phykit 2.1.73__tar.gz → 2.1.75__tar.gz

{phykit-2.1.73 → phykit-2.1.75}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phykit
-Version: 2.1.73
+Version: 2.1.75
 Home-page: https://github.com/jlsteenwyk/phykit
 Author: Jacob L. Steenwyk
 Author-email: jlsteenwyk@gmail.com

{phykit-2.1.73 → phykit-2.1.75}/phykit/phykit.py

@@ -5759,6 +5759,15 @@ class Phykit:
                                            circular splits network
                                            plot (optional)
 
+                --max-splits               maximum number of splits
+                                           to include in the network
+                                           graph (default: 30; higher
+                                           splits are still reported
+                                           in text/JSON output)
+
+                --histogram                output filename for a split
+                                           frequency histogram (optional)
+
                 --fig-width                 figure width in inches
                                             (auto-scaled if omitted)
 
@@ -5833,6 +5842,20 @@ class Phykit:
             required=False,
             help=SUPPRESS,
         )
+        parser.add_argument(
+            "--max-splits",
+            type=int,
+            default=30,
+            required=False,
+            help=SUPPRESS,
+        )
+        parser.add_argument(
+            "--histogram",
+            type=str,
+            default=None,
+            required=False,
+            help=SUPPRESS,
+        )
         add_plot_arguments(parser)
         _add_json_argument(parser)
         _run_service(parser, argv, ConsensusNetwork)
@@ -7598,6 +7621,9 @@ class Phykit:
 
                 -v/--verbose                print per-branch details
 
+                --annotate                  show gCF values on the
+                                            plot near each branch
+
                 --fig-width                 figure width in inches
                                             (auto-scaled if omitted)
 
@@ -7662,6 +7688,10 @@ class Phykit:
         parser.add_argument(
             "-v", "--verbose", action="store_true", required=False, help=SUPPRESS
         )
+        parser.add_argument(
+            "--annotate", action="store_true", required=False, default=False,
+            help=SUPPRESS,
+        )
         add_plot_arguments(parser)
         _add_json_argument(parser)
         _run_service(parser, argv, DiscordanceAsymmetry)

{phykit-2.1.73 → phykit-2.1.75}/phykit/services/tree/ancestral_reconstruction.py

@@ -939,7 +939,9 @@ class AncestralReconstruction(Tree):
 
             # Tip labels
             max_x = max(node_x.values()) if node_x else 1.0
-            draw_circular_tip_labels(ax, tree, coords, fontsize=9, offset=max_x * 0.03)
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                draw_circular_tip_labels(ax, tree, coords, fontsize=label_fontsize, offset=max_x * 0.03)
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:
@@ -1012,11 +1014,13 @@ class AncestralReconstruction(Tree):
             # Tip labels
             max_x = max(node_x.values()) if node_x else 0
             offset = max_x * 0.02
-            for tip in tips:
-                ax.text(
-                    node_x[id(tip)] + offset, node_y[id(tip)],
-                    tip.name, va="center", fontsize=9,
-                )
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                for tip in tips:
+                    ax.text(
+                        node_x[id(tip)] + offset, node_y[id(tip)],
+                        tip.name, va="center", fontsize=label_fontsize,
+                    )
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:
@@ -1655,7 +1659,9 @@ class AncestralReconstruction(Tree):
                     start_angle += sweep
 
             # Tip labels
-            draw_circular_tip_labels(ax, tree, coords, fontsize=9, offset=max_x * 0.03)
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                draw_circular_tip_labels(ax, tree, coords, fontsize=label_fontsize, offset=max_x * 0.03)
 
             # Apply color annotations
             if self.plot_config.color_file:
@@ -1750,12 +1756,14 @@ class AncestralReconstruction(Tree):
             # Tip labels with state color
             max_x_val = max(node_x.values()) if node_x else 0
             offset = max_x_val * 0.02
-            for tip in tips:
-                color = state_colors.get(tip_states.get(tip.name, ""), "black")
-                ax.text(
-                    node_x[id(tip)] + offset, node_y[id(tip)],
-                    tip.name, va="center", fontsize=9, color=color,
-                )
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                for tip in tips:
+                    color = state_colors.get(tip_states.get(tip.name, ""), "black")
+                    ax.text(
+                        node_x[id(tip)] + offset, node_y[id(tip)],
+                        tip.name, va="center", fontsize=label_fontsize, color=color,
+                    )
 
             # Apply color annotations
             if self.plot_config.color_file:

{phykit-2.1.73 → phykit-2.1.75}/phykit/services/tree/concordance_asr.py

@@ -844,7 +844,9 @@ class ConcordanceAsr(Tree):
 
             # Tip labels
             max_x = max(node_x.values()) if node_x else 1.0
-            draw_circular_tip_labels(ax, tree, coords, fontsize=9, offset=max_x * 0.03)
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                draw_circular_tip_labels(ax, tree, coords, fontsize=label_fontsize, offset=max_x * 0.03)
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:
@@ -915,11 +917,13 @@ class ConcordanceAsr(Tree):
             # Tip labels
             max_x = max(node_x.values()) if node_x else 0
             offset = max_x * 0.02
-            for tip in tips:
-                ax.text(
-                    node_x[id(tip)] + offset, node_y[id(tip)],
-                    tip.name, va="center", fontsize=9,
-                )
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                for tip in tips:
+                    ax.text(
+                        node_x[id(tip)] + offset, node_y[id(tip)],
+                        tip.name, va="center", fontsize=label_fontsize,
+                    )
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:

{phykit-2.1.73 → phykit-2.1.75}/phykit/services/tree/consensus_network.py

@@ -19,6 +19,8 @@ class ConsensusNetwork(Tree):
         super().__init__(trees=parsed["trees"])
         self.threshold = parsed["threshold"]
         self.missing_taxa = parsed["missing_taxa"]
+        self.max_splits = parsed["max_splits"]
+        self.histogram = parsed["histogram"]
         self.plot_output = parsed["plot_output"]
         self.json_output = parsed["json_output"]
         self.plot_config = parsed["plot_config"]
@@ -28,6 +30,8 @@ class ConsensusNetwork(Tree):
             trees=args.trees,
             threshold=args.threshold,
             missing_taxa=args.missing_taxa,
+            max_splits=getattr(args, "max_splits", 30),
+            histogram=getattr(args, "histogram", None),
             plot_output=getattr(args, "plot_output", None),
             json_output=getattr(args, "json", False),
             plot_config=PlotConfig.from_args(args),
@@ -414,19 +418,41 @@ class ConsensusNetwork(Tree):
         )
 
         config = self.plot_config
-        config.resolve(n_rows=len(all_taxa), n_cols=None)
+        n = len(ordering)
+        # Force square figure for network graphs
+        if config.fig_width is None and config.fig_height is None:
+            size = max(10, min(30, 8 + n * 0.05))
+            config.fig_width = size
+            config.fig_height = size
+        config.resolve(n_rows=n, n_cols=None)
         fig, ax = plt.subplots(1, 1, figsize=(config.fig_width, config.fig_height))
         ax.set_aspect("equal")
 
