modelbase2 0.5.0__py3-none-any.whl → 0.6.0__py3-none-any.whl

modelbase2/simulator.py

@@ -69,7 +69,7 @@ class Simulator:
         y0: Initial conditions for the simulation.
         integrator: Integrator protocol to use for the simulation.
         concs: List of DataFrames containing concentration results.
-        args: List of DataFrames containing argument values.
+        dependent: List of DataFrames containing argument values.
         simulation_parameters: List of dictionaries containing simulation parameters.
 
     """
@@ -78,7 +78,7 @@ class Simulator:
     y0: ArrayLike
     integrator: IntegratorProtocol
     concs: list[pd.DataFrame] | None
-    args: list[pd.DataFrame] | None
+    dependent: list[pd.DataFrame] | None
     simulation_parameters: list[dict[str, float]] | None
 
     def __init__(
@@ -110,13 +110,10 @@ class Simulator:
 
         self.integrator = integrator(self.model, self.y0)
         self.concs = None
-        self.args = None
         self.simulation_parameters = None
 
         if test_run:
             y0 = dict(zip(model.get_variable_names(), self.y0, strict=True))
-            self.model.get_full_concs(y0, 0)
-            self.model.get_fluxes(y0, 0)
             self.model.get_right_hand_side(y0, 0)
 
     def _save_simulation_results(
@@ -146,7 +143,7 @@ class Simulator:
     def clear_results(self) -> None:
         """Clear simulation results."""
         self.concs = None
-        self.args = None
+        self.dependent = None
         self.simulation_parameters = None
         if self.integrator is not None:
             self.integrator.reset()
@@ -173,7 +170,7 @@ class Simulator:
             return
 
         # NOTE: IMPORTANT!
-        # model._get_rhs sorts the return array by model.get_compounds()
+        # model._get_rhs sorts the return array by model.get_variable_names()
         # Do NOT change this ordering
         results_df = pd.DataFrame(
             results,
@@ -294,24 +291,24 @@ class Simulator:
                 break
         return self
 
-    def _get_args_vectorised(
+    def _get_dependent_vectorised(
         self,
         concs: list[pd.DataFrame],
         params: list[dict[str, float]],
         *,
         include_readouts: bool = True,
     ) -> list[pd.DataFrame]:
-        args: list[pd.DataFrame] = []
+        dependent: list[pd.DataFrame] = []
 
         for res, p in zip(concs, params, strict=True):
             self.model.update_parameters(p)
-            args.append(
-                self.model.get_args_time_course(
+            dependent.append(
+                self.model.get_dependent_time_course(
                     concs=res,
                     include_readouts=include_readouts,
                 )
             )
-        return args
+        return dependent
 
     @overload
     def get_concs(  # type: ignore
@@ -367,6 +364,16 @@ class Simulator:
 
         return results
 
+    # Get results depending on the raw results
+
+    def _get_dependent(self) -> list[pd.DataFrame] | None:
+        if (concs := self.concs) is None:
+            return None
+        if (params := self.simulation_parameters) is None:
+            return None
+
+        return self._get_dependent_vectorised(concs, params)
+
     @overload
     def get_full_concs(  # type: ignore
         self,
@@ -374,6 +381,7 @@ class Simulator:
         normalise: float | ArrayLike | None = None,
         concatenated: Literal[False],
         include_readouts: bool = True,
+        dependent: list[pd.DataFrame] | None = None,
     ) -> list[pd.DataFrame] | None: ...
 
     @overload
@@ -383,6 +391,7 @@ class Simulator:
         normalise: float | ArrayLike | None = None,
         concatenated: Literal[True],
         include_readouts: bool = True,
+        dependent: list[pd.DataFrame] | None = None,
     ) -> pd.DataFrame | None: ...
 
     @overload
@@ -392,6 +401,7 @@ class Simulator:
         normalise: float | ArrayLike | None = None,
         concatenated: bool = True,
         include_readouts: bool = True,
+        dependent: list[pd.DataFrame] | None = None,
     ) -> pd.DataFrame | None: ...
 
     def get_full_concs(
@@ -400,6 +410,7 @@ class Simulator:
         normalise: float | ArrayLike | None = None,
         concatenated: bool = True,
         include_readouts: bool = True,
+        dependent: list[pd.DataFrame] | None = None,
     ) -> pd.DataFrame | list[pd.DataFrame] | None:
         """Get the full concentration results, including derived quantities.
 
