scikit-learn · ogrisel · Apr 2, 2023 · Mar 30, 2023 · Mar 31, 2023 · Mar 31, 2023
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -232,6 +232,7 @@ jobs:
       debian_atlas_32bit:
         DOCKER_CONTAINER: 'i386/debian:11.2'
         DISTRIB: 'debian-32'
+        COVERAGE: "true"
         LOCK_FILE: './build_tools/azure/debian_atlas_32bit_lock.txt'
         # disable pytest xdist due to unknown bug with 32-bit container
         PYTEST_XDIST_VERSION: 'none'

diff --git a/build_tools/azure/combine_coverage_reports.sh b/build_tools/azure/combine_coverage_reports.sh
@@ -0,0 +1,17 @@
+#!/bin/bash
+
+set -e
+
+# Defines the show_installed_libraries and activate_environment functions.
+source build_tools/shared.sh
+
+activate_environment
+
+# Combine all coverage files generated by subprocesses workers such
+# such as pytest-xdist and joblib/loky:
+pushd $TEST_DIR
+coverage combine --append
+popd
+
+# Copy the combined coverage file to the root of the repository:
+cp $TEST_DIR/.coverage $BUILD_REPOSITORY_LOCALPATH
diff --git a/build_tools/azure/debian_atlas_32bit_lock.txt b/build_tools/azure/debian_atlas_32bit_lock.txt
@@ -6,6 +6,8 @@
 #
 attrs==22.2.0
     # via pytest
+coverage==7.2.2
+    # via pytest-cov
 cython==0.29.33
     # via -r build_tools/azure/debian_atlas_32bit_requirements.txt
 joblib==1.1.1
@@ -19,6 +21,10 @@ pluggy==0.13.1
 py==1.11.0
     # via pytest
 pytest==5.3.1
+    # via
+    #   -r build_tools/azure/debian_atlas_32bit_requirements.txt
+    #   pytest-cov
+pytest-cov==2.9.0
     # via -r build_tools/azure/debian_atlas_32bit_requirements.txt
 threadpoolctl==2.2.0
     # via -r build_tools/azure/debian_atlas_32bit_requirements.txt

diff --git a/build_tools/azure/debian_atlas_32bit_requirements.txt b/build_tools/azure/debian_atlas_32bit_requirements.txt
@@ -5,3 +5,4 @@ cython
 joblib==1.1.1  # min
 threadpoolctl==2.2.0
 pytest==5.3.1  # min
+pytest-cov==2.9.0  # min
diff --git a/build_tools/azure/posix-docker.yml b/build_tools/azure/posix-docker.yml
@@ -56,13 +56,17 @@ jobs:
     - script: >
         docker container run --rm
         --volume $TEST_DIR:/temp_dir
+        --volume $BUILD_REPOSITORY_LOCALPATH:/repo_localpath
         --volume $PWD:/io
         --volume $CCACHE_DIR:/ccache
         -w /io
         --detach
         --name skcontainer
+        -e BUILD_SOURCESDIRECTORY=/io
         -e TEST_DIR=/temp_dir
         -e CCACHE_DIR=/ccache
+        -e BUILD_REPOSITORY_LOCALPATH=/repo_localpath
+        -e COVERAGE
         -e DISTRIB
         -e LOCK_FILE
         -e JUNITXML
@@ -82,6 +86,11 @@ jobs:
     - script: >
         docker exec skcontainer ./build_tools/azure/test_script.sh
       displayName: 'Test Library'
+    - script: >
+        docker exec skcontainer ./build_tools/azure/combine_coverage_reports.sh
+      condition: and(succeeded(), eq(variables['COVERAGE'], 'true'),
+                     eq(variables['SELECTED_TESTS'], ''))
+      displayName: 'Combine coverage'
     - task: PublishTestResults@2
       inputs:
         testResultsFiles: '$(TEST_DIR)/$(JUNITXML)'
@@ -116,3 +125,9 @@ jobs:
         JUNIT_FILE: $(TEST_DIR)/$(JUNITXML)
       condition: and(succeededOrFailed(), eq(variables['CREATE_ISSUE_ON_TRACKER'], 'true'),
                      eq(variables['Build.Reason'], 'Schedule'))
+    - bash: bash build_tools/azure/upload_codecov.sh
+      condition: and(succeeded(), eq(variables['COVERAGE'], 'true'),
+                     eq(variables['SELECTED_TESTS'], ''))
+      displayName: 'Upload To Codecov'
+      env:
+        CODECOV_TOKEN: $(CODECOV_TOKEN)
diff --git a/build_tools/azure/posix.yml b/build_tools/azure/posix.yml
@@ -67,6 +67,11 @@ jobs:
       condition: and(succeeded(),
                      eq(variables['CHECK_PYTEST_SOFT_DEPENDENCY'], 'true'),
                      eq(variables['SELECTED_TESTS'], ''))
+    - script: |
+        build_tools/azure/combine_coverage_reports.sh
+      condition: and(succeeded(), eq(variables['COVERAGE'], 'true'),
+                     eq(variables['SELECTED_TESTS'], ''))
+      displayName: 'Combine coverage'
     - task: PublishTestResults@2
       inputs:
         testResultsFiles: '$(TEST_DIR)/$(JUNITXML)'

