def write(cells, nb_version=4):
"""Turn cells list into valid IPython notebook code."""
# Use IPython.nbformat functionality for writing the notebook
if nb_version == 3:
from IPython.nbformat.v3 import (
new_code_cell,
new_text_cell,
new_worksheet,
new_notebook,
new_metadata,
new_author,
)
nb = new_worksheet()
elif nb_version == 4:
from IPython.nbformat.v4 import new_code_cell, new_markdown_cell, new_notebook
nb_cells = []
for cell_tp, language, block in cells:
if cell_tp == "markdown":
if nb_version == 3:
nb.cells.append(new_text_cell(u"markdown", source=block))
elif nb_version == 4:
nb_cells.append(new_markdown_cell(source=block))
elif cell_tp == "codecell":
if nb_version == 3:
nb.cells.append(new_code_cell(input=block))
elif nb_version == 4:
nb_cells.append(new_code_cell(source=block))
if nb_version == 3:
nb = new_notebook(worksheets=[nb], metadata=new_metadata())
# Let us make v4 notebook here by upgrading
from IPython.nbformat.v4 import upgrade
nb = upgrade(nb)
import IPython.nbformat.v4.nbjson as nbjson
# Convert nb to json format
filestr = nbjson.writes(nb)
elif nb_version == 4:
nb = new_notebook(cells=nb_cells)
from IPython.nbformat import writes
filestr = writes(nb, version=4)
return filestr
def write(cells, nb_version=4):
"""Turn cells list into valid IPython notebook code."""
# Use IPython.nbformat functionality for writing the notebook
if nb_version == 3:
from IPython.nbformat.v3 import (new_code_cell, new_text_cell,
new_worksheet, new_notebook,
new_metadata, new_author)
nb = new_worksheet()
elif nb_version == 4:
from IPython.nbformat.v4 import (new_code_cell, new_markdown_cell,
new_notebook)
nb_cells = []
for cell_tp, language, block in cells:
if cell_tp == 'markdown':
if nb_version == 3:
nb.cells.append(new_text_cell(u'markdown', source=block))
elif nb_version == 4:
nb_cells.append(new_markdown_cell(source=block))
elif cell_tp == 'codecell':
if nb_version == 3:
nb.cells.append(new_code_cell(input=block))
elif nb_version == 4:
nb_cells.append(new_code_cell(source=block))
if nb_version == 3:
nb = new_notebook(worksheets=[nb], metadata=new_metadata())
# Let us make v4 notebook here by upgrading
from IPython.nbformat.v4 import upgrade
nb = upgrade(nb)
import IPython.nbformat.v4.nbjson as nbjson
# Convert nb to json format
filestr = nbjson.writes(nb)
elif nb_version == 4:
nb = new_notebook(cells=nb_cells)
from IPython.nbformat import writes
filestr = writes(nb, version=4)
return filestr
def ipynb_code(filestr, code_blocks, code_block_types,
tex_blocks, format):
"""
# We expand all newcommands now
from html import embed_newcommands
newcommands = embed_newcommands(filestr)
if newcommands:
filestr = newcommands + filestr
"""
# Fix pandoc citations to normal internal links: [[key]](#key)
filestr = re.sub(r'\[@(.+?)\]', r'[[\g<1>]](#\g<1>)', filestr)
# filestr becomes json list after this function so we must typeset
# envirs here. All envirs are typeset as pandoc_quote.
from common import _CODE_BLOCK, _MATH_BLOCK
envir_format = option('ipynb_admon=', 'paragraph')
# Remove all !bpop-!epop environments (they cause only problens and
# have no use)
for envir in 'pop', 'slidecell':
filestr = re.sub('^<!-- !b%s .*\n' % envir, '', filestr,
flags=re.MULTILINE)
filestr = re.sub('^<!-- !e%s .*\n' % envir, '', filestr,
flags=re.MULTILINE)
filestr = re.sub('^<!-- !bnotes.*?<!-- !enotes -->\n', '', filestr,
flags=re.DOTALL|re.MULTILINE)
filestr = re.sub('^<!-- !split -->\n', '', filestr, flags=re.MULTILINE)
from doconce import doconce_envirs
envirs = doconce_envirs()[8:-2]
for envir in envirs:
pattern = r'^!b%s(.*?)\n(.+?)\s*^!e%s' % (envir, envir)
if envir_format in ('quote', 'paragraph', 'hrule'):
def subst(m):
title = m.group(1).strip()
# Text size specified in parenthesis?
m2 = re.search('^\s*\((.+?)\)', title)
if title == '' and envir not in ('block', 'quote'):
title = envir.capitalize() + '.'
elif title.lower() == 'none':
title == ''
elif m2:
text_size = m2.group(1).lower()
title = title.replace('(%s)' % text_size, '').strip()
elif title and title[-1] not in ('.', ':', '!', '?'):
# Make sure the title ends with puncuation
title += '.'
