Remove much cout... Bump versions

.github/workflows/ci-build.yml

@@ -87,16 +87,18 @@ jobs:
 
     - name: Run tests
       run: |
-        # Install specific branch of pyNeuroML
-        pip install git+https://github.com/NeuroML/pyNeuroML.git@experimental
-
         pip install c302
         pip install neuron
         pip list
         which nrniv
         export NEURON_HOME=/home/runner/.local
         ./run_all_tests.sh 
 
+    - name: Generated file info
+      run: |
+        
+        ls -alt  simulations/*
+
     - name: Final version info
       run: |
         

main_sim.py

@@ -164,7 +164,7 @@ def __init__(self, tstop=100, dt=0.005, activity_file=None, verbose=True):
 
     def set_timestep(self, dt):
 
-        print('Setting timestep...')
+        print('Setting timestep to %s...'%dt)
 
         dt = float('{:0.1e}'.format(dt)) * 1000.0 # memory issue fix
 
@@ -173,13 +173,11 @@ def set_timestep(self, dt):
             import neuron
             self.h = neuron.h
         except Exception as e:
-            return 'Python import error: %s..'%e 
+            raise Exception('Python import error in C302NRNSimulation: %s..'%e)
 
         self.ns = NeuronSimulation(self.tstop, dt)
         print_("Initialised C302NRNSimulation of length %s ms and dt = %s ms..."%(self.tstop,dt))
 
-        return 'Success...' # for debugging... 
-
 
     def save_results(self):
 

run_all_tests.sh

@@ -3,17 +3,17 @@
 set -ex
 
 # No c302
-python sibernetic_c302.py -test -noc302 -duration 0.1
+python3 sibernetic_c302.py -test -noc302 -duration 0.1
 
-python sibernetic_c302.py -test -noc302 -duration 0.054 -logstep 3
+python3 sibernetic_c302.py -test -noc302 -duration 0.054 -logstep 3
 
 # c302
-python sibernetic_c302.py -test  -duration 1.1  -c302params C1 
+python3 sibernetic_c302.py -test  -duration 1.1  -c302params C1 
 
 # c302 + half_resolution
-python sibernetic_c302.py -test  -duration 1  -c302params C0 -configuration worm_alone_half_resolution 
+python3 sibernetic_c302.py -test  -duration 1  -c302params C0 -configuration worm_alone_half_resolution 
 
 # c302 + TestMuscle 
-python sibernetic_c302.py -test -duration 20 -c302params C0 -reference TargetMuscle -configuration worm_alone_half_resolution -logstep 500
+python3 sibernetic_c302.py -test -duration 20 -c302params C0 -reference TargetMuscle -configuration worm_alone_half_resolution -logstep 500
 
 

sibernetic_c302.py

@@ -9,7 +9,7 @@
 import pprint
 pp = pprint.PrettyPrinter(indent=4)
 
-script_version = '0.1.7' # This will change at different rate to C++ code...
+script_version = '0.1.8' # This will change at different rate to C++ code...
 
 DEFAULTS = {'duration': 2.0,
             'dt': 0.005,
@@ -412,7 +412,7 @@ def run(a=None,**kwargs):
 
     if not a.noc302 and successful:
 
-        announce("Generating images for neuronal activity...")
+        announce("Generating images for neuronal activity (via %s in %s)..."%(lems_file, sim_dir))
 
         results = pynml.reload_saved_data(lems_file,
                           base_dir=sim_dir,

src/main.cpp

@@ -45,7 +45,7 @@ bool load_to = false;
 bool skip_display_particles = false;
 bool skip_display_membranes = false;
 bool skip_display_connections = false;
-std::string version = "0.0.7";
+std::string version = "0.0.8";
 
 int usage() {
   std::cout

src/owSignalSimulator.cpp

@@ -80,62 +80,48 @@ SignalSimulator::SignalSimulator(const std::string &simFileName,
 
   // Import the file as a Python module.
   pModule = PyImport_Import(pName);
-  std::cout << "1) Py module "<< s <<" imported..." << std::endl;
-  if (PyErr_Occurred())
-    PyErr_Print();
-
-    PyObject *pModule2 = PyImport_Import(PyUnicode_FromString("sys"));
   if (PyErr_Occurred())
     PyErr_Print();
 
 
-  std::cout << "2) all good" << std::endl;
   // Build the name of a callable class
   if (pModule != nullptr) {
-  std::cout << "3) class: " << simClassName << std::endl;
     pClass = PyObject_GetAttrString(pModule, simClassName.c_str());
     if (PyErr_Occurred())
       PyErr_Print();
   } else {
 
-  std::cout << "4) Good..." << std::endl;
     throw std::runtime_error("Python module not loaded, have you set "
                              "PYTHONPATH?\nTry: \n\n   export "
-                             "PYTHONPATH=$PYTHONPATH:./src\n");
+                             "PYTHONPATH=$PYTHONPATH:.\n");
   }
-  std::cout << "5) pClass: " << pClass << std::endl;
   // Create an instance of the class
   if (PyCallable_Check(pClass)) {
-  std::cout << "6) callable.." << std::endl;
-
-      try {
-    pInstance = PyObject_CallObject(pClass, nullptr);
-      } catch (const std::exception& ex)
-      {
-  std::cout << "Error: " << ex.what() << std::endl;
-      }
-  std::cout << "7) No error" << std::endl;
+
+    try {
+      pInstance = PyObject_CallObject(pClass, nullptr);
+    } catch (const std::exception& ex)
+    {
+      std::cout << "Error: " << ex.what() << std::endl;
+    }
+
     if (PyErr_Occurred())
     {
-  std::cout << "errrr" << std::endl;
+      std::cout << "Error at PyObject_CallObject" << std::endl;
       PyErr_Print();
-
     }
     PyObject *dt = Py_BuildValue("f", timeStep); // Create tuple of arguments for initialization
     PyObject *pFuncName = Py_BuildValue("s", "set_timestep");
-  std::cout << "Calling " << pFuncName << std::endl;
     //pInstance = PyObject_CallMethod(pInstance, "set_timestep", "(f)", timeStep);
 
-      try {
-    PyObject *output = PyObject_CallMethodObjArgs(pInstance, pFuncName, dt, nullptr);
-        std::cout << "Here's the output: " << output << std::endl;
+    try {
+      PyObject_CallMethodObjArgs(pInstance, pFuncName, dt, nullptr);
 
-      } catch (const std::exception& ex)
-      {
-  std::cout << "Error: " << ex.what() << std::endl;
-      }
+    } catch (const std::exception& ex)
+    {
+      std::cout << "Error: " << ex.what() << std::endl;
+    }
 
-  std::cout << "8) Good..." << std::endl;
     if (PyErr_Occurred())
       PyErr_Print();
     Py_DECREF(dt);
@@ -147,8 +133,6 @@ SignalSimulator::SignalSimulator(const std::string &simFileName,
                              "callable! Try: export "
                              "PYTHONPATH=$PYTHONPATH:./src");
   }
-
-  std::cout << "999" << std::endl;
 }
 
 std::vector<float> SignalSimulator::run() {