warning to log in serialized_sections #176 (#178)

* warning to log in serialized_sections  #176

* update test_serialized_sections

* format

bluecellulab/cell/serialized_sections.py

@@ -15,17 +15,14 @@
 index."""
 from __future__ import annotations
 import logging
-import warnings
 import neuron
 from bluecellulab.type_aliases import HocObjectType, NeuronSection
 
 
 logger = logging.getLogger(__name__)
-warnings.filterwarnings("once", category=UserWarning, module=__name__)
 
 
 class SerializedSections:
-
     def __init__(self, cell: HocObjectType) -> None:
         self.isec2sec: dict[int, NeuronSection] = {}
         n = cell.nSecAll
@@ -37,7 +34,8 @@ def __init__(self, cell: HocObjectType) -> None:
                 raise ValueError("Error: failure in mk2_isec2sec()")
 
             if v_value < 0:
-                warnings.warn(
-                    f"[Warning] SerializedSections: v(0.0001) < 0. index={index} v()={v_value}")
+                logging.debug(
+                    f"[Warning] SerializedSections: v(0.0001) < 0. index={index} v()={v_value}"
+                )
             else:
                 self.isec2sec[int(v_value)] = neuron.h.SectionRef(sec=sec)

tests/test_cell/test_serialized_sections.py

@@ -1,4 +1,5 @@
 """Unit tests for serialized_sections module."""
+import logging
 from pathlib import Path
 
 import pytest
@@ -11,11 +12,12 @@
 
 
 @pytest.mark.v5
-def test_serialized_sections():
+def test_serialized_sections(caplog):
     """Test the SerializedSections class."""
     cell = Cell(
         "%s/examples/cell_example1/test_cell.hoc" % script_dir,
-        "%s/examples/cell_example1" % script_dir)
+        "%s/examples/cell_example1" % script_dir,
+    )
 
     serialized_sections = SerializedSections(cell.cell.getCell())
     assert len(serialized_sections.isec2sec) == 135
@@ -32,8 +34,9 @@ def test_serialized_sections():
     section_list = modified_cell.all
     first_section = next(iter(section_list))
     first_section(0.0001).v = -2
-    with pytest.warns(UserWarning):
-        SerializedSections(modified_cell)
+    caplog.set_level(logging.DEBUG)
+    SerializedSections(modified_cell)
+    assert "[Warning] SerializedSections: v(0.0001) < 0" in caplog.text
 
     modified_cell.nSecAll = -1
     with pytest.raises(ValueError):