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2017-01-06GitLab: Tarball Version Test (#2296)Axel Huebl2-2/+29
* GitLab: Tarball Version Test Upload a test demonstrating #2290 * Add GitLab parsing
2017-01-06various python package version and dependency updates (#2751)Gregory Lee7-3/+11
* various python package version and dependency updates * various python package version and dependency updates
2017-01-05espressopp: package for the ESPResSo++ software (#2602)Christoph Junghans1-0/+79
* espressopp: package for the ESPResSo++ software This commit adds a package for the ESPResSo++ simulation software. * Move Espressopp package to CMakePackage This commit moves Espressopp package to CMakePackage. Addresses some comments in the PR. * Remove run_tests and changed type of dependencies Addressed some comments from @adamjstewart. Removed global run_tests setting and removed type from many dependencies. Set type for py-mpi4py to 'nolink'. * Updated to last version and fix mpi4py dependency Added latest espressopp version and changed mpi4py (version) dependency for different espressopp versions. * Changed mpi4py version requirements for espressopp Changed py-mpi4py version requirements for espressopp@1.9.4 according to the package build requirements for that version.
2017-01-05Add dependencies and finish the py-tornado package.Matthew Krafczyk34-26/+1200
This adds the following packages: py-backports-shutil-get-terminal-size py-nbformat py-backports-ssl-match-hostname py-pathlib2 py-entrypoints py-pickleshare py-futures py-pip py-ipykernel py-prompt-toolkit py-ipython-genutils py-ptyprocess py-ipywidgets py-simplegeneric py-jupyter-client py-singledispatch py-jupyter-console py-terminado py-jupyter-core py-traitlets py-jupyter-notebook py-wcwidth py-monotonic py-widgetsnbextension py-nbconvert
2017-01-05Added npm, node.js, and Jupyter dependenciesJean-Paul Pelteret10-0/+485
Adds the following packages: node-js py-backports-abc py-functools32 py-pycurl py-vcversione npm py-certifi py-jsonschema py-tornado py-zmq - Added python packages that are dependencies for the Jupyter suite - Update new python packaages to use extension package install function. - Added npm and node-js packages
2017-01-05Correct env vars for modulecmd; Fixes #1481 (#2745)Mario Melara1-14/+2
Don't override MODULEPATH with PATH, PATH has no modulefiles PEP8 compliance
2017-01-05test: fixed 'refresh_builtin_mock' fixture (#2748)Massimiliano Culpo1-1/+0
2017-01-04Standardize package names: lower-case, not Mixed_CASE (#2475)Elizabeth Fischer205-204/+215
* Rename packages * Upcasing depends_on() in packages. * Downcased extends('r') * Fixed erroneously changed URL that had slipped through. * Fixed typo * Fixed link from documentation into package source code. * Fixed another doc problem. * Changed underscores to dashes in package names. * Added test to enforce lowercase, no-underscore naming convention. * Fix r-xgboost * Downcase more instances of 'R' in package auto-creation. * Fix test. * Converted unit test packages to use dashes not underscores * Downcase `r` in the docs. * Update module_file_support.rst Fix r->R for class R.
2017-01-04Use zlib's "fossil" site for old tarballs (#2735)George Hartzell1-4/+5
* Use zlib's "fossil" site for old tarballs Following citibeth's suggestion in #2732, use zlib's "fossil" site (not to be confused with the sqlite team's VCS...) for retrieving old tarballs. Digests for 1.2.{8,10} match and both install for me on CentOS 7. * Use zlib's "fossil" URL as the one true URL Everything seems to be available at zlib's "fossil" URL, so just use it as the one and only url. (and fix a flake8 complaint about a comment)
2017-01-04add package for conduit (#2670)Cyrus Harrison1-0/+312
* add package for conduit * try to fix main conduit docstring * use join_path instead of pjoin * address a few requests in pr #2670 change name of 'github-master' to 'master' change 'docs' variant to 'doc', set default to False remove explicit +shared variant spec for silo and hdf5 deps (in the conduit +shared case) cases since they default to True add reference to static rpath issue (https://github.com/LLNL/spack/issues/2658) * address pr #2670 requests add todos and more info on why variants for deps where selected use python module install python to enable spack activate use .format instead of %s
2017-01-04opencoarrays: new version (#2734)Jeffrey Salmond1-3/+1
* add version 1.8.0 * remove depends_on('cmake') as it is now unecessary * remove 'coarrays' as a virtual package
2017-01-04New package: ccache (#2721)Jean-Paul Pelteret1-0/+44
2017-01-04libpng: Upgrade versions to fix vulnerability. (#2723)Elizabeth Fischer2-7/+15
2017-01-04zlib@1.2.10 and R do not get along, work around it (#2727)George Hartzell1-0/+1
* zlib@1.2.10 and R do not get along, work around it R's configure script has trouble with version numbers > 1.2.9. This works around it by constraining R to 1.2.8. I'm working with some R folk on getting it fixed going forward. * Add adamjstewart's change.
2017-01-03Update to latest zlib version, server no longer provides older version (#2720)Barry Smith1-1/+4
* Update to latest zlib version, server no longer provides older version Funded-by: IDEAS Project: IDEAS/xSDK * Add alternative URL for previous release of zlib
2017-01-02Fix issues when a package provides the same vdep twice. (#2710)Todd Gamblin6-34/+117
* Fix issues when a package provides the same vdep twice. - provides() now adds to a set of provided vdeps instead of a single one. * flake8
2017-01-01tests: `coverage combine` run only if tests succeeded (#2712)Massimiliano Culpo1-2/+1
2016-12-31Disallow vdeps in `packages.yaml` (#2699)Todd Gamblin7-104/+177
* Consolidate packages.yaml code to preferred_packages * Add validation check and a test for packages.py parsing. * flake8
2016-12-30Add latest version of gmp (#2695)Adam J. Stewart1-4/+5
2016-12-30Fix missing debug parameter for parse_version() (#2696)Adam J. Stewart1-2/+2
2016-12-30Fix test command arg handling.Todd Gamblin1-5/+6
2016-12-30Run coverage for the `spack install` command as well as `spack test`.Todd Gamblin2-3/+4
- Also don't run coverage on OSX.
2016-12-30Allow setting default variants (#2644)Michael Kuhn1-2/+9
2016-12-30Add OSX build to .travis.yml. Clean up .travis.yml (#2689)Todd Gamblin1-3/+32
* Add OSX build to .travis.yml. Clean up .travis.yml * Add gcc/gfortran to the mac brew setup.
2016-12-30Fix Python issue with build failures; Add test case for build failures. (#2687)Todd Gamblin3-4/+55
2016-12-29Concretize preserves deptypes (#2681)Todd Gamblin11-179/+477
Concretization preserves deptypes
2016-12-29Fix issues related to the switchover to pytest. (#2685)Todd Gamblin38-10/+7809
- Remove stale reference to `import nose` from `bin/spack` script. - Add `py` to externals (missing dependency for `pytest`)
2016-12-29unit tests: replace nose with pytest (#2502)Massimiliano Culpo156-17619/+19218
* Porting: substitute nose with ytest This huge commit substitutes nose with pytest as a testing system. Things done here: * deleted external/nose as it is no longer used * moved mock resources in their own directory 'test/mock/' * ported two tests (cmd/find, build_system) to pytest native syntax as an example * build_environment, log: used monkeypatch instead of try/catch * moved global mocking of fetch_cache to an auto-used fixture * moved global mocking from test/__init__.py to conftest.py * made `spack test` a wrapper around pytest * run-unit-tests: avoid running python 2.6 tests under coverage to speed them up * use `pytest --cov` instead of coverage run to cut down testing time * mock/packages_test: moved mock yaml configuration to files instead of leaving it in the code as string literals * concretize.py: ported tests to native pytest, reverted multiprocessing in pytest.ini as it was creating the wrong report for coveralls * conftest.py, fixtures: added docstrings * concretize_preferences.py: uses fixtures instead of subclassing MockPackagesTest * directory_layout.py: uses fixtures instead of subclassing MockPackagesTest * install.py: uses fixtures instead of subclassing MockPackagesTest * optional_deps.py: uses fixtures instead of subclassing MockPackagesTest optional_deps.py: uses fixtures instead of subclassing MockPackagesTest * packages.py: uses fixtures instead of subclassing MockPackagesTest * provider_index.py: uses fixtures instead of subclassing MockPackagesTest * spec_yaml.py: uses fixtures instead of subclassing MockPackagesTest * multimethod.py: uses fixtures instead of subclassing MockPackagesTest * install.py: now uses mock_archive_url * git_fetch.py: uses fixtures instead of subclassing MockPackagesTest * hg_fetch.py: uses fixtures instead of subclassing MockPackagesTest * svn_fetch.py, mirror.py: uses fixtures instead of subclassing MockPackagesTest repo.py: deleted * test_compiler_cmd.py: uses fixtures instead of subclassing MockPackagesTest * cmd/module.py, cmd/uninstall.py: uses fixtures instead of subclassing MockDatabase * database.py: uses fixtures instead of subclassing MockDatabase, removed mock/database * pytest: uncluttering fixture implementations * database: changing the scope to 'module' * config.py: uses fixtures instead of subclassing MockPackagesTest * spec_dag.py, spec_semantics.py: uses fixtures instead of subclassing MockPackagesTest * stage.py: uses fixtures instead of subclassing MockPackagesTest. Removed mock directory * pytest: added docstrings to all the fixtures * pytest: final cleanup * build_system_guess.py: fixed naming and docstrings as suggested by @scheibelp * spec_syntax.py: added expected failure on parsing multiple specs closes #1976 * Add pytest and pytest-cov to Spack externals. * Make `spack flake8` ignore externals. * run-unit-tests runs spack test and not pytest. * Remove all the special stuff for `spack test` - Remove `conftest.py` magic and all the special case stuff in `bin/spack` - Spack commands can optionally take unknown arguments, if they want to handle them. - `spack test` is now a command like the others. - `spack test` now just delegates its arguments to `pytest`, but it does it by receiving unknown arguments and NOT taking an explicit help argument. * Fix error in fixtures. * Improve `spack test` command a bit. - Now supports an approximation of the old simple interface - Also supports full pytest options if you want them. * Use external coverage instead of pytest-cov * Make coverage use parallel-mode. * change __init__.py docs to include pytest
2016-12-28Allow exclusion of packages from `spack module loads` (#2667)Elizabeth Fischer1-1/+7
* Allow exclusion of packages from `spack module loads` * Comment out excluded packages instead of not showing them at all.
2016-12-28Directive inheritance: laziness for the win (#2623)Massimiliano Culpo11-202/+281
* inheritance of directives: using meta-classes to inject attributes coming from directives into packages + lazy directives * _dep_types -> dependency_types * using a meta-class to inject directives into packages * directives are lazy fixes #2466 * directives.py: allows for multiple inheritance. Added blank lines as suggested by @tgamblin * directives.py: added a test for simple inheritance of directives * Minor improvement requested by @tgamblin CMakePackage: importing names from spack.directives directives: wrap __new__ to respect pep8 * Refactoring requested by @tgamblin directives: removed global variables in favor of class variables. Simplified the interface for directives (they return a callable on a package or a list of them).
2016-12-28init yorick package (#2635)Thierry1-0/+81
* init yorick package * attempt at picking up SPACK's compiler choice, todo ~X variant. * sphinx docstring error ? * version# tarball, ~X default, docstring fix * sphinx docstring fix(?)
2016-12-27Cleanup post luafilesystem version de-underscoring (#2683)George Hartzell1-3/+3
The upstream luafilesystem tarball/version had a wayward/inconsistent underscore in their more recent version tag. The played badly with our package fetching machinery (due to recent changes?). Upstream cleaned up their bit which required some touchups here. - updated the url - updated the version (digest) - updated the format statement for the path to the rockspec.
