SBML Math <-> SymPy
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sbmlmath — a Python library for handling SBML MathML
sbmlmath 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, e.g., the differences in operator precedence between sympy/Python and libsbml L3 formulas!) - retaining unit annotations and other
<ci>attributes
- in particular for cases where
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
Documentation
Under construction at sbmlmath.readthedocs.io.
Installation
Releases from PyPI:
pip install sbmlmath
The latest development version from GitHub:
pip install git+https://github.com/dweindl/sbmlmath.git#egg=sbmlmath
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