Commit graph

35421 commits

Author SHA1 Message Date
George Young
efd2ed750d
py-bx-python: add 0.9.0 (#38419)
* py-bx-python: add 0.9.0

* remove dependency

* Remove python upper bound

* Clarify dependency requirements

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-27 08:14:37 -04:00
Harmen Stoppels
ab10b645c6
Revert "Updates to symlinking for Windows (#34701)" (#38578)
This reverts commit 66f75407d1.
2023-06-27 09:46:08 +02:00
Brian Van Essen
e79f275bc9
CachedCMakePackage: set build type (#38502)
Fixed the cached CMake package so that the build_type field is saved
in the cached configuration file.
2023-06-26 18:25:46 -07:00
Adam J. Stewart
09b4ed6c80
py-numpy: add v1.24.4 (#38555) 2023-06-26 18:28:13 -04:00
David Alexander
66f75407d1
Updates to symlinking for Windows (#34701)
* Support hardlinks/junctions on Windows systems without developer
  mode enabled
  * Generally, use of llnl.util.symlink.symlink is preferred over
    os.symlink since it handles this automatically
* Generally an error is now reported if a user attempts to create a
  symlink to a file that does not exist (this was previously allowed
  on Linux/Mac).
  * One exception to this: when Spack installs files from the source
    into their final prefix, dangling symlinks are allowed (on
    Linux/Mac - Windows does not allow this in any circumstance).
    The intent behind this is to avoid generating failures for
    installations on Linux/Mac that were succeeding before.
* Because Windows is strict about forbidding dangling symlinks,
  `traverse_tree` has been updated to skip creating symlinks if they
  would point to a file that is ignored. This check is not
  transitive (i.e., a symlink to a symlink to an ignored file would
  not be caught appropriately)
* Relocate function: resolve_link_target_relative_to_the_link
  (this is not otherwise modified)

Co-authored-by: jamessmillie <smillie@txcorp.com>
2023-06-26 13:38:14 -07:00
Manuela Kuhn
5db241c755
krb5: add missing findutils dependency (#38440)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-06-26 20:28:50 +02:00
Xavier Delaruelle
1dcc67535a
modules: ignore more Modules variables in from_sourcing_file (#38455)
Update list of excluded variables in `from_sourcing_file` function to
cover all variables specific to Environment Modules or Lmod. Add
specifically variables relative to the definition of `module()`, `ml()`
and `_module_raw()` Bash functions.

Fixes #13504
2023-06-26 20:21:46 +02:00
Carson Woods
46fe1f48bc
Adds new Qthreads package version (#38421)
* Add new versions of Qthreads
* Add version URLs explicitly as it has recently changed
* Use function to extrapolate version URL for older versions
* Fix url formatter
2023-06-26 09:48:47 -04:00
kjrstory
30201e3381
Openfoam: replace two boolean variants with multi-valued variant for precision option (#37736) 2023-06-26 15:43:27 +02:00
Martin Aumüller
501bb88de2
llvm: fix build against libstdc++ 13 (#38329)
llvm @13-15 is required for ispc, but fails to build with GCC 13.
14.0.6 and 15.0.7 built successfully with upstream patch, 13.0.1
still fails. Thus upstream patch is applied to 14 and 15 only.
2023-06-26 15:42:25 +02:00
Alex Richert
c5adb05433
ufs-utils: update urls, versions, and dependencies (#37255) 2023-06-26 15:41:38 +02:00
Tamara Dahlgren
8528106484
tests/heffte/tasmanian: convert to new stand-alone test process (#35750) 2023-06-26 15:10:55 +02:00
George Young
134dceb055
cromwell: add v85 (#38427)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-26 09:08:34 -04:00
Sergey Kosukhin
aa3744299b
netcdf-c: apply patches (#38324)
* netcdf-c: fix building on macOS

* netcdf-c: add patch fixing multi-threaded HDF5 calls

* netcdf-c: update patch url
2023-06-26 15:04:12 +02:00
George Young
105ac0c377
mmseqs2: patching to support building with %gcc@13: (#38296)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-26 14:59:05 +02:00
Cameron Book
1949f67a71
scotch: add new variants + bison version min. (#37958) 2023-06-26 14:55:21 +02:00
Terry Cojean
0314071763
ginkgo: add version 1.6.0 (#38439) 2023-06-26 14:13:48 +02:00
Annop Wongwathanarat
6e13d7d917
acfl: remove version 23.04 (#38363) 2023-06-26 14:02:17 +02:00
Annop Wongwathanarat
2d4758bdd9
armpl-gcc: remove version 23.04 (#38362) 2023-06-26 14:01:43 +02:00
George Young
ff002316a8
py-python-lzo: add 1.15 (#38418)
* py-python-lzo: add 1.15

* Update package.py

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-26 07:42:39 -04:00
snehring
251282812b
demuxlet: add new package (#38425) 2023-06-26 13:17:01 +02:00
SXS Bot
4ac43b5032
spectre: add v2023.06.19 (#38474)
Co-authored-by: sxs-bot <sxs-bot@users.noreply.github.com>
2023-06-26 13:07:39 +02:00
Tamara Dahlgren
05b6ac16bc
tests/*mpi*: convert to new stand-alone test process (#35802) 2023-06-26 12:40:03 +02:00
Xavier Delaruelle
8164712264
Add raw attribute to env.set command (#38465)
Update `env.set` command and underlying `SetEnv` object to add the `raw`
boolean attribute. `raw` is optional and set to False by default. When
set to True, value format is skipped for object when generating
environment modifications.

With this change it is now possible to define environment variable
whose value contains variable reference syntax (like `{foo}` or `{}`)
that should be set as-is.

Fixes #29578
2023-06-26 11:55:57 +02:00
Wouter Deconinck
ce0b9ea8cf
acts: ensure Python_EXECUTABLE uses ^python when +python (#38540)
By default, `find_package(Python)` searches from highest version to lowest version, identifying the highest version that satisfies the requirements. This means that `/usr/bin/python3.11` will be found before `$(spack location -i python)/bin/python3.10`, even when other packages have been built with the `python` in spack.

This ensures that the `python` dependency is explicitly the `python` version that is used.
2023-06-26 11:31:48 +02:00
Adam J. Stewart
c560053c39
py-scipy: add v1.11.0 (#38546)
Co-authored-by: adamjstewart <adamjstewart@users.noreply.github.com>
2023-06-26 11:30:06 +02:00
Fabien Bruneval
5b0ca6d287
MOLGW: add new package (#37878) 2023-06-26 11:12:03 +02:00
is-a-gamer
887d356e01
bzip2: add pkg-config file (#38355)
Co-authored-by: HongZhi He <a13041902330@outlook.com>
2023-06-26 05:02:23 -04:00
Tamara Dahlgren
95ca9dea89
libxml2: convert to new stand-alone test process (#37694) 2023-06-25 01:02:33 -04:00
Cyrus Harrison
cb23362b7f
ascent: add optional occa dep (#38426)
Co-authored-by: cyrush <cyrush@users.noreply.github.com>
2023-06-24 23:32:34 -04:00
George Young
42c4a8b388
gmap-gsnap: updating to 2023-06-01 (#38428)
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-24 16:46:37 +02:00
Thomas Madlener
cc1f403385
circe2: add new package (#38491) 2023-06-24 16:32:15 +02:00
snehring
b1d281f197
apptainer: add squashfuse dep (#38499) 2023-06-24 16:02:51 +02:00
Tamara Dahlgren
29a1c418b3
etsf-io: convert to new stand-alone test process (#35746) 2023-06-24 15:59:48 +02:00
Wouter Deconinck
36dd325187
gaudi: new versions 36.[11-14] (#38498) 2023-06-24 15:56:02 +02:00
Tamara Dahlgren
585e150816
hpctoolkit: convert to new stand-alone test process (#35752) 2023-06-24 15:44:14 +02:00
miheer vaidya
9a30ba1a4d
clp and osi depend on pkgconfig (#31505)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2023-06-24 15:34:56 +02:00
David Huber
d5bb152165
GSI-ncdiag: add v1.1.0 and v1.1.1. (#38196)
Co-authored-by: [David Huber] <[david.huber@noaa.gov]>
2023-06-24 15:29:01 +02:00
Stephen Sachs
0c6d0541f0
Fix syntax to set default target in aws-pcluster pipelines (#38048)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-06-24 15:25:19 +02:00
Dennis Klein
7b977dc103
libzmq: Fix static assertion failure with gcc-13 (#38391) 2023-06-24 13:13:17 +02:00
Matthew Thompson
f98bfebce4
pfunit: fix the max_array_rank variant definition (#38528) 2023-06-24 11:01:21 +02:00
Kapil Arya
4907315079
DMTCP: add v3.0.0. (#38307) 2023-06-24 11:00:20 +02:00
Richard Berger
48168de1cc
lammps: new verisons (#38532) 2023-06-24 10:49:18 +02:00
Gurkirat Singh
d99892e490
Fixes openmpi configure args for multinode execution on slurm (#38403)
Remove `--enable-mca-no-build=btl-uct` check for ucx spec
as it is already fixed in the openmpi open-mpi/ompi#6666
2023-06-24 10:40:43 +02:00
Chris Green
09d9b48957
range-v3: remove overbroad boost dependence (#38539)
Co-authored-by: greenc-FNAL <greenc-FNAL@users.noreply.github.com>
2023-06-24 10:25:39 +02:00
Stephen Hudson
62aa9d87ee
libEnsemble: add v0.10.0 (#37954)
* libEnsemble: add v0.10.0

* Make new deps required

* Fixes to deps

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

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

* Fix build, run

* Reorder required deps

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-06-23 15:16:53 -05:00
Manuela Kuhn
0470fe545f
py-pytest: add 7.3.2 (#38522)
* py-pytest: add 7.3.2

* [@spackbot] updating style on behalf of manuelakuhn

* Swap py-importlib-metadata dependency order

* Restrict python version for older versions
2023-06-23 15:07:38 -05:00
mschouler
db8bf333d3
Add recipe for iterative-stats (#38039)
* Add recipe for iterative-stats

* Fix branch name and remove comment

* Add git link

* Add package maintainer

* Enforce multiple requested changes

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

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

* Update checksum

* Fix openturns dependency specification

* Add python variant spec to openturns

---------

Co-authored-by: Marc Schouler <marc.schouler@inria.fr>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-06-23 15:07:04 -05:00
julian-zeidler
f73c8f2255
Added version 0.33 (#38534) 2023-06-23 14:17:38 -04:00
G-Ragghianti
42ed4d81b7
fix version dependency logic (#38535) 2023-06-23 11:08:56 -07:00