glob2bib: a bibliography generator for BibTeX and BibLaTeX/Biber

Bibliography management is a tedious, but a necessary endeavor when writing any technical document. Naturally, one accumulates many references while researching a topic and it is often convenient to organize them in some "centralized" manner (e.g., a large, monolithic .bib file or several smaller ones). Instead of copying the whole collection into every project, it is preferable to include only those entries that are actually needed. This not only keeps the document source uncluttered, but also prevents unecessarily long LaTeX compile times due to needlessly parsing over a large number of unused .bib entries. Of course, doing this manually is a nuisance and should be avoided at all costs. Thanks to glob2bib, one never needs to resort to such primitive sorting practices again!

Taking an .aux file (generated during the compilation of a .tex source) and adirectory as input, glob2bib:

1. extracts all the citation keys listed in the .aux file.
2. recursively finds all the .bib files found within the specified directory.
3. extracts all the entries from the .bib files whose keys match those in the .aux file.
4. prints the extracted entries to the terminal or (optionally) writes them to a file.

For convenience, glob2bib works for .aux files generated by both BibTeX and BibLaTeX/Biber workflows. Similarly, it can also optionally convert unicode greek literals found in the extracted entries to (escaped) greek math TeX commands. The latter feature is particularly useful when different documents use different TeX engines (e.g., pdfTeX or LuaTeX).

Installation

glob2bib is just a simple Python script with no external dependencies. For convenience, a Makefile is included for lazy integration into *nix systems. Installation is as easy as:

make install

Note that, as per usual, superuser privilages are required for this.

Usage

Typical use looks like:

glob2bib document.aux /path/to/bib/database -o references.bib

which will output the extracted entries to a new .bib file references.bib.

A full discription of all input options can be obtained using:

glob2bib --help

which will print:

usage: glob2bib [-h] [-v] [-o OUTPUT] [-s] [-b] [-l] [-a] [-u] aux_file bib_dir

glob2bib: a bibliography generator for BibTeX and BibLaTeX/Biber

positional arguments:
  aux_file              auxillary file (.aux) from LaTeX compilation
  bib_dir               directory to recursively glob for .bib files

options:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  -o OUTPUT, --output OUTPUT
                        name of the output file to write the extracted .bib entries to
  -s, --substitute-unicode
                        substitute unicode greek literals with (escaped) greek math TeX commands
  -b, --biblatex        assume BibLaTeX/Biber as the bibliography management backend
  -l, --long-journal-titles
                        substitute abbreviated journal titles with their full names
  -a, --abbreviated-journal-titles
                        substitute full journal titles with their abbreviated names
  -u, --url-swap        swap the url field for the doi in each entry

Copyright (c) 2019-2022 Ryan M. L. McFadden

Caveats

It is assumed that each .bib entry is of the form:

@article{key,
   author = "...",
   title = "...",
   ...
   doi = "...",
   url = "..."
}

where the most crucial feature is the ending, which consists solely of a lone } on the line trailing the last entry data. As is, glob2bib will fail to parse .bib entries that do not comply with this formatting.