[MRG] Refactor ratio to pick up any class (#290)

* EHN enable multiclass ratio handling

* FIX simplify call to dictionary

* FIX RUS done

* FIX Refactor ADASYN

* FIX partial

* FIX refactor SMOTE

* FIX refactor SMOTE

* DOC add proper docstring

* PEP8

* FIX ClusterCentroids

* FIX refactor IHT

* FIX Nearmiss refactoring

* FIX tomek links refactor

* FIX refactor OSS

* FIX NCR refactoring

* FIX refactor combined methods with Pipeline

* FIX combine method targetting all classes when cleaning

* FIX balance cascade refactoring

* EHN add the possibility to add a dict for ratio

* TST add test for check_ratio

* TST add test for float

* FIX/TST adapt common test

* TST fix IHT tests

* TST fix NCR

* FIX combine test

* TST fix balance

* FIX doctest

* FIX doctest

* FIX solve the pickle issue

* FIX remove comments

* TST add test for NCR

* TST add knn balance cascade

* EHN add callable option for the ratio

* DOC make doc cleaner

* FIX/DOC remove useless comments and clean doc

* DEP deprecation of ratio as float

* EHN add base class for cleaning methods

* TST add common test for multi class

* MAINT downgrade sphinx for the moment

* TST/EHN add test for the ratio and specific ratio for cleaning sampling

* EHN remove redundant code

* FIX warning

* Remove useless base class

* MAINT add christos back to some file

* EHN rename test and add a comment

* DOC add hash_X_y in the API

* [MRG] Incorporate chkoar remarks (#6)

* change cleaning-sampler to clean-sampler

* Refactor the over_sampling

* [WIP] adapt ensamble class

* [MRG] Remove the init in base class (#7)

* change cleaning-sampler to clean-sampler

* Refactor the over_sampling

* [WIP] adapt ensamble class

* iterate

* fix PEP8

* EHN doc

* FIX add extension for sphinx

* EHN make deprecatin great again

* EHN Improve SMOTE and ADASYN

Author: glemaitre

circle.yml

@@ -23,7 +23,7 @@ dependencies:
     - sudo apt-get install build-essential python-dev python-setuptools
     # install numpy first as it is a compile time dependency for other packages
     - pip install --upgrade numpy
-    - pip install --upgrade scipy matplotlib setuptools nose coverage sphinx pillow sphinx-gallery sphinx_rtd_theme
+    - pip install --upgrade scipy matplotlib setuptools nose coverage pillow sphinx-gallery sphinx_rtd_theme sphinx==1.5.6
     # Installing required packages for `make -C doc check command` to work.
     - sudo -E apt-get -yq update
     - sudo -E apt-get -yq --no-install-suggests --no-install-recommends --force-yes install dvipng texlive-latex-base texlive-latex-extra

doc/_static/css/imbalanced-learn.css

@@ -2,4 +2,19 @@
 
 .highlight a {
     text-decoration: underline;
-}
+}
+
+.deprecated p {
+    padding: 10px 7px 10px 10px;
+    color: #b94a48;
+    background-color: #F3E5E5;
+    border: 1px solid #eed3d7;
+}
+
+.deprecated p span.versionmodified {
+    font-weight: bold;
+}
+
+.wy-nav-content {
+    max-width: 1200px !important;
+}

doc/api.rst

@@ -77,8 +77,8 @@ Combination of over- and under-sampling methods
 ===============================================
 
 .. automodule:: imblearn.combine
-    :no-members:
-    :no-inherited-members:
+   :no-members:
+   :no-inherited-members:
 
 .. currentmodule:: imblearn
 
@@ -174,3 +174,6 @@ Utilities
    :toctree: generated/
 
    utils.estimator_checks.check_estimator
+   utils.check_neighbors_object
+   utils.check_ratio
+   utils.hash_X_y

doc/conf.py

@@ -31,6 +31,15 @@
     pass
 # -- General configuration ------------------------------------------------
 
+
+# If extensions (or modules to document with autodoc) are in another
+# directory, add these directories to sys.path here. If the directory
+# is relative to the documentation root, use os.path.abspath to make it
+# absolute, like shown here.
+sys.path.insert(0, os.path.abspath('sphinxext'))
+
+from github_link import make_linkcode_resolve
+
 # If your documentation needs a minimal Sphinx version, state it here.
 # needs_sphinx = '1.0'
 
@@ -39,9 +48,10 @@
 # ones.
 extensions = [
     'sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx',
-    'sphinx.ext.todo', 'numpydoc', 'sphinx.ext.pngmath', 'sphinx.ext.ifconfig',
+    'sphinx.ext.todo', 'sphinx.ext.pngmath', 'sphinx.ext.ifconfig',
     'sphinx.ext.viewcode', 'sphinx_gallery.gen_gallery',
-    'sphinx.ext.autosummary'
+    'sphinx.ext.autosummary', 'numpydoc',
+    'sphinx_issues', 'sphinx.ext.linkcode'
 ]
 
 autosummary_generate = True
@@ -294,6 +304,13 @@ def generate_example_rst(app, what, name, obj, options, lines):
         open(examples_path, 'w').close()
 
 
+# Config for sphinx_issues
+
+issues_uri = 'https://github.com/scikit-learn-contrib/imbalanced-learn/issues/{issue}'
+issues_github_path = 'scikit-learn-contrib/imbalanced-learn'
+issues_user_uri = 'https://github.com/{user}'
+
+
 def setup(app):
     app.connect('autodoc-process-docstring', generate_example_rst)
 
@@ -312,3 +329,9 @@ def setup(app):
 
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {'http://docs.python.org/': None}
+
+# The following is used by sphinx.ext.linkcode to provide links to github
+linkcode_resolve = make_linkcode_resolve('imblearn',
+                                         u'https://github.com/scikit-learn-contrib/'
+                                         'imbalanced-learn/blob/{revision}/'
+                                         '{package}/{path}#L{lineno}')

doc/sphinxext/LICENSE.txt

@@ -0,0 +1,97 @@
+-------------------------------------------------------------------------------
+    The files
+    - numpydoc.py
+    - autosummary.py
+    - autosummary_generate.py
+    - docscrape.py
+    - docscrape_sphinx.py
+    - phantom_import.py
+    have the following license:
+
+Copyright (C) 2008 Stefan van der Walt <stefan@mentat.za.net>, Pauli Virtanen <pav@iki.fi>
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+ 1. Redistributions of source code must retain the above copyright
+    notice, this list of conditions and the following disclaimer.
+ 2. Redistributions in binary form must reproduce the above copyright
+    notice, this list of conditions and the following disclaimer in
+    the documentation and/or other materials provided with the
+    distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
+IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT,
+INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.
+
+-------------------------------------------------------------------------------
+    The files
+    - compiler_unparse.py
+    - comment_eater.py
+    - traitsdoc.py
+    have the following license:
+
+This software is OSI Certified Open Source Software.
+OSI Certified is a certification mark of the Open Source Initiative.
+
+Copyright (c) 2006, Enthought, Inc.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+ * Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+ * Neither the name of Enthought, Inc. nor the names of its contributors may
+   be used to endorse or promote products derived from this software without
+   specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
+-------------------------------------------------------------------------------
+    The files
+    - only_directives.py
+    - plot_directive.py
+    originate from Matplotlib (http://matplotlib.sf.net/) which has
+    the following license:
+
+Copyright (c) 2002-2008 John D. Hunter; All Rights Reserved.
+
+1. This LICENSE AGREEMENT is between John D. Hunter (“JDH”), and the Individual or Organization (“Licensee”) accessing and otherwise using matplotlib software in source or binary form and its associated documentation.
+
+2. Subject to the terms and conditions of this License Agreement, JDH hereby grants Licensee a nonexclusive, royalty-free, world-wide license to reproduce, analyze, test, perform and/or display publicly, prepare derivative works, distribute, and otherwise use matplotlib 0.98.3 alone or in any derivative version, provided, however, that JDH’s License Agreement and JDH’s notice of copyright, i.e., “Copyright (c) 2002-2008 John D. Hunter; All Rights Reserved” are retained in matplotlib 0.98.3 alone or in any derivative version prepared by Licensee.
+
+3. In the event Licensee prepares a derivative work that is based on or incorporates matplotlib 0.98.3 or any part thereof, and wants to make the derivative work available to others as provided herein, then Licensee hereby agrees to include in any such work a brief summary of the changes made to matplotlib 0.98.3.
+
+4. JDH is making matplotlib 0.98.3 available to Licensee on an “AS IS” basis. JDH MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR IMPLIED. BY WAY OF EXAMPLE, BUT NOT LIMITATION, JDH MAKES NO AND DISCLAIMS ANY REPRESENTATION OR WARRANTY OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE OR THAT THE USE OF MATPLOTLIB 0.98.3 WILL NOT INFRINGE ANY THIRD PARTY RIGHTS.
+
+5. JDH SHALL NOT BE LIABLE TO LICENSEE OR ANY OTHER USERS OF MATPLOTLIB 0.98.3 FOR ANY INCIDENTAL, SPECIAL, OR CONSEQUENTIAL DAMAGES OR LOSS AS A RESULT OF MODIFYING, DISTRIBUTING, OR OTHERWISE USING MATPLOTLIB 0.98.3, OR ANY DERIVATIVE THEREOF, EVEN IF ADVISED OF THE POSSIBILITY THEREOF.
+
+6. This License Agreement will automatically terminate upon a material breach of its terms and conditions.
+
+7. Nothing in this License Agreement shall be deemed to create any relationship of agency, partnership, or joint venture between JDH and Licensee. This License Agreement does not grant permission to use JDH trademarks or trade name in a trademark sense to endorse or promote products or services of Licensee, or any third party.
+
+8. By copying, installing or otherwise using matplotlib 0.98.3, Licensee agrees to be bound by the terms and conditions of this License Agreement.
+

