diff --git a/paper-releases/pbisc-diffusion/updates/20260929T062828Z-manuscript-relocation/diffusion/dataset/server_1/maintenance/26f3248763a2f99b/POLICY.md b/paper-releases/pbisc-diffusion/updates/20260929T062828Z-manuscript-relocation/diffusion/dataset/server_1/maintenance/26f3248763a2f99b/POLICY.md new file mode 100644 index 0000000000000000000000000000000000000000..00343cb2c10b05f9e2002a1fe688d7fddd9c2e5d --- /dev/null +++ b/paper-releases/pbisc-diffusion/updates/20260929T062828Z-manuscript-relocation/diffusion/dataset/server_1/maintenance/26f3248763a2f99b/POLICY.md @@ -0,0 +1,60 @@ +# PBISC-Diffusion paper archive maintenance + +Project ID: **`pbisc-diffusion`**. User standing instruction, 2026-09-28: keep this paper archive updated across **Codex and Claude Code**, and do not mix in any other paper. + +## Scope gate — apply this before doing anything + +This policy applies only to work explicitly for the PBISC-Diffusion paper: + +- Model 8 source, training/fine-tuning, inference, evaluation, figures and reproducibility: `/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/`. +- Its named manuscript: `/home/sj_server_1/PBISC/paper-release-20260928/manuscript/` (a Git working tree of `junidude/PBISC-diffusion-overleaf`, whose README identifies PBISC-Diffusion). It was moved there from `/home/sj_server_1/PBISC/immun-pbmc-fm/bulk2sc-paper/nature-communications-overleaf/` on 2026-09-29 at the user's request; its superseded drafts are in the sibling `archived-analyses/`, which is not an archive payload root. +- Exact shared dependencies listed in `SCOPE.json`, with a documented relationship to this paper. A shared dependency does not bring its directory, its other uses, or another paper into scope. New external dependencies require evidence of the Model 8/manuscript relationship and a deliberate exact-path scope addition. + +Do **not** treat all PBISC work as this paper. VAE/BIBM papers, independent Model 7 work, historical `model/diffusion` / coalescent, other `bulk2sc-paper` subdirectories, transcriptome/FM papers and unrelated datalake analyses are outside scope. A generic PBISC mention is not enough to infer the paper. The old archived-diffusion wording concerns the historical coalescent branch, not the active Model 8 paper. + +## Shared start/end contract for both agents + +At the start of an in-scope task, read this policy, `SCOPE.json`, and `../LATEST.json` if present; otherwise use `BASELINE_REFERENCE.json`. Consult `../CURRENT.md` and the current model/inference catalogs before retrieving results. Check source host as well as absolute path: identical paths exist on both servers. + +Before finishing an in-scope task that changes paper evidence or reusable assets: + +1. Identify exact new or changed checkpoints, data/preprocessing inputs, splits/QC/masks/units, evaluation references, scripts/configs, score tables, figures or manuscript files. Include provenance tying them to this paper. Do not glob the whole workspace. +2. Write a request using `request.example.json`. Use `project_id: pbisc-diffusion`; name each source host/path, artifact kind and actual state. Register training/inference that is still running as a location/status observation; do not publish actively changing payload files as completed. Immutable stopped/intermediate checkpoints may be archived with that state retained. +3. Record **new inference output locations**, recorded output/checkpoint/input hashes and receipt paths. Preserve the distinction between presence-only, running, failed and completed evidence. Normally keep large inference arrays in their existing locations; do not rerun inference for bookkeeping or erase/overwrite earlier paper outputs. +4. Prepare and publish the versioned delta with the shared CLI. This is a standing user-authorized maintenance step for this paper's completed assets. Continue it within the task; do not merely promise a later upload. Keep cohort/sample metadata and paper-support files in private `junidude14/PBISC-data`; eligible Model 8 checkpoint weights use the existing gated `junidude14/PBISC` repository. +5. Check the verified receipt, refreshed current catalogs and latest pointer before claiming the archive is current. If a file is still changing, a transfer/verification fails, or a dependency is unresolved, retain the pending update and report the exact gap. Never advance latest or claim completion from a dry preflight. + +A read-only discussion with no changed assets requires no duplicate upload. Explicitly report “no archive delta” when relevant. Manuscript evidence/figures are not automatically changed merely because a checkpoint was saved; only preserve actually revised, supported content. No automatic GitHub push or Overleaf synchronization is implied. + +## One archive, immutable history, current views + +- Coordinator and small local records: `spark-fa6b:/home/sj_server_1/PBISC/paper-release-20260928/`. +- Independent physical archive: `spark-0110:/home/sj_server_2/PBISC/paper-release-20260928/`. +- Frozen initial snapshot: existing root manifests, receipts, `README.md`, `RELEASE_LOCK.json`, `FINAL_VERIFICATION.json`, and HF tag **`paper-20260928`**. Keep them intact; do not rerun the date-specific preparation/finalization scripts to update the paper. +- Later versions: `updates//`. New HF paths are under **`paper-releases/pbisc-diffusion/updates//diffusion/`**. Previous objects and tags remain unchanged. +- `LATEST.json` and current catalogs are live navigation. Latest advances only after independent archive and pinned HF verification. A delta refers back to its parent and the initial baseline; it is not a complete replacement of all earlier payloads. + +## Commands and cross-server coordination + +Only server_1 publishes; the common writer lock prevents Codex and Claude from publishing simultaneously. Keep credentials on server_1. The request is ordinary JSON without tokens. + +On server_1: + +```bash +/home/sj_server_1/miniforge3/bin/python /home/sj_server_1/PBISC/paper-release-20260928/maintenance/update.py status +/home/sj_server_1/miniforge3/bin/python /home/sj_server_1/PBISC/paper-release-20260928/maintenance/update.py