+        # Determine label fontsize: auto-suppress for large trees
+        if config.ylabel_fontsize is not None:
+            label_fontsize = config.ylabel_fontsize
+        elif n > 100:
+            label_fontsize = 0  # auto-hide for very large trees
+        elif n > 50:
+            label_fontsize = max(3, 8 - (n - 50) * 0.1)
+        else:
+            label_fontsize = 10
+
         if not splits_list:
             # No splits: place taxa evenly on a circle
             for taxon in ordering:
                 angle = angles[taxon]
                 x = math.cos(angle)
                 y = math.sin(angle)
-                deg = math.degrees(angle)
-                ha = "left" if -90 < deg < 90 or deg > 270 else "right"
-                ax.text(x, y, taxon, ha=ha, va="center", fontsize=10)
+                if label_fontsize > 0:
+                    deg = math.degrees(angle)
+                    ha = "left" if -90 < deg < 90 or deg > 270 else "right"
+                    rotation = deg if -90 < deg < 90 or deg > 270 else deg + 180
+                    ax.text(x, y, taxon, ha=ha, va="center",
+                            fontsize=label_fontsize, rotation=rotation,
+                            rotation_mode="anchor")
+                else:
+                    ax.plot(x, y, "o", color="black", markersize=2)
         else:
             # Compute node positions: pos = sum(sign_i * weight_i * dir_i) / 2
             node_positions = {}
@@ -453,6 +479,16 @@ class ConsensusNetwork(Tree):
                 x2, y2 = node_positions[s2]
                 ax.plot([x1, x2], [y1, y2], "-", color="black", linewidth=1.5, zorder=2)
 
+            # Find taxa on split boundaries (participating in displayed splits)
+            boundary_taxa = set()
+            for split, count, freq in circular_splits:
+                for i in range(n):
+                    curr = ordering[i]
+                    nxt = ordering[(i + 1) % n]
+                    if (curr in split) != (nxt in split):
+                        boundary_taxa.add(curr)
+                        boundary_taxa.add(nxt)
+
             # Draw pendant edges and taxon labels
             for taxon in ordering:
                 angle = angles[taxon]
@@ -460,14 +496,30 @@ class ConsensusNetwork(Tree):
                     nx, ny = node_positions[taxon_signs[taxon]]
                 else:
                     nx, ny = 0.0, 0.0
-                tx = nx + pendant_len * math.cos(angle)
-                ty = ny + pendant_len * math.sin(angle)
-                ax.plot([nx, tx], [ny, ty], "-", color="black", linewidth=1.5, zorder=2)
-                lx = tx + 0.03 * math.cos(angle)
-                ly = ty + 0.03 * math.sin(angle)
-                deg = math.degrees(angle)
-                ha = "left" if -90 < deg < 90 or deg > 270 else "right"
-                ax.text(lx, ly, taxon, ha=ha, va="center", fontsize=10, zorder=4)
+
+                # Only draw full pendant edges for boundary taxa;
+                # non-boundary taxa get a short stub or are skipped
+                if taxon in boundary_taxa or n <= 50:
+                    plen = pendant_len
+                else:
+                    plen = pendant_len * 0.3  # short stub
+
+                tx = nx + plen * math.cos(angle)
+                ty = ny + plen * math.sin(angle)
+                ax.plot([nx, tx], [ny, ty], "-", color="black",
+                        linewidth=0.8 if taxon not in boundary_taxa else 1.5,
+                        alpha=0.3 if taxon not in boundary_taxa else 1.0,
+                        zorder=2)
+
+                if label_fontsize > 0 and (taxon in boundary_taxa or n <= 50):
+                    lx = tx + 0.03 * math.cos(angle)
+                    ly = ty + 0.03 * math.sin(angle)
+                    deg = math.degrees(angle)
+                    ha = "left" if -90 < deg < 90 or deg > 270 else "right"
+                    rotation = deg if -90 < deg < 90 or deg > 270 else deg + 180
+                    ax.text(lx, ly, taxon, ha=ha, va="center",
+                            fontsize=label_fontsize, rotation=rotation,
+                            rotation_mode="anchor", zorder=4)
 
             # Frequency labels on internal edges (one per split)
             labeled_splits = set()
@@ -497,6 +549,35 @@ class ConsensusNetwork(Tree):
     # Output
     # ------------------------------------------------------------------
 
