Restructuring

.github/workflows/build.yml

@@ -0,0 +1,31 @@
+name: build
+
+on:
+  push:
+    branches: main
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+
+    steps:
+      - run: |
+          echo "github.event_name=${{ github.event_name }}"
+          echo "github.event.workflow_run.conclusion=${{ github.event.workflow_run.conclusion }}"
+      - name: Checkout repository
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
+
+      - name: Install build dependencies
+        run: |
+          pip install -U pip build
+
+      - name: Build package artifacts and install wheel
+        run: |
+          python -m build
+          pip install dist/isaricanalytics*.whl
+
+      - name: Test wheel import
+        run: |
+          python -c "import isaricanalytics; print(isaricanalytics.__version__)"

.github/workflows/pre-commit.yml

@@ -2,19 +2,20 @@ name: pre-commit
 
 on:
   push:
-    branches: [main]
+    branches: main
   pull_request:
 
 jobs:
   pre-commit:
     runs-on: ubuntu-latest
+    timeout-minutes: 10
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
         with:
           python-version: "3.11"
 

.github/workflows/test.yml

@@ -0,0 +1,59 @@
+name: Tests and Coverage
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  unit-test:
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+
+    steps:
+      - run: |
+          echo "github.event_name=${{ github.event_name }}"
+          echo "github.event.workflow_run.conclusion=${{ github.event.workflow_run.conclusion }}"
+      - name: Checkout repository
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
+
+      - name: Set up Python
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
+        with:
+          python-version: "3.11"
+
+      - name: Install project and unit test dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[test]"
+
+      - name: Run pytest with coverage
+        env:
+          PYTEST_DISABLE_PLUGIN_AUTOLOAD: "1"
+        run: |
+          python -m pytest \
+                    --code-highlight=yes \
+                    --color=yes \
+                    --verbosity=3 \
+                    -p pytest_cov \
+                    --cov=isaricanalytics \
+                    --cov-report=term-missing \
+                    --cov-report=xml \
+                    --cov-report=html
+
+      - name: Upload coverage.xml artifact
+        uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f
+        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@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2
+        with:
+          files: ./coverage.xml
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: false
+          verbose: true

.readthedocs.yaml

@@ -10,7 +10,6 @@ build:
   os: ubuntu-lts-latest
   tools:
     python: "3.11"
-
     # You can also specify other tool versions:
     # nodejs: "20"
     # rust: "1.70"

CITATION.cff

@@ -0,0 +1,40 @@
+cff-version: 1.2.0
+title: IsaricAnalytics
+message: Data analysis toolkit to support fast analysis of clinical data during emerging infectious disease outbreaks.
+type: software
+authors:
+  - name-particle: Tom
+    family-names: Edinburgh
+    email: tom.edinburgh@ndm.ox.ac.uk
+    orcid: 0000-0002-3599-7133
+  - name-particle: Esteban
+    family-names: Garcia-Gallo
+    email: esteban.garcia@ndm.ox.ac.uk
+    orcid: 0000-0002-8030-9985
+  - name-particle: Igor
+    family-names: Peres
+    email: igor.peres@puc-rio.br
+    orcid:
+  - name-particle: Tomoe
+    family-names: Gusberti
+    email: tomoegusberti@gmail.com
+    orcid:
+  - name-particle: Luiz
+    family-names: Raffaini
+    email: lemraffaini@gmail.com
+    orcid:
+repository-code: 'https://github.com/ISARICResearch/IsaricAnalytics'
+url: 'https://github.com/ISARICResearch/IsaricAnalytics'
+abstract: Data analysis toolkit to support fast analysis of clinical data during emerging infectious disease outbreaks.
+keywords:
+    - isaric
+    - infectious disease
+    - pandemic
+    - disease outbreak
+    - clinical epidemiology
+    - disease outbreak response
+    - data analysis
+    - data analytics
+license: MIT
+version: 0.2.0
+date-released:

README.md

@@ -2,7 +2,7 @@
 
 [![CodeQL](https://github.com/ISARICResearch/IsaricAnalytics/actions/workflows/github-code-scanning/codeql/badge.svg)](https://github.com/ISARICResearch/IsaricAnalytics/actions/workflows/github-code-scanning/codeql)
 [![pre-commit](https://github.com/ISARICResearch/IsaricAnalytics/actions/workflows/pre-commit.yml/badge.svg)](https://github.com/ISARICResearch/IsaricAnalytics/actions/workflows/pre-commit.yml)
-[![Tests (python versions)](https://github.com/ISARICResearch/IsaricAnalytics/actions/workflows/test-python-versions-coverage.yml/badge.svg)](https://github.com/ISARICResearch/IsaricAnalytics/actions/workflows/test-python-versions-coverage.yml)
+[![Tests (python versions)](https://github.com/ISARICResearch/IsaricAnalytics/actions/workflows/test.yml/badge.svg)](https://github.com/ISARICResearch/IsaricAnalytics/actions/workflows/test.yml)
 [![codecov](https://codecov.io/gh/ISARICResearch/IsaricAnalytics/graph/badge.svg?token=Q0A84OK6E5)](https://codecov.io/gh/ISARICResearch/IsaricAnalytics)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 
@@ -22,3 +22,7 @@ characteristics that allow some automation during research analyses and the re-u
 elements of analysis pipelines to similar contexts. This package is designed to support
 Reusable Analytical Pipelines for Infectious Diseases (RAPIDs), which is based on the concept
 of [Reproducible Analytical Pipelines](https://analysisfunction.civilservice.gov.uk/support/reproducible-analytical-pipelines/).
+
+## Documentation
+
+Project documentation is available at https://isaricanalytics.readthedocs.io/en/latest. It is built with [Sphinx](https://www.sphinx-doc.org/en/) from content and configuration defined in the [`docs`](https://github.com/ISARICResearch/VERTEX/tree/main/docs) subfolder.

docs/_static/css/custom.css

@@ -0,0 +1,3 @@
+.theme-toggle-container {
+  display: none;
+}