batplot 1.8.52__tar.gz → 1.8.55__tar.gz

{batplot-1.8.52 → batplot-1.8.55}/DEVELOPING.md

@@ -460,7 +460,10 @@ Before changing release behavior:
      `--dev-upgrade` runs `sync_pyproject_package_data()` to refresh
      `[tool.setuptools.package-data]`.
    - Git: `_git_stage_release_snapshot()` stages tracked updates and all untracked
-     non-ignored paths (no hand-maintained file list).
+     non-ignored paths (no hand-maintained file list), and **always** re-stages
+     the MkDocs user manual (`docs/`, `mkdocs.yml`, `.github/workflows/docs.yml`,
+     `scripts/capture_manual_figures.py`) so GitHub Pages updates on every
+     `--dev-upgrade` / `--dev-git` push.
 4. Keep GitHub/PyPI conflict handling explicit and testable.
 
 Canonical version files checked on every release:

{batplot-1.8.52 → batplot-1.8.55}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: batplot
-Version: 1.8.52
+Version: 1.8.55
 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
@@ -58,22 +58,22 @@ Dynamic: license-file
 
 **Interactive plotting tool for battery and materials characterization data**
 
-`batplot` is a Python CLI tool for visualizing and analyzing electrochemical and structural characterization data with interactive styling and session management. The electrochemistry and operando plots were inspired from Amalie Skurtveit's python scripts (https://github.com/piieceofcake?tab=repositories).
+`batplot` is a Command-line based software for quick visuallization of 1D (x,y) and 2D (x,y,z) data with interactive styling and session management. It is designed for researchers within the fields of materials sciences and electrochemistry who do not have programming skills. 
+The electrochemistry and operando plots were inspired from Amalie Skurtveit's python scripts (https://github.com/piieceofcake?tab=repositories).
 
 ## Features
 
 With a single line of command to easily plot publication-ready plots with customized, intuitive interactive editing features such as:
 - **Electrochemistry Plot**: Galvanostatic cycling (GC), cyclic voltammetry (CV), differential capacity (dQdV), capacity per cycle (CPC) with multi-file support
-- **1D XY plot**: Designed for XRD, PDF, XAS (XANES/EXAFS) but also support other types
+- **1D XY plot**: Designed for 1D data such as XRD, PDF, XAS (XANES/EXAFS) but also support other types
 - **Operando Contour plot**: Correlate in-situ characterizations (XRD/PDF/XAS) with electrochemical data
 - **XRD axis units**: Interactive Options `u` converts 2θ ↔ Q ↔ d (XY and operando); CIF phase ticks follow the current domain
 - **Histogram mode**: Column histograms from tabular `.csv`/`.txt` data (e.g. particle-size lists)
 - **Interactive plotting**: Real-time editing customized for each type of plottings
-- **Session Persistence**: Save and reload complete plot states with `.pkl` files
+- **Session Save**: Save and reload complete plot states with `.pkl` files
 - **Style Management**: Import/export plot styles as `.bps`/`.bpsg` files (histogram: `.bpsh`)
 - **Batch Processing**: Export each file separately with `--all`
-- **Column preview**: `--showcol` prints numbered columns, header names when found, and the first 10 values per column (CSV, Excel, text, .mpt, .brml, Bruker .raw, etc.)
-- **Strip header lines**: `--strip-header N` removes the first N lines from a file or a folder of files (with `--ext`) and writes copies into a `stripped/` subfolder (originals untouched)
+
 
 ## Installation
 
@@ -84,8 +84,9 @@ pip install batplot
 
 ## Quick Start
 
+- User manual: https://chem-plot.github.io/batplot/
 - Tutorial: https://drive.google.com/file/d/1NTFJWNBbWW4mgz0H5ZelGjuOBWxoFgkr/view
-- Tutorial files: https://github.com/chem-plot/batplot/blob/main/batplot_tutorial.zip
+- Demo files: https://github.com/chem-plot/batplot/blob/main/batplot_demo_files.zip
 
 ---
 
@@ -263,18 +264,12 @@ batplot file1.csv file2.csv --gc --save
 
 ### 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.
-
-By default each half-cycle resets capacity near 0 (cycles overlaid). With `--gc --cum`, capacity is laid **end-to-end** (cumulative / throughput capacity) so charge and discharge connect from the start to the end of the experiment; cycle colors, multifile overlay, overview, display mode, style/session save, and `--ro` still apply.
+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 --i
 
-# Cumulative capacity (charge/discharge connected end-to-end)
-batplot battery.csv --gc --cum --i
-batplot f1.csv f2.csv --gc --cum --i
-
 # From .mpt (requires --mass in mg)
 batplot battery.mpt --gc --mass 7.0 --i
 
@@ -496,6 +491,8 @@ With `--interactive`:
 
 ## Help & Documentation
 
+Illustrated user manual (GitHub Pages): https://chem-plot.github.io/batplot/
+
 ```bash
 batplot --h              # General help
 batplot --h xy           # XY mode guide
@@ -503,7 +500,7 @@ batplot --h ec           # Electrochemistry guide
 batplot --h op           # Operando guide
 batplot --h histo        # Histogram mode guide
 batplot --v           # Version and release notes
-batplot --m            # Open illustrated manual
+batplot --m            # Open online user manual (https://chem-plot.github.io/batplot/)
 ```
 
 ---

{batplot-1.8.52 → batplot-1.8.55}/README.md

@@ -2,22 +2,22 @@
 
 **Interactive plotting tool for battery and materials characterization data**
 
-`batplot` is a Python CLI tool for visualizing and analyzing electrochemical and structural characterization data with interactive styling and session management. The electrochemistry and operando plots were inspired from Amalie Skurtveit's python scripts (https://github.com/piieceofcake?tab=repositories).
+`batplot` is a Command-line based software for quick visuallization of 1D (x,y) and 2D (x,y,z) data with interactive styling and session management. It is designed for researchers within the fields of materials sciences and electrochemistry who do not have programming skills. 
+The electrochemistry and operando plots were inspired from Amalie Skurtveit's python scripts (https://github.com/piieceofcake?tab=repositories).
 
 ## Features
 
 With a single line of command to easily plot publication-ready plots with customized, intuitive interactive editing features such as:
 - **Electrochemistry Plot**: Galvanostatic cycling (GC), cyclic voltammetry (CV), differential capacity (dQdV), capacity per cycle (CPC) with multi-file support
-- **1D XY plot**: Designed for XRD, PDF, XAS (XANES/EXAFS) but also support other types
+- **1D XY plot**: Designed for 1D data such as XRD, PDF, XAS (XANES/EXAFS) but also support other types
 - **Operando Contour plot**: Correlate in-situ characterizations (XRD/PDF/XAS) with electrochemical data
 - **XRD axis units**: Interactive Options `u` converts 2θ ↔ Q ↔ d (XY and operando); CIF phase ticks follow the current domain
 - **Histogram mode**: Column histograms from tabular `.csv`/`.txt` data (e.g. particle-size lists)
 - **Interactive plotting**: Real-time editing customized for each type of plottings
-- **Session Persistence**: Save and reload complete plot states with `.pkl` files
+- **Session Save**: Save and reload complete plot states with `.pkl` files
 - **Style Management**: Import/export plot styles as `.bps`/`.bpsg` files (histogram: `.bpsh`)
 - **Batch Processing**: Export each file separately with `--all`
-- **Column preview**: `--showcol` prints numbered columns, header names when found, and the first 10 values per column (CSV, Excel, text, .mpt, .brml, Bruker .raw, etc.)
-- **Strip header lines**: `--strip-header N` removes the first N lines from a file or a folder of files (with `--ext`) and writes copies into a `stripped/` subfolder (originals untouched)
+
 
 ## Installation
 
@@ -28,8 +28,9 @@ pip install batplot
 
 ## Quick Start
 
+- User manual: https://chem-plot.github.io/batplot/
 - Tutorial: https://drive.google.com/file/d/1NTFJWNBbWW4mgz0H5ZelGjuOBWxoFgkr/view
-- Tutorial files: https://github.com/chem-plot/batplot/blob/main/batplot_tutorial.zip
+- Demo files: https://github.com/chem-plot/batplot/blob/main/batplot_demo_files.zip
 
 ---
 
@@ -207,18 +208,12 @@ batplot file1.csv file2.csv --gc --save
 
 ### 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.
-
-By default each half-cycle resets capacity near 0 (cycles overlaid). With `--gc --cum`, capacity is laid **end-to-end** (cumulative / throughput capacity) so charge and discharge connect from the start to the end of the experiment; cycle colors, multifile overlay, overview, display mode, style/session save, and `--ro` still apply.
+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 --i
 
