Training segmentation example notebook fixes #1361
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, pull_request] | |
| 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', '3.10'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache Python | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.pythonLocation }} | |
| key: ${{ env.pythonLocation }}-${{ hashFiles('requirements.txt') }}-${{ hashFiles('requirements-test.txt') }} | |
| restore-keys: | | |
| ${{ env.pythonLocation }}- | |
| - name: Install Dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt | |
| pip install -r requirements-test.txt | |
| - name: PyTest | |
| run: | | |
| pytest --cov deepcell | |
| - 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 | |
| # A job that runs the test suite using the development version of the | |
| # deepcell dependencies: deepcell-tracking and deepcell-toolbox. | |
| # This ensures consistency across unreleased versions of deepcell libraries | |
| test-dev: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.7", "3.8", "3.9", "3.10"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install deepcell-tf and dependencies | |
| run: | | |
| python -m pip install --upgrade pip wheel setuptools | |
| # Install deepcell-tf from source | |
| python -m pip install -r requirements.txt | |
| python -m pip install . | |
| python -m pip install -r requirements-test.txt | |
| - name: Manually install dev version of toolbox | |
| run: | | |
| git clone https://github.com/vanvalenlab/deepcell-toolbox.git && cd deepcell-toolbox | |
| python -m pip uninstall DeepCell-Toolbox -y | |
| python -m pip install . | |
| - name: Manually install dev version of tracking | |
| run: | | |
| git clone https://github.com/vanvalenlab/deepcell-tracking.git && cd deepcell-tracking | |
| python -m pip uninstall DeepCell-Tracking -y | |
| python -m pip install . | |
| - name: List dependencies | |
| run: | | |
| python -m pip install --upgrade numpy\<2 | |
| python -m pip list | |
| - name: Run tests | |
| run: | | |
| pytest --pyargs deepcell | |
| 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 | |
| test-docker: | |
| name: Build Docker and Run Tests | |
| runs-on: ubuntu-latest | |
| steps: | |
| # Attempt to free up space in workflow container | |
| - name: Delete tools folder | |
| run: rm -rf /opt/hostedtoolcache | |
| - uses: actions/checkout@v4 | |
| - name: Set up QEMU | |
| uses: docker/setup-qemu-action@v3 | |
| - name: Set up Docker Buildx | |
| 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 and Run Unit Tests | |
| env: | |
| IMAGE: ${{ github.repository }}:${{ github.sha }} | |
| NAME: deepcell-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-tf/requirements-test.txt | |
| docker exec ${{ env.NAME }} pip install -r /opt/deepcell-tf/requirements-test.txt | |
| docker exec ${{ env.NAME }} pytest /opt/deepcell-tf/deepcell | |
| docker kill ${{ env.NAME }} && docker rm ${{ env.NAME }} |