Bacpop-202 Assign fallback to refs to db #525
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| # This workflow will install Python dependencies, run tests and lint with a single version of Python | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Python unit & integration tests | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main, "bacpop-*" ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| path: main | |
| - name: Restore databases from cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ./main/storage/dbs | |
| key: cache-dbs | |
| id: cache-dbs | |
| - name: Download and extract GPS database | |
| working-directory: ./main | |
| run: | | |
| ./scripts/download_databases --refs | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: "3.9" | |
| - name: Setup Miniconda | |
| uses: conda-incubator/[email protected] | |
| with: | |
| python-version: 3.9 | |
| activate-environment: beebop_py | |
| channels: bioconda, conda-forge | |
| - name: Get Date | |
| id: get-date | |
| run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT | |
| shell: bash | |
| - name: Restore Conda env from cache | |
| uses: actions/cache@v2 | |
| with: | |
| path: /usr/share/miniconda/envs/beebop_py | |
| key: | |
| # Refresh cache each day | |
| conda-${{ runner.os }}--${{ runner.arch }}--${{ | |
| steps.get-date.outputs.today }}-${{ env.CACHE_NUMBER}} | |
| env: | |
| # Increment this value to manually reset cache. | |
| CACHE_NUMBER: 0 | |
| id: cache-conda | |
| # - name: Install poppunk | |
| # run: conda install poppunk | |
| # currently the latest poppunk release is missing some functions required for beebop. For now installing from source: | |
| - name: Get poppunk source code | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: bacpop/PopPUNK | |
| ref: fix-json-serialisation | |
| path: poppunk | |
| - name: install poppunk & dependencies | |
| working-directory: ./poppunk | |
| run: | | |
| source $CONDA/etc/profile.d/conda.sh | |
| conda activate beebop_py | |
| conda install graph-tool | |
| conda install mandrake | |
| conda install rapidnj | |
| sudo apt-get update | |
| sudo apt-get install libeigen3-dev libegl1 | |
| sudo apt-get install libopenblas-dev | |
| sudo apt-get install -y '^libxcb.*-dev' libx11-xcb-dev libglu1-mesa-dev libxrender-dev libxi-dev libxkbcommon-dev libxkbcommon-x11-dev | |
| pip install joblib==1.1.0 | |
| conda install -c bioconda pp-sketchlib=2.0.0 | |
| pip3 install git+https://github.com/bacpop/[email protected]#egg=PopPUNK | |
| - name: Install Poetry | |
| uses: snok/install-poetry@v1 | |
| with: | |
| virtualenvs-create: false | |
| - name: Install dependencies | |
| working-directory: ./main | |
| run: | | |
| source $CONDA/etc/profile.d/conda.sh | |
| conda activate beebop_py | |
| poetry install | |
| - name: Run Redis | |
| working-directory: ./main | |
| run: | | |
| source $CONDA/etc/profile.d/conda.sh | |
| conda activate beebop_py | |
| docker pull redis | |
| docker run --rm -d --name=redis -p 6379:6379 redis | |
| - name: Test with pytest | |
| env: | |
| MICROREACT_TOKEN: ${{ secrets.MICROREACT_TOKEN }} | |
| working-directory: ./main | |
| run: | | |
| source $CONDA/etc/profile.d/conda.sh | |
| conda activate beebop_py | |
| export PATH="/usr/share/miniconda/bin:$PATH" | |
| rq worker > rq_output.txt 2>&1 & | |
| STORAGE_LOCATION=./tests/results DBS_LOCATION=./storage/dbs poetry run coverage run -m pytest | |
| - name: Process coverage | |
| working-directory: ./main | |
| run: | | |
| source $CONDA/etc/profile.d/conda.sh | |
| conda activate beebop_py | |
| export PATH="/usr/share/miniconda/bin:$PATH" | |
| poetry run coverage report -m && poetry run coverage xml | |
| - name: Upload Coverage to Codecov | |
| uses: codecov/codecov-action@v2 | |
| with: | |
| root_dir: ./main | |
| # Uncomment the next three lines to debug on failure with | |
| # tmate. However, don't leave them uncommented on merge as that | |
| # causes failing builds to hang forever. | |
| # | |
| # - name: tmate session | |
| # if: ${{ failure() }} | |
| # uses: mxschmitt/action-tmate@v3 |