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Author SHA1 Message Date
Robert D. French
974749aaf6 Provide mpi-less variant for nco (#1643) 2016-08-28 19:15:15 -07:00
Erik Schnetter
6acfcd82b1 Update Julia to 0.5 release branch; install some Julia package as well (#1637) 
* Update Julia to 0.5 release branch; install some Julia package as well

* Add comments, correct flake8 error

* Correct flake8 error
 2016-08-28 17:46:10 -07:00
Robert D. French
079d063c6d Variant for building cdo without mpi (#1638) 2016-08-28 17:43:54 -07:00
Erik Schnetter
db7c3d2de6 New package for the Mercurial (hg) version control system (#1644) 
* New package "mercurial"

* Disable self-checks

The self-checks require subversion, which we don't want to require.
 2016-08-28 17:31:15 -07:00
becker33
e73a1a4ec3 Merge pull request #1558 from mcfadden8/mmcfadden-features/gcc-pic-libraries 
Added variant to gcc package to install PIC versions of libgfortran and libstdc++
 2016-08-25 16:00:00 -07:00
Gregory Lee
77c24d4127 Merge pull request #1379 from LLNL/features/graphlib3 
added stat 3.0 beta and added pygtk and dependent packages
 2016-08-25 09:14:36 -07:00
Todd Gamblin
8170bcfcdd Merge pull request #1574 from ARCCA/plumed-push 
Update plumed package to include optional modules
 2016-08-25 02:45:33 -07:00
Andrew Williams
07e0da24c5 Reverted url to point to tarball rather than git tag 2016-08-25 10:21:56 +01:00
Todd Gamblin
22d2786940 Merge pull request #1580 from davydden/pkg/trilinos_url_fix 
trilinos: switch to github url; fix missing py-numpy dependency
 2016-08-25 02:10:05 -07:00
Kelly (KT) Thompson
2ddaabed25 + Boost: fix recipe for intel compilers. 
This is the same patch provided by PR #550, but rebased against the current
develop branch. It also passes the flake8 checks.
 2016-08-24 15:57:28 -06:00
Todd Gamblin
93cb2db531 Fix build dependency. 2016-08-24 14:10:12 -07:00
Todd Gamblin
a7e568b1d1 Merge branch 'eschnett/sympol' of git://github.com/eschnett/spack into eschnett-eschnett/sympol 2016-08-24 14:05:05 -07:00
Todd Gamblin
19bbe5e421 Merge pull request #1596 from eschnett/eschnett/git-update 
Update git to 2.9.3
 2016-08-24 14:03:04 -07:00
Todd Gamblin
86fe78f5f1 Merge pull request #1582 from eschnett/eschnett/gcc-update 
Update gcc to @6.2.0
 2016-08-24 14:02:54 -07:00
Adam J. Stewart
eace068788 Use self.run_tests for make check 2016-08-24 15:21:23 -05:00
Adam J. Stewart
70bb1f1707 Reduce number of variants, just use system or no-system libs 2016-08-24 14:39:05 -05:00
Todd Gamblin
e6bac6f208 Merge pull request #1613 from eschnett/eschnett/cmake-update 
Update cmake to 3.6.1
 2016-08-24 08:49:33 -07:00
Todd Gamblin
63859bf113 Merge pull request #1575 from davydden/pkg/nwchem 
nwchem: add new package
 2016-08-24 08:49:11 -07:00
Todd Gamblin
5cfa74801f Merge pull request #1565 from adamjstewart/features/fftw 
Add latest version of fftw
 2016-08-24 08:49:00 -07:00
Adam J. Stewart
5970b7a00a Only run tests if explicitly requested 2016-08-24 10:34:20 -05:00
Erik Schnetter
41750ce70d Update cmake to 3.6.1 2016-08-24 10:45:13 -04:00
Denis Davydov
d154f151aa py-cclib: new package 2016-08-24 16:26:35 +02:00
Denis Davydov
6d2d5806b5 nwchem: add python module 2016-08-24 13:40:02 +02:00
Denis Davydov
dae219d5c3 nwchem: add another patch 2016-08-23 22:24:16 +02:00
Denis Davydov
459b6eae11 nwchem: add another patch 2016-08-23 22:15:38 +02:00
Erik Schnetter
3194f2001b Update git to 2.9.3 2016-08-23 15:35:43 -04:00
Erik Schnetter
05f5ba4bf9 Correct flake8 errors 2016-08-23 14:57:29 -04:00
Erik Schnetter
73cae8d9c4 Implement review requests 
- use two empty lines before `class`
- change version numbering scheme for packages, use `url_for_version` to make things work
- specify dependency types
- add comment about temporarily moved download location
- update two packages to newer versions
 2016-08-23 13:52:28 -04:00
Denis Davydov
52ae0ea055 trilinos: use version.dashed 2016-08-23 18:48:17 +02:00
David Beckingsale
243d516bf0 Ensure RAJA builds out-of-source 2016-08-23 08:18:26 -07:00
Denis Davydov
6500ac80e4 nwchem: fix lapack detection 2016-08-23 16:46:40 +02:00
Erik Schnetter
a2692e4ef5 sympol: Add package 2016-08-23 10:41:08 -04:00
Erik Schnetter
bdc825fc3c cddlib: Point download url to a (more reliable) Fedora server 2016-08-23 09:59:56 -04:00
Erik Schnetter
64d3f87e60 Merge branch 'develop' into eschnett/sympol 2016-08-23 09:45:46 -04:00
Denis Davydov
7eb386e55e nwchem: add patches 2016-08-23 14:52:18 +02:00
Denis Davydov
5da9116c06 nwchem: add scalapack; extra steps for 32bit blas/lapack 2016-08-23 11:55:00 +02:00
Denis Davydov
