summaryrefslogtreecommitdiff
AgeCommit message (Collapse)AuthorFilesLines
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.
2022-12-15IntelOneApiPackage: add envmods variant to toggle environment modifications ↵Sean Koyama2-7/+18
by oneapi packages (#34253) Co-authored-by: Sean Koyama <skoyama@anl.gov> Co-authored-by: Robert Cohn <robert.s.cohn@intel.com>
2022-12-15Add a proper deprecation warning for update-index -d (#34520)Harmen Stoppels4-5/+38
2022-12-15Remove warning in download_tarball (#34549)Harmen Stoppels1-4/+0
2022-12-15Forward lookup of the "run_tests" attribute (#34531)Massimiliano Culpo2-1/+20
fixes #34518 Fix an issue due to the MRO chain of the package wrapper during build. Before this PR we were always returning False when the builder object was created before the run_tests method was monkey patched.
2022-12-15metabat: adding missing build dependency (#34530)snehring1-0/+1
2022-12-15talass: fixed URLs so the package is reachable (#34387)Loïc Pottier1-2/+5
Signed-off-by: Loïc Pottier <pottier1@llnl.gov>
2022-12-15ncl: add RPC lib with ncl+hdf4 (#34451)Brian Vanderwende1-1/+12
2022-12-15Add G'MIC package with only the "cli" target available (#34533)downloadico1-0/+41
2022-12-15sundials: fix typo in smoke tests (#34539)David Gardner1-1/+1
2022-12-15podio, edm4hep: add v0.7.2 and v0.16.1 respectively (#34526)Thomas Madlener2-0/+7
Co-authored-by: Bernhard Kaindl <43588962+bernhardkaindl@users.noreply.github.com>
2022-12-15cpuinfo: new versions, shared libs (#34544)Adam J. Stewart1-29/+9
2022-12-15acts: new versions 19.11.0, 21.0.0, 21.1.0 (#34540)Wouter Deconinck1-0/+5
* acts: new versions 19.11.0, 21.0.0, 21.1.0 https://github.com/acts-project/acts/compare/v19.10.0...v19.11.0: - python 3.8 required if ACTS_BUILD_EXAMPLES_PYTHON_BINDINGS https://github.com/acts-project/acts/compare/v20.3.0...v21.0.0: - python 3.8 required if ACTS_BUILD_EXAMPLES_PYTHON_BINDINGS https://github.com/acts-project/acts/compare/v21.0.0...v21.1.0: - no build system changes * acts: depends_on python@3.8: when sometimes
2022-12-15libcint: Fix +coulomb_erf and add +pypzpx (#34524)Fabien Bruneval1-1/+7
2022-12-15lcio: add latest version (#34527)Thomas Madlener1-0/+1
2022-12-14ParaView: Add openPMD Support (#33821)Axel Huebl2-1/+13
openPMD, a metadata standard on top of backends like ADIOS2 and HDF5, is implemented in ParaView 5.9+ via a Python3 module. Simplify Conflicts & Variant Add to ECP Data Vis SDK
2022-12-14py-traitlets: add w5.7.1 (#34525)Manuela Kuhn1-0/+3
2022-12-15caliper: add version 2.9.0 (#34538)David Boehme1-2/+3
2022-12-15apptainer: add new version 1.1.4 (#34536)snehring1-0/+1
2022-12-14Patch dill._dill._is_builtin_module (#34534)Sam Grayson2-0/+39
* Patch dill._dill._is_builtin_module * Fix style * Add test
2022-12-15py-archspec: replace removed .build_directory with .stage.source_path (#34521)finkandreas1-1/+1
2022-12-14Revert "Revert "Use `urllib` handler for `s3://` and `gs://`, improve ↵Harmen Stoppels4-159/+92
`url_exists` through HEAD requests (#34324)"" (#34498) This reverts commit 8035eeb36d5068fcbae613e51dd13cb1ae9f4888. And also removes logic around an additional HEAD request to prevent a more expensive GET request on wrong content-type. Since large files are typically an attachment and only downloaded when reading the stream, it's not an optimization that helps much, and in fact the logic was broken since the GET request was done unconditionally.
2022-12-14WarpX 22.11, 22.12 & PICMI-Standard (#34517)Axel Huebl3-2/+10
* PICMI: 0.0.22 * WarpX: 22.11, 22.12
2022-12-14edits to 8x existing recipes, mostly new versions, plus two dependency fixes ↵Marco De La Pierre8-4/+14
(#34516)
2022-12-14Nextflow, Tower Agent, Tower CLI: updates (#34515)Marco De La Pierre5-1/+150
* renamed tower-agent and tower-cli with prefif nf- * new nextflow package version * added newest versions (today) for nf-tower-agent and nf-tower-cli
2022-12-14New neuroscience packages: py-bmtk, py-neurotools (#34464)Erik Heeren3-0/+75
* Add py-bmtk and py-neurotools * py-bmtk: version bump * [@spackbot] updating style on behalf of heerener * Maybe the copyright needs to be extended to 2022 for the check to pass * Process review remarks * Update var/spack/repos/builtin/packages/py-neurotools/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-12-14bufr: add v11.6, 11.7, 11.7.1 (#34509)eugeneswalker1-0/+3
generated by cgit v1.2.3-70-g09d2 (git 2.46.0) at 2024-08-26 19:26:25 +0000