deploy: 8b1d810

.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: df155090b35a77ab1121f730e76e5d0d
+config: 82b6cc535abaa73c2054d07239db1835
 tags: 645f666f9bcd5a90fca523b33c5a78b7

_sources/index.rst.txt

@@ -1,33 +1,148 @@
-.. Biofilter-dev documentation master file, created by
-   sphinx-quickstart on Tue Dec  3 10:39:44 2024.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
+Biofilter Project Documentation
+===============================
 
-Biofilter Developer 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.
 
-Add content using ``reStructuredText`` syntax. See the
-`reStructuredText <https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html>`_
-documentation for details.
 
+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:
 
-.. toctree::
-   :maxdepth: 2
-   :caption: Contents:
+1. **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.
+
+2. **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:
+
+- Biofilter User Guide
+- LOKI User Guide
+
+
+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
 
-   usage-of-tox
-   usage-of-sphinx
-   usage-of-poetry
-   usage-of-coverage
-   usage-of-black
-   usage-of-branching
-   usage-of-testing
+- **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.
 
-Indices and tables
-==================
 
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+Getting Started
+---------------
+
+Follow these steps to set up the **Biofilter** project for development or testing:
+
+1. **Clone the Repository**:
+
+  .. code-block:: bash
+
+    git clone https://github.com/RitchieLab/biofilter.git
+    cd biofilter
+
+2. **Switch to the development Branch.** Ensure you are working with the latest code:**
+
+  .. code-block:: bash
+
+    git checkout development
+
+3. **Set Up Python Environment:**
+
+  If you are using pyenv, set the desired Python version for the project
+
+  .. code-block:: bash
+
+    pyenv install 3.11.9  # Example version
+    pyenv local 3.11.9
+
+  Ensure the Python version matches the project requirements (Python >= 3.10).
+
+4. **Install Poetry.** Install Poetry, the dependency and environment manager:
+
+  .. code-block:: bash
+
+    curl -sSL https://install.python-poetry.org | python3 -
+    poetry --version  # Verify the installation
+
+5. **Install Project Dependencies.** Use Poetry to install all required dependencies:
+
+  .. code-block:: bash
+
+    poetry install
+
+6. **Configure Python Versions in tox.** Update the tox.ini file to include the Python versions available in your environment. For example:
+
+  .. code-block:: ini
+
+    [tox]
+    envlist = py310, py311, py312
+
+7. **Run Tests.** Verify your setup by running the test suite:
+
+  .. code-block:: bash
+
+    poetry run pytest
+
+
+.. toctree::
+  :maxdepth: 2
+  :caption: Contents:
+
+  usage-of-branching
+  usage-of-poetry
+  usage-of-black
+  usage-of-coverage
+  usage-of-tox
+  usage-of-sphinx
+  usage-of-git
+

_sources/usage-of-black.rst.txt

@@ -1,4 +1,4 @@
-Black Code Formatter Guide
+Black Guide
 ==========================
 
 Black is a code formatter for Python that automatically reformats your code to be more readable and standardized. This guide provides essential information for using Black within this project.

_sources/usage-of-coverage.rst.txt

@@ -1,5 +1,5 @@
-Running Coverage in the Biofilter Project
-=========================================
+Coverage Guide
+==============
 
 To measure test coverage in the Biofilter project, we use `Coverage.py`. This guide outlines the steps to install and run `coverage` and generate reports.
 

_sources/usage-of-git.rst.txt

@@ -0,0 +1,3 @@
+Using git and CI/CD by Actions
+==============================
+

_sources/usage-of-poetry.rst.txt

@@ -1,5 +1,5 @@
-Using Poetry for Dependency Management and Project Setup
-========================================================
+Poetry Guider
+=============
 
 This document provides a guide to understanding Poetry, setting up the project locally, and creating installation packages for the Biofilter project.
 

_sources/usage-of-sphinx.rst.txt

@@ -1,5 +1,5 @@
-Setting Up and Running Sphinx for Biofilter Documentation
-=========================================================
+Sphinx Guider
+=============
 
 This document provides instructions for contributors on how to set up, customize, and run Sphinx to generate documentation for the **Biofilter** project.
 

_sources/usage-of-tox.rst.txt

@@ -1,5 +1,5 @@
-Using Tox in the Biofilter Project
-==================================
+Tox Guider
+==========
 
 Tox is a tool used to automate testing across multiple Python versions and environments. It ensures consistency and compatibility in your project's workflows.
 

genindex.html

@@ -124,7 +124,7 @@
 
         <div class="md-flex__cell md-flex__cell--shrink">
           <div class="md-header-nav__source">
-            <a href="https://github.com/your-org/biofilter" title="Go to repository" class="md-source" data-md-source="github">
+            <a href="https://github.com/RitchieLab/biofilter" title="Go to repository" class="md-source" data-md-source="github">
 
     <div class="md-source__icon">
       <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" viewBox="0 0 24 24" width="28" height="28">
@@ -183,7 +183,7 @@
        title="Biofilter Developer Documentation 2.4.4 documentation">Biofilter Developer Docs</a>
   </label>
     <div class="md-nav__source">
-      <a href="https://github.com/your-org/biofilter" title="Go to repository" class="md-source" data-md-source="github">
+      <a href="https://github.com/RitchieLab/biofilter" title="Go to repository" class="md-source" data-md-source="github">
 
     <div class="md-source__icon">
       <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" viewBox="0 0 24 24" width="28" height="28">
@@ -199,6 +199,65 @@
 
 
 
+
+  <ul class="md-nav__list">
+    <li class="md-nav__item">
+
+      <span class="md-nav__link caption"><span class="caption-text">Contents:</span></span>
+
+    </li>
+    <li class="md-nav__item">
+
+
+      <a href="usage-of-branching.html" class="md-nav__link">Branching Structure Guide</a>
+
+
+    </li>
+    <li class="md-nav__item">
+
+
+      <a href="usage-of-poetry.html" class="md-nav__link">Poetry Guider</a>
+
+
+    </li>
+    <li class="md-nav__item">
+
+
+      <a href="usage-of-black.html" class="md-nav__link">Black Guide</a>
+
+
+    </li>
+    <li class="md-nav__item">
+
+
+      <a href="usage-of-coverage.html" class="md-nav__link">Coverage Guide</a>
+
+
+    </li>
+    <li class="md-nav__item">
+
+
+      <a href="usage-of-tox.html" class="md-nav__link">Tox Guider</a>
+
+
+    </li>
+    <li class="md-nav__item">
+
+
+      <a href="usage-of-sphinx.html" class="md-nav__link">Sphinx Guider</a>
+
+
+    </li>
+    <li class="md-nav__item">
+
+
+      <a href="usage-of-git.html" class="md-nav__link">Using git and CI/CD by Actions</a>
+
+
+    </li>
+  </ul>
+
+
 </nav>
               </div>
             </div>