mxlpy 0.18.0__py3-none-any.whl → 0.20.0__py3-none-any.whl

mxlpy/types.py

@@ -17,9 +17,13 @@ Classes:
 from __future__ import annotations
 
 from abc import abstractmethod
+from collections.abc import Callable, Iterable, Iterator, Mapping
 from dataclasses import dataclass, field
+from typing import TYPE_CHECKING, Any, ParamSpec, Protocol, TypeVar, cast
 
+import numpy as np
 import pandas as pd
+from numpy.typing import NDArray
 
 __all__ = [
     "AbstractEstimator",
@@ -27,7 +31,6 @@ __all__ = [
     "Array",
     "ArrayLike",
     "Derived",
-    "Float",
     "IntegratorProtocol",
     "IntegratorType",
     "McSteadyStates",
@@ -46,15 +49,7 @@ __all__ = [
     "unwrap2",
 ]
 
-from collections.abc import Callable, Iterator, Mapping
-from typing import TYPE_CHECKING, Any, ParamSpec, Protocol, TypeVar, cast
-
-import numpy as np
-import numpy.typing as npt
-from numpy.typing import NDArray
-
-type Float = npt.NDArray[np.floating[Any]] | float
-type RateFn = Callable[..., Float]
+type RateFn = Callable[..., float]
 type Array = NDArray[np.floating[Any]]
 type ArrayLike = NDArray[np.floating[Any]] | list[float]
 
@@ -159,7 +154,7 @@ class Derived:
     fn: RateFn
     args: list[str]
 
-    def calculate(self, dependent: dict[str, float]) -> float:
+    def calculate(self, dependent: dict[str, Any]) -> float:
         """Calculate the derived value.
 
         Args:
@@ -171,7 +166,7 @@ class Derived:
         """
         return cast(float, self.fn(*(dependent[arg] for arg in self.args)))
 
-    def calculate_inpl(self, name: str, dependent: dict[str, float]) -> None:
+    def calculate_inpl(self, name: str, dependent: dict[str, Any]) -> None:
         """Calculate the derived value in place.
 
         Args:
@@ -181,20 +176,6 @@ class Derived:
         """
         dependent[name] = cast(float, self.fn(*(dependent[arg] for arg in self.args)))
 
-    def calculate_inpl_time_course(self, name: str, dependent: pd.DataFrame) -> None:
-        """Calculate the derived value in place.
-
-        Args:
-            name: Name of the derived variable.
-            dependent: Dictionary of dependent variables.
-
-        """
-        try:
-            dependent[name] = self.fn(*dependent.loc[:, self.args].to_numpy().T)
-        except ValueError:  # e.g. numpy.where
-            sub = dependent.loc[:, self.args].to_numpy()
-            dependent[name] = [self.fn(*row) for row in sub]
-
 
 @dataclass(kw_only=True, slots=True)
 class Readout:
@@ -203,7 +184,7 @@ class Readout:
     fn: RateFn
     args: list[str]
 
-    def calculate(self, dependent: dict[str, float]) -> float:
+    def calculate(self, dependent: dict[str, Any]) -> float:
         """Calculate the derived value.
 
         Args:
@@ -215,8 +196,8 @@ class Readout:
         """
         return cast(float, self.fn(*(dependent[arg] for arg in self.args)))
 
-    def calculate_inpl(self, name: str, dependent: dict[str, float]) -> None:
-        """Calculate the readout in place.
+    def calculate_inpl(self, name: str, dependent: dict[str, Any]) -> None:
+        """Calculate the reaction in place.
 
         Args:
             name: Name of the derived variable.
@@ -225,20 +206,6 @@ class Readout:
         """
         dependent[name] = cast(float, self.fn(*(dependent[arg] for arg in self.args)))
 
-    def calculate_inpl_time_course(self, name: str, dependent: pd.DataFrame) -> None:
-        """Calculate the derived value in place.
-
-        Args:
-            name: Name of the derived variable.
-            dependent: Dictionary of dependent variables.
-
-        """
-        try:
-            dependent[name] = self.fn(*dependent.loc[:, self.args].to_numpy().T)
-        except ValueError:  # e.g. numpy.where
-            sub = dependent.loc[:, self.args].to_numpy()
-            dependent[name] = [self.fn(*row) for row in sub]
-
 
 @dataclass(kw_only=True, slots=True)
 class Reaction:
@@ -255,7 +222,7 @@ 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:
+    def calculate(self, dependent: dict[str, Any]) -> float:
         """Calculate the derived value.
 
         Args:
@@ -267,7 +234,7 @@ class Reaction:
         """
         return cast(float, self.fn(*(dependent[arg] for arg in self.args)))
 
-    def calculate_inpl(self, name: str, dependent: dict[str, float]) -> None:
+    def calculate_inpl(self, name: str, dependent: dict[str, Any]) -> None:
         """Calculate the reaction in place.
 
         Args:
@@ -277,19 +244,57 @@ class Reaction:
         """
         dependent[name] = cast(float, self.fn(*(dependent[arg] for arg in self.args)))
 
-    def calculate_inpl_time_course(self, name: str, dependent: pd.DataFrame) -> None:
-        """Calculate the derived value in place.
 
-        Args:
-            name: Name of the derived variable.
-            dependent: Dictionary of dependent variables.
+@dataclass(kw_only=True)
+class AbstractSurrogate:
+    """Abstract base class for surrogate models.
 
-        """
-        try:
-            dependent[name] = self.fn(*dependent.loc[:, self.args].to_numpy().T)
-        except ValueError:  # e.g. numpy.where
-            sub = dependent.loc[:, self.args].to_numpy()
-            dependent[name] = [self.fn(*row) for row in sub]
+    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.
+
+    """
+
+    args: list[str]
+    outputs: list[str]
+    stoichiometries: dict[str, dict[str, float | Derived]] = field(default_factory=dict)
+
+    @abstractmethod
+    def predict(
+        self, args: dict[str, float | pd.Series | pd.DataFrame]
+    ) -> dict[str, float]:
+        """Predict outputs based on input data."""
+
+    def calculate_inpl(
+        self,
+        name: str,  # noqa: ARG002, for API compatibility
+        args: dict[str, float | pd.Series | pd.DataFrame],
+    ) -> None:
+        """Predict outputs based on input data."""
+        args |= self.predict(args=args)
+
+
+@dataclass(kw_only=True)
+class MockSurrogate(AbstractSurrogate):
+    """Mock surrogate model for testing purposes."""
+
+    fn: Callable[..., Iterable[float]]
+
+    def predict(
+        self,
+        args: dict[str, float | pd.Series | pd.DataFrame],
+    ) -> dict[str, float]:
+        """Predict outputs based on input data."""
+        return dict(
+            zip(
+                self.outputs,
+                self.fn(*(args[i] for i in self.args)),
+                strict=True,
+            )
+        )  # type: ignore
 
 
 @dataclass(kw_only=True, slots=True)
@@ -429,70 +434,6 @@ class ProtocolByPars:
         return cast(pd.DataFrame, mean.unstack().T)
 
 
-@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.
-
-    """
-
-    args: list[str]
-    outputs: list[str]
-    stoichiometries: dict[str, dict[str, float]] = field(default_factory=dict)
-
-    @abstractmethod
-    def predict_raw(self, y: np.ndarray) -> np.ndarray:
-        """Predict outputs based on input data."""
-
-    def predict(self, y: np.ndarray) -> dict[str, float]:
-        """Predict outputs based on input data."""
-        return dict(
-            zip(
-                self.outputs,
-                self.predict_raw(y),
-                strict=True,
-            )
-        )
-
-    def calculate_inpl(
-        self,
-        name: str,  # noqa: ARG002, for API compatibility
-        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,
-        name: str,  # noqa: ARG002, for API compatibility
-        args: pd.DataFrame,
-    ) -> None:
-        """Predict outputs based on input data."""
-        args[self.outputs] = 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(
-        self,
-        y: np.ndarray,
-    ) -> dict[str, float]:
-        """Predict outputs based on input data."""
-        return dict(zip(self.outputs, y, strict=True))
-
-
 @dataclass(kw_only=True)
 class AbstractEstimator:
     """Abstract class for parameter estimation using neural networks."""

{mxlpy-0.18.0.dist-info → mxlpy-0.20.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mxlpy
-Version: 0.18.0
+Version: 0.20.0
 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>
@@ -24,6 +24,7 @@ Classifier: Topic :: Software Development
 Requires-Python: >=3.12
 Requires-Dist: dill>=0.3.9
 Requires-Dist: latexify-py>=0.4.4
+Requires-Dist: lazy-import>=0.2.2
 Requires-Dist: matplotlib>=3.9.2
 Requires-Dist: mike>=2.1.3
 Requires-Dist: more-itertools>=10.5.0
@@ -41,29 +42,21 @@ Requires-Dist: tabulate>=0.9.0
 Requires-Dist: toml>=0.10.2
 Requires-Dist: tqdm>=4.66.6
 Requires-Dist: typing-extensions>=4.12.2
-Provides-Extra: dev
-Requires-Dist: coverage>=7.6.4; extra == 'dev'
-Requires-Dist: jupyter>=1.1.1; extra == 'dev'
-Requires-Dist: mkdocs-jupyter>=0.25.1; extra == 'dev'
-Requires-Dist: mkdocs-material>=9.5.42; extra == 'dev'
-Requires-Dist: mkdocs>=1.6.1; extra == 'dev'
-Requires-Dist: pre-commit>=4.0.1; extra == 'dev'
-Requires-Dist: pyright>=1.1.387; extra == 'dev'
-Requires-Dist: pytest-cov>=5.0.0; extra == 'dev'
-Requires-Dist: pytest>=8.3.3; extra == 'dev'
-Requires-Dist: requests>=2.32.3; extra == 'dev'
-Requires-Dist: ruff>=0.7.1; extra == 'dev'
-Requires-Dist: ssort>=0.13.0; extra == 'dev'
-Requires-Dist: toml-sort<0.24,>=0.23.1; extra == 'dev'
+Provides-Extra: keras
+Requires-Dist: keras>=3.9.2; extra == 'keras'
+Provides-Extra: tensorflow
+Requires-Dist: tensorflow>=2.19.0; extra == 'tensorflow'
 Provides-Extra: torch
 Requires-Dist: torch>=2.5.1; extra == 'torch'
 Description-Content-Type: text/markdown
 
 <p align="center">
-    <img src="docs/assets/logo-diagram.png" width="600px" alt='mxlpy-logo'>
+    <img src="https://raw.githubusercontent.com/Computational-Biology-Aachen/MxlPy/refs/heads/main/docs/assets/logo-diagram.png" width="600px" alt='mxlpy-logo'>
 </p>
 
-# mxlpy
+
+
+# MxlPy
 
 [![pypi](https://img.shields.io/pypi/v/mxlpy.svg)](https://pypi.python.org/pypi/mxlpy)
 [![docs][docs-badge]][docs]
@@ -78,14 +71,26 @@ Description-Content-Type: text/markdown
 
 ## Installation
 
-You can install mxlpy using pip: `pip install mxlpy`
+You can install mxlpy using pip: `pip install mxlpy`.
+
+Due to their sizes, the machine learning packages are optional dependencies. You can install them using
+
+```shell
+# One of them respectively
+pip install mxlpy[torch]
+pip install mxlpy[tensorflow]
+pip install mxlpy[keras]
+
+# together
+pip install mxlpy[torch, tensorflow, keras]
+```
 
 If you want access to the sundials solver suite via the [assimulo](https://jmodelica.org/assimulo/) package, we recommend setting up a virtual environment via [pixi](https://pixi.sh/) or [mamba / conda](https://mamba.readthedocs.io/en/latest/) using the [conda-forge](https://conda-forge.org/) channel.
 
 ```bash
 pixi init
 pixi add python assimulo
-pixi add --pypi mxlpy[torch]
+pixi add --pypi mxlpy
 ```
 
 ## How to cite
@@ -103,7 +108,7 @@ You have two choices here, using `uv` (pypi-only) or using `pixi` (conda-forge,
 ### uv
 
 - Install `uv` as described in [the docs](https://docs.astral.sh/uv/getting-started/installation/).
-- Run `uv sync --extra dev --extra torch` to install dependencies locally
+- Run `uv sync --all-extras --all-groups` to install dependencies locally
 
 ### pixi
 
@@ -111,7 +116,3 @@ You have two choices here, using `uv` (pypi-only) or using `pixi` (conda-forge,
 - Run `pixi install --frozen`
 
 
-## Notes
-
-- `uv add $package`
-- `uv add --optional dev $package`

mxlpy-0.20.0.dist-info/RECORD

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mxlpy-0.18.0.dist-info/RECORD

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