Fix building/deployment of Python package and docker image #619
Workflow file for this run
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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: build | |
| on: | |
| push: | |
| branches: [master] | |
| pull_request: | |
| branches: [master] | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }} | |
| cancel-in-progress: true | |
| jobs: | |
| tests: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.7, 3.8, 3.9] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache pip | |
| uses: actions/cache@v3 | |
| with: | |
| # path: ${{ env.pythonLocation }} | |
| # key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }} | |
| # restore-keys: | | |
| # ${{ env.pythonLocation }}- | |
| # This path is specific to Ubuntu | |
| path: ~/.cache/pip | |
| # Look to see if there is a cache hit for the corresponding requirements file | |
| key: ${{ runner.os }}-pip-${{ hashFiles('setup.py') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| ${{ runner.os }}- | |
| - name: Install Dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install -r requirements.txt -r requirements-test.txt | |
| python -m pip install . | |
| - name: PyTest | |
| run: | | |
| pytest --cov deepcell_spots | |
| - name: Coveralls | |
| if: env.COVERALLS_REPO_TOKEN != null | |
| env: | |
| COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }} | |
| COVERALLS_FLAG_NAME: ${{ matrix.python-version }} | |
| COVERALLS_PARALLEL: true | |
| run: | | |
| coveralls --service=github | |
| test-docker: | |
| name: Build docker image and run tests | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: docker/setup-qemu-action@v3 | |
| - uses: docker/setup-buildx-action@v3 | |
| - name: Cache docker layers | |
| uses: actions/cache@v3 | |
| with: | |
| path: /tmp/.buildx-cache | |
| key: ${{ runner.os }}-buildx-${{ github.sha }} | |
| restore-keys: ${{ runner.os }}-buildx- | |
| - name: Build image run unit tests | |
| env: | |
| IMAGE: ${{ github.repository }}:${{ github.sha }} | |
| NAME: deepcell-spots-test | |
| run: | | |
| docker buildx build --load --tag ${{ env.IMAGE }} . | |
| docker run -d -it \ | |
| --entrypoint=bash \ | |
| --name ${{ env.NAME }} \ | |
| ${{ env.IMAGE }} | |
| docker cp requirements-test.txt ${{ env.NAME }}:/opt/deepcell-spots/requirements-test.txt | |
| docker exec ${{ env.NAME }} pip install -r /opt/deepcell-spots/requirements-test.txt | |
| docker exec ${{ env.NAME }} pytest /opt/deepcell-spots/deepcell_spots | |
| docker kill ${{ env.NAME }} && docker rm ${{ env.NAME }} | |
| coveralls: | |
| name: Finish Coveralls | |
| needs: tests | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Coveralls Finished | |
| uses: coverallsapp/github-action@master | |
| if: env.COVERALLS_REPO_TOKEN != null | |
| env: | |
| COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }} | |
| with: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| parallel-finished: true |