phykit 2.1.38__tar.gz → 2.1.40__tar.gz

{phykit-2.1.38 → phykit-2.1.40}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phykit
-Version: 2.1.38
+Version: 2.1.40
 Home-page: https://github.com/jlsteenwyk/phykit
 Author: Jacob L. Steenwyk
 Author-email: jlsteenwyk@gmail.com

{phykit-2.1.38 → phykit-2.1.40}/phykit/cli_registry.py

@@ -129,6 +129,9 @@ ALIAS_TO_HANDLER: Dict[str, str] = {
     "prune": "prune_tree",
     "rename_tree": "rename_tree_tips",
     "rename_tips": "rename_tree_tips",
+    "kuhner_felsenstein_distance": "kf_distance",
+    "kf_dist": "kf_distance",
+    "kf": "kf_distance",
     "robinson_foulds_distance": "rf_distance",
     "rf_dist": "rf_distance",
     "rf": "rf_distance",

phykit-2.1.40/phykit/helpers/plot_config.py

@@ -0,0 +1,207 @@
+import sys
+from dataclasses import dataclass, field
+from typing import List, Optional
+
+
+VALID_LEGEND_POSITIONS = frozenset([
+    "best", "upper right", "upper left", "lower left", "lower right",
+    "right", "center left", "center right", "lower center", "upper center",
+    "center", "none",
+])
+
+
+@dataclass
+class PlotConfig:
+    fig_width: Optional[float] = None
+    fig_height: Optional[float] = None
+    dpi: int = 300
+    show_title: bool = True
+    title: Optional[str] = None
+    legend_position: Optional[str] = None
+    ylabel_fontsize: Optional[float] = None
+    xlabel_fontsize: Optional[float] = None
+    title_fontsize: Optional[float] = None
+    axis_fontsize: Optional[float] = None
+    colors: Optional[List[str]] = None
+
+    def validate(self) -> None:
+        if self.fig_width is not None and self.fig_width <= 0:
+            print(f"Error: --fig-width must be positive, got {self.fig_width}")
+            sys.exit(2)
+        if self.fig_height is not None and self.fig_height <= 0:
+            print(f"Error: --fig-height must be positive, got {self.fig_height}")
+            sys.exit(2)
+        if self.dpi <= 0:
+            print(f"Error: --dpi must be positive, got {self.dpi}")
+            sys.exit(2)
+        for name, val in [
+            ("--ylabel-fontsize", self.ylabel_fontsize),
+            ("--xlabel-fontsize", self.xlabel_fontsize),
+            ("--title-fontsize", self.title_fontsize),
+            ("--axis-fontsize", self.axis_fontsize),
+        ]:
+            if val is not None and val < 0:
+                print(f"Error: {name} must be non-negative, got {val}")
+                sys.exit(2)
+        if (
+            self.legend_position is not None
+            and self.legend_position not in VALID_LEGEND_POSITIONS
+        ):
+            print(
+                f"Error: --legend-position '{self.legend_position}' is not valid. "
+                f"Choose from: {', '.join(sorted(VALID_LEGEND_POSITIONS))}"
+            )
+            sys.exit(2)
+
+    @classmethod
+    def auto_scale(cls, n_rows=None, n_cols=None) -> "PlotConfig":
+        # fig_height
+        if n_rows is not None:
+            raw_height = 3.0 + n_rows * 0.18
+            fig_height = max(5.0, min(200.0, raw_height))
+            if raw_height > 200.0:
+                print(
+                    f"Warning: computed figure height ({raw_height:.0f} in) "
+                    f"exceeds 200 in; capping at 200. Use --fig-height to override.",
+                    file=sys.stderr,
+                )
+        else:
+            fig_height = 8.0
+
+        # fig_width
+        if n_cols is not None:
+            fig_width = max(10.0, min(20.0, 8.0 + n_cols * 0.15))
+        else:
+            fig_width = 14.0
+
+        # ylabel_fontsize
+        if n_rows is not None:
+            if n_rows > 800:
+                ylabel_fontsize = 0.0
+            else:
+                ylabel_fontsize = max(3.0, min(7.0, 7.0 - (n_rows - 50) * 0.008))
+        else:
+            ylabel_fontsize = 7.0
+
+        # xlabel_fontsize
+        if n_cols is not None:
+            if n_cols > 60:
+                xlabel_fontsize = 0.0
+            else:
+                xlabel_fontsize = max(3.0, min(7.0, 7.0 - (n_cols - 20) * 0.1))
+        else:
+            xlabel_fontsize = 7.0
+
+        return cls(
+            fig_width=fig_width,
+            fig_height=fig_height,
+            ylabel_fontsize=ylabel_fontsize,
+            xlabel_fontsize=xlabel_fontsize,
+            title_fontsize=12.0,
+            axis_fontsize=10.0,
+        )
+
+    def resolve(self, n_rows=None, n_cols=None) -> "PlotConfig":
+        defaults = PlotConfig.auto_scale(n_rows, n_cols)
