batplot 1.3.5__tar.gz → 1.3.7__tar.gz

{batplot-1.3.5 → batplot-1.3.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: batplot
-Version: 1.3.5
+Version: 1.3.7
 Summary: Interactive plotting for XRD, PDF, and XAS data (.xye, .xy, .qye, .dat, .csv, .gr, .nor, .chik, .chir)
 Author-email: Tian Dai <tianda@uio.no>
 License: MIT License
@@ -45,6 +45,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
 Requires-Dist: matplotlib
+Requires-Dist: rich>=10.0.0
 Dynamic: license-file
 
 # batplot
@@ -179,3 +180,5 @@ Tian Dai (tianda@uio.no)
 University of Oslo
 
 **GitHub**: https://github.com/tiandai-chem/batplot
+
+**Subscribe for Updates**: Join batplot-lab@kjemi.uio.no for updates, feature announcements, and community feedback

{batplot-1.3.5 → batplot-1.3.7}/README.md

@@ -130,3 +130,5 @@ Tian Dai (tianda@uio.no)
 University of Oslo
 
 **GitHub**: https://github.com/tiandai-chem/batplot
+
+**Subscribe for Updates**: Join batplot-lab@kjemi.uio.no for updates, feature announcements, and community feedback

{batplot-1.3.5 → batplot-1.3.7}/batplot/__init__.py

@@ -1,5 +1,5 @@
 """batplot: Interactive plotting for battery data visualization."""
 
-__version__ = "1.3.1"
+__version__ = "1.3.7"
 
 __all__ = ["__version__"]

{batplot-1.3.5 → batplot-1.3.7}/batplot/args.py

@@ -4,6 +4,64 @@ from __future__ import annotations
 
 import argparse
 import sys
+import re
+
+# Try to import rich for colored output
+try:
+    from rich.console import Console
+    from rich.markup import escape
+    _console = Console()
+    _HAS_RICH = True
+except ImportError:
+    _console = None
+    _HAS_RICH = False
+
+
+def _colorize_help(text: str) -> str:
+    """Add colors to help text by highlighting flags and special elements.
+    
+    Args:
+        text: Plain help text
+        
+    Returns:
+        Text with rich markup for colored output
+    """
+    if not _HAS_RICH:
+        return text
+    
+    # Escape any existing markup
+    text = escape(text)
+    
+    # Color all flags (--flag or -f)
+    text = re.sub(r'(--[\w-]+)', r'[cyan]\1[/cyan]', text)
+    text = re.sub(r'(\s-[a-zA-Z]\b)', r'[cyan]\1[/cyan]', text)
+    
+    # Color file extensions
+    text = re.sub(r'(\.\w{2,4}\b)', r'[yellow]\1[/yellow]', text)
+    
+    # Color example commands (batplot at start of line or after whitespace)
+    text = re.sub(r'(batplot\s+[^\n]+)', r'[green]\1[/green]', text)
+    
+    # Color section headers (lines ending with :)
+    text = re.sub(r'^([A-Z][\w\s/()]+:)$', r'[bold blue]\1[/bold blue]', text, flags=re.MULTILINE)
+    
+    # Color special markers
+    text = text.replace('•', '[bold]•[/bold]')
+    
+    return text
+
+
+def _print_help(text: str) -> None:
+    """Print help text with optional coloring.
+    
+    Args:
+        text: Help text to print
+    """
+    if _HAS_RICH and _console:
+        colored_text = _colorize_help(text)
+        _console.print(colored_text)
+    else:
+        print(text)
 
 
 def _print_general_help() -> None:
@@ -46,11 +104,12 @@ def _print_general_help() -> None:
         "  batplot -h xy   # XY file plotting guide\n"
         "  batplot -h ec   # Electrochemistry (GC/dQdV/CV/CPC) guide\n"
         "  batplot -h op   # Operando guide\n\n"
-        "Contact:\n"
+        "Contact & Updates:\n"
+        "  Subscribe to batplot-lab@kjemi.uio.no for updates and feedback\n"
         "  GitHub: https://github.com/tiandai-chem/batplot\n"
         "  Email: tianda@uio.no\n"
     )
-    print(msg)
+    _print_help(msg)
 
