Commit graph

13866 commits

Author SHA1 Message Date
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
Adam J. Stewart
7dc6b609d5 r-rgdal does not yet support PROJ.6 (#11766) 2019-06-17 23:47:52 -04:00
Adam J. Stewart
6422130709 Add PROJ.6 (#11730)
* Add PROJ.6

* Add back comment about newer PROJ API
2019-06-17 23:46:42 -04:00
Adam J. Stewart
1891734195 PROJ.6 not yet supported in SAGA-GIS (#11768) 2019-06-17 21:39:05 -04:00
Adam J. Stewart
a239ba33af py-cartopy does not yet support PROJ.6 (#11765) 2019-06-17 21:35:14 -04:00
Adam J. Stewart
a896a33b3b Specify which versions of PROJ work with MapServer (#11764) 2019-06-17 21:34:54 -04:00
Adam J. Stewart
349844a5fd Restrict magics to proj@:5 (#11763) 2019-06-17 21:33:25 -04:00
Adam J. Stewart
3018c64537 GRASS GIS does not yet support PROJ.6 (#11762) 2019-06-17 20:59:12 -04:00
Adam J. Stewart
b0cf2b5855 Add GEOS 3.7.2 (#11734) 2019-06-17 20:58:43 -04:00
Adam J. Stewart
de51be45b9 Add GDAL 3.0.0 (#11733)
* Add GDAL 3.0.0

* Clarify PROJ version requirements
2019-06-17 20:57:48 -04:00
Adam J. Stewart
17f20d0f32 Add py-fiona 1.8.6 (#11736)
* Add py-fiona 1.8.6

* Remove commented code

* Python 3 will be required in the next release
2019-06-17 20:54:58 -04:00
Adam J. Stewart
ee20b4826f Add libgeotiff 1.5.1 (#11731) 2019-06-17 20:46:46 -04:00
Manav Bhatia
0e34cc8a8e Libmesh updates (#11750)
* Updates to libMesh: added v1.3.1 checksum, added vtk variant, bugfix for enabling petsc when slepc variant is specified

* fixed indentation issues identified by Travis CI

* - updates version number
- added master as a version
- added new variant options for perflog, metaphysicl and blocked storage
-- bug-fix for metis

* fixes for spack indentation errors

* renaming develop to master following review comment of PR.
2019-06-17 19:38:19 -05:00
Adam J. Stewart
e23adbd4a9 Add py-pyproj 2.2.0 (#11735)
* Add py-pyproj 2.2.0

* PR review requests

* Make Python requirements more explicit
2019-06-17 20:23:40 -04:00
Adam J. Stewart
10d5008ef5 Restrict pism to proj@:4 (#11754)
* Restrict pism to proj@:5

* PROJ.5 is not yet supported either :(
2019-06-17 18:35:03 -04:00
Paul
93e1336de8 Added newer GoLang versions (#11756) 2019-06-17 17:23:09 -05:00
Adam J. Stewart
a558de117a Restrict ibmisc to proj@:4 (#11753)
* Restrict ibmisc to proj@:5

* Restrict ibmisc to proj@:4
2019-06-17 18:02:09 -04:00
Dan Lipsa
cdf4ba81e5 Remove version from py-mpi4py. (#11587) 2019-06-17 10:59:34 -04:00
Valentin Clement (バレンタイン クレメン)
f4d8b1ee60 Add version 1.2.2 and 1.2.3 to the package (#11748) 2019-06-17 16:03:26 +02:00
Dan Lipsa
83c7959580 Fix condition to enable mpi4py. (#11707)
* Fix condition to enable mpi4py.

* flake8

* Catalyst as paraview for mpi4py.

* Catalyst needs numpy and mpi4py.

* Remove leftover enable python.
2019-06-17 09:30:29 -04:00
Tamara Dahlgren
6e067a05c7 bugfix: use config fixture for stage tests (#11701)
Some tests introduced in #11528 temporarily set the user's `config:build_stage`, which affected (or created) a config.yaml file in the user's `$HOME/.spack` directory that could leave entries behind if the tests fail.

This change ensures only temporary configuration files are used/affected by these tests.
2019-06-17 11:38:34 +02:00