hlrs-software-stack/spack
7
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity
4303 commits 3 branches 52 tags 188 MiB
Commit graph

2238 commits

Author SHA1 Message Date
mwilliammyers
f2e8f27c15 opencv : Add libpng cmake support 2016-07-20 18:10:08 -06:00
mwilliammyers
fc79b104f0 opencv : Add libjpeg-turbo cmake support 2016-07-20 18:10:07 -06:00
mwilliammyers
97143768c8 opencv : Add libtiff cmake support 2016-07-20 18:10:07 -06:00
mwilliammyers
d3b97227a1 opencv : Add optional jdk dependency 2016-07-20 18:10:07 -06:00
mwilliammyers
da2b695f93 opencv : Fix lib finding for python 2016-07-20 17:25:05 -06:00
mwilliammyers
10c285a774 opencv : Use string.format() 2016-07-20 17:25:01 -06:00
mwilliammyers
0654ee6a10 opencv : Fix style inconsistencies 2016-07-20 17:24:55 -06:00
mwilliammyers
8cf03c209f opencv : Make extending python optional 2016-07-20 17:24:50 -06:00
mwilliammyers
c588ce9648 opencv : Improve cmake detecting python 2016-07-20 17:24:46 -06:00
mwilliammyers
3fac2dcc41 opencv : Fix cmake not disabling gtk 2016-07-20 17:24:40 -06:00
mwilliammyers
0080ffcf9f opencv : Use in operator 2016-07-20 17:24:35 -06:00
mwilliammyers
ce902bf27a opencv : Minor style changes 2016-07-20 17:24:30 -06:00
mwilliammyers
2cde6aaabd opencv : Add GUI support 2016-07-20 17:24:26 -06:00
mwilliammyers
578ddea418 opencv : Fix pep8 style issues 2016-07-20 17:24:21 -06:00
mwilliammyers
cf0f5756f5 opencv : Fix python extensions issues 2016-07-20 17:24:13 -06:00
mwilliammyers
9e1d26e973 opencv : Add CUDA extensions 2016-07-20 17:23:46 -06:00
Todd Gamblin
e389afedaa Merge pull request #1323 from glennpj/rlib 
Set environment variables for R
 2016-07-20 15:43:26 -07:00
Todd Gamblin
b9c79824a2 Merge pull request #1313 from sknigh/gnu-tools 
Added packages for GNU tools screen, datamash, and parallel
 2016-07-20 15:38:55 -07:00
Todd Gamblin
0777d3a5ba Merge pull request #1326 from mwilliammyers/package-openexr 
openexr : Add new package
 2016-07-20 15:35:36 -07:00
Mitchell Devlin
2344ffd0c7 add libxsmm package 2016-07-20 16:36:31 -05:00
Glenn Johnson
0c75174ec3 Fix indent/flake8 error. 2016-07-20 15:56:20 -05:00
mwilliammyers
e973adf84b openexr : Add new package 2016-07-20 14:49:03 -06:00
Glenn Johnson
f9137f606f Set environment variables 
This commit adds `setup_environment` to export the libraries and
headers.

Fixes #1314.
 2016-07-20 15:37:31 -05:00
Todd Gamblin
d8acd41ba1 Merge pull request #1321 from mwilliammyers/package-ilmbase 
ilmbase : Add new IlmBase package
 2016-07-20 13:13:21 -07:00
Todd Gamblin
8efbec3c0b Merge pull request #1292 from eschnett/eschnett/hdf5-default-1.10 
Make newest HDF5 release the default version
 2016-07-20 12:57:45 -07:00
Todd Gamblin
4c7c9f4ff5 Merge pull request #1303 from adamjstewart/features/armadillo 
Updates to Armadillo package
 2016-07-20 12:56:41 -07:00
Samuel Knight
24c14ff7a8 Added gnu packages datamash, parallel, and screen 2016-07-20 19:53:14 +00:00
mwilliammyers
c9f4e8ce5a ilmbase : Add new IlmBase package 2016-07-20 13:13:47 -06:00
Todd Gamblin
4434f482c0 remove FIXMEs 2016-07-20 09:48:54 -07:00
Todd Gamblin
3def8ef60e Merge branch 'cdo' of https://github.com/robertdfrench/spack into robertdfrench-cdo 2016-07-20 09:48:01 -07:00
Todd Gamblin
20584ab084 Merge pull request #1302 from robertdfrench/adios-url 
Get adios from github, not NCCS
 2016-07-20 09:47:23 -07:00
Todd Gamblin
7c28338d60 Merge pull request #1301 from robertdfrench/silver-searcher 
Silver Searcher 0.32 is out
 2016-07-20 09:47:12 -07:00
Todd Gamblin
17a63c9646 Merge pull request #1284 from eschnett/eschnett/py-h5py.2 
Declare dependency of "py-h5py +mpi" on "py-mpi4py"
 2016-07-20 09:45:54 -07:00
Todd Gamblin
7f20678969 Merge pull request #1291 from eschnett/eschnett/netcdf-4.4.1 
Update NetCDF to version 4.4.1
 2016-07-20 09:34:14 -07:00
Erik Schnetter
69e36c9821 Ensure that per-4.4.1 NetCDF doesn't use HDF5 1.10 2016-07-20 11:25:46 -04:00
Robert D. French
6b0fb476ab Draft CDO 2016-07-19 15:57:55 -07:00
Robert D. French
1c9cf668a1 Silver Search 0.32 is out 
PEP8 Love + Re-adding v0.30.0
 2016-07-19 10:48:53 -07:00
Adam J. Stewart
8034536054 Fix shared object suffix for macOS 2016-07-19 12:37:34 -05:00
Adam J. Stewart
afa4cdc2d8 Updates to Armadillo package 2016-07-19 12:33:04 -05:00
Robert D. French
25e765baae Download Adios from Github 
Get adios from github, not NCCS

