Commit graph

7375 commits

Author SHA1 Message Date
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
Massimiliano Culpo
cd511791d1 configure and build command: fix the stop iteration semantics
- broke somewhere between bdf4832269 (#2810) and 17b13b161b
2017-01-12 09:11:48 -08:00
Massimiliano Culpo
de2cb864fa mirror: fix error for some specs during concretization (#2806) 2017-01-11 07:38:22 -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
Todd Gamblin
f5557b5723 Change nargs='*' to argparse.REMAINDER for constraint options. (#2798) 2017-01-10 12:25:41 -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
Axel Huebl
05d77917fd GitLab: Tarball Version Test (#2296)
* GitLab: Tarball Version Test

Upload a test demonstrating #2290

* Add GitLab parsing
2017-01-06 08:53:19 -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
Mario Melara
3d54c3c689 Correct env vars for modulecmd; Fixes #1481 (#2745)
Don't override MODULEPATH with PATH, PATH has no modulefiles

PEP8 compliance
2017-01-05 11:15:38 -08:00
Massimiliano Culpo
9271c69b5d test: fixed 'refresh_builtin_mock' fixture (#2748) 2017-01-05 10:25:24 -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
Massimiliano Culpo
34d23c617c tests: coverage combine run only if tests succeeded (#2712) 2017-01-01 13:05:33 -08:00
Todd Gamblin
b9ec69dce1 Disallow vdeps in packages.yaml (#2699)
* Consolidate packages.yaml code to preferred_packages

* Add validation check and a test for packages.py parsing.

* flake8
2016-12-31 08:12:38 -08:00
Adam J. Stewart
040f8a7176 Add latest version of gmp (#2695) 2016-12-30 22:53:54 -08:00
Adam J. Stewart
8cb54a9a67 Fix missing debug parameter for parse_version() (#2696) 2016-12-30 22:52:49 -08:00
Todd Gamblin
c88df5819d Fix test command arg handling. 2016-12-30 17:18:19 -08:00
Todd Gamblin
b5537553f2 Run coverage for the spack install command as well as spack test.
- Also don't run coverage on OSX.
2016-12-30 17:18:19 -08:00
Michael Kuhn
a42f340d37 Allow setting default variants (#2644) 2016-12-30 14:11:39 -08:00
Todd Gamblin
d52c44cba9 Add OSX build to .travis.yml. Clean up .travis.yml (#2689)
* Add OSX build to .travis.yml.  Clean up .travis.yml
* Add gcc/gfortran to the mac brew setup.
2016-12-30 13:59:21 -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
Todd Gamblin
d6390c159f Fix issues related to the switchover to pytest. (#2685)
- Remove stale reference to `import nose` from `bin/spack` script.
- Add `py` to externals (missing dependency for `pytest`)
2016-12-29 11:59:45 -08:00
Massimiliano Culpo
7ea10e768e unit tests: replace nose with pytest (#2502)
* Porting: substitute nose with ytest

This huge commit substitutes nose with pytest as a testing system. Things done here:

* deleted external/nose as it is no longer used
* moved mock resources in their own directory 'test/mock/'
* ported two tests (cmd/find, build_system) to pytest native syntax as an example
* build_environment, log: used monkeypatch instead of try/catch
* moved global mocking of fetch_cache to an auto-used fixture
* moved global mocking from test/__init__.py to conftest.py
* made `spack test` a wrapper around pytest
* run-unit-tests: avoid running python 2.6 tests under coverage to speed them up
* use `pytest --cov` instead of coverage run to cut down testing time

* mock/packages_test: moved mock yaml configuration to files instead of leaving it in the code as string literals

* concretize.py: ported tests to native pytest, reverted multiprocessing in pytest.ini as it was creating the wrong report for coveralls

* conftest.py, fixtures: added docstrings

* concretize_preferences.py: uses fixtures instead of subclassing MockPackagesTest

* directory_layout.py: uses fixtures instead of subclassing MockPackagesTest

* install.py: uses fixtures instead of subclassing MockPackagesTest

* optional_deps.py: uses fixtures instead of subclassing MockPackagesTest

optional_deps.py: uses fixtures instead of subclassing MockPackagesTest

* packages.py: uses fixtures instead of subclassing MockPackagesTest

* provider_index.py: uses fixtures instead of subclassing MockPackagesTest

* spec_yaml.py: uses fixtures instead of subclassing MockPackagesTest

* multimethod.py: uses fixtures instead of subclassing MockPackagesTest

* install.py: now uses mock_archive_url

* git_fetch.py: uses fixtures instead of subclassing MockPackagesTest

* hg_fetch.py: uses fixtures instead of subclassing MockPackagesTest

* svn_fetch.py, mirror.py: uses fixtures instead of subclassing MockPackagesTest
repo.py: deleted

* test_compiler_cmd.py: uses fixtures instead of subclassing MockPackagesTest

* cmd/module.py, cmd/uninstall.py: uses fixtures instead of subclassing MockDatabase

* database.py: uses fixtures instead of subclassing MockDatabase, removed mock/database

* pytest: uncluttering fixture implementations

* database: changing the scope to 'module'

* config.py: uses fixtures instead of subclassing MockPackagesTest

* spec_dag.py, spec_semantics.py: uses fixtures instead of subclassing MockPackagesTest

* stage.py: uses fixtures instead of subclassing MockPackagesTest. Removed mock directory

* pytest: added docstrings to all the fixtures

* pytest: final cleanup

* build_system_guess.py: fixed naming and docstrings as suggested by @scheibelp

* spec_syntax.py: added expected failure on parsing multiple specs closes #1976

* Add pytest and pytest-cov to Spack externals.

* Make `spack flake8` ignore externals.

* run-unit-tests runs spack test and not pytest.

* Remove all the special stuff for `spack test`

- Remove `conftest.py` magic and all the special case stuff in `bin/spack`

- Spack commands can optionally take unknown arguments, if they want to
  handle them.

- `spack test` is now a command like the others.

- `spack test` now just delegates its arguments to `pytest`, but it does
  it by receiving unknown arguments and NOT taking an explicit
  help argument.

* Fix error in fixtures.

* Improve `spack test` command a bit.

- Now supports an approximation of the old simple interface
- Also supports full pytest options if you want them.

* Use external coverage instead of pytest-cov

* Make coverage use parallel-mode.

* change __init__.py docs to include pytest
2016-12-29 07:48:48 -08:00
Elizabeth Fischer
88f57d7543 Allow exclusion of packages from spack module loads (#2667)
* Allow exclusion of packages from `spack module loads`

* Comment out excluded packages instead of not showing them at all.
2016-12-28 13:31:18 -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