mxlpy 0.21.0__py3-none-any.whl → 0.22.0__py3-none-any.whl

mxlpy/model.py

@@ -15,9 +15,23 @@ from typing import TYPE_CHECKING, Self, cast
 
 import numpy as np
 import pandas as pd
+import sympy
 
 from mxlpy import fns
-from mxlpy.types import AbstractSurrogate, Array, Derived, Reaction, Readout
+from mxlpy.meta.source_tools import fn_to_sympy
+from mxlpy.meta.sympy_tools import (
+    list_of_symbols,
+    stoichiometries_to_sympy,
+)
+from mxlpy.types import (
+    AbstractSurrogate,
+    Array,
+    Derived,
+    Parameter,
+    Reaction,
+    Readout,
+    Variable,
+)
 
 if TYPE_CHECKING:
     from collections.abc import Iterable, Mapping
@@ -32,9 +46,38 @@ __all__ = [
     "MissingDependenciesError",
     "Model",
     "ModelCache",
+    "TableView",
 ]
 
 
+def _latex_view(expr: sympy.Expr | None) -> str:
+    if expr is None:
+        return "PARSE-ERROR"
+    return f"${sympy.latex(expr)}$"
+
+
+@dataclass(kw_only=True, slots=True)
+class TableView:
+    """Markdown view of pandas Dataframe.
+
+    Mostly used to get nice LaTeX rendering of sympy expressions.
+    """
+
+    data: pd.DataFrame
+
+    def __repr__(self) -> str:
+        """Normal Python shell output."""
+        return self.data.to_markdown()
+
+    def _repr_markdown_(self) -> str:
+        """Fancy IPython shell output.
+
+        Looks the same as __repr__, but is handled by IPython to output
+        `IPython.display.Markdown`, so looks nice
+        """
+        return self.data.to_markdown()
+
+
 @dataclass
 class Dependency:
     """Container class for building dependency tree."""
@@ -275,8 +318,8 @@ class Model:
     """
 
     _ids: dict[str, str] = field(default_factory=dict)
-    _variables: dict[str, float | Derived] = field(default_factory=dict)
-    _parameters: dict[str, float] = field(default_factory=dict)
+    _variables: dict[str, Variable] = field(default_factory=dict)
+    _parameters: dict[str, Parameter] = field(default_factory=dict)
     _derived: dict[str, Derived] = field(default_factory=dict)
     _readouts: dict[str, Readout] = field(default_factory=dict)
     _reactions: dict[str, Reaction] = field(default_factory=dict)
@@ -300,7 +343,7 @@ class Model:
             ModelCache: An instance of ModelCache containing the initialized cache data.
 
         """
-        all_parameter_values: dict[str, float] = self._parameters.copy()
+        all_parameter_values: dict[str, float] = self.get_parameter_values()
         all_parameter_names: set[str] = set(all_parameter_values)
 
         # Sanity checks
@@ -317,11 +360,19 @@ class Model:
             self._derived
             | self._reactions
             | self._surrogates
-            | {k: v for k, v in self._variables.items() if isinstance(v, Derived)}
+            | {
+                k: init
+                for k, v in self._variables.items()
+                if isinstance(init := v.initial_value, Derived)
+            }
         )
         order = _sort_dependencies(
             available=all_parameter_names
-            | {k for k, v in self._variables.items() if not isinstance(v, Derived)}
+            | {
+                k
+                for k, v in self._variables.items()
+                if not isinstance(v.initial_value, Derived)
+            }
             | set(self._data)
             | {"time"},
             elements=[
@@ -337,7 +388,11 @@ class Model:
         dependent = (
             all_parameter_values
             | self._data
-            | {k: v for k, v in self._variables.items() if not isinstance(v, Derived)}
+            | {
+                k: init
+                for k, v in self._variables.items()
+                if not isinstance(init := v.initial_value, Derived)
+            }
             | {"time": 0.0}
         )
         for name in order:
@@ -393,7 +448,9 @@ class Model:
         dxdt = pd.Series(np.zeros(len(var_names), dtype=float), index=var_names)
 
         initial_conditions: dict[str, float] = {
-            k: v for k, v in self._variables.items() if not isinstance(v, Derived)
+            k: init
+            for k, v in self._variables.items()
+            if not isinstance(init := v.initial_value, Derived)
         }
         for name in static_order:
             if name in self._variables:
@@ -465,29 +522,88 @@ class Model:
         del self._ids[name]
 
     ##########################################################################
-    # Parameters
+    # Parameters - views
     ##########################################################################
 
