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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.
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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.
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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](streamlit) web applications.
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You can also install the package for development by cloning this repository and 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 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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### Docker
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If you prefer not to install VueGen on your system, a pre-configured Docker container is available. It includes all dependencies, ensuring a fully reproducible execution environment. See the [Execution section](#execution) for details on running VueGen with Docker. The official Docker image is available at [quay.io/dtu_biosustain_dsp/vuegen][vuegen-docker-quay].
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If you prefer not to install VueGen on your system, a pre-configured Docker container is available. It includes all dependencies, ensuring a fully reproducible execution environment. See the [Execution section](#execution) for details on running VueGen with Docker. The official Docker image is available at [quay.io/dtu_biosustain_dsp/vuegen][vuegen-docker-quay].
VueGen’s functionality is demonstrated through two case studies:
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**1. Predefined Directory**
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This introductory case study uses a predefined directory with plots, dataframes, Markdown, and HTML components. Users can generate reports in different formats and modify the configuration file to customize the report structure.
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This introductory case study uses a predefined directory with plots, dataframes, Markdown, and HTML components. Users can generate reports in different formats and modify the configuration file to customize the report structure.
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🔗 [![Open in Colab][colab_badge]][colab_link_intro_demo]
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Once a Streamlit report is generated, it can be deployed as a web application to make it accessible online. There are multiple ways to achieve this:
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***Streamlit Community Cloud**: Deploy your report easily using [Streamlit Cloud][st-cloud], as demonstrated in the [EMP VueGen Demo][emp-st-demo]. The process involves moving the necessary scripts, data, and a requirements.txt file into a GitHub repository. Then, the app can be deployed via the Streamlit Cloud interface. The deployment example is available in the `streamlit-report-example` branch.
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***Standalone Executables**: Convert your Streamlit application into a desktop app by packaging it as an executable file for different operating systems. A detailed explanation of this process can be found in this [Streamlit forum post][st-forum-exe].
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***Stlite**: Run Streamlit apps directly in the browser with [stlite][stlite], a WebAssembly port of Streamlit powered by Pyodide, eliminating the need for a server. It also allows packaging apps as standalone desktop executables using stlite desktop.
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-**Streamlit Community Cloud**: Deploy your report easily using [Streamlit Cloud][st-cloud], as demonstrated in the [EMP VueGen Demo][emp-st-demo]. The process involves moving the necessary scripts, data, and a requirements.txt file into a GitHub repository. Then, the app can be deployed via the Streamlit Cloud interface. The deployment example is available in the `streamlit-report-example` branch.
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-**Standalone Executables**: Convert your Streamlit application into a desktop app by packaging it as an executable file for different operating systems. A detailed explanation of this process can be found in this [Streamlit forum post][st-forum-exe].
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-**Stlite**: Run Streamlit apps directly in the browser with [stlite][stlite], a WebAssembly port of Streamlit powered by Pyodide, eliminating the need for a server. It also allows packaging apps as standalone desktop executables using stlite desktop.
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These options provide flexibility depending on whether the goal is online accessibility, lightweight execution, or local application distribution.
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**APA:**
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Ayala-Ruano, S., Webel, H., & Santos, A. (2025). *VueGen: Automating the generation of scientific reports*. bioRxiv. https://doi.org/10.1101/2025.03.05.641152
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Ayala-Ruano, S., Webel, H., & Santos, A. (2025). _VueGen: Automating the generation of scientific reports_. bioRxiv. https://doi.org/10.1101/2025.03.05.641152
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**BibTeX:**
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## Contact and feedback
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We appreciate your feedback! If you have any comments, suggestions, or run into issues while using VueGen, feel free to [open an issue][new-issue] in this repository. Your input helps us make VueGen better for everyone.
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We appreciate your feedback! If you have any comments, suggestions, or run into issues while using VueGen, feel free to [open an issue][new-issue] in this repository. Your input helps us make VueGen better for everyone.
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