mxlpy 0.22.0__py3-none-any.whl → 0.23.0__py3-none-any.whl

mxlpy/plot.py

@@ -28,6 +28,7 @@ import numpy as np
 import pandas as pd
 import seaborn as sns
 from cycler import cycler
+from matplotlib import colormaps
 from matplotlib import pyplot as plt
 from matplotlib.axes import Axes
 from matplotlib.colors import (
@@ -37,6 +38,8 @@ from matplotlib.colors import (
     colorConverter,  # type: ignore
 )
 from matplotlib.figure import Figure
+from matplotlib.legend import Legend
+from matplotlib.patches import Patch
 from mpl_toolkits.mplot3d import Axes3D
 
 from mxlpy.label_map import LabelMapper
@@ -541,7 +544,7 @@ def bars(
     sns.barplot(data=cast(pd.DataFrame, x), ax=ax)
 
     if xlabel is None:
-        xlabel = x.index.name if x.index.name is not None else ""
+        xlabel = x.index.name if x.index.name is not None else ""  # type: ignore
     _default_labels(ax, xlabel=xlabel, ylabel=ylabel)
     if isinstance(x, pd.DataFrame):
         ax.legend(x.columns)
@@ -651,7 +654,7 @@ def lines(
     )
     _default_labels(
         ax,
-        xlabel=x.index.name if xlabel is None else xlabel,
+        xlabel=x.index.name if xlabel is None else xlabel,  # type: ignore
         ylabel=ylabel,
     )
     if legend:
@@ -792,7 +795,11 @@ def line_mean_std(
         color=color,
         alpha=alpha,
     )
-    _default_labels(ax, xlabel=df.index.name, ylabel=None)
+    _default_labels(
+        ax,
+        xlabel=df.index.name,  # type: ignore
+        ylabel=None,
+    )
     return fig, ax
 
 
@@ -865,11 +872,11 @@ def _create_heatmap(
     if title is not None:
         ax.set_title(title)
     ax.set_xticks(
-        np.arange(0, len(df.columns), 1, dtype=float) + 0.5,
+        np.arange(0, len(df.columns), 1, dtype=float) + 0.5,  # type: ignore
         labels=xticklabels,
     )
     ax.set_yticks(
-        np.arange(0, len(df.index), 1, dtype=float) + 0.5,
+        np.arange(0, len(df.index), 1, dtype=float) + 0.5,  # type: ignore
         labels=yticklabels,
     )
 
@@ -906,8 +913,8 @@ def heatmap(
         ax=ax,
         df=df,
         title=title,
-        xlabel=df.index.name,
-        ylabel=df.columns.name,
+        xlabel=df.index.name,  # type: ignore
+        ylabel=df.columns.name,  # type: ignore
         xticklabels=cast(list, df.columns),
         yticklabels=cast(list, df.index),
         annotate=annotate,
@@ -943,8 +950,8 @@ def heatmap_from_2d_idx(
 
     return _create_heatmap(
         df=df2d,
-        xlabel=df2d.index.name,
-        ylabel=df2d.columns.name,
+        xlabel=df2d.index.name,  # type: ignore
+        ylabel=df2d.columns.name,  # type: ignore
         xticklabels=[f"{i:.2f}" for i in df2d.columns],
         yticklabels=[f"{i:.2f}" for i in df2d.index],
         ax=ax,
@@ -1064,11 +1071,6 @@ def shade_protocol(
     add_legend: bool = True,
 ) -> None:
     """Shade the given protocol on the given axis."""
-    from matplotlib import colormaps
-    from matplotlib.colors import Normalize
-    from matplotlib.legend import Legend
-    from matplotlib.patches import Patch
-
     cmap = colormaps[cmap_name]
     norm = Normalize(
         vmin=protocol.min() if vmin is None else vmin,

mxlpy/sbml/_export.py

@@ -10,7 +10,7 @@ import numpy as np
 
 from mxlpy.meta.source_tools import get_fn_ast
 from mxlpy.sbml._data import AtomicUnit, Compartment
-from mxlpy.types import Derived
+from mxlpy.types import Derived, InitialAssignment
 
 if TYPE_CHECKING:
     from collections.abc import Callable
@@ -448,7 +448,7 @@ def _create_sbml_variables(
         cpd.setBoundaryCondition(False)
         cpd.setHasOnlySubstanceUnits(False)
         # cpd.setUnit() # FIXME: implement
-        if isinstance((init := variable.initial_value), Derived):
+        if isinstance((init := variable.initial_value), InitialAssignment):
             ar = sbml_model.createInitialAssignment()
             ar.setId(_convert_id_to_sbml(id_=name, prefix="IA"))
             ar.setName(_convert_id_to_sbml(id_=name, prefix="IA"))
@@ -494,11 +494,19 @@ def _create_sbml_parameters(
         sbml_model : libsbml.Model
 
     """
-    for parameter_id, value in model.get_parameter_values().items():
+    for name, value in model.get_raw_parameters().items():
         k = sbml_model.createParameter()
-        k.setId(_convert_id_to_sbml(id_=parameter_id, prefix="PAR"))
+        k.setId(_convert_id_to_sbml(id_=name, prefix="PAR"))
         k.setConstant(True)
-        k.setValue(float(value))
+
+        if isinstance((init := value.value), InitialAssignment):
+            ar = sbml_model.createInitialAssignment()
+            ar.setId(_convert_id_to_sbml(id_=name, prefix="IA"))
+            ar.setName(_convert_id_to_sbml(id_=name, prefix="IA"))
+            ar.setVariable(_convert_id_to_sbml(id_=name, prefix="IA"))
+            ar.setMath(_sbmlify_fn(init.fn, init.args))
+        else:
+            k.setValue(float(init))
 
 
 def _create_sbml_derived_parameters(*, model: Model, sbml_model: libsbml.Model) -> None: