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2020-01-13racon: added v1.4.3, v1.4.2, v1.4.0 and v1.3.3 (#14478)darmac1-0/+4
2020-01-13syned: new package at develop (#14468)Sajid Ali1-0/+22
2020-01-13gromacs: add v2020 (#14477)Christoph Junghans1-0/+1
2020-01-11LLVM-Flang package (#14389)Nichols A. Romero3-12/+202
* Add 20181226 release of pgmath * 20190329 release of pgmath requires match for CMPLX macro. * Add llvm-flang package for Flang fork of LLVM * Add new and old flang releases. * Add cmake and python dependencies. * Update dependencies on llvm-flang and pgmath. * Fix cmake args and change spec to reflect llvm-flang package. * change copyright date through 2020. * Reference Flang package more explicitly. * More robust support for python executable. * import os no longer needed, picked up by flake8. * Use built-in target spec. Variant and targets follow style in main LLVM package. * Get rid of targets list and only support one target for now. * Sparc does not appear to be supported in Flang. * Raise InstallError if architecture not supported.
2020-01-09Add TensorFlow 2.1.0 (#14429)Adam J. Stewart1-15/+12
* Add TensorFlow 2.1.0 * kafka and ignite are no longer supported
2020-01-09root: Configure ROOT correctly for python3 (#14225)Hadrien G1-2/+4
* Configure ROOT correctly for python3 * Record Python version conflict * Code editing on a phone sucks
2020-01-09new versions of `TFEL` and `MGIS` (#14249)thelfer2-4/+22
* fixes #967 * Version bump to 0.9.1 - Bugfixes for spack find - 0.9.1 can read specs from current develop. * Don't assume spack is in the path when building docs. * Quick fix for relocation issues. * elf relocation fix: cherry-picked from develop branch (#6889) * Revert "Quick fix for relocation issues." This reverts commit 57608a6dc495af6c042945767ac3bd0c009fadd5. * Buildcache: relocate fixes (#6512) * Updated function which checks if a binary file needs relocation. Previously this was incorrectly identifying ELF binaries as symbolic links (so they were being excluded from relocation). Added test to check that ELF binaries are not considered symlinks. * relocate_text was not replacing paths in text files. Added test to check that text files are relocated properly (i.e. paths in the file are converted to the new prefix). * Exclude backup files created by filter_file when installing from binary cache. * Update write_buildinfo_file method signature to distinguish between the spec prefix and the working directory for the binary cache package. * Final changes for v0.11.0 (#6318) * Fix logo link in README.md to point to the develop branch. (#6969) * Compiler flag handlers (#6415) This adds the ability for packages to apply compiler flags in one of three ways: by injecting them into the compiler wrapper calls (the default in this PR and previously the only automated choice); exporting environment variable definitions for variables with corresponding names (e.g. CPPFLAGS=...); providing them as arguments to the build system (e.g. configure). When applying compiler flags using build system arguments, a package must implement the 'flags_to_build_system_args" function. This is provided for CMake and autotools packages, so for packages which subclass those build systems, they need only update their flag handler method specify which compiler flags should be specified as arguments to the build system. Convenience methods are provided to specify that all flags be applied in one of the 3 available ways, so a custom implementation is only required if more than one method of applying compiler flags is needed. This also removes redundant build system definitions from tutorial examples * Fix type issues with setting flag handlers (#6960) The flag_handlers method was being set as a bound method, but when reset in the package.py file it was being set as an unbound method (all python2 issues). This gets the underlying function information, which is the same in either case. The bug was uncovered for parmetis in #6858. This is a partial fix. Included are changes to the parmetis package.py file to make use of flag_handlers. * Bump version to 0.11.1 * Added flags to unit tests + OSX build done once per day (#6988) * Adding flags to codecov reports * OSX builds are triggered once a day * Pull R list_urls from upstream. * travis: removed /usr/local/include/c++ before installing gcc on OSX (#6515) (#7027) "brew install gcc" fails for travis build because of an existing /usr/local/include/c++. This commit removes the offending file as suggested by brew. * Fix gfortran 7 detection (#7017) * Add NameError to exceptions caught from configure_args in module generation (#7173) * Revert "Binary caching: remove symlinks, copy files instead (#9747)" This reverts commit 058cf81312d07d13b0b6de9949c641892d50ad0b. * Make Spack relocate text files in build caches with relative binaries * add the tfel package * fix the tfel package * fix the tfel package * fix the tfel package * Taking Adam J. Steward' remarks into account * fixes trailing white spaces * Update description * Update