Commit graph

7575 commits

Author SHA1 Message Date
Thierry
857dac88c8 init yorick package (#2635)
* init yorick package

* attempt at picking up SPACK's compiler choice, todo ~X variant.

* sphinx docstring error ?

* version# tarball, ~X default, docstring fix

* sphinx docstring fix(?)
2016-12-28 10:08:02 -08:00
George Hartzell
18c10f2bad Cleanup post luafilesystem version de-underscoring (#2683)
The upstream luafilesystem tarball/version had a wayward/inconsistent
underscore in their more recent version tag.  The played badly with
our package fetching machinery (due to recent changes?).

Upstream cleaned up their bit which required some touchups here.

- updated the url
- updated the version (digest)
- updated the format statement for the path to the rockspec.
2016-12-27 11:49:53 -08:00
Mayeul d'Avezac
81c1404b9c Adds catch, cppunit, spdlog, tinyxml(1 and 2), google benchmark (#2627)
* Adds catch, cppunit, spdlog, tinyxml(1 and 2), google benchmark

Tinyxml comes in two flavors, 1 and 2. Each comes in several
versions... So they cannot be easily united into a single package.

* Use CMakePackage and friends, add copyright

Also eleminate debug/release variants, since it no longuer fits in the
CMakePackage format.

* Remove unnecessary url

* spdlog now has tagged releases

* Remove unnecessary url argument

* Fewer quotes in cmake args, because magic

* Incorrect base class for tinyxml
2016-12-27 00:32:29 -08:00
Michael Kuhn
baaa613e44 Update wx to 3.1.0 (#2641) 2016-12-27 00:18:26 -08:00
Adam J. Stewart
29bac34c1d Ensure that every file in Spack has a license (#2659)
* Ensure that every package has a license

Also fixes URLs with http://http:// doubled.

This is a continuation of #2656.

* Add license to every file in Spack

* Make sure Todd is the author of all packages

* Fix flake8 tests

* Don't license external Sphinx docs

* Don't display licenses in tutorial example packages

Also fixes typos and converts command-line examples
from tcsh to bash, which is more common
2016-12-27 00:17:12 -08:00
Matthew Scott Krafczyk
3e92ffde7d Update py-cython with new pypi.io url and new version (#2650) 2016-12-25 19:48:11 -08:00
Adam J. Stewart
f34c5367d5 Better tabulation for spack checksum (#2673) 2016-12-25 19:25:53 -08:00
Denis Davydov
91bfebbed8 filter_system_path: additionally filter system prefixes (#2672)
That's because in set_build_environment_variables()
the funciton filter_system_paths() is actually applied to
package prefixes, and not to prefix/lib or prefix/include.
2016-12-25 19:24:56 -08:00
Bruno Turcksin
e16908b16b Add 64 bit variant to dealii. (#2654) 2016-12-25 18:55:14 -08:00
Adam J. Stewart
b240fdb2b9 Add latest version of Python 2 (#2668) 2016-12-25 18:53:16 -08:00
Michael Kuhn
33592d0142 Update gcc to 6.3.0 (#2669) 2016-12-25 18:52:58 -08:00
Todd Gamblin
c4afaabea9 Add argument to spack spec to show deptypes. (#2680)
- `-t` | `--types` argument now shows deptypes in `spack spec`
2016-12-25 14:15:58 -08:00
George Hartzell
041f96b349 Update the texlive distro digest. (#2679)
sigh.
2016-12-25 12:37:03 -08:00
Adam J. Stewart
7e8767e3fd Remove usernames from paths in docs (#2675)
* Remove usernames from paths in docs

* Fix path export
2016-12-25 12:36:35 -08:00
Massimiliano Culpo
8fe5fb7988 go: fixed GOROOT_BOOTSTRAP without workarounds (#2671) 2016-12-25 12:33:57 -08:00
Adam J. Stewart
c3cd948537 Modify github archive regex to support luaposix (#2677) 2016-12-25 12:32:19 -08:00
Michael Kuhn
e340f275b8 Update cairo to 1.14.8, gtkplus to 2.24.31 and pango to 1.40.3 (#2642) 2016-12-21 15:03:28 -08:00
Kim Serradell
70a4c4e105 Bug fontconfig (#2652)
* Added uuid: OSSP uuid is a ISO-C:1999 application programming interface

* Fixed install error in cmor package

* Added uuid: OSSP uuid is a ISO-C:1999 application programming interface

* Fixed install error in cmor package

* Modifiying fontconfig file to allow install in OpenSuse 13.2

* Adding pkg-config dependency to freetype and libxml2

* Removed first possible solution. With @adamjstewart selecting the one adding pkg-config to dependencies
2016-12-21 14:27:15 -08:00
Federico Padua
60dc751225 Fix homepage for the package libspatialindex (#2656)
Small fix for the homepage of the package libspatialindex.
2016-12-21 14:23:32 -08:00
scheibelp
3f1cdbf5ef Revert #2292: use frontend compiler for build deps (#2549)
The primary goal of #2292 was to use the frontend compiler to make
build dependencies like cmake on HPC platforms. It turns out that
while this works in some cases, it did not handle cases where a
package was a link dependency of the root and of a build dependency
(and could produce incorrect concretizations which would not build).
2016-12-20 00:21:25 -08:00
Michael Kuhn
3ce3165ae6 Update gdal to 2.1.2 (#2643) 2016-12-19 17:06:57 -08:00
Adam J. Stewart
b3ba45afa9 Various improvements to H5hut (#2636) 2016-12-19 17:06:14 -08:00
Todd Gamblin
c89de04f40 Support Yorick versions (#2640) 2016-12-19 14:55:23 -08:00
Andrey Prokopenko
d306893d83 moab: changed trilinos dependency to zoltan, and added fortran variant (#2582)
Trilinos dependency is very heavy, the zoltan one is light. I'm not sure
if there is a situation where one needs the former.
2016-12-19 14:41:09 -08:00
Adam J. Stewart
d24186ea84 Update PnetCDF to AutotoolsPackage (#2637) 2016-12-19 14:26:47 -08:00
George Hartzell
d8efeabf77 Update digest for vim@8.0 tarball. (#2600)
* Update digest for vim@8.0 tarball.

The digest appears to have changed.

The new digest value matches the value in their
[MD5SUMS](ftp://ftp.vim.org/pub/vim/unix/MD5SUMS)
file.

* Change ftp.vim.org -> github.com/vim/vim/archive

Vim seems to do weekly releases, but the name of the tarball on
ftp.vim.org doesn't change so we have to regularly play 'update the
digest' (aka Internet whack-a-mole).

This commit changes the url so that we are now downloading particular
versions from the Vim project's github archive.

I didn't walk back through of time to get all of the versions that
used to be explicit.  I grabbed the final `7.4` and the current `8.0`
releases.  If people need more we can add them.
2016-12-19 14:26:16 -08:00
Todd Gamblin
4b7b6768e6 Modify github regex to support NCO. (#2633) 2016-12-19 14:17:18 -08:00
Adam J. Stewart
46436a0909 GSL: Add latest version, update to AutotoolsPackage (#2630) 2016-12-19 09:21:38 -08:00
Todd Gamblin
a2b4146e10 Fixes for various hash issues (#2626)
* Better output for disambiguate_specs()

* Fix wrong exception name.

* Fix satsifies(): concrete specs require matching by hash.

- Fixes uninstall by hash and other places where we need to match a
  specific spec.

- Fix an error in provider_index (satisfies() call was backwards)

- Fix an error in satisfies_dependencies(): checks were too shallow.

* Fix default args in Spec.tree()

* Move installed_dependents() to DB to avoid unknown package error.

* Make `spack find` and `sapck.store.db.query()` faster for hashes.

* Add a test to ensure satisfies() respects concrete Specs' hashes.
2016-12-19 09:09:53 -08:00
Adam J. Stewart
08d323b1f8 NCO: Add latest version, update to AutotoolsPackage (#2629) 2016-12-19 08:49:37 -08:00
Todd Gamblin
b18738e03d Add gawk (GNU awk) (#2625)
* Add gawk, GNU awk.

* flake8 fix.
2016-12-18 22:35:23 -08:00
George Hartzell
6e1b3f621d Feature/add package for fastqc (#1573)
* Add package for fastqc

This tool is a java mess.  Their Way To Do It is to just copy the entire
tree into it's final resting place, make the perl script at the top
level executable and take it from there.

Yuck.

This package assumes that `set_executable` actually sets all the user
bits.  If that change doesn't go in, then something equivalent needs to
be done.

