.8.0', submodules=True)
version('1.7.1', tag='v1.7.1', submodules=True)
version('1.7.0', tag='v1.7.0', submodules=True)
version('1.6.0', tag='v1.6.0', submodules=True)
version('1.5.1', tag='v1.5.1', submodules=True)
version('1.5.0', tag='v1.5.0', submodules=True)
version('1.4.1', tag='v1.4.1', submodules=True)
version('1.4.0', tag='v1.4.0', submodules=True, deprecated=True,
submodules_delete=['third_party/fbgemm'])
version('1.3.1', tag='v1.3.1', submodules=True)
version('1.3.0', tag='v1.3.0', submodules=True)
version('1.2.0', tag='v1.2.0', submodules=True)
version('1.1.0', tag='v1.1.0', submodules=True)
version('1.0.1', tag='v1.0.1', submodules=True)
version('1.0.0', tag='v1.0.0', submodules=True)
version('0.4.1', tag='v0.4.1', submodules=True, deprecated=True,
submodules_delete=['third_party/nervanagpu'])
version('0.4.0', tag='v0.4.0', submodules=True, deprecated=True)
version('0.3.1', tag='v0.3.1', submodules=True, deprecated=True)
version("master", branch="master", submodules=True)
version("1.10.1", tag="v1.10.1", submodules=True)
version("1.10.0", tag="v1.10.0", submodules=True)
version("1.9.1", tag="v1.9.1", submodules=True)
version("1.9.0", tag="v1.9.0", submodules=True)
version("1.8.2", tag="v1.8.2", submodules=True)
version("1.8.1", tag="v1.8.1", submodules=True)
version("1.8.0", tag="v1.8.0", submodules=True)
version("1.7.1", tag="v1.7.1", submodules=True)
version("1.7.0", tag="v1.7.0", submodules=True)
version("1.6.0", tag="v1.6.0", submodules=True)
version("1.5.1", tag="v1.5.1", submodules=True)
version("1.5.0", tag="v1.5.0", submodules=True)
version("1.4.1", tag="v1.4.1", submodules=True)
version(
"1.4.0",
tag="v1.4.0",
submodules=True,
deprecated=True,
submodules_delete=["third_party/fbgemm"],
)
version("1.3.1", tag="v1.3.1", submodules=True)
version("1.3.0", tag="v1.3.0", submodules=True)
version("1.2.0", tag="v1.2.0", submodules=True)
version("1.1.0", tag="v1.1.0", submodules=True)
version("1.0.1", tag="v1.0.1", submodules=True)
version("1.0.0", tag="v1.0.0", submodules=True)
version(
"0.4.1",
tag="v0.4.1",
submodules=True,
deprecated=True,
submodules_delete=["third_party/nervanagpu"],
)
version("0.4.0", tag="v0.4.0", submodules=True, deprecated=True)
version("0.3.1", tag="v0.3.1", submodules=True, deprecated=True)
is_darwin = sys.platform == 'darwin'
is_darwin = sys.platform == "darwin"
# All options are defined in CMakeLists.txt.
# Some are listed in setup.py, but not all.
variant('caffe2', default=True, description='Build Caffe2')
variant('test', default=False, description='Build C++ test binaries')
variant('cuda', default=not is_darwin, description='Use CUDA')
variant('rocm', default=False, description='Use ROCm')
variant('cudnn', default=not is_darwin, description='Use cuDNN')
variant('fbgemm', default=True, description='Use FBGEMM (quantized 8-bit server operators)')
variant('kineto', default=True, description='Use Kineto profiling library')
variant('magma', default=not is_darwin, description='Use MAGMA')
variant('metal', default=is_darwin, description='Use Metal for Caffe2 iOS build')
variant('nccl', default=not is_darwin, description='Use NCCL')
variant('nnpack', default=True, description='Use NNPACK')
variant('numa', default=not is_darwin, description='Use NUMA')
variant('numpy', default=True, description='Use NumPy')
variant('openmp', default=True, description='Use OpenMP for parallel code')
variant('qnnpack', default=True, description='Use QNNPACK (quantized 8-bit operators)')
variant('valgrind', default=not is_darwin, description='Use Valgrind')
variant('xnnpack', default=True, description='Use XNNPACK')
variant('mkldnn', default=True, description='Use MKLDNN')
variant('distributed', default=not is_darwin, description='Use distributed')
variant('mpi', default=not is_darwin, description='Use MPI for Caffe2')
variant('gloo', default=not is_darwin, description='Use Gloo')
variant('tensorpipe', default=not is_darwin, description='Use TensorPipe')
variant('onnx_ml', default=True, description='Enable traditional ONNX ML API')
variant('breakpad', default=True, description='Enable breakpad crash dump library')
variant("caffe2", default=True, description="Build Caffe2")
variant("test", default=False, description="Build C++ test binaries")
variant("cuda", default=not is_darwin, description="Use CUDA")
variant("rocm", default=False, description="Use ROCm")
variant("cudnn", default=not is_darwin, description="Use cuDNN")
variant("fbgemm", default=True, description="Use FBGEMM (quantized 8-bit server operators)")
variant("kineto", default=True, description="Use Kineto profiling library")
variant("magma", default=not is_darwin, description="Use MAGMA")
variant("metal", default=is_darwin, description="Use Metal for Caffe2 iOS build")
variant("nccl", default=not is_darwin, description="Use NCCL")
variant("nnpack", default=True, description="Use NNPACK")
variant("numa", default=not is_darwin, description="Use NUMA")
variant("numpy", default=True, description="Use NumPy")
variant("openmp", default=True, description="Use OpenMP for parallel code")
variant("qnnpack", default=True, description="Use QNNPACK (quantized 8-bit operators)")
variant("valgrind", default=not is_darwin, description="Use Valgrind")
variant("xnnpack", default=True, description="Use XNNPACK")
variant("mkldnn", default=True, description="Use MKLDNN")
variant("distributed", default=not is_darwin, description="Use distributed")
variant("mpi", default=not is_darwin, description="Use MPI for Caffe2")
variant("gloo", default=not is_darwin, description="Use Gloo")
variant("tensorpipe", default=not is_darwin, description="Use TensorPipe")
variant("onnx_ml", default=True, description="Enable traditional ONNX ML API")
variant("breakpad", default=True, description="Enable breakpad crash dump library")
conflicts('+cuda', when='+rocm')
conflicts('+cudnn', when='~cuda')
conflicts('+magma', when='~cuda')
conflicts('+nccl', when='~cuda~rocm')
conflicts('+nccl', when='platform=darwin')
conflicts('+numa', when='platform=darwin', msg='Only available on Linux')
conflicts('+valgrind', when='platform=darwin', msg='Only available on Linux')
conflicts('+mpi', when='~distributed')
conflicts('+gloo', when='~distributed')
conflicts('+tensorpipe', when='~distributed')
conflicts('+kineto', when='@:1.7')
conflicts('+valgrind', when='@:1.7')
conflicts('~caffe2', when='@0.4.0:1.6') # no way to disable caffe2?
conflicts('+caffe2', when='@:0.3.1') # caffe2 did not yet exist?
conflicts('+tensorpipe', when='@:1.5')
conflicts('+xnnpack', when='@:1.4')
conflicts('~onnx_ml', when='@:1.4') # no way to disable ONNX?
conflicts('+rocm', when='@:0.4')
conflicts('+cudnn', when='@:0.4')
conflicts('+fbgemm', when='@:0.4,1.4.0')
conflicts('+qnnpack', when='@:0.4')
conflicts('+mkldnn', when='@:0.4')
conflicts('+breakpad', when='@:1.9') # Option appeared in 1.10.0
conflicts('+breakpad', when='target=ppc64:', msg='Unsupported')
conflicts('+breakpad', when='target=ppc64le:', msg='Unsupported')
conflicts("+cuda", when="+rocm")
conflicts("+cudnn", when="~cuda")
conflicts("+magma", when="~cuda")
conflicts("+nccl", when="~cuda~rocm")
conflicts("+nccl", when="platform=darwin")
conflicts("+numa", when="platform=darwin", msg="Only available on Linux")
conflicts("+valgrind", when="platform=darwin", msg="Only available on Linux")
conflicts("+mpi", when="~distributed")
conflicts("+gloo", when="~distributed")
conflicts("+tensorpipe", when="~distributed")
conflicts("+kineto", when="@:1.7")
conflicts("+valgrind", when="@:1.7")
conflicts("~caffe2", when="@0.4.0:1.6") # no way to disable caffe2?
conflicts("+caffe2", when="@:0.3.1") # caffe2 did not yet exist?
conflicts("+tensorpipe", when="@:1.5")
conflicts("+xnnpack", when="@:1.4")
conflicts("~onnx_ml", when="@:1.4") # no way to disable ONNX?
conflicts("+rocm", when="@:0.4")
conflicts("+cudnn", when="@:0.4")
conflicts("+fbgemm", when="@:0.4,1.4.0")
conflicts("+qnnpack", when="@:0.4")
conflicts("+mkldnn", when="@:0.4")
conflicts("+breakpad", when="@:1.9") # Option appeared in 1.10.0
conflicts("+breakpad", when="target=ppc64:", msg="Unsupported")
conflicts("+breakpad", when="target=ppc64le:", msg="Unsupported")
conflicts('cuda_arch=none', when='+cuda',
msg='Must specify CUDA compute capabilities of your GPU, see '
'https://developer.nvidia.com/cuda-gpus')
conflicts(
"cuda_arch=none",
when="+cuda",
msg="Must specify CUDA compute capabilities of your GPU, see "
"https://developer.nvidia.com/cuda-gpus",
)
# Required dependencies
depends_on('cmake@3.5:', type='build')
depends_on("cmake@3.5:", type="build")
# Use Ninja generator to speed up build times, automatically used if found
depends_on('ninja@1.5:', when='@1.1.0:', type='build')
depends_on("ninja@1.5:", when="@1.1.0:", type="build")
# See python_min_version in setup.py
depends_on('python@3.6.2:', when='@1.7.1:', type=('build', 'link', 'run'))
depends_on('python@3.6.1:', when='@1.6.0:1.7.0', type=('build', 'link', 'run'))
depends_on('python@3.5:', when='@1.5.0:1.5', type=('build', 'link', 'run'))
depends_on('python@2.7:2.8,3.5:', when='@1.4.0:1.4', type=('build', 'link', 'run'))
depends_on('python@2.7:2.8,3.5:3.7', when='@:1.3', type=('build', 'link', 'run'))
depends_on('py-setuptools', type=('build', 'run'))
depends_on('py-future', when='@1.5:', type=('build', 'run'))
depends_on('py-future', when='@1.1: ^python@:2', type=('build', 'run'))
depends_on('py-pyyaml', type=('build', 'run'))
