batplot 1.8.28__tar.gz → 1.8.29__tar.gz

{batplot-1.8.28/batplot.egg-info → batplot-1.8.29}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: batplot
-Version: 1.8.28
+Version: 1.8.29
 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
@@ -112,6 +112,10 @@ batplot scan1.brml:1.5406 scan2.xye:0.7093
 # Convert and export to converted/ subfolder (q and Q equivalent)
 batplot data.xye --convert 1.54 q
 batplot data.qye --convert q 1.54
+
+# With --readcol for custom column layout (e.g. 2θ in col 3, intensity in col 4)
+batplot data.csv --readcol 3 4 --convert 1.54 q
+batplot f1.txt --readcol 2 3 f2.txt --readcol 5 6 --convert 1.54 q
 ```
 
 ### Stacking and normalization
@@ -152,6 +156,9 @@ batplot data.xy --readcol 1 2 1 3
 
 # Range: col 1 as x, cols 2–20 as 19 y-curves
 batplot file.txt --readcol 1 2-20
+
+# With --convert: use custom columns when converting XRD data
+batplot data.csv --readcol 3 4 --convert 1.54 q
 ```
 
 ### Derivatives and EXAFS
@@ -186,6 +193,8 @@ batplot allfiles --xaxis 2theta --xrange 15 75 --interactive
 
 ### Galvanostatic cycling (GC)
 
+GC mode plots potential vs. capacity for each charge/discharge cycle—the primary visualization for battery cycling data. Batplot automatically detects cycles from Neware `.csv` or Biologic `.mpt` files, assigns each cycle a distinct color, and supports both specific capacity (mAh/g) and raw capacity. For `.mpt` files, pass `--mass` (mg) to compute specific capacity. Discontinuous or paused experiments are handled by splitting data into contiguous charge/discharge segments. Use the interactive menu to customize colors, visibility, and export.
+
 ```bash
 # From .csv (capacity in file)
 batplot battery.csv --gc
@@ -278,13 +287,17 @@ batplot file1.xye file2.qye structure.cif:1.54 --stack --interactive
 
 ## Batch export (--all)
 
-Export each file as a separate figure to `batplot_svg/`:
+Export each file as a separate figure to `Figures/`:
 
 ```bash
 batplot --all
 batplot --all --format png
 batplot --all --xaxis 2theta --xrange 10 80
 batplot --all style.bps --gc --mass 7
+
+# With --readcol for custom columns (put --readcol before style file)
+batplot --all --readcol 2 3 --xaxis 2theta
+batplot --all --readcol 2 3 style.bps --xaxis 2theta
 ```
 
 ---

{batplot-1.8.28 → batplot-1.8.29}/README.md

@@ -61,6 +61,10 @@ batplot scan1.brml:1.5406 scan2.xye:0.7093
 # Convert and export to converted/ subfolder (q and Q equivalent)
 batplot data.xye --convert 1.54 q
 batplot data.qye --convert q 1.54
+
+# With --readcol for custom column layout (e.g. 2θ in col 3, intensity in col 4)
+batplot data.csv --readcol 3 4 --convert 1.54 q
+batplot f1.txt --readcol 2 3 f2.txt --readcol 5 6 --convert 1.54 q
 ```
 
 ### Stacking and normalization
@@ -101,6 +105,9 @@ batplot data.xy --readcol 1 2 1 3
 
 # Range: col 1 as x, cols 2–20 as 19 y-curves
 batplot file.txt --readcol 1 2-20
+
+# With --convert: use custom columns when converting XRD data
+batplot data.csv --readcol 3 4 --convert 1.54 q
 ```
 
 ### Derivatives and EXAFS
@@ -135,6 +142,8 @@ batplot allfiles --xaxis 2theta --xrange 15 75 --interactive
 
 ### Galvanostatic cycling (GC)
 
+GC mode plots potential vs. capacity for each charge/discharge cycle—the primary visualization for battery cycling data. Batplot automatically detects cycles from Neware `.csv` or Biologic `.mpt` files, assigns each cycle a distinct color, and supports both specific capacity (mAh/g) and raw capacity. For `.mpt` files, pass `--mass` (mg) to compute specific capacity. Discontinuous or paused experiments are handled by splitting data into contiguous charge/discharge segments. Use the interactive menu to customize colors, visibility, and export.
+
 ```bash
 # From .csv (capacity in file)
 batplot battery.csv --gc
@@ -227,13 +236,17 @@ batplot file1.xye file2.qye structure.cif:1.54 --stack --interactive
 
