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Requirements

This document explains the purpose of each package listed in the install_requires and extras_require sections of the setup.py file for the ensemble-kalman-smoother project.

Basic Requirements

These are the core dependencies required for the project to function properly, and can be installed via:

pip install -e .
  • ipykernel: Provides the IPython kernel for Jupyter, allowing the execution of Python code in Jupyter notebooks.
  • matplotlib: A comprehensive library for creating static, animated, and interactive visualizations in Python.
  • numpy: The fundamental package for scientific computing with Python, providing support for arrays, matrices, and many mathematical functions.
  • opencv-python: A library of programming functions mainly aimed at real-time computer vision. It allows for image and video capture and processing.
  • pandas: A powerful data analysis and manipulation library for Python, providing data structures like DataFrames.
  • scikit-learn: A machine learning library for Python, offering simple and efficient tools for data mining and data analysis.
  • scipy (>=1.2.0): A library used for scientific and technical computing, building on the capabilities of numpy and providing additional functionality.
  • tqdm: A fast, extensible progress bar for Python and CLI, useful for tracking the progress of loops and processes.
  • typing: Provides support for type hints, making it easier to write and maintain Python code by specifying expected types of variables.
  • sleap_io: A library for reading and writing SLEAP (Single Leap Application Protocol) files, which are used for pose estimation in biological research.
  • jax: A library for high-performance numerical computing, offering support for automatic differentiation and optimized operations on CPUs and GPUs.
  • jaxlib: A companion library to jax, providing implementations of numerical operations on various hardware platforms.

Additional Requirements (for devs)

These are optional dependencies used for development and documentation purposes, and can be installed via:

pip install -e ".[dev]"
  • flake8: A linting tool for Python that checks the code for style and quality issues, ensuring adherence to coding standards.
  • isort: A tool to sort imports in Python files, organizing them according to the PEP8 style guide.
  • Sphinx: A documentation generator for Python projects, converting reStructuredText files into various output formats such as HTML and PDF.
  • sphinx_rtd_theme: The theme for Sphinx documentation, used to create documentation that looks similar to Read the Docs.
  • sphinx-rtd-dark-mode: An extension for Sphinx to add dark mode support to the Read the Docs theme.
  • sphinx-automodapi: A Sphinx extension that helps generate documentation from docstrings in the code.
  • sphinx-copybutton: A Sphinx extension that adds a copy button to code blocks in the documentation.
  • sphinx-design: A Sphinx extension that adds design elements such as cards, grids, and buttons to the documentation.