hlrs-software-stack/spack

Author	SHA1	Message	Date
Erik Schnetter	4e390e6689	m4: Update version (#2872 )	2017-01-20 10:23:53 -08:00
Erik Schnetter	56cdb1d1ab	swig: Update version (#2871 )	2017-01-20 10:23:23 -08:00
Jason Sarich	bc37a1012c	let pflotran depend on hdf 1.8.12 and above (#2875 )	2017-01-20 10:18:58 -08:00
Michael Kuhn	042307d5f1	Update c-blosc to 1.11.1 (#2877 )	2017-01-20 10:17:46 -08:00
Erik Schnetter	a0c4fe247f	OpenSSL: Update to version 1.1.0c (#2885 )	2017-01-20 10:12:09 -08:00
Denis Davydov	1223e43827	p4est: add 2.0 (#2890 )	2017-01-20 10:11:11 -08:00
Denis Davydov	c350bd1216	dealii: fix config without mpi (#2856 ) * dealii: fix config without mpi * dealii: add check of variants	2017-01-19 11:24:09 -08:00
Quinn	f511f7b558	Adding some fixes to packages that use `configure_args` function without setting spec set or directly referencing it (#2868 ) * Adding 'self.' to the spec call for configure_args * Updating this to set spec to self.spec * More updates to the configure_args spec calls * Another spec issue * Another spec issue. * And another spec issue * Switching cmor back to self.spec.	2017-01-19 06:26:39 -08:00
Erik Schnetter	9b7001fda1	OpenMPI: Update auto-detection of Verbs library location (#2124 )	2017-01-18 14:54:39 -08:00
Adam J. Stewart	02f92fc7f8	Massive conversion from Package to AutotoolsPackage (#2845 ) * Massive conversion from Package to AutotoolsPackage * Forgot to convert p4est to AutotoolsPackage * Fix typo * Fix broken link in docs	2017-01-18 10:34:09 -08:00
Denis Davydov	5812081b80	gmsh: add 2.16 (#2857 )	2017-01-18 09:34:05 -08:00
Denis Davydov	ddfbb14ad9	octave: add 4.2.0; fix Blas/Lapack; use AutotoolsPackage (#2858 ) * octave: add 4.2.0; fix Blas/Lapack; use AutotoolsPackage * fix a bug	2017-01-18 09:33:45 -08:00
Adam J. Stewart	026e2d0fe6	Convert 3 more new packages to PythonPackage (#2841 )	2017-01-18 08:51:38 -08:00
Erik Schnetter	6242aaef6c	papi: Update to 5.5.1 (#2849 )	2017-01-18 08:18:38 -08:00
Erik Schnetter	70042f9e7d	hwloc: Update to 1.11.5 (#2851 )	2017-01-18 08:18:08 -08:00
Erik Schnetter	b452a7619c	curl: update to 7.52.1 (#2852 )	2017-01-18 08:17:50 -08:00
Erik Schnetter	a23fcd2a93	cmake: Update to 3.7.2 (#2853 )	2017-01-18 08:17:31 -08:00
Erik Schnetter	3bd0101fb9	jemalloc: Update to 4.4.0 (#2850 )	2017-01-18 08:16:59 -08:00
Denis Davydov	a040c8c743	oce: add 0.18 and fix patching (#2844 ) * oce: add 0.18 and fix patching * oce: simplify the patch	2017-01-17 14:40:07 -08:00
Denis Davydov	190a5b575c	p4est: switch to AutotoolsPackage (#2839 )	2017-01-17 11:05:34 -08:00
Adam J. Stewart	c0aaa8fcea	Add PythonPackage base class - Add a PythonPackage class with build system support. - Support build phases in PythonPackage - Add a custom sanity check for PythonPackages - Get rid of nolink dependencies in python packages - Update spack create to use new PythonPackage class - Port most of Python packages to new PythonPackage class - Conducted a massive install and activate of Python packages. - Fixed bugs introduced by install and activate. - Update API docs on PythonPackage	2017-01-16 20:00:31 -08:00
Mario Melara	beafcfd3ef	Set MPI environment variables to the compiler wrappers on Cray (#2762 ) * Set MPI[lang] env var to compiler wrappers on cray Sets MPICC, MPICXX, MPIFC etc to point to the compiler wrappers on Cray systems. Some packages look for MPIs via environment variables - e.g adios * Use spec to check for Cray * os is no longer used.	2017-01-16 16:15:37 -08:00
Jon Rood	6e8058ad41	Specify Python location in VisIt in a more uniform fashion. (#2803 )	2017-01-16 03:21:52 -08:00
Todd Gamblin	de7be6694f	Fix issue with Mac OS version detection in m4 package. (#2835 )	2017-01-16 03:03:52 -08:00
Denis Davydov	8365dbd959	petsc: add 64bit variant (#2655 ) * petsc: add 64bit variant * hypre: add int64 variant * superlu-dist: add int64 variant * petsc: add int64 variant * metis: rename idx64 to int64 to make it consistent with other packages * mumps: rename idx64 to int64 to make it consistent with other packages * dealii: rename 64bit to int64 to make it consistent with other packages	2017-01-16 02:23:07 -08:00
Axel Huebl	e2697e4a37	isl: add latest version (#2834 ) added latest version of isl. Needed to get llvm/clang in the latest trunk to build via spack, but there are more versions available. what is the policy regarding those? Add what we need for now?	2017-01-16 01:17:35 -08:00
Jon Rood	b2f29b855b	Updating BoxLib with the ability to build again. (#2813 ) * Updating BoxLib with the ability to build again. * Using Spack MPI compilers directly. * Fixing typo. * Using tarball from github archive for boxlib.	2017-01-15 17:07:44 -08:00
Adam J. Stewart	e3a631c90e	Add Astra package (#2800 )	2017-01-15 16:23:52 -08:00
Adam J. Stewart	f480e3449e	Added customization for make targets in 'build' and 'install' phases for CMakePackage (#2742 ) * Added customization for make targets in 'build' and 'install' phases for CMakePackage * Use rst in build system docs so that Sphinx generates nice API docs * Allow AutotoolsPackages to be built in a different directory * Flake8 * Fix missing import * Allow configure to be located in different directory * Update espressopp to use build targets * Flake8 * Sphinx fix, lists must be a new paragraph * Back out change that allowed a configure script in a different directory than build_directory * Add missing deps, build in parallel * Missing space for rst list	2017-01-15 16:23:16 -08:00
Jean-Paul Pelteret	4b7b595e3c	New package: CppAD (#2832 )	2017-01-15 16:20:26 -08:00
Adam J. Stewart	f2d4c15395	Remove cmake build dep from CMakePackages (#2684 )	2017-01-15 03:18:52 -08:00
Adam J. Stewart	7fce4c5083	Add list_url to cmake (#2714 )	2017-01-15 03:16:41 -08:00
Axel Huebl	3f7b4ab7aa	Clang & Boost: No PCH (#2827 ) Although it hurts a little, officially pre-compiled headers in boost are only supported for gcc & msvc and the latest clang releases still fail to build boost with it. Therefore, I disabled building those to get boost build with clang 3.9.0 on an Ubuntu 14.04 (x86). Links to documentation and boost bug reports are inline, so people can later on check if they still apply. Seems just to be a bug in `Boost.Build` that tries to set `-o` with multiple output files.	2017-01-15 02:38:14 -08:00
Axel Huebl	5c4d2627ff	Packages: Add CUDA8 (#2823 ) Adds the latest CUDA release, 8.0.44.	2017-01-15 02:35:53 -08:00
Adam J. Stewart	367f46eee2	Add old version of PGI (#2784 )	2017-01-15 02:35:27 -08:00
Adam J. Stewart	12edc4e369	Add latest version of PETSc (#2783 )	2017-01-15 02:34:48 -08:00
Massimiliano Culpo	436f6a4ab6	get_std_cmake_args delegates to CMakePackage._std_args fixes #2665 (#2805 )	2017-01-15 02:34:15 -08:00
danielsjensen1	957cb968c6	Features/octopus 6.0 (#2819 ) * Added support for Octopus 6.0 and the optional libraries: metis, parmetis, netcdf, arpack-ng, and scalapack. * Fix PEP 8 line too long error. * Changed format syntax {} to {0} to support Python 2.6.	2017-01-15 02:30:47 -08:00
Gregory Lee	c6c6773c03	added psutil python package (#2812 )	2017-01-15 02:30:12 -08:00
Stephen McDowell	1f4ca71e21	Adding the py-ipdb package for more stable debugging with iPython. (#2824 ) * Adding the py-ipdb package for more stable debugging with iPython. * Removing deprecated python support, adding missing dependencies. * Adding version checks for (i)python	2017-01-15 02:29:29 -08:00
Matthew Scott Krafczyk	28ea72d5b2	Add the package py-sphinx-bootstrap-theme (#2825 )	2017-01-15 02:27:17 -08:00
Andrey Prokopenko	1128922b44	boost: fixing boost-1.55.0 for gcc-5 (#2822 ) 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.	2017-01-13 08:43:50 -08:00
Jim Galarowicz	481bc91854	Update the boost versions used by openspeedshop. Boost-1.60 to current 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.	2017-01-10 12:28:05 -08:00
Massimiliano Culpo	a7a77b5b41	openjpeg: fixes url (#2790 )	2017-01-10 09:14:16 -08:00
Adam J. Stewart	1ece25bdc2	Temporary workaround for R concretization bug (#2756 )	2017-01-09 19:07:49 -08:00
sknigh	c7ca96b327	Added list_url to r-dt package (#1533 )	2017-01-09 14:37:06 -08:00
Elizabeth Fischer	402dfe30f9	Get Rid of nobuild, nolink, and alldeps (#2765 ) * 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')`	2017-01-07 19:59:02 -08:00
Adam J. Stewart	68baac0549	Various updates to the NCO package and dependencies (#2639 ) * 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	2017-01-07 18:06:59 -08:00
Adam J. Stewart	a0195371e8	Unset PETSC_DIR during installation (#2768 ) * Set PETSC_DIR during installation * Move env var unsets to setup_environment * Fix unset var name and number of args	2017-01-07 17:38:53 -08:00
James Wynne III	b7fdc03bd5	Added needed deps for bbcp (#2773 )	2017-01-07 16:30:54 -08:00
Adam J. Stewart	daff3c0908	Preliminary RPackage class (#2761 )	2017-01-07 16:28:52 -08:00
Todd Gamblin	f379697985	Fix issues linking hDF5 1.8.14 and below on Ubuntu. (#2772 )	2017-01-07 09:03:50 -08:00
Cyrus Harrison	e39ba88e9c	add conduit 0.2.1 release (#2766 )	2017-01-06 12:33:51 -08:00
Bruno Turcksin	2f173bda9c	Add boost 1.63.0 (#2743 )	2017-01-06 11:44:41 -08:00
Gregory Lee	a016fd01ec	Merge pull request #2740 from jrood-nrel/jonrood Renaming mkl to intel-mkl	2017-01-06 11:01:16 -08:00
Gregory Lee	7b337de93e	various python package version and dependency updates (#2751 ) * various python package version and dependency updates * various python package version and dependency updates	2017-01-06 08:50:06 -08:00
Christoph Junghans	8dc056130c	espressopp: package for the ESPResSo++ software (#2602 ) * 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.	2017-01-05 21:20:55 -08:00
Matthew Krafczyk	8c650303ff	Add dependencies and finish the py-tornado package. 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	2017-01-05 16:10:30 -08:00
Jean-Paul Pelteret	6a5185a2a7	Added npm, node.js, and Jupyter dependencies 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	2017-01-05 16:10:30 -08:00
Elizabeth Fischer	3dd4a01a5e	Standardize package names: lower-case, not Mixed_CASE (#2475 ) * 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.	2017-01-04 18:24:07 -08:00
Jon Rood	01406251c9	Intel-mkl provides mkl	2017-01-04 14:02:23 -07:00
Jon Rood	c8405b4b5f	Renaming mkl to intel-mkl	2017-01-04 13:55:08 -07:00
George Hartzell	4e653254c5	Use zlib's "fossil" site for old tarballs (#2735 ) * 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)	2017-01-04 11:43:10 -08:00
Cyrus Harrison	eaa24b08fd	add package for conduit (#2670 ) * 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	2017-01-04 10:20:08 -08:00
Jeffrey Salmond	e57fc3d950	opencoarrays: new version (#2734 ) * add version 1.8.0 * remove depends_on('cmake') as it is now unecessary * remove 'coarrays' as a virtual package	2017-01-04 08:40:55 -08:00
Jean-Paul Pelteret	4ff33d41a7	New package: ccache (#2721 )	2017-01-04 08:39:58 -08:00
Elizabeth Fischer	03471469e7	libpng: Upgrade versions to fix vulnerability. (#2723 )	2017-01-04 08:32:10 -08:00
George Hartzell	2e24a3a2be	zlib@1.2.10 and R do not get along, work around it (#2727 ) * 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.	2017-01-04 07:51:16 -08:00
Barry Smith	2322deda65	Update to latest zlib version, server no longer provides older version (#2720 ) * 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	2017-01-03 13:52:14 -08:00
Todd Gamblin	d32d5e45fb	Fix issues when a package provides the same vdep twice. (#2710 ) * 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	2017-01-02 18:40:57 -08:00
Adam J. Stewart	040f8a7176	Add latest version of gmp (#2695 )	2016-12-30 22:53:54 -08:00
Todd Gamblin	972a277956	Fix Python issue with build failures; Add test case for build failures. (#2687 )	2016-12-30 11:37:50 -08:00
Todd Gamblin	5fbab1f4b5	Concretize preserves deptypes (#2681 ) Concretization preserves deptypes	2016-12-29 14:43:59 -08:00
Massimiliano Culpo	17b13b161b	Directive inheritance: laziness for the win (#2623 ) * 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).	2016-12-28 12:37:02 -08:00
Thierry	857dac88c8	init yorick package (#2635 ) * 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(?)	2016-12-28 10:08:02 -08:00
George Hartzell	18c10f2bad	Cleanup post luafilesystem version de-underscoring (#2683 ) 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.	2016-12-27 11:49:53 -08:00
Mayeul d'Avezac	81c1404b9c	Adds catch, cppunit, spdlog, tinyxml(1 and 2), google benchmark (#2627 ) * 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	2016-12-27 00:32:29 -08:00
Michael Kuhn	baaa613e44	Update wx to 3.1.0 (#2641 )	2016-12-27 00:18:26 -08:00
Adam J. Stewart	29bac34c1d	Ensure that every file in Spack has a license (#2659 ) * 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	2016-12-27 00:17:12 -08:00
Matthew Scott Krafczyk	3e92ffde7d	Update py-cython with new pypi.io url and new version (#2650 )	2016-12-25 19:48:11 -08:00
Bruno Turcksin	e16908b16b	Add 64 bit variant to dealii. (#2654 )	2016-12-25 18:55:14 -08:00
Adam J. Stewart	b240fdb2b9	Add latest version of Python 2 (#2668 )	2016-12-25 18:53:16 -08:00
Michael Kuhn	33592d0142	Update gcc to 6.3.0 (#2669 )	2016-12-25 18:52:58 -08:00
George Hartzell	041f96b349	Update the texlive distro digest. (#2679 ) sigh.	2016-12-25 12:37:03 -08:00
Massimiliano Culpo	8fe5fb7988	go: fixed GOROOT_BOOTSTRAP without workarounds (#2671 )	2016-12-25 12:33:57 -08:00
Michael Kuhn	e340f275b8	Update cairo to 1.14.8, gtkplus to 2.24.31 and pango to 1.40.3 (#2642 )	2016-12-21 15:03:28 -08:00
Kim Serradell	70a4c4e105	Bug fontconfig (#2652 ) * 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	2016-12-21 14:27:15 -08:00
Federico Padua	60dc751225	Fix homepage for the package libspatialindex (#2656 ) Small fix for the homepage of the package libspatialindex.	2016-12-21 14:23:32 -08:00
Michael Kuhn	3ce3165ae6	Update gdal to 2.1.2 (#2643 )	2016-12-19 17:06:57 -08:00
Adam J. Stewart	b3ba45afa9	Various improvements to H5hut (#2636 )	2016-12-19 17:06:14 -08:00
Andrey Prokopenko	d306893d83	moab: changed trilinos dependency to zoltan, and added fortran variant (#2582 ) Trilinos dependency is very heavy, the zoltan one is light. I'm not sure if there is a situation where one needs the former.	2016-12-19 14:41:09 -08:00
Adam J. Stewart	d24186ea84	Update PnetCDF to AutotoolsPackage (#2637 )	2016-12-19 14:26:47 -08:00
George Hartzell	d8efeabf77	Update digest for vim@8.0 tarball. (#2600 ) * Update digest for vim@8.0 tarball. The digest appears to have changed. The new digest value matches the value in their [MD5SUMS](ftp://ftp.vim.org/pub/vim/unix/MD5SUMS) file. * Change ftp.vim.org -> github.com/vim/vim/archive Vim seems to do weekly releases, but the name of the tarball on ftp.vim.org doesn't change so we have to regularly play 'update the digest' (aka Internet whack-a-mole). This commit changes the url so that we are now downloading particular versions from the Vim project's github archive. I didn't walk back through of time to get all of the versions that used to be explicit. I grabbed the final `7.4` and the current `8.0` releases. If people need more we can add them.	2016-12-19 14:26:16 -08:00
Adam J. Stewart	46436a0909	GSL: Add latest version, update to AutotoolsPackage (#2630 )	2016-12-19 09:21:38 -08:00
Adam J. Stewart	08d323b1f8	NCO: Add latest version, update to AutotoolsPackage (#2629 )	2016-12-19 08:49:37 -08:00
Todd Gamblin	b18738e03d	Add gawk (GNU awk) (#2625 ) * Add gawk, GNU awk. * flake8 fix.	2016-12-18 22:35:23 -08:00
George Hartzell	6e1b3f621d	Feature/add package for fastqc (#1573 ) * Add package for fastqc This tool is a java mess. Their Way To Do It is to just copy the entire tree into it's final resting place, make the perl script at the top level executable and take it from there. Yuck. This package assumes that `set_executable` actually sets all the user bits. If that change doesn't go in, then something equivalent needs to be done. * Use chmod to make fastqc executable I haven't gotten any feedback on changing set-executable, so switch to using chmod (from the cuda package). * Flake8 cleanup * Install files neatly, don't just copy top level of dir Rather than blindly copying everything in the distribution, carefully put the necessary bits into reasonable places. Neatness counts, etc... This requires patching the `fastqc` perl script, so this commit adds a patch file. * Additional pep8 cleanup * Let dependency handle adding jdk to PATH * Flake8 cleanup * Ensure that java is on PATH I thought that the run dependency on the jdk would put java on my PATH, but it does not appear to work. For now, do it by hand.	2016-12-18 16:38:14 -08:00
Alfredo Adolfo Gimenez	68e9a2ed8d	Added customization for make targets in 'build' and 'install' phases for AutotoolsPackage (#2464 ) * Customization for make targets in build and test phases for AutotoolsPackage * Updated Blitz++ to use customized make build and test targets * Removed flake8 error * Removed make test customization, added make install customization, need to figure out issues with multiple make targets * Changed build_targets and install_targets to normal attributes	2016-12-18 16:27:47 -08:00
Chris MacMackin	0de7b5504e	py-markdown: Add new package for python-markdown. (#2611 ) * py-markdown: Add new package for python-markdown. * py-markdown: Added restrictions on Python version. * py-markdown: Removed upper-limit on compatible Python versions. * py-markdown: Reinstated upper bound on Python version. Also fixed small formatting error.	2016-12-18 16:23:31 -08:00
Denis Davydov	1c0f28c559	gmsh: add 2.15.0 and switch to CMakePackage (#2620 )	2016-12-18 16:20:37 -08:00
Denis Davydov	da2350a1c9	tbb: add 2017.3 (#2619 )	2016-12-18 16:20:26 -08:00
Denis Davydov	aeb58dc2de	cmake: add 3.7.1 (#2618 )	2016-12-18 16:20:13 -08:00
Gregory Lee	592df25aef	build fixes for openblas (#2601 ) * build fixes for openblas * avx2 in openblas nnot supported with older gcc * merge fix for openblas	2016-12-17 17:04:59 -08:00
Denis Davydov	0ef55b831f	dealii: fix config for Netcdf with lib64 (#2616 )	2016-12-17 08:57:33 -08:00
Chris MacMackin	a1a41bb4c7	graphviz: fixed build error due to specifying ltdl lib but not include. (#2609 ) * graphviz: fixed build error due to specifying ltdl lib but not include. * graphviz: Fixed dependencies on libtool and expat.	2016-12-16 16:22:13 -08:00
Andrey Prokopenko	394f010952	libmesh: added mpi variant (#2584 )	2016-12-16 15:39:55 -08:00
Thierry	5f88bea442	init nfft 3.3.2 package file (#2612 ) * init nfft 3.3.2 package file * shorten comment line	2016-12-16 15:36:34 -08:00
Chris MacMackin	3089d118c1	py-beautifulsoup4: Added version 4.5.1 (#2610 )	2016-12-16 14:21:26 -08:00
Jon Rood	d7ff4b8f34	Updating Trilinos with superlu variant and fixing git branch version options. (#2604 )	2016-12-16 14:14:50 -08:00
Adam J. Stewart	36072c4776	[HACK] Make concretization great again! (#2590 ) * Always default to +mpi * Always default to ~X	2016-12-16 10:49:02 -08:00
Massimiliano Culpo	87c9b01033	openblas: derives from MakefilePackage (#2488 ) * MakefilePackage: changed build_args and install_args for consistency with #2464 openblas: derives from MakefilePackage * MakefilePackage: changed default edit behavior	2016-12-15 10:15:52 -08:00
Massimiliano Culpo	f9ca5b9f27	go: see #2567 , temporary fix (#2588 )	2016-12-15 09:12:33 -08:00
Todd Gamblin	6971918c27	Add GNU patch to Spack. (#2598 )	2016-12-15 01:35:45 -08:00
Jean-Paul Pelteret	8816cdea9e	Blacklist flex 2.6.2 by commenting out package version (#2571 ) Fixes #2554	2016-12-14 14:34:55 -08:00
George Hartzell	f487102c0c	Update texlive digest (#2591 ) Texlive is live, they update the contents of their tarball on a whim. Here's the current one.	2016-12-14 11:55:48 -08:00
Kim Serradell	c02de564e4	New package py-cdo (#2569 ) * Add python cdo support * Correct pypi url * Corrected a blanck space that was failing CI * Corrected url that was failing CI * Following @alalazo indications, Write this line wrapping it around 80 chars to pass Travis * Added cdo package depency	2016-12-13 14:36:06 -08:00
Gregory Lee	392ed4f0cc	Merge pull request #2506 from skosukhin/pr_python A couple of updates for python package.	2016-12-13 13:56:15 -08:00
amklinv	f613445eb2	Added support for xSDKTrilinos package (#2201 ) * Added support for xSDKTrilinos package * Updated xsdktrilinos/package.py for PR review * Added trilinos version # reqs to xsdktrilinos * xsdktrilinos now uses CMakePackage * Cleaned up xsdktrilinos/package.py * Removed unused cxxflags from xsdktrilinos * Removed unused sys import from xsdktrilinos	2016-12-13 11:50:10 -08:00
Denis Davydov	d855403546	likwid: remote root from INSTALL_CHOWN (#2564 )	2016-12-13 10:46:31 -08:00
Denis Davydov	fab9af7081	slepc/petsc: fix python dependency (#2560 )	2016-12-13 01:32:42 -08:00
Sergey Kosukhin	d8c4418952	Updated python: refactoring and warning messages.	2016-12-13 08:36:56 +01:00
Sergey Kosukhin	3ba88a7509	Updated python: pass LDSHARED to dependants' setup scripts.	2016-12-13 08:36:56 +01:00
Sergey Kosukhin	ec855df071	Updated python: account for lib64 when filtering compilers.	2016-12-13 08:36:56 +01:00
Sergey Kosukhin	58cb2cc2af	Updated python: reformat code.	2016-12-13 08:36:56 +01:00
Adam J. Stewart	9f71382912	Add missing bzip2 dependency to freetype (#2536 ) * Add freetype dependency on bzip2 * Switch package with an install method for the docs	2016-12-12 14:20:36 -08:00
Jean-Paul Pelteret	6698650679	Doxygen: Add new version (#2561 )	2016-12-12 13:45:29 -08:00
Denis Davydov	eb645a8e46	p4est: remove unneded lua dependency (#2559 )	2016-12-12 09:51:58 -08:00
Javier	641db8b9bd	New package - r-xgboost (#2493 )	2016-12-11 11:49:33 -08:00
Denis Davydov	c8a89d84b5	atlas: fix lapack stage path (#2371 ) * atlas: fix lapack stage path * atlas: add a few links to other package managers	2016-12-11 11:48:23 -08:00
Denis Davydov	d8fd5835b6	rename: add new package (#2486 )	2016-12-11 11:44:30 -08:00
Denis Davydov	62dedc80b1	likwid: add todo (#2531 ) * likwid: add todo * liwkid: add a note on hwloc dependency	2016-12-11 11:39:56 -08:00
Denis Davydov	6475937fc2	numdiff: fix dependency type on macOS (#2538 )	2016-12-11 11:38:40 -08:00
Sergey Kosukhin	42dbd4f855	Updated cmor: corrected way to set constraints for the extendee. (#2543 )	2016-12-11 11:37:00 -08:00
Jean-Paul Pelteret	70f1e92951	Update Adol-C package (#2556 ) Rename developer version, add new version, and make patch version specific.	2016-12-11 11:35:57 -08:00
Denis Davydov	1570f90fde	clang: do xcode mockup iff requested by a package (#2544 ) * clang: do xcode mockup iff requested by a package * add a note * add pkg to setup_custom_environment() and decide whether or not to use mockup XCode there based on the package	2016-12-10 16:23:39 -08:00
Stephen McDowell	b03881d1bb	Eigen 3.3.1 is latest stable version. (#2551 ) Main page states [3.3.1 is latest stable](http://eigen.tuxfamily.org/index.php?title=Main_Page).	2016-12-10 16:23:20 -08:00
Stephen McDowell	3887d9b2bc	Scotch 6.0.4 is available. (#2552 ) Source project page states [6.0.4 is latest stable](http://scotch.gforge.inria.fr/)	2016-12-10 16:23:03 -08:00
Barry Smith	3a1e191b72	Implementation of spack file for Pflotran (#2444 ) Supports installing both a "known version" of PETSc/PFlotran that works and the develop/master branches of both packages Funded-by: IDEAS Project: IDEAS/xSDK Time: 4 hour	2016-12-10 16:22:36 -08:00
Tom Scogland	943c007fb5	update flux dependencies and package (#2541 ) * update flux dependencies and package * refinements from @adamjstewart * fix flux document generation The docbook-xsl package has been added, and correctly configures catalog files to generate documentation correctly with asciidoc.	2016-12-09 17:19:53 -08:00
Denis Davydov	d7e9134d42	astyle: do not set user/group when installing on macOS (#2542 ) * astyle: do not set user/group when installing on macOS * astyle: add new version	2016-12-09 10:58:08 -08:00
Denis Davydov	4d0ea423fb	petsc: explicitly disable X11 (#2533 ) otherwise petsc may pickup libX11 on login nodes during config/build, but libX11 may not be available on computation nodes.	2016-12-09 08:43:38 -08:00
Sergey Kosukhin	607f4e7b81	Added packages: cmor and uuid. (#2527 ) * Added package 'uuid'. * Added package 'cmor'. * Updated 'cmor' and 'uuid': docstring formatting.	2016-12-08 12:09:21 -08:00
Todd Gamblin	be300eb6d5	Add support for parsing R-XML URL versions. (#2525 ) * Add support for parsing R-XML URL versions. * Better url-parse debug output. - just print the debug stuff all the time. * fix R-XML versions.	2016-12-08 11:08:58 -08:00
George Hartzell	65df417444	Update emacs: current release, use our x11 bits (#2052 ) * Update emacs: current release, use our x11 bits Add checksum for 25.1 release. Rework the X support: - use Spack's X11 bits - add ability to specify an X toolkit (gtk or athena, default is gtk). - change toolkit names to align with Emacs' configure usage. * PEP8 cleanups. * glib dependency should not be type=build I'd like to blame that on a typo, but it's a few too many characters for that to be viable. I'm not sure what I was thinking. * Pass X variant down: emacs->pango->cairo * X variants default to False, warn on bad toolkit Change the X variants for emacs, pango and cairo to default to False. Check that the toolkit is a valid choice and give a reasonable error if not. * Fix flake8 issue, reword warning text * gtkplus needs to use +X variant for pango to work In order for a useful variant of pango to be built into the spec I needed to make the dependency on gtkplus explicitly specify it's X variant. The X variant is the default, but that wasn't enough to make it happy. Since it's happiness is the most imporant thing in the world, this change! :)	2016-12-08 09:43:29 -08:00
Adam J. Stewart	ed8060abe0	Scotch fails to build with latest flex (#2523 )	2016-12-08 09:37:18 -08:00
Denis Davydov	cab8788f53	dealii: remove dependencies which are not needed (#2522 )	2016-12-08 07:29:22 -08:00
George Hartzell	5f01f273e0	Add version/digest for emacs 25.1 (#2511 ) * Add version/digest for emacs 25.1 * Put newest version at top of list	2016-12-07 16:33:41 -08:00
Andrey Prokopenko	bb7b51855a	yaml-cpp: add boost dependency (#2517 ) yaml-cpp has a boost dependency, and according to [yaml-cpp page](https://github.com/jbeder/yaml-cpp): yaml-cpp 0.5.3 has been released! This is a bug fix release. It also will be the last release that uses Boost; futures releases will require C++11 instead.	2016-12-07 13:55:12 -08:00
George Hartzell	72c01fbd33	Building lua-luafilesystem requires a newish-git (#2515 ) See #2059 for background. I'm unable to install `lmod` because lua-luafilesystem fails. The luarocks install bits attempt to do a shallow clone of the luafilesystem sources and the default git on my CentOS 7 test box (`git version 1.8.3.1`) fails. This adds a build dependency that ensures that a relatively modern git is available.	2016-12-07 12:12:53 -08:00
George Hartzell	f3410a0b1d	Update texlive digest value (#2514 ) * Update texlive digest value While the discussion in #2494 progresses, this changes fixes the digest values so that builds succeeed. * Add warning that texlive is not repeatably installable	2016-12-07 12:02:22 -08:00
Andrey Prokopenko	3088cb171e	netcdf: add checksum for 4.3.3.1 version (#2509 )	2016-12-07 09:34:31 -08:00
Andrey Prokopenko	8239bd1681	cmake: added checksum for 3.1.0 version (#2508 )	2016-12-07 09:33:54 -08:00
Barry Smith	76dae1dc5f	hypre, superlu-dist, trilinos - support using develop/master branches of these packages (#2443 ) Funded-by: IDEAS Project: IDEAS/xSDK Time: 1 hour	2016-12-06 12:10:51 -08:00
Joseph Ciurej	9c57a49bf4	Fixed a few minor issues with the 'fontconfig' package install script. (#2491 )	2016-12-06 10:39:59 -08:00
Andrey Prokopenko	9edb31a51c	hdf5: added 'pic' variant (#2373 )	2016-12-05 11:57:04 -08:00
Adam J. Stewart	9115ab5097	Add Java support to OpenMPI (#2285 ) * Update OpenMPI to the AutotoolsPackage * Add Java support to OpenMPI * Fix missing commas * Be more specific about what versions support what flags * Revert description for thread_multiple variant	2016-12-05 10:15:12 -08:00
Elizabeth Fischer	cd0524b5b7	py-rtree: Added package (#1548 ) * py-rtree: Added package * py-rtree = RTree (spatial indexing) data structure for Python * libspatialindex = Underlying C library wrapped by py-rtree * Flake8 and Copyright issues. * Fix Python syntax error. * Fixed dependency type error. * Added new version, based on updates requested in upstream PR * 1. Change cmake to build dependency. 2. Updated to CMakePackage	2016-12-05 10:08:52 -08:00
Denis Davydov	24093a932c	ghostcript-fonts: fix install on macOS (#2482 )	2016-12-05 08:28:35 -08:00
Denis Davydov	2d1ab68656	xextproto: fix on macOS by not running parallel build (#2483 )	2016-12-05 08:28:02 -08:00
George Hartzell	f0dcb5bbf7	Update go to 1.7.4 and 1.6.4 to fix security issues (#2467 ) * Update go to 1.7.4 and 1.6.4 to fix security issues The go team recently rolled out two releases to address security issues. Details available on the [go release site](https://golang.org/doc/devel/release.html). This commit updates our explicitly supported versions. It also includes a comment about two CentOS requirements (enable user_namespace and ensure that the static c library is installed) that are required for the pacakges to pass their tests. * Flake8 cleanup	2016-12-03 16:44:03 -08:00
Andrey Prokopenko	f17c22dfb5	zlib: added 'pic' variant (#2470 ) It looks more complicated because zlib has custom configure which does not support CFLAGS option. So instead, we take it from environment.	2016-12-03 16:43:44 -08:00
George Hartzell	6ddc518417	Update git package to include 2.11.0 (#2471 )	2016-12-03 16:41:12 -08:00
hegner	2f46613132	Fix download URL and dependencies for py-pypar (#2430 ) * fix download URL and dependencies for py-pypar * use url_for_version in py-pypar	2016-12-02 13:56:00 -08:00
Nicolas Richart	cc92b9a3a2	foam-extend: modification to accept flex version >= 2.6 (#2452 ) * Modification to accept flex version >= 2.6 + bug fix on paraview dependency * flake8 "corrections"	2016-12-02 13:51:03 -08:00
Elizabeth Fischer	18878a8615	doxygen: Disable unnecessary graphviz dependency by default. (#2323 )	2016-12-02 10:56:40 -08:00
Jon Rood	8b612d3568	Updating SuperLU package to use pic_flag instead of -fPIC, and removing specific version for default install method. (#2456 )	2016-12-02 10:47:35 -08:00
Jon Rood	946605a4c9	Updating yaml-cpp from Package to CMakePackage. (#2457 )	2016-12-02 10:41:18 -08:00
Gregory Lee	84dc0b5b83	new intel parallel studio versions (#2459 )	2016-12-02 10:35:36 -08:00
Andrey Prokopenko	3024c0096a	cmake: update the requirements for --no-system-jsoncpp option (#2312 ) The option appeared in CMake 3.2 (specifically, in 3.2.0-rc2, see https://cmake.org/pipermail/cmake-developers/2015-February/024552.html).	2016-12-01 17:51:00 -08:00
George Hartzell	c01f78e515	Make X11 font install dir the font search default (#2203 ) * Make X11 font install dir the font search default We install the X11 fonts into `/share/fonts` beneath the font-util installation prefix, but that directory is not one of the places that the font subsystem searches. This commit makes the fontconfig package depend on the font-util package, and then it makes ```python spec['font-util'].prefix + "/share/fonts" ``` be the fontconfig default font location. Before this change, plots drawn by R have bounding boxes where font glyphs should be. After this change fonts appear as expected. * Enrich description string (trigger new CI run) Improve the docstring for the package. Also interested in the side effect of triggering another CI run to see if the recent flake8 fix lets this PR run clean. * Flake8 cleanups	2016-12-01 17:38:00 -08:00
hegner	8dae60c5f0	Fix py-scientificpython and py-argcomplete dependencies (#2420 ) * add missing py-numpy dependency to scipy * add missing setuptools build dependency to py-argcomplete	2016-12-01 14:34:07 -08:00
Sergey Kosukhin	c6e2d9c1b0	Updated hdf5: new versions added. (#2442 ) * Updated hdf5: new versions added. * Updated hdf5: url_for_version() accounts for per-version urls.	2016-12-01 14:31:27 -08:00
Bruno Turcksin	bc4237c93e	Update trilinos version to 12.10.1 (#2454 )	2016-12-01 11:52:05 -06:00
Denis Davydov	6ce0ee49a9	likwid: add new package (#2455 )	2016-12-01 11:51:23 -06:00
Gregory Lee	8e816f8f88	Merge pull request #2364 from davydden/ips_mkl intel-parallel-studio: fix location of MKL libs	2016-12-01 09:21:37 -08:00
George Hartzell	8ab69c4d32	Update R&friends to use our X11 libs (#2053 ) * Update R&friends to use our X11 libs Add `depends_on()`'s for R, Cairo, and Tk so that they use the Spack X bits. * Conditionalize X stuff on variant Another step towards hooking up the X stuff. There's still discussion happening on the issue, but this is better than the 'everything must build with X' state that it was in.	2016-11-30 15:49:49 -06:00
