docfixes

nbara · nbara · commit 9f331491bcae · 2020-04-30T18:28:24.000+02:00
diff --git a/.travis.yml b/.travis.yml
@@ -20,7 +20,7 @@ install:
 script:
   - mkdir docs
   - cd doc
-  - sphinx-autogen *.rst
+  # - sphinx-autogen *.rst
   - make html
   - touch _build/html/.nojekyll
 deploy:
diff --git a/doc/conf.py b/doc/conf.py
@@ -12,9 +12,9 @@
 #
 import os
 import sys
-from numpydoc import docscrape
+from numpydoc import docscrape  # noqa
 import sphinx_gallery  # noqa
-import sphinx_bootstrap_theme
+import sphinx_bootstrap_theme  # noqa
 
 import matplotlib
 matplotlib.use('agg')
@@ -31,7 +31,7 @@
 project = 'MEEGkit'
 copyright = '2020, Nicolas Barascud'
 author = 'Nicolas Barascud'
-
+version = '0.1'
 
 # -- General configuration ---------------------------------------------------
 
@@ -44,7 +44,7 @@
     'sphinx.ext.napoleon',
     'numpydoc',
     'sphinx_gallery.gen_gallery',
-    ]
+]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -55,8 +55,14 @@
 exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', 'config.py']
 
 # generate autosummary even if no references
-autosummary_generate = True
-autodoc_default_flags = ['members', 'undoc-members', 'show-inheritance', 'inherited-members']
+# autosummary_generate = True
+autodoc_default_options = {
+    'members': True,
+    'special-members': '__init__',
+    'undoc-members': True,
+    'show-inheritance': True,
+    'exclude-members': '__weakref__'
+}
 numpydoc_show_class_members = True
 
 # The suffix(es) of source filenames.
@@ -80,13 +86,20 @@
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
 
+
 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)
+    ],
+
     # Render the current pages TOC in the navbar. (Default: true)
     'navbar_pagenav': True,
 
@@ -126,7 +139,7 @@
     # Currently, the supported themes are:
     # - Bootstrap 2: https://bootswatch.com/2
     # - Bootstrap 3: https://bootswatch.com/3
-    'bootswatch_theme': "simplex",
+    'bootswatch_theme': "united",
 
     # Choose Bootstrap version.
     # Values: "3" (default) or "2" (in quotes)
diff --git a/doc/modules/meegkit.asr.rst b/doc/modules/meegkit.asr.rst
@@ -0,0 +1,30 @@
+meegkit.asr
+===========
+
+.. automodule:: meegkit.asr
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      asr_calibrate
+      asr_process
+      clean_windows
+   
+   
+
+   
+   
+   .. rubric:: Classes
+
+   .. autosummary::
+   
+      ASR
+   
+   
+
+   
+   
+   
diff --git a/doc/modules/meegkit.cca.rst b/doc/modules/meegkit.cca.rst
@@ -0,0 +1,28 @@
+meegkit.cca
+===========
+
+.. automodule:: meegkit.cca
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      cca_crossvalidate
+      mcca
+      nt_cca
+      whiten
+      whiten_nt
+      whiten_svd
+      whiten_zca
+   
+   
+
+   
+   
+   
+
+   
+   
+   
diff --git a/doc/modules/meegkit.detrend.rst b/doc/modules/meegkit.detrend.rst
@@ -0,0 +1,24 @@
+meegkit.detrend
+===============
+
+.. automodule:: meegkit.detrend
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      detrend
+      reduce_ringing
+      regress
+   
+   
+
+   
+   
+   
+
+   
+   
+   
diff --git a/doc/modules/meegkit.dss.rst b/doc/modules/meegkit.dss.rst
@@ -0,0 +1,24 @@
+meegkit.dss
+===========
+
+.. automodule:: meegkit.dss
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      dss0
+      dss1
+      dss_line
+   
+   
+
+   
+   
+   
+
+   
+   
+   
diff --git a/doc/modules/meegkit.sns.rst b/doc/modules/meegkit.sns.rst
@@ -0,0 +1,24 @@
+meegkit.sns
+===========
+
+.. automodule:: meegkit.sns
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      sns
+      sns0
+      sns1
+   
+   
+
+   
+   
+   
+
+   
+   
+   
diff --git a/doc/modules/meegkit.star.rst b/doc/modules/meegkit.star.rst
@@ -0,0 +1,22 @@
+meegkit.star
+============
+
+.. automodule:: meegkit.star
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      star
+   
+   
+
+   
+   
+   
+
+   
+   
+   
diff --git a/doc/modules/meegkit.tspca.rst b/doc/modules/meegkit.tspca.rst
@@ -0,0 +1,23 @@
+meegkit.tspca
+=============
+
+.. automodule:: meegkit.tspca
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      tspca
+      tsr
+   
+   
+
+   
+   
+   
+
+   
+   
+   
diff --git a/doc/modules/meegkit.utils.rst b/doc/modules/meegkit.utils.rst
@@ -0,0 +1,67 @@
+meegkit.utils
+=============
+
+.. automodule:: meegkit.utils
+
+   .. autosummary::
+
+    covariances
+    denoise
+    matrix
+    sig
+    stats
+
+|
+
+----
+
+Covariances
+-----------
+.. automodule:: meegkit.utils.covariances
+
+   .. autosummary::
+
+
+|
+
+----
+
+Denoising
+---------
+.. automodule:: meegkit.utils.denoise
+
+   .. autosummary::
+
+
+|
+
+----
+
+Matrix manipulation
+-------------------
+.. automodule:: meegkit.utils.matrix
+
+   .. autosummary::
+
+
+|
+
+----
+
+Signal
+------
+.. automodule:: meegkit.utils.sig
+
+   .. autosummary::
+
+
+|
+
+----
+
+
+Statistics
+----------
+.. automodule:: meegkit.utils.stats
+
+   .. autosummary::
diff --git a/meegkit/asr.py b/meegkit/asr.py
@@ -15,6 +15,8 @@
 except ImportError:
     pyriemann = None
 
+__all__ = ['ASR', 'clean_windows', 'asr_calibrate', 'asr_process']
+
 
 class ASR():
     """Artifact Subspace Reconstruction.
diff --git a/meegkit/utils/covariances.py b/meegkit/utils/covariances.py
diff --git a/meegkit/utils/denoise.py b/meegkit/utils/denoise.py
diff --git a/meegkit/utils/sig.py b/meegkit/utils/sig.py
diff --git a/meegkit/utils/stats.py b/meegkit/utils/stats.py
