Add intial nmllite version

.gitignore

@@ -41,3 +41,15 @@ OpenWormMuscleModel.egg-info
 /NeuroML2/*_main.json
 arm64
 /NeuroML2/LEMS_NeuronMuscle_eden.py
+/NeuroML2/nmllite/CaPool.nml
+/NeuroML2/nmllite/IClamp_SingleCompMuscle.gv.png
+/NeuroML2/nmllite/IClamp_SingleCompMuscle.net.png
+/NeuroML2/nmllite/LEMS_Sim_IClamp_SingleCompMuscle.png
+/NeuroML2/nmllite/LEMS_Sim_IClamp_SingleCompMuscle.xml
+/NeuroML2/nmllite/Leak.channel.nml
+/NeuroML2/nmllite/*dat
+/NeuroML2/nmllite/SingleCompMuscle.cell.nml
+/NeuroML2/nmllite/ca_boyle.channel.nml
+/NeuroML2/nmllite/k_fast.channel.nml
+/NeuroML2/nmllite/k_slow.channel.nml
+/NeuroML2/nmllite/report.Sim_IClamp_SingleCompMuscle.txt

NeuroML2/nmllite/GenerateExamples.py

@@ -0,0 +1,74 @@
+from neuromllite import *
+from neuromllite.NetworkGenerator import *
+from neuromllite.utils import create_new_model
+import sys
+
+sys.path.append("..")
+
+
+def generate(cell, duration=45, config='IClamp',parameters = None):
+
+    reference = "%s_%s"%(config, cell)
+
+    cell_id = '%sCell'%cell
+    cell_nmll = Cell(id=cell_id, neuroml2_source_file='../%s.cell.nml'%(cell))
+
+    ################################################################################
+    ###   Add some inputs
+
+    if 'IClamp' in config:
+
+        if not parameters:
+            parameters = {}
+            parameters['stim_amp'] = '700pA'
+            parameters['offset_stim_amp'] = '-120 pA'
+
+        input_source0 = InputSource(id='iclamp_stim', 
+                                   neuroml2_input='PulseGenerator', 
+                                   parameters={'amplitude':'stim_amp', 'delay':'5ms', 'duration':'20ms'})
+
+        input_source1 = InputSource(id='iclamp_offset', 
+                                   neuroml2_input='PulseGenerator', 
+                                   parameters={'amplitude':'offset_stim_amp', 'delay':'0ms', 'duration':'10000ms'})
+
+
+    else:
+
+        if not parameters:
+            parameters = {}
+            parameters['average_rate'] = '100 Hz'
+            parameters['number_per_cell'] = '10'
+
+        input_source0 = InputSource(id='pfs0', 
+                                   neuroml2_input='PoissonFiringSynapse', 
+                                   parameters={'average_rate':'average_rate', 
+                                               'synapse':syn_exc.id, 
+                                               'spike_target':"./%s"%syn_exc.id})
+
+    sim, net = create_new_model(reference,
+                     duration, 
+                     dt=0.025, # ms 
+                     temperature=34, # degC
+                     default_region='Worm',
+                     parameters = parameters,
+                     cell_for_default_population=cell_nmll,
+                     input_for_default_population=input_source0)
+
+    net.input_sources.append(input_source1)
+    net.inputs.append(Input(id='input_offset',
+                            input_source=input_source1.id,
+                            population=net.populations[0].id,
+                            percentage=100))
+    net.to_json_file()
+
+    return sim, net
+
+
+
+if __name__ == "__main__":
+
+    sim, net = generate('SingleCompMuscle', 45, config="IClamp")
+
+
+    check_to_generate_or_run(sys.argv, sim)
+

