MNT blackify source code and add pre-commit (#722)

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

Author: 3 people

.pre-commit-config.yaml

@@ -0,0 +1,19 @@
+repos:
+-   repo: https://github.com/python/black
+    rev: stable
+    hooks:
+    -   id: black
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.3.0
+    hooks:
+    -   id: check-yaml
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+-   repo: https://gitlab.com/pycqa/flake8
+    rev: 3.7.8
+    hooks:
+    -   id: flake8
+        types: [file, python]
+        # only check for unused imports for now, as long as
+        # the code is not fully PEP8 compatible
+        args: [--select=F401]

build_tools/circle/linting.sh

@@ -130,7 +130,7 @@ check_files() {
     if [ -n "$files" ]; then
         # Conservative approach: diff without context (--unified=0) so that code
         # that was not changed does not create failures
-        git diff --unified=0 $COMMIT_RANGE -- $files | flake8 --diff --show-source $options
+        git diff --unified=0 $COMMIT_RANGE -- $files | flake8 --diff --max-line-length=88 --show-source $options
     fi
 }
 

conftest.py

@@ -12,22 +12,24 @@
 import numpy as np
 
 try:
-    np.set_printoptions(legacy='1.13')
+    np.set_printoptions(legacy="1.13")
 except TypeError:
     pass
 
 
 def pytest_runtest_setup(item):
     fname = item.fspath.strpath
-    if (fname.endswith(os.path.join('keras', '_generator.py')) or
-            fname.endswith('miscellaneous.rst')):
+    if fname.endswith(os.path.join("keras", "_generator.py")) or fname.endswith(
+        "miscellaneous.rst"
+    ):
         try:
             import keras
         except ImportError:
-            pytest.skip('The keras package is not installed.')
-    elif (fname.endswith(os.path.join('tensorflow', '_generator.py')) or
-          fname.endswith('miscellaneous.rst')):
+            pytest.skip("The keras package is not installed.")
+    elif fname.endswith(os.path.join("tensorflow", "_generator.py")) or fname.endswith(
+        "miscellaneous.rst"
+    ):
         try:
             import tensorflow
         except ImportError:
-            pytest.skip('The tensorflow package is not installed.')
+            pytest.skip("The tensorflow package is not installed.")

doc/conf.py

@@ -19,7 +19,7 @@
 # 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'))
+sys.path.insert(0, os.path.abspath("sphinxext"))
 from github_link import make_linkcode_resolve
 import sphinx_gallery
 
@@ -32,15 +32,15 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.doctest',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.linkcode',
-    'sphinxcontrib.bibtex',
-    'numpydoc',
-    'sphinx_issues',
-    'sphinx_gallery.gen_gallery',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.linkcode",
+    "sphinxcontrib.bibtex",
+    "numpydoc",
+    "sphinx_issues",
+    "sphinx_gallery.gen_gallery",
 ]
 
 # bibtex file
@@ -50,22 +50,22 @@
 # see https://github.com/numpy/numpydoc/issues/69
 numpydoc_show_class_members = False
 
-extensions.append('sphinx.ext.imgmath')
-imgmath_image_format = 'svg'
+extensions.append("sphinx.ext.imgmath")
+imgmath_image_format = "svg"
 
 autodoc_default_options = {
     "members": True,
     "inherited-members": True,
 }
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # generate autosummary even if no references
 autosummary_generate = True
 
 # The suffix of source filenames.
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The encoding of source files.
 # source_encoding = 'utf-8-sig'
@@ -74,7 +74,7 @@
 plot_gallery = True
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
 project = 'imbalanced-learn'
@@ -86,6 +86,7 @@
 #
 # The short X.Y version.
 from imblearn import __version__
+
 version = __version__
 # The full version, including alpha/beta/rc tags.
 release = __version__
@@ -102,11 +103,11 @@
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ['_build', '_templates']
+exclude_patterns = ["_build", "_templates"]
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
-default_role = 'literal'
+default_role = "literal"
 
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
@@ -121,10 +122,10 @@
 # show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # Custom style
-html_style = 'css/imbalanced-learn.css'
+html_style = "css/imbalanced-learn.css"
 
 # A list of ignored prefixes for module index sorting.
 # modindex_common_prefix = []
@@ -136,7 +137,7 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # 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
@@ -165,7 +166,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
@@ -214,17 +215,15 @@
 # html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'imbalanced-learndoc'
+htmlhelp_basename = "imbalanced-learndoc"
 
 # -- Options for LaTeX output ---------------------------------------------
 
 latex_elements = {
     # The paper size ('letterpaper' or 'a4paper').
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     # 'preamble': '',
 }
@@ -233,8 +232,13 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    ('index', 'imbalanced-learn.tex', 'imbalanced-learn Documentation',
-     'G. Lemaitre, F. Nogueira, D. Oliveira, C. Aridas', 'manual'),
+    (
+        "index",
+        "imbalanced-learn.tex",
+        "imbalanced-learn Documentation",
+        "G. Lemaitre, F. Nogueira, D. Oliveira, C. Aridas",
+        "manual",
+    ),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -256,21 +260,19 @@
 
