omnip: updated module name homology → orthology
#103
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| name: build | |
| on: | |
| push: | |
| branches: [ main ] | |
| jobs: | |
| build-linux: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libcurl4-openssl-dev | |
| python -m pip install --upgrade pip | |
| pip install wheel | |
| pip install pytest-cov flake8 scikit-learn skranger git+https://github.com/saezlab/omnipath scanpy adjustText pypath-omnipath psutil . | |
| - 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 and add coverage | |
| run: | | |
| pytest --cov --disable-warnings decoupler | |
| - name: Upload coverage reports to Codecov | |
| run: | | |
| curl -Os https://uploader.codecov.io/latest/linux/codecov | |
| chmod +x codecov | |
| ./codecov -t ${CODECOV_TOKEN} | |
| build-macOS: | |
| runs-on: macOS-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - name: Install dependencies | |
| run: | | |
| brew install openssl | |
| export LDFLAGS="-L/usr/local/opt/openssl@3/lib" | |
| export CPPFLAGS="-I/usr/local/opt/openssl@3/include" | |
| export PKG_CONFIG_PATH="/usr/local/opt/openssl@3/lib/pkgconfig" | |
| python -m pip install --upgrade pip | |
| pip install wheel | |
| pip install pytest flake8 scikit-learn skranger git+https://github.com/saezlab/omnipath scanpy adjustText pypath-omnipath psutil . | |
| - 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 | |
| run: | | |
| pytest --disable-warnings . |