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Build Sphinx API docs under TravisCI/Tox using apidoc
We trigger sphinx-apidoc from sphinx's conf.py In theory this would allow readthedocs to be used and generate the API documentation *.rst files on demand. Uses autodoc_default_values added in Sphinx 1.8.0
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# Minimal makefile for Sphinx documentation | ||
# | ||
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# You can set these variables from the command line. | ||
SPHINXOPTS = | ||
SPHINXBUILD = sphinx-build | ||
SPHINXPROJ = Bio | ||
SOURCEDIR = . | ||
BUILDDIR = _build | ||
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# Put it first so that "make" without argument is like "make help". | ||
help: | ||
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) | ||
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.PHONY: help Makefile | ||
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# 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) |
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#!/usr/bin/env python3 | ||
# -*- coding: utf-8 -*- | ||
"""Biopython Sphinx documentation build configuration file. | ||
After generating ``*.rst`` files from the source code, this | ||
file controls running ``sphinx-build`` to turn these into | ||
human readable documentation. | ||
""" | ||
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import os | ||
import shutil | ||
# import sys | ||
import tempfile | ||
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from Bio import __version__ | ||
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# -- General configuration ------------------------------------------------ | ||
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# If your documentation needs a minimal Sphinx version, state it here. | ||
# | ||
# needs_sphinx = '1.0' | ||
needs_sphinx = '1.8' | ||
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# 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.todo', | ||
'sphinx.ext.viewcode', | ||
'sphinx.ext.autosummary', | ||
'numpydoc'] | ||
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# Add any paths that contain templates here, relative to this directory. | ||
templates_path = ['_templates'] | ||
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# The suffix(es) of source filenames. | ||
# You can specify multiple suffix as a list of string: | ||
# | ||
# source_suffix = ['.rst', '.md'] | ||
source_suffix = '.rst' | ||
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# The master toctree document. | ||
master_doc = 'index' | ||
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# General information about the project. | ||
project = 'Biopython' | ||
copyright = '1999-2017, The Biopython Contributors' | ||
author = 'The Biopython Contributors' | ||
document = 'Biopython API Documentation' | ||
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# 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 = __version__ # TODO: Shorten this | ||
# The full version, including alpha/beta/rc tags. | ||
release = __version__ | ||
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# 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 = 'en' | ||
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# 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'] | ||
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# The name of the Pygments (syntax highlighting) style to use. | ||
pygments_style = 'sphinx' | ||
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# If true, `todo` and `todoList` produce output, else they produce nothing. | ||
todo_include_todos = True | ||
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# -- Options for autodoc -------------------------------------------------- | ||
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# This requires Sphinx 1.8.0b1 or later: | ||
autodoc_default_values = { | ||
'members': None, | ||
'undoc-members': None, | ||
'special-members': None, | ||
'show-inheritance': None, | ||
'member-order': 'bysource', | ||
'exclude-members': '__dict__,__weakref__,__module__', | ||
} | ||
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# To avoid import errors. | ||
autodoc_mock_imports = ['MySQLdb'] | ||
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# -- Options for HTML output ---------------------------------------------- | ||
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# The theme to use for HTML and HTML Help pages. See the documentation for | ||
# a list of builtin themes. | ||
# | ||
html_theme = 'alabaster' | ||
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# 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 = {} | ||
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# 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'] | ||
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# 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', | ||
], | ||
} | ||
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# -- Options for HTMLHelp output ------------------------------------------ | ||
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# Output file base name for HTML help builder. | ||
htmlhelp_basename = 'Biopython_doc' | ||
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# -- Options for LaTeX output --------------------------------------------- | ||
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latex_elements = { | ||
# The paper size ('letterpaper' or 'a4paper'). | ||
# | ||
# 'papersize': 'letterpaper', | ||
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# The font size ('10pt', '11pt' or '12pt'). | ||
# | ||
# 'pointsize': '10pt', | ||
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# Additional stuff for the LaTeX preamble. | ||
# | ||
# 'preamble': '', | ||
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# Latex figure (float) alignment | ||
# | ||
# 'figure_align': 'htbp', | ||
} | ||
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# 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, 'Biopython_API.tex', document, author, 'manual'), | ||
] | ||
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# -- Options for manual page output --------------------------------------- | ||
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# One entry per manual page. List of tuples | ||
# (source start file, name, description, authors, manual section). | ||
man_pages = [ | ||
(master_doc, 'biopython', document, [author], 1), | ||
] | ||
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# -- Options for Texinfo output ------------------------------------------- | ||
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# 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, 'Biopython', document, author, 'Biopython', | ||
'Collection of modules for dealing with biological data in Python.', | ||
'Miscellaneous'), | ||
] | ||
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# -- Options for Epub output ---------------------------------------------- | ||
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# Bibliographic Dublin Core info. | ||
epub_title = document # project | ||
epub_author = author | ||
epub_publisher = author | ||
epub_copyright = copyright | ||
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# The unique identifier of the text. This can be a ISBN number | ||
# or the project homepage. | ||
# | ||
# epub_identifier = '' | ||
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# A unique identification for the text. | ||
# | ||
# epub_uid = '' | ||
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# A list of files that should not be packed into the epub file. | ||
epub_exclude_files = ['search.html'] | ||
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# -- Options for numpydoc ------------------------------------------------- | ||
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numpydoc_class_members_toctree = False | ||
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# -- Magic to run sphinx-apidoc automatically ----------------------------- | ||
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# See https://github.com/rtfd/readthedocs.org/issues/1139 | ||
# on which this is based. | ||
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def run_apidoc(_): | ||
"""Call sphinx-apidoc on Bio and BioSQL modules.""" | ||
from sphinx.ext.apidoc import main as apidoc_main | ||
cur_dir = os.path.abspath(os.path.dirname(__file__)) | ||
# Can't see a better way than running apidoc twice, for Bio & BioSQL | ||
# We don't care about the index.rst / conf.py (we have our own) | ||
# or the Makefile / make.bat (effectively same) clashing, | ||
# $ sphinx-apidoc -e -F -o /tmp/api/BioSQL BioSQL | ||
# $ sphinx-apidoc -e -F -o /tmp/api/Bio Bio | ||
tmp_path = tempfile.mkdtemp() | ||
apidoc_main(['-e', '-F', '-o', tmp_path, '../../BioSQL']) | ||
apidoc_main(['-e', '-F', '-o', tmp_path, '../../Bio']) | ||
os.remove(os.path.join(tmp_path, 'index.rst')) # Using our own | ||
for filename in os.listdir(tmp_path): | ||
if filename.endswith(".rst"): | ||
shutil.move(os.path.join(tmp_path, filename), | ||
os.path.join(cur_dir, filename)) | ||
shutil.rmtree(tmp_path) | ||
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def setup(app): | ||
"""Over-ride Sphinx setup to trigger sphinx-apidoc.""" | ||
app.connect('builder-inited', run_apidoc) |
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.. Biopython API documentation master file, based on sphinx-quickstart | ||
This depends on having sphinx-apidoc run on both Bio and BioSQL to | ||
generate the per-module/package RST file referenced here. | ||
Welcome to Biopython's API documentation! | ||
========================================= | ||
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.. toctree:: | ||
:maxdepth: 4 | ||
:caption: Contents: | ||
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Bio | ||
BioSQL | ||
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Indices and tables | ||
================== | ||
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* :ref:`genindex` | ||
* :ref:`modindex` | ||
* :ref:`search` |