Javier	5eb7026dd1	New package - r-irkernel (#2434 ) * New package - r-irkernel * New package - r-pbdzmq, dependency of r-irkernel * Adding blank line expected by flake8 tests	2016-11-29 16:59:28 -08:00
Joseph Ciurej	3d439d8946	Added the '+debug' and '+except' variants to the 'tetgen' package. (#2370 ) Fixed a bug that was causing memory errors after asserts in 'tetgen@1.5.0'.	2016-11-29 16:18:03 -06:00
Javier	e3778923b6	New package - r-rbokeh (#2436 )	2016-11-29 11:29:46 -06:00
Erik Schnetter	00ad8e87f4	jemalloc: Update to 4.3.1 (#2435 ) This corrects a severe problem (segfault) on macos Sierra.	2016-11-29 09:51:55 -06:00
Barry Smith	4d56d4f1f9	add support for installing the development (master) version of PETSc (#2431 ) Funded-by: IDEAS Project: IDEAS/xSDK Time: .3 hours x	2016-11-29 09:28:09 -06:00
Adam J. Stewart	664939eeba	Fix building latest version of flex (#2401 ) * Fix building latest version of flex * Don't need when clause * Remove perl deps, shebang too long	2016-11-28 09:48:34 -08:00
hegner	a2e6de9b5d	add missing zeromq dependency to r-rzmq (#2425 )	2016-11-28 09:14:16 -08:00
Javier	bb5bd8091d	New package - r-pryr (#2424 )	2016-11-28 09:14:10 -08:00
Javier	2d43b56deb	New package - r-uuid (#2423 )	2016-11-28 09:14:05 -08:00
Javier	6e68a01e50	New package - r-rmarkdown (#2422 )	2016-11-28 09:14:00 -08:00
Javier	6c2729ae6f	New package - r-repr (#2421 )	2016-11-28 09:13:20 -08:00
Denis Davydov	d2d23b76da	hdf5: fix for lib64 installation (#2349 )	2016-11-28 09:12:48 -08:00
Denis Davydov	b47bd9cc00	scotch: fix compilation on macOS (#2326 )	2016-11-26 16:48:50 -08:00
Javier	eeb9c84677	New package - r-rinside (#2416 ) * New package - r-rinside * Changes to pass flake8 test	2016-11-26 16:48:04 -08:00
Javier	1cdfc30374	New package - r-rsnns (#2415 )	2016-11-26 16:47:56 -08:00
Javier	0c4e97b6a1	New package - r-rzmq (#2414 ) * New package - r-rzmq * Adding homepage	2016-11-26 16:47:47 -08:00
Javier	7baa6e824b	New package - r-irdisplay (#2413 )	2016-11-26 16:47:38 -08:00
Javier	cc0d08255c	New package - r-hexbin (#2412 )	2016-11-26 16:47:25 -08:00
Andrey Prokopenko	8f0b91edaa	netcdf: multiple improvements (#2377 ) - Added 'dap' and 'cdmremote' variants This is based on work in #2324 with the following motivation: Turn off DAP support by deafult. DAP requires curl, which has issues with circular dependencies. For 95% of NetCDF users that do not need DAP, turning it off avoides this rats nest of problems. - Added 'parallel-netcdf' variant To support work with parallel-netcdf - Added 'shared' and 'static' build separation	2016-11-24 13:52:28 -08:00
George Hartzell	cde8f697a9	Bugfix/update go packages (#2369 ) * Update go-bootstrap package The last C based Go src tree was the 1.4 series. For a while they were cutting new releases so that people could bootstrap from a C only system. Now they're recommending that you either use the release-1.4 branch or that you use a date-stamped tarball that they'll produce on an as-needed basis. There are several issues that keep 1.4.2 from building on a CentOS 7 system. I've switched to the date based tarball. The cgo bits were also mis-behaving, but they're not needed for the bootstrapping task so I've set an environment variable that disables them. Details [on the install-from-source page](https://golang.org/doc/install/source#go14) and these issues: - https://github.com/golang/go/issues/17545 - https://github.com/golang/go/issues/16352. * Update go package Switched from pulling from the git repository to using the source tarballs and added digest values. Added support for 1.7.3, continued supporting 1.6.2, including patches for a couple of problems (details in [17545](https://github.com/golang/go/issues/17545) and [17986](https://github.com/golang/go/issues/17986). Dropped support for 1.5.4 and 1.4.2 because they no longer pass their tests and the patches above to not apply.	2016-11-24 12:25:51 -08:00
Javier	9c267e9c73	Updated version - r-lattice (#2410 )	2016-11-24 12:19:42 -08:00
Javier	09a5826903	New package - r-testit (#2409 )	2016-11-24 12:19:10 -08:00
Javier	f4fc670ab4	New package - r-highr (#2408 )	2016-11-24 12:19:05 -08:00
Javier	bb3239903b	New package - r-knitr (#2407 )	2016-11-24 12:19:01 -08:00
Javier	8949e67ce3	New package - r-gistr (#2406 )	2016-11-24 12:18:57 -08:00
Javier	85638aad03	New package - r-formatr (#2405 ) * New package - r-formatr * Block comment should start with '# '	2016-11-24 12:18:47 -08:00
Javier	4214281ab3	New package - r-evaluate (#2404 )	2016-11-24 12:18:41 -08:00
Gregory Lee	96bc3ff8f6	added qt variants for pyqt to build (#2389 )	2016-11-23 14:10:12 -08:00
Jon Rood	a6db0bfae2	Updating SuperLU package file with ability to build version 4.3. (#2390 ) * Updating SuperLU package file with ability to build version 4.3 (before they added cmake) with external blas or internal blas, and added capability to build the latest version 5.2.1 (with cmake) with internal blas. * Updating SuperLU package file with suggested changes, i.e. reorganizing installation methods based on version, adding cmake dependency when necessary, removing any use of internal blas, and also adding fpic variant. * Fixing flake8 failures.	2016-11-23 13:26:00 -08:00
Javier	7bda4e98b3	New package - r-catools (#2394 ) * New package - r-catools * Splitting lines to pass flake8 travis test	2016-11-23 10:57:47 -08:00
Javier	b085ce9e94	New package - r-partykit (#2395 ) * New package - r-partykit * Splitting lines to pass flake8 travis test	2016-11-23 10:57:23 -08:00
Javier	0eddf8421d	New package - r-formula (#2396 )	2016-11-23 10:56:59 -08:00
Javier	d6710a6aaf	New package - r-deoptim (#2397 )	2016-11-23 10:56:37 -08:00
Javier	74e6db9060	New package - r-c50 (#2393 ) * Adding R library r-bitops * New package - r-c50	2016-11-23 10:56:13 -08:00
Jon Rood	f8d038c0b8	New package yaml-cpp (#2399 ) * Adding new package for yaml-cpp. * Removing gcc specific c++11 flag. Adding fpic variant. Fixing formatting.	2016-11-23 10:54:22 -08:00
Matthew Scott Krafczyk	1fbe67af3d	Update flex package url's and versions (#2384 ) * Update flex package url's and versions The old sourceforge page for flex is now defunct. While version 2.6.0 still downloads fine, later versions are no longer hosted there. Development continues on github. I've adjusted urls to point to this new location. In addition, from 2.6.0 onwards, a new naming scheme for releases seems to have been adopted. I've created a url_for_version function to sort this out. * Change flex to an AutotoolsPackage Also move the url_for_version function to the end of the package definition. * Implement the autoreconf function for flex	2016-11-22 14:30:25 -08:00
becker33	5e73266572	Merge pull request #2291 from ax3l/topic-icet Packages: Add IceT	2016-11-21 14:27:17 -08:00
Andrey Prokopenko	3954fc8545	llvm-lld: minor misprint fix	2016-11-21 16:22:31 -05:00
Glenn Johnson	a8e40bf803	intel-parallel-studio: fix location of MKL libs	2016-11-18 23:16:47 +01:00
Denis Davydov	a5fb33b0e4	python: symlink lib64/python2.7/lib-dynload/ to lib/python2.7/lib-dynload/ (#2295 )	2016-11-16 07:29:08 -07:00
becker33	93287b950b	Merge pull request #1547 from citibeth/efischer/160816-PyPathspec py-pathspec: New package	2016-11-14 15:13:21 -08:00
Axel Huebl	4b82d881dc	Add Package: IceT Adds the IceT compositing library from Sandia/Kitware. Most default functionality needed for image compositing is added, OpenGL acceleration for very large displays is disabled. Downstream usage: most VTK based software which supports parallel image compositing, such as VisIt, Paraview and in our use-case [ISAAC](https://github.com/ComputationalRadiationPhysics/isaac).	2016-11-13 16:50:14 -07:00
Kelly Thompson	05c6c40e36	Force the recipe for Lua to use the spack compiler. (#2299 ) * Force the recipe for Lua to use the spack compiler. I'm not sure how the old recipe worked for anyone. The Lua Makefiles set `CC=gcc` and for my spack environment the first `gcc` found in my `PATH` is `$SPACK_ROOT/lib/spack/env/gcc`, which is a directory. This caused the build to fail. My change drops the `-std=gnu99`, but this option doesn't appear to be required for a sucessful build. * Preserve the '-std=gnu99' compile option.	2016-11-12 21:46:59 -07:00
Elizabeth Fischer	8c0c3263e2	Simplify the CMake build to make it more robust. (#2325 ) * Simplify the CMake build to make it more robust. * ncurses on by default.	2016-11-12 21:26:40 -07:00
Todd Gamblin	a5934fcaa6	Remove automake dep in libelf. (#2328 )	2016-11-12 21:25:14 -07:00
Adam J. Stewart	09470ec672	Add VizGlow package (#2298 )	2016-11-10 21:55:27 -08:00
Axel Huebl	42cc997aea	Packages: Add Jansson (#2287 ) This adds the built recipe for [Jansson](http://www.digip.org/jansson/), a C library for encoding, decoding and manipulating JSON data. GitHub Repo: https://github.com/akheron/jansson Downstream Usage: In [ISAAC](https://github.com/ComputationalRadiationPhysics/isaac) which is an in situ visualization library based on [alpaka](https://github.com/ComputationalRadiationPhysics/alpaka) and/or CUDA which is used in [PIConGPU](https://github.com/ComputationalRadiationPhysics/picongpu).	2016-11-10 21:52:49 -08:00
Denis Davydov	7cb756cdbb	tree: use Spack's compiler and fix installation on macOS (#2293 )	2016-11-10 21:52:22 -08:00
Axel Huebl	26ed2327ae	Packages: Add libwebsockets (#2288 ) This adds the built recipe for [libwebsockets](https://libwebsockets.org/lws-api-doc-master/html/index.html), a C library for lightweight websocket clients and servers. GitHub Repo: https://github.com/warmcat/libwebsockets Downstream Usage: In [ISAAC](https://github.com/ComputationalRadiationPhysics/isaac) which is an in situ visualization library based on [alpaka](https://github.com/ComputationalRadiationPhysics/alpaka) and/or CUDA which is used in [PIConGPU](https://github.com/ComputationalRadiationPhysics/picongpu).	2016-11-10 21:51:50 -08:00
Adam J. Stewart	99cf7b4ab3	Run HDF 5 tests post-installation (#2297 )	2016-11-10 21:50:32 -08:00
christianbaensch	2e11e7e456	Update package.py with/out CUDA support (#2266 ) Adding some lines to prevent from using any CUDA stuff, if NVIDIA CUDA Developement Kit was installed before.	2016-11-09 07:37:40 -08:00
Massimiliano Culpo	e5edac8af6	zlib, tar: passed to AutotoolsPackage (#2273 )	2016-11-09 07:37:08 -08:00
Gregory Lee	1b64213b10	added numpy version 1.11.2 and moved url to pypi.io (#2286 )	2016-11-09 07:35:30 -08:00
Oliver Breitwieser	98f27a89ec	Add py-pudb package (#2289 )	2016-11-09 07:34:30 -08:00
Oliver Breitwieser	68f79043aa	Add 1.5.3 for py-matplotlib and moved to pypi.io (#2271 ) * Added version 1.5.3 for py-matplotlib * Updated url to pypi.io so all versions are properly downloaded.	2016-11-09 07:34:17 -08:00
Sergey Kosukhin	4457c6a2ad	Updated environment-modules package: (#2279 ) Added 'lib64' directory as a possible option where tclConfig.sh file can be found.	2016-11-08 07:19:31 -08:00
Pramod Kumbhar	ba58a9f30d	fix tau installation issue (#2269 ) * fix tau installation issue : setup_environment() is called before install phase when 'Makefile.' doesn't exist (causing list index out of range error). Added detailed comment suggested by @alalazo	2016-11-08 07:18:14 -08:00
Gregory Lee	1f5ca24197	Merge pull request #2197 from skosukhin/ext_bugfix Updated python package reflecting the changes in `9347f86`	2016-11-07 16:05:57 -08:00
Adam J. Stewart	ca5f713282	Further restrict versions of GCC patched (#2259 )	2016-11-06 15:31:48 -08:00
Michael Kuron	6f2c05b888	Add PFFT parallel FFT package (#2255 ) * Add PFFT parallel FFT package * pfft: fix non-double precision	2016-11-05 12:19:19 -07:00
Massimiliano Culpo	6c1113769b	mpich: updated package to build_systems (#2254 ) * mpich: updated package to build_systems * qa : flake8 issues	2016-11-05 11:23:57 -07:00
Adam J. Stewart	6d1c32d46a	Add STAR-CCM+ package (#2202 ) * Add STAR-CCM+ package * Cleanup commented out code	2016-11-04 23:16:20 -07:00
Sergey Kosukhin	6dfc536ecd	Updated py-netcdf: added dependency on py-setuptools. (#2213 )	2016-11-04 23:15:55 -07:00
George Hartzell	bcee2ca162	New texlive release, updating the digest to match (#2218 ) * November 1 seems to have brought a new texlive release, updating the digest to match. Also switching the url from their automagic mirror to an explicit site to avoid inconsistencies during their updates. It seems like only yesterday (#2073) that I updated this.... * Add comment to url warning about mirror updates Add a comment to the download info warning to use a specific site rather than the mirror, to avoid wobbles during their asynchronous updates. * Fix typo ('to no' -> 'do not')	2016-11-04 23:14:48 -07:00
Axel Huebl	c3d9dda0e5	libSplash: Add 1.6.0 Release (#2244 ) * libSplash: Add 1.6.0 Release Add the latest release of libSplash, version 1.6.0. * Fix flake8 checks (another loop inversion issue)	2016-11-04 16:27:17 -07:00
Gregory Lee	ee6eb508cb	patch older config.guess for newer architectures (#2221 )	2016-11-04 12:12:37 -07:00
Jeffrey Salmond	472ad39db3	updates to matio package (#2243 ) * updates to matio package - update to a AutoTools package - add variants for hdf5 and zlib - add latest version * fix flake8 error	2016-11-04 11:56:47 -07:00
Jeffrey Salmond	f01b9797d7	opencoarrays package fixes and new version (#2239 ) * fix and simplify opencoarrays package using new CMakePackge methods * add new version	2016-11-04 11:50:25 -07:00
Jeffrey Salmond	a135a1245a	tweaks to packages using CMakePackage (#2241 ) * fix to trilinos package * fix to dealii package * fix to everytrace package * fix to everytrace-example package * changes suggested by @davydden	2016-11-04 10:57:53 -07:00
Denis Davydov	29f81b7775	trilinos: switch to CMakePackage and minor cleanup (#2226 )	2016-11-04 02:00:03 -07:00
Denis Davydov	453331dba0	dealii: switch to CMakePackage and minor cleanup (#2237 )	2016-11-04 01:46:39 -07:00
Pramod Kumbhar	b706da1109	Set TAU_MAKEFILE env variable (#2210 ) * In order to use TAU module, we have to set TAU_MAKEFILE env variable. * updated with suggestions from @citibeth	2016-11-02 15:05:47 -05:00
Sergey Kosukhin	8fb5cb2137	Added first version of the NCL package. (#2195 ) Without GRIB2 and HDF-EOS support yet.	2016-11-02 10:20:57 -05:00
Peter Doak	1aa5d4875e	Nmap package added (#2206 ) * works to build newest version of nmap with gcc@5.3.0 * formatting * clean up	2016-11-01 16:10:39 -07:00
Sergey Kosukhin	62eba4774d	Updated python package reflecting the changes in `9347f86`	2016-11-01 16:15:34 +01:00
Barry Smith	a714377123	python: PYTHONHOME may not be the same as the prefix of the python executable (#2173 ) On MacOS, brew installs /usr/local/bin/python but the Python prefix is not /usr/local/bin Use the python command sys.exec to get the correct directory, instead of the ad hoc self.prefix previously used This was a bear to debug; been driving me nuts since I started using spack. Since spack passes PYTHONHOME down to package builds in the environment it was passing PYTHONHOME of /usr/local/bin to the PETSc build that uses Python so the PETSc Python ./configure errored immediately with ImportError: No module named site since python could find no python modules. Todd Gamblin pointed out that my first try to fix this was wrong since it assumed the spack python was the same python used to run spack. Elizabeth Fischer suggested how to get it to work also with python3 Funded-by: IDEAS Project: IDEAS/xSDK Time: 7 hours Thanks-to: Todd Gamblin, Elizabeth Fischer	2016-10-30 17:13:16 -07:00
Gregory Lee	dbd9f1c5a1	updated gtk and gobject dependences (#2126 )	2016-10-30 11:50:36 -07:00
Adam J. Stewart	893b2e4f62	Update license directory for intel-paralel-studio (#2163 )	2016-10-29 14:30:00 -07:00
Joseph Ciurej	c82985cb5e	Update and Clean Up the Visit and VTK Packages (#2167 ) * Made some refactoring improvements to the 'visit' and 'vtk' packages. * Added a small fix for the 'vtk' package when building with 'qt+webkit'.	2016-10-28 17:59:21 -07:00
Adam J. Stewart	dd53ddb003	Add latest version of Intel Parallel Studio XE (#2151 )	2016-10-27 12:58:31 -07:00
Barry Smith	eb36b2a622	Get Trilinos 12.6.2 to build with Intel compilers and spack (#2102 ) Funded-by: IDEAS Project: IDEAS/xSDK Time: 2 hours	2016-10-26 21:52:29 -07:00
Axel Huebl	0007877944	libSplash: Add 1.5.0 Release (#2137 ) Add the latest release of libSplash, version 1.5.0.	2016-10-26 14:23:09 -07:00
Denis Davydov	46433b9eb3	require fortran for MPI providers to avoid delayed compiler errors (#1937 ) * openmpi: require fortran for now * mpich: requre fortran for now * mvapich2: require fortran for now * openmpi: flake8 fixes	2016-10-26 09:12:26 -07:00
Jim Galarowicz	92f17eeba7	Develop: Resolve issue 2070 with new depends_on clause in the openspeedshop package file. (#2136 ) * 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.	2016-10-26 08:37:02 -07:00
Denis Davydov	33fb7bbd1b	add a unit test for conretization with develop version (#2064 )	2016-10-26 01:49:52 -07:00
Denis Davydov	e65c9f6865	veclibfort: add new package (#2080 ) * veclibfort: add new package * veclibfort: add a small test	2016-10-26 01:49:06 -07:00
George Hartzell	89c1d361b2	Add package for ant (#2133 ) Add a package for ant, a java build tool.	2016-10-25 23:57:27 -07:00
George Hartzell	37dede3163	Add package for maven (#2132 ) Add a package that installed the pre-built maven distribution. I've given up, for now, on building maven from source. That processed stumbled on two points before I gave up: 1. It downloaded several hundred .{pop,jar} files and I despaired of figuring out some way of mirroring and checksumming them; and 2. It exploded complaining about too many unacceptable license files, which seems odd in its own source tree. Perhaps someone with more Java fu that I admit to can figure it out. In the meantime, this is useful.	2016-10-25 23:56:31 -07:00
Barry Smith	3de26ff3d7	openblas: Fixes to get OpenBLAS to install with Intel compilers (#2101 ) Funded-by: IDEAS Project: IDEAS/xSDK Time: 1 hour	2016-10-25 11:12:22 -07:00
Stephen Herbein	14e3a541e1	Add latest versions of Flux prerequisites (#2108 ) * libsodium: add latest versions, fix old versions older versions of libsodium were added to an "old" subdirectory * zeromq: add 4.1.4 prerequiste for the latest develop version of flux	2016-10-25 11:11:23 -07:00
Mayeul d'Avezac	65c250699f	pkg-config variant to use internal glib (#2104 ) Pkg-config depends on glib which depends on pkg-config. As a result, pkg-config used to build glib internally. However, this fails on Mac. Building pkg-config with an internal glib is now a variant, turned on by default, and required to build glib.	2016-10-25 11:08:32 -07:00
Adam J. Stewart	08300ccffb	Allow newer versions of GCC to compile older versions of GCC (#2107 ) * Add patch allowing GCC 6 to compile GCC 5 * Expand patch version range	2016-10-25 11:06:33 -07:00
George Hartzell	14ed97f219	Update cask to v0.8.1 (#2125 )	2016-10-25 10:58:50 -07:00
Adam J. Stewart	eeded917cd	Rename xpyb to py-xpyb (#2120 )	2016-10-25 10:10:16 -07:00
Mayeul d'Avezac	1928d83259	Tells boost explictly about python libraries and headers (#2106 ) * Tells boost explictly about libraries and headers Ideally, bjam would determine the libraries and headers from the executable. But it doesn't. This rigs a best guess for python libraries and headers. * Move glob import to top of file * variable name change: alllibs --> all_libs * Use dso suffix rather than hard-coded string * Use only MAJOR.MINOR when setting up python in bjam	2016-10-25 08:10:52 -07:00
Massimiliano Culpo	b27e78cd78	spack setup : fixed regression after #1186 (#2117 )	2016-10-25 07:53:11 -07:00
Denis Davydov	d7b624457f	gmp: fix a bug (#2114 )	2016-10-25 07:08:52 -07:00
Todd Gamblin	0f6a5cd385	Merge pull request #1186 from epfl-scitas/features/install_with_phases do_install : allow for an arbitrary number of phases	2016-10-24 17:13:49 -07:00
Todd Gamblin	c1ad4bde28	Rename EditableMakefile to MakefilePackage	2016-10-24 16:41:20 -07:00
Barry Smith	453ad8df9d	Get netlib-lapack to compile with Intel and add deprecated routines (#2103 ) Funded-by: IDEAS Project: IDEAS/xSDK Time: .4 hours	2016-10-24 14:25:59 -07:00
Mayeul d'Avezac	509bbd7067	Adds new versions to eigen (#2105 ) * Adds new versions to eigen * Reorder versions from oldest to newest	2016-10-24 11:09:17 -07:00
alalazo	7bd735416d	package.py : moved each specialized package to its own module file	2016-10-23 22:38:19 +02:00
alalazo	fa3f07c092	CMakePackage, AutotoolsPackage : added default behavior on check	2016-10-23 19:02:46 +02:00
alalazo	ebbbed166e	Merge branch 'develop' of https://github.com/LLNL/spack into features/install_with_phases_rebase	2016-10-23 13:35:12 +02:00
Barry Smith	9d3d492214	mumps: Add support for Intel compiler and insure both lapack and blas… (#2076 ) * mumps: Add support for Intel compiler and insure both lapack and blas libraries are passed to the examples Likely it was not discoverged before that the examples require both lapack and blas libraries because it was tested with Openblas which is one large library containing everything. Funded-by: IDEAS Project: IDEAS/xSDK Time: .3 hours * flake8 fix.	2016-10-22 15:57:44 -07:00
Joseph Ciurej	9f3a46c6c1	Add Package : OpenSceneGraph (#2075 ) * Created the initial version of the 'OpenSceneGraph' package. * Added 'zlib' as a dependency and linked it during the build step. * Fixed a few minor PEP8 style violations in the 'OpenSceneGraph' package. * Added cmake as a build dependency and improved the build procedure. * Made a few important argument updates to improve package compatibility. * Fixed up a few remaining style issues in the 'openscenegraph' package. * Added a description for the 'openscenegraph' package. * Fixed a bug that was causing some 'openscenegraph@3.2.3%gcc' installs to fail. * Fixed a number of small issues with the 'openscenegraph' package. * Removed a number of superfluous flags from the 'openscenegraph' install.	2016-10-22 15:14:29 -07:00
Jean-Paul Pelteret	7565f9dcdb	Add new package "gource" and dependencies "glew, sdl, sdl-image". (#2084 )	2016-10-22 14:28:59 -07:00
George Hartzell	cfbacdb41e	Updated the texlive digest value (#2073 ) The texlive tarball, install-tl-unx.tar.gz is unversioned and changes periodically. When it does, the digest needs to change too. This does that.	2016-10-21 16:57:42 -07:00
alalazo	482f60d1d3	packages : moved decorators into AutotoolsPackage and CMakePackage	2016-10-22 01:03:07 +02:00
Joseph Ciurej	6464d6682c	Update Package : Qt (Add 'WebKit' Support) (#1455 ) * Added the '+webkit' variant to the 'qt' package. * Made 'qmake' an available executable to 'qt' depdendents.	2016-10-21 14:13:56 -07:00
Matthew LeGendre	9f36ae4e20	Extend concretization test to excercise bug in concretize's provider sorting	2016-10-21 11:57:57 -07:00
Adam J. Stewart	52158d9316	Add new Version property to handle joined version numbers (#2062 ) * Add new version property to handle joined version numbers * Add unit test for new joined property * Add documentation on version.up_to() and version.joined	2016-10-21 07:49:36 -07:00
Adam J. Stewart	c513fd72fb	Add latest version of Armadillo (#2061 )	2016-10-21 07:39:48 -07:00
Massimiliano Culpo	aa86432ec6	patch directive : fixed retrieval from urls ( fixes #1584 ) (#2039 ) * patch directive : fixed retrieval from urls fixes #1584 - add support for 'gz' archives - fixed bugs with URL patches - updated nwchem * patch directive : added checksum to UrlPatch - refactored classes in patch.py - updated nwchem * patch directive : added caching	2016-10-21 07:32:52 -07:00
alalazo	213e3f0860	Merge branch 'develop' of https://github.com/LLNL/spack into features/install_with_phases_rebase Conflicts: lib/spack/spack/cmd/install.py lib/spack/spack/cmd/setup.py	2016-10-21 12:38:43 +02:00
Matthew LeGendre	8de143a994	Fixes needed to build gcc on Linux/ppc64le (#2057 ) * Fixes needed to build gcc on Linux/ppc64le * flake8 fix.	2016-10-19 23:29:59 -07:00
George Hartzell	027632cbac	Fix cdd package definition, dotted is a property (#2054 ) Things that accessed the cdd package, such as `spack info cdd run tripped over a buglet in the cdd package, causing them to exit with something like this: ``` Caused by: TypeError: 'str' object is not callable File "/rss/spack/lib/spack/spack/repository.py", line 584, in get self._instances[key] = package_class(copy) File "/rss/spack/lib/spack/spack/package.py", line 398, in __init__ f = fs.for_package_version(self, self.version) File "/rss/spack/lib/spack/spack/fetch_strategy.py", line 852, in for_package_version attrs['url'] = pkg.url_for_version(version) File "/rss/spack/var/spack/repos/builtin/packages/cdd/package.py", line 40, in url_for_version str(version.dotted()).replace('.', '')) ``` @tgamblin pointed out that `dotted` is a property, not a functin call and that the parentheses are therefor inappropriate. This deletes the parentheses. `spack info cdd` now works for me.	2016-10-19 12:28:26 -07:00
George Hartzell	dbbef6ba23	Add package for htop (#2051 ) Add package for htop, an interactive text-mode process viewer for Unix systems. Think top, with pretty colors and dyanmic bar graphs. More info [here](https://github.com/hishamhm/htop).	2016-10-19 10:33:49 -07:00
Denis Davydov	0e59ade030	petsc: minor fixes... (#2036 ) * petsc: require boost for :3.5 only * petsc: turn off download for c2html and hwloc	2016-10-18 08:09:18 -07:00
Eric	306eea5e59	Support for bazel (#2023 ) * Add package bazel * Add support for bazel-based builds	2016-10-18 07:46:42 -07:00
Denis Davydov	4c2af4f888	superlu-dist: add 5.1.0 and 5.1.1 (#2038 )	2016-10-18 07:45:48 -07:00
Denis Davydov	dd28f5b5eb	mumps: add 5.0.2 (#2041 )	2016-10-18 07:38:30 -07:00
Denis Davydov	5f20c43315	hypre: add 2.11.1 (#2040 )	2016-10-18 07:38:15 -07:00
Jim Galarowicz	87adcfeea8	Update the Krell Institute products to use the latest features of spa… (#1984 ) * 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.	2016-10-17 01:18:30 -07:00
Pramod Kumbhar	b5e20018b5	fix download url for paraver (#2033 ) * fix download url for paraver * added note to remove older version	2016-10-17 01:17:01 -07:00
Pramod Kumbhar	e93c9060f5	fix sqlite download url (#2031 )	2016-10-15 16:31:23 -07:00
Elizabeth Fischer	3dbde09747	Workaround for illegal package merging in py-matplotlib/py-basemap (#1964 ) * Workaround for illegal package merging in py-matplotlib/py-basemap # Conflicts: # var/spack/repos/builtin/packages/py-basemap/package.py * flake8 * flake8 * Be conservative: only apply the namespace package fix for Python >= 3.5.2 * flake8 * Bug fix	2016-10-14 16:09:54 -07:00
Adam J. Stewart	fbe9142b7e	Fix list_url for fish shell (#2022 )	2016-10-14 12:46:59 -07:00
John Finigan	4be224238e	py-macs2: New package (#2011 ) * py-macs2: New package * py-macs2: add py-numpy@1.6: dependency	2016-10-14 12:00:56 -07:00
Kelly Thompson	e359a7ca59	Add missing 'import os'. (#2012 )	2016-10-14 12:00:43 -07:00
Denis Davydov	48f23aadbe	dealii: remove extra test which are now mostly integrated in make test (#2013 )	2016-10-14 09:49:31 -07:00
Denis Davydov	0d89e5e32b	Package/petsc slepc new versions (#2019 ) * petsc: add 3.7.4 * slepc: add 3.7.3	2016-10-14 08:25:22 -07:00
Elizabeth Fischer	b27f4e3aeb	py-matplotlib: Add variants for optional dependencies. (#2008 )	2016-10-12 14:55:38 -07:00
Elizabeth Fischer	67ef6df4db	Made optional CGAL dependencies optional. (#2006 ) * Made optional CGAL dependencies optional. * cgal: Added note explaining that the CORE library is not the same as core CGAL functionality. * Bug fix and flake8 * flake8	2016-10-12 13:02:06 -07:00
Ben Boeckel	b369be65d7	Mock up Xcode devdir to make Qt5 work on Mac OS X (#1832 ) * build_environment: allow compilers to set up an environment * clang: mock up a toolchain directory for xcode Some projects ignore CC and CXX flags and instead use xcode to find the toolchain. Clang on Apple should set up the environment properly. Arguably, every compiler could do this on Apple, but let's see how this works out just for AppleClang for now. The Documentation directory is ~1.7G and the excluded platforms add up to about 7G. Ignoring swift saves another 500M. The resulting Xcode.app copy is in the 2G range. * compiler: set member variables early This is required so that later methods can query things such as the version of the compiler. * compiler: support finding the real path of the compiler On Apple, the /usr/bin compilers are actually wrapping tools themselves which query xcrun for the currently selected Xcode installation. Pierce this veil and get the real, full path the to underlying compilers instead. * icu4c: install with rpath On macOS, icu installs with a library ID of the library name. Enabling rpath makes its ID its full installed path which lets Qt5 link against it successfully. * qt: no -no-gtkstyle flag on Qt5 on macOS	2016-10-12 09:58:12 -07:00
Todd Gamblin	488e1bab2c	Make `insecure` option work with curl AND git. (#1786 )	2016-10-11 23:13:40 -07:00
Elizabeth Fischer	a6f85f51d0	patchelf: Add version (#1540 ) * patchelf: Add version * flake8 * Removed unnecessary url_for_version() function. * Restored old URL	2016-10-11 23:11:25 -07:00
Denis Davydov	025b914079	oce: fix for Sierra (#1934 )	2016-10-11 23:10:51 -07:00
gmatteo	949766d92e	Abinit: Added package(s) (#1995 ) * First version of Abinit package * Ignore .swp files Add libxc, etsf_io packages * AtomPaw package * Make Abinit depend on mpi@2: and external version of libxc, netcdf, hdf5, etsf_io * etsf_io: install Fortran modules in prefix.include * Remove etsf_io from abinit requirements * Add libxc2.2.1 (required by Abinit and atompaw) * Cleanup * Run make check * Cleanup * Use ld_flags instead of hard-coded libs, fix pep8, add copyright * Put scalapack before lapackblas	2016-10-11 15:22:46 -07:00
Joseph Ciurej	37d125b890	Update Package : ExodusII (#1504 ) * Added support for the 'maxdims' and 'maxvars' flags for 'NetCDF'. * Added the '+mpi' variant and improved dependencies for 'exodusii'. Improved the 'exodusii' package so that it's less reliant on patches. * Added better type checking to variant values in the 'netcdf' package. * Corrected the required CMake version for the 'exodusii' package. * Fixed the dependencies of the '+mpi' variant of the 'exodusii' package.	2016-10-11 14:53:02 -07:00
Adam J. Stewart	6dc8bbcb3a	Package all of Xorg/X11/XCB (#1740 ) * Updates to Mesa and other Xorg packages * Add packages for all Xorg Protocol extensions * Add packages for first half of Xorg libraries * Add packages for remaining Xorg libraries * Add packages for all Xorg utilities * Add packages for Xorg documentation tools * Add build deps to Xorg protocol headers * Add packages for XCB * Add build deps to Xorg libraries * Add build deps to Xorg utilities * Add packages for Xorg fonts and font-related utilities * Change font deptype from build to default I wasn't sure which deptype was appropriate at first since none of the packages are actually linked together. I initially chose the build deptype for this reason. However, the font packages don't install into their own prefix. They install into font-config. If font-config is a build dependency, that means you can uninstall it without uninstalling the font packages, which wouldn't make sense since they install into font-config. So I switched them back to the default deptype. * Minor formatting changes to ncview * Add half-way done xorg-server package * Add packages for Xorg test suites, not yet tested! * Add packages for Xorg data * Add first quarter of Xorg apps * Add more packages for Xorg apps * Add dependencies to mesa * Remove comments from mesa package * Flake8 * Add more packages for Xorg apps * Add more packages for Xorg apps * Add more packages for Xorg apps * Add more packages for Xorg apps * Add more packages for Xorg apps * Add package for Sublime Text * Add packages for remaining Xorg apps * Revisit testing packages, add missing dependencies * Add dependencies, clean up FIXMEs	2016-10-11 09:42:20 -07:00
alalazo	c7a5dd36e2	qa : flake8 issues	2016-10-11 16:30:06 +02:00
alalazo	ab995df777	Merge branch 'develop' of https://github.com/LLNL/spack into features/install_with_phases_rebase Conflicts: lib/spack/spack/build_environment.py lib/spack/spack/cmd/install.py lib/spack/spack/cmd/setup.py lib/spack/spack/package.py var/spack/repos/builtin/packages/gmp/package.py var/spack/repos/builtin/packages/hdf5/package.py	2016-10-11 16:28:08 +02:00
Denis Davydov	4d939802ae	hypre: fix blas/lapack for MKL (#1993 )	2016-10-11 06:48:16 -07:00
Todd Gamblin	1dff309a3f	Merge pull request #1989 from KineticTheory/cray_compile_wrappers On Cray machines, use the Cray compile wrappers instead of MPI wrappers.	2016-10-11 06:46:29 -07:00
Adam J. Stewart	aa079dbdf1	Add variant to MPICH to enable ROMIO support (#1944 )	2016-10-11 02:16:01 -07:00
