Commit graph

24722 commits

Author SHA1 Message Date
Ben Darwin
bd8ae72146
dcm2niix: new package (at version 1.0.20210317) (#25250) 2021-08-09 11:15:38 +02:00
Severin Strobl
f67d3b127c
apex: add v2.4.1 (#25248)
Also updated the URLs for APEX according to the recent move.
2021-08-09 11:14:55 +02:00
Martin Pokorny
22bc189e0e
casacore: add variant for ADIOS2 support (#25251) 2021-08-09 11:13:26 +02:00
Todd Gamblin
7ddd6ad461 installation: filter padding from all tty output
This is both a bugfix and a generalization of #25168. In #25168, we attempted to filter padding
*just* from the debug output of `spack.util.executable.Executable` objects. It turns out we got it
wrong -- filtering the command line string instead of the arg list resulted in output like this:

```
==> [2021-08-05-21:34:19.918576] ["'", '/', 'b', 'i', 'n', '/', 't', 'a', 'r', "'", ' ', "'", '-', 'o', 'x', 'f', "'", ' ', "'", '/', 't', 'm', 'p', '/', 'r', 'o', 'o', 't', '/', 's', 'p', 'a', 'c', 'k', '-', 's', 't', 'a', 'g', 'e', '/', 's', 'p', 'a', 'c', 'k', '-', 's', 't', 'a', 'g', 'e', '-', 'p', 'a', 't', 'c', 'h', 'e', 'l', 'f', '-', '0', '.', '1', '3', '-', 'w', 'p', 'h', 'p', 't', 'l', 'h', 'w', 'u', 's', 'e', 'i', 'a', '4', 'k', 'p', 'g', 'y', 'd', 'q', 'l', 'l', 'i', '2', '4', 'q', 'b', '5', '5', 'q', 'u', '4', '/', 'p', 'a', 't', 'c', 'h', 'e', 'l', 'f', '-', '0', '.', '1', '3', '.', 't', 'a', 'r', '.', 'b', 'z', '2', "'"]
```

Additionally, plenty of builds output padded paths in other plcaes -- e.g., not just command
arguments, but in other `tty` messages via `llnl.util.filesystem` and other places. `Executable`
isn't really the right place for this.

This PR reverts the changes to `Executable` and moves the filtering into `llnl.util.tty`. There is
now a context manager there that you can use to install a filter for all output.
`spack.installer.build_process()` now uses this context manager to make `tty` do path filtering
when padding is enabled.

- [x] revert filtering in `Executable`
- [x] add ability for `tty` to filter output
- [x] install output filter in `build_process()`
- [x] tests
2021-08-09 01:42:07 -07:00
Jen Herting
29098a1e07
py-speech-recognition: new package (#25273) 2021-08-09 10:31:21 +02:00
Sergey Kosukhin
053fa2a47b
netcdf-fortran: fix building with AOCC (#25186) 2021-08-09 10:30:31 +02:00
Tom Stitt
25a4c5ad18
mfem: add v4.3 (#25158)
Co-authored-by: Veselin Dobrev <dobrev@llnl.gov>
2021-08-09 10:08:33 +02:00
Tamara Dahlgren
4cd2cfc7e7
ci pipelines: expand the list of RADIUSS packages (#25282) 2021-08-09 10:06:56 +02:00
Satish Balay
874a35e30d
trilinos: fix +hypre build (#25291) 2021-08-09 10:05:52 +02:00
Satish Balay
f6cb076229
petsc: fix build with trilinos (#25289) 2021-08-09 10:02:47 +02:00
Sreenivasa Murthy Kolam
ea71eb35d3
Update rocm ecosystem to v4.3.0 (#25299) 2021-08-09 09:48:05 +02:00
Satish Balay
24ea784dc4
petsc, petsc4py: add version 3.15.3 (#25307) 2021-08-09 00:43:35 -07:00
Glenn Johnson
ff9c7380e8
r-cairo: add an explicit dependency on libxt (#25309)
Since r-cairo will always look for X libraries, and likely find them on
the system, make it always depend on r+X.
2021-08-09 09:27:57 +02:00
Harmen Stoppels
c37aee4620
hip: fix broken tests with ^cmake@3.21: (#25246) 2021-08-09 07:19:29 +00:00
Harmen Stoppels
4384ff8e41
Use __skip_rocmclang for cmake 3.21 in rocblas/rocfft to avoid incomplete compiler support (#25253) 2021-08-09 07:03:03 +00:00
Harmen Stoppels
420113d5ab
libtree: add v1.2.3 (#25270) 2021-08-09 08:51:39 +02:00
Seth R Johnson
66a8993092 Remove xsdk@0.2.0 and associated versions and xsdktrilinos
These versions can cause weird concretizations, and it looks like the
old version of xsdk may not even work because of xsdktrilinos being
disabled. The hypre version tagged for xsdk@0.2 no longer exists at the
described location.
2021-08-08 10:55:39 -07:00
Seth R Johnson
38803e3597 trilinos: remove develop version, change xsdk name
With the previous naming scheme, `trilinos@:10` concretizes to
`trilinos@xsdk-0.2.0`. Now, it's clear what the xsdk version is closest
to. Changed from tag to the corresponding commit SHA for safety.
2021-08-08 10:55:39 -07:00
Satish Balay
6ed4cf4016
petsc: cleanup test code to support 'spack test run' and add a 'cuda' test (#25099) 2021-08-08 12:16:42 -05:00
Alec Scott
0dd6b1e134 Clean Up PR from Container Builder 2021-08-08 07:20:25 -07:00
Edgar A. Leon
1c90b25933 hwloc: Adding opencl and rocm (AMD GPUs) variants to hwloc. 2021-08-08 07:18:26 -07:00
lukebroskop
1c204bef8a
trilinos: flag_handler logic fix (#25290)
* Do not allow cray build system patch for later version of otf2

* Modify flag_handler logic in the trilinos package

Modify flag_handler logic in the trilinos package to work better with compilers
other than CCE
2021-08-08 10:16:57 -04:00
Wouter Deconinck
9b66053d99
vecgeom: new version 1.1.16 (#25266)
Diff 1.1.15 to 1.1.16 at https://gitlab.cern.ch/VecGeom/VecGeom/-/compare/v1.1.15...v1.1.16?from_project_id=981, no changes to build dependencies.
2021-08-08 10:05:19 -04:00
Alec Scott
cfbefee0fa
Fix GHCR Username in Container Builder (#25301) 2021-08-07 00:25:36 +00:00
Axel Huebl
98d4a7af24
openPMD-api: CTest & Install Tests (#25300)
Run CTest at build time with:
```
spack install --test=root openpmd-api@<version>
```

and run smoke-tests after install and loading of the package via
```
spack load -r /<spec>
spack test run /<spec>
```
2021-08-06 16:55:32 -07:00
Axel Huebl
91b3dcca26
openPMD-api: 0.14.1 (#25265)
* openPMD-api: 0.14.1

Add the latest bugfix release.

* Keep 0.13.4 still preferred

More regressions to mitigate...
2021-08-06 16:43:46 -07:00
Axel Huebl
d69a22f160
WarpX: 21.08 (#25234)
Add the latest WarpX release.
2021-08-06 16:42:58 -07:00
Alec Scott
b92fa6bbf9
Add New Build Containers Workflow (#24257)
This pull request adds a new workflow to build and deploy Spack Docker containers
from GitHub Actions. In comparison with our current system where we use Dockerhub's
CI to build our Docker containers, this workflow will allow us to now build for multiple
architectures and deploy to multiple registries. (At the moment x86_64 and Arm64 because
ppc64le is throwing an error within archspec.)

