phytreon 0.2.0__tar.gz → 0.2.2__tar.gz

{phytreon-0.2.0 → phytreon-0.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phytreon
-Version: 0.2.0
+Version: 0.2.2
 Summary: Phylogenetic trees and publication figures in Python
 Author-email: Yiheng Du <yiheng.du@slu.edu>
 License: MIT License
@@ -130,6 +130,7 @@ tr.join_data(meta, on="name")                    # attach metadata to tips
     .tip_labels()
     .support_labels()                            # node support values
 ).save("tree.pdf")                               # PDF/SVG/PNG -> matplotlib
+ # .save("tree.svg")                             # SVG: editable text -> drop into PowerPoint
  # .save("tree.html")                            # HTML        -> plotly (zoom/hover)
 ```
 
@@ -284,7 +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-0.2.0 → phytreon-0.2.2}/README.md

@@ -75,6 +75,7 @@ tr.join_data(meta, on="name")                    # attach metadata to tips
     .tip_labels()
     .support_labels()                            # node support values
 ).save("tree.pdf")                               # PDF/SVG/PNG -> matplotlib
+ # .save("tree.svg")                             # SVG: editable text -> drop into PowerPoint
  # .save("tree.html")                            # HTML        -> plotly (zoom/hover)
 ```
 
@@ -229,7 +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-0.2.0 → phytreon-0.2.2}/phytreon/__init__.py

@@ -38,7 +38,7 @@ from .treeops import (
     robinson_foulds, prune_to_taxa,
 )
 
-__version__ = "0.2.0"
+__version__ = "0.2.2"
 
 __all__ = [
     "core", "layout", "infer", "comparative", "plot", "datasets", "treeops",

{phytreon-0.2.0 → 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":
@@ -313,16 +321,30 @@ class TreeFigure:
     def save(self, path: str, dpi: int = 300, **kwargs) -> str:
         """Save to ``path``; backend chosen from the file extension.
 
-        ``dpi`` controls raster resolution; remaining kwargs (e.g. ``figsize``)
-        are forwarded to the renderer.
+        Supports ``.png`` / ``.jpg`` (raster), ``.pdf`` / ``.svg`` (vector),
+        and ``.html`` (interactive plotly). ``dpi`` controls raster
+        resolution; remaining kwargs (e.g. ``figsize``) are forwarded to the
+        renderer.
+
+        SVG output keeps every label as a real ``<text>`` element (rather than
+        outlined vector paths), so the figure stays fully editable after
+        importing it into PowerPoint (Insert → Picture, then Graphics Format →
+        Convert to Shape), Illustrator, Inkscape, etc. -- you can recolour,
+        move, and re-type the text.
         """
         ext = path.lower().rsplit(".", 1)[-1]
         if ext == "html":
             self.draw(backend="plotly", **kwargs).write_html(path)
         else:  # pdf/svg/png/jpg -> matplotlib
+            import matplotlib as mpl
             fig = self.draw(backend="mpl", **kwargs)
             extra = getattr(fig, "_phytreon_extra_artists", None)
-            fig.savefig(path, bbox_inches="tight", dpi=dpi, bbox_extra_artists=extra)
+            # for SVG, emit editable <text> (not glyph outlines) so labels
+            # remain real, re-typeable text in PowerPoint / vector editors
+            rc = {"svg.fonttype": "none"} if ext == "svg" else {}
+            with mpl.rc_context(rc):
+                fig.savefig(path, bbox_inches="tight", dpi=dpi,
+                            bbox_extra_artists=extra)
         return path
 
     def show(self, backend: str = "mpl", **kwargs):

{phytreon-0.2.0 → phytreon-0.2.2}/phytreon.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phytreon
-Version: 0.2.0
+Version: 0.2.2
 Summary: Phylogenetic trees and publication figures in Python
 Author-email: Yiheng Du <yiheng.du@slu.edu>
 License: MIT License
@@ -130,6 +130,7 @@ tr.join_data(meta, on="name")                    # attach metadata to tips
     .tip_labels()
     .support_labels()                            # node support values
 ).save("tree.pdf")                               # PDF/SVG/PNG -> matplotlib
+ # .save("tree.svg")                             # SVG: editable text -> drop into PowerPoint
  # .save("tree.html")                            # HTML        -> plotly (zoom/hover)
 ```
 
@@ -284,7 +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-0.2.0 → phytreon-0.2.2}/tests/test_smoke.py

@@ -65,6 +65,33 @@ def test_layouts_render_both_backends(tmp_path):
     assert (tmp_path / "circular.html").exists()
 
 
+def test_svg_export_keeps_editable_text(tmp_path):
+    # SVG must emit real <text> elements (svg.fonttype="none"), not outlined
+    # glyph paths -- so labels stay editable after importing into PowerPoint
+    # or a vector editor.
+    import re
+    tr = pt.datasets.primates()
+    out = tmp_path / "tree.svg"
+    pt.TreeFigure(tr).tip_labels().save(str(out))
+    svg = out.read_text(encoding="utf-8")
+    texts = re.findall(r"<text[^>]*>(.*?)</text>", svg, re.S)
+    assert texts, "SVG has no <text> elements -- labels were outlined to paths"
+    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]]