Fix threading bug #9
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| name: Conda build | |
| on: | |
| push: | |
| branches: [ "main" ] | |
| paths: [ "**.py" ] | |
| pull_request: | |
| branches: [ "main" ] | |
| paths: [ "**.py" ] | |
| jobs: | |
| build-linux: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 5 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: '3.10' | |
| - name: Add conda to system path | |
| run: | | |
| # $CONDA is an environment variable pointing to the root of the miniconda directory | |
| echo $CONDA/bin >> $GITHUB_PATH | |
| - name: Install dependencies | |
| run: | | |
| conda env update --file environment.yml --name base | |
| - name: Lint with flake8 | |
| run: | | |
| conda install flake8 | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=130 --statistics | |
| - name: Install package | |
| run: | | |
| pip install . | |
| - name: Get external data | |
| run: | | |
| mkdir -p ~/.dbcanlight | |
| curl -o ~/.dbcanlight/substrate_mapping.tsv https://bcb.unl.edu/dbCAN2/download/Databases/fam-substrate-mapping-08252022.tsv | |
| curl -o ~/.dbcanlight/cazyme.hmm https://bcb.unl.edu/dbCAN2/download/Databases/V11/dbCAN-HMMdb-V11.txt | |
| curl -o ~/.dbcanlight/substrate.hmm https://bcb.unl.edu/dbCAN2/download/Databases/dbCAN_sub.hmm | |
| - name: Test with pytest | |
| run: | | |
| conda install pytest | |
| pytest |