+    @property
+    def parameters(self) -> TableView:
+        """Return view of parameters."""
+        index = list(self._parameters.keys())
+        data = [
+            {
+                "value": el.value,
+                "unit": _latex_view(unit) if (unit := el.unit) is not None else "",
+                # "source": ...,
+            }
+            for el in self._parameters.values()
+        ]
+        return TableView(data=pd.DataFrame(data, index=index))
+
+    def get_raw_parameters(self, *, as_copy: bool = True) -> dict[str, Parameter]:
+        """Returns the parameters of the model."""
+        if as_copy:
+            return copy.deepcopy(self._parameters)
+        return self._parameters
+
+    def get_parameter_values(self) -> dict[str, float]:
+        """Returns the parameters of the model.
+
+        Examples:
+            >>> model.parameters
+                {"k1": 0.1, "k2": 0.2}
+
+        Returns:
+            parameters: A dictionary where the keys are parameter names (as strings)
+                  and the values are parameter values (as floats).
+
+        """
+        return {k: v.value for k, v in self._parameters.items()}
+
+    def get_parameter_names(self) -> list[str]:
+        """Retrieve the names of the parameters.
+
+        Examples:
+            >>> model.get_parameter_names()
+                ['k1', 'k2']
+
+        Returns:
+            parametes: A list containing the names of the parameters.
+
+        """
+        return list(self._parameters)
+
+    #####################################
+    # Parameters - create
+    #####################################
+
     @_invalidate_cache
-    def add_parameter(self, name: str, value: float) -> Self:
+    def add_parameter(
+        self,
+        name: str,
+        value: float,
+        unit: sympy.Expr | None = None,
+        source: str | None = None,
+    ) -> Self:
         """Adds a parameter to the model.
 
         Examples:
             >>> model.add_parameter("k1", 0.1)
 
         Args:
-            name (str): The name of the parameter.
-            value (float): The value of the parameter.
+            name: The name of the parameter.
+            value: The value of the parameter.
+            unit: unit of the parameter
+            source: source of the information given
 
         Returns:
             Self: The instance of the model with the added parameter.
 
         """
         self._insert_id(name=name, ctx="parameter")
-        self._parameters[name] = value
+        self._parameters[name] = Parameter(value=value, unit=unit, source=source)
         return self
 
-    def add_parameters(self, parameters: dict[str, float]) -> Self:
+    def add_parameters(self, parameters: Mapping[str, float | Parameter]) -> Self:
         """Adds multiple parameters to the model.
 
         Examples:
@@ -502,36 +618,15 @@ class Model:
 
         """
         for k, v in parameters.items():
-            self.add_parameter(k, v)
+            if isinstance(v, Parameter):
+                self.add_parameter(k, v.value, unit=v.unit, source=v.source)
+            else:
+                self.add_parameter(k, v)
         return self
 
-    @property
-    def parameters(self) -> dict[str, float]:
-        """Returns the parameters of the model.
-
-        Examples:
-            >>> model.parameters
-                {"k1": 0.1, "k2": 0.2}
-
-        Returns:
-            parameters: A dictionary where the keys are parameter names (as strings)
-                  and the values are parameter values (as floats).
-
-        """
-        return self._parameters.copy()
-
-    def get_parameter_names(self) -> list[str]:
-        """Retrieve the names of the parameters.
-
-        Examples:
-            >>> model.get_parameter_names()
-                ['k1', 'k2']
-
-        Returns:
-            parametes: A list containing the names of the parameters.
-
-        """
-        return list(self._parameters)
+    #####################################
+    # Parameters - delete
+    #####################################
 
     @_invalidate_cache
     def remove_parameter(self, name: str) -> Self:
@@ -568,8 +663,19 @@ class Model:
             self.remove_parameter(name)
         return self
 
+    #####################################
+    # Parameters - update
+    #####################################
+
     @_invalidate_cache
-    def update_parameter(self, name: str, value: float) -> Self:
+    def update_parameter(
+        self,
+        name: str,
+        value: float | None = None,
+        *,
+        unit: sympy.Expr | None = None,
+        source: str | None = None,
+    ) -> Self:
         """Update the value of a parameter.
 
         Examples:
@@ -578,6 +684,8 @@ class Model:
         Args:
             name: The name of the parameter to update.
             value: The new value for the parameter.
+            unit: Unit of the parameter
+            source: Source of the information
 
         Returns:
             Self: The instance of the class with the updated parameter.
@@ -589,10 +697,17 @@ class Model:
         if name not in self._parameters:
             msg = f"'{name}' not found in parameters"
             raise KeyError(msg)
-        self._parameters[name] = value
+
+        parameter = self._parameters[name]
+        if value is not None:
+            parameter.value = value
+        if unit is not None:
+            parameter.unit = unit
+        if source is not None:
+            parameter.source = source
         return self
 
-    def update_parameters(self, parameters: dict[str, float]) -> Self:
+    def update_parameters(self, parameters: Mapping[str, float | Parameter]) -> Self:
         """Update multiple parameters of the model.
 
         Examples:
@@ -606,7 +721,10 @@ class Model:
 
         """
         for k, v in parameters.items():
-            self.update_parameter(k, v)
+            if isinstance(v, Parameter):
+                self.update_parameter(k, value=v.value, unit=v.unit, source=v.source)
+            else:
+                self.update_parameter(k, v)
         return self
 
     def scale_parameter(self, name: str, factor: float) -> Self:
@@ -623,7 +741,7 @@ class Model:
             Self: The instance of the class with the updated parameter.
 
         """
-        return self.update_parameter(name, self._parameters[name] * factor)
+        return self.update_parameter(name, self._parameters[name].value * factor)
 
     def scale_parameters(self, parameters: dict[str, float]) -> Self:
         """Scales the parameters of the model.
@@ -667,7 +785,7 @@ class Model:
             Self: The instance of the model with the parameter converted to a variable.
 
         """
-        value = self._parameters[name] if initial_value is None else initial_value
+        value = self._parameters[name].value if initial_value is None else initial_value
         self.remove_parameter(name)
         self.add_variable(name, value)
 
@@ -708,7 +826,7 @@ class Model:
     ##########################################################################
 
     @property
-    def variables(self) -> dict[str, float | Derived]:
+    def variables(self) -> TableView:
         """Returns a copy of the variables dictionary.
 
         Examples:
@@ -722,10 +840,79 @@ class Model:
             dict[str, float]: A copy of the variables dictionary.
 
         """
-        return self._variables.copy()
+        index = list(self._variables.keys())
+        data = []
+        for name, el in self._variables.items():
+            if isinstance(init := el.initial_value, Derived):
+                value_str = _latex_view(
+                    fn_to_sympy(
+                        init.fn,
+                        origin=name,
+                        model_args=list_of_symbols(init.args),
+                    )
+                )
+            else:
+                value_str = str(init)
+            data.append(
+                {
+                    "value": value_str,
+                    "unit": _latex_view(unit) if (unit := el.unit) is not None else "",
+                    # "source"
+                }
+            )
+        return TableView(data=pd.DataFrame(data, index=index))
+
+    def get_raw_variables(self, *, as_copy: bool = True) -> dict[str, Variable]:
+        """Retrieve the initial conditions of the model.
+
+        Examples:
+            >>> model.get_initial_conditions()
+                {"x1": 1.0, "x2": 2.0}
+
+        Returns:
+            initial_conditions: A dictionary where the keys are variable names and the values are their initial conditions.
+
+        """
+        if as_copy:
+            return copy.deepcopy(self._variables)
+        return self._variables
+
+    def get_initial_conditions(self) -> dict[str, float]:
+        """Retrieve the initial conditions of the model.
+
+        Examples:
+            >>> model.get_initial_conditions()
+                {"x1": 1.0, "x2": 2.0}
+
+        Returns:
+            initial_conditions: A dictionary where the keys are variable names and the values are their initial conditions.
+
+        """
+        if (cache := self._cache) is None:
+            cache = self._create_cache()
+        return cache.initial_conditions
+
+    def get_variable_names(self) -> list[str]:
+        """Retrieve the names of all variables.
+
+        Examples:
+            >>> model.get_variable_names()
+                ["x1", "x2"]
+
+        Returns:
+            variable_names: A list containing the names of all variables.
+
+        """
+        return list(self._variables)
 
     @_invalidate_cache
-    def add_variable(self, name: str, initial_condition: float | Derived) -> Self:
+    def add_variable(
+        self,
+        name: str,
+        initial_value: float | Derived,
+        unit: sympy.Expr | None = None,
+        source: str | None = None,
+    ) -> Self:
         """Adds a variable to the model with the given name and initial condition.
 
         Examples:
@@ -733,17 +920,23 @@ class Model:
 
         Args:
             name: The name of the variable to add.
-            initial_condition: The initial condition value for the variable.
+            initial_value: The initial condition value for the variable.
+            unit: unit of the variable
+            source: source of the information given
 
         Returns:
             Self: The instance of the model with the added variable.
 
         """
         self._insert_id(name=name, ctx="variable")
-        self._variables[name] = initial_condition
+        self._variables[name] = Variable(
+            initial_value=initial_value, unit=unit, source=source
+        )
         return self
 
-    def add_variables(self, variables: Mapping[str, float | Derived]) -> Self:
+    def add_variables(
+        self, variables: Mapping[str, float | Variable | Derived]
+    ) -> Self:
         """Adds multiple variables to the model with their initial conditions.
 
         Examples:
@@ -757,8 +950,16 @@ class Model:
             Self: The instance of the model with the added variables.
 
         """
-        for name, y0 in variables.items():
-            self.add_variable(name=name, initial_condition=y0)
+        for name, v in variables.items():
+            if isinstance(v, Variable):
+                self.add_variable(
+                    name=name,
+                    initial_value=v.initial_value,
+                    unit=v.unit,
+                    source=v.source,
+                )
+            else:
+                self.add_variable(name=name, initial_value=v)
         return self
 
     @_invalidate_cache
@@ -797,7 +998,13 @@ class Model:
         return self
 
     @_invalidate_cache
-    def update_variable(self, name: str, initial_condition: float | Derived) -> Self:
+    def update_variable(
+        self,
+        name: str,
+        initial_value: float | Derived,
+        unit: sympy.Expr | None = None,
+        source: str | None = None,
+    ) -> Self:
         """Updates the value of a variable in the model.
 
