modelbase2 0.1.78__py3-none-any.whl → 0.2.0__py3-none-any.whl

modelbase2/utils/plotting.py

@@ -1,372 +0,0 @@
-from __future__ import annotations
-
-import itertools as it
-import math
-import matplotlib.pyplot as plt
-import numpy as np
-import pandas as pd
-from ..types import Axes, Figure
-from matplotlib.collections import QuadMesh
-from matplotlib.colors import LogNorm, Normalize, SymLogNorm
-from matplotlib.colors import colorConverter as _colorConverter
-from typing import Any, Iterable, Optional, Sized, Union
-
-
-def _get_plot_kwargs(
-    figure_kwargs: Optional[dict[str, Any]],
-    subplot_kwargs: Optional[dict[str, Any]],
-    plot_kwargs: Optional[dict[str, Any]],
-    grid_kwargs: Optional[dict[str, Any]],
-    tick_kwargs: Optional[dict[str, Any]],
-    label_kwargs: Optional[dict[str, Any]],
-    title_kwargs: Optional[dict[str, Any]],
-    legend_kwargs: Optional[dict[str, Any]],
-) -> dict[str, dict[str, Any]]:
-    """Get default plot kwargs or overwrite them."""
-    local_figure_kwargs = {"figsize": (10, 7)}
-    local_subplot_kwargs = {"facecolor": "white"}
-    local_plot_kwargs = {"linewidth": 4}
-    local_grid_kwargs = {
-        "color": (0, 0, 0),
-        "alpha": 0.33,
-        "linestyle": "dashed",
-        "linewidth": 1,
-    }
-    local_tick_kwargs = {
-        "direction": "out",
-        "length": 6,
-        "width": 2,
-        "labelsize": 14,
-        "color": "0.15",
-        "pad": 7,
-    }
-    local_label_kwargs = {"fontsize": 14}
-    local_title_kwargs = {"fontsize": 18}
-    local_legend_kwargs = {
-        "loc": "upper left",
-        "bbox_to_anchor": (1.02, 1),
-        "borderaxespad": 0,
-        "ncol": 1,
-        "fontsize": 12,
-        "numpoints": 1,
-        "scatterpoints": 1,
-        "markerscale": 1,
-        "frameon": False,
-    }
-    if figure_kwargs is not None:
-        local_figure_kwargs.update(figure_kwargs)
-    if subplot_kwargs is not None:
-        local_subplot_kwargs.update(subplot_kwargs)
-    if plot_kwargs is not None:
-        local_plot_kwargs.update(plot_kwargs)
-    if grid_kwargs is not None:
-        local_grid_kwargs.update(grid_kwargs)
-    if tick_kwargs is not None:
-        local_tick_kwargs.update(tick_kwargs)
-    if label_kwargs is not None:
-        local_label_kwargs.update(label_kwargs)
-    if title_kwargs is not None:
-        local_title_kwargs.update(title_kwargs)
-    if legend_kwargs is not None:
-        local_legend_kwargs.update(legend_kwargs)
-    return {
-        "figure": local_figure_kwargs,
-        "subplot": local_subplot_kwargs,
-        "plot": local_plot_kwargs,
-        "grid": local_grid_kwargs,
-        "ticks": local_tick_kwargs,
-        "label": local_label_kwargs,
-        "title": local_title_kwargs,
-        "legend": local_legend_kwargs,
-    }
-
-
-def _style_subplot(
-    ax: Axes,
-    kwargs: dict,
-    xlabel: str | None = None,
-    ylabel: str | None = None,
-    zlabel: str | None = None,
-    title: str | None = None,
-    legend: bool = False,
-    grid: bool | None = None,
-) -> None:
-    """Set style of the subplot."""
-    if grid:
-        ax.grid(True, which="major", axis="both", **kwargs["grid"])
-    if legend:
-        ax.legend(**kwargs["legend"])
-    if title is not None:
-        ax.set_title(title, **kwargs["title"])
-    if xlabel is not None:
-        ax.set_xlabel(xlabel, **kwargs["label"])
-    if ylabel is not None:
-        ax.set_ylabel(ylabel, **kwargs["label"])
-    if zlabel is not None:
-        ax.set_zlabel(zlabel, **kwargs["label"])
-    ax.tick_params(**kwargs["ticks"])
-    for axis in ["top", "bottom", "left", "right"]:
-        ax.spines[axis].set_linewidth(0)
-
-
-def plot(
-    plot_args: Iterable,
-    legend: Optional[Iterable[str]] = None,
-    xlabel: Optional[str] = None,
-    ylabel: Optional[str] = None,
-    title: Optional[str] = None,
-    grid: bool = True,
-    tight_layout: bool = True,
-    ax: Optional[plt.Axes] = None,
-    figure_kwargs: Optional[dict[str, Any]] = None,
-    subplot_kwargs: Optional[dict[str, Any]] = None,
-    plot_kwargs: Optional[dict[str, Any]] = None,
-    grid_kwargs: Optional[dict[str, Any]] = None,
-    legend_kwargs: Optional[dict[str, Any]] = None,
-    tick_kwargs: Optional[dict[str, Any]] = None,
-    label_kwargs: Optional[dict[str, Any]] = None,
-    title_kwargs: Optional[dict[str, Any]] = None,
-) -> tuple[Figure, plt.Axes]:
-    """Plot simulation results as a grid."""
-    kwargs = _get_plot_kwargs(
-        figure_kwargs=figure_kwargs,
-        subplot_kwargs=subplot_kwargs,
-        plot_kwargs=plot_kwargs,
-        grid_kwargs=grid_kwargs,
-        tick_kwargs=tick_kwargs,
-        label_kwargs=label_kwargs,
-        title_kwargs=title_kwargs,
-        legend_kwargs=legend_kwargs,
-    )
-    ylabel = ylabel if ylabel is not None else "Remember to label your axes"
-    xlabel = xlabel if xlabel is not None else "Remember to label your axes"
-
-    if ax is None:
-        fig, ax = plt.subplots(
-            nrows=1,
-            ncols=1,
-            squeeze=True,
-            subplot_kw=kwargs["subplot"],
-            **kwargs["figure"],
-        )
-    else:
-        fig = ax.get_figure()
-    ax.plot(*plot_args, **kwargs["plot"])
-    if grid:
-        ax.grid(True, which="major", axis="both", **kwargs["grid"])
-    if legend is not None:
-        if isinstance(legend, str):
-            legend = [legend]
-        ax.legend(legend, **kwargs["legend"])
-    ax.set_ylabel(ylabel, **kwargs["label"])
-    ax.set_xlabel(xlabel, **kwargs["label"])
-    ax.set_title(title, **kwargs["title"])
-    ax.tick_params(**kwargs["ticks"])
-    if tight_layout:
-        fig.tight_layout()
-    return fig, ax
-
-
-def plot_grid(
-    plot_groups: Sized,
-    legend_groups: Optional[Iterable] = None,
-    ncols: Optional[int] = None,
-    sharex: bool = True,
-    sharey: bool = True,
-    xlabels: Optional[Union[str, Iterable[str]]] = None,
-    ylabels: Optional[Union[str, Iterable[str]]] = None,
-    figure_title: str | None = None,
-    plot_titles: Optional[Union[Iterable[str], Iterable[None]]] = None,
-    grid: bool = True,
-    tight_layout: bool = True,
-    figure_kwargs: Optional[dict[str, Any]] = None,
-    subplot_kwargs: Optional[dict[str, Any]] = None,
-    plot_kwargs: Optional[dict[str, Any]] = None,
-    grid_kwargs: Optional[dict[str, Any]] = None,
-    legend_kwargs: Optional[dict[str, Any]] = None,
-    tick_kwargs: Optional[dict[str, Any]] = None,
-    label_kwargs: Optional[dict[str, Any]] = None,
-    title_kwargs: Optional[dict[str, Any]] = None,
-) -> tuple[Figure, Axes]:
-    """Plot simulation results as a grid."""
-    if ncols is None:
-        _, ncols = min(
-            (
-                (math.ceil(len(plot_groups) / i) * i - len(plot_groups), i)
-                for i in range(2, 6)
-            ),
-            key=lambda x: (x[0], -x[1]),
-        )
-    nrows = math.ceil(len(plot_groups) / ncols)
-    if figure_kwargs is None:
-        figure_kwargs = {}
-    figure_kwargs.setdefault("figsize", (5 * ncols, 4 * nrows))
-    if legend_kwargs is None:
-        legend_kwargs = {}
-    legend_kwargs.setdefault("loc", "best")
-    legend_kwargs.setdefault("bbox_to_anchor", None)
-    legend_kwargs.setdefault("borderaxespad", 0.5)
-    kwargs = _get_plot_kwargs(
-        figure_kwargs=figure_kwargs,
-        subplot_kwargs=subplot_kwargs,
-        plot_kwargs=plot_kwargs,
-        grid_kwargs=grid_kwargs,
-        tick_kwargs=tick_kwargs,
-        label_kwargs=label_kwargs,
-        title_kwargs=title_kwargs,
-        legend_kwargs=legend_kwargs,
-    )
-
-    if legend_groups is None:
-        legend_groups = it.repeat(None)
-    if ylabels is None:
-        ylabels = it.repeat("Remember to label your axes")
-    else:
-        if isinstance(ylabels, str):
-            ylabels = it.repeat(ylabels)
-    if xlabels is None:
-        xlabels = it.repeat("Remember to label your axes")
-    else:
-        if isinstance(xlabels, str):
-            xlabels = it.repeat(xlabels)
-    if plot_titles is None:
-        plot_titles = it.repeat(None)
-
-    fig, axs = plt.subplots(
-        nrows=nrows,
-        ncols=ncols,
-        sharex=sharex,
-        sharey=sharey,
-        squeeze=False,
-        subplot_kw=kwargs["subplot"],
-        **kwargs["figure"],
-    )
-    for ax, plot_args, legend_args, title in zip(axs.ravel(), plot_groups, legend_groups, plot_titles):  # type: ignore
-        ax.plot(*plot_args, **kwargs["plot"])
-        ax.set_title(title, **kwargs["title"])
-        if legend_args is not None:
-            ax.legend(legend_args, **kwargs["legend"])
-        ax.tick_params(**kwargs["ticks"])
-        if grid:
-            ax.grid(True, which="major", axis="both", **kwargs["grid"])
-
-    if sharey:
-        for ax, ylabel in zip(axs[:, 0], ylabels):  # type: ignore
-            ax.set_ylabel(ylabel, **kwargs["label"])
-    else:
-        for ax, ylabel in zip(axs.ravel(), ylabels):
-            ax.set_ylabel(ylabel, **kwargs["label"])
-    if sharex:
-        for ax, xlabel in zip(axs[-1], xlabels):  # type: ignore
-            ax.set_xlabel(xlabel, **kwargs["label"])
-    else:
-        for ax, xlabel in zip(axs.ravel(), xlabels):
-            ax.set_xlabel(xlabel, **kwargs["label"])
-    fig.suptitle(figure_title, y=1.025, **kwargs["title"])
-    if tight_layout:
-        fig.tight_layout()
-    return fig, axs
-
-
-def relative_luminance(color: list[float]) -> float:
-    """Calculate the relative luminance of a color."""
