Project improvements and VERTEX code migration

.github/workflows/test-python-versions-coverage.yml

@@ -9,33 +9,45 @@ on:
 
 jobs:
 
-  build:
-    name: Python version tests and coverage
+  test:
+    name: Python tests and coverage
     runs-on: ubuntu-latest
-
-    # Skip job if it's a draft PR
-    if: github.event.pull_request.draft == false
+    permissions:
+      contents: read
+      pull-requests: write
 
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.11"]
         # Note: Latest version is tested by os tests
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: install
+      - name: Run tests
         run: |
-          python --version
-          python -m pip install --upgrade pip setuptools wheel
-          python -m pip install .
+          pip install pdm &&\
+          pdm install -v -dG "test" --no-editable --no-self &&\
+          pdm run -v python -m pytest --code-highlight=yes --color=yes --verbosity=3 -p pytest_cov --cov=isaricanalytics --cov-report=term-missing --cov-report=xml
 
-      - name: "run unit tests (todo: upload to Codecov)"
-        run: |
-          python -m pytest --cov=isaricanalytics --cov-report=xml
+      - name: Upload coverage XML
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-xml
+          path: coverage.xml
+          if-no-files-found: error
+
+      - name: Upload coverage report to Codecov
+        continue-on-error: true
+        uses: codecov/codecov-action@v5
+        with:
+          files: ./coverage.xml
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: false
+          verbose: true

.gitignore

@@ -1,3 +1,9 @@
+# logs
+app.log*
+
+#public project dir
+projects/*
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -50,6 +56,7 @@ coverage.xml
 .hypothesis/
 .pytest_cache/
 cover/
+test-results/
 
 # Translations
 *.mo
@@ -162,3 +169,5 @@ cython_debug/
 # Ignore Mac DS_Store files
 .DS_Store
 **/.DS_Store
+
+docs/_build

README.md

@@ -1,5 +1,11 @@
 # IsaricAnalytics
 
+[![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)
+[![codecov](https://codecov.io/gh/ISARICResearch/IsaricAnalytics/graph/badge.svg?token=Q0A84OK6E5)](https://codecov.io/gh/ISARICResearch/IsaricAnalytics)
+[![License: CC BY-SA 4.0](https://img.shields.io/badge/License-CC%20BY--SA%204.0-lightgrey.svg)](https://creativecommons.org/licenses/by-sa/4.0/)
+
 IsaricAnalytics is a data analysis toolkit to support fast analysis of clinical data during
 emerging infectious disease outbreaks. It supports medical statistics and traditional
 machine learning, with analysis pipelines that follow methodological best practices.

SECURITY.md

@@ -0,0 +1,5 @@
+# Security Policy
+
+A number of security measures are used including code scanning, secrets scanning, and Dependabot alerts.
+
+Vulnerabilities can be reported privately to data@isaric.org.

codecov.yml

@@ -0,0 +1,15 @@
+coverage:
+  status:
+    project:
+      default:
+        target: 80%
+        threshold: 0%
+        flags:
+          - unit
+        paths:
+          - "isaricanalytics"
+        branches:
+          - main
+        if_ci_failed: error
+        informational: false
+        only_pulls: false

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)