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1993 commits

Author SHA1 Message Date
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
52ca215e29 mkl: add provide blas/lapack 2016-07-13 11:42:40 +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