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2016-10-15fix sqlite download url (#2031)Pramod Kumbhar1-1/+1
2016-10-14Workaround for illegal package merging in py-matplotlib/py-basemap (#1964)Elizabeth Fischer1-1/+75
* Workaround for illegal package merging in py-matplotlib/py-basemap # Conflicts: # var/spack/repos/builtin/packages/py-basemap/package.py * flake8 * flake8 * Be conservative: only apply the namespace package fix for Python >= 3.5.2 * flake8 * Bug fix
2016-10-14Fix list_url for fish shell (#2022)Adam J. Stewart1-2/+1
2016-10-14py-macs2: New package (#2011)John Finigan1-0/+46
* py-macs2: New package * py-macs2: add py-numpy@1.6: dependency
2016-10-14Add missing 'import os'. (#2012)Kelly Thompson1-0/+1
2016-10-14dealii: remove extra test which are now mostly integrated in make test (#2013)Denis Davydov1-113/+0
2016-10-14Package/petsc slepc new versions (#2019)Denis Davydov2-0/+2
* petsc: add 3.7.4 * slepc: add 3.7.3
2016-10-12py-matplotlib: Add variants for optional dependencies. (#2008)Elizabeth Fischer1-21/+42
2016-10-12Made optional CGAL dependencies optional. (#2006)Elizabeth Fischer1-17/+34
* Made optional CGAL dependencies optional. * cgal: Added note explaining that the CORE library is not the same as core CGAL functionality. * Bug fix and flake8 * flake8
2016-10-12Mock up Xcode devdir to make Qt5 work on Mac OS X (#1832)Ben Boeckel2-2/+2
* build_environment: allow compilers to set up an environment * clang: mock up a toolchain directory for xcode Some projects ignore CC and CXX flags and instead use xcode to find the toolchain. Clang on Apple should set up the environment properly. Arguably, every compiler could do this on Apple, but let's see how this works out just for AppleClang for now. The Documentation directory is ~1.7G and the excluded platforms add up to about 7G. Ignoring swift saves another 500M. The resulting Xcode.app copy is in the 2G range. * compiler: set member variables early This is required so that later methods can query things such as the version of the compiler. * compiler: support finding the real path of the compiler On Apple, the /usr/bin compilers are actually wrapping tools themselves which query xcrun for the currently selected Xcode installation. Pierce this veil and get the real, full path the to underlying compilers instead. * icu4c: install with rpath On macOS, icu installs with a library ID of the library name. Enabling rpath makes its ID its full installed path which lets Qt5 link against it successfully. * qt: no -no-gtkstyle flag on Qt5 on macOS
2016-10-11Make `insecure` option work with curl AND git. (#1786)Todd Gamblin1-20/+6
2016-10-11patchelf: Add version (#1540)Elizabeth Fischer1-1/+3
* patchelf: Add version * flake8 * Removed unnecessary url_for_version() function. * Restored old URL
2016-10-11oce: fix for Sierra (#1934)Denis Davydov2-0/+50
2016-10-11Abinit: Added package(s) (#1995)gmatteo4-0/+306
* First version of Abinit package * Ignore *.swp files * Add libxc, etsf_io packages * AtomPaw package * Make Abinit depend on mpi@2: and external version of libxc, netcdf, hdf5, etsf_io * etsf_io: install Fortran modules in prefix.include * Remove etsf_io from abinit requirements * Add libxc2.2.1 (required by Abinit and atompaw) * Cleanup * Run make check * Cleanup * Use ld_flags instead of hard-coded libs, fix pep8, add copyright * Put scalapack before lapackblas
2016-10-11Update Package : ExodusII (#1504)Joseph Ciurej4-41/+66
* Added support for the 'maxdims' and 'maxvars' flags for 'NetCDF'. * Added the '+mpi' variant and improved dependencies for 'exodusii'. Improved the 'exodusii' package so that it's less reliant on patches. * Added better type checking to variant values in the 'netcdf' package. * Corrected the required CMake version for the 'exodusii' package. * Fixed the dependencies of the '+mpi' variant of the 'exodusii' package.
2016-10-11Package all of Xorg/X11/XCB (#1740)Adam J. Stewart263-108/+12270
* Updates to Mesa and other Xorg packages * Add packages for all Xorg Protocol extensions * Add packages for first half of Xorg libraries * Add packages for remaining Xorg libraries * Add packages for all Xorg utilities * Add packages for Xorg documentation tools * Add build deps to Xorg protocol headers * Add packages for XCB * Add build deps to Xorg libraries * Add build deps to Xorg utilities * Add packages for Xorg fonts and font-related utilities * Change font deptype from build to default I wasn't sure which deptype was appropriate at first since none of the packages are actually linked together. I initially chose the build deptype for this reason. However, the font packages don't install into their own prefix. They install into font-config. If font-config is a build dependency, that means you can uninstall it without uninstalling the font packages, which wouldn't make sense since they install into font-config. So I switched them back to the default deptype. * Minor formatting changes to ncview * Add half-way done xorg-server package * Add packages for Xorg test suites, not yet tested! * Add packages for Xorg data * Add first quarter of Xorg apps * Add more packages for Xorg apps * Add dependencies to mesa * Remove comments from mesa package * Flake8 * Add more packages for Xorg apps * Add more packages for Xorg apps * Add more packages for Xorg apps * Add more packages for Xorg apps * Add more packages for Xorg apps * Add package for Sublime Text * Add packages for remaining Xorg apps * Revisit testing packages, add missing dependencies * Add dependencies, clean up FIXMEs
2016-10-11hypre: fix blas/lapack for MKL (#1993)Denis Davydov1-2/+2
2016-10-11Merge pull request #1989 from KineticTheory/cray_compile_wrappersTodd Gamblin1-4/+12
On Cray machines, use the Cray compile wrappers instead of MPI wrappers.
2016-10-11Add variant to MPICH to enable ROMIO support (#1944)Adam J. Stewart1-32/+32
2016-10-11tethex: add a new package (#1991)Denis Davydov1-0/+49
2016-10-11More specific dependency versions, wrap make check (#1962)Adam J. Stewart3-12/+25
2016-10-11Update libjpeg-turbo: added new version and removed redundant dependency. ↵Sergey Kosukhin1-7/+12
(#1897)
2016-10-11pango: add missing dependency (#1958)Denis Davydov1-0/+1
2016-10-11libcerf: fix for modern clang (#1959)Denis Davydov1-1/+7
2016-10-11[WIP] Use boost system layout by default (#1955)scheibelp2-8/+28
Use boost system layout by default
2016-10-11Charm++: Ignore compiler warnings while configuring (#1981)Erik Schnetter2-0/+18
2016-10-11Trilinos: Use more flexible option for locating the BLAS library directory. ↵Kelly Thompson2-9/+2
(#1987) + This change fixes a problem that manifests when trilinos is built against a MKL installation defined as an external package. In this scenario, the MKL libraries are found one directory deeper than for the case where spack provides MKL. The extra directory is a platform name like 'intel64'. + The changes in this PR were recommended by contributor @davydden. I implemented and tested with intel@16.0.3. These changes fix the issue I reported. I did not attempt building trilinos against other BLAS implementations. + fixes #1923
2016-10-11hpx5 version update (#1967)Pramod Kumbhar1-2/+3
2016-10-11Mfem 3.2 (#1202)Geoffrey Oxberry1-15/+55
* mfem: add tarball extension Add tarball extension as a result of a feature added in PR#1926, which fixes earlier issues in this PR (PR#1202). Prior to adding this feature, Spack would not autodetect the extension of the tarball downloaded from the redirected, shorted Google URL, requiring a messy hack. This hack worked for mfem version 3.1, but led to errors when adding mfem version 3.2 because the files downloaded from Google did not contain the package name, version number, or extension. Adding the extension enables Spack to rename the tarball downloaded from Google to a sensible name that is compatible with its filename parsing algorithms so that Spack "does the right thing" (detects that the file is a GZipped tarball, decompresses it, runs GNU Make) in fetching and staging the package. * mfem: add linkage to KLU & BTF Add linkage to the KLU & BTF solvers, which are now enabled in MFEM for versions 3.2 and later. * mfem: Add superlu-dist variant Add linkage to SuperLU_DIST, which is a new linear solver interface for MFEM versions 3.2 and later. * mfem: add netcdf variant for cubit mesh support Add NetCDF variant for MFEM versions 3.2 and later; installing the NetCDF interfaces enables CUBIT mesh support.
2016-10-10On Cray machines, use the Cray compile wrappers instead of MPI wrappers.Kelly (KT) Thompson1-4/+12
+ Cray compile wrappers are MPI wrappers. + Packages that need to be compiled with MPI compile wrappers normally use 'mpicc', 'mpic++' and 'mpif90' provided by the MPI vendor. However, when using cray-mpich as the MPI vendor, the compile wrappers 'CC', 'cc' and 'ftn' must be used. + In this scenario, the mpich package is hijacked by specifying cray-mpich as an external package under the 'mpich:' section of packages.yaml. For example: packages: mpich: modules: mpich@7.4.2%intel@16.0.3 arch=cray-CNL-haswell: cray-mpich/7.4.2 buildable: False all: providers: mpi: [mpich] + This change allows packages like parmetis to be built using the Cray compile wrappers. For example: 'spack install parmetis%intel@16.0.3 ^mpich@7.4.2 os=CNL' + This commit relies on the existence of the environment variable CRAYPE_VERSION to determine if the current machine is running a Cray environment. This check is insufficient, but I'm not sure how to improve this logic. + Fixes #1827
2016-10-10Update package to use MPI compile wrappers as specified in MPI package. (#1985)Kelly Thompson1-6/+4
+ Previouly, these strings were hard coded to 'mpicc', 'mpic++', and 'mpifort'.
2016-10-10fix blas-lapack in scipy and numpy (#1949)Denis Davydov2-19/+14
* fix blas-lapack in scipy and numpy * py-numpy: do not set rpath on macOS * py-scipy: do not set Blas/Lapack. This appears to be picked up from py-numpy * py-numpy: don't write rpath= in Sierra only * py-numpy: add a link to build notes
2016-10-10Correct Charm++ install procedure (#1957)Erik Schnetter1-0/+16
Charm++ only creates symbolic links instead of copying files. Correct this.
2016-10-07Added symengine and associated packages (#1885)Jean-Paul Pelteret7-4/+365
Symengine and associated packages
2016-10-06Restore default RPATH settings but allow packages to limit to immediate ↵Todd Gamblin1-0/+4
deps. (#1954) - Some packages (netcdf) NEED RPATHs for transitive deps. - Others (dealii) will exceed OS limits when the DAG is too large.
2016-10-06atlas: add 3.10.3 (#1952)Denis Davydov1-0/+3
2016-10-06Feature Proposal : Make All Python Extensions User Configuration Independent ↵Joseph Ciurej86-94/+90
(#1435) * Updated all Python extension packages to use 'setup_py' on install. * Fixed a few minor style issues with the updated Python packages.
2016-10-06Update gmp: fixed an issue with intel compiler. (#1898)Sergey Kosukhin1-2/+8
2016-10-06Updated nettle to have m4 as an immediate dependency (#1946)Jay1-0/+1
* Updated nettle to have m4 as an immediate dependency to match new PATH construction logic which only includes immediate dependencies. * Update package.py
2016-10-06Sqlite ppc64le configure build guess fix (#1684)James Wynne III1-1/+10
* Added check for ppc64le because configure cant guess the build type for rhel on ppc64le Expand/clarify description of dependency types Refactored getting the arch so that its less verbose * Fixed flake8 issues
2016-10-06Update pixman: mmx is disabled only for MacOS. (#1896)Sergey Kosukhin1-3/+9
2016-10-06Update libtiff: updated homepage and fetch urls. (#1895)Sergey Kosukhin1-2/+3
* Update libtiff: updated homepage and fetch urls. * Update libtiff: new version 4.0.6.
2016-10-06cgal: build out of source. (#1918)Elizabeth Fischer1-4/+4
* cgal: build out of source. * Simplify cmake out-of-source.
2016-10-06add python options to vtk package (#1931)Jeffrey Salmond1-1/+5
2016-10-05mumps: Add alternate download location (in comments) (#1919)Elizabeth Fischer1-0/+2
2016-10-05Add package for CONVERGE CFD (#1905)Adam J. Stewart1-0/+69
2016-10-05Add latest versions, resolve variant resolution bug (#1909)Adam J. Stewart3-8/+14
2016-10-05everytrace: New package (#1543)Elizabeth Fischer2-0/+98
* everytrace: New package Everytrace ensures that stack trace is obtained every time a program exits, for whatever reason. * everytrace: Change CMake to build dependency * Renamed to everytrace-example, flake8 and copyright issues. * flake8 * Missing type=build
2016-10-05Add missing dependencies for Flake8 (#1883)Adam J. Stewart9-26/+364
* Warn user if flake8 can't find setuptools * Add missing dependencies of flake8 * Updates to py-autopep8, make packages activateable * Check for presence of setuptools for Sphinx too * Fix bug in order of commands
2016-10-05PNGwriter, libSplash: Add `master` version (#1744)Axel Huebl2-0/+8
* PNGwriter, libSplash: Add `master` version * PNGwriter, libSplash: Add `dev` versions Can be used for now, `develop` is currently discouraged.
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