+        for fld in [
+            "fig_width", "fig_height", "ylabel_fontsize", "xlabel_fontsize",
+            "title_fontsize", "axis_fontsize",
+        ]:
+            if getattr(self, fld) is None:
+                setattr(self, fld, getattr(defaults, fld))
+        return self
+
+    def apply_to_figure(self, fig, ax, default_title, default_colors):
+        # Title
+        if self.show_title:
+            title_text = self.title if self.title is not None else default_title
+            ax.set_title(title_text, fontsize=self.title_fontsize)
+        else:
+            ax.set_title("")
+
+        # Legend
+        if self.legend_position is not None:
+            if self.legend_position == "none":
+                legend = ax.get_legend()
+                if legend is not None:
+                    legend.set_visible(False)
+            else:
+                legend = ax.get_legend()
+                if legend is not None:
+                    handles = legend.legend_handles
+                    labels = [t.get_text() for t in legend.get_texts()]
+                    legend.remove()
+                    ax.legend(handles=handles, labels=labels, loc=self.legend_position)
+
+        # Axis label font sizes
+        if self.axis_fontsize is not None:
+            ax.xaxis.label.set_fontsize(self.axis_fontsize)
+            ax.yaxis.label.set_fontsize(self.axis_fontsize)
+
+        # Y-axis tick labels
+        if self.ylabel_fontsize is not None:
+            if self.ylabel_fontsize == 0.0:
+                ax.set_yticklabels([])
+            else:
+                for label in ax.get_yticklabels():
+                    label.set_fontsize(self.ylabel_fontsize)
+
+        # X-axis tick labels
+        if self.xlabel_fontsize is not None:
+            if self.xlabel_fontsize == 0.0:
+                ax.set_xticklabels([])
+            else:
+                for label in ax.get_xticklabels():
+                    label.set_fontsize(self.xlabel_fontsize)
+
+        # Colors
+        return self.merge_colors(default_colors)
+
+    def merge_colors(self, defaults: List[str]) -> List[str]:
+        if self.colors is None:
+            return list(defaults)
+        result = list(defaults)
+        for i, user_color in enumerate(self.colors[:len(defaults)]):
+            if user_color:  # non-empty string overrides
+                result[i] = user_color
+        return result
+
+    @classmethod
+    def from_args(cls, args) -> "PlotConfig":
+        colors_str = getattr(args, "colors", None)
+        colors = None
+        if colors_str is not None:
+            colors = [c.strip() for c in colors_str.split(",")]
+
+        no_title = getattr(args, "no_title", False)
+
+        config = cls(
+            fig_width=getattr(args, "fig_width", None),
+            fig_height=getattr(args, "fig_height", None),
+            dpi=getattr(args, "dpi", 300),
+            show_title=not no_title,
+            title=getattr(args, "title", None),
+            legend_position=getattr(args, "legend_position", None),
+            ylabel_fontsize=getattr(args, "ylabel_fontsize", None),
+            xlabel_fontsize=getattr(args, "xlabel_fontsize", None),
+            title_fontsize=getattr(args, "title_fontsize", None),
+            axis_fontsize=getattr(args, "axis_fontsize", None),
+            colors=colors,
+        )
+        config.validate()
+        return config
+
+
+def add_plot_arguments(parser) -> None:
+    group = parser.add_argument_group("plot options")
+    group.add_argument("--fig-width", type=float, default=None, help="Figure width in inches (auto-scaled if omitted)")
+    group.add_argument("--fig-height", type=float, default=None, help="Figure height in inches (auto-scaled if omitted)")
+    group.add_argument("--dpi", type=int, default=300, help="Resolution in DPI (default: 300)")
+    group.add_argument("--no-title", action="store_true", default=False, help="Hide the plot title")
+    group.add_argument("--title", type=str, default=None, help="Custom title text")
+    group.add_argument("--legend-position", type=str, default=None, help="Legend location (e.g., 'upper right', 'none' to hide)")
+    group.add_argument("--ylabel-fontsize", type=float, default=None, help="Font size for y-axis labels; 0 to hide")
+    group.add_argument("--xlabel-fontsize", type=float, default=None, help="Font size for x-axis labels; 0 to hide")
+    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)")