from pathlib import Path
import re,json,shutil,subprocess,hashlib
import fitz
P=Path(__file__).resolve().parents[1];R=P.parents[1]
MAP=[('Figure1','projects/wu_20261104_association_apl/figures/association_controls.pdf'),('Figure2','projects/wu_20261104_combination_network/figures/anatomical_coverage.pdf'),('Figure3','projects/wu_20261104_combination_network/figures/full_primary_refinement.pdf'),('Figure4','projects/wu_20261104_public_validation/figures/animal_model_comparison.pdf'),('Figure5','projects/wu_20261104_public_validation/figures/author_QC_and_sensitivity.pdf'),('ExtendedData1','projects/wu_20261104_public_validation/figures/all21_heldout_traces.pdf'),('ExtendedData2','projects/wu_20261104_public_validation/figures/native_variants.pdf'),('ExtendedData3','projects/wu_20261104_public_validation/figures/observation_and_calibration.pdf'),('ExtendedData4','projects/wu_20261104_public_validation/figures/published_perturbation_source.pdf'),('ExtendedData5','projects/wu_20261104_public_validation/figures/raw_WT_QC.pdf'),('ExtendedData6','projects/wu_20261104_public_validation/figures/raw_NaChBac_QC.pdf')]
ledger=[]
for name,path in MAP:
 src=R/path;dst=P/'figures'/(name+'.pdf');shutil.copy2(src,dst)
 ledger.append(dict(figure=name,source_path=path,source_sha256=hashlib.sha256(src.read_bytes()).hexdigest(),release_path=str(dst.relative_to(P)),interpretation='Source figure copied without changing data; caption in manuscript describes inference scope'))
(P/'metadata/figure_provenance.json').write_text(json.dumps(ledger,indent=2))

def esc(s):
 # Keep reference markers and URLs human-readable; no fabricated bibliography metadata.
 trans={'γ':'gamma','μ':'micro','µ':'micro','Ω':'Ohm','−':'-','–':'--','—':'---','×':' x ','≤':'<=','≥':'>=','→':' -> ','’':"'",'‘':"'",'“':'"','”':'"','⁻':'-','⁶':'6','α':'alpha','Δ':'Delta','²':'2','³':'3','π':'pi'}
 for a,b in trans.items():s=s.replace(a,b)
 s=s.replace('\\(','').replace('\\)','').replace('\\min','min')
 return ''.join({'\\':r'\textbackslash{}','&':r'\&','%':r'\%','$':r'\$','#':r'\#','_':r'\_','{':r'\{','}':r'\}','~':r'\textasciitilde{}','^':r'\textasciicircum{}'}.get(c,c) for c in s)

def inline(s):
 parts=re.split(r'(\*\*[^*]+\*\*|`[^`]+`|\*[^*]+\*)',s)
 return ''.join(r'\textbf{'+esc(t[2:-2])+'}' if t.startswith('**') else r'\texttt{'+esc(t[1:-1])+'}' if t.startswith('`') else r'\emph{'+esc(t[1:-1])+'}' if t.startswith('*') else esc(t) for t in parts)

s=(P/'manuscript/manuscript.md').read_text();lines=s.splitlines();title=lines[0][2:];body=[]
for line in lines[1:]:
 if line.startswith('### '):body.append(r'\subsection*{'+inline(line[4:])+'}')
 elif line.startswith('## '):body.append(r'\section*{'+inline(line[3:])+'}')
 elif line:body.append(inline(line)+'\n')
 else:body.append('\n')
tex=r'''\documentclass[11pt]{article}
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage{lmodern}
\usepackage[margin=0.9in]{geometry}
\usepackage{graphicx}
\usepackage{microtype}
\usepackage{hyperref}
\usepackage{amsmath}
\usepackage{longtable}
\hypersetup{colorlinks=true,urlcolor=blue,linkcolor=blue}
\setlength{\parskip}{0.45em}
\setlength{\parindent}{0pt}
\title{'''+esc(title)+r'''}
\author{Internal research manuscript --- author list pending team confirmation}
\date{Draft prepared 5 November 2026; analyses completed 4 November 2026}
\begin{document}
\maketitle
'''+''.join(body)
tex+='\n\\clearpage\n\\section*{Main and extended data figures}\n'
for name,_ in MAP:
 tex+='\\clearpage\n\\subsection*{'+name+'}\n\\begin{center}\n\\includegraphics[width=.98\\textwidth,height=.89\\textheight,keepaspectratio]{../figures/'+name+'.pdf}\n\\end{center}\n'
tex+='\\end{document}\n';(P/'manuscript/main.tex').write_text(tex)
for i in range(2):
 r=subprocess.run(['pdflatex','-interaction=nonstopmode','-halt-on-error','-output-directory',str(P/'exports'),'main.tex'],cwd=P/'manuscript',capture_output=True,text=True,timeout=60)
 (P/f'validation/latex_pass{i+1}.txt').write_text(r.stdout+r.stderr)
 assert r.returncode==0,r.stdout[-2000:]
shutil.copy2(P/'exports/main.pdf',P/'exports/manuscript.pdf')
with fitz.open(P/'exports/manuscript.pdf') as d:
 text=' '.join(page.get_text() for page in d)
 for marker in ['5,177','35.216','32.723','15.820','14.192','0.05218953','0.05219441','24']:
  assert marker in text,marker
 assert all(len(page.get_text().strip())>15 for page in d)
 abstract=s.split('## Abstract\n\n')[1].split('\n\n## Introduction')[0]
 report=dict(status='PASS',pages=len(d),abstract_words=len(abstract.split()),manuscript_words=len(s.split()),figures=11,references_verified_against_original_article_XML=8,numeric_markers_present=True,authors_affiliations_not_inferred=True,license_not_invented=True,publication_not_asserted_without_remote_commit=True)
 for i in [0,2,4,min(7,len(d)-1)]:d[i].get_pixmap(matrix=fitz.Matrix(1.1,1.1)).save(P/f'validation/manuscript_page{i+1:02d}.png')
 (P/'validation/manuscript_validation.json').write_text(json.dumps(report,indent=2));print(json.dumps(report))