Merge pull request #1 from ModECI/nml_examples

Updates to get tests passing
ModECI · Nov 3, 2024 · c757b05 · c757b05
2 parents d8a6cf4 + 205ffe3
commit c757b05
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Showing 55 changed files with 211 additions and 78 deletions.
diff --git a/.github/workflows/ci_test_all.yml b/.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
diff --git a/docs/sphinx/source/api/export_format/MDF/images/abc_conditions.png b/docs/sphinx/source/api/export_format/MDF/images/abc_conditions.png
diff --git a/docs/sphinx/source/api/export_format/MDF/images/switched_rlc_circuit.png b/docs/sphinx/source/api/export_format/MDF/images/switched_rlc_circuit.png
diff --git a/docs/sphinx/source/api/export_format/MDF/images/switched_rlc_plot.png b/docs/sphinx/source/api/export_format/MDF/images/switched_rlc_plot.png
diff --git a/docs/sphinx/source/api/export_format/NeuroML/ABCD.mdf.png b/docs/sphinx/source/api/export_format/NeuroML/ABCD.mdf.png
diff --git a/docs/sphinx/source/api/export_format/NeuroML/LEMS_SimABCD.png b/docs/sphinx/source/api/export_format/NeuroML/LEMS_SimABCD.png
diff --git a/docs/sphinx/source/api/export_format/NeuroML/LEMS_SimFN.png b/docs/sphinx/source/api/export_format/NeuroML/LEMS_SimFN.png
diff --git a/docs/sphinx/source/api/export_format/NeuroML/LEMS_SimIzhikevichTest.png b/docs/sphinx/source/api/export_format/NeuroML/LEMS_SimIzhikevichTest.png
diff --git a/docs/sphinx/source/api/export_format/PyTorch/inception.png b/docs/sphinx/source/api/export_format/PyTorch/inception.png
diff --git a/docs/sphinx/source/api/export_format/PyTorch/simple_pytorch_to_mdf_torchviz.png b/docs/sphinx/source/api/export_format/PyTorch/simple_pytorch_to_mdf_torchviz.png
diff --git a/examples/MDF/ABCD.json b/examples/MDF/ABCD.json
@@ -182,4 +182,4 @@
             }
         }
     }
-}
+}
diff --git a/examples/MDF/Arrays.json b/examples/MDF/Arrays.json
@@ -90,4 +90,4 @@
             }
         }
     }
-}
+}
diff --git a/examples/MDF/NewtonCoolingModel.json b/examples/MDF/NewtonCoolingModel.json
@@ -35,4 +35,4 @@
             }
         }
     }
-}
+}
diff --git a/examples/MDF/ParametersFunctions.json b/examples/MDF/ParametersFunctions.json
@@ -64,4 +64,4 @@
             }
         }
     }
-}
+}
diff --git a/examples/MDF/RNN/IAFs.nmllite.json b/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",

diff --git a/examples/MDF/RNN/Simiaf_example.json b/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
             }
         }
     }

diff --git a/examples/MDF/RNN/regenerate.sh b/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
diff --git a/examples/MDF/Simple.json b/examples/MDF/Simple.json
@@ -70,4 +70,4 @@
             }
         }
     }
-}
+}
diff --git a/examples/MDF/States.json b/examples/MDF/States.json
@@ -47,4 +47,4 @@
             }
         }
     }
-}
+}
diff --git a/examples/MDF/SwitchedRLC_Circuit.json b/examples/MDF/SwitchedRLC_Circuit.json
@@ -2,6 +2,10 @@
     "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": {
@@ -22,9 +26,15 @@
                                 ]
                             },
                             "R": {
+                                "metadata": {
+                                    "description": "Resistance in Ohms"
+                                },
                                 "value": 100
                             },
                             "L": {
+                                "metadata": {
+                                    "description": "Inductance in Henrys"
+                                },
                                 "value": 1
                             },
                             "C": {
@@ -62,4 +72,4 @@
             }
         }
     }
-}
+}
diff --git a/examples/MDF/SwitchedRLC_Circuit.yaml b/examples/MDF/SwitchedRLC_Circuit.yaml
@@ -1,6 +1,9 @@
 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:
@@ -15,8 +18,12 @@ SwitchedRLC_Circuit:
                                 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

