hlrs-software-stack/spack
7
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity
4457 commits 3 branches 52 tags 188 MiB
Commit graph

2360 commits

Author SHA1 Message Date
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
Adam J. Stewart
5b1a882fc2 Update meep's url_for_version 2016-08-01 13:35:21 -05:00
Adam J. Stewart
a2578c21e4 Supply flags to bdist 2016-08-01 13:35:21 -05:00
Adam J. Stewart
8d0758fc4c Allow py-meep to link properly 2016-08-01 13:35:21 -05:00
Adam J. Stewart
880cbb2217 Better testing for MEEP 2016-08-01 13:35:21 -05:00
Adam J. Stewart
3b4820f290 Patch pkg-config and update installs for various packages 2016-08-01 13:35:21 -05:00
Adam J. Stewart
9e05fdf4a1 Bug fixes 2016-08-01 13:35:20 -05:00
Adam J. Stewart
7e53f4328f Add py-meep package and dependencies 2016-08-01 13:35:20 -05:00
George Hartzell
7d303afd64 Address flake8 issue 2016-08-01 13:42:55 -04:00
George Hartzell
1552ed943a Add package for cask 
Add a package for cask, the emacs project/dependency management tool.

Based on [Homebrew's formula][brew].

[brew]: https://github.com/Homebrew/homebrew-core/blob/master/Formula/cask.rb
 2016-08-01 13:41:28 -04:00
George Hartzell
31b7580b76 Fix jdk package's use of distutils 
See issue #1364.  @citibeth's fix works fine.
 2016-08-01 13:33:27 -04:00
becker33
cc3fc2ba4c Merge pull request #1322 from mdevlin1/feature/libxsmm 
Add libxsmm package
 2016-08-01 09:56:09 -07:00
Paul Hopkins
cca240c8f9 Add concretize_preferences tests 2016-08-01 16:18:11 +01:00
alalazo
ec09dfe5d1 cp2k : added package 2016-08-01 10:41:33 +02:00
Todd Gamblin
fbbb82259a Merge pull request #1407 from glennpj/r-ncdf4 
New package - r-ncdf4
 2016-07-31 22:15:52 -07:00
Todd Gamblin
ea11aab71f Merge pull request #1406 from glennpj/r-np 
New package - r-np
 2016-07-31 22:15:37 -07:00
Todd Gamblin
2042c94a6c Merge pull request #1405 from glennpj/r-survey 
New package - r-survey
 2016-07-31 22:15:09 -07:00
Todd Gamblin
64be8a80b2 Merge pull request #1404 from glennpj/r-tarifx 
New package - r-tarifx
 2016-07-31 22:14:56 -07:00
Todd Gamblin
7185fe2876 Merge pull request #1403 from glennpj/r-e1071 
New package - r-e1071
 2016-07-31 22:14:40 -07:00
Todd Gamblin
0724eba935 Merge pull request #1402 from glennpj/r-plotrix 
New package - r-plotrix
 2016-07-31 22:14:25 -07:00
Todd Gamblin
441bb83682 Merge pull request #1401 from glennpj/r-gdata 
New package - r-gdata
 2016-07-31 22:13:50 -07:00
Todd Gamblin
2cffc90284 Merge pull request #1400 from glennpj/r-roxygen2 
New package - r-roxygen2
 2016-07-31 22:13:16 -07:00
Todd Gamblin
68cedd2599 Merge pull request #1399 from glennpj/r-testthat 
New package - r-testthat
 2016-07-31 22:12:06 -07:00
Todd Gamblin
d00fd06095 Merge pull request #1398 from glennpj/r-xml 
New package - r-xml
 2016-07-31 22:11:38 -07:00
Glenn Johnson
8815f0a0b5 New package - r-ncdf4 
Interface to Unidata netCDF (version 4 or earlier) format data files.
 2016-07-31 17:12:29 -05:00
Glenn Johnson
bfd03db12a New package - r-np 
Nonparametric kernel smoothing methods for mixed data types.
 2016-07-31 16:18:55 -05:00
Glenn Johnson
f14eb07dc1 New package - r-survey 
Analysis of complex survey samples.
 2016-07-31 15:50:19 -05:00
Glenn Johnson
a9cc6a7d08 New package - r-tarifx 
A collection of various utility and convenience functions.
 2016-07-31 15:39:09 -05:00
Glenn Johnson
be2f2e42db New package - r-e1071 
Misc functions of the Department of Statistics, Probability Theory Group
(Formerly: E1071), TU Wien.
 2016-07-31 15:26:13 -05:00
Glenn Johnson
