This directory contains organized scripts for the amilib project, categorized by functionality.

Scripts for creating, managing, and analyzing document corpora.

• ingest_breward2023.py - Ingest PDF files into AmiCorpus structure
• extract_phrases_keybert_breward2023.py - Extract phrases using KeyBERT analysis
• extract_phrases_breward2023.py - Extract phrases using TF-IDF analysis

Scripts for adding hyperlinks and annotations to PDFs and HTML documents.

• markup_climate_pdfs_with_glossary.py - Add IPCC glossary links to climate PDFs
• markup_ipcc_executive_summary.py - Add glossary links to IPCC HTML documents
• process_biorxiv_pdfs_simple.py - Simplified PDF annotation (alternative)
• process_remaining_biorxiv.py - Background processing of bioRxiv PDFs
• create_flat_glossary.py - Convert HTML glossary to flat text format

Utility scripts for system maintenance and file operations.

• sanitize_filenames.py - Make filenames Windows-compatible
• clean_git_history.py - Clean git history of problematic filenames

Each subdirectory contains its own README with specific usage instructions for the scripts in that category.

All scripts should follow the established style guide:

• Use Python commands, not shell commands
• Avoid hardcoded strings and numbers
• Do not put business logic in main(); use parameterized methods
• Use absolute imports with module prefix
• Use clean Path construction with comma-separated arguments