dependencies following @adamjstewart adices * Style fixes * Style fixes * Add java optional support * add the maintainers attribute (following @alalazo advice), disable interface not selected (following @adamjstewart advice) * flake8 fixes * Fix Cast3M and python-bindings support. Python detection is made compatible with cmake'FindPythonLibs module (at least how it is used in TFEL) * Style fixes * Style fixes * Fix test on python version * Follow @adamjstewart advices: code is much cleaner and readable * Small fix * Small fix * Add comment * Small fix in cmake option * try again (trying to overcome Travis CI unstable build process) * Add support for the MFrontGenericInterfaceSupport project (MGIS) * Style fixes * Package documentation update * Package documentation update * Fix a typo thanks to Andreas Baumbach review * Follow Adam J. Stewart advices * Fix type * bugfix: add back r's for invalid regexes * tutorial basics section: fix gcc install version * version bump: v0.12.1 * bugfix: bring in .travis.yml from develop * Add new TFEL' versions (3.0.4, 3.1.4 and 3.2.1). Add new MGIS version (1.0.1). Fix MGIS dependency * merge with spack:develop * add missing dependency * new versions of and * Fix MGIS url. Fix duplicate variant in TFEL * Fix tfel packaging according to Adam J. Stewart' advices * Fix flake8 warning Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com> Co-authored-by: Todd Gamblin <tgamblin@llnl.gov> Co-authored-by: Peter Scheibel <scheibel1@llnl.gov> Co-authored-by: Greg Becker <becker33@llnl.gov> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-01-09FairLogger: new package (#14427) (#14427)Dr. Christian Tacke1-0/+65
* Fixed date on first copyright header. * Rename dev version to develop * Improve filter_file calling * Be explicit for +pretty / ~pretty
2020-01-09Add ADF (#14423)asmaahassan901-0/+35
* Add ADF * Fix typo and lint * fix lint again * one more lint fix * fix identation * still stying to fix identation * one final fix * import needed libraries * changes as per reviewer's request fix setup environment function, enhance recipe * add import os once again * chnages as per reviewer's request
2020-01-09tomcat: new package (#14441)darmac1-0/+30
2020-01-09storm: new package (#14437)darmac1-0/+28
2020-01-09rapidjson: delete '-march' flags when using Fujitsu compiler. (#14435)t-karatsu2-0/+14
2020-01-08fix build for qt5 and the Intel compiler (#14387)Glenn Johnson3-3/+35
* Set conflicts for qt5 and the Intel compiler This PR sets a `conflicts` statement for QT5 and the Intel compiler. * New patches for intel compiles This commit adds two patches to get QT5 to compile with the intel compilers. The two patches are very similar but the file being patched was changed substantially between qt-5.11 and qt-5.12. The patch checks versions of both GCC and Intel compilers to know when to use overflow builtis. Essentially, GCC must be >= 5 and Intel must be >= 18. The sqlite dependency needs the `+column_metadata` variant when the Intel compiler is used. That is made conditional on the compiler but it might make sense to make that the default for the sqlite dependency. Some other changes were made based on testing builds of various QT5 versions with several Intel compilers. - The libxext dependency is still needed for QT5 - A dependency on libxrender is needed - The gtk option format needs to be constrained at the qt@5.7 level, not qt@5.8. - An extra configure option is needed for the sql plugins RPATH
2020-01-08lrslib: fix return value (#14422)noguchi-k2-0/+40
2020-01-08cmake: Create an optimized release build (#14414)Chuck Atkins1-1/+8
2020-01-08Adding a new package, scikit-build, which is useful for building Python ↵Corey adams1-0/+27
Extensions (#14417) * Adding a new package, scikit-build, which is very useful for building python extensions * Update package.py * Update package.py Trying to address flake8 corrections * Update var/spack/repos/builtin/packages/py-scikit-build/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-scikit-build/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-01-07hpcviewer: add version 2019.12 (#14419)Mark W. Krentel1-0/+9
Add conflicts for aarch64 and darwin.
2020-01-07Record a new ROOT/GCC incompatibility (#14371)Hadrien G1-0/+4
2020-01-07py-rapidjson: new package at 0.9.1 (#14280)Justin S1-0/+18
* py-rapidjson: new package at 0.9.1 * py-rapidjson: rename to py-python-rapidjson, use PyPI mirror * py-python-rapidjson: add missing deps * python-rapidjson: use short PyPI url * py-python-rapidjson: remove extra dependencies
2020-01-07r-ldheatmap: new package at 0.99-7 (#14405)Justin S1-0/+22
2020-01-07NumPy 1.18.1 requires Cython 0.29.14 (#14418)Adam J. Stewart2-2/+5
2020-01-07Package/opencv: cudacodec fix (#14409)Sinan1-0/+8
* create new variant, fix build error * flake8 * add conflict, re-arrange config arg for cudacodec
2020-01-07gdb: add version 8.3.1 (#14413)Matthias Diener1-0/+1
2020-01-07ncl: Add missing fontconfig dependency (#14411)Michael Kuhn1-1/+3
Moreover, cairo needs to have its freetype variant enabled.