@@ -417,23 +428,25 @@ class Simulator:
             return None
         if (params := self.simulation_parameters) is None:
             return None
-        if (args := self.args) is None:
-            args = self._get_args_vectorised(concs, params)
+        if dependent is None:
+            dependent = self._get_dependent_vectorised(concs, params)
 
+        # Filter to full concs
         names = (
             self.model.get_variable_names() + self.model.get_derived_variable_names()
         )
         if include_readouts:
             names.extend(self.model.get_readout_names())
-        full_concs = [i.loc[:, names] for i in args]
+        dependent = [i.loc[:, names] for i in dependent]
+
         if normalise is not None:
-            full_concs = _normalise_split_results(
-                results=full_concs,
+            dependent = _normalise_split_results(
+                results=dependent,
                 normalise=normalise,
             )
         if concatenated:
-            return pd.concat(full_concs, axis=0)
-        return full_concs
+            return pd.concat(dependent, axis=0)
+        return dependent
 
     @overload
     def get_fluxes(  # type: ignore
@@ -441,6 +454,7 @@ class Simulator:
         *,
         normalise: float | ArrayLike | None = None,
         concatenated: Literal[False],
+        dependent: list[pd.DataFrame] | None = None,
     ) -> list[pd.DataFrame] | None: ...
 
     @overload
@@ -449,6 +463,7 @@ class Simulator:
         *,
         normalise: float | ArrayLike | None = None,
         concatenated: Literal[True],
+        dependent: list[pd.DataFrame] | None = None,
     ) -> pd.DataFrame | None: ...
 
     @overload
@@ -457,6 +472,7 @@ class Simulator:
         *,
         normalise: float | ArrayLike | None = None,
         concatenated: bool = True,
+        dependent: list[pd.DataFrame] | None = None,
     ) -> pd.DataFrame | None: ...
 
     def get_fluxes(
@@ -464,6 +480,7 @@ class Simulator:
         *,
         normalise: float | ArrayLike | None = None,
         concatenated: bool = True,
+        dependent: list[pd.DataFrame] | None = None,
     ) -> pd.DataFrame | list[pd.DataFrame] | None:
         """Get the flux results.
 
@@ -482,22 +499,20 @@ class Simulator:
             return None
         if (params := self.simulation_parameters) is None:
             return None
-        if (args := self.args) is None:
-            args = self._get_args_vectorised(concs, params)
-
-        fluxes: list[pd.DataFrame] = []
-        for y, p in zip(args, params, strict=True):
-            self.model.update_parameters(p)
-            fluxes.append(self.model.get_fluxes_time_course(args=y))
+        if dependent is None:
+            dependent = self._get_dependent_vectorised(concs, params)
 
+        # Filter to fluxes
+        names = self.model.get_reaction_names()
+        dependent = [i.loc[:, names] for i in dependent]
         if normalise is not None:
-            fluxes = _normalise_split_results(
-                results=fluxes,
+            dependent = _normalise_split_results(
+                results=dependent,
                 normalise=normalise,
             )
         if concatenated:
-            return pd.concat(fluxes, axis=0)
-        return fluxes
+            return pd.concat(dependent, axis=0)
+        return dependent
 
     def get_concs_and_fluxes(self) -> tuple[pd.DataFrame | None, pd.DataFrame | None]:
         """Get the concentrations and fluxes.
@@ -511,7 +526,14 @@ class Simulator:
             tuple[pd.DataFrame, pd.DataFrame]: Tuple of concentrations and fluxes.
 