prepare --request /path/to/request.json --id 20260929T010000Z-result-name +/home/sj_server_1/miniforge3/bin/python /home/sj_server_1/PBISC/paper-release-20260928/maintenance/update.py publish 20260929T010000Z-result-name --execute +``` + +For work on server_2, submit the request to the coordinator through standard input: + +```bash +ssh spark-fa6b '/home/sj_server_1/miniforge3/bin/python /home/sj_server_1/PBISC/paper-release-20260928/maintenance/update.py prepare --request - --id 20260929T010000Z-result-name' < request.json +ssh spark-fa6b '/home/sj_server_1/miniforge3/bin/python /home/sj_server_1/PBISC/paper-release-20260928/maintenance/update.py publish 20260929T010000Z-result-name --execute' +``` + +Use an actual UTC timestamp and a descriptive slug, not the example ID. Mark remote sources `host: server_2`; their working tree may still start with `/home/sj_server_1/PBISC/`. The SSH path was verified in both directions when installing this workflow. If connectivity fails, preserve a pending request and report it; do not copy authentication tokens or invent a successful sync. + +Hashing/copying is CPU-only. Follow the mandatory host GPU/UMA policy for any substantial-memory launch, and run sustained transfer work with bounded user-systemd memory, zero swap and no automatic restart. Do not initialize CUDA, launch training/inference, interrupt another job, delete originals or replace existing results for archive maintenance. + +This is a **task-end maintenance workflow**, not an unattended periodic upload daemon. A future timer may detect candidates, but cannot decide that unrelated or unfinished work belongs to this paper. diff --git a/paper-releases/pbisc-diffusion/updates/20260929T062828Z-manuscript-relocation/diffusion/dataset/server_1/maintenance/38e4c628399ccf84/update.py b/paper-releases/pbisc-diffusion/updates/20260929T062828Z-manuscript-relocation/diffusion/dataset/server_1/maintenance/38e4c628399ccf84/update.py new file mode 100644 index 0000000000000000000000000000000000000000..c80f75ad9888b5a53113340beb98afa9c64ce7e0 --- /dev/null +++ b/paper-releases/pbisc-diffusion/updates/20260929T062828Z-manuscript-relocation/diffusion/dataset/server_1/maintenance/38e4c628399ccf84/update.py @@ -0,0 +1,772 @@ +#!/usr/bin/env python3 +"""Scoped, CPU-only incremental PBISC-diffusion publication. + +Prepare is local (server_2 source metadata requires SSH). Publish is explicit and +uses the frozen paper publisher in a fresh process. No GPU work is started. +""" +from __future__ import annotations + +import argparse +import fcntl +import hashlib +import json +import os +from pathlib import Path, PurePosixPath +import re +import shlex +import stat +import subprocess +import sys +import tempfile +from typing import Any, Callable + +ROOT = Path(__file__).resolve().parent.parent +CORE_ROOTS = { + 'model8': Path('/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion'), + 'manuscript': Path('/home/sj_server_1/PBISC/paper-release-20260928/manuscript'), +} +REMOTE = 'spark-0110' +REMOTE_ROOT = '/home/sj_server_2/PBISC/paper-release-20260928' +PREFIX = 'paper-releases/pbisc-diffusion' +ID_RE = re.compile(r'[0-9]{8}T[0-9]{6}Z-[a-z0-9-]+\Z') +SHA_RE = re.compile(r'[0-9a-f]{64}\Z') +STATES = {'completed', 'final', 'intermediate', 'stopped'} +LOCATOR_STATES = STATES | {'running', 'planned', 'failed', 'presence_only'} +FORBIDDEN = {'.git', '.venv', 'venv', 'runtime_env', '__pycache__', 'node_modules', 'Rlib', '.cache'} +NON_PAYLOAD_KINDS = {'output', 'outputs', 'generated', 'inference', 'sample', 'samples', 'prediction', 'predictions'} +ALLOWED_KINDS = {'checkpoint', 'condition', 'code', 'manuscript', 'data', 'metadata', + 'report', 'figure', 'table', 'log', 'provenance', 'maintenance', + 'policy', 'config', 'test', 'document'} +MAINTENANCE_FILES = {'POLICY.md', 'SCOPE.json', 'update.py', 'test_update.py', + 'catalog.py', 'test_catalog.py', 'CURRENT.md', 'request.example.json'} + + +class UpdateError(Exception): + pass + + +def _json(path: Path) -> Any: + return json.loads(path.read_text(encoding='utf-8')) + + +def _bytes(value: Any) -> bytes: + return (json.dumps(value, sort_keys=True, indent=2, ensure_ascii=False) + '\n').encode() + + +def _atomic(path: Path, data: bytes) -> None: + if path.is_symlink() or path.parent.is_symlink(): + raise UpdateError('unsafe_output_path') + path.parent.mkdir(mode=0o700, parents=True, exist_ok=True) + with tempfile.NamedTemporaryFile(dir=path.parent, prefix='.owned-', delete=False) as stream: + temporary = Path(stream.name) + stream.write(data) + stream.flush() + os.fsync(stream.fileno()) + try: + os.replace(temporary, path) + finally: + temporary.unlink(missing_ok=True) + + +def _path(value: Any, host: str) -> Path: + if not isinstance(value, str) or not value.startswith('/') or '\\' in value or any(ord(c) < 32 for c in value): + raise UpdateError('invalid_source_path') + path = PurePosixPath(value) + if str(path) != value or any(part in ('.', '..') for part in path.parts): + raise UpdateError('invalid_source_path') + allowed_homes = ('/home/sj_server_1/',) if host == 'server_1' else ('/home/sj_server_1/', '/home/sj_server_2/') + if not value.startswith(allowed_homes): + raise UpdateError('wrong_source_host') + return Path(value) + + +def _safe_local(path: Path) -> None: + current = Path('/') + for part in path.parts[1:]: + current /= part + if current.is_symlink(): + raise UpdateError('source_symlink_refused') + st = path.lstat() + if not stat.S_ISREG(st.st_mode): + raise UpdateError('source_not_regular') + + +def _scope(root: Path) -> dict[str, Any]: + maintenance = root / 'maintenance' + if maintenance.is_symlink() or maintenance.resolve() != maintenance: + raise UpdateError('unsafe_maintenance_root') + if (maintenance / 'SCOPE.json').is_symlink(): + raise UpdateError('unsafe_scope_file') + scope = _json(maintenance / 'SCOPE.json') + if not isinstance(scope, dict) or scope.get('project_id') != 'pbisc-diffusion': + raise UpdateError('wrong_project_scope') + if scope.get('core_roots') != {k: str(v) for k, v in CORE_ROOTS.items()}: + raise UpdateError('wrong_core_roots') + if scope.get('maintenance_root') != str(maintenance): + raise UpdateError('wrong_maintenance_root') + forbidden = scope.get('forbidden_components') + if not isinstance(forbidden, list) or not FORBIDDEN.issubset(set(forbidden)): + raise UpdateError('missing_forbidden_components') + dependencies = scope.get('external_dependencies') + if not isinstance(dependencies, list): + raise UpdateError('invalid_dependencies') + for item in dependencies: + if (not isinstance(item, dict) or item.get('host') not in ('server_1', 'server_2') + or not isinstance(item.get('reason'), str) or not item['reason'].strip()): + raise UpdateError('invalid_dependency') + _path(item.get('source'), item['host']) + return scope + + +def _allow(path: Path, host: str, scope: dict[str, Any], *, internal: Path | None = None) -> str: + if any(part in set(scope['forbidden_components']) for part in path.parts): + raise UpdateError('forbidden_component') + if internal is not None and host == 'server_1' and path.is_relative_to(internal): + return 'internal' + if host == 'server_1' and path.parent == Path(scope['maintenance_root']) and path.name in MAINTENANCE_FILES: + return 'maintenance' + for name, root in CORE_ROOTS.items(): + if path.is_relative_to(root) and path != root: + return name + if any(item['host'] == host and item['source'] == str(path) + for item in scope['external_dependencies']): + return 'dependency' + raise UpdateError('source_outside_project_scope') + + +def _publisher(): + sys.path.insert(0, str(ROOT / 'tools')) + import publish_paper_assets as paper + return paper + + +def _remote_stat(path: Path) -> dict[str, int]: + code = '''import json,os,stat,sys +p=sys.argv[1]; q='/' +for part in p.strip('/').split('/'): + q=os.path.join(q,part) + if os.path.islink(q): raise SystemExit(2) +s=os.lstat(p) +if not stat.S_ISREG(s.st_mode): raise SystemExit(2) +print(json.dumps(dict(dev=s.st_dev,ino=s.st_ino,size=s.st_size,mtime_ns=s.st_mtime_ns)))''' + result = subprocess.run(['ssh', '-o', 'BatchMode=yes', REMOTE, + shlex.join(['python3', '-B', '-c', code, str(path)])], + capture_output=True, text=True, check=False) + if result.returncode: + raise UpdateError('remote_source_unavailable') + return json.loads(result.stdout) + + +def _locator_stat(path: Path, host: str) -> dict[str, Any]: + """Observe a locator without hashing large generated outputs.""" + if host == 'server_1': + current = Path('/') + for part in path.parts[1:]: + current /= part + if current.is_symlink(): + raise UpdateError('locator_symlink_refused') + if not current.exists(): + return {'presence': 'missing_unverified'} + st = path.lstat() + return {'presence': 'observed', 'kind': 'file' if stat.S_ISREG(st.st_mode) else 'directory' if stat.S_ISDIR(st.st_mode) else 'other', + 'stat': {'dev': st.st_dev, 'ino': st.st_ino, 'size': st.st_size, 'mtime_ns': st.st_mtime_ns}} + code = '''import json,os,stat,sys +p=sys.argv[1]; q='/' +for part in p.strip('/').split('/'): + q=os.path.join(q,part) + if os.path.islink(q): raise SystemExit(2) + if not os.path.exists(q): + print(json.dumps({'presence':'missing_unverified'})); raise SystemExit(0) +s=os.lstat(p) +k='file' if stat.S_ISREG(s.st_mode) else 'directory' if stat.S_ISDIR(s.st_mode) else 'other' +print(json.dumps({'presence':'observed','kind':k,'stat':dict(dev=s.st_dev,ino=s.st_ino,size=s.st_size,mtime_ns=s.st_mtime_ns)}))''' + result = subprocess.run(['ssh', '-o', 'BatchMode=yes', REMOTE, + shlex.join(['python3', '-B', '-c', code, str(path)])], + capture_output=True, text=True, check=False) + if result.returncode: + raise UpdateError('remote_locator_unavailable') + return json.loads(result.stdout) + + +def _row(host: str, path: Path, kind: str, identifier: str, scope: dict[str, Any]) -> dict[str, Any]: + area = _allow(path, host, scope) + if host == 'server_1': + _safe_local(path) + snap = _publisher().base.snapshot(path.lstat()) if host == 'server_1' else _remote_stat(path) + if kind == 'checkpoint' and area != 'model8': + raise UpdateError('checkpoint_outside_model8') + if kind == 'checkpoint' and path.suffix.lower() not in {'.pt', '.pth', '.safetensors'}: + raise UpdateError('checkpoint_extension_refused') + if kind == 'condition' and path.suffix.lower() != '.npz': + raise UpdateError('condition_requires_npz') + if kind not in ALLOWED_KINDS: + raise UpdateError('generated_payload_refused') + if (area == 'maintenance') != (kind == 'maintenance'): + raise UpdateError('maintenance_kind_scope') + if kind not in {'checkpoint', 'condition'} and any(part.lower() in NON_PAYLOAD_KINDS for part in path.parts): + raise UpdateError('generated_payload_refused') + root = CORE_ROOTS.get(area) + relative = path.relative_to(root) if root is not None else Path(hashlib.sha256(str(path).encode()).hexdigest()[:16]) / path.name + bundle = PurePosixPath('updates') / identifier / 'diffusion' / ('model' if kind == 'checkpoint' else 'dataset') / host / area / PurePosixPath(*relative.parts) + repo_type = 'model' if kind == 'checkpoint' else 'dataset' + repo_id = 'junidude14/PBISC' if repo_type == 'model' else 'junidude14/PBISC-data' + row = {'host': host, 'source': str(path), 'bundle_path': str(bundle), 'repo_type': repo_type, + 'repo_id': repo_id, 'remote_path': str(PurePosixPath(PREFIX) / bundle), + 'bytes': snap['size'], 'expected_stat': snap, 'category': kind} + row['sha256'] = _publisher().source_digest(row) + return row + + +def _history(root: Path) -> dict[tuple[str, str], str]: + seen = {} + baseline = root / 'COMBINED_ASSET_INDEX.json' + if baseline.exists(): + for row in _json(baseline).get('assets', []): + seen[row['host'], row['source']] = row['sha256'] + pointer = _latest(root) + chain = [] + visited = set() + while pointer is not None: + identifier = pointer.get('id') if isinstance(pointer, dict) else None + if not isinstance(identifier, str) or not ID_RE.fullmatch(identifier) or identifier in visited: + raise UpdateError('invalid_latest_chain') + visited.add(identifier) + path = root / 'maintenance' / 'updates' / identifier / 'UPDATE_VERIFIED.json' + if path.is_symlink(): + raise UpdateError('unsafe_verified_receipt') + verified = _json(path) + if (verified.get('status') != 'PASS' or