scikit-learn · glemaitre · Apr 28, 2021 · Dec 2, 2020 · Dec 2, 2020 · Dec 4, 2020
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -104,6 +104,9 @@ jobs:
   pypy3:
     docker:
       - image: condaforge/miniforge3
+    environment:
+      # Avoid the interactive dialog when installing tzdata
+      - DEBIAN_FRONTEND: noninteractive
     steps:
       - restore_cache:
           keys:

diff --git a/.github/labeler.yml b/.github/labeler.yml
diff --git a/.github/scripts/label_title_regex.py b/.github/scripts/label_title_regex.py
@@ -0,0 +1,25 @@
+"""Labels PRs based on title. Must be run in a github action with the
+pull_request_target event."""
+from ghapi.all import context_github
+from ghapi.all import GhApi
+from ghapi.all import user_repo
+from ghapi.all import github_token
+import re
+
+owner, repo = user_repo()
+pull_request = context_github.event.pull_request
+title = pull_request.title
+
+regex_to_labels = [
+    (r"\bDOC\b", "Documentation"),
+    (r"\bCI\b", "Build / CI")
+]
+
+labels_to_add = [
+    label for regex, label in regex_to_labels
+    if re.search(regex, title)
+]
+
+if labels_to_add:
+    api = GhApi(owner=owner, repo=repo, token=github_token())
+    api.issues.add_labels(pull_request.number, labels=labels_to_add)
diff --git a/.github/workflows/labeler-title-regex.yml b/.github/workflows/labeler-title-regex.yml
@@ -1,16 +1,20 @@
 name: Pull Request Regex Title Labeler
 on:
   pull_request_target:
-    types: [opened]
+    types: [opened, edited]
 
 jobs:
 
   labeler:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     steps:
-    - name: Check Labels
-      id: labeler
-      continue-on-error: true
-      uses: jimschubert/labeler-action@v2
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
       with:
-        GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+        python-version: '3.9'
+    - name: Install ghapi
+      run: pip install -Uq ghapi
+    - name: Label pull request
+      run: python .github/scripts/label_title_regex.py
+      env:
+        CONTEXT_GITHUB: ${{ toJson(github) }}
diff --git a/.github/workflows/sync_pull_request.yml b/.github/workflows/sync_pull_request.yml
diff --git a/.travis.yml b/.travis.yml
@@ -30,12 +30,6 @@ env:
 
 jobs:
   include:
-    - python: 3.7
-      env:
-        - CHECK_WARNING=true
-        - BUILD_WITH_ICC=true
-      if: type = cron OR commit_message =~ /\[icc-build\]/
-
     # Manual trigger of linux/arm64 tests in PR without triggering the full
     # wheel building process for all the Python versions.
     - python: 3.9

diff --git a/README.rst b/README.rst
@@ -17,8 +17,8 @@
 .. |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
 
-.. |PythonVersion| image:: https://img.shields.io/badge/python-3.6%20%7C%203.7%20%7C%203.8-blue
-.. _PythonVersion: https://img.shields.io/badge/python-3.6%20%7C%203.7%20%7C%203.8-blue
+.. |PythonVersion| image:: https://img.shields.io/badge/python-3.6%20%7C%203.7%20%7C%203.8%20%7C%203.9-blue
+.. _PythonVersion: https://img.shields.io/badge/python-3.6%20%7C%203.7%20%7C%203.8%20%7C%203.9-blue
 
 .. |PyPi| image:: https://badge.fury.io/py/scikit-learn.svg
 .. _PyPi: https://badge.fury.io/py/scikit-learn

diff --git a/asv_benchmarks/asv.conf.json b/asv_benchmarks/asv.conf.json
@@ -30,7 +30,7 @@
 
     // List of branches to benchmark. If not provided, defaults to "master
     // (for git) or "default" (for mercurial).
-    // "branches": ["main"], // for git
+    "branches": ["main"],
     // "branches": ["default"],    // for mercurial
 
     // The DVCS being used.  If not set, it will be automatically
@@ -73,7 +73,7 @@
     //
     "matrix": {
         "numpy": [],
-	    "scipy": [],
+        "scipy": [],
         "cython": [],
         "joblib": [],
         "threadpoolctl": []

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -78,6 +78,28 @@ jobs:
         # Here we make sure, that they are still run on a regular basis.
         SKLEARN_SKIP_NETWORK_TESTS: '0'
 
+# Check compilation with intel C++ compiler (ICC)
+- template: build_tools/azure/posix.yml
+  parameters:
+    name: Linux_Nightly_ICC
+    vmImage: ubuntu-18.04
+    dependsOn: [git_commit, linting]
+    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'], '[icc-build]')
+        )
+      )
+    matrix:
+      pylatest_conda_mkl:
+        DISTRIB: 'conda'
+        PYTHON_VERSION: '*'
+        BLAS: 'mkl'
+        COVERAGE: 'false'
+        BUILD_WITH_ICC: 'true'
+
 # Will run all the time regardless of linting outcome.
 - template: build_tools/azure/posix.yml
   parameters:

diff --git a/build_tools/azure/install.sh b/build_tools/azure/install.sh
@@ -51,6 +51,10 @@ if [[ "$DISTRIB" == "conda" ]]; then
             # sklearn/svm/_libsvm.cpython-38-darwin.so,
             # 2): Symbol not found: _svm_check_parameter error
             TO_INSTALL="$TO_INSTALL compilers>=1.0.4,!=1.1.0 llvm-openmp"
+        else
+            # Without openmp, we use the system clang. Here we use /usr/bin/ar
+            # instead because llvm-ar errors
+            export AR=/usr/bin/ar
         fi
     fi
 	make_conda $TO_INSTALL
@@ -96,7 +100,11 @@ elif [[ "$DISTRIB" == "conda-pip-scipy-dev" ]]; then
     python -m pip install -U pip
     echo "Installing numpy and scipy master wheels"
     dev_anaconda_url=https://pypi.anaconda.org/scipy-wheels-nightly/simple
-    pip install --pre --upgrade --timeout=60 --extra-index $dev_anaconda_url numpy scipy pandas
+    pip install --pre --upgrade --timeout=60 --extra-index $dev_anaconda_url numpy pandas
+
+    # issue with metadata in scipy dev builds https://github.com/scipy/scipy/issues/13196
+    # --use-deprecated=legacy-resolver needs to be included
+    pip install --pre --upgrade --timeout=60 --extra-index $dev_anaconda_url scipy --use-deprecated=legacy-resolver
     pip install --pre cython
     setup_ccache
     echo "Installing joblib master"
@@ -144,6 +152,20 @@ if [[ "$DISTRIB" == "conda-pip-latest" ]]; then
     # environment:
     pip install --verbose --editable .
 else
+    if [[ "$BUILD_WITH_ICC" == "true" ]]; then
+        wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
+        sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
+        rm GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
+        sudo add-apt-repository "deb https://apt.repos.intel.com/oneapi all main"
+        sudo apt-get update
+        sudo apt-get install intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic
+        source /opt/intel/oneapi/setvars.sh
+
+        # The "build_clib" command is implicitly used to build "libsvm-skl".
+        # To compile with a different compiler, we also need to specify the
+        # compiler for this command
+        python setup.py build_ext --compiler=intelem -i build_clib --compiler=intelem
+    fi
     # Use the pre-installed build dependencies and build directly in the
     # current environment.
     python setup.py develop

diff --git a/build_tools/azure/test_docs.sh b/build_tools/azure/test_docs.sh
@@ -8,4 +8,8 @@ elif [[ "$DISTRIB" == "ubuntu" ]]; then
     source $VIRTUALENV/bin/activate
 fi
 
