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neuronmimic-data / wu_20261104_structure_function /manuscript_release /code /prepare_release.py

cyd0806

Release all nine KC structure/function rounds and auditable dependencies

6f24982 verified 1 day ago

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"""Enumerate all task rounds and dependency closure; no auth or network."""
from pathlib import Path
import csv,json,hashlib,re,concurrent.futures,collections,os,tarfile,urllib.parse
P=Path(__file__).resolve().parents[1];R=P.parents[1]
SEEDS=[R/'projects/wu_20261102_followup_20261103']+sorted(x for x in (R/'projects').glob('wu_20261104_*') if x!=P)+[R/'artifacts/wu_20261030_all5177_structural_atlas']
EXTERNAL=R/'simulation/data/external/kc_nachbac_model_2025'
BAD_PARTS={'.git','__pycache__','.venv','.venv_fine_structure','.cache','.pytest_cache'}
SECRET=re.compile(rb'(?:gh[pousr]_[A-Za-z0-9_]{20,}|github_pat_[A-Za-z0-9_]{20,}|hf_[A-Za-z0-9]{20,})')
CODE_EXT={'.py','.sh','.mod','.hoc','.toml','.yaml','.yml','.cff','.R','.m'}
ALL={};excluded=[]
def admissible(p):return p.is_file() and not BAD_PARTS.intersection(p.parts) and p.suffix not in {'.pyc','.pyo'}
def add(p,role):
 try:p=p.resolve();rel=p.relative_to(R)
 except (ValueError,OSError):return
 if not admissible(p):return
 if p==R/'20261102_吴老师组会纪要.pdf':
  excluded.append({'path':str(rel),'reason':'Internal meeting record, not a scientific public-data payload'});return
 ALL.setdefault(p,role)
def resolve(s,base):
 if not isinstance(s,str) or len(s)>1000 or '\n' in s or '://' in s:return None
 x=Path(s)
 for p in ([x] if x.is_absolute() else [R/x,base/x]):
  if p.exists() and p.is_file():return p
 return None
def walk(x,base):
 if isinstance(x,dict):
  for k,v in x.items():
   if isinstance(v,str) and k in {'path','source','source_file','file','swc_path','local_path','local','input_path'}:
    p=resolve(v,base)
    if p:add(p,'manifest_dependency')
   elif isinstance(v,(list,dict)):walk(v,base)
 elif isinstance(x,list):
  for v in x:walk(v,base)
for root in SEEDS:
 for p in root.rglob('*'):add(p,'task_project' if root.parent.name=='projects' else 'structural_atlas')
for p in (R/'simulation/src').rglob('*'):add(p,'shared_simulation_code')
# Dependencies as recorded by sealed input manifests; expand until no new manifests found.
visited=set()
for iteration in range(6):
 todo=[p for p in ALL if p not in visited and any(z in p.name.lower() for z in ['manifest','dependenc','provenance','registry']) and p.suffix in {'.csv','.json'}]
 if not todo:break
 for p in todo:
  visited.add(p)
  try:
   if p.suffix=='.json':walk(json.loads(p.read_text()),p.parent)
   else:
    with p.open(newline='') as f:
     for row in csv.DictReader(f):walk(row,p.parent)
  except (ValueError,UnicodeError,csv.Error):pass
# All original physiology files are inventoried even where public redistribution terms remain unresolved.
for p in EXTERNAL.rglob('*'):add(p,'third_party_source_retrieval_required')
for p in [R/'pyproject.toml',R/'simulation/README.md',R/'simulation/src/bio_fly/__init__.py']:add(p,'shared_simulation_code')
# Retrieve rather than relicense unlicensed author-source bundles. Derived outputs are retained.
def terms(p):
 rel=str(p.relative_to(R))
 if str(EXTERNAL.relative_to(R)) in rel or 'AusbornLab__KC_NaChBac_Model__' in p.name:
  return 'SOURCE_RETRIEVAL_ONLY','Author model repository has no explicit license in source audit'
 if ('published_KC_KC_model' in p.parts and any(t in p.parts for t in ['author_release','current_commit'])):
  return 'SOURCE_RETRIEVAL_ONLY','Pinned external model-source snapshot; preserve original repository terms'
 return 'INCLUDE','Own/derived scientific output or attributed source; original terms retained, no blanket license'

