pytest.yml

# Modified from GitHub Actions template

name: QA

# Improves reproducibility and speed
env:
  OPENBLAS_NUM_THREADS: 1
  OMP_NUM_THREADS: 1

on:
  push:
    branches: [master]
  pull_request:
    branches: [master]

jobs:
  Pytest:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.11"]
    steps:
    - uses: actions/checkout@v2
    - name: Setup Python ${{ matrix.python-version }}
      uses: actions/setup-python@v2
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install dependencies
      run: |
        pip install --upgrade pip wheel
        pip install numpy==1.26.4
        pip install -r requirements.txt
    - name: Compile Cython components
      run: |
        make clean compile
    - name: Test with pytest
      run: |
        python -m pytest --cov-report xml:cov.xml --cov=ecoli --cov=reconstruction --cov=wholecell --cov=runscripts --durations=0
    - name: Code Coverage Report
      uses: irongut/CodeCoverageSummary@v1.3.0
      with:
        filename: cov.xml
        format: markdown
        indicators: true
        output: both
    - name: Add Coverage PR Comment
      uses: marocchino/sticky-pull-request-comment@v2
      if: github.event_name == 'pull_request'
      with:
        recreate: true
        path: code-coverage-results.md
  Mypy:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.11"]
    steps:
    - uses: actions/checkout@v2
    - name: Setup Python ${{ matrix.python-version }}
      uses: actions/setup-python@v2
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install dependencies
      run: |
        pip install --upgrade pip wheel
        pip install numpy==1.26.4 mypy
        pip install -r requirements.txt
    - name: Compile Cython components
      run: |
        make clean compile
    - name: Mypy
      run: |
        mypy
  Lint:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.11"]
    steps:
    - uses: actions/checkout@v2
    - name: Setup Python ${{ matrix.python-version }}
      uses: actions/setup-python@v2
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install dependencies
      run: |
        pip install --upgrade pip wheel
        pip install numpy==1.26.4 ruff
        pip install -r requirements.txt
    - name: Compile Cython components
      run: |
        make clean compile
    - name: Ruff
      run: |
        ruff check doc ecoli migration wholecell runscripts validation reconstruction