Merge pull request #64 from ModECI/test_sbml

Adds SBML API generation example

Author: pgleeson

.github/workflows/ci.yml

@@ -47,21 +47,30 @@ 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

.gitignore

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

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 2023-09-13.
+This page is generated periodically, most recently on 2023-09-19.
 
 - Padraig Gleeson ([@pgleeson](https://github.com/pgleeson))
 - Manifest Chakalov  ([@mqnifestkelvin](https://github.com/mqnifestkelvin))

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">
     <Section id="Abstract">
         <Paragraph contents="Blah blah blah"/>
         <Paragraph contents="Blah2"/>

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...

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">
     <Section id="Abstract">
         <Paragraph contents="Blah blah blah"/>
         <Paragraph contents="Blah2"/>

examples/images/combine.png

@@ -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"/>