update to support JLab 4 #332
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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: | |
| # unit-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 ${{ matrix.extra_dependencies }} | |
| # mamba list | |
| # - name: Build and install package | |
| # run: | | |
| # pip install .[tests,build] | |
| # jupyter labextension develop . --overwrite | |
| # pip list | |
| # jupyter labextension list | |
| # - name: Run tests | |
| # run: | | |
| # pytest --color=yes --disable-pytest-warnings \ | |
| # --cov=mols2grid --cov-report=xml \ | |
| # tests/ -m "not webdriver" | |
| # - name: Run webdriver tests | |
| # run: | | |
| # pytest --color=yes --disable-pytest-warnings \ | |
| # --cov=mols2grid --cov-report=xml --cov-append \ | |
| # tests/ -m "webdriver" | |
| # - name: Measure tests coverage | |
| # uses: codecov/codecov-action@v3 | |
| # with: | |
| # files: ./coverage.xml | |
| # fail_ci_if_error: true | |
| # verbose: true | |
| build: | |
| uses: ./.github/workflows/_build-package.yml | |
| with: | |
| cache-package: true | |
| upload-package: true | |
| build-test: | |
| name: Test build | |
| needs: [build] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Retrieve cached package | |
| uses: actions/cache/restore@v3 | |
| id: cache-mols2grid | |
| with: | |
| path: | | |
| dist/mols2grid-*.whl | |
| dist/mols2grid-*.tar.gz | |
| key: mols2grid-${{ 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 | |
| ui-tests: | |
| needs: [build] | |
| name: ${{ matrix.label }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| include: | |
| - label: JLab-3-Widgets-7 | |
| extra_dependencies: "'jupyterlab~=3.2' 'ipywidgets~=7.6'" | |
| - label: JLab-4-Widgets-8 | |
| extra_dependencies: "'jupyterlab~=4.0' 'ipywidgets~=8.1'" | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Retrieve cached package | |
| uses: actions/cache/restore@v3 | |
| id: cache-mols2grid | |
| with: | |
| path: | | |
| dist/mols2grid-*.whl | |
| dist/mols2grid-*.tar.gz | |
| key: mols2grid-${{ runner.os }}-${{ github.sha }} | |
| - name: Cache conda | |
| uses: actions/cache@v3 | |
| env: | |
| CACHE_NUMBER: 2 | |
| with: | |
| path: ~/conda_pkgs_dir | |
| key: | |
| conda-${{ matrix.label }}-${{ env.CACHE_NUMBER }} | |
| - name: Setup Conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: "3.10" | |
| 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: Install XeLatex | |
| run: sudo apt-get install texlive-xetex | |
| - name: Install Ghostscript for ImageMagick | |
| run: sudo apt-get install ghostscript | |
| - name: Install the extension | |
| run: | | |
| pip install dist/mols2grid-*.whl | |
| jupyter labextension list | |
| - name: Run test notebook and convert to PDF | |
| working-directory: tests/notebooks/ | |
| run: | | |
| jupyter nbconvert --to pdf --execute --no-input filtering.ipynb | |
| - name: Change ImageMagick policy to allow pdf->png conversion | |
| run: | | |
| sudo sed -i 's/^.*policy.*coder.*none.*PDF.*//' /etc/ImageMagick-6/policy.xml | |
| - name: Convert to PNG | |
| id: png-conv | |
| working-directory: tests/notebooks/ | |
| run: | | |
| mv filtering.pdf ${{ matrix.label }}.pdf | |
| convert -density 192 ${{ matrix.label }}.pdf \ | |
| -quality 100 -alpha remove ${{ matrix.label }}.png | |
| ls | |
| - name: Run diff | |
| id: diff-test | |
| working-directory: tests/notebooks/ | |
| run: | | |
| delta=$(compare -metric AE -fuzz 10% ref-${{ matrix.label }}.png ${{ matrix.label }}.png null:) | |
| echo "Delta: $delta" | |
| [[ $delta -eq 0 ]] | |
| - name: Upload output if fail | |
| if: ${{ always() && (steps.diff-test.outcome.failure || steps.png-conv.outcome.failure) }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: notebook-${{ matrix.label }} | |
| path: | | |
| tests/notebooks/${{ matrix.label }}* | |
| if-no-files-found: error | |
| retention-days: 5 |