diff --git a/.github/workflows/medcat-v1-tutorials_main.yml b/.github/workflows/medcat-v1-tutorials_main.yml index d3c778785..d0000acf8 100644 --- a/.github/workflows/medcat-v1-tutorials_main.yml +++ b/.github/workflows/medcat-v1-tutorials_main.yml @@ -5,13 +5,13 @@ on: branches: [ main ] pull_request: paths: - - 'medcat-v1/**' - - 'medcat-v1-tutorials/**' + - 'v1/medcat/**' + - 'v1/medcat-tutorials/**' - '.github/workflows/medcat-v1**' - '.github/workflows/medcat-v1-tutorials**' defaults: run: - working-directory: ./medcat-v1-tutorials + working-directory: ./v1/medcat-tutorials jobs: main: diff --git a/.github/workflows/medcat-v1_main.yml b/.github/workflows/medcat-v1_main.yml index a60aead3c..3a9a2db89 100644 --- a/.github/workflows/medcat-v1_main.yml +++ b/.github/workflows/medcat-v1_main.yml @@ -5,11 +5,11 @@ on: branches: [ main ] pull_request: paths: - - 'medcat-v1/**' + - 'v1/medcat/**' - '.github/workflows/medcat-v1**' defaults: run: - working-directory: ./medcat-v1 + working-directory: ./v1/medcat jobs: build: diff --git a/.github/workflows/medcat-v1_production.yml b/.github/workflows/medcat-v1_production.yml index 791a24f3a..3d715f6f3 100644 --- a/.github/workflows/medcat-v1_production.yml +++ b/.github/workflows/medcat-v1_production.yml @@ -11,7 +11,7 @@ on: defaults: run: - working-directory: ./medcat-v1 + working-directory: ./v1/medcat jobs: build-n-publish-to-pypi: @@ -70,4 +70,4 @@ jobs: with: # TODO CU-869a25n7e Use Trusted Platform Publisher based PyPI release password: ${{ secrets.PYPI_API_TOKEN }} - packages_dir: medcat-v1/dist + packages_dir: v1/medcat/dist diff --git a/anoncat-demo-app/README.md b/anoncat-demo-app/README.md index d4ee545eb..dd819d8aa 100644 --- a/anoncat-demo-app/README.md +++ b/anoncat-demo-app/README.md @@ -1,6 +1,6 @@ # Deidentify app -Demo for AnonCAT. It uses [MedCAT](https://github.com/CogStack/cogstack-nlp/tree/main/medcat-v1), an advanced natural language processing tool, to identify and classify sensitive information, such as names, addresses, and medical terms. +Demo for AnonCAT. It uses [MedCAT](https://github.com/CogStack/cogstack-nlp/tree/main/v1/medcat), an advanced natural language processing tool, to identify and classify sensitive information, such as names, addresses, and medical terms. ## Example @@ -22,7 +22,7 @@ MODEL_NAME = '' ### Build your own model -To build your own models please follow the tutorials outlined in [MedCATtutorials](https://github.com/CogStack/cogstack-nlp/tree/main/medcat-v1-tutorials) +To build your own models please follow the tutorials outlined in [MedCATtutorials](https://github.com/CogStack/cogstack-nlp/tree/main/v1/medcat-tutorials) *__Note:__ This is currently under development* diff --git a/medcat-service/models/examples/examples.md b/medcat-service/models/examples/examples.md index 89445110a..2f0c591df 100644 --- a/medcat-service/models/examples/examples.md +++ b/medcat-service/models/examples/examples.md @@ -2,7 +2,7 @@ ## [example-medcat-v1-model-pack][(models/examples/example-medcat-v1-model-pack.zip) - This model pack is built by running the MedCAT V1 Tutorial Part 3.1. -- https://github.com/CogStack/cogstack-nlp/blob/main/medcat-v1-tutorials/notebooks/introductory/Part_3_1_Building_a_Concept_Database_and_Vocabulary.ipynb +- https://github.com/CogStack/cogstack-nlp/blob/main/v1/medcat-tutorials/notebooks/introductory/Part_3_1_Building_a_Concept_Database_and_Vocabulary.ipynb It isn't a trained model, but has the concepts "Kidney Failure" and "Failure of Kidneys" built in diff --git a/medcat-trainer/notebook_docs/API_Examples.ipynb b/medcat-trainer/notebook_docs/API_Examples.ipynb index d4ceffc87..22dcd3beb 100644 --- a/medcat-trainer/notebook_docs/API_Examples.ipynb +++ b/medcat-trainer/notebook_docs/API_Examples.ipynb @@ -216,7 +216,7 @@ "### Create CDBs and Vocabularies\n", "The MedCAT models used by MedCATTrainer are output by MedCAT instances of classesmedcat.cdb.CDB, medcat.utils.vocab.Vocabulary. Calling save_dict('\\') will write a file that can be loaded in another instance of MedCAT (via load_dict()), or within MedCATTrainer.