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2019-11-08openPMD-api: JSON Always On (#13641)Axel Huebl1-9/+5
JSON is not a compile-time variant anymore and a mandatory dependency from now on.
2019-11-08fluxbox: fix the comparison method with zero. (#13642)t-karatsu2-0/+14
2019-11-08Timemory (#13503)Jonathan R. Madsen1-0/+83
* Create timemory/package.py * Update package.py * mpi default to on * Update package.py * Update package.py * Update var/spack/repos/builtin/packages/timemory/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py * Update package.py * Update package.py - cleanup - python deps specify type - python 2.6 compatibility - double quotes to single quotes * Update package.py * Update package.py
2019-11-08precice: add compiler conflicts (#13644)Frédéric Simonis1-0/+7
2019-11-08Update openfoam to use new environment api (ref: #11115, 9ddc98e46a73) (#13645)Mark Olesen2-31/+40
- build: no special treatment - already addressed in the spack-Allwmake script - run: use environment from the OpenFOAM etc/bashrc
2019-11-07llvm: fix PythonString::GetString for >=python-3.7 (#13631)Daryl W. Grunau2-0/+42
* llvm: fix PythonString::GetString for >=python-3.7 * llvm/package.py: fix when the patch should be applied
2019-11-07new package: py-tempora (#13582)Marc Mengel1-0/+22
* package py-tempora * package py-tempora * Update var/spack/repos/builtin/packages/py-tempora/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * missing deps * Update var/spack/repos/builtin/packages/py-tempora/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-tempora/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-tempora/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * license bits
2019-11-07New package: py-uwsgi (#13619)Marc Mengel1-0/+18
* package py-uwsgi * package py-uwsgi * Update var/spack/repos/builtin/packages/py-uwsgi/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * license bits
2019-11-07New package: py-jaraco-functools (#13581)Marc Mengel1-0/+23
* package py-jaraco-functools * package py-jaraco-functools * autopep8, docutils cleanup * Update var/spack/repos/builtin/packages/py-jaraco-functools/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * missing deps * license bits * ...and later versions * lru cache dep change from adamjstewart
2019-11-07Balay/ginkgo 1.1.0 (#13632)Satish Balay1-1/+4
* ginkgo: add version 1.1.0 * Ginkgo: add conflict for gcc older than version 5.3
2019-11-07bugfix: mirror path works for unknown versions (#13626)Todd Gamblin2-2/+8
`mirror_archive_path` was failing to account for the case where the fetched version isn't known to Spack. - [x] don't require the fetched version to be in `Package.versions` - [x] add regression test for mirror paths when package does not have a version
2019-11-07py-pyside: fix setup files to support python 3.5. (#13613)Kelly (KT) Thompson1-0/+11
This fix already exists in the development branch of pyside. See https://github.com/pyside/pyside-setup/pull/55.
2019-11-07elmer-fem: add devel branch (#13630)Justin S1-0/+1
2019-11-07PyTorch: Add 1.3.1 (#13629)Adam J. Stewart1-0/+1
2019-11-07(py)arrow: new versions (#13561)Andreas Baumbach2-3/+17
* (py)arrow: new versions * move py-arrow source to github as not all versions are on pypi same checksum as pypi, adding build_directory * move back to pypi sources * drop 0.15.0 and 0.14.1 as only .whl are available on pypi * add new dependencies * Update var/spack/repos/builtin/packages/py-pyarrow/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-07new package: py-convertdate (#13573)Andreas Baumbach1-0/+21
* new package: py-convertdate * Update docstring
2019-11-07Speed up PyTorch build (#13621)Adam J. Stewart1-6/+18
2019-11-07bam-readcount: a new package. (#13628)健美猞猁1-0/+15
2019-11-07m4: fixed macOS version identification on patch (#13623)Josh Deaton1-1/+3
Patch was not being applied in recent versions of macOS. Homebrew is still applying patch to any version after High Sierra.
2019-11-06py-jupyter-core add new version and setuptools dependency (#13424)Andreas Baumbach1-13/+15
* py-jupyter-core add new version and setuptools dependency * update checksums to use pypi * fixup url and python dep type * Update var/spack/repos/builtin/packages/py-jupyter-core/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-06new package: py-jdatetime (#13569)Andreas Baumbach1-0/+15
* new package: py-jdatetime * Update var/spack/repos/builtin/packages/py-jdatetime/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-06ncview: Fix dependency check (#13615)Michael Kuhn1-1/+1
netcdf has been renamed to netcdf-c.