Use correct hash, thanks Ben
 2016-07-19 10:31:59 -07:00
Todd Gamblin
a64a2e72cf Merge pull request #1226 from adamjstewart/features/tkinter 
Add Tkinter support for Python
 2016-07-19 09:41:12 -07:00
Todd Gamblin
4ad29b6c9b Merge pull request #1262 from davydden/pkg/suite_sparse_fix_blas 
suite-sparse: enable TBB and fix Blas/Lapack libs
 2016-07-19 09:18:42 -07:00
Erik Schnetter
71684cb071 Flex requires m4 2016-07-18 23:04:20 -04:00
Erik Schnetter
4dec06e4f4 Make HDF5 1.10 the default version 
Apply this only after NetCDF 4.4.1 is supported.
 2016-07-18 20:14:44 -04:00
Erik Schnetter
94df1b801a Update NetCDF to version 4.4.1 
This version supports HDF5 1.10 in a backward-compatible manner.
 2016-07-18 20:11:32 -04:00
Todd Gamblin
7555c3d949 Merge pull request #1204 from goxberry/cmake-3.6.0 
cmake@3.6.0
 2016-07-18 16:53:17 -07:00
Todd Gamblin
25a9181a1b Merge pull request #1287 from mwilliammyers/package-jasper 
jasper: Add new jasper package
 2016-07-18 15:43:18 -07:00
mwilliammyers
02340062b4 package - jasper - Add new jasper package 2016-07-18 16:17:07 -06:00
Todd Gamblin
607813d5ce setuptools is a build dependency in numpy. 2016-07-18 14:13:14 -07:00
Erik Schnetter
67fade5b1e Declare dependency of "py-h5py +mpi" on "py-mpi4py" 2016-07-18 17:08:56 -04:00
Todd Gamblin
a9ed2296a1 Merge pull request #1282 from eschnett/eschnett/py-numpy 
py-numpy: Add py-setuptools dependencies
 2016-07-18 13:58:17 -07:00
Todd Gamblin
fa0bbb57ea Merge pull request #1270 from davydden/pkg/mumps_scalapack_fix_blas 
Pkg/mumps scalapack fix blas
 2016-07-18 13:57:26 -07:00
Erik Schnetter
49cd6f6269 py-numpy: Add py-setuptools dependencies 
Closes #1281.
 2016-07-18 16:01:48 -04:00
Todd Gamblin
089189afaf Merge pull request #1238 from davydden/pkg/mkl_update 
mkl: add provide blas/lapack
 2016-07-18 11:52:30 -07:00
Adam J. Stewart
ea425a101a Flake8 and new tk version 2016-07-18 07:51:08 -05:00
Adam J. Stewart
583232ea52 Build Python with Tkinter support 2016-07-18 07:51:08 -05:00
Todd Gamblin
b3789a4693 Merge pull request #1269 from davydden/pkg/hypre_trilinos_blas 
Pkg/hypre trilinos blas
 2016-07-18 03:06:37 -07:00
Denis Davydov
2e4966c854 netlib-scalapack: use dso_suffix 2016-07-18 10:11:18 +02:00
Todd Gamblin
c898b9db04 Merge pull request #1188 from epfl-scitas/packages/py-numpy 
RPATH for blas in py numpy
 2016-07-17 21:20:39 -07:00
Todd Gamblin
28ce08b9e2 Merge pull request #1258 from eschnett/eschnett/openmpi-2.0.0 
Update to OpenMPI 2.0.0
 2016-07-17 21:01:21 -07:00
Denis Davydov
1bd3a702c9 mumps: flake8 fixes 2016-07-16 15:14:06 +02:00
Denis Davydov
561748a063 netlib-scalapack: flake8 fixes 2016-07-16 08:03:54 +02:00
Denis Davydov
9ea4f80f15 flake8 fixes 2016-07-16 07:58:51 +02:00
Denis Davydov
0752eccfa5 mumps: don't hardcode blas name; remove unused depends_on(lapack) 2016-07-16 07:38:42 +02:00
Denis Davydov
6175ce7559 netlib-scalapack: make sure Spack's Lapack is used 2016-07-16 07:37:38 +02:00
Denis Davydov
987fb137f9 trilinos: don't hardcode blas/lapack names 2016-07-16 07:31:38 +02:00
Denis Davydov
514c61b8fe hypre: don't hardcode blas/lapack/mpi; optionally run tests 2016-07-16 07:28:31 +02:00
Denis Davydov
96e9dbca08 suite-sparse: enable TBB and fix Blas/Lapack libs 2016-07-16 00:33:39 +02:00
Erik Schnetter
5a1ed51dcd Correct indentation 2016-07-15 18:10:33 -04:00
becker33
c0be585b67 Merge pull request #1168 from epfl-scitas/packages/gts 
gts : added package
 2016-07-15 14:07:59 -07:00
becker33
656b2d562f Merge pull request #1177 from epfl-scitas/packages/swiftsim_and_metis 
swiftsim : fixed configuration for metis
 2016-07-15 14:05:28 -07:00
becker33
f761130343 Merge pull request #1187 from paulhopkins/bugfix/python-updates 
Bugfix/python updates
 2016-07-15 14:04:46 -07:00
becker33
f1d85ac2e9 Merge pull request #1227 from glennpj/ggvis 
New package - r-ggvis
 2016-07-15 14:00:15 -07:00
becker33
37ce4108ce Merge pull request #1254 from mdevlin1/features/hmmer 
add HMMER package
 2016-07-15 13:52:56 -07:00
Erik Schnetter
4663288b49 Update to OpenMPI 2.0.0 2016-07-15 13:00:48 -04:00
George Hartzell
64b1bafd41 Make flake8 happy with .../jdk/package.py 
My PR for adding a new jdk version failed its
travis run because of existing flake8 violoations.

This package cleans them up.

I'm not particularly pythonic, but most of the complaints were
obvious.  HOWEVER, I'm not particularly confident about handling
long lines by taking an flake8 exception comment onto the end.

