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2018-02-23accfft: added new package (#7213)Massimiliano Culpo1-0/+66
2018-02-23Pin Sphinx version to v1.7.0 (#7337)Massimiliano Culpo1-1/+1
Later versions of Sphinx fail due to possible clashes with our custom argparse.
2018-02-23Make fix_darwin_install_name python3-compatible (#7329)scheibelp1-10/+6
This updates the fix_darwin_install_name function to use the Spack Executable object to run install_name_tool, which ensures that process output is formatted as a 'str' for python2 and python3. Originally fix_darwin_install_name was invoking subprocess.Popen directly.
2018-02-23QMCPACK - General Improvements (#6958)Nichols A. Romero2-69/+33
* No longer need to patch CMake. Using CMAKE_CXX_FLAGS to include BLAS/LAPACK/MKL header files properly. * Backport two patches to QMCPACK versions prior to 3.3.0: https://github.com/QMCPACK/qmcpack/pull/621, https://github.com/QMCPACK/qmcpack/pull/623 * Insufficient to include lapack_dir in CMAKE_CXX_FLAGS, CMAKE_C_FLAGS is also needed. * Make patched Espresso a default variant instead of a hard dependency. This is easier on computer architectures where Espresso is hard to build. * Fix patching with QE variant. Now using correct form of patch command. * Add QMCPACK v3.4.0 * Backport patch to QMCPACK versions prior to 3.3.0: https://github.com/QMCPACK/qmcpack/pull/643
2018-02-23fix url finding of lru-cache (#7118)healther1-1/+2
Change-Id: I65a93e3d5d1ea52a0be56bbc664c6b5d405e2bf4
2018-02-22maestrowf: new package (#7300)Francesco Di Natale1-0/+40
* Add Maestro Workflow Conductor to Spack * Removal of a trailing whitespace character.
2018-02-22nalu package: update dependency (#7245)Jon Rood1-3/+2
Yaml-cpp hasn't tagged a release in over 2 years, yet they have fixed many things and now have the ability to use find_package in CMake. Since we use this feature in Nalu, we require the latest yaml-cpp until they tag a new release. I have also deprecated the now unnecessary ENABLE_INSTALL flag.
2018-02-22remove dead Exact proxies (no fetch possible) (#7312)Christoph Junghans3-287/+0
2018-02-22ECP-CANDLE benchmark script (#7271)Brian Van Essen1-4/+8
* Added a package for the MDAnalysis toolkit. * Added a variant to the candle benchmark to make MPI support optional. * Added py-requests package.
2018-02-22Added virtualenvwrapper python package (#7270)Brian Van Essen4-0/+124
* Added a package for the MDAnalysis toolkit. * Adding a package for the Python virtualenvwrapper pacakge. Included dependent virtualenv-clone and stevedore packages. Updated py-pbr with a new version to support this. * Added extra necessary dependencies and fixed the file download paths.
2018-02-22Fixed Theano GPU support (#7325)Brian Van Essen4-2/+99
* Added a package for the MDAnalysis toolkit. * Added a new package for pygpu, which is the python front end of the libgpuarray. Additionally changed the dependency for theano so that it properly picks up the pygpu library. * Added the libcheck package. Fixed flake8 errors in py-pygpu recipe and removed spurious dependency on cudnn for libgpuarray.
2018-02-22bml: enable MPI by default (#7324)Christoph Junghans1-1/+1
2018-02-22bml: add version 1.2.3 (#7308)Christoph Junghans1-0/+1
2018-02-22yambo: added new package (#7301)Massimiliano Culpo2-2/+171
2018-02-21cohmm: use more sane defaults (#7296)Christoph Junghans1-1/+1
2018-02-21mkl: fix order of libs (#7280)Denis Davydov2-2/+2
2018-02-21clamr: needs cmake-3.1 (#7297)Christoph Junghans1-0/+1
Found in proxyapps/proxy-ci#2
2018-02-21nut: needs cmake-3.0 (#7298)Christoph Junghans1-0/+1
Found in proxyapps/proxy-ci#2
2018-02-21cbench set its environment using `setup_environment` (#7236)Massimiliano Culpo1-9/+9
The edit phase of cbench was used to set environment variables. Though this works, the variables set this way are not dumped to build.env. This commit fixes the issue by setting those variables in the `setup_environment` function.
2018-02-20py-pyvcf: versions 0.6.7 and 0.6.8 (#6743)peetsv1-0/+39
* py-pyvcf: versions 0.6.0 and 0.6.7 * adding dependencies * Changing location of source tarball * updating url to eliminate embedded checksum
2018-02-20new package: Soapdenovo2 (#7047)Yifan Zhu1-0/+43
2018-02-19perl-text-csv: Create new package (#7258)Eric1-0/+34
2018-02-19hdf5: fixing ~/+ fortran builds; updated to version 0.8.0 (#7260)Mark C. Miller1-1/+3
2018-02-19sundials: add the 'headers' and 'libs' properties (#7282)Veselin Dobrev1-3/+37
* [SUNDIALS] Add the 'headers' and 'libs' properties, plus a couple of small tweaks. * [SUNDIALS] Revert incorrectly changed conflicts() directive. Fix style.
