8000 Merge branch 'master' of https://github.com/scikit-learn/scikit-learn… · scikit-learn/scikit-learn@4b2b050 · GitHub
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Gaurav Chawla
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Merge branch 'master' of https://github.com/scikit-learn/scikit-learn into issue_14257
2 parents aeafae7 + 1fca00b commit 4b2b050
  • dummy.py
  • ensemble/tests
  • feature_extraction
  • gaussian_process
  • linear_model
  • metrics
  • model_selection
  • naive_bayes.py
  • neighbors/tests
  • preprocessing
  • semi_supervised
  • svm
  • tests
  • tree

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    63 files changed

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    lines changed

    ‎.github/ISSUE_TEMPLATE/config.yml

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    Original file line numberDiff line numberDiff line change
    @@ -1,5 +1,8 @@
    11
    blank_issues_enabled: false
    22
    contact_links:
    3+
    - name: Discussions
    4+
    url: https://github.com/scikit-learn/scikit-learn/discussions
    5+
    about: Ask questions and discuss with other scikit-learn community members
    36
    - name: Stack overflow
    47
    url: https://stackoverflow.com/questions/tagged/scikit-learn
    58
    about: Please ask and answer usage questions on stackoverflow

    ‎.github/workflows/wheels.yml

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    @@ -86,6 +86,7 @@ jobs:
    8686
    OPENBLAS_NUM_THREADS=2
    8787
    SKLEARN_SKIP_NETWORK_TESTS=1
    8888
    SKLEARN_BUILD_PARALLEL=3
    89+
    MACOSX_DEPLOYMENT_TARGET=10.13
    8990
    CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.platform_id }}
    9091
    CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: bash build_tools/github/repair_windows_wheels.sh {wheel} {dest_dir} ${{ matrix.bitness }}
    9192
    CIBW_BEFORE_TEST_WINDOWS: bash build_tools/github/build_minimal_windows_image.sh ${{ matrix.python }} ${{ matrix.bitness }}

    ‎.travis.yml

    Lines changed: 10 additions & 4 deletions
    Original file line numberDiff line numberDiff line change
    @@ -36,15 +36,21 @@ jobs:
    3636
    - BUILD_WITH_ICC=true
    3737
    if: type = cron OR commit_message =~ /\[icc-build\]/
    3838

    39-
    - python: 3.7
    39+
    # Manual trigger of linux/arm64 tests in PR without triggering the full
    40+
    # wheel building process for all the Python versions.
    41+
    - python: 3.9
    4042
    os: linux
    4143
    arch: arm64
    42-
    if: type = cron OR commit_message =~ /\[arm64\]/
    44+
    if: commit_message =~ /\[arm64\]/
    4345
    env:
    4446
    - CPU_COUNT=8
    4547

    46-
    # Linux environments to build the scikit-learn wheels
    47-
    # for the ARM64 arquitecture and Python 3.6 and newer
    48+
    # Linux environments to build the scikit-learn wheels for the ARM64
    49+
    # architecture and Python 3.6 and newer. This is used both at release time
    50+
    # with the manual trigger in the commit message in the release branch and as
    51+
    # a scheduled task to build the weekly dev build on the master branch. The
    52+
    # weekly frequency is meant to avoid depleting the Travis CI credits too
    53+
    # fast.
    4854
    - python: 3.6
    4955
    os: linux
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    arch: arm64

    ‎azure-pipelines.yml

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    Original file line numberDiff line numberDiff line change
    @@ -8,66 +8,65 @@ schedules:
    88
    always: true
    99

    1010
    jobs:
    11-
    - job: linting
    12-
    displayName: Linting
    11+
    - job: git_commit
    12+
    displayName: Get Git Commit
    1313
    pool:
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    vmImage: ubuntu-18.04
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    steps:
    16-
    - task: UsePythonVersion@0
    17-
    inputs:
    18-
    versionSpec: '3.9'
    19-
    - bash: |
    20-
    pip install flake8 mypy==0.782
    21-
    displayName: Install linters
    2216
    - bash: |
    2317
    set -ex
    2418
    if [[ $BUILD_REASON == "PullRequest" ]]; then
    2519
    # By default pull requests use refs/pull/PULL_ID/merge as the source branch
    2620
    # which has a "Merge ID into ID" as a commit message. The latest commit
    2721
    # message is the second to last commit
    2822
    COMMIT_ID=$(echo $BUILD_SOURCEVERSIONMESSAGE | awk '{print $2}')
    29-
    COMMIT_MESSAGE=$(git log $COMMIT_ID -1 --pretty=%B)
    23+
    message=$(git log $COMMIT_ID -1 --pretty=%B)
    3024
    else
    31-
    COMMIT_MESSAGE=$BUILD_SOURCEVERSIONMESSAGE
    25+
    message=$BUILD_SOURCEVERSIONMESSAGE
    3226
    fi
    33-
    echo "##vso[task.setvariable variable=COMMIT_MESSAGE]$COMMIT_MESSAGE"
    27+
    echo "##vso[task.setvariable variable=message;isOutput=true]$message"
    28+
    name: commit
    3429
    displayName: Get source version message
    30+
    31+
    - job: linting
    32+
    dependsOn: [git_commit]
    33+
    condition: |
    34+
    and(
    35+
    succeeded(),
    36+
    not(contains(dependencies['git_commit']['outputs']['commit.message'], '[lint skip]')),
    37+
    not(contains(dependencies['git_commit']['outputs']['commit.message'], '[ci skip]'))
    38+
    )
    39+
    displayName: Linting
    40+
    pool:
    41+
    vmImage: ubuntu-18.04
    42+
    steps:
    43+
    - task: UsePythonVersion@0
    44+
    inputs:
    45+
    versionSpec: '3.9'
    3546
    - bash: |
    36-
    set -ex
    37-
    if [[ "$COMMIT_MESSAGE" =~ "[lint skip]" ]]; then
    38-
    # skip linting
    39-
    echo "Skipping flake8 linting"
    40-
    exit 0
    41-
    else
    42-
    ./build_tools/circle/linting.sh
    43-
    fi
    47+
    pip install flake8 mypy==0.782
    48+
    displayName: Install linters
    49+
    - bash: |
    50+
    ./build_tools/circle/linting.sh
    4451
    displayName: Run linting
    4552
    - bash: |
    46-
    set -ex
    47-
    if [[ "$COMMIT_MESSAGE" =~ "[lint skip]" ]]; then
    48-
    # skip linting
    49-
    echo "Skipping mypy linting"
    50-
    exit 0
    51-
    else
    52-
    mypy sklearn/
    53-
    fi
    53+
    mypy sklearn/
    5454
    displayName: Run mypy
    55-
    - bash: |
    56-
    if [[ "$COMMIT_MESSAGE" =~ "[scipy-dev]" ]] || [[ $BUILD_REASON == "Schedule" ]]; then
    57-
    echo "Running scipy-dev"
    58-
    echo "##vso[task.setvariable variable=runScipyDev;isOutput=true]true"
    59-
    else
    60-
    echo "##vso[task.setvariable variable=runScipyDev;isOutput=true]false"
    61-
    fi
    62-
    name: gitCommitMessage
    63-
    displayName: Determine to run scipy-dev
    6455
    6556
    - template: build_tools/azure/posix.yml
    6657
    parameters:
    6758
    name: Linux_Nightly
    6859
    vmImage: ubuntu-18.04
    69-
    dependsOn: [linting]
    70-
    condition: eq(dependencies['linting']['outputs']['gitCommitMessage.runScipyDev'], 'true')
    60+
    dependsOn: [git_commit, linting]
