test compose basic #61
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| name: build | |
| on: [push] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.8"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install CD-Hit | |
| run: | | |
| wget https://github.com/weizhongli/cdhit/releases/download/V4.8.1/cd-hit-v4.8.1-2019-0228.tar.gz | |
| tar -xzvf cd-hit-v4.8.1-2019-0228.tar.gz | |
| cd cd-hit-v4.8.1-2019-0228 | |
| make | |
| chmod u+x cd-hit | |
| pwd | |
| - name: Export cd-hit path | |
| run: | | |
| echo /home/runner/work/rnaglib/rnaglib/cd-hit-v4.8.1-2019-0228 >> $GITHUB_PATH | |
| - name: Install rna-align | |
| run: | | |
| wget https://zhanggroup.org/RNA-align/bin/RNAalign.tar.bz2 | |
| tar -xvjf RNAalign.tar.bz2 | |
| cd RNAalign | |
| g++ -O3 -ffast-math -o RNAalign RNAalign.cpp -static | |
| chmod u+x ./RNAalign | |
| pwd | |
| - name: Export RNAalign path | |
| run: | | |
| echo /home/runner/work/rnaglib/rnaglib/RNAalign >> $GITHUB_PATH | |
| - name: Test with pytest | |
| run: | | |
| echo $PATH | |
| which RNAalign | |
| which cd-hit | |
| pip install -r requirements_test.txt | |
| pip install coverage | |
| coverage run --source src/rnaglib -m pytest | |
| coverage report -m | |
| coverage xml | |
| - name: Upload Coverage | |
| uses: codecov/codecov-action@v2 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| files: coverage.xml | |
| flags: pytest | |
| name: rnaglib | |
| fail_ci_if_error: true | |
| verbose: true |