Fix scientific data preparation, cache ownership, and heatmap geometry

[michael-denyer]

Regional plots now resolve selected rows, column roles, LD options and one lead row before rendering. Label eligibility follows that row before ranking, and reference LD values are assigned by SNP ID without changing row order or losing coloring when an R2 column already exists. Colocalization and genome-wide plots normalize source-owned fields before composition; disabled effect coloring does not require effect columns.

GTEx and overlap calculations preserve chromosome and absolute position. Fine-mapping loaders preserve reported membership without inventing credible sets. Category, species and annotation handling preserve the supplied data and configuration.

Caller-supplied recombination directories remain read-only. Archive ingestion streams regular map files into owned paths, downloads stage privately, and gene/exon caches publish atomically. PLINK paths resolve before changing directory. Matplotlib and Bokeh use the same heatmap edges; shared genomic axes remain aligned when adding a colorbar. Example verification generates outside the checkout and explicitly accepts baselines without discarding manual changes.

Compatibility changes are documented in the changelog, user guide and ADR 0009: position-only overlap requires common_chrom, FINEMAP/CAVIAR no longer infer membership, and legacy annotation CSV caches are cold misses. LD tests are separated into command construction, output parsing and process execution, preserving all original test bodies.

Validation:

• 1,527 default tests passed with 97% reported coverage, including regression cases for label selection, existing R2 values and inactive effect columns.
• Full repository hooks passed, including lint, formatting, links, Markdown, Mermaid, YAML and coverage tests.
• Wheel and source distribution built successfully.
• The PR updates four heatmap exports. The follow-up label and LD fixes produce no further example differences; native cell bounds and shared-axis alignment are tested.

Live PLINK, Spark and external annotation services were not exercised; their boundaries use controlled process/transport fixtures.

[coldtea-pr-lens]

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🟢 +0 new · 🟠 ~21 changed · 🔴 -0 removed · 3 flows · 25 files · commit 6df0b1e

Architecture

21 components touched across 6 lanes.

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Inside the changed components — 3 views

Component view — Regional & Genome-Wide Data Preparation

Upfront column projection, lead row selection, and label filtering in regional and genome-wide plotting.

Component view — Reference Data & Cache Publication

Atomic gene/exon ZIP cache publication, safe recombination map streaming, and path-resolved PLINK execution.

Component view — Rendering Panels & Backend Geometry

Shared heatmap cell edge geometry, panel-owned drawing, and inset colorbars preserving genomic coordinate scale.

Data flow

Regional data preparation and lead resolution · Gene annotation fetch and atomic archive publication · Colocalization input projection and scatter preparation

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The other flows — 2 sequences

Gene annotation fetch and atomic archive publication

Colocalization input projection and scatter preparation

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