SGD NaN Fix #19
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| name: Tests & Docs | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - master | |
| pull_request: | |
| branches: | |
| - main | |
| - master | |
| jobs: | |
| # Job (1): Run testing in parallel against multiples OSs and Python versions | |
| test: | |
| if: "!contains(github.event.head_commit.message, 'skip ci')" | |
| name: Test | |
| runs-on: ${{ matrix.os }} | |
| # Determines whether the entire workflow should pass/fail based on parallel jobs | |
| continue-on-error: ${{ matrix.ok-fail }} | |
| defaults: | |
| # This ensures each step gets properly configured bash shell for conda commands to work | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| # OSs to test | |
| os: [ubuntu-latest, macos-latest, windows-latest] | |
| # Python versions to test | |
| python-version: [3.7, 3.8] | |
| # By default everything should pass for the workflow to pass | |
| ok-fail: [false] | |
| include: | |
| # Rather than include 3.9 in the python versions, do it here so we can ignore failures on mac and windows with 3.9 (they have install issues) | |
| - os: ubuntu-latest | |
| python-version: 3.9 | |
| ok-fail: true | |
| - os: macos-latest | |
| python-version: 3.9 | |
| ok-fail: true | |
| - os: windows-latest | |
| python-version: 3.9 | |
| ok-fail: true | |
| steps: | |
| # Step up miniconda | |
| - name: Download and setup Miniconda | |
| uses: conda-incubator/setup-miniconda@059455a698430d8b68fa317268fa2e3da3492a98 | |
| with: | |
| miniconda-version: "latest" | |
| python-version: ${{ matrix.python-version }} | |
| # Check out latest code on github | |
| - name: Checkout Code | |
| uses: actions/checkout@v2 | |
| # Install common sci-py packages via conda as well as testing packages and requirements | |
| - name: Install Dependencies | |
| run: | | |
| conda activate test | |
| conda env list | |
| conda install -y numpy numba pandas scipy seaborn | |
| conda install -y -c conda-forge pytest pytest-cov pytest-xdist pytest-sugar coveralls black | |
| pip install . -r requirements.txt | |
| # Check code formatting | |
| - name: Check code formatting | |
| run: | | |
| black . --check --diff | |
| # Actually run the tests with coverage | |
| - name: Run Tests | |
| run: | | |
| conda activate test | |
| conda env list | |
| pytest --cov=neighbors -rs -n auto | |
| # Send coverage to coveralls.io but waiting on parallelization to finish | |
| # Not using the official github action in the marketplace to upload because it requires a .lcov file, which pytest doesn't generate. It's just easier to use the coveralls python library which does the same thing, but works with pytest. | |
| - name: Upload Coverage | |
| # The coveralls python package has some 422 server issues with uploads from github-actions so try both service providers, for more see: | |
| # https://github.com/TheKevJames/coveralls-python/issues/252 | |
| run: coveralls --service=github || coveralls --service=github-actions | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| COVERALLS_FLAG_NAME: $${{ matrix}} | |
| COVERALLS_PARALLEL: true | |
| # Job (2): Send a finish notification to coveralls.io to integrate coverage across parallel tests | |
| coveralls: | |
| if: "!contains(github.event.head_commit.message, 'skip ci')" | |
| name: Coveralls.io Upload | |
| needs: test | |
| runs-on: ubuntu-latest | |
| container: python:3-slim | |
| continue-on-error: true | |
| steps: | |
| - name: Finished | |
| run: | | |
| pip3 install --upgrade coveralls | |
| coveralls --service=github --finish || coveralls --service=github-actions --finish | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| # Job (3): Build and deploy docs | |
| docs: | |
| if: "!contains(github.event.head_commit.message, 'skip ci')" | |
| name: Build & deploy docs | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout Code | |
| uses: actions/checkout@v2 | |
| - name: Setup Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: "3.8" | |
| - name: Upgrade pip | |
| run: | | |
| # install pip=>20.1 to use "pip cache dir" | |
| python3 -m pip install --upgrade pip | |
| - name: Setup pip-cache | |
| id: pip-cache | |
| run: echo "::set-output name=dir::$(pip cache dir)" | |
| - name: Cache deps | |
| uses: actions/cache@v2 | |
| with: | |
| path: ${{ steps.pip-cache.outputs.dir }} | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Install deps | |
| run: | | |
| python3 -m pip install . -r requirements.txt | |
| python3 -m pip install -r ./requirements-dev.txt | |
| - name: Build docs | |
| run: | | |
| mkdocs build | |
| echo 'neighbors.cosanlab.com' > ./site/CNAME | |
| - name: Deploy docs | |
| uses: peaceiris/actions-gh-pages@068dc23d9710f1ba62e86896f84735d869951305 | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| publish_dir: ./site |