phykit 2.1.84__tar.gz → 2.1.87__tar.gz

{phykit-2.1.84 → phykit-2.1.87}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phykit
-Version: 2.1.84
+Version: 2.1.87
 Home-page: https://github.com/jlsteenwyk/phykit
 Author: Jacob L. Steenwyk
 Author-email: jlsteenwyk@gmail.com

{phykit-2.1.84 → phykit-2.1.87}/phykit/cli_registry.py

@@ -215,6 +215,9 @@ ALIAS_TO_HANDLER: Dict[str, str] = {
     "tree_space": "tree_space",
     "tspace": "tree_space",
     "tree_landscape": "tree_space",
+    "transfer_annotations": "transfer_annotations",
+    "transfer_annot": "transfer_annotations",
+    "annotate_tree": "transfer_annotations",
     "tgroups": "taxon_groups",
     "shared_taxa": "taxon_groups",
     "occupancy_filter": "occupancy_filter",

{phykit-2.1.84 → phykit-2.1.87}/phykit/phykit.py

@@ -308,6 +308,8 @@ class Phykit:
                     - prune taxa from a phylogeny
                 subtree_prune_regraft (alias: spr)
                     - generate all SPR rearrangements for a specified subtree
+                transfer_annotations (alias: transfer_annot; annotate_tree)
+                    - transfer node annotations between trees (e.g., wASTRAL to RAxML/IQ-TREE)
                 relative_rate_test (alias: rrt; tajima_rrt)
                     - Tajima's relative rate test for equal evolutionary
                       rates between two ingroup lineages
@@ -2823,6 +2825,14 @@ class Phykit:
                 --plot                      output path for concordance
                                             ASR plot
 
+                --plot-uncertainty          output path for uncertainty
+                                            plot showing the distribution
+                                            of ancestral estimates across
+                                            gene trees (distribution
+                                            method) or concordance
+                                            sources (weighted method)
+                                            as violin + boxplots
+
                 --missing-taxa              how to handle taxa mismatches:
                                             shared (default) or error
 
@@ -2900,6 +2910,10 @@ class Phykit:
             "--plot", type=str, required=False, default=None,
             help=SUPPRESS, metavar=""
         )
+        parser.add_argument(
+            "--plot-uncertainty", type=str, required=False, default=None,
+            help=SUPPRESS, metavar=""
+        )
         parser.add_argument(
             "--missing-taxa", type=str, required=False, default="shared",
             choices=["error", "shared"], help=SUPPRESS, metavar=""
@@ -6821,6 +6835,59 @@ class Phykit:
         _add_json_argument(parser)
         _run_service(parser, argv, Spr)
 
+    @staticmethod
+    def transfer_annotations(argv):
+        parser = _new_parser(
+            description=textwrap.dedent(
+                f"""\
+                {help_header}
+
+                Transfer internal node annotations from one tree onto
+                another. Matches nodes by bipartition (descendant taxa
+                set) and copies the annotation labels.
+
+                Typical use case: transfer wASTRAL support annotations
+                (q1/q2/q3, pp1, f1, etc.) from an annotated ASTRAL
+                tree onto a branch-length-optimized topology from
+                RAxML-NG, IQ-TREE, or any other tool. The output tree
+                has the target's branch lengths with the source's
+                annotations.
+
+                Aliases:
+                  transfer_annotations, transfer_annot, annotate_tree
+                Command line interfaces:
+                  pk_transfer_annotations, pk_transfer_annot, pk_annotate_tree
+
+                Usage:
+                phykit transfer_annotations --source <annotated_tree>
+                  --target <branch_length_tree> [-o/--output <file>]
+                  [--json]
+
+                Options
+                =====================================================
+                --source                    annotated tree file (e.g.,
+                                            wASTRAL output with
+                                            --support 3)
+
+                --target                    target tree file with
+                                            branch lengths to keep
+                                            (e.g., RAxML-NG or
+                                            IQ-TREE output)
+
+                -o/--output                 output file for the
+                                            annotated tree (default:
+                                            target file + ".annotated")
+
+                --json                      output results as JSON
+                """
+            ),
+        )
+        parser.add_argument("--source", type=str, required=True, help=SUPPRESS, metavar="")
+        parser.add_argument("--target", type=str, required=True, help=SUPPRESS, metavar="")
+        parser.add_argument("-o", "--output", type=str, default=None, help=SUPPRESS, metavar="")
+        _add_json_argument(parser)
+        _run_service(parser, argv, TransferAnnotations)
+
     @staticmethod
     def relative_rate_test(argv):
         parser = _new_parser(
@@ -9190,6 +9257,10 @@ def subtree_prune_regraft(argv=None):
     Phykit.subtree_prune_regraft(sys.argv[1:])
 
