test.yaml

# Testing for pipeline python wrapper and scripts used inside rules

name: Clustering script tests

on: [push, pull_request]

jobs:
  build:
    runs-on: ${{ matrix.config.os }}
    strategy:
      fail-fast: false
      matrix:
        config: 
          - {os: ubuntu-latest}
    name: Testing on ${{ matrix.config.os }}

    steps:
      - uses: actions/checkout@v4
      - name: Install Conda environment with Micromamba
        uses: mamba-org/setup-micromamba@v1
        with:
          generate-run-shell: false # see https://github.com/mamba-org/setup-micromamba/issues/130
          cache-downloads: true
          environment-file: tests/env.yaml
      - name: Conda list
        shell: bash -l {0}
        run: conda list
      - name: Unit tests
        shell: bash -l {0}
        run: pytest .
      - name: Integration test, normal flow
        shell: bash -l {0}
        run: bash tests/normal_flow/run_test.sh
      - name: Integration test, no previous clustering
        shell: bash -l {0}
        run: bash tests/no_previous_clustering/run_test.sh
      - name: Integration test, merged clusters
        shell: bash -l {0}
        run: bash tests/merge/run_test.sh
      - name: Integration test, curation
        shell: bash -l {0}
        run: bash tests/curation/run_test.sh