docs(medcat): Move away from v2 prefix

.github/workflows/medcat-den_main.yml

@@ -34,7 +34,7 @@ jobs:
           uv sync --all-extras --dev
           uv run python -m ensurepip
           uv run python -m pip install --upgrade pip
-          uv run python -m pip install "../medcat-v2[spacy,deid,meta-cat,rel-cat]"
+          uv run python -m pip install "../medcat[spacy,deid,meta-cat,rel-cat]"
       - name: Check types
         run: |
           uv run python -m mypy --follow-imports=normal src/medcat_den

.github/workflows/medcat-deps-update.yml

@@ -50,4 +50,4 @@ jobs:
           python .github/scripts/bump_dependants.py \
             --version "${{ steps.version.outputs.version }}" \
             --package "medcat" \
-            --dependants "medcat-scripts" "medcat-v2-tutorials" "medcat-service"
+            --dependants "medcat-scripts" "medcat-tutorials" "medcat-service"

.github/workflows/medcat-embedding-linker_ci.yml

@@ -36,7 +36,7 @@ jobs:
           uv sync --all-extras --dev
           uv run python -m ensurepip
           uv run python -m pip install --upgrade pip
-          uv run python -m pip install "../../medcat-v2[spacy]"
+          uv run python -m pip install "../../medcat[spacy]"
       - name: Check types
         run: |
           uv run python -m mypy --follow-imports=normal src/medcat_embedding_linker

.github/workflows/medcat-model-distributor_build.yml

@@ -11,7 +11,7 @@ on:
   pull_request:
     paths:
       - 'medcat-model-distributor/**'
-      - 'medcat-v2/**'
+      - 'medcat/**'
       - '.github/workflows/medcat-model-distributor**'
 defaults:
   run:

.github/workflows/medcat-scripts_main.yml

@@ -36,7 +36,7 @@ jobs:
           uv pip install -r requirements.txt
           uv pip install -r requirements-dev.txt
           # reinstall MedCAT from local to test against changes in core lib
-          uv pip install "../medcat-v2[spacy,deid,meta-cat,rel-cat]"
+          uv pip install "../medcat[spacy,deid,meta-cat,rel-cat]"
       - name: Check types
         run: |
           # NOTE: Only testing against .py files in this folder

.github/workflows/medcat-service_docker.yml

@@ -7,7 +7,7 @@ on:
       - 'medcat-service/v*.*.*'  # e.g., medcat-serice/v0.1.1
   pull_request:
     paths:
-      - 'medcat-v2/**'
+      - 'medcat/**'
       - 'medcat-service/**'
       - '.github/workflows/medcat-service**'
 
@@ -66,7 +66,7 @@ jobs:
           flavor: latest=false
 
       - name: Make medact-v2 available within build
-        run: cp -r ../medcat-v2 medcat-v2
+        run: cp -r ../medcat medcat
 
       - name: Build Docker MedCATservice image for testing
         id: docker_build

.github/workflows/medcat-service_run-tests.yml

@@ -5,7 +5,7 @@ on:
     branches: [ main ]
   pull_request:
     paths:
-      - 'medcat-v2/**'
+      - 'medcat/**'
       - 'medcat-service/**'
       - '.github/workflows/medcat-service**'
 
@@ -40,7 +40,7 @@ jobs:
           python -m pip install virtualenv setuptools
           python -m pip install isort flake8 mypy stubs types-Flask types-simplejson types-setuptools types-requests
           python -m pip install -r ./requirements.txt --extra-index-url https://download.pytorch.org/whl/cpu/;
-          python -m pip install "../medcat-v2[meta-cat,spacy,deid]"
+          python -m pip install "../medcat[meta-cat,spacy,deid]"
 
       - name: Check linting and types
         run: |

.github/workflows/medcat-trainer_ci.yml

@@ -152,7 +152,7 @@ jobs:
       matrix:
         medcat-source:
           - released   # current behaviour, pins to lockfile
-          - local      # tests against ../medcat-v2
+          - local      # tests against ../medcat
     steps:
       - name: Checkout main
         uses: actions/checkout@v7
@@ -197,7 +197,7 @@ jobs:
         if: matrix.medcat-source == 'local'
         run: |
           cd webapp
-          uv pip install --editable "../../medcat-v2[meta-cat,spacy,rel-cat,deid,dict-ner]"
+          uv pip install --editable "../../medcat[meta-cat,spacy,rel-cat,deid,dict-ner]"
 
       - name: Run Django tests with coverage
         env:

.github/workflows/medcat-transformer-ner-ci.yml

@@ -36,7 +36,7 @@ jobs:
           uv sync --all-extras --dev
           uv run python -m ensurepip
           uv run python -m pip install --upgrade pip
-          uv run python -m pip install "../../medcat-v2[spacy]"
+          uv run python -m pip install "../../medcat[spacy]"
       - name: Check types
         run: |
           uv run python -m mypy --follow-imports=normal src/medcat_transformer_ner

