Consolidate to single composite figure #735
Workflow file for this run
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| # This workflow will install Python dependencies, run tests and lint with a single version of Python | |
| # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python | |
| name: CI | |
| on: | |
| push: | |
| pull_request: | |
| branches: [ "main" ] | |
| permissions: | |
| contents: read | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] | |
| os: [windows-latest, macOS-latest, ubuntu-latest] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: "recursive" | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install oldest-supported-numpy==2023.10.25 | |
| # --ignore-requires-python ensures docs deps don't break install on early python versions | |
| if [ -f requirements.txt ]; then pip install --ignore-requires-python -r requirements.txt; fi | |
| pip install -e . | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Test with pytest | |
| run: | | |
| python -m pytest | |
| coverage: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.11"] | |
| os: [ubuntu-latest] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: "recursive" | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| # - name: Setup LCOV | |
| # uses: hrishikesh-kadam/setup-lcov@v1 | |
| - name: Install dependencies | |
| run: | | |
| sudo apt update -yy | |
| sudo apt install -yy lcov | |
| python -m pip install --upgrade pip | |
| pip install wheel | |
| pip install oldest-supported-numpy==2023.10.25 | |
| # --ignore-requires-python ensures docs deps don't break install on early python versions | |
| if [ -f requirements.txt ]; then pip install --ignore-requires-python -r requirements.txt; fi | |
| rm -rf Empirical/.git | |
| - name: Build phylotrackpy | |
| run: | | |
| make coverage | |
| - name: Test with pytest | |
| run: | | |
| python -m pytest --cov=. --cov-report=lcov | |
| lcov --output-file coverage.cpp --capture --directory . | |
| lcov --output-file coverage.cpp --extract coverage.cpp "*" | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| files: "coverage.cpp, coverage.lcov, Empirical/include/emp/Evolve/Systematics.hpp" | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| verbose: true | |
| build_wheels: | |
| name: Build wheels on ${{ matrix.os }} | |
| needs: [] | |
| # if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v') | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, windows-latest, macos-13, macos-14] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: "recursive" | |
| - name: Build wheels | |
| uses: pypa/[email protected] | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }} | |
| path: ./wheelhouse/*.whl | |
| build_sdist: | |
| name: Build source distribution | |
| needs: [] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: "recursive" | |
| - name: Build sdist | |
| run: pipx run build --sdist | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: cibw-sdist | |
| path: dist/*.tar.gz | |
| upload_pypi: | |
| needs: [build_wheels, build_sdist, test] | |
| runs-on: ubuntu-latest | |
| environment: pypi | |
| permissions: | |
| id-token: write | |
| # upload to PyPI on every tag starting with 'v' | |
| if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v') | |
| # alternatively, to publish when a GitHub Release is created, use the following rule: | |
| # if: github.event_name == 'release' && github.event.action == 'published' | |
| steps: | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| # unpacks default artifact into dist/ | |
| # if `name: artifact` is omitted, the action will create extra parent dir | |
| pattern: cibw-* | |
| path: dist | |
| merge-multiple: true | |
| - uses: pypa/[email protected] | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} | |
| paper: | |
| runs-on: ubuntu-latest | |
| name: Paper Draft | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - 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@v4 | |
| 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 |