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95a48b27ec09b691d4107d48854126c045b03188
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9194 Commits

Author SHA1 Message Date
Greg Becker
95a48b27ec env activation: use package defined env setup methods (#13249) 
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.
 2019-10-22 23:27:40 -07:00
Benjamin Fovet
7338730528 gmsh: add version 4.4.1 (#13366) 2019-10-22 18:18:19 -05:00
Frédéric Simonis
ab5135db1c Boost package: Fix iostream autodetect libraries (#12440) 
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.
 2019-10-22 14:25:03 -07:00
Axel Huebl
0f931cfc87 ADIOS2: Document endian_reverse variant (#13226) 
Update the documentation of the `endian_reverse` variant in ADIOS2.
The short description caused some confusion (for me) :-)
 2019-10-22 11:06:06 -05:00
Ruben Di Battista
49291d5a40 git-lfs: Add new version (#13356) 
PS: The old versions do not work: it's likely that they changed git
history on submodules
 2019-10-22 10:45:45 -05:00
Adam J. Stewart
526ee113ea Default to Python 3.7 (#10319) 
* Default to Python 3

* Fix build with Intel compilers
 2019-10-22 10:22:32 -05:00
Adam J. Stewart
48e8029fb1 Add latest version of py-scikit-learn (#13295) 
* Add latest version of py-scikit-learn

* setup_environment -> setup_build_environment
 2019-10-22 09:16:58 -05:00
Adam J. Stewart
09070b0c9b Add latest version of npth (#13353) 2019-10-22 09:16:33 -05:00
Adam J. Stewart
2de807d4cb Add latest version of py-macs2 (#13358) 2019-10-22 09:16:07 -05:00
Adam J. Stewart
e0c310bfd3 Add latest version of py-sphinxcontrib-programoutput (#13359) 2019-10-22 09:15:39 -05:00
Adam J. Stewart
809733c7e6 Restrict parallel build of py-astropy to Python 3 (#13360) 2019-10-22 09:15:11 -05:00
Adam J. Stewart
6cb972a9d2 Add dependency version constraint to libgcrypt (#13351) 2019-10-22 00:43:44 -05:00
Adam J. Stewart
2aa51697c5 Fix configure arg to libassuan (#13350) 2019-10-22 00:43:29 -05:00
Adam J. Stewart
598274a278 Fix configure arg to libksba (#13352) 2019-10-22 00:43:11 -05:00
Adam J. Stewart
fb219cd91c Add latest version of gnupg (#13349) 2019-10-22 00:42:56 -05:00
Adam J. Stewart
326db657da Add latest version of patchelf (#13348) 2019-10-22 00:42:40 -05:00
Adam J. Stewart
5e6dc7ab4b Add latest version of zstd (#13340) 
* Add latest version of zstd

* setup_environment -> setup_build_environment
 2019-10-21 21:45:48 -05:00
Toyohisa Kameyama
98c0d59a0c sniffles: fix zlib header lookup directory. (#13063) 
* sniffles: fix zlib header lookup directory.

* use bamtools and zlib to spack installed package.

* remove unneeded patch.
 2019-10-21 18:38:05 -05:00
noguchi-k
7b62b64b03 elsi:add CMAKE Fortran MODDIR FLAG for Fujitsu compiler (#13244) 
* add CMAKE Fortran MODDIR FLAG for Fujitsu compiler

* elsi:remove extra fix
 2019-10-21 18:28:38 -05:00
t-karatsu
0e3e1836ff arpack-ng: Fixed error that is not compatible with isnan. (#13246) 2019-10-21 18:27:39 -05:00
t-karatsu
26141ad489 bpp-core: Clarify 'isnan' function's namespace. (#13260) 2019-10-21 18:24:10 -05:00
Michael Kuhn
edf56d8ac4 qt: Fix build for newer versions (#13262) 
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
 2019-10-21 18:23:03 -05:00
健美猞猁
26687988eb New package: Fl (#12877) 2019-10-21 12:04:00 -07:00
Adam J. Stewart
4ab63c17d5 Fix Python 3.8 build on macOS (#13338) 2019-10-21 11:21:47 -05:00
Adam J. Stewart
4d99663ef9 Add latest version of py-cffi (#13322) 
* Add latest version of py-cffi

* setup_environment -> setup_build_environment
 2019-10-21 11:19:48 -05:00
Adam J. Stewart
038f7b1b66 Add latest version of py-numpy (#13307) 
* Add latest version of py-numpy

* setup_environment -> setup_build_environment
 2019-10-21 11:19:05 -05:00
Adam J. Stewart
72177b6e97 Add latest version of py-tables (#13291) 
* Add latest version of py-tables

* setup_environment -> setup_build_environment
 2019-10-21 11:17:52 -05:00
Adam J. Stewart
5090071693 Add latest version of py-torch (#13290) 
* Add latest version of py-torch

* setup_environment -> setup_build_environment
 2019-10-21 11:17:15 -05:00
Adam J. Stewart
f2d91f7e3c Use specific version of googletest for uriparser (#13339) 2019-10-20 19:08:23 -05:00
Adam J. Stewart
01e64886ac Tut cannot be built with Python 3.7+ (#13341) 2019-10-20 19:08:04 -05:00
Adam J. Stewart
7f2aacfffc Add latest version of proj (#13337) 2019-10-20 17:56:37 -05:00
Adam J. Stewart
030b2f8657 Add missing zlib dependency to openjpeg (#13336) 2019-10-20 17:06:43 -05:00
Adam J. Stewart
0cfc88c7d7 openblas: http -> https (#13335) 2019-10-20 17:06:30 -05:00
Adam J. Stewart
785d5d9ca3 mapserver: http -> https (#13334) 2019-10-20 16:31:55 -05:00
Adam J. Stewart
4789ac956c liblas: http -> https (#13331) 2019-10-20 15:51:35 -05:00
Adam J. Stewart
529d1246f6 libtiff: http -> https (#13332) 2019-10-20 15:51:23 -05:00
Adam J. Stewart
b56e46ece8 libgeotiff: http -> https (#13330) 2019-10-20 15:51:08 -05:00
Adam J. Stewart
f1e595cb61 Add latest version of libyaml (#13333) 2019-10-20 15:50:48 -05:00
Adam J. Stewart
04e999162d Add latest version of libgcrypt (#13329) 2019-10-20 14:45:00 -05:00
Adam J. Stewart
73c5a9c736 Add latest version of googletest (#13328) 2019-10-20 14:44:43 -05:00
Adam J. Stewart
1673dc5aeb GEOS: http -> https (#13327) 2019-10-20 14:44:28 -05:00
Adam J. Stewart
c767444f88 Add missing test dependency to py-alabaster (#13325) 2019-10-20 14:44:14 -05:00
Adam J. Stewart
a602ed873d Add latest version of py-typing (#13287) 2019-10-20 13:18:02 -05:00
Adam J. Stewart
d462749b59 Add missing dependencies to py-apipkg (#13324) 2019-10-20 13:17:44 -05:00
Adam J. Stewart
32879df9d0 Add latest version of py-babel (#13323) 2019-10-20 13:17:28 -05:00
Adam J. Stewart
ea90d2b88a Add latest version of py-chardet (#13321) 2019-10-20 11:44:12 -05:00
Adam J. Stewart
d2744a072b Add latest version of py-click (#13320) 2019-10-20 11:43:56 -05:00
Adam J. Stewart
41126d457f Add latest version of py-execnet (#13317) 2019-10-20 11:21:59 -05:00
Adam J. Stewart
1007a0f7e5 Add latest version of py-decorator (#13318) 2019-10-20 11:21:46 -05:00
Adam J. Stewart
47831a95e1 Add latest version of py-coverage (#13319) 2019-10-20 11:21:32 -05:00