phykit 2.1.41__tar.gz → 2.1.43__tar.gz

{phykit-2.1.41 → phykit-2.1.43}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phykit
-Version: 2.1.41
+Version: 2.1.43
 Home-page: https://github.com/jlsteenwyk/phykit
 Author: Jacob L. Steenwyk
 Author-email: jlsteenwyk@gmail.com

{phykit-2.1.41 → phykit-2.1.43}/phykit/cli_registry.py

@@ -116,6 +116,8 @@ ALIAS_TO_HANDLER: Dict[str, str] = {
     "quartet_net": "quartet_network",
     "qnet": "quartet_network",
     "nanuq": "quartet_network",
+    "qpie": "quartet_pie",
+    "quartet_pie_chart": "quartet_pie",
     "ltt": "ltt",
     "gamma_stat": "ltt",
     "gamma": "ltt",

phykit-2.1.43/phykit/helpers/quartet_utils.py

@@ -0,0 +1,136 @@
+"""
+Shared utilities for quartet concordance factor computation and ASTRAL parsing.
+
+Provides gene concordance factor (gCF/gDF1/gDF2) computation via the
+four-group bipartition decomposition, and parsing of ASTRAL -t 2
+q1/q2/q3 annotations from Newick node labels.
+"""
+from typing import Dict, List, Optional, Tuple
+
+from ..errors import PhykitUserError
+
+
+def canonical_split(tips: frozenset, all_taxa: frozenset) -> frozenset:
+    """Normalize a bipartition to a canonical frozenset-of-frozensets."""
+    complement = all_taxa - tips
+    return frozenset([tips, complement])
+
+
+def compute_gcf_per_node(
+    species_tree, gene_trees: list
+) -> Dict[int, Tuple[float, float, float, int, int, int]]:
+    """Compute (gCF, gDF1, gDF2, concordant, disc1, disc2) per internal node.
+
+    Uses the four-group decomposition (C1, C2, S, D) around each internal
+    branch to identify the concordant bipartition and the two NNI alternatives.
+
+    Returns dict mapping clade id -> (gCF, gDF1, gDF2, n_conc, n_d1, n_d2).
+    """
+    all_taxa = frozenset(t.name for t in species_tree.get_terminals())
+
+    # Build parent map
+    parent_map = {}
+    for clade in species_tree.find_clades(order="preorder"):
+        for child in clade.clades:
+            parent_map[id(child)] = clade
+
+    # Extract bipartitions from all gene trees
+    gt_splits = []
+    for gt in gene_trees:
+        gt_taxa = frozenset(t.name for t in gt.get_terminals())
+        shared = gt_taxa & all_taxa
+        if len(shared) < 4:
+            gt_splits.append(set())
+            continue
+        splits = set()
+        for clade in gt.get_nonterminals():
+            tips = frozenset(t.name for t in clade.get_terminals()) & shared
+            if len(tips) <= 1 or tips == shared:
+                continue
+            splits.add(canonical_split(tips, shared))
+        gt_splits.append(splits)
+
+    result = {}
+    for clade in species_tree.find_clades(order="preorder"):
+        if clade.is_terminal() or clade == species_tree.root:
+            continue
+
+        children = clade.clades
+        if len(children) < 2:
+            continue
+
+        C1 = frozenset(t.name for t in children[0].get_terminals())
+        C2 = frozenset(t.name for t in children[1].get_terminals())
+        # Handle polytomies: merge extra children into C2
+        for c in children[2:]:
+            C2 = C2 | frozenset(t.name for t in c.get_terminals())
+
+        remaining = all_taxa - C1 - C2
+        if not remaining:
+            continue
+
+        concordant_bp = canonical_split(C1 | C2, all_taxa)
+        nni1_bp = canonical_split(remaining | C2, all_taxa)
+        nni2_bp = canonical_split(C1 | remaining, all_taxa)
+
+        conc = sum(1 for s in gt_splits if concordant_bp in s)
+        d1 = sum(1 for s in gt_splits if nni1_bp in s)
+        d2 = sum(1 for s in gt_splits if nni2_bp in s)
+
+        total = conc + d1 + d2
+        if total > 0:
+            gcf = conc / total
+            gdf1 = d1 / total
+            gdf2 = d2 / total
+        else:
+            gcf, gdf1, gdf2 = 1.0, 0.0, 0.0
+
+        result[id(clade)] = (gcf, gdf1, gdf2, conc, d1, d2)
+
+    return result
+
+
+def parse_astral_annotations(
+    tree,
+) -> Dict[int, Tuple[float, float, float]]:
+    """Parse q1/q2/q3 annotations from ASTRAL -t 2 Newick node labels.
+
+    ASTRAL annotates internal nodes with formats like:
+      '[q1=0.5;q2=0.3;q3=0.2;f1=50;...]'
+      'q1=0.5;q2=0.3;q3=0.2'
+
+    Returns dict mapping clade id -> (q1, q2, q3).
+    Only nodes with valid q1/q2/q3 are included.
+    """
+    result = {}
+    for clade in tree.find_clades(order="preorder"):
+        if clade.is_terminal():
+            continue
+        label = clade.name or clade.comment or ""
+        qs = _parse_qs_from_label(str(label))
+        if qs is not None:
+            result[id(clade)] = qs
+    return result
+
+
+def _parse_qs_from_label(label: str) -> Optional[Tuple[float, float, float]]:
+    """Extract q1, q2, q3 from an ASTRAL node label string."""
+    s = label.strip("'\"").strip("[]")
+    q1 = q2 = q3 = None
+    for part in s.split(";"):
+        if "=" not in part:
+            continue
+        key, val = part.split("=", 1)
+        key = key.strip()
+        try:
+            if key == "q1":
+                q1 = float(val)
+            elif key == "q2":
+                q2 = float(val)
+            elif key == "q3":
+                q3 = float(val)
+        except ValueError:
+            continue
+    if q1 is not None and q2 is not None and q3 is not None:
+        return (q1, q2, q3)
+    return None

