Commit graph

17692 commits

Author SHA1 Message Date
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
Jeremy
598c233f78
Update kokkos for new 3.x build systems (#16358)
* change old Makefile-based Kokkos to kokkos-legacy

* add Kokkos 3.x packages

Co-authored-by: Jeremiah J Wilke <jjwilke@kokkos-dev-2.sandia.gov>
2020-04-30 08:13:47 -06:00
Teodor Nikolov
9627cbbe1b
lapackpp and blaspp: added packages (develop branch) (#16373) 2020-04-30 16:05:45 +02:00
Toyohisa Kameyama
54b71b2b69
JHPCN-DF: added package at v1.1.0 (#16384) 2020-04-30 15:03:35 +02:00
Benoit Coste
6c751f931c
py-pyquaternion: added package at v0.9.5 (#16386) 2020-04-30 14:50:28 +02:00
Chris Green
9698907e74
Spack command extensions: error-handling (#13635)
Generally speaking, errors that are encountered when attempting to load
command extensions now terminate the running Spack instance.

* Added new exceptions `spack.cmd.PythonNameError` and
  `spack.cmd.CommandNameError`.
* New functions `spack.cmd.require_python_name(pname)` and
  `spack.cmd.require_cmd_name(cname)` check that `pname` and `cname`
  respectively meet requirements, throwing the appropriate error if not.
* `spack.cmd.get_module()` uses `require_cmd_name()` and passes through
  exceptions from module load attempts.
* `spack.cmd.get_command()` uses `require_cmd_name()` and invokes
  `get_module()` with the correct command-name form rather than the
  previous (incorrect) Python name.
* Added New exceptions `spack.extensions.CommandNotFoundError` and
  `spack.extensions.ExtensionNamingError`.
* `_extension_regexp` has a new leading underscore to indicate expected
  privacy.
* `spack.extensions.extension_name()` raises an `ExtensionNamingError`
  rather than using `tty.warn()`.
* `spack.extensions.load_command_extension()` checks command source
  existence early and bails out if missing. Also, exceptions raised by
  `load_module_from_file()` are passed through.
* `spack.extensions.get_module()` raises `CommandNotFoundError` as
  appropriate.
* Spack `main()` allows `parser.add_command()` exceptions to cause
  program end.

Tests:

* More common boilerplate has been pulled out into fixtures including
  `sys.modules` dictionary cleanup and resource-managed creation of a
  simple command extension with specified contents in the source file
  for a single named command.
* "Hello, World!" test now uses a command named `hello-world` instead of
  `hello` in order to verify correct handling of commands with hyphens.
* New tests for:
  * Missing (or misnamed) command.
  * Badly-named extension.
  * Verification that errors encountered during import of a command are
    propagated upward.

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2020-04-29 18:18:48 -07:00
Carson Woods
d12e588c60
charliecloud: add more checksummed versions (#16146)
* Add more checksummed versions

* Remove all versions not supported by autotools build method

* Add old build system for older versions

* Add suggested changes
2020-04-29 17:22:22 -05:00
Adam J. Stewart
eef75ddd45
py-mypy: setuptools needed at run-time (#16375) 2020-04-29 13:50:34 -05:00
Dr. Christian Tacke
0385e84775
boost: Patch for boostorg/process/issues/116 (#16371)
Patch for "Unable to compile code using boost/process.hpp"
See: https://github.com/boostorg/process/issues/116
2020-04-29 12:53:58 -05:00
Nathan
b6b44948b8
prefix gets removed when adding additional configure options (#16335)
* prefix gets removed when adding additional configure options

* Update waf documentation to reflect the new change
2020-04-29 10:52:23 -05:00
darmac
42d7fd30c4
Add new package: brpc (#16309)
* Add new package: brpc

* change a patch for brpc

* refine brpc version

* refine brpc patch constraint
2020-04-29 09:58:35 -05:00
darmac
5697894b22
Add new package: graylog2-server (#16370) 2020-04-29 09:58:09 -05:00
darmac
890059c635
Add new package: libconfuse (#16368) 2020-04-29 09:57:38 -05:00
darmac
35b9901fa0
Add new package: fping (#16367) 2020-04-29 09:57:16 -05:00
darmac
0d9b003169
Add new package: trident (#16342)
* Add new package: trident

* remove unused source code
2020-04-29 08:20:05 -05:00
Jonathan R. Madsen
39bbe8f9d4
Update timemory to support new dependencies and expose more build options (#16241)
* Update timemory/package.py to support new dependencies and expose more build options

* Added missing 'use_arch' option handling

* Fixes for python 2.6

* Fix pyflake error F632

* F632 flake fixes

* Update package.py

* Update package.py

* 80 char width + added extra conflicts + fixed kokkos_modules reference

* 79 char width

* Removed submodule builds

- added allinea_map variant
- disabled caliper by default
- added ompt_{standalone,llvm} variants

* flake8 updates

* 79 char width
2020-04-29 08:19:17 -05:00
Joseph Ciurej
97e67b385c
ffmpeg: add v1.0.10, v2.8.15; add '+avresample'; improve variant handling (#16359)
* ffmpeg: add older versions (i.e. 2.8.15, 1.0.10), add 'avresample' variant

* ffmpeg: update variant handling to support older versions (i.e. 2.8.15, 1.0.10)
2020-04-29 09:33:22 +02:00
Joseph Ciurej
c37857f995
openscenegraph: add v3.4.0, v3.4.1; add '+ffmpeg' (#16360)
* openscenegraph: add v3.4.0/3.4.1, update versioning to use git, improve dependency handling (esp. for ffmpeg, opengl)

* openscenegraph: add '+ffmpeg' variant, add 'jasper' dependency, clean up cmake config variables

* openscenegraph: reverted fetches to use checksums to improve reliability

* openscenegraph: add a few more explicit dependencies (e.g. png, tiff, glib).
2020-04-29 09:27:27 +02:00