ci.yml

name: CI

on:
  push:
    branches: [ main ]
  pull_request:
    branches: [ main ]
  workflow_dispatch:

jobs:
  test-core:
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.7", "3.9"]
    defaults:
      run:
        shell: bash -l {0}
    name: test-core (Python ${{ matrix.python-version }})
    steps:
    - uses: actions/checkout@v3
    - uses: conda-incubator/setup-miniconda@v2
      with:
        mamba-version: "*"
        channels: conda-forge,defaults
        channel-priority: true
        python-version: ${{ matrix.python-version }}
        environment-file: environment.yml
    - name: Install syntheseus
      run: |
        pip install .[dev]
    - name: Run pre-commit
      run: |
        pre-commit run --verbose --all-files
    - name: Run unit tests
      run: |
        coverage run -p -m pytest ./syntheseus/tests/
        coverage report --data-file .coverage.*
    - name: Upload coverage report
      uses: actions/upload-artifact@v4
      with:
        name: .coverage.core-${{ matrix.python-version }}
        path: .coverage.*
        include-hidden-files: true
  test-models:
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0}
    name: test-models
    steps:
    - name: Free extra disk space
      uses: jlumbroso/free-disk-space@main
    - uses: actions/checkout@v3
    - uses: conda-incubator/setup-miniconda@v2
      with:
        mamba-version: "*"
        channels: conda-forge,defaults
        channel-priority: true
        environment-file: environment_full.yml
    - name: Install syntheseus with all single-step models
      run: |
        sudo apt install graphviz
        pip install .[all]
    - name: Run single-step model tests
      run: |
        coverage run -p -m pytest \
          ./syntheseus/tests/cli/test_cli.py \
          ./syntheseus/tests/reaction_prediction/inference/test_models.py \
          ./syntheseus/tests/reaction_prediction/utils/test_parallel.py
        coverage report --data-file .coverage.*
    - name: Upload coverage report
      uses: actions/upload-artifact@v4
      with:
        name: .coverage.models
        path: .coverage.*
        include-hidden-files: true
  coverage:
    needs: [test-core, test-models]
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v2
    - name: Set up Python
      uses: actions/setup-python@v2
      with:
        python-version: 3.9
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install coverage
    - uses: actions/download-artifact@v4
      with:
        merge-multiple: true
    - name: Generate a combined coverage report
      run: |
        coverage combine
        coverage report