Update type test to satisfy new flake8 (#3521) #23
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| name: Unit Tests | |
| on: | |
| push: # ci work when pushing master branch | |
| branches: | |
| - master | |
| pull_request: # ci work when creating a PR to master branch | |
| branches: | |
| - master | |
| jobs: | |
| core-build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ['3.8', '3.10'] | |
| include: | |
| - os: windows-latest | |
| python-version: '3.9' | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Cache pip modules for Linux | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('requirements/**.yml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Build DeepChem | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -e . | |
| - name: Import checking | |
| run: python -c "import deepchem" | |
| unit-tests: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ['3.8', '3.10'] | |
| include: | |
| - os: windows-latest | |
| python-version: '3.9' | |
| env: | |
| OS: ${{ matrix.os }} | |
| PYTHON_VERSION: ${{ matrix.python-version }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| # https://github.com/galaxyproject/tools-iuc/blob/master/.github/workflows/pr.yaml | |
| # The range of commits to check for changes is: | |
| # - for events on the master branch we compare against the sha before the event | |
| # (note that this does not work for feature branch events since we want all | |
| # commits on the feature branch and not just the commits of the last event) | |
| # - for pull requests we compare against the 1st ancestor, given the current | |
| # HEAD is the merge between the PR branch and the base branch | |
| - name: Set commit range (push to the master branch, e.g. merge) | |
| if: github.ref == 'refs/heads/master' && github.event_name == 'push' | |
| run: echo "COMMIT_RANGE=${{ 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@v3 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('requirements/**.yml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Cache pip packages for MacOS | |
| if: runner.os == 'macOS' | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/Library/Caches/pip | |
| key: ${{ matrix.os }}-pip-${{ hashFiles('requirements/**.yml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Cache pip packages for Windows | |
| if: runner.os == 'Windows' | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~\AppData\Local\pip\Cache | |
| key: ${{ matrix.os }}-pip-${{ hashFiles('requirements/**.yml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Create env.yml for python < 3.10 | |
| shell: bash | |
| if: ${{ matrix.python-version != '3.10' }} | |
| run: | | |
| python -m pip install --upgrade pip; | |
| pip install conda-merge; | |
| cd requirements | |
| if [ "$(uname)" == 'Linux' ]; then | |
| conda-merge env_common.yml env_test.yml env_ubuntu.yml tensorflow/env_tensorflow.cpu.yml torch/env_torch.cpu.yml jax/env_jax.cpu.yml env_py310_no_support.yml > env.yml | |
| elif [ "$(uname)" == 'Darwin' ]; then | |
| conda-merge env_common.yml env_test.yml env_mac.yml tensorflow/env_tensorflow.cpu.yml torch/env_torch.mac.cpu.yml jax/env_jax.cpu.yml env_py310_no_support.yml > env.yml | |
| elif [[ "$(uname)" == "MINGW64_NT"* ]]; then | |
| conda-merge env_common.yml env_test.yml tensorflow/env_tensorflow.cpu.yml torch/env_torch.cpu.yml > env.yml | |
| fi; | |
| cd .. | |
| cp requirements/env.yml env.yml | |
| - name: Create env.yml for python == 3.10 | |
| shell: bash | |
| # A special case of environment creation for python 3.10 which excludes vina | |
| if: ${{ matrix.python-version == '3.10' }} | |
| run: | | |
| python -m pip install --upgrade pip; | |
| pip install conda-merge; | |
| cd requirements | |
| if [ "$(uname)" == 'Linux' ]; then | |
| conda-merge env_common.yml env_test.yml env_ubuntu.yml tensorflow/env_tensorflow.cpu.yml torch/env_torch.cpu.yml jax/env_jax.cpu.yml > env.yml | |
| elif [ "$(uname)" == 'Darwin' ]; then | |
| conda-merge env_common.yml env_test.yml env_mac.yml tensorflow/env_tensorflow.cpu.yml torch/env_torch.mac.cpu.yml jax/env_jax.cpu.yml > env.yml | |
| elif [[ "$(uname)" == "MINGW64_NT"* ]]; then | |
| conda-merge env_common.yml env_test.yml tensorflow/env_tensorflow.cpu.yml torch/env_torch.cpu.yml > env.yml | |
| fi; | |
| cd .. | |
| cp requirements/env.yml env.yml | |
| - name: Install all dependencies | |
| uses: conda-incubator/setup-miniconda@v2 | |
| 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: Doctest Linux | |
| if: ${{ (runner.os == 'Linux') && always() }} | |
| shell: bash -l {0} | |
| run: DGLBACKEND=pytorch pytest -v --ignore-glob='deepchem/**/test*.py' --doctest-modules deepchem --doctest-continue-on-failure | |
| - name: Doctest Windows | |
| if: ${{ (runner.os == 'Windows') && always() }} | |
| # Seperate test avoiding Jax in windows since Jax is not supported in Windows | |
| shell: bash -l {0} | |
| run: DGLBACKEND=pytorch pytest -v --ignore-glob='deepchem/**/test*.py' --ignore-glob='deepchem/models/jax_models/*' --doctest-modules deepchem --doctest-continue-on-failure | |
| - name: PyTest | |
| if: ${{ (success() || failure()) && (steps.install.outcome == 'failure' || steps.install.outcome == 'success') && (matrix.python-version == '3.10') }} | |
| shell: bash -l {0} | |
| run: pytest -v -m "not jax and not torch and not tensorflow and not dqc" --ignore='deepchem/dock/tests/test_docking.py' --ignore='deepchem/dock/tests/test_pose_scoring.py' --ignore='deepchem/dock/tests/test_pose_generation.py' deepchem | |
| - name: PyTest | |
| # A special pytest case for python 3.10 version which excludes vina | |
| if: ${{ (success() || failure()) && (steps.install.outcome == 'failure' || steps.install.outcome == 'success') && (matrix.python-version != '3.10') }} | |
| shell: bash -l {0} | |
| run: pytest -v -m "not jax and not torch and not tensorflow and not dqc" deepchem |