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jeromekelleherjeromekelleher
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Add back bespoke Python tests
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‎.github/workflows/tests.yml‎

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os: [ macos-latest, ubuntu-24.04, windows-latest ]
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# test:
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# name: Python
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# runs-on: ${{ matrix.os }}
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# strategy:
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# fail-fast: false
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# matrix:
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# python: [ 3.11, 3.13 ]
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# os: [ macos-latest, ubuntu-24.04, windows-latest ]
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# defaults:
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# run:
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# shell: bash
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# steps:
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# - name: Cancel Previous Runs
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# uses: styfle/cancel-workflow-action@0.13.0
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# with:
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# access_token: ${{ github.token }}
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# - name: Checkout
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# uses: actions/checkout@v6.0.2
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# - name: Install OSX libs
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# if: matrix.os == 'macos-latest'
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# run: |
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# brew install libxml2 libxslt
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# - name: Fix windows symlinks
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# working-directory: python
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# if: matrix.os == 'windows-latest'
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# run: |
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# rm -r lib
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# mkdir lib
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# cp -r --dereference ../c/subprojects lib/.
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# cp -r --dereference ../c/tskit lib/.
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# cp ../c/tskit.h lib/.
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# - name: Install uv and set the python version
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# uses: astral-sh/setup-uv@v7
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# with:
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# python-version: ${{ matrix.python }}
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# version: "0.8.15"
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# - name: Install dependencies
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# working-directory: python
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# run: uv sync --locked --group test
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# - name: Minidom test
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# working-directory: python
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# # Importing either IPython or pytest causes import of xml.dom.minidom
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# # So to actually test that tskit imports it, we need a minimal test
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# run: |
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# uv run python -c "import tskit;tskit.Tree.generate_star(5).tree_sequence.draw_svg(path='test.svg')"
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# - name: Run JIT code coverage
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# run: |
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# NUMBA_DISABLE_JIT=1 uv run --project=python \
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# pytest --cov=tskit --cov-report=xml --cov-branch -n2 \
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# python/tests/test_jit.py
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# - name: Upload coverage to Codecov
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# uses: codecov/codecov-action@v5.5.2
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# with:
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# token: ${{ secrets.CODECOV_TOKEN }}
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# working-directory: python
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# fail_ci_if_error: false
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# files: coverage.xml
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# disable_search: true
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# verbose: true
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# flags: python-tests-no-jit
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# - name: Run tests
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# run: |
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# if [[ "${{ matrix.os }}" == "windows-latest" ]]; then
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# uv run --project=python \
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# pytest --cov=tskit --skip-slow --cov-report=xml --cov-branch -n2 python/tests
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# else
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# uv run --project=python \
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# pytest --cov=tskit --cov-report=xml --cov-branch -n2 python/tests
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# fi
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# - name: Upload coverage to Codecov
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# uses: codecov/codecov-action@v5.5.2
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# with:
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# token: ${{ secrets.CODECOV_TOKEN }}
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# fail_ci_if_error: false
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# flags: python-tests
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# files: coverage.xml
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# disable_search: true
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# verbose: true
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msys2:
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runs-on: windows-latest
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strategy:
@@ -181,3 +91,52 @@ jobs:
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working-directory: c
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run: |
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ninja -C build test
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bespoke-python-test:
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name: Bespoke Python tests
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runs-on: ubuntu-24.04
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steps:
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- name: Cancel Previous Runs
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uses: styfle/cancel-workflow-action@0.13.0
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with:
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access_token: ${{ github.token }}
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- name: Checkout
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uses: actions/checkout@v6.0.2
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with:
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submodules: true
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- name: Install uv and set the python version
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uses: astral-sh/setup-uv@v6
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with:
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python-version: 3.11
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version: "0.8.15"
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- name: Install Python dependencies
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run: uv sync --project=${{ inputs.pyproject-directory }} --locked --group test --no-default-groups
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- name: Minidom test
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working-directory: python
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# Importing either IPython or pytest causes import of xml.dom.minidom
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# So to actually test that tskit imports it, we need a minimal test
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run: |
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uv run --locked --group test --no-default-groups \
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python -c "import tskit;tskit.Tree.generate_star(5).tree_sequence.draw_svg(path='test.svg')"
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- name: Run JIT code coverage
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run: |
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NUMBA_DISABLE_JIT=1 uv run --locked --project=python --no-default-groups\
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pytest --cov=python/tskit --cov-report=xml --cov-branch \
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python/tests/test_jit.py
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v5.5.2
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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fail_ci_if_error: true
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files: coverage.xml
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disable_search: true
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verbose: true
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flags: python-tests-no-jit
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‎python/pyproject.toml‎

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"PT009", # pytest.raises(ValueError) too broad
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"PT011", # pytest.raises(ValueError) too broad
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"PT012", # pytest.raises() block should contain a single simple statement
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"B018", # Found useless expression. Either assign it
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# "B028", # No stacklevel for warnings
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"B018", # Found useless expression. Either assign it
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"PT031", # `pytest.warns()` block should contain a single simple statement
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]
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