Commit graph

9214 commits

Author SHA1 Message Date
Eric Martin
944ffe44a7 subread: add version 2.0.0 (#13368) 2019-10-23 23:07:11 -05:00
Cody Balos
177f661bb3 sundials: add version 5.0.0 and new variant (#13375)
* sundials: add version 5.0.0 and new variant

plus some cleanup

* sundiaks: fix formatting

* sundials: fix dependencies
2019-10-23 23:06:20 -05:00
Eric Martin
d0d0456fa7 vt: add version 0.5772 (#13367) 2019-10-23 23:05:27 -05:00
Greg Becker
8c7a3e55dd add spack dev-build command; deprecate spack diy (#13374)
Rename the `spack diy` command to `spack dev-build` to make the use case clearer.

The `spack diy` command has some useful functionality for developers using Spack to build their dependencies and configure/build/install the code they are developing.  Developers do not notice it, partly because of the obscure name.

The `spack dev-build` command has a `-u/--until PHASE` option to stop after a given phase of the build. This can be used to configure your project, run cmake on your project, or similarly stop after any stage of the build the user wants. These options are analogous to the existing `spack configure` and `spack build` commands, but for developer builds.

To unify the syntax, we have deprecated the `spack configure` and `spack build` commands, and added a `-u/--until PHASE` option to the `spack install` command as well.

The functionality in `spack dev-build` (specifically `spack dev-build -u cmake`) may be able to supersede the `spack setup` command, but this PR does not deprecate that command as that will require slightly more thought.
2019-10-23 17:08:15 -07:00
Michael Kuhn
bd7265ed52 bison: Fix parallel build (#13402) 2019-10-23 16:49:18 -05:00
Michael Kuhn
420346b275 mysql: Use correct python command (#13393)
* mysql: Use correct python command

python~pythoncmd does not provide a python symlink for python3, so make
sure we pick the right command.

* mysql: Adapt to build env changes
2019-10-23 14:15:30 -05:00
Sarah Osborn
b7536eb332 hypre: Add new variants to expose existing features. (#13373)
* hypre: Add new variants to expost existing features.

* hypre: Add new variants to expose existing features.

* hypre: Shorten description line.

* hypre: Add an explicit else clause to disable some features.
2019-10-23 14:13:21 -05:00
Adam J. Stewart
33499681a4
Add latest version of py-pbr (#13380) 2019-10-23 10:14:04 -05:00
Adam J. Stewart
df3b23334a
py-argparse: remove Python dependency version (#13378) 2019-10-23 10:13:39 -05:00
Adam J. Stewart
bc6c76baf9
py-traceback2: fix dependencies (#13381) 2019-10-23 10:13:11 -05:00
Michael Kuhn
b75f506a1a bison: Fix build (#13231)
It seems that 3.4.2 includes a change that is supposed to fix parallel
builds (https://lists.gnu.org/archive/html/bug-bison/2019-08/msg00000.html).
Instead, it actually breaks it for me (with -j48) with errors such as:
```
mv: cannot stat 'examples/c/reccalc/scan.stamp.tmp': No such file or directory
Makefile:9323: recipe for target 'examples/c/reccalc/scan.stamp' failed
```
2019-10-23 10:07:22 -05:00
Adam J. Stewart
4bd0a9b286
py-linecache2: pbr is only a build dependency (#13379) 2019-10-23 09:38:05 -05:00
Adam J. Stewart
baeec6a94e
py-unittest2: fix dependencies (#13382) 2019-10-23 09:37:03 -05:00
Adam J. Stewart
79c28331d2
Add py-codecov package (#13383) 2019-10-23 09:36:45 -05:00
t-karatsu
6f41987500 bpp-phyl: Clarify namespace of 'isnan' function. (#13386) 2019-10-23 09:36:01 -05:00
Michael Kuhn
64694dfaf8 magics: Use correct python path (#13394)
python~pythoncmd does not provide a python symlink for python3, so make
sure we pick the right command.
2019-10-23 09:33:42 -05:00
Michael Kuhn
466d07558d bracken: Use correct python command (#13395)
python~pythoncmd does not provide a python symlink for python3, so make
sure we pick the right command.
2019-10-23 09:33:09 -05:00
carlabguillen
44f859849b Ace package. Initial commit (#13211)
* Ace package. Initial commit

* Correcting header now with licence.

* Using sha256

* Making requested changes:removing import line, urls and checksums in one line, and making it an MakefilePackage.

* Removing extra line
2019-10-23 09:31:06 -05:00
Michael Kuhn
464ce2795a glib: Use correct python command (#13392)
python~pythoncmd does not provide a python symlink for python3, so make
sure we pick the right command.
2019-10-23 09:30:46 -05:00
Satish Balay
25d63aa44c petsc: add version 3.12.1 [and variant: batch] (#13390)
* petsc: add version 3.12.1 [and variant: batch]

* fix test_prs_update_old_api errors
2019-10-23 09:29:28 -05:00
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