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github-actions wants to merge 16 commits into from
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Heat 1.6.1 - Main #2012

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@github-actions github-actions bot commented Oct 29, 2025

Copy of latest pre-release PR targeting release.
DO NOT CHANGE ANYTHING UNTIL HAS BEEN MERGED.

TODO:

  • Make sure version.py is updated to reflect the dev version.
  • Ensure Citation file is up to date.
  • Ensure the Changelog is up to date.
  • Test and merge conda-forge build (PR is usually created within a few hours of PyPi release)
  • Update docker image and related documentation (see Update Docker image #1716 )
  • Update spack recipe
  • Update easybuild recipe

github-actions bot and others added 5 commits September 3, 2025 13:12
@github-actions @mrfh92
@ClaudiaComito @jolemse @JuanPedroGHM @dependabot @pre-commit-ci @Marc-Jindra @Hakdag97 @mtar @thawn @step-security-bot @Berkant03 @LScheib @lolacaro @bhagemeier
Heat 1.6.0 - Release (#1957)
83727cb 
* Update heat/core/io.py

Co-authored-by: Claudia Comito <[email protected]>

* 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] <[email protected]>

* [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] <[email protected]>

* 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] <[email protected]>
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] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Apply suggestions from code review

Co-authored-by: Copilot <[email protected]>

* 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 <[email protected]>

* 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] <[email protected]>

* 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 <[email protected]>
Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <[email protected]>
Co-authored-by: Claudia Comito <[email protected]>

* 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] <[email protected]>

* Debugging

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Claudia Comito <[email protected]>

* 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] <[email protected]>
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] <[email protected]>
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] <[email protected]>
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] <[email protected]>

* 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] <[email protected]>

* 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] <[email protected]>

* 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] <[email protected]>

* 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] <[email protected]>
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] <[email protected]>
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] <[email protected]>
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] <[email protected]>

* 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] <[email protected]>

* 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 <[email protected]>

* 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] <[email protected]>

* 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 <[email protected]>
Co-authored-by: Michael Tarnawa <[email protected]>
Co-authored-by: Michael Tarnawa <[email protected]>

* 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] <[email protected]>

* 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 <[email protected]>
Co-authored-by: Claudia Comito <[email protected]>

* 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 <[email protected]>
Co-authored-by: Claudia Comito <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Marc-Jindra <[email protected]>
Co-authored-by: Michael Tarnawa <[email protected]>

* 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] <[email protected]>
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] <[email protected]>
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] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Apply suggestions from code review

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* took review into account

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* pre-commit stuff

* [pre-commit.ci] pre-commit autoupdate (#1912)

updates:
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* 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

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* 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

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* Removed update_docker.yml since the functionality was moved to release prep

---------

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* [StepSecurity] Apply security best practices (#1891)

* [StepSecurity] Apply security best practices

Signed-off-by: StepSecurity Bot <[email protected]>

* 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

---------

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Co-authored-by: Claudia Comito <[email protected]>

* 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:
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  update-type: version-update:semver-patch
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Signed-off-by: dependabot[bot] <[email protected]>

* 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:
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  update-type: version-update:semver-minor
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Signed-off-by: dependabot[bot] <[email protected]>

* [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
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  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

* 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:
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  dependency-version: 3.29.4
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...

Signed-off-by: dependabot[bot] <[email protected]>

* 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

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* 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 <[email protected]>
Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <[email protected]>
Co-authored-by: Claudia Comito <[email protected]>
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
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Signed-off-by: dependabot[bot] <[email protected]>
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* 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
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...

Signed-off-by: dependabot[bot] <[email protected]>
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* 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] <[email protected]>
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>
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* Update CODE_OF_CONDUCT.md

New email for reporting

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* 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] <[email protected]>
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] <[email protected]>
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* 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] <[email protected]>
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>
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* 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>
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* 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

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---------

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Signed-off-by: StepSecurity Bot <[email protected]>
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Co-authored-by: Claudia Comito <[email protected]>
Co-authored-by: jolemse <[email protected]>
Co-authored-by: Hoppe <[email protected]>
Co-authored-by: Juan Pedro Gutiérrez Hermosillo Muriedas <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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@github-actions @JuanPedroGHM
@mrfh92 @ClaudiaComito
Sturdier MPI Check (#1926) (#1979)
3c2b559 
* 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 <[email protected]>
Co-authored-by: Fabian Hoppe <[email protected]>
Co-authored-by: Claudia Comito <[email protected]>
@github-actions @ClaudiaComito
Bugs/1990 Fix handling of zarr groups (#1991) (#1999)
80756c5 
* 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 <[email protected]>
Co-authored-by: Copilot <[email protected]>
Bump version to 1.6.1
f3af3ee
Update pytorch image in Dockerfile.release and Dockerfile.source to v…
5a8a207 
…ersion
JuanPedroGHM and others added 11 commits October 29, 2025 11:07
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@JuanPedroGHM