+    def _draw_histogram(self, split_counts, n_trees, output_path):
+        """Draw a histogram of split frequencies."""
+        import matplotlib
+        matplotlib.use("Agg")
+        import matplotlib.pyplot as plt
+
+        config = self.plot_config
+        config.resolve(n_rows=10, n_cols=None)
+
+        frequencies = [count / n_trees for count in split_counts.values()]
+
+        fig, ax = plt.subplots(figsize=(config.fig_width or 10, config.fig_height or 6))
+        ax.hist(frequencies, bins=50, color="#377eb8", edgecolor="black", linewidth=0.5)
+        ax.set_xlabel("Split frequency", fontsize=config.axis_fontsize or 12)
+        ax.set_ylabel("Number of splits", fontsize=config.axis_fontsize or 12)
+        ax.axvline(x=self.threshold, color="red", linestyle="--", lw=1,
+                   label=f"Threshold ({self.threshold})")
+        ax.legend(fontsize=9)
+
+        if config.show_title:
+            ax.set_title(
+                config.title or "Split Frequency Distribution",
+                fontsize=config.title_fontsize or 14,
+            )
+
+        fig.tight_layout()
+        fig.savefig(output_path, dpi=config.dpi, bbox_inches="tight")
+        plt.close(fig)
+
     def _format_split(self, split: frozenset) -> str:
         return "{" + ", ".join(sorted(split)) + "}"
 
@@ -551,6 +632,35 @@ class ConsensusNetwork(Tree):
             for split, count, freq in filtered:
                 print(f"{self._format_split(split)}\t{count}/{n_trees}\t{freq:.4f}")
 
+        if self.histogram:
+            self._draw_histogram(split_counts, n_trees, self.histogram)
+            if not self.json_output:
+                print(f"Histogram saved: {self.histogram}")
+
         if self.plot_output:
+            import sys
+            n_taxa = len(all_taxa)
+
+            if n_taxa > 100:
+                print(
+                    f"Warning: {n_taxa} taxa — network graph may not be "
+                    f"informative at this scale. Consider using "
+                    f"--histogram for a split frequency distribution instead.",
+                    file=sys.stderr,
+                )
+
             ordering = self._compute_circular_ordering(trees, all_taxa)
-            self._draw_network(ordering, filtered, all_taxa, self.plot_output)
+
+            # Cap splits for graph visualization to avoid exponential blowup
+            plot_filtered = filtered
+            if len(filtered) > self.max_splits:
+                print(
+                    f"Warning: {len(filtered)} splits above threshold; "
+                    f"using top {self.max_splits} for network graph "
+                    f"(use --max-splits to adjust).",
+                    file=sys.stderr,
+                )
+                # filtered is already sorted by frequency (descending)
+                plot_filtered = filtered[:self.max_splits]
+
+            self._draw_network(ordering, plot_filtered, all_taxa, self.plot_output)

{phykit-2.1.73 → phykit-2.1.75}/phykit/services/tree/cont_map.py

@@ -522,7 +522,9 @@ class ContMap(Tree):
 
             # Tip labels
             max_x = max(node_x.values()) if node_x else 1.0
-            draw_circular_tip_labels(ax, tree, coords, fontsize=9, offset=max_x * 0.03)
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                draw_circular_tip_labels(ax, tree, coords, fontsize=label_fontsize, offset=max_x * 0.03)
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:
@@ -592,11 +594,13 @@ class ContMap(Tree):
             # Tip labels
             max_x = max(node_x.values()) if node_x else 0
             offset = max_x * 0.02
-            for tip in tips:
-                ax.text(
-                    node_x[id(tip)] + offset, node_y[id(tip)],
-                    tip.name, va="center", fontsize=9,
-                )
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                for tip in tips:
+                    ax.text(
+                        node_x[id(tip)] + offset, node_y[id(tip)],
+                        tip.name, va="center", fontsize=label_fontsize,
+                    )
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:

{phykit-2.1.73 → phykit-2.1.75}/phykit/services/tree/density_map.py

@@ -347,7 +347,9 @@ class DensityMap(Tree):
 
