Commit Graph

20075 Commits

Author SHA1 Message Date
Massimiliano Culpo
cb2c233a97 Move context manager to swap the current store into spack.store
The context manager can be used to swap the current
store temporarily, for any use case that may need it.
2021-02-10 16:50:09 -08:00
Massimiliano Culpo
1a8963b0f4 repo: generalize "swap" context manager to also accept paths
The method is now called "use_repositories" and
makes it clear in the docstring that it accepts
as arguments either Repo objects or paths.

Since there was some duplication between this
contextmanager and "use_repo" in the testing framework,
remove the latter and use spack.repo.use_repositories
across the entire code base.

Make a few adjustment to MockPackageMultiRepo, since it was
stating in the docstring that it was supposed to mock
spack.repo.Repo and was instead mocking spack.repo.RepoPath.
2021-02-10 16:50:09 -08:00
Scott McMillan
0007ed72c3 Fix: Add a space between -isystem and the directory (#21599)
Some compilers, such as the NV compilers, do not recognize -isystem
dir when specified without a space.

Works: -isystem ../include
Does not work: -isystem../include

This PR updates the compiler wrapper to include the space with -isystem.
2021-02-10 15:56:42 -08:00
Greg Becker
2b6f896ca7 Bugfix: environments/views on separate mounts (#20720)
Environment views fail when the tmpdir used for view generation is
on a separate mount from the install_tree because the files cannot
by symlinked between the two. The fix is to use an alternative
tmpdir located alongside the view.
2021-02-10 13:39:11 -08:00
Jen Herting
5828a2cd31 [py-chalice] py-typing causes issues with python >= 3.5 (#21202)
* [py-chalice] py-typing causes issues with python >= 3.5

* [py-chalice] changed upperbound on typing
2021-02-10 21:31:02 +00:00
eugeneswalker
e15a3438a8 ascent: add version v0.6.0 (#21573) 2021-02-10 10:14:16 -08:00
a-saitoh-fj
24dd5d12a5 py-llvmlite: Changing build options when using the FUJITSU compiler (#21585) 2021-02-10 09:58:10 -06:00
vvolkl
08972014f8 [py-uproot4] add new versions (#21588) 2021-02-10 09:57:10 -06:00
a-saitoh-fj
bd836540f2 New package: py-dask-sphinx-theme (#21582) 2021-02-10 10:22:03 +01:00
a-saitoh-fj
cf9a7bc7f6 pandoc modified:package.py (#21581) 2021-02-10 10:20:47 +01:00
h-denpo
7d48bbfd3a raxml-ng: Fixed typo: (#21580) 2021-02-10 10:17:28 +01:00
Matt Schramm
175d614bc6 Update package.py (#21577) 2021-02-10 10:16:22 +01:00
Shintaro Iwasaki
ca6ec59a86 sollve: deprecate the sollve package (#21578) 2021-02-10 01:49:20 +00:00
Jen Herting
a938cc512b New package: py-moviepy (#20751)
* [py-moviepy] created template

* [py-moviepy] added dependencies

* [py-moviepy] removed fixmes, added homepage and description

* [py-moviepy] updated to pypi and updated checksum

* [py-moviepy] added setuptools dependency

* [py-moviepy] more specific version limit

* [py-moviepy] added checksum for version 1.0.1

* [py-moviepy] numpy restriction not nesessary here
2021-02-09 23:18:51 +00:00
kean-smullen-nnl
32056da93b New Package: py-xgboost (#21470)
* new python package py-xgboost added

* py-xgboost spack style applied

* py-xgboost: Addressing PR #21470 comments. Added variant descriptions and fixed scikit-learn when clause
2021-02-09 23:12:20 +00:00
Satish Balay
42e8a64660 xsdk: update petsc4py, strumpack dependencies (#21569) 2021-02-10 00:10:09 +01:00
Adam J. Stewart
d580ac302d 3DTK: add new package (#20931)
* 3DTK: add new package

* Add missing opencv variants

Co-authored-by: Michael Kuhn <michael@ikkoku.de>

* Fix cmake version req, add eigen dep

* Prefer trunk version

* Tell 3dtk where to find eigen

* Fix installation

* Fix installation

Co-authored-by: Michael Kuhn <michael@ikkoku.de>
2021-02-09 16:45:41 -06:00
Ethan Stam
865d38afa7 ParaView, LLVM: add -shared-intel to solve intel linking failures (#18195) 2021-02-09 23:26:49 +01:00
Desmond Orton
2697c73097 New Package r-reproducible (#21434) 2021-02-09 14:11:14 -08:00
Glenn Johnson
d01edbb48e Fix groff build with long interpeter line (#21549)
This PR fixes the case where groff fails to build if the spack install
path is really long. There are a couple of perl scripts that get built,
and used, during the build phase that will fail when the perl
interpreter line is too long. Filtering the lines will not work because
the files don not exist after the configure phase and patching after the
build phase is too late.  This PR runs the scripts explicitly with the
spack perl via the $(PERL) variable in the call to the script.
2021-02-09 13:54:51 -08:00
Glenn Johnson
f7a9fbc688 Update the Spack R BioConductor packages to Bioconductor-3.12 (#21575) 2021-02-09 15:35:30 -06:00
Adam J. Stewart
e341a76543 Clean up .gitignore, add Python.gitignore (#20613)
* Clean up .gitignore, add Python.gitignore

* Ignore `spack debug create-db-tarball` logs

* lib/ and var/ need to be tracked

* Add editor- and OS-specific ignores

* Add PyCharm ignores

* Add JetBrains editors like PyCharm
2021-02-09 20:55:03 +00:00
takanori-ihara
fe863b68b2 biobambam2: Add test method and test scripts. (#21504)
Co-Authored-By: Tamara Dahlgren <dahlgren1@llnl.gov>
2021-02-09 12:33:55 -08:00
Jordan Ogas
02a4abadfa add charliecloud 0.22 (#21574) 2021-02-09 12:15:03 -08:00
Dr. Christian Tacke
11711fcbe5 root: 6.22.04 works with xrootd 5 (#21572)
ROOT version 6.22.04 has been ported to support xrootd 5.
So let's support that.

