phylustrator 0.2.0__tar.gz → 0.2.2__tar.gz

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

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phylustrator
-Version: 0.2.0
+Version: 0.2.2
 Summary: A composable plotter for evolutionary figures: phylogenetic trees, genomes, synteny and alignments
 Author-email: "Adrian A. Davin" <aaredav@gmail.com>
 License: MIT

{phylustrator-0.2.0 → phylustrator-0.2.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "phylustrator"
-version = "0.2.0"
+version = "0.2.2"
 description = "A composable plotter for evolutionary figures: phylogenetic trees, genomes, synteny and alignments"
 readme = "README.md"
 requires-python = ">=3.10"

{phylustrator-0.2.0 → phylustrator-0.2.2}/src/phylustrator/color.py

@@ -14,6 +14,24 @@ from typing import Callable, Iterable
 # figure that shows two characters at once needs two maps that cannot be mistaken for each other,
 # which is why more than one sequential map is here.
 _COLORMAPS: dict[str, list[tuple[int, int, int]]] = {
+    # magma stopped before it goes pale, the same trade as `viridis_dark` below in a different hue.
+    # Two line-safe ramps, not one, because a figure that shows two different quantities beside each
+    # other needs them to look different — one ramp used twice reads as one quantity shown twice.
+    "magma_dark": [
+        (0, 0, 4), (11, 9, 36), (32, 17, 75), (59, 15, 112),
+        (87, 21, 126), (114, 31, 129), (140, 41, 129), (168, 50, 125),
+        (196, 60, 117), (222, 73, 104), (241, 96, 93), (250, 127, 94),
+    ],
+    # viridis stopped before it goes pale. A sequential ramp on a *line* has a problem a heatmap does
+    # not: the light end of every perceptually-uniform map (viridis 222, magma 248, cividis 224 in
+    # luminance) vanishes against white at a few pixels wide, so the values that land there are
+    # invisible rather than merely faint. This keeps viridis's order and spacing and stops at its last
+    # clearly-drawn green, which costs a little range and makes every value readable.
+    "viridis_dark": [
+        (68, 1, 84), (72, 26, 108), (71, 47, 125), (65, 68, 135),
+        (57, 86, 140), (49, 104, 142), (42, 120, 142), (35, 136, 142),
+        (31, 152, 139), (34, 168, 132), (53, 183, 121), (84, 197, 104),
+    ],
     "viridis": [
         (68, 1, 84), (72, 26, 108), (71, 47, 125), (65, 68, 135),
         (57, 86, 140), (49, 104, 142), (42, 120, 142), (35, 136, 142),

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

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: phylustrator
-Version: 0.2.0
+Version: 0.2.2
 Summary: A composable plotter for evolutionary figures: phylogenetic trees, genomes, synteny and alignments
 Author-email: "Adrian A. Davin" <aaredav@gmail.com>
 License: MIT

{phylustrator-0.2.0 → phylustrator-0.2.2}/tests/test_figure.py

@@ -106,3 +106,18 @@ def test_color_history_limits_fix_the_scale_across_panels():
     own = (plot(tree) + color_history(narrow)).as_svg()
     fixed = (plot(tree) + color_history(narrow, limits=(0.0, 1.0))).as_svg()
     assert own != fixed
+
+
+def test_a_line_safe_colormap_never_goes_pale():
+    """Every perceptually-uniform sequential map ends near-white, which is fine for a heatmap and not
+    for a branch a few pixels wide: the values at that end vanish instead of being faint."""
+    from phylustrator.color import colormap_hex
+
+    def luminance(hex_colour):
+        r, g, b = (int(hex_colour[i:i + 2], 16) for i in (1, 3, 5))
+        return 0.2126 * r + 0.7152 * g + 0.0722 * b
+
+    for pale, safe in (("viridis", "viridis_dark"), ("magma", "magma_dark")):
+        assert max(luminance(c) for c in colormap_hex(pale)) > 200        # the problem
+        assert max(luminance(c) for c in colormap_hex(safe)) < 180        # the fix
+        assert colormap_hex(safe)[0] == colormap_hex(pale)[0]             # same dark end, same order