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2020-01-07gdal: Fix libgeotiff dependency (#14410)Michael Kuhn1-1/+1
gdal@2.4.3 is missing the libgeotiff dependency.
2020-01-07Spack can automatically remove unused specs (#13534)Massimiliano Culpo7-7/+193
* Spack can uninstall unused specs fixes #4382 Added an option to spack uninstall that removes all unused specs i.e. build dependencies or transitive dependencies that are left in the store after the specs that pulled them in have been removed. * Moved the functionality to its own command The command has been named 'spack autoremove' to follow the naming used for the same functionality by other widely known package managers i.e. yum and apt. * Speed-up autoremoving specs by not locking and re-reading the scratch DB * Make autoremove work directly on Spack's store * Added unit tests for the new command * Display a terser output to the user * Renamed the "autoremove" command "gc" Following discussion there's more consensus around the latter name. * Preserve root specs in env contexts * Instead of preserving specs, restrict gc to the active environment * Added docs * Added a unit test for gc within an environment * Updated copyright to 2020 * Updated documentation according to review Rephrased a couple of sentences, added references to `spack find` and dependency types. * Updated function naming and docstrings * Simplified computation of unused specs Since the new approach uses private attributes of the DB it has been coded as a method of that class rather than a freestanding function.
2020-01-06Fix outdated bash tab completion (#14392)Adam J. Stewart1-201/+321
2020-01-06Add py-numpy 1.18.1 (#14406)Adam J. Stewart1-1/+2
2020-01-06r-snpstats: new package at 1.34.0 (#14404)Justin S1-0/+29
2020-01-06r-genetics: new package at 1.3.8.1.2 (#14403)Justin S1-0/+22
2020-01-06Add updated kaldi and openfst (#14398)Thom Troy2-0/+3
* add openfst v1.6.7 and kaldi from 2019-09-29 * revert openfst package version in url
2020-01-06Add singularity@3.5.2 (#14401)George Hartzell1-0/+1
2020-01-06Fastdfs (#14378)darmac1-0/+35
* add new package : fastdfs * refine install() * remove redundant fastdfs/fastdfs/package.py * fix install() error
2020-01-06py-ujson: new package at 1.35 (#14279)Justin S1-0/+18
* py-ujson: new package at 1.35 * py-ujson: use PyPI mirror, add missing deps * py-ujson: use short PyPI url
2020-01-06Fix QT on Linux+clang (#13684)Seth R. Johnson1-33/+56
* Add platform flag to QT for linux+clang * Extend QT platform support to more compilers and systems * Unify QT5 configure options * fixup! Unify QT5 configure options * fixup! Unify QT5 configure options * fixup! Unify QT5 configure options * Fix newer flake8 and mac qt5 configure
2020-01-06Nsimd: New package (#14226)Erik Schnetter1-0/+65
* Nsimd: New package * Various cleanups as suggested during review
2020-01-06Reference `spack help --spec` in `spack spec --help`Adam J. Stewart1-0/+4
2020-01-05Add py-thirdorder recipe (#12791)asmaahassan901-0/+37
* Add Thirdorder recipe * Remove white spaces * Converting recipe to a PythonPackage base class * remove trailing spaces * remove line at end of file * enhance recipe as per reviewer * fix post_install as requested by reviewer * rename dir to py-thirderorder * change checksum to sha256
2020-01-04Overhaul py-pillow package (#14385)Adam J. Stewart1-51/+54
* Overhaul py-pillow package * Fix bug where zlib and jpeg were always disabled
2020-01-04libwebp: CMakePackage -> AutotoolsPackage (#14384)Adam J. Stewart1-7/+49
2020-01-04Adjust constraints of gcc-5 (#14388)Glenn Johnson1-1/+2
This PR adjusts the constraints on isl with GCC-5. GCC-5.1 and GCC-5.2 need isl-0.14, not isl-0.15.