See: https://github.com/root-project/root/commit/a33b156e3bf809343eda08150666154a
2021-02-09 11:33:14 -08:00
Evan Bollig
cc6d055786 Relion 3.1.1 patch for Ubuntu18.04 (#21556) 2021-02-09 11:07:06 -08:00
Cyrus Harrison
533d4bbc3c add conduit 0.7.0 release (#21558) 2021-02-09 11:02:30 -08:00
Adam J. Stewart
7ccb9992a6 Procedure to deprecate old versions of software (#20767)
* Procedure to deprecate old versions of software

* Add documentation

* Fix bug in logic

* Update tab completion

* Deprecate legacy packages

* Deprecate old mxnet as well

* More explicit docs
2021-02-09 13:51:18 -05:00
BenWeber42
e5ab686d77 Changed stages permissions to 750 (#21425) 2021-02-09 10:12:43 -08:00
BenWeber42
e4d74825f3 Fixed uninstall rm parent folder race condition (#21424) 2021-02-09 10:05:06 -08:00
Toyohisa Kameyama
b802e75274 penblas: fix link error in dependent packages. (#21561) 2021-02-09 09:53:09 -08:00
Harmen Stoppels
0760c7c704 Add more cmake patch releases (#21562) 2021-02-09 09:48:34 -08:00
Adam J. Stewart
341eec8dfb py-pandas: add v1.2.2 (#21568) 2021-02-09 09:32:58 -08:00
Mark Meredith
784b421eda Fix typo (#21567) 2021-02-09 15:34:42 +00:00
Shintaro Iwasaki
3c874e22b5 bolt: add new versions (#21550) 2021-02-09 09:43:12 +01:00
Sreenivasa Murthy Kolam
bff4469d8f replace libelf with elfutils in hip-rocclr (#21421) 2021-02-09 08:21:05 +01:00
Jen Herting
58f3d0986d New package: py-msgpack-numpy (#21548)
* [py-msgpack-numpy] created template

* [py-msgpack-numpy] added dependencies

* [py-msgpack-numpy] added homepage and description. removed fixmes. fixed copyright date

* [py-msgpack-numpy] url -> pypi
2021-02-08 21:20:07 +00:00
Andrew W Elble
dc1a05d273 py-tensorflow-estimator: update for 2.4.0 (#21546)
* py-tensorflow-estimator: update for 2.4.0

* build/run deptypes, switch to common tmpfile logic
2021-02-08 21:14:20 +00:00
Andrew W Elble
7fd8b775ad py-tensorboard: add new versions (#21545) 2021-02-08 14:38:09 -06:00
ketsubouchi
0e3b12776c xforms: new package (#21535) 2021-02-08 12:27:36 -08:00
Jen Herting
843e1993ae New package: py-imageio-ffmpeg (#20749)
* [py-imageio-ffmpeg] created template

* [py-imageio-ffmpeg] added dependencies

* [py-imageio-ffmpeg] added runtime dependency

* [py-imageio-ffmpeg] removed fixmes, added homepage and description

* [py-imageio-ffmpeg] url -> pypi and updated checksum
2021-02-08 13:30:45 -06:00
AMD Toolchain Support
fc374febf2 amdtoolchain support for openfoam (#21536) 2021-02-08 13:22:59 -06:00
Sergei Shudler
6447ec6ff5 Smoke test for parallel-netcdf package (#21400) 2021-02-08 11:21:52 -08:00
Satish Balay
c01065ee73 petsc: update to version 3.14.4, and petsc4py to 3.14.1 (#21544) 2021-02-08 13:05:52 -06:00
Adam J. Stewart
48954a5a3e Restore verbosity of patching (#21233) 2021-02-08 10:29:19 -08:00
Pieter Ghysels
b37c601a01 Strumpack slate variant (#21542)
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2021-02-08 18:27:41 +00:00
Toyohisa Kameyama
512c8a1f1a ldak: build only x86_64 linux. (#21414) 2021-02-08 10:22:47 -08:00
Howard Pritchard
45040589c8 paraview: disable VTK_PYTHON_OPTIONAL_LINK for cce (#21357)
when building paraview 5.8 or newer.

See https://gitlab.kitware.com/vtk/vtk/-/merge_requests/7482for background info.

Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
2021-02-08 09:53:06 -08:00
Satish Balay
66dc7d8c53 petsc4py: workaround LDSHARED change in 3cc5b7adc7 (#21541) 2021-02-08 11:43:46 -06:00
victorusu
9d8b8553f1 Add ReFrame 3.4 (#21540) 2021-02-08 17:00:12 +01:00