Merge pull request #2294 from nd-02110114/migrate-github-actions

name: Test for build scripts

on:

  push: # ci work when pushing master branch

    branches:

      - master

  pull_request: # ci work when creating a PR to master branch

    branches:

      - master

jobs:

  bash-build:

    runs-on: ${{ matrix.os }}

    strategy:

      fail-fast: false

      matrix:

        os: [ubuntu-latest, macos-latest]

        python-version: [3.7]

    steps:

    - uses: actions/checkout@v2

    - name: Cache pip modules for Linux

      if: runner.os == 'Linux'

      uses: actions/cache@v2

      with:

        path: ~/.cache/pip

        key: ${{ runner.os }}-pip-${{ hashFiles('env.*.yml') }}

        restore-keys: |

          ${{ runner.os }}-pip-

    - name: Cache pip modules for MacOS

      if: runner.os == 'macOS'

      uses: actions/cache@v2

      with:

        path: ~/Library/Caches/pip

        key: ${{ matrix.os }}-pip-${{ hashFiles('env.*.yml') }}

        restore-keys: |

          ${{ runner.os }}-pip-

    - name: Install miniconda

      uses: conda-incubator/setup-miniconda@v2

      with:

        miniconda-version: "latest"

        auto-update-conda: true

        python-version: ${{ matrix.python-version }}

    - name: Install dependencies (failure check)

      continue-on-error: true

      shell: bash -l {0}

      run: |

        source scripts/install_deepchem_conda.sh

    - name: Install all dependencies

      shell: bash -l {0}

      run: |

        source scripts/install_deepchem_conda.sh ${{ matrix.python-version }} cpu

    - name: Build DeepChem from source

      shell: bash -l {0}

      run: |

        conda activate deepchem

        pip install -e .

        python -V

        python -c 'import deepchem; print(deepchem.__version__)'

        python -c 'import rdkit; print(rdkit.__version__)'

        python -c 'import torch; print(torch.__version__)'

        python -c 'import tensorflow; print(tensorflow.__version__)'

  powershell-build:

    runs-on: windows-latest

    strategy:

      fail-fast: false

      matrix:

        python-version: [3.7]

    steps:

    - uses: actions/checkout@v2

    - name: Cache pip packages for Windows

      uses: actions/cache@v2

      with:

        path: ~\AppData\Local\pip\Cache

        key: ${{ matrix.os }}-pip-${{ hashFiles('env.*.yml') }}

    - name: Install miniconda

      uses: conda-incubator/setup-miniconda@v2

      with:

        miniconda-version: "latest"

        auto-update-conda: true

        python-version: ${{ matrix.python-version }}

    - name: Install dependencies (failure check)

      continue-on-error: true

      shell: pwsh

      run: |

        . .\scripts\install_deepchem_conda.ps1

    - name: Install dependencies

      shell: pwsh

      run: |

        . .\scripts\install_deepchem_conda.ps1 ${{ matrix.python-version }} cpu

    - name: Build DeepChem from source

      shell: pwsh

      run: |

        conda activate deepchem

        pip install -e .

        python -V

        python -c 'import deepchem; print(deepchem.__version__)'

        python -c 'import rdkit; print(rdkit.__version__)'

        python -c 'import torch; print(torch.__version__)'

        python -c 'import tensorflow; print(tensorflow.__version__)'

name: Test for documents

on:

  push: # ci work when pushing master branch

    branches:

      - master

  pull_request: # ci work when creating a PR to master branch

    branches:

      - master

jobs:

  linux:

    runs-on: ubuntu-latest

    strategy:

      fail-fast: false

      matrix:

        python-version: [3.7]

    steps:

    - uses: actions/checkout@v2

    - name: Cache pip packages for Linux

      uses: actions/cache@v2

      with:

        path: ~/.cache/pip

        key: ${{ runner.os }}-pip-${{ hashFiles('env.*.yml') }}

        restore-keys: |

          ${{ runner.os }}-pip-

    - name: Set up Python ${{ matrix.python-version }}

      uses: actions/setup-python@v2

      with:

        python-version: ${{ matrix.python-version }}

    - name: Create env.yml

      run: |

        python -m pip install --upgrade pip

        pip install conda-merge

        conda-merge env.common.yml env.cpu.yml env.test.yml > env.yml

    - uses: conda-incubator/setup-miniconda@v2

      with:

        miniconda-version: "latest"

        auto-update-conda: true

        activate-environment: deepchem

        channels: omnia,conda-forge,defaults

        python-version: ${{ matrix.python-version }}

        environment-file: env.yml

    - name: Install dependencies (docs)

      shell: bash -l {0}

      working-directory: ./docs

      run: pip install -r requirements.txt

    - name: Build docs

      shell: bash -l {0}

      working-directory: ./docs

      run: make clean html

    - name: DocTest (Tutorials)

      shell: bash -l {0}

      working-directory: ./docs

      run: make doctest_tutorials

    - name: DocTest (Examples)

      shell: bash -l {0}

      working-directory: ./docs

      run: make doctest_examples

name: Test for DeepChem Core

on:

  push: # ci work when pushing master branch

    branches:

      - master

  pull_request: # ci work when creating a PR to master branch

    branches:

      - master

jobs:

  build:

    runs-on: ubuntu-latest

    strategy:

      fail-fast: false

      matrix:

        python-version: [3.7]

    steps:

    - uses: actions/checkout@v2

    - name: Cache pip modules for Linux

      uses: actions/cache@v2

      with:

        path: ~/.cache/pip

        key: ${{ runner.os }}-pip-${{ hashFiles('env.*.yml') }}

        restore-keys: |

          ${{ runner.os }}-pip-

    - name: Set up Python ${{ matrix.python-version }}

      uses: actions/setup-python@v2

      with:

        python-version: ${{ matrix.python-version }}

    - name: Build DeepChem

      run: |

        python -m pip install --upgrade pip

        pip install tensorflow'>=2.3,<2.4'

        pip install -e .

    - name: Import checking

      run: python -c "import deepchem"

  test:

    runs-on: ${{ matrix.os }}

    strategy:

      fail-fast: false

      matrix:

        os: [ubuntu-latest, windows-latest]

        python-version: [3.7]

        include:

          - os: ubuntu-latest

            python-version: 3.6

    env:

      OS: ${{ matrix.os }}

      PYTHON_VERSION: ${{ matrix.python-version }}

    steps:

    - uses: actions/checkout@v2

      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@v2

      with:

        path: ~/.cache/pip

        key: ${{ runner.os }}-pip-${{ hashFiles('env.*.yml') }}

        restore-keys: |

          ${{ runner.os }}-pip-

    - name: Cache pip packages for MacOS

      if: runner.os == 'macOS'

      uses: actions/cache@v2

      with:

        path: ~/Library/Caches/pip

        key: ${{ matrix.os }}-pip-${{ hashFiles('env.*.yml') }}

        restore-keys: |

          ${{ runner.os }}-pip-

    - name: Cache pip packages for Windows

      if: runner.os == 'Windows'

      uses: actions/cache@v2

      with:

        path: ~\AppData\Local\pip\Cache

        key: ${{ matrix.os }}-pip-${{ hashFiles('env.*.yml') }}

        restore-keys: |

          ${{ runner.os }}-pip-

    - name: Set up Python ${{ matrix.python-version }}

      uses: actions/setup-python@v2

      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

      shell: bash

      run: |

        python -m pip install --upgrade pip;

        pip install conda-merge;

        if [ "$(uname)" == 'Darwin' ]; then

          conda-merge env.common.yml env.cpu.mac.yml env.test.yml > env.yml

        else

          conda-merge env.common.yml env.cpu.yml env.test.yml > env.yml

        fi;

    - name: Install all dependencies

      uses: conda-incubator/setup-miniconda@v2

      with:

        miniconda-version: "latest"

        auto-update-conda: true

        activate-environment: deepchem

        channels: omnia,conda-forge,defaults

        python-version: ${{ matrix.python-version }}

        environment-file: env.yml

    - name: Install DeepChem

      shell: bash -l {0}

      run: pip install -e .

    - name: Yapf (version 0.22.0)

      # on Windows, yapf raise the strange error..., so ignore

      if: runner.os == 'Linux' || runner.os == 'macOS'

      shell: bash -l {0}

      run: |

        CHANGED_FILES=`git diff --name-only $COMMIT_RANGE | grep .py$ | grep -v contrib/`

        yapf -d $CHANGED_FILES

    - name: Flake8

      shell: bash -l {0}

      run: source scripts/flake8_for_ci.sh

    - name: Mypy

      shell: bash -l {0}

      run: mypy -p deepchem

    - name: Doctest

      shell: bash -l {0}

      run: DGLBACKEND=pytorch pytest -v --ignore-glob='deepchem/**/test*.py' --doctest-modules deepchem

    - name: PyTest

      shell: bash -l {0}

      run: pytest -v -m "not slow" --cov=deepchem --cov-report=xml deepchem

    - name: Upload coverage to Codecov

      uses: codecov/codecov-action@v1

      with:

        file: ./coverage.xml

  deploy:

    if: ${{ github.ref == 'master' }}

    needs: [build]

    runs-on: ubuntu-latest

    steps:

    - uses: actions/checkout@v2

    - name: Set up Python

      uses: actions/setup-python@v1

      with:

        python-version: '3.7'

    - name: Install dependencies

      run: |

        python -m pip install --upgrade pip

        pip install setuptools wheel twine

    - name: Publish (Nightly)

      env:

        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}

        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}

      run: |

        python setup.py sdist bdist_wheel

        twine upload dist/*

name: Release PyPI packages

on:

  push:

    tags:

      - '*' # ci work when pushing a tag

jobs:

  release:

    runs-on: ubuntu-latest

    strategy:

      fail-fast: false

      matrix:

        python-version: [3.7]

    steps:

    - uses: actions/checkout@v2

    - name: Cache pip modules for Linux

      uses: actions/cache@v2

      with:

        path: ~/.cache/pip

        key: ${{ runner.os }}-pip-${{ hashFiles('env.*.yml') }}

        restore-keys: |

          ${{ runner.os }}-pip-

    - name: Set up Python ${{ matrix.python-version }}

      uses: actions/setup-python@v2

      with:

        python-version: ${{ matrix.python-version }}

    - name: Build DeepChem

      run: |

        python -m pip install --upgrade pip

        pip install tensorflow'>=2.3,<2.4'

        pip install -e .

    - name: Import checking

      run: python -c "import deepchem"

    - name: Prepare for publishing

      run: |

        rm -rf ./build ./dist ./*egg-info

        pip install setuptools wheel twine

    - name: Publish (Stable)

      env:

        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}

        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}

      run: |

        python setup.py sdist bdist_wheel --release

        twine upload dist/*

datasets/qm8.csv

.vscode/

env.yml

.python-version