Merge pull request #65 from ModECI/development

To v0.3.3; XML export & sbml, neuroml examples
ModECI · Dec 14, 2023 · c67ef05 · c67ef05
2 parents e158706 + 490505e
commit c67ef05
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diff --git a/.github/workflows/ci.yml b/.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: |

diff --git a/.github/workflows/static.yml b/.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
 

diff --git a/.gitignore b/.gitignore
@@ -163,3 +163,4 @@ cython_debug/
 .idea/
 /examples/document.specification.bson
 /examples/neuroml2/hello_world.v.dat
+/examples/sbml/example_sbml_test.xml
diff --git a/README.md b/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).
 

diff --git a/docs/sphinx/source/api/Contributors.md b/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))

diff --git a/docs/sphinx/source/api/Introduction.md b/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).
 

diff --git a/docs/sphinx/source/api/Quickstart.md b/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).
diff --git a/docs/sphinx/source/api/examples/document.bson b/docs/sphinx/source/api/examples/document.bson
diff --git a/docs/sphinx/source/api/examples/document.json b/docs/sphinx/source/api/examples/document.json
@@ -1,6 +1,7 @@
 {
     "MyBook": {
         "title": "My life in Python",
+        "ISBN": 123,
         "sections": {
             "Abstract": {
                 "paragraphs": [

diff --git a/docs/sphinx/source/api/examples/document.py b/docs/sphinx/source/api/examples/document.py
@@ -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")

diff --git a/docs/sphinx/source/api/examples/document.xml b/docs/sphinx/source/api/examples/document.xml
@@ -1,5 +1,5 @@
-<?xml version="1.0" ?>
-<Document id="MyBook" title="My life in Python" ISBN="None">
+<?xml version="1.0" encoding="UTF-8"?>
+<Document id="MyBook" title="My life in Python" ISBN="123">
     <Section id="Abstract">
         <Paragraph contents="Blah blah blah"/>
         <Paragraph contents="Blah2"/>

diff --git a/docs/sphinx/source/api/examples/document.yaml b/docs/sphinx/source/api/examples/document.yaml
@@ -1,5 +1,6 @@
 MyBook:
     title: My life in Python
+    ISBN: 123
     sections:
         Abstract:
             paragraphs:

diff --git a/examples/COMBINE.md b/examples/COMBINE.md
@@ -0,0 +1,29 @@
+# COMBINE standards in modelspec
+
+![combine](images/combine.png)
+
+To illustrate the utility of modelspec, and to create a uniform, compatible set of APIs across a diverse range of model specification formats, we are investigating the [COMBINE set of standards in computational biology](https://co.mbine.org/standards/), and attempting to express these formats in modelspec.
+
+## NeuroML
+
+![neuroml](images/neuroml.png)
+
+A preliminary version of an API for [NeuroML2](https://docs.neuroml.org/Userdocs/NeuroMLv2.html) can be found [here](neuroml2). This allows generation of NeuroML2 models using the modelspec based API, saving as valid XML, as well as JSON, YAML and BSON equivalents. See [neuroml2_spec.py](neuroml2/neuroml2_spec.py).
+
+[NeuroMLlite](https://github.com/NeuroML/NeuroMLlite) already uses modelspec as its primary specification format. See [here](https://github.com/NeuroML/NeuroMLlite/blob/master/neuromllite/__init__.py).
+
+## SBML
+
+![combine](images/sbml.png)
+
+Work towards an API for [SBML](https://www.sbml.org/) can be found [here](sbml).
+
+An example of an SBML file generated from this is [here](sbml/test_minimal_example.xml).
+
+## CellML
+
+TODO...
+
+## SED-ML
+
+TODO...
diff --git a/examples/document.bson b/examples/document.bson
diff --git a/examples/document.json b/examples/document.json
@@ -1,6 +1,7 @@
 {
     "MyBook": {
         "title": "My life in Python",
+        "ISBN": 123,
         "sections": {
             "Abstract": {
                 "paragraphs": [

diff --git a/examples/document.py b/examples/document.py
@@ -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")

diff --git a/examples/document.xml b/examples/document.xml
@@ -1,5 +1,5 @@
-<?xml version="1.0" ?>
-<Document id="MyBook" title="My life in Python" ISBN="None">
+<?xml version="1.0" encoding="UTF-8"?>
+<Document id="MyBook" title="My life in Python" ISBN="123">
     <Section id="Abstract">
         <Paragraph contents="Blah blah blah"/>
         <Paragraph contents="Blah2"/>

diff --git a/examples/document.yaml b/examples/document.yaml
@@ -1,5 +1,6 @@
 MyBook:
     title: My life in Python
+    ISBN: 123
     sections:
         Abstract:
             paragraphs:

diff --git a/examples/images/combine.png b/examples/images/combine.png
diff --git a/examples/images/neuroml.png b/examples/images/neuroml.png
diff --git a/examples/images/sbml.png b/examples/images/sbml.png
diff --git a/examples/neuroml2/TestNeuroML.xml b/examples/neuroml2/TestNeuroML.xml
@@ -1,4 +1,4 @@
-<?xml version="1.0" ?>
+<?xml version="1.0" encoding="UTF-8"?>
 <neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" id="TestNeuroML" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd">
     <izhikevich2007Cell id="izh2007RS0" C="100pF" v0="-60mV" k="0.7nS_per_mV" vr="-60mV" vt="-40mV" vpeak="35mV" a="0.03per_ms" b="-2nS" c="-50.0mV" d="100pA"/>
     <pulseGenerator id="pulseGen_0" delay="100ms" duration="800ms" amplitude="0.07 nA"/>

diff --git a/examples/neuroml2/neuroml2_spec.py b/examples/neuroml2/neuroml2_spec.py
@@ -197,7 +197,7 @@ class neuroml(Base):
 
     with open("NeuroML2.specification.yaml", "w") as d:
         yy = yaml.dump(doc_dict, indent=4, sort_keys=False)
-        print(yy)
+        # print(yy)
         d.write(yy)
 
     from modelspec.utils import load_xml