Merge pull request #539 from ModECI/development

 Update to v0.4.11, fix tests related to numpy2 & add Newton's law of cooling example

Author: pgleeson

.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/

.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

.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

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