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2018-01-08perl-text-unidecode: Create new package (#6854)Eric1-0/+34
2018-01-08Cleanup: Remove Dbl Brackets (#6848)Axel Huebl2-26/+26
Remove unnecessary double brackets in ADIOS2 and gearshifft packages.
2018-01-08fix swift-t packages dependencies (#6530)Bryce Allen2-1/+3
2018-01-08Upgrade recipe for parmetis to be a CMakePackage (#6807)Kelly (KT) Thompson1-16/+10
* Upgrade recipe for parmetis to be a CMakePackage + Eliminate `install` method (use the one from CMakePackage). + Move configure options to new method `cmake_args` + Move special install instructions for DarwinOS to a `run_after` method. * Fix run_after section; Remove variant +debug.
2018-01-08Rmlab: Control PNG (#6846)Axel Huebl1-0/+9
Control the find_package of the PNG variant explicitly. This avoids picking up an "external" PNGwriter install in case `~png` is picked by changing the default "AUTO" search to explicit "ON" (required) of "OFF" (ignore if exists).
2018-01-07Add documentation on Codecov (#6842)Adam J. Stewart1-12/+60
2018-01-06Siesta: only apply patch to <4.1 and fix Intel compiler (#6466)Michael Kuron2-10/+54
* Siesta: add 3.2 and don't apply patch to 4.1 * siesta: fix bad optimization with Intel compiler * siesta: Fix download URL * siesta: build utilities too * siesta: fix binary name collision * siesta: Cleanup
2018-01-06Blitz 1.0.1 (#6765)Milton Woods1-2/+3
* blitz: update to version 1.0.1 * blitz: change URL for release tarballs * blitz: update checksum of @1.0.0 after changing URL
2018-01-06py-psyclone: Parallelisation System for climate models (#6797)Milton Woods1-0/+65
* py-psyclone: Code generation for the PSyKAl framework from the GungHo project * py-psyclone: add installation tests based on py.test * py-psyclone: define 'develop' version as latest master branch * py-psyclone: extract tagged version 1.5.1 from git repo * py-psyclone: whitespace adjustments for flake8 * py-psyclone: use compatible versions of py-fparser * py-psyclone: use type='test' for selected dependencies
2018-01-06Updating OpenFAST to use explicit lapack and blas libraries from Spack. (#6824)Jon Rood1-1/+8
* Updating OpenFAST to use explicit lapack and blas libraries from Spack. * Simplifying openfast blas lib logic and fixes flake8 errors. * Changing order of blas and lapack libs in openfast package.
2018-01-05sailfish: Create new package (#6827)Eric1-0/+37
* sailfish: Create new package * sailfish: fix tbb dependency * sailfish: fix dependency type
2018-01-05py-pybedtools: Create new package (#6487)Eric1-0/+42
* py-pybedtools: Create new package * py-pybedtools: add py-six requirement * py-pybedtools: remove py-cython dependency for release version * py-pybedtools: include minimum version of py-pysam
2018-01-05Fixes the bug in spack configure spotted in #6833 (#6837)Massimiliano Culpo1-1/+1
2018-01-05Fix spack configure output (#6835)Adam J. Stewart1-1/+1
2018-01-05Add a package: ctffind. (#6836)健美猫1-0/+37
* Add a package: ctffind. * Add a package: ctffind.
2018-01-05Provide build_type variant for Metis. (#6808)Kelly (KT) Thompson1-11/+22
* Provide build_type variant for Metis. + Ideally, we would make Metis a CMakePackage, but `metis@:5` doesn't use CMake. + For now, provide a `build_type=` variant similar what is found in CMakePackage. + There is a potential for duplicate specification of `CMAKE_BUILD_TYPE` if both variants `+debug` and `build_type=` are specified. I am looking for advice on how this can be resolved. * Update metis recipe in response to flake8 and user comments. + Wrap comment lines that used more than 80 columns. + Change `+debug` variant to avoid potential for multiple `-DCMAKE_BUID_TYPE=` arguments provided to cmake. Specifying this variant no longer appends this configure option. However, if `+debug` is specified, require `build_type=Debug` to maintain expected behavior. * For metis, remove +debug variant; use build_type= instead. + Update recipe for metis@4 to extract `build_type=` values and set `OPTFLAGS` accordingly. + For metis@5:, the behavior from the previously supported variant `+debug` can be obtained with the options `+gdb build_type=Debug` * Conflicts added for metis@4 when build_type != Release|Debug. * Use spack function conflicts instead of 'raise InstallError'.
