Commit graph

27193 commits

Author SHA1 Message Date
Rémi Lacroix
56e4203450
netcdf-cxx: Update the download URL (#32275) 2022-08-19 18:44:14 +00:00
Adam J. Stewart
b0990aa1fa
py-pygments: add v2.13.0 (#32168) 2022-08-19 18:09:51 +00:00
Seth R. Johnson
e29d9de2dd
ForTrilinos: new versions 2.0.1, 2.1.0 (#32265)
* ForTrilinos: new versions 2.0.1, 2.1.0

I also had to update the checksum for the released 2.0.0: see #32000 for
the explanation and solution to keep this from happening again.

* Soooo stylish
2022-08-19 11:37:55 -06:00
Harmen Stoppels
7acc082fba
ncurses 6.3 restrict patch (#32271) 2022-08-19 10:11:32 -07:00
Olivier Cessenat
362cdc5437
pcsclite: add new package (#32129) 2022-08-19 18:22:15 +02:00
eugeneswalker
e1bce8c577
e4s %oneapi: add aml +ze (level zero) (#32161) 2022-08-19 08:25:15 -07:00
Seth R. Johnson
7760625b3f
py-macholib: add v1.16 (#31967)
* py-macholib: add v1.16

* Update dependencies

Even 1.11 requires `altgraph (>=0.15)`. The lastest requires no
additional dependencies.
2022-08-19 08:25:51 -06:00
dunatotatos
77c2332df6
htslib, samtools: add v1.15 and v1.15.1 (#32259) 2022-08-19 13:56:14 +00:00
Olivier Cessenat
8773c183b5
ghostscript: new version 9.56.1 (#32088) 2022-08-19 15:00:14 +02:00
Harmen Stoppels
2daea9e4b4
docs: add a note about an issue being solved on develop (#32261) 2022-08-19 12:40:41 +00:00
psakievich
abf847ce82
Add messages to assertions in asp.py (#32237)
Assertions without messages if/when hit create a blank error message for users.  

This PR adds error messages to all assertions in asp.py even
if it seems unlikely they will ever be needed.
2022-08-19 14:15:25 +02:00
iarspider
8d99d33128
xpmem: fix configure with ~kernel-module (#32258) 2022-08-19 12:36:11 +02:00
eugeneswalker
a42a874faa
e4s oneapi: compiler environment: prepend lib dir to LD_LIBRARY_PATH (#32227) 2022-08-19 06:30:18 -04:00
Mikael Simberg
be62635154
Add tracy variant to pika (#32090) 2022-08-19 02:38:07 -06:00
eugeneswalker
022d59f4a5
e4s: add dealii +cuda (#32159) 2022-08-18 22:41:57 -06:00
Massimiliano Culpo
605d72133b
spack.util.package_hash: parametrize unit-tests (#32240)
* spack.util.package_hash: parametrize unit-tests

* Fix comment
2022-08-18 18:17:43 -07:00
eugeneswalker
b2d1d07d2e
e4s %oneapi: add amrex +sycl (#32162) 2022-08-18 18:16:55 -07:00
Mark W. Krentel
908055e37c
hpctoolkit: update git url from github to gitlab (#32252) 2022-08-18 17:35:34 -07:00
Wouter Deconinck
90352d7223
kassiopeia: new version 3.8.2 (#32254)
* kassiopeia: new version 3.8.2

There was no version 3.8.1, so here is the diff with 3.8.0: https://github.com/KATRIN-Experiment/Kassiopeia/compare/v3.8.0...v3.8.2

Build system changes:
- default `cxxstd` is now 17.

* kassiopeia: updated hash

* kassiopeia: use spec.satisfies

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-08-18 17:20:17 -07:00
kwryankrattiger
d77a8f7aa1
Sensei v4 (#30432)
* Sensei: Refactor package to work with v4.0.0

* Add missing MPI dependency
* Patch bug in libsim adapter
* Simplify conflicts with when-clauses
* Conflict variants that are incompatible (catalyst/libsim/ascent)
* Fix paraview version constraints to be more clear
* Add version constraints for VTK
* Drop unneeded visit restrictions
* Specify +vtkm dependency on ParaView's VTKm
* +hl is not needed for VTK, and is already specified in the VTK recipe
when it is needed
* Pass paths for adios2 and ascent packages