         """
-        return self.get_concs(), self.get_fluxes()
+        if (concs := self.concs) is None:
+            return None, None
+        if (params := self.simulation_parameters) is None:
+            return None, None
+
+        dependent = self._get_dependent_vectorised(concs, params)
+
+        return self.get_concs(), self.get_fluxes(dependent=dependent)
 
     def get_full_concs_and_fluxes(
         self,
@@ -530,9 +552,15 @@ class Simulator:
             Full concentrations and fluxes
 
         """
+        if (concs := self.concs) is None:
+            return None, None
+        if (params := self.simulation_parameters) is None:
+            return None, None
+        dependent = self._get_dependent_vectorised(concs, params)
+
         return (
-            self.get_full_concs(include_readouts=include_readouts),
-            self.get_fluxes(),
+            self.get_full_concs(include_readouts=include_readouts, dependent=dependent),
+            self.get_fluxes(dependent=dependent),
         )
 
     def get_results(self) -> pd.DataFrame | None:

modelbase2/surrogates.py

@@ -16,7 +16,6 @@ Functions:
 
 from __future__ import annotations
 
-from abc import abstractmethod
 from dataclasses import dataclass
 from pathlib import Path
 from typing import TYPE_CHECKING
@@ -29,6 +28,7 @@ from torch import nn
 from torch.optim.adam import Adam
 
 from modelbase2.parallel import Cache
+from modelbase2.types import AbstractSurrogate
 
 if TYPE_CHECKING:
     from collections.abc import Callable
@@ -36,11 +36,9 @@ if TYPE_CHECKING:
     from torch.optim.optimizer import ParamsT
 
 __all__ = [
-    "AbstractSurrogate",
     "Approximator",
     "DefaultCache",
     "DefaultDevice",
-    "MockSurrogate",
     "TorchSurrogate",
     "train_torch_surrogate",
 ]
@@ -50,39 +48,6 @@ DefaultDevice = torch.device("cpu")
 DefaultCache = Cache(Path(".cache"))
 
 
-@dataclass(kw_only=True)
-class AbstractSurrogate:
-    """Abstract base class for surrogate models.
-
-    Attributes:
-        inputs: List of input variable names.
-        stoichiometries: Dictionary mapping reaction names to stoichiometries.
-
-    Methods:
-        predict: Abstract method to predict outputs based on input data.
-
-    """
-
-    inputs: list[str]
-    stoichiometries: dict[str, dict[str, float]]
-
-    @abstractmethod
-    def predict(self, y: np.ndarray) -> dict[str, float]:
-        """Predict outputs based on input data."""
-
-
-@dataclass(kw_only=True)
-class MockSurrogate(AbstractSurrogate):
-    """Mock surrogate model for testing purposes."""
-
-    def predict(
-        self,
-        y: np.ndarray,
-    ) -> dict[str, float]:
-        """Predict outputs based on input data."""
-        return dict(zip(self.stoichiometries, y, strict=True))
-
-
 @dataclass(kw_only=True)
 class TorchSurrogate(AbstractSurrogate):
     """Surrogate model using PyTorch.
@@ -316,7 +281,7 @@ def train_torch_surrogate(
         )
     surrogate = TorchSurrogate(
         model=approximator,
-        inputs=surrogate_inputs,
+        args=surrogate_inputs,
         stoichiometries=surrogate_stoichiometries,
     )
     return surrogate, losses

modelbase2/types.py

@@ -147,31 +147,96 @@ class IntegratorProtocol(Protocol):
         ...
 
 
-@dataclass(slots=True)
+@dataclass(kw_only=True, slots=True)
 class Derived:
     """Container for a derived value."""
 
+    name: str
     fn: RateFn
     args: list[str]
-    math: str | None = None
 
+    def calculate(self, dependent: dict[str, float]) -> float:
+        """Calculate the derived value.
 
-@dataclass(slots=True)
+        Args:
+            dependent: Dictionary of dependent variables.
+
+        Returns:
+            The calculated derived value.
+
+        """
+        return cast(float, self.fn(*(dependent[arg] for arg in self.args)))
+
+    def calculate_inpl(self, dependent: dict[str, float]) -> None:
+        """Calculate the derived value in place.
+
+        Args:
+            dependent: Dictionary of dependent variables.
+
+        """
+        dependent[self.name] = cast(
+            float, self.fn(*(dependent[arg] for arg in self.args))
+        )
+
+    def calculate_inpl_time_course(self, dependent: pd.DataFrame) -> None:
+        """Calculate the derived value in place.
+
+        Args:
+            dependent: Dictionary of dependent variables.
+
+        """
+        dependent[self.name] = self.fn(*dependent.loc[:, self.args].to_numpy().T)
+
+
+@dataclass(kw_only=True, slots=True)
 class Readout:
     """Container for a readout."""
 
