batplot 1.8.40__tar.gz → 1.8.41__tar.gz

batplot-1.8.41/MANIFEST.in

@@ -0,0 +1,3 @@
+include README.md LICENSE
+recursive-include batplot/data CHANGELOG.md
+exclude batplot/data/USER_MANUAL.md

{batplot-1.8.40/batplot.egg-info → batplot-1.8.41}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: batplot
-Version: 1.8.40
+Version: 1.8.41
 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
@@ -47,6 +47,9 @@ Requires-Dist: numpy>=1.21.0
 Requires-Dist: matplotlib>=3.5.0
 Requires-Dist: rich>=10.0.0
 Requires-Dist: openpyxl>=3.0.0
+Provides-Extra: test
+Requires-Dist: pytest>=7.0; extra == "test"
+Requires-Dist: basedpyright>=1.28.0; extra == "test"
 Dynamic: license-file
 
 # batplot
@@ -213,7 +216,6 @@ batplot battery.mpt --gc --mass 7.0 --i
 
 ```bash
 batplot cyclic.mpt --cv --i
-batplot cyclic.mpt --cv --i
 ```
 
 ### Differential capacity (dQ/dV)
@@ -356,12 +358,12 @@ With `--interactive`:
 ## Help & Documentation
 
 ```bash
-batplot --help              # General help
-batplot --help xy           # XY mode guide
-batplot --help ec           # Electrochemistry guide
-batplot --help op           # Operando guide
-batplot --version           # Version and release notes
-batplot --manual            # Open illustrated manual
+batplot --h              # General help
+batplot --h xy           # XY mode guide
+batplot --h ec           # Electrochemistry guide
+batplot --h op           # Operando guide
+batplot --v           # Version and release notes
+batplot --m            # Open illustrated manual
 ```
 
 - [USER_MANUAL.md](USER_MANUAL.md) — Detailed usage and workflows

{batplot-1.8.40 → batplot-1.8.41}/README.md

@@ -162,7 +162,6 @@ batplot battery.mpt --gc --mass 7.0 --i
 
 ```bash
 batplot cyclic.mpt --cv --i
-batplot cyclic.mpt --cv --i
 ```
 
 ### Differential capacity (dQ/dV)
@@ -305,12 +304,12 @@ With `--interactive`:
 ## Help & Documentation
 
 ```bash
-batplot --help              # General help
-batplot --help xy           # XY mode guide
-batplot --help ec           # Electrochemistry guide
-batplot --help op           # Operando guide
-batplot --version           # Version and release notes
-batplot --manual            # Open illustrated manual
+batplot --h              # General help
+batplot --h xy           # XY mode guide
+batplot --h ec           # Electrochemistry guide
+batplot --h op           # Operando guide
+batplot --v           # Version and release notes
+batplot --m            # Open illustrated manual
 ```
 
 - [USER_MANUAL.md](USER_MANUAL.md) — Detailed usage and workflows

batplot-1.8.41/batplot/__init__.py

@@ -0,0 +1,74 @@
+"""batplot: Interactive plotting for battery data visualization."""
+
+from __future__ import annotations
+
+import importlib
+import importlib.abc
+import importlib.machinery
+import sys
+
+__version__ = "1.8.41"
+
+
+_LEGACY_MODULE_ALIASES = {
+    "batplot.interactive": "batplot.plot_modes.xy.interactive",
+    "batplot.electrochem_interactive": "batplot.plot_modes.electrochem.interactive",
+    "batplot.cpc_interactive": "batplot.plot_modes.cpc.interactive",
+    "batplot.cpc_menu": "batplot.plot_modes.cpc.menu",
+    "batplot.operando_ec_interactive": "batplot.plot_modes.operando.interactive",
+    "batplot.operando_layout": "batplot.plot_modes.operando.layout",
+    "batplot.operando_menu": "batplot.plot_modes.operando.menu",
+    "batplot.operando_style": "batplot.plot_modes.operando.style",
+    "batplot.interactive_state": "batplot.plot_modes.common.interactive_state",
+}
+
+
+class _LegacyModuleAliasLoader(importlib.abc.Loader):
+    """Lazy compatibility loader for mode modules moved under ``plot_modes``."""
+
+    def __init__(self, fullname: str, target_name: str):
+        self.fullname = fullname
+        self.target_name = target_name
+
+    def create_module(self, spec):
+        module = importlib.import_module(self.target_name)
+        self._apply_extra_exports(module)
+        sys.modules[self.fullname] = module
+        parent_name, _, child_name = self.fullname.rpartition(".")
+        parent = sys.modules.get(parent_name)
+        if parent is not None:
+            setattr(parent, child_name, module)
+        return module
+
+    def exec_module(self, module) -> None:
+        return None
+
+    def _apply_extra_exports(self, module) -> None:
+        if self.fullname == "batplot.cpc_interactive":
+            menu = importlib.import_module("batplot.plot_modes.cpc.menu")
+            module.print_cpc_menu = menu.print_cpc_menu
+            module.build_cpc_menu_columns = menu.build_cpc_menu_columns
+        elif self.fullname == "batplot.operando_ec_interactive":
+            style = importlib.import_module("batplot.plot_modes.operando.style")
+            module.build_operando_ec_style_config_v2 = style.build_operando_ec_style_config_v2
+
+
+class _LegacyModuleAliasFinder(importlib.abc.MetaPathFinder):
+    def find_spec(self, fullname, path=None, target=None):
+        target_name = _LEGACY_MODULE_ALIASES.get(fullname)
+        if target_name is None:
+            return None
+        loader = _LegacyModuleAliasLoader(fullname, target_name)
+        spec = importlib.machinery.ModuleSpec(fullname, loader)
+        spec.origin = f"legacy-alias:{target_name}"
+        return spec
+
+
+def _install_legacy_alias_finder() -> None:
+    if not any(isinstance(finder, _LegacyModuleAliasFinder) for finder in sys.meta_path):
+        sys.meta_path.insert(0, _LegacyModuleAliasFinder())
+
+
+_install_legacy_alias_finder()
+
+__all__ = ["__version__"]

{batplot-1.8.40 → batplot-1.8.41}/batplot/args.py

@@ -24,6 +24,7 @@ from __future__ import annotations
 import argparse
 import sys
 import re
+import webbrowser
 
 # ====================================================================
 # HELP OUTPUT
@@ -169,13 +170,13 @@ def _print_general_help() -> None:
         "  • More: --help xy / --help ec / --help op\n\n"
         
         "More help:\n"
-        "  batplot --version       # Version and release info (with option to show full release notes)\n"
+        "  batplot --v       # Version and release info (with option to show full release notes)\n"
         "  batplot --showcol FILE [FILE...]   # Preview column names + first 10 values per column\n"
-        "  batplot --help          # This help\n"
-        "  batplot --help xy       # XY file plotting guide\n"
-        "  batplot --help ec       # Electrochemistry (GC/dQdV/CV/CPC) guide\n"
-        "  batplot --help op       # Operando contour guide (also: batplot --help contour)\n"
-        "  batplot --manual        # Open the illustrated txt manual with highlights\n\n"
+        "  batplot --h          # This help\n"
+        "  batplot --h xy       # XY file plotting guide\n"
+        "  batplot --h ec       # Electrochemistry (GC/dQdV/CV/CPC) guide\n"
+        "  batplot --h op       # Operando contour guide (also: batplot --help contour)\n"
+        "  batplot --m        # Open the illustrated PDF manual\n\n"
 
