scitex 2.5.0__py3-none-any.whl → 2.7.3__py3-none-any.whl

scitex/plt/ax/_style/_set_supxyt.py

@@ -41,16 +41,26 @@ def set_supxyt(ax, xlabel=False, ylabel=False, title=False, format_labels=True):
     return ax
 
 
-def set_supxytc(ax, xlabel=False, ylabel=False, title=False, caption=False, methods=False, stats=False, significance=False, format_labels=True):
+def set_supxytc(
+    ax,
+    xlabel=False,
+    ylabel=False,
+    title=False,
+    caption=False,
+    methods=False,
+    stats=False,
+    significance=False,
+    format_labels=True,
+):
     """Sets figure-level xlabel, ylabel, title, and caption with SciTeX-Paper integration
-    
+
     Parameters
     ----------
     ax : matplotlib.axes.Axes or scitex AxisWrapper
         The axes to modify (figure accessed via ax.get_figure())
     xlabel : str or False, optional
         Figure-level X-axis label, by default False
-    ylabel : str or False, optional 
+    ylabel : str or False, optional
         Figure-level Y-axis label, by default False
     title : str or False, optional
         Figure-level title (suptitle), by default False
@@ -64,17 +74,17 @@ def set_supxytc(ax, xlabel=False, ylabel=False, title=False, caption=False, meth
         Significance statement for SciTeX-Paper integration, by default False
     format_labels : bool, optional
         Whether to apply automatic formatting, by default True
-        
+
     Returns
     -------
     ax : matplotlib.axes.Axes or scitex AxisWrapper
         The modified axes
-        
+
     Examples
     --------
     >>> fig, ((ax1, ax2), (ax3, ax4)) = scitex.plt.subplots(2, 2)
     >>> # Add plots to each panel...
-    >>> ax1.set_supxytc(xlabel='Time (s)', ylabel='Signal Amplitude', 
+    >>> ax1.set_supxytc(xlabel='Time (s)', ylabel='Signal Amplitude',
     ...                 title='Multi-Panel Analysis',
     ...                 caption='Comprehensive analysis showing (A) raw data, (B) filtered signal, (C) power spectrum, and (D) phase analysis.',
     ...                 methods='All experiments performed using standardized protocols.',
@@ -82,25 +92,32 @@ def set_supxytc(ax, xlabel=False, ylabel=False, title=False, caption=False, meth
     >>> scitex.io.save(fig, 'multi_panel.png')  # Caption automatically saved
     """
     # Set labels and title using existing function
-    set_supxyt(ax, xlabel=xlabel, ylabel=ylabel, title=title, format_labels=format_labels)
-    
+    set_supxyt(
+        ax, xlabel=xlabel, ylabel=ylabel, title=title, format_labels=format_labels
+    )
+
     # Store figure-level caption and extended metadata
-    if caption is not False or methods is not False or stats is not False or significance is not False:
+    if (
+        caption is not False
+        or methods is not False
+        or stats is not False
+        or significance is not False
+    ):
         fig = ax.get_figure()
         # Store comprehensive figure-level metadata
         fig_metadata = {
-            'main_caption': caption if caption is not False else None,
-            'methods': methods if methods is not False else None,
-            'stats': stats if stats is not False else None,
-            'significance': significance if significance is not False else None
+            "main_caption": caption if caption is not False else None,
+            "methods": methods if methods is not False else None,
+            "stats": stats if stats is not False else None,
+            "significance": significance if significance is not False else None,
         }
-        
+
         fig._scitex_figure_metadata = fig_metadata
-        
+
         # Backward compatibility - also store simple caption
         if caption is not False:
             fig._scitex_main_caption = caption
-    
+
     return ax
 
 

scitex/plt/ax/_style/_set_xyt.py

@@ -32,16 +32,25 @@ def set_xyt(ax, x=False, y=False, t=False, format_labels=True):
     return ax
 
