Merge pull request #488 from ModECI/development

To v0.4.8, includes Outreachy May 2023 work
ModECI · Sep 15, 2023 · 2e9cd9c · 2e9cd9c
2 parents 4273a98 + c147789
commit 2e9cd9c
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diff --git a/.github/workflows/ci.yml b/.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/[email protected]
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+      with:
+        python-version: "3.10"
+    - uses: pre-commit/[email protected]
       with:
         extra_args: --hook-stage manual --all-files
 
@@ -29,9 +31,9 @@ jobs:
         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 }}
 
@@ -58,9 +60,9 @@ jobs:
       run: |
         python -m pytest -m coremdf tests/
 
-    - name: Install optional dependencies
+    - name: Install most optional dependencies
       run: |
-        python -m pip install .[all]
+        python -m pip install .[all_except_psyneulink]
 
     - name: Version info for optional installed packages
       run: |
@@ -87,11 +89,6 @@ jobs:
       run: |
         python -m pytest -v -m "neuroml" tests/
 
-    - name: Test interface PsyNeuLink
-      if: ${{ matrix.python-version != '3.10' }}
-      run: |
-        python -m pytest -v -m "psyneulink" tests/
-
     - name: Test interface TensorFlow linux/mac
       if: ${{ matrix.runs-on != 'windows-latest' }}
       run: |
@@ -105,6 +102,20 @@ jobs:
         dot -V
         python -m pytest -v -m "tensorflow" tests/
 
+    - name: Test interface PsyNeuLink
+      if: ${{ matrix.python-version != '3.10' }}
+      run: |
+        python -m pip install .[psyneulink]
+        python -m pytest -v -m "psyneulink" tests/
+
+    - name: Build Documentation
+      run: |
+        cd docs
+        python generate.py
+        cd sphinx
+        make clean
+        make html
+
     - name: Final version info for optional installed packages
       run: |
           pip list
@@ -114,12 +125,12 @@ 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
 

diff --git a/.gitignore b/.gitignore
@@ -278,3 +278,32 @@ 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/*1.png
+/examples/NeuroML/PyNN/*.1
+/examples/NeuroML/PyNN/arm64
+/examples/NeuroML/PyNN/*.pkl
+/examples/NeuroML/PyNN/*.json
+/examples/NeuroML/PyNN/*.mdf
+/examples/NeuroML/PyNN/*.spikes
+*_code.gen.c
+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
diff --git a/docs/sphinx/source/api/QuickStart.md b/docs/sphinx/source/api/QuickStart.md
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/simple_pytorch_to_mdf.png b/docs/sphinx/source/api/export_format/PyTorch/simple_pytorch_to_mdf.png
diff --git a/docs/sphinx/source/conf.py b/docs/sphinx/source/conf.py
@@ -145,14 +145,14 @@ def setup(app):
     "pytest": ("https://docs.pytest.org/en/stable", None),
 }
 
-from sphinx.ext.autodoc import ClassLevelDocumenter, InstanceAttributeDocumenter
+from sphinx.ext.autodoc import ClassLevelDocumenter, AttributeDocumenter
 
 
 def add_directive_header(self, sig):
     ClassLevelDocumenter.add_directive_header(self, sig)
 
 
-InstanceAttributeDocumenter.add_directive_header = add_directive_header
+AttributeDocumenter.add_directive_header = add_directive_header
 
 
 import os

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 v0.4.7",
+        "generating_application": "Python modeci-mdf v0.4.8",
         "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 v0.4.7
+    generating_application: Python modeci-mdf v0.4.8
     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 v0.4.7",
+        "generating_application": "Python modeci-mdf v0.4.8",
         "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 v0.4.7
+    generating_application: Python modeci-mdf v0.4.8
     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 v0.4.7",
+        "generating_application": "Python modeci-mdf v0.4.8",
         "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 v0.4.7
+    generating_application: Python modeci-mdf v0.4.8
     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 v0.4.7",
+        "generating_application": "Python modeci-mdf v0.4.8",
         "graphs": {
             "array_example": {
                 "nodes": {

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 v0.4.7
+    generating_application: Python modeci-mdf v0.4.8
     graphs:
         array_example:
             nodes:

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 v0.4.7",
+        "generating_application": "Python modeci-mdf v0.4.8",
         "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 v0.4.7
+    generating_application: Python modeci-mdf v0.4.8
     graphs:
         params_funcs_example:
             nodes:

diff --git a/examples/MDF/RNN/IAF_net.json b/examples/MDF/RNN/IAF_net.json
@@ -1,7 +1,7 @@
 {
     "IAF_net": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.7",
+        "generating_application": "Python modeci-mdf v0.4.8",
         "graphs": {
             "iaf_example": {
                 "nodes": {

diff --git a/examples/MDF/RNN/IAF_net.yaml b/examples/MDF/RNN/IAF_net.yaml
@@ -1,6 +1,6 @@
 IAF_net:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.7
+    generating_application: Python modeci-mdf v0.4.8
     graphs:
         iaf_example:
             nodes:

diff --git a/examples/MDF/RNN/IAF_net2.json b/examples/MDF/RNN/IAF_net2.json
@@ -1,7 +1,7 @@
 {
     "IAF_net2": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.7",
+        "generating_application": "Python modeci-mdf v0.4.8",
         "graphs": {
             "iaf_example": {
                 "nodes": {

