Commit graph

7233 commits

Author SHA1 Message Date
Sajid Ali
e57ddda4cc update h5py to 2.9.0 (#10169)
* 	modified:   var/spack/repos/builtin/packages/py-h5py/package.py

* Update package.py

* Update package.py
2018-12-20 17:23:17 -06:00
thelfer
00d84b1978 Update TFEL package (#9995)
* add the tfel package

* fix the tfel package

* fix the tfel package

* fix the tfel package

* Taking Adam J. Steward' remarks into account

* fixes trailing white spaces

* Update description

* Update dependencies following @adamjstewart adices

* Style fixes

* Style fixes

* Add java optional support

* add the maintainers attribute (following @alalazo advice), disable interface not selected (following @adamjstewart advice)

* flake8 fixes

* Fix Cast3M and python-bindings support. Python detection is made compatible with cmake'FindPythonLibs module (at least how it is used in TFEL)

* Style fixes

* Style fixes

* Fix test on python version

* Follow @adamjstewart advices: code is much cleaner and readable

* Small fix

* Small fix

* Add comment

* Small fix in cmake option

* try again (trying to overcome Travis CI unstable build process)
2018-12-20 15:47:24 -06:00
Mark Olesen
7ded7fdbda OpenFOAM-v1812 - new version (#10167) 2018-12-20 13:18:51 -06:00
jthies
9110c727bb packages/phist: add maintainer (#10162) 2018-12-20 13:23:35 +01:00
Greg Sjaardema
93c491f729 CGNS: Allow use of git branch versions (#10156)
* CGNS: Allow use of git branch versions

Add ability to use git `master` and `develop` branches of the CGNS library.  The `seacas` package sometimes needs to use the `master` or `develop` branch due to some new changes to the parallel I/O implementation in CGNS which has not yet been released.

* CGNS: Reorder to put newest version on top

Based on review comments, place newest version (develop) first in list.
2018-12-19 20:02:24 -06:00
Mark W. Krentel
84b33523ec dyninst: patch to build dyninst with older gcc (#10160)
* dyninst: patch to build dyninst with older gcc

Add 'v9.3.2-auto.patch'.  This patch changes some 'auto t: type' usage
to the older but equivalent 'type.begin()'.  This allows building
dyninst 9.3.2 with gcc 4.4 which doesn't support the newer syntax.
This patch is harmless with newer gcc.

* Fix typo in patch.  (My bad for sloppy cut-and-paste.)

* Restrict the patch to gcc 4.7 and earlier.  gcc 4.8 supports the newer
usage and thus doesn't need the patch.
2018-12-19 17:24:43 -08:00
Michael Kuhn
84c547cf6e sqlite: add 3.26.0 (#10138) 2018-12-19 17:07:03 -06:00
Owen Solberg
6b1b9031ea updated checksum for kallisto (#10158) 2018-12-19 17:06:33 -06:00
Michael Kuhn
67ab73d381 fetch_strategy: improve GitFetchStrategy (#10153)
Currently, only the Git repsository's URL shows up in the `spack info`
output, which makes it hard to distinguish different versions:
```
Safe versions:
    develop    [git] https://github.com/LLNL/H5Z-ZFP.git
    0.8.0      [git] https://github.com/LLNL/H5Z-ZFP.git
    0.7.0      [git] https://github.com/LLNL/H5Z-ZFP.git
```

This change adds additional information as shown when cloning a Git
repository:
```
Safe versions:
    develop    [git] https://github.com/LLNL/H5Z-ZFP.git on branch master
    0.8.0      [git] https://github.com/LLNL/H5Z-ZFP.git at commit af165c4
    0.7.0      [git] https://github.com/LLNL/H5Z-ZFP.git at commit 58ac811
```
2018-12-19 14:33:58 -08:00
jthies
5f3d9a4076 phist tag 1.7.5 was moved (#10155) 2018-12-19 13:36:49 -06:00
sknigh
5adec7e491 Updated Dakota to 6.9 (#10157)
* Updated Dakota to 6.9

* Change comment wording
2018-12-19 13:03:14 -06:00
Adam J. Stewart
adfbe71b1b
Add python bindings to libxslt (#10149) 2018-12-19 11:39:19 -06:00
Adam J. Stewart
654360d2ad
Add missing libiconv dependency to libxml2 (#10148) 2018-12-19 11:38:14 -06:00
Adam J. Stewart
0fcca9f422
Add list_url to docbook-xml (#10146) 2018-12-19 11:37:54 -06:00
Adam J. Stewart
e19e176e67
Add latest version of docbook-xsl (#10147) 2018-12-19 11:37:35 -06:00
Adam J. Stewart
ed0ca18c3c
Restrict patch to oldest version of libbsd (#10145) 2018-12-19 11:37:11 -06:00
Satish Balay
c1e562f333
PETSc: add version 3.10.3 (#10154) 2018-12-19 10:46:02 -06:00
Neil Flood
a6e2f1a96a mapserver: new package (#10067) 2018-12-19 10:04:25 +01:00
Elsa Gonsiorowski, PhD
b091fcdb8e fix for mpifileutils package (#10142)
* proper include & linking of libarchive

