v3.0.0

3.0.0 (2023-12-20)

Added

• speed optimizations, ~250%
• pseudo-annotating eponymous diseases (e.g. Creutzfeldt-Jakob)
• PatientNameAnnotator, which replaces deduce.pattern
• a structured way for loading and building lookup structures (lists and tries), including caching
• pre_match_words for some regexp annotators, speeding up the annotating
• option to present a user config as dict (using config keyword)

Changed

• speedup for TokenPatternAnnotator
• some internals of ContextPatternAnnotator
• initials now detected by lookup list, rather than pattern
• redactor open and close chars from < > to [ ], as previous chars caused issues in html (so deidentified text now shows [PATIENT], [LOCATIE], etc.)
• names of lookup structures to singular (prefix, rather than prefixes)
• INSTELLING tag to ZIEKENHUIS and ZORGINSTELLING
• refactored and simplified annotator loading, specifically the annotator_type config keyword now accepts references to classes (e.g deduce.annotator.TokenPatternAnnotator)
• renamed interfix_with_capital annotator to interfix_with_name

Deprecated

• the config_file keyword, now replaced by config which accepts both filenames and dicts
• old lookup list names, e.g. prefixes now replaced by prefix
• annotator types 'custom', 'regexp', 'token_pattern', 'dd_token_pattern' and 'annotation_context', all replaced by setting class directly as annotator_type

Removed

• automated coverage reporting on coveralls.io
• options lowercase_lookup, lowercase_neg_lookup for token patterns
• everything in deduce.pattern, patient patterns now replaced by PatientNameAnnotator
• utils.any_in_text

Fixed

• some small additions/removals for specific lookup lists
• smaller bugs related to overlapping matches