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Author SHA1 Message Date
dependabot[bot]
1243717012 build(deps): bump actions/checkout from 2 to 3.0.2 (#30235) 
Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 3.0.2.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v2...2541b1294d2704b0964813337f33b291d3f8596b)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2022-04-27 13:47:50 +02:00
snehring
da3d315cba blat: add v37 (#30166) 2022-04-27 12:26:57 +02:00
Michael Kuhn
48ff4c7679 rust: add 1.60.0 and fix libgit2 incompatibility (#30123) 2022-04-27 12:22:52 +02:00
liuyangzhuan
9fc6494a28 Added GPTune v3.0.0 and its dependency py-pymoo (#30119) 2022-04-27 12:21:44 +02:00
Valentin Volkl
9d4cedac51 tauola: fix ~lhapdf (#30190) 2022-04-27 12:16:08 +02:00
Derek Ryan Strong
f66139dfe4 Add fix for binutils 2.38 +gas makeinfo issue (#30209) 
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
 2022-04-27 12:11:48 +02:00
nfurmento
79e0a3dad0 Starpu and Fxt: new packages (#29285) 2022-04-27 12:10:09 +02:00
dependabot[bot]
3dbbf3a101 build(deps): bump codecov/codecov-action from 3.0.0 to 3.1.0 (#30234) 
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3.0.0 to 3.1.0.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/master/CHANGELOG.md)
- [Commits](e3c560433a...81cd2dc814)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2022-04-27 11:26:19 +02:00
Harmen Stoppels
f273e7d329 openmpi: add toggle for rsh plm (#30251) 
By default `openmpi` needs `rsh` from `openssh`, which is a somewhat
redundant dependency for clusters using slurm. This PR adds a toggle to
allow users to disable the ssh/rsh plm altogether.
 2022-04-27 11:15:48 +02:00
snehring
351072cd9f gcta: rework package recipe (#30286) 2022-04-27 08:56:31 +00:00
Adam J. Stewart
0b23f1be05 py-pil: deprecate package (#30308) 2022-04-27 02:34:29 -06:00
Glenn Johnson
b8015a71e9 relion: add altcpu variant and fix fftw (#30097) 
This package was not setting FFTW when +mklfft was used with +cuda.
Since both were set to 'True', the default build was not linked to
any FFTW, leading to a run time error. It seems MKL support was
conflated with alternative CPU acceleration support. This PR does the
following:

- adds the altcpu variant to specify non-GPU/CPU acceleration
- sets a conflict between +altcpu and +cuda
- sets an FFTW implementation
- sets fltk+xft when +gui to get a decent looking GUI interface
- sets tbb dependency only when +altcpu
- adds dependency on ctffind
- adds variant and dependency on motioncor2
- sets defaults for
    - qsub template location
    - ctffind location
    - motioncor2 location

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
 2022-04-27 10:30:39 +02:00
snehring
739f040fa8 bucky: fix compile errors with newer gccs (#30314) 2022-04-27 02:11:02 -06:00
Massimiliano Culpo
d5fc859f46 ASP-based solver: handle installed specs from unknown namespaces (#30092) 
fixes #28259

This commit discard specs from unknown namespaces from the
ones that can be "reused" during concretization. Previously
Spack would just error out when encountering them.
 2022-04-27 02:10:46 -06:00
Erik Schnetter
753f4a4bc3 reprimand: update requests on boost (#30109) 2022-04-27 09:46:22 +02:00
Lhxone
8c280d98ca suntans: add new package (#30149) 2022-04-27 09:35:40 +02:00
eugeneswalker
d5e1fa5771 py-cryptography@35: tell cargo to use cli git, not cargo internal git… (#30307) 2022-04-26 20:58:28 -06:00
Michael Kuhn
f30b79b2c5 libgit2: add 1.4.3 and 1.3.1 (#30122) 2022-04-26 20:54:30 -06:00
Erik Schnetter
54146d44f9 fossil: New package (#30311) 
* fossil: new package

* fossil: Format code
 2022-04-27 00:47:24 +00:00
Tamara Dahlgren
0c31ab87c9 Feature: Allow re-use of run_test() in install_time_test_callbacks (#26594) 
Allow re-use of run_test() in install_time_test_callbacks

Co-authored-by: Greg Becker <becker33@llnl.gov>
 2022-04-26 17:40:05 -07:00
Lhxone
e49cccb0d9 New package: CaNS (#30218) 2022-04-27 00:33:36 +00:00
haralmha
7a1841c464 hadoop: Update url and add version 3.3.2 (#29812) 
* hadoop: Update url and add version 3.3.2

* Update url
 2022-04-26 17:26:28 -07:00
haralmha
40ebeb2dc8 arrow: Add version 7.0.0 (#29962) 2022-04-26 16:57:56 -07:00
Lhxone
e5444b9a77 New package: Swan (#30217) 2022-04-26 16:32:19 -07:00
haralmha
89cc16a9cd gnuplot: Add version 5.4.3 and add workaround for not found DSO (#30163) 2022-04-26 16:03:36 -07:00
Ken Raffenetti
a24070d532 docs: Fix ROCmPackage example syntax (#30168) 2022-04-26 16:00:40 -07:00
Kyle Gerheiser
f473fd8084 Add g2tmpl versions 1.10.2 and 1.10.1 (#30202) 2022-04-26 15:56:06 -07:00
John Hodrien
5055f5e3e2 Power9 build fix for ctffind4 (#30300) 
Only tested against the latest version, which is why it only applies the patch
when using 4.1.14.

