fixed filter cell function to be the same as pagoda2, added neighbors… #69
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: Build and Test | |
| on: | |
| push: | |
| paths: | |
| - 'scFates/**' | |
| jobs: | |
| install_and_load: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - name: Install package | |
| run: | | |
| pip install wheel | |
| pip install . | |
| - name: Load package | |
| run: | | |
| python -c "import scFates" | |
| build_and_test: | |
| runs-on: ubuntu-latest | |
| needs: install_and_load | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get clean && sudo apt-get update | |
| sudo apt-get install -y r-base r-cran-mgcv | |
| pip install wheel | |
| pip install coverage cmake pytest mock | |
| pip install rpy2 | |
| pip install . | |
| - name: Test with pytest | |
| run: | | |
| coverage run -m pytest scFates/tests/test_w_plots.py | |
| coverage report -i -m | |
| coverage xml -i | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v1 | |
| with: | |
| files: ./coverage.xml | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| pypi_upload: | |
| if: | | |
| contains(github.event.head_commit.message, 'pypi test') || | |
| startsWith(github.ref, 'refs/tags/v') | |
| runs-on: ubuntu-latest | |
| needs: build_and_test | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - name: Setup pip | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install wheel | |
| - name: Build wheel | |
| run: | | |
| python setup.py bdist_wheel | |
| python setup.py sdist | |
| - name: Publish package to TestPyPI | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.TEST_PYPI_API_TOKEN }} | |
| repository_url: https://test.pypi.org/legacy/ | |
| verbose: true | |
| if: contains(github.event.head_commit.message, 'pypi test') | |
| - name: Publish package to PyPI | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} | |
| verbose: true | |
| if: startsWith(github.ref, 'refs/tags/v') |