+if [[ "$BUILD_WITH_ICC" == "true" ]]; then
+    source /opt/intel/oneapi/setvars.sh
+fi
+
 make test-doc
diff --git a/build_tools/azure/test_script.sh b/build_tools/azure/test_script.sh
@@ -8,6 +8,10 @@ elif [[ "$DISTRIB" == "ubuntu" ]] || [[ "$DISTRIB" == "ubuntu-32" ]]; then
     source $VIRTUALENV/bin/activate
 fi
 
+if [[ "$BUILD_WITH_ICC" == "true" ]]; then
+    source /opt/intel/oneapi/setvars.sh
+fi
+
 python --version
 python -c "import numpy; print('numpy %s' % numpy.__version__)"
 python -c "import scipy; print('scipy %s' % scipy.__version__)"

diff --git a/build_tools/github/upload_anaconda.sh b/build_tools/github/upload_anaconda.sh
@@ -11,7 +11,11 @@ else
     ANACONDA_TOKEN="$SCIKIT_LEARN_STAGING_UPLOAD_TOKEN"
 fi
 
-pip install git+https://github.com/Anaconda-Server/anaconda-client
+# Install Python 3.8 because of a bug with Python 3.9
+export PATH=$CONDA/bin:$PATH
+conda create -n upload -y python=3.8
+source activate upload
+conda install -y anaconda-client
 
 # Force a replacement if the remote file already exists
 anaconda -t $ANACONDA_TOKEN upload --force -u $ANACONDA_ORG dist/artifact/*

diff --git a/build_tools/travis/after_success.sh b/build_tools/travis/after_success.sh
@@ -18,7 +18,16 @@ if [[ $BUILD_WHEEL == true && $TRAVIS_EVENT_TYPE != pull_request ]]; then
         ANACONDA_TOKEN="$SCIKIT_LEARN_STAGING_UPLOAD_TOKEN"
     fi
 
-    pip install git+https://github.com/Anaconda-Server/anaconda-client
+    MINICONDA_URL="https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-aarch64.sh"
+    wget $MINICONDA_URL -O miniconda.sh
+    MINICONDA_PATH=$HOME/miniconda
+    chmod +x miniconda.sh && ./miniconda.sh -b -p $MINICONDA_PATH
+
+    # Install Python 3.8 because of a bug with Python 3.9
+    export PATH=$MINICONDA_PATH/bin:$PATH
+    conda create -n upload -y python=3.8
+    source activate upload
+    conda install -y anaconda-client
 
     # Force a replacement if the remote file already exists
     anaconda -t $ANACONDA_TOKEN upload --force -u $ANACONDA_ORG wheelhouse/*.whl

diff --git a/build_tools/travis/install_main.sh b/build_tools/travis/install_main.sh
@@ -32,12 +32,7 @@ ccache --max-size 100M --show-stats
 # to setup a conda-based environment instead
 deactivate
 
-if [[ $TRAVIS_CPU_ARCH == arm64 ]]; then
-    # Different Miniconda URL for ARM64 architectures
-    MINICONDA_URL="https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-aarch64.sh"
-else
-    MINICONDA_URL="https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh"
-fi
+MINICONDA_URL="https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-aarch64.sh"
 
 # Install Miniconda
 wget $MINICONDA_URL -O miniconda.sh
@@ -62,23 +57,7 @@ python --version
 python -c "import numpy; print(f'numpy {numpy.__version__}')"
 python -c "import scipy; print(f'scipy {scipy.__version__}')"
 
