ModECI · pgleeson · May 1, 2024 · May 15, 2024 · May 23, 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/.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/examples/ACT-R/addition.json b/examples/ACT-R/addition.json
@@ -1,7 +1,7 @@
 {
     "addition": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.10",
+        "generating_application": "Python modeci-mdf v0.4.11",
         "graphs": {
             "addition_graph": {
                 "nodes": {

diff --git a/examples/ACT-R/addition.yaml b/examples/ACT-R/addition.yaml
@@ -1,6 +1,6 @@
 addition:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.10
+    generating_application: Python modeci-mdf v0.4.11
     graphs:
         addition_graph:
             nodes:

diff --git a/examples/ACT-R/count.json b/examples/ACT-R/count.json
@@ -1,7 +1,7 @@
 {
     "count": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.10",
+        "generating_application": "Python modeci-mdf v0.4.11",
         "graphs": {
             "count_graph": {
                 "nodes": {

diff --git a/examples/ACT-R/count.yaml b/examples/ACT-R/count.yaml
@@ -1,6 +1,6 @@
 count:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.10
+    generating_application: Python modeci-mdf v0.4.11
     graphs:
         count_graph:
             nodes:

diff --git a/examples/MDF/ABCD.json b/examples/MDF/ABCD.json
@@ -1,7 +1,7 @@
 {
     "ABCD": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.10",
+        "generating_application": "Python modeci-mdf v0.4.11",
         "graphs": {
             "abcd_example": {
                 "nodes": {

diff --git a/examples/MDF/ABCD.yaml b/examples/MDF/ABCD.yaml
@@ -1,6 +1,6 @@
 ABCD:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.10
+    generating_application: Python modeci-mdf v0.4.11
     graphs:
         abcd_example:
             nodes:

diff --git a/examples/MDF/Arrays.json b/examples/MDF/Arrays.json
@@ -1,7 +1,7 @@
 {
     "Arrays": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.10",
+        "generating_application": "Python modeci-mdf v0.4.11",
         "graphs": {
             "array_example": {
                 "nodes": {

diff --git a/examples/MDF/Arrays.yaml b/examples/MDF/Arrays.yaml
@@ -1,6 +1,6 @@
 Arrays:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.10
+    generating_application: Python modeci-mdf v0.4.11
     graphs:
         array_example:
             nodes:

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/ParametersFunctions.json b/examples/MDF/ParametersFunctions.json
@@ -1,7 +1,7 @@
 {
     "ParametersFunctions": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.10",
+        "generating_application": "Python modeci-mdf v0.4.11",
         "graphs": {
             "params_funcs_example": {
                 "nodes": {

diff --git a/examples/MDF/ParametersFunctions.yaml b/examples/MDF/ParametersFunctions.yaml
@@ -1,6 +1,6 @@
 ParametersFunctions:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.10
+    generating_application: Python modeci-mdf v0.4.11
     graphs:
         params_funcs_example:
             nodes:

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/IAF_net.json b/examples/MDF/RNN/IAF_net.json
@@ -1,7 +1,7 @@
 {
     "IAF_net": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.10",
+        "generating_application": "Python modeci-mdf v0.4.11",
         "graphs": {
             "iaf_example": {
                 "nodes": {

diff --git a/examples/MDF/RNN/IAF_net.yaml b/examples/MDF/RNN/IAF_net.yaml
@@ -1,6 +1,6 @@
 IAF_net:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.10
+    generating_application: Python modeci-mdf v0.4.11
     graphs:
         iaf_example:
             nodes:

diff --git a/examples/MDF/RNN/IAF_net2.json b/examples/MDF/RNN/IAF_net2.json
@@ -1,7 +1,7 @@
 {
     "IAF_net2": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.10",
+        "generating_application": "Python modeci-mdf v0.4.11",
         "graphs": {
             "iaf_example": {
                 "nodes": {

diff --git a/examples/MDF/RNN/IAF_net2.yaml b/examples/MDF/RNN/IAF_net2.yaml
@@ -1,6 +1,6 @@
 IAF_net2:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.10
+    generating_application: Python modeci-mdf v0.4.11
     graphs:
         iaf_example:
             nodes:

diff --git a/examples/MDF/RNN/IAFs.json b/examples/MDF/RNN/IAFs.json
@@ -1,7 +1,7 @@
 {
     "IAFs": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.10",
+        "generating_application": "Python modeci-mdf v0.4.11",
         "graphs": {
             "iaf_example": {
                 "nodes": {