05e5276aec New package - r-plotrix 
Various plotting functions.
 2016-07-31 15:15:55 -05:00
Glenn Johnson
dbf799bbf9 New package - r-gdata 
Data manipulation tools.
 2016-07-31 15:07:40 -05:00
Glenn Johnson
f39e570f36 New package - r-roxygen2 
In-source documentation for R.
 2016-07-31 14:52:16 -05:00
Glenn Johnson
58a6039c0a New package - r-testthat 
A unit testing system for R.
 2016-07-31 14:40:46 -05:00
Glenn Johnson
0662b953f0 New package - r-xml 
Tools for parsing and generating XML within R and S-Plus.
 2016-07-31 14:25:17 -05:00
Glenn Johnson
1b04b8be01 New package - r-datatable 
Extension of Data.frame
 2016-07-31 14:11:04 -05:00
Todd Gamblin
173a16b38a Merge pull request #1396 from glennpj/r-quantmod 
New package - r-quantmod
 2016-07-30 20:15:53 -07:00
Todd Gamblin
68ba5377c1 Merge pull request #1395 from glennpj/r-ggmap 
New package - r-ggmap and dependencies
 2016-07-30 20:14:57 -07:00
Todd Gamblin
253507c0c3 Merge pull request #1394 from glennpj/r-maps 
New package - r-maps
 2016-07-30 20:14:27 -07:00
Todd Gamblin
7684652ce3 Merge pull request #1393 from glennpj/r-maptools 
New package - r-maptools
 2016-07-30 20:14:19 -07:00
Todd Gamblin
b12dc34ba7 Merge pull request #1391 from glennpj/r-caret 
New package - r-caret
 2016-07-30 20:14:09 -07:00
Todd Gamblin
9c31ee8a75 Merge pull request #1390 from glennpj/r-glmnet 
New package - r-glmnet
 2016-07-30 20:13:50 -07:00
Todd Gamblin
ae5ba2b110 Merge pull request #1389 from glennpj/r-vcd 
New package - r-vcd
 2016-07-30 20:13:05 -07:00
Todd Gamblin
13499f1655 Merge pull request #1388 from glennpj/r-multcomp 
New package - r-multcomp
 2016-07-30 20:12:51 -07:00
Todd Gamblin
49e9f365d8 Merge pull request #1387 from glennpj/r-randomforest 
New package r-randomforest
 2016-07-30 20:12:21 -07:00
Glenn Johnson
41cd861861 New package - r-quantmod 
Qualitative Financial modelling framework.
 2016-07-30 18:25:43 -05:00
Glenn Johnson
2913aa8d09 New package - r-ggmap and dependencies 
Spatial visualization with ggplot2
 2016-07-30 18:14:02 -05:00
Glenn Johnson
1bd2def41e New package - r-maps 
Draw geographical maps.
 2016-07-30 17:34:07 -05:00
Glenn Johnson
386f0e577a New package - r-maptools 
Tools for reading and handling spatial objects.
 2016-07-30 17:26:31 -05:00
Glenn Johnson
7207ce2a18 New package - r-caret 
Classification and Regression Training
 2016-07-30 16:53:54 -05:00
Glenn Johnson
20e52e5052 New package - r-glmnet 
Lasso and Elastic-Net Regularized Generalized Linear Models
 2016-07-30 16:38:00 -05:00
Glenn Johnson
e9944150a5 New package - r-vcd 
Visualizing Categorical Data
 2016-07-30 16:28:43 -05:00
Glenn Johnson
fc1804974c New package - r-multcomp 
Simultaneous Inference in General Parametric Models.
 2016-07-30 16:09:57 -05:00
Glenn Johnson
12167e8f37 New package r-randomforest 
Breiman and Cutler's Random Forests for Classification and Regression.
 2016-07-30 15:39:28 -05:00
Glenn Johnson
8dc26bbcd9 Have R extensions build in parallel. 
Set `MAKEFLAGS` so R extensions can be built in parallel if that is set
in spack.
 2016-07-30 15:20:14 -05:00
Glenn Johnson
ee7acc6b13 New package r-car 
Companion to Applied Regression.
 2016-07-30 15:10:25 -05:00
Kelly (KT) Thompson
6c80b15220 GTK+3: Provide updates to package dependencies. 
WIP: I started trying to build gtkplus@3.20, but this package has many more
dependencies than v2 and it requires newer versions of existing packages. This
commit provides updates for 5 packages that are required by GTK+3. This is not
the complete set of changes required for GTK+3.