As currently set up, the PR will build all of the current containers (minus Centos6 because 
those yum repositories are no longer available?) as both x86_64 and Arm64 variants. The
workflow is currently setup to build and deploy containers nightly from develop as well as
on tagged releases. The workflow will also build, but NOT deploy containers on a pull request
for the purposes of testing this PR. At the moment it is setup to deploy the built containers to
GitHub's Container Registry although, support for also uploading to Dockerhub/Quay can be
included easily if we decide to keep releasing on Dockerhub/want to begin releasing on Quay.
2021-08-06 15:53:46 -07:00
Jen Herting
97993ac38a
[py-sentencepiece] added veriosn 0.1.91 (#25275) 2021-08-06 15:41:27 +00:00
Todd Gamblin
ad66b758e4
codecov: allow coverage offsets for more base commit flexibility (#25293)
This is an attempt to fix "Missing base commit" messages in the codecov UI. Because we do not run
full tests on package PRs, package PRs' merge commits on `develop` don't have coverage info. It
appears that codecov will give you an error if the pseudo-base's coverage data doesn't all apply
properly to the real PR base, unless the `allow_coverage_offsets` option is set.

* See here for docs:
  https://docs.codecov.com/docs/comparing-commits#pseudo-comparison

* See here for another potential solution:
  https://community.codecov.com/t/2480/15
2021-08-06 01:33:12 -07:00
Todd Gamblin
0a6e98cdb5
refactor: rename colorful kwarg to color (#25292)
`compare_specs()` had a `colorful` keyword argument, but everything else in
spack uses `color` for this.

- [x] rename the argument
- [x] make the default follow spack's `--color=always/never/auto` setting
2021-08-06 06:29:49 +00:00
Jen Herting
2aea624dca
New package: r-elemstatlearn (#25276) 2021-08-05 17:12:15 -05:00
Jen Herting
0053117ac8
New package: r-gparotation (#25277) 2021-08-05 17:05:21 -05:00
Jen Herting
c178000d18
[sentencepiece] added version 0.1.91 (#25274) 2021-08-05 16:49:23 +00:00
gpotter2
4af6d6bb1b
Add libvpx to ffmpeg (#25155) 2021-08-05 10:55:03 -05:00
Harmen Stoppels
8f238c03ad
Add py-fastcov (#25268)
* Add py-fastcov

* Update var/spack/repos/builtin/packages/py-fastcov/package.py
2021-08-05 13:36:41 +00:00
Harmen Stoppels
15653868c8
patchelf: add v0.13 (#25271) 2021-08-05 13:30:17 +00:00
iarspider
159ac3e3fb
Add checksum for py-wheel 0.33.6 (#25257) 2021-08-05 08:01:22 +00:00
iarspider
b11f8aa4ea
Update py-typing-extensions (#25262) 2021-08-04 21:56:52 +00:00
iarspider
4ac246760e
Add checksum for py-gast 0.5.1 and 0.5.2 (#25258) 2021-08-04 14:55:48 -07:00
iarspider
63f950768f
Add checksums for new protobuf versions (#25259) 2021-08-04 21:47:23 +00:00
Adam J. Stewart
e2fe415ae6
Spack version: 0.16.1 -> 0.16.2 (#25255)
17473a08ff merged `v0.16.1` back into `develop` but somehow lost the version bump.  Fix it here.
2021-08-04 14:37:40 -07:00
iarspider
988c67fff2
Add checksum for py-astor@0.8.1 (#25256) 2021-08-04 21:31:07 +00:00
Richarda Butler
b5c82aa986
Caliper: Add E4S testsuite stand alone test (#25094) 2021-08-04 10:22:50 -07:00
lukebroskop
5f3c25f6e9
libcircle fix for CCE (#25224) 2021-08-04 12:43:18 +00:00
Michele Mesiti
978191aff5
Added new versions for Sombrero (#25243) 2021-08-04 10:02:30 +00:00
Harmen Stoppels
4b870196c0
Bump py-python-swiftclient and add keystone support (#25221) 2021-08-04 08:09:01 +00:00
Harmen Stoppels
575e321cc5
Add py-python-keystoneclient (#25220)
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-08-04 07:55:53 +00:00
Harmen Stoppels
20394a97da
Add py-oslo-serialization (#25218)
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-08-04 07:36:11 +00:00
Harmen Stoppels
63ac1b6620
Add py-oslo-config (#25216) 2021-08-04 07:31:44 +00:00