docs: inital sphinx docs for rtd

.readthedocs.yml

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+version: 2
+formats:
+ - pdf
+python:
+  version: 3.6
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .
+  system_packages: false

docs/README.md

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+PyJibe documentation
+====================
+Building the documentation of PyJibe requires Python 3.
+To install the requirements for building the documentation, run
+
+    pip install -r requirements.txt
+
+To compile the documentation, run
+
+    sphinx-build . _build
+
+Notes
+=====
+To view the sphinx inventory of PyJibe, run
+
+   python -m sphinx.ext.intersphinx 'http://pyjibe.readthedocs.io/en/latest/objects.inv'

docs/conf.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# PyJibe documentation build configuration file, created by
+# sphinx-quickstart on Tue Sep 26 17:55:31 2017.
+#
+# 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.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# 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.
+
+# Get version number from pyjibe._version file
+import os.path as op
+import sys
+# include parent directory
+pdir = op.dirname(op.dirname(op.abspath(__file__)))
+# include extenstions
+sys.path.append(op.abspath('extensions'))
+
+# http://www.sphinx-doc.org/en/stable/ext/autodoc.html#confval-autodoc_member_order
+# Order class attributes and functions in separate blocks
+autodoc_member_order = 'groupwise'
+autoclass_content = 'both'
+
+# include source of matplotlib plots
+plot_include_source = True
+
+# Display link to GitHub repo instead of doc on rtfd
+rst_prolog = """
+:github_url: https://github.com/AFM-analysis/PyJibe
+"""
+
+# -- 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.autosummary',
+              'sphinx.ext.intersphinx',
+              'sphinx.ext.mathjax',
+              'sphinx.ext.viewcode',
+              'sphinx.ext.napoleon',
+              'sphinxcontrib.bibtex',
+              'matplotlib.sphinxext.plot_directive',
+              'fancy_include',
+              'github_changelog',
+              'rtd_pdf',
+              ]
+
+# 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'
+
+# General information about the project.
+project = 'PyJibe'
+github_project = 'AFM-analysis/PyJibe'
+copyright = '2019, Paul Müller'
+author = 'Paul Müller'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+# 
+# The full version, including alpha/beta/rc tags.
+# This gets 'version'
+exec(open(op.join(pdir, "pyjibe/_version.py")).read())
+release = version #@UndefinedVariable
+# 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 patterns also effect to html_static_path and html_extra_path
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- 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 = 'sphinx_rtd_theme'
+
+# 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 = ['data']
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'pyjibedoc'
+
+
+# -- 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, 'pyjibe.tex', 'PyJibe Documentation',
+     author, '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, 'pyjibe', 'PyJibe 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, 'pyjibe', 'PyJibe Documentation',
+     author, 'pyjibe', 'post-measurement analysis of RT-DC data sets',
+     'Scientific'),
+]
+
+
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {"python": ('https://docs.python.org/', None),
+                       "numpy": ('http://docs.scipy.org/doc/numpy', None),
+                       "scipy": ('https://docs.scipy.org/doc/scipy/reference/', None),
+                       "nanite": ('http://nanite.readthedocs.io/en/stable', None),
+                       }

docs/extensions/fancy_include.py

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+"""Include single scripts with doc string, code, and image
+
+Use case
+--------
+There is an "examples" directory in the root of a repository,
+e.g. 'include_doc_code_img_path = "../examples"' in conf.py
+(default). An example is a file ("an_example.py") that consists
+of a doc string at the beginning of the file, the example code,
+and, optionally, an image file (png, jpg) ("an_example.png").
+
+
+Configuration
+-------------
+In conf.py, set the parameter
+
+   fancy_include_path = "../examples"
+
+to wherever the included files reside.
+
+
+Usage
+-----
+The directive
+
+   .. fancy_include:: an_example.py
+
+will display the doc string formatted with the first line as a
+heading, a code block with line numbers, and the image file.
+"""
+import io
+import os.path as op
+
+from docutils.statemachine import ViewList
+from docutils.parsers.rst import Directive
+from sphinx.util.nodes import nested_parse_with_titles
+from docutils import nodes
+
+
+class IncludeDirective(Directive):
+    required_arguments = 1
+    optional_arguments = 0
+
+    def run(self):
+        path = self.state.document.settings.env.config.fancy_include_path
+        full_path = op.join(path, self.arguments[0])
+
+        with io.open(full_path, "r") as myfile:
+            text = myfile.read()
+
+        # add reference
+        name = op.basename(full_path)[:-3]
+        rst = [".. _example_{}:".format(name),
+               "",
+               ]
+
+        # add docstring
+        source = text.split('"""')
+        doc = source[1].split("\n")
+        doc.insert(1, "~" * len(doc[0]))  # make title heading
+
+        code = source[2].split("\n")
+
+        for line in doc:
+            rst.append(line)
+
+        # image
+        for ext in [".png", ".jpg"]:
+            image_path = full_path[:-3] + ext
+            if op.exists(image_path):
+                break
+        else:
+            image_path = ""
+        if image_path:
+            rst.append(".. figure:: {}".format(image_path))
+            rst.append("")
+
+        # download file
+        rst.append(":download:`{}<{}>`".format(
+            op.basename(full_path), full_path))
+
+        # code
+        rst.append("")
+        rst.append(".. code-block:: python")
+        rst.append("   :linenos:")
+        rst.append("")
+        for line in code:
+            rst.append("   {}".format(line))
+        rst.append("")
+
+        vl = ViewList(rst, "fakefile.rst")
+        # Create a node.
+        node = nodes.section()
+        node.document = self.state.document
+        # Parse the rst.
+        nested_parse_with_titles(self.state, vl, node)
+        return node.children
+
+
+def setup(app):
+    app.add_config_value('fancy_include_path', "../examples", 'html')
+
+    app.add_directive('fancy_include', IncludeDirective)
+
+    return {'version': '0.1'}   # identifies the version of our extension