nbara · nbara · Apr 8, 2021 · Apr 7, 2021 · Apr 7, 2021 · Apr 8, 2021
diff --git a/.gitignore b/.gitignore
@@ -79,4 +79,4 @@ target/
 # doc
 _build/
 auto_examples/
-modules/
+
diff --git a/.travis.yml b/.travis.yml
@@ -13,13 +13,11 @@ install:
   - sudo apt-get update
   - pip install -r requirements.txt
   - pip install -e .
-  - pip install sphinx-gallery
-  - pip install numpydoc
-  - pip install sphinx_bootstrap_theme
   - pip install git+https://github.com/pymanopt/pymanopt
 script:
   - mkdir docs
   - cd doc
+  - pip install -r requirements.txt
   # - sphinx-autogen *.rst
   - make html
   - touch _build/html/.nojekyll

diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 # MEEGkit
 
 [![unit-tests](https://github.com/nbara/python-meegkit/workflows/unit-tests/badge.svg?style=flat)](https://github.com/nbara/python-meegkit/actions?workflow=unit-tests)
-[![Travis](https://img.shields.io/travis/nbara/python-meegkit.svg?label=documentation&logo=travis)](https://travis-ci.org/nbara/python-meegkit)
+[![documentation](https://img.shields.io/travis/nbara/python-meegkit.svg?label=documentation&logo=travis)](https://travis-ci.org/nbara/python-meegkit)
 [![codecov](https://codecov.io/gh/nbara/python-meegkit/branch/master/graph/badge.svg)](https://codecov.io/gh/nbara/python-meegkit)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/nbara/python-meegkit/master)
 [![twitter](https://img.shields.io/twitter/follow/lebababa?label=Twitter&style=flat&logo=Twitter)](https://twitter.com/intent/follow?screen_name=lebababa)

diff --git a/doc/Makefile b/doc/Makefile
@@ -25,7 +25,6 @@ clean:
 	-rm -rf _build/*
 	-rm -rf _source/*
 	-rm -rf generated
-	-rm -rf auto_examples/*
 	-rm -rf *.stc
 	-rm -rf *.fif
 	-rm -rf *.nii.gz

diff --git a/doc/conf.py b/doc/conf.py
@@ -12,10 +12,6 @@
 #
 import os
 import sys
-from numpydoc import docscrape  # noqa
-import sphinx_gallery  # noqa
-import sphinx_bootstrap_theme  # noqa
-
 import matplotlib
 matplotlib.use('agg')
 
@@ -27,9 +23,10 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'MEEGkit'
-copyright = '2020, Nicolas Barascud'
+project = f'MEEGkit v{meegkit.__version__}'
+copyright = '2021, Nicolas Barascud'
 author = 'Nicolas Barascud'
+release = meegkit.__version__
 version = meegkit.__version__
 
 # -- General configuration ---------------------------------------------------
@@ -42,7 +39,9 @@
     'sphinx.ext.autosummary',
     'sphinx.ext.napoleon',
     'numpydoc',
+    'jupyter_sphinx',
     'sphinx_gallery.gen_gallery',
+    'sphinxemoji.sphinxemoji',
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -75,10 +74,8 @@
 
 # -- Options for HTML output -------------------------------------------------
 
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-#
-html_theme = 'bootstrap'
+# The theme to use for HTML and HTML Help pages
+html_theme = 'pydata_sphinx_theme'
 
 # 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,
@@ -87,62 +84,33 @@
 
 
 html_theme_options = {
-    # Tab name for entire site. (Default: "Site")
-    'navbar_site_name': "MEEGkit documentation",
-
-    # Render the next and previous page links in navbar. (Default: true)
-    'navbar_sidebarrel': False,
-
-    # Links in the navbar
-    'navbar_links': [
-        ("Examples", "auto_examples/index"),
-        ("GitHub", "https://github.com/nbara/python-meegkit", True)
+    "show_toc_level": 1,
+    "external_links": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/nbara/python-meegkit",
+        }
+    ],
+    "icon_links": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/nbara/python-meegkit",
+            "icon": "fab fa-github-square",
+        },
+        {
+            "name": "Twitter",
+            "url": "https://twitter.com/lebababa",
+            "icon": "fab fa-twitter-square",
+        },
     ],
+    "use_edit_page_button": True,
+}
 
