bionemo-recipes.yml

name: "BioNeMo Recipes CI"

on:
  push:
    branches:
      - main
      - "pull-request/[0-9]+"
      - "dependabot/**"
  merge_group:
    types: [checks_requested]
  schedule:
    - cron: "0 7 * * *" # Runs at 7 AM UTC daily (12 AM MST)

defaults:
  run:
    shell: bash -x -e -u -o pipefail {0}

concurrency:
  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

jobs:
  changed-dirs:
    runs-on: ubuntu-latest
    outputs:
      any_changed: ${{ steps.changed-files.outputs.any_changed }}
      all_changed_files: ${{ steps.changed-files.outputs.all_changed_files }}
      dirs: ${{ steps.set-dirs.outputs.dirs }}

    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0

      - name: Get changed files
        id: changed-files
        uses: step-security/changed-files@v46
        with:
          base_sha: main
          dir_names: true
          dir_names_max_depth: 2
          files: |
            models/**
            recipes/**

      - id: set-dirs
        # TODO: add models to the list of dirs
        run: |
          DIRS=$(ls -d recipes/*/ | jq -R -s -c 'split("\n")[:-1]')
          echo "dirs=$DIRS" >> $GITHUB_OUTPUT
      - name: Show output
        run: |
          echo '${{ toJSON(steps.changed-files.outputs) }}'
        shell:
          bash

  per-folder-test:
    needs: changed-dirs
    runs-on: linux-amd64-gpu-l4-latest-1
    container:
      image: nvcr.io/nvidia/pytorch:25.06-py3
    strategy:
      matrix:
        dir: ${{ fromJson(needs.changed-dirs.outputs.dirs) }}
      fail-fast: false

    steps:
      - name: Checkout repository
        if: contains(needs.changed-dirs.outputs.all_changed_files, matrix.dir)
        uses: actions/checkout@v4
        with:
          sparse-checkout: '${{ matrix.dir }}'
          sparse-checkout-cone-mode: false

      - name: Install uv
        uses: astral-sh/setup-uv@v6

      - name: Install dependencies
        working-directory: ${{ matrix.dir }}
        run: uv pip install -r requirements.txt

      - name: Run tests
        working-directory: ${{ matrix.dir }}
        run: pytest -v .