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2020-10-26Update GATK versions. (#19521)dunatotatos1-0/+40
2020-10-26fujitsu-ssl2: update package.py (#19519)takanori-ihara1-60/+68
2020-10-26abseil-cpp: add versions 20200923.{1,2} (#19517)Geoffrey Gunter1-1/+3
2020-10-26New package: py-visdom (#19479)Jen Herting1-0/+30
* [py-visdom] created template * [py-visdom] added dependencies * [py-visdom] added homepage and description. removed fixmes * [py-visdom] added dependency on py-torchfile * [py-visdom] py-pillow -> pil * [py-visdom] fixed url format * [py-visdom] fixed url format
2020-10-26Add BLT package (#19410)David Beckingsale1-0/+30
* Add BLT package * Switch install function Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Add type='run' to cmake dependency Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Add git attribute to BLT Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-10-26cp2k, libxc, libint: fix builds with %intel, resp. intel-parallel-studio+mkl ↵Tiziano Müller3-39/+23
(#19522) * cp2k: locate correct include dir when using intel-parallel-studio+mkl for fftw-api * libxc: drop arch-specific intel opt. flags fixes #17794 * libint: drop arch-specific intel opt. flags, always build Fortran example with FC fixes #17509
2020-10-26bugfix: test_push_and_fetch_keys should be skipped w/o gpg (#19511)Todd Gamblin1-0/+2
- [x] add a `@pytest.skipif` decorator
2020-10-25package/pmdk add variants, version 1.9 (#19512)Sinan1-4/+13
* package/pmdk add variants, version 1.9 * add dependency * Update var/spack/repos/builtin/packages/pmdk/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: sbulut <sbulut@3vgeomatics.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-10-25phist: two new versions and disable ccache because we don't have a ↵jthies1-1/+4
dependency on ccache. (#19510) Otherwise, phist would look for ccache via cmake, which is not the spack way to do it. Co-authored-by: Thies <thie_jo@be-cpu03.sc.bs.dlr.de>
2020-10-24bugfix: fix config merge order for OrderdDicts (#18482)Todd Gamblin5-30/+67
The logic in `config.py` merges lists correctly so that list elements from higher-precedence config files come first, but the way we merge `dict` elements reverses the precedence. Since `mirrors.yaml` relies on `OrderedDict` for precedence, this bug causes mirrors in lower-precedence config scopes to be checked before higher-precedence scopes. We should probably convert `mirrors.yaml` to use a list at some point, but in the meantie here's a fix for `OrderedDict`. - [x] ensuring that keys are ordered correctly in `OrderedDict` by re-inserting keys from the destination `dict` after adding the keys from the source `dict`. - [x] also simplify the logic in `merge_yaml` by always reinserting common keys -- this preserves mark information without all the special cases, and makes it simpler to preserve insertion order. Assuming a default spack configuration, if we run this: ```console $ spack mirror add foo https://bar.com ``` Results before this change: ```console $ spack config blame mirrors --- mirrors: /Users/gamblin2/src/spack/etc/spack/defaults/mirrors.yaml:2 spack-public: https://spack-llnl-mirror.s3-us-west-2.amazonaws.com/ /Users/gamblin2/.spack/mirrors.yaml:2 foo: https://bar.com ``` Results after: ```console $ spack config blame mirrors --- mirrors: /Users/gamblin2/.spack/mirrors.yaml:2 foo: https://bar.com /Users/gamblin2/src/spack/etc/spack/defaults/mirrors.yaml:2 spack-public: https://spack-llnl-mirror.s3-us-west-2.amazonaws.com/ ```
2020-10-24py-coverage: added v5.3 (#19509)Massimiliano Culpo1-0/+1
2020-10-23docs: update docs on shell support and using packages (#19486)Todd Gamblin3-337/+344
Shell integration no longer requires setting `SPACK_ROOT`, so we can simplify the documentation on it. The docs on shell support and using packages are getting a bit old, and information on `spack load` (which seems to be everyone's most common way of using packages) is hard to find. This PR simplifies the shell documentation to remove SPACK_ROOT, and also moves some sections around for clearer organization. - [x] make docs on sourcing setup scripts clearer and simpler - [x] introduce `spack load` early in the basic usage guide instead of burying it in the module docs - [x] clean up module docs so that spack module tcl loads comes later - [x] be clear about the different ways to use packages so that the users can find the docs better. Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2020-10-23csh: don't require SPACK_ROOT for sourcing setup-env.csh (#18225)Todd Gamblin15-122/+242
Don't require SPACK_ROOT for sourcing setup-env.csh and make output more consistent
2020-10-23Fix GROMACS to require FFTW when using cuda (#19505)Marty Kandes1-1/+1
GROMACS still requires a version of FFTW when compiling it to utilize NVIDIA GPUs. In fact, the type of calculation that depends on FFTW -- Particle-Mesh Ewald (PME) -- is generally run on the host system's CPUs, even when GPUs are available.
2020-10-23New package: py-rise (#19496)iarspider1-0/+19
* New package: py-rise * Fix URL and add description * Update var/spack/repos/builtin/packages/py-rise/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-10-23let intel-parallel-studio provide fftw-api for +mkl (#19497)Tiziano Müller1-0/+4
2020-10-23CMake fix: narrow versions that the PGI patch is applied to (#19495)Scott McMillan1-1/+1
Co-authored-by: Scott McMillan <smcmillan@nvidia.com>
2020-10-23New package: py-gsi (#19494)iarspider1-0/+19
* New package: py-gsi * Add dependency on py-setuptools
2020-10-23Update asciidoc-py3 and fix build problem (#19491)lorddavidiii1-0/+3
* asciidoc-py3: add new version 9.0.3 * asciidoc-py3: fix build - add libxml2 and libxslt as dependency
2020-10-23modified:var/spack/repos/builtin/packages/ppopen-appl-fem/package.py (#19489)daichi-nishi1-2/+3
2020-10-23modified:var/spack/repos/builtin/packages/ppopen-appl-fdm/package.py (#19488)daichi-nishi1-3/+2
2020-10-23gaussian-src: initial commit, gaussian-view: update to 6.1.1 (#17711)Tiziano Müller7-8/+1237
* gaussian-src: initial commit to build from source * do not install the source to ensure to not accidentally distribute it to users * set required runtime env vars based on the login.profile * gaussian-view: update to 6.1.1
2020-10-23gcc: Fix zstd patch version range (#19490)Michael Kuhn1-1/+1
PR #19482 updated gcc to only apply the zstd patch until @10.2 but the releases/gcc-10 branch actually does not contain the patch yet, that is, gcc@10.3 will most likely have the same problem. Apply the patch for all 10.x releases instead.
2020-10-23Add new package: acpica-tools (#18739)darmac1-0/+22
* Add new package: acpica-tools * refine build dependencies
2020-10-23gcc: fix build of gcc@master by limiting the version range of a patch (#19482)Thomas Green1-1/+1
Co-authored-by: Thomas Green <ca-tgreen@gw4a64fxlogin00.head.gw4.metoffice.gov.uk>
2020-10-23graphviz: add patch for XCode 12 (#19485)Todd Gamblin2-0/+26
- [x] Add a patch to fix an implicit declaration error with apple-clang 12
2020-10-23openipmi: added new package at v2.0.28 (#18790)darmac1-0/+30
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-10-22modified:var/spack/repos/builtin/packages/ppopen-appl-fvm/package.py (#19487)daichi-nishi1-3/+5
2020-10-22Bcolz (#19331)manifest1-0/+27
* gemini dep -py-bcolz + * Update var/spack/repos/builtin/packages/py-bcolz/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-bcolz/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * py-bcolz URL fix * Update var/spack/repos/builtin/packages/py-bcolz/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-10-22Syscalc hash (#19323)iarspider1-2/+3
* Update syscalc hash * Tiny fix * Change URL and update hash as advised by the devs Co-authored-by: iarspider <iarpsider@gmail.com>
2020-10-22New package: py-dominate (#19483)Jen Herting1-0/+24
* [py-dominate] created template * [py-dominate] added dependencies * [py-dominate] added homepage and description. removed fixmes * [py-dominate] fixed url format
2020-10-22Enable packages to use the NVIDIA HPC SDK (#19452)Scott McMillan85-18/+1824
* Enable packages to use the NVIDIA HPC SDK * fix linter and review items * fix linter issue Co-authored-by: Scott McMillan <smcmillan@nvidia.com>
2020-10-22New package: py-torchfile (#19481)Jen Herting1-0/+22
* [py-torchfile] created template * [py-torchfile] set python versions * [py-torchfile] depends on py-numpy * [py-torchfile] fixed url format * [py-torchfile] added homepage and description. removed fixmes * [py-torchfile] fixed url format
2020-10-22Add scratch module roots to test configuration (#19477)Massimiliano Culpo4-82/+23
fixes #19476 Module file content is written to file in a temporary location and read back to be analyzed by unit tests. The approach to patch "open" and write to a StringIO in memory has been abandoned, since over time other operations insisting on the filesystem have been added to the module file generator.
