Commit Graph

29406 Commits

Author SHA1 Message Date
Harmen Stoppels
dc39edb790 man-db: fix gnulib issue (#33149)
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-10-12 11:28:45 +02:00
Seth R. Johnson
f9620950cd py-sphinxcontrib-bibtex: new version 2.5.0 (#32902)
2.4 seems to have issues with sphinx-rtd and sphinx 5.1:
```
AttributeError: 'Text' object has no attribute 'rawsource'
```
2022-10-12 11:25:56 +02:00
iarspider
f10997a0df py-uproot: add v4.3.5 (#33151) 2022-10-12 11:22:43 +02:00
Michael Kuhn
2df25d8b37 meson: add 0.63.3 (#33216) 2022-10-12 03:02:44 -06:00
Jim Edwards
e31a4b6dc6 ESMF package update (#33202) 2022-10-12 10:59:02 +02:00
Jonathon Anderson
827e576c3d bear: fix RPATH handling (#33217) 2022-10-12 10:34:56 +02:00
Adam J. Stewart
549f6361ce py-poetry-core: jail git to stage directory (#33181) 2022-10-12 10:31:12 +02:00
MicK7
c3cc462a69 Add new vtk 9.2.2 release (#33001)
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2022-10-12 10:22:42 +02:00
Glenn Johnson
bffc4ab826 Update CRAN packages (#33223) 2022-10-12 10:20:52 +02:00
Luke Diorio-Toth
fffa9258c5 infernal: add v1.1.4 (#33230) 2022-10-12 09:41:01 +02:00
Luke Diorio-Toth
a34b36703a trnascan-se: add v2.0.11 (#33232) 2022-10-12 09:39:36 +02:00
Massimiliano Culpo
7efbd7d8eb Fix typo in docs (#33182) 2022-10-12 08:31:48 +02:00
iarspider
bd5705b2a8 Add checksum for py-cryptography 37.0.4 (#33186) 2022-10-11 20:43:56 -05:00
iarspider
f4cc48286d Add checksum for py-frozenlist 1.3.1 (#33193) 2022-10-11 20:41:08 -05:00
iarspider
caf8b57fd4 Add checksum for py-yarl 1.8.1 (#33195) 2022-10-11 20:40:22 -05:00
iarspider
9342344f78 Add checksum for py-immutables 0.18 (#33197) 2022-10-11 20:39:20 -05:00
iarspider
552908595e Add checksum for py-google-auth-oauthlib 0.5.2 (#33198) 2022-10-11 20:38:26 -05:00
iarspider
9cd47454f3 Add checksum for py-jupyter-server 1.18.1 (#33204) 2022-10-11 20:32:42 -05:00
iarspider
cbe2178e3f Add checksum for py-websocket-client 1.4.1 (#33205) 2022-10-11 20:30:45 -05:00
iarspider
7d4fa0ea00 Add checksum for py-requests-unixsocket 0.3.0 (#33206) 2022-10-11 20:29:40 -05:00
iarspider
7f49cc2d17 Add checksum for py-typed-ast 1.5.4 (#33207) 2022-10-11 20:28:37 -05:00
iarspider
a43ad2d876 Add checksum for py-scinum 1.4.3 (#33208) 2022-10-11 20:27:49 -05:00
iarspider
401412f999 Add checksum for py-python-rapidjson@1.8 (#33210) 2022-10-11 20:25:30 -05:00
iarspider
019463be39 Add checksum for py-pysqlite3 0.4.7 (#33211) 2022-10-11 20:24:46 -05:00
Luke Diorio-Toth
cd74e091d0 version bump to 3.10.42 (#33220) 2022-10-11 19:13:56 -06:00
Adam J. Stewart
5844c24ca8 py-rtree: add v1.0.1 (#33222) 2022-10-11 17:49:41 -07:00
Adam J. Stewart
d1fb82a2c4 GCC: update Xcode 14 conflict (#33226) 2022-10-11 17:26:47 -07:00
Harmen Stoppels
926dca9e5f Specify GCC prefix in LLVM-based compilers (#33146)
* spack.compiler.Compiler: introduce prefix property

We currently don't really have something that gives the GCC install
path, which is used by many LLVM-based compilers (llvm, llvm-amdgpu,
nvhpc, ...) to fix the GCC toolchain once and for all.

This `prefix` property is dynamic in the sense that it queries the
compiler itself. This is necessary because it's not easy to deduce the
install path from the `cc` property (might be a symlink, might be a
filename like `gcc` which works by having the compiler load a module
that sets the PATH variable, might be a generic compiler wrapper based
on environment variables like on cray...).

With this property introduced, we can clean up some recipes that have
the logic repeated for GCC.

* intel-oneapi-compilers: set --gcc-sysroot to %gcc prefix
2022-10-11 17:45:51 -06:00
kwryankrattiger
4b866e8ffc Darshan variant cleanup (#33165)
* Darshan-Runtime: Cleanup version dependent variants

* Darshan-Util: Cleanup version dependent variants.
2022-10-11 12:04:22 -07:00
kwryankrattiger
5d0f0914b8 Omega-H: Current constraint doesn't allow any cuda (#33164)
From the issue referenced, it seems later and earlier versions
of cuda work.
2022-10-11 12:03:39 -07:00
Massimiliano Culpo
de8c827983 Refactor a few classes related to package repositories (#32273)
Caches used by repositories don't reference the global spack.repo.path instance
anymore, but get the repository they refer to during initialization.
 
