Formatted with black

Author: pgleeson

docs/conf.py

@@ -53,7 +53,7 @@
     # space here is important since __version__ is used in generation of
     # version_info also
     if "__version__ =" in aline:
-        version = aline.split("\"")[1]
+        version = aline.split('"')[1]
 # The full version, including alpha/beta/rc tags.
 release = version
 

docs/generate.py

@@ -2,7 +2,6 @@
 
 
 if __name__ == "__main__":
-
     net = neuromllite.Network(id="net")
     doc = net.generate_documentation(format="markdown")
     print(doc)

examples/Example12.py

@@ -1,5 +1,12 @@
 from neuromllite import Network, Cell, InputSource, Population, Synapse
-from neuromllite import Projection, RandomConnectivity, Input, Simulation, RectangularRegion, RandomLayout
+from neuromllite import (
+    Projection,
+    RandomConnectivity,
+    Input,
+    Simulation,
+    RectangularRegion,
+    RandomLayout,
+)
 import sys
 
 ################################################################################
@@ -11,21 +18,23 @@
 net.seed = 1234
 net.temperature = 32.0
 
-net.parameters = {"N": 20,
-                  "fractionE": 0.7,
-                  "weightInput": 0.7,
-                  "prob_e_e": 0.1,
-                  "prob_e_i": 0.9,
-                  "prob_i_e": 0.8,
-                  "prob_i_i": 0.3,
-                  "global_delay": 2}
-
-r1 = RectangularRegion(
-    id="region1", x=0, y=0, z=0, width=1000, height=100, depth=1000
-)
+net.parameters = {
+    "N": 20,
+    "fractionE": 0.7,
+    "weightInput": 0.7,
+    "prob_e_e": 0.1,
+    "prob_e_i": 0.9,
+    "prob_i_e": 0.8,
+    "prob_i_i": 0.3,
+    "global_delay": 2,
+}
+
+r1 = RectangularRegion(id="region1", x=0, y=0, z=0, width=1000, height=100, depth=1000)
 net.regions.append(r1)
 
-pyr_cell = Cell(id="pyr_4_sym", neuroml2_source_file="test_files/acnet2/pyr_4_sym.cell.nml")
+pyr_cell = Cell(
+    id="pyr_4_sym", neuroml2_source_file="test_files/acnet2/pyr_4_sym.cell.nml"
+)
 net.cells.append(pyr_cell)
 bask_cell = Cell(id="bask", neuroml2_source_file="test_files/acnet2/bask.cell.nml")
 net.cells.append(bask_cell)
@@ -61,17 +70,24 @@
 net.populations.append(pE)
 net.populations.append(pI)
 
-syn_e_e = Synapse(id="AMPA_syn", neuroml2_source_file="test_files/acnet2/AMPA_syn.synapse.nml")
+syn_e_e = Synapse(
+    id="AMPA_syn", neuroml2_source_file="test_files/acnet2/AMPA_syn.synapse.nml"
+)
 net.synapses.append(syn_e_e)
-syn_e_i = Synapse(id="AMPA_syn_inh", neuroml2_source_file="test_files/acnet2/AMPA_syn_inh.synapse.nml")
+syn_e_i = Synapse(
+    id="AMPA_syn_inh", neuroml2_source_file="test_files/acnet2/AMPA_syn_inh.synapse.nml"
+)
 net.synapses.append(syn_e_i)
-syn_i_e = Synapse(id="GABA_syn", neuroml2_source_file="test_files/acnet2/GABA_syn.synapse.nml")
+syn_i_e = Synapse(
+    id="GABA_syn", neuroml2_source_file="test_files/acnet2/GABA_syn.synapse.nml"
+)
 net.synapses.append(syn_i_e)
-syn_i_i = Synapse(id="GABA_syn_inh", neuroml2_source_file="test_files/acnet2/GABA_syn_inh.synapse.nml")
+syn_i_i = Synapse(
+    id="GABA_syn_inh", neuroml2_source_file="test_files/acnet2/GABA_syn_inh.synapse.nml"
+)
 net.synapses.append(syn_i_i)
 
 
-
 net.projections.append(
     Projection(
         id="projEE",
@@ -94,7 +110,6 @@
 )
 
 
-
 net.projections.append(
     Projection(
         id="projIE",
@@ -136,7 +151,7 @@
 ###   Build Simulation object & save as JSON
 
 sim = Simulation(
-    id="Sim%s"%net.id,
+    id="Sim%s" % net.id,
     network=new_file,
     duration="1000",
     seed="1111",
@@ -145,7 +160,7 @@
     record_spikes={
         pE.id: "*",
         pI.id: "*",
-    }
+    },
 )
 
 sim.to_json_file()

examples/Example4.py

@@ -125,7 +125,7 @@
 
 sim.to_json_file()
 sim.network = net_yaml_file
-sim.to_yaml_file('%s.yaml'%sim.id)
+sim.to_yaml_file("%s.yaml" % sim.id)
 
 sim.network = net_json_file  # reverting, for call below...
 

examples/Example6.py

@@ -6,7 +6,6 @@
 
 
 def generate(ref="Example6_PyNN", add_inputs=True):
-
     ################################################################################
     ###   Build new network
 
@@ -69,7 +68,6 @@ def generate(ref="Example6_PyNN", add_inputs=True):
     layers = ["L23", "L4", "L5", "L6"]
 
     for l in layers:
-
         i = 3 - layers.index(l)
         r = RectangularRegion(
             id=l,
@@ -83,7 +81,6 @@ def generate(ref="Example6_PyNN", add_inputs=True):
         net.regions.append(r)
 
         for t in ["E", "I"]:
-
             try:
                 import opencortex.utils.color as occ
 
@@ -223,7 +220,6 @@ def generate(ref="Example6_PyNN", add_inputs=True):
 
 
 if __name__ == "__main__":
-
     if "-noinputs" in sys.argv:
         sim, net = generate("Example6_PyNN_noinputs", False)
     else:

examples/Example7.py

@@ -14,7 +14,6 @@
 
 
 def generate():
-
     dt = 0.025
     simtime = 1000
 
@@ -228,9 +227,7 @@ def generate():
 
 
 if __name__ == "__main__":
-
     if "-sweep" in sys.argv:
-
         from neuromllite.sweep.ParameterSweep import *
 
         sim, net = generate()
@@ -298,7 +295,6 @@ def generate():
         plt.show()
 
     if "-sweep2" in sys.argv:
-
         sim, net = generate()
         sim.record_traces = {}
 
@@ -372,7 +368,6 @@ def generate():
         plt.show()
 
     else:
-
         sim, net = generate()
 
         ################################################################################

examples/arbor/ArborExample.py

@@ -103,7 +103,7 @@
 
 net.projections[0].random_connectivity = RandomConnectivity(probability=0.5)
 
-'''
+"""
 net.synapses.append(Synapse(id='gabaSyn',
                             pynn_receptor_type='inhibitory',
                             pynn_synapse_type='cond_alpha',
@@ -116,10 +116,10 @@
                                   synapse='gabaSyn',
                                   delay=2,
                                   weight=0.01))
-net.projections[1].random_connectivity=RandomConnectivity(probability=1)'''
+net.projections[1].random_connectivity=RandomConnectivity(probability=1)"""
 
 net.inputs.append(
-    Input(id="stim", input_source=input_source.id, population=p0.id, cell_ids=[1,2])
+    Input(id="stim", input_source=input_source.id, population=p0.id, cell_ids=[1, 2])
 )
 
 print(net.to_json())
@@ -141,7 +141,7 @@
 
 sim.to_json_file()
 sim.network = new_file_yaml
-sim.to_yaml_file('%s.yaml'%sim.id)
+sim.to_yaml_file("%s.yaml" % sim.id)
 
 
 ################################################################################

examples/sonatatest/analyze_output.py

@@ -5,7 +5,6 @@
 from analyze_output_utils import plot_data
 
 if __name__ == "__main__":
-
     plot_data(
         "output/membrane_potential.h5", "mV", "Membrane Potential", show_already=True
     )

examples/sonatatest/analyze_output_utils.py

@@ -16,7 +16,6 @@ def plot_data(reports_file, y_axis, title, show_already=True, max_num_traces=Non
             pop_prefixes = {pop: "/report/%s/" % pop}
 
     for pop in pop_prefixes:
-
         gids = np.array(cellvar_h5["%smapping/gids" % pop_prefixes[pop]])
 
         soma_locs = np.array(

examples/sonatatest/run_bmtk.py

@@ -4,7 +4,6 @@
 
 
 def run(config_file, simulator):
-
     if simulator == "NEURON":
         from bmtk.simulator import bionet
 
@@ -25,5 +24,4 @@ def run(config_file, simulator):
 
 
 if __name__ == "__main__":
-
     run("config.json", "NEST")