Enhancements

.github/workflows/build.yaml

@@ -27,7 +27,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Set up environment for CI
         run: |

.github/workflows/deploy.yml

@@ -13,10 +13,10 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v6
 
       - name: Assume AWS IAM Role
-        uses: aws-actions/configure-aws-credentials@v4
+        uses: aws-actions/configure-aws-credentials@v6
         with:
           role-to-assume: ${{ secrets.AWS_ROLE_ARN }}
           aws-region: eu-west-2

.github/workflows/lint.yml

@@ -11,10 +11,10 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.11"
 

.github/workflows/test-and-coverage.yml → .github/workflows/test.yml

@@ -12,10 +12,10 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.11"
 
@@ -36,80 +36,87 @@ jobs:
           root: tests/fixtures/prebuilt_public_project
           require_project_files: "true"
 
-  test:
+  unit-test:
     needs: schema
     runs-on: ubuntu-latest
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.11"
-          cache: "pip"
 
-      - name: Install project and test dependencies
+      - name: Install project and unit test dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -e ".[dev]"
+          pip install -e ".[test]"
 
       - name: Run pytest with coverage
         env:
           PYTEST_DISABLE_PLUGIN_AUTOLOAD: "1"
         run: |
-          pytest -m "not e2e" -p pytest_cov --cov=vertex --cov-report=term-missing --cov-report=xml
+          python -m pytest \
+                    -m "not e2e" \
+                    --ignore=tests/frontend-smoke/ \
+                    --code-highlight=yes \
+                    --color=yes \
+                    --verbosity=3 \
+                    -p pytest_cov \
+                    --cov=vertex \
+                    --cov-report=term-missing \
+                    --cov-report=xml
 
       - name: Upload coverage.xml artifact
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6
         with:
           name: coverage-xml
           path: coverage.xml
           if-no-files-found: error
 
       - name: Upload coverage report to Codecov (best effort)
         continue-on-error: true
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@v6
         with:
           files: ./coverage.xml
           token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: false
           verbose: true
 
-  frontend-smoke:
+  frontend-smoke-test:
     needs: schema
     runs-on: ubuntu-latest
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.11"
-          cache: "pip"
 
-      - name: Install project and test dependencies
+      - name: Install frontend smoke test dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -e ".[dev]"
+          pip install -e ".[frontend-smoke-tests]"
 
-      - name: Install Playwright Chromium browser
-        run: |
-          python -m playwright install --with-deps chromium
-
-      - name: Run Playwright smoke tests
+      - name: Run frontend smoke tests
         env:
           PLAYWRIGHT_ARTIFACTS_DIR: test-results/playwright
           PYTEST_DISABLE_PLUGIN_AUTOLOAD: "1"
         run: |
-          pytest tests/test_playwright_smoke.py
+          python -m pytest \
+                    --code-highlight=yes \
+                    --color=yes \
+                    --verbosity=3 \
+                    tests/frontend-smoke/test_playwright_smoke.py
 
       - name: Upload Playwright artifacts on failure
         if: failure()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6
         with:
           name: playwright-artifacts
           path: test-results/playwright

.github/workflows/validate-project-outputs.yml

@@ -32,10 +32,10 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.11"
 

Dockerfile

@@ -3,6 +3,9 @@ FROM python:3.11-slim
 # Set the working directory
 WORKDIR /app
 
+# Install Git
+RUN apt update && apt install -y git
+
 # Upgrade pip and install pip-tools first
 RUN pip install "pip<25" "setuptools<80" wheel
 RUN pip install "pip-tools==7.5.1"

README.md

@@ -22,9 +22,9 @@ VERTEX has three main elements:
 
 VERTEX processes and visualizes data using the concept of **Reproducible Analytical Pipelines (RAPs)**. RAPs are a set of resuable functions or blocks of code that can request specific variables from an [ISARIC ARC](https://github.com/ISARICResearch/ARC)-formatted REDCap database. These functions then process the data to generate dataframes, which can then be visualized interactively through a Plotly Dash app.
 
