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2017-05-06gmp: switch to download directly from GNU (#4152)Adam J. Stewart1-1/+1
2017-05-06mpfr: switch to more reliable URL (#4139)Adam J. Stewart1-2/+3
* Add list_url to mpfr * Switch to download directly from GNU * http -> https
2017-05-06Updating bamtools to include a dependency for zlib. (#4031)Barry Britt1-8/+9
* Updating bamtools to include a dependency for zlib. In a standard compile, bamtools will fail if zlib headers are not installed on the target machine. In order to maintain compatibility with all systems -- and since zlib is included already as a dependency for cmake -- this patch adds zlib as a link dependency for the bamtools package. * Modified cmake rpath include. Bamtools has a non-standard library location, so we need to append $prefix/lib/bamtools to the rpath. Not sure there's a better way to do this... * Fixing syntax error in package.py Fixed a non-terminated parenthesis on line 46. * Updated bamtools to be a CMakePackage Removed extraneous code, and altered the package to extend cmake_args including the non-standard library location. * UpRemoving cmake dependency and removing blank line from end of file * Updates to cmake_args. Removed the duplicate definition of std_cmake_args in favor of simply overriding the CMAKE_INSTALL_RPATH variable that is provided. This should allow the package to be linked correctly to itself.
2017-05-06Update zlib to work with other compilers (#4088)Matthew Scott Krafczyk2-0/+15
* Fix -include issue with intel and pgi in zlib MERGE CANDIDATE * Patch zlib to compiler with the cray compiler suite.
2017-05-05Add info for perl@5.22.1 (#4147)George Hartzell1-0/+1
What the user wants, the user gets....
2017-05-05Add latest version of curl (#4140)Adam J. Stewart1-1/+2
2017-05-05Python 3 doesn't have iteritems, use items (#4143)Adam J. Stewart3-5/+5
2017-05-05Add latest version of Lmod (#4141)Adam J. Stewart1-1/+2
2017-05-05Add info for jdk@8u73 (#4137)George Hartzell1-3/+6
* Fix ordering of versions (proper!) * Add url/digest for jdk@8u73
2017-05-05Add OpenCV 3.2.0 checksum (#4138)Todd Gamblin1-0/+1
2017-05-05Add info for r@3.3.3 (#4128)George Hartzell1-0/+1
2017-05-04SV variants are evaluated correctly in "when=" (#4118)Massimiliano Culpo2-1/+11
* SV variants are evaluated correctly in `when=` statements fixes #4113 The problem here was tricky: ```python spec.satisfies(other) ``` changes already the MV variants in others into SV variants (where necessary) if spec is concrete. If it is not concrete it does nothing because we may be acting at a pure syntactical level. When evaluating a `when=` keyword spec is for sure not concrete as it is in the middle of the concretization process. In this case we have to trigger manually the substitution in other to not end up comparing a MV variant "foo=bar" to a SV variant "foo=bar" and having False in return. Which is wrong. * sv variants: improved error message for typos in "when=" statements
2017-05-04variants: fixed packages reported by @adamjstewart in #4098 (#4105)Massimiliano Culpo5-33/+85
2017-05-04patch sqlite to work around macro definition (#4117)Gregory Lee2-0/+19
2017-05-03Update py-beautifulsoup4 (#4089)Matthew Scott Krafczyk1-4/+3
* Update py-beautifulsoup4 * Change beautifulsoup4 url to pypi.io url.
