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| # This is a basic workflow to help you get started with Actions | |
| name: CI | |
| # Controls when the action will run. | |
| on: [push, pull_request, workflow_dispatch] | |
| # A workflow run is made up of one or more jobs that can run sequentially or in parallel | |
| jobs: | |
| # This workflow contains a single job called "build" | |
| build: | |
| environment: Base | |
| # The type of runner that the job will run on | |
| runs-on: ubuntu-latest | |
| # strategy: | |
| # matrix: | |
| # python-version: [3.10, 3.11, 3.12] | |
| # Steps represent a sequence of tasks that will be executed as part of the job | |
| steps: | |
| # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it | |
| - uses: actions/checkout@v2 | |
| # Runs a single command using the runners shell | |
| - name: Set up Python 3.11.10 | |
| uses: actions/setup-python@v1 | |
| with: | |
| python-version: 3.11.10 | |
| - name: Set up conda test | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-activate-base: false | |
| activate-environment: pandora | |
| environment-file: environment.yml | |
| python-version: 3.11.10 | |
| # python-version: ${{ matrix.python-version }} | |
| # auto-update-conda: false | |
| # miniforge-version: latest | |
| - name: Set up directories | |
| run: | | |
| python test/install_git_test.py | |
| - name: Install package | |
| shell: bash -l {0} | |
| run: | | |
| pip install joblib | |
| python -m pip install --upgrade pip | |
| pip install -e .[test] | |
| - name: Test with pytest | |
| shell: bash -l {0} | |
| env: | |
| KEY_MODELLER: ${{ secrets.MODELLER_KEY }} | |
| run: | | |
| echo $KEY_MODELLER | |
| conda install -c salilab modeller | |
| conda install -c bioconda muscle=5.1 | |
| conda install -c bioconda blast=2.10 | |
| alias blastp='$CONDA/bin/blastp' | |
| alias muscle='$CONDA/bin/muscle' | |
| pytest test/ --cov=PANDORA --cov-config=.coveragerc --cov-report xml:coverage.xml | |
| - name: Coveralls | |
| shell: bash -l {0} | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| path-to-lcov: coverage.xml | |
| run: | | |
| coveralls --service=github |