 ## Batch export (--all)
 
-Export each file as a separate figure to `batplot_svg/`:
+Export each file as a separate figure to `Figures/`:
 
 ```bash
 batplot --all
 batplot --all --format png
 batplot --all --xaxis 2theta --xrange 10 80
 batplot --all style.bps --gc --mass 7
+
+# With --readcol for custom columns (put --readcol before style file)
+batplot --all --readcol 2 3 --xaxis 2theta
+batplot --all --readcol 2 3 style.bps --xaxis 2theta
 ```
 
 ---

{batplot-1.8.28 → batplot-1.8.29}/batplot/__init__.py

@@ -1,5 +1,5 @@
 """batplot: Interactive plotting for battery data visualization."""
 
-__version__ = "1.8.28"
+__version__ = "1.8.29"
 
 __all__ = ["__version__"]

{batplot-1.8.28 → batplot-1.8.29}/batplot/args.py

@@ -227,6 +227,9 @@ def _print_xy_help() -> None:
         "                              - <wl1> <wl2>  : convert 2θ from wavelength1 to wavelength2\n"
         "                              - <wl> q or Q  : convert 2θ (with wavelength) to Q space (q and Q equivalent)\n"
         "                              - q or Q <wl>  : convert Q space to 2θ (with wavelength)\n"
+        "                              Works with --readcol for custom column layout (per-file, per-ext, or global):\n"
+        "                                batplot data.csv --readcol 3 4 --convert 1.54 q\n"
+        "                                batplot f1.txt --readcol 2 3 f2.txt --readcol 5 6 --convert 1.54 q\n"
         "                              Examples:\n"
         "                                batplot file.xye --convert 1.54 0.25\n"
         "                                batplot file.xye --convert 1.54 q\n"
@@ -244,6 +247,7 @@ def _print_xy_help() -> None:
         "    Multi-curve: file.xy --readcol 1 2 1 3  (plot cols 1,2 and 1,3 as two curves)\n"
         "    Range: file.txt --readcol 1 2-20  (col 1 as x, cols 2..20 as 19 y-curves)\n"
         "    With wavelength: file.xy:1.54 --readcol 2 3  (col 2 as 2θ, convert to Q using λ=1.54 Å)\n"
+        "    With --convert: file.csv --readcol 3 4 --convert 1.54 q  (custom cols for conversion)\n"
         "  --readcolxy <x> <y>       : read columns for .xy files only\n"
         "  --readcolxye <x> <y>      : read columns for .xye files only\n"
         "  --readcolqye <x> <y>      : read columns for .qye files only\n"
@@ -574,17 +578,22 @@ def parse_args(argv=None):
     # does not consume it. When --readcol appears before any file (global),
     # store in global_readcol_expanded for post-parse.
     # Keys use the exact file token (e.g. "file.xy:1.54") for wavelength match.
+    # Style files (.bps, .bpsg, .bpcfg) are NOT treated as file tokens so that
+    # "batplot --all style.bps --readcol 2 3" uses global readcol, not per-file.
     # ====================================================================
     readcol_by_file = {}
     global_readcol_expanded = None
     filtered_argv = []
     last_file_token = None
+    _STYLE_EXTENSIONS = ('.bps', '.bpsg', '.bpcfg')
     i = 0
     while i < len(argv):
         arg = argv[i]
-        # Track non-option tokens as potential file specs
+        # Track non-option tokens as potential file specs (exclude style files)
         if not arg.startswith('-'):
-            last_file_token = arg
+            arg_lower = arg.lower()
+            if not arg_lower.endswith(_STYLE_EXTENSIONS):
+                last_file_token = arg
         if arg == '--readcol' and i + 1 < len(argv):
             tokens = []
             j = i + 1

{batplot-1.8.28 → batplot-1.8.29}/batplot/batplot.py

@@ -3416,7 +3416,7 @@ def batplot_main() -> int:  # type: ignore
             print("Error: --convert requires file(s) to convert")
             exit(1)
         from_param, to_param = args.convert
-        convert_xrd_data(args.files, from_param, to_param)
+        convert_xrd_data(args.files, from_param, to_param, args=args)
         exit()
 
     # ---------------- Plotting ----------------
@@ -4035,7 +4035,17 @@ def batplot_main() -> int:  # type: ignore
                 y_plotted = y_plot_offset
 
             target_ax = ax2 if is_right_y else ax
-            target_ax.plot(x_plotted, y_plotted, "-", lw=1, alpha=0.8)
+            # With --ry: assign explicit colors so plot, Colors menu (c), labels, and p/i/s/b stay consistent.
+            # Matplotlib twinx uses a separate color cycle; explicit colors avoid mismatch across axes.
+            if right_y_data_indices:
+                try:
+                    curve_idx = len(y_data_list)
+                    curve_color = plt.cm.tab10(curve_idx % 10)
+                    target_ax.plot(x_plotted, y_plotted, "-", lw=1, alpha=0.8, color=curve_color)
+                except Exception:
+                    target_ax.plot(x_plotted, y_plotted, "-", lw=1, alpha=0.8)
+            else:
+                target_ax.plot(x_plotted, y_plotted, "-", lw=1, alpha=0.8)
             x_data_list.append(x_plotted)
             y_data_list.append(y_plotted.copy())
             labels_list.append(curve_label)
@@ -4102,19 +4112,11 @@ def batplot_main() -> int:  # type: ignore
                           transform=ax.transAxes)
             label_text_objects.append(txt)
 
-    # Ensure consistent initial placement (especially for stacked mode)
-    update_labels(ax, y_data_list, label_text_objects, args.stack, False)
-    
-    # Initialize curve names visibility (default to visible)
-    fig._curve_names_visible = True
-    # Initialize stack label position (default to top/max)
-    fig._stack_label_at_bottom = False
-    fig._label_anchor_left = False
-    # Right y-axis state (--ry): ax2, curve indices, and curve->line mapping
+    # Right y-axis state (--ry): build curve->line mapping BEFORE first update_labels
+    # so label colors correctly match curves on both axes (plotting.py uses fig._xy_lines_by_curve)
     fig._xy_ax2 = ax2
     fig._xy_use_top_x = bool(getattr(args, 'txaxis', False))
     fig._xy_right_y_curve_indices = frozenset(right_y_curve_indices)
-    # Build curve index -> line mapping for interactive (ax.lines vs ax2.lines)
     _lines_by_curve = []
     _left_indices = sorted(i for i in range(len(y_data_list)) if i not in right_y_curve_indices)
     _right_sorted = sorted(right_y_curve_indices)
@@ -4127,6 +4129,15 @@ def batplot_main() -> int:  # type: ignore
             _lines_by_curve.append(ax.lines[k] if k < len(ax.lines) else None)
     fig._xy_lines_by_curve = _lines_by_curve
 
+    # Ensure consistent initial placement (especially for stacked mode)
+    update_labels(ax, y_data_list, label_text_objects, args.stack, False)
+    
+    # Initialize curve names visibility (default to visible)
+    fig._curve_names_visible = True
+    # Initialize stack label position (default to top/max)
+    fig._stack_label_at_bottom = False
+    fig._label_anchor_left = False
+
     # ---------------- CIF tick overlay (after labels placed) ----------------
     def _ensure_wavelength_for_2theta():
         """Ensure wavelength assigned to all CIF tick sets without prompting.

