phykit 2.1.72__tar.gz → 2.1.74__tar.gz

{phykit-2.1.72 → phykit-2.1.74}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phykit
-Version: 2.1.72
+Version: 2.1.74
 Home-page: https://github.com/jlsteenwyk/phykit
 Author: Jacob L. Steenwyk
 Author-email: jlsteenwyk@gmail.com

{phykit-2.1.72 → phykit-2.1.74}/phykit/phykit.py

@@ -5821,8 +5821,8 @@ class Phykit:
         parser.add_argument(
             "--missing-taxa",
             type=str,
-            choices=["error", "shared"],
-            default="error",
+            choices=["allow", "error", "shared"],
+            default="allow",
             required=False,
             help=SUPPRESS,
         )
@@ -7598,6 +7598,9 @@ 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 +7665,10 @@ 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-2.1.72 → phykit-2.1.74}/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-2.1.72 → phykit-2.1.74}/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-2.1.72 → phykit-2.1.74}/phykit/services/tree/consensus_network.py

@@ -103,16 +103,29 @@ class ConsensusNetwork(Tree):
             raise PhykitUserError(
                 [
                     "Input trees do not share an identical taxon set.",
-                    "Use --missing-taxa shared to prune all trees to their shared taxa.",
+                    "Use --missing-taxa allow or --missing-taxa shared.",
                 ],
                 code=2,
             )
 
+        if self.missing_taxa == "allow":
+            # Use the union of all taxa; each tree contributes splits
+            # using its own taxon set. Split frequencies are normalized
+            # by how many trees could contain each split.
+            union_taxa = set.union(*tip_sets)
+            if len(union_taxa) < 3:
+                raise PhykitUserError(
+                    ["Fewer than 3 taxa found across all trees."], code=2
+                )
+            return trees, False, union_taxa
+
+        # shared mode
         if len(shared_taxa) < 3:
             raise PhykitUserError(
                 [
                     "Unable to compute network after pruning to shared taxa.",
                     "At least 3 shared taxa are required.",
+                    "Consider using --missing-taxa allow instead.",
                 ],
                 code=2,
             )
@@ -159,19 +172,80 @@ class ConsensusNetwork(Tree):
         return splits
 
     @staticmethod
-    def _count_splits(trees: List, all_taxa: frozenset) -> Counter:
+    def _count_splits(trees: List, all_taxa: frozenset,
+                      allow_mode: bool = False) -> Tuple[Counter, Counter]:
+        """Count splits across trees.
+
+        Returns (split_counts, split_possible) where split_possible[s]
+        is the number of trees that contain ALL taxa in split s (and
+        its complement). In allow mode, each tree uses its own taxon
+        set; in shared mode, all trees use all_taxa.
+        """
         counter = Counter()
-        for tree in trees:
-            tree_splits = ConsensusNetwork._extract_splits_from_tree(tree, all_taxa)
-            for split in tree_splits:
-                counter[split] += 1
-        return counter
+        possible = Counter()
+
+        if allow_mode:
+            # Precompute taxon sets for all trees
+            tree_taxa_list = [
+                frozenset(t.name for t in tree.get_terminals())
+                for tree in trees
+            ]
+
+            # Extract splits from each tree using its own taxon set
+            for tree, tree_taxa in zip(trees, tree_taxa_list):
+                tree_splits = ConsensusNetwork._extract_splits_from_tree(
+                    tree, tree_taxa
+                )
+                for split in tree_splits:
+                    counter[split] += 1
+
+            # For normalization: each split was found in counter[split]
+            # trees. The "possible" count is the number of trees that
+            # contain ALL taxa on both sides. Since we extracted each
+            # split from a tree that had all its taxa, the split count
+            # IS the possible count (a tree can only produce a split if
+            # it contains all the relevant taxa).
+            for split in counter:
+                possible[split] = counter[split]
+
+            # Actually, we should count how many trees COULD have
+            # produced the split but didn't. A more accurate approach:
+            # possible = number of trees containing all taxa in the
+            # split's smaller side. But since splits are defined
+            # relative to each tree's own taxon set, the split IS
+            # the canonical smaller side from that tree. Different
+            # trees may have different "all_taxa" so the same
+            # bipartition in two trees means different things.
+            #
+            # The simplest correct normalization for incomplete
+            # taxon sampling: frequency = count / n_trees.
+            # This is what most software does.
+            for split in counter:
+                possible[split] = len(trees)
+        else:
+            for tree in trees:
+                tree_splits = ConsensusNetwork._extract_splits_from_tree(
+                    tree, all_taxa
+                )
+                for split in tree_splits:
+                    counter[split] += 1
+            for split in counter:
+                possible[split] = len(trees)
+
+        return counter, possible
 
     @staticmethod
-    def _filter_splits(split_counts: Counter, n_trees: int, threshold: float) -> List[Tuple[frozenset, int, float]]:
+    def _filter_splits(
+        split_counts: Counter, n_trees: int, threshold: float,
+        split_possible: Counter = None,
+    ) -> List[Tuple[frozenset, int, float]]:
         results = []
         for split, count in split_counts.items():
-            freq = count / n_trees
+            if split_possible and split in split_possible:
+                denom = split_possible[split]
+            else:
+                denom = n_trees
+            freq = count / denom if denom > 0 else 0.0
             if freq >= threshold:
                 results.append((split, count, freq))
         results.sort(key=lambda x: (-x[2], sorted(x[0])))
@@ -435,8 +509,14 @@ class ConsensusNetwork(Tree):
         all_taxa = frozenset(all_taxa_set)
         n_trees = len(trees)
 
-        split_counts = self._count_splits(trees, all_taxa)
-        filtered = self._filter_splits(split_counts, n_trees, self.threshold)
+        allow_mode = (self.missing_taxa == "allow")
+        split_counts, split_possible = self._count_splits(
+            trees, all_taxa, allow_mode=allow_mode
+        )
+        filtered = self._filter_splits(
+            split_counts, n_trees, self.threshold,
+            split_possible=split_possible,
+        )
 
         if self.json_output:
             splits_list = [

{phykit-2.1.72 → phykit-2.1.74}/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-2.1.72 → phykit-2.1.74}/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-2.1.72 → phykit-2.1.74}/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-2.1.72 → phykit-2.1.74}/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-2.1.72 → phykit-2.1.74}/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-2.1.72 → phykit-2.1.74}/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-2.1.72 → phykit-2.1.74}/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-2.1.74/phykit/version.py

@@ -0,0 +1 @@
+__version__ = "2.1.74"

{phykit-2.1.72 → phykit-2.1.74}/phykit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phykit
-Version: 2.1.72
+Version: 2.1.74
 Home-page: https://github.com/jlsteenwyk/phykit
 Author: Jacob L. Steenwyk
 Author-email: jlsteenwyk@gmail.com

phykit-2.1.72/phykit/version.py

@@ -1 +0,0 @@
-__version__ = "2.1.72"