scikit-learn · MaxwellLZH · Oct 25, 2021 · Oct 26, 2021 · Nov 7, 2021 · Nov 7, 2021
diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
@@ -84,6 +84,8 @@ jobs:
 
       - name: Setup Python
         uses: actions/setup-python@v2
+        with:
+          python-version: '3.9'  # update once build dependencies are available
 
       - name: Build and test wheels
         env:

diff --git a/.travis.yml b/.travis.yml
@@ -22,7 +22,7 @@ env:
     # Custom environment variables for the ARM wheel builder
     - CIBW_BUILD_VERBOSITY=1
     - CIBW_TEST_COMMAND="bash {project}/build_tools/travis/test_wheels.sh"
-    - CIBW_ENVIRONMENT="CPU_COUNT=6
+    - CIBW_ENVIRONMENT="CPU_COUNT=2
                         OMP_NUM_THREADS=2
                         OPENBLAS_NUM_THREADS=2
                         SKLEARN_BUILD_PARALLEL=10
@@ -39,23 +39,32 @@ jobs:
     # fast.
     - python: 3.7
       os: linux
-      arch: arm64
+      arch: arm64-graviton2
+      dist: focal
+      virt: lxd
+      group: edge
       if: type = cron or commit_message =~ /\[cd build\]/
       env:
         - BUILD_WHEEL=true
         - CIBW_BUILD=cp37-manylinux_aarch64
 
     - python: 3.8
       os: linux
-      arch: arm64
+      arch: arm64-graviton2
+      dist: focal
+      virt: lxd
+      group: edge
       if: type = cron or commit_message =~ /\[cd build\]/
       env:
         - BUILD_WHEEL=true
         - CIBW_BUILD=cp38-manylinux_aarch64
 
     - python: 3.9
       os: linux
-      arch: arm64
+      arch: arm64-graviton2
+      dist: focal
+      virt: lxd
+      group: edge
       if: type = cron or commit_message =~ /\[cd build\]/
       env:
         - BUILD_WHEEL=true

diff --git a/README.rst b/README.rst
@@ -5,15 +5,15 @@
 .. |Azure| image:: https://dev.azure.com/scikit-learn/scikit-learn/_apis/build/status/scikit-learn.scikit-learn?branchName=main
 .. _Azure: https://dev.azure.com/scikit-learn/scikit-learn/_build/latest?definitionId=1&branchName=main
 
+.. |CircleCI| image:: https://circleci.com/gh/scikit-learn/scikit-learn/tree/main.svg?style=shield&circle-token=:circle-token
+.. _CircleCI: https://circleci.com/gh/scikit-learn/scikit-learn
+
 .. |Travis| image:: https://api.travis-ci.com/scikit-learn/scikit-learn.svg?branch=main
-.. _Travis: https://travis-ci.com/scikit-learn/scikit-learn
+.. _Travis: https://app.travis-ci.com/github/scikit-learn/scikit-learn
 
 .. |Codecov| image:: https://codecov.io/gh/scikit-learn/scikit-learn/branch/main/graph/badge.svg?token=Pk8G9gg3y9
 .. _Codecov: https://codecov.io/gh/scikit-learn/scikit-learn
 
-.. |CircleCI| image:: https://circleci.com/gh/scikit-learn/scikit-learn/tree/main.svg?style=shield&circle-token=:circle-token
-.. _CircleCI: https://circleci.com/gh/scikit-learn/scikit-learn
-
 .. |Nightly wheels| image:: https://github.com/scikit-learn/scikit-learn/workflows/Wheel%20builder/badge.svg?event=schedule
 .. _`Nightly wheels`: https://github.com/scikit-learn/scikit-learn/actions?query=workflow%3A%22Wheel+builder%22+event%3Aschedule
 
@@ -186,6 +186,7 @@ Communication
 - Stack Overflow: https://stackoverflow.com/questions/tagged/scikit-learn
 - Github Discussions: https://github.com/scikit-learn/scikit-learn/discussions
 - Website: https://scikit-learn.org
+- LinkedIn: https://www.linkedin.com/company/scikit-learn
 
