Commit graph

4175 commits

Author SHA1 Message Date
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
7ae163d436 Merge pull request #1361 from epfl-scitas/features/module_token_expansion_in_environment
module : token expansion in environment
2016-08-03 09:49:28 -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
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
becker33
4ff4eab476 Merge pull request #1236 from davydden/pkg/arpack-ng_blas
arpack-ng: fix blas/lapack libraries
2016-08-02 11:50:42 -07:00
Denis Davydov
f90692cf81 arpack-ng: fix blas/lapack libraries 2016-08-02 20:27:34 +02:00
becker33
13d9eed85b Merge pull request #1424 from adamjstewart/features/setup_py
spack create should use setup_py() instead of python()
2016-08-02 10:28:14 -07:00
Adam J. Stewart
941acef009 spack create should use setup_py() instead of python() 2016-08-02 12:20:28 -05:00
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
becker33
326b9838ed Merge pull request #1423 from glennpj/fix_url
Move archive_version setting to if block
2016-08-02 10:05:25 -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
Glenn Johnson
2929fb0a4d Move archive_version setting to if block
The archive_version variable should only get set if versions will be
checked and that is only if there is a list_url in the package file. For
VCS repos setting the variable triggers an error from web.py as it
parses the default_fetcher object.

This should fix #1422.
2016-08-02 11:54:09 -05:00
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
becker33
9490bd2154 Merge pull request #1373 from hartzell/bug/update-several-r-packages
Update several R packages (r-shiny prereqs)
2016-08-02 09:07:31 -07:00
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