Address some more nits

Author: jsnel

pyglotaran_extras/inspect/kinetic_scheme/_layout.py

@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import hashlib
+import logging
 from collections import deque
 from enum import Enum
 from typing import TYPE_CHECKING
@@ -20,6 +21,9 @@
 NodePositions = dict[str, tuple[float, float]]
 """Mapping from node label to (x, y) position in data coordinates."""
 
+_LOGGER = logging.getLogger(__name__)
+_SAME_COLUMN_TOLERANCE = 0.3
+
 
 class LayoutAlgorithm(str, Enum):
     """Available layout algorithms for kinetic scheme visualization.
@@ -667,7 +671,15 @@ def _position_ground_state_nodes(
             positions[gs_node.label] = (parent_x, parent_y - ground_state_offset)
         else:
             # Fallback: place at origin
-            positions[gs_node.label] = (0.0, -ground_state_offset)
+            fallback_position = (0.0, -ground_state_offset)
+            _LOGGER.debug(
+                "Ground-state fallback positioning used for node '%s': "
+                "parents=%s, fallback_position=%s",
+                gs_node.label,
+                parents,
+                fallback_position,
+            )
+            positions[gs_node.label] = fallback_position
 
 
 def _avoid_ground_state_arrow_overlap(
@@ -718,7 +730,7 @@ def _avoid_ground_state_arrow_overlap(
 
             # Check if successor is approximately in the same x column
             # and below the parent
-            if abs(sx - px) < 0.3 and sy < py:
+            if abs(sx - px) < _SAME_COLUMN_TOLERANCE and sy < py:
                 positions[successor_label] = (sx + nudge, sy)
 
 

tests/inspect/kinetic_scheme/test_layout.py

@@ -2,8 +2,6 @@
 
 from __future__ import annotations
 
-import hashlib
-
 import pytest
 
 from pyglotaran_extras.inspect.kinetic_scheme._k_matrix_parser import Transition
@@ -104,10 +102,14 @@ def test_no_overlapping_positions(self) -> None:
         positions = compute_layout(graph, LayoutAlgorithm.HIERARCHICAL)
 
         compartment_positions = [positions[n.label] for n in graph.compartment_nodes()]
+        epsilon = 1e-6
         for i, pos_i in enumerate(compartment_positions):
             for j, pos_j in enumerate(compartment_positions):
                 if i != j:
-                    assert pos_i != pos_j
+                    dx = pos_i[0] - pos_j[0]
+                    dy = pos_i[1] - pos_j[1]
+                    distance = (dx * dx + dy * dy) ** 0.5
+                    assert distance > epsilon
 
     def test_deterministic_output(self) -> None:
         """Same input should always produce the same positions."""
@@ -120,12 +122,11 @@ def test_deterministic_output(self) -> None:
 
     def test_node_sort_index_is_deterministic(self) -> None:
         """Node sort index should use deterministic hashing."""
-        label = "species_2"
-        digest = hashlib.md5(label.encode(), usedforsecurity=False).digest()
-        expected = int.from_bytes(digest[:4], "big") / 4294967296.0
-        actual = _node_sort_index(label)
-        assert actual == expected
-        assert 0.0 <= actual < 1.0
+        species_2_idx = _node_sort_index("species_2")
+        species_3_idx = _node_sort_index("species_3")
+        assert 0.0 <= species_2_idx < 1.0
+        assert 0.0 <= species_3_idx < 1.0
+        assert species_2_idx != species_3_idx
 
     def test_parallel_nodes_side_by_side(self) -> None:
         """Parallel decay nodes (all isolated) should be on the same row."""