 Citation
 ~~~~~~~~

diff --git a/SECURITY.md b/SECURITY.md
@@ -0,0 +1,17 @@
+# Security Policy
+
+## Supported Versions
+
+| Version   | Supported          |
+| --------- | ------------------ |
+| 1.0.1     | :white_check_mark: |
+| < 1.0.1   | :x:                |
+
+## Reporting a Vulnerability
+
+Please report security vulnerabilities by email to `security@scikit-learn.org`.
+This email is an alias to a subset of the scikit-learn maintainers' team.
+
+If the security vulnerability is accepted, a patch will be crafted privately
+in order to prepare a dedicated bugfix release as timely as possible (depending
+on the complexity of the fix).
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -48,7 +48,7 @@ jobs:
         pip install pytest flake8 mypy==0.782 black==21.6b0
       displayName: Install linters
     - bash: |
-        black --check .
+        black --check --diff .
       displayName: Run black
     - bash: |
         ./build_tools/circle/linting.sh
@@ -81,6 +81,7 @@ jobs:
         # Tests that require large downloads over the networks are skipped in CI.
         # Here we make sure, that they are still run on a regular basis.
         SKLEARN_SKIP_NETWORK_TESTS: '0'
+        CREATE_ISSUE_ON_TRACKER: 'true'
 
 # Check compilation with intel C++ compiler (ICC)
 - template: build_tools/azure/posix.yml
@@ -105,6 +106,28 @@ jobs:
         COVERAGE: 'false'
         BUILD_WITH_ICC: 'true'
 
+- template: build_tools/azure/posix-docker.yml
+  parameters:
+    name: Linux_Nightly_PyPy
+    vmImage: ubuntu-20.04
+    dependsOn: [linting, git_commit]
+    condition: |
+      and(
+        succeeded(),
+        not(contains(dependencies['git_commit']['outputs']['commit.message'], '[ci skip]')),
+        or(
+          eq(variables['Build.Reason'], 'Schedule'),
+          contains(dependencies['git_commit']['outputs']['commit.message'], '[pypy]')
+        )
+      )
+    matrix:
+      pypy3:
+        DISTRIB: 'conda-mamba-pypy3'
+        DOCKER_CONTAINER: 'condaforge/mambaforge-pypy3:4.10.3-5'
+        PILLOW_VERSION: 'none'
+        PANDAS_VERSION: 'none'
+        CREATE_ISSUE_ON_TRACKER: 'true'
+
 # Will run all the time regardless of linting outcome.
 - template: build_tools/azure/posix.yml
   parameters:
@@ -123,6 +146,7 @@ jobs:
         PYTHON_VERSION: '*'
         BLAS: 'mkl'
         COVERAGE: 'true'
+        SHOW_SHORT_SUMMARY: 'true'
 
 # Check compilation with Ubuntu bionic 18.04 LTS and scipy from conda-forge
 - template: build_tools/azure/posix.yml
@@ -198,11 +222,6 @@ jobs:
         ne(variables['Build.Reason'], 'Schedule')
       )
     matrix:
-      pypy3:
-        DISTRIB: 'conda-mamba-pypy3'
-        DOCKER_CONTAINER: 'condaforge/mambaforge-pypy3:4.10.3-5'
-        PILLOW_VERSION: 'none'
-        PANDAS_VERSION: 'none'
       debian_atlas_32bit:
         DISTRIB: 'debian-32'
         DOCKER_CONTAINER: 'i386/debian:10.9'
@@ -237,7 +256,7 @@ jobs:
 - template: build_tools/azure/windows.yml
   parameters:
     name: Windows
-    vmImage: vs2017-win2016
+    vmImage: windows-latest
     dependsOn: [linting, git_commit]
     condition: |
       and(

diff --git a/build_tools/azure/posix-docker.yml b/build_tools/azure/posix-docker.yml
@@ -34,6 +34,7 @@ jobs:
     # Set in azure-pipelines.yml
     DISTRIB: ''
     DOCKER_CONTAINER: ''
+    SHOW_SHORT_SUMMARY: 'false'
   strategy:
     matrix:
       ${{ insert }}: ${{ parameters.matrix }}

diff --git a/build_tools/azure/posix.yml b/build_tools/azure/posix.yml
@@ -33,6 +33,8 @@ jobs:
     THREADPOOLCTL_VERSION: 'latest'
     COVERAGE: 'true'
     TEST_DOCSTRINGS: 'false'
+    CREATE_ISSUE_ON_TRACKER: 'false'
+    SHOW_SHORT_SUMMARY: 'false'
   strategy:
     matrix:
