Fix AttributeError: 'LayoutLine' object has no attribute 'color' (#835)

* Initial plan

* Initial plan: fix AttributeError in assign_array and blank line handling in synteny Layout

Co-authored-by: tanghaibao <106987+tanghaibao@users.noreply.github.com>

* Fix AttributeError in assign_array and blank line handling in synteny Layout

Co-authored-by: tanghaibao <106987+tanghaibao@users.noreply.github.com>

* Style fixes by Black

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: tanghaibao <106987+tanghaibao@users.noreply.github.com>

Author: Copilot

.gitignore

@@ -74,3 +74,5 @@ src/jcvi/version.py
 # Test output files
 tests/**/*.synfind
 tests/**/*.lifted.anchors
+tests/**/*.pdf
+tests/**/grape_peach.bed

src/jcvi/graphics/base.py

@@ -132,7 +132,7 @@ def __init__(self, filename):
     def assign_array(self, attrib, array):
         assert len(array) == len(self)
         for x, c in zip(self, array):
-            if not getattr(x, attrib):
+            if not getattr(x, attrib, None):
                 setattr(x, attrib, c)
 
     def assign_colors(self, seed: Optional[int] = None):

src/jcvi/graphics/synteny.py

@@ -99,6 +99,9 @@ def __init__(self, filename, delimiter=",", seed: Optional[int] = None):
         fp = open(filename, encoding="utf-8")
         self.edges = []
         for row in fp:
+            row = row.strip()
+            if not row:
+                continue
             if row[0] == "#":
                 continue
             if row[0] == "e":

tests/graphics/test_base.py

@@ -55,3 +55,52 @@ def test_update_figname(figname, format, expected):
     from jcvi.graphics.base import update_figname
 
     assert update_figname(figname, format) == expected, "Expect {}".format(expected)
+
+
+def test_assign_array_missing_attribute():
+    """Test that assign_array works when the attribute is not set on the object.
+
+    This guards against AttributeError: 'LayoutLine' object has no attribute 'color'
+    when an object without the attribute is present in the layout list.
+    """
+    from jcvi.graphics.base import AbstractLayout
+
+    class SimpleItem:
+        pass
+
+    class MockLayout(AbstractLayout):
+        def __init__(self):
+            super().__init__("/dev/null")
+
+    ml = MockLayout()
+    item = SimpleItem()
+    ml.append(item)
+
+    # Should not raise AttributeError even if 'color' is not set on item
+    ml.assign_array("color", ["red"])
+    assert item.color == "red"
+
+
+def test_assign_array_existing_attribute_preserved():
+    """Test that assign_array does not overwrite an existing truthy attribute."""
+    from jcvi.graphics.base import AbstractLayout
+
+    class SimpleItem:
+        def __init__(self, color):
+            self.color = color
+
+    class MockLayout(AbstractLayout):
+        def __init__(self):
+            super().__init__("/dev/null")
+
+    ml = MockLayout()
+    item_with_color = SimpleItem("blue")
+    item_without_color = SimpleItem("")
+    ml.append(item_with_color)
+    ml.append(item_without_color)
+
+    ml.assign_array("color", ["red", "green"])
+    # Existing truthy color should be preserved
+    assert item_with_color.color == "blue"
+    # Empty/falsy color should be replaced
+    assert item_without_color.color == "green"

tests/graphics/test_karyotype.py

@@ -42,4 +42,5 @@ def test_main():
     image_name = karyotype_main(
         ["seqids_with_empty_lines", "layout", "-o", "karyotype_with_empty_lines.pdf"]
     )
+    assert op.exists(image_name)
     os.chdir(cwd)

tests/graphics/test_synteny.py

@@ -3,11 +3,13 @@
 
 import os
 import os.path as op
+import tempfile
+
 import pytest
 
 from jcvi.apps.base import cleanup
 from jcvi.formats.bed import merge
-from jcvi.graphics.synteny import LayoutLine, main as synteny_main
+from jcvi.graphics.synteny import Layout, LayoutLine, main as synteny_main
 from jcvi.utils.validator import ValidationError
 
 
@@ -57,3 +59,22 @@ def test_main():
     image_name = synteny_main(["blocks", "grape_peach.bed", "blocks.layout"])
     assert op.exists(image_name)
     os.chdir(cwd)
+
+
+def test_layout_with_blank_lines():
+    """Test that Layout handles blank lines in the layout file gracefully."""
+    with tempfile.NamedTemporaryFile(mode="w", suffix=".layout", delete=False) as f:
+        f.write("# x,y,rotation,ha,va,color\n")
+        f.write("\n")
+        f.write("0.5, 0.6, 0, left, center, m\n")
+        f.write("\n")
+        f.write("0.5, 0.4, 0, left, center, k\n")
+        tmpfile = f.name
+
+    try:
+        layout = Layout(tmpfile)
+        assert len(layout) == 2
+        assert layout[0].color == "m"
+        assert layout[1].color == "k"
+    finally:
+        os.unlink(tmpfile)