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2023-08-07libdeflate: new versions, switch to cmake (#39062)Harmen Stoppels1-3/+22
2023-08-07py-torchmetrics: add v1.0.2 (#39274)Adam J. Stewart1-2/+13
2023-08-07py-timm: add v0.9.5 (#39275)Adam J. Stewart1-0/+1
2023-08-07samtools: add 1.17 (#39287)Christopher Christofi1-0/+2
2023-08-07use {%compiler.name}{@compiler.version} in matching_specs (#39247)Harmen Stoppels1-1/+1
2023-08-07spack: bump package (#39184)Harmen Stoppels1-10/+39
2023-08-07CI: remove redundant sections (#38514)kwryankrattiger9-716/+70
Refactor gitlab ci configs so that mac and cray jobs can reuse as much higher level configuration as possible. * CI: remove redundant sections * CI: Include base linux CI configs in cray stacks Relocation and runner mapping is consistent between cray and linux runners. * Export user cache path in before script * CI: add GPG root for mac runners * Disable user configs Metal runners share a ~ directory * Disable user config and add configs in activate env
2023-08-07celeritas: new version 0.3.1 (#39288)Seth R. Johnson1-2/+4
2023-08-07Extract prefix locks and failure markers from Database (#39024)Massimiliano Culpo12-383/+357
This PR extracts two responsibilities from the `Database` class: 1. Managing locks for prefixes during an installation 2. Marking installation failures and pushes them into their own class (`SpecLocker` and `FailureMarker`). These responsibilities are also pushed up into the `Store`, leaving to `Database` only the duty to manage `index.json` files. `SpecLocker` classes no longer share a global list of locks, but locks are per instance. Their identifier is simply `(dag hash, package name)`, and not the spec prefix path, to avoid circular dependencies across Store / Database / Spec.
2023-08-07Picklable HTTPError (#39285)Harmen Stoppels2-2/+36
2023-08-05Bugfix spack module files (#39282)Brian Van Essen2-0/+12
* Fixed the LD_LIBRARY_PATH to use the lib64 directory. * On AMD systems the llvm/lib directory is not properly put into the LD_LIBRARY_PATH. * Added both lib and lib64 paths for libfabric. * Split the prepend statements.
2023-08-05Add a more detailed HTTPError (#39187)Harmen Stoppels1-3/+26
2023-08-04py-pyqt6: add new package (#32696)Adam J. Stewart12-138/+189
2023-08-04acts: new versions 23.[3-5].0, 24.0.0, 25.0.[0-1], 26.0.0, 27.[0-1].0, ↵Wouter Deconinck2-2/+28
28.0.0 (#37055) * acts: new version 23.[3-5].0, 24.0.0 - https://github.com/acts-project/acts/compare/v23.2.1...v23.3.0 - https://github.com/acts-project/acts/compare/v23.3.0...v23.4.0 - https://github.com/acts-project/acts/compare/v23.4.0...v23.5.0 - https://github.com/acts-project/acts/compare/v23.5.0...v24.0.0 * acts: update dependencies * acts: new versions 25.0.0, 25.0.1, 26.0.0, 27.0.0 * [@spackbot] updating style on behalf of wdconinc * acts: rm duplicate edm4hep variant definition * acts: depends_on podio 0.6: open ended range * acts: new version 27.1.0 * acts: depends_on mlpack when +mlpack * acts: new version 28.0.0 * actsvg: new version 0.4.35 * acts: depends_on actsvg@0.4.35: when @28: --------- Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
2023-08-04FIX libfabric module file (#39271)Brian Van Essen2-2/+12
* Add support to export the LD_LIBRARY_PATH for the libfabric package and subsequent module files. Fix the AWS OFI RCCL package so that it prepends the enviornment variables. * Fixed comment
2023-08-04[py-smartredis] New Package (#39098)Matt Drozt3-0/+247
* Create a spack package for smartredis python client * make py-SR deps versions match docs * tie SR v0.4.0 to redis-plus-plus v1.3.5 * looser extension lib deps for concretization * Apply suggestions from code review Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Address reviewer feedback --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-08-04Replace code that captures a recipes generator statement in the cached (#39192)Brian Van Essen1-0/+11
cmake build.
2023-08-04Add MET, METplus packages (#39238)Alex Richert5-0/+277
* Add metplus package * Add met package * add metplus develop version * copyright year var/spack/repos/builtin/packages/met/package.py * copyright year var/spack/repos/builtin/packages/metplus/package.py --------- Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2023-08-04 julia: add v1.9.2 (#39269)Davide1-0/+1
2023-08-03salmon: update version (#39202)pabloaledo2-0/+20
* salmon: update version --------- Signed-off-by: Pablo <pablo.aledo@seqera.io>
2023-08-03adios2: add 2.9.1 release (#39257)Vicente Bolea1-2/+3
2023-08-03openssl: Update to 3.1.2, 3.0.10, 1.1.1v (#39216)Erik Schnetter1-3/+18
2023-08-03Revert checksum verification CI test (#39259)Tamara Dahlgren1-18/+1
2023-08-03sowing: add version 1.1.26-p8 (#39258)Satish Balay1-1/+4
* sowing: add version 1.1.26-p8 * add in maintainer
2023-08-03Automated deployment to update package flux-core 2023-08-03 (#39237)Vanessasaurus1-0/+1
Co-authored-by: github-actions <github-actions@users.noreply.github.com>
2023-08-03hpcviewer: add version 2023.07 (#39236)Mark W. Krentel1-1/+6
Add version 2023.07, adjust the line for deprecated (anything using java 8 is now deprecated).
