Sphinx config file

config source code

#
# Configuration file for the Sphinx documentation builder.
#
# This file does only contain a selection of the most common options. For a
# full list see the documentation:
# http://www.sphinx-doc.org/en/master/config

# -- Path setup --------------------------------------------------------------

# 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('.'))

from __future__ import print_function
import os
import sys
import shutil
import subprocess

# -- Project information -----------------------------------------------------

project = u'Doc tutorial'
copyright = u'2019, nobody'
author = u'nobody'

# The short X.Y version
version = u''
# The full version, including alpha/beta/rc tags
release = u'1.0.0'


# -- 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.doctest',
    'sphinx.ext.intersphinx',
    'sphinx.ext.todo',
    'sphinx.ext.coverage',
    'sphinx.ext.mathjax',
    'sphinx.ext.ifconfig',
    'sphinx.ext.viewcode',
    'sphinx.ext.githubpages',
    'sphinx.ext.napoleon',
    'sphinx.ext.extlinks',
    'sphinx.ext.inheritance_diagram',
]

# -- nbsphinx ext -------
try:
    # nbsphinx converts ipython/jupyter notebooks to sphinx docs
    import nbsphinx
    import distutils.spawn
    if not distutils.spawn.find_executable('pandoc'):
        print('Warning: pandoc is missing. Notebooks will not be included '
              'in the docs')
    else:
        nbsphinx_allow_errors = True
        extensions += ['nbsphinx',
                      'sphinx.ext.mathjax']
        # set this env variable to tell notebooks that we should not use
        # any GUI during notebooks execution
        os.environ['ALLOW_GUI'] = '0'
        print('-- nbsphinx should work. --')
except ImportError as e:
    nbsphinx = None
    print('Warning: nbsphinx could not be imported, the notebooks will not '
          'appear in the docs')

# -- sphinx-gallery ext -----
try:
    import matplotlib
    import sphinx_gallery
    extensions.append('sphinx_gallery.gen_gallery')
    sphinx_gallery_conf = {
        'examples_dirs': 'code_examples',   # path to your example scripts
        'gallery_dirs': 'auto_examples',  # path where to save gallery generated examples
        'filename_pattern': '.*\.py',
        #'ignore_pattern': r'/[^abcefgmnst][^/]*\.py$',
        'expected_failing_examples': ['code_examples/conf.py'],
    }
except ImportError:
    pass  # no gallery. Oh, well.

Out:

-- nbsphinx should work. --

# 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'

# 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 pattern also affects html_static_path and html_extra_path.
exclude_patterns = [u'_build', 'Thumbs.db', '.DS_Store']

# The name of the Pygments (syntax highlighting) style to use.
pygments_style = None


# -- 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'
#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 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.
#
# The default sidebars (for documents that don't match any pattern) are
# defined by theme itself.  Builtin themes are using these templates by
# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
# 'searchbox.html']``.
#
# html_sidebars = {}


# -- Options for HTMLHelp output ---------------------------------------------

# Output file base name for HTML help builder.
htmlhelp_basename = 'Doctutorialdoc'


# -- 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, 'Doctutorial.tex', u'Doc tutorial Documentation',
     u'nobody', '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, 'doctutorial', u'Doc tutorial 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, 'Doctutorial', u'Doc tutorial Documentation',
     author, 'Doctutorial', 'One line description of project.',
     'Miscellaneous'),
]


# -- Options for Epub output -------------------------------------------------

# Bibliographic Dublin Core info.
epub_title = project

# 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']


# -- Extension configuration -------------------------------------------------

# -- Options for intersphinx extension ---------------------------------------

# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {
    'https://docs.python.org/': None,
    'https://populse.github.io/capsul/': None,
    'https://matplotlib.org/': None}

