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2020-03-18Use python extend_path as pyqt sip fix (#15297)Sinan5-41/+53
* try extend path to solve PyQt5.sip not found issue * disable private sip installation in sippackage class * undo manual PyQt5 dir creation in py-sip site-packages dir * fix typo * fix typo * also apply fix to PyQt4 * tidy up * flake8 and tidy up * tidy and undo hardcoding of python_include_dir * replace hardcoded python inc dir * fix minor issues * rethink include dir variable name * improve style * add new versions * implement new sip setup to qsci installation * set sip-incdir correctly for the new setup * setup extend_path thing before qsci python bindings * take care of conflict * flake8 * also extend for PyQt4 * improve style * improve style * SipPackage build sys should depend on py-sip * consolidate extend_path fixes into SipPackage * fix typo * fix bugs * flake8 * revert sip doc to pre-resource setup * import os module * flake8 Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
2020-03-18revbayes: Update pre-build process (#15485)Nick Booher1-0/+5
2020-03-18Cctools 7.1.0 (#15506)Benjamin Tovar1-12/+41
* update to 7.1.0 * adds gettext as dependency (needed to link with python) * disable python2 or python3 as needed
2020-03-18add new package: acl (#15514)darmac1-0/+30
2020-03-18add new package: userspace-rcu (#15515)darmac2-0/+44
2020-03-18CGNS: Version update (#15523)Greg Sjaardema1-1/+8
* CGNS: Version update The CGNS library has several new versions. There was a format-changing change in 3.4.0 which was removed for 3.4.1. The change was then added again and released with a change to the major version (4.0.0). Note that 4.0.0 should be close to the functionality of 3.4.0. * CGNS: Add shared variant Added the `shared`variant to make the CMake build correctly pick up the RPATH settings.
2020-03-18update util-linux to version: 2.33:2.35.1 (#15529)darmac1-0/+4
2020-03-18triangle: add X11 dependency. (#15533)Toyohisa Kameyama1-0/+2
2020-03-18xsetpointer: fix wrong dependency type. (#15534)Toyohisa Kameyama1-3/+3
2020-03-18adding the fortran option for hdf5 dependency for comptatibility with petsc ↵gauthier121-1/+1
requirement (#15536)
2020-03-18xts: add some dependencies. (#15537)Toyohisa Kameyama1-8/+11
2020-03-18Remove trailing newline. (#15539)Robert Kalescky1-0/+5
2020-03-18r-openssl requires C99. (#15541)Robert Kalescky1-0/+5
2020-03-18py-numpy: add 1.18.2 (#15546)Adam J. Stewart1-1/+2
2020-03-18Add package anaconda3 (#15404)Amjad Kotobi1-0/+53
2020-03-18Added a package for the DiHydrogen distributed linear algebra library. (#15426)Brian Van Essen1-0/+111
* Added a package for the DiHydrogen distributed linear algebra library. * Updated recipe to provide cuda architecture constaints. * Addressed reviewer comments * Fixed flake 8
2020-03-18QMCPACK Update March 2020 (#15511)Nichols A. Romero1-5/+17
* Clean-up description of variants. * Support AFQMC with CUDA.
2020-03-18openPMD-api: HDF5 1.12.0 Support (#15530)Axel Huebl2-0/+27
Fix API breakage in HDF5 1.12.0 for released versions.
2020-03-18Previous qt package file changes broke the openspeedshop gui build. (#15471)Jim Galarowicz2-2/+3
* Previous qt changes broke the openspeedshop gui build. This puts back the changes that caused the breakage. * Update the qt version to be more robust. Co-authored-by: Galarowicz, James <jgalarowicz@newmexicoconsortium.org>
2020-03-17update checksum for intel-tbb@2020.1 (#15528)eugeneswalker1-1/+1
2020-03-17SEACAS: Add versions 2020-03-16 and 2020-01-16 (#15525)Greg Sjaardema1-0/+2
2020-03-17MPICH: optional libxml2 support; NAG patches (#15235)Sergey Kosukhin5-2/+222
* Add patches when building with NAG * Make libxml2 support optional. Also include conflict for @:3.2~hydra+libxml2 since @:3.2~hydra does not require libxml2 support * Add '--disable-silent-rules' to get more verbose output during the build
2020-03-17Remove PatchelfError and change patchelf error message to a warning. (#15518)Patrick Gartung1-13/+4
2020-03-17Corrected compiler filtering for TAU makefiles (#15342)wspear1-2/+20
* Implemented working file filtering to replace spack compiler wrapper with real compiler. * Using string=True instead of re.escape. Using self.prefix.lib instead of appending /lib. Co-authored-by: Wyatt Spear <wspear@cs.uoregon.edu>
2020-03-17geant4: Removed unnecessary definition of xerces-c. (#15513)Tomoki, Karatsu1-1/+0
2020-03-17Update and exetend VecGeom (#14520)Seth R. Johnson1-32/+79
* Add new vecgeom versions, add cuda support, automate target options * Add ROOT, GDML, and external VecCore support to VecGeom * Address reviewer comments * Update vecgeom for CUDA * Update versions
2020-03-17nfs-utils: added package at v2.4.2 (#15491)darmac1-0/+34
2020-03-17Module files won't use CPATH by default, but language specific vars (#14749)Massimiliano Culpo1-1/+5
