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2023-12-19"spack diff": add ignore option for dependencies (#41711)Peter Scheibel8-27/+208
* add trim function to `Spec` and `--ignore` option to 'spack diff' Allows user to compare two specs while ignoring the sub-DAG of a particular dependency, e.g. spack diff --ignore=mpi --ignore=zlib trilinos/abcdef trilinos/fedcba to focus on differences closer to the root of the software stack
2023-12-19CI: Disable downloading artifacts from upstream jobs (#41432)kwryankrattiger2-0/+4
* CI: Disable downloading artifacts from upstream jobs * CI: Default .base-jobs are `when:manual`
2023-12-19environment_modifications_for_specs: do not mutate spec.prefix (#41737)Harmen Stoppels1-41/+31
Sometimes env variables computed in `setup_run_environment` depend on tests w.r.t. files in `spec.prefix`, but Spack temporarily projects `spec.prefix` to the view. This is problematic for two reasons: 1. Some packages iterate over `<prefix>/bin`: they expect only the current package's executables, but find all linked in the view, leading to false positives. 2. Some packages test for `os.path.islink(...)`, which is always true in a view `gcc` is an example that does both. This PR lets Spack compute the environment modifications using the original prefix, and projects to the view afterwards
2023-12-19Skip 'icc.patch' in var/spack/repos/builtin/packages/py-gevent/package.py ↵Dom Heinzeller1-1/+1
for py-gevent@23.7.0+ (#41568)
2023-12-19e4s: add julia (#41768)Harmen Stoppels1-0/+1
2023-12-19Add an audit to prevent virtual packages with variants specified (#41747)Massimiliano Culpo12-15/+108
Currently, a virtual spec is composed of just a name and a version. When a virtual spec contains other components, such as variants, Spack won't emit warnings or errors but will silently drop them - which is unexpected by users.
2023-12-19adios2: fix build failure in 2.7.1 (#41753)Ben Wibking2-0/+27
2023-12-19umpire: backport -fcompare-debug-second flag removal (#41506)Mikael Simberg1-0/+7
2023-12-19ffmpeg: mostly build fixes (#41050)Martin Aumüller1-2/+21
2023-12-19openblas: add patches to build with clang (#39138)Aiden Grossman3-0/+50
2023-12-19removing deprecated: recipes tower-agent and tower-cli, as nf- prefixed ↵Dr Marco Claudio De La Pierre2-109/+0
recipes available (#41576) Signed-off-by: Dr Marco Claudio De La Pierre <marco.delapierre@seqera.io>
2023-12-19lbann: relax the requirement on protobuf (#41591)Brian Van Essen1-1/+1
2023-12-19build(deps): bump black from 23.11.0 to 23.12.0 in /lib/spack/docs (#41615)dependabot[bot]1-1/+1
Bumps [black](https://github.com/psf/black) from 23.11.0 to 23.12.0. - [Release notes](https://github.com/psf/black/releases) - [Changelog](https://github.com/psf/black/blob/main/CHANGES.md) - [Commits](https://github.com/psf/black/compare/23.11.0...23.12.0) --- updated-dependencies: - dependency-name: black dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-12-19easi: specify better the impalajit dependency (#41637)Thomas-Ulrich1-2/+2
2023-12-19pcre: ensure consistency between autotools and cmake builds (#41644)Wouter Deconinck1-16/+30
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
2023-12-19legion: do not set HIP_PATH env variable (#41660)Richard Berger2-5/+4
* legion: do not set HIP_PATH env variable * flecsi: workaround Legion CMake for +rocm
2023-12-19openmpi: allow external libevent in general case (#41686)Howard Pritchard1-1/+2
