Error while exporting notebook with links

[pprzetacznik]

Hi,

while using version 4.2 I've noticed such problem. I've got (abcd)[http://link.to.some.page.com] markdown which causes such error after using nbconvert to convert my notebook to pdf:

(jupyter)[pankracy@piotrek-fedora rbm]$ jupyter nbconvert --to latex Untitled1.ipynb 
[NbConvertApp] Converting notebook Untitled1.ipynb to latex
Traceback (most recent call last):
  File "/home/Pankracy/Envs/jupyter/bin/jupyter-nbconvert", line 11, in <module>
    load_entry_point('nbconvert', 'console_scripts', 'jupyter-nbconvert')()
  File "/home/Pankracy/Envs/jupyter/lib/python2.7/site-packages/jupyter_core/application.py", line 267, in launch_instance
    return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
  File "/home/Pankracy/Envs/jupyter/lib/python2.7/site-packages/traitlets/config/application.py", line 658, in launch_instance
    app.start()
  File "/home/Pankracy/Envs/jupyter/src/nbconvert/nbconvert/nbconvertapp.py", line 305, in start
    self.convert_notebooks()
  File "/home/Pankracy/Envs/jupyter/src/nbconvert/nbconvert/nbconvertapp.py", line 473, in convert_notebooks
    self.convert_single_notebook(notebook_filename)
  File "/home/Pankracy/Envs/jupyter/src/nbconvert/nbconvert/nbconvertapp.py", line 444, in convert_single_notebook
    output, resources = self.export_single_notebook(notebook_filename, resources, input_buffer=input_buffer)
  File "/home/Pankracy/Envs/jupyter/src/nbconvert/nbconvert/nbconvertapp.py", line 373, in export_single_notebook
    output, resources = self.exporter.from_filename(notebook_filename, resources=resources)
  File "/home/Pankracy/Envs/jupyter/src/nbconvert/nbconvert/exporters/exporter.py", line 166, in from_filename
    return self.from_file(f, resources=resources, **kw)
  File "/home/Pankracy/Envs/jupyter/src/nbconvert/nbconvert/exporters/exporter.py", line 184, in from_file
    return self.from_notebook_node(nbformat.read(file_stream, as_version=4), resources=resources, **kw)
  File "/home/Pankracy/Envs/jupyter/src/nbconvert/nbconvert/exporters/latex.py", line 82, in from_notebook_node
    return super(LatexExporter, self).from_notebook_node(nb, resources, **kw)
  File "/home/Pankracy/Envs/jupyter/src/nbconvert/nbconvert/exporters/templateexporter.py", line 220, in from_notebook_node
    output = self.template.render(nb=nb_copy, resources=resources)
  File "/home/Pankracy/Envs/jupyter/lib/python2.7/site-packages/jinja2/environment.py", line 989, in render
    return self.environment.handle_exception(exc_info, True)
  File "/home/Pankracy/Envs/jupyter/lib/python2.7/site-packages/jinja2/environment.py", line 754, in handle_exception
    reraise(exc_type, exc_value, tb)
  File "/home/Pankracy/Envs/jupyter/src/nbconvert/nbconvert/exporters/../templates/latex/article.tplx", line 8, in top-level template code
    ((* extends cell_style *))
  File "/home/Pankracy/Envs/jupyter/src/nbconvert/nbconvert/exporters/../templates/latex/style_ipython.tplx", line 56, in top-level template code
    ((( text | add_prompts(first='{\color{' ~ prompt_color ~ '}' ~ prompt ~ '[{\\color{' ~ prompt_color ~ '}' ~ execution_count ~ '}]:} ', cont=indention) )))
  File "/home/Pankracy/Envs/jupyter/src/nbconvert/nbconvert/exporters/../templates/latex/base.tplx", line 6, in top-level template code
    ((*- extends 'document_contents.tplx' -*))
  File "/home/Pankracy/Envs/jupyter/src/nbconvert/nbconvert/exporters/../templates/latex/document_contents.tplx", line 50, in top-level template code
    ((*- block figure scoped -*))
  File "/home/Pankracy/Envs/jupyter/src/nbconvert/nbconvert/exporters/../templates/latex/skeleton/display_priority.tplx", line 5, in top-level template code
    ((*- extends 'null.tplx' -*))
  File "/home/Pankracy/Envs/jupyter/src/nbconvert/nbconvert/exporters/../templates/latex/skeleton/null.tplx", line 30, in top-level template code
    ((*- block body -*))
  File "/home/Pankracy/Envs/jupyter/src/nbconvert/nbconvert/exporters/../templates/latex/base.tplx", line 173, in block "body"
    ((( super() )))
  File "/home/Pankracy/Envs/jupyter/src/nbconvert/nbconvert/exporters/../templates/latex/skeleton/null.tplx", line 32, in block "body"
    ((*- block any_cell scoped -*))
  File "/home/Pankracy/Envs/jupyter/src/nbconvert/nbconvert/exporters/../templates/latex/skeleton/null.tplx", line 76, in block "any_cell"
    ((*- block markdowncell scoped-*))
  File "/home/Pankracy/Envs/jupyter/src/nbconvert/nbconvert/exporters/../templates/latex/document_contents.tplx", line 67, in block "markdowncell"
    ((( cell.source | citation2latex | strip_files_prefix | convert_pandoc('markdown', 'json',extra_args=[]) | resolve_references | convert_pandoc('json','latex'))))
  File "/home/Pankracy/Envs/jupyter/src/nbconvert/nbconvert/filters/filter_links.py", line 16, in resolve_references
    return applyJSONFilters([resolve_one_reference], source)
  File "/home/Pankracy/Envs/jupyter/lib/python2.7/site-packages/pandocfilters.py", line 197, in applyJSONFilters
    altered = walk(altered, action, format, meta)
  File "/home/Pankracy/Envs/jupyter/lib/python2.7/site-packages/pandocfilters.py", line 120, in walk
    array.append(walk(item, action, format, meta))
  File "/home/Pankracy/Envs/jupyter/lib/python2.7/site-packages/pandocfilters.py", line 113, in walk
    array.append(walk(item, action, format, meta))
  File "/home/Pankracy/Envs/jupyter/lib/python2.7/site-packages/pandocfilters.py", line 124, in walk
    x[k] = walk(x[k], action, format, meta)
  File "/home/Pankracy/Envs/jupyter/lib/python2.7/site-packages/pandocfilters.py", line 111, in walk
    item['c'] if 'c' in item else None, format, meta)
  File "/home/Pankracy/Envs/jupyter/src/nbconvert/nbconvert/filters/filter_links.py", line 29, in resolve_one_reference
    target = val[2][0]
IndexError: list index out of range

