update to support JLab 4 #323
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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: ${{ matrix.label }} | |
| # runs-on: ubuntu-latest | |
| # strategy: | |
| # matrix: | |
| # include: | |
| # - label: JLab-3-Widgets-7 | |
| # extra_dependencies: "'jupyterlab~=3.2' 'ipywidgets~=7.6'" | |
| # - label: JLab-4-Widgets-8 | |
| # extra_dependencies: "'jupyterlab~=4.0' 'ipywidgets~=8.1'" | |
| # steps: | |
| # - uses: actions/checkout@v3 | |
| # - name: Retrieve cached package | |
| # uses: actions/cache/restore@v3 | |
| # id: cache-mols2grid | |
| # with: | |
| # path: | | |
| # dist/mols2grid-*.whl | |
| # dist/mols2grid-*.tar.gz | |
| # key: mols2grid-${{ 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 ${{ matrix.extra_dependencies }} | |
| # mamba list | |
| # - name: Get wheel absolute path | |
| # id: wheel-path | |
| # run: echo "value=$(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: Run test | |
| # run: | | |
| # echo TODO |