# Recall that this formatting is called very late
# so native format must be used!
if title:
title = '**' + title + '**\n'
# Could also consider subsubsection formatting
block = m.group(2)
# Always use quote typesetting for quotes
if envir_format == 'quote' or envir == 'quote':
# Make Markdown quote of the block: lines start with >
lines = []
for line in block.splitlines():
# Just quote plain text
if not (_MATH_BLOCK in line or
_CODE_BLOCK in line or
line.startswith('FIGURE:') or
line.startswith('MOVIE:') or
line.startswith('|')):
lines.append('> ' + line)
else:
lines.append('\n' + line + '\n')
block = '\n'.join(lines) + '\n\n'
# Add quote and a blank line after title
if title:
title = '> ' + title + '>\n'
else:
# Add a blank line after title
if title:
title += '\n'
if envir_format == 'hrule':
# Native ------ does not work, use <hr/>
#text = '\n\n----------\n' + title + '----------\n' + \
# block + '\n----------\n\n'
text = '\n\n<hr/>\n' + title + \
block + '\n<hr/>\n\n'
else:
text = title + block + '\n\n'
return text
else:
errwarn('*** error: --ipynb_admon=%s is not supported' % envir_format)
filestr = re.sub(pattern, subst, filestr,
flags=re.DOTALL | re.MULTILINE)
# Fix pyshell and ipy interactive sessions: remove prompt and output.
# or split in multiple cells such that output comes out at the end of a cell
# Fix sys environments and use run prog.py so programs can be run in cell
# Insert %matplotlib inline in the first block using matplotlib
# Only typeset Python code as blocks, otherwise !bc environmens
# become plain indented Markdown.
from doconce import dofile_basename
from sets import Set
ipynb_tarfile = 'ipynb-%s-src.tar.gz' % dofile_basename
src_paths = Set()
mpl_inline = False
split_pyshell = option('ipynb_split_pyshell=', 'on')
if split_pyshell is None:
split_pyshell = False
elif split_pyshell in ('no', 'False', 'off'):
split_pyshell = False
else:
split_pyshell = True
ipynb_code_tp = [None]*len(code_blocks)
for i in range(len(code_blocks)):
# Check if continuation lines are in the code block, because
# doconce.py inserts a blank after the backslash
if '\\ \n' in code_blocks[i]:
code_blocks[i] = code_blocks[i].replace('\\ \n', '\\\n')
if not mpl_inline and (
re.search(r'import +matplotlib', code_blocks[i]) or \
re.search(r'from +matplotlib', code_blocks[i]) or \
re.search(r'import +scitools', code_blocks[i]) or \
re.search(r'from +scitools', code_blocks[i])):
code_blocks[i] = '%matplotlib inline\n\n' + code_blocks[i]
mpl_inline = True
tp = code_block_types[i]
if tp.endswith('-t'):
# Standard Markdown code with pandoc/github extension
language = tp[:-2]
language_spec = language2pandoc.get(language, '')
#code_blocks[i] = '\n' + indent_lines(code_blocks[i], format) + '\n'
code_blocks[i] = "```%s\n" % language_spec + \
indent_lines(code_blocks[i].strip(), format) + \
"```"
ipynb_code_tp[i] = 'markdown'
elif tp.startswith('pyshell') or tp.startswith('ipy'):
lines = code_blocks[i].splitlines()
last_cell_end = -1
if split_pyshell:
new_code_blocks = []
# Split for each output an put in separate cell
for j in range(len(lines)):
if lines[j].startswith('>>>') or lines[j].startswith('... '):
lines[j] = lines[j][4:]
elif lines[j].startswith('In ['): # IPython
lines[j] = ':'.join(lines[j].split(':')[1:]).strip()
elif lines[j].startswith(' ...: '): # IPython
lines[j] = lines[j][8:]
else:
# output (no prefix or Out)
lines[j] = ''
new_code_blocks.append(
'\n'.join(lines[last_cell_end+1:j+1]))
last_cell_end = j
code_blocks[i] = new_code_blocks
ipynb_code_tp[i] = 'cell'
else:
# Remove prompt and output lines; leave code executable in cell
for j in range(len(lines)):
if lines[j].startswith('>>> ') or lines[j].startswith('... '):
lines[j] = lines[j][4:]
elif lines[j].startswith('In ['):
lines[j] = ':'.join(lines[j].split(':')[1:]).strip()
else:
# output
lines[j] = ''
for j in range(lines.count('')):
lines.remove('')
code_blocks[i] = '\n'.join(lines)
ipynb_code_tp[i] = 'cell'
elif tp.startswith('sys'):
# Do we find execution of python file? If so, copy the file
# to separate subdir and make a run file command in a cell.
# Otherwise, it is just a plain verbatim Markdown block.
found_unix_lines = False
lines = code_blocks[i].splitlines()
for j in range(len(lines)):
m = re.search(r'(.+?>|\$) *python +([A-Za-z_0-9]+?\.py)',
lines[j])
if m:
name = m.group(2).strip()
if os.path.isfile(name):
src_paths.add(os.path.dirname(name))
lines[j] = '%%run "%s"' % fullpath
else:
found_unix_lines = True
src_paths = list(src_paths)
if src_paths and not found_unix_lines:
# This is a sys block with run commands only
code_blocks[i] = '\n'.join(lines)
ipynb_code_tp[i] = 'cell'
else:
# Standard Markdown code
code_blocks[i] = '\n'.join(lines)
code_blocks[i] = indent_lines(code_blocks[i], format)
ipynb_code_tp[i] = 'markdown'
elif tp.endswith('hid'):
ipynb_code_tp[i] = 'cell_hidden'
elif tp.startswith('py'):
ipynb_code_tp[i] = 'cell'
else:
# Should support other languages as well, but not for now
code_blocks[i] = indent_lines(code_blocks[i], format)
ipynb_code_tp[i] = 'markdown'
# figure_files and movie_files are global variables and contain
# all figures and movies referred to
src_paths = list(src_paths)
if figure_files:
src_paths += figure_files
if movie_files:
src_paths += movie_files
if src_paths:
# Make tar file with all the source dirs with files
# that need to be executed
os.system('tar cfz %s %s' % (ipynb_tarfile, ' '.join(src_paths)))
errwarn('collected all required additional files in ' + ipynb_tarfile + ' which must be distributed with the notebook')
elif os.path.isfile(ipynb_tarfile):
os.remove(ipynb_tarfile)
