diff --git a/.github/workflows/medcat-den_main.yml b/.github/workflows/medcat-den_main.yml index e1a3aaafd..35a62bfcf 100644 --- a/.github/workflows/medcat-den_main.yml +++ b/.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 diff --git a/.github/workflows/medcat-deps-update.yml b/.github/workflows/medcat-deps-update.yml index b531306f9..7ef1e146a 100644 --- a/.github/workflows/medcat-deps-update.yml +++ b/.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" diff --git a/.github/workflows/medcat-embedding-linker_ci.yml b/.github/workflows/medcat-embedding-linker_ci.yml index 2876d784b..852c7daa7 100644 --- a/.github/workflows/medcat-embedding-linker_ci.yml +++ b/.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 diff --git a/.github/workflows/medcat-model-distributor_build.yml b/.github/workflows/medcat-model-distributor_build.yml index 6d9248041..47b012db4 100644 --- a/.github/workflows/medcat-model-distributor_build.yml +++ b/.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: diff --git a/.github/workflows/medcat-scripts_main.yml b/.github/workflows/medcat-scripts_main.yml index b7dd6b8e0..14730b691 100644 --- a/.github/workflows/medcat-scripts_main.yml +++ b/.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 diff --git a/.github/workflows/medcat-service_docker.yml b/.github/workflows/medcat-service_docker.yml index 01937a206..f67aa40f3 100644 --- a/.github/workflows/medcat-service_docker.yml +++ b/.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 diff --git a/.github/workflows/medcat-service_run-tests.yml b/.github/workflows/medcat-service_run-tests.yml index 2912eb65b..9af59e6d7 100644 --- a/.github/workflows/medcat-service_run-tests.yml +++ b/.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: | diff --git a/.github/workflows/medcat-trainer_ci.yml b/.github/workflows/medcat-trainer_ci.yml index 0290e577e..90964486d 100644 --- a/.github/workflows/medcat-trainer_ci.yml +++ b/.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: diff --git a/.github/workflows/medcat-transformer-ner-ci.yml b/.github/workflows/medcat-transformer-ner-ci.yml index 35a9e4d6b..4e86b37bd 100644 --- a/.github/workflows/medcat-transformer-ner-ci.yml +++ b/.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 diff --git a/.github/workflows/medcat-v2-lib-stability.yml b/.github/workflows/medcat-v2-lib-stability.yml index ec94198b4..6a4264198 100644 --- a/.github/workflows/medcat-v2-lib-stability.yml +++ b/.github/workflows/medcat-v2-lib-stability.yml @@ -11,7 +11,7 @@ on: defaults: run: - working-directory: ./medcat-v2 + working-directory: ./medcat jobs: diff --git a/.github/workflows/medcat-v2-tutorials_main.yml b/.github/workflows/medcat-v2-tutorials_main.yml index 86aa03a38..b16c132c8 100644 --- a/.github/workflows/medcat-v2-tutorials_main.yml +++ b/.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: | diff --git a/.github/workflows/medcat-v2_main.yml b/.github/workflows/medcat-v2_main.yml index a48888b16..d1eb36eeb 100644 --- a/.github/workflows/medcat-v2_main.yml +++ b/.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 diff --git a/.github/workflows/medcat-v2_release.yml b/.github/workflows/medcat-v2_release.yml index 0efa6b7b9..571df0e11 100644 --- a/.github/workflows/medcat-v2_release.yml +++ b/.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: diff --git a/README.md b/README.md index 354a4fd3e..a28b0e833 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,7 @@ ## 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) @@ -16,7 +16,7 @@ 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 \ No newline at end of file +- [MedCAT Tutorials](medcat-tutorials/README.md): The MedCAT Tutorials privde an interactive learning path for using MedCAT diff --git a/SECURITY.md b/SECURITY.md index 9b4295c8d..c79579ad9 100644 --- a/SECURITY.md +++ b/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. \ No newline at end of file +- Provide as much detail as possible (affected versions, reproduction steps, etc.) to help us triage the issue quickly. diff --git a/anoncat-demo-app/README.md b/anoncat-demo-app/README.md index 4520ccb24..ec5e90262 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-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 diff --git a/medcat-den/tests/resource_fetch.py b/medcat-den/tests/resource_fetch.py index 6ac710958..63630d5ba 100644 --- a/medcat-den/tests/resource_fetch.py +++ b/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. # diff --git a/medcat-model-distributor/docker-compose-test.yml b/medcat-model-distributor/docker-compose-test.yml index 9b0b20888..5de50d528 100644 --- a/medcat-model-distributor/docker-compose-test.yml +++ b/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: diff --git a/medcat-scripts/README.md b/medcat-scripts/README.md index 2de430a48..95b8c1ba9 100644 --- a/medcat-scripts/README.md +++ b/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 -``` \ No newline at end of file +``` diff --git a/medcat-service/Dockerfile b/medcat-service/Dockerfile index cf6eb8fe9..042fa4110 100644 --- a/medcat-service/Dockerfile +++ b/medcat-service/Dockerfile @@ -29,7 +29,7 @@ COPY . /cat ARG REINSTALL_CORE_FROM_LOCAL=false RUN if [ "$REINSTALL_CORE_FROM_LOCAL" = "true" ]; then \ echo "Reinstalling medcat based on relative path"; \ - SETUPTOOLS_SCM_PRETEND_VERSION="2.4.0-dev0" pip install -e "./medcat-v2[meta-cat,spacy]"; \ + SETUPTOOLS_SCM_PRETEND_VERSION="2.4.0-dev0" pip install -e "./medcat[meta-cat,spacy]"; \ fi # Now run the simple api diff --git a/medcat-service/Dockerfile_gpu b/medcat-service/Dockerfile_gpu index 2086e64f5..b54ac35b8 100644 --- a/medcat-service/Dockerfile_gpu +++ b/medcat-service/Dockerfile_gpu @@ -50,7 +50,7 @@ COPY . /cat ARG REINSTALL_CORE_FROM_LOCAL=false RUN if [ "$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 diff --git a/medcat-service/README.md b/medcat-service/README.md index 149ee34c4..bbdce0b6b 100644 --- a/medcat-service/README.md +++ b/medcat-service/README.md @@ -1,6 +1,6 @@ # MedCAT Service -Medcat service is a REST API for serving [MedCAT](https://github.com/CogStack/cogstack-nlp/blob/main/medcat-v2/) models, allowing you to send text for processing and receive structured annotations in response. +Medcat service is a REST API for serving [MedCAT](https://github.com/CogStack/cogstack-nlp/blob/main/medcat/) models, allowing you to send text for processing and receive structured annotations in response. See the documentation on https://docs.cogstack.org/ for the docs on medcat service. @@ -82,14 +82,14 @@ Both files allow tailoring MedCAT for specific use-cases. When running MedCAT Se ## Local development -For local development, set up a Python virtual environment, install dependencies with pip, and make sure to also install the local MedCAT core library (the `medcat-v2` folder) in editable mode. +For local development, set up a Python virtual environment, install dependencies with pip, and make sure to also install the local MedCAT core library (the `medcat` folder) in editable mode. ```bash python -m venv .venv source .venv/bin/activate pip install -r requirements.txt -r requirements-dev.txt -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]" bash start_service_debug.sh # Service will run on localhost:8000 -``` \ No newline at end of file +``` diff --git a/medcat-service/docs/index.md b/medcat-service/docs/index.md index 3df08afb1..42ff6efd6 100644 --- a/medcat-service/docs/index.md +++ b/medcat-service/docs/index.md @@ -1,6 +1,6 @@ # Medcat service documentation -Medcat service is a REST API for serving [MedCAT](https://github.com/CogStack/cogstack-nlp/blob/main/medcat-v2/) models, allowing you to perform named entity resolution and deidentification of medical text over an API. +Medcat service is a REST API for serving [MedCAT](https://github.com/CogStack/cogstack-nlp/blob/main/medcat/) models, allowing you to perform named entity resolution and deidentification of medical text over an API. Feel free to ask questions on the github issue tracker or on our [discourse website](https://discourse.cogstack.org) which is frequently used by our development team! diff --git a/medcat-service/docs/setup/configuration.md b/medcat-service/docs/setup/configuration.md index 657de80eb..dfc7f7da2 100644 --- a/medcat-service/docs/setup/configuration.md +++ b/medcat-service/docs/setup/configuration.md @@ -75,7 +75,7 @@ The main settings that can be used to improve the performance when querying larg MedCAT parameters are defined in selected `envs/medcat*` file. -For details on available MedCAT parameters please refer to [the official GitHub repository](https://github.com/CogStack/cogstack-nlp/blob/main/medcat-v2/). +For details on available MedCAT parameters please refer to [the official GitHub repository](https://github.com/CogStack/cogstack-nlp/blob/main/medcat/). ## Custom