 # intersphinx configuration
 intersphinx_mapping = {
-    'python': ('https://docs.python.org/{.major}'.format(
-        sys.version_info), None),
-    'numpy': ('https://docs.scipy.org/doc/numpy/', None),
-    'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
-    'matplotlib': ('https://matplotlib.org/', None),
-    'sklearn': ('http://scikit-learn.org/stable', None)
+    "python": ("https://docs.python.org/{.major}".format(sys.version_info), None,),
+    "numpy": ("https://docs.scipy.org/doc/numpy/", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
+    "matplotlib": ("https://matplotlib.org/", None),
+    "sklearn": ("http://scikit-learn.org/stable", None),
 }
 
 # sphinx-gallery configuration
 sphinx_gallery_conf = {
-    'doc_module': 'imblearn',
-    'backreferences_dir': os.path.join('generated'),
-    'show_memory': True,
-    'reference_url': {
-        'imblearn': None}
+    "doc_module": "imblearn",
+    "backreferences_dir": os.path.join("generated"),
+    "show_memory": True,
+    "reference_url": {"imblearn": None},
 }
 
 # -- Options for manual page output ---------------------------------------
@@ -281,8 +283,15 @@
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [('index', 'imbalanced-learn', 'imbalanced-learn Documentation',
-              ['G. Lemaitre, F. Nogueira, D. Oliveira, C. Aridas'], 1)]
+man_pages = [
+    (
+        "index",
+        "imbalanced-learn",
+        "imbalanced-learn Documentation",
+        ["G. Lemaitre, F. Nogueira, D. Oliveira, C. Aridas"],
+        1,
+    )
+]
 
 # If true, show URL addresses after external links.
 # man_show_urls = False
@@ -293,9 +302,15 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    ('index', 'imbalanced-learn', 'imbalanced-learn Documentation',
-     'G. Lemaitre, F. Nogueira, D. Oliveira, C. Aridas', 'imbalanced-learn',
-     'Toolbox for imbalanced dataset in machine learning.', 'Miscellaneous'),
+    (
+        "index",
+        "imbalanced-learn",
+        "imbalanced-learn Documentation",
+        "G. Lemaitre, F. Nogueira, D. Oliveira, C. Aridas",
+        "imbalanced-learn",
+        "Toolbox for imbalanced dataset in machine learning.",
+        "Miscellaneous",
+    ),
 ]
 
 
@@ -311,9 +326,9 @@
 
 # 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}'
+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}"
 
 # Hack to get kwargs to appear in docstring #18434
 # TODO: Remove when https://github.com/sphinx-doc/sphinx/pull/8234 gets
@@ -366,7 +381,9 @@ def setup(app):
 # texinfo_no_detailmenu = False
 
 # The following is used by sphinx.ext.linkcode to provide links to github
-linkcode_resolve = make_linkcode_resolve('imblearn',
-                                         'https://github.com/scikit-learn-contrib/'
-                                         'imbalanced-learn/blob/{revision}/'
-                                         '{package}/{path}#L{lineno}')
+linkcode_resolve = make_linkcode_resolve(
+    "imblearn",
+    "https://github.com/scikit-learn-contrib/"
+    "imbalanced-learn/blob/{revision}/"
+    "{package}/{path}#L{lineno}",
+)

doc/install.rst

@@ -17,6 +17,9 @@ The imbalanced-learn package requires the following dependencies:
 Install
 =======
 
+From PyPi or conda-forge repositories
+.....................................
+
 imbalanced-learn is currently available on the PyPi's repositories and you can
 install it via `pip`::
 
@@ -26,16 +29,25 @@ The package is release also in Anaconda Cloud platform::
 
   conda install -c conda-forge imbalanced-learn
 
+From source available on GitHub
+...............................
+
 If you prefer, you can clone it and run the setup.py file. Use the following
 commands to get a copy from Github and install all dependencies::
 
   git clone https://github.com/scikit-learn-contrib/imbalanced-learn.git
   cd imbalanced-learn
   pip install .
 
-Or install using pip and GitHub::
+Be aware that you can install in developer mode with::
+
+  pip install --no-build-isolation --editable .
+
+If you wish to make pull-requests on GitHub, we advise you to install
+pre-commit::
 
-  pip install -U git+https://github.com/scikit-learn-contrib/imbalanced-learn.git
+  pip install pre-commit
+  pre-commit install
 
 Test and coverage
 =================

doc/miscellaneous.rst

@@ -121,8 +121,7 @@ data and minimizing the loss previously defined::
   ...         # For each epoch, run accuracy on train and test
   ...         feed_dict = dict()
   ...         predicts_train = sess.run(predict, feed_dict={data: X})
-  ...         print("epoch: {} train accuracy: {:.3f}"
-  ...               .format(e, accuracy(y, predicts_train)))
+  ...         print(f"epoch: {e} train accuracy: {accuracy(y, predicts_train):.3f}")
   ... # doctest: +ELLIPSIS
   Starting training
   [...
@@ -169,4 +168,4 @@ will be passed to ``fit_generator``::
 
 .. topic:: References
 
-  * :ref:`sphx_glr_auto_examples_applications_porto_seguro_keras_under_sampling.py`
+  * :ref:`sphx_glr_auto_examples_applications_porto_seguro_keras_under_sampling.py`