         Examples:
@@ -805,7 +1012,9 @@ class Model:
 
         Args:
             name: The name of the variable to update.
-            initial_condition: The initial condition or value to set for the variable.
+            initial_value: The initial condition or value to set for the variable.
+            unit: Unit of the variable
+            source: Source of the information
 
         Returns:
             Self: The instance of the model with the updated variable.
@@ -814,10 +1023,20 @@ class Model:
         if name not in self._variables:
             msg = f"'{name}' not found in variables"
             raise KeyError(msg)
-        self._variables[name] = initial_condition
+
+        variable = self._variables[name]
+
+        if initial_value is not None:
+            variable.initial_value = initial_value
+        if unit is not None:
+            variable.unit = unit
+        if source is not None:
+            variable.source = source
         return self
 
-    def update_variables(self, variables: Mapping[str, float | Derived]) -> Self:
+    def update_variables(
+        self, variables: Mapping[str, float | Derived | Variable]
+    ) -> Self:
         """Updates multiple variables in the model.
 
         Examples:
@@ -831,37 +1050,17 @@ class Model:
 
         """
         for k, v in variables.items():
-            self.update_variable(k, v)
+            if isinstance(v, Variable):
+                self.update_variable(
+                    k,
+                    initial_value=v.initial_value,
+                    unit=v.unit,
+                    source=v.source,
+                )
+            else:
+                self.update_variable(k, v)
         return self
 
-    def get_variable_names(self) -> list[str]:
-        """Retrieve the names of all variables.
-
-        Examples:
-            >>> model.get_variable_names()
-                ["x1", "x2"]
-
-        Returns:
-            variable_names: A list containing the names of all variables.
-
-        """
-        return list(self._variables)
-
-    def get_initial_conditions(self) -> dict[str, float]:
-        """Retrieve the initial conditions of the model.
-
-        Examples:
-            >>> model.get_initial_conditions()
-                {"x1": 1.0, "x2": 2.0}
-
-        Returns:
-            initial_conditions: A dictionary where the keys are variable names and the values are their initial conditions.
-
-        """
-        if (cache := self._cache) is None:
-            cache = self._create_cache()
-        return cache.initial_conditions
-
     def make_variable_static(self, name: str, value: float | None = None) -> Self:
         """Converts a variable to a static parameter.
 
@@ -881,8 +1080,12 @@ class Model:
             Self: The instance of the class for method chaining.
 
         """
-        value_or_derived = self._variables[name] if value is None else value
+        value_or_derived = (
+            self._variables[name].initial_value if value is None else value
+        )
         self.remove_variable(name)
+
+        # FIXME: better handling of unit
         if isinstance(value_or_derived, Derived):
             self.add_derived(name, value_or_derived.fn, args=value_or_derived.args)
         else:
@@ -901,12 +1104,12 @@ class Model:
         return self
 
     ##########################################################################
-    # Derived
+    # Derived - views
     ##########################################################################
 
     @property
-    def derived(self) -> dict[str, Derived]:
-        """Returns a copy of the derived quantities.
+    def derived(self) -> TableView:
+        """Returns a view of the derived quantities.
 
         Examples:
             >>> model.derived
@@ -917,10 +1120,30 @@ class Model:
             dict[str, Derived]: A copy of the derived dictionary.
 
         """
-        return self._derived.copy()
+        index = list(self._derived.keys())
+        data = [
+            {
+                "value": _latex_view(
+                    fn_to_sympy(
+                        el.fn,
+                        origin=name,
+                        model_args=list_of_symbols(el.args),
+                    )
+                ),
+                "unit": _latex_view(unit) if (unit := el.unit) is not None else "",
+            }
+            for name, el in self._derived.items()
+        ]
 
-    @property
-    def derived_variables(self) -> dict[str, Derived]:
+        return TableView(data=pd.DataFrame(data, index=index))
+
+    def get_raw_derived(self, *, as_copy: bool = True) -> dict[str, Derived]:
+        """Get copy of derived values."""
+        if as_copy:
+            return copy.deepcopy(self._derived)
+        return self._derived
+
+    def get_derived_variables(self) -> dict[str, Derived]:
         """Returns a dictionary of derived variables.
 
         Examples:
@@ -940,8 +1163,7 @@ class Model:
 
         return {k: v for k, v in derived.items() if k not in cache.all_parameter_values}
 
-    @property
-    def derived_parameters(self) -> dict[str, Derived]:
+    def get_derived_parameters(self) -> dict[str, Derived]:
         """Returns a dictionary of derived parameters.
 
         Examples:
@@ -966,6 +1188,7 @@ class Model:
         fn: RateFn,
         *,
         args: list[str],
+        unit: sympy.Expr | None = None,
     ) -> Self:
         """Adds a derived attribute to the model.
 
@@ -976,13 +1199,14 @@ class Model:
             name: The name of the derived attribute.
             fn: The function used to compute the derived attribute.
             args: The list of arguments to be passed to the function.
+            unit: Unit of the derived value
 
         Returns:
             Self: The instance of the model with the added derived attribute.
 