doc/sphinxext/MANIFEST.in

@@ -0,0 +1,2 @@
+recursive-include tests *.py
+include *.txt

doc/sphinxext/README.txt

@@ -0,0 +1,52 @@
+=====================================
+numpydoc -- Numpy's Sphinx extensions
+=====================================
+
+Numpy's documentation uses several custom extensions to Sphinx.  These
+are shipped in this ``numpydoc`` package, in case you want to make use
+of them in third-party projects.
+
+The following extensions are available:
+
+  - ``numpydoc``: support for the Numpy docstring format in Sphinx, and add
+    the code description directives ``np-function``, ``np-cfunction``, etc.
+    that support the Numpy docstring syntax.
+
+  - ``numpydoc.traitsdoc``: For gathering documentation about Traits attributes.
+
+  - ``numpydoc.plot_directives``: Adaptation of Matplotlib's ``plot::``
+    directive. Note that this implementation may still undergo severe
+    changes or eventually be deprecated.
+
+  - ``numpydoc.only_directives``: (DEPRECATED)
+
+  - ``numpydoc.autosummary``: (DEPRECATED) An ``autosummary::`` directive.
+    Available in Sphinx 0.6.2 and (to-be) 1.0 as ``sphinx.ext.autosummary``,
+    and it the Sphinx 1.0 version is recommended over that included in
+    Numpydoc.
+
+
+numpydoc
+========
+
+Numpydoc inserts a hook into Sphinx's autodoc that converts docstrings
+following the Numpy/Scipy format to a form palatable to Sphinx.
+
+Options
+-------
+
+The following options can be set in conf.py:
+
+- numpydoc_use_plots: bool
+
+  Whether to produce ``plot::`` directives for Examples sections that
+  contain ``import matplotlib``.
+
+- numpydoc_show_class_members: bool
+
+  Whether to show all members of a class in the Methods and Attributes
+  sections automatically.
+
+- numpydoc_edit_link: bool  (DEPRECATED -- edit your HTML template instead)
+
+  Whether to insert an edit link after docstrings.

doc/sphinxext/github_link.py

@@ -0,0 +1,84 @@
+from operator import attrgetter
+import inspect
+import subprocess
+import os
+import sys
+from functools import partial
+
+REVISION_CMD = 'git rev-parse --short HEAD'
+
+
+def _get_git_revision():
+    try:
+        revision = subprocess.check_output(REVISION_CMD.split()).strip()
+    except (subprocess.CalledProcessError, OSError):
+        print('Failed to execute git to get revision')
+        return None
+    return revision.decode('utf-8')
+
+
+def _linkcode_resolve(domain, info, package, url_fmt, revision):
+    """Determine a link to online source for a class/method/function
+
+    This is called by sphinx.ext.linkcode
+
+    An example with a long-untouched module that everyone has
+    >>> _linkcode_resolve('py', {'module': 'tty',
+    ...                          'fullname': 'setraw'},
+    ...                   package='tty',
+    ...                   url_fmt='http://hg.python.org/cpython/file/'
+    ...                           '{revision}/Lib/{package}/{path}#L{lineno}',
+    ...                   revision='xxxx')
+    'http://hg.python.org/cpython/file/xxxx/Lib/tty/tty.py#L18'
+    """
+
+    if revision is None:
+        return
+    if domain not in ('py', 'pyx'):
+        return
+    if not info.get('module') or not info.get('fullname'):
+        return
+
+    class_name = info['fullname'].split('.')[0]
+    if type(class_name) != str:
+        # Python 2 only
+        class_name = class_name.encode('utf-8')
+    module = __import__(info['module'], fromlist=[class_name])
+    obj = attrgetter(info['fullname'])(module)
+
+    try:
+        fn = inspect.getsourcefile(obj)
+    except Exception:
+        fn = None
+    if not fn:
+        try:
+            fn = inspect.getsourcefile(sys.modules[obj.__module__])
+        except Exception:
+            fn = None
+    if not fn:
+        return
+
+    fn = os.path.relpath(fn,
+                         start=os.path.dirname(__import__(package).__file__))
+    try:
+        lineno = inspect.getsourcelines(obj)[1]
+    except Exception:
+        lineno = ''
+    return url_fmt.format(revision=revision, package=package,
+                          path=fn, lineno=lineno)
+
+
+def make_linkcode_resolve(package, url_fmt):
+    """Returns a linkcode_resolve function for the given URL format
+
+    revision is a git commit reference (hash or name)
+
+    package is the name of the root module of the package
+
+    url_fmt is along the lines of ('https://github.com/USER/PROJECT/'
+                                   'blob/{revision}/{package}/'
+                                   '{path}#L{lineno}')
+    """
+    revision = _get_git_revision()
+    return partial(_linkcode_resolve, revision=revision, package=package,
+                   url_fmt=url_fmt)