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📝 Docs(README.md): Update image links and installation instructions on the README.
ALos, updated the logo, class diagram, and graphical abstract images
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README.md

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<!-- <div align="center">
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<img width="300px" src="images/vuegen_logo.svg">
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</div> -->
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![VueGen Logo](docs/images/vuegen_logo.svg)
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![VueGen Logo](https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg)
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-----------------
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<p align="center">
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VueGen is a Python library that automates the creation of scientific reports.
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<img width="650px" src="images/vuegen_graph_abstract.png" alt="VueGen overview"/>
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</figure>
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</p> -->
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![VueGen Abstract](docs/images/vuegen_graph_abstract.png)
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![VueGen Abstract](https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_graph_abstract.png)
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Also, the class diagram for the project is presented below to illustrate the architecture and relationships between classes:
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</figure>
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</p> -->
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![VueGen Class Diagram](docs/images/vuegen_classdiagram_noattmeth.png)
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![VueGen Class Diagram](https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_classdiagram_noattmeth.png)
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## Installation
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You can install the package for development from this repository by running the following command:
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Vuegen is available on [PyPI][vuegen-pypi] and can be installed using pip:
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```bash
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pip install vuegen
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```
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You can also install the package for development from this repository by running the following command:
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```bash
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pip install -e path/to/vuegen # specify location
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pip install -e . # in case your pwd is in the vuegen directory
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```
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This will both install `quarto` and `streamlit` as our backends for report generation.
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### Verify quarto installation
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### Quarto installation
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Test your quarto installation by running the following command:
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Vuegen uses [Quarto][quarto] to generate various report types. The pip insallation includes quarto using the [quarto-cli Python library][quarto-cli-pypi]. To test if quarto is installed in your computer, run the following command:
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```bash
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quarto check
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```
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If you use conda a conda environement you can install quatro from the conda-forge channel
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in case it did not work.
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```bash
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conda install -c conda-forge quarto
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```
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If quarto is not installed, you can download the command-line interface from the [Quarto website][quarto-cli] for your operating system.
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## Execution
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vuegen --config example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml --report_type streamlit
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```
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The current report types are streamlit, html, pdf, docx, odt, revealjs, pptx, and jupyter.
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The current report types supported by VueGen are:
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* Streamlit
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* HTML
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* PDF
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* DOCX
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* ODT
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* Reveal.js
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* PPTX
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* Jupyter
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## Acknowledgements
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[issues]: https://github.com/Multiomics-Analytics-Group/vuegen/issues/new
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[streamlit]: https://streamlit.io/
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[vuegen-pypi]: https://pypi.org/project/vuegen/
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[quarto]: https://quarto.org/
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[quarto-cli-pypi]: https://pypi.org/project/quarto-cli/
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[quarto-cli]: https://quarto.org/docs/get-started/
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[Mona]: https://multiomics-analytics-group.github.io/
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[Biosustain]: https://www.biosustain.dtu.dk/
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[scriberia]: https://www.scriberia.co.uk/
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[turingway]: https://github.com/the-turing-way/the-turing-way
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[zenodo-turingway]: https://zenodo.org/records/3695300
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[issues]: https://github.com/Multiomics-Analytics-Group/vuegen/issues/new
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