         "Contact & Updates:\n"
         "  Subscribe to batplot-lab@kjemi.uio.no for updates\n"
@@ -246,10 +247,14 @@ def _print_xy_help() -> None:
         "                              - file:wl          : single wavelength (for Q conversion or CIF 2theta calculation)\n"
         "                              - file:wl1:wl2     : dual wavelength (convert 2theta→Q using wl1, then Q→2theta using wl2)\n"
         "                              - file.cif:wl      : CIF file with wavelength for 2theta tick calculation\n"
+        "                              - file:q           : mark file as already in Q (no conversion; implies Q axis)\n"
+        "                              Any file:wl or file:q suffix implies Q mode automatically (no --xaxis q needed);\n"
+        "                              files without wavelength info are then assumed to be already in Q.\n"
         "                              Examples:\n"
         "                                batplot data.xye:1.5406 --xaxis 2theta\n"
         "                                batplot data.xye:0.25:1.54 --xaxis 2theta\n"
         "                                batplot data.xye pattern.cif:0.25448 --xaxis 2theta\n"
+        "                                batplot scan.xy:0.709 sim.csv:q --stack --i\n"
         "  --readcol <x_col> <y_col> : specify which columns to read as x and y (1-indexed)\n"
         "    Per-file:  file1.xy --readcol 2 3 file2.xy --readcol 4 5  (different cols per file)\n"
         "    Multi-curve: file.xy --readcol 1 2 1 3  (plot cols 1,2 and 1,3 as two curves)\n"
@@ -375,58 +380,10 @@ def _print_op_help() -> None:
     _print_help(msg)
 
 
-def build_parser() -> argparse.ArgumentParser:
-    """
-    Build the argument parser for batplot command-line interface.
-    
-    HOW ARGUMENT PARSING WORKS:
-    --------------------------
-    This function creates an ArgumentParser object that defines all valid
-    command-line arguments for batplot. When you run 'batplot file.xy --i',
-    argparse uses this parser to:
-    1. Recognize which arguments are valid
-    2. Extract values from the command line
-    3. Convert them to appropriate Python types (int, float, bool, etc.)
-    4. Store them in a namespace object (args.files, args.interactive, etc.)
-    
-    ARGUMENT TYPES:
-    --------------
-    - Positional arguments: 'files' - list of file paths (can be 0 or more)
-    - Flags (boolean): '--i' - True if present, False if absent
-    - Options with values: '--mass 7.0' or '--mass 0.01g' - mass in mg, or grams with a ``g`` suffix
-    - Optional arguments: '--help xy' - can have optional value
-    
-    WHY add_help=False?
-    -------------------
-    We use a custom help system that supports topic-specific help:
-    - 'batplot --help' → general help
-    - 'batplot --help xy' → XY mode help
-    - 'batplot --help ec' → EC mode help
-    - 'batplot --help op' → Operando mode help
-    
-    This gives users more targeted help instead of one giant help page.
-    
-    Returns:
-        Configured ArgumentParser object ready to parse command-line arguments
-    """
-    # Create parser with custom help system (we handle help ourselves)
-    parser = argparse.ArgumentParser(add_help=False)
-    
-    # ====================================================================
-    # TOPIC-AWARE HELP SYSTEM
-    # ====================================================================
-    # Instead of standard --help, we support topic-specific help:
-    #   batplot --help        → general help
-    #   batplot --help xy     → XY mode help
-    #   batplot --help ec     → EC mode help
-    #   batplot --help op     → Operando mode help
-    #
-    # nargs="?" means the argument is optional:
-    #   - If not provided: const="" (empty string)
-    #   - If provided: uses the value (e.g., "xy", "ec", "op")
-    # ====================================================================
+def _add_help_and_entry_arguments(parser: argparse.ArgumentParser) -> None:
+    """Register help/version/manual flags and positional file inputs."""
     parser.add_argument("--help", nargs="?", const="", metavar="topic",
-                        help=argparse.SUPPRESS)  # SUPPRESS hides from auto-generated help
+                        help=argparse.SUPPRESS)
     parser.add_argument("--version", action="store_true", dest="version",
                         help="Show version and current release info, then exit.")
     parser.add_argument(
@@ -435,18 +392,11 @@ def build_parser() -> argparse.ArgumentParser:
         help=argparse.SUPPRESS,
     )
     parser.add_argument("--manual", action="store_true", help=argparse.SUPPRESS)
-    
-    # ====================================================================
-    # POSITIONAL ARGUMENTS (FILE PATHS)
-    # ====================================================================
-    # 'files' is a positional argument, meaning it doesn't need a flag.
-    # nargs="*" means it accepts 0 or more values (list).
-    # Examples:
-    #   batplot file1.xy file2.xy        → args.files = ['file1.xy', 'file2.xy']
-    #   batplot allfiles                 → args.files = ['allfiles']
-    #   batplot --i            → args.files = [] (empty list)
-    # ====================================================================
     parser.add_argument("files", nargs="*", help=argparse.SUPPRESS)
+
+
+def _add_xy_arguments(parser: argparse.ArgumentParser) -> None:
+    """Register XY/general plotting arguments."""
     parser.add_argument("--delta", type=float, default=None, help=argparse.SUPPRESS)
     parser.add_argument("--autoscale", action="store_true", help=argparse.SUPPRESS)
     parser.add_argument("--xrange", nargs=2, type=float, help=argparse.SUPPRESS)
@@ -464,15 +414,29 @@ def build_parser() -> argparse.ArgumentParser:
     parser.add_argument("--kchik", action="store_true", help=argparse.SUPPRESS)
     parser.add_argument("--k2chik", action="store_true", help=argparse.SUPPRESS)
     parser.add_argument("--k3chik", action="store_true", help=argparse.SUPPRESS)
+    parser.add_argument("--1d", action="store_true", dest="derivative_1d", help=argparse.SUPPRESS)
+    parser.add_argument("--2d", action="store_true", dest="derivative_2d", help=argparse.SUPPRESS)
+
+
+def _add_interactive_export_arguments(parser: argparse.ArgumentParser) -> None:
+    """Register interactive, export, and batch-output arguments."""
     parser.add_argument("--i", "--interactive", action="store_true", dest="interactive", help=argparse.SUPPRESS)
     parser.add_argument("--savefig", type=str, help=argparse.SUPPRESS)
     parser.add_argument("--stack", action="store_true", help=argparse.SUPPRESS)
     parser.add_argument("--ry", action="store_true", help=argparse.SUPPRESS)
     parser.add_argument("--txaxis", action="store_true", help=argparse.SUPPRESS)
-    parser.add_argument("--operando", "--contour", action="store_true", dest="operando", help=argparse.SUPPRESS)
-    parser.add_argument("--average", type=int, help=argparse.SUPPRESS)
-    parser.add_argument("--sum", dest="scan_sum", type=int, help=argparse.SUPPRESS)
     parser.add_argument("--debug", action="store_true", help=argparse.SUPPRESS)
+    parser.add_argument("--ro", action="store_true", help=argparse.SUPPRESS)
+    parser.add_argument("--all", type=str, nargs='?', const='all', help=argparse.SUPPRESS)
+    parser.add_argument("--format", type=str, default='svg', 
+                       choices=['svg', 'png', 'pdf', 'jpg', 'jpeg', 'eps', 'tif', 'tiff'],
+                       help=argparse.SUPPRESS)
+    parser.add_argument("--canvas", action="store_true", dest="canvas",
+                        help="Canvas mode: combine multiple .pkl sessions into one layout. Use numbers to edit each panel.")
+
+
+def _add_electrochem_arguments(parser: argparse.ArgumentParser) -> None:
+    """Register electrochemistry mode arguments."""
     parser.add_argument("--gc", action="store_true", help=argparse.SUPPRESS)
     parser.add_argument("--mass", type=parse_mass_mg_from_cli, action='append', help=argparse.SUPPRESS)
     parser.add_argument("--dqdv", action="store_true", help=argparse.SUPPRESS)
@@ -486,14 +450,19 @@ def build_parser() -> argparse.ArgumentParser:
                        help=argparse.SUPPRESS)
     parser.add_argument("--anode", action="store_true", help=argparse.SUPPRESS)
     parser.add_argument("--cathode", action="store_true", help=argparse.SUPPRESS)
-    parser.add_argument("--ro", action="store_true", help=argparse.SUPPRESS)
-    parser.add_argument("--all", type=str, nargs='?', const='all', help=argparse.SUPPRESS)
-    parser.add_argument("--format", type=str, default='svg', 
-                       choices=['svg', 'png', 'pdf', 'jpg', 'jpeg', 'eps', 'tif', 'tiff'],
-                       help=argparse.SUPPRESS)
+
+
+def _add_operando_arguments(parser: argparse.ArgumentParser) -> None:
+    """Register operando contour arguments."""
+    parser.add_argument("--operando", "--contour", action="store_true", dest="operando", help=argparse.SUPPRESS)
+    parser.add_argument("--average", type=int, help=argparse.SUPPRESS)
+    parser.add_argument("--sum", dest="scan_sum", type=int, help=argparse.SUPPRESS)
+
+
+def _add_read_column_arguments(parser: argparse.ArgumentParser) -> None:
+    """Register column-selection arguments."""
     parser.add_argument("--readcol", nargs=2, type=int, metavar=('X_COL', 'Y_COL'),
                        help=argparse.SUPPRESS)
-    # Add extension-specific readcol arguments
     parser.add_argument("--readcolxy", nargs=2, type=int, metavar=('X_COL', 'Y_COL'),
                        help=argparse.SUPPRESS)
     parser.add_argument("--readcolxye", nargs=2, type=int, metavar=('X_COL', 'Y_COL'),
@@ -510,10 +479,51 @@ def build_parser() -> argparse.ArgumentParser:
                        help=argparse.SUPPRESS)
     parser.add_argument("--readcols", nargs=2, type=int, metavar=('X_COL', 'Y_COL'),
                        help=argparse.SUPPRESS)
-    parser.add_argument("--1d", action="store_true", dest="derivative_1d", help=argparse.SUPPRESS)
-    parser.add_argument("--2d", action="store_true", dest="derivative_2d", help=argparse.SUPPRESS)
-    parser.add_argument("--canvas", action="store_true", dest="canvas",
-                        help="Canvas mode: combine multiple .pkl sessions into one layout. Use numbers to edit each panel.")
+
+
+def build_parser() -> argparse.ArgumentParser:
+    """
+    Build the argument parser for batplot command-line interface.
+    
+    HOW ARGUMENT PARSING WORKS:
+    --------------------------
+    This function creates an ArgumentParser object that defines all valid
+    command-line arguments for batplot. When you run 'batplot file.xy --i',
+    argparse uses this parser to:
+    1. Recognize which arguments are valid
+    2. Extract values from the command line
+    3. Convert them to appropriate Python types (int, float, bool, etc.)
+    4. Store them in a namespace object (args.files, args.interactive, etc.)
+    
+    ARGUMENT TYPES:
+    --------------
+    - Positional arguments: 'files' - list of file paths (can be 0 or more)
+    - Flags (boolean): '--i' - True if present, False if absent
+    - Options with values: '--mass 7.0' or '--mass 0.01g' - mass in mg, or grams with a ``g`` suffix
+    - Optional arguments: '--help xy' - can have optional value
+    
+    WHY add_help=False?
+    -------------------
+    We use a custom help system that supports topic-specific help:
+    - 'batplot --help' → general help
+    - 'batplot --help xy' → XY mode help
+    - 'batplot --help ec' → EC mode help
+    - 'batplot --help op' → Operando mode help
+    
+    This gives users more targeted help instead of one giant help page.
+    
+    Returns:
+        Configured ArgumentParser object ready to parse command-line arguments
+    """
+    # Create parser with custom help system (we handle help ourselves)
+    parser = argparse.ArgumentParser(add_help=False)
+    
+    _add_help_and_entry_arguments(parser)
+    _add_xy_arguments(parser)
+    _add_interactive_export_arguments(parser)
+    _add_operando_arguments(parser)
+    _add_electrochem_arguments(parser)
+    _add_read_column_arguments(parser)
     return parser
 
 
@@ -711,18 +721,23 @@ 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"
         try:
-            from .manual import open_manual_url  # Lazy import avoids matplotlib startup unless needed
-            open_manual_url()
+            opened = webbrowser.open(manual_url)
             if _HAS_RICH and _console:
-                _console.print("\n[green]Opened manual in browser[/green]")
+                if opened:
+                    _console.print("\n[green]Opened PDF manual in browser[/green]")
+                else:
+                    _console.print(f"\n[yellow]Manual PDF:[/yellow] {manual_url}")
             else:
-                print("\nOpened manual in browser")
+                print("\nOpened PDF manual in browser" if opened else f"\nManual PDF: {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}")
             else:
                 print(f"\nFailed to open manual: {exc}")
+                print(f"Manual PDF: {manual_url}")
         sys.exit(0)
     
     topic = getattr(ns, 'help', None)