Feedback welcome...
 2016-07-15 12:39:40 -04:00
Mitchell Devlin
5f1b6f000d add HMMER package 2016-07-15 11:03:57 -05:00
Denis Davydov
b29b7595dd mkl: add info on interface and threading layers to the docstring 2016-07-15 17:35:10 +02:00
Todd Gamblin
077848fc0b Merge pull request #378 from mathstuf/dep-types 
dependency types
 2016-07-15 00:29:16 -07:00
Todd Gamblin
f3e9588457 Fix package name bug. 2016-07-14 23:15:54 -07:00
Gregory Becker
487ec2aff1 added py-pydatalog package 2016-07-14 23:12:35 -07:00
Todd Gamblin
b8e2799700 Add GNU Prolog package. 2016-07-14 14:38:30 -07:00
Ben Boeckel
a0584c78a8 foam-extend, sundials: add cmake as a builddep 
The sundials doesn't use CMake directly, but it is referenced in the
patch step. I suspect it calls CMake somewhere else in its build system.
 2016-07-14 16:21:47 -04:00
Ben Boeckel
d71a12438b cantera: use nolink for python module dependencies 
Unsure about this, but this is probably true.
 2016-07-14 16:21:47 -04:00
Ben Boeckel
39aef5fc00 lua: bring in run deps of build and run deps 2016-07-14 16:21:47 -04:00
Ben Boeckel
a82385cdae R: look only at run dependencies of build and run deps 2016-07-14 16:21:46 -04:00
Ben Boeckel
0ca1a481a3 python: setup the dependent environment properly 
We want the run dependencies of all build and run dependencies of the
current package.
 2016-07-14 16:21:46 -04:00
Ben Boeckel
ac1701ae29 msgpack-c: add missing dependency on cmake 2016-07-14 16:21:46 -04:00
Ben Boeckel
77965ce5bf py-matplotlib: require py-setuptools to build 2016-07-14 16:21:46 -04:00
Ben Boeckel
6fd45520da deptypes: mark deptypes in packages 2016-07-14 16:21:46 -04:00
Ben Boeckel
45c675fe7f spack: introduce dependency types 
deptypes: allow for different queries

For things like Python modules, they are required for the build and
runtime, but rather than adding a new parameter for what to query across
the dependency DAG, just expose the recursive query parameter.
 2016-07-14 16:21:46 -04:00
Ben Boeckel
bdf82246f7 darwin: explicitly use the 'when=' kwarg 2016-07-14 16:21:45 -04:00
Ben Boeckel
1ae43b3405 doxygen: add missing import 2016-07-14 16:21:45 -04:00
Denis Davydov
668b4f1b2c mkl: set MKLROOT 2016-07-13 23:36:23 +02:00
Adam J. Stewart
3864da6300 Flake8 2016-07-13 11:45:16 -05:00
Adam J. Stewart
d09b0c95ec Filter both makefiles to allow intel to build bzip2 2016-07-13 11:45:16 -05:00
Denis Davydov
de9cce3e80 p4est: flake8 2016-07-13 11:45:33 +02:00
Denis Davydov
52ca215e29 mkl: add provide blas/lapack 2016-07-13 11:42:40 +02:00
Denis Davydov
b8bd02c5b2 p4est: use run_tests instead of a variant 2016-07-13 10:56:40 +02:00
George Hartzell
a73d91a2e5 Add URL and md5 for jdk-8u92. 
Installed on Centos7.2 system, `java -version` works.
 2016-07-12 16:59:08 -04:00
Glenn Johnson
955d02049c New package - r-ggvis 
Bring in ggvis and dependencies.

