improve coverage reporting

Author: FynnBe

.github/workflows/build.yaml

@@ -93,7 +93,7 @@ jobs:
           path: bioimageio_cache
           key: ${{needs.populate-cache.outputs.cache-key}}
       - name: pytest
-        run: pytest --cov bioimageio --cov-report xml --cov-append --capture no --disable-pytest-warnings
+        run: pytest --cov bioimageio --cov-append --capture no --disable-pytest-warnings
         env:
           BIOIMAGEIO_CACHE_PATH: bioimageio_cache
           RUN_EXPENSIVE_TESTS: ${{ matrix.run-expensive-tests && 'true' || 'false' }}
@@ -104,20 +104,45 @@ jobs:
           path: bioimageio_cache
           key: ${{needs.populate-cache.outputs.cache-key}}
 
-      - if: matrix.report-coverage && github.event_name == 'pull_request'
-        uses: orgoro/[email protected]
+      - run: cp .coverage .coverage.${{matrix.python-version}}-${{matrix.numpy-version}}
+      - uses: actions/upload-artifact@v4
+        with:
+          name: .coverage.${{matrix.python-version}}-${{matrix.numpy-version}}
+          retention-days: 1
+          path: .coverage.${{matrix.python-version}}-${{matrix.numpy-version}}
+          include-hidden-files: true
+
+  coverage:
+    needs: [test]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v6
+      - run: |
+          pip install coverage
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: .coverage.*
+          merge-multiple: true
+      - run: |
+          ls -la .coverage*
+          coverage combine
+          coverage xml -o coverage.xml
+      - uses: orgoro/[email protected]
         with:
           coverageFile: coverage.xml
-          token: ${{secrets.GITHUB_TOKEN}}
-      - if: matrix.report-coverage && github.ref == 'refs/heads/main'
+          token: ${{ secrets.GITHUB_TOKEN }}
+          thresholdAll: 0.7
+          thresholdNew: 0.9
+          thresholdModified: 0.6
+      - name: generate coverage badge and html report
         run: |
           pip install genbadge[coverage]
           genbadge coverage --input-file coverage.xml --output-file ./dist/coverage/coverage-badge.svg
           coverage html -d dist/coverage
-      - if: matrix.report-coverage && github.ref == 'refs/heads/main'
-        uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v4
         with:
-          name: coverage
+          name: coverage-summary
           retention-days: 1
           path: dist
 
@@ -157,7 +182,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/download-artifact@v4
         with:
-          name: coverage
+          name: coverage-summary
           path: dist
       - uses: actions/setup-python@v6
         with: