Re-named files and adapted scripts

CERN · Nov 18, 2024 · 3d5ca48 · 3d5ca48
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diff --git a/README.md b/README.md
@@ -176,7 +176,7 @@ Run the `style_docs.py` script to apply custom styles, move required files, and
 
 ```
 python style_docs.py \
-&& mv sphinx/_build/markdown/index.md mkdocs/docs/code_documentation/models.md \
+&& mv sphinx/_build/markdown/index.md mkdocs/docs/code/models.md \
 && pyreverse -o png -p UML-CAiMIRA --output-directory mkdocs/docs ../src/caimira/calculator/models/models.py
 ```
 

diff --git a/caimira/docs/Dockerfile b/caimira/docs/Dockerfile
@@ -25,8 +25,8 @@ WORKDIR /app/docs
 
 # Run the Python script to update markdown files, move it, and generate UML diagram
 RUN python3 style_docs.py \
-&& mv sphinx/_build/markdown/index.md mkdocs/docs/code_documentation/models.md \
-&& pyreverse -o png -p UML-CAiMIRA --output-directory mkdocs/docs/code_documentation ../src/caimira/calculator/models/models.py
+&& mv sphinx/_build/markdown/index.md mkdocs/docs/code/models.md \
+&& pyreverse -o png -p UML-CAiMIRA --output-directory mkdocs/docs/code ../src/caimira/calculator/models/models.py
 
 # Mkdocs directory
 WORKDIR /app/docs/mkdocs

diff --git a/caimira/docs/mkdocs/docs/code/architecture.md b/caimira/docs/mkdocs/docs/code/architecture.md
@@ -0,0 +1,9 @@
+This page contains a Unified Modeling Language (UML) diagram describing all the data classes and their relations.
+
+## CAiMIRA UML Diagram
+
+The following diagram describes all the data classes and their relations under the `models.py` file. Click the diagram to zoom-in.
+
+[![CAiMIRA UML diagram](classes_UML-CAiMIRA.png)](classes_UML-CAiMIRA.png)
+
+CAiMIRA `models.py` file UML diagram.
diff --git a/...kdocs/docs/code_documentation/rest_api.md → caimira/docs/mkdocs/docs/code/rest_api.md b/...kdocs/docs/code_documentation/rest_api.md → caimira/docs/mkdocs/docs/code/rest_api.md
@@ -1,6 +1,6 @@
 # CAiMIRA REST API
 
-The API enables third-party applications to interact with the CAiMIRA [backend](https://gitlab.cern.ch/caimira/caimira), making integration easier and more flexible. This page covers the CAiMIRA [package structure](#directory-layout-key-components), [API usage](#rest-api-overview), [deployment processes](#deployment-process), including versioning guidelines.
+The API enables third-party applications to interact with the CAiMIRA [backend](https://gitlab.cern.ch/caimira/caimira), making integration easier and more flexible. This page covers the CAiMIRA [package structure](#directory-layout-key-components) and [API usage](#rest-api-overview).
 
 ## Package Overview
 
@@ -201,24 +201,4 @@ As the project is growing, more endpoints targeted to specific tasks will be dev
                 "room_capacity": "10",
                 "room_volume": "60",
                 "total_people": "2"
-            }'
-
-## Deployment Process
-
-The deployment process varies depending on whether changes are pushed to branches, tags, or the test environment (`live/caimira-test` branch).
-
-### Branch and Tag-based Deployment
-
-For branch pushes:
-
-* All branches (except `live/caimira-test`) trigger the **test** stage in the CI/CD pipeline, ensuring the code passes all necessary tests before it is deployed.
-
-For tag creation:
-
-* When a new tag is created, the pipeline skips the previous tests, and it builds `Docker` images, storing them in GitLab's container registry. The images can be manually deployed to the OKD platform for the `PROD` - production environment.
-
-### OKD Platform Deployment
-The `cern_caimira` package, which contains the CERN-specific UI, is deployed directly to the OKD platform. The `caimira package`, which contains the backend logic, is deployed as a standalone API for integration with external services.
-
-### Versioning and Tags
-The repository follows a *semantic versioning* scheme, with tags named according to the `MAJOR.MINOR.PATCH` format (e.g., `v5.0.0`).
+            }'
diff --git a/caimira/docs/mkdocs/docs/index.md b/caimira/docs/mkdocs/docs/index.md
@@ -6,16 +6,18 @@ It includes details on the diameter-dependent mathematical model and the code de
 
