batplot 1.8.37__tar.gz → 1.8.39__tar.gz

{batplot-1.8.37/batplot.egg-info → batplot-1.8.39}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: batplot
-Version: 1.8.37
+Version: 1.8.39
 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-1.8.37 → batplot-1.8.39}/batplot/__init__.py

@@ -1,5 +1,5 @@
 """batplot: Interactive plotting for battery data visualization."""
 
-__version__ = "1.8.37"
+__version__ = "1.8.39"
 
 __all__ = ["__version__"]

{batplot-1.8.37 → batplot-1.8.39}/batplot/args.py

@@ -234,6 +234,8 @@ def _print_xy_help() -> None:
         "                                batplot f1.txt --readcol 2 3 f2.txt --readcol 5 6 --convert 1.54 q\n"
         "                              Directory: pass a folder to convert all .xy/.xye/.qye/.dat/.csv/.txt files:\n"
         "                                batplot /path/to/folder --convert 0.25448 1.54\n"
+        "                              Batch in current folder: use allfiles token (non-convertible files are skipped):\n"
+        "                                batplot allfiles --convert q 1.54\n"
         "                              Examples:\n"
         "                                batplot file.xye --convert 1.54 0.25\n"
         "                                batplot file.xye --convert 1.54 q\n"

{batplot-1.8.37 → batplot-1.8.39}/batplot/batplot.py

@@ -2624,7 +2624,11 @@ def batplot_main() -> int:  # type: ignore
         expanded = []
         for p in args.files:
             if os.path.isfile(p):
-                expanded.append(p)
+                ext = os.path.splitext(p)[1].lower()
+                if ext in convert_ext:
+                    expanded.append(p)
+                else:
+                    print(f"Warning: Skipping non-convertible file: {p}")
             elif os.path.isdir(p):
                 for f in sorted(os.listdir(p), key=natural_sort_key):
                     fp = os.path.join(p, f)
@@ -3351,6 +3355,10 @@ def batplot_main() -> int:  # type: ignore
         stack_label_bottom = bool(sess.get('stack_label_at_bottom', False))
         update_labels(ax, y_data_list, label_text_objects, saved_stack, stack_label_bottom)
         if cif_tick_series:
+            try:
+                fig._batplot_cif_tick_series = cif_tick_series
+            except Exception:
+                pass
             # Provide draw/extend helpers compatible with interactive menu using original placement logic
             def _session_q_to_2theta(peaksQ, wl):
                 if wl is None:
@@ -3364,7 +3372,8 @@ def batplot_main() -> int:  # type: ignore
 
             def _session_ensure_wavelength(default_wl=1.5406):
                 # Prefer any stored wl, else args.wl, else provided default
-                for _lab,_fname,_peaks,_wl,_qmax,_color in cif_tick_series:
+                _ser = getattr(fig, '_batplot_cif_tick_series', None) or cif_tick_series
+                for _lab,_fname,_peaks,_wl,_qmax,_color in _ser:
                     if _wl is not None:
                         return _wl
                 return getattr(args, 'wl', None) or default_wl
@@ -3374,7 +3383,10 @@ def batplot_main() -> int:  # type: ignore
                 return
 
             def _session_cif_draw():
-                if not cif_tick_series:
+                cif_series_draw = getattr(fig, '_batplot_cif_tick_series', None)
+                if cif_series_draw is None:
+                    cif_series_draw = cif_tick_series
+                if not cif_series_draw:
                     return
                 try:
                     # Preserve current limits before drawing - use actual current limits
@@ -3435,7 +3447,7 @@ def batplot_main() -> int:  # type: ignore
                         stacked_or_multi_y=_stacked_s,
                     )
                     _cif_bottom_m = xy_cif_stack_bottom_margin_yr(fixed_yr, show_titles=show_titles_local)
-                    needed_min = base - (len(cif_tick_series) - 1) * spacing - _cif_bottom_m
+                    needed_min = base - (len(cif_series_draw) - 1) * spacing - _cif_bottom_m
                     if not show_titles_local:
                         ylim_draw = tuple(prev_ylim)
                     elif needed_min >= prev_ylim[0]:
@@ -3457,7 +3469,7 @@ def batplot_main() -> int:  # type: ignore
                     wl_any = _session_ensure_wavelength()
                     
                     # Draw each series
-                    for i,(lab,fname,peaksQ,wl,qmax_sim,color) in enumerate(cif_tick_series):
+                    for i,(lab,fname,peaksQ,wl,qmax_sim,color) in enumerate(cif_series_draw):
                         y_line = base - i * spacing + xy_cif_stack_y_offset(fig, i)
                         tick_h, hkl_y = xy_cif_tick_stack_layout(y_line, yr)
                         # Convert peaks to axis domain
@@ -3621,7 +3633,7 @@ def batplot_main() -> int:  # type: ignore
         cif_globals_dict = None
         if cif_tick_series:
             cif_globals_dict = {
-                'cif_tick_series': list(cif_tick_series),
+                'cif_tick_series': cif_tick_series,
                 'cif_hkl_map': cif_hkl_map,
                 'cif_hkl_label_map': cif_hkl_label_map,
                 'show_cif_hkl': bool(show_cif_hkl),
@@ -4457,7 +4469,13 @@ def batplot_main() -> int:  # type: ignore
             draw_cif_ticks()
 
     def draw_cif_ticks():
-        if not cif_tick_series:
+        # Interactive menu mutates _bp.cif_tick_series; session/menu paths may use a
+        # different list than this closure. fig._batplot_cif_tick_series stays synced
+        # from interactive_menu so redraw sees renames (r→t), reorder, colors, etc.
+        cif_series_draw = getattr(fig, '_batplot_cif_tick_series', None)
+        if cif_series_draw is None:
+            cif_series_draw = cif_tick_series
+        if not cif_series_draw:
             return
         # Preserve current limits before drawing - use actual current limits
         # to prevent any movement when toggling
@@ -4492,13 +4510,13 @@ def batplot_main() -> int:  # type: ignore
             _bp_module = sys.modules.get('__main__')
             if _bp_module is not None and hasattr(_bp_module, 'cif_set_visible'):
                 vis = list(getattr(_bp_module, 'cif_set_visible') or [])
-                if len(vis) == len(cif_tick_series):
+                if len(vis) == len(cif_series_draw):
                     set_visible = [bool(v) for v in vis]
         except Exception:
             pass
         # Effective number of visible CIF rows (for spacing and y-limit expansion)
         if set_visible is None:
-            n_rows = len(cif_tick_series)
+            n_rows = len(cif_series_draw)
         else:
             n_rows = max(1, sum(1 for v in set_visible if v))
         
@@ -4571,7 +4589,7 @@ def batplot_main() -> int:  # type: ignore
             except Exception:
                 pass
         visible_idx = 0
-        for i,(lab, fname, peaksQ, wl, qmax_sim, color) in enumerate(cif_tick_series):
+        for i,(lab, fname, peaksQ, wl, qmax_sim, color) in enumerate(cif_series_draw):
             if set_visible is not None and i < len(set_visible) and not set_visible[i]:
                 continue
             y_line = base - visible_idx * spacing + xy_cif_stack_y_offset(fig, i)
@@ -4651,7 +4669,7 @@ def batplot_main() -> int:  # type: ignore
         hover_meta = []
         show_hkl = globals().get('show_cif_hkl', False)
         # Build mapping from Q to label text if available
-        for i,(lab, fname, peaksQ, wl, qmax_sim, color) in enumerate(cif_tick_series):
+        for i,(lab, fname, peaksQ, wl, qmax_sim, color) in enumerate(cif_series_draw):
             if use_2th and wl is None:
                 wl = getattr(ax, '_cif_hover_wl', None)
             # Recreate domain peaks consistent with those drawn (limit to view)
@@ -4738,6 +4756,10 @@ def batplot_main() -> int:  # type: ignore
             ax._cif_hover_cid = cid
 
     if cif_tick_series:
+        try:
+            fig._batplot_cif_tick_series = cif_tick_series
+        except Exception:
+            pass
         # Auto-assign distinct colors for CIF tick series.
         # For multiple CIF series:
         #   - If <= 10 files, use 'tab10' but in a re-ordered sequence to

{batplot-1.8.37 → batplot-1.8.39}/batplot/cpc_interactive.py

@@ -149,21 +149,17 @@ def _legend_no_frame(ax, *args, **kwargs):
     kwargs.setdefault('columnspacing', 0.6)
     # Don't use labelcolor='linecolor' by default as it causes issues 
     # with scatter plots that have facecolor='none' (hollow markers)
-    leg = ax.legend(*args, **kwargs)
+    legend_host_ax = kwargs.pop('legend_host_ax', None)
+    target_ax = legend_host_ax if legend_host_ax is not None else ax
+    leg = target_ax.legend(*args, **kwargs)
     if leg is not None:
         try:
             leg.set_frame_on(False)
+            # Keep legend above plot artists on the hosting axis.
+            leg.set_zorder(1_000_000)
+            leg.set_clip_on(False)
             for t in leg.get_texts():
                 t.set_verticalalignment('center')
-            # Nudge text up so it aligns with the symbol handle (patches sit higher than text baseline)
-            try:
-                sizes = [t.get_fontsize() for t in leg.get_texts() if t.get_text().strip()]
-                fs = float(np.mean(sizes)) if sizes else 10.0
-                shift_pts = fs * 0.5  # Points to move text up (was 0.15, increased for proper alignment)
-                for t in leg.get_texts():
-                    t.set_position((0, shift_pts))
-            except Exception:
-                pass
         except Exception:
             pass
     return leg
@@ -540,13 +536,16 @@ def _rebuild_legend(ax, ax2, file_data, preserve_position=True):
                         _legend_no_frame(ax, h_all, l_all, loc='center',
                                          bbox_to_anchor=(fx, fy),
                                          bbox_transform=fig.transFigure,
-                                         borderaxespad=1.0, title=leg_title)
+                                         borderaxespad=1.0, title=leg_title,
+                                         legend_host_ax=ax2)
                     except Exception:
                         _legend_no_frame(ax, h_all, l_all, loc='best',
-                                         borderaxespad=1.0, title=leg_title)
+                                         borderaxespad=1.0, title=leg_title,
+                                         legend_host_ax=ax2)
                 else:
                     _legend_no_frame(ax, h_all, l_all, loc='best',
-                                     borderaxespad=1.0, title=leg_title)
+                                     borderaxespad=1.0, title=leg_title,
+                                     legend_host_ax=ax2)
         else:
             # Single-file: standard handles from axes
             try:
@@ -570,13 +569,16 @@ def _rebuild_legend(ax, ax2, file_data, preserve_position=True):
                         _legend_no_frame(ax, h_all, l_all, loc='center',
                                          bbox_to_anchor=(fx, fy),
                                          bbox_transform=fig.transFigure,
-                                         borderaxespad=1.0, title=leg_title)
+                                         borderaxespad=1.0, title=leg_title,
+                                         legend_host_ax=ax2)
                     except Exception:
                         _legend_no_frame(ax, h_all, l_all, loc='best',
-                                         borderaxespad=1.0, title=leg_title)
+                                         borderaxespad=1.0, title=leg_title,
+                                         legend_host_ax=ax2)
                 else:
                     _legend_no_frame(ax, h_all, l_all, loc='best',
-                                     borderaxespad=1.0, title=leg_title)
+                                     borderaxespad=1.0, title=leg_title,
+                                     legend_host_ax=ax2)
             else:
                 leg = ax.get_legend()
                 if leg:
@@ -654,13 +656,16 @@ def _build_compact_cpc_legend(ax, ax2, file_data, xy_in=None, leg_title=None):
             pass
 