def hash_one(item):
 p,role=item;h=hashlib.sha256();hits=0
 scan=p.suffix.lower() in {'.py','.sh','.json','.csv','.txt','.md','.toml','.yaml','.yml','.ini','.cfg','.log','.m','.R','.hoc','.mod','.xml'} or p.suffix==''
 tail=b''
 with p.open('rb') as f:
  while b:=f.read(4*1024*1024):
   h.update(b)
   if scan:
    hits+=len(SECRET.findall(tail+b));tail=b[-150:]
 disposition,reason=terms(p)
 if hits:disposition='EXCLUDE_CREDENTIAL_PATTERN';reason='Credential-shaped strings detected; values suppressed and no upload allowed'
 return dict(path=str(p.relative_to(R)),bytes=p.stat().st_size,sha256=h.hexdigest(),role=role,public_disposition=disposition,reason=reason,credential_matches=hits)
with concurrent.futures.ThreadPoolExecutor(max_workers=8) as pool:rows=list(pool.map(hash_one,sorted(ALL.items())))
fields=list(rows[0]);out=P/'metadata/release_inventory.csv'
with out.open('w',newline='') as f:w=csv.DictWriter(f,fieldnames=fields);w.writeheader();w.writerows(rows)
retrieval=[]
source_tree=R/'projects/wu_20261102_followup_20261103/sources/AusbornLab__KC_NaChBac_Model_tree.json'
tracked={x['path'] for x in json.loads(source_tree.read_text())['tree'] if x['type']=='blob'}
source_commit='b799ccd7bd37dc080d717d8ca2b75699bf94eae2'
for row in rows:
 if row['public_disposition']=='SOURCE_RETRIEVAL_ONLY':
  path=row['path'];url='';q='';revision='';action='RESTORE_FROM_RECORDED_SOURCE_ARCHIVE_VERIFY_SHA256'
  if 'simulation/data/external/kc_nachbac_model_2025/' in path:
   q=path.split('simulation/data/external/kc_nachbac_model_2025/',1)[1]
  elif 'AusbornLab__KC_NaChBac_Model__' in path:
   q=path.split('AusbornLab__KC_NaChBac_Model__',1)[1].replace('__','/')
  is_author='kc_nachbac' in path.lower() or 'AusbornLab' in path
  if is_author:
   revision=source_commit
   if q in tracked:
    url='https://raw.githubusercontent.com/AusbornLab/KC_NaChBac_Model/'+source_commit+'/'+urllib.parse.quote(q,safe='/');action='FETCH_PINNED_SOURCE_VERIFY_SHA256'
   else:action='REBUILD_FROM_PINNED_SOURCE_MACHINE_SPECIFIC_HASH_NOT_PORTABLE'
  elif '/author_release/' in path:
   revision='v1.0.0 / 3710a03';url='https://zenodo.org/api/records/17698635/files/nawrotlab/KC_KC_lateral_interactions-v1.0.0.zip/content'
  retrieval.append({**row,'original_url':url,'source_repo':'https://github.com/AusbornLab/KC_NaChBac_Model' if is_author else 'https://github.com/nawrotlab/KC_KC_lateral_interactions','source_revision':revision,'original_relative_path':q,'retrieval_action':action})
with (P/'metadata/source_retrieval_ledger.csv').open('w',newline='') as f:
 w=csv.DictWriter(f,fieldnames=fields+['original_url','source_repo','source_revision','original_relative_path','retrieval_action']);w.writeheader();w.writerows(retrieval)
summary={'status':'INVENTORIED_NOT_UPLOADED','task_rounds':len([s for s in SEEDS if s.parent.name=='projects']),'seed_roots':[str(x.relative_to(R)) for x in SEEDS],'files':len(rows),'bytes':sum(x['bytes'] for x in rows),'included_files':sum(x['public_disposition']=='INCLUDE' for x in rows),'included_bytes':sum(x['bytes'] for x in rows if x['public_disposition']=='INCLUDE'),'source_retrieval_files':len(retrieval),'credential_pattern_files':[x['path'] for x in rows if x['credential_matches']],'excluded_internal_files':list({x['path']:x for x in excluded}.values()),'dependency_manifest_files_parsed':len(visited),'bulk_destination':'cyd0806/neuronmimic-data/wu_20261104_structure_function','note':'Scientific project payload; no virtual environments, private meeting minutes, git internals or unrelated dirty artifacts.'}
(P/'metadata/release_inventory_summary.json').write_text(json.dumps(summary,indent=2,ensure_ascii=False));print(json.dumps(summary,ensure_ascii=False,indent=2))

