mxlpy 0.19.0__py3-none-any.whl → 0.20.0__py3-none-any.whl

mxlpy/model.py

@@ -17,13 +17,13 @@ import numpy as np
 import pandas as pd
 
 from mxlpy import fns
-from mxlpy.types import (
-    AbstractSurrogate,
-    Array,
-    Derived,
-    Reaction,
-    Readout,
-)
+from mxlpy.types import AbstractSurrogate, Array, Derived, Reaction, Readout
+
+if TYPE_CHECKING:
+    from collections.abc import Iterable, Mapping
+    from inspect import FullArgSpec
+
+    from mxlpy.types import Callable, Param, RateFn, RetType
 
 __all__ = [
     "ArityMismatchError",
@@ -34,12 +34,6 @@ __all__ = [
     "ModelCache",
 ]
 
-if TYPE_CHECKING:
-    from collections.abc import Iterable, Mapping
-    from inspect import FullArgSpec
-
-    from mxlpy.types import Callable, Param, RateFn, RetType
-
 
 @dataclass
 class Dependency:
@@ -694,6 +688,21 @@ class Model:
 
         return self
 
+    def get_unused_parameters(self) -> set[str]:
+        """Get parameters which aren't used in the model."""
+        args = set()
+        for variable in self._variables.values():
+            if isinstance(variable, Derived):
+                args.update(variable.args)
+        for derived in self._derived.values():
+            args.update(derived.args)
+        for reaction in self._reactions.values():
+            args.update(reaction.args)
+        for surrogate in self._surrogates.values():
+            args.update(surrogate.args)
+
+        return set(self._parameters).difference(args)
+
     ##########################################################################
     # Variables
     ##########################################################################
@@ -1115,10 +1124,29 @@ class Model:
         args = self.get_dependent(variables=variables, time=time)
 
         stoich = copy.deepcopy(cache.stoich_by_cpds[variable])
-        for rxn, derived in cache.dyn_stoich_by_cpds[variable].items():
+        for rxn, derived in cache.dyn_stoich_by_cpds.get(variable, {}).items():
             stoich[rxn] = float(derived.fn(*(args[i] for i in derived.args)))
         return stoich
 
+    def get_raw_stoichiometries_of_variable(
+        self, variable: str
+    ) -> dict[str, float | Derived]:
+        """Retrieve the raw stoichiometry of a specific variable.
+
+        Examples:
+            >>> model.get_stoichiometries_of_variable("x1")
+                {"v1": -1, "v2": Derived(...)}
+
+        Args:
+            variable: The name of the variable for which to retrieve the stoichiometry.
+
+        """
+        stoichs: dict[str, dict[str, float | Derived]] = {}
+        for rxn_name, rxn in self._reactions.items():
+            for cpd_name, factor in rxn.stoichiometry.items():
+                stoichs.setdefault(cpd_name, {})[rxn_name] = factor
+        return stoichs[variable]
+
     @_invalidate_cache
     def add_reaction(
         self,

mxlpy/nn/_keras.py

@@ -1,12 +1,19 @@
-from typing import cast
+from __future__ import annotations
+
+from typing import TYPE_CHECKING, cast
 
 import keras
 import pandas as pd
 from tqdm.keras import TqdmCallback
 
-from mxlpy.types import Array
+if TYPE_CHECKING:
+    from mxlpy.types import Array
 
-__all__ = ["LSTM", "MLP", "train"]
+__all__ = [
+    "LSTM",
+    "MLP",
+    "train",
+]
 
 
 def train(

mxlpy/nn/_torch.py

@@ -24,7 +24,13 @@ if TYPE_CHECKING:
 
     from mxlpy.types import Array
 
-__all__ = ["DefaultDevice", "LSTM", "LossFn", "MLP", "train"]
+__all__ = [
+    "DefaultDevice",
+    "LSTM",
+    "LossFn",
+    "MLP",
+    "train",
+]
 
 DefaultDevice = torch.device("cpu")
 

mxlpy/parallel.py

@@ -24,11 +24,14 @@ from typing import TYPE_CHECKING, Any, cast
 import pebble
 from tqdm import tqdm
 
-__all__ = ["Cache", "parallelise"]
-
 if TYPE_CHECKING:
     from collections.abc import Callable, Collection, Hashable
 
+__all__ = [
+    "Cache",
+    "parallelise",
+]
+
 
 def _pickle_name(k: Hashable) -> str:
     return f"{k}.p"

mxlpy/parameterise.py

@@ -1,11 +1,19 @@
 """Module to parameterise models."""
 
-from pathlib import Path
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
 
-import pandas as pd
 from parameteriser.brenda.v0 import Brenda
 
-__all__ = ["get_km_and_kcat_from_brenda"]
+if TYPE_CHECKING:
+    from pathlib import Path
+
+    import pandas as pd
+
+__all__ = [
+    "get_km_and_kcat_from_brenda",
+]
 
 
 def get_km_and_kcat_from_brenda(

mxlpy/plot.py

@@ -19,10 +19,41 @@ Functions:
 from __future__ import annotations
 
 import contextlib
+import itertools as it
+import math
+from dataclasses import dataclass
+from typing import TYPE_CHECKING, Any, Literal, cast, overload
 
+import numpy as np
+import pandas as pd
+import seaborn as sns
 from cycler import cycler
+from matplotlib import pyplot as plt
+from matplotlib.axes import Axes
+from matplotlib.colors import (
+    LogNorm,
+    Normalize,
+    SymLogNorm,
+    colorConverter,  # type: ignore
+)
+from matplotlib.figure import Figure
+from mpl_toolkits.mplot3d import Axes3D
+
+from mxlpy.label_map import LabelMapper
+
+if TYPE_CHECKING:
+    from collections.abc import Generator, Iterable, Iterator
+
+    from matplotlib.collections import QuadMesh
+    from numpy.typing import NDArray
+
+    from mxlpy.linear_label_map import LinearLabelMapper
+    from mxlpy.model import Model
+    from mxlpy.types import Array, ArrayLike
+
 
 __all__ = [
+    "Axs",
     "Color",
     "FigAx",
     "FigAxs",
@@ -31,7 +62,10 @@ __all__ = [
     "RGBA",
     "add_grid",
     "bars",
+    "bars_autogrouped",
+    "bars_grouped",
     "context",
+    "grid_labels",
     "grid_layout",
     "heatmap",
     "heatmap_from_2d_idx",
@@ -53,37 +87,45 @@ __all__ = [
     "violins_from_2d_idx",
 ]
 
-import itertools as it
-import math
-from typing import TYPE_CHECKING, Any, Literal, cast
 
-import numpy as np
-import pandas as pd
-import seaborn as sns
-from matplotlib import pyplot as plt
-from matplotlib.axes import Axes
-from matplotlib.colors import (
-    LogNorm,
-    Normalize,
-    SymLogNorm,
-    colorConverter,  # type: ignore
-)
-from matplotlib.figure import Figure
-from mpl_toolkits.mplot3d import Axes3D
+@dataclass
+class Axs:
+    """Convenience container  axes."""
 
-from mxlpy.label_map import LabelMapper
+    axs: NDArray[np.object_]
 
-if TYPE_CHECKING:
-    from collections.abc import Generator, Iterable
+    def __iter__(self) -> Iterator[Axes]:
+        """Get flat axes."""
+        yield from cast(list[Axes], self.axs.flatten())
 
-    from matplotlib.collections import QuadMesh
+    def __len__(self) -> int:
+        """Length of axes."""
+        return len(self.axs.flatten())
+
+    @overload
+    def __getitem__(self, row_col: int) -> Axes: ...
+
+    @overload
+    def __getitem__(self, row_col: slice) -> NDArray[np.object_]: ...
+
+    @overload
+    def __getitem__(self, row_col: tuple[int, int]) -> Axes: ...
+
+    @overload
+    def __getitem__(self, row_col: tuple[slice, int]) -> NDArray[np.object_]: ...
+
+    @overload
+    def __getitem__(self, row_col: tuple[int, slice]) -> NDArray[np.object_]: ...
+
+    def __getitem__(
+        self, row_col: int | slice | tuple[int | slice, int | slice]
+    ) -> Axes | NDArray[np.object_]:
+        """Get Axes or Array of Axes."""
+        return cast(Axes, self.axs[row_col])
 
