modelbase2 0.1.79__py3-none-any.whl → 0.3.0__py3-none-any.whl

modelbase2/ode/model.py

@@ -1,470 +0,0 @@
-from __future__ import annotations
-
-import numpy as np
-import pandas as pd
-from ..core import (
-    AlgebraicModule,
-    AlgebraicModuleContainer,
-    Constant,
-    ConstantContainer,
-    DerivedConstant,
-    NameContainer,
-    Reaction,
-    ReactionContainer,
-    Variable,
-    VariableContainer,
-)
-from ..core.data import (
-    DerivedStoichiometry,
-    ModuleFunction,
-    RateFunction,
-    StoichiometryByReaction,
-    StoichiometryByVariable,
-)
-from ..types import Array, Series
-from dataclasses import dataclass, field
-from functools import singledispatchmethod
-from modelbase.ode import Model as OldModel
-from typing import Iterable, Literal, Optional, Union, overload
-
-
-def _sort_derived_compounds(m: Model, max_iterations: int = 10_000) -> list[str]:
-    from queue import Empty, SimpleQueue
-
-    available = set(m.constants)
-    order = []
-    to_sort: SimpleQueue = SimpleQueue()
-    for v in m.derived_constants.values():
-        to_sort.put((v.name, set(v.args)))
-
-    last_name: str | None = None
-    i = 0
-    while True:
-        try:
-            name, args = to_sort.get_nowait()
-        except Empty:
-            break
-        if args.issubset(available):
-            available.add(name)
-            order.append(name)
-        else:
-            if last_name == name:
-                order.append(name)
-                break
-            to_sort.put((name, args))
-            last_name = name
-        i += 1
-        if i > max_iterations:
-            while True:
-                try:
-                    name, args = to_sort.get_nowait()
-                    print(name, args)
-                except Empty:
-                    break
-
-            raise ValueError(
-                "Exceeded max iterations on sorting. Check if there are circular references."
-            )
-    return order
-
-
-@dataclass
-class Model:
-    _algebraic_modules: AlgebraicModuleContainer = field(
-        default_factory=AlgebraicModuleContainer
-    )
-    _variables: VariableContainer = field(default_factory=VariableContainer)
-    _constants: ConstantContainer = field(default_factory=ConstantContainer)
-    _reactions: ReactionContainer = field(default_factory=ReactionContainer)
-    _names: NameContainer = field(default_factory=NameContainer)
-
-    def __add__(self, other: "Model") -> "Model":
-        for name, variable in other.variables.items():
-            if name in self.variables:
-                continue
-            else:
-                self.add_variable(variable)
-
-        for name, constant in other.constants.items():
-            if name in self.constants:
-                self.update_constant(name, constant.value)
-            else:
-                self.add_constant(constant)
-
-        # for name, derived_constant in other.derived_constants.items():
-        for name in other._constants._derived_constant_order:
-            derived_constant = other.derived_constants[name]
-            if name in self.derived_constants:
-                self.update_derived_constant(
-                    name,
-                    derived_constant.function,
-                    derived_constant.args,
-                    derived_constant.unit,
-                )
-            else:
-                self.add_derived_constant(derived_constant)
-
-        # for name, module in other.algebraic_modules.items():
-        for name in other._algebraic_modules.module_order:
-            module = other.algebraic_modules[name]
-            if name in self.algebraic_modules:
-                self.update_algebraic_module(
-                    name,
-                    module.function,
-                    module.derived_variables,
-                    module.args,
-                )
-            else:
-                self.add_algebraic_module(module)
-
-        for name, reaction in other.reactions.items():
-            if reaction.name in self.reactions:
-                self.update_reaction(
-                    reaction.name,
-                    reaction.function,
-                    reaction.stoichiometry,
-                    reaction.derived_stoichiometry,
-                    reaction.args,
-                )
-            else:
-                self.add_reaction(
-                    Reaction(
-                        name=reaction.name,
-                        function=reaction.function,
-                        stoichiometry=reaction.stoichiometry,
-                        derived_stoichiometry=reaction.derived_stoichiometry,
-                        args=reaction.args,
-                    )
-                )
-
-        return self
-
-    @property
-    def constants(self) -> dict[str, Constant]:
-        return self._constants.constants
-
-    @property
-    def derived_constants(self) -> dict[str, DerivedConstant]:
-        return self._constants.derived_constants
-
-    @property
-    def constant_values(self) -> dict[str, float]:
-        return self._constants.values
-
-    @property
-    def variables(self) -> dict[str, Variable]:
-        return self._variables.variables
-
-    @property
-    def derived_variables(self) -> list[str]:
-        return self._algebraic_modules.get_derived_variables()
