Merge pull request #65 from ModECI/development

To v0.3.3; XML export & sbml, neuroml examples

Author: pgleeson

.github/workflows/ci.yml

@@ -24,7 +24,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.7", "3.8", "3.9", "3.10"]
+        python-version: [ "3.8", "3.9", "3.10", "3.11"]
         runs-on: [ubuntu-latest, macos-latest, windows-latest]
 
     steps:
@@ -34,6 +34,7 @@ jobs:
       with:
         python-version:  ${{ matrix.python-version }}
 
+
     - name: Install package
       run: |
         python -m pip install --upgrade pip
@@ -47,24 +48,33 @@ jobs:
       run: |
         pip list
 
-    - name: Run some examples
+    - name: Run simple examples
       run: |
         cd examples
         python document.py
 
         cd test
         python test.py
 
-        ## Test NeuroML example
+    - name: Test NeuroML examples
+      if: ${{ matrix.python-version != '3.7'}}
+      run: |
 
-        cd ../neuroml2
+        cd examples/neuroml2
         python neuroml2_spec.py
 
         # Note: NeuroML files will be validated with OMV below
 
+    - name: Test SBML examples
+      if: ${{ matrix.python-version != '3.7'}}
+      run: |
+
+        cd examples/sbml
+        ./regenerateAndTest.sh
+
     - name: Run pytest
       run: |
-        pytest tests
+        pytest tests -v
 
     - name: Install & test NeuroMLlite
       run: |

.github/workflows/static.yml

@@ -33,7 +33,7 @@ jobs:
       uses: actions/checkout@v3
 
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: 3.9
 

.gitignore

@@ -163,3 +163,4 @@ cython_debug/
 .idea/
 /examples/document.specification.bson
 /examples/neuroml2/hello_world.v.dat
+/examples/sbml/example_sbml_test.xml

README.md

@@ -1,10 +1,8 @@
 # Modelspec
 
-
 [![Continuous builds](https://github.com/ModECI/modelspec/actions/workflows/ci.yml/badge.svg)](https://github.com/ModECI/modelspec/actions/workflows/ci.yml) [![PyPI](https://img.shields.io/pypi/v/modelspec)](https://pypi.org/project/modelspec/)
 
-
-Functionality for specifying the structure of models & enabling automatic serialization to them (e.g. in JSON and YAML format).
+Functionality for specifying the allowed structure of models, facilitating the creation of APIs in Python for handling the models & enabling automatic serialization of instances of them (e.g. in JSON and YAML format).
 
 This package is being used by [NeuroMLlite](https://github.com/NeuroML/NeuroMLlite) & [MDF](https://github.com/ModECI/MDF).
 

docs/sphinx/source/api/Contributors.md

@@ -3,7 +3,7 @@
 # Modelspec contributors
 
 This page list names and Github profiles of contributors to Modelspec, listed in no particular order.
-This page is generated periodically, most recently on 2023-09-12.
+This page is generated periodically, most recently on 2023-12-13.
 
 - Padraig Gleeson ([@pgleeson](https://github.com/pgleeson))
 - Manifest Chakalov  ([@mqnifestkelvin](https://github.com/mqnifestkelvin))

docs/sphinx/source/api/Introduction.md

@@ -1,10 +1,8 @@
 # Modelspec
 
-
 [![Continuous builds](https://github.com/ModECI/modelspec/actions/workflows/ci.yml/badge.svg)](https://github.com/ModECI/modelspec/actions/workflows/ci.yml) [![PyPI](https://img.shields.io/pypi/v/modelspec)](https://pypi.org/project/modelspec/)
 
-
-Functionality for specifying the structure of models & enabling automatic serialization to them (e.g. in JSON and YAML format).
+Functionality for specifying the allowed structure of models, facilitating the creation of APIs in Python for handling the models & enabling automatic serialization of instances of them (e.g. in JSON and YAML format).
 
 This package is being used by [NeuroMLlite](https://github.com/NeuroML/NeuroMLlite) & [MDF](https://github.com/ModECI/MDF).
 

docs/sphinx/source/api/Quickstart.md

@@ -15,18 +15,19 @@ More details, and importantly, how to set up a [virtual environment](https://vir
 
 ### Simple example
 
-A basic example which illustrates how to create the specification for a document(model) and create serialized instances can be found [here](examples/README).
+A basic example which illustrates how to create the specification for a document (i.e. the model definition for a document) and create serialized instances can be found [here](examples/README).
 
 ### Serialization formats
 
-Python scripts can be used to generate the specification of a type of model(e.g. [this](https://github.com/ModECI/modelspec/blob/main/examples/document.py)), but the models are saved in standardized format in either text based [JSON](https://github.com/ModECI/modelspec/blob/main/examples/document.json) or [YAML](https://github.com/ModECI/modelspec/blob/main/examples/document.yaml) formats or in binary [BSON](https://github.com/ModECI/modelspec/blob/main/examples/document.bson) format. Support for XML serialization is under development.
+Python scripts can be used to generate the specification of a type of model (e.g. [this](https://github.com/ModECI/modelspec/blob/main/examples/document.py)), but the models are saved in standardized format in either text based ([JSON](https://github.com/ModECI/modelspec/blob/main/examples/document.json) or [YAML](https://github.com/ModECI/modelspec/blob/main/examples/document.yaml)) formats or in binary ([BSON](https://github.com/ModECI/modelspec/blob/main/examples/document.bson)) format. Support for [XML](https://github.com/ModECI/modelspec/blob/main/examples/document.xml) serialization has recently been added.
 
 ### Current formats using modelspec
 
-#### MDF
+#### MDF (Model Description Format)
 
-MDF uses modelspec to create the structure of its models and convert the models into serialized formats such as JSON, YAML, and BSON.
+[ModECI's MDF](https://modeci.org/quickstart) uses modelspec to create the structure of its models and convert the models into serialized formats such as JSON, YAML, and BSON.
 
 #### NeuroML
 
-NeuroMLlite uses modelspec to create the structure of its models and convert the models into serialize formats such as JSON, YAML, and BSON.
+[NeuroMLlite](https://github.com/NeuroML/NeuroMLlite) uses modelspec to create the structure of its models and convert the models into serialize formats such as JSON, YAML, and BSON.
+The XML serialisation of modelspec will be useful for integrating NeuroML 2 files into the framework, see [here](https://github.com/ModECI/modelspec/tree/main/examples/neuroml2).

docs/sphinx/source/api/examples/document.bson

@@ -1,6 +1,7 @@
 {
     "MyBook": {
         "title": "My life in Python",
+        "ISBN": 123,
         "sections": {
             "Abstract": {
                 "paragraphs": [

docs/sphinx/source/api/examples/document.json

@@ -52,7 +52,7 @@ class Document(Base):
     sections: List[Section] = field(factory=list)
 
 
-doc = Document(id="MyBook")
+doc = Document(id="MyBook", ISBN=123)
 doc.title = "My life in Python"
 
 a = Section(id="Abstract")