Commit graph

13089 commits

Author SHA1 Message Date
Frédéric Simonis
3f7fd4037f precice: add compiler conflicts (#13644) 2019-11-08 10:33:00 -06:00
Mark Olesen
f4a1666b1a Update openfoam to use new environment api (ref: #11115, 9ddc98e46a) (#13645)
- build:
  no special treatment - already addressed in the spack-Allwmake script

- run:
  use environment from the OpenFOAM etc/bashrc
2019-11-08 10:32:14 -06:00
Daryl W. Grunau
ae6229dee2 llvm: fix PythonString::GetString for >=python-3.7 (#13631)
* llvm: fix PythonString::GetString for >=python-3.7

* llvm/package.py: fix when the patch should be applied
2019-11-07 19:05:16 -06:00
Marc Mengel
119af6d71b new package: py-tempora (#13582)
* 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
2019-11-07 18:59:38 -06:00
Marc Mengel
a2627da7d9 New package: py-uwsgi (#13619)
* 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
2019-11-07 18:58:47 -06:00
Marc Mengel
fd01ac0ff1 New package: py-jaraco-functools (#13581)
* 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
2019-11-07 18:52:32 -06:00
Satish Balay
ff307aa86c Balay/ginkgo 1.1.0 (#13632)
* ginkgo: add version 1.1.0

* Ginkgo: add conflict for gcc older than version 5.3
2019-11-07 18:51:20 -06:00
Todd Gamblin
c9c267518f
bugfix: mirror path works for unknown versions (#13626)
`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
2019-11-07 17:13:51 -07:00
Kelly (KT) Thompson
719ebd18c3 py-pyside: fix setup files to support python 3.5. (#13613)
This fix already exists in the development branch of pyside. See
https://github.com/pyside/pyside-setup/pull/55.
2019-11-07 15:43:49 -06:00
Justin S
8139d7cb69 elmer-fem: add devel branch (#13630) 2019-11-07 15:41:43 -06:00
Adam J. Stewart
9936c8269f
PyTorch: Add 1.3.1 (#13629) 2019-11-07 13:47:13 -06:00
Andreas Baumbach
0616c6ada1 (py)arrow: new versions (#13561)
* (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>
2019-11-07 11:52:29 -06:00
Andreas Baumbach
76c15f11e0 new package: py-convertdate (#13573)
* new package: py-convertdate

* Update docstring
2019-11-07 11:51:53 -06:00
Adam J. Stewart
344e4e0d1c
Speed up PyTorch build (#13621) 2019-11-07 10:05:50 -06:00
健美猞猁
be56fe0677 bam-readcount: a new package. (#13628) 2019-11-07 10:00:43 -06:00
Josh Deaton
d748df73a3 m4: fixed macOS version identification on patch (#13623)
Patch was not being applied in recent versions of macOS. Homebrew is still applying patch to any version after High Sierra.
2019-11-07 09:43:59 -06:00
Andreas Baumbach
45eecbdbc2 py-jupyter-core add new version and setuptools dependency (#13424)
* 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>
2019-11-06 13:30:59 -06:00
Andreas Baumbach
12da0e7152 new package: py-jdatetime (#13569)
* new package: py-jdatetime

* Update var/spack/repos/builtin/packages/py-jdatetime/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-06 13:25:01 -06:00
Michael Kuhn
6d6716e302 ncview: Fix dependency check (#13615)
netcdf has been renamed to netcdf-c.
2019-11-06 13:24:33 -06:00
Christoph Junghans
0d35ae7f5f gromacs: add v2019.4 and others (#13617)
* gromacs: add v2019.4 and others

* gromacs: fix patch applying
2019-11-06 13:24:14 -06:00
Andreas Baumbach
52afcfac4d new package: py-dateparser (#13574)
* new package: py-dateparser

* take setup.py dependencies into account

* fixup help->description

* reorder dependencies

* drop version constraints not enforced in setup.py
2019-11-06 13:18:37 -06:00
Andreas Baumbach
6b7a51587b new package: py-nodeenv (#13594)
* new package: py-nodeenv

* drop python version requirements, not enforced by setup.py
2019-11-06 13:16:49 -06:00
Andreas Baumbach
4ed56573c4 py-tatsu: new package (#13566)
* py-tatsu: new package