Spec.virtual now use the index, and computation done to compute the index 
use Repository.is_virtual_safe. 

Code to construct mock packages and mock repository has been factored into 
a unique MockRepositoryBuilder that is used throughout the codebase.

Add debug print for pushing and popping config scopes.

Changed spack.repo.use_repositories so that it can override or not previous repos

spack.repo.use_repositories updates spack.config.config according to the modifications done

Removed a peculiar behavior from spack.config.Configuration where push would always 
bubble-up a scope named command_line if it existed
2022-10-11 19:28:27 +02:00
Peter Scheibel
b594c0aee0 spack diff any specs you want (#32737)
Resolves #31782

With this change, if a spec is concrete after parsing (e.g. spec.yaml
or /hash-based), then it is not disambiguated (a process which requires
(a) that the spec be installed and (b) that it be part of the
currently-active environment).

This commit allows you to:

* Diff specs from an environment regardless of whether they have
  been installed (more useful for projection/matrix-based envs)
* Diff specs read from .yaml files which may or may not be entirely
  different installations of Spack

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2022-10-11 10:03:31 -06:00
dependabot[bot]
8e3c088a7a Bump actions/setup-python from 4.2.0 to 4.3.0 (#33166)
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.2.0 to 4.3.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](b55428b188...13ae5bb136)

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

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

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2022-10-11 09:54:17 +02:00
iarspider
a0489d8480 py-importlib-resources: add v5.9.0 (#33047) 2022-10-11 09:52:01 +02:00
eugeneswalker
a587bff119 e4s ci: add cabana +rocm (#33177) 2022-10-11 00:37:55 -06:00
Glenn Johnson
c885b591e2 new package: r-profvis (#33171) 2022-10-10 21:09:53 -06:00
Glenn Johnson
771aee30ea new package: r-urlchecker (#33174) 2022-10-10 19:42:06 -06:00
Glenn Johnson
87536ab107 new package: r-ragg (#33172) 2022-10-10 19:38:06 -06:00
Glenn Johnson
acf6acc93c Add bioc attribute to r-do-db (#33179) 2022-10-10 19:33:55 -06:00
Glenn Johnson
cecec254b0 new package: r-optimparallel (#33169) 2022-10-10 19:25:55 -06:00
Mark W. Krentel
c7472c849f hpctoolkit: add version 2022.10.01 (#33078)
* hpctoolkit: add version 2022.10.01

 1. add version 2022.10.01
 2. remove version for master branch, develop is now the main branch
 3. add CPATH and LD_LIBRARY_PATH to module run environment,
    this is for apps that want to use the start/stop interface
 4. cleanup style in variants, depends and conflicts
 5. remove all-static variant, nothing uses it
 6. deprecate more old versions

* [@spackbot] updating style on behalf of mwkrentel

* Add when(+level_zero) to the gtpin variant.

* Test commit to see if this passes E4S.

* Another test commit to see if E4S succeeds.

* Add temporary hack to ignore +mpi for version 2022.10.01 and issue a
warning instead.

Co-authored-by: mwkrentel <mwkrentel@users.noreply.github.com>
2022-10-10 17:59:13 -07:00
iarspider
be293ceb7a Add checksum for py-virtualenv 20.16.4 (#33154)
* Add checksum for py-virtualenv 20.16.4

* [@spackbot] updating style on behalf of iarspider

* Update package.py

* Update package.py

Co-authored-by: iarspider <iarspider@users.noreply.github.com>
2022-10-10 18:49:52 -06:00
iarspider
4a9790e8cd Add checksum for py-msgpack 1.0.4 (#33161)
* Add checksum for py-msgpack 1.0.4

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-10-10 18:38:19 -06:00
Glenn Johnson
cd6ef2c3cb new package: r-textshaping (#33173) 2022-10-10 18:38:01 -06:00
Glenn Johnson
042050be11 new package: r-pkgdown (#33170) 2022-10-10 18:33:58 -06:00
Glenn Johnson
46b7d3995c new package: r-interp (#33168) 2022-10-10 17:57:52 -06:00
iarspider
c393a57a48 Update py werkzeug (#33155)
* Add checksum for py-virtualenv 20.16.4

* Add checksum for py-werkzeug 2.2.2

* Restore py-virtualenv/package.py

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-10-10 17:50:06 -06:00
Axel Huebl
9d89dba292 Docs: Getting Started Dependencies (#32480)
* Docs: Getting Started Dependencies

Finally document what one needs to install to use Spack on
Linux and Mac :-)

With <3 for minimal container users and my colleagues with
their fancy Macs.

* Debian Update Packages: GCC, Python

- build-essential: includes gcc, g++ (thx Cory)
- Python: add python3-venv, python3-distutils (thx Pradyun)

* Add RHEL8 Dependencies
2022-10-10 23:25:37 +00:00
Glenn Johnson
a05a34361a new package: r-downlit (#33167) 2022-10-10 16:24:13 -07:00
eugeneswalker
dc141f5ad6 e4s: add hypre +rocm (#32148) 2022-10-10 16:09:52 -06:00