Black formatting (#83)

* Use black code formatting + GH Actions

* Reformat setup and conf

.github/workflows/black.yml

@@ -0,0 +1,10 @@
+name: Lint
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: psf/black@stable

docs/changelog.rst

@@ -20,6 +20,7 @@ c. Added a new dataset containing 8 hours of ECG data. The dataset is in compres
 **Improvements**
 
 a. When using an MNE.Raw object, conversion of the data from Volts to micro-Volts is now performed within MNE. `PR 70 <https://github.com/raphaelvallat/yasa/pull/70>`_
+b. Use `black <https://black.readthedocs.io/en/stable/>`_ code formatting.
 
 **Dependencies**
 

docs/conf.py

@@ -9,24 +9,26 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-sys.path.insert(0, os.path.abspath('sphinxext'))
-extensions = ['sphinx.ext.mathjax',
-              'sphinx.ext.doctest',
-              'sphinx.ext.viewcode',
-              'sphinx.ext.githubpages',
-              'sphinx.ext.autosummary',
-              'sphinx.ext.autodoc',
-              'sphinx.ext.intersphinx',
-              'matplotlib.sphinxext.plot_directive',
-              'sphinx_copybutton',
-              'numpydoc']
+sys.path.insert(0, os.path.abspath("sphinxext"))
+extensions = [
+    "sphinx.ext.mathjax",
+    "sphinx.ext.doctest",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.githubpages",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
+    "matplotlib.sphinxext.plot_directive",
+    "sphinx_copybutton",
+    "numpydoc",
+]
 
 # Generate the API documentation when building
 autosummary_generate = True
 autodoc_default_options = {
-    'members': True,
-    'member-order': 'groupwise',
-    'undoc-members': False,
+    "members": True,
+    "member-order": "groupwise",
+    "undoc-members": False,
     # 'special-members': '__init__',
     # 'exclude-members': '__weakref__'
 }
@@ -49,15 +51,17 @@
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = 'yasa'
-author = 'Raphael Vallat'
-copyright = u'2018-{}, Dr. Raphael Vallat, Center for Human Sleep Science, UC Berkeley'.format(time.strftime("%Y"))
+project = "yasa"
+author = "Raphael Vallat"
+copyright = "2018-{}, Dr. Raphael Vallat, Center for Human Sleep Science, UC Berkeley".format(
+    time.strftime("%Y")
+)
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -79,56 +83,57 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
 
 # -- Options for HTML output ----------------------------------------------
 
 # Bootstrap theme
-html_theme = 'bootstrap'
+html_theme = "bootstrap"
 html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()
 html_theme_options = {
-    'source_link_position': "footer",
+    "source_link_position": "footer",
     # 'navbar_title': ' ',  # we replace this with an image
-    'bootswatch_theme': "flatly",
-    'navbar_sidebarrel': False,
+    "bootswatch_theme": "flatly",
+    "navbar_sidebarrel": False,
     # 'nosidebar': True,
     # 'navbar_site_name': "",
-    'navbar_pagenav': False,
-    'bootstrap_version': "3",
-    'navbar_class': "navbar",
-    'navbar_links': [
+    "navbar_pagenav": False,
+    "bootstrap_version": "3",
+    "navbar_class": "navbar",
+    "navbar_links": [
         ("API", "api"),
         ("Quickstart", "quickstart"),
         ("FAQ", "faq"),
         ("What's new", "changelog"),
-        ("Contribute", "contributing")],
+        ("Contribute", "contributing"),
+    ],
 }
 
-html_logo = 'pictures/yasa_128x128.png'
-html_favicon = 'pictures/favicon.ico'
+html_logo = "pictures/yasa_128x128.png"
+html_favicon = "pictures/favicon.ico"
 
 # -- Options for HTML output ------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'yasadoc'
+htmlhelp_basename = "yasadoc"
 html_show_sourcelink = False
 