-    # Render the current pages TOC in the navbar. (Default: true)
-    'navbar_pagenav': True,
-
-    # Tab name for the current pages TOC. (Default: "Page")
-    'navbar_pagenav_name': "Page",
-
-    # Global TOC depth for "site" navbar tab. (Default: 1)
-    # Switching to -1 shows all levels.
-    'globaltoc_depth': 2,
-
-    # Include hidden TOCs in Site navbar?
-    #
-    # Note: If this is "false", you cannot have mixed ``:hidden:`` and
-    # non-hidden ``toctree`` directives in the same page, or else the build
-    # will break.
-    #
-    # Values: "true" (default) or "false"
-    'globaltoc_includehidden': "true",
-
-    # HTML navbar class (Default: "navbar") to attach to <div> element.
-    # For black navbar, do "navbar navbar-inverse"
-    'navbar_class': "navbar navbar-inverse",
-
-    # Fix navigation bar to top of page?
-    # Values: "true" (default) or "false"
-    'navbar_fixed_top': "true",
-
-    # Location of link to source.
-    # Options are "nav" (default), "footer" or anything else to exclude.
-    'source_link_position': "nav",
-
-    # Bootswatch (http://bootswatch.com/) theme.
-    #
-    # Options are nothing (default) or the name of a valid theme
-    # such as "cosmo" or "sandstone".
-    #
-    # Currently, the supported themes are:
-    # - Bootstrap 2: https://bootswatch.com/2
-    # - Bootstrap 3: https://bootswatch.com/3
-    'bootswatch_theme': "united",
-
-    # Choose Bootstrap version.
-    # Values: "3" (default) or "2" (in quotes)
-    'bootstrap_version': "3",
+html_context = {
+    "github_user": "nbara",
+    "github_repo": "python-meegkit",
+    "github_version": "master",
+    "doc_path": "doc",
 }
 
 # -- Options for Sphinx-gallery HTML ------------------------------------------
@@ -153,4 +121,5 @@
     'gallery_dirs': 'auto_examples',  # path to where to save gallery generated output
     'filename_pattern': '/example_',
     'ignore_pattern': 'config.py',
+    'run_stale_examples': False,
 }
diff --git a/doc/index.rst b/doc/index.rst
@@ -1,23 +1,37 @@
-.. MEEGkit documentation master file, created by
+.. ``meegkit`` documentation master file, created by
    sphinx-quickstart on Fri Jan 10 12:31:49 2020.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to MEEGkit
-==================
+|:brain:| ``meegkit``: EEG and MEG denoising in Python
+======================================================
 
-The code of the project is on Github: `MEEGkit <https://github.com/nbara/python-meegkit>`_
+Introduction
+------------
 
+``meegkit`` is a collection of EEG and MEG denoising techniques for
+**Python 3.6+**. Please feel free to contribute, or suggest new analyses. Keep
+in mind that this is mostly development code, and as such is likely to change
+without any notice. Also, while most of the methods have been fairly robustly
+tested, bugs can (and should!) be expected.
 
-Contents
---------
+The source code of the project is hosted on Github at the following address:
+https://github.com/nbara/python-meegkit
 
-:py:mod:`meegkit`:
+To get started, follow the installation instructions `in the README <https://github.com/nbara/python-meegkit#installation>`_.
+
+Available modules
+-----------------
+
+Here is a list of the methods and techniques available in ``meegkit``:
 
 .. currentmodule:: meegkit
 
+.. toctree::
+   :maxdepth: 1
+
 .. autosummary::
-   :toctree: modules/
+   :caption: meegkit
 
    ~meegkit.asr
    ~meegkit.cca
@@ -30,16 +44,19 @@ Contents
    ~meegkit.tspca
    ~meegkit.utils
 
+
 Examples gallery
 ----------------
 
-A gallery of examples is available at the following address:
+A number of example scripts and notebooks are available:
+
 
 .. toctree::
    :maxdepth: 2
 
    auto_examples/index
 
+
 Indices and tables
 ------------------
 

diff --git a/doc/modules/meegkit.trca.rst b/doc/modules/meegkit.trca.rst
@@ -0,0 +1,30 @@
+meegkit.trca
+============
+
+.. automodule:: meegkit.trca
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      trca
+      TRCA
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/doc/requirements.txt b/doc/requirements.txt
@@ -0,0 +1,9 @@
+sphinx
+sphinx-copybutton
+sphinxemoji
+pydata-sphinx-theme
+numpydoc
+matplotlib
+pillow
+sphinx-gallery
+jupyter-sphinx
diff --git a/examples/README.rst b/examples/README.rst
@@ -1,4 +1,8 @@
-MEEGkit examples
+Examples gallery
 ================
 
