Revert "Fix citation issues"

This reverts commit 86eac313.

.gitlab-ci.yml

@@ -78,4 +78,8 @@ pages:
       - $CI_PROJECT_DIR/public
   rules:
     - if: '$CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH'  # Run when the commit is on the default branch
-      when: on_success  # Only run if the previous jobs are successful
\ No newline at end of file
+      when: on_success  # Only run if the previous jobs are successful
+    - if: '$CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH'  # Allow manual triggers on non-default branches
+      when: manual  # Run only when triggered manually
+    - if: '$CI_PIPELINE_SOURCE == "trigger"'  # Triggered by another pipeline
+      when: on_success  # Run if the source pipeline was successful

Pipfile

@@ -9,7 +9,6 @@ mkdocs-material = "*"
 mkdocs-glightbox = "*"
 mkdocs-site-urls = "*"
 mkdoxy = "*"
-mkdocs-bibtex =  "*"
 
 [dev-packages]
 mkdocs = "*"

docs/assets/bibtex/propulsion_design_literature.bib

-@Misc{Pet13,
-  title = {Regression line from LTH-Data},
-  author = {Fabian Peter},
-  year = {2013},
-  note = {For A319-100, A320-200, A321-200, A340-300B, A300-600R, A310-300, A330-200 see Excel file "sheet real_reduziert" on RWTH Aachen ILR-Server: \textbackslash\11\_MICADO\04-Descriptions\massEstimation\engine\[engineWeightMethods.xlsx] (stand von Fabian Peter 2012)}
-}
-
-@misc{Ata10,
-  author = {Atanasov, Georgi},
-  year = {2010},
-  title = {Methodische Entwicklung von Konzepten zur Antriebsintegration im Flugzeugentwurf},
-  howpublished = {Diplomarbeit, RWTH Aachen University, Aachen, Germany}
-}

docs/documentation/analysis/ecological_assessment/basic-concepts.md

@@ -48,20 +48,20 @@ Soot     | 0.025e-3   |
 All other emissions are considered to be non-proportional and are calculated with following methods:
 
 - For NOx emissions, there are
-    - a P3T3 Method[@Nor03],
-    - Boeing Fuel Flow Method 2[@Sch13]
+    - a P3T3 Method \cite Nor03,
+    - Boeing Fuel Flow Method 2 \cite Sch13
     - and the calculation based on data generated by GasTurb available.
 - For HC as well as CO emissions, the
     - DLR Omega method
-    - and Boeing Fuel Flow Method 2[@Sch13] are implemented.
+    - and Boeing Fuel Flow Method 2 \cite Sch13 are implemented.
     - Additionally, there is the option to calculate the landing and takeoff cycle emissions based on constants provided by ICAO.
 - Soot emissions can be determined via
     - a DLR correlation based on ICAO smoke numbers
-    - or a correlation by R.B. Whyte[@Kug05].
+    - or a correlation by R.B. Whyte \cite Kug05.
     - Alternatively, it can be assumed to be proportional to the consumed fuel.
 
 #### Hydrogen Combustion Emissions
-When hydrogen is burned in an engine, only H2O and NOx emissions are produced. H2O is again assumed to be proportional to the fuel flow. For NOx emissions, there are two methods implemented. As the determination of NOx emissions when burning hydrogen is subject to great uncertainty, a the low-fidelity method of using constant emission indices for different flight phases is the default method. The emission indices were determined by K. Kossarev (2022)[@Koss22] for one engine type and are listed in this table:
+When hydrogen is burned in an engine, only H2O and NOx emissions are produced. H2O is again assumed to be proportional to the fuel flow. For NOx emissions, there are two methods implemented. As the determination of NOx emissions when burning hydrogen is subject to great uncertainty, a the low-fidelity method of using constant emission indices for different flight phases is the default method. The emission indices were determined in \cite Koss22 for one engine type and are listed in this table:
 
 Phase   | EI [g/kg]|
 --------|----------|
@@ -71,7 +71,7 @@ Climb   | 6.17     |
 Cruise  | 3.14     |
 Approach| 2.4      |
 
-Alternatively, you can choose to follow the method described in Kossarev (2022)[@Koss22] and calculate the emission index in every mission step. For that, the emissions of kerosene-burning engines are calculated via the P3T3 method and a correction factor is used to derive the emissions due to hydrogen combustion. If the calculation of a correction factor fails, the first method is used as a fallback method.
+Alternatively, you can choose to follow the method described in \cite Koss22 and calculate the emission index in every mission step. For that, the emissions of kerosene-burning engines are calculated via the P3T3 method and a correction factor is used to derive the emissions due to hydrogen combustion. If the calculation of a correction factor fails, the first method is used as a fallback method.
 
