Biofilter Project Documentation¶
Welcome to the Biofilter project documentation! This guide provides an overview of the project, its structure, and resources to help both power users and developers get started.
Overview¶
The Biofilter project is a Python-based tool designed for efficient data processing and analysis using SQLite as its core data storage. The project is organized into two main modules:
Biofilter Module: Responsible for managing and running the functionalities specific to the Biofilter system, such as filtering genes, groups, and annotations based on user-defined criteria.
LOKI Module: Manages functionalities related to the LOKI database, including data transformations and preparation for Biofilter analysis.
Both modules work with a SQLite database file, which must be provided as an input argument. This database stores all the necessary data for Biofilter and LOKI functionalities, ensuring a consistent and centralized data source.
Documentation for Users¶
For more detailed instructions and usage examples, refer to the user documentation:
Key Features¶
Python-Based:
The entire project is developed in Python, leveraging modern tools and libraries to ensure maintainability, scalability, and ease of use.
Integrated SQLite Database:
All data required by Biofilter and LOKI is stored in a single SQLite file. The path to this database must be provided as an argument when running either module.
Modular Design:
The Biofilter module focuses on filtering and querying functionalities.
The LOKI module handles data preparation and transformations.
Development Tools:
Poetry: Used for dependency management and virtual environment creation.
Tox: Ensures testing across multiple Python versions.
Black: Enforces consistent code formatting.
Sphinx: Generates project documentation.
Coverage: Measures code coverage during testing.
Development Resources¶
As a new contributor, here are some key points to help you navigate and contribute to the project:
Code Organization:
biofilter_modules: Contains core functionalities for Biofilter.
loki_modules: Handles LOKI-specific operations.
tests: Includes unit and functional tests for both modules.
Development Workflow: Follow these guidelines to maintain consistency and quality in your contributions:
Use Poetry as the central tool for managing dependencies and virtual environments.
Run tests with Tox to ensure compatibility across supported Python versions.
Follow code formatting standards enforced by Black.
Environment Setup: Ensure your environment is consistent with the project’s requirements:
Python >= 3.10
Dependencies managed through poetry install
Tips for New Developers:
Start by reviewing the README and this documentation to understand the project’s goals and architecture.
Use the provided tools (e.g., Black, Tox) to maintain consistency and quality in your contributions.
Always run tests before submitting changes.
Getting Started¶
Follow these steps to set up the Biofilter project for development or testing:
Clone the Repository:
git clone https://github.com/RitchieLab/biofilter.git cd biofilter
Switch to the development Branch. Ensure you are working with the latest code:**
git checkout development
Set Up Python Environment:
If you are using pyenv, set the desired Python version for the project
pyenv install 3.11.9 # Example version pyenv local 3.11.9Ensure the Python version matches the project requirements (Python >= 3.10).
Install Poetry. Install Poetry, the dependency and environment manager:
curl -sSL https://install.python-poetry.org | python3 - poetry --version # Verify the installation
Install Project Dependencies. Use Poetry to install all required dependencies:
poetry install
Configure Python Versions in tox. Update the tox.ini file to include the Python versions available in your environment. For example:
[tox] envlist = py310, py311, py312
Run Tests. Verify your setup by running the test suite:
poetry run pytest