BibCom simplifies the creation of a BibTeX bibliography for scientific papers, specifically in physics. The tool automatically generates BibTeX entries from ADS or INSPIRE for missing citations in LaTeX documents. The new BibTeX entries are copied to the clipboard (useful for online tools such as Overleaf) or appended to a local BibTeX file.
Creating a BibTeX bibliography is necessary but tedious. Databases such as NASA/ADS or HEP INSPIRE provide an immense help, but adding new entries a few at a time is still time-consuming. The same is true for adjusting the bib file accordingly to match the preferred citation key style.
Enter BibCom! This tool automatically generates bib entries for missing citations from the “missing citation” entries from the .log file.
New bib entries will be copied to the clipboard or appended to a local bib file.
The only requirement is that the citation keys correspond to any combination of the following persistent identifiers:
- an arXiv preprint number (with or without
arXiv:in front) - a DOI (with or without
doi:in front) - a HEP INSPIRE key
- a NASA/ADS key
The recommended database for queries is ADS, but INSPIRE can be used as a fallback option. To query ADS, you need to create a free account and generate an API token, as explained below.
Clone the repository and ensure that the following Python packages are installed: numpy, pyperclip, and requests.
If in doubt, run
python -m pip install numpy pyperclip requests
Create an ADS account here.
You can then generate the API token under Account -> Settings -> API Token.
Paste it into a plain text such as my.token in your local BibCom folder.
As an added benefit, you may be intersted in creating custom email alerts for new arXiv preprints with ADS.
Compiling your LaTeX paper [main].tex creates a log file named [main].log in the in the same folder.
If you are using Overleaf, it can be downloaded after clicking on the “Logs and output files”, scrolling down and clicking on “Other logs and files”.
Then simpliy update your bibliography as needed with Bibcom until you are ready to submit. At that point, you may want to check your bibliography for duplicates (see Complete overview).
To query the INSPIRE database, simply run
python compile_bib.py [main].log
and paste the results into your bib file (using Ctrl+V, Cmd+V, or right click -> paste).
If you provide your ADS API in a file my.token or via the environment variable ADS_API_TOKEN, the ADS database will be queried instead.
The full range of options for compile_bib.py also allows for adding the name of a bib file /some/folder/to/my.bib and/or the name of a file my.token containing your ADS API:
python compile_bib.py [main].log my.token /some/folder/to/my.bib
In this case, the new bib entires will be additionally appended to the file.
If the file /some/folder/to/my.bib does not exist, it will be created.
When providing a bib file name, BibCom will automatically check for duplicates.
Note that the order of the arguments and the names of the files do not matter as long as the files end in .log, .bib, and .token. For example, any of the below will work:
python compile_bib.py my.token [main].log
python compile_bib.py [main].log my.token
python compile_bib.py /some/folder/to/my.bib [main].log my.token
ADS BibTeX entries use LaTeX macros for some journal names, as described here.
This contains the file jdefs.tex, which you can download and include in your LaTeX preamble via \include{jdefs} to replace the macros.
Alternatively, you can supply jdefs.tex — or any other .tex file in the same format — as an argument.
BibCom will then replace all macros in the bibliography accordingly:
python compile_bib.py [main].log jdefs.tex
To check an exiting bib file /some/folder/to/my.bib for duplicates, run
python check_bib.py /some/folder/to/my.bib
The check is based on arXiv/eprint IDs and DOIs. The code will print the names of any duplicates that the user needs to fix.