     # --- Build proxy handles and labels ---
-    _marker_kw = dict(linewidth=0)
-    # Header: filled square = Charge
-    chg_patch = mpatches.Patch(facecolor='#444444', edgecolor='#444444', label='Charge')
-    # Header: hollow square = Discharge
-    dch_patch = mpatches.Patch(facecolor='none', edgecolor='#444444',
-                                linewidth=1.2, label='Discharge')
-    handles = [chg_patch, dch_patch]
+    # Use scatter proxy handles so legend uses scatter-specific vertical alignment
+    # controls (scatterpoints/scatteryoffsets), which is more stable here.
+    ms2 = 28.0  # marker area in points^2
+    chg_handle = ax.scatter([], [], marker='s', s=ms2,
+                            facecolors='#444444', edgecolors='#444444',
+                            linewidths=1.0, label='Charge')
+    dch_handle = ax.scatter([], [], marker='s', s=ms2,
+                            facecolors='none', edgecolors='#444444',
+                            linewidths=1.2, label='Discharge')
+    handles = [chg_handle, dch_handle]
     labels = ['Charge', 'Discharge']
 
     # Header: efficiency triangle if visible
@@ -680,33 +685,34 @@ def _build_compact_cpc_legend(ax, ax2, file_data, xy_in=None, leg_title=None):
                         pass
         except Exception:
             eff_color = '#888888'
-        from matplotlib.lines import Line2D  # type: ignore
-        eff_handle = Line2D([0], [0], marker='^', color='none',
-                            markerfacecolor=eff_color, markeredgecolor=eff_color,
-                            markersize=4, label='Efficiency')
+        eff_handle = ax.scatter([], [], marker='^', s=ms2,
+                                facecolors=eff_color, edgecolors=eff_color,
+                                linewidths=1.0, label='Efficiency')
         handles.append(eff_handle)
         labels.append('Efficiency')
 
-    # Separator: invisible patch with empty label to create visual gap
-    sep = mpatches.Patch(visible=False, label='')
+    # Separator: invisible marker handle with empty label to create visual gap
+    sep = ax.scatter([], [], s=0.0, alpha=0.0, label='')
     handles.append(sep)
     labels.append('')
 
     # Per-file rows
     for color, fname in file_rows:
-        patch = mpatches.Patch(facecolor=color, edgecolor=color, label=fname)
-        handles.append(patch)
+        file_handle = ax.scatter([], [], marker='s', s=ms2,
+                                 facecolors=color, edgecolors=color,
+                                 linewidths=1.0, label=fname)
+        handles.append(file_handle)
         labels.append(fname)
 
     if not file_rows:
         return  # Nothing to show
 
     fig = ax.figure
-    # Multi-file: smaller symbols; handler_map forces squares (never cuboids)
+    # Multi-file compact legend with scatter-specific alignment controls.
     _hl = 0.35
     _legend_kw = dict(
         handlelength=_hl, handleheight=_hl, borderaxespad=1.0, title=leg_title,
-        handler_map={mpatches.Patch: _HandlerSquarePatch()},
+        scatterpoints=1, scatteryoffsets=[0.5],
     )
     if xy_in is not None:
         try:
@@ -717,11 +723,14 @@ def _build_compact_cpc_legend(ax, ax2, file_data, xy_in=None, leg_title=None):
                              loc='center',
                              bbox_to_anchor=(fx, fy),
                              bbox_transform=fig.transFigure,
+                             legend_host_ax=ax2,
                              **_legend_kw)
         except Exception:
-            _legend_no_frame(ax, handles, labels, loc='best', **_legend_kw)
+            _legend_no_frame(ax, handles, labels, loc='best',
+                             legend_host_ax=ax2, **_legend_kw)
     else:
-        _legend_no_frame(ax, handles, labels, loc='best', **_legend_kw)
+        _legend_no_frame(ax, handles, labels, loc='best',
+                         legend_host_ax=ax2, **_legend_kw)
 
 
 def _get_geometry_snapshot(ax, ax2) -> Dict:

{batplot-1.8.37 → batplot-1.8.39}/batplot/data/CHANGELOG.md

@@ -1,5 +1,13 @@
 # Changelog
 
+## [1.8.39] - 2026-05-01
+- Bug fixes for BatX operando plot
+
+
+## [1.8.38] - 2026-04-03
+- Bug fixes
+
+
 ## [1.8.37] - 2026-03-31
 - Bug fixes
 

{batplot-1.8.37 → batplot-1.8.39}/batplot/interactive.py

@@ -91,10 +91,12 @@ class _FilterIMKWarning:
         self.original_stderr.flush()
 
