Ensure default soma voltage (v) recording for all cells

bluecellulab/reports/utils.py

@@ -141,6 +141,37 @@ def prepare_recordings_for_reports(
                 sites_index[cell_id].append(entry)
                 cell.report_sites[report_name].append(entry)
 
+    for cell_id, cell in cells.items():
+        sec = cell.soma
+        sec_name = sec.name().split(".")[-1]
+        segx = 0.5
+        rec_name = section_to_variable_recording_str(sec, segx, "v")
+
+        if rec_name in recording_index[cell_id]:
+            continue
+
+        report_name = "__default_voltage__"
+        cell.report_sites.setdefault(report_name, [])
+
+        configured = cell.configure_recording(
+            [(sec, sec_name, segx)],
+            "v",
+            report_name,
+        )
+
+        for (sec, sec_name, segx), rec_name in configured:
+            recording_index[cell_id].append(rec_name)
+
+            entry_default_voltage: SiteEntry = {
+                "report": report_name,
+                "rec_name": rec_name,
+                "section": sec_name,
+                "segx": float(segx),
+                "area_um2": None,
+            }
+            sites_index[cell_id].append(entry_default_voltage)
+            cell.report_sites[report_name].append(entry_default_voltage)
+
     return dict(recording_index), dict(sites_index)
 
 

tests/test_reports/test_reports_utils.py

@@ -35,19 +35,30 @@
 )
 
 
+class DummySection:
+    def name(self):
+        return "cell.soma[0]"
+
+    def __str__(self):
+        return "soma[0]"
+
+
 class DummyCell:
     def __init__(self, targets, rec_names):
         self.targets = targets
         self.rec_names = rec_names
         self.report_sites: dict[str, list[dict]] = {}
+        self.soma = DummySection()
 
     def resolve_segments_from_config(self, _cfg):
         return self.targets
 
     def resolve_segments_from_compartment_set(self, _node_id, _compartment_nodes):
         return self.targets
 
-    def configure_recording(self, sites, _variable, _report_name):
+    def configure_recording(self, sites, variable, report_name):
+        if report_name == "__default_voltage__":
+            return [(site, f"default_{variable}_{idx}") for idx, site in enumerate(sites)]
         return list(zip(sites, self.rec_names))
 
 
@@ -134,8 +145,11 @@ def test_prepare_recordings_for_reports_compartment_populates_report_sites(caplo
         recording_index, sites_index = prepare_recordings_for_reports(cells, cfg)
 
     assert not caplog.records
-    assert recording_index[cell_id] == ["rec_soma", "rec_dend"]
-    assert len(sites_index[cell_id]) == 2
+    assert recording_index[cell_id][:2] == ["rec_soma", "rec_dend"]
+    assert len(recording_index[cell_id]) == 3
+    assert len(sites_index[cell_id]) == 3
+    assert "__default_voltage__" in cell.report_sites
+    assert len(cell.report_sites["__default_voltage__"]) == 1
     assert "r1" in cell.report_sites
     assert [s["rec_name"] for s in cell.report_sites["r1"]] == ["rec_soma", "rec_dend"]
 
@@ -155,8 +169,10 @@ def test_prepare_recordings_for_reports_warns_on_rec_mismatch(caplog):
         recording_index, sites_index = prepare_recordings_for_reports(cells, cfg)
 
     assert "Configured 1/2 recording sites" in caplog.text
-    assert recording_index[cell_id] == ["only_one"]
-    assert len(sites_index[cell_id]) == 1
+    assert recording_index[cell_id][0] == "only_one"
+    assert len(recording_index[cell_id]) == 2
+    assert len(sites_index[cell_id]) == 2
+    assert "__default_voltage__" in cell.report_sites
 
 
 def test_prepare_recordings_for_reports_populates_area_um2(monkeypatch):