Merge branch 'sphinx' into testing

Generated documentation.

.gitignore

@@ -26,3 +26,6 @@ gensim_gb_txt.mm
 corpus.mm
 demonstrator/dariah_topics/
 demonstrator/static/*.pngcover
+.idea
+Topics.iml
+_build

CONTRIBUTING.md

@@ -1,6 +1,19 @@
+# Information for Contributors
+
 ## Development Environment
 
-TODO
+* [Code and Issues are at Github](http://github.com/DARIAH-DE/Topics)
+* [Integration Build](http://dev.digital-humanities.de/ci/jobs/DARIAH-Topics)
+
+### Start hacking
+
+```bash
+git clone -b testing git@github.com:DARIAH-DE/Topics
+cd Topics
+mkvirtualenv Topics      # if you use virtualenvwrapper
+workon Topics            # if you use virtualenvwrapper
+pip install -r requirement-dev.txt
+```
 
 ## Releasing / Pushing to Master
 
@@ -16,3 +29,34 @@ Pushing to master is protected, you can only push heads that have an "green" sta
 6. when the build has successfully finished, push master.
 
 If something goes wrong, `git reset --hard master origin/master` and try again.
+
+## Documentation
+
+The documentation is built using [Sphinx](http://www.sphinx-doc.org/). 
+The following files influence the docs:
+
+* ``index.rst`` contains the landing page with the table of contents. Here, all files should be linked.
+* ``*.ipynb`` for tutorials etc. can be linked from the index file
+* ``README.md`` and ``CONTRIBUTING.md`` will also be included
+* Docstrings in the modules will be included
+* ``docs/**/*`` may contain additional files
+* ``conf.py`` contains sphinx configuration
+* ``setup.py`` contains version numbers etc.
+
+### Documentation formats
+
+Standalone documentation files can be written in one of the following formats:
+
+* ReSTructured Text (`*.rst`), [see Sphinx docs](http://www.sphinx-doc.org/en/stable/rest.html)
+* Jupyter Notebook (`*.ipynb`), by way of [nbsphinx](https://nbsphinx.readthedocs.io/)
+* Markdown
+
+Docstrings should follow [Google conventions](http://google.github.io/styleguide/pyguide.html?showone=Comments#Comments), this is supported by [Napoleon](http://www.sphinx-doc.org/en/stable/ext/napoleon.html).
+
+### Build the documentation
+
+Run `python setup.py build_sphinx -a`, which will create the documentation tree in `build/sphinx/html`.
+
+### After adding another module
+
+Run `sphinx-apidoc -M -e -o docs/gen dariah_topics` to add a documentation stub to `docs/gen`. 

Introducing_MALLET.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "<div style=\"text-align: center\"><h1>Topics – Easy Topic Modeling in Python</h1></div>"
+    "# Topics – Easy Topic Modeling in Python"
    ]
   },
   {

Introducing_gensim.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "<div style=\"text-align: center\"><h1>Topics – Easy Topic Modeling in Python</h1></div>"
+    "# Topics – Easy Topic Modeling in Python"
    ]
   },
   {

Introducing_lda.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "<div style=\"text-align: center\"><h1>Topics – Easy Topic Modeling in Python</h1></div>"
+    "# Topics – Easy Topic Modeling in Python"
    ]
   },
   {

conf.py

@@ -0,0 +1,204 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# DARIAH Topics documentation build configuration file, created by
+# sphinx-quickstart on Wed Oct  4 16:58:39 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.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- 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.napoleon',
+    'nbsphinx',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.todo',
+    'sphinx.ext.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.githubpages']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['docs/_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+source_suffix = ['.rst', '.md']
+# source_suffix = '.rst'
+
+source_parsers = {
+    '.md': 'recommonmark.parser.CommonMarkParser',
+}
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = 'DARIAH Topics'
+copyright = '2017, DARIAH-DE Group Würzburg'
+author = 'DARIAH-DE Group Würzburg'
+
+# 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.
+version = '0.3'
+# The full version, including alpha/beta/rc tags.
+release = '0.3.0dev0'
+
+# 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', '.*', '.tox', '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 = True
+
+autosummary_generate = True
+
+autodoc_default_flags = [
+    'members',
+    'inherited-members',
+    'show-inheritance'
+]
+
+default_role = 'any'
+
+# -- 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 = {
+    'github_user': 'DARIAH-DE',
+    'github_repo': 'Topics',
+    'show_related': True,
+    'fixed_sidebar': 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 = ['docs/_static']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# This is required for the alabaster theme
+# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
+html_sidebars = {
+    '**': [
+        'about.html',
+        'navigation.html',
+        'relations.html',  # needs 'show_related': True theme option to display
+        'searchbox.html',
+        'donate.html',
+    ]
+}
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'DARIAHTopicsdoc'
+
+
+# -- 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, 'DARIAHTopics.tex', 'DARIAH Topics Documentation',
+     'DARIAH-DE Group Würzburg', '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, 'dariahtopics', 'DARIAH Topics 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, 'DARIAHTopics', 'DARIAH Topics Documentation',
+     author, 'DARIAHTopics', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# Intersphinx configuration: URLs for other libraries to link
+intersphinx_mapping = { 'http://docs.python.org/3': None,
+                        'http://pandas.pydata.org/pandas-docs/stable/': None,
+                        'https://matplotlib.org/': None,
+                        'https://radimrehurek.com/gensim/': None }
+

dariah_topics/__init__.py

@@ -1,8 +1,8 @@
 """
-The `dariah_topics` package currently offers four modules:
+The :mod:`dariah_topics` package currently offers four modules:
 
-* `dariah_topics.preprocessing` contains preprocessing code
-* `dariah_topics.visualization` offers visualization stuff that depends on PyLDAvis
-* `dariah_topics.mallet` provides a wrapper that calls mallet
-* `dariah_topics.evaluation` provides coherence measures
+* :mod:`dariah_topics.preprocessing` contains preprocessing code
+* :mod:`dariah_topics.visualization` offers visualization stuff that depends on PyLDAvis
+* :mod:`dariah_topics.mallet` provides a wrapper that calls mallet
+* :mod:`dariah_topics.evaluation` provides coherence measures
 """