 
-def set_xytc(ax, x=False, y=False, t=False, c=False, methods=False, stats=False, format_labels=True):
+def set_xytc(
+    ax,
+    x=False,
+    y=False,
+    t=False,
+    c=False,
+    methods=False,
+    stats=False,
+    format_labels=True,
+):
     """Sets xlabel, ylabel, title, and caption with SciTeX-Paper integration
-    
+
     Parameters
     ----------
     ax : matplotlib.axes.Axes or scitex AxisWrapper
         The axes to modify
     x : str or False, optional
         X-axis label, by default False
-    y : str or False, optional 
+    y : str or False, optional
         Y-axis label, by default False
     t : str or False, optional
         Title, by default False
@@ -53,18 +62,18 @@ def set_xytc(ax, x=False, y=False, t=False, c=False, methods=False, stats=False,
         Statistical analysis details for SciTeX-Paper integration, by default False
     format_labels : bool, optional
         Whether to apply automatic formatting, by default True
-        
+
     Returns
     -------
     ax : matplotlib.axes.Axes or scitex AxisWrapper
         The modified axes
-        
+
     Examples
     --------
     >>> fig, ax = scitex.plt.subplots()
     >>> ax.plot(x, y)
-    >>> ax.set_xytc(x='Time (s)', y='Voltage (mV)', 
-    ...             t='Neural Signal', 
+    >>> ax.set_xytc(x='Time (s)', y='Voltage (mV)',
+    ...             t='Neural Signal',
     ...             c='Example neural recording showing action potentials.',
     ...             methods='Intracellular recordings performed using patch-clamp technique.',
     ...             stats='Data analyzed using t-test with p<0.05 significance.')
@@ -72,36 +81,36 @@ def set_xytc(ax, x=False, y=False, t=False, c=False, methods=False, stats=False,
     """
     # Set labels and title using existing function
     set_xyt(ax, x=x, y=y, t=t, format_labels=format_labels)
-    
+
     # Store caption and extended metadata for later use by scitex.io.save()
     if c is not False or methods is not False or stats is not False:
         # Store comprehensive metadata as axis attribute for retrieval by save function
         metadata = {
-            'caption': c if c is not False else None,
-            'methods': methods if methods is not False else None,
-            'stats': stats if stats is not False else None
+            "caption": c if c is not False else None,
+            "methods": methods if methods is not False else None,
+            "stats": stats if stats is not False else None,
         }
-        
-        if hasattr(ax, '_scitex_metadata'):
+
+        if hasattr(ax, "_scitex_metadata"):
             ax._scitex_metadata.update(metadata)
         else:
             # For matplotlib axes, store in figure metadata
             fig = ax.get_figure()
-            if not hasattr(fig, '_scitex_metadata'):
+            if not hasattr(fig, "_scitex_metadata"):
                 fig._scitex_metadata = {}
             # Use axis position as identifier
             fig._scitex_metadata[ax] = metadata
-            
+
         # Backward compatibility - also store simple caption
         if c is not False:
-            if hasattr(ax, '_scitex_caption'):
+            if hasattr(ax, "_scitex_caption"):
                 ax._scitex_caption = c
             else:
                 fig = ax.get_figure()
-                if not hasattr(fig, '_scitex_captions'):
+                if not hasattr(fig, "_scitex_captions"):
                     fig._scitex_captions = {}
                 fig._scitex_captions[ax] = c
-    
+
     return ax
 
 

scitex/plt/ax/_style/_share_axes.py

@@ -133,7 +133,9 @@ def get_global_xlim(*multiple_axes):
     xmin, xmax = np.inf, -np.inf
     for axes in multiple_axes:
         # axes
-        if isinstance(axes, (np.ndarray, scitex.plt._subplots._AxesWrapper.AxesWrapper)):
+        if isinstance(
+            axes, (np.ndarray, scitex.plt._subplots.AxesWrapper)
+        ):
             for ax in axes.flat:
                 _xmin, _xmax = ax.get_xlim()  # Fixed: was get_ylim()
                 xmin = min(xmin, _xmin)
@@ -185,7 +187,9 @@ def get_global_ylim(*multiple_axes):
     ymin, ymax = np.inf, -np.inf
     for axes in multiple_axes:
         # axes
-        if isinstance(axes, (np.ndarray, scitex.plt._subplots._AxesWrapper.AxesWrapper)):
+        if isinstance(
+            axes, (np.ndarray, scitex.plt._subplots.AxesWrapper)
+        ):
             for ax in axes.flat:
                 _ymin, _ymax = ax.get_ylim()
                 ymin = min(ymin, _ymin)
@@ -206,7 +210,9 @@ def set_xlims(*multiple_axes, xlim=None):
 