 
-def _safe_input(prompt: str = "") -> str:
+def _safe_input(prompt: str = "", *, cancel_on_interrupt: bool = True) -> str:
     """Wrapper around input() that suppresses macOS IMKCFRunLoopWakeUpReliable warnings.
-    
-    This is a harmless macOS system message that appears when using input() in terminals.
+
+    On **Ctrl+C** (or EOF on stdin), returns ``""`` by default so prompts behave like cancel
+    and the interactive menu keeps running instead of exiting with a traceback.
+    Set ``cancel_on_interrupt=False`` to re-raise (e.g. tests).
     """
     # Filter stderr to hide macOS IMK warnings while preserving other errors
     original_stderr = sys.stderr
@@ -102,7 +104,21 @@ def _safe_input(prompt: str = "") -> str:
     try:
         result = input(prompt)
         return result
-    except (KeyboardInterrupt, EOFError):
+    except KeyboardInterrupt:
+        if cancel_on_interrupt:
+            try:
+                print()
+            except Exception:
+                pass
+            return ""
+        raise
+    except EOFError:
+        if cancel_on_interrupt:
+            try:
+                print()
+            except Exception:
+                pass
+            return ""
         raise
     finally:
         sys.stderr = original_stderr
@@ -161,6 +177,70 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
     # Provide a consistent interface for accessing CIF state
     _bp = type('CIFState', (), cif_globals)() if cif_globals else None
 
+    def _sync_fig_cif_tick_series():
+        """Keep fig._batplot_cif_tick_series aligned with menu state for CIF redraw."""
+        if _bp is None:
+            return
+        try:
+            _cts = getattr(_bp, 'cif_tick_series', None)
+            if _cts is not None:
+                fig._batplot_cif_tick_series = _cts
+        except Exception:
+            pass
+
+    _sync_fig_cif_tick_series()
+
+    def _cif_series_for_session():
+        """CIF list for save (s), export (p), and undo snapshot: same as redraw (fig-backed)."""
+        try:
+            c = getattr(fig, '_batplot_cif_tick_series', None)
+            if c is not None:
+                return c
+        except Exception:
+            pass
+        if _bp is not None:
+            return getattr(_bp, 'cif_tick_series', None)
+        return None
+
+    def _print_cif_phase_list(cts):
+        for i, (lab, fname, *_rest) in enumerate(cts):
+            print(f"  {i+1}: {lab} ({os.path.basename(fname)})")
+
+    def _apply_cif_phase_label_rename(idx: int, new_label: str) -> None:
+        """Update one CIF phase row label and redraw (shared by main r→t and cif→r)."""
+        cts = getattr(_bp, 'cif_tick_series', None) if _bp is not None else None
+        if not cts or not (0 <= idx < len(cts)):
+            return
+        try:
+            push_state("cif-rename")
+        except Exception:
+            pass
+        _, fname, peaksQ, wl_e, qmax, col = cts[idx]
+        if _bp is not None:
+            setattr(_bp, 'cif_extend_suspended', True)
+        if hasattr(ax, '_cif_tick_art'):
+            try:
+                for art in list(getattr(ax, '_cif_tick_art', [])):
+                    try:
+                        art.remove()
+                    except Exception:
+                        pass
+                ax._cif_tick_art = []
+            except Exception:
+                pass
+        cts[idx] = (new_label, fname, peaksQ, wl_e, qmax, col)
+        if _bp is not None:
+            setattr(_bp, 'cif_tick_series', cts)
+        _sync_fig_cif_tick_series()
+        if hasattr(ax, '_cif_draw_func'):
+            ax._cif_draw_func()
+        try:
+            fig.canvas.draw()
+        except Exception:
+            pass
+        if _bp is not None:
+            setattr(_bp, 'cif_extend_suspended', False)
+
     try:
         raw_source_paths = list(getattr(args, 'files', []) or [])
     except Exception:
@@ -985,7 +1065,7 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
 
     # NEW: export current style to .bpcfg
     def export_style_config(filename, base_path=None, overwrite_path=None, force_kind=None):
-        cts = getattr(_bp, 'cif_tick_series', None) if _bp is not None else None
+        cts = _cif_series_for_session()
         show_titles = bool(getattr(_bp, 'show_cif_titles', True)) if _bp is not None else True
         return _export_style_config(
             filename,
@@ -1007,7 +1087,7 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
 
