Fix accessing afferent_section_pos of synapse description (#169)

* Fix accessing afferent_section_pos

* pin libsonata<=0.1.25

* bluepy_circuit_access with AFFERENT_SECTION_POS

* simplify bluepy access' afferent section pos logic

* handle bluepy's exception for afferent_section_pos in props from/to bluepy

bluecellulab/circuit/circuit_access/bluepy_circuit_access.py

@@ -191,23 +191,15 @@ def extract_synapses(
 
             if isinstance(connectome._impl, SonataConnectome):
                 logger.debug('Using sonata style synapse file, not nrn.h5')
-                # load 'afferent_section_pos' instead of '_POST_DISTANCE'
-                if 'afferent_section_pos' in connectome.available_properties:
-                    connectome_properties[
-                        connectome_properties.index(SynapseProperty.POST_SEGMENT_OFFSET)
-                    ] = 'afferent_section_pos'
-
-                connectome_properties = properties_to_bluepy(connectome_properties)
-                synapses = connectome.afferent_synapses(
-                    gid, properties=connectome_properties
-                )
-                synapses.columns = properties_from_bluepy(synapses.columns)
-            else:
-                connectome_properties = properties_to_bluepy(connectome_properties)
-                synapses = connectome.afferent_synapses(
-                    gid, properties=connectome_properties
-                )
-                synapses.columns = properties_from_bluepy(synapses.columns)
+                connectome_properties.remove(SynapseProperty.POST_SEGMENT_OFFSET)
+            else:  # afferent section_pos will be computed via post_segment_offset
+                connectome_properties.remove(SynapseProperty.AFFERENT_SECTION_POS)
+
+            connectome_properties = properties_to_bluepy(connectome_properties)
+            synapses = connectome.afferent_synapses(
+                gid, properties=connectome_properties
+            )
+            synapses.columns = properties_from_bluepy(synapses.columns)
 
             synapses = synapses.reset_index(drop=True)
             synapses.index = pd.MultiIndex.from_tuples(

bluecellulab/circuit/synapse_properties.py

@@ -140,12 +140,15 @@ def properties_from_bluepy(
     'str's."""
     if not BLUEPY_AVAILABLE:
         raise ExtraDependencyMissingError("bluepy")
-    return [
-        SynapseProperty.from_bluepy(prop)
-        if isinstance(prop, BLPSynapse)
-        else prop
-        for prop in props
-    ]
+    res: list[SynapseProperty | str] = []
+    for prop in props:
+        if isinstance(prop, BLPSynapse):
+            res.append(SynapseProperty.from_bluepy(prop))
+        elif prop == "afferent_section_pos":  # jira_url/project/issues/browse/NSETM-2313
+            res.append(SynapseProperty.AFFERENT_SECTION_POS)
+        else:
+            res.append(prop)
+    return res
 
 
 def properties_to_bluepy(props: list[SynapseProperty | str]) -> list[BLPSynapse | str]:
@@ -154,14 +157,19 @@ def properties_to_bluepy(props: list[SynapseProperty | str]) -> list[BLPSynapse
     # bluepy does not have AFFERENT_SECTION_POS atm.
     # jira_url/project/issues/browse/NSETM-2313
     bluepy_recognised_props = props.copy()
+    removed_afferent_section_pos = False
     if SynapseProperty.AFFERENT_SECTION_POS in bluepy_recognised_props:
+        removed_afferent_section_pos = True
         bluepy_recognised_props.remove(SynapseProperty.AFFERENT_SECTION_POS)
-    return [
+    res = [
         prop.to_bluepy()
         if isinstance(prop, SynapseProperty)
         else prop
         for prop in bluepy_recognised_props
     ]
+    if removed_afferent_section_pos:
+        res.append("afferent_section_pos")
+    return res
 
 
 def synapse_property_encoder(dct: dict[SynapseProperty | str, Any]) -> dict[str, Any]:

bluecellulab/synapse/synapse_factory.py

@@ -114,10 +114,10 @@ def determine_synapse_location(cls, syn_description: pd.Series, cell: bluecellul
         section: NeuronSection = cell.get_psection(section_id=isec).hsection
 
         # old circuits don't have it, it needs to be computed via synlocation_to_segx
-        if ("afferent_section_pos" in syn_description and
-                not np.isnan(syn_description["afferent_section_pos"])):
+        if (SynapseProperty.AFFERENT_SECTION_POS in syn_description and
+                not np.isnan(syn_description[SynapseProperty.AFFERENT_SECTION_POS])):
             # position is pre computed in SONATA
-            location = syn_description["afferent_section_pos"]
+            location = syn_description[SynapseProperty.AFFERENT_SECTION_POS]
         else:
             ipt = syn_description[SynapseProperty.POST_SEGMENT_ID]
             syn_offset = syn_description[SynapseProperty.POST_SEGMENT_OFFSET]

tests/test_synapse/test_synapse_factory.py

@@ -58,7 +58,7 @@ def test_determine_synapse_location(self):
         res = SynapseFactory.determine_synapse_location(self.syn_description, self.cell)
         assert res.location == 0.9999999
         # set afferent_section_pos
-        self.syn_description["afferent_section_pos"] = 1.2
+        self.syn_description[SynapseProperty.AFFERENT_SECTION_POS] = 1.2
         res = SynapseFactory.determine_synapse_location(self.syn_description, self.cell)
         assert res.location == 1.2
         assert res.section.L == pytest.approx(9.530376893488256)

tox.ini

@@ -15,6 +15,7 @@ deps =
     pytest-timeout>=2.1.0
     pytest-xdist>=3.3.1  # multiprocessing
     pytest-forked>=1.6.0  # isolation
+    libsonata<=0.1.25  # 0.1.26 supports h5 synapse_replay only, some of our tests atm use .dat
 download = true
 allowlist_externals =
     make