From 363705dfaf3973be3c2ca3f9c0e70bc6db63cf09 Mon Sep 17 00:00:00 2001
From: Alfin Johny <alfin.johny@tum.de>
Date: Tue, 21 Jan 2025 11:32:53 +0100
Subject: [PATCH] Fix missing API interface section in documentation

---
 docs/contact.md                               |   2 +-
 ...nal_software.md => additional-software.md} |   0
 docs/documentation/analysis.md                |  12 +-
 docs/documentation/libraries.md               |  26 +--
 docs/documentation/overview.md                |   4 +-
 docs/get-involved/testing.md                  |   3 +-
 docs/index.md                                 |   2 +-
 mkdocs.yml                                    | 186 +++++++++++++++---
 8 files changed, 184 insertions(+), 51 deletions(-)
 rename docs/documentation/{additional_software.md => additional-software.md} (100%)

diff --git a/docs/contact.md b/docs/contact.md
index 6db7a6c..c36684a 100644
--- a/docs/contact.md
+++ b/docs/contact.md
@@ -2,4 +2,4 @@
 
 You want to get in touch with us to clarify your questions or share your feedback about UNICADO? Awesome! Feel free to write us a mail, and we'll respond to your inquiry as soon as possible.
 
-:email: **E-Mail:** [contact@unicado.io](mailto:contact@unicado.io)
+:email: **E-Mail:** [contacts@unicado.io](mailto:contacts@unicado.io)
diff --git a/docs/documentation/additional_software.md b/docs/documentation/additional-software.md
similarity index 100%
rename from docs/documentation/additional_software.md
rename to docs/documentation/additional-software.md
diff --git a/docs/documentation/analysis.md b/docs/documentation/analysis.md
index a8d3966..8d8f46d 100644
--- a/docs/documentation/analysis.md
+++ b/docs/documentation/analysis.md
@@ -22,7 +22,7 @@ lift mach numbers.
 
 |Module Version|Language|License|Documentation|
 |:---:|:---:|:---:|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](aircraft-design/aerodynamic_analysis/doc/content/index.md)|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](../documentation/aircraft-design/aerodynamic_analysis/doc/content/index.md)|
 
 ---
 
@@ -39,7 +39,7 @@ For the user, possible changes in the module run configuration can be made in th
 
 |Module Version|Language|License|Documentation|
 |:---:|:---:|:---:|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](aircraft-design/mission_analysis/doc/content/index.md)|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](../documentation/aircraft-design/mission_analysis/doc/content/index.md)|
 
 ---
 
@@ -50,7 +50,7 @@ The `weight_and_balance_analysis` module calculates sub-masses and total masses
 
 |Module Version|Language|License|Documentation|
 |:---:|:---:|:---:|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](aircraft-design/weight_and_balance_analysis/doc/content/index.md)|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](../documentation/aircraft-design/weight_and_balance_analysis/doc/content/index.md)|
 
 ---
 
@@ -67,7 +67,7 @@ The parameters comprised in this XML file can have different attributes as e.g.
 
 |Module Version|Language|License|Documentation|
 |:---:|:---:|:---:|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](aircraft-design/ecological_assessment/doc/content/index.md)|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](../documentation/aircraft-design/ecological_assessment/doc/content/index.md)|
 
 ---
 
@@ -78,7 +78,7 @@ The module `calculatePerformance` is used to evaluate the mission performance of
 
 |Module Version|Language|License|Documentation|
 |:---:|:---:|:---:|---|
-|2.1.0|:simple-cplusplus:| GPLv3 |[Link](aircraft-design/performance_assessment/doc/content/index.md)|
+|2.1.0|:simple-cplusplus:| GPLv3 |[Link](../documentation/aircraft-design/performance_assessment/doc/content/index.md)|
 
 ---
 
@@ -94,6 +94,6 @@ Direct costs include all expenses incurred in operating and financing the aircra
 
 |Module Version|Language|License|Documentation|
 |:---:|:---:|:---:|---|
-|2.1.0|:simple-python: |GPLv3|[Link](aircraft-design/cost_estimation/doc/content/index.md)|
+|2.1.0|:simple-python: |GPLv3|[Link](../documentation/aircraft-design/cost_estimation/doc/content/index.md)|
 