atk  - move default version from 2.14 -> 2.20.
glib - move default version from 2.42 -> 2.49
     - v2.49 requires pcre+utf as a new dependency.
pcre - if variant +utf is selected, add '--enable-unicode-properties' to the
       configure options.
libepoxy - new package to spack
         - manages OpenGL function pointers.
pango    - move default version from 1.36 -> 1.40
 2016-07-29 09:05:44 -06:00
Denis Davydov
aad5a4c4b3 mkl: flake8 fixes; minor docu update 2016-07-29 14:12:07 +02:00
Denis Davydov
b6ce0e6f0e trilinos: make sure hdf5 is picked up from Spack 2016-07-29 13:11:12 +02:00
Denis Davydov
943896e237 trilinos: fix lapack lib dir 2016-07-29 13:09:34 +02:00
Denis Davydov
8ee4df8101 hypre: minor cleanup related to blas/lapack 2016-07-29 11:37:19 +02:00
Denis Davydov
572f1cd427 mkl: symlink libs to prefix.lib 2016-07-29 11:36:37 +02:00
Todd Gamblin
e04662f84f Merge pull request #1344 from LLNL/bugfix/py-nose-nosetests 
do not ignore nosetests script in py-nose
 2016-07-28 10:19:13 -07:00
becker33
5caaa2cd75 Merge pull request #1331 from adamjstewart/fixes/mvapich2 
MVAPICH2 depends on libpciaccess
 2016-07-28 09:52:51 -07:00
becker33
3759f62cba Merge pull request #1235 from davydden/pkg/p4est_run_tests 
p4est: use run_tests instead of a variant
 2016-07-27 18:36:36 -07:00
George Hartzell
f855cf6bab Add package for tree 
Add a package for [tree](http://mama.indstate.edu/users/ice/tree/).

It has a Makefile that hardcodes a prefix and some CFLAGS.  Used
filter_file to:

- set the make variable *prefix* to `prefix`; and
- comment out their CFLAGS, just use ours....

It installs, runs on CentOS7, and uninstalls cleanly.
 2016-07-27 11:32:03 -04:00
Todd Gamblin
458deaae5e Merge pull request #1350 from adamjstewart/fixes/openssl 
Fix OpenSSL url_for_version
 2016-07-27 08:08:00 -07:00
Greg Lee
e4525e57bb intel parallel studio itac fixes 2016-07-25 14:02:15 -07:00
Greg Lee
dba384108b intel parallel studio setup mkl environment 2016-07-25 14:01:49 -07:00
Samuel Knight
a2d4dcc636 Added libhio package 2016-07-25 17:32:03 +00:00
becker33
969e785d94 Merge pull request #1352 from glennpj/r_googlevis 
New package - r-googlevis
 2016-07-25 10:25:47 -07:00
becker33
5b7ec8de95 Merge pull request #1351 from glennpj/r_htmlwidgets 
New packages - R htmlwidgets
 2016-07-25 10:25:19 -07:00
Glenn Johnson
eb865b0df2 Add py-setuptools as dependency 
With the addition of dependency types and with `py-setuptools` set as
type='build' there are more packages that need to have `py-setuptools`
added as a dependency.

