Backend separation

- extract, isolate and package it in a completely independent Python module, versioned and in a way that allows releases on PyPI.org - fixed error in placeholder for secondary school (data registry defaults) - added restriction in pytest version to install - expected number of new cases fix - data registry update (schema v2.1.1) - github update - deprecate ExpertApplication and CO2Application - changes to reflect schema update 2.0.2 - version update - Fixed error with f_inf (short-range)
CERN · Jul 15, 2024 · e5c8ce7 · e5c8ce7
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diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -24,6 +24,7 @@ jobs:
     env:
       PROJECT_ROOT: ./
       PROJECT_NAME: caimira
+      CAIMIRA_TESTS_CALCULATOR_TIMEOUT: 30
     steps:
       - name: Checkout
         uses: actions/checkout@v2
@@ -46,6 +47,7 @@ jobs:
     env:
       PROJECT_ROOT: ./
       PROJECT_NAME: caimira
+      CAIMIRA_TESTS_CALCULATOR_TIMEOUT: 30
     steps:
       - name: Checkout
         uses: actions/checkout@v2

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -2,28 +2,16 @@
 # Read the Docs configuration file
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
-# Required
 version: 2
 
-# Set the version of Python and other tools you might need
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
-    python: "3.9"
-    # You can also specify other tool versions:
-    # nodejs: "16"
-    # rust: "1.55"
-    # golang: "1.17"
+    python: "3.11"
 
-# Build documentation in the docs/ directory with Sphinx
 sphinx:
    configuration: caimira/docs/conf.py
 
-# If using Sphinx, optionally build your docs in additional formats such as PDF
-# formats:
-#    - pdf
-
-# Optionally declare the Python requirements required to build your docs
 python:
    install:
-   - requirements: requirements.txt
+   - requirements: caimira/docs/requirements.txt
diff --git a/README.md b/README.md
@@ -66,7 +66,7 @@ The information also features a distribution diagram of licenses and a brief des
 A risk assessment tool which simulates the airborne spread of the SARS-CoV-2 virus for space managers.
 
 
-### CAiMIRA Expert App
+### CAiMIRA Expert App and CO₂ App
 
 A tool to interact with various parameters of the CAiMIRA model.
 
@@ -103,25 +103,25 @@ pip install -e .   # At the root of the repository
 ### Running the Calculator app in development mode
 
 ```
-python -m caimira.apps.calculator
+python -m ui.apps.calculator
 ```
 
 To run with a specific template theme created:
 
 ```
-python -m caimira.apps.calculator --theme=caimira/apps/templates/{theme}
+python -m ui.apps.calculator --theme=ui/apps/templates/{theme}
 ```
 
 To run the entire app in a different `APPLICATION_ROOT` path:
 
 ```
-python -m caimira.apps.calculator --app_root=/myroot
+python -m ui.apps.calculator --app_root=/myroot
 ```
 
 To run the calculator on a different URL path:
 
 ```
-python -m caimira.apps.calculator --prefix=/mycalc
+python -m ui.apps.calculator --prefix=/mycalc
 ```
 
 Each of these commands will start a local version of CAiMIRA, which can be visited at http://localhost:8080/.
@@ -139,13 +139,32 @@ If any of the `.rst` files under the `caimira/docs` folder is changed, this comm
 
 Then, right click on `caimira/docs/_build/html/index.html` and select `Open with` your preferred web browser.
 
-### Running the CAiMIRA Expert-App app in development mode
+### Running the CAiMIRA Expert-App or CO2-App apps in development mode
+
+#### Disclaimer
+
+The `ExpertApplication` and `CO2Application` are no longer actively maintained but will remain in the codebase for legacy purposes.
+Please note that the functionality of these applications might be compromised due to deprecation issues.
+
+#### Running the Applications
+
+These applications only work within Jupyter notebooks. Attempting to run them outside of a Jupyter environment may result in errors or degraded functionality.
+
+##### Prerequisites
+
+Make sure you have the needed dependencies intalled:
 
 ```
-voila caimira/apps/expert/caimira.ipynb --port=8080
+pip install notebook jupyterlab
 ```
 
-Then visit http://localhost:8080.
+Running with Visual Studio Code (VSCode):
+
+1. Ensure you have the following extensions installed in VSCode: `Jupyter` and `Python`.
+
+2. Open VSCode and navigate to the directory containing the notebook.
+
+3. Open the notebook (e.g. `caimira/apps/expert/caimira.ipynb`) and run the cells by clicking the `run` button next to each cell.
 
 ### Running the tests
 

diff --git a/app-config/caimira-public-docker-image/Dockerfile b/app-config/caimira-public-docker-image/Dockerfile
@@ -14,8 +14,6 @@ COPY ./app-config/caimira-public-docker-image/run_caimira.sh /opt/caimira/start.
 # To ensure that we have installed the full requirements, re-run the pip install.
 # In the best case this will be a no-op.
 RUN cd /opt/caimira/src/ && /opt/caimira/app/bin/pip install -r /opt/caimira/src/requirements.txt
-RUN /opt/caimira/app/bin/jupyter trust /opt/caimira/src/caimira/apps/expert/*.ipynb
-RUN /opt/caimira/app/bin/jupyter trust /opt/caimira/src/caimira/apps/expert_co2/*.ipynb
 COPY ./app-config/caimira-public-docker-image/nginx.conf /opt/caimira/nginx.conf
 
 EXPOSE 8080

diff --git a/app-config/caimira-public-docker-image/nginx.conf b/app-config/caimira-public-docker-image/nginx.conf
@@ -44,18 +44,6 @@ http {
 
         large_client_header_buffers 4 16k;
 
-        location /voila-server/ {
-            proxy_pass http://localhost:8082/voila-server/;
-        }
-        rewrite ^/expert-app$ /voila-server/ last;
-        rewrite ^/(files/static)/(.*)$ /voila-server/voila/$1/$2 last;
-
-        location /co2-voila-server/ {
-            proxy_pass http://localhost:8083/co2-voila-server/;
-        }
-        rewrite ^/co2-app$ /voila-server/ last;
-        rewrite ^/(files/static)/(.*)$ /voila-server/voila/$1/$2 last;
-
         location / {
             proxy_pass http://localhost:8081;
         }

diff --git a/app-config/caimira-public-docker-image/run_caimira.sh b/app-config/caimira-public-docker-image/run_caimira.sh
@@ -5,17 +5,6 @@ echo 'Please see https://gitlab.cern.ch/caimira/caimira for terms of use.'
 # Run a proxy for the apps (listening on 8080).
 nginx -c /opt/caimira/nginx.conf
 
-# Run the expert app in the background.
 cd /opt/caimira/src/caimira
-/opt/caimira/app/bin/python -m voila /opt/caimira/src/caimira/apps/expert/caimira.ipynb \
-  --port=8082 --no-browser --base_url=/voila-server/ \
-  --Voila.tornado_settings 'allow_origin=*' \
-  >> /var/log/expert-app.log 2>&1 &
-
-/opt/caimira/app/bin/python -m voila /opt/caimira/src/caimira/apps/expert_co2/caimira.ipynb \
-  --port=8083 --no-browser --base_url=/co2-voila-server/ \
-  --Voila.tornado_settings 'allow_origin=*' \
-  >> /var/log/co2-app.log 2>&1 &
-
 # Run the calculator in the foreground.
-/opt/caimira/app/bin/python -m caimira.apps.calculator --port 8081 --no-debug
+/opt/caimira/app/bin/python -m ui.apps.calculator --port 8081 --no-debug
diff --git a/app-config/calculator-app/app.sh b/app-config/calculator-app/app.sh
@@ -26,14 +26,9 @@ if [[ "$APP_NAME" == "calculator-app" ]]; then
     export "DATA_SERVICE_ENABLED"="${DATA_SERVICE_ENABLED:=0}"
     export "CAIMIRA_PROFILER_ENABLED"="${CAIMIRA_PROFILER_ENABLED:=0}"
 
-    echo "Starting the caimira webservice with: python -m caimira.apps.calculator ${args[@]}"
-    python -m caimira.apps.calculator "${args[@]}"
-elif [[ "$APP_NAME" == "caimira-voila" ]]; then
-    echo "Starting the voila service"
-    voila caimira/apps/expert/ --port=8080 --no-browser --base_url=/voila-server/ --tornado_settings 'allow_origin=*'
-elif [[ "$APP_NAME" == "caimira-co2-voila" ]]; then
-    echo "Starting the CO2 voila service"
-    voila caimira/apps/expert_co2/ --port=8080 --no-browser --base_url=/co2-voila-server/ --tornado_settings 'allow_origin=*'
+    echo "Starting the caimira webservice with: python -m ui.apps.calculator ${args[@]}"
+    python -m ui.apps.calculator "${args[@]}"
+
 else
     echo "No APP_NAME specified"
     exit 1

diff --git a/app-config/docker-compose.yml b/app-config/docker-compose.yml
@@ -1,25 +1,13 @@
 version: "3.8"
 services:
-  expert-app:
-    image: calculator-app
-    environment:
-      - APP_NAME=caimira-voila
-    user: ${CURRENT_UID:?"Please run as follows 'CURRENT_UID=$(id -u):$(id -g) docker-compose up'"}
-
-  expert-co2-app:
-    image: calculator-app
-    environment:
-      - APP_NAME=caimira-co2-voila
-    user: ${CURRENT_UID:?"Please run as follows 'CURRENT_UID=$(id -u):$(id -g) docker-compose up'"}
-
   calculator-app:
     image: calculator-app
     environment:
       - COOKIE_SECRET
       - APP_NAME=calculator-app
       - APPLICATION_ROOT=/
       - CAIMIRA_CALCULATOR_PREFIX=/calculator-cern
-      - CAIMIRA_THEME=caimira/apps/templates/cern
+      - CAIMIRA_THEME=ui/apps/templates/cern
       - DATA_SERVICE_ENABLED=0
       - CAIMIRA_PROFILER_ENABLED=0
     user: ${CURRENT_UID}
@@ -54,10 +42,6 @@ services:
         condition: service_started
       calculator-open-app:
         condition: service_started
-      expert-app:
-        condition: service_started
-      expert-co2-app:
-        condition: service_started
       auth-service:
         condition: service_started
     user: ${CURRENT_UID}
diff --git a/app-config/nginx/nginx.conf b/app-config/nginx/nginx.conf
@@ -73,44 +73,8 @@ http {
             proxy_pass http://calculator-app:8080/$request_uri;
         }
 
-        location /voila-server/ {
-            proxy_intercept_errors on;
-
-            # Anything under voila-server or expert-app is authenticated.
-            auth_request /auth/probe;
-            error_page 401 = @error401;
-            error_page 404 = @proxy_404_error_handler;
-
-            # expert-app is the name of the voila server in each of docker-compose,
-            # caimira-test.web.cern.ch and caimira.web.cern.ch.
-            proxy_pass http://expert-app:8080/voila-server/;
-        }
-        rewrite ^/expert-app$ /voila-server/voila/render/caimira.ipynb last;
-        rewrite ^/(files/static)/(.*)$ /voila-server/voila/$1/$2 last;
-
-        # Before implementing the nginx router we could access /voila/render/caimira.ipynb.
-        # Redirect this (and all other) URLs to the new scheme.
+        # Redirect URLs to the new scheme.
         absolute_redirect off;
-        rewrite ^/voila/(.*)$ /voila-server/voila/$1 redirect;
-
-        location /co2-voila-server/ {
-            proxy_intercept_errors on;
-
-            # Anything under voila-server or co2-app is authenticated.
-            auth_request /auth/probe;
-            error_page 401 = @error401;
-            error_page 404 = @proxy_404_error_handler;
-
-            # expert-co2-app is the name of the voila server in each of docker-compose,
-            # caimira-test.web.cern.ch and caimira.web.cern.ch.
-            proxy_pass http://expert-co2-app:8080/co2-voila-server/;
-        }
-        rewrite ^/co2-app$ /co2-voila-server/voila/render/caimira.ipynb last;
-        rewrite ^/(files/static)/(.*)$ /co2-voila-server/voila/$1/$2 last;
-
-        # Before implementing the nginx router we could access /voila/render/caimira.ipynb.
-        # Redirect this (and all other) URLs to the new scheme.
-        rewrite ^/voila/(.*)$ /co2-voila-server/voila/$1 redirect;
 
         location / {
             # By default we have no authentication.

diff --git a/app-config/openshift/deploymentconfig.yaml b/app-config/openshift/deploymentconfig.yaml
@@ -68,120 +68,6 @@
                 kind: ImageStreamTag
                 name: 'auth-service:latest'
                 namespace: ${PROJECT_NAME}
-    -
-      apiVersion: apps.openshift.io/v1
-      kind: DeploymentConfig
-      metadata:
-        name: expert-app
-        labels: {app: expert-app}
-      spec:
-        replicas: 1
-        template:
-          metadata:
-            labels:
-              app: expert-app
-          spec:
-            containers:
-              - name: calculator-app
-                env:
-                - name: APP_NAME
-                  value: caimira-voila
-                image: '${PROJECT_NAME}/calculator-app'
-                ports:
-                  - containerPort: 8080
-                    protocol: TCP
-                imagePullPolicy: Always
-                resources:
-                  limits: { cpu: '1', memory: 1Gi }
-                  requests: { cpu: 1m, memory: 512Mi }
-                terminationMessagePath: /dev/termination-log
-                terminationMessagePolicy: File
-            dnsPolicy: ClusterFirst
-            restartPolicy: Always
-            schedulerName: default-scheduler
-            securityContext: { }
-            terminationGracePeriodSeconds: 30
-        strategy:
-          activeDeadlineSeconds: 21600
-          resources: { }
-          rollingParams:
-            intervalSeconds: 1
-            maxSurge: 25%
-            maxUnavailable: 25%
-            timeoutSeconds: 600
-            updatePeriodSeconds: 1
-          type: Rolling
-        test: false
-        selector:
-          app: expert-app
-        triggers:
-          - type: ConfigChange
-          - type: ImageChange
-            imageChangeParams:
-              automatic: true
-              containerNames:
-                - calculator-app
-              from:
-                kind: ImageStreamTag
-                name: 'calculator-app:latest'
-                namespace: ${PROJECT_NAME}
-    -
-      apiVersion: apps.openshift.io/v1
-      kind: DeploymentConfig
-      metadata:
-        name: expert-co2-app
-        labels: {app: expert-co2-app}
-      spec:
-        replicas: 1
-        template:
-          metadata:
-            labels:
-              app: expert-co2-app
-          spec:
-            containers:
-              - name: calculator-app
-                env:
-                - name: APP_NAME
-                  value: caimira-co2-voila
-                image: '${PROJECT_NAME}/calculator-app'
-                ports:
-                  - containerPort: 8080
-                    protocol: TCP
-                imagePullPolicy: Always
-                resources:
-                  limits: { cpu: '1', memory: 1Gi }
-                  requests: { cpu: 1m, memory: 512Mi }
-                terminationMessagePath: /dev/termination-log
-                terminationMessagePolicy: File
-            dnsPolicy: ClusterFirst
-            restartPolicy: Always
-            schedulerName: default-scheduler
-            securityContext: { }
-            terminationGracePeriodSeconds: 30
-        strategy:
-          activeDeadlineSeconds: 21600
-          resources: { }
-          rollingParams:
-            intervalSeconds: 1
-            maxSurge: 25%
-            maxUnavailable: 25%
-            timeoutSeconds: 600
-            updatePeriodSeconds: 1
-          type: Rolling
-        test: false
-        selector:
-          app: expert-co2-app
-        triggers:
-          - type: ConfigChange
-          - type: ImageChange
-            imageChangeParams:
-              automatic: true
-              containerNames:
-                - calculator-app
-              from:
-                kind: ImageStreamTag
-                name: 'calculator-app:latest'
-                namespace: ${PROJECT_NAME}
     -
       apiVersion: apps.openshift.io/v1
       kind: DeploymentConfig
@@ -417,3 +303,4 @@
     - name: PROJECT_NAME
       description: The name of this project, e.g. caimira-test
       required: true
+