test_linux.yml

name: test

on:
  push:
    branches: [main, "[0-9]+.[0-9]+.x"]
  pull_request:
  schedule:
    - cron: "0 0 * * *"
  workflow_dispatch:

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

jobs:
  test:
    runs-on: ubuntu-latest

    defaults:
      run:
        shell: bash -e {0} # -e to fail on error

    strategy:
      fail-fast: false
      matrix:
        python: ["3.10", "3.13"]

    name: Python ${{ matrix.python }} integration

    env:
      PYTHON: ${{ matrix.python }}
      TEST_DATA_URL: https://yanglab.westlake.edu.cn/data/gsMap/gsMap_test_data.tar.gz
      TEST_DATA_DIR: ${{ github.workspace }}/test_data
      WORK_DIR: ${{ github.workspace }}/gsmap_workdir

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

      - name: Install uv
        uses: astral-sh/setup-uv@v5

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

      - name: Install dependencies
        run: |
          uv pip install --system -e ".[tests]"

      - name: Create workdir
        run: |
          mkdir -p $WORK_DIR
          echo "Created workdir: $WORK_DIR"

      - name: Cache test data
        uses: actions/cache@v3
        id: cache-test-data
        with:
          path: ${{ env.TEST_DATA_DIR }}
          key: test-data-v1

      - name: Download and extract test data
        if: steps.cache-test-data.outputs.cache-hit != 'true'
        run: |
          echo "Downloading test data from $TEST_DATA_URL"
          curl -L $TEST_DATA_URL -o gsMap_test_data.tar.gz
          tar -xzf gsMap_test_data.tar.gz -C ${{ github.workspace }}
          rm gsMap_test_data.tar.gz
          echo "Test data extracted to ${{ github.workspace }}"
          ls -la $TEST_DATA_DIR

      - name: Run pytest
        env:
          MPLBACKEND: agg
          DISPLAY: :0
          COLUMNS: 120
        run: |
          python -m pytest --cov=src \
              --junitxml=junit.xml -o junit_family=legacy \
              --cov-report=term-missing \
              --cov-report=xml \
              --cov-config=.coveragerc \
              -v -s --color=yes \
              --run-real-data \
              --work-dir=$WORK_DIR \
              --test-data=$TEST_DATA_DIR

      - uses: codecov/codecov-action@v4
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          files: ./coverage.xml
          fail_ci_if_error: false

      - name: Upload test results to Codecov
        if: ${{ !cancelled() }}
        uses: codecov/test-results-action@v1
        with:
          token: ${{ secrets.CODECOV_TOKEN }}