.github/workflows/medcat-v2-lib-stability.yml

@@ -11,7 +11,7 @@ on:
 
 defaults:
   run:
-    working-directory: ./medcat-v2
+    working-directory: ./medcat
 
 
 jobs:

.github/workflows/medcat-v2-tutorials_main.yml

@@ -1,17 +1,17 @@
-name: medcat-v2-tutorials - Test
+name: medcat-tutorials - Test
 
 on:
   push:
     branches: [ main ]
   pull_request:
     paths:
-      - 'medcat-v2/**'
-      - 'medcat-v2-tutorials/**'
+      - 'medcat/**'
+      - 'medcat-tutorials/**'
       - '.github/workflows/medcat-v2**'
-      - '.github/workflows/medcat-v2-tutorials**'
+      - '.github/workflows/medcat-tutorials**'
 defaults:
   run:
-    working-directory: ./medcat-v2-tutorials
+    working-directory: ./medcat-tutorials
 
 jobs:
   basic-and-meta:
@@ -32,7 +32,7 @@ jobs:
         run: |
           pip install -U pip
           pip install -r requirements.txt
-          pip install "../medcat-v2[spacy,deid,rel-cat,meta-cat]"
+          pip install "../medcat[spacy,deid,rel-cat,meta-cat]"
 
       - name: Install IPython kernel
         run: |
@@ -79,7 +79,7 @@ jobs:
         run: |
           pip install -U pip
           pip install -r requirements.txt
-          pip install "../medcat-v2[spacy,deid,rel-cat,meta-cat]"
+          pip install "../medcat[spacy,deid,rel-cat,meta-cat]"
 
       - name: Install IPython kernel
         run: |

.github/workflows/medcat-v2_main.yml

@@ -1,15 +1,15 @@
-name: medcat-v2 - Test
+name: medcat - Test
 
 on:
   push:
     branches: [ main ]
   pull_request:
     paths:
-      - 'medcat-v2/**'
+      - 'medcat/**'
       - '.github/workflows/medcat-v2**'
 defaults:
   run:
-    working-directory: ./medcat-v2
+    working-directory: ./medcat
 jobs:
   test-resource-utils:
    runs-on: ubuntu-latest
@@ -28,7 +28,7 @@ jobs:
         with:
           python-version: "3.10"
           enable-cache: true
-          cache-dependency-glob: "medcat-v2/uv.lock"
+          cache-dependency-glob: "medcat/uv.lock"
       - name: Install the project
         run: |
           uv sync # NO extras
@@ -49,7 +49,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
           enable-cache: true
-          cache-dependency-glob: "medcat-v2/uv.lock"
+          cache-dependency-glob: "medcat/uv.lock"
       - name: Install the project
         run: |
           uv sync --all-extras --dev

.github/workflows/medcat-v2_release.yml

@@ -1,4 +1,4 @@
-name: medcat-v2 - Build Python Package
+name: medcat - Build Python Package
 
 on:
   push:
@@ -13,11 +13,11 @@ permissions:
 
 defaults:
   run:
-    working-directory: ./medcat-v2
+    working-directory: ./medcat
 
 jobs:
   build:
-    name: Build medcat-v2 wheel
+    name: Build medcat wheel
     runs-on: ubuntu-latest
     outputs:
       version_tag: ${{ steps.extract.outputs.version_tag }}
@@ -71,10 +71,10 @@ jobs:
       - name: Upload wheel artifact
         uses: actions/upload-artifact@v7
         with:
-          name: medcat-v2-wheel
+          name: medcat-wheel
           path: |
-            medcat-v2/dist/*.whl
-            medcat-v2/dist/*.tar.gz
+            medcat/dist/*.whl
+            medcat/dist/*.tar.gz
 
   bundle:
     name: Build install bundles
@@ -131,8 +131,8 @@ jobs:
       - name: Download built medcat wheel for inclusion in bundles
         uses: actions/download-artifact@v8
         with:
-          name: medcat-v2-wheel
-          path: medcat-v2/built-wheel
+          name: medcat-wheel
+          path: medcat/built-wheel
 
       - name: List downloaded artifacts
         run: ls -lh built-wheel
@@ -152,8 +152,8 @@ jobs:
         with:
           name: bundles-${{ matrix.python-version }}
           path: |
-            medcat-v2/medcat-v${{ needs.build.outputs.version_only }}-${{ matrix.python-version }}-cpu.tar.gz
-#            medcat-v2/medcat-v${{ needs.build.outputs.version_only }}-${{ matrix.python-version }}-gpu.tar.gz
+            medca2/medcat-v${{ needs.build.outputs.version_only }}-${{ matrix.python-version }}-cpu.tar.gz
+#            medcat/medcat-v${{ needs.build.outputs.version_only }}-${{ matrix.python-version }}-gpu.tar.gz
 
   release:
     name: Create GitHub Release
@@ -163,7 +163,7 @@ jobs:
       - name: Download all artifacts
         uses: actions/download-artifact@v8
         with:
-          path: medcat-v2/artifacts
+          path: medcat/artifacts
 