* Use chmod to make fastqc executable

I haven't gotten any feedback on changing set-executable, so switch to
using chmod (from the cuda package).

* Flake8 cleanup

* Install files neatly, don't just copy top level of dir

Rather than blindly copying everything in the distribution, carefully
put the necessary bits into reasonable places.  Neatness counts, etc...

This requires patching the `fastqc` perl script, so this commit adds a
patch file.

* Additional pep8 cleanup

* Let dependency handle adding jdk to PATH

* Flake8 cleanup

* Ensure that java is on PATH

I thought that the run dependency on the jdk would put
java on my PATH, but it does not appear to work.

For now, do it by hand.
2016-12-18 16:38:14 -08:00
Alfredo Adolfo Gimenez
68e9a2ed8d Added customization for make targets in 'build' and 'install' phases for AutotoolsPackage (#2464)
* Customization for make targets in build and test phases for AutotoolsPackage

* Updated Blitz++ to use customized make build and test targets

* Removed flake8 error

* Removed make test customization, added make install customization, need to figure out issues with multiple make targets

* Changed build_targets and install_targets to normal attributes
2016-12-18 16:27:47 -08:00
Chris MacMackin
0de7b5504e py-markdown: Add new package for python-markdown. (#2611)
* py-markdown: Add new package for python-markdown.

* py-markdown: Added restrictions on Python version.

* py-markdown: Removed upper-limit on compatible Python versions.

* py-markdown: Reinstated upper bound on Python version. Also fixed small formatting error.
2016-12-18 16:23:31 -08:00
Denis Davydov
1c0f28c559 gmsh: add 2.15.0 and switch to CMakePackage (#2620) 2016-12-18 16:20:37 -08:00
Denis Davydov
da2350a1c9 tbb: add 2017.3 (#2619) 2016-12-18 16:20:26 -08:00
Denis Davydov
aeb58dc2de cmake: add 3.7.1 (#2618) 2016-12-18 16:20:13 -08:00
Gregory Lee
592df25aef build fixes for openblas (#2601)
* build fixes for openblas

* avx2 in openblas nnot supported with older gcc

* merge fix for openblas
2016-12-17 17:04:59 -08:00
Denis Davydov
0ef55b831f dealii: fix config for Netcdf with lib64 (#2616) 2016-12-17 08:57:33 -08:00
Chris MacMackin
a1a41bb4c7 graphviz: fixed build error due to specifying ltdl lib but not include. (#2609)
* graphviz: fixed build error due to specifying ltdl lib but not include.

* graphviz: Fixed dependencies on libtool and expat.
2016-12-16 16:22:13 -08:00
Andrey Prokopenko
394f010952 libmesh: added mpi variant (#2584) 2016-12-16 15:39:55 -08:00
Thierry
5f88bea442 init nfft 3.3.2 package file (#2612)
* init nfft 3.3.2 package file

* shorten comment line
2016-12-16 15:36:34 -08:00
Chris MacMackin
3089d118c1 py-beautifulsoup4: Added version 4.5.1 (#2610) 2016-12-16 14:21:26 -08:00
Jon Rood
d7ff4b8f34 Updating Trilinos with superlu variant and fixing git branch version options. (#2604) 2016-12-16 14:14:50 -08:00
Adam J. Stewart
36072c4776 [HACK] Make concretization great again! (#2590)
* Always default to +mpi

* Always default to ~X
2016-12-16 10:49:02 -08:00
Massimiliano Culpo
87c9b01033 openblas: derives from MakefilePackage (#2488)
* MakefilePackage: changed build_args and install_args for consistency with #2464
openblas: derives from MakefilePackage

* MakefilePackage: changed default edit behavior
2016-12-15 10:15:52 -08:00
Massimiliano Culpo
f9ca5b9f27 go: see #2567, temporary fix (#2588) 2016-12-15 09:12:33 -08:00
Todd Gamblin
6971918c27 Add GNU patch to Spack. (#2598) 2016-12-15 01:35:45 -08:00
Mario Melara
32cecf55ee Fix target for compiler on CNL operating systems (#2580)
Changes any to a string to avoid <built-in function any> being
incorrectly added to target in compilers.yaml.
2016-12-14 14:37:14 -08:00
Jean-Paul Pelteret
8816cdea9e Blacklist flex 2.6.2 by commenting out package version (#2571)
Fixes #2554
2016-12-14 14:34:55 -08:00