Merge remote-tracking branch 'upstream/master' into safe-level

Author: laurallu

.circleci/config.yml

@@ -5,14 +5,18 @@ jobs:
     docker:
       - image: circleci/python:3.6.1
     environment:
-      - USERNAME: "scikit-learn-contrib"
-      - DOC_REPO: "imbalanced-learn"
+      - USERNAME: "glemaitre"
+      - ORGANIZATION: "imbalanced-learn"
+      - DOC_REPO: "imbalanced-learn.github.io"
       - DOC_URL: ""
       - EMAIL: "g.lemaitre58@gmail.com"
       - MINICONDA_PATH: ~/miniconda
       - CONDA_ENV_NAME: testenv
       - PYTHON_VERSION: 3
     steps:
+      - add_ssh_keys:
+          fingerprints:
+            - "34:ea:b1:d9:b1:e2:5d:79:81:c4:d0:39:ca:85:e1:ef"
       - checkout
       - run: ./build_tools/circle/checkout_merge_commit.sh
       - run: ./build_tools/circle/build_doc.sh
@@ -27,11 +31,11 @@ jobs:
       - attach_workspace:
           at: doc/_build/html
       - run: ls -ltrh doc/_build/html
-      # - deploy:
-      #     command: |
-      #       if [[ "${CIRCLE_BRANCH}" =~ ^master$|^[0-9]+\.[0-9]+\.X$ ]]; then
-      #         bash ./build_tools/circle/push_doc.sh doc/_build/html
-      #       fi
+      - deploy:
+          command: |
+            if [[ "${CIRCLE_BRANCH}" =~ ^master$|^[0-9]+\.[0-9]+\.X$ ]]; then
+              bash ./build_tools/circle/push_doc.sh doc/_build/html
+            fi
     filters:
       branches:
         ignore: gh-pages

.readthedocs.yml

@@ -4,7 +4,7 @@
 
 .. _scikit-learn-contrib: https://github.com/scikit-learn-contrib
 
-|Travis|_ |AppVeyor|_ |Codecov|_ |CircleCI|_ |ReadTheDocs|_ |PythonVersion|_ |Pypi|_ |Gitter|_
+|Travis|_ |AppVeyor|_ |Codecov|_ |CircleCI|_ |PythonVersion|_ |Pypi|_ |Gitter|_
 
 .. |Travis| image:: https://travis-ci.org/scikit-learn-contrib/imbalanced-learn.svg?branch=master
 .. _Travis: https://travis-ci.org/scikit-learn-contrib/imbalanced-learn
@@ -18,9 +18,6 @@
 .. |CircleCI| image:: https://circleci.com/gh/scikit-learn-contrib/imbalanced-learn.svg?style=shield&circle-token=:circle-token
 .. _CircleCI: https://circleci.com/gh/scikit-learn-contrib/imbalanced-learn/tree/master
 
-.. |ReadTheDocs| image:: https://readthedocs.org/projects/imbalanced-learn/badge/?version=latest
-.. _ReadTheDocs: https://imbalanced-learn.readthedocs.io/en/latest/?badge=latest
-
 .. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/imbalanced-learn.svg
 .. _PythonVersion: https://img.shields.io/pypi/pyversions/imbalanced-learn.svg
 

README.rst

@@ -74,6 +74,15 @@ fi
 
 MAKE_TARGET=html
 
+# Installing required system packages to support the rendering of math
+# notation in the HTML documentation
+sudo -E apt-get -yq update
+sudo -E apt-get -yq remove texlive-binaries --purge
+sudo -E apt-get -yq --no-install-suggests --no-install-recommends \
+    install dvipng texlive-latex-base texlive-latex-extra \
+    texlive-latex-recommended texlive-fonts-recommended \
+    latexmk gsfonts ccache
+
 # deactivate circleci virtualenv and setup a miniconda env instead
 if [[ `type -t deactivate` ]]; then
     deactivate

build_tools/circle/build_doc.sh

@@ -27,13 +27,13 @@ MSG="Pushing the docs to $dir/ for branch: $CIRCLE_BRANCH, commit $CIRCLE_SHA1"
 
