build(deps): bump github/codeql-action from 3.29.1 to 3.29.2 #1910
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Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.29.1 to 3.29.2. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@39edc49...181d5ee) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.29.2 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>
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* Update heat/core/io.py Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * added test for dndarray.info * added tests for two uncovered exception lines * one additional line from DMD covered * one more line in DMD covered * debugging * build(deps): bump actions/setup-python from 5.4.0 to 5.5.0 Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5.4.0 to 5.5.0. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@4237552...8d9ed9a) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/PyCQA/flake8: 7.1.2 → 7.2.0](PyCQA/flake8@7.1.2...7.2.0) * build(deps): bump github/codeql-action from 3.28.12 to 3.28.13 Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.28.12 to 3.28.13. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@5f8171a...1b549b9) --- updated-dependencies: - dependency-name: github/codeql-action dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * further work on eigh * eigh completed for split = 0 * flake8 * tests for eigh, now split=none,0,1 * build(deps): bump step-security/harden-runner from 2.11.0 to 2.11.1 (#1851) Bumps [step-security/harden-runner](https://github.com/step-security/harden-runner) from 2.11.0 to 2.11.1. - [Release notes](https://github.com/step-security/harden-runner/releases) - [Commits](step-security/harden-runner@4d991eb...c6295a6) --- updated-dependencies: - dependency-name: step-security/harden-runner dependency-version: 2.11.1 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> * build(deps): bump actions/dependency-review-action from 4.5.0 to 4.6.0 (#1850) Bumps [actions/dependency-review-action](https://github.com/actions/dependency-review-action) from 4.5.0 to 4.6.0. - [Release notes](https://github.com/actions/dependency-review-action/releases) - [Commits](actions/dependency-review-action@3b139cf...ce3cf95) --- updated-dependencies: - dependency-name: actions/dependency-review-action dependency-version: 4.6.0 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> * Apply suggestions from code review Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * minor modifications due to Copilot's Review * added SVD for general case * reformatting * tests for SVD * tests for SVD completed * added module _config in core which is intended to handle MPI, CUDA, and ROCm versioning * added variable GPU_AWARE_MPI * added MPICH * changed method info into __repr__ * moved __repr__ to printing module * removed dead code * restructuring of tests * added further test to DMDc * small typo corrected * adapted tolerances for last test; errors grow w.r.t. timesteps (is in the nature of DMD), so largest number of procs determines tolerance * Update test_dmd.py lower tolerances for the AMD-runner * dummy commit since sth was wrong with pre-commit * corrected tests * debugging of tests * Remove unnecessary contiguous calls (#1831) * removed contiguous calls from manipulations.py * removed the contiguous calls from linalg/qr.py * removed unnecessary contiguous call in factories.py * removed some more unnecessary contiguous calls * reinstate contiguous() calls if needed * removed the contiguous calls from linalg/qr.py * reinstate setting Q_buf to Q_curr --------- Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * build(deps): bump github/codeql-action from 3.28.13 to 3.28.15 Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.28.13 to 3.28.15. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@1b549b9...45775bd) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.28.15 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * removed debugging prints that were forgotten before merging into main * subTest'ified the zarr tests, added some strange exception handling that is likely necessary to accomodate zarr-versions compatible with Python 3.10 * small bug fix * bugfix in eigh * removed unneccesary numpy import * changed representation string according to review * debugging of memory consumption in Polar * bug fixes for devices in polar and eigh * bugfixes for certain device constellations * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update README.md * Support latest PyTorch release * Make unit tests compatible with NumPy 2.x (#1826) * changed row_stack to vstack for numpy >= 2.0.0 * Changed the numpy version check to the numpy suggested method * Changed numpy version requirement * fixed DeprecationWarning from missing axes for np.fft.fftn * Fixed one __array_wrap__ DeprecationWarning * Stopped testing cross of vector axes with 2 elements for numpy >= 2.0 * changed requirements to avoid errors with numpy >= 2 * Using Python 3.10 for RecievePR * changed python-version to '3.10' because 3.10 was interpreted as 3.1 * changed ci.yaml to exclude python 3.9 * Fixed two DeprecationWarnings of np.cross() by adding a third dimension with zeros * Fixed the last np.cross() warning by performing the operation manually * changed dtype of np.cross() to float32 --------- Co-authored-by: Fabian Hoppe <112093564+mrfh92@users.noreply.github.com> Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <juanpedroghm@gmail.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * build(deps): bump actions/setup-python from 5.5.0 to 5.6.0 (#1863) * build(deps): bump actions/setup-python from 5.5.0 to 5.6.0 Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5.5.0 to 5.6.0. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@8d9ed9a...a26af69) --- updated-dependencies: - dependency-name: actions/setup-python dependency-version: 5.6.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * Debugging --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * build(deps): bump docker/build-push-action from 6.15.0 to 6.16.0 (#1860) Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 6.15.0 to 6.16.0. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](docker/build-push-action@471d1dc...14487ce) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-version: 6.16.0 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> * build(deps): bump step-security/harden-runner from 2.11.1 to 2.12.0 (#1861) Bumps [step-security/harden-runner](https://github.com/step-security/harden-runner) from 2.11.1 to 2.12.0. - [Release notes](https://github.com/step-security/harden-runner/releases) - [Commits](step-security/harden-runner@c6295a6...0634a26) --- updated-dependencies: - dependency-name: step-security/harden-runner dependency-version: 2.12.0 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> * build(deps): bump github/codeql-action from 3.28.15 to 3.28.17 (#1866) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.28.15 to 3.28.17. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@45775bd...60168ef) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.28.17 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> * build(deps): bump actions/dependency-review-action from 4.6.0 to 4.7.0 Bumps [actions/dependency-review-action](https://github.com/actions/dependency-review-action) from 4.6.0 to 4.7.0. - [Release notes](https://github.com/actions/dependency-review-action/releases) - [Commits](actions/dependency-review-action@ce3cf95...38ecb5b) --- updated-dependencies: - dependency-name: actions/dependency-review-action dependency-version: 4.7.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * added benchmarks for eigh, svd, and rsvd * dummy commit to trigger benchmark runs * Support latest PyTorch release * changed torchvision version to <0.22.1 * retrigger checks * build(deps): bump github/codeql-action from 3.28.17 to 3.28.18 Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.28.17 to 3.28.18. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@60168ef...ff0a06e) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.28.18 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * build(deps): bump docker/build-push-action from 6.16.0 to 6.17.0 Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 6.16.0 to 6.17.0. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](docker/build-push-action@14487ce...1dc7386) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-version: 6.17.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * build(deps): bump actions/dependency-review-action from 4.7.0 to 4.7.1 Bumps [actions/dependency-review-action](https://github.com/actions/dependency-review-action) from 4.7.0 to 4.7.1. - [Release notes](https://github.com/actions/dependency-review-action/releases) - [Commits](actions/dependency-review-action@38ecb5b...da24556) --- updated-dependencies: - dependency-name: actions/dependency-review-action dependency-version: 4.7.1 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * RTD Notebook gallery and profiling notebook with perun. (#1867) * docs: notebook gallery in rtd * docs: missing makefiles * docs: reverted changes to gitignore * haicore notebook setup * ompi in readthedocs build * correct apt package for mpi * docs: replaced small bodies dataset with digits from sklearn (boring, but easier to access on the long term) * perun notebook * wrong cell type * added pytorch 2.7 to ci workflow * docs: post practice run fixes * notebook thumbnails, formatting and corrections for tutorial * forgot to uncomment autoapi * build(deps): bump github/codeql-action from 3.28.18 to 3.28.19 (#1881) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.28.18 to 3.28.19. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@ff0a06e...fca7ace) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.28.19 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> * build(deps): bump docker/build-push-action from 6.17.0 to 6.18.0 (#1877) Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 6.17.0 to 6.18.0. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](docker/build-push-action@1dc7386...2634353) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-version: 6.18.0 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> * build(deps): bump ossf/scorecard-action from 2.4.1 to 2.4.2 (#1878) Bumps [ossf/scorecard-action](https://github.com/ossf/scorecard-action) from 2.4.1 to 2.4.2. - [Release notes](https://github.com/ossf/scorecard-action/releases) - [Changelog](https://github.com/ossf/scorecard-action/blob/main/RELEASE.md) - [Commits](ossf/scorecard-action@f49aabe...05b42c6) --- updated-dependencies: - dependency-name: ossf/scorecard-action dependency-version: 2.4.2 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> * build(deps): bump step-security/harden-runner from 2.12.0 to 2.12.1 Bumps [step-security/harden-runner](https://github.com/step-security/harden-runner) from 2.12.0 to 2.12.1. - [Release notes](https://github.com/step-security/harden-runner/releases) - [Commits](step-security/harden-runner@0634a26...002fdce) --- updated-dependencies: - dependency-name: step-security/harden-runner dependency-version: 2.12.1 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * build(deps): bump github/codeql-action from 3.28.19 to 3.29.0 Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.28.19 to 3.29.0. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@fca7ace...ce28f5b) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.29.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * Add special methods for operations in NumPy * add tests for NumPy related array methods * fix variable name * Exit installation if conda environment cannot be activated (#1880) * exit 0_setup_conda.sh if environment cannot be activated otherwise the script might install into the base environment * exit 0_setup_pip.sh if environment cannot be activated --------- Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <juanpedroghm@gmail.com> * fix item access * add contiguous call again * same as before * [pre-commit.ci] pre-commit autoupdate (#1894) updates: - [github.com/PyCQA/flake8: 7.2.0 → 7.3.0](PyCQA/flake8@7.2.0...7.3.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * bugfix in rSVD for the case the rank is smaller than number of processes * build(deps): bump github/codeql-action from 3.29.0 to 3.29.1 Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.29.0 to 3.29.1. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@ce28f5b...39edc49) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.29.1 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * resolved bug in rSVD, actualle one-process QR * Support PyTorch 2.7.1 (#1883) * Support latest PyTorch release * Update ci.yaml pytorch: add v2.2, drop v1.11 * debugging test_lasso * Support latest PyTorch release * Update bug_report.yml Add latest versions for options * update torchvision * do not test latest torch in matrix * pin zarr version * remove dead code * pin zarr to 3.0.8 * add back latest pytorch to matrix * edit PR body * Update ci.yaml --------- Co-authored-by: ClaudiaComito <39374113+ClaudiaComito@users.noreply.github.com> Co-authored-by: Michael Tarnawa <m.tarnawa@fz-juelich.de> Co-authored-by: Michael Tarnawa <18899420+mtar@users.noreply.github.com> * build(deps): bump docker/setup-buildx-action from 3.10.0 to 3.11.1 Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 3.10.0 to 3.11.1. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](docker/setup-buildx-action@b5ca514...e468171) --- updated-dependencies: - dependency-name: docker/setup-buildx-action dependency-version: 3.11.1 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * Update polar.py * Revert "build(deps): bump docker/setup-buildx-action from 3.10.0 to 3.11.1" (#1908) * support torch_function (#1895) Co-authored-by: Fabian Hoppe <112093564+mrfh92@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * Features/1845 Update citations (#1846) * Update README.md: added citation possibilities * Update README.md: link to ZENODO * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update README.md * Update README.md * Update README.md --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <juanpedroghm@gmail.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * Transition to pyproject.toml, Ruff, and mypy (#1832) * Support latest PyTorch release * Support latest PyTorch release * retrigger checks * wip: toml, ruff, mypy and cli * ci: better mypy error filter (down to 3041) * ci: mypy in list of dev deps * ci: skiping mypy for now * dependency specification * missing argument description for permute method * fixed dynamic version in pyproject.toml * properly skipping mypy in the pre-commit.ci * fixed dependencies, removed references to python 3.9, added python 3.13 * doc -> docs * fixed tests * cli tests * Update .github/ISSUE_TEMPLATE/bug_report.yml Co-authored-by: Michael Tarnawa <18899420+mtar@users.noreply.github.com> * removed problematic pytorch version?! * consistency is important * did not work * vulnerabitliy removal, other changes to toml * It's not working :( * fixing tests * Update .pre-commit-config.yaml * fix: cli does not change the default device * fix: support for older pytorch version on the cli, limit zarr package version * Update pytorch exclude with py-3.13 --------- Co-authored-by: ClaudiaComito <39374113+ClaudiaComito@users.noreply.github.com> Co-authored-by: Marc-Jindra <m.jindra@fz-juelich.de> Co-authored-by: Michael Tarnawa <18899420+mtar@users.noreply.github.com> * build(deps): bump docker/setup-buildx-action from 3.10.0 to 3.11.1 (#1911) Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 3.10.0 to 3.11.1. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](docker/setup-buildx-action@b5ca514...e468171) --- updated-dependencies: - dependency-name: docker/setup-buildx-action dependency-version: 3.11.1 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> * build(deps): bump github/codeql-action from 3.29.1 to 3.29.2 (#1910) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.29.1 to 3.29.2. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@39edc49...181d5ee) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.29.2 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> * build(deps): bump step-security/harden-runner from 2.12.1 to 2.12.2 (#1909) Bumps [step-security/harden-runner](https://github.com/step-security/harden-runner) from 2.12.1 to 2.12.2. - [Release notes](https://github.com/step-security/harden-runner/releases) - [Commits](step-security/harden-runner@002fdce...6c439dc) --- updated-dependencies: - dependency-name: step-security/harden-runner dependency-version: 2.12.2 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> * Apply suggestions from code review Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * took review into account * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * pre-commit stuff * [pre-commit.ci] pre-commit autoupdate (#1912) updates: - [github.com/astral-sh/ruff-pre-commit: v0.11.13 → v0.12.3](astral-sh/ruff-pre-commit@v0.11.13...v0.12.3) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Updated release_prep.yml to incorporate up-to-date Dockerfile Pytorch versions (#1903) * Create update_docker.yml * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update release-prep.yml Added the update functionality of the Dockerfile.source and Dockerfile.release Pytorch Image versions. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Removed update_docker.yml since the functionality was moved to release prep --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * [StepSecurity] Apply security best practices (#1891) * [StepSecurity] Apply security best practices Signed-off-by: StepSecurity Bot <bot@stepsecurity.io> * Test with shellcheck-py * Update .pre-commit-config.yaml * shellcheck updates * Update build_and_push.sh * Update increment_version.sh * Update increment_version.sh * Update build_and_push.sh * Update test_nvidia_image_haicore_enroot.sh * Update test_nvidia_image_haicore_enroot.sh * Update build_and_push.sh * Update 0_setup_pip.sh --------- Signed-off-by: StepSecurity Bot <bot@stepsecurity.io> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * build(deps): bump korthout/backport-action from 3.2.0 to 3.2.1 Bumps [korthout/backport-action](https://github.com/korthout/backport-action) from 3.2.0 to 3.2.1. - [Release notes](https://github.com/korthout/backport-action/releases) - [Commits](korthout/backport-action@436145e...0193454) --- updated-dependencies: - dependency-name: korthout/backport-action dependency-version: 3.2.1 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * build(deps): bump step-security/harden-runner from 2.12.1 to 2.13.0 Bumps [step-security/harden-runner](https://github.com/step-security/harden-runner) from 2.12.1 to 2.13.0. - [Release notes](https://github.com/step-security/harden-runner/releases) - [Commits](step-security/harden-runner@v2.12.1...ec9f2d5) --- updated-dependencies: - dependency-name: step-security/harden-runner dependency-version: 2.13.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/pre-commit/mirrors-mypy: v1.16.1 → v1.17.0](pre-commit/mirrors-mypy@v1.16.1...v1.17.0) - [github.com/astral-sh/ruff-pre-commit: v0.12.3 → v0.12.4](astral-sh/ruff-pre-commit@v0.12.3...v0.12.4) - [github.com/gitleaks/gitleaks: v8.16.3 → v8.28.0](gitleaks/gitleaks@v8.16.3...v8.28.0) * Fix ValueError in save_zarr by conditional handling of chunks argument Fixes error when calling zarr.create by only passing chunks as a list if not None. * Unfix zarr version in pyproject.toml to test CI job `test_amd` * Add note in docstring of save_zarr() * build(deps): bump tj-actions/branch-names from 8.2.1 to 9.0.1 Bumps [tj-actions/branch-names](https://github.com/tj-actions/branch-names) from 8.2.1 to 9.0.1. - [Release notes](https://github.com/tj-actions/branch-names/releases) - [Changelog](https://github.com/tj-actions/branch-names/blob/main/HISTORY.md) - [Commits](tj-actions/branch-names@dde14ac...386e117) --- updated-dependencies: - dependency-name: tj-actions/branch-names dependency-version: 9.0.1 dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * build(deps): bump github/codeql-action from 3.29.2 to 3.29.4 Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.29.2 to 3.29.4. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@181d5ee...4e828ff) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.29.4 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * Setuptools build fix on pytproject.toml (#1919) * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.12.4 → v0.12.5](astral-sh/ruff-pre-commit@v0.12.4...v0.12.5) * Stride argument for convolution (#1865) * Add: enable stride as input option for convolution Belongs to Issue 1755 Changes include - stride as optional input - stride in docstring (except for output dim computations and as example) - raise ValueError for incorrect option (stride < 1) and combinations (stride > 1 and mode = 'same') * Add: Failing stride tests in test_signal.py - Added correct results for odd and even kernel - Added calls for convolution with stride=2 except with exception for mode `same` - Covers is_mps true and false - Stopped at tests for large distributed signals * Add: Pass stride tests for standard cases Belongs to Issue 1755 - edge cases and batch-processing not yet implemented or tested - Fix test error - Implement stride to pass tests - Write convolution_stride.py script for debugging purposes, will be removed later * Add: test for large signals with stride Belongs to Issue 1755 - passes * Add: Test cases until batch Belongs to issue 1755 - Passes tests * Add: Failing tests for batch convolution with stride Belongs to Issue 1755 * Add: batch processing with stride Belongs to Issue 1755 - Added stride to conv1D call in batch_convolution - Passes tests * Remove: Remove script to test convolution with stride * Update: Docstring of convolution Belongs to Issue 1755 - Correct stride information - Add examples * Fail: Tests fail for mpirun -n3 ... - Issue with halo size - Problem marked in code - Not solved * Update: Split stride tests - Different configurations in different tests functions - If process number == 1: all pass - If multiple process < 3 (because tested only then), 5 fail - This needs to be fixed, likely fails due to wrong halo in presence of stride * Add: Enable stride on distributed arrays but not kernels Adjust signal on each rank such that it starts with the next kernel according to stride - Added the compution of starting values for each rank - Avoid doubles for even and odd kernels Halo size computation is independent of stride Added a script for debugging, will be removed Ideas: generalize it for stride 1 (should work out of the box) To do: Adapt for distributed kernels * Add: Distributed Kernels and optimized start index computation Optimized start index computation: - Remove global index array - Use lshap map and simple modulo operation only Distributed kernels - Any stride > 1 is a subset of the solution for stride 1 - Not the most efficient but at least functional * Fix: Improve test coverage Still missing - Cuda code bits - else statement beginning line 229 * Delete: conv_test.py Test script no longer needed * Add: Add benchmarks for signal.py * Add: script to test benchmark - empty so far * Fix: Benchmarks - Fix run_signal_benchmarks - Add run_signal_benchmarks to main.py Remove: print statements from convolution in signal.py * Fix: benchmarks/cb/signal.py - add () to monitor decorator of perun * Fix: Rename signal.py to avoid clash with python3.12 signal - change signal.py to heat_signal.py * Fix: Adjust array numbers for benchmarking * Remove: benchmark script from scripts/ * Fix: Benchmarking signal.py and testing signal.py - Benchmark improved - removed import pytest from test_signal.py * Fix: test_signal.py batch convolution with stride - Stride was not passed as a single value but different values for different ranks - Solution: Do not randomly create stride values but use fixed values * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix: test_convolution-stride_large_signal_and_kernel_modes - Remove torch arrays - Instead work with np.convolve similar to test without stride * Fix: Add device for empty torch tensors - Stride test fails for large arrays - Error message says, that device does not match - Due to large stride, potentially empty tensor creation -> add device to that tensor created * Fix: torch_device instead of device - when empty tensor is called, use torch_device * Fix: Missed .device to previous commit * Fix: torch device not accessible - instead use str(ht_array.device) - Use signal.device to get correct rank --------- Co-authored-by: Fabian Hoppe <112093564+mrfh92@users.noreply.github.com> Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <juanpedroghm@gmail.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * build(deps): bump tj-actions/branch-names from 9.0.1 to 9.0.2 (#1930) Bumps [tj-actions/branch-names](https://github.com/tj-actions/branch-names) from 9.0.1 to 9.0.2. - [Release notes](https://github.com/tj-actions/branch-names/releases) - [Changelog](https://github.com/tj-actions/branch-names/blob/main/HISTORY.md) - [Commits](tj-actions/branch-names@386e117...5250492) --- updated-dependencies: - dependency-name: tj-actions/branch-names dependency-version: 9.0.2 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> * build(deps): bump github/codeql-action from 3.29.4 to 3.29.8 (#1933) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.29.4 to 3.29.8. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@4e828ff...76621b6) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.29.8 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> * build(deps): bump docker/login-action from 3.4.0 to 3.5.0 (#1934) Bumps [docker/login-action](https://github.com/docker/login-action) from 3.4.0 to 3.5.0. - [Release notes](https://github.com/docker/login-action/releases) - [Commits](docker/login-action@74a5d14...184bdaa) --- updated-dependencies: - dependency-name: docker/login-action dependency-version: 3.5.0 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> * [pre-commit.ci] pre-commit autoupdate (#1931) updates: - [github.com/pre-commit/mirrors-mypy: v1.17.0 → v1.17.1](pre-commit/mirrors-mypy@v1.17.0...v1.17.1) - [github.com/astral-sh/ruff-pre-commit: v0.12.5 → v0.12.7](astral-sh/ruff-pre-commit@v0.12.5...v0.12.7) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <juanpedroghm@gmail.com> * Update CODE_OF_CONDUCT.md New email for reporting * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * build(deps): bump github/codeql-action from 3.29.8 to 3.29.9 (#1943) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.29.8 to 3.29.9. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@76621b6...df55935) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.29.9 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> * build(deps): bump actions/checkout from 4.2.2 to 5.0.0 (#1942) Bumps [actions/checkout](https://github.com/actions/checkout) from 4.2.2 to 5.0.0. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@11bd719...08c6903) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: 5.0.0 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> * build(deps): bump korthout/backport-action from 3.2.1 to 3.3.0 (#1944) Bumps [korthout/backport-action](https://github.com/korthout/backport-action) from 3.2.1 to 3.3.0. - [Release notes](https://github.com/korthout/backport-action/releases) - [Commits](korthout/backport-action@0193454...ca4972a) --- updated-dependencies: - dependency-name: korthout/backport-action dependency-version: 3.3.0 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> * [pre-commit.ci] pre-commit autoupdate (#1936) updates: - [github.com/pre-commit/pre-commit-hooks: v5.0.0 → v6.0.0](pre-commit/pre-commit-hooks@v5.0.0...v6.0.0) - [github.com/astral-sh/ruff-pre-commit: v0.12.7 → v0.12.8](astral-sh/ruff-pre-commit@v0.12.7...v0.12.8) - [github.com/shellcheck-py/shellcheck-py: v0.10.0.1 → v0.11.0.1](shellcheck-py/shellcheck-py@v0.10.0.1...v0.11.0.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * Update latest-pytorch-support.yml (#1950) move to pyproject.toml * [pre-commit.ci] pre-commit autoupdate (#1949) updates: - [github.com/astral-sh/ruff-pre-commit: v0.12.8 → v0.12.9](astral-sh/ruff-pre-commit@v0.12.8...v0.12.9) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * Bump version to 1.6.0 * Update pytorch image in Dockerfile.release and Dockerfile.source to version * update coverage, add link to issue search * add FFT, masked arrays * Update authors and contributors in CITATION.cff * fix: typo in release drafter * Updated Changelog * changelog highlights * Update micro version to 0 * Update CHANGELOG.md * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: StepSecurity Bot <bot@stepsecurity.io> Co-authored-by: Fabian Hoppe <112093564+mrfh92@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> Co-authored-by: jolemse <35252911+jolemse@users.noreply.github.com> Co-authored-by: Hoppe <mrhf92@gmail.com> Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <juanpedroghm@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Marc-Jindra <m.jindra@fz-juelich.de> Co-authored-by: Hakdag97 <72792786+Hakdag97@users.noreply.github.com> Co-authored-by: Michael Tarnawa <18899420+mtar@users.noreply.github.com> Co-authored-by: Till Korten <webmaster@korten.at> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Michael Tarnawa <m.tarnawa@fz-juelich.de> Co-authored-by: StepSecurity Bot <bot@stepsecurity.io> Co-authored-by: Berkant <51971304+Berkant03@users.noreply.github.com> Co-authored-by: Lukas Scheib <ls.login.sl@gmail.com> Co-authored-by: Lukas Scheib <146953413+LScheib@users.noreply.github.com> Co-authored-by: lolacaro <carola.fischer.science@gmail.com> Co-authored-by: Björn Hagemeier <b.hagemeier@fz-juelich.de> Co-authored-by: Heat Release Bot <>
