v2.1.3

2.1.3

Enhancements

• Added shared @common_options decorator and setup_logging() helper in new bactopia/cli/common.py to prevent drift of --verbose, --silent, and --version/-V flags across CLI commands
• Migrated 21 CLI modules to use @common_options (all user-facing commands except jsonify, sysinfo, and pipeline scripts)
• Standardized version flag: all commands now accept both --version and -V
• Added missing --silent flag to bactopia-catalog and bactopia-lint
• Added missing --verbose flag to bactopia-citations and bactopia-docs
• Added OPTION_GROUPS for organized --help output to bactopia-catalog, bactopia-citations, and bactopia-docs
• Added module-level docstrings to 12 CLI modules that were missing them
• Removed trailing periods from all CLI help text for consistency
• Standardized --verbose help text across all commands (was split between two variants)
• Replaced scaffold.py's private _setup_logging with the shared setup_logging() helper
• Added -V short flag to bactopia-scaffold group command
• Updated CLAUDE.md CLI module pattern documentation to reflect common_options usage

Build

• Updated justfile to resolve poetry and python paths via which for more reliable environment handling
• just install now includes test dependencies (--with test)
• Test commands now use poetry run <python> -m pytest to ensure correct interpreter