2018-01-05Fix pymongo package (#6832)David Hows1-2/+3
And update to 3.6
2018-01-04Create a symbolic link to the MotionCor2_x.x.x executable. (#6826)健美猫1-0/+2
* Create a symbolic link for MotionCor2. * Create a symbolic link for MotionCor2. * Create a symbolic link for MotionCor2. * Create a symbolic link for MotionCor2.
2018-01-04Revert "openssl: Add perl dependency" (#6831)Adam J. Stewart1-1/+5
* Revert "Added i3 and its dependencies. (#6805)" This reverts commit a00a09a234886d3bb4e53f873579a56aca11d3ba. * Revert "Adding NEURON simulator package (#5097)" This reverts commit d24782c86d84d51ac3ef7404c9e4a4eb6b9eab7e. * Revert "openssl: Add perl dependency (#5188)" This reverts commit 395ee97f3b1cdd96ae00bdae6d27d3145c50fc5e.
2018-01-04Added i3 and its dependencies. (#6805)stefanosoffia5-0/+233
2018-01-04Adding NEURON simulator package (#5097)Pramod S Kumbhar1-0/+224
* Adding NEURON package widely used in computational neuroscience community * flake8 fixes * Add rx3d variant * Addressed review comments from Adam * Addressed 2nd review comments * Added check for +mpi on bg-q * Filter spack compiler wrappers in NEURON scripts Add gcc march=native flag to make front-end build robust * Make develop as preferred version due to bug in long filename handlings in <= v7.4 * Avoid use of gcc in cross compiling environment Use arch specific options on cray and bg-q arch * Simplify cross compiling build: - v7.5 added and no longer need develop as preferred version - legacy cray related options removed - cross compiling args reduced - python arguments reduced as neuron finds proper libraries * Simplify bg-q configurations * Cleanup and unify arch options * Make sure to add commonly available packages as dependency * Arch path added to dependent_environment as nrniv needed at runtime * Support for Power 8 architecture * Fix python3 on OS X * flake8 fix * remove unnecessary conflcist directives
2018-01-04openssl: Add perl dependency (#5188)Michael Kuhn1-5/+1
perl is required for the configure script.
2018-01-04Protobuf intel patch (#5233)Brian Van Essen2-0/+27
* Added a package for the MDAnalysis toolkit. * Added a patch file to get rid of compiler warnings with intel compiler and inlining. Added checksum values for other versions of protobuf. * Added dependency on Intel compiler for intel patch
2018-01-04Fix build of paraview (#5802)Simone Bnà1-1/+14
* added variant examples to paraview package.py * qt: added libxt dependency * add variant to use external hdf5, this is needed when compiling with gcc@4.8.5 * paraview: added python dependecies to PYTHONPATH
2018-01-04make nghttp2 optional for curl, as it does not build for older compilers. ↵Todd Gamblin1-4/+7
(#5977)
2018-01-04Adding Nek5000 to Spack (#6153)Thilina Rathnayake2-0/+154
* Start adding Nek5000 package * Add tools to install: genmap, prenek, postnek * Address comments by @davydden * Use install_tree (thanks @junghans) and polish * Update url * Fix flake formatting errors * Change F77 and CC compilers Apparently spack compilers can't be called outside spack and we have an underscore test in our Nek5000/core/makenek.inc file which calls F77 compiler. * Add support for visit and profiling options * Fix a typo * Fix a typo * Remove the C check * Add visit variant * Update the install of int_tp tool * Let MAXNEL to be set during installation
2018-01-04r-rgraphviz: Create new package. (#6316)lingnanyuan1-0/+38
2018-01-04Set SMPI library path in dependent packages (#6548)serbanmaerean1-0/+2
* Added magma package * Incorporated Serban's change * Remove deleted files * argparse.py * Sync forked Spack repo in github * Add spectrum-mpi lib path to LD_LIBRAY_PATH in spack_env. As a result of supporting alternate installation directories, spectrum-mpi does not use rpath anymore, so we need to set LD_LIBRARY_PATH in spack_env to allow MPI programs to run during dependent package configuration. * Fix flake8 error (blank line at EOF)
2018-01-04RNA-SeQC: Create new package (#6555)Eric2-0/+66
* RNA-SeQC: Create new package * RNA-SeQC: Fix flake8 error * RNA-SeQC: Fix Travis error
2018-01-04r-rgeos: Create new package. (#6592)lingnanyuan1-0/+42
2018-01-04qt: add 5.10.0, fix macOS build, clean-up comments/TODOs (#6766)Denis Davydov2-7/+57
