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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
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.
2022-12-15py-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>
2022-12-15IntelOneApiPackage: add envmods variant to toggle environment modifications ↵Sean Koyama1-2/+4
by oneapi packages (#34253) Co-authored-by: Sean Koyama <skoyama@anl.gov> Co-authored-by: Robert Cohn <robert.s.cohn@intel.com>
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
2022-12-14WarpX 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
2022-12-14fms: add v2019.01.03 (#34511)eugeneswalker1-0/+3
2022-12-14justbuild: add v1.0.0 (#34467)Alberto Sartori1-0/+1
2022-12-13r-rgdal: adding new version 1.6-2 (#34502)snehring1-0/+1
2022-12-13py-submitit: add 1.4.5 (#34460)Matthias Wolf1-1/+3
2022-12-13py-tifffile: add 2022.10.10 (#34499)Manuela Kuhn1-2/+7
2022-12-13py-sphinxcontrib-qthelp: add 1.0.3 (#34495)Manuela Kuhn1-1/+3
2022-12-13py-sqlalchemy: add 1.4.45 (#34497)Manuela Kuhn1-25/+2
2022-12-13trilinos: extend range of Teuchos patch (#34504)Paul Kuberry1-1/+1
2022-12-13Update pFunit, add gFTL, gFTL-Shared, fArgParse, pFlogger, yaFyaml (#34476)Matthew Thompson6-14/+296
* Add GFE packages, Update pFUnit * Remove citibeth as maintainer per her request * Version 3.3.0 is an odd duck. Needs a v Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
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