-# Cumulative capacity (charge/discharge connected end-to-end)
-batplot battery.csv --gc --cum --i
-batplot f1.csv f2.csv --gc --cum --i
-
 # From .mpt (requires --mass in mg)
 batplot battery.mpt --gc --mass 7.0 --i
 
@@ -440,6 +435,8 @@ With `--interactive`:
 
 ## Help & Documentation
 
+Illustrated user manual (GitHub Pages): https://chem-plot.github.io/batplot/
+
 ```bash
 batplot --h              # General help
 batplot --h xy           # XY mode guide
@@ -447,7 +444,7 @@ batplot --h ec           # Electrochemistry guide
 batplot --h op           # Operando guide
 batplot --h histo        # Histogram mode guide
 batplot --v           # Version and release notes
-batplot --m            # Open illustrated manual
+batplot --m            # Open online user manual (https://chem-plot.github.io/batplot/)
 ```
 
 ---

{batplot-1.8.52 → batplot-1.8.55}/batplot/__init__.py

@@ -7,7 +7,7 @@ import importlib.abc
 import importlib.machinery
 import sys
 
-__version__ = "1.8.52"
+__version__ = "1.8.55"
 
 
 _LEGACY_MODULE_ALIASES = {

{batplot-1.8.52 → batplot-1.8.55}/batplot/_mpl_backend.py

@@ -58,7 +58,7 @@ def is_interactive_backend() -> bool:
 
 
 def _headless_context() -> bool:
-    """True when batplot must stay on a non-interactive backend (CI/pytest)."""
+    """True when batplot must stay on a non-interactive backend (CI/pytest/SSH)."""
     if os.environ.get("BATPLOT_HEADLESS", "").lower() in ("1", "true", "yes"):
         return True
     if os.environ.get("CI", "").lower() in ("1", "true", "yes"):
@@ -67,11 +67,16 @@ def _headless_context() -> bool:
         return True
     if "pytest" in sys.modules:
         return True
+    # Linux SSH / containers without a graphical session: do not try Tk/Qt.
+    # macOS/Windows GUI apps do not rely on DISPLAY/WAYLAND_DISPLAY.
+    if sys.platform.startswith("linux"):
+        if not (os.environ.get("DISPLAY") or os.environ.get("WAYLAND_DISPLAY")):
+            return True
     return False
 
 
 def running_headless() -> bool:
-    """True under pytest, CI, or when ``BATPLOT_HEADLESS`` is set."""
+    """True under pytest, CI, no Linux display, or ``BATPLOT_HEADLESS``."""
     return _headless_context()
 
 
@@ -148,6 +153,12 @@ def ensure_gui_backend(args=None) -> bool:
     if _should_respect_env_agg():
         return False
 
+    # Linux without DISPLAY/WAYLAND: skip Tk/Qt attempts (SSH/containers).
+    if sys.platform.startswith("linux") and not (
+        os.environ.get("DISPLAY") or os.environ.get("WAYLAND_DISPLAY")
+    ):
+        return is_interactive_backend()
+
     if _USER_SET_MPLBACKEND:
         env_be = os.environ.get("MPLBACKEND")
         if env_be and not _is_noninteractive_backend(env_be):

{batplot-1.8.52 → batplot-1.8.55}/batplot/args.py

@@ -173,7 +173,7 @@ def _print_general_help() -> None:
         "Features:\n"
         "  • Interactive (--i): styling, ranges, fonts, export, sessions\n"
         "  • XRD wavelength: --wl 1.54 or file.xye:1.5406 for Q conversion\n"
-        "  • XRD axis units (interactive): Options u converts 2θ ↔ Q ↔ d (XY + operando; needs λ for 2θ)\n"
+        "  • XRD axis units (interactive): Options u converts 2θ ↔ Q (XY; needs λ for 2θ); operando also offers d\n"
         "  • CIF phase ticks: add .cif (or file.cif:wl); ticks follow the current axis (2θ / Q / d)\n"
         "  • X-axis range: --xrange min max\n"
         "  • Save figure: --out filename (default .svg)\n"
@@ -191,7 +191,7 @@ def _print_general_help() -> None:
         "  batplot --h ec       # Electrochemistry (GC/dQdV/CV/CPC) guide\n"
         "  batplot --h op       # Operando contour guide (also: batplot --help contour)\n"
         "  batplot --h histo    # Histogram mode guide (.csv/.txt column data)\n"
-        "  batplot --m        # Open the illustrated PDF manual\n\n"
+        "  batplot --m        # Open online user manual (https://chem-plot.github.io/batplot/)\n\n"
 
         "Contact & Updates:\n"
         "  Subscribe to batplot-lab@kjemi.uio.no for updates\n"
@@ -200,6 +200,7 @@ def _print_general_help() -> None:
         "  Email: tianda@uio.no\n"
         "  Personal page: https://www.mn.uio.no/kjemi/english/people/aca/tianda/\n"
         "  GitHub: https://github.com/chem-plot/batplot\n"
+        "  User manual: https://chem-plot.github.io/batplot/\n"
         "  Kindly cite Tian's github page if the plot is used for publication\n"
         )
     _print_help(msg)
@@ -209,13 +210,17 @@ def _print_xy_help() -> None:
     msg = (
         "XY plots (XRD/PDF/XAS and many more)\n\n"
         "Supported files: .xye .xy .qye .dat .csv .gr .nor .chik .chir .txt .brml .raw .xrdml .rasx and other formats. CIF overlays supported.\n\n"
-        "Axis detection: .qye→Q, .gr→r, .nor→energy, .chik→k, .chir→r, else use --xaxis (Q, 2theta, d, r, k, energy, time or user defined).\n"
+        "Axis detection: .qye→Q, .gr→r, .nor→energy, .chik→k, .chir→r; XRD vendor/\n"
+        "  file:wl / --wl imply Q or 2θ as documented. Otherwise (e.g. batplot file.xy)\n"
+        "  cols 1–2 plot with labels X / Y — use --xaxis (Q, 2theta, d, r, k, energy, time\n"
+        "  or a custom name) when you want a typed axis.\n"
         "If mixing 2θ data in Q, give wavelength per-file (file.xye:1.5406) or global flag --wl.\n"
         "A wavelength can be converted into a different wave length by file.xye:1.54:0.709.\n"
         "For electrochemistry CSV/MPT time-potential plots, use --xaxis time.\n\n"
         "Interactive XRD axis units (Options u):\n"
-        "  In --i, press u to convert the plotted XRD axis among 2θ ↔ Q ↔ d (XRD data only).\n"
+        "  In --i, press u to convert the plotted XRD axis between 2θ ↔ Q (XRD data only).\n"
         "  Conversions involving 2θ need λ (--wl, file:wl, or prompt). CIF ticks stay Bragg-aligned.\n"
+        "  d-spacing is not offered as a plot domain in 1D Options u.\n"
         "  Not for PDF (.gr), XAS (.nor/.chik/.chir), or other non-diffraction axes.\n"
         "  Example: batplot data.xye:0.709 --xaxis 2theta --i   then u → q  (uses λ=0.709 Å).\n\n"
         "CIF phase ticks:\n"
@@ -225,6 +230,7 @@ def _print_xy_help() -> None:
         "    batplot scan.xye:1.54 phase.cif --i\n"
         "    batplot scan.xye phase.cif:0.709 --xaxis 2theta --wl 0.709 --i\n\n"
         "Examples:\n"
+        "  batplot file.xy --i                                  # Quick plot cols 1–2 as X/Y\n"
         "  batplot file.xy file2.xye --xaxis 2theta --i         # Plot XRD data in 2theta space\n"
         "  batplot file1.xye:1.5406 file2.txt:0.709 --i         # Plot XRD data in different wavelengths in q space\n"
         "  batplot data1.xye data2.xye --wl 1.54 --i            # Same Wavelength for Q conversion\n"
@@ -236,7 +242,8 @@ def _print_xy_help() -> None:
         "  batplot file1.xy file2.xy --1d --stack --i           # First derivative\n"
         "  batplot allfiles --i                                 # All files in directory\n"
         "  batplot allfiles --xaxis 2theta --xrange 10 80       # All with axis and range\n"
-        "  batplot --all --xaxis 2theta --xrange 10 80          # Batch: export each file → Figures/\n"
+        "  batplot --all                                       # Batch: each file → Figures/ (X/Y default)\n"
+        "  batplot --all --xaxis 2theta --xrange 10 80          # Batch with typed XRD axis\n"
         "  batplot file1.xy file2.xye --xaxis 2theta style.bps  # Style + export\n\n"
         "Tips and options:\n"
         "[XY plot]\n"
@@ -443,7 +450,7 @@ def _print_op_help() -> None:
         "Standard XY files:\n"
         "  • Folder should contain .xy/.xye/.qye/.dat files.\n"
         "  • Intensity scale is auto-adjusted between min/max values.\n"
-        "  • If no .qye present, provide --xaxis 2theta or set --wl for Q conversion.\n"
+        "  • Default axis is 2θ when no .qye; use --xaxis Q or --wl for Q conversion.\n"
         "  • If a .mpt file is present, a side panel is added for dual-panel mode (time/potential/temp/etc.).\n"
         "  • Without a .mpt file, operando-only mode shows the contour plot alone.\n"
         "  • --1d / --2d: plot the first derivative (dy/dx) of each scan as a contour plot.\n\n"
@@ -767,20 +774,66 @@ def parse_args(argv=None):
     # 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.
+    #
+    # Values of known options (--wl 0.259, --xaxis q, --out out.svg, …) must
+    # NOT update last_file_token. Otherwise
+    #   batplot TD_R02.dat --wl 0.259 --readcol 1 3
+    # binds readcol to "0.259" and the plot silently falls back to cols 1,2.
     # ====================================================================
     readcol_by_file = {}
     global_readcol_expanded = None
     filtered_argv = []
     last_file_token = None
     _STYLE_EXTENSIONS = ('.bps', '.bpsg', '.bpcfg')
+    # Exact value counts for options that take fixed nargs (after short→long).
+    # store_true / flag-only options are omitted (0 values).
+    _OPTION_VALUE_COUNTS = {
+        '--wl': 1,
+        '--xaxis': 1,
+        '--out': 1,
+        '--savefig': 1,
+        '--delta': 1,
+        '--format': 1,
+        '--mass': 1,
+        '--cd': 1,
+        '--average': 1,
+        '--sum': 1,
+        '--histocol': 1,
+        '--binwidth': 1,
+        '--bins': 1,
+        '--ext': 1,
+        '--convert-ext': 1,
+        '--xrange': 2,
+        '--convert': 2,
+        '--pw': 2,
+        '--b': 2,
+        '--readcolxy': 2,
+        '--readcolxye': 2,
+        '--readcolqye': 2,
+        '--readcolnor': 2,
+        '--readcoldat': 2,
+        '--readcolcsv': 2,
+        '--readcolc': 2,
+        '--readcols': 2,
+    }
+    for _ext in custom_readcol_exts:
+        _OPTION_VALUE_COUNTS[f'--readcol{_ext}'] = 2
+    # Optional single value (nargs='?'): consume at most one non-option token.
+    _OPTIONAL_ONE_VALUE = {'--all', '--help', '--extract-brml-scans'}
+
+    def _option_value_count(flag: str) -> int:
+        if flag in _OPTION_VALUE_COUNTS:
+            return _OPTION_VALUE_COUNTS[flag]
+        if flag in _OPTIONAL_ONE_VALUE:
+            return 1
+        if flag == '--fullprof':
+            # nargs='+': consume following non-option tokens
+            return 10**9
+        return 0
+
     i = 0
     while i < len(argv):
         arg = argv[i]
-        # Track non-option tokens as potential file specs (exclude style files)
-        if not arg.startswith('-'):
-            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
@@ -818,9 +871,23 @@ def parse_args(argv=None):
                     global_readcol_expanded = pairs[0] if len(pairs) == 1 else pairs
                 i = j
                 continue
+        if arg.startswith('-'):
+            filtered_argv.append(arg)
+            n_vals = _option_value_count(arg)
+            i += 1
+            taken = 0
+            while taken < n_vals and i < len(argv) and not argv[i].startswith('-'):
+                filtered_argv.append(argv[i])
+                i += 1
+                taken += 1
+            continue
+        # Non-option: potential file spec (exclude style files)
+        arg_lower = arg.lower()
+        if not arg_lower.endswith(_STYLE_EXTENSIONS):
+            last_file_token = arg
         filtered_argv.append(arg)
         i += 1
-    
+
     argv = filtered_argv
     
     # ====================================================================
@@ -852,23 +919,27 @@ def parse_args(argv=None):
     # weren't in the parser yet when we built it
     ns, _unknown = parser.parse_known_args(argv)
     if getattr(ns, "manual", False):
-        manual_url = "https://github.com/chem-plot/batplot/blob/main/batplot_user_manual.pdf"
+        manual_url = "https://chem-plot.github.io/batplot/"
         try:
             opened = webbrowser.open(manual_url)
             if _HAS_RICH and _console:
                 if opened:
-                    _console.print("\n[green]Opened PDF manual in browser[/green]")
+                    _console.print("\n[green]Opened user manual in browser[/green]")
                 else:
-                    _console.print(f"\n[yellow]Manual PDF:[/yellow] {manual_url}")
+                    _console.print(f"\n[yellow]User manual:[/yellow] {manual_url}")
             else:
-                print("\nOpened PDF manual in browser" if opened else f"\nManual PDF: {manual_url}")
+                print(
+                    "\nOpened user manual in browser"
+                    if opened
+                    else f"\nUser manual: {manual_url}"
+                )
         except Exception as exc:  # pragma: no cover - best effort
             if _HAS_RICH and _console:
                 _console.print(f"\n[red]Failed to open manual:[/red] {exc}")
-                _console.print(f"[yellow]Manual PDF:[/yellow] {manual_url}")
+                _console.print(f"[yellow]User manual:[/yellow] {manual_url}")
             else:
                 print(f"\nFailed to open manual: {exc}")
-                print(f"Manual PDF: {manual_url}")
+                print(f"User manual: {manual_url}")
         sys.exit(0)
     
     topic = getattr(ns, 'help', None)

{batplot-1.8.52 → batplot-1.8.55}/batplot/batch.py

@@ -110,7 +110,7 @@ def batch_process(directory: str, args):
     - .nor → Energy space (XAS, eV)
     - .chik → k-space (EXAFS, Å⁻¹)
     - .chir → r-space (Fourier transform of EXAFS, Å)
-    - .xy, .xye, .dat, .csv, .txt → Generic 2-column data (requires --xaxis flag)
+    - .xy, .xye, .dat, .csv, .txt → Generic 2-column data (labels X/Y; optional --xaxis / --wl)
     
     STYLE FILE SUPPORT:
     ------------------
@@ -122,7 +122,7 @@ def batch_process(directory: str, args):
         directory: Path to directory containing data files
         args: Argument namespace with batch processing options:
             - all: Style file path (if provided) or 'all' string
-            - xaxis: X-axis type for unknown extensions (Q, 2theta, r, energy, k, rft)
+            - xaxis: Optional X-axis type (Q, 2theta, r, energy, k, rft); omit for X/Y
             - xrange: Optional X-axis range (min, max)
             - yrange: Optional Y-axis range (min, max)
             - format: Output format ('svg' or 'png', default 'svg')
@@ -137,7 +137,7 @@ def batch_process(directory: str, args):
     # ====================================================================
     # We classify file extensions into three categories:
     # 1. Known extensions with automatic axis detection (don't need --xaxis)
-    # 2. Known generic extensions (need --xaxis if axis type unclear)
+    # 2. Generic / unknown extensions → X/Y unless --xaxis / --wl given
     # 3. Excluded extensions (not data files, skip them)
     # ====================================================================
     
@@ -209,7 +209,7 @@ def batch_process(directory: str, args):
         if ext in known_ext:
             files.append(f)
         else:
-            # Include unknown extensions (require --xaxis)
+            # Include unknown extensions (default X/Y; optional --xaxis / --wl)
             files.append(f)
             unknown_ext_files.append(f)
     
@@ -221,20 +221,15 @@ def batch_process(directory: str, args):
         batch_save_xy_directory(directory, args, files)
         return
     