2020-01-04Add libs property to openjpeg package (#14383)Adam J. Stewart1-0/+5
2020-01-04Add libs property to lcms package (#14382)Adam J. Stewart1-0/+4
2020-01-04py-torchvision 0.4.X does not support py-pillow 7.X.Y (#14381)Adam J. Stewart1-1/+3
2020-01-04environment-modules: add version 4.4.1 (#14379)Xavier Delaruelle1-1/+2
2020-01-04add new package : lucene (#14316)darmac1-0/+28
* add new package : lucene * update lucene version url
2020-01-04add new package : kafka (#14315)darmac1-0/+35
* add new package : kafka * move url_for_version after depens_on() * refine list_depth for kafka
2020-01-04add new package : tajo (#14314)darmac1-0/+36
* add new package : tajo * refine list_depth for tajo
2020-01-03py-intervaltree: new package at 3.0.2 (#14277)Justin S1-0/+19
* py-intervaltree: new package at 3.0.2 * py-intervaltree: fix checksum * py-intervaltree: add py-setuptools dep * py-intervaltree: use inclusive ranges * py-intervaltree: change py-test dep type
2020-01-03petsc: add version 3.12.3 (#14374)Satish Balay1-0/+1
2020-01-03new package: bref3 (#14256)xfzhao2-0/+50
2020-01-02Get py-numpy > 1.16 to build with Intel compiler (#14360)Glenn Johnson1-0/+23
Beginning with numpy > 1.16 when using older versions of gcc the `std=c99` flag must be used. The Intel compiler depends on gcc for its language extensions so the version of gcc is important. If the version of gcc used by the Intel compiler is one that requires the `-std=c99` flag then that flag will have to be used for a build with the Intel compiler as well. This PR tests the version of gcc used by the Intel compiler and will abort the build if the gcc version is < 4.8 and inject the `-std=c99` flag if >= 4.8 and < 5.1. This will cover the system gcc compiler and any gcc environment module loaded at build time.
2020-01-02package/opencv fix mistake in conflict statement involving gcc (#13959)Sinan1-4/+1
* fix mistake in conflict * extend CudaPackage to resolve cuda-gcc conflicts
2020-01-02Updated version to include v3.0.1 (#14353)Jonathan R. Madsen1-0/+2
* Updated version to include v3.0.1 - this patch has a rather critical MT fix * Update package.py - Moved 3.0.1 above 3.0.0
2020-01-02fix url for mantevo packages (#14366)Christoph Junghans9-9/+9
2020-01-02RHEL8 bugfix for module_cmd (#14349)Sajid Ali1-1/+2
2020-01-02Set preferred version of perl-bioperl (#14354)Glenn Johnson1-1/+3
Due to formatting differences, the older version of perl-bioperl was getting picked up as the preferred version. This PR explicitly sets the newer version to be preferred.
2020-01-02added verbose variant to mercury package (#14355)Matthieu Dorier1-0/+3
2020-01-02gromacs: depend on hwloc v1 (#14343)Gilles Gouaillardet1-1/+3
Because of a bug in the current concretizer, spack install gromacs fails because gromacs depends on hwloc (default is v2), and Open MPI (the default MPI library) depends on hwloc v1. As discussed in https://github.com/spack/spack/issues/14339, this workaround should be removed once the concretizer is fixed Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
2020-01-02py-scikit-learn: add 0.22.1 (#14350)Adam J. Stewart1-0/+1
2020-01-02osu-micro-benchmarks: added version 5.6.2 (#14352)Mike Kiernan1-1/+2
2020-01-02new package: py-zarr (#14326)Sinan1-0/+25
* create package py-zarr * specify setuptools versions * add more dependencies, improve style * Update var/spack/repos/builtin/packages/py-zarr/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-zarr/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-zarr/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * add dependencies, remove python version constraint * remove windows specific dependency Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-01-02MKL: set appropriate CMake env vars (#14274)Adam J. Stewart2-5/+8
2020-01-02refactor: cleanup imports in spec.pyTodd Gamblin9-169/+167
The imports in `spec.py` are getting to be pretty unwieldy. - [x] Remove all of the `import from` style imports and replace them with `import` or `import as` - [x] Remove a number names that were exported by `spack.spec` that weren't even in `spack.spec`
2020-01-02bugfix: cdash tests shoudln't modify working directoryTodd Gamblin1-8/+9
The latest cdash test creates a local cdash_reports directory, but it should do that in a tmpdir.
