CogStack · alhendrickson · Aug 13, 2025 · Aug 13, 2025 · Aug 13, 2025
diff --git 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
@@ -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
@@ -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
@@ -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 = '<NAME OF MODEL HERE.zip>'
 
 ### 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
@@ -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
@@ -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('\\<file location\\>') 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
@@ -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
diff --git a/medcat-v1-tutorials/.gitignore → v1/medcat-tutorials/.gitignore b/medcat-v1-tutorials/.gitignore → v1/medcat-tutorials/.gitignore
diff --git a/medcat-v1-tutorials/LICENSE → v1/medcat-tutorials/LICENSE b/medcat-v1-tutorials/LICENSE → v1/medcat-tutorials/LICENSE
diff --git a/medcat-v1-tutorials/README.md → v1/medcat-tutorials/README.md b/medcat-v1-tutorials/README.md → v1/medcat-tutorials/README.md
diff --git a/...-v1-tutorials/git-config/hooks/pre-commit → ...cat-tutorials/git-config/hooks/pre-commit b/...-v1-tutorials/git-config/hooks/pre-commit → ...cat-tutorials/git-config/hooks/pre-commit
diff --git a/...art_1_1_OPTIONAL_Logging_With_MedCAT.html → ...art_1_1_OPTIONAL_Logging_With_MedCAT.html b/...art_1_1_OPTIONAL_Logging_With_MedCAT.html → ...art_1_1_OPTIONAL_Logging_With_MedCAT.html
diff --git a/...rt_1_1_OPTIONAL_Logging_With_MedCAT.ipynb → ...rt_1_1_OPTIONAL_Logging_With_MedCAT.ipynb b/...rt_1_1_OPTIONAL_Logging_With_MedCAT.ipynb → ...rt_1_1_OPTIONAL_Logging_With_MedCAT.ipynb
diff --git a/...t_2_Dataset_Analysis_and_Preparation.html → ...t_2_Dataset_Analysis_and_Preparation.html b/...t_2_Dataset_Analysis_and_Preparation.html → ...t_2_Dataset_Analysis_and_Preparation.html
diff --git a/..._2_Dataset_Analysis_and_Preparation.ipynb → ..._2_Dataset_Analysis_and_Preparation.ipynb b/..._2_Dataset_Analysis_and_Preparation.ipynb → ..._2_Dataset_Analysis_and_Preparation.ipynb
diff --git a/...ng_a_Concept_Database_and_Vocabulary.html → ...ng_a_Concept_Database_and_Vocabulary.html b/...ng_a_Concept_Database_and_Vocabulary.html → ...ng_a_Concept_Database_and_Vocabulary.html
diff --git a/...g_a_Concept_Database_and_Vocabulary.ipynb → ...g_a_Concept_Database_and_Vocabulary.ipynb b/...g_a_Concept_Database_and_Vocabulary.ipynb → ...g_a_Concept_Database_and_Vocabulary.ipynb
diff --git a/...eases_from_Electronic_Health_Records.html → ...eases_from_Electronic_Health_Records.html b/...eases_from_Electronic_Health_Records.html → ...eases_from_Electronic_Health_Records.html
diff --git a/...ases_from_Electronic_Health_Records.ipynb → ...ases_from_Electronic_Health_Records.ipynb b/...ases_from_Electronic_Health_Records.ipynb → ...ases_from_Electronic_Health_Records.ipynb
diff --git a/...rt_3_3_Model_technical_optimisations.html → ...rt_3_3_Model_technical_optimisations.html b/...rt_3_3_Model_technical_optimisations.html → ...rt_3_3_Model_technical_optimisations.html
diff --git a/...t_3_3_Model_technical_optimisations.ipynb → ...t_3_3_Model_technical_optimisations.ipynb b/...t_3_3_Model_technical_optimisations.ipynb → ...t_3_3_Model_technical_optimisations.ipynb
diff --git a/...ByteLevelBPETokenizer_and_Embeddings.html → ...ByteLevelBPETokenizer_and_Embeddings.html b/...ByteLevelBPETokenizer_and_Embeddings.html → ...ByteLevelBPETokenizer_and_Embeddings.html
diff --git a/...yteLevelBPETokenizer_and_Embeddings.ipynb → ...yteLevelBPETokenizer_and_Embeddings.ipynb b/...yteLevelBPETokenizer_and_Embeddings.ipynb → ...yteLevelBPETokenizer_and_Embeddings.ipynb
diff --git a/...rvised_Training_and_Meta_annotations.html → ...rvised_Training_and_Meta_annotations.html b/...rvised_Training_and_Meta_annotations.html → ...rvised_Training_and_Meta_annotations.html
diff --git a/...vised_Training_and_Meta_annotations.ipynb → ...vised_Training_and_Meta_annotations.ipynb b/...vised_Training_and_Meta_annotations.ipynb → ...vised_Training_and_Meta_annotations.ipynb
diff --git a/...MedCAT_pipeline_with_MetaAnnotations.html → ...MedCAT_pipeline_with_MetaAnnotations.html b/...MedCAT_pipeline_with_MetaAnnotations.html → ...MedCAT_pipeline_with_MetaAnnotations.html
diff --git a/...edCAT_pipeline_with_MetaAnnotations.ipynb → ...edCAT_pipeline_with_MetaAnnotations.ipynb b/...edCAT_pipeline_with_MetaAnnotations.ipynb → ...edCAT_pipeline_with_MetaAnnotations.ipynb
diff --git a/...ence_of_Physical_and_Mental_Diseases.html → ...ence_of_Physical_and_Mental_Diseases.html b/...ence_of_Physical_and_Mental_Diseases.html → ...ence_of_Physical_and_Mental_Diseases.html
diff --git a/...nce_of_Physical_and_Mental_Diseases.ipynb → ...nce_of_Physical_and_Mental_Diseases.ipynb b/...nce_of_Physical_and_Mental_Diseases.ipynb → ...nce_of_Physical_and_Mental_Diseases.ipynb
diff --git a/...ervised_Training_Relation_Extraction.html → ...ervised_Training_Relation_Extraction.html b/...ervised_Training_Relation_Extraction.html → ...ervised_Training_Relation_Extraction.html
diff --git a/...rvised_Training_Relation_Extraction.ipynb → ...rvised_Training_Relation_Extraction.ipynb b/...rvised_Training_Relation_Extraction.ipynb → ...rvised_Training_Relation_Extraction.ipynb
diff --git a/...om_annotations_with_Relation_toolkit.html → ...om_annotations_with_Relation_toolkit.html b/...om_annotations_with_Relation_toolkit.html → ...om_annotations_with_Relation_toolkit.html
diff --git a/...m_annotations_with_Relation_toolkit.ipynb → ...m_annotations_with_Relation_toolkit.ipynb b/...m_annotations_with_Relation_toolkit.ipynb → ...m_annotations_with_Relation_toolkit.ipynb
diff --git a/...ooks/introductory/data/MedCAT_Export.json → ...ooks/introductory/data/MedCAT_Export.json b/...ooks/introductory/data/MedCAT_Export.json → ...ooks/introductory/data/MedCAT_Export.json
diff --git a/...ta/MedCAT_Export_relation_extraction.json → ...ta/MedCAT_Export_relation_extraction.json b/...ta/MedCAT_Export_relation_extraction.json → ...ta/MedCAT_Export_relation_extraction.json
diff --git a/...ebooks/introductory/data/cdb_advanced.csv → ...ebooks/introductory/data/cdb_advanced.csv b/...ebooks/introductory/data/cdb_advanced.csv → ...ebooks/introductory/data/cdb_advanced.csv
diff --git a/...otebooks/introductory/data/cdb_simple.csv → ...otebooks/introductory/data/cdb_simple.csv b/...otebooks/introductory/data/cdb_simple.csv → ...otebooks/introductory/data/cdb_simple.csv
diff --git a/...books/introductory/data/cui_location.json → ...books/introductory/data/cui_location.json b/...books/introductory/data/cui_location.json → ...books/introductory/data/cui_location.json
diff --git a/...otebooks/introductory/data/noteevents.csv → ...otebooks/introductory/data/noteevents.csv b/...otebooks/introductory/data/noteevents.csv → ...otebooks/introductory/data/noteevents.csv
diff --git a/.../notebooks/introductory/data/patients.csv → .../notebooks/introductory/data/patients.csv b/.../notebooks/introductory/data/patients.csv → .../notebooks/introductory/data/patients.csv
diff --git a/.../notebooks/introductory/data/pt_notes.csv → .../notebooks/introductory/data/pt_notes.csv b/.../notebooks/introductory/data/pt_notes.csv → .../notebooks/introductory/data/pt_notes.csv
diff --git a/...ooks/introductory/data/rel_cat_ADE_V2.tsv → ...ooks/introductory/data/rel_cat_ADE_V2.tsv b/...ooks/introductory/data/rel_cat_ADE_V2.tsv → ...ooks/introductory/data/rel_cat_ADE_V2.tsv
diff --git a/...otebooks/introductory/data/vocab_data.txt → ...otebooks/introductory/data/vocab_data.txt b/...otebooks/introductory/data/vocab_data.txt → ...otebooks/introductory/data/vocab_data.txt
diff --git a/...omparing_Models_with_RegressionSuite.html → ...omparing_Models_with_RegressionSuite.html b/...omparing_Models_with_RegressionSuite.html → ...omparing_Models_with_RegressionSuite.html
diff --git a/...mparing_Models_with_RegressionSuite.ipynb → ...mparing_Models_with_RegressionSuite.ipynb b/...mparing_Models_with_RegressionSuite.ipynb → ...mparing_Models_with_RegressionSuite.ipynb
diff --git a/.../specialised/Preprocessing_SNOMED_CT.html → .../specialised/Preprocessing_SNOMED_CT.html b/.../specialised/Preprocessing_SNOMED_CT.html → .../specialised/Preprocessing_SNOMED_CT.html
diff --git a/...specialised/Preprocessing_SNOMED_CT.ipynb → ...specialised/Preprocessing_SNOMED_CT.ipynb b/...specialised/Preprocessing_SNOMED_CT.ipynb → ...specialised/Preprocessing_SNOMED_CT.ipynb
diff --git a/...cialised/data_regr/Keggle_MCT_export.json → ...cialised/data_regr/Keggle_MCT_export.json b/...cialised/data_regr/Keggle_MCT_export.json → ...cialised/data_regr/Keggle_MCT_export.json
diff --git a/...ooks/specialised/data_regr/categories.yml → ...ooks/specialised/data_regr/categories.yml b/...ooks/specialised/data_regr/categories.yml → ...ooks/specialised/data_regr/categories.yml
diff --git a/medcat-v1-tutorials/requirements-dev.txt → v1/medcat-tutorials/requirements-dev.txt b/medcat-v1-tutorials/requirements-dev.txt → v1/medcat-tutorials/requirements-dev.txt
diff --git a/medcat-v1/.dockerignore → v1/medcat/.dockerignore b/medcat-v1/.dockerignore → v1/medcat/.dockerignore
diff --git a/medcat-v1/.flake8 → v1/medcat/.flake8 b/medcat-v1/.flake8 → v1/medcat/.flake8
diff --git a/medcat-v1/.gitignore → v1/medcat/.gitignore b/medcat-v1/.gitignore → v1/medcat/.gitignore
@@ -55,4 +55,6 @@ tests/model_creator/output/*
 docs/auto/
 docs/_build
 
-models/
+
+models/*
+!models/README.md
diff --git a/medcat-v1/.readthedocs.yaml → v1/medcat/.readthedocs.yaml b/medcat-v1/.readthedocs.yaml → v1/medcat/.readthedocs.yaml
diff --git a/medcat-v1/CODE_OF_CONDUCT.md → v1/medcat/CODE_OF_CONDUCT.md b/medcat-v1/CODE_OF_CONDUCT.md → v1/medcat/CODE_OF_CONDUCT.md
diff --git a/medcat-v1/CONTRIBUTING.md → v1/medcat/CONTRIBUTING.md b/medcat-v1/CONTRIBUTING.md → v1/medcat/CONTRIBUTING.md
diff --git a/medcat-v1/LICENSE → v1/medcat/LICENSE b/medcat-v1/LICENSE → v1/medcat/LICENSE
diff --git a/medcat-v1/README.md → v1/medcat/README.md b/medcat-v1/README.md → v1/medcat/README.md
diff --git a/...-v1/configs/base_train_selfsupervised.txt → ...cat/configs/base_train_selfsupervised.txt b/...-v1/configs/base_train_selfsupervised.txt → ...cat/configs/base_train_selfsupervised.txt
diff --git a/medcat-v1/configs/base_validate.txt → v1/medcat/configs/base_validate.txt b/medcat-v1/configs/base_validate.txt → v1/medcat/configs/base_validate.txt
diff --git a/...t-v1/configs/default_regression_tests.yml → ...dcat/configs/default_regression_tests.yml b/...t-v1/configs/default_regression_tests.yml → ...dcat/configs/default_regression_tests.yml
diff --git a/medcat-v1/docs/Makefile → v1/medcat/docs/Makefile b/medcat-v1/docs/Makefile → v1/medcat/docs/Makefile
diff --git a/medcat-v1/docs/_static/css/overrides.css → v1/medcat/docs/_static/css/overrides.css b/medcat-v1/docs/_static/css/overrides.css → v1/medcat/docs/_static/css/overrides.css
diff --git a/...cs/_templates/autoapi_templates/index.rst → ...cs/_templates/autoapi_templates/index.rst b/...cs/_templates/autoapi_templates/index.rst → ...cs/_templates/autoapi_templates/index.rst
diff --git a/medcat-v1/docs/conf.py → v1/medcat/docs/conf.py b/medcat-v1/docs/conf.py → v1/medcat/docs/conf.py
diff --git a/medcat-v1/docs/index.rst → v1/medcat/docs/index.rst b/medcat-v1/docs/index.rst → v1/medcat/docs/index.rst
diff --git a/medcat-v1/docs/main.md → v1/medcat/docs/main.md b/medcat-v1/docs/main.md → v1/medcat/docs/main.md
diff --git a/medcat-v1/docs/make.bat → v1/medcat/docs/make.bat b/medcat-v1/docs/make.bat → v1/medcat/docs/make.bat
diff --git a/medcat-v1/docs/requirements.txt → v1/medcat/docs/requirements.txt b/medcat-v1/docs/requirements.txt → v1/medcat/docs/requirements.txt
diff --git a/medcat-v1/examples/README.md → v1/medcat/examples/README.md b/medcat-v1/examples/README.md → v1/medcat/examples/README.md
diff --git a/medcat-v1/examples/cdb.csv → v1/medcat/examples/cdb.csv b/medcat-v1/examples/cdb.csv → v1/medcat/examples/cdb.csv
diff --git a/medcat-v1/examples/cdb.dat → v1/medcat/examples/cdb.dat b/medcat-v1/examples/cdb.dat → v1/medcat/examples/cdb.dat
diff --git a/medcat-v1/examples/cdb_2.csv → v1/medcat/examples/cdb_2.csv b/medcat-v1/examples/cdb_2.csv → v1/medcat/examples/cdb_2.csv
diff --git a/...ples/cdb_old_broken_weights_in_config.dat → ...ples/cdb_old_broken_weights_in_config.dat b/...ples/cdb_old_broken_weights_in_config.dat → ...ples/cdb_old_broken_weights_in_config.dat
diff --git a/medcat-v1/examples/complex_cdb.csv → v1/medcat/examples/complex_cdb.csv b/medcat-v1/examples/complex_cdb.csv → v1/medcat/examples/complex_cdb.csv
diff --git a/...t-v1/examples/medmentions/medmentions.txt → ...dcat/examples/medmentions/medmentions.txt b/...t-v1/examples/medmentions/medmentions.txt → ...dcat/examples/medmentions/medmentions.txt
diff --git a/...amples/run_standalone_meta_annotations.py → ...amples/run_standalone_meta_annotations.py b/...amples/run_standalone_meta_annotations.py → ...amples/run_standalone_meta_annotations.py
diff --git a/medcat-v1/examples/vocab.dat → v1/medcat/examples/vocab.dat b/medcat-v1/examples/vocab.dat → v1/medcat/examples/vocab.dat
diff --git a/medcat-v1/examples/vocab_data.txt → v1/medcat/examples/vocab_data.txt b/medcat-v1/examples/vocab_data.txt → v1/medcat/examples/vocab_data.txt
diff --git a/medcat-v1/install_requires.txt → v1/medcat/install_requires.txt b/medcat-v1/install_requires.txt → v1/medcat/install_requires.txt
diff --git a/medcat-v1/medcat/LICENSE → v1/medcat/medcat/LICENSE b/medcat-v1/medcat/LICENSE → v1/medcat/medcat/LICENSE
diff --git a/medcat-v1/medcat/__init__.py → v1/medcat/medcat/__init__.py b/medcat-v1/medcat/__init__.py → v1/medcat/medcat/__init__.py
diff --git a/medcat-v1/medcat/cat.py → v1/medcat/medcat/cat.py b/medcat-v1/medcat/cat.py → v1/medcat/medcat/cat.py
diff --git a/medcat-v1/medcat/cdb.py → v1/medcat/medcat/cdb.py b/medcat-v1/medcat/cdb.py → v1/medcat/medcat/cdb.py
diff --git a/medcat-v1/medcat/cdb_maker.py → v1/medcat/medcat/cdb_maker.py b/medcat-v1/medcat/cdb_maker.py → v1/medcat/medcat/cdb_maker.py
diff --git a/medcat-v1/medcat/config.py → v1/medcat/medcat/config.py b/medcat-v1/medcat/config.py → v1/medcat/medcat/config.py
diff --git a/medcat-v1/medcat/config_meta_cat.py → v1/medcat/medcat/config_meta_cat.py b/medcat-v1/medcat/config_meta_cat.py → v1/medcat/medcat/config_meta_cat.py
diff --git a/medcat-v1/medcat/config_rel_cat.py → v1/medcat/medcat/config_rel_cat.py b/medcat-v1/medcat/config_rel_cat.py → v1/medcat/medcat/config_rel_cat.py
diff --git a/medcat-v1/medcat/config_transformers_ner.py → v1/medcat/medcat/config_transformers_ner.py b/medcat-v1/medcat/config_transformers_ner.py → v1/medcat/medcat/config_transformers_ner.py
diff --git a/medcat-v1/medcat/datasets/__init__.py → v1/medcat/medcat/datasets/__init__.py b/medcat-v1/medcat/datasets/__init__.py → v1/medcat/medcat/datasets/__init__.py
diff --git a/medcat-v1/medcat/datasets/data_collator.py → v1/medcat/medcat/datasets/data_collator.py b/medcat-v1/medcat/datasets/data_collator.py → v1/medcat/medcat/datasets/data_collator.py
diff --git a/medcat-v1/medcat/datasets/helpers.py → v1/medcat/medcat/datasets/helpers.py b/medcat-v1/medcat/datasets/helpers.py → v1/medcat/medcat/datasets/helpers.py
diff --git a/...-v1/medcat/datasets/medcat_annotations.py → ...cat/medcat/datasets/medcat_annotations.py b/...-v1/medcat/datasets/medcat_annotations.py → ...cat/medcat/datasets/medcat_annotations.py
diff --git a/...medcat/datasets/patient_concept_stream.py → ...medcat/datasets/patient_concept_stream.py b/...medcat/datasets/patient_concept_stream.py → ...medcat/datasets/patient_concept_stream.py
diff --git a/...at-v1/medcat/datasets/transformers_ner.py → ...edcat/medcat/datasets/transformers_ner.py b/...at-v1/medcat/datasets/transformers_ner.py → ...edcat/medcat/datasets/transformers_ner.py
diff --git a/medcat-v1/medcat/linking/__init__.py → v1/medcat/medcat/linking/__init__.py b/medcat-v1/medcat/linking/__init__.py → v1/medcat/medcat/linking/__init__.py
diff --git a/...v1/medcat/linking/context_based_linker.py → ...at/medcat/linking/context_based_linker.py b/...v1/medcat/linking/context_based_linker.py → ...at/medcat/linking/context_based_linker.py
diff --git a/...v1/medcat/linking/vector_context_model.py → ...at/medcat/linking/vector_context_model.py b/...v1/medcat/linking/vector_context_model.py → ...at/medcat/linking/vector_context_model.py
diff --git a/medcat-v1/medcat/meta_cat.py → v1/medcat/medcat/meta_cat.py b/medcat-v1/medcat/meta_cat.py → v1/medcat/medcat/meta_cat.py
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diff --git a/...sources/mct_export_for_meta_cat_test.json → ...sources/mct_export_for_meta_cat_test.json b/...sources/mct_export_for_meta_cat_test.json → ...sources/mct_export_for_meta_cat_test.json
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diff --git a/...ests/resources/medcat_trainer_export.json → ...ests/resources/medcat_trainer_export.json b/...ests/resources/medcat_trainer_export.json → ...ests/resources/medcat_trainer_export.json
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diff --git a/...tibility/check_backwards_compatibility.sh → ...tibility/check_backwards_compatibility.sh b/...tibility/check_backwards_compatibility.sh → ...tibility/check_backwards_compatibility.sh
diff --git a/...urces/regression/creation/cat_creation.py → ...urces/regression/creation/cat_creation.py b/...urces/regression/creation/cat_creation.py → ...urces/regression/creation/cat_creation.py
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diff --git a/...ssion/creation/supervised_mct_export.json → ...ssion/creation/supervised_mct_export.json b/...ssion/creation/supervised_mct_export.json → ...ssion/creation/supervised_mct_export.json
diff --git a/...ources/regression/creation/vocab_data.txt → ...ources/regression/creation/vocab_data.txt b/...ources/regression/creation/vocab_data.txt → ...ources/regression/creation/vocab_data.txt
diff --git a/...ts/resources/regression/run_regression.sh → ...ts/resources/regression/run_regression.sh b/...ts/resources/regression/run_regression.sh → ...ts/resources/regression/run_regression.sh
diff --git a/.../tests/resources/regression/test_vocab.py → .../tests/resources/regression/test_vocab.py b/.../tests/resources/regression/test_vocab.py → .../tests/resources/regression/test_vocab.py
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diff --git a/medcat-v1/tests/stats/test_kfold.py → v1/medcat/tests/stats/test_kfold.py b/medcat-v1/tests/stats/test_kfold.py → v1/medcat/tests/stats/test_kfold.py
diff --git a/medcat-v1/tests/stats/test_mctexport.py → v1/medcat/tests/stats/test_mctexport.py b/medcat-v1/tests/stats/test_mctexport.py → v1/medcat/tests/stats/test_mctexport.py
diff --git a/medcat-v1/tests/test_cat.py → v1/medcat/tests/test_cat.py b/medcat-v1/tests/test_cat.py → v1/medcat/tests/test_cat.py
diff --git a/medcat-v1/tests/test_cdb.py → v1/medcat/tests/test_cdb.py b/medcat-v1/tests/test_cdb.py → v1/medcat/tests/test_cdb.py
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diff --git a/medcat-v1/tests/test_meta_cat.py → v1/medcat/tests/test_meta_cat.py b/medcat-v1/tests/test_meta_cat.py → v1/medcat/tests/test_meta_cat.py
diff --git a/medcat-v1/tests/test_ner.py → v1/medcat/tests/test_ner.py b/medcat-v1/tests/test_ner.py → v1/medcat/tests/test_ner.py
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diff --git a/medcat-v1/tests/test_rel_cat.py → v1/medcat/tests/test_rel_cat.py b/medcat-v1/tests/test_rel_cat.py → v1/medcat/tests/test_rel_cat.py
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diff --git a/medcat-v1/tests/utils/ner/test_deid.py → v1/medcat/tests/utils/ner/test_deid.py b/medcat-v1/tests/utils/ner/test_deid.py → v1/medcat/tests/utils/ner/test_deid.py
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diff --git a/...t-v1/tests/utils/regression/test_utils.py → ...dcat/tests/utils/regression/test_utils.py b/...t-v1/tests/utils/regression/test_utils.py → ...dcat/tests/utils/regression/test_utils.py
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diff --git a/medcat-v1/tests/utils/saving/test_coding.py → v1/medcat/tests/utils/saving/test_coding.py b/medcat-v1/tests/utils/saving/test_coding.py → v1/medcat/tests/utils/saving/test_coding.py
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diff --git a/.../tests/utils/saving/test_serialization.py → .../tests/utils/saving/test_serialization.py b/.../tests/utils/saving/test_serialization.py → .../tests/utils/saving/test_serialization.py
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diff --git a/medcat-v1/tests/utils/test_checkpoint.py → v1/medcat/tests/utils/test_checkpoint.py b/medcat-v1/tests/utils/test_checkpoint.py → v1/medcat/tests/utils/test_checkpoint.py
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diff --git a/...t-v1/tests/utils/test_memory_optimiser.py → ...dcat/tests/utils/test_memory_optimiser.py b/...t-v1/tests/utils/test_memory_optimiser.py → ...dcat/tests/utils/test_memory_optimiser.py
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diff --git a/medcat-v1/tutorial/README.md → v1/medcat/tutorial/README.md b/medcat-v1/tutorial/README.md → v1/medcat/tutorial/README.md