* drop unnecessary dependencies

* drop kanji, add variant, and restrict to future releases
2019-11-06 13:16:05 -06:00
Michael Kuhn
52eba8fb00 netcdf-fortran: Fix parallel builds (#13612)
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.
2019-11-06 11:14:35 -06:00
Michael Kuhn
95bc677445 cdo: Fix with_or_without calls (#13614)
netcdf has been renamed to netcdf-c and udunits2 has been renamed to
udunits.
2019-11-06 11:13:21 -06:00
Andreas Baumbach
e292bef411 new package: py-pymeeus (#13572)
* new package: py-pymeeus

* drop unnecessary dependencies
2019-11-06 11:02:19 -06:00
Andreas Baumbach
ea5c7917ac new package: py-pre-commit (#13570)
* new package: py-pre-commit

* update missing dependencies

* add python version restriction
2019-11-06 11:01:33 -06:00
Andreas Baumbach
2bd1a0ca4c new package: py-aspy-yaml (#13591)
* new package: py-aspy-yaml

* add python version dependency
2019-11-06 10:55:19 -06:00
Michael Kuhn
abce878fad go: Add 1.13.4 and 1.12.13 (#13609) 2019-11-06 11:36:35 +01:00
Axel Huebl
f9dc41f806 pybind11: correct get_include path (#13605)
* 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>
2019-11-06 07:15:13 +01:00
Andreas Baumbach
a684efe826 new package: py-ics (#13576)
* 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>
2019-11-05 17:03:31 -06:00
Jordan Ogas
6dabdb7a82 add charliecloud 0.12 (#13599)
* add charliecloud 0.12

* fix typo

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-05 15:51:02 -06:00
Adam J. Stewart
6ffbc9c091
Add GDAL 3.0.2 (#13603) 2019-11-05 15:05:36 -06:00
Axel Huebl
8cbea5f767 mpi4py 3.0.3 (#13601)
* 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
2019-11-05 15:04:49 -06:00
Christoph Junghans
7c018bc2c8
netcdf: fix headers in v4.7.2 (#13600) 2019-11-05 12:56:02 -07:00
Christoph Junghans
10f509b182
elpa: add v 2019.05.002 (#13602) 2019-11-05 12:55:51 -07:00
Adam J. Stewart
27ab045dc1
PyTorch: avoid use of third party vendored deps (#13588)
* PyTorch: avoid use of third party vendored deps

* Flake8 fix
2019-11-05 13:19:07 -06:00
Andreas Baumbach
7a0bed7893 add depends_on(python) to PythonPackage stub (#13595) 2019-11-05 13:18:17 -06:00
Andreas Baumbach
68a34a11bc new package: py-nose-cov (#13571)
* new package: py-nose-cov

* add missing dependencies
2019-11-05 12:57:31 -06:00
Andreas Baumbach
74c81c0fc3 update py-notebook (#13423)
* 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
2019-11-05 12:51:00 -06:00
Andreas Baumbach
35f0003c08 new package py-cfgv (#13592) 2019-11-05 12:47:52 -06:00
Andreas Baumbach
aa2972172a new package: py-identify (#13593) 2019-11-05 12:46:57 -06:00
Douglas Duckworth
54e1d57647 added relion 3.0.8 [latest stable version in 3.0 branch] as well as 3.1_beta (#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
2019-11-05 12:40:27 -06:00
Todd Gamblin
a6ccb5b2fa
bugfix: uninstall should find concrete specs by DAG hash (#13598)
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 06:12:12 -07:00
Todd Gamblin
b77974e986
spack find now displays variants and other spec constraints (#13596)
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.
2019-11-05 05:39:56 -07:00
Andreas Baumbach
527d639b0e new package py-testpath (#13417)
* new package py-testpath

dependency of py-nbconvert

* py-testpath: fix flake8

* Remove the unnecessary pip dependency
2019-11-04 19:39:25 -06:00
Andreas Baumbach
4f5d3770c7 update py-pyzmq (#13420)
* update py-zmq

* update dependencies
2019-11-04 19:38:19 -06:00
Andreas Baumbach
0341c38dff update py-jupyter-client and new setuptools dependency (#13425)
* update py-jupyter-client and new setuptools dependency

* update dependencies
2019-11-04 19:28:59 -06:00
xfzhao
18243695c9 Mothur update (#13580)
* add +vserach option

* fixes #967
2019-11-04 19:27:13 -06:00
Gregory Lee
7e2e93b787 added archer 2.0.0 and package build fixes (#13577) 2019-11-04 17:39:16 -06:00