fix: use coverage combine with path mapping for accurate diff-cover

Per-package coverage.xml files stored source filenames relative to each
package directory, making diff-cover unable to match them against git
diff paths. This caused diff-cover to report artificially low coverage
despite tests achieving 100% coverage on the changed lines.

- Enable relative_files in coverage.run config
- Add coverage.paths mapping so coverage combine can unify per-package
  paths into paths relative to the python/ workspace root
- Move skip_empty to coverage.report where it belongs
- Replace per-file diff-cover invocation with coverage combine followed
  by diff-cover on a single merged coverage.xml
- Remove redundant PYTEST_ADDOPTS override from CI

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: raballew

.github/workflows/python-tests.yaml

@@ -117,21 +117,21 @@ jobs:
 
       - name: Run pytest
         working-directory: python
-        env:
-          PYTEST_ADDOPTS: "--cov --cov-report=xml"
         run: |
             make test
 
       - name: Check coverage on changed lines
         if: github.event_name == 'pull_request'
         working-directory: python
         run: |
-            coverage_files=$(find packages -name coverage.xml 2>/dev/null | sort)
-            if [ -z "$coverage_files" ]; then
-              echo "::error::No coverage.xml files found"
+            coverage_data=$(find packages -name .coverage -type f 2>/dev/null | sort)
+            if [ -z "$coverage_data" ]; then
+              echo "::error::No .coverage data files found"
               exit 1
             fi
-            uv run diff-cover $coverage_files --compare-branch=origin/${{ github.base_ref }} --fail-under=80
+            uv run coverage combine $coverage_data
+            uv run coverage xml -o combined-coverage.xml
+            uv run diff-cover combined-coverage.xml --compare-branch=origin/${{ github.base_ref }} --fail-under=80
 
   # https://github.com/orgs/community/discussions/26822
   pytest:

python/pyproject.toml

@@ -101,9 +101,17 @@ mosquitto = "mosquitto"
 
 [tool.coverage.run]
 branch = true
+relative_files = true
 omit = ["conftest.py", "test_*.py", "*_test.py", "*_pb2.py", "*_pb2_grpc.py"]
+
+[tool.coverage.report]
 skip_empty = true
 
+[tool.coverage.paths]
+source = [
+    "packages/*/",
+]
+
 [tool.pytest.ini_options]
 addopts = "--capture=no --doctest-modules --cov --cov-report=html --cov-report=xml"