This PR adds that dependency for the following packages:
- py-h5py
- py-networkx
- py-pytables
- py-scikit-image
 2016-07-25 11:23:09 -05:00
Glenn Johnson
81cd458c26 r-curl update and chaged remote archive 
This updates to the 1.0 version of r-curl. The remote archive directory
name also changed so change that here as well.
 2016-07-24 16:48:07 -05:00
Glenn Johnson
27986c9edf New packages - R htmlwidgets 2016-07-24 16:43:35 -05:00
Glenn Johnson
b7bf88c761 New package - r-googlevis 2016-07-24 16:38:36 -05:00
Adam J. Stewart
29278090eb Fix OpenSSL url_for_version 2016-07-24 15:19:27 -05:00
Glenn Johnson
a8855f48aa Add dependency type tp r- packages 
This PR adds the `nolink` dependency type to r- package dependencies.
This is needed due to the new dependency types in Spack. A couple of
packages were updated with new versions as well.
 2016-07-23 19:43:55 -05:00
Greg Lee
773bca159a do not ignore nosetests script in py-nose 2016-07-22 15:49:36 -07:00
Glenn Johnson
ec9959b152 R extension dependencies with compiler wrapper 
This commit introduces a mechanism to insure that R package dependencies
are built with the Spack compiler wrapper. A copy of Makeconf is made
before `filter_compilers` is called. This is then pointed to by the
R_MAKEVARS_SITE environment variable set up in
`setup_dependent_environment`. With this the normal compilers are used
outside of spack and the spack wrapper compilers are used inside of
spack.

This commit also standardizes on the `join_path` call. It also sets the
commented build command to reflect what is actually used with the newer
string formatting.
 2016-07-22 17:05:01 -05:00
Adam J. Stewart
1be486c90a Add CGNS package 2016-07-22 17:02:45 -05:00
Todd Gamblin
395c616a48 Merge pull request #950 from xjrc/packages/python 
Enhancement Proposal: Make Python Spack Installs Ignore User Configuration
 2016-07-22 13:56:19 -07:00
Joseph Ciurej
fa92f58167 Adding temporary script that fixes all Python extensions w/ 'setup_py'. 2016-07-22 11:17:19 -07:00
Joseph Ciurej
ac2e0962ce Improved the build flag construction code in the python install method. 2016-07-22 11:12:02 -07:00
Joseph Ciurej
fb2d2303d6 Fixed a bug that was causing Python installs to be affected by user config. 2016-07-22 11:11:08 -07:00
Todd Gamblin
f5b4664c7c Merge pull request #1336 from glennpj/rcase 
Fix alpha case of dependencies for some r-packages
 2016-07-22 10:08:14 -07:00
Todd Gamblin
adffba5081 Merge pull request #1230 from hartzell/update-jdk 
Add URL and md5 for jdk-8u92.
 2016-07-21 22:06:29 -07:00
Glenn Johnson
e083c91d5e Fix alpha case of dependencies. 
A while ago I was asked to convert packages to all lowercase. That was
done but some dependencies did not get converted in the specification.
This commit fixes that as well as a couple of urls that need to be made
explicit and a missing dependency on jdk.
 2016-07-21 19:58:04 -05:00
Todd Gamblin
ed737cb2a2 Merge pull request #1333 from LLNL/features/no-openssl-pinging 
Remove remote website pinging from OpenSSL
 2016-07-21 16:46:59 -07:00
Todd Gamblin
488550c2e6 Merge pull request #1334 from hartzell/add-gcc-5.4.0 
Update gcc package with info about gcc-5.4.0
 2016-07-21 16:37:31 -07:00
Todd Gamblin
8523f75e6c Remove remote website pinging from OpenSSL 
- OpenSSL no longer checks remote versions on the openssl site.

- Spack is used on systems that aren't connected to the internet, and
  this check is probably in the wrong place and affects too many
  commands.  We can work on figuring out a better, more configurable
  place to put a check like this.
 2016-07-21 16:35:20 -07:00
George Hartzell
4efe022165 Update with info about gcc-5.4.0 2016-07-21 15:36:22 -04:00
Mitchell Devlin
796308ed85 edit 2016-07-21 13:39:27 -05:00
George Hartzell
4c105895ab Fix flake8 violations 2016-07-21 14:24:51 -04:00
George Hartzell
9523e50732 Fix shebang line in tcl scripts 
Lmod's configure script goes to the trouble of finding
tclsh.  This change uses that info to rewrite the #! lines
in the tcl scripts so that they call the tclsh that the
configure script discovered.

It needs to massage the existing shebang lines into something
that the sed statement in the makefile can manipulate and
it needs to add the path_to_tclsh info into the set of sed
statements.

