Commit graph

5392 commits

Author SHA1 Message Date
becker33
a091eeceab Parser fix (#2769)
* Fixed parser to eliminate need for escape quotes. TODO: Fix double call to shlex, fix spaces in spec __str__

* Fixed double shlex

* cleanup

* rebased on develop

* Fixed parsing for multiple specs; broken since #360

* Revoked elimination of the `-` sigil in the syntax, and added it back into tests

* flake8

* more flake8

* Cleaned up dead code and added comments to parsing code

* bugfix for spaces in arguments; new bug found in testing

* Added unit tests for kv pairs in parsing/lexing

* Even more flake8

* ... yet another flake8

* Allow multiple specs in install

* unfathomable levels of flake8

* Updated documentation to match parser fix
2017-01-15 19:17:54 -08:00
Jon Rood
b2f29b855b Updating BoxLib with the ability to build again. (#2813)
* Updating BoxLib with the ability to build again.

* Using Spack MPI compilers directly.

* Fixing typo.

* Using tarball from github archive for boxlib.
2017-01-15 17:07:44 -08:00
Adam J. Stewart
e3a631c90e Add Astra package (#2800) 2017-01-15 16:23:52 -08:00
Adam J. Stewart
f480e3449e Added customization for make targets in 'build' and 'install' phases for CMakePackage (#2742)
* Added customization for make targets in 'build' and 'install' phases for CMakePackage

* Use rst in build system docs so that Sphinx generates nice API docs

* Allow AutotoolsPackages to be built in a different directory

* Flake8

* Fix missing import

* Allow configure to be located in different directory

* Update espressopp to use build targets

* Flake8

* Sphinx fix, lists must be a new paragraph

* Back out change that allowed a configure script in a different directory than build_directory

* Add missing deps, build in parallel

* Missing space for rst list
2017-01-15 16:23:16 -08:00
Jean-Paul Pelteret
4b7b595e3c New package: CppAD (#2832) 2017-01-15 16:20:26 -08:00
Adam J. Stewart
f2d4c15395 Remove cmake build dep from CMakePackages (#2684) 2017-01-15 03:18:52 -08:00
Adam J. Stewart
7fce4c5083 Add list_url to cmake (#2714) 2017-01-15 03:16:41 -08:00
Axel Huebl
3f7b4ab7aa Clang & Boost: No PCH (#2827)
Although it hurts a little, officially pre-compiled headers in
boost are only supported for gcc & msvc and the latest clang
releases still fail to build boost with it.

Therefore, I disabled building those to get boost build with
clang 3.9.0 on an Ubuntu 14.04 (x86).

Links to documentation and boost bug reports are inline, so
people can later on check if they still apply. Seems just to
be a bug in `Boost.Build` that tries to set `-o` with multiple
output files.
2017-01-15 02:38:14 -08:00
Todd Gamblin
0d367bbd20 Add a test to exercise non-buildable external packages. (#2833) 2017-01-15 02:37:20 -08:00
becker33
677623962e Fixed find -lp command (coloring was broken) (#2820) 2017-01-15 02:36:36 -08:00
Axel Huebl
5c4d2627ff Packages: Add CUDA8 (#2823)
Adds the latest CUDA release, 8.0.44.
2017-01-15 02:35:53 -08:00
Adam J. Stewart
367f46eee2 Add old version of PGI (#2784) 2017-01-15 02:35:27 -08:00
Adam J. Stewart
12edc4e369 Add latest version of PETSc (#2783) 2017-01-15 02:34:48 -08:00
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
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