 
+def transfer_annotations(argv=None):
+    Phykit.transfer_annotations(sys.argv[1:])
+
+
 def relative_rate_test(argv=None):
     Phykit.relative_rate_test(sys.argv[1:])
 

{phykit-2.1.84 → phykit-2.1.87}/phykit/service_factories.py

@@ -108,6 +108,7 @@ RobinsonFouldsDistance = _LazyServiceFactory("phykit.services.tree.rf_distance",
 RootTree = _LazyServiceFactory("phykit.services.tree.root_tree", "RootTree")
 Saturation = _LazyServiceFactory("phykit.services.tree.saturation", "Saturation")
 Spr = _LazyServiceFactory("phykit.services.tree.spr", "Spr")
+TransferAnnotations = _LazyServiceFactory("phykit.services.tree.transfer_annotations", "TransferAnnotations")
 SpuriousSequence = _LazyServiceFactory("phykit.services.tree.spurious_sequence", "SpuriousSequence")
 TerminalBranchStats = _LazyServiceFactory("phykit.services.tree.terminal_branch_stats", "TerminalBranchStats")
 TipLabels = _LazyServiceFactory("phykit.services.tree.tip_labels", "TipLabels")

{phykit-2.1.84 → phykit-2.1.87}/phykit/services/tree/__init__.py

@@ -48,6 +48,7 @@ _EXPORTS = {
     "TipToTipDistance": "tip_to_tip_distance",
     "TipToTipNodeDistance": "tip_to_tip_node_distance",
     "TotalTreeLength": "total_tree_length",
+    "TransferAnnotations": "transfer_annotations",
     "Treeness": "treeness",
     "ThresholdModel": "threshold_model",
     "TreenessOverRCV": "treeness_over_rcv",

{phykit-2.1.84 → phykit-2.1.87}/phykit/services/tree/ancestral_reconstruction.py

@@ -1,5 +1,5 @@
-import copy
 import math
+import pickle
 import sys
 from typing import Dict, List, Tuple
 
@@ -78,7 +78,7 @@ class AncestralReconstruction(Tree):
         x = np.array([trait_values[name] for name in ordered_names])
 
         # Prune tree to shared taxa
-        tree_copy = copy.deepcopy(tree)
+        tree_copy = pickle.loads(pickle.dumps(tree, protocol=pickle.HIGHEST_PROTOCOL))
         tip_names_in_tree = [t.name for t in tree_copy.get_terminals()]
         tips_to_prune = [t for t in tip_names_in_tree if t not in trait_values]
         if tips_to_prune:
@@ -1368,7 +1368,7 @@ class AncestralReconstruction(Tree):
             trait_name = "trait"
 
         # Prune tree to shared taxa
-        tree_copy = copy.deepcopy(tree)
+        tree_copy = pickle.loads(pickle.dumps(tree, protocol=pickle.HIGHEST_PROTOCOL))
         tip_names_in_tree = [t.name for t in tree_copy.get_terminals()]
         tips_to_prune = [t for t in tip_names_in_tree if t not in tip_states]
         if tips_to_prune:

{phykit-2.1.84 → phykit-2.1.87}/phykit/services/tree/base.py

@@ -1,4 +1,5 @@
 import copy
+import pickle
 from typing import List
 from functools import lru_cache
 import os
@@ -80,12 +81,29 @@ class Tree(BaseService):
     def read_reference_tree_file(self):
         return self._read_tree_with_error(self.reference, "reference")
 