depends_on('py-typing', when='@0.4: ^python@:3.4', type=('build', 'run'))
depends_on('py-typing-extensions', when='@1.7:', type=('build', 'run'))
depends_on('py-pybind11@2.6.2', when='@1.8.0:', type=('build', 'link', 'run'))
depends_on('py-pybind11@2.3.0', when='@1.1.0:1.7', type=('build', 'link', 'run'))
depends_on('py-pybind11@2.2.4', when='@1.0.0:1.0', type=('build', 'link', 'run'))
depends_on('py-pybind11@2.2.2', when='@0.4.0:0.4', type=('build', 'link', 'run'))
depends_on('py-dataclasses', when='@1.7: ^python@3.6.0:3.6', type=('build', 'run'))
depends_on('py-tqdm', type='run')
depends_on('py-protobuf', when='@0.4:', type=('build', 'run'))
depends_on('protobuf', when='@0.4:')
depends_on('blas')
depends_on('lapack')
depends_on('eigen', when='@0.4:')
depends_on("python@3.6.2:", when="@1.7.1:", type=("build", "link", "run"))
depends_on("python@3.6.1:", when="@1.6.0:1.7.0", type=("build", "link", "run"))
depends_on("python@3.5:", when="@1.5.0:1.5", type=("build", "link", "run"))
depends_on("python@2.7:2.8,3.5:", when="@1.4.0:1.4", type=("build", "link", "run"))
depends_on("python@2.7:2.8,3.5:3.7", when="@:1.3", type=("build", "link", "run"))
depends_on("py-setuptools", type=("build", "run"))
depends_on("py-future", when="@1.5:", type=("build", "run"))
depends_on("py-future", when="@1.1: ^python@:2", type=("build", "run"))
depends_on("py-pyyaml", type=("build", "run"))
depends_on("py-typing", when="@0.4: ^python@:3.4", type=("build", "run"))
depends_on("py-typing-extensions", when="@1.7:", type=("build", "run"))
depends_on("py-pybind11@2.6.2", when="@1.8.0:", type=("build", "link", "run"))
depends_on("py-pybind11@2.3.0", when="@1.1.0:1.7", type=("build", "link", "run"))
depends_on("py-pybind11@2.2.4", when="@1.0.0:1.0", type=("build", "link", "run"))
depends_on("py-pybind11@2.2.2", when="@0.4.0:0.4", type=("build", "link", "run"))
depends_on("py-dataclasses", when="@1.7: ^python@3.6.0:3.6", type=("build", "run"))
depends_on("py-tqdm", type="run")
depends_on("py-protobuf", when="@0.4:", type=("build", "run"))
depends_on("protobuf", when="@0.4:")
depends_on("blas")
depends_on("lapack")
depends_on("eigen", when="@0.4:")
# https://github.com/pytorch/pytorch/issues/60329
# depends_on('cpuinfo@2020-12-17', when='@1.8.0:')
# depends_on('cpuinfo@2020-06-11', when='@1.6.0:1.7')
@@ -152,30 +165,30 @@ class PyTorch(PythonPackage, CudaPackage):
# depends_on('sleef@3.4.0_2019-07-30', when='@1.6.0:1.7')
# https://github.com/Maratyszcza/FP16/issues/18
# depends_on('fp16@2020-05-14', when='@1.6.0:')
depends_on('pthreadpool@2021-04-13', when='@1.9.0:')
depends_on('pthreadpool@2020-10-05', when='@1.8.0:1.8')
depends_on('pthreadpool@2020-06-15', when='@1.6.0:1.7')
depends_on('psimd@2020-05-17', when='@1.6.0:')
depends_on('fxdiv@2020-04-17', when='@1.6.0:')
depends_on('benchmark', when='@1.6:+test')
depends_on("pthreadpool@2021-04-13", when="@1.9.0:")
depends_on("pthreadpool@2020-10-05", when="@1.8.0:1.8")
depends_on("pthreadpool@2020-06-15", when="@1.6.0:1.7")
depends_on("psimd@2020-05-17", when="@1.6.0:")
depends_on("fxdiv@2020-04-17", when="@1.6.0:")
depends_on("benchmark", when="@1.6:+test")
# Optional dependencies
depends_on('cuda@7.5:', when='+cuda', type=('build', 'link', 'run'))
depends_on('cuda@9:', when='@1.1:+cuda', type=('build', 'link', 'run'))
depends_on('cuda@9.2:', when='@1.6:+cuda', type=('build', 'link', 'run'))
depends_on('cudnn@6.0:7', when='@:1.0+cudnn')
depends_on('cudnn@7.0:7', when='@1.1.0:1.5+cudnn')
depends_on('cudnn@7.0:', when='@1.6.0:+cudnn')
depends_on('magma', when='+magma')
depends_on('nccl', when='+nccl')
depends_on('numactl', when='+numa')
depends_on('py-numpy', when='+numpy', type=('build', 'run'))
depends_on('llvm-openmp', when='%apple-clang +openmp')
depends_on('valgrind', when='+valgrind')
depends_on("cuda@7.5:", when="+cuda", type=("build", "link", "run"))
depends_on("cuda@9:", when="@1.1:+cuda", type=("build", "link", "run"))
depends_on("cuda@9.2:", when="@1.6:+cuda", type=("build", "link", "run"))
depends_on("cudnn@6.0:7", when="@:1.0+cudnn")
depends_on("cudnn@7.0:7", when="@1.1.0:1.5+cudnn")
depends_on("cudnn@7.0:", when="@1.6.0:+cudnn")
depends_on("magma", when="+magma")
depends_on("nccl", when="+nccl")
depends_on("numactl", when="+numa")
depends_on("py-numpy", when="+numpy", type=("build", "run"))
depends_on("llvm-openmp", when="%apple-clang +openmp")
depends_on("valgrind", when="+valgrind")
# https://github.com/pytorch/pytorch/issues/60332
# depends_on('xnnpack@2021-02-22', when='@1.8.0:+xnnpack')
# depends_on('xnnpack@2020-03-23', when='@1.6.0:1.7+xnnpack')
depends_on('mpi', when='+mpi')
depends_on("mpi", when="+mpi")
# https://github.com/pytorch/pytorch/issues/60270
# depends_on('gloo@2021-05-04', when='@1.9.0:+gloo')
# depends_on('gloo@2020-09-18', when='@1.7.0:1.8+gloo')
@@ -183,31 +196,35 @@ class PyTorch(PythonPackage, CudaPackage):
# https://github.com/pytorch/pytorch/issues/60331
# depends_on('onnx@1.8.0_2020-11-03', when='@1.8.0:+onnx_ml')
# depends_on('onnx@1.7.0_2020-05-31', when='@1.6.0:1.7+onnx_ml')
depends_on('mkl', when='+mkldnn')
depends_on("mkl", when="+mkldnn")
# Test dependencies
depends_on('py-hypothesis', type='test')
depends_on('py-six', type='test')
depends_on('py-psutil', type='test')
depends_on("py-hypothesis", type="test")
depends_on("py-six", type="test")
depends_on("py-psutil", type="test")
# Fix BLAS being overridden by MKL
# https://github.com/pytorch/pytorch/issues/60328
patch('https://patch-diff.githubusercontent.com/raw/pytorch/pytorch/pull/59220.patch',
sha256='e37afffe45cf7594c22050109942370e49983ad772d12ebccf508377dc9dcfc9',
when='@1.2.0:')
patch(
"https://patch-diff.githubusercontent.com/raw/pytorch/pytorch/pull/59220.patch",
sha256="e37afffe45cf7594c22050109942370e49983ad772d12ebccf508377dc9dcfc9",
when="@1.2.0:",
)
# Fixes build on older systems with glibc <2.12
patch('https://patch-diff.githubusercontent.com/raw/pytorch/pytorch/pull/55063.patch',
sha256='e17eaa42f5d7c18bf0d7c37d7b0910127a01ad53fdce3e226a92893356a70395',
when='@1.1.0:1.8.1')
patch(
"https://patch-diff.githubusercontent.com/raw/pytorch/pytorch/pull/55063.patch",
sha256="e17eaa42f5d7c18bf0d7c37d7b0910127a01ad53fdce3e226a92893356a70395",
when="@1.1.0:1.8.1",
)
# Fixes CMake configuration error when XNNPACK is disabled
# https://github.com/pytorch/pytorch/pull/35607
# https://github.com/pytorch/pytorch/pull/37865
patch('xnnpack.patch', when='@1.5.0:1.5')
patch("xnnpack.patch", when="@1.5.0:1.5")
# Fixes build error when ROCm is enabled for pytorch-1.5 release
patch('rocm.patch', when='@1.5.0:1.5+rocm')
patch("rocm.patch", when="@1.5.0:1.5+rocm")
# Fixes fatal error: sleef.h: No such file or directory
# https://github.com/pytorch/pytorch/pull/35359
@@ -216,47 +233,56 @@ class PyTorch(PythonPackage, CudaPackage):
# Fixes compilation with Clang 9.0.0 and Apple Clang 11.0.3
# https://github.com/pytorch/pytorch/pull/37086
patch('https://github.com/pytorch/pytorch/commit/e921cd222a8fbeabf5a3e74e83e0d8dfb01aa8b5.patch',
sha256='17561b16cd2db22f10c0fe1fdcb428aecb0ac3964ba022a41343a6bb8cba7049',
when='@1.1:1.5')
patch(
"https://github.com/pytorch/pytorch/commit/e921cd222a8fbeabf5a3e74e83e0d8dfb01aa8b5.patch",
sha256="17561b16cd2db22f10c0fe1fdcb428aecb0ac3964ba022a41343a6bb8cba7049",
when="@1.1:1.5",
)
# Removes duplicate definition of getCusparseErrorString
# https://github.com/pytorch/pytorch/issues/32083
patch('cusparseGetErrorString.patch', when='@0.4.1:1.0^cuda@10.1.243:')
patch("cusparseGetErrorString.patch", when="@0.4.1:1.0^cuda@10.1.243:")
# Fixes 'FindOpenMP.cmake'
# to detect openmp settings used by Fujitsu compiler.
patch('detect_omp_of_fujitsu_compiler.patch', when='%fj')
patch("detect_omp_of_fujitsu_compiler.patch", when="%fj")
# Fix compilation of +distributed~tensorpipe
# https://github.com/pytorch/pytorch/issues/68002
patch('https://github.com/pytorch/pytorch/commit/c075f0f633fa0136e68f0a455b5b74d7b500865c.patch',
sha256='e69e41b5c171bfb00d1b5d4ee55dd5e4c8975483230274af4ab461acd37e40b8', when='@1.10.0+distributed~tensorpipe')
patch(
"https://github.com/pytorch/pytorch/commit/c075f0f633fa0136e68f0a455b5b74d7b500865c.patch",
sha256="e69e41b5c171bfb00d1b5d4ee55dd5e4c8975483230274af4ab461acd37e40b8",
when="@1.10.0+distributed~tensorpipe",
)
# Both build and install run cmake/make/make install
# Only run once to speed up build times
phases = ['install']
phases = ["install"]
@property
def libs(self):
root = join_path(self.prefix, self.spec['python'].package.site_packages_dir,
'torch', 'lib')
return find_libraries('libtorch', root)
root = join_path(
self.prefix, self.spec["python"].package.site_packages_dir, "torch", "lib"
)
return find_libraries("libtorch", root)
@property
def headers(self):
root = join_path(self.prefix, self.spec['python'].package.site_packages_dir,
'torch', 'include')
root = join_path(
self.prefix, self.spec["python"].package.site_packages_dir, "torch", "include"
)
headers = find_all_headers(root)
headers.directories = [root]
return headers
@when('@1.5.0:')
@when("@1.5.0:")
def patch(self):
# https://github.com/pytorch/pytorch/issues/52208
filter_file('torch_global_deps PROPERTIES LINKER_LANGUAGE C',
'torch_global_deps PROPERTIES LINKER_LANGUAGE CXX',
'caffe2/CMakeLists.txt')
filter_file(
"torch_global_deps PROPERTIES LINKER_LANGUAGE C",
"torch_global_deps PROPERTIES LINKER_LANGUAGE CXX",
"caffe2/CMakeLists.txt",
)
