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2022-01-07py-pyzmq: adjust constraints for python-3.9 (#28264)Glenn Johnson1-2/+3
Version 18.1 builds with python-3.9
2022-01-07NVIDIA HPC SDK package: add version 22.1 (#28288)Filippo Spiga1-0/+4
2022-01-07r-kegg-db: mark deprecated, removed from bioconductor-3.13 (#28271)Glenn Johnson1-3/+5
2022-01-07py-matplotlib: fix config for oneapi compiler (#28265)Robert Cohn1-1/+2
* py-matplotlib: fix config for oneapi compiler * Small change to trigger CI restart
2022-01-07r-illuminahumanmethylationepicmanifest: remove invalid homepage (#28269)Glenn Johnson1-1/+0
2022-01-07uriparser: Add latest release 0.9.6 with security fixes (#28291)Sebastian Pipping1-2/+3
2022-01-06ip package: add v4.0.0 (#28237)Kyle Gerheiser1-1/+2
Keep 3.3.3 the preferred version until other packages can be updated
2022-01-06viennarna package: add version 2.5.0 (#28261)snehring1-1/+2
2022-01-06Update the rocm recipes for 4.5.0 release (#27535)Sreenivasa Murthy Kolam49-120/+684
* 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
2022-01-06bazel: python executable required (#28286)Adam J. Stewart2-1/+8
* bazel: python executable required * python: add autodetection of +pythoncmd
2022-01-06GDAL: add new version (#28238)Adam J. Stewart1-9/+15
* GDAL: add new version * Use conflicts for PCRE
2022-01-06lapackpp: set BLA_VENDOR for cray (#28125)luker1-1/+12
2022-01-06r-genomeinfodbdata: add version 1.2.7 (#28266)Glenn Johnson1-7/+12
Also adjust formatting.
2022-01-06r package: add version 4.1.2 (#28244)Glenn Johnson1-1/+2
Set +libidn2 for the curl dependency. This is necessary after #25166.
2022-01-06Fix spack install --v[tab] spec (#28278)Harmen Stoppels3-2/+12
2022-01-06Fix double space in prompt after 'spack env activate -p' (#28279)Harmen Stoppels1-1/+1
2022-01-06r-illuminahumanmethylationepicanno-ilm10b4-hg19: remove invalid homepage ↵Glenn Johnson1-3/+2
(#28267)
2022-01-05WarpX: 22.01 (#28225)Axel Huebl2-19/+33
* 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
2022-01-05GCC package: allow building gcc-5 on newer Linux (#27386)Glenn Johnson2-0/+85
Remove cyclades support so gcc-5 can build against newer glibc versions (e.g. 2.31).
2022-01-05llvm: make targets a multivalued variant (#27735)Harmen Stoppels5-37/+69
* 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
2022-01-05Add function to determine Linux kernel version (#27855)Andrew W Elble2-1/+22
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).
2022-01-05Address legion package build issue on macOS with apple-clang-12 (#28241)Pat McCormick1-1/+11
* Added C++ standard variant as a primary work-around for issues with apple-clang 12.x but could also be helpful for broader uses.
2022-01-05py-pyzmq: fix deptype of libzmq (#28254)Dylan Simon1-2/+2
2022-01-05py-appdirs: patch for encoding issue (#28253)Severin Strobl2-0/+22
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.
2022-01-05Snakemake: New Version 6.12.3 (#28252)Marcus Boden2-3/+52
* 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
2022-01-05py-zipfile-deflate64: add new package (#27971)Adam J. Stewart1-0/+19
2022-01-05VTK: Patch ADIOS2 module to fix cyclic dependency (#27784)kwryankrattiger4-1/+59
2022-01-05ccache: add v4.5 and v4.5.1 (#28249)Harmen Stoppels1-0/+2
2022-01-05subversion: add v1.14.1, build in parallel (#28250)Harmen Stoppels1-4/+2
2022-01-05sirius, spfft: make rocm arch variants conditional (#28251)Harmen Stoppels2-2/+2
2022-01-05GnuPG: add v2.3.4 and update dependencies (#28248)Massimiliano Culpo5-2/+9
2022-01-04new package: py-lmdb (#28239)Andrew W Elble1-0/+20
2022-01-04snap-korf: version update + fix for compilers newer than gcc5 (#28243)snehring1-5/+18
2022-01-04py-smart-open: Adding new version and dependencies (#28220)Marcus Boden1-6/+40
* py-smart-open: Adding new version and dependencies * fix python version and variant description/default
2022-01-04New package: py-fastdownload (#28150)Jen Herting1-0/+23
* [py-fastdownload] created template * [py-fastdownload] - added homepage - added description - added dependencies - removed fixmes
2022-01-04Fix: py-adios Cython run (#28223)Axel Huebl1-21/+23
* 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`
2022-01-04new package: r-cca and dependencies (#28229)Andrew W Elble6-0/+109
Co-authored-by: Andrew W Elble <aweits@skl-a-00.rc.rit.edu>
2022-01-04new package: r-rpsychi (#28231)Andrew W Elble1-0/+26
Co-authored-by: Andrew W Elble <aweits@skl-a-00.rc.rit.edu>
2022-01-04new package: r-ccp (#28230)Andrew W Elble1-0/+13
Co-authored-by: Andrew W Elble <aweits@skl-a-00.rc.rit.edu>
2022-01-04[py-gpustat] Added new version (#28135)Matthieu Dorier1-3/+9
* [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
2022-01-04New version of neovim (#28222)Teodor Nikolov1-0/+1
2022-01-04Drop preferred hdf5 version (#28091)Harmen Stoppels3-4/+6
* 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>
2022-01-04charmpp: add conflict with +shared on macOS with GCC (#28211)Nils Leif Fischer1-0/+4
2022-01-04cudnn: add v8.3.1 (#28071)Stephen McDowell1-4/+28
2022-01-04doxygen: fix build issue with external Py3 (#28216)Nils Leif Fischer1-0/+9
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
2022-01-04doxygen: add v1.9.3 (#28217)Nils Leif Fischer1-0/+1
2022-01-04amrex: add v22.01 (#28214)Weiqun Zhang1-1/+2
2022-01-04namd: Fix issue when building with interface=python ^python@3.8 (#28218)Tom Payerle2-0/+19
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
2022-01-03qt: depends_on assimp@5.0 when @5.14: +opengl (#28191)Wouter Deconinck2-0/+22
* 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[py-aiohttp] added new version (#28210)Matthieu Dorier1-5/+13
* [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>
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