Merge branch 'development' into nml_examples

pgleeson · pgleeson · commit 0ce76f162af7 · 2025-12-17T17:55:23.000Z
diff --git a/.gitignore b/.gitignore
@@ -316,3 +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
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/Izh_run.png b/docs/sphinx/source/api/export_format/NeuroML/Izh_run.png
diff --git a/docs/sphinx/source/api/export_format/NeuroML/MDFFNrun.multi.png b/docs/sphinx/source/api/export_format/NeuroML/MDFFNrun.multi.png
diff --git a/docs/sphinx/source/api/export_format/NeuroML/MDFFNrun.png b/docs/sphinx/source/api/export_format/NeuroML/MDFFNrun.png
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 v0.4.13",
+        "generating_application": "Python modeci-mdf v0.4.14",
         "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 v0.4.13
+    generating_application: Python modeci-mdf v0.4.14
     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 v0.4.13",
+        "generating_application": "Python modeci-mdf v0.4.14",
         "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 v0.4.13
+    generating_application: Python modeci-mdf v0.4.14
     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 v0.4.13",
+        "generating_application": "Python modeci-mdf v0.4.14",
         "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 v0.4.13
+    generating_application: Python modeci-mdf v0.4.14
     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 v0.4.13",
+        "generating_application": "Python modeci-mdf v0.4.14",
         "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 v0.4.13
+    generating_application: Python modeci-mdf v0.4.14
     graphs:
         array_example:
             nodes:
diff --git a/examples/MDF/NewtonCoolingModel.json b/examples/MDF/NewtonCoolingModel.json
@@ -1,7 +1,7 @@
 {
     "NewtonCoolingModel": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.13",
+        "generating_application": "Python modeci-mdf v0.4.14",
         "graphs": {
             "cooling_process": {
                 "nodes": {
diff --git a/examples/MDF/NewtonCoolingModel.yaml b/examples/MDF/NewtonCoolingModel.yaml
@@ -1,6 +1,6 @@
 NewtonCoolingModel:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.13
+    generating_application: Python modeci-mdf v0.4.14
     graphs:
         cooling_process:
             nodes:
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 v0.4.13",
+        "generating_application": "Python modeci-mdf v0.4.14",
         "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 v0.4.13
+    generating_application: Python modeci-mdf v0.4.14
     graphs:
         params_funcs_example:
             nodes:
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 v0.4.13",
+        "generating_application": "Python modeci-mdf v0.4.14",
         "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 v0.4.13
+    generating_application: Python modeci-mdf v0.4.14
     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 v0.4.13",
+        "generating_application": "Python modeci-mdf v0.4.14",
         "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 v0.4.13
+    generating_application: Python modeci-mdf v0.4.14
     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 v0.4.13",
+        "generating_application": "Python modeci-mdf v0.4.14",
         "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 v0.4.13
+    generating_application: Python modeci-mdf v0.4.14
     graphs:
         iaf_example:
             nodes:
diff --git a/examples/MDF/RNN/IaF.net.run.png b/examples/MDF/RNN/IaF.net.run.png
diff --git a/examples/MDF/RNN/IaF.net2.run.png b/examples/MDF/RNN/IaF.net2.run.png
diff --git a/examples/MDF/RNN/IaF.run.png b/examples/MDF/RNN/IaF.run.png
diff --git a/examples/MDF/RNN/RNN.run.png b/examples/MDF/RNN/RNN.run.png
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 v0.4.13",
+        "generating_application": "Python modeci-mdf v0.4.14",
         "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 v0.4.13
+    generating_application: Python modeci-mdf v0.4.14
     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 v0.4.13",
+        "generating_application": "Python modeci-mdf v0.4.14",
         "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 v0.4.13
+    generating_application: Python modeci-mdf v0.4.14
     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 v0.4.13",
+        "generating_application": "Python modeci-mdf v0.4.14",
         "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 v0.4.13
+    generating_application: Python modeci-mdf v0.4.14
     graphs:
         state_example:
             nodes:
diff --git a/examples/MDF/SwitchedRLC_Circuit.json b/examples/MDF/SwitchedRLC_Circuit.json
@@ -1,7 +1,7 @@
 {
     "SwitchedRLC_Circuit": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.13",
+        "generating_application": "Python modeci-mdf v0.4.14",
         "metadata": {
             "preferred_duration": 2,
             "preferred_dt": 0.001
diff --git a/examples/MDF/SwitchedRLC_Circuit.yaml b/examples/MDF/SwitchedRLC_Circuit.yaml
