Add badges (#29)

Add self-hosted (well, github pages hosted) badges and reports (tests and coverage) using coverage.py and genbadge.

The reports and badges are hosted in a different repo. To add this to another repo, you'd just have to use a suitable access token as a repository secret (ie, one that has access to the qupath badges repo).

.github/workflows/tests.yml

@@ -1,6 +1,6 @@
-# This workflow will run unit tests on pull requests or when manually activated
+# This workflow will run unit tests when main is updated, on pull requests or when manually activated
 
-name: test
+name: pytest
 
 on:
   push:
@@ -24,9 +24,53 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: "3.10"
-        
+
       - name: Install
         run: pip install .[test]
 
       - name: Run tests
-        run: pytest
+        run: |
+          coverage run -m pytest --junitxml=reports/junit/junit.xml --html=reports/junit/report.html
+
+
+      ## everything from here deals with generating and uploading reports and badges to a separate "badges" repo.
+      - name: Create reports and badges
+        if: github.ref_name == 'main' && matrix.os == 'ubuntu-latest'
+        run: |
+          coverage xml -o reports/coverage/coverage.xml
+          coverage html -d reports/coverage/
+          genbadge coverage -i reports/coverage/coverage.xml
+          genbadge tests -i reports/junit/junit.xml
+
+
+      - name: Make badge dir
+        if: github.ref_name == 'main' && matrix.os == 'ubuntu-latest'
+        run: |
+          mkdir -p badges
+          mv *badge.svg badges
+
+      - name: Setup assets dir
+        if: github.ref_name == 'main' && matrix.os == 'ubuntu-latest'
+        run: |
+          mkdir assets
+          mv badges assets/
+          mv reports assets/
+
+      - name: Clone badges repo
+        if: github.ref_name == 'main' && matrix.os == 'ubuntu-latest'
+        run: |
+            git clone --branch=gh-pages https://${{ secrets.TARGET_REPO_ACCESS_TOKEN }}@github.com/qupath/badges.git badges
+            ## cba handling merging or dealing with stale resources
+            rm -rf badges/${{ github.event.repository.name }}
+            mkdir -p badges/${{ github.event.repository.name }}
+            mv assets/* badges/${{github.event.repository.name}}/
+
+      - name: Deploy badges to gh-pages
+        if: github.ref_name == 'main' && matrix.os == 'ubuntu-latest'
+        run: |
+          cd badges
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          git add .
+          git commit -m "Update badges and reports"
+          git push

.gitignore

@@ -138,3 +138,5 @@ dmypy.json
 # Generated test images
 *.tif
 *.zarr
+reports
+*.svg

README.md

@@ -1,5 +1,9 @@
+[![Coverage](https://qupath.github.io/badges/badges/coverage-badge.svg?dummy=1234)](https://qupath.github.io/badges/reports/coverage/index.html?dummy=1234)
+[![Tests](https://qupath.github.io/badges/badges/tests-badge.svg?dummy=1234)](https://qupath.github.io/badges/reports/junit/report.html?dummy=1234)
+![Actions](https://github.com/qupath/qubalab/actions/workflows/tests.yml/badge.svg?dummy=1234)
 # QuBaLab
 
+
 This is a Python package for exploring quantitative bioimage analysis... *especially* (but not exclusively) in combination with QuPath (https://qupath.github.io/).
 
 The name comes from **Quantitative Bioimage Analysis Laboratory**. This is chosen to be reminiscent of QuPath (*Quantitative Pathology*), but recognizes that neither is really restricted to pathology.

setup.cfg

@@ -36,7 +36,9 @@ dev =
     jupyter ~= 1.0.0
 test =
     pytest ~= 8.2.2
-openslide =
+    pytest-html ~= 4.1.1
+    coverage ~= 7.6.5
+    genbadge[all] ~= 1.1.1
 doc =
     sphinx ~= 7.4.5
     sphinx-rtd-theme ~= 2.0.0