Merge pull request #311 from ModECI/development

Release v0.4.2

.github/workflows/ci.yml

@@ -25,12 +25,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.9]
+        python-version: [ "3.7", "3.9", "3.10"]
         runs-on: [ubuntu-latest, macos-latest, windows-latest]
-        exclude:
-          # excludes Python 3.9 windows for now on account of PsyNeuLink
-          - python-version: 3.9
-            runs-on: windows-latest
 
     steps:
     - uses: actions/checkout@v2
@@ -39,31 +35,55 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install modelspec
-      run: python -m pip install git+https://github.com/ModECI/modelspec.git@main
+    # Rely on version of modelspec from PyPI as set by setup.cfg...
+    #- name: Install modelspec
+    #  run: python -m pip install git+https://github.com/ModECI/modelspec.git@main
 
-    - name: Install NeuroMLlite
-      run: python -m pip install NeuroMLlite>=0.5.0
+    # Rely on version of NeuroMLlite from PyPI as set by setup.py...
+    # - name: Install NeuroMLlite
+    #   run: python -m pip install NeuroMLlite>=0.5.0
 
-    - name: Install GPy (py3.9)
-      if: ${{ matrix.python-version == '3.9' }}
-      run: python -m pip install git+https://github.com/SheffieldML/GPy.git@devel
+    # Rely on version of PsyNeuLink from PyPI as set by setup.py...
+    #- name: Install specific PsyNeuLink branch
+    #  run: python -m pip install git+https://github.com/ModECI/PsyNeuLink@devel
 
-    - name: Install package
-      run: python -m pip install .[test]
+    - name: Install core package
+      run: python -m pip install .[dev]
 
     - name: Version info for installed packages
       run: |
           pip list
 
-    - name: Test package
+    - name: Test core package
       run: |
-        python -m pytest -ra tests/*.py
-        python -m pytest -ra tests/interfaces/onnx/*.py
-        python -m pytest -ra tests/interfaces/pytorch/test_export.py
-        python -m pytest -ra tests/interfaces/pytorch/test_import.py # inception taking v long
+        python -m pytest -m coremdf tests/
 
-    - name: Final version info for installed packages
+    - name: Install optional dependencies
+      run: python -m pip install .[all]
+
+    - name: Version info for optional installed packages
+      run: |
+          pip list
+
+    - name: Test interface ACT-R
+      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
+      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: Final version info for optional installed packages
       run: |
           pip list
 

.gitignore

@@ -1,6 +1,8 @@
 # No BSON in the repo
 *.bson
-
+/examples/MDF/conditions/everyncalls
+/examples/MDF/conditions/threshold
+/examples/MDF/conditions/timeinterval
 /abc_conditions
 examples/ONNX/data
 examples/ONNX/*.onnx
@@ -250,19 +252,27 @@ Thumbs.db #thumbnail cache on Windows
 /examples/NeuroML/Izh.png
 /examples/NeuroML/Izh_multi
 /examples/NeuroML/Izh_multi.png
-/examples/NeuroML/Izh_run.png
 /examples/NeuroML/IzhikevichTest.mdf.json
 /examples/NeuroML/IzhikevichTest.net.nml
-/examples/NeuroML/IzhikevichTest.nmllite.yaml
 /examples/NeuroML/LEMS_SimIzhikevichTest.xml
 /examples/NeuroML/SimIzhikevichTest.json
-/examples/NeuroML/SimIzhikevichTest.yaml
 /examples/AB
 /examples/AB.png
+/examples/states
+/examples/states.png
+/examples/conditions
+/examples/conditions.png
 *.onnx
 /examples/AB.json
 /examples/AB.yaml
 /examples/MDF/params_funcs_example
 /examples/MDF/params_funcs_example_3
 /examples/MDF/params_funcs_example_3.png
 /examples/MDF/params_funcs_example.png
+/examples/NeuroML/LEMS_SimFN_nrn.py
+/examples/MDF/RNN/*.gv.png
+/examples/MDF/RNN/*.dat
+/examples/MDF/RNN/LEMS_Simiaf_example.xml
+/examples/MDF/RNN/iaf_example.net.nml
+/examples/MDF/RNN/iaf_example__lems.xml
+/examples/MDF/RNN/iaf_example_lems_definitions.xml

docs/generate.py

@@ -49,6 +49,29 @@
 
 print("Written main documentation")
 
