Commit graph

24320 commits

Author SHA1 Message Date
Peter Scheibel
9f7fb6d01a
stage.steal_source: preserve symlinks
This avoids dangling symlink errors. ignore_dangling_symlinks option would be more-targeted but is only available for Python >= 3.2 (#28318)
2022-01-10 10:10:49 -08:00
Adam J. Stewart
cc32b08205
Python: set default config_vars (#28290)
* Python: set default config_vars

* Add missing commas

* dso_suffix not present for some reason

* Remove use of default_site_packages_dir

* Use config_vars during bootstrapping too

* Catch more errors

* Fix unit tests

* Catch more errors

* Update docstring
2022-01-10 12:00:06 -06:00
Marcus Boden
5958306466
New packages: google-crc32c and py-google-crc32c (#28293) 2022-01-10 08:58:02 -06:00
Erik Schnetter
464d294b63
z3: New version 4.8.14 (#28314) 2022-01-10 14:31:52 +01:00
Erik Schnetter
b7f4a421e4
hwloc: New version 2.7.0 (#28298) 2022-01-10 12:00:51 +01:00
Peter Brady
fe64afb479
New package: petaca (#28326)
* Add the petaca fortran/c package

* Adopt date for version name and remove variants
2022-01-09 19:49:49 -05:00
luker
0277067e5f
blaspp: set BLA_VENDOR for cray (#28104)
* for Cray's libsci in blaspp, set BLA_VENDOR=all

* Update package.py

* Update package.py

* Update package.py
2022-01-08 15:41:50 -05:00
Adam J. Stewart
334102addd
SQLite: add new version/variant (#28204) 2022-01-08 12:57:57 -06:00
Erik Schnetter
52d475e89b
openssh: New version 8.8p1 (#28325) 2022-01-08 13:10:28 +01:00
Martin Diehl
2bb844ee0e
Damask improvements (#28178) 2022-01-08 06:50:38 -05:00
Jógvan Magnus Haugaard Olsen
897616f073
Dalton package: add versions and variants (#28226)
* Update existing 2020.0 version to use tag
* Add versions 2018.2 and master
* Add patches for GCC/Intel
* Use MPI compiler wrappers when +mpi
* Constrain CMake build dependency (need >= 3.1)
* Add variants for optional components (e.g QFIT library)
2022-01-07 18:59:17 -08:00
Anton Kozhevnikov
34f0222fdd
ELPA package: don't check threading support during build (#28227)
./configure tries to execute an MPI test, which is not possible on
most HPC platforms (if you don't build on a compute node), so this
check is disabled to allow the build to proceed. Ideally we could
check this by placing constraints on the MPI that Spack builds (e.g.
require building a version that is guaranteed to have threading
support).
2022-01-07 18:13:46 -08:00
Peter Brady
d125bdfaa0
Catch2 package: add versions 2.13.8 and 3.0.0-preview4 (#28297) 2022-01-07 16:55:49 -08:00
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