-
-    @property
-    def all_variables(self) -> list[str]:
-        return list(self.variables) + self.derived_variables
-
-    @property
-    def algebraic_modules(self) -> dict[str, AlgebraicModule]:
-        return self._algebraic_modules.modules
-
-    @property
-    def reactions(self) -> dict[str, Reaction]:
-        return self._reactions.reactions
-
-    @property
-    def stoichiometries(self) -> dict[str, StoichiometryByVariable]:
-        return self._reactions.stoichiometries_by_variables
-
-    @singledispatchmethod
-    def add(
-        self,
-        element: Union[list, Constant, DerivedConstant, Variable, AlgebraicModule],
-    ) -> None:
-        raise NotImplementedError(element.__class__.__name__)
-
-    @add.register
-    def _add_iterable(self, elements: list) -> None:
-        for element in elements:
-            self.add(element)
-
-    ##########################################################################
-    # Constants
-    ##########################################################################
-
-    @add.register
-    def add_constant(self, constant: Constant) -> None:
-        self._names.add(constant.name, "constant")
-        self._constants.add_basic(constant)
-
-    def scale_constant(self, name: str, factor: float) -> None:
-        value = self.constant_values[name]
-        self.update_constant(name, value * factor)
-
-    def update_constant(self, name: str, value: float) -> None:
-        self._constants.update_basic(name, value)
-        self._reactions.update_derived_stoichiometries(self.constant_values)
-
-    def update_constants(self, constants: dict[str, float]) -> None:
-        for name, value in constants.items():
-            self.update_constant(name, value)
-
-    def remove_constant(self, name: str) -> None:
-        self._names.remove(name)
-        self._constants.remove_basic(name)
-
-    def remove_constants(self, names: Iterable[str]) -> None:
-        for name in names:
-            self.remove_constant(name)
-
-    ##########################################################################
-    # Derived Constants
-    ##########################################################################
-
-    @add.register
-    def add_derived_constant(self, constant: DerivedConstant) -> None:
-        self._names.require_multiple(constant.args)
-        self._names.add(constant.name, "derived_constant")
-        self._constants.add_derived(constant)
-
-    def update_derived_constant(
-        self,
-        name: str,
-        function: Optional[RateFunction] = None,
-        args: Optional[Iterable[str]] = None,
-        unit: Optional[str] = None,
-    ) -> None:
-        old = self.remove_derived_constant(name)
-        if function is None:
-            function = old.function
-        if args is None:
-            args = old.args
-        if unit is None:
-            unit = old.unit
-        self.add_derived_constant(DerivedConstant(name, function, list(args), unit))
-        self._reactions.update_derived_stoichiometries(self.constant_values)
-
-    def remove_derived_constant(self, name: str) -> DerivedConstant:
-        self._names.remove(name)
-        return self._constants.remove_derived(name)
-
-    def remove_derived_constants(self, names: Iterable[str]) -> None:
-        for name in names:
-            self.remove_derived_constant(name)
-
-    ##########################################################################
-    # Variables
-    ##########################################################################
-
-    @add.register
-    def add_variable(self, variable: Variable) -> None:
-        self._names.add(variable.name, "variable")
-        self._variables.add(variable)
-
-    def remove_variable(self, name: str) -> None:
-        self._names.remove(name)
-        self._variables.remove(name)
-
-    def remove_variables(self, names: Iterable[str]) -> None:
-        for name in names:
-            self.remove_variable(name)
-
-    ##########################################################################
-    # Algebraic Modules
-    ##########################################################################
-
-    def _get_available_args(self) -> set[str]:
-        return set(self.all_variables) | set(self._constants.values)
-
-    @add.register
-    def add_algebraic_module(self, module: AlgebraicModule) -> None:
-        for name in module.derived_variables:
-            self._names.add(name, "derived_variable")
-        self._names.require_multiple(module.args)
-        self._algebraic_modules.add(
-            module,
-            self._get_available_args(),
-            sort_modules=True,
-        )
-
-    def remove_algebraic_module(self, name: str) -> AlgebraicModule:
-        module = self._algebraic_modules.remove(
-            name,
-            set(),
-            sort_modules=False,
-        )
-        for name in module.derived_variables:
-            self._names.remove(name)
-        return module
-
-    def remove_algebraic_modules(self, names: Iterable[str]) -> None:
-        for name in names:
-            self.remove_algebraic_module(name)
-
-    def update_algebraic_module(
-        self,
-        name: str,
-        function: Optional[ModuleFunction] = None,
-        derived_variables: Optional[list[str]] = None,