GGvis is an implementaion of the 'Grammar of Graphics', combined with
shiny.
 2016-07-12 12:27:54 -05:00
Todd Gamblin
069de3f008 Merge pull request #1223 from glennpj/tidyr 
New package - r-tidyr
 2016-07-12 00:23:09 -07:00
Todd Gamblin
04b3d8d86f Merge pull request #1222 from glennpj/libxml2 
Use the site_packages_dir from the Python class
 2016-07-12 00:22:45 -07:00
Glenn Johnson
502d15fd3b New package - r-tidyr 
Tools for changing the layout of data sets.
 2016-07-11 21:12:28 -05:00
Glenn Johnson
5e323b052a Remove import of os 
The import of `os` is no longer needed.
 2016-07-11 20:21:25 -05:00
Glenn Johnson
81daaddfe9 Use the site_packages_dir from the Python class 
It is not necessary to set site_packages_dir in this package as it is
already provided by the Python package class.
 2016-07-11 20:08:30 -05:00
Todd Gamblin
15790d7018 Merge pull request #1207 from davydden/pkg/dealii_update_petsc37 
dealii: update for petsc37
 2016-07-11 15:32:32 -07:00
Glenn Johnson
1b08296392 Fix flake8 error 2016-07-11 17:22:31 -05:00
Glenn Johnson
8de84b5d8a Fix error reported on Google Groups list 
Fixes the reported `TypeError: not enough arguments for format string`
error.
 2016-07-11 16:56:26 -05:00
Todd Gamblin
efdcd199c1 Merge pull request #1218 from glennpj/dplyr 
New package - r-dplyr
 2016-07-11 13:19:09 -07:00
Glenn Johnson
d99fbbb68f New package - r-lubridate 
Functions to work with date-times and timespans.
 2016-07-11 14:59:47 -05:00
Glenn Johnson
11960e53ef New package - r-dplyr 
This brings in dplyr and dependencies.
 2016-07-11 14:50:33 -05:00
Todd Gamblin
255d05a9c1 Merge pull request #1214 from glennpj/rfilter 
Filter compilers for R
 2016-07-11 11:37:39 -07:00
Glenn Johnson
664bdd359f Filter compilers for R 
This adds a filter_compilers function to have the Makeconf file for R
point to the actual compilers rather than the spack wrappers. Also added
version 3.3.1.
 2016-07-11 13:29:43 -05:00
Todd Gamblin
691e628726 Merge pull request #1206 from davydden/pkg/slepc_371_fix 
slepc: fix install_name for binaries on macOS for 3.7.1
 2016-07-11 09:14:53 -07:00
Paul Hopkins
0d3a52ae29 Fix typo in Octave variant suitesparse 2016-07-11 16:00:19 +01:00
Denis Davydov
1b553f2b21 dealii: fix directory structure 2016-07-11 13:21:16 +02:00
Denis Davydov
f14cd67446 dealii: flake8 fixes 2016-07-11 10:56:57 +02:00
Denis Davydov
84afaf385f dealii: run tests only when self.run_tests=true 2016-07-11 10:22:29 +02:00
Denis Davydov
1cc6e42682 dealii: add petsc/slepc 3.7 support 2016-07-11 10:20:15 +02:00
Denis Davydov
38550bbc1b slepc: fix install_name for binaries on macOS for 3.7.1 2016-07-11 10:17:09 +02:00
Geoffrey Oxberry
7551e4c14f cmake@3.6.0 
Add CMake version 3.6.0.
 2016-07-10 18:02:51 -07:00
Todd Gamblin
b0f4052bd8 Merge pull request #1169 from davydden/feature/install_argument_tests_petsc_fixes 
--run-tests install argument and petsc fixes
 2016-07-09 12:10:16 -07:00
Denis Davydov
e482994a15 petsc: add -lm when building example 2016-07-09 08:12:34 +02:00
Erik Schnetter
c8137194f0 Update Cereal to 1.2.0 2016-07-08 15:20:09 -04:00
Todd Gamblin
f04258eb29 Merge pull request #1192 from SteVwonder/develop 
docbook-xml: replace 'cp -t' with install_tree
 2016-07-08 11:09:41 -07:00
Todd Gamblin
1fa67e458c Merge pull request #1194 from SteVwonder/lua-fix 
lua: switch self.version[:2] to .up_to(2)
 2016-07-08 11:09:18 -07:00
Stephen Herbein
bb8a8ecda3 json-c: fix build by running serially 2016-07-08 10:39:47 -07:00
Paul Hopkins
49e8e4b590 Add comments explaining UCS4 and prevent variant being used on Python 3.3 and above 2016-07-08 13:47:25 +01:00
Stephen Herbein
1a1bf31032 lua: switch self.version[:2] to .up_to(2) 
Previous package would not install correctly, would throw:
return os.path.join('share', 'lua', '%d.%d' % self.version[:2])
TypeError: %d format: a number is required, not Version
 2016-07-07 18:58:52 -07:00
Stephen Herbein
1b53452618 docbook-xml: replace 'cp -t' with install_tree 
'-t' is not supported by the default cp on Mac OS X

replace with install/install_tree

cannot just use install_tree since shutil.copytree insists that the dst
directory not exist
 2016-07-07 17:41:53 -07:00
Nicolas Richart
d339f2af29 flake8 corrections 2016-07-07 18:22:27 +02:00
Nicolas Richart
4c1b53660d fixes #719 2016-07-07 18:18:01 +02:00
Paul Hopkins
a2be05f24b Fix whitespace 2016-07-07 14:00:37 +01:00
Paul Hopkins
719b6bfffd Modify range for ucs4 2.* configure arguments 2016-07-07 13:18:40 +01:00
Paul Hopkins
8c1274bbbb Fix Python configure arguments for ucs4 variant on Python 3.0 and above 2016-07-07 13:12:43 +01:00
Paul Hopkins
fb6d850637 Add more python versions 2016-07-07 13:09:08 +01:00
Todd Gamblin
6bb31a9a4c Merge pull request #1175 from davydden/pkg/arpack-3.4.0 
Pkg/arpack 3.4.0
 2016-07-06 14:45:21 -07:00
Todd Gamblin
91da3d8e64 Merge pull request #1174 from LLNL/bugfix/github-1172-suite-sparse 
Bugfix/GitHub 1172 suite sparse
 2016-07-06 14:35:59 -07:00
Todd Gamblin
c6e89d9283 Merge pull request #1180 from davydden/pkg/oce_update_and_fix 
oce: add 0.17.2; fix running tests
 2016-07-06 14:27:05 -07:00
Denis Davydov
14cef6eab8 oce: flake8 fixes 2016-07-06 22:51:20 +02:00
Denis Davydov
c096bb332a petsc: fix unit tests 2016-07-06 22:45:43 +02:00
Greg Lee
3df0f1902d clean up suitesparse deps 2016-07-06 12:15:20 -07:00
Greg Lee
4e27d91351 flake 8 fixes 2016-07-06 11:51:32 -07:00
Denis Davydov
57eaea2e8c oce: add 0.17.2; fix running tests 2016-07-06 20:35:59 +02:00
Paul Hopkins
61fe89bda0 Add ucs4 unicode variant to Python package 2016-07-06 18:29:54 +01:00
Denis Davydov
3d755a148b arpack-ng: fix binaries for macOS 2016-07-06 18:30:38 +02:00
alalazo
379f23be02 swiftsim : fixed configuration for metis 2016-07-06 17:51:46 +02:00
Denis Davydov
c8fc56686c arpack-ng: fix corrupted parpack_cmake.patch 2016-07-06 13:42:59 +02:00
Denis Davydov
63e45c586c arpack-ng: flake8 fixes and minor update of incode comments 2016-07-06 13:27:02 +02:00
Denis Davydov
a47b3ba01b arpack-ng: use spec['mpi'].mpif77 2016-07-06 13:23:51 +02:00
Denis Davydov
f5f7abd71f arpack-ng: add 3.4.0 with cmake build 2016-07-06 12:59:42 +02:00
Greg Lee
4c063c6055 kludge to get suite-sparse-4.5.1 to link with -lstdc++ 2016-07-05 13:48:32 -07:00
Greg Lee
976b2b4d25 added suitesparse version 4.5.3 2016-07-05 13:45:22 -07:00
Erik Schnetter
79b3ef0362 Don't enforce hdf5~mpi 2016-07-05 10:58:11 -04:00
alalazo
55c4a676ad gts : added package 2016-07-05 14:30:48 +02:00
Todd Gamblin
d687e332ad Fix compile bugs for gcc on Mac OS X with macports. 
- add macports to things that are cleaned out of the environment.
- linker incompatibilities cause issues with packages like OpenSSL.
- also clean up NOQA stuff in OpenSSL
 2016-07-04 22:59:02 -07:00
Todd Gamblin
f2a692c515 Merge pull request #1163 from epfl-scitas/fixes/reserved_name_for_system_packages 
fixes : reserved name for system packages
 2016-07-04 21:25:50 -07:00
Todd Gamblin
d166c04db5 Merge pull request #1166 from glennpj/rstan 
New package - RStan
 2016-07-04 21:23:10 -07:00
Todd Gamblin
1de675e976 Merge pull request #1165 from robertdfrench/ruby-needs-ffi-zlib 
Ruby 2.2.0 needs ffi and zlib
 2016-07-04 21:22:38 -07:00
Glenn Johnson
d5abcc5c88 Fix flake errors 2016-07-04 17:55:10 -05:00
Glenn Johnson
519b760222 New package - RStan 
This PR creates the RStan package and its dependencies.
 2016-07-04 17:30:05 -05:00
Robert D. French
53bbbfbe21 Require libffi, zlib; Make Openssl, readline optional 2016-07-04 15:21:13 -04:00
Nicolas
85982017b6 Revert "Corrected the shared libraries and tests in mumps package" 2016-07-04 18:19:09 +02:00
alalazo
861f174f66 qa : fixed flake8 issues 2016-07-04 10:26:32 +02:00
alalazo
3e8391458c openssl : changed tag for system reserved versions fixes #1150 2016-07-04 10:25:20 +02:00
Todd Gamblin
890df7153a Merge branch 'efischer/160311-StagedPackage' of https://github.com/citibeth/spack into citibeth-efischer/160311-StagedPackage 2016-07-04 00:27:32 -07:00
Glenn Johnson
729f23b432 Use Executable to set script 
Use `Executable("./install.sh")` to set `install_script`. This allows it
to work when the current directory is not on the PATH.
 2016-07-01 22:13:40 -05:00
Tzanio Kolev
137db14b75 Update package.py 2016-06-30 15:40:02 -07:00
Tzanio
d3b0cb56b7 Updating MFEM package with v3.2 info. 2016-06-30 15:23:30 -07:00
Elizabeth Fischer
50ac98bc04 Merge remote-tracking branch 'upstream/develop' into efischer/160630-StagedPackage 
# Conflicts:
#	lib/spack/docs/packaging_guide.rst
#	lib/spack/spack/package.py

