ModECI · pgleeson · Feb 5, 2025 · May 30, 2024 · May 30, 2024 · May 30, 2024
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -58,11 +58,13 @@ jobs:
         brew install hdf5
 
     - name: Install core package
-      run: python -m pip install .[dev]
+      run: |
+        pip install 'numpy<2.0.0' # due to lingering issues with other modules & numpy v2...
+        python -m pip install .[dev]
 
     - name: Version info for installed packages
       run: |
-          pip list
+        pip list
 
     - name: Test core package
       run: |
@@ -102,7 +104,6 @@ jobs:
         python -m pytest -v -m "tensorflow" tests/
 
     - name: Test interface PsyNeuLink
-      if: ${{ matrix.python-version != '3.11'}}
       run: |
         python -m pip install .[psyneulink]
         python -m pytest -v -m "psyneulink" tests/

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/.gitignore b/.gitignore
@@ -311,3 +311,5 @@ examples/TensorFlow/Keras/keras_to_MDF
 /examples/TensorFlow/Keras/IRIS/keras_model_on_iris.keras
 /examples/TensorFlow/Keras/MNIST/kr_N_model.keras
 /checkoutpngs.sh
+/docs/sphinx/source/api/export_format/MDF/images/newton.png
+/docs/sphinx/source/api/export_format/MDF/images/newton_plot.png
diff --git a/docs/sphinx/source/api/export_format/MDF/MDF.md b/docs/sphinx/source/api/export_format/MDF/MDF.md
@@ -2,7 +2,7 @@
 
 Examples of [Python](https://python.org), [JSON](https://developer.mozilla.org/en-US/docs/Learn/JavaScript/Objects/JSON#:~:text=JavaScript%20Object%20Notation%20(JSON)%20is,page%2C%20or%20vice%20versa) and [YAML](https://circleci.com/blog/what-is-yaml-a-beginner-s-guide/) files to illustrate the structure and usage of MDF.
 
-<a href="#simple"> Simple </a>| <a href="#abcd"> ABCD </a> | <a href="#arrays"> Arrays </a> | <a href="#st"> States </a> | <a href="#conditions"> Conditions </a> | <a href="#parameters-and-functions"> Parameters and Functions </a>
+<a href="#simple"> Simple </a>| <a href="#abcd"> ABCD </a> | <a href="#arrays"> Arrays </a> | <a href="#st"> States </a> | <a href="#conditions"> Conditions </a> | <a href="#parameters-and-functions"> Parameters and Functions </a>| <a href="#newton"> Newton's Law of Cooling</a>
 
 <p id="simple"></p>
 
@@ -73,6 +73,16 @@ A simple 3 [Nodes](https://mdf.readthedocs.io/en/latest/api/Specification.html#n
 A simple [Node](https://mdf.readthedocs.io/en/latest/api/Specification.html#node) with a number of different types of [Parameters](https://mdf.readthedocs.io/en/latest/api/Specification.html#parameter) (in blue; fixed and **stateful**) and [Functions](https://mdf.readthedocs.io/en/latest/api/Specification.html#function) (in purple; can be built in or ONNX based).
 
 <img src="https://raw.githubusercontent.com/ModECI/MDF/main/examples/MDF/images/params_funcs.png" width="250" height="198" />
+<p id="newton"></p>
+
+## Newton's Law of Cooling
+
+[Python Source](https://github.com/ModECI/MDF/blob/main/examples/MDF/newton.py) | [JSON](https://github.com/ModECI/MDF/blob/main/examples/MDF/NewtonCoolingModel.json) | [YAML](https://github.com/ModECI/MDF/blob/main/examples/MDF/NewtonCoolingModel.yaml)
+
+A simple [Newtonian cooling process](https://en.wikipedia.org/wiki/Newton%27s_law_of_cooling) model that demonstrates the use of time derivative simulating the cooling of an object to the ambient temperature over time.
+
+<img src="https://raw.githubusercontent.com/ModECI/MDF/development/examples/MDF/images/newton.png" width="250"/>
+<img src="https://raw.githubusercontent.com/ModECI/MDF/development/examples/MDF/images/newton_plot.png" width="250"/>
 