-        args: Optional[list[str]] = None,
-    ) -> None:
-        old_module = self.remove_algebraic_module(name)
-        if function is None:
-            function = old_module.function
-        if derived_variables is None:
-            derived_variables = old_module.derived_variables
-        if args is None:
-            args = old_module.args
-        self.add_algebraic_module(
-            AlgebraicModule(name, function, derived_variables, args)
-        )
-
-        self._algebraic_modules.update(
-            name,
-            function,
-            derived_variables,
-            args,
-            self._get_available_args(),
-        )
-
-    ##########################################################################
-    # Reactions
-    ##########################################################################
-
-    @add.register
-    def add_reaction(
-        self,
-        reaction: Reaction,
-    ) -> None:
-        self._names.require_multiple(reaction.args)
-        self._reactions.add(reaction, self.constant_values)
-
-    def remove_reaction(self, name: str) -> None:
-        self._reactions.remove(name=name)
-
-    def remove_reactions(self, names: Iterable[str]) -> None:
-        for name in names:
-            self.remove_reaction(name=name)
-
-    def update_reaction(
-        self,
-        name: str,
-        function: Optional[RateFunction] = None,
-        stoichiometry: Optional[StoichiometryByReaction] = None,
-        # derived_stoichiometry: Optional[DerivedStoichiometry] = None,
-        derived_stoichiometry: Optional[dict[str, DerivedStoichiometry]] = None,
-        args: list[str] | None = None,
-    ) -> None:
-        self._reactions.update(
-            name,
-            function,
-            stoichiometry,
-            derived_stoichiometry,
-            args,
-            self.constant_values,
-        )
-
-    def get_stoichiometries(self) -> pd.DataFrame:
-        return self._reactions.get_stoichiometries()
-
-    # ##########################################################################
-    # # Simulation functions
-    # ##########################################################################
-
-    def _get_problem(self, t: float, y: Iterable[float]) -> list[float]:
-        """Integration function"""
-        variables = dict(zip(self.stoichiometries, y)) | {"time": t}
-        args = variables | self.constant_values
-        args |= self._algebraic_modules.get_values_float(args)
-        fluxes = self._reactions.get_fluxes_float(args)
-        rhs = self._reactions.get_right_hand_side_float(fluxes)
-        return list(rhs.values())
-
-    def _get_all_args(self, variables: dict[str, float], time: float) -> dict[str, float]:
-        args = variables | self.constant_values | {"time": time}
-        args |= self._algebraic_modules.get_values_float(args)
-        return args
-
-    def get_derived_variables(
-        self, variables: dict[str, float], time: float = 0.0
-    ) -> dict[str, float]:
-        args = variables | self.constant_values | {"time": time}
-        return self._algebraic_modules.get_values_float(args)
-
-    @overload
-    def get_fluxes(
-        self,
-        variables: dict[str, float],
-        return_type: Literal["dict"],
-        time: float = 0,
-    ) -> dict[str, float]:
-        ...
-
-    @overload
-    def get_fluxes(
-        self,
-        variables: dict[str, float],
-        return_type: Literal["array"],
-        time: float = 0,
-    ) -> Array:
-        ...
-
-    @overload
-    def get_fluxes(
-        self,
-        variables: dict[str, float],
-        return_type: Literal["series"],
-        time: float = 0,
-    ) -> Series:
-        ...
-
-    @overload
-    def get_fluxes(
-        self,
-        variables: dict[str, float],
-        return_type: Literal["dict"] = "dict",
-        time: float = 0,
-    ) -> dict[str, float]:
-        ...
-
-    def get_fluxes(
-        self,
-        variables: dict[str, float],
-        return_type: Literal["array", "dict", "series"] = "dict",
-        time: float = 0.0,
-    ) -> Union[Array, dict[str, float], pd.Series]:
-        args = self._get_all_args(variables, time)
-        fluxes_dict = self._reactions.get_fluxes_float(args)
-        if return_type == "dict":
-            return fluxes_dict
-        elif return_type == "series":
-            return pd.Series(fluxes_dict)
-        elif return_type == "array":
-            return np.fromiter(fluxes_dict.values(), dtype="float")
-        else:
-            raise NotImplementedError(f"Unknown return type {return_type}")
-
-    def get_right_hand_side(
-        self, variables: dict[str, float], time: float = 0.0
-    ) -> dict[str, float]:
-        fluxes = self.get_fluxes(variables, time=time)
-        return self._reactions.get_right_hand_side_float(fluxes)
-
-    def to_version_1(self) -> OldModel:
-        old = OldModel()
-
-        old.add_compounds(list(self.variables))
-
-        old.add_parameters({k: v.value for k, v in self.constants.items()})
-
-        for k in _sort_derived_compounds(self):
-            dc = self.derived_constants[k]
-            old.add_derived_parameter(k, dc.function, dc.args)
-
-        for k, am in self.algebraic_modules.items():
-            old.add_algebraic_module_from_args(
