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2017-04-05update versions for scalasca and related tools (#3697)Mark Olesen4-64/+59
- clean up fetch urls - inherit from AutotoolsPackage instead of Package - explicit fPIC flags look suspicious, but leave them in there. - in scalasca, use the cube version that is implicit from the scorep dependency instead of specifying it twice.
2017-04-05Fix libxpm (#3704)Michael Kuhn1-0/+5
It tries to use gettext but fails because it does not explicitly link against libintl.
2017-04-05Fix ncl (#3708)Michael Kuhn2-1/+23
- Add patch to make ncl compile with hdf5 1.10. - Add missing dependencies to make ncl compile without errors.
2017-04-05Add stress package (#3695)Adam J. Stewart1-0/+37
2017-04-05Add versions 3.2.0 3.1.0 for protobuf. (#3698)健美猫1-7/+9
2017-04-04Add package for open source Shiny Server (#3688)George Hartzell1-0/+77
* The beginnings of a package for shiny-server Just stashing a WIP. This doesn't work. This goes for a while and/but blows up with some OpenSSL related issue. * Make it work! Yay! * shiny-server needs R with X support My environment gets this for "free" from my packages.yaml, but it should be explicity. * Address feedback - python version - gcc dependency - Flake8 comment rules * Richer caveats and warnings. * Convert to CMakePackage and fix python version typo * Fix typo: noqab -> noqa * Ensure proper build location, clean up comments
2017-04-04Convert STREAM to MakefilePackage (#3692)Adam J. Stewart1-4/+2
2017-04-04Add fio package (#3689)Adam J. Stewart1-0/+56
2017-04-04intel-mkl: add 2017.2 (#3687)Denis Davydov1-15/+7
* intel-mkl: add 2017.2 * intel-mkl: add urls, update docstring
2017-04-04Update SymEngine package to enable build against LLVM (#3682)Jean-Paul Pelteret1-2/+7
2017-04-04Cppcheck (#3684)Mayeul d'Avezac1-1/+5
* Adds cppcheck version 1.72 * cppcheck installation requires cfg files Without these files, cppcheck does not work correctly
2017-04-04Update tinyxml (#3649)Mayeul d'Avezac1-1/+2
* Update tinyxml * url seems to have changed * spack replaces "_2_6_2" with "_2.6.2" unless the url is explicitly given * copyfile is no longuer available by default * URL version-parsing should work as of #2972
2017-04-03Add IOzone package (#3679)Adam J. Stewart1-0/+53
2017-04-03Overhaul Spack's URL parsing (#2972)Adam J. Stewart65-238/+154
* Remove fake URLs from Spack * Ignore long lines for URLs that start with ftp: * Preliminary changes to version regexes * New redesign of version regexes * Allow letters in version-only * Fix detection of versions that end in Final * Rearrange a few regexes and add examples * Add tests for common download repositories * Add test cases for common tarball naming schemes * Finalize version regexes * spack url test -> spack url summary * Clean up comments * Rearrange suffix checks * Use query strings for name detection * Remove no longer necessary url_for_version functions * Strip off extraneous information after package name * Add one more test * Dot in square brackets does not need to be escaped * Move renaming outside of parse_name_offset * Fix versions for a couple more packages * Fix flake8 and doc tests * Correctly parse Python, Lua, and Bio++ package names * Use effective URLs for mfem * Add checksummed version to mitos * Remove url_for_version from STAR-CCM+ package * Revert changes to version numbers with underscores and dashes * Fix name detection for tbb * Correctly parse Ruby gems * Reverted mfem back to shortened URLs. * Updated instructions for better security * Remove preferred=True from newest version * Add tests for new `spack url list` flags * Add tests for strip_name_suffixes * Add unit tests for version separators * Fix bugs related to parseable name but in parseable version * Remove dead code, update docstring * Ignore 'binary' at end of version string * Remove platform from version * Flip libedit version numbers * Re-support weird NCO alpha/beta versions * Rebase and remove one new fake URL * Add / to beginning of regex to avoid picking up similarly named packages * Ignore weird tar versions * Fix bug in url parse --spider when no versions found * Less strict version matching for spack versions * Don't rename Python packages * Be a little more selective, version must begin with a digit * Re-add fake URLs * Fix up several other packages * Ignore more file endings * Add parsing support for Miniconda * Update tab completion * XFAILS are now PASSES for 2 web tests
2017-04-03Add latest version of pkg-config (#3672)Adam J. Stewart1-16/+16
2017-04-03openfst conflicts with intel@16: and gcc@6: . (#3671)健美猫1-10/+5
2017-04-03Fix conflict directives for libpfm4. (#3673)健美猫1-1/+1
2017-04-03Add latest alpha release of MVAPICH2 (#3674)Adam J. Stewart1-1/+6
2017-04-03Add depends_on() new-ish bison (#3661)George Hartzell1-0/+1
* Add depends_on() new-ish bison * Refine dependency, only needed to build.
2017-04-03Add libpfm4 package. (#3667)健美猫1-0/+48
2017-04-03add CUDA_HOME arg to nccl makefile (#3666)Jeffrey Salmond1-0/+4
2017-04-03add gflags as dependency of glog (#3665)Jeffrey Salmond1-0/+2
2017-04-02Hey, I was using that! :) (#3660)George Hartzell1-0/+3
Turns out that we really want 5.22.2 for backward compatibility.
2017-04-02Set default providers for all virtual dependencies (#3634)Adam J. Stewart2-2/+6
* Set default providers for everything * Add default OpenFOAM provider
2017-04-02new directive: conflicts() (#3125)Massimiliano Culpo3-0/+94
* Add conflicts(<spec>) directive * openblas: added conflicts for intel@16 refs #3119 * added brief docs and unit tests
2017-04-01Add better tests for web.py; fix some bugs found with spidering.Todd Gamblin19-32/+23
- _spider in web.py was actually failing to spider deeper than a certain point. - Fixed multiprocessing pools to not use daemons and to allow recursive spawning. - Added detailed tests for spidering and for finding archive versions. - left some xfail URL finding exercises for the reader. - Fix noqa annotations for some @when decorators
2017-04-01fix version specs for EasyBuild packages (#3659)Kenneth Hoste3-3/+3
* fix Python version requirement for easybuild-framework * make 'when' for depends_on('py-easybuild-framework') open-ended
2017-04-01EasyBuild and dependencies (#3658)Kenneth Hoste6-0/+221
* add packages for EasyBuild and dependencies * fix remarks w.r.t. docstrings & download urls, make dependency specs stricter w.r.t. required versions * fix easybuild-* dep specs, should be open-ended * correct dep specs for easybuild and easybuild-easyconfigs using @3.1.2[:]
2017-04-01Add a pcakge: libzip. (#3656)健美猫1-0/+35
2017-03-31Make packages Python3 compatible.Todd Gamblin6-18/+20
2017-03-31PythonPackage: Let There Be Tests! (#2869)Adam J. Stewart4-0/+92
* Run python setup.py test if --run-tests * Attempt to import the Python module after installation * Add testing support to numpy and scipy * Remove duplicated comments * Update to new run-tests callback methodology * Remove unrelated changes for another PR
2017-03-31new and updated PRUNERS tools (#3648)Gregory Lee4-4/+86
2017-03-31Fix mxml (#3639)Michael Kuhn1-2/+5
mxml is now hosted on GitHub.
