#!/usr/bin/env python3 """Rewrite the old cluster's absolute path roots across the RNASBDD repository. The repository hardcodes ~1,449 absolute paths under two roots that existed only on the retired DeltaAI allocation. Nothing runs on a new cluster until they are remapped. This rewrites them in place. Dry run (default) reports what would change and touches nothing: python remap_paths.py --repo /path/to/RNASBDD \ --data-root /new/scratch/RNASBDD \ --env-prefix /new/conda/envs/rnasbdd \ --crossdocked-root /new/scratch/sbdd_data Add --apply to write. Re-run the test suite afterwards: the specs carry SHA-256 digests for the files they name, and the suite checks that those still resolve. Digests are NOT rewritten, on purpose. A path move does not change file content, so every dataset/split/freeze/checkpoint digest must still match after remapping. If one does not, the file was corrupted in transit and the launcher is right to refuse it. """ from __future__ import annotations import argparse import sys from pathlib import Path # Old roots, longest first so that a prefix never shadows a longer match. OLD_ENV_PREFIX = "/work/nvme/bdrx/dzhang5/conda/envs/rnasbdd" OLD_ANNAPURNA_ENV = "/work/nvme/bdrx/dzhang5/conda/envs/annapurna" OLD_RNAMIGOS2_ENV = "/work/nvme/bdrx/dzhang5/conda/envs/rnamigos2" OLD_TOOLS_ROOT = "/work/nvme/bdrx/dzhang5/tools" OLD_CROSSDOCKED = "/work/hdd/bdrx/dzhang5/sbdd_data" OLD_POCKET10 = "/work/hdd/bdrx/dzhang5/unimomo/molecule/crossdocked_pocket10" OLD_DATA_ROOT = "/work/hdd/bdrx/dzhang5/RNASBDD" # Genuinely cluster-specific and deliberately not remapped. This is a shell # `case` glob guarding a wheel build against non-DeltaAI prefixes; on a new # cluster the whole guard needs rewriting by hand, not prefix substitution. UNMAPPED_BY_DESIGN = ("scripts/build_deltaai_pyg_wheels.sh",) SEARCH_DIRS = ("run_specs", "configs", "harness", "scripts", "docs") SEARCH_FILES = (".research-project.toml",) SKIP_SUFFIXES = {".pyc", ".pt", ".lmdb", ".zst", ".png", ".jpg", ".pdf"} def build_mapping(args: argparse.Namespace) -> list[tuple[str, str]]: mapping = [ (OLD_ENV_PREFIX, args.env_prefix.rstrip("/")), (OLD_CROSSDOCKED, args.crossdocked_root.rstrip("/")), (OLD_DATA_ROOT, args.data_root.rstrip("/")), ] if args.tools_root: mapping.append((OLD_TOOLS_ROOT, args.tools_root.rstrip("/"))) if args.annapurna_env: mapping.append((OLD_ANNAPURNA_ENV, args.annapurna_env.rstrip("/"))) if args.rnamigos2_env: mapping.append((OLD_RNAMIGOS2_ENV, args.rnamigos2_env.rstrip("/"))) if args.crossdocked_pocket10: mapping.append((OLD_POCKET10, args.crossdocked_pocket10.rstrip("/"))) # Longest old-prefix first: OLD_ENV_PREFIX lives under a root that no other # entry covers, but keeping the rule explicit makes adding entries safe. mapping.sort(key=lambda pair: len(pair[0]), reverse=True) return mapping def candidate_files(repo: Path): for name in SEARCH_FILES: path = repo / name if path.is_file(): yield path for directory in SEARCH_DIRS: root = repo / directory if not root.is_dir(): continue for path in sorted(root.rglob("*")): if path.is_file() and path.suffix not in SKIP_SUFFIXES: if "__pycache__" not in path.parts: yield path def main() -> int: parser = argparse.ArgumentParser() parser.add_argument("--repo", required=True, type=Path) parser.add_argument("--data-root", required=True, help="replaces /work/hdd/bdrx/dzhang5/RNASBDD") parser.add_argument("--env-prefix", required=True, help="replaces the conda env prefix") parser.add_argument("--crossdocked-root", required=True, help="replaces /work/hdd/bdrx/dzhang5/sbdd_data") parser.add_argument("--tools-root", default=None, help="replaces /work/nvme/bdrx/dzhang5/tools " "(mmseqs2, annapurna, rnamigos2 binaries)") parser.add_argument("--annapurna-env", default=None, help="replaces the AnnapuRNA conda env prefix. This is " "a SEPARATE Python 2.7.15 env, not the main one.") parser.add_argument("--rnamigos2-env", default=None, help="replaces the RNAmigos2 conda env prefix " "(separate Python 3.10 env).") parser.add_argument("--crossdocked-pocket10", default=None, help="replaces the legacy CrossDocked pocket10 raw " "tree, which lives under a different old root " "than --crossdocked-root.") parser.add_argument("--apply", action="store_true", help="write the changes; without it this is a dry run") args = parser.parse_args() repo = args.repo.resolve() if not (repo / "run_specs").is_dir(): raise SystemExit(f"{repo} does not look like the RNASBDD repository") mapping = build_mapping(args) print("mapping:") for old, new in mapping: print(f" {old}\n -> {new}") print() total_hits = 0 changed_files = 0 per_prefix = {old: 0 for old, _ in mapping} for path in candidate_files(repo): try: text = path.read_text(encoding="utf-8") except (UnicodeDecodeError, OSError): continue updated = text hits = 0 for old, new in mapping: count = updated.count(old) if count: updated = updated.replace(old, new) per_prefix[old] += count hits += count if hits: total_hits += hits changed_files += 1 if args.apply: path.write_text(updated, encoding="utf-8") else: print(f" {hits:>4} {path.relative_to(repo)}") print() for old, count in sorted(per_prefix.items(), key=lambda kv: -kv[1]): print(f" {count:>5} x {old}") verb = "rewrote" if args.apply else "would rewrite" print(f"\n{verb} {total_hits} references across {changed_files} files") leftovers: dict[str, int] = {} if args.apply: for path in candidate_files(repo): rel = str(path.relative_to(repo)) if rel in UNMAPPED_BY_DESIGN: continue try: text = path.read_text(encoding="utf-8") except (UnicodeDecodeError, OSError): continue count = (text.count("/work/hdd/bdrx/dzhang5") + text.count("/work/nvme/bdrx/dzhang5")) if count: leftovers[rel] = count total_left = sum(leftovers.values()) print(f"remaining old-root references: {total_left}") for rel, count in sorted(leftovers.items(), key=lambda kv: -kv[1]): print(f" {count:>3} {rel}") for rel in UNMAPPED_BY_DESIGN: if (repo / rel).is_file(): print(f" skipped by design (needs hand edit): {rel}") if total_left: print("\nNOTE: the mapping did not cover everything. Pass the " "optional flags (--annapurna-env, --rnamigos2-env, " "--crossdocked-pocket10, --tools-root) for the ones above.") return 1 print("\nNext: re-run the test suite. Digests are unchanged by design, " "so a digest failure now means a corrupted transfer, not a stale " "pin.") else: print("dry run - nothing written. Re-run with --apply to write.") return 0 if __name__ == "__main__": sys.exit(main())