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2017-01-15Added customization for make targets in 'build' and 'install' phases for ↵Adam J. Stewart8-78/+96
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
2017-01-15New package: CppAD (#2832)Jean-Paul Pelteret1-0/+48
2017-01-15Remove cmake build dep from CMakePackages (#2684)Adam J. Stewart10-18/+1
2017-01-15Add list_url to cmake (#2714)Adam J. Stewart1-2/+4
2017-01-15Clang & Boost: No PCH (#2827)Axel Huebl1-0/+7
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.
2017-01-15Add a test to exercise non-buildable external packages. (#2833)Todd Gamblin1-2/+30
2017-01-15Fixed find -lp command (coloring was broken) (#2820)becker331-3/+2
2017-01-15Packages: Add CUDA8 (#2823)Axel Huebl1-0/+2
Adds the latest CUDA release, 8.0.44.
2017-01-15Add old version of PGI (#2784)Adam J. Stewart1-1/+5
2017-01-15Add latest version of PETSc (#2783)Adam J. Stewart1-0/+1
2017-01-15get_std_cmake_args delegates to CMakePackage._std_args fixes #2665 (#2805)Massimiliano Culpo3-16/+57
2017-01-15Features/octopus 6.0 (#2819)danielsjensen11-8/+53
* 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.
2017-01-15added psutil python package (#2812)Gregory Lee1-0/+43
2017-01-15Adding the py-ipdb package for more stable debugging with iPython. (#2824)Stephen McDowell1-0/+58
* Adding the py-ipdb package for more stable debugging with iPython. * Removing deprecated python support, adding missing dependencies. * Adding version checks for (i)python
2017-01-15Add the package py-sphinx-bootstrap-theme (#2825)Matthew Scott Krafczyk1-0/+41
2017-01-13boost: fixing boost-1.55.0 for gcc-5 (#2822)Andrey Prokopenko2-0/+54
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.
2017-01-12configure and build command: fix the stop iteration semanticsMassimiliano Culpo1-0/+5
- broke somewhere between bdf48322696290d4e3d00ed12b7c7fe6ca213478 (#2810) and 17b13b161b3ddcd691ea7ed90165cfab6dec3950
2017-01-11mirror: fix error for some specs during concretization (#2806)Massimiliano Culpo1-0/+3
2017-01-10Update the boost versions used by openspeedshop. Boost-1.60 to current ↵Jim Galarowicz6-16/+16
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.
2017-01-10Change nargs='*' to argparse.REMAINDER for constraint options. (#2798)Todd Gamblin2-2/+3
2017-01-10openjpeg: fixes url (#2790)Massimiliano Culpo1-0/+4
2017-01-09Temporary workaround for R concretization bug (#2756)Adam J. Stewart1-2/+1
2017-01-09Added list_url to r-dt package (#1533)sknigh1-0/+1
2017-01-07Get Rid of nobuild, nolink, and alldeps (#2765)Elizabeth Fischer184-515/+508
* 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')`
2017-01-07Various updates to the NCO package and dependencies (#2639)Adam J. Stewart9-100/+45
* 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
2017-01-07Unset PETSC_DIR during installation (#2768)Adam J. Stewart1-1/+11
* Set PETSC_DIR during installation * Move env var unsets to setup_environment * Fix unset var name and number of args
2017-01-07Added needed deps for bbcp (#2773)James Wynne III1-0/+3
2017-01-07Preliminary RPackage class (#2761)Adam J. Stewart173-1213/+238
2017-01-07Fix issues linking hDF5 1.8.14 and below on Ubuntu. (#2772)Todd Gamblin1-1/+15
2017-01-06add conduit 0.2.1 release (#2766)Cyrus Harrison1-1/+2
2017-01-06Add boost 1.63.0 (#2743)Bruno Turcksin1-0/+1
2017-01-06Merge pull request #2740 from jrood-nrel/jonroodGregory Lee1-1/+2
Renaming mkl to intel-mkl
2017-01-06GitLab: Tarball Version Test (#2296)Axel Huebl2-2/+29
* GitLab: Tarball Version Test Upload a test demonstrating #2290 * Add GitLab parsing
2017-01-06various python package version and dependency updates (#2751)Gregory Lee7-3/+11
* various python package version and dependency updates * various python package version and dependency updates
2017-01-05espressopp: package for the ESPResSo++ software (#2602)Christoph Junghans1-0/+79
* 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.
2017-01-05Add dependencies and finish the py-tornado package.Matthew Krafczyk34-26/+1200
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
2017-01-05Added npm, node.js, and Jupyter dependenciesJean-Paul Pelteret10-0/+485
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
2017-01-05Correct env vars for modulecmd; Fixes #1481 (#2745)Mario Melara1-14/+2
Don't override MODULEPATH with PATH, PATH has no modulefiles PEP8 compliance
2017-01-05test: fixed 'refresh_builtin_mock' fixture (#2748)Massimiliano Culpo1-1/+0
2017-01-04Standardize package names: lower-case, not Mixed_CASE (#2475)Elizabeth Fischer205-204/+215
* 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.
2017-01-04Intel-mkl provides mklJon Rood1-0/+1
2017-01-04Renaming mkl to intel-mklJon Rood1-1/+1
2017-01-04Use zlib's "fossil" site for old tarballs (#2735)George Hartzell1-4/+5
* 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)
2017-01-04add package for conduit (#2670)Cyrus Harrison1-0/+312
* 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
2017-01-04opencoarrays: new version (#2734)Jeffrey Salmond1-3/+1
* add version 1.8.0 * remove depends_on('cmake') as it is now unecessary * remove 'coarrays' as a virtual package
2017-01-04New package: ccache (#2721)Jean-Paul Pelteret1-0/+44
2017-01-04libpng: Upgrade versions to fix vulnerability. (#2723)Elizabeth Fischer2-7/+15
2017-01-04zlib@1.2.10 and R do not get along, work around it (#2727)George Hartzell1-0/+1
* 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.
2017-01-03Update to latest zlib version, server no longer provides older version (#2720)Barry Smith1-1/+4
* 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
2017-01-02Fix issues when a package provides the same vdep twice. (#2710)Todd Gamblin6-34/+117
* 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
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