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2018-07-12flang: add support for llvm-6 (#8073)Christoph Junghans2-8/+65
* flang: add support for llvm-6 * flang: review changes * pgmath: make flake8 happy
2018-07-12locks: improve errors and permission checkingTodd Gamblin2-52/+145
- Clean up error messages for when a lock can't be created, or when an exclusive (write) lock can't be taken on a file. - Add a number of subclasses of LockError to distinguish timeouts from permission issues. - Add an explicit check to prevent the user from taking a write lock on a read-only file. - We had a check for this for when we try to *upgrade* a lock on an RO file, but not for an initial write lock attempt. - Add more tests for different lock permission scenarios.
2018-07-12locks: llnl.util.lock now only writes host info when in debug modeTodd Gamblin2-13/+98
- write locks previously wrote information about the lock holder (host and pid), and read locks woudl read this in. - This is really only for debugging, so only enable it then - add some tests that target debug info, and improve multiproc lock test output
2018-07-12tests: Separate tests for llnl.util.lock and spack.util.lockTodd Gamblin4-161/+169
- llnl.util.lock tests are now independent of Spack
2018-07-12refactor: move spack.util.multiproc to llnl.util.multiprocTodd Gamblin5-12/+12
- multiproc doesn't depend on Spack - llnl.util.lock test uses it, but shouldn't use parts of Spack.
2018-07-12tests: add lib/spack/spack/test/.cache to gitignore for pytestTodd Gamblin1-1/+1
- this shoudl have been moved when we moved pytest.ini to lib/spack/spack/test
2018-07-12Add Git development versions for Typhon and BookLeaf_Cpp. (#8694)Tim Law2-0/+6
2018-07-12First try on pytorch (#8649)Nicolas Richart1-0/+93
* initial version of the package pyTorch (#171) * adding version 0.4 * flake8 correction * reordering version, removing run dependecies * Changing depends_on type to default
2018-07-12mitofates: more deps and a patch to make it functional (#8686)Levi Baber2-0/+39
* mitofates: more deps and a patch to make it functional
2018-07-12Remove unnecessary version-specific URL overrides (#8693)Adam J. Stewart5-19/+10
2018-07-11transdecoder: needs perl-uri-escape (#8690)Levi Baber1-0/+1
2018-07-11beast1: new version (#8691)Levi Baber1-0/+2
2018-07-11mothur: new version (#8692)Levi Baber1-0/+1
2018-07-11py-ply: added version 3.11 (#8383)Massimiliano Culpo1-2/+3
2018-07-11Don't propagate version-specific URL overrides to newer versions (#8565)Massimiliano Culpo3-18/+52
When a user specifies a URL for a specific version of a package, Spack originally would use that URL for all newer versions of the package. This behavior has proven to be generally more harmful than useful, so this PR removes the feature such that a version-specific URL override affects only that version.
2018-07-11py-cutadapt: needs py-setuptools at runtime (#8689)Levi Baber1-1/+1
2018-07-11openmpi: add 3.1.1 (#8684)Howard Pritchard1-0/+1
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2018-07-11Adjusted sublime-text package (#8685)Jannek Squar1-2/+3
2018-07-11perl-math-cephes: new package (#8671)Levi Baber1-0/+35
2018-07-11Update kaldi (#8682)Jimmy Tang1-8/+8
* Update kaldi always use the --fst-version otherwise it does the wrong thing with selecting the fst version. also enable speex by default * Give version a more meaningful name * Update older version with a date string instead
2018-07-11New packages: libbeato bwtool. (#8681)健美猞猁2-0/+72
2018-07-11Retire the py-dev package (#8679)Adam J. Stewart2-48/+0
2018-07-11Patch for 'netlib-lapack'. (#8677)Sergey Kosukhin2-0/+31
2018-07-11Bump gromacs versions. (#8676)健美猞猁1-0/+2
2018-07-10Adding psm as a dependency of mvapich2. (#8674)Jon Rood1-1/+5
2018-07-10Gtkorvo updates (#8663)Kshitij Mehta5-9/+57
* gtkorvo-atl: Updated to version 2.2 * gtkorvo-dill: Updated to version 2.4 * gtkorvo-enet: Updated to version 1.3.14 * libevpath: Updated to version 4.4.0 * libffs: Updated to version 1.5 * gtkorvo-atl: Bugfix: Fixed cmake args * gtkorvo-enet: Switched order of versions to have the latest version on the top * gtkorvo-atl: Cleaned up cmake_args. Added conditional self.run_tests * gtkorvo-dill: Cleaned up cmake_args. Added conditional self.run_tests * libffs: Correction in dependency versions. Cleaned up cmake_args. Added conditional self.run_tests * libevpath: Correction in dependency versions. Cleaned up cmake_args. Added conditional self.run_tests * gtkorvo-atl: Removed unused option from cmake args
2018-07-10fetch: remove 'trying' when cloning repos (#8651)Matthias Diener2-5/+5
* fetch: remove 'trying' when cloning repos This makes it similar to what the URL strategy prints. * change svn/hg names
2018-07-10libxshmfence: Update to 1.3 (#8667)Michael Kuhn1-2/+3
libxshmfence@1.2 does not compile with recent versions of glibc.