\n", "\n", - "Examples models are provided on the MedCAT Repository: https://github.com/CogStack/cogstack-nlp/tree/main/medcat-v1" + "Examples models are provided on the MedCAT Repository: https://github.com/CogStack/cogstack-nlp/tree/main/v1/medcat" ] }, { diff --git a/medcat-trainer/notebook_docs/Generate_CUI_Filters.ipynb b/medcat-trainer/notebook_docs/Generate_CUI_Filters.ipynb index 6f4842e32..5f4adc384 100644 --- a/medcat-trainer/notebook_docs/Generate_CUI_Filters.ipynb +++ b/medcat-trainer/notebook_docs/Generate_CUI_Filters.ipynb @@ -25,7 +25,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Relation file from SNOMED-CT Preprocessing tutorial: https://github.com/CogStack/cogstack-nlp/blob/main/medcat-v1-tutorials/notebooks/specialised/Preprocessing_SNOMED_CT.ipynb, \n", + "Relation file from SNOMED-CT Preprocessing tutorial: https://github.com/CogStack/cogstack-nlp/blob/main/v1/medcat-tutorials/notebooks/specialised/Preprocessing_SNOMED_CT.ipynb, \n", "\n", "In section \"SNOMED Relationships\"\n" ] diff --git a/medcat-v1/medcat/datasets/medcat_annotations.py.lock b/medcat-v1/medcat/datasets/medcat_annotations.py.lock deleted file mode 100755 index e69de29bb..000000000 diff --git a/medcat-v1-tutorials/.gitignore b/v1/medcat-tutorials/.gitignore similarity index 100% rename from medcat-v1-tutorials/.gitignore rename to v1/medcat-tutorials/.gitignore diff --git a/medcat-v1-tutorials/LICENSE b/v1/medcat-tutorials/LICENSE similarity index 100% rename from medcat-v1-tutorials/LICENSE rename to v1/medcat-tutorials/LICENSE diff --git a/medcat-v1-tutorials/README.md b/v1/medcat-tutorials/README.md similarity index 100% rename from medcat-v1-tutorials/README.md rename to v1/medcat-tutorials/README.md diff --git a/medcat-v1-tutorials/git-config/hooks/pre-commit b/v1/medcat-tutorials/git-config/hooks/pre-commit 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similarity index 100% rename from medcat-v1/medcat/utils/preprocess_umls.py rename to v1/medcat/medcat/utils/preprocess_umls.py diff --git a/medcat-v1/medcat/utils/regression/README.md b/v1/medcat/medcat/utils/regression/README.md similarity index 100% rename from medcat-v1/medcat/utils/regression/README.md rename to v1/medcat/medcat/utils/regression/README.md diff --git a/medcat-v1/medcat/utils/regression/__init__.py b/v1/medcat/medcat/utils/regression/__init__.py similarity index 100% rename from medcat-v1/medcat/utils/regression/__init__.py rename to v1/medcat/medcat/utils/regression/__init__.py diff --git a/medcat-v1/medcat/utils/regression/checking.py b/v1/medcat/medcat/utils/regression/checking.py similarity index 100% rename from medcat-v1/medcat/utils/regression/checking.py rename to v1/medcat/medcat/utils/regression/checking.py diff --git a/medcat-v1/medcat/utils/regression/regression_checker.py b/v1/medcat/medcat/utils/regression/regression_checker.py similarity index 100% rename from medcat-v1/medcat/utils/regression/regression_checker.py rename to v1/medcat/medcat/utils/regression/regression_checker.py diff --git a/medcat-v1/medcat/utils/regression/results.py b/v1/medcat/medcat/utils/regression/results.py similarity index 100% rename from medcat-v1/medcat/utils/regression/results.py rename to v1/medcat/medcat/utils/regression/results.py diff --git a/medcat-v1/medcat/utils/regression/targeting.py b/v1/medcat/medcat/utils/regression/targeting.py similarity index 100% rename from medcat-v1/medcat/utils/regression/targeting.py rename to v1/medcat/medcat/utils/regression/targeting.py diff --git a/medcat-v1/medcat/utils/regression/utils.py b/v1/medcat/medcat/utils/regression/utils.py similarity index 100% rename from medcat-v1/medcat/utils/regression/utils.py rename to v1/medcat/medcat/utils/regression/utils.py diff --git a/medcat-v1/medcat/utils/relation_extraction/__init__.py b/v1/medcat/medcat/utils/relation_extraction/__init__.py similarity index 100% rename from medcat-v1/medcat/utils/relation_extraction/__init__.py rename to v1/medcat/medcat/utils/relation_extraction/__init__.py diff --git a/medcat-v1/medcat/utils/relation_extraction/base_component.py b/v1/medcat/medcat/utils/relation_extraction/base_component.py similarity index 100% rename from medcat-v1/medcat/utils/relation_extraction/base_component.py rename to v1/medcat/medcat/utils/relation_extraction/base_component.py diff --git a/medcat-v1/medcat/utils/relation_extraction/bert/__init__.py b/v1/medcat/medcat/utils/relation_extraction/bert/__init__.py similarity index 100% rename from medcat-v1/medcat/utils/relation_extraction/bert/__init__.py rename to v1/medcat/medcat/utils/relation_extraction/bert/__init__.py