       - name: Move all bundles to dist/
         run: |
@@ -175,8 +175,8 @@ jobs:
       - name: Download built wheel
         uses: actions/download-artifact@v8
         with:
-          name: medcat-v2-wheel
-          path: medcat-v2/dist-wheel
+          name: medcat-wheel
+          path: medcat/dist-wheel
 
       - name: Move wheels to dist/
         run: |
@@ -194,7 +194,7 @@ jobs:
           draft: true
           # softprops/action-gh-release v2 doesnt support the working-directory field, so put the path in files
           files: |
-            medcat-v2/dist/*
+            medcat/dist/*
 
       - name: Remove install bundles in preparations for PyPI push
         run: |
@@ -204,7 +204,7 @@ jobs:
       - name: Publish to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
-          packages-dir: medcat-v2/dist
+          packages-dir: medcat/dist
 
   # test-time models for download
   upload-test-models:

README.md

@@ -8,15 +8,15 @@
 
 ## Latest Releases
 
-[![medcat-v2](https://img.shields.io/github/v/release/CogStack/cogstack-nlp?filter=medcat/*&label=medcat-v2)](https://github.com/CogStack/cogstack-nlp/releases/latest)
+[![medcat](https://img.shields.io/github/v/release/CogStack/cogstack-nlp?filter=medcat/*&label=medcat-v2)](https://github.com/CogStack/cogstack-nlp/releases/latest)
 [![medcat-den](https://img.shields.io/github/v/release/CogStack/cogstack-nlp?filter=medcat-den/*&label=medcat-den)](https://github.com/CogStack/cogstack-nlp/releases/latest)
 [![medcat-trainer](https://img.shields.io/github/v/release/CogStack/cogstack-nlp?filter=medcat-trainer/*&label=medcat-trainer)](https://github.com/CogStack/cogstack-nlp/releases/latest)
 [![medcat-service](https://img.shields.io/github/v/release/CogStack/cogstack-nlp?filter=medcat-service/*&label=medcat-service)](https://github.com/CogStack/cogstack-nlp/releases/latest)
 <!-- [![pypi Version](https://img.shields.io/pypi/v/medcat.svg?style=flat-square&logo=pypi&logoColor=white)](https://pypi.org/project/medcat/) -->
 
 CogStack Natural Language Processing offers tools to process and extract information from clinical text and documents in Electronic Health Records (EHRs).
 
-The primary NLP focus is the [Medical Concept Annotation Tool](medcat-v2/README.md) (MedCAT), a self-supervised machine learning algorithm for extracting concepts using any concept vocabulary including UMLS/SNOMED-CT. See the paper on [arXiv](https://arxiv.org/abs/2010.01165).
+The primary NLP focus is the [Medical Concept Annotation Tool](medcat/README.md) (MedCAT), a self-supervised machine learning algorithm for extracting concepts using any concept vocabulary including UMLS/SNOMED-CT. See the paper on [arXiv](https://arxiv.org/abs/2010.01165).
 
 
 **Official Docs [here](https://docs.cogstack.org)**
@@ -27,11 +27,11 @@ The primary NLP focus is the [Medical Concept Annotation Tool](medcat-v2/README.
 ## Projects
 
 ### NLP
-- [Medical Concept Annotation Tool](medcat-v2/README.md): MedCAT can be used to extract information from Electronic Health Records (EHRs) and link it to biomedical ontologies like SNOMED-CT, UMLS, or HPO (and potentially other ontologies).
+- [Medical Concept Annotation Tool](medcat/README.md): MedCAT can be used to extract information from Electronic Health Records (EHRs) and link it to biomedical ontologies like SNOMED-CT, UMLS, or HPO (and potentially other ontologies).
 - [Medical Concept Annotation Tool Trainer](medcat-trainer/README.md): MedCATTrainer is an interface for building, improving and customising a given Named Entity Recognition and Linking (NER+L) model (MedCAT) for biomedical domain text.
-- [MedCAT Service](medcat-service/README.md): A REST API wrapper for [MedCAT](https://github.com/CogStack/cogstack-nlp/blob/main/medcat-v2/), allowing you to send text for processing and receive structured annotations in response.
+- [MedCAT Service](medcat-service/README.md): A REST API wrapper for [MedCAT](https://github.com/CogStack/cogstack-nlp/blob/main/medcat/), allowing you to send text for processing and receive structured annotations in response.
 
