last commit did not include nbconvert.py change to not reread the file -- adding now

nbconvert.py

@@ -1,863 +1,864 b''
 #!/usr/bin/env python
 """Convert IPython notebooks to other formats, such as ReST, and HTML.
 
 Example:
   ./nbconvert.py --format html file.ipynb
 
 Produces 'file.rst' and 'file.html', along with auto-generated figure files
 called nb_figure_NN.png. To avoid the two-step process, ipynb -> rst -> html,
 use '--format quick-html' which will do ipynb -> html, but won't look as
 pretty.
 """
 #-----------------------------------------------------------------------------
 # Imports
 #-----------------------------------------------------------------------------
 from __future__ import print_function
 
 # Stdlib
 import codecs
 import logging
 import os
 import pprint
 import re
 import subprocess
 import sys
 import json
 import copy
 from shutil import rmtree
 
 inkscape = 'inkscape'
 if sys.platform == 'darwin':
     inkscape = '/Applications/Inkscape.app/Contents/Resources/bin/inkscape'
     if not os.path.exists(inkscape):
         inkscape = None
 
 # From IPython
 from IPython.external import argparse
 from IPython.nbformat import current as nbformat
 from IPython.utils.text import indent
 from decorators import DocInherit
 from IPython.nbformat.v3.nbjson import BytesEncoder
 from IPython.utils import py3compat
 
 #-----------------------------------------------------------------------------
 # Utility functions
 #-----------------------------------------------------------------------------
 
 def DocInherit(f):
     return f
 
 def remove_fake_files_url(cell):
     """Remove from the cell source the /files/ pseudo-path we use.
     """
     src = cell.source
     cell.source = src.replace('/files/', '')
 
 
 def remove_ansi(src):
     """Strip all ANSI color escape sequences from input string.
 
     Parameters
     ----------
     src : string
 
     Returns
     -------
     string
     """
     return re.sub(r'\033\[(0|\d;\d\d)m', '', src)
 
 
 # Pandoc-dependent code
 def markdown2latex(src):
     """Convert a markdown string to LaTeX via pandoc.
 
     This function will raise an error if pandoc is not installed.
 
     Any error messages generated by pandoc are printed to stderr.
 
     Parameters
     ----------
     src : string
       Input string, assumed to be valid markdown.
 
     Returns
     -------
     out : string
       Output as returned by pandoc.
     """
     p = subprocess.Popen('pandoc -f markdown -t latex'.split(),
                          stdin=subprocess.PIPE, stdout=subprocess.PIPE)
     out, err = p.communicate(src.encode('utf-8'))
     if err:
         print(err, file=sys.stderr)
     #print('*'*20+'\n', out, '\n'+'*'*20)  # dbg
     return unicode(out,'utf-8')
 
 
 def markdown2rst(src):
     """Convert a markdown string to LaTeX via pandoc.
 
     This function will raise an error if pandoc is not installed.
 
     Any error messages generated by pandoc are printed to stderr.
 
     Parameters
     ----------
     src : string
       Input string, assumed to be valid markdown.
 
     Returns
     -------
     out : string
       Output as returned by pandoc.
     """
     p = subprocess.Popen('pandoc -f markdown -t rst'.split(),
                          stdin=subprocess.PIPE, stdout=subprocess.PIPE)
     out, err = p.communicate(src.encode('utf-8'))
     if err:
         print(err, file=sys.stderr)
     #print('*'*20+'\n', out, '\n'+'*'*20)  # dbg
     return unicode(out,'utf-8')
 
 
 def rst_directive(directive, text=''):
     out = [directive, '']
     if text:
         out.extend([indent(text), ''])
     return out
 
