test.yaml

name: Test

on: [push, pull_request]

jobs:
  cli_test:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout code
        uses: actions/checkout@v2
      - name: Install Conda environment with Micromamba
        uses: mamba-org/provision-with-micromamba@main
        with:
          cache-downloads: true
          environment-file: env.yaml

      - name: Conda list
        shell: bash -l {0}
        run: conda list

      - name: Run tests
        shell: bash -l {0}
        run: |          
          set -ex

          python -m pip install . --no-deps -vv

          check_exit_code () { exit_code=$?; echo "exit code: $exit_code"; if [ $exit_code -ne 0 ]; then exit 1; fi; }

          itolparser --version
          check_exit_code

          itolparser --continuous nr_amr_genes --outdir tmp_output --input tests/table.tsv
          check_exit_code

          for file in tests/correct_output/normal/*
          do
            NAME=$(basename $file)
            cmp tests/correct_output/normal/$NAME tmp_output/$NAME
            check_exit_code
          done

          itolparser --continuous nr_amr_genes --ignore ST serotype --outdir tmp_output_OrRd --palette OrRd -i tests/table.tsv
          check_exit_code

          for file in tests/correct_output/OrRd_palette/*
          do
            NAME=$(basename $file)
            cmp tests/correct_output/OrRd_palette/$NAME tmp_output_OrRd/$NAME
            check_exit_code
          done