             # Tip labels
             max_x = max(node_x.values()) if node_x else 1.0
-            draw_circular_tip_labels(ax, tree, coords, fontsize=9, offset=max_x * 0.03)
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                draw_circular_tip_labels(ax, tree, coords, fontsize=label_fontsize, offset=max_x * 0.03)
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:
@@ -453,11 +455,13 @@ class DensityMap(Tree):
             # Tip labels
             max_x = max(node_x.values()) if node_x else 0
             offset = max_x * 0.02
-            for tip in tips:
-                ax.text(
-                    node_x[id(tip)] + offset, node_y[id(tip)],
-                    tip.name, va="center", fontsize=9,
-                )
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                for tip in tips:
+                    ax.text(
+                        node_x[id(tip)] + offset, node_y[id(tip)],
+                        tip.name, va="center", fontsize=label_fontsize,
+                    )
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:

{phykit-2.1.73 → phykit-2.1.75}/phykit/services/tree/discordance_asymmetry.py

@@ -33,6 +33,7 @@ class DiscordanceAsymmetry(Tree):
         super().__init__(tree_file_path=parsed["tree_file_path"])
         self.gene_trees_path = parsed["gene_trees_path"]
         self.verbose = parsed["verbose"]
+        self.annotate = parsed["annotate"]
         self.json_output = parsed["json_output"]
         self.plot_output = parsed["plot_output"]
         self.plot_config = parsed["plot_config"]
@@ -42,6 +43,7 @@ class DiscordanceAsymmetry(Tree):
             tree_file_path=args.tree,
             gene_trees_path=args.gene_trees,
             verbose=getattr(args, "verbose", False),
+            annotate=getattr(args, "annotate", False),
             json_output=getattr(args, "json", False),
             plot_output=getattr(args, "plot_output", None),
             plot_config=PlotConfig.from_args(args),
@@ -314,7 +316,9 @@ class DiscordanceAsymmetry(Tree):
 
             # Tip labels
             max_x = max(node_x.values()) if node_x else 1.0
-            draw_circular_tip_labels(ax, species_tree, coords, fontsize=9, offset=max_x * 0.02)
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                draw_circular_tip_labels(ax, species_tree, coords, fontsize=label_fontsize, offset=max_x * 0.02)
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:
@@ -345,23 +349,28 @@ class DiscordanceAsymmetry(Tree):
 
                 total = entry["n_concordant"] + entry["n_alt1"] + entry["n_alt2"]
                 gcf = entry["n_concordant"] / total if total > 0 else 1.0
-                ax.annotate(
-                    f"gCF={gcf:.2f}",
-                    (cx, cy),
-                    textcoords="offset points",
-                    xytext=(5, 5),
-                    fontsize=7,
-                )
+
+                if self.annotate:
+                    ax.annotate(
+                        f"{gcf:.2f}",
+                        (cx, cy),
+                        textcoords="offset points",
+                        xytext=(5, 5),
+                        fontsize=max(4, 7 - n_tips * 0.01),
+                    )
 
                 if (entry["fdr_p"] is not None and entry["fdr_p"] < 0.05
                         and entry["favored_alt"] is not None):
                     ax.scatter(cx, cy, s=100, c="red", marker="*", zorder=5)
 
-            # Colorbar
-            sm = plt.cm.ScalarMappable(cmap=cmap, norm=norm)
-            sm.set_array([])
-            cbar = fig.colorbar(sm, ax=ax, pad=0.15)
-            cbar.set_label("Asymmetry ratio")
+            # Colorbar (hide if legend-position is none)
+            legend_loc = config.legend_position or "upper right"
+            if legend_loc != "none":
+                sm = plt.cm.ScalarMappable(cmap=cmap, norm=norm)
+                sm.set_array([])
+                cbar = fig.colorbar(sm, ax=ax, pad=0.15)
+                cbar_fontsize = config.axis_fontsize if config.axis_fontsize else 10
+                cbar.set_label("Asymmetry ratio", fontsize=cbar_fontsize)
 
             if config.show_title:
                 ax.set_title(config.title or "Discordance Asymmetry", fontsize=config.title_fontsize)
@@ -409,16 +418,18 @@ class DiscordanceAsymmetry(Tree):
                 x = node_x.get(id(clade), 0)
                 y = node_y.get(id(clade), 0)
 
