RDiffusion/install.sh at main · A4Bio/RDiffusion · GitHub

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#!/usr/bin/env bash
set -euo pipefail

# This script assumes:
# 1) conda create -n RDiffusion python=3.10
# 2) conda activate RDiffusion

SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
cd "$SCRIPT_DIR"

echo "[1/6] Preparing pip tooling..."
python -m pip install --upgrade "pip<24.1" "setuptools<60" wheel

echo "[2/6] Installing core numerical/runtime dependencies..."
python -m pip install \
	numpy==1.24.4 \
	scipy==1.10.1 \
	pandas==1.3.1 \
	scikit-learn==1.3.2 \
	tqdm==4.66.5 \
	biopython==1.79 \
	einops==0.8.1 \
	pillow==10.2.0 \
	requests==2.32.4 \
	fsspec==2024.6.1 \
	packaging==25.0 \
	protobuf==3.17.3 \
	regex==2021.10.8 \
	PyYAML==5.4.1

echo "[3/6] Installing PyTorch stack (matching RDiffusion env major versions)..."
python -m pip install \
	torch==2.4.1 \
	torchvision==0.19.1 \
	torchaudio==2.4.1 \
	pytorch-lightning==1.9.3 \
	torchmetrics==1.5.2 \
	tensorboard==2.6.0 \
	accelerate==0.16.0 \
	ninja==1.13.0

echo "[4/6] Installing NLP/model dependencies..."
python -m pip install \
	tokenizers==0.20.3 \
	transformers==4.46.3 \
	huggingface-hub==0.36.0 \
	safetensors==0.5.3 \
    ptflops==0.7.3

echo "[5/6] Installing fairseq-compatible dependencies..."
python -m pip install \
	hydra-core==1.0.7 \
	omegaconf==2.0.6 \
	fairseq==0.12.2

echo "[Optional] Installing geometric dependencies for ts task (best effort)..."
set +e
python -m pip install torch-geometric==2.6.1
TS_GEOM_RC=$?
set -e

if [[ $TS_GEOM_RC -ne 0 ]]; then
	echo "[WARN] torch-geometric install failed. Non-ts tasks can still run."
	echo "[WARN] For ts task, install torch-scatter/torch-cluster/torch-sparse wheels matching your torch build."
fi

echo "[6/6] Quick runtime check..."
python - <<'PY'
import importlib

mods = [
		"torch",
		"pytorch_lightning",
		"transformers",
		"fairseq",
		"numpy",
		"sklearn",
		"tqdm",
]
for m in mods:
		importlib.import_module(m)

print("Core dependency import check passed.")
PY

python inference.py --help >/dev/null
echo "RDiffusion install finished. inference.py --help passed."