bluecellulab 2.6.1__py3-none-any.whl → 2.6.3__py3-none-any.whl

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/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/graph.py

@@ -82,4 +82,4 @@ def plot_graph(G: nx.Graph, node_size: float = 400, edge_width: float = 0.4, nod
     # Add text at the bottom of the figure
     plt.figtext(0.5, 0.01, "Network of simulated cells", ha="center", fontsize=10, va="bottom")
 
-    plt.show()
+    return plt

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-2.6.1.dist-info → bluecellulab-2.6.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.6.1
+Version: 2.6.3
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.6.1.dist-info → bluecellulab-2.6.3.dist-info}/RECORD

@@ -3,7 +3,7 @@ bluecellulab/circuit_simulation.py,sha256=GLy_O5onhiSa-RajorDHlgP1rkFxjUONB4G6B4
 bluecellulab/connection.py,sha256=volV2YKtmqAF7MOEJar5ldF1ARAo7k2vF9MB1NXybUY,4640
 bluecellulab/dendrogram.py,sha256=w0vvv0Q169DolTX1j9dAZIvHIl4H258gAjQ1xQaNiGk,6427
 bluecellulab/exceptions.py,sha256=KIxF7s_7gPVJ07TiQ-Z1D8de7ylV74gNMhzl0339CVM,2379
-bluecellulab/graph.py,sha256=ODiQy4xjRVxtNITXeXpYnqHas0wR7gZ_aXuDAF7jMq4,3419
+bluecellulab/graph.py,sha256=o-9NnRrli0AqfGcw0-nhjaICH2IeqCH76uAlbZbo2dQ,3419
 bluecellulab/importer.py,sha256=zwVi1Nx2f8xzFfzxzYoXa7gfi7DQapqkRJII5sBbRyY,2900
 bluecellulab/neuron_interpreter.py,sha256=hXig_u3T6JmEHbkV8ZblEZtX0kY80ate4VpRtANNFrM,2185
 bluecellulab/plotwindow.py,sha256=UVHzml-BB83m5Qr-YGkjR9kB-vSW8mM0Owh2j95yIaU,2721
@@ -36,10 +36,10 @@ bluecellulab/circuit/format.py,sha256=eYhiBIQnPnnVBmaSDymFjQprXN9QjEYKmFhb2mIS86
 bluecellulab/circuit/iotools.py,sha256=KVE7x5LNQ4RgjNh05Q-h3Swpbs3nRFtrcWNHj62aiRI,1585
 bluecellulab/circuit/node_id.py,sha256=gaRAW3UhbPOPsoXMHLjo3qH9iNod7YB8ZOcguWprrU4,1265
 bluecellulab/circuit/simulation_access.py,sha256=QHVEN-sEZbCCvblhBHEShGX0-NEXCD1AYpavpVGCgAE,7073
-bluecellulab/circuit/synapse_properties.py,sha256=tF2vfYVKtyS6hWrk_hHmvdUQvXIlZi8ZY0Vcci0-_sA,5967
+bluecellulab/circuit/synapse_properties.py,sha256=a4-Yw_f8JIR6i2YG8qhCW97TMSd_Z-aF6lp_a1wBwnM,6374
 bluecellulab/circuit/validate.py,sha256=7EUN15u0JFFlLf389jUBqLwDOHyZdfKtoidI-xLUVYA,3593
 bluecellulab/circuit/circuit_access/__init__.py,sha256=sgp6m5kP-pq60V1IFGUiSUR1OW01zdxXNNUJmPA8anI,201
-bluecellulab/circuit/circuit_access/bluepy_circuit_access.py,sha256=HxQaRTz1HaeOVV87fiptJBXRNWCitT-5YHn71WtSsLg,14687
+bluecellulab/circuit/circuit_access/bluepy_circuit_access.py,sha256=pUoTw6wXMGZAqjjC3vpdZcm8ex108aEPw0L6fSypx9g,14273
 bluecellulab/circuit/circuit_access/definition.py,sha256=SnKBFEgdXFG-QexYRrGSzVAd7bSj7NwN0IuTsjDOrDY,4435
 bluecellulab/circuit/circuit_access/sonata_circuit_access.py,sha256=c0MMJuoT6_dRW8O5HSRS5hHv1zDKdW0sBR-DaP0F1bk,10351
 bluecellulab/circuit/config/__init__.py,sha256=aaoJXRKBJzpxxREo9NxKc-_CCPmVeuR1mcViRXcLrC4,215
@@ -60,11 +60,11 @@ bluecellulab/stimulus/__init__.py,sha256=DgIgVaSyR-URf3JZzvO6j-tjCerzvktuK-ep8pj
 bluecellulab/stimulus/circuit_stimulus_definitions.py,sha256=uij_s44uNdmMwMLGmTHSRgmp9K9B_vvHHshX6YPJNJU,15686
 bluecellulab/stimulus/factory.py,sha256=cjnMqFx-Y31kV1XHvkSbGI2f1OpEawU3Wg_cLqcIyRc,11883
 bluecellulab/synapse/__init__.py,sha256=RW8XoAMXOvK7OG1nHl_q8jSEKLj9ZN4oWf2nY9HAwuk,192
-bluecellulab/synapse/synapse_factory.py,sha256=YkvxbdGF-u-vxYdbRNTlX-9AtSC_3t_FQRFhybwzgrk,6805
+bluecellulab/synapse/synapse_factory.py,sha256=MjUorWoMl4lFSBgQw4QS09Dzh0-LYWlCHJKYy8N-d3w,6847
 bluecellulab/synapse/synapse_types.py,sha256=4gne-hve2vq1Lau-LAVPsfLjffVYqAYBW3kCfC7_600,16871
-bluecellulab-2.6.1.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
-bluecellulab-2.6.1.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
-bluecellulab-2.6.1.dist-info/METADATA,sha256=jQkc9kIE0mWCM6BNhdQaFA-bP-Enl_6NFyeelVMvq9E,7025
-bluecellulab-2.6.1.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-bluecellulab-2.6.1.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
-bluecellulab-2.6.1.dist-info/RECORD,,
+bluecellulab-2.6.3.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
+bluecellulab-2.6.3.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
+bluecellulab-2.6.3.dist-info/METADATA,sha256=yg81T-fh1WY_SIy1BaGDTXzBe2_b7kmtUJie9gPIIqM,7025
+bluecellulab-2.6.3.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+bluecellulab-2.6.3.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
+bluecellulab-2.6.3.dist-info/RECORD,,