Merge pull request #493 from ModECI/development

Latest development to cyclic graphs test branch

Author: pgleeson

.github/workflows/ci.yml

@@ -13,9 +13,11 @@ jobs:
     name: Format
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v1
-    - uses: actions/setup-python@v2
-    - uses: pre-commit/action@v2.0.0
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+    - uses: pre-commit/action@v3.0.0
       with:
         extra_args: --hook-stage manual --all-files
 
@@ -25,13 +27,13 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.8", "3.9", "3.10"]
+        python-version: [ "3.8", "3.10", "3.11"]
         runs-on: [ubuntu-latest, macos-latest, windows-latest]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
-    - uses: actions/setup-python@v2
+    - uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
@@ -60,48 +62,37 @@ jobs:
 
     - name: Install most optional dependencies
       run: |
-        python -m pip install .[all_except_psyneulink]
+        python -m pip install .[optional]
 
     - 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
+      uses: ts-graphviz/setup-graphviz@v1
 
     - name: Test interface ACT-R
-      if: ${{ matrix.python-version != '3.10' || matrix.runs-on != 'windows-latest' }}
       run: |
         python -m pytest -v -m "actr" tests/
 
     - name: Test interface PyTorch
-      if: ${{ matrix.python-version != '3.10' || matrix.runs-on != 'windows-latest' }}
       run: |
         python -m pytest -v -m "pytorch" tests/
 
     - name: Test interface NeuroML
-      if: ${{ matrix.python-version != '3.10' || matrix.runs-on != 'windows-latest' }}
       run: |
+        python -m pip install .[neuroml]
         python -m pytest -v -m "neuroml" tests/
 
-    - name: Test interface TensorFlow linux/mac
-      if: ${{ matrix.runs-on != 'windows-latest' }}
-      run: |
-        dot -V
-        python -m pytest -v -m "tensorflow" tests/
-
-    - name: Test interface TensorFlow windows
-      if: ${{ matrix.python-version != '3.10' && matrix.runs-on == 'windows-latest' }}
+    - name: Test interface TensorFlow
+      if: ${{ matrix.python-version != '3.11'}}
       run: |
-        choco install graphviz
+        python -m pip install .[tensorflow]
         dot -V
         python -m pytest -v -m "tensorflow" tests/
 
     - name: Test interface PsyNeuLink
-      if: ${{ matrix.python-version != '3.10' }}
+      if: ${{ matrix.python-version != '3.11'}}
       run: |
         python -m pip install .[psyneulink]
         python -m pytest -v -m "psyneulink" tests/
@@ -123,12 +114,12 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v3
 
     - name: Build sdist and wheel
       run: pipx run --spec build pyproject-build
 
-    - uses: actions/upload-artifact@v2
+    - uses: actions/upload-artifact@v3
       with:
         path: dist
 

.gitignore

@@ -281,16 +281,33 @@ Thumbs.db #thumbnail cache on Windows
 /examples/NeuroML/arm64
 /examples/MDF/RNN/iaf.net
 /examples/MDF/RNN/iaf.net2
+/examples/TensorFlow/Keras/keras_to_MDF
 /examples/NeuroML/PyNN/All*
 /examples/NeuroML/PyNN/*dat
-/examples/NeuroML/PyNN/*.png
+/examples/NeuroML/PyNN/*1.png
 /examples/NeuroML/PyNN/*.1
-/examples/NeuroML/PyNN/InputWeights*
-/examples/NeuroML/PyNN/OneCell*
-/examples/NeuroML/PyNN/Sim*
-/examples/NeuroML/PyNN/LEMS_Sim*
-/examples/NeuroML/PyNN/HH*
 /examples/NeuroML/PyNN/arm64
 /examples/NeuroML/PyNN/*.pkl
+/examples/NeuroML/PyNN/*.json
+/examples/NeuroML/PyNN/*.mdf
+/examples/NeuroML/PyNN/*.spikes
 *_code.gen.c
-/examples/NeuroML/PyNN/Net1*
+examples/TensorFlow/Keras/Keras_to_MDF_IRIS/keras_to_MDF
+examples/TensorFlow/Keras/keras_to_MDF
+/examples/TensorFlow/Keras/Keras_MDF/Keras_to_MDF_IRIS/keras_to_MDF
+/examples/TensorFlow/Keras/Keras_MDF/keras_to_MDF
+/examples/NeuroML/PyNN/HH.yaml
+/examples/NeuroML/PyNN/InputWeights.yaml
+/examples/NeuroML/PyNN/Net1.yaml
+/examples/NeuroML/PyNN/OneCell.yaml
+/examples/NeuroML/PyNN/SimHH.yaml
+/examples/NeuroML/PyNN/SimNet1.yaml
+/examples/NeuroML/PyNN/SimOneCell.yaml
+/examples/NeuroML/PyNN/SimSimpleNet.yaml
+/examples/NeuroML/PyNN/SimpleNet.yaml
+/examples/NeuroML/PyNN/SimInputWeights.yaml
+/examples/TensorFlow/Keras/IRIS/keras_to_MDF
+/examples/TensorFlow/Keras/MNIST/keras_to_MDF
+/examples/TensorFlow/Keras/MNIST/keras_to_MDF.1
+/examples/TensorFlow/Keras/IRIS/keras_to_MDF.1
+/checkout_pngs.sh