Commit graph

24307 commits

Author SHA1 Message Date
Satish Balay
6a60201e80
petsc, py-petsc4py: add versions 3.16.3 (#28277) 2022-01-07 17:15:27 -06:00
Glenn Johnson
a3f5b712d3
py-pyzmq: adjust constraints for python-3.9 (#28264)
Version 18.1 builds with python-3.9
2022-01-07 15:08:02 -06:00
Filippo Spiga
b2336402a7
NVIDIA HPC SDK package: add version 22.1 (#28288) 2022-01-07 12:02:46 -08:00
Glenn Johnson
5091dc2124
r-kegg-db: mark deprecated, removed from bioconductor-3.13 (#28271) 2022-01-07 11:17:36 -07:00
Robert Cohn
7bed76786d
py-matplotlib: fix config for oneapi compiler (#28265)
* py-matplotlib: fix config for oneapi compiler

* Small change to trigger CI restart
2022-01-07 11:17:14 -07:00
Glenn Johnson
0e45ad2d7f
r-illuminahumanmethylationepicmanifest: remove invalid homepage (#28269) 2022-01-07 10:59:19 -07:00
Sebastian Pipping
43e064880e
uriparser: Add latest release 0.9.6 with security fixes (#28291) 2022-01-07 10:14:11 -07:00
Kyle Gerheiser
04a95e3425
ip package: add v4.0.0 (#28237)
Keep 3.3.3 the preferred version until other packages can be updated
2022-01-06 19:46:31 -08:00
snehring
496b28bb58
viennarna package: add version 2.5.0 (#28261) 2022-01-06 19:44:50 -08:00
Sreenivasa Murthy Kolam
94bd667ba6
Update the rocm recipes for 4.5.0 release (#27535)
* rocm recipes updates for 4.5.0

* update to rocm recipes for 4.5.0 release

* updates to the rocm recipes for rocm-4.5.0 release

* fix style errors

* update to rocm-validation-suite for rocm-4.5.0 release

* bump up rccl recipe for rocm-4.5.0

* bump up version for rdc for rocm-4.5.0

* update miopengemm, miopen-opencl,rocm-opencl recipes for 4.5.0 release

* bump up version for mivisiox for rocm-4.5.0 release

* update the rocm-validation-suite recipe

* no need to change the perl path for 4.5.0

* fix the build failure with the recent change made for hip package

* modify checksum for the llvm-amdgpu for 4.5.0

* fix the build issue aftere recent changes made for enabling test

* fix the build issue with 4.5.0

* add new recipe for hipsolver

* address review comments
2022-01-06 13:24:00 -08:00
Adam J. Stewart
186730a284
bazel: python executable required (#28286)
* bazel: python executable required

* python: add autodetection of +pythoncmd
2022-01-06 15:16:43 -06:00
Adam J. Stewart
6e31094d77
GDAL: add new version (#28238)
* GDAL: add new version

* Use conflicts for PCRE
2022-01-06 12:26:24 -07:00
luker
27cbf46dd6
lapackpp: set BLA_VENDOR for cray (#28125) 2022-01-06 13:44:28 -05:00
Glenn Johnson
83a98c3807
r-genomeinfodbdata: add version 1.2.7 (#28266)
Also adjust formatting.
2022-01-06 11:30:31 -06:00
Glenn Johnson
2262bd1797
r package: add version 4.1.2 (#28244)
Set +libidn2 for the curl dependency. This is necessary after #25166.
2022-01-06 11:28:58 -06:00
Harmen Stoppels
f0b70b7c8e
Fix spack install --v[tab] spec (#28278) 2022-01-06 14:47:03 +01:00
Harmen Stoppels
f8d4b4746c
Fix double space in prompt after 'spack env activate -p' (#28279) 2022-01-06 04:59:07 -07:00
Glenn Johnson
f33f67ebd3
r-illuminahumanmethylationepicanno-ilm10b4-hg19: remove invalid homepage (#28267) 2022-01-06 11:35:40 +01:00
Axel Huebl
cc866f3c02
WarpX: 22.01 (#28225)
* WarpX: 22.01

Update `warpx` & `py-warpx` to the latest release, `22.01`.

