feat: amino acid translation by nextclade #7
Workflow file for this run
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| name: Poetry in Conda | |
| on: | |
| push: | |
| branches: [ main ] # Or your main branch name | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| - name: Run black formatting check | |
| uses: psf/black@stable | |
| - name: Set up Conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| channels: conda-forge, bioconda | |
| environment-file: environment.yml | |
| activate-environment: myenv | |
| - name: Install Poetry | |
| run: | | |
| source $(conda info --base)/etc/profile.d/conda.sh | |
| conda activate myenv | |
| conda install -c conda-forge poetry | |
| - name: Install the module | |
| run: | | |
| source $(conda info --base)/etc/profile.d/conda.sh | |
| conda activate myenv | |
| poetry install --with dev --no-interaction | |
| - name: Run unit tests | |
| run: | | |
| source $(conda info --base)/etc/profile.d/conda.sh | |
| conda activate myenv | |
| poetry run pytest | |
| - name: Run unit tests | |
| run: poetry run pytest | |
| - name: Run Ruff | |
| run: | | |
| source $(conda info --base)/etc/profile.d/conda.sh | |
| conda activate myenv | |
| poetry run ruff check . | |
| - name: Run interrogate | |
| run: | | |
| source $(conda info --base)/etc/profile.d/conda.sh | |
| conda activate myenv | |
| poetry run interrogate src | |
| - name: Run Pyright (type checking) | |
| run: | | |
| source $(conda info --base)/etc/profile.d/conda.sh | |
| conda activate myenv | |
| poetry run pyright |