aca8576de4 trilinos: switch to github url; fix missing py-numpy dependency 2016-08-23 10:50:08 +02:00
Todd Gamblin
e81f3daa28 Merge pull request #1519 from mathstuf/fix-deptypes 
Fix deptypes
 2016-08-22 21:40:25 -07:00
Erik Schnetter
7b49166f9b Update gcc to @6.2.0 
Also add some missing older version.
Update download location to original GNU location.
 2016-08-22 20:26:54 -04:00
Denis Davydov
a44beee172 nwchem: add new package 2016-08-23 02:22:44 +02:00
Andrew Williams
65abd279cd Renamed intelmpi as suggested 2016-08-22 13:44:21 +01:00
Andrew Williams
87d15212eb Cleaned branch to only include plumed package 2016-08-22 12:30:17 +01:00
Andrew Williams
226d4f04f3 Spelling tweaks and consistent quoting 2016-08-22 12:09:50 +01:00
Andrew Williams
5661afa315 Passed flake8 tests 2016-08-22 12:03:47 +01:00
Andrew Williams
0c8462723b Found upstream plumed package and modified this one to match 2016-08-22 11:24:03 +01:00
Erik Schnetter
78685addbb hdf5-blosc: Correct download url 2016-08-21 14:39:54 -04:00
Todd Gamblin
55b1182a4c Merge pull request #1554 from eschnett/eschnett/hdf5-blosc 
hdf5-blosc: Remove commit id from version specification
 2016-08-21 09:44:25 -07:00
Adam J. Stewart
d5903e4612 Flake8 2016-08-19 17:06:34 -05:00
Adam J. Stewart
f0f2c6c486 Add latest version of fftw 2016-08-19 17:05:14 -05:00
Gregory L. Lee
a177b9be8a updated stat 3.0.0b url 2016-08-19 13:11:21 -07:00
Adam J. Stewart
835b8f246e py-sphinx requires py-setuptools during runtime 2016-08-19 14:20:31 -05:00
Adam J. Stewart
d7873b5319 Swap lowercase for uppercase in URL 2016-08-19 14:00:50 -05:00
Adam J. Stewart
c1af0d3806 Fix binary conflicts during sphinx activation 2016-08-19 13:54:22 -05:00
Adam J. Stewart
d4e3699510 Add all Sphinx dependencies 2016-08-19 13:44:00 -05:00
Erik Schnetter
466da3afcc Remove commented-out outdated commit id 2016-08-19 11:52:40 -04:00
Andrew Williams
90e5ccd98c Cleaned up commented out code in intelmpi package 2016-08-19 15:01:46 +01:00
Andrew Williams
13f636ec68 Added required arguments to get plumed to build with intelmpi 2016-08-19 15:00:21 +01:00
Adam J. Stewart
28537ae7b7 Workaround until variant forwarding works properly 2016-08-18 14:40:21 -05:00
Stephen Herbein
3445a781eb py-cffi: set LDSHARED env so that rpath is set 
py-cffi's .so was being built without the rpath being set.  distutils
looks at the LDSHARED for which compiler to use to build the final .so.
Since it was not set, distutils fell back to the system provided
compiler.  Setting it forces the shared library to be compiled with the
spack compiler (meaning that the rpath is set correctly).
 2016-08-18 11:32:19 -07:00
Andrew Williams
6641f42417 Not compiling due to mpi error. Also getting this error from the command line so could be separate issue. Otherwise package definition first draft complete. 2016-08-18 13:19:36 +01:00
Erik Schnetter
296212d78d hdf5-blosc: Remove commit id from version specification 
The respective commit seems to have vanished.
Now using the master branch without specifying a particular commit.
 2016-08-17 16:36:33 -04:00
Adam J. Stewart
4d12c5455a Fix NetCDF/HDF5 dependency resolution problems 2016-08-17 13:03:56 -05:00
Marty McFadden
f4ec99ecb4 Added +piclibs variant for building PIC versions of libgfortran.a and libstdc++.a 2016-08-17 09:28:21 -07:00
Andrew Williams
b99e945e6d Added variants and dependencies to plumed but I'm getting an error when trying to resolve mpi to a valid virtual package 2016-08-17 15:43:59 +01:00
becker33
7f57405eac Merge pull request #1531 from davydden/pkg/ape 
ape: add new package
 2016-08-16 10:52:27 -07:00
becker33
e8afbfbce7 Merge pull request #1530 from davydden/pkg/octopus 
octopus: new package
 2016-08-16 10:49:41 -07:00
Denis Davydov
5dcc0f7802 ape: add new package 2016-08-16 19:42:32 +02:00
Denis Davydov
9509c10064 octopus: new package 2016-08-16 19:38:38 +02:00
Gregory L. Lee
f182590aae added pkg-config to build deps of cairo and pixman 2016-08-15 15:17:53 -07:00
Gregory L. Lee
54ef9443d3 fix atk url_for_version 2016-08-15 13:51:54 -07:00
Gregory L. Lee
74dd7a36b5 allow parallel build of stat 2016-08-15 13:51:54 -07:00
Gregory L. Lee
749a4e78c7 gobject-introspection requires glib version 2.48.1 2016-08-15 13:51:54 -07:00
Gregory L. Lee
3df208efc0 stat and dependences package updates 2016-08-15 13:51:53 -07:00
Gregory L. Lee
69931996bf added dyninst patches for stat+dysect 2016-08-15 13:51:53 -07:00
Gregory L. Lee
f9cb21e886 flake 8 fixes for dyninst 2016-08-15 13:51:53 -07:00
Gregory L. Lee
0074ecd6fa dyninst package use spec.satisfies instead of @when 2016-08-15 13:51:52 -07:00
Gregory L. Lee
8b94937609 flake 8 fixes for stat and dependents 
flake 8 fixes for dyninst

