.gitignore
.readthedocs.yaml
README.md
mkdocs.yml
mypy.ini
pyproject.toml
uv.lock
.release/README.md
.release/install_bundle_readme.md
.release/prepare_minor_release.sh
.release/prepare_patch_release.sh
.release/prepare_release.sh
docs/architecture.md
docs/breaking_changes.md
docs/index.md
docs/migration_guide_v2.md
docs/pyproject.toml
docs/uv.lock
docs/_static/img/cat-logo.png
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medcat/__init__.py
medcat/__main__.py
medcat/cat.py
medcat/py.typed
medcat/trainer.py
medcat/version.py
medcat/vocab.py
medcat.egg-info/PKG-INFO
medcat.egg-info/SOURCES.txt
medcat.egg-info/dependency_links.txt
medcat.egg-info/requires.txt
medcat.egg-info/top_level.txt
medcat/cdb/__init__.py
medcat/cdb/cdb.py
medcat/cdb/concepts.py
medcat/components/__init__.py
medcat/components/types.py
medcat/components/addons/__init__.py
medcat/components/addons/addons.py
medcat/components/addons/meta_cat/__init__.py
medcat/components/addons/meta_cat/data_utils.py
medcat/components/addons/meta_cat/meta_cat.py
medcat/components/addons/meta_cat/ml_utils.py
medcat/components/addons/meta_cat/models.py
medcat/components/addons/meta_cat/mctokenizers/__init__.py
medcat/components/addons/meta_cat/mctokenizers/bert_tokenizer.py
medcat/components/addons/meta_cat/mctokenizers/bpe_tokenizer.py
medcat/components/addons/meta_cat/mctokenizers/tokenizers.py
medcat/components/addons/relation_extraction/__init__.py
medcat/components/addons/relation_extraction/base_component.py
medcat/components/addons/relation_extraction/config.py
medcat/components/addons/relation_extraction/ml_utils.py
medcat/components/addons/relation_extraction/models.py
medcat/components/addons/relation_extraction/pad_seq.py
medcat/components/addons/relation_extraction/rel_cat.py
medcat/components/addons/relation_extraction/rel_dataset.py
medcat/components/addons/relation_extraction/tokenizer.py
medcat/components/addons/relation_extraction/bert/__init__.py
medcat/components/addons/relation_extraction/bert/config.py
medcat/components/addons/relation_extraction/bert/model.py
medcat/components/addons/relation_extraction/bert/tokenizer.py
medcat/components/addons/relation_extraction/llama/__init__.py
medcat/components/addons/relation_extraction/llama/config.py
medcat/components/addons/relation_extraction/llama/model.py
medcat/components/addons/relation_extraction/llama/tokenizer.py
medcat/components/addons/relation_extraction/modernbert/__init__.py
medcat/components/addons/relation_extraction/modernbert/config.py
medcat/components/addons/relation_extraction/modernbert/model.py
medcat/components/addons/relation_extraction/modernbert/tokenizer.py
medcat/components/linking/__init__.py
medcat/components/linking/context_based_linker.py
medcat/components/linking/no_action_linker.py
medcat/components/linking/only_primary_name_linker.py
medcat/components/linking/two_step_context_based_linker.py
medcat/components/linking/vector_context_model.py
medcat/components/ner/__init__.py
medcat/components/ner/dict_based_ner.py
medcat/components/ner/vocab_based_annotator.py
medcat/components/ner/vocab_based_ner.py
medcat/components/ner/trf/__init__.py
medcat/components/ner/trf/deid.py
medcat/components/ner/trf/helpers.py
medcat/components/ner/trf/model.py
medcat/components/ner/trf/tokenizer.py
medcat/components/ner/trf/transformers_ner.py
medcat/components/normalizing/__init__.py
medcat/components/normalizing/normalizer.py
medcat/components/tagging/__init__.py
medcat/components/tagging/tagger.py
medcat/config/__init__.py
medcat/config/config.py
medcat/config/config_meta_cat.py
medcat/config/config_rel_cat.py
medcat/config/config_transformers_ner.py
medcat/data/__init__.py
medcat/data/entities.py
medcat/data/mctexport.py
medcat/data/model_card.py
medcat/deid/__init__.py
medcat/model_creation/__init__.py
medcat/model_creation/cdb_maker.py
medcat/model_creation/preprocess_snomed.py
medcat/model_creation/preprocess_umls.py
medcat/pipeline/__init__.py
medcat/pipeline/pipeline.py
medcat/pipeline/speed_utils.py
medcat/plugins/__init__.py
medcat/plugins/catalog.py
medcat/plugins/cli.py
medcat/plugins/downloadable.py
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medcat/plugins/loader.py
medcat/plugins/registry.py
medcat/plugins/data/__init__.py
medcat/plugins/data/plugin_catalog.json
medcat/preprocessors/__init__.py
medcat/preprocessors/cleaners.py
medcat/stats/__init__.py
medcat/stats/kfold.py
medcat/stats/stats.py
medcat/storage/__init__.py
medcat/storage/jsonserialiser.py
medcat/storage/mp_ents_save.py
medcat/storage/schema.py
medcat/storage/serialisables.py
medcat/storage/serialisers.py
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medcat/tokenizing/__init__.py
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medcat/tokenizing/spacy_impl/tokenizers.py
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medcat/tokenizing/spacy_impl/utils.py
medcat/utils/__init__.py
medcat/utils/cdb_state.py
medcat/utils/cdb_utils.py
medcat/utils/check_for_updates.py
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medcat/utils/legacy/__init__.py
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medcat/utils/legacy/convert_config.py
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medcat/utils/legacy/convert_meta_cat.py
medcat/utils/legacy/convert_rel_cat.py
medcat/utils/legacy/convert_vocab.py
medcat/utils/legacy/fixes.py
medcat/utils/legacy/helpers.py
medcat/utils/legacy/identifier.py
medcat/utils/legacy/legacy_converter.py
medcat/utils/legacy/v2_beta.py
medcat/utils/ner/__init__.py
medcat/utils/ner/data_collator.py
medcat/utils/ner/metrics.py
medcat/utils/ner/transformers_ner.py
medcat/utils/regression/__init__.py
medcat/utils/regression/checking.py
medcat/utils/regression/regression_checker.py
medcat/utils/regression/results.py
medcat/utils/regression/targeting.py
medcat/utils/regression/utils.py
tests/__init__.py
tests/test_cat.py
tests/test_trainer.py
tests/test_vocab.py
tests/backwards_compatibility/check_backwards_compatibility.sh
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tests/backwards_compatibility/creation/cat_creation.py
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tests/backwards_compatibility/testing/example_regression_suite.yml
tests/backwards_compatibility/testing/test_vocab.py
tests/cdb/__init__.py
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tests/components/__init__.py
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tests/components/addons/test_addons.py
tests/components/addons/meta_cat/__init__.py
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tests/components/ner/trf/__init__.py
tests/components/ner/trf/test_transformers_ner.py
tests/components/normalizing/__init__.py
tests/components/normalizing/test_normalizer.py
tests/components/tagging/__init__.py
tests/components/tagging/test_tagger.py
tests/config/__init__.py
tests/config/test_config.py
tests/config/test_config_env_at_import_time.py
tests/config/test_config_import_no_warnings.py
tests/config/test_config_serialisation.py
tests/data/__init__.py
tests/data/test_mctexport.py
tests/model_creation/__init__.py
tests/model_creation/test_cdb_maker.py
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tests/other/download_all_transformers_models.py
tests/pipeline/__init__.py
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tests/plugins/__init__.py
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tests/resources/cdb_example.csv
tests/resources/cdb_meta.csv
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tests/resources/deid_test_data.json
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tests/resources/mct2_cdb/.schema.json
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tests/resources/mct2_cdb/config/components/tagging/.serialised_by
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