Replace HMMER with PyHMMER #354
Workflow file for this run
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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: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: false | |
| python-version: ${{ matrix.python-version }} | |
| miniconda-version: "latest" | |
| mamba-version: "1.4.2" | |
| channels: conda-forge,bioconda | |
| channel-priority: true | |
| auto-activate-base: false | |
| environment-file: environment.yml | |
| activate-environment: bakta | |
| # - name: Install DeepSig | |
| # if: ${{ matrix.os == 'ubuntu-latest' && matrix.python-version == '3.8'}} | |
| # run: conda install numpy=1.23 keras=2.4.3 tensorflow=2.2.0 chardet deepsig | |
| - name: Install PyTest | |
| run: conda install pytest | |
| - name: Conda info | |
| run: | | |
| conda info | |
| conda list | |
| conda config --show | |
| printenv | sort | |
| - name: Run PyTest | |
| if: ${{ matrix.os == 'ubuntu-latest' || matrix.python-version == '3.10'}} | |
| run: pytest |