Merge pull request #552 from ModECI/experimental

pgleeson · web-flow · commit ebdfe2fafaa1 · 2025-06-23T10:45:13.000+01:00
Remove numpy pin and fix issue with shape defaults
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -59,7 +59,6 @@ jobs:
 
     - name: Install core package
       run: |
-        pip install 'numpy<2.0.0' # due to lingering issues with other modules & numpy v2...
         python -m pip install .[dev]
 
     - name: Version info for installed packages
diff --git a/examples/NeuroML/ABCD.json b/examples/NeuroML/ABCD.json
@@ -1,6 +1,6 @@
 {
     "ABCD": {
-        "version": "NeuroMLlite v0.6.0",
+        "version": "NeuroMLlite v0.6.1",
         "notes": "Example of a simplified network",
         "parameters": {
             "A_initial": 0.1,
diff --git a/examples/NeuroML/ABCD.net.nml b/examples/NeuroML/ABCD.net.nml
@@ -1,5 +1,5 @@
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="ABCD">
-    <notes>Generated by NeuroMLlite v0.6.0
+    <notes>Generated by NeuroMLlite v0.6.1
     Generated network: ABCD
     Generation seed: 1234
     NeuroMLlite parameters:
diff --git a/examples/NeuroML/FN.json b/examples/NeuroML/FN.json
@@ -1,6 +1,6 @@
 {
     "FN": {
-        "version": "NeuroMLlite v0.6.0",
+        "version": "NeuroMLlite v0.6.1",
         "notes": "FitzHugh Nagumo cell model - originally specified in NeuroML/LEMS",
         "parameters": {
             "initial_w": 0.0,
diff --git a/examples/NeuroML/FN.net.nml b/examples/NeuroML/FN.net.nml
@@ -1,5 +1,5 @@
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="FN">
-    <notes>Generated by NeuroMLlite v0.6.0
+    <notes>Generated by NeuroMLlite v0.6.1
     Generated network: FN
     Generation seed: 1234
     NeuroMLlite parameters:
diff --git a/examples/NeuroML/IzhikevichTest.net.nml b/examples/NeuroML/IzhikevichTest.net.nml
@@ -1,5 +1,5 @@
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="IzhikevichTest">
-    <notes>Generated by NeuroMLlite v0.6.0
+    <notes>Generated by NeuroMLlite v0.6.1
     Generated network: IzhikevichTest
     Generation seed: 1234
     NeuroMLlite parameters:
diff --git a/examples/NeuroML/IzhikevichTest.nmllite.yaml b/examples/NeuroML/IzhikevichTest.nmllite.yaml
@@ -1,5 +1,5 @@
 IzhikevichTest:
-    version: NeuroMLlite v0.6.0
+    version: NeuroMLlite v0.6.1
     notes: Example Izhikevich
     parameters:
         N: 1
diff --git a/examples/NeuroML/LEMS_SimABCD.xml b/examples/NeuroML/LEMS_SimABCD.xml
@@ -2,7 +2,7 @@
 
     <!--
 
-        This LEMS file has been automatically generated using PyNeuroML v1.3.13 (libNeuroML v0.6.5)
+        This LEMS file has been automatically generated using PyNeuroML v1.3.18 (libNeuroML v0.6.7)
 
      -->
 
diff --git a/examples/NeuroML/LEMS_SimFN.xml b/examples/NeuroML/LEMS_SimFN.xml
@@ -2,7 +2,7 @@
 
     <!--
 
-        This LEMS file has been automatically generated using PyNeuroML v1.3.13 (libNeuroML v0.6.5)
+        This LEMS file has been automatically generated using PyNeuroML v1.3.18 (libNeuroML v0.6.7)
 
      -->
 
diff --git a/examples/NeuroML/LEMS_SimIzhikevichTest.xml b/examples/NeuroML/LEMS_SimIzhikevichTest.xml
@@ -2,7 +2,7 @@
 
     <!--
 
-        This LEMS file has been automatically generated using PyNeuroML v1.3.13 (libNeuroML v0.6.5)
+        This LEMS file has been automatically generated using PyNeuroML v1.3.18 (libNeuroML v0.6.7)
 
