add documentation boilerplate

.gitignore

 __pycache__/
 /build/
 /dist/
+/doc/build/
 *~

MANIFEST.in

 include *.rst
 include test_*.py
+include doc/Makefile
+include doc/source/conf.py
+include doc/source/*.rst
+include doc/source/kwantdoctheme/static/kwantdoctheme.css
+include doc/source/kwantdoctheme/theme.conf

doc/Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = kwant-spectrum
+SOURCEDIR     = source
+BUILDDIR      = build
+
+export PYTHONPATH := $(abspath ..):$(PYTHONPATH)
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doc/source/conf.py

+# -*- 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 --------------------------------------------------------------
+
+# The path is set in the Makefile, so that it also affects the Jupyter kernel
+# executed through the jupyter-sphinx extension.
+
+# -- Project information -----------------------------------------------------
+
+project = 'kwant-spectrum'
+copyright = '2018-2019, T. Kloss, C. W. Groth, X. Waintal, et al.'
+author = 'T. Kloss, C. W. Groth, X. Waintal, et al.'
+
+# The short X.Y version
+version = ''
+# The full version, including alpha/beta/rc tags
+release = '0.0'
+
+
+# -- 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.napoleon',
+    'sphinx.ext.mathjax',
+    'jupyter_sphinx.execute',
+]
+
+# 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 = None
+
+# 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 = 'sphinx'
+
+
+# -- 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 = 'kwantdoctheme'
+html_theme_path = ['.']
+
+# 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 = {'collapsiblesidebar': True}
+
+# 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 = []
+
+# 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 = 'kwant-spectrumdoc'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # 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, 'kwant-spectrum.tex', 'kwant-spectrum Documentation',
+     'T. Kloss, C. W. Groth, X. Waintal, et al.', '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, 'kwant-spectrum', 'kwant-spectrum 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, 'kwant-spectrum', 'kwant-spectrum Documentation',
+     author, 'kwant-spectrum', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# -- Extension configuration -------------------------------------------------

doc/source/index.rst

+Kwant-Spectrum |release| documentation
+======================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

