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2022-10-25New packages: mlst, any2fasta, perl-carp, perl-class-method-modifiers, ↵Luke Diorio-Toth7-0/+157
perl-role-tiny, perl-moo, perl-sub-quote (#33274) * added mlst and deps * added install() to any2fasta * added script dependencies, builds OK * fixed style * Update var/spack/repos/builtin/packages/any2fasta/package.py Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-10-25udunits: Update download URL (#32390)Rémi Lacroix1-4/+19
* udunits: Update download URL * udunits: Deprecate older versions Unidata now only provides the latest version of each X.Y branch. Older 2.2 versions have been deprecated accordingly but are still available in the build cache. Co-authored-by: RemiLacroix-IDRIS <RemiLacroix-IDRIS@users.noreply.github.com> Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-10-25Update wgrib2 from JCSDA/NOAA-EMC fork (#32857)Dom Heinzeller1-14/+189
* Update wgrib2 from JCSDA/NOAA-EMC fork * var/spack/repos/builtin/packages/wgrib2/package.py: fix typo in comment, add conflict for variants netcdf3, netcdf4 * wget hdf5/netcdf4 internal dependencies for wgrib2 * Black-format var/spack/repos/builtin/packages/wgrib2/package.py * More format changes in var/spack/repos/builtin/packages/wgrib2/package.py
2022-10-25Gmsh: Fix CGNS support for version up to 4.7.1 (#33508)Rémi Lacroix1-0/+1
Gmsh started supporting the "scoping" option of CGNS in version 4.8.0.
2022-10-25cdo: add new release 2.1.0 (#33303)Brian Spilner1-0/+5
2022-10-24fix problems with missing rocm dependencies (#33381)Miroslav Stoyanov1-1/+37
2022-10-24Add py-myst-parser & update py-mdit-py-plugins and py-sphinxcontrib-mermaid ↵Zach Jibben4-4/+64
(#33427) * Update py-sphinxcontrib-mermaid * Add py-myst-parser * Fix py-mdit-py-plugins and py-myst-parser dependencies * Add py-exhale package * Update var/spack/repos/builtin/packages/py-mdit-py-plugins/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-myst-parser/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-myst-parser/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-myst-parser/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update py-exhale and py-myst-parser dependencies * Add @svenevs as py-exhale maintainer * Update var/spack/repos/builtin/packages/py-mdit-py-plugins/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-10-24Add filename to text_to_relocate only if it needs to be relocated (#31074)iarspider1-0/+27
Scan the text files for relocatable prefixes *before* creating a tarball, to reduce the amount of work to be done during install from binary cache. Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2022-10-24cppcheck: add version 2.9 (#33491)Jon Rood1-0/+1
2022-10-24update fms package for v2022.04 (#33484)Ryan Mulhall1-1/+2
Co-authored-by: rem1776 <Ryan.Mulhall@noaa.gov>
2022-10-24chai +rocm: use hipcc as CMAKE_CXX_COMPILER (#33479)eugeneswalker1-0/+7
2022-10-24py-drep and ANIcalculator: new packages (#33467)Luke Diorio-Toth2-0/+79
* py-drep: new package * fixed file extension * added darwin conflict * py-checkm-genome and py-pysam: bumped version and updated deps (#10) added checkm and pysam deps * added dep documentation and fixed style * changed checkm and pysam back to dev version for upstreaming * added url and perl run dep * fixed style
2022-10-23py-gcovr: add 5.2 (#33476)Michael Kuhn1-2/+7
2022-10-23ca-certificates-mozilla: add 2022-10-11 (#33331)Michael Kuhn1-0/+5
2022-10-23helics: Add version 3.3.1 (#33475)HELICS-bot1-0/+1
2022-10-23sqlite: add 3.39.4 (#33339)Michael Kuhn1-0/+1
2022-10-23gettext: add 0.21.1 (#33333)Michael Kuhn1-0/+3
2022-10-23util-linux, util-linux-uuid: add 2.38.1 (#33342)Michael Kuhn2-1/+3
2022-10-22python: add 3.10.8, 3.9.15, 3.8.15, 3.7.15 (#33340)Michael Kuhn1-2/+6
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2022-10-22zlib: add 1.2.13 (#33337)Michael Kuhn1-1/+6
2022-10-22openblas@0.3.21: fix misdetection of gfortran on cray (#33444)eugeneswalker2-0/+57
2022-10-22netlib-scalapack %cce: add -hnopattern to fflags (#33422)eugeneswalker1-0/+7
2022-10-22acts: new versions (#32969)Wouter Deconinck3-20/+94
* acts: new versions In the 20.x release line, these are the changes, https://github.com/acts-project/acts/compare/v20.0.0...v20.2.0 - `option(ACTS_SETUP_ACTSVG "Build ActSVG display plugin" OFF)` introduced in v20.1.0 - `option(ACTS_USE_SYSTEM_ACTSVG "Use the ActSVG system library" OFF)` introduced in v20.1.0 - `option(ACTS_BUILD_PLUGIN_ACTSVG "Build SVG display plugin" OFF)` introduced in v20.1.0 - `option(ACTS_USE_EXAMPLES_TBB "Use Threading Building Blocks library in examples" ON)` introduced in v20.1.0 - `option(ACTS_EXATRKX_ENABLE_ONNX "Build the Onnx backend for the exatrkx plugin" OFF)` introduced in v20.2.0 - `option(ACTS_EXATRKX_ENABLE_TORCH "Build the torchscript backend for the exatrkx plugin" ON)` introduced in v20.2.0 In the 19.x release line, these are the changes: https://github.com/acts-project/acts/compare/v19.7.0...v19.9.0 - `option(ACTS_USE_EXAMPLES_TBB "Use Threading Building Blocks library in examples" ON)` introduced in v19.8.0 The new build options have not been implemented in this commit but will be implemented next. * acts: new variant svg * actsvg: new package * actsvg: style fixes * acts: new versions 20.3.0 and 19.10.0 * astsvg: depends_on boost googletest * actsvg: new version 0.4.26 (and style fix) Includes fix to build issue when +examples, https://github.com/acts-project/actsvg/pull/23 * acts: new variant tbb when +examples @19.8:19 @20.1: * acts: set ACTS_USE_EXAMPLES_TBB * acts: no need for ACTS_SETUP_ACTSVG * acts: move tbb variant to examples block * acts: ACTS_USE_SYSTEM_ACTSDD4HEP removed in 20.3 * acts: use new ACTS_USE_SYSTEM_LIBS * acts-dd4hep: new version 1.0.1, maintainer handle fixed * acts: simplify variant tbb condition
2022-10-21arborx: add new release 1.3 (#33402)Andrey Prokopenko1-2/+15
* arborx: add new release 1.3 * [@spackbot] updating style on behalf of aprokop
2022-10-21honor global spack flags (#33470)Chris White1-0/+17
2022-10-21raja@0.14.0 +rocm: add -std=c++14 to HIP_HIPCC_FLAGS (#33456)eugeneswalker1-3/+5
2022-10-21Update maintainers for NOAA/EMC-maintained libraries (#33469)Alex Richert26-26/+121
* Update maintainers for NOAA/EMC-maintained libraries * Fix line lengths * Fix line length for gptl
2022-10-21openfast: Fix package file (#33454)Jon Rood1-23/+25
* Fix openfast package file. * Fix openfast package file. * Fix typo. * [@spackbot] updating style on behalf of jrood-nrel Co-authored-by: jrood-nrel <jrood-nrel@users.noreply.github.com>
2022-10-21py-instrain: added required + optional dependency (#33465)Luke Diorio-Toth1-0/+8