Denis Davydov	49aed3969c	tethex: add a new package (#1991 )	2016-10-11 02:13:25 -07:00
Adam J. Stewart	5988b3a222	More specific dependency versions, wrap make check (#1962 )	2016-10-11 01:36:40 -07:00
Sergey Kosukhin	7fd639d6fc	Update libjpeg-turbo: added new version and removed redundant dependency. (#1897 )	2016-10-11 01:32:05 -07:00
Denis Davydov	6c250ab486	pango: add missing dependency (#1958 )	2016-10-11 01:19:44 -07:00
Denis Davydov	907546b55e	libcerf: fix for modern clang (#1959 )	2016-10-11 01:19:12 -07:00
scheibelp	9e7f53a35a	[WIP] Use boost system layout by default (#1955 ) Use boost system layout by default	2016-10-11 01:17:26 -07:00
Erik Schnetter	f555b8110d	Charm++: Ignore compiler warnings while configuring (#1981 )	2016-10-11 00:45:01 -07:00
Kelly Thompson	1891ce3545	Trilinos: Use more flexible option for locating the BLAS library directory. (#1987 ) + This change fixes a problem that manifests when trilinos is built against a MKL installation defined as an external package. In this scenario, the MKL libraries are found one directory deeper than for the case where spack provides MKL. The extra directory is a platform name like 'intel64'. + The changes in this PR were recommended by contributor @davydden. I implemented and tested with intel@16.0.3. These changes fix the issue I reported. I did not attempt building trilinos against other BLAS implementations. + fixes #1923	2016-10-11 00:42:59 -07:00
Pramod Kumbhar	afd5d6b5cd	hpx5 version update (#1967 )	2016-10-11 00:36:31 -07:00
Geoffrey Oxberry	9a05ffea27	Mfem 3.2 (#1202 ) * mfem: add tarball extension Add tarball extension as a result of a feature added in PR#1926, which fixes earlier issues in this PR (PR#1202). Prior to adding this feature, Spack would not autodetect the extension of the tarball downloaded from the redirected, shorted Google URL, requiring a messy hack. This hack worked for mfem version 3.1, but led to errors when adding mfem version 3.2 because the files downloaded from Google did not contain the package name, version number, or extension. Adding the extension enables Spack to rename the tarball downloaded from Google to a sensible name that is compatible with its filename parsing algorithms so that Spack "does the right thing" (detects that the file is a GZipped tarball, decompresses it, runs GNU Make) in fetching and staging the package. * mfem: add linkage to KLU & BTF Add linkage to the KLU & BTF solvers, which are now enabled in MFEM for versions 3.2 and later. * mfem: Add superlu-dist variant Add linkage to SuperLU_DIST, which is a new linear solver interface for MFEM versions 3.2 and later. * mfem: add netcdf variant for cubit mesh support Add NetCDF variant for MFEM versions 3.2 and later; installing the NetCDF interfaces enables CUBIT mesh support.	2016-10-11 00:33:26 -07:00
Kelly (KT) Thompson	3553c8b9e9	On Cray machines, use the Cray compile wrappers instead of MPI wrappers. + Cray compile wrappers are MPI wrappers. + Packages that need to be compiled with MPI compile wrappers normally use 'mpicc', 'mpic++' and 'mpif90' provided by the MPI vendor. However, when using cray-mpich as the MPI vendor, the compile wrappers 'CC', 'cc' and 'ftn' must be used. + In this scenario, the mpich package is hijacked by specifying cray-mpich as an external package under the 'mpich:' section of packages.yaml. For example: packages: mpich: modules: mpich@7.4.2%intel@16.0.3 arch=cray-CNL-haswell: cray-mpich/7.4.2 buildable: False all: providers: mpi: [mpich] + This change allows packages like parmetis to be built using the Cray compile wrappers. For example: 'spack install parmetis%intel@16.0.3 ^mpich@7.4.2 os=CNL' + This commit relies on the existence of the environment variable CRAYPE_VERSION to determine if the current machine is running a Cray environment. This check is insufficient, but I'm not sure how to improve this logic. + Fixes #1827	2016-10-10 19:10:26 -06:00
Kelly Thompson	29fc9cd22c	Update package to use MPI compile wrappers as specified in MPI package. (#1985 ) + Previouly, these strings were hard coded to 'mpicc', 'mpic++', and 'mpifort'.	2016-10-10 15:33:00 -07:00
Denis Davydov	c2ca8693e9	fix blas-lapack in scipy and numpy (#1949 ) * fix blas-lapack in scipy and numpy * py-numpy: do not set rpath on macOS * py-scipy: do not set Blas/Lapack. This appears to be picked up from py-numpy * py-numpy: don't write rpath= in Sierra only * py-numpy: add a link to build notes	2016-10-10 12:38:44 -07:00
Erik Schnetter	377ac68690	Correct Charm++ install procedure (#1957 ) Charm++ only creates symbolic links instead of copying files. Correct this.	2016-10-10 09:13:20 -07:00
Jean-Paul Pelteret	d3daa829f0	Added symengine and associated packages (#1885 ) Symengine and associated packages	2016-10-07 22:45:24 -07:00
Todd Gamblin	dbc864c9db	Restore default RPATH settings but allow packages to limit to immediate deps. (#1954 ) - Some packages (netcdf) NEED RPATHs for transitive deps. - Others (dealii) will exceed OS limits when the DAG is too large.	2016-10-06 15:57:23 -07:00
Denis Davydov	9683e0df07	atlas: add 3.10.3 (#1952 )	2016-10-06 15:23:18 -07:00
Joseph Ciurej	82fcc5e1de	Feature Proposal : Make All Python Extensions User Configuration Independent (#1435 ) * Updated all Python extension packages to use 'setup_py' on install. * Fixed a few minor style issues with the updated Python packages.	2016-10-06 14:43:49 -07:00
Sergey Kosukhin	ebef9628a3	Update gmp: fixed an issue with intel compiler. (#1898 )	2016-10-06 12:49:03 -07:00
Jay	6e9353f1a8	Updated nettle to have m4 as an immediate dependency (#1946 ) * Updated nettle to have m4 as an immediate dependency to match new PATH construction logic which only includes immediate dependencies. * Update package.py	2016-10-06 11:50:50 -07:00
James Wynne III	7dc11472bf	Sqlite ppc64le configure build guess fix (#1684 ) * Added check for ppc64le because configure cant guess the build type for rhel on ppc64le Expand/clarify description of dependency types Refactored getting the arch so that its less verbose * Fixed flake8 issues	2016-10-06 02:48:05 -07:00
Sergey Kosukhin	92ca6d6423	Update pixman: mmx is disabled only for MacOS. (#1896 )	2016-10-06 02:43:34 -07:00
Sergey Kosukhin	4cce23ea89	Update libtiff: updated homepage and fetch urls. (#1895 ) * Update libtiff: updated homepage and fetch urls. * Update libtiff: new version 4.0.6.	2016-10-06 02:43:23 -07:00
Elizabeth Fischer	264604df3e	cgal: build out of source. (#1918 ) * cgal: build out of source. * Simplify cmake out-of-source.	2016-10-06 02:36:27 -07:00
Jeffrey Salmond	a648dc6b33	add python options to vtk package (#1931 )	2016-10-06 02:29:25 -07:00
Elizabeth Fischer	2966f174ae	mumps: Add alternate download location (in comments) (#1919 )	2016-10-05 23:15:38 -07:00
Adam J. Stewart	6ee020cea4	Add package for CONVERGE CFD (#1905 )	2016-10-05 10:37:50 -07:00
Adam J. Stewart	95b07c365c	Add latest versions, resolve variant resolution bug (#1909 )	2016-10-05 10:37:35 -07:00
Elizabeth Fischer	42c69b3809	everytrace: New package (#1543 ) * everytrace: New package Everytrace ensures that stack trace is obtained every time a program exits, for whatever reason. * everytrace: Change CMake to build dependency * Renamed to everytrace-example, flake8 and copyright issues. * flake8 * Missing type=build	2016-10-05 10:03:05 -07:00
Adam J. Stewart	d5e5e4ed1a	Add missing dependencies for Flake8 (#1883 ) * Warn user if flake8 can't find setuptools * Add missing dependencies of flake8 * Updates to py-autopep8, make packages activateable * Check for presence of setuptools for Sphinx too * Fix bug in order of commands	2016-10-05 10:00:31 -07:00
Elizabeth Fischer	42a60b2434	Added copyright and build deps specification; should be ready to merge.	2016-10-05 12:14:08 -04:00
Axel Huebl	ac3e21f8d4	PNGwriter, libSplash: Add `master` version (#1744 ) * PNGwriter, libSplash: Add `master` version * PNGwriter, libSplash: Add `dev` versions Can be used for now, `develop` is currently discouraged.	2016-10-05 06:46:20 -07:00
Denis Davydov	4e5d340665	boost: set 1.61 as preffered until 1.62 is fixed (#1908 )	2016-10-05 05:16:06 -07:00
alalazo	7a26c60dbd	Merge branch 'develop' of https://github.com/LLNL/spack into features/install_with_phases_rebase Conflicts: lib/spack/spack/cmd/setup.py lib/spack/spack/package.py var/spack/repos/builtin/packages/gmp/package.py	2016-10-05 09:33:59 +02:00
Pramod Kumbhar	9daafc32f1	Packages for Darshan I/O performance characterization tool from ANL (#1900 )	2016-10-04 14:40:35 -07:00
Adam J. Stewart	7806fded3e	Update documentation URL after switch to readthedocs (#1901 )	2016-10-04 11:47:25 -07:00
Sergey Kosukhin	1d981ebd50	A set of tools used in climate modeling and numerical weather prediction. (#1317 ) * Update grib-api: switched to cmake building system. * Update harfbuzz: added pkg-config dependency. * Update pango: added pkg-config dependency. * Add libemos package. * Add Magics (from ECMWF) package. * Revert "Variant for building cdo without mpi (#1638)": CDO does not use MPI. This reverts commit `079d063c6d`. * Update CDO package: full featured implementation. * Update magics: added python as build dependency. * Update cdo: added disabling configuration options.	2016-10-04 09:29:22 -07:00
Ivo Jimenez	d36028cff4	Adds mpip package (#1886 )	2016-10-04 01:30:52 -07:00
Ivo Jimenez	2c701d372e	Adds lulesh package (#1887 )	2016-10-04 01:28:23 -07:00
Pramod Kumbhar	e546d6246f	Spack package for HPCToolkit (#1892 ) * Spack package for HPCToolkit (performance analysis tool) * Correction for PR comments, make flake8 happy * update note / comments	2016-10-04 01:02:50 -07:00
Massimiliano Culpo	50fcade81b	cp2k : added support for libint, fixed compilation issues on elpa (#1889 )	2016-10-03 08:25:36 -07:00
Geoffrey Oxberry	df79ba0dcf	gcc: fix darwin dispatch/object.h header issue (#1518 ) Fixes #1203. Apple ships headers in Yosemite (and possibly earlier) that are gcc-incompatible, but compile fine with clang. The fix is to copy the offending system header from /usr/include/${REST_OF_HEADER_PATH} to ${GCC_PREFIX}/include/${REST_OF_HEADER_PATH} and replace the non-gcc- compatible features with gcc-compatible equivalents. See https://github.com/hashdist/hashstack/pull/771/files for inspiration, and http://hamelot.io/programming/osx-gcc-dispatch_block_t-has-not-been-declared-invalid-typedef/ for a description of the header issue.	2016-10-02 18:54:43 -07:00
Nicolas Richart	16f99bd0b2	Adding latest version of fenics (#1528 ) * Adding last version of fenics and making trilinos not ambiguous on hdf5 * forcing fenics to ignore hdf5 cxx * Adding deptypes and correcting the hdf5 patch * flake8 corrections * cleaning some useless code	2016-10-02 18:51:34 -07:00
Kelly Thompson	621a4d637d	Provide newer versions of llvm (3.8.1, 3.9.0) (#1765 ) * Provide new versions of llvm. + Provide file list and md5 hashes for 3.8.1 and 3.9.0. + Clean up indentation for the 'releases' data structure to improve consistency. * Adding a block of code to the 'resources' structure for cfe. * Merge cfe and clang resources into single entity.	2016-10-02 18:50:42 -07:00
Alfredo Adolfo Gimenez	1ea9582218	Added hadoop, spark, and variant spark+hadoop (#1833 ) * Added hadoop, spark, and variant spark+hadoop * Docstrings, dependency types, urls, copyright * Flake8 fixes, link dependency for hadoop * Build type for spark, env problem setting JAVA_HOME	2016-10-02 18:49:30 -07:00
Erik Schnetter	b22956bab2	git: Don't link against -lrt on Darwin (#1877 ) There is no librt on Darwin, and it's not necessary either.	2016-10-02 18:37:45 -07:00
Erik Schnetter	28b48f3e1a	Update PAPI to 5.5.0 (#1878 )	2016-10-02 18:37:26 -07:00
Erik Schnetter	b2ff9dbcd4	Update tmux to 2.3.0 (#1879 )	2016-10-02 18:37:17 -07:00
Kelly Thompson	051c5dbc27	New package: libquo (#1880 ) * New package: libquo libquo is a high-level, easy to use programming interface tailored specifically for MPI/MPI+X codes that may benefit from evolving process binding policies during their execution. QUO allows for arbitrary process binding policies to be enacted and reverted during the execution of an MPI/MPI+X application as different computational phases are entered and exited, respectively. https://github.com/losalamos/libquo * Remove use of 'which' and fix style non-conformance.	2016-10-02 18:36:48 -07:00
Bruno Turcksin	e854e053e4	Add boost 1.62.0 (#1882 )	2016-10-02 18:36:31 -07:00
Jean-Paul Pelteret	c86d4c8920	Added bash-completion package (#951 )	2016-10-02 17:50:39 -07:00
Pramod Kumbhar	4b34ba1035	pdt url change to download full installer tarball (#1881 )	2016-09-30 14:31:28 -07:00
Pramod Kumbhar	6c627dbac9	Add cube variant for building GUI component with qt, parallel built supported (#1525 )	2016-09-29 15:37:35 -04:00
Pramod Kumbhar	6ec46ca802	updated to latest available package and fixed installation issue (old packages are no longer available for download) (#1523 )	2016-09-29 15:37:07 -04:00
Mitchell Devlin	86cad961e5	added libxstream (#1454 )	2016-09-29 15:36:37 -04:00
Adam J. Stewart	deb1cb4805	Add libint package (#1264 ) * Add libint package * Add Intel optimization flags recommended by CP2K * Add new version and Intel compiler optimization flags for libxc * Add older version of libint * Libint depends on GMP C++ library	2016-09-29 15:35:10 -04:00
Robert D. French	a77b48f491	Library for manipulating grib1 and grib2 files (#1736 ) Pro tips from @adamjstewart: * line too long in package description * name it grib-api instead of grib_api * depend on netcdf without reference to unnecessary constraints	2016-09-28 17:02:29 -04:00
Elizabeth Fischer	3352889d73	py-pil: Protect against building with Python3. (#1868 ) * py-pil: Does not build with Python3. * Set py-pillow to be the default pil provider * Update package.py * Change to comments requested by adamjstewart * Remove version constraint from extends(), avoid a Spack bug.	2016-09-28 16:51:41 -04:00
Erik Schnetter	4040792501	Update Qthreads to 1.11 (#1863 )	2016-09-28 15:22:02 -04:00
Todd Gamblin	295742e2b5	Fixes #1860 . Subversion builds sequentially due to race.	2016-09-28 15:18:52 -04:00
Robert D. French	fea0a74bec	vim8 is out! (#1753 ) * depends on ncurses for 8.0 or higher	2016-09-28 15:17:15 -04:00
Adam J. Stewart	66c2ac0bc9	Tell Mercurial where to find CA certs (#1873 )	2016-09-28 14:58:51 -04:00
Adam J. Stewart	9b575dd976	Various updates to scipy and numpy (#1856 )	2016-09-27 10:56:24 -04:00
Michael Kuhn	00b3aa77ae	Update cdo to 1.7.2 (#1858 )	2016-09-27 10:56:04 -04:00
Erik Schnetter	88af9f783d	Make PETSc build on Darwin (#1835 ) Don't set cpp when building on Darwin.	2016-09-26 10:38:02 -07:00
Erik Schnetter	3282eaea8d	Update OpenSSL (#1853 )	2016-09-26 10:37:40 -07:00
Denis Davydov	1e10309ff7	some fixes to blas/lapack usage in packages (#1852 ) * atlas: fix unit test * openblas: remove symlinks; use lapack_libs.ld_flags in the test * mkl: fix openmp variant of blas/lapack libs * intel-parallel-studio: fix openmp variant of blas/lapack libs * netlib-scalapack: fix blas/lapack for multilib case (e.g. mkl) * arpack-ng: fix blas/lapack for multilib case (e.g. mkl) * petsc: explicitly specify blas/lapack * minor * cantera: fix blas/lapack usage * ipopt: fix blas/lapack usage * netlib-lapack: fix external blas usage * mfem: fix lapack/blas usage * superlu-mt: fix blas usage * flake8 fixes	2016-09-26 10:37:23 -07:00
Todd Gamblin	cb36aadaf6	Fix doc bugs, widen columns in the package list	2016-09-23 18:07:33 -07:00
Patrick Gartung	ec91152a36	a few package used in HEP including ROOT6	2016-09-23 18:07:22 -07:00
Adam J. Stewart	64194a823a	Remove duplicate ICU package (#1837 ) * Remove duplicate ICU package * Ignore deleted files during flake8 tests * Rename Boost ICU variant	2016-09-23 14:16:59 -07:00
Denis Davydov	6ef6428331	m4: fix compilation on Sierra with GCC (#1844 ) * m4: fix compilation on Sierra with GCC * m4: check macOS version	2016-09-23 13:38:29 -07:00
Bruno Turcksin	98d54182d3	Add Trilinos 12.8.1 (#1843 )	2016-09-23 13:36:21 -07:00
Erik Schnetter	73ec2a27d0	Don't require git for Julia @0.5: (#1834 )	2016-09-23 13:35:12 -07:00
Erik Schnetter	8147a09489	Update jemalloc to 4.2.1 (#1839 )	2016-09-23 13:32:57 -07:00
Robert D. French	3d282b9239	Add libmesh, needed for some FEM applications (#1846 )	2016-09-23 13:26:27 -07:00
Denis Davydov	df5e151049	hypre: fix a bug with blas/lapack names (#1841 )	2016-09-23 10:06:18 -07:00
Erik Schnetter	c0ebbc97c9	Update OpenSSL (#1836 ) This is a security update with priority "HIGH".	2016-09-23 08:21:15 -07:00
Denis Davydov	462a4a1353	boost: fix a bug which broke it on macOS with clang+gfortran (#1816 ) * dealii: add missing python dependency * boost: fix a bug which broke it on macOS with clang+gfortran Boost was using gcc compiler instead of clang++, which lead to cryptic Undefined symbols linking errors for boost::python::objects::function_object() when building other packages against boost+python. * boost: add exceptions for intel * boost: use spack_cxx	2016-09-22 13:47:22 -07:00
Adam J. Stewart	a638b62ab1	Updates to CGAL and ICU4C packages (#1828 )	2016-09-22 11:50:50 -07:00
Elizabeth Fischer	64c3b11478	suitesparse: Added +fpic (for linking with shared libraries) (#1542 )	2016-09-22 11:03:49 -07:00
Erik Schnetter	7ad6c35627	New package "charm" for the Charm++ parallel programming framework (#1766 )	2016-09-22 00:48:00 -07:00
Massimiliano Culpo	d848559f70	Reworking of `lapack_shared_libs` and similar properties (#1682 ) * Turned <provider>_libs into an iterable Modifications : - added class LibraryList + unit tests - added convenience functions `find_libraries` and `dedupe` - modifed non Intel blas/lapack providers - modified packages using blas_shared_libs and similar functions * atlas : added pthread variant * intel packages : added lapack_libs and blas_libs * find_library_path : removed unused function * PR review : fixed last issues * LibraryList : added test on __add__ return type * LibraryList : added __radd__ fixed unit tests fix : failing unit tests due to missing `self` * cp2k and dependecies : fixed blas-lapack related statements in package.py	2016-09-21 12:27:59 -07:00
Todd Gamblin	6b6f868f2a	Flake8 fixes.	2016-09-21 04:35:15 -07:00
Todd Gamblin	786ab114b7	Merge branch 'qt-osx' of git://github.com/mathstuf/spack into mathstuf-qt-osx	2016-09-21 04:32:03 -07:00
George Hartzell	51d869493a	Add package for bedtools2 (#1572 ) Add package for bedtools2, with support for v2.25.0 and v2.26.0.	2016-09-21 04:23:03 -07:00
George Hartzell	db0baaafe3	Add package for bamtools (#1571 ) bamtools provides a C++ API & command-line toolkit for working with BAM data.	2016-09-21 04:22:55 -07:00
Mayeul d'Avezac	3d1c92e22c	Update espresso recipe to track change in spack internals (#1734 )	2016-09-21 04:18:35 -07:00
Adam J. Stewart	cf925ddc97	Add missing build dependencies to hdf package (#1812 )	2016-09-21 04:16:57 -07:00
Kelly Thompson	3d3614e522	Update to allow netlib-scalapack to build against netlib-lapack. (#1539 )	2016-09-21 04:10:30 -07:00
Glenn Johnson	c1284a9046	Stop python from linking with system ncurses (#1672 ) Python will look to link with libncursesw in preference to libncurses. Since ncurses in spack is built without suffixes there is no libncursesw and python will link to the system libncursesw for _curses.so and _curses_panel.so, as well as libpanelw for _curses_panel.so. This PR introduces a patch that simple removes the check for ncursesw in setup.py and therefore sets `curses_library` to `ncurses`.	2016-09-21 04:02:28 -07:00
Glenn Johnson	851b58248d	Build pkg-config files for ncurses (#1673 )	2016-09-21 04:02:07 -07:00
Glenn Johnson	73012ec4c8	Rework libgd package (#1679 ) * Added missing libtiff dependency * added dependency on fontconfig * Added version 2.2.3 * use autotools rather than cmake The cmake build was not producing a complete install. * There was no versioning of the installed libraries. * gdlib-config was missing * pkgconfig directory was missing These problems do not happen when built with autotools.	2016-09-21 01:56:20 -07:00
Todd Gamblin	ae6252ca5f	Merge branch 'efischer/160914-FixBinutils226Question' of git://github.com/citibeth/spack into bugfix/efischer-160914-FixBinutils226Question	2016-09-21 01:45:38 -07:00
Axel Huebl	d3e04b3daf	Close #1683 Apply ADIOS 1.10.0 Patch (HDF5 1.10+) (#1699 ) * Close #1683 Apply ADIOS 1.10.0 Patch Also correct version dependencies and comments. * Clean Up ADIOS - add develop - simplify HDF5 options (parallel only) - remove optional netCDF (not fully v4)	2016-09-21 00:55:54 -07:00
Massimiliano Culpo	3254d2f8f9	cp2k : added dependencies (#1724 ) * wannier90 : added package (#24) * wannier90 : added package * cp2k : added dependency on wannier90 * elpa : updated package, added cp2k dependency (#26) Conflicts: var/spack/repos/builtin/packages/elpa/package.py	2016-09-21 00:53:06 -07:00
Alfredo Adolfo Gimenez	02307cf7ce	Set JAVA_HOME on module load and on dependent installs. (#1716 ) * Set JAVA_HOME on module load and on dependent installs. * Include environment setup from dependencies in dependee module (#1714)	2016-09-21 00:52:09 -07:00
Massimiliano Culpo	1cc48bf7d7	grackle : added package (#1725 ) Modifications : * grackle : added package * grackle : added version 2.2	2016-09-21 00:51:49 -07:00
Erik Schnetter	3c7ea3000a	Wrap yt package (#1751 ) yt is a python package for analyzing and visualizing volumetric, multi-resolution data from astrophysical simulations, radio telescopes, and a burgeoning interdisciplinary community.	2016-09-21 00:37:46 -07:00
Sergey Kosukhin	746495896c	Qt library: added variant to enable/disable compilation of examples (#1763 )	2016-09-21 00:25:14 -07:00
Patrick Gartung	e6dc448f18	Compiling python with gnu c++ on macos fails with toolboxglue enabled.	2016-09-20 23:34:15 -07:00
Gregory L. Lee	25ee9456f5	added STAT release 3.0.0	2016-09-20 16:09:31 -07:00
Erik Schnetter	ef1f441424	Julia: Add version 0.5.0 (#1809 )	2016-09-20 12:40:58 -07:00
Adam J. Stewart	db483e77e4	Remove url_for_version as it breaks spack info (#1503 )	2016-09-20 10:17:51 -07:00
Joseph Ciurej	7f9e89eb53	Update Package: Git-LFS (#1769 ) * Fixed a few small bugs in the 'git-lfs' install script. * Fixed a bug in the '(go\|go-bootstrap)@1.4.2+test' install scripts. * Fixing a minor style issue in the 'git-lfs' install script.	2016-09-20 10:08:25 -07:00
Erik Schnetter	00bac8f294	PETSc: Explicitly point to cpp when configuring (#1807 ) I encountered an HPC system where PETSc's configure stage does not find a valid `cpp` (C preprocessor). Explicitly pointing to Spack's `cpp` wrapper resolves the problem.	2016-09-20 10:05:57 -07:00
Adam J. Stewart	f180d748be	Remove lingering boilerplate FIXMEs (#1756 )	2016-09-20 08:01:55 -07:00
Joseph Ciurej	2cbae1d691	Update Package: Metis (#1783 ) * Fixed a bug that was causing post-install METIS tests to fail. * Improved the patching procedure used in the 'metis' install script. * Enabled patch skipping for the 'metis' and 'parmetis' packages. * Fixed some minor style issues in the 'parmetis' package. * Improved the 'metis' test fix and added 'run_tests' support.	2016-09-20 02:48:31 -07:00
Robert D. French	5c11fe88df	Add UberFTP utility (#1780 )	2016-09-20 02:47:10 -07:00
Denis Davydov	1565a643bd	dealii: add 8.4.2 (#1782 )	2016-09-20 02:46:57 -07:00
Bruno Turcksin	20fcd3f1dd	Add Python support to gdb. (#1790 )	2016-09-20 02:46:30 -07:00
Joseph Ciurej	e73a7c80bf	Update Package : Zoltan (#1793 ) * Refactored and reorganized the 'zoltan' install script. * Fixed a few bugs with the '+mpi' and '+fortan' variants of 'zoltan'. * Reintroduced and improved the '+shared' variant for the 'zoltan' package. * Improved compatibility with different MPI providers for 'zoltan'.	2016-09-20 02:46:13 -07:00
Tom Merrick	d71f8dcab5	samtools could not find the ncurses library (#1785 )	2016-09-20 02:27:19 -07:00
Massimiliano Culpo	ea446c0f0e	lmod : added support for the creation of hierarchical lua module files (#1723 ) Includes : - treatment of a generic hierarchy (i.e. lapack + mpi + compiler) - possibility to specify which compilers are to be considered Core - correct treatment of the 'family' directive - unit tests for most new features	2016-09-20 02:26:25 -07:00
Erik Schnetter	bd6aac3102	Update Julia to 0.4.7 (#1805 )	2016-09-20 02:16:25 -07:00
Erik Schnetter	bddb15ef4c	Make VisIt build again (#1762 ) - add new version 2.10.3 - explicitly require hdf5 variant ~mpi, since we don't know how to build with mpicc - explicitly disable glew since it may not be installed	2016-09-20 02:15:58 -07:00
Erik Schnetter	70424b511e	Work around cmake problems in VTK (#1761 ) The cmake scripts can't handle the semicolons in gcc's version output. Filter them out before detecting the version.	2016-09-20 02:15:37 -07:00
Erik Schnetter	2a558e9d7a	Tighten HDF5 version requirements for Silo (#1760 )	2016-09-20 02:14:55 -07:00
Erik Schnetter	8426b65592	Make cmake @2.8 build again (#1759 )	2016-09-20 02:14:37 -07:00
Erik Schnetter	140f1773cf	Update hwloc to 1.11.4 (#1752 )	2016-09-20 02:14:17 -07:00
Erik Schnetter	682ac5194e	Declare py-beautifulsoup4's dependency on py-setuptools (#1748 )	2016-09-20 02:14:06 -07:00
Erik Schnetter	48c87da07b	Update curl to 7.50.3 (#1747 ) * Update curl to 7.50.2 * Update curl to 7.50.3	2016-09-20 02:13:54 -07:00
Erik Schnetter	bbdc429db3	Update OpenMPI to 2.0.1 (#1721 )	2016-09-20 02:13:40 -07:00
Erik Schnetter	2e490050f6	Update OpenBLAS to 0.2.19 (#1702 )	2016-09-20 02:13:25 -07:00
Erik Schnetter	ebde2a101e	Reorder versions in openssl (#1601 )	2016-09-20 02:13:14 -07:00
Erik Schnetter	ee2ddaa7cc	Update mbedtls to 2.3.0 (#1600 )	2016-09-20 02:13:03 -07:00
Erik Schnetter	6848752fed	Update cereal to 1.2.1 (#1599 )	2016-09-20 02:12:52 -07:00
Erik Schnetter	dfad4a0abc	Update binutils to 2.27 (#1598 )	2016-09-20 02:12:40 -07:00
Michael Kuhn	7fd44a983d	Update mvapich2 to 2.2 (#1775 )	2016-09-15 10:42:57 +08:00
Elizabeth Fischer	2a823fbdfd	[RtM] Added py-proj/package.py (RtM = Ready to Merge) (#717 ) * Added py-proj package * Added bug-fix patched version to the package. * Removed dependency of py-proj on proj. * py-proj: Added missing dependency * py-proj: Removed versions from forked repos, now that necessary bug fixes have been merged into the main repo. * Update package.py Added a blank line that Travis wanted. * 1. Added copyright 2. Used setup_py 3. Added type='build' for dependencies.	2016-09-15 10:35:57 +08:00
Elizabeth Fischer	a954d0976a	Put back full-length URL.	2016-09-14 16:52:33 -04:00
Elizabeth Fischer	595ec7e034	Bug fix capturing which packages work with which binutils.	2016-09-14 16:50:17 -04:00
Elizabeth Fischer	4a1df7e0b2	Resolved issues of py-pillow, py-scipy and binutils dependencies. Resolves #1506 py-pillow: Remove version dependency on binutils@2.25. In tests, it works just fine with binutils@2.26. Fixed flake8 issues.	2016-09-14 10:56:08 -04:00
Erik Schnetter	1d09d1a4e2	Update netlib-lapack to 3.6.1 (#1597 )	2016-09-09 13:50:37 -07:00
Erik Schnetter	567d67fae2	Add libiconv dependency for git (#1468 ) Also remove "--without-pcre" flag that git does not understand any more.	2016-09-09 12:57:49 -07:00
Erik Schnetter	8249108cc6	Qthreads: Switch back to using tarball to get released version (#1739 ) * Qthreads: Switch back to using tarball for download * Don't require autotools any more * Re-enable autotools * Remove autotools again * Use .tar.bz tarball; remove outdated code	2016-09-09 06:56:11 -07:00
Erik Schnetter	e06a0271a4	New package h5hut (#1737 ) * New package h5hut -- High-Performance I/O Library for Particle-based Simulations * Set up MPI compilers * Add version 1.8.12 to HDF5 * Correct Sphinx error	2016-09-08 13:27:47 -07:00
Erik Schnetter	ff7c0335ff	Declare fontconfig dependency on pkg-config (#1686 )	2016-09-08 12:15:42 -07:00
Todd Gamblin	3d3d65f3f7	Merge pull request #1553 from adamjstewart/fixes/netcdf-hdf5 Fix NetCDF/HDF5 dependency resolution problems	2016-09-08 11:58:46 -07:00
Adam J. Stewart	0586b388df	Add latest version of libpng, ncview depends on libpng (#1502 ) * Add latest version of libpng * ncview depends on libpng	2016-09-08 09:02:10 -07:00
Ben Boeckel	77611913c6	qt: only pass -qt-xcb on non-OS X	2016-09-06 16:53:38 -04:00
Ben Boeckel	112122bc28	qt: progress on qt5.5 on osx Qt5.5 searches for the SDK itself and just ignores environment variables like CC and CXX, skipping the spack wrappers.	2016-09-06 16:01:16 -04:00
Ben Boeckel	fca26c0b79	qt: make -no-phonon specific to qt4	2016-09-06 16:00:22 -04:00
Ben Boeckel	67462ca65a	qt: fix pcre header conflict in javascriptcore	2016-09-06 16:00:21 -04:00
Ben Boeckel	4687860885	qt: force the 10.9 SDK on macos The 10.11 SDK fails to configure.	2016-09-06 16:00:21 -04:00
Ben Boeckel	a05a6456d5	glib: build on macos	2016-09-06 16:00:21 -04:00
Ben Boeckel	b810a113af	pixman: disable mmx	2016-09-06 16:00:21 -04:00
Ben Boeckel	3df1eeccb9	qt: setup the sdk and platform arguments	2016-09-06 16:00:21 -04:00
Ben Boeckel	71c357e485	qt: support building with 10.10+ SDKs	2016-09-06 16:00:21 -04:00
Ben Boeckel	aa9faceb03	qt: disable phonon support	2016-09-06 16:00:21 -04:00
Ben Boeckel	6075abfbdb	qt: depend on icu4c	2016-09-06 16:00:21 -04:00
Ben Boeckel	a9bfd88248	qt: depend on OpenSSL OS X doesn't come with an OpenSSL supported by Qt4.	2016-09-06 16:00:21 -04:00
Ben Boeckel	4c566617f7	qt: make libxcb a conditional dependency OS X doesn't have X (usually).	2016-09-06 16:00:21 -04:00
Ben Boeckel	5ba1144515	qt: create a dbus variant	2016-09-06 16:00:20 -04:00
Ben Boeckel	4b471ecc6e	qt: support detecting newer SDK paths	2016-09-06 15:59:46 -04:00
Robert D. French	ccfbfcc890	ITS XML Translation Tool (#1728 )	2016-09-06 06:56:13 -07:00
Jeffrey Salmond	26d45bc106	fontconfig: add --disable-docs to configure (#1729 )	2016-09-06 06:55:58 -07:00
Kelly Thompson	f0192edf0d	For OpenMPI v 2+, add a configure option to provide C++ bindings. (#1730 ) + Starting with version 2.0, OpenMPI no longer provides C++ bindings by default (libmpi_cxx.so). Add a configure option to instruct the build to also build and install libmpi_cxx.so. + This MPI feature is needed by at least one spack package (moab).	2016-09-06 06:55:37 -07:00
alalazo	d39b666913	plumed : avoid linking with libgslcblas	2016-09-06 11:21:26 +02:00
alalazo	47f6a6d3cf	Merge branch 'develop' of https://github.com/LLNL/spack into features/install_with_phases_rebase Conflicts: lib/spack/spack/build_environment.py lib/spack/spack/package.py var/spack/repos/builtin/packages/astyle/package.py var/spack/repos/builtin/packages/lzo/package.py var/spack/repos/builtin/packages/openjpeg/package.py var/spack/repos/builtin/packages/swiftsim/package.py	2016-09-04 10:12:52 +02:00
Massimiliano Culpo	497bbb3ae3	added package : pexsi (#1550 ) * pexsi : added package * cp2k : added pexsi (works for gcc+openmpi with and without plumed)	2016-09-03 08:13:47 -07:00
becker33	fa310c825d	Merge pull request #1704 from eschnett/eschnett/libiconf-gets Make libiconv work with C11	2016-09-02 16:46:40 -07:00
becker33	6de191a926	Merge pull request #1708 from robertdfrench/globus-toolkit Globus Toolkit	2016-09-02 15:31:34 -07:00
becker33	ea6143402f	Merge pull request #1715 from alfredo-gimenez/bugfix/vim Fix vim package.	2016-09-02 14:59:14 -07:00
Alfredo Gimenez	19102559f0	Add sbt (scala build tool) package	2016-09-02 14:15:20 -07:00
Alfredo Gimenez	817c120b1c	Fix vim package	2016-09-02 14:09:46 -07:00
Erik Schnetter	d78d18c4bd	Update OpenMPI description (#1705 )	2016-09-02 10:57:35 -07:00
Jeffrey Salmond	5146c64dfc	Fixes for the ImageMagick package. (#1709 ) * add pango dependency * add new package ghostscript-fonts & add to ImageMagick as dependency also tell ImageMagick's configure where the font dir is! * refactor to fix flake8 * add homepage to ghostscript-fonts * use install_tree * remove unneeded import	2016-09-02 10:41:35 -07:00
Erik Schnetter	c7bb523c8f	Declare qthreads dependency on automake (#1711 )	2016-09-02 10:34:07 -07:00
Robert.French	d876d9b778	Globus Toolkit	2016-09-02 16:04:26 +00:00
Erik Schnetter	9ceb3f6b49	Add two famous old versions of autoconf These old versions are often used because their immediate successors are incompatible in some way.	2016-09-02 11:23:33 -04:00
Erik Schnetter	0bd63ce8be	Make libiconv work with C11 C11 does not provide gets() any more, so we cannot reference it	2016-09-02 10:53:59 -04:00
Todd Gamblin	8d755c010d	Merge pull request #1658 from LLNL/features/git-lfs Add git-lfs package.	2016-09-01 11:58:18 -07:00
Erik Schnetter	932cd6fa19	Switch lzo download from https to http lzo's download server does not present a valid certificate, so that downloads via https are failing. Spack's MD5 checksum still ensure a safe download. Closes #1675.	2016-08-31 12:41:04 -04:00
Adam J. Stewart	1be6267149	Undo changes to trailing triple quotes in docstring	2016-08-30 16:28:55 -05:00
Adam J. Stewart	9b455e9254	Resolve new documentation issues that have cropped up	2016-08-30 15:58:22 -05:00