Mostly minor/formatting issues in lib/spack/spack/package.py (the heavyweight merge was already done recently).  Only one serious issue: it looks like the feature branch had accidentally deleted the line `spack.hooks.post_install(self)`.  This got added back in from develop.
 2016-06-30 09:13:24 -04:00
Todd Gamblin
a7b8cb6901 Merge pull request #1145 from davydden/pkg/petsc_tests 
petsc: run a test
 2016-06-30 01:58:35 -07:00
Denis Davydov
6f4b0e9bda petsc: fix flake8 and ~mpi case in tests 2016-06-30 08:22:01 +02:00
Denis Davydov
37728afada petsc: run a test 2016-06-30 00:19:50 +02:00
Adam J. Stewart
2fcaa011ce Add py-restview package 2016-06-29 12:57:58 -05:00
Todd Gamblin
7df89896f4 Merge pull request #1113 from davydden/octave_extensions 
Octave extensions
 2016-06-29 00:38:05 -07:00
Todd Gamblin
0fd58fb585 Merge pull request #1133 from davydden/pkg/dealii_fix_tests 
dealii: run more unit tests when building @dev
 2016-06-28 10:02:43 -07:00
Denis Davydov
32c801bbf6 dealii: run more unit tests when building @dev 2016-06-28 18:06:56 +02:00
Todd Gamblin
ad48ad7586 Merge pull request #1131 from epfl-scitas/fixes/swift_git_environment_variables 
fix : swiftsim will set git environment variables in the appropriate hook
 2016-06-28 09:05:26 -07:00
alalazo
5cdd37959a swiftsim : substituted tag with corresponding commit 2016-06-28 18:03:28 +02:00
Todd Gamblin
6810965457 Merge pull request #1130 from davydden/gmsh 
Gmsh -- various fixes
 2016-06-28 08:49:06 -07:00
alalazo
18612eca59 qa : fixed flake8 issues 2016-06-28 12:59:13 +02:00
alalazo
48888b0f8e swift : setting environment variables in the right place 2016-06-28 12:57:19 +02:00
Denis Davydov
c4c167c1ca octave: rename executable Octave to octave 2016-06-28 11:25:45 +02:00
Denis Davydov
51b0f53b33 gmsh: flake8 fixes 2016-06-28 10:50:35 +02:00
Denis Davydov
06e38d2ca2 gmsh: various fixes 
(i) add new version
(ii) add OCE, PETSc and SLEPc as dependencies
(iii) fix Blas/Lapack configuration
(iv) disable internal Metis which does not compile
 2016-06-28 10:33:25 +02:00
Todd Gamblin
793c9f5546 Merge pull request #1116 from mwilliammyers/package-lrzip 
Add package lrzip & its dependency lzo
 2016-06-27 22:32:57 -07:00
mwilliammyers
9bb918915f Add package lrzip & its dependency lzo 2016-06-27 15:19:13 -06:00
Todd Gamblin
d7c2f683d9 Merge pull request #1004 from UCL-RITS/bare-eigen 
Option to install eigen without dependencies
 2016-06-27 13:35:35 -07:00
Nicolas Richart
9026fb8e8a Corrections for PETSc 3.7 and detection of PETSC version to enable TAO 2016-06-27 20:52:05 +02:00
Todd Gamblin
3ea9d1e665 Merge pull request #1122 from LLNL/bugfix/newarch-sys_type 
Bugfix/newarch sys type
 2016-06-27 10:07:03 -07:00
Todd Gamblin
bf4eeb48b9 Merge pull request #1099 from adamjstewart/fixes/hdf5 
Fix self-check for hdf5@1.10.0-patch1
 2016-06-27 09:47:17 -07:00
Todd Gamblin
76458f5bfc Merge pull request #1002 from epfl-scitas/packages/foam-extend 
Package foam-extend
 2016-06-27 09:40:49 -07:00
Denis Davydov
0faa6dd753 octave: make extendable and add a package 2016-06-27 13:44:58 +02:00
Todd Gamblin
305d5698df Rename spack.architecture.sys_type() to spack.architecture.platform() 2016-06-27 02:19:08 -07:00
alalazo
13fcb3c083 swift : renamed swiftsim 2016-06-27 09:25:58 +02:00
alalazo
f3f309a22a Merge branch 'develop' of https://github.com/LLNL/spack into packages/swift_durham 2016-06-27 09:08:37 +02:00
Todd Gamblin
a1db306a0c Merge pull request #1009 from epfl-scitas/packages/emacs 
Emacs: adding dependencies to be able to build without the system libs
 2016-06-26 22:46:45 -07:00
Todd Gamblin
bad32724ec Merge pull request #1092 from adamjstewart/features/netcdf-f 
Add latest version of netcdf-fortran and curl
 2016-06-26 22:38:00 -07:00
Todd Gamblin
8b35940857 Merge pull request #1103 from adamjstewart/features/mpi 
Add MPI environment variables to packages
 2016-06-26 22:35:39 -07:00
Todd Gamblin
f86f6c6274 Merge pull request #1104 from mwilliammyers/py-protobuf 
Add new package py-protobuf
 2016-06-26 22:28:57 -07:00
Todd Gamblin
7d85902f37 Merge pull request #1093 from eschnett/eschnett/julia-update 
Update Julia to 0.4.6
 2016-06-26 22:28:33 -07:00
Todd Gamblin
c096aa9557 Merge pull request #997 from glennpj/glib_gcc 
Get glib to compile with gcc-6.1
 2016-06-26 22:28:07 -07:00
Nicolas Richart
f3accb111e correcting flake8 2016-06-27 01:23:14 +02:00
Nicolas Richart
7cf1313572 changes to use from_sourcing_file 2016-06-27 00:55:26 +02:00
alalazo
9de0503188 qa : flake8 issues 2016-06-26 22:00:10 +02:00
alalazo
11863d2de3 packages : moved adios and mxml into builtin repo 2016-06-26 21:56:06 +02:00
alalazo
a2ba60f6a8 qa : flake8 issues 2016-06-26 17:38:48 +02:00
alalazo
e5b36583b5 swift : added package 2016-06-26 17:36:53 +02:00
alalazo
acd9014553 autotools : set Executable() in dependent modules 2016-06-26 17:36:33 +02:00
mwilliammyers
2c6c21a3bf Add new package py-protobuf 2016-06-23 15:54:20 -06:00
Adam J. Stewart
8921bf4552 Add MPI environment variables to packages 2016-06-23 10:08:40 -05:00
Adam J. Stewart
d566510a40 Flake8 and url_for_version fixes 2016-06-22 15:22:42 -05:00
Adam J. Stewart
3f4bf04dde Fix self-check for hdf5@1.10.0-patch1 2016-06-22 14:40:51 -05:00
Erik Schnetter
c904a42c5b Address flake errors 2016-06-22 11:09:45 -04:00
Adam J. Stewart
b66f5b6231 Add latest version of cURL 2016-06-22 10:05:20 -05:00
Erik Schnetter
e398c0dc5b Update Julia to 0.4.6 2016-06-22 11:00:00 -04:00
Adam J. Stewart
060fb596f7 Add latest version of netcdf-fortran 2016-06-22 09:52:17 -05:00
Nicolas Richart
97feca0888 Merge branch 'develop' into packages/foam-extend 2016-06-22 14:51:57 +02:00
Todd Gamblin
e41d67e031 Merge pull request #1078 from adamjstewart/features/pillow 
Allow py-pillow to link to Spack-built libraries
 2016-06-22 01:11:25 -07:00
Todd Gamblin
8b5467e65d Merge pull request #1049 from glennpj/newR_database 
New R database packages
 2016-06-21 13:23:58 -07:00
Adam J. Stewart
a7ffb2c1a4 Flake8 2016-06-21 15:21:53 -05:00
Todd Gamblin
bbe2db5814 Merge pull request #1087 from LLNL/bugfix/new-harfbuzz-fix 
Bugfix/new harfbuzz fix
 2016-06-21 13:10:50 -07:00
Adam J. Stewart
66089c89aa Depend on pil 2016-06-21 14:55:49 -05:00
Adam J. Stewart
2efc67da60 Remove +tk variant, provide pil 2016-06-21 14:50:33 -05:00
Gregory L. Lee
e0fbf14f99 consolidated f2py regex 2016-06-21 09:23:58 -07:00
Gregory L. Lee
8f3954c1bd flake 8 fixes for cairo, freetype, and harfbuzz 2016-06-21 08:47:22 -07:00
Gregory L. Lee
4041f45b6c fixed conflicts in python package 2016-06-21 08:47:11 -07:00
Todd Gamblin
f18e1a9371 Merge branch 'features/cantera' of https://github.com/adamjstewart/spack into adamjstewart-features/cantera 2016-06-20 23:53:48 -07:00
Glenn Johnson
77cd474a2d Make all packages lowercase. 2016-06-20 20:10:44 -05:00
alalazo
b86e3047f3 openmpi : revert part of #1079 (OpenMPI can be built without fortran) 
Building OpenMPI without fortran is possible, and was already handled.
 Raising an install error we effectively renounce at clang+OpenMPI.

 build_environment : sets 'CC', 'CXX', and similar variables only if a compiler is found
 2016-06-20 20:46:11 +02:00
Todd Gamblin
f74d4b0660 Merge pull request #1052 from adamjstewart/features/psi4 
Add Psi4 Package
 2016-06-20 10:49:45 -07:00
Todd Gamblin
9b299cb2bb Merge pull request #1023 from epfl-scitas/packages/mumps 
Corrected the shared libraries and tests in mumps package
 2016-06-20 10:48:12 -07:00
Todd Gamblin
cec283f608 Merge pull request #1059 from epfl-scitas/packages/mpi_wrappers_with_rpath 
MPI : have wrappers set RPATH instead of RUNPATH
 2016-06-20 10:47:24 -07:00
Todd Gamblin
c2d0870924 Merge pull request #1063 from eschnett/eschnett/openmpi-1.10.3 
Update OpenMPI to 1.10.3
 2016-06-20 10:45:56 -07:00
Todd Gamblin
31bb47356f Merge pull request #1022 from glennpj/r-devtools 
new package: r-devtools
 2016-06-20 10:34:23 -07:00
Todd Gamblin
b3881701c5 Merge pull request #1021 from glennpj/packrat 
new package: r-packrat
 2016-06-20 10:33:55 -07:00
Todd Gamblin
0fbd2fe224 Merge pull request #1000 from glennpj/new_R 
Add version 3.3.0 of R and extensions
 2016-06-20 10:33:43 -07:00
Todd Gamblin
c09111bbef Merge pull request #1053 from davydden/pkg/dealii_suite_update 
update Petsc, Slepc, Trilinos, Superlu-dist and deal.II
 2016-06-20 10:32:52 -07:00
Todd Gamblin
8047edfb56 Merge pull request #1029 from adamjstewart/features/armadillo 
Add Armadillo and SuperLU packages
 2016-06-20 10:29:29 -07:00
Todd Gamblin
265b9bcb0f Merge pull request #1076 from JRWynneIII/ferret 
Added spec to build Ferret
 2016-06-20 10:28:42 -07:00
Adam J. Stewart
c9eb5f8173 Use non-checksummed PyPi download URLs 2016-06-20 12:24:45 -05:00
Adam J. Stewart
7e1ee463ca Install examples for sundials 2016-06-20 12:24:45 -05:00
Adam J. Stewart
81ac3b62fc Filter compilers and link boost properly 2016-06-20 12:24:45 -05:00
Adam J. Stewart
a21e845ce7 Flake8 2016-06-20 12:24:45 -05:00
Adam J. Stewart
2220784eda Add scons support, .zip support, and Cantera package 2016-06-20 12:24:45 -05:00
Todd Gamblin
12b9d6da10 Merge pull request #1083 from robertdfrench/tmux-2.2 
Tmux 2.2
 2016-06-20 09:36:55 -07:00
Robert.French
83b0c16728 Tmux 2.2 with PEP8 
Tmux 2.2