footer markdown diff --git a/medcat-v2-tutorials/.ci/patch_notebook_installs.py b/medcat-tutorials/.ci/patch_notebook_installs.py similarity index 98% rename from medcat-v2-tutorials/.ci/patch_notebook_installs.py rename to medcat-tutorials/.ci/patch_notebook_installs.py index 4a201fd60..545751192 100644 --- a/medcat-v2-tutorials/.ci/patch_notebook_installs.py +++ b/medcat-tutorials/.ci/patch_notebook_installs.py @@ -5,7 +5,7 @@ import argparse -rel_install_path = "../medcat-v2/" +rel_install_path = "../medcat/" abs_install_path = str(pathlib.Path(rel_install_path).resolve()) # Matches either: diff --git a/medcat-v2-tutorials/README.md b/medcat-tutorials/README.md similarity index 56% rename from medcat-v2-tutorials/README.md rename to medcat-tutorials/README.md index 771b05229..bdbfe4306 100644 --- a/medcat-v2-tutorials/README.md +++ b/medcat-tutorials/README.md @@ -1,4 +1,4 @@ -# MedCAT Tutorials (version 2) +# MedCAT Tutorials The MedCAT Tutorials provide an interactive learning path for using MedCAT. @@ -9,13 +9,13 @@ The following readmes are around the setup of the tutorials themselves aimed at ### Documentation Build -The `medcat-v2` documentation site imports this project’s MkDocs navigation file directly. The relevant plugins are the mkdocs-monorepo-plugin and the mkdocs-jupyter plugin. +The `medcat` documentation site imports this project’s MkDocs navigation file directly. The relevant plugins are the mkdocs-monorepo-plugin and the mkdocs-jupyter plugin. -In `medcat-v2/mkdocs.yml` the `Tutorials` section is wired in via an include: +In `medcat/mkdocs.yml` the `Tutorials` section is wired in via an include: ```yaml nav: - - Tutorials: '!include ../medcat-v2-tutorials/mkdocs.yml' + - Tutorials: '!include ../medcat-tutorials/mkdocs.yml' ``` #### Run the docs locally (rendered site) @@ -23,6 +23,6 @@ nav: To preview the rendered docs site locally: ```bash -cd cogstack-nlp/medcat-v2-tutorials +cd cogstack-nlp/medcat-tutorials uv run mkdocs serve ``` diff --git a/medcat-v2-tutorials/mkdocs.yml b/medcat-tutorials/mkdocs.yml similarity index 100% rename from medcat-v2-tutorials/mkdocs.yml rename to medcat-tutorials/mkdocs.yml diff --git a/medcat-v2-tutorials/notebooks/advanced/1._Creating_and_using_a_custom_tokenizer.ipynb b/medcat-tutorials/notebooks/advanced/1._Creating_and_using_a_custom_tokenizer.ipynb similarity index 100% rename from medcat-v2-tutorials/notebooks/advanced/1._Creating_and_using_a_custom_tokenizer.ipynb rename to medcat-tutorials/notebooks/advanced/1._Creating_and_using_a_custom_tokenizer.ipynb diff --git a/medcat-v2-tutorials/notebooks/advanced/2._Create_and_use_component.ipynb b/medcat-tutorials/notebooks/advanced/2._Create_and_use_component.ipynb similarity index 100% rename from medcat-v2-tutorials/notebooks/advanced/2._Create_and_use_component.ipynb rename to medcat-tutorials/notebooks/advanced/2._Create_and_use_component.ipynb diff --git a/medcat-v2-tutorials/notebooks/index.md b/medcat-tutorials/notebooks/index.md similarity index 97% rename from medcat-v2-tutorials/notebooks/index.md rename to medcat-tutorials/notebooks/index.md index 426bbedf9..8ba932c06 100644 --- a/medcat-v2-tutorials/notebooks/index.md +++ b/medcat-tutorials/notebooks/index.md @@ -23,7 +23,7 @@ To get set up to run the tutorials interactively, clone the repo and install the ```bash git clone https://github.com/CogStack/cogstack-nlp.git -cd cogstack-nlp/medcat-v2-tutorials +cd cogstack-nlp/medcat-tutorials python -m venv .venv source .venv/bin/activate diff --git a/medcat-v2-tutorials/notebooks/introductory/basic/1._Build_a_Concept_Database_and_a_Vocabulary.ipynb b/medcat-tutorials/notebooks/introductory/basic/1._Build_a_Concept_Database_and_a_Vocabulary.ipynb similarity index 100% rename from medcat-v2-tutorials/notebooks/introductory/basic/1._Build_a_Concept_Database_and_a_Vocabulary.ipynb rename to medcat-tutorials/notebooks/introductory/basic/1._Build_a_Concept_Database_and_a_Vocabulary.ipynb diff --git a/medcat-v2-tutorials/notebooks/introductory/basic/2._Unsupervised_training_on_model.ipynb b/medcat-tutorials/notebooks/introductory/basic/2._Unsupervised_training_on_model.ipynb similarity index 100% rename from medcat-v2-tutorials/notebooks/introductory/basic/2._Unsupervised_training_on_model.ipynb rename to 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to