 cd $HOME
 if [ ! -d $DOC_REPO ];
-then git clone --depth 1 --no-checkout -b gh-pages "git@github.com:"$USERNAME"/"$DOC_REPO".git";
+then git clone --depth 1 --no-checkout -b master "git@github.com:"$ORGANIZATION"/"$DOC_REPO".git";
 fi
 cd $DOC_REPO
 git config core.sparseCheckout true
 echo $dir > .git/info/sparse-checkout
-git checkout gh-pages
-git reset --hard origin/gh-pages
+git checkout master
+git reset --hard origin/master
 git rm -rf $dir/ && rm -rf $dir/
 cp -R $GENERATED_DOC_DIR $dir
 touch $dir/.nojekyll
@@ -42,6 +42,6 @@ git config --global user.name $USERNAME
 git config --global push.default matching
 git add -f $dir/
 git commit -m "$MSG" $dir
-git push origin gh-pages
+git push origin master
 
 echo $MSG

build_tools/circle/push_doc.sh

@@ -46,13 +46,8 @@
 # see https://github.com/numpy/numpydoc/issues/69
 numpydoc_show_class_members = False
 
-# pngmath / imgmath compatibility layer for different sphinx versions
-import sphinx
-from distutils.version import LooseVersion
-if LooseVersion(sphinx.__version__) < LooseVersion('1.4'):
-    extensions.append('sphinx.ext.pngmath')
-else:
-    extensions.append('sphinx.ext.imgmath')
+extensions.append('sphinx.ext.imgmath')
+imgmath_image_format = 'svg'
 
 autodoc_default_flags = ['members', 'inherited-members']
 
@@ -138,7 +133,7 @@
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-# html_theme_options = {'prev_next_buttons_location': None}
+# html_theme_options = {}
 
 # Add any paths that contain custom themes here, relative to this directory.
 html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]

doc/conf.py

@@ -1,7 +1,7 @@
 .. _changes_0_6:
 
 Version 0.6.0 (under-development)
-================================+
+=================================
 
 Changelog
 ---------
@@ -12,7 +12,7 @@ Changed models
 The following models might give some different sampling due to changes in
 scikit-learn:
 
-- :class:`imblearn.under_sampling.ClusterCentroid`
+- :class:`imblearn.under_sampling.ClusterCentroids`
 - :class:`imblearn.under_sampling.InstanceHardnessThreshold`
 
 Maintenance

doc/whats_new/v0.6.rst

@@ -88,8 +88,7 @@ def outlier_rejection(X, y):
     """This will be our function used to resample our dataset."""
     model = IsolationForest(max_samples=100,
                             contamination=0.4,
-                            random_state=rng,
-                            behaviour='new')
+                            random_state=rng)
     model.fit(X)
     y_pred = model.predict(X)
     return X[y_pred == 1], y[y_pred == 1]

examples/plot_outlier_rejections.py

@@ -204,8 +204,7 @@ class BalancedRandomForestClassifier(RandomForestClassifier):
     ccp_alpha : non-negative float, optional (default=0.0)
         Complexity parameter used for Minimal Cost-Complexity Pruning. The
         subtree with the largest cost complexity that is smaller than
-        ``ccp_alpha`` will be chosen. By default, no pruning is performed. See
-        :ref:`minimal_cost_complexity_pruning` for details.
+        ``ccp_alpha`` will be chosen. By default, no pruning is performed.
 
         .. versionadded:: 0.22
            Added in `scikit-learn` in 0.22

imblearn/ensemble/_forest.py

@@ -395,8 +395,8 @@ def specificity_score(
     """Compute the specificity
 
     The specificity is the ratio ``tn / (tn + fp)`` where ``tn`` is the number
-    of true negatives and ``fn`` the number of false negatives. The specificity
-    quantifies the ability to avoid false positives_[1].
+    of true negatives and ``fp`` the number of false positives. The specificity
+    quantifies the ability to avoid false positives.
 
     The best value is 1 and the worst value is 0.
 

imblearn/metrics/_classification.py

@@ -867,7 +867,7 @@ class SMOTENC(SMOTE):
 
     See
     :ref:`sphx_glr_auto_examples_over-sampling_plot_comparison_over_sampling.py`,
-    and :ref:`sphx_glr_auto_examples_over-sampling_plot_smote.py`.
+    and :ref:`sphx_glr_auto_examples_over-sampling_plot_illustration_generation_sample.py`.
 
     See also
     --------

imblearn/over_sampling/_smote.py

@@ -33,7 +33,8 @@
                'Operating System :: Unix',
                'Operating System :: MacOS',
                'Programming Language :: Python :: 3.6',
-               'Programming Language :: Python :: 3.7']
+               'Programming Language :: Python :: 3.7',
+               'Programming Language :: Python :: 3.8']
 INSTALL_REQUIRES = [
     'numpy>=1.11',
     'scipy>=0.17',