updated

Author: Sayitobar

fishplotpy/data.py

@@ -327,15 +327,15 @@ def _validate_inputs(self):
             current_time_fracs = self.frac_table.iloc[:, time_idx].values
 
             calculated_nest_levels = self.nest_level  # Get the calculated levels
-            # print(f"DEBUG: Time {time_idx}, Nest Levels: {calculated_nest_levels}") # Add this
+            # print(f"DEBUG: Time {time_idx}, Nest Levels: {calculated_nest_levels}"
             for level in np.unique(calculated_nest_levels):
                 level_mask = calculated_nest_levels == level
                 level_clones_indices = np.where(level_mask)[0]  # 0-based indices
                 level_sum = current_time_fracs[level_mask].sum()
-                # print(f"DEBUG: Time {time_idx}, Level {level}, Clones(0-based): {level_clones_indices}, Sum: {level_sum}") # Add this
+                # print(f"DEBUG: Time {time_idx}, Level {level}, Clones(0-based): {level_clones_indices}, Sum: {level_sum}")
                 if level_sum > 100.0 + tolerance:
                     level_clones_one_based = level_clones_indices + 1
-                    # print(f"ERROR Triggered: Clones {level_clones_one_based}, Level {level}, Sum {level_sum}") # Add this
+                    # print(f"ERROR Triggered: Clones {level_clones_one_based}, Level {level}, Sum {level_sum}")
                     raise ValueError(
                         f"Clones {list(level_clones_one_based)} with nest level {level} sum to "
                         f"{level_sum:.2f} (> 100) at timepoint {time_idx} (value {self.timepoints[time_idx]})."
@@ -524,8 +524,6 @@ def layout_clones(self, separate_independent_clones: bool = False):
                 else:  # Handling subclones (parent_1based > 0)
                     parent_0based = parent_1based - 1
                     # Start at the bottom coordinate of the parent
-                    # If parent fraction is 0, parent ybtm is NaN - need fallback?
-                    # If parent absent, start from 0? R seems to imply start from ybtm[parent]
                     # If parent ybtm[parent_0based, time_idx] is NaN, this will propagate NaN.
                     current_y = ybtm_matrix[parent_0based, time_idx]
 
@@ -575,7 +573,7 @@ def layout_clones(self, separate_independent_clones: bool = False):
                         # Deferring this precise logic for now to get core layout working.
                         # It might be better handled during shape generation (spline/polygon).
 
-        # --- Finalize Coordinates (Convert to lists, remove NaNs) ---
+        # --- Finalize Coordinates ---
         final_xpos = []
         final_ytop = []
         final_ybtm = []

fishplotpy/plot.py

@@ -42,11 +42,7 @@ def _annot_clone(ax: plt.Axes, x: float, y: float, annot: str,
     # Let's assume cex is a multiplier for a default reasonable size e.g., 8
     fontsize = plt.rcParams['font.size'] * cex  # Scale default font size
 
-    # Basic offset implementation:
-    # Calculate offset in display coordinates (pixels) and convert back? Simpler:
-    # Approximate offset in data coordinates based on position.
-    # This is a rough heuristic. A fixed pixel offset would be more robust but complex.
-    # Let's use a fraction of axis range as offset unit.
+    # Basic offset implementation (use a fraction of axis range as offset unit)
     x_range = ax.get_xlim()[1] - ax.get_xlim()[0]
     y_range = ax.get_ylim()[1] - ax.get_ylim()[0]
     offset_scale_x = x_range * 0.01  # Scale offset relative to x-axis range
@@ -68,15 +64,16 @@ def _annot_clone(ax: plt.Axes, x: float, y: float, annot: str,
         # Outline with white, adjust linewidth as needed
         path_effects = [pe.withStroke(linewidth=1.5, foreground='white')]
 
-    ax.text(x + x_off, y + y_off, annot,  # Apply offset
-            ha=ha, va=va,
-            rotation=angle,
-            color=col,
-            fontsize=fontsize,
-            rotation_mode='anchor',  # Rotate around the anchor point (ha/va)
-            transform=ax.transData,
-            path_effects=path_effects  # Add path effects
-            )
+    ax.text(
+        x + x_off, y + y_off, annot,  # Apply offset
+        ha=ha, va=va,
+        rotation=angle,
+        color=col,
+        fontsize=fontsize,
+        rotation_mode='anchor',  # Rotate around the anchor point (ha/va)
+        transform=ax.transData,
+        path_effects=path_effects  # Add path effects
+    )
 
 
 def _draw_clust_polygon(ax: plt.Axes, xpos: np.ndarray, ytop: np.ndarray, ybtm: np.ndarray,
@@ -197,9 +194,7 @@ def _draw_clust_spline(ax: plt.Axes, xpos: np.ndarray, ytop: np.ndarray, ybtm: n
         print("Skipping drawing for clone with no timepoints.")  # Mimic R warning
         return
     if len(xpos) < 2:
-        # Cannot draw spline with < 2 points, draw as polygon?
-        # Or just skip/draw a point? R's spline might handle this.
-        # For now, draw simple polygon if only 1 point.
+        # draw simple polygon if only 1 point
         if len(xpos) == 1:
             _draw_clust_polygon(ax, xpos, ytop, ybtm, color, nest_level, pad_left,
                                 border, col_border, ramp_angle=0.5,  # Use default ramp

tests/test_data.py

@@ -39,19 +39,19 @@ def test_init_valid_data(valid_input_data):
     # Check defaults
     assert fp_data.clone_labels == ['1', '2', '3']
     assert fp_data.clone_annots == ['', '', '']
-    assert len(fp_data.colors) == 3 # Should have assigned default colors
+    assert len(fp_data.colors) == 3  # Should have assigned default colors
 
 
 def test_init_mismatched_parents_length():
     """Test error if len(parents) != num_clones."""
     with pytest.raises(ValueError, match="Length of parents must equal"):
-        FishPlotData(frac_table=VALID_FRACS, parents=[0, 1]) # Too short
+        FishPlotData(frac_table=VALID_FRACS, parents=[0, 1])
 
 
 def test_init_mismatched_timepoints_length():
     """Test error if len(timepoints) != num_timepoints."""
     with pytest.raises(ValueError, match="Length of timepoints must equal"):
-        FishPlotData(frac_table=VALID_FRACS, parents=VALID_PARENTS, timepoints=[0, 50]) # Too short
+        FishPlotData(frac_table=VALID_FRACS, parents=VALID_PARENTS, timepoints=[0, 50])
 
 
 def test_init_invalid_parent_index_negative():
@@ -63,7 +63,7 @@ def test_init_invalid_parent_index_negative():
 def test_init_invalid_parent_index_too_large():
     """Test error if parents index > num_clones."""
     with pytest.raises(ValueError, match="greater than the number of clones"):
-        FishPlotData(frac_table=VALID_FRACS, parents=[0, 1, 4]) # Parent 4 invalid
+        FishPlotData(frac_table=VALID_FRACS, parents=[0, 1, 4])  # Parent 4 invalid
 
 
 def test_init_non_numeric_fracs():
@@ -79,7 +79,7 @@ def test_init_non_numeric_fracs():
 def test_validation_clone_reappearance_error():
     """Test error when a clone reappears after being zero."""
     fracs = pd.DataFrame([
-        [10, 0, 10], # Clone 1 reappears
+        [10, 0, 10],  # Clone 1 reappears
         [90, 100, 90]
     ])
     parents = [0, 0]