fix read_protein_set to use source_path=self.dataDir #1
Workflow file for this run
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| name: pre-merge Python3.10 CI | |
| on: | |
| push: | |
| branches: | |
| - feature/** # these branches as well | |
| - enhancement/** | |
| - fix/** | |
| jobs: | |
| ubuntu_python_3_10: | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 120 | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| - name: Cache Python dependencies | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Install Clustal Omega, MAFFT & add to PATH | |
| run: | | |
| export HOME_DIR=$PWD | |
| echo "HOME_DIR=$PWD" >> $GITHUB_ENV # used later in the workflow | |
| wget http://www.clustal.org/omega/clustalo-1.2.4-Ubuntu-x86_64 -O clustalo && chmod +x clustalo | |
| wget https://mafft.cbrc.jp/alignment/software/mafft-7.520-linux.tgz -O mafft.tgz && tar -xzvf mafft.tgz && chmod +x mafft-linux64/mafftdir/bin/mafft | |
| echo "MAFFT_BINARIES=$PWD/mafft-linux64/mafftdir/libexec/" >> $GITHUB_ENV | |
| echo "$HOME_DIR/mafft-linux64/mafftdir/bin/" >> $GITHUB_PATH | |
| echo "$HOME_DIR" >> $GITHUB_PATH # make clustalo available in the next steps | |
| - name: Print Clustal Omega & MAFFT versions | |
| run: | | |
| clustalo --version # For debugging clustalo version | |
| mafft --version # For debugging mafft version | |
| - name: Install dependencies | |
| run: | | |
| python -c "print('Python version: ' + '$(python --version)')" | |
| python -c "import platform; print('System info: ', platform.system(), platform.release())" # For debugging OS version | |
| python -c "import platform; print(platform.system(), platform.release())" # For debugging OS version | |
| python -m pip install ".[full]" | |
| 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 --junitxml=$HOME_DIR/test_report.xml # -x: stop on first failure, -v: verbose | |
| - name: Publish Test Report | |
| uses: mikepenz/action-junit-report@v4 | |
| if: success() || failure() # always run even if the previous step fails | |
| with: | |
| report_paths: 'test_report.xml' | |
| - name: Test CLI | |
| run: cd testing/test_cli && ./run.sh | |
| - name: Test Tutorials | |
| run: cd testing/test_tutorial && ./run.sh | |
| - name: Test Consistency | |
| run: cd testing/test_consistency && ./run.sh |