Commit graph

17565 commits

Author SHA1 Message Date
Amjad Kotobi
4c666034dc
r-rstudioapi : new version (#16574) 2020-05-11 12:49:27 -05:00
Amjad Kotobi
3ddf6c0845
r-rlang : new version (#16575) 2020-05-11 12:48:51 -05:00
Amjad Kotobi
5e348f7133
r-digest : version updated (#16578) 2020-05-11 12:43:38 -05:00
Andrew Gaspar
2c009a3226
Map the spack skylake arch to Kokkos BDW, rather than SKX (#16583)
SKX includes AVX-512 extensions that consumer Skylake processors do
not have. Therefore, map Skylake to the prior arch to work on
these systems. Skylake-X processors will still map as the
skylake_avx512 spack arch and get the correct optimzations.
2020-05-11 12:33:34 -05:00
Justin S
20a4e5efe8
stata: add new libpng dependency (#16582) 2020-05-11 12:32:36 -05:00
Michael Kuhn
cd2e906702
netcdf-fortran: Fix build with gcc@10: (#16573) 2020-05-11 12:31:40 -05:00
Jen Herting
c220a22b69
New package: py-mmcv (#16536)
* [py-mmcv] Created template

* [py-mmcv] added description and homepage

* [py-mmcv] requires python 3.6+

* [py-mmcv] added dependencies

* [py-mmcv] depends on opencv

* [py-mmcv] cleaned up fixmes

* [py-mmcv] requires numpy >= 1.11.1
2020-05-11 12:14:22 -05:00
Michael Kuhn
03d0a7ee1e
gcc: added v10.1.0 (#16525) 2020-05-11 16:22:19 +02:00
Sinan
ff6a0fc7b0
py-configobj: remove url function (#16522)
It seems the pypi version of the package somehow compiles just fine

Co-authored-by: Sinan81 <sbulut@3vgeomatics.com>
2020-05-11 10:43:56 +02:00
takanori-ihara
e08792cbcb
py-jupyterlab: added package at v2.1.0 (#16562) 2020-05-11 10:35:44 +02:00
takanori-ihara
fa8dede6cd
Add new package:py-jupyterlab-server (#16561) 2020-05-10 21:32:53 -05:00
Adam J. Stewart
c03d4688e4
PyTorch: fix master and mkldnn builds (#16560) 2020-05-10 19:40:00 -05:00
Amjad Kotobi
7d3b40fba4
new version r-rcpp (#16549) 2020-05-10 17:39:20 -05:00
Amjad Kotobi
6c820dd6b5
new version r-glue (#16558) 2020-05-10 17:38:51 -05:00
Amjad Kotobi
36941e3d94
new version r-pkgbuild (#16559) 2020-05-10 17:38:38 -05:00
Amjad Kotobi
5dc51c21bb
new version r-jsonlite (#16557) 2020-05-10 17:38:26 -05:00
Amjad Kotobi
f32d561e9b
new version r-dt (#16555) 2020-05-10 15:31:58 -05:00
Amjad Kotobi
3210e5999e
new version r-covr (#16554) 2020-05-10 15:31:08 -05:00
Amjad Kotobi
ff869a7d68
new version r-callr (#16552) 2020-05-10 15:29:18 -05:00
Adam J. Stewart
358242d2a8
DGL: add new version (#16547) 2020-05-10 10:04:28 -05:00
Massimiliano Culpo
8c12030498 Fix MacOS tests on develop
The -u option allows to update the current head,
so tests won't fail if we are on develop
2020-05-09 17:41:57 -07:00
Axel Huebl
29105da445 macOS nightly: +1hr py-jupyter
check if failures ares actually a real timeout or an error that
just causes a hang.
2020-05-09 17:41:10 -07:00
Axel Huebl
2b234b7a66 macOS nightly: two cores
All GitHub actions provide two cores. Just make sure this does not
get oversubscribed with potentially visible additional physical
cores.
2020-05-09 17:41:10 -07:00
Massimiliano Culpo
05203ec3fb
Add unit test on MacOS using Github Actions (#14220)
- Remove macos tests from travis
- Add macos tests in github actions.
2020-05-09 13:35:14 -07:00
vvolkl
69ea6de069
[dd4hep] variant and run env updates (#16524)
* [dd4hep] variant and run env updates

* address comments from #16524
2020-05-09 14:54:07 -05:00
Larry Knox
6e46603470
Add maintainers and variants for building with default earlier api versions. (#16534)
* Add maintainers.
Add variants for building with default earlier api versions.

* Update var/spack/repos/builtin/packages/hdf5/package.py

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-05-09 13:05:55 -05:00
Jen Herting
54fee4b400
New package: py-addict (#16535)
* [py-addict] created template

* [py-addict] added homepage and description

* [py-addict] cleaned up fixmes

* [py-addict] depends on py-setuptools
2020-05-09 13:05:33 -05:00
Nichols A. Romero
a868b1c756
QMCPACK Update May 2020 (#16542)
* Add naromero77 as a maintainer for QMCPACK Spack package.

* Add QMCPACK 3.9.2

* Remove QE-to-QMCPACK wave function converter from QMCPACK Spack package. Already been moved to QE Spack package.
2020-05-09 13:05:11 -05:00
iarspider
b668bde7ec
Fix dependency of geant4 (amends #16497) (#16504)
* Fix dependency of geant4 (amends #16497)

* Update geant4-data dependencies

* Reviewer comments (part 1/2)

* Reviewer comments (part 2/2)

* Update var/spack/repos/builtin/packages/geant4-data/package.py

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-05-09 19:04:20 +01:00
Massimiliano Culpo
b06bc31029
Increase coverage of spack.relocate (#16475)
- add docstrings and make parameter names consistent in `relocate.py`
- Make `replace_prefix_*` and other functions private (as they are implementation details)
- remove unused function _replace_prefix_nullterm()

- Add unit tests for `relocate.py` functions
  - add patchelf to Travis and use it during tests
  - add hello_world fixture with a compiled binary, so we can test relocation
2020-05-09 10:41:50 -07:00
Cyrus Harrison
8671ac6a1a
update visit package with 3.1.1 release and add comments (#16498) 2020-05-09 10:28:33 -07:00
Todd Gamblin
7b8e5c8999 bugfix: don't use sys.stdout as a default arg value (#16541)
After migrating to `travis-ci.com`, we saw I/O issues in our tests --
tests that relied on `capfd` and `capsys` were failing. We've also seen
this in GitHub actions, and it's kept us from switching to them so far.

Turns out that the issue is that using streams like `sys.stdout` as
default arguments doesn't play well with `pytest` and output redirection,
as `pytest` changes the values of `sys.stdout` and `sys.stderr`. if these
values are evaluated before output redirection (as they are when used as
default arg values), output won't be captured properly later.

- [x] replace all stream default arg values with `None`, and only assign stream
      values inside functions.
- [x] fix tests we didn't notice were relying on this erroneous behavior
2020-05-09 00:56:18 -07:00
Todd Gamblin
5883e9df53 ci: update Travis badge in README.md to point to travis-ci.com 2020-05-09 00:56:18 -07:00
Adam J. Stewart
790e9ac6de
spaCy: add new package for en_core_web_sm model (#16539) 2020-05-08 22:20:38 -05:00
Keita Iwabuchi
4c42946201
Metall: add version 0.2 (#16502) 2020-05-08 12:31:20 -05:00
takanori-ihara
89c92a0206
Add new package:py-pytest-check-links (#16503) 2020-05-08 12:30:47 -05:00
Sergey Kosukhin
e1c49d11bf
py-netcdf4: a couple of improvements (#16505)
* py-netcdf4: avoid recompilation and make the older versions to work with HDF5@1.10:

* py-netcdf4: add a new version and introduce a maintainer list.
2020-05-08 12:27:28 -05:00
Frédéric Simonis
1e9313a191
precice: Fix conflict with boost 1.73.0 (#16507) 2020-05-08 12:26:37 -05:00
Christoph Junghans
b9415c6b53
graphviz: fix cairo backend (#16511) 2020-05-08 12:25:38 -05:00
iarspider
08528a7379
Gaudi: separate variant for building documentation (#16515)
* Gaudi: separate variant for building documentation

* Update package.py
2020-05-08 12:24:42 -05:00
h-denpo
fae55550f9
New package (#16519)
Large Scale Assembly, Structural Correspondence,
       Multi Dynamics Simulator.In this program,
       a part of functions of ADVENTURE_Solid ver.1.1 module
2020-05-08 12:22:04 -05:00
iarspider
652e179ae6
Gaudi: syntax fix (#16523) 2020-05-08 12:17:48 -05:00
Amjad Kotobi
33e88db2d6
new version xrootd-4.12.0 (#16528) 2020-05-08 12:05:54 -05:00
Amjad Kotobi
9eaf7e42c8
new version r-git2r-0.27.1 (#16529) 2020-05-08 12:05:30 -05:00
Axel Huebl
f5844d3d81
all_urls: add urls[0] for versions (#16435)
This adds the `url` alternative `urls` to `package.all_urls`. With
this addition, one can find again new versions with
`spack versions <package>` for packages that are populated with
from mixin mirror `urls`.

Example: `util-macros` from x.org mixin.
2020-05-08 10:12:45 +02:00
Erik Schnetter
4ebff5cef9
Documentation: typo in option description (#16518) 2020-05-07 22:23:16 -07:00
iarspider
e2d42672b7
Config option to disable setting S_ISGID bit when creating installation directory (#14479)
* Add config option to disable setting S_ISGID bit when creating installation directory. 

Co-authored-by: Ivan Razumov <ivan.razumov@cern.ch>
2020-05-07 17:21:53 -07:00
iarspider
08f449ae9a
"spack checksum" QoL (#14311)
* Non-interactive mode for spack checksum; allow passing 'package@version' to spack checksum

* Flake8 fixes

* Update checksum.py

Fix typo

* Update spack-completion script

* Automatically set non-interactive mode if more than one version passed

* Update lib/spack/spack/cmd/checksum.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Add documentation and update spack-completion

* Flake8

* Rename option

* Update spack-completion

* Update lib/spack/spack/cmd/checksum.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update checksum.py

* Update stage.py

* Update create.py

Use batch mode when adding a new package

Co-authored-by: Ivan Razumov <ivan.razumov@cern.ch>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-05-07 18:34:36 -05:00
Elizabeth Fischer
bff5708a4f
Revert changes to qt (#16516)
Co-authored-by: Elizabeth Fischer <elizabeth.fischer@alaska.edu>
2020-05-07 18:32:44 -05:00
Peter Scheibel
1ed564a1e6
Testing: fix unintended interactions between tests, part 2 (#16429)
This fixes some errors with setting up test configuration. These
errors do not cause current Spack tests to fail but do create
red herring issues elsewhere (see #15666). Fixing these errors
leads to more errors in tests that depended on the original
misconfigured state, so those are also addressed here.

This is an update to #16003 which accounts for some unit tests with
conflicting config/mutable_config fixtures. These conflicts were
not exposed until the mutable_config fixture was fixed. Details are
included below. The change which builds on #16003 is prefixed with
"(new)".

* 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.
* (new) For tests that use install_mockery and mutable_config,
  replace install_mockery with a separate install_mockery_mutable_config
  fixture that is exactly the same as install_mockery but uses the
  mutable_config fixture to avoid conflicts.
2020-05-07 14:01:58 -07:00