BibTeX Cite Key Manager

This repository contains two Python scripts designed to help manage BibTeX citation keys and ensure consistency in LaTeX documents:

• process_bib.py: Processes a BibTeX file to:
  • Identify and count duplicate citation keys.
  • Deduplicate entries based on title similarity, keeping the most informative entry.
  • Generate a key mapping (JSON file) to map old keys to the retained best keys.
  • Output a processed BibTeX file (processed.bib) containing only unique entries.
• update_tex.py: Updates a TeX file to use the consistent citation keys from the processed BibTeX file:
  • Replaces \supercite{old_key} citations with \supercite{best_key} using the key mapping.
  • Handles \supercite{key1, key2, ...} with comma-separated keys.
  • Warns about any citation keys in the TeX file that are not found in the processed BibTeX file or key mappings.

Usage

Prerequisites:

• Python 3.x
• Install required Python libraries:

  pip install bibtexparser difflib

Step-by-step Instructions:

1. Prepare your BibTeX file: Combine all your BibTeX files into a single file, e.g., merged.bib. This script is designed to handle duplicates within this merged file.
2. Run process_bib.py:

   python process_bib.py

   This script will:
   • Read merged.bib (you can modify input_bib_file variable in the script).
   • Process the BibTeX entries, deduplicate, and generate key mappings.
   • Save the processed BibTeX entries to processed.bib.
   • Save the key mappings to key_mapping.json.
   • Print key statistics and mappings to the console.
3. Prepare your TeX file: Ensure your LaTeX document uses \supercite{} for citations and you want to update the keys in these commands.
4. Run update_tex.py:

   python update_tex.py

   This script will:
   • Read main.tex (you can modify input_tex_file variable in the script).
   • Read processed.bib and key_mapping.json generated in the previous step.
   • Replace \supercite{} keys in main.tex based on the key mappings.
   • Save the updated TeX file as main_updated.tex.
   • Print warnings for any citation keys in the TeX file that are not found in the BibTeX files.
5. Review output files: Check processed.bib, key_mapping.json, and main_updated.tex to ensure the scripts worked as expected. Pay attention to any warnings printed in the console.

File Structure:

• process_bib.py: Python script to process BibTeX files.
• update_tex.py: Python script to update TeX files.
• merged.bib (Input): Your merged BibTeX file (or any name you configure in process_bib.py).
• processed.bib (Output): Processed BibTeX file with unique entries.
• key_mapping.json (Output): JSON file containing key mappings from old to best keys.
• main.tex (Input): Your LaTeX TeX file (or any name you configure in update_tex.py).
• main_updated.tex (Output): Updated TeX file with consistent citation keys.

Notes:

• Title Similarity Threshold: The process_bib.py script uses a title similarity threshold of 0.8 to identify duplicate papers. You can adjust this value in the script if needed.
• Entry Richness: The script determines the "best" entry based on the number of fields. You can customize the get_entry_richness function in process_bib.py for more sophisticated criteria.
• Backup: Always back up your merged.bib and TeX files before running these scripts.
• Citation Command: update_tex.py is designed to work with \supercite{} command. If you use other citation commands like \cite, \citet, \citep, you'll need to modify the update_tex.py script accordingly.