* due to linux headers, mfu can't build on mac

* hard code deps in configure line

rather than relying on pkg-config

* +xattr during config

* must also link the lib

* find mfu.h

* long lines
2018-12-18 21:51:24 -06:00
Dave
b27f81ac00 WarpX: Added dependency on fftw when +psatd (#10144) 2018-12-18 20:11:08 -06:00
Matthias Wolf
22d9938560 flatbuffers: add 1.10.0 (#10137)
Also unpin the version from the arrow package.
2018-12-18 10:53:02 -06:00
Adam J. Stewart
f8c650b9c4 Add pdf variant to cairo (#10135) 2018-12-18 16:39:36 +01:00
Justin Stanley
59d7854b89 clp: add build_directory, remove old hack (#10112)
* clp: add build_directory, remove old hack

* clp: use spack-build for building
2018-12-18 08:36:40 -06:00
Adam J. Stewart
d4b5fc141c
Add latest version of libxkbcommon (#10134) 2018-12-17 19:27:58 -06:00
Alberto Chiusole
a41571a1b6 Add variant to ecflow to choose whether to use static boost libraries. (#9933)
When this variant is set, it requires boost to be built with the +pic variant.
2018-12-17 19:23:53 -06:00
David Hows
c70ea22c6f Add thread count variant to atlas (#9999)
* Add thread count variant

Atlas automatically configures itself and optimizes to run with a fixed number of threads. This can be overridden during compile by setting a flag and atlas will tune itself to use the specified number, rather than all system CPUs. 

Default value is the existing logic, autoconfigure.

* Fix Linting

* Another lint for longline
2018-12-17 19:12:00 -06:00
Jannek Squar
09d2df690a Add spack package for saga-gis (#10018)
* Add spack package for saga-gis

* Adjusted license header

* Adjust saga-gis package, added fixme comments

* Removed version constraint

* Fixed fixme comment
2018-12-17 19:10:50 -06:00
Matthias Diener
776f99a414 git: add version 2.20.1 (#10130) 2018-12-17 17:36:57 -06:00
Omar Awile
d313291c2d Added RocksDB package (#10084)
* Added rocksdb package

* Fixes based on @tristan0x and @pramodk comments

* Cleanup

* A couple minor fixes based on @adamjstewart 's advice

* Fixed flake8 errors
2018-12-17 17:36:45 -06:00
Adam J. Stewart
c2b546fa97
Add missing gettext dependency to at-spi2-core (#10124) 2018-12-17 14:00:53 -06:00
Todd Gamblin
37954a78ff
Revert "mark: Create new package. (#7069)" (#10131)
This reverts commit 90b34c96d6.
2018-12-17 11:15:32 -08:00
Adam J. Stewart
bcd65906c9
Add latest version of gdk-pixbuf (#10126) 2018-12-17 13:04:40 -06:00
Adam J. Stewart
5964d14936
Add latest version of ghostscript (#10123) 2018-12-17 13:04:16 -06:00
Adam J. Stewart
fe73043170
Add missing libbsd dependency to libxdmcp (#10122) 2018-12-17 13:04:00 -06:00
Adam J. Stewart
9913b3b846
Add latest version of libbsd (#10121) 2018-12-17 13:03:43 -06:00
Adam J. Stewart
a8a0aee3f3
Add patch to fix windows.h include in freetype (#10075)
* Add patch to fix windows.h include in freetype

* Fix patch
2018-12-17 13:00:43 -06:00
Mark Olesen
cbedd507cf ENH: fixes and updates for openfoam-com build (#10065)
- previous removal of FOAM_EXT_LIBBIN (ThirdParty) from the environment
  during the build could lead to the system scotch library being found
  instead of the spack installation.

  Avoid this largely cosmetic change to the setting in favour of
  improved build robustness. These modifications will be largely
  superfluous in the 1812 release anyhow.

- Split the patching algorithm into 'regular' and '@:1806' since the
  next versions of openfoam will again need fewer patches.

- Add hook into foamCreateManpage to be used where available
2018-12-17 12:58:09 -06:00
Greg Sjaardema
ccce3b79ab SEACAS: Add preliminary support for seacas package (#9972)
* SEACAS: Add preliminary support for seacas package

* Eliminate leftover from package I copied from.