+    name: str
     fn: RateFn
     args: list[str]
 
+    def calculate(self, dependent: dict[str, float]) -> float:
+        """Calculate the derived value.
+
+        Args:
+            dependent: Dictionary of dependent variables.
+
+        Returns:
+            The calculated derived value.
+
+        """
+        return cast(float, self.fn(*(dependent[arg] for arg in self.args)))
+
+    def calculate_inpl(self, dependent: dict[str, float]) -> None:
+        """Calculate the readout in place.
+
+        Args:
+            dependent: Dictionary of dependent variables.
+
+        """
+        dependent[self.name] = cast(
+            float, self.fn(*(dependent[arg] for arg in self.args))
+        )
+
+    def calculate_inpl_time_course(self, dependent: pd.DataFrame) -> None:
+        """Calculate the derived value in place.
 
-@dataclass(slots=True)
+        Args:
+            dependent: Dictionary of dependent variables.
+
+        """
+        dependent[self.name] = self.fn(*dependent.loc[:, self.args].to_numpy().T)
+
+
+@dataclass(kw_only=True, slots=True)
 class Reaction:
     """Container for a reaction."""
 
+    name: str
     fn: RateFn
     stoichiometry: Mapping[str, float | Derived]
     args: list[str]
-    math: str | None = None
 
     def get_modifiers(self, model: Model) -> list[str]:
         """Get the modifiers of the reaction."""
@@ -180,8 +245,44 @@ class Reaction:
 
         return [k for k in self.args if k in include and k not in exclude]
 
+    def calculate(self, dependent: dict[str, float]) -> float:
+        """Calculate the derived value.
+
+        Args:
+            dependent: Dictionary of dependent variables.
+
+        Returns:
+            The calculated derived value.
+
+        """
+        return cast(float, self.fn(*(dependent[arg] for arg in self.args)))
+
+    def calculate_inpl(self, dependent: dict[str, float]) -> None:
+        """Calculate the reaction in place.
+
+        Args:
+            dependent: Dictionary of dependent variables.
+
+        """
+        dependent[self.name] = cast(
+            float, self.fn(*(dependent[arg] for arg in self.args))
+        )
+
+    def calculate_inpl_time_course(self, dependent: pd.DataFrame) -> None:
+        """Calculate the derived value in place.
+
+        Args:
+            dependent: Dictionary of dependent variables.
+
+        """
+        try:
+            dependent[self.name] = self.fn(*dependent.loc[:, self.args].to_numpy().T)
+        except ValueError:  # e.g. numpy.where
+            sub = dependent.loc[:, self.args].to_numpy()
+            dependent[self.name] = [self.fn(*row) for row in sub]
+
 
-@dataclass(slots=True)
+@dataclass(kw_only=True, slots=True)
 class ResponseCoefficients:
     """Container for response coefficients."""
 
@@ -198,7 +299,7 @@ class ResponseCoefficients:
         return pd.concat((self.concs, self.fluxes), axis=1)
 
 
-@dataclass(slots=True)
+@dataclass(kw_only=True, slots=True)
 class ResponseCoefficientsByPars:
     """Container for response coefficients by parameter."""
 
@@ -216,7 +317,7 @@ class ResponseCoefficientsByPars:
         return pd.concat((self.concs, self.fluxes), axis=1)
 
 
-@dataclass(slots=True)
+@dataclass(kw_only=True, slots=True)
 class SteadyStates:
     """Container for steady states."""
 
@@ -234,7 +335,7 @@ class SteadyStates:
         return pd.concat((self.concs, self.fluxes), axis=1)
 
 
-@dataclass(slots=True)
+@dataclass(kw_only=True, slots=True)
 class McSteadyStates:
     """Container for Monte Carlo steady states."""
 
@@ -253,7 +354,7 @@ class McSteadyStates:
         return pd.concat((self.concs, self.fluxes), axis=1)
 
 
-@dataclass(slots=True)
+@dataclass(kw_only=True, slots=True)
 class TimeCourseByPars:
     """Container for time courses by parameter."""
 
