Commit graph

27640 commits

Author SHA1 Message Date
dlkuehn
b09fb467f1
Package rna-seqc: Change jdk dependency to java (#30049)
Co-authored-by: David Kuehn <las_dkuehn@iastate.edu>
2022-04-14 10:02:06 -07:00
Zack Galbreath
dec3e31e60
spack ci: remove relate-CDash-builds functionality (#29950)
gitlab ci: Remove code for relating CDash builds

Relating CDash builds to their dependencies was a seldom used feature.  Removing
it will make it easier for us to reorganize our CDash projects & build groups in the 
future by eliminating the needs to keep track of CDash build ids in our binary mirrors.
2022-04-14 10:42:30 -06:00
Olivier Cessenat
f5520de4bd
libefence: add package for the Electric Fence library from B. Perens (#29595) 2022-04-14 08:53:52 -07:00
Massimiliano Culpo
be99a72d57 Add CHANGELOG for v0.17.2 2022-04-14 16:19:37 +02:00
Kevin Huck
6f1a5c8fee
apex: add v2.5.0 (#30018) 2022-04-14 11:45:02 +02:00
Valentin Volkl
a482970a35
sherpa: fix build of recola interface (#30000) 2022-04-14 11:43:39 +02:00
dependabot[bot]
bbb3f724af
build(deps): bump actions/setup-python from 3.1.1 to 3.1.2 (#30017)
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 3.1.1 to 3.1.2.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](21c0493ecf...98f2ad02fd)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

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

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2022-04-14 10:47:01 +02:00
Peter Scheibel
89f6db21f1
Ad-hoc Git commit versions: support submodules (#30037)
* Allow packages to add a 'submodules' property that determines when ad-hoc Git-commit-based versions should initialize submodules

* add support for ad-hoc git-commit-based versions to instantiate submodules if the associated package has a 'submodules' property and it indicates this should happen for the associated spec

* allow Package-level submodule request to influence all explicitly-defined version() in the Package

* skip test on windows which fails because of long paths
2022-04-13 20:05:14 -07:00
dlkuehn
b28b24ccf8
express: version update to 1.5.3 (#29760)
Co-authored-by: snehring <snehring@iastate.edu>
2022-04-13 20:02:53 -06:00
Chris White
3dfa64edab
BLT package: add version 0.5.1 (#30053) 2022-04-13 20:02:27 -06:00
iarspider
2046ca7722
Add checksum for libisl 0.24 and update URL (#30025) 2022-04-13 17:41:34 -07:00
Mikael Simberg
4f5d5bb2ef
Add hpx-kokkos package (#29766)
Co-authored-by: Mikael Simberg <mikael.simberg@iki.if>
2022-04-14 00:23:33 +00:00
Veselin Dobrev
34d9d58924
New package version: mfem v4.4 (#29658) 2022-04-13 16:27:54 -07:00
Dylan Simon
0804637228
distcc: add 3.3.5 for gcc@10 (#29666) 2022-04-13 16:11:36 -07:00
Matthieu Dorier
a837008ff7
[mochi-thallium] added new version of mochi-thallium (#29791) 2022-04-13 14:51:06 -07:00
Jeremy L Thompson
1ffad2073d
libceed - add v0.9 and 0.10.1 (#29820) 2022-04-13 14:47:11 -07:00
Massimiliano Culpo
c846b5149d
Add support for Python 3.10 (#29581)
* Add support for Python 3.10

* Update unit-tests to use 3.10

* Update Getting started section of the docs

* Update bootstrap action
2022-04-13 14:32:23 -07:00
Seth R. Johnson
4c1250854a
perl: fix mac patch (#30001)
- Apply macosx version workaround to all 5.35 and less
- Delete an obsolete mac patch file that I didn't notice when adding
  #28797
2022-04-13 12:34:48 -06:00
iarspider
fbd94b9ad2
Add checksums for xtensor 0.24.1 and xtl 0.7.4 (#30032) 2022-04-13 11:22:59 -06:00
mcourtois
10a3822728
mumps: install header files as compiled (#29940)
Co-authored-by: Mathieu Courtois <mathieu.courtois@edf.fr>
2022-04-13 09:45:47 -07:00
Umar Arshad
586df30f9a
ArrayFire: new version and update CUDA usage (#29988)
* Set CUDA architectures in ArrayFire based on cuda_arch

