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2018-03-22Speedup the default 'libs' property search ... (#7553)Veselin Dobrev1-24/+21
* Speedup the default 'libs' property search - important for external packages. * As advised by @alalazo, use tuples instead of lists inside _libs_default_handler.
2018-03-22mc: create new package (#7564)Matthias Diener1-0/+56
* mc: new package * Update package.py * Update package.py * Update package.py
2018-03-22[hypre] add the 'headers' property (#7278)Veselin Dobrev1-3/+21
* [hypre] Add the 'headers' property plus a small tweak in the 'libs' property. * [hypre] Add fallbacks for searching for '.libs' in 'prefix.lib64' and in all of 'prefix'. * [hypre] Fix style. * [hypre] Use find_headers instead of find + HeaderList.
2018-03-22added a new package file for PHIST (Pipelined, Hybrid-parallel Iterat… (#7361)jthies1-0/+132
* added a new package file for PHIST (Pipelined, Hybrid-parallel Iterative Solver Toolkit) * packages/phist: fix some formatting errors (too long lines etc) and set allowed values for option "outlev" * packages/phist: fix some more flake8 errors * add headers property to netlib-lapack and intel-mkl * ghost: fix finding cblas header and libs (at least for mkl and netlib-lapack, which provide headers()) * added a new package file for PHIST (Pipelined, Hybrid-parallel Iterative Solver Toolkit) * packages/phist: fix some formatting errors (too long lines etc) and set allowed values for option "outlev" * packages/phist: fix some more flake8 errors * phist: use headers property to find lapacke include dir * phist: fix flake8 error * phist: be more specific about dependencies and update version * phist: state trilinos minimum version when building with Tpetra kernels * gmp: add oldish version 5.1.3 with checksum * phist: get rid of the 'petsc+complex' variant, it can be installed by kernel_lib=petsc ^petsc+complex * phist: new version * phist: fix version checksum * Revert "add headers property to netlib-lapack and intel-mkl" This reverts commit d8cb62905ebfb2cba186fd2d736d54a88a49d089. * Revert "ghost: fix finding cblas header and libs (at least for mkl and netlib-lapack, which provide headers())" This reverts commit d406a77ed7879c124fbaf1d757d002b9f0771620. * phist: remove unused function * phist: reorder package file versions/variants/depends_on/rest * phist: some minor changes requested by @adamjsteward
2018-03-22perl-json: Create new package (#7431)Eric1-0/+34
2018-03-22Add py-cvxopt package (#7527)Adam J. Stewart1-0/+143
* Add py-cvxopt package * Flake8 fixes
2018-03-22Fix giflib unit tests on macOS/BSD (#7519)Adam J. Stewart2-0/+24
* Fix giflib unit tests on macOS/BSD * Unit tests occasionally fail when run in parallel
2018-03-22Fix error raising during install with Python 3 (#6894)Adam J. Stewart1-2/+8
* Fix error raising during install with Python 3 * Fix env_path too
2018-03-22Add latest version of MPFR and patches for older versions (#7545)Adam J. Stewart3-178/+19
* Add latest version of MPFR and patches for older versions * Fetch and checksum patches instead of storing them * Fix bug, version attribute was being overridden
2018-03-22package/py-pyutilib: create new package (#7555)Sinan1-0/+51
2018-03-22llvm+python+lldb depends on py-six for versions 5 and up (#7056)Gregory Lee1-0/+3
2018-03-22Used names with __ in class level constructs to avoid rebinding (#7563)Massimiliano Culpo1-3/+3
fixes #3129
2018-03-22Add latest version of MPC (#7546)Adam J. Stewart1-5/+13
2018-03-22Add latest version of ISL (#7547)Adam J. Stewart1-1/+2
2018-03-22add versions 1.9.6 1.9.7 (#7562)Sinan1-0/+2
2018-03-22Record installation date and time in DB (#7334)Massimiliano Culpo6-51/+262
* Added installation date and time to the database Information on the date and time of installation of a spec is recorded into the database. The information is retained on reindexing. * Expose the possibility to query for installation date The DB can now be queried for specs that have been installed in a given time window. This query possibility is exposed to command line via two new options of the `find` command. * Extended docstring for Database._add * Use timestamps since the epoch instead of formatted date in the DB * Allow 'pretty date' formats from command line * Substituted kwargs with explicit arguments * Simplified regex for pretty date strings. Added unit tests.
