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(100%) rename {medcat-v1 => v1/medcat-v1}/tests/utils/test_decorators.py (100%) rename {medcat-v1 => v1/medcat-v1}/tests/utils/test_hashing.py (100%) rename {medcat-v1 => v1/medcat-v1}/tests/utils/test_helpers.py (100%) rename {medcat-v1 => v1/medcat-v1}/tests/utils/test_memory_optimiser.py (100%) rename {medcat-v1 => v1/medcat-v1}/tests/utils/test_normalizers.py (100%) rename {medcat-v1 => v1/medcat-v1}/tests/utils/test_preprocess_snomed.py (100%) rename {medcat-v1 => v1/medcat-v1}/tests/utils/test_spacy_compatibility.py (100%) rename {medcat-v1 => v1/medcat-v1}/tests/utils/test_usage_monitoring.py (100%) rename {medcat-v1 => v1/medcat-v1}/tests/utils/test_vocab_utils.py (100%) rename {medcat-v1 => v1/medcat-v1}/tutorial/README.md (100%) diff --git a/.github/workflows/medcat-v1-tutorials_main.yml b/.github/workflows/medcat-v1-tutorials_main.yml index d3c77878..7b66d247 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/**' + - 'v1/medcat-v1-tutorials/**' - '.github/workflows/medcat-v1**' - '.github/workflows/medcat-v1-tutorials**' defaults: run: - working-directory: ./medcat-v1-tutorials + working-directory: ./v1/medcat-v1-tutorials jobs: main: diff --git a/.github/workflows/medcat-v1_main.yml b/.github/workflows/medcat-v1_main.yml index a60aead3..78fd28a2 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-v1/**' - '.github/workflows/medcat-v1**' defaults: run: - working-directory: ./medcat-v1 + working-directory: ./v1/medcat-v1 jobs: build: diff --git a/.github/workflows/medcat-v1_production.yml b/.github/workflows/medcat-v1_production.yml index 791a24f3..1d5e704c 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-v1 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-v1/dist diff --git a/anoncat-demo-app/README.md b/anoncat-demo-app/README.md index d4ee545e..e0f85bbb 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-v1), 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-v1-tutorials) *__Note:__ This is currently under development* diff --git a/medcat-service/models/examples/examples.md b/medcat-service/models/examples/examples.md index 89445110..97a76cc6 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-v1-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 d4ceffc8..0fd7b87a 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-v1" ] }, { diff --git a/medcat-trainer/notebook_docs/Generate_CUI_Filters.ipynb b/medcat-trainer/notebook_docs/Generate_CUI_Filters.ipynb index 6f4842e3..0745c80d 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-v1-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 e69de29b..00000000 diff --git a/medcat-v1-tutorials/.gitignore b/v1/medcat-v1-tutorials/.gitignore similarity index 100% rename from medcat-v1-tutorials/.gitignore rename to v1/medcat-v1-tutorials/.gitignore diff --git a/medcat-v1-tutorials/LICENSE b/v1/medcat-v1-tutorials/LICENSE similarity index 100% rename from medcat-v1-tutorials/LICENSE rename to v1/medcat-v1-tutorials/LICENSE diff --git a/medcat-v1-tutorials/README.md b/v1/medcat-v1-tutorials/README.md similarity index 100% rename from medcat-v1-tutorials/README.md rename to v1/medcat-v1-tutorials/README.md diff --git a/medcat-v1-tutorials/git-config/hooks/pre-commit 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rename from medcat-v1/tests/utils/test_usage_monitoring.py rename to v1/medcat-v1/tests/utils/test_usage_monitoring.py diff --git a/medcat-v1/tests/utils/test_vocab_utils.py b/v1/medcat-v1/tests/utils/test_vocab_utils.py similarity index 100% rename from medcat-v1/tests/utils/test_vocab_utils.py rename to v1/medcat-v1/tests/utils/test_vocab_utils.py diff --git a/medcat-v1/tutorial/README.md b/v1/medcat-v1/tutorial/README.md similarity index 100% rename from medcat-v1/tutorial/README.md rename to v1/medcat-v1/tutorial/README.md From 9af5a1f0c1165eb109ad5b329339246d8625a4a9 Mon Sep 17 00:00:00 2001 From: alhendrickson <159636032+alhendrickson@users.noreply.github.com.> Date: Wed, 13 Aug 2025 12:49:09 +0000 Subject: [PATCH 2/2] chore: Move all Medcat V1 projects into a subfolder --- .github/workflows/medcat-v1-tutorials_main.yml | 6 +++--- .github/workflows/medcat-v1_main.yml | 4 ++-- .github/workflows/medcat-v1_production.yml | 4 ++-- anoncat-demo-app/README.md | 4 ++-- 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v1/{medcat-v1 => medcat}/tests/utils/test_memory_optimiser.py (100%) rename v1/{medcat-v1 => medcat}/tests/utils/test_normalizers.py (100%) rename v1/{medcat-v1 => medcat}/tests/utils/test_preprocess_snomed.py (100%) rename v1/{medcat-v1 => medcat}/tests/utils/test_spacy_compatibility.py (100%) rename v1/{medcat-v1 => medcat}/tests/utils/test_usage_monitoring.py (100%) rename v1/{medcat-v1 => medcat}/tests/utils/test_vocab_utils.py (100%) rename v1/{medcat-v1 => medcat}/tutorial/README.md (100%) diff --git a/.github/workflows/medcat-v1-tutorials_main.yml b/.github/workflows/medcat-v1-tutorials_main.yml index 7b66d247..d0000acf 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: - - 'v1/medcat-v1/**' - - 'v1/medcat-v1-tutorials/**' + - 'v1/medcat/**' + - 'v1/medcat-tutorials/**' - '.github/workflows/medcat-v1**' - '.github/workflows/medcat-v1-tutorials**' defaults: run: - working-directory: ./v1/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 78fd28a2..3a9a2db8 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: - - 'v1/medcat-v1/**' + - 'v1/medcat/**' - '.github/workflows/medcat-v1**' defaults: run: - working-directory: ./v1/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 1d5e704c..3d715f6f 100644 --- a/.github/workflows/medcat-v1_production.yml +++ b/.github/workflows/medcat-v1_production.yml @@ -11,7 +11,7 @@ on: defaults: run: - working-directory: ./v1/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: v1/medcat-v1/dist + packages_dir: v1/medcat/dist diff --git a/anoncat-demo-app/README.md b/anoncat-demo-app/README.md index e0f85bbb..dd819d8a 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/v1/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/v1/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 97a76cc6..2f0c591d 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/v1/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 0fd7b87a..22dcd3be 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/v1/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 0745c80d..5f4adc38 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/v1/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/v1/medcat-v1-tutorials/.gitignore b/v1/medcat-tutorials/.gitignore similarity index 100% rename from v1/medcat-v1-tutorials/.gitignore rename to v1/medcat-tutorials/.gitignore diff --git a/v1/medcat-v1-tutorials/LICENSE b/v1/medcat-tutorials/LICENSE similarity index 100% rename from v1/medcat-v1-tutorials/LICENSE rename to v1/medcat-tutorials/LICENSE diff --git a/v1/medcat-v1-tutorials/README.md b/v1/medcat-tutorials/README.md similarity index 100% rename from v1/medcat-v1-tutorials/README.md rename to v1/medcat-tutorials/README.md diff --git a/v1/medcat-v1-tutorials/git-config/hooks/pre-commit b/v1/medcat-tutorials/git-config/hooks/pre-commit similarity index 100% rename from v1/medcat-v1-tutorials/git-config/hooks/pre-commit rename to v1/medcat-tutorials/git-config/hooks/pre-commit diff --git 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