Fix: Conditionally pass idx_pdb to writepdb to avoid AttributeError with SelfConditioning/ScaffoldedSampler #11
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| # 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: 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 | |
| cd tests && uv run python test_diffusion.py | |
| # - name: Test with pytest | |
| # run: | | |
| # pytest |