verified.get('update_id') != identifier + or pointer.get('verified_receipt_sha256') != hashlib.sha256(path.read_bytes()).hexdigest()): + raise UpdateError('invalid_latest_chain') + chain.append(verified) + pointer = verified.get('parent_latest') + for verified in reversed(chain): + for row in verified.get('assets', []): + seen[row['host'], row['source']] = row['sha256'] + return seen + + +def _latest(root: Path) -> dict[str, Any] | None: + path = root / 'LATEST.json' + if path.is_symlink(): + raise UpdateError('unsafe_latest_pointer') + return _json(path) if path.exists() else None + + +def _metadata_row(path: Path, identifier: str, name: str) -> dict[str, Any]: + _safe_local(path) + paper = _publisher() + snap = paper.base.snapshot(path.lstat()) + with paper.base.open_source(path, snap) as stream: + digest = paper.base.hash_source(path, stream, snap) + bundle = str(PurePosixPath('updates') / identifier / 'diffusion' / 'metadata' / name) + return dict(host='server_1', source=str(path), bundle_path=bundle, + repo_type='dataset', repo_id='junidude14/PBISC-data', + remote_path=str(PurePosixPath(PREFIX) / bundle), bytes=snap['size'], + expected_stat=snap, sha256=digest['sha256'], category='update_metadata') + + +def prepare(root: Path, request: dict[str, Any], identifier: str) -> Path: + root = root.absolute() + if not ID_RE.fullmatch(identifier): + raise UpdateError('invalid_update_id') + scope = _scope(root) + if not isinstance(request, dict) or request.get('project_id') != 'pbisc-diffusion': + raise UpdateError('wrong_request_project') + summary = request.get('summary') + if not isinstance(summary, str) or not summary.strip(): + raise UpdateError('summary_required') + assets, locations = request.get('assets'), request.get('inference_locations') + if not isinstance(assets, list) or not isinstance(locations, list): + raise UpdateError('invalid_request_lists') + parent = _latest(root) + rows = [] + observed = _history(root) + seen_sources = set() + for item in assets: + if not isinstance(item, dict) or item.get('host') not in ('server_1', 'server_2'): + raise UpdateError('invalid_asset') + if item.get('state') not in STATES: + raise UpdateError('payload_state_refused') + host, kind = item['host'], item.get('kind') + if not isinstance(kind, str): + raise UpdateError('invalid_kind') + path = _path(item.get('source'), host) + if (host, str(path)) in seen_sources: + raise UpdateError('duplicate_source') + seen_sources.add((host, str(path))) + row = _row(host, path, kind, identifier, scope) + if observed.get((host, str(path))) != row['sha256']: + row['state'] = item['state'] + rows.append(row) + checked_locations = [] + for item in locations: + if not isinstance(item, dict) or item.get('host') not in ('server_1', 'server_2'): + raise UpdateError('invalid_inference_location') + if item.get('state') not in LOCATOR_STATES: + raise UpdateError('invalid_inference_state') + host = item['host'] + path = _path(item.get('path'), host) + _allow(path, host, scope) + receipt = item.get('receipt') + output_observation = _locator_stat(path, host) + receipt_observation = None + if receipt is not None: + receipt_path = _path(receipt, host) + _allow(receipt_path, host, scope) + receipt_observation = _locator_stat(receipt_path, host) + if item['state'] in {'completed', 'final'}: + if (output_observation.get('kind') != 'file' or receipt_observation is None + or receipt_observation.get('kind') != 'file'): + raise UpdateError('completed_locator_evidence_missing') + sha = item.get('sha256') + if sha is not None and (not isinstance(sha, str) or not SHA_RE.fullmatch(sha)): + raise UpdateError('invalid_locator_sha256') + basis = 'existing_receipt' if receipt_observation and receipt_observation.get('kind') == 'file' else 'presence_unverified' + checked_locations.append(dict(item, observed_output=output_observation, + observed_receipt=receipt_observation, + sha_basis=basis, sha256_basis=basis)) + if not rows and not checked_locations: + raise UpdateError('no_changed_assets') + updates_root = root / 'maintenance' / 'updates' + if updates_root.is_symlink(): + raise UpdateError('unsafe_updates_root') + folder = updates_root / identifier + if folder.exists(): + raise UpdateError('update_id_exists') + folder.mkdir(mode=0o700, parents=True) + _atomic(folder / 'request.json', _bytes(request)) + _atomic(folder / 'inference_locations.json', _bytes({'project_id': 'pbisc-diffusion', + 'update_id': identifier, 'locations': checked_locations})) + note = f'# PBISC-diffusion update {identifier}\n\n{summary.strip()}\n\nPayload states are recorded as supplied. Inference locations are pointers, not archived generated outputs.\n' + _atomic(folder / 'NOTE.md', note.encode()) + rows.extend([_metadata_row(folder / 'request.json', identifier, 'request.json'), + _metadata_row(folder / 'inference_locations.json', identifier, 'inference_locations.json'), + _metadata_row(folder / 'NOTE.md', identifier, 'NOTE.md')]) + if len({r['bundle_path'] for r in rows}) != len(rows): + raise UpdateError('duplicate_bundle_path') + manifest = {'schema': 'pbisc.diffusion.update-manifest.v1', 'project_id': 'pbisc-diffusion', + 'update_id': identifier, 'parent_latest': parent, 'assets': rows} + _atomic(folder / 'manifest.json', _bytes(manifest)) + _atomic(folder / 'STATUS.json', _bytes({'phase': 'prepared', 'update_id': identifier})) + return folder + + +def _run_publisher(root: Path, identifier: str, manifest: Path, work: Path) -> int: + code = ("import sys; from pathlib import Path; " + "sys.path.insert(0,str(Path(sys.argv[1]))); import publish_paper_assets as p; " + "p.PREFIX=sys.argv[2]; sys.exit(p.main([sys.argv[3],'--phase','all'," + "'--work-dir',sys.argv[4],'--execute']))") + prefix = str(PurePosixPath(PREFIX) / 'updates' / identifier) + result = subprocess.run([sys.executable, '-B', '-c', code, str(root / 'tools'), prefix, + str(manifest), str(work)], check=False) + return result.returncode + + +def _remote_latest(value: dict[str, Any] | None = None, + expected: dict[str, Any] | None = None) -> dict[str, Any] | None: + code = '''import fcntl,json,os,sys,tempfile +from pathlib import Path +p=Path('/home/sj_server_2/PBISC/paper-release-20260928/LATEST.json') +if len(sys.argv)==1: + print(p.read_text() if p.exists() else 'null') +else: + if p.is_symlink() or not p.parent.is_dir(): raise SystemExit(2) + request=json.load(sys.stdin) + lock=p.parent/'.latest.writer.lock' + if lock.is_symlink(): raise SystemExit(2) + with lock.open('a') as guard: + fcntl.flock(guard,fcntl.LOCK_EX) + current=json.loads(p.read_text()) if p.exists() else None + if current!