Revert "Merge branch 'master' into matern-inf-nu"

This reverts commit 9ba25e9, reversing
changes made to 9f30421.

.circleci/config.yml

@@ -13,11 +13,6 @@ jobs:
       - NUMPY_VERSION: 1.11.0
       - SCIPY_VERSION: 0.17.0
       - MATPLOTLIB_VERSION: 1.5.1
-      # on conda, this is the latest for python 3.5
-      # The following places need to be in sync with regard to Cython version:
-      # - .circleci config file
-      # - sklearn/_build_utils/__init__.py
-      # - advanced installation guide
       - CYTHON_VERSION: 0.28.5
       - SCIKIT_IMAGE_VERSION: 0.12.3
     steps:

MANIFEST.in

@@ -5,3 +5,4 @@ recursive-include sklearn *.c *.h *.pyx *.pxd *.pxi *.tp
 recursive-include sklearn/datasets *.csv *.csv.gz *.rst *.jpg *.txt *.arff.gz *.json.gz
 include COPYING
 include README.rst
+

README.rst

@@ -31,7 +31,7 @@ SciPy and is distributed under the 3-Clause BSD license.
 
 The project was started in 2007 by David Cournapeau as a Google Summer
 of Code project, and since then many volunteers have contributed. See
-the `About us <http://scikit-learn.org/dev/about.html#authors>`__ page
+the `About us <http://scikit-learn.org/dev/about.html#authors>`_ page
 for a list of core contributors.
 
 It is currently maintained by a team of volunteers.
@@ -55,7 +55,7 @@ scikit-learn requires:
 **Scikit-learn 0.20 was the last version to support Python 2.7 and Python 3.4.**
 scikit-learn 0.21 and later require Python 3.5 or newer.
 
-Scikit-learn plotting capabilities (i.e., functions start with ``plot_``
+Scikit-learn plotting capabilities (i.e., functions start with "plot_"
 and classes end with "Display") require Matplotlib (>= 1.5.1). For running the
 examples Matplotlib >= 1.5.1 is required. A few examples require
 scikit-image >= 0.12.3, a few examples require pandas >= 0.18.0.
@@ -138,7 +138,7 @@ Project History
 
 The project was started in 2007 by David Cournapeau as a Google Summer
 of Code project, and since then many volunteers have contributed. See
-the `About us <http://scikit-learn.org/dev/about.html#authors>`__ page
+the  `About us <http://scikit-learn.org/dev/about.html#authors>`_ page
 for a list of core contributors.
 
 The project is currently maintained by a team of volunteers.

azure-pipelines.yml

@@ -26,7 +26,7 @@ jobs:
       pylatest_conda_mkl:
         DISTRIB: 'conda'
         PYTHON_VERSION: '*'
-        BLAS: 'mkl'
+        INSTALL_MKL: 'true'
         NUMPY_VERSION: '*'
         SCIPY_VERSION: '*'
         CYTHON_VERSION: '*'
@@ -48,17 +48,17 @@ jobs:
         DISTRIB: 'ubuntu'
         PYTHON_VERSION: '3.5'
         JOBLIB_VERSION: '0.11'
+        SKLEARN_NO_OPENMP: 'True'
       # Linux + Python 3.5 build with OpenBLAS and without SITE_JOBLIB
       py35_conda_openblas:
         DISTRIB: 'conda'
         PYTHON_VERSION: '3.5'
-        BLAS: 'openblas'
+        INSTALL_MKL: 'false'
         NUMPY_VERSION: '1.11.0'
         SCIPY_VERSION: '0.17.0'
         PANDAS_VERSION: '*'
         CYTHON_VERSION: '*'
-        # temporary pin pytest due to unknown failure with pytest 5.3
-        PYTEST_VERSION: '5.2'
+        PYTEST_VERSION: '*'
         PILLOW_VERSION: '4.0.0'
         MATPLOTLIB_VERSION: '1.5.1'
         # later version of joblib are not packaged in conda for Python 3.5
@@ -69,7 +69,7 @@ jobs:
       pylatest_pip_openblas_pandas:
         DISTRIB: 'conda-pip-latest'
         # FIXME: pinned until SciPy wheels are available for Pyhon 3.8
-        PYTHON_VERSION: '3.8'
+        PYTHON_VERSION: '3.7'
         PYTEST_VERSION: '4.6.2'
         COVERAGE: 'true'
         CHECK_PYTEST_SOFT_DEPENDENCY: 'true'
@@ -86,6 +86,7 @@ jobs:
         DISTRIB: 'ubuntu-32'
         PYTHON_VERSION: '3.5'
         JOBLIB_VERSION: '0.11'
+        SKLEARN_NO_OPENMP: 'True'
 
