phytreon 0.2.1__tar.gz → 0.2.2__tar.gz

{phytreon-0.2.1 → phytreon-0.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phytreon
-Version: 0.2.1
+Version: 0.2.2
 Summary: Phylogenetic trees and publication figures in Python
 Author-email: Yiheng Du <yiheng.du@slu.edu>
 License: MIT License
@@ -285,7 +285,7 @@ fluently — every method returns the figure, so calls chain.
 
 | Method | Draws |
 |---|---|
-| `.branches(color=, size=)` | the tree skeleton (e.g. color by lineage) |
+| `.branches(color=, size=)` | the tree skeleton (`size=` sets line width globally; e.g. color by lineage) |
 | `.tip_labels()` / `.node_labels()` / `.support_labels()` | text labels |
 | `.tip_points()` / `.node_points()` / `.points()` | markers (color / size / shape mapping) |
 | `.highlight(node=)` / `.clade_label(...)` | shade / bracket a clade |

{phytreon-0.2.1 → phytreon-0.2.2}/README.md

@@ -230,7 +230,7 @@ fluently — every method returns the figure, so calls chain.
 
 | Method | Draws |
 |---|---|
-| `.branches(color=, size=)` | the tree skeleton (e.g. color by lineage) |
+| `.branches(color=, size=)` | the tree skeleton (`size=` sets line width globally; e.g. color by lineage) |
 | `.tip_labels()` / `.node_labels()` / `.support_labels()` | text labels |
 | `.tip_points()` / `.node_points()` / `.points()` | markers (color / size / shape mapping) |
 | `.highlight(node=)` / `.clade_label(...)` | shade / bracket a clade |

{phytreon-0.2.1 → phytreon-0.2.2}/phytreon/__init__.py

@@ -38,7 +38,7 @@ from .treeops import (
     robinson_foulds, prune_to_taxa,
 )
 
-__version__ = "0.2.1"
+__version__ = "0.2.2"
 
 __all__ = [
     "core", "layout", "infer", "comparative", "plot", "datasets", "treeops",

{phytreon-0.2.1 → phytreon-0.2.2}/phytreon/plot/figure.py

@@ -214,7 +214,15 @@ class TreeFigure:
 
     # -- composition methods (each returns self so calls chain) ----------
     def branches(self, color="black", size: float = 1.0) -> "TreeFigure":
+        """Draw (or restyle) the tree skeleton. ``size`` is a single width
+        applied to every branch in the tree -- there is no per-branch/data
+        variation. A figure only ever has one skeleton layer: calling this
+        again (e.g. to override the ``skeleton=True`` default added by
+        ``__init__``) replaces it in place rather than drawing a second,
+        overlapping set of lines.
+        """
         from .elements import _Branches
+        self._elements = [e for e in self._elements if not isinstance(e, _Branches)]
         return self.add(_Branches(color=color, size=size))
 
     def tip_labels(self, **kwargs) -> "TreeFigure":

{phytreon-0.2.1 → phytreon-0.2.2}/phytreon.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phytreon
-Version: 0.2.1
+Version: 0.2.2
 Summary: Phylogenetic trees and publication figures in Python
 Author-email: Yiheng Du <yiheng.du@slu.edu>
 License: MIT License
@@ -285,7 +285,7 @@ fluently — every method returns the figure, so calls chain.
 
 | Method | Draws |
 |---|---|
-| `.branches(color=, size=)` | the tree skeleton (e.g. color by lineage) |
+| `.branches(color=, size=)` | the tree skeleton (`size=` sets line width globally; e.g. color by lineage) |
 | `.tip_labels()` / `.node_labels()` / `.support_labels()` | text labels |
 | `.tip_points()` / `.node_points()` / `.points()` | markers (color / size / shape mapping) |
 | `.highlight(node=)` / `.clade_label(...)` | shade / bracket a clade |

{phytreon-0.2.1 → phytreon-0.2.2}/tests/test_smoke.py

@@ -79,6 +79,19 @@ def test_svg_export_keeps_editable_text(tmp_path):
     assert "Human" in " ".join(texts)     # a real tip label is editable text
 
 
+def test_branches_size_is_a_single_global_override():
+    # __init__(skeleton=True) already draws one branches layer; calling
+    # .branches(size=...) again must replace it, not stack a second layer
+    # on top (a second, differently-sized layer would leave a fringe of the
+    # first layer's colour/width showing through).
+    from phytreon.plot.elements import _Branches
+    tr = pt.datasets.primates()
+    p = pt.TreeFigure(tr).branches(size=0.3, color="red")
+    layers = [e for e in p._elements if isinstance(e, _Branches)]
+    assert len(layers) == 1
+    assert layers[0].size == 0.3 and layers[0].color == "red"
+
+
 def test_neighbor_joining():
     names = ["A", "B", "C", "D"]
     d = [[0, 5, 9, 9], [5, 0, 10, 10], [9, 10, 0, 8], [9, 10, 8, 0]]