{phykit-2.1.41 → phykit-2.1.43}/phykit/phykit.py

@@ -242,6 +242,9 @@ class Phykit:
                 quartet_network (alias: quartet_net; qnet; nanuq)
                     - quartet-based network inference (NANUQ-style)
                       distinguishing ILS from hybridization
+                quartet_pie (alias: qpie; quartet_pie_chart)
+                    - phylogram with quartet concordance pie charts
+                      at internal nodes
                 ltt (alias: gamma_stat; gamma)
                     - lineage-through-time plot and Pybus & Harvey
                       gamma statistic for diversification rate testing
@@ -4524,6 +4527,107 @@ class Phykit:
         _add_json_argument(parser)
         _run_service(parser, argv, ConsensusNetwork)
 
+    @staticmethod
+    def quartet_pie(argv):
+        parser = _new_parser(
+            description=textwrap.dedent(
+                f"""\
+                {help_header}
+
+                Draw a phylogram with pie charts at internal nodes showing
+                quartet concordance proportions.
+
+                In native mode (-g provided), computes gene concordance
+                factors (gCF, gDF1, gDF2) from a species tree and gene
+                trees via bipartition matching. In ASTRAL mode (no -g),
+                parses q1/q2/q3 annotations from ASTRAL -t 2 output.
+
+                Pie slices show: concordant (blue), discordant alt 1
+                (red), discordant alt 2 (gray).
+
+                Aliases:
+                  quartet_pie, qpie, quartet_pie_chart
+                Command line interfaces:
+                  pk_quartet_pie, pk_qpie
+
+                Usage:
+                phykit quartet_pie -t <tree> [-g <gene_trees>] -o <output>
+                  [--annotate] [--json]
+                  [--fig-width <float>] [--fig-height <float>]
+                  [--dpi <int>] [--no-title] [--title <str>]
+                  [--legend-position <str>]
+                  [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
+                  [--title-fontsize <float>] [--axis-fontsize <float>]
+                  [--colors <str>]
+
+                Options
+                =====================================================
+                -t/--tree                   species tree file (required)
+
+                -g/--gene-trees             gene trees file, one Newick
+                                            tree per line (optional;
+                                            if omitted, ASTRAL -t 2
+                                            annotations are parsed)
+
+                -o/--output                 output figure path (required;
+                                            supports .png, .pdf, .svg)
+
+                --annotate                  show gCF/gDF values as text
+                                            near each pie chart
+
+                --fig-width                 figure width in inches
+                                            (auto-scaled if omitted)
+
+                --fig-height                figure height in inches
+                                            (auto-scaled if omitted)
+
+                --dpi                       resolution in DPI
+                                            (default: 300)
+
+                --no-title                  hide the plot title
+
+                --title                     custom title text
+
+                --legend-position           legend location (e.g.,
+                                            "upper right", "none")
+
+                --ylabel-fontsize           font size for tip labels;
+                                            0 to hide
+
+                --xlabel-fontsize           font size for x-axis labels;
+                                            0 to hide
+
+                --title-fontsize            font size for the title
+
+                --axis-fontsize             font size for axis labels
+
+                --colors                    comma-separated colors for
+                                            concordant, disc1, disc2
+                                            (default: "#2b8cbe,#d62728,
+                                            #969696")
+
+                --json                      optional argument to output
+                                            per-node concordance as JSON
+                """
+            ),
+        )
+        parser.add_argument(
+            "-t", "--tree", type=str, required=True, help=SUPPRESS, metavar=""
+        )
+        parser.add_argument(
+            "-g", "--gene-trees", type=str, required=False, default=None,
+            help=SUPPRESS, metavar=""
+        )
+        parser.add_argument(
+            "-o", "--output", type=str, required=True, help=SUPPRESS, metavar=""
+        )
+        parser.add_argument(
+            "--annotate", action="store_true", required=False, help=SUPPRESS
+        )
+        add_plot_arguments(parser)
+        _add_json_argument(parser)
+        _run_service(parser, argv, QuartetPie)
+
     @staticmethod
     def quartet_network(argv):
         parser = _new_parser(
@@ -6620,6 +6724,10 @@ def quartet_network(argv=None):
     Phykit.quartet_network(sys.argv[1:])
 
 
+def quartet_pie(argv=None):
+    Phykit.quartet_pie(sys.argv[1:])
+
+
 def ltt(argv=None):
     Phykit.ltt(sys.argv[1:])
 

{phykit-2.1.41 → phykit-2.1.43}/phykit/service_factories.py

@@ -84,6 +84,7 @@ ThresholdModel = _LazyServiceFactory("phykit.services.tree.threshold_model", "Th
 PolytomyTest = _LazyServiceFactory("phykit.services.tree.polytomy_test", "PolytomyTest")
 PrintTree = _LazyServiceFactory("phykit.services.tree.print_tree", "PrintTree")
 PruneTree = _LazyServiceFactory("phykit.services.tree.prune_tree", "PruneTree")
+QuartetPie = _LazyServiceFactory("phykit.services.tree.quartet_pie", "QuartetPie")
 RenameTreeTips = _LazyServiceFactory("phykit.services.tree.rename_tree_tips", "RenameTreeTips")
 FitDiscrete = _LazyServiceFactory("phykit.services.tree.fit_discrete", "FitDiscrete")
 KuhnerFelsensteinDistance = _LazyServiceFactory("phykit.services.tree.kf_distance", "KuhnerFelsensteinDistance")

{phykit-2.1.41 → phykit-2.1.43}/phykit/services/tree/__init__.py

@@ -28,6 +28,7 @@ _EXPORTS = {
     "PolytomyTest": "polytomy_test",
     "PrintTree": "print_tree",
     "PruneTree": "prune_tree",
+    "QuartetPie": "quartet_pie",
     "RenameTreeTips": "rename_tree_tips",
     "KuhnerFelsensteinDistance": "kf_distance",
     "RobinsonFouldsDistance": "rf_distance",

phykit-2.1.43/phykit/services/tree/quartet_pie.py

@@ -0,0 +1,305 @@
+"""
+Quartet pie chart visualization of gene tree concordance.
+
+Draws a phylogram with pie charts at internal nodes showing the
+proportion of gene trees supporting the species tree topology (gCF)
+versus the two NNI alternative topologies (gDF1, gDF2). Supports
+both native computation from gene trees and parsing of ASTRAL -t 2
+annotations.
+"""
+import sys
+from typing import Dict, List, Tuple
+
+import numpy as np
+
+from .base import Tree
+from ...helpers.json_output import print_json
+from ...helpers.plot_config import PlotConfig
+from ...helpers.quartet_utils import (
+    compute_gcf_per_node,
+    parse_astral_annotations,
+)
+from ...errors import PhykitUserError
+
+
+class QuartetPie(Tree):
+    def __init__(self, args) -> None:
+        parsed = self.process_args(args)
+        super().__init__(tree_file_path=parsed["tree_file_path"])
+        self.gene_trees_path = parsed["gene_trees_path"]
+        self.output_path = parsed["output_path"]
+        self.annotate = parsed["annotate"]
+        self.json_output = parsed["json_output"]
+        self.plot_config = parsed["plot_config"]
+
+    def run(self) -> None:
+        tree = self.read_tree_file()
+        self._validate_tree(tree)
+
+        if self.gene_trees_path:
+            # Native mode: compute gCF from gene trees
+            gene_trees = self._parse_gene_trees(self.gene_trees_path)
+            proportions = compute_gcf_per_node(tree, gene_trees)
+            input_mode = "native"
+            n_gene_trees = len(gene_trees)
+        else:
+            # ASTRAL mode: parse q1/q2/q3 from node labels
+            astral_props = parse_astral_annotations(tree)
+            if not astral_props:
+                raise PhykitUserError(
+                    [
+                        "No ASTRAL q1/q2/q3 annotations found in the tree.",
+                        "Either provide gene trees with -g, or use an ASTRAL",
+                        "-t 2 output tree with quartet annotations.",
+                    ],
+                    code=2,
+                )
+            # Convert to same format: (q1, q2, q3, 0, 0, 0) — no raw counts
+            proportions = {
+                cid: (q1, q2, q3, 0, 0, 0)
+                for cid, (q1, q2, q3) in astral_props.items()
+            }
+            input_mode = "astral"
+            n_gene_trees = 0
+
+        self._plot_quartet_pie(tree, proportions, self.output_path)
+
+        if self.json_output:
+            self._print_json(tree, proportions, input_mode, n_gene_trees)
+        else:
+            print(f"Quartet pie chart saved: {self.output_path}")
+
+    def process_args(self, args) -> Dict:
+        return dict(
+            tree_file_path=args.tree,
+            gene_trees_path=getattr(args, "gene_trees", None),
+            output_path=args.output,
+            annotate=getattr(args, "annotate", False),
+            json_output=getattr(args, "json", False),
+            plot_config=PlotConfig.from_args(args),
+        )
+
+    def _validate_tree(self, tree) -> None:
+        tips = list(tree.get_terminals())
+        if len(tips) < 4:
+            raise PhykitUserError(
+                ["Tree must have at least 4 tips for quartet analysis."],
+                code=2,
+            )
+        for clade in tree.find_clades():
+            if clade.branch_length is None and clade != tree.root:
+                clade.branch_length = 1e-8
+
+    def _parse_gene_trees(self, path: str) -> list:
+        from Bio import Phylo
+        try:
+            return list(Phylo.parse(path, "newick"))
+        except Exception:
+            raise PhykitUserError(
+                [
+                    f"Could not parse gene trees from {path}.",
+                    "File should contain one Newick tree per line.",
+                ],
+                code=2,
+            )
+
+    def _plot_quartet_pie(
+        self,
+        tree,
+        proportions: Dict[int, Tuple],
+        output_path: str,
+    ) -> None:
+        try:
+            import matplotlib
+            matplotlib.use("Agg")
+            import matplotlib.pyplot as plt
+            from matplotlib.patches import Patch
+        except ImportError:
+            print("matplotlib is required for quartet_pie. Install matplotlib and retry.")
+            raise SystemExit(2)
+
+        config = self.plot_config
+        tips = list(tree.get_terminals())
+        config.resolve(n_rows=len(tips), n_cols=None)
+
+        default_colors = ["#2b8cbe", "#d62728", "#969696"]
+        colors = config.merge_colors(default_colors)
+
+        # Build parent map
+        parent_map = {}
+        for clade in tree.find_clades(order="preorder"):
+            for child in clade.clades:
+                parent_map[id(child)] = clade
+
+        # Compute node positions
+        node_x = {}
+        node_y = {}
+
+        for i, tip in enumerate(tips):
+            node_y[id(tip)] = i
+
+        root = tree.root
+        for clade in tree.find_clades(order="preorder"):
+            if clade == root:
+                node_x[id(clade)] = 0.0
+            elif id(clade) in parent_map:
+                parent = parent_map[id(clade)]
+                t = clade.branch_length if clade.branch_length else 0.0
+                node_x[id(clade)] = node_x.get(id(parent), 0.0) + t
+
+        for clade in tree.find_clades(order="postorder"):
+            if not clade.is_terminal() and id(clade) not in node_y:
+                child_ys = [
+                    node_y[id(c)] for c in clade.clades if id(c) in node_y
+                ]
+                if child_ys:
+                    node_y[id(clade)] = np.mean(child_ys)
+                else:
+                    node_y[id(clade)] = 0.0
+
+        fig, ax = plt.subplots(figsize=(config.fig_width, config.fig_height))
+
+        # Draw branches
+        for clade in tree.find_clades(order="preorder"):
+            if clade == root:
+                continue
+            if id(clade) not in parent_map:
+                continue
+            parent = parent_map[id(clade)]
+            if id(parent) not in node_x or id(clade) not in node_x:
+                continue
+
+            x0 = node_x[id(parent)]
+            x1 = node_x[id(clade)]
+            y0 = node_y.get(id(parent), 0)
+            y1 = node_y.get(id(clade), 0)
+
+            ax.plot([x0, x1], [y1, y1], color="black", lw=1.5)
+            ax.plot([x0, x0], [y0, y1], color="black", lw=1.5)
+
+        # Pie charts at internal nodes — rendered as inset axes so they
+        # appear as perfect circles regardless of axis scaling, and are
+        # drawn above the phylogeny branches.
+        max_x = max(node_x.values()) if node_x else 1.0
+        n_tips = len(tips)
+        # Pie size in figure-fraction units (scales with figure, not data)
+        pie_size = min(0.06, 0.8 / max(n_tips, 1))
+
+        # Force a draw so transData is populated
+        fig.canvas.draw()
+
+        for clade in tree.find_clades(order="preorder"):
+            if clade.is_terminal() or clade == root:
+                continue
+            cid = id(clade)
+            if cid not in proportions:
+                continue
+
+            props = proportions[cid]
+            gcf, gdf1, gdf2 = props[0], props[1], props[2]
+            cx = node_x.get(cid, 0)
+            cy = node_y.get(cid, 0)
+
+            # Convert data coords to figure-fraction coords for the inset
+            disp = ax.transData.transform((cx, cy))
+            fig_coord = fig.transFigure.inverted().transform(disp)
+            fx, fy = fig_coord
+
+            # Create a small inset axes centered on the node
+            inset = fig.add_axes(
+                [fx - pie_size / 2, fy - pie_size / 2, pie_size, pie_size],
+                zorder=10,
+            )
+            wedge_vals = [gcf, gdf1, gdf2]
+            wedge_colors = [c for v, c in zip(wedge_vals, colors) if v > 1e-6]
+            wedge_vals = [v for v in wedge_vals if v > 1e-6]
+            if wedge_vals:
+                inset.pie(
+                    wedge_vals, colors=wedge_colors, startangle=90,
+                    wedgeprops={"edgecolor": "black", "linewidth": 0.5},
+                )
+            inset.set_aspect("equal")
+            inset.axis("off")
+
+            # Annotate with values if requested
+            if self.annotate:
+                ax.annotate(
+                    f"{gcf:.2f}/{gdf1:.2f}/{gdf2:.2f}",
+                    (cx, cy),
+                    textcoords="offset points",
+                    xytext=(8, 8),
+                    fontsize=6,
+                    color="black",
+                    zorder=11,
+                )
+
+        # Tip labels
+        offset = max_x * 0.03
+        label_fontsize = config.ylabel_fontsize if config.ylabel_fontsize and config.ylabel_fontsize > 0 else 9
+        for tip in tips:
+            ax.text(
+                node_x[id(tip)] + offset, node_y[id(tip)],
+                tip.name, va="center", fontsize=label_fontsize,
+            )
+
+        # Legend
+        legend_handles = [
+            Patch(facecolor=colors[0], edgecolor="black", linewidth=0.5,
+                  label="Concordant (gCF / q1)"),
+            Patch(facecolor=colors[1], edgecolor="black", linewidth=0.5,
+                  label="Discordant alt 1 (gDF1 / q2)"),
+            Patch(facecolor=colors[2], edgecolor="black", linewidth=0.5,
+                  label="Discordant alt 2 (gDF2 / q3)"),
+        ]
+        legend_loc = config.legend_position or "upper right"
+        if legend_loc != "none":
+            ax.legend(handles=legend_handles, loc=legend_loc, fontsize=8, frameon=True)
+
+        ax.set_xlabel("Branch length (subs/site)")
+        ax.set_yticks([])
+        ax.spines["top"].set_visible(False)
+        ax.spines["right"].set_visible(False)
+        ax.spines["left"].set_visible(False)
+
+        if config.show_title:
+            ax.set_title(
+                config.title or "Quartet Concordance Pie Chart",
+                fontsize=config.title_fontsize,
+            )
+        if config.axis_fontsize:
+            ax.xaxis.label.set_fontsize(config.axis_fontsize)
+
+        # Use constrained_layout=False since inset pie axes are incompatible
+        # with tight_layout; manual padding via subplots_adjust instead
+        fig.subplots_adjust(left=0.05, right=0.85, top=0.92, bottom=0.12)
+        fig.savefig(output_path, dpi=config.dpi, bbox_inches="tight")
+        plt.close(fig)
+
+    def _print_json(self, tree, proportions, input_mode, n_gene_trees):
+        nodes = []
+        for clade in tree.find_clades(order="preorder"):
+            if clade.is_terminal():
+                continue
+            cid = id(clade)
+            if cid not in proportions:
+                continue
+            props = proportions[cid]
+            tip_names = sorted(t.name for t in clade.get_terminals())
+            nodes.append({
+                "node_tips": tip_names,
+                "gCF": round(props[0], 4),
+                "gDF1": round(props[1], 4),
+                "gDF2": round(props[2], 4),
+                "concordant_count": props[3],
+                "disc1_count": props[4],
+                "disc2_count": props[5],
+            })
+
+        payload = {
+            "n_taxa": tree.count_terminals(),
+            "n_gene_trees": n_gene_trees,
+            "input_mode": input_mode,
+            "nodes": nodes,
+            "output_file": self.output_path,
+        }
+        print_json(payload)