* qt: add 5.10.0, fix macOS build, clean-up comments/TODOs * qt: fix pkgconfig files * qt: restore-pc-files.patch * add version constraint to the patch * qt: adjust url_for_version for 5.10.0
2018-01-04xios: I/O management for climate models (#6796)Milton Woods4-0/+289
* xios: XML-IO-SERVER library for IO management of climate models * xios: install to prefix directory * xios: add a test case * xios: define versions to use cache and mirror directories * xios: use proper svn URL for version 910 * xios: package url must be defined, otherwise uninstall fails * xios: add trunk version to allow building latest revision * xios: enable parallel build * xios: allow installation with mpif90 compiler wrappers * xios: use mpi variants of dependencies * xios: allow user to specify MPI launcher via MPIRUN environment variable * xios: prefer spack versions of blitz and boost (needed for gcc@7) * xios: enable builds with clang+gfortran on OSX * xios: use numeric versions for releases, @develop for trunk * xios: different patches required for @1.0 and @develop * xios: patch function for clang works across revisions * xios: link blitz library * xios: workaround bug 17782 in llvm * xios: whitespace adjustments for flake8 * xios: avoid bare except clause * xios: netcdf-fortran inherits ^netcdf+mpi from xios dependencies
2018-01-04py-umi-tools: Create new package (#6823)Eric1-0/+45
* py-umi-tools: Create new package * py-umi-tools: fix dependencies
2018-01-03Update grackle (#6822)Loikki1-2/+3
2018-01-03package openfoam-com: add version 1712 and update patches (#6820)Mark Olesen12-906/+956
* combine all patches for 1612 into a single file, with additional comments to explain the rational. * Add kahip decomposition variant. * Add support for ARM64 architecture. * filter instead of patching etc/config.*/settings. This eliminates patch files for 1706, perhaps for the future as well. * URLs at or before version 1612 have a different structure, so provide a url_for_version implementation to handle this
2018-01-03package/r-rjags: create new package (#6804)Sinan1-0/+46
* package/r-rjags: create new package * fix typo fix typo * package/r-rjags small fix to pass flake8 tests * package/r-rjags: more fixes to satisfy flake8 tests
2018-01-03fltk depends on libx11. (#6816)健美猫1-0/+2
2018-01-03Add a new version and runtime dependency for MotionCor2. (#6817)健美猫1-0/+3
* Update motioncor2 to 1.0.4 and add libtiff dependency. * Add comments for libtiff dependency in MotionCor2.
2018-01-03Add libtiff@3. (#6818)健美猫1-0/+1
2018-01-03suite-sparse: support 64bit BLAS (#6767)Denis Davydov1-0/+6
* suite-sparse: support 64bit BLAS * use double quotes instead of escaped quotes
2018-01-03Flex v2.6.4 conflicts with gcc@7.2.0 (#6819)stefanosoffia1-0/+4
2018-01-02singularity - added master branch (#6631)Douglas Duckworth1-0/+1
* singularity - added master branch as this has latest fixes - 2.4 does not compile on centos 6 without use of this branch * renamed to develop * added master branch properly
2018-01-02New Package: py-adios (#5686)Axel Huebl1-0/+78
The ADIOS1 numpy bindings depend on an installed, fully loaded ADIOS C library + its config tools to build properly.
2018-01-02Intel mkl dnn (#6268)Brian Van Essen1-0/+39
* Added a package for the MDAnalysis toolkit. * Added a package for the Intel MKL-DNN project. * Fixed flake8 errors. * Fixed Flake8
2018-01-02Fix HTML detection (#6394)Michael Kuhn1-1/+2
Some servers report a content-type header instead of Content-Type.
2018-01-02rsem: update version 1.3.0 md5sum (#6650)Eric1-1/+1
2018-01-02atom-dft: new package plus dependencies (#6653)Michael Kuron3-0/+156
* atom-dft: new package plus dependencies * Indentation fix * Use the compiler wrappers * Pass variables instead of using FileFilter
2018-01-02Install all the cli tools from all the sub-directories (#6705)Jimmy Tang1-1/+6
* Install all the cli tools from all the sub-directories * Satisfy pep8
2018-01-02py-lrudict: a LRU-based cache dictionary (#6734)Feiyi Wang1-0/+38
* add py-lrudict * style fix * style fix: add blank lines
2018-01-02py-scandir: a better directory iterator, backport to 2.7 (#6739)Feiyi Wang1-0/+37
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