update + debug workflows #8
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| name: Multi-OS Python Version Test | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| pull_request: | |
| branches: | |
| - dev | |
| jobs: | |
| build-and-test: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| python-version: ['3.10'] | |
| fail-fast: false | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Clustal Omega and MAFFT | |
| run: | | |
| export $HOME_DIR=$PWD | |
| ls -la | |
| echo "$PWD" >> $GITHUB_PATH | |
| if [ "${{ runner.os }}" = "macOS" ]; then | |
| wget http://www.clustal.org/omega/clustal-omega-1.2.3-macosx -O clustalo && chmod +x clustalo | |
| brew install mafft && unset MAFFT_BINARIES | |
| elif [ "${{ runner.os }}" = "Linux" ]; then | |
| wget http://www.clustal.org/omega/clustalo-1.2.4-Ubuntu-x86_64 -O clustalo && chmod +x clustalo | |
| wget https://mafft.cbrc.jp/alignment/software/mafft-7.520-linux.tgz -O mafft.tgz && tar -xzvf mafft.tgz && chmod +x mafft-linux64/mafftdir/bin/mafft | |
| echo "$PWD/mafft-linux64/mafftdir/bin/" >> $GITHUB_PATH | |
| export MAFFT_BINARIES=$PWD/mafft-linux64/mafftdir/libexec/ | |
| fi | |
| echo 'PATH, and GITHUB_PATH:' | |
| echo $PATH | |
| echo $GITHUB_PATH | |
| ls -la | |
| clustalo --version # For debugging clustalo version | |
| mafft --version # For debugging mafft version | |
| - name: Install dependencies | |
| run: | | |
| python --version | |
| python -m pip install ".[full]" --no-cache-dir | |
| python -c "import qsprpred; print(qsprpred.__version__)" # For debugging package version | |
| python -m pip install pytest | |
| python -m pip install jupyterlab | |
| python -m pip freeze # For debugging environment | |
| - name: Run pytest | |
| run: pytest -xv qsprpred # -x: stop on first failure, -v: verbose | |
| - name: Test CLI | |
| run: cd test_cli && ./run.sh && cd "$HOME_DIR" | |
| - name: Test Tutorials | |
| run: cd test_tutorial && ./run.sh && cd "$HOME_DIR" | |
| - name: Test Consistency | |
| run: cd test_consistency && ./run.sh && cd "$HOME_DIR" |