 #-----------------------------------------------------------------------------
 # Class declarations
 #-----------------------------------------------------------------------------
 
 class ConversionException(Exception):
     pass
 
 
 class Converter(object):
     default_encoding = 'utf-8'
     extension = str()
     figures_counter = 0
     infile = str()
     infile_dir = str()
     infile_root = str()
     files_dir = str()
     with_preamble = True
     user_preamble = None
     output = str()
     raw_as_verbatim = False
         
     def __init__(self, infile):
         self.infile = infile
         self.infile_dir = os.path.dirname(infile)
         infile_root = os.path.splitext(infile)[0]
         files_dir = infile_root + '_files'
         if not os.path.isdir(files_dir):
             os.mkdir(files_dir)
         self.infile_root = infile_root
         self.files_dir = files_dir
         self.outbase = infile_root
 
     def dispatch(self, cell_type):
         """return cell_type dependent render method,  for example render_code
         """
         return getattr(self, 'render_' + cell_type, self.render_unknown)
 
     def convert(self, cell_separator='\n'):
         lines = []
         lines.extend(self.optional_header())
         converted_cells = []
         for worksheet in self.nb.worksheets:
             for cell in worksheet.cells:
                 #print(cell.cell_type)  # dbg
                 conv_fn = self.dispatch(cell.cell_type)
                 if cell.cell_type in ('markdown', 'raw'):
                     remove_fake_files_url(cell)
                 converted_cells.append('\n'.join(conv_fn(cell)))
         cell_lines = cell_separator.join(converted_cells).split('\n')
         lines.extend(cell_lines)
         lines.extend(self.optional_footer())
         return u'\n'.join(lines)
 
     def render(self):
         "read, convert, and save self.infile"
-        self.read()
+        if not hasattr(self, 'nb'):
+            self.read()
         self.output = self.convert()
         return self.save()
 
     def read(self):
         "read and parse notebook into NotebookNode called self.nb"
         with open(self.infile) as f:
             self.nb = nbformat.read(f, 'json')
 
     def save(self, outfile=None, encoding=None):
         "read and parse notebook into self.nb"
         if outfile is None:
             outfile = self.outbase + '.' + self.extension
         if encoding is None:
             encoding = self.default_encoding
         with open(outfile, 'w') as f:
             f.write(self.output.encode(encoding))
         return os.path.abspath(outfile)
 
     def optional_header(self):
         return []
 
     def optional_footer(self):
         return []
 
     def _new_figure(self, data, fmt):
         """Create a new figure file in the given format.
 
         Returns a path relative to the input file.
         """
         figname = '%s_fig_%02i.%s' % (self.infile_root, 
                                       self.figures_counter, fmt)
         self.figures_counter += 1
         fullname = os.path.join(self.files_dir, figname)
 
         # Binary files are base64-encoded, SVG is already XML
         if fmt in ('png', 'jpg', 'pdf'):
             data = data.decode('base64')
             fopen = lambda fname: open(fname, 'wb')
         else:
             fopen = lambda fname: codecs.open(fname, 'wb', self.default_encoding)
             
         with fopen(fullname) as f:
             f.write(data)
             
         return fullname
 
     def render_heading(self, cell):
         """convert a heading cell
 
         Returns list."""
         raise NotImplementedError
 
     def render_code(self, cell):
         """Convert a code cell
 
         Returns list."""
         raise NotImplementedError
 
     def render_markdown(self, cell):
         """convert a markdown cell
 
         Returns list."""
         raise NotImplementedError
 
     def render_pyout(self, output):
         """convert pyout part of a code cell
 
         Returns list."""
         raise NotImplementedError
 
 
     def render_pyerr(self, output):
         """convert pyerr part of a code cell
 
         Returns list."""
         raise NotImplementedError
 
     def _img_lines(self, img_file):
         """Return list of lines to include an image file."""
         # Note: subclasses may choose to implement format-specific _FMT_lines
         # methods if they so choose (FMT in {png, svg, jpg, pdf}).
         raise NotImplementedError
 
     def render_display_data(self, output):
         """convert display data from the output of a code cell
 
         Returns list.
         """
         lines = []
 
         for fmt in ['png', 'svg', 'jpg', 'pdf']:
             if fmt in output:
                 img_file = self._new_figure(output[fmt], fmt)
                 # Subclasses can have format-specific render functions (e.g.,
                 # latex has to auto-convert all SVG to PDF first).
                 lines_fun = getattr(self, '_%s_lines' % fmt, None)
                 if not lines_fun:
                     lines_fun = self._img_lines
                 lines.extend(lines_fun(img_file))
 
         return lines
 
     def render_stream(self, cell):
         """convert stream part of a code cell
 
         Returns list."""
         raise NotImplementedError
 
     def render_raw(self, cell):
         """convert a cell with raw text
 
         Returns list."""
         raise NotImplementedError
 
     def render_unknown(self, cell):
         """Render cells of unkown type
 
         Returns list."""
         data = pprint.pformat(cell)
         logging.warning('Unknown cell:\n%s' % data)
         return self._unknown_lines(data)
 
     def _unknown_lines(self, data):
         """Return list of lines for an unknown cell.
 