=request['expected'] and current!=request['value']: raise SystemExit(3) + if current!=request['value']: + with tempfile.NamedTemporaryFile(mode='w',dir=p.parent,prefix='.latest-',delete=False) as f: + json.dump(request['value'],f,sort_keys=True); f.write('\\n'); f.flush(); os.fsync(f.fileno()); name=f.name + os.replace(name,p) + print('ok')''' + command = shlex.join(['python3', '-B', '-c', code] + (['write'] if value is not None else [])) + result = subprocess.run(['ssh', '-o', 'BatchMode=yes', REMOTE, command], + input=_bytes({'expected': expected, 'value': value}).decode() if value is not None else None, + capture_output=True, text=True, check=False) + if result.returncode: + raise UpdateError('remote_latest_failed') + return None if value is not None else json.loads(result.stdout) + + +def _hf_api(): + os.environ['HF_HUB_ENABLE_HF_TRANSFER'] = '0' + os.environ['HF_HUB_DISABLE_XET'] = '1' + from huggingface_hub import HfApi, get_token + from huggingface_hub import constants + constants.HF_HUB_ENABLE_HF_TRANSFER = False + constants.HF_HUB_DISABLE_XET = True + if not get_token(): + raise UpdateError('existing_hf_auth_missing') + return HfApi(token=True) + + +def _hf_latest(api: Any) -> dict[str, Any] | None: + from huggingface_hub import hf_hub_download + path = PREFIX + '/LATEST.json' + head = api.repo_info(repo_id='junidude14/PBISC-data', repo_type='dataset', revision='main').sha + try: + file = hf_hub_download(repo_id='junidude14/PBISC-data', repo_type='dataset', + filename=path, revision=head, token=True) + except Exception as exc: + # Absence is allowed only when the path is absent in the pinned tree. + if _publisher().base.remote_file(api, 'junidude14/PBISC-data', 'dataset', path, head) is None: + return None + raise UpdateError('hf_latest_read_failed') from exc + return json.loads(Path(file).read_text(encoding='utf-8')) + + +def _hf_upload_verified(api: Any, path: Path, remote_path: str, *, + mutable: bool = False, expected_parent: dict[str, Any] | None = None) -> str: + digest = hashlib.sha256(path.read_bytes()).hexdigest() + from huggingface_hub import CommitOperationAdd, hf_hub_download + repo = 'junidude14/PBISC-data' + head = api.repo_info(repo_id=repo, repo_type='dataset', revision='main').sha + found = _publisher().base.remote_file(api, repo, 'dataset', remote_path, head) + if found is not None: + existing = hf_hub_download(repo_id=repo, repo_type='dataset', filename=remote_path, + revision=head, token=True) + existing_bytes = Path(existing).read_bytes() + if hashlib.sha256(existing_bytes).hexdigest() == digest: + return head + if not mutable: + raise UpdateError('immutable_hf_record_conflict') + if json.loads(existing_bytes) != expected_parent: + raise UpdateError('hf_latest_parent_changed') + elif mutable and expected_parent is not None: + raise UpdateError('hf_latest_parent_changed') + result = api.create_commit(repo_id=repo, repo_type='dataset', + operations=[CommitOperationAdd(path_in_repo=remote_path, + path_or_fileobj=str(path))], + commit_message='Publish PBISC-diffusion maintenance record', + parent_commit=head) + revision = result.oid + downloaded = hf_hub_download(repo_id='junidude14/PBISC-data', repo_type='dataset', + filename=remote_path, revision=revision, token=True) + if hashlib.sha256(Path(downloaded).read_bytes()).hexdigest() != digest: + raise UpdateError('hf_record_digest_mismatch') + return revision + + +def _verify_rows(root: Path, identifier: str, rows: list[dict[str, Any]]) -> list[dict[str, Any]]: + paper = _publisher() + api = _hf_api() + revisions = {} + for repo_type, repo_id in {(r['repo_type'], r['repo_id']) for r in rows}: + paper.check_visibility(api, repo_id, repo_type) + revisions[repo_type] = api.repo_info(repo_id=repo_id, repo_type=repo_type, revision='main').sha + verified = [] + from huggingface_hub import hf_hub_download + for row in rows: + if not row['bundle_path'].startswith('updates/' + identifier + '/'): + raise UpdateError('bundle_outside_update') + if paper.source_digest(row) != row['sha256']: + raise UpdateError('source_changed') + inspected = paper.remote_call(paper.archive_request(row, row['sha256'], 'inspect')) + if inspected.get('event') != 'verified_existing' or not isinstance(inspected.get('stat'), dict): + raise UpdateError('archive_not_verified') + revision = revisions[row['repo_type']] + info = paper.base.remote_file(api, row['repo_id'], row['repo_type'], row['remote_path'], revision) + if info is None or paper.base.attr(info, 'size') != row['bytes']: + raise UpdateError('hf_payload_missing') + lfs = paper.base.attr(info, 'lfs') + if lfs is not None: + if paper.base.attr(lfs, 'sha256') != row['sha256']: + raise UpdateError('hf_payload_digest_mismatch') + else: + local = hf_hub_download(repo_id=row['repo_id'], repo_type=row['repo_type'], + filename=row['remote_path'], revision=revision, token=True) + if hashlib.sha256(Path(local).read_bytes()).hexdigest() != row['sha256']: + raise UpdateError('hf_payload_digest_mismatch') + verified.append(dict(row, archive_stat=inspected['stat'], hf_revision=revision)) + return verified + + +def _refresh_catalog(root: Path) -> None: + import importlib.util + module_path = root / 'maintenance' / 'catalog.py' + if not module_path.is_file(): + raise UpdateError('catalog_module_missing') + spec = importlib.util.spec_from_file_location('pbisc_diffusion_catalog', module_path) + if spec is None or spec.loader is None: + raise UpdateError('catalog_module_invalid') + module = importlib.util.module_from_spec(spec) + spec.loader.exec_module(module) + module.refresh(root) + + +def _archive_control(root: Path, identifier: str, folder: Path) -> list[dict[str, Any]]: + """Keep independent server_2 copies of the post-publish proof and