Anchor-mode HIV rendering, palette/NT-ruler/V1V2 extensions, row labels, multi-panel fixes#1
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…margin - render_panels now stacks panels with patchworklib instead of overwriting - Derive shared inches-per-data-unit scale from tallest panel so chrome (regions, markers, ref rows) is identical physical size across panels - Only last panel draws the legend (show_footer parameter) - Set patchworklib margin to 0 for flush panel stacking - Fix panel_figsize to account for extra_ref_rows - Add _data_height helper mirroring _draw_panel coordinate system - Add figsize/show_footer params to to_patchwork for composition control
Extend Panel with optional secondary_ref_row + heterologous_color so the renderer can flag cells where a sample matches a secondary reference (e.g. another lineage's parental) but differs from the primary reference. Useful for visualizing heterologous-recombination evidence in pixel panels. - models.Panel: secondary_ref_row + heterologous_color (default #FF6F00) - hiv.hiv_panel: secondary_ref_path param; reads single-record FASTA, asserts length matches alignment columns - renderer._draw_panel: three-way comparison before mismatch coloring, legend gains "Heterologous" entry when secondary ref is present - 7 new tests covering match/pure-mismatch/heterologous classification, short-secondary fallback, end-to-end hiv_panel integration, and length-mismatch error path
…ny round 1) resolves: scrutiny-m2 blocker #2 (ruler below region bar)
… (scrutiny round 1)
resolves: scrutiny-m2 blocker #3
Adds a row_label_mode field to Panel with three modes:
- group_rollup (default; preserves existing '{name} ({count})' labels)
- per_row_numbered ('{N}. {short_seqid}' with N monotonic per panel)
- raw_seqid ('{short_seqid}' only)
Reference rows (extra_ref_rows and the primary ref labelled by
panel.label) are ALWAYS drawn with their logical label and never
numbered, regardless of mode. short_seqid truncates to
row_label_max_chars (default 30).
Threads row_label_mode + row_label_max_chars through hiv_panel().
Adds compute_row_labels() helper exposing the label list in render
order for tests. Adds TestRowLabelMode suite in
tests/test_hiv_panel_extensions.py (9 new tests, 85/85 total).
Adds tpixel.anchors with bundled lineage→HxB2 maps (CH505, SF162p3, T250-4) so hiv_panel can place the region bar even when the alignment lacks an HxB2 row. New CLI/API surface: * hiv_panel: anchor_id, anchor_lineage, show_variant_labels, show_markers * CLI: --anchor-id, --anchor-lineage, --variant-labels, --markers/--no-markers * hxb2_variant_labels(): K169E-style mutation labels vs HxB2 * hxb2_col_labels(): always include first mapped column tick * hxb2_regions(): absorb gap columns instead of fragmenting bar * renderer: uuid-suffixed brick labels (fixes patchworklib reuse error across multiple render_panels calls in one process); footer height bump for legend clearance; font-size tweaks Package data: anchor reference fastas shipped via setuptools package-data declaration. Tests fixtures trimmed to 10 records each (full alignment width preserved) — repo no longer carries large sequence sets. .gitignore: add refs/, restore tests/output/, drop dead prototype entries.
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Summary
hiv_paneland CLI now render HIV Env alignments without anHxB2row by mapping a known lineage_ref(CH505 / SF162p3 / T250-4) onto bundled per-lineage HxB2 references. Newtpixel.anchorsmodule + package data.K169E-style mutation labels under the x-axis, computed against HxB2 (works in both classic and anchor mode).--markers/--no-markersto suppress PNGS dots.secondary_ref_rowfor three-way classification (match / mismatch-vs-primary / heterologous-vs-secondary).hiv_panelpalette overrides with adjacent same-color region merging.row_label_modesupportsgroup_rollup,per_row_numbered,raw_seqid._labelsetreuse error across multiplerender_panelscalls in one process).tests/data/*.fastacut to 10 records each; full alignment width preserved. Repo no longer carries large sequence sets..gitignorecleanup — addrefs/, restoretests/output/, drop dead prototype entries.Test plan
pytest tests/— 125 passedtpixel <CH505 alignment> --hiv -o out.pngtpixel <T205-4 fasta> --hiv --anchor-lineage T250-4 -o out.pngtpixel <alignment> --hiv --variant-labels -o out.png