flake 8 fixes for dyninst

flake 8 fixes for dyninst
 2016-08-15 13:50:39 -07:00
Gregory L. Lee
bd8aab00e4 updated stat and added pygtk and dependent packages 2016-08-15 13:48:58 -07:00
Andrew Williams
27793d97dc temp commit in current state 2016-08-15 16:16:00 +01:00
Ben Boeckel
9ec1c0e18e opencv: make py-numpy a nolink dependency 2016-08-15 10:47:00 -04:00
Ben Boeckel
042666eb7e go: mark git as also being a runtime dependency 2016-08-15 10:46:45 -04:00
Ben Boeckel
826732efec packages: mark builddeps as type='build' 
Less sure about these.
 2016-08-15 10:46:23 -04:00
Ben Boeckel
eb13cbe9bd r-datatable: fix nolink dependency 2016-08-15 10:46:05 -04:00
Ben Boeckel
0d17d90b29 packages: mark builddeps as type='build' 2016-08-15 10:45:19 -04:00
Andrew Williams
3edfa390f7 Basic package file for plumed and boilerplate for external intel mpi 2016-08-15 11:19:40 +01:00
Adam J. Stewart
bc64990bc6 Replace python('setup.py' with setup_py( 2016-08-12 12:16:48 -05:00
Todd Gamblin
e1c2ea5123 Merge pull request #1342 from adamjstewart/features/cgns 
Add CGNS package
 2016-08-12 09:19:07 -07:00
Adam J. Stewart
d4377c1293 Add Python 3.5 support, latest version of PySide 2016-08-12 09:59:38 -05:00
Adam J. Stewart
633e540a17 Use GitHub URL for ImageMagick 2016-08-11 14:13:33 -05:00
Adam J. Stewart
f147d64527 Rebase messed up flake8 2016-08-11 11:01:57 -05:00
Adam J. Stewart
04cee45ac9 Skip webengine until webkit support is added 2016-08-11 10:33:43 -05:00
Adam J. Stewart
2b0444b6f4 Latest version of pyside still has problems, add deps 2016-08-11 10:33:43 -05:00
Adam J. Stewart
b6fad65f52 Combine patch for all versions 
Patch doesn't work with @when unless you specify a patch for every
version. When running `spack patch` for a version without a patch,
spack thinks that a patch exists, tries to apply it, but it doesn't
exist. Spack gets very confused.
 2016-08-11 10:33:43 -05:00
Adam J. Stewart
1363b05e93 Add test dependencies 2016-08-11 10:33:43 -05:00
Adam J. Stewart
5cc76f7d84 Fix patch for py-pyside 1.2.4 2016-08-11 10:33:43 -05:00
Adam J. Stewart
59ce0c7514 Add patch to build qt 4 with GCC 6 2016-08-11 10:33:42 -05:00
Adam J. Stewart
ddf1879bed Remove glib dependency, causes problems with PCRE and JavaScript 2016-08-11 10:33:02 -05:00
Adam J. Stewart
90dd26397c Fix qt patch 2016-08-11 10:33:02 -05:00
Adam J. Stewart
7135299a66 Add latest version of pcre 2016-08-11 10:33:02 -05:00
Adam J. Stewart
ac15d5d619 Add patch for qt gamepad compilation problems 2016-08-11 10:33:01 -05:00
Adam J. Stewart
eac9a5905f Flake8 and url_for_version changes 2016-08-11 10:33:01 -05:00
Adam J. Stewart
80742b2647 Add latest version of qt 2016-08-11 10:30:31 -05:00
Adam J. Stewart
8a0824df09 Update matplotlibrc filtering for GUI backends 2016-08-11 10:28:35 -05:00
Adam J. Stewart
a388871083 Update ImageMagick to latest version 2016-08-11 10:28:35 -05:00
Adam J. Stewart
2b83ea30e7 Re-add ipython support 2016-08-11 10:28:35 -05:00
Adam J. Stewart
f56de63972 Fix cycler dependencies, update qhull version names 2016-08-11 10:28:35 -05:00
Adam J. Stewart
0b8a3ad8ad Flake8 2016-08-11 10:28:34 -05:00
Adam J. Stewart
aa6a6df640 Undo changes to GUI framework 2016-08-11 10:28:34 -05:00
Adam J. Stewart
e905ce16c9 Flake8 2016-08-11 10:28:34 -05:00
Adam J. Stewart
11e595089d Matplotlib overhaul 2016-08-11 10:28:33 -05:00
Adam J. Stewart
b47357d73c Add patch for Intel compilers 2016-08-11 10:22:47 -05:00
Adam J. Stewart
5fc20487e4 Flake8 and formatting changes 2016-08-11 10:22:47 -05:00
