|
4 | 4 | VueGen is a Python package that automates the creation of scientific reports. |
5 | 5 | </p> |
6 | 6 |
|
7 | | -| Information | Links | |
8 | | -| :-------------------- | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | |
9 | | -| **Package** | [][vuegen-pypi] [][vuegen-conda] [][vuegen-pypi] [][vuegen-docker-quay] [][mit-license]| |
10 | | -| **Documentation** | [][vuegen-docs] [](https://www.sphinx-doc.org/)  [![CC BY 4.0][cc-by-shield]][vuegen-license]| |
11 | | -| **Build** | [][ci-gh-action] [][ci-docs] | |
12 | | -| **Examples** | [][emp-html-demo] [][emp-st-demo] | |
13 | | -| **Discuss on GitHub** | [][issues] [][pulls] | |
14 | | -| **Cite** | [][vuegen-article] | |
| 7 | +| Information | Links | |
| 8 | +| :-------------------- | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | |
| 9 | +| **Package** | [][vuegen-pypi] [][vuegen-conda] [][vuegen-pypi] [][vuegen-docker-quay] [][mit-license] | |
| 10 | +| **Documentation** | [][vuegen-docs] [](https://www.sphinx-doc.org/)  [![CC BY 4.0][cc-by-shield]][vuegen-license] | |
| 11 | +| **Build** | [][ci-gh-action] [][ci-docs] | |
| 12 | +| **Examples** | [][emp-html-demo] [][emp-st-demo] | |
| 13 | +| **Discuss on GitHub** | [][issues] [][pulls] | |
| 14 | +| **Cite** | [][vuegen-article] | |
15 | 15 |
|
16 | 16 | ## Table of contents: |
17 | 17 |
|
|
26 | 26 | - [Credits and acknowledgements](#credits-and-acknowledgements) |
27 | 27 | - [Citation](#citation) |
28 | 28 | - [Contact and feedback](#contact-and-feedback) |
| 29 | +- [FAQ](#faq) |
29 | 30 |
|
30 | 31 | ## About the project |
31 | 32 |
|
@@ -130,7 +131,6 @@ vuegen --directory docs/example_data/Earth_microbiome_vuegen_demo_notebook --rep |
130 | 131 | > You can also specify the output directory with the `--output_directory` argumument, which defaults to the current working directory. |
131 | 132 | > See all available arguments with the `--help` option. |
132 | 133 |
|
133 | | - |
134 | 134 | ### Folder structure |
135 | 135 |
|
136 | 136 | 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. |
@@ -343,8 +343,8 @@ This case study focuses on the `APICall` component, which enables interaction wi |
343 | 343 | 🔗 [![Open in Colab][colab_badge]][colab_link_apicall] |
344 | 344 |
|
345 | 345 | > [!NOTE] |
346 | | -> A [configuration file example][apicall-config] for the apicall component is available in |
347 | | -the `docs/example_config_files` folder. |
| 346 | +> A [configuration file example][apicall-config] for the apicall component is available in |
| 347 | +> the `docs/example_config_files` folder. |
348 | 348 |
|
349 | 349 | ### 4. ChatBot Component |
350 | 350 |
|
@@ -375,8 +375,8 @@ Two API modes are supported: |
375 | 375 | This response structure is currently customized for an internal knowledge graph assistant, but VueGen is being actively developed to support more flexible and general-purpose response formats in future releases. |
376 | 376 |
|
377 | 377 | > [!NOTE] |
378 | | -> A [configuration file example][chatbot-config] for the chatbot component is available |
379 | | -in the `docs/example_config_files` folder. |
| 378 | +> A [configuration file example][chatbot-config] for the chatbot component is available |
| 379 | +> in the `docs/example_config_files` folder. |
380 | 380 |
|
381 | 381 | ## Web application deployment |
382 | 382 |
|
@@ -406,13 +406,13 @@ Full details for both licenses can be found in the [LICENSE][vuegen-license] fil |
406 | 406 |
|
407 | 407 | ## Contributing |
408 | 408 |
|
409 | | -VueGen is an open-source project, and we welcome contributions of all kinds via GitHub issues and pull requests. |
410 | | -You can report bugs, suggest improvements, propose new features, or implement changes. |
| 409 | +VueGen is an open-source project, and we welcome contributions of all kinds via GitHub issues and pull requests. |
| 410 | +You can report bugs, suggest improvements, propose new features, or implement changes. |
411 | 411 |
|
412 | | -We follow the [Conventional Commits][conventional-commits] specification for commit messages and use the |
| 412 | +We follow the [Conventional Commits][conventional-commits] specification for commit messages and use the |
413 | 413 | [changelog-from-release][changelog-from-release-repo] tool to automatically generate the [CHANGELOG](CHANGELOG.md). |
414 | 414 |
|
415 | | -Please follow the guidelines in the [CONTRIBUTING](CONTRIBUTING.md) file to ensure that your contribution is |
| 415 | +Please follow the guidelines in the [CONTRIBUTING](CONTRIBUTING.md) file to ensure that your contribution is |
416 | 416 | easily integrated into the project. |
417 | 417 |
|
418 | 418 | ## Credits and acknowledgements |
@@ -451,6 +451,27 @@ Ayala-Ruano, S., Webel, H., & Santos, A. (2025). _VueGen: Automating the generat |
451 | 451 |
|
452 | 452 | 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. |
453 | 453 |
|
| 454 | +## FAQ |
| 455 | + |
| 456 | +<details> |
| 457 | + <summary>Interactive Plots are not shown correctly</summary> |
| 458 | + |
| 459 | +1. Make sure to export your interactive plots from Plotly or Altair in JSON format, not as standalone HTML files. |
| 460 | +2. It is best to use VueGen within the environment you created your plots. If you gather it from many sources and |
| 461 | + see compatibility issues, consider recreating the plots in a single environment. Failing examples are more than welcome |
| 462 | + via [GitHub issues](https://github.com/Multiomics-Analytics-Group/vuegen/issues/new/choose) (you need a GitHub account). |
| 463 | + |
| 464 | +</details> |
| 465 | + |
| 466 | +<details> |
| 467 | + <summary>Old JSON Plots stopped working.</summary> |
| 468 | + |
| 469 | +We have seen differently structured JSON file from plotlyjs before version 3. If you |
| 470 | +have such old files and encouter issue, please consider sharing them via |
| 471 | +[GitHub issues](https://github.com/Multiomics-Analytics-Group/vuegen/issues/new/choose). |
| 472 | + |
| 473 | +</details> |
| 474 | + |
454 | 475 | [streamlit]: https://streamlit.io/ |
455 | 476 | [vuegen-pypi]: https://pypi.org/project/vuegen/ |
456 | 477 | [vuegen-conda]: https://anaconda.org/bioconda/vuegen |
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