Commit graph

2865 commits

Author SHA1 Message Date
Massimiliano Culpo
436f6a4ab6 get_std_cmake_args delegates to CMakePackage._std_args fixes #2665 (#2805) 2017-01-15 02:34:15 -08:00
danielsjensen1
957cb968c6 Features/octopus 6.0 (#2819)
* Added support for Octopus 6.0 and the optional libraries: metis, parmetis, netcdf, arpack-ng, and scalapack.

* Fix PEP 8 line too long error.

* Changed format syntax {} to {0} to support Python 2.6.
2017-01-15 02:30:47 -08:00
Gregory Lee
c6c6773c03 added psutil python package (#2812) 2017-01-15 02:30:12 -08:00
Stephen McDowell
1f4ca71e21 Adding the py-ipdb package for more stable debugging with iPython. (#2824)
* Adding the py-ipdb package for more stable debugging with iPython.

* Removing deprecated python support, adding missing dependencies.

* Adding version checks for (i)python
2017-01-15 02:29:29 -08:00
Matthew Scott Krafczyk
28ea72d5b2 Add the package py-sphinx-bootstrap-theme (#2825) 2017-01-15 02:27:17 -08:00
Andrey Prokopenko
1128922b44 boost: fixing boost-1.55.0 for gcc-5 (#2822)
boost-1.55.0 requires patching when compiling with gcc-5. See these
threads:

https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=197594
https://svn.boost.org/trac/boost/ticket/10125

Fixes #2821.
2017-01-13 08:43:50 -08:00
Jim Galarowicz
481bc91854 Update the boost versions used by openspeedshop. Boost-1.60 to current latest causes compile errors when building openspeedshop. (#2300)
* Update the krell institute products to use the latest features of spack for building on cluster platforms.

* Address travis error messages and resubmit the pull request.

* Update the contents of openspeedshop package.py so it passes the flake8 tests.

* Fix flake8 error-whitespack issue in mrnet package.py file.

* Add updates based on spack reviewer feedback.

* More fixes based on comments from reviewers.  Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH.

* More review related changes.  Update MPIOption.append lines and take out xercesc references.

* Create a base options function for common openspeedshop base cmake options to reduce redundencies.

* Add libxml2+python depends on to get around issues with the libxml2 package file.

* Using boost over 1.60.0 causes compile errors.  This is a known boost bug. Also, dyninst-9.2.0 is set to be the vesrion of dyninst to use with OSS, as of now. The newer version fails to build.

* Fix bad syntax in specifying the boost version range.

* Update the version numbers for the krell institute components and tools: cbtf and openspeedshop.

* Do not build glib for qt3, it is not needed and causes build problems at this time anyway.
2017-01-10 12:28:05 -08:00
Massimiliano Culpo
a7a77b5b41 openjpeg: fixes url (#2790) 2017-01-10 09:14:16 -08:00
Adam J. Stewart
1ece25bdc2 Temporary workaround for R concretization bug (#2756) 2017-01-09 19:07:49 -08:00
sknigh
c7ca96b327 Added list_url to r-dt package (#1533) 2017-01-09 14:37:06 -08:00
Elizabeth Fischer
402dfe30f9 Get Rid of nobuild, nolink, and alldeps (#2765)
* Removing the nobuild, nolink, and alldeps dependency types in favor of being explicit.
* This will help with maintenance going forward, as adding more dependency types won't affect existing declared dependencies in weird ways.
* default deptype is still `('build', 'link')`
2017-01-07 19:59:02 -08:00
Adam J. Stewart
68baac0549 Various updates to the NCO package and dependencies (#2639)
* Remove +mpi variant from NCO

* Update NCO deps to AutotoolsPackage

* Update the other NetCDF packages to AutotoolsPackage

* ANTLR has a nolink deptype on java, don't worry about csharp

* Remove restrictions from NCO package, fix homepage

* Add version 4.6.3 of NCO

* Missed AutotoolsPackage for NetCDF-CXX4

* NetCDF tests fail when run in parallel

* Remove commented out dependency

* Add documentation dependency
2017-01-07 18:06:59 -08:00
Adam J. Stewart
a0195371e8 Unset PETSC_DIR during installation (#2768)
* Set PETSC_DIR during installation

* Move env var unsets to setup_environment

* Fix unset var name and number of args
2017-01-07 17:38:53 -08:00
James Wynne III
b7fdc03bd5 Added needed deps for bbcp (#2773) 2017-01-07 16:30:54 -08:00
Adam J. Stewart
daff3c0908 Preliminary RPackage class (#2761) 2017-01-07 16:28:52 -08:00
Todd Gamblin
f379697985 Fix issues linking hDF5 1.8.14 and below on Ubuntu. (#2772) 2017-01-07 09:03:50 -08:00
Cyrus Harrison
e39ba88e9c add conduit 0.2.1 release (#2766) 2017-01-06 12:33:51 -08:00
Bruno Turcksin
2f173bda9c Add boost 1.63.0 (#2743) 2017-01-06 11:44:41 -08:00
Gregory Lee
a016fd01ec Merge pull request #2740 from jrood-nrel/jonrood
Renaming mkl to intel-mkl
2017-01-06 11:01:16 -08:00
Gregory Lee
7b337de93e various python package version and dependency updates (#2751)
* various python package version and dependency updates

* various python package version and dependency updates
2017-01-06 08:50:06 -08:00
Christoph Junghans
8dc056130c espressopp: package for the ESPResSo++ software (#2602)
* espressopp: package for the ESPResSo++ software

This commit adds a package for the ESPResSo++
simulation software.

* Move Espressopp package to CMakePackage

This commit moves Espressopp package to CMakePackage.
Addresses some comments in the PR.

* Remove run_tests and changed type of dependencies

Addressed some comments from @adamjstewart.
Removed global run_tests setting and removed type from many
dependencies. Set type for py-mpi4py to 'nolink'.

* Updated to last version and fix mpi4py dependency

Added latest espressopp version and changed mpi4py (version) dependency for
different espressopp versions.

* Changed mpi4py version requirements for espressopp

Changed py-mpi4py version requirements for espressopp@1.9.4 according
to the package build requirements for that version.
2017-01-05 21:20:55 -08:00
Matthew Krafczyk
8c650303ff Add dependencies and finish the py-tornado package.
This adds the following packages:

 py-backports-shutil-get-terminal-size  py-nbformat
 py-backports-ssl-match-hostname        py-pathlib2
 py-entrypoints                         py-pickleshare
 py-futures                             py-pip
 py-ipykernel                           py-prompt-toolkit
 py-ipython-genutils                    py-ptyprocess
 py-ipywidgets                          py-simplegeneric
 py-jupyter-client                      py-singledispatch
 py-jupyter-console                     py-terminado
 py-jupyter-core                        py-traitlets
 py-jupyter-notebook                    py-wcwidth
 py-monotonic                           py-widgetsnbextension
 py-nbconvert
2017-01-05 16:10:30 -08:00
Jean-Paul Pelteret
6a5185a2a7 Added npm, node.js, and Jupyter dependencies
Adds the following packages:
  node-js  py-backports-abc  py-functools32  py-pycurl   py-vcversione
  npm      py-certifi        py-jsonschema   py-tornado  py-zmq

- Added python packages that are dependencies for the Jupyter suite
- Update new python packaages to use extension package install function.
- Added npm and node-js packages
2017-01-05 16:10:30 -08:00
Elizabeth Fischer
3dd4a01a5e Standardize package names: lower-case, not Mixed_CASE (#2475)
* Rename packages

* Upcasing depends_on() in packages.

* Downcased extends('r')

* Fixed erroneously changed URL that had slipped through.

* Fixed typo

* Fixed link from documentation into package source code.

* Fixed another doc problem.

* Changed underscores to dashes in package names.

* Added test to enforce lowercase, no-underscore naming convention.

* Fix r-xgboost

* Downcase more instances of 'R' in package auto-creation.

* Fix test.

* Converted unit test packages to use dashes not underscores

* Downcase `r` in the docs.

* Update module_file_support.rst

Fix r->R for class R.
2017-01-04 18:24:07 -08:00
Jon Rood
01406251c9 Intel-mkl provides mkl 2017-01-04 14:02:23 -07:00
Jon Rood
c8405b4b5f Renaming mkl to intel-mkl 2017-01-04 13:55:08 -07:00
George Hartzell
4e653254c5 Use zlib's "fossil" site for old tarballs (#2735)
* Use zlib's "fossil" site for old tarballs

Following citibeth's suggestion in #2732, use zlib's "fossil"
site (not to be confused with the sqlite team's VCS...) for retrieving
old tarballs.

