fixing issue with init parameters axons + example of docstring for fa…

…scicle attributes

CHANGELOG.md

@@ -9,7 +9,7 @@ All notable changes to NRV are sumed up in this file.
 - progress bars are now handled with [rich.progress](https://rich.readthedocs.io/en/stable/progress.html)
 
 ### Fixed
-
+- ``axon.__init__``'s ``kwargs``: all parameters can now be set at the instantiation of the axon
 
 
 ### Removed

nrv/nmod/_axons.py

@@ -285,7 +285,11 @@ def __init__(
         self.Nsec = 0
         self.Nseg = 0
         self.myelinated = ""
-        ## stims
+
+        self.set_parameters(**kwargs)
+
+        ## Contexts
+        # Intra stims
         self.intra_current_stim = []
         self.intra_current_stim_positions = []
         self.intra_current_stim_starts = []
@@ -294,6 +298,8 @@ def __init__(
         self.intra_voltage_stim = None
         self.intra_voltage_stim_position = []
         self.intra_voltage_stim_stimulus = None
+
+        # Extra stims
         self.extra_stim = None
         self.footprints = None
         ## recording mechanism

nrv/nmod/_fascicles.py

@@ -180,8 +180,11 @@ def __init__(self, diameter=None, ID=0, **kwargs):
         super().__init__(**kwargs)
 
         # to add to a fascicle/nerve common mother class
-        self.save_path = ""
-        self.verbose = False
+
+        #:str: path where the simulation results should be saved
+        self.save_path:str = ""
+        #:str: value: False: verbosity mainly for pbars. Tests more comment
+        self.verbose = False 
         self.return_parameters_only = False
         self.loaded_footprints = False
         self.save_results = False

tests/unitary_tests/094_test_rec_all.py

@@ -2,45 +2,38 @@
 import matplotlib.pyplot as plt
 
 if __name__ == "__main__":
-	gnafbar_mrg = 3.0 # S.cm-2
-	gnapbar_mrg = 0.01 # S.cm-2
-	gksbar_mrg = 0.08  # S.cm-2
-	gl_mrg = 0.007  # S.cm-2
-	cm=1 * 1e-6 # F
-
-	## Test1
-
-
-	y = 0
-	z = 0
-	d = 6
-	L = nrv.get_length_from_nodes(d, 15)
-
-	axon1 = nrv.myelinated(y,z,d,L,dt=0.001,rec='all')
-	#print(axon1.rec_position_list)
-	total = 0
-	for positions in axon1.rec_position_list:
-		total += len(positions)
-	#print(total)
-	print(total == len(axon1.x_rec))
-
-	t_start = 2
-	duration = 0.1
-	amplitude = 2
-	axon1.insert_I_Clamp_node(2, t_start, duration, amplitude)
-
-	t_sim=15
-	results = axon1.simulate(t_sim=t_sim, record_I_mem=True)
-	del axon1
-
-
-	plt.figure()
-	map = plt.pcolormesh(results['t'], results['x_rec'], results['V_mem'] ,shading='auto')
-	plt.xlabel('time (ms)')
-	plt.ylabel('position (µm)')
-	cbar = plt.colorbar(map)
-	cbar.set_label('membrane voltage (mV)')
-	plt.savefig('./unitary_tests/figures/94_A.png')
+
+    ## Test1
+    y = 0
+    z = 0
+    d = 6
+    L = nrv.get_length_from_nodes(d, 15)
+
+    axon1 = nrv.myelinated(y,z,d,L,dt=0.001,rec='all')
+    #print(axon1.rec_position_list)
+    total = 0
+    for positions in axon1.rec_position_list:
+        total += len(positions)
+    #print(total)
+    print(total == len(axon1.x_rec))
+
+    t_start = 2
+    duration = 0.1
+    amplitude = 2
+    axon1.insert_I_Clamp_node(2, t_start, duration, amplitude)
+
+    t_sim=15
+    results = axon1.simulate(t_sim=t_sim, record_I_mem=True)
+    del axon1
+
+
+    plt.figure()
+    map = plt.pcolormesh(results['t'], results['x_rec'], results['V_mem'] ,shading='auto')
+    plt.xlabel('time (ms)')
+    plt.ylabel('position (µm)')
+    cbar = plt.colorbar(map)
+    cbar.set_label('membrane voltage (mV)')
+    plt.savefig('./unitary_tests/figures/94_A.png')