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2021-02-09New Package: py-xgboost (#21470)kean-smullen-nnl1-0/+39
* 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
2021-02-10xsdk: update petsc4py, strumpack dependencies (#21569)Satish Balay1-3/+4
2021-02-093DTK: add new package (#20931)Adam J. Stewart2-0/+110
* 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>
2021-02-09ParaView, LLVM: add -shared-intel to solve intel linking failures (#18195)Ethan Stam2-2/+14
2021-02-09New Package r-reproducible (#21434)Desmond Orton1-0/+45
2021-02-09Fix groff build with long interpeter line (#21549)Glenn Johnson3-0/+27
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.
2021-02-09Update the Spack R BioConductor packages to Bioconductor-3.12 (#21575)Glenn Johnson193-635/+1177
2021-02-09Clean up .gitignore, add Python.gitignore (#20613)Adam J. Stewart1-24/+491
* 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
2021-02-09biobambam2: Add test method and test scripts. (#21504)takanori-ihara1-0/+20
Co-Authored-By: Tamara Dahlgren <dahlgren1@llnl.gov>
2021-02-09add charliecloud 0.22 (#21574)Jordan Ogas1-0/+1
2021-02-09root: 6.22.04 works with xrootd 5 (#21572)Dr. Christian Tacke1-1/+2
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
2021-02-09Relion 3.1.1 patch for Ubuntu18.04 (#21556)Evan Bollig2-0/+33
2021-02-09add conduit 0.7.0 release (#21558)Cyrus Harrison1-0/+1
2021-02-09Procedure to deprecate old versions of software (#20767)Adam J. Stewart31-97/+215
* 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
2021-02-09Changed stages permissions to 750 (#21425)BenWeber421-3/+3
2021-02-09Fixed uninstall rm parent folder race condition (#21424)BenWeber421-3/+12
2021-02-09penblas: fix link error in dependent packages. (#21561)Toyohisa Kameyama1-0/+4
2021-02-09Add more cmake patch releases (#21562)Harmen Stoppels1-0/+5
2021-02-09py-pandas: add v1.2.2 (#21568)Adam J. Stewart1-0/+1
2021-02-09Fix typo (#21567)Mark Meredith1-1/+1
2021-02-09bolt: add new versions (#21550)Shintaro Iwasaki1-0/+2
2021-02-09replace libelf with elfutils in hip-rocclr (#21421)Sreenivasa Murthy Kolam1-1/+1
2021-02-08New package: py-msgpack-numpy (#21548)Jen Herting1-0/+23
* [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
2021-02-08py-tensorflow-estimator: update for 2.4.0 (#21546)Andrew W Elble1-17/+14
* py-tensorflow-estimator: update for 2.4.0 * build/run deptypes, switch to common tmpfile logic
2021-02-08py-tensorboard: add new versions (#21545)Andrew W Elble2-18/+27
2021-02-08xforms: new package (#21535)ketsubouchi1-0/+26
2021-02-08New package: py-imageio-ffmpeg (#20749)Jen Herting1-0/+25
* [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
2021-02-08amdtoolchain support for openfoam (#21536)AMD Toolchain Support1-4/+4
2021-02-08Smoke test for parallel-netcdf package (#21400)Sergei Shudler1-0/+32
2021-02-08petsc: update to version 3.14.4, and petsc4py to 3.14.1 (#21544)Satish Balay2-1/+6
2021-02-08Restore verbosity of patching (#21233)Adam J. Stewart1-6/+6
2021-02-08Strumpack slate variant (#21542)Pieter Ghysels1-2/+6
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2021-02-08ldak: build only x86_64 linux. (#21414)Toyohisa Kameyama1-9/+11
2021-02-08paraview: disable VTK_PYTHON_OPTIONAL_LINK for cce (#21357)Howard Pritchard1-0/+2
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>
2021-02-08petsc4py: workaround LDSHARED change in ↵Satish Balay2-0/+15
3cc5b7adc7d2167646d6a049d64c710d98e1d6f0 (#21541)
2021-02-08Add ReFrame 3.4 (#21540)victorusu1-0/+2
2021-02-08py-dvc: new package (#21516)Andrew-Dunning-NNL1-0/+61
* 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>
2021-02-08cp2k: added support for AMD toolchain (#21371)AMD Toolchain Support3-28/+55
2021-02-08libqglviewer: add dependency on glu (#21438)Tomoyasu Nojiri1-0/+1
2021-02-08pangolin: add dependency on glu (#21439)Tomoyasu Nojiri1-0/+1
2021-02-08mumps: don't put absolute path in soname (#21247)lpoirel1-2/+2
2021-02-08build(deps): bump actions/cache from v2 to v2.1.4 (#21529)dependabot[bot]1-1/+1
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>
2021-02-08py-matplotlib: clarify backend variant description (#21520)Adam J. Stewart1-1/+3
2021-02-08py-fiscalyear: add v0.3.1 (#21523)Adam J. Stewart1-0/+1
2021-02-08py-numpy: add v1.20.1 (#21525)Adam J. Stewart1-0/+1
2021-02-08libproxy: add v0.4.17 (#21526)darmac1-0/+6
Added dependency on Python and zlib
2021-02-08pciutils: add a PREFIX parameter to make invocation (#21527)darmac1-0/+3
2021-02-08bird: add build dependencies (#21528)darmac1-0/+2
2021-02-07Package/r require and subpackage dep fix (#21433)Desmond Orton1-0/+29
2021-02-07fix build failure with boost-1.58.0 by using higher revision (#21376)Sreenivasa Murthy Kolam2-2/+3
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