Adam J. Stewart
534e1cbf1b Some tests don't pass with Intel compilers 2016-08-11 10:20:08 -05:00
Adam J. Stewart
ee5e20dae3 Add dependencies to libarchive and cmake 2016-08-11 10:17:42 -05:00
Adam J. Stewart
58d7704060 Overhaul of compression libraries 2016-08-11 10:15:13 -05:00
Todd Gamblin
e6a122417a Merge pull request #1491 from eschnett/eschnett/curl 
Update curl to 7.50.1
 2016-08-11 03:04:07 -07:00
Todd Gamblin
84e331c586 Remove unneeded noqa comments. 2016-08-10 16:33:39 -07:00
Todd Gamblin
240f1fd223 Spack packages now PEP8 compliant. 2016-08-10 16:33:39 -07:00
Erik Schnetter
158deae625 Update curl to 7.50.1 2016-08-10 13:51:57 -04:00
Matt Belhorn
2be065418b Openssl package should not require openssl (https) to obtain source. 2016-08-09 15:57:07 -04:00
alalazo
38dcd6bce9 qa : flake8 issues 2016-08-09 09:54:24 +02:00
alalazo
5362864cc9 plumed : fixed name clash on attribute 2016-08-09 09:24:36 +02:00
Massimiliano Culpo
15d9fb1879 plumed : adding dependents 
* cp2k : added plumed
* gromacs : patched pme load balancing
* gromacs : added plumed
 2016-08-09 09:23:53 +02:00
becker33
3ea1325620 Merge pull request #1345 from hartzell/feature/add-perl-dependency-to-git 
Add depends_on('perl'), depends_on('pcre') to git package
 2016-08-08 09:44:50 -07:00
Todd Gamblin
dd30066feb Merge pull request #1449 from hartzell/feature/add-package-for-prank 
Add package for prank and supporting tools
 2016-08-07 23:43:40 -07:00
Todd Gamblin
e65a8b6a9a Merge pull request #1463 from davydden/pkg/opium 
opium: add new package
 2016-08-07 15:56:27 -07:00
Todd Gamblin
8121ac2c27 Merge pull request #1464 from hartzell/feature/update-lmod 
No need to patch Lmod after 6.4.4
 2016-08-07 15:55:16 -07:00
Todd Gamblin
93f5a750cb Merge pull request #1465 from glennpj/pango_url 
Add list_url to pango package
 2016-08-07 15:55:04 -07:00
Todd Gamblin
281f6f18e1 Merge pull request #1466 from pramodk/develop 
PDT should download full installer package
 2016-08-07 15:54:50 -07:00
Denis Davydov
db87a9d3ce tar: fix 1.28 on macOS; add 1.29 (#1462) 2016-08-07 15:54:01 -07:00
Adam J. Stewart
d7329d7bc2 Fix erroneously stripped trailing whitespace in patch (#1467) 2016-08-07 15:53:25 -07:00
Pramod Kumbhar
e9edfec0ec PDT should download full installer package pdtoolkit-X.tar.gz (default pdt-X.tar.gz is only for x86 and cray) 2016-08-07 01:14:26 +02:00
Glenn Johnson
2ad21e7070 Add list_url to pango package 
Added a `list_url` so the updated pango tar file can be retrieved.
 2016-08-06 18:12:47 -05:00
George Hartzell
09d96bef9f No need to patch Lmod after 6.4.4 
The Lmod author changed the src so that it uses the tclsh (and shared
libraries) discovered at configure time.  He did it differently that I
did in this patch, but he changes solve our problem too, so...
 2016-08-06 17:39:05 -04:00
George Hartzell
9ebbde0e01 Make configure use our gettext library 
The configure script needs extra encouragement to link against our
gettext/libintl library.
 2016-08-06 16:28:47 -04:00
George Hartzell
1de5817b58 Clean up rebase problems 
My rebase duplicated the depends_on('zlib') and dropped the --with-curl
from the configure.

This fixes those.
 2016-08-06 16:28:47 -04:00
George Hartzell
f699d7c08e [Whitespace] Gather the depends_on's together. 2016-08-06 16:28:47 -04:00
George Hartzell
152fa33a55 Call configure --with-libpcre=... to use our pcre 
An earlier commit claimed that this package depends_on('pcre') but I
didn't fix the call to configure that enabled it.