diff --git a/examples/MDF/RNN/IAF_net2.yaml b/examples/MDF/RNN/IAF_net2.yaml
@@ -1,6 +1,6 @@
 IAF_net2:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.7
+    generating_application: Python modeci-mdf v0.4.8
     graphs:
         iaf_example:
             nodes:

diff --git a/examples/MDF/RNN/IAFs.json b/examples/MDF/RNN/IAFs.json
@@ -1,7 +1,7 @@
 {
     "IAFs": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.7",
+        "generating_application": "Python modeci-mdf v0.4.8",
         "graphs": {
             "iaf_example": {
                 "nodes": {

diff --git a/examples/MDF/RNN/IAFs.yaml b/examples/MDF/RNN/IAFs.yaml
@@ -1,6 +1,6 @@
 IAFs:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.7
+    generating_application: Python modeci-mdf v0.4.8
     graphs:
         iaf_example:
             nodes:

diff --git a/examples/MDF/RNN/RNNs.json b/examples/MDF/RNN/RNNs.json
@@ -1,7 +1,7 @@
 {
     "RNNs": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.7",
+        "generating_application": "Python modeci-mdf v0.4.8",
         "graphs": {
             "rnn_example": {
                 "nodes": {

diff --git a/examples/MDF/RNN/RNNs.yaml b/examples/MDF/RNN/RNNs.yaml
@@ -1,6 +1,6 @@
 RNNs:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.7
+    generating_application: Python modeci-mdf v0.4.8
     graphs:
         rnn_example:
             nodes:

diff --git a/examples/MDF/Simple.bson b/examples/MDF/Simple.bson
diff --git a/examples/MDF/Simple.json b/examples/MDF/Simple.json
@@ -1,7 +1,7 @@
 {
     "Simple": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.7",
+        "generating_application": "Python modeci-mdf v0.4.8",
         "graphs": {
             "simple_example": {
                 "nodes": {

diff --git a/examples/MDF/Simple.yaml b/examples/MDF/Simple.yaml
@@ -1,6 +1,6 @@
 Simple:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.7
+    generating_application: Python modeci-mdf v0.4.8
     graphs:
         simple_example:
             nodes:

diff --git a/examples/MDF/States.json b/examples/MDF/States.json
@@ -1,7 +1,7 @@
 {
     "States": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.7",
+        "generating_application": "Python modeci-mdf v0.4.8",
         "graphs": {
             "state_example": {
                 "nodes": {

diff --git a/examples/MDF/States.yaml b/examples/MDF/States.yaml
@@ -1,6 +1,6 @@
 States:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.7
+    generating_application: Python modeci-mdf v0.4.8
     graphs:
         state_example:
             nodes:

diff --git a/examples/MDF/abc_conditions.json b/examples/MDF/abc_conditions.json
@@ -1,7 +1,7 @@
 {
     "abc_conditions": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.7",
+        "generating_application": "Python modeci-mdf v0.4.8",
         "graphs": {
             "abc_conditions_example": {
                 "nodes": {

diff --git a/examples/MDF/abc_conditions.yaml b/examples/MDF/abc_conditions.yaml
@@ -1,6 +1,6 @@
 abc_conditions:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.7
+    generating_application: Python modeci-mdf v0.4.8
     graphs:
         abc_conditions_example:
             nodes:

diff --git a/examples/MDF/conditions/Composite_mdf_condition.json b/examples/MDF/conditions/Composite_mdf_condition.json
@@ -1,7 +1,7 @@
 {
     "Composite_mdf_condition": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.7",
+        "generating_application": "Python modeci-mdf v0.4.8",
         "graphs": {
             "Composite_mdf_condition_example": {
                 "nodes": {

diff --git a/examples/MDF/conditions/Composite_mdf_condition.yaml b/examples/MDF/conditions/Composite_mdf_condition.yaml
@@ -1,6 +1,6 @@
 Composite_mdf_condition:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.7
+    generating_application: Python modeci-mdf v0.4.8
     graphs:
         Composite_mdf_condition_example:
             nodes:

diff --git a/examples/MDF/conditions/everyncalls_condition.json b/examples/MDF/conditions/everyncalls_condition.json
@@ -1,7 +1,7 @@
 {
     "everyncalls_condition": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.7",
+        "generating_application": "Python modeci-mdf v0.4.8",
         "graphs": {
             "everyncalls_example": {
                 "nodes": {

diff --git a/examples/MDF/conditions/everyncalls_condition.yaml b/examples/MDF/conditions/everyncalls_condition.yaml
@@ -1,6 +1,6 @@
 everyncalls_condition:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.7
+    generating_application: Python modeci-mdf v0.4.8
     graphs:
         everyncalls_example:
             nodes:

diff --git a/examples/MDF/conditions/threshold_condition.json b/examples/MDF/conditions/threshold_condition.json
@@ -1,7 +1,7 @@
 {
     "threshold_condition": {
         "format": "ModECI MDF v0.4",
-        "generating_application": "Python modeci-mdf v0.4.7",
+        "generating_application": "Python modeci-mdf v0.4.8",
         "graphs": {
             "threshold_example": {
                 "nodes": {

diff --git a/examples/MDF/conditions/threshold_condition.yaml b/examples/MDF/conditions/threshold_condition.yaml
@@ -1,6 +1,6 @@
 threshold_condition:
     format: ModECI MDF v0.4
-    generating_application: Python modeci-mdf v0.4.7
+    generating_application: Python modeci-mdf v0.4.8
     graphs:
         threshold_example:
             nodes: