Commit graph

11736 commits

Author SHA1 Message Date
Carson Woods
f10b806bde Singularity package: add version 3.2.1 (#11833) 2019-06-24 18:20:23 -07:00
Denis Davydov
8e89a82076 clamav: add new package (#11818)
* clamav: add new package

* fix flake8

* remove --dsable lines
2019-06-24 19:47:15 -04:00
Gregory Lee
16ff38b784 add glx variant to libepoxy (#11814) 2019-06-24 17:57:17 -04:00
Glenn Johnson
c575cc46db The py-pytables package depends on hdf5-blosc (#11823)
* The py-pytables package depends on hdf5-blosc

* Further modifications to py-pytables package

The 3.2.2 version of py-pytables should still build with internal blosc.
The issue with locking in a multithreaded environment has been
fixed/worked around in version 3.3.

Also, add bzip2 and lzo variants.
2019-06-24 17:56:51 -04:00
Satish Balay
1ec3d78441 hypre: superlu-dist-link-2.15.0.patch is now in hypre@develop (#11829) 2019-06-24 17:55:04 -04:00
Andreas Baumbach
b39a992528 add new package py-absl-py (#11812)
* add new package py-absl-py

Change-Id: I248d30e0a3e5e05d9ea4027d97a85545c63d1125

* Update package.py

* Update package.py

* Update package.py

* Update package.py
2019-06-23 17:33:36 -04:00
Andreas Baumbach
2687af2c53 New package py-astor (and test dependency py-astunparse) (#11813)
* add package py-astor

Change-Id: I2f6becfb5e9771170bf2df5eb629920e1c0998d7

* add new package py-astunparse

Change-Id: Id2d3e8dec28e720ed1cb121dad0d1a405c27ca29

* Update package.py

* Update package.py

* Update package.py
2019-06-23 17:33:22 -04:00
Christoph Junghans
d65e6ad7e3 hypre: add v2.16.0 (#11821)
* hypre: add v2.16.0

* update checksums

* hypre: xsdk-0.2.0 tag is missing on the new repo
2019-06-23 17:33:05 -04:00
Neil Flood
681245c7ed awscli: new package (#11796)
* awscli: new package

* More precise py-pyyaml version dep, as per setup.py
2019-06-23 14:54:48 -04:00
Adam J. Stewart
9c54d8ef6c
r-sf may not support PROJ.6 (#11767)
* r-sf may not support PROJ.6

* Add comment explaining dep
2019-06-23 11:35:33 -05:00
Sinan
c83f8a425d new package/py-blessed (#11656)
* new package/py-blessed

* make flake8 happy

* fix docstring

* tab to spaces

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

specify dependency version.

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

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

specify dependency version

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

* add setuptools as depedency
2019-06-22 17:05:03 -05:00
Peter Scheibel
1ae03b327c
Use Stage.archive_file to access non-expanded download (#11817)
Fixes #11816

Allow packages to refer to non-expanded downloads (e.g. a single
script) using Stage.archive_file. This addresses a regression from
#11688 and adds a unit test for it.
2019-06-21 16:56:38 -07:00
Gerasimos Chourdakis
98d21193ff precice: add version 1.5.1 (#11809) 2019-06-21 07:56:35 -04:00
Toyohisa Kameyama
e19d7b9a49 exonerate use autotools. (#11805) 2019-06-21 07:55:29 -04:00
Toyohisa Kameyama
1827b4c5cb mpileaks: use autotools. (#11808) 2019-06-21 07:55:04 -04:00
Toyohisa Kameyama
9955b15f4e mpe2 use autotools and add libx11 dependency. (#11807) 2019-06-21 07:54:51 -04:00
Gregory Lee
894d01e482 converting to launchmon to autotools package (#11794) 2019-06-21 07:47:42 -04:00
Valentin Reis
e6264030d7 New packages: nrm and libnrm (#11777)
Also add new py-warlock, py-jsonpatch, and py-jsonpointer packages as
dependencies of nrm.
2019-06-20 19:21:44 -07:00
Adam J. Stewart
9b8215ce9d Ignore pgcc-llvm and friends, default to pgcc (#11703)
This change reverts to the previous behavior of only looking for pgcc
and friends, not pgcc-llvm and friends.

