refactor: restructure codebase to src layout

[DSuveges]

Context

• Move package code to src/genome_plotter/
• Move tests to src/tests/
• Update all imports to use new package paths
• Add CLI entry points: prepare-data, plot-chromosome
• Update pyproject.toml with src layout configuration
• Update GitHub Actions workflows for new test paths
• Fix various linting issues (undefined logger, unused variables)

New structure

  src/
  ├── genome_plotter/
  │   ├── __init__.py
  │   ├── config.json
  │   ├── logger_config.yaml
  │   ├── prepare_data.py
  │   ├── plot_chromosome.py
  │   ├── functions/
  │   │   ├── ChromosomePlotter.py
  │   │   ├── ColorFunctions.py
  │   │   ├── ConfigManager.py
  │   │   └── ... (other modules)
  │   └── input_parsers/
  │       ├── data_integrator.py
  │       ├── fetch_cytobands.py
  │       └── ... (other modules)
  └── tests/
      ├── __init__.py
      ├── test_color_fun.py
      └── test_config_manager.py

CLI entry points

• prepare-data → genome_plotter.prepare_data:main
• plot-chromosome → genome_plotter.plot_chromosome:main

[codecov-commenter]

Welcome to Codecov 🎉

Once you merge this PR into your default branch, you're all set! Codecov will compare coverage reports and display results in all future pull requests.

Thanks for integrating Codecov - We've got you covered ☂️