def setup_build_environment(self, env):
"""Set environment variables used to control the build.
@@ -269,7 +295,8 @@ class PyTorch(PythonPackage, CudaPackage):
most flags defined in ``CMakeLists.txt`` can be specified as
environment variables.
"""
def enable_or_disable(variant, keyword='USE', var=None, newer=False):
def enable_or_disable(variant, keyword="USE", var=None, newer=False):
"""Set environment variable to enable or disable support for a
particular variant.
@@ -284,137 +311,135 @@ class PyTorch(PythonPackage, CudaPackage):
# Version 1.1.0 switched from NO_* to USE_* or BUILD_*
# But some newer variants have always used USE_* or BUILD_*
if self.spec.satisfies('@1.1:') or newer:
if '+' + variant in self.spec:
env.set(keyword + '_' + var, 'ON')
if self.spec.satisfies("@1.1:") or newer:
if "+" + variant in self.spec:
env.set(keyword + "_" + var, "ON")
else:
env.set(keyword + '_' + var, 'OFF')
env.set(keyword + "_" + var, "OFF")
else:
if '+' + variant in self.spec:
env.unset('NO_' + var)
if "+" + variant in self.spec:
env.unset("NO_" + var)
else:
env.set('NO_' + var, 'ON')
env.set("NO_" + var, "ON")
# Build in parallel to speed up build times
env.set('MAX_JOBS', make_jobs)
env.set("MAX_JOBS", make_jobs)
# Spack logs have trouble handling colored output
env.set('COLORIZE_OUTPUT', 'OFF')
env.set("COLORIZE_OUTPUT", "OFF")
if self.spec.satisfies('@0.4:'):
enable_or_disable('test', keyword='BUILD')
if self.spec.satisfies("@0.4:"):
enable_or_disable("test", keyword="BUILD")
if self.spec.satisfies('@1.7:'):
enable_or_disable('caffe2', keyword='BUILD')
if self.spec.satisfies("@1.7:"):
enable_or_disable("caffe2", keyword="BUILD")
enable_or_disable('cuda')
if '+cuda' in self.spec:
enable_or_disable("cuda")
if "+cuda" in self.spec:
# cmake/public/cuda.cmake
# cmake/Modules_CUDA_fix/upstream/FindCUDA.cmake
env.unset('CUDA_ROOT')
torch_cuda_arch = ';'.join('{0:.1f}'.format(float(i) / 10.0) for i
in
self.spec.variants['cuda_arch'].value)
env.set('TORCH_CUDA_ARCH_LIST', torch_cuda_arch)
env.unset("CUDA_ROOT")
torch_cuda_arch = ";".join(
"{0:.1f}".format(float(i) / 10.0) for i in self.spec.variants["cuda_arch"].value
)
env.set("TORCH_CUDA_ARCH_LIST", torch_cuda_arch)
enable_or_disable('rocm')
enable_or_disable("rocm")
enable_or_disable('cudnn')
if '+cudnn' in self.spec:
enable_or_disable("cudnn")
if "+cudnn" in self.spec:
# cmake/Modules_CUDA_fix/FindCUDNN.cmake
env.set('CUDNN_INCLUDE_DIR', self.spec['cudnn'].prefix.include)
env.set('CUDNN_LIBRARY', self.spec['cudnn'].libs[0])
env.set("CUDNN_INCLUDE_DIR", self.spec["cudnn"].prefix.include)
env.set("CUDNN_LIBRARY", self.spec["cudnn"].libs[0])
enable_or_disable('fbgemm')
if self.spec.satisfies('@1.8:'):
enable_or_disable('kineto')
enable_or_disable('magma')
enable_or_disable('metal')
if self.spec.satisfies('@1.10:'):
enable_or_disable('breakpad')
enable_or_disable("fbgemm")
if self.spec.satisfies("@1.8:"):
enable_or_disable("kineto")
enable_or_disable("magma")
enable_or_disable("metal")
if self.spec.satisfies("@1.10:"):
enable_or_disable("breakpad")
enable_or_disable('nccl')
if '+nccl' in self.spec:
env.set('NCCL_LIB_DIR', self.spec['nccl'].libs.directories[0])
env.set('NCCL_INCLUDE_DIR', self.spec['nccl'].prefix.include)
enable_or_disable("nccl")
if "+nccl" in self.spec:
env.set("NCCL_LIB_DIR", self.spec["nccl"].libs.directories[0])
env.set("NCCL_INCLUDE_DIR", self.spec["nccl"].prefix.include)
# cmake/External/nnpack.cmake
enable_or_disable('nnpack')
enable_or_disable("nnpack")
enable_or_disable('numa')
if '+numa' in self.spec:
enable_or_disable("numa")
if "+numa" in self.spec:
# cmake/Modules/FindNuma.cmake
env.set('NUMA_ROOT_DIR', self.spec['numactl'].prefix)
env.set("NUMA_ROOT_DIR", self.spec["numactl"].prefix)
# cmake/Modules/FindNumPy.cmake
enable_or_disable('numpy')
enable_or_disable("numpy")
# cmake/Modules/FindOpenMP.cmake
enable_or_disable('openmp', newer=True)
enable_or_disable('qnnpack')
if self.spec.satisfies('@1.3:'):
enable_or_disable('qnnpack', var='PYTORCH_QNNPACK')
if self.spec.satisfies('@1.8:'):
enable_or_disable('valgrind')
if self.spec.satisfies('@1.5:'):
enable_or_disable('xnnpack')
enable_or_disable('mkldnn')
enable_or_disable('distributed')
enable_or_disable('mpi')
enable_or_disable("openmp", newer=True)
enable_or_disable("qnnpack")
if self.spec.satisfies("@1.3:"):
enable_or_disable("qnnpack", var="PYTORCH_QNNPACK")
if self.spec.satisfies("@1.8:"):
enable_or_disable("valgrind")
if self.spec.satisfies("@1.5:"):
enable_or_disable("xnnpack")
enable_or_disable("mkldnn")
enable_or_disable("distributed")
enable_or_disable("mpi")
# cmake/Modules/FindGloo.cmake
enable_or_disable('gloo', newer=True)
if self.spec.satisfies('@1.6:'):
enable_or_disable('tensorpipe')
enable_or_disable("gloo", newer=True)
if self.spec.satisfies("@1.6:"):
enable_or_disable("tensorpipe")
if '+onnx_ml' in self.spec:
env.set('ONNX_ML', 'ON')
if "+onnx_ml" in self.spec:
env.set("ONNX_ML", "ON")
else:
env.set('ONNX_ML', 'OFF')
env.set("ONNX_ML", "OFF")
if not self.spec.satisfies('@master'):
env.set('PYTORCH_BUILD_VERSION', self.version)
env.set('PYTORCH_BUILD_NUMBER', 0)
if not self.spec.satisfies("@master"):
env.set("PYTORCH_BUILD_VERSION", self.version)
env.set("PYTORCH_BUILD_NUMBER", 0)
# BLAS to be used by Caffe2
# Options defined in cmake/Dependencies.cmake and cmake/Modules/FindBLAS.cmake
if self.spec['blas'].name == 'atlas':
env.set('BLAS', 'ATLAS')
env.set('WITH_BLAS', 'atlas')
elif self.spec['blas'].name in ['blis', 'amdblis']:
env.set('BLAS', 'BLIS')
env.set('WITH_BLAS', 'blis')
elif self.spec['blas'].name == 'eigen':
env.set('BLAS', 'Eigen')
elif self.spec['lapack'].name in ['libflame', 'amdlibflame']:
env.set('BLAS', 'FLAME')
env.set('WITH_BLAS', 'FLAME')
elif self.spec['blas'].name in [
'intel-mkl', 'intel-parallel-studio', 'intel-oneapi-mkl']:
env.set('BLAS', 'MKL')
env.set('WITH_BLAS', 'mkl')
elif self.spec['blas'].name == 'openblas':
env.set('BLAS', 'OpenBLAS')
env.set('WITH_BLAS', 'open')
elif self.spec['blas'].name == 'veclibfort':
env.set('BLAS', 'vecLib')
env.set('WITH_BLAS', 'veclib')
if self.spec["blas"].name == "atlas":
env.set("BLAS", "ATLAS")
env.set("WITH_BLAS", "atlas")
elif self.spec["blas"].name in ["blis", "amdblis"]:
env.set("BLAS", "BLIS")
env.set("WITH_BLAS", "blis")
elif self.spec["blas"].name == "eigen":
env.set("BLAS", "Eigen")
elif self.spec["lapack"].name in ["libflame", "amdlibflame"]:
env.set("BLAS", "FLAME")
env.set("WITH_BLAS", "FLAME")
elif self.spec["blas"].name in ["intel-mkl", "intel-parallel-studio", "intel-oneapi-mkl"]:
env.set("BLAS", "MKL")
env.set("WITH_BLAS", "mkl")
elif self.spec["blas"].name == "openblas":
env.set("BLAS", "OpenBLAS")
env.set("WITH_BLAS", "open")
elif self.spec["blas"].name == "veclibfort":
env.set("BLAS", "vecLib")
env.set("WITH_BLAS", "veclib")
else:
env.set('BLAS', 'Generic')
env.set('WITH_BLAS', 'generic')
env.set("BLAS", "Generic")
env.set("WITH_BLAS", "generic")
# Don't use vendored third-party libraries when possible
env.set('BUILD_CUSTOM_PROTOBUF', 'OFF')
env.set('USE_SYSTEM_NCCL', 'ON')
env.set('USE_SYSTEM_EIGEN_INSTALL', 'ON')
if self.spec.satisfies('@0.4:'):
env.set('pybind11_DIR', self.spec['py-pybind11'].prefix)
env.set('pybind11_INCLUDE_DIR',
self.spec['py-pybind11'].prefix.include)
if self.spec.satisfies('@1.10:'):
env.set('USE_SYSTEM_PYBIND11', 'ON')
env.set("BUILD_CUSTOM_PROTOBUF", "OFF")
env.set("USE_SYSTEM_NCCL", "ON")
env.set("USE_SYSTEM_EIGEN_INSTALL", "ON")
if self.spec.satisfies("@0.4:"):
env.set("pybind11_DIR", self.spec["py-pybind11"].prefix)
env.set("pybind11_INCLUDE_DIR", self.spec["py-pybind11"].prefix.include)
if self.spec.satisfies("@1.10:"):
env.set("USE_SYSTEM_PYBIND11", "ON")
# https://github.com/pytorch/pytorch/issues/60334
# if self.spec.satisfies('@1.8:'):
# env.set('USE_SYSTEM_SLEEF', 'ON')
if self.spec.satisfies('@1.6:'):
if self.spec.satisfies("@1.6:"):
# env.set('USE_SYSTEM_LIBS', 'ON')
# https://github.com/pytorch/pytorch/issues/60329
# env.set('USE_SYSTEM_CPUINFO', 'ON')
@@ -422,27 +447,26 @@ class PyTorch(PythonPackage, CudaPackage):
# env.set('USE_SYSTEM_GLOO', 'ON')
# https://github.com/Maratyszcza/FP16/issues/18
# env.set('USE_SYSTEM_FP16', 'ON')
env.set('USE_SYSTEM_PTHREADPOOL', 'ON')
env.set('USE_SYSTEM_PSIMD', 'ON')
env.set('USE_SYSTEM_FXDIV', 'ON')
env.set('USE_SYSTEM_BENCHMARK', 'ON')
env.set("USE_SYSTEM_PTHREADPOOL", "ON")
env.set("USE_SYSTEM_PSIMD", "ON")
env.set("USE_SYSTEM_FXDIV", "ON")
env.set("USE_SYSTEM_BENCHMARK", "ON")
# https://github.com/pytorch/pytorch/issues/60331
# env.set('USE_SYSTEM_ONNX', 'ON')
# https://github.com/pytorch/pytorch/issues/60332
# env.set('USE_SYSTEM_XNNPACK', 'ON')
@run_before('install')
@run_before("install")
def build_amd(self):
if '+rocm' in self.spec:
python(os.path.join('tools', 'amd_build', 'build_amd.py'))
if "+rocm" in self.spec:
python(os.path.join("tools", "amd_build", "build_amd.py"))
@run_after('install')
@run_after("install")
@on_package_attributes(run_tests=True)
def install_test(self):
with working_dir('test'):
python('run_test.py')
with working_dir("test"):
python("run_test.py")
# Tests need to be re-added since `phases` was overridden
run_after('install')(
PythonPackage._run_default_install_time_test_callbacks)
run_after('install')(PythonPackage.sanity_check_prefix)
run_after("install")(PythonPackage._run_default_install_time_test_callbacks)
run_after("install")(PythonPackage.sanity_check_prefix)