@@ -285,7 +386,7 @@ class TimeCourseByPars:
         return cast(pd.DataFrame, mean.unstack().T)
 
 
-@dataclass(slots=True)
+@dataclass(kw_only=True, slots=True)
 class ProtocolByPars:
     """Container for protocols by parameter."""
 
@@ -348,14 +449,25 @@ class AbstractSurrogate:
             )
         )
 
+    def calculate_inpl(self, args: dict[str, float]) -> None:
+        """Predict outputs based on input data."""
+        args |= self.predict(np.array([args[arg] for arg in self.args]))
+
+    def calculate_inpl_time_course(self, args: pd.DataFrame) -> None:
+        args[list(self.stoichiometries)] = pd.DataFrame(
+            [self.predict(y) for y in args.loc[:, self.args].to_numpy()],
+            index=args.index,
+            dtype=float,
+        )
+
 
 @dataclass(kw_only=True)
 class MockSurrogate(AbstractSurrogate):
     """Mock surrogate model for testing purposes."""
 
-    def predict_raw(
+    def predict(
         self,
         y: np.ndarray,
-    ) -> np.ndarray:
+    ) -> dict[str, float]:
         """Predict outputs based on input data."""
-        return y
+        return dict(zip(self.stoichiometries, y, strict=True))

{modelbase2-0.5.0.dist-info → modelbase2-0.6.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: modelbase2
-Version: 0.5.0
+Version: 0.6.0
 Summary: A package to build metabolic models
 Author-email: Marvin van Aalst <marvin.vanaalst@gmail.com>
 Maintainer-email: Marvin van Aalst <marvin.vanaalst@gmail.com>

