filterbib 0.1.0

A Python package that includes a Python and Bash script to filter particular fields from a bib-file

filterbib

Package to filter out particular fields from a bib-file (e.g., exported from zotero). Cleans up the file so that only relevant fields are shown in the bibliography.

Installation

# install package
pip install git+https://github.com/gjheij/filterbib

This will place 2 scripts in the bin folder of the current anaconda environment: filter_bib and read_bib:

• filter_bib: main shell script that calls upon read_bib. This is a shell script to deal with ampersands properly, which turned out to be tricky with python.
• read_bib: python script that uses pybtex to do most of the actual filtering.

Usage

Just entering filter_bib will pull up the help information:

(base) [heij@Jurjens-MacBook filterbib]$ filter_bib

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filter_bib

Filter a bib-file representing a bibliography for particular fields to clean up the file. By default,
it filters out the following fields:

["abstract","note","file","extra","keywords","copyright","url","doi","urldate","issn","shorttitle",
"language","pmid"]

This part of the script is shell to deal with the ampersand's in the file ('\&' is not processed well in LaTex, so this should be changed to '\&'). It is very hard to do this
with expressions used in python. This is mainly important if you're using full journal names, rather than the abbreviations.

Arguments:
  <input bib>           file to be filtered
  <clean bib>           cleaned file
  <fields to remove>    comma-separated list of fields to remove

Example:
  filter_bib exported_items.bib exported_items_clean.bib
  filter_bib exported_items.bib exported_items_clean.bib abstract,note,extra

---------------------------------------------------------------------------------------------------------

(base) [heij@Jurjens-MacBook filterbib]$ 

The usage is simple: export a file from Zotero as bibtex, which generates a bib-file. This file can then be passed to filter_bib:

# simplest call
filter_bib exported_file.bib exported_file_clean.bib

By default, the following fields are removed:

fields_to_remove = [
    "abstract",
    "note",
    "file",
    "extra",
    "keywords",
    "copyright",
    "url",
    "doi",
    "urldate",
    "issn",
    "shorttitle",
    "language",
    "pmid"
]

For some instances, it's nice to keep the doi-field, in which case you can copy this list and exclude doi:

filter_bib exported_items.bib exported_items_clean.bib abstract,note,file,extra,keywords,copyright,url,urldate,issn,shorttitle,language,pmid