ci(coverage): update tests.yaml to run with coverage on ubunutu + add badge to README

Author: amyheather

.github/workflows/tests.yaml

@@ -33,6 +33,8 @@ jobs:
 
   # Run tests using matrix strategy
   tests:
+    permissions:
+      contents: write
     needs: setup-matrix
     runs-on: ${{ matrix.os }}
     strategy:
@@ -57,8 +59,33 @@ jobs:
         if: runner.os != 'Windows'
         run: pip install -r requirements.txt
 
-      - name: Run tests
-        run: pytest
+      - name: Run tests (with coverage for linux)
+        run: |
+          if [ "${{ matrix.os }}" = "ubuntu-latest" ]; then
+            pytest --cov --cov-report=xml
+          else
+            pytest
+          fi
+        shell: bash
+
+      - name: Generate coverage badge (for-the-badge style)
+        if: matrix.os == 'ubuntu-latest'
+        run: genbadge coverage -i coverage.xml -o images/coverage-badge.svg
 
-      - name: List the environment variables
-        run: env
+      - name: Upload coverage badge
+        if: matrix.os == 'ubuntu-latest'
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-badge
+          path: images/coverage-badge.svg
+
+      - name: Commit coverage badge
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          git config --local user.email "github-actions[bot]@users.noreply.github.com"
+          git config --local user.name "github-actions[bot]"
+          git add images/coverage-badge.svg
+          git commit -m "ci(tests): update coverage badge" || echo "No changes to commit"
+          git push
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

README.md

@@ -7,7 +7,7 @@
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14622466.svg)](https://doi.org/10.5281/zenodo.14622466)
 [![Tests](https://github.com/pythonhealthdatascience/pydesrap_mms/actions/workflows/tests.yaml/badge.svg)](https://github.com/pythonhealthdatascience/pydesrap_mms/actions/workflows/tests.yaml)
 [![Linting](https://github.com/pythonhealthdatascience/pydesrap_mms/actions/workflows/lint.yaml/badge.svg)](https://github.com/pythonhealthdatascience/pydesrap_mms/actions/workflows/lint.yaml)
-[![ORCID](https://img.shields.io/badge/ORCID_Amy_Heather-0000--0002--6596--3479-A6CE39?&logo=orcid&logoColor=white)](https://orcid.org/0000-0002-6596-3479)
+[![Coverage](https://github.com/pythonhealthdatascience/pydesrap_mms/raw/main/images/coverage-badge.svg)](https://github.com/pythonhealthdatascience/pydesrap_mms/actions/workflows/tests.yaml)
 </div>
 
 ## Repository overview