+    @staticmethod
+    def _fast_copy(tree):
+        """Copy a tree using pickle instead of deepcopy.
+
+        Avoids RecursionError on deeply nested trees (e.g., ladder-like
+        topologies with hundreds of cascading bifurcations) where
+        copy.deepcopy exceeds Python's default recursion limit.
+        Falls back to deepcopy for objects that can't be pickled (e.g.,
+        mocks in unit tests).
+        """
+        try:
+            return pickle.loads(pickle.dumps(tree, protocol=pickle.HIGHEST_PROTOCOL))
+        except (pickle.PicklingError, TypeError, AttributeError):
+            return copy.deepcopy(tree)
+
     def _read_tree_with_error(self, tree_path: str, attr_name: str):
         try:
             file_hash = self._get_file_hash(tree_path)
             tree = self._cached_tree_read(tree_path, self.tree_format, file_hash)
-            # Return a deep copy to prevent modifications to the cached tree
-            return copy.deepcopy(tree)
+            # Return a copy to prevent modifications to the cached tree.
+            # Uses pickle instead of deepcopy to avoid RecursionError on
+            # deeply nested trees.
+            return self._fast_copy(tree)
         except FileNotFoundError:
             path = getattr(self, attr_name)
             raise PhykitUserError(

{phykit-2.1.84 → phykit-2.1.87}/phykit/services/tree/branch_length_multiplier.py

@@ -1,5 +1,5 @@
 from typing import Dict
-import copy
+import pickle
 
 from Bio.Phylo import Newick
 
@@ -20,7 +20,7 @@ class BranchLengthMultiplier(Tree):
     def run(self) -> None:
         tree = self.read_tree_file()
         # Make a deep copy to avoid modifying the cached tree
-        tree_copy = copy.deepcopy(tree)
+        tree_copy = pickle.loads(pickle.dumps(tree, protocol=pickle.HIGHEST_PROTOCOL))
         scaled_count = self.multiply_branch_lengths_by_factor(tree_copy, self.factor)
         self.write_tree_file(tree_copy, self.output_file_path)
 

{phykit-2.1.84 → phykit-2.1.87}/phykit/services/tree/character_map.py

@@ -7,7 +7,7 @@ produces a phylogram/cladogram plot with annotated character changes.
 
 Uses the generalized parsimony utilities in phykit.helpers.parsimony_utils.
 """
-import copy
+import pickle
 from collections import Counter
 from typing import Dict, List, Optional, Set, Tuple
 
@@ -79,7 +79,7 @@ class CharacterMap(Tree):
 
     def run(self) -> None:
         tree = self.read_tree_file()
-        tree = copy.deepcopy(tree)
+        tree = pickle.loads(pickle.dumps(tree, protocol=pickle.HIGHEST_PROTOCOL))
 
         char_names, tip_states = self._parse_character_matrix(self.data_path)
         n_chars = len(char_names)

{phykit-2.1.84 → phykit-2.1.87}/phykit/services/tree/collapse_branches.py

@@ -1,5 +1,5 @@
 from typing import Dict
-import copy
+import pickle
 
 from .base import Tree
 from ...helpers.json_output import print_json
@@ -18,7 +18,7 @@ class CollapseBranches(Tree):
     def run(self):
         tree = self.read_tree_file()
         # Make a deep copy to avoid modifying the cached tree
-        tree_copy = copy.deepcopy(tree)
+        tree_copy = pickle.loads(pickle.dumps(tree, protocol=pickle.HIGHEST_PROTOCOL))
         initial_nonterminals = len(tree_copy.get_nonterminals())
         tree_copy.collapse_all(
             lambda c: c.confidence and c.confidence < self.support

{phykit-2.1.84 → phykit-2.1.87}/phykit/services/tree/concordance_asr.py

@@ -1,4 +1,3 @@
-import copy
 import math
 import pickle
 from io import StringIO
@@ -37,6 +36,7 @@ class ConcordanceAsr(Tree):
         self.method = parsed["method"]
         self.ci = parsed["ci"]
         self.plot_output = parsed["plot_output"]
+        self.plot_uncertainty = parsed["plot_uncertainty"]
         self.missing_taxa = parsed["missing_taxa"]
         self.json_output = parsed["json_output"]
         self.plot_config = parsed["plot_config"]
@@ -50,6 +50,7 @@ class ConcordanceAsr(Tree):
             method=getattr(args, "method", "weighted"),
             ci=getattr(args, "ci", False),
             plot_output=getattr(args, "plot", None),
+            plot_uncertainty=getattr(args, "plot_uncertainty", None),
             missing_taxa=getattr(args, "missing_taxa", "shared"),
             json_output=getattr(args, "json", False),
             plot_config=PlotConfig.from_args(args),
@@ -105,7 +106,7 @@ class ConcordanceAsr(Tree):
             )
 
         # Prune species tree to shared taxa with trait data
-        species_copy = copy.deepcopy(species_tree)
+        species_copy = pickle.loads(pickle.dumps(species_tree, protocol=pickle.HIGHEST_PROTOCOL))
         sp_tips = [t.name for t in species_copy.get_terminals()]
         tips_to_prune = [t for t in sp_tips if t not in trait_values]
         if tips_to_prune:
@@ -131,6 +132,12 @@ class ConcordanceAsr(Tree):
             )
             result["plot_output"] = self.plot_output
 
+        if self.plot_uncertainty:
+            self._plot_uncertainty(
+                species_copy, result, self.plot_uncertainty
+            )
+            result["plot_uncertainty"] = self.plot_uncertainty
+
         if self.json_output:
             print_json(result)
         else:
@@ -409,7 +416,7 @@ class ConcordanceAsr(Tree):
 
     def _run_asr_on_tree(self, tree, trait_values):
         """Run _fast_anc on one tree, return results keyed by descendant frozensets."""
-        tree_copy = copy.deepcopy(tree)
+        tree_copy = pickle.loads(pickle.dumps(tree, protocol=pickle.HIGHEST_PROTOCOL))
 
         # Prune to trait taxa
         tip_names = [t.name for t in tree_copy.get_terminals()]
@@ -586,6 +593,8 @@ class ConcordanceAsr(Tree):
                 "gdf2": float(gdf2),
                 "var_topology": float(between_var),
                 "var_parameter": float(within_var),
+                "source_estimates": [float(m) for m in means],
+                "source_weights": [float(w) for w in weights],
             }
 
             if self.ci:
@@ -658,6 +667,7 @@ class ConcordanceAsr(Tree):
                 "n_gene_trees_with_node": len(estimates_list),
                 "var_topology": float(np.var(estimates_list)),
                 "var_parameter": 0.0,
+                "gene_tree_estimates": estimates_list,
             }
 