Provide variant to skip utempter

Remove utempter variant; 2.2 doesn't need it

Flake8ify
 2016-06-20 16:26:49 +00:00
Denis Davydov
cf4a34c657 openmpi: raise an error without Fortran compiler 2016-06-19 11:59:29 +02:00
Denis Davydov
1cc04cff27 openblas: raise an error without Fortran compiler 2016-06-19 11:59:10 +02:00
Adam J. Stewart
652a5eb592 Allow py-pillow to link to Spack-built libraries 2016-06-17 18:09:03 -05:00
Todd Gamblin
62b2f2a7c9 Merge pull request #1065 from epfl-scitas/packages/espresso_update 
espresso : update to 5.4.0
 2016-06-17 14:51:45 -07:00
Todd Gamblin
9a8d109650 Merge pull request #1044 from adamjstewart/features/sncosmo 
Add py-sncosmo package
 2016-06-17 14:50:37 -07:00
Todd Gamblin
0bbbfc2ef7 Merge pull request #946 from LLNL/features/intel2 
Intel software packages and license enhancements
 2016-06-17 14:28:39 -07:00
Adam J. Stewart
536fa73d5f Python flake8 overhaul 2016-06-17 13:33:09 -05:00
Robert D. French
448f8c43d4 Added working Ferret spec 
Fixed ferret spec. It builds now

Made ferret spec more flake8-y

Fixed homepage and info text about Ferret

Removed vim swap file

Reverted changes to netcdf-fortran spec and added netcdf~mpi dependency to ferret spec to compensate for it

Fixed flake8 issues!
 2016-06-17 14:23:50 -04:00
Adam J. Stewart
80d444624b Fix activation of sites.py for sncosmo 2016-06-17 11:08:16 -05:00
Adam J. Stewart
24f65c502e Add additional Astropy dependencies 2016-06-17 10:45:10 -05:00
Adam J. Stewart
b2aa78d6ab Remove version constraints 2016-06-17 10:45:10 -05:00
Adam J. Stewart
4eeaff175c Allow packages to build 2016-06-17 10:44:28 -05:00
Adam J. Stewart
a660c60eb1 Add py-sncosmo package 2016-06-17 10:43:34 -05:00
Glenn Johnson
8970785d33 Add 'jdk' as a dependency. 
Add jdk as a dependency so that R has support for java and allow
packages that need java to work.
 2016-06-16 23:08:55 -05:00
Glenn Johnson
a813f03955 Add list_url for old versions. 2016-06-16 23:08:55 -05:00
Glenn Johnson
4850b9d4d1 Make install comment consistent with actual call. 2016-06-16 23:08:55 -05:00
Glenn Johnson
7da405e630 Add validator for bioconductor packages 
This commit adds a validator function to make sure the versions of R and
bioconductor are in sync.
 2016-06-16 23:08:55 -05:00
Glenn Johnson
7213b12324 Tweak how R packages are built. 
Add bzip2 as a dependency to base R.