      -->
 
diff --git a/examples/NeuroML/PyNN/HH.net.nml b/examples/NeuroML/PyNN/HH.net.nml
@@ -1,5 +1,5 @@
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="HH">
-    <notes>Generated by NeuroMLlite v0.6.0
+    <notes>Generated by NeuroMLlite v0.6.1
     Generated network: HH
     Generation seed: 1234
     NeuroMLlite parameters:
diff --git a/examples/NeuroML/PyNN/InputWeights.net.nml b/examples/NeuroML/PyNN/InputWeights.net.nml
@@ -1,5 +1,5 @@
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="InputWeights">
-    <notes>Generated by NeuroMLlite v0.6.0
+    <notes>Generated by NeuroMLlite v0.6.1
     Generated network: InputWeights
     Generation seed: 1234
     NeuroMLlite parameters:
diff --git a/examples/NeuroML/PyNN/Net1.net.nml b/examples/NeuroML/PyNN/Net1.net.nml
@@ -1,5 +1,5 @@
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="Net1">
-    <notes>Generated by NeuroMLlite v0.6.0
+    <notes>Generated by NeuroMLlite v0.6.1
     Generated network: Net1
     Generation seed: 1234
     NeuroMLlite parameters:
diff --git a/examples/NeuroML/PyNN/OneCell.net.nml b/examples/NeuroML/PyNN/OneCell.net.nml
@@ -1,5 +1,5 @@
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="OneCell">
-    <notes>Generated by NeuroMLlite v0.6.0
+    <notes>Generated by NeuroMLlite v0.6.1
     Generated network: OneCell
     Generation seed: 1234
     NeuroMLlite parameters:
diff --git a/examples/NeuroML/PyNN/SimpleNet.net.nml b/examples/NeuroML/PyNN/SimpleNet.net.nml
@@ -1,5 +1,5 @@
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2"  xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="SimpleNet">
-    <notes>Generated by NeuroMLlite v0.6.0
+    <notes>Generated by NeuroMLlite v0.6.1
     Generated network: SimpleNet
     Generation seed: 1234
     NeuroMLlite parameters:
diff --git a/examples/NeuroML/SimABCD.json b/examples/NeuroML/SimABCD.json
@@ -1,6 +1,6 @@
 {
     "SimABCD": {
-        "version": "NeuroMLlite v0.6.0",
+        "version": "NeuroMLlite v0.6.1",
         "network": "ABCD.json",
         "duration": 5000.0,
         "dt": 100.0,
diff --git a/examples/NeuroML/SimFN.json b/examples/NeuroML/SimFN.json
@@ -1,6 +1,6 @@
 {
     "SimFN": {
-        "version": "NeuroMLlite v0.6.0",
+        "version": "NeuroMLlite v0.6.1",
         "network": "FN.json",
         "duration": 100.0,
         "dt": 0.05,
diff --git a/examples/NeuroML/SimIzhikevichTest.yaml b/examples/NeuroML/SimIzhikevichTest.yaml
@@ -1,5 +1,5 @@
 SimIzhikevichTest:
-    version: NeuroMLlite v0.6.0
+    version: NeuroMLlite v0.6.1
     network: IzhikevichTest.nmllite.yaml
     duration: 700.0
     dt: 0.025
diff --git a/examples/ONNX/abc.json b/examples/ONNX/abc.json
@@ -33,7 +33,7 @@
                             }
                         }
                     },
-                    "Loop_3": {
+                    "Loop_6": {
                         "input_ports": {
                             "B_loop_count": {
                                 "shape": [
@@ -55,7 +55,7 @@
                                     "graph_sub_graph": {
                                         "id": "sub_graph",
                                         "nodes": {
-                                            "Div_5": {
+                                            "Div_8": {
                                                 "input_ports": {
                                                     "x.11": {
                                                         "shape": [
@@ -69,7 +69,7 @@
                                                     "B": {
                                                         "value": 10.0
                                                     },
-                                                    "Div_5": {
+                                                    "Div_8": {
                                                         "function": "onnx::Div",
                                                         "args": {
                                                             "A": "x.11",
@@ -79,16 +79,16 @@
                                                 },
                                                 "output_ports": {
                                                     "x": {
-                                                        "value": "Div_5"
+                                                        "value": "Div_8"
                                                     }
                                                 }
                                             },
-                                            "Identity_6": {
+                                            "Identity_9": {
                                                 "parameters": {
                                                     "input": {
                                                         "value": true
                                                     },
-                                                    "Identity_6": {
+                                                    "Identity_9": {
                                                         "function": "onnx::Identity",
                                                         "args": {
                                                             "input": "input"
@@ -97,7 +97,7 @@
                                                 },
                                                 "output_ports": {
                                                     "_11": {
-                                                        "value": "Identity_6"
+                                                        "value": "Identity_9"
                                                     }
                                                 }
                                             }
@@ -108,7 +108,7 @@
                             "cond": {
                                 "value": true
                             },
-                            "Loop_3": {
+                            "Loop_6": {
