Sphinx doesn't generate sidebar table of contents for headers

Question

I'm struggling with sidebar table of contents in Sphinx's generated documentation.

I just want to have kind of automatically generated index tree by the left side of my documentation. Instead, I see only blank headers: (I hope you don't mind target docs are in Polish)

My index.rst file:

.. SIMail documentation master file, created by
   sphinx-quickstart on Mon Nov 26 12:38:31 2018.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Welcome to SIMail docs!
=======================

.. toctree::
   :numbered:

Providers
==============

.. automodule:: Providers
   :members:

Connection managers
===================

.. automodule:: ConnectionManagers
   :members:


Indices and tables
******************

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`

My conf.py file:

# -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
#
# This file does only contain a selection of the most common options. For a
# full list see the documentation:
# http://www.sphinx-doc.org/en/master/config

# -- Path setup --------------------------------------------------------------

# 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.
#
import os
import sys
sys.path.insert(0, os.path.abspath('../../src'))


# -- Project information -----------------------------------------------------

project = 'SIMail'
copyright = '2018, Kamil Kurzacz'
author = 'Kamil Kurzacz'

# The short X.Y version
version = ''
# The full version, including alpha/beta/rc tags
release = '1'


# -- General configuration ---------------------------------------------------

# If your documentation needs a minimal Sphinx version, state it here.
#
# needs_sphinx = '1.0'

# 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',
    'sphinx.ext.intersphinx',
    'sphinx.ext.todo',
    'sphinx.ext.coverage',
    'sphinx.ext.ifconfig',
    'sphinx.ext.viewcode',
    'sphinx.ext.githubpages',
    'sphinx.ext.autosummary',
]

# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']

# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
# source_suffix = ['.rst', '.md']
source_suffix = '.rst'

# The master toctree document.
master_doc = 'index'

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
#language = 'pl'
language = 'en'

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path.
exclude_patterns = []

# The name of the Pygments (syntax highlighting) style to use.
pygments_style = None


# -- 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 = '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 = {}

# 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']

# Custom sidebar templates, must be a dictionary that maps document names
# to template names.
#
# The default sidebars (for documents that don't match any pattern) are
# defined by theme itself.  Builtin themes are using these templates by
# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
# 'searchbox.html']``.
#
# html_sidebars = {}


# -- Options for HTMLHelp output ---------------------------------------------

# Output file base name for HTML help builder.
htmlhelp_basename = 'SIMaildoc'


# -- Options for LaTeX output ------------------------------------------------

latex_elements = {
    # The paper size ('letterpaper' or 'a4paper').

    'papersize': 'a4paper',

    # The font size ('10pt', '11pt' or '12pt').

    'pointsize': '10pt',

    # Additional stuff for the LaTeX preamble.

    'preamble': '',

    # Latex figure (float) alignment

    'figure_align': 'htbp',
}

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
#  author, documentclass [howto, manual, or own class]).
latex_documents = [
    (master_doc, 'SIMail.tex', 'SIMail Documentation',
     'Kamil Kurzacz', 'manual'),
]


# -- Options for manual page output ------------------------------------------

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
    (master_doc, 'simail', 'SIMail Documentation',
     [author], 1)
]


# -- Options for Texinfo output ----------------------------------------------

# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
#  dir menu entry, description, category)
texinfo_documents = [
    (master_doc, 'SIMail', 'SIMail Documentation',
     author, 'SIMail', 'One line description of project.',
     'Miscellaneous'),
]


# -- Options for Epub output -------------------------------------------------

# Bibliographic Dublin Core info.
epub_title = project

# The unique identifier of the text. This can be a ISBN number
# or the project homepage.
#
# epub_identifier = ''

# A unique identification for the text.
#
# epub_uid = ''

# A list of files that should not be packed into the epub file.
epub_exclude_files = ['search.html']


# -- Extension configuration -------------------------------------------------

# -- Options for intersphinx extension ---------------------------------------

# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {'https://docs.python.org/': None}

# -- Options for todo extension ----------------------------------------------

# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = True

# -- Options for autogenerate
autodoc_default_flags = ['members']
autosummary_generate = True

I was looking for questions like "Sphinx doesn't generate index on sidebar", but I found nothing. It looks like I omitted small detail. Is there a special command in reST to force Sphinx generate index list on a sidebar?

I found partial answer to my question, which is to generate separate files for all module with sphinx-autodoc. But it looks the problem is that Sphinx ignores all headers when it comes to build table of contents from index.rst

In simple words, I wanna have navigation list with links to all headers in my index.rst, the same way as in this tutorial example. The author seems to put almost nothing more than just sections with source files. And he's got automatically generated navigation to all of the headers within index.rst. To show my problem, I attach another picture: Please take a look at example's index.rst. Every header existing in the file has generated link in navigation.

2018-12-17 update

I have followed comments to problem, and upgraded Sphinx manually to v2.0.0+/60e3c2a. Still cannot get what I need. What I did was to:

1. Git clone https://github.com/sphinx-doc/sphinx
2. cd to directory with new sphinx, then python setup.py build and install Do I need to do something else?

This is my output from Sphinx:

>make html
Running Sphinx v2.0.0+/60e3c2a
loading translations [en]... done
c:\users\kamil\appdata\local\programs\python\python37-32\lib\site-packages\sphinx-2.0.0.dev20181217-py3.7.egg\sphinx\events.py:77: RemovedInSphinx30Warning: autodoc_default_flags is now deprecated. Please use autodoc_default_options instead.
  results.append(callback(*args))
loading pickled environment... done
[autosummary] generating autosummary for: index.rst
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 0 source files that are out of date
updating environment: 0 added, 0 changed, 6 removed
looking for now-outdated files... none found
no targets are out of date.
build succeeded.

The HTML pages are in build\html.

Abiogenetic

What happens if you use another theme, such as "classic" or "nature"? – Blakney

Still there is no navigation list to headers. I have attached another picture at the end of my post to show what I mean: imgur.com/a/4V8awHz – Abiogenetic

Python 3.7, Sphinx 1.8.2 and Alabaster 0.7.12 – Abiogenetic

OK. With Sphinx 1.8.2 and Alabaster 0.7.12, I can reproduce the problem (headers are missing in sidebar). With Sphinx 1.7.5, the headers are there. – Blakney

This bug seems to be related: github.com/sphinx-doc/sphinx/issues/5066 – Blakney

Thanks, but problem still exists. See my latest post update – Abiogenetic

Answer 1

You need to add an explicit setting for html_sidebars for the Alabaster theme, per its documentation:

Either way, add an explicit html_sidebars setting so Alabaster’s customized sidebar templates are loaded:

    html_sidebars = {
        '**': [
            'about.html',
            'navigation.html',
            'relations.html',
            'searchbox.html',
            'donate.html',
        ]
    }

Ophthalmologist

Unfortunately, it didn't help. Your suggestion haven't ended with any noticable changes. I followed your links, eventually getting to sidebar configuration: html_sidebars = { '**': ['globaltoc.html', 'sourcelink.html', 'searchbox.html'], 'using/windows': ['windowssidebar.html', 'searchbox.html'], } The sidebar changed their sections, but still table of contents isn't generated: imgur.com/a/7XX6rV9 – Abiogenetic

You need to add some entries to your toctree directive, too. It's currently empty. – Ophthalmologist

I thought I don't have to do it manually, because I'm putting sections below. In fact, I try to follow tutorial and I was trying to make my docs files quite similar to suggested index.rst. Can you tell me how to call the header I put manually below my toctree section? – Abiogenetic

From the docs on toctree: The documents to include are given as document names, which in short means that you leave off the file name extension and use forward slashes (/) as directory separators. – Ophthalmologist

Yes, but I don't have additional documents with rst extension. All I have is index.rst and Python files with annotations. When I try to put section name under toctree directive, like this: .. toctree:: :maxdepth: 2 Providers I'm getting error about reference to non-existing document – Abiogenetic

Then create them, moving the content from index.rst into each as you see fit. – Ophthalmologist

Well, the problem is Sphinx doesn't index the headers in index.rst at all – Abiogenetic

I don't understand the problem you describe. Navigation and toctree are only HTML lists, not headings, and Sphinx will generate index entries for those toctree entries. If you want navigation, then you must have entries in your toctree. For a single HTML page, then use make singlehtml. – Ophthalmologist

Let us continue this discussion in chat. – Abiogenetic

Answer 2

In my case it was only a matter of adding

.. toctree::
   :hidden:

   index

in my index.rst file.

Buhrstone

this doesn't work for me, and I get "WARNING: circular toctree references detected, ignoring: index <- index" – Churr

@joelb I can point you out on what it is still working for me: github.com/xcash/bootstrap-autocomplete/tree/master/docs – Buhrstone

I also get an error when doing this. WARNING: self referenced toctree found. Ignored. – Rigobertorigor

Answer 3

In case anyone is still looking for a solution - no idea if this would have worked in the version of sphinx that was available at the time of the original post:

Sphinx sidebar table of contents: include section headers

Blouin