Commit graph

23281 commits

Author SHA1 Message Date
Matthew Archer
e034930775
kahip: update build system to cmake for v3.11, retain scons for older versions (#25645)
* kahip: update to cmake for v3.11, retain scons for older versions

* kahip: update build system to cmake for v3.11, retain SCons for older versions

* address PR comments and add maintainer

* address PR comments - correct version to 2.10, add deprecated and url, and remove scons version
2021-10-11 10:20:43 -05:00
Daniele Cesarini
79aba5942a
Update of siesta libs (#26489) 2021-10-11 09:09:39 -05:00
iarspider
78200b6b41
Add new versions of kiwisolver (#26597) 2021-10-11 09:09:01 -05:00
Harmen Stoppels
89220bc0e1
Only install env modifications in <prefix>/.spack (#24081)
- Do not store the full list of environment variables in
  <prefix>/.spack/spack-build-env.txt because it may contain user secrets.

- Only store environment variable modifications upon installation.

- Variables like PATH may still contain user and system paths to make
  spack-build-env.txt sourceable. Variables containing paths are
  modified through prepending/appending, and if we don't apply these
  to the current environment variable, we end up with statements like
  `export PATH=/path/to/spack/bin` with system paths missing, meaning
  no system binaries are in the path, which is a bad user experience.

- Do write the full environment to spack-build-env.txt in the staging dir,
  but ensure it is readonly for the current user, to make it a bit safer
  on shared systems.
2021-10-11 09:07:45 -05:00
Harmen Stoppels
c0c9ab113e
Add spack env activate --temp (#25388)
Creates an environment in a temporary directory and activates it, which
is useful for a quick ephemeral environment:

```
$ spack env activate -p --temp
[spack-1a203lyg] $ spack add zlib
==> Adding zlib to environment /tmp/spack-1a203lyg
==> Updating view at /tmp/spack-1a203lyg/.spack-env/view
```
2021-10-11 06:56:03 -04:00
Harmen Stoppels
f28b08bf02
Remove unused --dependencies flag (#25731) 2021-10-11 10:16:11 +02:00
iarspider
ad75f74334
New package: py-cppy (required for py-kiwisolver) (#26645) 2021-10-10 17:14:20 -05:00
Manuela Kuhn
4e1fdfeb18
py-nilearn: add 0.4.2 and 0.6.2 (#26635) 2021-10-09 19:14:13 -05:00
Manuela Kuhn
7f46b9a669
py-pyvistaqt: add new package (#26637) 2021-10-09 21:00:00 +00:00
Michael Kuhn
5deb8a05c4
environment-modules: fix build (#26632)
PR #25904 moved the `--with-tcl` option to only older versions. However,
without this option, the build breaks:
```
checking for Tcl configuration... configure: error: Can't find Tcl configuration definitions. Use --with-tcl to specify a directory containing tclConfig.sh
```
2021-10-09 12:43:54 -05:00
Bernhard Kaindl
9194ca1e2f
idna: Add versions 2.9 for sierrapy #23768 and 3.2(current) (#26616)
py-sierrapy was merged accidentally and pins its versions to exact
numbers. Add 2.9 as the version for sierrapy and the current 3.2
2021-10-09 11:31:11 -05:00
Joseph Wang
e6cc92554d
py-awkward: add py-yaml as depends (#26626) 2021-10-09 17:35:22 +02:00
Joseph Wang
03ab5dee31
evtgen: fix pythia typo (#26625) 2021-10-09 16:11:58 +02:00
Bernhard Kaindl
93df47f4d5
librsvg: fix build when does not use -pthread for linking (#26592)
librsvg uses pthread_atfork() but does not use -pthread on Ubuntu 18.04 %gcc@8
2021-10-09 13:10:13 +02:00
Derek Ryan Strong
4b5cc8e3bd
Add R 4.1.1 (#26589) 2021-10-08 20:02:03 -05:00
Derek Ryan Strong
e89d4b730a
Add Julia 1.6.3 (#26624) 2021-10-09 00:58:19 +00:00
Massimiliano Culpo
2386630e10
Remove DB reindex during a read operation (#26601)
The DB should be what is trusted for certain operations.
If it is not present when read we should assume the
corresponding store is empty, rather than trying a
write operation during a read.

* Add a unit test
* Document what needs to be there in tests
2021-10-08 22:35:23 +00:00
Bernhard Kaindl
21ce23816e
py-twisted,py-storm: dep on zope.interface, bump storm version (#26610)
* py-twisted,py-storm: dep on zope.interface, bump storm version

py-twisted and py-storm's import tests need zope.interface.
py-storm: Use pypi and add version 0.25. It didn't change reqs.
zope.infterface@4.5.0 imports removed Feature: Use setuptools@:45

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

* py-storm: all deps updated with type=('build', 'run')

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-10-08 21:20:39 +00:00
psakievich
8ebb705871
Trilinos: update for CUDA and Nalu-Wind (#26614) 2021-10-08 21:08:54 +00:00
Bernhard Kaindl
7e8f2e0c11
py-hypothesis: Add variants django, dumpy, pandas and fix import tests (#26604) 2021-10-08 21:00:47 +00:00
Manuela Kuhn
654268b065
py-bcrypt, py-bleach, py-decorator, py-pygdal: fix python dependency (#26596)
* py-bcrypt, py-bleach, py-decorator, py-pygdal: fix python dependency

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-10-08 15:56:22 -05:00
Bernhard Kaindl
6d0d8d021a
py-pymatgen: fix build of old versions, bump version to 2021.3.9 (#26249)
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-10-08 19:54:40 +00:00
Bernhard Kaindl
f1f614ee9f
py-anytree: Add dep py-six@1.9.0 as required by setup.py (#26603)
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-10-08 19:36:12 +00:00
Manuela Kuhn
88c33686fd
py-matplotlib: fix 3.4.3 (#26586)
* py-matplotlib: fix 3.4.3

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-10-08 13:52:10 -05:00
Bernhard Kaindl
de86726483
py-traceback2: Fix depends_on: add six and py-linecache2 (#26607) 2021-10-08 13:35:36 -05:00
Bernhard Kaindl
a95c1dd615
py-keras-preprocessing: Add missing deps: six@1.9.0: and numpy@1.9.1: (#26605)
* py-keras-preprocessing: Add missing deps: six@1.9.0: and numpy@1.9.1:

Add deps: pip download --no-binary :all: keras-preprocessing==1.1.2
Collecting numpy>=1.9.1
  Installing build dependencies: started
Collecting six>=1.9.0

* Update var/spack/repos/builtin/packages/py-keras-preprocessing/package.py

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-10-08 13:34:25 -05:00
Harmen Stoppels
7d89a95028
Fix leaky spack.binary_distribution.binary_index in tests (#26609)
* Fix issues with leaky binary index across tests

* More rigorous binary_index reset as now other tests are failing :(
2021-10-08 13:41:47 -04:00
Manuela Kuhn
32b35e1a78
py-neurora: add new package (#26479) 2021-10-08 13:39:45 +00:00
Tamara Dahlgren
7f2611a960
Allow Version('') and map it to the empty tuple (#25953) 2021-10-08 10:36:54 +02:00
Rodrigo Ceccato de Freitas
169d0a5649
cling: add missing CMake dependency (#26577) 2021-10-08 09:28:37 +02:00
Adam J. Stewart
f390289629
More strict ReadTheDocs tests (#26580) 2021-10-08 09:27:17 +02:00
Daniel G Travieso
10de12c7d0
add hash field to spec on find --json and assert in test its there (#26443)
Co-authored-by: Daniel Travieso <daniel@dgtravieso.com>
2021-10-07 23:50:05 -07:00
Bernhard Kaindl
449a5832c8
llvm: llvm@13+libcxx needs a very recent C++ compiler (#26584)
libc++-13 does not support %gcc@:10, see:
https://bugs.llvm.org/show_bug.cgi?id=51359#c1

https://libcxx.llvm.org/#platform-and-compiler-support says:
- GCC    11     - latest stable release per GCC’s release page
- Clang: 11, 12 - latest two stable releases per LLVM’s release page
- AppleClang 12 - latest stable release per Xcode’s release page
2021-10-08 00:25:51 +00:00
Pedro Demarchi Gomes
28529f9eaf
re2 pic support (#26513) 2021-10-08 01:01:40 +02:00
Oliver Perks
da31c7e894
Updatepackage/minigmg (#26467)
* MiniGMG, add support for optimised flags + SIMDe implementation of AVX instrinsics

* Add .gitlab-ci.yml

* NVHPC fast

* remove CI

* Syntax fix
2021-10-07 14:49:14 -05:00
Paul Ferrell
0b9914e2f5
Fix for license symlinking issue. (#26576)
When a symlink to a license file exists but is broken, the license symlink post-install hook fails
because os.path.exists() checks the existence of the target not the symlink itself.
os.path.lexists() is the proper function to use.
2021-10-07 19:18:35 +00:00
Seth R. Johnson
9853fd50e2
itk: use CMakePackage helpers (#26572) 2021-10-07 10:49:51 -05:00
Scott Wittenburg
0561af1975
Pipelines: retry service job on system errors (#26508)
Retry rebuild-index, cleanup, and no-op jobs automatically if they fail
due to infrastructure-related problems.
2021-10-07 08:59:51 -06:00
Kevin Huck
b33a0923e1
apex: support profiling/tracing HIP applications (#26569)
libz is added for compressing google trace events output.
2021-10-07 16:22:40 +02:00
Harmen Stoppels
05834e7c9d
Memoize the result of spack.platforms.host() (#26573) 2021-10-07 14:04:05 +02:00
Olivier Cessenat
20ee786d09
visit: add an external find function (determine_version) (#25817)
* visit: add an external find function (determine_version)

* visit: correct too long comment line

* visit: forgot to set executables

* visit: external find uses signgle dash version

* visit: found as external asking visit version
2021-10-07 10:19:58 +00:00
Manuela Kuhn
653d5e1590
py-mayavi: add 4.7.3 (#26566) 2021-10-06 19:15:34 -05:00
Tyler Funnell
60909f7250
fish: adding version 3.3.1 (#26488)
* fish: adding version 3.3.1

* adding maintainer

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2021-10-06 20:42:45 +00:00
Manuela Kuhn
b787065bdb
py-scikit-image: add 0.18.3 and fix dependencies (#26406) 2021-10-06 15:30:27 -05:00
Jen Herting
3945e2ad93
New package: py-clean-text (#26511)
* [py-clean-text] created template

* [py-clean-text]

- added description
- added dependencies
- removed fixmes
2021-10-06 19:44:33 +00:00
Tamara Dahlgren
affd2236e6
Provide more info in SbangPathError to aid CI debugging (#26316) 2021-10-06 21:03:33 +02:00
Kevin Pedretti
cb5b28392e
Patch from upstream needed to build numactl on riscv64. (#26541)
The most recent release of numactl (2.0.14) fails to build on riscv64
because of a missing "-latomic". This patch from upstream resolves this
issue. It can be dropped once the next version of numactl is released.
2021-10-06 11:50:21 -07:00
Rodrigo Ceccato de Freitas
b1f7b39a06
ucx: fix typo in config description (#26564) 2021-10-06 18:44:22 +00:00
Manuela Kuhn
770c4fd0b2
py-nipype: add 1.4.2 (#26472) 2021-10-06 20:35:42 +02:00
Massimiliano Culpo
98ee00b977
Restore the correct computation of stores in environments (#26560)
Environments push/pop scopes upon activation. If some lazily
evaluated value depending on the current configuration was
computed and cached before the scopes are pushed / popped
there will be an inconsistency in the current state.

This PR fixes the issue for stores, but it would be better
to move away from global state.
2021-10-06 11:32:26 -07:00