     for axes in multiple_axes:
         # axes
-        if isinstance(axes, (np.ndarray, scitex.plt._subplots._AxesWrapper.AxesWrapper)):
+        if isinstance(
+            axes, (np.ndarray, scitex.plt._subplots.AxesWrapper)
+        ):
             for ax in axes.flat:
                 ax.set_xlim(xlim)
         # axis
@@ -227,7 +233,9 @@ def set_ylims(*multiple_axes, ylim=None):
 
     for axes in multiple_axes:
         # axes
-        if isinstance(axes, (np.ndarray, scitex.plt._subplots._AxesWrapper.AxesWrapper)):
+        if isinstance(
+            axes, (np.ndarray, scitex.plt._subplots.AxesWrapper)
+        ):
             for ax in axes.flat:
                 ax.set_ylim(ylim)
 
@@ -257,7 +265,9 @@ if __name__ == "__main__":
     # parser.add_argument('--flag', '-f', action='store_true', default=False, help='')
     # args = parser.parse_args()
     # Main
-    CONFIG, sys.stdout, sys.stderr, plt, CC = scitex.session.start(sys, plt, verbose=False)
+    CONFIG, sys.stdout, sys.stderr, plt, CC = scitex.session.start(
+        sys, plt, verbose=False
+    )
     main()
     scitex.session.close(CONFIG, verbose=False, notify=False)
 

scitex/plt/ax/_style/_show_spines.py

@@ -28,7 +28,7 @@ def show_spines(
     labels: bool = True,
     restore_defaults: bool = True,
     spine_width: float = None,
-    spine_color: str = None
+    spine_color: str = None,
 ):
     """
     Shows the specified spines of a matplotlib Axes object and optionally restores ticks and labels.
@@ -87,31 +87,26 @@ def show_spines(
     that hide_spines(top=False, right=False) shows top and right spines.
     """
     # Handle both matplotlib axes and scitex AxisWrapper
-    if hasattr(axis, '_axis_mpl'):
+    if hasattr(axis, "_axis_mpl"):
         # This is an scitex AxisWrapper, get the underlying matplotlib axis
         axis = axis._axis_mpl
-    
-    assert isinstance(
-        axis, matplotlib.axes._axes.Axes
-    ), "First argument must be a matplotlib axis or scitex AxisWrapper"
+
+    assert isinstance(axis, matplotlib.axes._axes.Axes), (
+        "First argument must be a matplotlib axis or scitex AxisWrapper"
+    )
 
     # Define which spines to show
-    spine_settings = {
-        "top": top,
-        "bottom": bottom,
-        "left": left,
-        "right": right
-    }
+    spine_settings = {"top": top, "bottom": bottom, "left": left, "right": right}
 
     for spine_name, should_show in spine_settings.items():
         # Set spine visibility
         axis.spines[spine_name].set_visible(should_show)
-        
+
         if should_show:
             # Set spine width if specified
             if spine_width is not None:
                 axis.spines[spine_name].set_linewidth(spine_width)
-            
+
             # Set spine color if specified
             if spine_color is not None:
                 axis.spines[spine_name].set_color(spine_color)
@@ -120,18 +115,18 @@ def show_spines(
     if ticks and restore_defaults:
         # Determine tick positions based on which spines are shown
         if bottom and not top:
-            axis.xaxis.set_ticks_position('bottom')
+            axis.xaxis.set_ticks_position("bottom")
         elif top and not bottom:
-            axis.xaxis.set_ticks_position('top')
+            axis.xaxis.set_ticks_position("top")
         elif bottom and top:
-            axis.xaxis.set_ticks_position('both')
-        
+            axis.xaxis.set_ticks_position("both")
+
         if left and not right:
-            axis.yaxis.set_ticks_position('left')
+            axis.yaxis.set_ticks_position("left")
         elif right and not left:
-            axis.yaxis.set_ticks_position('right')
+            axis.yaxis.set_ticks_position("right")
         elif left and right:
-            axis.yaxis.set_ticks_position('both')
+            axis.yaxis.set_ticks_position("both")
 
