Merge pull request #60 from NeuroML/experimental

Update to v0.5.7
NeuroML · Sep 15, 2023 · ac205ae · ac205ae
2 parents 5c9eb7c + d192a5a
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diff --git a/docs/NeuroMLlite_specification.json b/docs/NeuroMLlite_specification.json
@@ -1,5 +1,5 @@
 {
-    "version": "NeuroMLlite v0.5.6",
+    "version": "NeuroMLlite v0.5.7",
     "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 v0.5.6
+version: NeuroMLlite v0.5.7
 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 v0.5.6
+# Specification of NeuroMLlite v0.5.7
 **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 v0.5.6",
+        "version": "NeuroMLlite v0.5.7",
         "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 v0.5.6",
+        "version": "NeuroMLlite v0.5.7",
         "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 v0.5.6
+    <notes>Generated by NeuroMLlite v0.5.7
     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 v0.5.6",
+        "version": "NeuroMLlite v0.5.7",
         "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 v0.5.6",
+        "version": "NeuroMLlite v0.5.7",
         "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 v0.5.6",
+        "version": "NeuroMLlite v0.5.7",
         "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 v0.5.6
+    <notes>Generated by NeuroMLlite v0.5.7
     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 v0.5.6",
+        "version": "NeuroMLlite v0.5.7",
         "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 v0.5.6
+    <notes>Generated by NeuroMLlite v0.5.7
     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 v0.5.6",
+        "version": "NeuroMLlite v0.5.7",
         "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 v0.5.6
+    <notes>Generated by NeuroMLlite v0.5.7
     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 v0.5.6
+    version: NeuroMLlite v0.5.7
     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 v0.5.6",
+        "version": "NeuroMLlite v0.5.7",
         "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 v0.5.6
+    <notes>Generated by NeuroMLlite v0.5.7
     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 v0.5.6",
+        "version": "NeuroMLlite v0.5.7",
         "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 v0.5.6
+    <notes>Generated by NeuroMLlite v0.5.7
     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 v0.5.6",
+        "version": "NeuroMLlite v0.5.7",
         "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 v0.5.6
+    <notes>Generated by NeuroMLlite v0.5.7
     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 v0.5.6",
+        "version": "NeuroMLlite v0.5.7",
         "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 v0.5.6",
+        "version": "NeuroMLlite v0.5.7",
         "notes": "Example 9: HindmarshRose",
         "parameters": {
             "N": 1,

diff --git a/examples/SimExample10.json b/examples/SimExample10.json
@@ -1,6 +1,6 @@
 {
     "SimExample10": {
-        "version": "NeuroMLlite v0.5.6",
+        "version": "NeuroMLlite v0.5.7",
         "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 v0.5.6",
+        "version": "NeuroMLlite v0.5.7",
         "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 v0.5.6",
+        "version": "NeuroMLlite v0.5.7",
         "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 v0.5.6",
+        "version": "NeuroMLlite v0.5.7",
         "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 v0.5.6",
+        "version": "NeuroMLlite v0.5.7",
         "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 v0.5.6
+    version: NeuroMLlite v0.5.7
     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 v0.5.6",
+        "version": "NeuroMLlite v0.5.7",
         "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 v0.5.6",
+        "version": "NeuroMLlite v0.5.7",
         "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 v0.5.6",
+        "version": "NeuroMLlite v0.5.7",
         "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 v0.5.6",
+        "version": "NeuroMLlite v0.5.7",
         "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 v0.5.6",
+        "version": "NeuroMLlite v0.5.7",
         "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 v0.5.6
+    version: NeuroMLlite v0.5.7
     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 v0.5.6",
+        "version": "NeuroMLlite v0.5.7",
         "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 v0.5.6
+    version: NeuroMLlite v0.5.7
     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 v0.5.6",
+        "version": "NeuroMLlite v0.5.7",
         "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 v0.5.6",
+        "version": "NeuroMLlite v0.5.7",
         "notes": "Example with spiking entities..",
         "parameters": {
             "N": 10,

diff --git a/examples/test_files/.test.validate.omt b/examples/test_files/.test.validate.omt
@@ -1,5 +1,5 @@
 # Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation 
 
 # This test will validate all of the NeuroML 2 files in the current directory using: jnml -validate *.nml
-target: "*.nml"
+target: "../Example2_TestNetwork.net.nml ../Example3_Network.net.nml ../Example4_PyNN.net.nml ../Example6_PyNN.net.nml ../Example7_Brunel2000.net.nml ../Example12_MultiComp.net.nml *.nml"
 engine: jNeuroML_validate
diff --git a/neuromllite/MDFHandler.py b/neuromllite/MDFHandler.py
@@ -253,9 +253,13 @@ def _comp_to_mdf_node(self, nmllite_comp, lems_comp_id, size=1, properties=None)
 
         print_v(
             "All LEMS Components in known LEMS model: %s"
-            % list(model.components.keys())
+            % sorted(list(model.components.keys()))
         )
-        print_v("This comp: %s" % lems_comp)
+        print_v(
+            "All LEMS ComponentTypes in known LEMS model: %s"
+            % sorted(list(model.component_types.keys()))
+        )
+        print_v("This LEMS comp: %s" % lems_comp)
         comp_type_name = lems_comp.type
         lems_comp_type = model.component_types.get(comp_type_name)
         print_v("lems_comp_type: %s" % lems_comp_type)
@@ -405,6 +409,7 @@ def _comp_to_mdf_node(self, nmllite_comp, lems_comp_id, size=1, properties=None)
                 # node["parameters"][sv.name]["value"] = [0]*size
 
                 node["output_ports"][sv.name] = {"value": sv.name}
+                print_v("Adding %s as an output port"%sv.name)
                 if sv.exposure:
                     node["output_ports"][sv.exposure] = {"value": sv.name}
 
@@ -515,21 +520,25 @@ def _replace_in_condition_test(self, test):
     def _get_all_elements_in_lems(cls, component_type, model, child_type):
         ee = []
         if child_type == "exposure":
-            for e in component_type.exposures:
-                ee.append(e)
+            if hasattr(component_type, "exposures"):
+                for e in component_type.exposures:
+                    ee.append(e)
         elif child_type == "constant":
-            for c in component_type.constants:
-                ee.append(c)
+            if hasattr(component_type, "constants"):
+                for c in component_type.constants:
+                    ee.append(c)
         elif child_type == "event_port":
-            for e in component_type.event_ports:
-                ee.append(e)
+            if hasattr(component_type, "event_ports"):
+                for e in component_type.event_ports:
+                    ee.append(e)
         elif child_type == "properties":
-            for p in component_type.properties:
-                ee.append(p)
+            if hasattr(component_type, "properties"):
+                for p in component_type.properties:
+                    ee.append(p)
         else:
             raise Exception("Cannot get child of type: %s in LEMS model" % child_type)
 
-        if component_type.extends:
+        if hasattr(component_type, "extends") and component_type.extends:
             ect = model.component_types[component_type.extends]
             ee.extend(cls._get_all_elements_in_lems(ect, model, child_type))
 

diff --git a/neuromllite/__init__.py b/neuromllite/__init__.py
@@ -1,6 +1,6 @@
 import collections
 
-__version__ = "0.5.6"
+__version__ = "0.5.7"
 
 # import pyNN
 # import nest