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2022-12-22bacio: patch for v2.4.1 (#34575)Alex Richert1-0/+4
2022-12-21add py-psij-python and py-pystache packages (#34357)Andre Merzky3-0/+49
* add psij package and deps * update hashes, URLs * linting * Update var/spack/repos/builtin/packages/py-psij-python/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pystache/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-pystache/package.py Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> * Update package.py apply suggested change * Update package.py apply suggested change * Update package.py ensure maintainer inheritance * add psij to exaworks meta-package Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-12-21paraview: patch catalyst etc. to build with oneapi (#33562)Howard Pritchard2-0/+48
without this patch, build of paraview has a meltdown when reaching 3rd party catalyst and other packages with these types of errors: 335 /tmp/foo/spack-stage/spack-stage-paraview-5.10.1-gscoqxhhakjyyfirdefuhmi2bzw4scho/spack-src/VTK/ThirdParty/fmt/vtkfmt/vtkfmt/format.h:1732:11: error: cannot capture a bi t-field by reference 336 if (sign) *it++ = static_cast<Char>(data::signs[sign]); 337 ^ Signed-off-by: Howard Pritchard <howardp@lanl.gov> Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2022-12-21py-cartopy: older versions don't support Python 3.10 (#34626)Adam J. Stewart1-14/+2
2022-12-21podio: add v0.16.2 (#34606)Thomas Madlener1-0/+1
2022-12-21relion: add v4.0.0 (#34600)Hector Martinez-Seara1-8/+5
2022-12-21glib: add 2.74.3 (#34603)Michael Kuhn1-0/+1
2022-12-21rocm: make amdgpu_target sticky (#34591)Cory Bloor10-11/+13
The sticky property will prevent clingo from changing the amdgpu_target to work around conflicts. This is the same behaviour as was adopted for cuda_arch in 055c9d125d29606947f2fd88a06e279667a74648.
2022-12-21eckit: skip broken test (#34610)Sergey Kosukhin1-1/+20
2022-12-21hpctoolkit: replace filter_file with upstream patch (#34604)Mark W. Krentel1-15/+7
Replace the filter_file for older configure with rocm 5.3 with an upstream patch. Further, the patch is no longer needed for develop or later releases.
2022-12-21dashan-runtime,darshan-util,py-darshan: update package versions for ↵shanedsnyder3-3/+12
darshan-3.4.2 (#34583)
2022-12-21arm-forge: add 22.1.2 (#34569)louisespellacy-arm1-0/+9
2022-12-21starpu: add conflict for ~blocking +simgrid (#34616)lpoirel1-0/+1
see https://gitlab.inria.fr/starpu/starpu/-/commit/1f5a911d43ba8e49f7229ab16f5dafdfdd596bd2
2022-12-21py-pyproj: add new versions (#34633)Adam J. Stewart1-6/+6
2022-12-21feat: 🎸 Add new 2023.0.0 oneVPL package (#34642)Andrey Perestoronin1-0/+6
2022-12-21py-vcrpy: add 4.2.1 (#34636)Manuela Kuhn1-0/+3
2022-12-21neko: add v0.5.0 (#34640)Niclas Jansson1-0/+1
2022-12-21hypre: add v2.27.0 (#34625)Rob Falgout1-0/+1
2022-12-21Add patch for pika on macOS (#34619)Mikael Simberg2-0/+63
2022-12-20py-scikit-image: add 0.19.3 (#34618)Manuela Kuhn1-7/+21
* py-scikit-image: add 0.19.3 * Update var/spack/repos/builtin/packages/py-scikit-image/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-12-20DAV: VTK-m needs to install examples for smoke test (#34611)kwryankrattiger1-0/+3
SDK deployment targets being able to validate and run VTK-m via spack deployments, so examples should be installed.
2022-12-202023.0.0 oneAPI release promotion (#34617)Andrey Perestoronin14-0/+80
2022-12-19Remove dep on jupyter meta-package (#34573)Nicholas Knoblauch1-1/+1
2022-12-19py-nipype: add 1.8.5 and py-looseversion: add new package (#34608)Manuela Kuhn2-1/+25
2022-12-19Gromacs: added version 2022.4 (#34599)Hector Martinez-Seara1-0/+1
2022-12-19[ELPA] add sha256 for elpa-2022.11.001.rc2.tar.gz (#33439)Anton Kozhevnikov1-0/+15
2022-12-19py-horovod: patch no longer applies (#34593)Adam J. Stewart1-1/+1
2022-12-19aws-sdk-cpp: add v1.10.32 (#34592)Adam J. Stewart1-0/+1
2022-12-19py-pyvista: add v0.37.0 (#34590)Adam J. Stewart1-4/+9
2022-12-19netcdf-cxx: add patch to fix macOS build (#34588)Adam J. Stewart2-0/+14
2022-12-19XNNPACK: fix build on macOS, update deps (#34555)Adam J. Stewart2-27/+32
2022-12-19Node.js: new versions, newer Python support, macOS fixes (#34478)Adam J. Stewart1-15/+37
2022-12-18py-numpy: add v1.24.0 (#34602)Adam J. Stewart1-0/+1
2022-12-18Add py-docstring-to-markdown v0.11 (#34595)Alec Scott1-0/+1
2022-12-18intel-oneapi-dpl: add v2022.0.0 (#34601)eugeneswalker1-0/+6
2022-12-17LLVM: replace libelf dependency with elf (#34265)iarspider1-7/+3
* LLVM: replace libelf dependency with elf I didn't test this extensively, but in CMS LLVM builds just fine with elfutils. * [@spackbot] updating style on behalf of iarspider Co-authored-by: iarspider <iarspider@users.noreply.github.com>
2022-12-17Update PyTorch ecosystem (#34582)Adam J. Stewart5-0/+9
2022-12-17Add static-only option for ESMF (#34576)Alex Richert1-0/+5
2022-12-17Add gimp & dependent packages (#34558)Benjamin S. Kirk12-0/+395
* exiv2: add new versions * babl: new package required to build GIMP * gegl: new package required to build GIMP * gexiv2: new package required to build GIMP * libmypaint: new package required to build GIMP * mypaint-brushes: new package required to build GIMP * vala: new package required to build GIMP * GIMP: new package definition for building GIMP-2.10 from source * libjxl: update for 0.7.0 * libwmf: a library for reading vector images in Windows Metafile Format (WMF) * libde265: an open source implementation of the h.265 video codec * libwebp: add new versions * GIMP: additional variants for building GIMP-2.10 from source * libde265: remove boilerplate * fixes for style precheck * updates based on feedback * fixes for style precheck
2022-12-16Update package versions: RADICAL-Cybertools (RE, RG, RP, RS, RU) (#34572)Mikhail Titov5-6/+21
* rct: update packages (RE, RG, RP, RS, RU) with new versions * re: fixed radical-pilot requirement for radical-entk
2022-12-16intel-oneapi-compilers: add v2023.0.0 (#34571)eugeneswalker1-0/+11
2022-12-16Add `--enable-orterun-prefix-by-default` configure option for OpenMPI (#34469)Jack Morrison1-0/+10
2022-12-16Automake requires Thread::Queue, but it is only provided with in ↵Bernhard Kaindl1-1/+1
perl+threads. (#34076) Update the depends_on("perl") to depends_on("perl+threads"). This and #34074 is needed to properly handle e.g. the perl-Thread-Queue rpm package: It may not be installed on RedHat-based hosts, which can lead to automake build failures when `spack external find perl` or `spack external find --all` was used to use the system-provided perl install.
2022-12-16octopus: Ensure MPI is used consistently (#33969)Rémi Lacroix1-6/+9
Some variants have MPI dependencies, make sure they can be used only when the `mpi` variable is enabled.
2022-12-16adding 2nd bunch of nf-core deps from update/nextflow-tools (#34562)Marco De La Pierre21-0/+505
* adding 2nd bunch of nf-core deps from update/nextflow-tools * Update var/spack/repos/builtin/packages/py-a2wsgi/package.py * Update var/spack/repos/builtin/packages/py-apispec/package.py * Update var/spack/repos/builtin/packages/py-bagit-profile/package.py * Update var/spack/repos/builtin/packages/py-bagit-profile/package.py * Update var/spack/repos/builtin/packages/py-bagit-profile/package.py * Update var/spack/repos/builtin/packages/py-bdbag/package.py * Update var/spack/repos/builtin/packages/py-schema-salad/package.py * Update var/spack/repos/builtin/packages/py-schema-salad/package.py * Update var/spack/repos/builtin/packages/py-tuspy/package.py * Update var/spack/repos/builtin/packages/py-schema-salad/package.py * Update var/spack/repos/builtin/packages/py-schema-salad/package.py * Update var/spack/repos/builtin/packages/py-bdbag/package.py * Update var/spack/repos/builtin/packages/py-bdbag/package.py * Update var/spack/repos/builtin/packages/py-bioblend/package.py * Update var/spack/repos/builtin/packages/py-circus/package.py * Update var/spack/repos/builtin/packages/py-circus/package.py * Update var/spack/repos/builtin/packages/py-cloudbridge/package.py * Update var/spack/repos/builtin/packages/py-cloudbridge/package.py * Apply suggestions from code review Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-12-16Adding first bunch of recipes for dependencies of nf-core-tools (#34537)Marco De La Pierre15-0/+344
* nextflow recipe: added latest stable version * tower-cli recipe: added latest release * recipes tower-agent and tower-cli renamed to nf-tower-agent and nf-tower-cli * recipes nf-tower-agent and nf-tower-cli: small fix * nf-core-tools recipe: added most py- dependencies * nf-core-tools: recipe without galaxy-tool-util (for testing) * fixed typos in py-yacman recipe * fixed typos in py-pytest-workflow recipe * fixed typo in nf-core-tools recipe * fixed typos in py-yacman recipe * fixes in recipes for py-questionary and py-url-normalize * fixes to py-yacman recipe * style fixes to py- packages that are dependencies to nf-core-tools * fix in py-requests-cache recipe * added missing dep in py-requests-cache recipe * nf-core-tools deps: removed redundant python dep for py packages oyaml and piper * nf-core-tools recipe: final, incl dep on py-galaxy-tool-util * nf-core-tools: new version with extra dependency * commit to merge packages on focus from update/nextflow-tools * nf-core: commenting galaxy dep for this pr * Update var/spack/repos/builtin/packages/py-requests-cache/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-requests-cache/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * removed nf-core-tools from this branch, will be back at the end Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-12-16Add HACCabana proxy app (#34567)Sam Reeve1-0/+33
2022-12-16new release cdo-2.1.1 (#34548)Brian Spilner1-0/+5
2022-12-16py-pytorch-lightning: add v1.8.5 (#34557)Adam J. Stewart1-0/+1
2022-12-16GDAL: add v3.6.1 (#34556)Adam J. Stewart1-0/+1
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