File diff suppressed because it is too large Load Diff

View File

@@ -400,7 +400,7 @@ def test_sanitize_literals(env, exclude, include):
({"SHLVL": "1"}, ["SH.*"], [], [], ["SHLVL"]),
# Check we can include using a regex
({"SHLVL": "1"}, ["SH.*"], ["SH.*"], ["SHLVL"], []),
# Check regex to exclude Environment Modules related vars
# Check regex to exclude Modules v4 related vars
(
{"MODULES_LMALTNAME": "1", "MODULES_LMCONFLICT": "2"},
["MODULES_(.*)"],
@@ -415,13 +415,6 @@ def test_sanitize_literals(env, exclude, include):
[],
["A_modquar", "b_modquar", "C_modshare"],
),
(
{"__MODULES_LMTAG": "1", "__MODULES_LMPREREQ": "2"},
["__MODULES_(.*)"],
[],
[],
["__MODULES_LMTAG", "__MODULES_LMPREREQ"],
),
],
)
def test_sanitize_regex(env, exclude, include, expected, deleted):
@@ -496,19 +489,3 @@ def test_exclude_lmod_variables():
# Check that variables related to lmod are not in there
modifications = env.group_by_name()
assert not any(x.startswith("LMOD_") for x in modifications)
@pytest.mark.skipif(sys.platform == "win32", reason="Not supported on Windows (yet)")
@pytest.mark.regression("13504")
def test_exclude_modules_variables():
# Construct the list of environment modifications
file = os.path.join(datadir, "sourceme_modules.sh")
env = EnvironmentModifications.from_sourcing_file(file)
# Check that variables related to modules are not in there
modifications = env.group_by_name()
assert not any(x.startswith("MODULES_") for x in modifications)
assert not any(x.startswith("__MODULES_") for x in modifications)
assert not any(x.startswith("BASH_FUNC_ml") for x in modifications)
assert not any(x.startswith("BASH_FUNC_module") for x in modifications)
assert not any(x.startswith("BASH_FUNC__module_raw") for x in modifications)

View File

@@ -1386,30 +1386,6 @@ def test_single_external_implicit_install(install_mockery, explicit_args, is_exp
assert spack.store.db.get_record(pkg).explicit == is_explicit
@pytest.mark.skipif(
sys.platform == "win32",
reason="Windows breaks overwrite install due to prefix normalization inconsistencies",
)
def test_overwrite_install_does_install_build_deps(install_mockery, mock_fetch):
"""When overwrite installing something from sources, build deps should be installed."""
s = spack.spec.Spec("dtrun3").concretized()
create_installer([(s, {})]).install()
# Verify there is a pure build dep
edge = s.edges_to_dependencies(name="dtbuild3").pop()
assert edge.deptypes == ("build",)
build_dep = edge.spec
# Uninstall the build dep
build_dep.package.do_uninstall()
# Overwrite install the root dtrun3
create_installer([(s, {"overwrite": [s.dag_hash()]})]).install()
# Verify that the build dep was also installed.
assert build_dep.installed
@pytest.mark.parametrize("run_tests", [True, False])
def test_print_install_test_log_skipped(install_mockery, mock_packages, capfd, run_tests):
"""Confirm printing of install log skipped if not run/no failures."""