diff --git a/examples/MDF/abc_conditions.json b/examples/MDF/abc_conditions.json
@@ -124,4 +124,4 @@
             }
         }
     }
-}
+}
diff --git a/examples/MDF/conditions/images/composite_example.png b/examples/MDF/conditions/images/composite_example.png
diff --git a/examples/MDF/images/abc_conditions.png b/examples/MDF/images/abc_conditions.png
diff --git a/examples/MDF/images/switched_rlc_plot.png b/examples/MDF/images/switched_rlc_plot.png
diff --git a/examples/MDF/newton.py b/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:

diff --git a/examples/MDF/switched_rlc.py b/examples/MDF/switched_rlc.py
@@ -31,6 +31,11 @@ def run_simulation(mod_graph, duration=2, dt=0.001):
         V_values.append(V)
         t += dt
 
+    print(
+        "Finished simulation of MDF model: %s of duration: %s sec"
+        % (mod_graph.id, duration)
+    )
+
     plt.figure(figsize=(10, 5))
     plt.plot(times, i_L_values, label="Inductor Current (i_L)")
     plt.plot(times, i_R_values, label="Resistor Current (i_R)")

diff --git a/examples/NeuroML/ABCD.json b/examples/NeuroML/ABCD.json
@@ -1,6 +1,6 @@
 {
     "ABCD": {
-        "version": "NeuroMLlite v0.5.9",
+        "version": "NeuroMLlite v0.6.0",
         "notes": "Example of a simplified network",
         "parameters": {
             "A_initial": 0.1,

diff --git a/examples/NeuroML/ABCD.mdf.png b/examples/NeuroML/ABCD.mdf.png
diff --git a/examples/NeuroML/ABCD.net.nml b/examples/NeuroML/ABCD.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="ABCD">
-    <notes>Generated by NeuroMLlite v0.5.9
+<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="ABCD">
+    <notes>Generated by NeuroMLlite v0.6.0
     Generated network: ABCD
     Generation seed: 1234
     NeuroMLlite parameters:

diff --git a/examples/NeuroML/FN.json b/examples/NeuroML/FN.json
@@ -1,6 +1,6 @@
 {
     "FN": {
-        "version": "NeuroMLlite v0.5.9",
+        "version": "NeuroMLlite v0.6.0",
         "notes": "FitzHugh Nagumo cell model - originally specified in NeuroML/LEMS",
         "parameters": {
             "initial_w": 0.0,

diff --git a/examples/NeuroML/FN.net.nml b/examples/NeuroML/FN.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="FN">
-    <notes>Generated by NeuroMLlite v0.5.9
+<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="FN">
+    <notes>Generated by NeuroMLlite v0.6.0
     Generated network: FN
     Generation seed: 1234
     NeuroMLlite parameters:

diff --git a/examples/NeuroML/IzhikevichTest.net.nml b/examples/NeuroML/IzhikevichTest.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="IzhikevichTest">
-    <notes>Generated by NeuroMLlite v0.5.9
+<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="IzhikevichTest">
+    <notes>Generated by NeuroMLlite v0.6.0
     Generated network: IzhikevichTest
     Generation seed: 1234
     NeuroMLlite parameters:

diff --git a/examples/NeuroML/IzhikevichTest.nmllite.yaml b/examples/NeuroML/IzhikevichTest.nmllite.yaml
@@ -1,5 +1,5 @@
 IzhikevichTest:
-    version: NeuroMLlite v0.5.9
+    version: NeuroMLlite v0.6.0
     notes: Example Izhikevich
     parameters:
         N: 1

diff --git a/examples/NeuroML/LEMS_SimABCD.png b/examples/NeuroML/LEMS_SimABCD.png
diff --git a/examples/NeuroML/LEMS_SimABCD.xml b/examples/NeuroML/LEMS_SimABCD.xml
@@ -2,7 +2,7 @@
 
     <!--
 
-        This LEMS file has been automatically generated using PyNeuroML v1.2.14 (libNeuroML v0.5.8)
+        This LEMS file has been automatically generated using PyNeuroML v1.3.8 (libNeuroML v0.6.3)
 
      -->
 

diff --git a/examples/NeuroML/LEMS_SimFN.png b/examples/NeuroML/LEMS_SimFN.png
-Original file line number
+Diff line change
@@ Expand Up / @@ -182,4 +182,4 @@ @@
                 }
             }
         }
-    }
+    }