ci.yml

# ci.yml
#
# Continuous Integration for Chemprop - checks build, code formatting, and runs tests for all
# proposed changes and on a regular schedule
#
# Note: this file contains extensive inline documentation to aid with knowledge transfer.

name: Continuous Integration

on:
  # run on pushes/pull requests to/against main
  push:
    branches: [main]
  pull_request:
    branches: [main]
  # run this in the morning on weekdays to catch dependency issues
  schedule:
    - cron: "0 8 * * 1-5"
  # allow manual runs
  workflow_dispatch:

# cancel previously running tests if new commits are made
# https://docs.github.com/en/actions/examples/using-concurrency-expressions-and-a-test-matrix
concurrency:
  group: actions-id-${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

jobs:
  build:
    name: Check Build
    runs-on: ubuntu-latest
    steps:
      # clone the repo, attempt to build
      - uses: actions/checkout@v4
      - run: python -m pip install build
      - run: python -m build .

  lint:
    name: Check Formatting
    needs: build
    runs-on: ubuntu-latest
    steps:
      # clone the repo, run black and flake8 on it
      - uses: actions/checkout@v4
      - run: python -m pip install black==23.* flake8
      - run: black --check .
      - run: flake8 .

  test:
    name: Execute Tests
    needs: lint
    runs-on: ${{ matrix.os }}
    defaults:
      run:
        # run with a login shell (so that the conda environment is activated)
        # and echo the commands we run as we do them (for debugging purposes)
        shell: bash -el {0}
    strategy:
      # if one platform/python version fails, continue testing the others
      fail-fast: false
      matrix:
        # test on all platforms with both supported versions of Python
        os: [ubuntu-latest, macos-13, windows-latest]
        python-version: [3.11, 3.12]
    steps:
      - uses: actions/checkout@v4
      # use a version of the conda virtual environment manager to set up an
      # isolated environment with the Python version we want
      - uses: mamba-org/setup-micromamba@main
        with:
          environment-name: temp
          condarc: |
            channels:
              - defaults
              - conda-forge
            channel_priority: flexible
          create-args: |
            python=${{ matrix.python-version }}
      - name: Install dependencies
        shell: bash -l {0}
        run: |
          python -m pip install nbmake
          python -m pip install ".[dev,docs,test]"
      - name: Install hyperopt optional dependencies (Python 3.11 only)
        if: ${{ matrix.python-version == '3.11' }} 
        run: |
          python -m pip install ".[hpopt]"
      - name: Test with pytest
        shell: bash -l {0}
        run: |
          # specifically disable running on GPU, otherwise Lightning will attempt to use the Apple GPU
          # that the GitHub actions runners still have but are not allowed to actually use
          pytest -v tests
      - name: Test notebooks
        shell: bash -l {0}
        run: |
          pytest --nbmake examples/training.ipynb
          pytest --nbmake examples/predicting.ipynb
          pytest --nbmake examples/convert_v1_to_v2.ipynb
          pytest --nbmake examples/training_regression_multicomponent.ipynb
          pytest --nbmake examples/predicting_regression_multicomponent.ipynb

  conda-test:
    name: Execute Tests with Conda-based Install
    needs: lint
    runs-on: ubuntu-latest
    defaults:
      run:
        # run with a login shell (so that the conda environment is activated)
        # and echo the commands we run as we do them (for debugging purposes)
        shell: bash -el {0}
    strategy:
      # if one platform/python version fails, continue testing the others
      fail-fast: false
      matrix:
        python-version: [3.11, 3.12]
    steps:
      - uses: actions/checkout@v4
      # use a version of the conda virtual environment manager to set up an
      # isolated environment with the Python version we want
      - uses: mamba-org/setup-micromamba@main
        with:
          environment-file: environment.yml
          condarc: |
            channels:
              - defaults
              - conda-forge
              - pytorch
            channel_priority: flexible
          create-args: |
            python=${{ matrix.python-version }}
      - name: Install Testing Dependencies
        run: conda install -c conda-forge pytest>=6.2 pytest-cov
      - name: Install Chemprop
        run: python -m pip install . --no-deps
      - name: Test with pytest
        shell: bash -l {0}
        run: |
          pytest -v tests

  pypi:
    name: Build and publish Python 🐍 distributions 📦 to PyPI
    runs-on: ubuntu-latest
    # only run if the tests pass
    needs: [test, conda-test]
    # run only on pushes to main on chemprop
    if:  ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' && github.repository == 'chemprop/chemprop'}}
    steps:
      - uses: actions/checkout@master
      - name: Set up Python 3.12
        uses: actions/setup-python@v3
        with:
          python-version: "3.11"
      - name: Install pypa/build
        run: >-
          python -m
          pip install
          build
          --user
      - name: Build a binary wheel and a source tarball
        run: >-
          python -m
          build
          --sdist
          --wheel
          --outdir dist/
          .
      - name: Publish distribution 📦 to PyPI
        uses: pypa/gh-action-pypi-publish@release/v1
        with:
          password: ${{ secrets.PYPI_API_TOKEN }}
          skip-existing: true
          verbose: true
  
  build-and-push-docker:
    # shamelessly copied from:
    # https://github.com/ReactionMechanismGenerator/RMG-Py/blob/bfaee1cad9909a17103a8e6ef9a22569c475964c/.github/workflows/CI.yml#L359C1-L386C54
    # which is also shamelessly copied from somewhere
    runs-on: ubuntu-latest
    # only run if the tests pass
    needs: [test, conda-test]
    # run only on pushes to main on chemprop
    if:  ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' && github.repository == 'chemprop/chemprop'}}
    steps:
      - name: Set up QEMU
        uses: docker/setup-qemu-action@v2

      - name: Set up Docker Buildx
        uses: docker/setup-buildx-action@v2

      - name: Login to Docker Hub
        uses: docker/login-action@v2
        with:
          # repository secretes managed by the maintainers
          username: ${{ secrets.DOCKERHUB_USERNAME }}
          password: ${{ secrets.DOCKERHUB_TOKEN }}

      - name: Build and Push
        uses: docker/build-push-action@v4
        with:
          push: true
          tags: chemprop/chemprop:latest