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2021-09-28py-anuga: add git main version to support build with python@3.5: (#26248)bernhardkaindl2-11/+60
* py-anuga: add git main version to support build with python@3.5: py-anuga's main branch has been converted to Python-3 recently. * py-triangle: use pypi, py-anuga: Fixed depends and test suite works now
2021-09-28py-tomopy: version bump and master, add new deps, make runtest pass (#26252)bernhardkaindl1-4/+32
Current py-tomopy has many features and dependencies, add them.
2021-09-28py-numba: add 0.54.0 and restrict old dependencies (#26281)Manuela Kuhn1-2/+7
* py-numba: add 0.54.0 and restrict old dependencies * Update var/spack/repos/builtin/packages/py-numba/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-09-28py-xlrd: add 2.0.1 (#26282)Manuela Kuhn1-0/+5
2021-09-28py-appdirs: add 1.4.4 (#26298)Manuela Kuhn1-0/+1
2021-09-28Update Nextflow (#26042)Diego Alvarez1-9/+17
2021-09-28Add OpenSSL 3 (#26097)Harmen Stoppels4-5/+10
* OpenSSL 3.0.0 * Remove openssl constraint in e4s to test 3.0.0 * Restrict openssl * Restrict openssl to @:1 in unifyfs * Revert "Remove openssl constraint in e4s to test 3.0.0" This reverts commit 0f0355609771764280ab1b6a523c80843a4f85d6. * Prefer 1.x
2021-09-28Move detection logic in its own package (#26119)Massimiliano Culpo5-287/+376
The logic to perform detection of already installed packages has been extracted from cmd/external.py and put into the spack.detection package. In this way it can be reused programmatically for other purposes, like bootstrapping. The new implementation accounts for cases where the executables are placed in a subdirectory within <prefix>/bin
2021-09-28libp11: Fix build and add new version (#26135)bernhardkaindl1-1/+3
The build needs `pkgconfig` and `openssl`, `m4` is already added by `autoconf`. Also add the current version of `libp11` to the list of versions. Co-authored-by: Bernhard Kaindl <bernhard.kaindl@ait.ac.at>
2021-09-27py-dataclasses: add 0.8 (#26283)Manuela Kuhn1-0/+1
2021-09-27py-meshio: add 5.0.1 and 4.4.6 (#26285)Manuela Kuhn1-2/+5
2021-09-27py-deprecated: add 1.2.13 and get sources from pypi (#26286)Manuela Kuhn1-2/+3
2021-09-27Use gnuconfig package for config file replacement (#26035)Harmen Stoppels5-44/+357
* Use gnuconfig package for config file replacement Currently the autotools build system tries to pick up config.sub and config.guess files from the system (in /usr/share) on arm and power. This is introduces an implicit system dependency which we can avoid by distributing config.guess and config.sub files in a separate package, such as the new `gnuconfig` package which is very lightweight/text only (unlike automake where we previously pulled these files from as a backup). This PR adds `gnuconfig` as an unconditional build dependency for arm and power archs. In case the user needs a system version of config.sub and config.guess, they are free to mark `gnuconfig` as an external package with the prefix pointing to the directory containing the config files: ```yaml gnuconfig: externals: - spec: gnuconfig@master prefix: /tmp/tmp.ooBlkyAKdw/lol buildable: false ``` Apart from that, this PR gives some better instructions for users when replacing config files goes wrong. * Mock needs this package too now, because autotools adds a depends_on * Add documentation * Make patch_config_files a prop, fix the docs, add integrations tests * Make macOS happy
2021-09-27qhull: use secure github URLS instead of www.qhull.org downloads (#26211)Tamara Dahlgren1-8/+5
2021-09-27py-python-picard: add new package (#26268)Manuela Kuhn1-0/+23
2021-09-27Updated versions for cuDNN and NVSHMEM (#26272)Brian Van Essen2-0/+7
2021-09-27py-torchvision: add v0.10.1 (#26267)Adam J. Stewart1-0/+2
2021-09-27py-llvmlite: add 0.37.0 (#26278)Manuela Kuhn1-4/+7
2021-09-27py-datalad: move datalad wtf test over from py-datalad-metalad (#26274)Manuela Kuhn2-6/+7
* py-datalad: move datalad wtf test over from py-datalad-metalad * Update var/spack/repos/builtin/packages/py-datalad/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-09-27py-numexpr: add 2.7.3 (#26279)Manuela Kuhn1-1/+3
2021-09-27py-tqdm: add 4.62.3 (#26277)Manuela Kuhn1-0/+2
2021-09-27py-nilearn: add 0.8.1 (#26276)Manuela Kuhn1-0/+1
2021-09-27[openloops][vbfnlo] Fix recipes and updated dependencies (#24461)Thomas Madlener3-0/+29
* [vbfnlo] Add doc variant to toggle building of docs * [openloops] Add scons to dependencies Make sure that the build_processes does not accidentally pick up a non-suitable scons version from the underlying system * [openloops] Set OLPYTHON to make sure the right scons is picked * [openloops] Fix Flake8 style complaints
