tests.yml

# This file configures the continuous integration (CI) system on GitHub.
# Introductory materials can be found here: https://docs.github.com/en/actions/learn-github-actions/understanding-github-actions.
# Documentation for editing this file can be found here: https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions

name: Tests

on:
  pull_request:
  push:

jobs:
  # lint:
  #   name: Code Quality
  #   runs-on: ubuntu-latest
  #   strategy:
  #     matrix:
  #       python-version: [ "3.12", "3.10" ]
  #   steps:
  #     - uses: actions/checkout@v4
  #     - name: "Install python"
  #       uses: "astral-sh/setup-uv@v3"
  #       with:
  #         enable-cache: true
  #         cache-dependency-glob: "pyproject.toml"
  #     - name: "Run command"
  #       run: |
  #         uvx -p ${{ matrix.python-version }} --with tox-uv tox -e ${{ matrix.tox-command }}

  generate_suppl_files:
    name: Generate extra files
    runs-on: ubuntu-24.04

    steps:
    - name: Checkout
      uses: actions/checkout@main
      with:
        fetch-depth: 0

    - uses: conda-incubator/setup-miniconda@v3
      with:
        auto-update-conda: true
        python-version: 3.8
        activate-environment: genome_loader_env
        environment-file: env.yml
        auto-activate-base: false

    - name: Run tests
      shell: bash -l {0}
      continue-on-error: true
      run: |
          bash scripts/run_tools.sh tests/data/genome_paths.json test_results

    - name: upload artefacts
      uses: actions/upload-artifact@v4
      with:
        path: test_results/


  tests:
    name: Run tests (${{ matrix.python-version }}, ${{ matrix.os }})
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        # os: ["ubuntu-22.02", "ubuntu-24.04"]
        # python-version: ["3.10", "3.11", "3.12"]
        os: ["ubuntu-24.04"]
        python-version: ["3.8"]
    steps:
      - name: Checkout
        uses: actions/checkout@main
        with:
          fetch-depth: 0

      - uses: conda-incubator/setup-miniconda@v3
        with:
          auto-update-conda: true
          python-version: ${{ matrix.python-version }}
          activate-environment: genome_loader_env
          environment-file: env.yml
          auto-activate-base: false

      - name: install prerequisites
        shell: bash -l {0}
        run: pip install -r requirements.txt

      - name: Run tests
        shell: bash -l {0}
        continue-on-error: true
        run: pytest --cov=genome_loader_scripts --cov-report=xml tests/

      - name: Send to Codecov
        id: send_to_codecov
        continue-on-error: true
        uses: codecov/codecov-action@main
        with:
            files: coverage.xml
            # fail_ci_if_error: true
            token: ${{ secrets.CODECOV_TOKEN }}

      - name: Run tests
        shell: bash -l {0}
        continue-on-error: true
        run: |
            stats.sh --format=8 in=tests/data/FW305-C-112.1/FW305-C-112.1_scaffolds.fna,tests/data/FW305-3-2-15-C-TSA1/FW305-3-2-15-C-TSA1_scaffolds.fna > tests/data/fna-stats.json
            checkm2 database --download
            mkdir tests/data/checkm2
            checkm2 predict --threads 10 --input tests/data/FW305-3-2-15-C-TSA1/FW305-3-2-15-C-TSA1_scaffolds.fna tests/data/FW305-C-112.1/FW305-C-112.1_scaffolds.fna -o tests/data/checkm2

      - name: upload artefacts
        uses: actions/upload-artifact@v4
        with:
          path: tests/