Checked with versions 6.4.1 and 6.3.7 (the checksum for 6.0.1 is
incorrect, a fix for another time).
 2016-07-21 13:58:16 -04:00
George Hartzell
52f0249c61 tcl is actually a runtime dependency. 
lmod uses tclsh at runtime, so adjust the depends_on accordingly
(thanks @davydden!).
 2016-07-21 13:51:03 -04:00
George Hartzell
a27cb639d8 The lmod package should depend_on('tcl') 
The lmod package needs a tclsh.  Up until now it just assumed
that one was available on the system.

This change adds a depends_on('tcl') to the lmod package.

The tcl package installs a tclsh script with an embedded version
number (e.g. tclsh8.6) but the lmod configuration looks for tclsh.
This change extends the tcl package to symlink tclshX.Y to tclsh in
the tcl package bin directory.
 2016-07-21 13:51:03 -04:00
Adam J. Stewart
cf8f14780f MVAPICH2 depends on libpciaccess 2016-07-21 11:13:17 -05:00
Glenn Johnson
ead1b93f75 MPI related changes 
- Redid the code for setting the itac symlink for the cluster edition.
- Removed the *PATH variables for MPI to avoid a conflict with other MPI
  environment modules.
- Added missing test for `+all` when checking variants.
 2016-07-20 20:03:05 -05:00
Glenn Johnson
0be4c7dfbd Changes as discussed in PR review 
- removed unneeded entry for `debugger/gdb/intel64_mic`
- set `+mpi` directory name to impi
 2016-07-20 20:03:05 -05:00
Glenn Johnson
5e5e36a659 Fix flake8 errors. 2016-07-20 19:54:35 -05:00
Glenn Johnson
16f67b5bb1 Setup environment for Intel Parallel Studio 
Set up the environment for the Intel compilers and tools. This commit
does the following:

- Unset variables that were incorrect from the auto guess prefix
  inspections.
- Add a RemovePath environment_modifications_formats for dotkit.
- Set the module environment variables appropriate for the different
  variants.
- Change the component logic so that the '+all' variant works. It was
  getting split by letter and leaving COMPONENTS empty.
- Added a variant checking function.
- Added NONRPM_DB_DIR to the silent.cfg so that the product database
  goes to the installation directory.
- With the product database in prefix the code to remove the product
  database file from the home directory is no longer needed and was
  removed.
- Reformat the 'tools' variant description.

There are probably more variables needed for the '+tools' for the
'professional' product version but I do not have access to that.
 2016-07-20 19:54:35 -05:00
mwilliammyers
b8444aa518 Merge remote-tracking branch 'upstream/develop' into package-opencv 
* upstream/develop: (126 commits)
  Fix indent/flake8 error.
  openexr : Add new package
  Set environment variables
  Added gnu packages datamash, parallel, and screen
  added package as argument to setup_platform_environment
  ilmbase : Add new IlmBase package
  Documented linker default
  fixed flake errors
  removed commented-out code
  Set default link type to dynamic on cray. Includes hooks for platform-based environment changes
  fixed flake errors
  fixed flake errors
  Improved cray_xc detection bug fix
  Improved cray_xc detection
  remove FIXMEs
  Ensure that per-4.4.1 NetCDF doesn't use HDF5 1.10
  Re-ignore licenses directory
  Add "default" configuration scope.
  Draft CDO
  Make frontend OS on Cray machines a proper linux distro.
  ...
 2016-07-20 18:34:53 -06:00
mwilliammyers
a09bebcaea opencv : Add section comments 2016-07-20 18:19:59 -06:00
mwilliammyers
a9541997ae opencv : Reorder depends_on statements 2016-07-20 18:19:03 -06:00
mwilliammyers
bd02892f7b opencv : Use dso_suffix for python lib 2016-07-20 18:10:10 -06:00
mwilliammyers
ea9fa81ba5 opencv : Fix python include dir for cmake 2016-07-20 18:10:09 -06:00
mwilliammyers
670157b364 opencv : Add zlib cmake support 2016-07-20 18:10:09 -06:00
mwilliammyers
e5ae48a9da opencv : Add jasper cmake support 2016-07-20 18:10:09 -06:00
mwilliammyers
47514d07b1 opencv : Use dso_suffix 2016-07-20 18:10:08 -06:00
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