 ---
diff --git a/docs/documentation/libraries.md b/docs/documentation/libraries.md
index 2be0912..c26d397 100644
--- a/docs/documentation/libraries.md
+++ b/docs/documentation/libraries.md
@@ -27,7 +27,7 @@ It has helper functions to extract and interpolate data of provided airfoil pola
 
 |Module Version|Language|License|Documentation|Dependencies|
 |:---:|:---:|:---:|---|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/aerodynamics/content/index.md)|-|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](documentation/libraries/aerodynamics/doc/content/index.md)|-|
 
 ---
 
@@ -39,7 +39,7 @@ The modularity and flexibility is achieved by using the high performance [Comput
 
 |Module Version|Language|License|Documentation|Dependencies|
 |:---:|:---:|:---:|---|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/aircraftGeometry2/content/index.md)| [Eigen3](https://eigen.tuxfamily.org/index.php?title=Main_Page), [CGAL](https://www.cgal.org/)|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/aircraftGeometry2/doc/content/index.md)| [Eigen3](https://eigen.tuxfamily.org/index.php?title=Main_Page), [CGAL](https://www.cgal.org/)|
 
 ---
 
@@ -50,7 +50,7 @@ The **airfoils** libary provides a database for different airfoils.
 
 |Module Version|Language|License|Documentation|Dependencies|
 |:---:|:---:|:---:|---|---|
-|1.0.0|:simple-cplusplus: |GPLv3|[Link](libraries/airfoils/content/index.md)|-|
+|1.0.0|:simple-cplusplus: |GPLv3|[Link](libraries/airfoils/doc/content/index.md)|-|
 
 ---
 
@@ -62,7 +62,7 @@ It uses a simple XML library, namely *tinyxml*, to read and parse the XML files.
 
 |Module Version|Language|License|Documentation|Dependencies|
 |:---:|:---:|:---:|---|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/aixml/content/index.md)|-|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/aixml/doc/content/index.md)|-|
 
 ---
 
@@ -74,7 +74,7 @@ You can set different atmospheric conditions (e.g. *ISA+25*) and calculate the p
 
 |Module Version|Language|License|Documentation|Dependencies|
 |:---:|:---:|:---:|---|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/atmosphere/content/index.md)||
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/atmosphere/doc/content/index.md)||
 
 ---
 
@@ -85,7 +85,7 @@ The **blackboxTest** library provides an interface to run a complete module with
 
 |Module Version|Language|License|Documentation|Dependencies|
 |:---:|:---:|:---:|---|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/blackboxTest/content/index.md)|[googleTest](https://google.github.io/googletest/)|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/blackboxTest/doc/content/index.md)|[googleTest](https://google.github.io/googletest/)|
 
 ---
 
@@ -98,7 +98,7 @@ The engine decks can originate from different softwaretools as long as they prov
 
 |Module Version|Language|License|Documentation|Dependencies|
 |:---:|:---:|:---:|---|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/engine/content/index.md)|-|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/engine/doc/content/index.md)|-|
 
 ---
 
@@ -118,7 +118,7 @@ It has helper functions to extract and interpolate data of the results from the
 
 |Module Version|Language|License|Documentation|Dependencies|
 |:---:|:---:|:---:|---|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/liftingLineInterface/content/index.md)|-|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/liftingLineInterface/doc/content/index.md)|-|
 
 ---
 
@@ -131,7 +131,7 @@ The library gives a template how modules should be structured and gives helpers
 
 |Module Version|Language|License|Documentation|Dependencies|
 |:---:|:---:|:---:|---|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/moduleBasics/content/index.md)|-|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/moduleBasics/doc/content/index.md)|-|
 
 ---
 
@@ -142,7 +142,7 @@ This library provides standardized UNICADO data preprocessing, run, and postproc
 
 |Module Version|Language|License|Documentation|Dependencies|
 |:---:|:---:|:---:|---|---|
-|1.0.0|:simple-python: |GPLv3|[Link](libraries/pymodulepackage/content/index.md)|-|
+|1.0.0|:simple-python: |GPLv3|[Link](libraries/pymodulepackage/doc/content/index.md)|-|
 
 ---
 
@@ -154,7 +154,7 @@ In provides custom output streams, which automatically handle the log files and
 
 |Module Version|Language|License|Documentation|Dependencies|
 |:---:|:---:|:---:|---|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/runtimeInfo/content/index.md)|-|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/runtimeInfo/doc/content/index.md)|-|
 
 ---
 
@@ -167,7 +167,7 @@ The library can handle *UNIX* and *Windows* systems alike.
 
 |Module Version|Language|License|Documentation|Dependencies|
 |:---:|:---:|:---:|---|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/standardFiles/content/index.md)|-|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/standardFiles/doc/content/index.md)|-|
 
 !!! warning
     Some functions of this library are a bit outdated! When using this library, please look first at the wonderful [STL :octicons-link-external-16:](https://en.cppreference.com/w/) whether the function you are seeking is already there.
@@ -196,4 +196,4 @@ In addition, it defines some common **constants** which are useful for calculati
 
 |Module Version|Language|License|Documentation|Dependencies|
 |:---:|:---:|:---:|---|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/unitConversion/content/index.md)|-|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](libraries/unitConversion/doc/content/index.md)|-|
diff --git a/docs/documentation/overview.md b/docs/documentation/overview.md
index 4365e8a..6baf4fe 100644
--- a/docs/documentation/overview.md
+++ b/docs/documentation/overview.md
@@ -25,8 +25,8 @@ glightbox: false
 
     Here you can found different designed aircraft. The designs are made using the **UNICADO** workflow and are generally in a *valid* and *converged* state.
 
-!!! note
-    This repository will be translated to a actual database in the future!
+๐Ÿ”” This repository will be translated to a actual database in the future!
+   
 
 - [:simple-gitlab: Engines :octicons-link-external-16:](https://git.rwth-aachen.de/unicado/engines):
 
diff --git a/docs/get-involved/testing.md b/docs/get-involved/testing.md
index 5f1fe4a..0b010da 100644
--- a/docs/get-involved/testing.md
+++ b/docs/get-involved/testing.md
@@ -76,8 +76,7 @@ Then you can execute the test
 #### Unit tests
 These tests involve systematically checking the lowest-level component, like a function, within a module.
 
-!!! note 
-    This is currently only implemented for the module/target **propulsionDesign**. 
+๐Ÿ”” This is currently only implemented for the module/target **propulsionDesign**. 
 
 To run the test, you need to add the flag when configuring your module
 === "Windows"
diff --git a/docs/index.md b/docs/index.md
index fad3ff0..f527d9b 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -61,7 +61,7 @@ Get an overview of the tools and libraries.
 
 Get insights on how to contribute and develop.
 
-[:octicons-arrow-right-24: Get involved](developer/developer-installation.md)
+[:octicons-arrow-right-24: Get involved](get-involved/developer-installation.md)
 </div>
 
 <div class="grid-item card" markdown="1">
diff --git a/mkdocs.yml b/mkdocs.yml
index 5f2c785..73de85c 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -24,8 +24,6 @@ markdown_extensions:
   - attr_list                             # Allows adding HTML attributes to Markdown elements (like classes).
   - admonition                            # Enables note/warning/admonition boxes with custom styling.
   - md_in_html                            # Allows writing Markdown inside HTML tags for flexibility.
-  - toc:                                  # Adds a table of contents (ToC) for each page.
-      permalink: '#'                      # Adds a clickable '#' for each ToC heading, allowing direct links.
   - pymdownx.tabbed:                      # Enables tabbed content blocks, allowing content to be organized in tabs.
       alternate_style: true               # Uses an alternate style for tabbed blocks.
   - pymdownx.emoji:                       # Adds support for emojis using the Material themeโ€™s emoji set.
@@ -65,12 +63,76 @@ plugins:
   - search
   - mkdoxy:
       projects:
-        aircraft_design:
-          doxygen_bin: "/path/to/doxygen"  # Update with the correct path
-          src-dirs: docs/documentation/aircraft_design/
+        propulsion_design:
+          src-dirs: ../aircraft-design/propulsion_design/
           full-doc: True
+          output: docs/propulsion_design
           doxy-cfg:
-            FILE_PATTERNS: "*.cpp *.h *.md *.png *.svg" # Include .cpp, .h, .md, .png, .svg files in the documentation
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
+        initial_sizing:
+          src-dirs: ../aircraft-design/initial_sizing/
+          full-doc: true
+          output: docs/initial_sizing
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
+        create_mission_xml:
+          src-dirs: ../aircraft-design/create_mission_xml/
+          full-doc: True
+          output: docs/create_mission_xml
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
+        fuselage_design:
+          src-dirs: ../aircraft-design/fuselage_design/
+          full-doc: true
+          output: docs/fuselage_design
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
+        wing_design:
+          src-dirs: ../aircraft-design/wing_design/
+          full-doc: True
+          output: docs/wing_design
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
+        empennage_design:
+          src-dirs: ../aircraft-design/empennage_design/
+          full-doc: true
+          output: docs/empennage_design
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
+        tank_design:
+          src-dirs: ../aircraft-design/tank_design/
+          full-doc: true
+          output: docs/tank_design
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
+        landing_gear_design:
+          src-dirs: ../aircraft-design/landing_gear_design/
+          full-doc: true
+          output: docs/landing_gear_design
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
+        systems_design:
+          src-dirs: ../aircraft-design/systems_design/
+          full-doc: true
+          output: docs/systems_design
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
             RECURSIVE: True
             EXTRACT_ALL: YES
   - glightbox                             # Plugin for lightbox-style image and content viewing.
@@ -83,16 +145,7 @@ theme:
   custom_dir: overrides                      # Directory for custom files (like footer).
   # Theme colors configuration
   palette:
-   - scheme: default
-     toggle:
-       icon: material/brightness-7
-       name: Switch to dark mode
-     primary: blue grey
-     accent: red
    - scheme: slate
-     toggle:
-       icon: material/brightness-3
-       name: Switch to light mode
      primary: green
      accent: red
 
@@ -101,7 +154,6 @@ theme:
     - navigation.instant
     - navigation.top
     - navigation.tabs
-    - toc.integrate  # This integrates the table of contents into the sidebar
 
   # Additional links (social) to display in the header
   extra:
@@ -120,27 +172,102 @@ nav:                                      # Customizes the main navigation struc
     - Cleared for Take-Off: download/takeoff.md  # Link to the takeoff/getting started page.
   - Tutorials:
     - Standalone Workflow: tutorials/standalone.md  # Link to the standalone tutorial page.
-    - Separate Tool Execution: tutorials/separate-tool-execution.md  # Link to the separate tool execution tutorial page.
+    - Separate Tool Execution: tutorials/seperate-tool-execution.md  # Link to the separate tool execution tutorial page.
+    - Changing Design Specifications: tutorials/changing-design-specifications.md
   - Documentation:                        # Top-level item for documentation.
     - Overview: documentation/overview.md   # Overview of modules.
     - Aircraft Design:
       - Sizing:  
-          - Overview: documentation/sizing.md # Link to aircraft sizing documentation.
-          - Initial Sizing: documentation/aircraft-design/initial_sizing/doc/content/index.md
-          - Create Mission XML: documentation/aircraft-design/create_mission_xml/doc/content/index.md
-          - Fuselage Design: documentation/aircraft-design/fuselage_design/doc/content/index.md
-          - Wing Design: documentation/aircraft-design/wing_design/doc/content/index.md
-          - Empennage Design: documentation/aircraft-design/empennage_design/doc/content/index.md
-          - Tank Design: documentation/aircraft-design/tank_design/doc/content/index.md
+          - Modules: documentation/sizing.md # Link to aircraft sizing documentation.
+          - Initial Sizing: 
+            - Introduction: documentation/aircraft-design/initial_sizing/doc/content/index.md
+            - Getting Staretd: documentation/aircraft-design/initial_sizing/doc/content/getting-started.md
+            - API Reference:
+              - initial_sizing/classes.md
+              - initial_sizing/namespaces.md
+              - initial_sizing/files.md
+              - initial_sizing/functions.md
+              - initial_sizing/pages.md             
+          - Create Mission XML:
+            - Introduction: documentation/aircraft-design/create_mission_xml/doc/content/index.md
+            - Getting Staretd: documentation/aircraft-design/create_mission_xml/doc/content/getting-started.md
+            - API Reference:
+              - create_mission_xml/classes.md
+              - create_mission_xml/namespaces.md
+              - create_mission_xml/files.md
+              - create_mission_xml/functions.md
+              - create_mission_xml/pages.md 
+          - Fuselage Design: 
+            - Introduction: documentation/aircraft-design/fuselage_design/doc/content/index.md
+            - Getting Staretd: documentation/aircraft-design/fuselage_design/doc/content/getting-started.md
+            - API Reference:
+              - fuselage_design/classes.md
+              - fuselage_design/namespaces.md
+              - fuselage_design/files.md
+              - fuselage_design/functions.md
+              - fuselage_design/pages.md 
+          - Wing Design:
+            - Introduction: documentation/aircraft-design/wing_design/doc/content/index.md
+            - Getting Staretd: documentation/aircraft-design/wing_design/doc/content/getting-started.md
+            - API Reference:
+              - wing_design/classes.md
+              - wing_design/namespaces.md
+              - wing_design/files.md
+              - wing_design/functions.md
+              - wing_design/pages.md           
+          - Empennage Design: 
+            - Introduction: documentation/aircraft-design/empennage_design/doc/content/index.md
+            - Getting Staretd: documentation/aircraft-design/empennage_design/doc/content/getting-started.md