The llvm variant doesn't support all the same features as the
traditional variant of the pgi code generator; this change avoids
treating the llvm variant as a default pgi compiler.

This retains the changes in #10704 which accept the "LLVM" suffix of
the version string of the PGI compiler, which allows users to
explicitly add the llvm-pgi compiler if desired.
2019-06-20 19:07:29 -07:00
Mark W. Krentel
a76bacd594 boost: add variant for symbol visibility (#11801)
Starting with 1.69.0, boost added a bjam option for the default symbol
visibility.  Up to 1.68.0, the value was always 'global'.  1.69.0
changed the default to 'hidden' but added an option.

Most packages will work with hidden and won't notice.  But some
packages may discover that an interface that they rely on is now
hidden and inaccessible.

https://boostorg.github.io/build/manual/develop/index.html#bbv2.builtin.features.visibility
2019-06-20 17:43:25 -04:00
Justin S
686eaff30c subread: add 1.6.4 (#11800) 2019-06-20 13:54:20 -05:00
Peter Scheibel
284ae9d1cc
Resources: use expanded archive name by default (#11688)
For resources, it is desirable to use the expanded archive name of
the resource as the name of the directory when adding it to the root
staging area.

#11528 established 'spack-src' as the universal directory where
source files are placed, which also affected the behavior of
resources managed with Stages.

This adds a new property ('srcdir') to Stage to remember the name of
the expanded source directory, and uses this as the default name when
placing a resource directory in the root staging area.

This also:

* Ensures that downloaded sources are archived using the expanded
  archive name (otherwise Spack will not be able to determine the
  original directory name when using a cached archive).
* Updates working_dir context manager to guarantee restoration of
  original working directory when an exception occurs
* Adds a "temp_cwd" context manager which creates a temporary
  directory and sets it as the working directory
2019-06-20 11:09:31 -07:00
Adam J. Stewart
4858d8c275 Add GDL 0.9.9 (#11760)
* Add GDL 0.9.9

* Add comment on PROJ dependency
2019-06-20 13:36:10 -04:00
Neil Flood
0cec7c6590 py-python-dateutil: Version 2.7.0 acquired dependency on setuptools-scm (#11795) 2019-06-20 09:18:04 -05:00
Carson Woods
e7eb9ce1af Bump netcdf-fortran version to 4.4.5 (#11790) 2019-06-19 17:38:17 -05:00
Oliver Breitwieser
8b1575fa0a py-matplotlib: Fix dependencies in [2.1.0:3.0.0) (#11787)
Starting with 2.1.0, backports.functools_lru_cache replaces functools32
when using python 2.7.x until python2 support is dropped in 3.0.0.

Change-Id: I8db61eac975da0042f6f5babe0f5f0c92807200e
2019-06-19 17:38:04 -05:00
Kevin Manalo
6e4ed3e84a osu-micro-benchmarks: add version 5.6.1 (#11779)
Also add mpi osu-micro-benchmarks to runtime PATH
2019-06-19 11:04:03 -07:00
brietzke
4f9116dae2 New package: fgsl: fortran interface to GSL (#11775) 2019-06-19 10:59:11 -07:00
Chuck Atkins
a60ffdd5a2 vtk, paraview, catalyst packages: Add maintainers (#11774) 2019-06-19 10:57:19 -07:00
Mark W. Krentel
d29f8d0598 xfd package: use Spack-installed libintl (#11545)
Fixes #11526

The xfd configure script tests for libintl but incorrectly concludes
that no additional library is needed because gettext is provided in
libc. So we add '-lintl' to ldlibs to point to the Spack-installed
gettext. Note that the xfd configure script does not have a
--with-gettext option to do this for us.