         Parameters
         ----------
         data : str
           The content of the unknown data as a single string.
         """
         raise NotImplementedError
 
 
 class ConverterRST(Converter):
     extension = 'rst'
     heading_level = {1: '=', 2: '-', 3: '`', 4: '\'', 5: '.', 6: '~'}
 
     @DocInherit
     def render_heading(self, cell):
         marker = self.heading_level[cell.level]
         return ['{0}\n{1}\n'.format(cell.source, marker * len(cell.source))]
 
     @DocInherit
     def render_code(self, cell):
         if not cell.input:
             return []
 
         lines = ['In[%s]:' % cell.prompt_number, '']
         lines.extend(rst_directive('.. code:: python', cell.input))
 
         for output in cell.outputs:
             conv_fn = self.dispatch(output.output_type)
             lines.extend(conv_fn(output))
 
         return lines
 
     @DocInherit
     def render_markdown(self, cell):
         #return [cell.source]
         return [markdown2rst(cell.source)]
 
     @DocInherit
     def render_raw(self, cell):
         if self.raw_as_verbatim:
             return ['::', '', indent(cell.source), '']
         else:
             return [cell.source]
 
     @DocInherit
     def render_pyout(self, output):
         lines = ['Out[%s]:' % output.prompt_number, '']
 
         # output is a dictionary like object with type as a key
         if 'latex' in output:
             lines.extend(rst_directive('.. math::', output.latex))
 
         if 'text' in output:
             lines.extend(rst_directive('.. parsed-literal::', output.text))
 
         return lines
 
     @DocInherit
     def render_pyerr(self, output):
         # Note: a traceback is a *list* of frames.
         return ['::', '', indent(remove_ansi('\n'.join(output.traceback))), '']
 
     @DocInherit
     def _img_lines(self, img_file):
         return ['.. image:: %s' % img_file, '']
     
     @DocInherit
     def render_stream(self, output):
         lines = []
 
         if 'text' in output:
             lines.extend(rst_directive('.. parsed-literal::', output.text))
 
         return lines
 
     @DocInherit
     def _unknown_lines(self, data):
         return rst_directive('.. warning:: Unknown cell') + [data]
 
 
 class ConverterQuickHTML(Converter):
     extension = 'html'
 
     def in_tag(self, tag, src):
         """Return a list of elements bracketed by the given tag"""
         return ['<%s>' % tag, src, '</%s>' % tag]
 
     def optional_header(self):
         # XXX: inject the IPython standard CSS into here
         s = """<html>
         <head>
         </head>
 
         <body>
         """
         return s.splitlines()
 
     def optional_footer(self):
         s = """</body>
         </html>
         """
         return s.splitlines()
 
     @DocInherit
     def render_heading(self, cell):
         marker = cell.level
         return ['<h{1}>\n  {0}\n</h{1}>'.format(cell.source, marker)]
 
     @DocInherit
     def render_code(self, cell):
         if not cell.input:
             return []
 
         lines = ['<table>']
         lines.append('<tr><td><tt>In [<b>%s</b>]:</tt></td><td><tt>' % cell.prompt_number)
         lines.append("<br>\n".join(cell.input.splitlines()))
         lines.append('</tt></td></tr>')
 
         for output in cell.outputs:
             lines.append('<tr><td></td><td>')
             conv_fn = self.dispatch(output.output_type)
             lines.extend(conv_fn(output))
             lines.append('</td></tr>')
         
         lines.append('</table>')
         return lines
 
     @DocInherit
     def render_markdown(self, cell):
         return self.in_tag('pre', cell.source)
 
     @DocInherit
     def render_raw(self, cell):
         if self.raw_as_verbatim:
             return self.in_tag('pre', cell.source)
         else:
             return [cell.source]
 
     @DocInherit
     def render_pyout(self, output):
         lines = ['<tr><td><tt>Out[<b>%s</b>]:</tt></td></tr>' % 
                  output.prompt_number, '<td>']
 
         # output is a dictionary like object with type as a key
         for out_type in ('text', 'latex'):
             if out_type in output:
                 lines.extend(self.in_tag('pre', indent(output[out_type])))
 
         return lines
 
     @DocInherit
     def render_pyerr(self, output):
         # Note: a traceback is a *list* of frames.
         return self.in_tag('pre', remove_ansi('\n'.join(output.traceback)))
 
     @DocInherit
     def _img_lines(self, img_file):
         return ['<img src="%s">' % img_file, '']
 
     @DocInherit
     def render_stream(self, output):
         lines = []
 
         if 'text' in output:
             lines.append(output.text)
 
         return lines
 
     @DocInherit
     def _unknown_lines(self, data):
         return ['<h2>Warning:: Unknown cell</h2>'] + self.in_tag('pre', data)
 
 
 class ConverterLaTeX(Converter):
     """Converts a notebook to a .tex file suitable for pdflatex.
 
     Note: this converter *needs*:
 
     - `pandoc`: for all conversion of markdown cells.  If your notebook only
        has Raw cells, pandoc will not be needed.
     
     -  `inkscape`: if your notebook has SVG figures.  These need to be
        converted to PDF before inclusion in the TeX file, as LaTeX doesn't
        understand SVG natively.
     
     You will in general obtain much better final PDF results if you configure
     the matplotlib backend to create SVG output with 
 
     %config InlineBackend.figure_format = 'svg'
 
     (or set the equivalent flag at startup or in your configuration profile).
     """
     extension = 'tex'
     documentclass = 'article'
     documentclass_options = '11pt,english'
     heading_map = {1: r'\section',
                    2: r'\subsection',
                    3: r'\subsubsection',
                    4: r'\paragraph',
                    5: r'\subparagraph',
                    6: r'\subparagraph'}
 
     def in_env(self, environment, lines):
         """Return list of environment lines for input lines
 
         Parameters
         ----------
         env : string
           Name of the environment to bracket with begin/end.
 
         lines: """
         out = [ur'\begin{%s}' % environment]
         if isinstance(lines, basestring):
             out.append(lines)
         else:  # list
             out.extend(lines)
         out.append(ur'\end{%s}' % environment)
         return out
 
     def convert(self):
         # The main body is done by the logic in the parent class, and that's
         # all we need if preamble support has been turned off.
         body = super(ConverterLaTeX, self).convert()
         if not self.with_preamble:
             return body
         # But if preamble is on, then we need to construct a proper, standalone
         # tex file.
         
         # Tag the document at the top and set latex class
         final = [ r'%% This file was auto-generated by IPython, do NOT edit',
                   r'%% Conversion from the original notebook file:',
                   r'%% {0}'.format(self.infile),
                   r'%%',
                   r'\documentclass[%s]{%s}' % (self.documentclass_options,
                                                self.documentclass),
                   '',
                  ]
         # Load our own preamble, which is stored next to the main file.  We
         # need to be careful in case the script entry point is a symlink
         myfile = __file__ if not os.path.islink(__file__) else \
           os.readlink(__file__)
         with open(os.path.join(os.path.dirname(myfile), 'preamble.tex')) as f:
             final.append(f.read())
             
         # Load any additional user-supplied preamble
         if self.user_preamble:
             final.extend(['', '%% Adding user preamble from file:',
                           '%% {0}'.format(self.user_preamble), ''])
             with open(self.user_preamble) as f:
                 final.append(f.read())
                 
         # Include document body
         final.extend([ r'\begin{document}', '',
                        body,
                        r'\end{document}', ''])
         # Retun value must be a string
         return '\n'.join(final)
         
     @DocInherit
     def render_heading(self, cell):
         marker = self.heading_map[cell.level]
         return ['%s{%s}' % (marker, cell.source) ]
 
     @DocInherit
     def render_code(self, cell):
         if not cell.input:
             return []
 
         # Cell codes first carry input code, we use lstlisting for that
         lines = [ur'\begin{codecell}']
         
         lines.extend(self.in_env('codeinput',
                               self.in_env('lstlisting', cell.input)))
 
         outlines = []
         for output in cell.outputs:
             conv_fn = self.dispatch(output.output_type)
             outlines.extend(conv_fn(output))
 
         # And then output of many possible types; use a frame for all of it.
         if outlines:
             lines.extend(self.in_env('codeoutput', outlines))
 
         lines.append(ur'\end{codecell}')
 
         return lines
 
 
     @DocInherit
     def _img_lines(self, img_file):
         return self.in_env('center',
                 [r'\includegraphics[width=6in]{%s}' % img_file, r'\par'])
 
     def _svg_lines(self, img_file):
         base_file = os.path.splitext(img_file)[0]
         pdf_file = base_file + '.pdf'
         subprocess.check_call([ inkscape, '--export-pdf=%s' % pdf_file,
                                img_file])
         return self._img_lines(pdf_file)
 
     @DocInherit
     def render_stream(self, output):
         lines = []
 
         if 'text' in output:
             lines.extend(self.in_env('verbatim', output.text.strip()))
 
         return lines
 
     @DocInherit
     def render_markdown(self, cell):
         return [markdown2latex(cell.source)]
         
     @DocInherit
     def render_pyout(self, output):
         lines = []
 
         # output is a dictionary like object with type as a key
         if 'latex' in output:
             lines.extend(output.latex)
 
         if 'text' in output:
             lines.extend(self.in_env('verbatim', output.text))
 
         return lines
 
     @DocInherit
     def render_pyerr(self, output):
         # Note: a traceback is a *list* of frames.
         return self.in_env('traceback',
                         self.in_env('verbatim', 
                                  remove_ansi('\n'.join(output.traceback))))
 
     @DocInherit
     def render_raw(self, cell):
         if self.raw_as_verbatim:
             return self.in_env('verbatim', cell.source)
         else:
             return [cell.source]
 
     @DocInherit
     def _unknown_lines(self, data):
         return [r'{\vspace{5mm}\bf WARNING:: unknown cell:}'] + \
           self.in_env('verbatim', data)
 
 
 class ConverterNotebook(Converter):
     """
     A converter that is essentially a null-op.
     This exists so it can be subclassed
     for custom handlers of .ipynb files 
     that create new .ipynb files.
 
     What distinguishes this from JSONWriter is that
     subclasses can specify what to do with each type of cell.
 
     Writes out a notebook file.
 
     """
     extension = 'ipynb'
 
     def __init__(self, infile, outbase):
         Converter.__init__(self, infile)
         self.outbase = outbase
         rmtree(self.files_dir)
 
     def convert(self):
         return json.dumps(json.loads(Converter.convert(self, ',')), indent=1, sort_keys=True)
 
     def optional_header(self):
         s = \
 """{
  "metadata": {
  "name": "%(name)s"
  },
  "nbformat": 3,
  "worksheets": [
  {
  "cells": [""" % {'name':self.outbase}
 
         return s.split('\n')
 
     def optional_footer(self):
         s = \
 """]
   }
  ]
 }"""
         return s.split('\n')
 
     @DocInherit
     def render_heading(self, cell):
         return cell_to_lines(cell)
 
     @DocInherit
     def render_code(self, cell):
         return cell_to_lines(cell)
 
     @DocInherit
     def render_markdown(self, cell):
         return cell_to_lines(cell)
 
     @DocInherit
     def render_raw(self, cell):
         return cell_to_lines(cell)
 
     @DocInherit
     def render_pyout(self, output):
         return cell_to_lines(cell)
 
     @DocInherit
     def render_pyerr(self, output):
         return cell_to_lines(cell)
 
 #-----------------------------------------------------------------------------
 # Standalone conversion functions
 #-----------------------------------------------------------------------------
 
 def rst2simplehtml(infile):
     """Convert a rst file to simplified html suitable for blogger.
 
