# -*- coding: utf-8 -*-
r"""
Parser for Jupyter notebooks
============================
Class that holds the Jupyter notebook information
"""
# Author: Óscar Nájera
# License: 3-clause BSD
from __future__ import division, absolute_import, print_function
from collections import defaultdict
from functools import partial
from itertools import count
import argparse
import base64
import json
import mimetypes
import os
import re
import sys
import copy
from sphinx.errors import ExtensionError
from . import sphinx_compatibility
from .py_source_parser import split_code_and_text_blocks
from .utils import replace_py_ipynb
logger = sphinx_compatibility.getLogger('sphinx-gallery')
[docs]def jupyter_notebook_skeleton():
"""Returns a dictionary with the elements of a Jupyter notebook"""
py_version = sys.version_info
notebook_skeleton = {
"cells": [],
"metadata": {
"kernelspec": {
"display_name": "Python " + str(py_version[0]),
"language": "python",
"name": "python" + str(py_version[0])
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": py_version[0]
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython" + str(py_version[0]),
"version": '{0}.{1}.{2}'.format(*sys.version_info[:3])
}
},
"nbformat": 4,
"nbformat_minor": 0
}
return notebook_skeleton
[docs]def directive_fun(match, directive):
"""Helper to fill in directives"""
directive_to_alert = dict(note="info", warning="danger")
return ('<div class="alert alert-{0}"><h4>{1}</h4><p>{2}</p></div>'
.format(directive_to_alert[directive], directive.capitalize(),
match.group(1).strip()))
[docs]def rst2md(text, gallery_conf, target_dir, heading_levels):
"""Converts the RST text from the examples docstrings and comments
into markdown text for the Jupyter notebooks
Parameters
----------
text: str
RST input to be converted to MD
gallery_conf : dict
The sphinx-gallery configuration dictionary.
target_dir : str
Path that notebook is intended for. Used where relative paths
may be required.
heading_levels: dict
Mapping of heading style ``(over_char, under_char)`` to heading level.
Note that ``over_char`` is `None` when only underline is present.
"""
# Characters recommended for use with headings
# https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html#sections
adornment_characters = "=`:.'\"~^_*+#<>-"
headings = re.compile(
# Start of string or blank line
r'(?P<pre>\A|^[ \t]*\n)'
# Optional over characters, allowing leading space on heading text
r'(?:(?P<over>[{0}])(?P=over)*\n[ \t]*)?'
# The heading itself, with at least one non-white space character
r'(?P<heading>\S[^\n]*)\n'
# Under character, setting to same character if over present.
r'(?P<under>(?(over)(?P=over)|[{0}]))(?P=under)*$'
r''.format(adornment_characters),
flags=re.M)
text = re.sub(
headings,
lambda match: '{1}{0} {2}'.format(
'#'*heading_levels[match.group('over', 'under')],
*match.group('pre', 'heading')),
text)
math_eq = re.compile(r'^\.\. math::((?:.+)?(?:\n+^ .+)*)', flags=re.M)
text = re.sub(math_eq,
lambda match: r'\begin{{align}}{0}\end{{align}}'.format(
match.group(1).strip()),
text)
inline_math = re.compile(r':math:`(.+?)`', re.DOTALL)
text = re.sub(inline_math, r'$\1$', text)
directives = ('warning', 'note')
for directive in directives:
directive_re = re.compile(r'^\.\. %s::((?:.+)?(?:\n+^ .+)*)'
% directive, flags=re.M)
text = re.sub(directive_re,
partial(directive_fun, directive=directive), text)
links = re.compile(r'^ *\.\. _.*:.*$\n', flags=re.M)
text = re.sub(links, '', text)
refs = re.compile(r':ref:`')
text = re.sub(refs, '`', text)
contents = re.compile(r'^\s*\.\. contents::.*$(\n +:\S+: *$)*\n',
flags=re.M)
text = re.sub(contents, '', text)
images = re.compile(
r'^\.\. image::(.*$)((?:\n +:\S+:.*$)*)\n',
flags=re.M)
image_opts = re.compile(r'\n +:(\S+): +(.*)$', flags=re.M)
text = re.sub(
images,
lambda match: '<img src="{}"{}>\n'.format(
generate_image_src(
match.group(1).strip(), gallery_conf, target_dir),
re.sub(image_opts, r' \1="\2"', match.group(2) or '')),
text)
return text
[docs]def generate_image_src(image_path, gallery_conf, target_dir):
if re.match(r'https?://', image_path):
return image_path
if not gallery_conf['notebook_images']:
return "file://" + image_path.lstrip('/')
# If absolute path from source directory given
if image_path.startswith('/'):
# Path should now be relative to source dir, not target dir
target_dir = gallery_conf['src_dir']
image_path = image_path.lstrip('/')
full_path = os.path.join(target_dir, image_path.replace('/', os.sep))
if isinstance(gallery_conf['notebook_images'], str):
# Use as prefix e.g. URL
prefix = gallery_conf['notebook_images']
rel_path = os.path.relpath(full_path, gallery_conf['src_dir'])
return prefix + rel_path.replace(os.sep, '/')
else:
