mxlpy 0.14.0__py3-none-any.whl → 0.16.0__py3-none-any.whl

mxlpy/simulator.py

@@ -16,8 +16,10 @@ from typing import TYPE_CHECKING, Literal, Self, cast, overload
 
 import numpy as np
 import pandas as pd
+from sympy import lambdify
 
 from mxlpy.integrators import DefaultIntegrator
+from mxlpy.symbolic import to_symbolic_model
 
 __all__ = ["Result", "Simulator"]
 
@@ -362,31 +364,24 @@ class Simulator:
         self._initialise_integrator()
 
     def _initialise_integrator(self) -> None:
-        from sympy import lambdify
-
-        from mxlpy.symbolic import to_symbolic_model
-
-        _jacobian = None
+        jac_fn = None
         if self.use_jacobian:
             try:
-                # NOTE: this implementation is not correct in the sense
-                # that it does not take parameter updates into account
-                # jac = (
-                #     to_symbolic_model(self.model)
-                #     .jacobian()
-                #     .subs(self.model._parameters)
-                # )
-                # _jacobian = lambdify(
-                #     ("time", self.model.get_variable_names()),
-                #     jac,
-                # )
-
-                # NOTE: this implementation is correct, but slow as hell
-                jac = to_symbolic_model(self.model).jacobian()
-                _jacobian = lambda t, y: lambdify(  # noqa: E731
-                    ("time", self.model.get_variable_names()),
-                    jac.subs(self.model._parameters),  # noqa: SLF001
-                )(t, y)
+                _jac = to_symbolic_model(self.model).jacobian()
+                _jac_fn = lambdify(
+                    (
+                        "time",
+                        self.model.get_variable_names(),
+                        self.model.get_parameter_names(),
+                    ),
+                    _jac,
+                )
+                jac_fn = lambda t, x: _jac_fn(  # noqa: E731
+                    t,
+                    x,
+                    self.model._parameters.values(),  # noqa: SLF001
+                )
+
             except Exception as e:  # noqa: BLE001
                 warnings.warn(str(e), stacklevel=2)
 
@@ -394,7 +389,7 @@ class Simulator:
         self.integrator = self._integrator_type(
             self.model,
             [y0[k] for k in self.model.get_variable_names()],
-            _jacobian,
+            jac_fn,
         )
 
     def clear_results(self) -> None:

mxlpy/types.py

@@ -158,7 +158,6 @@ type IntegratorType = Callable[
 class Derived:
     """Container for a derived value."""
 
-    name: str
     fn: RateFn
     args: list[str]
 
@@ -174,36 +173,35 @@ class Derived:
         """
         return cast(float, self.fn(*(dependent[arg] for arg in self.args)))
 
-    def calculate_inpl(self, dependent: dict[str, float]) -> None:
+    def calculate_inpl(self, name: str, dependent: dict[str, float]) -> None:
         """Calculate the derived value in place.
 
         Args:
+            name: Name of the derived variable.
             dependent: Dictionary of dependent variables.
 
         """
-        dependent[self.name] = cast(
-            float, self.fn(*(dependent[arg] for arg in self.args))
-        )
+        dependent[name] = cast(float, self.fn(*(dependent[arg] for arg in self.args)))
 
-    def calculate_inpl_time_course(self, dependent: pd.DataFrame) -> None:
+    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[self.name] = self.fn(*dependent.loc[:, self.args].to_numpy().T)
+            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[self.name] = [self.fn(*row) for row in sub]
+            dependent[name] = [self.fn(*row) for row in sub]
 
 
 @dataclass(kw_only=True, slots=True)
 class Readout:
     """Container for a readout."""
 
-    name: str
     fn: RateFn
     args: list[str]
 
@@ -219,36 +217,35 @@ class Readout:
         """
         return cast(float, self.fn(*(dependent[arg] for arg in self.args)))
 
-    def calculate_inpl(self, dependent: dict[str, float]) -> None:
+    def calculate_inpl(self, name: str, dependent: dict[str, float]) -> None:
         """Calculate the readout in place.
 
         Args:
+            name: Name of the derived variable.
             dependent: Dictionary of dependent variables.
 
         """
-        dependent[self.name] = cast(
-            float, self.fn(*(dependent[arg] for arg in self.args))
-        )
+        dependent[name] = cast(float, self.fn(*(dependent[arg] for arg in self.args)))
 
-    def calculate_inpl_time_course(self, dependent: pd.DataFrame) -> None:
+    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[self.name] = self.fn(*dependent.loc[:, self.args].to_numpy().T)
+            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[self.name] = [self.fn(*row) for row in sub]
+            dependent[name] = [self.fn(*row) for row in sub]
 
 
 @dataclass(kw_only=True, slots=True)
 class Reaction:
     """Container for a reaction."""
 
-    name: str
     fn: RateFn
     stoichiometry: Mapping[str, float | Derived]
     args: list[str]
@@ -272,29 +269,29 @@ class Reaction:
         """
         return cast(float, self.fn(*(dependent[arg] for arg in self.args)))
 
-    def calculate_inpl(self, dependent: dict[str, float]) -> None:
+    def calculate_inpl(self, name: str, dependent: dict[str, float]) -> None:
         """Calculate the reaction in place.
 
         Args:
+            name: Name of the derived variable.
             dependent: Dictionary of dependent variables.
 
         """
-        dependent[self.name] = cast(
-            float, self.fn(*(dependent[arg] for arg in self.args))
-        )
+        dependent[name] = cast(float, self.fn(*(dependent[arg] for arg in self.args)))
 
-    def calculate_inpl_time_course(self, dependent: pd.DataFrame) -> None:
+    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[self.name] = self.fn(*dependent.loc[:, self.args].to_numpy().T)
+            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[self.name] = [self.fn(*row) for row in sub]
+            dependent[name] = [self.fn(*row) for row in sub]
 
 
 @dataclass(kw_only=True, slots=True)
@@ -357,7 +354,7 @@ class McSteadyStates:
     variables: pd.DataFrame
     fluxes: pd.DataFrame
     parameters: pd.DataFrame
-    mc_parameters: pd.DataFrame
+    mc_to_scan: pd.DataFrame
 
     def __iter__(self) -> Iterator[pd.DataFrame]:
         """Iterate over the concentration and flux steady states."""
@@ -464,11 +461,19 @@ class AbstractSurrogate:
             )
         )
 
-    def calculate_inpl(self, args: dict[str, float]) -> None:
+    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, args: pd.DataFrame) -> None:
+    def calculate_inpl_time_course(
+        self,
+        name: str,  # noqa: ARG002, for API compatibility
+        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()],

{mxlpy-0.14.0.dist-info → mxlpy-0.16.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mxlpy
-Version: 0.14.0
+Version: 0.16.0
 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>
@@ -60,7 +60,9 @@ Provides-Extra: torch
 Requires-Dist: torch>=2.5.1; extra == 'torch'
 Description-Content-Type: text/markdown
 
-<img src="docs/assets/logo-diagram.png" style="display: block; max-height: 30rem; margin: auto; padding: 0" alt='mxlpy-logo'>
+<p align="center">
+    <img src="docs/assets/logo-diagram.png" width="600px" alt='mxlpy-logo'>
+</p>
 
 # mxlpy
 
@@ -70,7 +72,7 @@ Description-Content-Type: text/markdown
 ![Coverage](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fgist.github.com%2Fmarvinvanaalst%2F98ab3ce1db511de42f9871e91d85e4cd%2Fraw%2Fcoverage.json&query=%24.message&label=Coverage&color=%24.color&suffix=%20%25)
 [![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/mxlpy)](https://pepy.tech/project/mxlpy)
+[![PyPI Downloads](https://static.pepy.tech/badge/mxlpy)](https://pepy.tech/projects/mxlpy)
 
 [docs-badge]: https://img.shields.io/badge/docs-main-green.svg?style=flat-square
 [docs]: https://computational-biology-aachen.github.io/mxlpy/

{mxlpy-0.14.0.dist-info → mxlpy-0.16.0.dist-info}/RECORD

@@ -4,10 +4,10 @@ mxlpy/fit.py,sha256=LwSoLfNVrqSlTtuUApwH36LjzGU0HLs4C_2qqTTjXFE,7859
 mxlpy/fns.py,sha256=ct_RFj9koW8vXHyr27GnbZUHUS_zfs4rDysybuFiOaU,4599
 mxlpy/identify.py,sha256=af52SCG4nlY9sSw22goaIheuvXR09QYK4ksCT24QHWI,1946
 mxlpy/label_map.py,sha256=urv-QTb0MUEKjwWvKtJSB8H2kvhLn1EKfRIH7awQQ8Y,17769
-mxlpy/linear_label_map.py,sha256=2lgERcUVDLXruRI08HBYJo_wK654y46voLUeBTzBy3k,10312
-mxlpy/mc.py,sha256=HWuJq4fV_wfTDERbLJRSF3fjCCYMxzLdqAyO53Z_uF8,16985
-mxlpy/mca.py,sha256=H0dfV45Kz5nMIW8s2V61op7x6LmI21wWgRf94i6iIY4,9328
-mxlpy/model.py,sha256=-BmS4bGCq_fMUnRLZG5uwl86ip_SiaWxsbgLPeV0nHQ,57656
+mxlpy/linear_label_map.py,sha256=DqzN_akacPccZwzYAR3ANIdzAU_GU6Xe6gWV9DHAAWU,10282
+mxlpy/mc.py,sha256=oYd8a3ycyZLyh-ZxTYUjDRNfsCcwSQaLWssxv0yC5Cc,17399
+mxlpy/mca.py,sha256=1_qBX9lHI6svXSebtwvMldAMwPlLqMylAPmxMbMQdWw,9359
+mxlpy/model.py,sha256=qzol8nDSbM3HdESh50c4UFjn6Pw5JwcvhQ5AyKnbyvc,57576
 mxlpy/npe.py,sha256=oiRLA43-qf-AcS2KpQfJIOt7-Ev9Aj5sF6TMq9bJn84,8747
 mxlpy/parallel.py,sha256=kX4Td5YoovDwZp6kX_3cfO6QtHSS9ieJ0bMZiKs3Xv8,5002
 mxlpy/parameterise.py,sha256=2jMhhO-bHTFP_0kXercJekeATAZYBg5FrK1MQ_mWGpk,654
@@ -15,17 +15,17 @@ mxlpy/paths.py,sha256=TK2wO4N9lG-UV1JGfeB64q48JVDbwqIUj63rl55MKuQ,1022
 mxlpy/plot.py,sha256=4uu-6d8LH-GWX-sG_TlSpkSsnikv1DLTtnjJzA7nuRA,24670
 mxlpy/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mxlpy/report.py,sha256=h7dhcBzPFydLPxdsEXokzDf7Ce4PirXMsvLqlDZLSWM,7181
-mxlpy/scan.py,sha256=-1SLyXJOX3U3CxeP1dEC4ytAoBMCH0Ql89wGvsG3LbI,18858
-mxlpy/simulator.py,sha256=vuTLuVanCIGAEqW8NUdGQvVKgoyvd45O-xBsbUoKaCI,21372
-mxlpy/types.py,sha256=RRhi1s6T9Yy8uZdLkWi7pvQTLmyPOlCgGTF8URYQGVA,14149
+mxlpy/scan.py,sha256=FBPpjv66v4IWZ5OwG_EWUdrucLWR9gq_XEsLFC-otaw,18969
+mxlpy/simulator.py,sha256=9Ne4P5Jrwgx4oAlljPvCqSCCy98_5Lv1B87y1AkbI4c,21041
+mxlpy/types.py,sha256=GbdyzEDTN8QfUH6-XXdNgf_TzqIXaYvcZGxaXc5kVio,14509
 mxlpy/experimental/__init__.py,sha256=kZTE-92OErpHzNRqmgSQYH4CGXrogGJ5EL35XGZQ81M,206
 mxlpy/experimental/diff.py,sha256=4bztagJzFMsQJM7dlun_kv-WrWssM8CIw7gcL63hFf8,8952
 mxlpy/integrators/__init__.py,sha256=kqmV6a0TRyLGR_XqbyAI652AfptYnXAUpqbSFg0CpP8,450
-mxlpy/integrators/int_assimulo.py,sha256=d-4HHOj4vmGpg8ig2IXMO5CPiIrq89_quEKvCxIKrhw,4747
+mxlpy/integrators/int_assimulo.py,sha256=TCBWQd558ZeRdBba1jCNsFyLBOssKvm8dXK36Aqg4_k,4817
 mxlpy/integrators/int_scipy.py,sha256=dFHlYTeb2zX97f3VuNdMJdI7WEYshF4JAIgprKKk2z4,4581
 mxlpy/meta/__init__.py,sha256=Jyy4063fZy6iT4LSwjPyEAVr4N_3xxcLc8wDBoDPyKc,278
-mxlpy/meta/codegen_latex.py,sha256=1z0waYPmohY9GTJ_5DBuwXOXGTCHCH8E14tg6MYsf2A,13460
-mxlpy/meta/codegen_modebase.py,sha256=qQ8p6_KqMYCw7SRmf2HHRGvl25sYPKVI_zWKhzFhFLw,3138
+mxlpy/meta/codegen_latex.py,sha256=R0OJqzE7PnOCWLk52C3XWuRb-zI2eYTvV2oJZJvPsOE,13414
+mxlpy/meta/codegen_modebase.py,sha256=_ZAW4NvXhKwJQLGz5hkwwZpL2JMAJlfG-GUWkYIiNvw,3124
 mxlpy/meta/codegen_py.py,sha256=xSdeuEGPGc-QKRMgJO4VSPGMlxCPEV5prkKjNQ2D2hg,3483
 mxlpy/meta/source_tools.py,sha256=EN3OoGQaXeIsDTJvA7S15-xDBra3DCIyFZEJ6h0Fy0k,11125
 mxlpy/nn/__init__.py,sha256=yUc4o-iqfVVzkq9tZCstWwizrCqNlMft0YUwWGFFO-E,219
@@ -44,7 +44,7 @@ mxlpy/surrogates/_torch.py,sha256=E_1eDUlPSVFwROkdMDCqYwwHE-61pjNMJWotnhjzge0,58
 mxlpy/symbolic/__init__.py,sha256=3hQjCMw8-6iOxeUdfnCg8449fF_BRF2u6lCM1GPpkRY,222
 mxlpy/symbolic/strikepy.py,sha256=r6nRtckV1nxKq3i1bYYWZOkzwZ5XeKQuZM5ck44vUo0,20010
 mxlpy/symbolic/symbolic_model.py,sha256=YL9noEeP3_0DoKXwMPELtfmPuP6mgNcLIJgDRCkyB7A,2434
-mxlpy-0.14.0.dist-info/METADATA,sha256=WyKwohN13eTY0JZRyWaNpVFJfAD4z0gviWZ212aAKbo,4564
-mxlpy-0.14.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-mxlpy-0.14.0.dist-info/licenses/LICENSE,sha256=bEzjyjy1stQhfRDVaVHa3xV1x-V8emwdlbMvYO8Zo84,35073
-mxlpy-0.14.0.dist-info/RECORD,,
+mxlpy-0.16.0.dist-info/METADATA,sha256=ySMK4udu6wgaUpG7Wn0sa-XYUkaVz4u19C5PjMEM5p0,4551
+mxlpy-0.16.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+mxlpy-0.16.0.dist-info/licenses/LICENSE,sha256=bEzjyjy1stQhfRDVaVHa3xV1x-V8emwdlbMvYO8Zo84,35073
+mxlpy-0.16.0.dist-info/RECORD,,