Build Sphinx API docs under TravisCI/Tox using apidoc

.travis-tox.ini

@@ -33,6 +33,7 @@ envlist =
     style
     sdist
     bdist_wheel
+    api
     {py27,py34,py35,py36,pypy,pypy3}-cover
     {py27,py34,py35,py36,pypy,pypy3}-nocov
 
@@ -86,6 +87,7 @@ commands =
 skip_install = True
 whitelist_externals =
     flake8
+    doc8
     rst-lint
     bash
 deps =
@@ -95,6 +97,7 @@ deps =
     flake8-rst-docstrings
     py34,py35,py36: flake8-bugbear
     restructuredtext_lint
+    doc8
 commands =
     flake8 --max-line-length 82 setup.py
     # These folders each have their own .flake8 file:
@@ -105,11 +108,13 @@ commands =
     flake8 Tests/
     # Now do various checks on our RST files:
     # Calling via bash to get it to expand the wildcard for us
-    bash -c \'rst-lint --level warning *.rst Doc\'
+    bash -c \'rst-lint --level warning *.rst\'
     # Check sort order (bash call work around for pipe character)
     bash -c \'grep "^- " CONTRIB.rst | LC_ALL=C sort -u -c -f\'
     # Check copyright date
     bash -c \'grep "1999-`date +'%Y'`" LICENSE.rst\'
+    # Would like to tell doc8 to just check *.rst but does *.txt too:
+    bash -c "doc8 --ignore-path 'Doc/examples/ec_*.txt' *.rst Doc/"
     # Check no __docformat__ lines
     bash -c "if grep --include '*.py' -rn '^__docformat__ ' Bio BioSQL Tests Scripts Doc ; then echo 'Remove __docformat__ line(s), we assume restructuredtext.'; false; fi"
     # Check DOI link style, see https://www.crossref.org/display-guidelines/
@@ -131,3 +136,24 @@ deps =
     numpy
 commands =
     python setup.py bdist_wheel
+
+[testenv:api]
+# Note Sphinx likes to have the code installed so can import it
+skip_install = False
+whitelist_externals =
+    bash
+    sphinx-apidoc
+    make
+deps =
+    mmtf-python
+    mysql-connector-python-rf
+    numpy
+    rdflib
+    reportlab
+    scipy
+    sphinx>=1.8.0
+    numpydoc
+commands =
+    bash -c \'python setup.py install > /dev/null\'
+    bash -c \'mkdir -p Doc/api/_templates Doc/api/_static Doc/api/_build\'
+    make -C Doc/api/ html

.travis.yml

@@ -38,6 +38,13 @@ matrix:
         apt:
           packages:
       before_install: echo "Going to run basic checks"
+    - stage: test
+      python: 2.7
+      env: TOXENV=api
+      addons:
+        apt:
+          packages:
+      before_install: echo "Going to build API docs"
     - stage: test
       python: 2.7
       env: TOXENV=py27-cover
@@ -145,7 +152,7 @@ install:
   - tox -c .travis-tox.ini -e $TOXENV --notest
 
 script:
-  - travis_wait tox -c .travis-tox.ini -e $TOXENV
+  - travis_wait 30 tox -c .travis-tox.ini -e $TOXENV
 
 notifications:
   email: false

Doc/api/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = Bio
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# 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)

Doc/api/conf.py

@@ -0,0 +1,234 @@
+#!/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.
+"""
+
+import os
+import shutil
+# import sys
+import tempfile
+
+from Bio import __version__
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+needs_sphinx = '1.8'
+
+# 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']
+
+# 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 = '1999-2017, 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__
+
+# 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 1.8.0b1 or later:
+autodoc_default_values = {
+    'members': None,
+    'undoc-members': None,
+    'special-members': None,
+    'show-inheritance': None,
+    'member-order': 'bysource',
+    'exclude-members': '__dict__,__weakref__,__module__',
+}
+
+# To avoid import errors.
+autodoc_mock_imports = ['MySQLdb']
+
+# -- 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 = {}
+
+# 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']
+
+# 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
+
+# -- Magic to run sphinx-apidoc automatically -----------------------------
+
+# See https://github.com/rtfd/readthedocs.org/issues/1139
+# on which this is based.
+
+
+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)
+
+
+def setup(app):
+    """Over-ride Sphinx setup to trigger sphinx-apidoc."""
+    app.connect('builder-inited', run_apidoc)

Doc/api/index.rst

@@ -0,0 +1,21 @@
+.. 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!
+=========================================
+
+.. toctree::
+   :maxdepth: 4
+   :caption: Contents:
+
+   Bio
+   BioSQL
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`