Merge pull request #28 from openworm/test_neuroml_pg

Reformatting python & restructured tests

Author: adampdp

.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 
@@ -52,18 +52,9 @@ jobs:
       run: |
         pip install OSBModelValidation
         pip install pyNeuroML
-        pip install ruff
         pip install numpy matplotlib
-        pip install ruff
-        
-
-
-    - name: Test NeuroML
-      run: |
-        cd neuromlLocal
-        ./regenerate.sh 
-
-        # make clean all # not yet...
+        pip install ruff 
+        pip install neuron 
 
     - name: Test directly running main program
       run: |
@@ -80,11 +71,12 @@ 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

.gitignore

@@ -27,3 +27,14 @@
 /neuromlLocal/Worm2DNet.gv.png
 /neuromlLocal/x86_64
 /neuromlLocal/testc302NervousSystem
+/arm64
+/x86_64
+/report.txt
+/exampleRun_nml
+/*.dat
+/exampleRun2
+/neuromlLocal/testc302SigSim/*.dat
+/neuromlLocal/testc302SigSim/arm64
+/neuromlLocal/testc302SigSim/x86_64
+/neuromlLocal/testc302SigSim/report.txt
+/neuromlLocal/testc302SigSim/testc302NervousSystem

Makefile

@@ -61,4 +61,4 @@ tests2: tests2.o NervousSystem.o random.o jsonUtils.o utils.o
 	g++ $(CXXFLAGS) $(LDFLAGS) -pthread -o tests2 tests2.o NervousSystem.o random.o utils.o jsonUtils.o $(LIBS)
 
 clean:
-	rm -f *.o main tests tests2
+	rm -f *.o neuromlLocal/*.o main tests tests2

load_data.py

@@ -5,11 +5,12 @@
 
 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 +37,7 @@ 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 +50,7 @@ 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 +64,7 @@ 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 +93,14 @@ 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)

neuromlLocal/Worm2D_neuroml.py

@@ -7,7 +7,6 @@
 
 import neuroml.writers as writers
 from neuroml import (
-    ExplicitInput,
     Network,
     NeuroMLDocument,
     Population,
@@ -16,13 +15,13 @@
     ContinuousProjection,
     ContinuousConnectionInstanceW,
     ElectricalConnectionInstanceW,
-    IncludeType,
     Property,
     Instance,
     Location,
     InputW,
     InputList,
 )
+# from neuroml import IncludeType
 
 import utils
 

neuromlLocal/build_network.py

@@ -0,0 +1,6 @@
+#!/bin/bash
+set -e
+
+rm -rf arm64 x86_64 __pycache__
+
+mv *.dat *.mod *_nrn.py *gv* report.txt /tmp || true

neuromlLocal/clean.sh

@@ -196,7 +196,7 @@ def run(self, skip_to_time=-1):
 
         self.ns.advance()
 
-        # print_("< Current NEURON time: %s ms" % self.h.t)
+        print_("< Current NEURON time: %s ms" % self.h.t)
 
         # values = []
         pop_list = [

neuromlLocal/main_sim.py

@@ -1,9 +1,16 @@
 #!/bin/bash
 set -ex
 
+./clean.sh 
+
 ruff format *py
 
 python regenerate.py
 
 omv all -V 
 
+cd testc302SigSim
+make clean all
+./testc302NervousSystem
+cd ..
+