    61+
    condition: |
    62+
    and(
    63+
    succeeded(),
    64+
    not(contains(dependencies['git_commit']['outputs']['commit.message'], '[ci skip]')),
    65+
    or(eq(variables['Build.Reason'], 'Schedule'),
    66+
    contains(dependencies['git_commit']['outputs']['commit.message'], '[scipy-dev]'
    67+
    )
    68+
    )
    69+
    )
    7170
    matrix:
    7271
    pylatest_pip_scipy_dev:
    7372
    DISTRIB: 'conda-pip-scipy-dev'
    @@ -84,6 +83,12 @@ jobs:
    8483
    parameters:
    8584
    name: Linux_Runs
    8685
    vmImage: ubuntu-18.04
    86+
    dependsOn: [git_commit]
    87+
    condition: |
    88+
    and(
    89+
    succeeded(),
    90+
    not(contains(dependencies['git_commit']['outputs']['commit.message'], '[ci skip]'))
    91+
    )
    8792
    matrix:
    8893
    pylatest_conda_mkl:
    8994
    DISTRIB: 'conda'
    @@ -95,8 +100,13 @@ jobs:
    95100
    parameters:
    96101
    name: Linux
    97102
    vmImage: ubuntu-18.04
    98-
    dependsOn: [linting]
    99-
    condition: and(ne(variables['Build.Reason'], 'Schedule'), succeeded('linting'))
    103+
    dependsOn: [linting, git_commit]
    104+
    condition: |
    105+
    and(
    106+
    succeeded(),
    107+
    not(contains(dependencies['git_commit']['outputs']['commit.message'], '[ci skip]')),
    108+
    ne(variables['Build.Reason'], 'Schedule')
    109+
    )
    100110
    matrix:
    101111
    # Linux environment to test that scikit-learn can be built against
    102112
    # versions of numpy, scipy with ATLAS that comes with Ubuntu Bionic 18.04
    @@ -139,8 +149,13 @@ jobs:
    139149
    parameters:
    140150
    name: Linux32
    141151
    vmImage: ubuntu-18.04
    142-
    dependsOn: [linting]
    143-
    condition: and(ne(variables['Build.Reason'], 'Schedule'), succeeded('linting'))
    152+
    dependsOn: [linting, git_commit]
    153+
    condition: |
    154+
    and(
    155+
    succeeded(),
    156+
    not(contains(dependencies['git_commit']['outputs']['commit.message'], '[ci skip]')),
    157+
    ne(variables['Build.Reason'], 'Schedule')
    158+
    )
    144159
    matrix:
    145160
    py36_ubuntu_atlas_32bit:
    146161
    DISTRIB: 'ubuntu-32'
    @@ -157,8 +172,13 @@ jobs:
    157172
    parameters:
    158173
    name: macOS
    159174
    vmImage: macOS-10.14
    160-
    dependsOn: [linting]
    161-
    condition: and(ne(variables['Build.Reason'], 'Schedule'), succeeded('linting'))
    175+
    dependsOn: [linting, git_commit]
    176+
    condition: |
    177+
    and(
    178+
    succeeded(),
    179+
    not(contains(dependencies['git_commit']['outputs']['commit.message'], '[ci skip]')),
    180+
    ne(variables['Build.Reason'], 'Schedule')
    181+
    )
    162182
    matrix:
    163183
    pylatest_conda_forge_mkl:
    164184
    DISTRIB: 'conda'
    @@ -174,8 +194,13 @@ jobs:
    174194
    parameters:
    175195
    name: Windows
    176196
    vmImage: vs2017-win2016
    177-
    dependsOn: [linting]
    178-
    condition: and(ne(variables['Build.Reason'], 'Schedule'), succeeded('linting'))
    197+
    dependsOn: [linting, git_commit]
    198+
    condition: |
    199+
    and(
    200+
    succeeded(),
    201+
    not(contains(dependencies['git_commit']['outputs']['commit.message'], '[ci skip]')),
    202+
    ne(variables['Build.Reason'], 'Schedule')
    203+
    )
    179204
    matrix:
    180205
    py37_conda_mkl:
    181206
    PYTHON_VERSION: '3.7'

    ‎build_tools/azure/install.sh

    Lines changed: 5 additions & 1 deletion
    Original file line numberDiff line numberDiff line change
    @@ -96,7 +96,11 @@ elif [[ "$DISTRIB" == "conda-pip-scipy-dev" ]]; then
    9696
    python -m pip install -U pip
    9797
    echo "Installing numpy and scipy master wheels"
    9898
    dev_anaconda_url=https://pypi.anaconda.org/scipy-wheels-nightly/simple
    99-
    pip install --pre --upgrade --timeout=60 --extra-index $dev_anaconda_url numpy scipy pandas
    99+
    pip install --pre --upgrade --timeout=60 --extra-index $dev_anaconda_url numpy pandas
    100+
    101+
    # issue with metadata in scipy dev builds https://github.com/scipy/scipy/issues/13196
    102+
    # --use-deprecated=legacy-resolver needs to be included
    103+
    pip install --pre --upgrade --timeout=60 --extra-index $dev_anaconda_url scipy --use-deprecated=legacy-resolver
    100104
    pip install --pre cython
    101105
    setup_ccache
    102106
    echo "Installing joblib master"

    ‎build_tools/circle/build_doc.sh

    Lines changed: 4 additions & 7 deletions
    Original file line numberDiff line numberDiff line change
    @@ -116,8 +116,8 @@ fi
    116116

    117117
    if [[ "$CIRCLE_BRANCH" =~ ^master$|^[0-9]+\.[0-9]+\.X$ && -z "$CI_PULL_REQUEST" ]]
    118118
    then
    119-
    # PDF linked into HTML
    120-
    make_args="dist LATEXMKOPTS=-halt-on-error"
    119+
    # ZIP linked into HTML
    120+
    make_args=dist
    121121
    elif [[ "$build_type" =~ ^QUICK ]]
    122122
    then
    123123
    make_args=html-noplot
    @@ -133,13 +133,10 @@ fi
    133133
    make_args="SPHINXOPTS=-T $make_args" # show full traceback on exception
    134134

    135135
    # Installing required system packages to support the rendering of math
    136-
    # notation in the HTML documentation
    136+
    # notation in the HTML documentation and to optimize the image files
    137137
    sudo -E apt-get -yq update
    138-
    sudo -E apt-get -yq remove texlive-binaries --purge
    139138
    sudo -E apt-get -yq --no-install-suggests --no-install-recommends \
    140-
    install dvipng texlive-latex-base texlive-latex-extra \
    141-
    texlive-latex-recommended texlive-fonts-recommended \
    142-
    latexmk gsfonts ccache
    139+
    install dvipng gsfonts ccache zip optipng
    143140

    144141
    # deactivate circleci virtualenv and setup a miniconda env instead
    145142
    if [[ `type -t deactivate` ]]; then

    ‎build_tools/circle/list_versions.py

    Lines changed: 23 additions & 8 deletions
    Original file line numberDiff line numberDiff line change
    @@ -8,6 +8,7 @@
    88
    from distutils.version import LooseVersion
    99
    from urllib.request import urlopen
    1010

    11+
    1112
    def json_urlread(url):
    1213
    try:
    1314
    return json.loads(urlopen(url).read().decode('utf8'))
    @@ -32,10 +33,23 @@ def human_readable_data_quantity(quantity, multiple=1024):
    3233
    quantity /= multiple
    3334

    3435

    35-
    def get_pdf_size(version):
    36+
    def get_file_extension(version):
    37+
    if 'dev' in version:
    38+
    # The 'dev' branch should be explictly handled
    39+
    return 'zip'
    40+
    41+
    current_version = LooseVersion(version)
    42+
    min_zip_version = LooseVersion('1.0.0')
    43+
    44+
    return 'zip' if current_version >= min_zip_version else 'pdf'
    45+
    46+
    47+
    def get_file_size(version):
    3648
    api_url = ROOT_URL + '%s/_downloads' % version
    3749
    for path_details in json_urlread(api_url):
    38-
    if path_details['name'] == 'scikit-learn-docs.pdf':
    50+
    file_extension = get_file_extension(version)
    51+
    file_path = f'scikit-learn-docs.{file_extension}'
    52+
    if path_details['name'] == file_path:
    3953
    return human_readable_data_quantity(path_details['size'], 1000)
    4054

    4155

    @@ -64,8 +78,8 @@ def get_pdf_size(version):
    6478
    if path_details['type'] == 'dir':
    6579
    html = urlopen(RAW_FMT % name).read().decode('utf8')
    6680
    version_num = VERSION_RE.search(html).group(1)
    67-
    pdf_size = get_pdf_size(name)
    68-
    dirs[name] = (version_num, pdf_size)
    81+
    file_size = get_file_size(name)
    82+
    dirs[name] = (version_num, file_size)
    6983