This fixes that.
 2016-08-06 16:28:47 -04:00
George Hartzell
3cf2fd40a8 Enable depends_on('pcre') also 
While I have the patient on the operating table, @adamjstewart asked
me to uncomment and test the depends_on('pcre').

Did it and it Works For Me(tm).
 2016-08-06 16:28:47 -04:00
George Hartzell
653905e3a2 Add depends_on('perl') to git package 
This commit changes the git package to depend_on('perl').  The system
perl is not always sufficient to install git (e.g. a CentOS7 system with
the development tools group installed has perl but not the
ExtUtils::MakeMaker package that git needs) and one can't always update
the system's perl.

This PR depends_on PR #1339, which adds a perl package to spack.
 2016-08-06 16:28:47 -04:00
George Hartzell
f800708ef3 Switch to using *std_cmake_args 2016-08-06 16:27:40 -04:00
George Hartzell
6a62a6b693 Flake8 whitespace cleanup 2016-08-06 16:27:40 -04:00
George Hartzell
a07a0ef54b Add Bio++ tool suite and supporting libs 
Add the Bio++ suite and its supporting libraries.
 2016-08-06 16:27:40 -04:00
George Hartzell
3c81bb44ba Add package for mafft 2016-08-06 16:27:40 -04:00
George Hartzell
e0db1f0268 Add package for exonerate 2016-08-06 16:27:40 -04:00
George Hartzell
9e16902397 Fix name of bpp-suite (missing -...) 2016-08-06 16:27:40 -04:00
George Hartzell
63592096c5 Add package for prank 2016-08-06 16:27:40 -04:00
Denis Davydov
4983ebcf7c opium: add new package 2016-08-06 21:35:52 +02:00
becker33
d3f115933e Merge pull request #1451 from hartzell/feature/add-package-for-fastx_toolkit 
Add package for fastx toolkit
 2016-08-05 15:09:46 -07:00
becker33
18d155e713 Merge pull request #1452 from hartzell/feature/add-package-for-samtools 
Add package for samtools
 2016-08-05 15:09:41 -07:00
George Hartzell
a6afaeb974 Remove lingering FIXME commentary 2016-08-05 17:51:24 -04:00
George Hartzell
769408130a Samtools depends on htslib from 1.3.1 onward 
Samtools used to (before 1.3.1) include it's own copy of htslib.  Going
forward, it needs to use the standalone htslib.
 2016-08-05 17:47:11 -04:00
becker33
8e20a14945 Merge pull request #1453 from hartzell/feature/add-package-for-seqtk 
Add package for seqtk
 2016-08-05 10:25:19 -07:00
becker33
f403f256ca Merge pull request #1450 from hartzell/feature/add-package-for-bwa 
Add package for bwa
 2016-08-05 10:21:10 -07:00
becker33
594a6710ed Merge pull request #1442 from suraia/update-scorep-2.0 
Update Score-P to 2.0

Most likely this can be generalized to link against older versions of dependencies, but it looks good for now.
 2016-08-05 08:57:25 -07:00
George Hartzell
d6dedee6ff Flake8 cleanup 2016-08-04 15:23:04 -04:00
Bruno Turcksin
0c02ee86a7 Add Trilinos 12.6.4 (#1447) 2016-08-04 11:29:10 -07:00
George Hartzell
e12d7aadda Add package for seqtk 
Seqtk is a tool for working with fast[aq] files.
 2016-08-04 14:18:03 -04:00
George Hartzell
fd11db92e1 Add package for bcftools 2016-08-04 14:18:03 -04:00
George Hartzell
ba0577dc96 Update samtools to support v1.3.1 
Update the samtools package to support v1.3.1, which
- now uses configure script; and
- now depends on external htslib package.

The dependency on mpc seems to have been bogus, it's never linked in,
nor is it mentioned in the source tree.  I *do* have a version in
/usr/lib64, but ldd does not sure it being linked in either....

By depending on 'ncurses' I can do away with the need for the patch.
 2016-08-04 14:18:03 -04:00
George Hartzell
ef1369c365 Add package for htslib 
Htslib was pulled out of samtools and made into a standalone thing.
This commit adds a packag for it, in support of the samtools package.
 2016-08-04 14:18:03 -04:00
George Hartzell
e17862c421 Add package for fastx toolkit 
Tools for working with FASTA/FASTQ files.
 2016-08-04 14:18:02 -04:00
George Hartzell
d5bb2955b1 Add package for libgtextutils 
Gordon's Text utils Library, in support of fastx toolkit.
 2016-08-04 14:18:02 -04:00
George Hartzell
d4274b32f2 Make flake8 happy (long lines) 2016-08-04 14:18:01 -04:00
Michael Kuhn
d7665a63e3 flake8 fixes 2016-08-04 19:04:48 +02:00
becker33
1ac1cc3d2c Merge pull request #1437 from jgalarowicz/update-xercesc 
Update the version of xerces-c, where the developers remove the old v…
 2016-08-04 09:00:36 -07:00
becker33
3c6f6fc811 Merge pull request #1438 from jgalarowicz/update-libmonitor 
Update libmonitor to use its new github location, it does not exist w…
 2016-08-04 08:59:35 -07:00
becker33
cabcdf0ec9 Merge pull request #1443 from davydden/pkg/dealii_python 
dealii: add optional python bindings
 2016-08-04 08:43:36 -07:00
becker33
fcc8b1d3e4 Merge pull request #1431 from hartzell/feature/add-package-for-unison 
Add package for unison (and ocaml)
 2016-08-04 08:41:45 -07:00
Denis Davydov
af8741c23c dealii: add optional python bindings 2016-08-04 16:11:14 +02:00
Michael Kuhn
584e5506f2 Update Score-P to 2.0 2016-08-04 14:24:25 +02:00
Todd Gamblin
b7fa2c4e21 Fix #1429: Remove git dep from gettext; break circular dependency. 
- It's not really a circular dependency -- git is a run dependency of gettext

- We can revert this change when Spack is smart enough to make git a run
  dependency and build it.
 2016-08-03 21:53:53 -07:00
Jim Galarowicz
2e1dbd0697 Fix flake8 errors for: Update libmonitor to use its new github location, it does not exist where the package file now points to. 2016-08-03 21:32:15 -05:00
Jim Galarowicz
e69423a154 Fix flake8 errors for Update the version of xerces-c, where the developers remove the old version, so there is no fallback. 2016-08-03 21:28:56 -05:00
Jim Galarowicz
e68b7d8c63 Update libmonitor to use its new github location, it does not exist where the package file now points to. 2016-08-03 21:08:48 -05:00
Jim Galarowicz
638f779841 Update the version of xerces-c, where the developers remove the old version, so there is no fallback. 2016-08-03 21:04:17 -05:00
George Hartzell
43371c31a2 Flake8 cleanup 2016-08-03 16:51:53 -04:00
Todd Gamblin
dce105d16f Merge pull request #1382 from KineticTheory/gktplus3-deps 
GTK+3: Provide updates to package dependencies.
 2016-08-03 13:45:18 -07:00
George Hartzell
4acf6d76bf Add package for unison 
Add package for unison (the file synchronizer).

Needs the ocaml compiler to build.
 2016-08-03 16:41:31 -04:00
George Hartzell
a7bfaa3797 Add package for ocaml compiler 
Installs the ocaml compiler.
 2016-08-03 16:41:31 -04:00
Kelly (KT) Thompson
7c46a4c0e4 Provide minor updates after code review 
+ Always depend on the gettext package. This simplifies the logic and I no
  longer need to 'import sys'
+ Only apply the patch for the older version of glib.
 2016-08-03 13:26:02 -06:00
becker33
3e6ebd577f Merge pull request #1378 from LLNL/bugfix/gh-1324-intel-parallel-studio 
Bugfix/gh 1324 intel parallel studio
 2016-08-03 10:46:40 -07:00
becker33
353726f08f Merge pull request #1156 from adamjstewart/features/py-meep 
Add py-meep package and dependencies

Merging to add the gettext support, will submit a separate issue for the LD_LIBRARY_PATH issue with MPI and py-meep
 2016-08-03 10:07:05 -07:00
becker33
b9195b415a Merge pull request #1420 from epfl-scitas/packages/plumed 
plumed : added package
 2016-08-03 08:36:31 -07:00
alalazo
2f1c000f62 qa : flake8 issues 2016-08-03 08:26:58 +02:00
Kelly (KT) Thompson
d7d12aa2dc One more formatting change to make flake8 happy. 2016-08-02 19:05:48 -06:00
becker33
48997cffa1 Merge pull request #1233 from hartzell/add-nextflow 
First cut package for nextflow, has issues
 2016-08-02 11:52:19 -07:00
Denis Davydov
f90692cf81 arpack-ng: fix blas/lapack libraries 2016-08-02 20:27:34 +02:00
becker33
b5a117c923 Merge pull request #1366 from hartzell/feature/add-package-for-ack 
Add package for ack
 2016-08-02 10:11:11 -07:00
becker33
1534a115bd Merge pull request #1421 from hartzell/feature/add-package-for-texlive 
Add package for texlive
 2016-08-02 10:10:43 -07:00
becker33
a03a35565e Merge pull request #1339 from hartzell/features/add-perl 
Add perl package
 2016-08-02 10:10:04 -07:00
George Hartzell
fa70a837d4 Remove accidentally committed cabal-install bits 2016-08-02 13:00:47 -04:00
becker33
91004158c6 Merge pull request #1243 from davydden/pkg/atlas_urls 
atlas: fix urls and shared libs
 2016-08-02 09:59:05 -07:00
becker33
3f26bbc8b3 Merge pull request #864 from davydden/kdiff3 
kdiff3: initial version of the package
 2016-08-02 09:35:00 -07:00
becker33
a3322fab0a Merge pull request #1360 from glennpj/pysetuptoolsdep 
Add py-setuptools dependencies to packages
 2016-08-02 09:33:40 -07:00
becker33
21158195fb Merge pull request #1354 from paulhopkins/bugfix/preferred_variants_do_not_recognise_-variant 
Bugfix/preferred variants do not recognise  -variant
 2016-08-02 09:15:06 -07:00
George Hartzell
74a181febc Remove local copy of cpanm installer 
This is handled as a resource in the package now.
 2016-08-02 12:13:24 -04:00
George Hartzell
4c8672ed1f Add previous versions back into package 
Following the advice of @glennpj, added the old versions back into the
packages.

I can install the current packages and the previous packages.
 2016-08-02 11:45:16 -04:00
George Hartzell
c77425bb22 Remove useless def unpack 
Before I learned that I was stumbling over a real but (#1308), I thought
I needed to arrange for the fetcher to skip the unpack step.

This commit removes the useful `def unpack`.
 2016-08-02 11:32:19 -04:00
George Hartzell
a6605d842b Flake8 cleanup. 2016-08-02 11:25:03 -04:00
George Hartzell
f2f5f6c279 Touch up variant comment 2016-08-02 11:18:50 -04:00
George Hartzell
c994565c62 Use "resource" machinery to manage cpanm tarball 
Use the resource machinery to fetch/cache/unpack/... the App::cpanminus
tarball.

- this hardcodes the version, I can't figure out how to use a variant to
  hold/set the value and access it in the resource().
- change up the install to use the `with working_dir()` meme.
 2016-08-02 11:16:46 -04:00
George Hartzell
1b9becc541 Add the std spack header to perl/package.py 
Stole the example header from antlr/package.py, included it at the top
of perl/package.py.
 2016-08-02 11:16:46 -04:00
George Hartzell
08ff7b65af Make running perl's tests conditional 
Make running perl's tests conditional, one must now specify the
`--run-tests` flag to the `spack install` command in order to run the
tests.

On one system (8 core, 16GB Digital Ocean Droplet), installing without
tests takes 3 minutes, with tests takes 16 minutes.
 2016-08-02 11:16:46 -04:00
George Hartzell
4d72e0fb9d Make the cpanm version a variant 
Rather than hard-coding the verison of `cpanm` that's [optionally]
installed into the core, make it a variant with a default value of
'1.7042'.

Also discovered that `prefix + 'bin'` is the same as `prefix.bin`, so
embetter that bit of code.
 2016-08-02 11:16:46 -04:00
George Hartzell
a5a4525bed Add perl package 
Add perl package, based on [work by
justintoo](https://github.com/LLNL/spack/pull/105).  He had too many
things pulled into that pull request, this just adds a perl package.

Support the current releases on the past three minor branches.

Run perl's tests before installing.

Install cpanm into the core (makes building on top of this perl *much*
simpler).  Controlled by a variant.
 2016-08-02 11:16:46 -04:00
George Hartzell
949621eb7f Add package for texlive 2016-08-02 11:15:42 -04:00
George Hartzell
857a03c127 Ack should depends_on('perl') 
Add a depends_on('perl') and rewrite the script's `#!` line to refer to
that Perl's `perl` executable.
 2016-08-02 11:11:05 -04:00
George Hartzell
114da813a3 Remove unnecessary imports. 
Now that it's sporting a cleaner install method, these imports are
unnecessary.
 2016-08-02 11:11:05 -04:00
George Hartzell
bf467c5df3 Remove override of unpack(self) 
I cargo culted that from my *nextflow* package.  I [thought I] needed it
to work around Spack trying to use tar to unpack something that was
neither a tar ball nor unpackable.

This package works fine without it.  In retrospect, the error that I was
seeing in the *nextflow* package was probably this problem #1308.
 2016-08-02 11:11:05 -04:00
George Hartzell
6c3623422f Use cleaner mech to install script 
Use @adamjstewart's nicer bit of python code in the
install method.
 2016-08-02 11:11:05 -04:00
George Hartzell
63121a0c49 Add package for ack 
Add a package for [ack](http://beyondgrep.com/install/).  Simply install
the fatpacked script.

It uses '#!/usr/bin/env perl' and it very much not choosy about what
perl it needs.  For now just trust that there's one available, perhaps
someday we can/should uncomment the depends_on('perl').

Follows the methodolgy I used in nextflow.  Has the same
uninstall/install problem that nextflow has, there is an issue in
progress for that: https://github.com/LLNL/spack/issues/1308.

Tested on CentOS7.
 2016-08-02 11:11:05 -04:00
George Hartzell
12d1263980 Update several R packages (r-shiny prereqs) 
r-jsonlite 0.0.21 -> 1.0
r-mime     0.4    -> 0.5
rcpp       0.12.5 -> 0.12.6

CRAN is funny.  The older versions of these packages are still available
in package specific directories but the current version is not there, so
I don't see any way to make the older versions work.
 2016-08-02 11:10:41 -04:00
George Hartzell
6f332c7e4c Fix whitespace, make flake8 happ{y,ier}. 2016-08-02 11:10:12 -04:00
George Hartzell
bfcec69630 Add standard header, use spack helpers 
Added the standard header (stolen from R).

