0.22.1 release (scikit-learn#15998)

* DOC fixed default values in dbscan (scikit-learn#15753)

* DOC fix incorrect branch reference in contributing doc (scikit-learn#15779)

* DOC relabel Feature -> Efficiency in change log (scikit-learn#15770)

* DOC fixed Birch default value (scikit-learn#15780)

* STY Minior change on code padding in website theme (scikit-learn#15768)

* DOC Fix yticklabels order in permutation importances example (scikit-learn#15799)

* Fix yticklabels order in permutation importances example

* STY Update wrapper width (scikit-learn#15793)

* DOC Long sentence was hard to parse and ambiguous in _classification.py (scikit-learn#15769)

* DOC Removed duplicate 'classes_' attribute in Naive Bayes classifiers (scikit-learn#15811)

* BUG Fixes pandas dataframe bug with boolean dtypes (scikit-learn#15797)

* BUG Returns only public estimators in all_estimators (scikit-learn#15380)

* DOC improve doc for multiclass and types_of_target (scikit-learn#15333)

* TST Increases tol for check_pca_float_dtype_preservation assertion (scikit-learn#15775)

* update _alpha_grid class in _coordinate_descent.py (scikit-learn#15835)

* FIX Explicit conversion of ndarray to object dtype. (scikit-learn#15832)

* BLD Parallelize sphinx builds on circle ci (scikit-learn#15745)

* DOC correct url for preprocessing (scikit-learn#15853)

* MNT avoid generating too many cross links in examples (scikit-learn#15844)

* DOC Correct wrong doc in precision_recall_fscore_support (scikit-learn#15833)

* DOC add comment in check_pca_float_dtype_preservation (scikit-learn#15819)

Documenting the changes in scikit-learn#15775

* DOC correct indents in docstring _split.py (scikit-learn#15843)

* DOC fix docstring of KMeans based on sklearn guideline (scikit-learn#15754)

* DOC fix docstring of AgglomerativeClustering based on sklearn guideline (scikit-learn#15764)

* DOC fix docstring of AffinityPropagation based on sklearn guideline (scikit-learn#15777)

* DOC fixed SpectralCoclustering and SpectralBiclustering docstrings following sklearn guideline (scikit-learn#15778)

* DOC fix FeatureAgglomeration and MiniBatchKMeans docstring following sklearn guideline (scikit-learn#15809)

* TST Specify random_state in test_cv_iterable_wrapper (scikit-learn#15829)

* DOC Include LinearSV{C, R} in models that support sample_weights (scikit-learn#15871)

* DOC correct some indents (scikit-learn#15875)

* DOC Fix documentation of default values in tree classes (scikit-learn#15870)

* DOC fix typo in docstring (scikit-learn#15887)

* DOC FIX default value for xticks_rotation in plot_confusion_matrix (scikit-learn#15890)

* Fix imports in pip3 ubuntu by suffixing affected files (scikit-learn#15891)

* MNT Raise erorr when normalize is invalid in confusion_matrix (scikit-learn#15888)

* [MRG] DOC Increases search results for API object results (scikit-learn#15574)

* MNT Ignores warning in pyamg for deprecated scipy.random (scikit-learn#15914)

* DOC Instructions to troubleshoot Windows path length limit (scikit-learn#15916)

* DOC add versionadded directive to some estimators (scikit-learn#15849)

* DOC clarify doc-string of roc_auc_score and add references (scikit-learn#15293)

* MNT Adds skip lint to azure pipeline CI (scikit-learn#15904)

* BLD Fixes bug when building with NO_MATHJAX=1 (scikit-learn#15892)

* [MRG] BUG Checks to number of axes in passed in ax more generically (scikit-learn#15760)

* EXA Minor fixes in plot_sparse_logistic_regression_20newsgroups.py (scikit-learn#15925)

* BUG Do not shadow public functions with deprecated modules (scikit-learn#15846)

* Import sklearn._distributor_init first (scikit-learn#15929)

* DOC Fix typos, via a Levenshtein-style corrector (scikit-learn#15923)

* DOC in canned comment, mention that PR title becomes commit me… (scikit-learn#15935)

* DOC/EXA Correct spelling of "Classification" (scikit-learn#15938)

* BUG fix pip3 ubuntu update by suffixing file (scikit-learn#15928)

* [MRG] Ways to compute center_shift_total were different in "full" and "elkan" algorithms. (scikit-learn#15930)