2020-10-22[py-pyarrow] cuda and orc support (#19445)Jen Herting1-0/+6
* [py-pyarrow] telling setup.py that we want cuda support * [py-pyarrow] added orc variant * [py-pyarrow] passing the orc variant down the line * [py-pyarrow] added variant description
2020-10-22Arrow: add orc support (#19442)Jen Herting1-0/+17
* [arrow] added orc support variant * [arrow] depends on orc * [arrow] added explicit disable of features for variants
2020-10-22modified:var/spack/repos/builtin/packages/ppopen-appl-amr-fdm/package.py ↵daichi-nishi1-4/+5
(#19459)
2020-10-22modified : var/spack/repos/builtin/packages/ppopen-appl-bem/package.py (#19460)daichi-nishi1-2/+2
2020-10-22ppopen-appl-dem-util:change download site to github. (#19461)daichi-nishi1-3/+5
* modified:var/spack/repos/builtin/packages/ppopen-appl-dem-util/package.py * modified:var/spack/repos/builtin/packages/ppopen-appl-dem-util/package.py:deleted whitespace
2020-10-22Add opencl-headers and use ocl-icd as OpenCL provider (#19463)lorddavidiii4-0/+96
* ocl-icd: fix build problems * New package: opencl-c-headers * New package: opencl-clhpp * New bundled package: opencl-headers - bundle C and C++ header files * ocl-icd: Add +headers variant to use this as opencl provider * ocl-icd: add new upstream release 2.2.13 * ocl-icd: add asciidoc-py3 and xmlto dependency needed for manpage generation * ocl-icd and opencl-headers provides OpenCL 3.0 - also add more explicit version providing for older ocl-icd versions * opencl-headers: add maximum of supported opencl versions for all versions * opencl-headers: there aren't final releases with OpenCL 3.0
2020-10-22modified:var/spack/repos/builtin/packages/ppopen-appl-fdm-at/package.py (#19464)daichi-nishi1-3/+2
2020-10-22Restrict Python version for Strelka to Python 2. (#19466)dunatotatos1-1/+1
Fix #19465
2020-10-22New Package: py-fastrlock (#19467)Jen Herting1-0/+24
* [py-fastrlock] created template * [py-fastrlock] added dependencies and setting --with-cython * [py-fastrlock] added homepage and description. removed fixmes
2020-10-22hercules (#19434)Andrew W Elble1-0/+22
2020-10-22Add new package: py-cantoolz (#18812)darmac1-0/+26
* Add new package: py-cantoolz * refine depends
2020-10-22New package: orc (#19441)Jen Herting2-0/+242
* [orc] created template * [orc] depends on maven * [orc] building with -fPIC * [orc] fixed name of c flags option * [orc] depends on openssl * [orc] added dependencies and disableing installing vendored libs * [orc] disabling hdfs * [orc] depending on specific versions of dependencies * [orc] no building of third party libs * [orc] helping cmake find the dependencies * [orc] disabling features that would require static protobuf libraries * [orc] dependency versions are ranges * [orc] added homepage and description. removed fixmes * [orc] flake8 * [orc] switching to compilier indipendent code
2020-10-22[treelite] added python and protobuf support (#19444)Jen Herting1-1/+45
* [treelite] added protobuf variant * [treelite] adding python support * [treelite] disable protobuf by default * [treelite] flake8 * [treelite] reordered phases
2020-10-22transrate: new package at 1.0.3 (#19295)Justin S1-0/+24
* transrate: new package at 1.0.3 * transrate: add macOS binary distribution * transrate: fix platform switching
2020-10-22py-tomlkit: new package at 0.7.0 (#19450)Justin S1-0/+22
* py-tomlkit: new package at 0.7.0 * py-tomlkit: add dependencies
2020-10-22New package: py-labours (#19433)Andrew W Elble1-0/+31
* py-labours * fix dep version constraints
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