r"""Parser for Jupyter notebooks.
Class that holds the Jupyter notebook information
"""
# Author: Óscar Nájera
# License: 3-clause BSD
from collections import defaultdict
from functools import partial
from itertools import count
import argparse
import base64
import copy
import json
import mimetypes
import os
from pathlib import Path
import re
import sys
import textwrap
from sphinx.errors import ExtensionError
import sphinx.util
from .py_source_parser import split_code_and_text_blocks
logger = sphinx.util.logging.getLogger("sphinx-gallery")
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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": "{}.{}.{}".format(*sys.version_info[:3]),
},
},
"nbformat": 4,
"nbformat_minor": 0,
}
return notebook_skeleton
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def directive_fun(match, directive):
"""Helper to fill in directives."""
directive_to_alert = dict(note="info", warning="danger")
return '<div class="alert alert-{}"><h4>{}</h4><p>{}</p></div>'.format(
directive_to_alert[directive], directive.capitalize(), match.group(1).strip()
)
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def convert_code_to_md(text):
"""Rewrite code blocks to use Markdown's preferred backtick notation.
Backtick notation preserves syntax highlighting.
Parameters
----------
text: str
A mostly converted string of markdown text. May contain zero, one,
or multiple code blocks in code-block format.
"""
code_regex = r"[ \t]*\.\. code-block::[ \t]*(\S*)\n[ \t]*\n([ \t]+)"
while True:
code_block = re.search(code_regex, text)
if not code_block:
break
indent = code_block.group(2)
start_index = code_block.span()[1] - len(indent)
# Find first non-empty, non-indented line
end = re.compile(rf"^(?!{re.escape(indent)})[ \t]*\S+", re.MULTILINE)
code_end_match = end.search(text, start_index)
end_index = code_end_match.start() if code_end_match else len(text)
contents = textwrap.dedent(text[start_index:end_index]).rstrip()
new_code = f"```{code_block.group(1)}\n{contents}\n```\n"
text = text[: code_block.span()[0]] + new_code + text[end_index:]
return text
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def rst2md(text, gallery_conf, target_dir, heading_levels):
"""Converts reST from docstrings and text blocks to markdown for Jupyter notebooks.
Parameters
----------
text: str
reST 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$", text)
directives = ("warning", "note")
for directive in directives:
directive_re = re.compile(
r"^\.\. %s::((?:.+)?(?:\n+^ .+)*)" % directive, flags=re.M
)
text = re.sub(directive_re, partial(directive_fun, directive=directive), text)
footnote_links = re.compile(r"^ *\.\. _.*:.*$\n", flags=re.M)
text = re.sub(footnote_links, "", text)
embedded_uris = re.compile(r"`([^`]*?)\s*<([^`]*)>`_")
text = re.sub(embedded_uris, r"[\1](\2)", 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,
)
text = convert_code_to_md(text)
return text
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def generate_image_src(image_path, gallery_conf, target_dir):
"""Modify image path for notebook, according to "notebook_images" config.
URLs are unchanged.
If "notebook_images" config is a str, it is used as a prefix to image path, relative
to "src_dir". If "notebook_images" is `True`, image is embedded as URI. If
"notebook_images" is `False`, "file://" is prepended.
"""
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(
f"Unable to open {full_path} to generate notebook data URI"
)
mime_type = mimetypes.guess_type(full_path)
return f"data:{mime_type[0]};base64,{data.decode('ascii')}"
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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
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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)
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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)
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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 adds \n to the end
markdown = pypandoc.convert_text(
bcontent, to="md", format="rst", **gallery_conf["pypandoc"]
)
if gallery_conf["promote_jupyter_magic"]:
remaining = promote_jupyter_cell_magic(work_notebook, markdown)
if remaining and not remaining.isspace():
add_markdown_cell(work_notebook, remaining)
else:
add_markdown_cell(work_notebook, markdown)
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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
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def python_to_jupyter_cli(args=None, namespace=None, sphinx_gallery_conf=None):
"""Exposes the jupyter notebook renderer to the command line.
Takes the same arguments as ArgumentParser.parse_args.
`sphinx_gallery_conf` functions same as in `conf.py`.
"""
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)
# handle `sphinx_gallery_conf`
gallery_conf = copy.deepcopy(gen_gallery.DEFAULT_GALLERY_CONF)
if sphinx_gallery_conf is not None:
gallery_conf.update(sphinx_gallery_conf)
# run script
for src_file in args.python_src_file:
file_conf, blocks = split_code_and_text_blocks(src_file)
print(f"Converting {src_file}")
target_dir = os.path.dirname(src_file)
example_nb = jupyter_notebook(blocks, copy.deepcopy(gallery_conf), target_dir)
save_notebook(example_nb, Path(src_file).with_suffix(".ipynb"))