medcat-tutorials/notebooks/introductory/relcat/data/rel_cat_ADE_V2.tsv diff --git a/medcat-v2-tutorials/pyproject.toml b/medcat-tutorials/pyproject.toml similarity index 100% rename from medcat-v2-tutorials/pyproject.toml rename to medcat-tutorials/pyproject.toml diff --git a/medcat-v2-tutorials/requirements.txt b/medcat-tutorials/requirements.txt similarity index 100% rename from medcat-v2-tutorials/requirements.txt rename to medcat-tutorials/requirements.txt diff --git a/medcat-v2-tutorials/uv.lock b/medcat-tutorials/uv.lock similarity index 100% rename from medcat-v2-tutorials/uv.lock rename to medcat-tutorials/uv.lock diff --git a/medcat-v2/README.md b/medcat-v2/README.md index 26557ef2d..ca7afa66b 100644 --- a/medcat-v2/README.md +++ b/medcat-v2/README.md @@ -1,191 +1,3 @@ -# Medical oncept Annotation Tool (version 2) +# MedCAT v2 -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). -Original paper for v1 on [arXiv](https://arxiv.org/abs/2010.01165). - -## Why MedCAT v2? - -MedCAT v2 is a comprehensive refactor designed to improve modularity, flexibility, and maintainability. The core library is now lightweight, with optional extras (spaCy tokenization, MetaCAT, DeID, RelCAT) available as separate installable features—allowing you to install only what you need. This modular approach reduces dependencies, enables smaller installs, and provides better separation of concerns. Additionally, v2 reduces internal coupling with spaCy, allowing for alternative tokenizers and greater extensibility. The new architecture makes it easier to create custom components and addons, while improving code maintainability and preparing the foundation for future enhancements. For most users, single-threaded inference APIs remain unchanged, ensuring a smooth transition. - -**There's a number of breaking changes in MedCAT v2 compared to v1.** -When moving from v1 to v2, please refer to the [migration guide](docs/migration_guide_v2.md). -Details on breaking are outlined [here](docs/breaking_changes.md). - -[![Build Status](https://github.com/CogStack/cogstack-nlp/actions/workflows/medcat-v2_main.yml/badge.svg?branch=main)](https://github.com/CogStack/cogstack-nlp/actions/workflows/medcat-v2_main.yml/badge.svg?branch=main) -[![Documentation Status](https://readthedocs.org/projects/cogstack-nlp/badge/?version=latest)](https://readthedocs.org/projects/cogstack-nlp/badge/?version=latest) -[![Latest release](https://img.shields.io/github/v/release/CogStack/cogstack-nlp?filter=medcat/*)](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/) - -**Official Docs [here](https://cogstack-nlp.readthedocs.io/)** - -**Discussion Forum [discourse](https://discourse.cogstack.org/)** - -## Available Models - -We have 2 public v2 models available: -1) SnomedCT UK Clinical edition 39.0 (Oct 2024) and UK Drug Extension 39.0 (July 2024) based model enriched with UMLS 2024AA; trained only on MIMIC-IV -2) SnomedCT UK Clinical edition 40.2 (June 2025) and UK Drug Extension 40.3 (July 2024) based model enriched with UMLS 2024AA; trained only on MIMIC-IV - -There are also a number of MedCAT v1 models available that can automatically be converted if required. - -To download any of these models, please [follow this link](https://medcat.sites.er.kcl.ac.uk/auth-callback-api) and sign in using your NIH / UMLS API key. You will then be redirected to the MedCAT model download form. Please complete this form and you will be provided a download link. - -While we encourage you use MedCAT v2 and the models in that native format, if you download an older version MedCAT v2 will be able to load it and covnert it to the format it knows. However, the loading process will be considerably longerin those cases. - -If you wish you can also convert the v1 models into the v2 format (see [tutorial](../medcat-v2-tutorials/notebooks/introductory/migration/1._Migrate_v1_model_to_v2.ipynb)). - -```python -from medcat.utils.legacy import legacy_converter -from medcat.storage.serialisers import AvailableSerialisers -old_model = '' -new_model_dir = '' -legacy_converter.do_conversion(old_model_path, new_model_dir, AvailableSerialisers.dill) -``` -OR -```bash -model_path = "models/medcat1_model_pack.zip" -new_model_folder = "models" # file in this folder -! python -m medcat.utils.legacy.legacy_converter $model_path $new_model_folder --verbose -``` - -## News -- **New public 2024 and 2025** Snomed models were