ci: fix coverage (#2115)

Author: flying-sheep

.github/workflows/test-cpu.yml

@@ -44,8 +44,9 @@ jobs:
       matrix:
         env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
         io_mark: ["zarr_io", "not zarr_io"]
-    env:  # environment variable for use in codecov’s env_vars tagging
+    env:  # environment variables for use in codecov’s env_vars tagging
       ENV_NAME: ${{ matrix.env.name }}
+      IO_MARK: ${{ matrix.io_mark }}
     steps:
       - uses: actions/checkout@v5
         with:
@@ -65,25 +66,27 @@ jobs:
         run: uvx hatch -v env create ${{ matrix.env.name }}
 
       - name: Run tests
+        env:
+          COVERAGE_PROCESS_START: ${{ github.workspace }}/pyproject.toml
         run: |
           uvx hatch run ${{ matrix.env.name }}:run-cov -v --color=yes -n auto --junitxml=test-data/test-results.xml -m "${{ matrix.io_mark }}" ${{ matrix.env.args }}
-          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 test results
         if: ${{ !cancelled() }}
         uses: codecov/test-results-action@v1
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
-          env_vars: ENV_NAME
+          env_vars: ENV_NAME,IO_MARK
           fail_ci_if_error: true
           file: test-data/test-results.xml
 
       - name: Upload coverage data
         uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
-          env_vars: ENV_NAME
+          env_vars: ENV_NAME,IO_MARK
           fail_ci_if_error: true
           files: test-data/coverage.xml
 

.github/workflows/test-gpu.yml

@@ -77,6 +77,8 @@ jobs:
         run: uv pip list
 
       - name: Run test
+        env:
+          COVERAGE_PROCESS_START: ${{ github.workspace }}/pyproject.toml
         run: |
           uv run coverage run -m pytest -m gpu -n auto
           uv run coverage combine

pyproject.toml

@@ -118,17 +118,15 @@ raw-options.version_scheme = "release-branch-semver"
 packages = [ "src/anndata", "src/testing" ]
 
 [tool.coverage.run]
-data_file = "test-data/coverage"
+data_file = "test-data/raw-coverage"
 source_pkgs = [ "anndata" ]
 omit = [ "src/anndata/_version.py", "**/test_*.py" ]
 concurrency = [ "multiprocessing" ]
-parallel = "true"
-
+parallel = true
 [tool.coverage.xml]
 output = "test-data/coverage.xml"
 [tool.coverage.paths]
 source = [ "./src", "**/site-packages" ]
-
 [tool.coverage.report]
 exclude_also = [
     "if TYPE_CHECKING:",