Commit graph

17609 commits

Author SHA1 Message Date
Shintaro Iwasaki
acf0c90283
argobots: mark 1.0 as preferred (#16458)
By default, Spack chooses 1.0rc2 instead of 1.0 though 1.0 is the stable and
newer release.  We manually mark the version 1.0 as preferred.
2020-05-04 16:44:50 -05:00
Oliver Breitwieser
1cff717ca8 Fix git-related commands not working in worktrees
If spack is checked out in a git worktree (see [1]), all git-related
commands fail because the `spack_is_git_repo()`-check is not thorough
enough.

When developing in a feature-branch in a seperate worktree, this is
annoying as all unittests regarding git-related spack commands fail,
cluttering the test results with false-positives.

[1]: https://git-scm.com/docs/git-worktree

Change-Id: I94b573a2c0e058e9ccc169e7ee6561626fbb06fd
2020-05-04 14:39:25 -07:00
Elizabeth Fischer
dea5d913db
Updates to Python for macOS (#16449)
Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
2020-05-04 16:30:59 -05:00
Elizabeth Fischer
7b31f5474b
grass: new versions (#16181)
* grass

* Update var/spack/repos/builtin/packages/grass/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-05-04 16:25:19 -05:00
Axel Huebl
87f78137a5
LAPACKC++: added "shared" variant (#16419)
We can control the shared/static build of CMake and the default in
Spack is to build shared libraries. The old, uncontrolled default
of this package is a static build.
2020-05-04 09:39:20 +02:00
Dr. Christian Tacke
d5adad6953
singularity: added missing dependencies (#16430)
See:

https://sylabs.io/guides/3.5/user-guide/quick_start.html#install-system-dependencies

for pkg-config and libseccomp
2020-05-04 09:02:38 +02:00
Nichols A. Romero
860c54335d
QE-to-QMCPACK wave function converter relocation + some bug fixes (#16422)
* Revise description of patch variant.

* Add qmcpack variant. Apply QE-to-QMCPACK wave function converter patch.

* Clean-up, document, and re-organize.

* ELPA patches did not nead when=`+patch` variant.

* Need to be more precise here with QE version numbers.

* satisfies seems to be necessary here in order to get correct behaviour.

* Buglet with zlib link line.

* Update var/spack/repos/builtin/packages/quantum-espresso/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/quantum-espresso/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Fix for QE-to-QMCPACK wave function converter w.r.t. QE 6.3. Also adjust comments to reflect changes in code.

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-05-03 14:53:01 -06:00
Adam J. Stewart
caad59e7c7
NumPy: add 1.18.4 (#16441) 2020-05-03 13:29:15 -05:00
vvolkl
ed9e19df06
Add new HEP package: fastjet (#16439)
* [fastjet] initial commit

* [fastjet] remove beta versions
2020-05-03 13:27:18 -05:00
vvolkl
3c2f46aabf
Add new HEP package: Delphes (#16440)
* [delphes] initial commit

* [delphes] formatting fixes
2020-05-03 11:13:03 -05:00
Adam J. Stewart
1af31d24fd
GEOS: add new version (#16437) 2020-05-02 23:38:46 -05:00
Adam J. Stewart
eb4451dd1e
py-shapely: new version, Python 3.7 fix (#16438) 2020-05-02 23:38:30 -05:00
Adam J. Stewart
2e63e08192
py-cartopy: update package, fix PROJ.6 support (#16436) 2020-05-02 20:13:12 -05:00
Matthias Diener
1bc104e00e
colordiff: add version 1.0.19 (#16431) 2020-05-02 13:26:56 -05:00
Jonathon Anderson
08f88b4be6
Add a gpfs variant to openmpi package (#15793)
Open MPI will detect and link against GPFS if it is present
on the system. This variant allows this to be disabled, even
if GPFS is present.
2020-05-02 11:07:50 -05:00
Sajid Ali
adafdf0644
add hydra/pmix conflict (#16428) 2020-05-01 20:51:54 -05:00
Matthias Diener
668dcb78a1
py-opentuner: add version 0.8.2 (#16423) 2020-05-01 20:50:54 -05:00
Jen Herting
acabe2deba
[ncbi-magicblast] added version 1.5.0 (#16424) 2020-05-01 20:50:26 -05:00
Justin S
cf59220edc
stata: add version 16 (#16425) 2020-05-01 20:50:13 -05:00
mic84
c7552c0c72
amrex: New version 20.05 (#16427) 2020-05-01 20:47:18 -05:00
Kelly (KT) Thompson
b5b7ef2ce6
Provide update for py-pyside2 version 5.14.2.1. (#16426) 2020-05-01 17:32:31 -05:00
Justin S
f38820f89c
tbl2asn: new package at 20200301 (#16280)
* tbl2asn: new package at 20200301