-                k, am.function, am.derived_variables, am.args
-            )
-
-        for r in self.reactions.values():
-            old.add_reaction_from_args(r.name, r.function, r.stoichiometry, r.args)
-        return old

modelbase2/ode/simulator.py

@@ -1,153 +0,0 @@
-from __future__ import annotations
-
-import logging
-import numpy as np
-import pandas as pd
-from ..types import Array
-from .integrator import Assimulo
-from .model import Model
-from dataclasses import dataclass, field
-from typing import Any, Optional, Type
-
-logger = logging.getLogger()
-
-
-@dataclass(repr=False)
-class SimulationResult:
-    time: Array
-    values: dict[str, Array]
-    constants: dict[str, float]
-
-    def __repr__(self) -> str:
-        return f"Simulation until t={self.time[-1]}"
-
-    def to_frame(self) -> pd.DataFrame:
-        return pd.DataFrame(
-            data=self.values,
-            index=self.time,  # type: ignore
-        )
-
-
-def concatenate_results(results: list[SimulationResult]) -> pd.DataFrame:
-    df = results[0].to_frame()
-    if len(results) > 1:
-        for result in results[1:]:
-            df = pd.concat((df, result.to_frame().iloc[1:]))
-    return df
-
-
-@dataclass(init=False)
-class Simulator:
-    model: Model
-    integrator: Assimulo
-    y0: list[float] = field(default_factory=list)
-    # Could also be ResultContainer once you add other model types again
-    results: list[SimulationResult] = field(default_factory=list)
-
-    def __init__(
-        self,
-        model: Model,
-        integrator: Type[Assimulo],
-        y0: dict[str, float],
-        results: Optional[SimulationResult] = None,
-    ):
-        self.model = model
-        self.update_y0(y0)
-        self.integrator = integrator(rhs=self.model._get_problem, y0=self.y0)
-        if results is None:
-            self.results = list()
-
-    def __reduce__(self) -> Any:
-        return (
-            self.__class__,
-            (
-                self.model,
-                self.integrator,
-                self.y0,
-            ),
-            (("results", self.results),),
-        )
-
-    def update_y0(self, y0: dict[str, float]) -> None:
-        self.y0 = [y0[i] for i in self.model.stoichiometries]
-
-    def clear_results(self) -> None:
-        self.results = list()
-        self.integrator.reset()
-
-    def simulate(
-        self,
-        t_end: float,
-    ) -> Optional[SimulationResult]:
-        if (integration := self.integrator.integrate(t_end, None, None)) is None:
-            logger.warning("Simulation failed")
-            return None
-        res = SimulationResult(
-            integration.time,
-            dict(zip(self.model.stoichiometries, integration.values.T)),
-            self.model.constant_values,
-        )
-        self.results.append(res)
-        return res
-
-    def simulate_to_steady_state(
-        self, tolerance: float = 1e-6
-    ) -> Optional[dict[str, float]]:
-        if (
-            integration := self.integrator.integrate_to_steady_state(tolerance)
-        ) is not None:
-            return dict(zip(self.model.stoichiometries, integration))
-        else:
-            logger.warning("Simulation failed")
-            return None
-
-    def get_results(self) -> pd.DataFrame:
-        return concatenate_results(self.results)
-
-    def _get_result_constants(self, result: SimulationResult) -> dict[str, Array]:
-        return {k: np.full(len(result.time), v) for k, v in result.constants.items()}
-
-    def _get_result_derived_variables(
-        self,
-        args: dict[str, Array],
-    ) -> dict[str, Array]:
-        return self.model._algebraic_modules.get_values_array(args)
-
-    def _get_result_all_variables(
-        self, result: SimulationResult, constants: dict[str, Array]
-    ) -> dict[str, Array]:
-        args = result.values | constants | {"time": result.time}
-        return result.values | self._get_result_derived_variables(args)
-
-    def _get_result_fluxes(self, result: SimulationResult) -> dict[str, Array]:
-        constants = self._get_result_constants(result)
-        all_variables = self._get_result_all_variables(result, constants)
-        args = all_variables | constants | {"time": result.time}
-        return self.model._reactions.get_fluxes_array(args)
-
-    def get_full_results(self) -> pd.DataFrame:
-        full_results: list[SimulationResult] = []
-        for result in self.results:
-            full_results.append(
-                SimulationResult(
-                    values=self._get_result_all_variables(
-                        result, self._get_result_constants(result)
-                    ),
-                    time=result.time,
-                    constants=result.constants,
-                )
-            )
-        return concatenate_results(full_results)
-
-    def get_fluxes(self) -> pd.DataFrame:
-        fluxes: list[SimulationResult] = []
-        for result in self.results:
-            result_fluxes = self._get_result_fluxes(result)
-            fluxes.append(
-                SimulationResult(
-                    values=result_fluxes,
-                    time=result.time,
-                    constants=result.constants,
-                )
-            )
-        return concatenate_results(fluxes)