Adam J. Stewart	a0c8aca3a2	Remove py-mercurial, going with mercurial package instead	2016-08-30 15:35:58 -05:00
Adam J. Stewart	eb56744f4d	Fix package docstrings, #1612	2016-08-30 15:29:50 -05:00
Adam J. Stewart	7f9d098c2f	Add mercurial package, used as test dependency	2016-08-30 15:21:15 -05:00
Todd Gamblin	7e4c6afd91	Merge pull request #1412 from adamjstewart/features/cmake Overhaul of CMake package and compression libraries	2016-08-30 12:18:56 -07:00
Todd Gamblin	abd1546d86	Merge pull request #1668 from ax3l/topic-pngwriter PNGwriter: Add Spack Package	2016-08-30 10:21:27 -07:00
Axel Huebl	d2d2234def	HDF5 Dependency: Rewrite to Union @adamjstewart ``` think you'll find that if you try running something like: spack spec libsplash ^hdf5@1.8.15 It will complain that libsplash does not depend on hdf5. This is a bug in Spack's dependency resolution. A workaround for this is to tell it to always depend on hdf5. ``` @davydden ``` to expand on @adamjstewart comment, spack will make a union of dependencies, i.e. hdf5@1.8.6: + hdf5+mpi = hdf5:1.8.6:+mpi, that's why it works. ``` thank you for the hint!	2016-08-30 17:00:09 +02:00
Axel Huebl	03c4d65af1	PNGwriter: Add Spack Package Adds a package for [PNGwriter](https://github.com/pngwriter/pngwriter/), a simple high-level C++ png API used in scientific projects. ``` PNGwriter is a very easy to use open source graphics library that uses PNG as its output format. The interface has been designed to be as simple and intuitive as possible. It supports plotting and reading pixels in the RGB (red, green, blue), HSV (hue, saturation, value/brightness) and CMYK (cyan, magenta, yellow, black) colour spaces, basic shapes, scaling, bilinear interpolation, full TrueType antialiased and rotated text support, bezier curves, opening existing PNG images and more. ``` PNGwriter is a dependency for [PIConGPU](http://picongpu.hzdr.de), an open-source, many-core, fully-relativistic particle-in-cell code and further software developed at [Helmholz-Zentrum Dresden - Rossendorf](https://www.hzdr.de).	2016-08-30 12:45:53 +02:00
Axel Huebl	3aaa077c9f	libSplash: Add Spack Package Adds a package for [libSplash](https://github.com/ComputationalRadiationPhysics/libSplash), a high-level library around serial and parallel HDF5 for regular grids and particle data sets. ``` libSplash aims at developing a HDF5-based I/O library for HPC simulations. It is created as an easy-to-use frontend for the standard HDF5 library with support for MPI processes in a cluster environment. While the standard HDF5 library provides detailed low-level control, libSplash simplifies tasks commonly found in large-scale HPC simulations, such as iter- ative computations and MPI distributed processes. ``` libSplash is a dependency for [PIConGPU](http://picongpu.hzdr.de), an open-source, many-core, fully-relativistic particle-in-cell code and further software developed at [Helmholz-Zentrum Dresden - Rossendorf](https://www.hzdr.de). libSplash builds in two versions, one without MPI writing domain-decomposed posix-style HDF5 files per process and one (default) with MPI and MPI-I/O ("parallel HDF5") support aggregating into a single file per MPI communicator. libSplash is used in conjunction with [openPMD](http://openPMD.org), see also [github.com/openPMD/](https://github.com/openPMD/).	2016-08-30 12:42:39 +02:00
Todd Gamblin	47bf7ecb2b	Merge pull request #1652 from ax3l/topic-updateAdios110 Update ADIOS Package	2016-08-29 22:59:39 -07:00
Elizabeth Fischer	cf11c32720	libpciaccess: Changed libtool to a build dependency. (#1602 )	2016-08-29 22:11:27 -07:00
Axel Huebl	0f40175524	Remove Space, Enable Parallel - remove space before comma - enable parallel build again (seems to work)	2016-08-30 02:02:48 +02:00
Axel Huebl	ecacce7e07	ADIOS: Use NetCDF Prefix from spec's	2016-08-30 00:51:44 +02:00
Gregory Lee	e32247e53a	added qt-creator (#1659 )	2016-08-29 15:45:16 -07:00
Axel Huebl	37f489886e	Defaults: MPI=True, Fortran=False - ADIOS is mainly a parallel I/O library - a Fortran compiler is non-standard in a minimal install	2016-08-30 00:14:29 +02:00
Axel Huebl	b33777fd2f	RM Outdated Comments, Versions & Code	2016-08-29 23:18:31 +02:00
Axel Huebl	88254a14a7	Always External MXML; type='build' - always use `mxml` as an external dependency in spack - declare `build`-only dependencies correctly	2016-08-29 23:01:20 +02:00
Axel Huebl	e1464ece55	ADIOS: disable parallel make	2016-08-29 19:06:22 +02:00
Robert D. French	a21d3d353b	New URL scheme for newer (and older) PDTs (#1651 )	2016-08-29 10:01:04 -07:00
Axel Huebl	f2eb1c93df	ADIOS: Run Autotools First	2016-08-29 18:42:07 +02:00
Robert D. French	4095eb2196	Ole' GNU nano; Actually ran flake8 (#1649 )	2016-08-29 09:21:19 -07:00
Todd Gamblin	57033a62fa	Merge pull request #1563 from adamjstewart/features/sphinx Add all Sphinx dependencies	2016-08-29 09:08:46 -07:00
Axel Huebl	4bd863761a	Update ADIOS Package This PR updates the ADIOS package. Changes: - add latest stable release `1.10.0` - add previous versions (hashes) - add default license header - add build options (shamelessly taken from HDF5 package) - add validation for excisting FC (as in HDF5) and make optional - handle mxml dependency correctly (not required in 1.10.0+) - add `CFLAGS=-fPIC` to build shared (python) libs in ADIOS' lib - remove `-DMPICH_IGNORE_CXX_SEEK` since it is normally not required - remove `MPICC/CXX?FC` since `--with-mpi` just performs well - add transforms: - `zlib`: useful (optional) default - `szip`: optional (compile often broken) - add transports that are not as performant as the `.bp` format: - `hdf5`: non-default - `netcdf`: non-default, close #1610	2016-08-29 17:16:15 +02:00
Todd Gamblin	31cab4bae2	Merge pull request #1619 from davydden/pkg/nwchem_macos_fix nwchem: use basename for CC and FC	2016-08-29 06:51:14 -07:00
Denis Davydov	66ea42f8d7	nwchem: use basename for CC and FC	2016-08-29 15:15:23 +02:00
Todd Gamblin	f5c9a8c2ee	Merge pull request #1650 from davydden/pkg/ape_octopus_comments ape octopus: in-code comments	2016-08-29 06:02:19 -07:00
Denis Davydov	5333a799ea	octopus: in-code comments to explain compiler flags	2016-08-29 08:45:28 +02:00
Denis Davydov	90070c317d	ape: in-code comments to explain compiler flags	2016-08-29 08:45:15 +02:00
Todd Gamblin	a3f1ae8c4f	Merge pull request #1041 from adamjstewart/features/matplotlib Matplotlib Python package overhaul	2016-08-28 21:22:44 -07:00
Abhinav Bhatele	a9a29d207d	add versions 2.2rc2 and 2.1 to the mvapich2 package (#1630 )	2016-08-28 20:18:57 -07:00
Erik Schnetter	e119c32a9c	Hot-fix for qthreads (#1632 ) The download tarball for qthreads vanished. Install it from a git branch instead as temporary work-around.	2016-08-28 20:18:24 -07:00
Jeffrey Salmond	82808f944a	New package: opencoarrays (#1633 ) * opencoarrays: new package * opencoarrays: remove tests from install due to (unimportant) failures in some configurations * opencoarrays: fix flake8 errors	2016-08-28 20:17:22 -07:00
Todd Gamblin	ed365614f4	Add git-lfs package.	2016-08-28 19:27:59 -07:00
Robert D. French	974749aaf6	Provide mpi-less variant for nco (#1643 )	2016-08-28 19:15:15 -07:00
Erik Schnetter	6acfcd82b1	Update Julia to 0.5 release branch; install some Julia package as well (#1637 ) * Update Julia to 0.5 release branch; install some Julia package as well * Add comments, correct flake8 error * Correct flake8 error	2016-08-28 17:46:10 -07:00
Robert D. French	079d063c6d	Variant for building cdo without mpi (#1638 )	2016-08-28 17:43:54 -07:00
Erik Schnetter	db7c3d2de6	New package for the Mercurial (hg) version control system (#1644 ) * New package "mercurial" * Disable self-checks The self-checks require subversion, which we don't want to require.	2016-08-28 17:31:15 -07:00
becker33	e73a1a4ec3	Merge pull request #1558 from mcfadden8/mmcfadden-features/gcc-pic-libraries Added variant to gcc package to install PIC versions of libgfortran and libstdc++	2016-08-25 16:00:00 -07:00
Gregory Lee	77c24d4127	Merge pull request #1379 from LLNL/features/graphlib3 added stat 3.0 beta and added pygtk and dependent packages	2016-08-25 09:14:36 -07:00
Todd Gamblin	8170bcfcdd	Merge pull request #1574 from ARCCA/plumed-push Update plumed package to include optional modules	2016-08-25 02:45:33 -07:00
Andrew Williams	07e0da24c5	Reverted url to point to tarball rather than git tag	2016-08-25 10:21:56 +01:00
Todd Gamblin	22d2786940	Merge pull request #1580 from davydden/pkg/trilinos_url_fix trilinos: switch to github url; fix missing py-numpy dependency	2016-08-25 02:10:05 -07:00
Kelly (KT) Thompson	2ddaabed25	+ Boost: fix recipe for intel compilers. This is the same patch provided by PR #550, but rebased against the current develop branch. It also passes the flake8 checks.	2016-08-24 15:57:28 -06:00
Todd Gamblin	93cb2db531	Fix build dependency.	2016-08-24 14:10:12 -07:00
Todd Gamblin	a7e568b1d1	Merge branch 'eschnett/sympol' of git://github.com/eschnett/spack into eschnett-eschnett/sympol	2016-08-24 14:05:05 -07:00
Todd Gamblin	19bbe5e421	Merge pull request #1596 from eschnett/eschnett/git-update Update git to 2.9.3	2016-08-24 14:03:04 -07:00
Todd Gamblin	86fe78f5f1	Merge pull request #1582 from eschnett/eschnett/gcc-update Update gcc to @6.2.0	2016-08-24 14:02:54 -07:00
Adam J. Stewart	eace068788	Use self.run_tests for make check	2016-08-24 15:21:23 -05:00
Adam J. Stewart	70bb1f1707	Reduce number of variants, just use system or no-system libs	2016-08-24 14:39:05 -05:00
Todd Gamblin	e6bac6f208	Merge pull request #1613 from eschnett/eschnett/cmake-update Update cmake to 3.6.1	2016-08-24 08:49:33 -07:00
Todd Gamblin	63859bf113	Merge pull request #1575 from davydden/pkg/nwchem nwchem: add new package	2016-08-24 08:49:11 -07:00
Todd Gamblin	5cfa74801f	Merge pull request #1565 from adamjstewart/features/fftw Add latest version of fftw	2016-08-24 08:49:00 -07:00
Adam J. Stewart	5970b7a00a	Only run tests if explicitly requested	2016-08-24 10:34:20 -05:00
Erik Schnetter	41750ce70d	Update cmake to 3.6.1	2016-08-24 10:45:13 -04:00
Denis Davydov	d154f151aa	py-cclib: new package	2016-08-24 16:26:35 +02:00
Denis Davydov	6d2d5806b5	nwchem: add python module	2016-08-24 13:40:02 +02:00
Denis Davydov	dae219d5c3	nwchem: add another patch	2016-08-23 22:24:16 +02:00
Denis Davydov	459b6eae11	nwchem: add another patch	2016-08-23 22:15:38 +02:00
Erik Schnetter	3194f2001b	Update git to 2.9.3	2016-08-23 15:35:43 -04:00
Erik Schnetter	05f5ba4bf9	Correct flake8 errors	2016-08-23 14:57:29 -04:00
Erik Schnetter	73cae8d9c4	Implement review requests - use two empty lines before `class` - change version numbering scheme for packages, use `url_for_version` to make things work - specify dependency types - add comment about temporarily moved download location - update two packages to newer versions	2016-08-23 13:52:28 -04:00
Denis Davydov	52ae0ea055	trilinos: use version.dashed	2016-08-23 18:48:17 +02:00
David Beckingsale	243d516bf0	Ensure RAJA builds out-of-source	2016-08-23 08:18:26 -07:00
Denis Davydov	6500ac80e4	nwchem: fix lapack detection	2016-08-23 16:46:40 +02:00
Erik Schnetter	a2692e4ef5	sympol: Add package	2016-08-23 10:41:08 -04:00
Erik Schnetter	bdc825fc3c	cddlib: Point download url to a (more reliable) Fedora server	2016-08-23 09:59:56 -04:00
Erik Schnetter	64d3f87e60	Merge branch 'develop' into eschnett/sympol	2016-08-23 09:45:46 -04:00
Denis Davydov	7eb386e55e	nwchem: add patches	2016-08-23 14:52:18 +02:00
Denis Davydov	5da9116c06	nwchem: add scalapack; extra steps for 32bit blas/lapack	2016-08-23 11:55:00 +02:00
Denis Davydov	aca8576de4	trilinos: switch to github url; fix missing py-numpy dependency	2016-08-23 10:50:08 +02:00
Todd Gamblin	e81f3daa28	Merge pull request #1519 from mathstuf/fix-deptypes Fix deptypes	2016-08-22 21:40:25 -07:00
Erik Schnetter	7b49166f9b	Update gcc to @6.2.0 Also add some missing older version. Update download location to original GNU location.	2016-08-22 20:26:54 -04:00
Denis Davydov	a44beee172	nwchem: add new package	2016-08-23 02:22:44 +02:00
Andrew Williams	65abd279cd	Renamed intelmpi as suggested	2016-08-22 13:44:21 +01:00
Andrew Williams	87d15212eb	Cleaned branch to only include plumed package	2016-08-22 12:30:17 +01:00
Andrew Williams	226d4f04f3	Spelling tweaks and consistent quoting	2016-08-22 12:09:50 +01:00
Andrew Williams	5661afa315	Passed flake8 tests	2016-08-22 12:03:47 +01:00
Andrew Williams	0c8462723b	Found upstream plumed package and modified this one to match	2016-08-22 11:24:03 +01:00
Erik Schnetter	78685addbb	hdf5-blosc: Correct download url	2016-08-21 14:39:54 -04:00
Todd Gamblin	55b1182a4c	Merge pull request #1554 from eschnett/eschnett/hdf5-blosc hdf5-blosc: Remove commit id from version specification	2016-08-21 09:44:25 -07:00
Adam J. Stewart	d5903e4612	Flake8	2016-08-19 17:06:34 -05:00
Adam J. Stewart	f0f2c6c486	Add latest version of fftw	2016-08-19 17:05:14 -05:00
Gregory L. Lee	a177b9be8a	updated stat 3.0.0b url	2016-08-19 13:11:21 -07:00
Adam J. Stewart	835b8f246e	py-sphinx requires py-setuptools during runtime	2016-08-19 14:20:31 -05:00
Adam J. Stewart	d7873b5319	Swap lowercase for uppercase in URL	2016-08-19 14:00:50 -05:00
Adam J. Stewart	c1af0d3806	Fix binary conflicts during sphinx activation	2016-08-19 13:54:22 -05:00
Adam J. Stewart	d4e3699510	Add all Sphinx dependencies	2016-08-19 13:44:00 -05:00
Erik Schnetter	466da3afcc	Remove commented-out outdated commit id	2016-08-19 11:52:40 -04:00
Andrew Williams	90e5ccd98c	Cleaned up commented out code in intelmpi package	2016-08-19 15:01:46 +01:00
Andrew Williams	13f636ec68	Added required arguments to get plumed to build with intelmpi	2016-08-19 15:00:21 +01:00
Adam J. Stewart	28537ae7b7	Workaround until variant forwarding works properly	2016-08-18 14:40:21 -05:00
Stephen Herbein	3445a781eb	py-cffi: set LDSHARED env so that rpath is set py-cffi's .so was being built without the rpath being set. distutils looks at the LDSHARED for which compiler to use to build the final .so. Since it was not set, distutils fell back to the system provided compiler. Setting it forces the shared library to be compiled with the spack compiler (meaning that the rpath is set correctly).	2016-08-18 11:32:19 -07:00
Andrew Williams	6641f42417	Not compiling due to mpi error. Also getting this error from the command line so could be separate issue. Otherwise package definition first draft complete.	2016-08-18 13:19:36 +01:00
Erik Schnetter	296212d78d	hdf5-blosc: Remove commit id from version specification The respective commit seems to have vanished. Now using the master branch without specifying a particular commit.	2016-08-17 16:36:33 -04:00
Adam J. Stewart	4d12c5455a	Fix NetCDF/HDF5 dependency resolution problems	2016-08-17 13:03:56 -05:00
Marty McFadden	f4ec99ecb4	Added +piclibs variant for building PIC versions of libgfortran.a and libstdc++.a	2016-08-17 09:28:21 -07:00
Andrew Williams	b99e945e6d	Added variants and dependencies to plumed but I'm getting an error when trying to resolve mpi to a valid virtual package	2016-08-17 15:43:59 +01:00
Elizabeth Fischer	a733e7e303	py-pathspec: New package Related to Python unit testing.	2016-08-17 00:34:33 -04:00
becker33	7f57405eac	Merge pull request #1531 from davydden/pkg/ape ape: add new package	2016-08-16 10:52:27 -07:00
becker33	e8afbfbce7	Merge pull request #1530 from davydden/pkg/octopus octopus: new package	2016-08-16 10:49:41 -07:00
Denis Davydov	5dcc0f7802	ape: add new package	2016-08-16 19:42:32 +02:00
Denis Davydov	9509c10064	octopus: new package	2016-08-16 19:38:38 +02:00
Gregory L. Lee	f182590aae	added pkg-config to build deps of cairo and pixman	2016-08-15 15:17:53 -07:00
Gregory L. Lee	54ef9443d3	fix atk url_for_version	2016-08-15 13:51:54 -07:00
Gregory L. Lee	74dd7a36b5	allow parallel build of stat	2016-08-15 13:51:54 -07:00
Gregory L. Lee	749a4e78c7	gobject-introspection requires glib version 2.48.1	2016-08-15 13:51:54 -07:00
Gregory L. Lee	3df208efc0	stat and dependences package updates	2016-08-15 13:51:53 -07:00
Gregory L. Lee	69931996bf	added dyninst patches for stat+dysect	2016-08-15 13:51:53 -07:00
Gregory L. Lee	f9cb21e886	flake 8 fixes for dyninst	2016-08-15 13:51:53 -07:00
Gregory L. Lee	0074ecd6fa	dyninst package use spec.satisfies instead of @when	2016-08-15 13:51:52 -07:00
Gregory L. Lee	8b94937609	flake 8 fixes for stat and dependents flake 8 fixes for dyninst flake 8 fixes for dyninst flake 8 fixes for dyninst	2016-08-15 13:50:39 -07:00
Gregory L. Lee	bd8aab00e4	updated stat and added pygtk and dependent packages	2016-08-15 13:48:58 -07:00
Andrew Williams	27793d97dc	temp commit in current state	2016-08-15 16:16:00 +01:00
Ben Boeckel	9ec1c0e18e	opencv: make py-numpy a nolink dependency	2016-08-15 10:47:00 -04:00
Ben Boeckel	042666eb7e	go: mark git as also being a runtime dependency	2016-08-15 10:46:45 -04:00
Ben Boeckel	826732efec	packages: mark builddeps as type='build' Less sure about these.	2016-08-15 10:46:23 -04:00
Ben Boeckel	eb13cbe9bd	r-datatable: fix nolink dependency	2016-08-15 10:46:05 -04:00
Ben Boeckel	0d17d90b29	packages: mark builddeps as type='build'	2016-08-15 10:45:19 -04:00
Andrew Williams	3edfa390f7	Basic package file for plumed and boilerplate for external intel mpi	2016-08-15 11:19:40 +01:00
Adam J. Stewart	bc64990bc6	Replace python('setup.py' with setup_py(	2016-08-12 12:16:48 -05:00
Todd Gamblin	e1c2ea5123	Merge pull request #1342 from adamjstewart/features/cgns Add CGNS package	2016-08-12 09:19:07 -07:00
Adam J. Stewart	d4377c1293	Add Python 3.5 support, latest version of PySide	2016-08-12 09:59:38 -05:00
Adam J. Stewart	633e540a17	Use GitHub URL for ImageMagick	2016-08-11 14:13:33 -05:00
Adam J. Stewart	f147d64527	Rebase messed up flake8	2016-08-11 11:01:57 -05:00
Adam J. Stewart	04cee45ac9	Skip webengine until webkit support is added	2016-08-11 10:33:43 -05:00
Adam J. Stewart	2b0444b6f4	Latest version of pyside still has problems, add deps	2016-08-11 10:33:43 -05:00
Adam J. Stewart	b6fad65f52	Combine patch for all versions Patch doesn't work with @when unless you specify a patch for every version. When running `spack patch` for a version without a patch, spack thinks that a patch exists, tries to apply it, but it doesn't exist. Spack gets very confused.	2016-08-11 10:33:43 -05:00
Adam J. Stewart	1363b05e93	Add test dependencies	2016-08-11 10:33:43 -05:00
Adam J. Stewart	5cc76f7d84	Fix patch for py-pyside 1.2.4	2016-08-11 10:33:43 -05:00
Adam J. Stewart	59ce0c7514	Add patch to build qt 4 with GCC 6	2016-08-11 10:33:42 -05:00
Adam J. Stewart	ddf1879bed	Remove glib dependency, causes problems with PCRE and JavaScript	2016-08-11 10:33:02 -05:00
Adam J. Stewart	90dd26397c	Fix qt patch	2016-08-11 10:33:02 -05:00
Adam J. Stewart	7135299a66	Add latest version of pcre	2016-08-11 10:33:02 -05:00
Adam J. Stewart	ac15d5d619	Add patch for qt gamepad compilation problems	2016-08-11 10:33:01 -05:00
Adam J. Stewart	eac9a5905f	Flake8 and url_for_version changes	2016-08-11 10:33:01 -05:00
Adam J. Stewart	80742b2647	Add latest version of qt	2016-08-11 10:30:31 -05:00
Adam J. Stewart	8a0824df09	Update matplotlibrc filtering for GUI backends	2016-08-11 10:28:35 -05:00
Adam J. Stewart	a388871083	Update ImageMagick to latest version	2016-08-11 10:28:35 -05:00
Adam J. Stewart	2b83ea30e7	Re-add ipython support	2016-08-11 10:28:35 -05:00
Adam J. Stewart	f56de63972	Fix cycler dependencies, update qhull version names	2016-08-11 10:28:35 -05:00
Adam J. Stewart	0b8a3ad8ad	Flake8	2016-08-11 10:28:34 -05:00
Adam J. Stewart	aa6a6df640	Undo changes to GUI framework	2016-08-11 10:28:34 -05:00
Adam J. Stewart	e905ce16c9	Flake8	2016-08-11 10:28:34 -05:00
Adam J. Stewart	11e595089d	Matplotlib overhaul	2016-08-11 10:28:33 -05:00
Adam J. Stewart	b47357d73c	Add patch for Intel compilers	2016-08-11 10:22:47 -05:00
Adam J. Stewart	5fc20487e4	Flake8 and formatting changes	2016-08-11 10:22:47 -05:00
Adam J. Stewart	534e1cbf1b	Some tests don't pass with Intel compilers	2016-08-11 10:20:08 -05:00
Adam J. Stewart	ee5e20dae3	Add dependencies to libarchive and cmake	2016-08-11 10:17:42 -05:00
Adam J. Stewart	58d7704060	Overhaul of compression libraries	2016-08-11 10:15:13 -05:00
Todd Gamblin	e6a122417a	Merge pull request #1491 from eschnett/eschnett/curl Update curl to 7.50.1	2016-08-11 03:04:07 -07:00
alalazo	f5433477b9	qa : flake8 issues	2016-08-11 09:08:00 +02:00
alalazo	b4b9ebe7d7	Merge branch 'develop' of https://github.com/LLNL/spack into features/install_with_phases Conflicts: lib/spack/llnl/util/tty/log.py lib/spack/spack/__init__.py lib/spack/spack/cmd/install.py lib/spack/spack/cmd/setup.py lib/spack/spack/package.py var/spack/repos/builtin/packages/blitz/package.py var/spack/repos/builtin/packages/gmp/package.py var/spack/repos/builtin/packages/qhull/package.py var/spack/repos/builtin/packages/szip/package.py	2016-08-11 08:55:20 +02:00
Todd Gamblin	84e331c586	Remove unneeded noqa comments.	2016-08-10 16:33:39 -07:00
Todd Gamblin	240f1fd223	Spack packages now PEP8 compliant.	2016-08-10 16:33:39 -07:00
Erik Schnetter	158deae625	Update curl to 7.50.1	2016-08-10 13:51:57 -04:00
Matt Belhorn	2be065418b	Openssl package should not require openssl (https) to obtain source.	2016-08-09 15:57:07 -04:00
alalazo	38dcd6bce9	qa : flake8 issues	2016-08-09 09:54:24 +02:00
alalazo	5362864cc9	plumed : fixed name clash on attribute	2016-08-09 09:24:36 +02:00
Massimiliano Culpo	15d9fb1879	plumed : adding dependents * cp2k : added plumed * gromacs : patched pme load balancing * gromacs : added plumed	2016-08-09 09:23:53 +02:00
becker33	3ea1325620	Merge pull request #1345 from hartzell/feature/add-perl-dependency-to-git Add depends_on('perl'), depends_on('pcre') to git package	2016-08-08 09:44:50 -07:00
Todd Gamblin	dd30066feb	Merge pull request #1449 from hartzell/feature/add-package-for-prank Add package for prank and supporting tools	2016-08-07 23:43:40 -07:00
Todd Gamblin	e65a8b6a9a	Merge pull request #1463 from davydden/pkg/opium opium: add new package	2016-08-07 15:56:27 -07:00
Todd Gamblin	8121ac2c27	Merge pull request #1464 from hartzell/feature/update-lmod No need to patch Lmod after 6.4.4	2016-08-07 15:55:16 -07:00
Todd Gamblin	93f5a750cb	Merge pull request #1465 from glennpj/pango_url Add list_url to pango package	2016-08-07 15:55:04 -07:00
Todd Gamblin	281f6f18e1	Merge pull request #1466 from pramodk/develop PDT should download full installer package	2016-08-07 15:54:50 -07:00
Denis Davydov	db87a9d3ce	tar: fix 1.28 on macOS; add 1.29 (#1462 )	2016-08-07 15:54:01 -07:00
Adam J. Stewart	d7329d7bc2	Fix erroneously stripped trailing whitespace in patch (#1467 )	2016-08-07 15:53:25 -07:00
Pramod Kumbhar	e9edfec0ec	PDT should download full installer package pdtoolkit-X.tar.gz (default pdt-X.tar.gz is only for x86 and cray)	2016-08-07 01:14:26 +02:00
Glenn Johnson	2ad21e7070	Add list_url to pango package Added a `list_url` so the updated pango tar file can be retrieved.	2016-08-06 18:12:47 -05:00
George Hartzell	09d96bef9f	No need to patch Lmod after 6.4.4 The Lmod author changed the src so that it uses the tclsh (and shared libraries) discovered at configure time. He did it differently that I did in this patch, but he changes solve our problem too, so...	2016-08-06 17:39:05 -04:00
George Hartzell	9ebbde0e01	Make configure use our gettext library The configure script needs extra encouragement to link against our gettext/libintl library.	2016-08-06 16:28:47 -04:00
George Hartzell	1de5817b58	Clean up rebase problems My rebase duplicated the depends_on('zlib') and dropped the --with-curl from the configure. This fixes those.	2016-08-06 16:28:47 -04:00
George Hartzell	f699d7c08e	[Whitespace] Gather the depends_on's together.	2016-08-06 16:28:47 -04:00
George Hartzell	152fa33a55	Call configure `--with-libpcre=...` to use our pcre An earlier commit claimed that this package depends_on('pcre') but I didn't fix the call to configure that enabled it. This fixes that.	2016-08-06 16:28:47 -04:00
George Hartzell	3cf2fd40a8	Enable depends_on('pcre') also While I have the patient on the operating table, @adamjstewart asked me to uncomment and test the depends_on('pcre'). Did it and it Works For Me(tm).	2016-08-06 16:28:47 -04:00
George Hartzell	653905e3a2	Add depends_on('perl') to git package This commit changes the git package to depend_on('perl'). The system perl is not always sufficient to install git (e.g. a CentOS7 system with the development tools group installed has perl but not the ExtUtils::MakeMaker package that git needs) and one can't always update the system's perl. This PR depends_on PR #1339, which adds a perl package to spack.	2016-08-06 16:28:47 -04:00
George Hartzell	f800708ef3	Switch to using *std_cmake_args	2016-08-06 16:27:40 -04:00
George Hartzell	6a62a6b693	Flake8 whitespace cleanup	2016-08-06 16:27:40 -04:00
George Hartzell	a07a0ef54b	Add Bio++ tool suite and supporting libs Add the Bio++ suite and its supporting libraries.	2016-08-06 16:27:40 -04:00
George Hartzell	3c81bb44ba	Add package for mafft	2016-08-06 16:27:40 -04:00
George Hartzell	e0db1f0268	Add package for exonerate	2016-08-06 16:27:40 -04:00
George Hartzell	9e16902397	Fix name of bpp-suite (missing -...)	2016-08-06 16:27:40 -04:00
George Hartzell	63592096c5	Add package for prank	2016-08-06 16:27:40 -04:00
Denis Davydov	4983ebcf7c	opium: add new package	2016-08-06 21:35:52 +02:00
becker33	d3f115933e	Merge pull request #1451 from hartzell/feature/add-package-for-fastx_toolkit Add package for fastx toolkit	2016-08-05 15:09:46 -07:00
becker33	18d155e713	Merge pull request #1452 from hartzell/feature/add-package-for-samtools Add package for samtools	2016-08-05 15:09:41 -07:00
George Hartzell	a6afaeb974	Remove lingering FIXME commentary	2016-08-05 17:51:24 -04:00
George Hartzell	769408130a	Samtools depends on htslib from 1.3.1 onward Samtools used to (before 1.3.1) include it's own copy of htslib. Going forward, it needs to use the standalone htslib.	2016-08-05 17:47:11 -04:00
becker33	8e20a14945	Merge pull request #1453 from hartzell/feature/add-package-for-seqtk Add package for seqtk	2016-08-05 10:25:19 -07:00
becker33	f403f256ca	Merge pull request #1450 from hartzell/feature/add-package-for-bwa Add package for bwa	2016-08-05 10:21:10 -07:00
becker33	594a6710ed	Merge pull request #1442 from suraia/update-scorep-2.0 Update Score-P to 2.0 Most likely this can be generalized to link against older versions of dependencies, but it looks good for now.	2016-08-05 08:57:25 -07:00
George Hartzell	d6dedee6ff	Flake8 cleanup	2016-08-04 15:23:04 -04:00
Bruno Turcksin	0c02ee86a7	Add Trilinos 12.6.4 (#1447 )	2016-08-04 11:29:10 -07:00
George Hartzell	e12d7aadda	Add package for seqtk Seqtk is a tool for working with fast[aq] files.	2016-08-04 14:18:03 -04:00
George Hartzell	fd11db92e1	Add package for bcftools	2016-08-04 14:18:03 -04:00
George Hartzell	ba0577dc96	Update samtools to support v1.3.1 Update the samtools package to support v1.3.1, which - now uses configure script; and - now depends on external htslib package. The dependency on mpc seems to have been bogus, it's never linked in, nor is it mentioned in the source tree. I do have a version in /usr/lib64, but ldd does not sure it being linked in either.... By depending on 'ncurses' I can do away with the need for the patch.	2016-08-04 14:18:03 -04:00
George Hartzell	ef1369c365	Add package for htslib Htslib was pulled out of samtools and made into a standalone thing. This commit adds a packag for it, in support of the samtools package.	2016-08-04 14:18:03 -04:00
George Hartzell	e17862c421	Add package for fastx toolkit Tools for working with FASTA/FASTQ files.	2016-08-04 14:18:02 -04:00
George Hartzell	d5bb2955b1	Add package for libgtextutils Gordon's Text utils Library, in support of fastx toolkit.	2016-08-04 14:18:02 -04:00
George Hartzell	d4274b32f2	Make flake8 happy (long lines)	2016-08-04 14:18:01 -04:00
Michael Kuhn	d7665a63e3	flake8 fixes	2016-08-04 19:04:48 +02:00
becker33	1ac1cc3d2c	Merge pull request #1437 from jgalarowicz/update-xercesc Update the version of xerces-c, where the developers remove the old v…	2016-08-04 09:00:36 -07:00
becker33	3c6f6fc811	Merge pull request #1438 from jgalarowicz/update-libmonitor Update libmonitor to use its new github location, it does not exist w…	2016-08-04 08:59:35 -07:00
becker33	cabcdf0ec9	Merge pull request #1443 from davydden/pkg/dealii_python dealii: add optional python bindings	2016-08-04 08:43:36 -07:00
becker33	fcc8b1d3e4	Merge pull request #1431 from hartzell/feature/add-package-for-unison Add package for unison (and ocaml)	2016-08-04 08:41:45 -07:00
Denis Davydov	af8741c23c	dealii: add optional python bindings	2016-08-04 16:11:14 +02:00
Michael Kuhn	584e5506f2	Update Score-P to 2.0	2016-08-04 14:24:25 +02:00
Todd Gamblin	b7fa2c4e21	Fix #1429 : Remove git dep from gettext; break circular dependency. - It's not really a circular dependency -- git is a run dependency of gettext - We can revert this change when Spack is smart enough to make git a run dependency and build it.	2016-08-03 21:53:53 -07:00
Jim Galarowicz	2e1dbd0697	Fix flake8 errors for: Update libmonitor to use its new github location, it does not exist where the package file now points to.	2016-08-03 21:32:15 -05:00
Jim Galarowicz	e69423a154	Fix flake8 errors for Update the version of xerces-c, where the developers remove the old version, so there is no fallback.	2016-08-03 21:28:56 -05:00
Jim Galarowicz	e68b7d8c63	Update libmonitor to use its new github location, it does not exist where the package file now points to.	2016-08-03 21:08:48 -05:00
Jim Galarowicz	638f779841	Update the version of xerces-c, where the developers remove the old version, so there is no fallback.	2016-08-03 21:04:17 -05:00
George Hartzell	43371c31a2	Flake8 cleanup	2016-08-03 16:51:53 -04:00
Todd Gamblin	dce105d16f	Merge pull request #1382 from KineticTheory/gktplus3-deps GTK+3: Provide updates to package dependencies.	2016-08-03 13:45:18 -07:00
George Hartzell	4acf6d76bf	Add package for unison Add package for unison (the file synchronizer). Needs the ocaml compiler to build.	2016-08-03 16:41:31 -04:00
George Hartzell	a7bfaa3797	Add package for ocaml compiler Installs the ocaml compiler.	2016-08-03 16:41:31 -04:00
Kelly (KT) Thompson	7c46a4c0e4	Provide minor updates after code review + Always depend on the gettext package. This simplifies the logic and I no longer need to 'import sys' + Only apply the patch for the older version of glib.	2016-08-03 13:26:02 -06:00
becker33	3e6ebd577f	Merge pull request #1378 from LLNL/bugfix/gh-1324-intel-parallel-studio Bugfix/gh 1324 intel parallel studio	2016-08-03 10:46:40 -07:00
becker33	353726f08f	Merge pull request #1156 from adamjstewart/features/py-meep Add py-meep package and dependencies Merging to add the gettext support, will submit a separate issue for the LD_LIBRARY_PATH issue with MPI and py-meep	2016-08-03 10:07:05 -07:00
becker33	b9195b415a	Merge pull request #1420 from epfl-scitas/packages/plumed plumed : added package	2016-08-03 08:36:31 -07:00
alalazo	2f1c000f62	qa : flake8 issues	2016-08-03 08:26:58 +02:00
Kelly (KT) Thompson	d7d12aa2dc	One more formatting change to make flake8 happy.	2016-08-02 19:05:48 -06:00
becker33	48997cffa1	Merge pull request #1233 from hartzell/add-nextflow First cut package for nextflow, has issues	2016-08-02 11:52:19 -07:00
Denis Davydov	f90692cf81	arpack-ng: fix blas/lapack libraries	2016-08-02 20:27:34 +02:00
becker33	b5a117c923	Merge pull request #1366 from hartzell/feature/add-package-for-ack Add package for ack	2016-08-02 10:11:11 -07:00
becker33	1534a115bd	Merge pull request #1421 from hartzell/feature/add-package-for-texlive Add package for texlive	2016-08-02 10:10:43 -07:00
becker33	a03a35565e	Merge pull request #1339 from hartzell/features/add-perl Add perl package	2016-08-02 10:10:04 -07:00
George Hartzell	fa70a837d4	Remove accidentally committed cabal-install bits	2016-08-02 13:00:47 -04:00
becker33	91004158c6	Merge pull request #1243 from davydden/pkg/atlas_urls atlas: fix urls and shared libs	2016-08-02 09:59:05 -07:00
becker33	3f26bbc8b3	Merge pull request #864 from davydden/kdiff3 kdiff3: initial version of the package	2016-08-02 09:35:00 -07:00
becker33	a3322fab0a	Merge pull request #1360 from glennpj/pysetuptoolsdep Add py-setuptools dependencies to packages	2016-08-02 09:33:40 -07:00
becker33	21158195fb	Merge pull request #1354 from paulhopkins/bugfix/preferred_variants_do_not_recognise_-variant Bugfix/preferred variants do not recognise -variant	2016-08-02 09:15:06 -07:00
George Hartzell	74a181febc	Remove local copy of cpanm installer This is handled as a resource in the package now.	2016-08-02 12:13:24 -04:00
George Hartzell	4c8672ed1f	Add previous versions back into package Following the advice of @glennpj, added the old versions back into the packages. I can install the current packages and the previous packages.	2016-08-02 11:45:16 -04:00