add a internal-libevent variant to add an out. related to #41549 Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2023-12-19tau : v2.33.1 and later requires otf2 v3 (#41691)wspear1-1/+2
2023-12-19legion: inject correct mpicc to embedded GASnet slingshot11 config (#41701)Richard Berger1-0/+9
2023-12-19ufs-weather-model: add build dependency (#41724)Tom Payerle1-0/+1
2023-12-19PyTorch: update ecosystem (#41713)Adam J. Stewart4-0/+7
2023-12-19samtools: add v1.19 (#41634)James Beal3-0/+11
Co-authored-by: James Beal <jb23@sanger.ac.uk>
2023-12-19ut: add v2.0.0 and v2.0.1 (#41771)Mikael Simberg1-0/+2
2023-12-19xyce: remove CMake test for all compilers (#41679)Paul Kuberry2-17/+11
2023-12-19intel-mpi-benchmarks: add v2021.7, v2021.6, v2021.5, v2021.4 (#41730)Jack Morrison1-0/+4
2023-12-19creduce: fix build of `@develop` (#41258)Pramod Kumbhar1-0/+1
2023-12-19uthash: add new package (#41732)Christopher Christofi1-0/+20
2023-12-19acts: new versions 31.* (#41733)Wouter Deconinck1-0/+3
This adds three new versions in the 31.* series. Release notes of 31.0.0 at https://github.com/acts-project/acts/releases/tag/v31.0.0. No changes to the CMakeLists.txt files that need addressing in the package recipe. The only new feature I'm a bit concerned about is https://github.com/acts-project/acts/pull/2626, which replaces testing for C++20 concepts support by the feature-testing macro `__cpp_concepts`, which is also a C++20 feature. So technically we now should require `cxxstd=20` even though Acts itself still allows (and defaults to) 17. Judging by https://en.cppreference.com/w/cpp/compiler_support/20, the support for feature-testing macros was added very early by most compilers.
2023-12-19whizard: fix support for building with hepmc output (#41538)Thomas Madlener1-17/+21
2023-12-19build(deps): bump black in /.github/workflows/style (#41616)dependabot[bot]1-1/+1
Bumps [black](https://github.com/psf/black) from 23.11.0 to 23.12.0. - [Release notes](https://github.com/psf/black/releases) - [Changelog](https://github.com/psf/black/blob/main/CHANGES.md) - [Commits](https://github.com/psf/black/compare/23.11.0...23.12.0) --- updated-dependencies: - dependency-name: black dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-12-19flexiblas: explicitly set SYSCONFDIR (#41748)Wouter Deconinck1-0/+3
As of CMake 3.4, [GNUInstallDirs](https://cmake.org/cmake/help/latest/module/GNUInstallDirs.html) treats `SYSCONFDIR` differently for a prefix that starts with `/opt`, then "the SYSCONFDIR value etc becomes /etc/opt/...." In the case of flexiblas, that results in failing attempts to write files to a system directory. Since [flexiblas version 1](https://github.com/mpimd-csc/flexiblas/commit/0f2d2c76594ed27c9315f3736ff7d2727223620a#diff-1e7de1ae2d059d21e1dd75d5812d5a34b0222cef273b7c3a2af62eb747f9d20aR16), we can override SYSCONFDIR with our own defines.
2023-12-19rebayes: add v1.2.2 (#41749)snehring1-0/+5
2023-12-19kalign: add v3.4.0 (#41758)Christopher Christofi1-5/+15
Co-authored-by: Rocco Meli <r.meli@bluemail.ch>
2023-12-19`spack config get`/`blame`: with no args, show entire config Massimiliano Culpo4-42/+50
This PR changes the default behavior of `spack config get` and `spack config blame` to print a flattened version of the entire spack configuration, including any active environment, if the commands are invoked with no section arguments. The new behavior is used in Gitlab CI to help debug CI configuration, but it can also be useful when asking for more information in issues, or when simply debugging Spack.