-    # Check if --xaxis is required for unknown extensions
-    if unknown_ext_files and not args.xaxis:
-        print(f"Error: Found {len(unknown_ext_files)} file(s) with unknown extension(s) that require --xaxis:")
-        for uf in unknown_ext_files[:5]:  # Show first 5
-            print(f"  - {uf}")
-        if len(unknown_ext_files) > 5:
-            print(f"  ... and {len(unknown_ext_files) - 5} more")
-        print("\nKnown extensions that don't require --xaxis: .qye, .gr, .nor, .chik, .chir")
-        print("Please specify x-axis type with --xaxis (options: 2theta, Q, r, energy, k, rft)")
-        print("Example: batplot --all --xaxis 2theta")
-        return
-    
-    if unknown_ext_files:
+    # Unknown extensions: without --xaxis/--wl → generic X/Y (same as interactive
+    # ``batplot file.xy``). With --xaxis, note the chosen type.
+    if unknown_ext_files and args.xaxis:
         print(f"Note: Processing {len(unknown_ext_files)} file(s) with unknown extension(s) using --xaxis {args.xaxis}")
+    elif unknown_ext_files and getattr(args, "wl", None) is None:
+        print(
+            f"Note: Processing {len(unknown_ext_files)} file(s) as generic X/Y "
+            "(cols 1–2). Use --xaxis or --wl for XRD/PDF/XAS axis types."
+        )
     
     print(f"Found {len(files)} files. Exporting SVG plots to Figures/")
     
@@ -315,8 +310,16 @@ def batch_process(directory: str, args):
                 else:
                     x, y = data[:, 0], data[:, 1]
                     e = data[:, 2] if data.shape[1] >= 3 else None
-                ax = (args.xaxis or '').strip()
-                axis_mode = 'Q' if ax.upper() == 'Q' else (args.xaxis if args.xaxis else '2theta')
+                # Preserve historic --xaxis / --wl behavior for non-Bruker .raw:
+                #   --xaxis Q → Q; other --xaxis → that type; --wl alone → 2θ
+                # Only the no-flag path is new (generic X/Y).
+                if args.xaxis:
+                    ax = (args.xaxis or "").strip()
+                    axis_mode = "Q" if ax.upper() == "Q" else args.xaxis
+                elif getattr(args, "wl", None) is not None:
+                    axis_mode = "2theta"
+                else:
+                    axis_mode = "generic"
             else:
                 data = robust_loadtxt_skipheader(fpath)
                 if data.ndim == 1: data = data.reshape(1, -1)
@@ -370,10 +373,11 @@ def batch_process(directory: str, args):
                         args._batch_warned_extensions.add(ext)
                         print(f"  Note: Reading '{ext}' files as 2-column (x, y) data with x-axis = {args.xaxis}")
                 elif getattr(args, 'wl', None) is not None:
-                    # .txt / generic text: --wl implies XRD Q conversion (matches main batplot.py)
+                    # .txt / generic text: --wl implies XRD Q conversion (matches main pipeline)
                     axis_mode = 'Q'
                 else:
-                    raise ValueError(f"Unknown file type: {fname}. Use --xaxis [Q|2theta|r|k|energy|rft], or --wl for XRD Q, or batplot --help for help.")
+                    # Quick plot: cols 1–2 with labels X / Y (matches interactive)
+                    axis_mode = 'generic'
 
             # Convert to Q if needed
             if axis_mode == 'Q' and ext not in ('.qye', '.gr', '.nor'):
@@ -446,9 +450,18 @@ def batch_process(directory: str, args):
                 ax_b.set_xlabel(r"k ($\mathrm{\AA}^{-1}$)")
             elif axis_mode == 'rft':
                 ax_b.set_xlabel("Radial distance (Å)")
+            elif axis_mode == 'generic':
+                ax_b.set_xlabel("X")
+            elif args.xaxis and str(args.xaxis).lower() not in (
+                "2theta", "two_theta", "tth", "q", "d", "r", "energy", "k", "rft", "time",
+            ):
+                ax_b.set_xlabel(str(args.xaxis))
             else:
                 ax_b.set_xlabel("2θ (deg)")
-            ax_b.set_ylabel("Normalized intensity (a.u.)" if getattr(args, 'norm', False) else "Intensity")
+            if axis_mode == 'generic' and not getattr(args, 'norm', False):
+                ax_b.set_ylabel("Y")
+            else:
+                ax_b.set_ylabel("Normalized intensity (a.u.)" if getattr(args, 'norm', False) else "Intensity")
             ax_b.set_title(fname)
             fig_b.subplots_adjust(left=0.18, right=0.97, bottom=0.16, top=0.90)
             # Get output format from args, default to svg

