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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>
2022-10-25binary_distribution: compress level 9 -> 6 (#33513)Harmen Stoppels1-1/+5
Use the same compression level as `gzip` (6) instead of what Python uses (9). The LLVM tarball takes 4m instead of 12m to create, and is <1% larger. That's not worth the wait...
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
2022-10-25depfile: resurrect lost touch (#33504)Harmen Stoppels1-0/+3
2022-10-25feature: Add -x|--explicit option to 'spack test run' (#32910)Tamara Dahlgren3-7/+21
2022-10-25BinaryCacheIndex: track update failures with cooldown (#33509)Jonathon Anderson1-6/+12
#32137 added an option to update() a BinaryCacheIndex with a cooldown: repeated attempts within this cooldown would not actually retry. However, the cooldown was not properly tracked for failures (which is common when the mirror does not store any binaries and therefore has no index.json). This commit ensures that update(..., with_cooldown=True) will also skip the update even if a failure has occurred within the cooldown period.
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.
2022-10-25spec.py: prefer transitive link and direct build/run/test deps (#33498)Harmen Stoppels2-2/+48
Due to reuse concretization, we may generate DAGs with two occurrences of the same package corresponding to distinct specs. This happens when build dependencies are reused, since their dependencies are ignored in concretization. This caused a regression, for example: `spec['openssl']` would take the 'openssl' of the build dep `cmake`, instead of the direct `openssl` dependency, simply because the edge to `cmake` was traversed first and we do depth first traversal. One solution that was discussed is to limit `spec[name]` to just direct deps, or direct deps + transitive link deps, but this is too breaking. Instead, this PR simply prioritizes transitive link and direct build/run/test deps, and then falls back to a full DAG traversal. So, it's just about order of iteration.
2022-10-25Update Spack Dockerfiles (#33500)Massimiliano Culpo3-3/+2
* Use spack bootstrap now in containers * Fix wrong path glob expression
2022-10-25Make CI on Windows fail fast (#33502)Massimiliano Culpo1-2/+2
2022-10-25Remove recursive symbolic link in lib/spack/docs from git repository (#33483)Massimiliano Culpo6-16/+3
Delete code removing the symlink during CI
2022-10-25Improve legibility of Gitlab CI (#33482)Harmen Stoppels19-21/+21
Use --backtrace in ci instead of --debug to reduce verbosity and don't show log on error, since log is already printed
2022-10-25CI: speed-up tests by dropping coverage on Python 2.7 (#33497)Massimiliano Culpo1-6/+6
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>
2022-10-24e4s ci: use an appropriate name for cdash build group name (#33494)eugeneswalker1-1/+1
2022-10-24Add filename to text_to_relocate only if it needs to be relocated (#31074)iarspider5-8/+81
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>
2022-10-24redact line numbers from grouped exception message (#33485)Danny McClanahan1-4/+8
2022-10-24e4s ci: add chai +rocm (#32506)eugeneswalker1-1/+3
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
2022-10-24locks: improved errors (#33477)Harmen Stoppels6-12/+59
Instead of showing ``` ==> Error: Timed out waiting for a write lock. ``` show ``` ==> Error: Timed out waiting for a write lock after 1.200ms and 4 attempts on file: /some/file ``` s.t. we actually get to see where acquiring a lock failed even when not running in debug mode. And use pretty time units everywhere, so we don't get 1.45e-9 seconds but 1.450ns etc.
2022-10-23backtraces with --backtrace (#33478)Harmen Stoppels2-2/+10
* backtraces without --debug Currently `--debug` is too verbose and not-`--debug` gives to little context about where exceptions are coming from. So, instead, it'd be nice to have `spack --backtrace` and `SPACK_BACKTRACE=1` as methods to get something inbetween: no verbose debug messages, but always a full backtrace. This is useful for CI, where we don't want to drown in debug messages when installing deps, but we do want to get details where something goes wrong if it goes wrong. * completion
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
2022-10-22Don't install xdist in CI on Python 2.7 (#33474)Massimiliano Culpo1-1/+6
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
2022-10-22Remove x86_64_v4 target from AHUG and ISC stacks (#33464)Zack Galbreath2-3/+0
2022-10-22stop building binaries for the 1% (#33463)Harmen Stoppels3-3/+3
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>
2022-10-21gitlab: Retry protected publish jobs in certain cases (#32496)Scott Wittenburg1-0/+3
When we lose a running pod (possibly loss of spot instance) or encounter some other infrastructure-related failure of this job, we need to retry it. This retries the job the maximum number of times in those cases.
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