uploaded and made available 7. October 2025. -- **MedCAT 2.0.0** was released 18. August 2025. - -[News pre v2.0.0](docs/v1_news.md). - -## Installation - -MedCAT v2 has its first full release -``` -pip install medcat -``` -Do note that **this installs only the core MedCAT v2**. -**It does not necessary dependencies for `spacy`-based tokenizing or MetaCATs or DeID**. -However, all of those are supported as well. -You can install them as follows: -``` -pip install "medcat[spacy]" # for spacy-based tokenizer -pip install "medcat[meta-cat]" # for MetaCAT -pip install "medcat[deid]" # for DeID models -pip install "medcat[spacy,meta-cat,deid,rel-cat,dict-ner]" # for all of the above -``` - -### Installing plugins - -MedCAT v2 supports **external plugins** that can provide new components (e.g. alternative NER models, addons, tokenizers) via Python entry points. - -- **Curated plugins**: The `medcat.plugins.catalog` module ships with a curated plugin catalog that can be updated from a remote JSON file. -- **Installer**: The `medcat.plugins.installer.PluginInstallationManager` wraps a `pip`-based installer and knows how to resolve a compatible plugin version for your current MedCAT version. -- **CLI**: You can install curated plugins directly from the command line: - -```bash -python -m medcat plugins install medcat-gliner -``` - -This will: - -- look up `medcat-gliner` in the curated catalog, -- resolve a version compatible with your installed MedCAT, -- and install it using `pip`. - -You can also: - -- pass `--dry-run` to show what would be installed without making changes: - - ```bash - python -m medcat plugins install --dry-run medcat-gliner - ``` - -- override the version/ref explicitly (e.g. when testing a branch or tag): - - ```bash - python -m medcat plugins install medcat-gliner --force-version main - ``` - -If a plugin requires authentication (for example, private Git repositories), MedCAT will log a warning and the installer will surface pip’s error messages if credentials are missing or incorrect. - -### Version / update checking - -MedCAT now has the ability to check for newer versions of itself on PyPI (or a local mirror of it). -This is so users don't get left behind too far with older versions of our software. -This is configurable by evnironmental variables so that sys admins (e.g for JupyterHub) can specify the settings they wish. -Version checks are done once a week and the results are cached. - -Below is a table of the environmental variables that govern the version checking and their defaults. - -| Variable | Default | Description | -|-----------|----------|-------------| -| **`MEDCAT_DISABLE_VERSION_CHECK`** | *(unset)* | When set to `true`, `yes` or `disable`, disables the version update check entirely. Useful for CI environments, offline setups, or deployments where external network access is restricted. | -| **`MEDCAT_PYPI_URL`** | `https://pypi.org/pypi` | Base URL used to query package metadata. Can be changed to a PyPI mirror or internal repository that exposes the `/pypi/{pkg}/json` API. | -| **`MEDCAT_MINOR_UPDATE_THRESHOLD`** | `3` | Number of newer **minor** versions (e.g. `1.4.x`, `1.5.x`) that must exist before MedCAT emits a “newer version available” log message. | -| **`MEDCAT_PATCH_UPDATE_THRESHOLD`** | `3` | Number of newer **patch** versions (e.g. `1.3.1`, `1.3.2`, `1.3.3`) on the same minor line required before emitting an informational update message. | -| **`MEDCAT_VERSION_UPDATE_LOG_LEVEL`** | `INFO` | Logging level used when reporting available newer versions (minor/patch thresholds). Accepts any valid `logging` level string (`DEBUG`, `INFO`, `WARNING`, `ERROR`, `CRITICAL`). | -| **`MEDCAT_VERSION_UPDATE_YANKED_LOG_LEVEL`** | `WARNING` | Logging level used when reporting that the current version has been **yanked** on PyPI. Accepts the same values as above. | - -## Demo - -The MedCAT v2 demo web app is available [here](https://medcat.sites.er.kcl.ac.uk/). - -## Key Concepts - -- **Components**: The building blocks of MedCAT (NER, Entity Linking, preprocessing, etc.) -- **Addons**: Components that extend the core NER+EL pipeline with additional processing stages -- **Plugins**: External packages that provide new component implementations or other functionality via entry points - -See [Architecture Documentation](docs/architecture.md) for detailed information. - -## Tutorials -A guide on how to use MedCAT v2 is available at on the medcat documentation page on [docs.cogstack.org](https://docs.cogstack.org) - -## Acknowledgements -Entity extraction was trained on [MedMentions](https://github.com/chanzuckerberg/MedMentions) In total it has ~ 35K entites from UMLS - -The vocabulary was compiled from [Wiktionary](https://en.wiktionary.org/wiki/Wiktionary:Main_Page) In total ~ 800K unique words - -## Powered By -A big thank you goes to [spaCy](https://spacy.io/) and [Hugging Face](https://huggingface.co/) - who made life a million times easier. - - -## Citation -MedCAT v2 citation: -``` -@inproceedings{ratas-etal-2026-medcat, - title = "{M}ed{CAT} v2: a modular, extensible architecture for clinical named entity recognition and linking under real-world privacy and compute constraints", - author = "Ratas, Mart and - Searle, Thomas and - Sutton, Adam and - Dobson, Richard", - editor = "Demner-Fushman, Dina and - Ananiadou, Sophia and - Roberts, Kirk and - Tsujii, Junichi", - booktitle = "{B}io{NLP} 2026", - month = jul, - year = "2026", - address = "San Diego, California", - publisher = "Association for Computational Linguistics", - url = "https://aclanthology.org/2026.bionlp-1.17/", - doi = "10.18653/v1/2026.bionlp-1.17", - pages = "191--198", - ISBN = "979-8-89176-434-7", - abstract = "MedCAT is an open-source framework for clinical named entity recognition and linking (NER+L) widely used in research and healthcare settings. We present MedCAT v2, a re-engineered version designed to improve modularity, extensibility, and maintainability while preserving the core functionality and performance of previous releases. The new architecture introduces a registry-based component system and a flexible pipeline that enables easy substitution of components, integration of alternative methods, and future expansion, including support for pre-trained components across the full NER+L and contextualisation workflow. This enables systematic exploration of clinical NER+L design trade-offs by evaluating different components in the pipeline. Evaluation across multiple public datasets shows equivalent or improved performance compared to earlier versions, with reduced integration overhead and improved runtime flexibility. The framework also supports optional extensions such as meta-annotation, relation extraction, providing a unified and reproducible environment for clinical NLP in real-world settings." -} -``` -
-MedCAT v1 citation - -``` -@ARTICLE{Kraljevic2021-ln, - title="Multi-domain clinical natural language processing with {MedCAT}: The Medical Concept Annotation Toolkit", - author="Kraljevic, Zeljko and Searle, Thomas and Shek, Anthony and Roguski, Lukasz and Noor, Kawsar and Bean, Daniel and Mascio, Aurelie and Zhu, Leilei and Folarin, Amos A and Roberts, Angus and Bendayan, Rebecca and Richardson, Mark P and Stewart, Robert and Shah, Anoop D and Wong, Wai Keong and Ibrahim, Zina and Teo, James T and Dobson, Richard J B", - journal="Artif. Intell. Med.", - volume=117, - pages="102083", - month=jul, - year=2021, - issn="0933-3657", - doi="10.1016/j.artmed.2021.102083" -} -
-``` +MedCAT v2 is now simply in at (../medcat)[./medcat]. \ No newline at end of file diff --git a/medcat-v2/.gitignore b/medcat/.gitignore similarity index 100% rename from medcat-v2/.gitignore rename to medcat/.gitignore diff --git a/medcat-v2/.readthedocs.yaml b/medcat/.readthedocs.yaml similarity index 71% rename from medcat-v2/.readthedocs.yaml rename to medcat/.readthedocs.yaml index 97683321c..15491d72c 100644 --- a/medcat-v2/.readthedocs.yaml +++ b/medcat/.readthedocs.yaml @@ -10,14 +10,14 @@ build: python: "3.13" jobs: pre_create_environment: - - cd medcat-v2/docs + - cd medcat/docs - asdf plugin add uv - asdf install uv latest - asdf global uv latest create_environment: - uv venv "${READTHEDOCS_VIRTUALENV_PATH}" install: - - cd medcat-v2/docs && UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen + - cd medcat/docs && UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen mkdocs: - configuration: medcat-v2/mkdocs.yml + configuration: medcat/mkdocs.yml diff --git a/medcat-v2/.release/README.md b/medcat/.release/README.md similarity index 100% rename from medcat-v2/.release/README.md rename to medcat/.release/README.md diff --git a/medcat-v2/.release/install_bundle_readme.md b/medcat/.release/install_bundle_readme.md similarity index 98% rename from medcat-v2/.release/install_bundle_readme.md rename to medcat/.release/install_bundle_readme.md index e9f69a575..4340d0b10 100644 --- a/medcat-v2/.release/install_bundle_readme.md +++ b/medcat/.release/install_bundle_readme.md @@ -64,7 +64,7 @@ Users who need gpu-enabled `torch` will need to install it separately. Once you've downloaded the install bundle on a computer with internet / PyPI access you need to - Move the archive (a `.tar.gz` file) to the target machine -- Unarchive using `tar -xvzf medcat-v2.