-## VERTEX Version 1.0
+## VERTEX Version 2.0.0
 
-**VERTEX Version 1.0** includes insight panels developed for the following research questions:
+**VERTEX Version 2.0.0** includes insight panels developed for the following research questions:
 - Clinical characterization of on presentation, including:
      - demographics and comorbidities
      - pregnancy
@@ -97,7 +97,7 @@ pip install -e .
 ```
 Any changes to the entrypoint definition or function implementing the entrypoint logic requires a re-installation (`pip uninstall -y isaric-vertex` and `pip install -e .`). The entrypoints currently include:
 
-* `descriptive-analytics` - generates analytics outputs from a given project source folder and saving them to local folder (within the project folder), e.g. for the Dengue synthetic demo project
+* `descriptive-analytics` - generates analytics outputs from a given project source folder and saving them to local folder (in an `outputs` subfolder of the project source folder), e.g. for the Dengue synthetic demo project
 ```shell
 $ descriptive-analytics demo-projects/ARChetypeCRF_dengue_synthetic/
 2026-03-26 10:00:05 [INFO] vertex.descriptive_analytics: Loading project data from project path: "/Users/smurthy/Documents/srm/dev/VERTEX/demo-projects/ARChetypeCRF_dengue_synthetic"
@@ -112,8 +112,8 @@ $ descriptive-analytics demo-projects/ARChetypeCRF_dengue_synthetic/
 ```
 
 > [!Note]
-The `descriptive-analytics` tool requires Google Chrome to be installed as some Chrome imaging functionality is used by the [kaleido](https://plotly.com/python/static-image-export/#kaleido) dependency when exporting/saving
-images - see [https://plotly.com/python/static-image-export/] for further information.
+The `descriptive-analytics` tool requires Google Chrome to be installed as some Chrome imaging functionality is used by the [`kaleido`](https://plotly.com/python/static-image-export/#kaleido) dependency when exporting/saving
+images - see [this](https://plotly.com/python/static-image-export/) for further information.
 
 ## Contributors
 

codecov.yml

@@ -12,8 +12,7 @@ coverage:
         threshold: 1%
     patch:
       default:
-        target: auto
-        threshold: 1%
+        target: 20%
 
 ignore:
   - "demo-projects/*"

demo-projects/ARChetypeCRF_dengue_synthetic/config_file.json

@@ -5,7 +5,7 @@
   "map_layout_center_latitude": 6,
   "map_layout_center_longitude": -75,
   "map_layout_zoom": 1.7,
-  "save_outputs": false,
+  "save_outputs": true,
   "outputs_path": "outputs/",
   "insight_panels_path": "insight_panels/",
   "insight_panels": [

demo-projects/ARChetypeCRF_dengue_synthetic/insight_panels/enrolment_details.py

@@ -1,7 +1,6 @@
+import isaricanalytics.IsaricDraw as idw
 import pandas as pd
 
-import vertex.IsaricDraw as idw
-
 
 def define_button():
     """Defines the button in the main dashboard menu"""

demo-projects/ARChetypeCRF_dengue_synthetic/insight_panels/outcomes_complications.py

@@ -1,8 +1,7 @@
+import isaricanalytics.IsaricAnalytics as ia
+import isaricanalytics.IsaricDraw as idw
 import pandas as pd
 
-import vertex.IsaricAnalytics as ia
-import vertex.IsaricDraw as idw
-
 
 def define_button():
     """Defines the button in the main dashboard menu"""

demo-projects/ARChetypeCRF_dengue_synthetic/insight_panels/presentation_demogcomor.py

@@ -1,9 +1,8 @@
+import isaricanalytics.IsaricAnalytics as ia
+import isaricanalytics.IsaricDraw as idw
 import numpy as np
 import pandas as pd
 
-import vertex.IsaricAnalytics as ia
-import vertex.IsaricDraw as idw
-
 
 def define_button():
     """Defines the button in the main dashboard menu"""

demo-projects/ARChetypeCRF_dengue_synthetic/insight_panels/presentation_symptoms.py

@@ -1,8 +1,7 @@
+import isaricanalytics.IsaricAnalytics as ia
+import isaricanalytics.IsaricDraw as idw
 import pandas as pd
 
-import vertex.IsaricAnalytics as ia
-import vertex.IsaricDraw as idw
-
 
 def define_button():
     """Defines the button in the main dashboard menu"""

demo-projects/ARChetypeCRF_dengue_synthetic/insight_panels/treatments_interventions.py

@@ -1,8 +1,7 @@
+import isaricanalytics.IsaricAnalytics as ia
+import isaricanalytics.IsaricDraw as idw
 import pandas as pd
 
-import vertex.IsaricAnalytics as ia
-import vertex.IsaricDraw as idw
-
 
 def define_button():
     """Defines the button in the main dashboard menu"""

demo-projects/ARChetypeCRF_h5nx_synthetic/config_file.json

@@ -5,7 +5,7 @@
   "map_layout_center_latitude": 6,
   "map_layout_center_longitude": -75,
   "map_layout_zoom": 1.7,
-  "save_outputs": false,
+  "save_outputs": true,
   "outputs_path": "outputs/",
   "insight_panels_path": "insight_panels/",
   "insight_panels": [

demo-projects/ARChetypeCRF_h5nx_synthetic/insight_panels/enrolment_details.py

@@ -1,7 +1,6 @@
+import isaricanalytics.IsaricDraw as idw
 import pandas as pd
 
-import vertex.IsaricDraw as idw
-
 
 def define_button():
     """Defines the button in the main dashboard menu"""

demo-projects/ARChetypeCRF_h5nx_synthetic/insight_panels/outcomes_complications.py

@@ -1,8 +1,7 @@
+import isaricanalytics.IsaricAnalytics as ia
+import isaricanalytics.IsaricDraw as idw
 import pandas as pd
 
-import vertex.IsaricAnalytics as ia
-import vertex.IsaricDraw as idw
-
 
 def define_button():
     """Defines the button in the main dashboard menu"""

demo-projects/ARChetypeCRF_h5nx_synthetic/insight_panels/presentation_demogcomor.py

@@ -1,9 +1,8 @@
+import isaricanalytics.IsaricAnalytics as ia
+import isaricanalytics.IsaricDraw as idw
 import numpy as np
 import pandas as pd
 
-import vertex.IsaricAnalytics as ia
-import vertex.IsaricDraw as idw
-
 
 def define_button():
     """Defines the button in the main dashboard menu"""

demo-projects/ARChetypeCRF_h5nx_synthetic/insight_panels/presentation_symptoms.py

@@ -1,8 +1,7 @@
+import isaricanalytics.IsaricAnalytics as ia
+import isaricanalytics.IsaricDraw as idw
 import pandas as pd
 
-import vertex.IsaricAnalytics as ia
-import vertex.IsaricDraw as idw
-
 
 def define_button():
     """Defines the button in the main dashboard menu"""

demo-projects/ARChetypeCRF_h5nx_synthetic/insight_panels/treatments_interventions.py

@@ -1,8 +1,7 @@
+import isaricanalytics.IsaricAnalytics as ia
+import isaricanalytics.IsaricDraw as idw
 import pandas as pd
 
-import vertex.IsaricAnalytics as ia
-import vertex.IsaricDraw as idw
-
 
 def define_button():
     """Defines the button in the main dashboard menu"""

demo-projects/ARChetypeCRF_h5nx_synthetic_mf/insight_panels/enrolment_details.py

@@ -1,7 +1,6 @@
+import isaricanalytics.IsaricDraw as idw
 import pandas as pd
 
-import vertex.IsaricDraw as idw
-
 
 def define_button():
     """Defines the button in the main dashboard menu"""

demo-projects/ARChetypeCRF_h5nx_synthetic_mf/insight_panels/modelling_featureselection.py

@@ -1,8 +1,7 @@
+import isaricanalytics.IsaricAnalytics as ia
+import isaricanalytics.IsaricDraw as idw
 import pandas as pd
 
-import vertex.IsaricAnalytics as ia
-import vertex.IsaricDraw as idw
-
 
 def define_button():
     """Defines the button in the main dashboard menu"""

demo-projects/ARChetypeCRF_h5nx_synthetic_mf/insight_panels/modelling_lengthofstay.py

@@ -1,8 +1,7 @@
+import isaricanalytics.IsaricAnalytics as ia
+import isaricanalytics.IsaricDraw as idw
 import pandas as pd
 
-import vertex.IsaricAnalytics as ia
-import vertex.IsaricDraw as idw
-
 
 def define_button():
     """Defines the button in the main dashboard menu"""

demo-projects/ARChetypeCRF_h5nx_synthetic_mf/insight_panels/modelling_riskfactors.py

@@ -1,8 +1,7 @@
+import isaricanalytics.IsaricAnalytics as ia
+import isaricanalytics.IsaricDraw as idw
 import pandas as pd
 
-import vertex.IsaricAnalytics as ia
-import vertex.IsaricDraw as idw
-
 
 def define_button():
     """Defines the button in the main dashboard menu"""