# Parse document into markdown text, code blocks, and tex blocks.
# Store in nested list notebook_blocks.
notebook_blocks = [[]]
authors = ''
for line in filestr.splitlines():
if line.startswith('authors = [new_author(name='): # old author method
authors = line[10:]
elif _CODE_BLOCK in line:
code_block_tp = line.split()[-1]
if code_block_tp in ('pyhid',) or not code_block_tp.endswith('hid'):
notebook_blocks[-1] = '\n'.join(notebook_blocks[-1]).strip()
notebook_blocks.append(line)
# else: hidden block to be dropped (may include more languages
# with time in the above tuple)
elif _MATH_BLOCK in line:
notebook_blocks[-1] = '\n'.join(notebook_blocks[-1]).strip()
notebook_blocks.append(line)
else:
if not isinstance(notebook_blocks[-1], list):
notebook_blocks.append([])
notebook_blocks[-1].append(line)
if isinstance(notebook_blocks[-1], list):
notebook_blocks[-1] = '\n'.join(notebook_blocks[-1]).strip()
# Add block type info
pattern = r'(\d+) +%s'
for i in range(len(notebook_blocks)):
if re.match(pattern % _CODE_BLOCK, notebook_blocks[i]):
m = re.match(pattern % _CODE_BLOCK, notebook_blocks[i])
idx = int(m.group(1))
if ipynb_code_tp[idx] == 'cell':
notebook_blocks[i] = ['cell', notebook_blocks[i]]
elif ipynb_code_tp[idx] == 'cell_hidden':
notebook_blocks[i] = ['cell_hidden', notebook_blocks[i]]
else:
notebook_blocks[i] = ['text', notebook_blocks[i]]
elif re.match(pattern % _MATH_BLOCK, notebook_blocks[i]):
notebook_blocks[i] = ['math', notebook_blocks[i]]
else:
notebook_blocks[i] = ['text', notebook_blocks[i]]
# Go through tex_blocks and wrap in $$
# (doconce.py runs align2equations so there are no align/align*
# environments in tex blocks)
label2tag = {}
tag_counter = 1
for i in range(len(tex_blocks)):
# Extract labels and add tags
labels = re.findall(r'label\{(.+?)\}', tex_blocks[i])
for label in labels:
label2tag[label] = tag_counter
# Insert tag to get labeled equation
tex_blocks[i] = tex_blocks[i].replace(
'label{%s}' % label, 'label{%s} \\tag{%s}' % (label, tag_counter))
tag_counter += 1
# Remove \[ and \] or \begin/end{equation*} in single equations
tex_blocks[i] = tex_blocks[i].replace(r'\[', '')
tex_blocks[i] = tex_blocks[i].replace(r'\]', '')
tex_blocks[i] = tex_blocks[i].replace(r'\begin{equation*}', '')
tex_blocks[i] = tex_blocks[i].replace(r'\end{equation*}', '')
# Check for illegal environments
m = re.search(r'\\begin\{(.+?)\}', tex_blocks[i])
if m:
envir = m.group(1)
if envir not in ('equation', 'equation*', 'align*', 'align',
'array'):
errwarn("""\
*** warning: latex envir \\begin{%s} does not work well in Markdown.
Stick to \\[ ... \\], equation, equation*, align, or align*
environments in math environments.
""" % envir)
eq_type = 'heading' # or '$$'
eq_type = '$$'
# Markdown: add $$ on each side of the equation
if eq_type == '$$':
# Make sure there are no newline after equation
tex_blocks[i] = '$$\n' + tex_blocks[i].strip() + '\n$$'
# Here: use heading (###) and simple formula (remove newline
# in math expressions to keep everything within a heading) as
# the equation then looks bigger
elif eq_type == 'heading':
tex_blocks[i] = '### $ ' + ' '.join(tex_blocks[i].splitlines()) + ' $'
# Add labels for the eqs above the block (for reference)
if labels:
#label_tp = '<a name="%s"></a>'
label_tp = '<div id="%s"></div>'
tex_blocks[i] = '<!-- Equation labels as ordinary links -->\n' + \
' '.join([label_tp % label
for label in labels]) + '\n\n' + \
tex_blocks[i]
# blocks is now a list of text chunks in markdown and math/code line
# instructions. Insert code and tex blocks
for i in range(len(notebook_blocks)):
if _CODE_BLOCK in notebook_blocks[i][1] or _MATH_BLOCK in notebook_blocks[i][1]:
words = notebook_blocks[i][1].split()
# start of notebook_blocks[i]: number block-indicator code-type
n = int(words[0])
if _CODE_BLOCK in notebook_blocks[i][1]:
notebook_blocks[i][1] = code_blocks[n] # can be list!
if _MATH_BLOCK in notebook_blocks[i][1]:
notebook_blocks[i][1] = tex_blocks[n]
# Make IPython structures
nb_version = int(option('ipynb_version=', '4'))
if nb_version == 3:
try:
from IPython.nbformat.v3 import (
new_code_cell, new_text_cell, new_worksheet,
new_notebook, new_metadata, new_author)
nb = new_worksheet()
except ImportError:
errwarn('*** error: could not import IPython.nbformat.v3!')
errwarn(' set --ipynb_version=4 or leave out --ipynb_version=3')
_abort()
elif nb_version == 4:
try:
from nbformat.v4 import (
new_code_cell, new_markdown_cell, new_notebook)
except ImportError:
# Try old style
try:
from IPython.nbformat.v4 import (
new_code_cell, new_markdown_cell, new_notebook)
except ImportError:
errwarn('*** error: cannot do import nbformat.v4 or IPython.nbformat.v4')
errwarn(' make sure IPython notebook or Jupyter is installed correctly')
_abort()
cells = []
mdstr = [] # plain md format of the notebook
prompt_number = 1
for block_tp, block in notebook_blocks:
if (block_tp == 'text' or block_tp == 'math') and block != '':
# Pure comments between math/code and math/code come
# out as empty blocks, should detect that situation
# (challenging - can have multiple lines of comments,
# or begin and end comment lines with important things between)
if nb_version == 3:
nb.cells.append(new_text_cell(u'markdown', source=block))
elif nb_version == 4:
cells.append(new_markdown_cell(source=block))
mdstr.append(('markdown', block))
elif block_tp == 'cell' and block != '' and block != []:
if isinstance(block, list):
for block_ in block:
block_ = block_.rstrip()
if block_ != '':
if nb_version == 3:
nb.cells.append(new_code_cell(
input=block_,
prompt_number=prompt_number,
collapsed=False))
elif nb_version == 4:
cells.append(new_code_cell(
source=block_,
execution_count=prompt_number,
metadata=dict(collapsed=False)))
prompt_number += 1
mdstr.append(('codecell', block_))
else:
block = block.rstrip()
if block != '':
if nb_version == 3:
nb.cells.append(new_code_cell(
input=block,
prompt_number=prompt_number,
collapsed=False))
elif nb_version == 4:
cells.append(new_code_cell(
source=block,
execution_count=prompt_number,
metadata=dict(collapsed=False)))
prompt_number += 1
mdstr.append(('codecell', block))
elif block_tp == 'cell_hidden' and block != '':
block = block.rstrip()
if nb_version == 3:
nb.cells.append(new_code_cell(
input=block, prompt_number=prompt_number, collapsed=True))
elif nb_version == 4:
cells.append(new_code_cell(
source=block,
execution_count=prompt_number,
metadata=dict(collapsed=True)))
prompt_number += 1
mdstr.append(('codecell', block))
"""
# Dump the notebook cells in a simple ASCII format
# (doc/src/ipynb/ipynb_generator.py can translate it back to .ipynb file)
f = open(dofile_basename + '.md-ipynb', 'w')
for cell_tp, block in mdstr:
if cell_tp == 'markdown':
f.write('\n-----\n\n')
elif cell_tp == 'codecell':
f.write('\n-----py\n\n')
f.write(block)
f.close()
"""
if nb_version == 3:
# Catch the title as the first heading
m = re.search(r'^#+\s*(.+)$', filestr, flags=re.MULTILINE)
title = m.group(1).strip() if m else ''
# md below is not used for anything
if authors:
authors = eval(authors)
md = new_metadata(name=title, authors=authors)
else:
md = new_metadata(name=title)
nb = new_notebook(worksheets=[nb], metadata=new_metadata())
# Let us make v4 notebook here by upgrading
from IPython.nbformat.v4 import upgrade
nb = upgrade(nb)
import IPython.nbformat.v4.nbjson as nbjson
# Convert nb to json format
filestr = nbjson.writes(nb)
elif nb_version == 4:
nb = new_notebook(cells=cells)
from IPython.nbformat import writes
filestr = writes(nb, version=4)
# Check that there are no empty cells:
if '"input": []' in filestr:
errwarn('*** error: empty cells in notebook - report bug in DocOnce')
_abort()
# must do the replacements here at the very end when json is written out
# \eqref and labels will not work, but labels (only in math) do no harm
filestr = re.sub(r'([^\\])label\{', r'\g<1>\\\\label{', filestr,
flags=re.MULTILINE)
# \\eqref{} just gives (???) link at this stage - future versions
# will probably support labels
#filestr = re.sub(r'\(ref\{(.+?)\}\)', r'\\eqref{\g<1>}', filestr)
# Now we use explicit references to tags
def subst(m):
label = m.group(1)
try:
return r'[(%s)](#%s)' % (label2tag[label], label)
except KeyError as e:
errwarn('*** error: label "%s" is not defined' % str(e))
filestr = re.sub(r'\(ref\{(.+?)\}\)', subst, filestr)
"""
# MathJax reference to tag (recall that the equations have both label
# and tag (know that tag only works well in HTML, but this mjx-eqn-no
# label does not work in ipynb)
filestr = re.sub(r'\(ref\{(.+?)\}\)',
lambda m: r'[(%s)](#mjx-eqn-%s)' % (label2tag[m.group(1)], label2tag[m.group(1)]), filestr)
"""
#filestr = re.sub(r'\(ref\{(.+?)\}\)', r'Eq (\g<1>)', filestr)
'''
