mini_build.yml

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.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.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.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 }}