-    rgb = _colorConverter.to_rgba_array(color)[:, :3]
-
-    # If RsRGB <= 0.03928 then R = RsRGB/12.92 else R = ((RsRGB+0.055)/1.055) ^ 2.4
-    rsrgb = np.where(rgb <= 0.03928, rgb / 12.92, ((rgb + 0.055) / 1.055) ** 2.4)
-
-    # L = 0.2126 * R + 0.7152 * G + 0.0722 * B
-    rel_luminance: list[float] = np.matmul(rsrgb, [0.2126, 0.7152, 0.0722])
-    return rel_luminance[0]
-
-
-def get_norm(vmin: float, vmax: float) -> plt.Normalize:
-    if vmax < 1000 and vmin > -1000:
-        norm = Normalize(vmin=vmin, vmax=vmax)
-    elif vmin <= 0:
-        norm = SymLogNorm(linthresh=1, vmin=vmin, vmax=vmax, base=10)
-    else:
-        norm = LogNorm(vmin=vmin, vmax=vmax)
-    return norm
-
-
-def heatmap_from_dataframe(
-    df: pd.DataFrame,
-    title: Optional[str] = None,
-    xlabel: Optional[str] = None,
-    ylabel: Optional[str] = None,
-    annotate: bool = True,
-    colorbar: bool = True,
-    cmap: str = "viridis",
-    vmax: Optional[float] = None,
-    vmin: Optional[float] = None,
-    norm: plt.Normalize | None = None,
-    ax: Optional[Axes] = None,
-    cax: Optional[Axes] = None,
-    sci_annotation_bounds: tuple[float, float] = (0.01, 100),
-    annotation_style: str = "2g",
-    figsize: tuple[float, float] = (8, 6),
-) -> tuple[Figure, plt.Axes, QuadMesh]:
-    data = df.values
-    rows = df.index
-    columns = df.columns
-
-    if ax is None:
-        fig, ax = plt.subplots(figsize=figsize)
-    else:
-        fig = ax.get_figure()
-
-    # Create norm
-    if norm is None:
-        if vmax is None:
-            vmax = np.nanmax(data)
-        if vmin is None:
-            vmin = np.nanmin(data)
-        norm = get_norm(vmin=vmin, vmax=vmax)  # type: ignore
-
-    # Create heatmap
-    hm = ax.pcolormesh(data, norm=norm, cmap=cmap)
-
-    # Despine axis
-    for side in ["top", "right", "left", "bottom"]:
-        ax.spines[side].set_visible(False)
-
-    # Set the axis limits
-    ax.set(xlim=(0, data.shape[1]), ylim=(0, data.shape[0]))
-
-    # Set ticks and ticklabels
-    ax.set_xticks(np.arange(len(columns)) + 0.5)
-    ax.set_xticklabels(columns)
-
-    ax.set_yticks(np.arange(len(rows)) + 0.5)
-    ax.set_yticklabels(rows)
-
-    # Set title and axis labels
-    ax.set_title(title)
-    ax.set_xlabel(xlabel)
-    ax.set_ylabel(ylabel)
-
-    if annotate:
-        text_kwargs = {"ha": "center", "va": "center"}
-        hm.update_scalarmappable()  # So that get_facecolor is an array
-        xpos, ypos = np.meshgrid(np.arange(len(columns)), np.arange(len(rows)))
-        for x, y, val, color in zip(
-            xpos.flat, ypos.flat, hm.get_array(), hm.get_facecolor()
-        ):
-            text_kwargs["color"] = (
-                "black" if relative_luminance(color) > 0.45 else "white"
-            )
-            if sci_annotation_bounds[0] < abs(val) <= sci_annotation_bounds[1]:
-                val_text = f"{val:.{annotation_style}}"
-            else:
-                val_text = f"{val:.0e}"
-            ax.text(x + 0.5, y + 0.5, val_text, **text_kwargs)
-
-    if colorbar:
-        # Add a colorbar
-        cb = ax.figure.colorbar(hm, cax, ax)
-        cb.outline.set_linewidth(0)
-
-    # Invert the y axis to show the plot in matrix form
-    ax.invert_yaxis()
-    return fig, ax, hm

modelbase2-0.1.78.dist-info/METADATA

@@ -1,44 +0,0 @@
-Metadata-Version: 2.1
-Name: modelbase2
-Version: 0.1.78
-Summary: A package to build metabolic models
-Home-page: https://gitlab.com/qtb-hhu/modelbase-software
-License: GPL-3.0-or-later
-Keywords: modelling,ode,metabolic
-Author: Marvin van Aalst
-Author-email: marvin.vanaalst@gmail.com
-Maintainer: Marvin van Aalst
-Maintainer-email: marvin.vanaalst@gmail.com
-Requires-Python: >=3.8,<4.0
-Classifier: Development Status :: 5 - Production/Stable
-Classifier: Environment :: Console
-Classifier: Intended Audience :: Developers
-Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
-Classifier: Operating System :: MacOS
-Classifier: Operating System :: Microsoft :: Windows
-Classifier: Operating System :: OS Independent
-Classifier: Operating System :: POSIX
-Classifier: Operating System :: Unix
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Topic :: Scientific/Engineering
-Classifier: Topic :: Software Development
-Requires-Dist: black (>=22.3.0,<23.0.0)
-Requires-Dist: ipywidgets (>=8.0.0,<9.0.0)
-Requires-Dist: matplotlib (>=3.5.0,<4.0.0)
-Requires-Dist: modelbase (>=1.14.0,<2.0.0)
-Requires-Dist: numpy (>=1.21.4,<2.0.0)
-Requires-Dist: pandas (>=1.3.4,<2.0.0)
-Requires-Dist: python-libsbml (>=5.19.2,<6.0.0)
-Requires-Dist: scipy (>=1.7.2,<2.0.0)
-Requires-Dist: sympy (>=1.9,<2.0)
-Requires-Dist: tqdm (>=4.62.3,<5.0.0)
-Requires-Dist: typing-extensions (>=4.0.0,<5.0.0)
-Project-URL: Documentation, https://modelbase.readthedocs.io/en/latest/
-Project-URL: Repository, https://gitlab.com/qtb-hhu/modelbase-software

modelbase2-0.1.78.dist-info/RECORD

@@ -1,22 +0,0 @@
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-modelbase2/core/variable_container.py,sha256=zww22-mW1XxiBel_4pLE1nnu-bPPqtTLN8sP5dvP1Sg,736
-modelbase2/ode/__init__.py,sha256=7iAUR7B3nPVZ2YLfkOdEv3IZw-hlh1ogxDyjj6Ra4pA,217
-modelbase2/ode/integrator.py,sha256=ZueqzmufHuJYTYGLMQC5KaaGOgjMPB_rkM4ZEMcHQog,2239
-modelbase2/ode/mca.py,sha256=5VNSCa28aub-oGw9vctwSON_OYDtupmzZp0r_-XD4Rs,8450
-modelbase2/ode/model.py,sha256=RYo3ywCfzoCG72FPun3XTl2Pj6EcCa66bN5eO-KhDUc,15618
-modelbase2/ode/simulator.py,sha256=v67OAW8qCdI7iPrr4bTigBbf_lLPUgdcJgIEPpyoWKk,4880
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-modelbase2/types.py,sha256=-h7uRV5ZC_UiUEH1tTm0SunlyLo7TRK3nwMd4-VuLDM,407
-modelbase2/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-modelbase2/utils/plotting.py,sha256=NxobtfoLwPHYz01Cp4PTEefN6sUqRB1vop_EEkJK0Ac,12357
-modelbase2-0.1.78.dist-info/LICENSE,sha256=qvG2VolmSkrcocL34V1ieOx-Rn-fpVcUbb25gHzVgZw,35079
-modelbase2-0.1.78.dist-info/WHEEL,sha256=vxFmldFsRN_Hx10GDvsdv1wroKq8r5Lzvjp6GZ4OO8c,88
-modelbase2-0.1.78.dist-info/METADATA,sha256=I7M9AHIPmFK3ZbuxC9odM9RJplGY7h_fYPHcQELYBys,1900
-modelbase2-0.1.78.dist-info/RECORD,,