Implement tree.ancestors #6274
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Tests | |
| on: | |
| pull_request: | |
| push: | |
| branches: [main, test] | |
| jobs: | |
| pre-commit: | |
| name: Lint | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Cancel Previous Runs | |
| uses: styfle/cancel-workflow-action@0.12.1 | |
| with: | |
| access_token: ${{ github.token }} | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.10' | |
| - name: install clang-format | |
| if: steps.clang_format.outputs.cache-hit != 'true' | |
| run: | | |
| sudo pip install clang-format==6.0.1 | |
| sudo ln -s /usr/local/bin/clang-format /usr/local/bin/clang-format-6.0 | |
| - uses: pre-commit/action@v3.0.0 | |
| benchmark: | |
| name: Benchmark | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Cancel Previous Runs | |
| uses: styfle/cancel-workflow-action@0.12.1 | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| 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 | |
| with: | |
| name: benchmark-results | |
| path: python/benchmark | |
| test: | |
| name: Python | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python: [ 3.9, 3.12 ] | |
| os: [ macos-latest, ubuntu-latest, 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@v3 | |
| - 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 | |
| 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 | |
| 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: Run tests | |
| working-directory: python | |
| run: | | |
| source ~/.profile | |
| conda activate anaconda-client-env | |
| # pytest -xv -n2 | |
| python -m pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 tests | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v4 | |
| 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 | |
| - name: Setup MSYS2 ${{matrix.sys}} | |
| uses: msys2/setup-msys2@v2 | |
| 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 |