                                 "function": "onnx::Loop",
                                 "args": {
                                     "M": "B_loop_count",
@@ -119,7 +119,7 @@
                         },
                         "output_ports": {
                             "x.3": {
-                                "value": "Loop_3"
+                                "value": "Loop_6"
                             }
                         }
                     },
@@ -152,14 +152,14 @@
                     }
                 },
                 "edges": {
-                    "/A/Add._A_Add_output_0_Loop_3._A_Add_output_0": {
+                    "/A/Add._A_Add_output_0_Loop_6._A_Add_output_0": {
                         "sender": "/A/Add",
-                        "receiver": "Loop_3",
+                        "receiver": "Loop_6",
                         "sender_port": "_A_Add_output_0",
                         "receiver_port": "_A_Add_output_0"
                     },
-                    "Loop_3.x.3_/C/Mul.x.3": {
-                        "sender": "Loop_3",
+                    "Loop_6.x.3_/C/Mul.x.3": {
+                        "sender": "Loop_6",
                         "receiver": "/C/Mul",
                         "sender_port": "x.3",
                         "receiver_port": "x.3"
diff --git a/examples/ONNX/abc.yaml b/examples/ONNX/abc.yaml
@@ -22,7 +22,7 @@ ONNX Model:
                     output_ports:
                         _A_Add_output_0:
                             value: /A/Add
-                Loop_3:
+                Loop_6:
                     input_ports:
                         B_loop_count:
                             shape:
@@ -39,7 +39,7 @@ ONNX Model:
                                 graph_sub_graph:
                                     id: sub_graph
                                     nodes:
-                                        Div_5:
+                                        Div_8:
                                             input_ports:
                                                 x.11:
                                                     shape:
@@ -49,36 +49,36 @@ ONNX Model:
                                             parameters:
                                                 B:
                                                     value: 10.0
-                                                Div_5:
+                                                Div_8:
                                                     function: onnx::Div
                                                     args:
                                                         A: x.11
                                                         B: B
                                             output_ports:
                                                 x:
-                                                    value: Div_5
-                                        Identity_6:
+                                                    value: Div_8
+                                        Identity_9:
                                             parameters:
                                                 input:
                                                     value: true
-                                                Identity_6:
+                                                Identity_9:
                                                     function: onnx::Identity
                                                     args:
                                                         input: input
                                             output_ports:
                                                 _11:
-                                                    value: Identity_6
+                                                    value: Identity_9
                         cond:
                             value: true
-                        Loop_3:
+                        Loop_6:
                             function: onnx::Loop
                             args:
                                 M: B_loop_count
                                 cond: cond
                                 v_initial: _A_Add_output_0
                     output_ports:
                         x.3:
-                            value: Loop_3
+                            value: Loop_6
                 /C/Mul:
                     input_ports:
                         x.3:
@@ -97,13 +97,13 @@ ONNX Model:
                         _13:
                             value: /C/Mul
             edges:
-                /A/Add._A_Add_output_0_Loop_3._A_Add_output_0:
+                /A/Add._A_Add_output_0_Loop_6._A_Add_output_0:
                     sender: /A/Add
-                    receiver: Loop_3
+                    receiver: Loop_6
                     sender_port: _A_Add_output_0
                     receiver_port: _A_Add_output_0
-                Loop_3.x.3_/C/Mul.x.3:
-                    sender: Loop_3
+                Loop_6.x.3_/C/Mul.x.3:
+                    sender: Loop_6
                     receiver: /C/Mul
                     sender_port: x.3
                     receiver_port: x.3
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
diff --git a/examples/PyTorch/PyTorch_MDF/benchmark_script/squeezenet1_1_benchmark.json b/examples/PyTorch/PyTorch_MDF/benchmark_script/squeezenet1_1_benchmark.json
@@ -2,11 +2,11 @@
     {
         "model_name": "squeezenet1_1",
         "model_type": "SqueezeNet",
-        "pytorch_time": 0.0694,
+        "pytorch_time": 0.0977,
         "pytorch_predictions": 10,
-        "mdf_time": 3.6003,
+        "mdf_time": 4.1677,
         "mdf_predictions": 10,
         "node density": 66,
-        "mdf : pytorch ratio": "51.86"
+        "mdf : pytorch ratio": "42.66"
     }
 ]
diff --git a/src/modeci_mdf/interfaces/pytorch/importer.py b/src/modeci_mdf/interfaces/pytorch/importer.py
@@ -361,9 +361,9 @@ def torchnode_to_mdfnode(
             out_dtype = str(out_type.getElementType())
 
