mxlpy 0.22.0__py3-none-any.whl → 0.24.0__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 (
@@ -37,7 +38,10 @@ 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 wadler_lindig import pformat
 
 from mxlpy.label_map import LabelMapper
 
@@ -102,6 +106,10 @@ class Axs:
         """Length of axes."""
         return len(self.axs.flatten())
 
+    def __repr__(self) -> str:
+        """Return default representation."""
+        return pformat(self)
+
     @overload
     def __getitem__(self, row_col: int) -> Axes: ...
 
@@ -210,6 +218,28 @@ def _partition_by_order_of_magnitude(s: pd.Series) -> list[list[str]]:
     ]
 
 
+def _combine_small_groups(
+    groups: list[list[str]], min_group_size: int
+) -> list[list[str]]:
+    """Combine smaller groups."""
+    result = []
+    current_group = groups[0]
+
+    for next_group in groups[1:]:
+        if len(current_group) < min_group_size:
+            current_group.extend(next_group)
+        else:
+            result.append(current_group)
+            current_group = next_group
+
+    # Last group
+    if len(current_group) < min_group_size:
+        result[-1].extend(current_group)
+    else:
+        result.append(current_group)
+    return result
+
+
 def _split_large_groups[T](groups: list[list[T]], max_size: int) -> list[list[T]]:
     """Split groups larger than the given size into smaller groups."""
     return list(
@@ -513,7 +543,7 @@ def grid_layout(
     n_rows = math.ceil(n_groups / n_cols)
     figsize = (n_cols * col_width, n_rows * row_height)
 
-    return _default_fig_axs(
+    fig, axs = _default_fig_axs(
         ncols=n_cols,
         nrows=n_rows,
         figsize=figsize,
@@ -522,6 +552,12 @@ def grid_layout(
         grid=grid,
     )
 
+    # Disable unused plots by default
+    axsl = list(axs)
+    for i in range(n_groups, len(axs)):
+        axsl[i].set_visible(False)
+    return fig, axs
+
 
 ##########################################################################
 # Plots
@@ -541,7 +577,7 @@ 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)
@@ -583,10 +619,6 @@ def bars_grouped(
             ylabel=ylabel,
         )
 
-    axsl = list(axs)
-    for i in range(len(groups), len(axs)):
-        axsl[i].set_visible(False)
-
     return fig, axs
 
 
@@ -596,18 +628,20 @@ def bars_autogrouped(
     n_cols: int = 2,
     col_width: float = 4,
     row_height: float = 3,
+    min_group_size: int = 1,
     max_group_size: int = 6,
     grid: bool = True,
     xlabel: str | None = None,
     ylabel: str | None = None,
 ) -> FigAxs:
     """Plot a series or dataframe with lines grouped by order of magnitude."""
-    group_names = _split_large_groups(
+    group_names = (
         _partition_by_order_of_magnitude(s)
         if isinstance(s, pd.Series)
-        else _partition_by_order_of_magnitude(s.max()),
-        max_size=max_group_size,
+        else _partition_by_order_of_magnitude(s.max())
     )
+    group_names = _combine_small_groups(group_names, min_group_size=min_group_size)
+    group_names = _split_large_groups(group_names, max_size=max_group_size)
 
     groups: list[pd.Series] | list[pd.DataFrame] = (
         [s.loc[group] for group in group_names]
@@ -651,7 +685,7 @@ 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:
@@ -711,10 +745,6 @@ def lines_grouped(
             ylabel=ylabel,
         )
 
-    axsl = list(axs)
-    for i in range(len(groups), len(axs)):
-        axsl[i].set_visible(False)
-
     return fig, axs
 
 
@@ -724,6 +754,7 @@ def line_autogrouped(
     n_cols: int = 2,
     col_width: float = 4,
     row_height: float = 3,
+    min_group_size: int = 1,
     max_group_size: int = 6,
     grid: bool = True,
     xlabel: str | None = None,
@@ -733,12 +764,13 @@ def line_autogrouped(
     linestyle: Linestyle | None = None,
 ) -> FigAxs:
     """Plot a series or dataframe with lines grouped by order of magnitude."""
-    group_names = _split_large_groups(
+    group_names = (
         _partition_by_order_of_magnitude(s)
         if isinstance(s, pd.Series)
-        else _partition_by_order_of_magnitude(s.max()),
-        max_size=max_group_size,
+        else _partition_by_order_of_magnitude(s.max())
     )
+    group_names = _combine_small_groups(group_names, min_group_size=min_group_size)
+    group_names = _split_large_groups(group_names, max_size=max_group_size)
 
     groups: list[pd.Series] | list[pd.DataFrame] = (
         [s.loc[group] for group in group_names]
@@ -792,7 +824,11 @@ 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 +901,11 @@ 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 +942,8 @@ 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 +979,8 @@ 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 +1100,6 @@ 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/_data.py

@@ -3,6 +3,8 @@ from __future__ import annotations
 from dataclasses import dataclass
 from typing import TYPE_CHECKING
 
+from wadler_lindig import pformat
+
 if TYPE_CHECKING:
     from collections.abc import Mapping
 
@@ -26,18 +28,30 @@ class AtomicUnit:
     scale: int
     multiplier: float
 
+    def __repr__(self) -> str:
+        """Return default representation."""
+        return pformat(self)
+
 
 @dataclass
 class CompositeUnit:
     sbml_id: str
     units: list
 
+    def __repr__(self) -> str:
+        """Return default representation."""
+        return pformat(self)
+
 
 @dataclass
 class Parameter:
     value: float
     is_constant: bool
 
+    def __repr__(self) -> str:
+        """Return default representation."""
+        return pformat(self)
+
 
 @dataclass
 class Compartment:
@@ -47,6 +61,10 @@ class Compartment:
     units: str
     is_constant: bool
 
+    def __repr__(self) -> str:
+        """Return default representation."""
+        return pformat(self)
+
 
 @dataclass
 class Compound:
@@ -58,21 +76,37 @@ class Compound:
     is_constant: bool
     is_concentration: bool
 
+    def __repr__(self) -> str:
+        """Return default representation."""
+        return pformat(self)
+
 
 @dataclass
 class Derived:
     body: str
     args: list[str]
 
+    def __repr__(self) -> str:
+        """Return default representation."""
+        return pformat(self)
+
 
 @dataclass
 class Function:
     body: str
     args: list[str]
 
+    def __repr__(self) -> str:
+        """Return default representation."""
+        return pformat(self)
+
 
 @dataclass
 class Reaction:
     body: str
     stoichiometry: Mapping[str, float | str]
     args: list[str]
+
+    def __repr__(self) -> str:
+        """Return default representation."""
+        return pformat(self)

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
@@ -447,15 +447,16 @@ def _create_sbml_variables(
         cpd.setConstant(False)
         cpd.setBoundaryCondition(False)
         cpd.setHasOnlySubstanceUnits(False)
+        cpd.setCompartment("compartment")
         # 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"))
             ar.setVariable(_convert_id_to_sbml(id_=name, prefix="IA"))
             ar.setMath(_sbmlify_fn(init.fn, init.args))
         else:
-            cpd.setInitialAmount(float(init))
+            cpd.setInitialConcentration(float(init))
 
 
 def _create_sbml_derived_variables(*, model: Model, sbml_model: libsbml.Model) -> None:
@@ -494,11 +495,19 @@ 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:
@@ -583,8 +592,8 @@ def _default_compartments(
 ) -> dict[str, Compartment]:
     if compartments is None:
         return {
-            "c": Compartment(
-                name="cytosol",
+            "compartment": Compartment(
+                name="compartment",
                 dimensions=3,
                 size=1,
                 units="litre",