Restructure main test file

Tidy load_data.py

Author: pgleeson

.github/workflows/ci-make.yml

@@ -28,11 +28,11 @@ jobs:
       run: g++ -v
 
     - name: Install dependencies (Ubuntu)
-      run: sudo apt-get install -y nlohmann-json3-dev
+      run: sudo apt-get install -y nlohmann-json3-dev tree
       if: ${{ contains(matrix.runs-on, 'ubuntu') }}
 
     - name: Install dependencies (macOS)
-      run: brew install nlohmann-json
+      run: brew install nlohmann-json tree
       if: ${{ contains(matrix.runs-on, 'macos') }}
 
     - name: Run C++ tests 
@@ -54,15 +54,6 @@ jobs:
         pip install pyNeuroML
         pip install numpy matplotlib
         pip install ruff
-        
-
-
-    - name: Test NeuroML
-      run: |
-        cd neuromlLocal
-        ./regenerate.sh 
-
-        # make clean all # not yet...
 
     - name: Test directly running main program
       run: |
@@ -79,11 +70,12 @@ jobs:
         export NEURON_HOME=$pythonLocation
         env
         
-        ./test_all.sh 
+        ./test_all.sh # also generated neuroml
 
         git diff exampleRun/phenotype.dat 
 
       
     - name: list generated files
       run: |
           ls -alth
+          tree

load_data.py

@@ -5,11 +5,13 @@
 
 import numpy as np
 from matplotlib import pyplot as plt
-#import random
+
+# import random
 import helper_funcs as hf
 
 
-def reload_single_run(show_plot=True):
+def reload_single_run(show_plot=True, verbose=False):
+
     N_muscles = 24  # Number of muscles alongside the body
     N_units = 10  # Number of neural units in VNC
     N_neuronsperunit = 6  # Number of neurons in a VNC neural unit (6 neurons)
@@ -36,7 +38,7 @@ def reload_single_run(show_plot=True):
             act_data[0], act_data[i], label="SR %i" % (i - offset), linewidth=0.5
         )
         axs[0, 0].xaxis.set_ticklabels([])
-    plt.legend()
+    #plt.legend()
 
     axs[0, 1].imshow(sr, aspect="auto", interpolation="nearest")
     axs[0, 1].xaxis.set_ticklabels([])
@@ -49,7 +51,7 @@ def reload_single_run(show_plot=True):
             act_data[0], act_data[i], label="Neu %i" % (i - offset), linewidth=0.5
         )
         axs[1, 0].xaxis.set_ticklabels([])
-    plt.legend()
+    #plt.legend()
 
     neu = act_data[offset : N_neurons + offset]
     axs[1, 1].imshow(neu, aspect="auto", interpolation="nearest")
@@ -63,7 +65,7 @@ def reload_single_run(show_plot=True):
             act_data[0], act_data[i], label="Mu %i" % (i - offset), linewidth=0.5
         )
         axs[2, 0].xaxis.set_ticklabels([])
-    plt.legend()
+    #plt.legend()
 
     mus = act_data[offset : N_muscles + offset]
     axs[2, 1].imshow(mus, aspect="auto", interpolation="nearest")
@@ -92,14 +94,14 @@ def reload_single_run(show_plot=True):
         f = float(t) / tmax
 
         color = "#%02x%02x00" % (int(0xFF * (f)), int(0xFF * (1 - f) * 0.8))
-        #color2 = "#%06x" % random.randint(0, 0xFFFFFF)
+        # color2 = "#%06x" % random.randint(0, 0xFFFFFF)
 
         point_start = 1
         for i in range(point_start, 50):
             x = body_data[i * 3 + 1][t]
             y = body_data[i * 3 + 2][t]
-            #y1 = body_data[i * 3 + 2][t]
-            if i == 1:
+            # y1 = body_data[i * 3 + 2][t]
+            if i == 1 and verbose:
                 print(
                     "%s + Plotting %i at t=%s (%s,%s), %s"
                     % ("\n" if i == point_start else "", i, t, x, y, color)