View File

@@ -198,15 +198,6 @@ def test_manpath_setup(self, modulefile_content, module_configuration):
assert len([x for x in content if 'setenv("MANPATH", "/path/to/man")' in x]) == 1
assert len([x for x in content if 'append_path("MANPATH", "", ":")' in x]) == 0
@pytest.mark.regression("29578")
def test_setenv_raw_value(self, modulefile_content, module_configuration):
"""Tests that we can set environment variable value without formatting it."""
module_configuration("autoload_direct")
content = modulefile_content("module-setenv-raw")
assert len([x for x in content if 'setenv("FOO", "{{name}}, {name}, {{}}, {}")' in x]) == 1
def test_help_message(self, modulefile_content, module_configuration):
"""Tests the generation of module help message."""
@@ -232,18 +223,6 @@ def test_help_message(self, modulefile_content, module_configuration):
)
assert help_msg in "".join(content)
content = modulefile_content("module-long-help target=core2")
help_msg = (
"help([[Name : module-long-help]])"
"help([[Version: 1.0]])"
"help([[Target : core2]])"
"help()"
"help([[Package to test long description message generated in modulefile."
"Message too long is wrapped over multiple lines.]])"
)
assert help_msg in "".join(content)
def test_exclude(self, modulefile_content, module_configuration):
"""Tests excluding the generation of selected modules."""
module_configuration("exclude")

View File

@@ -29,7 +29,7 @@ def test_simple_case(self, modulefile_content, module_configuration):
module_configuration("autoload_direct")
content = modulefile_content(mpich_spec_string)
assert "module-whatis {mpich @3.0.4}" in content
assert 'module-whatis "mpich @3.0.4"' in content
def test_autoload_direct(self, modulefile_content, module_configuration):
"""Tests the automatic loading of direct dependencies."""
@@ -112,16 +112,16 @@ def test_alter_environment(self, modulefile_content, module_configuration):
content = modulefile_content("mpileaks platform=test target=x86_64")
assert len([x for x in content if x.startswith("prepend-path CMAKE_PREFIX_PATH")]) == 0
assert len([x for x in content if "setenv FOO {foo}" in x]) == 1
assert len([x for x in content if "setenv OMPI_MCA_mpi_leave_pinned {1}" in x]) == 1
assert len([x for x in content if "setenv OMPI_MCA_MPI_LEAVE_PINNED {1}" in x]) == 0
assert len([x for x in content if 'setenv FOO "foo"' in x]) == 1
assert len([x for x in content if 'setenv OMPI_MCA_mpi_leave_pinned "1"' in x]) == 1
assert len([x for x in content if 'setenv OMPI_MCA_MPI_LEAVE_PINNED "1"' in x]) == 0
assert len([x for x in content if "unsetenv BAR" in x]) == 1
assert len([x for x in content if "setenv MPILEAKS_ROOT" in x]) == 1
content = modulefile_content("libdwarf platform=test target=core2")
assert len([x for x in content if x.startswith("prepend-path CMAKE_PREFIX_PATH")]) == 0
assert len([x for x in content if "setenv FOO {foo}" in x]) == 0
assert len([x for x in content if 'setenv FOO "foo"' in x]) == 0
assert len([x for x in content if "unsetenv BAR" in x]) == 0
assert len([x for x in content if "depends-on foo/bar" in x]) == 1
assert len([x for x in content if "module load foo/bar" in x]) == 1
@@ -133,14 +133,14 @@ def test_prepend_path_separator(self, modulefile_content, module_configuration):
module_configuration("module_path_separator")
content = modulefile_content("module-path-separator")
assert len([x for x in content if "append-path --delim {:} COLON {foo}" in x]) == 1
assert len([x for x in content if "prepend-path --delim {:} COLON {foo}" in x]) == 1
assert len([x for x in content if "remove-path --delim {:} COLON {foo}" in x]) == 1
assert len([x for x in content if "append-path --delim {;} SEMICOLON {bar}" in x]) == 1
assert len([x for x in content if "prepend-path --delim {;} SEMICOLON {bar}" in x]) == 1
assert len([x for x in content if "remove-path --delim {;} SEMICOLON {bar}" in x]) == 1
assert len([x for x in content if "append-path --delim { } SPACE {qux}" in x]) == 1
assert len([x for x in content if "remove-path --delim { } SPACE {qux}" in x]) == 1
assert len([x for x in content if 'append-path --delim ":" COLON "foo"' in x]) == 1
assert len([x for x in content if 'prepend-path --delim ":" COLON "foo"' in x]) == 1
assert len([x for x in content if 'remove-path --delim ":" COLON "foo"' in x]) == 1
assert len([x for x in content if 'append-path --delim ";" SEMICOLON "bar"' in x]) == 1
assert len([x for x in content if 'prepend-path --delim ";" SEMICOLON "bar"' in x]) == 1
assert len([x for x in content if 'remove-path --delim ";" SEMICOLON "bar"' in x]) == 1
assert len([x for x in content if 'append-path --delim " " SPACE "qux"' in x]) == 1
assert len([x for x in content if 'remove-path --delim " " SPACE "qux"' in x]) == 1
@pytest.mark.regression("11355")
def test_manpath_setup(self, modulefile_content, module_configuration):
@@ -150,12 +150,12 @@ def test_manpath_setup(self, modulefile_content, module_configuration):
# no manpath set by module
content = modulefile_content("mpileaks")
assert len([x for x in content if "append-path --delim {:} MANPATH {}" in x]) == 0
assert len([x for x in content if 'append-path --delim ":" MANPATH ""' in x]) == 0
# manpath set by module with prepend-path
content = modulefile_content("module-manpath-prepend")
assert (
len([x for x in content if "prepend-path --delim {:} MANPATH {/path/to/man}" in x])
len([x for x in content if 'prepend-path --delim ":" MANPATH "/path/to/man"' in x])
== 1
)
assert (
@@ -163,33 +163,24 @@ def test_manpath_setup(self, modulefile_content, module_configuration):
[
x
for x in content
if "prepend-path --delim {:} MANPATH {/path/to/share/man}" in x
if 'prepend-path --delim ":" MANPATH "/path/to/share/man"' in x
]
)
== 1
)
assert len([x for x in content if "append-path --delim {:} MANPATH {}" in x]) == 1
assert len([x for x in content if 'append-path --delim ":" MANPATH ""' in x]) == 1
# manpath set by module with append-path
content = modulefile_content("module-manpath-append")
assert (
len([x for x in content if "append-path --delim {:} MANPATH {/path/to/man}" in x]) == 1
len([x for x in content if 'append-path --delim ":" MANPATH "/path/to/man"' in x]) == 1
)
assert len([x for x in content if "append-path --delim {:} MANPATH {}" in x]) == 1
assert len([x for x in content if 'append-path --delim ":" MANPATH ""' in x]) == 1
# manpath set by module with setenv
content = modulefile_content("module-manpath-setenv")
assert len([x for x in content if "setenv MANPATH {/path/to/man}" in x]) == 1
assert len([x for x in content if "append-path --delim {:} MANPATH {}" in x]) == 0
@pytest.mark.regression("29578")
def test_setenv_raw_value(self, modulefile_content, module_configuration):
"""Tests that we can set environment variable value without formatting it."""
module_configuration("autoload_direct")
content = modulefile_content("module-setenv-raw")
assert len([x for x in content if "setenv FOO {{{name}}, {name}, {{}}, {}}" in x]) == 1
assert len([x for x in content if 'setenv MANPATH "/path/to/man"' in x]) == 1
assert len([x for x in content if 'append-path --delim ":" MANPATH ""' in x]) == 0
def test_help_message(self, modulefile_content, module_configuration):
"""Tests the generation of module help message."""
@@ -199,11 +190,11 @@ def test_help_message(self, modulefile_content, module_configuration):
help_msg = (
"proc ModulesHelp { } {"
" puts stderr {Name : mpileaks}"
" puts stderr {Version: 2.3}"
" puts stderr {Target : core2}"
" puts stderr {}"
" puts stderr {Mpileaks is a mock package that passes audits}"
' puts stderr "Name : mpileaks"'
' puts stderr "Version: 2.3"'
' puts stderr "Target : core2"'
' puts stderr ""'
' puts stderr "Mpileaks is a mock package that passes audits"'
"}"
)
assert help_msg in "".join(content)
@@ -212,23 +203,9 @@ def test_help_message(self, modulefile_content, module_configuration):
help_msg = (
"proc ModulesHelp { } {"
" puts stderr {Name : libdwarf}"
" puts stderr {Version: 20130729}"
" puts stderr {Target : core2}"
"}"
)
assert help_msg in "".join(content)
content = modulefile_content("module-long-help target=core2")
help_msg = (
"proc ModulesHelp { } {"
" puts stderr {Name : module-long-help}"
" puts stderr {Version: 1.0}"
" puts stderr {Target : core2}"
" puts stderr {}"
" puts stderr {Package to test long description message generated in modulefile.}"
" puts stderr {Message too long is wrapped over multiple lines.}"
' puts stderr "Name : libdwarf"'
' puts stderr "Version: 20130729"'
' puts stderr "Target : core2"'
"}"
)
assert help_msg in "".join(content)
@@ -383,14 +360,14 @@ def test_setup_environment(self, modulefile_content, module_configuration):
content = modulefile_content("mpileaks")
assert len([x for x in content if "setenv FOOBAR" in x]) == 1
assert len([x for x in content if "setenv FOOBAR {mpileaks}" in x]) == 1
assert len([x for x in content if 'setenv FOOBAR "mpileaks"' in x]) == 1
spec = spack.spec.Spec("mpileaks")
spec.concretize()
content = modulefile_content(str(spec["callpath"]))
assert len([x for x in content if "setenv FOOBAR" in x]) == 1
assert len([x for x in content if "setenv FOOBAR {callpath}" in x]) == 1
assert len([x for x in content if 'setenv FOOBAR "callpath"' in x]) == 1
def test_override_config(self, module_configuration, factory):
"""Tests overriding some sections of the configuration file."""
@@ -431,7 +408,7 @@ def test_extend_context(self, modulefile_content, module_configuration):
assert 'puts stderr "sentence from package"' in content
short_description = "module-whatis {This package updates the context for Tcl modulefiles.}"
short_description = 'module-whatis "This package updates the context for Tcl modulefiles."'
assert short_description in content
@pytest.mark.regression("4400")

View File

@@ -100,7 +100,7 @@ def test_buildcache(mock_archive, tmpdir):
parser = argparse.ArgumentParser()
buildcache.setup_parser(parser)
create_args = ["create", "-a", "-f", "-d", mirror_path, pkghash]
create_args = ["create", "-a", "-f", mirror_path, pkghash]
# Create a private key to sign package with if gpg2 available
spack.util.gpg.create(
name="test key 1", expires="0", email="spack@googlegroups.com", comment="Spack test key"
@@ -116,7 +116,7 @@ def test_buildcache(mock_archive, tmpdir):
# Uninstall the package
pkg.do_uninstall(force=True)
install_args = ["install", "-a", "-f", pkghash]
install_args = ["install", "-f", pkghash]
args = parser.parse_args(install_args)
# Test install
buildcache.buildcache(parser, args)
@@ -131,30 +131,6 @@ def test_buildcache(mock_archive, tmpdir):
assert buildinfo["relocate_textfiles"] == ["dummy.txt"]
assert buildinfo["relocate_links"] == ["link_to_dummy.txt"]
# create build cache with relative path
create_args.insert(create_args.index("-a"), "-f")
create_args.insert(create_args.index("-a"), "-r")
args = parser.parse_args(create_args)
buildcache.buildcache(parser, args)
# Uninstall the package
pkg.do_uninstall(force=True)
args = parser.parse_args(install_args)
buildcache.buildcache(parser, args)
# test overwrite install
install_args.insert(install_args.index("-a"), "-f")
args = parser.parse_args(install_args)
buildcache.buildcache(parser, args)
files = os.listdir(spec.prefix)
assert "link_to_dummy.txt" in files
assert "dummy.txt" in files
# assert os.path.realpath(
# os.path.join(spec.prefix, 'link_to_dummy.txt')
# ) == os.path.realpath(os.path.join(spec.prefix, 'dummy.txt'))
args = parser.parse_args(["keys"])
buildcache.buildcache(parser, args)

View File

@@ -173,14 +173,6 @@ def test_ensure_binary_is_relocatable(source_file, is_relocatable):
assert relocatable == is_relocatable
@pytest.mark.requires_executables("patchelf", "strings", "file")
@skip_unless_linux
def test_patchelf_is_relocatable():
patchelf = os.path.realpath(spack.relocate._patchelf())
assert llnl.util.filesystem.is_exe(patchelf)
spack.relocate.ensure_binary_is_relocatable(patchelf)
@skip_unless_linux
def test_ensure_binary_is_relocatable_errors(tmpdir):
# The file passed in as argument must exist...
@@ -241,30 +233,6 @@ def test_normalize_relative_paths(start_path, relative_paths, expected):
assert normalized == expected
def test_set_elf_rpaths(mock_patchelf):
# Try to relocate a mock version of patchelf and check
# the call made to patchelf itself
patchelf = mock_patchelf("echo $@")
rpaths = ["/usr/lib", "/usr/lib64", "/opt/local/lib"]
output = spack.relocate._set_elf_rpaths(str(patchelf), rpaths)
# Assert that the arguments of the call to patchelf are as expected
assert "--force-rpath" in output
assert "--set-rpath " + ":".join(rpaths) in output
assert str(patchelf) in output
@skip_unless_linux
def test_set_elf_rpaths_warning(mock_patchelf):
# Mock a failing patchelf command and ensure it warns users
patchelf = mock_patchelf("exit 1")
rpaths = ["/usr/lib", "/usr/lib64", "/opt/local/lib"]
# To avoid using capfd in order to check if the warning was triggered
# here we just check that output is not set
output = spack.relocate._set_elf_rpaths(str(patchelf), rpaths)
assert output is None
@pytest.mark.requires_executables("patchelf", "strings", "file", "gcc")
@skip_unless_linux
def test_relocate_text_bin(binary_with_rpaths, prefix_like):

View File

@@ -125,7 +125,7 @@ def _mock_installed(self):
# use the installed C. It should *not* force A to use the installed D
# *if* we're doing a fresh installation.
a_spec = Spec(a)
a_spec._add_dependency(c_spec, deptypes=("build", "link"))
a_spec._add_dependency(c_spec, deptypes=("build", "link"), virtuals=())
a_spec.concretize()
assert spack.version.Version("2") == a_spec[c][d].version
assert spack.version.Version("2") == a_spec[e].version
@@ -148,7 +148,7 @@ def test_specify_preinstalled_dep(tmpdir, monkeypatch):
monkeypatch.setattr(Spec, "installed", property(lambda x: x.name != "a"))
a_spec = Spec("a")
a_spec._add_dependency(b_spec, deptypes=("build", "link"))
a_spec._add_dependency(b_spec, deptypes=("build", "link"), virtuals=())
a_spec.concretize()
assert set(x.name for x in a_spec.traverse()) == set(["a", "b", "c"])
@@ -989,9 +989,9 @@ def test_synthetic_construction_of_split_dependencies_from_same_package(mock_pac
link_run_spec = Spec("c@=1.0").concretized()
build_spec = Spec("c@=2.0").concretized()
root.add_dependency_edge(link_run_spec, deptypes="link")
root.add_dependency_edge(link_run_spec, deptypes="run")
root.add_dependency_edge(build_spec, deptypes="build")
root.add_dependency_edge(link_run_spec, deptypes="link", virtuals=())
root.add_dependency_edge(link_run_spec, deptypes="run", virtuals=())
root.add_dependency_edge(build_spec, deptypes="build", virtuals=())
# Check dependencies from the perspective of root
assert len(root.dependencies()) == 2
@@ -1017,7 +1017,7 @@ def test_synthetic_construction_bootstrapping(mock_packages, config):
root = Spec("b@=2.0").concretized()
bootstrap = Spec("b@=1.0").concretized()
root.add_dependency_edge(bootstrap, deptypes="build")
root.add_dependency_edge(bootstrap, deptypes="build", virtuals=())
assert len(root.dependencies()) == 1
assert root.dependencies()[0].name == "b"
@@ -1036,7 +1036,7 @@ def test_addition_of_different_deptypes_in_multiple_calls(mock_packages, config)
bootstrap = Spec("b@=1.0").concretized()
for current_deptype in ("build", "link", "run"):
root.add_dependency_edge(bootstrap, deptypes=current_deptype)
root.add_dependency_edge(bootstrap, deptypes=current_deptype, virtuals=())
# Check edges in dependencies
assert len(root.edges_to_dependencies()) == 1
@@ -1063,9 +1063,9 @@ def test_adding_same_deptype_with_the_same_name_raises(
c1 = Spec("b@=1.0").concretized()
c2 = Spec("b@=2.0").concretized()
p.add_dependency_edge(c1, deptypes=c1_deptypes)
p.add_dependency_edge(c1, deptypes=c1_deptypes, virtuals=())
with pytest.raises(spack.error.SpackError):
p.add_dependency_edge(c2, deptypes=c2_deptypes)
p.add_dependency_edge(c2, deptypes=c2_deptypes, virtuals=())
@pytest.mark.regression("33499")
@@ -1084,16 +1084,16 @@ def test_indexing_prefers_direct_or_transitive_link_deps():
z3_flavor_1 = Spec("z3 +through_a1")
z3_flavor_2 = Spec("z3 +through_z1")
root.add_dependency_edge(a1, deptypes=("build", "run", "test"))
root.add_dependency_edge(a1, deptypes=("build", "run", "test"), virtuals=())
# unique package as a dep of a build/run/test type dep.
a1.add_dependency_edge(a2, deptypes="all")
a1.add_dependency_edge(z3_flavor_1, deptypes="all")
a1.add_dependency_edge(a2, deptypes="all", virtuals=())
a1.add_dependency_edge(z3_flavor_1, deptypes="all", virtuals=())
# chain of link type deps root -> z1 -> z2 -> z3
root.add_dependency_edge(z1, deptypes="link")
z1.add_dependency_edge(z2, deptypes="link")
z2.add_dependency_edge(z3_flavor_2, deptypes="link")
root.add_dependency_edge(z1, deptypes="link", virtuals=())
z1.add_dependency_edge(z2, deptypes="link", virtuals=())
z2.add_dependency_edge(z3_flavor_2, deptypes="link", virtuals=())
# Indexing should prefer the link-type dep.
assert "through_z1" in root["z3"].variants

