Adds switched RLC circuit example; regenerated nml; adds workflow for test_all.sh

.github/workflows/ci_test_all.yml

@@ -0,0 +1,52 @@
+name: CI Test script
+
+on:
+  push:
+    branches: [ main, development, experimental, test*, nml* ]
+  pull_request:
+    branches: [ main, development, experimental, test*, nml* ]
+
+jobs:
+
+  checks:
+    name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
+    runs-on: ${{ matrix.runs-on }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [ "3.10"]
+        runs-on: [ubuntu-latest]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install HDF5 for pytables on macos-14/latest
+      if: ${{ matrix.runs-on == 'macos-latest' }}
+      run: |
+        brew install hdf5
+
+    - name: Install graphviz
+      uses: ts-graphviz/setup-graphviz@v2
+      with:
+        # Skip to run brew update command on macOS.
+        macos-skip-brew-update: 'true' # default false
+
+    - name: Run test script
+      run: |
+        export NEURON_HOME=$pythonLocation
+        ./test_all.sh
+
+    - name: Version info for installed packages
+      run: |
+        pip list
+
+
+
+
+    - name: Final version info for optional installed packages
+      run: |
+          pip list

examples/MDF/RNN/IAFs.nmllite.json

@@ -1,16 +1,19 @@
 {
     "iaf_example": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.6.0",
         "notes": "NeuroMLlite export of MDF graph: iaf_example",
         "cells": {
-            "input_node__instance": {
+            "current_input_node__instance": {
                 "lems_source_file": "iaf_example_lems_definitions.xml"
             },
             "pre__instance": {
                 "lems_source_file": "iaf_example_lems_definitions.xml"
             },
             "post__instance": {
                 "lems_source_file": "iaf_example_lems_definitions.xml"
+            },
+            "syn_post__instance": {
+                "lems_source_file": "iaf_example_lems_definitions.xml"
             }
         },
         "synapses": {
@@ -20,14 +23,17 @@
             "silentSyn_proj_input_edge": {
                 "lems_source_file": "iaf_example_lems_definitions.xml"
             },
+            "silentSyn_proj_post_internal_edge": {
+                "lems_source_file": "iaf_example_lems_definitions.xml"
+            },
             "silentSyn_proj_syn_edge": {
                 "lems_source_file": "iaf_example_lems_definitions.xml"
             }
         },
         "populations": {
-            "input_node": {
+            "current_input_node": {
                 "size": 1,
-                "component": "input_node__instance",
+                "component": "current_input_node__instance",
                 "properties": {
                     "color": "0.2 0.2 0.2",
                     "radius": 3
@@ -48,11 +54,19 @@
                     "color": "0.2 0.2 0.2",
                     "radius": 3
                 }
+            },
+            "syn_post": {
+                "size": 1,
+                "component": "syn_post__instance",
+                "properties": {
+                    "color": "0.2 0.2 0.2",
+                    "radius": 3
+                }
             }
         },
         "projections": {
             "proj_input_edge": {
-                "presynaptic": "input_node",
+                "presynaptic": "current_input_node",
                 "postsynaptic": "pre",
                 "synapse": "rsDL",
                 "pre_synapse": "silentSyn_proj_input_edge",
@@ -62,9 +76,20 @@
                     "probability": 1
                 }
             },
+            "proj_post_internal_edge": {
+                "presynaptic": "syn_post",
+                "postsynaptic": "post",
+                "synapse": "rsDL",
+                "pre_synapse": "silentSyn_proj_post_internal_edge",
+                "type": "continuousProjection",
+                "weight": 1,
+                "random_connectivity": {
+                    "probability": 1
+                }
+            },
             "proj_syn_edge": {
                 "presynaptic": "pre",
-                "postsynaptic": "post",
+                "postsynaptic": "syn_post",
                 "synapse": "rsDL",
                 "pre_synapse": "silentSyn_proj_syn_edge",
                 "type": "continuousProjection",

examples/MDF/RNN/Simiaf_example.json

@@ -1,29 +1,22 @@
 {
     "Simiaf_example": {
-        "version": "NeuroMLlite v0.5.3",
+        "version": "NeuroMLlite v0.6.0",
         "network": "IAFs.nmllite.json",
         "duration": 100000.0,
         "dt": 10.0,
         "seed": 123,
         "record_variables": {
             "time": {
-                "input_node": 0
+                "current_input_node": 0
             },
-            "out_port": {
-                "input_node": 0
+            "current_output": {
+                "current_input_node": 0,
+                "syn_post": 0
             },
             "current_input": {
                 "pre": 0,
                 "post": 0
             },
-            "spike_input": {
-                "pre": 0,
-                "post": 0
-            },
-            "syn_i": {
-                "pre": 0,
-                "post": 0
-            },
             "spiking": {
                 "pre": 0,
                 "post": 0
@@ -32,13 +25,19 @@
                 "pre": 0,
                 "post": 0
             },
-            "out_port_v": {
+            "v_output": {
                 "pre": 0,
                 "post": 0
             },
-            "out_port_spiking": {
+            "spiking_output": {
                 "pre": 0,
                 "post": 0
+            },
+            "spike_input": {
+                "syn_post": 0
+            },
+            "syn_i": {
+                "syn_post": 0
             }
         }
     }

examples/MDF/RNN/regenerate.sh

@@ -12,4 +12,4 @@ python generate_iaf.py -run -net -nogui
 python generate_iaf.py -run -net2 -nogui
 #Fix dimensions!
 #python generate_iaf.py -neuroml
-pynml LEMS_Simiaf_example.xml -lems-graph
+#pynml LEMS_Simiaf_example.xml -lems-graph

examples/MDF/SwitchedRLC_Circuit.json

@@ -0,0 +1,75 @@
+{
+    "SwitchedRLC_Circuit": {
+        "format": "ModECI MDF v0.4",
+        "generating_application": "Python modeci-mdf v0.4.11",
+        "metadata": {
+            "preferred_duration": 2,
+            "preferred_dt": 0.001
+        },
+        "graphs": {
+            "SwitchedRLC_Circuit": {
+                "nodes": {
+                    "V": {
+                        "parameters": {
+                            "Vs": {
+                                "conditions": [
+                                    {
+                                        "id": "off",
+                                        "test": "time<0.5",
+                                        "value": "0"
+                                    },
+                                    {
+                                        "id": "on",
+                                        "test": "time>=0.5",
+                                        "value": 0.1
+                                    }
+                                ]
+                            },
+                            "R": {
+                                "metadata": {
+                                    "description": "Resistance in Ohms"
+                                },
+                                "value": 100
+                            },
+                            "L": {
+                                "metadata": {
+                                    "description": "Inductance in Henrys"
+                                },
+                                "value": 1
+                            },
+                            "C": {
+                                "value": 0.001
+                            },
+                            "time": {
+                                "default_initial_value": 0,
+                                "time_derivative": "1"
+                            },
+                            "V": {
+                                "default_initial_value": 0,
+                                "time_derivative": "i_C /C"
+                            },
+                            "i_R": {
+                                "value": "V / R"
+                            },
+                            "i_L": {
+                                "default_initial_value": 0,
+                                "time_derivative": "(Vs - V)/L"
+                            },
+                            "i_C": {
+                                "value": "i_L-i_R"
+                            }
+                        },
+                        "output_ports": {
+                            "V_out": {
+                                "value": "V"
+                            },
+                            "i_L_out": {
+                                "value": "i_L"
+                            }
+                        }
+                    }
+                }
+            }
+        }
+    }
+}

examples/MDF/SwitchedRLC_Circuit.yaml

@@ -0,0 +1,47 @@
+SwitchedRLC_Circuit:
+    format: ModECI MDF v0.4
+    generating_application: Python modeci-mdf v0.4.11
+    metadata:
+        preferred_duration: 2
+        preferred_dt: 0.001
+    graphs:
+        SwitchedRLC_Circuit:
+            nodes:
+                V:
+                    parameters:
+                        Vs:
+                            conditions:
+                            -   id: 'off'
+                                test: time<0.5
+                                value: '0'
+                            -   id: 'on'
+                                test: time>=0.5
+                                value: 0.1
+                        R:
+                            metadata:
+                                description: Resistance in Ohms
+                            value: 100
+                        L:
+                            metadata:
+                                description: Inductance in Henrys
+                            value: 1
+                        C:
+                            value: 0.001
+                        time:
+                            default_initial_value: 0
+                            time_derivative: '1'
+                        V:
+                            default_initial_value: 0
+                            time_derivative: i_C /C
+                        i_R:
+                            value: V / R
+                        i_L:
+                            default_initial_value: 0
+                            time_derivative: (Vs - V)/L
+                        i_C:
+                            value: i_L-i_R
+                    output_ports:
+                        V_out:
+                            value: V
+                        i_L_out:
+                            value: i_L

examples/MDF/newton.py

@@ -52,13 +52,13 @@ def main():
             s.append(eg.enodes["cool_node"].evaluable_outputs["out_port"].curr_value)
             t += dt
 
+        # Plotting the results
+        plt.plot(times, s)
+        plt.xlabel("Time")
+        plt.ylabel("Temperature")
+        plt.title("Newton's Cooling Law Simulation")
+        plt.savefig("newton_plot.png")
         if "-nogui" not in sys.argv:
-            # Plotting the results
-            plt.plot(times, s)
-            plt.xlabel("Time")
-            plt.ylabel("Temperature")
-            plt.title("Newton's Cooling Law Simulation")
-            plt.savefig("newton_plot.png")
             plt.show()
 
     if "-graph" in sys.argv: