mxlpy 0.19.0__py3-none-any.whl → 0.21.0__py3-none-any.whl

mxlpy/scan.py

@@ -15,19 +15,6 @@ Functions:
 
 from __future__ import annotations
 
-from mxlpy.integrators import DefaultIntegrator
-
-__all__ = [
-    "ProtocolWorker",
-    "SteadyStateWorker",
-    "TimeCourse",
-    "TimeCourseWorker",
-    "TimePoint",
-    "steady_state",
-    "time_course",
-    "time_course_over_protocol",
-]
-
 from dataclasses import dataclass
 from functools import partial
 from typing import TYPE_CHECKING, Protocol, Self, cast
@@ -37,12 +24,7 @@ import pandas as pd
 
 from mxlpy.parallel import Cache, parallelise
 from mxlpy.simulator import Result, Simulator
-from mxlpy.types import (
-    IntegratorType,
-    ProtocolByPars,
-    SteadyStates,
-    TimeCourseByPars,
-)
+from mxlpy.types import IntegratorType, ProtocolByPars, SteadyStates, TimeCourseByPars
 
 if TYPE_CHECKING:
     from collections.abc import Callable
@@ -51,6 +33,18 @@ if TYPE_CHECKING:
     from mxlpy.types import Array
 
 
+__all__ = [
+    "ProtocolWorker",
+    "SteadyStateWorker",
+    "TimeCourse",
+    "TimeCourseWorker",
+    "TimePoint",
+    "steady_state",
+    "time_course",
+    "time_course_over_protocol",
+]
+
+
 def _update_parameters_and_initial_conditions[T](
     pars: pd.Series,
     fn: Callable[[Model], T],
@@ -286,7 +280,8 @@ class SteadyStateWorker(Protocol):
         model: Model,
         *,
         rel_norm: bool,
-        integrator: IntegratorType,
+        integrator: IntegratorType | None,
+        y0: dict[str, float] | None,
     ) -> TimePoint:
         """Call the worker function."""
         ...
@@ -300,7 +295,8 @@ class TimeCourseWorker(Protocol):
         model: Model,
         time_points: Array,
         *,
-        integrator: IntegratorType,
+        integrator: IntegratorType | None,
+        y0: dict[str, float] | None,
     ) -> TimeCourse:
         """Call the worker function."""
         ...
@@ -314,7 +310,8 @@ class ProtocolWorker(Protocol):
         model: Model,
         protocol: pd.DataFrame,
         *,
-        integrator: IntegratorType,
+        integrator: IntegratorType | None,
+        y0: dict[str, float] | None,
         time_points_per_step: int = 10,
     ) -> TimeCourse:
         """Call the worker function."""
@@ -325,7 +322,8 @@ def _steady_state_worker(
     model: Model,
     *,
     rel_norm: bool,
-    integrator: IntegratorType,
+    integrator: IntegratorType | None,
+    y0: dict[str, float] | None,
 ) -> TimePoint:
     """Simulate the model to steady state and return concentrations and fluxes.
 
@@ -341,7 +339,7 @@ def _steady_state_worker(
     """
     try:
         res = (
-            Simulator(model, integrator=integrator)
+            Simulator(model, integrator=integrator, y0=y0)
             .simulate_to_steady_state(rel_norm=rel_norm)
             .get_result()
         )
@@ -353,7 +351,8 @@ def _steady_state_worker(
 def _time_course_worker(
     model: Model,
     time_points: Array,
-    integrator: IntegratorType,
+    y0: dict[str, float] | None,
+    integrator: IntegratorType | None,
 ) -> TimeCourse:
     """Simulate the model to steady state and return concentrations and fluxes.
 
@@ -369,7 +368,7 @@ def _time_course_worker(
     """
     try:
         res = (
-            Simulator(model, integrator=integrator)
+            Simulator(model, integrator=integrator, y0=y0)
             .simulate_time_course(time_points=time_points)
             .get_result()
         )
@@ -386,7 +385,8 @@ def _protocol_worker(
     model: Model,
     protocol: pd.DataFrame,
     *,
-    integrator: IntegratorType = DefaultIntegrator,
+    integrator: IntegratorType | None,
+    y0: dict[str, float] | None,
     time_points_per_step: int = 10,
 ) -> TimeCourse:
     """Simulate the model over a protocol and return concentrations and fluxes.
@@ -404,7 +404,7 @@ def _protocol_worker(
     """
     try:
         res = (
-            Simulator(model, integrator=integrator)
+            Simulator(model, integrator=integrator, y0=y0)
             .simulate_over_protocol(
                 protocol=protocol,
                 time_points_per_step=time_points_per_step,
@@ -435,7 +435,7 @@ def steady_state(
     rel_norm: bool = False,
     cache: Cache | None = None,
     worker: SteadyStateWorker = _steady_state_worker,
-    integrator: IntegratorType = DefaultIntegrator,
+    integrator: IntegratorType | None = None,
 ) -> SteadyStates:
     """Get steady-state results over supplied values.
 
@@ -484,6 +484,7 @@ def steady_state(
                 worker,
                 rel_norm=rel_norm,
                 integrator=integrator,
+                y0=None,
             ),
             model=model,
         ),
@@ -491,8 +492,8 @@ def steady_state(
         cache=cache,
         parallel=parallel,
     )
-    concs = pd.DataFrame({k: v.variables.T for k, v in res.items()}).T
-    fluxes = pd.DataFrame({k: v.fluxes.T for k, v in res.items()}).T
+    concs = pd.DataFrame({k: v.variables.T for k, v in res}).T
+    fluxes = pd.DataFrame({k: v.fluxes.T for k, v in res}).T
     idx = (
         pd.Index(to_scan.iloc[:, 0])
         if to_scan.shape[1] == 1
@@ -511,8 +512,8 @@ def time_course(
     y0: dict[str, float] | None = None,
     parallel: bool = True,
     cache: Cache | None = None,
+    integrator: IntegratorType | None = None,
     worker: TimeCourseWorker = _time_course_worker,
-    integrator: IntegratorType = DefaultIntegrator,
 ) -> TimeCourseByPars:
     """Get time course for each supplied parameter.
 
@@ -564,6 +565,8 @@ def time_course(
 
 
     """
+    # We update the initial conditions separately here, because `to_scan` might also
+    # contain initial conditions.
     if y0 is not None:
         model.update_variables(y0)
 
@@ -574,6 +577,7 @@ def time_course(
                 worker,
                 time_points=time_points,
                 integrator=integrator,
+                y0=None,  # See comment above
             ),
             model=model,
         ),
@@ -581,8 +585,8 @@ def time_course(
         cache=cache,
         parallel=parallel,
     )
-    concs = cast(dict, {k: v.variables for k, v in res.items()})
-    fluxes = cast(dict, {k: v.fluxes for k, v in res.items()})
+    concs = cast(dict, {k: v.variables for k, v in res})
+    fluxes = cast(dict, {k: v.fluxes for k, v in res})
     return TimeCourseByPars(
         parameters=to_scan,
         variables=pd.concat(concs, names=["n", "time"]),
@@ -600,7 +604,7 @@ def time_course_over_protocol(
     parallel: bool = True,
     cache: Cache | None = None,
     worker: ProtocolWorker = _protocol_worker,
-    integrator: IntegratorType = DefaultIntegrator,
+    integrator: IntegratorType | None = None,
 ) -> ProtocolByPars:
     """Get protocol series for each supplied parameter.
 
@@ -631,6 +635,8 @@ def time_course_over_protocol(
         TimeCourseByPars: Protocol series results for each parameter set.
 
     """
+    # We update the initial conditions separately here, because `to_scan` might also
+    # contain initial conditions.
     if y0 is not None:
         model.update_variables(y0)
 
@@ -642,6 +648,7 @@ def time_course_over_protocol(
                 protocol=protocol,
                 time_points_per_step=time_points_per_step,
                 integrator=integrator,
+                y0=None,
             ),
             model=model,
         ),
@@ -649,8 +656,8 @@ def time_course_over_protocol(
         cache=cache,
         parallel=parallel,
     )
-    concs = cast(dict, {k: v.variables for k, v in res.items()})
-    fluxes = cast(dict, {k: v.fluxes for k, v in res.items()})
+    concs = cast(dict, {k: v.variables for k, v in res})
+    fluxes = cast(dict, {k: v.fluxes for k, v in res})
     return ProtocolByPars(
         parameters=to_scan,
         protocol=protocol,

mxlpy/simulator.py

@@ -21,14 +21,17 @@ from sympy import lambdify
 from mxlpy.integrators import DefaultIntegrator
 from mxlpy.symbolic import to_symbolic_model
 
-__all__ = ["Result", "Simulator"]
-
 if TYPE_CHECKING:
     from collections.abc import Iterator
 
     from mxlpy.model import Model
     from mxlpy.types import Array, ArrayLike, IntegratorProtocol, IntegratorType
 
+__all__ = [
+    "Result",
+    "Simulator",
+]
+
 
 def _normalise_split_results(
     results: list[pd.DataFrame],
@@ -332,7 +335,7 @@ class Simulator:
         self,
         model: Model,
         y0: dict[str, float] | None = None,
-        integrator: IntegratorType = DefaultIntegrator,
+        integrator: IntegratorType | None = None,
         *,
         use_jacobian: bool = False,
         test_run: bool = True,
@@ -351,7 +354,7 @@ class Simulator:
         self.model = model
         self.y0 = model.get_initial_conditions() if y0 is None else y0
 
-        self._integrator_type = integrator
+        self._integrator_type = DefaultIntegrator if integrator is None else integrator
         self._time_shift = None
         self.variables = None
         self.dependent = None
@@ -500,6 +503,35 @@ class Simulator:
         self._handle_simulation_results(time, results, skipfirst=True)
         return self
 
+    def simulate_over_protocol(
+        self,
+        protocol: pd.DataFrame,
+        time_points_per_step: int = 10,
+    ) -> Self:
+        """Simulate the model over a given protocol.
+
+        Examples:
+            >>> Simulator(model).simulate_over_protocol(
+            ...     protocol,
+            ...     time_points_per_step=10
+            ... )
+
+        Args:
+            protocol: DataFrame containing the protocol.
+            time_points_per_step: Number of time points per step.
+
+        Returns:
+            The Simulator instance with updated results.
+
+        """
+        for t_end, pars in protocol.iterrows():
+            t_end = cast(pd.Timedelta, t_end)
+            self.model.update_parameters(pars.to_dict())
+            self.simulate(t_end.total_seconds(), steps=time_points_per_step)
+            if self.variables is None:
+                break
+        return self
+
     def simulate_to_steady_state(
         self,
         tolerance: float = 1e-6,
@@ -535,35 +567,6 @@ class Simulator:
         )
         return self
 
-    def simulate_over_protocol(
-        self,
-        protocol: pd.DataFrame,
-        time_points_per_step: int = 10,
-    ) -> Self:
-        """Simulate the model over a given protocol.
-
-        Examples:
-            >>> Simulator(model).simulate_over_protocol(
-            ...     protocol,
-            ...     time_points_per_step=10
-            ... )
-
-        Args:
-            protocol: DataFrame containing the protocol.
-            time_points_per_step: Number of time points per step.
-
-        Returns:
-            The Simulator instance with updated results.
-
-        """
-        for t_end, pars in protocol.iterrows():
-            t_end = cast(pd.Timedelta, t_end)
-            self.model.update_parameters(pars.to_dict())
-            self.simulate(t_end.total_seconds(), steps=time_points_per_step)
-            if self.variables is None:
-                break
-        return self
-
     def get_result(self) -> Result | None:
         """Get result of the simulation.
 

mxlpy/surrogates/_keras.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from dataclasses import dataclass
 from typing import Self, cast
 

mxlpy/surrogates/_poly.py

@@ -1,6 +1,7 @@
-from collections.abc import Iterable
+from __future__ import annotations
+
 from dataclasses import dataclass
-from typing import Literal
+from typing import TYPE_CHECKING, Literal
 
 import numpy as np
 import pandas as pd
@@ -8,6 +9,9 @@ from numpy import polynomial
 
 from mxlpy.types import AbstractSurrogate, ArrayLike, Derived
 
+if TYPE_CHECKING:
+    from collections.abc import Iterable
+
 __all__ = [
     "PolynomialExpansion",
     "Surrogate",

mxlpy/surrogates/_qss.py

@@ -9,7 +9,10 @@ from mxlpy.types import AbstractSurrogate, Array
 if TYPE_CHECKING:
     import pandas as pd
 