{batplot-1.8.28 → batplot-1.8.29}/batplot/converters.py

@@ -46,10 +46,85 @@ Physical meaning:
 from __future__ import annotations
 
 import os
+from typing import Any, Optional
+
 import numpy as np
 
 
-def convert_xrd_data(filenames, from_param: str, to_param: str):
+def _resolve_readcol_for_file(
+    fname: str,
+    readcol_by_file: Optional[dict[str, Any]] = None,
+    readcol_by_ext: Optional[dict[str, tuple[int, int]]] = None,
+    readcol_global: Optional[Any] = None,
+) -> Optional[tuple[int, int, Optional[int]]]:
+    """
+    Resolve which columns to use for a file (x_col, y_col, e_col).
+    Returns (x_col, y_col, e_col) 1-indexed, or None to use defaults (1, 2, 3).
+    e_col is optional; if None, no error column. Uses first pair for multi-curve.
+    """
+    if not readcol_by_file and not readcol_by_ext and not readcol_global:
+        return None
+
+    # Try per-file match (multiple strategies for cross-platform path matching)
+    rc = None
+    if readcol_by_file:
+        norm_fname = os.path.normpath(fname)
+        abs_fname = os.path.abspath(fname)
+        base_fname = os.path.basename(fname)
+        for key in readcol_by_file:
+            key_norm = os.path.normpath(key)
+            key_abs = os.path.abspath(key)
+            key_base = os.path.basename(key)
+            # Prefer exact/normpath/abspath match; use basename only as last resort
+            if fname == key or norm_fname == key_norm or abs_fname == key_abs:
+                rc = readcol_by_file[key]
+                break
+        # Basename fallback only if no match and exactly one key has this basename
+        if rc is None and base_fname:
+            matches = [k for k in readcol_by_file if os.path.basename(k) == base_fname]
+            if len(matches) == 1:
+                rc = readcol_by_file[matches[0]]
+
+    # Fall back to per-extension
+    if rc is None and readcol_by_ext:
+        _, ext = os.path.splitext(fname)
+        ext_lower = ext.lower() if ext else ""
+        rc = readcol_by_ext.get(ext_lower)
+
+    # Fall back to global
+    if rc is None and readcol_global is not None:
+        rc = readcol_global
+
+    if rc is None:
+        return None
+
+    # Normalize to single (x, y) pair; for multi-curve use first pair
+    if isinstance(rc, (list, tuple)) and len(rc) >= 2:
+        first = rc[0]
+        if isinstance(first, (list, tuple)) and len(first) >= 2:
+            x_col, y_col = int(first[0]), int(first[1])
+        else:
+            x_col, y_col = int(rc[0]), int(rc[1])
+    elif isinstance(rc, (list, tuple)) and len(rc) == 1:
+        first = rc[0]
+        if isinstance(first, (list, tuple)) and len(first) >= 2:
+            x_col, y_col = int(first[0]), int(first[1])
+        else:
+            return None
+    else:
+        return None
+
+    # Optional error column: use y_col + 1 if user might have x, y, e layout
+    e_col = y_col + 1
+    return (x_col, y_col, e_col)
+
+
+def convert_xrd_data(
+    filenames,
+    from_param: str,
+    to_param: str,
+    args: Optional[Any] = None,
+):
     """
     Convert XRD data files between different representations.
     
@@ -85,6 +160,9 @@ def convert_xrd_data(filenames, from_param: str, to_param: str):
         filenames: List of file paths to convert (e.g., ['data.xy', 'pattern.xye'])
         from_param: Source parameter - either a wavelength (float as string) or 'q'
         to_param: Target parameter - either a wavelength (float as string) or 'q'
+        args: Optional parsed args with readcol_by_file, readcol_by_ext, readcol for
+              column selection (1-indexed). When provided, uses these instead of
+              default columns 1, 2, 3. Compatible with --readcol, --readcolxy, etc.
     
     Output:
         Creates converted files in a 'converted' subfolder within the directory
@@ -137,6 +215,7 @@ def convert_xrd_data(filenames, from_param: str, to_param: str):
         return
     
     # Process each file
+    output_dirs = set()
     for fname in filenames:
         # Validate file exists
         if not os.path.isfile(fname):
@@ -158,11 +237,35 @@ def convert_xrd_data(filenames, from_param: str, to_param: str):
         if data.shape[1] < 2:
             print(f"Invalid data format in {fname}: need at least 2 columns (x, y)")
             continue
-        
-        # Extract columns
-        x = data[:, 0]  # X values (2θ or Q)
-        y = data[:, 1]  # Intensity values
-        e = data[:, 2] if data.shape[1] >= 3 else None  # Error bars (optional)
+
+        # Resolve column selection (--readcol, --readcolxy, etc.)
+        readcol_by_file = getattr(args, "readcol_by_file", None) or {}
+        readcol_by_ext = getattr(args, "readcol_by_ext", None) or {}
+        readcol_global = getattr(args, "readcol", None)
+        resolved = _resolve_readcol_for_file(
+            fname, readcol_by_file, readcol_by_ext, readcol_global
+        )
+
+        if resolved:
+            x_col, y_col, e_col = resolved
+            # Convert 1-indexed to 0-indexed
+            x_idx, y_idx = x_col - 1, y_col - 1
+            if x_idx < 0 or y_idx < 0 or x_idx >= data.shape[1] or y_idx >= data.shape[1]:
+                print(f"Error in {fname}: --readcol columns {x_col}, {y_col} out of range (file has {data.shape[1]} columns)")
+                continue
+            x = data[:, x_idx]
+            y = data[:, y_idx]
+            # Use error column if specified and exists
+            if e_col is not None and e_col <= data.shape[1]:
+                e_idx = e_col - 1
+                e = data[:, e_idx] if e_idx >= 0 else None
+            else:
+                e = None
+        else:
+            # Default: columns 0, 1, 2 (1-indexed: 1, 2, 3)
+            x = data[:, 0]
+            y = data[:, 1]
+            e = data[:, 2] if data.shape[1] >= 3 else None
         
         # Perform conversion based on type
         if conversion_type == "wavelength_to_wavelength":
@@ -227,9 +330,14 @@ def convert_xrd_data(filenames, from_param: str, to_param: str):
             # Use UTF-8 encoding to support Greek letters (θ) in headers on all platforms
             np.savetxt(output_fname, out_data, fmt="% .6f", header=header, encoding='utf-8')
             print(f"Saved {output_fname}")
+            output_dirs.add(output_dir)
         except Exception as e:
             print(f"Error saving {output_fname}: {e}")
 
+    if output_dirs:
+        dirs_str = ", ".join(sorted(output_dirs))
+        print(f"Exported to: {dirs_str}")
+
 
 def convert_to_qye(filenames, wavelength: float):
     """

{batplot-1.8.28 → batplot-1.8.29}/batplot/data/CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+## [1.8.29] - 2026-03-10
+- Improved compatibility of `--convert` with `--readcol`: conversion now respects per-file, per-extension, and global column selection
+- Use custom columns when converting XRD data: `batplot data.csv --readcol 3 4 --convert 1.54 q`
+- Per-file columns for convert: `batplot f1.txt --readcol 2 3 f2.txt --readcol 5 6 --convert 1.54 q`
+- Fixed `--all style.bps --readcol 2 3`: style files (.bps, .bpsg, .bpcfg) no longer steal readcol; global readcol now applies to all data files
+
 ## [1.8.16] - 2026-03-09
 - GC and dQdV modes now support multiple files
 

{batplot-1.8.28 → batplot-1.8.29}/batplot/data/USER_MANUAL.md

@@ -231,6 +231,21 @@ All converted files are saved in a `converted` subfolder within the directory co
 - Q-space files: `.qye` extension
 - 2θ files: `.xy` or original extension
 
+### Custom columns with --readcol
+
+When your file has 2θ or Q in non-standard columns, use `--readcol` with `--convert`:
+
+```bash
+# 2θ in column 3, intensity in column 4
+batplot data.csv --readcol 3 4 --convert 1.54 q
+
+# Per-file columns
+batplot f1.txt --readcol 2 3 f2.txt --readcol 5 6 --convert 1.54 q
+
+# Extension-specific: --readcoldat, --readcolcsv, etc.
+batplot file.dat --readcoldat 2 4 --convert 1.54 q
+```
+
 ### Examples
 
 ```bash

{batplot-1.8.28 → batplot-1.8.29}/batplot/plotting.py

@@ -73,6 +73,18 @@ def update_labels(ax, y_data_list: List, label_text_objects: List, stack_mode: b
     fig = getattr(ax, 'figure', None)
     label_anchor_left = bool(getattr(fig, '_label_anchor_left', False)) if fig is not None else False
 
+    # Line lookup for dual y-axis (--ry): curve index -> Line2D (ax or ax2)
+    # When --ry is used, curves are split between ax and ax2; _xy_lines_by_curve maps correctly.
+    def _line_for_curve(i):
+        lines_src = getattr(fig, '_xy_lines_by_curve', None) if fig else None
+        if lines_src is not None and 0 <= i < len(lines_src):
+            ln = lines_src[i]
+            if ln is not None:
+                return ln
+        if i < len(ax.lines):
+            return ax.lines[i]
+        return None
+
     # ====================================================================
     if stack_mode:
         # Get plot edges in data coordinates
@@ -118,9 +130,9 @@ def update_labels(ax, y_data_list: List, label_text_objects: List, stack_mode: b
             
             # Set label color to match curve color (makes identification easier)
             try:
-                if i < len(ax.lines):
-                    # Get color from corresponding line object
-                    txt.set_color(ax.lines[i].get_color())
+                ln = _line_for_curve(i)
+                if ln is not None:
+                    txt.set_color(ln.get_color())
             except Exception:
                 # If color matching fails, keep default color
                 pass
@@ -182,8 +194,9 @@ def update_labels(ax, y_data_list: List, label_text_objects: List, stack_mode: b
                 
                 # Match label color to curve color
                 try:
-                    if i < len(ax.lines):
-                        txt.set_color(ax.lines[i].get_color())
+                    ln = _line_for_curve(i)
+                    if ln is not None:
+                        txt.set_color(ln.get_color())
                 except Exception:
                     pass
         else:
@@ -213,8 +226,9 @@ def update_labels(ax, y_data_list: List, label_text_objects: List, stack_mode: b
                 
                 # Match label color to curve color
                 try:
-                    if i < len(ax.lines):
-                        txt.set_color(ax.lines[i].get_color())
+                    ln = _line_for_curve(i)
+                    if ln is not None:
+                        txt.set_color(ln.get_color())
                 except Exception:
                     pass
     

{batplot-1.8.28 → batplot-1.8.29}/batplot/version_check.py

@@ -101,10 +101,13 @@ 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': '- Improved compatibility of --convert with --readcol: conversion now respects per-file, per-extension, and global column selection',
     # Additional notes (auto-filled from RELEASE_NOTES.txt)
     'update_notes': [
-        '- Bug fixes'
+        '- Improved compatibility of --convert with --readcol: conversion now respects per-file, per-extension, and global column selection',
+        '- Use custom columns when converting XRD data: batplot data.csv --readcol 3 4 --convert 1.54 q',
+        '- Per-file columns for convert: batplot f1.txt --readcol 2 3 f2.txt --readcol 5 6 --convert 1.54 q',
+        '- Fixed --all style.bps --readcol 2 3: style files no longer steal readcol; global readcol applies to all data files'
     ],
     'show_update_notes': True,
 }

{batplot-1.8.28 → batplot-1.8.29/batplot.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: batplot
-Version: 1.8.28
+Version: 1.8.29
 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
@@ -112,6 +112,10 @@ batplot scan1.brml:1.5406 scan2.xye:0.7093
 # Convert and export to converted/ subfolder (q and Q equivalent)
 batplot data.xye --convert 1.54 q
 batplot data.qye --convert q 1.54
+
+# With --readcol for custom column layout (e.g. 2θ in col 3, intensity in col 4)
+batplot data.csv --readcol 3 4 --convert 1.54 q
+batplot f1.txt --readcol 2 3 f2.txt --readcol 5 6 --convert 1.54 q
 ```
 
