ci.yml

name: CI

on:
  push:
    branches:
      - master
    tags:
      - "**"
  pull_request: {}

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: ${{ github.ref != 'refs/heads/master' }}

jobs:
  changes:
    runs-on: ubuntu-latest
    outputs:
      webknossos: ${{ steps.filter.outputs.webknossos || github.ref ==
        'refs/heads/master' }}
      cluster_tools: ${{ steps.filter.outputs.cluster_tools || github.ref ==
        'refs/heads/master' }}
    steps:
      - uses: actions/checkout@v6
      - uses: dorny/paths-filter@v4.0.1
        id: filter
        with:
          filters: |
            webknossos:
              - 'webknossos/**'
            cluster_tools:
              - 'cluster_tools/**'

  cluster_tools_slurm:
    needs: changes
    if: ${{ needs.changes.outputs.cluster_tools == 'true' }}
    runs-on: ubuntu-latest
    timeout-minutes: 30
    strategy:
      matrix:
        python-version: [ "3.13", "3.12", "3.11", "3.10" ]
    defaults:
      run:
        working-directory: cluster_tools
    steps:
      - uses: actions/checkout@v6
      - uses: astral-sh/setup-uv@v8.0.0
        with:
          enable-cache: true
          cache-dependency-glob: "cluster_tools/uv.lock"
      - run: uv python install ${{ matrix.python-version }}
      - name: Start Docker Cluster
        run: cd ./dockered-slurm && docker compose up -d
      - name: Log Core Container
        run: |
          for name in "slurmctld" "c1" "c2"; do
            docker logs "$name"
          done
      - name: Install UV dependencies
        run: |
          for name in "slurmctld" "c1" "c2"; do
            docker exec -w /cluster_tools "$name" bash -c "uv sync --frozen"
          done
      - name: "Run Tests (test_all, test_slurm) without modified slurm.conf"
        run: |
          docker exec \
            -w /cluster_tools/tests \
            -e PYTEST_EXECUTORS=slurm \
            slurmctld bash -c "uv run --frozen python -m pytest -sv test_all.py test_slurm.py -m 'not requires_modified_slurm_config'"
      - name: "Run Tests (test_deref_main)"
        run: |
          docker exec \
            -w /cluster_tools/tests \
            slurmctld bash -c "uv run --frozen python test_deref_main.py"

      - name: Update Slurm Config
        run: |
          echo "MaxArraySize=2" >> ./dockered-slurm/slurm.conf
          sed "s/JobAcctGatherFrequency=30/JobAcctGatherFrequency=1/g" ./dockered-slurm/slurm.conf > ./dockered-slurm/slurm.conf.tmp
          mv ./dockered-slurm/slurm.conf.tmp ./dockered-slurm/slurm.conf
      - name: Restart Slurm Cluster
        run: cd ./dockered-slurm && docker compose restart slurmctld c1 c2

      - name: "Run Tests (test_all, test_slurm) with modified slurm.conf"
        run: |
          # Run tests requiring a modified slurm config
          docker exec \
            -w /cluster_tools/tests \
            -e PYTEST_EXECUTORS=slurm \
            slurmctld bash -c "uv run --frozen python -m pytest -sv test_slurm.py -m 'requires_modified_slurm_config'"

  cluster_tools_other:
    needs: changes
    if: ${{ needs.changes.outputs.cluster_tools == 'true' }}
    runs-on: ubuntu-latest
    timeout-minutes: 30
    strategy:
      matrix:
        python-version: [ "3.13", "3.12", "3.11", "3.10" ]
    defaults:
      run:
        working-directory: cluster_tools
    steps:
      - uses: actions/checkout@v6
      - name: Install uv
        uses: astral-sh/setup-uv@v8.0.0
        with:
          enable-cache: true
          cache-dependency-glob: "cluster_tools/uv.lock"
      - name: Set up Python ${{ matrix.python-version }}
        run: uv python install ${{ matrix.python-version }}
      - name: Install dependencies (without docker)
        run: uv sync --frozen
      - name: Check typing
        if: ${{ matrix.python-version == '3.11' }}
        run: ./typecheck.sh
      - name: Check formatting
        if: ${{ matrix.python-version == '3.11' }}
        run: ./format.sh check
      - name: Lint code
        if: ${{ matrix.python-version == '3.11' }}
        run: ./lint.sh
      - name: Run multiprocessing tests
        run: |
          cd tests
          PYTEST_EXECUTORS=multiprocessing,sequential,multiprocessing_with_pickling,sequential_with_pickling \
            uv run --frozen python -m pytest -sv test_all.py test_multiprocessing.py
      - name: Run batching tests
        run: |
          cd tests
          uv run --frozen python -m pytest -sv test_batching.py