-if [[ $BUILD_WITH_ICC == true ]]; then
-    wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
-    sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
-    rm GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
-    sudo add-apt-repository "deb https://apt.repos.intel.com/oneapi all main"
-    sudo apt-get update
-    sudo apt-get install intel-oneapi-icc
-    source /opt/intel/oneapi/setvars.sh
-
-    # The "build_clib" command is implicitly used to build "libsvm-skl".
-    # To compile with a different compiler, we also need to specify the
-    # compiler for this command
-    python setup.py build_ext --compiler=intelem -i build_clib --compiler=intelem
-else
-    pip install -e .
-fi
-
+pip install -e .
 python setup.py develop
 
 ccache --show-stats

diff --git a/conftest.py b/conftest.py
@@ -1,7 +1,7 @@
 # Even if empty this file is useful so that when running from the root folder
 # ./sklearn is added to sys.path by pytest. See
-# https://docs.pytest.org/en/latest/pythonpath.html for more details.  For
-# example, this allows to build extensions in place and run pytest
+# https://docs.pytest.org/en/latest/explanation/pythonpath.html for more
+# details. For example, this allows to build extensions in place and run pytest
 # doc/modules/clustering.rst and use sklearn from the local folder rather than
 # the one from site-packages.
 

diff --git a/doc/about.rst b/doc/about.rst
@@ -160,6 +160,10 @@ Grisel, Guillaume Lemaitre, Jérémie du Boisberranger and Chiara Marmo.
    :width: 70pt
    :target: https://www.dataiku.com/
 
+.. |aphp| image:: images/logo_APHP_text.png
+   :width: 150pt
+   :target: https://aphp.fr/
+
 .. |inria| image:: images/inria-logo.jpg
    :width: 100pt
    :target: https://www.inria.fr
@@ -185,6 +189,8 @@ Grisel, Guillaume Lemaitre, Jérémie du Boisberranger and Chiara Marmo.
    +---------+----------+
    |     |dataiku|      |
    +---------+----------+
+   |       |aphp|       |
+   +---------+----------+
    |                    |
    +---------+----------+
    |       |inria|      |

diff --git a/doc/common_pitfalls.rst b/doc/common_pitfalls.rst
@@ -564,7 +564,7 @@ preformance by letting the estimator use a different RNG on each fold. This
 is done by passing a `RandomState` instance (or `None`) to the estimator
 initialization.
 
-When we pass an integer, the estimator will use the same RNG on each fold: if
+When we pass an integer, the estimator will use the same RNG on each fold:
 if the estimator performs well (or bad), as evaluated by CV, it might just be
 because we got lucky (or unlucky) with that specific seed. Passing instances
 leads to more robust CV results, and makes the comparison between various

diff --git a/doc/conftest.py b/doc/conftest.py
@@ -1,6 +1,7 @@
 import os
 from os.path import exists
 from os.path import join
+from os import environ
 import warnings
 
 from sklearn.utils import IS_PYPY
@@ -48,6 +49,12 @@ def setup_loading_other_datasets():
         raise SkipTest("Skipping loading_other_datasets.rst, "
                        "pandas not installed")
 
+    # checks SKLEARN_SKIP_NETWORK_TESTS to see if test should run
+    run_network_tests = environ.get("SKLEARN_SKIP_NETWORK_TESTS", '1') == "0"
+    if not run_network_tests:
+        raise SkipTest("Skipping loading_other_datasets.rst, tests can be "
+                       "enabled by settting SKLEARN_SKIP_NETWORK_TESTS=0")
+
 
 def setup_compose():
     try:

diff --git a/doc/developers/advanced_installation.rst b/doc/developers/advanced_installation.rst
@@ -479,9 +479,9 @@ repository:
 
 .. prompt:: bash $
 
-    wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
-    sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
-    rm GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
+    wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
+    sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
+    rm GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
 
 Then, add the oneAPI repository to your APT repositories:
 
@@ -490,11 +490,12 @@ Then, add the oneAPI repository to your APT repositories:
     sudo add-apt-repository "deb https://apt.repos.intel.com/oneapi all main"
     sudo apt-get update
 
-Install ICC, packaged under the name ``intel-oneapi-icc``:
+Install ICC, packaged under the name
+``intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic``:
 
 .. prompt:: bash $
 
-    sudo apt-get install intel-oneapi-icc
+    sudo apt-get install intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic
 
 Before using ICC, you need to set up environment variables: