bluecellulab 2.2.2__py3-none-any.whl → 2.2.4__py3-none-any.whl

bluecellulab/cell/core.py

@@ -101,9 +101,6 @@ class Cell(InjectableMixin, PlottableMixin):
 
         self.cellname = neuron.h.secname(sec=self.soma).split(".")[0]
 
-        # Set the gid of the cell
-        self.cell.getCell().gid = self.cell_id.id
-
         if rng_settings is None:
             self.rng_settings = RNGSettings("Random123")  # SONATA value
         else:
@@ -121,11 +118,11 @@ class Cell(InjectableMixin, PlottableMixin):
         # time recording needs this push
         self.soma.push()
         self.hocname = neuron.h.secname(sec=self.soma).split(".")[0]
-        self.somatic = [x for x in public_hoc_cell(self.cell).somatic]
-        self.basal = [x for x in public_hoc_cell(self.cell).basal]  # dend is same as basal
-        self.apical = [x for x in public_hoc_cell(self.cell).apical]
-        self.axonal = [x for x in public_hoc_cell(self.cell).axonal]
-        self.all = [x for x in public_hoc_cell(self.cell).all]
+        self.somatic = list(public_hoc_cell(self.cell).somatic)
+        self.basal = list(public_hoc_cell(self.cell).basal)  # dend is same as basal
+        self.apical = list(public_hoc_cell(self.cell).apical)
+        self.axonal = list(public_hoc_cell(self.cell).axonal)
+        self.all = list(public_hoc_cell(self.cell).all)
         self.record_dt = record_dt
         self.add_recordings(['self.soma(0.5)._ref_v', 'neuron.h._ref_t'],
                             dt=self.record_dt)
@@ -560,11 +557,7 @@ class Cell(InjectableMixin, PlottableMixin):
             syn_description, self
         )
 
-        if 'Weight' in connection_modifiers:
-            weight_scalar = connection_modifiers['Weight']
-        else:
-            weight_scalar = 1.0
-
+        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)
 
@@ -573,11 +566,10 @@ class Cell(InjectableMixin, PlottableMixin):
         # SpontMinis in sim config takes precedence of values in nodes file
         if 'SpontMinis' in connection_modifiers:
             spont_minis_rate = connection_modifiers['SpontMinis']
+        elif synapse.mech_name in ["GluSynapse", "ProbAMPANMDA_EMS"]:
+            spont_minis_rate = exc_mini_frequency
         else:
-            if synapse.mech_name in ["GluSynapse", "ProbAMPANMDA_EMS"]:
-                spont_minis_rate = exc_mini_frequency
-            else:
-                spont_minis_rate = inh_mini_frequency
+            spont_minis_rate = inh_mini_frequency
 
         if spont_minis_rate is not None and spont_minis_rate > 0:
             sec = self.get_hsection(post_sec_id)
@@ -590,8 +582,7 @@ class Cell(InjectableMixin, PlottableMixin):
             self.syn_mini_netcons[synapse_id].delay = 0.1
             self.syn_mini_netcons[synapse_id].weight[0] = weight * weight_scalar
             # set netcon type
-            nc_param_name = 'nc_type_param_{}'.format(
-                synapse.hsynapse).split('[')[0]
+            nc_param_name = f'nc_type_param_{synapse.hsynapse}'.split('[')[0]
             if hasattr(neuron.h, nc_param_name):
                 nc_type_param = int(getattr(neuron.h, nc_param_name))
                 # NC_SPONTMINI
@@ -655,7 +646,7 @@ class Cell(InjectableMixin, PlottableMixin):
         """Get the children section of a neuron section."""
         number_children = neuron.h.SectionRef(sec=parentsection).nchild()
         children = []
-        for index in range(0, int(number_children)):
+        for index in range(int(number_children)):
             children.append(neuron.h.SectionRef(sec=self.soma).child[index])
         return children
 
@@ -679,10 +670,10 @@ class Cell(InjectableMixin, PlottableMixin):
             self.get_recording(secname)
             self.get_recording(child)
 
-    def somatic_branches(self):
+    def somatic_branches(self) -> None:
         """Show the index numbers."""
         nchild = neuron.h.SectionRef(sec=self.soma).nchild()
-        for index in range(0, int(nchild)):
+        for index in range(int(nchild)):
             secname = neuron.h.secname(sec=neuron.h.SectionRef(
                 sec=self.soma).child[index])
             if "axon" not in secname:
@@ -699,9 +690,9 @@ class Cell(InjectableMixin, PlottableMixin):
                                     public_hoc_cell(self.cell).nSecBasal + apicnumber)
                     logger.info((apicnumber, secnumber))
                 else:
-                    raise Exception(
-                        "somaticbranches: No apic or \
-                                dend found in section %s" % secname)
+                    raise BluecellulabError(
+                        f"somaticbranches: No apic or dend found in section {secname}"
+                    )
 
