feat(bokeh): implement tree-phylogenetic (#3102)

## Implementation: `tree-phylogenetic` - bokeh

Implements the **bokeh** version of `tree-phylogenetic`.

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

**Parent Issue:** #3070

---
:robot: *[impl-generate
workflow](https://github.com/MarkusNeusinger/pyplots/actions/runs/20620334569)*

---------

Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

Author: github-actions[bot]

plots/tree-phylogenetic/implementations/bokeh.py

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+""" pyplots.ai
+tree-phylogenetic: Phylogenetic Tree Diagram
+Library: bokeh 3.8.1 | Python 3.13.11
+Quality: 91/100 | Created: 2025-12-31
+"""
+
+from bokeh.io import export_png
+from bokeh.models import ColumnDataSource, HoverTool, Label, Legend, LegendItem
+from bokeh.plotting import figure, output_file, save
+
+
+# Phylogenetic tree data - Primate species (mitochondrial DNA based)
+# Manually define tree structure with node positions and branch connections
+# Structure: ((((Human, Chimp), Gorilla), Orangutan), Gibbon)
+# Using rectangular cladogram layout
+
+# Node positions (x = evolutionary distance, y = vertical position)
+species = ["Human", "Chimpanzee", "Gorilla", "Orangutan", "Gibbon"]
+
+# Leaf node positions - shifted left to better center the tree
+leaf_y = [5, 4, 3, 2, 1]
+leaf_x = [0.75, 0.75, 0.65, 0.45, 0.25]
+
+# Internal node positions - shifted left to match
+# Node 1: Human-Chimp ancestor
+# Node 2: Node1-Gorilla ancestor
+# Node 3: Node2-Orangutan ancestor
+# Node 4: Root - Node3-Gibbon ancestor
+
+internal_x = [0.60, 0.40, 0.20, 0.00]
+internal_y = [4.5, 3.75, 2.875, 1.9375]
+
+# Branch lines (horizontal and vertical segments)
+# Format: lists of x and y coordinates for each branch segment
+
+# Horizontal branches from leaves to their ancestors
+h_branch_x = [
+    [internal_x[0], leaf_x[0]],  # Human
+    [internal_x[0], leaf_x[1]],  # Chimp
+    [internal_x[1], leaf_x[2]],  # Gorilla
+    [internal_x[2], leaf_x[3]],  # Orangutan
+    [internal_x[3], leaf_x[4]],  # Gibbon
+    [internal_x[1], internal_x[0]],  # Node1 to Node2
+    [internal_x[2], internal_x[1]],  # Node2 to Node3
+    [internal_x[3], internal_x[2]],  # Node3 to Root
+]
+
+h_branch_y = [
+    [leaf_y[0], leaf_y[0]],  # Human
+    [leaf_y[1], leaf_y[1]],  # Chimp
+    [leaf_y[2], leaf_y[2]],  # Gorilla
+    [leaf_y[3], leaf_y[3]],  # Orangutan
+    [leaf_y[4], leaf_y[4]],  # Gibbon
+    [internal_y[0], internal_y[0]],  # Node1 to Node2
+    [internal_y[1], internal_y[1]],  # Node2 to Node3
+    [internal_y[2], internal_y[2]],  # Node3 to Root
+]
+
+# Vertical branches connecting nodes
+v_branch_x = [
+    [internal_x[0], internal_x[0]],  # Node1 vertical (Human-Chimp)
+    [internal_x[1], internal_x[1]],  # Node2 vertical (Node1-Gorilla)
+    [internal_x[2], internal_x[2]],  # Node3 vertical (Node2-Orangutan)
+    [internal_x[3], internal_x[3]],  # Root vertical (Node3-Gibbon)
+]
+
+v_branch_y = [
+    [leaf_y[0], leaf_y[1]],  # Node1 vertical
+    [internal_y[0], leaf_y[2]],  # Node2 vertical
+    [internal_y[1], leaf_y[3]],  # Node3 vertical
+    [internal_y[2], leaf_y[4]],  # Root vertical
+]
+
+# Create figure with better centered x_range
+p = figure(
+    width=4800,
+    height=2700,
+    title="Primate Evolution · tree-phylogenetic · bokeh · pyplots.ai",
+    x_axis_label="Evolutionary Distance (substitutions per site)",
+    y_axis_label="",
+    x_range=(-0.15, 1.05),
+    y_range=(0.3, 5.7),
+)
+
+# Style the figure
+p.title.text_font_size = "28pt"
+p.xaxis.axis_label_text_font_size = "22pt"
+p.xaxis.major_label_text_font_size = "18pt"
+p.yaxis.visible = False
+p.grid.visible = False
+p.outline_line_color = None
+
+# Draw horizontal branches
+for hx, hy in zip(h_branch_x, h_branch_y, strict=True):
