Merge pull request #56 from NeuroML/experimental

pgleeson · web-flow · commit 828747f89aa7 · 2023-05-31T17:21:07.000+01:00
Updates to MDF mapping &amp; uses latest Arbor
diff --git a/docs/NeuroMLlite_specification.json b/docs/NeuroMLlite_specification.json
@@ -1,5 +1,5 @@
 {
-    "version": "NeuroMLlite v0.5.5",
+    "version": "NeuroMLlite v0.5.6",
     "specification": {
         "Network": {
             "definition": "A Network containing multiple Population's, connected by Projection's and receiving Input's",
diff --git a/docs/NeuroMLlite_specification.yaml b/docs/NeuroMLlite_specification.yaml
@@ -1,4 +1,4 @@
-version: NeuroMLlite v0.5.5
+version: NeuroMLlite v0.5.6
 specification:
     Network:
         definition: A Network containing multiple Population's, connected by Projection's
diff --git a/docs/README.md b/docs/README.md
@@ -1,4 +1,4 @@
-# Specification of NeuroMLlite v0.5.5
+# Specification of NeuroMLlite v0.5.6
 **Note: the NeuroMLlite specification is still in development! Subject to change...**
 
 ## Network
diff --git a/examples/Example10_Lorenz.json b/examples/Example10_Lorenz.json
@@ -1,6 +1,6 @@
 {
     "Example10_Lorenz": {
-        "version": "NeuroMLlite v0.5.5",
+        "version": "NeuroMLlite v0.5.6",
         "notes": "Example 10: Lorenz",
         "parameters": {
             "N": 1,
diff --git a/examples/Example11_Synapses.json b/examples/Example11_Synapses.json
@@ -1,6 +1,6 @@
 {
     "Example11_Synapses": {
-        "version": "NeuroMLlite v0.5.5",
+        "version": "NeuroMLlite v0.5.6",
         "notes": "Example 11: synaptic properties",
         "parameters": {
             "input_amp": 0.23,
diff --git a/examples/Example11_Synapses.net.nml b/examples/Example11_Synapses.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_v2.3.xsd" id="Example11_Synapses">
-    <notes>Generated by NeuroMLlite v0.5.5
+    <notes>Generated by NeuroMLlite v0.5.6
     Generated network: Example11_Synapses
     Generation seed: 1234
     NeuroMLlite parameters: 
diff --git a/examples/Example12_MultiComp.json b/examples/Example12_MultiComp.json
@@ -1,6 +1,6 @@
 {
     "Example12_MultiComp": {
-        "version": "NeuroMLlite v0.5.5",
+        "version": "NeuroMLlite v0.5.6",
         "notes": "Example 12: Multicompartmental cells...",
         "parameters": {
             "N": 20,
diff --git a/examples/Example1_TestNetwork.json b/examples/Example1_TestNetwork.json
@@ -1,6 +1,6 @@
 {
     "TestNetwork": {
-        "version": "NeuroMLlite v0.5.5",
+        "version": "NeuroMLlite v0.5.6",
         "notes": "A simple network with 2 populations & projection between them. No info yet on what the cells are so network can't be simulated.",
         "populations": {
             "pop0": {
diff --git a/examples/Example2_TestNetwork.json b/examples/Example2_TestNetwork.json
@@ -1,6 +1,6 @@
 {
     "Example2_TestNetwork": {
-        "version": "NeuroMLlite v0.5.5",
+        "version": "NeuroMLlite v0.5.6",
         "notes": "A simple network with 2 populations & projection between them. Cells are specified to be NeuroML 2 HH cell models & pre population is given a spiking input.",
         "cells": {
             "hhcell": {
diff --git a/examples/Example2_TestNetwork.net.nml b/examples/Example2_TestNetwork.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_v2.3.xsd" id="Example2_TestNetwork">
-    <notes>Generated by NeuroMLlite v0.5.5
+    <notes>Generated by NeuroMLlite v0.5.6
     Generated network: Example2_TestNetwork
     Generation seed: 1234</notes>
     <include href="test_files/inputs.nml"/>
diff --git a/examples/Example3_Network.json b/examples/Example3_Network.json
@@ -1,6 +1,6 @@
 {
     "Example3_Network": {
-        "version": "NeuroMLlite v0.5.5",
+        "version": "NeuroMLlite v0.5.6",
         "notes": "Example 3: simple network with 2 populations of NeuroML2 cells, a projection between them and spiking input.",
         "cells": {
             "hhcell": {
