Fix/docstring warnings (#478)

* fix headings for release notes, elephant versions > 0.10.0

* fixed warnings on build html for asset docstring

* fixed warnings on build html for causality.granger docstring

* fixed warnings on build html for cell_assembly_detection docstring

* more fixes

* fixed indentation errors

* fixed import errors

* Apply suggestions from code review

Co-authored-by: Michael Denker <[email protected]>

* removed 'binsize', deprecated, use 'bin_size'

* removed deprecation for __init__

* added template for gpfa

* overline for heading in install.rst

* remove template for gpfa

* increase timeout for urlopen

* remove unused variable

* change context for urlopen

* remove timeout

* fix typo

* add template for GPFA class

* fix math expression

---------

Co-authored-by: Michael Denker <[email protected]>

doc/_templates/autosummary/gpfa_class.rst

@@ -0,0 +1,7 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :special-members: __contains__,__getitem__,__iter__,__len__,__add__,__sub__,__mul__,__div__,__neg__
+   :members:

doc/_templates/autosummary/spike_train_generation_class.rst

@@ -0,0 +1,30 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+
+   {% block methods %}
+
+   {% if methods %}
+   .. rubric:: {{ _('Methods') }}
+
+   .. autosummary::
+   {% for item in methods %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Attributes') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+   {%- if item not in ["process_operational_time","isi_generator"] %}
+      ~{{ name }}.{{ item }}
+   {%- endif %}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}

doc/conf.py

@@ -3,7 +3,8 @@
 # Elephant documentation build configuration file, created by
 # sphinx-quickstart on Wed Feb  5 17:11:26 2014.
 #
-# This file is execfile()d with the current directory set to its containing dir.
+# This file is execfile()d with the current directory set to its containing
+# dir.
 #
 # Note that not all possible configuration values are present in this
 # autogenerated file.
@@ -21,11 +22,11 @@
 sys.path.insert(0, '..')
 
 # -- General configuration -----------------------------------------------
-
 # If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
+# needs_sphinx = '1.0'
 
-# Add any Sphinx extension module names here, as strings. They can be extensions
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = [
     'sphinx.ext.autodoc',
@@ -43,13 +44,13 @@
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ['_templates/autosummary']
 
 # The suffix of source filenames.
 source_suffix = '.rst'
 
 # The encoding of source files.
-#source_encoding = 'utf-8-sig'
+# source_encoding = 'utf-8-sig'
 
 # The master toctree document.
 master_doc = 'index'
@@ -75,13 +76,13 @@
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
-#language = None
+# language = None
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
-#today = ''
+# today = ''
 # Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
+# today_fmt = '%B %d, %Y'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -90,25 +91,26 @@
     '**.ipynb_checkpoints',
 ]
 
-# The reST default role (used for this markup: `text`) to use for all documents.
-#default_role = None
+# The reST default role (used for this markup: `text`) to use for all
+# documents.
+# default_role = None
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
+# add_function_parentheses = True
 
 # If true, the current module name will be prepended to all description
 # unit titles (such as .. function::).
-#add_module_names = True
+# add_module_names = True
 
 # If true, sectionauthor and moduleauthor directives will be shown in the
 # output. They are ignored by default.
-#show_authors = False
+# show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
 
 # A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
+# modindex_common_prefix = []
 
 # Only execute Jupyter notebooks that have no evaluated cells
 nbsphinx_execute = 'auto'
@@ -129,6 +131,10 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 html_theme = 'alabaster'
+
+# 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
+# documentation.
 html_theme_options = {
     'font_family': 'Arial',
     'page_width': '1200px',  # default is 940
@@ -137,11 +143,11 @@
 }
 
 # Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
+# html_theme_path = []
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-#html_title = None
+# html_title = None
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
 html_short_title = None
@@ -162,30 +168,30 @@
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
+# html_last_updated_fmt = '%b %d, %Y'
 
 # If true, SmartyPants will be used to convert quotes and dashes to
 # typographically correct entities.
 html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
+# html_sidebars = {}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
-#html_additional_pages = {}
+# html_additional_pages = {}
 
 # If false, no module index is generated.
-#html_domain_indices = True
+# html_domain_indices = True
 
 # If false, no index is generated.
 html_use_index = True
 
 # If true, the index is split into individual pages for each letter.
-#html_split_index = False
+# html_split_index = False
 
 # If true, links to the reST sources are added to the pages.
-#html_show_sourcelink = True
+# html_show_sourcelink = True
 
 # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
 html_show_sphinx = False
@@ -196,10 +202,10 @@
 # If true, an OpenSearch description file will be output, and all pages will
 # contain a <link> tag referring to it.  The value of this option must be the
 # base URL from which the finished HTML is served.
-#html_use_opensearch = ''
+# html_use_opensearch = ''
 
 # This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
+# html_file_suffix = None
 
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'elephantdoc'
@@ -231,31 +237,32 @@
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title, author, documentclass [howto/manual]).
+# (source start file, target name, title, author, documentclass
+# [howto/manual]).
 latex_documents = [
     ('index', 'elephant.tex', u'Elephant Documentation',
      authors, 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
-#latex_logo = None
+# latex_logo = None
 
 # For "manual" documents, if this is true, then toplevel headings are parts,
 # not chapters.
-#latex_use_parts = False
+# latex_use_parts = False
 
 # If true, show page references after internal links.
-#latex_show_pagerefs = False
+# latex_show_pagerefs = False
 
 # If true, show URL addresses after external links.
-#latex_show_urls = False
+# latex_show_urls = False
 
 # Documents to append as an appendix to all manuals.
-#latex_appendices = []
+# latex_appendices = []
 
 # If false, no module index is generated.
-#latex_domain_indices = True
+# latex_domain_indices = True
 
 
 # -- Options for manual page output --------------------------------------
@@ -268,7 +275,7 @@
 ]
 
 # If true, show URL addresses after external links.
-#man_show_urls = False
+# man_show_urls = False
 
 
 # -- Options for Texinfo output ------------------------------------------
@@ -287,13 +294,13 @@
 ]
 
 # Documents to append as an appendix to all manuals.
-#texinfo_appendices = []
+# texinfo_appendices = []
 
 # If false, no module index is generated.
-#texinfo_domain_indices = True
+# texinfo_domain_indices = True
 
 # How to display URL addresses: 'footnote', 'no', or 'inline'.
-#texinfo_show_urls = 'footnote'
+# texinfo_show_urls = 'footnote'
 
 
 # -- Options for Epub output ---------------------------------------------
@@ -306,37 +313,37 @@
 
 # The language of the text. It defaults to the language option
 # or en if the language is not set.
-#epub_language = ''
+# epub_language = ''
 
 # The scheme of the identifier. Typical schemes are ISBN or URL.
-#epub_scheme = ''
+# epub_scheme = ''
 
 # The unique identifier of the text. This can be a ISBN number
 # or the project homepage.
-#epub_identifier = ''
+# epub_identifier = ''
 
 # A unique identification for the text.
-#epub_uid = ''
+# epub_uid = ''
 
 # A tuple containing the cover image and cover page html template filenames.
-#epub_cover = ()
+# epub_cover = ()
 
 # HTML files that should be inserted before the pages created by sphinx.
 # The format is a list of tuples containing the path and title.
-#epub_pre_files = []
+# epub_pre_files = []
 
 # HTML files shat should be inserted after the pages created by sphinx.
 # The format is a list of tuples containing the path and title.
-#epub_post_files = []
+# epub_post_files = []
 
 # A list of files that should not be packed into the epub file.
-#epub_exclude_files = []
+# epub_exclude_files = []
 
 # The depth of the table of contents in toc.ncx.
-#epub_tocdepth = 3
+# epub_tocdepth = 3
 
 # Allow duplicate toc entries.
-#epub_tocdup = True
+# epub_tocdup = True
 
 
 # configuration for intersphinx: refer to Viziphant
@@ -345,6 +352,7 @@
     'numpy': ('https://numpy.org/doc/stable', None)
 }
 
+
 # The name of math_renderer extension for HTML output.
 html_math_renderer = 'mathjax'
 

doc/install.rst

@@ -209,9 +209,10 @@ You can have one, both, or none installed in your system.
             unresponsive until the compute program terminates.
 
 .. _no-compile-spade:
-***********
+
+****************************
 Resolving compilation issues
-***********
+****************************
 
 Some modules in Elephant make use of C extensions to speed up computation.
 However, those extensions need to be compiled before use. In some cases, this

elephant/asset/asset.py

@@ -1975,6 +1975,7 @@ def intersection_matrix(self, normalization=None):
                 * 'intersection': `len(intersection(s_i, s_j))`
                 * 'mean': `sqrt(len(s_1) * len(s_2))`
                 * 'union': `len(union(s_i, s_j))`
+
             Default: None
 
         Returns
@@ -2029,9 +2030,9 @@ def probability_matrix_montecarlo(self, n_surrogates, imat=None,
             If None, the output of :func:`ASSET.intersection_matrix` is used.
             Default: None
         surrogate_method : {'dither_spike_train', 'dither_spikes',
-                            'jitter_spikes',
-                            'randomise_spikes', 'shuffle_isis',
-                            'joint_isi_dithering'}, optional
+            'jitter_spikes', 'randomise_spikes', 'shuffle_isis',
+            'joint_isi_dithering'}, optional
+
             The method to generate surrogate spike trains. Refer to the
             :func:`spike_train_surrogates.surrogates` documentation for more
             information about each surrogate method. Note that some of these
@@ -2305,9 +2306,10 @@ def joint_probability_matrix(self, pmat, filter_shape, n_largest,
         precision : {'float', 'double'}, optional
             Single or double floating-point precision for the resulting `jmat`
             matrix.
-              * `'float'`: 32 bits; the tolerance error is ``≲1e-3``.
 
+              * `'float'`: 32 bits; the tolerance error is ``≲1e-3``.
               * `'double'`: 64 bits; the tolerance error is ``<1e-5``.
+
             Double floating-point precision is typically x4 times slower than
             the single floating-point equivalent.
             Default: 'float'

elephant/causality/granger.py

@@ -370,8 +370,10 @@ def pairwise_granger(signals, max_order, information_criterion='aic'):
         Maximal order of autoregressive model.
     information_criterion : {'aic', 'bic'}, optional
         A function to compute the information criterion:
-            `bic` for Bayesian information_criterion,
-            `aic` for Akaike information criterion,
+
+        * `bic` for Bayesian information_criterion,
+        * `aic` for Akaike information criterion,
+
         Default: 'aic'
 
     Returns
@@ -538,8 +540,10 @@ def conditional_granger(signals, max_order, information_criterion='aic'):
         Maximal order of autoregressive model.
     information_criterion : {'aic', 'bic'}, optional
         A function to compute the information criterion:
-            `bic` for Bayesian information_criterion,
-            `aic` for Akaike information criterion,
+
+        * `bic` for Bayesian information_criterion,
+        * `aic` for Akaike information criterion,
+
         Default: 'aic'
 
     Returns