     # NEW: apply imported style config (restricted application)
     def apply_style_config(filename):
-        cts = getattr(_bp, 'cif_tick_series', None) if _bp is not None else None
+        cts = _cif_series_for_session()
         hkl_map = getattr(_bp, 'cif_hkl_label_map', None) if _bp is not None else None
         res = _bp_apply_style_config(
             filename,
@@ -1026,6 +1106,7 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
             hkl_map,
             adjust_margins,
         )
+        _sync_fig_cif_tick_series()
         # Sync top/right tick label2 fonts with current rcParams after style import
         try:
             fam_chain = plt.rcParams.get('font.sans-serif')
@@ -1586,6 +1667,7 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                 except Exception:
                     return None
                 return None
+            _cts_for_snap = _cif_series_for_session()
             snap = {
                 "note": note,
                 "xlim": ax.get_xlim(),
@@ -1622,7 +1704,7 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                 "tick_direction": getattr(fig, '_tick_direction', 'out'),
                 "tick_spacing": _capture_tick_spacing(ax),
                 "tick_minor_count": _capture_tick_minor_count(ax),
-                "cif_tick_series": (list(getattr(_bp, 'cif_tick_series')) if (_bp is not None and hasattr(_bp, 'cif_tick_series')) else None),
+                "cif_tick_series": (list(_cts_for_snap) if _cts_for_snap is not None else None),
                 "show_cif_hkl": (bool(getattr(_bp, 'show_cif_hkl')) if _bp is not None and hasattr(_bp, 'show_cif_hkl') else False),
                 "show_cif_titles": (bool(getattr(_bp, 'show_cif_titles')) if _bp is not None and hasattr(_bp, 'show_cif_titles') else True),
                 "rotation_angle": getattr(ax, '_rotation_angle', 0),
@@ -2009,6 +2091,7 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                     _bp.cif_tick_series[:] = [tuple(t) for t in snap["cif_tick_series"]]
                 except Exception:
                     pass
+                _sync_fig_cif_tick_series()
             if _bp is not None and 'show_cif_hkl' in snap:
                 try:
                     new_state = bool(snap['show_cif_hkl'])
@@ -2144,7 +2227,7 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                 print("  " + colorize_menu("p: shift all CIF ticks (w/s or type a value)"))
                 print("  " + colorize_menu("c: CIF color (per set)"))
                 print("  " + colorize_menu("x: show/hide CIF set"))
-                print("  " + colorize_menu("r: rename CIF set label"))
+                print("  " + colorize_menu("r: rename CIF phase label (same as main menu r→t)"))
                 print("  " + colorize_menu("q: back to main menu"))
                 sub = _safe_input(colorize_prompt("CIF (z/t/v/p/c/x/r/q): ")).strip().lower()
                 if not sub or sub == 'q':
@@ -2249,6 +2332,7 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                             new_cts = [cts[i - 1] for i in parts]
                             if _bp is not None:
                                 setattr(_bp, 'cif_tick_series', new_cts)
+                            _sync_fig_cif_tick_series()
                             prev_offs = getattr(fig, '_bp_cif_stack_y_offsets', None)
                             if prev_offs is not None and len(prev_offs) == len(cts):
                                 fig._bp_cif_stack_y_offsets = [prev_offs[i - 1] for i in parts]
@@ -2390,6 +2474,7 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                                         cts[idx] = (lab, fname, peaksQ, wl_e, qmax, resolved)
                                     if _bp is not None:
                                         setattr(_bp, 'cif_tick_series', cts)
+                                    _sync_fig_cif_tick_series()
                                     if hasattr(ax, '_cif_draw_func'):
                                         ax._cif_draw_func()
                                 else:
@@ -2495,6 +2580,7 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                                         cts[idx] = (lab, fname, peaksQ, wl_e, qmax, col_val)
                                     if _bp is not None:
                                         setattr(_bp, 'cif_tick_series', cts)
+                                    _sync_fig_cif_tick_series()
                                     if hasattr(ax, '_cif_draw_func'):
                                         ax._cif_draw_func()
                     except Exception as e:
@@ -2542,39 +2628,40 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                     except Exception as e:
                         print(f"Error toggling CIF visibility: {e}")
                 elif sub == 'r':
-                    # Rename CIF set labels — updates label field in cif_tick_series and redraws.
+                    # Rename CIF phase labels — same behavior as main menu r→t.
                     try:
                         cts = getattr(_bp, 'cif_tick_series', None) if _bp is not None else None
                         if not cts:
-                            print("No CIF tick sets to rename.")
+                            print("No CIF phases to rename.")
                         else:
                             while True:
-                                print("CIF sets (q=back)")
-                                for i, (lab, fname, *_rest) in enumerate(cts):
-                                    print(f"  {i+1}: {lab}")
-                                idx_s = _safe_input("Set index to rename (q=back): ").strip().lower()
+                                print("CIF phases (q=back to CIF menu)")
+                                _print_cif_phase_list(cts)
+                                idx_s = _safe_input(
+                                    "Phase number to rename (q=back): "
+                                ).strip().lower()
                                 if not idx_s or idx_s == 'q':
                                     break
                                 try:
                                     idx = int(idx_s) - 1
-                                    if 0 <= idx < len(cts):
-                                        lab, fname, peaksQ, wl_e, qmax, col = cts[idx]
-                                        new_lab = _safe_input(f"New label for set {idx+1} (current: {lab}, blank=cancel): ").strip()
-                                        if not new_lab:
-                                            continue
-                                        push_state("cif-rename")
-                                        cts[idx] = (new_lab, fname, peaksQ, wl_e, qmax, col)
-                                        if _bp is not None:
-                                            setattr(_bp, 'cif_tick_series', cts)
-                                        if hasattr(ax, '_cif_draw_func'):
-                                            ax._cif_draw_func()
-                                        print(f"Set {idx+1} renamed to: {new_lab}")
-                                    else:
+                                    if not (0 <= idx < len(cts)):
                                         print("Invalid index.")
+                                        continue
                                 except ValueError:
                                     print("Invalid index.")
+                                    continue
+                                print_label_latex_tips()
+                                new_lab = _safe_input(
+                                    "New CIF phase label (q=cancel): "
+                                ).strip()
+                                if not new_lab or new_lab.lower() == 'q':
+                                    print("Canceled.")
+                                    continue
+                                new_lab = convert_label_shortcuts(new_lab)
+                                _apply_cif_phase_label_rename(idx, new_lab)
+                                print(f"Phase {idx + 1} label updated.")
                     except Exception as e:
-                        print(f"Error renaming CIF sets: {e}")
+                        print(f"Error renaming CIF phase labels: {e}")
                 else:
                     print("Unknown option.")
             continue
@@ -2708,7 +2795,7 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                     delta=delta,
                     args=args,
                     tick_state=tick_state,
-                    cif_tick_series=(getattr(_bp, 'cif_tick_series', None) if _bp is not None else None),
+                    cif_tick_series=_cif_series_for_session(),
                     cif_hkl_map=(getattr(_bp, 'cif_hkl_map', None) if _bp is not None else None),
                     cif_hkl_label_map=(getattr(_bp, 'cif_hkl_label_map', None) if _bp is not None else None),
                     show_cif_hkl=(bool(getattr(_bp, 'show_cif_hkl', False)) if _bp is not None else False),
@@ -2870,7 +2957,7 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                         delta=delta,
                         args=args,
                         tick_state=tick_state,
-                        cif_tick_series=(getattr(_bp, 'cif_tick_series', None) if _bp is not None else None),
+                        cif_tick_series=_cif_series_for_session(),
                         cif_hkl_map=(getattr(_bp, 'cif_hkl_map', None) if _bp is not None else None),
                         cif_hkl_label_map=(getattr(_bp, 'cif_hkl_label_map', None) if _bp is not None else None),
                         show_cif_hkl=(bool(getattr(_bp,'show_cif_hkl', False)) if _bp is not None else False),
@@ -2903,7 +2990,7 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                             delta=delta,
                             args=args,
                             tick_state=tick_state,
-                            cif_tick_series=(getattr(_bp, 'cif_tick_series', None) if _bp is not None else None),
+                            cif_tick_series=_cif_series_for_session(),
                             cif_hkl_map=(getattr(_bp, 'cif_hkl_map', None) if _bp is not None else None),
                             cif_hkl_label_map=(getattr(_bp, 'cif_hkl_label_map', None) if _bp is not None else None),
                             show_cif_hkl=(bool(getattr(_bp,'show_cif_hkl', False)) if _bp is not None else False),
@@ -2943,7 +3030,7 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                         delta=delta,
                         args=args,
                         tick_state=tick_state,
-                        cif_tick_series=(getattr(_bp, 'cif_tick_series', None) if _bp is not None else None),
+                        cif_tick_series=_cif_series_for_session(),
                         cif_hkl_map=(getattr(_bp, 'cif_hkl_map', None) if _bp is not None else None),
                         cif_hkl_label_map=(getattr(_bp, 'cif_hkl_label_map', None) if _bp is not None else None),
                         show_cif_hkl=(bool(getattr(_bp,'show_cif_hkl', False)) if _bp is not None else False),
@@ -3157,6 +3244,7 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                                         cts[idx] = (lab, fname, peaksQ, wl_e, qmax, resolved)
                                     if _bp is not None:
                                         setattr(_bp, 'cif_tick_series', cts)
+                                    _sync_fig_cif_tick_series()
                                     if hasattr(ax, '_cif_draw_func'):
                                         ax._cif_draw_func()
                                 else:
@@ -3225,6 +3313,7 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                                         cts[idx] = (lab, fname, peaksQ, wl_e, qmax, col_val)
                                     if _bp is not None:
                                         setattr(_bp, 'cif_tick_series', cts)
+                                    _sync_fig_cif_tick_series()
                                     if hasattr(ax, '_cif_draw_func'):
                                         ax._cif_draw_func()
                         else:
@@ -3317,7 +3406,7 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                 while True:
                     rename_opts = "c=curve"
                     if has_cif:
-                        rename_opts += ", t=cif tick label"
+                        rename_opts += ", t=CIF phase label (same as cif→r)"
                     rename_opts += ", x=x-axis, y=y-axis, q=return"
                     mode = _safe_input(f"Rename ({rename_opts}): ").strip().lower()
                     if mode == 'q':
@@ -3350,44 +3439,34 @@ def interactive_menu(fig, ax, y_data_list, x_data_list, labels, orig_y,
                     elif mode == 't':
                         cts = getattr(_bp, 'cif_tick_series', None) if _bp is not None else None
                         if not cts:
-                            print("No CIF tick sets to rename.")
+                            print("No CIF phases to rename.")
+                            continue
+                        print("CIF phases (then pick one; same list as cif→r)")
+                        _print_cif_phase_list(cts)
+                        s = _safe_input(
+                            "Phase number to rename (q=cancel): "
+                        ).strip()
+                        if not s or s.lower() == 'q':
+                            print("Canceled.")
                             continue
-                        for i,(lab, fname, *_rest) in enumerate(cts):
-                            print(f"  {i+1}: {lab} ({os.path.basename(fname)})")
-                        s = _safe_input("CIF tick number to rename (q=cancel): ").strip()
-                        if not s or s.lower()=='q':
-                            print("Canceled."); continue
                         try:
-                            idx = int(s)-1
+                            idx = int(s) - 1
                             if not (0 <= idx < len(cts)):
-                                print("Index out of range."); continue
+                                print("Index out of range.")
+                                continue
                         except ValueError:
-                            print("Bad index."); continue
+                            print("Bad index.")
+                            continue
                         print_label_latex_tips()
-                        new_name = _safe_input("New CIF tick label (q=cancel): ")
-                        if not new_name or new_name.lower()=='q':
-                            print("Canceled."); continue
+                        new_name = _safe_input(
+                            "New CIF phase label (q=cancel): "
+                        ).strip()
+                        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:
-                            setattr(_bp, 'cif_extend_suspended', True)
-                        if hasattr(ax, '_cif_tick_art'):
-                            try:
-                                for art in list(getattr(ax, '_cif_tick_art', [])):
-                                    try:
-                                        art.remove()
-                                    except Exception:
-                                        pass
-                                ax._cif_tick_art = []
-                            except Exception:
-                                pass
-                        cts[idx] = (new_name, fname, peaksQ, wl, qmax_sim, color)
-                        setattr(_bp, 'cif_tick_series', cts)
-                        if hasattr(ax,'_cif_draw_func'): ax._cif_draw_func()
-                        fig.canvas.draw()
-                        if _bp is not None:
-                            setattr(_bp, 'cif_extend_suspended', False)
+                        _apply_cif_phase_label_rename(idx, new_name)
+                        print(f"Phase {idx + 1} label updated.")
                     elif mode in ('x','y'):
                         print("Enter new axis label (q=cancel).")
                         print_label_latex_tips()

{batplot-1.8.37 → batplot-1.8.39}/batplot/operando.py

@@ -607,66 +607,73 @@ def plot_operando_folder(folder: str, args, cif_files=None) -> Tuple[plt.Figure,
 
             for ec_path in ec_files:
                 is_datalogger = ec_path.suffix.lower() == ".csv" and is_biologic_datalogger_csv(str(ec_path))
-
-                if is_datalogger:
-                    time_h, voltage_v = read_biologic_datalogger_time_voltage(str(ec_path))
-                    time_h = np.asarray(time_h, float)
-                    voltage_v = np.asarray(voltage_v, float)
-                    if time_offset != 0:
-                        time_h = time_h + time_offset
-                    if len(time_h) > 0:
+                try:
+                    if is_datalogger:
+                        time_h, voltage_v = read_biologic_datalogger_time_voltage(str(ec_path))
+                        time_h = np.asarray(time_h, float)
+                        voltage_v = np.asarray(voltage_v, float)
+                        if len(time_h) == 0 or len(voltage_v) == 0:
+                            raise ValueError(f"DataLogger file {ec_path.name} has no valid data rows")
+                        if time_offset != 0:
+                            time_h = time_h + time_offset
                         time_offset = float(np.nanmax(time_h))
-                    x_parts.append(voltage_v)
-                    y_parts.append(time_h)
-                else:
-                    # .mpt file
-                    readcol_mpt = None
-                    if hasattr(args, 'readcols') and args.readcols is not None:
-                        readcol_mpt = tuple(args.readcols)
-                    if readcol_mpt is None and hasattr(args, 'readcol_by_ext') and '.mpt' in getattr(args, 'readcol_by_ext', {}):
-                        readcol_mpt = args.readcol_by_ext['.mpt']
-
-                    if readcol_mpt:
-                        data = robust_loadtxt_skipheader(str(ec_path))
-                        if data.ndim == 1:
-                            data = data.reshape(1, -1)
-                        if data.shape[1] < 2:
-                            raise ValueError(f"MPT file {ec_path.name} has insufficient columns")
-                        x_col, y_col = readcol_mpt
-                        x_col_idx, y_col_idx = x_col - 1, y_col - 1
-                        # EC panel: voltage on X, time on Y; assume x_col=time, y_col=voltage (EC-Lab order)
-                        v_raw = np.asarray(data[:, y_col_idx], float)
-                        t_raw = np.asarray(data[:, x_col_idx], float)
+                        x_parts.append(voltage_v)
+                        y_parts.append(time_h)
                     else:
-                        result = read_mpt_file(str(ec_path), mode='time')
-                        if len(result) == 5:
-                            x_data, y_data, current_mA, x_lbl, y_lbl = result
-                            x_lower = x_lbl.lower().replace(' ', '').replace('_', '')
-                            y_lower = y_lbl.lower().replace(' ', '').replace('_', '')
-                            has_time_in_x = 'time' in x_lower
-                            has_voltage_in_y = 'voltage' in y_lower or 'potential' in y_lower or 'ewe' in y_lower
-                            if x_lbl == 'Time (h)' and y_lbl == 'Potential (V)':
-                                t_raw = np.asarray(x_data, float)
-                                v_raw = np.asarray(y_data, float)
-                            elif has_time_in_x and has_voltage_in_y:
-                                t_raw = np.asarray(x_data, float)
-                                v_raw = np.asarray(y_data, float)
-                            elif 'voltage' in x_lower or 'potential' in x_lower:
-                                v_raw = np.asarray(x_data, float)
-                                t_raw = np.asarray(y_data, float)
+                        # .mpt file
+                        readcol_mpt = None
+                        if hasattr(args, 'readcols') and args.readcols is not None:
+                            readcol_mpt = tuple(args.readcols)
+                        if readcol_mpt is None and hasattr(args, 'readcol_by_ext') and '.mpt' in getattr(args, 'readcol_by_ext', {}):
+                            readcol_mpt = args.readcol_by_ext['.mpt']
+
+                        if readcol_mpt:
+                            data = robust_loadtxt_skipheader(str(ec_path))
+                            if data.ndim == 1:
+                                data = data.reshape(1, -1)
+                            if data.shape[1] < 2:
+                                raise ValueError(f"MPT file {ec_path.name} has insufficient columns")
+                            x_col, y_col = readcol_mpt
+                            x_col_idx, y_col_idx = x_col - 1, y_col - 1
+                            # EC panel: voltage on X, time on Y; assume x_col=time, y_col=voltage (EC-Lab order)
+                            v_raw = np.asarray(data[:, y_col_idx], float)
+                            t_raw = np.asarray(data[:, x_col_idx], float)
+                        else:
+                            result = read_mpt_file(str(ec_path), mode='time')
+                            if len(result) == 5:
+                                x_data, y_data, current_mA, x_lbl, y_lbl = result
+                                x_lower = x_lbl.lower().replace(' ', '').replace('_', '')
+                                y_lower = y_lbl.lower().replace(' ', '').replace('_', '')
+                                has_time_in_x = 'time' in x_lower
+                                has_voltage_in_y = 'voltage' in y_lower or 'potential' in y_lower or 'ewe' in y_lower
+                                if x_lbl == 'Time (h)' and y_lbl == 'Potential (V)':
+                                    t_raw = np.asarray(x_data, float)
+                                    v_raw = np.asarray(y_data, float)
+                                elif has_time_in_x and has_voltage_in_y:
+                                    t_raw = np.asarray(x_data, float)
+                                    v_raw = np.asarray(y_data, float)
+                                elif 'voltage' in x_lower or 'potential' in x_lower:
+                                    v_raw = np.asarray(x_data, float)
+                                    t_raw = np.asarray(y_data, float)
+                                else:
+                                    v_raw = np.asarray(x_data, float)
+                                    t_raw = np.asarray(y_data, float)
                             else:
+                                x_data, y_data, current_mA, *_ = result
                                 v_raw = np.asarray(x_data, float)
-                                t_raw = np.asarray(y_data, float)
-                        else:
-                            x_data, y_data, current_mA, *_ = result
-                            v_raw = np.asarray(x_data, float)
-                            t_raw = np.asarray(y_data, float) / 3600.0
-                    if time_offset != 0:
-                        t_raw = t_raw + time_offset
-                    if len(t_raw) > 0:
+                                t_raw = np.asarray(y_data, float) / 3600.0
+                        if len(t_raw) == 0 or len(v_raw) == 0:
+                            raise ValueError(f"MPT file {ec_path.name} has no valid data rows")
+                        if time_offset != 0:
+                            t_raw = t_raw + time_offset
                         time_offset = float(np.nanmax(t_raw))
-                    x_parts.append(v_raw)
-                    y_parts.append(t_raw)
+                        x_parts.append(v_raw)
+                        y_parts.append(t_raw)
+                except Exception as ec_file_err:
+                    print(f"[operando] Skip EC file {ec_path.name}: {ec_file_err}")
+
+            if not x_parts or not y_parts:
+                raise ValueError("No valid electrochem data points in detected EC files")
 