diff --git a/build_tools/azure/test_script.sh b/build_tools/azure/test_script.sh
@@ -2,14 +2,10 @@
 
 set -e
 
-# defines the show_installed_libraries function
+# Defines the show_installed_libraries and activate_environment functions.
 source build_tools/shared.sh
 
-if [[ "$DISTRIB" =~ ^conda.* ]]; then
-    source activate $VIRTUALENV
-elif [[ "$DISTRIB" == "ubuntu" || "$DISTRIB" == "debian-32" || "$DISTRIB" == "pip-nogil" ]]; then
-    source $VIRTUALENV/bin/activate
-fi
+activate_environment
 
 if [[ "$BUILD_REASON" == "Schedule" ]]; then
     # Enable global random seed randomization to discover seed-sensitive tests

diff --git a/build_tools/azure/upload_codecov.sh b/build_tools/azure/upload_codecov.sh
@@ -2,41 +2,48 @@
 
 set -e
 
-# called when COVERAGE=="true" and DISTRIB=="conda"
-export PATH=$HOME/miniconda3/bin:$PATH
-source activate $VIRTUALENV
-
-# Need to run codecov from a git checkout, so we copy .coverage
-# from TEST_DIR where pytest has been run
-pushd $TEST_DIR
-coverage combine --append
-popd
-cp $TEST_DIR/.coverage $BUILD_REPOSITORY_LOCALPATH
-
 # When we update the codecov uploader version, we need to update the checksums.
 # The checksum for each codecov binary is available at
 # https://uploader.codecov.io e.g. for linux
-# https://uploader.codecov.io/v0.4.0/linux/codecov.SHA256SUM. In principle we
-# need to check the signatures with the codecov gpg key as well, see
+# https://uploader.codecov.io/v0.4.1/linux/codecov.SHA256SUM.
+
+# Instead of hardcoding a specific version and signature in this script, it
+# would be possible to use the "latest" symlink URL but then we need to
+# download both the codecov.SHA256SUM files each time and check the signatures
+# with the codecov gpg key as well, see:
 # https://docs.codecov.com/docs/codecov-uploader#integrity-checking-the-uploader
-# for more details
-CODECOV_UPLOADER_VERSION=0.4.0
+# However this approach would yield a larger number of downloads from
+# codecov.io and keybase.io, therefore increasing the risk of running into
+# network failures.
+CODECOV_UPLOADER_VERSION=0.4.1
 CODECOV_BASE_URL="https://uploader.codecov.io/v$CODECOV_UPLOADER_VERSION"
+
+
+# Check that the git repo is located at the expected location:
+if [[ ! -d "$BUILD_REPOSITORY_LOCALPATH/.git" ]]; then
+    echo "Could not find the git checkout at $BUILD_REPOSITORY_LOCALPATH"
+    exit 1
+fi
+# Check that the combined coverage file exists at the expected location:
+if [[ ! -f "$BUILD_REPOSITORY_LOCALPATH/.coverage" ]]; then
+    echo "Could not find the combined coverage file at $BUILD_REPOSITORY_LOCALPATH/.coverage"
+    exit 1
+fi
 if [[ $OSTYPE == *"linux"* ]]; then
     curl -Os "$CODECOV_BASE_URL/linux/codecov"
-    SHA256SUM="671cf0d89d1c149f57e1a9a31f3fb567ab4209e4d5829f13ff7b8c104db7131f  codecov"
+    SHA256SUM="32cb14b5f3aaacd67f4c1ff55d82f037d3cd10c8e7b69c051f27391d2e66e15c  codecov"
     echo "$SHA256SUM" | shasum -a256 -c
     chmod +x codecov
-    ./codecov -t ${CODECOV_TOKEN} --rootDir $BUILD_REPOSITORY_LOCALPATH
+    ./codecov -t ${CODECOV_TOKEN} -R $BUILD_REPOSITORY_LOCALPATH -f .coverage -Z
 elif [[ $OSTYPE == *"darwin"* ]]; then
     curl -Os "$CODECOV_BASE_URL/macos/codecov"
-    SHA256SUM="7549819f0fe115e113ec3538e259d748e87d84f68afa5deadc798967ec716b8d  codecov"
