#!/usr/bin/env python3 """ Sync the latest manuscript PDFs from the private research pipelines into this public repo, then commit + push any changes. Usage: python3 sync.py # sync all papers + CV, commit, push python3 sync.py --no-push # sync + commit, skip push python3 sync.py --dry-run # show what would change, no writes python3 sync.py [...] # sync only the named slugs python3 sync.py --cv-only # just refresh cv.pdf Source-of-truth for each slug is, in order: 1. /papers//manuscript/draft_combined.pdf 2. /papers//manuscript/submission//manuscript.pdf 3. /papers//manuscript/submission//submission-manuscript.pdf 4. /future//manuscript/ Add new papers by appending to PAPERS below. To rename a public slug, edit the first column; to point at a different source dir, edit src_dir. """ from __future__ import annotations import argparse import hashlib import shutil import subprocess import sys from pathlib import Path PAPERS_PUBLIC = Path("/Users/jonpalisoc/papers-public") HEALTH = Path("/Users/jonpalisoc/research-pipeline") PETS = Path("/Users/jonpalisoc/pet-research-pipeline") CV_SRC = Path("/Users/jonpalisoc/Documents/Jobs/JPalisocCV.pdf") # (public_slug, pipeline_root, paper_subdir, src_dirname, preferred_submission_journal) # preferred_submission_journal is used only if draft_combined.pdf is missing. PAPERS = [ # public_slug pipeline_root subdir src_dirname journal ("administrative-wedge", HEALTH, "papers", "administrative-wedge", "health-affairs"), ("adult-dental", HEALTH, "future", "adult-dental", "hsr"), ("buprenorphine-pa", HEALTH, "papers", "buprenorphine-pa", "health-affairs"), ("ca-medi-cal-2024-expansion", HEALTH, "future", "ca-medi-cal-26-49-expansion", None), ("doula-coverage", HEALTH, "papers", "doula-coverage", "health-affairs"), ("evv-rollout", HEALTH, "papers", "evv-rollout", "health-affairs"), ("postpartum-extension-chronic-care", HEALTH, "papers", "fertility-option-larc-ipi", None), ("fmap-floor-ltss-rkd", HEALTH, "papers", "fmap-floor-ltss-rkd", "medical_care"), ("fqhc-nap-bartik-iv", HEALTH, "papers", "fqhc-nap-bartik-iv", None), ("medicaid-drug-pools", HEALTH, "papers", "medicaid-drug-pools", "health-affairs"), ("noncitizen-coverage", HEALTH, "papers", "noncitizen-coverage", "health-affairs"), ("oregon-healthier-oregon", HEALTH, "future", "oregon-healthier-oregon-sdid", None), ("pbm-spread-pricing", HEALTH, "papers", "pbm-spread-pricing", "hsr"), ("post-release-mortality", HEALTH, "papers", "post-release-mortality", "health-affairs"), ("public-charge-chilling", HEALTH, "papers", "public-charge-chilling", "health-affairs"), ("public-data-medicaid-fraud-playbook", HEALTH, "papers", "public-data-medicaid-fraud-playbook", None), ("reentry-waivers", HEALTH, "future", "reentry-waivers", None), ("rural-emergency-hospitals", HEALTH, "papers", "rural-emergency-hospitals", "health-services-research"), ("section-17000-backstop", HEALTH, "future", "section-17000-backstop", None), ("ssa-office-closures-medicaid", HEALTH, "papers", "ssa-office-closures-medicaid", None), ("state-directed-payments-panel", HEALTH, "future", "state-directed-payments-panel", None), ("suspension-termination", HEALTH, "papers", "suspension-termination", None), ("unwind-compliance", HEALTH, "papers", "unwind-compliance", "hsr"), ("unwinding-adult-health", HEALTH, "future", "unwinding-adult-health", "health-affairs"), ("work-requirements", HEALTH, "future", "work-requirements", "hsr"), ("senior-dog-adoption-fee-waivers", PETS, "papers", "senior-dog-adoption-fee-waivers", None), ] def find_pdf(pipeline: Path, subdir: str, src_dirname: str, journal: str | None) -> Path | None: """Return the canonical manuscript PDF for one paper. Strict preference order: 1. manuscript/draft_combined.pdf 2. manuscript/draft_combined_with_figures.pdf 3. manuscript/submission//manuscript.pdf (if journal given) 4. manuscript/submission//submission-manuscript.pdf 5. manuscript/submission//manuscript.pdf (most-recent first) 6. manuscript/submission//submission-manuscript.pdf """ paper_dir = pipeline / subdir / src_dirname if not paper_dir.exists(): return None ms = paper_dir / "manuscript" # 1 & 2: draft_combined variants always win for name in ("draft_combined.pdf", "draft_combined_with_figures.pdf"): p = ms / name if p.exists(): return p submission = ms / "submission" if not submission.exists(): return None # 3 & 4: preferred journal if journal: for name in ("manuscript.pdf", "submission-manuscript.pdf"): p = submission / journal / name if p.exists(): return p # 5 & 6: any journal, most recent fallbacks: list[Path] = [] for jd in submission.iterdir(): if not jd.is_dir(): continue for name in ("manuscript.pdf", "submission-manuscript.pdf"): p = jd / name if p.exists(): fallbacks.append(p) if not fallbacks: return None fallbacks.sort(key=lambda p: p.stat().st_mtime, reverse=True) return fallbacks[0] def sha256(path: Path) -> str: h = hashlib.sha256() with path.open("rb") as f: for chunk in iter(lambda: f.read(65536), b""): h.update(chunk) return h.hexdigest() def sync_one(public_slug: str, src: Path, dry_run: bool) -> str: """Copy src into papers-public if it differs. Return status: 'updated', 'unchanged', 'new'.""" dst = PAPERS_PUBLIC / f"{public_slug}.pdf" if not dst.exists(): if dry_run: return "new (would copy)" shutil.copy2(src, dst) return "new" if sha256(src) == sha256(dst): return "unchanged" if dry_run: return "changed (would update)" shutil.copy2(src, dst) return "updated" def sync_cv(dry_run: bool) -> str: if not CV_SRC.exists(): return "skipped (CV pdf missing)" dst = PAPERS_PUBLIC / "cv.pdf" if dst.exists() and sha256(CV_SRC) == sha256(dst): return "unchanged" if dry_run: return "would update" shutil.copy2(CV_SRC, dst) return "updated" def git_commit_and_push(no_push: bool, dry_run: bool) -> bool: """Stage, commit, push any changes in papers-public. Return True if anything pushed/committed.""" repo = PAPERS_PUBLIC status = subprocess.run( ["git", "-C", str(repo), "status", "--porcelain"], capture_output=True, text=True, check=True, ).stdout.strip() if not status: return False print("\nChanges:") print(status) if dry_run: print("(dry-run; not committing)") return False subprocess.run(["git", "-C", str(repo), "add", "-A"], check=True) subprocess.run( ["git", "-C", str(repo), "-c", "user.email=jpalisoc@umich.edu", "-c", "user.name=Jonathan Palisoc", "commit", "-q", "-m", "Auto-sync from research pipelines"], check=True, ) if no_push: print("(committed locally; --no-push so skipping push)") return True subprocess.run(["git", "-C", str(repo), "push", "-q", "origin", "main"], check=True) print("Pushed.") return True def main() -> int: ap = argparse.ArgumentParser() ap.add_argument("slugs", nargs="*", help="Specific public slugs to sync (default: all)") ap.add_argument("--no-push", action="store_true", help="Commit locally but don't push") ap.add_argument("--dry-run", action="store_true", help="Print what would change; no writes") ap.add_argument("--cv-only", action="store_true", help="Only refresh cv.pdf") ap.add_argument("--no-cv", action="store_true", help="Skip CV refresh") args = ap.parse_args() print(f"Sync target: {PAPERS_PUBLIC}") print(f"Dry run: {args.dry_run}\n") updated = 0 unchanged = 0 missing = 0 if not args.cv_only: for public_slug, pipeline, subdir, src_dirname, journal in PAPERS: if args.slugs and public_slug not in args.slugs: continue src = find_pdf(pipeline, subdir, src_dirname, journal) if src is None: print(f" - {public_slug:42s} no PDF found (skipped)") missing += 1 continue status = sync_one(public_slug, src, args.dry_run) print(f" - {public_slug:42s} {status} <- {src.relative_to(pipeline)}") if status in ("updated", "new"): updated += 1 else: unchanged += 1 if not args.no_cv: cv_status = sync_cv(args.dry_run) print(f"\nCV: {cv_status}") if cv_status == "updated": updated += 1 print(f"\nSummary: {updated} updated, {unchanged} unchanged, {missing} missing.") if args.dry_run: return 0 if updated == 0: print("Nothing to commit.") return 0 git_commit_and_push(args.no_push, args.dry_run) return 0 if __name__ == "__main__": sys.exit(main())