mxlpy 0.12.0__py3-none-any.whl → 0.14.0__py3-none-any.whl

mxlpy/plot.py

@@ -52,7 +52,7 @@ __all__ = [
 
 import itertools as it
 import math
-from typing import TYPE_CHECKING, Literal, cast
+from typing import TYPE_CHECKING, Any, Literal, cast
 
 import numpy as np
 import pandas as pd
@@ -292,15 +292,19 @@ def reset_prop_cycle(ax: Axes) -> None:
 def context(
     colors: list[str] | None = None,
     line_width: float | None = None,
+    line_style: Linestyle | None = None,
+    rc: dict[str, Any] | None = None,
 ) -> Generator[None, None, None]:
     """Context manager to set the defaults for plots.
 
     Args:
         colors: colors to use for the plot.
         line_width: line width to use for the plot.
+        line_style: line style to use for the plot.
+        rc: additional keyword arguments to pass to the rc context.
 
     """
-    rc = {}
+    rc = {} if rc is None else rc
 
     if colors is not None:
         rc["axes.prop_cycle"] = cycler(color=colors)
@@ -308,6 +312,9 @@ def context(
     if line_width is not None:
         rc["lines.linewidth"] = line_width
 
+    if line_style is not None:
+        rc["lines.linestyle"] = line_style
+
     with plt.rc_context(rc):
         yield
 
@@ -476,19 +483,17 @@ def lines(
 ) -> FigAx:
     """Plot multiple lines on the same axis."""
     fig, ax = _default_fig_ax(ax=ax, grid=grid)
-    ax.plot(
+    _lines = ax.plot(
         x.index,
         x,
-        # linestyle=linestyle,
-        # linewidth=linewidth,
         alpha=alpha,
     )
     _default_labels(ax, xlabel=x.index.name, ylabel=None)
     if legend:
-        if isinstance(x, pd.Series):
-            ax.legend([str(x.name)])
-        else:
-            ax.legend(x.columns)
+        names = x.columns if isinstance(x, pd.DataFrame) else [str(x.name)]
+        for line, name in zip(_lines, names, strict=True):
+            line.set_label(name)
+        ax.legend()
     return fig, ax
 
 

mxlpy/simulator.py

@@ -10,6 +10,7 @@ Classes:
 
 from __future__ import annotations
 
+import warnings
 from dataclasses import dataclass, field
 from typing import TYPE_CHECKING, Literal, Self, cast, overload
 
@@ -319,6 +320,7 @@ class Simulator:
     variables: list[pd.DataFrame] | None
     dependent: list[pd.DataFrame] | None
     simulation_parameters: list[dict[str, float]] | None
+    use_jacobian: bool
 
     # For resets (e.g. update variable)
     _integrator_type: IntegratorType
@@ -330,6 +332,7 @@ class Simulator:
         y0: dict[str, float] | None = None,
         integrator: IntegratorType = DefaultIntegrator,
         *,
+        use_jacobian: bool = False,
         test_run: bool = True,
     ) -> None:
         """Initialize the Simulator.
@@ -339,6 +342,7 @@ class Simulator:
             y0: Initial conditions for the model variables.
                 If None, the initial conditions are obtained from the model.
             integrator: The integrator to use for the simulation.
+            use_jacobian: Whether to use the Jacobian for the simulation.
             test_run (bool, optional): If True, performs a test run for better error messages
 
         """
@@ -348,7 +352,9 @@ class Simulator:
         self._integrator_type = integrator
         self._time_shift = None
         self.variables = None
+        self.dependent = None
         self.simulation_parameters = None
+        self.use_jacobian = use_jacobian
 
         if test_run:
             self.model.get_right_hand_side(self.y0, time=0)
@@ -360,16 +366,29 @@ class Simulator:
 
         from mxlpy.symbolic import to_symbolic_model
 
-        try:
-            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)
-
-        except:  # noqa: E722
-            _jacobian = None  # type: ignore
+        _jacobian = 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)
+            except Exception as e:  # noqa: BLE001
+                warnings.warn(str(e), stacklevel=2)
 
         y0 = self.y0
         self.integrator = self._integrator_type(

mxlpy/types.py

@@ -192,7 +192,11 @@ class Derived:
             dependent: Dictionary of dependent variables.
 
         """
-        dependent[self.name] = self.fn(*dependent.loc[:, self.args].to_numpy().T)
+        try:
+            dependent[self.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]
 
 
 @dataclass(kw_only=True, slots=True)
@@ -233,7 +237,11 @@ class Readout:
             dependent: Dictionary of dependent variables.
 
         """
-        dependent[self.name] = self.fn(*dependent.loc[:, self.args].to_numpy().T)
+        try:
+            dependent[self.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]
 
 
 @dataclass(kw_only=True, slots=True)

{mxlpy-0.12.0.dist-info → mxlpy-0.14.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mxlpy
-Version: 0.12.0
+Version: 0.14.0
 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>

{mxlpy-0.12.0.dist-info → mxlpy-0.14.0.dist-info}/RECORD

@@ -12,12 +12,12 @@ 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
 mxlpy/paths.py,sha256=TK2wO4N9lG-UV1JGfeB64q48JVDbwqIUj63rl55MKuQ,1022
-mxlpy/plot.py,sha256=z1JW7Si1JQyNMj_MMLkgbLkOkSjVcfAZJGjm_WqCgT4,24355
+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=CeMmm5SdgJphQWWBygnv0rxiXjBUJPWHV8-bh6miJNM,20494
-mxlpy/types.py,sha256=aWDtWOTZo4UQJ3rYGq1m6aV4hGxIjvycfJGc8CIDQLE,13775
+mxlpy/simulator.py,sha256=vuTLuVanCIGAEqW8NUdGQvVKgoyvd45O-xBsbUoKaCI,21372
+mxlpy/types.py,sha256=RRhi1s6T9Yy8uZdLkWi7pvQTLmyPOlCgGTF8URYQGVA,14149
 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
@@ -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-0.12.0.dist-info/METADATA,sha256=Ul9QrtiIlIBZSsRGrTF2J-D_ssjpQtpsw_4IA3LR_lg,4564
-mxlpy-0.12.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-mxlpy-0.12.0.dist-info/licenses/LICENSE,sha256=bEzjyjy1stQhfRDVaVHa3xV1x-V8emwdlbMvYO8Zo84,35073
-mxlpy-0.12.0.dist-info/RECORD,,
+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,,