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Jupyter/IPython notebook to latex converter and spell checker

Project description

This module installs two command line scripts:

  • jupyter2article extracts some content (raw cells, markdown cells, code output) from a Jupyter/IPython notebook and pastes it into a new file. It also converst markdown headings to proper LaTeX chapter, section, subsetion etc. and inserts appropriate labels. This converter is not intended to replace the nbconvert from the IPython project. Instead, it serves one very specific purpose: Turn a notebook into a LaTeX file that I can submit to the journal.
  • jupyterspellcheck spell checks markdown and raw cells in a notebook.

Note that scipts and procedures have been renamed to “jupyter”, but the name of the package and its directory structure still reflect that fact that Jupyter notebooks started out as part of the IPython project.

The converter

When I first encountered the IPython notebook, I thought this was a solution looking for a problem. However, I have since been converted! The tipping point for me was this: I want to version control my papers and I always had multiple directories for analysis code, plotting code, LaTeX files, plot scripts and figures and tables. That’s just so unwieldy. Also, I found it cumbersome to email figures to individual collaborators all the time. The Notebook can hold all this information in one place and I can just provide my co-authors with a link to the github repository once and they have access to the latest version all the time. Even if they do not use python, they can still see the all the current figures using nbviewer.ipython.org

Now all papers I work on a are written in an IPython notebook. So, the final step to do is to convert the notebook to the LaTeX file I can submit to a journal. That’s what this simple converter code does.

This converter is not intended to replace the nbconvert from the IPython project. Instead, it serves one very specific purpose: Turn a notebook into a LaTeX file that I can submit to the journal.

How to use it

As a script

Installing this module places a script in your path, so you can do:

jupyter2article myanalysis.ipynb myanalysis.tex

In this case it’s run with my set of design choices (see below).

As a Python module

Import into python and make a NotebookConverter object:

from ipynb2article import NotebookConverter converter = NotebookConverter

Then, customize how each type of cell is converted by changing the converter:

converter.cellconverters[‘code’] = NotebookConverter.IgnoreConverter()

Finally, call:

converter.convert(infile, outfile, …)

This method allows you to use only part of a notebook file (ignore to first n cells or ignore everything until a cell has a specific string value, e.g. “The paper starts here”). Also, it allows you to provide a text file that will be pasted before or after the converted notebook (you can put the ‘usepackage’ and similar stuff in those files so they don’t clutter your notebook). However, I do not use this option any longer, because that means I would have multiple input files. If I put all those LaTeX headers into the notebook as well, I only have a single file.

Design

The code is written around these design ideas:

  • Be able to ignore certain parts of the notebook (e.g. introductory comments in the first few cells).

  • Convert headings to section / subsection etc. I generally level 2 such as “## Heading” for section, “### Heading” for subsections etc.

  • Copy text in “markdown” and “raw text” cells. To simplify, I just write real LaTeX code in those cells. All equations will be rendered correctly in the notebook file for me and my co-authors to see. When I want to highlight something I type LaTeX “emph{}” or “textbf{}”, not the markdown equivalents. That looks not as nice in the notebook, but makes live so much easier. Also, markdown does not recognize “cite”, “ref” and “label”. Again, it looks not as nice in markdown, but (1) I only need to know LaTeX and (2) it works flawlessly when converted.

  • No figure conversion. Instead, in the notebook itself I issue:

    > fig.savefig(‘/path/to/my/article/XXX.eps’)

    because ApJ requires me to submit figures as separate files anyway.

  • Just type figure captions into markdown cells.

  • No conversion of code cells. Who wants code in an ApJ paper?

  • Occasionally, I want to have the output of a computation (e.g. a table written with astropy in LaTeX format) in the article. Keep it simple. Output of all code cells that have a certain comment string (I use “# output->LaTeX”) is copied verbatim to the LaTeX file.

  • Work with the python standard library only. No external dependencies.

To implement this I wrote a converter for each cell type. LiteralSourceConverter just takes the literal string value (it also adds a line break at the end of the cell) and puts it into the LaTeX file (use for markdown and raw text cells), MarkedCodeOutputConverter checks if a code cell has a specific string in it and if so, it copies the output of this cell, and LatexHeadingConverter looks for the level of the heading and turns that into LaTeX (it also adds as label like “label{sect:title}”).

The spellchecker

Spell check the markdown text in IPython notebooks

As much as I love the IPython notebook, there is one big drawback (at least in my installation). When I type into a cell in the browser (I use firefox) there is no automatic spell checking of the input. Sure, the notebook has syntax highlighting for code cells in python, but I want to do my entire paper writing in the notebook and for me that means that a spell checker for cells with markdown, headings or raw text is absolutely essential. On the other hand, I cannot just run e.g. ispell on the ipynb file, since most of its contents is actually code and not plain English. So, I wanted to write a spell checker, that parses the ipynb file and spell checks only the markdown, heading and raw text input cells.

Oh, one more thing: Because I type a lot of raw LaTeX in my notebooks (see my other post on ipynb2article.py) as opposed to real markdown that resembles English much better I define a custom filter function that makes sure that strings which look like LaTeX commands will not be spell checked (since very few LaTeX command are valid English words so that would give a lot of apparent typos). More complicated filters that avoid spell checking within equations or commands like \label{XXX} or \cite{} are possible (they would be called a chunker in pyenchant). Check the github repository for this code if you want to see if I have an improved version.

How to use this script:

Close down the notebook you want to spell check in IPython, then simply type on the command line:

jupyterspellcheck filein.ipynb fileout.ipynb

Open the new file in IPython, run all cells again and keep working.

filein and fileout can be the same filename (in this case the old file will get overwritten with the spelling corrected version), but I recommend to keep a copy just in case something gets screwed up.

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