Better toml parm parse

[baperry2]

Use TOML files for config, but with auto-documentation and auto-save features.

[Copilot]

Pull request overview

This PR modernizes the parameter parsing infrastructure by replacing the simple toml library with tomlkit and significantly enhancing the TomlParmParse class with auto-documentation, auto-save features, and improved command-line integration.

Key Changes:

• Complete rewrite of TomlParmParse class with new features including nested parameter access via dict-like interface, automatic documentation generation, command-line argument parsing, and unused input detection
• Migration from toml library to tomlkit for better control over formatting and comments
• Updated example scripts to use the new parse_args() API with inline documentation strings

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 13 comments.

Show a summary per file

File	Description
cmlm/utils/input_file.py	Complete rewrite with new TomlParmParse implementation featuring auto-documentation, command-line parsing, and nested parameter access
run_scripts/ctable/create_spray_table_nd.py	Updated to use new TomlParmParse.parse_args() API with doc strings for each parameter
run_scripts/ctable/create_spray_table_nd.toml	Reformatted with enhanced comments and documentation structure
run_scripts/ctable/create_dummy_table_nd.py	Updated to use new TomlParmParse.parse_args() API
run_scripts/ctable/create_dummy_table_nd.toml	Reformatted with enhanced comments
pyproject.toml	Changed dependency from toml >= 0.10.0 to tomlkit >= 0.13.0
cmlm/utils/__init__.py	Minor whitespace formatting change

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