# Final fixes: replace all text between cells by markdown code cells
# Note: the patterns are overlapping so a plain re.sub will not work,
# here we run through all blocks found and subsitute the first remaining
# one, one by one.
pattern = r' \},\n(.+?)\{\n "cell_type":'
begin_pattern = r'^(.+?)\{\n "cell_type":'
remaining_block_begin = re.findall(begin_pattern, filestr, flags=re.DOTALL)
remaining_blocks = re.findall(pattern, filestr, flags=re.DOTALL)
import string
for block in remaining_block_begin + remaining_blocks:
filestr = string.replace(filestr, block, json_markdown(block) + ' ',
maxreplace=1)
filestr_end = re.sub(r' \{\n "cell_type": .+?\n \},\n', '', filestr,
flags=re.DOTALL)
filestr = filestr.replace(filestr_end, json_markdown(filestr_end))
filestr = """{
"metadata": {
"name": "SOME NAME"
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
""" + filestr.rstrip() + '\n'+ \
json_pycode('', final_prompt_no+1, 'python').rstrip()[:-1] + """
],
"metadata": {}
}
]
}"""
'''
return filestr
def ipynb_code(filestr, code_blocks, code_block_types, tex_blocks, format):
"""
# We expand all newcommands now
from html import embed_newcommands
newcommands = embed_newcommands(filestr)
if newcommands:
filestr = newcommands + filestr
"""
# Fix pandoc citations to normal internal links: [[key]](#key)
filestr = re.sub(r'\[@(.+?)\]', r'[[\g<1>]](#\g<1>)', filestr)
# filestr becomes json list after this function so we must typeset
# envirs here. All envirs are typeset as pandoc_quote.
from .common import _CODE_BLOCK, _MATH_BLOCK
envir_format = option('ipynb_admon=', 'paragraph')
# Remove all !bpop-!epop environments (they cause only problens and
# have no use)
for envir in 'pop', 'slidecell':
filestr = re.sub('^<!-- !b%s .*\n' % envir,
'',
filestr,
flags=re.MULTILINE)
filestr = re.sub('^<!-- !e%s .*\n' % envir,
'',
filestr,
flags=re.MULTILINE)
filestr = re.sub('^<!-- !bnotes.*?<!-- !enotes -->\n',
'',
filestr,
flags=re.DOTALL | re.MULTILINE)
filestr = re.sub('^<!-- !split -->\n', '', filestr, flags=re.MULTILINE)
from .doconce import doconce_envirs
envirs = doconce_envirs()[8:-2]
for envir in envirs:
pattern = r'^!b%s(.*?)\n(.+?)\s*^!e%s' % (envir, envir)
if envir_format in ('quote', 'paragraph', 'hrule'):
def subst(m):
title = m.group(1).strip()
# Text size specified in parenthesis?
m2 = re.search('^\s*\((.+?)\)', title)
if title == '' and envir not in ('block', 'quote'):
title = envir.capitalize() + '.'
elif title.lower() == 'none':
title == ''
elif m2:
text_size = m2.group(1).lower()
title = title.replace('(%s)' % text_size, '').strip()
elif title and title[-1] not in ('.', ':', '!', '?'):
# Make sure the title ends with puncuation
title += '.'
# Recall that this formatting is called very late
# so native format must be used!
if title:
title = '**' + title + '**\n'
# Could also consider subsubsection formatting
block = m.group(2)
# Always use quote typesetting for quotes
if envir_format == 'quote' or envir == 'quote':
# Make Markdown quote of the block: lines start with >
lines = []
for line in block.splitlines():
# Just quote plain text
if not (_MATH_BLOCK in line or _CODE_BLOCK in line
or line.startswith('FIGURE:')
or line.startswith('MOVIE:')
or line.startswith('|')):
lines.append('> ' + line)
else:
lines.append('\n' + line + '\n')
block = '\n'.join(lines) + '\n\n'
# Add quote and a blank line after title
if title:
title = '> ' + title + '>\n'
else:
# Add a blank line after title
if title:
title += '\n'
if envir_format == 'hrule':
# Native ------ does not work, use <hr/>
#text = '\n\n----------\n' + title + '----------\n' + \
# block + '\n----------\n\n'
text = '\n\n<hr/>\n' + title + \
block + '\n<hr/>\n\n'
else:
text = title + block + '\n\n'
return text
else:
errwarn('*** error: --ipynb_admon=%s is not supported' %
envir_format)
filestr = re.sub(pattern,
subst,
filestr,
flags=re.DOTALL | re.MULTILINE)
