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2016-12-10clang: do xcode mockup iff requested by a package (#2544)Denis Davydov5-5/+15
* clang: do xcode mockup iff requested by a package * add a note * add pkg to setup_custom_environment() and decide whether or not to use mockup XCode there based on the package
2016-12-10Eigen 3.3.1 is latest stable version. (#2551)Stephen McDowell1-0/+1
Main page states [3.3.1 is latest stable](http://eigen.tuxfamily.org/index.php?title=Main_Page).
2016-12-10Scotch 6.0.4 is available. (#2552)Stephen McDowell1-0/+1
Source project page states [6.0.4 is latest stable](http://scotch.gforge.inria.fr/)
2016-12-10Implementation of spack file for Pflotran (#2444)Barry Smith2-1/+50
Supports installing both a "known version" of PETSc/PFlotran that works and the develop/master branches of both packages Funded-by: IDEAS Project: IDEAS/xSDK Time: 4 hour
2016-12-09update flux dependencies and package (#2541)Tom Scogland8-40/+90
* update flux dependencies and package * refinements from @adamjstewart * fix flux document generation The docbook-xsl package has been added, and correctly configures catalog files to generate documentation correctly with asciidoc.
2016-12-09astyle: do not set user/group when installing on macOS (#2542)Denis Davydov1-0/+5
* astyle: do not set user/group when installing on macOS * astyle: add new version
2016-12-09petsc: explicitly disable X11 (#2533)Denis Davydov1-2/+3
otherwise petsc may pickup libX11 on login nodes during config/build, but libX11 may not be available on computation nodes.
2016-12-08Make targets an attribute of compilers (#2500)becker336-25/+56
* Make targets an attribute of compilers, similar to OS. Allows users to use `spack compiler find` to add compilers for the same platform/os but different targets when spack is installed on a file system mounted on machines with different targets. * Changed get_compilers() method to treat old compilers with no target as target='any' * flake8 changes * Address change requests for comments/code clarity
2016-12-08Json loader now returns str objects instead of unicode. (#2524)Sergey Kosukhin1-2/+22
2016-12-08Added packages: cmor and uuid. (#2527)Sergey Kosukhin2-0/+108
* Added package 'uuid'. * Added package 'cmor'. * Updated 'cmor' and 'uuid': docstring formatting.
2016-12-08Revert to-string for CNL operating system (#2526)scheibelp2-3/+3
2016-12-08Add support for parsing R-XML URL versions. (#2525)Todd Gamblin4-9/+23
* Add support for parsing R-XML URL versions. * Better url-parse debug output. - just print the debug stuff all the time. * fix R-XML versions.
2016-12-08Update emacs: current release, use our x11 bits (#2052)George Hartzell4-12/+21
* Update emacs: current release, use our x11 bits Add checksum for 25.1 release. Rework the X support: - use Spack's X11 bits - add ability to specify an X toolkit (gtk or athena, default is gtk). - change toolkit names to align with Emacs' configure usage. * PEP8 cleanups. * glib dependency should not be type=build I'd like to blame that on a typo, but it's a few too many characters for that to be viable. I'm not sure what I was thinking. * Pass X variant down: emacs->pango->cairo * X variants default to False, warn on bad toolkit Change the X variants for emacs, pango and cairo to default to False. Check that the toolkit is a valid choice and give a reasonable error if not. * Fix flake8 issue, reword warning text * gtkplus needs to use +X variant for pango to work In order for a useful variant of pango to be built into the spec I needed to make the dependency on gtkplus explicitly specify it's X variant. The X variant is the default, but that wasn't enough to make it happy. Since it's happiness is the most imporant thing in the world, this change! :)
2016-12-08Scotch fails to build with latest flex (#2523)Adam J. Stewart1-1/+1
2016-12-08dealii: remove dependencies which are not needed (#2522)Denis Davydov1-4/+0
2016-12-08fix for bluegene-q platform (#1980)Pramod Kumbhar2-3/+35
* fix for bluegene-q platform * change powerpc to ppc64 * change CNK to cnk
2016-12-08Fix deptypes for deps specified on command line (#2307)scheibelp2-20/+60
Fixes #2306 Any dependency explicitly mentioned in a spec string ended up with the build and link deptypes unconditionally. This fixes dependency resolution to ensure that packages which are mentioned in the spec string have their deptypes determined by the dependency information in the package.py files. For example if a package has cmake as a build dependency, and cmake is mentioned as a dependency in the spec string for the package, then it ends up with just the build deptype.
