Backport PR scverse#3797: ci: fix coverage

Author: flying-sheep

.github/workflows/ci.yml

@@ -75,22 +75,23 @@ jobs:
         run: uvx hatch run ${{ matrix.env.name }}:run
       - name: Run tests (coverage)
         if: matrix.env.test-type == 'coverage'
+        env:
+          COVERAGE_PROCESS_START: ${{ github.workspace }}/pyproject.toml
         run: |
           uvx hatch run ${{ matrix.env.name }}:run-cov
-          uvx hatch run ${{ matrix.env.name }}:coverage combine
+          uvx hatch run ${{ matrix.env.name }}:cov-combine
           uvx hatch run ${{ matrix.env.name }}:coverage xml
 
       - name: Upload coverage data
+        if: ${{ !cancelled() }} && matrix.env.test-type == 'coverage'
         uses: codecov/codecov-action@v5
-        if: matrix.env.test-type == 'coverage'
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           env_vars: ENV_NAME
           fail_ci_if_error: true
           files: test-data/coverage.xml
 
       - name: Upload test results
-        # yaml strings can’t start with “!”, so using explicit substitution
         if: ${{ !cancelled() }}
         uses: codecov/test-results-action@v1
         with:

pyproject.toml

@@ -194,15 +194,15 @@ filterwarnings = [
 ]
 
 [tool.coverage.run]
-data_file = "test-data/coverage"
+data_file = "test-data/raw-coverage"
 source_pkgs = [ "scanpy" ]
 omit = [ "tests/*", "src/testing/*" ]
 concurrency = [ "multiprocessing" ]
-parallel = "true"
+parallel = true
 [tool.coverage.xml]
 output = "test-data/coverage.xml"
 [tool.coverage.paths]
-source = [ ".", "**/site-packages" ]
+source = [ "src", "**/site-packages" ]
 [tool.coverage.report]
 exclude_also = [
     "if __name__ == .__main__.:",