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2018-09-12AMG: update version (#9228)Abhinav Bhatele1-0/+1
2018-09-12petsc: fix compilation with intel (#9198)Ricardo Silva1-3/+8
* mpiifort doesn't automatically link all run-time libraries * scalapack was being picked up accidentaly if intel-mkl was in the spec
2018-09-11ecp-proxy-apps: update dependencies for release 1.0 and 1.1 (#9217)Abhinav Bhatele2-13/+19
2018-09-11steps: new package starting at 3.3 (#9173)Tristan Carel1-0/+80
2018-09-10Improve spec['python'].command support for bwpy (#9157)Adam J. Stewart1-24/+19
2018-09-10py-espresso: added v4.0.0 (#9192)Christoph Junghans2-0/+31
Added v4.0.0 and workaround for cmake bug
2018-09-08trilinos: disable xlf_tpetra.patch for trilinos@develop (#9193)Satish Balay1-3/+3
This patch does not apply cleanly anymore and breaks clang/Mac builds balay@asterix /home/balay/git-repo/github/trilinos (develop=) $ patch -Np1 < /home/balay/git-repo/github/spack/var/spack/repos/builtin/packages/trilinos/xlf_tpetra.patch can't find file to patch at input line 3 Perhaps you used the wrong -p or --strip option? The text leading up to this was: -------------------------- |--- a/packages/tpetra/core/src/Tpetra_Details_libGemm.cpp |+++ b/packages/tpetra/core/src/Tpetra_Details_libGemm.cpp -------------------------- File to patch:
2018-09-08assimp: fix compile issues with intel compilers on knl/linux [a depen… (#9191)Satish Balay1-1/+14
* assimp: fix compile issues with intel compilers on knl/linux [a dependency for dealii] Fixes issue #9189 * assimp: add variant 'shared' with default value 'True'
2018-09-08xsdk: disable assimp in deal.II (#9190)Denis Davydov1-1/+1
2018-09-07libMesh: New variant and updated recent versions. (#9186)Josh Deaton1-2/+12
* libmesh: Added SLEPC eigensolver variant. * libmesh: Added new versions. * Corrected flake8 errors. * Corrected SLEPc variant with proper config & conflicts.
2018-09-07Tanim (#9158)Mike Pozulp8-5/+88
* Added jdk version, added r-ks and r-multicool packages, made some r packages less conservative in their r version requirement * flake8 fixes * fix formatting in jdk version cmd * Added type=('build', 'run') to some R package dependencies, added some missing dependencies to r-ks. Thanks Adam. * fix flake8 error
2018-09-06xsdk: add dealii (#7529)Denis Davydov2-2/+5
2018-09-06Balay/xsdk trilinos develop (#9182)Satish Balay3-1/+58
* xsdk: update xsdk@develop dependency on trilinos@develop * trilinos: enable tpetra, ifpack2, zoltan2, amesos2
2018-09-06gmodel: new package starting at 2.1.0 (#9170)Tristan Carel1-0/+39
2018-09-06gmsh: add git master and 4.0.0 versions (#9172)Tristan Carel1-1/+2
2018-09-06openPMD-api: ^py-numpy@1.15+ (#9178)Axel Huebl1-1/+1
Due to an internal bug regarding the handling of scalars (ndim must be 0) in numpy prior to 1.15.0, openPMD-api will require the latest numpy 1.15+. Since there is a small regression with datetime pickling in 1.15.0 from the required fix and spack only packages 1.15.1 currently, we depend on 1.15.1 in the recipe.
2018-09-05omega-h: add versions and variants (#9169)Tristan Carel1-2/+40
* add 5 most recent versions and git master branch * add trilinos, gmodel, throw, examples, optimize, symbols, and warnings variants * disable XSDK so that Trilinos dependencies are found.
2018-09-04Pack dlang's stdlib into dmd. (#9131)健美猞猁1-5/+50
* Update dmd. * Build dmd and druntime. * Build dmd. * Restore edit. * Flake8.
2018-09-04Onedrive: a new package. (#9130)健美猞猁1-0/+56
* skilion-onedrive: a new package. * Fix flake8 issues.
2018-09-04Bamdst: a new package. (#9113)健美猞猁1-0/+46
* Bamdst: a new package. * Remove duplicate make() in install().
2018-09-04trinity: full dependencies (#9064)Levi Baber1-0/+31
2018-09-04r-summarizedexperiment: new version (#9054)Levi Baber1-5/+12
* r-summarizedexperiment: new version * r-summarizedexperiment: add ending range for r3.4 dep * r-summarizedexperiment: fix range
2018-09-04Feature/py pycogent New-Version (#9095)Miles Perry1-3/+19
* added py-pycogent * flake8 edits * added type=('build', 'run') to deps, changed py-matplotlib and mpi4py * changed python min version to 2.6 * fixed cython to py-cython dep * fixed mpi4py to py-mpi4py * fixed py-sqlalchemy * added 1.5.3 version * fixed version 1.5.3 install * changed deps names to reflect convention * added variants * changed download URL and added SHA256 hash * fixed deps * added github url for 1.5.3 * removed unneeded deps * doesn't require py-setuptools * fixed url and added py-setuptools specific to version 1.9 * fixed variant names and changed cython to normal dependency instead of variant * removed cython dep, failed to build when it was present. Changed variant name 'mpi4py' to 'mpi' and changed sqlalchemy variant name to mpi * fixed dependencies and added py-pymysql dep * added setup-environment step * changed download url for 1.5.3 to pypi * fixed flake8 issue * updated * added changes
2018-09-04py-maestrowf: Addition of new releases. (#9135)Francesco Di Natale1-1/+6
* Addition of latest maestrowf releases. * Addition of filelock to dependencies. * Addition of when clause to depends_on for filelock and tabulate. * Correction of the tar url.