     This just runs rst2html with certain parameters to produce really simple
     html and strips the document header, so the resulting file can be easily
     pasted into a blogger edit window.
     """
 
     # This is the template for the rst2html call that produces the cleanest,
     # simplest html I could find.  This should help in making it easier to
     # paste into the blogspot html window, though I'm still having problems
     # with linebreaks there...
     cmd_template = ("rst2html --link-stylesheet --no-xml-declaration "
                     "--no-generator --no-datestamp --no-source-link "
                     "--no-toc-backlinks --no-section-numbering "
                     "--strip-comments ")
 
     cmd = "%s %s" % (cmd_template, infile)
     proc = subprocess.Popen(cmd,
                             stdout=subprocess.PIPE,
                             stderr=subprocess.PIPE,
                             shell=True)
     html, stderr = proc.communicate()
     if stderr:
         raise IOError(stderr)
 
     # Make an iterator so breaking out holds state.  Our implementation of
     # searching for the html body below is basically a trivial little state
     # machine, so we need this.
     walker = iter(html.splitlines())
 
     # Find start of main text, break out to then print until we find end /div.
     # This may only work if there's a real title defined so we get a 'div class'
     # tag, I haven't really tried.
     for line in walker:
         if line.startswith('<body>'):
             break
 
     newfname = os.path.splitext(infile)[0] + '.html'
     with open(newfname, 'w') as f:
         for line in walker:
             if line.startswith('</body>'):
                 break
             f.write(line)
             f.write('\n')
 
     return newfname
 
 #-----------------------------------------------------------------------------
 # Cell-level functions -- similar to IPython.nbformat.v3.rwbase functions
 # but at cell level instead of whole notebook level
 #-----------------------------------------------------------------------------
 
 def writes_cell(cell, **kwargs):
     kwargs['cls'] = BytesEncoder
     kwargs['indent'] = 3
     kwargs['sort_keys'] = True
     kwargs['separators'] = (',',': ')
     if kwargs.pop('split_lines', True):
         cell = split_lines_cell(copy.deepcopy(cell))
     return py3compat.str_to_unicode(json.dumps(cell, **kwargs), 'utf-8')
 
 _multiline_outputs = ['text', 'html', 'svg', 'latex', 'javascript', 'json']
 def split_lines_cell(cell):
     """
     Split lines within a cell as in 
     IPython.nbformat.v3.rwbase.split_lines
 
     """
     if cell.cell_type == 'code':
         if 'input' in cell and isinstance(cell.input, basestring):
             cell.input = (cell.input + '\n').splitlines()
         for output in cell.outputs:
             for key in _multiline_outputs:
                 item = output.get(key, None)
                 if isinstance(item, basestring):
                     output[key] = (item + '\n').splitlines()
     else: # text, heading cell
         for key in ['source', 'rendered']:
             item = cell.get(key, None)
             if isinstance(item, basestring):
                 cell[key] = (item + '\n').splitlines()
     return cell
 
 def cell_to_lines(cell):
     '''
     Write a cell to json, returning the split lines.
     '''
     split_lines_cell(cell)
     s = writes_cell(cell).strip()
     return s.split('\n')
 
 
 known_formats = "rst (default), html, quick-html, latex"
 
 def main(infile, format='rst'):
     """Convert a notebook to html in one step"""
     # XXX: this is just quick and dirty for now. When adding a new format,
     # make sure to add it to the `known_formats` string above, which gets
     # printed in in the catch-all else, as well as in the help
     if format == 'rst':
         converter = ConverterRST(infile)
         converter.render()
     elif format == 'html':
         #Currently, conversion to html is a 2 step process, nb->rst->html
         converter = ConverterRST(infile)
         rstfname = converter.render()
         rst2simplehtml(rstfname)
     elif format == 'quick-html':
         converter = ConverterQuickHTML(infile)
         rstfname = converter.render()
     elif format == 'latex':
         converter = ConverterLaTeX(infile)
         latexfname = converter.render()
     else:
         raise SystemExit("Unknown format '%s', " % format +
                 "known formats are: " + known_formats)
 
 #-----------------------------------------------------------------------------
 # Script main
 #-----------------------------------------------------------------------------
 
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description=__doc__,
             formatter_class=argparse.RawTextHelpFormatter)
     # TODO: consider passing file like object around, rather than filenames
     # would allow us to process stdin, or even http streams
     #parser.add_argument('infile', nargs='?', type=argparse.FileType('r'), default=sys.stdin)
 
     #Require a filename as a positional argument
     parser.add_argument('infile', nargs=1)
     parser.add_argument('-f', '--format', default='rst',
                         help='Output format. Supported formats: \n' +
                         known_formats)
     args = parser.parse_args()
     main(infile=args.infile[0], format=args.format)