George Hartzell	c77425bb22	Remove useless `def unpack` Before I learned that I was stumbling over a real but (#1308), I thought I needed to arrange for the fetcher to skip the unpack step. This commit removes the useful `def unpack`.	2016-08-02 11:32:19 -04:00
George Hartzell	a6605d842b	Flake8 cleanup.	2016-08-02 11:25:03 -04:00
George Hartzell	f2f5f6c279	Touch up variant comment	2016-08-02 11:18:50 -04:00
George Hartzell	c994565c62	Use "resource" machinery to manage cpanm tarball Use the resource machinery to fetch/cache/unpack/... the App::cpanminus tarball. - this hardcodes the version, I can't figure out how to use a variant to hold/set the value and access it in the resource(). - change up the install to use the `with working_dir()` meme.	2016-08-02 11:16:46 -04:00
George Hartzell	1b9becc541	Add the std spack header to perl/package.py Stole the example header from antlr/package.py, included it at the top of perl/package.py.	2016-08-02 11:16:46 -04:00
George Hartzell	08ff7b65af	Make running perl's tests conditional Make running perl's tests conditional, one must now specify the `--run-tests` flag to the `spack install` command in order to run the tests. On one system (8 core, 16GB Digital Ocean Droplet), installing without tests takes 3 minutes, with tests takes 16 minutes.	2016-08-02 11:16:46 -04:00
George Hartzell	4d72e0fb9d	Make the cpanm version a variant Rather than hard-coding the verison of `cpanm` that's [optionally] installed into the core, make it a variant with a default value of '1.7042'. Also discovered that `prefix + 'bin'` is the same as `prefix.bin`, so embetter that bit of code.	2016-08-02 11:16:46 -04:00
George Hartzell	a5a4525bed	Add perl package Add perl package, based on [work by justintoo](https://github.com/LLNL/spack/pull/105). He had too many things pulled into that pull request, this just adds a perl package. Support the current releases on the past three minor branches. Run perl's tests before installing. Install cpanm into the core (makes building on top of this perl much simpler). Controlled by a variant.	2016-08-02 11:16:46 -04:00
George Hartzell	949621eb7f	Add package for texlive	2016-08-02 11:15:42 -04:00
George Hartzell	857a03c127	Ack should depends_on('perl') Add a depends_on('perl') and rewrite the script's `#!` line to refer to that Perl's `perl` executable.	2016-08-02 11:11:05 -04:00
George Hartzell	114da813a3	Remove unnecessary imports. Now that it's sporting a cleaner install method, these imports are unnecessary.	2016-08-02 11:11:05 -04:00
George Hartzell	bf467c5df3	Remove override of `unpack(self)` I cargo culted that from my nextflow package. I [thought I] needed it to work around Spack trying to use tar to unpack something that was neither a tar ball nor unpackable. This package works fine without it. In retrospect, the error that I was seeing in the nextflow package was probably this problem #1308.	2016-08-02 11:11:05 -04:00
George Hartzell	6c3623422f	Use cleaner mech to install script Use @adamjstewart's nicer bit of python code in the install method.	2016-08-02 11:11:05 -04:00
George Hartzell	63121a0c49	Add package for ack Add a package for [ack](http://beyondgrep.com/install/). Simply install the fatpacked script. It uses '#!/usr/bin/env perl' and it very much not choosy about what perl it needs. For now just trust that there's one available, perhaps someday we can/should uncomment the depends_on('perl'). Follows the methodolgy I used in nextflow. Has the same uninstall/install problem that nextflow has, there is an issue in progress for that: https://github.com/LLNL/spack/issues/1308. Tested on CentOS7.	2016-08-02 11:11:05 -04:00
George Hartzell	12d1263980	Update several R packages (r-shiny prereqs) r-jsonlite 0.0.21 -> 1.0 r-mime 0.4 -> 0.5 rcpp 0.12.5 -> 0.12.6 CRAN is funny. The older versions of these packages are still available in package specific directories but the current version is not there, so I don't see any way to make the older versions work.	2016-08-02 11:10:41 -04:00
George Hartzell	6f332c7e4c	Fix whitespace, make flake8 happ{y,ier}.	2016-08-02 11:10:12 -04:00
George Hartzell	bfcec69630	Add standard header, use spack helpers Added the standard header (stolen from R). Touched up the install to use set_executable rather than doing it myself.	2016-08-02 11:10:12 -04:00
George Hartzell	4373a2b629	First cut package for nextflow, has issues This is my first cut at a package to support nextflow. It's also my first package. It works, but has issues. I'm going to submit a pull request and get some coaching on how to deal with it. One issue particular: if I install, then uninstall, then try to install again (which uses the cached copy of the "distribution file"), it explodes.	2016-08-02 11:10:12 -04:00
Glenn Johnson	a57d94af03	Fix flake8 issues.	2016-08-02 09:53:57 -05:00
Denis Davydov	a1703bf70d	kdiff3: add license block	2016-08-02 16:37:14 +02:00
Gilles Fourestey	dea7bbb4a0	added plumed * plumed : first version * plumed : added dependencies and docs	2016-08-02 15:06:46 +02:00
Denis Davydov	565bd5f51e	atlas: revert to lapack 3.5.0	2016-08-02 13:52:32 +02:00
Denis Davydov	bef7e2645a	atlas: flake8 fixes	2016-08-02 13:52:32 +02:00
Denis Davydov	f6a4a6b00f	atlas: add install_test	2016-08-02 13:52:32 +02:00
Denis Davydov	0c0b37800d	atlas: set (blas\|lapack)_shared_lib	2016-08-02 13:52:32 +02:00
Denis Davydov	4ecf481337	atlas: fix shared libs; set compilers	2016-08-02 13:52:32 +02:00
Denis Davydov	6f7e12d49b	atlas: fix urls and use lapack 3.6.0	2016-08-02 13:52:32 +02:00
Denis Davydov	0aa513ad70	libxau: mark pkg-config as build-type dependency	2016-08-02 13:50:46 +02:00
Denis Davydov	450c750214	kdiff3: initial version of the package	2016-08-02 13:49:40 +02:00
Denis Davydov	a4e59c2758	libxau: add missing dependency	2016-08-02 13:49:40 +02:00
Kelly (KT) Thompson	9433e84776	Formatting changes for flake8.	2016-08-01 22:54:51 -06:00
Kelly (KT) Thompson	17f0eb5148	Provide correct download urls and additional dependencies.	2016-08-01 22:10:54 -06:00
	ba11f19efc	Merge remote-tracking branch 'upstream/develop' into gktplus3-deps	2016-08-01 20:50:28 -06:00
becker33	b892cebe8a	Merge pull request #1343 from glennpj/r_unfilter R extension dependencies with compiler wrapper	2016-08-01 13:51:13 -07:00
becker33	e861e35acf	Merge pull request #1234 from mwilliammyers/package-opencv Update opencv package	2016-08-01 13:44:31 -07:00
becker33	1847aa035d	Merge pull request #1348 from glennpj/rcurl r-curl update and changed remote archive	2016-08-01 13:38:38 -07:00
becker33	94238eebfa	Merge pull request #1381 from davydden/pkg/mkl_linux MKL linux fixes	2016-08-01 13:36:10 -07:00
becker33	dc9fcea989	Merge pull request #1365 from hartzell/feature/add-package-for-tree Add package for tree	2016-08-01 13:21:09 -07:00
becker33	15514792d5	Merge pull request #1374 from hartzell/bug/fix-jdk-import-of-distutils Bug: fix jdk package's use of distutils	2016-08-01 13:20:44 -07:00
becker33	851bc506e4	Merge pull request #1367 from adamjstewart/features/pgi Add latest version of PGI	2016-08-01 13:07:35 -07:00
becker33	932300256c	Merge pull request #1413 from mdevlin1/fixes/libxsmm Fixed libxsmm package	2016-08-01 13:06:05 -07:00
becker33	6361f5c2d4	Merge pull request #1359 from sknigh/libhio added libhio package	2016-08-01 13:05:29 -07:00
Mitchell Devlin	2d51ea5da4	fixed libxsmm makefile filter	2016-08-01 14:38:16 -05:00
Adam J. Stewart	fed7ba1dab	Add latest version of PGI	2016-08-01 13:42:00 -05:00
Adam J. Stewart	ab885a5397	Allow git to depend on gettext now that it works	2016-08-01 13:35:22 -05:00
Adam J. Stewart	4014a29d2b	Use proper deptype so that spack activate works	2016-08-01 13:35:22 -05:00
Adam J. Stewart	f5aed63b0b	pkg-config should be a build dependency only	2016-08-01 13:35:22 -05:00
Adam J. Stewart	5cac0a528c	Fix undefined symbols by building shared libraries	2016-08-01 13:35:22 -05:00
Adam J. Stewart	bdb64c2e39	Tell MEEP where to find libctl	2016-08-01 13:35:22 -05:00
Adam J. Stewart	0903ae0599	Final fixes to get libctl working	2016-08-01 13:35:22 -05:00
Adam J. Stewart	1e3a5d4e26	Final fixes to get guile to build	2016-08-01 13:35:21 -05:00
Adam J. Stewart	6db99a4fe7	Rename gc => bdw-gc, fix libunistring bug	2016-08-01 13:35:21 -05:00
Adam J. Stewart	5b1a882fc2	Update meep's url_for_version	2016-08-01 13:35:21 -05:00
Adam J. Stewart	a2578c21e4	Supply flags to bdist	2016-08-01 13:35:21 -05:00
Adam J. Stewart	8d0758fc4c	Allow py-meep to link properly	2016-08-01 13:35:21 -05:00
Adam J. Stewart	880cbb2217	Better testing for MEEP	2016-08-01 13:35:21 -05:00
Adam J. Stewart	3b4820f290	Patch pkg-config and update installs for various packages	2016-08-01 13:35:21 -05:00
Adam J. Stewart	9e05fdf4a1	Bug fixes	2016-08-01 13:35:20 -05:00
Adam J. Stewart	7e53f4328f	Add py-meep package and dependencies	2016-08-01 13:35:20 -05:00
George Hartzell	7d303afd64	Address flake8 issue	2016-08-01 13:42:55 -04:00
George Hartzell	1552ed943a	Add package for cask Add a package for cask, the emacs project/dependency management tool. Based on [Homebrew's formula][brew]. [brew]: https://github.com/Homebrew/homebrew-core/blob/master/Formula/cask.rb	2016-08-01 13:41:28 -04:00
George Hartzell	31b7580b76	Fix jdk package's use of distutils See issue #1364. @citibeth's fix works fine.	2016-08-01 13:33:27 -04:00
becker33	cc3fc2ba4c	Merge pull request #1322 from mdevlin1/feature/libxsmm Add libxsmm package	2016-08-01 09:56:09 -07:00
Paul Hopkins	cca240c8f9	Add concretize_preferences tests	2016-08-01 16:18:11 +01:00
alalazo	ec09dfe5d1	cp2k : added package	2016-08-01 10:41:33 +02:00
Todd Gamblin	fbbb82259a	Merge pull request #1407 from glennpj/r-ncdf4 New package - r-ncdf4	2016-07-31 22:15:52 -07:00
Todd Gamblin	ea11aab71f	Merge pull request #1406 from glennpj/r-np New package - r-np	2016-07-31 22:15:37 -07:00
Todd Gamblin	2042c94a6c	Merge pull request #1405 from glennpj/r-survey New package - r-survey	2016-07-31 22:15:09 -07:00
Todd Gamblin	64be8a80b2	Merge pull request #1404 from glennpj/r-tarifx New package - r-tarifx	2016-07-31 22:14:56 -07:00
Todd Gamblin	7185fe2876	Merge pull request #1403 from glennpj/r-e1071 New package - r-e1071	2016-07-31 22:14:40 -07:00
Todd Gamblin	0724eba935	Merge pull request #1402 from glennpj/r-plotrix New package - r-plotrix	2016-07-31 22:14:25 -07:00
Todd Gamblin	441bb83682	Merge pull request #1401 from glennpj/r-gdata New package - r-gdata	2016-07-31 22:13:50 -07:00
Todd Gamblin	2cffc90284	Merge pull request #1400 from glennpj/r-roxygen2 New package - r-roxygen2	2016-07-31 22:13:16 -07:00
Todd Gamblin	68cedd2599	Merge pull request #1399 from glennpj/r-testthat New package - r-testthat	2016-07-31 22:12:06 -07:00
Todd Gamblin	d00fd06095	Merge pull request #1398 from glennpj/r-xml New package - r-xml	2016-07-31 22:11:38 -07:00
Glenn Johnson	8815f0a0b5	New package - r-ncdf4 Interface to Unidata netCDF (version 4 or earlier) format data files.	2016-07-31 17:12:29 -05:00
Glenn Johnson	bfd03db12a	New package - r-np Nonparametric kernel smoothing methods for mixed data types.	2016-07-31 16:18:55 -05:00
Glenn Johnson	f14eb07dc1	New package - r-survey Analysis of complex survey samples.	2016-07-31 15:50:19 -05:00
Glenn Johnson	a9cc6a7d08	New package - r-tarifx A collection of various utility and convenience functions.	2016-07-31 15:39:09 -05:00
Glenn Johnson	be2f2e42db	New package - r-e1071 Misc functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien.	2016-07-31 15:26:13 -05:00
Glenn Johnson	05e5276aec	New package - r-plotrix Various plotting functions.	2016-07-31 15:15:55 -05:00
Glenn Johnson	dbf799bbf9	New package - r-gdata Data manipulation tools.	2016-07-31 15:07:40 -05:00
Glenn Johnson	f39e570f36	New package - r-roxygen2 In-source documentation for R.	2016-07-31 14:52:16 -05:00
Glenn Johnson	58a6039c0a	New package - r-testthat A unit testing system for R.	2016-07-31 14:40:46 -05:00
Glenn Johnson	0662b953f0	New package - r-xml Tools for parsing and generating XML within R and S-Plus.	2016-07-31 14:25:17 -05:00
Glenn Johnson	1b04b8be01	New package - r-datatable Extension of Data.frame	2016-07-31 14:11:04 -05:00
Todd Gamblin	173a16b38a	Merge pull request #1396 from glennpj/r-quantmod New package - r-quantmod	2016-07-30 20:15:53 -07:00
Todd Gamblin	68ba5377c1	Merge pull request #1395 from glennpj/r-ggmap New package - r-ggmap and dependencies	2016-07-30 20:14:57 -07:00
Todd Gamblin	253507c0c3	Merge pull request #1394 from glennpj/r-maps New package - r-maps	2016-07-30 20:14:27 -07:00
Todd Gamblin	7684652ce3	Merge pull request #1393 from glennpj/r-maptools New package - r-maptools	2016-07-30 20:14:19 -07:00
Todd Gamblin	b12dc34ba7	Merge pull request #1391 from glennpj/r-caret New package - r-caret	2016-07-30 20:14:09 -07:00
Todd Gamblin	9c31ee8a75	Merge pull request #1390 from glennpj/r-glmnet New package - r-glmnet	2016-07-30 20:13:50 -07:00
Todd Gamblin	ae5ba2b110	Merge pull request #1389 from glennpj/r-vcd New package - r-vcd	2016-07-30 20:13:05 -07:00
Todd Gamblin	13499f1655	Merge pull request #1388 from glennpj/r-multcomp New package - r-multcomp	2016-07-30 20:12:51 -07:00
Todd Gamblin	49e9f365d8	Merge pull request #1387 from glennpj/r-randomforest New package r-randomforest	2016-07-30 20:12:21 -07:00
Glenn Johnson	41cd861861	New package - r-quantmod Qualitative Financial modelling framework.	2016-07-30 18:25:43 -05:00
Glenn Johnson	2913aa8d09	New package - r-ggmap and dependencies Spatial visualization with ggplot2	2016-07-30 18:14:02 -05:00
Glenn Johnson	1bd2def41e	New package - r-maps Draw geographical maps.	2016-07-30 17:34:07 -05:00
Glenn Johnson	386f0e577a	New package - r-maptools Tools for reading and handling spatial objects.	2016-07-30 17:26:31 -05:00
Glenn Johnson	7207ce2a18	New package - r-caret Classification and Regression Training	2016-07-30 16:53:54 -05:00
Glenn Johnson	20e52e5052	New package - r-glmnet Lasso and Elastic-Net Regularized Generalized Linear Models	2016-07-30 16:38:00 -05:00
Glenn Johnson	e9944150a5	New package - r-vcd Visualizing Categorical Data	2016-07-30 16:28:43 -05:00
Glenn Johnson	fc1804974c	New package - r-multcomp Simultaneous Inference in General Parametric Models.	2016-07-30 16:09:57 -05:00
Glenn Johnson	12167e8f37	New package r-randomforest Breiman and Cutler's Random Forests for Classification and Regression.	2016-07-30 15:39:28 -05:00
Glenn Johnson	8dc26bbcd9	Have R extensions build in parallel. Set `MAKEFLAGS` so R extensions can be built in parallel if that is set in spack.	2016-07-30 15:20:14 -05:00
Glenn Johnson	ee7acc6b13	New package r-car Companion to Applied Regression.	2016-07-30 15:10:25 -05:00
Kelly (KT) Thompson	6c80b15220	GTK+3: Provide updates to package dependencies. WIP: I started trying to build gtkplus@3.20, but this package has many more dependencies than v2 and it requires newer versions of existing packages. This commit provides updates for 5 packages that are required by GTK+3. This is not the complete set of changes required for GTK+3. atk - move default version from 2.14 -> 2.20. glib - move default version from 2.42 -> 2.49 - v2.49 requires pcre+utf as a new dependency. pcre - if variant +utf is selected, add '--enable-unicode-properties' to the configure options. libepoxy - new package to spack - manages OpenGL function pointers. pango - move default version from 1.36 -> 1.40	2016-07-29 09:05:44 -06:00
Denis Davydov	aad5a4c4b3	mkl: flake8 fixes; minor docu update	2016-07-29 14:12:07 +02:00
Denis Davydov	b6ce0e6f0e	trilinos: make sure hdf5 is picked up from Spack	2016-07-29 13:11:12 +02:00
Denis Davydov	943896e237	trilinos: fix lapack lib dir	2016-07-29 13:09:34 +02:00
Denis Davydov	8ee4df8101	hypre: minor cleanup related to blas/lapack	2016-07-29 11:37:19 +02:00
Denis Davydov	572f1cd427	mkl: symlink libs to prefix.lib	2016-07-29 11:36:37 +02:00
Todd Gamblin	e04662f84f	Merge pull request #1344 from LLNL/bugfix/py-nose-nosetests do not ignore nosetests script in py-nose	2016-07-28 10:19:13 -07:00
becker33	5caaa2cd75	Merge pull request #1331 from adamjstewart/fixes/mvapich2 MVAPICH2 depends on libpciaccess	2016-07-28 09:52:51 -07:00
becker33	3759f62cba	Merge pull request #1235 from davydden/pkg/p4est_run_tests p4est: use run_tests instead of a variant	2016-07-27 18:36:36 -07:00
George Hartzell	f855cf6bab	Add package for tree Add a package for [tree](http://mama.indstate.edu/users/ice/tree/). It has a Makefile that hardcodes a prefix and some CFLAGS. Used filter_file to: - set the make variable prefix to `prefix`; and - comment out their CFLAGS, just use ours.... It installs, runs on CentOS7, and uninstalls cleanly.	2016-07-27 11:32:03 -04:00
Todd Gamblin	458deaae5e	Merge pull request #1350 from adamjstewart/fixes/openssl Fix OpenSSL url_for_version	2016-07-27 08:08:00 -07:00
Greg Lee	e4525e57bb	intel parallel studio itac fixes	2016-07-25 14:02:15 -07:00
Greg Lee	dba384108b	intel parallel studio setup mkl environment	2016-07-25 14:01:49 -07:00
Samuel Knight	a2d4dcc636	Added libhio package	2016-07-25 17:32:03 +00:00
becker33	969e785d94	Merge pull request #1352 from glennpj/r_googlevis New package - r-googlevis	2016-07-25 10:25:47 -07:00
becker33	5b7ec8de95	Merge pull request #1351 from glennpj/r_htmlwidgets New packages - R htmlwidgets	2016-07-25 10:25:19 -07:00
Glenn Johnson	eb865b0df2	Add py-setuptools as dependency With the addition of dependency types and with `py-setuptools` set as type='build' there are more packages that need to have `py-setuptools` added as a dependency. This PR adds that dependency for the following packages: - py-h5py - py-networkx - py-pytables - py-scikit-image	2016-07-25 11:23:09 -05:00
Glenn Johnson	81cd458c26	r-curl update and chaged remote archive This updates to the 1.0 version of r-curl. The remote archive directory name also changed so change that here as well.	2016-07-24 16:48:07 -05:00
Glenn Johnson	27986c9edf	New packages - R htmlwidgets	2016-07-24 16:43:35 -05:00
Glenn Johnson	b7bf88c761	New package - r-googlevis	2016-07-24 16:38:36 -05:00
Adam J. Stewart	29278090eb	Fix OpenSSL url_for_version	2016-07-24 15:19:27 -05:00
Glenn Johnson	a8855f48aa	Add dependency type tp r- packages This PR adds the `nolink` dependency type to r- package dependencies. This is needed due to the new dependency types in Spack. A couple of packages were updated with new versions as well.	2016-07-23 19:43:55 -05:00
Greg Lee	773bca159a	do not ignore nosetests script in py-nose	2016-07-22 15:49:36 -07:00
Glenn Johnson	ec9959b152	R extension dependencies with compiler wrapper This commit introduces a mechanism to insure that R package dependencies are built with the Spack compiler wrapper. A copy of Makeconf is made before `filter_compilers` is called. This is then pointed to by the R_MAKEVARS_SITE environment variable set up in `setup_dependent_environment`. With this the normal compilers are used outside of spack and the spack wrapper compilers are used inside of spack. This commit also standardizes on the `join_path` call. It also sets the commented build command to reflect what is actually used with the newer string formatting.	2016-07-22 17:05:01 -05:00
Adam J. Stewart	1be486c90a	Add CGNS package	2016-07-22 17:02:45 -05:00
Todd Gamblin	395c616a48	Merge pull request #950 from xjrc/packages/python Enhancement Proposal: Make Python Spack Installs Ignore User Configuration	2016-07-22 13:56:19 -07:00
Joseph Ciurej	fa92f58167	Adding temporary script that fixes all Python extensions w/ 'setup_py'.	2016-07-22 11:17:19 -07:00
Joseph Ciurej	ac2e0962ce	Improved the build flag construction code in the python install method.	2016-07-22 11:12:02 -07:00
Joseph Ciurej	fb2d2303d6	Fixed a bug that was causing Python installs to be affected by user config.	2016-07-22 11:11:08 -07:00
Todd Gamblin	f5b4664c7c	Merge pull request #1336 from glennpj/rcase Fix alpha case of dependencies for some r-packages	2016-07-22 10:08:14 -07:00
Todd Gamblin	adffba5081	Merge pull request #1230 from hartzell/update-jdk Add URL and md5 for jdk-8u92.	2016-07-21 22:06:29 -07:00
Glenn Johnson	e083c91d5e	Fix alpha case of dependencies. A while ago I was asked to convert packages to all lowercase. That was done but some dependencies did not get converted in the specification. This commit fixes that as well as a couple of urls that need to be made explicit and a missing dependency on jdk.	2016-07-21 19:58:04 -05:00
Todd Gamblin	ed737cb2a2	Merge pull request #1333 from LLNL/features/no-openssl-pinging Remove remote website pinging from OpenSSL	2016-07-21 16:46:59 -07:00
Todd Gamblin	488550c2e6	Merge pull request #1334 from hartzell/add-gcc-5.4.0 Update gcc package with info about gcc-5.4.0	2016-07-21 16:37:31 -07:00
Todd Gamblin	8523f75e6c	Remove remote website pinging from OpenSSL - OpenSSL no longer checks remote versions on the openssl site. - Spack is used on systems that aren't connected to the internet, and this check is probably in the wrong place and affects too many commands. We can work on figuring out a better, more configurable place to put a check like this.	2016-07-21 16:35:20 -07:00
George Hartzell	4efe022165	Update with info about gcc-5.4.0	2016-07-21 15:36:22 -04:00
Mitchell Devlin	796308ed85	edit	2016-07-21 13:39:27 -05:00
George Hartzell	4c105895ab	Fix flake8 violations	2016-07-21 14:24:51 -04:00
George Hartzell	9523e50732	Fix shebang line in tcl scripts Lmod's configure script goes to the trouble of finding tclsh. This change uses that info to rewrite the #! lines in the tcl scripts so that they call the tclsh that the configure script discovered. It needs to massage the existing shebang lines into something that the sed statement in the makefile can manipulate and it needs to add the path_to_tclsh info into the set of sed statements. Checked with versions 6.4.1 and 6.3.7 (the checksum for 6.0.1 is incorrect, a fix for another time).	2016-07-21 13:58:16 -04:00
George Hartzell	52f0249c61	tcl is actually a runtime dependency. lmod uses tclsh at runtime, so adjust the depends_on accordingly (thanks @davydden!).	2016-07-21 13:51:03 -04:00
George Hartzell	a27cb639d8	The lmod package should depend_on('tcl') The lmod package needs a tclsh. Up until now it just assumed that one was available on the system. This change adds a depends_on('tcl') to the lmod package. The tcl package installs a tclsh script with an embedded version number (e.g. tclsh8.6) but the lmod configuration looks for tclsh. This change extends the tcl package to symlink tclshX.Y to tclsh in the tcl package bin directory.	2016-07-21 13:51:03 -04:00
Adam J. Stewart	cf8f14780f	MVAPICH2 depends on libpciaccess	2016-07-21 11:13:17 -05:00
Glenn Johnson	ead1b93f75	MPI related changes - Redid the code for setting the itac symlink for the cluster edition. - Removed the *PATH variables for MPI to avoid a conflict with other MPI environment modules. - Added missing test for `+all` when checking variants.	2016-07-20 20:03:05 -05:00
Glenn Johnson	0be4c7dfbd	Changes as discussed in PR review - removed unneeded entry for `debugger/gdb/intel64_mic` - set `+mpi` directory name to impi	2016-07-20 20:03:05 -05:00
Glenn Johnson	5e5e36a659	Fix flake8 errors.	2016-07-20 19:54:35 -05:00
Glenn Johnson	16f67b5bb1	Setup environment for Intel Parallel Studio Set up the environment for the Intel compilers and tools. This commit does the following: - Unset variables that were incorrect from the auto guess prefix inspections. - Add a RemovePath environment_modifications_formats for dotkit. - Set the module environment variables appropriate for the different variants. - Change the component logic so that the '+all' variant works. It was getting split by letter and leaving COMPONENTS empty. - Added a variant checking function. - Added NONRPM_DB_DIR to the silent.cfg so that the product database goes to the installation directory. - With the product database in prefix the code to remove the product database file from the home directory is no longer needed and was removed. - Reformat the 'tools' variant description. There are probably more variables needed for the '+tools' for the 'professional' product version but I do not have access to that.	2016-07-20 19:54:35 -05:00
mwilliammyers	b8444aa518	Merge remote-tracking branch 'upstream/develop' into package-opencv * upstream/develop: (126 commits) Fix indent/flake8 error. openexr : Add new package Set environment variables Added gnu packages datamash, parallel, and screen added package as argument to setup_platform_environment ilmbase : Add new IlmBase package Documented linker default fixed flake errors removed commented-out code Set default link type to dynamic on cray. Includes hooks for platform-based environment changes fixed flake errors fixed flake errors Improved cray_xc detection bug fix Improved cray_xc detection remove FIXMEs Ensure that per-4.4.1 NetCDF doesn't use HDF5 1.10 Re-ignore licenses directory Add "default" configuration scope. Draft CDO Make frontend OS on Cray machines a proper linux distro. ...	2016-07-20 18:34:53 -06:00
mwilliammyers	a09bebcaea	opencv : Add section comments	2016-07-20 18:19:59 -06:00
mwilliammyers	a9541997ae	opencv : Reorder depends_on statements	2016-07-20 18:19:03 -06:00
mwilliammyers	bd02892f7b	opencv : Use dso_suffix for python lib	2016-07-20 18:10:10 -06:00
mwilliammyers	ea9fa81ba5	opencv : Fix python include dir for cmake	2016-07-20 18:10:09 -06:00
mwilliammyers	670157b364	opencv : Add zlib cmake support	2016-07-20 18:10:09 -06:00
mwilliammyers	e5ae48a9da	opencv : Add jasper cmake support	2016-07-20 18:10:09 -06:00
mwilliammyers	47514d07b1	opencv : Use dso_suffix	2016-07-20 18:10:08 -06:00
mwilliammyers	f2e8f27c15	opencv : Add libpng cmake support	2016-07-20 18:10:08 -06:00
mwilliammyers	fc79b104f0	opencv : Add libjpeg-turbo cmake support	2016-07-20 18:10:07 -06:00
mwilliammyers	97143768c8	opencv : Add libtiff cmake support	2016-07-20 18:10:07 -06:00
mwilliammyers	d3b97227a1	opencv : Add optional jdk dependency	2016-07-20 18:10:07 -06:00
mwilliammyers	da2b695f93	opencv : Fix lib finding for python	2016-07-20 17:25:05 -06:00
mwilliammyers	10c285a774	opencv : Use string.format()	2016-07-20 17:25:01 -06:00
mwilliammyers	0654ee6a10	opencv : Fix style inconsistencies	2016-07-20 17:24:55 -06:00
mwilliammyers	8cf03c209f	opencv : Make extending python optional	2016-07-20 17:24:50 -06:00
mwilliammyers	c588ce9648	opencv : Improve cmake detecting python	2016-07-20 17:24:46 -06:00
mwilliammyers	3fac2dcc41	opencv : Fix cmake not disabling gtk	2016-07-20 17:24:40 -06:00
mwilliammyers	0080ffcf9f	opencv : Use `in` operator	2016-07-20 17:24:35 -06:00
mwilliammyers	ce902bf27a	opencv : Minor style changes	2016-07-20 17:24:30 -06:00
mwilliammyers	2cde6aaabd	opencv : Add GUI support	2016-07-20 17:24:26 -06:00
mwilliammyers	578ddea418	opencv : Fix pep8 style issues	2016-07-20 17:24:21 -06:00
mwilliammyers	cf0f5756f5	opencv : Fix python extensions issues	2016-07-20 17:24:13 -06:00
mwilliammyers	9e1d26e973	opencv : Add CUDA extensions	2016-07-20 17:23:46 -06:00
Todd Gamblin	e389afedaa	Merge pull request #1323 from glennpj/rlib Set environment variables for R	2016-07-20 15:43:26 -07:00
Todd Gamblin	b9c79824a2	Merge pull request #1313 from sknigh/gnu-tools Added packages for GNU tools screen, datamash, and parallel	2016-07-20 15:38:55 -07:00
Todd Gamblin	0777d3a5ba	Merge pull request #1326 from mwilliammyers/package-openexr openexr : Add new package	2016-07-20 15:35:36 -07:00
Mitchell Devlin	2344ffd0c7	add libxsmm package	2016-07-20 16:36:31 -05:00
Glenn Johnson	0c75174ec3	Fix indent/flake8 error.	2016-07-20 15:56:20 -05:00
mwilliammyers	e973adf84b	openexr : Add new package	2016-07-20 14:49:03 -06:00
Glenn Johnson	f9137f606f	Set environment variables This commit adds `setup_environment` to export the libraries and headers. Fixes #1314.	2016-07-20 15:37:31 -05:00
Todd Gamblin	d8acd41ba1	Merge pull request #1321 from mwilliammyers/package-ilmbase ilmbase : Add new IlmBase package	2016-07-20 13:13:21 -07:00
Todd Gamblin	8efbec3c0b	Merge pull request #1292 from eschnett/eschnett/hdf5-default-1.10 Make newest HDF5 release the default version	2016-07-20 12:57:45 -07:00
Todd Gamblin	4c7c9f4ff5	Merge pull request #1303 from adamjstewart/features/armadillo Updates to Armadillo package	2016-07-20 12:56:41 -07:00
Samuel Knight	24c14ff7a8	Added gnu packages datamash, parallel, and screen	2016-07-20 19:53:14 +00:00
mwilliammyers	c9f4e8ce5a	ilmbase : Add new IlmBase package	2016-07-20 13:13:47 -06:00
alalazo	40cb314638	Merge branch 'develop' of https://github.com/LLNL/spack into features/install_with_phases Conflicts: lib/spack/spack/package.py	2016-07-20 21:02:19 +02:00
Todd Gamblin	4434f482c0	remove FIXMEs	2016-07-20 09:48:54 -07:00
Todd Gamblin	3def8ef60e	Merge branch 'cdo' of https://github.com/robertdfrench/spack into robertdfrench-cdo	2016-07-20 09:48:01 -07:00
Todd Gamblin	20584ab084	Merge pull request #1302 from robertdfrench/adios-url Get adios from github, not NCCS	2016-07-20 09:47:23 -07:00
Todd Gamblin	7c28338d60	Merge pull request #1301 from robertdfrench/silver-searcher Silver Searcher 0.32 is out	2016-07-20 09:47:12 -07:00
Todd Gamblin	17a63c9646	Merge pull request #1284 from eschnett/eschnett/py-h5py.2 Declare dependency of "py-h5py +mpi" on "py-mpi4py"	2016-07-20 09:45:54 -07:00
Todd Gamblin	7f20678969	Merge pull request #1291 from eschnett/eschnett/netcdf-4.4.1 Update NetCDF to version 4.4.1	2016-07-20 09:34:14 -07:00
Erik Schnetter	69e36c9821	Ensure that per-4.4.1 NetCDF doesn't use HDF5 1.10	2016-07-20 11:25:46 -04:00
Robert D. French	6b0fb476ab	Draft CDO	2016-07-19 15:57:55 -07:00
Robert D. French	1c9cf668a1	Silver Search 0.32 is out PEP8 Love + Re-adding v0.30.0	2016-07-19 10:48:53 -07:00
Adam J. Stewart	8034536054	Fix shared object suffix for macOS	2016-07-19 12:37:34 -05:00
Adam J. Stewart	afa4cdc2d8	Updates to Armadillo package	2016-07-19 12:33:04 -05:00
Robert D. French	25e765baae	Download Adios from Github Get adios from github, not NCCS Use correct hash, thanks Ben	2016-07-19 10:31:59 -07:00
Todd Gamblin	a64a2e72cf	Merge pull request #1226 from adamjstewart/features/tkinter Add Tkinter support for Python	2016-07-19 09:41:12 -07:00
Todd Gamblin	4ad29b6c9b	Merge pull request #1262 from davydden/pkg/suite_sparse_fix_blas suite-sparse: enable TBB and fix Blas/Lapack libs	2016-07-19 09:18:42 -07:00
Erik Schnetter	71684cb071	Flex requires m4	2016-07-18 23:04:20 -04:00
Erik Schnetter	4dec06e4f4	Make HDF5 1.10 the default version Apply this only after NetCDF 4.4.1 is supported.	2016-07-18 20:14:44 -04:00
Erik Schnetter	94df1b801a	Update NetCDF to version 4.4.1 This version supports HDF5 1.10 in a backward-compatible manner.	2016-07-18 20:11:32 -04:00
Todd Gamblin	7555c3d949	Merge pull request #1204 from goxberry/cmake-3.6.0 cmake@3.6.0	2016-07-18 16:53:17 -07:00
Todd Gamblin	25a9181a1b	Merge pull request #1287 from mwilliammyers/package-jasper jasper: Add new jasper package	2016-07-18 15:43:18 -07:00
mwilliammyers	02340062b4	package - jasper - Add new jasper package	2016-07-18 16:17:07 -06:00
Todd Gamblin	607813d5ce	setuptools is a build dependency in numpy.	2016-07-18 14:13:14 -07:00
Erik Schnetter	67fade5b1e	Declare dependency of "py-h5py +mpi" on "py-mpi4py"	2016-07-18 17:08:56 -04:00
Todd Gamblin	a9ed2296a1	Merge pull request #1282 from eschnett/eschnett/py-numpy py-numpy: Add py-setuptools dependencies	2016-07-18 13:58:17 -07:00
Todd Gamblin	fa0bbb57ea	Merge pull request #1270 from davydden/pkg/mumps_scalapack_fix_blas Pkg/mumps scalapack fix blas	2016-07-18 13:57:26 -07:00
Erik Schnetter	49cd6f6269	py-numpy: Add py-setuptools dependencies Closes #1281.	2016-07-18 16:01:48 -04:00
Todd Gamblin	089189afaf	Merge pull request #1238 from davydden/pkg/mkl_update mkl: add provide blas/lapack	2016-07-18 11:52:30 -07:00
Adam J. Stewart	ea425a101a	Flake8 and new tk version	2016-07-18 07:51:08 -05:00
Adam J. Stewart	583232ea52	Build Python with Tkinter support	2016-07-18 07:51:08 -05:00
Todd Gamblin	b3789a4693	Merge pull request #1269 from davydden/pkg/hypre_trilinos_blas Pkg/hypre trilinos blas	2016-07-18 03:06:37 -07:00
Denis Davydov	2e4966c854	netlib-scalapack: use dso_suffix	2016-07-18 10:11:18 +02:00
alalazo	6c00a13ed5	Merge branch 'develop' of https://github.com/LLNL/spack into features/install_with_phases Conflicts: var/spack/repos/builtin/packages/swiftsim/package.py	2016-07-18 08:49:24 +02:00
Todd Gamblin	c898b9db04	Merge pull request #1188 from epfl-scitas/packages/py-numpy RPATH for blas in py numpy	2016-07-17 21:20:39 -07:00
Todd Gamblin	28ce08b9e2	Merge pull request #1258 from eschnett/eschnett/openmpi-2.0.0 Update to OpenMPI 2.0.0	2016-07-17 21:01:21 -07:00
Denis Davydov	1bd3a702c9	mumps: flake8 fixes	2016-07-16 15:14:06 +02:00
Denis Davydov	561748a063	netlib-scalapack: flake8 fixes	2016-07-16 08:03:54 +02:00
Denis Davydov	9ea4f80f15	flake8 fixes	2016-07-16 07:58:51 +02:00
Denis Davydov	0752eccfa5	mumps: don't hardcode blas name; remove unused depends_on(lapack)	2016-07-16 07:38:42 +02:00
Denis Davydov	6175ce7559	netlib-scalapack: make sure Spack's Lapack is used	2016-07-16 07:37:38 +02:00
