Source code for sbmlmath

from importlib.metadata import PackageNotFoundError, version
from typing import Union

import libsbml
import sympy as sp

try:
    __version__ = version("sbmlmath")
except PackageNotFoundError:
    # package is not installed
    pass

#: Default SBML level if not specified otherwise.
_DEFAULT_SBML_LEVEL = 3
#: Default SBML version if not specified otherwise.
_DEFAULT_SBML_VERSION = 2




def sympy_to_sbml_math(sp_expr: sp.Expr) -> libsbml.ASTNode:
    """Convert sympy expression to SBML math ASTNode.

    This function takes a SymPy expression and converts it to an SBML math
    ASTNode.

    Args:
        sp_expr: The SymPy expression to be converted.

    Returns:
        The resulting SBML math ASTNode.

    Raises:
        ValueError:
            If there is an error in converting the math expression.
    """
    mathml = SBMLMathMLPrinter().doprint(sp_expr)

    if ast_node := libsbml.readMathMLFromString(mathml):
        return ast_node

    raise ValueError(
        f"Unknown error handling math expression:\n{sp_expr}\n{mathml}"
    )





def sbml_math_to_sympy(
    sbml_obj: Union[libsbml.SBase, libsbml.ASTNode], **kwargs
) -> sp.Expr:
    """Convert SBML MathML to sympy expression.

    Conversion is done using the default settings of :class:`SBMLMathMLParser`.

    Args:
        sbml_obj:
            The SBML object to be converted.
            (Either directly the ASTNode or the surrounding SBase object).
        kwargs:
            Additional keyword arguments passed to
            :attr:`SBMLMathMLParser.__init__`.
    Returns:
        The resulting sympy expression.
    """
    if isinstance(sbml_obj, libsbml.ASTNode):
        ast_node = sbml_obj
        sbml_obj = ast_node.getParentSBMLObject()
    else:
        ast_node = sbml_obj.getMath()

    level = (
        sbml_obj.getLevel() if sbml_obj is not None else _DEFAULT_SBML_LEVEL
    )
    version = (
        sbml_obj.getVersion()
        if sbml_obj is not None
        else _DEFAULT_SBML_VERSION
    )
    mathml = libsbml.writeMathMLWithNamespaceToString(
        ast_node, libsbml.SBMLNamespaces(level, version)
    )
    return SBMLMathMLParser(
        sbml_level=level, sbml_version=version, **kwargs
    ).parse_str(mathml)





def set_math(
    element: libsbml.SBase,
    expr: sp.Expr,
) -> None:
    """Set the math expression of an SBML object.

    Args:
        element:
            The SBML object to set the math expression for.
        expr:
            The sympy expression to set as the math expression.
    """
    mathml = SBMLMathMLPrinter(
        sbml_level=element.getLevel(),
        sbml_version=element.getVersion(),
    ).doprint(expr)

    if ast_node := libsbml.readMathMLFromString(mathml):
        if element.setMath(ast_node) == libsbml.LIBSBML_OPERATION_SUCCESS:
            return
        sbml_document = element.getSBMLDocument()
        raise ValueError(
            f"Error setting math expression:\n{expr}\n"
            f"{mathml}\n{sbml_document.getErrorLog().toString()}"
        )
    raise ValueError(
        f"Unknown error parsing math expression:\n{expr}\n{mathml}"
    )



from .cfunction import *
from .csymbol import *
from .mathml_parser import SBMLMathMLParser
from .mathml_printer import SBMLMathMLPrinter
from .species_symbol import SpeciesSymbol

__all__ = [
    "set_math",
    "SBMLMathMLParser",
    "SBMLMathMLPrinter",
    "SpeciesSymbol",
    "TimeSymbol",
    "sympy_to_sbml_math",
    "sbml_math_to_sympy",
    *csymbol.__all__,
    *cfunction.__all__,
]