-    from mxlpy.linear_label_map import LinearLabelMapper
-    from mxlpy.model import Model
-    from mxlpy.types import Array, ArrayLike
 
 type FigAx = tuple[Figure, Axes]
-type FigAxs = tuple[Figure, list[Axes]]
+type FigAxs = tuple[Figure, Axs]
 
 type Linestyle = Literal[
     "solid",
@@ -97,6 +139,7 @@ type RGB = tuple[float, float, float]
 type RGBA = tuple[float, float, float, float]
 type Color = str | RGB | RGBA
 
+
 ##########################################################################
 # Helpers
 ##########################################################################
@@ -158,7 +201,12 @@ def _partition_by_order_of_magnitude(s: pd.Series) -> list[list[str]]:
     """Partition a series into groups based on the order of magnitude of the values."""
     return [
         i.to_list()
-        for i in np.floor(np.log10(s)).to_frame(name=0).groupby(0)[0].groups.values()  # type: ignore
+        for i in s.abs()
+        .apply(np.log10)
+        .apply(np.floor)
+        .to_frame(name=0)
+        .groupby(0)[0]
+        .groups.values()  # type: ignore
     ]
 
 
@@ -258,6 +306,18 @@ def add_grid(ax: Axes) -> Axes:
     return ax
 
 
+def grid_labels(
+    axs: Axs,
+    xlabel: str | None = None,
+    ylabel: str | None = None,
+) -> None:
+    """Apply labels to left and bottom axes."""
+    for ax in axs[-1, :]:
+        ax.set_xlabel(xlabel)
+    for ax in axs[:, 0]:
+        ax.set_ylabel(ylabel)
+
+
 def rotate_xlabels(
     ax: Axes,
     rotation: float = 45,
@@ -367,7 +427,6 @@ def _default_fig_ax(
 
 
 def _default_fig_axs(
-    axs: list[Axes] | None,
     *,
     ncols: int,
     nrows: int,
@@ -391,19 +450,16 @@ def _default_fig_axs(
         Figure and Axes objects for the plot.
 
     """
-    if axs is None or len(axs) == 0:
-        fig, axs_array = plt.subplots(
-            nrows=nrows,
-            ncols=ncols,
-            sharex=sharex,
-            sharey=sharey,
-            figsize=figsize,
-            squeeze=False,
-            layout="constrained",
-        )
-        axs = list(axs_array.flatten())
-    else:
-        fig = cast(Figure, axs[0].get_figure())
+    fig, axs_array = plt.subplots(
+        nrows=nrows,
+        ncols=ncols,
+        sharex=sharex,
+        sharey=sharey,
+        figsize=figsize,
+        squeeze=False,
+        layout="constrained",
+    )
+    axs = Axs(axs_array)
 
     if grid:
         for ax in axs:
@@ -433,7 +489,6 @@ def two_axes(
 ) -> FigAxs:
     """Create a figure with two axes."""
     return _default_fig_axs(
-        None,
         ncols=2,
         nrows=1,
         figsize=figsize,
@@ -448,18 +503,17 @@ def grid_layout(
     *,
     n_cols: int = 2,
     col_width: float = 3,
-    row_height: float = 4,
+    row_height: float = 2.5,
     sharex: bool = True,
     sharey: bool = False,
     grid: bool = True,
-) -> tuple[Figure, list[Axes]]:
+) -> FigAxs:
     """Create a grid layout for the given number of groups."""
     n_cols = min(n_groups, n_cols)
     n_rows = math.ceil(n_groups / n_cols)
     figsize = (n_cols * col_width, n_rows * row_height)
 
     return _default_fig_axs(
-        None,
         ncols=n_cols,
         nrows=n_rows,
         figsize=figsize,
@@ -475,19 +529,103 @@ def grid_layout(
 
 
 def bars(
-    x: pd.DataFrame,
+    x: pd.Series | pd.DataFrame,
     *,
     ax: Axes | None = None,
     grid: bool = True,
+    xlabel: str | None = None,
+    ylabel: str | None = None,
 ) -> FigAx:
     """Plot multiple lines on the same axis."""
     fig, ax = _default_fig_ax(ax=ax, grid=grid)
-    sns.barplot(data=x, ax=ax)
-    _default_labels(ax, xlabel=x.index.name, ylabel=None)
-    ax.legend(x.columns)
+    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 ""
+    _default_labels(ax, xlabel=xlabel, ylabel=ylabel)
+    if isinstance(x, pd.DataFrame):
+        ax.legend(x.columns)
     return fig, ax
 
 
+def bars_grouped(
+    groups: list[pd.DataFrame] | list[pd.Series],
+    *,
+    n_cols: int = 2,
+    col_width: float = 3,
+    row_height: float = 4,
+    sharey: bool = False,
+    grid: bool = True,
+    xlabel: str | None = None,
+    ylabel: str | None = None,
+) -> FigAxs:
+    """Plot multiple groups of lines on separate axes."""
+    fig, axs = grid_layout(
+        len(groups),
+        n_cols=n_cols,
+        col_width=col_width,
+        row_height=row_height,
+        sharex=False,
+        sharey=sharey,
+        grid=grid,
+    )
+
+    for group, ax in zip(
+        groups,
+        axs,
+        strict=False,
+    ):
+        bars(
+            group,
+            ax=ax,
+            grid=grid,
+            xlabel=xlabel,
+            ylabel=ylabel,
+        )
+
+    axsl = list(axs)
+    for i in range(len(groups), len(axs)):
+        axsl[i].set_visible(False)
+
+    return fig, axs
+
+
+def bars_autogrouped(
+    s: pd.Series | pd.DataFrame,
+    *,
+    n_cols: int = 2,
+    col_width: float = 4,
+    row_height: float = 3,
+    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(
+        _partition_by_order_of_magnitude(s)
+        if isinstance(s, pd.Series)
+        else _partition_by_order_of_magnitude(s.max()),
+        max_size=max_group_size,
+    )
+
+    groups: list[pd.Series] | list[pd.DataFrame] = (
+        [s.loc[group] for group in group_names]
+        if isinstance(s, pd.Series)
+        else [s.loc[:, group] for group in group_names]
+    )
+
+    return bars_grouped(
+        groups,
+        n_cols=n_cols,
+        col_width=col_width,
+        row_height=row_height,
+        grid=grid,
+        xlabel=xlabel,
+        ylabel=ylabel,
+    )
+
+
 def lines(
     x: pd.DataFrame | pd.Series,
     *,
@@ -498,6 +636,8 @@ def lines(
     legend: bool = True,
     linewidth: float | None = None,
     linestyle: Linestyle | None = None,
+    xlabel: str | None = None,
+    ylabel: str | None = None,
 ) -> FigAx:
     """Plot multiple lines on the same axis."""
     fig, ax = _default_fig_ax(ax=ax, grid=grid)
@@ -509,7 +649,11 @@ def lines(
         linestyle=linestyle,
         color=color,
     )
-    _default_labels(ax, xlabel=x.index.name, ylabel=None)
+    _default_labels(
+        ax,
+        xlabel=x.index.name if xlabel is None else xlabel,
+        ylabel=ylabel,
+    )
     if legend:
         names = x.columns if isinstance(x, pd.DataFrame) else [str(x.name)]
         for line, name in zip(_lines, names, strict=True):
@@ -533,6 +677,8 @@ def lines_grouped(
     sharex: bool = True,
     sharey: bool = False,
     grid: bool = True,
+    xlabel: str | None = None,
+    ylabel: str | None = None,
     color: Color | list[list[Color]] | None = None,
     linewidth: float | None = None,
     linestyle: Linestyle | None = None,
@@ -561,10 +707,13 @@ def lines_grouped(
             color=color_,
             linewidth=linewidth,
             linestyle=linestyle,
+            xlabel=xlabel,
+            ylabel=ylabel,
         )
 
+    axsl = list(axs)
     for i in range(len(groups), len(axs)):
-        axs[i].set_visible(False)
+        axsl[i].set_visible(False)
 
     return fig, axs
 
@@ -577,6 +726,8 @@ def line_autogrouped(
     row_height: float = 3,
     max_group_size: int = 6,
     grid: bool = True,
+    xlabel: str | None = None,
+    ylabel: str | None = None,
     color: Color | list[list[Color]] | None = None,
     linewidth: float | None = None,
     linestyle: Linestyle | None = None,
@@ -604,6 +755,8 @@ def line_autogrouped(
         color=color,
         linestyle=linestyle,
         linewidth=linewidth,
+        xlabel=xlabel,
+        ylabel=ylabel,
     )
 
 
@@ -886,7 +1039,7 @@ def violins_from_2d_idx(
         grid=grid,
     )
 
-    for ax, col in zip(axs[: len(df.columns)], df.columns, strict=True):
+    for ax, col in zip(axs[: len(df.columns)].flatten(), df.columns, strict=True):
         ax.set_title(col)
         violins(df[col].unstack(), ax=ax)
 

mxlpy/report.py

@@ -1,5 +1,7 @@
 """Generate a report comparing two models."""
 
