diff --git a/CHANGELOG.md b/CHANGELOG.md index cd25470..7a65695 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,13 +7,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 :exclamation: = Breaking change -## (unreleased) +## 0.8.0 (2024-06-03) ### Changed * :exclamation: Renamed the `clinlp_entity_matcher` to `clinlp_rule_based_entity_matcher` * :exclamation: `clinlp` now stores entities in `doc.spans['ents']` rather than `doc.ents`, allowing for overlap * :exclamation: Overlap in entities found by the entity matcher is no longer resolved by default (replacing old behaviour). To remove overlap, pass `resolve_overlap=True`. +* Refactored tests to use `pytest` best practices * Changed `clinlp_autocomponent` to `clinlp_component`, which automatically registers your component with spaCy +* Codebase and linting improvements +* Renamed the `other_threshold` config to `family_threshold` in the `clinlp_experiencer_transformer` component ### Fixed * The `clinlp_rule_based_entity_matcher` no longer overwrites entities detected by other components (but appends them) diff --git a/poetry.lock b/poetry.lock index 9b41340..8ad47d3 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,13 +2,13 @@ [[package]] name = "accelerate" -version = "0.29.3" +version = "0.30.1" description = "Accelerate" optional = false python-versions = ">=3.8.0" files = [ - {file = "accelerate-0.29.3-py3-none-any.whl", hash = "sha256:99d633d4b6126817c5e554487406748be95c8d1d1e659dd2fd60657e35f532dd"}, - {file = "accelerate-0.29.3.tar.gz", hash = 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"phonemizer", "pyctcdecode (>=0.4.0)"] ftfy = ["ftfy"] integrations = ["optuna", "ray[tune] (>=2.7.0)", "sigopt"] @@ -2392,7 +2401,7 @@ natten = ["natten (>=0.14.6,<0.15.0)"] onnx = ["onnxconverter-common", "onnxruntime (>=1.4.0)", "onnxruntime-tools (>=1.4.2)", "tf2onnx"] onnxruntime = ["onnxruntime (>=1.4.0)", "onnxruntime-tools (>=1.4.2)"] optuna = ["optuna"] -quality = ["GitPython (<3.1.19)", "datasets (!=2.5.0)", "hf-doc-builder (>=0.3.0)", "isort (>=5.5.4)", "ruff (==0.1.5)", "urllib3 (<2.0.0)"] +quality = ["GitPython (<3.1.19)", "datasets (!=2.5.0)", "isort (>=5.5.4)", "ruff (==0.1.5)", "urllib3 (<2.0.0)"] ray = ["ray[tune] (>=2.7.0)"] retrieval = ["datasets (!=2.5.0)", "faiss-cpu"] sagemaker = ["sagemaker (>=2.31.0)"] @@ -2401,16 +2410,16 @@ serving = ["fastapi", "pydantic", "starlette", "uvicorn"] sigopt = ["sigopt"] sklearn = ["scikit-learn"] speech = ["kenlm", "librosa", "phonemizer", "pyctcdecode (>=0.4.0)", "torchaudio"] -testing = ["GitPython (<3.1.19)", "beautifulsoup4", 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"tokenizers (>=0.19,<0.20)", "torch", "tqdm (>=4.27)"] +torchhub = ["filelock", "huggingface-hub (>=0.23.0,<1.0)", "importlib-metadata", "numpy (>=1.17)", "packaging (>=20.0)", "protobuf", "regex (!=2019.12.17)", "requests", "sentencepiece (>=0.1.91,!=0.1.92)", "tokenizers (>=0.19,<0.20)", "torch", "tqdm (>=4.27)"] video = ["av (==9.2.0)", "decord (==0.6.0)"] vision = ["Pillow (>=10.0.1,<=15.0)"] @@ -2460,13 +2469,13 @@ test = ["black (>=22.3.0,<23.0.0)", "coverage (>=6.2,<7.0)", "isort (>=5.0.6,<6. [[package]] name = "typing-extensions" -version = "4.11.0" +version = "4.12.1" description = "Backported and Experimental Type Hints for Python 3.8+" optional = false python-versions = ">=3.8" files = [ - {file = "typing_extensions-4.11.0-py3-none-any.whl", hash = "sha256:c1f94d72897edaf4ce775bb7558d5b79d8126906a14ea5ed1635921406c0387a"}, - {file = "typing_extensions-4.11.0.tar.gz", hash = "sha256:83f085bd5ca59c80295fc2a82ab5dac679cbe02b9f33f7d83af68e241bea51b0"}, + {file = "typing_extensions-4.12.1-py3-none-any.whl", hash = "sha256:6024b58b69089e5a89c347397254e35f1bf02a907728ec7fee9bf0fe837d203a"}, + {file = "typing_extensions-4.12.1.tar.gz", hash = "sha256:915f5e35ff76f56588223f15fdd5938f9a1cf9195c0de25130c627e4d597f6d1"}, ] [[package]] @@ -2499,13 +2508,13 @@ zstd = ["zstandard (>=0.18.0)"] [[package]] name = "wasabi" -version = "1.1.2" +version = "1.1.3" description = "A lightweight console printing and formatting toolkit" optional = false python-versions = ">=3.6" files = [ - {file = "wasabi-1.1.2-py3-none-any.whl", hash = "sha256:0a3f933c4bf0ed3f93071132c1b87549733256d6c8de6473c5f7ed2e171b5cf9"}, - {file = "wasabi-1.1.2.tar.gz", hash = "sha256:1aaef3aceaa32edb9c91330d29d3936c0c39fdb965743549c173cb54b16c30b5"}, + {file = "wasabi-1.1.3-py3-none-any.whl", hash = "sha256:f76e16e8f7e79f8c4c8be49b4024ac725713ab10cd7f19350ad18a8e3f71728c"}, + {file = "wasabi-1.1.3.tar.gz", hash = "sha256:4bb3008f003809db0c3e28b4daf20906ea871a2bb43f9914197d540f4f2e0878"}, ] [package.dependencies] diff --git a/pyproject.toml b/pyproject.toml index adcb4ab..bab844f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "clinlp" -version = "0.7.0" +version = "0.8.0" description = "Performant and production-ready NLP pipelines for clinical text written in Dutch" authors = ["UMCU DIT Analytics "] readme = "README.md" diff --git a/src/clinlp/ie/entity.py b/src/clinlp/ie/entity.py index 7cf5c7d..8da85be 100644 --- a/src/clinlp/ie/entity.py +++ b/src/clinlp/ie/entity.py @@ -1,4 +1,3 @@ - import intervaltree as ivt import numpy as np import pandas as pd @@ -57,7 +56,6 @@ def __init__(self) -> None: @clinlp_component( name="clinlp_rule_based_entity_matcher", - requires=["doc.sents"], assigns=["doc.spans"], default_config=_defaults_term | _defaults_entity_matcher, ) diff --git a/src/clinlp/ie/qualifier/transformer.py b/src/clinlp/ie/qualifier/transformer.py index 2adedbd..8058d3a 100644 --- a/src/clinlp/ie/qualifier/transformer.py +++ b/src/clinlp/ie/qualifier/transformer.py @@ -37,7 +37,7 @@ } _defaults_experiencer_transformer = { "token_window": 64, - "other_threshold": 0.5, + "family_threshold": 0.5, } @@ -209,11 +209,11 @@ class ExperiencerTransformer(QualifierTransformer): def __init__( self, nlp: Language, - other_threshold: float = _defaults_experiencer_transformer["other_threshold"], + family_threshold: float = _defaults_experiencer_transformer["family_threshold"], **kwargs, ) -> None: self.nlp = nlp - self.other_threshold = other_threshold + self.family_threshold = family_threshold super().__init__(**kwargs) @@ -221,7 +221,7 @@ def __init__( def qualifier_classes(self) -> dict[str, QualifierClass]: return { "Experiencer": QualifierClass( - "Experiencer", ["Patient", "Family"], default="Patient" + "Experiencer", ["Patient", "Family", "Other"], default="Patient" ) } @@ -237,7 +237,7 @@ def _detect_qualifiers(self, doc: Doc) -> None: prob_aggregator=self.prob_aggregator, ) - if prob > self.other_threshold: + if prob > self.family_threshold: self.add_qualifier_to_ent( ent, self.qualifier_classes["Experiencer"].create("Family", prob=prob),