2020-01-01tests: improved `spack test` command line optionsTodd Gamblin5-62/+266
Previously, `spack test` automatically passed all of its arguments to `pytest -k` if no options were provided, and to `pytest` if they were. `spack test -l` also provided a list of test filenames, but they didn't really let you completely narrow down which tests you wanted to run. Instead of trying to do our own weird thing, this passes `spack test` args directly to `pytest`, and omits the implicit `-k`. This means we can now run, e.g.: ```console $ spack test spec_syntax.py::TestSpecSyntax::test_ambiguous ``` This wasn't possible before, because we'd pass the fully qualified name to `pytest -k` and get an error. Because `pytest` doesn't have the greatest ability to list tests, I've tweaked the `-l`/`--list`, `-L`/`--list-long`, and `-N`/`--list-names` options to `spack test` so that they help you understand the names better. you can combine these options with `-k` or other arguments to do pretty powerful searches. This one makes it easy to get a list of names so you can run tests in different orders (something I find useful for debugging `pytest` issues): ```console $ spack test --list-names -k "spec and concretize" cmd/env.py::test_concretize_user_specs_together concretize.py::TestConcretize::test_conflicts_in_spec concretize.py::TestConcretize::test_find_spec_children concretize.py::TestConcretize::test_find_spec_none concretize.py::TestConcretize::test_find_spec_parents concretize.py::TestConcretize::test_find_spec_self concretize.py::TestConcretize::test_find_spec_sibling concretize.py::TestConcretize::test_no_matching_compiler_specs concretize.py::TestConcretize::test_simultaneous_concretization_of_specs spec_dag.py::TestSpecDag::test_concretize_deptypes spec_dag.py::TestSpecDag::test_copy_concretized ``` You can combine any list option with keywords: ```console $ spack test --list -k microarchitecture llnl/util/cpu.py modules/lmod.py ``` ```console $ spack test --list-long -k microarchitecture llnl/util/cpu.py:: test_generic_microarchitecture modules/lmod.py::TestLmod:: test_only_generic_microarchitectures_in_root ``` Or just list specific files: ```console $ spack test --list-long cmd/test.py cmd/test.py:: test_list test_list_names_with_pytest_arg test_list_long test_list_with_keywords test_list_long_with_pytest_arg test_list_with_pytest_arg test_list_names ``` Hopefully this stuff will help with debugging test issues. - [x] make `spack test` send args directly to `pytest` instead of trying to do fancy things. - [x] rework `--list`, `--list-long`, and add `--list-names` to make searching for tests easier. - [x] make it possible to mix Spack's list args with `pytest` args (they're just fancy parsing around `pytest --collect-only`) - [x] add docs - [x] add tests - [x] update spack completion
2020-01-01new package: py-numcodecs (#14330)Sinan1-0/+25
* new package: py-numcodecs * make msgpack variant
2020-01-01py-numpy: add 1.17.5 (#14341)Adam J. Stewart1-0/+1
2019-12-31tests: rename checks in github actionsTodd Gamblin3-5/+5
I usually want to look at the Travis CI output, but I currently have to scroll down to see it. This renames checks to be a bit shorter and more consistent with Travis's naming, and also so that actions appear lower than travis and codecov in the list of checks.
2019-12-31Modify create clue list so R packages are detected (#12277)Glenn Johnson1-1/+1
R packages can contain configure scripts so R needs to be before autotools in the clue list.
2019-12-31tests: move mock config.yaml files to common directoryTodd Gamblin5-15/+8
Test configuration files (except modules.yaml) were in the root level of test/data, but should really just be in their own directory. The absence of modules.yaml was also breaking module tests if we got module preferences after tests started, as the mock modules.yaml was not in the test directory.
2019-12-31config: remove all module-scope calls to spack.config.get()Todd Gamblin4-16/+27
This avoids parsing modules.yaml on startup.
2019-12-31modules: make the module hook more robustTodd Gamblin1-8/+12
The module hook would previously fail if there were no enabled module types. - Instead of looking for a `KeyError`, default to empty list when the config variable is not present. - Convert lambdas to real functions for clarity.
2019-12-31hooks: remove pre_run hook to improve startup time.Todd Gamblin3-49/+0
- Remove legacy yaml_version_check() hook - Remove the pre_run hook from `hook/__init__.py` and `main.py` We want to discourage the use of pre-run hooks because they have to run at startup. To keep Spack fast, we should do things like this lazily instead of in hooks that require spidering directories full of modules.
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