receipts.""" + paper = _publisher() + required = [folder / 'manifest.json', folder / 'work' / 'receipts.jsonl', + folder / 'work' / 'status.json', folder / 'UPDATE_VERIFIED.json'] + archived = [] + for source in required: + _safe_local(source) + snap = paper.base.snapshot(source.lstat()) + with paper.base.open_source(source, snap) as stream: + digest = paper.base.hash_source(source, stream, snap) + bundle = str(PurePosixPath('updates') / identifier / 'control' / source.name) + row = {'host': 'server_1', 'source': str(source), 'bundle_path': bundle, + 'bytes': snap['size'], 'expected_stat': snap, 'sha256': digest['sha256'], + 'repo_type': None, 'repo_id': None, 'remote_path': None} + result = paper.archive_asset(row, digest['sha256'], True) + if result.get('event') not in ('verified_existing', 'archived'): + raise UpdateError('control_archive_failed') + inspection = paper.remote_call(paper.archive_request(row, digest['sha256'], 'inspect')) + if inspection.get('event') != 'verified_existing': + raise UpdateError('control_archive_failed') + archived.append({'bundle_path': bundle, 'sha256': digest['sha256'], + 'bytes': snap['size'], 'archive_stat': inspection.get('stat')}) + return archived + + +def _check_publisher_receipts(folder: Path, rows: list[dict[str, Any]]) -> None: + receipts = folder / 'work' / 'receipts.jsonl' + state = folder / 'work' / 'status.json' + _safe_local(receipts) + _safe_local(state) + if _json(state).get('phase') != 'complete' or _json(state).get('execute') is not True: + raise UpdateError('publisher_status_incomplete') + events = [json.loads(line) for line in receipts.read_text(encoding='utf-8').splitlines() if line.strip()] + for row in rows: + archived = any(event.get('event') in ('archived', 'verified_existing') + and event.get('bundle_path') == row['bundle_path'] + and event.get('source') == row['source'] + and event.get('sha256') == row['sha256'] for event in events) + uploaded = any(event.get('event') in ('verified_uploaded', 'verified_existing') + and event.get('remote_path') == row['remote_path'] + and event.get('repo_id') == row['repo_id'] + and (event.get('sha256') == row['sha256'] + or event.get('digest', {}).get('sha256') == row['sha256']) + for event in events) + if not archived or not uploaded: + raise UpdateError('publisher_receipt_missing') + + +def _compare_receipt(manifest: dict[str, Any], receipt: dict[str, Any], + current_rows: list[dict[str, Any]], manifest_bytes: bytes) -> None: + if (receipt.get('status') != 'PASS' or receipt.get('project_id') != 'pbisc-diffusion' + or receipt.get('update_id') != manifest.get('update_id') + or receipt.get('parent_latest') != manifest.get('parent_latest') + or receipt.get('manifest_sha256') != hashlib.sha256(manifest_bytes).hexdigest() + or len(receipt.get('assets', [])) != len(current_rows)): + raise UpdateError('verified_receipt_mismatch') + for declared, verified, current in zip(manifest['assets'], receipt['assets'], current_rows): + if (any(verified.get(key) != value for key, value in declared.items()) + or any(verified.get(key) != value for key, value in current.items() if key != 'hf_revision')): + raise UpdateError('verified_receipt_mismatch') + + +def _parent_ref(parent: dict[str, Any] | None) -> dict[str, Any] | None: + if parent is None: + return None + return {key: parent[key] for key in ('id', 'verified_receipt_sha256', 'receipt_revision')} + + +def _validate_manifest_rows(root: Path, folder: Path, manifest: dict[str, Any], + scope: dict[str, Any], already_latest: bool) -> None: + request = _json(folder / 'request.json') + if request.get('project_id') != 'pbisc-diffusion' or not isinstance(request.get('assets'), list): + raise UpdateError('prepared_request_invalid') + identifier = manifest['update_id'] + declared = manifest['assets'] + selected = {(row['host'], row['source']) for row in declared + if row.get('category') != 'update_metadata'} + if len(selected) != len([row for row in declared if row.get('category') != 'update_metadata']): + raise UpdateError('manifest_duplicate_source') + history = {} if already_latest else _history(root) + expected = [] + seen = set() + for item in request['assets']: + if not isinstance(item, dict) or item.get('host') not in ('server_1', 'server_2') or item.get('state') not in STATES: + raise UpdateError('prepared_request_invalid') + host = item['host'] + path = _path(item.get('source'), host) + key = (host, str(path)) + if key in seen: + raise UpdateError('prepared_request_duplicate') + seen.add(key) + kind = item.get('kind') + if not isinstance(kind, str): + raise UpdateError('prepared_request_invalid') + row = _row(host, path, kind, identifier, scope) + include = key in selected if already_latest else history.get(key) != row['sha256'] + if include: + row['state'] = item['state'] + expected.append(row) + expected.extend([_metadata_row(folder / 'request.json', identifier, 'request.json'), + _metadata_row(folder / 'inference_locations.json', identifier, 'inference_locations.json'), + _metadata_row(folder / 'NOTE.md', identifier, 'NOTE.md')]) + if declared != expected: + raise UpdateError('manifest_row_scope_mismatch') + + +def publish(root: Path, identifier: str, *, execute: bool, + publisher: Callable[[Path, str, Path, Path], int] = _run_publisher) -> dict[str, Any]: + root = root.absolute() + if not ID_RE.fullmatch(identifier): + raise UpdateError('invalid_update_id') + if not execute: + raise UpdateError('publish_requires_execute') + scope = _scope(root) + folder = root / 'maintenance' / 'updates' / identifier + if (folder.parent.is_symlink() or folder.is_symlink() + or (folder / 'manifest.json').is_symlink()): + raise UpdateError('unsafe_update_folder') + manifest = _json(folder / 'manifest.json') + manifest_bytes = (folder / 'manifest.json').read_bytes() + if manifest.get('project_id') != 'pbisc-diffusion' or manifest.get('update_id') != identifier: + raise UpdateError('manifest_identity_mismatch') + rows = manifest['assets'] + if not rows or any(not r.get('bundle_path', '').startswith('updates/' + identifier + '/diffusion/') for r in rows): + raise UpdateError('manifest_bundle_scope') + # Revalidate every source