ci.yml

name: CI
on:
  push:
    branches: [main, develop]
    paths: ["src/**", "tests/**", ".github/workflows/ci.yml"]
  pull_request:
    branches: [main, develop]
    paths: ["src/**", "tests/**", ".github/workflows/ci.yml"]
  workflow_dispatch:

jobs:
  CI:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest, macos-latest]
        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
    steps:
      - name: Checkout
        uses: actions/checkout@v4

      - name: Setup Python ${{ matrix.python-version}}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}

      - name: Install python dependencies
        run: pip install -e . pytest pytest-cov ruff streamlit

      - name: Install external dependencies
        run: |
          sudo apt update -y
          sudo apt install -y ncbi-blast+ mmseqs2 mummer progressivemauve
        if: ${{ matrix.os=='ubuntu-latest' }}

      - name: Run ruff lint check
        run: ruff check --diff

      - name: Run ruff format check
        run: ruff format --check --diff

      - name: Run pytest
        run: pytest