2020-01-07gdal: Fix libgeotiff dependency (#14410)Michael Kuhn1-1/+1
gdal@2.4.3 is missing the libgeotiff dependency.
2020-01-06Add py-numpy 1.18.1 (#14406)Adam J. Stewart1-1/+2
2020-01-06r-snpstats: new package at 1.34.0 (#14404)Justin S1-0/+29
2020-01-06r-genetics: new package at 1.3.8.1.2 (#14403)Justin S1-0/+22
2020-01-06Add updated kaldi and openfst (#14398)Thom Troy2-0/+3
* add openfst v1.6.7 and kaldi from 2019-09-29 * revert openfst package version in url
2020-01-06Add singularity@3.5.2 (#14401)George Hartzell1-0/+1
2020-01-06Fastdfs (#14378)darmac1-0/+35
* add new package : fastdfs * refine install() * remove redundant fastdfs/fastdfs/package.py * fix install() error
2020-01-06py-ujson: new package at 1.35 (#14279)Justin S1-0/+18
* py-ujson: new package at 1.35 * py-ujson: use PyPI mirror, add missing deps * py-ujson: use short PyPI url
2020-01-06Fix QT on Linux+clang (#13684)Seth R. Johnson1-33/+56
* Add platform flag to QT for linux+clang * Extend QT platform support to more compilers and systems * Unify QT5 configure options * fixup! Unify QT5 configure options * fixup! Unify QT5 configure options * fixup! Unify QT5 configure options * Fix newer flake8 and mac qt5 configure
2020-01-06Nsimd: New package (#14226)Erik Schnetter1-0/+65
* Nsimd: New package * Various cleanups as suggested during review
2020-01-05Add py-thirdorder recipe (#12791)asmaahassan901-0/+37
* Add Thirdorder recipe * Remove white spaces * Converting recipe to a PythonPackage base class * remove trailing spaces * remove line at end of file * enhance recipe as per reviewer * fix post_install as requested by reviewer * rename dir to py-thirderorder * change checksum to sha256
2020-01-04Overhaul py-pillow package (#14385)Adam J. Stewart1-51/+54
* Overhaul py-pillow package * Fix bug where zlib and jpeg were always disabled
2020-01-04libwebp: CMakePackage -> AutotoolsPackage (#14384)Adam J. Stewart1-7/+49
2020-01-04Adjust constraints of gcc-5 (#14388)Glenn Johnson1-1/+2
This PR adjusts the constraints on isl with GCC-5. GCC-5.1 and GCC-5.2 need isl-0.14, not isl-0.15.
2020-01-04Add libs property to openjpeg package (#14383)Adam J. Stewart1-0/+5
2020-01-04Add libs property to lcms package (#14382)Adam J. Stewart1-0/+4
2020-01-04py-torchvision 0.4.X does not support py-pillow 7.X.Y (#14381)Adam J. Stewart1-1/+3
2020-01-04environment-modules: add version 4.4.1 (#14379)Xavier Delaruelle1-1/+2
2020-01-04add new package : lucene (#14316)darmac1-0/+28
* add new package : lucene * update lucene version url
2020-01-04add new package : kafka (#14315)darmac1-0/+35
* add new package : kafka * move url_for_version after depens_on() * refine list_depth for kafka
2020-01-04add new package : tajo (#14314)darmac1-0/+36
* add new package : tajo * refine list_depth for tajo
2020-01-03py-intervaltree: new package at 3.0.2 (#14277)Justin S1-0/+19
* py-intervaltree: new package at 3.0.2 * py-intervaltree: fix checksum * py-intervaltree: add py-setuptools dep * py-intervaltree: use inclusive ranges * py-intervaltree: change py-test dep type
2020-01-03petsc: add version 3.12.3 (#14374)Satish Balay1-0/+1
2020-01-03new package: bref3 (#14256)xfzhao2-0/+50
2020-01-02Get py-numpy > 1.16 to build with Intel compiler (#14360)Glenn Johnson1-0/+23
Beginning with numpy > 1.16 when using older versions of gcc the `std=c99` flag must be used. The Intel compiler depends on gcc for its language extensions so the version of gcc is important. If the version of gcc used by the Intel compiler is one that requires the `-std=c99` flag then that flag will have to be used for a build with the Intel compiler as well. This PR tests the version of gcc used by the Intel compiler and will abort the build if the gcc version is < 4.8 and inject the `-std=c99` flag if >= 4.8 and < 5.1. This will cover the system gcc compiler and any gcc environment module loaded at build time.
2020-01-02package/opencv fix mistake in conflict statement involving gcc (#13959)Sinan1-4/+1
* fix mistake in conflict * extend CudaPackage to resolve cuda-gcc conflicts
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