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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.
2022-10-21Relocation should take hardlinks into account (#33460)Harmen Stoppels7-62/+190
Currently `relocate_text` and `relocate_text_bin` are unsafe in the sense that they run in parallel, and lead to races when modifying different items pointing to the same inode. This leads to the issue observed in #33453. This PR: 1. Renames those functions to `unsafe_*` so people are aware 2. Adds logic to deal with hardlinks in current binary packages 3. Adds logic to deal with hardlinks when creating new binary tarballs, so the install side doesn't have to de-dupe hardlinks. 4. Adds a test for 3 The assumption is that all our relocation logic preserves inodes. That is, we should never copy a file, modify it, and then move it back. I quickly verified, and its seems like this is true for (binary) text relocation, as well as rpath patching in patchelf (even when the file grows) and mach-o fixes.
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
2022-10-21gitlab: when_possible -> false (#33443)Harmen Stoppels2-2/+2
`reuse` and `when_possible` concretization broke the invariant that `spec[pkg_name]` has unique keys. This invariant is relied on in tons of places, such as when setting up the build environment. When using `when_possible` concretization, one may end up with two or more `perl`s or `python`s among the transitive deps of a spec, because concretization does not consider build-only deps of reusable specs. Until the code base is fixed not to rely on this broken property of `__getitem__`, we should disable reuse in CI.
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
2022-10-21Remove "spack buildcache copy" in v0.19.0 (#33437)Massimiliano Culpo2-91/+1
2022-10-20e4s ci: add raja +rocm (#32505)eugeneswalker1-1/+1
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>
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