Support all-nodes matching in LSHMM #5376
Workflow file for this run
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| 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/[email protected] | |
| with: | |
| access_token: ${{ github.token }} | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| 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/[email protected] | |
| benchmark: | |
| name: Benchmark | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Cancel Previous Runs | |
| uses: styfle/[email protected] | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| 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@v2 | |
| with: | |
| name: benchmark-results | |
| path: python/benchmark | |
| test: | |
| name: Python | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python: [ 3.8, 3.9, "3.11" ] | |
| os: [ macos-latest, ubuntu-latest, windows-latest ] | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - name: Cancel Previous Runs | |
| uses: styfle/[email protected] | |
| with: | |
| access_token: ${{ github.token }} | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Cache conda and dependencies | |
| id: cache | |
| uses: actions/cache@v2 | |
| with: | |
| path: | | |
| c:\Miniconda\envs\anaconda-client-env | |
| /usr/share/miniconda/envs/anaconda-client-env | |
| ~/osx-conda | |
| ~/.profile | |
| key: ${{ runner.os }}-${{ matrix.python}}-conda-v12-${{ hashFiles('python/requirements/CI-tests-conda/requirements.txt') }}-${{ hashFiles('python/requirements/CI-tests-pip/requirements.txt') }} | |
| - name: Install Conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| 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 | |
| use-only-tar-bz2: 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 setuptools==57.5.0 #v58 broke some deps https://setuptools.pypa.io/en/latest/history.html#v58-0-0 | |
| pip install -r python/requirements/CI-tests-pip/requirements.txt | |
| - name: Fix OSX Cache Write #OSX Won't let the cache restore due to file perms | |
| if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'macos-latest' | |
| run: | | |
| cp -r /usr/local/miniconda/envs/anaconda-client-env ~/osx-conda | |
| - name: Fix OSX Cache Restore | |
| if: steps.cache.outputs.cache-hit == 'true' && matrix.os == 'macos-latest' | |
| run: | | |
| mkdir -p /usr/local/miniconda/envs | |
| sudo cp -r ~/osx-conda /usr/local/miniconda/envs/anaconda-client-env | |
| - name: Build module | |
| working-directory: python | |
| run: | | |
| source ~/.profile | |
| conda activate anaconda-client-env | |
| python setup.py build_ext --inplace | |
| - name: Remove py311 incompatible tests (lack of numba support for 3.11, needed for lshmm) | |
| if: matrix.python == '3.11' | |
| run: | | |
| rm python/tests/test_*matching* | |
| - 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@v3 | |
| 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/[email protected] | |
| with: | |
| access_token: ${{ github.token }} | |
| - name: 'Checkout' | |
| uses: actions/checkout@v3 | |
| - 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 |