Merge pull request #528 from ModECI/nml_examples

Fix to CI and regenerated images
ModECI · Apr 29, 2024 · 9af8aa7 · 9af8aa7
2 parents 1c2ee26 + b000a64
commit 9af8aa7
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -27,8 +27,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.8", "3.10", "3.11"]
+        python-version: [ "3.9", "3.10", "3.11"]
         runs-on: [ubuntu-latest, macos-latest, windows-latest]
+        exclude:
+          - runs-on: macos-latest
+            python-version: "3.9"
 
     steps:
     - uses: actions/checkout@v4
@@ -49,6 +52,11 @@ jobs:
     #- name: Install specific PsyNeuLink branch
     #  run: python -m pip install git+https://github.com/ModECI/PsyNeuLink@devel
 
+    - name: Install HDF5 for pytables on macos-14/latest
+      if: ${{ matrix.runs-on == 'macos-latest' }}
+      run: |
+        brew install hdf5
+
     - name: Install core package
       run: python -m pip install .[dev]
 

diff --git a/docs/MDF_function_specifications.json b/docs/MDF_function_specifications.json
diff --git a/docs/MDF_function_specifications.md b/docs/MDF_function_specifications.md
diff --git a/docs/MDF_function_specifications.yaml b/docs/MDF_function_specifications.yaml
diff --git a/docs/sphinx/source/api/MDF_function_specifications.md b/docs/sphinx/source/api/MDF_function_specifications.md
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/Izh_run.png b/docs/sphinx/source/api/export_format/NeuroML/Izh_run.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/NeuroML/MDFFNrun.png b/docs/sphinx/source/api/export_format/NeuroML/MDFFNrun.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/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/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/LEMS_Simiaf_example.png b/examples/MDF/RNN/LEMS_Simiaf_example.png
diff --git a/examples/MDF/RNN/RNN.run.png b/examples/MDF/RNN/RNN.run.png
diff --git a/examples/MDF/RNN/iaf.net.png b/examples/MDF/RNN/iaf.net.png
diff --git a/examples/MDF/RNN/iaf.net2.png b/examples/MDF/RNN/iaf.net2.png
diff --git a/examples/MDF/RNN/iaf.png b/examples/MDF/RNN/iaf.png
diff --git a/examples/MDF/RNN/rnn.png b/examples/MDF/RNN/rnn.png
diff --git a/examples/MDF/conditions/images/composite_example.png b/examples/MDF/conditions/images/composite_example.png
diff --git a/examples/MDF/conditions/images/everyncalls.png b/examples/MDF/conditions/images/everyncalls.png
diff --git a/examples/MDF/conditions/images/threshold.png b/examples/MDF/conditions/images/threshold.png
diff --git a/examples/MDF/conditions/images/timeinterval.png b/examples/MDF/conditions/images/timeinterval.png
diff --git a/examples/MDF/images/abc_conditions.png b/examples/MDF/images/abc_conditions.png
diff --git a/examples/MDF/images/abcd.png b/examples/MDF/images/abcd.png
diff --git a/examples/MDF/images/abcd_3.png b/examples/MDF/images/abcd_3.png
diff --git a/examples/MDF/images/arrays.png b/examples/MDF/images/arrays.png
diff --git a/examples/MDF/images/params_funcs.png b/examples/MDF/images/params_funcs.png
diff --git a/examples/MDF/images/simple.png b/examples/MDF/images/simple.png
diff --git a/examples/MDF/images/simple_3.png b/examples/MDF/images/simple_3.png
diff --git a/examples/MDF/images/states.png b/examples/MDF/images/states.png
diff --git a/examples/NeuroML/ABCD.1.mdf.png b/examples/NeuroML/ABCD.1.mdf.png
diff --git a/examples/NeuroML/ABCD.mdf.png b/examples/NeuroML/ABCD.mdf.png
diff --git a/examples/NeuroML/ABCD.nmllite.png b/examples/NeuroML/ABCD.nmllite.png
diff --git a/examples/NeuroML/FN.gv.png b/examples/NeuroML/FN.gv.png
diff --git a/examples/NeuroML/FNmulti.png b/examples/NeuroML/FNmulti.png
diff --git a/examples/NeuroML/Izh.png b/examples/NeuroML/Izh.png
diff --git a/examples/NeuroML/Izh_run.png b/examples/NeuroML/Izh_run.png
diff --git a/examples/NeuroML/IzhikevichTest.gv.png b/examples/NeuroML/IzhikevichTest.gv.png
diff --git a/examples/NeuroML/LEMS_SimABCD.png b/examples/NeuroML/LEMS_SimABCD.png
diff --git a/examples/NeuroML/LEMS_SimFN.png b/examples/NeuroML/LEMS_SimFN.png
diff --git a/examples/NeuroML/LEMS_SimIzhikevichTest.png b/examples/NeuroML/LEMS_SimIzhikevichTest.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/NeuroML/PyNN/HH.mdf.png b/examples/NeuroML/PyNN/HH.mdf.png
diff --git a/examples/NeuroML/PyNN/InputWeights.mdf.png b/examples/NeuroML/PyNN/InputWeights.mdf.png
diff --git a/examples/NeuroML/PyNN/Net1.mdf.png b/examples/NeuroML/PyNN/Net1.mdf.png
diff --git a/examples/NeuroML/PyNN/OneCell.mdf.png b/examples/NeuroML/PyNN/OneCell.mdf.png
diff --git a/examples/NeuroML/PyNN/SimpleNet.mdf.png b/examples/NeuroML/PyNN/SimpleNet.mdf.png
diff --git a/examples/ONNX/ab.json b/examples/ONNX/ab.json
@@ -3,7 +3,7 @@
         "format": "ModECI MDF v0.4",
         "generating_application": "Python modeci-mdf v0.4.9",
         "graphs": {
-            "torch_jit": {
+            "main_graph": {
                 "nodes": {
                     "/A/Add": {
                         "input_ports": {

diff --git a/examples/ONNX/ab.png b/examples/ONNX/ab.png
diff --git a/examples/ONNX/ab.yaml b/examples/ONNX/ab.yaml
@@ -2,7 +2,7 @@ ONNX Model:
     format: ModECI MDF v0.4
     generating_application: Python modeci-mdf v0.4.9
     graphs:
-        torch_jit:
+        main_graph:
             nodes:
                 /A/Add:
                     input_ports:

diff --git a/examples/ONNX/abc.json b/examples/ONNX/abc.json
@@ -3,7 +3,7 @@
         "format": "ModECI MDF v0.4",
         "generating_application": "Python modeci-mdf v0.4.9",
         "graphs": {
-            "torch_jit": {
+            "main_graph": {
                 "nodes": {
                     "/A/Add": {
                         "input_ports": {
@@ -52,8 +52,8 @@
                         "parameters": {
                             "body": {
                                 "value": {
-                                    "graph_torch_jit1": {
-                                        "id": "torch_jit1",
+                                    "graph_sub_graph": {
+                                        "id": "sub_graph",
                                         "nodes": {
                                             "Div_5": {
                                                 "input_ports": {

diff --git a/examples/ONNX/abc.yaml b/examples/ONNX/abc.yaml
@@ -2,7 +2,7 @@ ONNX Model:
     format: ModECI MDF v0.4
     generating_application: Python modeci-mdf v0.4.9
     graphs:
-        torch_jit:
+        main_graph:
             nodes:
                 /A/Add:
                     input_ports:
@@ -36,8 +36,8 @@ ONNX Model:
                     parameters:
                         body:
                             value:
-                                graph_torch_jit1:
-                                    id: torch_jit1
+                                graph_sub_graph:
+                                    id: sub_graph
                                     nodes:
                                         Div_5:
                                             input_ports:

diff --git a/examples/ONNX/abcd.json b/examples/ONNX/abcd.json
@@ -3,7 +3,7 @@
         "format": "ModECI MDF v0.4",
         "generating_application": "Python modeci-mdf v0.4.9",
         "graphs": {
-            "torch_jit": {
+            "main_graph": {
                 "nodes": {
                     "/A/Mul": {
                         "input_ports": {

diff --git a/examples/ONNX/abcd.yaml b/examples/ONNX/abcd.yaml
@@ -2,7 +2,7 @@ ONNX Model:
     format: ModECI MDF v0.4
     generating_application: Python modeci-mdf v0.4.9
     graphs:
-        torch_jit:
+        main_graph:
             nodes:
                 /A/Mul:
                     input_ports:

diff --git a/examples/PyTorch/MDF_PyTorch/ABCD.onnx b/examples/PyTorch/MDF_PyTorch/ABCD.onnx
diff --git a/examples/PyTorch/MDF_PyTorch/Arrays.onnx b/examples/PyTorch/MDF_PyTorch/Arrays.onnx
diff --git a/examples/PyTorch/MDF_PyTorch/Simple.onnx b/examples/PyTorch/MDF_PyTorch/Simple.onnx