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Merge pull request #65 from ModECI/development
To v0.3.3; XML export & sbml, neuroml examples
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‎.github/workflows/ci.yml

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

‎.github/workflows/static.yml

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uses: actions/checkout@v3
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- name: Set up Python
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uses: actions/setup-python@v2
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uses: actions/setup-python@v4
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with:
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python-version: 3.9
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‎.gitignore

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.idea/
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/examples/document.specification.bson
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/examples/neuroml2/hello_world.v.dat
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/examples/sbml/example_sbml_test.xml

‎README.md

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# Modelspec
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[![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/)
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Functionality for specifying the structure of models & enabling automatic serialization to them (e.g. in JSON and YAML format).
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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).
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This package is being used by [NeuroMLlite](https://github.com/NeuroML/NeuroMLlite) & [MDF](https://github.com/ModECI/MDF).
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‎docs/sphinx/source/api/Contributors.md

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

‎docs/sphinx/source/api/Introduction.md

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# Modelspec
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[![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/)
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Functionality for specifying the structure of models & enabling automatic serialization to them (e.g. in JSON and YAML format).
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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).
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This package is being used by [NeuroMLlite](https://github.com/NeuroML/NeuroMLlite) & [MDF](https://github.com/ModECI/MDF).
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‎docs/sphinx/source/api/Quickstart.md

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### Simple example
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A basic example which illustrates how to create the specification for a document(model) and create serialized instances can be found [here](examples/README).
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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).
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### Serialization formats
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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.
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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.
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### Current formats using modelspec
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#### MDF
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#### MDF (Model Description Format)
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MDF uses modelspec to create the structure of its models and convert the models into serialized formats such as JSON, YAML, and BSON.
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[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.
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#### NeuroML
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NeuroMLlite uses modelspec to create the structure of its models and convert the models into serialize formats such as JSON, YAML, and BSON.
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[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.
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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

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

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{
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"MyBook": {
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"title": "My life in Python",
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"ISBN": 123,
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"sections": {
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"Abstract": {
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"paragraphs": [

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

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

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

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<?xml version="1.0" ?>
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<Document id="MyBook" title="My life in Python" ISBN="None">
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<?xml version="1.0" encoding="UTF-8"?>
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<Document id="MyBook" title="My life in Python" ISBN="123">
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<Section id="Abstract">
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<Paragraph contents="Blah blah blah"/>
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<Paragraph contents="Blah2"/>

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

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MyBook:
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title: My life in Python
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ISBN: 123
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sections:
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Abstract:
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paragraphs:

‎examples/COMBINE.md

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# COMBINE standards in modelspec
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![combine](images/combine.png)
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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.
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## NeuroML
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![neuroml](images/neuroml.png)
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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).
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[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).
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## SBML
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![combine](images/sbml.png)
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Work towards an API for [SBML](https://www.sbml.org/) can be found [here](sbml).
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An example of an SBML file generated from this is [here](sbml/test_minimal_example.xml).
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## CellML
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TODO...
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## SED-ML
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TODO...

‎examples/document.bson

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‎examples/document.json

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{
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"ISBN": 123,
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"sections": {
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"Abstract": {
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‎examples/document.py

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doc = Document(id="MyBook")
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doc = Document(id="MyBook", ISBN=123)
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doc.title = "My life in Python"
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a = Section(id="Abstract")

‎examples/document.xml

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<?xml version="1.0" ?>
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<Document id="MyBook" title="My life in Python" ISBN="None">
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<?xml version="1.0" encoding="UTF-8"?>
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<Document id="MyBook" title="My life in Python" ISBN="123">
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<Section id="Abstract">
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<Paragraph contents="Blah blah blah"/>
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<Paragraph contents="Blah2"/>

‎examples/document.yaml

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MyBook:
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title: My life in Python
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ISBN: 123
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sections:
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Abstract:
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paragraphs:

‎examples/images/combine.png

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‎examples/images/neuroml.png

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‎examples/images/sbml.png

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‎examples/neuroml2/TestNeuroML.xml

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<?xml version="1.0" ?>
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<?xml version="1.0" encoding="UTF-8"?>
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<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">
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<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"/>
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<pulseGenerator id="pulseGen_0" delay="100ms" duration="800ms" amplitude="0.07 nA"/>

‎examples/neuroml2/neuroml2_spec.py

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from modelspec.utils import load_xml

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