mxlpy 0.23.0__py3-none-any.whl → 0.25.0__py3-none-any.whl

mxlpy/types.py

@@ -33,6 +33,7 @@ from typing import (
 import numpy as np
 import pandas as pd
 from numpy.typing import NDArray
+from wadler_lindig import pformat
 
 __all__ = [
     "AbstractEstimator",
@@ -182,6 +183,10 @@ class Variable:
     unit: sympy.Expr | None = None
     source: str | None = None
 
+    def __repr__(self) -> str:
+        """Return default representation."""
+        return pformat(self)
+
 
 @dataclass
 class Parameter:
@@ -191,6 +196,10 @@ class Parameter:
     unit: sympy.Expr | None = None
     source: str | None = None
 
+    def __repr__(self) -> str:
+        """Return default representation."""
+        return pformat(self)
+
 
 @dataclass(kw_only=True, slots=True)
 class Derived:
@@ -200,6 +209,10 @@ class Derived:
     args: list[str]
     unit: sympy.Expr | None = None
 
+    def __repr__(self) -> str:
+        """Return default representation."""
+        return pformat(self)
+
     def calculate(self, args: dict[str, Any]) -> float:
         """Calculate the derived value.
 
@@ -231,6 +244,10 @@ class InitialAssignment:
     args: list[str]
     unit: sympy.Expr | None = None
 
+    def __repr__(self) -> str:
+        """Return default representation."""
+        return pformat(self)
+
     def calculate(self, args: dict[str, Any]) -> float:
         """Calculate the derived value.
 
@@ -262,6 +279,10 @@ class Readout:
     args: list[str]
     unit: sympy.Expr | None = None
 
+    def __repr__(self) -> str:
+        """Return default representation."""
+        return pformat(self)
+
     def calculate(self, args: dict[str, Any]) -> float:
         """Calculate the derived value.
 
@@ -294,6 +315,10 @@ class Reaction:
     args: list[str]
     unit: sympy.Expr | None = None
 
+    def __repr__(self) -> str:
+        """Return default representation."""
+        return pformat(self)
+
     def get_modifiers(self, model: Model) -> list[str]:
         """Get the modifiers of the reaction."""
         include = set(model.get_variable_names())
@@ -341,6 +366,10 @@ class AbstractSurrogate:
     outputs: list[str]
     stoichiometries: dict[str, dict[str, float | Derived]] = field(default_factory=dict)
 
+    def __repr__(self) -> str:
+        """Return default representation."""
+        return pformat(self)
+
     @abstractmethod
     def predict(
         self, args: dict[str, float | pd.Series | pd.DataFrame]
@@ -382,6 +411,10 @@ class AbstractEstimator:
 
     parameter_names: list[str]
 
+    def __repr__(self) -> str:
+        """Return default representation."""
+        return pformat(self)
+
     @abstractmethod
     def predict(self, features: pd.Series | pd.DataFrame) -> pd.DataFrame:
         """Predict the target values for the given features."""
@@ -430,6 +463,10 @@ class Result:
     raw_parameters: list[dict[str, float]]
     raw_args: list[pd.DataFrame] = field(default_factory=list)
 
+    def __repr__(self) -> str:
+        """Return default representation."""
+        return pformat(self)
+
     @classmethod
     def default(cls, model: Model, time_points: Array) -> Result:
         """Get result filled with NaNs."""
@@ -453,6 +490,7 @@ class Result:
         """Simulation variables."""
         return self.get_variables(
             include_derived_variables=True,
+            include_surrogate_variables=True,
             include_readouts=True,
             concatenated=True,
             normalise=None,
@@ -461,7 +499,9 @@ class Result:
     @property
     def fluxes(self) -> pd.DataFrame:
         """Simulation fluxes."""
-        return self.get_fluxes()
+        return self.get_fluxes(
+            include_surrogates=True,
+        )
 
     def _compute_args(self) -> list[pd.DataFrame]:
         # Already computed
@@ -618,6 +658,7 @@ class Result:
         *,
         include_derived_variables: bool = True,
         include_readouts: bool = True,
+        include_surrogate_variables: bool = True,
         concatenated: Literal[False],
         normalise: float | ArrayLike | None = None,
     ) -> list[pd.DataFrame]: ...
@@ -628,6 +669,7 @@ class Result:
         *,
         include_derived_variables: bool = True,
         include_readouts: bool = True,
+        include_surrogate_variables: bool = True,
         concatenated: Literal[True],
         normalise: float | ArrayLike | None = None,
     ) -> pd.DataFrame: ...
@@ -638,6 +680,7 @@ class Result:
         *,
         include_derived_variables: bool = True,
         include_readouts: bool = True,
+        include_surrogate_variables: bool = True,
         concatenated: bool = True,
         normalise: float | ArrayLike | None = None,
     ) -> pd.DataFrame: ...
@@ -647,6 +690,7 @@ class Result:
         *,
         include_derived_variables: bool = True,
         include_readouts: bool = True,
+        include_surrogate_variables: bool = True,
         concatenated: bool = True,
         normalise: float | ArrayLike | None = None,
     ) -> pd.DataFrame | list[pd.DataFrame]:
@@ -660,7 +704,9 @@ class Result:
             0.000200   0.999800   0.999800
 
         """
-        if not include_derived_variables and not include_readouts:
+        if not (
+            include_derived_variables or include_readouts or include_surrogate_variables
+        ):
             return self._adjust_data(
                 self.raw_variables,
                 normalise=normalise,
@@ -671,6 +717,7 @@ class Result:
             self._compute_args(),
             include_variables=True,
             include_derived_variables=include_derived_variables,
+            include_surrogate_variables=include_surrogate_variables,
             include_readouts=include_readouts,
         )
         return self._adjust_data(
@@ -751,6 +798,177 @@ class Result:
         """
         return pd.concat((self.variables, self.fluxes), axis=1)
 
+    @overload
+    def get_right_hand_side(  # type: ignore
+        self,
+        *,
+        normalise: float | ArrayLike | None = None,
+        concatenated: Literal[False],
+    ) -> list[pd.DataFrame]: ...
+
+    @overload
+    def get_right_hand_side(
+        self,
+        *,
+        normalise: float | ArrayLike | None = None,
+        concatenated: Literal[True],
+    ) -> pd.DataFrame: ...
+
+    @overload
+    def get_right_hand_side(
+        self,
+        *,
+        normalise: float | ArrayLike | None = None,
+        concatenated: bool = True,
+    ) -> pd.DataFrame: ...
+
+    def get_right_hand_side(
+        self,
+        *,
+        normalise: float | ArrayLike | None = None,
+        concatenated: bool = True,
+    ) -> pd.DataFrame | list[pd.DataFrame]:
+        """Get right hand side over time."""
+        args_by_simulation = self._compute_args()
+        return self._adjust_data(
+            [
+                self.model.update_parameters(p).get_right_hand_side_time_course(
+                    args=args
+                )
+                for args, p in zip(args_by_simulation, self.raw_parameters, strict=True)
+            ],
+            normalise=normalise,
+            concatenated=concatenated,
+        )
+
+    @overload
+    def get_producers(  # type: ignore
+        self,
+        variable: str,
+        *,
+        scaled: bool = False,
+        normalise: float | ArrayLike | None = None,
+        concatenated: Literal[False],
+    ) -> list[pd.DataFrame]: ...
+
+    @overload
+    def get_producers(
+        self,
+        variable: str,
+        *,
+        scaled: bool = False,
+        normalise: float | ArrayLike | None = None,
+        concatenated: Literal[True],
+    ) -> pd.DataFrame: ...
+
+    @overload
+    def get_producers(
+        self,
+        variable: str,
+        *,
+        scaled: bool = False,
+        normalise: float | ArrayLike | None = None,
+        concatenated: bool = True,
+    ) -> pd.DataFrame: ...
+
+    def get_producers(
+        self,
+        variable: str,
+        *,
+        scaled: bool = False,
+        normalise: float | ArrayLike | None = None,
+        concatenated: bool = True,
+    ) -> pd.DataFrame | list[pd.DataFrame]:
+        """Get fluxes of variable with positive stoichiometry."""
+        self.model.update_parameters(self.raw_parameters[0])
+        names = [
+            k
+            for k, v in self.model.get_stoichiometries_of_variable(variable).items()
+            if v > 0
+        ]
+
+        fluxes: list[pd.DataFrame] = [
+            i.loc[:, names]
+            for i in self.get_fluxes(normalise=normalise, concatenated=False)
+        ]
+
+        if scaled:
+            fluxes = [i.copy() for i in fluxes]
+            for v, p in zip(fluxes, self.raw_parameters, strict=True):
+                self.model.update_parameters(p)
+                stoichs = self.model.get_stoichiometries_of_variable(variable)
+                for k in names:
+                    v.loc[:, k] *= stoichs[k]
+
+        self.model.update_parameters(self.raw_parameters[-1])
+        if concatenated:
+            return pd.concat(fluxes, axis=0)
+        return fluxes
+
+    @overload
+    def get_consumers(  # type: ignore
+        self,
+        variable: str,
+        *,
+        scaled: bool = False,
+        normalise: float | ArrayLike | None = None,
+        concatenated: Literal[False],
+    ) -> list[pd.DataFrame]: ...
+
+    @overload
+    def get_consumers(
+        self,
+        variable: str,
+        *,
+        scaled: bool = False,
+        normalise: float | ArrayLike | None = None,
+        concatenated: Literal[True],
+    ) -> pd.DataFrame: ...
+
+    @overload
+    def get_consumers(
+        self,
+        variable: str,
+        *,
+        scaled: bool = False,
+        normalise: float | ArrayLike | None = None,
+        concatenated: bool = True,
+    ) -> pd.DataFrame: ...
+
+    def get_consumers(
+        self,
+        variable: str,
+        *,
+        scaled: bool = False,
+        normalise: float | ArrayLike | None = None,
+        concatenated: bool = True,
+    ) -> pd.DataFrame | list[pd.DataFrame]:
+        """Get fluxes of variable with negative stoichiometry."""
+        self.model.update_parameters(self.raw_parameters[0])
+        names = [
+            k
+            for k, v in self.model.get_stoichiometries_of_variable(variable).items()
+            if v < 0
+        ]
+
+        fluxes: list[pd.DataFrame] = [
+            i.loc[:, names]
+            for i in self.get_fluxes(normalise=normalise, concatenated=False)
+        ]
+
+        if scaled:
+            fluxes = [i.copy() for i in fluxes]
+            for v, p in zip(fluxes, self.raw_parameters, strict=True):
+                self.model.update_parameters(p)
+                stoichs = self.model.get_stoichiometries_of_variable(variable)
+                for k in names:
+                    v.loc[:, k] *= -stoichs[k]
+
+        self.model.update_parameters(self.raw_parameters[-1])
+        if concatenated:
+            return pd.concat(fluxes, axis=0)
+        return fluxes
+
     def get_new_y0(self) -> dict[str, float]:
         """Get the new initial conditions after the simulation.
 
@@ -778,6 +996,10 @@ class ResponseCoefficients:
     variables: pd.DataFrame
     fluxes: pd.DataFrame
 
+    def __repr__(self) -> str:
+        """Return default representation."""
+        return pformat(self)
+
     @property
     def combined(self) -> pd.DataFrame:
         """Return the response coefficients as a DataFrame."""
@@ -796,6 +1018,10 @@ class ResponseCoefficientsByPars:
     fluxes: pd.DataFrame
     parameters: pd.DataFrame
 
+    def __repr__(self) -> str:
+        """Return default representation."""
+        return pformat(self)
+
     @property
     def combined(self) -> pd.DataFrame:
         """Return the response coefficients as a DataFrame."""
@@ -814,6 +1040,10 @@ class SteadyStateScan:
     raw_index: pd.Index | pd.MultiIndex
     raw_results: list[Result]
 
+    def __repr__(self) -> str:
+        """Return default representation."""
+        return pformat(self)
+
     @property
     def variables(self) -> pd.DataFrame:
         """Return steady-state variables by scan."""
@@ -874,6 +1104,10 @@ class SteadyStateScan:
 class TimeCourseScan:
     """Container for time courses by scanned values."""
 
+    def __repr__(self) -> str:
+        """Return default representation."""
+        return pformat(self)
+
     to_scan: pd.DataFrame
     raw_results: dict[Hashable, Result]
 
@@ -953,6 +1187,10 @@ class ProtocolScan:
     protocol: pd.DataFrame
     raw_results: dict[Hashable, Result]
 
+    def __repr__(self) -> str:
+        """Return default representation."""
+        return pformat(self)
+
     @property
     def variables(self) -> pd.DataFrame:
         """Return all args of the time courses."""
@@ -1032,6 +1270,10 @@ class McSteadyStates:
     parameters: pd.DataFrame
     mc_to_scan: pd.DataFrame
 
+    def __repr__(self) -> str:
+        """Return default representation."""
+        return pformat(self)
+
     @property
     def combined(self) -> pd.DataFrame:
         """Return the steady states as a DataFrame."""

{mxlpy-0.23.0.dist-info → mxlpy-0.25.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mxlpy
-Version: 0.23.0
+Version: 0.25.0
 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>
@@ -33,7 +33,7 @@ Requires-Dist: numpy>=2.1.2
 Requires-Dist: pandas>=2.2.3
 Requires-Dist: parameteriser>=0.1.0
 Requires-Dist: pebble>=5.0.7
-Requires-Dist: pysbml>=0.2.0
+Requires-Dist: pysbml>=0.3.0
 Requires-Dist: python-libsbml>=5.20.4
 Requires-Dist: salib>=1.5.1
 Requires-Dist: scipy>=1.14.1
@@ -121,3 +121,13 @@ You have two choices here, using `uv` (pypi-only) or using `pixi` (conda-forge,
 - Run `pixi install --frozen`
 
 
+## LLMs
+
+We support the [llms.txt](https://llmstxt.org/) convention for making documentation available to large language models and the applications that make use of them. It is located at [docs/llms.txt](https://github.com/Computational-Biology-Aachen/MxlPy/tree/main/docs/llms.txt)
+
+## Tool family 🏠
+
+`MxlPy` is part of a larger family of tools that are designed with a similar set of abstractions. Check them out!
+
+- [MxlBricks](https://github.com/Computational-Biology-Aachen/mxl-bricks) is built on top of `MxlPy` to build mechanistic models composed of pre-defined reactions (bricks)
+- [MxlWeb](https://github.com/Computational-Biology-Aachen/mxl-web) brings simulation of mechanistic models to the browser!

{mxlpy-0.23.0.dist-info → mxlpy-0.25.0.dist-info}/RECORD

@@ -1,37 +1,40 @@
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-mxlpy/carousel.py,sha256=nYWEdxDd7lm5INfZjpwaEhYqysg9e4EH9Ubcl6bPca8,4721
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 mxlpy/distributions.py,sha256=ce6RTqn19YzMMec-u09fSIUA8A92M6rehCuHuXWcX7A,8734
-mxlpy/fit.py,sha256=3hGUqJ2tOOToZLMMaJw5M9b6_UlUJwT_MhUvfPmRBd8,22355
 mxlpy/fns.py,sha256=NLxYwa3ylS7SkISBjw_TgQSKEm7WnkZF9wPigX_ZCAM,13915
-mxlpy/identify.py,sha256=G-Zyr_l-K2mDtIV1xGrQ52QJxoBYqRoNA5RW6GpbNjs,2213
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 mxlpy/label_map.py,sha256=PwYanfg07hC0ayyOOP72RFlCQNvhCTbpOhW6kZZ2GUU,17826
 mxlpy/linear_label_map.py,sha256=6Ye6IziWGKkYD_5z3FmTVwnJ2T9SvVGN3U4CfXjXseo,10320
-mxlpy/mc.py,sha256=6n6VAuSVcXinqcWxNJAioMYpBmSAB40WItPloK1vmBM,17017
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 mxlpy/mca.py,sha256=IoOHJbjPnAEDqKk64OjFjgRPX5K_aE9D4RrCJ1xFIkw,9457
-mxlpy/model.py,sha256=tAz_Rbe_S1Ho-k_14gBxmE9RMYo2xJUWYkdLYUyMKHg,79072
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 mxlpy/parallel.py,sha256=yLQLw5O4vnPVp_Zmtw1UhPWtB3483foimxQB-TwFKPg,5016
 mxlpy/parameterise.py,sha256=IgbvfEnkmaqVq_5GgFjHqApGUN9CJrsVD3Fr7pg9iFA,758
 mxlpy/paths.py,sha256=TK2wO4N9lG-UV1JGfeB64q48JVDbwqIUj63rl55MKuQ,1022
-mxlpy/plot.py,sha256=oZq8NqycdiJwqEm7FVpNTBkjGYgPBEbqDqZxbrvUtDI,32662
+mxlpy/plot.py,sha256=Dng9tyga8xagINQO_OZvjLRoaYGFR8crMljDHrzwEF8,33603
 mxlpy/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mxlpy/report.py,sha256=v597yzKecgtoNmlNZ_nVhBCa3czNw0tksOK5mLtAQvE,10631
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 mxlpy/units.py,sha256=4bKXkCYsONUVWRdzV7aVcWFQSA6sxilebgXXFUEKw_c,2091
 mxlpy/experimental/__init__.py,sha256=kZTE-92OErpHzNRqmgSQYH4CGXrogGJ5EL35XGZQ81M,206
-mxlpy/experimental/diff.py,sha256=g5hKvFsEUdEk5OGQ_aQuCxLAnenD_jG4G__EcVfKsx4,9104
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 mxlpy/integrators/__init__.py,sha256=TKo2dkJqdW3_n7YrmF6k3kEjr8_kr3-7MDaLu-zFWRg,533
 mxlpy/integrators/int_assimulo.py,sha256=1cvR8cOBdrl_DQs9v0o7wItSG5iyYqwZVh7EO0fg3ro,5021
 mxlpy/integrators/int_diffrax.py,sha256=q_8NZgIZ6T-SRRcI8kSjEb6l-DbXqPv6rjj9KApkQac,3326
 mxlpy/integrators/int_scipy.py,sha256=xKyisVN1jW5hxmVD2K_RpoQ2MwNrMxSGODsAEgEt6_I,4922
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-mxlpy/meta/codegen_latex.py,sha256=i4tPvk2-toAYqtf4TynuE9sfUSHUp21AMUgjgFEB0uo,23215
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-mxlpy/meta/sympy_tools.py,sha256=XaRXdyXiiiOHBXatxoRTRKwy7BaM9I0lL6PE5HP33wE,3016
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+mxlpy/meta/codegen_mxlpy.py,sha256=FjBw37IqziB4dv5VBAvKenFODfxjJXdW6rQqx9CqYUk,8433
+mxlpy/meta/source_tools.py,sha256=e6ufIsBjgde3QuQ9OsAYES0Lib4WALw4E-0wH_2cF6Y,22442
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 mxlpy/nn/__init__.py,sha256=Qjr-ERsY2lbD75sFBOhCUwEasQDSJKcpBn_kReLZ6oA,633
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@@ -39,8 +42,8 @@ mxlpy/npe/__init__.py,sha256=hBHCUD2JYDBBGS2kTY8mTCfWB3u1R7m5l--wUupZt6o,1270
 mxlpy/npe/_keras.py,sha256=ytvXMPK9KUCGOzTQm08_SgafiMb-MOIUdZQV7JjAO40,9721
 mxlpy/npe/_torch.py,sha256=v3joh6lFJJxvYJj--wzmKXL9UMTaIN3h6hPNq0uX9NU,11250
 mxlpy/sbml/__init__.py,sha256=Mt97CddpLi3wIrA1b_5cagLmDdNxAVF_S7QV57Pzw8s,226
-mxlpy/sbml/_data.py,sha256=yYli7ZQ1_pnH9kt5EmcuHM0moQoa43rrFVdrseXlG0o,1136
-mxlpy/sbml/_export.py,sha256=0R34btB5COKD1gsWisdlWdEbJ-BUrjb78s6sWnm5Ph4,20945
+mxlpy/sbml/_data.py,sha256=98w5vyhdOHilD5zjy21XFzam0FlvcW_cb1XRTsIgD_M,2019
+mxlpy/sbml/_export.py,sha256=leKf7dFqpoYxO3xFu4j_mM5eAgo-lq__ywADXsmamRU,21008
 mxlpy/sbml/_import.py,sha256=_4MR54YyVkIh9eVAiSMd7yijhHC_ds-3v7M_C4Zn8BY,3565
 mxlpy/sbml/_name_conversion.py,sha256=93muW47M7qJoE227HKHmThWpPeWsXDN9eM8cRH2pqPs,1340
 mxlpy/surrogates/__init__.py,sha256=cz9qr0ToYSutIK45IvKrMe1mPP7Lj0I_V0HYGixfpZU,916
@@ -51,7 +54,7 @@ mxlpy/surrogates/_torch.py,sha256=gU0secuRBYgewhNqZmSo6_Xf804dSzwWwIYmdKA7y60,63
 mxlpy/symbolic/__init__.py,sha256=_vM5YM5I6OH0QDbFt9uGYKO8Z5Vly0wbGuvUScVrPRU,258
 mxlpy/symbolic/strikepy.py,sha256=tzo3uvPpXLDex09hWTuitVzuTNwbgl7jWGjD8g6a8iI,20033
 mxlpy/symbolic/symbolic_model.py,sha256=cKfWoktvFmXjuo8egE7gXKrKBq2iBUiy_BcIKIvvz8A,3026
-mxlpy-0.23.0.dist-info/METADATA,sha256=80ODNl3NCffUmuu_mJmvUmld7uNm390vMtlhNx2Soes,4696
-mxlpy-0.23.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-mxlpy-0.23.0.dist-info/licenses/LICENSE,sha256=lHX9Eu70g3Iv1aOxXTWNHa3vq9vaVYSPQx4jOLYmDpw,1096
-mxlpy-0.23.0.dist-info/RECORD,,
+mxlpy-0.25.0.dist-info/METADATA,sha256=ENFh6nylpjiupCmhYEhozQCuP1FuyO0vGMegm3VPyvU,5413
+mxlpy-0.25.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+mxlpy-0.25.0.dist-info/licenses/LICENSE,sha256=lHX9Eu70g3Iv1aOxXTWNHa3vq9vaVYSPQx4jOLYmDpw,1096
+mxlpy-0.25.0.dist-info/RECORD,,