fixes #11555 Every path in CPATH is equivalent to a -I path to the compiler, while every path in *_INCLUDE_PATH is equivalent to -isystem. The latter avoids the noise due to warnings coming from 3rd party libraries that a project depends on. Added INCLUDE env variable (Intel Fortran, .mod files)
2020-03-16cap binutils version @:2.33.1 due to build failures with 2.34 (#15504)eugeneswalker1-1/+1
2020-03-16Warn only if link target is not relative and outside of the install prefix ↵Patrick Gartung1-9/+8
(#15512)
2020-03-16veccore: added package at v0.6.0 (#15472)Seth R. Johnson1-0/+40
2020-03-16When replacing path text in ELF binaries do not include null byte padding in ↵Patrick Gartung1-1/+1
search string (#15508)
2020-03-16CMakePackage: convert variants to CMake arguments (#14376)Seth R. Johnson4-16/+161
Add a 'define_from_variant` helper function to CMake-based Spack packages to convert package variants into CMake arguments. For example: args.append('-DFOO=%s' % ('ON' if '+foo' in self.spec else 'OFF')) can be replaced with: args.append(self.define_from_variant('foo')) The following conversions are handled automatically: * Flag variants will be converted to CMake booleans * Multivalued variants will be converted to semicolon-separated strings * Other variant values are converted to CMake string arguments This also adds a 'define' helper method to convert any variable to a CMake argument. It has the same conversion rules as 'define_from_variant' (but operates directly on values rather than requiring the user to supply the name of a package variant).
2020-03-16silo: depends on hdf5@:1.10.999 (#15495)Erik Schnetter1-0/+1
Silo does not build with HDF5 1.12.
2020-03-16Buildcache: Install into non-default directory layouts (#13797)Patrick Gartung4-585/+896
* Buildcache: Install into non-default directory layouts Store a dictionary mapping of original dependency prefixes to dependency hashes Use the loaded spec to grab the new dependency prefixes in the new directory layout. Map the original dependency prefixes to the new dependency prefixes using the dependency hashes. Use the dependency prefixes map to replace original rpaths with new rpaths preserving the order. For mach-o binaries, use the dependency prefixes map to replace the dependency library entires for libraries and executables and the replace the library id for libraries. On Linux, patchelf is used to replace the rpaths of elf binaries. On macOS, install_name_tool is used to replace the rpaths and dependency libraries of mach-o binaries and the id of mach-o libraries. On Linux, macholib is used to replace the dependency libraries of mach-o binaries and the id of mach-o libraries. Binary text with padding replacement is attempted for all binaries for the following paths: spack layout root spack prefix sbang script location dependency prefixes package prefix Text replacement is attempted for all text files using the paths above. Symbolic links to the absolute path of the package install prefix are replaced, all others produce warnings.
2020-03-16tixi: added package at v3.0.3 (#15490)Melven Roehrig-Zoellner1-0/+24
2020-03-16swig: added v4.0.1 (#15496)Erik Schnetter1-0/+1
2020-03-16ncurses: added v6.2 (#15494)Erik Schnetter1-0/+1
2020-03-16cmake: added v3.16.5 (#15492)Erik Schnetter1-0/+1
2020-03-16unqlite: added package at v1.1.9 (#15501)Matthieu Dorier1-0/+18
2020-03-15gcc: Don't apply macOS 9.2.0 patch for 9.3.0 (#15493)Erik Schnetter1-1/+1
The patch neither applies nor is necessary.
2020-03-14Limit binutils to <= 2.33.1 (#15470)Tim Haines1-1/+1
HPCToolKit <= 2020.03.01 does not build with binutils 2.34.
2020-03-13LIBXSMM 1.15 (#15482)Hans Pabst1-2/+3
* LIBXSMM 1.15 * LIBXSMM: renamed development version according to the related branch on GitHub.
2020-03-13py-astpretty: add new package (#15484)Adam J. Stewart1-0/+21
* py-astpretty: add new package * pkg_resources needed at run-time
2020-03-13package: Add fetch_options variable (#15317)Michael Kuhn14-42/+122
PR #15212 added a new connect_timeout option that can be overridden using fetch_options but had to specified per-version. This adds a new per-package variable that can be used to override fetch_options for all versions in the package. This includes connect_timeout as well as 'cookie' (e.g. for the jdk package). Packages can combine package-level fetch_options with per-version fetch_options, in which case the version fetch_options completely override the package-level fetch_options. This commit includes tests for the added behavior.
2020-03-13pgi: add missing paths in setup_run_environment (#15480)Melven Roehrig-Zoellner1-0/+3
2020-03-13Add py-h5glance versions 0.5 & 0.6 (#15461)Thomas Kluyver1-1/+3
* Add py-h5glance versions 0.5 & 0.6 * List versions newest to oldest
2020-03-13Add new ACTS version (#15479)Hadrien G1-0/+1
2020-03-13gitignore: pytest cache directory (#15476)Adam J. Stewart1-0/+1
2020-03-12Add source highlight package (#15473)Hector1-0/+21
* add GNU source-highlight package * fix flake8 * Allows the package to download from GNU mirrors