Merge pull request #461 from ModECI/development

Updates to NeuroML examples; regenerated images; to v0.4.6
ModECI · May 31, 2023 · f5ee2dc · f5ee2dc
2 parents c61fc54 + 82770ce
commit f5ee2dc
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Showing 159 changed files with 2,438 additions and 678 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -59,12 +59,19 @@ jobs:
         python -m pytest -m coremdf tests/
 
     - name: Install optional dependencies
-      run: python -m pip install .[all]
+      run: |
+        python -m pip install .[all]
 
     - name: Version info for optional installed packages
       run: |
           pip list
 
+    - name: Install graphviz
+      if: ${{ matrix.runs-on != 'windows-latest' }}
+      run: |
+        if [[  ${{ matrix.runs-on }} == *"macos"* ]]; then brew install graphviz ; fi
+        if [[  ${{ matrix.runs-on }} == *"ubuntu"* ]]; then sudo apt install graphviz ; fi
+
     - name: Test interface ACT-R
       if: ${{ matrix.python-version != '3.10' || matrix.runs-on != 'windows-latest' }}
       run: |
@@ -88,8 +95,6 @@ jobs:
     - name: Test interface TensorFlow linux/mac
       if: ${{ matrix.runs-on != 'windows-latest' }}
       run: |
-        if [[  ${{ matrix.runs-on }} == *"macos"* ]]; then brew install graphviz ; fi
-        if [[  ${{ matrix.runs-on }} == *"ubuntu"* ]]; then sudo apt install graphviz ; fi
         dot -V
         python -m pytest -v -m "tensorflow" tests/
 

diff --git a/.gitignore b/.gitignore
@@ -276,3 +276,5 @@ Thumbs.db #thumbnail cache on Windows
 /examples/MDF/NLP/TestNLP
 /examples/MDF/conditions/composite_example
 /examples/NeuroML/arm64
+/examples/MDF/RNN/iaf.net
+/examples/MDF/RNN/iaf.net2
diff --git a/docs/sphinx/source/api/export_format/MDF/images/abc_conditions.png b/docs/sphinx/source/api/export_format/MDF/images/abc_conditions.png
diff --git a/docs/sphinx/source/api/export_format/MDF/images/abcd.png b/docs/sphinx/source/api/export_format/MDF/images/abcd.png
diff --git a/docs/sphinx/source/api/export_format/MDF/images/abcd_3.png b/docs/sphinx/source/api/export_format/MDF/images/abcd_3.png
diff --git a/docs/sphinx/source/api/export_format/MDF/images/arrays.png b/docs/sphinx/source/api/export_format/MDF/images/arrays.png
diff --git a/docs/sphinx/source/api/export_format/MDF/images/params_funcs.png b/docs/sphinx/source/api/export_format/MDF/images/params_funcs.png
diff --git a/docs/sphinx/source/api/export_format/MDF/images/simple.png b/docs/sphinx/source/api/export_format/MDF/images/simple.png
diff --git a/docs/sphinx/source/api/export_format/MDF/images/simple_3.png b/docs/sphinx/source/api/export_format/MDF/images/simple_3.png
diff --git a/docs/sphinx/source/api/export_format/MDF/images/states.png b/docs/sphinx/source/api/export_format/MDF/images/states.png
diff --git a/docs/sphinx/source/api/export_format/NeuroML/ABCD.1.mdf.png b/docs/sphinx/source/api/export_format/NeuroML/ABCD.1.mdf.png
diff --git a/docs/sphinx/source/api/export_format/NeuroML/ABCD.mdf.png b/docs/sphinx/source/api/export_format/NeuroML/ABCD.mdf.png
diff --git a/docs/sphinx/source/api/export_format/NeuroML/ABCD.nmllite.png b/docs/sphinx/source/api/export_format/NeuroML/ABCD.nmllite.png
diff --git a/docs/sphinx/source/api/export_format/NeuroML/FN.gv.png b/docs/sphinx/source/api/export_format/NeuroML/FN.gv.png
diff --git a/docs/sphinx/source/api/export_format/NeuroML/FNmulti.png b/docs/sphinx/source/api/export_format/NeuroML/FNmulti.png
diff --git a/docs/sphinx/source/api/export_format/NeuroML/Izh.png b/docs/sphinx/source/api/export_format/NeuroML/Izh.png
diff --git a/docs/sphinx/source/api/export_format/NeuroML/IzhikevichTest.gv.png b/docs/sphinx/source/api/export_format/NeuroML/IzhikevichTest.gv.png
diff --git a/docs/sphinx/source/api/export_format/NeuroML/LEMS_SimABCD.png b/docs/sphinx/source/api/export_format/NeuroML/LEMS_SimABCD.png
diff --git a/docs/sphinx/source/api/export_format/NeuroML/LEMS_SimFN.png b/docs/sphinx/source/api/export_format/NeuroML/LEMS_SimFN.png
diff --git a/docs/sphinx/source/api/export_format/NeuroML/LEMS_SimIzhikevichTest.png b/docs/sphinx/source/api/export_format/NeuroML/LEMS_SimIzhikevichTest.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/ONNX/ab.png b/docs/sphinx/source/api/export_format/ONNX/ab.png
diff --git a/docs/sphinx/source/api/export_format/ONNX/simple_ab.py b/docs/sphinx/source/api/export_format/ONNX/simple_ab.py
@@ -7,6 +7,7 @@
 import torch
 import onnx
 import sys
+import os
 
 
 from modeci_mdf.interfaces.onnx import onnx_to_mdf
@@ -80,7 +81,9 @@ def main():
         view_on_render=False,
         level=3,
         filename_root="ab",
-        only_warn_on_fail=True,  # Makes sure test of this doesn't fail on Windows on GitHub Actions
+        only_warn_on_fail=(
+            os.name == "nt"
+        ),  # Makes sure test of this doesn't fail on Windows on GitHub Actions
     )
     if "-run" in sys.argv:
         verbose = True

diff --git a/docs/sphinx/source/api/export_format/ONNX/simple_abc.py b/docs/sphinx/source/api/export_format/ONNX/simple_abc.py
@@ -6,6 +6,7 @@
 """
 import torch
 import onnx
+import os
 
 
 from modeci_mdf.interfaces.onnx import onnx_to_mdf
@@ -82,7 +83,9 @@ def main():
         view_on_render=False,
         level=3,
         filename_root="abc",
-        only_warn_on_fail=True,  # Makes sure test of this doesn't fail on Windows on GitHub Actions
+        only_warn_on_fail=(
+            os.name == "nt"
+        ),  # Makes sure test of this doesn't fail on Windows on GitHub Actions
     )
 
 

diff --git a/docs/sphinx/source/api/export_format/PyTorch/inception.png b/docs/sphinx/source/api/export_format/PyTorch/inception.png
diff --git a/docs/sphinx/source/api/export_format/PyTorch/mlp_pure_mdf.png b/docs/sphinx/source/api/export_format/PyTorch/mlp_pure_mdf.png
diff --git a/docs/sphinx/source/api/export_format/PyTorch/simple_pytorch_to_mdf.1.png b/docs/sphinx/source/api/export_format/PyTorch/simple_pytorch_to_mdf.1.png
diff --git a/docs/sphinx/source/api/export_format/PyTorch/simple_pytorch_to_mdf.png b/docs/sphinx/source/api/export_format/PyTorch/simple_pytorch_to_mdf.png
diff --git a/docs/sphinx/source/api/export_format/PyTorch/simple_pytorch_to_mdf_torchviz.png b/docs/sphinx/source/api/export_format/PyTorch/simple_pytorch_to_mdf_torchviz.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 v0.4.5",
+        "generating_application": "Python modeci-mdf v0.4.6",
         "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 v0.4.5
+    generating_application: Python modeci-mdf v0.4.6
     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 v0.4.5",
+        "generating_application": "Python modeci-mdf v0.4.6",
         "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 v0.4.5
+    generating_application: Python modeci-mdf v0.4.6
     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 v0.4.5",
+        "generating_application": "Python modeci-mdf v0.4.6",
         "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 v0.4.5
+    generating_application: Python modeci-mdf v0.4.6
     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 v0.4.5",
+        "generating_application": "Python modeci-mdf v0.4.6",
         "graphs": {
             "array_example": {
                 "nodes": {
@@ -28,7 +28,12 @@
                     },
                     "middle_node": {
                         "input_ports": {
-                            "input_port1": {}
+                            "input_port1": {
+                                "shape": [
+                                    2,
+                                    2
+                                ]
+                            }
                         },
                         "parameters": {
                             "slope": {

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 v0.4.5
+    generating_application: Python modeci-mdf v0.4.6
     graphs:
         array_example:
             nodes:
@@ -17,7 +17,10 @@ Arrays:
                             value: input_level
                 middle_node:
                     input_ports:
-                        input_port1: {}
+                        input_port1:
+                            shape:
+                            - 2
+                            - 2
                     parameters:
                         slope:
                             value: 0.5

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 v0.4.5",
+        "generating_application": "Python modeci-mdf v0.4.6",
         "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 v0.4.5
+    generating_application: Python modeci-mdf v0.4.6
     graphs:
         params_funcs_example:
             nodes: