📝 Updated main and docs README files and remove docs/sections_readme folder

Author: sayalaruano

README.md

@@ -233,7 +233,7 @@ More information regarding the app and builds can be found in the
 
 VueGen’s functionality is demonstrated through two case studies:
 
-**1. Predefined Directory**
+### 1. Predefined Directory
 
 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.
 
@@ -242,7 +242,7 @@ This introductory case study uses a predefined directory with plots, dataframes,
 > [!NOTE]
 > The [configuration file][predef-dir-config] is available in the `docs/example_config_files` folder, and the [directory][predef-dir] with example data is in the `docs/example_data` folder.
 
-**2. Earth Microbiome Project Data**
+### 2. Earth Microbiome Project Data
 
 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.
 
@@ -252,7 +252,7 @@ This advanced case study demonstrates the application of VueGen in a real-world
 > The EMP case study is available online as [HTML][emp-html-demo] and [Streamlit][emp-st-demo] reports.
 > The [configuration file][emp-config] is available in the `docs/example_config_files` folder, and the [directory][emp-dir] with example data is in the `docs/example_data` folder.
 
-**3. ChatBot Component**
+### 3. ChatBot Component
 
 This case study highlights VueGen’s capability to embed a chatbot component into a report subsection, 
 enabling interactive conversations inside the report.
@@ -285,9 +285,17 @@ to support more flexible and general-purpose response formats in future releases
 
 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:
 
-- **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.
-- **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].
-- **Stlite**: Run Streamlit apps directly in the browser with [stlite][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.
+### 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.
+
+### 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].
+
+### Stlite
+
+Run Streamlit apps directly in the browser with [stlite][stlite_repo], 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.
 
 These options provide flexibility depending on whether the goal is online accessibility, lightweight execution, or local application distribution.
 
@@ -361,7 +369,7 @@ We appreciate your feedback! If you have any comments, suggestions, or run into
 [emp-config]: https://github.com/Multiomics-Analytics-Group/vuegen/blob/main/docs/example_config_files/Earth_microbiome_vuegen_demo_notebook_config
 [emp-dir]: https://github.com/Multiomics-Analytics-Group/vuegen/blob/main/docs/example_data/Earth_microbiome_vuegen_demo_notebook
 [st-cloud]: https://streamlit.io/cloud
-[stlite]: https://github.com/whitphx/stlite
+[stlite_repo]: https://github.com/whitphx/stlite
 [st-forum-exe]: https://discuss.streamlit.io/t/streamlit-deployment-as-an-executable-file-exe-for-windows-macos-and-android/6812
 [Mona]: https://multiomics-analytics-group.github.io/
 [Biosustain]: https://www.biosustain.dtu.dk/

docs/README.md

@@ -2,9 +2,9 @@
 
 In order to build the docs you need to 
 
-  1. install sphinx and additional support packages
-  2. build the package reference files
-  3. run sphinx to create a local html version
+  1. Install sphinx and additional support packages
+  2. Build the package reference files
+  3. Run sphinx to create a local html version
 
 The documentation is build using readthedocs automatically.
 
@@ -31,7 +31,9 @@ sphinx-apidoc --force --implicit-namespaces --module-first -o reference ../src/v
 sphinx-build -n -W --keep-going -b html ./ ./_build/
 ```
 
-## Include repo README.md into docs
+## Include repo README into docs
+
+The README is included in the `Overview` section of the docs. We created a [Python script](https://github.com/Multiomics-Analytics-Group/vuegen/blob/split-readme-docs/docs/split_readme.py) to split the README sections into separate md files, stored in `docs/sections_readme`. The `index.md` file contains the structure of the docs with the generated sections and additional information.
 
 Relative links are used in the main README, which need to be resolved when building. It's
 possible to include the a `relative-docs` option if one uses `index.md` ([see docs](https://myst-parser.readthedocs.io/en/latest/faq/index.html#include-a-file-from-outside-the-docs-folder-like-readme-md)). This does not work