Add image directory, modify image creation with sphinx syntax

Author: katharinapaul2403

docs/source/conf.py

@@ -74,11 +74,13 @@
 ## Viewcode
 extensions.append("sphinx.ext.viewcode")
 
+## View figures 
+extensions.append("sphinx_subfigure")
+
 ## Copy Button
 extensions.append("sphinx_copybutton")
 
 ## BibTeX
-extensions.append("myst_parser")
 extensions.append("sphinxcontrib.bibtex")
 bibtex_bibfiles = ["references.bib"]
 

docs/source/index.md

@@ -1,4 +1,4 @@
-```{include} ../../README.md
+```{include} ./user_guide/introduction.md
 ```
 
 ```{toctree}
@@ -8,7 +8,7 @@
 
 user_guide/installation
 user_guide/getting-started
-user_guide/CLI-interface
+user_guide/command-line-interface
 user_guide/python-interface
 user_guide/jupyter-interface
 ```

docs/source/user_guide/command-line-interface.md

@@ -1,5 +1,5 @@
 
-# Using the Command Line Interface (CLI)
+# Command Line Interface (CLI)
 
 ## Initialize Project Repository
 

docs/source/user_guide/images/RDM-architecture-poster.png

@@ -29,16 +29,50 @@ CADET-RDM projects are structured into two distinct repositories.
 1. The **project repository** that contains the input data, code, software and configurations to execute the computations. The output repository is a directory within the project repository.
 2. The **output repository** that contains the results of these computations, including all calculations, models and figures created by running the project code. Also stored in the output directory is the metadata used to create the specific result. This includes e.g. the software versions and requirements.
 
-<img src="RDM-structure.png" alt="RDM-project architecture" width="400"/>
+
+```{subfigure} 
+   :layout-sm:
+   :gap: 8px
+   :subcaptions: above
+   :name: myfigure
+   :class-grid: outline
+
+   .. image:: ./images/RDM-architecture-poster.png
+      :alt: Image A
+```
+
+```{image} images/RDM-architecture-poster.png
+:alt: Grapes on a vineyard
+:width: 200px
+:align: center
+```
+
+<img src="./images/RDM-architecture-poster.png" alt="RDM-project-architecture" width="200"/>
+
 
 Both the **project** and the **output** repository are their own git repositories. The commit architecture of CADET-RDM allows for easy tracking and reproducing of results and their respective project code.
 
 ## RDM commit architecture
 
 Every run of the project code creates a new output branch (*result branch*) in the **output directory**. The repository on this new branch uniquely contains the files created by the execution of the project code. <br> At the same time, for every run of the project code the `run_history` directory on the master branch of the output repository is updated. This directory is unique to the master branch and contains the metadata and software specifications for every branch in the output repository. This directory also links the results in the output branch to the corresponding commit in the project repository used to create them. For transparency and easy accessibility, the most important specifications for every result branch are also documented in the `log.tsv` on the master branch of the output repository.
+
+```{subfigure} AB
+:layout-sm: AB
+:gap: 8px
+:class-grid: outline
+
+    ```{image} images/RDM-project-commits.png
+    :alt: Image A
+    ```
+
+    ```{image} images/RDM-output-commits.png
+    :alt: Image B
+    ```
+```
+
 <p float="left">
-  <img src="RDM-project-commits.png" alt="Bild 1" width="200"/>
-  <img src="RDM-output-commits.png" alt="Bild 2" width="295"/>
+  <img src="./images/RDM-project-commits.png" alt="RDM-project-commits" width="200"/>
+  <img src="./images/RDM-output-commits.png" alt="RDM-output-commits" width="295"/>
 </p>
 
 Because of this simultanious log of the metadata and the environment used to create a specific output, results can be reproduced easily.