	"""Enumerate all task rounds and dependency closure; no auth or network."""
	from pathlib import Path
	import csv,json,hashlib,re,concurrent.futures,collections,os,tarfile,urllib.parse
	P=Path(__file__).resolve().parents[1];R=P.parents[1]
	SEEDS=[R/'projects/wu_20261102_followup_20261103']+sorted(x for x in (R/'projects').glob('wu_20261104_*') if x!=P)+[R/'artifacts/wu_20261030_all5177_structural_atlas']
	EXTERNAL=R/'simulation/data/external/kc_nachbac_model_2025'
	BAD_PARTS={'.git','__pycache__','.venv','.venv_fine_structure','.cache','.pytest_cache'}
	SECRET=re.compile(rb'(?:gh[pousr]_[A-Za-z0-9_]{20,}\|github_pat_[A-Za-z0-9_]{20,}\|hf_[A-Za-z0-9]{20,})')
	CODE_EXT={'.py','.sh','.mod','.hoc','.toml','.yaml','.yml','.cff','.R','.m'}
	ALL={};excluded=[]
	def admissible(p):return p.is_file() and not BAD_PARTS.intersection(p.parts) and p.suffix not in {'.pyc','.pyo'}
	def add(p,role):
	try:p=p.resolve();rel=p.relative_to(R)
	except (ValueError,OSError):return
	if not admissible(p):return
	if p==R/'20261102_吴老师组会纪要.pdf':
	excluded.append({'path':str(rel),'reason':'Internal meeting record, not a scientific public-data payload'});return
	ALL.setdefault(p,role)
	def resolve(s,base):
	if not isinstance(s,str) or len(s)>1000 or '\n' in s or '://' in s:return None
	x=Path(s)
	for p in ([x] if x.is_absolute() else [R/x,base/x]):
	if p.exists() and p.is_file():return p
	return None
	def walk(x,base):
	if isinstance(x,dict):
	for k,v in x.items():
	if isinstance(v,str) and k in {'path','source','source_file','file','swc_path','local_path','local','input_path'}:
	p=resolve(v,base)
	if p:add(p,'manifest_dependency')
	elif isinstance(v,(list,dict)):walk(v,base)
	elif isinstance(x,list):
	for v in x:walk(v,base)
	for root in SEEDS:
	for p in root.rglob('*'):add(p,'task_project' if root.parent.name=='projects' else 'structural_atlas')
	for p in (R/'simulation/src').rglob('*'):add(p,'shared_simulation_code')
	# Dependencies as recorded by sealed input manifests; expand until no new manifests found.
	visited=set()
	for iteration in range(6):
	todo=[p for p in ALL if p not in visited and any(z in p.name.lower() for z in ['manifest','dependenc','provenance','registry']) and p.suffix in {'.csv','.json'}]
	if not todo:break
	for p in todo:
	visited.add(p)
	try:
	if p.suffix=='.json':walk(json.loads(p.read_text()),p.parent)
	else:
	with p.open(newline='') as f:
	for row in csv.DictReader(f):walk(row,p.parent)
	except (ValueError,UnicodeError,csv.Error):pass
	# All original physiology files are inventoried even where public redistribution terms remain unresolved.
	for p in EXTERNAL.rglob('*'):add(p,'third_party_source_retrieval_required')
	for p in [R/'pyproject.toml',R/'simulation/README.md',R/'simulation/src/bio_fly/__init__.py']:add(p,'shared_simulation_code')
	# Retrieve rather than relicense unlicensed author-source bundles. Derived outputs are retained.
	def terms(p):
	rel=str(p.relative_to(R))
	if str(EXTERNAL.relative_to(R)) in rel or 'AusbornLab__KC_NaChBac_Model__' in p.name:
	return 'SOURCE_RETRIEVAL_ONLY','Author model repository has no explicit license in source audit'
	if ('published_KC_KC_model' in p.parts and any(t in p.parts for t in ['author_release','current_commit'])):
	return 'SOURCE_RETRIEVAL_ONLY','Pinned external model-source snapshot; preserve original repository terms'
	return 'INCLUDE','Own/derived scientific output or attributed source; original terms retained, no blanket license'

