Hippocamplus My Second Memory

Additional checks for a LaTeX manuscript

Apr 18 2018 pub latex thesis

To continue on the series of “Things I did instead of writing my thesis to help me write my thesis”, another Python script that reads a LaTeX manuscript and helps check that everything is fine. More specifically, the checkLatex.py script (on GitHub) will:

  1. List missing references.
  2. List multi-references to reorder.
  3. List duplicated labels.
  4. List labels that don’t start by fig: or tab:.
  5. List figures/tables that are not in order.
  6. List ??, REF or XX.
  7. List acronyms in italic (for gene names).
  8. List acronyms in serif (for method names).
  9. List acronyms not in italic nor in serif.
  10. Shows the first usage of each acronym (not in italic/serif).

This was particularly useful for my thesis because I combined three manuscripts and a general intro. I had to make sure that the labels, acronyms, references were all correct and consistent throughout the thesis. I might still use this again on smaller documents like research manuscripts.

Why this output?

“List missing references” because bibtex output was sandwiched between long latex logs and it was easy to do. “List multi-references to reorder” is to transform “something19,3,12” into “something3,12,19”. Not a big deal but I prefer when it’s ordered…

“List duplicated labels” helped merge manuscripts in the thesis but won’t be very useful in general. “List labels that don’t start by fig: or tab:” to make sure that figures and tables have labels starting with fig: or tab: (it helps for the next check). “List figures/tables that are not in order” to make sure the figure/table numbers are in ascending order in the text. It checks for the order of labels in each file separately. That way if the supplementary material is in a separate file (using \input), the supp figs are considered separately from other figures. It’s not perfect though, because the script doesn’t “understand” sub-figures.

“List ??, REF or XX” because that’s what I use when I’m writing and missing a number or reference.

“List acronyms in italic (for gene names)” to make sure that acronyms in italic are gene names. “List acronyms in serif (for method names)” to make sure that acronyms in serif are methods names. “List acronyms not in italic nor in serif” to check if I forgot to put a gene name in italic or a method in serif. It also helped listing the abbreviations at the beginning of the thesis. “Shows the first usage of an acronym (not in italic/serif)” to make sure acronyms are defined properly.

Practical details

The script assumes that the document is compiled. For example, it will use the .bbl file for the checks on the references.

It will follow one level of \input{}. It was enough for my thesis: I had one main.tex file with \input commands calling the different chapters. It should be enough for a manuscript in general.

Acronyms are defined by the regular expression [A-Za-z0-9]*[A-Z]{2}[A-Za-z0-9]*, i.e. at least two consecutive uppercase letters and any letter/number around.

Some arguments to switch on/off the acronym mode and internal references as explained in the help output:

> python checkLatex.py -h
usage: checkLatex.py [-h] -i TEX [-inrefs] [-noacro]

Check for problems in a LaTeX manuscript.

optional arguments:
  -h, --help  show this help message and exit
  -i TEX      the input tex file
  -inrefs     list non-fig/table internal refs
  -noacro     don't list acronyms

Final check

I used pdfgrep to check the final PDF for quotation marks that could result from missing reference/figure/table.

pdfgrep '\?' main.pdf