Denis Davydov	987fb137f9	trilinos: don't hardcode blas/lapack names	2016-07-16 07:31:38 +02:00
Denis Davydov	514c61b8fe	hypre: don't hardcode blas/lapack/mpi; optionally run tests	2016-07-16 07:28:31 +02:00
Denis Davydov	96e9dbca08	suite-sparse: enable TBB and fix Blas/Lapack libs	2016-07-16 00:33:39 +02:00
Erik Schnetter	5a1ed51dcd	Correct indentation	2016-07-15 18:10:33 -04:00
becker33	c0be585b67	Merge pull request #1168 from epfl-scitas/packages/gts gts : added package	2016-07-15 14:07:59 -07:00
becker33	656b2d562f	Merge pull request #1177 from epfl-scitas/packages/swiftsim_and_metis swiftsim : fixed configuration for metis	2016-07-15 14:05:28 -07:00
becker33	f761130343	Merge pull request #1187 from paulhopkins/bugfix/python-updates Bugfix/python updates	2016-07-15 14:04:46 -07:00
becker33	f1d85ac2e9	Merge pull request #1227 from glennpj/ggvis New package - r-ggvis	2016-07-15 14:00:15 -07:00
becker33	37ce4108ce	Merge pull request #1254 from mdevlin1/features/hmmer add HMMER package	2016-07-15 13:52:56 -07:00
Erik Schnetter	4663288b49	Update to OpenMPI 2.0.0	2016-07-15 13:00:48 -04:00
George Hartzell	64b1bafd41	Make flake8 happy with .../jdk/package.py My PR for adding a new jdk version failed its travis run because of existing flake8 violoations. This package cleans them up. I'm not particularly pythonic, but most of the complaints were obvious. HOWEVER, I'm not particularly confident about handling long lines by taking an flake8 exception comment onto the end. Feedback welcome...	2016-07-15 12:39:40 -04:00
Mitchell Devlin	5f1b6f000d	add HMMER package	2016-07-15 11:03:57 -05:00
Denis Davydov	b29b7595dd	mkl: add info on interface and threading layers to the docstring	2016-07-15 17:35:10 +02:00
alalazo	893a5565fe	Merge branch 'develop' of https://github.com/LLNL/spack into features/install_with_phases Conflicts: lib/spack/spack/__init__.py var/spack/repos/builtin/packages/gmp/package.py var/spack/repos/builtin/packages/openjpeg/package.py	2016-07-15 11:02:55 +02:00
Todd Gamblin	077848fc0b	Merge pull request #378 from mathstuf/dep-types dependency types	2016-07-15 00:29:16 -07:00
Todd Gamblin	f3e9588457	Fix package name bug.	2016-07-14 23:15:54 -07:00
Gregory Becker	487ec2aff1	added py-pydatalog package	2016-07-14 23:12:35 -07:00
Todd Gamblin	b8e2799700	Add GNU Prolog package.	2016-07-14 14:38:30 -07:00
Ben Boeckel	a0584c78a8	foam-extend, sundials: add cmake as a builddep The sundials doesn't use CMake directly, but it is referenced in the patch step. I suspect it calls CMake somewhere else in its build system.	2016-07-14 16:21:47 -04:00
Ben Boeckel	d71a12438b	cantera: use nolink for python module dependencies Unsure about this, but this is probably true.	2016-07-14 16:21:47 -04:00
Ben Boeckel	39aef5fc00	lua: bring in run deps of build and run deps	2016-07-14 16:21:47 -04:00
Ben Boeckel	a82385cdae	R: look only at run dependencies of build and run deps	2016-07-14 16:21:46 -04:00
Ben Boeckel	0ca1a481a3	python: setup the dependent environment properly We want the run dependencies of all build and run dependencies of the current package.	2016-07-14 16:21:46 -04:00
Ben Boeckel	ac1701ae29	msgpack-c: add missing dependency on cmake	2016-07-14 16:21:46 -04:00
Ben Boeckel	77965ce5bf	py-matplotlib: require py-setuptools to build	2016-07-14 16:21:46 -04:00
Ben Boeckel	6fd45520da	deptypes: mark deptypes in packages	2016-07-14 16:21:46 -04:00
Ben Boeckel	45c675fe7f	spack: introduce dependency types deptypes: allow for different queries For things like Python modules, they are required for the build and runtime, but rather than adding a new parameter for what to query across the dependency DAG, just expose the recursive query parameter.	2016-07-14 16:21:46 -04:00
Ben Boeckel	bdf82246f7	darwin: explicitly use the 'when=' kwarg	2016-07-14 16:21:45 -04:00
Ben Boeckel	1ae43b3405	doxygen: add missing import	2016-07-14 16:21:45 -04:00
Denis Davydov	668b4f1b2c	mkl: set MKLROOT	2016-07-13 23:36:23 +02:00
Adam J. Stewart	3864da6300	Flake8	2016-07-13 11:45:16 -05:00
Adam J. Stewart	d09b0c95ec	Filter both makefiles to allow intel to build bzip2	2016-07-13 11:45:16 -05:00
alalazo	7cedd620f1	package.py : added CMakePackage, changed qhull, ibmisc, openjpeg to work as examples	2016-07-13 17:36:06 +02:00
Denis Davydov	de9cce3e80	p4est: flake8	2016-07-13 11:45:33 +02:00
Denis Davydov	52ca215e29	mkl: add provide blas/lapack	2016-07-13 11:42:40 +02:00
Denis Davydov	b8bd02c5b2	p4est: use run_tests instead of a variant	2016-07-13 10:56:40 +02:00
alalazo	5cc59507f7	package.py : hdf5 and lzo have examples of run_tests	2016-07-13 09:27:09 +02:00
alalazo	97c2224cd6	package.py : extra arguments, fixed inheritance issue - added attribute to hold extra arguments in PackageBase instances - fixed registration from within packages - examples : hdf5, lzo	2016-07-13 09:27:09 +02:00
alalazo	a43c63f149	package : added EditableMakefile Modifications : - added EditableMakefile to PackageBase subclasses - astyle modified as an example - preliminary hook to stop at a certain phase of install	2016-07-13 09:27:09 +02:00
alalazo	8f75d34331	package : added a stub for AutotoolsPackage, examples in szip and swiftsim	2016-07-13 09:27:09 +02:00
alalazo	8ed028e2d6	package : introduced InstallPhase, added decorators for prerequisites and sanity_checks of phases	2016-07-13 09:27:09 +02:00
George Hartzell	a73d91a2e5	Add URL and md5 for jdk-8u92. Installed on Centos7.2 system, `java -version` works.	2016-07-12 16:59:08 -04:00
Glenn Johnson	955d02049c	New package - r-ggvis Bring in ggvis and dependencies. GGvis is an implementaion of the 'Grammar of Graphics', combined with shiny.	2016-07-12 12:27:54 -05:00
Todd Gamblin	069de3f008	Merge pull request #1223 from glennpj/tidyr New package - r-tidyr	2016-07-12 00:23:09 -07:00
Todd Gamblin	04b3d8d86f	Merge pull request #1222 from glennpj/libxml2 Use the site_packages_dir from the Python class	2016-07-12 00:22:45 -07:00
Glenn Johnson	502d15fd3b	New package - r-tidyr Tools for changing the layout of data sets.	2016-07-11 21:12:28 -05:00
Glenn Johnson	5e323b052a	Remove import of os The import of `os` is no longer needed.	2016-07-11 20:21:25 -05:00
Glenn Johnson	81daaddfe9	Use the site_packages_dir from the Python class It is not necessary to set site_packages_dir in this package as it is already provided by the Python package class.	2016-07-11 20:08:30 -05:00
Todd Gamblin	15790d7018	Merge pull request #1207 from davydden/pkg/dealii_update_petsc37 dealii: update for petsc37	2016-07-11 15:32:32 -07:00
Glenn Johnson	1b08296392	Fix flake8 error	2016-07-11 17:22:31 -05:00
Glenn Johnson	8de84b5d8a	Fix error reported on Google Groups list Fixes the reported `TypeError: not enough arguments for format string` error.	2016-07-11 16:56:26 -05:00
Todd Gamblin	efdcd199c1	Merge pull request #1218 from glennpj/dplyr New package - r-dplyr	2016-07-11 13:19:09 -07:00
Glenn Johnson	d99fbbb68f	New package - r-lubridate Functions to work with date-times and timespans.	2016-07-11 14:59:47 -05:00
Glenn Johnson	11960e53ef	New package - r-dplyr This brings in dplyr and dependencies.	2016-07-11 14:50:33 -05:00
Todd Gamblin	255d05a9c1	Merge pull request #1214 from glennpj/rfilter Filter compilers for R	2016-07-11 11:37:39 -07:00
Glenn Johnson	664bdd359f	Filter compilers for R This adds a filter_compilers function to have the Makeconf file for R point to the actual compilers rather than the spack wrappers. Also added version 3.3.1.	2016-07-11 13:29:43 -05:00
Todd Gamblin	691e628726	Merge pull request #1206 from davydden/pkg/slepc_371_fix slepc: fix install_name for binaries on macOS for 3.7.1	2016-07-11 09:14:53 -07:00
Paul Hopkins	0d3a52ae29	Fix typo in Octave variant suitesparse	2016-07-11 16:00:19 +01:00
Denis Davydov	1b553f2b21	dealii: fix directory structure	2016-07-11 13:21:16 +02:00
Denis Davydov	f14cd67446	dealii: flake8 fixes	2016-07-11 10:56:57 +02:00
Denis Davydov	84afaf385f	dealii: run tests only when self.run_tests=true	2016-07-11 10:22:29 +02:00
Denis Davydov	1cc6e42682	dealii: add petsc/slepc 3.7 support	2016-07-11 10:20:15 +02:00
Denis Davydov	38550bbc1b	slepc: fix install_name for binaries on macOS for 3.7.1	2016-07-11 10:17:09 +02:00
Geoffrey Oxberry	7551e4c14f	cmake@3.6.0 Add CMake version 3.6.0.	2016-07-10 18:02:51 -07:00
Todd Gamblin	b0f4052bd8	Merge pull request #1169 from davydden/feature/install_argument_tests_petsc_fixes --run-tests install argument and petsc fixes	2016-07-09 12:10:16 -07:00
Denis Davydov	e482994a15	petsc: add -lm when building example	2016-07-09 08:12:34 +02:00
Erik Schnetter	c8137194f0	Update Cereal to 1.2.0	2016-07-08 15:20:09 -04:00
Todd Gamblin	f04258eb29	Merge pull request #1192 from SteVwonder/develop docbook-xml: replace 'cp -t' with install_tree	2016-07-08 11:09:41 -07:00
Todd Gamblin	1fa67e458c	Merge pull request #1194 from SteVwonder/lua-fix lua: switch self.version[:2] to .up_to(2)	2016-07-08 11:09:18 -07:00
Stephen Herbein	bb8a8ecda3	json-c: fix build by running serially	2016-07-08 10:39:47 -07:00
Paul Hopkins	49e8e4b590	Add comments explaining UCS4 and prevent variant being used on Python 3.3 and above	2016-07-08 13:47:25 +01:00
Stephen Herbein	1a1bf31032	lua: switch self.version[:2] to .up_to(2) Previous package would not install correctly, would throw: return os.path.join('share', 'lua', '%d.%d' % self.version[:2]) TypeError: %d format: a number is required, not Version	2016-07-07 18:58:52 -07:00
Stephen Herbein	1b53452618	docbook-xml: replace 'cp -t' with install_tree '-t' is not supported by the default cp on Mac OS X replace with install/install_tree cannot just use install_tree since shutil.copytree insists that the dst directory not exist	2016-07-07 17:41:53 -07:00
Nicolas Richart	d339f2af29	flake8 corrections	2016-07-07 18:22:27 +02:00
Nicolas Richart	4c1b53660d	fixes #719	2016-07-07 18:18:01 +02:00
Paul Hopkins	a2be05f24b	Fix whitespace	2016-07-07 14:00:37 +01:00
Paul Hopkins	719b6bfffd	Modify range for ucs4 2.* configure arguments	2016-07-07 13:18:40 +01:00
Paul Hopkins	8c1274bbbb	Fix Python configure arguments for ucs4 variant on Python 3.0 and above	2016-07-07 13:12:43 +01:00
Paul Hopkins	fb6d850637	Add more python versions	2016-07-07 13:09:08 +01:00
Todd Gamblin	6bb31a9a4c	Merge pull request #1175 from davydden/pkg/arpack-3.4.0 Pkg/arpack 3.4.0	2016-07-06 14:45:21 -07:00
Todd Gamblin	91da3d8e64	Merge pull request #1174 from LLNL/bugfix/github-1172-suite-sparse Bugfix/GitHub 1172 suite sparse	2016-07-06 14:35:59 -07:00
Todd Gamblin	c6e89d9283	Merge pull request #1180 from davydden/pkg/oce_update_and_fix oce: add 0.17.2; fix running tests	2016-07-06 14:27:05 -07:00
Denis Davydov	14cef6eab8	oce: flake8 fixes	2016-07-06 22:51:20 +02:00
Denis Davydov	c096bb332a	petsc: fix unit tests	2016-07-06 22:45:43 +02:00
Greg Lee	3df0f1902d	clean up suitesparse deps	2016-07-06 12:15:20 -07:00
Greg Lee	4e27d91351	flake 8 fixes	2016-07-06 11:51:32 -07:00
Denis Davydov	57eaea2e8c	oce: add 0.17.2; fix running tests	2016-07-06 20:35:59 +02:00
Paul Hopkins	61fe89bda0	Add ucs4 unicode variant to Python package	2016-07-06 18:29:54 +01:00
Denis Davydov	3d755a148b	arpack-ng: fix binaries for macOS	2016-07-06 18:30:38 +02:00
alalazo	379f23be02	swiftsim : fixed configuration for metis	2016-07-06 17:51:46 +02:00
Denis Davydov	c8fc56686c	arpack-ng: fix corrupted parpack_cmake.patch	2016-07-06 13:42:59 +02:00
Denis Davydov	63e45c586c	arpack-ng: flake8 fixes and minor update of incode comments	2016-07-06 13:27:02 +02:00
Denis Davydov	a47b3ba01b	arpack-ng: use spec['mpi'].mpif77	2016-07-06 13:23:51 +02:00
Denis Davydov	f5f7abd71f	arpack-ng: add 3.4.0 with cmake build	2016-07-06 12:59:42 +02:00
Greg Lee	4c063c6055	kludge to get suite-sparse-4.5.1 to link with -lstdc++	2016-07-05 13:48:32 -07:00
Greg Lee	976b2b4d25	added suitesparse version 4.5.3	2016-07-05 13:45:22 -07:00
Erik Schnetter	79b3ef0362	Don't enforce `hdf5~mpi`	2016-07-05 10:58:11 -04:00
alalazo	55c4a676ad	gts : added package	2016-07-05 14:30:48 +02:00
Todd Gamblin	d687e332ad	Fix compile bugs for gcc on Mac OS X with macports. - add macports to things that are cleaned out of the environment. - linker incompatibilities cause issues with packages like OpenSSL. - also clean up NOQA stuff in OpenSSL	2016-07-04 22:59:02 -07:00
Todd Gamblin	f2a692c515	Merge pull request #1163 from epfl-scitas/fixes/reserved_name_for_system_packages fixes : reserved name for system packages	2016-07-04 21:25:50 -07:00
Todd Gamblin	d166c04db5	Merge pull request #1166 from glennpj/rstan New package - RStan	2016-07-04 21:23:10 -07:00
Todd Gamblin	1de675e976	Merge pull request #1165 from robertdfrench/ruby-needs-ffi-zlib Ruby 2.2.0 needs ffi and zlib	2016-07-04 21:22:38 -07:00
Glenn Johnson	d5abcc5c88	Fix flake errors	2016-07-04 17:55:10 -05:00
Glenn Johnson	519b760222	New package - RStan This PR creates the RStan package and its dependencies.	2016-07-04 17:30:05 -05:00
Robert D. French	53bbbfbe21	Require libffi, zlib; Make Openssl, readline optional	2016-07-04 15:21:13 -04:00
Nicolas	85982017b6	Revert "Corrected the shared libraries and tests in mumps package"	2016-07-04 18:19:09 +02:00
alalazo	861f174f66	qa : fixed flake8 issues	2016-07-04 10:26:32 +02:00
alalazo	3e8391458c	openssl : changed tag for system reserved versions fixes #1150	2016-07-04 10:25:20 +02:00
Todd Gamblin	890df7153a	Merge branch 'efischer/160311-StagedPackage' of https://github.com/citibeth/spack into citibeth-efischer/160311-StagedPackage	2016-07-04 00:27:32 -07:00
Glenn Johnson	729f23b432	Use Executable to set script Use `Executable("./install.sh")` to set `install_script`. This allows it to work when the current directory is not on the PATH.	2016-07-01 22:13:40 -05:00
Tzanio Kolev	137db14b75	Update package.py	2016-06-30 15:40:02 -07:00
Tzanio	d3b0cb56b7	Updating MFEM package with v3.2 info.	2016-06-30 15:23:30 -07:00
Elizabeth Fischer	50ac98bc04	Merge remote-tracking branch 'upstream/develop' into efischer/160630-StagedPackage # Conflicts: # lib/spack/docs/packaging_guide.rst # lib/spack/spack/package.py Mostly minor/formatting issues in lib/spack/spack/package.py (the heavyweight merge was already done recently). Only one serious issue: it looks like the feature branch had accidentally deleted the line `spack.hooks.post_install(self)`. This got added back in from develop.	2016-06-30 09:13:24 -04:00
Todd Gamblin	a7b8cb6901	Merge pull request #1145 from davydden/pkg/petsc_tests petsc: run a test	2016-06-30 01:58:35 -07:00
Denis Davydov	6f4b0e9bda	petsc: fix flake8 and ~mpi case in tests	2016-06-30 08:22:01 +02:00
Denis Davydov	37728afada	petsc: run a test	2016-06-30 00:19:50 +02:00
Adam J. Stewart	2fcaa011ce	Add py-restview package	2016-06-29 12:57:58 -05:00
Todd Gamblin	7df89896f4	Merge pull request #1113 from davydden/octave_extensions Octave extensions	2016-06-29 00:38:05 -07:00
Todd Gamblin	0fd58fb585	Merge pull request #1133 from davydden/pkg/dealii_fix_tests dealii: run more unit tests when building @dev	2016-06-28 10:02:43 -07:00
Denis Davydov	32c801bbf6	dealii: run more unit tests when building @dev	2016-06-28 18:06:56 +02:00
Todd Gamblin	ad48ad7586	Merge pull request #1131 from epfl-scitas/fixes/swift_git_environment_variables fix : swiftsim will set git environment variables in the appropriate hook	2016-06-28 09:05:26 -07:00
alalazo	5cdd37959a	swiftsim : substituted tag with corresponding commit	2016-06-28 18:03:28 +02:00
Todd Gamblin	6810965457	Merge pull request #1130 from davydden/gmsh Gmsh -- various fixes	2016-06-28 08:49:06 -07:00
alalazo	18612eca59	qa : fixed flake8 issues	2016-06-28 12:59:13 +02:00
alalazo	48888b0f8e	swift : setting environment variables in the right place	2016-06-28 12:57:19 +02:00
Denis Davydov	c4c167c1ca	octave: rename executable Octave to octave	2016-06-28 11:25:45 +02:00
Denis Davydov	51b0f53b33	gmsh: flake8 fixes	2016-06-28 10:50:35 +02:00
Denis Davydov	06e38d2ca2	gmsh: various fixes (i) add new version (ii) add OCE, PETSc and SLEPc as dependencies (iii) fix Blas/Lapack configuration (iv) disable internal Metis which does not compile	2016-06-28 10:33:25 +02:00
Todd Gamblin	793c9f5546	Merge pull request #1116 from mwilliammyers/package-lrzip Add package lrzip & its dependency lzo	2016-06-27 22:32:57 -07:00
mwilliammyers	9bb918915f	Add package lrzip & its dependency lzo	2016-06-27 15:19:13 -06:00
Todd Gamblin	d7c2f683d9	Merge pull request #1004 from UCL-RITS/bare-eigen Option to install eigen without dependencies	2016-06-27 13:35:35 -07:00
Nicolas Richart	9026fb8e8a	Corrections for PETSc 3.7 and detection of PETSC version to enable TAO	2016-06-27 20:52:05 +02:00
Todd Gamblin	3ea9d1e665	Merge pull request #1122 from LLNL/bugfix/newarch-sys_type Bugfix/newarch sys type	2016-06-27 10:07:03 -07:00
Todd Gamblin	bf4eeb48b9	Merge pull request #1099 from adamjstewart/fixes/hdf5 Fix self-check for hdf5@1.10.0-patch1	2016-06-27 09:47:17 -07:00
Todd Gamblin	76458f5bfc	Merge pull request #1002 from epfl-scitas/packages/foam-extend Package foam-extend	2016-06-27 09:40:49 -07:00
Denis Davydov	0faa6dd753	octave: make extendable and add a package	2016-06-27 13:44:58 +02:00
Todd Gamblin	305d5698df	Rename spack.architecture.sys_type() to spack.architecture.platform()	2016-06-27 02:19:08 -07:00
alalazo	13fcb3c083	swift : renamed swiftsim	2016-06-27 09:25:58 +02:00
alalazo	f3f309a22a	Merge branch 'develop' of https://github.com/LLNL/spack into packages/swift_durham	2016-06-27 09:08:37 +02:00
Todd Gamblin	a1db306a0c	Merge pull request #1009 from epfl-scitas/packages/emacs Emacs: adding dependencies to be able to build without the system libs	2016-06-26 22:46:45 -07:00
Todd Gamblin	bad32724ec	Merge pull request #1092 from adamjstewart/features/netcdf-f Add latest version of netcdf-fortran and curl	2016-06-26 22:38:00 -07:00
Todd Gamblin	8b35940857	Merge pull request #1103 from adamjstewart/features/mpi Add MPI environment variables to packages	2016-06-26 22:35:39 -07:00
Todd Gamblin	f86f6c6274	Merge pull request #1104 from mwilliammyers/py-protobuf Add new package py-protobuf	2016-06-26 22:28:57 -07:00
Todd Gamblin	7d85902f37	Merge pull request #1093 from eschnett/eschnett/julia-update Update Julia to 0.4.6	2016-06-26 22:28:33 -07:00
Todd Gamblin	c096aa9557	Merge pull request #997 from glennpj/glib_gcc Get glib to compile with gcc-6.1	2016-06-26 22:28:07 -07:00
Nicolas Richart	f3accb111e	correcting flake8	2016-06-27 01:23:14 +02:00
Nicolas Richart	7cf1313572	changes to use from_sourcing_file	2016-06-27 00:55:26 +02:00
alalazo	9de0503188	qa : flake8 issues	2016-06-26 22:00:10 +02:00
alalazo	11863d2de3	packages : moved adios and mxml into builtin repo	2016-06-26 21:56:06 +02:00
alalazo	a2ba60f6a8	qa : flake8 issues	2016-06-26 17:38:48 +02:00
alalazo	e5b36583b5	swift : added package	2016-06-26 17:36:53 +02:00
alalazo	acd9014553	autotools : set Executable() in dependent modules	2016-06-26 17:36:33 +02:00
mwilliammyers	2c6c21a3bf	Add new package py-protobuf	2016-06-23 15:54:20 -06:00
Adam J. Stewart	8921bf4552	Add MPI environment variables to packages	2016-06-23 10:08:40 -05:00
Adam J. Stewart	d566510a40	Flake8 and url_for_version fixes	2016-06-22 15:22:42 -05:00
Adam J. Stewart	3f4bf04dde	Fix self-check for hdf5@1.10.0-patch1	2016-06-22 14:40:51 -05:00
Erik Schnetter	c904a42c5b	Address flake errors	2016-06-22 11:09:45 -04:00
Adam J. Stewart	b66f5b6231	Add latest version of cURL	2016-06-22 10:05:20 -05:00
Erik Schnetter	e398c0dc5b	Update Julia to 0.4.6	2016-06-22 11:00:00 -04:00
Adam J. Stewart	060fb596f7	Add latest version of netcdf-fortran	2016-06-22 09:52:17 -05:00
Nicolas Richart	97feca0888	Merge branch 'develop' into packages/foam-extend	2016-06-22 14:51:57 +02:00
Todd Gamblin	e41d67e031	Merge pull request #1078 from adamjstewart/features/pillow Allow py-pillow to link to Spack-built libraries	2016-06-22 01:11:25 -07:00
Todd Gamblin	8b5467e65d	Merge pull request #1049 from glennpj/newR_database New R database packages	2016-06-21 13:23:58 -07:00
Adam J. Stewart	a7ffb2c1a4	Flake8	2016-06-21 15:21:53 -05:00
Todd Gamblin	bbe2db5814	Merge pull request #1087 from LLNL/bugfix/new-harfbuzz-fix Bugfix/new harfbuzz fix	2016-06-21 13:10:50 -07:00
Adam J. Stewart	66089c89aa	Depend on pil	2016-06-21 14:55:49 -05:00
Adam J. Stewart	2efc67da60	Remove +tk variant, provide pil	2016-06-21 14:50:33 -05:00
Gregory L. Lee	e0fbf14f99	consolidated f2py regex	2016-06-21 09:23:58 -07:00
Gregory L. Lee	8f3954c1bd	flake 8 fixes for cairo, freetype, and harfbuzz	2016-06-21 08:47:22 -07:00
Gregory L. Lee	4041f45b6c	fixed conflicts in python package	2016-06-21 08:47:11 -07:00
Todd Gamblin	f18e1a9371	Merge branch 'features/cantera' of https://github.com/adamjstewart/spack into adamjstewart-features/cantera	2016-06-20 23:53:48 -07:00
Glenn Johnson	77cd474a2d	Make all packages lowercase.	2016-06-20 20:10:44 -05:00
alalazo	b86e3047f3	openmpi : revert part of #1079 (OpenMPI can be built without fortran) Building OpenMPI without fortran is possible, and was already handled. Raising an install error we effectively renounce at clang+OpenMPI. build_environment : sets 'CC', 'CXX', and similar variables only if a compiler is found	2016-06-20 20:46:11 +02:00
Todd Gamblin	f74d4b0660	Merge pull request #1052 from adamjstewart/features/psi4 Add Psi4 Package	2016-06-20 10:49:45 -07:00
Todd Gamblin	9b299cb2bb	Merge pull request #1023 from epfl-scitas/packages/mumps Corrected the shared libraries and tests in mumps package	2016-06-20 10:48:12 -07:00
Todd Gamblin	cec283f608	Merge pull request #1059 from epfl-scitas/packages/mpi_wrappers_with_rpath MPI : have wrappers set RPATH instead of RUNPATH	2016-06-20 10:47:24 -07:00
Todd Gamblin	c2d0870924	Merge pull request #1063 from eschnett/eschnett/openmpi-1.10.3 Update OpenMPI to 1.10.3	2016-06-20 10:45:56 -07:00
Todd Gamblin	31bb47356f	Merge pull request #1022 from glennpj/r-devtools new package: r-devtools	2016-06-20 10:34:23 -07:00
Todd Gamblin	b3881701c5	Merge pull request #1021 from glennpj/packrat new package: r-packrat	2016-06-20 10:33:55 -07:00
Todd Gamblin	0fbd2fe224	Merge pull request #1000 from glennpj/new_R Add version 3.3.0 of R and extensions	2016-06-20 10:33:43 -07:00
Todd Gamblin	c09111bbef	Merge pull request #1053 from davydden/pkg/dealii_suite_update update Petsc, Slepc, Trilinos, Superlu-dist and deal.II	2016-06-20 10:32:52 -07:00
Todd Gamblin	8047edfb56	Merge pull request #1029 from adamjstewart/features/armadillo Add Armadillo and SuperLU packages	2016-06-20 10:29:29 -07:00
Todd Gamblin	265b9bcb0f	Merge pull request #1076 from JRWynneIII/ferret Added spec to build Ferret	2016-06-20 10:28:42 -07:00
Adam J. Stewart	c9eb5f8173	Use non-checksummed PyPi download URLs	2016-06-20 12:24:45 -05:00
Adam J. Stewart	7e1ee463ca	Install examples for sundials	2016-06-20 12:24:45 -05:00
Adam J. Stewart	81ac3b62fc	Filter compilers and link boost properly	2016-06-20 12:24:45 -05:00
Adam J. Stewart	a21e845ce7	Flake8	2016-06-20 12:24:45 -05:00
Adam J. Stewart	2220784eda	Add scons support, .zip support, and Cantera package	2016-06-20 12:24:45 -05:00
Todd Gamblin	12b9d6da10	Merge pull request #1083 from robertdfrench/tmux-2.2 Tmux 2.2	2016-06-20 09:36:55 -07:00
Robert.French	83b0c16728	Tmux 2.2 with PEP8 Tmux 2.2 Provide variant to skip utempter Remove utempter variant; 2.2 doesn't need it Flake8ify	2016-06-20 16:26:49 +00:00
Erik Schnetter	e43eaad557	New package porta	2016-06-19 14:11:36 -04:00
Erik Schnetter	a0c0728ea8	New package polymake	2016-06-19 13:47:26 -04:00
Erik Schnetter	b4da4425ff	Add header files to lrslib install	2016-06-19 13:47:02 -04:00
Erik Schnetter	fa471a4ed1	Add missing header files to Bliss install	2016-06-19 13:46:38 -04:00
Erik Schnetter	d8b9cda632	Build Bliss both with and without GMP	2016-06-19 12:48:47 -04:00
Denis Davydov	cf4a34c657	openmpi: raise an error without Fortran compiler	2016-06-19 11:59:29 +02:00
Denis Davydov	1cc04cff27	openblas: raise an error without Fortran compiler	2016-06-19 11:59:10 +02:00
Erik Schnetter	71e92774eb	New package cddlib	2016-06-18 22:47:59 -04:00
Erik Schnetter	8fa8fc239f	New package "nauty and Traces"	2016-06-18 22:22:58 -04:00
Erik Schnetter	e5b08544ff	New package Panda	2016-06-18 22:02:36 -04:00
Erik Schnetter	2009354719	Add fourier tool to lrslib	2016-06-18 21:38:15 -04:00
Erik Schnetter	a5086f474e	New package lrslib	2016-06-18 18:03:09 -04:00
Erik Schnetter	92a7c0ddd5	Update Bliss to use -O3	2016-06-18 18:02:52 -04:00
Erik Schnetter	64aaf7ba81	New package cdd	2016-06-18 16:37:08 -04:00
Erik Schnetter	83d4cdc090	Update Bliss	2016-06-18 16:36:43 -04:00
Erik Schnetter	a07056d67b	Add Bliss package	2016-06-18 16:20:37 -04:00
Adam J. Stewart	652a5eb592	Allow py-pillow to link to Spack-built libraries	2016-06-17 18:09:03 -05:00
Todd Gamblin	62b2f2a7c9	Merge pull request #1065 from epfl-scitas/packages/espresso_update espresso : update to 5.4.0	2016-06-17 14:51:45 -07:00
Todd Gamblin	9a8d109650	Merge pull request #1044 from adamjstewart/features/sncosmo Add py-sncosmo package	2016-06-17 14:50:37 -07:00
Todd Gamblin	0bbbfc2ef7	Merge pull request #946 from LLNL/features/intel2 Intel software packages and license enhancements	2016-06-17 14:28:39 -07:00
Adam J. Stewart	536fa73d5f	Python flake8 overhaul	2016-06-17 13:33:09 -05:00
Robert D. French	448f8c43d4	Added working Ferret spec Fixed ferret spec. It builds now Made ferret spec more flake8-y Fixed homepage and info text about Ferret Removed vim swap file Reverted changes to netcdf-fortran spec and added netcdf~mpi dependency to ferret spec to compensate for it Fixed flake8 issues!	2016-06-17 14:23:50 -04:00
Adam J. Stewart	80d444624b	Fix activation of sites.py for sncosmo	2016-06-17 11:08:16 -05:00
Adam J. Stewart	24f65c502e	Add additional Astropy dependencies	2016-06-17 10:45:10 -05:00
Adam J. Stewart	b2aa78d6ab	Remove version constraints	2016-06-17 10:45:10 -05:00
Adam J. Stewart	4eeaff175c	Allow packages to build	2016-06-17 10:44:28 -05:00
Adam J. Stewart	a660c60eb1	Add py-sncosmo package	2016-06-17 10:43:34 -05:00
Glenn Johnson	8970785d33	Add 'jdk' as a dependency. Add jdk as a dependency so that R has support for java and allow packages that need java to work.	2016-06-16 23:08:55 -05:00
Glenn Johnson	a813f03955	Add list_url for old versions.	2016-06-16 23:08:55 -05:00
Glenn Johnson	4850b9d4d1	Make install comment consistent with actual call.	2016-06-16 23:08:55 -05:00
Glenn Johnson	7da405e630	Add validator for bioconductor packages This commit adds a validator function to make sure the versions of R and bioconductor are in sync.	2016-06-16 23:08:55 -05:00
Glenn Johnson	7213b12324	Tweak how R packages are built. Add bzip2 as a dependency to base R. Switch from installing the R packages from tar files to installing from the extracted directory. This is more in line with a standard install and also allows installing from VCS. Use the Bioconductor version for BiocGenerics and future Bioconductor packages. Suffix the package with 'bioc-$version' to indicate which Bioconductor release the package is a part of. This is actually more important than the actual version attached to individual packages although those are subject to change within the Bioconductor branch.	2016-06-16 23:08:55 -05:00
Glenn Johnson	0e64c25ffc	Fix flake8 errors Use Bioconductor provided Short URL for homepage in BiocGenerics. Wrap description text for utf variant in pcre.	2016-06-16 23:08:54 -05:00
Glenn Johnson	37dc13edaf	Update version of BiocGenerics The BioConductor repositories only keep the most recent version so this has to be bumped.	2016-06-16 23:08:54 -05:00
Glenn Johnson	8704a4ed35	Use configure_args rather than options Replaced 'options' with 'configure_args'. That seems like a better name and is consistent with the packaging guide.	2016-06-16 23:08:54 -05:00
Glenn Johnson	fe256870b4	Add variant for UTF support to pcre This will build PCRE with UTF support by default. That seems to be reasonable for most environments.	2016-06-16 23:08:54 -05:00
Glenn Johnson	cb3505769b	Clean up R extensions Run the existing R extension packages through autopep8 to clean up.	2016-06-16 23:07:13 -05:00
Glenn Johnson	6649f9edc2	Add version 3.3.0 of R This commit adds the 3.3.0 version of R and adds dependencies on curl and pcre.	2016-06-16 23:07:13 -05:00
Glenn Johnson	64acbbfcf0	Clean up R package files - remove unused imports - apply pep8 - reformat text strings	2016-06-16 23:07:13 -05:00
Todd Gamblin	9ee6cbfb40	Merge pull request #944 from adamjstewart/features/bertini Add bertini package	2016-06-16 16:57:50 -07:00
Todd Gamblin	344280154a	Merge pull request #962 from adamjstewart/features/hpl Add HPL benchmark package	2016-06-16 16:57:24 -07:00
Todd Gamblin	88b73bacdb	Merge branch 'features/newarch' into develop Conflicts: lib/spack/spack/config.py var/spack/repos/builtin/packages/lua/package.py	2016-06-16 03:03:26 -07:00
alalazo	a1cbb73f8b	qa : fixed flake8 issues	2016-06-16 11:24:18 +02:00
alalazo	8d9ffcf565	espresso : updated to 5.4.0, added Parallel=False	2016-06-16 11:22:26 +02:00
Todd Gamblin	76dfaa71a7	fix up packages for new architecture.	2016-06-16 01:47:20 -07:00
Todd Gamblin	40d25d9062	Add libxcb dependencies. Fix up packages to get py-basemap and stat to build.	2016-06-16 00:56:53 -07:00
Erik Schnetter	a7ab064a9e	Update OpenMPI to 1.10.3	2016-06-15 18:05:23 -04:00
Massimiliano Culpo	daa46105a7	mpich based providers : shortened filter_compilers	2016-06-15 21:37:12 +02:00
Adam J. Stewart	44e188f111	Remove MPI support, fix INCLUDE filters	2016-06-15 14:17:30 -05:00
Adam J. Stewart	7b97ea248a	More template filtering	2016-06-15 14:17:29 -05:00
Adam J. Stewart	9cf1257be4	Filter compilers	2016-06-15 14:17:29 -05:00
Adam J. Stewart	deb4f919cf	Psi4 tweaks	2016-06-15 14:17:29 -05:00
Adam J. Stewart	9d99042fed	Add Psi4 package	2016-06-15 14:17:29 -05:00
Denis Davydov	0e04e65ae0	trilinos: specify superlu-dist version dependency	2016-06-15 18:44:59 +02:00
Denis Davydov	5fe531050c	flake8 fixes for dealii	2016-06-15 18:33:34 +02:00
Denis Davydov	e76083205f	flake8 fixes for slepc	2016-06-15 18:33:08 +02:00
Denis Davydov	6390acc660	flake8 fixes for petsc	2016-06-15 18:32:42 +02:00
Denis Davydov	6d714e4425	flake8 fixes for superlu-dist	2016-06-15 18:31:39 +02:00
Denis Davydov	d0d83cfe1e	slepc: build by default with Arpack	2016-06-15 18:21:13 +02:00
Denis Davydov	d04dc8440f	dealii: specify petsc/slepc version dependencies	2016-06-15 18:21:13 +02:00
Denis Davydov	4d40f86bd3	trilinos: add 12.6.2 and 12.6.3	2016-06-15 18:21:13 +02:00
Denis Davydov	5358ffbe5a	slepc: add 3.6.3 and 3.7.1; specify petsc version dependency	2016-06-15 18:21:13 +02:00
Denis Davydov	9ceb8fea78	petsc: add 3.6.4 and 3.7.2; specify superlu-dist version dependency	2016-06-15 18:21:13 +02:00
Denis Davydov	a860a3d614	superlu-dist: avoid harcoding blas/lapack/mpi; remove preferred version	2016-06-15 18:21:13 +02:00
Todd Gamblin	c803f7ae98	Merge pull request #1045 from eschnett/eschnett/openmpi-verbs-usr Do not pass "/usr" or "/usr/local" as path to configure	2016-06-15 09:06:12 -07:00
Todd Gamblin	4ede87a8b0	Merge pull request #1058 from eschnett/eschnett/blosc Add packages c-blosc and hdf5-blosc	2016-06-15 09:04:48 -07:00
Todd Gamblin	9dd1f2747a	Merge pull request #1028 from JRWynneIII/boost-graph-parallel-fix Add variant for boost graph and parallel graph	2016-06-15 09:03:01 -07:00
Todd Gamblin	08badb5a35	Merge pull request #1040 from KineticTheory/pkg-trilinos Make Boost an optional feature of Trilinos.	2016-06-15 08:57:38 -07:00
Todd Gamblin	ff3469385b	Merge pull request #1037 from KineticTheory/develop Package serf also depends on zlib.	2016-06-15 08:57:14 -07:00
Todd Gamblin	bfedeadacb	Merge pull request #1031 from opoplawski/pcre Add patch to compile pcre with Intel 16.0.3 compiler	2016-06-15 08:56:53 -07:00
alalazo	b09bee8158	qa : fixed flake8 issues	2016-06-15 13:29:30 +02:00
alalazo	b59d4f243b	openmpi, mvapich2, mpich : filtered out "--Wl,--enable-new-dtag" in wrappers, as it turns RPATH into RUNPATH Apart from that turned `os.path.join` into `join_path` and `os.environ` into `env` in the packages	2016-06-15 13:21:39 +02:00
Erik Schnetter	05d7378da5	Install shared libraries correctly on Linux	2016-06-14 17:13:20 -04:00
Erik Schnetter	ca5180f7a2	Correct Blosc install on Darwin	2016-06-14 17:03:00 -04:00
Erik Schnetter	e6ec372926	Add packages c-blosc and hdf5-blosc c-blosc provides the Blosc compression filter, and hdf5-blosc provides a plugin for HDF5 to use that filter.	2016-06-14 09:59:48 -04:00
Glenn Johnson	e226837d33	Fix flake8 error.	2016-06-13 23:04:26 -05:00
Glenn Johnson	8861c99333	New package - r-foreign	2016-06-13 22:50:07 -05:00
Glenn Johnson	5ba5ef6c46	Add list_url for older versions.	2016-06-13 17:50:27 -05:00
Glenn Johnson	94d0f21823	New package - r-xlsxjars	2016-06-13 17:50:06 -05:00
Glenn Johnson	4767185082	New package - r-xlsx	2016-06-13 17:48:59 -05:00
Glenn Johnson	5cd09af066	New package - r-XLConnect	2016-06-13 17:48:44 -05:00
Glenn Johnson	3c234a7d3b	New package - r-XLConnectJars	2016-06-13 17:36:50 -05:00
