test.yml

name: Run basic tests for Lemur 

on:
  push:
    branches: [ "main" ]
  pull_request:
    branches: [ "main" ]

jobs:
  test:
    name: Test Lemur executable
    runs-on: ${{ matrix.os }}
    defaults:
      run:
        shell: bash -l {0}

    strategy:
          fail-fast: false
          matrix:
            os: [ubuntu-latest, macos-12]

    steps:
      - uses: actions/checkout@v4
      - name: Setup Miniconda
        uses: conda-incubator/setup-miniconda@v3
        with:
          environment-file: ./lemur.yml
          activate-environment: lemur-env
          python-version: 3.9

      - name: Create output folder
        run: |
          mkdir ./examples/example-output

      - name: Run Lemur
        run: ./lemur -i ./examples/example-data/example.fastq 
                     -o ./examples/example-output 
                     -d ./examples/example-db 
                     --tax-path ./examples/example-db/taxonomy.tsv 
                     -r species 
                     --verbose;

      - name: Check that output was produced
        id: check_files
        uses: andstor/file-existence-action@v2.0.0
        with:
          files: "./examples/example-output/P_rgs_df.tsv, ./examples/example-output/relative_abundance.tsv, ./examples/example-output/relative_abundance-species.tsv" 
          fail: true

      - name: Check if outputed profile matches reference
        uses: LouisBrunner/diff-action@v2.0.0
        with:
          old: ./examples/example-output-ref/relative_abundance.tsv
          new: ./examples/example-output/relative_abundance.tsv
          mode: strict
          tolerance: same
          output: ./examples/example-output/relative_abundance_diff.txt 
    
      - name: Archive production artifacts
        uses: actions/upload-artifact@v3
        with:
          name: lemur-out-log
          path: ./examples/example-output/*
          retention-days: 5