2016-12-27Adds catch, cppunit, spdlog, tinyxml(1 and 2), google benchmark (#2627)Mayeul d'Avezac7-0/+264
* Adds catch, cppunit, spdlog, tinyxml(1 and 2), google benchmark Tinyxml comes in two flavors, 1 and 2. Each comes in several versions... So they cannot be easily united into a single package. * Use CMakePackage and friends, add copyright Also eleminate debug/release variants, since it no longuer fits in the CMakePackage format. * Remove unnecessary url * spdlog now has tagged releases * Remove unnecessary url argument * Fewer quotes in cmake args, because magic * Incorrect base class for tinyxml
2016-12-27Update wx to 3.1.0 (#2641)Michael Kuhn1-5/+12
2016-12-27Ensure that every file in Spack has a license (#2659)Adam J. Stewart61-168/+1230
* Ensure that every package has a license Also fixes URLs with http://http:// doubled. This is a continuation of #2656. * Add license to every file in Spack * Make sure Todd is the author of all packages * Fix flake8 tests * Don't license external Sphinx docs * Don't display licenses in tutorial example packages Also fixes typos and converts command-line examples from tcsh to bash, which is more common
2016-12-25Update py-cython with new pypi.io url and new version (#2650)Matthew Scott Krafczyk1-1/+3
2016-12-25Better tabulation for spack checksum (#2673)Adam J. Stewart1-1/+5
2016-12-25filter_system_path: additionally filter system prefixes (#2672)Denis Davydov2-2/+6
That's because in set_build_environment_variables() the funciton filter_system_paths() is actually applied to package prefixes, and not to prefix/lib or prefix/include.
2016-12-25Add 64 bit variant to dealii. (#2654)Bruno Turcksin1-8/+15
2016-12-25Add latest version of Python 2 (#2668)Adam J. Stewart1-1/+4
2016-12-25Update gcc to 6.3.0 (#2669)Michael Kuhn1-0/+1
2016-12-25Add argument to `spack spec` to show deptypes. (#2680)Todd Gamblin2-1/+20
- `-t` | `--types` argument now shows deptypes in `spack spec`
2016-12-25Update the texlive distro digest. (#2679)George Hartzell1-1/+1
sigh.
2016-12-25Remove usernames from paths in docs (#2675)Adam J. Stewart9-303/+303
* Remove usernames from paths in docs * Fix path export
2016-12-25go: fixed GOROOT_BOOTSTRAP without workarounds (#2671)Massimiliano Culpo2-9/+5
2016-12-25Modify github archive regex to support luaposix (#2677)Adam J. Stewart2-1/+6
2016-12-21Update cairo to 1.14.8, gtkplus to 2.24.31 and pango to 1.40.3 (#2642)Michael Kuhn3-8/+10
2016-12-21Bug fontconfig (#2652)Kim Serradell2-1/+4
* Added uuid: OSSP uuid is a ISO-C:1999 application programming interface * Fixed install error in cmor package * Added uuid: OSSP uuid is a ISO-C:1999 application programming interface * Fixed install error in cmor package * Modifiying fontconfig file to allow install in OpenSuse 13.2 * Adding pkg-config dependency to freetype and libxml2 * Removed first possible solution. With @adamjstewart selecting the one adding pkg-config to dependencies
2016-12-21Fix homepage for the package libspatialindex (#2656)Federico Padua1-1/+1
Small fix for the homepage of the package libspatialindex.
2016-12-20Revert #2292: use frontend compiler for build deps (#2549)scheibelp4-90/+24
The primary goal of #2292 was to use the frontend compiler to make build dependencies like cmake on HPC platforms. It turns out that while this works in some cases, it did not handle cases where a package was a link dependency of the root and of a build dependency (and could produce incorrect concretizations which would not build).
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