@@ -1,6 +1,6 @@
 SwitchedRLC_Circuit:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.13
+    generating_application: Python modeci-mdf v0.4.14
     metadata:
         preferred_duration: 2
         preferred_dt: 0.001
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 v0.4.13",
+        "generating_application": "Python modeci-mdf v0.4.14",
         "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 v0.4.13
+    generating_application: Python modeci-mdf v0.4.14
     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 v0.4.13",
+        "generating_application": "Python modeci-mdf v0.4.14",
         "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 v0.4.13
+    generating_application: Python modeci-mdf v0.4.14
     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 v0.4.13",
+        "generating_application": "Python modeci-mdf v0.4.14",
         "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 v0.4.13
+    generating_application: Python modeci-mdf v0.4.14
     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 v0.4.13",
+        "generating_application": "Python modeci-mdf v0.4.14",
         "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 v0.4.13
+    generating_application: Python modeci-mdf v0.4.14
     graphs:
         threshold_example:
             nodes:
diff --git a/examples/MDF/conditions/timeinterval_condition.json b/examples/MDF/conditions/timeinterval_condition.json
@@ -1,7 +1,7 @@
 {
     "timeinterval_condition": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.13",
+        "generating_application": "Python modeci-mdf v0.4.14",
         "graphs": {
             "timeinterval_example": {
                 "nodes": {
diff --git a/examples/MDF/conditions/timeinterval_condition.yaml b/examples/MDF/conditions/timeinterval_condition.yaml
@@ -1,6 +1,6 @@
 timeinterval_condition:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.13
+    generating_application: Python modeci-mdf v0.4.14
     graphs:
         timeinterval_example:
             nodes:
diff --git a/examples/MDF/images/newton_plot.png b/examples/MDF/images/newton_plot.png
diff --git a/examples/MDF/images/switched_rlc_plot.png b/examples/MDF/images/switched_rlc_plot.png
diff --git a/examples/NeuroML/Izh_run.png b/examples/NeuroML/Izh_run.png
diff --git a/examples/NeuroML/MDFFNrun.multi.png b/examples/NeuroML/MDFFNrun.multi.png
diff --git a/examples/NeuroML/MDFFNrun.png b/examples/NeuroML/MDFFNrun.png
diff --git a/examples/ONNX/ab.json b/examples/ONNX/ab.json
@@ -1,7 +1,7 @@
 {
     "ONNX Model": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.13",
+        "generating_application": "Python modeci-mdf v0.4.14",
         "graphs": {
             "main_graph": {
                 "nodes": {
diff --git a/examples/ONNX/ab.yaml b/examples/ONNX/ab.yaml
@@ -1,6 +1,6 @@
 ONNX Model:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.13
+    generating_application: Python modeci-mdf v0.4.14
     graphs:
         main_graph:
             nodes:
diff --git a/examples/ONNX/abc.json b/examples/ONNX/abc.json
@@ -1,7 +1,7 @@
 {
     "ONNX Model": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.13",
+        "generating_application": "Python modeci-mdf v0.4.14",
         "graphs": {
             "main_graph": {
                 "nodes": {
diff --git a/examples/ONNX/abc.yaml b/examples/ONNX/abc.yaml
@@ -1,6 +1,6 @@
 ONNX Model:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.13
+    generating_application: Python modeci-mdf v0.4.14
     graphs:
         main_graph:
             nodes:
diff --git a/examples/ONNX/abc_basic-mdf.json b/examples/ONNX/abc_basic-mdf.json
@@ -1,7 +1,7 @@
 {
     "ONNX Model": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.13",
+        "generating_application": "Python modeci-mdf v0.4.14",
         "graphs": {
             "main_graph": {
                 "nodes": {
diff --git a/examples/ONNX/abc_basic-mdf.yaml b/examples/ONNX/abc_basic-mdf.yaml
@@ -1,6 +1,6 @@
 ONNX Model:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.13
+    generating_application: Python modeci-mdf v0.4.14
     graphs:
         main_graph:
             nodes:
diff --git a/examples/ONNX/abcd.json b/examples/ONNX/abcd.json
@@ -1,7 +1,7 @@
 {
     "ONNX Model": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.13",
+        "generating_application": "Python modeci-mdf v0.4.14",
         "graphs": {
             "main_graph": {
                 "nodes": {
diff --git a/examples/ONNX/abcd.yaml b/examples/ONNX/abcd.yaml
@@ -1,6 +1,6 @@
 ONNX Model:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.13
+    generating_application: Python modeci-mdf v0.4.14
     graphs:
         main_graph:
             nodes:
diff --git a/examples/PyTorch/MDF_PyTorch/ABCD_pytorch.py b/examples/PyTorch/MDF_PyTorch/ABCD_pytorch.py
@@ -1,5 +1,5 @@
 """
-This script has been generated by modeci_mdf v0.4.13.
+This script has been generated by modeci_mdf v0.4.14.
 It is an export of a MDF model (mdf.s - MDF stateful, i.e. full MDF allowing stateful parameters) to PyTorch
 
