Add doc note re: mutations per site #6733
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| name: Tests | |
| on: | |
| pull_request: | |
| merge_group: | |
| push: | |
| branches: [main, test] | |
| jobs: | |
| pre-commit: | |
| name: Lint | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - name: Cancel Previous Runs | |
| uses: styfle/cancel-workflow-action@0.12.1 | |
| with: | |
| access_token: ${{ github.token }} | |
| - uses: actions/checkout@v4.2.2 | |
| - uses: actions/setup-python@v5.4.0 | |
| with: | |
| python-version: '3.12' | |
| - name: install clang-format | |
| if: steps.clang_format.outputs.cache-hit != 'true' | |
| run: | | |
| pip install setuptools clang-format==6.0.1 | |
| clang-format -version | |
| sudo cp /opt/hostedtoolcache/Python/3.12.10/x64/bin/clang-format /opt/hostedtoolcache/Python/3.12.10/x64/bin/clang-format-6.0 | |
| clang-format-6.0 -version | |
| - uses: pre-commit/action@v3.0.1 | |
| benchmark: | |
| name: Benchmark | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - name: Cancel Previous Runs | |
| uses: styfle/cancel-workflow-action@0.12.1 | |
| - uses: actions/checkout@v4.2.2 | |
| - uses: actions/setup-python@v5.4.0 | |
| with: | |
| python-version: '3.12' | |
| cache: 'pip' | |
| cache-dependency-path: python/requirements/benchmark.txt | |
| - name: Install deps | |
| run: pip install -r python/requirements/benchmark.txt | |
| - name: Build module | |
| run: | | |
| cd python | |
| python setup.py build_ext --inplace | |
| - name: Run benchmarks | |
| run: | | |
| cd python/benchmark | |
| pip uninstall -y tskit | |
| python run.py | |
| - name: Upload Results | |
| uses: actions/upload-artifact@v4.6.1 | |
| with: | |
| name: benchmark-results | |
| path: python/benchmark | |
| test: | |
| name: Python | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python: [ 3.9, 3.13 ] | |
| os: [ macos-latest, ubuntu-24.04, windows-latest ] | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - name: Cancel Previous Runs | |
| uses: styfle/cancel-workflow-action@0.12.1 | |
| with: | |
| access_token: ${{ github.token }} | |
| - name: Checkout | |
| uses: actions/checkout@v4.2.2 | |
| - name: Install OSX libs | |
| if: matrix.os == 'macos-latest' | |
| run: | | |
| brew install libxml2 libxslt | |
| - name: Cache conda and dependencies | |
| id: cache | |
| uses: actions/cache@v4.2.2 | |
| with: | |
| path: ${{ env.CONDA }}/envs | |
| key: ${{ runner.os }}-${{ runner.arch }}-${{ matrix.python}}-conda-v1-${{ hashFiles('python/requirements/CI-tests-conda/requirements.txt') }}-${{ hashFiles('python/requirements/CI-tests-pip/requirements.txt') }} | |
| - name: Install Conda | |
| uses: conda-incubator/setup-miniconda@v3.1.1 | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| with: | |
| activate-environment: anaconda-client-env | |
| python-version: ${{ matrix.python }} | |
| channels: conda-forge | |
| channel-priority: strict | |
| auto-update-conda: true | |
| - name: Fix windows symlinks | |
| working-directory: python | |
| if: matrix.os == 'windows-latest' | |
| run: | | |
| rm -r lib | |
| mkdir lib | |
| cp -r --dereference ../c/subprojects lib/. | |
| cp -r --dereference ../c/tskit lib/. | |
| cp ../c/tskit.h lib/. | |
| - name: Fix windows .profile | |
| if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'windows-latest' | |
| run: | | |
| cp ~/.bash_profile ~/.profile | |
| - name: Install conda deps | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| shell: bash -l {0} #We need a login shell to get conda | |
| run: | | |
| conda install --yes --file=python/requirements/CI-tests-conda/requirements.txt | |
| - name: Install pip deps | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| shell: bash -l {0} | |
| run: | | |
| pip install -r python/requirements/CI-tests-pip/requirements.txt | |
| # Remove tskit installed by conda | |
| pip uninstall -y tskit | |
| - name: Build module | |
| working-directory: python | |
| run: | | |
| source ~/.profile | |
| conda activate anaconda-client-env | |
| python setup.py build_ext --inplace | |
| - name: Minidom test | |
| working-directory: python | |
| # Importing either IPython or pytest causes import of xml.dom.minidom | |
| # So to actually test that tskit imports it, we need a minimal test | |
| run: | | |
| source ~/.profile | |
| conda activate anaconda-client-env | |
| python -c "import tskit;tskit.Tree.generate_star(5).tree_sequence.draw_svg(path='test.svg')" | |
| - name: Run tests | |
| working-directory: python | |
| run: | | |
| source ~/.profile | |
| conda activate anaconda-client-env | |
| if [[ "${{ matrix.os }}" == "windows-latest" ]]; then | |
| python -m pytest -x --skip-slow --cov=tskit --cov-report=xml --cov-branch -n2 --durations=20 tests | |
| else | |
| python -m pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 --durations=20 tests | |
| fi | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v5.4.0 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| working-directory: python | |
| fail_ci_if_error: false | |
| flags: python-tests | |
| name: codecov-umbrella | |
| verbose: true | |
| msys2: | |
| runs-on: windows-latest | |
| strategy: | |
| matrix: | |
| include: | |
| - { sys: mingw32, env: i686 } | |
| - { sys: mingw64, env: x86_64 } | |
| name: Windows (${{ matrix.sys }}, ${{ matrix.env }}) | |
| defaults: | |
| run: | |
| shell: msys2 {0} | |
| steps: | |
| - name: Cancel Previous Runs | |
| uses: styfle/cancel-workflow-action@0.12.1 | |
| with: | |
| access_token: ${{ github.token }} | |
| - name: 'Checkout' | |
| uses: actions/checkout@v4.2.2 | |
| - name: Setup MSYS2 ${{matrix.sys}} | |
| uses: msys2/setup-msys2@v2.27.0 | |
| with: | |
| msystem: ${{matrix.sys}} | |
| update: true | |
| install: >- | |
| git | |
| mingw-w64-${{matrix.env}}-toolchain | |
| mingw-w64-${{matrix.env}}-ninja | |
| mingw-w64-${{matrix.env}}-meson | |
| mingw-w64-${{matrix.env}}-cunit | |
| - name: Build | |
| working-directory: c | |
| run: | | |
| meson build -Dbuild_examples=false | |
| ninja -C build | |
| - name: Run tests | |
| working-directory: c | |
| run: | | |
| ninja -C build test |