2019-11-06gromacs: add v2019.4 and others (#13617)Christoph Junghans1-1/+4
* gromacs: add v2019.4 and others * gromacs: fix patch applying
2019-11-06new package: py-dateparser (#13574)Andreas Baumbach1-0/+33
* new package: py-dateparser * take setup.py dependencies into account * fixup help->description * reorder dependencies * drop version constraints not enforced in setup.py
2019-11-06new package: py-nodeenv (#13594)Andreas Baumbach1-0/+17
* new package: py-nodeenv * drop python version requirements, not enforced by setup.py
2019-11-06py-tatsu: new package (#13566)Andreas Baumbach1-0/+27
* py-tatsu: new package * drop unnecessary dependencies * drop kanji, add variant, and restrict to future releases
2019-11-06netcdf-fortran: Fix parallel builds (#13612)Michael Kuhn1-1/+18
netcdf-fortran@4.5: will error if netcdf-c has been built with MPI support: ``` configure: error: ----------------------------------------------------------------------- The NetCDF C library is built with parallel I/O feature enabled, but the Fortran compiler '.../lib/spack/env/gcc/gfortran' supplied in this configure command does not support MPI-IO. Please use one that does. If parallel I/O feature is not desired, please use a NetCDF C library with parallel I/O feature disabled. Abort. ----------------------------------------------------------------------- ``` Copy logic from netcdf-c to add an `mpi` variant.
2019-11-06cdo: Fix with_or_without calls (#13614)Michael Kuhn1-3/+6
netcdf has been renamed to netcdf-c and udunits2 has been renamed to udunits.
2019-11-06new package: py-pymeeus (#13572)Andreas Baumbach1-0/+17
* new package: py-pymeeus * drop unnecessary dependencies
2019-11-06new package: py-pre-commit (#13570)Andreas Baumbach1-0/+30
* new package: py-pre-commit * update missing dependencies * add python version restriction
2019-11-06new package: py-aspy-yaml (#13591)Andreas Baumbach1-0/+19
* new package: py-aspy-yaml * add python version dependency
2019-11-06go: Add 1.13.4 and 1.12.13 (#13609)Michael Kuhn1-0/+2
2019-11-06pybind11: correct get_include path (#13605)Axel Huebl1-0/+20
* pybind11: test get_include path Helper for non-CMake downstream projects to find the pybind11 header location. * pybind11: return proper get_include() use our prefix instead of letting pybind11 trying to self-determine it from given conda/virtualenv/global rules. Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-05new package: py-ics (#13576)Andreas Baumbach1-0/+39
* new package: py-ics * drop 0.5 and move to tar-ball * Update var/spack/repos/builtin/packages/py-ics/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-ics/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-05add charliecloud 0.12 (#13599)Jordan Ogas1-0/+1
* add charliecloud 0.12 * fix typo Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-05Add GDAL 3.0.2 (#13603)Adam J. Stewart1-1/+2
2019-11-05mpi4py 3.0.3 (#13601)Axel Huebl1-3/+4
* mpi4py 3.0.3 Adds support for Python 3.8 with new Cython files. I tried to build 3.0.0 with Python 3.8 and this builds as well, therefor I added no conflict. * mpi4py: update dependency version ranges
2019-11-05netcdf: fix headers in v4.7.2 (#13600)Christoph Junghans1-0/+3
2019-11-05elpa: add v 2019.05.002 (#13602)Christoph Junghans1-0/+1
2019-11-05PyTorch: avoid use of third party vendored deps (#13588)Adam J. Stewart1-5/+16
* PyTorch: avoid use of third party vendored deps * Flake8 fix
2019-11-05add depends_on(python) to PythonPackage stub (#13595)Andreas Baumbach1-0/+1
2019-11-05new package: py-nose-cov (#13571)Andreas Baumbach1-0/+19
* new package: py-nose-cov * add missing dependencies
2019-11-05update py-notebook (#13423)Andreas Baumbach1-6/+16
* update py-jupyter-notebook * add setuptools dependency for newer version the whole jupyter collection seems to use setuptools in case of certain setup.py-arguments from the very beginning. However the latest ones actually require it, otherwise the build will fail * add newly introduced dependencies * dependency constraints * drop terminal variant and update python dep
2019-11-05new package py-cfgv (#13592)Andreas Baumbach1-0/+19
2019-11-05new package: py-identify (#13593)Andreas Baumbach1-0/+21
2019-11-05added relion 3.0.8 [latest stable version in 3.0 branch] as well as 3.1_beta ↵Douglas Duckworth1-6/+12
(#13539) * added relion 3.0.8 [latest stable version in 3.0 branch] as well as 3.1_beta * relion 3.1 beta compiles without Benchmarking build type see https://github.com/3dem/relion/issues/533 * relion 3.0.X - 3.1 now supports latest cmake@3
2019-11-05bugfix: uninstall should find concrete specs by DAG hash (#13598)Todd Gamblin1-1/+9
This fixes a regression introduced in #10792. `spack uninstall` in an environment would not match concrete query specs properly after the index hash of enviroments changed. - [x] Search by DAG hash for specs to remove instead of by build hash
2019-11-05`spack find` now displays variants and other spec constraints (#13596)Todd Gamblin3-4/+23
If you do this in a spack environment: spack add hdf5+hl hdf5+hl will be the root added to the `spack.yaml` file, and you should really expect `hdf5+hl` to display as a root in the environment. - [x] Add decoration to roots so that you can see the details about what is required to build. - [x] Add a test.
2019-11-04new package py-testpath (#13417)Andreas Baumbach1-0/+16
* new package py-testpath dependency of py-nbconvert * py-testpath: fix flake8 * Remove the unnecessary pip dependency
2019-11-04update py-pyzmq (#13420)Andreas Baumbach1-0/+4
* update py-zmq * update dependencies
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