2021-09-27MPICH: Add E4S testsuite stand alone test (#25634)Richarda Butler1-0/+32
2021-09-27mrtrix3: add version 3.0.3 (#25943)Ben Darwin1-0/+2
2021-09-27Update highfive (#26262)iarspider1-6/+11
* Add new versions of highfive * Fix CMake option name
2021-09-27New packages for openCARP (#25909)Marie Houillon4-0/+174
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2021-09-27source-highlight: allow to build the git master branch (#25947)Melven Roehrig-Zoellner1-0/+9
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2021-09-27added workaround for rocm/cmake bug in tasmanian (#25949)Miroslav Stoyanov1-0/+4
2021-09-27added package g2c from NOAAs NCEPLIBS project (#26190)Edward Hartnett1-0/+28
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2021-09-27sundials package: @:5.7.0 requires hypre@:2.22.0 (#25903)Olivier Cessenat1-9/+10
sundials@:5.7.0 fails to build with hypre@2.22.1
2021-09-27New Package: EcoSLIM (#25975)Steven Smith1-0/+25
Co-authored-by: Steven Smith <Steven Smith> Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2021-09-27Correct path comparisons for fs view (#25891)psakievich2-6/+13
* Fix path comparisons in copy views * Get correct permissions * Set group id though os Co-authored-by: Philip Sakievich <psakiev@sanida.gov>
2021-09-27add mantainer to bedops (#26141)jacorvar1-0/+1
2021-09-27spindle: It seems it needs mpi.h to compile, adding depends on mpi. (#26151)bernhardkaindl1-1/+14
Workaround this compile error for gcc by adding -Wno-narrowing for it: spindle_logd.cc:65:76: error: narrowing conversion of '255' from 'int' to 'char' spindle_logd.cc:65:76: error: narrowing conversion of '223' from 'int' to 'char' spindle_logd.cc:65:76: error: narrowing conversion of '191' from 'int' to 'char' spindle 0.8.1 wants to compile tests with mpi.h, newer versions need mpicc, thus add: depends_on("mpi"). Spindle supports the --no-mpi to disable MPI.
2021-09-27added NOAAs UPP package (#26198)Edward Hartnett1-0/+52
2021-09-27py-torch: add v1.9.1 (#26159)Adam J. Stewart1-0/+1
2021-09-27perl: Fix test case bug perl#15544: Don't fail with PATH >1000 chars (#26245)bernhardkaindl1-0/+5
Fix the perl test case bug Perl/perl5#15544 Variable PATH longer than 1000 characters (as is usual with spack) fails a perl test case The fix is: Don't test PATH in testcase perlbug.t Fixes `spack install --test=all` for specs triggering a build and test of perl!
2021-09-27exempi: fix expat dependency (#26221)Manuela Kuhn1-0/+8
* exempi: fix expat dependency and fix test with --test=root Co-authored-by: Bernhard Kaindl <bernhardkaindl7@gmail.com>
2021-09-27pythia8: update to v8.306, change url, set environment variables for ↵iarspider1-11/+24
dependents (#26255)
2021-09-27New package: r-klar (#25390)Jen Herting1-0/+28
2021-09-26New package: r-questionr (#25395)Jen Herting1-0/+28
2021-09-27py-python-gitlab: add 2.10.1 (#26229)Manuela Kuhn1-2/+7
2021-09-27[acts] eigen is not only a build dependency (#26257)Wouter Deconinck1-1/+1
The ActsConfig.cmake includes a `find_dependency(Eigen3)` line. Requiring depends_on type='build' does not expose eigen to dependents during their build. Ref: https://github.com/acts-project/acts/blob/v13.0.0/cmake/ActsConfig.cmake.in#L59
2021-09-27cfitsio: add version 4.0.0 (#26218)lorddavidiii1-0/+1
2021-09-26trilinos: default gotype=long_long (#26253)Seth R. Johnson1-1/+1
"Long long" is the default type when building trilinos on its own, and many downstream packages (both in and out of spack) rely on it. E4S already sets this explicitly to long_long.
2021-09-26masurca: add versions up to v4.0.5 (#26171)Desmond Orton1-0/+1
Co-authored-by: las_djorton <las_djorton@babybuild.las.iastate.edu>
2021-09-26vtk: depends_on freetype @:2.10.2 through @:9.0.1 only (#26180)Wouter Deconinck1-2/+2
The issues in https://gitlab.kitware.com/vtk/vtk/-/issues/18033 were fixed in: - https://github.com/Kitware/VTK/commit/dae1718d50bec1b40b860280acafbdd94fc4cd5d - https://github.com/Kitware/VTK/commit/31e8e4ebeb3152f7cfdb3f14f24f7e5d31a4f8b5 These fixes are in vtk@9.0.2 https://github.com/Kitware/VTK/releases/tag/v9.0.2 and beyond.
2021-09-26lbann: add support for building with the ONNX C++ library (#26130)Brian Van Essen1-0/+3
2021-09-26podio, edm4hep: fix tests (#26116)Valentin Volkl2-1/+4
Co-authored-by: Seth R. Johnson <johnsonsr@ornl.gov>
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