* ECP-SDK: Enable sensei

* CI: Add sensei to the data-vis-sdk pipeline

* Sensei: Change VISIT_DIR to work on linux

* Fixup: style check

* Sensei: Add patch for version detection

* CI: revert SDK pipeline in favor of new matrices

* Sensei: Formatting fixes
2022-08-18 17:20:01 -07:00
snehring
364e4e03ef
pasta: missing setuptools dep (#32220)
* pasta: missing setuptools dep

* pasta: remove extraneous which

* pasta: convert to PythonPackage

* pasta: specify dendropy version
2022-08-18 22:53:09 +00:00
Adam J. Stewart
373d2ccf9f
py-rasterio: add v1.3.1 (#32244) 2022-08-18 21:08:46 +00:00
Gregory Lee
0a8df434d2
added qt-creator 5.0.3 (#32241)
* added qt-creator 5.0.3

* [@spackbot] updating style on behalf of lee218llnl

Co-authored-by: lee218llnl <lee218llnl@users.noreply.github.com>
2022-08-18 19:35:44 +00:00
Sergey Kosukhin
15be91b585
autoconf-archive: fetch patch from github (#32232)
* autoconf-archive: fetch patch from github

* autoconf-archive: do not try to patch libtool
2022-08-18 10:55:04 -07:00
Thomas Gruber
bfa67bb275
Add patch for MEM_* group for Intel Icelake SP for 5.2.0 and newer (#32235) 2022-08-18 10:30:56 -07:00
Massimiliano Culpo
3c6b5b8afc
Remove unused argument in test fixture (#32236)
The argument is very likely a typo, and was meant to
be given to the fixture decorator. Since the value
being passed is the default, let's just remove it.
2022-08-18 10:22:50 -07:00
Robert Cohn
1cdc50e3f6
ascent: fix oneapi build (#32239) 2022-08-18 17:15:39 +00:00
eugeneswalker
cfa4bffe26
e4s ci stack: add catalyst build (#31993) 2022-08-18 10:49:51 -06:00
Robert Cohn
3d4705ffab
flux-sched: fix oneapi build (#32233) 2022-08-18 07:34:34 -07:00
Massimiliano Culpo
9d55a0436b
spec: fix typo in Spec._finalize_concretization (#32210) 2022-08-18 15:04:08 +02:00
Olivier Cessenat
5981225d5a
latex2html: new version V2022.2 (#32089) 2022-08-18 12:34:35 +00:00
Massimiliano Culpo
7f81a0a25e
CI: move nightly macOS builds from GA to pipelines (#32231)
Modifications:
- [x] Delete the `macOS builds nightly` workflow
- [x] Removed shield in README.md
- [x] Moved corresponding specs to `e4s-macos`
2022-08-18 09:13:37 +00:00
Axel Huebl
5a59e1b77a
hiredis: set install_name on macos, ccache: optional hiredis (#32219)
* hiredis: set install_name on macos
* ccache: make hiredis optional

Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2022-08-18 08:49:53 +00:00
snehring
a164b0b3e6
Update busco to 5.4.3 (#32221)
* metaeuk: new package

* sepp: new package

* busco: adding version 5.4.3

* busco: adding maintainers

* metauk: more accurate cmake dep

* sepp: adding missing dep and accurate python dep

* sepp: remove install_tree

* sepp: extend python
2022-08-17 23:31:04 -06:00
Adam J. Stewart
d398e91e88
py-pytorch-lightning: add v1.7.2 (#32226) 2022-08-18 04:25:16 +00:00
Sergey Kosukhin
f2adbafe38
mpich: add patch fixing MPI_MIN for unsigned integers (#32188) 2022-08-17 19:25:56 -06:00
Tom Scogland
b9e57006c9
bugfix: use cmake version from dependency (#31739)
Ensure that build tools with module-level commands in spack use
the version built as part of their build graph if one exists.
This is now also required for mesa, scons, cmake and ctest, out
of graph versions of these tools in path will not be found unless
added as an external.

This bug appeared because a new version of rocprim needs cmake
3.16, while I have 3.14 in my path I had added an external for
cmake 3.20 to the dag, but 3.14 was still used to configure
rocprim causing it to fail. As far as I can tell, all the build
tools added in build_environment.py had this problem, despite the
fact that they should have been resolving these tools by name
with a path search and find the one in the dag that way. I'm
still investigating why the path searching and Executable logic
didn't do it, but this makes three of the build systems much more
explicit, and leaves only gmake and ninja as dependencies from
out in the system while ensuring the version in the dag is used
if there is one.

The additional sqlite version is to perturb the hash of python to
work around a relocation bug which will be fixed in a subsequent
PR.
2022-08-17 17:54:17 -07:00
牟展佑
c386181c0f
LLVM: add @15.0.0-rc1 (#31945) 2022-08-17 16:53:59 -06:00
Mikhail Titov
33c3cf2412
rct: update packages (RE, RG, RP, RS, RU) with new versions (#32216) 2022-08-17 22:42:48 +00:00
eugeneswalker
d8689b5038
e4s mac ci: try lambda, the new mac studio runner (#32169) 2022-08-17 21:24:47 +00:00
Larry Knox
c340fe43d2
Add HDF5 version 1.13.2. (#32202)
* Add HDF5 version 1.13.2.
Remove HDF5 versions 1.13.0 and 1.13.1.

* Correct formatting.
2022-08-17 14:21:54 -07:00
wanlinwang
4c040e02d1
Add riscv-gnu-toolchain package. (#32047)
Create a package for riscv-gnu-toolchain, a cross-compilation tool.
2022-08-17 12:18:24 -06:00
Todd Gamblin
73d25984ca clingo: fix bootstrapping on M1/monterey with command line tools
The Python that comes with XCode command line tools is a bit weird.

This fixes two issues that were preventing it from bootstrapping:

- [x] CommandLineTools python does not come with a `python-config` executable. If you
      don't have one of these, CMake's FindPython will, for some reason, assume that you
      want Python 2, so you need to set `CLINGO_PYTHON_VERSION` to ensure that clingo
      tells `find_package(Python <VERSION>)` the right thing.

- [x] We weren't setting `PYTHONHOME` correctly in Python's `package.py`. We were
      setting it to the `prefix` from Python `sysconfig`, but `prefix` tells you where
      the executable lives. CommandLineTools python reports its prefix as

          /Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8

      but that doesn't exist. It looks like Apple builds the full python and just copies
      pieces of it into command line tools. PYTHONHOME is supposed to tell you where the
      default python library location is. So you have to look at the `base`, which
      `sysconfig` reports as

          /Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.8

      On most systems this is probably the same as `prefix`, but not with
      CommandLineTools, which has its system library in a different place.

The second change here was cherry-picked to 0d981a012d before merging and doesn't show
up here.

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-08-17 10:42:15 -07:00
Adam J. Stewart
50f8a0f0d6 python: simplify libs() and headers() methods in python/package.py
- [x] Rework `headers` to search a sequence of directories and to display all searched
      locations on error, as opposed to handling each directory with a variable

- [x] Make `headers` and `libs` do the same type of search and raise the same sort of
      errors.

Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2022-08-17 10:42:15 -07:00
Jen Herting
30585890a8
New package: py-bitshuffle (#31876)
* [py-bitshuffle] New package

* [py-bitshuffle] compiling against spack hdf5

* [py-bitshuffle] flake8

* [py-bitshuffle] update import ine

* [@spackbot] updating style on behalf of qwertos

Co-authored-by: James A Zilberman <jazrc@rit.edu>
Co-authored-by: qwertos <qwertos@users.noreply.github.com>
2022-08-17 10:19:19 -07:00
snehring
80afc1a5a8
ncbi-toolkit: adding new version (#32098) 2022-08-17 09:56:55 -07:00
Jonathan R. Madsen
809df37765
Add omnitrace version 1.4.0 (#32160)
* Add version 1.4.0

- override build variant with explicit variant instead of __init__ workaround

* Update package.py
2022-08-17 09:54:47 -07:00
Mike Renfro
7330969e8a
fasta-36.3.8h_2020-05-04 (#32180)
* Adding 36.3.8h_2020-05-04

* [@spackbot] updating style on behalf of mikerenfro

Co-authored-by: mikerenfro <mikerenfro@users.noreply.github.com>
2022-08-17 09:50:35 -07:00
Erik Schnetter
b8b1a85e4d
rclone: add v1.59.1 (#32011) 2022-08-17 14:51:06 +02:00
Wouter Deconinck
ff163bf623
acts: new versions 19.7.0, 20.0.0 (#32177) 2022-08-17 14:48:50 +02:00