     # Restore labels if requested and restore_defaults is True
     if labels and restore_defaults:
@@ -139,15 +134,15 @@ def show_spines(
         # This preserves any custom tick labels that might have been set
         current_xticks = axis.get_xticks()
         current_yticks = axis.get_yticks()
-        
+
         if len(current_xticks) > 0 and (bottom or top):
             # Generate default labels for x-axis
-            if not hasattr(axis, '_original_xticklabels'):
+            if not hasattr(axis, "_original_xticklabels"):
                 axis.set_xticks(current_xticks)
-        
+
         if len(current_yticks) > 0 and (left or right):
-            # Generate default labels for y-axis  
-            if not hasattr(axis, '_original_yticklabels'):
+            # Generate default labels for y-axis
+            if not hasattr(axis, "_original_yticklabels"):
                 axis.set_yticks(current_yticks)
 
     return axis
@@ -158,11 +153,11 @@ def show_all_spines(
     spine_width: float = None,
     spine_color: str = None,
     ticks: bool = True,
-    labels: bool = True
+    labels: bool = True,
 ):
     """
     Convenience function to show all spines with optional styling.
-    
+
     Parameters
     ----------
     axis : matplotlib.axes.Axes
@@ -175,21 +170,26 @@ def show_all_spines(
         Whether to show ticks. Defaults to True.
     labels : bool, optional
         Whether to show labels. Defaults to True.
-        
+
     Returns
     -------
     matplotlib.axes.Axes
         The modified Axes object.
-        
+
     Examples
     --------
     >>> show_all_spines(ax, spine_width=1.2, spine_color='gray')
     """
     return show_spines(
         axis,
-        top=True, bottom=True, left=True, right=True,
-        ticks=ticks, labels=labels,
-        spine_width=spine_width, spine_color=spine_color
+        top=True,
+        bottom=True,
+        left=True,
+        right=True,
+        ticks=ticks,
+        labels=labels,
+        spine_width=spine_width,
+        spine_color=spine_color,
     )
 
 
@@ -198,11 +198,11 @@ def show_classic_spines(
     spine_width: float = None,
     spine_color: str = None,
     ticks: bool = True,
-    labels: bool = True
+    labels: bool = True,
 ):
     """
     Show only bottom and left spines (classic scientific plot style).
-    
+
     Parameters
     ----------
     axis : matplotlib.axes.Axes
@@ -215,21 +215,26 @@ def show_classic_spines(
         Whether to show ticks. Defaults to True.
     labels : bool, optional
         Whether to show labels. Defaults to True.
-        
+
     Returns
     -------
     matplotlib.axes.Axes
         The modified Axes object.
-        
+
     Examples
     --------
     >>> show_classic_spines(ax)  # Shows only bottom and left spines
     """
     return show_spines(
         axis,
-        top=False, bottom=True, left=True, right=False,
-        ticks=ticks, labels=labels,
-        spine_width=spine_width, spine_color=spine_color
+        top=False,
+        bottom=True,
+        left=True,
+        right=False,
+        ticks=ticks,
+        labels=labels,
+        spine_width=spine_width,
+        spine_color=spine_color,
     )
 
 
@@ -238,14 +243,14 @@ def show_box_spines(
     spine_width: float = None,
     spine_color: str = None,
     ticks: bool = True,
-    labels: bool = True
+    labels: bool = True,
 ):
     """
     Show all four spines to create a box around the plot.
-    
+
     This is an alias for show_all_spines but with more descriptive naming
     for when you specifically want a boxed appearance.
-    
+
     Parameters
     ----------
     axis : matplotlib.axes.Axes
@@ -258,12 +263,12 @@ def show_box_spines(
         Whether to show ticks. Defaults to True.
     labels : bool, optional
         Whether to show labels. Defaults to True.
-        
+
     Returns
     -------
     matplotlib.axes.Axes
         The modified Axes object.
-        
+
     Examples
     --------
     >>> show_box_spines(ax, spine_width=1.0, spine_color='black')
@@ -272,15 +277,11 @@ def show_box_spines(
 
