feat(matplotlib): implement tree-phylogenetic (#3110)

## Implementation: `tree-phylogenetic` - matplotlib

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

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

**Parent Issue:** #3070

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:robot: *[impl-generate
workflow](https://github.com/MarkusNeusinger/pyplots/actions/runs/20620332010)*

---------

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

Author: github-actions[bot]

plots/tree-phylogenetic/implementations/matplotlib.py

@@ -0,0 +1,120 @@
+""" pyplots.ai
+tree-phylogenetic: Phylogenetic Tree Diagram
+Library: matplotlib 3.10.8 | Python 3.13.11
+Quality: 91/100 | Created: 2025-12-31
+"""
+
+import matplotlib.pyplot as plt
+
+
+# Primate phylogenetic tree - pre-computed coordinates
+# Each leaf: (name, y_position, x_end) where x_end is total distance from root
+# Species ordered by evolutionary grouping (top to bottom)
+species = [
+    ("Galago", 0, 0.24),
+    ("Tarsier", 1, 0.24),
+    ("Lemur", 2, 0.18),
+    ("Spider Monkey", 3, 0.20),
+    ("Capuchin", 4, 0.19),
+    ("Baboon", 5, 0.18),
+    ("Rhesus Macaque", 6, 0.18),
+    ("Gibbon", 7, 0.16),
+    ("Orangutan", 8, 0.15),
+    ("Gorilla", 9, 0.14),
+    ("Chimpanzee", 10, 0.13),
+    ("Human", 11, 0.13),
+]
+
+# Branch structure: each branch is (x1, y1, x2, y2, color)
+# Horizontal branches (to tips)
+branch_color = "#306998"
+yellow = "#FFD43B"
+green = "#5A9C5A"
+
+# Pre-computed branch segments for the phylogenetic tree
+# Format: (x_start, y_start, x_end, y_end, color)
+branches = [
+    # Root split (Prosimians vs Simians)
+    (0, 5.5, 0.05, 5.5, branch_color),  # Root to split
+    (0.05, 1, 0.05, 5.5, branch_color),  # Vertical at root
+    (0.05, 1, 0.05, 10, branch_color),  # Vertical to Simians
+    # Prosimians clade
+    (0.05, 1, 0.08, 1, green),  # To Prosimians node
+    (0.08, 0.5, 0.08, 2, green),  # Prosimians vertical
+    (0.08, 0.5, 0.10, 0.5, green),  # To Lorisoids
+    (0.10, 0, 0.10, 1, green),  # Lorisoids vertical
+    (0.10, 0, 0.24, 0, green),  # To Galago
+    (0.10, 1, 0.24, 1, green),  # To Tarsier
+    (0.08, 2, 0.18, 2, green),  # To Lemur
+    # Simians main branch
+    (0.05, 10, 0.08, 10, branch_color),  # To Simians node
+    (0.08, 5.5, 0.08, 10, branch_color),  # Simians vertical
+    # Apes clade
+    (0.08, 10, 0.10, 10, branch_color),  # To Apes
+    (0.10, 8.5, 0.10, 10, branch_color),  # Apes vertical
+    # African Apes
+    (0.10, 10, 0.11, 10, branch_color),  # To African Apes
+    (0.11, 9.5, 0.11, 11, branch_color),  # African Apes vertical
+    (0.11, 9, 0.14, 9, branch_color),  # To Gorilla
+    (0.11, 10.5, 0.12, 10.5, branch_color),  # To Hominini
+    (0.12, 10, 0.12, 11, branch_color),  # Hominini vertical
+    (0.12, 10, 0.13, 10, branch_color),  # To Chimpanzee
+    (0.12, 11, 0.13, 11, branch_color),  # To Human
+    # Asian Apes
+    (0.10, 8.5, 0.13, 8.5, branch_color),  # To Asian Apes
+    (0.13, 7, 0.13, 8, branch_color),  # Asian Apes vertical
+    (0.13, 7, 0.16, 7, branch_color),  # To Gibbon
+    (0.13, 8, 0.15, 8, branch_color),  # To Orangutan
+    # Monkeys clade
+    (0.08, 5.5, 0.12, 5.5, yellow),  # To Monkeys
+    (0.12, 3.5, 0.12, 5.5, yellow),  # Monkeys vertical
+    # Old World Monkeys
+    (0.12, 5.5, 0.14, 5.5, yellow),  # To Old World
+    (0.14, 5, 0.14, 6, yellow),  # OW vertical
+    (0.14, 5, 0.18, 5, yellow),  # To Baboon
+    (0.14, 6, 0.18, 6, yellow),  # To Rhesus
+    # New World Monkeys
+    (0.12, 3.5, 0.15, 3.5, yellow),  # To New World
+    (0.15, 3, 0.15, 4, yellow),  # NW vertical
+    (0.15, 3, 0.20, 3, yellow),  # To Spider Monkey
+    (0.15, 4, 0.19, 4, yellow),  # To Capuchin
+]
+
+# Create figure
+fig, ax = plt.subplots(figsize=(16, 9))
+
+# Draw all branches
+for x1, y1, x2, y2, color in branches:
+    ax.plot([x1, x2], [y1, y2], color=color, linewidth=2.5, solid_capstyle="round")
+
+# Draw species labels
+for name, y, x in species:
+    ax.plot(x, y, "o", color=branch_color, markersize=8)
+    ax.text(x + 0.008, y, name, va="center", ha="left", fontsize=16, fontweight="medium")
+
+# Style the plot
+ax.set_xlabel("Evolutionary Distance (substitutions per site)", fontsize=20)
+ax.set_title("Primate Evolution · tree-phylogenetic · matplotlib · pyplots.ai", fontsize=24)
+
+# Set axis limits
+ax.set_xlim(-0.02, 0.38)
+ax.set_ylim(-1, 12.5)
+
+# Style ticks
+ax.tick_params(axis="x", labelsize=16)
+ax.tick_params(axis="y", left=False, labelleft=False)
+
+# Add subtle grid on x-axis only
+ax.grid(True, axis="x", alpha=0.3, linestyle="--")
+
+# Remove spines
+ax.spines["top"].set_visible(False)
+ax.spines["right"].set_visible(False)
+ax.spines["left"].set_visible(False)
+
+# Add scale bar
+ax.plot([0, 0.05], [-0.5, -0.5], color="#333333", linewidth=3, solid_capstyle="butt")
+ax.text(0.025, -0.8, "0.05", ha="center", va="top", fontsize=14, color="#333333")
+
+plt.tight_layout()
+plt.savefig("plot.png", dpi=300, bbox_inches="tight")

plots/tree-phylogenetic/metadata/matplotlib.yaml

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+library: matplotlib
+specification_id: tree-phylogenetic
+created: '2025-12-31T13:56:05Z'
+updated: '2025-12-31T14:07:51Z'
+generated_by: claude-opus-4-5-20251101
+workflow_run: 20620332010
+issue: 3070
+python_version: 3.13.11
+library_version: 3.10.8
+preview_url: https://storage.googleapis.com/pyplots-images/plots/tree-phylogenetic/matplotlib/plot.png
+preview_thumb: https://storage.googleapis.com/pyplots-images/plots/tree-phylogenetic/matplotlib/plot_thumb.png
+preview_html: null
+quality_score: 91
+review:
+  strengths:
+  - Excellent clade coloring with three distinct, colorblind-safe colors (blue, yellow,
+    green) representing apes, monkeys, and prosimians
+  - Clean, readable phylogenetic tree structure with proper proportional branch lengths
+  - Well-formatted title following exact spec convention
+  - Scale bar included for reference (0.05 units)
+  - Scientifically accurate primate phylogeny with correct evolutionary groupings
+  - Clean code structure with pre-computed coordinates for clarity
+  weaknesses:
+  - Missing legend to explain the meaning of the three clade colors (blue=apes, yellow=monkeys,
+    green=prosimians)