update to support JLab 4 #313
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - "*" | |
| workflow_dispatch: | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| concurrency: | |
| group: ${{ github.ref }}-${{ github.head_ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| tests: | |
| name: ${{ matrix.label }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| include: | |
| - label: rdkit-2021 | |
| python-version: 3.8 | |
| extra_dependencies: "rdkit==2021.03.1" | |
| - label: rdkit-latest | |
| python-version: "3.10" | |
| extra_dependencies: "rdkit" | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install Firefox | |
| uses: browser-actions/setup-firefox@latest | |
| - run: firefox --version | |
| - name: Prepare Selenium | |
| uses: browser-actions/setup-geckodriver@latest | |
| with: | |
| geckodriver-version: "0.32.0" | |
| - run: geckodriver --version | |
| - name: Cache conda | |
| uses: actions/cache@v3 | |
| env: | |
| CACHE_NUMBER: 0 | |
| with: | |
| path: ~/conda_pkgs_dir | |
| key: | |
| conda-${{ hashFiles('tests/environment.yml') }}-${{ matrix.label }}-${{ env.CACHE_NUMBER }} | |
| - name: Cache pip | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pip | |
| key: pip-${{ hashFiles('pyproject.toml') }} | |
| restore-keys: pip- | |
| - name: Get yarn cache directory path | |
| id: yarn-cache-dir-path | |
| run: echo "dir=$(yarn cache dir)" >> $GITHUB_OUTPUT | |
| - name: Cache yarn | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ steps.yarn-cache-dir-path.outputs.dir }} | |
| key: yarn-${{ hashFiles('yarn.lock') }} | |
| restore-keys: | | |
| yarn- | |
| - name: Setup Conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| environment-file: tests/environment.yml | |
| use-only-tar-bz2: true | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| use-mamba: true | |
| - name: Check conda and pip | |
| run: | | |
| which python | |
| python --version | |
| pip --version | |
| conda --version | |
| mamba --version | |
| - name: Install remaining conda dependencies | |
| run: | | |
| mamba install 'jupyterlab>=3,<5' ipywidgets=8 ${{ matrix.extra_dependencies }} | |
| mamba list | |
| - name: Build and install package | |
| run: | | |
| pip install .[tests,build] | |
| jupyter labextension develop . --overwrite | |
| pip list | |
| jupyter labextension list | |
| - name: Run tests | |
| run: | | |
| pytest --color=yes --disable-pytest-warnings \ | |
| --cov=mols2grid --cov-report=xml \ | |
| tests/ -m "not webdriver" | |
| - name: Run webdriver tests | |
| run: | | |
| pytest --color=yes --disable-pytest-warnings \ | |
| --cov=mols2grid --cov-report=xml --cov-append \ | |
| tests/ -m "webdriver" | |
| - name: Measure tests coverage | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| files: ./coverage.xml | |
| fail_ci_if_error: true | |
| verbose: true | |
| build: | |
| uses: ./.github/workflows/_build-package.yml | |
| with: | |
| cache-package: true | |
| test-build: | |
| name: Test build | |
| needs: [build] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Retrieve cached package | |
| uses: actions/cache/restore@v3 | |
| id: cache-mols2grid | |
| with: | |
| path: | | |
| dist/mols2grid-*.whl | |
| dist/mols2grid-*.tar.gz | |
| key: mols2grid-${{ runner.os }}-${{ github.sha }} | |
| - name: Install python with pip | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| cache: "pip" | |
| - name: Prepare quick test script | |
| run: | | |
| curl https://raw.githubusercontent.com/rdkit/rdkit/master/Docs/Book/data/solubility.test.sdf --output solubility.sdf | |
| echo "$SCRIPT" > test_install.py | |
| cat test_install.py | |
| env: | |
| SCRIPT: | | |
| import mols2grid as mg | |
| mg.save("solubility.sdf", output="/dev/null") | |
| - name: Test tar.gz build | |
| run: | | |
| pip install rdkit dist/mols2grid-*.tar.gz \ | |
| && python test_install.py \ | |
| && pip uninstall -y mols2grid | |
| - name: Test wheel build | |
| run: | | |
| pip install dist/mols2grid-*.whl \ | |
| && python test_install.py | |
| notebook-tests: | |
| needs: [build] | |
| name: ${{ matrix.label }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| include: | |
| - label: JLab-3-Widgets-7 | |
| extra_dependencies: "jupyterlab>=3.2,<4 ipywidgets>=7.6,<8" | |
| - label: JLab-4-Widgets-8 | |
| extra_dependencies: "jupyterlab>=4,<5 ipywidgets>=8.1,<9" | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Retrieve cached package | |
| uses: actions/cache/restore@v3 | |
| id: cache-mols2grid | |
| with: | |
| path: | | |
| dist/mols2grid-*.whl | |
| dist/mols2grid-*.tar.gz | |
| key: mols2grid-${{ runner.os }}-${{ github.sha }} | |
| - name: Get yarn cache directory path | |
| id: yarn-ui-cache-dir-path | |
| run: echo "dir=$(yarn cache dir)" >> $GITHUB_OUTPUT | |
| - name: Cache yarn | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ steps.yarn-ui-cache-dir-path.outputs.dir }} | |
| key: yarn-ui-${{ hashFiles('tests/notebooks/yarn.lock') }} | |
| restore-keys: | | |
| yarn-ui- | |
| - name: Setup Conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: "3.10" | |
| use-only-tar-bz2: true | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| use-mamba: true | |
| - name: Install remaining conda dependencies | |
| run: | | |
| mamba install rdkit pandas ${{ matrix.extra_dependencies }} | |
| mamba list | |
| - name: Get wheel absolute path | |
| id: wheel-path | |
| run: echo "value=$(ls -d $PWD/dist/mols2grid-*.whl)" >> $GITHUB_OUTPUT | |
| - name: Install the extension | |
| run: | | |
| pip install 'mols2grid[packaging] @ file://${{ steps.wheel-path.outputs.value }}' | |
| jupyter labextension list | |
| - name: Install Test Dependencies | |
| run: | | |
| jlpm --no-immutable | |
| npx playwright install chromium | |
| working-directory: tests/notebooks | |
| - name: Execute integration tests | |
| working-directory: tests/notebooks | |
| run: | | |
| npx playwright test | |
| - name: Upload Playwright Test assets | |
| if: always() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: notebooks-test-assets | |
| path: | | |
| tests/notebooks/test-results | |
| - name: Upload Playwright Test report | |
| if: always() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: notebooks-test-report | |
| path: | | |
| tests/notebooks/playwright-report | |
| - name: Update snapshots | |
| if: failure() | |
| working-directory: tests/notebooks | |
| run: | | |
| jlpm test:update | |
| - name: Upload updated snapshots | |
| if: failure() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: notebook-updated-snapshots | |
| path: tests/notebooks/tests |