This script cleans up the journal names in a .bib file to match the CASSI abbreviations. Not all CASSI entries are included (please contribute more!); the majority came from the Core Journals table.

The script will print a warning if an abbreviation was not found.

There are several user-specified variables within the script toward the top. These include:

• cassi_csv: the name of the CSV with columns for Abbreviations, Publication Names, and CODEN. A path may be included!
• bib_in: the input BibTeX file. A path may be included!
• bib_out: the name of the BibTeX file to output. A path may be included!
• lower_list: a list of words in title fields that should always be lowercase
• upper_list: a list of words in title fields that should always be uppercase
• ignore_list: a list of words in title fields that should retain their capitalization
• bib_write_order: a list specifying the order of fields written within a BibTeX entry. Anything not specified is appended at the end alphabetically.
• marked_for_removal_bool: a boolean operator for whether specific fields should not be included in the output BibTeX file
• marked_for_removal: a list of fields that should not be included in the output BibTeX file. If marked_for_removal_bool = True, this variable must be created!
• remove_comments: a boolean operator for whether to include comments in the output BibTeX file. If False, all comments will be in a block together at the top of the output.
• alpha_out: a boolean operator for whether to change the order of the entries to alphabetical by identifier (True) or leave them unsorted (False).

After modifying everything in the variable set-up, you can run the script!

python bibtex_parser.py

This script is written using Python3. You can either install Python on its own or through Anaconda (recommended).

Dependencies:

• bibtexparser
• pandas
• titlecase

These can be installed using the included requirements.txt file:

pip install -r requirements.txt

• Check entries against CrossRef