-Below is a gallery of examples
+Below is a list of example scripts showing basic usage for most methods in
+MEEGkit.
+
+The examples can be browsed directly on `Github <https://github.com/nbara/python-meegkit/tree/master/examples>`_.
+
diff --git a/meegkit/cca.py b/meegkit/cca.py
@@ -1,4 +1,4 @@
-"""CCA functions."""
+"""Canonical Correlation Analysis."""
 import numpy as np
 from scipy import linalg
 

diff --git a/meegkit/ress.py b/meegkit/ress.py
@@ -8,7 +8,9 @@
 def RESS(X, sfreq: int, peak_freq: float, neig_freq: float = 1,
          peak_width: float = .5, neig_width: float = 1, n_keep: int = 1,
          return_maps: bool = False):
-    """Rhythmic entrainment source separation [1]_.
+    """Rhythmic Entrainment Source Separation.
+
+    As described in [1]_.
 
     Parameters
     ----------

diff --git a/meegkit/trca.py b/meegkit/trca.py
@@ -1,4 +1,4 @@
-"""Task-Related Component Analysis (TRCA)."""
+"""Task-Related Component Analysis."""
 # Author: Giuseppe Ferraro <giuseppe.ferraro@isae-supaero.fr>
 import numpy as np
 import scipy.linalg as linalg
@@ -8,7 +8,7 @@
 
 
 def trca(X):
-    """Task-related component analysis (TRCA).
+    """Task-related component analysis.
 
     This function implements the method described in [1]_.
 

diff --git a/meegkit/utils/stats.py b/meegkit/utils/stats.py
@@ -225,8 +225,8 @@ def cronbach(epochs, K=None, n_bootstrap=2000, tmin=None, tmax=None):
     Internal reliability of the ERN and Pe as a function of increasing trial
     numbers can be quantified with Cronbach's alpha:
 
-    $$\alpha = \frac{K}{K-1} \left(1-\frac{\sum_{i=1}^K
-    \sigma^2_{Y_i}}{ \sigma^2_X}\right)$$
+        $$\alpha = \frac{K}{K-1} \left(1-\frac{\sum_{i=1}^K
+          \sigma^2_{Y_i}}{ \sigma^2_X}\right)$$
 
     Hinton, Brownlow, McMurray, and Cozens (2004) have suggested that
     Cronbach's alpha exceeding .90 indicates excellent internal reliability,
@@ -284,6 +284,8 @@ def cronbach(epochs, K=None, n_bootstrap=2000, tmin=None, tmax=None):
 def snr_spectrum(X, freqs, n_avg=1, n_harm=1, skipbins=1):
     """Compute Signal-to-Noise-corrected spectrum.
 
+    The implementation tries to replicate examples in [1; 2; 3]_.
+
     Parameters
     ----------
     X : ndarray , shape=(n_freqs, n_chans,[ n_trials,])

diff --git a/meegkit/utils/trca.py b/meegkit/utils/trca.py
@@ -31,7 +31,7 @@ def normfit(data, ci=0.95):
 
     Parameters
     ----------
-    data: array, shape=()
+    data : array, shape=()
         Input data.
     ci : float
         Confidence interval (default=0.95).
@@ -61,8 +61,10 @@ def normfit(data, ci=0.95):
 def itr(n, p, t):
     """Compute information transfer rate (ITR).
 
-    Inputs
-    ------
+    Definition in [1]_.
+
+    Parameters
+    ----------
     n : int
         Number of targets.
     p : float

diff --git a/requirements.txt b/requirements.txt
@@ -3,11 +3,7 @@ scipy
 matplotlib
 scikit-learn
 pandas
-sphinx
-pillow
-sphinx-gallery
 joblib
-numpydoc
 flake8
 pytest
 pytest-cov
-Original file line number
+Diff line change
@@ Expand Up / @@ -79,4 +79,4 @@ target/ @@
     # doc
     _build/
     auto_examples/
-    modules/