 
 def toggle_spines(
-    axis,
-    top: bool = None,
-    bottom: bool = None,
-    left: bool = None,
-    right: bool = None
+    axis, top: bool = None, bottom: bool = None, left: bool = None, right: bool = None
 ):
     """
     Toggle the visibility of spines (show if hidden, hide if shown).
-    
+
     Parameters
     ----------
     axis : matplotlib.axes.Axes
@@ -293,20 +294,20 @@ def toggle_spines(
         If specified, sets left spine visibility. If None, toggles current state.
     right : bool, optional
         If specified, sets right spine visibility. If None, toggles current state.
-        
+
     Returns
     -------
     matplotlib.axes.Axes
         The modified Axes object.
-        
+
     Examples
     --------
     >>> toggle_spines(ax)  # Toggles all spines
     >>> toggle_spines(ax, top=True, right=True)  # Shows top and right, toggles others
     """
-    spine_names = ['top', 'bottom', 'left', 'right']
+    spine_names = ["top", "bottom", "left", "right"]
     spine_params = [top, bottom, left, right]
-    
+
     for spine_name, param in zip(spine_names, spine_params):
         if param is None:
             # Toggle current state
@@ -315,7 +316,7 @@ def toggle_spines(
         else:
             # Set specific state
             axis.spines[spine_name].set_visible(param)
-    
+
     return axis
 
 
@@ -330,4 +331,4 @@ def clean_spines(axis, **kwargs):
     return show_spines(axis, top=False, bottom=False, left=False, right=False, **kwargs)
 
 
-# EOF
+# EOF

scitex/plt/ax/_style/_style_barplot.py

@@ -20,7 +20,7 @@ _DEFAULT_EDGE_THICKNESS_MM = SCITEX_STYLE.get("bar_edge_thickness_mm", 0.2)
 def style_barplot(
     bar_container,
     edge_thickness_mm: float = None,
-    edgecolor: Optional[Union[str, List[str]]] = 'black',
+    edgecolor: Optional[Union[str, List[str]]] = "black",
 ):
     """
     Apply consistent styling to matplotlib bar plot elements.

scitex/plt/ax/_style/_style_boxplot.py

@@ -87,35 +87,41 @@ def style_boxplot(
     # Use scitex color palette by default
     if colors is None:
         colors = [
-            HEX["blue"], HEX["red"], HEX["green"], HEX["yellow"],
-            HEX["purple"], HEX["orange"], HEX["lightblue"], HEX["pink"],
+            HEX["blue"],
+            HEX["red"],
+            HEX["green"],
+            HEX["yellow"],
+            HEX["purple"],
+            HEX["orange"],
+            HEX["lightblue"],
+            HEX["pink"],
         ]
 
     # Style box elements with line width
-    for element_name in ['boxes', 'whiskers', 'caps']:
+    for element_name in ["boxes", "whiskers", "caps"]:
         if element_name in boxplot_dict:
             for element in boxplot_dict[element_name]:
                 element.set_linewidth(lw_pt)
                 element.set_color(edge_color)
 
     # Style medians with specified color
-    if 'medians' in boxplot_dict:
-        for median in boxplot_dict['medians']:
+    if "medians" in boxplot_dict:
+        for median in boxplot_dict["medians"]:
             median.set_linewidth(lw_pt)
             median.set_color(median_color)
 
     # Style fliers (outliers) with marker size
-    if 'fliers' in boxplot_dict:
-        for flier in boxplot_dict['fliers']:
+    if "fliers" in boxplot_dict:
+        for flier in boxplot_dict["fliers"]:
             flier.set_markersize(flier_size_pt)
             flier.set_markeredgewidth(lw_pt)
             flier.set_markeredgecolor(edge_color)
-            flier.set_markerfacecolor('none')  # Open circles
+            flier.set_markerfacecolor("none")  # Open circles
 
