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2020-01-21pipelines: `spack ci` command with env-based workflow (#12854)Scott Wittenburg1-0/+1
Rework Spack's continuous integration workflow to be environment-based. - Add the `spack ci` command, which replaces the many scripts in `bin/` - `spack ci` decouples the CI workflow from the spack instance: - CI is defined in a spack environment - environment is in its own (single) git repository, separate from Spack - spack instance used to run the pipeline is up to the user - A new `gitlab-ci` section in environments allows users to configure how specs in the environment should be mapped to runners - Compilers can be bootstrapped in the new pipeline workflow - Add extensive documentation on pipelines (see `pipelines.rst` for further details) - Add extensive tests for pipeline code
2020-01-21python: add `debug` variant to enable pydebug (#14584)Todd Gamblin1-0/+10
2020-01-21Add py-scipy 1.2.3 (#14583)Adam J. Stewart1-0/+1
2020-01-21Update and fix samtools (#14507)Glenn Johnson1-12/+25
* Update and fix samtools This PR adds samtools-1.10 and sets the htlib directory so that the spack built htslib can be used. This PR also arranges the dependencies so that the htslib sequence is grouped on its own. Finally, the bzip2 dependency is removed and python and perl run dependencies are added. * Fix samtools when built with ncurses+termlib * The CI flake8 tests require lowercase variable Interestingly, this did not show up when I ran `spack flake8` locally.
2020-01-21cmake: Fix patch checksum (#14542)Michael Kuhn2-1/+146
Add patch locally to make sure checksum cannot change again.
2020-01-21Use CudaPackage mixin for py-theano (#14577)Glenn Johnson1-8/+5
This PR adds the CudaPackage mixin class to py-theano. This replaces the `gpu` variant with the `cuda` variant.
2020-01-20Add new kcov package (#14574)Adam J. Stewart1-0/+33
* Add new kcov package * Fix linking error and add test
2020-01-20Update AWS ParallelCluster to 2.5.1 (#14571)Sean Smith1-1/+4
Signed-off-by: Sean Smith <seaam@amazon.com>
2020-01-19add conduit 0.5.1 release and allow conduit to build against statically ↵Cyrus Harrison1-4/+3
linked python (#14559)
2020-01-19capnproto: New package. (#14557)Olaf Mersmann1-0/+21
* capnproto: New package. * capnproto: Fix flake8 errors. * Remove characters invalid in Python 2.
2020-01-19py-voluptuous update versions (#14556)Simon Pintarelli1-2/+4
2020-01-18openmpi: swat btl/uct ucx 1.7 bug (#14522)Howard Pritchard1-0/+6
Unfortunately UCX 1.7.0 is appearing in RPMS before it's officially released. There's a problem with Open MPI 4.0.x where x < 3 and this version of UCX, namely that the UCT BTL fails to compile. See https://github.com/open-mpi/ompi/issues/7128 This patch works around the problem by disabling the build of the UCT BTL for releases 4.0.0 to 4.0.2. add hppritcha (me) as maintainer Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2020-01-18Added py-spdlog package (#14514)Matthieu Dorier1-0/+28
* Added py-spdlog package * pleasing flake-8 * pleasing flake-8 * addressed some comments from adamjstewart * changed URL for archive * replaced with pypi.io url
2020-01-17Updates to casacore package (#14552)Martin Pokorny1-5/+20
* Add +cfitsio variant to wcslib dependency * Replace ncurses dependency with readline dependency casacore explicitly may depend on readline, not ncurses * Add workaround for casacore's readline dependency casacore optionally depends upon readline, but it's CMakeLists.txt provides no user control over whether or not readline becomes a dependency. As readline is often present by default on systems, it's better for this package to explicitly depend on readline in order to prevent linking to whatever system version of the library happens to be found during the build process. This should be considered a workaround until casacore's CMakeLists.txt is fixed. * Apply workaround for casacore's dependency on SOFA Similar to the issues with casacore's readline dependency, casacore's optional dependency on SOFA does not provide the user with a means of controlling the dependency during build time. Unlike the readline library, the SOFA library is unlikely to exist on most systems by default. As the SOFA dependency is only optionally used for testing casacore, requiring it by default is not a good workaround. Until casacore's CMakeLists.txt is fixed, this variant has been removed to avoid unexpected library dependencies in the installed package. * Add newer casacore versions * Add mpokorny to maintainer field
2020-01-17aml: adds 'develop' and 'master' targets. (#14549)Valentin Reis1-0/+3
Co-authored-by: mlhardware <57849932+mlhardware@users.noreply.github.com>
2020-01-17suite-sparse: add 5.4.0, 5.5.0, and 5.6.0, GitHub releases (#14547)Kai Torben Ohlhus1-9/+21
- The suite-sparse author publishes new versions starting with 5.5.0 on GitHub, see https://github.com/DrTimothyAldenDavis/SuiteSparse/releases and http://faculty.cse.tamu.edu/davis/SuiteSparse/ - change spack to download from there - updated sha256 checksums from GitHub for all available releases - For versions 5.4.0, 5.5.0, 5.6.0 there is a slightly different compilation necessary: first `make default` then `make install`. Summary of the version changes (+ added, -removed [because not available on GitHub]): ``` + 5.6.0 + 5.5.0 + 5.4.0 5.3.0 5.2.0 + 5.1.2 5.1.0 + 5.0.0 + 4.5.6 4.5.5 - 4.5.4 4.5.3 - 4.5.1 ```
2020-01-17add new package : erlang (#14548)darmac1-0/+28
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
2020-01-16Add 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
2020-01-15Add 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