2018-07-09charm: add possibility to run tests (#8665)Matthias Diener1-0/+6
2018-07-09libnova: new package (#8666)Levi Baber1-0/+42
* libnova: new package * libnova: flake8
2018-07-09Add ccache support (#3761)Christoph Junghans5-1/+41
If the user sets "ccache: true" in spack's config.yaml, Spack will use an available ccache executable when compiling c/c++ code. This feature is disabled by default (i.e. "ccache: false") and the documentation is updated with how to enable ccache support
2018-07-09Make 'netlib-lapack' a CMakePackage. (#8661)Sergey Kosukhin1-48/+70
* Make 'netlib-lapack' a CMakePackage. * Add a comment. * Some refactoring.
2018-07-09express: bamtools lib handling (#8552)Levi Baber1-5/+2
* express: bamtools lib handling * express: use libs property * express: remove old comment
2018-07-08trilinos: update dtk dependencies (#8660)Andrey Prokopenko1-0/+3
2018-07-08fix typo in help of `spack clone` prefix is singular (#8658)Andreas Baumbach1-1/+1
Change-Id: I3bfe5b4ba497fae57d5382502ea9a1b054688fdb
2018-07-07blasr: new package (#8367)Miles Perry1-0/+96
* blasr: new package * blasr: changed version release, created list with 9 things, seperated make into build phase. * blasr: fixed build phase by adding : * blasr: fixed syntax for configure_args * blasr: flake8 edits * blasr-libcpp: fixed configure_args syntax * blasr: fixed install issues resulting from PacBio changes * blasr: removed accidental blasr-libcpp upload * blasr: removed accidental blasr-libcpp upload * blasr: removed blasr-libcpp * blasr: edited out comment
2018-07-07ECP VELOC (#8581)Elsa Gonsiorowski, PhD7-0/+388
* kvtree package file * MPI is default on * proper mpi compiler * rankstr package * better rankstr description * typo * redset package * shuffile package * er package * axl package * proper pythor * mpi is default on * alpha releases and master versions * veloc package with boost headers dep * cmake version * added C++11 requirement * flake8 * flake8 * ecp tag * axl: better async api option handling * veloc package description * prettier args list * C++11 flag handler * v1.0 of veloc
2018-07-06Added support for uncrustify 0.67. (#8655)estebanpauli1-1/+17
* Added support for uncrustify 0.67. Since the build system changed for uncrustify at version 0.64, I had to change the package from an AutotoolsPackage to a plain Package and use @when annotations to build the packages differently. * Removed blank line at end of file * Added support for python2.6 in uncrustify configuration.
2018-07-06Fix security issue in singularity + misc cleanups (#8657)George Hartzell1-9/+15
- Versions before 2.5.2 suffer from a serious security problem (https://nvd.nist.gov/vuln/detail/CVE-2018-12021). Deleted all versions prior to v2.5.2. - Update homepage (looks like singularity's going Freemium). - Use release tarball instead of automagically generated archive tarball (digest values are more stable). - No longer need autotools for released versions, just @devel. - Install needs to be single-threaded, otherwise when installed as root the various 'chmod' operations race against the copies.
2018-07-06Fix digests for git@2.17.0 and git@2.17.1 (#8652)George Hartzell1-4/+4
The entries for git@2.17.1 and git@2.17.0 were swapped. This fixes them.
2018-07-06Update nettle package with info for v3.4 (#8653)George Hartzell1-0/+1
2018-07-06Clear up a bit of modules/dotkit confusion (#8650)George Hartzell1-5/+7
`use` is an overloaded word between dotkit, modules and spack. Add additional words to make the distinction clear in the docs.
2018-07-06Add url_for_version and list_url to Ruby package (#8216)Adam J. Stewart1-0/+6
2018-07-06precice: new package (issue #8643) (#8644)Mark Olesen2-0/+181
preCICE (Precise Code Interaction Coupling Environment) is a coupling library for partitioned multi-physics simulations. Partitioned means that preCICE couples existing programs (solvers) capable of simulating a subpart of the complete physics involved in a simulation. of-precice: new package preCICE adapter for OpenFOAM
2018-07-06switch git to kernel.org source and sha256 (#8580)Andreas Baumbach1-48/+49
* switch git to kernel.org source and sha256 Change-Id: I5fe15689adb1163e9ed2b7127b52c95bd0d48564 * fix forgotton md5s Change-Id: Ib01f21e20678d9aac3344b6ee311134a90b87bdd * remove old url Change-Id: I717a084a0357a84b83bc6c8542749aac7e04f68b
2018-07-06Glog: make is a function (#8648)Adam J. Stewart1-2/+2
2018-07-05cleverleaf: Intel compiler fails compilation without c++11 flag (#8550) (#8598)twang151-0/+6
2018-07-05Add missing dependencies and variants to wcslib (#8603)Adam J. Stewart1-2/+34
* Add missing dependencies and variants to wcslib * Add flex version requirement
2018-07-05ncbitoolkit: Create new package. (#8591)lingnanyuan1-0/+65
* ncbitoolkit: Create new package. * Fix Flake8 Error. * Add version constraints and change format. * Fix version constraints.
2018-07-05added rpy2 2.9.4 and added py-jinja2 dependency (#8645)Gregory Lee1-3/+14
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