Presentation of the project for developers

Structure of the GitHub repository

The project is composed of three blocks containing the three independent Python libraries:

  • HDF5_BLS: The library used to interface an HDF5 file to comply with the BLS standard we are developing.

  • HDF5_BLS_analyse: The library performing the conversion of data obtained by a spectrometer to a Power spectrum.

  • HDF5_BLS_treat: The library performing the treatment of the data (fitting, normalization, etc.).

The project has additionally, a graphical user interface (GUI) to facilitate the use of the library:

  • HDF5_BLS_GUI: The GUI used to interact with the library.

And the basis for a web viewer currently under development:

  • HDF5_BLS_webview: The web viewer used to interact with the library.

All these modules are independent but at the same time part of the same main goal: to unify and standardize the storage of BLS data in a HDF5 file, and to develop unified tools to process these data.

As such, the project is structured as a “monorepo” structure:

.
├── data <- static data used in the project (algorithms, images, spreadsheets, etc.)
├── docs <- documentation of the project
├── packages <- the repository where all the Python scripts are stored
│   ├── HDF5_BLS
│   ├── HDF5_BLS_analyse
│   ├── HDF5_BLS_treat
│   └── HDF5_BLS_GUI
├── HDF5_BLS_webview
├── tests <- tests of the project
└── ... <- other files like the README, LICENSE, etc.

We have also adopted the setuptools src-layout to organize the Python packages:

.
└── HDF5_BLS
    ├── src
    │   └── _HDF5_BLS
    │       ├── __init__.py
    │       ├── file.py
    │       └── ...
    ├── tests
    ├── pyproject.toml
    └── README.md

Documentation

The documentation is written in reStructuredText and is built using Sphinx. The documentation is hosted on Read the Docs. To compile the documentation locally, you need to install both Sphinx and the Read the Docs theme:

pip install sphinx sphinx-rtd-theme

Then, you can compile the documentation by running the following command in the docs directory:

make html

The documentation will be generated in the docs/build/html directory.

You can also compile the documentation as a latex file to get a pdf version:

make latex

Important

Part of the documentation is automatically generated from the docstrings of the code. The docstrings are written in the numpydoc format. The documentation is built using Sphinx.

Docstrings

Docstrings are used to automatically generate the documentation of the code. They are written in the numpydoc format and are placed in the docstring of the functions. The docstrings are automatically extracted and used to generate the documentation.