Glenn Johnson	450b082daf	Do not need to depend on jdk here because R itself does.	2016-06-13 17:35:35 -05:00
Glenn Johnson	427fa7fd0a	New package - rJava	2016-06-13 17:26:01 -05:00
David Boehme	52160bff18	Use https for github	2016-06-13 11:47:28 -07:00
Glenn Johnson	d398ebe21f	New package - r-RSQLite	2016-06-12 22:06:06 -05:00
Glenn Johnson	b96b32e9ec	New package - r-RPostgreSQL	2016-06-12 22:05:45 -05:00
Glenn Johnson	77e8096a6f	New package - r-RODBC	2016-06-12 22:05:26 -05:00
Glenn Johnson	bfb0985c38	New package - r-RMySQL	2016-06-12 22:05:10 -05:00
Glenn Johnson	a7a640bfb8	New package - rDBI	2016-06-12 22:04:37 -05:00
Glenn Johnson	b05a565648	New package - mariadb	2016-06-12 22:04:09 -05:00
Glenn Johnson	5d3965c7a6	New package - unixODBC	2016-06-12 22:03:24 -05:00
Glenn Johnson	7727f6fc7e	New package - libaio	2016-06-12 22:02:46 -05:00
Glenn Johnson	4dcb15cf6d	Ran through autopep8 and cleaned up.	2016-06-12 22:00:49 -05:00
Glenn Johnson	bdb9af63ed	Add version 9.5.3 and add readline as a dependency.	2016-06-12 21:58:41 -05:00
Glenn Johnson	8ff7cbb9ce	Run binutils/package.py through autopep8.	2016-06-12 21:57:03 -05:00
Glenn Johnson	1601cf1b14	Patch binutils This commit adds a patch to update symbol versions from linker scripts. This is seen with libmysqlclient.so which has to maintain compatibility across two versions. Only one can be the default. https://sourceware.org/git/gitweb.cgi?p=binutils-gdb.git;a=commitdiff;h=544ddf9322b1b83982e5cb84a54d084ee7e718ea	2016-06-12 21:46:11 -05:00
Kelly (KT) Thompson	31d2c38687	Update formatting to meet code style requirements.	2016-06-12 19:56:29 -06:00
Kelly (KT) Thompson	b89bcdff62	Make Boost an optional feature of Trilinos. I have been unable to build Boost with some toolset/platform combinations. The users I support don't need the Boost features in Trilinos, so I have been manually hacking trilinos/package.py to disable boost. I would like to propose that these changes be added to the released version. + Add boost as a variant, default to true so there is no change to existing behavior. + Move the CMake configure options related to Boost into a conditional block that is triggered by "if '+boost' in spec".	2016-06-12 19:48:45 -06:00
Tom Scogland	1b28991e0a	Merge pull request #1026 from epfl-scitas/packages/lmod lmod : updated package and dependencies	2016-06-12 17:01:41 -07:00
Glenn Johnson	59c9816dbf	Make quotations in variables consistent.	2016-06-11 16:01:23 -05:00
Glenn Johnson	0e9f8bd38d	Add list_url for old versions.	2016-06-11 15:53:28 -05:00
Erik Schnetter	953b65abcc	Do not pass "/usr" or "/usr/local" as path to configure	2016-06-11 16:41:39 -04:00
Glenn Johnson	6c0ea77d1d	Add list_url for older versions.	2016-06-11 15:36:43 -05:00
Adam J. Stewart	85502e34f9	CMake knows how to create PIC	2016-06-10 14:35:19 -05:00
Kelly (KT) Thompson	883f601bca	Fix style issues.	2016-06-09 19:18:25 -06:00
Kelly (KT) Thompson	915115386a	Package serf also depends on zlib. + Add zlib as a required dependency. + Point scons build system to the spack provided zlib installation.	2016-06-09 18:30:28 -06:00
Orion Poplawski	454acf58af	Add additional blank line for flake8	2016-06-08 16:49:42 -06:00
Orion Poplawski	e3ca5e6676	Add patch to compile pcre with Intel 16.0.3 compiler	2016-06-08 16:23:04 -06:00
Adam J. Stewart	65896ff2ed	Add Armadillo and SuperLU packages	2016-06-08 14:11:14 -05:00
James Riley Wynne III	4b9707f8ea	Fixed flake8 formatting problems	2016-06-08 14:36:45 -04:00
James Riley Wynne III	42a10d5690	Fixes issue #438	2016-06-08 12:43:05 -04:00
Nicolas Richart	2d21693b9d	Missing file to patch mumps	2016-06-08 17:09:13 +02:00
alalazo	564483936f	qa : fixed flake8 issues	2016-06-08 16:33:49 +02:00
alalazo	4a61efe641	lmod : fixed issues with LUA_PATH during installation	2016-06-08 16:21:09 +02:00
alalazo	f4a39457de	lmod : updated package and dependencies	2016-06-08 15:35:15 +02:00
Nicolas Richart	165411f4a5	bug fix in the +mpi case	2016-06-08 15:17:12 +02:00
Nicolas Richart	498c098d11	Cleaning flake warnings in mumps package	2016-06-08 14:57:54 +02:00
Nicolas Richart	e124c86a4f	Corrected the shared libraries and tests in mumps package	2016-06-08 14:17:46 +02:00
Glenn Johnson	bb19dffb26	Fix flake8 error.	2016-06-07 23:40:12 -05:00
Glenn Johnson	ad0cfa41aa	Fix flake8 errors	2016-06-07 23:37:49 -05:00
Glenn Johnson	738720a000	new package: r-devtools This PR brings in the R devtools package and it dependencies.	2016-06-07 23:20:46 -05:00
Greg Lee	bb57b82794	flake8 fixes	2016-06-07 20:15:02 -07:00
Glenn Johnson	2262bc95f1	new package: r-packrat Manage the R packages your project depends on in an isolated, portable, and reproducible way. https://github.com/rstudio/packrat/	2016-06-07 22:04:11 -05:00
Greg Lee	25b2f7b1d7	put older versions back + version-specific dwarfdump dir	2016-06-07 20:02:38 -07:00
Mayeul d'Avezac	0b5ce9e16a	💄 style points requested by flake8	2016-06-03 11:52:19 +01:00
Nicolas Richart	8b6035ab82	Making emacs dependent on internal packages	2016-06-03 00:24:00 +02:00
Todd Gamblin	3d2b25e45c	Merge pull request #1014 from epfl-scitas/packages/mvapich2 Changes to take into account slurm in version @2.1: of mvapich2	2016-06-02 01:08:28 -07:00
Todd Gamblin	27bc49d8c8	Merge pull request #1001 from ashkan2200/develop Dealii, fixed issue with tests	2016-06-02 01:01:29 -07:00
Todd Gamblin	b843b73bb5	Merge pull request #1005 from eschnett/eschnett/hdf5-update Update HDF5 to version 1.10.0-patch1	2016-06-02 00:57:15 -07:00
Todd Gamblin	1fb4fa02e3	Merge pull request #1010 from epfl-scitas/packages/tetgen Adding a version to tetgen	2016-06-02 00:54:09 -07:00
Nicolas Richart	53dcc39b72	removing useless selfs	2016-06-01 17:33:54 +02:00
Nicolas Richart	3ab8468e73	Correcting the flake8 warnings	2016-06-01 16:43:08 +02:00
Nicolas Richart	0451c8e55f	Addapting the mvapich2@2.1: configure options for slurm	2016-06-01 15:58:00 +02:00
Nicolas Richart	d802144f39	Introduced a bug by correcting flake8 warnings	2016-06-01 03:31:29 +02:00
Nicolas Richart	5d4a0e4050	Corrections for flake8	2016-06-01 03:28:42 +02:00
Nicolas Richart	97bad2c1ac	Corrections for flake8	2016-06-01 03:25:37 +02:00
Nicolas Richart	58052e6632	Adding package fenics	2016-06-01 03:20:56 +02:00
Nicolas Richart	cb673765c2	Adding a version to tetgen	2016-06-01 03:02:48 +02:00
Nicolas Richart	0df0677d5b	Adding a variant to link against the spack libraries instead of the system ones	2016-06-01 03:00:03 +02:00
Nicolas Richart	9db8dc1895	Removing extra dependencies + minor fix according to remarks on #1002	2016-06-01 00:57:01 +02:00
Erik Schnetter	c03c689cb2	Update HDF5 to version 1.10.0-patch1	2016-05-31 12:18:17 -04:00
Adam J. Stewart	564e7f5e5b	Don't build in parallel	2016-05-31 09:32:24 -05:00
Mayeul d'Avezac	29b85fbce0	Eigen can be installed with dependencies	2016-05-31 10:10:12 +01:00
Ali Dorostkar	6f96484f83	Spacing correction More spacing correction	2016-05-31 09:58:29 +02:00
Ali Dorostkar	e82fb5b58f	Fixed spacing Replaced tabs with spaces	2016-05-31 08:44:46 +02:00
Todd Gamblin	f3f0122f11	Merge branch 'develop' into features/newarch	2016-05-30 13:54:53 -07:00
Ali Dorostkar	c4d5bd13c7	dealii, Added comment Added comment for why step-40 is done differently for dealii 8.4.0 and later	2016-05-30 18:11:34 +02:00
Nicolas Richart	fd345c8ef0	Merge branch 'packages/foam-extend' of github.com:epfl-scitas/spack into packages/foam-extend	2016-05-30 17:04:21 +02:00
Nicolas Richart	9f4e599232	Ignoring the flake8 error for a line too long	2016-05-30 16:58:06 +02:00
Nicolas Richart	08c8d1d1f7	limiting package to foam-extend to start	2016-05-30 16:49:25 +02:00
Nicolas Richart	4122ecbc80	First try at OpenFOAM-extend	2016-05-30 16:49:25 +02:00
Ali Dorostkar	4f591a6fe3	Step-40 test for 8.3.0 and earlier Integrated part of step-40 to be tested for earlier versions of dealii	2016-05-30 16:42:24 +02:00
Nicolas Richart	fe79e43459	limiting package to foam-extend to start	2016-05-30 15:46:39 +02:00
Ali Dorostkar	d7e84fe07c	dealii, test for specific version Specified that test case “step-40” is only to be run when using dealii version 8.4.0 or later	2016-05-30 14:03:27 +02:00
Glenn Johnson	66aaaa1751	Add a comment regarding the reason for the patch.	2016-05-29 15:30:09 -05:00
Ali Dorostkar	c2ac47235f	additional versions for Dealii Included additional versions for Deal.II package.	2016-05-29 13:22:19 +02:00
Glenn Johnson	c16d7c481c	Get glib to compile with gcc-6.1 This commit adds a patch to fix the case where gcc-6.1 emits an error for string format literal that was a warning in previous versions of gcc. The patch reference is https://bugzilla.gnome.org/show_bug.cgi?id=761550 Also ran the package file through autopep8.	2016-05-28 23:30:56 -05:00
Mario Melara	33e1dcc476	Adding mock package file for external module	2016-05-28 10:14:40 -07:00
Gregory Becker	9dad7c2ace	re-merged mainline develop	2016-05-27 13:13:19 -07:00
Greg Lee	6dcdb50a3e	Merge branch 'develop' of https://github.com/llnl/spack into develop	2016-05-27 12:44:57 -07:00
Greg Lee	0ae1298d25	updated libdwarf version and dwarfdump build	2016-05-27 12:43:13 -07:00
Adam J. Stewart	dd5a6914f1	Undo changes to flex	2016-05-27 12:56:43 -05:00
Todd Gamblin	f6a0cd1bf8	Merge pull request #973 from eschnett/eschnett/openmpi-verbs Auto-detect verbs location	2016-05-27 11:01:44 -05:00
Todd Gamblin	7b063e3e6c	Merge pull request #975 from adamjstewart/features/stream Add STREAM benchmark package	2016-05-27 10:59:13 -05:00
Todd Gamblin	dc4ca26441	Merge pull request #992 from davydden/update/dealii Update/dealii	2016-05-26 17:39:37 -05:00
Todd Gamblin	96f65479e7	Merge pull request #993 from xjrc/packages/metis Update Package : METIS/ParMETIS	2016-05-26 17:37:33 -05:00
Denis Davydov	040c122719	dealii: formatting	2016-05-26 23:00:22 +02:00
Denis Davydov	0036483ded	dealii: don't hardcode blas and mpi; minor fixes to dependencies	2016-05-26 18:07:27 +02:00
Todd Gamblin	76d42b5200	Merge pull request #982 from trws/rust Rust	2016-05-25 15:15:51 -05:00
Joseph Ciurej	734fb459a4	Fixing a small bug with metis@4+shared installs on the Mac platform.	2016-05-25 12:27:52 -07:00
Joseph Ciurej	483ec0d762	Added preliminary improved testing code for METIS@:4.	2016-05-24 16:13:52 -07:00
Joseph Ciurej	c9ba73d931	Added staging support and improved error handling for METIS@:4 installs.	2016-05-24 16:05:29 -07:00
Joseph Ciurej	b5d0a38860	Fixed a few linking/testing bugs in the METIS@:4 install method.	2016-05-24 15:03:21 -07:00
Greg Lee	1bca69f272	updated launchmon url and version	2016-05-24 14:54:09 -07:00
Joseph Ciurej	064d3584c0	Updating 'metis' and 'parmetis' to conform to PEP8 standards.	2016-05-24 12:28:05 -07:00
Joseph Ciurej	0ef6843d85	Improved MPI path specification for ParMETIS using PR #893 features.	2016-05-24 12:28:05 -07:00
Joseph Ciurej	9c95ec0b29	Updated and added new versions to the METIS/ParMETIS packages. - Added a 'url_for_version' function to the METIS/ParMETIS packages. - Added installation support for METIS@5.0.2 and ParMETIS@4.0.2. - Changed the 'double' variant to 'real64' to make it more consistent with the 'idx64' variant naming. - Removed an unnecessary dependency on gdb.	2016-05-24 12:28:05 -07:00
Denis Davydov	c78349a3a4	octave: fix formatting	2016-05-23 15:08:10 +02:00
Denis Davydov	ce3146e91a	octave: add missing dependencies and update to 4.0.2	2016-05-23 14:50:06 +02:00
Tom Scogland	00de72272d	rust compiler/builder package, new llvm variants	2016-05-22 11:16:00 -07:00
Tom Scogland	425beb4d97	updates for rust-bindgen	2016-05-22 11:16:00 -07:00
Tom Scogland	404b7c7c4f	initial rust support	2016-05-22 11:16:00 -07:00
Nicolas Richart	4c87ef915f	First try at OpenFOAM-extend	2016-05-22 18:55:29 +02:00
Erik Schnetter	09eed08b9c	Auto-detect verbs location	2016-05-20 16:24:48 -04:00
Todd Gamblin	d94972503a	Merge pull request #964 from davydden/update/tbb tbb: add 4.4.4; raise InstallError when building 4.4.3 with GCC6.1	2016-05-19 22:44:03 -07:00
Nicolas Richart	2e77cc635e	missing @ in version definition	2016-05-20 00:51:58 +02:00
Nicolas Richart	a233ed2de7	changes scotch package to make he coverage test pass	2016-05-20 00:42:34 +02:00
Nicolas Richart	a51566ec6e	changes to simplify the esmumps variant for version < 6.0.0 + typos corrections, according to the remarks on PR #979	2016-05-20 00:31:12 +02:00
Nicolas Richart	1bf306bbbd	Adding +metis variant to scotch + minor changes	2016-05-19 17:26:44 +02:00
Gregory Becker	9f59c128be	Partial merge of mainline develop	2016-05-18 15:13:40 -07:00
Tom Scogland	29635b7bbd	initial docs for find and flake8 cleanup	2016-05-18 14:04:39 -07:00
Adam J. Stewart	434ff28af4	Add STREAM benchmark package	2016-05-18 15:14:21 -05:00
Todd Gamblin	d391670755	Merge pull request #966 from verolero86/develop Add option to disable VT support in openmpi package	2016-05-18 08:36:23 -07:00
Todd Gamblin	78c46aab35	Merge pull request #969 from Rombur/boost Add boost 1.61.0	2016-05-18 08:35:51 -07:00
Todd Gamblin	637da63506	Merge pull request #948 from davydden/bugfix/astyle astyle: fix filter command which failed on OSX with python 2.7.10	2016-05-18 08:35:01 -07:00
Bruno Turcksin	bbbffe7423	Add boost 1.61.0	2016-05-18 08:51:22 -04:00
Denis Davydov	267666cd97	formatting	2016-05-18 08:35:47 +02:00
Greg Lee	582d01784a	added newdtags variant, default to false (i.e., remove --enable-new-dtags)	2016-05-17 21:18:34 -07:00
Todd Gamblin	d592a1655f	Merge pull request #961 from xjrc/features/flake8-improvements Enhancement Proposal: Exempt '@when' Functions from Style Redefinition Errors	2016-05-17 17:00:49 -07:00
Todd Gamblin	502420ceff	Merge branch 'features/cflags' into develop Conflicts: lib/spack/spack/cmd/find.py var/spack/repos/builtin/packages/ghostscript/package.py	2016-05-17 16:44:54 -07:00
Denis Davydov	1a187e73ae	tbb: add 4.4.4; raise InstallError when building 4.4.3 with GCC6.1	2016-05-17 22:57:32 +02:00
Todd Gamblin	138307dd0c	Merge pull request #955 from trws/lua-rework complete lua rework	2016-05-17 13:21:51 -07:00
Veronica G. Vergara Larrea	6c95a5d496	the right flag here is +, the default behavior is controlled in the variant	2016-05-17 14:37:36 -04:00
Adam J. Stewart	f16228d811	Add more install directories	2016-05-17 13:36:38 -05:00
becker33	3d9c8f4fd4	Merge pull request #952 from davydden/package/sed sed: add package	2016-05-17 11:27:57 -07:00
Adam J. Stewart	631cbdbda8	Flake8	2016-05-17 13:22:00 -05:00
Adam J. Stewart	7b9b18f03c	Add HPL benchmark package	2016-05-17 13:14:59 -05:00
Veronica G. Vergara Larrea	471950434e	add a flag to openmpi to allow users to disable vt support	2016-05-17 13:40:01 -04:00
Todd Gamblin	1774c7a7b3	Merge pull request #958 from trws/golang-new Golang new	2016-05-17 05:56:06 -07:00
Tom Scogland	80c02ad36a	flake8-related cleanup	2016-05-17 05:30:35 -07:00
Tom Scogland	af4af94203	rework for gopath and bootstrapping	2016-05-17 05:21:11 -07:00
Joseph Ciurej	761c5c8450	Added line limit exemptions for 'variant' and 'version' directives. Updated the 'scotch' package to use oneline 'variant' directives.	2016-05-16 12:14:57 -07:00
Joseph Ciurej	52c8bedb9c	Updated style checking to ignore refinition errors for '@when' fxns. Updated the Scotch package to conform to PEP8 standards and to test style checking improvements.	2016-05-16 11:09:44 -07:00
Todd Gamblin	a74bc9369b	Merge pull request #953 from citibeth/150514-NetCDFCXX4 netcdf-cxx4: Update to latest released version 4.3.0	2016-05-16 10:58:27 -07:00
Elizabeth Fischer	65ff89a0b0	Placate flake8 demands.	2016-05-16 12:53:24 -04:00
Tom Scogland	62dd040a8f	add GOPATH support Also fixes flex to depend on bison for its yacc implementation.	2016-05-16 09:30:37 -07:00
Tom Scogland	9780427940	fixing more flake8 errors that only appear on travis...	2016-05-16 05:37:04 -07:00
Tom Scogland	dacedfcc0e	formatting to appease flake8	2016-05-16 05:12:30 -07:00
Tom Scogland	52c359bc77	fix linking issue on ubuntu Evidently some readline variants are built with only a dynamic dependency on ncurses, this addresses that problem for such systems.	2016-05-16 03:36:31 -07:00
Todd Gamblin	53df9fbb4f	Merge pull request #959 from davydden/bugfix/doxygen_ghostscript_graphviz Bugfix/doxygen ghostscript graphviz	2016-05-16 00:12:59 -07:00
Denis Davydov	0fbf70d95d	indentation fixes	2016-05-15 23:37:09 +02:00
Denis Davydov	459c647bc9	doxygen: add graphviz variant; enable flex and bison on OSX and they build fine	2016-05-15 19:43:01 +02:00
Tom Scogland	71d9911539	go cleanup, adding hub	2016-05-15 10:23:33 -07:00
Tom Scogland	b7aa47a178	remove debug print	2016-05-15 09:52:09 -07:00
Denis Davydov	a045154b5e	graphviz: add missing dependency and fix installation on darwin	2016-05-15 18:34:50 +02:00
Denis Davydov	21d4f3a356	ghostscript: url was changed upstream	2016-05-15 18:33:06 +02:00
Greg Lee	c2ca5f44b4	flake8 fixes	2016-05-15 08:19:55 -07:00
Tom Scogland	2bfa4d7e4f	removing comments also randomly changed unnecessary licence block	2016-05-14 22:42:14 -07:00
Tom Scogland	577657b3f7	go rework This commit includes: * a new go package that uses gccgo to bootstrap the go toolchain * env support added to Executable * a new Go fetch strategy that uses `go get` to fetch a package and all of its deps * A platinum searcher package that leverages the new go package and fetch strategy	2016-05-14 22:35:55 -07:00
Tom Scogland	0816e9554d	adding go_compiler providers	2016-05-14 18:06:42 -07:00
Tom Scogland	915f91a619	moving go packages to the new path	2016-05-14 18:06:42 -07:00
Tom Scogland	0c33e8ac48	go and a basic go package	2016-05-14 18:06:41 -07:00
Tom Scogland	f50439b990	appeasing the great vengeful flake8 gods	2016-05-14 17:49:06 -07:00
Tom Scogland	0668b6d7ba	changes to appease flake8 for lua-luaposix package	2016-05-14 17:38:32 -07:00
Tom Scogland	21161a60ff	changes to appease flake8 (mostly) for lua package	2016-05-14 17:38:13 -07:00
Glenn Johnson	fffc2d2765	Updated turbomole package file. This PR updates the turbomole package file but does not introduce any new funtionality. The updtes are: - use spack interface for subprocess.PIPE and subprocess.Popen - clean up based on flake8 - remove some extra whitespace	2016-05-14 19:33:45 -05:00
Tom Scogland	b5979b13e3	complete lua rework, also module path fix This is a complete rework of the lua package, it also allows the environment modification classes to handle paths that are not separated by colons, and uses the support for same in TCL modules as well. The biggest difference is the handling for lua extension packages, which now have their paths set correctly by the lua parent package, and have access to both lua and luarocks as installation tools. See the luaposix package for what should be required for most lua packages after this.	2016-05-14 16:18:26 -07:00
Denis Davydov	c5a35acd67	sed: add package	2016-05-14 22:29:16 +02:00
Elizabeth Fischer	4bf9b168a5	netcdf-cxx4: Update to latest released version 4.3.0	2016-05-14 16:19:10 -04:00
Gregory L. Lee	e3cd0a67d0	address flake8 issues	2016-05-13 16:12:48 -07:00
Gregory L. Lee	e9b71872a8	addressed PR#946 comments from @adamjstewart	2016-05-13 15:16:07 -07:00
Todd Gamblin	4a6ec6377d	Merge pull request #940 from gzagaris/feature/doxygen-version-1.8.11 Add doxygen version 1.8.11	2016-05-13 10:10:23 -07:00
Denis Davydov	8db35ab9a2	openblas: use spack_cc/spack_f77 and add a note on compiler mixing	2016-05-13 17:28:30 +02:00
Denis Davydov	67999d1b1c	astyle: fix filter command which failed on OSX with python 2.7.10	2016-05-13 17:13:45 +02:00
George Zagaris	e763eeacdd	fix format in doxygen/package.py	2016-05-12 23:25:10 -07:00
Gregory L. Lee	b8a91db089	Intel software packages and license enhancements	2016-05-12 20:04:45 -07:00
Adam J. Stewart	088dce709e	Make flake8 happy	2016-05-12 16:33:37 -05:00
Adam J. Stewart	ab41fd6692	Add bertini package Also add missing dependency. Flex would not build for me without bison. It complained about not being able to find `yacc`.	2016-05-12 16:21:06 -05:00
Adam J. Stewart	03307f91df	Fix bug when compiling elk~mpi	2016-05-12 10:27:05 -05:00
Adam J. Stewart	3526d92660	Indentation fix	2016-05-12 10:27:05 -05:00
Adam J. Stewart	d7020434d9	Use new-ish blas_shared_lib and more flake8 fixes	2016-05-12 10:27:04 -05:00
Adam J. Stewart	e2e72b14b2	Use new openmp_flag and mpi attributes	2016-05-12 10:26:10 -05:00
George Zagaris	3ece0e7b76	Add doxygen version 1.8.11	2016-05-12 00:42:22 -07:00
Todd Gamblin	e7ced54369	Correct LLNL LGPL license template for clarity.	2016-05-11 21:22:25 -07:00
Todd Gamblin	14fe0b8ad2	Merge pull request #558 from adamjstewart/features/pgi Add Licensed Software Support	2016-05-11 17:17:47 -07:00
Todd Gamblin	2dc49ee88d	Merge pull request #938 from KineticTheory/pkg-moab Provide new package: MOAB	2016-05-11 17:14:05 -07:00
Kelly (KT) Thompson	c5a19b57f7	Clean up formatting.	2016-05-11 16:33:57 -06:00
Gregory Becker	2e1810e3a7	re-merging develop	2016-05-11 15:26:09 -07:00
Kelly (KT) Thompson	8bec127a1d	Attempt to fix formatting issues (flake8).	2016-05-11 14:00:44 -06:00
Kelly (KT) Thompson	9482ce1fce	Remove some extraneous comments.	2016-05-11 12:39:20 -06:00
Kelly (KT) Thompson	e200a41d3d	New package MOAB.	2016-05-11 12:34:33 -06:00
Adam J. Stewart	c043275f1b	Final flake8 changes	2016-05-11 11:46:41 -05:00
Adam J. Stewart	5879f8207f	Flake8 formatting changes	2016-05-11 11:32:08 -05:00
Adam J. Stewart	8ea5e946a2	Add Allinea packages	2016-05-11 11:32:08 -05:00
Adam J. Stewart	8bcb812529	Allow multiple license symlinks	2016-05-11 11:32:08 -05:00
Adam J. Stewart	6906911e85	Allow license files to use different symbols for comments	2016-05-11 11:32:08 -05:00
Adam J. Stewart	240c0643f2	Add NAG Fortran compiler package	2016-05-11 11:27:11 -05:00
Adam J. Stewart	82ce798f41	Bug fix	2016-05-11 11:27:11 -05:00
Adam J. Stewart	2fb128fb34	Add PGI Compiler Package	2016-05-11 11:27:11 -05:00
Denis Davydov	eba264fcd0	fix formatting	2016-05-11 16:11:34 +02:00
Denis Davydov	361b629034	openblas: make unit test more robust by outputing only the solution vector from dgesv	2016-05-11 15:10:13 +02:00
Denis Davydov	809ded74c9	add functions for simple unit tests; refactor openblas to use them	2016-05-11 15:10:13 +02:00
Todd Gamblin	9030541e4b	Merge pull request #929 from epfl-scitas/differentiate_framework_from_packages QA : make qa checking less painful	2016-05-11 02:26:07 -07:00
Todd Gamblin	d7847ff768	Use just one flake8 file; mark package.py files to avoid E501 w/url.	2016-05-11 01:16:41 -07:00
alalazo	7d74e209f3	qa : this should still fail due to F821	2016-05-10 19:20:26 +02:00
Todd Gamblin	3e717842c9	Merge pull request #924 from hegner/feature/python-diverse Add a few more python packages	2016-05-10 09:44:32 -07:00
Todd Gamblin	836d081bca	Merge pull request #927 from davydden/astyle_fix_ubuntu astyle: compile with spack_cxx	2016-05-10 09:43:44 -07:00
alalazo	979b53cab6	qa : modifying 2 packages and a framework file just for the sake of it	2016-05-10 18:33:07 +02:00
Tom Scogland	8fec824484	Merge pull request #769 from epfl-scitas/openmpi_variants openmpi : added variants	2016-05-10 09:02:33 -07:00
Denis Davydov	c8d8860742	astyle: fix formatting	2016-05-10 18:01:19 +02:00
Benedikt Hegner	fa44cd5cef	renaming py-Genshi into py-genshi	2016-05-10 17:30:44 +02:00
Benedikt Hegner	f5fb771573	fixing imports; configure commands aren't available at import time yet	2016-05-10 14:52:14 +02:00
Denis Davydov	cd9cdd6410	astyle: compile with spack_cxx	2016-05-10 13:37:57 +02:00
Benedikt Hegner	ad42579f08	addressing coding style rules	2016-05-10 13:17:36 +02:00
Benedikt Hegner	aca5941a0e	Add a few more python packages py-Genshi py-astroid py-jinja2 py-logilab-common py-markupsafe py-mistune py-prettytable py-py2neo py-storm	2016-05-10 11:48:18 +02:00
Todd Gamblin	35cf52d182	Merge pull request #707 from dhandeo/visit VisIt v2.10.1	2016-05-10 01:40:27 -07:00
Todd Gamblin	a1ebdf63f3	Merge pull request #812 from eschnett/eschnett/hdf5-check-install Check the installed HDF5 library for consistency	2016-05-10 01:34:10 -07:00
Todd Gamblin	6c46a5d623	Merge pull request #807 from gartung/fftw-openmp FFTW: openmp needs to be an option for clang build	2016-05-10 01:33:13 -07:00
Todd Gamblin	2a38ec4c93	Merge pull request #788 from citibeth/efischer/140416-UpdatePNetCDF parallel-netcdf: Updated package	2016-05-10 01:31:57 -07:00
Todd Gamblin	57e495943f	Merge pull request #757 from glennpj/extend_r Make R extendable	2016-05-10 01:30:13 -07:00
Todd Gamblin	b1da3664ec	Merge pull request #795 from adamjstewart/features/argcomplete Add argcomplete python package	2016-05-10 01:29:08 -07:00
Todd Gamblin	87c772b117	Merge pull request #845 from davydden/openblas_cleanup_unit_test openblas: fix a bug and cleanup the unit test	2016-05-10 01:28:49 -07:00
Todd Gamblin	ccccd7b60d	Merge pull request #806 from davydden/openblas_openmp_clang openblas: do not use OpenMP with Clang	2016-05-10 01:28:12 -07:00
Todd Gamblin	f21fcb3b88	Merge pull request #798 from jgalarowicz/osscbtf-changes Update the main Krell Institute and Argo Navis Tech. packages for MPI…	2016-05-10 01:26:48 -07:00
Todd Gamblin	d2004a186c	Merge pull request #825 from xjrc/packages/scotch Update Package : Scotch	2016-05-10 01:26:21 -07:00
Todd Gamblin	0f427ed334	Tweak nccmp to be more spack-compatible. - Spack doesn't set F90, but it confuses the nccmp build. Just remove it from the environment. - TODO: should build environment unset this variable?	2016-05-10 01:07:34 -07:00
Todd Gamblin	1cc94a0f79	Merge branch 'efischer/160425-nccmp' of git://github.com/citibeth/spack into citibeth-efischer/160425-nccmp	2016-05-10 01:04:46 -07:00
Todd Gamblin	1568e64f95	Merge pull request #862 from davydden/glib_libxcb_missing_dependencies Glib libxcb missing dependencies	2016-05-10 00:57:27 -07:00
Todd Gamblin	5e471719a6	Merge pull request #907 from eschnett/eschnett/binutils-werror Disable -Werror	2016-05-10 00:54:24 -07:00
Todd Gamblin	2fde72075f	Merge pull request #918 from hegner/bugfix/bison Add missing m4 dependency to bison	2016-05-10 00:54:04 -07:00
Todd Gamblin	e672e10219	Merge pull request #912 from citibeth/efischer/160506-NCO nco: Added new package	2016-05-10 00:53:51 -07:00
Todd Gamblin	a996b8aa7f	Merge pull request #919 from jppelteret/bugfix/gmsh-2 GMsh: Fix binary linking against its own libraries	2016-05-10 00:53:22 -07:00
Todd Gamblin	813fefbc71	Merge pull request #922 from bcouturi/gdbupdate Added gdb 7.11 released on 24 Feb 2016	2016-05-10 00:53:00 -07:00
Todd Gamblin	e3115aa505	Kripke variants.	2016-05-10 00:31:06 -07:00
alalazo	474048ae8b	openmpi : fixes #920 , added sqlite as a dependency The default for the variant `pmi` has been set to `False` `sqlite` is now a dependency if `+sqlite3`	2016-05-10 09:02:16 +02:00
alalazo	405b04efab	Merge branch 'develop' of https://github.com/LLNL/spack into openmpi_variants	2016-05-10 08:40:26 +02:00
Denis Davydov	b063ab42bf	openblas: fix and cleanup the unit test	2016-05-10 07:33:57 +02:00
Todd Gamblin	2e0ee5404d	clean up Kripke package and dependencies.	2016-05-09 17:14:25 -07:00
Todd Gamblin	92b7534885	Merge branch 'features/kripke' of git://github.com/tzislam/spack into tzislam-features/kripke	2016-05-09 17:00:47 -07:00
Tanzima Z. Islam	23ec6c6bb0	Removed FIXME comments	2016-05-09 16:34:27 -07:00
Tanzima Z. Islam	045e5bd458	Adding a new package: Kripke from the public tar ball	2016-05-09 16:22:07 -07:00
Joseph Ciurej	ceab445b9f	Integrated improvements from PR #893 to remove hardcoded MPI path.	2016-05-09 14:39:42 -07:00
Joseph Ciurej	88d2f6b83a	Enabled the '+esmumps' variant for 'scotch@:6.0.0'. Added support for 'scotch@6.0.0'.	2016-05-09 14:19:42 -07:00
Joseph Ciurej	7e6be184bc	Updated and fixed the Scotch package. - Fixed a bug that was causing shared library usage to fail when linking with another application. - Updated the repository URL to allow for more general version downloading. - Added installation support for version 5.1.10b. - Cleaned up the installation file to make it a bit easier to follow and modify.	2016-05-09 14:19:42 -07:00
Ben Couturier	3948b082ad	Added gdb 7.11	2016-05-09 22:32:46 +02:00
Jean-Paul Pelteret	970196d825	GMsh: Fix binary linking against its own libraries GMsh binary now links against full path name of libraries. This fixes problems, such as `dyld: Library not loaded: libGmsh.2.11.dylib`, when running the executable.	2016-05-09 14:23:07 +02:00
Benedikt Hegner	6e07f46df8	add missing m4 dependency to bison	2016-05-09 14:02:41 +02:00
alalazo	3d7684277a	Merge branch 'openmpi_variants' of github.com:epfl-scitas/spack into openmpi_variants Conflicts: var/spack/repos/builtin/packages/openmpi/package.py	2016-05-09 10:56:26 +02:00
alalazo	497ed9f933	Merge branch 'develop' of https://github.com/LLNL/spack into openmpi_variants Conflicts: var/spack/repos/builtin/packages/openmpi/package.py	2016-05-09 08:23:30 +02:00
Todd Gamblin	ea408cc0d0	Merge pull request #911 from castillo23/packages/crypto add support for crypto version 5.6.1	2016-05-08 14:40:21 -07:00
Todd Gamblin	7145b72482	Merge pull request #914 from trws/packages-leading-to-neovim pile of dependencies for neovim, including luajit and libuv	2016-05-08 14:37:51 -07:00
Todd Gamblin	bd63545b0c	Merge pull request #913 from trws/mpi-should-have-pmi add pmi support and process managers to the MPIs	2016-05-08 14:36:38 -07:00
Jean-Paul Pelteret	95c7f4fba3	Fixes #915	2016-05-08 16:53:31 +02:00
Denis Davydov	72b91758c9	openblas: raise an error when using +openmp with clang; set +openmp to false by default	2016-05-08 16:51:06 +02:00
Massimiliano Culpo	7d5bb088b4	Merge branch 'develop' of https://github.com/LLNL/spack into openmpi_variants Conflicts: var/spack/repos/builtin/packages/openmpi/package.py	2016-05-07 15:08:27 +02:00
Tom Scogland	22afc6dadd	pile of dependencies for neovim, including luajit and libuv	2016-05-06 15:33:26 -07:00
Tom Scogland	7ec28231d9	Merge pull request #906 from adamjstewart/features/xerces-c Remove FIXME comments	2016-05-06 15:30:09 -07:00
Tom Scogland	1de110fbba	Merge pull request #794 from adamjstewart/features/jpeg Add latest jpeg version	2016-05-06 15:20:43 -07:00
Tom Scogland	7dbf6f97f6	Merge pull request #841 from eschnett/eschnett/hwloc Update hwloc to 1.11.3	2016-05-06 15:19:16 -07:00
Tom Scogland	1cf2526a79	Merge pull request #865 from davydden/silver_searcher_dependencies the_silver_searcher: add missing dependency	2016-05-06 15:18:50 -07:00
Tom Scogland	86449790fe	add pmi support and process managers to the MPIs	2016-05-06 15:15:40 -07:00
Elizabeth Fischer	c82db2116b	nco: Added new package	2016-05-06 17:42:42 -04:00
Cecilia W. Castillo	7bf724b1d3	add support for crypto version 5.6.1	2016-05-06 14:14:13 -07:00
Tanzima Z. Islam	9f212e7201	Adding a new package file for Kripke	2016-05-06 13:50:34 -07:00
Erik Schnetter	db80c5e97e	Disable -Werror This leads to problems if new compiler versions report new kinds of warnings.	2016-05-05 21:11:54 -04:00
Gregory Becker	11b62114bb	versioning the database	2016-05-05 16:58:00 -07:00
Gregory Becker	44f089508b	Changed other packages to fit new syntax	2016-05-05 15:40:22 -07:00
Gregory Becker	d45b2c7947	Fixed openssl to work with new syntax	2016-05-05 15:36:48 -07:00
Adam J. Stewart	1203a14563	Remove tutorial comments	2016-05-05 14:01:21 -05:00
Todd Gamblin	9fb1a9537d	Merge branch 'develop' into features/cflags	2016-05-05 10:49:15 -07:00
Robert D. French	18d2b28c49	Build and install BBCP Build and install BBCP Use correct destination for install	2016-05-05 10:58:24 -04:00
Todd Gamblin	10b0cb108c	Merge pull request #893 from davydden/mpi_dependent_env Introduce variables for MPI compiler wrappers and document their usage	2016-05-05 01:40:11 -07:00
Denis Davydov	c3bc4d6195	mpich: remove module.mpicc as no formula is using it and it is a duplicate of self.spec.mpicc	2016-05-05 10:28:04 +02:00
Denis Davydov	b12fb7ebc8	mpi: move mpicc/mpicxx/mpifc/mpif77 to setup_dependent_package()	2016-05-05 10:24:32 +02:00
Todd Gamblin	56557f7ff6	Merge pull request #871 from davydden/dealii_updated_dependencies dealii: add new dependency -- gsl	2016-05-05 01:00:55 -07:00
Todd Gamblin	4ee1bca1d9	Merge pull request #881 from KineticTheory/pkg-superlu-dist + Add version 5.0 download for SuperLU_DIST.	2016-05-05 00:57:24 -07:00
Todd Gamblin	c6a7af3fa7	Merge pull request #885 from davydden/p4est_test_option p4est: put back +tests variant	2016-05-05 00:53:58 -07:00
Todd Gamblin	d00680a883	Merge pull request #886 from eschnett/eschnett/openblas-make Disable OpenBLAS's overriding of our "make -jN" option	2016-05-05 00:53:47 -07:00
Todd Gamblin	c7f23ca0d6	Merge pull request #887 from adamjstewart/features/openmpi Re-add hwloc as a dependency of openmpi	2016-05-05 00:53:10 -07:00
Todd Gamblin	d0acc9827a	Merge pull request #884 from davydden/libtool_missing_dependency libtool: add a missing dependency	2016-05-05 00:52:39 -07:00
Todd Gamblin	c1010c3422	Merge pull request #889 from adamjstewart/features/netcdf Remove hdf5 ~cxx constraint on netcdf	2016-05-05 00:51:49 -07:00
