Step-by-Step Refactoring Plan for NTSim

Set Up Git Branching and Initial State
- Create Release Tag: Tag the current stable version of ntsim_2.py (e.g., v0.0.9) so we can always reference or revert to it if needed.
- Create Feature Branches:
  - For each feature, create a new branch. The naming convention could be: dvn/feature/<feature-name> for user dvn and updated appropriately for other users.
  - Example branches:
    - dvn/feature/config-refactor
    - dvn/feature/argument-parser-modularization
    - dvn/feature/simulation-split
Set Up Continuous Integration (CI)
- Use GitHub Actions (or another CI platform) to run unit tests and style checks (flake8, black, anything else?).
- Create a simple workflow to run tests on push or pull requests to any feature branch.

Refactor Argument Parsing (Feature Branch: dvn/feature/argument-parser-modularization)
- Create a New Script: Create ntsim.py as a fresh starting point.
- Move Argument Parsing to ntsim_arguments.py:
  - Split argument parsing into a standalone module.
  - Use configargparse but enhance it with config file support. Allow users to provide a YAML/JSON configuration.
- Introduce a Configuration File:
  - Provide a default configuration file (ntsim.yaml) that can be customized.
  - Modify ntsim.py to load settings from the configuration file first, then override with command-line arguments if provided.
Refactor Initialization Logic (Feature Branch: dvn/feature/config-refactor)
- Create a configuration management class (NTSimConfig) to handle all the configurations.
- Goals:
  - Centralize all configuration in one place.
  - Reduce the use of direct references to opts across the script.
  - Ensure the command-line interface can override configuration settings.

Split NTSim Responsibilities (Feature Branch: dvn/feature/simulation-split)
- Break down the large responsibilities of the NTSim class into multiple methods and smaller classes:
  - NTSimArgumentParser: Handle all argument parsing.
  - NTSimConfigurator: Responsible for reading the configuration, setting up dependencies, and initializing objects.
  - NTSimSimulator: Focus purely on the simulation logic.
  - NTSimWriter: Handle all file writing and logging.
- Action Steps:
  - Extract methods from process().
  - Move configure() logic to NTSimConfigurator.
  - Create clean, readable methods for event initialization, particle simulation, photon propagation, etc.
- Deliverables:
  - Each class or function has a single responsibility.
  - Each method is easily testable in isolation.
Introduce Modular Factories (Feature Branch: dvn/feature/factory-improvements)
- Refactor Factories: Update the current Factory classes so that dependencies are instantiated dynamically.
- Blueprint Handling: Avoid the dual usage of terms like "Blueprint." Consider using clearer terms like ConfigTemplate vs. Instance.

Package and Module Management (Feature Branch: dvn/feature/package-management)
- Optional Installation:
  - Update pyproject.toml to include optional installations:
```
 [project.optional_dependencies]
 generator-neutrino-ava = "nupropagator>=0.0.2"
 # or generator-neutrino-ava = ["nupropagator @ git@git.jinr.ru:ava/nupropogator.git"] 

 telescope-baikal = ["baikal-model @ git@git.jinr.ru:Baikal/bgvd-model.git"]
```
    Users should be able to run pip install ntsim[telescope-baikal] or to pip install ntsim[generator-neutrino-ava] install optional dependencies.
- Interactive Welcome Mode:
  - Implement a welcome feature in ntsim.py to display available configurations based on installed packages.
  - Optional Dependency Installer: Add a utility that informs the user which optional dependencies are missing and offers the necessary pip install command.
Installation Verification (Feature Branch: dvn/feature/installation-check)
- Add Diagnostic Script (ntsim_check.py):
  - This script checks the current environment for missing dependencies.
  - Print a summary with steps to install any missing components.
- Post-Installation Report:
  - Add a post-installation success message summarizing the status of optional components.

Implement Unit Tests for Core Components (Feature Branch: dvn/feature/unit-testing)
- Create tests for individual classes:
  - Configuration Parsing: Verify NTSimConfig correctly reads and overrides settings.
  - Factory Modules: Test each Factory’s get_blueprint() and configure() methods.
  - Simulation Methods: Test components of process(), especially the refactored methods like simulate_particles(), simulate_photons().
- Add test cases for:
  - Edge Scenarios: Such as missing dependencies or misconfigured inputs.
  - Optional Dependencies: Test welcome mode behavior based on installed components.
End-to-End Testing (Feature Branch: dvn/feature/e2e-testing)
- Set up tests to run complete simulations, validate the output, and check for correctness and consistency.
- Use the tqdm simulation loops and validate progress and logging consistency.

Update Documentation (Feature Branch: dvn/feature/documentation)
- Update the README.md to reflect new setup methods and modular installations.
- Write user guides for:
  - Installing Different Modes
    - welcome (minimal possible informing the user what is available and what could be installed)
    - baikal-gvd (install all data and models for GVD),
    - generator-neutrino (ava, nugen, proposal, all),
    - generator-muon (Corsika, ...)
    - ...
  - Using the New Configuration System: Include examples of YAML/JSON config.
- Write a Developer Guide on contributing to ntsim, focusing on how to use feature branches and how to run tests.
User-Friendly Logging & CLI Improvements (Feature Branch: dvn/feature/logging-improvements)
- Improve logging:
  - Refactor logging configurations to be more modular (ntsim_logging.py).
  - Add detailed log levels to track progress in different parts of the simulation (INFO, DEBUG, WARNING).
- Command-Line Interface:
  - Shorten the command-line usage by leveraging the configuration file.
  - Provide meaningful error messages if required arguments are missing or incorrectly formatted.

Prepare for Release (Feature Branch: dvn/feature/release-preparation)
- Ensure all feature branches are merged into main.
- Tag a new release version (v0.1-beta).
- Include release notes summarizing major refactoring steps, new features, and breaking changes.
User Feedback & Iteration
- Release to a subset of users for beta testing.
- Gather feedback on:
  - Ease of Use: Are the new configurations and installations user-friendly?
  - Performance: Does the refactored code maintain or improve simulation times?
- Prioritize bug fixes and minor enhancements based on feedback.

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