Commit graph

25240 commits

Author SHA1 Message Date
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
Matthieu Dorier
7a8862e316
[py-aiohttp] added new version (#28210)
* [py-aiohttp] added new version

* [py-aiohttp] changed dependency on setuptools

* [py-aiohttp] fixed some of the dependencies

* [py-aiohttp] updated dependency to py-typing-extensions

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-01-03 12:38:15 -07:00
Marcus Boden
20780ec61c
New package: py-azure-storage-blob (#28209)
* New package: py-azure-storage-blob

* fixed typo

* Update var/spack/repos/builtin/packages/py-azure-storage-blob/package.py

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

* Update var/spack/repos/builtin/packages/py-azure-storage-blob/package.py

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

* Update var/spack/repos/builtin/packages/py-azure-storage-blob/package.py

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-01-03 12:34:59 -07:00
Matthieu Dorier
98dfe7e7e0
[py-asynctest] Added py-asynctest package (#28194)
* [py-asynctest] Added py-asynctest package

* [py-asynctest] added dependency to py-setuptools
2022-01-03 11:25:11 -06:00
Marcus Boden
94f5d0a3f4
py-azure-core: Added v1.21.1 (#28208) 2022-01-03 11:24:04 -06:00
Marcus Boden
997dba8ffd
py-msrest: new version 0.6.21 (#28207) 2022-01-03 11:22:48 -06:00
AMD Toolchain Support
6f95296972
cp2k: fix dependency libraries (#28128)
* fixing build issues in cp2k dependencies

* fixing style issues

* reverting elpa.prefix.lib and grammer correction

* addressing the suggestions
2022-01-03 10:32:26 -05:00
Cyrus Harrison
c85c725b08
apcomp add v0.4.0 and new variant (#27820) 2022-01-03 10:40:18 +00:00
Vicente Bolea
a06d93f6cb
VTKm: add v1.7.0 (#27864)
Co-authored-by: Cyrus Harrison <cyrush@llnl.gov>
2022-01-03 11:36:11 +01:00
Seth R. Johnson
8daaee3ed6
ROOT: unset MACOSX_DEPLOYMENT_TARGET for macOS (#28163) 2022-01-03 11:21:15 +01:00
Adam J. Stewart
e40eceba4c
py-torchgeo: add v0.2.0 (#28200) 2022-01-03 11:20:07 +01:00
Tiziano Müller
c220abb011
elpa: add version 2021.11.001, add +autotune variant (#28134) 2022-01-02 22:56:03 -07:00
AMD Toolchain Support
71cb9fd9fd
openmpi: extend version range for cray flags (#28107)
Co-authored-by: mohan babu <mohbabul@amd.com>
2022-01-02 21:17:24 -05:00
Maciej Wójcik
8fdb6e2b61
gromacs-swaxs: add new versions (#28157)
* Deprecate invalid versions

* Add new gromacs-swaxs releases
2022-01-02 21:02:25 -05:00
Eric Berquist
676d321b28
direnv: new version 2.30.2 (#28179) 2022-01-02 21:00:32 -05:00
Adam J. Stewart
d6d1d33e88
libtiff: fix build on macOS Monterey (#28185)
* libtiff: fix build on macOS Monterey

* patch configure, not configure.ac

* Revert "patch configure, not configure.ac"

This reverts commit 8bf315cb22f17bece5b4fa671120dbd05ff96f27.

* Force Spack to run autoreconf using new patch
2022-01-02 20:50:26 -05:00
Adam J. Stewart
89830c2117
Revert "[py-aiohttp] added new version (#28132)" (#28192)
This reverts commit fee855030d.
2022-01-02 13:22:28 -05:00
Nils Leif Fischer
4e16948a1f
libsharp: add pic option (#28197) 2022-01-02 13:19:03 -05:00