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conf.py
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conf.py
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#!/usr/bin/env python3
"""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.
"""
import os
import shutil
import sys
import tempfile
from sphinx.ext import autodoc
from Bio import __version__, Application
# -- General configuration ------------------------------------------------
# If your documentation needs a minimal Sphinx version, state it here.
#
needs_sphinx = "3.5"
# 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",
# Don't want to include source code in the API docs
# 'sphinx.ext.viewcode',
"sphinx.ext.autosummary",
"numpydoc",
]
# 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 = "Biopython"
copyright = "1999-2020, The Biopython Contributors"
author = "The Biopython Contributors"
document = "Biopython API Documentation"
# 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__
# Versions for versions.html:
# (this will break if we have version gaps)
try:
main_version, minor_version, _ = version.split(".") # e.g. 1.79.dev0
dev_version = True
except ValueError:
main_version, minor_version = version.split(".") # e.g. 1.78
dev_version = False
prev_minor_version = int(minor_version) - (2 if dev_version else 1)
previous_version = f"{main_version}.{prev_minor_version}"
versions = [
("Previous", f"../../{previous_version}/api/"),
("Latest", "../../latest/api/"),
("Develop", "../../dev/api/"),
]
if version < "1.75": # 1.74 is the earliest Sphinx-generated api documentation
del versions[0]
# 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"
# 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 = True
# -- Options for autodoc --------------------------------------------------
# This requires Sphinx 1.8 or later:
autodoc_default_options = {
"members": None,
"undoc-members": None,
"special-members": None,
"show-inheritance": None,
"member-order": "bysource",
"exclude-members": "__dict__,__weakref__,__module__",
}
# Experimental feature to preserve the default argument values of
# functions in source code and keep them not evaluated for readability:
autodoc_preserve_defaults = True
# To avoid import errors.
autodoc_mock_imports = ["MySQLdb"]
# -- Options for HTML output ----------------------------------------------
# Sphinx default was html_theme = "alabaster"
html_theme = "sphinx_rtd_theme"
# Sphinx Read The Docs theme settings, see
# https://sphinx-rtd-theme.readthedocs.io/en/latest/configuring.html
html_theme_options = {
"prev_next_buttons_location": "both",
# Same a Hyde theme sidebar on biopython.org:
"style_nav_header_background": "#10100F",
# Since we have the Biopython logo via html_logo,
"logo_only": True,
}
# Based on:
# https://github.com/readthedocs/sphinx_rtd_theme/issues/231#issuecomment-126447493
html_context = {
"display_github": True, # Add 'Edit on Github' link instead of 'View page source'
"github_user": "biopython",
"github_repo": "biopython",
"github_version": "master",
"conf_py_path": "/Doc/api/",
# "source_suffix": source_suffix,
"theme_display_version": False,
# Biopython-specific values for version-footer (versions.html):
"display_version_footer": True,
"current_version": version,
"versions": versions,
"project_home_url": "https://biopython.org",
"project_github_url": "https://github.com/biopython/biopython",
}
html_logo = "../images/biopython_logo_white.png"
# The RST source is transient, don't need/want to include it
html_show_sourcelink = False
html_copy_source = False
# 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"]
# The following is not applicable to the Read-the-docs theme:
# 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 = "Biopython_doc"
# -- 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, "Biopython_API.tex", document, 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, "biopython", document, [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,
"Biopython",
document,
author,
"Biopython",
"Collection of modules for dealing with biological data in Python.",
"Miscellaneous",
)
]
# -- Options for Epub output ----------------------------------------------
# Bibliographic Dublin Core info.
epub_title = document # project
epub_author = author
epub_publisher = author
epub_copyright = copyright
# The unique identifier of the text. This can be a ISBN number
# or the project homepage.
#
# epub_identifier = ''
# A unique identification for the text.
#
# epub_uid = ''
# A list of files that should not be packed into the epub file.
epub_exclude_files = ["search.html"]
# -- Options for numpydoc -------------------------------------------------
numpydoc_class_members_toctree = False
# Prevents the attributes and methods from being shown twice
numpydoc_show_class_members = False
# -- Magic to run sphinx-apidoc automatically -----------------------------
# See https://github.com/rtfd/readthedocs.org/issues/1139
# on which this is based.
def insert_github_link(filename):
"""Insert file specific :github_url: metadata for theme breadcrumbs."""
assert "/" not in filename and filename.endswith(".rst")
with open(filename) as handle:
text = handle.read()
if ":github_url:" in text:
return
python = filename[:-4].replace(".", "/") + "/__init__.py"
if not os.path.isfile(os.path.join("../../", python)):
python = filename[:-4].replace(".", "/") + ".py"
if not os.path.isfile(os.path.join("../../", python)):
sys.stderr.write(
"WARNING: Could not map %s to a Python file, e.g. %s\n" % (filename, python)
)
return
text = ":github_url: https://github.com/%s/%s/blob/%s/%s\n\n%s" % (
html_context["github_user"],
html_context["github_repo"],
html_context["github_version"],
python,
text,
)
with open(filename, "w") as handle:
handle.write(text)
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,
# The input path:
"../../Bio",
# These are patterns to exclude:
"../../Bio/Alphabet/",
"../../Bio/Restriction/Restriction.py",
]
)
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)
for f in os.listdir(cur_dir):
if f.startswith("Bio") and f.endswith(".rst"):
insert_github_link(f)
class BioPythonAPI(autodoc.ClassDocumenter):
"""Custom Class Documenter for AbstractCommandline classes."""
def import_object(self):
"""Import the class."""
ret = super().import_object()
if not issubclass(self.object, Application.AbstractCommandline):
return ret
try:
# If the object is an AbstractCommandline we instantiate it.
self.object()
except TypeError:
# Throws if the object is the base AbstractCommandline class
pass
return ret
def setup(app):
"""Over-ride Sphinx setup to trigger sphinx-apidoc."""
app.connect("builder-inited", run_apidoc)
app.add_css_file("biopython.css")
def add_documenter(app, env, docnames):
app.add_autodocumenter(BioPythonAPI, True)
# Over-ride autodoc documenter
app.connect("env-before-read-docs", add_documenter)