diff --git a/examples/Example3_Network.net.nml b/examples/Example3_Network.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_v2.3.xsd" id="Example3_Network">
-    <notes>Generated by NeuroMLlite v0.5.5
+    <notes>Generated by NeuroMLlite v0.5.6
     Generated network: Example3_Network
     Generation seed: 1234</notes>
     <include href="test_files/inputs.nml"/>
diff --git a/examples/Example4_PyNN.json b/examples/Example4_PyNN.json
@@ -1,6 +1,6 @@
 {
     "Example4_PyNN": {
-        "version": "NeuroMLlite v0.5.5",
+        "version": "NeuroMLlite v0.5.6",
         "notes": "Example 4: a network with PyNN cells & inputs",
         "parameters": {
             "input_amp": 0.99
diff --git a/examples/Example4_PyNN.net.nml b/examples/Example4_PyNN.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_v2.3.xsd" id="Example4_PyNN">
-    <notes>Generated by NeuroMLlite v0.5.5
+    <notes>Generated by NeuroMLlite v0.5.6
     Generated network: Example4_PyNN
     Generation seed: 1234
     NeuroMLlite parameters: 
diff --git a/examples/Example4_PyNN.yaml b/examples/Example4_PyNN.yaml
@@ -1,5 +1,5 @@
 Example4_PyNN:
-    version: NeuroMLlite v0.5.5
+    version: NeuroMLlite v0.5.6
     notes: 'Example 4: a network with PyNN cells & inputs'
     parameters:
         input_amp: 0.99
diff --git a/examples/Example6_PyNN.json b/examples/Example6_PyNN.json
@@ -1,6 +1,6 @@
 {
     "Example6_PyNN": {
-        "version": "NeuroMLlite v0.5.5",
+        "version": "NeuroMLlite v0.5.6",
         "notes": "Another network for PyNN - work in progress...",
         "parameters": {
             "N_scaling": 0.005,
diff --git a/examples/Example6_PyNN.net.nml b/examples/Example6_PyNN.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_v2.3.xsd" id="Example6_PyNN">
-    <notes>Generated by NeuroMLlite v0.5.5
+    <notes>Generated by NeuroMLlite v0.5.6
     Generated network: Example6_PyNN
     Generation seed: 1234
     NeuroMLlite parameters: 
diff --git a/examples/Example6_PyNN_noinputs.json b/examples/Example6_PyNN_noinputs.json
@@ -1,6 +1,6 @@
 {
     "Example6_PyNN_noinputs": {
-        "version": "NeuroMLlite v0.5.5",
+        "version": "NeuroMLlite v0.5.6",
         "notes": "Another network for PyNN - work in progress...",
         "parameters": {
             "N_scaling": 0.005,
diff --git a/examples/Example6_PyNN_noinputs.net.nml b/examples/Example6_PyNN_noinputs.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_v2.3.xsd" id="Example6_PyNN_noinputs">
-    <notes>Generated by NeuroMLlite v0.5.5
+    <notes>Generated by NeuroMLlite v0.5.6
     Generated network: Example6_PyNN_noinputs
     Generation seed: 1234
     NeuroMLlite parameters: 
diff --git a/examples/Example7_Brunel2000.json b/examples/Example7_Brunel2000.json
@@ -1,6 +1,6 @@
 {
     "Example7_Brunel2000": {
-        "version": "NeuroMLlite v0.5.5",
+        "version": "NeuroMLlite v0.5.6",
         "notes": "Example 7: based on network of Brunel 2000",
         "parameters": {
             "g": 4,
diff --git a/examples/Example7_Brunel2000.net.nml b/examples/Example7_Brunel2000.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_v2.3.xsd" id="Example7_Brunel2000">
-    <notes>Generated by NeuroMLlite v0.5.5
+    <notes>Generated by NeuroMLlite v0.5.6
     Generated network: Example7_Brunel2000
     Generation seed: 1234
     NeuroMLlite parameters: 
diff --git a/examples/Example8_Extension.json b/examples/Example8_Extension.json
@@ -1,6 +1,6 @@
 {
     "Example8_Extension": {
-        "version": "NeuroMLlite v0.5.5",
+        "version": "NeuroMLlite v0.5.6",
         "notes": "Example 8: general testing...",
         "parameters": {
             "N": 10,
diff --git a/examples/Example9_HindmarshRose.json b/examples/Example9_HindmarshRose.json
@@ -1,6 +1,6 @@
 {
     "Example9_HindmarshRose": {
-        "version": "NeuroMLlite v0.5.5",
+        "version": "NeuroMLlite v0.5.6",
         "notes": "Example 9: HindmarshRose",
         "parameters": {
             "N": 1,
diff --git a/examples/LEMS_SimExample3.xml b/examples/LEMS_SimExample3.xml
@@ -2,7 +2,7 @@
     
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v1.0.8 (libNeuroML v0.5.1)
+        This LEMS file has been automatically generated using PyNeuroML v1.0.8 (libNeuroML v0.5.2)
 
      -->
     
diff --git a/examples/LEMS_SimExample4.xml b/examples/LEMS_SimExample4.xml
@@ -2,7 +2,7 @@
     
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v1.0.8 (libNeuroML v0.5.1)
+        This LEMS file has been automatically generated using PyNeuroML v1.0.8 (libNeuroML v0.5.2)
 
      -->
     
diff --git a/examples/SimExample10.json b/examples/SimExample10.json
@@ -1,6 +1,6 @@
 {
     "SimExample10": {
-        "version": "NeuroMLlite v0.5.5",
+        "version": "NeuroMLlite v0.5.6",
         "network": "Example10_Lorenz.json",
         "duration": 10000.0,
         "dt": 1.0,
diff --git a/examples/SimExample11.json b/examples/SimExample11.json
@@ -1,6 +1,6 @@
 {
     "SimExample11": {
-        "version": "NeuroMLlite v0.5.5",
+        "version": "NeuroMLlite v0.5.6",
         "network": "Example11_Synapses.json",
         "duration": 1000.0,
         "dt": 0.01,
diff --git a/examples/SimExample12_MultiComp.json b/examples/SimExample12_MultiComp.json
@@ -1,6 +1,6 @@
 {
     "SimExample12_MultiComp": {
-        "version": "NeuroMLlite v0.5.5",
+        "version": "NeuroMLlite v0.5.6",
         "network": "Example12_MultiComp.json",
         "duration": 1000.0,
         "dt": 0.025,
diff --git a/examples/SimExample3.json b/examples/SimExample3.json
@@ -1,6 +1,6 @@
 {
     "SimExample3": {
-        "version": "NeuroMLlite v0.5.5",
+        "version": "NeuroMLlite v0.5.6",
         "network": "Example3_Network.json",
         "duration": 1000.0,
         "dt": 0.025,
diff --git a/examples/SimExample4.json b/examples/SimExample4.json
@@ -1,6 +1,6 @@
 {
     "SimExample4": {
-        "version": "NeuroMLlite v0.5.5",
+        "version": "NeuroMLlite v0.5.6",
         "network": "Example4_PyNN.json",
         "duration": 1000.0,
         "dt": 0.01,
diff --git a/examples/SimExample4.yaml b/examples/SimExample4.yaml
@@ -1,5 +1,5 @@
 SimExample4:
-    version: NeuroMLlite v0.5.5
+    version: NeuroMLlite v0.5.6
     network: Example4_PyNN.yaml
     duration: 1000.0
     dt: 0.01
diff --git a/examples/SimExample6_PyNN.json b/examples/SimExample6_PyNN.json
@@ -1,6 +1,6 @@
 {
     "SimExample6_PyNN": {
-        "version": "NeuroMLlite v0.5.5",
+        "version": "NeuroMLlite v0.5.6",
         "network": "Example6_PyNN.json",
         "duration": 100.0,
         "dt": 0.025,
diff --git a/examples/SimExample7.json b/examples/SimExample7.json
@@ -1,6 +1,6 @@
 {
     "SimExample7": {
-        "version": "NeuroMLlite v0.5.5",
+        "version": "NeuroMLlite v0.5.6",
         "network": "Example7_Brunel2000.json",
         "duration": 1000.0,
         "dt": 0.025,
diff --git a/examples/SimExample8.json b/examples/SimExample8.json
@@ -1,6 +1,6 @@
 {
     "SimExample8": {
-        "version": "NeuroMLlite v0.5.5",
+        "version": "NeuroMLlite v0.5.6",
         "network": "Example8_Extension.json",
         "duration": 1000.0,
         "dt": 0.025,
diff --git a/examples/SimExample9.json b/examples/SimExample9.json
@@ -1,6 +1,6 @@
 {
     "SimExample9": {
-        "version": "NeuroMLlite v0.5.5",
+        "version": "NeuroMLlite v0.5.6",
         "network": "Example9_HindmarshRose.json",
         "duration": 1000000.0,
         "dt": 25.0,
diff --git a/examples/arbor/ArborExample.json b/examples/arbor/ArborExample.json
@@ -1,6 +1,6 @@
 {
     "ArborExample": {
-        "version": "NeuroMLlite v0.5.5",
+        "version": "NeuroMLlite v0.5.6",
         "notes": "Example for testing Arbor",
         "parameters": {
             "v_init": -50,
diff --git a/examples/arbor/ArborExample.yaml b/examples/arbor/ArborExample.yaml
@@ -1,5 +1,5 @@
 ArborExample:
-    version: NeuroMLlite v0.5.5
+    version: NeuroMLlite v0.5.6
     notes: Example for testing Arbor
     parameters:
         v_init: -50
diff --git a/examples/arbor/SimArborExample.json b/examples/arbor/SimArborExample.json
@@ -1,6 +1,6 @@
 {
     "SimArborExample": {
-        "version": "NeuroMLlite v0.5.5",
+        "version": "NeuroMLlite v0.5.6",
         "network": "ArborExample.json",
         "duration": 100.0,
         "dt": 0.01,
diff --git a/examples/arbor/SimArborExample.yaml b/examples/arbor/SimArborExample.yaml
@@ -1,5 +1,5 @@
 SimArborExample:
-    version: NeuroMLlite v0.5.5
+    version: NeuroMLlite v0.5.6
     network: ArborExample.yaml
     duration: 100.0
     dt: 0.01
diff --git a/examples/spikeratetest/SimSpikers.json b/examples/spikeratetest/SimSpikers.json
@@ -1,6 +1,6 @@
 {
     "SimSpikers": {
-        "version": "NeuroMLlite v0.5.5",
+        "version": "NeuroMLlite v0.5.6",
         "network": "Spikers.json",
         "duration": 10000.0,
         "dt": 0.025,
diff --git a/examples/spikeratetest/Spikers.json b/examples/spikeratetest/Spikers.json
@@ -1,6 +1,6 @@
 {
     "Spikers": {
-        "version": "NeuroMLlite v0.5.5",
+        "version": "NeuroMLlite v0.5.6",
         "notes": "Example with spiking entities..",
         "parameters": {
             "N": 10,
diff --git a/neuromllite/ArborHandler.py b/neuromllite/ArborHandler.py
@@ -310,7 +310,7 @@ def create_arbor_cell(self, cell, gid, pop_id, index):
 
             decor.paint('"soma"', arbor.density(cell.parameters["mechanism"]))
 
