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2018-05-04Hic-Pro: fix a typo and replace hard-coded version. (#8022)健美猫1-2/+2
* Fix a typo and replace hard-coded version. * version -> self.version.
2018-05-04openmpi: don't build static libraries if slurm is activated (#8021)Massimiliano Culpo1-1/+9
According to this comment: https://github.com/open-mpi/ompi/issues/4338#issuecomment-383982008 on an OpenMPI issue, using `--enable-static` silently disable slurm support.
2018-05-03gdal: update (#8008)Elizabeth Fischer1-4/+9
* gdal: update * Remove unneeded depends(python)
2018-05-03Bump r-rcpp versions. (#8016)健美猫1-0/+2
2018-05-03pism: new package (#8010)Elizabeth Fischer1-0/+171
* pism: new package * Implement code review * Remove pointless docstring5 * Fixed missing trailing quote
2018-05-03py-numpy: update (#8003)Elizabeth Fischer2-4/+9
* py-numpy: update * Better constrain when can / cannot parallel build. * Update SciPy parallel logic to be specific to Python 3.5+, same as in Numpy.
2018-05-03py-bsddb3: update (#8006)Elizabeth Fischer1-1/+5
* py-bsddb3: update * Change py-setuptools to build dependency
2018-05-03pfunit: update (#7994)Elizabeth Fischer1-12/+15
2018-05-03Everytrace: update (#7995)Elizabeth Fischer1-3/+7
2018-05-03py-yamlreader: new package (#7997)Elizabeth Fischer1-0/+39
2018-05-03gmp: update (#7999)Elizabeth Fischer1-0/+2
2018-05-03py-scipy: update (#8000)Elizabeth Fischer1-4/+1
2018-05-03py-pyside: update (#8002)Elizabeth Fischer1-0/+14
2018-05-03py-cython: update (#8005)Elizabeth Fischer1-0/+5
2018-05-03genomefinisher: Create new package (#7989)Eric2-0/+65
2018-05-03 py-crispresso: Create new package (#7990)Eric1-0/+46
* py-crispresso: Create new package * py-crispresso: Create new package
2018-05-03New Package: ruby-svn2git (#7979)Kelly (KT) Thompson1-0/+48
* New Package: svn2git https://github.com/nirvdrum/svn2git svn2git is a tiny utility for migrating projects from Subversion to Git while keeping the trunk, branches and tags where they should be. It uses git-svn to clone an svn repository and does some clean-up to make sure branches and tags are imported in a meaningful way, and that the code checked into master ends up being what's currently in your svn trunk rather than whichever svn branch your last commit was in. * Actually requires +perl variant of subversion. * fix style issue.
2018-05-03A new package: nanopb. (#7981)健美猫1-0/+38
* A new package: nanopb. * flake8. * Remove py-pytorch.
2018-05-03Bump pgi to 18.4. (#7980)健美猫1-0/+1
* Bump pgi to 18.4. * Remove the empty line. * Update.
2018-05-03Bump gatk version to 4.0.4.0. (#7985)健美猫1-5/+13
* Bump gatk version to 4.0.4.0. * Update. * Fixed. * Fixed.
2018-05-03A new package: py-openslide-python. (#7907)健美猫1-0/+41
* A new package: py-openslide-python. * Update. * Remove py-pytorch package. * Remove nektar package. * Remove install_time_test_callbacks
2018-05-03go: Update to 1.10.2 (#7982)Michael Kuhn1-0/+1
2018-05-02make symlinking python3->python optional (#7960)Elizabeth Fischer1-1/+5
* Make symlinking python3->python optional * Added reference to PEP 394
2018-05-02mvapich2: add 2.3rc2 (#7976)Adam Moody1-0/+1
2018-05-02sphinx: Updated to v1.7.4 (#7977)Elizabeth Fischer1-0/+6
* sphinx: Updated to v1.7.4 * Update package.py
2018-05-02Added BookLeaf_Cpp and Typhon packages. (#7969)Tim Law2-0/+105
2018-05-02Add libcint version 3.0.12 (#7972)Michael F. Herbst1-0/+1
2018-05-02bedops: Create new package (#7956)Eric1-0/+42
* bedops: Create new package * fix install method
2018-05-02Fix Spectrum MPI package spec file for PGI compilers (#7964)David Wootton1-0/+10
* Added magma package * Incorporated Serban's change * Remove deleted files * argparse.py * Sync forked Spack repo in github * Use reported version of IBM XL Fortran compiler for compiler versions >= 16.0. Starting with the April 2018 release, the IBM XL C and Fortran compilers report the same version, 16.0. Consequently, there is no need to downgrade the Fortran compiler version to match that of the C compiler. * Eliminate blank lines. * Update the Spectrum MPI package.py file to specify the correct compilation scripts for the PGI compilers.
2018-05-02openmc is not a proxy (#7968)Christoph Junghans1-2/+0
https://github.com/spack/spack/issues/7965#issuecomment-385953224
2018-05-01Fix initialization of defaults in yaml schema validation (#7959)scheibelp2-2/+47
Fixes #7924 Spack's yaml schema validator was initializing all instances of unspecified properties with the same object, so that updating the property for one entry was updating it for others (e.g. updating versions for one package would update it for other packages). This updates the schema validator to instantiate defaults with separate object instances and adds a test to confirm this behavior (and also confirms #7924 without this change).
2018-04-30mvapich2: add registration cache and file systems variants (#7948)Adam Moody1-2/+36
* mvapich2: add registration cache and file systems variants, avoid empty --with-pm= if no process manager is specified, add missing leading dash in --disable-silent-rules
2018-04-30mpifileutils: roll back to dtcmp v1.0.3, add option to build master branch ↵Adam Moody1-1/+6
(#7949) * mpifileutils: roll back to dtcmp v1.0.3 due to API change, add option to build master branch * add comment to explain why certain dtcmp is required, rename version for git branch * dtcmp v1.0.2 is missing github tarball
2018-04-30vt: Create new package (#7947)Eric1-0/+38
2018-04-30Build shared libs for tinyxml. (#7914)健美猫2-9/+20
2018-04-29Patch eospac package to allow compilation with %clang. (#7928)Kelly (KT) Thompson2-0/+65
When building eospac with %clang, spack's Fortran compiler wrapper is called 'flang', which is rejected by the eospac build system..Allow compilation with %clang by patching the eospac build system. My testing only covers %clang where flang is actually gfortran. However, this patch only registers 'flang' as a known Fortran compiler and does not set any flags or options that are compiler specific. .
2018-04-28Document how to run unit tests with print statements (#7860)Adam J. Stewart1-0/+7
2018-04-28mfem: fix concretization (#7923)Christoph Junghans1-2/+2
* mfem: fix concretization * Fix hypre deps again * Update package.py
2018-04-27Update with recent versions through 4.8.3 and add variants. (#7933)Chris Green2-1/+68
Add configurable HTTP, Python and readline support. Add previously missing dependencies. Minor patch to improve Python support (see https://github.com/xrootd/xrootd/pull/695).
2018-04-26bcftools: new version (#7930)Levi Baber1-0/+2
2018-04-26add versions 3.4.3. and 3.5.0 (#7929)Sinan1-0/+2
2018-04-26Allow len(Version) to return number of split components. (#7918)Chris Green2-0/+11
2018-04-26samtools: new version (#7921)Levi Baber1-0/+4
2018-04-26XL Fortran compiler >= 16.0 is synced with C compiler version (#7887)serbanmaerean2-0/+12
* Use reported version of IBM XL Fortran compiler for compiler versions >= 16.0. Starting with the April 2018 release, the IBM XL C and Fortran compilers report the same version, 16.0. Consequently, there is no need to downgrade the Fortran compiler version to match that of the C compiler.
2018-04-26Use GitLab's API endpoint for fetching a git snapshot. (#7881)Sergey Kosukhin11-19/+44
* Use GitLab's API endpoint for fetching a git snapshot. * More GitLab packages use the API. * find_list_url for GitLab's API URLs. * Flake8 * Url for 'hacckernels'. * Check GitLab API regexps before the non-API ones.
2018-04-26add patch to get aspell to build on OSX (#7919)healther2-0/+22
2018-04-26config_args does NOT apply to CMakePackage. (#7917)健美猫1-1/+1
2018-04-26Add Trinity package (#7828)Simon Flood1-0/+74
* Add Trinity package New package to install Trinity - another odd installer (assumes installation to /usr/local/bin and doesn't copy dot files hence deleting them) * Update package.py added dependencies from https://github.com/trinityrnaseq/trinityrnaseq/wiki/Installing-Trinity * Update package.py Copy tree to prefix.bin so that PATH can correctly be set for the Trinity command - can't split it off as it seems everything needs to stay together. * Update package.py Fixed over-length lines and space before comma
2018-04-26Package 'gdbm': do not set CC. (#7912)Sergey Kosukhin1-8/+1
2018-04-26mfem: add valid range of hypre version numbers (#7903)Geoffrey Oxberry1-0/+2
This commit fixes #7900. In short: in the absence of constraints to the contrary, spack will download the preferred version of a package, which is usually the most recent non-develop version. On a clean spack installation without hypre installed, `spack install mfem` will download hypre 2.14.0, which is API-incompatible with mfem 3.3.2 (and earlier versions of mfem), so spack will throw compiler errors re: the API mismatch. This commit fixes that error by restricting mfem release versions 3.3.2 and earlier to hypre version 2.10.b to 2.13.999 (only 2.13.0 currently exists, but if it has a non-2.14.x maintenance release, these versions of hypre should also be permitted).
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