phylustrator 0.3.0__tar.gz → 0.3.1__tar.gz

{phylustrator-0.3.0/src/phylustrator.egg-info → phylustrator-0.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phylustrator
-Version: 0.3.0
+Version: 0.3.1
 Summary: A composable plotter for evolutionary figures: phylogenetic trees, genomes, synteny and alignments
 Author-email: "Adrian A. Davin" <aaredav@gmail.com>
 License: MIT

{phylustrator-0.3.0 → phylustrator-0.3.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "phylustrator"
-version = "0.3.0"
+version = "0.3.1"
 description = "A composable plotter for evolutionary figures: phylogenetic trees, genomes, synteny and alignments"
 readme = "README.md"
 requires-python = ">=3.10"

{phylustrator-0.3.0 → phylustrator-0.3.1}/src/phylustrator/trees/layers/guides.py

@@ -100,15 +100,35 @@ def legend(title: str = "", *, swatch: float | None = None, size: float | None =
 
 def time_marker(*times, color: str = "#444444", width: float = 1.5, dash: bool = True,
                 label: str | None = None, label_size: float | None = None):
-    """Vertical reference line(s) crossing the tree at the given distance/time value(s) — e.g. to mark
-    a mass-extinction moment or a rate shift. Rectangular only (distance maps to x). ``label`` (if
-    given) is written above the first line."""
+    """Reference marker(s) at the given distance/time value(s) — e.g. a mass-extinction moment or a
+    rate shift. Rectangular: a vertical line crossing the tree. Radial: a circle at that distance
+    from the centre, which is what a depth threshold looks like on a tree too big to read as a
+    rectangle. The unrooted layout places branches by angle and has no distance-from-origin axis, so
+    it raises rather than drawing nothing. ``label`` (if given) is written above the first marker.
+
+    Times come on the stem-inclusive scale of the rectangular layout, the same scale
+    ``branch_events`` takes. The radial layout starts at the crown, so the stem comes off there."""
 
     def layer(canvas, tree, layout, style):
-        if layout.kind != "rectangular":
+        ls = label_size if label_size is not None else style.font_size
+        if layout.kind == "unrooted":
+            raise ValueError("time_marker needs a layout with a distance axis, and the unrooted "
+                             "layout has none: it places branches by angle, so a distance from the "
+                             "origin is not a place on it. Use rectangular or radial.")
+        if layout.kind == "radial":
+            # the radial layout drops the stem and starts at the crown, so shift the times by it —
+            # branch_events shifts the same way, for the same reason
+            stem = float(tree.root.length or 0.0)
+            for i, t in enumerate(times):
+                r = t - stem
+                if r < 0:
+                    raise ValueError(f"time_marker at {t:g} falls inside the root stem, which the "
+                                     f"radial layout does not draw: its centre is the crown, at {stem:g}")
+                canvas.data_ring(r, color, width, dash=dash)
+                if label and i == 0:
+                    canvas.text(0.0, -r, label, dy=-8, anchor="middle", color=color, size=ls)
             return
         y0, y1 = layout.ylim
-        ls = label_size if label_size is not None else style.font_size
         for i, t in enumerate(times):
             canvas.line(t, y0, t, y1, color, width, dash=dash)
             if label and i == 0:

{phylustrator-0.3.0 → phylustrator-0.3.1/src/phylustrator.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phylustrator
-Version: 0.3.0
+Version: 0.3.1
 Summary: A composable plotter for evolutionary figures: phylogenetic trees, genomes, synteny and alignments
 Author-email: "Adrian A. Davin" <aaredav@gmail.com>
 License: MIT

{phylustrator-0.3.0 → phylustrator-0.3.1}/tests/test_figure.py

@@ -1,5 +1,6 @@
 """Figure: the skeleton renders to SVG, and the stem shows up as one extra branch."""
 
+import math
 import re
 
 import pytest
@@ -15,6 +16,7 @@ from phylustrator.trees import (
     note,
     plot,
     rubberband,
+    time_marker,
 )
 
 
@@ -231,3 +233,59 @@ def test_rubberband_survives_a_lopsided_tree_and_stays_smooth():
                + rubberband(pops, palette=palette, gap=8.0, smooth=smooth)).as_svg()
         assert svg.count("<path") > 0
         assert "#207080" in svg and "#c77bad" in svg
+
+
+# --- time_marker across the layouts (issue #8) ------------------------------------------------
+
+_MARKER_TREE = "((((A:1,B:1)F:1,C:2)G:1,D:3)H:1,E:4)R;"
+
+
+def _circle(svg):
+    """The (cx, cy, r) of the one circle in the figure — the radial marker."""
+    found = re.findall(r'<circle cx="([-\d.]+)" cy="([-\d.]+)" r="([-\d.]+)"', svg)
+    assert len(found) == 1, f"expected one circle, found {len(found)}"
+    return tuple(float(v) for v in found[0])
+
+
+def test_time_marker_draws_in_rectangular_and_radial():
+    """It rendered nothing at all in radial, and said nothing about it."""
+    tree = loads(_MARKER_TREE)
+    for layout in ("rectangular", "radial"):
+        svg = (plot(tree, layout=layout) + time_marker(2.0, color="#D55E00", width=4)).as_svg()
+        assert "#D55E00" in svg, f"the marker is missing from the {layout} layout"
+
+
+def test_the_radial_marker_is_a_circle_through_the_nodes_at_that_distance():
+    tree = loads(_MARKER_TREE)
+    fig = plot(tree, layout="radial") + time_marker(2.0, color="#D55E00")
+    cx, cy, r = _circle(fig.as_svg())
+    at_two = [n for n in fig.geometry().nodes if n.name == "G"][0]      # G sits at distance 2
+    assert math.hypot(at_two.x - cx, at_two.y - cy) == pytest.approx(r)
+    assert r > 0
+
+
+def test_the_radial_marker_takes_the_stem_off_the_time():
+    """The radial layout starts at the crown, as branch_events already assumed for its events."""
+    tree = loads("((((A:1,B:1)F:1,C:2)G:1,D:3)H:1,E:4)R:1.5;")
+    fig = plot(tree, layout="radial") + time_marker(3.5)                # 2.0 past the crown
+    cx, cy, r = _circle(fig.as_svg())
+    at_two = [n for n in fig.geometry().nodes if n.name == "G"][0]
+    assert math.hypot(at_two.x - cx, at_two.y - cy) == pytest.approx(r)
+
+
+def test_the_radial_marker_keeps_its_dash():
+    tree = loads(_MARKER_TREE)
+    assert "stroke-dasharray" in (plot(tree, layout="radial") + time_marker(2.0)).as_svg()
+    assert "stroke-dasharray" not in (plot(tree, layout="radial")
+                                      + time_marker(2.0, dash=False)).as_svg()
+
+
+def test_time_marker_refuses_the_unrooted_layout():
+    """A distance from the origin is not a place on an equal-angle layout. Say so, do not skip."""
+    with pytest.raises(ValueError, match="unrooted"):
+        (plot(loads(_MARKER_TREE), layout="unrooted") + time_marker(2.0)).as_svg()
+
+
+def test_time_marker_refuses_a_time_the_radial_layout_cannot_show():
+    with pytest.raises(ValueError, match="stem"):
+        (plot(loads("((A:1,B:1)F:1,C:2)R:1.5;"), layout="radial") + time_marker(0.5)).as_svg()