NeuroML2/nmllite/IClamp_SingleCompMuscle.json

@@ -0,0 +1,68 @@
+{
+    "IClamp_SingleCompMuscle": {
+        "version": "NeuroMLlite v0.5.9",
+        "notes": "A network model: IClamp_SingleCompMuscle",
+        "parameters": {
+            "stim_amp": "700pA",
+            "offset_stim_amp": "-120 pA"
+        },
+        "cells": {
+            "SingleCompMuscleCell": {
+                "neuroml2_source_file": "../SingleCompMuscle.cell.nml"
+            }
+        },
+        "input_sources": {
+            "iclamp_stim": {
+                "parameters": {
+                    "amplitude": "stim_amp",
+                    "delay": "5ms",
+                    "duration": "20ms"
+                },
+                "neuroml2_input": "PulseGenerator"
+            },
+            "iclamp_offset": {
+                "parameters": {
+                    "amplitude": "offset_stim_amp",
+                    "delay": "0ms",
+                    "duration": "10000ms"
+                },
+                "neuroml2_input": "PulseGenerator"
+            }
+        },
+        "regions": {
+            "Worm": {
+                "x": 0.0,
+                "y": 0.0,
+                "z": 0.0,
+                "width": 1000.0,
+                "height": 100.0,
+                "depth": 1000.0
+            }
+        },
+        "populations": {
+            "pop_SingleCompMuscleCell": {
+                "size": 1,
+                "component": "SingleCompMuscleCell",
+                "properties": {
+                    "color": "0.8 0 0"
+                },
+                "random_layout": {
+                    "region": "Worm"
+                }
+            }
+        },
+        "inputs": {
+            "Stim_iclamp_stim": {
+                "input_source": "iclamp_stim",
+                "population": "pop_SingleCompMuscleCell",
+                "percentage": 100
+            },
+            "input_offset": {
+                "input_source": "iclamp_offset",
+                "population": "pop_SingleCompMuscleCell",
+                "percentage": 100
+            }
+        },
+        "temperature": 34.0
+    }
+}

NeuroML2/nmllite/IClamp_SingleCompMuscle.net.nml

@@ -0,0 +1,29 @@
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="IClamp_SingleCompMuscle">
+    <notes>Generated by NeuroMLlite v0.5.9
+    Generated network: IClamp_SingleCompMuscle
+    Generation seed: 1234
+    NeuroMLlite parameters: 
+        offset_stim_amp = -120 pA
+        stim_amp = 700pA</notes>
+    <include href="../SingleCompMuscle.cell.nml"/>
+    <pulseGenerator id="iclamp_stim" delay="5ms" duration="20ms" amplitude="700pA"/>
+    <pulseGenerator id="iclamp_offset" delay="0ms" duration="10000ms" amplitude="-120 pA"/>
+    <network id="IClamp_SingleCompMuscle" type="networkWithTemperature" temperature="34.0degC">
+        <notes>A network model: IClamp_SingleCompMuscle</notes>
+        <property tag="recommended_dt_ms" value="0.025"/>
+        <property tag="recommended_duration_ms" value="45.0"/>
+        <population id="pop_SingleCompMuscleCell" component="SingleCompMuscleCell" size="1" type="populationList">
+            <property tag="color" value="0.8 0 0"/>
+            <property tag="region" value="Worm"/>
+            <instance id="0">
+                <location x="966.453535692138757" y="44.073259917535268" z="7.491470058587191"/>
+            </instance>
+        </population>
+        <inputList id="Stim_iclamp_stim" population="pop_SingleCompMuscleCell" component="iclamp_stim">
+            <input id="0" target="../pop_SingleCompMuscleCell/0/SingleCompMuscleCell" destination="synapses"/>
+        </inputList>
+        <inputList id="input_offset" population="pop_SingleCompMuscleCell" component="iclamp_offset">
+            <input id="0" target="../pop_SingleCompMuscleCell/0/SingleCompMuscleCell" destination="synapses"/>
+        </inputList>
+    </network>
+</neuroml>

NeuroML2/nmllite/Sim_IClamp_SingleCompMuscle.json

@@ -0,0 +1,12 @@
+{
+    "Sim_IClamp_SingleCompMuscle": {
+        "version": "NeuroMLlite v0.5.9",
+        "network": "IClamp_SingleCompMuscle.json",
+        "duration": 45.0,
+        "dt": 0.025,
+        "seed": 12345,
+        "record_traces": {
+            "all": "*"
+        }
+    }
+}