2017-05-03building wget depends on perl > 5.12.0 (#4087)Matthew Scott Krafczyk1-0/+1
* building wget depends on perl > 5.12.0 * Remove extra parenthesis
2017-05-03hdf5: updated version (#4108)Massimiliano Culpo1-0/+1
2017-05-03spack: no stacktrace if not in debug mode + fix emacs variant (#4098)Massimiliano Culpo1-6/+7
* spack: no stacktrace if not in debug mode + fix emacs variant * emacs: removed dead code
2017-05-02Add the py-dryscrape package (#4094)Matthew Scott Krafczyk1-0/+41
* Add the py-dryscrape package * Adjust dependencies and change development to develop
2017-05-02Update the py-lxml package (#4090)Matthew Scott Krafczyk1-0/+4
2017-05-02Add findutils package (#4091)Matthew Scott Krafczyk1-0/+53
2017-05-02Add the py-webkit-server package (#4092)Matthew Scott Krafczyk1-0/+35
* Add the py-webkit-server package * Change development to develop
2017-05-02Add the py-xvfbwrapper package (#4093)Matthew Scott Krafczyk1-0/+37
2017-05-02Add py-pyprof2html package (#4095)Matthew Scott Krafczyk2-0/+49
2017-05-02Add py-libconf package (#4096)Matthew Scott Krafczyk1-0/+36
2017-05-02Add the libconfig package (#4097)Matthew Scott Krafczyk1-0/+43
2017-05-02cgal: updated version (#4081)Massimiliano Culpo1-0/+1
2017-05-02Allow ghostscript to build with Spack dependencies (#4065)Adam J. Stewart1-6/+37
2017-05-02Add missing dependencies to emacs (#4068)Adam J. Stewart1-0/+3
2017-05-02mvapich2: fixed broken reference to spec (#4078)Massimiliano Culpo1-0/+1
2017-05-01Add latest version of libtiff (#4067)Adam J. Stewart1-1/+2
2017-05-01Multi-valued variants (#2386)Massimiliano Culpo6-251/+258
Modifications: - added support for multi-valued variants - refactored code related to variants into variant.py - added new generic features to AutotoolsPackage that leverage multi-valued variants - modified openmpi to use new features - added unit tests for the new semantics
2017-05-01Add latest version of lcms (#4066)Adam J. Stewart1-4/+5
2017-05-01Add a WafPackage base class (#3975)Adam J. Stewart2-12/+19
* Add a WafPackage base class * Correct comment in docstring * Be more specific about the Python versions supported
2017-04-30flecsale: works with python3 (#4058)Christoph Junghans1-1/+1
Ref laristra/flecsale#41
2017-04-30suite-sparse: updated version (#4055)Massimiliano Culpo1-0/+1
2017-04-29Clean up now that submodules are properly supported. (#4053)Christoph Junghans3-21/+3
2017-04-29flecsale: add more features (#4052)Christoph Junghans1-1/+7
2017-04-29Python command, libraries, and headers (#3367)Adam J. Stewart38-182/+262
## Motivation Python installations are both important and unfortunately inconsistent. Depending on the Python version, OS, and the strength of the Earth's magnetic field when it was installed, the name of the Python executable, directory containing its libraries, library names, and the directory containing its headers can vary drastically. I originally got into this mess with #3274, where I discovered that Boost could not be built with Python 3 because the executable is called `python3` and we were telling it to use `python`. I got deeper into this mess when I started hacking on #3140, where I discovered just how difficult it is to find the location and name of the Python libraries and headers. Currently, half of the packages that depend on Python and need to know this information jump through hoops to determine the correct information. The other half are hard-coded to use `python`, `spec['python'].prefix.lib`, and `spec['python'].prefix.include`. Obviously, none of these packages would work for Python 3, and there's no reason to duplicate the effort. The Python package itself should contain all of the information necessary to use it properly. This is in line with the recent work by @alalazo and @davydden with respect to `spec['blas'].libs` and friends. ## Prefix For most packages in Spack, we assume that the installation directory is `spec['python'].prefix`. This generally works for anything installed with Spack, but gets complicated when we include external packages. Python is a commonly used external package (it needs to be installed just to run Spack). If it was installed with Homebrew, `which python` would return `/usr/local/bin/python`, and most users would erroneously assume that `/usr/local` is the installation directory. If you peruse through #2173, you'll immediately see why this is not the case. Homebrew actually installs Python in `/usr/local/Cellar/python/2.7.12_2` and symlinks the executable to `/usr/local/bin/python`. `PYTHONHOME` (and presumably most things that need to know where Python is installed) needs to be set to the actual installation directory, not `/usr/local`. Normally I would say, "sounds like user error, make sure to use the real installation directory in your `packages.yaml`". But I think we can make a special case for Python. That's what we decided in #2173 anyway. If we change our minds, I would be more than happy to simplify things. To solve this problem, I created a `spec['python'].home` attribute that works the same way as `spec['python'].prefix` but queries Python to figure out where it was actually installed. @tgamblin Is there any way to overwrite `spec['python'].prefix`? I think it's currently immutable. ## Command In general, Python 2 comes with both `python` and `python2` commands, while Python 3 only comes with a `python3` command. But this is up to the OS developers. For example, `/usr/bin/python` on Gentoo is actually Python 3. Worse yet, if someone is using an externally installed Python, all 3 commands may exist in the same directory! Here's what I'm thinking: If the spec is for Python 3, try searching for the `python3` command. If the spec is for Python 2, try searching for the `python2` command. If neither are found, try searching for the `python` command. ## Libraries Spack installs Python libraries in `spec['python'].prefix.lib`. Except on openSUSE 13, where it installs to `spec['python'].prefix.lib64` (see #2295 and #2253). On my CentOS 6 machine, the Python libraries are installed in `/usr/lib64`. Both need to work. The libraries themselves change name depending on OS and Python version. For Python 2.7 on macOS, I'm seeing: ``` lib/libpython2.7.dylib ``` For Python 3.6 on CentOS 6, I'm seeing: ``` lib/libpython3.so lib/libpython3.6m.so.1.0 lib/libpython3.6m.so -> lib/libpython3.6m.so.1.0 ``` Notice the `m` after the version number. Yeah, that's a thing. ## Headers In Python 2.7, I'm seeing: ``` include/python2.7/pyconfig.h ``` In Python 3.6, I'm seeing: ``` include/python3.6m/pyconfig.h ``` It looks like all Python 3 installations have this `m`. Tested with Python 3.2 and 3.6 on macOS and CentOS 6 Spack has really nice support for libraries (`find_libraries` and `LibraryList`), but nothing for headers. Fixed.
2017-04-29Add a new package for dash (#4050)Adam J. Stewart3-9/+48
2017-04-29Add latest version of PGI compilers (#4047)Adam J. Stewart1-5/+19
* Add latest version of PGI compilers * Add environment variables for PGI
2017-04-29A few updates to packages (mostly version updates) (#4049)Massimiliano Culpo5-18/+28
2017-04-28Bug/make dia build (#4045)George Hartzell1-2/+3
* Make dia build w/ Spack's X bits (and misc) X related - need to depend on the +X variant of gtkplus - need to depend on freetype misc - fix path to tarball * Make freetype a "build" dependency * Freetype is not just a build dep
2017-04-28Allow compilation of mgridgen (serial) as well as parmgridgen (parallel) (#3906)Mark Olesen1-14/+22
2017-04-28ncurses package builds ncurses and ncursesw (#3953)sknigh6-3/+63
* ncurses package will build ncurses and ncursesw * Added libs property to ncurses, added fix for hstr * flake8 is a harsh mistress * make libs() more robust * atop depends on ncurses * fish depends on ncurses * libtermkey and nano depend on ncurses * Adjust url spacing
2017-04-28Various patches to Openblas for Intel (#4030)Brian Van Essen3-0/+41
* Added a patch to the openblas package to change the openmp flag for icc to qopenmp. * Fixed a linking problem where when using Intel compilers, it was still pulling in -lgfortran
2017-04-28Depend on readline, remove hardcoded -ltermcap (#4042)George Hartzell2-1/+7
* depend on readline, remove hardcoded -ltermcap Bowtie should use Spack's readline and not explicitly depend on the system termcap (which, on CentOS, leads to linking against the system's tinfo library). * Add depends_on('zlib') * Add conflict with gcc@6: Build seems to have trouble with 6's migration to -std=gnu++14.
2017-04-28Add a new package for Cbench (#4043)Adam J. Stewart1-0/+92
2017-04-28Add a new package for dos2unix (#4037)Adam J. Stewart1-0/+37
2017-04-28dealii: fix missing -march=native in flags (#4036)Denis Davydov1-5/+14