More formatting

c302/__init__.py

@@ -79,6 +79,7 @@ def load_data_reader(data_reader="SpreadsheetDataReader"):
         reader (obj): The data reader object
     """
     return importlib.import_module("c302.%s" % data_reader)
+    # return importlib.import_module("cect.%s" % data_reader)
 
 
 def get_str_from_expnotation(num):

c302/backers.py

@@ -41,9 +41,7 @@ def get_adopted_cell_names(root=os.path.dirname(os.path.abspath(__file__)) + "/d
         info += "----------\n\n"
         info += "Adopted name: **" + name + "**\n\n\n"
         i = 0
-        search_file = open(
-            "../examples/c302_A_Full.nml", "r"
-        )
+        search_file = open("../examples/c302_A_Full.nml", "r")
         for line in search_file:
             i += 1
             if 'tag="OpenWormBackerAssignedName" value="%s"' % name in line:

c302/c302_info.py

@@ -27,13 +27,13 @@ def generate_c302_info(nml_doc, verbose=False):
 
         for c in cp.continuous_connection_instance_ws:
             if "inh" in c.post_component:
-                cc_inh_conns[cp.presynaptic_population][
-                    cp.postsynaptic_population
-                ] = float(c.weight)
+                cc_inh_conns[cp.presynaptic_population][cp.postsynaptic_population] = (
+                    float(c.weight)
+                )
             else:
-                cc_exc_conns[cp.presynaptic_population][
-                    cp.postsynaptic_population
-                ] = float(c.weight)
+                cc_exc_conns[cp.presynaptic_population][cp.postsynaptic_population] = (
+                    float(c.weight)
+                )
 
     gj_conns = {}
     for ep in net.electrical_projections:

c302/c302_utils.py

@@ -483,13 +483,13 @@ def generate_conn_matrix(
 
         for c in cp.continuous_connection_instance_ws:
             if "inh" in c.post_component:
-                cc_inh_conns[cp.presynaptic_population][
-                    cp.postsynaptic_population
-                ] = float(c.weight)
+                cc_inh_conns[cp.presynaptic_population][cp.postsynaptic_population] = (
+                    float(c.weight)
+                )
             else:
-                cc_exc_conns[cp.presynaptic_population][
-                    cp.postsynaptic_population
-                ] = float(c.weight)
+                cc_exc_conns[cp.presynaptic_population][cp.postsynaptic_population] = (
+                    float(c.weight)
+                )
 
     gj_conns = {}
     for ep in net.electrical_projections:
@@ -546,13 +546,13 @@ def generate_conn_matrix(
                 "Exc Conn %s -> %s: %s" % (pre, post, cc_exc_conns[pre][post]), verbose
             )
             if post in all_neurons:
-                data_exc_n[
-                    all_neurons.index(pre), all_neurons.index(post)
-                ] = cc_exc_conns[pre][post]
+                data_exc_n[all_neurons.index(pre), all_neurons.index(post)] = (
+                    cc_exc_conns[pre][post]
+                )
             else:
-                data_exc_m[
-                    all_neurons.index(pre), all_muscles.index(post)
-                ] = cc_exc_conns[pre][post]
+                data_exc_m[all_neurons.index(pre), all_muscles.index(post)] = (
+                    cc_exc_conns[pre][post]
+                )
             if pre in all_muscles:
                 raise Exception("Unexpected...")
 
@@ -562,13 +562,13 @@ def generate_conn_matrix(
                 "Inh Conn %s -> %s: %s" % (pre, post, cc_inh_conns[pre][post]), verbose
             )
             if post in all_neurons:
-                data_inh_n[
-                    all_neurons.index(pre), all_neurons.index(post)
-                ] = cc_inh_conns[pre][post]
+                data_inh_n[all_neurons.index(pre), all_neurons.index(post)] = (
+                    cc_inh_conns[pre][post]
+                )
             else:
-                data_inh_m[
-                    all_neurons.index(pre), all_muscles.index(post)
-                ] = cc_inh_conns[pre][post]
+                data_inh_m[all_neurons.index(pre), all_muscles.index(post)] = (
+                    cc_inh_conns[pre][post]
+                )
             if pre in all_muscles:
                 raise Exception("Unexpected...")
 
@@ -652,13 +652,13 @@ def generate_conn_matrix(
                 and post in all_neurons
             ):
                 if pre in all_neurons:
-                    data_n_m[
-                        all_neurons.index(pre), all_muscles.index(post)
-                    ] = gj_conns[pre][post]
+                    data_n_m[all_neurons.index(pre), all_muscles.index(post)] = (
+                        gj_conns[pre][post]
+                    )
                 else:
-                    data_n_m[
-                        all_muscles.index(pre), all_neurons.index(post)
-                    ] = gj_conns[pre][post]
+                    data_n_m[all_muscles.index(pre), all_neurons.index(post)] = (
+                        gj_conns[pre][post]
+                    )
                 neuron_muscle = True
             elif pre in all_muscles and post in all_muscles:
                 muscle_muscle = True
@@ -736,14 +736,18 @@ def generate_conn_matrix(
     colormap = None
 
     if "-phar" in sys.argv:
-        configs = ["c302_C0_Pharyngeal.net.nml"]
+        configs = ["c302_C1_Pharyngeal.net.nml"]
 
     elif "-osc" in sys.argv:
         configs = ["c302_C1_Oscillator.net.nml"]
 
     elif "-soc" in sys.argv:
         configs = ["c302_C1_Social.net.nml"]
 
+    elif "-syns" in sys.argv:
+        configs = ["c302_C1_Syns.net.nml"]
+        figsize = (10, 10)
+
     elif "-musc" in sys.argv:
         configs = ["c302_C1_Muscles.net.nml"]
         figsize = (10, 10)

test.sh

@@ -1,5 +1,7 @@
 set -ex
 
+pip install .
+
 ##   Test readers
 
 python -m c302.SpreadsheetDataReader