* Python in 22.01+: Relax even further

See: https://github.com/ECP-WarpX/WarpX/pull/2664
2022-01-05 20:50:45 -08:00
Glenn Johnson
a43ed9286f
GCC package: allow building gcc-5 on newer Linux (#27386)
Remove cyclades support so gcc-5 can build against newer glibc
versions (e.g. 2.31).
2022-01-05 14:14:28 -08:00
Harmen Stoppels
071778b919
llvm: make targets a multivalued variant (#27735)
* llvm: make targets a multivalued variant

* Fix the targets variant values

1. Make them lowercase and add a mapping to cmake equivalent
2. auto -> all
2. Restore composability by using a multivalued variant, so that
   `targets=all` and `targets=x86` is combined to `targets=all,x86`
   which is then transformed into LLVM_TARGETS_TO_BUILD=all.

* use targets=x86 in iwyu

* Default to nvptx/amdgpu/host arch targets

* default to none

* Update var/spack/repos/builtin/packages/zig/package.py
2022-01-05 14:11:05 -07:00
Andrew W Elble
a4f0fbafbb
Add function to determine Linux kernel version (#27855)
This reports the kernel version (vs. the distro version) on Linux and
returns a valid Version (stripping characters like '+' which may be
present for custom-built kernels).
2022-01-05 10:22:43 -08:00
Pat McCormick
52cfd17917
Address legion package build issue on macOS with apple-clang-12 (#28241)
* Added C++ standard variant as a primary work-around for issues with apple-clang 12.x
but could also be helpful for broader uses.
2022-01-05 10:20:24 -08:00
Dylan Simon
f34598214b
py-pyzmq: fix deptype of libzmq (#28254) 2022-01-05 10:59:33 -07:00
Severin Strobl
f064c5ee4f
py-appdirs: patch for encoding issue (#28253)
Reading appdirs.py without explicitly requesting UTF-8 decoding results
in the build process to fail for Python 3.6.

See https://github.com/ActiveState/appdirs/pull/152 for the upstream
fix.
2022-01-05 10:59:12 -07:00
Marcus Boden
3e992aa283
Snakemake: New Version 6.12.3 (#28252)
* snakemake: New version
The newer versions of snakemake have a lot of new dependencies. The
optional dependencies still have to be added.

* removed comment

* some changes

* added reports variant

* deprecate older version and add me as maintainer

* Added dependency py-ratelimiter
2022-01-05 09:53:30 -07:00
Adam J. Stewart
c226835aa5
py-zipfile-deflate64: add new package (#27971) 2022-01-05 09:29:25 -07:00
kwryankrattiger
9e616ca7b7
VTK: Patch ADIOS2 module to fix cyclic dependency (#27784) 2022-01-05 11:21:08 -05:00
Harmen Stoppels
b23bd81cd9
ccache: add v4.5 and v4.5.1 (#28249) 2022-01-05 15:49:56 +01:00
Harmen Stoppels
39a346bde0
subversion: add v1.14.1, build in parallel (#28250) 2022-01-05 15:48:45 +01:00
Harmen Stoppels
89d3590300
sirius, spfft: make rocm arch variants conditional (#28251) 2022-01-05 15:47:40 +01:00
Massimiliano Culpo
0f74b7ec44
GnuPG: add v2.3.4 and update dependencies (#28248) 2022-01-05 15:42:18 +01:00
Andrew W Elble
422ae20a45
new package: py-lmdb (#28239) 2022-01-04 17:59:16 -07:00
snehring
efc5d0a3b4
snap-korf: version update + fix for compilers newer than gcc5 (#28243) 2022-01-04 17:44:04 -07:00
Marcus Boden
431473ea9b
py-smart-open: Adding new version and dependencies (#28220)
* py-smart-open: Adding new version and dependencies

* fix python version and variant description/default
2022-01-04 14:20:15 -07:00
Jen Herting
cbe47f2066
New package: py-fastdownload (#28150)
* [py-fastdownload] created template

* [py-fastdownload]

- added homepage
- added description
- added dependencies
- removed fixmes
2022-01-04 15:14:59 -06:00
Axel Huebl
e43795de28
Fix: py-adios Cython run (#28223)
* Fix: py-adios Cython run

Always run Cython before `py-adios` installs.
This makes sure the `.cpp` files from `.pyx` files are freshly
created and work with newer CPython versions than the one checked
in.

* Cleanup: `rm` -> `os.remove`
2022-01-04 12:05:18 -07:00
Andrew W Elble
dc1b6aa8c6
new package: r-cca and dependencies (#28229)
Co-authored-by: Andrew W Elble <aweits@skl-a-00.rc.rit.edu>
2022-01-04 11:41:21 -07:00
Andrew W Elble
b924a5db14
new package: r-rpsychi (#28231)
Co-authored-by: Andrew W Elble <aweits@skl-a-00.rc.rit.edu>
2022-01-04 12:39:37 -06:00
Andrew W Elble
0264bb8343
new package: r-ccp (#28230)
Co-authored-by: Andrew W Elble <aweits@skl-a-00.rc.rit.edu>
2022-01-04 12:37:40 -06:00
Matthieu Dorier
c24bb64792
[py-gpustat] Added new version (#28135)
* [py-gpustat] Added new version

* [py-gpustat] marking 0.6.0 as preferred

* [py-gpustat] updated dependencies

* [py-gpustat] added dependency on python 3.4+

* [py-gpustat] corrected dependency to py-pytest-runner
2022-01-04 11:20:57 -06:00
Teodor Nikolov
cdb04931ab
New version of neovim (#28222) 2022-01-04 07:14:01 -07:00
Harmen Stoppels
dce4f161d4
Drop preferred hdf5 version (#28091)
* Drop preferred hdf5 version

* Fix conduit

* Add compat bound for silo on hdf5

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

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

* hdf5 <= 1.10 for conduit <= 0.7

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
2022-01-04 02:24:37 -08:00
Nils Leif Fischer
ffc3272a2b
charmpp: add conflict with +shared on macOS with GCC (#28211) 2022-01-04 10:31:55 +01:00
Stephen McDowell
8d19db8628
cudnn: add v8.3.1 (#28071) 2022-01-04 09:25:13 +01:00
Nils Leif Fischer
1250b77607
doxygen: fix build issue with external Py3 (#28216)
Doxygen's build system uses CMake's deprecated `FindPythonInterp`,
which can get confused by other `python` executables in the PATH.
See issue: https://github.com/spack/spack/issues/28215
2022-01-04 09:10:39 +01:00
Nils Leif Fischer
1b5eaf62de
doxygen: add v1.9.3 (#28217) 2022-01-04 09:08:14 +01:00
Weiqun Zhang
dd03a1a91e
amrex: add v22.01 (#28214) 2022-01-04 09:06:59 +01:00
Tom Payerle
7cd8bae799
namd: Fix issue when building with interface=python ^python@3.8 (#28218)
Patch to add --embed flag to config-python when interface=python and
using python@3.8:

This is because python@3.8 changed behavior of python-config --ldflags
(and --libs) such that it no longer includes -lpython unless --embed
flag is used.

See e.g. https://github.com/mesonbuild/meson/issues/5629
2022-01-04 09:04:46 +01:00
Wouter Deconinck
ae2509339d
qt: depends_on assimp@5.0 when @5.14: +opengl (#28191)
* qt: depends_on assimp@5.0 when @5.14: +opengl

* [qt] patch for assimp@5.14:5

* [qt] depends_on assimp@5.0.0:5.0

* [qt] remove depends_on gmake again
2022-01-03 12:56:11 -07:00