# Fix pyshell and ipy interactive sessions: remove prompt and output.
# or split in multiple cells such that output comes out at the end of a cell
# Fix sys environments and use run prog.py so programs can be run in cell
# Insert %matplotlib inline in the first block using matplotlib
# Only typeset Python code as blocks, otherwise !bc environmens
# become plain indented Markdown.
from .doconce import dofile_basename
ipynb_tarfile = 'ipynb-%s-src.tar.gz' % dofile_basename
src_paths = set()
mpl_inline = False
split_pyshell = option('ipynb_split_pyshell=', 'on')
if split_pyshell is None:
split_pyshell = False
elif split_pyshell in ('no', 'False', 'off'):
split_pyshell = False
else:
split_pyshell = True
ipynb_code_tp = [None] * len(code_blocks)
for i in range(len(code_blocks)):
# Check if continuation lines are in the code block, because
# doconce.py inserts a blank after the backslash
if '\\ \n' in code_blocks[i]:
code_blocks[i] = code_blocks[i].replace('\\ \n', '\\\n')
if not mpl_inline and (
re.search(r'import +matplotlib', code_blocks[i]) or \
re.search(r'from +matplotlib', code_blocks[i]) or \
re.search(r'import +scitools', code_blocks[i]) or \
re.search(r'from +scitools', code_blocks[i])):
code_blocks[i] = '%matplotlib inline\n\n' + code_blocks[i]
mpl_inline = True
tp = code_block_types[i]
if tp.endswith('-t'):
# Standard Markdown code with pandoc/github extension
language = tp[:-2]
language_spec = language2pandoc.get(language, '')
#code_blocks[i] = '\n' + indent_lines(code_blocks[i], format) + '\n'
code_blocks[i] = "```%s\n" % language_spec + \
indent_lines(code_blocks[i].strip(), format) + \
"```"
ipynb_code_tp[i] = 'markdown'
elif tp.startswith('pyshell') or tp.startswith('ipy'):
lines = code_blocks[i].splitlines()
last_cell_end = -1
if split_pyshell:
new_code_blocks = []
# Split for each output an put in separate cell
for j in range(len(lines)):
if lines[j].startswith('>>>') or lines[j].startswith(
'... '):
lines[j] = lines[j][4:]
elif lines[j].startswith('In ['): # IPython
lines[j] = ':'.join(lines[j].split(':')[1:]).strip()
elif lines[j].startswith(' ...: '): # IPython
lines[j] = lines[j][8:]
else:
# output (no prefix or Out)
lines[j] = ''
new_code_blocks.append('\n'.join(lines[last_cell_end +
1:j + 1]))
last_cell_end = j
code_blocks[i] = new_code_blocks
ipynb_code_tp[i] = 'cell'
else:
# Remove prompt and output lines; leave code executable in cell
for j in range(len(lines)):
if lines[j].startswith('>>> ') or lines[j].startswith(
'... '):
lines[j] = lines[j][4:]
elif lines[j].startswith('In ['):
lines[j] = ':'.join(lines[j].split(':')[1:]).strip()
else:
# output
lines[j] = ''
for j in range(lines.count('')):
lines.remove('')
code_blocks[i] = '\n'.join(lines)
ipynb_code_tp[i] = 'cell'
elif tp.startswith('sys'):
# Do we find execution of python file? If so, copy the file
# to separate subdir and make a run file command in a cell.
# Otherwise, it is just a plain verbatim Markdown block.
found_unix_lines = False
lines = code_blocks[i].splitlines()
for j in range(len(lines)):
m = re.search(r'(.+?>|\$) *python +([A-Za-z_0-9]+?\.py)',
lines[j])
if m:
name = m.group(2).strip()
if os.path.isfile(name):
src_paths.add(os.path.dirname(name))
lines[j] = '%%run "%s"' % fullpath
else:
found_unix_lines = True
src_paths = list(src_paths)
if src_paths and not found_unix_lines:
# This is a sys block with run commands only
code_blocks[i] = '\n'.join(lines)
ipynb_code_tp[i] = 'cell'
else:
# Standard Markdown code
code_blocks[i] = '\n'.join(lines)
code_blocks[i] = indent_lines(code_blocks[i], format)
ipynb_code_tp[i] = 'markdown'
elif tp.endswith('hid'):
ipynb_code_tp[i] = 'cell_hidden'
elif tp.endswith('out'):
ipynb_code_tp[i] = 'cell_output'
elif tp.startswith('py'):
ipynb_code_tp[i] = 'cell'
else:
# Should support other languages as well, but not for now
code_blocks[i] = indent_lines(code_blocks[i], format)
ipynb_code_tp[i] = 'markdown'
# figure_files and movie_files are global variables and contain
# all figures and movies referred to
src_paths = list(src_paths)
if figure_files:
src_paths += figure_files
if movie_files:
src_paths += movie_files
if src_paths:
# Make tar file with all the source dirs with files
# that need to be executed
os.system('tar cfz %s %s' % (ipynb_tarfile, ' '.join(src_paths)))
errwarn('collected all required additional files in ' + ipynb_tarfile +
' which must be distributed with the notebook')
elif os.path.isfile(ipynb_tarfile):
os.remove(ipynb_tarfile)
