diff --git a/.gitignore b/.gitignore index b05281e..158faf3 100644 --- a/.gitignore +++ b/.gitignore @@ -127,4 +127,6 @@ docs/images/UML_diagrams/ docs/images/Graphical_abstract/ docs/images/Nfcore_module_figure docs/presentations/ +docs/example_data/Earth_microbiome_vuegen_demo_notebook_test/ +docs/vuegen_case_study_earth_microbiome test.ipynb test.py \ No newline at end of file diff --git a/README.md b/README.md index 808ce35..c0aeac2 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ -![VueGen Logo](docs/images/vuegen_logo.svg) +![VueGen Logo](https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_logo.svg) -----------------

VueGen is a Python library that automates the creation of scientific reports. @@ -26,7 +26,7 @@ An overview of the VueGen workflow is shown in the figure below: VueGen overview

--> -![VueGen Abstract](docs/images/vuegen_graph_abstract.png) +![VueGen Abstract](https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_graph_abstract.png) Also, the class diagram for the project is presented below to illustrate the architecture and relationships between classes: @@ -36,33 +36,32 @@ Also, the class diagram for the project is presented below to illustrate the arc

--> -![VueGen Class Diagram](docs/images/vuegen_classdiagram_noattmeth.png) +![VueGen Class Diagram](https://raw.githubusercontent.com/Multiomics-Analytics-Group/vuegen/main/docs/images/vuegen_classdiagram_noattmeth.png) ## Installation -You can install the package for development from this repository by running the following command: +Vuegen is available on [PyPI][vuegen-pypi] and can be installed using pip: + +```bash +pip install vuegen +``` + +You can also install the package for development from this repository by running the following command: ```bash pip install -e path/to/vuegen # specify location pip install -e . # in case your pwd is in the vuegen directory ``` -This will both install `quarto` and `streamlit` as our backends for report generation. - -### Verify quarto installation +### Quarto installation -Test your quarto installation by running the following command: +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: ```bash quarto check ``` -If you use conda a conda environement you can install quatro from the conda-forge channel -in case it did not work. - -```bash -conda install -c conda-forge quarto -``` +If quarto is not installed, you can download the command-line interface from the [Quarto website][quarto-cli] for your operating system. ## Execution @@ -83,7 +82,15 @@ It's also possible to provide a configuration file instead of a directory: vuegen --config example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml --report_type streamlit ``` -The current report types are streamlit, html, pdf, docx, odt, revealjs, pptx, and jupyter. +The current report types supported by VueGen are: +* Streamlit +* HTML +* PDF +* DOCX +* ODT +* Reveal.js +* PPTX +* Jupyter ## Acknowledgements @@ -95,10 +102,15 @@ If you have comments or suggestions about this project, you can [open an issue][ [issues]: https://github.com/Multiomics-Analytics-Group/vuegen/issues/new [streamlit]: https://streamlit.io/ +[vuegen-pypi]: https://pypi.org/project/vuegen/ +[quarto]: https://quarto.org/ +[quarto-cli-pypi]: https://pypi.org/project/quarto-cli/ +[quarto-cli]: https://quarto.org/docs/get-started/ [Mona]: https://multiomics-analytics-group.github.io/ [Biosustain]: https://www.biosustain.dtu.dk/ [scriberia]: https://www.scriberia.co.uk/ [turingway]: https://github.com/the-turing-way/the-turing-way [zenodo-turingway]: https://zenodo.org/records/3695300 +[issues]: https://github.com/Multiomics-Analytics-Group/vuegen/issues/new diff --git a/docs/images/vuegen_classdiagram_noattmeth.png b/docs/images/vuegen_classdiagram_noattmeth.png index e9eeaa0..b7c578d 100644 Binary files a/docs/images/vuegen_classdiagram_noattmeth.png and b/docs/images/vuegen_classdiagram_noattmeth.png differ diff --git a/docs/images/vuegen_graph_abstract.png b/docs/images/vuegen_graph_abstract.png index caa114f..7d7fe84 100644 Binary files a/docs/images/vuegen_graph_abstract.png and b/docs/images/vuegen_graph_abstract.png differ diff --git a/docs/images/vuegen_logo.png b/docs/images/vuegen_logo.png index c753e09..5fdc22b 100644 Binary files a/docs/images/vuegen_logo.png and b/docs/images/vuegen_logo.png differ diff --git a/docs/images/vuegen_logo.svg b/docs/images/vuegen_logo.svg index a1df622..fff2065 100644 --- a/docs/images/vuegen_logo.svg +++ b/docs/images/vuegen_logo.svg @@ -11,8 +11,8 @@ sodipodi:docname="vuegen_logo.svg" inkscape:version="1.3.2 (091e20e, 2023-11-25)" inkscape:export-filename="vuegen_logo.png" - inkscape:export-xdpi="100" - inkscape:export-ydpi="100" + inkscape:export-xdpi="192" + inkscape:export-ydpi="192" width="350" height="300" xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape" @@ -28,15 +28,15 @@ inkscape:pageopacity="0.0" inkscape:pagecheckerboard="0" inkscape:deskcolor="#d1d1d1" - inkscape:zoom="0.89698939" - inkscape:cx="146.04409" - inkscape:cy="124.86212" + inkscape:zoom="1.2685346" + inkscape:cx="152.14406" + inkscape:cy="195.89533" inkscape:window-width="1200" - inkscape:window-height="847" - inkscape:window-x="1201" - inkscape:window-y="52" + inkscape:window-height="932" + inkscape:window-x="1200" + inkscape:window-y="25" inkscape:window-maximized="0" - inkscape:current-layer="g410" + inkscape:current-layer="Layer_1" showgrid="true" inkscape:document-units="mm">VueGen - +