+# Generate export formats documentation
+export_formats_list = [
+    "MDF",
+    "ACT-R",
+    "NeuroML",
+    "ONNX",
+    "PsyNeuLink",
+    "PyTorch",
+    "Quantum",
+    "WebGME",
+]
+for format in export_formats_list:
+    with open("../examples/" + format + "/README.md") as readfile, open(
+        "sphinx/source/api/export_format/" + format + "/" + format + ".md", "w"
+    ) as writefile:
+        # read content from first file
+        for line in readfile:
+            # append content to second file
+            writefile.write(line)
+
+
+print("Written Export format documentation")
+
 # Generate standard function generate_documentation
 
 from modeci_mdf.functions.standard import mdf_functions, create_python_expression

docs/sphinx/source/api/Export.md

@@ -0,0 +1,10 @@
+## Supported export Models
+This is the list of currently supported models which MDF supports
+
+ - ACT-R [README](https://github.com/ModECI/MDF/tree/main/examples/ACT-R#readme)
+ - NeuroML [README](https://github.com/ModECI/MDF/tree/main/examples/NeuroML#readme)
+ - ONNX [README](https://github.com/ModECI/MDF/tree/main/examples/ONNX#readme)
+ - PsyNeuLink [README](https://github.com/ModECI/MDF/tree/main/examples/PsyNeuLink#readme)
+ - PyTorch [README](https://github.com/ModECI/MDF/tree/main/examples/PyTorch#readme)
+ - Quantum [README](https://github.com/ModECI/MDF/tree/main/examples/Quantum#readme)
+ - WebGME [README](https://github.com/ModECI/MDF/tree/main/examples/WebGME#readme)

docs/sphinx/source/api/export_format/ACT-R/ACT-R.md

@@ -0,0 +1,61 @@
+# Interactions between MDF and ACT-R
+
+This directory contains examples of ACT-R models converted to MDF. The ACT-R
+models [count.lisp](./count.lisp) and [addition.lisp](addition.lisp) are based on
+the [ACT-R tutorial](http://act-r.psy.cmu.edu/software/).
+
+The scripts [count.py](count.py) and [addition.py](addition.py) can be run
+to create the MDF .json and .yaml files for the given example and execute it
+using the MDF scheduler.
+
+The below graph represents the basic structure of all ACT-R models in MDF:
+![actr.png](actr.png)
+
+There are also more detailed graphs [count.png](count.png) and
+[addition.png](addition.png) for each example.
+
+### Count Model
+
+[ACT-R](count.lisp) | [JSON](count.json) | [YAML](count.yaml) | [Python Script](count.py) | [Graph](count.png)
+
+![count.png](count.png)
+
+The count model counts from a start value to an end value. The script
+[count.py](count.py) first reads the original ACT-R model file
+[count.lisp](count.lisp), generates an MDF representation using the MDF ACT-R interface, and outputs the [JSON](count.json) and [YAML](count.yaml) files. It then executes
+the MDF model using the MDF scheduler and outputs the final goal set by the
+model once execution is finished. The final goal has the form:
+
+`{'name': 'first-goal', 'ISA': 'count-from', 'start': 'two', 'end': 'four', 'count': 'four'}`
+
+In this example, the start value is two, the end value is four, and the final
+value of count is four, indicating that the model counted from two to four. The
+start and end values can be modified in line 17 of [count.lisp](count.lisp),
+which sets the initial goal of the model:
+
+`(first-goal ISA count-from start two end four)`
+
+The script can use any values specified in [count.lisp](count.lisp), so the
+model can be modified and run multiple times in order to test different values.
+The [count](count.png) graph represents this example.
+
+### Addition Model
+
+[ACT-R](addition.lisp) | [JSON](addition.json) | [YAML](addition.yaml) | [Python Script](addition.py) | [Graph](addition.png)
+
+![addition.png](addition.png)
+
+The addition model computes the sum of two numbers. The script
+[addition.py](addition.py) functions identically to the previous example, but
+uses the addition model instead. The final goal has the form:
+
+`{'name': 'second-goal', 'ISA': 'add', 'arg1': 'five', 'arg2': 'two', 'sum': 'seven', 'count': 'nil'}`
+
+In this case, the first argument is five, the second argument is two, and the
+model has calculated the sum, seven. Like the previous example, the arguments
+can be modified in line 23 of [addition.lisp](addition.lisp) in order to test
+different values:
+
+`(second-goal ISA add arg1 five arg2 two)`
+
+The [addition](addition.png) graph represents this example.