ci.yaml

name: CI

on:
#  push:
#    branches: [master]
  pull_request:
    branches: [master]
#  schedule:
#  - cron: "0 5 * * 0"

env:
  PREPARATION_COMMIT: '[github-actions.ci] update output data'

# Cancel any in-progress runs when a new run is triggered
concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

jobs:
  build:
    name: CI
    runs-on: ubuntu-latest

    defaults:
      run:
        shell: bash -l {0}

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

    - name: Setup micromamba
      uses: mamba-org/setup-micromamba@v2
      with:
        micromamba-version: latest
        environment-file: environment.yaml
        log-level: debug
        init-shell: bash
        cache-environment: true
        cache-downloads: true

    - name: Run unit tests
      run: |
        make unit-test

    - name: Test snakemake workflows
      run: |
        make test

    - name: Commit changes
      uses: stefanzweifel/git-auto-commit-action@v5
      with:
        branch: ${{ github.ref_name }}
        commit_message: '${{ env.PREPARATION_COMMIT }}'