-                # Show gCF value
+                # Show gCF value (only if --annotate)
                 total = entry["n_concordant"] + entry["n_alt1"] + entry["n_alt2"]
                 gcf = entry["n_concordant"] / total if total > 0 else 1.0
-                ax.annotate(
-                    f"gCF={gcf:.2f}",
-                    (x, y),
-                    textcoords="offset points",
-                    xytext=(5, 5),
-                    fontsize=7,
-                )
+
+                if self.annotate:
+                    ax.annotate(
+                        f"{gcf:.2f}",
+                        (x, y),
+                        textcoords="offset points",
+                        xytext=(5, 5),
+                        fontsize=max(4, 7 - n_tips * 0.01),
+                    )
 
                 # Mark significant branches (FDR < 0.05)
                 if (entry["fdr_p"] is not None and entry["fdr_p"] < 0.05
@@ -426,13 +437,15 @@ class DiscordanceAsymmetry(Tree):
                     ax.scatter(x, y, s=100, c="red", marker="*", zorder=5)
 
             # Tip labels
-            max_x = max(node_x.values()) if node_x else 0
-            offset = max_x * 0.02
-            for tip in tips:
-                ax.text(
-                    node_x[id(tip)] + offset, node_y[id(tip)],
-                    tip.name, va="center", fontsize=9,
-                )
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                max_x = max(node_x.values()) if node_x else 0
+                offset = max_x * 0.02
+                for tip in tips:
+                    ax.text(
+                        node_x[id(tip)] + offset, node_y[id(tip)],
+                        tip.name, va="center", fontsize=label_fontsize,
+                    )
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:
@@ -450,11 +463,14 @@ class DiscordanceAsymmetry(Tree):
                 if color_legend:
                     ax.legend(handles=color_legend, loc="upper right", fontsize=8, frameon=True)
 
-            # Colorbar
-            sm = plt.cm.ScalarMappable(cmap=cmap, norm=norm)
-            sm.set_array([])
-            cbar = fig.colorbar(sm, ax=ax, pad=0.15)
-            cbar.set_label("Asymmetry ratio")
+            # Colorbar (hide if legend-position is none)
+            legend_loc = config.legend_position or "upper right"
+            if legend_loc != "none":
+                sm = plt.cm.ScalarMappable(cmap=cmap, norm=norm)
+                sm.set_array([])
+                cbar = fig.colorbar(sm, ax=ax, pad=0.15)
+                cbar_fontsize = config.axis_fontsize if config.axis_fontsize else 10
+                cbar.set_label("Asymmetry ratio", fontsize=cbar_fontsize)
 
             ax.set_xlabel("Branch length (subs/site)")
             ax.set_yticks([])

{phykit-2.1.73 → phykit-2.1.75}/phykit/services/tree/phenogram.py

@@ -487,12 +487,14 @@ class Phenogram(Tree):
         # Label tips with taxon names (offset to the right)
         max_x = max(node_x.values()) if node_x else 0
         offset = max_x * 0.02
-        for tip in tips:
-            if id(tip) in node_x and tip.name in trait_values:
-                ax.text(
-                    node_x[id(tip)] + offset, trait_values[tip.name],
-                    tip.name, va="center", fontsize=9,
-                )
+        label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+        if label_fontsize > 0:
+            for tip in tips:
+                if id(tip) in node_x and tip.name in trait_values:
+                    ax.text(
+                        node_x[id(tip)] + offset, trait_values[tip.name],
+                        tip.name, va="center", fontsize=label_fontsize,
+                    )
 
         ax.set_xlabel("Distance from root")
         ax.set_ylabel("Trait value")

