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2020-05-05[dd4hep] fix python setup (#16461)vvolkl1-1/+1
2020-05-05cctools to 7.1.5 (#16450)Benjamin Tovar1-2/+3
* change homepage to readthedocs * update cctools version to 7.1.5 * change http to https
2020-05-05lammps: added v20200505 (#16463)Christoph Junghans1-0/+2
2020-05-04bugfix: config:install_hash_length ignored (#15919)Greg Becker2-0/+42
2020-05-04py-shapely: add master version (#16465)Adam J. Stewart1-2/+16
2020-05-04libspatialite: Update for proj@6 (#16173)Elizabeth Fischer1-2/+16
* libspatialite * flake8 * Added proper version constrain * Update var/spack/repos/builtin/packages/libspatialite/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/libspatialite/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-05-04libsecret (#16174)Elizabeth Fischer1-0/+2
* libsecret * Update package.py Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
2020-05-04bugfix: Update run-time dependencies of py-xenv (#16460)vvolkl1-1/+1
Otherwise, if I run `xenv` after `spack load py-xenv` it fails with: ``` Traceback (most recent call last): File "/home/vavolkl/spack/opt/spack/linux-centos7-broadwell/gcc-8.3.0/py-xenv-develop_2018-12-20-lqbxakapsepqo5w3sjhhokj5o7c5jei2/bin/xenv", line 6, in <module> from pkg_resources import load_entry_point ModuleNotFoundError: No module named 'pkg_resources' ```
2020-05-04[gaudi] fixes and patches (#16433)vvolkl6-19/+315
* [gaudi] fixes and patches * Update var/spack/repos/builtin/packages/gaudi/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/gaudi/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Apply suggestions from code review Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * [gaudi] add older versions and fold +tests into +optional * [gaudi] set run environment Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-05-04environments: allow sigils to apply to entire reference (#15245)Greg Becker3-5/+110
* environments: allow sigils to apply to entire reference
2020-05-04ecFlow added UI & GUI flag with new version (#16444)Amjad Kotobi1-4/+10
* ecFlow added UI & GUI flag with new version * Fix1
2020-05-04py-palletable: Add new version (#16445)Elizabeth Fischer1-0/+1
Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
2020-05-04py-cf-units: Add new version (#16446)Elizabeth Fischer1-0/+1
Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
2020-05-04update isaac and issac-server to v1.5.0 (#16452)René Widera2-0/+2
Update package.py with the latest release [ISAAC v1.5.0].
2020-05-04pocl: add version 1.5 (#16455)Matthias Diener1-1/+3
* pocl: add version 1.5 * update clang version
2020-05-04hwloc: add version 2.2.0 (#16456)Matthias Diener1-0/+1
2020-05-04BOLT: add 1.0 (#16457)Shintaro Iwasaki1-5/+1
2020-05-04argobots: mark 1.0 as preferred (#16458)Shintaro Iwasaki1-1/+2
By default, Spack chooses 1.0rc2 instead of 1.0 though 1.0 is the stable and newer release. We manually mark the version 1.0 as preferred.
2020-05-04Fix git-related commands not working in worktreesOliver Breitwieser2-3/+87
If spack is checked out in a git worktree (see [1]), all git-related commands fail because the `spack_is_git_repo()`-check is not thorough enough. When developing in a feature-branch in a seperate worktree, this is annoying as all unittests regarding git-related spack commands fail, cluttering the test results with false-positives. [1]: https://git-scm.com/docs/git-worktree Change-Id: I94b573a2c0e058e9ccc169e7ee6561626fbb06fd
2020-05-04Updates to Python for macOS (#16449)Elizabeth Fischer1-1/+2
Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
2020-05-04grass: new versions (#16181)Elizabeth Fischer1-1/+6
* grass * Update var/spack/repos/builtin/packages/grass/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-05-04LAPACKC++: added "shared" variant (#16419)Axel Huebl1-2/+10
We can control the shared/static build of CMake and the default in Spack is to build shared libraries. The old, uncontrolled default of this package is a static build.