             if self.ci and len(estimates_list) >= 2:
@@ -961,3 +971,149 @@ class ConcordanceAsr(Tree):
         fig.savefig(output_path, dpi=config.dpi, bbox_inches="tight")
         plt.close(fig)
         print(f"Saved concordance ASR plot: {output_path}")
+
+    # ------------------------------------------------------------------
+    # Uncertainty plot
+    # ------------------------------------------------------------------
+
+    def _plot_uncertainty(self, species_tree, result, output_path) -> None:
+        """Violin + boxplot showing distribution of ancestral estimates.
+
+        For the distribution method: per-gene-tree estimates.
+        For the weighted method: concordant + discordant source estimates.
+        """
+        try:
+            import matplotlib
+            matplotlib.use("Agg")
+            import matplotlib.pyplot as plt
+        except ImportError:
+            print("matplotlib is required for plotting.")
+            return
+
+        anc = result.get("ancestral_estimates", {})
+        if not anc:
+            return
+
+        config = self.plot_config
+
+        # Collect data: (node_label, estimates_list, gcf, estimate)
+        node_data = []
+        for clade in species_tree.find_clades(order="preorder"):
+            if clade.is_terminal():
+                continue
+            # Match by descendants
+            desc = sorted(t.name for t in clade.get_terminals())
+            for label, entry in anc.items():
+                if entry.get("descendants") == desc:
+                    if result["method"] == "distribution":
+                        estimates = entry.get("gene_tree_estimates", [])
+                    else:
+                        estimates = entry.get("source_estimates", [])
+                    if len(estimates) >= 2:
+                        # Short label for display
+                        if len(desc) <= 2:
+                            short = f"({', '.join(desc)})"
+                        else:
+                            short = f"({desc[0]}, ..., {desc[-1]})"
+                        node_data.append((
+                            short, estimates,
+                            entry.get("gcf", 1.0),
+                            entry.get("estimate", 0.0),
+                        ))
+                    break
+
+        if not node_data:
+            print("No nodes with enough estimates for uncertainty plot.")
+            return
+
+        # Sort by weighted/mean estimate
+        node_data.sort(key=lambda x: x[3])
+
+        labels = [d[0] for d in node_data]
+        data = [d[1] for d in node_data]
+        gcfs = [d[2] for d in node_data]
+
+        n_nodes = len(node_data)
+        fig_h = max(4, n_nodes * 0.5)
+        fig_w = config.fig_width or 8
+        if config.fig_height:
+            fig_h = config.fig_height
+        fig, ax = plt.subplots(figsize=(fig_w, fig_h))
+
+        positions = list(range(n_nodes))
+
+        # Color by gCF: high concordance = blue, low = red
+        gcf_colors = []
+        for g in gcfs:
+            if g >= 0.7:
+                gcf_colors.append("#2b8cbe")
+            elif g >= 0.4:
+                gcf_colors.append("#969696")
+            else:
+                gcf_colors.append("#d62728")
+
+        # Violin plots (horizontal)
+        vp = ax.violinplot(
+            data, positions=positions, vert=False,
+            showmeans=False, showmedians=False, showextrema=False,
+        )
+        for i, body in enumerate(vp["bodies"]):
+            body.set_facecolor(gcf_colors[i])
+            body.set_alpha(0.3)
+            body.set_edgecolor(gcf_colors[i])
+
+        # Boxplots
+        bp = ax.boxplot(
+            data, positions=positions, vert=False,
+            widths=0.3, patch_artist=True, showfliers=True, zorder=3,
+        )
+        for i, box in enumerate(bp["boxes"]):
+            box.set_facecolor(gcf_colors[i])
+            box.set_alpha(0.6)
+        for element in ["whiskers", "caps", "medians"]:
+            for line in bp[element]:
+                line.set_color("black")
+
+        # Mean markers
+        for i, d in enumerate(data):
+            mean_val = np.mean(d)
+            ax.plot(
+                mean_val, i, "D", color="white",
+                markeredgecolor="black", markersize=5, zorder=4,
+            )
+
+        ax.set_yticks(positions)
+        ax.set_yticklabels(labels, fontsize=7)
+        xlabel = "Ancestral state estimate"
+        ax.set_xlabel(xlabel)
+
+        ax.spines["top"].set_visible(False)
+        ax.spines["right"].set_visible(False)
+
+        # Legend for gCF colors
+        from matplotlib.patches import Patch
+        legend_handles = [
+            Patch(facecolor="#2b8cbe", alpha=0.6, label="gCF >= 0.7"),
+            Patch(facecolor="#969696", alpha=0.6, label="0.4 <= gCF < 0.7"),
+            Patch(facecolor="#d62728", alpha=0.6, label="gCF < 0.4"),
+        ]
+        ax.legend(
+            handles=legend_handles, loc="lower right",
+            fontsize=7, title="Concordance", title_fontsize=8,
+        )
+
+        method_label = (
+            "gene trees" if result["method"] == "distribution"
+            else "concordance sources"
+        )
+        if config.show_title:
+            ax.set_title(
+                config.title
+                or f"Ancestral state uncertainty across {method_label}",
+                fontsize=config.title_fontsize,
+            )
+
+        fig.tight_layout()
+        fig.savefig(output_path, dpi=config.dpi, bbox_inches="tight")
+        plt.close(fig)
+        print(f"Saved uncertainty plot: {output_path}")

{phykit-2.1.84 → phykit-2.1.87}/phykit/services/tree/cont_map.py

@@ -1,5 +1,5 @@
-import copy
 import math
+import pickle
 import sys
 from typing import Dict, List, Tuple
 
