Add ZOMBI2 integration: read zombi2 output, draw gene-family reconciliations#6
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…iations New phylustrator.zombi2 module reads a ZOMBI2 (github.com/AADavin/zombi2) Genomes.write() output folder and draws a gene family's history on the time-calibrated species tree. Because the layout uses x = time, transfers are placed at their true time on both branches (plot_transfers mode="time") and so render horizontal in time; originations/duplications/losses become branch markers at the exact time they occurred. API (file-based; Phylustrator never imports zombi2): - load(output_dir) -> Zombi2Data(species_tree, events, transfers); the species tree is annotated with time_from_origin per node. - draw_reconciliation(data_or_path, family, ...) -> VerticalTreeDrawer. - event_markers() / transfer_records() lower-level helpers. Exposed as the phylustrator.zombi2 submodule. Tests build a minimal ZOMBI2-format fixture in tmp_path (self-contained, no zombi2 dependency): 10 tests, full suite 195 passing, ruff clean. Docs: guide/zombi2.md + api/zombi2.md + nav + changelog. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Summary
Adds
phylustrator.zombi2, a file-based adapter that reads ZOMBI2 output and draws a gene family's reconciliation on the time-calibrated species tree. Because the layout usesx = time, transfers are placed at their true time on both branches (plot_transfers(mode="time")) and render horizontal in time; originations / duplications / losses become branch markers at the exact time they happened.Phylustrator never imports ZOMBI2 — it only reads the files ZOMBI2 writes, so the two stay decoupled.
API
zombi2.load(output_dir) -> Zombi2Data(species_tree, events, transfers)— parses aGenomes.write()folder (species_tree.nwk+gene_family_events/*.tsv+Transfers.tsv); the species tree is annotated withtime_from_originper node.zombi2.draw_reconciliation(data_or_path, family, ...) -> VerticalTreeDrawer— overlays O/D/L markers + time-placed transfer arcs; returns the drawer for further customisation /save_svg/save_png.zombi2.event_markers()/zombi2.transfer_records()— lower-level helpers.Changes
src/phylustrator/zombi2.py, exposed as thephylustrator.zombi2submodule.tests/tests_zombi2.py— 10 tests, building a minimal ZOMBI2-format fixture intmp_path(no zombi2 dependency, no committed data).docs/guide/zombi2.md+docs/api/zombi2.md+ mkdocs nav + CHANGELOG.Purely additive (7 files, +496 lines, 0 deletions); changes no existing behaviour.
Testing
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