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openworm · Sep 21, 2023 · 10abce2 · 10abce2
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Showing 13 changed files with 46 additions and 46 deletions.
diff --git a/examples/parametersweep/CanonicalCircuit.py b/examples/parametersweep/CanonicalCircuit.py
@@ -159,7 +159,7 @@ def generate(duration=1000, paramset='C'):
                      network=new_file,
                      duration=duration,
                      dt='0.1',
-                     recordTraces={'all':'*'},
+                     record_traces={'all':'*'},
                      plots2D={'DB-VB':{'x_axis':'DB/0/%s/v'%neuron_id,
                                     'y_axis':'VB/0/%s/v'%neuron_id}})
 

diff --git a/examples/parametersweep/Canonical_C.json b/examples/parametersweep/Canonical_C.json
@@ -1,6 +1,6 @@
 {
     "Canonical_C": {
-        "version": "NeuroMLlite v0.3.0",
+        "version": "NeuroMLlite v0.5.7",
         "parameters": {
             "stim_duration": "2000ms",
             "stim_amp": "3.5pA",
@@ -24,12 +24,12 @@
         },
         "input_sources": {
             "iclamp_0": {
-                "neuroml2_input": "PulseGenerator",
                 "parameters": {
                     "amplitude": "stim_amp",
                     "delay": "500ms",
                     "duration": "stim_duration"
-                }
+                },
+                "neuroml2_input": "PulseGenerator"
             }
         },
         "regions": {
@@ -212,7 +212,7 @@
             "stim": {
                 "input_source": "iclamp_0",
                 "population": "AVB",
-                "percentage": 100.0
+                "percentage": 100
             }
         }
     }

diff --git a/examples/parametersweep/Canonical_C.net.nml b/examples/parametersweep/Canonical_C.net.nml
@@ -1,5 +1,5 @@
-<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_v2.2.xsd" id="Canonical_C">
-    <notes>Generated by NeuroMLlite v0.3.0
+<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.xsd" id="Canonical_C">
+    <notes>Generated by NeuroMLlite v0.5.7
     Generated network: Canonical_C
     Generation seed: 1234
     NeuroMLlite parameters: 
@@ -60,28 +60,28 @@
             </instance>
         </population>
         <continuousProjection id="proj_AVB_VB" presynapticPopulation="AVB" postsynapticPopulation="VB">
-            <continuousConnectionInstanceW id="0" preCell="../AVB/0/GenericNeuronCell" postCell="../VB/0/GenericNeuronCell" preComponent="silentSyn_proj_AVB_VB" postComponent="neuron_to_neuron_exc_syn" weight="3."/>
+            <continuousConnectionInstanceW id="0" preCell="../AVB/0/GenericNeuronCell" postCell="../VB/0/GenericNeuronCell" preComponent="silentSyn_proj_AVB_VB" postComponent="neuron_to_neuron_exc_syn" weight="3.0"/>
         </continuousProjection>
         <continuousProjection id="proj_AVB_DB" presynapticPopulation="AVB" postsynapticPopulation="DB">
             <continuousConnectionInstanceW id="0" preCell="../AVB/0/GenericNeuronCell" postCell="../DB/0/GenericNeuronCell" preComponent="silentSyn_proj_AVB_DB" postComponent="neuron_to_neuron_exc_syn" weight="1.5"/>
         </continuousProjection>
         <continuousProjection id="proj_DB_VD" presynapticPopulation="DB" postsynapticPopulation="VD">
-            <continuousConnectionInstanceW id="0" preCell="../DB/0/GenericNeuronCell" postCell="../VD/0/GenericNeuronCell" preComponent="silentSyn_proj_DB_VD" postComponent="neuron_to_neuron_exc_syn" weight="20."/>
+            <continuousConnectionInstanceW id="0" preCell="../DB/0/GenericNeuronCell" postCell="../VD/0/GenericNeuronCell" preComponent="silentSyn_proj_DB_VD" postComponent="neuron_to_neuron_exc_syn" weight="20.0"/>
         </continuousProjection>
         <continuousProjection id="proj_DB_DD" presynapticPopulation="DB" postsynapticPopulation="DD">
-            <continuousConnectionInstanceW id="0" preCell="../DB/0/GenericNeuronCell" postCell="../DD/0/GenericNeuronCell" preComponent="silentSyn_proj_DB_DD" postComponent="neuron_to_neuron_exc_syn" weight="20."/>
+            <continuousConnectionInstanceW id="0" preCell="../DB/0/GenericNeuronCell" postCell="../DD/0/GenericNeuronCell" preComponent="silentSyn_proj_DB_DD" postComponent="neuron_to_neuron_exc_syn" weight="20.0"/>
         </continuousProjection>
         <continuousProjection id="proj_VB_VD" presynapticPopulation="VB" postsynapticPopulation="VD">
-            <continuousConnectionInstanceW id="0" preCell="../VB/0/GenericNeuronCell" postCell="../VD/0/GenericNeuronCell" preComponent="silentSyn_proj_VB_VD" postComponent="neuron_to_neuron_exc_syn" weight="20."/>
+            <continuousConnectionInstanceW id="0" preCell="../VB/0/GenericNeuronCell" postCell="../VD/0/GenericNeuronCell" preComponent="silentSyn_proj_VB_VD" postComponent="neuron_to_neuron_exc_syn" weight="20.0"/>
         </continuousProjection>
         <continuousProjection id="proj_VB_DD" presynapticPopulation="VB" postsynapticPopulation="DD">
-            <continuousConnectionInstanceW id="0" preCell="../VB/0/GenericNeuronCell" postCell="../DD/0/GenericNeuronCell" preComponent="silentSyn_proj_VB_DD" postComponent="neuron_to_neuron_exc_syn" weight="20."/>
+            <continuousConnectionInstanceW id="0" preCell="../VB/0/GenericNeuronCell" postCell="../DD/0/GenericNeuronCell" preComponent="silentSyn_proj_VB_DD" postComponent="neuron_to_neuron_exc_syn" weight="20.0"/>
         </continuousProjection>
         <continuousProjection id="proj_VD_VB" presynapticPopulation="VD" postsynapticPopulation="VB">
-            <continuousConnectionInstanceW id="0" preCell="../VD/0/GenericNeuronCell" postCell="../VB/0/GenericNeuronCell" preComponent="silentSyn_proj_VD_VB" postComponent="neuron_to_neuron_inh_syn" weight="40."/>
+            <continuousConnectionInstanceW id="0" preCell="../VD/0/GenericNeuronCell" postCell="../VB/0/GenericNeuronCell" preComponent="silentSyn_proj_VD_VB" postComponent="neuron_to_neuron_inh_syn" weight="40.0"/>
         </continuousProjection>
         <continuousProjection id="proj_DD_DB" presynapticPopulation="DD" postsynapticPopulation="DB">
-            <continuousConnectionInstanceW id="0" preCell="../DD/0/GenericNeuronCell" postCell="../DB/0/GenericNeuronCell" preComponent="silentSyn_proj_DD_DB" postComponent="neuron_to_neuron_inh_syn" weight="40."/>
+            <continuousConnectionInstanceW id="0" preCell="../DD/0/GenericNeuronCell" postCell="../DB/0/GenericNeuronCell" preComponent="silentSyn_proj_DD_DB" postComponent="neuron_to_neuron_inh_syn" weight="40.0"/>
         </continuousProjection>
         <inputList id="stim" population="AVB" component="iclamp_0">
             <input id="0" target="../AVB/0/GenericNeuronCell" destination="synapses"/>

diff --git a/examples/parametersweep/Canonical_X.json b/examples/parametersweep/Canonical_X.json
@@ -1,6 +1,6 @@
 {
     "Canonical_X": {
-        "version": "NeuroMLlite v0.3.0",
+        "version": "NeuroMLlite v0.5.7",
         "parameters": {
             "stim_duration": "250ms",
             "stim_amp": "1pA",
@@ -24,12 +24,12 @@
         },
         "input_sources": {
             "iclamp_0": {
-                "neuroml2_input": "PulseGenerator",
                 "parameters": {
                     "amplitude": "stim_amp",
                     "delay": "500ms",
                     "duration": "stim_duration"
-                }
+                },
+                "neuroml2_input": "PulseGenerator"
             }
         },
         "regions": {
@@ -146,7 +146,7 @@
             "stim": {
                 "input_source": "iclamp_0",
                 "population": "AVB",
-                "percentage": 100.0
+                "percentage": 100
             }
         }
     }

diff --git a/examples/parametersweep/Canonical_X.net.nml b/examples/parametersweep/Canonical_X.net.nml
@@ -1,5 +1,5 @@
-<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_v2.2.xsd" id="Canonical_X">
-    <notes>Generated by NeuroMLlite v0.3.0
+<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.xsd" id="Canonical_X">
+    <notes>Generated by NeuroMLlite v0.5.7
     Generated network: Canonical_X
     Generation seed: 1234
     NeuroMLlite parameters: 

diff --git a/examples/parametersweep/IClamp_GenericMuscleCell.json b/examples/parametersweep/IClamp_GenericMuscleCell.json
@@ -1,24 +1,23 @@
 {
     "IClamp_GenericMuscleCell": {
-        "version": "NeuroMLlite v0.3.0",
-        "temperature": 34.0,
+        "version": "NeuroMLlite v0.5.7",
+        "notes": "A network model: IClamp_GenericMuscleCell",
         "parameters": {
             "stim_amp": "4pA"
         },
-        "notes": "A network model: IClamp_GenericMuscleCell",
         "cells": {
             "GenericMuscleCell": {
                 "neuroml2_source_file": "GenericMuscleCell.cell.nml"
             }
         },
         "input_sources": {
             "iclamp_0": {
-                "neuroml2_input": "PulseGenerator",
                 "parameters": {
                     "amplitude": "stim_amp",
                     "delay": "500ms",
                     "duration": "2000ms"
-                }
+                },
+                "neuroml2_input": "PulseGenerator"
             }
         },
         "regions": {
@@ -47,8 +46,9 @@
             "Stim_iclamp_0": {
                 "input_source": "iclamp_0",
                 "population": "pop_GenericMuscleCell",
-                "percentage": 100.0
+                "percentage": 100
             }
-        }
+        },
+        "temperature": 34.0
     }
 }
diff --git a/examples/parametersweep/IClamp_GenericMuscleCell.net.nml b/examples/parametersweep/IClamp_GenericMuscleCell.net.nml
@@ -1,5 +1,5 @@
-<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_v2.2.xsd" id="IClamp_GenericMuscleCell">
-    <notes>Generated by NeuroMLlite v0.3.0
+<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.xsd" id="IClamp_GenericMuscleCell">
+    <notes>Generated by NeuroMLlite v0.5.7
     Generated network: IClamp_GenericMuscleCell
     Generation seed: 1234
     NeuroMLlite parameters: 

diff --git a/examples/parametersweep/IClamp_GenericNeuronCell.json b/examples/parametersweep/IClamp_GenericNeuronCell.json
@@ -1,24 +1,23 @@
 {
     "IClamp_GenericNeuronCell": {
-        "version": "NeuroMLlite v0.3.0",
-        "temperature": 34.0,
+        "version": "NeuroMLlite v0.5.7",
+        "notes": "A network model: IClamp_GenericNeuronCell",
         "parameters": {
             "stim_amp": "4pA"
         },
-        "notes": "A network model: IClamp_GenericNeuronCell",
         "cells": {
             "GenericNeuronCell": {
                 "neuroml2_source_file": "GenericNeuronCell.cell.nml"
             }
         },
         "input_sources": {
             "iclamp_0": {
-                "neuroml2_input": "PulseGenerator",
                 "parameters": {
                     "amplitude": "stim_amp",
                     "delay": "500ms",
                     "duration": "2000ms"
-                }
+                },
+                "neuroml2_input": "PulseGenerator"
             }
         },
         "regions": {
@@ -47,8 +46,9 @@
             "Stim_iclamp_0": {
                 "input_source": "iclamp_0",
                 "population": "pop_GenericNeuronCell",
-                "percentage": 100.0
+                "percentage": 100
             }
-        }
+        },
+        "temperature": 34.0
     }
 }
diff --git a/examples/parametersweep/IClamp_GenericNeuronCell.net.nml b/examples/parametersweep/IClamp_GenericNeuronCell.net.nml
@@ -1,5 +1,5 @@
-<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_v2.2.xsd" id="IClamp_GenericNeuronCell">
-    <notes>Generated by NeuroMLlite v0.3.0
+<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.xsd" id="IClamp_GenericNeuronCell">
+    <notes>Generated by NeuroMLlite v0.5.7
     Generated network: IClamp_GenericNeuronCell
     Generation seed: 1234
     NeuroMLlite parameters: 

diff --git a/examples/parametersweep/SimCanonical_C.json b/examples/parametersweep/SimCanonical_C.json
@@ -1,10 +1,10 @@
 {
     "SimCanonical_C": {
-        "version": "NeuroMLlite v0.3.0",
+        "version": "NeuroMLlite v0.5.7",
         "network": "Canonical_C.json",
         "duration": 3000.0,
         "dt": 0.1,
-        "recordTraces": {
+        "record_traces": {
             "all": "*"
         },
         "plots2D": {

diff --git a/examples/parametersweep/SimCanonical_X.json b/examples/parametersweep/SimCanonical_X.json
@@ -1,10 +1,10 @@
 {
     "SimCanonical_X": {
-        "version": "NeuroMLlite v0.3.0",
+        "version": "NeuroMLlite v0.5.7",
         "network": "Canonical_X.json",
         "duration": 3000.0,
         "dt": 0.1,
-        "recordTraces": {
+        "record_traces": {
             "all": "*"
         },
         "plots2D": {

diff --git a/examples/parametersweep/Sim_IClamp_GenericMuscleCell.json b/examples/parametersweep/Sim_IClamp_GenericMuscleCell.json
@@ -1,11 +1,11 @@
 {
     "Sim_IClamp_GenericMuscleCell": {
-        "version": "NeuroMLlite v0.3.0",
+        "version": "NeuroMLlite v0.5.7",
         "network": "IClamp_GenericMuscleCell.json",
         "duration": 3000.0,
         "dt": 0.025,
         "seed": 12345,
-        "recordTraces": {
+        "record_traces": {
             "all": "*"
         }
     }

diff --git a/examples/parametersweep/Sim_IClamp_GenericNeuronCell.json b/examples/parametersweep/Sim_IClamp_GenericNeuronCell.json
@@ -1,11 +1,11 @@
 {
     "Sim_IClamp_GenericNeuronCell": {
-        "version": "NeuroMLlite v0.3.0",
+        "version": "NeuroMLlite v0.5.7",
         "network": "IClamp_GenericNeuronCell.json",
         "duration": 3000.0,
         "dt": 0.025,
         "seed": 12345,
-        "recordTraces": {
+        "record_traces": {
             "all": "*"
         }
     }