-            decor.place('"center"', arbor.spike_detector(0), "detector")
+            decor.place('"center"', arbor.threshold_detector(0), "detector")
 
             for ip in self.input_info:
                 if self.input_info[ip][0] == pop_id:
@@ -337,7 +337,7 @@ def create_arbor_cell(self, cell, gid, pop_id, index):
             # (4) Attach a single synapse.
             decor.place('"synapse_site"', arbor.synapse("expsyn"), "syn")
 
-            default_cell = arbor.cable_cell(default_tree, labels, decor)
+            default_cell = arbor.cable_cell(default_tree, labels=labels, decor=decor)
 
             print_v("Created a new cell for gid %i: %s" % (gid, cell))
             print_v("%s" % (default_cell))
diff --git a/neuromllite/MDFHandler.py b/neuromllite/MDFHandler.py
diff --git a/neuromllite/NetworkGenerator.py b/neuromllite/NetworkGenerator.py
diff --git a/neuromllite/__init__.py b/neuromllite/__init__.py

Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`{`
`2`		`- "version": "NeuroMLlite v0.5.5",`
	`2`	`+ "version": "NeuroMLlite v0.5.6",`
`3`	`3`	`"specification": {`
`4`	`4`	`"Network": {`
`5`	`5`	`"definition": "A Network containing multiple Population's, connected by Projection's and receiving Input's",`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-version: NeuroMLlite v0.5.5`
	`1`	`+version: NeuroMLlite v0.5.6`
`2`	`2`	`specification:`
`3`	`3`	`Network:`
`4`	`4`	`definition: A Network containing multiple Population's, connected by Projection's`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"Example10_Lorenz": {`
`3`		`- "version": "NeuroMLlite v0.5.5",`
	`3`	`+ "version": "NeuroMLlite v0.5.6",`
`4`	`4`	`"notes": "Example 10: Lorenz",`
`5`	`5`	`"parameters": {`
`6`	`6`	`"N": 1,`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"Example11_Synapses": {`
`3`		`- "version": "NeuroMLlite v0.5.5",`
	`3`	`+ "version": "NeuroMLlite v0.5.6",`
`4`	`4`	`"notes": "Example 11: synaptic properties",`
`5`	`5`	`"parameters": {`
`6`	`6`	`"input_amp": 0.23,`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"Example12_MultiComp": {`
`3`		`- "version": "NeuroMLlite v0.5.5",`
	`3`	`+ "version": "NeuroMLlite v0.5.6",`
`4`	`4`	`"notes": "Example 12: Multicompartmental cells...",`
`5`	`5`	`"parameters": {`
`6`	`6`	`"N": 20,`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"TestNetwork": {`
`3`		`- "version": "NeuroMLlite v0.5.5",`
	`3`	`+ "version": "NeuroMLlite v0.5.6",`
`4`	`4`	`"notes": "A simple network with 2 populations & projection between them. No info yet on what the cells are so network can't be simulated.",`
`5`	`5`	`"populations": {`
`6`	`6`	`"pop0": {`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"Example2_TestNetwork": {`
`3`		`- "version": "NeuroMLlite v0.5.5",`
	`3`	`+ "version": "NeuroMLlite v0.5.6",`
`4`	`4`	`"notes": "A simple network with 2 populations & projection between them. Cells are specified to be NeuroML 2 HH cell models & pre population is given a spiking input.",`
`5`	`5`	`"cells": {`
`6`	`6`	`"hhcell": {`