diff --git a/examples/MDF/RNN/IAFs.yaml b/examples/MDF/RNN/IAFs.yaml
@@ -1,6 +1,6 @@
 IAFs:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.10
+    generating_application: Python modeci-mdf v0.4.11
     graphs:
         iaf_example:
             nodes:

diff --git a/examples/MDF/RNN/RNNs.json b/examples/MDF/RNN/RNNs.json
@@ -1,7 +1,7 @@
 {
     "RNNs": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.10",
+        "generating_application": "Python modeci-mdf v0.4.11",
         "graphs": {
             "rnn_example": {
                 "nodes": {

diff --git a/examples/MDF/RNN/RNNs.yaml b/examples/MDF/RNN/RNNs.yaml
@@ -1,6 +1,6 @@
 RNNs:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.10
+    generating_application: Python modeci-mdf v0.4.11
     graphs:
         rnn_example:
             nodes:

diff --git a/examples/MDF/Simple.bson b/examples/MDF/Simple.bson
diff --git a/examples/MDF/Simple.json b/examples/MDF/Simple.json
@@ -1,7 +1,7 @@
 {
     "Simple": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.10",
+        "generating_application": "Python modeci-mdf v0.4.11",
         "graphs": {
             "simple_example": {
                 "nodes": {

diff --git a/examples/MDF/Simple.yaml b/examples/MDF/Simple.yaml
@@ -1,6 +1,6 @@
 Simple:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.10
+    generating_application: Python modeci-mdf v0.4.11
     graphs:
         simple_example:
             nodes:

diff --git a/examples/MDF/States.json b/examples/MDF/States.json
@@ -1,7 +1,7 @@
 {
     "States": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.10",
+        "generating_application": "Python modeci-mdf v0.4.11",
         "graphs": {
             "state_example": {
                 "nodes": {

diff --git a/examples/MDF/States.yaml b/examples/MDF/States.yaml
@@ -1,6 +1,6 @@
 States:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.10
+    generating_application: Python modeci-mdf v0.4.11
     graphs:
         state_example:
             nodes:

diff --git a/examples/MDF/abc_conditions.json b/examples/MDF/abc_conditions.json
@@ -1,7 +1,7 @@
 {
     "abc_conditions": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.10",
+        "generating_application": "Python modeci-mdf v0.4.11",
         "graphs": {
             "abc_conditions_example": {
                 "nodes": {

diff --git a/examples/MDF/abc_conditions.yaml b/examples/MDF/abc_conditions.yaml
@@ -1,6 +1,6 @@
 abc_conditions:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.10
+    generating_application: Python modeci-mdf v0.4.11
     graphs:
         abc_conditions_example:
             nodes:

diff --git a/examples/MDF/conditions/Composite_mdf_condition.json b/examples/MDF/conditions/Composite_mdf_condition.json
@@ -1,7 +1,7 @@
 {
     "Composite_mdf_condition": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.10",
+        "generating_application": "Python modeci-mdf v0.4.11",
         "graphs": {
             "Composite_mdf_condition_example": {
                 "nodes": {

diff --git a/examples/MDF/conditions/Composite_mdf_condition.yaml b/examples/MDF/conditions/Composite_mdf_condition.yaml
@@ -1,6 +1,6 @@
 Composite_mdf_condition:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.10
+    generating_application: Python modeci-mdf v0.4.11
     graphs:
         Composite_mdf_condition_example:
             nodes:

diff --git a/examples/MDF/conditions/everyncalls_condition.json b/examples/MDF/conditions/everyncalls_condition.json
@@ -1,7 +1,7 @@
 {
     "everyncalls_condition": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.10",
+        "generating_application": "Python modeci-mdf v0.4.11",
         "graphs": {
             "everyncalls_example": {
                 "nodes": {

diff --git a/examples/MDF/conditions/everyncalls_condition.yaml b/examples/MDF/conditions/everyncalls_condition.yaml
@@ -1,6 +1,6 @@
 everyncalls_condition:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.10
+    generating_application: Python modeci-mdf v0.4.11
     graphs:
         everyncalls_example:
             nodes:

diff --git a/examples/MDF/conditions/threshold_condition.json b/examples/MDF/conditions/threshold_condition.json
@@ -1,7 +1,7 @@
 {
     "threshold_condition": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.10",
+        "generating_application": "Python modeci-mdf v0.4.11",
         "graphs": {
             "threshold_example": {
                 "nodes": {

diff --git a/examples/MDF/conditions/threshold_condition.yaml b/examples/MDF/conditions/threshold_condition.yaml
@@ -1,6 +1,6 @@
 threshold_condition:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.10
+    generating_application: Python modeci-mdf v0.4.11
     graphs:
         threshold_example:
             nodes: