mxlpy 0.22.0__py3-none-any.whl → 0.24.0__py3-none-any.whl

mxlpy/sbml/_import.py

@@ -1,582 +1,104 @@
 from __future__ import annotations
 
-import logging
-import math  # noqa: F401  # models might need it
 import re
-from collections import defaultdict
-from dataclasses import dataclass, field
-from pathlib import Path
-from typing import TYPE_CHECKING, Self
+import sys
+import unicodedata
+from importlib import util
+from typing import TYPE_CHECKING
 
-import libsbml
-import numpy as np  # noqa: F401  # models might need it
+import pysbml
 import sympy
 
-from mxlpy.model import Dependency, Model, _sort_dependencies
-from mxlpy.paths import default_tmp_dir
-from mxlpy.sbml._data import (
-    AtomicUnit,
-    Compartment,
-    CompositeUnit,
-    Compound,
-    Derived,
-    Function,
-    Parameter,
-    Reaction,
+from mxlpy.meta.codegen_mxlpy import (
+    SymbolicFn,
+    SymbolicParameter,
+    SymbolicReaction,
+    SymbolicRepr,
+    SymbolicVariable,
+    generate_mxlpy_code_from_symbolic_repr,
 )
-from mxlpy.sbml._mathml import parse_sbml_math
-from mxlpy.sbml._name_conversion import _name_to_py
-from mxlpy.sbml._unit_conversion import get_operator_mappings, get_unit_conversion
+from mxlpy.paths import default_tmp_dir
 from mxlpy.types import unwrap
 
+__all__ = ["free_symbols", "import_from_path", "read", "valid_filename"]
+
 if TYPE_CHECKING:
     from collections.abc import Callable
+    from pathlib import Path
 
-_LOGGER = logging.getLogger(__name__)
-
-__all__ = [
-    "INDENT",
-    "OPERATOR_MAPPINGS",
-    "Parser",
-    "UNIT_CONVERSION",
-    "import_from_path",
-    "read",
-    "valid_filename",
-]
-
-UNIT_CONVERSION = get_unit_conversion()
-OPERATOR_MAPPINGS = get_operator_mappings()
-INDENT = "    "
-
-
-def _nan_to_zero(value: float) -> float:
-    return 0 if str(value) == "nan" else value
-
-
-@dataclass(slots=True)
-class Parser:
-    # Collections
-    boundary_species: set[str] = field(default_factory=set)
-    # Parsed stuff
-    atomic_units: dict[str, AtomicUnit] = field(default_factory=dict)
-    composite_units: dict[str, CompositeUnit] = field(default_factory=dict)
-    compartments: dict[str, Compartment] = field(default_factory=dict)
-    parameters: dict[str, Parameter] = field(default_factory=dict)
-    variables: dict[str, Compound] = field(default_factory=dict)
-    derived: dict[str, Derived] = field(default_factory=dict)
-    initial_assignment: dict[str, Derived] = field(default_factory=dict)
-    functions: dict[str, Function] = field(default_factory=dict)
-    reactions: dict[str, Reaction] = field(default_factory=dict)
-
-    def parse(self, file: str | Path) -> Self:
-        if not Path(file).exists():
-            msg = "Model file does not exist"
-            raise OSError(msg)
-        doc = libsbml.readSBMLFromFile(str(file))
-
-        # Check for unsupported packages
-        for i in range(doc.num_plugins):
-            if doc.getPlugin(i).getPackageName() == "comp":
-                msg = "No support for comp package"
-                raise NotImplementedError(msg)
-
-        sbml_model = doc.getModel()
-        if sbml_model is None:
-            return self
-
-        if bool(sbml_model.getConversionFactor()):
-            msg = "Conversion factors are currently not supported"
-            raise NotImplementedError(msg)
-
-        self.parse_functions(sbml_model)
-        self.parse_units(sbml_model)
-        self.parse_compartments(sbml_model)
-        self.parse_variables(sbml_model)
-        self.parse_parameters(sbml_model)
-        self.parse_initial_assignments(sbml_model)
-        self.parse_rules(sbml_model)
-        self.parse_constraints(sbml_model)
-        self.parse_reactions(sbml_model)
-        self.parse_events(sbml_model)
-
-        # Modifications
-        self._convert_substance_amount_to_concentration()
-        # self._rename_species_references()
-        return self
-
-    ###############################################################################
-    # PARSING STAGE
-    ###############################################################################
-
-    def parse_constraints(self, sbml_model: libsbml.Model) -> None:
-        if len(sbml_model.getListOfConstraints()) > 0:
-            msg = "mxlpy does not support model constraints. "
-            raise NotImplementedError(msg)
-
-    def parse_events(self, sbml_model: libsbml.Model) -> None:
-        if len(sbml_model.getListOfEvents()) > 0:
-            msg = (
-                "mxlpy does not current support events. "
-                "Check the file for how to integrate properly."
-            )
-            raise NotImplementedError(msg)
-
-    def parse_units(self, sbml_model: libsbml.Model) -> None:
-        for unit_definition in sbml_model.getListOfUnitDefinitions():
-            composite_id = unit_definition.getId()
-            local_units = []
-            for unit in unit_definition.getListOfUnits():
-                atomic_unit = AtomicUnit(
-                    kind=UNIT_CONVERSION[unit.getKind()],
-                    scale=unit.getScale(),
-                    exponent=unit.getExponent(),
-                    multiplier=unit.getMultiplier(),
-                )
-                local_units.append(atomic_unit.kind)
-                self.atomic_units[atomic_unit.kind] = atomic_unit
-            self.composite_units[composite_id] = CompositeUnit(
-                sbml_id=composite_id,
-                units=local_units,
-            )
-
-    def parse_compartments(self, sbml_model: libsbml.Model) -> None:
-        for compartment in sbml_model.getListOfCompartments():
-            sbml_id = _name_to_py(compartment.getId())
-            size = compartment.getSize()
-            if str(size) == "nan":
-                size = 0
-            self.compartments[sbml_id] = Compartment(
-                name=compartment.getName(),
-                dimensions=compartment.getSpatialDimensions(),
-                size=size,
-                units=compartment.getUnits(),
-                is_constant=compartment.getConstant(),
-            )
-
-    def parse_parameters(self, sbml_model: libsbml.Model) -> None:
-        for parameter in sbml_model.getListOfParameters():
-            self.parameters[_name_to_py(parameter.getId())] = Parameter(
-                value=_nan_to_zero(parameter.getValue()),
-                is_constant=parameter.getConstant(),
-            )
-
-    def parse_variables(self, sbml_model: libsbml.Model) -> None:
-        for compound in sbml_model.getListOfSpecies():
-            compound_id = _name_to_py(compound.getId())
-            if bool(compound.getConversionFactor()):
-                msg = "Conversion factors are not implemented. "
-                raise NotImplementedError(msg)
-
-            # NOTE: What the shit is this?
-            initial_amount = compound.getInitialAmount()
-            if str(initial_amount) == "nan":
-                initial_amount = compound.getInitialConcentration()
-                is_concentration = str(initial_amount) != "nan"
-            else:
-                is_concentration = False
-
-            has_boundary_condition = compound.getBoundaryCondition()
-            if has_boundary_condition:
-                self.boundary_species.add(compound_id)
-
-            self.variables[compound_id] = Compound(
-                compartment=compound.getCompartment(),
-                initial_amount=_nan_to_zero(initial_amount),
-                substance_units=compound.getSubstanceUnits(),
-                has_only_substance_units=compound.getHasOnlySubstanceUnits(),
-                has_boundary_condition=has_boundary_condition,
-                is_constant=compound.getConstant(),
-                is_concentration=is_concentration,
-            )
-
-    def parse_functions(self, sbml_model: libsbml.Model) -> None:
-        for func in sbml_model.getListOfFunctionDefinitions():
-            func_name = func.getName()
-            sbml_id = func.getId()
-            if sbml_id is None or sbml_id == "":
-                sbml_id = func_name
-            elif func_name is None or func_name == "":
-                func_name = sbml_id
-            func_name = _name_to_py(func_name)
-
-            if (node := func.getMath()) is None:
-                continue
-            body, args = parse_sbml_math(node=node)
-
-            self.functions[func_name] = Function(
-                body=body,
-                args=args,
-            )
-
-    ###############################################################################
-    # Different kinds of derived values
-    ###############################################################################
-
-    def parse_initial_assignments(self, sbml_model: libsbml.Model) -> None:
-        for assignment in sbml_model.getListOfInitialAssignments():
-            name = _name_to_py(assignment.getSymbol())
-
-            node = assignment.getMath()
-            if node is None:
-                msg = f"Unusable math for {name}"
-                _LOGGER.warning(msg)
-                continue
-
-            body, args = parse_sbml_math(node)
-            self.initial_assignment[name] = Derived(
-                body=body,
-                args=args,
-            )
-
-    def _parse_algebraic_rule(self, rule: libsbml.AlgebraicRule) -> None:
-        msg = f"Algebraic rules are not implemented for {rule.getId()}"
-        raise NotImplementedError(msg)
-
-    def _parse_assignment_rule(self, rule: libsbml.AssignmentRule) -> None:
-        if (node := rule.getMath()) is None:
-            return
-
-        name: str = _name_to_py(rule.getId())
-        body, args = parse_sbml_math(node=node)
-
-        self.derived[name] = Derived(
-            body=body,
-            args=args,
-        )
-
-    def _parse_rate_rule(self, rule: libsbml.RateRule) -> None:
-        msg = f"Skipping rate rule {rule.getId()}"
-        raise NotImplementedError(msg)
-
-    def parse_rules(self, sbml_model: libsbml.Model) -> None:
-        """Parse rules and separate them by type."""
-        for rule in sbml_model.getListOfRules():
-            if rule.element_name == "algebraicRule":
-                self._parse_algebraic_rule(rule=rule)
-            elif rule.element_name == "assignmentRule":
-                self._parse_assignment_rule(rule=rule)
-            elif rule.element_name == "rateRule":
-                self._parse_rate_rule(rule=rule)
-            else:
-                msg = "Unknown rate type"
-                raise ValueError(msg)
+    from mxlpy.model import Model
 