             x_data = np.concatenate(x_parts) if len(x_parts) > 1 else x_parts[0]
             y_data = np.concatenate(y_parts) if len(y_parts) > 1 else y_parts[0]

{batplot-1.8.37 → batplot-1.8.39}/batplot/style.py

@@ -534,6 +534,17 @@ def print_style_info(
     if cif_tick_series:
         print(f"\n--- CIF (cif key) ---")
         try:
+            print("CIF phase labels (r→t / cif→r) & per-set colors (c); stored in p / i / s / b:")
+            for i, ent in enumerate(cif_tick_series):
+                if len(ent) < 6:
+                    continue
+                lab, fname, _pq, _wl, _qm, col = ent[0], ent[1], ent[2], ent[3], ent[4], ent[5]
+                try:
+                    ch = mcolors.to_hex(mcolors.to_rgba(col))
+                except Exception:
+                    ch = str(col)
+                hb = color_block(ch) if ch else ""
+                print(f"  {i + 1}: {lab}  ({os.path.basename(fname)})  {hb} {ch}")
             hkl_state = None
             _bp_module = sys.modules.get('__main__')
             if _bp_module is not None and hasattr(_bp_module, 'show_cif_hkl'):
@@ -786,8 +797,9 @@ def export_style_config(
         except Exception:
             pass
         if cif_tick_series:
+            # label + color so export (p) / import (i) match session (s) / undo (b) for renamed phases
             cfg["cif_ticks"] = [
-                {"index": i, "color": color}
+                {"index": i, "label": str(lab), "color": color}
                 for i, (lab, fname, peaksQ, wl, qmax_sim, color) in enumerate(cif_tick_series)
             ]
             # Always save one offset per CIF set so import (i) matches session/undo (s/b).

{batplot-1.8.37 → batplot-1.8.39}/batplot/version_check.py

@@ -101,10 +101,10 @@ def _wrap_line(text: str, width: int) -> List[str]:
 UPDATE_INFO = {
     # Custom message to include in update notification
     # (Auto-filled from RELEASE_NOTES.txt when using batplot --dev-upgrade)
-    'custom_message': '- Bug fixes',
+    'custom_message': '- Bug fixes for BatX operando plot',
     # Additional notes (auto-filled from RELEASE_NOTES.txt)
     'update_notes': [
-        '- Bug fixes'
+        '- Bug fixes for BatX operando plot'
     ],
     'show_update_notes': True,
 }

{batplot-1.8.37 → batplot-1.8.39/batplot.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: batplot
-Version: 1.8.37
+Version: 1.8.39
 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-1.8.37 → batplot-1.8.39}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "batplot"
-version = "1.8.37"
+version = "1.8.39"
 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" }