 """
diff --git a/examples/PyTorch/MDF_PyTorch/Arrays_pytorch.py b/examples/PyTorch/MDF_PyTorch/Arrays_pytorch.py
@@ -1,5 +1,5 @@
 """
-This script has been generated by modeci_mdf v0.4.13.
+This script has been generated by modeci_mdf v0.4.14.
 It is an export of a MDF model (mdf.s - MDF stateful, i.e. full MDF allowing stateful parameters) to PyTorch
 
 """
diff --git a/examples/PyTorch/MDF_PyTorch/Simple_pytorch.py b/examples/PyTorch/MDF_PyTorch/Simple_pytorch.py
@@ -1,5 +1,5 @@
 """
-This script has been generated by modeci_mdf v0.4.13.
+This script has been generated by modeci_mdf v0.4.14.
 It is an export of a MDF model (mdf.s - MDF stateful, i.e. full MDF allowing stateful parameters) to PyTorch
 
 """
diff --git a/examples/PyTorch/inception.json b/examples/PyTorch/inception.json
diff --git a/examples/PyTorch/mlp_pure_mdf.json b/examples/PyTorch/mlp_pure_mdf.json
diff --git a/examples/PyTorch/mlp_pure_mdf.yaml b/examples/PyTorch/mlp_pure_mdf.yaml
diff --git a/examples/PyTorch/simple_pytorch_to_mdf.json b/examples/PyTorch/simple_pytorch_to_mdf.json
diff --git a/examples/TensorFlow/Keras/IRIS/keras_to_MDF.json b/examples/TensorFlow/Keras/IRIS/keras_to_MDF.json
diff --git a/examples/TensorFlow/Keras/IRIS/keras_to_MDF.yaml b/examples/TensorFlow/Keras/IRIS/keras_to_MDF.yaml
diff --git a/examples/TensorFlow/Keras/MNIST/keras_to_MDF.json b/examples/TensorFlow/Keras/MNIST/keras_to_MDF.json
diff --git a/examples/TensorFlow/Keras/MNIST/keras_to_MDF.yaml b/examples/TensorFlow/Keras/MNIST/keras_to_MDF.yaml
diff --git a/src/modeci_mdf/__init__.py b/src/modeci_mdf/__init__.py

Original file line number	Diff line number	Diff line change
`@@ -1,7 +1,7 @@`
`1`	`1`	`{`
`2`	`2`	`"addition": {`
`3`	`3`	`"format": "ModECI MDF v0.4",`
`4`		`- "generating_application": "Python modeci-mdf v0.4.13",`
	`4`	`+ "generating_application": "Python modeci-mdf v0.4.14",`
`5`	`5`	`"graphs": {`
`6`	`6`	`"addition_graph": {`
`7`	`7`	`"nodes": {`
Original file line number	Diff line number	Diff line change
`@@ -1,7 +1,7 @@`
`1`	`1`	`{`
`2`	`2`	`"count": {`
`3`	`3`	`"format": "ModECI MDF v0.4",`
`4`		`- "generating_application": "Python modeci-mdf v0.4.13",`
	`4`	`+ "generating_application": "Python modeci-mdf v0.4.14",`
`5`	`5`	`"graphs": {`
`6`	`6`	`"count_graph": {`
`7`	`7`	`"nodes": {`
Original file line number	Diff line number	Diff line change
`@@ -1,7 +1,7 @@`
`1`	`1`	`{`
`2`	`2`	`"ABCD": {`
`3`	`3`	`"format": "ModECI MDF v0.4",`
`4`		`- "generating_application": "Python modeci-mdf v0.4.13",`
	`4`	`+ "generating_application": "Python modeci-mdf v0.4.14",`
`5`	`5`	`"graphs": {`
`6`	`6`	`"abcd_example": {`
`7`	`7`	`"nodes": {`