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2018-06-10A new package: axel. (#8434)健美猞猁1-0/+42
* A new package: axel. * Remove duplicate pkgconf.
2018-06-10Bump miniconda to 4.5.4. (#8435)健美猞猁2-0/+2
2018-06-09py-projectq: Added new package and fixed its dependency py-pybind11 (#8378)toffer932-0/+69
* py-pybind11: Additionally install python extensions e.g. run python setup * py-projectq: Added new package for quantum computing * py-projectq: corrected typos * edited flake8 incompatibilities * additional flake8 faults * changes according to suggestions * flake8 errors fixed * typo and missing environment variable set * py-pybind11:added setup_environemt * py-projectq:changed version according to request * flake8 correction * py-pybind11:changed to setup_py and removed noop * py-projectq:removed dependency and changed type of py-pytest dependency * py-pybind11: flake8 error corrected * py-projectq: Small error correction
2018-06-09Git's gitk needs TK's wish to be found in PATH (#8360)Kelly (KT) Thompson1-1/+13
* Git's gitk needs TK's wish to be found in PATH * Add a _runtime_ dependency on `tk` * Add an environment rule to add the path to TK's `wish` program to $PATH for the generated `git` modulefile. * Make TclTk run environment an optional variant for git. * Cleanup based on PR recommendations.
2018-06-08compiler flags: add cxx98 standard support (#7601)Chris Green10-52/+328
The following improvements are made to cxx standard support (e.g. compiler.cxxNN_flag functions) in compilers: * Add cxx98_flag property * Add support for throwing an exception when a flag is not supported (previously if a flag was not supported the application was terminated with tty.die) * The name of the flag associated with e.g. c++14 standard support changes for different compiler versions (e.g. c++1y vs c++14). This makes a few corrections on what flag to return for which version. * Added tests to confirm that versions report expected flags for various c++ standards (or raise an exception for versions that don't provide a given cxx standard) Note that if a given cxx standard is the default, the associated flag property will return ""; cxx98 is assumed to be the default standard so this is the behavior for the associated property in the base compiler class. Package changes: * Improvements to the boost spec to take advantage of the improved standard flag facility. * Update the clingo spec to catch the new exception rather than look for an empty flag to indicate non-support (which is not part of the compiler flag API)
2018-06-08r-mice: new package (#8423)Yifan Zhu1-0/+57
* r-mice: new package * flake8 fixed
2018-06-08tcl package: Install sources (#8153)Elizabeth Fischer1-0/+21
The tcl package references the original sources upon install, and the tk build requires the tcl sources. This updates the tcl package to install its sources following the example of #4102, and also updates the tclConfig.sh file to properly reference the installed sources (rather than the staging directory created by Spack).
2018-06-08new version scotch@6.0.5a (#8254)Oliver Pola2-0/+636
* new version scotch@6.0.5a * patch metis headers on scotch@6.0.4 according to https://gforge.inria.fr/tracker/?func=detail&atid=1082&aid=19521&group_id=248
2018-06-08GDL and missing dependencies (#8283)Ricardo Silva4-0/+349
* GDL and missing dependencies Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch> * GDL and GraphicsMagick improvements * GDL: sort variants and dependencies, add descriptions * GDL: add wx variant * GDL: make variants explicit (in cmake args) * GraphicsMagick: sort dependencies * GraphicsMagick: cleanup boilerplate comments Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch> * Improvements/Fixes for gdl, plplot and graphicsmagick * gdl: * variants: * openmp * be explicit about enabling/disabling x11 * dependencies: * logic for plplot with/without wx * some previously missing (where being picked up from the system) * graphicsmagick: previously missing dependencies (where being picked up from the system) * plplot: more versions + variants + dependencies Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch> * GDL: hdf4/5 variants * also sorted explicit enabling/disabling of cmake flags for readability Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch> * plplot: fix variant descriptions Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch> * Add tcl variant, use find_libraries for portability Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch> * plplot: flake8 Signed-off-by: Ricardo Silva <ricardo.silva@epfl.ch>
2018-06-08go: Update to 1.10.3 (#8426)Michael Kuhn1-0/+1
2018-06-07Added elastic search (#8424)sknigh1-0/+50
2018-06-07Update intel-tbb to 2018.3 and improve version URLs, dependencies and ↵Chris Green3-47/+85
patching. (#7932) * Update to 2018.3 and improve version URLs, dependencies and patching. Improve to version -> URL translation to be algorithmic rather than manual. Make binutils build dependency explicit where appropriate because we're sensitive to the assembler used. Build's use of '-mrtm' is only patched away if it needs to be because the assembler is too old. Incorporate @adamjstewart request to convert GCC version check to a conflict. * Allow specification of C++ standard. * Improve TBB patch per PR comments. * Restrict RTM patch application to older OS only. * New version 2018_U4.
2018-06-07pbbam: new package (#8365)Miles Perry1-0/+62
* pbbam: new package * pbbam: updated version * pbbam: added option tests handling * pbbam: flake8 edits
2018-06-07Fix hydrogen@develop build (#8262)Corey McNeish3-69/+13
* Delete support for old versions of Elemental in Hydrogen * Fix cmake_args versions in lbann * Remove unused import (again) * Revert elemental to pre-llnl fork * Strip tailing whitespace from libgfortran.so * Fix flake8 * Remove debug print * * Add back elemental@develop * Prohibit installation of hydrogen previous to 0.99 * Fix flake8 * Change cmake_args error to a conflicts for old versions of Hydrogen * Use ~ not -
2018-06-07Fermi Science Tools: New package (#8126)Yifan Zhu1-0/+45
* fermisciencetools: new package * fermisciencetools: new package * added comments about the error in building the source distribution; fixed flake8 errors
2018-06-07add python cache removal to `spack clean` (#8419)healther1-4/+24
Remove .pyc and .pyo files along with __pycache__directory if the user provides the -p/--python-cache option to "spack clean"
2018-06-07add sqlitebrowser (#8418)healther2-0/+68
* add sqlitebrowser Change-Id: I20cac709509e82d348cebc11b0d584b53b2ad3d4 * add message and clean up unnecessary code Change-Id: Ib9d2229ee25d751274680d06824891ee78fa5970 * and make flake8 happy Change-Id: I814eb89eefe1767af4d8043b08b61991750516df * make gcc-independence great again Change-Id: I75f7271757782a6735eb7f03c0551d190722974d * remove explicit import of dso_suffix Change-Id: I626c6391b22524895199db5508606c4cf22bf9b5
2018-06-07fix qt@5.8: build on systems without wayland (#8417)healther1-0/+6
* fix qt@5.8: build on systems without wayland Change-Id: I56b83208edd46f50e003d82c071e296e905bfb15 * add links Change-Id: Ia16fc20632690340f33df77fbdcb1a166d49cedc * move 5.8 comparison into 5.7 configure block Change-Id: I7dc606beeb5b5bf4e8263bc50d28de6591633c99
2018-06-07googletest: add a shared variant for all supported versions (#8373)Daryl W. Grunau1-2/+10
* add a shared variant for all supported versions * address comment from @citibeth about MacOS lib installs * address additional comments from @citibeth about MacOS lib installs * set +shared variant to be default behavior
2018-06-07add commented test dependencies (#8407)healther25-68/+41
* add commented test dependencies Change-Id: I38ffd3caa77a59f2a0a7ae92a9c8e8215cf5b4d6 * readd make('test') to openssl Change-Id: Ia3733a3848a2a26729b4050c7d4439ea9de17b1a
2018-06-07 modified: var/spack/repos/builtin/packages/py-psutil/package.py (#8420)Sajid Ali1-1/+2
2018-06-07Add new package: ftgl (#8416)Javier Cervantes1-0/+57
* Add new package: ftgl * Check version using decorator
2018-06-07openPMD-api: Update Dependencies (#8330)Axel Huebl1-9/+6
We need a newer version of HDF5 and dropped the boost dependency. Modernize the test variant to the spack test functionality.
2018-06-07add package py-cartopy and dependencies (#8406)healther5-0/+224
* add package py-cartopy Change-Id: Ifbe541e852921c384a381594a2c1110814556311 * fix comments and flake8 Change-Id: I8d5e994580e8252e00654e68ad79d74e06089939 * remove pip dependency... not sure why added in the first place Change-Id: Ie2a788887dac30778cc43931a0732980a347514d * move build, link, run to default dependencies Change-Id: I1ec0cb7dc4a697c4ca9e68a0cc0d8694cc21c100
2018-06-06Fix bug where patches specified by dependents were not applied (#8272)scheibelp2-12/+13
Fixes #7885 #7193 added the patches_to_apply function to collect patches which are then applied in Package.do_patch. However this only collects patches that are associated with the Package object and does not include Spec-related patches (which are applied by dependents, added in #5476). Spec.patches already collects patches from the package as well as those applied by dependents, so the Package.patches_to_apply function isn't necessary. All uses of Package.patches_to_apply are replaced with Package.spec.patches. This also updates Package.content_hash to require the associated spec to be concrete: Spec.patches is only set after concretization. Before this PR, it was possible for Package.content_hash to be valid before concretizing the associated Spec if all patches were associated with the Package (vs. being applied by dependents). This behavior was unreliable though so the change is unlikely to be disruptive.
2018-06-06Add new package: davix (#8376)Javier Cervantes2-0/+109
* Add new package: davix * Add list_url * Remove extra spaces, add list_depth and specify dependency type
2018-06-06remove pwrType from the interface SZ_compress_args() (#8414)Sheng Di1-1/+2
2018-06-06r-mitml: new package and its dependencies r-jomo and r-pan (#8412)Yifan Zhu3-0/+120
2018-06-06libjpeg-turbo: updated checksums and added autoreconf for older versions (#8411)ynanyam1-4/+8
2018-06-06ADIOS: Serial API with Parallel Lib (#8409)Axel Huebl2-0/+19
Provides a patch for the fix in https://github.com/ornladios/ADIOS/pull/182 Installed ADIOS MPI-enabled libraries are with that able to also perform serial I/O without the need to start the whole app via `mpiexec`.
2018-06-06Add new package: rngstreams (#8395)Javier Cervantes1-0/+34
* Add new package: rngstreams * Remove unnecessary list_url
2018-06-06xsimd: test type (#8405)Axel Huebl1-1/+9
Add the new type 'test` to the `googletest` dependency of xsimd.
2018-06-06Add new package: prng (#8396)Javier Cervantes3-0/+243
* Add new package: prng * Add missing dependencies and use force_autoreconf option * Add dependency types
2018-06-06Fix ADIOS 1.13.1: Maxium SZ (#8408)Axel Huebl1-2/+2
Fix the maximum accepted SZ version for the latest ADIOS release.
2018-06-06numpy: nosetest (#8404)Axel Huebl1-3/+1
the type 'test' exists now :-)
2018-06-06ISAAC Server 1.3.3 (#8403)Axel Huebl1-0/+1
Forgot to bump this package with the library release.
2018-06-06Trilinos update (#8363)Andrey Prokopenko1-5/+75
* trilinos: add more package conflicts This was done by putting in required lib dependencies from each package's `cmake/Dependencies.cmake`. * trilinos: added few more trilinos packages * trilinos: hiccup fix
2018-06-06r-splitstackshape: Create new package. (#8370)lingnanyuan1-0/+47
* r-splitstackshape: Create new package. * r-splitstackshape: Add version constraints. * add list_url and change dependency type.
2018-06-06add 1.4.13.4 for SZ (#8375)Sheng Di1-1/+2
* add 1.4.13.4 for SZ * undo spack link (change llnl/spack to spack/spack) and change .zip to .tar.gz * revise package.py for SZ 1.4.13.4 based on Adam's comments.
2018-06-06py-mpmath: added version 1.0.0 (#8382)Massimiliano Culpo1-2/+3
* py-mpmath: added version 1.0.0 * Fixed checksum for version 0.19
2018-06-06py-scikit-learn: added version 0.19.1 and updated dependencies (#8399)Massimiliano Culpo3-0/+3
py-numpy: added version 1.14.3 py-scipy: added version 1.1.0
2018-06-06py-theano: added version 1.0.2 (#8400)Massimiliano Culpo1-0/+1
2018-06-05py-sympy: added version 1.1.1 (#8381)Massimiliano Culpo1-1/+2
2018-06-05py-cython: added version 0.28.3 (#8379)Massimiliano Culpo1-0/+1
2018-06-05Added py-pip 10.0.1 and py-setuptools 39.2.0 (#8377)Massimiliano Culpo2-0/+2
2018-06-05py-virtualenv: added version 16.0.0 (#8380)Massimiliano Culpo1-0/+1
2018-06-05Preserve Spack CC/FC/F77/CXX settings when loading modules (#8346)Massimiliano Culpo4-15/+110
Fixes #8345 Spack environment modifications are applied before modules are loaded; this includes settings to CC, FC, F77, and CXX, which point to the Spack compiler wrappers. If the loaded modules set CC, this overrides the Spack compiler wrappers. This PR adds a context manager to preserve the values of CC etc. that are set by Spack: any effects on the CC, FC, F77, and CXX variables from modules are undone and their original values are restored.
2018-06-04added line 43 (#8369)Daniel Topa1-0/+1
version('1.4.1.2', '38c7d33210155e5796b16d536d1b5cfe') Signed-off-by: Daniel Topa <dantopa@lanl.gov>
2018-06-04clean up version names (#8368)Daryl W. Grunau1-6/+6
2018-06-04New package: phast (#7993)Yifan Zhu1-0/+58
* adding partially completed recipe for phast. will need clapack as dependency * try to install phast * seems to still need CLAPCK * using CLAPACK instead * phast: updated * fixed flake8 error * phast cannot build with clapack built with external blas? * phast: depend on clapack built without external blas * fixed flake8 errors * phast: updated build_directory
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