Digests for 1.2.{8,10} match and both install for me on CentOS 7.

* Use zlib's "fossil" URL as the one true URL

Everything seems to be available at zlib's "fossil" URL, so just use
it as the one and only url.

(and fix a flake8 complaint about a comment)
2017-01-04 11:43:10 -08:00
Cyrus Harrison
eaa24b08fd add package for conduit (#2670)
* add package for conduit

* try to fix main conduit docstring

* use join_path instead of pjoin

* address a few requests in pr #2670

change name of 'github-master' to 'master'

change 'docs' variant to 'doc', set default to False

remove explicit +shared variant spec for silo and hdf5 deps
(in the conduit +shared case) cases since they default to True

add reference to static rpath issue
(https://github.com/LLNL/spack/issues/2658)

* address pr #2670 requests

add todos and more info on why variants for deps where selected
use python module install python to enable spack activate
use .format instead of %s
2017-01-04 10:20:08 -08:00
Jeffrey Salmond
e57fc3d950 opencoarrays: new version (#2734)
* add version 1.8.0

* remove depends_on('cmake') as it is now unecessary

* remove 'coarrays' as a virtual package
2017-01-04 08:40:55 -08:00
Jean-Paul Pelteret
4ff33d41a7 New package: ccache (#2721) 2017-01-04 08:39:58 -08:00
Elizabeth Fischer
03471469e7 libpng: Upgrade versions to fix vulnerability. (#2723) 2017-01-04 08:32:10 -08:00
George Hartzell
2e24a3a2be zlib@1.2.10 and R do not get along, work around it (#2727)
* zlib@1.2.10 and R do not get along, work around it

R's configure script has trouble with version numbers > 1.2.9.

This works around it by constraining R to 1.2.8.

I'm working with some R folk on getting it fixed going forward.

* Add adamjstewart's change.
2017-01-04 07:51:16 -08:00
Barry Smith
2322deda65 Update to latest zlib version, server no longer provides older version (#2720)
* Update to latest zlib version, server no longer provides older version

Funded-by: IDEAS
Project: IDEAS/xSDK

* Add alternative URL for previous release of zlib
2017-01-03 13:52:14 -08:00
Todd Gamblin
d32d5e45fb Fix issues when a package provides the same vdep twice. (#2710)
* Fix issues when a package provides the same vdep twice.

- provides() now adds to a set of provided vdeps instead of a single one.

* flake8
2017-01-02 18:40:57 -08:00
Adam J. Stewart
040f8a7176 Add latest version of gmp (#2695) 2016-12-30 22:53:54 -08:00
Todd Gamblin
972a277956 Fix Python issue with build failures; Add test case for build failures. (#2687) 2016-12-30 11:37:50 -08:00
Todd Gamblin
5fbab1f4b5 Concretize preserves deptypes (#2681)
Concretization preserves deptypes
2016-12-29 14:43:59 -08:00
Massimiliano Culpo
17b13b161b Directive inheritance: laziness for the win (#2623)
* inheritance of directives: using meta-classes to inject attributes coming from directives into packages + lazy directives

* _dep_types -> dependency_types
* using a meta-class to inject directives into packages
* directives are lazy

fixes #2466

* directives.py: allows for multiple inheritance. Added blank lines as suggested by @tgamblin

* directives.py: added a test for simple inheritance of directives

* Minor improvement requested by @tgamblin

CMakePackage: importing names from spack.directives
directives: wrap __new__ to respect pep8

* Refactoring requested by @tgamblin

directives: removed global variables in favor of class variables. Simplified the interface for directives (they return a callable on a package or a list of them).
2016-12-28 12:37:02 -08:00
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
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
George Hartzell
041f96b349 Update the texlive distro digest. (#2679)
sigh.
2016-12-25 12:37:03 -08:00
Massimiliano Culpo
8fe5fb7988 go: fixed GOROOT_BOOTSTRAP without workarounds (#2671) 2016-12-25 12:33:57 -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