If you're anything like me, then you probably use a citation manager such as Mendeley or Zotero, and use the browser plugin to conveniently add citations to your library. Everything is rainbows and unicorns until it's time for dissemination ๐ฑ. Enter pmcbib
, a friendly utility written in python that checks your .bib file against the PubMed database to find all the fudge-ups.
version 0.0.2.dev1 added support for aliasing and makes use of stdout/stderr (see example use case)
- python 3.7
- metapub
- bibtexparser
- python-Levenshtein
- internet connection (duh!)
pip install git+https://github.com/LelouchLamperougeVI/pmcbib.git
pmcbib [-h] [-c config.json] [-o] [-r report.md] [-v] [-w L] file.bib
positional arguments:
file.bib ye olde bibtex file
optional arguments:
-h, --help show this help message and exit
-c config.json, --config config.json
config file
-o, --output output automatically corrected bibtex entries on
STDOUT
-r report.md, --report report.md
report outputted as a MarkDown file (default no
output)
-v, --verbose turn on verbose (overwrites -w)
-w L, --warn L minimum warning level to report on console (STDERR)
pmcbib -r report.md example.bib
to suppress warning messages:
pmcbib -r report.md -w 4 example.bib
or
pmcbib -r report.md example.bib 2> /dev/null
pmcbib -o example.bib > corrected.bib
pmcbib
will automatically try to fix identified issues. However, it is strongly recommended for the user to go over the report before committing to the output.
pmcbib -c ~/.config/pmcbib/config.json example.bib