         """
         self._insert_id(name=name, ctx="derived")
-        self._derived[name] = Derived(fn=fn, args=args)
+        self._derived[name] = Derived(fn=fn, args=args, unit=unit)
         return self
 
     def get_derived_parameter_names(self) -> list[str]:
@@ -996,7 +1220,7 @@ class Model:
             A list of names of the derived parameters.
 
         """
-        return list(self.derived_parameters)
+        return list(self.get_derived_parameters())
 
     def get_derived_variable_names(self) -> list[str]:
         """Retrieve the names of derived variables.
@@ -1009,7 +1233,7 @@ class Model:
             A list of names of derived variables.
 
         """
-        return list(self.derived_variables)
+        return list(self.get_derived_variables())
 
     @_invalidate_cache
     def update_derived(
@@ -1018,6 +1242,7 @@ class Model:
         fn: RateFn | None = None,
         *,
         args: list[str] | None = None,
+        unit: sympy.Expr | None = None,
     ) -> Self:
         """Updates the derived function and its arguments for a given name.
 
@@ -1026,16 +1251,21 @@ class Model:
 
         Args:
             name: The name of the derived function to update.
-            fn: The new derived function. If None, the existing function is retained. Defaults to None.
-            args: The new arguments for the derived function. If None, the existing arguments are retained. Defaults to None.
+            fn: The new derived function. If None, the existing function is retained.
+            args: The new arguments for the derived function. If None, the existing arguments are retained.
+            unit: Unit of the derived value
 
         Returns:
             Self: The instance of the class with the updated derived function and arguments.
 
         """
         der = self._derived[name]
-        der.fn = der.fn if fn is None else fn
-        der.args = der.args if args is None else args
+        if fn is not None:
+            der.fn = fn
+        if args is not None:
+            der.args = args
+        if unit is not None:
+            der.unit = unit
         return self
 
     @_invalidate_cache
@@ -1061,7 +1291,27 @@ class Model:
     ###########################################################################
 
     @property
-    def reactions(self) -> dict[str, Reaction]:
+    def reactions(self) -> TableView:
+        """Get view of reactions."""
+        index = list(self._reactions.keys())
+        data = [
+            {
+                "value": _latex_view(
+                    fn_to_sympy(
+                        rxn.fn,
+                        origin=name,
+                        model_args=list_of_symbols(rxn.args),
+                    )
+                ),
+                "stoichiometry": stoichiometries_to_sympy(name, rxn.stoichiometry),
+                "unit": _latex_view(unit) if (unit := rxn.unit) is not None else "",
+                # "source"
+            }
+            for name, rxn in self._reactions.items()
+        ]
+        return TableView(data=pd.DataFrame(data, index=index))
+
+    def get_raw_reactions(self, *, as_copy: bool = True) -> dict[str, Reaction]:
         """Retrieve the reactions in the model.
 
         Examples:
@@ -1072,7 +1322,9 @@ class Model:
             dict[str, Reaction]: A deep copy of the reactions dictionary.
 
         """
-        return copy.deepcopy(self._reactions)
+        if as_copy:
+            return copy.deepcopy(self._reactions)
+        return self._reactions
 
     def get_stoichiometries(
         self, variables: dict[str, float] | None = None, time: float = 0.0
@@ -1091,7 +1343,7 @@ class Model:
         """
         if (cache := self._cache) is None:
             cache = self._create_cache()
-        args = self.get_dependent(variables=variables, time=time)
+        args = self.get_args(variables=variables, time=time)
 
         stoich_by_cpds = copy.deepcopy(cache.stoich_by_cpds)
         for cpd, stoich in cache.dyn_stoich_by_cpds.items():
@@ -1121,7 +1373,7 @@ class Model:
         """
         if (cache := self._cache) is None:
             cache = self._create_cache()
-        args = self.get_dependent(variables=variables, time=time)
+        args = self.get_args(variables=variables, time=time)
 
         stoich = copy.deepcopy(cache.stoich_by_cpds[variable])
         for rxn, derived in cache.dyn_stoich_by_cpds.get(variable, {}).items():
@@ -1155,6 +1407,8 @@ class Model:
         *,
         args: list[str],
         stoichiometry: Mapping[str, float | str | Derived],
+        unit: sympy.Expr | None = None,
+        # source: str | None = None,
     ) -> Self:
         """Adds a reaction to the model.
 
@@ -1170,6 +1424,7 @@ class Model:
             fn: The function representing the reaction.
             args: A list of arguments for the reaction function.
             stoichiometry: The stoichiometry of the reaction, mapping species to their coefficients.
+            unit: Unit of the rate
 
         Returns:
             Self: The instance of the model with the added reaction.
@@ -1181,7 +1436,12 @@ class Model:
             k: Derived(fn=fns.constant, args=[v]) if isinstance(v, str) else v
             for k, v in stoichiometry.items()
         }
-        self._reactions[name] = Reaction(fn=fn, stoichiometry=stoich, args=args)
+        self._reactions[name] = Reaction(
+            fn=fn,
+            stoichiometry=stoich,
+            args=args,
+            unit=unit,
+        )
         return self
 
     def get_reaction_names(self) -> list[str]:
@@ -1205,6 +1465,7 @@ class Model:
         *,
         args: list[str] | None = None,
         stoichiometry: Mapping[str, float | Derived | str] | None = None,
+        unit: sympy.Expr | None = None,
     ) -> Self:
         """Updates the properties of an existing reaction in the model.
 