I would be grateful for any help.

Cheers, PIotrek

[takluyver]

What version of pandoc do you have? Run pandoc --version at a command line to find out.

@michaelpacer I remember running into this with bookbook, but I'd forgotten about it when we put it into nbconvert. We probably need to make the code robust to older versions of pandoc.

[pprzetacznik]

@takluyver

(jupyter)[pankracy@piotrek-fedora rbm]$ pandoc --version
pandoc 1.13.2
Compiled with texmath 0.8.0.1, highlighting-kate 0.5.11.1.
Syntax highlighting is supported for the following languages:
    abc, actionscript, ada, agda, apache, asn1, asp, awk, bash, bibtex, boo, c,
    changelog, clojure, cmake, coffee, coldfusion, commonlisp, cpp, cs, css,
    curry, d, diff, djangotemplate, dockerfile, dot, doxygen, doxygenlua, dtd,
    eiffel, email, erlang, fasm, fortran, fsharp, gcc, glsl, gnuassembler, go,
    haskell, haxe, html, ini, isocpp, java, javadoc, javascript, json, jsp,
    julia, latex, lex, lilypond, literatecurry, literatehaskell, lua, m4,
    makefile, mandoc, markdown, mathematica, matlab, maxima, mediawiki,
    metafont, mips, modelines, modula2, modula3, monobasic, nasm, noweb,
    objectivec, objectivecpp, ocaml, octave, opencl, pascal, perl, php, pike,
    postscript, prolog, pure, python, r, relaxng, relaxngcompact, rest, rhtml,
    roff, ruby, rust, scala, scheme, sci, sed, sgml, sql, sqlmysql,
    sqlpostgresql, tcl, tcsh, texinfo, verilog, vhdl, xml, xorg, xslt, xul,
    yacc, yaml, zsh
Default user data directory: /home/Pankracy/.pandoc
Copyright (C) 2006-2014 John MacFarlane
Web:  http://johnmacfarlane.net/pandoc
This is free software; see the source for copying conditions.
There is no warranty, not even for merchantability or fitness
for a particular purpose.

[mpacer]

Could you try updating to a newer version of pandoc, I believe the most recent release (at the time of this writing) is in the 1.18 1.19 line?

[takluyver]

Yeah, I think the structure of pandoc's ast changed somewhere around 1.16 or 1.17, so your version will have the older structure.

[pprzetacznik]

Thanks, pandoc's upgrade also required upgrade of system but it's eventually working right now.