 ### Stacking and normalization
@@ -152,6 +156,9 @@ batplot data.xy --readcol 1 2 1 3
 
 # Range: col 1 as x, cols 2–20 as 19 y-curves
 batplot file.txt --readcol 1 2-20
+
+# With --convert: use custom columns when converting XRD data
+batplot data.csv --readcol 3 4 --convert 1.54 q
 ```
 
 ### Derivatives and EXAFS
@@ -186,6 +193,8 @@ batplot allfiles --xaxis 2theta --xrange 15 75 --interactive
 
 ### Galvanostatic cycling (GC)
 
+GC mode plots potential vs. capacity for each charge/discharge cycle—the primary visualization for battery cycling data. Batplot automatically detects cycles from Neware `.csv` or Biologic `.mpt` files, assigns each cycle a distinct color, and supports both specific capacity (mAh/g) and raw capacity. For `.mpt` files, pass `--mass` (mg) to compute specific capacity. Discontinuous or paused experiments are handled by splitting data into contiguous charge/discharge segments. Use the interactive menu to customize colors, visibility, and export.
+
 ```bash
 # From .csv (capacity in file)
 batplot battery.csv --gc
@@ -278,13 +287,17 @@ batplot file1.xye file2.qye structure.cif:1.54 --stack --interactive
 
 ## Batch export (--all)
 
-Export each file as a separate figure to `batplot_svg/`:
+Export each file as a separate figure to `Figures/`:
 
 ```bash
 batplot --all
 batplot --all --format png
 batplot --all --xaxis 2theta --xrange 10 80
 batplot --all style.bps --gc --mass 7
+
+# With --readcol for custom columns (put --readcol before style file)
+batplot --all --readcol 2 3 --xaxis 2theta
+batplot --all --readcol 2 3 style.bps --xaxis 2theta
 ```
 
 ---

{batplot-1.8.28 → batplot-1.8.29}/batplot.egg-info/SOURCES.txt

@@ -2,7 +2,6 @@ LICENSE
 MANIFEST.in
 NOTICE
 README.md
-USER_MANUAL.md
 pyproject.toml
 setup.py
 batplot/__init__.py

{batplot-1.8.28 → batplot-1.8.29}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "batplot"
-version = "1.8.28"
+version = "1.8.29"
 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" }