Model units create complicated SBML

[luciansmith]

Hi Lucian,

The create SBML when setting model units is overly complicated. If the substanceUnits, timeUnits, ... are one of the base units or defined units these should just be used in the model element instead of creating a new unitDefinition.

These unit definitions

import tellurium as te
r = te.loada('''
    // Units
    m2 = meter^2;
    m3 = meter^3;
    
    // base units
    substance = mole;
    volume = m2;
    area = m3;
    length = metre;
    extent = mole;
    time_unit = second;
''')
print(r.getSBML())

should create the following SBML

<?xml version="1.0" encoding="UTF-8"?>
<!-- Created by libAntimony version v2.8.1 on 2016-02-17 12:19 with libSBML version 5.12.1. -->
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
  <model id="__main" name="__main" substanceUnits="mole" timeUnits="second" volumeUnits="m3" areaUnits="m2" lengthUnits="metre" extentUnits="mole">
    <listOfUnitDefinitions>
      <unitDefinition id="m2">
        <listOfUnits>
          <unit kind="metre" exponent="2" scale="0" multiplier="1"/>
        </listOfUnits>
      </unitDefinition>
      <unitDefinition id="m3">
        <listOfUnits>
          <unit kind="metre" exponent="3" scale="0" multiplier="1"/>
        </listOfUnits>
      </unitDefinition>
    </listOfUnitDefinitions>
  </model>

But currently result in the much more complicated and unreadable

<?xml version="1.0" encoding="UTF-8"?>
<!-- Created by libAntimony version v2.8.1 on 2016-02-17 12:19 with libSBML version 5.12.1. -->
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
  <model id="__main" name="__main" substanceUnits="substance" timeUnits="time_unit" volumeUnits="volume" areaUnits="area" lengthUnits="length" extentUnits="extent">
    <listOfUnitDefinitions>
      <unitDefinition id="m2">
        <listOfUnits>
          <unit kind="metre" exponent="2" scale="0" multiplier="1"/>
        </listOfUnits>
      </unitDefinition>
      <unitDefinition id="m3">
        <listOfUnits>
          <unit kind="metre" exponent="3" scale="0" multiplier="1"/>
        </listOfUnits>
      </unitDefinition>
      <unitDefinition id="substance">
        <listOfUnits>
          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
        </listOfUnits>
      </unitDefinition>
      <unitDefinition id="volume">
        <listOfUnits>
          <unit kind="metre" exponent="2" scale="0" multiplier="1"/>
        </listOfUnits>
      </unitDefinition>
      <unitDefinition id="area">
        <listOfUnits>
          <unit kind="metre" exponent="3" scale="0" multiplier="1"/>
        </listOfUnits>
      </unitDefinition>
      <unitDefinition id="length">
        <listOfUnits>
          <unit kind="metre" exponent="1" scale="0" multiplier="1"/>
        </listOfUnits>
      </unitDefinition>
      <unitDefinition id="extent">
        <listOfUnits>
          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
        </listOfUnits>
      </unitDefinition>
      <unitDefinition id="time_unit">
        <listOfUnits>
          <unit kind="second" exponent="1" scale="0" multiplier="1"/>
        </listOfUnits>
      </unitDefinition>
    </listOfUnitDefinitions>
  </model>

Only define the substance, volume, ... units if they are not defined in the model or are no base units.

The best
Matthias

Reported by: matthiaskoenig