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merged 4 commits into from
May 9, 2025
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Update GUI installation instructions #118

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755384c
:memo: update instructions to install vuegen into GUI
enryH May 7, 2025
e476c3f
:bug: update global config dictionary in app
enryH May 7, 2025
af21ebc
:art: move and extend message in case of errors
enryH May 7, 2025
3395e92
:art: format markdown README
enryH May 7, 2025
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31 changes: 18 additions & 13 deletions README.md
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Expand Up @@ -7,7 +7,7 @@
| Information | Links |
| :-------------------- | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| **Package** | [![PyPI Latest Release](https://img.shields.io/pypi/v/vuegen.svg)][vuegen-pypi] [![Conda Latest Release](https://img.shields.io/conda/v/bioconda/vuegen.svg)][vuegen-conda] [![Supported versions](https://img.shields.io/pypi/pyversions/vuegen.svg)][vuegen-pypi] [![Docker Repository on Quay](https://quay.io/repository/dtu_biosustain_dsp/vuegen/status "Docker Repository on Quay")][vuegen-docker-quay] [![License](https://img.shields.io/github/license/Multiomics-Analytics-Group/vuegen)][vuegen-license] |
| **Documentation** | [![View - Documentation](https://img.shields.io/badge/view-Documentation-blue?style=flat)][vuegen-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/vuegen/badge/?style=flat) |
| **Documentation** | [![View - Documentation](https://img.shields.io/badge/view-Documentation-blue?style=flat)][vuegen-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/vuegen/badge/?style=flat) |
| **Build** | [![CI](https://github.com/Multiomics-Analytics-Group/vuegen/actions/workflows/cdci.yml/badge.svg)][ci-gh-action] [![Docs](https://github.com/Multiomics-Analytics-Group/vuegen/actions/workflows/docs.yml/badge.svg)][ci-docs] |
| **Examples** | [![HTML5](https://img.shields.io/badge/html5-%23E34F26.svg?style=for-the-badge&logo=html5&logoColor=white)][emp-html-demo] [![Streamlit](https://img.shields.io/badge/Streamlit-%23FE4B4B.svg?style=for-the-badge&logo=streamlit&logoColor=white)][emp-st-demo] |
| **Discuss on GitHub** | [![GitHub issues](https://img.shields.io/github/issues/Multiomics-Analytics-Group/vuegen)][issues] [![GitHub pull requests](https://img.shields.io/github/issues-pr/Multiomics-Analytics-Group/vuegen)][pulls] |
Expand Down Expand Up @@ -129,7 +129,7 @@ vuegen --directory docs/example_data/Earth_microbiome_vuegen_demo_notebook --rep

### Folder structure

Your input directory should follow a **nested folder structure**, where first-level folders are treated as **sections** and second-level folders as **subsections**, containing the components (plots, tables, networks, Markdown text, and HTML files). If the component files are in the first-level folders, an `overview` subsection will be created automatically.
Your input directory should follow a **nested folder structure**, where first-level folders are treated as **sections** and second-level folders as **subsections**, containing the components (plots, tables, networks, Markdown text, and HTML files). If the component files are in the first-level folders, an `overview` subsection will be created automatically.

Here is an example layout:

Expand Down Expand Up @@ -245,33 +245,39 @@ The **bundle GUI** with the VueGen package is available under the
You will need to unzip the file and run `vuegen_gui` in the unpacked main folder.
Most dependencies are included into the bundle using [PyInstaller][pyinstaller].

Streamlit works out of the box as a purely Python based package. For the rest of report types you
Streamlit works out of the box as a purely Python based package. For the rest of report types you
will have to have a **Python 3.12** installation with the `jupyter` package installed, as `quarto` needs to start
a kernel for execution. This is also true if you install `quarto` globally on your machine.

> [!TIP]
> It is advisable to create 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`. We recommend using [miniforge][conda-download] to install Python and the `conda` package manager.

We assume you have installed the `miniforge` distribution for your machine (MacOS with arm64/ apple silicon
or x86_64/ intel or Windows x86_64). Also, download the
We assume you have installed the `miniforge` distribution for your machine (MacOS with arm64/ apple silicon
or x86_64/ intel or Windows x86_64). Also, download the
[latest `vuegen_gui` bundle](https://github.com/Multiomics-Analytics-Group/vuegen/releases/latest)
from the releases page according to your operating system.

You can create a new conda environment with Python 3.12 and the `jupyter` and `vuegen` package:

```bash
conda create -n vuegen_gui -c conda-forge python=3.12 jupyter vuegen
conda create -n vuegen_gui -c conda-forge -c bioconda python=3.12 jupyter vuegen
```

> [!WARNING]
> If you have errors with the `vuegen` package, you can install it separately using pip, as explained in the installation section.
>
> ```
> conda create -n vuegen_gui -c conda-forge -c bioconda python=3.12 jupyter
> conda activate vuegen_gui
> pip install vuegen
> ```

Then, activate the environment:

```bash
conda activate vuegen_gui
```

> [!WARNING]
> If you have errors with the `vuegen` package, you can install it separately using pip, as explained in the installation section.

Now, you can list all conda environments to find the location of the `vuegen_gui` environment:

```bash
Expand Down Expand Up @@ -320,11 +326,10 @@ This advanced case study demonstrates the application of VueGen in a real-world

### 3. ChatBot Component

This case study highlights VueGen’s capability to embed a chatbot component into a report subsection,
enabling interactive conversations inside the report. This component is streamlit-specific and is not
This case study highlights VueGen’s capability to embed a chatbot component into a report subsection,
enabling interactive conversations inside the report. This component is streamlit-specific and is not
available for other report types.


Two API modes are supported:

- **Ollama-style streaming chat completion**
Expand Down Expand Up @@ -353,7 +358,7 @@ to support more flexible and general-purpose response formats in future releases

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:

### Streamlit Community Cloud
### 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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2 changes: 1 addition & 1 deletion gui/app.py
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Expand Up @@ -135,7 +135,7 @@ def inner():
kwargs["max_depth"] = int(max_depth.get())
print("kwargs:")
pprint(kwargs)

global config_app
if python_dir_entry.get():
if python_dir_entry.get() != config_app["python_dir_entry"]:
config_app["python_dir_entry"] = python_dir_entry.get()
Expand Down