Commit graph

13721 commits

Author SHA1 Message Date
noguchi-k
f79649d2e3 lrslib: fix return value (#14422) 2020-01-08 12:41:39 -06:00
Chuck Atkins
26ffbe3d21
cmake: Create an optimized release build (#14414) 2020-01-08 13:17:53 -05:00
Corey adams
de93830b9a Adding a new package, scikit-build, which is useful for building Python Extensions (#14417)
* Adding a new package, scikit-build, which is very useful for building python extensions

* Update package.py

* Update package.py

Trying to address flake8 corrections

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-01-08 10:06:47 -06:00
Tim Haines
2028687efe spack.compilers.clang: add new version check (#14365) 2020-01-08 07:13:36 +01:00
Mark W. Krentel
8a82c930bb hpcviewer: add version 2019.12 (#14419)
Add conflicts for aarch64 and darwin.
2020-01-07 21:51:18 -06:00
Hadrien G
11501532d3 Record a new ROOT/GCC incompatibility (#14371) 2020-01-07 21:35:47 -06:00
Justin S
3e8b4a9b24 py-rapidjson: new package at 0.9.1 (#14280)
* py-rapidjson: new package at 0.9.1

* py-rapidjson: rename to py-python-rapidjson, use PyPI mirror

* py-python-rapidjson: add missing deps

* python-rapidjson: use short PyPI url

* py-python-rapidjson: remove extra dependencies
2020-01-07 16:40:22 -06:00
Justin S
a24498f7ba r-ldheatmap: new package at 0.99-7 (#14405) 2020-01-07 15:33:41 -06:00
Adam J. Stewart
c40ee08c8d
NumPy 1.18.1 requires Cython 0.29.14 (#14418) 2020-01-07 15:22:27 -06:00
Sinan
e4f56378b1 Package/opencv: cudacodec fix (#14409)
* create new variant, fix build error

* flake8

* add conflict, re-arrange config arg for cudacodec
2020-01-07 13:19:18 -06:00
eugeneswalker
7546ca6d4d bugfix: Issue #14346, buildcache create s3 push fails when package w same DAG hash already exists at mirror (#14412) 2020-01-07 12:40:37 -06:00
Matthias Diener
777812df4e gdb: add version 8.3.1 (#14413) 2020-01-07 12:38:05 -06:00
Michael Kuhn
be3482de09 ncl: Add missing fontconfig dependency (#14411)
Moreover, cairo needs to have its freetype variant enabled.
2020-01-07 10:55:34 -06:00
Michael Kuhn
a5ae5aca36 gdal: Fix libgeotiff dependency (#14410)
gdal@2.4.3 is missing the libgeotiff dependency.
2020-01-07 10:55:01 -06:00
Massimiliano Culpo
08d0267c9a Spack can automatically remove unused specs (#13534)
* Spack can uninstall unused specs

fixes #4382

Added an option to spack uninstall that removes all unused specs i.e.
build dependencies or transitive dependencies that are left
in the store after the specs that pulled them in have been removed.

* Moved the functionality to its own command

The command has been named 'spack autoremove' to follow the naming used
for the same functionality by other widely known package managers i.e.
yum and apt.

* Speed-up autoremoving specs by not locking and re-reading the scratch DB

* Make autoremove work directly on Spack's store

* Added unit tests for the new command

* Display a terser output to the user

* Renamed the "autoremove" command "gc"

Following discussion there's more consensus around
the latter name.

* Preserve root specs in env contexts

* Instead of preserving specs, restrict gc to the active environment

* Added docs

* Added a unit test for gc within an environment

* Updated copyright to 2020

* Updated documentation according to review

Rephrased a couple of sentences, added references to
`spack find` and dependency types.

* Updated function naming and docstrings

* Simplified computation of unused specs

Since the new approach uses private attributes of the DB
it has been coded as a method of that class rather than a
freestanding function.
2020-01-07 08:16:54 -08:00
Adam J. Stewart
eddb42ed43
Fix outdated bash tab completion (#14392) 2020-01-06 23:18:14 -06:00
Adam J. Stewart
d2ed01a12c
Add py-numpy 1.18.1 (#14406) 2020-01-06 17:48:27 -06:00
Justin S
e49a5adf04 r-snpstats: new package at 1.34.0 (#14404) 2020-01-06 16:21:38 -06:00
Justin S
e04a9031b0 r-genetics: new package at 1.3.8.1.2 (#14403) 2020-01-06 16:20:34 -06:00
Thom Troy
0950f5ffa3 Add updated kaldi and openfst (#14398)
* add openfst v1.6.7 and kaldi from 2019-09-29

* revert openfst package version in url
2020-01-06 16:19:42 -06:00
George Hartzell
37b11d0468 Add singularity@3.5.2 (#14401) 2020-01-06 16:12:50 -06:00
darmac
f3c0d23a3c Fastdfs (#14378)
* add new package : fastdfs

* refine install()

* remove redundant fastdfs/fastdfs/package.py

* fix install() error
2020-01-06 16:12:08 -06:00
Justin S
627fd1949d py-ujson: new package at 1.35 (#14279)
* py-ujson: new package at 1.35

* py-ujson: use PyPI mirror, add missing deps

* py-ujson: use short PyPI url
2020-01-06 15:53:26 -06:00
Seth R. Johnson
47750c8800 Fix QT on Linux+clang (#13684)
* Add platform flag to QT for linux+clang

* Extend QT platform support to more compilers and systems

* Unify QT5 configure options

* fixup! Unify QT5 configure options

* fixup! Unify QT5 configure options

* fixup! Unify QT5 configure options

* Fix newer flake8 and mac qt5 configure
2020-01-06 15:47:16 -06:00
Erik Schnetter
7cde359eb8 Nsimd: New package (#14226)
* Nsimd: New package

* Various cleanups as suggested during review
2020-01-06 15:40:58 -06:00
Adam J. Stewart
adffa45264 Reference spack help --spec in spack spec --help 2020-01-06 00:20:19 -08:00
asmaahassan90
c0672eb641 Add py-thirdorder recipe (#12791)
* Add Thirdorder recipe

* Remove white spaces

* Converting recipe to a PythonPackage base class

* remove trailing spaces

* remove line at end of file

* enhance recipe as per reviewer

* fix post_install as requested by reviewer

* rename dir to py-thirderorder

* change checksum to sha256
2020-01-05 12:28:10 -06:00
Adam J. Stewart
f7f4d1a02e
Overhaul py-pillow package (#14385)
* Overhaul py-pillow package

* Fix bug where zlib and jpeg were always disabled
2020-01-04 22:49:39 -06:00
Adam J. Stewart
f0532e27da
libwebp: CMakePackage -> AutotoolsPackage (#14384) 2020-01-04 22:48:45 -06:00
Glenn Johnson
8c8f3f228c Adjust constraints of gcc-5 (#14388)
This PR adjusts the constraints on isl with GCC-5. GCC-5.1 and GCC-5.2
need isl-0.14, not isl-0.15.
2020-01-04 22:47:06 -06:00
Adam J. Stewart
90f4860402
Add libs property to openjpeg package (#14383) 2020-01-04 16:46:53 -06:00
Adam J. Stewart
4d85979ec4
Add libs property to lcms package (#14382) 2020-01-04 16:46:40 -06:00
Adam J. Stewart
378016d350
py-torchvision 0.4.X does not support py-pillow 7.X.Y (#14381) 2020-01-04 14:21:29 -06:00
Xavier Delaruelle
d83d7ce694 environment-modules: add version 4.4.1 (#14379) 2020-01-04 12:56:09 -06:00
darmac
c22329c5e8 add new package : lucene (#14316)
* add new package : lucene

* update lucene version url
2020-01-04 11:34:28 -06:00
darmac
66bb19a593 add new package : kafka (#14315)
* add new package : kafka

* move url_for_version after depens_on()

* refine list_depth for kafka
2020-01-04 11:33:52 -06:00
darmac
c9729aaab7 add new package : tajo (#14314)
* add new package : tajo

* refine list_depth for tajo
2020-01-04 11:33:09 -06:00
Justin S
b9dc263801 py-intervaltree: new package at 3.0.2 (#14277)
* py-intervaltree: new package at 3.0.2

* py-intervaltree: fix checksum

* py-intervaltree: add py-setuptools dep

* py-intervaltree: use inclusive ranges

* py-intervaltree: change py-test dep type
2020-01-03 15:52:59 -06:00
Satish Balay
f7b9592eb9 petsc: add version 3.12.3 (#14374) 2020-01-03 13:35:54 -06:00
xfzhao
100593b83a new package: bref3 (#14256) 2020-01-03 10:22:09 +01:00
Glenn Johnson
729e43ffac Get py-numpy > 1.16 to build with Intel compiler (#14360)
Beginning with numpy > 1.16 when using older versions of gcc the
`std=c99` flag must be used. The Intel compiler depends on gcc for its
language extensions so the version of gcc is important. If the version
of gcc used by the Intel compiler is one that requires the `-std=c99`
flag then that flag will have to be used for a build with the Intel
compiler as well.

This PR tests the version of gcc used by the Intel compiler and will
abort the build if the gcc version is < 4.8 and inject the `-std=c99`
flag if >= 4.8 and < 5.1. This will cover the system gcc compiler and
any gcc environment module loaded at build time.
2020-01-02 19:30:13 -06:00
Sinan
39a09691c5 package/opencv fix mistake in conflict statement involving gcc (#13959)
* fix mistake in conflict

* extend CudaPackage to resolve cuda-gcc conflicts
2020-01-02 19:18:27 -06:00
Jonathan R. Madsen
e46548c3b8 Updated version to include v3.0.1 (#14353)
* Updated version to include v3.0.1

- this patch has a rather critical MT fix

* Update package.py

- Moved 3.0.1 above 3.0.0
2020-01-02 19:17:54 -06:00
Christoph Junghans
70184c6ea2 fix url for mantevo packages (#14366) 2020-01-02 19:17:32 -06:00
Sajid Ali
c3c1cf13e7 RHEL8 bugfix for module_cmd (#14349) 2020-01-02 15:30:11 -06:00
Glenn Johnson
ba0e144b07 Set preferred version of perl-bioperl (#14354)
Due to formatting differences, the older version of perl-bioperl was
getting picked up as the preferred version. This PR explicitly sets the
newer version to be preferred.
2020-01-02 15:29:35 -06:00
Matthieu Dorier
8e70fa52df added verbose variant to mercury package (#14355) 2020-01-02 15:29:18 -06:00
Gilles Gouaillardet
19c1312eb4 gromacs: depend on hwloc v1 (#14343)
Because of a bug in the current concretizer,
spack install gromacs
fails because gromacs depends on hwloc (default is v2), and Open MPI
(the default MPI library) depends on hwloc v1.
As discussed in https://github.com/spack/spack/issues/14339, this
workaround should be removed once the concretizer is fixed

Signed-off-by: Gilles Gouaillardet <gilles@rist.or.jp>
2020-01-02 15:16:22 -06:00
Adam J. Stewart
e26f517daf
py-scikit-learn: add 0.22.1 (#14350) 2020-01-02 15:15:49 -06:00
Mike Kiernan
85fc6448f8 osu-micro-benchmarks: added version 5.6.2 (#14352) 2020-01-02 15:15:21 -06:00