 # Contents:
 
-* [Project Overview]()
-    * [About](project_overview/about.md)
-    * [Installation](project_overview/installation.md)
-    * [Deployment](project_overview/deployment.md)
-    * [User Guide]()
-        * [Quick Guide](project_overview/user_guide/quick_guide.md)
-        * [Full Guide](project_overview/user_guide/full_guide.md)
-    * [Open Source Acknowledgments](project_overview/open_source_acknowledgments.md)
-
-* [Code Documentation]()
-    * [Diameter Normalization](code_documentation/diameter_normalization.md)
-    * [REST API](code_documentation/rest_api.md)
-    * [Models Module](code_documentation/models.md)
+* [About](root/about.md)
+* [Installation](root/installation.md)
+* [Deployment](root/deployment.md)
+* [Open Source Acknowledgments](root/open_source_acknowledgments.md)
+* [License](LICENSE.md)
+* [Physics of the model](root/physics_model.md)
+* **Code**
+    * [Architecture](code/architecture.md)
+    * [models.py](code/models.md)
+    * [REST API](code/rest_api.md)
+* **User Interfaces**
+    * **CAiMIRA Calculator**
+        * [Quick Guide](user_interfaces/CAiMIRA/quick_guide.md)
+        * [Full Guide](user_interfaces/CAiMIRA/full_guide.md)
+    * [ARIA](https://partnersplatform.who.int/aria)
diff --git a/...ocs/mkdocs/docs/project_overview/about.md → caimira/docs/mkdocs/docs/root/about.md b/...ocs/mkdocs/docs/project_overview/about.md → caimira/docs/mkdocs/docs/root/about.md
@@ -47,27 +47,28 @@ As a result, WHO has invited CERN to become a member of a multidisciplinary expe
 The collaboration takes place within CERNs wide-ranging engagement with other international organisations, promoting shared solutions to societal challenges.
 
 ## Authors
-CAiMIRA was developed by the following members of CERN - European Council for Nuclear Research (visit [https://home.cern/](https://home.cern/)) and WHO - World Health Organization:
 
-Andre Henriques<sup>1</sup>, Luis Aleixo<sup>1</sup>, Marco Andreini<sup>1</sup>, Gabriella Azzopardi<sup>2</sup>, James Devine<sup>3</sup>, Philip Elson<sup>4</sup>, Nicolas Mounet<sup>2</sup>, Markus Kongstein Rognlien<sup>2,6</sup>, Nicola Tarocco<sup>5</sup>, Luca Fontana<sup>7</sup>, Alice Simniceanu<sup>7</sup>
+Andre Henriques<sup>1,2</sup>, Wei Jia<sup>3</sup>, Luis Aleixo<sup>1</sup>, Nicolas Mounet<sup>1</sup>, Luca Fontana<sup>4,5</sup>, Alice Simniceanu<sup>2,6</sup>, James Devine<sup>1</sup>, Philip Elson<sup>1</sup>, Gabriella Azzopardi<sup>1</sup>, Markus Kongstein Rognlien<sup>1,7</sup>, Marco Andreini<sup>1</sup>, Nicola Tarocco<sup>1</sup>, Olivia Keiser<sup>2</sup>, Yugou Li<sup>3</sup>, Julian Tang<sup>8</sup>
 
-<sup>1</sup>HSE Unit, Occupational Health & Safety Group, CERN<br>
-<sup>2</sup>Beams Department, Accelerators and Beam Physics Group, CERN<br>
-<sup>3</sup>Experimental Physics Department, Safety Office, CERN<br>
-<sup>4</sup>Beams Department, Controls Group, CERN<br>
-<sup>5</sup>Information Technology Department, Collaboration, Devices & Applications Group, CERN<br>
-<sup>6</sup>Norwegian University of Science and Technology (NTNU)<br>
-<sup>7</sup>World Health Organization (WHO)<br>
+<sup>1</sup>CERN (European Organization for Nuclear Research), Geneva, Switzerland<br>
+<sup>2</sup>Institute of Global Health, University of Geneva, Geneva, Switzerland<br>
+<sup>3</sup>Department of Mechanical Engineering, University of Hong Kong, Hong Kong SAR, China<br>
+<sup>4</sup>Strategic Health Operations, Operations Support and Logistic, Health Emergencies Programme, World Health Organization, Geneva, Switzerland<br>
+<sup>5</sup>Department of Civil and Mechanical Engineering, Università degli studi di Cassino e del Lazio Meridionale (UNICAS), Cassino, Italy<br>
+<sup>6</sup>Epidemic and Pandemic Preparedness, Health Emergencies Programme, World Health Organization, Geneva, Switzerland<br>
+<sup>7</sup>Norwegian University of Science and Technology (NTNU), Torgarden, Norway<br>
+<sup>8</sup>Respiratory Sciences, University of Leicester, Leicester, UK<br>
 
 #### Other contributors
 
-Anna Efimova<sup>1,2</sup>, Anel Massalimova<sup>1,3</sup>, Cole Austin Coughlin<sup>1,4</sup>, Germain Personne<sup>5</sup>
+Anna Efimova<sup>1,2</sup>, Anel Massalimova<sup>1,3</sup>, Cole Austin Coughlin<sup>1,4</sup>, Germain Personne<sup>5</sup>, Matteo Manzinello<sup>6</sup>, Elias Sandner<sup>1</sup>
 
-<sup>1</sup>Summer Student Programme, CERN<br>
+<sup>1</sup>CERN<br>
 <sup>2</sup>M.V. Lomonosov Moscow State University<br>
 <sup>3</sup>National Research Nuclear University "MEPhI"<br>
 <sup>4</sup>University of Manitoba<br>
 <sup>5</sup>Université Clermont Auvergne<br>
+<sup>6</sup>World Health Organization (WHO)<br>
 
 ## Reference and Citation
 

diff --git a/...kdocs/docs/project_overview/deployment.md → caimira/docs/mkdocs/docs/root/deployment.md b/...kdocs/docs/project_overview/deployment.md → caimira/docs/mkdocs/docs/root/deployment.md
@@ -138,3 +138,22 @@ but it may be origin if you haven't configured it differently):
 
     git push --force upstream name-of-local-branch:live/caimira-test
 
+## Deployment Process
+
+The deployment process varies depending on whether changes are pushed to branches, tags, or the test environment (`live/caimira-test` branch).
+
+### Branch and Tag-based Deployment
+
+For branch pushes:
+
+* All branches (except `live/caimira-test`) trigger the **test** stage in the CI/CD pipeline, ensuring the code passes all necessary tests before it is deployed.
+
+For tag creation:
+
+* When a new tag is created, the pipeline skips the previous tests, and it builds `Docker` images, storing them in GitLab's container registry. The images can be manually deployed to the OKD platform for the `PROD` - production environment.
+
+### OKD Platform Deployment
+The `cern_caimira` package, which contains the CERN-specific UI, is deployed directly to the OKD platform. The `caimira package`, which contains the backend logic, is deployed as a standalone API for integration with external services.
+
+### Versioning and Tags
+The repository follows a *semantic versioning* scheme, with tags named according to the `MAJOR.MINOR.PATCH` format (e.g., `v5.0.0`).
diff --git a/...ocs/docs/project_overview/installation.md → ...ira/docs/mkdocs/docs/root/installation.md b/...ocs/docs/project_overview/installation.md → ...ira/docs/mkdocs/docs/root/installation.md
@@ -134,7 +134,7 @@ The response format will be:
 }
 ```
 
-For further details please refer to the [REST API documentation page](../code_documentation/rest_api.md).
+For further details please refer to the [REST API documentation page](../code/rest_api.md).
 
 #### Running the Expert-Apps
 
@@ -217,7 +217,7 @@ To compile and view CAiMIRA's documentation, follow these steps:
     Run the `style_docs.py` script to apply custom styles, move required files, and generate a UML diagram:
 
         python style_docs.py \
-        && mv sphinx/_build/markdown/index.md mkdocs/docs/code_documentation/models.md \
+        && mv sphinx/_build/markdown/index.md mkdocs/docs/code/models.md \
         && pyreverse -o png -p UML-CAiMIRA --output-directory mkdocs/docs ../src/caimira/calculator/models/models.py
 
 4. Start the documentation server

diff --git a/...t_overview/open_source_acknowledgments.md → .../docs/root/open_source_acknowledgments.md b/...t_overview/open_source_acknowledgments.md → .../docs/root/open_source_acknowledgments.md
diff --git a/...e_documentation/diameter_normalization.md → ...ra/docs/mkdocs/docs/root/physics_model.md b/...e_documentation/diameter_normalization.md → ...ra/docs/mkdocs/docs/root/physics_model.md
@@ -1,6 +1,6 @@
-# Diameter-dependent Model
+# Physics of the Model
 
-This section describes the CAiMIRA model and its dependence on the Particles diameter. A Unified Modeling Language (UML) diagram describing all the data classes and their relations can be found [here](#caimira-uml-diagram), at the bottom of the document.
+This page describes the CAiMIRA model and its dependence on the Particles diameter.
 
 ## Context
 
@@ -304,16 +304,6 @@ Note still that nothing depends on the aerosol diameter $D$ in this case (no par
 Since the CO<sub>2</sub> concentration differs from the virus concentration, the specific removal rate, CO<sub>2</sub> atmospheric concentration and normalization factors are respectively defined in `caimira.models.models.CO2ConcentrationModel.removal_rate()`,
 `caimira.models.models.CO2ConcentrationModel.min_background_concentration()` and `caimira.models.models.CO2ConcentrationModel.normalization_factor()`.
 
-<a id="caimira-uml-diagram"></a>
-
-## CAiMIRA UML Diagram
-
-The following diagram describes all the data classes and their relations under the models.py file. Click the diagram to zoom-in.
-
-[![CAiMIRA UML diagram](classes_UML-CAiMIRA.png)](classes_UML-CAiMIRA.png)
-
-CAiMIRA `models.py` file UML diagram.
-
 ## References
 
 * <a id='id7'>**[1]**</a> Jia, Wei, et al. “Exposure and respiratory infection risk via the short-range airborne route.” Building and environment 219 (2022): 109166. [doi.org/10.1016/j.buildenv.2022.109166](https://doi.org/10.1016/j.buildenv.2022.109166)

diff --git a/...project_overview/user_guide/full_guide.md → ...ocs/user_interfaces/CAiMIRA/full_guide.md b/...project_overview/user_guide/full_guide.md → ...ocs/user_interfaces/CAiMIRA/full_guide.md
@@ -1,4 +1,4 @@
-## CAiMIRA Calculator
+## [CAiMIRA Calculator](https://caimira.web.cern.ch/)
 
 This guide helps on how to use the calculator app. For more information on the Airborne Transmission of SARS-CoV-2, feel free to check out the HSE Seminar: [https://cds.cern.ch/record/2743403](https://cds.cern.ch/record/2743403)
 

diff --git a/...verview/user_guide/img/window_opening.png → ...interfaces/CAiMIRA/img/window_opening.png b/...verview/user_guide/img/window_opening.png → ...interfaces/CAiMIRA/img/window_opening.png
diff --git a/...t_overview/user_guide/img/window_type.PNG → ...er_interfaces/CAiMIRA/img/window_type.PNG b/...t_overview/user_guide/img/window_type.PNG → ...er_interfaces/CAiMIRA/img/window_type.PNG
diff --git a/...roject_overview/user_guide/quick_guide.md → ...cs/user_interfaces/CAiMIRA/quick_guide.md b/...roject_overview/user_guide/quick_guide.md → ...cs/user_interfaces/CAiMIRA/quick_guide.md
@@ -1,4 +1,4 @@
-## CAiMIRA Calculator
+## [CAiMIRA Calculator](https://caimira.web.cern.ch/)
 
 This tool simulates the airborne spread of SARS-CoV-2 virus in a finite volume and estimates the risk of COVID-19 infection. It is based on current scientific data and can be used to compare the effectiveness of different mitigation measures.
 

diff --git a/caimira/docs/mkdocs/mkdocs.yml b/caimira/docs/mkdocs/mkdocs.yml
@@ -4,19 +4,21 @@ theme:
 
 nav:
   - Home: index.md
-  - Project Overview:
-      - About: project_overview/about.md
-      - Installation: project_overview/installation.md
-      - Deployment: project_overview/deployment.md
-      - User Guide:
-          - Quick Guide: project_overview/user_guide/quick_guide.md
-          - Full Guide: project_overview/user_guide/full_guide.md
-      - Open Source Acknowledgments: project_overview/open_source_acknowledgments.md
-  - License: LICENSE.md 
-  - Code Documentation:
-      - Diameter Normalization: code_documentation/diameter_normalization.md
-      - REST API: code_documentation/rest_api.md
-      - Models Module: code_documentation/models.md
+  - About: root/about.md
+  - Installation: root/installation.md
+  - Deployment: root/deployment.md
+  - Open Source Acknowledgments: root/open_source_acknowledgments.md
+  - License: LICENSE.md
+  - Physics of the model: root/physics_model.md
+  - Code:
+      - Architecture: code/architecture.md
+      - models.py: code/models.md
+      - REST API: code/rest_api.md
+  - User Interfaces:
+      - CAiMIRA Calculator:
+          - Quick Guide: user_interfaces/CAiMIRA/quick_guide.md
+          - Full Guide: user_interfaces/CAiMIRA/full_guide.md
+      - ARIA: https://partnersplatform.who.int/aria
 
 markdown_extensions:
   - pymdownx.arithmatex:

diff --git a/caimira/docs/style_docs.py b/caimira/docs/style_docs.py
@@ -199,7 +199,7 @@ def main():
         print(f"File '{index_file_path}' does not exist, skipping update.")
 
     # Path to the open source acknowledgements markdown file to be updated
-    acknowledgements_file_path = 'mkdocs/docs/project_overview/open_source_acknowledgments.md'
+    acknowledgements_file_path = 'mkdocs/docs/root/open_source_acknowledgments.md'
 
     if os.path.isfile(acknowledgements_file_path):
         # Retrieve package details
@@ -209,7 +209,7 @@ def main():
         add_python_dependencies_section(acknowledgements_file_path, package_details)
 
         # Generate the pie chart
-        output_image_path = 'mkdocs/docs/project_overview/license_distribution.png'
+        output_image_path = 'mkdocs/docs/root/license_distribution.png'
         generate_license_distribution_pie_chart(package_details, output_image_path)
     else:
         print(f"File '{acknowledgements_file_path}' does not exist, skipping update.")