2020-05-04singularity: added missing dependencies (#16430)Dr. Christian Tacke1-0/+3
See: https://sylabs.io/guides/3.5/user-guide/quick_start.html#install-system-dependencies for pkg-config and libseccomp
2020-05-03QE-to-QMCPACK wave function converter relocation + some bug fixes (#16422)Nichols A. Romero1-15/+74
* Revise description of patch variant. * Add qmcpack variant. Apply QE-to-QMCPACK wave function converter patch. * Clean-up, document, and re-organize. * ELPA patches did not nead when=`+patch` variant. * Need to be more precise here with QE version numbers. * satisfies seems to be necessary here in order to get correct behaviour. * Buglet with zlib link line. * Update var/spack/repos/builtin/packages/quantum-espresso/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/quantum-espresso/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Fix for QE-to-QMCPACK wave function converter w.r.t. QE 6.3. Also adjust comments to reflect changes in code. Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-05-03NumPy: add 1.18.4 (#16441)Adam J. Stewart1-1/+2
2020-05-03Add new HEP package: fastjet (#16439)vvolkl1-0/+49
* [fastjet] initial commit * [fastjet] remove beta versions
2020-05-03Add new HEP package: Delphes (#16440)vvolkl1-0/+63
* [delphes] initial commit * [delphes] formatting fixes
2020-05-02GEOS: add new version (#16437)Adam J. Stewart1-1/+2
2020-05-02py-shapely: new version, Python 3.7 fix (#16438)Adam J. Stewart1-2/+12
2020-05-02py-cartopy: update package, fix PROJ.6 support (#16436)Adam J. Stewart2-13/+145
2020-05-02colordiff: add version 1.0.19 (#16431)Matthias Diener1-0/+1
2020-05-02Add a gpfs variant to openmpi package (#15793)Jonathon Anderson1-0/+6
Open MPI will detect and link against GPFS if it is present on the system. This variant allows this to be disabled, even if GPFS is present.
2020-05-01add hydra/pmix conflict (#16428)Sajid Ali1-0/+1
2020-05-01py-opentuner: add version 0.8.2 (#16423)Matthias Diener1-3/+6
2020-05-01[ncbi-magicblast] added version 1.5.0 (#16424)Jen Herting1-0/+1
2020-05-01stata: add version 16 (#16425)Justin S1-3/+9
2020-05-01amrex: New version 20.05 (#16427)mic841-3/+12
2020-05-01Provide update for py-pyside2 version 5.14.2.1. (#16426)Kelly (KT) Thompson1-0/+1
2020-05-01tbl2asn: new package at 20200301 (#16280)Justin S1-0/+24
* tbl2asn: new package at 20200301 * tbl2asn: remove unused url * tbl2asn: use spack decompression, fix permissions * tbl2asn: change version
2020-05-01Revert "Testing: fix unintended interactions between tests (#16003)" (#16420)Peter Scheibel5-23/+8
This was breaking tests on develop.
2020-05-01Testing: fix unintended interactions between tests (#16003)Peter Scheibel5-8/+23
* For tests that use the real Spack package repository, the config needs to avoid using MPI providers that are not intended to be installed by Spack. Without this, it is possible that Spack tests which concretize the MPI virtual will end up trying to use an implementation that it shouldn't (e.g. one that is always provided externally). See #15666 for an example. * The mutable_config test fixture was not initializing the scope roots to the right directories (so the resulting config was empty). * The current_host fixture in the concretize.py tests was using the config fixture rather than mutable_config, and was polluting the config cache for other tests. * One test in concretize.py was clearing a nonexistent cache (PackagePrefs._packages_config_cache). This reference has been removed. * The test 'test_preferred_compilers' was was depending on cross test config pollution to succeed. The initial spec before concretization has been updated to updated to be explicit about the desired result.
2020-05-01dev-build: --drop-in <shell> (#14887)Axel Huebl3-2/+21
* dev-build: --drop-in <shell> Add a `--drop-in <shell>` option to `spack dev-build`. This option will automatically run a `spack build-env <spec> -- <shell>` at the end of a `dev-build`, e.g. to quickly drop-and-devel into a build phase of a package. Example usage: ``` spack dev-build --before cmake --drop-in bash openpmd-api@develop ``` * build_env: drop in unit test Co-authored-by: Greg Becker <becker33@llnl.gov>
2020-05-01mt-metis: New package. (#16380)Toyohisa Kameyama2-0/+51
* mt-metis: New package. * variant to 1 line. * delete useless lines.
2020-05-01raja: add awareness of the cuda architecture (#16377)Matt Larsen1-1/+6
2020-05-01arborx: fix build with new kokkos-legacy (#16413)Jean-Laurent Picard1-1/+1
2020-04-30gromacs: add v2020.2 (#16408)Christoph Junghans1-0/+1
2020-04-30amrex: repo went through history rewrite - so use updates sha256sums (#16379)Satish Balay1-9/+9
2020-04-30Fix typos in new AutotoolsPackage function (#16406)Adam J. Stewart1-2/+2
2020-04-30sqlite: Add 3.31.1 (#16404)Michael Kuhn1-1/+4
2020-04-30readline: Fix homepage (#16403)Michael Kuhn1-1/+1