2018-03-22Recover the old patching order for packages. (#7558)Massimiliano Culpo1-1/+1
fixes #7543 This is very likely an hot-fix, while a more permanent solution is needed. See this comment for more insight: https://github.com/spack/spack/pull/7193#discussion_r176448831 on the problem.
2018-03-22meme: fix errors (#6736)Levi Baber1-4/+5
* meme: added perl-xml-parser dependency, resolved issue. still need to fix ghostscript or image-magick, conversion not working. * meme: fixed issue with libxslt/libxml2 conflict, and added imagemagick support * meme: removing libxslt/libxml2 dependency lines * meme: configure args * meme: separating configure args * meme: removing a comment, and hoping for travis to rebuild. site seems back up. * meme: make image-magick optional * meme: add comment referencing PR * meme: bah flake8
2018-03-22tcl-tclxml: new package (#7557)Federico Ficarelli1-0/+58
2018-03-22Add latest version of eigen (#7530)Adam J. Stewart2-1/+31
* Add latest version of eigen * Fix bug in ptscotch detection
2018-03-22tcl-tcllib: new package (#7481)Federico Ficarelli1-0/+47
2018-03-21Propagate architecture information during concretization (#7412)becker332-17/+57
This updates architecture concretization to * Search for the nearest parent in the DAG for architecture information rather than defaulting to the root of the DAG * Propagate architecture settings transitively, such that if for example the target is set at the root of the dag it will set the same target on indirect dependencies (assuming no intermediate dependency specifies a separate target). Previously this occurred in general but under some conditions did not, for example if an intermediate dependency specified some subset of architecture properties.
2018-03-21Opt avx (#7486)Michael Sternberg2-25/+36
* Promote to Autotools for simplicity; broaden Intel CPU opt targeting from SSE4.2 to AVX2 * make Intel CPU opt targeting same as in ../libxc * flake8 W291 * use canonical means to pass (ahem) the test phase, h/t @adamjstewart * revert f25d598 (unrelated merge) * re-merge
2018-03-21Add latest versions of bazel (#7542)Leonhard Reichenbach2-4/+34
* Add latest versions of bazel * Added java as dependency to run bazel
2018-03-21libXi requires pkgconfig and fixesproto (#7480)Eric Müller1-0/+4
2018-03-21py-pybedtools: fix hash for 0.6.9 (#7492)Levi Baber1-1/+1
2018-03-21Singularity: new version (#7551)Levi Baber1-0/+1
* singularity: new version * singularity: hash
2018-03-21perl-module-implementation: Create new package (#7549)Eric1-0/+40
2018-03-21New Package: jchronoss (#7207)Julien Adam1-0/+63
* New Package: jchronoss * jchronoss: Fix flake8 errors * jchronoss: Fix according to recommendations * jchronoss: Remove FIXME * jchronoss: Fix another flake8 error
2018-03-21r-dirichletmultinomial: Create new package. (#7227)lingnanyuan1-0/+44
* r-dirichletmultinomial: Create new package. * Change description. * Change description.
2018-03-21Enable creation of mirrors for systems with different compilers (#5153)scheibelp3-13/+50
* Create mirror for system with different compilers Spack concretizes the spec provided by the user in "spack mirror create" to ensure downloading the right dependencies. Under normal circumstances concretization requires that the chosen compiler exists on the system, but this is not required when creating download mirrors for other systems, so this requirement is removed in that case. * Add test for disabling compiler existence check * Update compiler existence checking logic * improve test for disabling compiler existence check
2018-03-21py-python-levenshtein: Create new package (#7426)Eric1-0/+37
* py-python-levenshtein: Create new package * py-python-levenshtein: fix flake8 errors * py-python-levenshtein: Use pypi.io per packaging guide
2018-03-21perl-cairo: Create new package (#7432)Eric1-0/+38
* perl-cairo: Create new package * perl-cairo: Add cairo dependency
2018-03-21bamutil: needs zlib (#7444)Levi Baber1-0/+2
2018-03-21package/JAGS: new version (4.3) (#7456)Sinan1-0/+1
* package/JAGS: new version (4.3) * fix typo fix typo
2018-03-21pandaseq: needs bzip and libtool as link (#7465)Levi Baber1-1/+2
2018-03-21Using self.prefix in Trilinos to avoid global name prefix undefined bug (#7478)Jon Rood1-1/+2
* Using self.prefix in Trilinos to avoid global name prefix undefined bug during module refreshing. * Fixing flake8 errors.
2018-03-21Open MPI: add 2.1.3 (#7535)Howard Pritchard1-0/+1
note the libmpi.so itself didn't have changes, only other components of the package had updates. Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2018-03-21suite-sparse: add cmake dependency (#7538)Denis Davydov1-0/+1
2018-03-21Generate spack docset for Dash. (#6981)健美猫1-1/+7
2018-03-21make py-setuptools a run-time-only dep for py-basemap and patch pytho… (#6989)Gregory Lee3-4/+9
* make py-setuptools a run-time-only dep for py-basemap and patch python package to only apply setuptools flag for build deps * py-qtconsole does not require setuptools
2018-03-21snphylo: new package (#7045)Yifan Zhu2-1/+58
* pushing partially done recipe for snphylo * r-snphylo: try * phylip: added version 3.697 * snphylo: updated package.py * snphylo: flake8 error fixed
2018-03-21Support MD5 with a warning when OpenSSL is compiled in FIPS mode (#7531)scheibelp1-3/+48
* This allows Spack to work with MD5 hashes on machines with openssl in FIPS mode. * We are still using MD5 for validation in many places, and a later PR will replace all uses of MD5 with SHA256. * This is a quick fix until that happens.
2018-03-21elfutils: document conflict with clang (#7096)Geoffrey Oxberry1-0/+6
2018-03-21intel-xed: new package (#7106)Mark W. Krentel1-0/+105
* intel-xed: new package The Intel X86 Encoder Decoder library for encoding and decoding x86 machine instructions. * intel-xed: style fixes for flake8. * intel-xed: better style fix * intel-xed: update to version 2018.02.14, add PYTHONPATH for building with python 3, cleanup the opt flag.
2018-03-21scotch%intel: remove restrict (#7148)lpoirel1-1/+1
The restrict compilation option with icc causes deadlock when multithreading is used. This issue has already been reported to the Scotch development team, but for current versions it is more reliable not to use the restrict compilation option.
2018-03-21librom: new package (#7180)Geoffrey Oxberry1-0/+77
* libtool: actually do symlinking correctly on darwin Version 4 of the libtool/darwin debacle: AutotoolsPackage hardcodes libtool & libtoolize into the autoreconf stage, so the commands `libtool` and `libtoolize` MUST be present, and shimming in glibtoolize into AutotoolsPackage when sys.platfrom == 'darwin' does not work. join_path(spec['libtool'].prefix.bin, 'libtool') still shadows system BSD libtool (in apple-cctools, see PR #7177), but this shadowing could be okay, depending on the combination of dependent specs. * librom: new package
2018-03-21py-backports-functools-lru-cache: add version 1.5 (#7206)Eric1-0/+2
* py-backports-functools-lru-cache: add version 1.5 * py-backports-functools-lru-cache: fix conflicts
2018-03-21Adding unzip package. (#7446)Jon Rood1-0/+46
* Adding unzip package. * Removing bzip2 dependency in unzip and raising an error when on Cray. * Fixing error. * Using conflicts statement for Cray detection in unzip package.
2018-03-21Xorg-server: Add dependencies and fix installation. (#7220)lingnanyuan3-53/+37
* xorg-server: Add several dependencies. * libepoxy: Add dependendies mesa and meson. * mesa: Add dependencies for hwrender. * mesa: undo some changes.
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