vuegen 0.2.0

Module to generate automatic web interface reports with visualizations

VueGen is a Python library that automates the creation of scientific reports.

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Table of contents:

• About the project
• Installation
• Execution
• Acknowledgements
• Contact

About the project

VueGen automates the creation of reports based on a directory with plots, dataframes, and other files in different formats. A YAML configuration file is generated from the directory to define the structure of the report. Users can customize the report by modifying the configuration file, or they can create their own configuration file instead of passing a directory as input.

The configuration file specifies the structure of the report, including sections, subsections, and various components such as plots, dataframes, markdown, html, and API calls. Reports can be generated in various formats, including documents (PDF, HTML, DOCX, ODT), presentations (PPTX, Reveal.js), notebooks (Jupyter) or Streamlit web applications.

An overview of the VueGen workflow is shown in the figure below:

Also, the class diagram for the project is presented below to illustrate the architecture and relationships between classes:

Installation

Vuegen is available on PyPI and can be installed using pip:

pip install vuegen

You can also install the package for development from this repository by running the following command:

pip install -e path/to/vuegen # specify location 
pip install -e . # in case your pwd is in the vuegen directory

Quarto installation

Vuegen uses Quarto to generate various report types. The pip insallation includes quarto using the quarto-cli Python library. To test if quarto is installed in your computer, run the following command:

quarto check

If quarto is not installed, you can download the command-line interface from the Quarto website for your operating system.

Execution

Run VueGen using a directory with the following command:

cd docs
vuegen --directory example_data/Earth_microbiome_vuegen_demo_notebook --report_type streamlit

💡 If vuegen does not work, try python -m vuegen instead.

By default, the streamlit_autorun argument is set to False, but you can use it in case you want to automatically run the streamlit app.

It's also possible to provide a configuration file instead of a directory:

vuegen --config example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml --report_type streamlit

The current report types supported by VueGen are:

• Streamlit
• HTML
• PDF
• DOCX
• ODT
• Reveal.js
• PPTX
• Jupyter

Acknowledgements

• Vuegen was developed by the Multiomics Network Analytics Group (MoNA) at the Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain).
• The vuegen logo was designed based on an image created by Scriberia for The Turing Way Community, which is shared under a CC-BY licence. The original image can be found at Zenodo.

Contact

If you have comments or suggestions about this project, you can open an issue in this repository.