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Author SHA1 Message Date
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
Andrew-Dunning-NNL
aba9207254 py-dvc: new package (#21516) 
* py-dvc: new package

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

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

* py-dvc: add version dependency for py-networkx

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
 2021-02-08 09:54:28 -06:00
AMD Toolchain Support
9eb5c8f843 cp2k: added support for AMD toolchain (#21371) 2021-02-08 11:03:56 +01:00
Tomoyasu Nojiri
83f7541420 libqglviewer: add dependency on glu (#21438) 2021-02-08 10:55:56 +01:00
Tomoyasu Nojiri
b760dbc502 pangolin: add dependency on glu (#21439) 2021-02-08 10:46:24 +01:00
lpoirel
aa86523aaa mumps: don't put absolute path in soname (#21247) 2021-02-08 10:30:27 +01:00
dependabot[bot]
652fef2c76 build(deps): bump actions/cache from v2 to v2.1.4 (#21529) 
Bumps [actions/cache](https://github.com/actions/cache) from v2 to v2.1.4.
- [Release notes](https://github.com/actions/cache/releases)
- [Commits](https://github.com/actions/cache/compare/v2...26968a09c0ea4f3e233fdddbafd1166051a095f6)

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

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2021-02-08 09:57:45 +01:00
Adam J. Stewart
824f6ad3f4 py-matplotlib: clarify backend variant description (#21520) 2021-02-08 09:36:35 +01:00
Adam J. Stewart
8a2fc484fa py-fiscalyear: add v0.3.1 (#21523) 2021-02-08 09:30:50 +01:00
Adam J. Stewart
480e4f0b4c py-numpy: add v1.20.1 (#21525) 2021-02-08 09:27:31 +01:00
darmac
f4f2647134 libproxy: add v0.4.17 (#21526) 
Added dependency on Python and zlib
 2021-02-08 09:25:10 +01:00
darmac
1bee682d67 pciutils: add a PREFIX parameter to make invocation (#21527) 2021-02-08 09:22:55 +01:00
darmac
ca24b6c740 bird: add build dependencies (#21528) 2021-02-08 09:20:48 +01:00
Desmond Orton
de99535f9a Package/r require and subpackage dep fix (#21433) 2021-02-07 13:48:14 -06:00
Sreenivasa Murthy Kolam
fef79b7e9b fix build failure with boost-1.58.0 by using higher revision (#21376) 2021-02-07 13:32:59 +01:00
Mark Abraham
9414b11490 Clarify GROMACS relaxed double option (#21510) 
* Clarify relaxed double precision option

This is only intended for use on the Fujitsu PRIMEHPC platform

* Fix typo

* Shorten line to keep linter happy
 2021-02-07 05:29:53 -07:00
Richarda Butler
5f75221522 Bugfix: Install font-util (#20179) 
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: Greg Becker <becker33@llnl.gov>
 2021-02-07 12:52:07 +01:00