* TST Fixes integer test for train and test indices (scikit-learn#15941)

* BUG ensure that parallel/sequential give the same permutation importances (scikit-learn#15933)

* Formatting fixes in changelog (scikit-learn#15944)

* MRG FIX: order of values of self.quantiles_ in QuantileTransformer (scikit-learn#15751)

* [MRG] BUG Fixes constrast in plot_confusion_matrix (scikit-learn#15936)

* BUG use zero_division argument in classification_report (scikit-learn#15879)

* DOC change logreg solver in plot_logistic_path (scikit-learn#15927)

* DOC fix whats new ordering (scikit-learn#15961)

* COSMIT use np.iinfo to define the max int32 (scikit-learn#15960)

* DOC Apply numpydoc validation to VotingRegressor methods (scikit-learn#15969)

Co-authored-by: Tiffany R. Williams <[email protected]>

* DOC improve naive_bayes.py documentation (scikit-learn#15943)

Co-authored-by: Jigna Panchal <[email protected]>

* DOC Fix default values in Perceptron documentation (scikit-learn#15965)

* DOC Improve default values in logistic documentation (scikit-learn#15966)

Co-authored-by: Guillaume Lemaitre <[email protected]>

* DOC Improve documentation of default values for imputers (scikit-learn#15964)

* EXA/MAINT Simplify code in manifold learning example (scikit-learn#15949)

* DOC Improve default values in SGD documentation (scikit-learn#15967)

* DOC Improve defaults in neural network documentation (scikit-learn#15968)

* FIX use safe_sparse_dot for callable kernel in LabelSpreading (scikit-learn#15868)

* BUG Adds attributes back to check_is_fitted (scikit-learn#15947)

Co-authored-by: Olivier Grisel <[email protected]>

* DOC update check_is_fitted what's new

* DOC change python-devel to python3-devel for yum. (scikit-learn#15986)

* DOC Correct the default value of values_format in plot_confusion_matrix (scikit-learn#15981)

* [MRG] MNT Updates pypy to use 7.2.0 (scikit-learn#15954)

* FIX Add missing 'values_format' param to disp.plot() in plot_confusion_matrix (scikit-learn#15937)

* FIX support scalar values in fit_params in SearchCV (scikit-learn#15863)

* support a scalar fit param

* pep8

* TST add test for desired behavior

* FIX introduce _check_fit_params to validate parameters

* DOC update whats new

* TST tests both grid-search and randomize-search

* PEP8

* DOC revert unecessary change

* TST add test for _check_fit_params

* olivier comments

* TST fixes

* DOC whats new

* DOC whats new

* TST revert type of error

* add olivier suggestions

* address olivier comments

* address thomas comments

* PEP8

* comments olivier

* TST fix test by passing X

* avoid to call twice tocsr

* add case column/row sparse in check_fit_param

* provide optional indices

* TST check content when indexing params

* PEP8

* TST update tests to check identity

* stupid fix

* use a distribution in RandomizedSearchCV

* MNT add lightgbm to one of the CI build

* move to another build

* do not install dependencies lightgbm

* MNT comments on the CI setup

* address some comments

* Test fit_params compat without dependency on lightgbm

Co-authored-by: Guillaume Lemaitre <[email protected]>
Co-authored-by: Olivier Grisel <[email protected]>

* Remove abstractmethod that silently brake downstream packages (scikit-learn#15996)

* FIX restore BaseNB._check_X without abstractmethod decoration (scikit-learn#15997)

* Update v0.22 changelog for 0.22.1 (scikit-learn#16002)

- set the date
- move entry for quantile transformer to the 0.22.1 section
- fix alphabetical ordering of modules

* STY Removes hidden scroll bar (scikit-learn#15999)

* Flake8 fixes

* Fix: remove left-over lines that should have been deleted during conflict resolution when rebasing

* Fix missing imports

* Update version

* Fix test_check_is_fitted

* Make test_sag_regressor_computed_correctly deterministic (scikit-learn#16003)

Fix scikit-learn#15818.

Co-authored-by: cgsavard <[email protected]>
Co-authored-by: Joel Nothman <[email protected]>
Co-authored-by: Thomas J Fan <[email protected]>
Co-authored-by: Matt Hall <[email protected]>
Co-authored-by: Kathryn Poole <[email protected]>
Co-authored-by: lucyleeow <[email protected]>
Co-authored-by: JJmistry <[email protected]>
Co-authored-by: Juan Carlos Alfaro Jiménez <[email protected]>
Co-authored-by: SylvainLan <[email protected]>
Co-authored-by: Nicolas Hug <[email protected]>
Co-authored-by: Hanmin Qin <[email protected]>
Co-authored-by: Adrin Jalali <[email protected]>
Co-authored-by: Vachan D A <[email protected]>
Co-authored-by: Sambhav Kothari <[email protected]>
Co-authored-by: wenliwyan <[email protected]>
Co-authored-by: shivamgargsya <[email protected]>
Co-authored-by: Reshama Shaikh <[email protected]>
Co-authored-by: Oliver Urs Lenz <[email protected]>
Co-authored-by: Loïc Estève <[email protected]>
Co-authored-by: Brian Wignall <[email protected]>
Co-authored-by: Ritchie Ng <[email protected]>
Co-authored-by: Guillaume Lemaitre <[email protected]>
Co-authored-by: inderjeet <[email protected]>
Co-authored-by: scibol <[email protected]>
Co-authored-by: Tirth Patel <[email protected]>
Co-authored-by: Bibhash Chandra Mitra <[email protected]>
Co-authored-by: Alexandre Gramfort <[email protected]>
Co-authored-by: Tiffany R. Williams <[email protected]>
Co-authored-by: Jigna Panchal <[email protected]>
Co-authored-by: @nkish <[email protected]>
Co-authored-by: Pulkit Mehta <[email protected]>
Co-authored-by: David Breuer <[email protected]>
Co-authored-by: Niklas <[email protected]>
Co-authored-by: Windber <[email protected]>
Co-authored-by: Stephen Blystone <[email protected]>
Co-authored-by: Brigitta Sipőcz <[email protected]>

Author: 37 people

.circleci/config.yml

@@ -101,7 +101,7 @@ jobs:
 
   pypy3:
     docker:
-      - image: pypy:3.6-7.1.1
+      - image: pypy:3.6-7.2.0
     steps:
       - restore_cache:
           keys:

azure-pipelines.yml

@@ -12,8 +12,14 @@ jobs:
     - bash: conda create --name flake8_env --yes flake8
       displayName: Install flake8
     - bash: |
-        source activate flake8_env
-        ./build_tools/circle/linting.sh
+        if [[ $BUILD_SOURCEVERSIONMESSAGE =~ \[lint\ skip\] ]]; then
+          # skip linting
+          echo "Skipping linting"
+          exit 0
+        else
+          source activate flake8_env
+          ./build_tools/circle/linting.sh
+        fi
       displayName: Run linting
 
 
@@ -65,10 +71,9 @@ jobs:
         JOBLIB_VERSION: '0.12.3'
         COVERAGE: 'true'
       # Linux environment to test the latest available dependencies and MKL.
-      # It runs tests requiring pandas and PyAMG.
+      # It runs tests requiring lightgbm, pandas and PyAMG.
       pylatest_pip_openblas_pandas:
         DISTRIB: 'conda-pip-latest'
-        # FIXME: pinned until SciPy wheels are available for Pyhon 3.8
         PYTHON_VERSION: '3.8'
         PYTEST_VERSION: '4.6.2'
         COVERAGE: 'true'

benchmarks/bench_plot_randomized_svd.py

@@ -104,7 +104,7 @@
 # in case the reconstructed (dense) matrix is too large
 MAX_MEMORY = np.int(2e9)
 
-# The following datasets can be dowloaded manually from:
+# The following datasets can be downloaded manually from:
 # CIFAR 10: https://www.cs.toronto.edu/~kriz/cifar-10-python.tar.gz
 # SVHN: http://ufldl.stanford.edu/housenumbers/train_32x32.mat
 CIFAR_FOLDER = "./cifar-10-batches-py/"

benchmarks/bench_text_vectorizers.py

@@ -32,7 +32,7 @@ def f():
 text = fetch_20newsgroups(subset='train').data[:1000]
 
 print("="*80 + '\n#' + "    Text vectorizers benchmark" + '\n' + '='*80 + '\n')
-print("Using a subset of the 20 newsrgoups dataset ({} documents)."
+print("Using a subset of the 20 newsgroups dataset ({} documents)."
       .format(len(text)))
 print("This benchmarks runs in ~1 min ...")
 

build_tools/azure/install.sh

@@ -13,7 +13,7 @@ make_conda() {
 version_ge() {
     # The two version numbers are separated with a new line is piped to sort
     # -rV. The -V activates for version number sorting and -r sorts in
-    # decending order. If the first argument is the top element of the sort, it
+    # descending order. If the first argument is the top element of the sort, it
     # is greater than or equal to the second argument.
     test "$(printf "${1}\n${2}" | sort -rV | head -n 1)" == "$1"
 }
@@ -92,6 +92,8 @@ elif [[ "$DISTRIB" == "conda-pip-latest" ]]; then
     python -m pip install numpy scipy cython joblib
     python -m pip install pytest==$PYTEST_VERSION pytest-cov pytest-xdist
     python -m pip install pandas matplotlib pyamg
+    # do not install dependencies for lightgbm since it requires scikit-learn
+    python -m pip install lightgbm --no-deps
 fi
 
 if [[ "$COVERAGE" == "true" ]]; then

build_tools/circle/build_test_pypy.sh

@@ -18,11 +18,14 @@ source pypy-env/bin/activate
 python --version
 which python
 
-# XXX: numpy version pinning can be reverted once PyPy
-#      compatibility is resolved for numpy v1.6.x. For instance,
-#      when PyPy3 >6.0 is released (see numpy/numpy#12740)
-pip install --extra-index https://antocuni.github.io/pypy-wheels/ubuntu numpy Cython pytest
-pip install scipy sphinx numpydoc docutils joblib pillow
+pip install -U pip
+
+# pins versions to install wheel from https://antocuni.github.io/pypy-wheels/manylinux2010
+pip install --extra-index-url https://antocuni.github.io/pypy-wheels/manylinux2010 numpy==1.18.0 scipy==1.3.2
+
+# Install Cython directly
+pip install https://antocuni.github.io/pypy-wheels/ubuntu/Cython/Cython-0.29.14-py3-none-any.whl
+pip install sphinx numpydoc docutils joblib pillow pytest
 
 ccache -M 512M
 export CCACHE_COMPRESS=1

conftest.py

@@ -37,7 +37,7 @@ def pytest_collection_modifyitems(config, items):
         skip_marker = pytest.mark.skip(
             reason='FeatureHasher is not compatible with PyPy')
         for item in items:
-            if item.name.endswith(('hashing.FeatureHasher',
+            if item.name.endswith(('_hash.FeatureHasher',
                                    'text.HashingVectorizer')):
                 item.add_marker(skip_marker)
 

doc/Makefile

@@ -2,7 +2,7 @@
 #
 
 # You can set these variables from the command line.
-SPHINXOPTS    =
+SPHINXOPTS    = -j auto
 SPHINXBUILD  ?= sphinx-build
 PAPER         =
 BUILDDIR      = _build

doc/conf.py

@@ -51,6 +51,7 @@
 if os.environ.get('NO_MATHJAX'):
     extensions.append('sphinx.ext.imgmath')
     imgmath_image_format = 'svg'
+    mathjax_path = ''
 else:
     extensions.append('sphinx.ext.mathjax')
     mathjax_path = ('https://cdn.jsdelivr.net/npm/mathjax@3/es5/'
@@ -304,7 +305,9 @@ def __call__(self, directory):
         'branch': binder_branch,
         'dependencies': './binder/requirements.txt',
         'use_jupyter_lab': True
-    }
+    },
+    # avoid generating too many cross links
+    'inspect_global_variables': False,
 }
 
 

doc/developers/advanced_installation.rst

@@ -49,7 +49,7 @@ feature, code or documentation improvement).
    If you plan on submitting a pull-request, you should clone from your fork
    instead.
 
-#. Install a compiler with OpenMP_ support for your platform. See intructions
+#. Install a compiler with OpenMP_ support for your platform. See instructions
    for :ref:`compiler_windows`, :ref:`compiler_macos`, :ref:`compiler_linux`
    and :ref:`compiler_freebsd`.
 
@@ -339,7 +339,7 @@ architecture (e.g. ARM), you can install the system versions::
 
 On Red Hat and clones (e.g. CentOS), install the dependencies using::
 
-    sudo yum -y install gcc gcc-c++ python-devel numpy scipy
+    sudo yum -y install gcc gcc-c++ python3-devel numpy scipy
 
 Linux compilers from conda-forge
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~