 - template: build_tools/azure/posix.yml
   parameters:
@@ -96,27 +97,14 @@ jobs:
       pylatest_conda_mkl:
         DISTRIB: 'conda'
         PYTHON_VERSION: '*'
-        BLAS: 'mkl'
-        NUMPY_VERSION: '*'
-        SCIPY_VERSION: '*'
-        CYTHON_VERSION: '*'
-        PILLOW_VERSION: '*'
-        PYTEST_VERSION: '*'
-        JOBLIB_VERSION: '*'
-        COVERAGE: 'true'
-      pylatest_conda_mkl_no_openmp:
-        DISTRIB: 'conda'
-        PYTHON_VERSION: '*'
-        BLAS: 'mkl'
+        INSTALL_MKL: 'true'
         NUMPY_VERSION: '*'
         SCIPY_VERSION: '*'
         CYTHON_VERSION: '*'
         PILLOW_VERSION: '*'
         PYTEST_VERSION: '*'
         JOBLIB_VERSION: '*'
         COVERAGE: 'true'
-        SKLEARN_TEST_NO_OPENMP: 'true'
-        SKLEARN_SKIP_OPENMP_TEST: 'true'
 
 - template: build_tools/azure/windows.yml
   parameters:

build_tools/azure/install.sh

@@ -22,8 +22,13 @@ if [[ "$DISTRIB" == "conda" ]]; then
 
     TO_INSTALL="python=$PYTHON_VERSION pip \
                 numpy=$NUMPY_VERSION scipy=$SCIPY_VERSION \
-                cython=$CYTHON_VERSION joblib=$JOBLIB_VERSION\
-                blas[build=$BLAS]"
+                cython=$CYTHON_VERSION joblib=$JOBLIB_VERSION"
+
+    if [[ "$INSTALL_MKL" == "true" ]]; then
+        TO_INSTALL="$TO_INSTALL mkl"
+    else
+        TO_INSTALL="$TO_INSTALL nomkl"
+    fi
 
     if [[ -n "$PANDAS_VERSION" ]]; then
         TO_INSTALL="$TO_INSTALL pandas=$PANDAS_VERSION"
@@ -42,11 +47,8 @@ if [[ "$DISTRIB" == "conda" ]]; then
     fi
 
     if [[ "$UNAMESTR" == "Darwin" ]]; then
-        if [[ "$SKLEARN_TEST_NO_OPENMP" != "true" ]]; then
-            # on macOS, install an OpenMP-enabled clang/llvm from conda-forge.
-            TO_INSTALL="$TO_INSTALL conda-forge::compilers \
-                        conda-forge::llvm-openmp"
-        fi
+        # on macOS, install an OpenMP-enabled clang/llvm from conda-forge
+        TO_INSTALL="$TO_INSTALL conda-forge::compilers conda-forge::llvm-openmp"
     fi
 
     # Old packages coming from the 'free' conda channel have been removed but
@@ -72,7 +74,6 @@ if [[ "$DISTRIB" == "conda" ]]; then
 
 elif [[ "$DISTRIB" == "ubuntu" ]]; then
     sudo add-apt-repository --remove ppa:ubuntu-toolchain-r/test
-    sudo apt-get update
     sudo apt-get install python3-scipy python3-matplotlib libatlas3-base libatlas-base-dev libatlas-dev python3-virtualenv
     python3 -m virtualenv --system-site-packages --python=python3 $VIRTUALENV
     source $VIRTUALENV/bin/activate
@@ -88,8 +89,7 @@ elif [[ "$DISTRIB" == "conda-pip-latest" ]]; then
     # we use pypi to test against the latest releases of the dependencies.
     # conda is still used as a convenient way to install Python and pip.
     make_conda "python=$PYTHON_VERSION"
-    python -m pip install -U pip
-    python -m pip install numpy scipy cython joblib
+    python -m pip install numpy scipy joblib cython
     python -m pip install pytest==$PYTEST_VERSION pytest-cov pytest-xdist
     python -m pip install pandas matplotlib pyamg
 fi
@@ -117,8 +117,5 @@ except ImportError:
     print('pandas not installed')
 "
 python -m pip list
-
-# Use setup.py instead of `pip install -e .` to be able to pass the -j flag
-# to speed-up the building multicore CI machines.
 python setup.py build_ext --inplace -j 3
 python setup.py develop

build_tools/azure/posix-32.yml

@@ -37,6 +37,7 @@ jobs:
         -e VIRTUALENV=testvenv
         -e JOBLIB_VERSION=$JOBLIB_VERSION
         -e PYTEST_VERSION=$PYTEST_VERSION
+        -e SKLEARN_NO_OPENMP=$SKLEARN_NO_OPENMP
         -e OMP_NUM_THREADS=$OMP_NUM_THREADS
         -e OPENBLAS_NUM_THREADS=$OPENBLAS_NUM_THREADS
         -e SKLEARN_SKIP_NETWORK_TESTS=$SKLEARN_SKIP_NETWORK_TESTS

build_tools/circle/build_doc.sh

@@ -58,44 +58,6 @@ get_build_type() {
         return
     fi
     changed_examples=$(echo "$filenames" | grep -E "^examples/(.*/)*plot_")
-
-    # The following is used to extract the list of filenames of example python
-    # files that sphinx-gallery needs to run to generate png files used as
-    # figures or images in the .rst files  from the documentation.
-    # If the contributor changes a .rst file in a PR we need to run all
-    # the examples mentioned in that file to get sphinx build the
-    # documentation without generating spurious warnings related to missing
-    # png files.
-
-    if [[ -n "$filenames" ]]
-    then
-        # get rst files
-        rst_files="$(echo "$filenames" | grep -E "rst$")"
-
-        # get lines with figure or images
-        img_fig_lines="$(echo "$rst_files" | xargs grep -shE "(figure|image)::")"
-
-        # get only auto_examples
-        auto_example_files="$(echo "$img_fig_lines" | grep auto_examples | awk -F "/" '{print $NF}')"
-
-        # remove "sphx_glr_" from path and accept replace _(\d\d\d|thumb).png with .py
-        scripts_names="$(echo "$auto_example_files" | sed 's/sphx_glr_//' | sed -E 's/_([[:digit:]][[:digit:]][[:digit:]]|thumb).png/.py/')"
-
-        # get unique values
-        examples_in_rst="$(echo "$scripts_names" | uniq )"
-    fi
-
-    # executed only if there are examples in the modified rst files
-    if [[ -n "$examples_in_rst" ]]
-    then
-        if [[ -n "$changed_examples" ]]
-        then
-            changed_examples="$changed_examples|$examples_in_rst"
-        else
-            changed_examples="$examples_in_rst"
-        fi
-    fi
-
     if [[ -n "$changed_examples" ]]
     then
         echo BUILD: detected examples/ filename modified in $git_range: $changed_examples
@@ -163,17 +125,16 @@ if [[ "$CIRCLE_JOB" == "doc-min-dependencies" ]]; then
     conda config --set restore_free_channel true
 fi
 
-# packaging won't be needed once setuptools starts shipping packaging>=17.0
 conda create -n $CONDA_ENV_NAME --yes --quiet python="${PYTHON_VERSION:-*}" \
   numpy="${NUMPY_VERSION:-*}" scipy="${SCIPY_VERSION:-*}" \
   cython="${CYTHON_VERSION:-*}" pytest coverage \
   matplotlib="${MATPLOTLIB_VERSION:-*}" sphinx=2.1.2 pillow \
   scikit-image="${SCIKIT_IMAGE_VERSION:-*}" pandas="${PANDAS_VERSION:-*}" \
-  joblib memory_profiler packaging
+  joblib memory_profiler
 
 source activate testenv
-pip install sphinx-gallery
-pip install numpydoc
+pip install sphinx-gallery==0.3.1
+pip install numpydoc==0.9
 
 # Build and install scikit-learn in dev mode
 python setup.py build_ext --inplace -j 3
@@ -242,12 +203,5 @@ then
     echo "$warnings" | sed 's/\/home\/circleci\/project\//<li>/g'
     echo '</ul></body></html>'
     ) > 'doc/_build/html/stable/_changed.html'
-
-    if [ "$warnings" != "/home/circleci/project/ no warnings" ]
-    then
-        echo "Sphinx generated warnings when building the documentation related to files modified in this PR."
-        echo "Please check doc/_build/html/stable/_changed.html"
-        exit 1
-    fi
 fi
 

doc/about.rst

@@ -139,13 +139,9 @@ Grisel, Guillaume Lemaitre, Jérémie du Boisberranger and Chiara Marmo.
    :target: https://www.axa.fr/
 
 .. |bnp| image:: images/bnp.png
-   :width: 170pt
+   :width: 150pt
    :target: https://www.bnpparibascardif.com/
 
-.. |fujitsu| image:: images/fujitsu.png
-   :width: 100pt
-   :target: https://www.fujitsu.com/global/
-
 .. |intel| image:: images/intel.png
    :width: 70pt
    :target: https://www.intel.com/
@@ -175,9 +171,7 @@ Grisel, Guillaume Lemaitre, Jérémie du Boisberranger and Chiara Marmo.
    +---------+----------+
    |                    |
    +---------+----------+ 
-   |  |axa|  ||fujitsu| |
-   +---------+----------+
-   |        |bnp|       |
+   |  |axa|  |   |bnp|  |
    +---------+----------+
    | |intel| | |nvidia| |
    +---------+----------+