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2018-01-10Update to the latest version of six (#6787)Adam J. Stewart1-3/+8
2018-01-10Fix bug in placeholder spack cd command and add unit tests (#6776)Adam J. Stewart3-3/+40
2018-01-10Geant4: fix qt dependency (#6828)Adam J. Stewart1-2/+2
2018-01-10Older versions of libiconv don't work with newer versions of GCC (#6829)Adam J. Stewart1-0/+2
2018-01-10opa-psm2: new package (#6874)Levi Baber1-0/+54
* opa-psm2: new package * opa-psm2: installs now. think the module file needs work * opa-psm2: module file seems good now * opa-psm2: remove fixme * opa-psm2: flake8 fixes * opa-psm2: removing unnecessary make in install phase
2018-01-10bcftools is a AutotoolsPackage. (#6881)健美猫1-5/+1
2018-01-10emacs: on darwin, do not build Cocoa app (#6882)Geoffrey Oxberry1-0/+7
Building emacs on darwin throws an error when trying to build an Emacs app in the nextstep/Emacs.app path of the build tree. For now, disable building this app. It's possible to enable building the app also; Homebrew offers options to this effect, and also adds Mac-specific options for starting the emacs daemon. However, for the sake of simplicity and getting a workable up-to-date emacs installation on my machine as quickly as possible, this commit focuses on a minimal viable modification.
2018-01-10Add a new package: unblur. (#6867)健美猫1-0/+72
* Add a new package: unblur. * Add a new package: unblur. * Add a new package: unblur. * Add a new package: unblur. Conflicts: var/spack/repos/builtin/packages/unblur/package.py * Add a new package: unblur.
2018-01-10Add unit tests for spack arch command (#6775)Adam J. Stewart1-0/+34
2018-01-10Add unit tests for spack graph command (#6778)Adam J. Stewart1-0/+76
2018-01-10Fix bash tab completion for spack install (#6868)Adam J. Stewart1-3/+5
2018-01-10Fix a typo in fetch_strategy error message formatting (#6878)Adam J. Stewart1-1/+1
2018-01-10Explicitly cast Version to str in openfoam-org (#6880)Adam J. Stewart1-2/+2
2018-01-10Fix tests for git package (#6869)Adam J. Stewart1-0/+3
2018-01-09casper: new package (#6873)Yifan Zhu2-2/+54
* casper: create package * jellyfish: added version 2.2.7 * casper: new package * casper: depends on jellyfish 2.2.3 or higher * casper: moved depends_on above install * casper: updated package.py * fixing download url for 1.11.1 * casper: set up environment * casper: add conflicts gcc@7.1.0, cannot install with 7.1.0 * capser: flake8 error corrcted * casper: create package * jellyfish: added version 2.2.7 * casper: new package * casper: depends on jellyfish 2.2.3 or higher * casper: moved depends_on above install * casper: updated package.py * fixing download url for 1.11.1 * casper: set up environment * casper: add conflicts gcc@7.1.0, cannot install with 7.1.0 * capser: flake8 error corrcted
2018-01-09prodigal: Create new package (#6870)Eric1-0/+41
2018-01-09A new package: jbigkit. (#6847)健美猫1-0/+54
* A new package: jbigkit. * A new package: jbigkit. * Add a new package: jbigkit.
2018-01-09changed url for astyle (#6863)BenBrands1-3/+3
* changed url for astyle * use SourceForge
2018-01-09[WIP] Fix git gettext/libintl handling (builds on ubuntu) (#6859)George Hartzell1-2/+18
* Fix git on ubuntu, first cut Spack needs to pass information about where the linker can find `libintl`. We're currently using `LDFLAGS` to do so. The `LDFLAGS` info is pasted into the command line upstream of the a file (`libgit.a`) that includes unresolved symbols that need that library. This fails on Ubuntu, although it seems to work on CentOS (see #6841). This change allows git to build on a Ubuntu 16.04.3 droplet. TODO: test on other platforms... * Add a bit of useful commentary
2018-01-09Fix missing dependency in ghostscript (#6866)Federico Ficarelli1-0/+1
2018-01-09Remove std_cmake_args from VTK definition (#6856)Adam J. Stewart1-5/+6
2018-01-08perl-xml-simple: Create new package (#6849)Eric1-0/+36
* perl-xml-simple: Create new package * perl-xml-simple: fix homepage url
2018-01-08perl-digest-md5: Create new package (#6852)Eric1-0/+34
2018-01-08barrnap: Create new package (#6855)Eric1-0/+40
2018-01-08perl-swissknife: Create new package (#6851)Eric1-0/+36
2018-01-08perl-time-piece: Create new package (#6853)Eric1-0/+34
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
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