My Codebase

Welcome to My Codebase, a comprehensive repository containing Jupyter Notebooks, Python scripts, and Bash scripts for data analysis, simulation, and various computational tasks. This repository is organized to facilitate easy navigation, modularity, and reusability of code across different projects.

Table of Contents

• Features

• Directory Structure

• Installation

  • Prerequisites
  • Clone the Repository
  • Set Up a Virtual Environment
  • Install Dependencies
  • Install muonpipe Module in Editable Mode

• Usage

  • Running Jupyter Notebooks
  • Executing Python Scripts
  • Running Bash Scripts

• Contributing

• License

Features

• Jupyter Notebooks: Interactive notebooks for data analysis, visualization, and exploration.
• Python Scripts: Modular Python scripts for various computational tasks.
• Bash Scripts: Automation scripts for setup, data processing, and deployment.
• Custom Modules: Reusable Python modules (muonpipe) to streamline code across notebooks and scripts.

Directory Structure

• python/jupyter_notebooks/: Contains all Jupyter Notebook files for data analysis and visualization.
• python/python_scripts/: Holds standalone Python scripts for various tasks.
• python/python_modules/: Custom Python modules, including muonpipe, essential for other code in the repository.
• bash_scripts/: Bash scripts for automating setup and deployment processes.
• data/: Directory for storing raw and processed data.
• C++/: Directory for C++ code
• requirements.txt: Lists all Python dependencies required for the project.
• README.md: This documentation file.

Installation

Prerequisites

• Python 3.10 or higher
• Git
• pip (Python package installer)
• Virtual Environment Tool (venv or conda)

Clone the Repository

git clone https://github.com/jstvdk/my_codebase.git
cd my_codebase

Set Up a Virtual Environment and installing the dependencies

From the project root directory:

conda create -n my_codebase_env python=3.10
conda activate my_codebase_env
pip install --upgrade pip
pip install -r requirements.txt

Install muonpipe Module in Editable Mode

The muonpipe module is essential for the functionality of almost all python related code in this repository. Installing it in editable mode ensures that any changes made to the module are immediately available without needing to reinstall.

To install it, navigate to the python_modules Directory:

cd python/python_modules/muonpipe
pip install -e .

Note: Ensure that you’re using the same Python environment (e.g., virtual environment) for both installing the package and running Jupyter Notebooks