Merge pull request #153 from vmenger/update-dependencies

Update dependencies

Author: vmenger

CHANGELOG.md

@@ -5,6 +5,12 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## 3.0.5 (2025-06-18)
+
+### Changed
+
+- Updated dependencies
+
 ## 3.0.4 (2025-05-06)
 
 ### Changed

deduce/__init__.py

@@ -1 +1,6 @@
 from deduce.deduce import Deduce, __version__
+
+__all__ = [
+    "Deduce",
+    "__version__",
+]

deduce/annotator.py

@@ -112,7 +112,6 @@ def __init__(
         self._matching_pipeline = None
 
         if len(self.pattern) > 0 and "lookup" in self.pattern[0]:
-
             if self.ds is None:
                 raise RuntimeError(
                     "Created pattern with lookup in TokenPatternAnnotator, but "
@@ -218,7 +217,6 @@ def annotate(self, doc: dd.Document) -> list[dd.Annotation]:
             )
 
         for token in tokens:
-
             annotation = self._match_sequence(
                 doc.text, self.pattern, token, direction="right", skip=self.skip
             )
@@ -252,12 +250,10 @@ def __init__(
     def _apply_context_pattern(
         self, text: str, annotations: dd.AnnotationSet, context_pattern: dict
     ) -> dd.AnnotationSet:
-
         direction = context_pattern["direction"]
         skip = set(context_pattern.get("skip", []))
 
         for annotation in annotations.copy():
-
             tag = list(_DIRECTION_MAP[direction]["order"](annotation.tag.split("+")))[
                 -1
             ]
@@ -319,7 +315,6 @@ def _annotate(self, text: str, annotations: dd.AnnotationSet) -> dd.AnnotationSe
             )
 
         if self.iterative:
-
             changed = dd.AnnotationSet(annotations.difference(original_annotations))
             annotations = dd.AnnotationSet(
                 annotations.intersection(original_annotations)
@@ -356,7 +351,6 @@ class implements logic for detecting first name(s), initials and surnames.
     """
 
     def __init__(self, tokenizer: Tokenizer, *args, **kwargs) -> None:
-
         self.tokenizer = tokenizer
         self.skip = [".", "-", " "]
 
@@ -366,9 +360,7 @@ def __init__(self, tokenizer: Tokenizer, *args, **kwargs) -> None:
     def _match_first_names(
         doc: dd.Document, token: dd.Token
     ) -> Optional[tuple[dd.Token, dd.Token]]:
-
         for first_name in doc.metadata["patient"].first_names:
-
             if str_match(token.text, first_name) or (
                 len(token.text) > 3
                 and str_match(token.text, first_name, max_edit_distance=1)
@@ -381,7 +373,6 @@ def _match_first_names(
     def _match_initial_from_name(
         doc: dd.Document, token: dd.Token
     ) -> Optional[tuple[dd.Token, dd.Token]]:
-
         for _, first_name in enumerate(doc.metadata["patient"].first_names):
             if str_match(token.text, first_name[0]):
                 next_token = token.next()
@@ -397,7 +388,6 @@ def _match_initial_from_name(
     def _match_initials(
         doc: dd.Document, token: dd.Token
     ) -> Optional[tuple[dd.Token, dd.Token]]:
-
         if str_match(token.text, doc.metadata["patient"].initials):
             return token, token
 
@@ -417,7 +407,6 @@ def next_with_skip(self, token: dd.Token) -> Optional[dd.Token]:
     def _match_surname(
         self, doc: dd.Document, token: dd.Token
     ) -> Optional[tuple[dd.Token, dd.Token]]:
-
         if doc.metadata["surname_pattern"] is None:
             doc.metadata["surname_pattern"] = self.tokenizer.tokenize(
                 doc.metadata["patient"].surname
@@ -473,9 +462,7 @@ def annotate(self, doc: Document) -> list[Annotation]:
         annotations = []
 
         for token in doc.get_tokens():
-
             for matcher, tag in matchers:
-
                 match = matcher(doc, token)
 
                 if match is None:
@@ -518,7 +505,6 @@ def __init__(
         lowercase: bool = True,
         **kwargs,
     ) -> None:
-
         self.pre_pseudo = set(pre_pseudo or [])
         self.post_pseudo = set(post_pseudo or [])
         self.lowercase = lowercase
@@ -553,7 +539,6 @@ def _get_previous_word(self, char_index: int, text: str) -> str:
         result = ""
 
         for ch in text[::-1]:
-
             if not self._is_word_char(ch):
                 break
 
@@ -576,7 +561,6 @@ def _get_next_word(self, char_index: int, text: str) -> str:
         result = ""
 
         for ch in text:
-
             if not self._is_word_char(ch):
                 break
 
@@ -648,7 +632,6 @@ def annotate(self, doc: Document) -> list[Annotation]:
         annotations = []
 
         for match in self.bsn_regexp.finditer(doc.text):
-
             text = match.group(self.capture_group)
             digits = re.sub(r"\D", "", text)
 

deduce/str/__init__.py

@@ -7,3 +7,13 @@
     UpperCase,
     UpperCaseFirstChar,
 )
+
+__all__ = [
+    "Acronimify",
+    "FilterBasedOnLookupSet",
+    "RemoveValues",
+    "TakeLastToken",
+    "TitleCase",
+    "UpperCase",
+    "UpperCaseFirstChar",
+]

deduce/tokenizer.py

@@ -86,7 +86,6 @@ def _merge(
         i = 0
 
         while i < len(tokens):
-
             if tokens_text[i] not in self._start_words:
                 tokens_merged.append(tokens[i])
                 i += 1

deduce/utils.py

@@ -66,9 +66,7 @@ def initialize_class(cls: type, args: dict, extras: dict) -> object:
     cls_params = inspect.signature(cls).parameters
 
     for arg_name, arg in extras.items():
-
         if arg_name in cls_params:
-
             args[arg_name] = arg
 
     return cls(**args)
@@ -209,7 +207,6 @@ def apply_transform(items: set[str], transform_config: dict) -> set[str]:
     transforms = transform_config.get("transforms", {})
 
     for _, transform in transforms.items():
-
         to_add = []
 
         for item in items:

docs/emojize.py

@@ -20,11 +20,9 @@ def emojize_all(s: str) -> str:
 
 
 if __name__ == "__main__":
-
     dir = argv[1]
 
     for file in glob.glob(dir + "/*.html"):
-
         with open(file, "r") as f:
             html = f.readlines()