@@ -47,7 +47,7 @@ class ContMap(Tree):
         x = np.array([trait_values[name] for name in ordered_names])
 
         # Prune tree to shared taxa
-        tree_copy = copy.deepcopy(tree)
+        tree_copy = pickle.loads(pickle.dumps(tree, protocol=pickle.HIGHEST_PROTOCOL))
         tip_names_in_tree = [t.name for t in tree_copy.get_terminals()]
         tips_to_prune = [t for t in tip_names_in_tree if t not in trait_values]
         if tips_to_prune:

{phykit-2.1.84 → phykit-2.1.87}/phykit/services/tree/independent_contrasts.py

@@ -7,7 +7,7 @@ contrast (standardized difference), producing n-1 contrasts for n tips.
 
 Cross-validated against R's ape::pic().
 """
-import copy
+import pickle
 import sys
 from typing import Dict, List, Tuple
 
@@ -27,7 +27,7 @@ class IndependentContrasts(Tree):
 
     def run(self) -> None:
         tree = self.read_tree_file()
-        tree = copy.deepcopy(tree)
+        tree = pickle.loads(pickle.dumps(tree, protocol=pickle.HIGHEST_PROTOCOL))
         self.validate_tree(tree, min_tips=3, assign_default_branch_length=1e-8, context="independent contrasts")
 
         tree_tips = [t.name for t in tree.get_terminals()]

{phykit-2.1.84 → phykit-2.1.87}/phykit/services/tree/internode_labeler.py

@@ -1,5 +1,5 @@
 from typing import Dict
-import copy
+import pickle
 
 from Bio.Phylo import Newick
 
@@ -19,7 +19,7 @@ class InternodeLabeler(Tree):
     def run(self):
         tree = self.read_tree_file()
         # Make a deep copy to avoid modifying the cached tree
-        tree_copy = copy.deepcopy(tree)
+        tree_copy = pickle.loads(pickle.dumps(tree, protocol=pickle.HIGHEST_PROTOCOL))
         labeled_count = self.add_labels_to_tree(tree_copy)
         self.write_tree_file(tree_copy, self.output_file_path)
 

{phykit-2.1.84 → phykit-2.1.87}/phykit/services/tree/last_common_ancestor_subtree.py

@@ -1,5 +1,5 @@
+import pickle
 import sys
-import copy
 from typing import Dict
 
 from .base import Tree
@@ -21,7 +21,7 @@ class LastCommonAncestorSubtree(Tree):
     def run(self):
         tree = self.read_tree_file()
         # Make a deep copy to avoid issues with cached tree modifications
-        tree_copy = copy.deepcopy(tree)
+        tree_copy = pickle.loads(pickle.dumps(tree, protocol=pickle.HIGHEST_PROTOCOL))
         try:
             taxa = read_single_column_file_to_list(self.list_of_taxa)
         except FileNotFoundError:

{phykit-2.1.84 → phykit-2.1.87}/phykit/services/tree/ou_shift_detection.py

@@ -1,4 +1,4 @@
-import copy
+import pickle
 import sys
 from typing import Dict, List, Tuple
 
@@ -61,7 +61,7 @@ class OUShiftDetection(Tree):
         shared = set(traits.keys())
 
         # Prune tree to shared taxa
-        tree_copy = copy.deepcopy(tree)
+        tree_copy = pickle.loads(pickle.dumps(tree, protocol=pickle.HIGHEST_PROTOCOL))
         tip_names_in_tree = [t.name for t in tree_copy.get_terminals()]
         to_prune = [t for t in tip_names_in_tree if t not in shared]
         if to_prune:

{phykit-2.1.84 → phykit-2.1.87}/phykit/services/tree/ouwie.py

@@ -1,4 +1,4 @@
-import copy
+import pickle
 import sys
 from typing import Dict, List, Tuple
 
@@ -44,7 +44,7 @@ class OUwie(Tree):
         traits = {k: traits[k] for k in shared}
         regime_assignments = {k: regime_assignments[k] for k in shared}
 
-        tree_copy = copy.deepcopy(tree)
+        tree_copy = pickle.loads(pickle.dumps(tree, protocol=pickle.HIGHEST_PROTOCOL))
         tip_names_in_tree = [t.name for t in tree_copy.get_terminals()]
         tips_to_prune = [t for t in tip_names_in_tree if t not in shared]
         if tips_to_prune:

{phykit-2.1.84 → phykit-2.1.87}/phykit/services/tree/parsimony_score.py

@@ -8,7 +8,7 @@ total is summed.
 