-    def _parse_local_parameters(
-        self, reaction_id: str, kinetic_law: libsbml.KineticLaw
-    ) -> dict[str, str]:
-        """Parse local parameters."""
-        parameters_to_update = {}
-        for parameter in kinetic_law.getListOfLocalParameters():
-            old_id = _name_to_py(parameter.getId())
-            if old_id in self.parameters:
-                new_id = f"{reaction_id}__{old_id}"
-                parameters_to_update[old_id] = new_id
-            else:
-                new_id = old_id
-            self.parameters[new_id] = Parameter(
-                value=_nan_to_zero(parameter.getValue()),
-                is_constant=parameter.getConstant(),
-            )
-        # Some models apparently also write local parameters in this
-        for parameter in kinetic_law.getListOfParameters():
-            old_id = _name_to_py(parameter.getId())
-            if old_id in self.parameters:
-                new_id = f"{reaction_id}__{old_id}"
-                parameters_to_update[old_id] = new_id
-            else:
-                new_id = old_id
-            self.parameters[new_id] = Parameter(
-                value=_nan_to_zero(parameter.getValue()),
-                is_constant=parameter.getConstant(),
-            )
-        return parameters_to_update
-
-    def parse_reactions(self, sbml_model: libsbml.Model) -> None:
-        for reaction in sbml_model.getListOfReactions():
-            sbml_id = _name_to_py(reaction.getId())
-            kinetic_law = reaction.getKineticLaw()
-            if kinetic_law is None:
-                continue
-            parameters_to_update = self._parse_local_parameters(
-                reaction_id=sbml_id,
-                kinetic_law=kinetic_law,
-            )
-
-            node = reaction.getKineticLaw().getMath()
-            # FIXME: convert substance amount to concentration here
-            body, args = parse_sbml_math(node=node)
-
-            # Update parameter references
-            for old, new in parameters_to_update.items():
-                pat = re.compile(f"({old})" + r"\b")
-                body = pat.sub(new, body)
 