The cuda_arch flag was not recognized by the ArrayFire package and
therefore any setting was not respected. This commit adds the appropriate
cmake flags if cuda_arch is specified. If no cuda_arch is specified,
then the flag is set to "Auto" which checks the installed compute
architectures on the build system.

* ArrayFire only requires boost headers to build. Update version to 1.75

ArrayFire only requires boost headers at build time. This commit also
updates the version to 1.75 to avoid some errors in Boost Compute

* Disable tests in ArrayFire by default

* Add support for ArrayFire v3.8.1

* Add maintainer for ArrayFire package

* Remove test variant from ArrayFire. Use comprehensions

* Reduce boost requirement in ArrayFire

* Address cuda_arch suggestions

* Add commit hashes to Release versions of ArrayFire

* Fix style issues in ArrayFire package
2022-04-13 09:31:40 -07:00
Paul
803900ddc5
Add Go 1.18 and 1.17.8 (#30035) 2022-04-13 09:29:12 -07:00
Massimiliano Culpo
0480afe29d
CI: avoid issues with Ubuntu patched git by adding safe.directory (#30042)
Ubuntu patched git v2.25.1 with a security fix that also
introduced a breaking change, so v2.25.1 behaves like
v2.35.2 with respect to the use cases in CVE-2022-24765
2022-04-13 11:10:00 +00:00
Harmen Stoppels
cb56e9b745
libbsd: fixes for %nvhpc (#29848) 2022-04-13 11:24:02 +02:00
renjithravindrankannath
6a8aa59717
reverting the changes present in 29017 as CFLAGS and CXXFLAGS which overrides defaults in other packages (#30036) 2022-04-13 08:29:56 +02:00
Daryl W. Grunau
110ade1804
Apply llvm7_intel.patch with intel@19.1.3 (#29955)
* llvm7_intel.patch required for intel@19.1.3 too

* apply llvm7_intel.patch forall intel@19.0 and intel@19.1

Co-authored-by: Daryl W. Grunau <dwg@lanl.gov>
2022-04-12 15:38:11 -07:00
Adam J. Stewart
5db279f986
py-numpy: add v1.21.6 (#30034) 2022-04-12 22:30:13 +00:00
Sergey Kosukhin
67a90a644f
hdf5: remove redundant dependency on numactl (#29914) 2022-04-12 14:55:28 -07:00
Jose E. Roman
fef84f2265
New patch release SLEPc 3.17.1 (#30010)
Co-authored-by: Satish Balay <balay@mcs.anl.gov>
2022-04-12 14:50:32 -07:00
Kyle Gerheiser
b0e35dffa3
Add grib_util v1.2.4 (#30033) 2022-04-12 13:32:19 -07:00
Nathan Hanford
a3520d14bd
Splice differing virtual packages (#27919)
Co-authored-by: Nathan Hanford <hanford1@llnl.gov>
2022-04-12 13:31:39 -07:00
psakievich
7d534f38d6
Don't allow replacement of root develop specs with --reuse (#28605)
* Fix to concretize.lp

do not allow dev specs to be reused

Co-authored-by: Gregory Becker <becker33@llnl.gov>
2022-04-12 10:37:24 -07:00
Peter Scheibel
2aec5b65f3
Git commit versions bugfix: Environments and Concretization (#29717)
Spack added support in #24639 for ad-hoc Git-commit-hash-based
versions: A user can install a package x@hash, where X is a package
that stores its source code in a Git repository, and the hash refers
to a commit in that repository which is not recorded as an explicit
version in the package.py file for X.

A couple issues were found relating to this:

* If an environment defines an alternative package repo (i.e. with
  repos.yaml), and spack.yaml contains user Specs with ad-hoc
  Git-commit-hash-based versions for packages in that repo,
  then as part of retrieving the data needed for version comparisons
  it will attempt to retrieve the package before the environment's
  configuration is instantiated.
* The bookkeeping information added to compare ad-hoc git versions was
  being stripped from Specs during concretization (such that user
  Specs which succeeded before concretizing would then fail after)

This addresses the issues:

* The first issue is resolved by deferring access to the associated
  Package until the versions are actually compared to one another.
* The second issue is resolved by ensuring that the Git bookkeeping
  information is explicitly applied to Specs after they are concretized.

This also:

* Resolves an ambiguity in the mock_git_version_info fixture used to
  create a tree of Git commits and provide a list where each index
  maps to a known commit.
* Isolates the cache used for Git repositories in tests using the
  mock_git_version_info fixture
* Adds a TODO which points out that if the remote Git repository
  overwrites tags, that Spack will then fail when using
  ad-hoc Git-commit-hash-based versions
2022-04-12 09:58:26 -07:00
Mikael Simberg
17e2fb0ef6
Add missing Boost dependencies to pika+generic_coroutines variant (#30026)
Co-authored-by: Mikael Simberg <mikael.simberg@iki.if>
2022-04-12 12:36:14 +02:00
Carlos Bederián
ce09b42cdd
curl: nss deprecated since 7.82 (#30020)
* curl: nss deprecated since 7.82
2022-04-12 03:30:24 -06:00
Brian Van Essen
433d404a93
lbann (and related stack): avoid bug in cmake 3.23.0 (#30019) 2022-04-12 08:56:48 +02:00
Massimiliano Culpo
8d56728984 vmd: remove custom phases 2022-04-12 08:39:15 +02:00
Massimiliano Culpo
39b58abd9c siesta: remove custom phases 2022-04-12 08:39:15 +02:00
Massimiliano Culpo
d7a6cb3e53 qbank: remove custom phases 2022-04-12 08:39:15 +02:00
Massimiliano Culpo
fd724fb38d py-sip: remove custom phases 2022-04-12 08:39:15 +02:00
Massimiliano Culpo
2bb9eeac28 py-gosam: remove custom phases 2022-04-12 08:39:15 +02:00
Massimiliano Culpo
b7ce6a5ec1 openmx: remove custom phases 2022-04-12 08:39:15 +02:00
Massimiliano Culpo
1999135cab ntl: remove custom phases 2022-04-12 08:39:15 +02:00
Massimiliano Culpo
a708844e87 nsimd: remove custom phases, refactor variants 2022-04-12 08:39:15 +02:00
Massimiliano Culpo
4dd5bcb3ef npb: remove custom phases 2022-04-12 08:39:15 +02:00
liuyangzhuan
dc44642bfb
bump py-statsmodels versions to 0.13.2 for gptune (#29972) 2022-04-11 17:10:28 -06:00
Doug Jacobsen
a9b4f33f23
Update gpg publish to work with mirror arguments (#28740)
This commit updates the `gpg publish` command to work with the mirror
arguments, when trying to push keys to a mirror.

- [x] update `gpg publish command
- [x] add test for publishing GPG keys and rebuilding the key index within a mirror
2022-04-11 14:48:08 -07:00
Sergey Kosukhin
6e5cba7b82
cray platform: unload cray-mpich (#29898) 2022-04-11 14:34:09 -07:00
Ken Raffenetti
b45e734b59
mpich: add v4.0.2 (#30012) 2022-04-11 15:22:34 -06:00
marcosmazz
624077e629
Fix typo in package wrf (#30014) 2022-04-11 14:11:19 -07:00