Commit graph

31726 commits

Author SHA1 Message Date
Adam J. Stewart
2727bd92d8
py-numpy: add v1.25.0 (#38461) 2023-06-21 10:03:50 -05:00
Martin Pokorny
ebbfc0363b
kokkos-nvcc-wrapper: add new versions (#38446) 2023-06-20 21:38:30 -04:00
Tamara Dahlgren
1b6e1fc852
tests/superlu: convert to new stand-alone test process (#38404)
* superlu: convert to new stand-alone test process
* Bugfix/superlu: add BaseBuilder and move post-install work to it
2023-06-20 16:46:11 -07:00
Matthieu Dorier
1376ec4887
[mochi-margo] margo version 0.14.0 added (#38473) 2023-06-20 18:48:21 -04:00
Stephen Sachs
0eec7c5c53
[WRF] Always use compiler wrappers for FFLAGS/FCFLAGS (#38470)
`FFLAGS` and `FCFLAGS` are being ignored by WRF build system. Not only in version
`3.9.1.1`, but also `4.x`.

Also, I see no reason to explicitly add `-w` and `-O2` to compile lines when
using `gcc@10:`. Tested for version `3.9.1.1`, `4.2.2`, & `4.5.0`.

Tagging original authors of this part @MichaelLaufer and @giordano in case they
want to chime in.
2023-06-20 18:24:31 -04:00
Valentin Volkl
05dd240997
fastjet: add v3.4.1, update patch (#38467) 2023-06-20 18:16:37 -04:00
Erik Schnetter
fb16c81b6c
mpiwrapper: New version 2.10.4 (#38448) 2023-06-20 18:16:15 -04:00
Erik Schnetter
7c3b33416f
mpitrampoline: New version 5.3.1 (#38449) 2023-06-20 18:08:00 -04:00
snehring
6755b74d22
ncbi-rmblastn: switching urls from ftp to https (#38490) 2023-06-20 16:03:48 -04:00
George Young
d0e843ce03
ncbi-rmblastn: patching to support building with %gcc@13: (#38382)
* ncbi-rmblastn: patching to support building with %gcc@13:
* ncbi-rmblastn: patching to build with %gcc@13:

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-20 12:42:22 -07:00
George Young
37f6231f2a
py-umi-tools: add 1.1.4, add py-pybktree dependency (#38394)
* py-umi-tools: add 1.1.4, add py-pybktree dependency

* remove python spec

* Remove `six` dependency

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-20 15:35:12 -04:00
snehring
d85f25a901
apptainer: adding version 1.1.9 (#38492) 2023-06-20 15:20:48 -04:00
Manuela Kuhn
2041b92d3a
py-pybids: add 0.16.1 (#38480) 2023-06-20 11:22:24 -05:00
Valentin Volkl
f461069888
root: fix variant detection (#38436) 2023-06-20 08:47:49 -05:00
Manuela Kuhn
9eb3de85c5
py-pre-commit: add 3.3.3 (#38468)
* py-pre-commit: add 3.3.3

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

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-06-19 18:30:42 -04:00
Manuela Kuhn
92d970498a
py-nodeenv: add 1.8.0 (#38383)
* py-nodeenv: add 1.8.0

* Remove python@3.7 restriction
2023-06-19 18:01:43 -04:00
Manuela Kuhn
bd5e99120d
py-pkginfo: add 1.9.6 (#38434)
* py-pkginfo: add 1.9.6

* Remove py-setuptools as run dependency
2023-06-19 17:39:14 -04:00
Juan Miguel Carceller
a7e307bd81
gsl: set GSL_ROOT_DIR (#38464)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-06-19 16:37:37 -04:00
snehring
55152781cb
repeatmasker: adding version 4.1.5 (#38445) 2023-06-19 11:13:27 -07:00
Manuela Kuhn
8ce0c7771c
py-pooch: add 1.7.0 (#38466) 2023-06-19 12:43:19 -05:00
Wouter Deconinck
7e0dfa270f
spdlog: patch for fmt::basic_runtime when ^fmt@10 (#38082) 2023-06-19 12:15:01 +02:00
Andrey Parfenov
7dc485d288
cc: Ensure that user-specified flags take precedence over others (#37376)
Spack flags supplied by users should supersede flags from package build systems and
other places in Spack.  However, Spack currently adds user-supplied flags to the 
beginning of the compile line, which means that in some cases build system flags will
supersede user-supplied ones.

The right place to add a flag to ensure it has highest precedence for the compiler really
depends on the type of flag.  For example, search paths like `-L` and `-I` are examined
in order, so adding them first is highest precedence.  Compilers take the *last* occurrence
of optimization flags like `-O2`, so those should be placed *after* other such flags.  Shim
libraries with `-l` should go *before* other libraries on the command line, so we want
user-supplied libs to go first, etc.

`lib/spack/env/cc` already knows how to split arguments into categories like `libs_list`,
`rpath_dirs_list`, etc., so we can leverage that functionality to merge user flags into
the arg list correctly.

The general rules for injected flags are:

1. All `-L`, `-I`, `-isystem`, `-l`, and `*-rpath` flags from `spack_flags_*` to appear
   before their regular counterparts.
2. All other flags ordered with the ones from flags after their regular counterparts,
   i.e. `other_flags` before `spack_flags_other_flags`

- [x] Generalize argument categorization into its own function in the `cc` shell script
- [x] Apply the same splitting logic to injected flags and flags from the original compile line.
- [x] Use the resulting flag lists to merge user- and build-system-supplied flags by category.
- [x] Add tests.

Signed-off-by: Andrey Parfenov <andrey.parfenov@intel.com>

Co-authored-by: iermolae <igor.ermolaev@intel.com>
2023-06-18 14:07:08 -07:00
simonleary-umass-edu
5c6c3b403b
fix oneapi modules (#38400) 2023-06-18 07:17:19 -04:00
Morten Kristensen
242854f266
py-vermin: add latest version 1.5.2 (#38460)
* py-vermin: add latest version 1.5.2

* Removed obsolete dep and setuptools is only for build-time

- setuptools are not used as runtime
- py27 isn't strictly necessary
2023-06-18 03:52:58 -04:00
William Moses
e9406a7d9e
Add latest enzyme release (#38442) 2023-06-17 03:12:14 -04:00
Greg Becker
0ac1c52d17
unparser: drop Python 2, fix testing bugs with newer Pythons (#38424)
The `unparser` that Spack uses for package hashing had several tweaks to ensure compatibility
with Python 2.7:
1. Currently, the unparser automatically moves `*` and `**` args to the end to preserve
   compatibility with `python@:3.4`
2. `print a, b, c` statements and single-tuple `print((a, b, c))` function calls were
   remapped to `print(a, b, c)` in the unparsed output for consistency across versions.

(1) is causing issues in our tests because a recent patch to the Python source code  
(https://github.com/python/cpython/pull/102953/files#diff-7972dffec6674d5f09410c71766ac6caacb95b9bccbf032061806ae304519c9bR813-R823) 
has a `**` arg before an named argument, and we round-trip the core python source code
as a test of our unparser.  This isn't actually a break with our consistent unpausing -- it's still
consistent, the python source just doesn't unparse to the same thing anymore. It does makes
it harder to test, so it's not worth maintaining the Python2-specific stuff anymore.

Since we only support `python@3.6:`, this PR removes (1) and (2) from the unparser, but keeps
one last tweak for unicode AST inconsistencies, as it's still needed for Python 3.5-3.7.

This fixes the CI error we've been seeing on `python@3.11.4` and `python@3.10.12`. Again, that
bug exists only in the test system and doesn't affect our canonical hashing of Python code.
2023-06-16 20:52:26 -04:00
Manuela Kuhn
a3c42715db
py-aiohttp: add 3.8.4 (#38451) 2023-06-16 16:49:45 -04:00
Alec Scott
0f27188383
millepede: add v04-13-03 (#38141) 2023-06-16 11:12:01 -07:00
Greg Becker
99f3b9f064
show external status as [e] (#33792) 2023-06-16 18:22:28 +02:00
Axel Huebl
d1bc4c4ef1
WarpX 23.06 (#38303)
* WarpX 23.06

Update WarpX and related Python packages to the lastest releases.

WarpX 23.06 introduces multi-dimension support in a single package,
which will ease deployment in E4S et al. that can ship now a single,
full-feature module/package that is NOT incompatible with itself
anymore.