Fix comes from:

https://grigoriefflab.umassmed.edu/forum/software/ctffind_ctftilt/installing_ctffind_4114_ibm_power9
 2022-04-26 17:13:37 -05:00
Joel Falcou
0b26103c07 EVE now use main instead of develop as main branch (#30220) 2022-04-26 15:34:45 -06:00
Greg Becker
f99614be02 old concretizer: update deprecation warning (#30227) 2022-04-26 14:17:17 -07:00
Mark W. Krentel
c02e83092e intel-xed: add version 2022.04.17 (#30239) 
1. Add version 2022.04.17 (new numbering scheme) and update mbuild resource.
2. Branch 'master' is now 'main'.
3. Old rev 10.2019.03 needs a patch for python vs python3.
 2022-04-26 14:15:10 -07:00
Kyle Gerheiser
85e99fa154 Add NCIO v1.1.0 (#30306) 
See release notes https://github.com/NOAA-EMC/NCEPLIBS-ncio/releases/tag/v1.1.0
 2022-04-26 21:03:26 +00:00
John W. Parent
83b91246b1 Windows: fix termination of process output redirection (#29923) 
The parent thread in the process stdout redirection logic on Windows
was closing a file that was being read in child thread, which lead to
error-based termination of the reader thread. This updates the
interaction to avoid the error.
 2022-04-26 12:56:13 -07:00
Andrea Valenzuela
0f4b228eff Add checksum for py-ipywidgets@7.7.0 (#30155) 
* Add checksum for py-ipywidgets@7.7.0

* Correct py-widgetsnbextension and py-ipython dependencies

* Update widgetsnbextension dependency to 3.6

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

* Allow requirement to next versions

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

* Revert ipyhton dependencies

* Add widgetsnbextension@3.6.0 checksum

Co-authored-by: aandvalenzuela <andrea.valenzuela.ramirez@cern.ch>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
 2022-04-26 14:48:53 -05:00
Lucas Frérot
2abbad1ca5 thrust: added version 1.12.1-1.16.0 (#30292) 2022-04-26 11:27:25 -07:00
Lucas Frérot
43d8fe212f py-uvw: updated versions (#30297) 2022-04-26 10:06:41 -07:00
Valentin Volkl
84befcdfe2 opendatadetector: add new package (#30298) 
* opendatadetector: add new package

* style

* opendatadetector: add hep tag
 2022-04-26 09:25:41 -07:00
Tamara Dahlgren
def8fce250 ginkgo: fix stand-alone test directory / install_test (#28412) 2022-04-26 09:20:10 -07:00
lorddavidiii
3a0aba0835 spack spec: add '--format' argument (#27908) 2022-04-26 09:08:56 -07:00
snehring
254cd624fe exabayes: specify c++11 (#30282) 2022-04-26 17:22:27 +02:00
Erik Schnetter
802a48fb43 boost: update list of modules (#30104) 
Co-authored-by: Tim Haines <thaines.astro@gmail.com>
 2022-04-26 17:12:47 +02:00
Mark W. Krentel
c81affa551 setup_package: don't unload modules on Cray when run with --dirty (#30261) 
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
 2022-04-26 16:53:10 +02:00
Simon Pintarelli
3e51304b68 spfft: pass cuda_arch to cmake (#30295) 2022-04-26 14:59:48 +02:00
snehring
62abbeaf6f express: specify patch version range (#30283) 2022-04-26 11:27:32 +02:00
H. Joe Lee
80e24f3f69 googletest: change "master" to "main" (#30285) 
There's no master branch on GitHub for googletest.
 2022-04-26 11:27:08 +02:00
dlkuehn
24f5069584 snpeff: change jdk dependency to java (#30048) 
Co-authored-by: David Kuehn <las_dkuehn@iastate.edu>
 2022-04-26 11:25:03 +02:00
Kevin Huck
5da78991d4 apex: add v2.5.1 (#30287) 2022-04-26 11:19:07 +02:00
Asher Mancinelli
cfb5d5f988 hiop: add v0.6.1, add new variant "cusolver" (#30288) 2022-04-26 11:12:14 +02:00
Michael Kuhn
a10d262f5f glib: add 2.72.1 and 2.70.5 (#30274) 2022-04-26 11:10:34 +02:00
Harmen Stoppels
16e926d374 gawk: drop gettext by default (#30290) 
Reduces the number of packages to bootstrap gcc (which actually has
--disable-nls).
 2022-04-26 11:02:03 +02:00