     @staticmethod
     @deprecated("Use bluecellulab.cell.section_distance.EuclideanSectionDistance instead.")
@@ -743,7 +734,7 @@ class Cell(InjectableMixin, PlottableMixin):
 
                 children = [
                     neuron.h.SectionRef(sec=max_diam_section).child[index]
-                    for index in range(0, int(neuron.h.SectionRef(
+                    for index in range(int(neuron.h.SectionRef(
                         sec=max_diam_section).nchild()))]
                 if len(children) == 0:
                     break
@@ -808,18 +799,14 @@ class Cell(InjectableMixin, PlottableMixin):
     @property
     def info_dict(self):
         """Return a dictionary with all the information of this cell."""
-
-        cell_info = {}
-
-        cell_info['synapses'] = {}
-        for sid, synapse in self.synapses.items():
-            cell_info['synapses'][sid] = synapse.info_dict
-
-        cell_info['connections'] = {}
-        for sid, connection in self.connections.items():
-            cell_info['connections'][sid] = connection.info_dict
-
-        return cell_info
+        return {
+            'synapses': {
+                sid: synapse.info_dict for sid, synapse in self.synapses.items()
+            },
+            'connections': {
+                sid: connection.info_dict for sid, connection in self.connections.items()
+            }
+        }
 
     def delete(self):
         """Delete the cell."""

bluecellulab/circuit/circuit_access.py

@@ -557,7 +557,7 @@ class SonataCircuitAccess:
         edges = self._circuit.edges
         # select edges that are in the projections, if there are projections
         if projections is None or len(projections) == 0:
-            edge_population_names = [x for x in edges]
+            edge_population_names = list(edges)
         elif isinstance(projections, str):
             edge_population_names = [x for x in edges if edges[x].source.name == projections]
         else:

bluecellulab/plotwindow.py

@@ -52,7 +52,7 @@ class PlotWindow:
             # Sorry, don't see a way but disable this warning to access this
             colors = pylab.rcParams['axes.prop_cycle'].by_key()['color']
 
-            linecolors = [x for x in itertools.islice(itertools.cycle(colors), 0, 50)]
+            linecolors = list(itertools.islice(itertools.cycle(colors), 0, 50))
 
             self.line[var_name] = pylab.Line2D(
                 time, recording, label=var_name,

bluecellulab/psection.py

@@ -124,7 +124,7 @@ class PSection:
 
     def getAllPDescendants(self):
         """Return all the psection that are descendants of this psection."""
-        pdescendants = [x for x in self.pchildren]
+        pdescendants = list(self.pchildren)
         for child in self.pchildren:
             pdescendants += child.getAllPDescendants()
         return pdescendants
@@ -158,10 +158,7 @@ class PSection:
         if self.isLeaf:
             treeWidth = self.maxsegdiam + self.xSpacing
         else:
-            treeWidth = 0
-            for child in self.pchildren:
-                treeWidth += child.treeWidth()
-
+            treeWidth = sum(child.treeWidth() for child in self.pchildren)
         return max(self.diam + self.xSpacing, treeWidth)
 
     def treeHeight(self):

{bluecellulab-2.2.2.dist-info → bluecellulab-2.2.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bluecellulab
-Version: 2.2.2
+Version: 2.2.4
 Summary: The Pythonic Blue Brain simulator access
 Home-page: https://github.com/BlueBrain/BlueCelluLab
 Author: Blue Brain Project, EPFL

