batplot 1.8.0__tar.gz → 1.8.1__tar.gz

{batplot-1.8.0/batplot.egg-info → batplot-1.8.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: batplot
-Version: 1.8.0
+Version: 1.8.1
 Summary: Interactive plotting tool for material science (1D plot) and electrochemistry (GC, CV, dQ/dV, CPC, operando) with batch processing
 Author-email: Tian Dai <tianda@uio.no>
 License: MIT License

{batplot-1.8.0 → batplot-1.8.1}/batplot/__init__.py

@@ -1,5 +1,5 @@
 """batplot: Interactive plotting for battery data visualization."""
 
-__version__ = "1.8.0"
+__version__ = "1.8.1"
 
 __all__ = ["__version__"]

{batplot-1.8.0 → batplot-1.8.1}/batplot/args.py

@@ -169,7 +169,7 @@ def _print_general_help() -> None:
         "    batplot --cv FILE.txt                  # EC CV (cyclic voltammetry) from .txt\n"
         "    batplot --cv --all                     # Batch: all .mpt/.txt in directory (CV mode)\n\n"
         "  [Operando]\n"
-        "    batplot --operando --i [FOLDER]        # Operando contour (with or without .mpt file) with interactive menu\n\n"
+        "    batplot --operando --i [FOLDER]        # Operando contour (with or without .mpt file)\n\n"
             "Features:\n"
         "  • Quick plotting with sensible defaults, no config files needed\n"
         "  • Supports many common file formats (see -h xy/ec/op)\n"
@@ -183,9 +183,9 @@ def _print_general_help() -> None:
         "  batplot -h xy   # XY file plotting guide\n"
         "  batplot -h ec   # Electrochemistry (GC/dQdV/CV/CPC) guide\n"
         "  batplot -h op   # Operando guide\n"
-        "  batplot -m      # Open the illustrated txt manual with highlights\n"
+        "  batplot -m      # Open the illustrated txt manual with highlights\n\n"
 
-        "Contact & Updates:\n\n"
+        "Contact & Updates:\n"
         "  Subscribe to batplot-lab@kjemi.uio.no for updates\n"
         "  (If you are not from UiO, send an email to sympa@kjemi.uio.no with the subject line \"subscribe batplot-lab@kjemi.uio.no your-name\")\n"
         "  Kindly cite the pypi package page (https://pypi.org/project/batplot/) if the plot is used for publication\n"

{batplot-1.8.0 → batplot-1.8.1}/batplot/cpc_interactive.py

@@ -86,6 +86,7 @@ from .ui import (
 from .utils import (
     _confirm_overwrite,
     choose_save_path,
+    convert_label_shortcuts,
     choose_style_file,
     list_files_in_subdirectory,
     get_organized_path,
@@ -335,13 +336,36 @@ def _rebuild_legend(ax, ax2, file_data, preserve_position=True):
     """
     try:
         fig = ax.figure
-        # Get stored position before rebuilding
+        # Get stored position before rebuilding. If none is stored yet, try to
+        # capture the current on-canvas position once so subsequent rebuilds
+        # (e.g., after renaming) do not jump to a new "best" location.
         xy_in = None
         if preserve_position:
             try:
                 xy_in = getattr(fig, '_cpc_legend_xy_in', None)
             except Exception:
-                pass
+                xy_in = None
+            if xy_in is None:
+                try:
+                    leg0 = ax.get_legend()
+                    if leg0 is not None and leg0.get_visible():
+                        try:
+                            renderer = fig.canvas.get_renderer()
+                        except Exception:
+                            fig.canvas.draw()
+                            renderer = fig.canvas.get_renderer()
+                        bb = leg0.get_window_extent(renderer=renderer)
+                        cx = 0.5 * (bb.x0 + bb.x1)
+                        cy = 0.5 * (bb.y0 + bb.y1)
+                        fx, fy = fig.transFigure.inverted().transform((cx, cy))
+                        fw, fh = fig.get_size_inches()
+                        offset = ((fx - 0.5) * fw, (fy - 0.5) * fh)
+                        offset = _sanitize_legend_offset(offset)
+                        if offset is not None:
+                            fig._cpc_legend_xy_in = offset
+                            xy_in = offset
+                except Exception:
+                    pass
         
         h1, l1 = ax.get_legend_handles_labels()
         h2, l2 = ax2.get_legend_handles_labels()
@@ -1643,6 +1667,31 @@ def cpc_interactive_menu(fig, ax, ax2, sc_charge, sc_discharge, sc_eff, file_dat
                 else:
                     # Single file mode: toggle efficiency
                     push_state("visibility-eff")
+                    # Capture current legend position BEFORE toggling visibility
+                    try:
+                        if not hasattr(fig, '_cpc_legend_xy_in') or getattr(fig, '_cpc_legend_xy_in') is None:
+                            leg0 = ax.get_legend()
+                            if leg0 is not None and leg0.get_visible():
+                                try:
+                                    # Ensure renderer exists
+                                    try:
+                                        renderer = fig.canvas.get_renderer()
+                                    except Exception:
+                                        fig.canvas.draw()
+                                        renderer = fig.canvas.get_renderer()
+                                    bb = leg0.get_window_extent(renderer=renderer)
+                                    cx = 0.5 * (bb.x0 + bb.x1)
+                                    cy = 0.5 * (bb.y0 + bb.y1)
+                                    fx, fy = fig.transFigure.inverted().transform((cx, cy))
+                                    fw, fh = fig.get_size_inches()
+                                    offset = ((fx - 0.5) * fw, (fy - 0.5) * fh)
+                                    offset = _sanitize_legend_offset(offset)
+                                    if offset is not None:
+                                        fig._cpc_legend_xy_in = offset
+                                except Exception:
+                                    pass
+                    except Exception:
+                        pass
                     vis = sc_eff.get_visible()
                     sc_eff.set_visible(not vis)
                     try:
@@ -1650,7 +1699,7 @@ def cpc_interactive_menu(fig, ax, ax2, sc_charge, sc_discharge, sc_eff, file_dat
                     except Exception:
                         pass
                 
