RFdiffusion/.github/workflows/main.yml

# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

name: Python application

on:
  push:
    branches: [ "main", "github-ci" ]
  pull_request:
    branches: [ "main", "github-ci" ]

permissions:
  contents: read

jobs:
  ppi-scaffolds-test:

    #runs-on: ubuntu-latest
    runs-on: ubuntu-24.04
    #container: nvcr.io/nvidia/cuda:12.9.1-cudnn-runtime-ubuntu20.04
    container: nvcr.io/nvidia/cuda:11.6.2-cudnn8-runtime-ubuntu20.04

    steps:
    - uses: actions/checkout@v4
    - name: Set up Python 3.9
      uses: actions/setup-python@v3
      with:
        python-version: "3.9"
    # - name: Install dependencies
    #   run: |
    #     python -m pip install --upgrade pip
    #     #pip install flake8 pytest
    #     pip install pytest
    #     if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
    # - name: Lint with flake8
    #   run: |
    #     # stop the build if there are Python syntax errors or undefined names
    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
    #     flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics

    - name: Install dependencies
      run: |
        apt-get update -qq && apt-get install -y --no-install-recommends \
        build-essential \
        git \
        curl \
        wget \
        ca-certificates

        curl -LsSf https://astral.sh/uv/install.sh | sh
        . $HOME/.local/bin/env bash

        uv python install 3.9
        uv venv
        uv pip install --no-cache-dir -q \
          dgl==1.0.2+cu116 -f https://data.dgl.ai/wheels/cu116/repo.html \
          torch==1.12.1+cu116 --extra-index-url https://download.pytorch.org/whl/cu116 \
          e3nn==0.3.3 \
          wandb==0.12.0 \
          pynvml==11.0.0 \
          git+https://github.com/NVIDIA/dllogger#egg=dllogger \
          decorator==5.1.0 \
          hydra-core==1.3.2 \
          pyrsistent==0.19.3 \
          pytest

        uv pip install --no-cache-dir env/SE3Transformer
        uv pip install --no-cache-dir -e . --no-deps
        rm -rf ~/.cache # /app/RFdiffusion/tests

    - name: Preseed DGL backend
      shell: bash
      run: |
        mkdir -p "$HOME/.dgl"
        printf '{"backend": "pytorch"}' > "$HOME/.dgl/config.conf"
        echo "DGLBACKEND=pytorch" >> "$GITHUB_ENV"

    - name: Download weights
      run: |
        mkdir models
        wget -q -O models/Base_ckpt.pt http://files.ipd.uw.edu/pub/RFdiffusion/6f5902ac237024bdd0c176cb93063dc4/Base_ckpt.pt
        wget -q -O models/Complex_base_ckpt.pt http://files.ipd.uw.edu/pub/RFdiffusion/e29311f6f1bf1af907f9ef9f44b8328b/Complex_base_ckpt.pt
        wget -q -O models/Complex_Fold_base_ckpt.pt http://files.ipd.uw.edu/pub/RFdiffusion/60f09a193fb5e5ccdc4980417708dbab/Complex_Fold_base_ckpt.pt
        wget -q -O models/InpaintSeq_ckpt.pt http://files.ipd.uw.edu/pub/RFdiffusion/74f51cfb8b440f50d70878e05361d8f0/InpaintSeq_ckpt.pt
        wget -q -O models/InpaintSeq_Fold_ckpt.pt http://files.ipd.uw.edu/pub/RFdiffusion/76d00716416567174cdb7ca96e208296/InpaintSeq_Fold_ckpt.pt
        wget -q -O models/ActiveSite_ckpt.pt http://files.ipd.uw.edu/pub/RFdiffusion/5532d2e1f3a4738decd58b19d633b3c3/ActiveSite_ckpt.pt
        wget -q -O models/Base_epoch8_ckpt.pt http://files.ipd.uw.edu/pub/RFdiffusion/12fc204edeae5b57713c5ad7dcb97d39/Base_epoch8_ckpt.pt
        #optional
        wget -q -O models/Complex_beta_ckpt.pt http://files.ipd.uw.edu/pub/RFdiffusion/f572d396fae9206628714fb2ce00f72e/Complex_beta_ckpt.pt
        #original structure prediction weights
        wget -q -O models/RF_structure_prediction_weights.pt http://files.ipd.uw.edu/pub/RFdiffusion/1befcb9b28e2f778f53d47f18b7597fa/RF_structure_prediction_weights.pt

    - name: Setup and Run ppi_scaffolds tests
      run: |
        tar -xvf examples/ppi_scaffolds_subset.tar.gz -C examples
        total_chunks=$(nproc)
        cd tests 

        #launch all chunks in background and record PIDs + labels
        pids=""
        for chunk_index in $(seq 1 $total_chunks); do
          echo "Running chunk $chunk_index of $total_chunks"
          uv run python test_diffusion.py --total_chunks $total_chunks --chunk_index $chunk_index &
          pids="$pids $!"
        done

        # wait for each and track failures
        fail=0
        for pid in $pids; do
          if ! wait "$pid"; then
            echo "A chunk (PID $pid) failed"
            fail=1
          else
            echo "A chunk (PID $pid) passed"
          fi
        done

        exit "$fail"

    # - name: Test with pytest
    #   run: |
    #     pytest