Conda build #5
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| name: Conda build | |
| on: | |
| push: | |
| branches: ["main"] | |
| paths: ["**.py", "environment.yml"] | |
| pull_request: | |
| branches: ["main"] | |
| paths: ["**.py", "environment.yml"] | |
| workflow_dispatch: | |
| jobs: | |
| build-conda: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: environment.yml | |
| create-args: >- | |
| python=3.10 | |
| flake8 | |
| pytest | |
| - 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 | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=130 --statistics | |
| shell: micromamba-shell {0} | |
| - name: Install package | |
| run: | | |
| pip install . | |
| shell: micromamba-shell {0} | |
| - name: Cache external data | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.dbcanlight | |
| key: dbcanlight-external | |
| - name: Get external data | |
| run: | | |
| mkdir -p ~/.dbcanlight | |
| if ! [ -f ~/.dbcanlight/cazyme.hmm ]; \ | |
| then curl -o ~/.dbcanlight/cazyme.hmm https://bcb.unl.edu/dbCAN2/download/Databases/V12/dbCAN-HMMdb-V12.txt; \ | |
| fi | |
| if ! [ -f ~/.dbcanlight/substrate_mapping.tsv ]; \ | |
| then curl -o ~/.dbcanlight/substrate_mapping.tsv https://bcb.unl.edu/dbCAN2/download/Databases/fam-substrate-mapping-08252022.tsv; \ | |
| fi | |
| if ! [ -f ~/.dbcanlight/substrate.hmm ]; \ | |
| then curl -o ~/.dbcanlight/substrate.hmm https://bcb.unl.edu/dbCAN2/download/Databases/dbCAN_sub.hmm; \ | |
| fi | |
| - name: Test with pytest | |
| run: | | |
| pytest | |
| shell: micromamba-shell {0} |