Regenerates all images; ensures graph generation failure always causes error if not Windows

.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/
 

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

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
     )
 
 

examples/MDF/Arrays.json

@@ -28,7 +28,12 @@
                     },
                     "middle_node": {
                         "input_ports": {
-                            "input_port1": {}
+                            "input_port1": {
+                                "shape": [
+                                    2,
+                                    2
+                                ]
+                            }
                         },
                         "parameters": {
                             "slope": {

examples/MDF/Arrays.yaml

@@ -17,7 +17,10 @@ Arrays:
                             value: input_level
                 middle_node:
                     input_ports:
-                        input_port1: {}
+                        input_port1:
+                            shape:
+                            - 2
+                            - 2
                     parameters:
                         slope:
                             value: 0.5

examples/MDF/RNN/IAF_net.json

@@ -46,7 +46,7 @@
                             }
                         },
                         "output_ports": {
-                            "out_port": {
+                            "current_output": {
                                 "value": "level"
                             }
                         }
@@ -57,17 +57,9 @@
                                 "shape": [
                                     8
                                 ]
-                            },
-                            "spike_input": {
-                                "shape": [
-                                    8
-                                ]
                             }
                         },
                         "parameters": {
-                            "syn_tau": {
-                                "value": 10
-                            },
                             "v0": {
                                 "value": [
                                     -54.67038134416407,
@@ -107,108 +99,6 @@
                                     -20
                                 ]
                             },
-                            "spike_weights": {
-                                "value": [
-                                    [
-                                        1.0,
-                                        0.0,
-                                        0.0,
-                                        0.0,
-                                        0.0,
-                                        0.0,
-                                        0.0,
-                                        0.0
-                                    ],
-                                    [
-                                        0.0,
-                                        1.0,
-                                        0.0,
-                                        0.0,
-                                        0.0,
-                                        0.0,
-                                        0.0,
-                                        0.0
-                                    ],
-                                    [
-                                        0.0,
-                                        0.0,
-                                        1.0,
-                                        0.0,
-                                        0.0,
-                                        0.0,
-                                        0.0,
-                                        0.0
-                                    ],
-                                    [
-                                        0.0,
-                                        0.0,
-                                        0.0,
-                                        1.0,
-                                        0.0,
-                                        0.0,
-                                        0.0,
-                                        0.0
-                                    ],
-                                    [
-                                        0.0,
-                                        0.0,
-                                        0.0,
-                                        0.0,
-                                        1.0,
-                                        0.0,
-                                        0.0,
-                                        0.0
-                                    ],
-                                    [
-                                        0.0,
-                                        0.0,
-                                        0.0,
-                                        0.0,
-                                        0.0,
-                                        1.0,
-                                        0.0,
-                                        0.0
-                                    ],
-                                    [
-                                        0.0,
-                                        0.0,
-                                        0.0,
-                                        0.0,
-                                        0.0,
-                                        0.0,
-                                        1.0,
-                                        0.0
-                                    ],
-                                    [
-                                        0.0,
-                                        0.0,
-                                        0.0,
-                                        0.0,
-                                        0.0,
-                                        0.0,
-                                        0.0,
-                                        1.0
-                                    ]
-                                ]
-                            },
-                            "weighted_spike": {
-                                "function": "MatMul",
-                                "args": {
-                                    "A": "spike_weights",
-                                    "B": "spike_input"
-                                }
-                            },
-                            "syn_i": {
-                                "default_initial_value": "0",
-                                "time_derivative": "-1 * syn_i",
-                                "conditions": [
-                                    {
-                                        "id": "spike_detected",
-                                        "test": "spike_input > 0",
-                                        "value": "weighted_spike"
-                                    }
-                                ]
-                            },
                             "spiking": {
                                 "default_initial_value": "0",
                                 "conditions": [
@@ -226,7 +116,7 @@
                             },
                             "v": {
                                 "default_initial_value": "v0",
-                                "time_derivative": "-1 * (v-erev)/tau + syn_i + current_input",
+                                "time_derivative": "-1 * (v-erev)/tau + current_input",
                                 "conditions": [
                                     {
                                         "id": "reset",
@@ -237,10 +127,10 @@
                             }
                         },
                         "output_ports": {
-                            "out_port_v": {
+                            "v_output": {
                                 "value": "v"
                             },
-                            "out_port_spiking": {
+                            "spiking_output": {
                                 "value": "spiking"
                             }
                         }
@@ -251,17 +141,9 @@
                                 "shape": [
                                     8
                                 ]
-                            },
-                            "spike_input": {
-                                "shape": [
-                                    8
-                                ]
                             }
                         },
                         "parameters": {
-                            "syn_tau": {
-                                "value": 10
-                            },
                             "v0": {
                                 "value": [
                                     -54.67038134416407,
@@ -301,6 +183,54 @@
                                     -20
                                 ]
                             },
+                            "spiking": {
+                                "default_initial_value": "0",
+                                "conditions": [
+                                    {
+                                        "id": "is_spiking",
+                                        "test": "v >= thresh",
+                                        "value": "1"
+                                    },
+                                    {
+                                        "id": "not_spiking",
+                                        "test": "v < thresh",
+                                        "value": "0"
+                                    }
+                                ]
+                            },
+                            "v": {
+                                "default_initial_value": "v0",
+                                "time_derivative": "-1 * (v-erev)/tau + current_input",
+                                "conditions": [
+                                    {
+                                        "id": "reset",
+                                        "test": "v > thresh",
+                                        "value": "erev"
+                                    }
+                                ]
+                            }
+                        },
+                        "output_ports": {
+                            "v_output": {
+                                "value": "v"
+                            },
+                            "spiking_output": {
+                                "value": "spiking"
+                            }
+                        }
+                    },
+                    "syn_post": {
+                        "input_ports": {
+                            "spike_input": {
+                                "shape": [
+                                    8
+                                ]
+                            }
+                        },
+                        "parameters": {
+                            "syn_tau": {
+                                "value": 10
+                            },
                             "spike_weights": {
                                 "value": [
                                     [
@@ -402,40 +332,11 @@
                                         "value": "weighted_spike"
                                     }
                                 ]
-                            },
-                            "spiking": {
-                                "default_initial_value": "0",
-                                "conditions": [
-                                    {
-                                        "id": "is_spiking",
-                                        "test": "v >= thresh",
-                                        "value": "1"
-                                    },
-                                    {
-                                        "id": "not_spiking",
-                                        "test": "v < thresh",
-                                        "value": "0"
-                                    }
-                                ]
-                            },
-                            "v": {
-                                "default_initial_value": "v0",
-                                "time_derivative": "-1 * (v-erev)/tau + syn_i + current_input",
-                                "conditions": [
-                                    {
-                                        "id": "reset",
-                                        "test": "v > thresh",
-                                        "value": "erev"
-                                    }
-                                ]
                             }
                         },
                         "output_ports": {
-                            "out_port_v": {
-                                "value": "v"
-                            },
-                            "out_port_spiking": {
-                                "value": "spiking"
+                            "current_output": {
+                                "value": "syn_i"
                             }
                         }
                     }
@@ -444,13 +345,19 @@
                     "input_edge": {
                         "sender": "current_input_node",
                         "receiver": "pre",
-                        "sender_port": "out_port",
+                        "sender_port": "current_output",
+                        "receiver_port": "current_input"
+                    },
+                    "post_internal_edge": {
+                        "sender": "syn_post",
+                        "receiver": "post",
+                        "sender_port": "current_output",
                         "receiver_port": "current_input"
                     },
                     "syn_edge": {
                         "sender": "pre",
-                        "receiver": "post",
-                        "sender_port": "out_port_spiking",
+                        "receiver": "syn_post",
+                        "sender_port": "spiking_output",
                         "receiver_port": "spike_input"
                     }
                 }