Merge pull request #465 from ModECI/development

pgleeson · web-flow · commit 4273a98fabae · 2023-06-25T17:45:52.000+01:00
To v0.4.7; removes setup.py; add MDF paper to website
diff --git a/docs/sphinx/source/api/MDFpaper.md b/docs/sphinx/source/api/MDFpaper.md
@@ -0,0 +1,12 @@
+(ModECI:mdf_intro_paper)=
+
+# Paper introducing MDF
+
+The background to the ModECI project, the motivation for developing the Model Description Format, and the initial Python implementation of the language have been described in a NeuroView article in the Neuron journal:
+
+*<b>Integrating model development across computational neuroscience, cognitive science, and machine learning</b>*
+Padraig Gleeson, Sharon Crook, David Turner, Katherine Mantel, Mayank Raunak, Ted Willke and Jonathan D. Cohen, April 25, 2023 DOI: [https://doi.org/10.1016/j.neuron.2023.03.037](https://doi.org/10.1016/j.neuron.2023.03.037)
+
+*Neuroscience, cognitive science, and computer science are increasingly benefiting through their interactions. This could be accelerated by direct sharing of computational models across disparate modeling software used in each. We describe a Model Description Format designed to meet this challenge.*
+
+The paper will be freely downloadable from [here](https://www.cell.com/neuron/fulltext/S0896-6273(23)00261-1) in April 2024. If you do not have access to this via your institution, please [download the preprint of the paper here](https://github.com/ModECI/MDFpaper/blob/main/GleesonEtAl23_ModECI_NeuroView.pdf).
diff --git a/docs/sphinx/source/index.rst b/docs/sphinx/source/index.rst
@@ -35,6 +35,7 @@ re-used in other environments.
 
    api/Introduction
    api/QuickStart
+   api/MDFpaper
    api/Installation
    api/Contributing
    api/Contributors
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 v0.4.6",
+        "generating_application": "Python modeci-mdf v0.4.7",
         "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 v0.4.6
+    generating_application: Python modeci-mdf v0.4.7
     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 v0.4.6",
+        "generating_application": "Python modeci-mdf v0.4.7",
         "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 v0.4.6
+    generating_application: Python modeci-mdf v0.4.7
     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 v0.4.6",
+        "generating_application": "Python modeci-mdf v0.4.7",
         "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 v0.4.6
+    generating_application: Python modeci-mdf v0.4.7
     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 v0.4.6",
+        "generating_application": "Python modeci-mdf v0.4.7",
         "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 v0.4.6
+    generating_application: Python modeci-mdf v0.4.7
     graphs:
         array_example:
             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 v0.4.6",
+        "generating_application": "Python modeci-mdf v0.4.7",
         "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 v0.4.6
+    generating_application: Python modeci-mdf v0.4.7
     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 v0.4.6",
+        "generating_application": "Python modeci-mdf v0.4.7",
         "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 v0.4.6
+    generating_application: Python modeci-mdf v0.4.7
     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 v0.4.6",
+        "generating_application": "Python modeci-mdf v0.4.7",
         "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 v0.4.6
+    generating_application: Python modeci-mdf v0.4.7
     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 v0.4.6",
+        "generating_application": "Python modeci-mdf v0.4.7",
         "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 v0.4.6
+    generating_application: Python modeci-mdf v0.4.7
     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 v0.4.6",
+        "generating_application": "Python modeci-mdf v0.4.7",
         "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 v0.4.6
+    generating_application: Python modeci-mdf v0.4.7
     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 v0.4.6",
+        "generating_application": "Python modeci-mdf v0.4.7",
         "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 v0.4.6
+    generating_application: Python modeci-mdf v0.4.7
     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 v0.4.6",
+        "generating_application": "Python modeci-mdf v0.4.7",
         "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 v0.4.6
+    generating_application: Python modeci-mdf v0.4.7
     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 v0.4.6",
+        "generating_application": "Python modeci-mdf v0.4.7",
         "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 v0.4.6
+    generating_application: Python modeci-mdf v0.4.7
     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 v0.4.6",
+        "generating_application": "Python modeci-mdf v0.4.7",
         "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 v0.4.6
+    generating_application: Python modeci-mdf v0.4.7
     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 v0.4.6",
+        "generating_application": "Python modeci-mdf v0.4.7",
         "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 v0.4.6
+    generating_application: Python modeci-mdf v0.4.7
     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 v0.4.6",
+        "generating_application": "Python modeci-mdf v0.4.7",
         "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 v0.4.6
+    generating_application: Python modeci-mdf v0.4.7
     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 v0.4.6",
+        "generating_application": "Python modeci-mdf v0.4.7",
         "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 v0.4.6
+    generating_application: Python modeci-mdf v0.4.7
     graphs:
         timeinterval_example:
             nodes:
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 v0.4.6",
+        "generating_application": "Python modeci-mdf v0.4.7",
         "graphs": {
             "torch-jit-export": {
                 "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 v0.4.6
+    generating_application: Python modeci-mdf v0.4.7
     graphs:
         torch-jit-export:
             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 v0.4.6",
+        "generating_application": "Python modeci-mdf v0.4.7",
         "graphs": {
             "torch-jit-export": {
                 "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 v0.4.6
+    generating_application: Python modeci-mdf v0.4.7
     graphs:
         torch-jit-export:
             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 v0.4.6",
+        "generating_application": "Python modeci-mdf v0.4.7",
         "graphs": {
             "torch-jit-export": {
                 "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 v0.4.6
+    generating_application: Python modeci-mdf v0.4.7
     graphs:
         torch-jit-export:
             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 v0.4.6.
+This script has been generated by modeci_mdf v0.4.7.
 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 v0.4.6.
+This script has been generated by modeci_mdf v0.4.7.
 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 v0.4.6.
+This script has been generated by modeci_mdf v0.4.7.
 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
@@ -1,7 +1,7 @@
 {
     "InceptionBlocks": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.6",
+        "generating_application": "Python modeci-mdf v0.4.7",
         "graphs": {
             "InceptionBlocksGraph": {
                 "nodes": {
diff --git a/examples/PyTorch/mlp_pure_mdf.json b/examples/PyTorch/mlp_pure_mdf.json
@@ -1,7 +1,7 @@
 {
     "mlp_pure_mdf": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.6",
+        "generating_application": "Python modeci-mdf v0.4.7",
         "graphs": {
             "mlp_pure_mdf": {
                 "nodes": {
diff --git a/examples/PyTorch/mlp_pure_mdf.yaml b/examples/PyTorch/mlp_pure_mdf.yaml
@@ -1,6 +1,6 @@
 mlp_pure_mdf:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.6
+    generating_application: Python modeci-mdf v0.4.7
     graphs:
         mlp_pure_mdf:
             nodes:
diff --git a/examples/PyTorch/simple_pytorch_to_mdf.json b/examples/PyTorch/simple_pytorch_to_mdf.json
@@ -1,7 +1,7 @@
 {
     "SimpleNet": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.6",
+        "generating_application": "Python modeci-mdf v0.4.7",
         "graphs": {
             "SimpleNetGraph": {
                 "nodes": {
diff --git a/setup.cfg b/setup.cfg
diff --git a/setup.py b/setup.py
diff --git a/src/modeci_mdf/__init__.py b/src/modeci_mdf/__init__.py
diff --git a/src/modeci_mdf/execution_engine.py b/src/modeci_mdf/execution_engine.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 v0.4.6",`
	`4`	`+ "generating_application": "Python modeci-mdf v0.4.7",`
`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 v0.4.6",`
	`4`	`+ "generating_application": "Python modeci-mdf v0.4.7",`
`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 v0.4.6",`
	`4`	`+ "generating_application": "Python modeci-mdf v0.4.7",`
`5`	`5`	`"graphs": {`
`6`	`6`	`"abcd_example": {`
`7`	`7`	`"nodes": {`
Original file line number	Diff line number	Diff line change
`@@ -1,7 +1,7 @@`
`1`	`1`	`{`
`2`	`2`	`"Arrays": {`
`3`	`3`	`"format": "ModECI MDF v0.4",`
`4`		`- "generating_application": "Python modeci-mdf v0.4.6",`
	`4`	`+ "generating_application": "Python modeci-mdf v0.4.7",`
`5`	`5`	`"graphs": {`
`6`	`6`	`"array_example": {`
`7`	`7`	`"nodes": {`