{bluecellulab-2.2.2.dist-info → bluecellulab-2.2.4.dist-info}/RECORD

@@ -5,8 +5,8 @@ bluecellulab/exceptions.py,sha256=ggTrfzoW3y0oDFUp3ff7GR9buLo-I2LM8XwxE1vQS9k,23
 bluecellulab/graph.py,sha256=ODiQy4xjRVxtNITXeXpYnqHas0wR7gZ_aXuDAF7jMq4,3419
 bluecellulab/importer.py,sha256=R9UPMK8MeZE8WJr2-VYyUOq3JqZe_VX5deaPuiW-1Gs,2848
 bluecellulab/neuron_interpreter.py,sha256=XPbQtOPIDk-sGydl4wuanOIeKl_rWvncXEsaweYTzVw,2185
-bluecellulab/plotwindow.py,sha256=-Tym4DH5tvuxLKua5NXxBcnVUNGMUQt3EltEQhG7fyg,2728
-bluecellulab/psection.py,sha256=_XTPc7bkm9M_06_h2kILW8J8wBhFGf6L9REv7y2m4yw,6060
+bluecellulab/plotwindow.py,sha256=u9bxWD6xYgzWBF-mI6Pi_qRAf3a4Wo4aqnH65f2W7v4,2721
+bluecellulab/psection.py,sha256=jiO75BAqNNg1_jwvDFrK1D2ay0j-dHJi-PcprOVG9u8,6013
 bluecellulab/psegment.py,sha256=f6NEryhuYplQyPLv_4t3d7lfh1rZW87xz8wiyOJ_0To,3121
 bluecellulab/rngsettings.py,sha256=Vz8qO1WI4TB9Cydy92AA3OSsDy9ZAxyFOYbj1Cazygk,3986
 bluecellulab/ssim.py,sha256=tbnLkddarBaa8TANZm9lTMli09lCtf1lG1auqR-XXzI,33282
@@ -16,7 +16,7 @@ bluecellulab/type_aliases.py,sha256=EMrunY-pIgZrsmetpAM8lA7tr0TFEzFoU5SX9sBuiOk,
 bluecellulab/utils.py,sha256=GKZkRYI2LY08tsIkG95MGn7EfmV4pBrIAqfRQCW14fs,300
 bluecellulab/cell/__init__.py,sha256=Sbc0QOsJ8E7tSwf3q7fsXuE_SevBN6ZmoCVyyU5zfII,208
 bluecellulab/cell/cell_dict.py,sha256=BKpJLYLrJCffKGak4EfGZtgus_u0Scz0NKas7tY31vE,1346
-bluecellulab/cell/core.py,sha256=Wsedq7heUj3Jg9PXKyN0X0PaQPos4eLYNwuErd3-krI,34488
+bluecellulab/cell/core.py,sha256=6WMp8fQoGFu1M1xQQX_HP-KTq1bJBwr8H36-dPV2QkQ,34145
 bluecellulab/cell/injector.py,sha256=QRg4GgK6qXFP-TnH8sg248_bHl8GfWonGoC4X-KI_nk,16843
 bluecellulab/cell/plotting.py,sha256=2yz7AIttx16spVTSrTogRRqhxFA9nrrGdo5jgANeUwg,4031
 bluecellulab/cell/random.py,sha256=s8Kf0q24fiA5rBdVCVbIdDMQGCDfQcwLwXRB72p1e1g,1773
@@ -29,7 +29,7 @@ bluecellulab/cell/ballstick/__init__.py,sha256=vywMSPAeTuCcK_E9gD8UX2XD1KfKbfCVF
 bluecellulab/cell/ballstick/emodel.hoc,sha256=7WcuepK-wB9bASRvNdCwO9Woc9-SpBCFqBqCXKgjsV8,1517
 bluecellulab/cell/ballstick/morphology.asc,sha256=EO0VIRilJAwpiDP2hIevwusfvYptNYhvsu1f5GgbSQo,190
 bluecellulab/circuit/__init__.py,sha256=Khpa13nzNvDlDS2JduyoFTukEduEkWCc5ML_JwGpmZs,361
-bluecellulab/circuit/circuit_access.py,sha256=ADrwWxGZD2x6wK1LIbC2hdOEtQMls2rk8cTaqhXKLSI,27514
+bluecellulab/circuit/circuit_access.py,sha256=HDFiE6Msh7nULYHOGcQp1S6s5eZvq-Iy6nlYbZQUD4U,27507
 bluecellulab/circuit/format.py,sha256=Q_YENbm45st6JjW80oMOOnLPdzKeVJh5nS_HHq1oj8g,1674
 bluecellulab/circuit/iotools.py,sha256=R_iDo1CM0X5z0SF_QtV4Ol4k5xX8kerE7n5djaY4Fxo,1591
 bluecellulab/circuit/node_id.py,sha256=OFNNt4g8w4Z6ZTh0qsbHqdSrWdftDp--tDaq_0-bLd8,1265
@@ -50,9 +50,9 @@ bluecellulab/simulation/simulation.py,sha256=sMTp3cjC3u-HAfw4WM1cab1ZpORCERPwgEj
 bluecellulab/synapse/__init__.py,sha256=RW8XoAMXOvK7OG1nHl_q8jSEKLj9ZN4oWf2nY9HAwuk,192
 bluecellulab/synapse/synapse_factory.py,sha256=qrtK_BMWGkpk1embG4oEkrLutt3L_ntqypuvYBxXPEA,6802
 bluecellulab/synapse/synapse_types.py,sha256=WDWpA9rpnyQg8tNuDK-NDPP-C22Ukx69aNljHwMiqkg,17027
-bluecellulab-2.2.2.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
-bluecellulab-2.2.2.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
-bluecellulab-2.2.2.dist-info/METADATA,sha256=eqlgvApEiZi93pD3l8fxX_oN5zB1wwWMnn_vkVOidEI,6907
-bluecellulab-2.2.2.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-bluecellulab-2.2.2.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
-bluecellulab-2.2.2.dist-info/RECORD,,
+bluecellulab-2.2.4.dist-info/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
+bluecellulab-2.2.4.dist-info/LICENSE,sha256=xOouu1gC1GGklDxkITlaVl60I9Ab860O-nZsFbWydvU,11749
+bluecellulab-2.2.4.dist-info/METADATA,sha256=vJBENOmPbIpAwgowk0RqWJJs1lkSD7_Ci0OOQu_GNIM,6907
+bluecellulab-2.2.4.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+bluecellulab-2.2.4.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
+bluecellulab-2.2.4.dist-info/RECORD,,