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2018-02-27Fix class name in build system tutorials (#7346)Mario Melara2-2/+2
AutoTools -> Autotools
2018-02-27updating zfp version (#7304)Mark C. Miller1-8/+5
2018-02-27Added initial Spackage for examinimd (#7350)Robert Pavel1-0/+85
2018-02-27minighost package: fixed a typo (#7349)Christoph Junghans1-1/+1
2018-02-27aspcud@1.9.4: new package (#7094)Geoffrey Oxberry1-0/+53
2018-02-27MPark.Variant (#7251)Axel Huebl1-0/+38
Adds Michael Park's C++11 `std::variant` (a C++17 stdlib feature).
2018-02-27minighost: fix mpi build (#7310)Christoph Junghans1-1/+1
2018-02-27snbone: fix build gcc-4.8 (#7317)Christoph Junghans1-1/+3
2018-02-27spglib: add new package (#7321)Denis Davydov3-0/+98
2018-02-27Docker-Based Developer Resource (#5871)Omar Padron25-0/+1308
* add docker-based development resources * incorporate feedback from @ax3l * fix docs/improve ssh handling * experiment with custom prompt * add arch/fix missing core_compilers key * add centos/minor tweaks * make prompt experiment optional * workaround problem with latest fedora docker image * add docker documentation page to index toc * try another documentation fix * switch arch linux base to base/archlinux * update the git urls in the Dockerfiles * add opensuse * switch CUSTOM_PROMPT variable to simply "PROMPT"
2018-02-26cpu_features (#7302)Axel Huebl1-0/+43
Adds Google's new cpu_features library. Install was added recently, so don't take the `0.1.0` release but the current `master` until a new version is published.
2018-02-26llvm package: update python dependency (#7100)healther1-1/+2
llvm versions >= 5 can use python 3.x
2018-02-26branson: needs mpi-2 (#7319)Christoph Junghans1-1/+1
2018-02-26ebms: needs mpi-2 (#7320)Christoph Junghans1-1/+1
2018-02-26hpgmg: more sane defaults for a proxy (#7330)Christoph Junghans1-1/+1
2018-02-23llvm and llvm-lld package updates (#7313)Mike Pozulp2-51/+35
* Combined llvm and llvm-lld: removed the separate llvm-lld package and added llvm-lld as an optional add on to the llvm package (the way several other llvm tools are maintained e.g. lldb) * Added more lld hashes to llvm package * The 'CppBackend' target doesn't exist for version 3.9.0 or later so exclude it for later versions * Was incorrectly specifying 'sparc' as a target for the 'sparc' architecture - needed to specify 'Sparc' * Fix issue #7248 building llvm: don't make the LLVMDemangle target for llvm < 4.0.0
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
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