* tbl2asn: remove unused url

* tbl2asn: use spack decompression, fix permissions

* tbl2asn: change version
2020-05-01 16:40:09 -05:00
Peter Scheibel
40df44e021
Revert "Testing: fix unintended interactions between tests (#16003)" (#16420)
This was breaking tests on develop.
2020-05-01 13:39:43 -07:00
Peter Scheibel
31d12d380f
Testing: fix unintended interactions between tests (#16003)
* For tests that use the real Spack package repository, the config
  needs to avoid using MPI providers that are not intended to be
  installed by Spack. Without this, it is possible that Spack tests
  which concretize the MPI virtual will end up trying to use an
  implementation that it shouldn't (e.g. one that is always
  provided externally). See #15666 for an example.
* The mutable_config test fixture was not initializing the scope
  roots to the right directories (so the resulting config was empty).
* The current_host fixture in the concretize.py tests was using the
  config fixture rather than mutable_config, and was polluting the
  config cache for other tests.
* One test in concretize.py was clearing a nonexistent cache
  (PackagePrefs._packages_config_cache). This reference has been
  removed.
* The test 'test_preferred_compilers' was was depending on cross
  test config pollution to succeed. The initial spec before
  concretization has been updated to updated to be explicit about
  the desired result.
2020-05-01 10:47:46 -07:00
Axel Huebl
d0dfa1ea4d
dev-build: --drop-in <shell> (#14887)
* dev-build: --drop-in <shell>

Add a `--drop-in <shell>` option to `spack dev-build`.
This option will automatically run a
`spack build-env <spec> -- <shell>` at the end of a `dev-build`, e.g.
to quickly drop-and-devel into a build phase of a package.

Example usage:
```
spack dev-build --before cmake --drop-in bash openpmd-api@develop
```

* build_env: drop in unit test

Co-authored-by: Greg Becker <becker33@llnl.gov>
2020-05-01 09:37:21 -07:00
Toyohisa Kameyama
40f70c4d4f
mt-metis: New package. (#16380)
* mt-metis: New package.

* variant to 1 line.

* delete useless lines.
2020-05-01 10:51:27 -05:00
Matt Larsen
69a0fbd2cb
raja: add awareness of the cuda architecture (#16377) 2020-05-01 10:07:12 +02:00
Jean-Laurent Picard
4f6c4743e3
arborx: fix build with new kokkos-legacy (#16413) 2020-05-01 09:30:27 +02:00
Christoph Junghans
7a56e6fce1
gromacs: add v2020.2 (#16408) 2020-04-30 19:01:07 -06:00
Satish Balay
4c69bc9d16
amrex: repo went through history rewrite - so use updates sha256sums (#16379) 2020-04-30 15:13:45 -05:00
Adam J. Stewart
022c287e47
Fix typos in new AutotoolsPackage function (#16406) 2020-04-30 15:13:04 -05:00
Michael Kuhn
a24a12f229
sqlite: Add 3.31.1 (#16404) 2020-04-30 15:12:51 -05:00
Michael Kuhn
efbd8c1555
readline: Fix homepage (#16403) 2020-04-30 15:12:38 -05:00
Michael Kuhn
9920684600
gettext: Add 0.20.2 (#16402) 2020-04-30 15:12:26 -05:00
Michael Kuhn
f04b0d99a8
glib: Add 2.64.2 (#16401) 2020-04-30 15:12:13 -05:00
Michael Kuhn
d2fc61a019
libffi: Add 3.3 (#16400) 2020-04-30 15:12:00 -05:00
Michael Kuhn
c2704a6037
perl: Add 5.30.2 (#16396) 2020-04-30 15:11:46 -05:00
Michael Kuhn
7adcb23978
libxml2: Add 2.9.10 (#16399) 2020-04-30 14:29:50 -05:00
Michael Kuhn
15c1fbc677
meson: Add 0.54.1 (#16398) 2020-04-30 14:29:36 -05:00
Michael Kuhn
6855e8e10f
pcre: Add 8.44 (#16397) 2020-04-30 14:29:24 -05:00
Ben Bergen
6d7daf0def
Resolves: https://github.com/spack/spack/issues/16394 (#16395)
Build problem with gcc 10.x
2020-04-30 11:16:00 -06:00
Adam J. Stewart
b55b7d5707
Fix kokkos-kernels tuple unpacking (#16393) 2020-04-30 11:36:50 -05:00
Christoph Junghans
cfb307b8e7
lammps: fix build with kokkos (#16390) 2020-04-30 10:29:08 -06:00
Adam J. Stewart
6c24142ebd
Fix coreutils configure_args (#16391) 2020-04-30 11:13:23 -05:00
Christoph Junghans
74c9ba551a
cabana: add v0.2 and fix kokkos deps (#16389) 2020-04-30 09:49:02 -06:00
darmac
b0ecaa1093
Add new package: bashtop (#16383) 2020-04-30 10:45:48 -05:00
Satish Balay
b2df39ea3a
petsc: switch hdf5 spec from --with-hdf5-dir to --with-hdf5-lib (#16376)
This way - we can detect and use hdf5:hl,fortran - if enabled, but not require it as a dependency
2020-04-30 10:40:25 -05:00
Satish Balay
3a3f871718
xsdk: update to mfem and py-petsc4py changes (#16378)
mfem variant hypre is now rolled into variant mpi - so update spec accordingly

mfem@4.0.1-xsdk+superlu-dist is broken and unsupported - so disable it

with the addition of py-petsc4py@3.13.0 - conretizer gets confused and is not picking py-petsc4py@3.12.0 as a compatible dependency with petsc@3.12. So manually specify it.
Also depends_on('py-libensemble@0.5.2+petsc4py ^py-petsc4py@3.12.0' causes concretizer to hang forever
2020-04-30 10:33:02 -05:00
Christoph Junghans
d5d4e16f3d
graphviz: fix cairo dep (#16387) 2020-04-30 10:29:20 -05:00
Christoph Junghans
f005ec016b
kokkos: fix typos (#16388) 2020-04-30 09:09:13 -06:00