Merge branch 'development' into fix/readthedocs

Author: davidt0x

.github/workflows/ci_test_all.yml

@@ -37,6 +37,7 @@ jobs:
 
     - name: Run test script
       run: |
+        pip install torch==2.8.0 # pinned to avoid issues with latest version taking up too much space...
         export NEURON_HOME=$pythonLocation
         ./test_all.sh
 

.gitignore

@@ -274,6 +274,9 @@ Thumbs.db #thumbnail cache on Windows
 /examples/PyTorch/simple_pytorch_to_mdf.1
 /examples/MDF/NLP/TestNLP_3
 /examples/MDF/NLP/TestNLP
+/examples/MDF/networks/Net_acyclical
+/examples/MDF/net/Net_acyclical
+/examples/MDF/net/weight.py
 /examples/MDF/conditions/composite_example
 /examples/NeuroML/arm64
 /examples/MDF/RNN/iaf.net
@@ -313,3 +316,4 @@ examples/TensorFlow/Keras/keras_to_MDF
 /checkoutpngs.sh
 /docs/sphinx/source/api/export_format/MDF/images/newton.png
 /docs/sphinx/source/api/export_format/MDF/images/newton_plot.png
+/examples/MDF/networks/Net_acyclical

docs/MDF_specification.json

@@ -106,13 +106,21 @@
                     "type": "str",
                     "description": "The unique (for this Node) id of the input port,"
                 },
+                "default_value": {
+                    "type": "Union",
+                    "description": "Value to set at this input port if no edge connected to it."
+                },
                 "shape": {
                     "type": "Optional",
                     "description": "The shape of the input port. This uses the same syntax as numpy ndarray shapes\n(e.g., :code:`numpy.zeros(shape)` would produce an array with the correct shape"
                 },
                 "type": {
                     "type": "Optional",
                     "description": "The data type of the input received at a port."
+                },
+                "reduce": {
+                    "type": "Optional",
+                    "description": "Specifies how to deal with multiple inputs to one port during a single timestep: add: add up all the values; multiply: multiply the values, overwrite: just use the last value supplied (default)"
                 }
             }
         },

docs/MDF_specification.yaml

@@ -91,6 +91,10 @@ specification:
             id:
                 type: str
                 description: The unique (for this Node) id of the input port,
+            default_value:
+                type: Union
+                description: Value to set at this input port if no edge connected
+                    to it.
             shape:
                 type: Optional
                 description: 'The shape of the input port. This uses the same syntax
@@ -101,6 +105,12 @@ specification:
             type:
                 type: Optional
                 description: The data type of the input received at a port.
+            reduce:
+                type: Optional
+                description: 'Specifies how to deal with multiple inputs to one port
+                    during a single timestep: add: add up all the values; multiply:
+                    multiply the values, overwrite: just use the last value supplied
+                    (default)'
     Function:
         definition: A single value which is evaluated as a function of values on :class:`InputPort`(s)
             and other Functions

docs/README.md

@@ -179,6 +179,13 @@ The <a href="#inputport">InputPort</a> is an attribute of a Node which allows ex
  </tr>
 
 
+  <tr>
+    <td><b>default_value</b></td>
+    <td>Union</td>
+    <td><i>Value to set at this input port if no edge connected to it.</i></td>
+ </tr>
+
+
   <tr>
     <td><b>shape</b></td>
     <td>Optional</td>
@@ -194,6 +201,13 @@ The <a href="#inputport">InputPort</a> is an attribute of a Node which allows ex
  </tr>
 
 
+  <tr>
+    <td><b>reduce</b></td>
+    <td>Optional</td>
+    <td><i>Specifies how to deal with multiple inputs to one port during a single timestep: add: add up all the values; multiply: multiply the values, overwrite: just use the last value supplied (default)</i></td>
+ </tr>
+
+
 </table>
 
 ## Function

docs/sphinx/source/api/Specification.rst

@@ -87,15 +87,17 @@ The `InputPort <#inputport>`__ is an attribute of a Node which allows external i
 
 **Allowed parameters**
 
-===============  ===========  =============================================================================================
-Allowed field    Data Type    Description
-===============  ===========  =============================================================================================
-**metadata**     Optional     Optional metadata field, an arbitrary dictionary of string keys and JSON serializable values.
-**id**           str          The unique (for this Node) id of the input port,
-**shape**        Optional     The shape of the input port. This uses the same syntax as numpy ndarray shapes
-                              (e.g., **numpy.zeros(shape)** would produce an array with the correct shape
-**type**         Optional     The data type of the input received at a port.
-===============  ===========  =============================================================================================
+=================  ===========  =================================================================================================================================================================================================
+Allowed field      Data Type    Description
+=================  ===========  =================================================================================================================================================================================================
+**metadata**       Optional     Optional metadata field, an arbitrary dictionary of string keys and JSON serializable values.
+**id**             str          The unique (for this Node) id of the input port,
+**default_value**  Union        Value to set at this input port if no edge connected to it.
+**shape**          Optional     The shape of the input port. This uses the same syntax as numpy ndarray shapes
+                                (e.g., **numpy.zeros(shape)** would produce an array with the correct shape
+**type**           Optional     The data type of the input received at a port.
+**reduce**         Optional     Specifies how to deal with multiple inputs to one port during a single timestep: add: add up all the values; multiply: multiply the values, overwrite: just use the last value supplied (default)
+=================  ===========  =================================================================================================================================================================================================
 
 ========
 Function