sbmlmath — a Python library for handling SBML MathML¶
This is a Python library for interconverting SymPy expressions and SBML-MathML. SBML uses a subset of MathML that this library aims to support. This is not (intended to be) a general MathML parser.
Main functionality:
sympy -> SBML MathML
SBML MathML -> sympy
in particular for cases where
sympy.sympify(libsbml.formulaToL3String(...))won’t do the job (mind the differences operator precedence between sympy/Python and libsbml L3 formulas!)retaining unit annotations and other
<ci>attributes
NOTE: This is under development and the API is to be considered unstable
Python support policy: sbmlmath follows NEP 29.
Usage¶
from sbmlmath import SBMLMathMLPrinter, SBMLMathMLParser
import sympy as sp
sympy_expr = sp.sympify("A ** B + exp(C) * D")
mathml = SBMLMathMLPrinter().doprint(sympy_expr)
print(mathml)
cycled_sympy = SBMLMathMLParser().parse_str(mathml)
print(cycled_sympy)
assert sympy_expr == cycled_sympy
Installation¶
Releases from PyPI:
pip install sbmlmath
The latest development version from GitHub:
pip install https://github.com/dweindl/sbmlmath/archive/main.zip
Source code¶
The source code is hosted on GitHub.
Contents: