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2022-12-21etags for index.json invalidation, test coverage (#34641)Harmen Stoppels4-97/+442
Implement an alternative strategy to do index.json invalidation. The current approach of pairs of index.json / index.json.hash is problematic because it leads to races. The standard solution for cache invalidation is etags, which are supported by both http and s3 protocols, which allows one to do conditional fetches. This PR implements that for the http/https schemes. It should also work for s3 schemes, but that requires other prs to be merged. Also it improves unit tests for index.json fetches.
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
2022-12-20archspec: add support for zen4 (#34609)Massimiliano Culpo7-33/+98
Also add: - Upper bound for Xeon Phi compiler support - Better detection for a64fx
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>
2022-12-17fix != -> == typo (#34568)Harmen Stoppels1-1/+1
2022-12-17Update PyTorch ecosystem (#34582)Adam J. Stewart5-0/+9
2022-12-17Add static-only option for ESMF (#34576)Alex Richert1-0/+5
2022-12-17e4s: disable mac stack due to binary relocation issue#32571 (#34560)eugeneswalker1-103/+103
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
2022-12-16Compiler detection: avoid false recognition of MSVC (#34574)John W. Parent1-0/+2
Interim fix for #34559 Spack's MSVC compiler definition uses ifx as the Fortran compiler. Prior to #33385, the Spack MSVC compiler definition required the executable to be called "ifx.exe"; #33385 replaced this with just "ifx", which inadvertently led to ifx falsely indicating the presence of MSVC on non-Windows systems (which leads to future errors when attempting to query/use those compiler objects). This commit applies a short-term fix by updating MSVC Fortran version detection to always indicate a failure on non-Windows.
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
2022-12-16vtk-m: add v2.0.0-rc1 (#34561)Vicente Bolea1-0/+1
2022-12-16spectre: add v2022.12.16 (#34570)SXS Bot1-0/+3
* spectre: add v2022.12.16 * [@spackbot] updating style on behalf of sxs-bot Co-authored-by: sxs-bot <sxs-bot@users.noreply.github.com>
2022-12-16add version 3.6.4 to wi4mpi (#34565)Marc Joos1-0/+1
2022-12-16nwchem: restricting current versions to python@3.9 at latest (#34506)snehring1-1/+1
2022-12-15libzmq: make location of libsodium explicit (#34553)Paul Kuberry1-1/+1
2022-12-15nco: add v5.0.6 (#34512)eugeneswalker1-0/+1
2022-12-15roctracer: fixed a bug in how the external is identified (#33517)Brian Van Essen1-6/+2
Make the package a proper ROCm package.
2022-12-15gitlab ci: more resources for slow builds (#34505)Zack Galbreath8-2/+28
2022-12-15py-traits: add 6.4.1 (#34550)Manuela Kuhn1-1/+3
2022-12-15eckit: add v1.19.0 (#34510)eugeneswalker1-0/+1
2022-12-15odc: add v1.4.5 (#34513)eugeneswalker1-0/+1
2022-12-15arpack-ng: add variant for ISO C binding support (#34529)Sebastian Grimberg1-0/+2
Co-authored-by: Sebastian Grimberg <sjg@amazon.com>
2022-12-15Propagate exceptions from Spack python console (#34547)Massimiliano Culpo1-0/+17
fixes #34489 Customize sys.excepthook to raise SystemExit when any unhandled exception reaches the hook.
generated by cgit v1.2.3-60-g2f50 (git 2.42.0) at 2024-07-12 05:04:48 +0000