Multiomics-Analytics-Group · sayalaruano · Aug 13, 2025 · Aug 13, 2025 · Aug 13, 2025
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -0,0 +1,67 @@
+# Contributing to VueCore
+
+[VueCore][vuecore-repo] is an open source project, and we welcome contributions of all 
+kinds via GitHub issues and pull requests: correct or improve our [documentation][vuecore-docs], report or fix bugs, propose changes, and implement new features. Please follow 
+these guidelines to make sure that your contribution is easily integrated into the project.
+
+## 1. Contributor Agreement
+
+By contributing, you agree that we may redistribute your work under [our
+license](LICENSE.md). In exchange, we will address your issues and/or assess
+your change proposal as promptly as we can, and help you become a member of our
+community.
+
+## 2. What to Contribute
+
+The easiest way to get started is by reporting an issue that needs to be fixed, 
+such as a bug in the code, unclear explanations, conceptual errors, or other details. 
+You can also  contribute by proposing new features or modules, improving existing 
+functionality, or suggesting other ideas that might be useful. If you’re looking for 
+inspiration, please check the [list of open issues][issues] in this repository.
+
+Feedback from beginners is especially valuable, as experienced users may overlook how 
+challenging certain aspects of the software can be for newcomers. Therefore, we encourage 
+you to share any suggestions or observations you have about this project.
+
+## 3. How to Contribute
+
+Here are the ways you can submit your suggestions and contribute to the project:
+
+### 1. Reporting Issues or Suggesting Improvements
+
+If you have a  [GitHub][github] account (or are willing to [open one][github-join]) but are unfamiliar with Git, you can report bugs or suggest improvements by [creating an issue][new-issue]. This GitHub feature allows for discussion threads on reported issues and proposed enhancements.
+
+### 2. Submitting Changes via Pull Requests
+
+If you are comfortable using Git and would like to add or modify a functionality, you can submit a **pull request (PR)**. Instructions on how to contribute this way are provided in the next section.
+
+> [!NOTE]
+> The documentation for [Git][git-docs] and [GitHub][github-docs] are easy to follow, and you can learn the basics using their official guides.
+
+## 3. Creating a Pull Request
+
+If you choose to contribute via GitHub, you may want to look at [How to Contribute to an Open Source Project on GitHub][how-contribute]. In brief, we use [GitHub flow][github-flow] to manage changes:
+
+1. Create a new branch in your desktop copy of this repository for each significant change.
+2. Commit the change in that branch.
+3. Push that branch to your fork of this repository on GitHub.
+4. Submit a pull request from that branch to the [upstream repository][vuecore-repo].
+5. If you receive feedback, make changes on your desktop and push to your branch on GitHub: the 
+   pull request will update automatically.
+
+## 5. Credits
+
+This contribution guide was modified under the [Creative Commons Attribution 4.0 International License][ccby] from the [Software Carpentry guides][soft-cp-guides].
+
+[vuecore-repo]: https://github.com/Multiomics-Analytics-Group/vuecore
+[vuecore-docs]: https://vuecore.readthedocs.io/
+[issues]: https://github.com/Multiomics-Analytics-Group/vuecore/issues
+[new-issue]: https://github.com/Multiomics-Analytics-Group/vuecore/issues/new
+[github]: https://github.com
+[github-join]: https://github.com/join
+[git-docs]: https://git-scm.com/doc
+[github-docs]: https://guides.github.com/
+[how-contribute]: https://egghead.io/courses/how-to-contribute-to-an-open-source-project-on-github
+[github-flow]: https://guides.github.com/introduction/flow/
+[soft-cp-guides]: https://software-carpentry.org/lessons/
+[ccby]: https://creativecommons.org/licenses/by/4.0/
diff --git a/LICENSE → LICENSE.md b/LICENSE → LICENSE.md
@@ -1,6 +1,6 @@
-MIT License
+## MIT License
 
-Copyright (c) 2023 Multi-omics Network Analytics Group
+Copyright (c) 2025 Multi-omics Network Analytics Group
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -19,3 +19,13 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
+
+## Creative Commons Attribution 4.0 International License (CC BY 4.0)
+
+Copyright (c) 2025 Multi-omics Network Analytics Group
+
+The creative works from this project are licensed under a Creative Commons Attribution 
+4.0 International License.
+
+To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
+
diff --git a/README.md b/README.md
@@ -4,26 +4,84 @@
    VueCore is a Python package for creating interactive and static visualizations of multi-omics data
 </p>
 