2018-09-03r-genomicalignments: new version (#9055)Levi Baber1-7/+15
* r-genomicalignments: new version * r-genomicalignments: ending range for r3.4 dep * r-genomicalignments: fix range
2018-09-03r-biomart: new version; (#9058)Levi Baber1-4/+6
* r-biomart: new version; * r-biomart: ending range for r3.4 dep * r-biomart: fix version range
2018-09-03r-deseq2: new version (#9062)Levi Baber1-1/+3
* r-deseq2: new version * r-deseq2: fix r 3.4 dep range
2018-09-03New package: AIDA (#9094)Hadrien G1-0/+38
* Trying to package old AIDA * Document the incompleteness * Install the jars too
2018-09-03Feature/py picrust New Package (#9096)Miles Perry1-0/+42
* added py-picrust * flake8 edits * fixed boilerplate, added type='build', 'run' * fixed errors * added deps * fixed error * fixed numpy max version * fixed future version * fixed version issues
2018-09-03nlopt: Only support release>=2.5.0, since earlier release tarballs were ↵Neil Flood1-2/+2
actually AutoTools, not CMake. (#9110)
2018-09-03aperture-photometry: new package (#9119)Miles Perry2-0/+55
2018-09-03py-pymysql: new package (#9122)Miles Perry1-0/+37
* py-pymysql: new package * added type build and run
2018-09-03openblas: add @0.3.1, patch CMake export bug in @0.3.1:0.3.2 (#9123)Geoffrey Oxberry2-0/+48
* openblas@0.3.1:0.3.2: patch CMake export bug See https://github.com/xianyi/OpenBLAS/pull/1703. * openblas@0.3.1: new version
2018-09-03New package: CODES simulation framework (#9133)Abhinav Bhatele2-0/+86
* New package: CODES simulation framework * CODES: add comments * CODES: remove -fi from extra autoreconf flags
2018-09-03NWChem 6.8.1 (#9140)Edoardo Aprà1-0/+2
2018-09-03added version for kull support (#9141)rice311-0/+1
2018-09-03aspect: new version (#9146)Timo Heister1-1/+2
2018-09-03Update openspeedshop and cbtf version numbers (#9150)Jim Galarowicz6-3/+11
Update the version numbers and now depend on the develop version of dyninst because of a feature in openspeedshop depends on new code in the dyninst develop tree. Without dyninst develop, openspeedshop will not build.
2018-09-03py-matplotlib: incorporate 8532 w/ version range (#9151)Levi Baber2-0/+18
* py-matplotlib: Add patch to fix FreeType library detection Adds patch to add $CPATH to locations searched for FreeType header file Patch has been upstreamed: https://github.com/matplotlib/matplotlib/pull/11457 * py-matplotlib: Add patch to fix FreeType library detection * Make patch only apply to versin 2.2.2 (as already upstreamed) * Fix flake8 format issue * py-matplotlib: add range to freetype patch * py-matplotlib: whitespace
2018-09-03mpifileutils: add v0.8 (#9152)Adam Moody1-1/+3
2018-09-03msgpack-c, snappy: explicitly depend on googletest (#9167)Matthias Wolf3-2/+22
2018-09-03Fix two dependencies with silo. (#9153)David Wells1-0/+2
1. I presently get errors of the sort ==> Error: KeyError: 'No spec with name mpi in silo@4.10.2%gcc@8.1.0+fortran+mpi [...] $HOME/spack/var/spack/repos/builtin/packages/silo/package.py:84, in configure_args: 81 'FCFLAGS={0}'.format(self.compiler.pic_flag)] 82 83 if '+mpi' in self.spec: >> 84 config_args.append('CC=%s' % self.spec['mpi'].mpicc) 85 config_args.append('CXX=%s' % self.spec['mpi'].mpicxx) 86 config_args.append('FC=%s' % self.spec['mpi'].mpifc) without the extra explicit MPI dependency. 2. Silo uses zlib, so we should explicitly depend on it.
2018-09-01Vim: add version 8.1.0338 (#9155)Adam J. Stewart1-1/+6
2018-09-01GDAL: add version 2.3.1 (#9156)Adam J. Stewart1-7/+13
2018-08-31SUNDIALS: add new versions, update hashes, and apply clang fix (#9115)Cody Balos1-14/+30
Added SUNDIALS 3.1.2 and 4.0.0-dev.1 versions and relevant dependencies (3.1.2 requires CMake 2.8.12). Updated all versions to use sha256 hashes. Addressed issue specific to clang compiler on macOS.
2018-08-31py-filelock: new package (#9136)Francesco Di Natale1-0/+45
* Addition of py-filelock and first page of versions. * Addition of setup.py patch for setuptools. * flake8 failure fixes. * Reduced url declaration to a single line. * Correction to py-filelock to use distutils.
2018-08-31openblas@0.3.3: new version (#9143)Geoffrey Oxberry1-0/+1
2018-08-31libpng package: add version (#9142)rice311-0/+1
2018-08-31singularity: new versionLevi Baber1-0/+1
2018-08-29Intel prefixes (#7469)Michael Sternberg6-845/+154
Consolidate prefix calculation logic for intel packages into the IntelPackage class. Add documentation on installing Intel packages with Spack an (alternatively) adding them as external packages in Spack.
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