{batplot-1.8.52 → batplot-1.8.55}/batplot/batplot.py

@@ -201,9 +201,12 @@ def _prepare_allfiles_directory(target_dir: str, args, use_relative_paths: bool
             print(f"  - {uf}")
         if len(unknown_ext_files) > 5:
             print(f"  ... and {len(unknown_ext_files) - 5} more")
-        print("These will be read as 2-column (x, y) data.")
-        if not args.xaxis:
-            print("Tip: Use --xaxis to specify the x-axis type (e.g., --xaxis 2theta, --xaxis Q, --xaxis r)")
+        print("These will be read as 2-column (x, y) data with labels X / Y by default.")
+        if not args.xaxis and getattr(args, "wl", None) is None:
+            print(
+                "Tip: Optional --xaxis / --wl for typed axes "
+                "(e.g. --xaxis 2theta, --xaxis Q); omit them for quick X/Y plots."
+            )
 
     print(f"Found {len(all_xy_files)} files to plot together")
     args.files = all_xy_files
@@ -373,6 +376,12 @@ def batplot_main() -> int:  # type: ignore
         Exit code: 0 for success, non-zero for error
         (Follows Unix convention: 0 = success, non-zero = error)
     """
+    # Defense in depth: also install when called without cli.main().
+    try:
+        from .plot_modes.common.terminal import install_safe_builtins
+        install_safe_builtins()
+    except Exception:
+        pass
     # ====================================================================
     # STEP 1: PARSE COMMAND-LINE ARGUMENTS
     # ====================================================================

{batplot-1.8.52 → batplot-1.8.55}/batplot/cli.py

@@ -61,6 +61,12 @@ def main(argv: Optional[list] = None) -> int:
 		>>> main()
 		0
 	"""
+	# Windows cp1252-safe print/input for all interactive menus and errors.
+	try:
+		from .plot_modes.common.terminal import install_safe_builtins
+		install_safe_builtins()
+	except Exception:
+		pass
 	# ====================================================================
 	# STEP 0.5: CHECK FOR DEVELOPER UPGRADE COMMAND
 	# ====================================================================
@@ -163,7 +169,14 @@ def main(argv: Optional[list] = None) -> int:
 		# Other exceptions (unexpected bugs) will still show full traceback
 		# for debugging purposes.
 		# ====================================================================
-		print(f"Error: {e}", file=sys.stderr)
+		try:
+			from .plot_modes.common.terminal import safe_console_print
+			safe_console_print(f"Error: {e}", file=sys.stderr)
+		except Exception:
+			try:
+				sys.stderr.write(f"Error: {e}\n")
+			except Exception:
+				sys.stderr.write("Error: (message not printable on this console)\n")
 		return 1  # Non-zero exit code indicates error
 		
 	finally:

{batplot-1.8.52 → batplot-1.8.55}/batplot/config.py

@@ -112,7 +112,7 @@ def load_config() -> Dict[str, Any]:
     
     # Try to read and parse JSON file
     try:
-        with open(config_file, 'r') as f:
+        with open(config_file, 'r', encoding='utf-8') as f:
             return json.load(f)  # Parse JSON string into Python dictionary
     except (json.JSONDecodeError, IOError):
         # File exists but is corrupted or unreadable
@@ -128,7 +128,7 @@ def save_config(config: Dict[str, Any]) -> bool:
     """
     config_file = get_config_file()
     try:
-        with open(config_file, 'w') as f:
+        with open(config_file, 'w', encoding='utf-8') as f:
             # indent=2 makes JSON file human-readable (pretty-printed)
             json.dump(config, f, indent=2)
         return True

{batplot-1.8.52 → batplot-1.8.55}/batplot/data/CHANGELOG.md

@@ -1,5 +1,20 @@
 # Changelog
 
+## [1.8.55] - 2026-09-15
+- Bug fixes
+
+
+## [1.8.54] - 2026-09-14
+- Fix --readcol after --wl / other option values (cols no longer stuck on 1–2)
+- Quit prompt: e=export and s=save work in every interactive / batch menu
+- Color menus (c/k): WASD side rectangle like spines t, for all modes
+- User manual homepage: GitHub repo + tutorial zip links
+
+
+## [1.8.53] - 2026-09-09
+- Bug fixes
+
+
 ## [1.8.52] - 2026-08-08
 - Bug fixes