Update Project Configuration and Utility Functions

[druvus]

This PR introduces several updates to the nanometa_live package, focusing on enhancing the project configuration and utility functions. Key changes include:

1. Version Update in __init__.py:

• Updated the version number from 0.3.2 to 0.4.0 to reflect new features and improvements.

2. Configuration File Enhancements (config.yaml):

• Reorganized and expanded the configuration file structure.
• Added comprehensive comments and examples for better clarity and usability.
• Introduced new sections such as General Project Settings, GUI Configuration, and Workflow Management.
• Included definitions and default settings for various components like GUI, taxonomy analysis, and workflow management.
• Added External Kraken2 Databases section for easily configurable external database options.

3. Utility Functions in kraken_utils.py:

• Implemented new functions for downloading and decompressing Kraken2 databases.
• Added download_database, decompress_database, and copy_inspect_file functions to handle external database setups.
• Enhanced logging for better tracking and troubleshooting.

4. New Project Creation Script (nanometa_new.py):

• Modified the script to support the creation of new projects with updated configuration settings.
• Added argument parsing for new configuration options including external Kraken2 databases.
• Implemented logic to update the configuration file based on user inputs.

5. Preparation Script Updates (nanometa_prepare.py):

• Refactored to support the new configuration format, especially for handling external Kraken2 databases.
• Added conditional logic for downloading and decompressing external databases only if required.
• Enhanced with a dry-run option for safe testing without actual file modifications.