 # -- Intersphinx ------------------------------------------------
 
 intersphinx_mapping = {
-    'numpy': ('http://docs.scipy.org/doc/numpy/', None),
-    'scipy': ('http://docs.scipy.org/doc/scipy/reference/', None),
-    'pandas': ('https://pandas.pydata.org/pandas-docs/stable/', None),
-    'sklearn': ('https://scikit-learn.org/stable/', None),
-    'matplotlib': ('https://matplotlib.org/', None),
-    'mne': ('https://martinos.org/mne/stable/', None),
-    'seaborn': ('https://seaborn.pydata.org/', None),
-    'pyriemann': ('https://pyriemann.readthedocs.io/en/latest/', None),
-    'tensorpac': ('https://etiennecmb.github.io/tensorpac/', None),
+    "numpy": ("http://docs.scipy.org/doc/numpy/", None),
+    "scipy": ("http://docs.scipy.org/doc/scipy/reference/", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
+    "sklearn": ("https://scikit-learn.org/stable/", None),
+    "matplotlib": ("https://matplotlib.org/", None),
+    "mne": ("https://martinos.org/mne/stable/", None),
+    "seaborn": ("https://seaborn.pydata.org/", None),
+    "pyriemann": ("https://pyriemann.readthedocs.io/en/latest/", None),
+    "tensorpac": ("https://etiennecmb.github.io/tensorpac/", None),
 }

notebooks/run_visbrain.py

@@ -5,9 +5,9 @@
 from yasa import spindles_detect, sw_detect
 
 # Load the data and hypnogram
-data = np.load('data_full_6hrs_100Hz_Cz+Fz+Pz.npz').get('data')
-ch_names = ['Cz', 'Fz', 'Pz']
-hypno = np.load('data_full_6hrs_100Hz_hypno.npz').get('hypno')
+data = np.load("data_full_6hrs_100Hz_Cz+Fz+Pz.npz").get("data")
+ch_names = ["Cz", "Fz", "Pz"]
+hypno = np.load("data_full_6hrs_100Hz_hypno.npz").get("hypno")
 
 # Initialize a Visbrain.gui.Sleep instance
 sl = Sleep(data=data, channels=ch_names, sf=100, hypno=hypno)
@@ -22,23 +22,22 @@ def fcn_spindle(data, sf, time, hypno):
     # sp = spindles_detect(data, sf).summary()
     # NREM sleep only
     sp = spindles_detect(data, sf, hypno=hypno).summary()
-    return (sp[['Start', 'End']].values * sf).astype(int)
+    return (sp[["Start", "End"]].values * sf).astype(int)
 
 
 # Define slow-waves function
 def fcn_sw(data, sf, time, hypno):
-    """Replace Visbrain built-in slow-wave detection by YASA algorithm.
-    """
+    """Replace Visbrain built-in slow-wave detection by YASA algorithm."""
     # On N2 / N3 sleep only
     # Note that if you want to apply the detection on N3 sleep only, you should
     # use sw_detect(..., include=(3)).summary()
     sw = sw_detect(data, sf, hypno=hypno).summary()
-    return (sw[['Start', 'End']].values * sf).astype(int)
+    return (sw[["Start", "End"]].values * sf).astype(int)
 
 
 # Replace the native Visbrain detections
-sl.replace_detections('spindle', fcn_spindle)
-sl.replace_detections('sw', fcn_sw)
+sl.replace_detections("spindle", fcn_spindle)
+sl.replace_detections("sw", fcn_sw)
 
 # Launch the Graphical User Interface
 sl.show()

pyproject.toml

@@ -0,0 +1,2 @@
+[tool.black]
+line-length = 100

setup.cfg

@@ -12,7 +12,7 @@ testpaths =
 
 [flake8]
 max-line-length = 100
-ignore = N806, N803, D107, D200, D205, D400, D401, D412, W504
+ignore = N806, N803, D107, D200, D205, D400, D401, D412, W504, E203
 exclude =
     .git,
     __pycache__,

setup.py

@@ -6,71 +6,73 @@
 LONG_DESCRIPTION = """YASA (Yet Another Spindle Algorithm) : fast and robust detection of spindles, slow-waves, and rapid eye movements from sleep EEG recordings..
 """
 
-DISTNAME = 'yasa'
-MAINTAINER = 'Raphael Vallat'
-MAINTAINER_EMAIL = '[email protected]'
-URL = 'https://github.com/raphaelvallat/yasa/'
-LICENSE = 'BSD (3-clause)'
-DOWNLOAD_URL = 'https://github.com/raphaelvallat/yasa/'
-VERSION = '0.6.1'
-PACKAGE_DATA = {'yasa.data.icons': ['*.svg']}
+DISTNAME = "yasa"
+MAINTAINER = "Raphael Vallat"
+MAINTAINER_EMAIL = "[email protected]"
+URL = "https://github.com/raphaelvallat/yasa/"
+LICENSE = "BSD (3-clause)"
+DOWNLOAD_URL = "https://github.com/raphaelvallat/yasa/"
+VERSION = "0.6.1"
+PACKAGE_DATA = {"yasa.data.icons": ["*.svg"]}
 
 INSTALL_REQUIRES = [
-    'numpy',
-    'scipy',
-    'pandas',
-    'matplotlib',
-    'seaborn',
-    'mne>=0.20.0',
-    'numba',
-    'outdated',
-    'antropy',
-    'scikit-learn',
-    'tensorpac>=0.6.5',
-    'pyriemann>=0.2.7',
-    'sleepecg>=0.5.0',
-    'lspopt',
-    'ipywidgets',
-    'joblib'
+    "numpy",
+    "scipy",
+    "pandas",
+    "matplotlib",
+    "seaborn",
+    "mne>=0.20.0",
+    "numba",
+    "outdated",
+    "antropy",
+    "scikit-learn",
+    "tensorpac>=0.6.5",
+    "pyriemann>=0.2.7",
+    "sleepecg>=0.5.0",
+    "lspopt",
+    "ipywidgets",
+    "joblib",
 ]
 
 PACKAGES = [
-    'yasa',
+    "yasa",
 ]
 
 CLASSIFIERS = [
-    'Intended Audience :: Science/Research',
-    'Programming Language :: Python :: 3.7',
-    'Programming Language :: Python :: 3.8',
-    'Programming Language :: Python :: 3.9',
-    'License :: OSI Approved :: BSD License',
-    'Operating System :: POSIX',
-    'Operating System :: Unix',
-    'Operating System :: MacOS'
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: POSIX",
+    "Operating System :: Unix",
+    "Operating System :: MacOS",
 ]
 
 try:
     from setuptools import setup
+
     _has_setuptools = True
 except ImportError:
     from distutils.core import setup
 
 if __name__ == "__main__":
 
-    setup(name=DISTNAME,
-          author=MAINTAINER,
-          author_email=MAINTAINER_EMAIL,
-          maintainer=MAINTAINER,
-          maintainer_email=MAINTAINER_EMAIL,
-          description=DESCRIPTION,
-          long_description=LONG_DESCRIPTION,
-          license=LICENSE,
-          url=URL,
-          version=VERSION,
-          download_url=DOWNLOAD_URL,
-          install_requires=INSTALL_REQUIRES,
-          include_package_data=True,
-          packages=PACKAGES,
-          package_data=PACKAGE_DATA,
-          classifiers=CLASSIFIERS,
-          )
+    setup(
+        name=DISTNAME,
+        author=MAINTAINER,
+        author_email=MAINTAINER_EMAIL,
+        maintainer=MAINTAINER,
+        maintainer_email=MAINTAINER_EMAIL,
+        description=DESCRIPTION,
+        long_description=LONG_DESCRIPTION,
+        license=LICENSE,
+        url=URL,
+        version=VERSION,
+        download_url=DOWNLOAD_URL,
+        install_requires=INSTALL_REQUIRES,
+        include_package_data=True,
+        packages=PACKAGES,
+        package_data=PACKAGE_DATA,
+        classifiers=CLASSIFIERS,
+    )

yasa/__init__.py

@@ -12,10 +12,9 @@
 from outdated import warn_if_outdated
 
 # Define YASA logger
-logging.basicConfig(format='%(asctime)s | %(levelname)s | %(message)s',
-                    datefmt='%d-%b-%y %H:%M:%S')
+logging.basicConfig(format="%(asctime)s | %(levelname)s | %(message)s", datefmt="%d-%b-%y %H:%M:%S")
 
-__author__  = "Raphael Vallat <[email protected]>"
+__author__ = "Raphael Vallat <[email protected]>"
 __version__ = "0.6.1"
 
 # Warn if a newer version of YASA is available