phykit 2.1.48__tar.gz → 2.1.49__tar.gz

{phykit-2.1.48 → phykit-2.1.49}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: phykit
-Version: 2.1.48
+Version: 2.1.49
 Home-page: https://github.com/jlsteenwyk/phykit
 Author: Jacob L. Steenwyk
 Author-email: jlsteenwyk@gmail.com
@@ -14,6 +14,22 @@ Classifier: Topic :: Scientific/Engineering
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
+Requires-Dist: biopython>=1.82
+Requires-Dist: matplotlib>=3.7.0
+Requires-Dist: numpy>=1.24.0
+Requires-Dist: scipy>=1.11.3
+Requires-Dist: scikit-learn>=1.4.2
+Requires-Dist: umap-learn>=0.5.0
+Requires-Dist: tqdm>=4.65.0
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
 
 <p align="center">
   <a href="https://github.com/jlsteenwyk/phykit">

{phykit-2.1.48 → phykit-2.1.49}/phykit/helpers/plot_config.py

@@ -23,6 +23,7 @@ class PlotConfig:
     title_fontsize: Optional[float] = None
     axis_fontsize: Optional[float] = None
     colors: Optional[List[str]] = None
+    ladderize: bool = False
 
     def validate(self) -> None:
         if self.fig_width is not None and self.fig_width <= 0:
@@ -187,6 +188,7 @@ class PlotConfig:
             title_fontsize=getattr(args, "title_fontsize", None),
             axis_fontsize=getattr(args, "axis_fontsize", None),
             colors=colors,
+            ladderize=getattr(args, "ladderize", False),
         )
         config.validate()
         return config
@@ -205,3 +207,4 @@ def add_plot_arguments(parser) -> None:
     group.add_argument("--title-fontsize", type=float, default=None, help="Font size for the title")
     group.add_argument("--axis-fontsize", type=float, default=None, help="Font size for axis labels")
     group.add_argument("--colors", type=str, default=None, help="Comma-separated colors (hex or named)")
+    group.add_argument("--ladderize", action="store_true", default=False, help="Ladderize (sort) the tree before plotting")

{phykit-2.1.48 → phykit-2.1.49}/phykit/phykit.py

@@ -464,7 +464,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -512,6 +512,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -816,7 +819,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -862,6 +865,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -947,7 +953,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -992,6 +998,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -1298,7 +1307,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -1348,6 +1357,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -1485,7 +1497,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -1530,6 +1542,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -1831,7 +1846,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -1888,6 +1903,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      output results as JSON
                 """
             ),
@@ -1961,7 +1979,7 @@ class Phykit:
                     [--legend-position <str>]
                     [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                     [--title-fontsize <float>] [--axis-fontsize <float>]
-                    [--colors <str>]
+                    [--colors <str>] [--ladderize]
                     [--json]
 
                 Options
@@ -2019,6 +2037,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      output results as JSON
                 """
             ),
@@ -2249,7 +2270,7 @@ class Phykit:
                     [--legend-position <str>]
                     [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                     [--title-fontsize <float>] [--axis-fontsize <float>]
-                    [--colors <str>]
+                    [--colors <str>] [--ladderize]
                     [--json]
 
                 Options
@@ -2307,6 +2328,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -2920,7 +2944,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -3006,6 +3030,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -3255,7 +3282,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -3307,6 +3334,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -3606,7 +3636,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -3661,6 +3691,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -3731,7 +3764,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -3774,6 +3807,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to also
                                             output results as JSON
                 """
@@ -3823,7 +3859,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -3876,6 +3912,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to also
                                             output results as JSON
                 """
@@ -3930,7 +3969,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -3973,6 +4012,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -4019,7 +4061,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -4065,6 +4107,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -4118,7 +4163,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -4170,6 +4215,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -4651,7 +4699,7 @@ class Phykit:
                     [--legend-position <str>]
                     [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                     [--title-fontsize <float>] [--axis-fontsize <float>]
-                    [--colors <str>]
+                    [--colors <str>] [--ladderize]
                     [--json]
 
                 Options
@@ -4702,6 +4750,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                     optional argument to output
                                            results as JSON
                 """
@@ -4766,7 +4817,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
 