-                _rebuild_legend(ax, ax2, file_data)
+                _rebuild_legend(ax, ax2, file_data, preserve_position=True)
                 fig.canvas.draw_idle()
             except ValueError:
                 print("Invalid input.")
@@ -1676,6 +1725,7 @@ def cpc_interactive_menu(fig, ax, ax2, sc_charge, sc_discharge, sc_eff, file_dat
         elif key == 'c':
             # Colors submenu: ly (left Y series) and ry (right Y efficiency), with user colors and palettes
             try:
+                # Note: Individual series may use different colors, so we can't show a single "current" palette
                 # Use same palettes as EC interactive
                 palette_opts = ['tab10', 'Set2', 'Dark2', 'viridis', 'plasma']
                 def _palette_color(name, idx=0, total=1, default_val=0.4):
@@ -2668,6 +2718,33 @@ def cpc_interactive_menu(fig, ax, ax2, sc_charge, sc_discharge, sc_eff, file_dat
             try:
                 push_state("toggle-eff")
                 
+                # Capture current legend position BEFORE toggling visibility
+                # This ensures the position is preserved when legend is rebuilt
+                try:
+                    if not hasattr(fig, '_cpc_legend_xy_in') or getattr(fig, '_cpc_legend_xy_in') is None:
+                        leg0 = ax.get_legend()
+                        if leg0 is not None and leg0.get_visible():
+                            try:
+                                # Ensure renderer exists
+                                try:
+                                    renderer = fig.canvas.get_renderer()
+                                except Exception:
+                                    fig.canvas.draw()
+                                    renderer = fig.canvas.get_renderer()
+                                bb = leg0.get_window_extent(renderer=renderer)
+                                cx = 0.5 * (bb.x0 + bb.x1)
+                                cy = 0.5 * (bb.y0 + bb.y1)
+                                fx, fy = fig.transFigure.inverted().transform((cx, cy))
+                                fw, fh = fig.get_size_inches()
+                                offset = ((fx - 0.5) * fw, (fy - 0.5) * fh)
+                                offset = _sanitize_legend_offset(offset)
+                                if offset is not None:
+                                    fig._cpc_legend_xy_in = offset
+                            except Exception:
+                                pass
+                except Exception:
+                    pass
+                
                 # Determine current visibility state (check if any efficiency is visible)
                 if is_multi_file:
                     # In multi-file mode, check if any efficiency is visible
@@ -3738,6 +3815,7 @@ def cpc_interactive_menu(fig, ax, ax2, sc_charge, sc_discharge, sc_eff, file_dat
             print("Tip: Use LaTeX/mathtext for special characters:")
             print("  Subscript: H$_2$O → H₂O  |  Superscript: m$^2$ → m²")
             print("  Bullet: $\\bullet$ → •   |  Greek: $\\alpha$, $\\beta$  |  Angstrom: $\\AA$ → Å")
+            print("  Shortcuts: g{super(-1)} → g$^{\\mathrm{-1}}$  |  Li{sub(2)}O → Li$_{\\mathrm{2}}$O")
             while True:
                 print("Rename: x=x-axis, ly=left y-axis, ry=right y-axis, l=legend labels, q=back")
                 sub = _safe_input("Rename> ").strip().lower()
@@ -3788,6 +3866,7 @@ def cpc_interactive_menu(fig, ax, ax2, sc_charge, sc_discharge, sc_eff, file_dat
                         print(f"Current file name in legend: '{base_name}'")
                         new_name = _safe_input("Enter new file name (q=cancel): ").strip()
                         if new_name and new_name.lower() != 'q':
+                            new_name = convert_label_shortcuts(new_name)
                             try:
                                 push_state("rename-legend")
                                 
@@ -3895,6 +3974,7 @@ def cpc_interactive_menu(fig, ax, ax2, sc_charge, sc_discharge, sc_eff, file_dat
                                     print(f"Current file name in legend: '{base_name}'")
                                     new_name = _safe_input("Enter new file name (q=cancel): ").strip()
                                     if new_name and new_name.lower() != 'q':
+                                        new_name = convert_label_shortcuts(new_name)
                                         try:
                                             push_state("rename-legend")
                                             
@@ -3966,6 +4046,7 @@ def cpc_interactive_menu(fig, ax, ax2, sc_charge, sc_discharge, sc_eff, file_dat
                     print(f"Current x-axis title: '{current}'")
                     new_title = _safe_input("Enter new x-axis title (q=cancel): ")
                     if new_title and new_title.lower() != 'q':
+                        new_title = convert_label_shortcuts(new_title)
                         try:
                             push_state("rename-x")
                             ax.set_xlabel(new_title)
@@ -3985,6 +4066,7 @@ def cpc_interactive_menu(fig, ax, ax2, sc_charge, sc_discharge, sc_eff, file_dat
                     print(f"Current left y-axis title: '{current}'")
                     new_title = _safe_input("Enter new left y-axis title (q=cancel): ")
                     if new_title and new_title.lower() != 'q':
+                        new_title = convert_label_shortcuts(new_title)
                         try:
                             push_state("rename-ly")
                             ax.set_ylabel(new_title)
@@ -3999,6 +4081,7 @@ def cpc_interactive_menu(fig, ax, ax2, sc_charge, sc_discharge, sc_eff, file_dat
                     print(f"Current right y-axis title: '{current}'")
                     new_title = _safe_input("Enter new right y-axis title (q=cancel): ")
                     if new_title and new_title.lower() != 'q':
+                        new_title = convert_label_shortcuts(new_title)
                         try:
                             push_state("rename-ry")
                             ax2.set_ylabel(new_title)

{batplot-1.8.0 → batplot-1.8.1}/batplot/electrochem_interactive.py

@@ -31,6 +31,7 @@ from .utils import (
     choose_style_file,
     list_files_in_subdirectory,
     get_organized_path,
+    convert_label_shortcuts,
 )
 import time
 from .color_utils import (
@@ -502,6 +503,28 @@ def _rebuild_legend(ax):
     fig = ax.figure
     # Capture existing title before any rebuild so it isn't lost
     _store_legend_title(fig, ax)
+    # If no stored position yet, try to capture the current legend location once
+    # so rebuilds (e.g., after renaming) don't jump to a new "best" spot.
+    try:
+        if getattr(fig, '_ec_legend_xy_in', None) is None:
+            leg0 = ax.get_legend()
+            if leg0 is not None and leg0.get_visible():
+                try:
+                    renderer = fig.canvas.get_renderer()
+                except Exception:
+                    fig.canvas.draw()
+                    renderer = fig.canvas.get_renderer()
+                bb = leg0.get_window_extent(renderer=renderer)
+                cx = 0.5 * (bb.x0 + bb.x1)
+                cy = 0.5 * (bb.y0 + bb.y1)
+                fx, fy = fig.transFigure.inverted().transform((cx, cy))
+                fw, fh = fig.get_size_inches()
+                offset = ((fx - 0.5) * fw, (fy - 0.5) * fh)
+                offset = _sanitize_legend_offset(fig, offset)
+                if offset is not None:
+                    fig._ec_legend_xy_in = offset
+    except Exception:
+        pass
     if not _get_legend_user_pref(fig):
         leg = ax.get_legend()
         if leg is not None:
@@ -2697,6 +2720,7 @@ def electrochem_interactive_menu(fig, ax, cycle_lines: Dict[int, Dict[str, Optio
                 print("Tip: Use LaTeX/mathtext for special characters:")
                 print("  Subscript: H$_2$O → H₂O  |  Superscript: m$^2$ → m²")
                 print("  Bullet: $\\bullet$ → •   |  Greek: $\\alpha$, $\\beta$  |  Angstrom: $\\AA$ → Å")
+                print("  Shortcuts: g{super(-1)} → g$^{\\mathrm{-1}}$  |  Li{sub(2)}O → Li$_{\\mathrm{2}}$O")
                 while True:
                     print("Rename axis: x, y, both, q=back")
                     sub = _safe_input("Rename> ").strip().lower()
@@ -2707,6 +2731,7 @@ def electrochem_interactive_menu(fig, ax, cycle_lines: Dict[int, Dict[str, Optio
                     if sub in ('x','both'):
                         txt = _safe_input("New X-axis label (blank=cancel): ")
                         if txt:
+                            txt = convert_label_shortcuts(txt)
                             push_state("rename-x")
                             try:
                                 # Freeze layout and preserve existing pad for one-shot restore
@@ -2730,6 +2755,7 @@ def electrochem_interactive_menu(fig, ax, cycle_lines: Dict[int, Dict[str, Optio
                     if sub in ('y','both'):
                         txt = _safe_input("New Y-axis label (blank=cancel): ")
                         if txt:
+                            txt = convert_label_shortcuts(txt)
                             push_state("rename-y")
                             base_ylabel = txt
                             try:
@@ -3027,6 +3053,8 @@ def electrochem_interactive_menu(fig, ax, cycle_lines: Dict[int, Dict[str, Optio
             _print_menu(len(all_cycles), is_dqdv)
             continue
         elif key == 'c':
+            # Show current palette if one is applied (this is informational only)
+            # Note: Individual cycles may use different colors, so we can't show a single "current" palette
             print(f"Total cycles: {len(all_cycles)}")
             print("Enter one of:")
             print(_colorize_inline_commands("  - numbers: e.g. 1 5 10"))

{batplot-1.8.0 → batplot-1.8.1}/batplot/interactive.py

@@ -25,6 +25,7 @@ from .utils import (
     choose_save_path,
     choose_style_file,
     list_files_in_subdirectory,
+    convert_label_shortcuts,
     get_organized_path,
 )
 import time
@@ -1955,12 +1956,11 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                                 ax._cif_draw_func()
                         fig.canvas.draw()
                     elif sub == 'p':
+                        # Show current palette if one is applied
                         history = getattr(fig, '_curve_palette_history', [])
                         current_palette = history[-1]['palette'] if history else None
                         if current_palette:
                             print(f"Current palette: {current_palette}")
-                        else:
-                            print("Current palette: manual/custom")
                         base_palettes = ['viridis', 'cividis', 'plasma', 'inferno', 'magma', 'batlow']
                         extras = []
                         def _palette_available(name: str) -> bool:
@@ -2211,6 +2211,7 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                         print("Tip: Use LaTeX/mathtext for special characters:")
                         print("  Subscript: H$_2$O → H₂O  |  Superscript: m$^2$ → m²")
                         print("  Bullet: $\\bullet$ → •   |  Greek: $\\alpha$, $\\beta$  |  Angstrom: $\\AA$ → Å")
+                        print("  Shortcuts: g{super(-1)} → g$^{\\mathrm{-1}}$  |  Li{sub(2)}O → Li$_{\\mathrm{2}}$O")
                         idx_in = _safe_input("Curve number to rename (q=cancel): ").strip()
                         if not idx_in or idx_in.lower() == 'q':
                             print("Canceled.")
@@ -2227,6 +2228,7 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                         if not new_label or new_label.lower() == 'q':
                             print("Canceled.")
                             continue
+                        new_label = convert_label_shortcuts(new_label)
                         push_state("rename-curve")
                         labels[idx] = new_label
                         label_text_objects[idx].set_text(f"{idx+1}: {new_label}")
@@ -2250,9 +2252,11 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                         print("Tip: Use LaTeX/mathtext for special characters:")
                         print("  Subscript: H$_2$O → H₂O  |  Superscript: m$^2$ → m²")
                         print("  Greek: $\\alpha$, $\\beta$  |  Angstrom: $\\AA$ → Å")
+                        print("  Shortcuts: g{super(-1)} → g$^{\\mathrm{-1}}$  |  Li{sub(2)}O → Li$_{\\mathrm{2}}$O")
                         new_name = _safe_input("New CIF tick label (q=cancel): ")
                         if not new_name or new_name.lower()=='q':
                             print("Canceled."); continue
+                        new_name = convert_label_shortcuts(new_name)
                         lab,fname,peaksQ,wl,qmax_sim,color = cts[idx]
                         # Suspend extension while updating label
                         if _bp is not None:
@@ -2278,10 +2282,12 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                         print("Tip: Use LaTeX/mathtext for special characters:")
                         print("  Subscript: H$_2$O → H₂O  |  Superscript: m$^2$ → m²")
                         print("  Greek: $\\alpha$, $\\beta$  |  Angstrom: $\\AA$ → Å")
+                        print("  Shortcuts: g{super(-1)} → g$^{\\mathrm{-1}}$  |  Li{sub(2)}O → Li$_{\\mathrm{2}}$O")
                         new_axis = _safe_input("New axis label: ")
                         if not new_axis or new_axis.lower() == 'q':
                             print("Canceled.")
                             continue
+                        new_axis = convert_label_shortcuts(new_axis)
                         new_axis = normalize_label_text(new_axis)
                         push_state("rename-axis")
                         # Freeze layout and preserve current pad via one-shot pending to avoid drift

{batplot-1.8.0 → batplot-1.8.1}/batplot/operando.py

@@ -315,6 +315,8 @@ def plot_operando_folder(folder: str, args) -> Tuple[plt.Figure, plt.Axes, Dict[
     extent = (grid_x.min(), grid_x.max(), 0, Zm.shape[0]-1)
     # Bottom-to-top visual order (scan 0 at bottom) to match EC time progression -> origin='lower'
     im = ax.imshow(Zm, aspect='auto', origin='lower', extent=extent, cmap='viridis', interpolation='nearest')
+    # Store the colormap name explicitly so it can be retrieved reliably when saving
+    setattr(im, '_operando_cmap_name', 'viridis')
     # Create custom colorbar axes on the left (will be positioned by layout function)
     # Create a dummy axes that will be replaced by the custom colorbar in interactive menu
     cbar_ax = fig.add_axes([0.0, 0.0, 0.01, 0.01])  # Temporary position, will be repositioned

{batplot-1.8.0 → batplot-1.8.1}/batplot/operando_ec_interactive.py

@@ -39,7 +39,7 @@ from .color_utils import (
     resolve_color_token,
     manage_user_colors,
 )
-from .utils import choose_style_file
+from .utils import choose_style_file, convert_label_shortcuts
 
 
 class _FilterIMKWarning:
@@ -354,7 +354,7 @@ def _draw_custom_colorbar(cbar_ax, im, label='Intensity', label_mode='normal'):
 
 def _update_custom_colorbar(cbar_ax, im=None, label=None, label_mode=None):
     """Update the custom colorbar when colormap or limits change.
-    
+
     Args:
         cbar_ax: Axes object containing the colorbar
         im: Optional AxesImage object (if None, uses stored reference)
@@ -365,17 +365,82 @@ def _update_custom_colorbar(cbar_ax, im=None, label=None, label_mode=None):
         im = getattr(cbar_ax, '_colorbar_im', None)
         if im is None:
             return
-    
+
     if label is None:
         label = getattr(cbar_ax, '_colorbar_label', 'Intensity')
-    
+
     if label_mode is None:
         label_mode = getattr(cbar_ax, '_colorbar_label_mode', 'normal')
-    
+
     # Redraw the colorbar
     _draw_custom_colorbar(cbar_ax, im, label, label_mode)
 
 
+def _safe_set_clim(im, vmin, vmax):
+    """Safely set color limits without triggering matplotlib colorbar callbacks.
+    
+    This wrapper around im.set_clim() prevents the NotImplementedError: cannot remove artist
+    error when using custom colorbars. The issue occurs because matplotlib's callback system
+    tries to update the colorbar when set_clim() is called, but our custom colorbar drawing
+    has already cleared the axes, causing the update to fail.
+    
+    This function suppresses the callback traceback by redirecting stderr to a null device
+    during the set_clim() call, preventing matplotlib's callback system from printing
+    tracebacks to the terminal.
+    
+    Args:
+        im: AxesImage object
+        vmin: Minimum value for color scale
+        vmax: Maximum value for color scale
+    """
+    import sys
+    import os
+    from io import StringIO
+    
+    # Create a null device for stderr redirection
+    class NullDevice:
+        def write(self, s):
+            pass
+        def flush(self):
+            pass
+        def close(self):
+            pass
+    
+    # Suppress matplotlib's exception printing by redirecting stderr AND excepthook
+    old_stderr = sys.stderr
+    old_excepthook = sys.excepthook
+    null_dev = NullDevice()
+    
+    # Create a no-op excepthook that suppresses all exceptions
+    def suppress_excepthook(exc_type, exc_value, exc_traceback):
+        # Only suppress if it's the specific error we're looking for
+        if exc_type == NotImplementedError and 'cannot remove artist' in str(exc_value).lower():
+            return  # Suppress this specific exception
+        # For any other exception, use the original handler
+        old_excepthook(exc_type, exc_value, exc_traceback)
+    
+    sys.stderr = null_dev
+    sys.excepthook = suppress_excepthook
+    
+    try:
+        # Set the color limits - matplotlib's callback will try to print traceback
+        # but both stderr and excepthook are suppressed
+        im.set_clim(vmin, vmax)
+        # The operation succeeds; any tracebacks are suppressed
+    except NotImplementedError:
+        # Suppress the specific error - color limits were still updated successfully
+        pass
+    except Exception:
+        # For any other unexpected error, restore handlers and re-raise
+        sys.stderr = old_stderr
+        sys.excepthook = old_excepthook
+        raise
+    finally:
+        # Always restore both stderr and excepthook
+        sys.stderr = old_stderr
+        sys.excepthook = old_excepthook
+
+
 def _detach_mpl_colorbar_callbacks(cbar, im) -> None:
     """Detach a Matplotlib Colorbar from its mappable callbacks.
 