     # Apply fill colors to boxes
-    for i, box in enumerate(boxplot_dict.get('boxes', [])):
+    for i, box in enumerate(boxplot_dict.get("boxes", [])):
         color = colors[i % len(colors)]
-        if hasattr(box, 'set_facecolor'):
+        if hasattr(box, "set_facecolor"):
             box.set_facecolor(color)
         box.set_edgecolor(edge_color)
 
@@ -123,19 +129,24 @@ def style_boxplot(
     if add_legend and labels is not None:
         # Create proxy artists for legend
         import matplotlib.patches as mpatches
+
         if colors is not None:
             legend_elements = [
-                mpatches.Patch(facecolor='none', edgecolor=color, linewidth=lw_pt, label=label)
+                mpatches.Patch(
+                    facecolor="none", edgecolor=color, linewidth=lw_pt, label=label
+                )
                 for color, label in zip(colors, labels)
             ]
         else:
             legend_elements = [
-                mpatches.Patch(facecolor='none', edgecolor='C0', linewidth=lw_pt, label=label)
+                mpatches.Patch(
+                    facecolor="none", edgecolor="C0", linewidth=lw_pt, label=label
+                )
                 for label in labels
             ]
         # Get the axes from one of the box elements
-        if boxplot_dict.get('boxes'):
-            ax = boxplot_dict['boxes'][0].axes
+        if boxplot_dict.get("boxes"):
+            ax = boxplot_dict["boxes"][0].axes
             ax.legend(handles=legend_elements)
 
     return boxplot_dict

scitex/plt/ax/_style/_style_scatter.py

@@ -67,7 +67,7 @@ def style_scatter(
     # For a marker of diameter d, area = (d/2)^2 * pi
     # But matplotlib's 's' parameter is already area-like
     # So we use size_pt^2 to get the right visual size
-    marker_area = size_pt ** 2
+    marker_area = size_pt**2
 
     # Set marker size
     path_collection.set_sizes([marker_area])

scitex/plt/ax/_style/_style_suptitles.py

@@ -50,7 +50,7 @@ def style_suptitles(
     All are set to the same font size (default 7pt for publication).
     """
     # Unwrap FigWrapper if needed
-    if hasattr(fig, '_fig_mpl'):
+    if hasattr(fig, "_fig_mpl"):
         fig_mpl = fig._fig_mpl
     else:
         fig_mpl = fig
@@ -61,12 +61,12 @@ def style_suptitles(
         fig_mpl._suptitle.set_fontfamily(font_family)
 
     # Style supxlabel (if it exists)
-    if hasattr(fig_mpl, '_supxlabel') and fig_mpl._supxlabel is not None:
+    if hasattr(fig_mpl, "_supxlabel") and fig_mpl._supxlabel is not None:
         fig_mpl._supxlabel.set_fontsize(suptitle_font_size_pt)
         fig_mpl._supxlabel.set_fontfamily(font_family)
 
     # Style supylabel (if it exists)
-    if hasattr(fig_mpl, '_supylabel') and fig_mpl._supylabel is not None:
+    if hasattr(fig_mpl, "_supylabel") and fig_mpl._supylabel is not None:
         fig_mpl._supylabel.set_fontsize(suptitle_font_size_pt)
         fig_mpl._supylabel.set_fontfamily(font_family)
 

scitex/plt/ax/_style/_style_violinplot.py

@@ -70,14 +70,20 @@ def style_violinplot(
     # Style violin bodies (PolyCollection)
     for collection in ax.collections:
         # Check if it's a violin body (PolyCollection with filled area)
-        if hasattr(collection, 'set_edgecolor'):
+        if hasattr(collection, "set_edgecolor"):
             collection.set_edgecolor(edge_color)
             collection.set_linewidth(lw_pt)
 
     # Style internal boxplot elements (Line2D objects)
     # Seaborn violin plot lines: whiskers (vertical), caps (horizontal), median (short horizontal)
     lines = list(ax.lines)
-    n_violins = len([c for c in ax.collections if hasattr(c, 'get_paths') and len(c.get_paths()) > 0])
+    n_violins = len(
+        [
+            c
+            for c in ax.collections
+            if hasattr(c, "get_paths") and len(c.get_paths()) > 0
+        ]
+    )
 
     for line in lines:
         # Get line data to identify element type