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2019-10-23petsc: add version 3.12.1 [and variant: batch] (#13390)Satish Balay1-8/+14
* petsc: add version 3.12.1 [and variant: batch] * fix test_prs_update_old_api errors
2019-10-22env activation: use package defined env setup methods (#13249)Greg Becker1-2/+2
This PR ensures that environment activation sets all environment variables set by the equivalent `module load` operations, except that the spec prefixes are "rebased" to the view associated with the environment. Currently, Spack blindly adds paths relative to the environment view root to the user environment on activation. Issue #12731 points out ways in which this behavior is insufficient. This PR changes that behavior to use the `setup_run_environment` logic for each package to augment the prefix inspections (as in Spack's modulefile generation logic) to ensure that all necessary variables are set to make use of the packages in the environment. See #12731 for details on the previous problems in behavior. This PR also updates the `ViewDescriptor` object in `spack.environment` to have a `__contains__` method. This allows for checks like `if spec in self.default_view`. The `__contains__` operator for `ViewDescriptor` objects checks whether the spec satisfies the filters of the View descriptor, not whether the spec is already linked into the underlying `FilesystemView` object.
2019-10-22gmsh: add version 4.4.1 (#13366)Benjamin Fovet1-0/+1
2019-10-22Boost package: Fix iostream autodetect libraries (#12440)Frédéric Simonis1-1/+3
Boost iostream autodetects the compression libraries libzstd and liblzma outside of the Spack environment. This commit disables mentioned libraries. In the future if the Spack zstd/lzma packages were added as dependencies of the Spack Boost package, additional work could be done to build Boost with the Spack-built versions of these libraries.
2019-10-22ADIOS2: Document endian_reverse variant (#13226)Axel Huebl1-1/+2
Update the documentation of the `endian_reverse` variant in ADIOS2. The short description caused some confusion (for me) :-)
2019-10-22git-lfs: Add new version (#13356)Ruben Di Battista1-0/+1
PS: The old versions do not work: it's likely that they changed git history on submodules
2019-10-22Default to Python 3.7 (#10319)Adam J. Stewart2-7/+44
* Default to Python 3 * Fix build with Intel compilers
2019-10-22Add latest version of py-scikit-learn (#13295)Adam J. Stewart1-32/+19
* Add latest version of py-scikit-learn * setup_environment -> setup_build_environment
2019-10-22Add latest version of npth (#13353)Adam J. Stewart1-1/+2
2019-10-22Add latest version of py-macs2 (#13358)Adam J. Stewart1-3/+7
2019-10-22Add latest version of py-sphinxcontrib-programoutput (#13359)Adam J. Stewart1-2/+4
2019-10-22Restrict parallel build of py-astropy to Python 3 (#13360)Adam J. Stewart1-2/+6
2019-10-22Add dependency version constraint to libgcrypt (#13351)Adam J. Stewart1-1/+1
2019-10-22Fix configure arg to libassuan (#13350)Adam J. Stewart1-3/+4
2019-10-22Fix configure arg to libksba (#13352)Adam J. Stewart1-3/+4
2019-10-22Add latest version of gnupg (#13349)Adam J. Stewart1-13/+23
2019-10-22Add latest version of patchelf (#13348)Adam J. Stewart1-5/+5
2019-10-21Add latest version of zstd (#13340)Adam J. Stewart1-3/+6
* Add latest version of zstd * setup_environment -> setup_build_environment
2019-10-21sniffles: fix zlib header lookup directory. (#13063)Toyohisa Kameyama2-0/+50
* sniffles: fix zlib header lookup directory. * use bamtools and zlib to spack installed package. * remove unneeded patch.
2019-10-21elsi:add CMAKE Fortran MODDIR FLAG for Fujitsu compiler (#13244)noguchi-k1-0/+5
* add CMAKE Fortran MODDIR FLAG for Fujitsu compiler * elsi:remove extra fix
2019-10-21arpack-ng: Fixed error that is not compatible with isnan. (#13246)t-karatsu2-0/+26
2019-10-21bpp-core: Clarify 'isnan' function's namespace. (#13260)t-karatsu2-0/+46
2019-10-21qt: Fix build for newer versions (#13262)Michael Kuhn1-2/+0
For some reason, newer versions of qt fail to build because they cannot find certain system libraries such as libatomic and libdl. Leaving the qmake compiler set to gcc seems to fix the problem. Fixes #13221
2019-10-21New package: Fl (#12877)健美猞猁1-0/+24
2019-10-21Fix Python 3.8 build on macOS (#13338)Adam J. Stewart1-150/+166
2019-10-21Add latest version of py-cffi (#13322)Adam J. Stewart1-5/+10
* Add latest version of py-cffi * setup_environment -> setup_build_environment
2019-10-21Add latest version of py-numpy (#13307)Adam J. Stewart1-4/+5
* Add latest version of py-numpy * setup_environment -> setup_build_environment
2019-10-21Add latest version of py-tables (#13291)Adam J. Stewart1-8/+10
* Add latest version of py-tables * setup_environment -> setup_build_environment
2019-10-21Add latest version of py-torch (#13290)Adam J. Stewart1-28/+30
* Add latest version of py-torch * setup_environment -> setup_build_environment
2019-10-20Use specific version of googletest for uriparser (#13339)Adam J. Stewart1-1/+1
2019-10-20Tut cannot be built with Python 3.7+ (#13341)Adam J. Stewart1-0/+4
2019-10-20Add latest version of proj (#13337)Adam J. Stewart1-1/+2
2019-10-20Add missing zlib dependency to openjpeg (#13336)Adam J. Stewart1-0/+2
2019-10-20openblas: http -> https (#13335)Adam J. Stewart1-2/+2
2019-10-20mapserver: http -> https (#13334)Adam J. Stewart1-1/+1
2019-10-20liblas: http -> https (#13331)Adam J. Stewart1-1/+1
2019-10-20libtiff: http -> https (#13332)Adam J. Stewart1-6/+6
2019-10-20libgeotiff: http -> https (#13330)Adam J. Stewart1-1/+1
2019-10-20Add latest version of libyaml (#13333)Adam J. Stewart1-27/+24
2019-10-20Add latest version of libgcrypt (#13329)Adam J. Stewart1-5/+7
2019-10-20Add latest version of googletest (#13328)Adam J. Stewart1-5/+6
2019-10-20GEOS: http -> https (#13327)Adam J. Stewart1-1/+1
2019-10-20Add missing test dependency to py-alabaster (#13325)Adam J. Stewart1-0/+1
2019-10-20Add latest version of py-typing (#13287)Adam J. Stewart1-3/+3
2019-10-20Add missing dependencies to py-apipkg (#13324)Adam J. Stewart1-0/+3
2019-10-20Add latest version of py-babel (#13323)Adam J. Stewart1-2/+6
2019-10-20Add latest version of py-chardet (#13321)Adam J. Stewart1-1/+4
2019-10-20Add latest version of py-click (#13320)Adam J. Stewart1-2/+5
2019-10-20Add latest version of py-execnet (#13317)Adam J. Stewart1-1/+3
2019-10-20Add latest version of py-decorator (#13318)Adam J. Stewart1-1/+4