Todd Gamblin	1181ad2bf0	Merge pull request #891 from adamjstewart/features/gcc Add latest version of GCC	2016-05-05 00:51:05 -07:00
Todd Gamblin	053e687e79	Merge pull request #800 from eschnett/eschnett/qthreads Add some qthreads patches	2016-05-05 00:49:32 -07:00
Todd Gamblin	7ac8ddde96	Merge pull request #897 from robertdfrench/https-urls-for-subversion Build Subversion with HTTP/S support	2016-05-05 00:20:59 -07:00
Todd Gamblin	3dd5b2845b	Merge pull request #900 from eschnett/eschnett/flex Update Flex to 2.6.0	2016-05-05 00:11:50 -07:00
Todd Gamblin	55f1cafb70	Merge pull request #899 from LLNL/bugfix/github-808-mrnet added git commit for clang support	2016-05-05 00:11:19 -07:00
Dhanannjay 'Djay' Deo	ef202fbe0c	Build static and shared libraries for silo	2016-05-04 22:50:15 -04:00
Dhanannjay 'Djay' Deo	45e77e7739	Correctly extend std_cmake_args	2016-05-04 22:49:47 -04:00
Dhanannjay 'Djay' Deo	1785de0f31	remove hdf5 which is silo actually a silo dependency	2016-05-04 22:08:01 -04:00
Erik Schnetter	27de2a42d9	Update Flex to 2.6.0	2016-05-04 20:27:58 -04:00
Greg Lee	514a8c737a	added git commit for clang support	2016-05-04 16:38:43 -07:00
Dhanannjay 'Djay' Deo	32f7b06a36	Add version 2.10.2	2016-05-04 18:14:38 -04:00
Patrick Gartung	67d64b804f	more succinctly	2016-05-04 23:53:10 +02:00
Robert.French	bfe009f98d	Subversion uses serf for http repos Add Scons package Add serf package Subversion uses serf for http repos	2016-05-04 16:16:36 +00:00
Denis Davydov	796bf5f85c	mvapich2: add self.spec.[mpicc\|mpicxx\|mpifc\|mpif77]	2016-05-04 17:33:19 +02:00
Patrick Gartung	7eb463a66e	only fail when it is apples clang	2016-05-04 15:05:56 +02:00
Denis Davydov	f417b1cf90	p4est: use mpicc,mpicxx,mpifc,mpif77 compiler variables instead of hardcoding names	2016-05-04 11:51:45 +02:00
Denis Davydov	c3317819cb	mpi: add self.spec.[mpicc\|mpicxx\|mpifc\|mpif77] to avoid hardcoding MPI wrappers names	2016-05-04 10:37:52 +02:00
Adam J. Stewart	88fa9084e2	Add latest version of GCC	2016-05-03 15:58:14 -05:00
Adam J. Stewart	a3d2d0cd22	Add latest OpenSSL versions	2016-05-03 15:44:23 -05:00
Adam J. Stewart	eaa45d8a9a	Remove hdf5 ~cxx constraint on netcdf	2016-05-03 13:28:38 -05:00
Kelly (KT) Thompson	f4260da1c2	Mark SuperLU_DIST version 4.3 as the preferred version since petsc and trilinos are not tested with 5.0.	2016-05-03 12:05:35 -06:00
Adam J. Stewart	51c6867f72	Re-add hwloc as a dependency of openmpi	2016-05-03 10:30:35 -05:00
Erik Schnetter	40d578be95	Disable OpenBLAS's overriding of our "make -jN" option	2016-05-03 10:38:05 -04:00
Denis Davydov	0583bc9859	p4est: put back +tests variant	2016-05-03 16:21:10 +02:00
Denis Davydov	98f8192bde	libtool: add a missing dependency	2016-05-03 15:15:55 +02:00
Kelly (KT) Thompson	89621faaea	+ Add version 5.0 download for SuperLU_DIST.	2016-05-02 20:21:03 -06:00
David Poliakoff	e74cc0df27	Updated docstring	2016-05-02 15:53:43 -07:00
David Poliakoff	afef04bb54	Added cnmem package`	2016-05-02 15:49:37 -07:00
David Poliakoff	179d308fe0	Added a package for the RAJA system	2016-05-02 14:32:57 -07:00
Todd Gamblin	372a455bea	Merge pull request #873 from jppelteret/bugfix/paradiseo Add extra dependencies for Paradiseo	2016-05-02 09:57:30 -07:00
Todd Gamblin	aa7444cd3d	Merge pull request #870 from jppelteret/bugfix/glm Add missing dependency for glm	2016-05-02 09:57:11 -07:00
Todd Gamblin	4fecf33416	Merge pull request #877 from vishalkenchan/develop bugfix: missing dependencies (m4) added for netcdf and autoconf	2016-05-02 09:56:44 -07:00
Denis Davydov	2eb4248f90	dealii: fix a bug where P4EST_DIR was unconditionally requested	2016-05-02 18:53:13 +02:00
Denis Davydov	cde1d18399	dealii: add new dependency -- gsl	2016-05-02 18:53:13 +02:00
Todd Gamblin	999dda8f83	Merge pull request #708 from adamjstewart/fixes/qt Prevent use of system GTK+	2016-05-02 09:41:51 -07:00
Todd Gamblin	568800c045	Merge pull request #875 from jppelteret/features/adol-c Added Adol-C package	2016-05-02 09:30:23 -07:00
Adam J. Stewart	7255f6969b	Merge branch 'develop' into features/argcomplete	2016-05-02 11:29:52 -05:00
Adam J. Stewart	17fa1b5007	Un-fix version 3	2016-05-02 11:28:20 -05:00
Adam J. Stewart	61e5ee5d63	Prevent use of system GTK+	2016-05-02 11:28:20 -05:00
Massimiliano Culpo	cfc25d0a92	Merge branch 'develop' into openmpi_variants	2016-05-02 18:26:05 +02:00
Adam J. Stewart	9c3d8dae57	Add latest jpeg version	2016-05-02 11:17:38 -05:00
Adam J. Stewart	4e2154e58f	Add argcomplete python package	2016-05-02 11:16:29 -05:00
Adam J. Stewart	c110865bf2	Remove OpenMPI dependency on hwloc	2016-05-02 11:06:33 -05:00
Adam J. Stewart	b99c8b641a	Add hydra package	2016-05-02 11:06:33 -05:00
Vishal Boddu	e111add17f	missing dependencies (m4) added for netcdf and autoconf	2016-05-02 14:31:02 +02:00
Jean-Paul Pelteret	5ae7276682	Fixes to installation with OpenMP (tested) and execution of test-suite	2016-05-02 11:01:14 +02:00
Jean-Paul Pelteret	631e235ef3	Added Adol-C package	2016-05-01 11:07:42 +02:00
Jean-Paul Pelteret	c33ffbae04	Add extra dependencies for Paradiseo.	2016-04-30 22:25:14 +02:00
Patrick Gartung	83108f815c	Error out if +openmp used with OS X clang	2016-04-30 13:18:32 -05:00
Patrick Gartung	f8c14e1d98	Make openmp variant false by default.	2016-04-30 13:18:32 -05:00
Patrick Gartung	a588a1fd84	openmp needs to be an option for clang build	2016-04-30 13:18:32 -05:00
Jean-Paul Pelteret	8fc43046eb	Add missing dependency for glm	2016-04-30 12:11:10 +02:00
Denis Davydov	3ad71700dd	the_silver_searcher: add missing dependency	2016-04-29 09:52:49 +02:00
Denis Davydov	176b9febb4	libxcb: add missing dependencies	2016-04-29 09:06:15 +02:00
Denis Davydov	17f696d3b3	glib: add missing dependencies	2016-04-29 09:05:54 +02:00
Todd Gamblin	1b731e525f	Merge pull request #703 from epfl-scitas/fixes/openssl_external fix : no warning when installing 'openssl@external'	2016-04-28 10:25:35 -07:00
Todd Gamblin	b75a3e112b	Merge pull request #855 from citibeth/efischer/160427-OpenblasFix openblas: Added +fpic variant to package.	2016-04-28 10:19:36 -07:00
Gregory Becker	ae5198e5e7	Merged in current develop to cflags 042716	2016-04-27 19:38:51 -07:00
Elizabeth F	71ca837ada	Add '+fpic' variant.	2016-04-27 20:36:41 -04:00
Elizabeth F	62d806d512	hdf5: Set preferred version, so as to not break NetCDF (for now).	2016-04-27 19:03:26 -04:00
Elizabeth F	ee6a75c9b5	Added missing -lpthread to OpenBLAS check. See: https://github.com/xianyi/OpenBLAS/wiki/faq#static_link	2016-04-27 18:44:54 -04:00
Todd Gamblin	92afa52eec	Merge pull request #804 from jppelteret/features/paradiseo Added package for Paradiseo.	2016-04-26 13:00:09 -07:00
Todd Gamblin	d1a9328793	Merge pull request #824 from adamjstewart/features/ior Add IOR benchmark package	2016-04-26 12:48:57 -07:00
Erik Schnetter	55d339194d	Update hwloc to 1.11.3	2016-04-26 15:29:16 -04:00
Todd Gamblin	1d2916da8c	Merge pull request #829 from davydden/openblas_unit_test openblas: a small unit test to make sure Lapack symbols are compiled	2016-04-26 10:47:35 -07:00
Todd Gamblin	7fc69a6b51	Merge pull request #838 from davydden/dealii_dependencies dealii: add missing dependencies	2016-04-26 10:34:00 -07:00
Todd Gamblin	237c843621	Merge pull request #837 from davydden/p4est_dependencies p4est: add missing dependencies	2016-04-26 10:33:46 -07:00
Todd Gamblin	ef0fefc506	Merge pull request #836 from davydden/astyle_fix astyle: fix installation of the binary	2016-04-26 10:33:24 -07:00
Todd Gamblin	9fb514ff81	Merge pull request #828 from glennpj/csvkit Add py-csvkit package	2016-04-26 10:32:27 -07:00
Glenn Johnson	dfc0efa8ed	Put f2py of py-numpy in python ignore list. (#827 ) There are many python packages that depend on py-numpy. Each one of those will have a copy of f2py that will need to be put in the ignore list for activation. Thise PR adds f2py to the ignore list in the python package.py file so that it does not have to be done for each package that depends on py-numpy. This follows the model of what is done for py-setuptools. This PR also removes the f2py ignore expression for python packages that were using it as it is no longer needed in the individual packages.	2016-04-26 10:32:14 -07:00
Glenn Johnson	b56bfcea96	Add the turbomole package. (#826 ) * Add the turbomole package. This package has three modes of operation that need to be selected independently. This is handled with spack vaiants. Turbomole has a builtin MPI implementation so it does not need to depend on an mpi provider when using the +mpi variant. * Whitespace cleanup.	2016-04-26 10:31:48 -07:00
Joseph Ciurej	8ec5e81186	Update Package : Zoltan (#833 ) * Added preliminary implementations for the debug and shared variants. * Fixed a few problems with the '+shared' variant of the Zoltan package. Added support for a few more important Zoltan package versions. * Fixed a minor compiler incompatibility issue with the '+shared+mpi' variants.	2016-04-26 10:24:36 -07:00
jppelteret	8e227f603d	Fix: Add missing dependencies for gmp and eigen (#830 ) See https://groups.google.com/forum/#!topic/spack/9JMDwafjBUs	2016-04-26 10:01:09 -07:00
Geoffrey Oxberry	f70046e6b7	MFEM version 3.1 (#749 ) MFEM is a free, lightweight, scalable C++ library for finite element methods. Includes lapack, hypre, metis, suite-sparse, mpi variants & tests for serial and parallel versions.	2016-04-26 10:00:24 -07:00
Denis Davydov	0ff4120692	dealii: add missing dependencies	2016-04-26 15:06:21 +02:00
Denis Davydov	8a45aa4185	p4est: add missing dependencies	2016-04-26 12:52:49 +02:00
Denis Davydov	168f9c46ea	astyle: fix installation of the binary	2016-04-26 09:18:39 +02:00
Jean-Paul Pelteret	17b7305086	Added package for Paradiseo.	2016-04-26 09:12:27 +02:00
Elizabeth Fischer	1a585a6c74	Added nccmp package	2016-04-25 22:25:08 -04:00
Denis Davydov	dd37959899	output with new lines	2016-04-25 16:21:19 +02:00
Denis Davydov	42be50d10b	add a test/output pair	2016-04-25 13:53:41 +02:00
Denis Davydov	b81cb554f5	openblas: a small unit test to make sure Lapack symbols are compiled	2016-04-25 13:30:20 +02:00
Glenn Johnson	2b7b7f6d97	Reformat description text.	2016-04-24 18:11:18 -05:00
Glenn Johnson	4e671c54ee	Reformat the description.	2016-04-24 18:06:51 -05:00
Glenn Johnson	797af2e80f	Add py-csvkit package This adds the py-csvkit package and needed dependencies for working with csv files.	2016-04-24 17:39:49 -05:00
Adam J. Stewart	a7ffffc336	Change homepage, explicitly disable	2016-04-24 17:14:33 -05:00
Adam J. Stewart	22e4ee5604	Add OSU Micro-Benchmarks package (#822 ) * Add OSU Micro-Benchmarks package * Add workaround for GCC bug	2016-04-23 13:29:47 -07:00
Ben Boeckel	e32416430c	Update git (#819 ) * git: update to 2.8.0 final and add 2.8.1 * git: hard-depend on curl and expat HTTP-based cloning is very prevalent now.	2016-04-23 12:18:58 -07:00
Elizabeth Fischer	248248c6b2	Added package: NCView (#791 ) * ncview: Added package * Removed FIXMEs	2016-04-23 12:15:53 -07:00
Erik Schnetter	4e062d86b4	Refine wget's OpenSSL configuration options (#786 )	2016-04-23 12:15:32 -07:00
Joseph Ciurej	d701d2ccf3	Updated the Swig package file to include versions for all of the popular Swig releases. (#790 )	2016-04-23 12:15:14 -07:00
Glenn Johnson	62d175c984	This commit explicitly sets `libdir`. This is necessary because different systems use different defaults.	2016-04-23 12:30:34 -05:00
Erik Schnetter	0cbaecca60	Don't use subprocess module	2016-04-22 21:52:11 -04:00
Adam J. Stewart	e7d2fa7084	Add IOR benchmark package	2016-04-22 12:30:24 -05:00
Ben Boeckel	5c4bb69af9	xerces-c: update to 3.1.3 (#811 ) The 3.1.2 tarball seems to have gone missing. Also switch to using bz2 rather than gz to reduce the download size.	2016-04-21 19:29:20 -07:00
Denis Davydov	ef9347bcfb	dealii: set DEAL_II_DIR when loading a module (#816 )	2016-04-21 19:25:17 -07:00
Erik Schnetter	867e1333d0	Remove outdated comment	2016-04-20 17:01:26 -04:00
Erik Schnetter	7c155f7456	Check the installed HDF5 library for consistency	2016-04-20 16:33:59 -04:00
Erik Schnetter	1acb2a1a09	Add some qthreads patches	2016-04-19 16:45:05 -04:00
Jim Galarowicz	44321c5c24	Update the main Krell Institute and Argo Navis Tech. packages for MPI variant support, get source from github not sourceforge, tested external package usage, and general package clean-up	2016-04-18 16:46:15 -07:00
Kelly Thompson	dd84a57580	+ On some systems, Dia also requires intltool. (#768 )	2016-04-17 07:15:47 +02:00
Ben Boeckel	63bade7a0c	metis: fix OS X install (#764 ) Without this, the binaries use relative paths for loading which causes them to not be found when running binaries. Not sure why the existing hack wasn't working, but this fixes it the proper way.	2016-04-17 07:15:07 +02:00
Erik Schnetter	375de085e2	Make PAPI build on Darwin (#772 ) * Make PAPI build on Darwin - don't use <malloc.h> - run install_name_tool * Use fix_darwin_install_name	2016-04-17 07:14:34 +02:00
Erik Schnetter	fb4f361cd0	Update to version 4.1.0 (#785 )	2016-04-17 07:12:52 +02:00
Kelly Thompson	523be30974	+ Add CMake version 3.5.2. (#787 )	2016-04-17 07:11:19 +02:00
Erik Schnetter	a25e33d96e	Create lib directory	2016-04-17 06:50:15 +02:00
Elizabeth F	e03e87b791	1. Added variants to choose language interfaces. 2. Now produces relocatable code (+fpic) by default	2016-04-16 00:57:57 -04:00
Todd Gamblin	69f8d8fa7a	Merge pull request #783 from adamjstewart/features/elk Add Elk package	2016-04-14 18:34:03 +02:00
Adam J. Stewart	cf1914fc00	Also install species directory	2016-04-14 10:18:06 -05:00
Todd Gamblin	a73b7052c9	Merge branch 'osx-fixes' of git://github.com/mathstuf/spack into mathstuf-osx-fixes	2016-04-14 15:25:24 +02:00
Todd Gamblin	9e456acbab	Merge pull request #779 from LLNL/bugfix/binutils-deps binutils depends on flex and bison.	2016-04-14 15:23:35 +02:00
Todd Gamblin	01fab24c15	binutils depends on flex, bison, and m4	2016-04-14 11:47:35 +02:00
Todd Gamblin	d6a232dbe0	Merge pull request #767 from mathstuf/paraview-fixes Paraview fixes	2016-04-14 11:29:46 +02:00
Todd Gamblin	f8543f7755	Merge pull request #780 from adamjstewart/fixes/hdf5 fortran2003 option has been removed from HDF5	2016-04-14 11:20:11 +02:00
Todd Gamblin	420a61491d	Merge pull request #781 from jgalarowicz/qt3-fixes Fix compile issues with new libpng versions and qt3 builds by using a…	2016-04-14 09:46:58 +02:00
Todd Gamblin	2bffd569d7	Merge pull request #782 from jgalarowicz/update-mrnet Update mrnet with new version source recognition and add krell related patch controlled by a variant.	2016-04-14 09:45:40 +02:00
Jim Galarowicz	f9aafeee1e	Loosen the boost requirement from a specific version that was specified in my initial commit.	2016-04-13 21:58:57 -07:00
Jim Galarowicz	2cf9ebc62c	Fix compile issues with new libpng versions and qt3 builds by using an older version of libpng. In libpng, make older versions available.	2016-04-13 15:00:45 -07:00
Adam J. Stewart	5717cb981e	fortran2003 option has been removed from HDF5	2016-04-13 15:03:03 -05:00
Todd Gamblin	2fe9bfcd82	Merge pull request #773 from eschnett/eschnett/julia Update Julia	2016-04-13 12:02:19 +02:00
Todd Gamblin	c96dd43174	Merge pull request #776 from adamjstewart/features/pnetcdf Add latest version of PnetCDF	2016-04-13 01:29:37 +02:00
Tom Scogland	04392babca	add setuptools version 20.7.0	2016-04-12 15:59:20 -07:00
Todd Gamblin	7acc7c4dae	Merge pull request #712 from Rombur/fix_pysetuptools Replace py-setuptools version 20.5 by version 20.6.7	2016-04-13 00:54:51 +02:00
Adam J. Stewart	abe744c5a0	Add latest version of PnetCDF	2016-04-12 16:53:45 -05:00
Adam J. Stewart	01f2dd03d5	Also install examples directory	2016-04-12 16:51:27 -05:00
Adam J. Stewart	cb6c6fb374	Add elk package	2016-04-11 16:28:30 -05:00
Erik Schnetter	882e2e42cf	Merge branch 'develop' into eschnett/julia	2016-04-11 15:40:27 -04:00
Erik Schnetter	df7e3f8635	Correct version dependency for OpenBLAS patch	2016-04-09 09:58:48 -04:00
Massimiliano Culpo	6cffac79bd	openmpi : added a few variants	2016-04-09 11:21:29 +02:00
Ben Boeckel	20b9f34b5c	paraview: use internal hdf5 Spack's HDF5 is too new. Rather than forcing everything in a ParaView chain to use older HDF5, use the internal one until ParaView is patched properly.	2016-04-08 15:09:02 -04:00
Ben Boeckel	6e56ba9f24	paraview: use internal netcdf VTK needs to learn to cope with netcdf being split like this.	2016-04-08 15:08:29 -04:00
Ben Boeckel	3a4aac0213	paraview: use the right cmake variables	2016-04-08 15:08:09 -04:00
Erik Schnetter	f461b99722	Building OpenBLAS requires recent binutils	2016-04-08 14:31:40 -04:00
Ben Boeckel	9eaf735bcd	py-setuptools: add 20.6.7	2016-04-08 12:03:45 -04:00
Ben Boeckel	dcd6b19348	py-setuptools: sort versions	2016-04-08 12:03:36 -04:00
Ben Boeckel	6c409d6b92	py-matplotlib: depend on pkg-config On OS X, freetype isn't found by default, but pkg-config can.	2016-04-08 12:03:05 -04:00
Ben Boeckel	7d19154e18	pkg-config: use the internal glib glib requires pkg-config itself, so on machines without pkg-config, there's a bootstrapping problem.	2016-04-08 12:01:28 -04:00
Todd Gamblin	e73caad0d7	Merge pull request #747 from KineticTheory/pkg-global Package global depends on ncurses	2016-04-07 00:20:15 -07:00
Glenn Johnson	8a7f34665b	Make sure base bioconductor package can be installed.	2016-04-06 23:05:49 -05:00
Geoffrey Oxberry	bbd328d307	metis 5: fix download url Spack picks up the wrong download for metis 5.1.0 from parsing the url field for metis 4.0.3. Add an explicit url field to fix this bug.	2016-04-06 16:58:48 -07:00
Todd Gamblin	4437bae16d	Merge pull request #750 from goxberry/metis-4.0.3 metis 4.0.3	2016-04-06 16:05:02 -07:00
Todd Gamblin	cac819766e	Merge pull request #755 from adamjstewart/features/bash Add bash package	2016-04-06 16:02:10 -07:00
Todd Gamblin	25d48f700c	Merge pull request #752 from KineticTheory/pkg-netlib-lapack Second attempt at PR#741	2016-04-06 16:01:33 -07:00
Geoffrey Oxberry	ddaba07d82	metis 4.0.3 Add version 4.0.3 to metis package. Attempted to implement reasonable versions of all variants declared for metis@5.1.0; some of these do not have analogues in metis@4.0.3, and errors are raised accordingly. Also updated dependencies of packages with depends_on('metis') to depends_on('metis@5:') to ensure that these packages still build.	2016-04-06 15:49:59 -07:00
Glenn Johnson	32779ab1f6	Add r-filehash to test version naming.	2016-04-06 17:02:34 -05:00
Massimiliano Culpo	c113d390a7	mvapich2 : MPI compiler wrapper will use spack compilers during the installation phase mpich : fixed wrong function signature	2016-04-06 23:51:47 +02:00
Glenn Johnson	fbabfc593d	Make R extensable and add a couple of packages for verification. Added R as a build system so that the create template will have the correct configure line. Added a regex for version parsing as the R URLs are a little odd.	2016-04-06 16:44:22 -05:00
Adam J. Stewart	380a2b23e6	Add bash package	2016-04-06 15:57:03 -05:00
Kelly (KT) Thompson	71e9f1ab8d	+ I am resubmitting this proposed change because it was accidentally overwritten. These modifications were accepted as PR#741 but somehow I clobbered them when PR#742 was merged. There was some unintentional overlap in my local repository that I didn't straighten out before pushing.	2016-04-06 09:52:09 -06:00
Todd Gamblin	3c8e055ed0	Merge pull request #751 from davydden/openblas_fix_compiler openblas: provide basename of compilers to avoid issues with detectio…	2016-04-06 02:47:37 -07:00
Denis Davydov	9b3c7b8afa	openblas: provide basename of compilers to avoid issues with detection of Fortran	2016-04-06 10:55:59 +02:00
Dhanannjay 'Djay' Deo	071548a62f	Building VisIt with silo	2016-04-05 23:16:57 -04:00
Dhanannjay Deo	f221f64509	Add variant for shared library	2016-04-05 23:11:18 -04:00
Dhanannjay Deo	c3c70cf704	Install lite pdb headers	2016-04-05 23:11:18 -04:00
Kelly (KT) Thompson	340ad44aab	Merge remote-tracking branch 'upstream/develop' into pkg-exuberant-ctags	2016-04-05 13:31:06 -06:00
Dhanannjay Deo	2e05830eb1	Constrain to vtk6.1 qt4.8.6 and opengl1 rendering backend	2016-04-05 15:12:06 -04:00
Dhanannjay Deo	872f049b30	create visit package	2016-04-05 15:12:06 -04:00
Kelly (KT) Thompson	21ad5162c4	+ Global requires ncurses.	2016-04-05 11:53:37 -06:00
Todd Gamblin	8ef9d68542	Merge pull request #726 from citibeth/efischer/160402-Qt Removed useless url in qt	2016-04-05 10:51:12 -07:00
Jim Galarowicz	0ebb192b2f	Update the MRNet package with the latest source and patch related to the krell tools needs. Also, reorder the list of version to match with the spack standard: newest to oldest.	2016-04-05 10:36:20 -07:00
Jim Galarowicz	ffed252df4	Merge remote-tracking branch 'upstream/develop' into develop	2016-04-05 10:31:41 -07:00
Erik Schnetter	a87ae5173f	Update Julia - allow checking out the master branche - add dependencies requires by important Julia package - add OpenBLAS patch	2016-04-05 09:05:46 -04:00
Todd Gamblin	faf4a1e370	Merge pull request #740 from glennpj/scikit Scikit	2016-04-04 23:11:04 -07:00
Todd Gamblin	b09d87970c	Merge pull request #742 from KineticTheory/pkg-dia Provide dia	2016-04-04 23:09:41 -07:00
Todd Gamblin	cefcbfea8e	Merge pull request #743 from eschnett/eschnett/netlib-scalapack Require cmake	2016-04-04 23:09:24 -07:00
Todd Gamblin	c010a6f8b0	Merge pull request #728 from eschnett/eschnett/hdf5-1.10 Update HDF5 to 1.10.0	2016-04-04 23:09:08 -07:00
Glenn Johnson	c546b75443	Add missing dependency on py-setuptools for - py-dask - py-decorator	2016-04-04 19:23:48 -05:00
Jim Galarowicz	9d2ef9f453	Merge remote-tracking branch 'upstream/develop' into develop	2016-04-04 17:07:53 -07:00
Glenn Johnson	2b3a8a4a5a	Add missing dependencies.	2016-04-04 19:01:44 -05:00
Erik Schnetter	aaf2830b8b	Require cmake	2016-04-04 19:40:05 -04:00
Kelly (KT) Thompson	48d70d960c	+ Provide dia, a program for drawing structured diagrams.	2016-04-04 17:11:04 -06:00
Todd Gamblin	3404a61ebf	Merge pull request #714 from goxberry/ipopt-3.12.4 Add ipopt v3.12.4 package.	2016-04-04 13:42:37 -07:00
Todd Gamblin	2fd2a5403f	Merge pull request #711 from goxberry/mumps-add-libexec Add mpiseq headers to MUMPS installation (was: Add libexec dir to MUMPS installation)	2016-04-04 13:41:55 -07:00
Kelly (KT) Thompson	cd3086f78d	+ Since CBLAS is only provided in 3.6.0 or later, modify package.py to on refer to CBLAS when the latest release is requested.	2016-04-04 14:35:09 -06:00
Glenn Johnson	9c60f122a6	New package - py-scikit-image (http://scikit-image.org/).	2016-04-04 14:02:55 -05:00
Glenn Johnson	8404f084c8	New package - py-networkx (https://networkx.github.io/).	2016-04-04 14:02:55 -05:00
Glenn Johnson	a10ab78e28	New package - py-decorator (https://github.com/micheles/decorator ).	2016-04-04 14:02:55 -05:00
Glenn Johnson	3a4210e9d7	New package - py-dask (http://dask.pydata.org ).	2016-04-04 14:02:55 -05:00
Glenn Johnson	d0ca3952a3	Add version 0.17.1 of scikit-learn.	2016-04-04 14:02:54 -05:00
Erik Schnetter	badf5b047b	Calculate version string in a function	2016-04-04 14:42:36 -04:00
Jim Galarowicz	6ebed7a2a6	Add release 9.1.0 recognition to the Dyninst API package file.	2016-04-04 11:23:51 -07:00
Todd Gamblin	220fb068aa	Merge pull request #724 from davydden/metis_suitesparse_dealii Metis and suitesparse fixes	2016-04-04 11:20:53 -07:00
Todd Gamblin	5084130e71	Merge pull request #715 from citibeth/efischer/160401-EnvironmentModules Added Environment Modules	2016-04-04 10:41:54 -07:00
Jim Galarowicz	e0b9f79b9b	Add changes that remove unsupported libraries from the boost build libraries list based on the boost version numbers. Libraries that are removed include: log - for versions of boost 1.53.0 and older - :atomic - for versions of boost 1.52.0 and older - :locale for versions of boost 1.49.0 and older - :chrono - for versions of boost 1.48.0 and older - and :random - for versions of boost 1.44.0 and older.	2016-04-04 10:33:03 -07:00
Todd Gamblin	a8b856432a	Merge pull request #716 from citibeth/efischer/160401-TclTk Fixed TCL/Tk	2016-04-04 10:24:11 -07:00
Todd Gamblin	266f64d848	Merge pull request #725 from citibeth/efischer/160402-NetCDFCXX Added deprecation warning to netcdf-cxx	2016-04-04 10:18:15 -07:00
Todd Gamblin	2d49842cd1	Merge pull request #730 from citibeth/efischer/160403-PyPillow [WIP] py-pillow: Updated for variants	2016-04-04 10:15:59 -07:00
Todd Gamblin	bd005b6ba6	Merge pull request #727 from glennpj/sympy Added version 1.0 of sympy.	2016-04-04 10:14:13 -07:00
Todd Gamblin	6755c397c9	Merge pull request #729 from citibeth/efischer/160403-LibxcbDependency libxcb: Added comments on two dependencies Spack does not yet know ho…	2016-04-04 10:13:45 -07:00
Todd Gamblin	932ed6b280	Merge pull request #731 from citibeth/efischer/160403-GitDependency git: added comment about newly discovered dependency	2016-04-04 10:13:15 -07:00
Todd Gamblin	a43cb60097	Merge pull request #733 from citibeth/efischer/160403-DbusDependency dbus: Added missing dependency (expat)	2016-04-04 10:12:47 -07:00
Bruno Turcksin	7197f15783	Add version 2.6.7 of py-setuptools	2016-04-04 10:15:00 -04:00
alalazo	d375ddadc4	openssl : reads newer version from ftp (recommended on openssl web-site)	2016-04-04 12:25:13 +02:00
Todd Gamblin	bb968fc5a2	Fix #620 , Resolve #664 . Fix issues with build environment. - Also added better regression tests for build environment.	2016-04-04 02:52:38 -07:00
Denis Davydov	131d34f318	suite-sparse: temporary disable TBB due to linking errors	2016-04-04 09:05:27 +02:00
Elizabeth F	14f073d410	py-pillow: Updated for variants, but still having trouble getting it to use Spack-supplied libjpeg.	2016-04-03 21:42:55 -04:00
Elizabeth F	0bf61ad57b	libxcb: Added comments on two dependencies Spack does not yet know how to build.	2016-04-03 21:42:40 -04:00
Elizabeth F	2809fe95db	git: added comment about newly discovered dependency	2016-04-03 21:42:29 -04:00
Elizabeth F	c3f7b035fd	dbus: Added missing dependency (expat)	2016-04-03 21:42:09 -04:00
citibeth	79836520d9	Fixed up to work on a machine without any system-install tcl.	2016-04-03 21:38:29 -04:00
Denis Davydov	e0ff3f16cc	dealii: blacklist boost	2016-04-03 19:41:51 +02:00
Elizabeth Fischer	40c279ef95	Fixed evil non-ASCII quotes	2016-04-03 00:10:22 -04:00
Erik Schnetter	e436f84244	Update HDF5 to 1.10.0	2016-04-02 20:22:26 -04:00
Glenn Johnson	c952c0ca16	Added version 1.0 of sympy. Beginning with this version, sympy requires the mpmath package. The py-mpmath package is added in this PR to accommodate that.	2016-04-02 15:50:20 -05:00
citibeth	1c483ffe4e	Merged the best of two Spack packages for Environment Modules. Named "environment-modules" to be consistent with Fedora and Ubuntu repositories. See `d96ea5b` for original packages/modules/package.py	2016-04-02 13:09:56 -04:00
citibeth	9f7db44574	Removed useless url in qt	2016-04-02 12:58:37 -04:00
citibeth	2126683203	Added deprecation warning to netcdf-cxx	2016-04-02 12:55:34 -04:00
Denis Davydov	adccd18015	dealii: add extra test for Petsc+Metis	2016-04-02 12:04:18 +02:00
Denis Davydov	a88c6da9ac	suite-sparse: fix a bug where interla metis was used; add TBB variant	2016-04-02 12:04:07 +02:00
Denis Davydov	624b576b1e	metis: fix compilation with Clang 7.3.0, add tests	2016-04-02 12:03:57 +02:00
Geoffrey Oxberry	edf6e9ceac	Add ipopt v3.12.4 package. Add package for the nonlinear programming solver IPOPT. This commit depends on the changes made in GitHub PR #711, since IPOPT requires the headers that correspond to the fake MPI implementation in sequential MUMPS.	2016-04-01 18:37:08 -07:00
Geoffrey Oxberry	71ffe2f1c4	mumps: install mpiseq headers for '~mpi' Prior to this commit, spack installs a library called `libmpiseq` into `spec['mumps'].prefix.lib` when it builds MUMPS without MPI. However, it does not also install the headers corresponding to this library, so it is impossible to compile source files that depend on function calls implemented in this library. This commit fixes this problem by installing these headers, which are needed by packages (e.g., IPOPT) that depend on these headers.	2016-04-01 18:26:25 -07:00
Elizabeth F	e4f7b78e9b	Fixed tk, and used uverridden url_for_version().	2016-04-01 16:38:02 -04:00
Elizabeth F	cfd5e69b81	Added Environment Modules package.	2016-04-01 15:28:03 -04:00
Elizabeth F	d4e6b15d98	Fixed TCL/Tk	2016-04-01 15:25:01 -04:00
Todd Gamblin	f5a77d3958	Merge pull request #709 from xjrc/packages/zoltan Add Package : Zoltan	2016-03-31 15:16:37 -07:00
Joseph Ciurej	09d657e98e	Fixed the MPI variant for the 'zoltan' package.	2016-03-31 14:36:32 -07:00
Joseph Ciurej	b1b94d2b7f	Added the initial version of the 'zoltan' package.	2016-03-31 13:59:49 -07:00
Todd Gamblin	d0c8245a58	Merge pull request #685 from gartung/add-modules-package add modules package and have setup script find it if built	2016-03-31 12:15:11 -07:00
Todd Gamblin	c5f3475f48	Merge pull request #704 from adamjstewart/features/qt-url Add url_for_version function and gtk variant	2016-03-31 11:55:27 -07:00
Todd Gamblin	220c72d67f	Merge branch 'features/blas-lapack-hardening' into develop	2016-03-31 11:37:09 -07:00
Adam J. Stewart	66038ef729	Add url_for_version function and gtk variant	2016-03-31 13:34:56 -05:00
Todd Gamblin	2441068d54	Merge pull request #697 from KineticTheory/pkg-libdrm + libdrm depends_on libpciaccess. Use spack provided libpciaccess.	2016-03-31 09:55:53 -07:00
Todd Gamblin	0840ffa3dd	Merge pull request #698 from UCL-RITS/espresso Fixes install issues on OS/X for Quantum Espresso	2016-03-31 09:47:33 -07:00
Todd Gamblin	e2a7b7e50d	Merge pull request #701 from dhandeo/vtk VTK	2016-03-31 09:46:49 -07:00
Todd Gamblin	a6f6c2b9c5	Merge pull request #702 from adamjstewart/features/cuda Add CUDA and HOOMD-blue packages	2016-03-31 09:45:45 -07:00
Massimiliano Culpo	837eff1704	openssl : special treatment for @external (fixes #647 )	2016-03-31 18:07:44 +02:00
Adam J. Stewart	a0902ad8d8	Change variant defaults and add comment	2016-03-31 11:04:29 -05:00
Dhanannjay Deo	3b0311a1e4	Add variant opengl2, which is ON by default Needed for visit which depends on vtk@6.1.0~opengl2	2016-03-31 10:39:34 -04:00
Dhanannjay Deo	123996aad0	Fix build for vtk6.1.0	2016-03-31 10:39:34 -04:00
Dhanannjay Deo	0bcfd09536	add: VTK lastest versions	2016-03-31 10:39:34 -04:00
Denis Davydov	6d0b4a28ab	oce: fix bugs related to NULL pointers and compiler optimisation	2016-03-31 13:36:28 +02:00
Mayeul d'Avezac	7430f9142f	Can install espresso on OS/X Espresso uses unix utility `find dir -name \*.x` to determine the executable to install. On OS/X, it also finds a bunch of debug symbols associated with the exectuble. These files have the same name, but are in a different directory. So the install process is done by hand in the package.py file, for OS/X.	2016-03-31 10:16:40 +01:00
Mayeul d'Avezac	397e0d1368	Fixes #454 in a simpler way than `34a8f0c` Rather than mess with the environment, have espresso install into the right directory (prefix/bin).	2016-03-31 10:12:20 +01:00
Todd Gamblin	360994b638	Merge branch 'davydden-dealii' into develop - Modified arpack-ng to call libtoolize.	2016-03-30 23:47:21 -07:00
Todd Gamblin	44b8947445	arpack-ng needs an extra libtoolize to build.	2016-03-30 23:33:57 -07:00
Kelly (KT) Thompson	a88c15e101	+ libdrm depends_on libpciaccess. Use spack provided libpciaccess.	2016-03-30 21:18:04 -06:00
Kelly (KT) Thompson	a364ab0d0f	libpng depends on zlib.	2016-03-30 17:12:32 -06:00
Todd Gamblin	ef5c973c93	Merge pull request #688 from davydden/doxygen_fix doxygen: add missing dependencies	2016-03-30 15:54:02 -07:00
Todd Gamblin	35322eccc1	Merge pull request #601 from KineticTheory/pkg-numdiff Provide new package numdiff	2016-03-30 15:22:56 -07:00
Todd Gamblin	892b8f155f	Merge branch 'dealii' of git://github.com/davydden/spack into davydden-dealii	2016-03-30 15:09:29 -07:00
Todd Gamblin	228130ddc8	Merge pull request #693 from mathstuf/osx-ninja ninja: fix installation on OS X	2016-03-30 14:59:08 -07:00
Todd Gamblin	b4580eb04c	Merge pull request #604 from KineticTheory/pkg-graphviz Pkg graphviz	2016-03-30 14:51:15 -07:00
Kelly (KT) Thompson	2ad5d2ea2a	+ For darwin, add a dependency on gettext. This change was recommended in the discussion for PR#601.	2016-03-30 15:40:04 -06:00
Kelly (KT) Thompson	be2862ef4e	Merge remote-tracking branch 'upstream/develop' into pkg-numdiff	2016-03-30 15:35:46 -06:00
Ben Boeckel	f1a0619821	mpich: disable fortran without a fortran compiler	2016-03-30 17:19:29 -04:00
Kelly (KT) Thompson	4ab362ae17	+ Fix variant description.	2016-03-30 14:27:23 -06:00
Kelly (KT) Thompson	d1a3adfcf0	+ Make --disable-perl the default configure option.	2016-03-30 14:25:44 -06:00
Ben Boeckel	dbb25bfeed	ninja: fix installation on OS X The cp -t flag is a GNU-ism. Instead, add a trailing slash to bindir to ensure that it is not treated as a file.	2016-03-30 16:17:52 -04:00
Kelly (KT) Thompson	8da62b310e	Merge remote-tracking branch 'upstream/develop' into pkg-graphviz	2016-03-30 13:59:10 -06:00
Denis Davydov	5506e89aa9	rename variant doxygen to doc	2016-03-30 21:41:23 +02:00

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