https://github.com/sebhoof/bibcom
A simple tool for generate missing BibTeX entries.
https://github.com/sebhoof/bibcom
automation bibliography bibtex latex publishing referencing science
Last synced: about 1 month ago
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A simple tool for generate missing BibTeX entries.
- Host: GitHub
- URL: https://github.com/sebhoof/bibcom
- Owner: sebhoof
- License: mit
- Created: 2022-04-25T19:40:53.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2024-09-12T09:41:57.000Z (almost 2 years ago)
- Last Synced: 2025-09-04T21:48:29.436Z (10 months ago)
- Topics: automation, bibliography, bibtex, latex, publishing, referencing, science
- Language: Python
- Homepage:
- Size: 87.9 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
README
BibCom – a BibTeX bibliography creator
[](https://zenodo.org/badge/latestdoi/485510848) [](https://opensource.org/licenses/MIT) [](https://github.com/psf/black)
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](https://www.overleaf.com)) or appended to a local BibTeX file.
## Introduction
Creating a BibTeX bibliography is necessary but tedious.
Databases such as [NASA/ADS](https://adsabs.harvard.edu) or [HEP INSPIRE](https://inspirehep.net/) 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](https://arxiv.org/) preprint number (with or without `arXiv:` in front)
- a DOI (with or without `doi:` in front)
- a [HEP INSPIRE](https://inspirehep.net/) key
- a [NASA/ADS](https://ui.adsabs.harvard.edu/) 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](#recommended-additional-steps).
## Installation
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
```
### Recommended additional steps
Create an ADS account [here](https://ui.adsabs.harvard.edu/user/account/register).
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.
## How to use BibCom
Compiling your LaTeX paper `[main].tex` creates a log file named `[main].log` in the in the same folder.
If you are using [Overleaf](https://www.overleaf.com), 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](#complete-overview)).
### Quickstart
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.
### Complete overview
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](https://ui.adsabs.harvard.edu/help/actions/journal-macros).
This contains the file [jdefs.tex](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](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.