+| Information           | Links                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
+| :-------------------- | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **Package**           | [![PyPI Latest Release](https://img.shields.io/pypi/v/vuecore.svg)][vuecore-pypi] [![Supported versions](https://img.shields.io/pypi/pyversions/vuecore.svg)][vuecore-pypi] [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)][mit-license]|
+| **Documentation**     | [![View - Documentation](https://img.shields.io/badge/view-Documentation-blue?style=flat)][vuecore-docs] [![made-with-sphinx-doc](https://img.shields.io/badge/Made%20with-Sphinx-1f425f.svg)](https://www.sphinx-doc.org/) ![Docs](https://readthedocs.org/projects/vuecore/badge/?style=flat) [![CC BY 4.0][cc-by-shield]][vuecore-license]|
+| **Build**             | [![CI](https://github.com/Multiomics-Analytics-Group/vuecore/actions/workflows/cdci.yml/badge.svg)][ci-gh-action]|                                                                                     
+| **Discuss on GitHub** | [![GitHub issues](https://img.shields.io/github/issues/Multiomics-Analytics-Group/vuecore)][issues] [![GitHub pull requests](https://img.shields.io/github/issues-pr/Multiomics-Analytics-Group/vuecore)][pulls]|
+
+## Table of contents:
+
+- [About the project](#about-the-project)
+- [Installation](#installation)
+- [Documentation](#documentation)
+- [License](#license)
+- [Contributing](#contributing)
+- [Credits and acknowledgements](#credits-and-acknowledgements)
+- [Contact and feedback](#contact-and-feedback)
+
+## About the project
+
 VueCore is part of a broader ecosystem of tools for multi-omics analysis, working in conjunction with [ACore][acore] and [VueGen][vuegen] to enable end-to-end data processing, visualization, and reporting.
 
 ## Installation
 
-### Latest stable release from PyPI
+> [!TIP]
+> It is recommended to install VueGen inside a virtual environment to manage depenendencies and avoid conflicts with existing packages. You can use the virtual environment manager of your choice, such as `poetry`, `conda`, or `pipenv`.
+
+### Pip
+
+VueGen is available on [PyPI][vuecore-pypi] and can be installed using pip:
 
 ```bash
-pip install vuecore
+pip install vuegen
 ```
 
-### Latest development version from GitHub
+You can also install the package for development by cloning this repository and running the following command:
 
-Clone this repository and then install using pip the development version in
-editable mode:
+> [!WARNING]
+> We assume you are in the root directory of the cloned repository when running this command. Otherwise, you need to specify the path to the `vuegen` directory.
 
 ```bash
-# git clone https://github.com/Multiomics-Analytics-Group/vuecore.git
-# cd vuecore
-pip install -e '.[dev]'
+pip install -e .
 ```
 
+## Documentation
+
+VueCore's documentation is hosted on [Read the Docs][vuecore-docs]. It includes detailed examples for every plot type, configuration options, and the API reference. It is designed to help you with creating visualizations for your multi-omics data.
+
+## License
+
+The code in this repository is licensed under the **MIT License**, allowing you to use, modify, and distribute it freely as long as you include the original copyright and license notice.
+
+The documentation and other creative content are licensed under the **Creative Commons Attribution 4.0 International (CC BY 4.0) License**, meaning you are free to share and adapt it with proper attribution.
+
+Full details for both licenses can be found in the [LICENSE][vuecore-license] file.
+
+## Contributing
+
+VueCore is an open-source project, and we welcome contributions of all kinds via GitHub issues and pull requests. You can report bugs, suggest improvements, propose new features, or implement changes. Please follow the guidelines in the [CONTRIBUTING](CONTRIBUTING.md) file to ensure that your contribution is easily integrated into the project.
+
+## Credits and acknowledgements
+
+- VueCore was developed by the [Multiomics Network Analytics Group (MoNA)][Mona] at the [Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain)][Biosustain].
+
+## Contact and feedback
+
+We appreciate your feedback! If you have any comments, suggestions, or run into issues while using VueCore, feel free to [open an issue][new-issue] in this repository. Your input helps us make VueCore better for everyone.
+
+
+[vuecore-pypi]: https://pypi.org/project/vuecore/
+[vuecore-license]: https://github.com/Multiomics-Analytics-Group/vuecore/blob/main/LICENSE.md
+[vuecore-docs]: https://vuecore.readthedocs.io/
+[cc-by-shield]: https://img.shields.io/badge/License-CC%20BY%204.0-lightgrey.svg
+[mit-license]: https://opensource.org/licenses/MIT
+[ci-gh-action]: https://github.com/Multiomics-Analytics-Group/vuecore/actions/workflows/cdci.yml
+[issues]: https://github.com/Multiomics-Analytics-Group/vuecore/issues
+[pulls]: https://github.com/Multiomics-Analytics-Group/vuecore/pulls
 [vuegen]: https://github.com/Multiomics-Analytics-Group/vuegen
-[acore]: https://github.com/Multiomics-Analytics-Group/acore
+[acore]: https://github.com/Multiomics-Analytics-Group/acore
+[Mona]: https://multiomics-analytics-group.github.io/
+[Biosustain]: https://www.biosustain.dtu.dk/
+[new-issue]:https://github.com/Multiomics-Analytics-Group/vuecore/issues/new