-__all__ = ["QSSFn", "Surrogate"]
+__all__ = [
+    "QSSFn",
+    "Surrogate",
+]
 
 type QSSFn = Callable[..., Iterable[float] | Array]
 

mxlpy/surrogates/_torch.py

@@ -1,18 +1,22 @@
+from __future__ import annotations
+
 from collections.abc import Callable
 from dataclasses import dataclass
-from typing import Self
+from typing import TYPE_CHECKING, Self
 
 import numpy as np
 import pandas as pd
 import torch
 from torch import nn
 from torch.optim.adam import Adam
-from torch.optim.optimizer import ParamsT
 
 from mxlpy.nn._torch import MLP, DefaultDevice
 from mxlpy.nn._torch import train as _train
 from mxlpy.types import AbstractSurrogate, Derived
 
+if TYPE_CHECKING:
+    from torch.optim.optimizer import ParamsT
+
 type LossFn = Callable[[torch.Tensor, torch.Tensor], torch.Tensor]
 
 __all__ = [

mxlpy/symbolic/__init__.py

@@ -1,10 +1,12 @@
 """Symbolic utilities."""
 
+from __future__ import annotations
+
+from .strikepy import check_identifiability
+from .symbolic_model import SymbolicModel, to_symbolic_model
+
 __all__ = [
     "SymbolicModel",
     "check_identifiability",
     "to_symbolic_model",
 ]
-
-from .strikepy import check_identifiability
-from .symbolic_model import SymbolicModel, to_symbolic_model

mxlpy/symbolic/strikepy.py

@@ -10,13 +10,15 @@ FIXME:
 - performance issues of generic_rank
 """
 
+from __future__ import annotations
+
 import textwrap
 from concurrent.futures import ProcessPoolExecutor
 from dataclasses import dataclass, field
 from functools import partial
 from math import ceil, inf
 from time import time
-from typing import cast
+from typing import TYPE_CHECKING, cast
 
 import numpy as np
 import numpy.typing as npt
@@ -27,7 +29,8 @@ import tqdm
 from sympy import Matrix
 from sympy.matrices import zeros
 
-from .symbolic_model import SymbolicModel
+if TYPE_CHECKING:
+    from .symbolic_model import SymbolicModel
 
 __all__ = [
     "Options",

mxlpy/symbolic/symbolic_model.py

@@ -1,15 +1,24 @@
 # ruff: noqa: D100, D101, D102, D103, D104, D105, D106, D107, D200, D203, D400, D401
 
 
-from collections.abc import Iterable
+from __future__ import annotations
+
 from dataclasses import dataclass
+from typing import TYPE_CHECKING
 
 import sympy
 
 from mxlpy.meta.source_tools import fn_to_sympy
-from mxlpy.model import Model
 
-__all__ = ["SymbolicModel", "to_symbolic_model"]
+if TYPE_CHECKING:
+    from collections.abc import Iterable
+
+    from mxlpy.model import Model
+
+__all__ = [
+    "SymbolicModel",
+    "to_symbolic_model",
+]
 
 
 @dataclass

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, Iterable, 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]
 

{mxlpy-0.19.0.dist-info → mxlpy-0.21.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mxlpy
-Version: 0.19.0
+Version: 0.21.0
 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>
@@ -51,10 +51,12 @@ 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]
@@ -67,11 +69,13 @@ Description-Content-Type: text/markdown
 [docs-badge]: https://img.shields.io/badge/docs-main-green.svg?style=flat-square
 [docs]: https://computational-biology-aachen.github.io/mxlpy/
 
+MxlPy (pronounced "em axe el pie") is a Python package for mechanistic learning (Mxl) - the combination of mechanistic modeling and machine learning to deliver explainable, data-informed solutions.
+
 ## Installation
 
 You can install mxlpy using pip: `pip install mxlpy`.
 
-Due to their sizes, the machine learning are optional dependencies. You cann install them using
+Due to their sizes, the machine learning packages are optional dependencies. You can install them using
 
 ```shell
 # One of them respectively

mxlpy-0.21.0.dist-info/RECORD

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