View File

@@ -660,6 +660,7 @@ def test_spec_formatting(self, default_mock_concretization):
("{architecture.os}", "", "os", lambda spec: spec.architecture),
("{architecture.target}", "", "target", lambda spec: spec.architecture),
("{prefix}", "", "prefix", lambda spec: spec),
("{external}", "", "external", lambda spec: spec), # test we print "False"
]
hash_segments = [
@@ -970,7 +971,7 @@ def test_error_message_unknown_variant(self):
def test_satisfies_dependencies_ordered(self):
d = Spec("zmpi ^fake")
s = Spec("mpileaks")
s._add_dependency(d, deptypes=())
s._add_dependency(d, deptypes=(), virtuals=())
assert s.satisfies("mpileaks ^zmpi ^fake")
@pytest.mark.parametrize("transitive", [True, False])
@@ -1017,6 +1018,7 @@ def test_is_extension_after_round_trip_to_dict(config, mock_packages, spec_str):
def test_malformed_spec_dict():
# FIXME: This test was really testing the specific implementation with an ad-hoc test
with pytest.raises(SpecError, match="malformed"):
Spec.from_dict(
{"spec": {"_meta": {"version": 2}, "nodes": [{"dependencies": {"name": "foo"}}]}}
@@ -1024,6 +1026,7 @@ def test_malformed_spec_dict():
def test_spec_dict_hashless_dep():
# FIXME: This test was really testing the specific implementation with an ad-hoc test
with pytest.raises(SpecError, match="Couldn't parse"):
Spec.from_dict(
{
@@ -1117,7 +1120,7 @@ def test_concretize_partial_old_dag_hash_spec(mock_packages, config):
# add it to an abstract spec as a dependency
top = Spec("dt-diamond")
top.add_dependency_edge(bottom, deptypes=())
top.add_dependency_edge(bottom, deptypes=(), virtuals=())
# concretize with the already-concrete dependency
top.concretize()

View File

@@ -43,12 +43,6 @@ def check_json_round_trip(spec):
assert spec.eq_dag(spec_from_json)
def test_simple_spec():
spec = Spec("mpileaks")
check_yaml_round_trip(spec)
check_json_round_trip(spec)
def test_read_spec_from_signed_json():
spec_dir = os.path.join(spack.paths.test_path, "data", "mirrors", "signed_json")
file_name = (
@@ -70,13 +64,6 @@ def check_spec(spec_to_check):
check_spec(s)
def test_normal_spec(mock_packages):
spec = Spec("mpileaks+debug~opt")
spec.normalize()
check_yaml_round_trip(spec)
check_json_round_trip(spec)
@pytest.mark.parametrize(
"invalid_yaml", ["playing_playlist: {{ action }} playlist {{ playlist_name }}"]
)
@@ -95,37 +82,28 @@ def test_invalid_json_spec(invalid_json, error_message):
assert error_message in exc_msg
def test_external_spec(config, mock_packages):
spec = Spec("externaltool")
spec.concretize()
check_yaml_round_trip(spec)
check_json_round_trip(spec)
spec = Spec("externaltest")
spec.concretize()
check_yaml_round_trip(spec)
check_json_round_trip(spec)
def test_ambiguous_version_spec(mock_packages):
spec = Spec("mpileaks@1.0:5.0,6.1,7.3+debug~opt")
spec.normalize()
check_yaml_round_trip(spec)
check_json_round_trip(spec)
def test_concrete_spec(config, mock_packages):
spec = Spec("mpileaks+debug~opt")
spec.concretize()
check_yaml_round_trip(spec)
check_json_round_trip(spec)
def test_yaml_multivalue(config, mock_packages):
spec = Spec('multivalue-variant foo="bar,baz"')
spec.concretize()
check_yaml_round_trip(spec)
check_json_round_trip(spec)
@pytest.mark.parametrize(
"abstract_spec",
[
# Externals
"externaltool",
"externaltest",
# Ambiguous version spec
"mpileaks@1.0:5.0,6.1,7.3+debug~opt",
# Variants
"mpileaks+debug~opt",
'multivalue-variant foo="bar,baz"',
# Virtuals on edges
"callpath",
"mpileaks",
],
)
def test_roundtrip_concrete_specs(abstract_spec, default_mock_concretization):
check_yaml_round_trip(Spec(abstract_spec))
check_json_round_trip(Spec(abstract_spec))
concrete_spec = default_mock_concretization(abstract_spec)
check_yaml_round_trip(concrete_spec)
check_json_round_trip(concrete_spec)
def test_yaml_subdag(config, mock_packages):
@@ -506,6 +484,8 @@ def test_legacy_yaml(tmpdir, install_mockery, mock_packages):
("specfiles/hdf5.v017.json.gz", "xqh5iyjjtrp2jw632cchacn3l7vqzf3m", spack.spec.SpecfileV2),
# Use "full hash" everywhere, see https://github.com/spack/spack/pull/28504
("specfiles/hdf5.v019.json.gz", "iulacrbz7o5v5sbj7njbkyank3juh6d3", spack.spec.SpecfileV3),
# Add properties on edges, see https://github.com/spack/spack/pull/34821
("specfiles/hdf5.v020.json.gz", "vlirlcgazhvsvtundz4kug75xkkqqgou", spack.spec.SpecfileV4),
],
)
def test_load_json_specfiles(specfile, expected_hash, reader_cls):

View File

@@ -19,7 +19,7 @@ def create_dag(nodes, edges):
"""
specs = {name: Spec(name) for name in nodes}
for parent, child, deptypes in edges:
specs[parent].add_dependency_edge(specs[child], deptypes=deptypes)
specs[parent].add_dependency_edge(specs[child], deptypes=deptypes, virtuals=())
return specs

View File

@@ -119,7 +119,10 @@ def test_dump_environment(prepare_environment_for_tests, tmpdir):
dumpfile_path = str(tmpdir.join("envdump.txt"))
envutil.dump_environment(dumpfile_path)
with open(dumpfile_path, "r") as dumpfile:
assert "TEST_ENV_VAR={0}; export TEST_ENV_VAR\n".format(test_paths) in list(dumpfile)
if sys.platform == "win32":
assert 'set "TEST_ENV_VAR={}"\n'.format(test_paths) in list(dumpfile)
else:
assert "TEST_ENV_VAR={0}; export TEST_ENV_VAR\n".format(test_paths) in list(dumpfile)
def test_reverse_environment_modifications(working_env):

View File

@@ -244,7 +244,6 @@ def check_ast_roundtrip(code1, filename="internal", mode="exec"):
assert ast.dump(ast1) == ast.dump(ast2), error_msg
@pytest.mark.xfail(reason="https://github.com/spack/spack/pull/38424")
def test_core_lib_files():
"""Roundtrip source files from the Python core libs."""
test_directories = [

View File

@@ -17,7 +17,6 @@
import spack.package_base
import spack.spec
from spack.version import (
SEMVER_REGEX,
GitVersion,
StandardVersion,
Version,
@@ -977,25 +976,3 @@ def test_unresolvable_git_versions_error(config, mock_packages):
# The package exists, but does not have a git property set. When dereferencing
# the version, we should get VersionLookupError, not a generic AttributeError.
spack.spec.Spec(f"git-test-commit@{'a' * 40}").version.ref_version
@pytest.mark.parametrize(
"tag,expected",
[
("v100.2.3", "100.2.3"),
("v1.2.3", "1.2.3"),
("v1.2.3-pre.release+build.1", "1.2.3-pre.release+build.1"),
("v1.2.3+build.1", "1.2.3+build.1"),
("v1.2.3+build_1", None),
("v1.2.3-pre.release", "1.2.3-pre.release"),
("v1.2.3-pre_release", None),
("1.2.3", "1.2.3"),
("1.2.3.", None),
],
)
def test_semver_regex(tag, expected):
result = SEMVER_REGEX.search(tag)
if expected is None:
assert result is None
else:
assert result.group() == expected

