bluecellulab 2.6.0__tar.gz → 2.6.2__tar.gz

{bluecellulab-2.6.0 → bluecellulab-2.6.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.6.0
+Version: 2.6.2
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.6.0 → bluecellulab-2.6.2}/bluecellulab/cell/core.py

@@ -497,10 +497,6 @@ class Cell(InjectableMixin, PlottableMixin):
         # numpy int to int
         post_sec_id = int(syn_description[SynapseProperty.POST_SECTION_ID])
 
-        location = SynapseFactory.determine_synapse_location(
-            syn_description, self
-        )
-
         weight_scalar = connection_modifiers.get('Weight', 1.0)
         exc_mini_frequency, inh_mini_frequency = mini_frequencies \
             if mini_frequencies is not None else (None, None)
@@ -516,13 +512,15 @@ class Cell(InjectableMixin, PlottableMixin):
             spont_minis_rate = inh_mini_frequency
 
         if spont_minis_rate is not None and spont_minis_rate > 0:
-            sec = self.get_psection(post_sec_id).hsection
+            synapse_hoc_args = SynapseFactory.determine_synapse_location(
+                syn_description, self
+            )
             # add the *minis*: spontaneous synaptic events
             self.ips[synapse_id] = neuron.h.\
-                InhPoissonStim(location, sec=sec)
+                InhPoissonStim(synapse_hoc_args.location, sec=synapse_hoc_args.section)
 
             self.syn_mini_netcons[synapse_id] = neuron.h.\
-                NetCon(self.ips[synapse_id], synapse.hsynapse, sec=sec)
+                NetCon(self.ips[synapse_id], synapse.hsynapse, sec=synapse_hoc_args.section)
             self.syn_mini_netcons[synapse_id].delay = 0.1
             self.syn_mini_netcons[synapse_id].weight[0] = weight * weight_scalar
             # set netcon type

{bluecellulab-2.6.0 → bluecellulab-2.6.2}/bluecellulab/circuit/circuit_access/bluepy_circuit_access.py

@@ -191,23 +191,15 @@ class BluepyCircuitAccess:
 
             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-2.6.0 → bluecellulab-2.6.2}/bluecellulab/circuit/synapse_properties.py

@@ -40,6 +40,7 @@ class SynapseProperty(Enum):
     NRRP = "NRRP"
     U_HILL_COEFFICIENT = "u_hill_coefficient"
     CONDUCTANCE_RATIO = "conductance_scale_factor"
+    AFFERENT_SECTION_POS = "afferent_section_pos"
 
     @classmethod
     def from_bluepy(cls, prop: BLPSynapse) -> SynapseProperty:
@@ -76,6 +77,7 @@ class SynapseProperties:
         SynapseProperty.NRRP,
         SynapseProperty.U_HILL_COEFFICIENT,
         SynapseProperty.CONDUCTANCE_RATIO,
+        SynapseProperty.AFFERENT_SECTION_POS,
     )
     plasticity = (
         "volume_CR", "rho0_GB", "Use_d_TM", "Use_p_TM", "gmax_d_AMPA",
@@ -98,6 +100,7 @@ snap_to_synproperty = MappingProxyType({
     "n_rrp_vesicles": SynapseProperty.NRRP,
     "u_hill_coefficient": SynapseProperty.U_HILL_COEFFICIENT,
     "conductance_scale_factor": SynapseProperty.CONDUCTANCE_RATIO,
+    "afferent_section_pos": SynapseProperty.AFFERENT_SECTION_POS,
 })
 
 
@@ -137,23 +140,36 @@ 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]:
     """Convert a list of SynapseProperty to bluepy Synapse properties, spare
     'str's."""
-    return [
+    # 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)
+    res = [
         prop.to_bluepy()
         if isinstance(prop, SynapseProperty)
         else prop
-        for prop in props
+        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-2.6.0 → bluecellulab-2.6.2}/bluecellulab/synapse/synapse_factory.py

@@ -114,10 +114,10 @@ class SynapseFactory:
         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]

{bluecellulab-2.6.0 → bluecellulab-2.6.2}/bluecellulab.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.6.0
+Version: 2.6.2
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.6.0 → bluecellulab-2.6.2}/tests/test_circuit/test_circuit_access.py

@@ -89,7 +89,7 @@ class TestSonataCircuitAccess:
         cell_id = CellId("hippocampus_neurons", 1)
         projections = None
         res = self.circuit_access.extract_synapses(cell_id, projections)
-        assert res.shape == (1742, 15)
+        assert res.shape == (1742, 16)
         assert all(res["source_popid"] == 2126)
 
         assert all(res["source_population_name"] == "hippocampus_projections")
@@ -101,13 +101,13 @@ class TestSonataCircuitAccess:
         # projection parameter
         projection = "hippocampus_projections"
         res = self.circuit_access.extract_synapses(cell_id, projection)
-        assert res.shape == (1742, 15)
+        assert res.shape == (1742, 16)
         list_of_single_projection = [projection]
         res = self.circuit_access.extract_synapses(cell_id, list_of_single_projection)
-        assert res.shape == (1742, 15)
+        assert res.shape == (1742, 16)
         empty_projection = []
         res = self.circuit_access.extract_synapses(cell_id, empty_projection)
-        assert res.shape == (1742, 15)
+        assert res.shape == (1742, 16)
 
     def test_target_contains_cell(self):
         target = "most_central_10_SP_PC"

{bluecellulab-2.6.0 → bluecellulab-2.6.2}/tests/test_synapse/test_synapse_factory.py

@@ -58,7 +58,7 @@ class TestSynapseFactory:
         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)

{bluecellulab-2.6.0 → bluecellulab-2.6.2}/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