# Parse document into markdown text, code blocks, and tex blocks.
# Store in nested list notebook_blocks.
notebook_blocks = [[]]
authors = ''
for line in filestr.splitlines():
if line.startswith('authors = [new_author(name='): # old author method
authors = line[10:]
elif _CODE_BLOCK in line:
code_block_tp = line.split()[-1]
if code_block_tp in (
'pyhid', ) or not code_block_tp.endswith('hid'):
notebook_blocks[-1] = '\n'.join(notebook_blocks[-1]).strip()
notebook_blocks.append(line)
# else: hidden block to be dropped (may include more languages
# with time in the above tuple)
elif _MATH_BLOCK in line:
notebook_blocks[-1] = '\n'.join(notebook_blocks[-1]).strip()
notebook_blocks.append(line)
else:
if not isinstance(notebook_blocks[-1], list):
notebook_blocks.append([])
notebook_blocks[-1].append(line)
if isinstance(notebook_blocks[-1], list):
notebook_blocks[-1] = '\n'.join(notebook_blocks[-1]).strip()
# Add block type info
pattern = r'(\d+) +%s'
for i in range(len(notebook_blocks)):
if re.match(pattern % _CODE_BLOCK, notebook_blocks[i]):
m = re.match(pattern % _CODE_BLOCK, notebook_blocks[i])
idx = int(m.group(1))
if ipynb_code_tp[idx] == 'cell':
notebook_blocks[i] = ['cell', notebook_blocks[i]]
elif ipynb_code_tp[idx] == 'cell_hidden':
notebook_blocks[i] = ['cell_hidden', notebook_blocks[i]]
elif ipynb_code_tp[idx] == 'cell_output':
notebook_blocks[i] = ['cell_output', notebook_blocks[i]]
else:
notebook_blocks[i] = ['text', notebook_blocks[i]]
elif re.match(pattern % _MATH_BLOCK, notebook_blocks[i]):
notebook_blocks[i] = ['math', notebook_blocks[i]]
else:
notebook_blocks[i] = ['text', notebook_blocks[i]]
# Go through tex_blocks and wrap in $$
# (doconce.py runs align2equations so there are no align/align*
# environments in tex blocks)
label2tag = {}
tag_counter = 1
for i in range(len(tex_blocks)):
# Extract labels and add tags
labels = re.findall(r'label\{(.+?)\}', tex_blocks[i])
for label in labels:
label2tag[label] = tag_counter
# Insert tag to get labeled equation
tex_blocks[i] = tex_blocks[i].replace(
'label{%s}' % label,
'label{%s} \\tag{%s}' % (label, tag_counter))
tag_counter += 1
# Remove \[ and \] or \begin/end{equation*} in single equations
tex_blocks[i] = tex_blocks[i].replace(r'\[', '')
tex_blocks[i] = tex_blocks[i].replace(r'\]', '')
tex_blocks[i] = tex_blocks[i].replace(r'\begin{equation*}', '')
tex_blocks[i] = tex_blocks[i].replace(r'\end{equation*}', '')
# Check for illegal environments
m = re.search(r'\\begin\{(.+?)\}', tex_blocks[i])
if m:
envir = m.group(1)
if envir not in ('equation', 'equation*', 'align*', 'align',
'array'):
errwarn("""\
*** warning: latex envir \\begin{%s} does not work well in Markdown.
Stick to \\[ ... \\], equation, equation*, align, or align*
environments in math environments.
""" % envir)
eq_type = 'heading' # or '$$'
eq_type = '$$'
# Markdown: add $$ on each side of the equation
if eq_type == '$$':
# Make sure there are no newline after equation
tex_blocks[i] = '$$\n' + tex_blocks[i].strip() + '\n$$'
# Here: use heading (###) and simple formula (remove newline
# in math expressions to keep everything within a heading) as
# the equation then looks bigger
elif eq_type == 'heading':
tex_blocks[i] = '### $ ' + ' '.join(
tex_blocks[i].splitlines()) + ' $'
# Add labels for the eqs above the block (for reference)
if labels:
#label_tp = '<a name="%s"></a>'
label_tp = '<div id="%s"></div>'
tex_blocks[i] = '<!-- Equation labels as ordinary links -->\n' + \
' '.join([label_tp % label
for label in labels]) + '\n\n' + \
tex_blocks[i]
# blocks is now a list of text chunks in markdown and math/code line
# instructions. Insert code and tex blocks
for i in range(len(notebook_blocks)):
if _CODE_BLOCK in notebook_blocks[i][
1] or _MATH_BLOCK in notebook_blocks[i][1]:
words = notebook_blocks[i][1].split()
# start of notebook_blocks[i]: number block-indicator code-type
n = int(words[0])
if _CODE_BLOCK in notebook_blocks[i][1]:
notebook_blocks[i][1] = code_blocks[n] # can be list!
if _MATH_BLOCK in notebook_blocks[i][1]:
notebook_blocks[i][1] = tex_blocks[n]
# Make IPython structures
nb_version = int(option('ipynb_version=', '4'))
if nb_version == 3:
try:
from IPython.nbformat.v3 import (new_code_cell, new_text_cell,
new_worksheet, new_notebook,
new_metadata, new_author)
nb = new_worksheet()
except ImportError:
errwarn('*** error: could not import IPython.nbformat.v3!')
errwarn(' set --ipynb_version=4 or leave out --ipynb_version=3')
_abort()
elif nb_version == 4:
try:
from nbformat.v4 import (new_code_cell, new_markdown_cell,
new_notebook)
except ImportError:
# Try old style
try:
from IPython.nbformat.v4 import (new_code_cell,
new_markdown_cell,
new_notebook)
except ImportError:
errwarn(
'*** error: cannot do import nbformat.v4 or IPython.nbformat.v4'
)
errwarn(
' make sure IPython notebook or Jupyter is installed correctly'
)
_abort()
cells = []
mdstr = [] # plain md format of the notebook
prompt_number = 1
for block_tp, block in notebook_blocks:
if (block_tp == 'text' or block_tp
== 'math') and block != '' and block != '<!-- -->':
if nb_version == 3:
nb.cells.append(new_text_cell(u'markdown', source=block))
elif nb_version == 4:
cells.append(new_markdown_cell(source=block))
mdstr.append(('markdown', block))
elif block_tp == 'cell' and block != '' and block != []:
if isinstance(block, list):
for block_ in block:
block_ = block_.rstrip()
if block_ != '':
if nb_version == 3:
nb.cells.append(
new_code_cell(input=block_,
prompt_number=prompt_number,
collapsed=False))
elif nb_version == 4:
cells.append(
new_code_cell(source=block_,
execution_count=prompt_number,
metadata=dict(collapsed=False)))
prompt_number += 1
mdstr.append(('codecell', block_))
else:
block = block.rstrip()
if block != '':
if nb_version == 3:
nb.cells.append(
new_code_cell(input=block,
prompt_number=prompt_number,
collapsed=False))
elif nb_version == 4:
cells.append(
new_code_cell(source=block,
execution_count=prompt_number,
metadata=dict(collapsed=False)))
prompt_number += 1
mdstr.append(('codecell', block))
elif block_tp == 'cell_output' and block != '':
block = block.rstrip()
if nb_version == 3:
print("WARNING: Output not implemented for nbformat v3.")
elif nb_version == 4:
outputs = [{
"data": {
"text/plain": [block]
},
"execution_count": prompt_number - 1,
"metadata": {},
"output_type": "execute_result"
}]
previous_cell = cells[-1]
if previous_cell.cell_type == "code":
previous_cell.outputs = outputs
else:
print("WARNING: DocOnce ipynb got code output,",
"but previous was not code.")
cells.append(
new_code_cell(source="#",
outputs=outputs,
execution_count=prompt_number,
metadata=dict(collapsed=False)))
mdstr.append(('codecell', block))
elif block_tp == 'cell_hidden' and block != '':
block = block.rstrip()
if nb_version == 3:
nb.cells.append(
new_code_cell(input=block,
prompt_number=prompt_number,
collapsed=True))
elif nb_version == 4:
cells.append(
new_code_cell(source=block,
execution_count=prompt_number,
metadata=dict(collapsed=True)))
prompt_number += 1
mdstr.append(('codecell', block))
"""
# Dump the notebook cells in a simple ASCII format
# (doc/src/ipynb/ipynb_generator.py can translate it back to .ipynb file)
f = open(dofile_basename + '.md-ipynb', 'w')
for cell_tp, block in mdstr:
if cell_tp == 'markdown':
f.write('\n-----\n\n')
elif cell_tp == 'codecell':
f.write('\n-----py\n\n')
f.write(block)
f.close()
"""
if nb_version == 3:
# Catch the title as the first heading
m = re.search(r'^#+\s*(.+)$', filestr, flags=re.MULTILINE)
title = m.group(1).strip() if m else ''
# md below is not used for anything
if authors:
authors = eval(authors)
md = new_metadata(name=title, authors=authors)
else:
md = new_metadata(name=title)
nb = new_notebook(worksheets=[nb], metadata=new_metadata())
# Let us make v4 notebook here by upgrading
from IPython.nbformat.v4 import upgrade
nb = upgrade(nb)
import IPython.nbformat.v4.nbjson as nbjson
# Convert nb to json format
filestr = nbjson.writes(nb)
elif nb_version == 4:
nb = new_notebook(cells=cells)
try:
from nbformat import writes
except ImportError:
from IPython.nbformat import writes
filestr = writes(nb, version=4)
# Check that there are no empty cells:
if '"input": []' in filestr:
errwarn('*** error: empty cells in notebook - report bug in DocOnce')
_abort()
# must do the replacements here at the very end when json is written out
# \eqref and labels will not work, but labels (only in math) do no harm
filestr = re.sub(r'([^\\])label\{',
r'\g<1>\\\\label{',
filestr,
flags=re.MULTILINE)
# \\eqref{} just gives (???) link at this stage - future versions
# will probably support labels
#filestr = re.sub(r'\(ref\{(.+?)\}\)', r'\\eqref{\g<1>}', filestr)
# Now we use explicit references to tags
def subst(m):
label = m.group(1)
try:
return r'[(%s)](#%s)' % (label2tag[label], label)
except KeyError as e:
errwarn('*** error: label "%s" is not defined' % str(e))
filestr = re.sub(r'\(ref\{(.+?)\}\)', subst, filestr)
"""
# MathJax reference to tag (recall that the equations have both label
# and tag (know that tag only works well in HTML, but this mjx-eqn-no
# label does not work in ipynb)
filestr = re.sub(r'\(ref\{(.+?)\}\)',
lambda m: r'[(%s)](#mjx-eqn-%s)' % (label2tag[m.group(1)], label2tag[m.group(1)]), filestr)
"""
#filestr = re.sub(r'\(ref\{(.+?)\}\)', r'Eq (\g<1>)', filestr)
'''
# Final fixes: replace all text between cells by markdown code cells
# Note: the patterns are overlapping so a plain re.sub will not work,
# here we run through all blocks found and subsitute the first remaining
# one, one by one.
pattern = r' \},\n(.+?)\{\n "cell_type":'
begin_pattern = r'^(.+?)\{\n "cell_type":'
remaining_block_begin = re.findall(begin_pattern, filestr, flags=re.DOTALL)
remaining_blocks = re.findall(pattern, filestr, flags=re.DOTALL)
import string
for block in remaining_block_begin + remaining_blocks:
filestr = string.replace(filestr, block, json_markdown(block) + ' ',
maxreplace=1)
filestr_end = re.sub(r' \{\n "cell_type": .+?\n \},\n', '', filestr,
flags=re.DOTALL)
filestr = filestr.replace(filestr_end, json_markdown(filestr_end))
filestr = """{
"metadata": {
"name": "SOME NAME"
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
""" + filestr.rstrip() + '\n'+ \
json_pycode('', final_prompt_no+1, 'python').rstrip()[:-1] + """
],
"metadata": {}
}
]
}"""
'''
return filestr