Switch from installing the R packages from tar files to installing from
the extracted directory. This is more in line with a standard install
and also allows installing from VCS.

Use the Bioconductor version for BiocGenerics and future Bioconductor
packages. Suffix the package with 'bioc-$version' to indicate which
Bioconductor release the package is a part of. This is actually more
important than the actual version attached to individual packages
although those are subject to change within the Bioconductor branch.
 2016-06-16 23:08:55 -05:00
Glenn Johnson
0e64c25ffc Fix flake8 errors 
Use Bioconductor provided Short URL for homepage in BiocGenerics.
Wrap description text for utf variant in pcre.
 2016-06-16 23:08:54 -05:00
Glenn Johnson
37dc13edaf Update version of BiocGenerics 
The BioConductor repositories only keep the most recent version so this
has to be bumped.
 2016-06-16 23:08:54 -05:00
Glenn Johnson
8704a4ed35 Use configure_args rather than options 
Replaced 'options' with 'configure_args'. That seems like a better name
and is consistent with the packaging guide.
 2016-06-16 23:08:54 -05:00
Glenn Johnson
fe256870b4 Add variant for UTF support to pcre 
This will build PCRE with UTF support by default. That seems to be
reasonable for most environments.
 2016-06-16 23:08:54 -05:00
Glenn Johnson
cb3505769b Clean up R extensions 
Run the existing R extension packages through autopep8 to clean up.
 2016-06-16 23:07:13 -05:00
Glenn Johnson
6649f9edc2 Add version 3.3.0 of R 
This commit adds the 3.3.0 version of R and adds dependencies on curl
and pcre.
 2016-06-16 23:07:13 -05:00
Glenn Johnson
64acbbfcf0 Clean up R package files 
- remove unused imports
- apply pep8
- reformat text strings
 2016-06-16 23:07:13 -05:00
Todd Gamblin
9ee6cbfb40 Merge pull request #944 from adamjstewart/features/bertini 
Add bertini package
 2016-06-16 16:57:50 -07:00
Todd Gamblin
344280154a Merge pull request #962 from adamjstewart/features/hpl 
Add HPL benchmark package
 2016-06-16 16:57:24 -07:00
Todd Gamblin
88b73bacdb Merge branch 'features/newarch' into develop 
Conflicts:
	lib/spack/spack/config.py
	var/spack/repos/builtin/packages/lua/package.py
 2016-06-16 03:03:26 -07:00
alalazo
a1cbb73f8b qa : fixed flake8 issues 2016-06-16 11:24:18 +02:00
alalazo
8d9ffcf565 espresso : updated to 5.4.0, added Parallel=False 2016-06-16 11:22:26 +02:00
Todd Gamblin
76dfaa71a7 fix up packages for new architecture. 2016-06-16 01:47:20 -07:00
Todd Gamblin
40d25d9062 Add libxcb dependencies. Fix up packages to get py-basemap and stat to build. 2016-06-16 00:56:53 -07:00
Erik Schnetter
a7ab064a9e Update OpenMPI to 1.10.3 2016-06-15 18:05:23 -04:00
Massimiliano Culpo
daa46105a7 mpich based providers : shortened filter_compilers 2016-06-15 21:37:12 +02:00
Adam J. Stewart
44e188f111 Remove MPI support, fix INCLUDE filters 2016-06-15 14:17:30 -05:00
Adam J. Stewart
7b97ea248a More template filtering 2016-06-15 14:17:29 -05:00
Adam J. Stewart
9cf1257be4 Filter compilers 2016-06-15 14:17:29 -05:00
Adam J. Stewart
deb4f919cf Psi4 tweaks 2016-06-15 14:17:29 -05:00
Adam J. Stewart
9d99042fed Add Psi4 package 2016-06-15 14:17:29 -05:00
Denis Davydov
0e04e65ae0 trilinos: specify superlu-dist version dependency 2016-06-15 18:44:59 +02:00
Denis Davydov
5fe531050c flake8 fixes for dealii 2016-06-15 18:33:34 +02:00
Denis Davydov
e76083205f flake8 fixes for slepc 2016-06-15 18:33:08 +02:00
Denis Davydov
6390acc660 flake8 fixes for petsc 2016-06-15 18:32:42 +02:00
Denis Davydov
6d714e4425 flake8 fixes for superlu-dist 2016-06-15 18:31:39 +02:00
Denis Davydov
d0d83cfe1e slepc: build by default with Arpack 2016-06-15 18:21:13 +02:00
Denis Davydov
d04dc8440f dealii: specify petsc/slepc version dependencies 2016-06-15 18:21:13 +02:00
Denis Davydov
4d40f86bd3 trilinos: add 12.6.2 and 12.6.3 2016-06-15 18:21:13 +02:00
Denis Davydov
5358ffbe5a slepc: add 3.6.3 and 3.7.1; specify petsc version dependency 2016-06-15 18:21:13 +02:00
Denis Davydov
9ceb8fea78 petsc: add 3.6.4 and 3.7.2; specify superlu-dist version dependency 2016-06-15 18:21:13 +02:00
Denis Davydov
a860a3d614 superlu-dist: avoid harcoding blas/lapack/mpi; remove preferred version 2016-06-15 18:21:13 +02:00
Todd Gamblin
c803f7ae98 Merge pull request #1045 from eschnett/eschnett/openmpi-verbs-usr 
Do not pass "/usr" or "/usr/local" as path to configure
 2016-06-15 09:06:12 -07:00
Todd Gamblin
4ede87a8b0 Merge pull request #1058 from eschnett/eschnett/blosc 
Add packages c-blosc and hdf5-blosc
 2016-06-15 09:04:48 -07:00