ci #304
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| name: ci | |
| on: | |
| push: | |
| branches: | |
| - master | |
| tags: | |
| - '*' | |
| pull_request: | |
| branches: | |
| - master | |
| schedule: | |
| - cron: '0 0 * * 1' # weekly | |
| workflow_dispatch: | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: [3.8, 3.9, "3.10", 3.11] | |
| subdivision: | |
| - "test_auxiliary_lib" | |
| - "test_frozen_instrumentation" | |
| - "test_genome_instrumentation" | |
| - "test_juxtaposition" | |
| - "test_phylogenetic_inference/test_estimators" | |
| - "test_phylogenetic_inference/test_pairwise" | |
| - "test_phylogenetic_inference/test_population" | |
| - "test_phylogenetic_inference/test_priors" | |
| - "test_phylogenetic_inference/test_tree" | |
| - "test_serialization" | |
| - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_depth_proportional_resolution_algo" | |
| - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_depth_proportional_resolution_tapered_algo" | |
| - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_fixed_resolution_algo" | |
| - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_geom_seq_nth_root_algo" | |
| - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_geom_seq_nth_root_tapered_algo" | |
| - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_nominal_resolution_algo" | |
| - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_perfect_resolution_algo" | |
| - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_pseudostochastic_algo" | |
| - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_recency_proportional_resolution_algo" | |
| - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_recency_proportional_resolution_curbed_algo" | |
| - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_stochastic_algo" | |
| - "test_stratum_retention_strategy/test_stratum_retention_policy_evaluators" | |
| - "test_stratum_retention_viz" | |
| - "test_test_drive" | |
| steps: | |
| - uses: actions/checkout@v1 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| sudo sed -i 's/azure\.//' /etc/apt/sources.list | |
| sudo apt-get update -o Acquire::Retries=3 | |
| sudo apt-get install -y ffmpeg -o Acquire::Retries=3 | |
| python -m pip install --upgrade pip | |
| pip install tox tox-gh-actions | |
| - name: Test with tox | |
| run: | | |
| export HSTRAT_TESTS_SUBDIVISION=${{ matrix.subdivision }} | |
| tox | |
| examples: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v1 | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.9 | |
| - name: Install Python dependencies | |
| uses: py-actions/py-dependency-install@v4 | |
| with: | |
| path: "requirements-dev/requirements-testing.txt" | |
| - name: Run examples | |
| run: ./examples/run_all.sh | |
| coverage: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| subdivision: | |
| - "test_auxiliary_lib" | |
| - "test_frozen_instrumentation" | |
| - "test_genome_instrumentation" | |
| - "test_juxtaposition" | |
| - "test_phylogenetic_inference/test_estimators" | |
| - "test_phylogenetic_inference/test_pairwise" | |
| - "test_phylogenetic_inference/test_population" | |
| - "test_phylogenetic_inference/test_priors" | |
| - "test_phylogenetic_inference/test_tree" | |
| - "test_serialization" | |
| - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_depth_proportional_resolution_algo" | |
| - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_depth_proportional_resolution_tapered_algo" | |
| - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_fixed_resolution_algo" | |
| - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_geom_seq_nth_root_algo" | |
| - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_geom_seq_nth_root_tapered_algo" | |
| - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_nominal_resolution_algo" | |
| - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_perfect_resolution_algo" | |
| - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_pseudostochastic_algo" | |
| - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_recency_proportional_resolution_algo" | |
| - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_recency_proportional_resolution_curbed_algo" | |
| - "test_stratum_retention_strategy/test_stratum_retention_algorithms/test_stochastic_algo" | |
| - "test_stratum_retention_strategy/test_stratum_retention_policy_evaluators" | |
| - "test_stratum_retention_viz" | |
| - "test_test_drive" | |
| steps: | |
| - uses: actions/checkout@v1 | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.9 | |
| - name: Install dependencies | |
| run: | | |
| sudo sed -i 's/azure\.//' /etc/apt/sources.list | |
| sudo apt-get update -o Acquire::Retries=3 | |
| sudo apt-get install -y ffmpeg -o Acquire::Retries=3 | |
| python -m pip install --upgrade pip | |
| python -m pip install -r requirements-dev/py39/requirements-testing.txt | |
| - name: Log coverage configuration | |
| run: coverage debug sys | |
| - name: Run tests with coverage report | |
| run: coverage run -m pytest tests/test_hstrat/${{ matrix.subdivision }} | |
| - uses: codecov/codecov-action@v3 | |
| with: | |
| flags: tests # optional | |
| fail_ci_if_error: true # optional (default = false) | |
| verbose: true # optional (default = false) | |
| tidy: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Install apt dependencies | |
| run: sudo apt-get install -y rename | |
| - uses: actions/checkout@v1 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - name: Test isort tidyness | |
| uses: jamescurtin/isort-action@master | |
| with: | |
| requirementsFiles: "requirements-dev/py38/requirements-testing.txt" | |
| - name: Test Black tidyness | |
| uses: psf/black@27d20144a7517594e24a1649451177b2a11284be | |
| with: | |
| version: "22.10.0" | |
| - uses: editorconfig-checker/action-editorconfig-checker@main | |
| - name: Test editorconfig tidyness | |
| run: editorconfig-checker | |
| - name: Test tidy/ tidyness | |
| run: ./tidy/test_tidy.sh | |
| paper: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| - name: Build draft PDF | |
| uses: openjournals/openjournals-draft-action@master | |
| with: | |
| journal: joss | |
| # This should be the path to the paper within your repo. | |
| paper-path: joss/paper.md | |
| - name: Upload | |
| uses: actions/upload-artifact@v1 | |
| with: | |
| name: paper | |
| # This is the output path where Pandoc will write the compiled | |
| # PDF. Note, this should be the same directory as the input | |
| # paper.md | |
| path: joss/paper.pdf | |
| # regression test for https://github.com/mmore500/hstrat/commit/c276530 | |
| packaging-bdist: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| - name: Build bdist | |
| run: | | |
| python3 -m venv env | |
| source env/bin/activate | |
| python3 -m pip install -r requirements-dev/requirements-release.txt | |
| python3 setup.py bdist_wheel | |
| tree dist | |
| deactivate | |
| - name: Upgrade pip | |
| run: python3 -m pip install pip --upgrade | |
| - name: Install from bdist | |
| run: python3 -m pip install dist/*.whl | |
| - name: Test install | |
| run: | | |
| find . -type f -name '*.py' -exec rm {} \; | |
| python3 -c "import hstrat; print(hstrat.__version__)" | |
| # regression test for https://github.com/mmore500/hstrat/commit/c276530 | |
| packaging-sdist: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| - name: Build sdist | |
| run: | | |
| python3 -m venv env | |
| source env/bin/activate | |
| python3 -m pip install -r requirements-dev/requirements-release.txt | |
| python3 setup.py sdist | |
| tree dist | |
| deactivate | |
| - name: Upgrade pip | |
| run: python3 -m pip install pip --upgrade | |
| - name: Install from sdist | |
| run: python3 -m pip install dist/*.tar.gz | |
| - name: Test install | |
| run: | | |
| find . -type f -name '*.py' -exec rm {} \; | |
| python3 -c "import hstrat; print(hstrat.__version__)" | |
| # regression test for https://github.com/mmore500/hstrat/commit/c276530 | |
| packaging-source: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| - name: Upgrade pip | |
| run: python3 -m pip install pip --upgrade | |
| - name: Install from source | |
| run: python3 -m pip install . | |
| - name: Test install | |
| run: | | |
| rm -rf * | |
| cd | |
| python3 -c "import hstrat; print(hstrat.__version__)" | |
| deploy: | |
| needs: | |
| - coverage | |
| - examples | |
| - packaging-bdist | |
| - packaging-sdist | |
| - packaging-source | |
| - test | |
| - tidy | |
| runs-on: ubuntu-latest | |
| if: startsWith(github.ref, 'refs/tags/v') | |
| steps: | |
| - uses: actions/checkout@v1 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install -r requirements-dev/py38/requirements-release.txt | |
| - run: python setup.py sdist bdist_wheel | |
| - name: Publish package | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} |