* And remove another stray line

Sorry, thought I had checked this better...

* SEACAS: Shorten long lines; fixup indentation

* SEACAS: Remove unused os import

* Add PLASMA version 18.11.0 and Lua variant (#9689)

* Add PLASMA 18.11.1 with optional Lua and test for headers

* New versions for a few python modules (#9969)

* py-jupyter-console: Add version 5.2.0

* py-jupyter-core: add version 4.4.0

* py-lxml: add version 4.2.5

* py-zmq: add version 17.1.2

* py-terminado: add version 0.8.1

* py-pexpect: add version 4.6.0

* py-pytables: add version 3.4.4

* SEACAS: Default to mpi on

* SEACAS: Modify to reduce variants

Instead of using an `allpkgs` or explicitly specifying each individual subset,
changed to minimize variants:
 * By default, the exodus and IOSS libraries are built and a few
   executables directly related to the IOSS library.
 * variant `common` defaults to True and builds the "common" seacas
   applications.  This is based on my definition, so there may be
   could be some discussion on what belongs here.
 * variant `legacy` defaults to True and builds the remainder of the
   seacas applications.  These are still used, but mainly in more
   esoteric areas.  Might be better to default to False, but I wanted
   default to just build everything which is what other SEACAS builds
   always do...

Removed the `kokkos` variants for now as I need to do some more
thinking on how best to support this.  Not often used currently,
so shouldn't be an issue.

Cleaned up other issues raised by Adam and found by me.

* SEACAS: Address flake8 issues

* SEACAS: Clean up variant package logic

Fixed package variant logic.
Consolidated some other variant handling logic
Other minor refactors for hopefully better readability

* SEACAS: Fix flake8 error

Missing whitespace around operator fixed.
2018-12-17 12:57:31 -06:00
Ricardo Silva
f979b974a5 GDL: python integration fixes (#9936)
* GDL: python integration fixes

* renamed python-related variants to follow the convention
* building the Python module requires patches currently targetting 0.9.8 othwerwise asking for the Python module *only* builds the Pyhton module
* building the python module also requires patching the vendored (with the GDL) antlr to be built as a shared library

* Typo

Co-Authored-By: rmsds <ricardo.d.silva@gmail.com>

* Rename embed-python variant to embed_python
2018-12-17 12:47:16 -06:00
TZ
a02cf107b5 zoltan: rely on MPI wrappers instead of guessing MPI libraries (#8986)
* zoltan: only add gussed MPI libs if no MPI wrappers are used

- if MPI-wrappers are used for compilation, we can assume that
  linking works without manually specifying MPI libs
  (guessing may result in wrong libs, cf. #8979)
- thus, only guess the NPI libs and add them explicitly if no
  MPI-wrappers are used
- use llnl.util.filesystem.find_libraries instead of a locally
  defined routine to guess the MPI libs if needed
  (cf. #8979)

* zoltan: rely on MPI-wrappers to know the required MPI libs
2018-12-17 12:45:49 -06:00
lingnanyuan
90b34c96d6 mark: Create new package. (#7069)
* mark: Create new package.

* mark: change description.

* mark: change description.

* mark: Delete set_up environment.

* mark: replace join_path(prefix.bin, mark) with prefix.bin.mark
2018-12-17 12:34:16 -06:00
Adam J. Stewart
ae307f5b0f Add latest version of atk (#10125) 2018-12-17 08:48:31 +01:00
jthies
17c77533ee packages/phist: new version 1.7.5 (#10120) 2018-12-16 13:35:44 -06:00
Justin Stanley
87615d54cc r-multitaper: new package at 1.0-14 (#10110) 2018-12-15 20:08:33 +01:00
Justin Stanley
c973d761e9 r-popgenome: new package at 2.6.1 (#10108) 2018-12-15 08:44:20 -06:00
Justin Stanley
3b59bf9efa r-xnomial: new package at 1.0.4 (#10111)
* r-xnomial: new package at 1.0.4

* r-xnomial: add list_url
2018-12-15 08:43:08 -06:00
Adam J. Stewart
caf94253e0
Add latest version of libsigcpp (#10103) 2018-12-14 21:09:33 -06:00
Adam J. Stewart
a55976747e
Add latest version of bdw-gc (#10100) 2018-12-14 21:09:19 -06:00
Adam J. Stewart
316df3cd37
Add latest version of libatomic-ops (#10099) 2018-12-14 21:09:04 -06:00
Levi Baber
7a0c334d81 pbsuite: pythonpath should be prepended not set (#10113) 2018-12-14 18:12:51 -08:00