Fix an issue reading extra properties for cells where there is no syn…

…apses.

Install latest libsonata branch

.github/workflows/simulation_test.yml

@@ -105,7 +105,7 @@ jobs:
     - name: Install libsonata
       if: steps.cache-venv.outputs.cache-hit != 'true'
       run: |
-        CC=mpicc CXX=mpic++ pip install git+https://github.com/BlueBrain/libsonata
+        CC=mpicc CXX=mpic++ pip install git+https://github.com/BlueBrain/libsonata@${{ env.LIBSONATA_BRANCH }}
 
     - name: Cache libsonatareport
       id: cache-libsonatareport

neurodamus/io/synapse_reader.py

@@ -348,7 +348,10 @@ def _read(attribute, optional=False):
         # We nevertheless can skip any base fields
         extra_fields = set(self._extra_fields) - (self.Parameters.all_fields | compute_fields)
         for field in sorted(extra_fields):
-            now_needed_gids = sorted(set(gid for gid in gids if field not in self._data[gid]))
+            now_needed_gids = sorted(set(
+                gid for gid in gids
+                if (data := self._data[gid]) is not self.EMPTY_DATA and field not in data
+            ))
             if needed_gids != now_needed_gids:
                 needed_gids = now_needed_gids
                 needed_edge_ids, lookup_gids = get_edge_and_lookup_gids(needed_gids)