feat(bokeh): implement tree-phylogenetic

[github-actions]

Implementation: tree-phylogenetic - bokeh

Implements the bokeh version of tree-phylogenetic.

File: plots/tree-phylogenetic/implementations/bokeh.py

Parent Issue: #3070

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🤖 impl-generate workflow

[claude]

AI Review - Attempt 1/3

Image Description

The plot displays a phylogenetic tree (cladogram) showing primate evolutionary relationships. The tree uses a rectangular layout with blue (#306998) branches connecting five species: Human, Chimpanzee, Gorilla, Orangutan, and Gibbon. Leaf nodes are marked with yellow circles with blue outlines, while internal nodes are solid blue circles. Species names appear to the right of each leaf node. The x-axis shows "Evolutionary Distance (substitutions per site)" ranging from 0 to 1.2. Three clade labels (Hominini, Homininae, Hominidae) appear in italic gray text near their respective internal nodes. A scale bar in the lower left indicates "0.1 substitutions/site". The title "Primate Evolution · tree-phylogenetic · bokeh · pyplots.ai" appears at the top left.

Quality Score: 88/100

Criteria Checklist

Visual Quality (35/40 pts)

• VQ-01: Text Legibility (9/10) - Title, axis labels, and species names are readable; clade labels slightly small
• VQ-02: No Overlap (8/8) - No overlapping text elements
• VQ-03: Element Visibility (7/8) - Nodes and branches are visible, but nodes could be slightly larger for better visibility
• VQ-04: Color Accessibility (5/5) - Blue/yellow color scheme is colorblind-safe
• VQ-05: Layout Balance (4/5) - Good use of canvas but tree is slightly left-heavy with empty space on the right
• VQ-06: Axis Labels (2/2) - X-axis has descriptive label with units
• VQ-07: Grid & Legend (0/2) - No grid (appropriate for tree), but no legend explaining node colors

Spec Compliance (23/25 pts)

• SC-01: Plot Type (8/8) - Correct phylogenetic tree/cladogram visualization
• SC-02: Data Mapping (5/5) - X positions correctly represent evolutionary distance
• SC-03: Required Features (4/5) - Has scale bar, clade annotations, branch lengths; missing color-coded clades as mentioned in spec
• SC-04: Data Range (3/3) - All species and nodes visible within axis range
• SC-05: Legend Accuracy (1/2) - No legend for node types (leaf vs internal)
• SC-06: Title Format (2/2) - Correctly formatted as "Primate Evolution · tree-phylogenetic · bokeh · pyplots.ai"

Data Quality (18/20 pts)

• DQ-01: Feature Coverage (7/8) - Shows hierarchical structure, branch lengths, clade labels; could show more diversity in branch lengths
• DQ-02: Realistic Context (7/7) - Primate phylogeny is a real, well-documented evolutionary scenario
• DQ-03: Appropriate Scale (4/5) - Branch lengths are plausible for mitochondrial DNA distances

Code Quality (9/10 pts)

• CQ-01: KISS Structure (3/3) - Simple linear structure with imports, data, plot, save
• CQ-02: Reproducibility (2/3) - Deterministic data (no random seed needed), but hardcoded values
• CQ-03: Clean Imports (2/2) - All imports are used
• CQ-04: No Deprecated API (1/1) - Uses current Bokeh API
• CQ-05: Output Correct (1/1) - Saves as plot.png and plot.html

Library Features (3/5 pts)

• LF-01: Uses distinctive library features (3/5) - Uses ColumnDataSource, Label annotations, export_png; could leverage more Bokeh interactivity features like hover tooltips

Strengths

• Clean rectangular cladogram layout accurately representing primate evolutionary relationships
• Excellent use of scale bar with proper units (substitutions per site)
• Clade annotations (Hominini, Homininae, Hominidae) add scientific context
• Good color scheme with distinct leaf nodes (yellow) and internal nodes (blue)
• Proper title format following pyplots.ai conventions
• Both PNG and HTML outputs provided for static and interactive viewing

Weaknesses

• Missing legend to explain node color meanings (leaf vs internal nodes)
• Clade labels are somewhat small and could be more prominent
• Could add hover tooltips showing species details for better interactivity
• Right side of canvas has significant empty space; tree could be better centered

Verdict: REJECTED

[github-actions]

🔧 Repair Attempt 1/3

Applied fixes based on AI review feedback.

Status: Repair completed, re-triggering review...

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🤖 impl-repair

[claude]

AI Review - Attempt 2/3

Image Description

The plot displays a rectangular phylogenetic tree (cladogram) showing primate evolutionary relationships. The tree has a clean white background with blue (#306998) branch lines connecting nodes. Five leaf nodes are shown as yellow circles with blue outlines (Human, Chimpanzee, Gorilla, Orangutan, Gibbon), and four internal/ancestral nodes are shown as smaller solid blue circles. Species labels appear to the right of each leaf node in dark gray text. Clade annotations ("Hominini", "Homininae", "Hominidae") appear in italics near their respective ancestral nodes. A scale bar at the bottom left indicates "0.1 substitutions/site". The x-axis is labeled "Evolutionary Distance (substitutions per site)" with tick marks from 0 to 1. A legend in the top-right distinguishes "Extant Species (Leaf Nodes)" from "Ancestral Nodes (Internal)". The title "Primate Evolution · tree-phylogenetic · bokeh · pyplots.ai" appears at the top-left.

Quality Score: 91/100

Criteria Checklist

Visual Quality (36/40 pts)

• VQ-01: Text Legibility (10/10) - Title at 28pt, axis labels at 22pt, species labels at 20pt, all clearly readable
• VQ-02: No Overlap (8/8) - No overlapping text elements, all labels well-spaced
• VQ-03: Element Visibility (7/8) - Nodes and branches clearly visible, good sizing for the data density
• VQ-04: Color Accessibility (5/5) - Blue/yellow color scheme is colorblind-safe, good contrast
• VQ-05: Layout Balance (4/5) - Tree is reasonably centered but could use slightly more of the canvas width
• VQ-06: Axis Labels (2/2) - X-axis has descriptive label with units "Evolutionary Distance (substitutions per site)"
• VQ-07: Grid & Legend (0/2) - Grid appropriately hidden for tree diagram, but legend is positioned far in the corner

Spec Compliance (23/25 pts)

• SC-01: Plot Type (8/8) - Correct phylogenetic tree (rectangular cladogram) visualization
• SC-02: Data Mapping (5/5) - X represents evolutionary distance, Y positions species correctly
• SC-03: Required Features (4/5) - Has branch lengths, scale bar, clade labels; missing color-coded clades as suggested in spec
• SC-04: Data Range (3/3) - All data visible within the axis range
• SC-05: Legend Accuracy (2/2) - Legend correctly identifies leaf vs internal nodes
• SC-06: Title Format (1/2) - Title is "Primate Evolution · tree-phylogenetic · bokeh · pyplots.ai" - includes context but format differs slightly from "{spec-id} · {library} · pyplots.ai"

Data Quality (19/20 pts)

• DQ-01: Feature Coverage (7/8) - Shows hierarchical structure, branch lengths, multiple clades; could show more variation in branch lengths
• DQ-02: Realistic Context (7/7) - Primate phylogeny based on mitochondrial DNA is a well-established, scientifically accurate scenario
• DQ-03: Appropriate Scale (5/5) - Branch lengths in substitutions per site are realistic evolutionary distances

Code Quality (9/10 pts)

• CQ-01: KISS Structure (3/3) - Simple linear structure: imports → data → plot → save
• CQ-02: Reproducibility (3/3) - Deterministic data (no random elements)
• CQ-03: Clean Imports (2/2) - All imports are used
• CQ-04: No Deprecated API (0/1) - Uses strict=True in zip which is fine, but adds unnecessary complexity
• CQ-05: Output Correct (1/1) - Saves as plot.png and plot.html

Library Features (4/5 pts)

• LF-01: Distinctive Features (4/5) - Uses ColumnDataSource, HoverTool for interactivity, Label annotations, Legend with custom styling - good use of Bokeh features

Strengths

• Excellent use of Bokeh interactive features including HoverTool with informative tooltips showing scientific names
• Clean, professional visual design with appropriate color scheme (Python blue/yellow)
• Well-structured clade annotations with italic styling for taxonomic names
• Scale bar properly indicates evolutionary distance units
• Comprehensive legend explaining node types

Weaknesses

• Legend positioned in far top-right corner could be closer to the tree for better visual association
• Title format includes descriptive prefix "Primate Evolution" instead of strictly following spec-id format

Verdict: APPROVED