+            - API Reference:
+              - empennage_design/classes.md
+              - empennage_design/namespaces.md
+              - empennage_design/files.md
+              - empennage_design/functions.md
+              - empennage_design/pages.md 
+          - Tank Design: 
+            - Introduction: documentation/aircraft-design/tank_design/doc/content/index.md
+            - Getting Staretd: documentation/aircraft-design/tank_design/doc/content/getting-started.md
+            - API Reference:
+              - tank_design/classes.md
+              - tank_design/namespaces.md
+              - tank_design/files.md
+              - tank_design/functions.md
+              - tank_design/pages.md 
           - Propulsion Design:
             - Introduction: documentation/aircraft-design/propulsion_design/doc/content/index.md
             - Getting Started: documentation/aircraft-design/propulsion_design/doc/content/getting_started.md
             - Engineering Principles: documentation/aircraft-design/propulsion_design/doc/content/engineering_principles.md
             - Software Architecture: documentation/aircraft-design/propulsion_design/doc/content/software_architecture.md
+            - Tutorial:
+              - Main: documentation/aircraft-design/propulsion_design/doc/content/tutorial.md
+              - Engine Extension: documentation/aircraft-design/propulsion_design/doc/content/tutorial_engine_extension.md
+              - Fidelity Extension: documentation/aircraft-design/propulsion_design/doc/content/tutorial_fidelity_extension.md
             - Changelog: documentation/aircraft-design/propulsion_design/doc/content/changelog.md
             - Additional: documentation/aircraft-design/propulsion_design/doc/content/additional.md
-          - Landing Gear Design: documentation/aircraft-design/landing_gear_design/doc/content/index.md
-          - Systems Design: documentation/aircraft-design/systems_design/doc/content/index.md
+            - API Reference:
+              - propulsion_design/classes.md
+              - propulsion_design/namespaces.md
+              - propulsion_design/files.md
+              - propulsion_design/functions.md
+              - propulsion_design/pages.md   
+          - Landing Gear Design: 
+            - Introduction: documentation/aircraft-design/landing_gear_design/doc/content/index.md
+            - Getting Staretd: documentation/aircraft-design/landing_gear_design/doc/content/getting-started.md
+            - API Reference:
+              - landing_gear_design/classes.md
+              - landing_gear_design/namespaces.md
+              - landing_gear_design/files.md
+              - landing_gear_design/functions.md
+              - landing_gear_design/pages.md 
+          - Systems Design: 
+            - Introduction: documentation/aircraft-design/systems_design/doc/content/index.md
+            - Getting Staretd: documentation/aircraft-design/systems_design/doc/content/getting-started.md
+            - API Reference:
+              - systems_design/classes.md
+              - systems_design/namespaces.md
+              - systems_design/files.md
+              - systems_design/functions.md
+              - systems_design/pages.md 
       - Analysis: documentation/analysis.md  # Link to analysis module page.
     - Libraries: documentation/libraries.md # Link to libraries overview.
     - Utilities: documentation/additional_software.md
@@ -171,5 +298,12 @@ nav:                                      # Customizes the main navigation struc
     - IDE Setup: get-involved/ide-setup.md
     - Release Package: get-involved/release-package.md
 
+  - About:                                # Top-level item for general site information.
+      - About us: 'about.md'              # Link to the about page.
+      - License: 'license.md'             # Link to license information.
+      - Contact: 'contact.md'             # Link to contact page.
+      - Partners: 'partners.md'           # Link to partners page.
+
+
 
 
-- 
GitLab