Touched up the install to use set_executable rather than doing it
myself.
 2016-08-02 11:10:12 -04:00
George Hartzell
4373a2b629 First cut package for nextflow, has issues 
This is my first cut at a package to support nextflow.  It's also my
first package.  It works, but has issues.  I'm going to submit a pull
request and get some coaching on how to deal with it.

One issue particular: if I install, then uninstall, then try to install
again (which uses the cached copy of the "distribution file"), it
explodes.
 2016-08-02 11:10:12 -04:00
Glenn Johnson
a57d94af03 Fix flake8 issues. 2016-08-02 09:53:57 -05:00
Denis Davydov
a1703bf70d kdiff3: add license block 2016-08-02 16:37:14 +02:00
Gilles Fourestey
dea7bbb4a0 added plumed 
* plumed : first version
* plumed : added dependencies and docs
 2016-08-02 15:06:46 +02:00
Denis Davydov
565bd5f51e atlas: revert to lapack 3.5.0 2016-08-02 13:52:32 +02:00
Denis Davydov
bef7e2645a atlas: flake8 fixes 2016-08-02 13:52:32 +02:00
Denis Davydov
f6a4a6b00f atlas: add install_test 2016-08-02 13:52:32 +02:00
Denis Davydov
0c0b37800d atlas: set (blas|lapack)_shared_lib 2016-08-02 13:52:32 +02:00
Denis Davydov
4ecf481337 atlas: fix shared libs; set compilers 2016-08-02 13:52:32 +02:00
Denis Davydov
6f7e12d49b atlas: fix urls and use lapack 3.6.0 2016-08-02 13:52:32 +02:00
Denis Davydov
0aa513ad70 libxau: mark pkg-config as build-type dependency 2016-08-02 13:50:46 +02:00
Denis Davydov
450c750214 kdiff3: initial version of the package 2016-08-02 13:49:40 +02:00
Denis Davydov
a4e59c2758 libxau: add missing dependency 2016-08-02 13:49:40 +02:00
Kelly (KT) Thompson
9433e84776 Formatting changes for flake8. 2016-08-01 22:54:51 -06:00
Kelly (KT) Thompson
17f0eb5148 Provide correct download urls and additional dependencies. 2016-08-01 22:10:54 -06:00
ba11f19efc Merge remote-tracking branch 'upstream/develop' into gktplus3-deps 2016-08-01 20:50:28 -06:00
becker33
b892cebe8a Merge pull request #1343 from glennpj/r_unfilter 
R extension dependencies with compiler wrapper
 2016-08-01 13:51:13 -07:00
becker33
e861e35acf Merge pull request #1234 from mwilliammyers/package-opencv 
Update opencv package
 2016-08-01 13:44:31 -07:00
becker33
1847aa035d Merge pull request #1348 from glennpj/rcurl 
r-curl update and changed remote archive
 2016-08-01 13:38:38 -07:00
becker33
94238eebfa Merge pull request #1381 from davydden/pkg/mkl_linux 
MKL linux fixes
 2016-08-01 13:36:10 -07:00
becker33
dc9fcea989 Merge pull request #1365 from hartzell/feature/add-package-for-tree 
Add package for tree
 2016-08-01 13:21:09 -07:00
becker33
15514792d5 Merge pull request #1374 from hartzell/bug/fix-jdk-import-of-distutils 
Bug: fix jdk package's use of distutils
 2016-08-01 13:20:44 -07:00
becker33
851bc506e4 Merge pull request #1367 from adamjstewart/features/pgi 
Add latest version of PGI
 2016-08-01 13:07:35 -07:00
becker33
932300256c Merge pull request #1413 from mdevlin1/fixes/libxsmm 
Fixed libxsmm package
 2016-08-01 13:06:05 -07:00
becker33
6361f5c2d4 Merge pull request #1359 from sknigh/libhio 
added libhio package
 2016-08-01 13:05:29 -07:00
Mitchell Devlin
2d51ea5da4 fixed libxsmm makefile filter 2016-08-01 14:38:16 -05:00
Adam J. Stewart
fed7ba1dab Add latest version of PGI 2016-08-01 13:42:00 -05:00
Adam J. Stewart
ab885a5397 Allow git to depend on gettext now that it works 2016-08-01 13:35:22 -05:00
Adam J. Stewart
4014a29d2b Use proper deptype so that spack activate works 2016-08-01 13:35:22 -05:00
Adam J. Stewart
f5aed63b0b pkg-config should be a build dependency only 2016-08-01 13:35:22 -05:00
Adam J. Stewart
5cac0a528c Fix undefined symbols by building shared libraries 2016-08-01 13:35:22 -05:00
Adam J. Stewart
bdb64c2e39 Tell MEEP where to find libctl 2016-08-01 13:35:22 -05:00
Adam J. Stewart
0903ae0599 Final fixes to get libctl working 2016-08-01 13:35:22 -05:00
Adam J. Stewart
1e3a5d4e26 Final fixes to get guile to build 2016-08-01 13:35:21 -05:00
Adam J. Stewart
6db99a4fe7 Rename gc => bdw-gc, fix libunistring bug 2016-08-01 13:35:21 -05:00