You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
👷 CI: Add CI steps to create streamlit example branch and deploy EMP case study
* 👷 CI: Add CI steps to create streamlit example branch and deploy EMP report
* 💚 CI: Fix streamlit example publication github action
* 🚚 Docs: move requirements.txt to docs folder
* 🎨 CI: change streamlit report example branch name
* 🐛 Fix: replace absolute paths of Python scripts from EMP streamlit report example and add aggrid as requirement
* 🐛 Fix: correct code to replace absolute paths in streamlit EMP python files
* ✏️ Fix: fix typo on command to correct absolute paths
* 📝 Docs: update logo files and README with case studies and web app deployment sections
pip install -e .# in case your pwd is in the vuegen directory
62
49
```
63
50
64
-
### Quarto installation
51
+
> [!TIP]
52
+
> 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`.
65
53
54
+
### Quarto installation
66
55
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:
67
56
68
57
```bash
69
58
quarto check
70
59
```
71
60
72
-
If quarto is not installed, you can download the command-line interface from the [Quarto website][quarto-cli] for your operating system.
61
+
> [!TIP]
62
+
> If quarto is not installed, you can download the command-line interface from the [Quarto website][quarto-cli] for your operating system.
73
63
74
64
## Execution
75
-
76
65
Run VueGen using a directory with the following command:
> 💡 If `vuegen` does not work, try `python -m vuegen` instead.
84
-
85
-
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.
71
+
> [!NOTE]
72
+
> 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.
86
73
87
74
It's also possible to provide a configuration file instead of a directory:
88
75
@@ -100,8 +87,34 @@ The current report types supported by VueGen are:
100
87
* PPTX
101
88
* Jupyter
102
89
103
-
## Acknowledgements
90
+
## Case studies
91
+
VueGen’s functionality is demonstrated through two case studies:
92
+
93
+
**1. Predefined Directory**
94
+
95
+
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.
96
+
97
+
🔗 [![Open in Colab][colab_badge]][colab_link_intro_demo]
98
+
99
+
**2. Earth Microbiome Project Data**
100
+
101
+
This advanced case study demonstrates the application of VueGen in a real-world scenario using data from the [Earth Microbiome Project (EMP)][emp]. The EMP is an initiative to characterize global microbial taxonomic and functional diversity. The notebook process the EMP data, create plots, dataframes, and other components, and organize outputs within a directory to produce reports. Report content and structure can be adapted by modifying the configuration file. Each report consists of sections on exploratory data analysis, metagenomics, and network analysis.
102
+
103
+
🔗 [![Open in Colab][colab_badge]][colab_link_emp_demo]
104
+
105
+
> [!NOTE]
106
+
> An HTML report example of the current vuegen release is available [here][emp-html-demo].
107
+
108
+
## Web application deployment
109
+
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:
110
+
111
+
***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.
112
+
***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].
113
+
*[Stlite][stlite]: Run Streamlit apps directly in the browser with 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.
114
+
115
+
These options provide flexibility depending on whether the goal is online accessibility, lightweight execution, or local application distribution.
104
116
117
+
## Credits and acknowledgements
105
118
- Vuegen was developed by the [Multiomics Network Analytics Group (MoNA)][Mona] at the [Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain)][Biosustain].
106
119
- The vuegen logo was designed based on an image created by [Scriberia][scriberia] for The [Turing Way Community][turingway], which is shared under a CC-BY licence. The original image can be found at [Zenodo][zenodo-turingway].
107
120
@@ -110,14 +123,28 @@ If you have comments or suggestions about this project, you can [open an issue][
0 commit comments