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2020-01-24Fixing GCC compiler setting for PDT packageKevin Huck1-0/+4
2020-01-24IOR package: add version 3.2.1 (#14582)Kevin Manalo1-2/+3
2020-01-24charliecloud package: add version 0.13; remove older versions (#14591)Jordan Ogas1-23/+12
* Add version 0.13 and update to use Autotools build system * Remove all versions prior to 0.13 (which do not use Autotools)
2020-01-24magma: add new version 2.5.2Piotr Luszczek1-0/+1
2020-01-24Add version 0.6.3 of yaml-cpp.Jon Rood1-0/+1
2020-01-24Updated and cleaned up the recipe for the LBANN and Hydrogen packages. (#14612)Brian Van Essen2-9/+16
* Updated and cleaned up the recipe for the LBANN and Hydrogen packages. * Flake8 * Added type test for catch2
2020-01-24Added version for 10.2 compatibility (#14613)Brian Van Essen1-2/+7
* Added version for 10.2 compatibility * Updated the preferred version
2020-01-24Use Spack target architecture to determine OpenBLAS target (#14380)Seth R. Johnson1-52/+82
Openblas target is now determined automatically upon inspection of `TargetList.txt`. If the spack target is a generic architecture family (like x86_64 or aarch64) the DYNAMIC_ARCH setting is used instead of targeting a specific microarchitecture.
2020-01-23openPMD-api: adios_config to run env (#14610)Axel Huebl1-0/+1
Popular CMake find-scripts for ADIOS1 search for this binary instead of looking up `CMAKE_PREFIX_PATH`.
2020-01-23Add TensorFlow 1.15.1 (#14614)Adam J. Stewart1-1/+2
2020-01-23ftgl: Move to frankheckenbach fork + CMakePackage (#14221)Hadrien G5-186/+40
* Try to switch to a newer fork of ftgl * Allow ROOT to be more flexible about ftgl versions * Turn ftgl into a CMakePackage * Update ROOT ftgl dep since 2.1.3 isn't a thing anymore * Please flake8 * Try to bring back the doc variant * Comment it out instead of removing it
2020-01-23root: Fix root+x breakage from #11129 (#14224)Hadrien G1-0/+29
* Fix root+x breakage from #11129 * Separate out +opengl breakage * Not strictly X11-related, but more breakage from #11129 * Another X11 breakage found while building 6.08.x * Don't put system headers in SPACK_INCLUDE_DIRS + deduplicate * xextproto is only a dependency in +x builds
2020-01-22binutils, libiberty: add version 2.33.1Mark W. Krentel2-1/+5
2020-01-22openPMD-api: Default +adios1 (#14599)Axel Huebl1-1/+1
Enable the ADIOS1 backend by default.
2020-01-22MPark.Variant: Patch NVCC C++14 Build 2 (#14434)Axel Huebl2-20/+33
Update the patch to fix builds with NVCC <= 10.2.89 with the accepted PR for upcoming releases of the library.
2020-01-22libquo: Update default version from 1.3 to 1.3.1. (#14585)Sam Gutiérrez1-1/+2
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
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