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2020-01-17jdk temporary fix (#14550)Sajid Ali1-0/+2
2020-01-17fix hadoop url and update versions (#14530)darmac1-3/+8
2020-01-16Added new hashes for the protobuf and py-protobuf packates. (#14546)Brian Van Essen2-0/+11
* Added new hashes for the protobuf and py-protobuf packates. * Fixed flake8
2020-01-16Don't patch latest version of HDF5 (#14545)Adam J. Stewart1-1/+1
2020-01-16Add py-torchvision 0.5.0 (#14544)Adam J. Stewart1-1/+2
2020-01-16Add py-torch 1.4.0 (#14543)Adam J. Stewart1-0/+1
2020-01-16Fix use of sys.executable for module/env commands (#14496)Adam J. Stewart2-4/+6
* Fix use of sys.executable for module/env commands * Fix unit tests * More consistent quotation, less duplication * Fix import syntax
2020-01-16Add include/pythonX.Y to CPATH (#14523)Adam J. Stewart1-6/+15
2020-01-16unifyfs: new release version (#14527)Cameron Stanavige1-2/+2
This updates the UnifyFS package to account for the latest 0.9.0 version and removes support for version 0.2.0.
2020-01-16mesa: check aarch64 system type as well (#14493)Howard Pritchard1-1/+1
to disabled use of libunwind. Without this mesa fails to build using recent Cray compilers - cce 9 and higher - on aarch64 systems. Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
2020-01-16falcon: Set Py_None to return value (#14532)noguchi-k2-0/+14
2020-01-16update hpx package for the new release 1.4.0 (#14533)albestro1-0/+1
2020-01-16add new package : geode (#14534)darmac1-0/+28
* add new package : geode * remove provides for gemfire
2020-01-16add new package : ignite (#14539)darmac1-0/+28
2020-01-16Use CudaPackage mixin for py-torch (#14540)Glenn Johnson1-2/+1
This PR adds CudaPackage in order to pick up the cuda/compiler conflicts defined in CudaPackage.
2020-01-16perl: Fix binary detection (#14536)Michael Kuhn1-1/+1
It seems that stable versions of perl also install a `perlX.Y.Z` binary. However, it seems that this binary can hang if used in conjunction with Spack's sbang workaround, as observed during automake's build.
2020-01-15octave: add 5.1.0 (#14531)Kai Torben Ohlhus1-0/+1
Add version Octave 5.1.0 including sha256.
2020-01-15Update py-csvkit (#14525)Glenn Johnson12-7/+230
* Update py-csvkit This PR updates the py-csvkit package. This version requires a python stack based on agate and this PR includes the new dependency packages. - py-agate-dbf - py-agate-excel - py-agate-sql - py-agate - py-dbfread - py-isodate - py-leather - py-parsedatetime - py-python-slugify - py-pytimeparse - py-text-unidecode * Replace the copy/pasted apostrophes Python 2 can not process the copy/pasted apostrophes so replace them with standard single quote character. * Add version constraints on dependencies
2020-01-15Update RocksDB to current version (#14524)Olaf Mersmann1-1/+23
* rocksdb: Fix for rocksdb issue 5303 * rocksdb: Explicitly disable features * rocksdb: Add TBB variant. * rocksdb: New version 5.18.3 and 6.5.3
2020-01-15Fix typo in modules docstring (#14521)Adam J. Stewart1-1/+1
2020-01-15Add version constraint to graphviz patches (#14377)Glenn Johnson1-4/+9
* Add version contraint to graphviz patches This PR restricts the graphviz version that the patches for building with the Intel compiler apply to. The two patches that were needed for building graphviz-2.40.1 with the Intel compiler are not needed for graphviz-2.42.2. * Adjust the qt dependencies The qt5 patch is only needed for graphviz-2.40.1. However, that version will only compile with GCC-6 or greater.
2020-01-15perl: Add 5.30.1 (and 5.31.7) (#14509)Michael Kuhn1-1/+24
This also fixes actually building the development releases.
2020-01-15mariadb-c-client: Add 3.1.6 and 3.1.5 (#14510)Michael Kuhn1-0/+2
2020-01-15hpctoolkit: add version 2019.12.28 (#14519)Mark W. Krentel1-13/+18
Add version 2019.12.28 and update the prereqs for the latest master.
2020-01-15New package Jali - unstructured mesh infrastructure for multiphysics ↵Rao Garimella1-0/+56
applications (#14498) * add variant for enabling testing * add variant for enabling testing * enable tests and clean up other options * enable tests and clean up other options * add numbered versions * add numbered versions * updates to avoid enable_tests variant; correct versioning * updates to avoid enable_tests variant; correct versioning * fixes for style * appropriate partitioners are enabled if 'all' is specified - so no need to check in spec * revert accidental change to copyright * remove erroneously re-introduced line about tests * new spack recipe for build Jali - unstructured mesh infrastructure for multiphysics applications * remove the +parallel condition for mstk, update 1.1.1 sha256sum and whitespace cleanup * reformat description * cut down description
2020-01-15Adds MPI_THREAD_MULTIPLE support for OpenMPI to the variant with UCX fabrics ↵Robert Mijakovic2-1/+17
(#14194) * Fixes: 1. MPI_THREAD_MULTIPLE problem with OpenMPI and UCX. Changes: 1. OpenMPI provides two new depends_on options which result in UCX being compiled with multiple threads support. One implicit when OpenMPI 3.x is used, MPI_THREAD_MULTIPLE is enabled by default, and one explicit for OpenMPI <= 2.x, MPI_THREAD_MULTIPLE is disabled by default. 2. Extends UCX package to allow "Enable thread support in UCP and UCT" option. 3. Adds sha256 sums of UCX releases 1.6.1 and 1.2.0. More details: Fixes the issue with OpenMPI where programs which use MPI_THREAD_MULTIPLE will fail to execute because UCP worker didn't support it. During the OpenMPI package installation it's the +thread_multiple spec was not propagated to UCX nor UCX handled it at all. Now, the OpenMPI package is capable of handling +thread_multiple spec when UCX is request and the UCX package correctly handles +thread_multiple and compiles with the --enable-mt option. Error message during runtime: pml_ucx.c:226 Error: UCP worker does not support MPI_THREAD_MULTIPLE * Adapts check of specs to read better and is the suggested form in the docs. * Explicitly disables multithreading of UCX if +thread_multiple option is not used.
2020-01-15Rework texlive package to install from source (#14332)Glenn Johnson1-19/+153
* Rework texlive package to install from source This PR reworks the texlive package so that it installs from versioned source distibution files. This is preferred over installing the binary package for several reasons. For the binary installation: 1. Each component is downloaded, so can not use a spack mirror. 2. Changes in components over time are not reflected in spack hash. 3. Some of the binaries do not run due to glibc issues, depending on OS. This PR keeps the binary installation as an option but it should be considered deprecated, and probably rewmoved at some point. This PR depends on zziplib from PR #14318. * Fix flake8 issues
2020-01-15Convert encoding of script in interproscan (#14356)Glenn Johnson2-0/+13
One of the perl scripts was encoded with ISO-8859-1, which caused the sbang replacement process to fail when spack uses python3. This PR converts the ps_scan script to UTF-8 encoding.
2020-01-15Change encoding for scripts in repeatmasker (#14358)Glenn Johnson2-0/+200
This PR converts ISO-8859 encoding to UTF-8 encoding for three scripts in repeatmasker. - the main RepeatMasker script - SimpleBatcher.pm - wublastToCrossmatch.pl The ISO-8859 encoding prevented the sbang replacement of long paths when spack uses python3.
2020-01-15python: Add 3.7.6 and 3.7.5 (#14497)Michael Kuhn1-1/+3
2020-01-14Update the icu4c package (#14450)Glenn Johnson1-5/+14
* Update the icu4c package This PR makes several changes to the icu4c package 1. add updated version to 65.1 2. modify the default url as project has moved to github 3. set UTF-8 locale to support building from source files in UTF-8 format Note that the older versions are not available on github so explicit urls were used. This PR will close #14399. * Consolidate the urls Consolidate the URLs in the `version` directives by using an if test in `url_for_version`. * Put version and sha256 on same line * Put top level url back
2020-01-14Update and fix bcftools package (#14505)Glenn Johnson6-1/+372
* Update and fix bcftools package This PR updates bcftools to 1.10.2 and is dependent on PR #14504. This PR also fixes builds of other versions. Versions 1.2-1.4 did not use autotools so when the packaeg was converted to use autotools with version 1.6 those older versions could no longer build. Also, those versions needed to be patched to use an external htsllib. The method of finding the external htslib is also different for those older versions. In addition, this PR adds two variants to bcftools: - libgsl - perl-filters Finally, dependencies for perl and python are added, and an unused dependency for libzip was removed. * Do not use '@' in variant description The '@' character in a variant description will cause a problem with `spack info`. ``` ==> Error: Incomplete color format: '@' in expressions, for @1.8: ``` * Fix error with python2 processing this package
2020-01-14Update armadillo (#14499)Erik Schnetter1-0/+1
2020-01-14Update HDF5 to 1.10.6 (#14500)Erik Schnetter1-0/+1
2020-01-14h5cpp: New package (#14501)Erik Schnetter1-0/+28
2020-01-14trnascan-se: add and configure infernal dependency (#14502)Justin S1-0/+7
* trnascan-se: add and configure infernal dep * trnascan-se: use patch() for infernal config
2020-01-14mpich: Correct package name in output (#14503)Erik Schnetter1-1/+1
2020-01-14Update htslib and add libcurl variant (#14504)Glenn Johnson1-2/+19
* Update htslib and add libcurl variant This PR updates htslib to version 1.10.2 and adds a libcurl variant. The libcurl variant defaults to True because, while it is optional, it is highly recommended by the project developers. Other things done: - be consistent with quotes * Change version in variant description Apparently, `spack info` does not like the `@` character in a variant description. ``` ==> Error: Incomplete color format: '@' in @1.3:. ```
2020-01-14stop word splitting from leaking out of setup-env (#14472)Tom Scogland1-1/+1
The pathadd function was using setopt to configure zsh for word splitting, which leaks out of the function and breaks default functionality in a number of external zsh plugins and packages. This switches to emulate -L, just as the spack function uses, to keep the setting local to the function.
2020-01-14py-yajl: new package at 0.3.5 (#14278)Justin S1-0/+17
* py-yajl: new package at 0.3.5 * py-yajl: use PyPI mirror * py-yajl: use short PyPI url * remove py-ujson package * py-yajl: remove unused imports
2020-01-14gapfiller: traverse subdirectories in patch (#14375)Justin S1-1/+1
* gapfiller: traverse subdirectories in patch * gapfiller: revert glob function change * gapfiller: use more precise glob
2020-01-14new package: variorum (#13624)Stephanie Brink1-0/+80
2020-01-14Update MSTK to 3.3.1 (#14494)Rao Garimella1-1/+2
2020-01-14add new package : rocketmq (#14442)darmac1-0/+29
* add new package : rocketmq * remove url_for_version()
2020-01-14Fix parsing of rocketmq URL (#14490)Adam J. Stewart2-0/+3
2020-01-14add new package : py-ansible (#14436)darmac1-0/+31
* add new package : py-ansible * update license info * update py-ansible depends
2020-01-14codar-cheetah: Added version 0.5 (#14487)Kshitij Mehta1-8/+6
* codar-cheetah: Added version 0.5 * codar-cheetah: Dropped v0.1 as it was not built as a Python package.
2020-01-14Sometimes debugging symbols are helpful (#14452)Rob Latham1-0/+6
2020-01-14Flang OpenMP target support for NVidia GPUs. (#14486)Nichols A. Romero1-0/+16
* Flang OpenMP target support for NVidia GPUs. * explictly disable gpu option with else clause.
2020-01-14upcxx depends on python 2 >= 2.7.5 (#14462)eugeneswalker1-0/+2
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