Also add version 1.1.3
2019-06-19 10:54:50 -07:00
Daniel Topa
06342923fc eospac package: replace md5 checksums with sha256 (#11757) 2019-06-18 19:20:35 -07:00
Andrey Prokopenko
d1c9367446 New package: ArborX (#11474) 2019-06-18 19:14:05 -07:00
Gregory Lee
8706ac1479 fixed spec dependence attribute writing. Fixes #11686 (#11776) 2019-06-19 04:13:12 +02:00
Justin S
2287dd6165 New package: amber (starting at v16) (#11619) 2019-06-18 19:01:03 -07:00
dorier
da800c21bd New package: PRRTE (#11614) 2019-06-18 18:47:24 -07:00
william-dawson
de2e088d43 New Package: ELSI (#11605) 2019-06-18 18:30:57 -07:00
Greg Becker
9a4917644a Remove test dependency on /usr/bin/gcc (#11769)
The regression test for #11678 fails on at least some Mac OS systems
because they have a /usr/bin/gcc that is secretly clang.

This PR replaces the dependency on a system gcc executable with a
test-generated script that generates the expected output for the
compiler logic.
2019-06-18 18:23:02 -07:00
Greg Becker
1ea3d29110 Ensure brew update is run before using brew in test environment (#11784)
All macos tests are failing because brew cannot install ccache
without updating brew. This ensures that brew update is run
before using brew in test environment.
2019-06-18 17:50:45 -07:00
Axel Huebl
e925589fc7 xtensor package: add version 0.20.7 and update dependencies (#11574)
* xtensor-python: add version 0.23.1
* xtensor-python: update xtensor/xtl dependency version constraints
  for 0.23.1
* xtensor-python: remove xtensor/xtl dependency version constraints
  for the develop version to favor the latest (develop) version of
  these dependencies
* xsimd: add version 7.2.3
* xtensor: add tbb variant to enable TBB parallelization
* xtensor: add version 0.20.7
* xtensor: update CMake args enable xsimd/tbb support based on
  variant settings
* xtl: add version 0.6.4
2019-06-18 17:05:47 -07:00
Robert Pavel
2eee507914 Added Cinch Spackage (#11759)
* Added Cinch Spackage and updated Flecsi to Use It

Added spackage for Cinch build system and updated flecsi spackage to use
the external version of cinch

* Flake8 compliance for Cinch and Flecsi

* Fixed Cinch Issue and Requested PR Changes

Swapped cinch back to master branch rather than test branch and style
issues for PR
2019-06-18 16:45:58 -05:00
Adam J. Stewart
d21bec996e Restrict gplates to proj@:5 (#11761)
* Restrict gplates to proj@:5

* Add comment on PROJ dependency
2019-06-18 15:15:14 -04:00
Adam J. Stewart
6d8c69848b Add py-rasterio 1.0.24 (#11738)
* Add py-rasterio 1.0.24

* Python 3 required in the next release
2019-06-18 15:14:27 -04:00
Adam J. Stewart
ff6dfe3c00 Add py-shapely 1.6.4.post2 (#11739) 2019-06-18 14:24:56 -04:00
Adam J. Stewart
ea3e1521fe Add CDO 1.9.7.1 (#11758) 2019-06-18 14:22:22 -04:00
Justin S
d82f8cd405 repeatmasker: perl and HMMER dependency fixes (#11660)
repeatmasker depended on HMMER but was never actually configured to
use it. The package also had many shebangs pointing to random perl
locations, now patched to use Spack's perl installation.
2019-06-18 11:11:00 -07:00
Hadrien G
e35355f040 ACTS package: add versions including 0.10.1 (#11606)
* Also add version 0.10.0
* Add leading '0' to 0.9.x versions (e.g. 0.09.1) and 0.8.x versions
* Don't mention acts-framework, that package isn't in Spack yet
2019-06-18 11:00:02 -07:00
Tamara Dahlgren
2a919c8851 Ensure proper gopath set for rclone (#11755)
Fixes #11745

Set the GOPATH environment variable to the stage path to avoid
creation of a $HOME/go directory.
2019-06-18 10:49:07 -07:00
Elizabeth Fischer
f886c7e59d Rename build.out to build.txt (#11749)
Rename build.out to build.txt; makes it easier when people post log files to the Spack mailing list.
2019-06-18 10:32:00 -07:00
Gabriel Rockefeller
003f670ef9 r3d: add version 2018-01-07 (#11770) 2019-06-18 09:36:49 -05:00
Adam J. Stewart
7c3137a203 Restrict libspatialite to proj@:5' (#11752) 2019-06-17 23:48:16 -04:00