    7084
    if path_details['type'] == 'symlink':
    7185
    symlinks[name] = json_urlread(path_details['_links']['self'])['target']
    @@ -81,7 +95,7 @@ def get_pdf_size(version):
    8195
    for name in (NAMED_DIRS +
    8296
    sorted((k for k in dirs if k[:1].isdigit()),
    8397
    key=LooseVersion, reverse=True)):
    84-
    version_num, pdf_size = dirs[name]
    98+
    version_num, file_size = dirs[name]
    8599
    if version_num in seen:
    86100
    # symlink came first
    87101
    continue
    @@ -91,7 +105,8 @@ def get_pdf_size(version):
    91105
    path = 'https://scikit-learn.org/%s/' % name
    92106
    out = ('* `Scikit-learn %s%s documentation <%s>`_'
    93107
    % (version_num, name_display, path))
    94-
    if pdf_size is not None:
    95-
    out += (' (`PDF %s <%s/_downloads/scikit-learn-docs.pdf>`_)'
    96-
    % (pdf_size, path))
    108+
    if file_size is not None:
    109+
    file_extension = get_file_extension(version_num)
    110+
    out += (f' (`{file_extension.upper()} {file_size} <{path}/'
    111+
    f'_downloads/scikit-learn-docs.{file_extension}>`_)')
    97112
    print(out)

    ‎build_tools/github/build_wheels.sh

    Lines changed: 9 additions & 1 deletion
    Original file line numberDiff line numberDiff line change
    @@ -5,7 +5,15 @@ set -x
    55

    66
    # OpenMP is not present on macOS by default
    77
    if [[ "$RUNNER_OS" == "macOS" ]]; then
    8-
    brew install libomp
    8+
    # Make sure to use a libomp version binary compatible with the oldest
    9+
    # supported version of the macos SDK as libomp will be vendored into the
    10+
    # scikit-learn wheels for macos. The list of bottles can be found at:
    11+
    # https://formulae.brew.sh/api/formula/libomp.json. Currently, the oldest
    12+
    # supported macos version is: High Sierra / 10.13. When upgrading this, be
    13+
    # sure to update the MACOSX_DEPLOYMENT_TARGET environment variable in
    14+
    # wheels.yml accordingly.
    15+
    wget https://homebrew.bintray.com/bottles/libomp-11.0.0.high_sierra.bottle.tar.gz
    16+
    brew install libomp-11.0.0.high_sierra.bottle.tar.gz
    917
    export CC=/usr/bin/clang
    1018
    export CXX=/usr/bin/clang++
    1119
    export CPPFLAGS="$CPPFLAGS -Xpreprocessor -fopenmp"

    ‎build_tools/travis/install_master.sh

    Lines changed: 2 additions & 17 deletions
    Original file line numberDiff line numberDiff line change
    @@ -50,23 +50,8 @@ conda update --yes conda
    5050
    conda create -n testenv --yes python=3.7
    5151

    5252
    source activate testenv
    53-
    54-
    if [[ $TRAVIS_CPU_ARCH == amd64 ]]; then
    55-
    echo "Upgrading pip and setuptools."
    56-
    pip install --upgrade pip setuptools
    57-
    echo "Installing numpy, scipy and pandas master wheels."
    58-
    dev_anaconda_url=https://pypi.anaconda.org/scipy-wheels-nightly/simple
    59-
    pip install --pre --upgrade --timeout=60 --extra-index $dev_anaconda_url numpy scipy pandas
    60-
    echo "Installing cython pre-release wheels."
    61-
    pip install --pre cython
    62-
    echo "Installing joblib master."
    63-
    pip install https://github.com/joblib/joblib/archive/master.zip
    64-
    echo "Installing pillow master."
    65-
    pip install https://github.com/python-pillow/Pillow/archive/master.zip
    66-
    else
    67-
    conda install -y scipy numpy pandas cython
    68-
    pip install joblib threadpoolctl
    69-
    fi
    53+
    conda install -y scipy numpy pandas cython
    54+
    pip install joblib threadpoolctl
    7055

    7156
    pip install $(get_dep pytest $PYTEST_VERSION) pytest-xdist
    7257

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