2023-12-19julia: set compatibility with `suite-sparse` (#41754)Mosè Giordano1-0/+1
2023-12-19gnina: add version 1.1 (#41762)Rocco Meli1-0/+1
2023-12-19tnftp: new package (#41763)Arne Becker1-0/+22
2023-12-19libxml2: correct improper use of base builder meta (#41760)John W. Parent1-4/+3
2023-12-18environment modifications for externals (#41723)Greg Becker4-1/+60
* allow externals to configure environment modifications * docs for external env modification --------- Co-authored-by: becker33 <becker33@users.noreply.github.com>
2023-12-18build(deps): bump docker/metadata-action from 5.3.0 to 5.4.0 (#41764)dependabot[bot]1-1/+1
Bumps [docker/metadata-action](https://github.com/docker/metadata-action) from 5.3.0 to 5.4.0. - [Release notes](https://github.com/docker/metadata-action/releases) - [Commits](https://github.com/docker/metadata-action/compare/31cebacef4805868f9ce9a0cb03ee36c32df2ac4...9dc751fe249ad99385a2583ee0d084c400eee04e) --- updated-dependencies: - dependency-name: docker/metadata-action dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-12-18podio: Add latest tag 0.17.4 (#41735)Thomas Madlener1-0/+1
2023-12-18build(deps): bump isort in /.github/workflows/style (#41650)dependabot[bot]1-1/+1
Bumps [isort](https://github.com/pycqa/isort) from 5.12.0 to 5.13.2. - [Release notes](https://github.com/pycqa/isort/releases) - [Changelog](https://github.com/PyCQA/isort/blob/main/CHANGELOG.md) - [Commits](https://github.com/pycqa/isort/compare/5.12.0...5.13.2) --- updated-dependencies: - dependency-name: isort dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-12-18build(deps): bump isort from 5.12.0 to 5.13.2 in /lib/spack/docs (#41651)dependabot[bot]1-1/+1
Bumps [isort](https://github.com/pycqa/isort) from 5.12.0 to 5.13.2. - [Release notes](https://github.com/pycqa/isort/releases) - [Changelog](https://github.com/PyCQA/isort/blob/main/CHANGELOG.md) - [Commits](https://github.com/pycqa/isort/compare/5.12.0...5.13.2) --- updated-dependencies: - dependency-name: isort dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-12-18spack.config: cleanup and add type hints (#41741)Massimiliano Culpo4-164/+177
2023-12-18gcc: fix run environment variables not being exported in environments (#41729)Michael Kuhn1-1/+3
Since views use symlinks, all compiler binaries were skipped in this case. Instead, only skip them if their target does not exist.
2023-12-18pika-algorithms: Add upper bound for pika version (#41736)Mikael Simberg1-5/+5
2023-12-18glib: add v2.78.3 (#41697)Michael Kuhn1-0/+1
2023-12-18asp.py: remove "CLI" reference (#41718)Harmen Stoppels2-6/+6
Can also be an environment root, or programatically `Spec("x").concretized()`.
2023-12-18`spack develop`: convert to config (#35273)Peter Scheibel12-211/+368
Convert the 'develop' section of an environment to a dedicated configuration section. This means for example that instead of having to define `develop` specs in the `spack.yaml`, the environment can `include:` another `develop.yaml` configuration which specifies which specs should be developed in the environment. This change is not expected to be disruptive given that existing environment `spack.yaml` files will conform to the new schema. (Update 11/28/2023) I have implemented the `develop`/`undevelop` commands in terms of more-generic modification functions added to the `config` module: `change_or_add` and `update_all`. It is assumed that the semantics added here (described in 11/18 update) would be desirable to extend to other config update actions (e.g. adding compilers, changing package requirements, adding mirrors). (Update 11/18/2023) I have updated this such that `spack develop`, and `spack undevelop` to potentially modify all writable scopes, like https://github.com/spack/spack/pull/41147. https://github.com/spack/spack/pull/35307 will be useful for modifying included scopes, but generally speaking specifying a `--scope` will not be required for `spack develop`: `spack develop` will add new develop specs to whatever scope already has develop specs defined, or to the highest-priority writable scope (which should be the env scope). TODOs: - [x] If you `spack undevelop` a package which is mentioned at multiple layers of configuration, then currently this would only modify one of them. That's not technically a new issue (has always existed for configuration modification), but may be confusing to users when presented via an interface other than `spack config set` - [x] Need to add (or confirm) the ability to modify individual config files by providing a path (rather than using a scope identifier as a key to retrieve associated config). - [x] `spack develop` adds new develop specs to the scope that defines them (potentially skipping higher priority scopes to e.g. augment included scope files) --------- Co-authored-by: scheibelp <scheibelp@users.noreply.github.com> Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
2023-12-17py-plum-dispatch: add new package (#41536)Christopher Christofi1-0/+23
* py-plum-dispatch: add new package * Update var/spack/repos/builtin/packages/py-plum-dispatch/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> --------- Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
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