{modelbase2-0.5.0.dist-info → modelbase2-0.6.0.dist-info}/RECORD

@@ -3,10 +3,10 @@ modelbase2/distributions.py,sha256=i456B0KYKdiGwuoVjoj3rey5lKdJmu9EVvacnfWXHGA,8
 modelbase2/fit.py,sha256=WEI2lxLhdHFr6ax5xXrrkHUTxcEhmXyBHebfHEcXwCY,8172
 modelbase2/fns.py,sha256=8JtIzPk3DAnNHz3LoJ1ukLFTjPNO1rNCeZ7VnRmJY2o,4503
 modelbase2/label_map.py,sha256=LUwcOHQWiGfBGV5XUmPM_SOwM9IyDVcQVJ11DPfVpAo,17774
-modelbase2/linear_label_map.py,sha256=gA8CHxcehgtI6ovwZ9qNUPDvxfqbO1J1kBC_mltD4TY,10225
+modelbase2/linear_label_map.py,sha256=6qs7SZIaiMcA0jRCdZXMe44lG7pBtKzYNMYSfNz2CfY,10317
 modelbase2/mc.py,sha256=zlDL7e_udpIMRhSjfFJo5AwkigD0B_3H2rQxyelBuzI,16285
 modelbase2/mca.py,sha256=nMS2VnzR2VEujCFUaj9WL82CNd-oxTb3jCHP8IlJvxA,8845
-modelbase2/model.py,sha256=d-iAu64oxVgH9QgNYhNnJnrISic_U1Z5hX6ij6eDqh0,55260
+modelbase2/model.py,sha256=3FSYqOMUqR2hkeqcqwnnEwyXK0V6cN0i-QpMR-_huoM,56730
 modelbase2/nnarchitectures.py,sha256=OA1X4UHrn7gsLuuqxK6Dhv5aiKnQflhHezYCUV-NuO8,4012
 modelbase2/npe.py,sha256=o876zHjyfJelGijSmCL0vUBfWbIhcbQyyPkwp8hZ4NA,8743
 modelbase2/parallel.py,sha256=kX4Td5YoovDwZp6kX_3cfO6QtHSS9ieJ0bMZiKs3Xv8,5002
@@ -14,33 +14,32 @@ modelbase2/parameterise.py,sha256=7VrYxrQv0visraqUthWSnWfx-cxh2evlXbszIY5031U,69
 modelbase2/paths.py,sha256=uatKXDa79uniUB2Z3dr8eBJVuUPXDI-o_bf-DqPKq1Y,1039
 modelbase2/plot.py,sha256=72Oivv-jsCF9J9U7Uli15p5SnuEHSnHRXCaRP8uUaJo,22724
 modelbase2/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-modelbase2/scan.py,sha256=PvWZA4EgNS0JVMvm87bF72hSmhvo6O2KGg4vRzxve_8,18104
+modelbase2/scan.py,sha256=q6GmI0nqLtzmHjgs-AEcK2aaj6tcw8dvzmOE79yL2Pg,18117
 modelbase2/scope.py,sha256=4twnEh8LrTmlLE-uRvubVkE3SSWejlLvtBzTCPqG3Aw,3710
-modelbase2/simulator.py,sha256=0_KXL3QUsMHtckdH4nPlzJoGNLoQaVttV7PUt2RU1m8,19823
-modelbase2/surrogates.py,sha256=Dk-YEXb-ot22W3r5Bl3rxApbCyvNdBnNCvRi_1f_NnA,9276
-modelbase2/types.py,sha256=N74pWUZDcGlSMfDkjqqwHn5dkozlqgS6Wqg-58YKdvg,9904
+modelbase2/simulator.py,sha256=3x_biwvwQmHCRs6C6R3dG5hUGwQqIgL0QQOrBR0zZQY,20986
+modelbase2/surrogates.py,sha256=1ikylwZ5LdgnFAcZDOCx_lY_xvnQHxcTX_2z-L98r0s,8387
+modelbase2/types.py,sha256=WDowHRr1YIvNNnK0clw_sBs5l2dwihT4av04Tt0jyFc,13502
 modelbase2/experimental/__init__.py,sha256=IzgcQ7MtMII7n6cg1PMp-oZm06CNVR19ax2exvb9Ny0,444
-modelbase2/experimental/_backup.py,sha256=As-L75tMQjWfkheRPk8xcroQPKDsSSejBJ2dXqPXmVo,46644
 modelbase2/experimental/codegen.py,sha256=i0soAT64oMBILGsWonoSSVkYMWOcCTY4RJ4TZoYlTos,6962
 modelbase2/experimental/diff.py,sha256=e7fjD9kqxkRUNxSevbAznd5cOlEdWJ6pj0y7Kd5KKrw,8973
 modelbase2/experimental/notes.md,sha256=YlM2biTzub6jSlx-aDZaBYsvQcGwb7NHyVAbbl2acGE,238
 modelbase2/experimental/strikepy.py,sha256=cKBs9InXR9mEPgx70Ynv0qkmAGfloksqinbpppTiC6U,19464
 modelbase2/experimental/symbolic.py,sha256=QT82TSW42RSVsvXK2WTQW1XluXnflWzrHbx6RFr_YmY,9953
-modelbase2/experimental/tex.py,sha256=q9k9NfQucUhYzNjAKkroU9XnBcfdegPK6h3DHhkfGOg,13618
+modelbase2/experimental/tex.py,sha256=48SrUEN-s2H_shHoXtimmLg_EDyCBa_vIVOXD2hlNbE,13664
 modelbase2/integrators/__init__.py,sha256=kqmV6a0TRyLGR_XqbyAI652AfptYnXAUpqbSFg0CpP8,450
 modelbase2/integrators/int_assimulo.py,sha256=VEQIZFZcEovLPy8i_jR8H8XcxBRQoRVmNzzCYzInPc0,4611
 modelbase2/integrators/int_scipy.py,sha256=-_9MS55eTc9jI7tk-3X49p-c7zrydoXaCCvDTn7Tybw,4334
 modelbase2/sbml/__init__.py,sha256=FBaQsVvrVc7QbCBXuG9tZOdSzHcqmmsaRbFx80rxrac,231
 modelbase2/sbml/_data.py,sha256=XwT1sSxn6KLTXYMbk4ORbEAEgZhQDBfoyrjMBDAoY_s,1135
 modelbase2/sbml/_export.py,sha256=9BLD3Qz86vlfDTZXwOnNOSVWq8mHrJoQjQmKJRZL_Wo,20285
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