Initial step towards a 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 · eacc969 · eacc969
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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.
 
@@ -103,7 +103,7 @@ 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:
@@ -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 ui/apps/expert_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/ui/apps/expert_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/ui/apps/expert_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 ui.apps.calculator --port 8081 --no-debug
diff --git a/app-config/calculator-app/app.sh b/app-config/calculator-app/app.sh
@@ -28,12 +28,7 @@ if [[ "$APP_NAME" == "calculator-app" ]]; then
 
     echo "Starting the caimira webservice with: python -m ui.apps.calculator ${args[@]}"
     python -m ui.apps.calculator "${args[@]}"
-elif [[ "$APP_NAME" == "caimira-voila" ]]; then
-    echo "Starting the voila service"
-    voila ui/apps/expert_apps/expert --port=8080 --no-browser --base_url=/voila-server/ --tornado_settings 'allow_origin=*'
-elif [[ "$APP_NAME" == "caimira-co2-voila" ]]; then
-    echo "Starting the CO2 voila service"
-    voila ui/apps/expert_apps/expert_co2/ --port=8080 --no-browser --base_url=/co2-voila-server/ --tornado_settings 'allow_origin=*'
+
 else
     echo "No APP_NAME specified"
     exit 1

diff --git a/app-config/docker-compose.yml b/app-config/docker-compose.yml
@@ -1,17 +1,5 @@
 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:
@@ -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
+