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chore(ci): Switch to tox-gh-actions for testing
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‎.github/workflows/pythonpackage.yml‎

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# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
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# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
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name: Python package
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name: Tox
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on:
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push:
@@ -13,9 +10,12 @@ on:
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- cron: '0 0 * * *'
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concurrency:
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group: python-${{ github.ref }}
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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permissions:
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contents: read
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jobs:
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job_metadata:
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if: github.repository == 'nipreps/niworkflows'
@@ -123,135 +123,62 @@ jobs:
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strategy:
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matrix:
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python-version: ["3.9", "3.10", "3.11", "3.12"]
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install: [repo]
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dependencies: [latest, pre]
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include:
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- python-version: "3.12"
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install: sdist
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- python-version: "3.12"
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install: wheel
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- python-version: "3.12"
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install: editable
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- python-version: "3.9"
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dependencies: min
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env:
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INSTALL_TYPE: ${{ matrix.install }}
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DEPENDS: ${{ matrix.dependencies }}
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steps:
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- uses: actions/checkout@v4
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if: matrix.install == 'repo' || matrix.install == 'editable'
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with:
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fetch-depth: 0
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Load test data cache
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uses: actions/cache@v4
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id: stanford-crn
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with:
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path: ~/.cache/stanford-crn/
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key: data-v0-${{ github.ref_name }}-${{ github.sha }}
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- name: Load TemplateFlow cache
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uses: actions/cache@v4
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id: templateflow
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with:
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path: ~/.cache/templateflow
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key: templateflow-v0-${{ github.ref_name }}-${{ strategy.job-index }}-${{ github.sha }}
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restore-keys: |
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templateflow-v0-${{ github.ref_name }}-
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templateflow-v0-
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- name: Fetch packages
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if: matrix.install == 'sdist' || matrix.install == 'wheel'
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uses: actions/download-artifact@v3
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with:
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name: dist
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path: dist/
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- name: Select archive
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run: |
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if [ "$INSTALL_TYPE" = "sdist" ]; then
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ARCHIVE=$( ls dist/*.tar.gz )
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elif [ "$INSTALL_TYPE" = "wheel" ]; then
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ARCHIVE=$( ls dist/*.whl )
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elif [ "$INSTALL_TYPE" = "repo" ]; then
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ARCHIVE="."
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elif [ "$INSTALL_TYPE" = "editable" ]; then
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ARCHIVE="-e ."
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fi
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echo "ARCHIVE=$ARCHIVE" | tee -a $GITHUB_ENV
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- name: Install package
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run: python -m pip install $ARCHIVE
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- name: Check version
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run: |
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INSTALLED_VERSION=$(python -c 'import niworkflows; print(niworkflows.__version__, end="")')
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echo "INSTALLED: \"${INSTALLED_VERSION}\""
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test "${INSTALLED_VERSION}" = "${VERSION}"
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env:
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VERSION: ${{ needs.job_metadata.outputs.version }}
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- name: Install test dependencies
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run: python -m pip install "niworkflows[tests]"
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- name: Run tests
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run: pytest -sv --doctest-modules --cov niworkflows --pyargs niworkflows
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- uses: codecov/codecov-action@v4
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name: Submit to CodeCov
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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test-pre:
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needs: [get_data, job_metadata]
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if: ${{ !contains(needs.job_metadata.outputs.commit_message, '[skip pre]') }}
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runs-on: ubuntu-latest
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strategy:
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matrix:
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# Only run --pre tests on Python versions within SPEC0 support
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python-version: ["3.11", "3.12"]
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install: [repo]
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pip-flags: ['--pre']
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env:
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INSTALL_TYPE: ${{ matrix.install }}
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PIP_FLAGS: ${{ matrix.pip-flags }}
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steps:
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- name: Debug commit message
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run: echo "${{ needs.job_metadata.outputs.commit_message }}"
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Load test data cache
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uses: actions/cache@v4
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id: stanford-crn
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with:
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path: ~/.cache/stanford-crn/
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key: data-v0-${{ github.ref_name }}-${{ github.sha }}
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- name: Load TemplateFlow cache
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uses: actions/cache@v4
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id: templateflow
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with:
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path: ~/.cache/templateflow
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key: templateflow-v0-${{ github.ref_name }}-${{ strategy.job-index }}-${{ github.sha }}
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restore-keys: |
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templateflow-v0-${{ github.ref_name }}-
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templateflow-v0-
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- name: Install package
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run: python -m pip install $PIP_FLAGS .
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- name: Check version
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run: |
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INSTALLED_VERSION=$(python -c 'import niworkflows; print(niworkflows.__version__, end="")')
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echo "INSTALLED: \"${INSTALLED_VERSION}\""
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test "${INSTALLED_VERSION}" = "${VERSION}"
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env:
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VERSION: ${{ needs.job_metadata.outputs.version }}
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- name: Install test dependencies
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run: python -m pip install $PIP_FLAGS "niworkflows[tests]"
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- name: Run tests
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run: pytest -sv --doctest-modules --cov niworkflows --pyargs niworkflows
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- uses: codecov/codecov-action@v4
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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name: Submit to CodeCov
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- uses: actions/checkout@v4
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with:
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submodules: recursive
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fetch-depth: 0
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- name: Install the latest version of uv
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uses: astral-sh/setup-uv@v3
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- name: Load test data cache
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uses: actions/cache@v4
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id: stanford-crn
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with:
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path: ~/.cache/stanford-crn/
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key: data-v0-${{ github.ref_name }}-${{ github.sha }}
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- name: Load TemplateFlow cache
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uses: actions/cache@v4
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id: templateflow
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with:
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path: ~/.cache/templateflow
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key: templateflow-v0-${{ github.ref_name }}-${{ strategy.job-index }}-${{ github.sha }}
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restore-keys: |
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templateflow-v0-${{ github.ref_name }}-
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templateflow-v0-
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- uses: actions/cache@v4
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with:
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path: ~/.cache/templateflow
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key: templateflow-v1
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- name: Install dependencies
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run: |
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sudo apt update
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sudo apt install -y --no-install-recommends graphviz
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Display Python version
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run: python -c "import sys; print(sys.version)"
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- name: Install tox
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run: |
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uv tool install tox --with=tox-uv --with=tox-gh-actions
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- name: Show tox config
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run: tox c
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- name: Run tox
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run: tox -v --exit-and-dump-after 1200
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- uses: codecov/codecov-action@v4
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with:
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file: coverage.xml
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token: ${{ secrets.CODECOV_TOKEN }}
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if: ${{ always() }}
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flake8:
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if: github.event_name != 'schedule'

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