{phykit-2.1.73 → phykit-2.1.75}/phykit/services/tree/rate_heterogeneity.py

@@ -759,7 +759,9 @@ class RateHeterogeneity(Tree):
 
             # Tip labels
             max_x = max(node_x.values()) if node_x else 1.0
-            draw_circular_tip_labels(ax, tree, coords, fontsize=9, offset=max_x * 0.02)
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                draw_circular_tip_labels(ax, tree, coords, fontsize=label_fontsize, offset=max_x * 0.02)
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:
@@ -825,11 +827,13 @@ class RateHeterogeneity(Tree):
 
             max_x = max(node_x.values()) if node_x else 0
             offset = max_x * 0.02
-            for tip in tips:
-                ax.text(
-                    node_x[id(tip)] + offset, node_y[id(tip)],
-                    tip.name, va="center", fontsize=9,
-                )
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                for tip in tips:
+                    ax.text(
+                        node_x[id(tip)] + offset, node_y[id(tip)],
+                        tip.name, va="center", fontsize=label_fontsize,
+                    )
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:

{phykit-2.1.73 → phykit-2.1.75}/phykit/services/tree/stochastic_character_map.py

@@ -600,7 +600,9 @@ class StochasticCharacterMap(Tree):
 
             # Tip labels
             max_x = max(node_x.values()) if node_x else 1.0
-            draw_circular_tip_labels(ax, tree, coords, fontsize=9, offset=max_x * 0.03)
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                draw_circular_tip_labels(ax, tree, coords, fontsize=label_fontsize, offset=max_x * 0.03)
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:
@@ -677,11 +679,13 @@ class StochasticCharacterMap(Tree):
             # Tip labels
             max_x = max(node_x.values()) if node_x else 0
             offset = max_x * 0.02
-            for tip in tips:
-                ax.text(
-                    node_x[id(tip)] + offset, node_y[id(tip)],
-                    tip.name, va="center", fontsize=9
-                )
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                for tip in tips:
+                    ax.text(
+                        node_x[id(tip)] + offset, node_y[id(tip)],
+                        tip.name, va="center", fontsize=label_fontsize
+                    )
 
             # Apply color annotations (range + label only; branches are trait-colored)
             if self.plot_config.color_file:

{phykit-2.1.73 → phykit-2.1.75}/phykit/services/tree/trait_rate_map.py

@@ -544,9 +544,11 @@ class TraitRateMap(Tree):
 
             # Tip labels
             max_x = max(node_x.values()) if node_x else 1.0
-            draw_circular_tip_labels(
-                ax, tree, coords, fontsize=9, offset=max_x * 0.03
-            )
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                draw_circular_tip_labels(
+                    ax, tree, coords, fontsize=label_fontsize, offset=max_x * 0.03
+                )
 
             # Color annotations
             if self.plot_config.color_file:
@@ -611,11 +613,13 @@ class TraitRateMap(Tree):
             # Tip labels
             max_x = max(node_x.values()) if node_x else 0
             offset = max_x * 0.02
-            for tip in tips:
-                ax.text(
-                    node_x[id(tip)] + offset, node_y[id(tip)],
-                    tip.name, va="center", fontsize=9,
-                )
+            label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize is not None else 9
+            if label_fontsize > 0:
+                for tip in tips:
+                    ax.text(
+                        node_x[id(tip)] + offset, node_y[id(tip)],
+                        tip.name, va="center", fontsize=label_fontsize,
+                    )
 
             # Color annotations
             if self.plot_config.color_file:

phykit-2.1.75/phykit/version.py

@@ -0,0 +1 @@
+__version__ = "2.1.75"

{phykit-2.1.73 → phykit-2.1.75}/phykit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phykit
-Version: 2.1.73
+Version: 2.1.75
 Home-page: https://github.com/jlsteenwyk/phykit
 Author: Jacob L. Steenwyk
 Author-email: jlsteenwyk@gmail.com

phykit-2.1.73/phykit/version.py

@@ -1 +0,0 @@
-__version__ = "2.1.73"