* e4s ci stacks: multiple specs for each dim variant no longer required

* [@spackbot] updating style on behalf of ax3l

* WarpX: Update CMake CLI and Test/Check

* Add Missing `build-directory`

* [@spackbot] updating style on behalf of ax3l

* Remove `build_directory` again

---------

Co-authored-by: eugeneswalker <eugenesunsetwalker@gmail.com>
Co-authored-by: ax3l <ax3l@users.noreply.github.com>
2023-06-16 06:47:59 -07:00
Gurkirat Singh
69a5c55702
docs: add quotes around some values in a YAML example (#38412) 2023-06-16 10:29:09 +02:00
Larry Knox
2972d5847c
Remove experimental hdf5 versions 1.13.x and add hdf5 version 1.10.10. (#38013)
* Remove experimental hdf5 versions 1.13.x.
Upgrade to 1.14 or remove dependencies on hdf5 1.13.x.

* Revert change to netcdf-c/package.py.
2023-06-15 22:41:39 -05:00
George Young
1577eb9602
star: add 2.7.10 (#38197)
* star: add 2.7.10
* star: fix building for non-avx2 arch processors
* convert to MakefilePackage, second take at fixing for aarch64
* style

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-15 12:53:32 -07:00
George Young
2f97c6ead2
perl-gd: update to 2.77, update urls (#38413)
* perl-gd: update to 2.77, update urls

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-06-15 12:39:57 -07:00
markus-ferrell
1df4afb53f
Enable build system guess tests on windows (#36971) 2023-06-15 11:40:09 -07:00
Adam J. Stewart
4991f0e484
MXNet: fix flag versions (#38402) 2023-06-15 11:34:21 -07:00
markus-ferrell
09fd7d68eb
Windows testing: enable graph, mark, and info cmd tests (#36977) 2023-06-15 11:28:52 -07:00
Jacob King
2ace8a55c1
Create package.py file for NIMROD abstract accelerated infrastructure. (#38405)
Co-authored-by: jacobrking <jacobrking@users.noreply.github.com>
2023-06-15 11:24:55 -07:00
Manuela Kuhn
861acb9467
py-nibabel: add 5.1.0 (#38379) 2023-06-15 13:14:26 -05:00
Thomas Madlener
eea743de46
podio: Add py-tabulate as new run and test dependency (#38409) 2023-06-15 10:56:00 -07:00
George Young
e2b6e5a7ec
py-numba: add 0.57.0, update dependency ranges (#38390)
* py-numba: add 0.57.0, update dependency ranges

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

Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>

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

Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>

* Update package.py

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com>
2023-06-15 12:39:12 -05:00
Manuela Kuhn
2f2dc3695c
py-datalad: add 0.18.4 (#37936) 2023-06-15 12:22:45 -05:00
Tamara Dahlgren
6eb5e57199
tests/py-horovod: convert to new stand-alone test process (#38366) 2023-06-15 12:17:09 -05:00
Tamara Dahlgren
9a047eb95f
tests/py-libensemble: convert to new stand-alone test process (#38344) 2023-06-15 12:09:57 -05:00
Tamara Dahlgren
ef42fd7a2f
tests/py-eccodes: convert to new stand-alone test process (#38346) 2023-06-15 11:58:00 -05:00
Manuela Kuhn
e642c2ea28
py-neurora: add 1.1.6.10 (#38378) 2023-06-15 11:14:28 -05:00
Massimiliano Culpo
f27d012e0c
Add virtual information on DAG edges (#34821)
* DependencySpec: add virtuals attribute on edges

This works for both the new and the old concretizer. Also,
added type hints to involved functions.

* Improve virtual reconstruction from old format

* Reconstruct virtuals when reading from Cray manifest

* Reconstruct virtual information on test dependencies
2023-06-15 07:16:54 -07:00
Tamara Dahlgren
c638311796
test/dust: convert to new stand-alone test process (#38367) 2023-06-14 20:27:35 -07:00
Manuela Kuhn
2a02bea405
py-nbclient: add 0.8.0 (#38325) 2023-06-14 17:31:03 -05:00
Manuela Kuhn
219b42d991
py-nbconvert: add 7.4.0 (#38326)
* py-nbconvert: add 7.4.0

* Move historical dependencies after variant
2023-06-14 17:28:30 -05:00