+    p.line(hx, hy, line_width=4, line_color="#306998")
+
+# Draw vertical branches
+for vx, vy in zip(v_branch_x, v_branch_y, strict=True):
+    p.line(vx, vy, line_width=4, line_color="#306998")
+
+# Draw leaf nodes with hover tooltips
+leaf_source = ColumnDataSource(
+    data={
+        "x": leaf_x,
+        "y": leaf_y,
+        "species": species,
+        "type": ["Leaf Node"] * len(species),
+        "info": [
+            "Modern human (Homo sapiens)",
+            "Chimpanzee (Pan troglodytes)",
+            "Western gorilla (Gorilla gorilla)",
+            "Bornean orangutan (Pongo pygmaeus)",
+            "White-handed gibbon (Hylobates lar)",
+        ],
+    }
+)
+leaf_scatter = p.scatter(
+    "x", "y", source=leaf_source, size=24, color="#FFD43B", line_color="#306998", line_width=3, name="leaf_nodes"
+)
+
+# Draw internal nodes with hover tooltips
+internal_names = ["Human-Chimp Ancestor", "Great Ape Ancestor", "Hominid Ancestor", "Root (Common Ancestor)"]
+internal_source = ColumnDataSource(
+    data={"x": internal_x, "y": internal_y, "type": ["Internal Node"] * len(internal_x), "info": internal_names}
+)
+internal_scatter = p.scatter("x", "y", source=internal_source, size=18, color="#306998", name="internal_nodes")
+
+# Add hover tool for interactivity
+hover = HoverTool(
+    renderers=[leaf_scatter, internal_scatter], tooltips=[("Type", "@type"), ("Info", "@info")], mode="mouse"
+)
+p.add_tools(hover)
+
+# Add species labels
+for i, sp in enumerate(species):
+    label = Label(
+        x=leaf_x[i] + 0.02, y=leaf_y[i], text=sp, text_font_size="20pt", text_baseline="middle", text_color="#333333"
+    )
+    p.add_layout(label)
+
+# Add scale bar
+scale_bar_y = 0.6
+p.line([0, 0.1], [scale_bar_y, scale_bar_y], line_width=4, line_color="#333333")
+scale_label = Label(
+    x=0.0, y=scale_bar_y - 0.15, text="0.1 substitutions/site", text_font_size="16pt", text_color="#333333"
+)
+p.add_layout(scale_label)
+
+# Add clade annotations with more prominent styling
+clade_labels = [
+    {"x": 0.58, "y": 4.5, "text": "Hominini"},
+    {"x": 0.38, "y": 3.75, "text": "Homininae"},
+    {"x": 0.18, "y": 2.875, "text": "Hominidae"},
+]
+
+for clade in clade_labels:
+    bracket_label = Label(
+        x=clade["x"] - 0.15,
+        y=clade["y"],
+        text=clade["text"],
+        text_font_size="20pt",
+        text_font_style="italic",
+        text_color="#444444",
+        text_baseline="middle",
+    )
+    p.add_layout(bracket_label)
+
+# Add legend for node types
+legend = Legend(
+    items=[
+        LegendItem(label="Extant Species (Leaf Nodes)", renderers=[leaf_scatter]),
+        LegendItem(label="Ancestral Nodes (Internal)", renderers=[internal_scatter]),
+    ],
+    location="top_right",
+    label_text_font_size="18pt",
+    spacing=10,
+    padding=15,
+    background_fill_alpha=0.8,
+)
+p.add_layout(legend)
+
+# Save PNG
+export_png(p, filename="plot.png")
+
+# Save HTML for interactivity
+output_file("plot.html")
+save(p)

plots/tree-phylogenetic/metadata/bokeh.yaml

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+library: bokeh
+specification_id: tree-phylogenetic
+created: '2025-12-31T13:54:21Z'
+updated: '2025-12-31T14:22:11Z'
+generated_by: claude-opus-4-5-20251101
+workflow_run: 20620334569
+issue: 3070
+python_version: 3.13.11
+library_version: 3.8.1
+preview_url: https://storage.googleapis.com/pyplots-images/plots/tree-phylogenetic/bokeh/plot.png
+preview_thumb: https://storage.googleapis.com/pyplots-images/plots/tree-phylogenetic/bokeh/plot_thumb.png
+preview_html: https://storage.googleapis.com/pyplots-images/plots/tree-phylogenetic/bokeh/plot.html
+quality_score: 91
+review:
+  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 instead of strictly following spec-id
+    format