Merge remote-tracking branch 'upstream/development' into rlc-circuit

ModECI · Jun 21, 2024 · 9d83492 · 9d83492
2 parents c29534f + 59aebdd
commit 9d83492
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Showing 16 changed files with 36 additions and 23 deletions.
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/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/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="#newton"> Newton'a Law of Cooling</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>
 

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/abc_conditions.json b/examples/MDF/abc_conditions.json
@@ -124,4 +124,4 @@
             }
         }
     }
-}
+}
diff --git a/examples/MDF/newton.py b/examples/MDF/newton.py
@@ -52,13 +52,14 @@ 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")
-        plt.show()
+        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:
         mod.to_graph_image(

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 v1.2.12 (libNeuroML v0.5.8)
+        This LEMS file has been automatically generated using PyNeuroML v1.2.14 (libNeuroML v0.5.8)
 
      -->
 

diff --git a/examples/NeuroML/LEMS_SimFN.xml b/examples/NeuroML/LEMS_SimFN.xml
@@ -2,7 +2,7 @@
 
     <!--
 
-        This LEMS file has been automatically generated using PyNeuroML v1.2.12 (libNeuroML v0.5.8)
+        This LEMS file has been automatically generated using PyNeuroML v1.2.14 (libNeuroML v0.5.8)
 
      -->
 

diff --git a/examples/NeuroML/LEMS_SimIzhikevichTest.xml b/examples/NeuroML/LEMS_SimIzhikevichTest.xml
@@ -2,7 +2,7 @@
 
     <!--
 
-        This LEMS file has been automatically generated using PyNeuroML v1.2.12 (libNeuroML v0.5.8)
+        This LEMS file has been automatically generated using PyNeuroML v1.2.14 (libNeuroML v0.5.8)
 
      -->
 

diff --git a/setup.cfg b/setup.cfg
@@ -55,7 +55,6 @@ package_dir =
 
 [options.extras_require]
 psyneulink =
-    grpcio-tools==1.42.0
     psyneulink
 
 neuroml =
-Original file line number
+Diff line change
@@ Expand Up / @@ -182,4 +182,4 @@ @@
                 }
             }
         }
-    }
+    }