diff --git a/medcat-v1/medcat/utils/relation_extraction/bert/config.py b/v1/medcat/medcat/utils/relation_extraction/bert/config.py similarity index 100% rename from medcat-v1/medcat/utils/relation_extraction/bert/config.py rename to 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medcat-v1/medcat/utils/relation_extraction/llama/tokenizer.py rename to v1/medcat/medcat/utils/relation_extraction/llama/tokenizer.py diff --git a/medcat-v1/medcat/utils/relation_extraction/ml_utils.py b/v1/medcat/medcat/utils/relation_extraction/ml_utils.py similarity index 100% rename from medcat-v1/medcat/utils/relation_extraction/ml_utils.py rename to v1/medcat/medcat/utils/relation_extraction/ml_utils.py diff --git a/medcat-v1/medcat/utils/relation_extraction/models.py b/v1/medcat/medcat/utils/relation_extraction/models.py similarity index 100% rename from medcat-v1/medcat/utils/relation_extraction/models.py rename to v1/medcat/medcat/utils/relation_extraction/models.py diff --git a/medcat-v1/medcat/utils/relation_extraction/modernbert/__init__.py b/v1/medcat/medcat/utils/relation_extraction/modernbert/__init__.py similarity index 100% rename from medcat-v1/medcat/utils/relation_extraction/modernbert/__init__.py rename to 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diff --git a/medcat-v1/tests/resources/jsonpickle_rel_cat_config.json b/v1/medcat/tests/resources/jsonpickle_rel_cat_config.json similarity index 100% rename from medcat-v1/tests/resources/jsonpickle_rel_cat_config.json rename to v1/medcat/tests/resources/jsonpickle_rel_cat_config.json diff --git a/medcat-v1/tests/resources/jsonpickle_tner_config.json b/v1/medcat/tests/resources/jsonpickle_tner_config.json similarity index 100% rename from medcat-v1/tests/resources/jsonpickle_tner_config.json rename to v1/medcat/tests/resources/jsonpickle_tner_config.json diff --git a/medcat-v1/tests/resources/mct_export_for_meta_cat_test.json b/v1/medcat/tests/resources/mct_export_for_meta_cat_test.json similarity index 100% rename from medcat-v1/tests/resources/mct_export_for_meta_cat_test.json rename to v1/medcat/tests/resources/mct_export_for_meta_cat_test.json diff --git a/medcat-v1/tests/resources/medcat_rel_test.csv b/v1/medcat/tests/resources/medcat_rel_test.csv similarity index 100% rename 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a/medcat-v1/tests/resources/medcat_trainer_export_filtered.json b/v1/medcat/tests/resources/medcat_trainer_export_filtered.json similarity index 100% rename from medcat-v1/tests/resources/medcat_trainer_export_filtered.json rename to v1/medcat/tests/resources/medcat_trainer_export_filtered.json diff --git a/medcat-v1/tests/resources/medcat_trainer_export_relations.json b/v1/medcat/tests/resources/medcat_trainer_export_relations.json similarity index 100% rename from medcat-v1/tests/resources/medcat_trainer_export_relations.json rename to v1/medcat/tests/resources/medcat_trainer_export_relations.json diff --git a/medcat-v1/tests/resources/model_compatibility/check_backwards_compatibility.sh b/v1/medcat/tests/resources/model_compatibility/check_backwards_compatibility.sh similarity index 100% rename from medcat-v1/tests/resources/model_compatibility/check_backwards_compatibility.sh rename to v1/medcat/tests/resources/model_compatibility/check_backwards_compatibility.sh diff --git a/medcat-v1/tests/resources/regression/creation/cat_creation.py b/v1/medcat/tests/resources/regression/creation/cat_creation.py similarity index 100% rename from medcat-v1/tests/resources/regression/creation/cat_creation.py rename to v1/medcat/tests/resources/regression/creation/cat_creation.py diff --git a/medcat-v1/tests/resources/regression/creation/preprocessed4cdb.txt b/v1/medcat/tests/resources/regression/creation/preprocessed4cdb.txt similarity index 100% rename from medcat-v1/tests/resources/regression/creation/preprocessed4cdb.txt rename to v1/medcat/tests/resources/regression/creation/preprocessed4cdb.txt diff --git a/medcat-v1/tests/resources/regression/creation/selfsupervised_data.txt b/v1/medcat/tests/resources/regression/creation/selfsupervised_data.txt similarity index 100% rename from medcat-v1/tests/resources/regression/creation/selfsupervised_data.txt rename to v1/medcat/tests/resources/regression/creation/selfsupervised_data.txt diff --git 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