Make my BibTeX file a little less stupid. Fix UTF, don't break in weird places, and don't list DOIs as URLs.

format_bibfile.py

import sys
import re
from pathlib import Path

def fix(path: Path, accent_file: Path, output_path: Path) -> None:
    """
    Reformat my bib file.
    
    * Remove PMC and DOI URLs because they're listed as IDs anyway.
    * Replace accent-like escape characters with their UTF equivalents. I mean, it's 2020.
    * Remove line breaks in the middle of sections.
    * TODO: Remove abstracts.
    * TODO: Auto-remove duplicates
    
    Args:
        path: Path (or str) to the file to correct.
        accent_file: Path (or str) to a tab-delimited file of (escape sequence \t character), with no header.
        output_path: Path (or str) to write to; will overwrite if it exists.
        
    """
    output_path = Path(output_path)
    path = Path(path)
    dct = {s.split('\t')[0]: s.split('\t')[1] for s in Path(accent_file).read_text(encoding='utf8').splitlines()}
    text = path.read_text(encoding='utf8')
    for key, value in dct.items():
        text = text.replace('{'+key+'}', value).replace(key, value)
        text = text.replace('PLoS', 'PLOS')
    text = '\n'.join([s for s in text.splitlines() if 'pubmedcentral.nih.gov' not in s and 'dx.doi.org/' not in s])
    pattern = re.compile('( *[a-z]+  *= *")([^"]+)(" *,)')
    def fix(match):
        inner = re.compile(r'[ \n]+').sub(' ', match.group(2))
        return match.group(1) + inner + match.group(3)
    text = pattern.sub(fix, text)
    output_path.write_text(text, encoding='utf8')


if __name__ == '__main__':
    fix(Path(sys.argv[1]), Path('accents.tsv'), Path(str(path) + '.fixed.bib'))