Robust regressor (#4160) #1
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| name: Test for Build | |
| 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', '3.11'] | |
| include: | |
| - os: windows-latest | |
| python-version: '3.9' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| # using cached dependencies to speed up workflow | |
| # ref: https://docs.github.com/en/actions/advanced-guides/caching-dependencies-to-speed-up-workflows | |
| - name: Cache pip modules for Linux | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/pip | |
| # the key is used to search for cache | |
| # hashFile(paths) return a single hash for the set of files that matches the path pattern | |
| key: ${{ runner.os }}-pip-${{ hashFiles('requirements/**') }} | |
| 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 . | |
| - name: Import checking | |
| run: python -c "import deepchem" | |
| 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/**') }} | |
| 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/**') }} | |
| 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/**') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install prerequisites for XGBoost and LightGBM (MacOS) | |
| if: startsWith(runner.os, 'macOS') | |
| run: brew update && brew install libomp | |
| - name: Create env.yml for python >3.8 | |
| shell: bash | |
| if: ${{ matrix.python-version != '3.8' && matrix.python-version != '3.11'}} | |
| run: | | |
| python -m pip install --upgrade pip; | |
| pip install conda-merge; | |
| cd requirements | |
| if [ "$(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.win.cpu.yml > env.yml | |
| fi; | |
| cd .. | |
| cp requirements/env.yml env.yml | |
| - name: Create env.yml for python 3.11 | |
| shell: bash | |
| # A special case of environment creation for python 3.8 which excludes hhsuite | |
| if: ${{ matrix.python-version == '3.11' }} | |
| run: | | |
| python -m pip install --upgrade pip; | |
| pip install conda-merge; | |
| cd requirements | |
| if [ "$(uname)" == 'Linux' ]; then | |
| conda-merge env_common.yml env_test.yml env_ubuntu_3_11.yml tensorflow/env_tensorflow.cpu.yml torch/env_torch.cpu.yml > env.yml | |
| elif [ "$(uname)" == 'Darwin' ]; then | |
| conda-merge env_common.yml env_test.yml env_mac_3_11.yml tensorflow/env_tensorflow.cpu.yml torch/env_torch.mac.cpu.yml > env.yml | |
| elif [[ "$(uname)" == "MINGW64_NT"* ]]; then | |
| conda-merge env_common.yml env_test.yml tensorflow/env_tensorflow.cpu.yml torch/env_torch.win.cpu.yml > env.yml | |
| fi; | |
| cd .. | |
| cp requirements/env.yml env.yml | |
| - name: Create env.yml for python 3.8 | |
| shell: bash | |
| # A special case of environment creation for python 3.8 which excludes jax [deprecated] | |
| if: ${{ matrix.python-version == '3.8' }} | |
| run: | | |
| python -m pip install --upgrade pip; | |
| pip install conda-merge; | |
| cd requirements | |
| if [ "$(uname)" == 'Linux' ]; then | |
| conda-merge env_common_3_8.yml env_test.yml env_ubuntu.yml tensorflow/env_tensorflow.cpu.yml torch/env_torch.cpu.yml > env.yml | |
| elif [ "$(uname)" == 'Darwin' ]; then | |
| conda-merge env_common_3_8.yml env_test.yml env_mac.yml tensorflow/env_tensorflow.cpu.yml torch/env_torch.mac.cpu.yml > env.yml | |
| elif [[ "$(uname)" == "MINGW64_NT"* ]]; then | |
| conda-merge env_common_3_8.yml env_test.yml tensorflow/env_tensorflow.cpu.yml torch/env_torch.win.cpu.yml > env.yml | |
| fi; | |
| cd .. | |
| cp requirements/env.yml env.yml | |
| - name: Install all dependencies using micromamba | |
| uses: mamba-org/setup-micromamba@main | |
| with: | |
| environment-file: env.yml | |
| environment-name: deepchem | |
| create-args: python=${{ matrix.python-version }} | |
| # - name: Install all dependencies using conda | |
| # 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 | |
| pypi-build: | |
| if: github.event_name == 'push' && github.ref == 'refs/heads/master' | |
| needs: [core-build] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.9' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install setuptools wheel twine | |
| - name: Publish (Nightly) | |
| env: | |
| TWINE_USERNAME: __token__ | |
| TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }} | |
| run: | | |
| python setup.py sdist bdist_wheel | |
| twine upload dist/* | |
| docker-build: | |
| if: github.event_name == 'push' && github.ref == 'refs/heads/master' | |
| needs: [core-build, pypi-build] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Maximize build space | |
| run: | | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf /opt/ghc | |
| sudo rm -rf "/usr/local/share/boost" | |
| sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
| sudo rm -rf /usr/local/lib/android | |
| - uses: actions/checkout@v4 | |
| - name: Set up Docker Buildx | |
| id: buildx | |
| uses: docker/setup-buildx-action@master | |
| - name: Cache Docker layers | |
| uses: actions/cache@v4 | |
| with: | |
| path: /tmp/.buildx-cache | |
| key: ${{ runner.os }}-buildx-${{ github.sha }} | |
| restore-keys: ${{ runner.os }}-buildx- | |
| - name: Login to DockerHub | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ secrets.DOCKER_HUB_USERNAME }} | |
| password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }} | |
| - name: Build and push | |
| id: docker_build | |
| uses: docker/build-push-action@v5 | |
| with: | |
| builder: ${{ steps.buildx.outputs.name }} | |
| context: ./docker/nightly | |
| push: true | |
| tags: deepchemio/deepchem:latest | |
| cache-from: type=local,src=/tmp/.buildx-cache | |
| cache-to: type=local,dest=/tmp/.buildx-cache | |
| - name: Image digest | |
| run: echo ${{ steps.docker_build.outputs.digest }} |