	def hash_one(item):
	p,role=item;h=hashlib.sha256();hits=0
	scan=p.suffix.lower() in {'.py','.sh','.json','.csv','.txt','.md','.toml','.yaml','.yml','.ini','.cfg','.log','.m','.R','.hoc','.mod','.xml'} or p.suffix==''
	tail=b''
	with p.open('rb') as f:
	while b:=f.read(410241024):
	h.update(b)
	if scan:
	hits+=len(SECRET.findall(tail+b));tail=b[-150:]
	disposition,reason=terms(p)
	if hits:disposition='EXCLUDE_CREDENTIAL_PATTERN';reason='Credential-shaped strings detected; values suppressed and no upload allowed'
	return dict(path=str(p.relative_to(R)),bytes=p.stat().st_size,sha256=h.hexdigest(),role=role,public_disposition=disposition,reason=reason,credential_matches=hits)
	with concurrent.futures.ThreadPoolExecutor(max_workers=8) as pool:rows=list(pool.map(hash_one,sorted(ALL.items())))
	fields=list(rows[0]);out=P/'metadata/release_inventory.csv'
	with out.open('w',newline='') as f:w=csv.DictWriter(f,fieldnames=fields);w.writeheader();w.writerows(rows)
	retrieval=[]
	source_tree=R/'projects/wu_20261102_followup_20261103/sources/AusbornLab__KC_NaChBac_Model_tree.json'
	tracked={x['path'] for x in json.loads(source_tree.read_text())['tree'] if x['type']=='blob'}
	source_commit='b799ccd7bd37dc080d717d8ca2b75699bf94eae2'
	for row in rows:
	if row['public_disposition']=='SOURCE_RETRIEVAL_ONLY':
	path=row['path'];url='';q='';revision='';action='RESTORE_FROM_RECORDED_SOURCE_ARCHIVE_VERIFY_SHA256'
	if 'simulation/data/external/kc_nachbac_model_2025/' in path:
	q=path.split('simulation/data/external/kc_nachbac_model_2025/',1)[1]
	elif 'AusbornLab__KC_NaChBac_Model__' in path:
	q=path.split('AusbornLab__KC_NaChBac_Model__',1)[1].replace('__','/')
	is_author='kc_nachbac' in path.lower() or 'AusbornLab' in path
	if is_author:
	revision=source_commit
	if q in tracked:
	url='https://raw.githubusercontent.com/AusbornLab/KC_NaChBac_Model/'+source_commit+'/'+urllib.parse.quote(q,safe='/');action='FETCH_PINNED_SOURCE_VERIFY_SHA256'
	else:action='REBUILD_FROM_PINNED_SOURCE_MACHINE_SPECIFIC_HASH_NOT_PORTABLE'
	elif '/author_release/' in path:
	revision='v1.0.0 / 3710a03';url='https://zenodo.org/api/records/17698635/files/nawrotlab/KC_KC_lateral_interactions-v1.0.0.zip/content'
	retrieval.append({**row,'original_url':url,'source_repo':'https://github.com/AusbornLab/KC_NaChBac_Model' if is_author else 'https://github.com/nawrotlab/KC_KC_lateral_interactions','source_revision':revision,'original_relative_path':q,'retrieval_action':action})
	with (P/'metadata/source_retrieval_ledger.csv').open('w',newline='') as f:
	w=csv.DictWriter(f,fieldnames=fields+['original_url','source_repo','source_revision','original_relative_path','retrieval_action']);w.writeheader();w.writerows(retrieval)
	summary={'status':'INVENTORIED_NOT_UPLOADED','task_rounds':len([s for s in SEEDS if s.parent.name=='projects']),'seed_roots':[str(x.relative_to(R)) for x in SEEDS],'files':len(rows),'bytes':sum(x['bytes'] for x in rows),'included_files':sum(x['public_disposition']=='INCLUDE' for x in rows),'included_bytes':sum(x['bytes'] for x in rows if x['public_disposition']=='INCLUDE'),'source_retrieval_files':len(retrieval),'credential_pattern_files':[x['path'] for x in rows if x['credential_matches']],'excluded_internal_files':list({x['path']:x for x in excluded}.values()),'dependency_manifest_files_parsed':len(visited),'bulk_destination':'cyd0806/neuronmimic-data/wu_20261104_structure_function','note':'Scientific project payload; no virtual environments, private meeting minutes, git internals or unrelated dirty artifacts.'}
	(P/'metadata/release_inventory_summary.json').write_text(json.dumps(summary,indent=2,ensure_ascii=False));print(json.dumps(summary,ensure_ascii=False,indent=2))