# -- Options for todo extension ----------------------------------------------

# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = True

code added after regular sphinx conf file

# -- Extlinks ------
extlinks = {
  'capsul': ('https://populse.github.io/capsul/%s',
    'capsul '),
}

# -- nbsphinx ------
if nbsphinx:
    # Notebooks handling:
    #
    # Several problems are handled here:
    # 1. nbsphinx 0.4 does not read (ignores) notebooks in _static/
    #    For this reason we moved the NB to tutorial/
    # 2. nbsphinx 0.4 does not allow direct links to the .ipynb (for download)
    #    but replaces them with the converted HTML page.
    #    For this reason we duplicate the NB into _static/ where NB are not
    #    processed, and links not changed
    # 3. notebooks include kernel infoemation which does not necessarily match the
    #    running/installed python and jupyter kernels.
    #    For this reason we conbert them using pupyter nbconvert, forcing the
    #    kernel to the current running python version.
    # 4. sphinx does not copy image files not in _static/ into the build tree.
    #    So we copy them into the build tree.
    # 5. nbsphinx 0.4 messes up image links when the notebook is not in the root
    #    of the sphinx tree. Typically in a notebook placed in tutorial/,
    #    containing links to "images/something.jpg", the HTML page will contain
    #    links to "tutorial/images/something.jpg".
    #    To overcome this, we copy the images directory into
    #    "tutorial/tutorial/images/" in the build tree.
    #
    # Thus, in git sources we have:
    #
    #     tutorial/capsul_tutorial.ipynb.in
    #     tutorial/images/*.jpg
    #
    # After running this conf.py (run by sphinx actually), we have additionally,
    # still in sources:
    #
    #     tutorial/capsul_tutorial.ipynb
    #
    # and in the build tree:
    #
    #     _static/tutorial/capsul_tutorial.ipynb
    #     tutorial/tutorial/images/*.jpg
    #
    # Hack to copy files from sources to build dir
    out_dir = sys.argv[-1]
    src_dir = sys.argv[-2]
    print('source:', src_dir)
    print('dest:', out_dir)
    print('cwd:', os.getcwd())
    #if not os.path.isabs(src_dir) and not os.path.exists(os.path.join(src_dir)):
        ## this strange config appears in Makefile builds
        #src_dir = os.getcwd()
    src_dir = os.path.abspath(src_dir)
    out_dir = os.path.join(os.path.abspath(out_dir), 'html')  # add html here
    print('abs source:', src_dir)
    print('abs dest:', out_dir)
    # nbsphinx 3/4 has a bug: it adds the 1st directory level to images paths.
    # so we have to move it into a 2nd level of 'tutorial'. Probably nbsphinx
    # is only working well for notebooks at the root of the source tree.
    out_tuto_path = os.path.join(out_dir, 'tutorial')
    out_tuto_img_path = os.path.join(out_tuto_path, 'tutorial')
    if os.path.exists(out_tuto_img_path):
        shutil.rmtree(out_tuto_img_path)
    if not os.path.exists(out_tuto_path):
        os.makedirs(out_tuto_path)
    if os.path.exists(os.path.join(src_dir, 'tutorial/images')):
        shutil.copytree(os.path.join(src_dir, 'tutorial/images'),
                        out_tuto_img_path)

    # convert notebook(s) with correct python kernel
    nb_name = 'sample_notebook.ipynb'
    in_nb = os.path.join(src_dir, 'tutorial/%s.in' % nb_name)
    out_nb = os.path.join(src_dir, 'tutorial/%s' % nb_name)
    args = [sys.executable, '-m', 'jupyter', 'nbconvert', '--to', 'notebook',
            '--execute',
            '--ExecutePreprocessor.kernel_name=python%d' % sys.version_info[0],
            '--output', out_nb, in_nb]
    print('exec:', *args)
    subprocess.check_call(args)

    #shutil.copy2(os.path.join(src_dir, 'tutorial/capsul_tutorial.ipynb.in'),
                #os.path.join(out_tuto_path, 'capsul_tutorial.ipynb.in'))
    if not os.path.exists(os.path.join(out_dir, '_static/tutorial')):
        os.makedirs(os.path.join(out_dir, '_static/tutorial'))
    shutil.copy2(os.path.join(src_dir, 'tutorial/%s' % nb_name),
                os.path.join(out_dir, '_static/tutorial/%s' % nb_name))

# -- copy this conf.py as code example
with open(os.path.join(src_dir, 'code_examples', 'conf.py'), 'w') as f:
    print('''"""Sphinx config file
==================

config source code
"""
''', file=f)
    with open(__file__) as sf:
        next(iter(sf))  # skip encoding line
        for line in sf:
            f.write(line)

# -- generate pipeline and processes docs -----
# we must actually write in sources for now.
sphinx_dir = os.path.dirname(__file__)
proc_rst_dir = os.path.join(sphinx_dir, 'process_docs', 'example_module')
if not os.path.exists(proc_rst_dir):
    os.makedirs(proc_rst_dir)
cmd = [sys.executable, '-m', 'capsul.sphinxext.capsul_pipeline_rst',
       '-i', 'sample_module.capsul', '-o', proc_rst_dir, '--schema']
print('generating CAPSUL processes docs...')
print(cmd)
subprocess.check_output(cmd)

Traceback (most recent call last):
  File "/home/travis/virtualenv/python3.7.1/lib/python3.7/site-packages/sphinx_gallery/gen_rst.py", line 440, in _memory_usage
    out = func()
  File "/home/travis/virtualenv/python3.7.1/lib/python3.7/site-packages/sphinx_gallery/gen_rst.py", line 425, in __call__
    exec(self.code, self.globals)
  File "/home/travis/build/denisri/demo-doc/doc/code_examples/conf.py", line 306, in <module>
    src_dir = sys.argv[-2]
IndexError: list index out of range