+from __future__ import annotations
+
 from collections.abc import Callable
 from datetime import UTC, datetime
 from pathlib import Path
@@ -10,7 +12,10 @@ import sympy
 from mxlpy.meta.source_tools import fn_to_sympy
 from mxlpy.model import Model
 
-__all__ = ["AnalysisFn", "markdown"]
+__all__ = [
+    "AnalysisFn",
+    "markdown",
+]
 
 type AnalysisFn = Callable[[Model, Model, Path], tuple[str, Path]]
 
@@ -84,9 +89,29 @@ def markdown(
 
     """
     content: list[str] = [
-        f"# Report:  {datetime.now(UTC).strftime('%Y-%m-%d')}",
+        f"# Report:  {datetime.now(UTC).strftime('%Y-%m-%d')}\n",
     ]
 
+    # Unused
+    if unused := m2.get_unused_parameters():
+        content.append("## <span style='color: red'>Unused parameters</span>\n")
+        names = "\n".join(f"<li>{i}</li>\n" for i in sorted(unused))
+        content.append(f"<ul>\n{names}\n</ul>\n")
+
+    # Model stats
+    content.extend(
+        [
+            "| Model component | Old | New |",
+            "| --- | --- | --- |",
+            f"| variables | {len(m1.variables)} | {len(m2.variables)}|",
+            f"| parameters | {len(m1.parameters)} | {len(m2.parameters)}|",
+            f"| derived parameters | {len(m1.derived_parameters)} | {len(m2.derived_parameters)}|",
+            f"| derived variables | {len(m1.derived_variables)} | {len(m2.derived_variables)}|",
+            f"| reactions | {len(m1.reactions)} | {len(m2.reactions)}|",
+            f"| surrogates | {len(m1._surrogates)} | {len(m2._surrogates)}|",  # noqa: SLF001
+        ]
+    )
+
     # Variables
     new_variables, removed_variables, changed_variables = _new_removed_changed(
         m1.variables, m2.variables
@@ -106,7 +131,7 @@ def markdown(
     if len(variables) >= 1:
         content.extend(
             (
-                "## Variables\n",
+                "## Variables\n\n",
                 "| Name | Old Value | New Value |",
                 "| ---- | --------- | --------- |",
             )
@@ -132,7 +157,7 @@ def markdown(
     if len(pars) >= 1:
         content.extend(
             (
-                "## Parameters\n",
+                "## Parameters\n\n",
                 "| Name | Old Value | New Value |",
                 "| ---- | --------- | --------- |",
             )
@@ -159,7 +184,7 @@ def markdown(
     if len(derived) >= 1:
         content.extend(
             (
-                "## Derived\n",
+                "## Derived\n\n",
                 "| Name | Old Value | New Value |",
                 "| ---- | --------- | --------- |",
             )
@@ -187,7 +212,7 @@ def markdown(
     if len(reactions) >= 1:
         content.extend(
             (
-                "## Reactions\n",
+                "## Reactions\n\n",
                 "| Name | Old Value | New Value |",
                 "| ---- | --------- | --------- |",
             )
@@ -207,7 +232,7 @@ def markdown(
     if len(dependent) >= 1:
         content.extend(
             (
-                "## Numerical differences of dependent values\n",
+                "## Numerical differences of dependent values\n\n",
                 "| Name | Old Value | New Value | Relative Change | ",
                 "| ---- | --------- | --------- | --------------- | ",
             )
@@ -226,7 +251,7 @@ def markdown(
     if len(rhs) >= 1:
         content.extend(
             (
-                "## Numerical differences of right hand side values\n",
+                "## Numerical differences of right hand side values\n\n",
                 "| Name | Old Value | New Value | Relative Change | ",
                 "| ---- | --------- | --------- | --------------- | ",
             )

mxlpy/sbml/__init__.py

@@ -5,10 +5,10 @@ Allows importing and exporting metabolic models in SBML format.
 
 from __future__ import annotations
 
+from ._export import write
+from ._import import read
+
 __all__ = [
     "read",
     "write",
 ]
-
-from ._export import write
-from ._import import read