 
 ## More examples

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/NewtonCoolingModel.json b/examples/MDF/NewtonCoolingModel.json
@@ -0,0 +1,38 @@
+{
+    "NewtonCoolingModel": {
+        "format": "ModECI MDF v0.4",
+        "generating_application": "Python modeci-mdf v0.4.11",
+        "graphs": {
+            "cooling_process": {
+                "nodes": {
+                    "cool_node": {
+                        "parameters": {
+                            "cooling_coeff": {
+                                "value": 0.1
+                            },
+                            "T_a": {
+                                "value": 20
+                            },
+                            "T_curr": {
+                                "default_initial_value": 90,
+                                "time_derivative": "dT_dt"
+                            },
+                            "dT_dt": {
+                                "value": "-cooling_coeff*(T_curr - T_a)",
+                                "default_initial_value": 0
+                            }
+                        },
+                        "output_ports": {
+                            "out_port": {
+                                "value": "T_curr"
+                            },
+                            "out_port2": {
+                                "value": "dT_dt"
+                            }
+                        }
+                    }
+                }
+            }
+        }
+    }
+}
diff --git a/examples/MDF/NewtonCoolingModel.yaml b/examples/MDF/NewtonCoolingModel.yaml
@@ -0,0 +1,23 @@
+NewtonCoolingModel:
+    format: ModECI MDF v0.4
+    generating_application: Python modeci-mdf v0.4.11
+    graphs:
+        cooling_process:
+            nodes:
+                cool_node:
+                    parameters:
+                        cooling_coeff:
+                            value: 0.1
+                        T_a:
+                            value: 20
+                        T_curr:
+                            default_initial_value: 90
+                            time_derivative: dT_dt
+                        dT_dt:
+                            value: -cooling_coeff*(T_curr - T_a)
+                            default_initial_value: 0
+                    output_ports:
+                        out_port:
+                            value: T_curr
+                        out_port2:
+                            value: dT_dt
diff --git a/examples/MDF/README.md b/examples/MDF/README.md
@@ -2,7 +2,7 @@
 
 Examples of [Python](https://python.org), [JSON](https://developer.mozilla.org/en-US/docs/Learn/JavaScript/Objects/JSON#:~:text=JavaScript%20Object%20Notation%20(JSON)%20is,page%2C%20or%20vice%20versa) and [YAML](https://circleci.com/blog/what-is-yaml-a-beginner-s-guide/) files to illustrate the structure and usage of MDF.
 
-<a href="#simple"> Simple </a>| <a href="#abcd"> ABCD </a> | <a href="#arrays"> Arrays </a> | <a href="#st"> States </a> | <a href="#conditions"> Conditions </a> | <a href="#parameters-and-functions"> Parameters and Functions </a>
+<a href="#simple"> Simple </a>| <a href="#abcd"> ABCD </a> | <a href="#arrays"> Arrays </a> | <a href="#st"> States </a> | <a href="#conditions"> Conditions </a> | <a href="#parameters-and-functions"> Parameters and Functions </a>| <a href="#newton"> Newton's Law of Cooling</a>
 
 <p id="simple"></p>
 
@@ -73,6 +73,16 @@ A simple 3 [Nodes](https://mdf.readthedocs.io/en/latest/api/Specification.html#n
 A simple [Node](https://mdf.readthedocs.io/en/latest/api/Specification.html#node) with a number of different types of [Parameters](https://mdf.readthedocs.io/en/latest/api/Specification.html#parameter) (in blue; fixed and **stateful**) and [Functions](https://mdf.readthedocs.io/en/latest/api/Specification.html#function) (in purple; can be built in or ONNX based).
 
 <img src="https://raw.githubusercontent.com/ModECI/MDF/main/examples/MDF/images/params_funcs.png" width="250" height="198" />
+<p id="newton"></p>
+
+## Newton's Law of Cooling
+
+[Python Source](https://github.com/ModECI/MDF/blob/main/examples/MDF/newton.py) | [JSON](https://github.com/ModECI/MDF/blob/main/examples/MDF/NewtonCoolingModel.json) | [YAML](https://github.com/ModECI/MDF/blob/main/examples/MDF/NewtonCoolingModel.yaml)
+
+A simple [Newtonian cooling process](https://en.wikipedia.org/wiki/Newton%27s_law_of_cooling) model that demonstrates the use of time derivative simulating the cooling of an object to the ambient temperature over time.
+
+<img src="https://raw.githubusercontent.com/ModECI/MDF/development/examples/MDF/images/newton.png" width="250"/>
+<img src="https://raw.githubusercontent.com/ModECI/MDF/development/examples/MDF/images/newton_plot.png" width="250"/>
 
 
 ## More examples

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