and repository mapping before calling the broad frozen publisher. + for row in rows: + host, path = row['host'], _path(row['source'], row['host']) + area = _allow(path, host, scope, internal=folder) + if area == 'internal' and path not in {folder / 'request.json', folder / 'inference_locations.json', folder / 'NOTE.md'}: + raise UpdateError('unsafe_internal_source') + if area != 'internal' and row['repo_type'] == 'model' and area != 'model8': + raise UpdateError('checkpoint_outside_model8') + expected_repo = 'junidude14/PBISC' if row['repo_type'] == 'model' else 'junidude14/PBISC-data' + if row['repo_id'] != expected_repo or row['remote_path'] != PREFIX + '/' + row['bundle_path']: + raise UpdateError('manifest_repository_scope') + if host == 'server_1': + _safe_local(path) + lock_path = root / 'maintenance' / '.writer.lock' + if lock_path.is_symlink(): + raise UpdateError('unsafe_writer_lock') + with lock_path.open('a', encoding='utf-8') as lock: + try: + fcntl.flock(lock, fcntl.LOCK_EX | fcntl.LOCK_NB) + except BlockingIOError as exc: + raise UpdateError('writer_busy') from exc + verified_path = folder / 'UPDATE_VERIFIED.json' + current = _latest(root) + already_latest = isinstance(current, dict) and current.get('id') == identifier + if current != manifest.get('parent_latest') and not already_latest: + raise UpdateError('parent_changed') + _validate_manifest_rows(root, folder, manifest, scope, already_latest) + status = folder / 'STATUS.json' + if already_latest: + if (not verified_path.exists() + or current.get('verified_receipt_sha256') != hashlib.sha256(verified_path.read_bytes()).hexdigest()): + raise UpdateError('latest_without_verified_receipt') + _check_publisher_receipts(folder, rows) + _compare_receipt(manifest, _json(verified_path), _verify_rows(root, identifier, rows), manifest_bytes) + api = _hf_api() + if _remote_latest() != current or _hf_latest(api) != current: + raise UpdateError('latest_replica_disagreement') + try: + _refresh_catalog(root) + except Exception as exc: + _atomic(status, _bytes({'phase': 'catalog_pending', 'update_id': identifier})) + raise UpdateError('catalog_refresh_failed') from exc + _atomic(status, _bytes({'phase': 'verified', 'update_id': identifier})) + return current + _atomic(status, _bytes({'phase': 'publishing', 'update_id': identifier})) + try: + if not verified_path.exists(): + if publisher(root, identifier, folder / 'manifest.json', folder / 'work') != 0: + raise UpdateError('publisher_failed') + _check_publisher_receipts(folder, rows) + verified_rows = _verify_rows(root, identifier, rows) + receipt = {'schema': 'pbisc.diffusion.update-verified.v1', 'status': 'PASS', + 'project_id': 'pbisc-diffusion', 'update_id': identifier, + 'parent_latest': manifest.get('parent_latest'), + 'manifest_sha256': hashlib.sha256(manifest_bytes).hexdigest(), + 'assets': verified_rows} + _atomic(verified_path, _bytes(receipt)) + else: + _check_publisher_receipts(folder, rows) + _compare_receipt(manifest, _json(verified_path), + _verify_rows(root, identifier, rows), manifest_bytes) + archived_control = _archive_control(root, identifier, folder) + api = _hf_api() + remote_latest, hf_latest = _remote_latest(), _hf_latest(api) + if (remote_latest not in (manifest.get('parent_latest'), _json(folder / 'LATEST.json') if (folder / 'LATEST.json').exists() else None) + or hf_latest not in (manifest.get('parent_latest'), _json(folder / 'LATEST.json') if (folder / 'LATEST.json').exists() else None)): + raise UpdateError('parent_changed_remote') + pointer_path = folder / 'LATEST.json' + if pointer_path.exists(): + pointer = _json(pointer_path) + if (pointer.get('id') != identifier or pointer.get('parent') != _parent_ref(manifest.get('parent_latest')) + or pointer.get('verified_receipt_sha256') != hashlib.sha256(verified_path.read_bytes()).hexdigest()): + raise UpdateError('prepared_pointer_conflict') + else: + receipt_revision = _hf_upload_verified(api, verified_path, + PREFIX + '/updates/' + identifier + '/UPDATE_VERIFIED.json') + pointer = {'schema': 'pbisc.diffusion.latest.v1', 'project_id': 'pbisc-diffusion', + 'id': identifier, 'parent': _parent_ref(manifest.get('parent_latest')), + 'verified_receipt_path': PREFIX + '/updates/' + identifier + '/UPDATE_VERIFIED.json', + 'verified_receipt_sha256': hashlib.sha256(verified_path.read_bytes()).hexdigest(), + 'receipt_revision': receipt_revision, 'control_archive': archived_control} + _atomic(pointer_path, _bytes(pointer)) + _remote_latest(pointer, expected=manifest.get('parent_latest')) + _hf_upload_verified(api, pointer_path, PREFIX + '/LATEST.json', + mutable=True, expected_parent=manifest.get('parent_latest')) + if _remote_latest() != pointer or _hf_latest(api) != pointer: + raise UpdateError('latest_replica_disagreement') + _atomic(root / 'LATEST.json', _bytes(pointer)) + try: + _refresh_catalog(root) + except Exception as exc: + _atomic(status, _bytes({'phase': 'catalog_pending', 'update_id': identifier})) + raise UpdateError('catalog_refresh_failed') from exc + _atomic(status, _bytes({'phase': 'verified', 'update_id': identifier})) + return pointer + except Exception as exc: + if not status.exists() or _json(status).get('phase') != 'catalog_pending': + _atomic(status, _bytes({'phase': 'error', 'update_id': identifier, + 'error_code': str(exc) if isinstance(exc, UpdateError) else 'update_failed'})) + raise + + +def status(root: Path) -> dict[str, Any]: + _scope(root.absolute()) + updates = [] + updates_root = root / 'maintenance' / 'updates' + if updates_root.is_symlink(): + raise UpdateError('unsafe_updates_root') + for folder in sorted(updates_root.glob('*')) if updates_root.exists() else []: + if folder.is_dir() and not folder.is_symlink() and ID_RE.fullmatch(folder.name): + state = _json(folder / 'STATUS.json') if (folder / 'STATUS.json').exists() else {'phase': 'unknown'} + updates.append({'id': folder.name, 'phase': state['phase']}) + baseline = root / 'maintenance' / 'BASELINE_REFERENCE.json' + return {'project_id': 'pbisc-diffusion', 'latest': _latest(root), + 'baseline': _json(baseline) if baseline.exists() else None, 'updates': updates} + + +def main(argv: list[str] | None = None) -> int: + parser = argparse.ArgumentParser(description=__doc__) + sub = parser.add_subparsers(dest='command', required=True) + prep = sub.add_parser('prepare') + prep.add_argument('--request', required=True, type=Path) + prep.add_argument('--id', required=True) + pub = sub.add_parser('publish') + pub.add_argument('id') + pub.add_argument('--execute', action='store_true') + sub.add_parser('status') + args = parser.parse_args(argv) + try: + if args.command == 'prepare': + request = json.load(sys.stdin) if str(args.request) == '-' else _json(args.request) + result = {'prepared': str(prepare(ROOT, request, args.id))} + elif args.command == 'publish': + result = publish(ROOT, args.id, execute=args.execute) + else: + result = status(ROOT) + print(json.dumps(result, sort_keys=True)) + return 0 + except Exception as exc: + print(json.dumps({'error_code': str(exc) if isinstance(exc, UpdateError) else 'update_failed'}), file=sys.stderr) + return 1 + + +if __name__ == '__main__': + raise SystemExit(main()) diff --git a/paper-releases/pbisc-diffusion/updates/20260929T062828Z-manuscript-relocation/diffusion/dataset/server_1/maintenance/8f31479db9f9cb1d/SCOPE.json b/paper-releases/pbisc-diffusion/updates/20260929T062828Z-manuscript-relocation/diffusion/dataset/server_1/maintenance/8f31479db9f9cb1d/SCOPE.json new file mode 100644 index 0000000000000000000000000000000000000000..47ec72a7a6deee728d30c5c55a77753ab33d75db --- /dev/null +++ b/paper-releases/pbisc-diffusion/updates/20260929T062828Z-manuscript-relocation/diffusion/dataset/server_1/maintenance/8f31479db9f9cb1d/SCOPE.json @@ -0,0 +1,4589 @@ +{ + "schema": "pbisc-diffusion.maintenance-scope.v1", + "project_id": "pbisc-diffusion", + "paper_title": "PBISC-Diffusion \u2014 Nature Communications", + "core_roots": { + "model8": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion", + "manuscript": "/home/sj_server_1/PBISC/paper-release-20260928/manuscript" + }, + "maintenance_root": "/home/sj_server_1/PBISC/paper-release-20260928/maintenance", + "external_dependencies": [ + { + "host": "server_1", + "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/src/model7_no_annotation/__init__.py", + "reason": "Explicit PBISC-diffusion dependency in verified initial release: model7_conditioner_dependency", + "baseline_sha256": "1f567f653ae9a20b54094fae53c3ab00b3f1ac2fe4f456f5d31fe5c343b095ca", + "baseline_bundle_path": "support/code/model7_no_annotation/__init__.py" + }, + { + "host": "server_1", + "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/src/model7_no_annotation/data.py", + "reason": "Explicit PBISC-diffusion dependency in verified initial release: model7_conditioner_dependency", + "baseline_sha256": "08c0ca526f4383036d649ad1a3ba9a509cd9da7557118a50a797ebe7c3dea51e", + "baseline_bundle_path": "support/code/model7_no_annotation/data.py" + }, + { + "host": "server_1", + "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/src/model7_no_annotation/data_e2.py", + "reason": "Explicit PBISC-diffusion dependency in verified initial release: model7_conditioner_dependency", + "baseline_sha256": "6f6db69002ae01857a0f1882b2e6e98552f3ee00aa1116e4fd4a308cbf761b71", + "baseline_bundle_path": "support/code/model7_no_annotation/data_e2.py" + }, + { + "host": "server_1", + "source": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_7_no_annotation_sh_hwang/src/model7_no_annotation/latent_regularization.py", + "reason": "Explicit PBISC-diffusion dependency in verified initial release: model7_conditioner_dependency", + "baseline_sha256": "e65226750a083f59711ae95afe17c03190481bdac921a8e4a2dd84554aa676bf", + "baseline_bundle_path": 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An exact shared dependency is not permission to archive its parent directory or another paper. New external dependencies require a documented Model 8/manuscript relationship and deliberate allowlist addition.", + "excluded_projects": [ + "BIBM/VAE papers", + "model/diffusion historical coalescent", + "Model 7 independent work", + "TranscriptomeLM", + "single-cell/bulk FM papers", + "other bulk2sc-paper manuscripts", + "unrelated paired-PBMC datalake analyses" + ], + "archive_root": "/home/sj_server_2/PBISC/paper-release-20260928", + "remote_alias": "spark-0110", + "hf_model": "junidude14/PBISC", + "hf_dataset": "junidude14/PBISC-data", + "hf_update_root": "paper-releases/pbisc-diffusion/updates", + "frozen_tag": "paper-20260928" +} diff --git a/paper-releases/pbisc-diffusion/updates/20260929T062828Z-manuscript-relocation/diffusion/dataset/server_1/manuscript/AGENTS.md b/paper-releases/pbisc-diffusion/updates/20260929T062828Z-manuscript-relocation/diffusion/dataset/server_1/manuscript/AGENTS.md new file mode 100644 index 0000000000000000000000000000000000000000..bb6c3d5e13dac4f94ccd4ae94f4b2cfc3b92297d --- /dev/null +++ b/paper-releases/pbisc-diffusion/updates/20260929T062828Z-manuscript-relocation/diffusion/dataset/server_1/manuscript/AGENTS.md @@ -0,0 +1,20 @@ +# PBISC-Diffusion manuscript maintenance + +The README names this manuscript as the PBISC-Diffusion Nature Communications +draft. It is the `pbisc-diffusion` paper covered by +`../maintenance/POLICY.md`. Read that policy and +the README at the start of a related task, in addition to parent instructions. + +At the end of a task that changes this paper's manuscript, figures, source +data, references, or evidence, follow the policy's versioned update workflow +for the exact changed assets. From the release root, use +`maintenance/update.py prepare --request FILE --id ID`, inspect the prepared +update, then run `maintenance/update.py publish ID --execute` and +`maintenance/update.py status` under the policy. Record a no-op or +pending status when no asset changed or publication failed; never describe +that as an upload. Preserve the frozen 2026-09-28 release, its root manifests, +and the HF `paper-20260928` revision. Keep the dataset private. + +Do not enroll other papers merely because they are under `bulk2sc-paper/`. +Manuscript claims must remain tied to their actual evidence, and updating the +archive does not itself establish scientific validity.