diff --git a/README.md b/README.md index a7aa4fd..1d29d66 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -## ![VueGen Logo](https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg) +## ![VueGen Logo](https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/HEAD/docs/images/logo/vuegen_logo.svg)

VueGen is a Python package that automates the creation of scientific reports. @@ -11,7 +11,7 @@ | **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] | -| **Cite** | [![DOI:10.1101/2025.03.05.641152](https://img.shields.io/badge/DOI-10.1101/2025.03.05.641152-B31B1B.svg)][vuegen-preprint] | +| **Cite** | [![DOI:10.1093/bioadv/vbaf149](https://img.shields.io/badge/DOI-10.1093/bioadv/vbaf149-074359.svg)][vuegen-article] | ## Table of contents: @@ -395,20 +395,23 @@ If you use VueGen in your research or publications, please cite it as follows: **APA:** -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 +Ayala-Ruano, S., Webel, H., & Santos, A. (2025). _VueGen: Automating the generation of scientific reports_. Bioinformatics Advances, vbaf149. https://doi.org/10.1093/bioadv/vbaf149 **BibTeX:** ```bibtex -@article{Ayala-Ruano2025VueGen, +@article{10.1093/bioadv/vbaf149, author = {Ayala-Ruano, Sebastian and Webel, Henry and Santos, Alberto}, title = {VueGen: Automating the generation of scientific reports}, - journal = {bioRxiv}, + journal = {Bioinformatics Advances}, + pages = {vbaf149}, year = {2025}, - doi = {10.1101/2025.03.05.641152}, - publisher = {Cold Spring Harbor Laboratory}, - url = {https://www.biorxiv.org/content/10.1101/2025.03.05.641152}, - eprint = {https://www.biorxiv.org/content/10.1101/2025.03.05.641152.full.pdf} + month = {06}, + issn = {2635-0041}, + doi = {10.1093/bioadv/vbaf149}, + url = {https://doi.org/10.1093/bioadv/vbaf149}, + eprint = {https://academic.oup.com/bioinformaticsadvances/advance-article-pdf/doi/ + 10.1093/bioadv/vbaf149/63568410/vbaf149.pdf}, } ``` @@ -433,7 +436,7 @@ We appreciate your feedback! If you have any comments, suggestions, or run into [config-chatbot]: https://github.com/Multiomics-Analytics-Group/vuegen/blob/main/docs/example_config_files/Chatbot_example_config.yaml [issues]: https://github.com/Multiomics-Analytics-Group/vuegen/issues [pulls]: https://github.com/Multiomics-Analytics-Group/vuegen/pulls -[vuegen-preprint]: https://doi.org/10.1101/2025.03.05.641152 +[vuegen-article]: https://doi.org/10.1093/bioadv/vbaf149 [quarto]: https://quarto.org/ [quarto-cli-pypi]: https://pypi.org/project/quarto-cli/ [quarto-cli]: https://quarto.org/docs/get-started/ diff --git a/docs/conf.py b/docs/conf.py index a0e5370..e2770d1 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -99,8 +99,8 @@ # https://github.com/executablebooks/MyST-NB/blob/master/docs/conf.py # html_title = "" html_theme = "sphinx_book_theme" -html_logo = "https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg" -html_favicon = "https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg" +html_logo = "images/logo/vuegen_logo.svg" +html_favicon = "images/logo/vuegen_logo_small.svg" html_theme_options = { "github_url": "https://github.com/Multiomics-Analytics-Group/vuegen", "repository_url": "https://github.com/Multiomics-Analytics-Group/vuegen", diff --git a/docs/images/logo/vuegen_logo.png b/docs/images/logo/vuegen_logo.png new file mode 100644 index 0000000..114c5fb Binary files /dev/null and b/docs/images/logo/vuegen_logo.png differ diff --git a/docs/images/vuegen_logo.svg b/docs/images/logo/vuegen_logo.svg similarity index 87% rename from docs/images/vuegen_logo.svg rename to docs/images/logo/vuegen_logo.svg index 13d1e00..c9860ea 100644 --- a/docs/images/vuegen_logo.svg +++ b/docs/images/logo/vuegen_logo.svg @@ -6,15 +6,15 @@ id="Layer_1" x="0px" y="0px" - viewBox="0 0 350.00011 300.00003" + viewBox="0 0 282.00009 276.00003" xml:space="preserve" - sodipodi:docname="vuegen_logo.svg" + sodipodi:docname="vuegen_logo_v2.svg" inkscape:version="1.3.2 (091e20e, 2023-11-25)" - inkscape:export-filename="vuegen_logo.png" - inkscape:export-xdpi="278.23743" - inkscape:export-ydpi="278.23743" - width="350" - height="300" + inkscape:export-filename="vuegen_logo_v2.png" + inkscape:export-xdpi="340.42554" + inkscape:export-ydpi="340.42554" + width="282" + height="276" xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape" xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd" xmlns="http://www.w3.org/2000/svg" @@ -28,15 +28,15 @@ inkscape:pageopacity="0.0" inkscape:pagecheckerboard="0" inkscape:deskcolor="#d1d1d1" - inkscape:zoom="1.2685346" - inkscape:cx="75.677872" - inkscape:cy="267.23749" - inkscape:window-width="1440" - inkscape:window-height="847" - inkscape:window-x="0" + inkscape:zoom="2.5370692" + inkscape:cx="168.69859" + inkscape:cy="132.04212" + inkscape:window-width="1920" + inkscape:window-height="1027" + inkscape:window-x="1440" inkscape:window-y="25" inkscape:window-maximized="1" - 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"vuegen/main/docs/images/vuegen_logo.svg" + "vuegen/HEAD/docs/images/logo/vuegen_logo.svg" ) TIMEOUT: int = 60 diff --git a/tests/report_examples/Basic_example_vuegen_demo_notebook/html/quarto_report/quarto_report.qmd b/tests/report_examples/Basic_example_vuegen_demo_notebook/html/quarto_report/quarto_report.qmd index 0a3a5e3..ece0fa8 100644 --- a/tests/report_examples/Basic_example_vuegen_demo_notebook/html/quarto_report/quarto_report.qmd +++ b/tests/report_examples/Basic_example_vuegen_demo_notebook/html/quarto_report/quarto_report.qmd @@ -28,7 +28,7 @@ include-after-body: