EMP case study as example data (#45)

* 📝 Docs: Add EMP example data directory and config. Also, created jupyter notebook to replicate EMP results and generate report examples.

* 📝 Docs: Update README with extended description and the EMP example data paths

* 👷 CI(cdci.yml): Update the CI test with the EMP example data and add tests to create reports from a directory

* 🐛 move \n out of f-string (for older Python versions?)

* 🎨 order imports, specify relative paths

- in docs the full path will be set based on the directory

* ➕ add pyyaml as dependency

using 'poetry add pyyaml'

* 🐛 update installation of docs, do not autorun streamlit

* 🔥 remove old demo

* ✨ Feat(quarto_reportview.py and streamlit_reportview.py): Add footer with link to vuegen and mona on the html, revealjs, pdf, and streamlit reports

* ♻️ Refactor(vuegen_case_study_earth_microbiome.ipynb): add random seed to subsample code to create the same dataframe examples at every run

* 📝 Docs(README.md): Add acknowledgements section

---------

Co-authored-by: Henry Webel <[email protected]>

Author: sayalaruano

.github/workflows/cdci.yml

@@ -33,7 +33,8 @@ jobs:
       - name: Execute streamlit report
         run: |
           cd docs
-          vuegen --config example_data/MicW2Graph/report_config_micw2graph.yaml
+          vuegen --directory example_data/Earth_microbiome_vuegen_demo_notebook
+          vuegen --config example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml
   
   other-reports:
     name: Integration tests
@@ -56,33 +57,41 @@ jobs:
       - name: Execute streamlit report (to check)
         run: |
           cd docs
-          vuegen -c example_data/MicW2Graph/report_config_micw2graph.yaml
+          vuegen -dir example_data/Earth_microbiome_vuegen_demo_notebook
+          vuegen -c example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml
       # repeat for easier inspection on GitHub:
       - name: quarto html report
         run: |
           cd docs
-          vuegen -c example_data/MicW2Graph/report_config_micw2graph.yaml -rt html
+          vuegen -dir example_data/Earth_microbiome_vuegen_demo_notebook -rt html
+          vuegen -c example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml -rt html
       - name: quarto pdf report
         run: |
           cd docs
-          vuegen -c example_data/MicW2Graph/report_config_micw2graph.yaml -rt pdf
+          vuegen -dir example_data/Earth_microbiome_vuegen_demo_notebook -rt pdf
+          vuegen -c example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml -rt pdf
       - name: quarto docx report
         run: |
           cd docs
-          vuegen -c example_data/MicW2Graph/report_config_micw2graph.yaml -rt docx
+          vuegen -dir example_data/Earth_microbiome_vuegen_demo_notebook -rt docx
+          vuegen -c example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml -rt docx
       - name: quarto odt report
         run: |
           cd docs
-          vuegen -c example_data/MicW2Graph/report_config_micw2graph.yaml -rt odt
+          vuegen -dir example_data/Earth_microbiome_vuegen_demo_notebook -rt odt
+          vuegen -c example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml -rt odt
       - name: quarto revealjs report
         run: |
           cd docs
-          vuegen -c example_data/MicW2Graph/report_config_micw2graph.yaml -rt revealjs
+          vuegen -dir example_data/Earth_microbiome_vuegen_demo_notebook -rt revealjs
+          vuegen -c example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml -rt revealjs
       - name: quarto pptx report
         run: |
           cd docs
-          vuegen -c example_data/MicW2Graph/report_config_micw2graph.yaml -rt pptx
+          vuegen -dir example_data/Earth_microbiome_vuegen_demo_notebook -rt pptx
+          vuegen -c example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml -rt pptx
       - name: quarto jupyter report
         run: |
           cd docs
-          vuegen -c example_data/MicW2Graph/report_config_micw2graph.yaml -rt jupyter
+          vuegen -dir example_data/Earth_microbiome_vuegen_demo_notebook -rt jupyter
+          vuegen -c example_data/Earth_microbiome_vuegen_demo_notebook/Earth_microbiome_vuegen_demo_notebook_config.yaml -rt jupyter

.gitignore

@@ -127,7 +127,4 @@ docs/images/UML_diagrams/
 docs/images/Graphical_abstract/
 docs/images/Nfcore_module_figure
 docs/presentations/
-test.py
-docs/example_data/Earth_microbiome_vuegen_demo_notebook/
-docs/example_data/emp_deblur_100bp.subset_2k.rare_5000.biom
-docs/vuegen_case_study_earth_microbiome.ipynb
+test.py

README.md

@@ -11,10 +11,13 @@
 - [About the project](#about-the-project)
 - [Installation](#installation)
 - [Execution](#execution)
+- [Acknowledgements](#acknowledgements)
 - [Contact](#contact)
 
 ## About the project
-VueGen automates the creation of scientific reports based on a YAML configuration file.  This configuration file specifies the structure of the report, including sections, subsections, and various components such as plots, dataframes, markdown, and API calls. Reports can be generated in various formats, including documents (PDF, HTML, DOCX, ODT), presentations (PPTX, Reveal.js), notebooks (Jupyter) or [Streamlit](streamlit) web applications.
+VueGen automates the creation of reports based on a directory with plots, dataframes, and other files in different formats. A YAML configuration file is generated from the directory to define the structure of the report. Users can customize the report by modifying the configuration file, or they can create their own configuration file instead of passing a directory as input. 
+
+The configuration file specifies the structure of the report, including sections, subsections, and various components such as plots, dataframes, markdown, html, and API calls. Reports can be generated in various formats, including documents (PDF, HTML, DOCX, ODT), presentations (PPTX, Reveal.js), notebooks (Jupyter) or [Streamlit](streamlit) web applications.
 
 An overview of the VueGen workflow is shown in the figure below:
 
@@ -41,7 +44,7 @@ You can install the package for development from this repository by running the
 
 ```bash
 pip install -e path/to/vuegen # specify location 
-pip install -e . # in case you pwd is in the vuegen directory
+pip install -e . # in case your pwd is in the vuegen directory
 ```
 
 ### Quarto installation
@@ -67,27 +70,39 @@ quarto check
 
 ## Execution
 
-Run VueGen using a configuration file with the following command:
+Run VueGen using a directory with the following command:
 
 ```bash
 cd docs
-vuegen --config example_data/MicW2Graph/report_config_micw2graph.yaml --report_type streamlit
+vuegen --directory example_data/Earth_microbiome_vuegen_demo_notebook --report_type streamlit
 ```
 
 > 💡 If `vuegen` does not work, try `python -m vuegen` instead.
 
 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.
 
-It's also possible to provide a directory instead of a configuration file:
+It's also possible to provide a configuration file instead of a directory:
 
 ```bash
-vuegen --directory docs/example_data/MicW2Graph/ --report_type streamlit
+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.
 
+## Acknowledgements
+
+- Vuegen was developed by the [Multiomics Network Analytics Group (MoNA)][Mona] at the [Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain)][Biosustain].
+- 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].
+
 ## Contact
 If you have comments or suggestions about this project, you can [open an issue][issues] in this repository.
 
 [issues]: https://github.com/Multiomics-Analytics-Group/vuegen/issues/new
 [streamlit]: https://streamlit.io/ 
+[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
+
+