2016-12-08Use frontend OS for build/run deps by default (#2292)scheibelp5-25/+91
Packages built targeting a backend may depend on packages like cmake which can be built against the frontend. With this commit, any build dependency or child of a build dependency will target the frontend by default. In compiler concretization when packages copy compilers from nearby packages, build dependencies use compiler information from other build dependencies, and link dependencies avoid using compiler information from build dependencies.
2016-12-07Add version/digest for emacs 25.1 (#2511)George Hartzell1-0/+1
* Add version/digest for emacs 25.1 * Put newest version at top of list
2016-12-07yaml-cpp: add boost dependency (#2517)Andrey Prokopenko1-3/+4
yaml-cpp has a boost dependency, and according to [yaml-cpp page](https://github.com/jbeder/yaml-cpp): yaml-cpp 0.5.3 has been released! This is a bug fix release. It also will be the last release that uses Boost; futures releases will require C++11 instead.
2016-12-07add ACLOCAL_PATH updates for packages that register m4 macros (#2518)Tom Scogland1-0/+2
2016-12-07Fixed spelling of variable (#2516)Oliver Breitwieser2-2/+2
2016-12-07Building lua-luafilesystem requires a newish-git (#2515)George Hartzell1-0/+1
See #2059 for background. I'm unable to install `lmod` because lua-luafilesystem fails. The luarocks install bits attempt to do a shallow clone of the luafilesystem sources and the default git on my CentOS 7 test box (`git version 1.8.3.1`) fails. This adds a build dependency that ensures that a relatively modern git is available.
2016-12-07Update texlive digest value (#2514)George Hartzell1-2/+9
* Update texlive digest value While the discussion in #2494 progresses, this changes fixes the digest values so that builds succeeed. * Add warning that texlive is not repeatably installable
2016-12-07netcdf: add checksum for 4.3.3.1 version (#2509)Andrey Prokopenko1-3/+4
2016-12-07cmake: added checksum for 3.1.0 version (#2508)Andrey Prokopenko1-1/+2
2016-12-06hypre, superlu-dist, trilinos - support using develop/master branches of ↵Barry Smith0-0/+0
these packages (#2443) Funded-by: IDEAS Project: IDEAS/xSDK Time: 1 hour
2016-12-06hypre, superlu-dist, trilinos - support using develop/master branches of ↵Barry Smith3-2/+24
these packages (#2443) Funded-by: IDEAS Project: IDEAS/xSDK Time: 1 hour
2016-12-06Fixed a few minor issues with the 'fontconfig' package install script. (#2491)Joseph Ciurej1-4/+4
2016-12-05hdf5: added 'pic' variant (#2373)Andrey Prokopenko1-0/+7
2016-12-05Remove CYAML tests from Spack now that the DB is JSON. (#2487)Todd Gamblin1-4/+2
2016-12-05Add Java support to OpenMPI (#2285)Adam J. Stewart1-55/+93
* Update OpenMPI to the AutotoolsPackage * Add Java support to OpenMPI * Fix missing commas * Be more specific about what versions support what flags * Revert description for thread_multiple variant
2016-12-05py-rtree: Added package (#1548)Elizabeth Fischer2-0/+95
* py-rtree: Added package * py-rtree = RTree (spatial indexing) data structure for Python * libspatialindex = Underlying C library wrapped by py-rtree * Flake8 and Copyright issues. * Fix Python syntax error. * Fixed dependency type error. * Added new version, based on updates requested in upstream PR * 1. Change cmake to build dependency. 2. Updated to CMakePackage
2016-12-05Use JSON for the database instead of YAML. (#2189)Todd Gamblin8-90/+282
* Use JSON for the database instead of YAML. - JSON is much faster than YAML *and* can preserve ordered keys. - 170x+ faster than Python YAML when using unordered dicts - 55x faster than Python YAML (both using OrderedDicts) - 8x faster than C YAML (with OrderedDicts) - JSON is built into Python, unlike C YAML, so doesn't add a dependency. - Don't need human readability for the package database. - JSON requires no major changes to the code -- same object model as YAML. - add to_json, from_json methods to spec. * Add tests to ensure JSON and YAML don't need to be ordered in DB. * Write index.json first time it's not found instead of requiring reindex. * flake8 bug.
2016-12-05Allow spack create to handle packages with period in name (#2351)Adam J. Stewart3-10/+13
* Allow spack create to handle packages with period in name * Update tests to handle new package name detection scheme
2016-12-05ghostcript-fonts: fix install on macOS (#2482)Denis Davydov1-1/+7
2016-12-05xextproto: fix on macOS by not running parallel build (#2483)Denis Davydov1-0/+2
2016-12-05travis: sphinx does not support python 2.6 anymore (#2485)Massimiliano Culpo1-0/+3
2016-12-04Bugfix: restore `__contains__` method after ArchSpec refactor. (#2481)Todd Gamblin1-0/+3
2016-12-03Update go to 1.7.4 and 1.6.4 to fix security issues (#2467)George Hartzell1-5/+20
* Update go to 1.7.4 and 1.6.4 to fix security issues The go team recently rolled out two releases to address security issues. Details available on the [go release site](https://golang.org/doc/devel/release.html). This commit updates our explicitly supported versions. It also includes a comment about two CentOS requirements (enable user_namespace and ensure that the static c library is installed) that are required for the pacakges to pass their tests. * Flake8 cleanup
2016-12-03zlib: added 'pic' variant (#2470)Andrey Prokopenko1-0/+12
It looks more complicated because zlib has custom configure which does not support CFLAGS option. So instead, we take it from environment.
2016-12-03Update git package to include 2.11.0 (#2471)George Hartzell1-0/+1
2016-12-03Fixes to Handling Multiple Architectures (#2261)Joseph Ciurej13-272/+473
* Added some notes about how multiarch detection could be fixed. * Implemented a preliminary version of the "spack.spec.ArchSpec" class. * Updated the "spack.spec.Spec" class to use "ArchSpec" instead of "Arch". * Fixed a number of small bugs in the "spack.spec.ArchSpec" class. * Fixed the 'Concretizer.concretize_architecture' method so that it uses the new architecture specs. * Updated the package class to properly use arch specs. Removed a number of unused architecture functions. * Fixed up a number of bugs that were causing the regression tests to fail. Added a couple of additional regression tests related to architecture parsing/specification. Fixed a few bugs with setting reserved os/target values on "ArchSpec" objects. Removed a number of unnecessary functions in the "spack.architecture" and "spack.concretize" modules. * Fixed a few bugs with reading architecture information from specs. Updated the tests to use a uniform architecture to improve reliability. Fixed a few minor style issues. * Adapted the compiler component of Spack to use arch specs. * Implemented more test cases for the extended architecture spec features. Improved error detection for multiple arch components in a spec. * Fix for backwards compatibility with v0.8 and prior * Changed os to unknown for compatibility specs * Use `spack09` instead of `spackcompat` for the platform of old specs.
2016-12-02Fix download URL and dependencies for py-pypar (#2430)hegner1-3/+7
* fix download URL and dependencies for py-pypar * use url_for_version in py-pypar
2016-12-02foam-extend: modification to accept flex version >= 2.6 (#2452)Nicolas Richart1-6/+23
* Modification to accept flex version >= 2.6 + bug fix on paraview dependency * flake8 "corrections"
2016-12-02doxygen: Disable unnecessary graphviz dependency by default. (#2323)Elizabeth Fischer1-1/+1
2016-12-02Updating SuperLU package to use pic_flag instead of -fPIC, and removing ↵Jon Rood1-9/+4
specific version for default install method. (#2456)
2016-12-02Updating yaml-cpp from Package to CMakePackage. (#2457)Jon Rood1-9/+11
2016-12-02new intel parallel studio versions (#2459)Gregory Lee1-6/+17
2016-12-01cmake: update the requirements for --no-system-jsoncpp option (#2312)Andrey Prokopenko1-1/+1
The option appeared in CMake 3.2 (specifically, in 3.2.0-rc2, see https://cmake.org/pipermail/cmake-developers/2015-February/024552.html).
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