# True, but not string. Embed as data URI.
try:
with open(full_path, 'rb') as image_file:
data = base64.b64encode(image_file.read())
except OSError:
raise ExtensionError(
'Unable to open {} to generate notebook data URI'
''.format(full_path))
mime_type = mimetypes.guess_type(full_path)
return 'data:{};base64,{}'.format(mime_type[0], data.decode('ascii'))
[docs]def jupyter_notebook(script_blocks, gallery_conf, target_dir):
"""Generate a Jupyter notebook file cell-by-cell
Parameters
----------
script_blocks : list
Script execution cells.
gallery_conf : dict
The sphinx-gallery configuration dictionary.
target_dir : str
Path that notebook is intended for. Used where relative paths
may be required.
"""
first_cell = gallery_conf["first_notebook_cell"]
last_cell = gallery_conf["last_notebook_cell"]
work_notebook = jupyter_notebook_skeleton()
if first_cell is not None:
add_code_cell(work_notebook, first_cell)
fill_notebook(work_notebook, script_blocks, gallery_conf, target_dir)
if last_cell is not None:
add_code_cell(work_notebook, last_cell)
return work_notebook
[docs]def add_code_cell(work_notebook, code):
"""Add a code cell to the notebook
Parameters
----------
code : str
Cell content
"""
code_cell = {
"cell_type": "code",
"execution_count": None,
"metadata": {"collapsed": False},
"outputs": [],
"source": [code.strip()]
}
work_notebook["cells"].append(code_cell)
[docs]def add_markdown_cell(work_notebook, markdown):
"""Add a markdown cell to the notebook
Parameters
----------
markdown : str
Markdown cell content.
"""
markdown_cell = {
"cell_type": "markdown",
"metadata": {},
"source": [markdown]
}
work_notebook["cells"].append(markdown_cell)
[docs]def fill_notebook(work_notebook, script_blocks, gallery_conf, target_dir):
"""Writes the Jupyter notebook cells
If available, uses pypandoc to convert rst to markdown.
Parameters
----------
script_blocks : list
Each list element should be a tuple of (label, content, lineno).
"""
heading_level_counter = count(start=1)
heading_levels = defaultdict(lambda: next(heading_level_counter))
for blabel, bcontent, lineno in script_blocks:
if blabel == 'code':
add_code_cell(work_notebook, bcontent)
else:
if gallery_conf["pypandoc"] is False:
markdown = rst2md(
bcontent + '\n', gallery_conf, target_dir, heading_levels)
else:
import pypandoc
# pandoc automatically addds \n to the end
markdown = pypandoc.convert_text(
bcontent, to='md', format='rst', **gallery_conf["pypandoc"]
)
add_markdown_cell(work_notebook, markdown)
[docs]def save_notebook(work_notebook, write_file):
"""Saves the Jupyter work_notebook to write_file"""
with open(write_file, 'w') as out_nb:
json.dump(work_notebook, out_nb, indent=2)
###############################################################################
# Notebook shell utility
[docs]def python_to_jupyter_cli(args=None, namespace=None):
"""Exposes the jupyter notebook renderer to the command line
Takes the same arguments as ArgumentParser.parse_args
"""
from . import gen_gallery # To avoid circular import
parser = argparse.ArgumentParser(
description='Sphinx-Gallery Notebook converter')
parser.add_argument('python_src_file', nargs='+',
help='Input Python file script to convert. '
'Supports multiple files and shell wildcards'
' (e.g. *.py)')
args = parser.parse_args(args, namespace)
for src_file in args.python_src_file:
file_conf, blocks = split_code_and_text_blocks(src_file)
print('Converting {0}'.format(src_file))
gallery_conf = copy.deepcopy(gen_gallery.DEFAULT_GALLERY_CONF)
target_dir = os.path.dirname(src_file)
example_nb = jupyter_notebook(blocks, gallery_conf, target_dir)
save_notebook(example_nb, replace_py_ipynb(src_file))