| |
| """Fetch the third-party components that are not redistributed with this release. |
| |
| DegradeMaster and EGFR-PROPK are published without a license, so we cannot ship |
| copies of them. This script clones each upstream repository at the pinned commit |
| used for the paper and copies the subset the pipeline imports into the layout |
| `scripts/evaluate_linkers.py` and `src/classifier/protac_classifier.py` expect. |
| |
| Both are optional. Generation (`scripts/generate.py`) runs without either: |
| - DegradeMaster is needed only for predicted-degradation scoring. |
| - EGFR-PROPK is needed only for the EGFR-only PK columns of batch_report.py. |
| |
| Usage: |
| python scripts/fetch_third_party.py # fetch both |
| python scripts/fetch_third_party.py degrademaster |
| """ |
| from __future__ import annotations |
|
|
| import argparse |
| import shutil |
| import subprocess |
| import sys |
| import tempfile |
| from pathlib import Path |
|
|
| ROOT = Path(__file__).resolve().parents[1] |
|
|
| COMPONENTS = { |
| "degrademaster": { |
| "url": "https://github.com/ABILiLab/DegradeMaster", |
| "commit": "aa149beaf067a051e070b3b281f7dba43c2f3e90", |
| "dest": ROOT / "src" / "degrademaster", |
| "paths": [ |
| "model.py", "dataset.py", "nn_utils.py", "pdb_utils.py", |
| "tools.py", "protacloader.py", |
| "tokenizer", "utils", |
| "checkpoint/1000/model_for_case_study.pth", |
| ], |
| }, |
| "propk": { |
| "url": "https://github.com/Zhang-Ran-0119/EGFR-PROPK", |
| "commit": "6940cb90c449e6c6d0678508fc2f228da796e028", |
| "dest": ROOT / "src" / "propk", |
| "paths": [ |
| "maplight.py", "maplight_gnn.py", |
| "models/CL_1_finetune.pkl", |
| "models/t0.5_10_finetune.pkl", |
| "models/Vss_1_finetune.pkl", |
| ], |
| }, |
| } |
|
|
|
|
| def fetch(name: str, spec: dict) -> int: |
| print(f"\n=== {name} ===") |
| print(f" {spec['url']} @ {spec['commit'][:12]}") |
| print(" NOTE: published without a license file. Review the upstream terms") |
| print(" before using or redistributing it.") |
|
|
| with tempfile.TemporaryDirectory() as tmp: |
| try: |
| subprocess.run(["git", "clone", "--quiet", spec["url"], tmp], check=True) |
| subprocess.run(["git", "-C", tmp, "checkout", "--quiet", spec["commit"]], |
| check=True) |
| except subprocess.CalledProcessError as exc: |
| print(f" FAILED to clone: {exc}") |
| return 1 |
|
|
| missing = [] |
| for rel in spec["paths"]: |
| src = Path(tmp) / rel |
| dst = spec["dest"] / rel |
| if not src.exists(): |
| missing.append(rel) |
| continue |
| dst.parent.mkdir(parents=True, exist_ok=True) |
| if src.is_dir(): |
| shutil.copytree(src, dst, dirs_exist_ok=True) |
| else: |
| shutil.copy2(src, dst) |
| print(f" + {rel}") |
|
|
| if missing: |
| print(f" {len(missing)} path(s) not found upstream at this commit:") |
| for rel in missing: |
| print(f" - {rel}") |
| print(" The upstream layout may have changed, or the checkpoint may be") |
| print(" distributed outside git. Fetch those by hand.") |
| return 1 |
| return 0 |
|
|
|
|
| def main() -> int: |
| ap = argparse.ArgumentParser(description=__doc__, |
| formatter_class=argparse.RawDescriptionHelpFormatter) |
| ap.add_argument("components", nargs="*", default=[], |
| choices=list(COMPONENTS), |
| help="which to fetch (default: all)") |
| args = ap.parse_args() |
|
|
| names = args.components or list(COMPONENTS) |
| failures = sum(fetch(n, COMPONENTS[n]) for n in names) |
|
|
| print() |
| if failures: |
| print(f"{failures} component(s) incomplete.") |
| else: |
| print("All components fetched.") |
| return 1 if failures else 0 |
|
|
|
|
| if __name__ == "__main__": |
| raise SystemExit(main()) |
|
|