2017-03-31Add QBank package (#3641)Adam J. Stewart3-5/+128
* Add QBank package * Install the documentation and add it to the MANPATH * Add Perl DBI package * Make sure setup method variables are consistent
2017-03-31Perl: add more versions, add phases (#3640)Adam J. Stewart1-14/+43
2017-03-31CONFIG: add older bison version 2.7 (#3645)Mark Olesen1-0/+1
- for programs that don't yet work with bison 3.x
2017-03-31Included LIBXSMM 1.8 into the list of available versions. (#3646)Hans Pabst1-1/+2
2017-03-31Subversion with perl bindings (#3644)Milton Woods2-7/+68
* perl-term-readkey: add perl Term::ReadKey package * subversion: add variant with perl bindings * subversion: use `which('perl')` to find perl executable in package.py
2017-03-30perl-xml-parser: add perl XML::Parser package (#3643)Milton Woods1-0/+37
2017-03-30Extendable Perl (#3614)Milton Woods2-1/+85
* perl: make extendable and add Module::Build package * perl: allow 'spack create' to identify perl packages from their contents * perl-module-build: fix indenting of package docstring * perl: split install() method for extensions into phases * perl: auto-detect build method (Makefile.PL vs Build.PL) and define a 'check' method * PerlPackage: use import statements similar to those in AutotoolsPackage * PerlModule: fix detection of Build.PL * PerlPackageTemplate: remove extraneous lines to avoid flake8 warnings * PerlPackageTemplate: split into separate templates for Makefile.PL and Build.PL * PerlPackage: add cross-references to docstrings * AutotoolsPackage: fix ambiguous cross-references to avoid errors in doc tests * PerlbuildPackageTemplate: depend on perl-module-build if Build.PL exists
2017-03-30support OpenFOAM package(s) (#3528)Mark Olesen12-221/+2495
* ENH: add package for building OpenFOAM (1612) from www.openfoam.com - provide 'openfoam' as virtual package. - package as openfoam-com to reflect the distribution point. This initial spack packaging for OpenFOAM supports a number of possible variants and should handle 64-bit labels properly now that the scotch package has been updated accordingly. * ENH: update package for foam-extend (extend-project.de) - provide 'openfoam' as virtual package. - much of the build is now aligned with how the openfoam-com package looks, with the aim of future refactoring. - avoid installing intermediate targets. - contains its own environment sourcing script for the build, for more flexibility and robustness (doesn't touch the python build environ) * ENH: added package for building from openfoam.org - provide 'openfoam' as a virtual package. - this is largely a direct copy of the openfoam-com package. It has been supplied as a courtesy for users and to ensure maximum consistency in quality and naming between the foam-extend, openfoam-com and openfoam-org packages. * CONFIG: add openfoam into bash completion providers list * ENH: have openfoam-com use spack as USERMPI - also simplify the generation of mplib/compiler rules * ENH: have openfoam-org use spack as SYSTEMMPI - this setup requires more environment settings than USERMPI (openfoam-com), but is currently the only means of integration for openfoam-org - simplify generation of mplib/compiler rules * ENH: simplify generation of mplib/compiler rules (foam-extend) - rename mpi rules from SPACK,SPACKMPI to USER,USERMPI for consistency with openfoam-com and to generalize for any build system. * STYLE: record spack tree as a log file (openfoam) - can be useful for future diagnostics and general record keeping
2017-03-30add package py-spykeutils (#3633)healther1-0/+39
* add package py-spykeutils * fixed dependency version restriction
2017-03-30cp2k: update to 4.1 + update of dependencies (#3561)Massimiliano Culpo8-122/+160
* libint: updated version, ported to AutotoolsPackage * elpa: updated version, ported to AutotoolsPackage * wannier90: updated version, ported to MakefilePackage * pexsi: updated version, ported to MakefilePackage * cp2k: updated version, removed wannier 90 from dependencies if cp2k@4.1 * plumed: updated version Modifications: * modules has been turned into a single variant, as different versions have different modules available * added dictionaries for patches * netlib-scalapack: ported to CMakePackage
2017-03-30Move py-dev to the proper repo directory (#3630)Adam J. Stewart2-0/+0
2017-03-30Fix url fetching for GnuTLS (#3631)Adam J. Stewart1-5/+9
2017-03-29Concretization problem breaks httpie dependency (#3629)George Hartzell1-1/+5
* Concretization problem breaks httpie dependency Concretization problem breaks this. Unconditional for now... https://github.com/LLNL/spack/issues/3628 * Flake8 cleanups
2017-03-29Add package for snakemake (#3605)George Hartzell2-0/+73
* Add package for snakemake * Flake8 cleanups * Add package for py-wrapt * Address PR feedback Switch to pypi URL. Tighten Python3 dependency spec. Add missing dependencies (wrapt, requests). - add package for wrapt.
2017-03-29Add package for httpie (#3609)George Hartzell1-0/+43
* Add package for httpie * Remove wayward FIXME and flake8 cleanup * Update dependencies, address PR feedback Fine tune dependencies (version constraints). Add missing dependency. Make SOCKS support a variant. * Flake8 cleanup
2017-03-29petsc: a workaround for macOS Clang 8.1.0 and XCode 8.3 (#3615)Denis Davydov2-0/+25
2017-03-29add package py-bokeh (#3618)healther1-0/+45
* add package py-bokeh * remove setuptools dependency * add missing dependencies
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