       ${{ insert }}: ${{ parameters.matrix }}
@@ -72,6 +74,30 @@ jobs:
         testRunTitle: ${{ format('{0}-$(Agent.JobName)', parameters.name) }}
       displayName: 'Publish Test Results'
       condition: succeededOrFailed()
+    - task: UsePythonVersion@0
+      inputs:
+        versionSpec: '3.9'
+      displayName: Place Python into path to update issue tracker
+      condition: and(succeededOrFailed(), eq(variables['CREATE_ISSUE_ON_TRACKER'], 'true'),
+                     eq(variables['Build.Reason'], 'Schedule'))
+    - bash: |
+        set -ex
+        if [[ $(BOT_GITHUB_TOKEN) == "" ]]; then
+          echo "GitHub Token is not set. Issue tracker will not be updated."
+          exit
+        fi
+
+        LINK_TO_RUN="https://dev.azure.com/$BUILD_REPOSITORY_NAME/_build/results?buildId=$BUILD_BUILDID&view=logs&j=$SYSTEM_JOBID"
+        CI_NAME="$SYSTEM_JOBIDENTIFIER"
+        ISSUE_REPO="$BUILD_REPOSITORY_NAME"
+
+        pip install defusedxml PyGithub
+        python maint_tools/create_issue_from_juint.py $(BOT_GITHUB_TOKEN) $CI_NAME $ISSUE_REPO $LINK_TO_RUN $JUNIT_FILE
+      displayName: 'Update issue tracker'
+      env:
+        JUNIT_FILE: $(TEST_DIR)/$(JUNITXML)
+      condition: and(succeededOrFailed(), eq(variables['CREATE_ISSUE_ON_TRACKER'], 'true'),
+                     eq(variables['Build.Reason'], 'Schedule'))
     - script: |
         build_tools/azure/upload_codecov.sh
       condition: and(succeeded(), eq(variables['COVERAGE'], 'true'))

diff --git a/build_tools/azure/test_script.sh b/build_tools/azure/test_script.sh
@@ -17,7 +17,6 @@ cp setup.cfg $TEST_DIR
 cd $TEST_DIR
 
 python -c "import sklearn; sklearn.show_versions()"
-python -m threadpoolctl -i sklearn
 
 if ! command -v conda &> /dev/null
 then
@@ -36,18 +35,28 @@ if [[ "$COVERAGE" == "true" ]]; then
     # report that otherwise hides the test failures and forces long scrolls in
     # the CI logs.
     export COVERAGE_PROCESS_START="$BUILD_SOURCESDIRECTORY/.coveragerc"
-    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 [[ -n "$CHECK_WARNINGS" ]]; then
     # numpy's 1.19.0's tostring() deprecation is ignored until scipy and joblib removes its usage
     TEST_CMD="$TEST_CMD -Werror::DeprecationWarning -Werror::FutureWarning -Wignore:tostring:DeprecationWarning"
+
+    # Python 3.10 deprecates disutils and is imported by numpy interally during import time
+    TEST_CMD="$TEST_CMD -Wignore:The\ distutils:DeprecationWarning"
+
+    # Workaround for https://github.com/pypa/setuptools/issues/2885
+    TEST_CMD="$TEST_CMD -Wignore:Creating\ a\ LegacyVersion:DeprecationWarning"
 fi
 
 if [[ "$PYTEST_XDIST_VERSION" != "none" ]]; then
     TEST_CMD="$TEST_CMD -n2"
 fi
 
+if [[ "$SHOW_SHORT_SUMMARY" == "true" ]]; then
+    TEST_CMD="$TEST_CMD -ra"
+fi
+
 set -x
-$TEST_CMD --pyargs sklearn
+eval "$TEST_CMD --pyargs sklearn"
 set +x
diff --git a/build_tools/azure/windows.yml b/build_tools/azure/windows.yml
@@ -20,6 +20,7 @@ jobs:
     PYTEST_XDIST: 'true'
     PYTEST_XDIST_VERSION: 'latest'
     TEST_DIR: '$(Agent.WorkFolder)/tmp_folder'
+    SHOW_SHORT_SUMMARY: 'false'
   strategy:
     matrix:
       ${{ insert }}: ${{ parameters.matrix }}

diff --git a/build_tools/circle/build_doc.sh b/build_tools/circle/build_doc.sh
@@ -145,8 +145,8 @@ fi
 
 MINICONDA_PATH=$HOME/miniconda
 # Install dependencies with miniconda
-wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
-   -O miniconda.sh
+wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh \
+    -O miniconda.sh
 chmod +x miniconda.sh && ./miniconda.sh -b -p $MINICONDA_PATH
 export PATH="/usr/lib/ccache:$MINICONDA_PATH/bin:$PATH"
 
@@ -165,7 +165,7 @@ fi
 source build_tools/shared.sh
 
 # packaging won't be needed once setuptools starts shipping packaging>=17.0
-conda create -n $CONDA_ENV_NAME --yes --quiet \
+mamba create -n $CONDA_ENV_NAME --yes --quiet \
     python="${PYTHON_VERSION:-*}" \
     "$(get_dep numpy $NUMPY_VERSION)" \
     "$(get_dep scipy $SCIPY_VERSION)" \
@@ -176,6 +176,11 @@ conda create -n $CONDA_ENV_NAME --yes --quiet \
     joblib memory_profiler packaging seaborn pillow pytest coverage
 
 source activate testenv
+# Pin PyWavelet to 1.1.1 that is the latest version that support our minumum
+# NumPy version required. If PyWavelets 1.2+ is installed, it would require
+# NumPy 1.17+ that trigger a bug with Pandas 0.25:
+# https://github.com/numpy/numpy/issues/18355#issuecomment-774610226
+pip install PyWavelets==1.1.1
 pip install "$(get_dep scikit-image $SCIKIT_IMAGE_VERSION)"
 pip install "$(get_dep sphinx-gallery $SPHINX_GALLERY_VERSION)"
 pip install "$(get_dep numpydoc $NUMPYDOC_VERSION)"

diff --git a/build_tools/github/test_wheels.sh b/build_tools/github/test_wheels.sh
@@ -9,7 +9,7 @@ if [[ "$OSTYPE" != "linux-gnu" ]]; then
     cp $CONFTEST_PATH $CONFTEST_NAME
 fi
 
+# Test that there are no links to system libraries in the
+# threadpoolctl output section of the show_versions output:
+python -c "import sklearn; sklearn.show_versions()"
 pytest --pyargs sklearn
-
-# Test that there are no links to system libraries
-python -m threadpoolctl -i sklearn
diff --git a/build_tools/github/test_windows_wheels.sh b/build_tools/github/test_windows_wheels.sh
@@ -10,15 +10,17 @@ if [[ "$BITNESS" == "32" ]]; then
     # 32-bit architectures use the regular
     # test command (outside of the minimal Docker container)
     cp $CONFTEST_PATH $CONFTEST_NAME
+    python -c "import sklearn; sklearn.show_versions()"
     pytest --pyargs sklearn
-    python -m threadpoolctl -i sklearn
 else
-    docker container run -e SKLEARN_SKIP_NETWORK_TESTS=1 \
-                         -e OMP_NUM_THREADS=2 \
-                         -e OPENBLAS_NUM_THREADS=2 \
-                         --rm scikit-learn/minimal-windows \
-                         powershell -Command "pytest --pyargs sklearn"
+    docker container run \
+        --rm scikit-learn/minimal-windows \
+        powershell -Command "python -c 'import sklearn; sklearn.show_versions()'"
 
-    docker container run --rm scikit-learn/minimal-windows \
-                         powershell -Command "python -m threadpoolctl -i sklearn"
+    docker container run \
+        -e SKLEARN_SKIP_NETWORK_TESTS=1 \
+        -e OMP_NUM_THREADS=2 \
+        -e OPENBLAS_NUM_THREADS=2 \
+        --rm scikit-learn/minimal-windows \
+        powershell -Command "pytest --pyargs sklearn"
 fi
diff --git a/build_tools/travis/test_wheels.sh b/build_tools/travis/test_wheels.sh
@@ -3,7 +3,7 @@
 pip install --upgrade pip || travis_terminate $?
 pip install pytest pytest-xdist || travis_terminate $?
 
+# Test that there are no links to system libraries in the threadpoolctl
+# section of the show_versions output.
+python -c "import sklearn; sklearn.show_versions()" || travis_terminate $?
 python -m pytest -n $CPU_COUNT --pyargs sklearn || travis_terminate $?
-
-# Test that there are no links to system libraries
-python -m threadpoolctl -i sklearn || travis_terminate $?
diff --git a/doc/authors.rst b/doc/authors.rst
@@ -42,6 +42,10 @@
     <p>Adrin Jalali</p>
     </div>
     <div>
+    <a href='https://github.com/jjerphan'><img src='https://avatars.githubusercontent.com/u/13029839?v=4' class='avatar' /></a> <br />
+    <p>Julien Jerphanion</p>
+    </div>
+    <div>
     <a href='https://github.com/glemaitre'><img src='https://avatars.githubusercontent.com/u/7454015?v=4' class='avatar' /></a> <br />
     <p>Guillaume Lemaitre</p>
     </div>