reproduce_paper.yml

name: Reproduce Paper
# This action runs a Jupyter notebook in the examples folder that uses astartes to generate
# train/val/test splits on two datasets (RDB7 and QM9). These dynamically generated splits
# are then compared to the splits which were created at the time of paper writing, to ensure
# that subsequent releases of astartes have backwards compatibility.
on:
  schedule:
    - cron: "0 8 * * 1-5"
  workflow_dispatch:

concurrency:
  group: actions-id-${{ github.workflow }}
  cancel-in-progress: true

jobs:
  build:
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -el {0}
    name: Reproduce Paper Data Splits
    steps:
      - uses: actions/checkout@v3
      - uses: mamba-org/setup-micromamba@main
        with:
          environment-name: temp
          condarc: |
            channels:
              - defaults
              - conda-forge
            channel_priority: flexible
          create-args: |
            python=3.11
      - name: Install Dependencies
        run: |
          python -m pip install -e .[molecules]
          python -m pip install scikit-learn==1.2.2
          python -m pip install notebook
          python -m pip install "numpy<2"
      - name: Backup Reference Splits
        run: |
          cd examples/reproduce_paper_splits
          cp QM9_splits/QM9_splits_kmeans.pkl REFERENCE_QM9_splits_kmeans.pkl
          cp QM9_splits/QM9_splits_random.pkl REFERENCE_QM9_splits_random.pkl
          cp QM9_splits/QM9_splits_scaffold.pkl REFERENCE_QM9_splits_scaffold.pkl
          cp RDB7_splits/RDB7_splits_kmeans.pkl REFERENCE_RDB7_splits_kmeans.pkl
          cp RDB7_splits/RDB7_splits_random.pkl REFERENCE_RDB7_splits_random.pkl
          cp RDB7_splits/RDB7_splits_scaffold.pkl REFERENCE_RDB7_splits_scaffold.pkl
      - name: Execute Splitting Notebooks
        run: |
          cd examples/reproduce_paper_splits
          ipython QM9_make_splits.ipynb
          ipython RDB7_make_splits.ipynb
      - name: Upload New Splits as Artifacts
        uses: actions/upload-artifact@v3
        with:
          name: dynamically-generated-splits
          path: |
            examples/reproduce_paper_splits/QM9_splits/
            examples/reproduce_paper_splits/RDB7_splits/
      - name: Compare Reference to Current
        run: |
          cd examples/reproduce_paper_splits
          python validate_splits.py