         try:
-            shape = tuple(out_type.sizes()) if out_type.sizes() else None
+            shape = tuple(out_type.sizes()) if out_type.sizes() else ()
         except RuntimeError:
-            shape = None
+            shape = ()
 
         mdf_node.output_ports.append(
             OutputPort(
@@ -387,9 +387,9 @@ def torchnode_to_mdfnode(
                 inp_dtype = str(inp_type.getElementType())
 
             try:
-                shape = tuple(inp_type.sizes()) if inp_type.sizes() else None
+                shape = tuple(inp_type.sizes()) if inp_type.sizes() else ()
             except RuntimeError:
-                shape = None
+                shape = ()
 
             mdf_node.input_ports.append(
                 InputPort(id=ip_name, shape=shape, type=inp_dtype)
diff --git a/src/modeci_mdf/mdf.py b/src/modeci_mdf/mdf.py
@@ -108,7 +108,7 @@ class InputPort(MdfBase):
     id: str = field(validator=instance_of(str))
     shape: Optional[Tuple[int, ...]] = field(
         validator=optional(instance_of(tuple)),
-        default=None,
+        default=(),
         converter=lambda x: make_tuple(x) if type(x) is str else x,
     )
     type: Optional[str] = field(validator=optional(instance_of(str)), default=None)
@@ -133,7 +133,7 @@ class OutputPort(MdfBase):
     value: Optional[str] = field(validator=optional(instance_of(str)), default=None)
     shape: Optional[Tuple[int, ...]] = field(
         validator=optional(instance_of(tuple)),
-        default=None,
+        default=(),
         converter=lambda x: make_tuple(x) if type(x) is str else x,
     )
     type: Optional[str] = field(validator=optional(instance_of(str)), default=None)

Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"ABCD": {`
`3`		`- "version": "NeuroMLlite v0.6.0",`
	`3`	`+ "version": "NeuroMLlite v0.6.1",`
`4`	`4`	`"notes": "Example of a simplified network",`
`5`	`5`	`"parameters": {`
`6`	`6`	`"A_initial": 0.1,`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"FN": {`
`3`		`- "version": "NeuroMLlite v0.6.0",`
	`3`	`+ "version": "NeuroMLlite v0.6.1",`
`4`	`4`	`"notes": "FitzHugh Nagumo cell model - originally specified in NeuroML/LEMS",`
`5`	`5`	`"parameters": {`
`6`	`6`	`"initial_w": 0.0,`