mxlpy 0.19.0__py3-none-any.whl → 0.20.0__py3-none-any.whl

mxlpy/sbml/_data.py

@@ -1,5 +1,12 @@
 from __future__ import annotations
 
+from dataclasses import dataclass
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from collections.abc import Mapping
+
+
 __all__ = [
     "AtomicUnit",
     "Compartment",
@@ -11,12 +18,6 @@ __all__ = [
     "Reaction",
 ]
 
-from dataclasses import dataclass
-from typing import TYPE_CHECKING
-
-if TYPE_CHECKING:
-    from collections.abc import Mapping
-
 
 @dataclass
 class AtomicUnit:

mxlpy/sbml/_mathml.py

@@ -1,5 +1,13 @@
 from __future__ import annotations
 
+from typing import TYPE_CHECKING, Any
+
+from ._name_conversion import _name_to_py
+from ._unit_conversion import get_ast_types
+
+if TYPE_CHECKING:
+    from libsbml import ASTNode
+
 __all__ = [
     "AST_TYPES",
     "handle_ast_constant_e",
@@ -73,13 +81,6 @@ __all__ = [
     "parse_sbml_math",
 ]
 
-from typing import TYPE_CHECKING, Any
-
-from ._name_conversion import _name_to_py
-from ._unit_conversion import get_ast_types
-
-if TYPE_CHECKING:
-    from libsbml import ASTNode
 
 AST_TYPES = get_ast_types()
 

mxlpy/sbml/_name_conversion.py

@@ -3,7 +3,11 @@ from __future__ import annotations
 import keyword
 import re
 
-__all__ = ["RE_FROM_SBML", "RE_KWDS", "SBML_DOT"]
+__all__ = [
+    "RE_FROM_SBML",
+    "RE_KWDS",
+    "SBML_DOT",
+]
 
 RE_KWDS = re.compile("|".join(f"^{i}$" for i in keyword.kwlist))
 SBML_DOT = "__SBML_DOT__"

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
@@ -35,14 +22,10 @@ from typing import TYPE_CHECKING, Protocol, Self, cast
 import numpy as np
 import pandas as pd
 
+from mxlpy.integrators import DefaultIntegrator
 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 +34,18 @@ 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],

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],
@@ -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-0.20.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mxlpy
-Version: 0.19.0
+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>
@@ -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]
@@ -71,7 +73,7 @@ Description-Content-Type: text/markdown
 
 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-0.20.0.dist-info/RECORD

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mxlpy-0.19.0.dist-info/RECORD

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