| 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): |
| |
| 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)) |
|
|