+    SHA256SUM="4ab0f06f06e9c4d25464f155b0aff36bfc1e8dbcdb19bfffd586beed1269f3af  codecov"
     echo "$SHA256SUM" | shasum -a256 -c
     chmod +x codecov
-    ./codecov -t ${CODECOV_TOKEN} --rootDir $BUILD_REPOSITORY_LOCALPATH
+    ./codecov -t ${CODECOV_TOKEN} -R $BUILD_REPOSITORY_LOCALPATH -f .coverage -Z
 else
     curl -Os "$CODECOV_BASE_URL/windows/codecov.exe"
-    SHA256SUM="15fb34be4eb9949ad4e964a0e21c4efc79657de05b2c799e041d7293dccf60eb  codecov.exe"
+    SHA256SUM="e0cda212aeaebe695509ce8fa2d608760ff70bc932003f544f1ad368ac5450a8 codecov.exe"
     echo "$SHA256SUM" | sha256sum -c
-    ./codecov.exe -t ${CODECOV_TOKEN} --rootDir $BUILD_REPOSITORY_LOCALPATH
+    ./codecov.exe -t ${CODECOV_TOKEN} -R $BUILD_REPOSITORY_LOCALPATH -f .coverage -Z
 fi
diff --git a/build_tools/azure/windows.yml b/build_tools/azure/windows.yml
@@ -41,13 +41,10 @@ jobs:
       displayName: 'Install'
     - bash: ./build_tools/azure/test_script.sh
       displayName: 'Test Library'
-    - bash: ./build_tools/azure/upload_codecov.sh
-      condition: and(succeeded(),
-                     eq(variables['COVERAGE'], 'true'),
+    - bash: ./build_tools/azure/combine_coverage_reports.sh
+      condition: and(succeeded(), eq(variables['COVERAGE'], 'true'),
                      eq(variables['SELECTED_TESTS'], ''))
-      displayName: 'Upload To Codecov'
-      env:
-        CODECOV_TOKEN: $(CODECOV_TOKEN)
+      displayName: 'Combine coverage'
     - task: PublishTestResults@2
       inputs:
         testResultsFiles: '$(TEST_DIR)/$(JUNITXML)'
@@ -78,3 +75,10 @@ jobs:
         JUNIT_FILE: $(TEST_DIR)/$(JUNITXML)
       condition: and(succeededOrFailed(), eq(variables['CREATE_ISSUE_ON_TRACKER'], 'true'),
                      eq(variables['Build.Reason'], 'Schedule'))
+    - bash: ./build_tools/azure/upload_codecov.sh
+      condition: and(succeeded(),
+                     eq(variables['COVERAGE'], 'true'),
+                     eq(variables['SELECTED_TESTS'], ''))
+      displayName: 'Upload To Codecov'
+      env:
+        CODECOV_TOKEN: $(CODECOV_TOKEN)
diff --git a/build_tools/shared.sh b/build_tools/shared.sh
@@ -25,3 +25,11 @@ show_installed_libraries(){
         python -m pip list
     fi
 }
+
+activate_environment() {
+    if [[ "$DISTRIB" =~ ^conda.* ]]; then
+        source activate $VIRTUALENV
+    elif [[ "$DISTRIB" == "ubuntu" || "$DISTRIB" == "debian-32" || "$DISTRIB" == "pip-nogil" ]]; then
+        source $VIRTUALENV/bin/activate
+    fi
+}
diff --git a/build_tools/update_environments_and_lock_files.py b/build_tools/update_environments_and_lock_files.py
@@ -329,11 +329,18 @@ def remove_from(alist, to_remove):
     {
         "build_name": "debian_atlas_32bit",
         "folder": "build_tools/azure",
-        "pip_dependencies": ["cython", "joblib", "threadpoolctl", "pytest"],
+        "pip_dependencies": [
+            "cython",
+            "joblib",
+            "threadpoolctl",
+            "pytest",
+            "pytest-cov",
+        ],
         "package_constraints": {
             "joblib": "min",
             "threadpoolctl": "2.2.0",
             "pytest": "min",
+            "pytest-cov": "min",
             # no pytest-xdist because it causes issue on 32bit
         },
         # same Python version as in debian-32 build