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* Added HF workflow * Moved prot bert tests to HF marker * Resolved?? * Moved all HF tests to new CI
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,139 @@ | ||
| name: Test for DeepChem HuggingFace | ||
| on: | ||
| push: # ci work when pushing master branch | ||
| branches: | ||
| - master | ||
| pull_request: # ci work when creating a PR to master branch | ||
| branches: | ||
| - master | ||
| jobs: | ||
| HF-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/torch/**') }} | ||
| 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 '.[torch]' | ||
| - name: Import checking | ||
| run: python -c "import deepchem; import torch;" | ||
|
|
||
| HF-tests: | ||
| 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/torch/**') }} | ||
| 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/torch/**') }} | ||
| 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/torch/**') }} | ||
| 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 3.9+ | ||
| 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/torch/env_torch.cpu.yml requirements/env_test.yml > env.yml | ||
| - 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/torch/env_torch.cpu.yml requirements/env_test.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 'hf' deepchem |
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