                 Options
                 =====================================================
@@ -4815,6 +4866,9 @@ class Phykit:
                                             (default: "#2b8cbe,#d62728,
                                             #969696")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             per-node concordance as JSON
                 """
@@ -4879,7 +4933,7 @@ class Phykit:
                     [--legend-position <str>]
                     [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                     [--title-fontsize <float>] [--axis-fontsize <float>]
-                    [--colors <str>]
+                    [--colors <str>] [--ladderize]
                     [--json]
 
                 Options
@@ -4936,6 +4990,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                     optional argument to output
                                            results as JSON
                 """
@@ -5096,7 +5153,7 @@ class Phykit:
                     [--legend-position <str>]
                     [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                     [--title-fontsize <float>] [--axis-fontsize <float>]
-                    [--colors <str>]
+                    [--colors <str>] [--ladderize]
                     [--json]
 
                 Options
@@ -5142,6 +5199,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -5250,7 +5310,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -5298,6 +5358,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -5357,7 +5420,7 @@ class Phykit:
                     [--legend-position <str>]
                     [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                     [--title-fontsize <float>] [--axis-fontsize <float>]
-                    [--colors <str>]
+                    [--colors <str>] [--ladderize]
                     [--json]
 
                 Options
@@ -5421,6 +5484,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -5820,7 +5886,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -5877,6 +5943,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -6056,7 +6125,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -6107,6 +6176,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -6225,7 +6297,7 @@ class Phykit:
                     [--legend-position <str>]
                     [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                     [--title-fontsize <float>] [--axis-fontsize <float>]
-                    [--colors <str>]
+                    [--colors <str>] [--ladderize]
                     [--json]
 
                 Options
@@ -6270,6 +6342,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -6325,7 +6400,7 @@ class Phykit:
                     [--legend-position <str>]
                     [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                     [--title-fontsize <float>] [--axis-fontsize <float>]
-                    [--colors <str>]
+                    [--colors <str>] [--ladderize]
                     [--json]
 
                 Options
@@ -6369,6 +6444,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -6425,7 +6503,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -6483,6 +6561,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      output results as JSON
                 """
             ),
@@ -6556,7 +6637,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
 
                 Options
                 =====================================================
@@ -6616,6 +6697,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """

{phykit-2.1.48 → phykit-2.1.49}/phykit/services/tree/ancestral_reconstruction.py

@@ -66,6 +66,9 @@ class AncestralReconstruction(Tree):
         if tips_to_prune:
             tree_copy = self.prune_tree_using_taxa_list(tree_copy, tips_to_prune)
 
+        if self.plot_config.ladderize:
+            tree_copy.ladderize()
+
         # Label internal nodes
         node_labels = self._label_internal_nodes(tree_copy)
 
@@ -1206,6 +1209,9 @@ class AncestralReconstruction(Tree):
         if tips_to_prune:
             tree_copy = self.prune_tree_using_taxa_list(tree_copy, tips_to_prune)
 
+        if self.plot_config.ladderize:
+            tree_copy.ladderize()
+
         # Label internal nodes
         node_labels = self._label_internal_nodes(tree_copy)
 

{phykit-2.1.48 → phykit-2.1.49}/phykit/services/tree/concordance_asr.py

@@ -101,6 +101,9 @@ class ConcordanceAsr(Tree):
                 species_copy, tips_to_prune
             )
 
+        if self.plot_config.ladderize:
+            species_copy.ladderize()
+
         if self.method == "distribution":
             result = self._run_distribution(
                 species_copy, gene_trees, trait_values, all_taxa

{phykit-2.1.48 → phykit-2.1.49}/phykit/services/tree/cont_map.py

@@ -40,6 +40,9 @@ class ContMap(Tree):
         if tips_to_prune:
             tree_copy = self.prune_tree_using_taxa_list(tree_copy, tips_to_prune)
 
+        if self.plot_config.ladderize:
+            tree_copy.ladderize()
+
         # Label internal nodes
         node_labels = self._label_internal_nodes(tree_copy)
 

{phykit-2.1.48 → phykit-2.1.49}/phykit/services/tree/cophylo.py

@@ -84,6 +84,10 @@ class Cophylo(Tree):
         n_tips1 = len(tips1)
         n_tips2 = len(tips2)
 
