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2017-05-11filesystem.py: fixed bug introduced in #3367 (scrambled order in output) (#4156)Massimiliano Culpo19-7/+95
PR #3367 inadvertently changed the semantics of _find_recursive and _find_non_recursive so that the returned list are not ordered as the input search list. This commit restores the original semantic, and adds tests to verify it.
2017-05-11Update NAG checksum, add F77 and FC (#4196)Adam J. Stewart1-1/+5
2017-05-10Open MPI: add 2.1.1 to the list (#4204)Howard Pritchard1-1/+2
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2017-05-10Add nemesistcpib fabrics variant (#4197)Michael Kuhn1-1/+4
2017-05-10updating git (#4200)Suzanne Parete-Koon1-0/+5
2017-05-10Edits to get setup-env.csh working better (#4044)Matthew Thompson1-3/+9
* Edits to get setup-env.csh working better. Autosets the sys_type a la setup-env.sh * More stealing from bash setup script for module roots * Add error message if SPACK_ROOT isn't set * Remove _sp_lmod_root per Adam J Stewart
2017-05-10cosmomc: Enable Python bindings (#4169)Erik Schnetter1-4/+13
* cosmomc: Enable Python bindings * cosmomc: Make python dependency optional
2017-05-10hdf5: Correct spelling (#4172)Erik Schnetter1-3/+3
* hdf5: Correct spelling * hdf5: avoid trailing spaces
2017-05-10highfive: New package; this is a C++ wrapper for the HDF5 library (#4173)Erik Schnetter1-0/+52
* highfive: New package; this is a C++ wrapper for the HDF5 library The C++ wrapper that is shipped with the HDF5 library has several shortcomings. The highfive library seems to avoid these. * highfive: Make MPI variant default to true
2017-05-10Add latest version of PGI compilers (#4186)Adam J. Stewart1-5/+6
* Add latest version of PGI compilers * Prepend, don't overwrite
2017-05-10py-flask version updates, remote switch (#4166)Stephen McDowell1-1/+2
* version updates, remote switch * trim versions to original and most recent * proper url discovered and tested
2017-05-10enable cuda support for suite-sparse (#4163)Stephen McDowell1-14/+14
* enable cuda support for suite-sparse * do not use spec.satisfies * cuda restructure, give clearer comment of why * str format compatibility * flake8 checks
2017-05-09Add a new package for ExtUtils::MakeMaker (#4179)Adam J. Stewart1-0/+38
2017-05-09Fix newline character in GCC package (#4181)Adam J. Stewart1-1/+1
* Fix newline character in GCC package * Remove the newline completely
2017-05-09Adding FASTMath uber package and missing FASTMath packages (#4120)Mark C. Miller10-3/+477
* adding 0.5.1 and variant for uint8 bit stream word type * Revisions as per davydden * fixing style (flake8) issues * - switched to derive from MakefilePackage - fixed typo in variant check - Confirmed installs correctly with bswtuint8 variant * added build method; changed zfp_incdir to incdir * * Adding uber fastmath package to support 'spack install fastmath' * Adding dims variant boxlib to control compile-time spatial dimension count * Explicitly disabling many parts of moab to get lib to build. Don't need tools yet. * Add logic to spack/setup-env to not refer to $SYS_TYPE if its not defined. * adding mesquite package * * Added Chombo (still working on Fortran name mangling) * Made mesquite depend on mpi * Fixed use of boxlib's dims numerical variant * adding PUMI * flake8 compliance * adding phasta * fixing flake8 issues * undue $SYS_TYPE protection change * fixing install step for fastmath uber package; resolve issues requested by adamjstewart in PR * revisions as per adamjstewart * re-enabling trilinos and phasta dependencies * all changes requested modulu values= and assert statement * fixing cmake_args usage in pumi; fixing lib installs for chombo * first pass at numerical variant * fixing dims variant as per @adamjstewart * fixing func/var name collision * fixing means of disabling -Werror * fix name collision for cmake_args var/func * fixing chombo homepage/url; make FASTMath use chombo#3.2; remove extraneous comment about boxlib dim * remove dummy fastmath package; switch to @BarrySmith soln for install of dummy bundle * fix flake8 import os issue * remove extraneous comment * adding url for fastmath scidac site * final fixes as per @adamjstewart * adding 1 dims option for boxlib * switching make(all) to gmake(all)
2017-05-09Add latest versions of Intel compiler (#4184)Adam J. Stewart2-0/+8
2017-05-09Make openmpi package defn more robust (#4183)George Hartzell1-0/+2
Make openmpi handle bad ibv_devices return statuses without bailing out completely. See #4162 for background.
2017-05-09ncurses: Always build tools (#4174)Erik Schnetter1-1/+0
Otherwise, the install can fail if the system-provided `tic` binary is too old.
