Update notebook reference (#4024) #6
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: Test for DeepChem Tensorflow | |
| on: | |
| push: # ci work when pushing master branch | |
| branches: | |
| - master | |
| pull_request: # ci work when creating a PR to master branch | |
| branches: | |
| - master | |
| jobs: | |
| tf-build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ['3.8', '3.10', '3.11'] | |
| include: | |
| - os: windows-latest | |
| python-version: 3.9 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Cache pip modules for Linux | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('requirements/tensorflow/**') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Build DeepChem | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -e '.[tensorflow]' | |
| - name: Import checking | |
| run: python -c "import deepchem; import tensorflow;" | |
| tf-test: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ['3.8', '3.10', '3.11'] | |
| include: | |
| - os: windows-latest | |
| python-version: '3.9' | |
| env: | |
| OS: ${{ matrix.os }} | |
| PYTHON_VERSION: ${{ matrix.python-version }} | |
| steps: | |
| - name: Maximize build space | |
| if: matrix.os == 'ubuntu-latest' | |
| run: | | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf /opt/ghc | |
| sudo rm -rf "/usr/local/share/boost" | |
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| sudo rm -rf /usr/local/lib/android | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| # https://github.com/galaxyproject/tools-iuc/blob/master/.github/workflows/pr.yaml | |
| # The range of commits to check for changes is: | |
| # - for events on the master branch we compare against the sha before the event | |
| # (note that this does not work for feature branch events since we want all | |
| # commits on the feature branch and not just the commits of the last event) | |
| # - for pull requests we compare against the 1st ancestor, given the current | |
| # HEAD is the merge between the PR branch and the base branch | |
| - name: Set commit range (push to the master branch, e.g. merge) | |
| if: github.ref == 'refs/heads/master' && github.event_name == 'push' | |
| run: echo "COMMIT_RANGE=${{ github.event.before }}.." >> $GITHUB_ENV | |
| - name: Set commit range (pull request) | |
| if: github.event_name == 'pull_request' | |
| run: | | |
| git fetch origin master | |
| echo "COMMIT_RANGE=origin/master..." >> $GITHUB_ENV | |
| - name: Cache pip packages for Linux | |
| if: runner.os == 'Linux' | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('requirements/tensorflow/**') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Cache pip packages for MacOS | |
| if: runner.os == 'macOS' | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/Library/Caches/pip | |
| key: ${{ matrix.os }}-pip-${{ hashFiles('requirements/tensorflow/**') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Cache pip packages for Windows | |
| if: runner.os == 'Windows' | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~\AppData\Local\pip\Cache | |
| key: ${{ matrix.os }}-pip-${{ hashFiles('requirements/tensorflow/**') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Create env.yml for python 3.8 | |
| shell: bash | |
| # A special case of environment creation for python 3.8 which includes an older version of matminer | |
| if: ${{ matrix.python-version == '3.8' }} | |
| run: | | |
| python -m pip install --upgrade pip; | |
| pip install conda-merge; | |
| conda-merge requirements/env_common_3_8.yml requirements/env_test.yml requirements/tensorflow/env_tensorflow.cpu.yml > env.yml | |
| - name: Create env.yml for python 3.9+ | |
| shell: bash | |
| if: ${{ matrix.python-version != '3.8' }} | |
| run: | | |
| python -m pip install --upgrade pip; | |
| pip install conda-merge; | |
| conda-merge requirements/env_common.yml requirements/env_test.yml requirements/tensorflow/env_tensorflow.cpu.yml > env.yml | |
| - name: Install all dependencies | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| activate-environment: deepchem | |
| channels: conda-forge,defaults | |
| python-version: ${{ matrix.python-version }} | |
| environment-file: env.yml | |
| - name: Install DeepChem | |
| id: install | |
| shell: bash -l {0} | |
| run: pip install -e . | |
| - name: PyTest | |
| if: ${{ (success() || failure()) && (steps.install.outcome == 'failure' || steps.install.outcome == 'success') }} | |
| shell: bash -l {0} | |
| run: pytest -v -m 'tensorflow' deepchem |