change(indexing): validate_lineage always warns if lineage misassigned

src/agora/io/signal.py

@@ -249,7 +249,7 @@ class Signal(BridgeH5):
         dataset: str or t.List[str],
         in_minutes: bool = True,
         lineage: bool = False,
-        run_lineage_check: bool = True,
+        stop_on_lineage_check: bool = True,
         **kwargs,
     ) -> pd.DataFrame or t.List[pd.DataFrame]:
         """
@@ -282,7 +282,7 @@ class Signal(BridgeH5):
                                 lineage,
                                 indices=np.array(df.index.to_list()),
                                 how="daughters",
-                                run_lineage_check=run_lineage_check,
+                                stop_on_lineage_check=stop_on_lineage_check,
                             )
                             mother_label[valid_indices] = lineage[
                                 valid_lineage, 1

src/agora/utils/indexing.py

@@ -8,7 +8,7 @@ def validate_lineage(
     lineage: np.ndarray,
     indices: np.ndarray,
     how: str = "families",
-    run_lineage_check: bool = True,
+    stop_on_lineage_check: bool = True,
 ):
     """
     Identify mother-bud pairs both in lineage and a Signal's indices.
@@ -31,9 +31,9 @@ def validate_lineage(
         If "mothers", matches indicate mothers from mother-bud pairs;
         If "daughters", matches indicate daughters from mother-bud pairs;
         If "families", matches indicate mothers and daughters in mother-bud pairs.
-    run_lineage_check: bool
-        If True, check for errors in the lineage assignment such as a daughter
-        being assigned two mothers.
+    stop_on_lineage_check: bool
+        If True, raise an Exception for any errors in the lineage assignment such
+        as a daughter being assigned two mothers.
 
     Returns
     -------
@@ -91,25 +91,27 @@ def validate_lineage(
         valid_indices = index_isin(indices, selected_lineages[:, c_index, :])
     flat_valid_indices = valid_indices.flatten()
     # test for mismatch
-    if run_lineage_check:
-        if how == "families":
-            test_mismatch = (
-                indices[flat_valid_indices, :].size
-                != np.unique(
-                    lineage[flat_valid_lineage, :].reshape(-1, 2), axis=0
-                ).size
-            )
-        else:
-            test_mismatch = (
-                indices[flat_valid_indices, :].size
-                != lineage[flat_valid_lineage, c_index, :].size
-            )
-        if test_mismatch:
-            # all unique indices in valid_lineages should be in valid_indices
+    if how == "families":
+        test_mismatch = (
+            indices[flat_valid_indices, :].size
+            != np.unique(
+                lineage[flat_valid_lineage, :].reshape(-1, 2), axis=0
+            ).size
+        )
+    else:
+        test_mismatch = (
+            indices[flat_valid_indices, :].size
+            != lineage[flat_valid_lineage, c_index, :].size
+        )
+    if test_mismatch:
+        # all unique indices in valid_lineages should be in valid_indices
+        if stop_on_lineage_check:
             raise Exception(
                 "Error in validate_lineage: "
                 "lineage information is likely not unique."
             )
+        else:
+            print("Warning: error in validate_lineage.")
     return flat_valid_lineage, flat_valid_indices