Replace hmmer with py hmmer (#219) #348
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| name: CI (Conda/PyTest) | |
| on: | |
| push: | |
| paths-ignore: | |
| - 'README.md' | |
| pull_request: | |
| types: | |
| - opened | |
| - edited | |
| - synchronize | |
| paths-ignore: | |
| - 'README.md' | |
| jobs: | |
| build: | |
| name: Test (${{ matrix.os }}, ${{ matrix.python-version }}) | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| os: ['ubuntu-latest', 'macos-latest'] | |
| python-version: ['3.10'] # ['3.8', '3.10'] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| micromamba-version: 'latest' | |
| environment-name: 'bakta' | |
| environment-file: 'environment.yml' | |
| create-args: python=${{ matrix.python-version }} | |
| condarc: | | |
| channels: | |
| - conda-forge | |
| - bioconda | |
| init-shell: bash | |
| cache-environment: true | |
| cache-downloads: true | |
| post-cleanup: 'all' | |
| # - name: Install DeepSig | |
| # if: ${{ matrix.os == 'ubuntu-latest' && matrix.python-version == '3.8'}} | |
| # run: mamba install numpy=1.23 keras=2.4.3 tensorflow=2.2.0 chardet deepsig | |
| - name: Install PyTest | |
| run: micromamba install pytest | |
| shell: bash -l {0} | |
| - name: Mamba info | |
| run: | | |
| micromamba info | |
| micromamba list | |
| printenv | sort | |
| shell: bash -l {0} | |
| - name: Run PyTest | |
| if: ${{ matrix.os == 'ubuntu-latest' || matrix.python-version == '3.10'}} | |
| run: pytest | |
| shell: bash -l {0} |