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v3.5.2 - Terne Topi Patch 2

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@mashehu mashehu released this 30 Jan 16:07
3.5.2
fee44da
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v3.5.2 - Terne Topi Patch 2 - [2026-01-30]

General

  • Switch from pre-commit to prek for pre-commit hooks in development(#3899)
  • Fix docker errors in test (#3924)
  • switch to uv and pyproject.toml (#3925)
  • dockerhub action: add disk clean-up step and combine the two actions (#3926)
  • Pin j178/prek-action action to 91fd7d7 (#3931)
  • Simplify coverage reporting in pytest.yml (#3934)
  • add pre-commit hook to keep uv.lock in sync (#3933)
  • Fix quote handling in meta.yml (#3948)
  • Add support for SVG files in bump-version command (#3978)
  • handle type for val in topics correctly (#3991)
  • Update docker/login-action digest to c94ce9f (#3998)
  • fix wrong parsing when output values contain spaces (#3999)
  • fix failing devcontainer builds (#4013)

Linting

  • fix test for linting for version.yml (#3947)
  • Fix bugs in subworkflows lint causing false positive warnings (#3968)
  • more fixes for incorrect parsing of version statement (#3973)
  • handle val in version topics correctly (#3988)
  • handle additional attributes in input parsing correctly (#3990)

Modules

  • sort meta.yml based on keys in schema (#3958)
  • fix(modules_json): Use name string instead of dict as key in recreate_dependencies (#3963)
  • linting: polish regex for output parsing in modules main.nf (#3967)
  • modules linting: catch failing edamontology requests (#3994)

Subworkflows

  • Update to new topic version handling (#3929)

Version updates

  • Update actions/setup-python digest to 83679a8 (#3928)
  • Update python:3.14-slim Docker digest to 119fd5b (#3910)
  • Update pre-commit hook astral-sh/ruff-pre-commit to v0.14.7 (#3943)
  • Update mcr.microsoft.com/devcontainers/miniconda Docker digest to 2be0f5a (#3946)
  • Update actions/checkout digest to 8e8c483 (#3956)
  • Update GitHub Actions (#3957)
  • Update astral-sh/setup-uv digest to ed21f2f (#3959)
  • Update codecov/codecov-action digest to 671740a (#3962)
  • Update codecov/codecov-action digest to 671740a (#4000)
  • Update pre-commit hook pre-commit/mirrors-mypy to v1.19.1 (#4007)
  • Update pre-commit hook astral-sh/uv-pre-commit to v0.9.28 (#4006)
  • Update dependency textual-dev to v1.8.0 (#4005)
  • Update mcr.microsoft.com/devcontainers/base Docker tag to v2.1.5 (#4002)
  • Update dependency textual to v7 (#4008)
  • Update mcr.microsoft.com/devcontainers/miniconda Docker digest to 8a29f1c (#4009)
  • Update pre-commit hook astral-sh/ruff-pre-commit to v0.14.14 (#4011)
  • Update python:3.14-slim Docker digest to 9b81fe9 (#4012)
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