-            for i, arg in enumerate(args):
-                args[i] = parameters_to_update.get(arg, arg)
-
-            dynamic_stoichiometry: dict[str, str] = {}
-            parsed_reactants: defaultdict[str, int] = defaultdict(int)
-            for substrate in reaction.getListOfReactants():
-                species = _name_to_py(substrate.getSpecies())
-                if (ref := substrate.getId()) != "":
-                    dynamic_stoichiometry[species] = ref
-                    self.parameters[ref] = Parameter(0.0, is_constant=False)
-
-                elif species not in self.boundary_species:
-                    factor = substrate.getStoichiometry()
-                    if str(factor) == "nan":
-                        msg = f"Cannot parse stoichiometry: {factor}"
-                        raise ValueError(msg)
-                    parsed_reactants[species] -= factor
-
-            parsed_products: defaultdict[str, int] = defaultdict(int)
-            for product in reaction.getListOfProducts():
-                species = _name_to_py(product.getSpecies())
-                if (ref := product.getId()) != "":
-                    dynamic_stoichiometry[species] = ref
-                    self.parameters[ref] = Parameter(0.0, is_constant=False)
-                elif species not in self.boundary_species:
-                    factor = product.getStoichiometry()
-                    if str(factor) == "nan":
-                        msg = f"Cannot parse stoichiometry: {factor}"
-                        raise ValueError(msg)
-                    parsed_products[species] += factor
-
-            # Combine stoichiometries
-            # Hint: you can't just combine the dictionaries, as you have cases like
-            # S1 + S2 -> 2S2, which have to be combined to S1 -> S2
-            stoichiometries = dict(parsed_reactants)
-            for species, value in parsed_products.items():
-                if species in stoichiometries:
-                    stoichiometries[species] = stoichiometries[species] + value
-                else:
-                    stoichiometries[species] = value
-
-            self.reactions[sbml_id] = Reaction(
-                body=body,
-                stoichiometry=stoichiometries | dynamic_stoichiometry,
-                args=args,
-            )
+def free_symbols(expr: sympy.Expr) -> list[str]:
+    return [i.name for i in expr.free_symbols if isinstance(i, sympy.Symbol)]
 
-    def _convert_substance_amount_to_concentration(
-        self,
-    ) -> None:
-        """Convert substance amount to concentration if has_only_substance_units is false.
 
-        The compounds in the test are supplied in mole if has_only_substance_units is false.
-        In that case, the reaction equation has to be reformed like this:
-        k1 * S1 * compartment -> k1 * S1
-        or in other words the species have to be divided by the compartment to get
-        concentration units.
-        """
-        for reaction in self.reactions.values():
-            function_body = reaction.body
-            removed_compartments = set()
-            for arg in reaction.args:
-                # the parsed species part is important to not
-                # introduce conversion on things that aren't species
-                if (species := self.variables.get(arg, None)) is None:
-                    continue
-
-                if not species.has_only_substance_units:
-                    compartment = species.compartment
-                    if compartment is not None:
-                        if self.compartments[compartment].dimensions == 0:
-                            continue
-                        if species.is_concentration:
-                            if compartment not in removed_compartments:
-                                pattern = f"({compartment})" + r"\b"
-                                repl = f"({compartment} / {compartment})"
-                                function_body = re.sub(pattern, repl, function_body)
-                                removed_compartments.add(compartment)
-                        else:
-                            # \b is word boundary
-                            pattern = f"({arg})" + r"\b"
-                            repl = f"({arg} / {compartment})"
-                            function_body = re.sub(pattern, repl, function_body)
-                        if compartment not in reaction.args:
-                            reaction.args.append(compartment)
-
-            # Simplify the function
-            try:
-                reaction.body = str(sympy.parse_expr(function_body))
-            except AttributeError:
-                # E.g. when math.factorial is called
-                # FIXME: do the sympy conversion before?
-                reaction.body = function_body
-
-
-def _handle_fn(name: str, body: str, args: list[str]) -> Callable[..., float]:
-    func_args = ", ".join(args)
-    func_str = "\n".join(
-        [
-            f"def {name}({func_args}):",
-            f"{INDENT}return {body}",
-            "",
-        ]
-    )
-    try:
-        exec(func_str, globals(), None)  # noqa: S102
-    except SyntaxError as e:
-        msg = f"Invalid function definition: {func_str}"
-        raise SyntaxError(msg) from e
-    python_func = globals()[name]
-    python_func.__source__ = func_str
-    return python_func  # type: ignore
-
-
-def _codegen_fn(name: str, body: str, args: list[str]) -> str:
-    func_args = ", ".join(args)
-    return "\n".join(
-        [
-            f"def {name}({func_args}):",
-            f"{INDENT}return {body}",
-            "",
-        ]
-    )
-
-
-def _codegen_initial_assignment(
+def _transform_stoichiometry(
     k: str,
-    sbml: Parser,
-    parameters: dict[str, float],
-) -> str:
-    if k in parameters:
-        return f"m.update_parameter('{k}', _init_{k}(*(args[i] for i in {sbml.initial_assignment[k].args})) )"
-
-    ass = sbml.initial_assignment[k]
-    fn = f"_init_{k}(*(args[i] for i in {ass.args}))"
-
-    if (species := sbml.variables.get(k)) is not None:
-        compartment = species.compartment
-        if compartment is not None and (
-            not species.is_concentration
-            or (species.has_only_substance_units and species.is_concentration)
-        ):
-            size = 1 if (c := sbml.compartments.get(compartment)) is None else c.size
-            if size != 0:
-                fn = f"{fn} * {size}"
-    elif k in sbml.compartments:
-        pass
-    else:
-        msg = "Initial assignment targeting unknown type"
-        raise NotImplementedError(msg)
-
-    return f"m.update_variable('{k}', {fn})"
-
-
-def _codgen(name: str, sbml: Parser) -> Path:
-    import itertools as it
-
-    functions = {
-        k: _codegen_fn(k, body=v.body, args=v.args)
-        for k, v in it.chain(
-            sbml.functions.items(),
-            sbml.derived.items(),
-            sbml.reactions.items(),
-            {f"_init_{k}": v for k, v in sbml.initial_assignment.items()}.items(),
+    v: pysbml.transform.data.Expr,
+) -> SymbolicFn | str | sympy.Float:
+    if isinstance(v, sympy.Float):
+        return v
+    if isinstance(v, sympy.Symbol):
+        return v.name
+
+    return SymbolicFn(k, expr=v, args=free_symbols(v))
+
+
+def _codegen(name: str, model: pysbml.transform.data.Model) -> Path:
+    sym = SymbolicRepr()
+    for key, var in model.variables.items():
+        sym.variables[key] = SymbolicVariable(
+            value=var.value,
+            unit=var.unit,
         )
-    }
-
-    parameters = {
-        k: v.value for k, v in sbml.parameters.items() if k not in sbml.derived
-    }
-    variables = {
-        k: v.initial_amount for k, v in sbml.variables.items() if k not in sbml.derived
-    }
-    for k, v in sbml.compartments.items():
-        if k in sbml.derived:
-            continue
-        if v.is_constant:
-            parameters[k] = v.size
-        else:
-            variables[k] = v.size
 
-    # Ensure non-zero value for initial assignments
-    # EXPLAIN: we need to do this for the first round of get_args to work
-    # otherwise we run into a ton of DivisionByZero errors.
-    # Since the values are overwritte afterwards, it doesn't really matter anyways
-    for k in sbml.initial_assignment:
-        if k in parameters and parameters[k] == 0:
-            parameters[k] = 1
-        if k in variables and variables[k] == 0:
-            variables[k] = 1
+    for key, par in model.parameters.items():
+        sym.parameters[key] = SymbolicParameter(value=par.value, unit=par.unit)
 
