pydgey 0.1.0

Interactive pipeline widgets for Google Colab and Jupyter.

Pydgey

Overview

Pydgey is a Python framework for building simple graphical user interfaces for pipelines that run interactively in Jupyter Notebooks (e.g., Google Colab, VSCode, JupyterLab).

Built on top of anywidget, React, and shadcn/ui, Pydgey aims to abstract away some of the complexities of widget building. It allows for pipelines to be defined using standard Python classes, and handles the generation of a clean, React-based UI.

Purpose

I needed a simple framework to quickly wrap tools and basic pipelines into user-friendly interfaces that run easily on Google Colab. The goal being to save Bachelors and Masters students in our lab the hassle of installing and managing command-line tools, letting them focus on the limited time they have to actually do science.

As the intended use is to run Pydgey widgets within the constraints of free Google Colab environments, the goal is not to support massive scale, high-concurrency execution, or complex dependency graphs like Snakemake or Nextflow. Pydgey prioritizes accessibility and ease-of-use for smaller, ad-hoc analyses over the computational efficiency required for large-scale workflows.

Getting Started

Pydgey can be installed from PyPI:

$ pip install pydgey

💡 Example

Create a launcher for an HMMER search pipeline. This will render an interactive widget in the notebook where users can upload files and configure E-values without writing code.

from examples.hmmsearch.hmmsearch import HmmSearchPipeline
from pydgey import create_launcher

# Define your pipeline (or import a pre-made one)
pipeline = HmmSearchPipeline()

# Launch the interactive widget
launcher = create_launcher(pipeline)
launcher

This simple snippet produces a full-featured UI with file selectors, parameter inputs, and log streaming.

🏗️ Contributing

Contributions are welcome. See CONTRIBUTING.md for more details.

⚖️ License

This library is provided under the MIT License. See LICENSE for more information.