CI add codecov to GitHub Action workflow (scikit-learn#31941)

StefanieSenger · lesteve · web-flow · commit 573695653d88 · 2025-08-28T18:24:01.000+02:00
Co-authored-by: Loïc Estève &lt;loic.esteve@ymail.com&gt;
diff --git a/.codecov.yml b/.codecov.yml
@@ -19,11 +19,9 @@ coverage:
 
 codecov:
   notify:
-    # Prevent coverage status to upload multiple times for parallel and long
-    # running CI pipelines. This configuration is particularly useful on PRs
-    # to avoid confusion. Note that this value is set to the number of Azure
-    # Pipeline jobs uploading coverage reports.
-    after_n_builds: 6
+    # Prevent codecov from calculating the coverage results before all expected uploads
+    # are in. This value is set to the total number of jobs uploading coverage reports.
+    after_n_builds: 7
 
 ignore:
 - "sklearn/externals"
diff --git a/.github/workflows/unit-tests.yml b/.github/workflows/unit-tests.yml
@@ -14,6 +14,7 @@ env:
   VIRTUALENV: testvenv
   TEST_DIR: ${{ github.workspace }}/tmp_folder
   CCACHE_DIR: ${{ github.workspace }}/ccache
+  COVERAGE: 'true'
 
 jobs:
   lint:
@@ -80,3 +81,19 @@ jobs:
 
       - name: Run tests
         run: bash -l build_tools/azure/test_script.sh
+
+      - name: Combine coverage reports from parallel test runners
+        run: bash -l build_tools/azure/combine_coverage_reports.sh
+        if: ${{ env.COVERAGE == 'true' }}
+
+      - name: Upload coverage report to Codecov
+        uses: codecov/codecov-action@v5
+        # TODO: should depend on whether we run the whole test suite (could be by adding
+        # && env.SELECTED_TESTS == '' as in build_tools/azure/posix.yml, or setting
+        # env.COVERAGE == 'false' before the "Run tests" step, so reports are not
+        # generated at all)
+        if: ${{ env.COVERAGE == 'true' }}
+        with:
+          files: ./coverage.xml
+          token: ${{ secrets.CODECOV_TOKEN }}
+          disable_search: true
diff --git a/build_tools/azure/combine_coverage_reports.sh b/build_tools/azure/combine_coverage_reports.sh
@@ -8,11 +8,11 @@ source build_tools/shared.sh
 activate_environment
 
 # Combine all coverage files generated by subprocesses workers such
-# such as pytest-xdist and joblib/loky:
+# as pytest-xdist and joblib/loky:
 pushd $TEST_DIR
 coverage combine --append
 coverage xml
 popd
 
 # Copy the combined coverage file to the root of the repository:
-cp $TEST_DIR/coverage.xml $BUILD_REPOSITORY_LOCALPATH
+cp $TEST_DIR/coverage.xml .
diff --git a/build_tools/azure/test_script.sh b/build_tools/azure/test_script.sh
@@ -29,6 +29,7 @@ if [[ "$COMMIT_MESSAGE" =~ \[float32\] ]]; then
     export SKLEARN_RUN_FLOAT32_TESTS=1
 fi
 
+CHECKOUT_FOLDER=$PWD
 mkdir -p $TEST_DIR
 cp pyproject.toml $TEST_DIR
 cd $TEST_DIR
@@ -42,19 +43,19 @@ show_installed_libraries
 TEST_CMD="python -m pytest --showlocals --durations=20 --junitxml=$JUNITXML -o junit_family=legacy"
 
 if [[ "$COVERAGE" == "true" ]]; then
-    # Note: --cov-report= is used to disable to long text output report in the
+    # Note: --cov-report= is used to disable too long text output report in the
     # CI logs. The coverage data is consolidated by codecov to get an online
     # web report across all the platforms so there is no need for this text
     # report that otherwise hides the test failures and forces long scrolls in
     # the CI logs.
-    export COVERAGE_PROCESS_START="$BUILD_SOURCESDIRECTORY/.coveragerc"
+    export COVERAGE_PROCESS_START="$CHECKOUT_FOLDER/.coveragerc"
 
     # Use sys.monitoring to make coverage faster for Python >= 3.12
     HAS_SYSMON=$(python -c 'import sys; print(sys.version_info >= (3, 12))')
     if [[ "$HAS_SYSMON" == "True" ]]; then
         export COVERAGE_CORE=sysmon
     fi
-    TEST_CMD="$TEST_CMD --cov-config='$COVERAGE_PROCESS_START' --cov sklearn --cov-report="
+    TEST_CMD="$TEST_CMD --cov-config='$COVERAGE_PROCESS_START' --cov=sklearn --cov-report="
 fi
 
 if [[ "$PYTEST_XDIST_VERSION" != "none" ]]; then
diff --git a/build_tools/github/pymin_conda_forge_arm_environment.yml b/build_tools/github/pymin_conda_forge_arm_environment.yml
@@ -18,5 +18,7 @@ dependencies:
   - pip
   - ninja
   - meson-python
+  - pytest-cov
+  - coverage
   - pip
   - ccache
diff --git a/build_tools/github/pymin_conda_forge_arm_linux-aarch64_conda.lock b/build_tools/github/pymin_conda_forge_arm_linux-aarch64_conda.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: linux-aarch64
-# input_hash: f12646c755adbf5f02f95c5d07e868bf1570777923e737bc27273eb1a5e40cd7
+# input_hash: 8eb842b860f2b03822d6d35414070c39f2efbb0f464d44310dc4696eec777227
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45
 https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6
@@ -105,6 +105,7 @@ https://conda.anaconda.org/conda-forge/noarch/pyparsing-3.2.3-pyhe01879c_2.conda
 https://conda.anaconda.org/conda-forge/noarch/setuptools-80.9.0-pyhff2d567_0.conda#4de79c071274a53dcaf2a8c749d1499e
 https://conda.anaconda.org/conda-forge/noarch/six-1.17.0-pyhe01879c_1.conda#3339e3b65d58accf4ca4fb8748ab16b3
 https://conda.anaconda.org/conda-forge/noarch/threadpoolctl-3.6.0-pyhecae5ae_0.conda#9d64911b31d57ca443e9f1e36b04385f
+https://conda.anaconda.org/conda-forge/noarch/toml-0.10.2-pyhd8ed1ab_1.conda#b0dd904de08b7db706167240bf37b164
 https://conda.anaconda.org/conda-forge/noarch/tomli-2.2.1-pyhe01879c_2.conda#30a0a26c8abccf4b7991d590fe17c699
 https://conda.anaconda.org/conda-forge/linux-aarch64/tornado-6.5.2-py310ha7967c6_0.conda#443b9fabfa1a26f93551ba75797b658a
 https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.14.1-pyhe01879c_0.conda#e523f4f1e980ed7a4240d7e27e9ec81f
@@ -116,6 +117,7 @@ https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxext-1.3.6-h57736b2
 https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxfixes-6.0.1-h57736b2_0.conda#78f8715c002cc66991d7c11e3cf66039
 https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxrender-0.9.12-h86ecc28_0.conda#ae2c2dd0e2d38d249887727db2af960e
 https://conda.anaconda.org/conda-forge/linux-aarch64/ccache-4.11.3-h4889ad1_0.conda#e0b9e519da2bf0fb8c48381daf87a194
+https://conda.anaconda.org/conda-forge/linux-aarch64/coverage-7.10.5-py310h3b5aacf_0.conda#8b34a4c575c644ea70a55aee4cd532bf
 https://conda.anaconda.org/conda-forge/linux-aarch64/dbus-1.16.2-heda779d_0.conda#9203b74bb1f3fa0d6f308094b3b44c1e
 https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.3.0-pyhd8ed1ab_0.conda#72e42d28960d875c7654614f8b50939a
 https://conda.anaconda.org/conda-forge/linux-aarch64/fonttools-4.59.1-py310h2d8da20_0.conda#13f1971056891c4746589e08c84d62b3
@@ -151,6 +153,7 @@ https://conda.anaconda.org/conda-forge/linux-aarch64/xorg-libxtst-1.2.5-h57736b2
 https://conda.anaconda.org/conda-forge/linux-aarch64/blas-devel-3.9.0-34_h9678261_openblas.conda#ca55bf55f4dd0b3eb5965a0646d038ce
 https://conda.anaconda.org/conda-forge/linux-aarch64/cairo-1.18.4-h83712da_0.conda#cd55953a67ec727db5dc32b167201aa6
 https://conda.anaconda.org/conda-forge/linux-aarch64/contourpy-1.3.2-py310hf54e67a_0.conda#779694434d1f0a67c5260db76b7b7907
+https://conda.anaconda.org/conda-forge/noarch/pytest-cov-6.2.1-pyhd8ed1ab_0.conda#ce978e1b9ed8b8d49164e90a5cdc94cd
 https://conda.anaconda.org/conda-forge/noarch/pytest-xdist-3.8.0-pyhd8ed1ab_0.conda#8375cfbda7c57fbceeda18229be10417
 https://conda.anaconda.org/conda-forge/linux-aarch64/scipy-1.15.2-py310hf37559f_0.conda#5c9b72f10d2118d943a5eaaf2f396891
 https://conda.anaconda.org/conda-forge/linux-aarch64/blas-2.134-openblas.conda#20a3b428eeca10be2baee7b1a27a80ee
diff --git a/build_tools/update_environments_and_lock_files.py b/build_tools/update_environments_and_lock_files.py
@@ -393,9 +393,7 @@ def remove_from(alist, to_remove):
         "folder": "build_tools/github",
         "platform": "linux-aarch64",
         "channels": ["conda-forge"],
-        "conda_dependencies": remove_from(
-            common_dependencies_without_coverage, ["pandas", "pyamg"]
-        )
+        "conda_dependencies": remove_from(common_dependencies, ["pandas", "pyamg"])
         + ["pip", "ccache"],
         "package_constraints": {
             "python": "3.10",
