Merge pull request #50 from pyiron/docs

Add minimal readthedoc support for API docs

.readthedocs.yml

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+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: []
+
+# Install pyiron from conda 
+conda:
+  environment: docs/environment.yml
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+    - method: pip
+      path: .

docs/conf.py

@@ -0,0 +1,305 @@
+# -*- coding: utf-8 -*-
+#
+# pyCMW documentation build configuration file, created by
+# sphinx-quickstart on Mon Sep 01 21:59:30 2014.
+#
+# 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.
+
+import sys
+import os
+import shutil
+import subprocess
+from sphinx.ext.apidoc import main
+
+# 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.
+
+
+# sys.path.insert(1, 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 = ['nbsphinx', 'sphinx.ext.mathjax', 'sphinx.ext.autodoc', 'sphinx.ext.viewcode',
+              'sphinx.ext.autosummary', 'sphinx.ext.napoleon']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+# source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = 'pyiron_contrib'
+copyright = u'2021, Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department ' \
+            u'All rights reserved'
+
+# 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_full = subprocess.check_output(
+    "python -c 'import versioneer; print(versioneer.get_version())'",
+    cwd=os.path.join(os.path.curdir, '..'),
+    universal_newlines=True,
+    shell=True
+)
+version_full = version_full.split('\n')[0]
+version = '.'.join(version_full.split('.')[0:2])
+# The full version, including alpha/beta/rc tags.
+release = version_full
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+# language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+# today = ''
+# Else, today_fmt is used as the format for a strftime call.
+# today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+
+exclude_patterns = ['_build', '**.ipynb_checkpoints', '**/tests']
+
+# 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
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+# add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+# 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 = []
+
+# If true, keep warnings as "system message" paragraphs in the built documents.
+# keep_warnings = False
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+
+# try:
+#    import sphinx_bootstrap_theme
+#    html_theme = 'bootstrap'
+#    html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()
+#    html_theme_options = {'bootswatch_theme': "spacelab"}
+# except ImportError:
+#    raise ImportError("You need to install bootstrap: pip install sphinx_bootstrap_theme")
+#    html_theme = 'default'
+
+try:
+   import sphinx_rtd_theme
+   html_theme = 'sphinx_rtd_theme'
+except ImportError:
+   html_theme = 'default'
+
+
+# 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 themes here, relative to this directory.
+# html_theme_path = []
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+# html_title = None
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+# html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+html_logo = "_static/pyiron-logo.png"
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+html_favicon = "_static/pyiron_logo.ico"
+
+# 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']
+
+# Add any extra paths that contain custom files (such as robots.txt or
+# .htaccess) here, relative to this directory. These files are copied
+# directly to the root of the documentation.
+# html_extra_path = []
+
+# 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'
+
+# 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 = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+# html_additional_pages = {}
+
+# If false, no module index is generated.
+# 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
+
+# If true, links to the reST sources are added to the pages.
+# html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+# html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+# html_show_copyright = True
+
+# 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 = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+# html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'pyironDoc'
+
+
+# -- 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': '',
+}
+
+# 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 = [
+  ('index', 'pyiron.tex', u'pyiron Documentation',
+   u'Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    ('index',
+     'pyiron',
+     u'pyiron Documentation',
+     [u'Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department'], 1)
+]
+
+# If true, show URL addresses after external links.
+#man_show_urls = False
+
+
+# -- 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 = [
+  ('index',
+   'pyiron_contrib',
+   'pyiron Documentation',
+   'Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department',
+   'pyiron_contrib',
+   'One line description of project.',
+   'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+# texinfo_appendices = []
+
+# If false, no module index is generated.
+# texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+# texinfo_show_urls = 'footnote'
+
+# If true, do not generate a @detailmenu in the "Top" node's menu.
+# texinfo_no_detailmenu = False
+
+main(['-e', '-o', 'apidoc', '../pyiron_contrib', '--force'])
+
+curdir = os.path.dirname(os.path.abspath(__file__))
+
+if 'readthedocs.org' in curdir:  # write config for readthedocs.org
+    with open(os.path.join(os.path.expanduser('~/.pyiron')), 'w') as f:
+        f.writelines(['[DEFAULT]',
+                      'TOP_LEVEL_DIRS = ' + os.path.join(curdir, '..'),
+                      'RESOURCE_PATHS = ' + os.path.join(curdir, '..') + '/tests/static'])

docs/environment.yml

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+channels:
+- conda-forge
+dependencies:
+- ipywidgets
+- cython
+- pyiron_atomistics
+- pyiron_contrib
+- nbsphinx

docs/index.rst

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+.. pyiron documentation master file
+
+.. _index:
+
+
+==============
+pyiron_contrib
+==============
+
+.. image:: https://github.com/pyiron/pyiron/workflows/Python%20package/badge.svg
+    :target: https://github.com/pyiron//pyiron/actions
+    :alt: Build Status
+
+.. image:: https://anaconda.org/conda-forge/pyiron/badges/downloads.svg
+
+.. image:: https://anaconda.org/conda-forge/pyiron/badges/latest_release_date.svg
+
+
+pyiron_contrib - Additional in-development modules for `pyiron <https://pyiron.readthedocs.io/en/latest/>`_.
+
+pyiron_contrib  is developed in the `Computational Materials Design department <https://www.mpie.de/CM>`_ of
+`Joerg Neugebauer <https://www.mpie.de/person/43010/2763386>`_ at the `Max Planck Institut für Eisenforschung (Max
+Planck Institute for iron research) <https://www.mpie.de/2281/en>`_.
+
+.. note::
+
+    **pyiron_contrib**: This is the documentation page for experimental modules of pyiron.  If you're new to
+    pyiron and want to get an overview head over to `pyiron <https://pyiron.readthedocs.io/en/latest/>`_.  If you're
+    looking for the API docs of the atomistic simulation packages check `pyiron_atomistics
+    <https://pyiron_atomistics.readthedocs.io/en/latest/>`_.
+
+.. toctree::
+    :hidden:
+
+    source/indices.rst

docs/source/indices.rst

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+.. _indices:
+
+
+API Documentation
+=================
+
+* :ref:`modindex`
+
+
+.. toctree::
+   :maxdepth:2