rustbam 0.2.0

Rust-powered BAM depth extraction with Python bindings
Documentation 
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name: CI

on:
  push:
    branches:
      - main
  pull_request:
    branches:
      - main

env:
  COVERAGE_PYTHON_VERSION: "3.8" # make coverage badge only for this version

jobs:
  test:
    name: Test RustBam on Ubuntu with Python ${{ matrix.python-version }}
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.8", "3.9", "3.10", "3.11"]

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4

      - name: Install Python ${{ matrix.python-version }}
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}

      - name: Install system dependencies
        run: |
          sudo apt-get update
          sudo apt-get install -y build-essential python3-dev python3-pip cargo

      - name: Setup Virtual Environment
        run: |
          python -m venv venv
          source venv/bin/activate
          pip install maturin pytest coverage
      
      - name: Build and Install RustBam
        run: |
          source venv/bin/activate
          maturin develop

      - name: Verify RustBam CLI
        run: |
          source venv/bin/activate
          rustbam --help

      - name: Run Tests with Coverage
        run: |
          source venv/bin/activate
          coverage run -m pytest -v
          coverage report -m

      - name: Coverage Badge
        uses: tj-actions/coverage-badge-py@v2
        if: matrix.python-version == env.COVERAGE_PYTHON_VERSION

      - name: Verify Changed files
        uses: tj-actions/verify-changed-files@v17
        id: verify-changed-files
        if: matrix.python-version == env.COVERAGE_PYTHON_VERSION
        with:
          files: coverage.svg

      - name: Commit files
        if: steps.verify-changed-files.outputs.files_changed == 'true' && matrix.python-version == env.COVERAGE_PYTHON_VERSION
        run: |
          git config --local user.email "github-actions[bot]@users.noreply.github.com"
          git config --local user.name "github-actions[bot]"
          git add coverage.svg
          git commit -m "update coverage.svg"

      - name: Push changes
        if: steps.verify-changed-files.outputs.files_changed == 'true' && matrix.python-version == env.COVERAGE_PYTHON_VERSION
        uses: ad-m/github-push-action@master
        with:
          github_token: ${{ secrets.github_token }}
          branch: ${{ github.ref }}