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* add contiguous call again * same as before * [pre-commit.ci] pre-commit autoupdate (#1894) updates: - [github.com/PyCQA/flake8: 7.2.0 → 7.3.0](https://github.com/PyCQA/flake8/compare/7.2.0...7.3.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * bugfix in rSVD for the case the rank is smaller than number of processes * build(deps): bump github/codeql-action from 3.29.0 to 3.29.1 Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.29.0 to 3.29.1. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/ce28f5bb42b7a9f2c824e633a3f6ee835bab6858...39edc492dbe16b1465b0cafca41432d857bdb31a) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.29.1 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * resolved bug in rSVD, actualle one-process QR * Support PyTorch 2.7.1 (#1883) * Support latest PyTorch release * Update ci.yaml pytorch: add v2.2, drop v1.11 * debugging test_lasso * Support latest PyTorch release * Update bug_report.yml Add latest versions for options * update torchvision * do not test latest torch in matrix * pin zarr version * remove dead code * pin zarr to 3.0.8 * add back latest pytorch to matrix * edit PR body * Update ci.yaml --------- Co-authored-by: ClaudiaComito <39374113+ClaudiaComito@users.noreply.github.com> Co-authored-by: Michael Tarnawa <m.tarnawa@fz-juelich.de> Co-authored-by: Michael Tarnawa <18899420+mtar@users.noreply.github.com> * build(deps): bump docker/setup-buildx-action from 3.10.0 to 3.11.1 Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 3.10.0 to 3.11.1. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](https://github.com/docker/setup-buildx-action/compare/b5ca514318bd6ebac0fb2aedd5d36ec1b5c232a2...e468171a9de216ec08956ac3ada2f0791b6bd435) --- updated-dependencies: - dependency-name: docker/setup-buildx-action dependency-version: 3.11.1 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * Update polar.py * Revert "build(deps): bump docker/setup-buildx-action from 3.10.0 to 3.11.1" (#1908) * support torch_function (#1895) Co-authored-by: Fabian Hoppe <112093564+mrfh92@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * Features/1845 Update citations (#1846) * Update README.md: added citation possibilities * Update README.md: link to ZENODO * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update README.md * Update README.md * Update README.md --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <juanpedroghm@gmail.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * Transition to pyproject.toml, Ruff, and mypy (#1832) * Support latest PyTorch release * Support latest PyTorch release * retrigger checks * wip: toml, ruff, mypy and cli * ci: better mypy error filter (down to 3041) * ci: mypy in list of dev deps * ci: skiping mypy for now * dependency specification * missing argument description for permute method * fixed dynamic version in pyproject.toml * properly skipping mypy in the pre-commit.ci * fixed dependencies, removed references to python 3.9, added python 3.13 * doc -> docs * fixed tests * cli tests * Update .github/ISSUE_TEMPLATE/bug_report.yml Co-authored-by: Michael Tarnawa <18899420+mtar@users.noreply.github.com> * removed problematic pytorch version?! * consistency is important * did not work * vulnerabitliy removal, other changes to toml * It's not working :( * fixing tests * Update .pre-commit-config.yaml * fix: cli does not change the default device * fix: support for older pytorch version on the cli, limit zarr package version * Update pytorch exclude with py-3.13 --------- Co-authored-by: ClaudiaComito <39374113+ClaudiaComito@users.noreply.github.com> Co-authored-by: Marc-Jindra <m.jindra@fz-juelich.de> Co-authored-by: Michael Tarnawa <18899420+mtar@users.noreply.github.com> * build(deps): bump docker/setup-buildx-action from 3.10.0 to 3.11.1 (#1911) Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 3.10.0 to 3.11.1. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](https://github.com/docker/setup-buildx-action/compare/b5ca514318bd6ebac0fb2aedd5d36ec1b5c232a2...e468171a9de216ec08956ac3ada2f0791b6bd435) --- updated-dependencies: - dependency-name: docker/setup-buildx-action dependency-version: 3.11.1 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> * build(deps): bump github/codeql-action from 3.29.1 to 3.29.2 (#1910) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.29.1 to 3.29.2. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/39edc492dbe16b1465b0cafca41432d857bdb31a...181d5eefc20863364f96762470ba6f862bdef56b) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.29.2 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> * build(deps): bump step-security/harden-runner from 2.12.1 to 2.12.2 (#1909) Bumps [step-security/harden-runner](https://github.com/step-security/harden-runner) from 2.12.1 to 2.12.2. - [Release notes](https://github.com/step-security/harden-runner/releases) - [Commits](https://github.com/step-security/harden-runner/compare/002fdce3c6a235733a90a27c80493a3241e56863...6c439dc8bdf85cadbbce9ed30d1c7b959517bc49) --- updated-dependencies: - dependency-name: step-security/harden-runner dependency-version: 2.12.2 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> * Apply suggestions from code review Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * took review into account * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * pre-commit stuff * [pre-commit.ci] pre-commit autoupdate (#1912) updates: - [github.com/astral-sh/ruff-pre-commit: v0.11.13 → v0.12.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.11.13...v0.12.3) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Updated release_prep.yml to incorporate up-to-date Dockerfile Pytorch versions (#1903) * Create update_docker.yml * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update release-prep.yml Added the update functionality of the Dockerfile.source and Dockerfile.release Pytorch Image versions. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Removed update_docker.yml since the functionality was moved to release prep --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * [StepSecurity] Apply security best practices (#1891) * [StepSecurity] Apply security best practices Signed-off-by: StepSecurity Bot <bot@stepsecurity.io> * Test with shellcheck-py * Update .pre-commit-config.yaml * shellcheck updates * Update build_and_push.sh * Update increment_version.sh * Update increment_version.sh * Update build_and_push.sh * Update test_nvidia_image_haicore_enroot.sh * Update test_nvidia_image_haicore_enroot.sh * Update build_and_push.sh * Update 0_setup_pip.sh --------- Signed-off-by: StepSecurity Bot <bot@stepsecurity.io> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * build(deps): bump korthout/backport-action from 3.2.0 to 3.2.1 Bumps [korthout/backport-action](https://github.com/korthout/backport-action) from 3.2.0 to 3.2.1. - [Release notes](https://github.com/korthout/backport-action/releases) - [Commits](https://github.com/korthout/backport-action/compare/436145e922f9561fc5ea157ff406f21af2d6b363...0193454f0c5947491d348f33a275c119f30eb736) --- updated-dependencies: - dependency-name: korthout/backport-action dependency-version: 3.2.1 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * build(deps): bump step-security/harden-runner from 2.12.1 to 2.13.0 Bumps [step-security/harden-runner](https://github.com/step-security/harden-runner) from 2.12.1 to 2.13.0. - [Release notes](https://github.com/step-security/harden-runner/releases) - [Commits](https://github.com/step-security/harden-runner/compare/v2.12.1...ec9f2d5744a09debf3a187a3f4f675c53b671911) --- updated-dependencies: - dependency-name: step-security/harden-runner dependency-version: 2.13.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/pre-commit/mirrors-mypy: v1.16.1 → v1.17.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.16.1...v1.17.0) - [github.com/astral-sh/ruff-pre-commit: v0.12.3 → v0.12.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.12.3...v0.12.4) - [github.com/gitleaks/gitleaks: v8.16.3 → v8.28.0](https://github.com/gitleaks/gitleaks/compare/v8.16.3...v8.28.0) * - added function to load multiple hdf5 - created tests for the function * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix ValueError in save_zarr by conditional handling of chunks argument Fixes error when calling zarr.create by only passing chunks as a list if not None. * Unfix zarr version in pyproject.toml to test CI job `test_amd` * Add cpu cast for test ending. * Add note in docstring of save_zarr() * build(deps): bump tj-actions/branch-names from 8.2.1 to 9.0.1 Bumps [tj-actions/branch-names](https://github.com/tj-actions/branch-names) from 8.2.1 to 9.0.1. - [Release notes](https://github.com/tj-actions/branch-names/releases) - [Changelog](https://github.com/tj-actions/branch-names/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/branch-names/compare/dde14ac574a8b9b1cedc59a1cf312788af43d8d8...386e117ea34339627a40843704a60a3bc9359234) --- updated-dependencies: - dependency-name: tj-actions/branch-names dependency-version: 9.0.1 dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * build(deps): bump github/codeql-action from 3.29.2 to 3.29.4 Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.29.2 to 3.29.4. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/181d5eefc20863364f96762470ba6f862bdef56b...4e828ff8d448a8a6e532957b1811f387a63867e8) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.29.4 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * Setuptools build fix on pytproject.toml (#1919) * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.12.4 → v0.12.5](https://github.com/astral-sh/ruff-pre-commit/compare/v0.12.4...v0.12.5) * Stride argument for convolution (#1865) * Add: enable stride as input option for convolution Belongs to Issue 1755 Changes include - stride as optional input - stride in docstring (except for output dim computations and as example) - raise ValueError for incorrect option (stride < 1) and combinations (stride > 1 and mode = 'same') * Add: Failing stride tests in test_signal.py - Added correct results for odd and even kernel - Added calls for convolution with stride=2 except with exception for mode `same` - Covers is_mps true and false - Stopped at tests for large distributed signals * Add: Pass stride tests for standard cases Belongs to Issue 1755 - edge cases and batch-processing not yet implemented or tested - Fix test error - Implement stride to pass tests - Write convolution_stride.py script for debugging purposes, will be removed later * Add: test for large signals with stride Belongs to Issue 1755 - passes * Add: Test cases until batch Belongs to issue 1755 - Passes tests * Add: Failing tests for batch convolution with stride Belongs to Issue 1755 * Add: batch processing with stride Belongs to Issue 1755 - Added stride to conv1D call in batch_convolution - Passes tests * Remove: Remove script to test convolution with stride * Update: Docstring of convolution Belongs to Issue 1755 - Correct stride information - Add examples * Fail: Tests fail for mpirun -n3 ... - Issue with halo size - Problem marked in code - Not solved * Update: Split stride tests - Different configurations in different tests functions - If process number == 1: all pass - If multiple process < 3 (because tested only then), 5 fail - This needs to be fixed, likely fails due to wrong halo in presence of stride * Add: Enable stride on distributed arrays but not kernels Adjust signal on each rank such that it starts with the next kernel according to stride - Added the compution of starting values for each rank - Avoid doubles for even and odd kernels Halo size computation is independent of stride Added a script for debugging, will be removed Ideas: generalize it for stride 1 (should work out of the box) To do: Adapt for distributed kernels * Add: Distributed Kernels and optimized start index computation Optimized start index computation: - Remove global index array - Use lshap map and simple modulo operation only Distributed kernels - Any stride > 1 is a subset of the solution for stride 1 - Not the most efficient but at least functional * Fix: Improve test coverage Still missing - Cuda code bits - else statement beginning line 229 * Delete: conv_test.py Test script no longer needed * Add: Add benchmarks for signal.py * Add: script to test benchmark - empty so far * Fix: Benchmarks - Fix run_signal_benchmarks - Add run_signal_benchmarks to main.py Remove: print statements from convolution in signal.py * Fix: benchmarks/cb/signal.py - add () to monitor decorator of perun * Fix: Rename signal.py to avoid clash with python3.12 signal - change signal.py to heat_signal.py * Fix: Adjust array numbers for benchmarking * Remove: benchmark script from scripts/ * Fix: Benchmarking signal.py and testing signal.py - Benchmark improved - removed import pytest from test_signal.py * Fix: test_signal.py batch convolution with stride - Stride was not passed as a single value but different values for different ranks - Solution: Do not randomly create stride values but use fixed values * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix: test_convolution-stride_large_signal_and_kernel_modes - Remove torch arrays - Instead work with np.convolve similar to test without stride * Fix: Add device for empty torch tensors - Stride test fails for large arrays - Error message says, that device does not match - Due to large stride, potentially empty tensor creation -> add device to that tensor created * Fix: torch_device instead of device - when empty tensor is called, use torch_device * Fix: Missed .device to previous commit * Fix: torch device not accessible - instead use str(ht_array.device) - Use signal.device to get correct rank --------- Co-authored-by: Fabian Hoppe <112093564+mrfh92@users.noreply.github.com> Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <juanpedroghm@gmail.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * build(deps): bump tj-actions/branch-names from 9.0.1 to 9.0.2 (#1930) Bumps [tj-actions/branch-names](https://github.com/tj-actions/branch-names) from 9.0.1 to 9.0.2. - [Release notes](https://github.com/tj-actions/branch-names/releases) - [Changelog](https://github.com/tj-actions/branch-names/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/branch-names/compare/386e117ea34339627a40843704a60a3bc9359234...5250492686b253f06fa55861556d1027b067aeb5) --- updated-dependencies: - dependency-name: tj-actions/branch-names dependency-version: 9.0.2 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> * build(deps): bump github/codeql-action from 3.29.4 to 3.29.8 (#1933) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.29.4 to 3.29.8. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/4e828ff8d448a8a6e532957b1811f387a63867e8...76621b61decf072c1cee8dd1ce2d2a82d33c17ed) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.29.8 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> * build(deps): bump docker/login-action from 3.4.0 to 3.5.0 (#1934) Bumps [docker/login-action](https://github.com/docker/login-action) from 3.4.0 to 3.5.0. - [Release notes](https://github.com/docker/login-action/releases) - [Commits](https://github.com/docker/login-action/compare/74a5d142397b4f367a81961eba4e8cd7edddf772...184bdaa0721073962dff0199f1fb9940f07167d1) --- updated-dependencies: - dependency-name: docker/login-action dependency-version: 3.5.0 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> * [pre-commit.ci] pre-commit autoupdate (#1931) updates: - [github.com/pre-commit/mirrors-mypy: v1.17.0 → v1.17.1](https://github.com/pre-commit/mirrors-mypy/compare/v1.17.0...v1.17.1) - [github.com/astral-sh/ruff-pre-commit: v0.12.5 → v0.12.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.12.5...v0.12.7) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <juanpedroghm@gmail.com> * Update CODE_OF_CONDUCT.md New email for reporting * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * build(deps): bump github/codeql-action from 3.29.8 to 3.29.9 (#1943) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.29.8 to 3.29.9. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/76621b61decf072c1cee8dd1ce2d2a82d33c17ed...df559355d593797519d70b90fc8edd5db049e7a2) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.29.9 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> * build(deps): bump actions/checkout from 4.2.2 to 5.0.0 (#1942) Bumps [actions/checkout](https://github.com/actions/checkout) from 4.2.2 to 5.0.0. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/11bd71901bbe5b1630ceea73d27597364c9af683...08c6903cd8c0fde910a37f88322edcfb5dd907a8) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: 5.0.0 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> * build(deps): bump korthout/backport-action from 3.2.1 to 3.3.0 (#1944) Bumps [korthout/backport-action](https://github.com/korthout/backport-action) from 3.2.1 to 3.3.0. - [Release notes](https://github.com/korthout/backport-action/releases) - [Commits](https://github.com/korthout/backport-action/compare/0193454f0c5947491d348f33a275c119f30eb736...ca4972adce8039ff995e618f5fc02d1b7961f27a) --- updated-dependencies: - dependency-name: korthout/backport-action dependency-version: 3.3.0 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> * [pre-commit.ci] pre-commit autoupdate (#1936) updates: - [github.com/pre-commit/pre-commit-hooks: v5.0.0 → v6.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v5.0.0...v6.0.0) - [github.com/astral-sh/ruff-pre-commit: v0.12.7 → v0.12.8](https://github.com/astral-sh/ruff-pre-commit/compare/v0.12.7...v0.12.8) - [github.com/shellcheck-py/shellcheck-py: v0.10.0.1 → v0.11.0.1](https://github.com/shellcheck-py/shellcheck-py/compare/v0.10.0.1...v0.11.0.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * bugfixes in tests * set seed in basic test class * removed manual seeds from most of tests * Update latest-pytorch-support.yml (#1950) move to pyproject.toml * [pre-commit.ci] pre-commit autoupdate (#1949) updates: - [github.com/astral-sh/ruff-pre-commit: v0.12.8 → v0.12.9](https://github.com/astral-sh/ruff-pre-commit/compare/v0.12.8...v0.12.9) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * First attempt for fit() implementation, corresponding unit tests and some minor corrections in documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * build(deps): bump github/codeql-action from 3.29.9 to 3.29.11 Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.29.9 to 3.29.11. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/df559355d593797519d70b90fc8edd5db049e7a2...3c3833e0f8c1c83d449a7478aa59c036a9165498) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.29.11 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * Bump version to 1.6.0 * Update pytorch image in Dockerfile.release and Dockerfile.source to version * update coverage, add link to issue search * add FFT, masked arrays * build(deps): bump actions/dependency-review-action from 4.7.1 to 4.7.2 (#1956) Bumps [actions/dependency-review-action](https://github.com/actions/dependency-review-action) from 4.7.1 to 4.7.2. - [Release notes](https://github.com/actions/dependency-review-action/releases) - [Commits](https://github.com/actions/dependency-review-action/compare/da24556b548a50705dd671f47852072ea4c105d9...bc41886e18ea39df68b1b1245f4184881938e050) --- updated-dependencies: - dependency-name: actions/dependency-review-action dependency-version: 4.7.2 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> Co-authored-by: Hakdag97 <72792786+Hakdag97@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#1958) updates: - [github.com/astral-sh/ruff-pre-commit: v0.12.9 → v0.12.10](https://github.com/astral-sh/ruff-pre-commit/compare/v0.12.9...v0.12.10) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * Update authors and contributors in CITATION.cff * fix: typo in release drafter * Updated Changelog * changelog highlights * Update micro version to 0 * Update CHANGELOG.md * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update version.py * Clean up commented-out code * post-release fixes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Updated release workflow notes * [pre-commit.ci] pre-commit autoupdate (#1962) updates: - [github.com/astral-sh/ruff-pre-commit: v0.12.10 → v0.12.11](https://github.com/astral-sh/ruff-pre-commit/compare/v0.12.10...v0.12.11) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * add reigh * build(deps): bump actions/stale from 9.1.0 to 10.0.0 Bumps [actions/stale](https://github.com/actions/stale) from 9.1.0 to 10.0.0. - [Release notes](https://github.com/actions/stale/releases) - [Changelog](https://github.com/actions/stale/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/stale/compare/5bef64f19d7facfb25b37b414482c7164d639639...3a9db7e6a41a89f618792c92c0e97cc736e1b13f) --- updated-dependencies: - dependency-name: actions/stale dependency-version: 10.0.0 dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * build(deps): bump actions/github-script from 6.4.1 to 8.0.0 Bumps [actions/github-script](https://github.com/actions/github-script) from 6.4.1 to 8.0.0. - [Release notes](https://github.com/actions/github-script/releases) - [Commits](https://github.com/actions/github-script/compare/d7906e4ad0b1822421a7e6a35d5ca353c962f410...ed597411d8f924073f98dfc5c65a23a2325f34cd) --- updated-dependencies: - dependency-name: actions/github-script dependency-version: 8.0.0 dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * build(deps): bump github/codeql-action from 3.29.11 to 3.30.1 Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.29.11 to 3.30.1. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/3c3833e0f8c1c83d449a7478aa59c036a9165498...f1f6e5f6af878fb37288ce1c627459e94dbf7d01) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.30.1 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * build(deps): bump actions/dependency-review-action from 4.7.2 to 4.7.3 Bumps [actions/dependency-review-action](https://github.com/actions/dependency-review-action) from 4.7.2 to 4.7.3. - [Release notes](https://github.com/actions/dependency-review-action/releases) - [Commits](https://github.com/actions/dependency-review-action/compare/bc41886e18ea39df68b1b1245f4184881938e050...595b5aeba73380359d98a5e087f648dbb0edce1b) --- updated-dependencies: - dependency-name: actions/dependency-review-action dependency-version: 4.7.3 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * build(deps): bump github/codeql-action from 3.30.1 to 3.30.3 (#1975) * build(deps): bump step-security/harden-runner from 2.13.0 to 2.13.1 (#1976) * [pre-commit.ci] pre-commit autoupdate (#1972) updates: - [github.com/pre-commit/mirrors-mypy: v1.17.1 → v1.18.1](https://github.com/pre-commit/mirrors-mypy/compare/v1.17.1...v1.18.1) - [github.com/astral-sh/ruff-pre-commit: v0.12.11 → v0.13.0](https://github.com/astral-sh/ruff-pre-commit/compare/v0.12.11...v0.13.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * build(deps): bump actions/setup-python from 5.6.0 to 6.0.0 (#1977) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5.6.0 to 6.0.0. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](https://github.com/actions/setup-python/compare/a26af69be951a213d495a4c3e4e4022e16d87065...e797f83bcb11b83ae66e0230d6156d7c80228e7c) --- updated-dependencies: - dependency-name: actions/setup-python dependency-version: 6.0.0 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> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * Sturdier MPI Check (#1926) * sturdier mpi check * GPU_AWARE as relevant global check, checks can depend on version now * gpu aware compatiblity changes * wip: communication layer fixes for gpu_aware_mpi * _moveToCompDevice function * fix: disabled OpenMPI cuda awareness due to unreliable tests and benchmarks --------- Co-authored-by: Fabian Hoppe <112093564+mrfh92@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#1980) updates: - [github.com/pre-commit/mirrors-mypy: v1.18.1 → v1.18.2](https://github.com/pre-commit/mirrors-mypy/compare/v1.18.1...v1.18.2) - [github.com/astral-sh/ruff-pre-commit: v0.13.0 → v0.13.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.13.0...v0.13.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * build(deps): bump github/codeql-action from 3.30.3 to 3.30.5 (#1983) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.30.3 to 3.30.5. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/192325c86100d080feab897ff886c34abd4c83a3...3599b3baa15b485a2e49ef411a7a4bb2452e7f93) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.30.5 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> * build(deps): bump actions/dependency-review-action from 4.7.3 to 4.8.0 (#1982) * Parallel initialization for k-means (#1754) * Created a test file mytest.py * Implementation of parallel initialization * Refined comments for better readability * Adjusted according to review comments * Removed numerical instabilies leading to error in perun test * added prints for debugging * Bug fix * Bug fix * sturdier mpi check * GPU_AWARE as relevant global check, checks can depend on version now * Added Allgatherv method * Buffer allocation outside loop * gpu aware compatiblity changes * wip: communication layer fixes for gpu_aware_mpi * _moveToCompDevice function * Adjusted keyword arguments to restore benchmark performance * Adjusted keyword arguments to restore benchmark performance * fix: disabled OpenMPI cuda awareness due to unreliable tests and benchmarks * Test AMD-Fix by adjusting initial oversampling factor * Automated increase of oversampling factor if chosen too small * Improved code coverage * bug fix * . * . * Adjusted docstring * Adjusted values for keyword arguments in KMedians and KMedoids --------- Co-authored-by: Akdag <akda_me@sc-030332l.intra.dlr.de> Co-authored-by: Fabian Hoppe <112093564+mrfh92@users.noreply.github.com> Co-authored-by: Hoppe <mrhf92@gmail.com> Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <juanpedroghm@gmail.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * build(deps): bump github/codeql-action from 3.30.5 to 3.30.6 (#1988) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.30.5 to 3.30.6. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/3599b3baa15b485a2e49ef411a7a4bb2452e7f93...64d10c13136e1c5bce3e5fbde8d4906eeaafc885) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.30.6 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> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * build(deps): bump korthout/backport-action from 3.3.0 to 3.4.1 (#1987) Bumps [korthout/backport-action](https://github.com/korthout/backport-action) from 3.3.0 to 3.4.1. - [Release notes](https://github.com/korthout/backport-action/releases) - [Commits](https://github.com/korthout/backport-action/compare/ca4972adce8039ff995e618f5fc02d1b7961f27a...d07416681cab29bf2661702f925f020aaa962997) --- updated-dependencies: - dependency-name: korthout/backport-action dependency-version: 3.4.1 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> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * build(deps): bump actions/stale from 10.0.0 to 10.1.0 (#1985) Bumps [actions/stale](https://github.com/actions/stale) from 10.0.0 to 10.1.0. - [Release notes](https://github.com/actions/stale/releases) - [Changelog](https://github.com/actions/stale/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/stale/compare/3a9db7e6a41a89f618792c92c0e97cc736e1b13f...5f858e3efba33a5ca4407a664cc011ad407f2008) --- updated-dependencies: - dependency-name: actions/stale dependency-version: 10.1.0 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> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * build(deps): bump ossf/scorecard-action from 2.4.2 to 2.4.3 (#1986) Bumps [ossf/scorecard-action](https://github.com/ossf/scorecard-action) from 2.4.2 to 2.4.3. - [Release notes](https://github.com/ossf/scorecard-action/releases) - [Changelog](https://github.com/ossf/scorecard-action/blob/main/RELEASE.md) - [Commits](https://github.com/ossf/scorecard-action/compare/05b42c624433fc40578a4040d5cf5e36ddca8cde...4eaacf0543bb3f2c246792bd56e8cdeffafb205a) --- updated-dependencies: - dependency-name: ossf/scorecard-action dependency-version: 2.4.3 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> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#1984) updates: - [github.com/astral-sh/ruff-pre-commit: v0.13.1 → v0.13.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.13.1...v0.13.3) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * Skip test_incrementalpca_fit_zarr() if Zarr is not installed * Fix Zarr test initialization to prevent ContainsGroupError in MPI runs * Second approach to solving the ContainsGroupError Previously, the `test_incrementalpca_fit_zarr` unit test failed with a `ContainsGroupError` when using Zarr files in multi-process setups. The issue was caused by passing the `dataset` parameter to `load_zarr()`, which does not expect it and can conflict with the internal Zarr group structure. This commit updates the `fit()` method to call `load_hdf5()` and `load_zarr()` separately, each with only the parameters they require. The unified `load_data_from_file` approach is kept for the loop, but the dataset argument is no longer passed to `load_zarr()`. Test modifications that previously tried to manually delete datasets and add MPI barriers have been reverted, as they are no longer needed. * Third approach to solving the ContainsGroupError Create the Zarr array directly at the path in the test instead of creating a root group. This should avoid the ContainsGroupError when load_zarr() expects an array at the given path. * Another attempt at solving the ContainsGroupError * Bugs/1990 Fix handling of zarr groups (#1991) * introduce variable to handle zarr groups * expand tests * edit docs * do not test with float64 on MPS * files housekeeping on MPS * load zarr variable from multiple dirs * fix path reading * fix import * expand docs * set device * fix dtype on empty ranks, balance output, refactor * adapt tests * Apply suggestions from code review Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * expand tests * fix deadlock at split sanitation * enable dtype setting * expand tests --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * build(deps): bump github/codeql-action from 3.30.6 to 4.30.9 (#2000) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.30.6 to 4.30.9. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/64d10c13136e1c5bce3e5fbde8d4906eeaafc885...16140ae1a102900babc80a33c44059580f687047) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 4.30.9 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> * build(deps): bump docker/login-action from 3.5.0 to 3.6.0 (#1993) Bumps [docker/login-action](https://github.com/docker/login-action) from 3.5.0 to 3.6.0. - [Release notes](https://github.com/docker/login-action/releases) - [Commits](https://github.com/docker/login-action/compare/184bdaa0721073962dff0199f1fb9940f07167d1...5e57cd118135c172c3672efd75eb46360885c0ef) --- updated-dependencies: - dependency-name: docker/login-action dependency-version: 3.6.0 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> Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <juanpedroghm@gmail.com> * build(deps): bump actions/dependency-review-action from 4.8.0 to 4.8.1 (#1992) Bumps [actions/dependency-review-action](https://github.com/actions/dependency-review-action) from 4.8.0 to 4.8.1. - [Release notes](https://github.com/actions/dependency-review-action/releases) - [Commits](https://github.com/actions/dependency-review-action/compare/56339e523c0409420f6c2c9a2f4292bbb3c07dd3...40c09b7dc99638e5ddb0bfd91c1673effc064d8a) --- updated-dependencies: - dependency-name: actions/dependency-review-action dependency-version: 4.8.1 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> Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <juanpedroghm@gmail.com> * Remove Zarr support for `IncrementalPCA` from this branch * build(deps): bump actions/upload-artifact from 4.6.2 to 5.0.0 (#2009) Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 4.6.2 to 5.0.0. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/ea165f8d65b6e75b540449e92b4886f43607fa02...330a01c490aca151604b8cf639adc76d48f6c5d4) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-version: 5.0.0 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> * build(deps): bump github/codeql-action from 4.30.9 to 4.31.0 (#2008) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 4.30.9 to 4.31.0. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/16140ae1a102900babc80a33c44059580f687047...4e94bd11f71e507f7f87df81788dff88d1dacbfb) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 4.31.0 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> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#1995) updates: - [github.com/astral-sh/ruff-pre-commit: v0.13.3 → v0.14.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.13.3...v0.14.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#2010) updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.1 → v0.14.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.1...v0.14.2) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Rework ipca test methods for clarity and code coverage * followed JPs suggestion * added tests * ... * ... * add additional tests * removed dead code * added continuous benchmarks * fixed error * fixed error attempt 2 * build(deps): bump github/codeql-action from 4.31.0 to 4.31.2 (#2015) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 4.31.0 to 4.31.2. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/4e94bd11f71e507f7f87df81788dff88d1dacbfb...0499de31b99561a6d14a36a5f662c2a54f91beee) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 4.31.2 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> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * build(deps): bump docker/setup-qemu-action from 3.6.0 to 3.7.0 (#2021) Bumps [docker/setup-qemu-action](https://github.com/docker/setup-qemu-action) from 3.6.0 to 3.7.0. - [Release notes](https://github.com/docker/setup-qemu-action/releases) - [Commits](https://github.com/docker/setup-qemu-action/compare/29109295f81e9208d7d86ff1c6c12d2833863392...c7c53464625b32c7a7e944ae62b3e17d2b600130) --- updated-dependencies: - dependency-name: docker/setup-qemu-action dependency-version: 3.7.0 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> * build(deps): bump step-security/harden-runner from 2.13.1 to 2.13.2 (#2022) Bumps [step-security/harden-runner](https://github.com/step-security/harden-runner) from 2.13.1 to 2.13.2. - [Release notes](https://github.com/step-security/harden-runner/releases) - [Commits](https://github.com/step-security/harden-runner/compare/f4a75cfd619ee5ce8d5b864b0d183aff3c69b55a...95d9a5deda9de15063e7595e9719c11c38c90ae2) --- updated-dependencies: - dependency-name: step-security/harden-runner dependency-version: 2.13.2 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> * [pre-commit.ci] pre-commit autoupdate (#2017) * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.2 → v0.14.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.2...v0.14.3) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#2023) updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.3 → v0.14.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.3...v0.14.4) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Set correct dtype when loading and saving hdf5 (#2014) * fixed load_hdf5 * fixed save_hdf5 * fixed different behavior in tests * test torch dtype for save_hdf5 --------- Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * build(deps): bump github/codeql-action from 4.31.2 to 4.31.3 (#2026) * build(deps): bump actions/dependency-review-action from 4.8.1 to 4.8.2 (#2025) Bumps [actions/dependency-review-action](https://github.com/actions/dependency-review-action) from 4.8.1 to 4.8.2. - [Release notes](https://github.com/actions/dependency-review-action/releases) - [Commits](https://github.com/actions/dependency-review-action/compare/40c09b7dc99638e5ddb0bfd91c1673effc064d8a...3c4e3dcb1aa7874d2c16be7d79418e9b7efd6261) --- updated-dependencies: - dependency-name: actions/dependency-review-action dependency-version: 4.8.2 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> * [pre-commit.ci] pre-commit autoupdate (#2027) updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.4 → v0.14.5](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.4...v0.14.5) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add a Heat aware DistributedSampler for torch usage. (#1807) * Added possible Distributed Dataset and Sampler for torch usage. Works on a process local basis. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Added Distributed new sample that shuffles all rows across the ranks * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add edge case for manual seed of torch * added some argument checks and updated documentation a bit * added tests and possible usage for gpus * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Implement shuffle using indexed data type instead of using unnecesarry copies. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove as mpi memory for correct functionality when using gpus * added mpi rank sorting correction to corrospond with first permutation. * change logic behind batches testing * add an all call to the isclose if * Skip batches test because of weird behaviour on diffrent systems * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * shuffle when setting the seed rather than creating the iter * use datatype for receive too, to circumvent int32 limit * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fixed wrong lenght usage and allow displacements bigger than uint32 in the sending datatype * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added option to decide to shuffle globally or locally * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * changed local shuffle to randperm inside the iter function, instead of shuffling local tensor * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Added and corrected documentation according to pydocstyle * fixed recv issues for high element count and ordering * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * - Add correction for recv buffer - Add Comments for init - made idxmap creation faster * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * - Add saving of the buffer - remove randperm for correction * - Fixed Recv_type for small arrays. - Added Train, val split function using the sampler. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * - Removed unused variables * fix: fixed tests, simplified permutation code * fix: brought back alltoall implementation, for future exploration * fix: return repr as it was * Remove seed initialization in basic_test.py Remove seed initialization from the test setup. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <juanpedroghm@gmail.com> Co-authored-by: Fabian Hoppe <112093564+mrfh92@users.noreply.github.com> * build(deps): bump actions/checkout from 5.0.0 to 6.0.0 (#2035) Bumps [actions/checkout](https://github.com/actions/checkout) from 5.0.0 to 6.0.0. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/08c6903cd8c0fde910a37f88322edcfb5dd907a8...1af3b93b6815bc44a9784bd300feb67ff0d1eeb3) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: 6.0.0 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> * build(deps): bump peter-evans/create-pull-request from 7.0.8 to 7.0.9 (#2033) Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 7.0.8 to 7.0.9. - [Release notes](https://github.com/peter-evans/create-pull-request/releases) - [Commits](https://github.com/peter-evans/create-pull-request/compare/271a8d0340265f705b14b6d32b9829c1cb33d45e...84ae59a2cdc2258d6fa0732dd66352dddae2a412) --- updated-dependencies: - dependency-name: peter-evans/create-pull-request dependency-version: 7.0.9 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> * build(deps): bump github/codeql-action from 4.31.3 to 4.31.4 (#2034) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 4.31.3 to 4.31.4. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/014f16e7ab1402f30e7c3329d33797e7948572db...e12f0178983d466f2f6028f5cc7a6d786fd97f4b) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 4.31.4 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> * [pre-commit.ci] pre-commit autoupdate (#2041) updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.5 → v0.14.6](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.5...v0.14.6) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * integration of reigh into SpectralClustering as new default method (replacing Lanczos) * Add device parameter to QR output arrays Update QR decomposition to include device parameter for R and Q arrays. * Add device parameter to factories.array calls for non-distributed eigh * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Supporting negative indices for flip operations (#2030) * Converting negative indices * use sanitize_axis * Added tests * edit docs --------- Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * Bump version to 1.7.0 * Update pytorch image in Dockerfile.release and Dockerfile.source to version * prep for 1.7.0 * feat: add ptp function to statistics module (#1897) (#1954) * feat: add ptp function to statistics module (#1897) * Fix type annotation for DNDarray.ptp Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * build(deps): bump github/codeql-action from 3.29.9 to 3.29.11 Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.29.9 to 3.29.11. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/github/codeql-action/compare/df559355d593797519d70b90fc8edd5db049e7a2...3c3833e0f8c1c83d449a7478aa59c036a9165498) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.29.11 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * Implement custom MPI_MINMAX reduction for ptp to minimize communication * Implement custom MPI_MINMAX reduction for ptp to minimize communication * Move min/max MPI op into communications, implement closure-based MPI_MINMAX and update ptp to use it * Implement dtype/size/stride-specific MPI _minmax_op and integrate it into ptp * Update ptp assertions in test_statistics.py Changed assertions from assertAlmostEqual to assertEqual for ptp comparison. --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <juanpedroghm@gmail.com> Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <juan.muriedas@kit.edu> * [pre-commit.ci] pre-commit autoupdate (#2059) * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/pre-commit/mirrors-mypy: v1.18.2 → v1.19.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.18.2...v1.19.0) - [github.com/astral-sh/ruff-pre-commit: v0.14.6 → v0.14.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.14.6...v0.14.7) * fix: invalid types for old versions of pytorch --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <juanpedroghm@gmail.com> * build(deps): bump actions/setup-python from 6.0.0 to 6.1.0 (#2049) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 6.0.0 to 6.1.0. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](https://github.com/actions/setup-python/compare/e797f83bcb11b83ae66e0230d6156d7c80228e7c...83679a892e2d95755f2dac6acb0bfd1e9ac5d548) --- updated-dependencies: - dependency-name: actions/setup-python dependency-version: 6.1.0 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> Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <juanpedroghm@gmail.com> * Handling of unknown MPI Libraries (#2032) * fix: Added 'other' as option for mpi library * fix: corrected parastation configuration * Update heat/core/_config.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Array API (#1022) * Create `array_api` namespace * Enable `copy` parameter for `asarray` * Add `iinfo` and `finfo` * Add constants * Modify `iinfo` and `finfo` to read minimum value from torch object This fixes a bug where negative numbers could be represented by uint8. * Add docstrings * Fix bug where `keepdim` was not working for `all` * Implement `all` * Implement `Array.__eq__` * Implement `astype` * Implement `Array` object * Implement `add` * Standardize import order * Document function parameters * Fix bug causing precision loss in `abs` In cases involving large numbers where the `dtype` parameter was unchanged, precision loss occurred due to intermediate casting to float32 (in `__local_op`) before casting back to the original `dtype`. Fixed by not doing the intermediate casting. * Implement `abs` * Implement `add` * Implement `bitwise_and` * Implement `bitwise_left_shift`, `less`, `any` Fixed bug in `ht.any` where `keepdim` argument was not working when `axis=None` (same fix as 136e1b7) * Implement `bitwise_invert` * Implement `bitwise_or` * Fix documentation for `_normalize_two_args` * Fix bug in `linalg.matrix_norm` f0a169b introduced a change in ht.abs where the dtype is not promoted to float by default. This caused the tests to fail. * Implement `bitwise_xor` * Implement `equal` * Implement `floor_divide` * Implement `greater_equal` * Implement `greater` * Implement `less_equal` * Implement `remainder` * Implement `multiply` * Implement `not_equal` * Implement `negative` * Implement `positive` * Implement `pow` * Implement `subtract` * Implement `divide` * Implement reflected arithmetic operators * Implement `empty` * Fix bug causing precision loss in `arange` * Implement `empty_like` * Implement `full_like` * Allow `linspace` to accept `num=0` * Fix precision bug in `linspace` * Enable bool dtype for `arange` * Fix tests for `logspace` * Fix `abs` tests * Fix `abs` tests * Implement `meshgrid` * Implement `ones` * Implement `ones_like` * Implement `zeros_like` and `full` * Implement `result_type` * Implement `expand_dims` * Implement `flip` * Implement `permute_dims` * Implement `roll` * Implement `squeeze` * Implement `can_cast` * Implement `acos` * Implement `acosh` * Implement `asin` and `asinh` * Implement `atan`, `atan2`, `atanh` * Implement `ceil` * Implement `cos` and `cosh` * Implement `exp` and `expm1` * Implement `floor` * Implement `log`, `log1p`, `log2`, `log10`, `logaddexp` * Implement `logical_and`, `logical_not`, `logical_or`, `logical_xor` * Implement `round` * Implement `sign` * Implement `sin` and `sinh` * Implement `square` and `sqrt` * Implement `tan` and `tanh` * Implement `trunc` * Implement `argmax` and `argmin` * Implement `vecdot` * Implement `unique_values` * Implement `max` and `min` * Implement `mean` * Implement `std` * Fix documentation * Add dlpack functions * Extract changes made in core module Shift changes made in core module to separate branches for individual PRs. * Restore original `abs` * Fix documentation * Add `from_dlpack` * Add ci tests * [skip ci] install MPI, update API reference, introduce manual trigger * [skip ci] trigger on PR label * adding back original trigger * back to original trigger * [skip ci] fix workflow indentation * fix URL of test repository * Test Python 3.9 and 3.10 * Update array-api.yml * change skipfile path * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update array-api.yml Retry test suite * Update array-api.yml * Update array-api.yml * Update array-api.yml * Update array-api.yml * Update array-api.yml * Update array-api.yml * Update array-api.yml * Update array-api.yml * Update array-api.yml * Update array-api.yml * update skips file * Update array-api.yml * Update array-api.yml * skips * update skips.txt * Update skips.txt * Update skips.txt * Update array-api.yml * Update array-api.yml * Update array-api.yml * Update array-api.yml * Update array-api.yml * Update array-api.yml * Update array-api.yml * Update __init__.py * skip failing tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update array-api.yml * Update array-api.yml * update skips * update skips * update skips.txt * Update skips.txt * Update array-api.yml * add complex types * update skips.txt/xfails.txt * update skips * update skips/xfails * update skips/xfails * put functions in limbo into skips * update skips * update files * add more skips * add more skips * even more skips * much more skips * and more * change to manual trigger * add contributor * Update codecov.yml ignore coverage array_api * Update array-api.yml * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * ruff check fixes * ruff fixes * update action --------- Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> Co-authored-by: Michael Tarnawa <m.tarnawa@fz-juelich.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Michael Tarnawa <18899420+mtar@users.noreply.github.com> Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <juanpedroghm@gmail.com> * Apply suggestion from @Copilot Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * make the code fit for maintenance/usage by non-mathematicians: added clarification on SVD-rank/Matrix-rank vs MPI-rank * made hdf5 support optional again, catch error in IncrementalPCA.fit * build(deps): bump actions/checkout from 6.0.0 to 6.0.1 (#2062) Bumps [actions/checkout](https://github.com/actions/checkout) from 6.0.0 to 6.0.1. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/1af3b93b6815bc44a9784bd300feb67ff0d1eeb3...8e8c483db84b4bee98b60c0593521ed34d9990e8) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch ... 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* Heat 1.6.0 - Release (#1957) * Update heat/core/io.py Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * added test for dndarray.info * added tests for two uncovered exception lines * one additional line from DMD covered * one more line in DMD covered * debugging * build(deps): bump actions/setup-python from 5.4.0 to 5.5.0 Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5.4.0 to 5.5.0. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@4237552...8d9ed9a) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/PyCQA/flake8: 7.1.2 → 7.2.0](PyCQA/flake8@7.1.2...7.2.0) * build(deps): bump github/codeql-action from 3.28.12 to 3.28.13 Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.28.12 to 3.28.13. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@5f8171a...1b549b9) --- updated-dependencies: - dependency-name: github/codeql-action dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * further work on eigh * eigh completed for split = 0 * flake8 * tests for eigh, now split=none,0,1 * build(deps): bump step-security/harden-runner from 2.11.0 to 2.11.1 (#1851) Bumps [step-security/harden-runner](https://github.com/step-security/harden-runner) from 2.11.0 to 2.11.1. - [Release notes](https://github.com/step-security/harden-runner/releases) - [Commits](step-security/harden-runner@4d991eb...c6295a6) --- updated-dependencies: - dependency-name: step-security/harden-runner dependency-version: 2.11.1 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> * build(deps): bump actions/dependency-review-action from 4.5.0 to 4.6.0 (#1850) Bumps [actions/dependency-review-action](https://github.com/actions/dependency-review-action) from 4.5.0 to 4.6.0. - [Release notes](https://github.com/actions/dependency-review-action/releases) - [Commits](actions/dependency-review-action@3b139cf...ce3cf95) --- updated-dependencies: - dependency-name: actions/dependency-review-action dependency-version: 4.6.0 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> * Apply suggestions from code review Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * minor modifications due to Copilot's Review * added SVD for general case * reformatting * tests for SVD * tests for SVD completed * added module _config in core which is intended to handle MPI, CUDA, and ROCm versioning * added variable GPU_AWARE_MPI * added MPICH * changed method info into __repr__ * moved __repr__ to printing module * removed dead code * restructuring of tests * added further test to DMDc * small typo corrected * adapted tolerances for last test; errors grow w.r.t. timesteps (is in the nature of DMD), so largest number of procs determines tolerance * Update test_dmd.py lower tolerances for the AMD-runner * dummy commit since sth was wrong with pre-commit * corrected tests * debugging of tests * Remove unnecessary contiguous calls (#1831) * removed contiguous calls from manipulations.py * removed the contiguous calls from linalg/qr.py * removed unnecessary contiguous call in factories.py * removed some more unnecessary contiguous calls * reinstate contiguous() calls if needed * removed the contiguous calls from linalg/qr.py * reinstate setting Q_buf to Q_curr --------- Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * build(deps): bump github/codeql-action from 3.28.13 to 3.28.15 Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.28.13 to 3.28.15. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@1b549b9...45775bd) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.28.15 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * removed debugging prints that were forgotten before merging into main * subTest'ified the zarr tests, added some strange exception handling that is likely necessary to accomodate zarr-versions compatible with Python 3.10 * small bug fix * bugfix in eigh * removed unneccesary numpy import * changed representation string according to review * debugging of memory consumption in Polar * bug fixes for devices in polar and eigh * bugfixes for certain device constellations * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update README.md * Support latest PyTorch release * Make unit tests compatible with NumPy 2.x (#1826) * changed row_stack to vstack for numpy >= 2.0.0 * Changed the numpy version check to the numpy suggested method * Changed numpy version requirement * fixed DeprecationWarning from missing axes for np.fft.fftn * Fixed one __array_wrap__ DeprecationWarning * Stopped testing cross of vector axes with 2 elements for numpy >= 2.0 * changed requirements to avoid errors with numpy >= 2 * Using Python 3.10 for RecievePR * changed python-version to '3.10' because 3.10 was interpreted as 3.1 * changed ci.yaml to exclude python 3.9 * Fixed two DeprecationWarnings of np.cross() by adding a third dimension with zeros * Fixed the last np.cross() warning by performing the operation manually * changed dtype of np.cross() to float32 --------- Co-authored-by: Fabian Hoppe <112093564+mrfh92@users.noreply.github.com> Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <juanpedroghm@gmail.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * build(deps): bump actions/setup-python from 5.5.0 to 5.6.0 (#1863) * build(deps): bump actions/setup-python from 5.5.0 to 5.6.0 Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5.5.0 to 5.6.0. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@8d9ed9a...a26af69) --- updated-dependencies: - dependency-name: actions/setup-python dependency-version: 5.6.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * Debugging --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * build(deps): bump docker/build-push-action from 6.15.0 to 6.16.0 (#1860) Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 6.15.0 to 6.16.0. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](docker/build-push-action@471d1dc...14487ce) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-version: 6.16.0 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> * build(deps): bump step-security/harden-runner from 2.11.1 to 2.12.0 (#1861) Bumps [step-security/harden-runner](https://github.com/step-security/harden-runner) from 2.11.1 to 2.12.0. - [Release notes](https://github.com/step-security/harden-runner/releases) - [Commits](step-security/harden-runner@c6295a6...0634a26) --- updated-dependencies: - dependency-name: step-security/harden-runner dependency-version: 2.12.0 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> * build(deps): bump github/codeql-action from 3.28.15 to 3.28.17 (#1866) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.28.15 to 3.28.17. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@45775bd...60168ef) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.28.17 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> * build(deps): bump actions/dependency-review-action from 4.6.0 to 4.7.0 Bumps [actions/dependency-review-action](https://github.com/actions/dependency-review-action) from 4.6.0 to 4.7.0. - [Release notes](https://github.com/actions/dependency-review-action/releases) - [Commits](actions/dependency-review-action@ce3cf95...38ecb5b) --- updated-dependencies: - dependency-name: actions/dependency-review-action dependency-version: 4.7.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * added benchmarks for eigh, svd, and rsvd * dummy commit to trigger benchmark runs * Support latest PyTorch release * changed torchvision version to <0.22.1 * retrigger checks * build(deps): bump github/codeql-action from 3.28.17 to 3.28.18 Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.28.17 to 3.28.18. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@60168ef...ff0a06e) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.28.18 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * build(deps): bump docker/build-push-action from 6.16.0 to 6.17.0 Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 6.16.0 to 6.17.0. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](docker/build-push-action@14487ce...1dc7386) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-version: 6.17.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * build(deps): bump actions/dependency-review-action from 4.7.0 to 4.7.1 Bumps [actions/dependency-review-action](https://github.com/actions/dependency-review-action) from 4.7.0 to 4.7.1. - [Release notes](https://github.com/actions/dependency-review-action/releases) - [Commits](actions/dependency-review-action@38ecb5b...da24556) --- updated-dependencies: - dependency-name: actions/dependency-review-action dependency-version: 4.7.1 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * RTD Notebook gallery and profiling notebook with perun. (#1867) * docs: notebook gallery in rtd * docs: missing makefiles * docs: reverted changes to gitignore * haicore notebook setup * ompi in readthedocs build * correct apt package for mpi * docs: replaced small bodies dataset with digits from sklearn (boring, but easier to access on the long term) * perun notebook * wrong cell type * added pytorch 2.7 to ci workflow * docs: post practice run fixes * notebook thumbnails, formatting and corrections for tutorial * forgot to uncomment autoapi * build(deps): bump github/codeql-action from 3.28.18 to 3.28.19 (#1881) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.28.18 to 3.28.19. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@ff0a06e...fca7ace) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.28.19 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> * build(deps): bump docker/build-push-action from 6.17.0 to 6.18.0 (#1877) Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 6.17.0 to 6.18.0. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](docker/build-push-action@1dc7386...2634353) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-version: 6.18.0 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> * build(deps): bump ossf/scorecard-action from 2.4.1 to 2.4.2 (#1878) Bumps [ossf/scorecard-action](https://github.com/ossf/scorecard-action) from 2.4.1 to 2.4.2. - [Release notes](https://github.com/ossf/scorecard-action/releases) - [Changelog](https://github.com/ossf/scorecard-action/blob/main/RELEASE.md) - [Commits](ossf/scorecard-action@f49aabe...05b42c6) --- updated-dependencies: - dependency-name: ossf/scorecard-action dependency-version: 2.4.2 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> * build(deps): bump step-security/harden-runner from 2.12.0 to 2.12.1 Bumps [step-security/harden-runner](https://github.com/step-security/harden-runner) from 2.12.0 to 2.12.1. - [Release notes](https://github.com/step-security/harden-runner/releases) - [Commits](step-security/harden-runner@0634a26...002fdce) --- updated-dependencies: - dependency-name: step-security/harden-runner dependency-version: 2.12.1 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * build(deps): bump github/codeql-action from 3.28.19 to 3.29.0 Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.28.19 to 3.29.0. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@fca7ace...ce28f5b) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.29.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * Add special methods for operations in NumPy * add tests for NumPy related array methods * fix variable name * Exit installation if conda environment cannot be activated (#1880) * exit 0_setup_conda.sh if environment cannot be activated otherwise the script might install into the base environment * exit 0_setup_pip.sh if environment cannot be activated --------- Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <juanpedroghm@gmail.com> * fix item access * add contiguous call again * same as before * [pre-commit.ci] pre-commit autoupdate (#1894) updates: - [github.com/PyCQA/flake8: 7.2.0 → 7.3.0](PyCQA/flake8@7.2.0...7.3.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * bugfix in rSVD for the case the rank is smaller than number of processes * build(deps): bump github/codeql-action from 3.29.0 to 3.29.1 Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.29.0 to 3.29.1. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@ce28f5b...39edc49) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.29.1 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * resolved bug in rSVD, actualle one-process QR * Support PyTorch 2.7.1 (#1883) * Support latest PyTorch release * Update ci.yaml pytorch: add v2.2, drop v1.11 * debugging test_lasso * Support latest PyTorch release * Update bug_report.yml Add latest versions for options * update torchvision * do not test latest torch in matrix * pin zarr version * remove dead code * pin zarr to 3.0.8 * add back latest pytorch to matrix * edit PR body * Update ci.yaml --------- Co-authored-by: ClaudiaComito <39374113+ClaudiaComito@users.noreply.github.com> Co-authored-by: Michael Tarnawa <m.tarnawa@fz-juelich.de> Co-authored-by: Michael Tarnawa <18899420+mtar@users.noreply.github.com> * build(deps): bump docker/setup-buildx-action from 3.10.0 to 3.11.1 Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 3.10.0 to 3.11.1. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](docker/setup-buildx-action@b5ca514...e468171) --- updated-dependencies: - dependency-name: docker/setup-buildx-action dependency-version: 3.11.1 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * Update polar.py * Revert "build(deps): bump docker/setup-buildx-action from 3.10.0 to 3.11.1" (#1908) * support torch_function (#1895) Co-authored-by: Fabian Hoppe <112093564+mrfh92@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * Features/1845 Update citations (#1846) * Update README.md: added citation possibilities * Update README.md: link to ZENODO * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update README.md * Update README.md * Update README.md --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <juanpedroghm@gmail.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * Transition to pyproject.toml, Ruff, and mypy (#1832) * Support latest PyTorch release * Support latest PyTorch release * retrigger checks * wip: toml, ruff, mypy and cli * ci: better mypy error filter (down to 3041) * ci: mypy in list of dev deps * ci: skiping mypy for now * dependency specification * missing argument description for permute method * fixed dynamic version in pyproject.toml * properly skipping mypy in the pre-commit.ci * fixed dependencies, removed references to python 3.9, added python 3.13 * doc -> docs * fixed tests * cli tests * Update .github/ISSUE_TEMPLATE/bug_report.yml Co-authored-by: Michael Tarnawa <18899420+mtar@users.noreply.github.com> * removed problematic pytorch version?! * consistency is important * did not work * vulnerabitliy removal, other changes to toml * It's not working :( * fixing tests * Update .pre-commit-config.yaml * fix: cli does not change the default device * fix: support for older pytorch version on the cli, limit zarr package version * Update pytorch exclude with py-3.13 --------- Co-authored-by: ClaudiaComito <39374113+ClaudiaComito@users.noreply.github.com> Co-authored-by: Marc-Jindra <m.jindra@fz-juelich.de> Co-authored-by: Michael Tarnawa <18899420+mtar@users.noreply.github.com> * build(deps): bump docker/setup-buildx-action from 3.10.0 to 3.11.1 (#1911) Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 3.10.0 to 3.11.1. - [Release notes](https://github.com/docker/setup-buildx-action/releases) - [Commits](docker/setup-buildx-action@b5ca514...e468171) --- updated-dependencies: - dependency-name: docker/setup-buildx-action dependency-version: 3.11.1 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> * build(deps): bump github/codeql-action from 3.29.1 to 3.29.2 (#1910) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.29.1 to 3.29.2. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@39edc49...181d5ee) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.29.2 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> * build(deps): bump step-security/harden-runner from 2.12.1 to 2.12.2 (#1909) Bumps [step-security/harden-runner](https://github.com/step-security/harden-runner) from 2.12.1 to 2.12.2. - [Release notes](https://github.com/step-security/harden-runner/releases) - [Commits](step-security/harden-runner@002fdce...6c439dc) --- updated-dependencies: - dependency-name: step-security/harden-runner dependency-version: 2.12.2 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> * Apply suggestions from code review Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * took review into account * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * pre-commit stuff * [pre-commit.ci] pre-commit autoupdate (#1912) updates: - [github.com/astral-sh/ruff-pre-commit: v0.11.13 → v0.12.3](astral-sh/ruff-pre-commit@v0.11.13...v0.12.3) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Updated release_prep.yml to incorporate up-to-date Dockerfile Pytorch versions (#1903) * Create update_docker.yml * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update release-prep.yml Added the update functionality of the Dockerfile.source and Dockerfile.release Pytorch Image versions. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Removed update_docker.yml since the functionality was moved to release prep --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * [StepSecurity] Apply security best practices (#1891) * [StepSecurity] Apply security best practices Signed-off-by: StepSecurity Bot <bot@stepsecurity.io> * Test with shellcheck-py * Update .pre-commit-config.yaml * shellcheck updates * Update build_and_push.sh * Update increment_version.sh * Update increment_version.sh * Update build_and_push.sh * Update test_nvidia_image_haicore_enroot.sh * Update test_nvidia_image_haicore_enroot.sh * Update build_and_push.sh * Update 0_setup_pip.sh --------- Signed-off-by: StepSecurity Bot <bot@stepsecurity.io> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * build(deps): bump korthout/backport-action from 3.2.0 to 3.2.1 Bumps [korthout/backport-action](https://github.com/korthout/backport-action) from 3.2.0 to 3.2.1. - [Release notes](https://github.com/korthout/backport-action/releases) - [Commits](korthout/backport-action@436145e...0193454) --- updated-dependencies: - dependency-name: korthout/backport-action dependency-version: 3.2.1 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * build(deps): bump step-security/harden-runner from 2.12.1 to 2.13.0 Bumps [step-security/harden-runner](https://github.com/step-security/harden-runner) from 2.12.1 to 2.13.0. - [Release notes](https://github.com/step-security/harden-runner/releases) - [Commits](step-security/harden-runner@v2.12.1...ec9f2d5) --- updated-dependencies: - dependency-name: step-security/harden-runner dependency-version: 2.13.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/pre-commit/mirrors-mypy: v1.16.1 → v1.17.0](pre-commit/mirrors-mypy@v1.16.1...v1.17.0) - [github.com/astral-sh/ruff-pre-commit: v0.12.3 → v0.12.4](astral-sh/ruff-pre-commit@v0.12.3...v0.12.4) - [github.com/gitleaks/gitleaks: v8.16.3 → v8.28.0](gitleaks/gitleaks@v8.16.3...v8.28.0) * Fix ValueError in save_zarr by conditional handling of chunks argument Fixes error when calling zarr.create by only passing chunks as a list if not None. * Unfix zarr version in pyproject.toml to test CI job `test_amd` * Add note in docstring of save_zarr() * build(deps): bump tj-actions/branch-names from 8.2.1 to 9.0.1 Bumps [tj-actions/branch-names](https://github.com/tj-actions/branch-names) from 8.2.1 to 9.0.1. - [Release notes](https://github.com/tj-actions/branch-names/releases) - [Changelog](https://github.com/tj-actions/branch-names/blob/main/HISTORY.md) - [Commits](tj-actions/branch-names@dde14ac...386e117) --- updated-dependencies: - dependency-name: tj-actions/branch-names dependency-version: 9.0.1 dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * build(deps): bump github/codeql-action from 3.29.2 to 3.29.4 Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.29.2 to 3.29.4. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@181d5ee...4e828ff) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.29.4 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> * Setuptools build fix on pytproject.toml (#1919) * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.12.4 → v0.12.5](astral-sh/ruff-pre-commit@v0.12.4...v0.12.5) * Stride argument for convolution (#1865) * Add: enable stride as input option for convolution Belongs to Issue 1755 Changes include - stride as optional input - stride in docstring (except for output dim computations and as example) - raise ValueError for incorrect option (stride < 1) and combinations (stride > 1 and mode = 'same') * Add: Failing stride tests in test_signal.py - Added correct results for odd and even kernel - Added calls for convolution with stride=2 except with exception for mode `same` - Covers is_mps true and false - Stopped at tests for large distributed signals * Add: Pass stride tests for standard cases Belongs to Issue 1755 - edge cases and batch-processing not yet implemented or tested - Fix test error - Implement stride to pass tests - Write convolution_stride.py script for debugging purposes, will be removed later * Add: test for large signals with stride Belongs to Issue 1755 - passes * Add: Test cases until batch Belongs to issue 1755 - Passes tests * Add: Failing tests for batch convolution with stride Belongs to Issue 1755 * Add: batch processing with stride Belongs to Issue 1755 - Added stride to conv1D call in batch_convolution - Passes tests * Remove: Remove script to test convolution with stride * Update: Docstring of convolution Belongs to Issue 1755 - Correct stride information - Add examples * Fail: Tests fail for mpirun -n3 ... - Issue with halo size - Problem marked in code - Not solved * Update: Split stride tests - Different configurations in different tests functions - If process number == 1: all pass - If multiple process < 3 (because tested only then), 5 fail - This needs to be fixed, likely fails due to wrong halo in presence of stride * Add: Enable stride on distributed arrays but not kernels Adjust signal on each rank such that it starts with the next kernel according to stride - Added the compution of starting values for each rank - Avoid doubles for even and odd kernels Halo size computation is independent of stride Added a script for debugging, will be removed Ideas: generalize it for stride 1 (should work out of the box) To do: Adapt for distributed kernels * Add: Distributed Kernels and optimized start index computation Optimized start index computation: - Remove global index array - Use lshap map and simple modulo operation only Distributed kernels - Any stride > 1 is a subset of the solution for stride 1 - Not the most efficient but at least functional * Fix: Improve test coverage Still missing - Cuda code bits - else statement beginning line 229 * Delete: conv_test.py Test script no longer needed * Add: Add benchmarks for signal.py * Add: script to test benchmark - empty so far * Fix: Benchmarks - Fix run_signal_benchmarks - Add run_signal_benchmarks to main.py Remove: print statements from convolution in signal.py * Fix: benchmarks/cb/signal.py - add () to monitor decorator of perun * Fix: Rename signal.py to avoid clash with python3.12 signal - change signal.py to heat_signal.py * Fix: Adjust array numbers for benchmarking * Remove: benchmark script from scripts/ * Fix: Benchmarking signal.py and testing signal.py - Benchmark improved - removed import pytest from test_signal.py * Fix: test_signal.py batch convolution with stride - Stride was not passed as a single value but different values for different ranks - Solution: Do not randomly create stride values but use fixed values * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix: test_convolution-stride_large_signal_and_kernel_modes - Remove torch arrays - Instead work with np.convolve similar to test without stride * Fix: Add device for empty torch tensors - Stride test fails for large arrays - Error message says, that device does not match - Due to large stride, potentially empty tensor creation -> add device to that tensor created * Fix: torch_device instead of device - when empty tensor is called, use torch_device * Fix: Missed .device to previous commit * Fix: torch device not accessible - instead use str(ht_array.device) - Use signal.device to get correct rank --------- Co-authored-by: Fabian Hoppe <112093564+mrfh92@users.noreply.github.com> Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <juanpedroghm@gmail.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * build(deps): bump tj-actions/branch-names from 9.0.1 to 9.0.2 (#1930) Bumps [tj-actions/branch-names](https://github.com/tj-actions/branch-names) from 9.0.1 to 9.0.2. - [Release notes](https://github.com/tj-actions/branch-names/releases) - [Changelog](https://github.com/tj-actions/branch-names/blob/main/HISTORY.md) - [Commits](tj-actions/branch-names@386e117...5250492) --- updated-dependencies: - dependency-name: tj-actions/branch-names dependency-version: 9.0.2 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> * build(deps): bump github/codeql-action from 3.29.4 to 3.29.8 (#1933) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.29.4 to 3.29.8. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@4e828ff...76621b6) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.29.8 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> * build(deps): bump docker/login-action from 3.4.0 to 3.5.0 (#1934) Bumps [docker/login-action](https://github.com/docker/login-action) from 3.4.0 to 3.5.0. - [Release notes](https://github.com/docker/login-action/releases) - [Commits](docker/login-action@74a5d14...184bdaa) --- updated-dependencies: - dependency-name: docker/login-action dependency-version: 3.5.0 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> * [pre-commit.ci] pre-commit autoupdate (#1931) updates: - [github.com/pre-commit/mirrors-mypy: v1.17.0 → v1.17.1](pre-commit/mirrors-mypy@v1.17.0...v1.17.1) - [github.com/astral-sh/ruff-pre-commit: v0.12.5 → v0.12.7](astral-sh/ruff-pre-commit@v0.12.5...v0.12.7) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <juanpedroghm@gmail.com> * Update CODE_OF_CONDUCT.md New email for reporting * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * build(deps): bump github/codeql-action from 3.29.8 to 3.29.9 (#1943) Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.29.8 to 3.29.9. - [Release notes](https://github.com/github/codeql-action/releases) - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md) - [Commits](github/codeql-action@76621b6...df55935) --- updated-dependencies: - dependency-name: github/codeql-action dependency-version: 3.29.9 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> * build(deps): bump actions/checkout from 4.2.2 to 5.0.0 (#1942) Bumps [actions/checkout](https://github.com/actions/checkout) from 4.2.2 to 5.0.0. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@11bd719...08c6903) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: 5.0.0 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> * build(deps): bump korthout/backport-action from 3.2.1 to 3.3.0 (#1944) Bumps [korthout/backport-action](https://github.com/korthout/backport-action) from 3.2.1 to 3.3.0. - [Release notes](https://github.com/korthout/backport-action/releases) - [Commits](korthout/backport-action@0193454...ca4972a) --- updated-dependencies: - dependency-name: korthout/backport-action dependency-version: 3.3.0 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> * [pre-commit.ci] pre-commit autoupdate (#1936) updates: - [github.com/pre-commit/pre-commit-hooks: v5.0.0 → v6.0.0](pre-commit/pre-commit-hooks@v5.0.0...v6.0.0) - [github.com/astral-sh/ruff-pre-commit: v0.12.7 → v0.12.8](astral-sh/ruff-pre-commit@v0.12.7...v0.12.8) - [github.com/shellcheck-py/shellcheck-py: v0.10.0.1 → v0.11.0.1](shellcheck-py/shellcheck-py@v0.10.0.1...v0.11.0.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * Update latest-pytorch-support.yml (#1950) move to pyproject.toml * [pre-commit.ci] pre-commit autoupdate (#1949) updates: - [github.com/astral-sh/ruff-pre-commit: v0.12.8 → v0.12.9](astral-sh/ruff-pre-commit@v0.12.8...v0.12.9) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * Bump version to 1.6.0 * Update pytorch image in Dockerfile.release and Dockerfile.source to version * update coverage, add link to issue search * add FFT, masked arrays * Update authors and contributors in CITATION.cff * fix: typo in release drafter * Updated Changelog * changelog highlights * Update micro version to 0 * Update CHANGELOG.md * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: StepSecurity Bot <bot@stepsecurity.io> Co-authored-by: Fabian Hoppe <112093564+mrfh92@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> Co-authored-by: jolemse <35252911+jolemse@users.noreply.github.com> Co-authored-by: Hoppe <mrhf92@gmail.com> Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <juanpedroghm@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Marc-Jindra <m.jindra@fz-juelich.de> Co-authored-by: Hakdag97 <72792786+Hakdag97@users.noreply.github.com> Co-authored-by: Michael Tarnawa <18899420+mtar@users.noreply.github.com> Co-authored-by: Till Korten <webmaster@korten.at> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Michael Tarnawa <m.tarnawa@fz-juelich.de> Co-authored-by: StepSecurity Bot <bot@stepsecurity.io> Co-authored-by: Berkant <51971304+Berkant03@users.noreply.github.com> Co-authored-by: Lukas Scheib <ls.login.sl@gmail.com> Co-authored-by: Lukas Scheib <146953413+LScheib@users.noreply.github.com> Co-authored-by: lolacaro <carola.fischer.science@gmail.com> Co-authored-by: Björn Hagemeier <b.hagemeier@fz-juelich.de> Co-authored-by: Heat Release Bot <> * Sturdier MPI Check (#1926) (#1979) * sturdier mpi check * GPU_AWARE as relevant global check, checks can depend on version now * gpu aware compatiblity changes * wip: communication layer fixes for gpu_aware_mpi * _moveToCompDevice function * fix: disabled OpenMPI cuda awareness due to unreliable tests and benchmarks --------- (cherry picked from commit 3637662) Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <juanpedroghm@gmail.com> Co-authored-by: Fabian Hoppe <112093564+mrfh92@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * Bugs/1990 Fix handling of zarr groups (#1991) (#1999) * introduce variable to handle zarr groups * expand tests * edit docs * do not test with float64 on MPS * files housekeeping on MPS * load zarr variable from multiple dirs * fix path reading * fix import * expand docs * set device * fix dtype on empty ranks, balance output, refactor * adapt tests * Apply suggestions from code review * expand tests * fix deadlock at split sanitation * enable dtype setting * expand tests --------- (cherry picked from commit dc4bd1c) Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Set correct dtype when loading and saving hdf5 (#2014) (#2024) * fixed load_hdf5 * fixed save_hdf5 * fixed different behavior in tests * test torch dtype for save_hdf5 --------- (cherry picked from commit 678cd47) Co-authored-by: Marc-Jindra <m.jindra@fz-juelich.de> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * Supporting negative indices for flip operations (#2030) (#2050) * Converting negative indices * use sanitize_axis * Added tests * edit docs --------- (cherry picked from commit 3c0bc27) Co-authored-by: Marc-Jindra <m.jindra@fz-juelich.de> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * Bump version to 1.7.0 * Update pytorch image in Dockerfile.release and Dockerfile.source to version * prep for 1.7.0 * Add device parameter to QR output arrays (#2051) Update QR decomposition to include device parameter for R and Q arrays. (cherry picked from commit bd5df7c) Co-authored-by: Giovanni Pederiva <g.pederiva@fz-juelich.de> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * Handling of unknown MPI Libraries (#2032) (#2060) * fix: Added 'other' as option for mpi library * fix: corrected parastation configuration * Update heat/core/_config.py --------- (cherry picked from commit 50080e0) Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <juanpedroghm@gmail.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> * changelog * Update bug_report.yml * final changelog, citation and readme * fix: removed p3.14 tests * fix: dev version number --------- Signed-off-by: dependabot[bot] <support@github.com> Signed-off-by: StepSecurity Bot <bot@stepsecurity.io> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Fabian Hoppe <112093564+mrfh92@users.noreply.github.com> Co-authored-by: Claudia Comito <39374113+ClaudiaComito@users.noreply.github.com> Co-authored-by: jolemse <35252911+jolemse@users.noreply.github.com> Co-authored-by: Hoppe <mrhf92@gmail.com> Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <juanpedroghm@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: Marc-Jindra <m.jindra@fz-juelich.de> Co-authored-by: Hakdag97 <72792786+Hakdag97@users.noreply.github.com> Co-authored-by: Michael Tarnawa <18899420+mtar@users.noreply.github.com> Co-authored-by: Till Korten <webmaster@korten.at> Co-authored-by: Michael Tarnawa <m.tarnawa@fz-juelich.de> Co-authored-by: StepSecurity Bot <bot@stepsecurity.io> Co-authored-by: Berkant <51971304+Berkant03@users.noreply.github.com> Co-authored-by: Lukas Scheib <ls.login.sl@gmail.com> Co-authored-by: Lukas Scheib <146953413+LScheib@users.noreply.github.com> Co-authored-by: lolacaro <carola.fischer.science@gmail.com> Co-authored-by: Björn Hagemeier <b.hagemeier@fz-juelich.de> Co-authored-by: Heat Release Bot <> Co-authored-by: Giovanni Pederiva <g.pederiva@fz-juelich.de>
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Bumps github/codeql-action from 3.29.1 to 3.29.2.
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181d5eeMerge pull request #2957 from github/update-v3.29.2-4c57370d0c77386aFix changelog PR number8d43d4eUpdate changelog for v3.29.24c57370Merge pull request #2935 from github/mbg/interpret-cq-results2830b75Add changelog entryaa72ddaMerge branch 'main' into mbg/interpret-cq-results65d1e45RenameSARIF_UPLOAD_ENDPOINTmembers362ebf8Check both SARIF files inquality-queries.ymltest10a3e4bFix formatting8593ea6Merge pull request #2954 from github/mergeback/v3.29.1-to-main-39edc492Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting
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