 ### Learning and Demos
-- [Deidentify app](anoncat-demo-app/README.md): Demo for AnonCAT. It uses [MedCAT](https://github.com/CogStack/cogstack-nlp/tree/main/medcat-v2), an advanced natural language processing tool, to identify and classify sensitive information, such as names, addresses, and medical terms.
+- [Deidentify app](anoncat-demo-app/README.md): Demo for AnonCAT. It uses [MedCAT](https://github.com/CogStack/cogstack-nlp/tree/main/medcat), an advanced natural language processing tool, to identify and classify sensitive information, such as names, addresses, and medical terms.
 - [MedCAT Demo App](medcat-demo-app/README.md): A simple web application showcasing how to use MedCAT for clinical text annotation.
-- [MedCAT Tutorials](medcat-v2-tutorials/README.md): The MedCAT Tutorials privde an interactive learning path for using MedCAT
+- [MedCAT Tutorials](medcat-tutorials/README.md): The MedCAT Tutorials privde an interactive learning path for using MedCAT

SECURITY.md

@@ -7,7 +7,7 @@ There are multiple projects in this repo. Versions are released as tags with a p
 We actively support security updates for the following versions:
 
 ### MedCAT NLP Library
-- [Medical Concept Annotation Tool](medcat-v2/README.md)
+- [Medical Concept Annotation Tool](medcat/README.md)
 
 | Version         | Supported          |
 | -------         | ------------------ |
@@ -55,4 +55,4 @@ Instead, report it privately by using the **[GitHub Security Advisories](https:/
 
 - Do not publicly disclose details of the vulnerability until we have released a fix.
 - Do not attempt to exploit the vulnerability beyond what is necessary to demonstrate it.
-- Provide as much detail as possible (affected versions, reproduction steps, etc.) to help us triage the issue quickly.
+- Provide as much detail as possible (affected versions, reproduction steps, etc.) to help us triage the issue quickly.

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-v2), 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/medcat), an advanced natural language processing tool, to identify and classify sensitive information, such as names, addresses, and medical terms.
 
 ## Example
 

medcat-den/tests/resource_fetch.py

@@ -1,5 +1,5 @@
 # NOTE: this file is designed to be copied across the following sub-folders
-#         1. medcat-v2/tests/resource_fetch.py
+#         1. medcat/tests/resource_fetch.py
 #         2. medcat-den/tests/resource_fetch.py
 #       So if you make changes here, copy them over to the others as well.
 #

medcat-model-distributor/docker-compose-test.yml

@@ -3,7 +3,7 @@ services:
     build:
       context: ./webapp
     volumes:
-      - ../medcat-v2/tests/resources:/webapp/models
+      - ../medcat/tests/resources:/webapp/models
     ports:
       - "8000:8000"
     env_file:

medcat-scripts/README.md

@@ -3,7 +3,7 @@
 This project contains the relevant tools and notebooks to help users work with MedCAT models.
 This includes instructions on finetuning models in an unsupervised or supervised manner as well as evaluating MedCATtrainer exports and run models on data.
 
-Some tutorials in [medcat-v2-tutorials](../medcat-v2-tutorials/) may also be of help.
+Some tutorials in [medcat-tutorials](../medcat-tutorials/) may also be of help.
 
 # Setup
 
@@ -20,4 +20,4 @@ python -m medcat download-scripts
 You may subsequently need to install the relevant requirements
 ```
 python -m pip install -r requirements.txt
-```
+```

medcat-service/Dockerfile

@@ -29,7 +29,7 @@ COPY . /cat
 ARG REINSTALL_CORE_FROM_LOCAL=false
 RUN if [ "$REINSTALL_CORE_FROM_LOCAL" = "true" ]; then \
         echo "Reinstalling medcat based on relative path"; \
-        SETUPTOOLS_SCM_PRETEND_VERSION="2.4.0-dev0" pip install -e "./medcat-v2[meta-cat,spacy]"; \
+        SETUPTOOLS_SCM_PRETEND_VERSION="2.4.0-dev0" pip install -e "./medcat[meta-cat,spacy]"; \
     fi
 
 # Now run the simple api

medcat-service/Dockerfile_gpu

@@ -50,7 +50,7 @@ COPY . /cat
 ARG REINSTALL_CORE_FROM_LOCAL=false
 RUN if [ "$REINSTALL_CORE_FROM_LOCAL" = "true" ]; then \
         echo "Reinstalling medcat based on relative path"; \
-        SETUPTOOLS_SCM_PRETEND_VERSION="2.4.0-dev0" pip install -e "./medcat-v2[meta-cat,spacy]"; \
+        SETUPTOOLS_SCM_PRETEND_VERSION="2.4.0-dev0" pip install -e "./medcat[meta-cat,spacy]"; \
     fi
 
 # Now run the simple api