  webknossos_linux:
    needs: changes
    if: |
      ${{ needs.changes.outputs.cluster_tools == 'true' }} ||
      ${{ needs.changes.outputs.webknossos == 'true' }}
    runs-on: ubicloud-standard-8
    strategy:
      matrix:
        python-version: [ "3.13", "3.12", "3.11", "3.10" ]
        group: [ 1, 2, 3 ]
      fail-fast: false
    defaults:
      run:
        working-directory: webknossos

    steps:
      - uses: actions/checkout@v6

      - name: Install uv
        uses: astral-sh/setup-uv@v8.0.0
        with:
          enable-cache: true
          cache-dependency-glob: "webknossos/uv.lock"

      - name: Set up Python ${{ matrix.python-version }}
        run: uv python install ${{ matrix.python-version }}

      - name: Check formatting
        if: ${{ matrix.group == 1 && matrix.python-version == '3.11' }}
        run: ./format.sh check

      - name: Lint code
        if: ${{ matrix.group == 1 && matrix.python-version == '3.11' }}
        run: ./lint.sh

      - name: Check typing
        if: ${{ matrix.group == 1 && matrix.python-version == '3.11' }}
        run: ./typecheck.sh

      - name: Patch Python standard library to assert that fork is not allowed
        run: |
          sed -i '/def _launch/a\ \ \ \ \ \ \ \ raise Exception("fork is not allowed.")' ${UV_PYTHON_INSTALL_DIR}/cpython-${{ matrix.python-version }}.*-linux-x86_64-gnu/lib/python${{ matrix.python-version }}/multiprocessing/popen_fork.py
          cat ${UV_PYTHON_INSTALL_DIR}/cpython-${{ matrix.python-version }}.*-linux-x86_64-gnu/lib/python${{ matrix.python-version }}/multiprocessing/popen_fork.py

      - name: Python tests (with coverage)
        if: ${{ matrix.python-version == '3.11' }}
        timeout-minutes: 30
        env:
          PYTHON_VERSION: ${{ matrix.python-version }}
        run: uv run test.py --splits 3 --group ${{ matrix.group }} --splitting-algorithm
          least_duration --cov=webknossos --cov-report=

      - name: Python tests
        if: ${{ matrix.python-version != '3.11' }}
        timeout-minutes: 30
        env:
          PYTHON_VERSION: ${{ matrix.python-version }}
        run: uv run test.py --splits 3 --group ${{ matrix.group }} --splitting-algorithm
          least_duration

      - name: Persist coverage reports
        if: ${{ matrix.python-version == '3.11' }}
        uses: actions/upload-artifact@v7
        with:
          name: coverage-report-${{ matrix.group }}
          path: "webknossos/.coverage"
          include-hidden-files: true
          if-no-files-found: error
          retention-days: 1 # Automatically deletes after 1 day

      - name: Check if git is dirty
        run: ../_tooling/check_clean.sh

  webknossos_windows:
    needs: changes
    if: |
      ${{ needs.changes.outputs.cluster_tools == 'true' }} ||
      ${{ needs.changes.outputs.webknossos == 'true' }}
    runs-on: windows-latest
    strategy:
      matrix:
        python-version: [ "3.12" ]
        group: [ 1, 2, 3 ]
      fail-fast: false
    defaults:
      run:
        working-directory: webknossos

    steps:
      - uses: actions/checkout@v6

      - name: Install uv
        uses: astral-sh/setup-uv@v8.0.0
        with:
          enable-cache: true
          cache-dependency-glob: "webknossos/uv.lock"

      - name: Install minio
        run: Invoke-WebRequest -Uri
          "https://dl.min.io/server/minio/release/windows-amd64/minio.exe"
          -OutFile "minio.exe"

      - name: Set up Python ${{ matrix.python-version }}
        run: uv python install ${{ matrix.python-version }}

      - name: Python tests
        timeout-minutes: 30
        env:
          PYTHON_VERSION: ${{ matrix.python-version }}
          MULTIPROCESSING_DEFAULT_START_METHOD: spawn
        run: uv run test.py --splits 3 --group ${{ matrix.group }} --splitting-algorithm
          least_duration

  coverage_report:
    needs: [ webknossos_linux ]
    if: success()
    runs-on: ubuntu-latest
    defaults:
      run:
        working-directory: webknossos
    steps:
      - uses: actions/checkout@v6

      - name: Install coverage.py
        run: pip install coverage

      - name: Download all coverage reports
        uses: actions/download-artifact@v8
        with:
          path: ~/coverage-files

      - name: Generate coverage report
        env:
          COVERAGE_FILE: "~/coverage-files/result.coverage"
        run: |
          coverage combine ~/coverage-files/**/.coverage
          coverage xml -i -o ~/coverage-files/result.xml

      - name: Report coverage
        uses: orgoro/coverage@v3.2
        with:
          coverageFile: /home/runner/coverage-files/result.xml
          token: ${{ secrets.GITHUB_TOKEN }}
          thresholdAll: 0.8

      - name: Cleanup temporary files
        run: rm -rf ~/coverage-files

  docs:
    needs:
      - cluster_tools_slurm
      - cluster_tools_other
      - webknossos_linux
      - webknossos_windows
    runs-on: ubuntu-latest
    if: |
      always() &&
      !contains(needs.*.result, 'failure') &&
      !contains(needs.*.result, 'cancelled') &&
      !github.event.pull_request.head.repo.fork

    steps:
      - uses: actions/checkout@v6
      - uses: actions/checkout@v6
        with:
          repository: scalableminds/webknossos
          path: docs/wk-repo
      - name: Install uv
        uses: astral-sh/setup-uv@v8.0.0
      - name: Build Docs
        run: |
          cd docs
          ./generate.sh --persist

      - name: Push docs (for master)
        if: github.ref == 'refs/heads/master'
        env:
          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
        run: |
          CI_BRANCH=${GITHUB_HEAD_REF:-$GITHUB_REF_NAME}
          NORMALIZED_CI_BRANCH=${CI_BRANCH//[\/-]/_}
          uvx --from awscli aws s3 cp --recursive --endpoint-url https://hel1.your-objectstorage.com docs/out s3://webknossos-www/docs/${NORMALIZED_CI_BRANCH}

      - name: Push docs (for tag)
        if: github.ref_type == 'tag'
        env:
          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
          N8N_TOKEN: ${{ secrets.N8N_USERNAME }}
          N8N_USERNAME: ${{ secrets.N8N_TOKEN }}
        run: |
          CI_TAG=$(git describe --tags)
          set -e

          uvx --from awscli aws s3 cp --recursive --endpoint-url https://hel1.your-objectstorage.com docs/out s3://webknossos-www/docs/${CI_TAG}
          curl --basic -u "${N8N_TOKEN}:${N8N_USERNAME}" https://docs.webknossos.org/webhooks/index-docs

      - name: Check links (on master)
        if: github.ref == 'refs/heads/master'
        env:
          # Or as an environment variable
          SLACK_HOOK: ${{ secrets.LINK_CHECKER_SLACK_HOOK }}
        run: |
          cd docs
          uv run --frozen linkchecker --config linkcheckerrc https://docs.webknossos.org > link_status || \
            curl -X POST --data-urlencode "payload={\"text\": \":warning: Broken Links on doc.webknossos.org :warning:\n"'```'"\n$(cat link_status)\n"'```"}' \
              "$SLACK_HOOK"

  pypi_and_gh_release:
    needs:
      - cluster_tools_slurm
      - cluster_tools_other
      - webknossos_linux
      - webknossos_windows
    if: |
      always() &&
      !contains(needs.*.result, 'failure') &&
      !contains(needs.*.result, 'cancelled') &&
      github.ref_type == 'tag' &&
      !github.event.pull_request.head.repo.fork
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v6
      - name: Install uv
        uses: astral-sh/setup-uv@v8.0.0
      - name: Publish python packages
        env:
          UV_PUBLISH_TOKEN: ${{ secrets.PYPI_PASSWORD }}
        run: _tooling/publish.sh
      - name: Prepare github release
        run: |
          VERSION="$(uvx dunamai from git)"
          _tooling/changelog_for_version.sh $VERSION > Changelog.md
      - name: Publish github release
        id: create_release
        uses: softprops/action-gh-release@v2
        with:
          tag_name: ${{ github.ref }}
          name: ${{ github.ref }}
          body_path: Changelog.md
          draft: false
          prerelease: false

  complete:
    needs:
      - cluster_tools_other
      - cluster_tools_slurm
      - webknossos_linux
      - webknossos_windows
      - docs
      - pypi_and_gh_release
    if: always()
    runs-on: ubuntu-latest
    steps:
      - name: Check failure
        if: |
          contains(needs.*.result, 'failure') ||
          contains(needs.*.result, 'cancelled')
        run: exit 1
      - name: Success
        run: echo Success!