modelbase2 0.5.0__py3-none-any.whl → 0.7.0__py3-none-any.whl

modelbase2/surrogates/_poly.py

@@ -1,14 +1,18 @@
 from collections.abc import Iterable
 from dataclasses import dataclass
+from typing import Literal
 
 import numpy as np
 import pandas as pd
 from numpy import polynomial
-from typing import Union, Literal
 
 from modelbase2.types import AbstractSurrogate, ArrayLike
 
-__all__ = ["PolySurrogate", "PolynomialExpansion", "train_polynomial_surrogate"]
+__all__ = [
+    "PolySurrogate",
+    "PolynomialExpansion",
+    "train_polynomial_surrogate",
+]
 
 # define custom type
 PolynomialExpansion = (

modelbase2/surrogates/_torch.py

@@ -160,7 +160,7 @@ def train_torch_surrogate(
     if approximator is None:
         approximator = MLP(
             n_inputs=len(features.columns),
-            layers=[50, 50, len(targets.columns)],
+            neurons_per_layer=[50, 50, len(targets.columns)],
         ).to(device)
 
     optimizer = optimimzer_cls(approximator.parameters())

modelbase2/types.py

@@ -127,13 +127,13 @@ class IntegratorProtocol(Protocol):
         *,
         t_end: float,
         steps: int | None = None,
-    ) -> tuple[ArrayLike | None, ArrayLike | None]:
+    ) -> tuple[Array | None, ArrayLike | None]:
         """Integrate the system."""
         ...
 
     def integrate_time_course(
         self, *, time_points: ArrayLike
-    ) -> tuple[ArrayLike | None, ArrayLike | None]:
+    ) -> tuple[Array | None, ArrayLike | None]:
         """Integrate the system over a time course."""
         ...
 
@@ -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))
+        )
 
-@dataclass(slots=True)
+    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(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 +449,26 @@ 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:
+        """Predict outputs based on input data."""
+        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 → modelbase2-0.7.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: modelbase2
-Version: 0.5.0
+Version: 0.7.0
 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>
@@ -60,6 +60,16 @@ Description-Content-Type: text/markdown
 
 # modelbase
 
+[![pypi](https://img.shields.io/pypi/v/modelbase2.svg)](https://pypi.python.org/pypi/modelbase2)
+[![docs][docs-badge]][docs]
+![License](https://img.shields.io/badge/license-GPL--3.0-blue?style=flat-square)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+[![security: bandit](https://img.shields.io/badge/security-bandit-yellow.svg)](https://github.com/PyCQA/bandit)
+[![Downloads](https://pepy.tech/badge/modelbase2)](https://pepy.tech/project/modelbase2)
+
+[docs-badge]: https://img.shields.io/badge/docs-main-green.svg?style=flat-square
+[docs]: https://computational-biology-aachen.github.io/modelbase2/
+
 ## Installation
 
 You can install modelbase using pip: `pip install modelbase2`

modelbase2-0.7.0.dist-info/RECORD

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