2018-02-19updating package: gmap-gsnap (#7285)snehring1-0/+1
* updating package: gmap-gsnap * fixing version order
2018-02-19Augustus update hash (#7286)Levi Baber1-3/+3
* augustus: 3.3 package hash changed * augustus: bamtools libraries now seem to be in lib64
2018-02-18py-quast: Create new package (#7254)Eric1-0/+49
2018-02-18netlib-scalapack: add the libs property (#7265)Veselin Dobrev1-1/+1
2018-02-17Silo: depend on Non-mpi hdf5 (#7275)Christoph Junghans1-1/+1
See #7255 for discussion
2018-02-17add new version (10.2) (#7272)Sinan1-0/+1
2018-02-16Package 'cdo': new versions. (#7250)Sergey Kosukhin1-0/+2
2018-02-15Use abspath to avoid permission errors(#7241)Pramod S Kumbhar2-1/+3
Fixes #5189 When working with non-normalized paths containing ".." on some file systems, Spack was found to encounter a permission error when writing to the path. This normalizes a path written by the intel-parallel-studio package and also normalizes all paths written by the license install hook (for all packages) to avoid this issue for intel-parallel-studio.
2018-02-15new package: igvtools (#6974)Eric2-0/+64
2018-02-15new package: pilon (#7033)Eric2-0/+63
2018-02-15mfem: have hypre link line also link lapack+blas (#7165)Geoffrey Oxberry1-5/+8
Spack's hypre package depends on LAPACK and BLAS, so linking to hypre requires linking to the LAPACK and BLAS libraries used to build hypre.
2018-02-14pmix: add 2.1.0 and more (#7191)Howard Pritchard1-0/+3
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2018-02-14ADIOS 2.1.0 (#7240)Axel Huebl1-0/+4
Adds the first stable API release of ADIOS2, v.2.1.0. Also adds a missing `pybind11` CMake flag for proper Python selection (needed in both the new and previous version).
2018-02-14libtool: symlink correctly on darwin (#7179)Geoffrey Oxberry1-4/+6
To accommodate build systems on Darwin which look for glibtool/ize, #7060 attempted to provide glibtool/ize symlinks for libtool/ize but accidentally created the same symlink twice. #7073 reverted this and replaced libtool/ize with glibtool/ize on Darwin. This led to #7163 since AutotoolsPackages depend on the presence of the 'libtool' binary, so this returns to the approach of #7160 but makes the correct symlinks.
2018-02-14xbraid: add libs method (#7233)Geoffrey Oxberry1-0/+5
XBraid installs `libbraid.a`, but the default `libs` method implementation will search for `libxbraid`, which does not exist. This commit fixes the behavior of the `libs` method for the `xbraid` package by overriding package's `libs` method.
2018-02-14r-seqlogo: new package (#7229)Yifan Zhu1-0/+38
2018-02-14stow: new package (#7235)Geoffrey Oxberry1-0/+46
2018-02-14hypre: add libs method (#7234)Geoffrey Oxberry1-0/+6
2018-02-14r-tfmpvalue: new package (#7230)Yifan Zhu1-0/+43
2018-02-14py-pybedtools: adding older version 0.6.9 (#7107)peetsv1-1/+3
2018-02-14gdbm: fix lmod global name 'spack_cc' undefined (#7225)Geoffrey Oxberry1-1/+3
Prior to this commit, running `spack module refresh` with `gdbm` installed throws the warning: ```console ==> Warning: Could not write module file [/Users/oxberry1/spack/share/spack/lmod/darwin-sierra-x86_64/Core/gdbm/1.14.1.lua] ==> Warning: --> global name 'spack_cc' is not defined <-- ``` This warning is repeated for every `gdbm` installation in Spack. The cause of the issue seems to be the same as in spack/spack (#6089): using `spack_cc`, `spack_cxx`, or similar inside `configure_args` causes the warnings to throw when module files are generated. Moving the use of `spack_cc` into `setup_environment` seems to fix the problem, even though it's a bit of a kludge.
2018-02-14ipopt: fix lmod global name 'prefix' undefined bug (#7224)Geoffrey Oxberry1-1/+1
Running `spack module refresh -m lmod --delete-tree -y` throws the following warning: ```console ==> Warning: Could not write module file [/Users/oxberry1/spack/share/spack/lmod/darwin-sierra-x86_64/openblas/0.2.20-ibhtl5q/clang/5.0.1/ipopt/3.12.9.lua] ==> Warning: --> global name 'prefix' is not defined <-- ``` This warning arises because the variable expansions in `spack.modules.BaseFileWriter` occur at module/package scope. Even though `prefix` is an argument to `install` methods in e.g., `MakefilePackage`, so using this argument within package methods is legal, doing so defeats the introspection logic in `spack.modules.BaseFileWriter`. Replacing `prefix` with `self.prefix` resolves the problem, because the introspection logic in `spack.modules.BaseFileWriter` can use introspection to query IPOPT's prefix.
2018-02-14vardictjava: Adding version 1.4.4 (#7223)peetsv1-0/+1
2018-02-14r-powerlaw: new package (#7222)Yifan Zhu2-0/+46
2018-02-14r-jaspar2018: Create new package. (#7221)lingnanyuan1-0/+37
2018-02-13fftw package: improved libs implementation (#7212)Massimiliano Culpo1-2/+31
Add query parameters to retrieve libraries based on precision (e.g. double or quad) and mpi/openmp support.
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