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2017-01-15Adding the py-ipdb package for more stable debugging with iPython. (#2824)Stephen McDowell1-0/+58
* Adding the py-ipdb package for more stable debugging with iPython. * Removing deprecated python support, adding missing dependencies. * Adding version checks for (i)python
2017-01-15Add the package py-sphinx-bootstrap-theme (#2825)Matthew Scott Krafczyk1-0/+41
2017-01-13boost: fixing boost-1.55.0 for gcc-5 (#2822)Andrey Prokopenko2-0/+54
boost-1.55.0 requires patching when compiling with gcc-5. See these threads: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=197594 https://svn.boost.org/trac/boost/ticket/10125 Fixes #2821.
2017-01-12configure and build command: fix the stop iteration semanticsMassimiliano Culpo1-0/+5
- broke somewhere between bdf48322696290d4e3d00ed12b7c7fe6ca213478 (#2810) and 17b13b161b3ddcd691ea7ed90165cfab6dec3950
2017-01-11mirror: fix error for some specs during concretization (#2806)Massimiliano Culpo1-0/+3
2017-01-10Update the boost versions used by openspeedshop. Boost-1.60 to current ↵Jim Galarowicz6-16/+16
latest causes compile errors when building openspeedshop. (#2300) * Update the krell institute products to use the latest features of spack for building on cluster platforms. * Address travis error messages and resubmit the pull request. * Update the contents of openspeedshop package.py so it passes the flake8 tests. * Fix flake8 error-whitespack issue in mrnet package.py file. * Add updates based on spack reviewer feedback. * More fixes based on comments from reviewers. Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH. * More review related changes. Update MPIOption.append lines and take out xercesc references. * Create a base options function for common openspeedshop base cmake options to reduce redundencies. * Add libxml2+python depends on to get around issues with the libxml2 package file. * Using boost over 1.60.0 causes compile errors. This is a known boost bug. Also, dyninst-9.2.0 is set to be the vesrion of dyninst to use with OSS, as of now. The newer version fails to build. * Fix bad syntax in specifying the boost version range. * Update the version numbers for the krell institute components and tools: cbtf and openspeedshop. * Do not build glib for qt3, it is not needed and causes build problems at this time anyway.
2017-01-10Change nargs='*' to argparse.REMAINDER for constraint options. (#2798)Todd Gamblin2-2/+3
2017-01-10openjpeg: fixes url (#2790)Massimiliano Culpo1-0/+4
2017-01-09Temporary workaround for R concretization bug (#2756)Adam J. Stewart1-2/+1
2017-01-09Added list_url to r-dt package (#1533)sknigh1-0/+1
2017-01-07Get Rid of nobuild, nolink, and alldeps (#2765)Elizabeth Fischer184-515/+508
* Removing the nobuild, nolink, and alldeps dependency types in favor of being explicit. * This will help with maintenance going forward, as adding more dependency types won't affect existing declared dependencies in weird ways. * default deptype is still `('build', 'link')`
2017-01-07Various updates to the NCO package and dependencies (#2639)Adam J. Stewart9-100/+45
* Remove +mpi variant from NCO * Update NCO deps to AutotoolsPackage * Update the other NetCDF packages to AutotoolsPackage * ANTLR has a nolink deptype on java, don't worry about csharp * Remove restrictions from NCO package, fix homepage * Add version 4.6.3 of NCO * Missed AutotoolsPackage for NetCDF-CXX4 * NetCDF tests fail when run in parallel * Remove commented out dependency * Add documentation dependency
2017-01-07Unset PETSC_DIR during installation (#2768)Adam J. Stewart1-1/+11
* Set PETSC_DIR during installation * Move env var unsets to setup_environment * Fix unset var name and number of args
2017-01-07Added needed deps for bbcp (#2773)James Wynne III1-0/+3
2017-01-07Preliminary RPackage class (#2761)Adam J. Stewart173-1213/+238
2017-01-07Fix issues linking hDF5 1.8.14 and below on Ubuntu. (#2772)Todd Gamblin1-1/+15
2017-01-06add conduit 0.2.1 release (#2766)Cyrus Harrison1-1/+2
2017-01-06Add boost 1.63.0 (#2743)Bruno Turcksin1-0/+1
2017-01-06Merge pull request #2740 from jrood-nrel/jonroodGregory Lee1-1/+2
Renaming mkl to intel-mkl
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.
2017-01-04Intel-mkl provides mklJon Rood1-0/+1
2017-01-04Renaming mkl to intel-mklJon Rood1-1/+1
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.
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