@@ -737,7 +802,7 @@ def operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax, file_paths=None):
                 
                 if intensity_max > intensity_min:
                     # Update color limits
-                    im.set_clim(intensity_min, intensity_max)
+                    _safe_set_clim(im, intensity_min, intensity_max)
                     
                     # Update colorbar if available
                     try:
@@ -1111,7 +1176,10 @@ def operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax, file_paths=None):
                 clim = im.get_clim()
             except Exception:
                 clim = None
-            cmap_name = getattr(im.get_cmap(), 'name', None)
+            # Get colormap name: first check if we stored it explicitly, otherwise try to get from colormap object
+            cmap_name = getattr(im, '_operando_cmap_name', None)
+            if cmap_name is None:
+                cmap_name = getattr(im.get_cmap(), 'name', None)
             # EC mode and caches (only if ec_ax exists)
             if ec_ax is not None:
                 mode = getattr(ec_ax, '_ec_y_mode', 'time')
@@ -1325,12 +1393,15 @@ def operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax, file_paths=None):
                             cbar.solids = None
                     except Exception:
                         pass
-                    lo, hi = snap['clim']; im.set_clim(float(lo), float(hi))
+                    lo, hi = snap['clim']; _safe_set_clim(im, float(lo), float(hi))
             except Exception:
                 pass
             try:
                 if snap.get('cmap'):
-                    im.set_cmap(snap['cmap'])
+                    cmap_name = snap['cmap']
+                    im.set_cmap(cmap_name)
+                    # Store the colormap name explicitly so it can be retrieved reliably when saving
+                    setattr(im, '_operando_cmap_name', cmap_name)
                     if cbar is not None:
                         _update_custom_colorbar(cbar.ax, im)
             except Exception:
@@ -2023,8 +2094,10 @@ def operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax, file_paths=None):
                                     continue
                                 except ValueError:
                                     print("Invalid input. Enter a number.")
+                                    continue
                                 except Exception as e:
                                     print(f"Error: {e}")
+                                    continue
                             elif sub == 'e':
                                 if ec_ax is None:
                                     print("EC panel not available.")
@@ -2042,10 +2115,13 @@ def operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax, file_paths=None):
                                     continue
                                 except ValueError:
                                     print("Invalid input. Enter a number.")
+                                    continue
                                 except Exception as e:
                                     print(f"Error: {e}")
+                                    continue
                             else:
                                 print("Invalid choice.")
+                                continue
                     elif choice != 'q':
                         print("Invalid choice")
                 else:
@@ -2107,10 +2183,13 @@ def operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax, file_paths=None):
                                     continue
                                 except ValueError:
                                     print("Invalid input. Enter a number.")
+                                    continue
                                 except Exception as e:
                                     print(f"Error: {e}")
+                                    continue
                             else:
                                 print("Invalid choice.")
+                                continue
                     elif choice != 'q':
                         print("Invalid choice")
                 fig.canvas.draw_idle()
@@ -3280,7 +3359,7 @@ def operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax, file_paths=None):
                             print("Invalid value, ignored.")
                             continue
                         _snapshot("operando-intensity-range")
-                        im.set_clim(cur[0], new_upper)
+                        _safe_set_clim(im, cur[0], new_upper)
                         try:
                             if cbar is not None:
                                 _update_custom_colorbar(cbar.ax, im)
@@ -3306,7 +3385,7 @@ def operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax, file_paths=None):
                             print("Invalid value, ignored.")
                             continue
                         _snapshot("operando-intensity-range")
-                        im.set_clim(new_lower, cur[1])
+                        _safe_set_clim(im, new_lower, cur[1])
                         try:
                             if cbar is not None:
                                 _update_custom_colorbar(cbar.ax, im)
@@ -3320,7 +3399,7 @@ def operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax, file_paths=None):
                     if line.lower() == 'a':
                         # Apply auto-normalization to visible data
                         if auto_available:
-                            im.set_clim(auto_lo, auto_hi)
+                            _safe_set_clim(im, auto_lo, auto_hi)
                             try:
                                 if cbar is not None:
                                     _update_custom_colorbar(cbar.ax, im)
@@ -3332,7 +3411,7 @@ def operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax, file_paths=None):
                             print("Auto-fit unavailable: no finite data in visible area")
                     else:
                         lo, hi = map(float, line.split())
-                        im.set_clim(lo, hi)
+                        _safe_set_clim(im, lo, hi)
                         try:
                             if cbar is not None:
                                 _update_custom_colorbar(cbar.ax, im)
@@ -3381,6 +3460,15 @@ def operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax, file_paths=None):
             print_menu()
         elif cmd == 'oc':
             # Change operando colormap (perceptually uniform suggestions)
+            # Show current colormap if one is applied
+            try:
+                current_cmap = getattr(im, '_operando_cmap_name', None)
+                if current_cmap is None:
+                    current_cmap = getattr(im.get_cmap(), 'name', None)
+                if current_cmap:
+                    print(f"Current operando colormap: {current_cmap}")
+            except Exception:
+                pass
             def _refresh_available():
                 return set(name.lower() for name in plt.colormaps())
             available = _refresh_available()
@@ -3453,6 +3541,8 @@ def operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax, file_paths=None):
                     if reversed_choice:
                         palette_obj = palette_obj.reversed()
                     im.set_cmap(palette_obj)
+                # Store the colormap name explicitly so it can be retrieved reliably when saving
+                setattr(im, '_operando_cmap_name', choice)
                 try:
                     # Update custom colorbar with new colormap
                     if cbar is not None:
@@ -3489,7 +3579,10 @@ def operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax, file_paths=None):
                     cb_w_in, cb_gap_in, ec_gap_in, ec_w_in, ax_w_in, ax_h_in = _ensure_fixed_params(fig, ax, cbar.ax, ec_ax)
                     fam = plt.rcParams.get('font.sans-serif', [''])[0]
                     fsize = plt.rcParams.get('font.size', None)
-                    cmap_name = getattr(im.get_cmap(), 'name', None)
+                    # Get colormap name: first check if we stored it explicitly, otherwise try to get from colormap object
+                    cmap_name = getattr(im, '_operando_cmap_name', None)
+                    if cmap_name is None:
+                        cmap_name = getattr(im.get_cmap(), 'name', None)
                     cb_vis = bool(cbar.ax.get_visible())
                     ec_vis = bool(ec_ax.get_visible()) if ec_ax is not None else None
                     cb_label_text = str(getattr(cbar.ax, '_colorbar_label', cbar.ax.get_ylabel() or 'Intensity'))
@@ -4056,6 +4149,8 @@ def operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax, file_paths=None):
                 if cmap:
                     try:
                         im.set_cmap(cmap)
+                        # Store the colormap name explicitly so it can be retrieved reliably when saving
+                        setattr(im, '_operando_cmap_name', cmap)
                         if cbar is not None:
                             _update_custom_colorbar(cbar.ax, im)
                     except Exception:
@@ -4329,7 +4424,7 @@ def operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax, file_paths=None):
                     try:
                         intensity_range = op.get('intensity_range')
                         if intensity_range and isinstance(intensity_range, (list, tuple)) and len(intensity_range) == 2:
-                            im.set_clim(float(intensity_range[0]), float(intensity_range[1]))
+                            _safe_set_clim(im, float(intensity_range[0]), float(intensity_range[1]))
                             print(f"Applied intensity range: {intensity_range[0]:.4g} to {intensity_range[1]:.4g}")
                     except Exception as e:
                         print(f"Warning: Could not apply intensity range: {e}")
@@ -4623,6 +4718,7 @@ def operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax, file_paths=None):
                 print("Tip: Use LaTeX/mathtext for special characters:")
                 print("  Subscript: H$_2$O → H₂O  |  Superscript: m$^2$ → m²")
                 print("  Bullet: $\\bullet$ → •   |  Greek: $\\alpha$, $\\beta$  |  Angstrom: $\\AA$ → Å")
+                print("  Shortcuts: g{super(-1)} → g$^{\\mathrm{-1}}$  |  Li{sub(2)}O → Li$_{\\mathrm{2}}$O")
                 while True:
                     sub = _safe_input("or> ").strip().lower()
                     if not sub:
@@ -4633,6 +4729,7 @@ def operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax, file_paths=None):
                         cur = ax.get_xlabel() or ''
                         lab = _safe_input(f"New operando X label (blank=cancel, current='{cur}'): ")
                         if lab:
+                            lab = convert_label_shortcuts(lab)
                             _snapshot("rename-op-x")
                             try:
                                 ax.set_xlabel(lab)
@@ -4646,6 +4743,7 @@ def operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax, file_paths=None):
                         cur = ax.get_ylabel() or ''
                         lab = _safe_input(f"New operando Y label (blank=cancel, current='{cur}'): ")
                         if lab:
+                            lab = convert_label_shortcuts(lab)
                             _snapshot("rename-op-y")
                             try:
                                 ax.set_ylabel(lab)
@@ -4675,6 +4773,7 @@ def operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax, file_paths=None):
                 print("Tip: Use LaTeX/mathtext for special characters:")
                 print("  Subscript: H$_2$O → H₂O  |  Superscript: m$^2$ → m²")
                 print("  Greek: $\\alpha$, $\\beta$  |  Angstrom: $\\AA$ → Å")
+                print("  Shortcuts: g{super(-1)} → g$^{\\mathrm{-1}}$  |  Li{sub(2)}O → Li$_{\\mathrm{2}}$O")
                 while True:
                     sub = _safe_input("er> ").strip().lower()
                     if not sub:
@@ -4685,6 +4784,7 @@ def operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax, file_paths=None):
                         cur = ec_ax.get_xlabel() or ''
                         lab = _safe_input(f"New EC X label (blank=cancel, current='{cur}'): ")
                         if lab:
+                            lab = convert_label_shortcuts(lab)
                             _snapshot("rename-ec-x")
                             try:
                                 ec_ax.set_xlabel(lab)
@@ -4697,6 +4797,7 @@ def operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax, file_paths=None):
                         cur = ec_ax.get_ylabel() or ''
                         lab = _safe_input(f"New EC Y label (blank=cancel, current='{cur}'): ")
                         if lab:
+                            lab = convert_label_shortcuts(lab)
                             _snapshot("rename-ec-y")
                             try:
                                 ec_ax.set_ylabel(lab)

{batplot-1.8.0 → batplot-1.8.1}/batplot/session.py

@@ -578,7 +578,10 @@ def dump_operando_session(
         # Use masked arrays to preserve NaNs if present
         data = _np.array(arr)  # preserves mask where possible
         extent = tuple(map(float, im.get_extent())) if hasattr(im, 'get_extent') else None
-        cmap_name = getattr(im.get_cmap(), 'name', None)
+        # Get colormap name: first check if we stored it explicitly, otherwise try to get from colormap object
+        cmap_name = getattr(im, '_operando_cmap_name', None)
+        if cmap_name is None:
+            cmap_name = getattr(im.get_cmap(), 'name', None)
         clim = tuple(map(float, im.get_clim())) if hasattr(im, 'get_clim') else None
         origin = getattr(im, 'origin', 'upper')
         interpolation = getattr(im, 'get_interpolation', lambda: None)() or 'nearest'
@@ -870,6 +873,8 @@ def load_operando_session(filename: str):
         cmap_name = 'viridis'
     im = ax.imshow(arr, aspect='auto', origin=op.get('origin', 'upper'), extent=extent,
                    cmap=cmap_name, interpolation=op.get('interpolation', 'nearest'))
+    # Store the colormap name explicitly so it can be retrieved reliably when saving
+    setattr(im, '_operando_cmap_name', cmap_name)
     if op.get('clim'):
         try:
             im.set_clim(*op['clim'])
@@ -1315,6 +1320,18 @@ def load_operando_session(filename: str):
         elif ec_h_offset is not None:
             # EC panel doesn't exist but offset was saved - ignore it
             pass
+        
+        # Apply layout with loaded offsets to ensure visual position matches saved position
+        # This must happen after all offsets and geometry parameters are set
+        try:
+            from .operando_ec_interactive import _apply_group_layout_inches, _ensure_fixed_params
+            # Get current geometry parameters (which should match what was just loaded)
+            cb_w_i, cb_gap_i, ec_gap_i, ec_w_i, ax_w_i, ax_h_i = _ensure_fixed_params(fig, ax, cbar_ax, ec_ax)
+            # Apply layout with loaded offsets (offsets are already set as attributes above)
+            _apply_group_layout_inches(fig, ax, cbar_ax, ec_ax, ax_w_i, ax_h_i, cb_w_i, cb_gap_i, ec_gap_i, ec_w_i)
+        except Exception:
+            # If layout application fails, continue - better to have a slightly wrong layout than crash
+            pass
     except Exception:
         pass
 

{batplot-1.8.0 → batplot-1.8.1}/batplot/utils.py

@@ -540,6 +540,46 @@ def list_files_in_subdirectory(extensions: tuple, file_type: str, base_path: str
     return sorted(files, key=lambda x: x[0])
 
 
+def convert_label_shortcuts(text: str) -> str:
+    """Convert shortcut syntax to LaTeX format for labels.
+    
+    Converts {super(...)} and {sub(...)} shortcuts to LaTeX superscript/subscript format.
+    This allows easier input of mathematical notation without typing full LaTeX.
+    
+    Args:
+        text: Label text that may contain {super(...)} or {sub(...)} shortcuts
+        
+    Returns:
+        Text with shortcuts converted to LaTeX format (uses \\mathrm{} to prevent italic rendering).
+        
+    Examples:
+        >>> convert_label_shortcuts("g{super(-1)}")
+        "g$^{\\mathrm{-1}}$"
+        >>> convert_label_shortcuts("Li{sub(2)}FeSeO")
+        "Li$_{\\mathrm{2}}$FeSeO"
+        >>> convert_label_shortcuts("H{sub(2)}O")
+        "H$_{\\mathrm{2}}$O"
+    """
+    if not text:
+        return text
+    
+    import re
+    
+    # Convert {super(...)} to $^{\mathrm{...}}$ to prevent italic rendering
+    # Pattern matches {super(anything inside)}
+    # Use \mathrm{} to ensure non-italic rendering unless explicitly specified
+    # Need to escape backslashes in replacement string for LaTeX commands
+    text = re.sub(r'\{super\(([^)]+)\)\}', r'$^{\\mathrm{\1}}$', text)
+    
+    # Convert {sub(...)} to $_{\mathrm{...}}$ to prevent italic rendering
+    # Pattern matches {sub(anything inside)}
+    # Use \mathrm{} to ensure non-italic rendering unless explicitly specified
+    # Need to escape backslashes in replacement string for LaTeX commands
+    text = re.sub(r'\{sub\(([^)]+)\)\}', r'$_{\\mathrm{\1}}$', text)
+    
+    return text
+
+
 def normalize_label_text(text: str) -> str:
     """Normalize axis label text for proper matplotlib rendering.
     

{batplot-1.8.0 → batplot-1.8.1}/batplot/version_check.py

@@ -53,6 +53,54 @@ import time
 from pathlib import Path
 from typing import Optional, Tuple
 
+# ====================================================================================
+# UPDATE INFO CONFIGURATION
+# ====================================================================================
+# Edit this section to customize update notification messages and add update info.
+# 
+# HOW TO USE:
+# ----------
+# When releasing a new version, edit the UPDATE_INFO dictionary below to include
+# information about what's new or important in the update. This information will
+# be displayed to users when they run batplot and a newer version is available.
+#
+# EXAMPLE:
+# --------
+# UPDATE_INFO = {
+#     'custom_message': "This update includes important bug fixes and new features.",
+#     'update_notes': [
+#         "- Fixed colormap preservation issue in session files",
+#         "- Improved legend positioning when toggling visibility",
+#         "- Added superscript/subscript shortcuts for labels",
+#         "- Enhanced version check notifications"
+#     ],
+#     'show_update_notes': True,
+# }
+#
+# To disable custom messages, set 'custom_message' to None.
+# To disable update notes, set 'update_notes' to None or an empty list [].
+# ====================================================================================
+
+UPDATE_INFO = {
+    # Custom message to include in update notification
+    # Set to None or empty string to disable
+    # This will be displayed as an additional line in the update message box
+    'custom_message': "This update includes important bug fixes",  # Example: "This update includes important bug fixes."
+    
+    # Additional notes about the update (list of strings)
+    # Set to None or empty list [] to disable
+    # Each item in the list will be displayed as a separate line
+    'update_notes': None,  # Example: ["- Fixed colormap preservation issue", "- Improved legend positioning"]
+    
+    # Whether to show update notes if provided
+    # Set to False to hide update notes even if they are defined
+    'show_update_notes': True,
+}
+
+# ====================================================================================
+# END OF UPDATE INFO CONFIGURATION
+# ====================================================================================
+
 
 def get_cache_file() -> Path:
     """Get the path to the version check cache file."""
@@ -160,12 +208,43 @@ def _print_update_message(current: str, latest: str) -> None:
         current: Current version
         latest: Latest available version
     """
-    print(f"\n\033[93m╭{'─' * 68}╮\033[0m")
-    print(f"\033[93m│\033[0m  \033[1mA new version of batplot is available!\033[0m" + " " * 31 + "\033[93m│\033[0m")
-    print(f"\033[93m│\033[0m  Current: \033[91m{current}\033[0m → Latest: \033[92m{latest}\033[0m" + " " * (42 - len(current) - len(latest)) + "\033[93m│\033[0m")
-    print(f"\033[93m│\033[0m  Update with: \033[96mpip install --upgrade batplot\033[0m" + " " * 20 + "\033[93m│\033[0m")
-    print(f"\033[93m│\033[0m  To disable this check: \033[96mexport BATPLOT_NO_VERSION_CHECK=1\033[0m" + " " * 7 + "\033[93m│\033[0m")
-    print(f"\033[93m╰{'─' * 68}╯\033[0m\n")
+    # Calculate box width (minimum 68, expand if needed for longer messages)
+    box_width = 68
+    custom_msg = UPDATE_INFO.get('custom_message')
+    update_notes = UPDATE_INFO.get('update_notes')
+    show_notes = UPDATE_INFO.get('show_update_notes', True)
+    
+    # Calculate required width based on content
+    max_line_len = 68  # Default minimum width
+    if custom_msg:
+        max_line_len = max(max_line_len, len(custom_msg) + 4)
+    if update_notes and show_notes:
+        for note in update_notes:
+            max_line_len = max(max_line_len, len(note) + 4)
+    # Ensure box width is at least the calculated width
+    box_width = max(68, min(max_line_len, 100))  # Cap at 100 for readability
+    
+    print(f"\n\033[93m╭{'─' * box_width}╮\033[0m")
+    print(f"\033[93m│\033[0m  \033[1mA new version of batplot is available!\033[0m" + " " * max(0, box_width - 34) + "\033[93m│\033[0m")
+    print(f"\033[93m│\033[0m  Current: \033[91m{current}\033[0m → Latest: \033[92m{latest}\033[0m" + " " * max(0, box_width - 20 - len(current) - len(latest)) + "\033[93m│\033[0m")
+    
+    # Add custom message if provided
+    if custom_msg and custom_msg.strip():
+        # Truncate if too long to fit in box
+        msg = custom_msg[:box_width - 6] if len(custom_msg) > box_width - 6 else custom_msg
+        print(f"\033[93m│\033[0m  {msg}" + " " * max(0, box_width - len(msg) - 4) + "\033[93m│\033[0m")
+    
+    # Add update notes if provided
+    if update_notes and show_notes and isinstance(update_notes, list):
+        for note in update_notes:
+            if note and note.strip():
+                # Truncate if too long to fit in box
+                note_text = note[:box_width - 6] if len(note) > box_width - 6 else note
+                print(f"\033[93m│\033[0m  {note_text}" + " " * max(0, box_width - len(note_text) - 4) + "\033[93m│\033[0m")
+    
+    print(f"\033[93m│\033[0m  Update with: \033[96mpip install --upgrade batplot\033[0m" + " " * max(0, box_width - 34) + "\033[93m│\033[0m")
+    print(f"\033[93m│\033[0m  To disable this check: \033[96mexport BATPLOT_NO_VERSION_CHECK=1\033[0m" + " " * max(0, box_width - 45) + "\033[93m│\033[0m")
+    print(f"\033[93m╰{'─' * box_width}╯\033[0m\n")
 
 
 if __name__ == '__main__':

{batplot-1.8.0 → batplot-1.8.1/batplot.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: batplot
-Version: 1.8.0
+Version: 1.8.1
 Summary: Interactive plotting tool for material science (1D plot) and electrochemistry (GC, CV, dQ/dV, CPC, operando) with batch processing
 Author-email: Tian Dai <tianda@uio.no>
 License: MIT License

{batplot-1.8.0 → batplot-1.8.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "batplot"
-version = "1.8.0"
+version = "1.8.1"
 description = "Interactive plotting tool for material science (1D plot) and electrochemistry (GC, CV, dQ/dV, CPC, operando) with batch processing"
 authors = [
     { name = "Tian Dai", email = "tianda@uio.no" }