Complete cell-SAM with two channel selection #1095
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: tests | |
| on: | |
| pull_request: | |
| push: | |
| branches: | |
| - main | |
| jobs: | |
| e2e-tests: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.8 | |
| - name: Cache pip | |
| uses: actions/cache@v3 | |
| with: | |
| # 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('backend/requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| ${{ runner.os }}- | |
| - name: Install Dependencies | |
| working-directory: backend | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt | |
| pip install -r requirements-test.txt | |
| - name: Use Node.js 16.x | |
| uses: actions/setup-node@v3 | |
| with: | |
| node-version: 16.x | |
| - name: Cypress run | |
| uses: cypress-io/github-action@v5 | |
| env: | |
| AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| CYPRESS_AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| CYPRESS_AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| with: | |
| working-directory: frontend | |
| start: | | |
| npm run cypress:frontend | |
| npm run cypress:backend | |
| wait-on: "http://localhost:3000, http://localhost:5000/health" | |
| wait-on-timeout: 300 | |
| spec: | | |
| cypress/e2e/label.cy.js | |
| cypress/e2e/caliban.cy.js | |
| cypress/e2e/spots.cy.js | |
| cypress/e2e/celltypes.cy.js | |
| - name: Cypress Coveralls | |
| uses: coverallsapp/github-action@master | |
| env: | |
| COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }} | |
| with: | |
| base-path: frontend | |
| path-to-lcov: frontend/coverage/lcov.info | |
| github-token: ${{ secrets.github_token }} | |
| flag-name: cypress | |
| parallel: true | |
| frontend-tests: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| node-version: [16.x] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Use Node.js ${{ matrix.node-version }} | |
| uses: actions/setup-node@v3 | |
| with: | |
| node-version: ${{ matrix.node-version }} | |
| - name: Cache node_modules | |
| uses: actions/cache@v3 | |
| with: | |
| path: "frontend/**/node_modules" | |
| key: ${{ runner.os }}-modules-${{ hashFiles('frontend/**/yarn.lock') }} | |
| restore-keys: | | |
| ${{ runner.os }}-yarn- | |
| ${{ runner.os }}- | |
| - name: Yarn Install | |
| working-directory: frontend | |
| run: yarn install --update-checksums | |
| - name: Lint | |
| working-directory: frontend | |
| run: yarn lint | |
| - name: Unit Tests | |
| working-directory: frontend | |
| run: yarn test --coverage | |
| env: | |
| CI: true | |
| - name: Coveralls Parallel | |
| uses: coverallsapp/github-action@master | |
| env: | |
| COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }} | |
| with: | |
| base-path: frontend | |
| path-to-lcov: frontend/coverage/lcov.info | |
| github-token: ${{ secrets.github_token }} | |
| flag-name: node-${{ matrix.node-version }} | |
| parallel: true | |
| backend-tests: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.8"] | |
| 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: | |
| # 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('backend/requirements.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| ${{ runner.os }}- | |
| - name: Install Dependencies | |
| working-directory: backend | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt | |
| pip install -r requirements-test.txt | |
| - name: Run PyTest | |
| working-directory: backend | |
| run: | | |
| PYTHONPATH=deepcell_label pytest deepcell_label --cov deepcell_label | |
| - name: Coveralls | |
| if: env.COVERALLS_REPO_TOKEN != null | |
| env: | |
| COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }} | |
| COVERALLS_FLAG_NAME: python-${{ matrix.python-version }} | |
| COVERALLS_PARALLEL: true | |
| working-directory: backend | |
| run: | | |
| coveralls | |
| coveralls: | |
| name: Finish Coveralls | |
| needs: [e2e-tests, frontend-tests, backend-tests] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Coveralls Finished | |
| uses: coverallsapp/github-action@master | |
| with: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| parallel-finished: true |