 
 
@@ -191,7 +191,7 @@ The central output of the mission submodule is the `ecological_assessment_result
 
 
 ## Life Cycle Emissions (Schaefer) {#lca-schaefer}
-The method is based on the dissertation by Katharina Schäfer (2011)[@Sch17]. It is highly recommended to refer to this work for detailed insights. The method calculates the energy demand and emissions across the aircraft's life cycle phases: development, production, operation, and end-of-life. The following image shows the processes considered.
+The method is based on the dissertation by Katharina Schäfer (2011) \cite Sch17. It is highly recommended to refer to this work for detailed insights. The method calculates the energy demand and emissions across the aircraft's life cycle phases: development, production, operation, and end-of-life. The following image shows the processes considered.
 
 ![](figures/lifeCyclePhases.png "Life cycle phases according to K.Schaefer")
 
@@ -707,7 +707,7 @@ The Method writes data to CSV files in the *aircraft\_exchange\_file\_directory/
 This method provides a single indicator - called the Air Quality Index (AQI) - for the assessment of air quality. The AQI can take values between 0 and 1, with 1 indicating that the allowable limits defined by ICAO are reached by all species. Therefore, low values are preferable.
 
 ### General principles {#aqi-schaefer-generalprinciples}
-The calculation method, including all required inputs, is described in Schaefer (2017)[@Sch17]. It is:
+The calculation method, including all required inputs, is described in Schaefer (2017) \cite Sch17. It is:
 
 $ AQI = 1/n \cdot \sum x_i/x_{i,max}$
 
@@ -744,7 +744,7 @@ mission_emissions/
 The submodule writes its calculation results into the HTML report located in *aircraft_exchange_file_directory/reporting/report_html*.
 
 ## Climate Model (Dallara) {#climate-model-dallara}
-The climate model calculates key climate impact metrics: Radiative Forcing (RF), Absolute Global Warming Potential (AGWP), Absolute Global Temperature Potential (AGTP), and Average Temperature Response (ATR). The calculation methodology is derived from Dallara's work in 2011[@Dal11], providing a systematic approach to assess the environmental effects of various emissions.
+The climate model calculates key climate impact metrics: Radiative Forcing (RF), Absolute Global Warming Potential (AGWP), Absolute Global Temperature Potential (AGTP), and Average Temperature Response (ATR). The calculation methodology is derived from Dallara's work in 2011 \cite Dal11, providing a systematic approach to assess the environmental effects of various emissions.
 
 The key metrics are:
 

docs/documentation/analysis/index.md

@@ -67,13 +67,18 @@ The `constraint_analysis` module updates the performance criteria wing loading a
 
 ## Ecological assessment
 ![Icon](site:assets/images/documentation/calculate-emissions.svg){.overview-img  align=left}
-The `ecological_assessment` is an additional module of the UNICADO toolchain.
-Its purpose is to calculate the emissions and energy demand within the aircraft's lifecycle and to determine the missions based climate impact as well as impact on the local air quality. While the life cycle assessment is only valid for conventional kerosene powered tube and wing aircraft, the mission and impact calculations can be performed for all aircraft configurations and kerosene or hydrogen powered engines.
+The **ecological_assessment** is an additional module of the UNICADO toolchain.
+Its purpose is to calculate the emissions and energy demand within the aircraft's lifecycle and to determine the missions based climate impact.
+For the user, possible changes in the module run configuration can be made in the related calculateEmissions_conf.xml file.
+The parameters comprised in this XML file can have different attributes as e.g. Filenames, Directories, Output configs, and are further subdivided into control and program settings.
 {.overview-item}
 
+!!! note
+    By now, only the calculation routines / outputs based on the flown mission are up to date.
+
 |Module Version|Language|License|Documentation|
 |:---:|:---:|:---:|---|
-|2.1.0|:simple-cplusplus: |GPLv3|[Link](ecological_assessment/index.md)|
+|2.1.0|:simple-cplusplus: |GPLv3|[Link](analysis/ecological_assessment/index.md)|
 
 ---
 

docs/documentation/overview.md

@@ -11,7 +11,7 @@ glightbox: false
 
 - [:simple-gitlab: Aircraft Design :octicons-link-external-16:](https://git.rwth-aachen.de/unicado/aircraft-design):
 
-    The aircraft design repository collect all the [sizing tools](sizing/index.md) and [analysis tools](analysis/index.md) which are needed for the preliminary design process.
+    The aircraft design repository collect alls the [sizing tools](sizing.md) and [analysis tools](analysis.md) which are needed for the preliminary design process.
 
 - [:simple-gitlab: Libraries :octicons-link-external-16:](https://git.rwth-aachen.de/unicado/libraries):
 

docs/documentation/sizing/propulsion_design/engineering_principles.md

@@ -55,9 +55,7 @@ The _scale factor_ is necessary for the rubber method as it uses the concept of
 
 The scaling is based on continuity principle assuming that the engine characteristics are constant.
 
-\[
-T = \dot{m} \cdot (V_9 - V_0)
-\]
+$T = \dot{m} \cdot (V_9 - V_0)$
 
 Therefore, thrust $T$ is proportional to the mass flow $\dot{m}$, which is linearly related to the cross-sectional area $A$ of the engine.
 
@@ -106,7 +104,7 @@ Additionally to calculating the engine performance parameter, the engine has to
 
 Here, currently only one method is implemented:
 
- - *default* is based on a thesis of RWTH Aachen [@Ata10]
+ - *default* is based on a thesis of RWTH Aachen \cite{Ata10}
 
 This method includes multiple empirical functions for different propulsion integration. These are the options that are currently implemented:
 

mkdocs.yml

@@ -68,135 +68,121 @@ extra_css:
 plugins:
   - search
   - site-urls
-  - bibtex:
-      bib_dir: "./docs/assets/bibtex/"
   - mkdoxy:
       projects:
         propulsion_design:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "propulsion_design"
-            OUTPUT_DIR: "docs/api/propulsion"
-            BIBTEX_FILE: "docs/assets/bibtex/propulsion_design_literature.bib"
-          src-dirs: docs/documentation/aircraft-design/propulsion_design/src/
-          full-doc: True
-        ecological_assessment:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "ecological_assessment"
-            OUTPUT_DIR: "docs/api/ecological_assessment"
-            BIBTEX_FILE: "docs/assets/bibtex/ecological_assessment_literature.bib"
-          src-dirs: docs/documentation/aircraft-design/ecological_assessment/src/
+          src-dirs: ../aircraft-design/propulsion_design/
           full-doc: True
+          output: docs/propulsion_design
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
         initial_sizing:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "initial_sizing"
-            OUTPUT_DIR: "docs/api/initial_sizing"
-            BIBTEX_FILE: "docs/assets/bibtex/initial_sizing_literature.bib"
-          src-dirs: docs/documentation/aircraft-design/initial_sizing/src/
+          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:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "create_mission_xml"
-            OUTPUT_DIR: "docs/api/create_mission_xml"
-            BIBTEX_FILE: "docs/assets/bibtex/create_mission_xml_literature.bib"
-          src-dirs: docs/documentation/aircraft-design/create_mission_xml/src/
-          full-doc: true
+          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:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "fuselage_design"
-            OUTPUT_DIR: "docs/api/fuselage_design"
-            BIBTEX_FILE: "docs/assets/bibtex/fuselage_design_literature.bib"
-          src-dirs: docs/documentation/aircraft-design/fuselage_design/src/
+          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:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "wing_design"
-            OUTPUT_DIR: "docs/api/wing_design"
-            BIBTEX_FILE: "docs/assets/bibtex/wing_design_literature.bib"
-          src-dirs: docs/documentation/aircraft-design/wing_design/src/
+          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:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "empennage_design"
-            OUTPUT_DIR: "docs/api/empennage_design"
-          src-dirs: docs/documentation/aircraft-design/empennage_design/src/
+          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:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "tank_design"
-            OUTPUT_DIR: "docs/api/tank_design"
-          src-dirs: docs/documentation/aircraft-design/tank_design/src/
+          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:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "landing_gear_design"
-            OUTPUT_DIR: "docs/api/landing_gear_design"
-          src-dirs: docs/documentation/aircraft-design/landing_gear_design/src/
+          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:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "systems_design"
-            OUTPUT_DIR: "docs/api/systems_design"
-          src-dirs: docs/documentation/aircraft-design/systems_design/src/
+          src-dirs: ../aircraft-design/systems_design/
           full-doc: true
+          output: docs/systems_design
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
+        ecological_assessment:
+          src-dirs: ../aircraft-design/ecological_assessment/
+          full-doc: true
+          output: docs/ecological_assessment
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
+        performance_assessment:
+          src-dirs: ../aircraft-design/performance_assessment/
+          full-doc: True
+          output: docs/propulsion_design
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
         aerodynamic_analysis:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "aerodynamic_analysis"
-            OUTPUT_DIR: "docs/api/aerodynamic_analysis"
-          src-dirs: docs/documentation/aircraft-design/aerodynamic_analysis/src/
+          src-dirs: ../aircraft-design/aerodynamic_analysis/
           full-doc: true
+          output: docs/aerodynamic_analysis
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
         aircraftGeometry2:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "aircraftGeometry2"
-            OUTPUT_DIR: "docs/api/aircraftGeometry2"
-          src-dirs: docs/documentation/aircraft-design/libs/aircraftGeometry2/src/
+          src-dirs: ../aircraft-design/libs/aircraftGeometry2/
           full-doc: true
+          output: docs/aircraftGeometry2
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
         engine:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "engine"
-            OUTPUT_DIR: "docs/api/engine"
-          src-dirs: docs/documentation/aircraft-design/libs/engine/src/
-          full-doc: true
-        mission_analysis:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "mission_analysis"
-            OUTPUT_DIR: "docs/api/mission_analysis"
-          src-dirs: docs/documentation/aircraft-design/mission_analysis/src/
-          full-doc: true
-        weight_and_balance_analysis:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "weight_and_balance_analysis"
-            OUTPUT_DIR: "docs/api/weight_and_balance_analysis"
-          src-dirs: docs/documentation/aircraft-design/weight_and_balance_analysis/src/
-          full-doc: true
-        performance_assesment:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "performance_assesment"
-            OUTPUT_DIR: "docs/api/performance_assesment"
-          src-dirs: docs/documentation/aircraft-design/performance_assesment/src/
-          full-doc: true
-        cost_estimation:
-          doxyfile: Doxyfile
-          variables:
-            PROJECT_NAME: "cost_estimation"
-            OUTPUT_DIR: "docs/api/cost_estimation"
-          src-dirs: docs/documentation/aircraft-design/cost_estimation/src/
+          src-dirs: ../aircraft-design/libs/engine/
           full-doc: true
+          output: docs/engine
+          doxy-cfg:
+            FILE_PATTERNS: "*.cpp *.h"
+            RECURSIVE: True
+            EXTRACT_ALL: YES
+
   - glightbox                             # Plugin for lightbox-style image and content viewing.
 
 
@@ -261,7 +247,7 @@ nav:                                      # Customizes the main navigation struc
             - Design Method: documentation/sizing/fuselage_design/design_method.md
             - Run your First Design: documentation/sizing/fuselage_design/run_your_first_design.md
             - Software Architecture: documentation/sizing/fuselage_design/software_architecture.md
-          # - API Reference: # TODO define for Python
+          #  # - API Reference: # TODO define for Python
           - Wing Design:
             - Introduction: documentation/sizing/wing_design/index.md
             - Getting Started: documentation/sizing/wing_design/getting-started.md
@@ -435,3 +421,6 @@ nav:                                      # Customizes the main navigation struc
       - License: 'license.md'             # Link to license information.
       - Contact: 'contact.md'             # Link to contact page.
       - Partners: 'partners.md'           # Link to partners page.
+
+
+