doc/source/kwantdoctheme/static/kwantdoctheme.css

+/* This theme is based on pydoctheme by Georg Brandl. */
+
+@import url("default.css");
+
+body {
+    background-color: white;
+    margin-left: 1em;
+    margin-right: 1em;
+}
+
+/* Disable typewriter font in headings. */
+h1 tt, h2 tt, h3 tt, h4 tt, h5 tt, h6 tt {
+    font-family: "Bitstream Vera Sans", Verdana, sans-serif;
+    font-size: 100%;
+}
+
+div.body p, div.body dd, div.body li {
+    -webkit-hyphens: auto;
+    -moz-hyphens: auto;
+    -ms-hyphens: auto;
+    -o-hyphens: auto;
+    hyphens: auto;
+}
+
+div.related {
+    margin-bottom: 1.2em;
+    padding: 0.5em 0;
+    border-top: 1px solid #ccc;
+    margin-top: 0.5em;
+}
+
+dt:target, .highlighted {
+    background-color: #fbf1aa;
+}
+
+div.related:first-child {
+    border-top: 0;
+    border-bottom: 1px solid #ccc;
+}
+
+div.sphinxsidebar {
+    background-color: #eeeeee;
+    border-radius: 5px;
+    line-height: 130%;
+    font-size: smaller;
+    overflow: hidden;
+}
+
+div.sphinxsidebar h3, div.sphinxsidebar h4 {
+    margin-top: 1.5em;
+}
+
+div.sphinxsidebarwrapper > h3:first-child {
+    margin-top: 0.2em;
+}
+
+div.sphinxsidebarwrapper > ul > li > ul > li {
+    margin-bottom: 0.4em;
+}
+
+div.sphinxsidebar input {
+    font-family: 'Bitstream Vera Serif',  Georgia, serif
+    border: 1px solid #999999;
+    font-size: smaller;
+    border-radius: 3px;
+}
+
+div.sphinxsidebar input[type=text] {
+    max-width: 220px;
+}
+
+div.body {
+    padding: 0 0 0 1.2em;
+}
+
+div.body p {
+    line-height: 140%;
+}
+
+div.body h1, div.body h2, div.body h3, div.body h4, div.body h5, div.body h6 {
+    margin: 0;
+    border: 0;
+    padding: 0.3em 0;
+}
+
+div.body hr {
+    border: 0;
+    background-color: #ccc;
+    height: 1px;
+}
+
+div.body pre {
+    border-radius: 3px;
+    border: 1px solid #ac9;
+}
+
+div.body div.admonition, div.body div.impl-detail {
+    border-radius: 3px;
+}
+
+div.body div.impl-detail > p {
+    margin: 0;
+}
+
+div.body div.seealso {
+    border: 1px solid #dddd66;
+}
+
+tt, pre {
+    font-family: monospace, sans-serif;
+    font-size: 96.5%;
+    -webkit-hyphens: none;
+    -moz-hyphens: none;
+    -ms-hyphens: none;
+    -o-hyphens: none;
+    hyphens: none;
+}
+
+div.body tt {
+    border-radius: 3px;
+}
+
+div.body tt.descname {
+    font-size: 120%;
+}
+
+div.body tt.xref, div.body a tt {
+    font-weight: normal;
+}
+
+p.deprecated {
+    border-radius: 3px;
+}
+
+table.docutils {
+    border: 1px solid #ddd;
+    min-width: 20%;
+    border-radius: 3px;
+    margin-top: 10px;
+    margin-bottom: 10px;
+}
+
+table.docutils td, table.docutils th {
+    border: 1px solid #ddd !important;
+    border-radius: 3px;
+}
+
+table p, table li {
+    text-align: left !important;
+}
+
+table.docutils th {
+    background-color: #eee;
+    padding: 0.3em 0.5em;
+}
+
+table.docutils td {
+    background-color: white;
+    padding: 0.3em 0.5em;
+}
+
+table.footnote, table.footnote td {
+    border: 0 !important;
+}
+
+div.footer {
+    line-height: 150%;
+    margin-top: -2em;
+    text-align: right;
+    width: auto;
+    margin-right: 10px;
+}
+
+/* have arguments of functions or classes also a monospace font */
+table.longtable.docutils > tbody > tr > td:first-child,
+dl.function > dt,
+dl.class > dt,
+dl.method > dt
+{
+    font-family: "Bitstream Vera Sans Mono", monospace, serif;
+    font-size: 96.5%;
+}
+
+/* rescale font for <tt> so that it is again 96.5% with respect to body */
+table.longtable.docutils > tbody > tr > td:first-child tt,
+dl.function > dt tt,
+dl.class > dt tt,
+dl.method > dt tt
+{
+    font-family: "Bitstream Vera Sans Mono", monospace, serif;
+    font-size: 100%;
+}
+
+td.field-body strong
+{
+    font-family: "Bitstream Vera Sans Mono", monospace, serif;
+    font-size: 96.5%;
+}

doc/source/kwantdoctheme/theme.conf

+# This theme is based on pydoctheme by Georg Brandl
+
+[theme]
+inherit = default
+stylesheet = kwantdoctheme.css
+pygments_style = sphinx
+
+[options]
+bodyfont = "Bitstream Vera Serif", Georgia, serif
+headfont = "Bitstream Vera Sans", Verdana, sans-serif
+footerbgcolor = white
+footertextcolor = #555555
+relbarbgcolor = white
+relbartextcolor = #666666
+relbarlinkcolor = #444444
+sidebarbgcolor = white
+sidebartextcolor = #444444
+sidebarlinkcolor = #444444
+sidebarwidth = 300
+bgcolor = white
+textcolor = black
+linkcolor = #045e94
+visitedlinkcolor = #045e94
+headtextcolor = black
+headbgcolor = white
+headlinkcolor = #aaaaaa