 Cross-validated against R's phangorn::parsimony().
 """
-import copy
+import pickle
 from typing import Dict, List
 
 from Bio import SeqIO
@@ -28,7 +28,7 @@ class ParsimonyScore(Tree):
 
     def run(self) -> None:
         tree = self.read_tree_file()
-        tree = copy.deepcopy(tree)
+        tree = pickle.loads(pickle.dumps(tree, protocol=pickle.HIGHEST_PROTOCOL))
         self.validate_tree(tree, min_tips=3, context="parsimony score")
         self._resolve_polytomies(tree)
 

{phykit-2.1.84 → phykit-2.1.87}/phykit/services/tree/phenogram.py

@@ -1,5 +1,5 @@
-import copy
 import math
+import pickle
 import sys
 from typing import Dict, List, Tuple
 
@@ -34,7 +34,7 @@ class Phenogram(Tree):
         x = np.array([trait_values[name] for name in ordered_names])
 
         # Prune tree to shared taxa
-        tree_copy = copy.deepcopy(tree)
+        tree_copy = pickle.loads(pickle.dumps(tree, protocol=pickle.HIGHEST_PROTOCOL))
         tip_names_in_tree = [t.name for t in tree_copy.get_terminals()]
         tips_to_prune = [t for t in tip_names_in_tree if t not in trait_values]
         if tips_to_prune:

{phykit-2.1.84 → phykit-2.1.87}/phykit/services/tree/phylo_logistic.py

@@ -1,4 +1,4 @@
-import copy
+import pickle
 from typing import Dict, List, Tuple
 
 import numpy as np
@@ -156,7 +156,7 @@ class PhyloLogistic(Tree):
             return vcv, diag_corr
 
         # Transform branch lengths
-        tree_t = copy.deepcopy(tree)
+        tree_t = pickle.loads(pickle.dumps(tree, protocol=pickle.HIGHEST_PROTOCOL))
         for clade in tree_t.find_clades():
             if clade.branch_length is not None and clade.branch_length > 0:
                 bl = clade.branch_length

{phykit-2.1.84 → phykit-2.1.87}/phykit/services/tree/phylogenetic_ordination.py

@@ -1,5 +1,5 @@
-import copy
 import os
+import pickle
 from typing import Dict, List, Tuple
 
 import numpy as np
@@ -346,7 +346,7 @@ class PhylogeneticOrdination(Tree):
     def _reconstruct_ancestral_scores(
         self, tree, scores: np.ndarray, ordered_names: List[str]
     ) -> Tuple[Dict, Dict]:
-        tree_copy = copy.deepcopy(tree)
+        tree_copy = pickle.loads(pickle.dumps(tree, protocol=pickle.HIGHEST_PROTOCOL))
 
         tip_names_in_tree = [t.name for t in tree_copy.get_terminals()]
         tips_to_prune = [t for t in tip_names_in_tree if t not in ordered_names]

{phykit-2.1.84 → phykit-2.1.87}/phykit/services/tree/phylomorphospace.py

@@ -1,5 +1,5 @@
-import copy
 import os
+import pickle
 from typing import Dict, List, Tuple
 
 import numpy as np
@@ -136,7 +136,7 @@ class Phylomorphospace(Tree):
     def _reconstruct_ancestral_scores(
         self, tree, scores: np.ndarray, ordered_names: List[str]
     ) -> Tuple[Dict, Dict, object]:
-        tree_copy = copy.deepcopy(tree)
+        tree_copy = pickle.loads(pickle.dumps(tree, protocol=pickle.HIGHEST_PROTOCOL))
 
         tip_names_in_tree = [t.name for t in tree_copy.get_terminals()]
         tips_to_prune = [t for t in tip_names_in_tree if t not in ordered_names]