@@ -1220,6 +1481,7 @@ class Model:
             fn: The new function for the reaction. If None, the existing function is retained.
             args: The new arguments for the reaction. If None, the existing arguments are retained.
             stoichiometry: The new stoichiometry for the reaction. If None, the existing stoichiometry is retained.
+            unit: Unit of the reaction
 
         Returns:
             Self: The instance of the model with the updated reaction.
@@ -1235,6 +1497,7 @@ class Model:
             }
             rxn.stoichiometry = stoich
         rxn.args = rxn.args if args is None else args
+        rxn.unit = rxn.unit if unit is None else unit
         return self
 
     @_invalidate_cache
@@ -1285,7 +1548,14 @@ class Model:
     # Think of something like NADPH / (NADP + NADPH) as a proxy for energy state
     ##########################################################################
 
-    def add_readout(self, name: str, fn: RateFn, *, args: list[str]) -> Self:
+    def add_readout(
+        self,
+        name: str,
+        fn: RateFn,
+        *,
+        args: list[str],
+        unit: sympy.Expr | None = None,
+    ) -> Self:
         """Adds a readout to the model.
 
         Examples:
@@ -1298,13 +1568,14 @@ class Model:
             name: The name of the readout.
             fn: The function to be used for the readout.
             args: The list of arguments for the function.
+            unit: Unit of the readout
 
         Returns:
             Self: The instance of the model with the added readout.
 
         """
         self._insert_id(name=name, ctx="readout")
-        self._readouts[name] = Readout(fn=fn, args=args)
+        self._readouts[name] = Readout(fn=fn, args=args, unit=unit)
         return self
 
     def get_readout_names(self) -> list[str]:
@@ -1320,6 +1591,12 @@ class Model:
         """
         return list(self._readouts)
 
+    def get_raw_readouts(self, *, as_copy: bool = True) -> dict[str, Readout]:
+        """Get copy of readouts in the model."""
+        if as_copy:
+            return copy.deepcopy(self._readouts)
+        return self._readouts
+
     def remove_readout(self, name: str) -> Self:
         """Remove a readout by its name.
 
@@ -1428,6 +1705,21 @@ class Model:
         self._surrogates.pop(name)
         return self
 
+    def get_raw_surrogates(
+        self, *, as_copy: bool = True
+    ) -> dict[str, AbstractSurrogate]:
+        """Get direct copies of model surrogates."""
+        if as_copy:
+            return copy.deepcopy(self._surrogates)
+        return self._surrogates
+
+    def get_surrogate_output_names(self) -> list[str]:
+        """Return output names by surrogates."""
+        names = []
+        for i in self._surrogates.values():
+            names.extend(i.outputs)
+        return names
+
     def get_surrogate_reaction_names(self) -> list[str]:
         """Return reaction names by surrogates."""
         names = []
@@ -1464,7 +1756,39 @@ class Model:
     # - readouts
     ##########################################################################
 
-    def _get_dependent(
+    def get_arg_names(
+        self,
+        *,
+        include_time: bool,
+        include_variables: bool,
+        include_parameters: bool,
+        include_derived_parameters: bool,
+        include_derived_variables: bool,
+        include_reactions: bool,
+        include_surrogate_outputs: bool,
+        include_readouts: bool,
+    ) -> list[str]:
+        """Get names of all kinds of model components."""
+        names = []
+        if include_time:
+            names.append("time")
+        if include_variables:
+            names.extend(self.get_variable_names())
+        if include_parameters:
+            names.extend(self.get_parameter_names())
+        if include_derived_variables:
+            names.extend(self.get_derived_variable_names())
+        if include_derived_parameters:
+            names.extend(self.get_derived_parameter_names())
+        if include_reactions:
+            names.extend(self.get_reaction_names())
+        if include_surrogate_outputs:
+            names.extend(self.get_surrogate_output_names())
+        if include_readouts:
+            names.extend(self.get_readout_names())
+        return names
+
+    def _get_args(
         self,
         variables: dict[str, float],
         time: float = 0.0,
@@ -1474,7 +1798,7 @@ class Model:
         """Generate a dictionary of model components dependent on other components.
 
         Examples:
-            >>> model._get_dependent({"x1": 1.0, "x2": 2.0}, time=0.0)
+            >>> model._get_args({"x1": 1.0, "x2": 2.0}, time=0.0)
                 {"x1": 1.0, "x2": 2.0, "k1": 0.1, "time": 0.0}
 
         Args:
@@ -1502,11 +1826,18 @@ class Model:
 
         return cast(dict[str, float], args)
 
-    def get_dependent(
+    def get_args(
         self,
         variables: dict[str, float] | None = None,
         time: float = 0.0,
         *,
+        include_time: bool = True,
+        include_variables: bool = True,
+        include_parameters: bool = True,
+        include_derived_parameters: bool = True,
+        include_derived_variables: bool = True,
+        include_reactions: bool = True,
+        include_surrogate_outputs: bool = True,
         include_readouts: bool = False,
     ) -> pd.Series:
         """Generate a pandas Series of arguments for the model.
@@ -1514,20 +1845,27 @@ class Model:
         Examples:
             # Using initial conditions
             >>> model.get_args()
-                {"x1": 1.get_dependent, "x2": 2.0, "k1": 0.1, "time": 0.0}
+                {"x1": 1.get_args, "x2": 2.0, "k1": 0.1, "time": 0.0}
 
             # With custom concentrations
-            >>> model.get_dependent({"x1": 1.0, "x2": 2.0})
+            >>> model.get_args({"x1": 1.0, "x2": 2.0})
                 {"x1": 1.0, "x2": 2.0, "k1": 0.1, "time": 0.0}
 
             # With custom concentrations and time
-            >>> model.get_dependent({"x1": 1.0, "x2": 2.0}, time=1.0)
+            >>> model.get_args({"x1": 1.0, "x2": 2.0}, time=1.0)
                 {"x1": 1.0, "x2": 2.0, "k1": 0.1, "time": 1.0}
 
         Args:
             variables: A dictionary where keys are the names of the concentrations and values are their respective float values.
-            time: The time point at which the arguments are generated (default is 0.0).
-            include_readouts: Whether to include readouts in the arguments (default is False).
+            time: The time point at which the arguments are generated.
+            include_time: Whether to include the time as an argument
+            include_variables: Whether to include variables
+            include_parameters: Whether to include parameters
+            include_derived_parameters: Whether to include derived parameters
+            include_derived_variables: Whether to include derived variables
+            include_reactions: Whether to include reactions
+            include_surrogate_outputs: Whether to include surrogate outputs
+            include_readouts: Whether to include readouts
 
         Returns:
             A pandas Series containing the generated arguments with float dtype.
@@ -1535,111 +1873,60 @@ class Model:
         """
         if (cache := self._cache) is None:
             cache = self._create_cache()
-
-        args = self._get_dependent(
+        raw = self._get_args(
             variables=self.get_initial_conditions() if variables is None else variables,
             time=time,
             cache=cache,
         )
-
         if include_readouts:
             for name, ro in self._readouts.items():  # FIXME: order?
-                ro.calculate_inpl(name, args)
-
-        return pd.Series(args, dtype=float)
+                ro.calculate_inpl(name, raw)
+        args = pd.Series(raw, dtype=float)
+        return args.loc[
+            self.get_arg_names(
+                include_time=include_time,
+                include_variables=include_variables,
+                include_parameters=include_parameters,
+                include_derived_parameters=include_derived_parameters,
+                include_derived_variables=include_derived_variables,
+                include_reactions=include_reactions,
+                include_surrogate_outputs=include_surrogate_outputs,
+                include_readouts=include_readouts,
+            )
+        ]
 
-    def get_dependent_time_course(
+    def _get_args_time_course(
         self,
-        variables: pd.DataFrame,
         *,
-        include_readouts: bool = False,
-    ) -> pd.DataFrame:
-        """Generate a DataFrame containing time course arguments for model evaluation.
-
-        Examples:
-            >>> model.get_dependent_time_course(
-            ...     pd.DataFrame({"x1": [1.0, 2.0], "x2": [2.0, 3.0]}
-            ... )
-                pd.DataFrame({
-                    "x1": [1.0, 2.0],
-                    "x2": [2.0, 3.0],
-                    "k1": [0.1, 0.1],
-                    "time": [0.0, 1.0]},
-                )
-
-        Args:
-            variables: A DataFrame containing concentration data with time as the index.
-            include_readouts: If True, include readout variables in the resulting DataFrame.
-
-        Returns:
-            A DataFrame containing the combined concentration data, parameter values,
-            derived variables, and optionally readout variables, with time as an additional column.
+        variables: pd.DataFrame,
+        include_readouts: bool,
+    ) -> dict[float, dict[str, float]]:
+        if (cache := self._cache) is None:
+            cache = self._create_cache()
 
-        """
-        args = {
-            time: self.get_dependent(
+        args_by_time = {}
+        for time, values in variables.iterrows():
+            args = self._get_args(
                 variables=values.to_dict(),
                 time=cast(float, time),
-                include_readouts=include_readouts,
+                cache=cache,
             )
-            for time, values in variables.iterrows()
-        }
-
-        return pd.DataFrame(args, dtype=float).T
-
-    ##########################################################################
-    # Get args
-    ##########################################################################
-
-    def get_args(
-        self,
-        variables: dict[str, float] | None = None,
-        time: float = 0.0,
-        *,
-        include_derived: bool = True,
-        include_readouts: bool = False,
-    ) -> pd.Series:
-        """Generate a pandas Series of arguments for the model.
-
-        Examples:
-            # Using initial conditions
-            >>> model.get_args()
-                {"x1": 1.0, "x2": 2.0, "k1": 0.1, "time": 0.0}
-
-            # With custom concentrations
-            >>> model.get_args({"x1": 1.0, "x2": 2.0})
-                {"x1": 1.0, "x2": 2.0, "k1": 0.1, "time": 0.0}
-
-            # With custom concentrations and time
-            >>> model.get_args({"x1": 1.0, "x2": 2.0}, time=1.0)
-                {"x1": 1.0, "x2": 2.0, "k1": 0.1, "time": 1.0}
-
-        Args:
-            variables: A dictionary where keys are the names of the concentrations and values are their respective float values.
-            time: The time point at which the arguments are generated.
-            include_derived: Whether to include derived variables in the arguments.
-            include_readouts: Whether to include readouts in the arguments.
-
-        Returns:
-            A pandas Series containing the generated arguments with float dtype.
-
-        """
-        names = self.get_variable_names()
-        if include_derived:
-            names.extend(self.get_derived_variable_names())
-        if include_readouts:
-            names.extend(self._readouts)
-
-        args = self.get_dependent(
-            variables=variables, time=time, include_readouts=include_readouts
-        )
-        return args.loc[names]
+            if include_readouts:
+                for name, ro in self._readouts.items():  # FIXME: order?
+                    ro.calculate_inpl(name, args)
+            args_by_time[time] = args
+        return args_by_time
 
     def get_args_time_course(
         self,
         variables: pd.DataFrame,
         *,
-        include_derived: bool = True,
+        include_variables: bool = True,
+        include_parameters: bool = True,
+        include_derived_parameters: bool = True,
+        include_derived_variables: bool = True,
+        include_reactions: bool = True,
+        include_surrogate_outputs: bool = True,
         include_readouts: bool = False,
     ) -> pd.DataFrame:
         """Generate a DataFrame containing time course arguments for model evaluation.
@@ -1657,22 +1944,40 @@ class Model:
 
         Args:
             variables: A DataFrame containing concentration data with time as the index.
-            include_derived: Whether to include derived variables in the arguments.
-            include_readouts: If True, include readout variables in the resulting DataFrame.
+            include_variables: Whether to include variables
+            include_parameters: Whether to include parameters
+            include_derived_parameters: Whether to include derived parameters
+            include_derived_variables: Whether to include derived variables
+            include_reactions: Whether to include reactions
+            include_surrogate_outputs: Whether to include surrogate outputs
+            include_readouts: Whether to include readouts
 
         Returns:
             A DataFrame containing the combined concentration data, parameter values,
             derived variables, and optionally readout variables, with time as an additional column.
 
         """
-        names = self.get_variable_names()
-        if include_derived:
-            names.extend(self.get_derived_variable_names())
-
-        args = self.get_dependent_time_course(
-            variables=variables, include_readouts=include_readouts
-        )
-        return args.loc[:, names]
+        args = pd.DataFrame(
+            self._get_args_time_course(
+                variables=variables,
+                include_readouts=include_readouts,
+            ),
+            dtype=float,
+        ).T
+
+        return args.loc[
+            :,
+            self.get_arg_names(
+                include_time=False,
+                include_variables=include_variables,
+                include_parameters=include_parameters,
+                include_derived_parameters=include_derived_parameters,
+                include_derived_variables=include_derived_variables,
+                include_reactions=include_reactions,
+                include_surrogate_outputs=include_surrogate_outputs,
+                include_readouts=include_readouts,
+            ),
+        ]
 
     ##########################################################################
     # Get fluxes
@@ -1707,10 +2012,9 @@ class Model:
 
         """
         names = self.get_reaction_names()
-        for surrogate in self._surrogates.values():
-            names.extend(surrogate.stoichiometries)
+        names.extend(self.get_surrogate_reaction_names())
 
-        args = self.get_dependent(
+        args = self.get_args(
             variables=variables,
             time=time,
             include_readouts=False,
@@ -1739,11 +2043,11 @@ class Model:
                           the index of the input arguments.
 
         """
-        names = self.get_reaction_names()
+        names: list[str] = self.get_reaction_names()
         for surrogate in self._surrogates.values():
             names.extend(surrogate.stoichiometries)
 
-        variables = self.get_dependent_time_course(
+        variables = self.get_args_time_course(
             variables=variables,
             include_readouts=False,
         )
@@ -1781,7 +2085,7 @@ class Model:
                 strict=True,
             )
         )
-        dependent: dict[str, float] = self._get_dependent(
+        dependent: dict[str, float] = self._get_args(
             variables=vars_d,
             time=time,
             cache=cache,
@@ -1829,7 +2133,7 @@ class Model:
         if (cache := self._cache) is None:
             cache = self._create_cache()
         var_names = self.get_variable_names()
-        dependent = self._get_dependent(
+        dependent = self._get_args(
             variables=self.get_initial_conditions() if variables is None else variables,
             time=time,
             cache=cache,