2023-08-03patchelf@0.18.0 breaks intel compiler libraries (#39253)Stephen Sachs1-1/+2
2023-08-03kafka: new versions (#39249)Matthieu Dorier1-0/+9
* kafka: version 2.13-3.5.0 * kafka: version 2.13-3.5.1 and 2.13-3.4.1
2023-08-03librdkafka: version 2.2.0 (#39250)Matthieu Dorier1-0/+1
2023-08-03Add checksum CI test and verify with new versions for glab and gh (#39181)Alec Scott3-1/+21
2023-08-03gftl-shared: new version 1.6.1 (#39217)Matthew Thompson1-0/+1
This PR adds gFTL-shared v1.6.1
2023-08-03mapl: add package (#39227)Matthew Thompson4-0/+279
* mapl: add package * Fix style
2023-08-03py-sphinx-rtd-theme: avoid concretizing 0.5 with Sphinx 7.0 (#39212)Seth R. Johnson1-1/+1
* py-sphinx-rtd-theme: avoid concretizing 0.5 with Sphinx 7.0 * Update var/spack/repos/builtin/packages/py-sphinx-rtd-theme/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-08-03Add pika 0.17.0 (#39221)Auriane R1-0/+1
2023-08-03pfunit: add versions 4.7.1, 4.7.2, 4.7.3 (#39218)Matthew Thompson1-0/+3
This adds the latest versions of pFUnit
2023-08-03vecgeom: new version 1.2.5 (#39211)Seth R. Johnson1-2/+11
* vecgeom: new version 1.2.5 * Mark previous versions as deprecated * [@spackbot] updating style on behalf of sethrj * vecgeom: fix 1.2.4 checksum for change to git describe
2023-08-03ucsc-bedgraphtobigwig: add package (#39208)pabloaledo1-0/+50
Signed-off-by: Pablo <pablo.aledo@seqera.io>
2023-08-03R: fix build on macOS arm64 (#39228)Adam J. Stewart1-0/+2
2023-08-03repo cache: use -inf default instead of 0 (#39214)Harmen Stoppels2-28/+24
FastPackageChecker.modified_since should use a default number < 0 When the repo cache does not exist, Spack uses mtime 0. This causes the repo cache not to be generated when the repo has mtime 0. Some popular package managers such as spack use 0 mtime normalization for reproducible tarballs. So when installing spack with spack from a buildcache, the repo cache doesn't generate Also add some typehints
2023-08-03ucsc-bedclip: add package (#39209)pabloaledo3-0/+81
Signed-off-by: Pablo <pablo.aledo@seqera.io>
2023-08-03py-kornia: add v0.7.0 (#39233)Adam J. Stewart1-0/+2
2023-08-03Buildcache commands cleanup, again... (#39203)Harmen Stoppels6-158/+114
* Inform mypy that tty.die is noreturn * avoid temporary allocation in env * update spack buildcache save-specfile * fix spack buildcache check/download/get-buildcache-name - ensure that required args and mutually exclusive ones are marked as such in argparse for better error messages - deprecate --spec-file everywhere - use disambiguate for better error messages
2023-08-02nextdenovo: new package @2.5.2 (and py-paralleltask) (#39139)George Young2-0/+49
* py-paralleltask: new package @0.2.2 * adding hidden dependency * nextdenovo: new package @2.5.2 * style * Update var/spack/repos/builtin/packages/py-paralleltask/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-08-02py-melissa-core: add new versions and py-iterative-stats dependency (#38654)mschouler1-4/+13
* py-melissa-core: add new versions and py-iterative-stats dependency * Enhance dependency specification * Fix dependency specification * Fix comment alignment * Improve dependency specification style * Enhance dependencies * Fix mpi4py, py-cloudpickle and py-python-hostlist dependencies * Update var/spack/repos/builtin/packages/py-melissa-core/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-melissa-core/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-melissa-core/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Set develop version as preferred * Update var/spack/repos/builtin/packages/py-melissa-core/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Marc Schouler <marc.schouler@inria.fr> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-08-02py-libEnsemble: add v0.10.2 (#39074)Stephen Hudson1-2/+4
* libEnsemble: add v0.10.2 * Make setuptools build only dep * Update var/spack/repos/builtin/packages/py-libensemble/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-08-02Add qmake virtual provider (#38848)Adam J. Stewart4-1/+6
2023-08-02openmolcas: adding version 23.06 (#39195)snehring1-0/+1
2023-08-02bioconductor-dupradar, bioconductor-rsubread: add packages (#39206)pabloaledo2-0/+41
* bioconductor-dupradar, bioconductor-rsubread: add packages * [@spackbot] updating style on behalf of pabloaledo
2023-08-02tximeta: add package (#39207)pabloaledo1-0/+39
* tximeta: add package Signed-off-by: Pablo <pablo.aledo@seqera.io> * [@spackbot] updating style on behalf of pabloaledo --------- Signed-off-by: Pablo <pablo.aledo@seqera.io>
2023-08-02patchelf: 0.18 (#39215)Harmen Stoppels1-0/+1
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