 
 def _print_xy_help() -> None:
@@ -87,7 +146,7 @@ def _print_xy_help() -> None:
     "  --fullprof <args>         : FullProf overlay options\n"
     "  --stack                   : stack curves vertically (auto-enables normalization)\n"
     )
-    print(msg)
+    _print_help(msg)
 
 
 def _print_ec_help() -> None:
@@ -123,7 +182,7 @@ def _print_ec_help() -> None:
         "rename axes, toggle ticks/titles/spines, print/export/import style (.bps/.bpsg), save session (.pkl).\n"
         "Note: Batch mode (--all) exports SVG files automatically; --interactive is for single-file plotting only.\n"
     )
-    print(msg)
+    _print_help(msg)
 
 
 def _print_op_help() -> None:
@@ -141,7 +200,7 @@ def _print_op_help() -> None:
         "EC y-axis options (time ↔ ions), geometry tweaks, toggle spines/ticks/labels,\n"
         "print/export/import style, save session.\n"
     )
-    print(msg)
+    _print_help(msg)
 
 
 def build_parser() -> argparse.ArgumentParser:
@@ -191,7 +250,10 @@ def parse_args(argv=None):
             _print_op_help()
         else:
             _print_general_help()
-            print("\nUnknown help topic. Use: xy, ec, op")
+            if _HAS_RICH and _console:
+                _console.print("\n[yellow]Unknown help topic. Use: xy, ec, op[/yellow]")
+            else:
+                print("\nUnknown help topic. Use: xy, ec, op")
         sys.exit(0)
     # No help requested: parse fully
     return parser.parse_args(argv)

{batplot-1.3.5 → batplot-1.3.7}/batplot/batplot.py

@@ -79,6 +79,22 @@ except ImportError:
 keep_canvas_fixed = False
 
 
+def _natural_sort_key(filename: str) -> list:
+    """Generate a natural sorting key for filenames with numbers.
+    
+    Converts 'file_10.xy' to ['file_', 10, '.xy'] so numerical parts are sorted numerically.
+    This ensures file_2.xy comes before file_10.xy (natural order).
+    """
+    parts = []
+    for match in re.finditer(r'(\d+|\D+)', filename):
+        text = match.group(0)
+        if text.isdigit():
+            parts.append(int(text))
+        else:
+            parts.append(text.lower())
+    return parts
+
+
 def batplot_main() -> int:
     """Main entry point for batplot CLI.
     
@@ -1131,7 +1147,7 @@ def batplot_main() -> int:
             all_xy_files = []
             unknown_ext_files = []
             
-            for f in sorted(os.listdir(os.getcwd())):
+            for f in sorted(os.listdir(os.getcwd()), key=_natural_sort_key):
                 if not os.path.isfile(os.path.join(os.getcwd(), f)):
                     continue
                 ext = os.path.splitext(f)[1].lower()

{batplot-1.3.5 → batplot-1.3.7}/batplot/operando.py

@@ -32,6 +32,21 @@ KNOWN_DIFFRACTION_EXT = {".xy", ".xye", ".qye", ".dat"}
 _two_theta_re = re.compile(r"2[tT]heta|2th", re.IGNORECASE)
 _q_re = re.compile(r"^q$", re.IGNORECASE)
 
+def _natural_sort_key(path: Path) -> list:
+    """Generate a natural sorting key for filenames with numbers.
+    
+    Converts 'file_10.xy' to ['file_', 10, '.xy'] so numerical parts are sorted numerically.
+    This ensures file_2.xy comes before file_10.xy (natural order).
+    """
+    parts = []
+    for match in re.finditer(r'(\d+|\D+)', path.name):
+        text = match.group(0)
+        if text.isdigit():
+            parts.append(int(text))
+        else:
+            parts.append(text.lower())
+    return parts
+
 def _infer_axis_mode(args, any_qye: bool, has_unknown_ext: bool):
     # Priority: explicit --xaxis, else .qye presence (Q), else wavelength (Q), else default 2theta with warning
     # If unknown extensions are present, use "user defined" mode
@@ -83,12 +98,12 @@ def plot_operando_folder(folder: str, args) -> Tuple[plt.Figure, plt.Axes, Dict[
     p = Path(folder)
     if not p.is_dir():
         raise FileNotFoundError(f"Not a directory: {folder}")
-    # First try to find known diffraction files
-    files = sorted([f for f in p.iterdir() if f.suffix.lower() in KNOWN_DIFFRACTION_EXT])
+    # First try to find known diffraction files (filter out macOS resource fork files starting with ._)
+    files = sorted([f for f in p.iterdir() if f.suffix.lower() in KNOWN_DIFFRACTION_EXT and not f.name.startswith("._")], key=_natural_sort_key)
     has_unknown_ext = False
     # If no known files found, accept any file extension (except .mpt which is for electrochemistry)
     if not files:
-        files = sorted([f for f in p.iterdir() if f.is_file() and f.suffix.lower() != ".mpt"])
+        files = sorted([f for f in p.iterdir() if f.is_file() and f.suffix.lower() != ".mpt" and not f.name.startswith("._")], key=_natural_sort_key)
         has_unknown_ext = True
         if not files:
             raise FileNotFoundError("No data files found in folder (excluding .mpt files)")
@@ -137,7 +152,8 @@ def plot_operando_folder(folder: str, args) -> Tuple[plt.Figure, plt.Axes, Dict[
     Z = np.vstack(stack)  # shape (n_scans, n_x)
 
     # Detect an electrochemistry .mpt file in the same folder (if any)
-    mpt_files = sorted([f for f in p.iterdir() if f.suffix.lower() == ".mpt"])  # pick first if present
+    # Filter out macOS resource fork files (starting with ._)
+    mpt_files = sorted([f for f in p.iterdir() if f.suffix.lower() == ".mpt" and not f.name.startswith("._")], key=_natural_sort_key)  # pick first if present
     has_ec = len(mpt_files) > 0
     ec_ax = None
 

{batplot-1.3.5 → batplot-1.3.7}/batplot/operando_ec_interactive.py

@@ -2628,6 +2628,12 @@ def operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax):
                             current_mA = getattr(ec_ax, '_ec_current_mA', None)
                             voltage_v = getattr(ec_ax, '_ec_voltage_v', None)
                             
+                            if current_mA is None:
+                                print("Error: Current data is required for ion counting but is not available in the .mpt file.")
+                                print("The .mpt file must contain the '<I>/mA' column to use this feature.")
+                                print_menu()
+                                continue
+                            
                             if time_h is not None and current_mA is not None:
                                 t = np.asarray(time_h, float)
                                 i_mA = np.asarray(current_mA, float)
@@ -2983,9 +2989,13 @@ def operando_ec_interactive_menu(fig, ax, im, cbar, ec_ax):
                 voltage_v = getattr(ec_ax, '_ec_voltage_v', None)
                 current_mA = getattr(ec_ax, '_ec_current_mA', None)
                 ln = getattr(ec_ax, '_ec_line', None)
-                if time_h is None or current_mA is None or ln is None:
+                if time_h is None or ln is None:
                     print("EC data not available for ion calculation.")
                     print_menu(); continue
+                if current_mA is None:
+                    print("Error: Current data is required for ion counting but is not available in the .mpt file.")
+                    print("The .mpt file must contain the '<I>/mA' column to use this feature.")
+                    print_menu(); continue
                 sub = input("ey submenu: n=ions, t=time, q=back: ").strip().lower()
                 if not sub or sub == 'q':
                     print_menu(); continue

{batplot-1.3.5 → batplot-1.3.7}/batplot/readers.py

@@ -95,12 +95,50 @@ def read_mpt_file(fname: str, mode: str = 'gc', mass_mg: float = None):
     """
     import re
     
+    # Check if this is a full EC-Lab format or a simple 2-column export
+    is_eclab_format = False
+    with open(fname, 'r', encoding='utf-8', errors='ignore') as f:
+        first_line = f.readline().strip()
+        if first_line.startswith('EC-Lab ASCII FILE'):
+            is_eclab_format = True
+    
+    # Handle simple 2-column time/voltage export format (for operando time mode)
+    if not is_eclab_format and mode == 'time':
+        try:
+            # Read with tab delimiter and handle European comma decimal separator
+            with open(fname, 'r', encoding='utf-8', errors='ignore') as f:
+                # Skip header line
+                f.readline()
+                time_vals = []
+                voltage_vals = []
+                for line in f:
+                    line = line.strip()
+                    if not line:
+                        continue
+                    parts = line.split('\t')
+                    if len(parts) >= 2:
+                        # Replace comma with period for European locale
+                        time_vals.append(float(parts[0].replace(',', '.')))
+                        voltage_vals.append(float(parts[1].replace(',', '.')))
+                
+                if not time_vals:
+                    raise ValueError("No data found in file")
+                
+                time_s = np.array(time_vals)
+                voltage_v = np.array(voltage_vals)
+                current_mA = np.zeros_like(time_s)  # No current data in simple format
+                return time_s, voltage_v, current_mA
+        except Exception as e:
+            raise ValueError(f"Failed to read simple .mpt format: {e}")
+    
+    # For non-time modes or EC-Lab format, require full EC-Lab format
+    if not is_eclab_format:
+        raise ValueError(f"Not a valid EC-Lab .mpt file: {fname}")
+    
     # Read header to find number of header lines
     header_lines = 0
     with open(fname, 'r', encoding='utf-8', errors='ignore') as f:
         first_line = f.readline().strip()
-        if not first_line.startswith('EC-Lab ASCII FILE'):
-            raise ValueError(f"Not a valid EC-Lab .mpt file: {fname}")
         
         # Find header lines count
         for line in f:
@@ -289,13 +327,16 @@ def read_mpt_file(fname: str, mode: str = 'gc', mass_mg: float = None):
         if voltage_col is None:
             available = ', '.join(f"'{c}'" for c in column_names)
             raise ValueError(f"Could not find 'Ewe/V' or 'Ewe' column.\nAvailable columns: {available}")
-        if current_col is None:
-            available = ', '.join(f"'{c}'" for c in column_names)
-            raise ValueError(f"Could not find '<I>/mA' column.\nAvailable columns: {available}")
         
         time_data = data[:, time_col]
         voltage_data = data[:, voltage_col]
-        current_data = data[:, current_col]
+        
+        # Current column is optional (only needed for advanced features like ion counting)
+        if current_col is None:
+            # Return None for current_data if column not found
+            current_data = None
+        else:
+            current_data = data[:, current_col]
         
         return (time_data, voltage_data, current_data)
     

{batplot-1.3.5 → batplot-1.3.7}/batplot.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: batplot
-Version: 1.3.5
+Version: 1.3.7
 Summary: Interactive plotting for XRD, PDF, and XAS data (.xye, .xy, .qye, .dat, .csv, .gr, .nor, .chik, .chir)
 Author-email: Tian Dai <tianda@uio.no>
 License: MIT License
@@ -45,6 +45,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy
 Requires-Dist: matplotlib
+Requires-Dist: rich>=10.0.0
 Dynamic: license-file
 
 # batplot
@@ -179,3 +180,5 @@ Tian Dai (tianda@uio.no)
 University of Oslo
 
 **GitHub**: https://github.com/tiandai-chem/batplot
+
+**Subscribe for Updates**: Join batplot-lab@kjemi.uio.no for updates, feature announcements, and community feedback

{batplot-1.3.5 → batplot-1.3.7}/batplot.egg-info/requires.txt

@@ -1,2 +1,3 @@
 numpy
 matplotlib
+rich>=10.0.0

{batplot-1.3.5 → batplot-1.3.7}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "batplot"
-version = "1.3.5"
+version = "1.3.7"
 description = "Interactive plotting for XRD, PDF, and XAS data (.xye, .xy, .qye, .dat, .csv, .gr, .nor, .chik, .chir)"
 authors = [
     { name = "Tian Dai", email = "tianda@uio.no" }
@@ -13,7 +13,8 @@ readme = "README.md"
 requires-python = ">=3.7"
 dependencies = [
     "numpy",
-    "matplotlib"
+    "matplotlib",
+    "rich>=10.0.0"
 ]
 license = { file = "LICENSE" }
 classifiers = [