phykit-2.1.43/phykit/version.py

@@ -0,0 +1 @@
+__version__ = "2.1.43"

{phykit-2.1.41 → phykit-2.1.43}/phykit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phykit
-Version: 2.1.41
+Version: 2.1.43
 Home-page: https://github.com/jlsteenwyk/phykit
 Author: Jacob L. Steenwyk
 Author-email: jlsteenwyk@gmail.com

{phykit-2.1.41 → phykit-2.1.43}/phykit.egg-info/SOURCES.txt

@@ -22,6 +22,7 @@ phykit/helpers/files.py
 phykit/helpers/json_output.py
 phykit/helpers/parallel.py
 phykit/helpers/plot_config.py
+phykit/helpers/quartet_utils.py
 phykit/helpers/stats_summary.py
 phykit/helpers/streaming.py
 phykit/services/__init__.py
@@ -93,6 +94,7 @@ phykit/services/tree/polytomy_test.py
 phykit/services/tree/print_tree.py
 phykit/services/tree/prune_tree.py
 phykit/services/tree/quartet_network.py
+phykit/services/tree/quartet_pie.py
 phykit/services/tree/rate_heterogeneity.py
 phykit/services/tree/relative_rate_test.py
 phykit/services/tree/rename_tree_tips.py

{phykit-2.1.41 → phykit-2.1.43}/phykit.egg-info/entry_points.txt

@@ -163,8 +163,11 @@ pk_ps = phykit.phykit:phylogenetic_signal
 pk_pt = phykit.phykit:print_tree
 pk_ptt = phykit.phykit:polytomy_test
 pk_qnet = phykit.phykit:quartet_network
+pk_qpie = phykit.phykit:quartet_pie
 pk_quartet_net = phykit.phykit:quartet_network
 pk_quartet_network = phykit.phykit:quartet_network
+pk_quartet_pie = phykit.phykit:quartet_pie
+pk_quartet_pie_chart = phykit.phykit:quartet_pie
 pk_rate_heterogeneity = phykit.phykit:rate_heterogeneity
 pk_rcv = phykit.phykit:rcv
 pk_rcvt = phykit.phykit:rcvt

{phykit-2.1.41 → phykit-2.1.43}/setup.py

@@ -202,6 +202,9 @@ setup(
             "pk_quartet_net = phykit.phykit:quartet_network",
             "pk_qnet = phykit.phykit:quartet_network",
             "pk_nanuq = phykit.phykit:quartet_network",
+            "pk_quartet_pie = phykit.phykit:quartet_pie",
+            "pk_qpie = phykit.phykit:quartet_pie",
+            "pk_quartet_pie_chart = phykit.phykit:quartet_pie",
             "pk_ltt = phykit.phykit:ltt",
             "pk_gamma_stat = phykit.phykit:ltt",
             "pk_gamma = phykit.phykit:ltt",

phykit-2.1.41/phykit/version.py

@@ -1 +0,0 @@
-__version__ = "2.1.41"