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2023-09-18Fix several build errors for hdf-eos2 (not only but in particular on macOS ↵Dom Heinzeller1-2/+25
w/ apple-clang) (#39877) Fix permissions for configure file in var/spack/repos/builtin/packages/hdf-eos2/package.py, fix dependencies to match what hdf provides, update compiler flags for apple-clang
2023-09-18py-types-typed-ast: add 1.5.8.7 (#40047)Manuela Kuhn1-0/+1
2023-09-18py-types-urllib3: add 1.26.25.14 (#40048)Manuela Kuhn1-1/+3
* py-types-urllib3: add 1.26.25.14 * Fix style
2023-09-18cpat: new package @3.0.4 (#40022)George Young1-0/+24
* cpat: new package @3.0.4 * Update package.py --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-09-18py-types-python-dateutil: add 2.8.19.14 (#40038)Manuela Kuhn1-1/+1
2023-09-18py-types-requests: add 2.31.0.2 (#40039)Manuela Kuhn1-2/+3
2023-09-18py-types-setuptools: add 68.2.0.0 (#40040)Manuela Kuhn1-0/+1
2023-09-18build(deps): bump docker/login-action from 2.2.0 to 3.0.0 (#39966)dependabot[bot]1-2/+2
Bumps [docker/login-action](https://github.com/docker/login-action) from 2.2.0 to 3.0.0. - [Release notes](https://github.com/docker/login-action/releases) - [Commits](https://github.com/docker/login-action/compare/465a07811f14bebb1938fbed4728c6a1ff8901fc...343f7c4344506bcbf9b4de18042ae17996df046d) --- updated-dependencies: - dependency-name: docker/login-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-09-18build(deps): bump docker/setup-qemu-action from 2.2.0 to 3.0.0 (#39968)dependabot[bot]1-1/+1
Bumps [docker/setup-qemu-action](https://github.com/docker/setup-qemu-action) from 2.2.0 to 3.0.0. - [Release notes](https://github.com/docker/setup-qemu-action/releases) - [Commits](https://github.com/docker/setup-qemu-action/compare/2b82ce82d56a2a04d2637cd93a637ae1b359c0a7...68827325e0b33c7199eb31dd4e31fbe9023e06e3) --- updated-dependencies: - dependency-name: docker/setup-qemu-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-09-18build(deps): bump docker/build-push-action from 4.2.1 to 5.0.0 (#39969)dependabot[bot]1-1/+1
Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 4.2.1 to 5.0.0. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](https://github.com/docker/build-push-action/compare/0a97817b6ade9f46837855d676c4cca3a2471fc9...0565240e2d4ab88bba5387d719585280857ece09) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-09-18py-werkzeug: Add version 0.12.2 required by py-graphene-tornado @2.6.1 (#39984)Lydéric Debusschère1-0/+1
2023-09-18Enabled building GCC 13.1 on darwin/aarch64. (#38667)Ben Cowan1-5/+15
2023-09-18python: Don't prefer 3.10 (#40036)Juan Miguel Carceller5-9/+8
2023-09-18[add] py-ldap3: new recipe, required by py-metomi-rose (#39982)Lydéric Debusschère1-0/+20
2023-09-18py-traits: add 6.4.2 (#39976)Manuela Kuhn1-2/+1
2023-09-18py-trove-classifiers: add 2023.8.7 (#39977)Manuela Kuhn1-0/+1
2023-09-18py-rseqc: add 5.0.1 (#39953)George Young1-2/+4
* py-rseqec: add 5.0.1 * Update package.py * style ... --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-09-18[chore] py-aniso8601: Add version 7.0.0 (#39808)Lydéric Debusschère1-0/+1
* [chore] py-aniso8601: Add version 3.0.2 required by py-graphene * py-aniso8601: Add version 7.0.0 and constraints on python version * py-aniso8601: fix style * [fix] py-aniso8601: remove version 3.0.2 which depends on removed version of python; set the minimal version of python to 3.7 * py-aniso8601: remove version constraint on python
2023-09-18Nextflow: add 22.04.3 (#40034)Diego Alvarez S1-0/+5
2023-09-18chexmix: new package (#38441)George Young2-0/+52
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-09-18checksum: use FIXME instead of FIX ME when adding versions (#40050)Michael Kuhn1-1/+1
The former is highlighted by editors, while the latter is not.
2023-09-18coin3d: apply upstream patches to fix build on Centos 8 (#39839)Martin Aumüller1-0/+18
fixes undefined references to dlerror, dlopen, dlsym, dlclose and XDefaultScreenOfDisplay, XScreenNumberOfScreen, XCreatePixmap, XFree, XFreePixmap, XCloseDisplay, XOpenDisplay
2023-09-18Julia: Fix sha256 for some LLVM patches (#40041)Rémi Lacroix1-3/+3
2023-09-15grass: Update spec for gdal dependency (#38396)Joscha Legewie1-1/+2
2023-09-15CI: add spec to job vars (#39905)Caetano Melone1-0/+5
* CI: add details about built spec to ci job variables Co-authored-by: Alec Scott <alec@bcs.sh> Co-authored-by: Alec Scott <hi@alecbcs.com>
2023-09-15gitlab ci: submit the correct audience for protected publish jobs (#40046)Scott Wittenburg1-1/+1
2023-09-15Windows RPATHing: fix symlink error (#39933)John W. Parent2-23/+38
With 349ba83, you cannot symlink() if the link already exists. Update the simulated RPATHing logic on Windows to account for that.
2023-09-15linux-headers: drop rsync dep, add new version (#39867)Harmen Stoppels1-1/+12
2023-09-15update sha256 after new tarball uploads (#40030)David Gardner1-1/+1
2023-09-15Group primitive url/path handling functions together (#40028)Massimiliano Culpo21-888/+903
2023-09-15Sandia OpenSHMEM: Update to include version 1.5.2 (#40025)Jack Morrison1-0/+1
2023-09-15build(deps): bump sphinx from 7.2.5 to 7.2.6 in /lib/spack/docs (#40029)dependabot[bot]1-1/+1
Bumps [sphinx](https://github.com/sphinx-doc/sphinx) from 7.2.5 to 7.2.6. - [Release notes](https://github.com/sphinx-doc/sphinx/releases) - [Changelog](https://github.com/sphinx-doc/sphinx/blob/master/CHANGES.rst) - [Commits](https://github.com/sphinx-doc/sphinx/compare/v7.2.5...v7.2.6) --- updated-dependencies: - dependency-name: sphinx dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-09-14Add shared and pic variants to libxml2 (#38094)Alex Richert1-0/+16
2023-09-14Add Scine QCMaquis recipe to builtin packages (#39709)Adam Grofe1-0/+62
* Add Scine QCMaquis recipe to builtin packages * Format scine-qcmaquis recipe using black * Remove import os from scine-qcmaquis recipe * Reduce length of symmetries line in scine-qcmaquis * Add myself as a maintainer of the scine-qcmaquis recipe * Update Scine-QCMaquis recipe following the review PR URL: https://github.com/spack/spack/pull/39709 Changes: - Updated Symmetries variant to us multi feature - Added dependency to boost+chrono since it was undocumented - Use define_from_variant to setup CMake args - Make version 3.1.2 be preferred since 3.1.3 build is broken * Change build_tests boolean condition --------- Co-authored-by: Adam Grofe <adamgrofe@microsoft.com>
2023-09-14gitlab ci: Put Cray binaries in public mirrors (#39938)Scott Wittenburg3-34/+7
2023-09-14meme: add 5.5.4, correct dependencies (#40014)George Young1-21/+24
* meme: add 5.5.4, correct dependencies * variant renaming --------- Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-09-14gffread: new package @0.12.7 (#40015)George Young1-0/+23
Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
2023-09-14Set # of ninja procs to 'make_jobs' for scipy (#293) (#38831)Alex Richert1-0/+1
2023-09-14Add pic option & maintainer to lz4 (#38095)Alex Richert1-0/+8
Co-authored-by: Greg Becker <becker33@llnl.gov>
2023-09-14Ensure PythonExtension is consistent when finding externals (#40012)Massimiliano Culpo1-41/+41
PythonExtension is a base class for PythonPackage, and is meant to be used for any package that is a Python extension but is not built using "python_pip". The "update_external_dependency" method in the base class calls another method that is defined in the derived class. Push "get_external_python_for_prefix" up in the hierarchy to make method calls consistent.
2023-09-14Add OIDC tokens to gitlab-ci jobs (#39813)Dan LaManna2-0/+23
* Add OIDC tokens to gitlab-ci jobs This should allow us to start issuing just-in-time generated credentials for CI jobs that need to modify binary mirrors. The "aud" claim of the token describes what the token is allowed to do. The claim is verified against a set of rules on the IAM role using signed information from GitLab. See spack-infrastructure for the claim verification logic. --------- Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
2023-09-14Add efficient `deptype` flag and `spack.deptypes` module (#39472)Harmen Stoppels34-457/+531
This commit replaces the internal representation of deptypes with `int`, which is more compact and faster to operate with. Double loops like: ``` any(x in ys for x in xs) ``` are replaced by constant operations bool(xs & ys), where xs and ys are dependency types. Global constants are exposed for convenience in `spack.deptypes`
2023-09-14data-vis-sdk: make llvm~libomptarget the default (#40007)Massimiliano Culpo1-1/+1
Currently the configuration of the pipeline is such that there are multiple "optimal" solutions. This is due to the pipeline making ~lld the default for LLVM, but leaving +libomptarget from package.py Since LLVM recipe has a: conflicts("~lld", "+libomptarget") clingo is forced to change one of the two defaults, and the penalty for doing so is the same for each. Hence, it is random whether we'll get +libomptarget+lld or ~libomptarget~lld. This fixes it by changing also the default for libomptarget.
2023-09-13Support static case for find_libraries() in xz (#38100)Alex Richert1-1/+8
* Update xz * add maintainer to xz * [@spackbot] updating style on behalf of AlexanderRichert-NOAA
2023-09-13Add pic variant for libpng (#37964)Alex Richert1-0/+2
2023-09-13Allow git to compile against static curl (#37960)Alex Richert1-1/+8
2023-09-13add trompeloeil package (#39944)Billae1-0/+20
* add trompeloeil package * remove maintainer as he wish not to be * fix style
2023-09-13Add static-only option for udunits (#38099)Alex Richert1-0/+7
* Add static-only option for udunits * add maintainer to udunits
2023-09-13Add libs property/find_libraries to libiconv (#37962)Alex Richert1-0/+5
2023-09-13Add pic and shared variants to GSL (#37961)Alex Richert1-0/+5
* Add pic and shared variants for gsl * fix gsl variant logic * make +pic default for gsl
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