GranTED/
├── README.md                  # Main landing page (installation, usage, citation, badges)
├── LICENSE                    # Apache License 2.0
├── CITATION.cff               # Academic citation file (Zenodo/RSC compatible)
├── pyproject.toml             # Modern packaging configuration (no setup.py needed)
├── requirements.txt           # Runtime dependencies
├── .gitignore
├── Makefile                   # Optional: common commands (test, build, clean)
│
├── src/
│   └── granted/              # Actual Python package
│       ├── __init__.py
│       ├── main.py
│       ├── modes.py
│       ├── analyzer.py
│       ├── visualizer.py
│       ├── reporter.py
│       ├── gran_functions.py
│       ├── preprocess.py
│       ├── data_io.py
│       └── version.py         # Central __version__
│
├── notebooks/                 # Future Jupyter notebooks
│   ├── 01_basic_analysis.ipynb
│   ├── 02_method_development.ipynb
│   └── 03_validation_example.ipynb
│
├── tests/
│   ├── __init__.py
│   ├── test_analyzer.py          # Core tests
│   ├── test_visualizer.py
│   ├── test_modes.py
│   ├── test_gran_functions.py
│   └── conftest.py               # Shared fixtures (optional)
├── pytest.ini                    # Configuration
│
├── data/                      # Small example datasets (or .gitignore large files)
├── output/                    # .gitignore (generated plots & reports)
├── docs/                      # Optional future documentation (Sphinx)
└── papers/                    # Manuscripts-related files (figures, supplementary)