+        if self.plot_config.ladderize:
+            tree1.ladderize()
+            tree2.ladderize()
+
         # Optimize tip ordering to reduce line crossings
         tree1_order, tree2_order = self._optimize_tip_order(
             tree1, tree2, mapping_valid

{phykit-2.1.48 → phykit-2.1.49}/phykit/services/tree/density_map.py

@@ -64,6 +64,9 @@ class DensityMap(Tree):
             for tip_name in tips_to_prune:
                 tree.prune(tip_name)
 
+        if self.plot_config.ladderize:
+            tree.ladderize()
+
         # Fit Q matrix using ER model
         Q, loglik = scm._fit_q_matrix(tree, tip_states, states, "ER")
         k = len(states)

{phykit-2.1.48 → phykit-2.1.49}/phykit/services/tree/discordance_asymmetry.py

@@ -85,6 +85,8 @@ class DiscordanceAsymmetry(Tree):
             self._output_text(branch_results, summary)
 
         if self.plot_output:
+            if self.plot_config.ladderize:
+                species_tree.ladderize()
             self._plot(species_tree, branch_results, self.plot_output,
                        shared_taxa=shared_taxa)
 

{phykit-2.1.48 → phykit-2.1.49}/phykit/services/tree/phylo_heatmap.py

@@ -43,6 +43,9 @@ class PhyloHeatmap(Tree):
         if tips_to_prune:
             tree = self.prune_tree_using_taxa_list(tree, tips_to_prune)
 
+        if self.plot_config.ladderize:
+            tree.ladderize()
+
         # Get tip order from tree traversal
         tip_order = [t.name for t in tree.get_terminals()]
 

{phykit-2.1.48 → phykit-2.1.49}/phykit/services/tree/quartet_pie.py

@@ -63,6 +63,9 @@ class QuartetPie(Tree):
             input_mode = "astral"
             n_gene_trees = 0
 
+        if self.plot_config.ladderize:
+            tree.ladderize()
+
         self._plot_quartet_pie(tree, proportions, self.output_path)
 
         if self.json_output:

{phykit-2.1.48 → phykit-2.1.49}/phykit/services/tree/rate_heterogeneity.py

@@ -108,6 +108,9 @@ class RateHeterogeneity(Tree):
 
         # Plot
         if self.plot_output:
+            if self.plot_config.ladderize:
+                tree_copy.ladderize()
+                parent_map = self._build_parent_map(tree_copy)
             self._plot_regime_tree(
                 tree_copy, branch_regimes, regimes, parent_map, self.plot_output
             )

{phykit-2.1.48 → phykit-2.1.49}/phykit/services/tree/stochastic_character_map.py

@@ -67,6 +67,9 @@ class StochasticCharacterMap(Tree):
             for tip_name in tips_to_prune:
                 tree.prune(tip_name)
 
+        if self.plot_config.ladderize:
+            tree.ladderize()
+
         # Fit Q matrix
         Q, loglik = self._fit_q_matrix(tree, tip_states, states, self.model)
         k = len(states)

phykit-2.1.49/phykit/version.py

@@ -0,0 +1 @@
+__version__ = "2.1.49"

{phykit-2.1.48 → phykit-2.1.49}/phykit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: phykit
-Version: 2.1.48
+Version: 2.1.49
 Home-page: https://github.com/jlsteenwyk/phykit
 Author: Jacob L. Steenwyk
 Author-email: jlsteenwyk@gmail.com
@@ -14,6 +14,22 @@ Classifier: Topic :: Scientific/Engineering
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
+Requires-Dist: biopython>=1.82
+Requires-Dist: matplotlib>=3.7.0
+Requires-Dist: numpy>=1.24.0
+Requires-Dist: scipy>=1.11.3
+Requires-Dist: scikit-learn>=1.4.2
+Requires-Dist: umap-learn>=0.5.0
+Requires-Dist: tqdm>=4.65.0
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
 
 <p align="center">
   <a href="https://github.com/jlsteenwyk/phykit">

phykit-2.1.48/phykit/version.py

@@ -1 +0,0 @@
-__version__ = "2.1.48"