-    derived_str = "\n    ".join(
-        f"m.add_derived('{k}', fn={k}, args={v.args})" for k, v in sbml.derived.items()
-    )
-    rxn_str = "\n    ".join(
-        f"m.add_reaction('{k}', fn={k}, args={rxn.args}, stoichiometry={rxn.stoichiometry})"
-        for k, rxn in sbml.reactions.items()
-    )
-
-    functions_str = "\n\n".join(functions.values())
-
-    parameters_str = f"m.add_parameters({parameters})" if len(parameters) > 0 else ""
-    variables_str = f"m.add_variables({variables})" if len(variables) > 0 else ""
-
-    # Initial assignments
-    initial_assignment_order = _sort_dependencies(
-        available=set(sbml.initial_assignment)
-        ^ set(parameters)
-        ^ set(variables)
-        ^ set(sbml.derived)
-        | {"time"},
-        elements=[
-            Dependency(name=k, required=set(v.args), provided={k})
-            for k, v in sbml.initial_assignment.items()
-        ],
-    )
+    for key, der in model.derived.items():
+        sym.derived[key] = SymbolicFn(fn_name=key, expr=der, args=free_symbols(der))
 
-    if len(initial_assignment_order) > 0:
-        initial_assignment_source = "\n    ".join(
-            _codegen_initial_assignment(k, sbml, parameters=parameters)
-            for k in initial_assignment_order
+    for key, rxn in model.reactions.items():
+        sym.reactions[key] = SymbolicReaction(
+            fn=SymbolicFn(fn_name=key, expr=rxn.expr, args=free_symbols(rxn.expr)),
+            stoichiometry={
+                k: _transform_stoichiometry(k, v) for k, v in rxn.stoichiometry.items()
+            },
         )
-    else:
-        initial_assignment_source = ""
-
-    file = f"""
-import math
-
-import numpy as np
-import scipy
-
-from mxlpy import Model
-
-{functions_str}
+    for key, der in model.initial_assignments.items():
+        if key in model.parameters:
+            sym.parameters[key].value = SymbolicFn(
+                fn_name=key, expr=der, args=free_symbols(der)
+            )
+        elif key in model.variables:
+            sym.variables[key].value = SymbolicFn(
+                fn_name=key, expr=der, args=free_symbols(der)
+            )
 
-def get_model() -> Model:
-    m = Model()
-    {parameters_str}
-    {variables_str}
-    {derived_str}
-    {rxn_str}
-    args = m.get_args()
-    {initial_assignment_source}
-    return m
-"""
     path = default_tmp_dir(None, remove_old_cache=False) / f"{name}.py"
     with path.open("w+") as f:
-        f.write(file)
+        f.write(
+            generate_mxlpy_code_from_symbolic_repr(
+                sym,
+                imports=[
+                    "import math",
+                    "import scipy",
+                ],
+            )
+        )
     return path
 
 
 def import_from_path(module_name: str, file_path: Path) -> Callable[[], Model]:
-    import sys
-    from importlib import util
-
     spec = unwrap(util.spec_from_file_location(module_name, file_path))
     module = util.module_from_spec(spec)
     sys.modules[module_name] = module
     unwrap(spec.loader).exec_module(module)
-    return module.get_model
+    return module.create_model
 
 
 def valid_filename(value: str) -> str:
-    import re
-    import unicodedata
-
     value = (
         unicodedata.normalize("NFKD", value).encode("ascii", "ignore").decode("ascii")
     )
@@ -595,8 +117,7 @@ def read(file: Path) -> Model:
         Model: Imported model instance.
 
     """
-    name = valid_filename(file.stem)
-    sbml = Parser().parse(file=file)
-
-    model_fn = import_from_path(name, _codgen(name, sbml))
+    model = pysbml.load_and_transform_model(file)
+    out_name = valid_filename(file.stem)
+    model_fn = import_from_path(out_name, _codegen(out_name, model))
     return model_fn()