* added py-instrain dependencies * fixed style * removed coverm dep until I have a working coverm package * added dep documentation
2022-10-21updated python version requirements (#33466)Luke Diorio-Toth1-4/+7
* updated python version requirements * updated sha256 Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-10-21py-checkm-genome and py-pysam: bumped version and updated deps (#33449)Luke Diorio-Toth2-7/+16
* py-checkm-genome and py-pysam: bumped version and updated deps * updated setuptools dep type Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-10-21axom@0.7.0: require cmake@3.21: (#33450)eugeneswalker1-2/+2
* axom@0.7.0: require cmake@3.21: * Update var/spack/repos/builtin/packages/axom/package.py Co-authored-by: Chris White <white238@llnl.gov> Co-authored-by: Chris White <white238@llnl.gov>
2022-10-21git: new versions and deprecations (#33408)Harmen Stoppels1-3/+35
2022-10-21intel-tbb: add in versions 2021.7.0, 2021.6.0 (#33445)Satish Balay1-6/+3
2021.7.0 fixes build on linux-ubuntu20.04-skylake / oneapi@2022.2.0
2022-10-20replaced package shortbred with py-shortbred (#33404)Luke Diorio-Toth2-1/+30
* fixed version numbers to python 2 and old biopython * changed shortbred pacakge to pypi, removed python 2 version * added package description * re-added shortbred package with depreciated flag * fixed style and removed unnecessary python dep (it can't build with python 2 anyway) * removed whitespace and readded the python2.7.9+ dep * fixed style
2022-10-20Add Boost 1.80.0 (#32879)Mikael Simberg2-2/+10
* Add Boost 1.80.0 * Add conflict for Boost 1.80.0 and dealii * Add conflict for Boost 1.80 and %oneapi
2022-10-20hiop: add v0.7.0 (#33441)eugeneswalker1-0/+1
* hiop: add v0.7.0 * Update var/spack/repos/builtin/packages/hiop/package.py Co-authored-by: Cameron Rutherford <cameron.rutherford@me.com> Co-authored-by: Cameron Rutherford <cameron.rutherford@me.com>
2022-10-20kokkos and kokkos-kernels: add new versions (#33301)Cody Balos2-0/+5
* kokkos: add version 3.7.00 * kokkos-kernels: add versions 3.6.01 and 3.7.00 * add correct kokkos dependence
2022-10-20butterflypack: add version 2.2.2 and openmp variant (#33416)Satish Balay1-0/+6
- add conflcit with gcc < 7 - fails with MacOS sed - so add in (gnu) sed as build dependency
2022-10-20Update OpenFAST package file (#33438)Jon Rood1-17/+24
* Update OpenFAST package file. * Add comment.
2022-10-20ophidia-primitives: new package at v1.7 (#33434)SoniaScard1-0/+41
* ophidia-primitives: new package at v1.7 * ophidia-primitives: Add mantainers * ophidia-primitives: Fix style Co-authored-by: SoniaScard <SoniaScard@users.noreply.github.com>
2022-10-20py-rasterio: add v1.3.3 (#33428)Adam J. Stewart1-0/+1
2022-10-20spdlog: Add version 1.10.0 (#33431)Rémi Lacroix1-0/+1
2022-10-20Change scalapack to test-only dependency (#33433)G-Ragghianti1-3/+5
2022-10-20arpack-ng %cce: add -hnopattern to fflags (#33424)eugeneswalker1-0/+5
2022-10-20py-bakta: new package (#33417)Luke Diorio-Toth1-0/+36
2022-10-19singularity-eos: new version 1.6.2 (#33415)Richard Berger1-0/+1
2022-10-19Simplify TIOGA package (#33396)Jon Rood1-26/+5
* Update TIOGA package. * Add comment. * Remove cuda variant and MPI_ROOT. * Style.
2022-10-19py-pandas: add v1.5.1 (#33412)Adam J. Stewart1-0/+1
2022-10-19mpich: enable building when @3.4~cuda (#33325)Sergey Kosukhin1-1/+1
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