"""Build review_index.html at the project root: a locally-navigable index with RELATIVE links to every artifact (figures, tables, dossiers, notebooks, inputs) so the work can be reviewed independently by opening it in a browser.""" import html from pathlib import Path ROOT = Path("/Users/shiventripathi/dev/science/th2_selective") def sz(p): b=p.stat().st_size return f"{b/1e6:.1f} MB" if b>1e6 else f"{b/1e3:.0f} KB" def links(paths, base): out="" for p in paths: if not p.exists(): continue rel=p.relative_to(ROOT) out+=f'
  • {html.escape(p.name)} {sz(p)}
    • ' return out O=ROOT/"outputs"; N=ROOT/"notebooks"; D=ROOT/"data" sections=[ ("Start here", [ROOT/"dashboard.html", O/"synthesis.md", O/"review_report.md"], "The dashboard (self-contained), the plain-language synthesis, and the independent-review report."), ("Figures", [O/"plane_plot.svg", O/"plane_plot.png", O/"recall_overlay.svg", O/"recall_overlay.png"], "The 2D arm plane (headline) and the known-regulator recall overlay."), ("Result tables", [O/"real_vs_fp_shortlist.csv", O/"selective_tiered.csv", O/"condition_selectivity_matrix.csv", O/"qc_audit_highconf.csv"], "Ranked shortlist (known vs novel), tiered selective list, per-condition selectivity, and the QC audit of the high-confidence set."), ("Intermediate data", [O/"arms.parquet", O/"annotations.parquet", O/"candidates_full.parquet", O/"obs_qc.parquet"], "Reconstructed arm scores, per-gene annotations, merged candidates, and the pulled h5ad QC columns."), ("Mechanism dossiers", sorted((O/"mechanism_dossiers").glob("*.md")), "Per-candidate agentic dossier: hypothesis, mechanism, evidence, proposed experiment, and the adversarial review."), ("Analysis code (reproducible)", sorted(N.glob("*.py")), "01 arms -> 02 annotations -> 03 credibility -> 04 score -> 05 dashboard -> 06 dossiers -> 07 QC audit -> 08 this index."), ("Inputs (from the Marson-lab repo)", [D/"Ota_Th2vsTh1_DE_results.csv", D/"th1_th2_known_regulators.yaml", D/"DE_stats.suppl_table.csv", D/"guide_kd_efficiency.suppl_table.csv", D/"Lambert_2018_HumanTF.csv", D/"donor_info.csv"], "The external Th2/Th1 signature, known-regulator calibration set, and the supplementary QC tables."), ] cards="" for title,paths,desc in sections: li=links(paths, ROOT) if not li: continue cards+=f'

    {title}

    {desc}

    ' HTML=f"""Selective Th2 Suppressor Atlas — local review index

    Selective Th2 Suppressor Atlas

    Local review index — every artifact, linked with relative paths. Open this file in a browser to click through the analysis independently.

    {cards}

    All paths are relative to this file. CSV/parquet open in your spreadsheet tool or a notebook; .md and .py open as text; .svg/.png in the browser. Generated from the outputs/ and notebooks/ directories.

    """ (ROOT/"review_index.html").write_text(HTML) print("wrote review_index.html with", HTML.count("
  • "), "linked files")