2017-05-09simulationio: Declare dependency on the HDF5 C++ bindings (#4177)Erik Schnetter1-0/+1
2017-05-09qthreads: Convert to AutoTools package (#4176)Erik Schnetter1-8/+8
2017-05-09funhpc: Update to version 1.3 (#4170)Erik Schnetter1-3/+5
Also use a Spack-provided GoogleTest.
2017-05-09gdbm: Declare readline dependency (#4171)Erik Schnetter1-0/+2
2017-05-09Merge pull request #4165 from epfl-scitas/packages/cp2k_intel_stack_17Gregory Lee4-25/+82
cp2k: fixed compilation issues for intel stack
2017-05-09Travis version of pip is too old (#4180)Adam J. Stewart1-0/+2
* Travis version of pip is too old * Also need to upgrade setuptools
2017-05-09cp2k: fixed compilation issues for intel stackMassimiliano Culpo4-25/+82
Added DFLAGS to the `make.inc` file being written. These macros are also added to the language specific variables like CFLAGS, CXXFLAGS and FCFLAGS. Changed `spec.satisfies('foo')` with `'foo' in spec` in `intel-mkl`, see #4135. Added a basic build interface to `intel-mpi`.
2017-05-08Add GCC 7 (#4144)Adam J. Stewart4-52/+210
* Add GCC 7 * Allow users to build subset of GCC compilers with multi-value variant. * Add comment explaining what 'all' actually means * More specific golang support * Only require Zip when building Java * Comment out provide directives that don't currently work * Add Ada support * Use conflicts directive * Fix joining of languages * Need special flag to build jit * Explicitly declare GNAT download extension * Import tty, update lib64 to lib * BRIG and Go are not supported on macOS * Simplify formatting and imports * JIT patch required for newer versions as well
2017-05-08spec_syntax: added xfailing tests for cases in #4144 (#4151)Massimiliano Culpo1-0/+26
It seems that parse_anonymous_spec may fail if more than one part (variant, version range, etc.) is given to the function. Added tests to code against to fix the problem in #4144.
2017-05-08rework spack help (#3033)Todd Gamblin57-218/+736
- Full help is now only generated lazily, when needed. - Executing specific commands doesn't require loading all of them. - All commands are only loaded if we need them for help. - There is now short and long help: - short help (spack help) shows only basic spack options - long help (spack help -a) shows all spack options - Both divide help on commands into high-level sections - Commands now specify attributes from which help is auto-generated: - description: used in help to describe the command. - section: help section - level: short or long - Clean up command descriptions - Add a `spack docs` command to open full documentation in the browser. - move `spack doc` command to `spack pydoc` for clarity - Add a `spack --spec` command to show documentation on the spec syntax.
2017-05-08qt: add 5.8.0 which builds on Sierra with clang 8.1.0 (#4109)Denis Davydov3-2/+50
* qt: add 5.8.0 which builds on Sierra with clang 8.1.0 * enable parallel build, add freetype dependency * minor * minor
2017-05-08Merge pull request #4145 from scheibelp/features/temporary-no-python-for-libxcbscheibelp2-2/+4
Remove python dependency for libxcb and xcbproto
2017-05-07BarrierTimeoutError must derive from Exception (#4157)Massimiliano Culpo1-1/+1
Seen in https://travis-ci.org/LLNL/spack/builds/229484526, very likely due to a problem in the Travis builder.
2017-05-07Fix PGI compiler detection on PowerPC (#4150)Adam J. Stewart1-2/+10
2017-05-07Spec.__init__: removed dead code (#4146)Massimiliano Culpo1-5/+2
The conditionals are repeated in the statement before _add_dependencies
2017-05-07Paramiko python extensions + his deps and other related extensions (#4158)Luigi Calori7-0/+272
* adding paramiko and missing dependencies, setup to work with #2548 * adding other deps for paramiko * fix flake8 errors * removed spurious add * address suggestion for proper dependencies * fix cryptography deps * remove FIXME comments and commented depends lines
2017-05-07Added scala package (#67)nvarini1-0/+50
2017-05-06Add Read the Docs badge to README (#4153)Adam J. Stewart1-0/+1
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.
2017-05-05Remind developers to update tab completion script (#4148)Adam J. Stewart1-0/+4
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
2017-05-05Remove python dependency for libxcb and xcbprotoPeter Josef Scheibel2-2/+4
python+tk will not build because it depends (indirectly) on python~tk via libxcb. There are efforts to allow multiple instances of a package to concretize together but they are ongoing so in the meantime this comments out the dependencies and adds TODOs
2017-05-05Fix typos in Basic Installation Tutorial (#4127)Adam J. Stewart1-4/+4
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
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