View File

@@ -4,7 +4,6 @@
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import collections
import os
import sys
import pytest
@@ -34,7 +33,6 @@ def _create_url(relative_url):
root_with_fragment = _create_url("index_with_fragment.html")
@pytest.mark.skipif(sys.platform == "win32", reason="Not supported on Windows (yet)")
@pytest.mark.parametrize(
"depth,expected_found,expected_not_found,expected_text",
[
@@ -99,20 +97,17 @@ def test_spider_no_response(monkeypatch):
assert not pages and not links
@pytest.mark.skipif(sys.platform == "win32", reason="Not supported on Windows (yet)")
def test_find_versions_of_archive_0():
versions = spack.util.web.find_versions_of_archive(root_tarball, root, list_depth=0)
assert Version("0.0.0") in versions
@pytest.mark.skipif(sys.platform == "win32", reason="Not supported on Windows (yet)")
def test_find_versions_of_archive_1():
versions = spack.util.web.find_versions_of_archive(root_tarball, root, list_depth=1)
assert Version("0.0.0") in versions
assert Version("1.0.0") in versions
@pytest.mark.skipif(sys.platform == "win32", reason="Not supported on Windows (yet)")
def test_find_versions_of_archive_2():
versions = spack.util.web.find_versions_of_archive(root_tarball, root, list_depth=2)
assert Version("0.0.0") in versions
@@ -120,14 +115,12 @@ def test_find_versions_of_archive_2():
assert Version("2.0.0") in versions
@pytest.mark.skipif(sys.platform == "win32", reason="Not supported on Windows (yet)")
def test_find_exotic_versions_of_archive_2():
versions = spack.util.web.find_versions_of_archive(root_tarball, root, list_depth=2)
# up for grabs to make this better.
assert Version("2.0.0b2") in versions
@pytest.mark.skipif(sys.platform == "win32", reason="Not supported on Windows (yet)")
def test_find_versions_of_archive_3():
versions = spack.util.web.find_versions_of_archive(root_tarball, root, list_depth=3)
assert Version("0.0.0") in versions
@@ -137,7 +130,6 @@ def test_find_versions_of_archive_3():
assert Version("4.5") in versions
@pytest.mark.skipif(sys.platform == "win32", reason="Not supported on Windows (yet)")
def test_find_exotic_versions_of_archive_3():
versions = spack.util.web.find_versions_of_archive(root_tarball, root, list_depth=3)
assert Version("2.0.0b2") in versions
@@ -145,7 +137,6 @@ def test_find_exotic_versions_of_archive_3():
assert Version("4.5-rc5") in versions
@pytest.mark.skipif(sys.platform == "win32", reason="Not supported on Windows (yet)")
def test_find_versions_of_archive_with_fragment():
versions = spack.util.web.find_versions_of_archive(
root_tarball, root_with_fragment, list_depth=0
@@ -206,7 +197,6 @@ def test_etag_parser():
assert spack.util.web.parse_etag("abc def") is None
@pytest.mark.skipif(sys.platform == "win32", reason="Not supported on Windows (yet)")
def test_list_url(tmpdir):
testpath = str(tmpdir)
testpath_url = url_util.path_to_file_url(testpath)

View File

@@ -211,7 +211,9 @@ def get_visitor_from_args(cover, direction, deptype, key=id, visited=None, visit
def with_artificial_edges(specs):
"""Initialize a list of edges from an imaginary root node to the root specs."""
return [
EdgeAndDepth(edge=spack.spec.DependencySpec(parent=None, spec=s, deptypes=()), depth=0)
EdgeAndDepth(
edge=spack.spec.DependencySpec(parent=None, spec=s, deptypes=(), virtuals=()), depth=0
)
for s in specs
]
@@ -552,8 +554,3 @@ def traverse_tree(specs, cover="nodes", deptype="all", key=id, depth_first=True)
return traverse_breadth_first_tree_nodes(None, edges)
return traverse_edges(specs, order="pre", cover=cover, deptype=deptype, key=key, depth=True)
def by_dag_hash(s: "spack.spec.Spec") -> str:
"""Used very often as a key function for traversals."""
return s.dag_hash()

View File

@@ -171,7 +171,11 @@ def path_put_first(var_name: str, directories: List[Path]):
BASH_FUNCTION_FINDER = re.compile(r"BASH_FUNC_(.*?)\(\)")
def _env_var_to_source_line(var: str, val: str) -> str:
def _win_env_var_to_set_line(var: str, val: str) -> str:
return f'set "{var}={val}"'
def _nix_env_var_to_source_line(var: str, val: str) -> str:
if var.startswith("BASH_FUNC"):
source_line = "function {fname}{decl}; export -f {fname}".format(
fname=BASH_FUNCTION_FINDER.sub(r"\1", var), decl=val
@@ -181,6 +185,13 @@ def _env_var_to_source_line(var: str, val: str) -> str:
return source_line
def _env_var_to_source_line(var: str, val: str) -> str:
if sys.platform == "win32":
return _win_env_var_to_set_line(var, val)
else:
return _nix_env_var_to_source_line(var, val)
@system_path_filter(arg_slice=slice(1))
def dump_environment(path: Path, environment: Optional[MutableMapping[str, str]] = None):
"""Dump an environment dictionary to a source-able file.
@@ -340,20 +351,13 @@ def execute(self, env: MutableMapping[str, str]):
class SetEnv(NameValueModifier):
__slots__ = ("force", "raw")
__slots__ = ("force",)
def __init__(
self,
name: str,
value: str,
*,
trace: Optional[Trace] = None,
force: bool = False,
raw: bool = False,
self, name: str, value: str, *, trace: Optional[Trace] = None, force: bool = False
):
super().__init__(name, value, trace=trace)
self.force = force
self.raw = raw
def execute(self, env: MutableMapping[str, str]):
tty.debug(f"SetEnv: {self.name}={str(self.value)}", level=3)
@@ -497,16 +501,15 @@ def _trace(self) -> Optional[Trace]:
return Trace(filename=filename, lineno=lineno, context=current_context)
@system_env_normalize
def set(self, name: str, value: str, *, force: bool = False, raw: bool = False):
def set(self, name: str, value: str, *, force: bool = False):
"""Stores a request to set an environment variable.
Args:
name: name of the environment variable
value: value of the environment variable
force: if True, audit will not consider this modification a warning
raw: if True, format of value string is skipped
"""
item = SetEnv(name, value, trace=self._trace(), force=force, raw=raw)
item = SetEnv(name, value, trace=self._trace(), force=force)
self.env_modifications.append(item)
@system_env_normalize
@@ -765,21 +768,16 @@ def from_sourcing_file(
"PS1",
"PS2",
"ENV",
# Environment Modules or Lmod
# Environment modules v4
"LOADEDMODULES",
"_LMFILES_",
"MODULEPATH",
"MODULERCFILE",
"BASH_FUNC_ml()",
"BASH_FUNC_module()",
# Environment Modules-specific configuration
"MODULESHOME",
"BASH_FUNC__module_raw()",
r"MODULES_(.*)",
r"__MODULES_(.*)",
"MODULEPATH",
"MODULES_(.*)",
r"(\w*)_mod(quar|share)",
# Lmod-specific configuration
# Lmod configuration
r"LMOD_(.*)",
"MODULERCFILE",
]
)

View File

@@ -4,7 +4,6 @@
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import errno
import math
import os
import shutil
@@ -152,17 +151,18 @@ def __exit__(cm, type, value, traceback):
return WriteTransaction(self._get_lock(key), acquire=WriteContextManager)
def mtime(self, key) -> float:
"""Return modification time of cache file, or -inf if it does not exist.
def mtime(self, key):
"""Return modification time of cache file, or 0 if it does not exist.
Time is in units returned by os.stat in the mtime field, which is
platform-dependent.
"""
if not self.init_entry(key):
return -math.inf
return 0
else:
return os.stat(self.cache_path(key)).st_mtime
sinfo = os.stat(self.cache_path(key))
return sinfo.st_mtime
def remove(self, key):
file = self.cache_path(key)

View File

@@ -454,10 +454,6 @@ def visit_ClassDef(self, node):
self.fill("@")
self.dispatch(deco)
self.fill("class " + node.name)
if getattr(node, "type_params", False):
self.write("[")
interleave(lambda: self.write(", "), self.dispatch, node.type_params)
self.write("]")
with self.delimit_if("(", ")", condition=node.bases or node.keywords):
comma = False
for e in node.bases:
@@ -503,10 +499,6 @@ def __FunctionDef_helper(self, node, fill_suffix):
self.dispatch(deco)
def_str = fill_suffix + " " + node.name
self.fill(def_str)
if getattr(node, "type_params", False):
self.write("[")
interleave(lambda: self.write(", "), self.dispatch, node.type_params)
self.write("]")
with self.delimit("(", ")"):
self.dispatch(node.args)
if getattr(node, "returns", False):
@@ -1257,23 +1249,3 @@ def visit_MatchOr(self, node):
with self.require_parens(_Precedence.BOR, node):
self.set_precedence(pnext(_Precedence.BOR), *node.patterns)
interleave(lambda: self.write(" | "), self.dispatch, node.patterns)
def visit_TypeAlias(self, node):
self.fill("type ")
self.dispatch(node.name)
self.write(" = ")
self.dispatch(node.value)
def visit_TypeVar(self, node):
self.write(node.name)
if node.bound:
self.write(": ")
self.dispatch(node.bound)
def visit_TypeVarTuple(self, node):
self.write("*")
self.write(node.name)
def visit_ParamSpec(self, node):
self.write("**")
self.write(node.name)

View File

@@ -17,6 +17,7 @@
import traceback
import urllib.parse
from html.parser import HTMLParser
from pathlib import Path, PurePosixPath
from urllib.error import URLError
from urllib.request import HTTPSHandler, Request, build_opener
@@ -498,7 +499,8 @@ def list_url(url, recursive=False):
if local_path:
if recursive:
return list(_iter_local_prefix(local_path))
# convert backslash to forward slash as required for URLs
return [str(PurePosixPath(Path(p))) for p in list(_iter_local_prefix(local_path))]
return [
subpath
for subpath in os.listdir(local_path)
@@ -738,7 +740,8 @@ def find_versions_of_archive(
# We'll be a bit more liberal and just look for the archive
# part, not the full path.
url_regex = os.path.basename(url_regex)
# this is a URL so it is a posixpath even on Windows
url_regex = PurePosixPath(url_regex).name
# We need to add a / to the beginning of the regex to prevent
# Spack from picking up similarly named packages like:

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