*-cpu.tar.gz` +- Unarchive using `tar -xvzf medcat-*-cpu.tar.gz` - Probably best to specify your exact file path - This will extract the contents (both the `.whl` files and this README) in the current folder - Activate your virtual environment (`venv`, `conda`, etc). diff --git a/medcat-v2/.release/prepare_minor_release.sh b/medcat/.release/prepare_minor_release.sh similarity index 100% rename from medcat-v2/.release/prepare_minor_release.sh rename to medcat/.release/prepare_minor_release.sh diff --git a/medcat-v2/.release/prepare_patch_release.sh b/medcat/.release/prepare_patch_release.sh similarity index 100% rename from medcat-v2/.release/prepare_patch_release.sh rename to medcat/.release/prepare_patch_release.sh diff --git a/medcat-v2/.release/prepare_release.sh b/medcat/.release/prepare_release.sh similarity index 100% rename from medcat-v2/.release/prepare_release.sh rename to medcat/.release/prepare_release.sh diff --git a/medcat-v2/MANIFEST.in b/medcat/MANIFEST.in similarity index 100% rename from medcat-v2/MANIFEST.in rename to medcat/MANIFEST.in diff --git a/medcat/README.md b/medcat/README.md new file mode 100644 index 000000000..ad59df66c --- /dev/null +++ b/medcat/README.md @@ -0,0 +1,167 @@ +# Medical oncept Annotation Tool + +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). +Original paper for v1 on [arXiv](https://arxiv.org/abs/2010.01165). + +Coming from MedCAT v1? See [here](docs/v1_info.md) for more info. + +[![Build Status](https://github.com/CogStack/cogstack-nlp/actions/workflows/medcat-v2_main.yml/badge.svg?branch=main)](https://github.com/CogStack/cogstack-nlp/actions/workflows/medcat-v2_main.yml/badge.svg?branch=main) +[![Documentation Status](https://readthedocs.org/projects/cogstack-nlp/badge/?version=latest)](https://readthedocs.org/projects/cogstack-nlp/badge/?version=latest) +[![Latest release](https://img.shields.io/github/v/release/CogStack/cogstack-nlp?filter=medcat/*)](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/) + +**Official Docs [here](https://cogstack-nlp.readthedocs.io/)** + +**Discussion Forum [discourse](https://discourse.cogstack.org/)** + +## Available Models + +We have 2 (relatively recent) public models available: +1) SnomedCT UK Clinical edition 39.0 (Oct 2024) and UK Drug Extension 39.0 (July 2024) based model enriched with UMLS 2024AA; trained only on MIMIC-IV +2) SnomedCT UK Clinical edition 40.2 (June 2025) and UK Drug Extension 40.3 (July 2024) based model enriched with UMLS 2024AA; trained only on MIMIC-IV + +There are also a number of legacy MedCAT models available that can automatically be converted if required. + +To download any of these models, please [follow this link](https://medcat.sites.er.kcl.ac.uk/auth-callback-api) and sign in using your NIH / UMLS API key. You will then be redirected to the MedCAT model download form. Please complete this form and you will be provided a download link. + +## News +- **New public 2024 and 2025** Snomed models were uploaded and made available 7. October 2025. +- **MedCAT 2.0.0** was released 18. August 2025. + +[News pre v2.0.0](docs/v1_news.md). + +## Installation + +MedCAT v2 has its first full release +``` +pip install medcat +``` +Do note that **this installs only the core MedCAT v2**. +**It does not necessary dependencies for `spacy`-based tokenizing or MetaCATs or DeID**. +However, all of those are supported as well. +You can install them as follows: +``` +pip install "medcat[spacy]" # for spacy-based tokenizer +pip install "medcat[meta-cat]" # for MetaCAT +pip install "medcat[deid]" # for DeID models +pip install "medcat[spacy,meta-cat,deid,rel-cat,dict-ner]" # for all of the above +``` + +### Installing plugins + +MedCAT v2 supports **external plugins** that can provide new components (e.g. alternative NER models, addons, tokenizers) via Python entry points. + +- **Curated plugins**: The `medcat.plugins.catalog` module ships with a curated plugin catalog that can be updated from a remote JSON file. +- **Installer**: The `medcat.plugins.installer.PluginInstallationManager` wraps a `pip`-based installer and knows how to resolve a compatible plugin version for your current MedCAT version. +- **CLI**: You can install curated plugins directly from the command line: + +```bash +python -m medcat plugins install medcat-gliner +``` + +This will: + +- look up `medcat-gliner` in the curated catalog, +- resolve a version compatible with your installed MedCAT, +- and install it using `pip`. + +You can also: + +- pass `--dry-run` to show what would be installed without making changes: + + ```bash + python -m medcat plugins install --dry-run medcat-gliner + ``` + +- override the version/ref explicitly (e.g. when testing a branch or tag): + + ```bash + python -m medcat plugins install medcat-gliner --force-version main + ``` + +If a plugin requires authentication (for example, private Git repositories), MedCAT will log a warning and the installer will surface pip’s error messages if credentials are missing or incorrect. + +### Version / update checking + +MedCAT now has the ability to check for newer versions of itself on PyPI (or a local mirror of it). +This is so users don't get left behind too far with older versions of our software. +This is configurable by evnironmental variables so that sys admins (e.g for JupyterHub) can specify the settings they wish. +Version checks are done once a week and the results are cached. + +Below is a table of the environmental variables that govern the version checking and their defaults. + +| Variable | Default | Description | +|-----------|----------|-------------| +| **`MEDCAT_DISABLE_VERSION_CHECK`** | *(unset)* | When set to `true`, `yes` or `disable`, disables the version update check entirely. Useful for CI environments, offline setups, or deployments where external network access is restricted. | +| **`MEDCAT_PYPI_URL`** | `https://pypi.org/pypi` | Base URL used to query package metadata. Can be changed to a PyPI mirror or internal repository that exposes the `/pypi/{pkg}/json` API. | +| **`MEDCAT_MINOR_UPDATE_THRESHOLD`** | `3` | Number of newer **minor** versions (e.g. `1.4.x`, `1.5.x`) that must exist before MedCAT emits a “newer version available” log message. | +| **`MEDCAT_PATCH_UPDATE_THRESHOLD`** | `3` | Number of newer **patch** versions (e.g. `1.3.1`, `1.3.2`, `1.3.3`) on the same minor line required before emitting an informational update message. | +| **`MEDCAT_VERSION_UPDATE_LOG_LEVEL`** | `INFO` | Logging level used when reporting available newer versions (minor/patch thresholds). Accepts any valid `logging` level string (`DEBUG`, `INFO`, `WARNING`, `ERROR`, `CRITICAL`). | +| **`MEDCAT_VERSION_UPDATE_YANKED_LOG_LEVEL`** | `WARNING` | Logging level used when reporting that the current version has been **yanked** on PyPI. Accepts the same values as above. | + +## Demo + +The MedCAT v2 demo web app is available [here](https://medcat.sites.er.kcl.ac.uk/). + +## Key Concepts + +- **Components**: The building blocks of MedCAT (NER, Entity Linking, preprocessing, etc.) +- **Addons**: Components that extend the core NER+EL pipeline with additional processing stages +- **Plugins**: External packages that provide new component implementations or other functionality via entry points + +See [Architecture Documentation](docs/architecture.md) for detailed information. + +## Tutorials +A guide on how to use MedCAT v2 is available at on the medcat documentation page on [docs.cogstack.org](https://docs.cogstack.org) + +## Acknowledgements +Entity extraction was trained on [MedMentions](https://github.com/chanzuckerberg/MedMentions) In total it has ~ 35K entites from UMLS + +The vocabulary was compiled from [Wiktionary](https://en.wiktionary.org/wiki/Wiktionary:Main_Page) In total ~ 800K unique words + +## Powered By +A big thank you goes to [spaCy](https://spacy.io/) and [Hugging Face](https://huggingface.co/) - who made life a million times easier. + + +## Citation +MedCAT v2 citation: +``` +@inproceedings{ratas-etal-2026-medcat, + title = "{M}ed{CAT} v2: a modular, extensible architecture for clinical named entity recognition and linking under real-world privacy and compute constraints", + author = "Ratas, Mart and + Searle, Thomas and + Sutton, Adam and + Dobson, Richard", + editor = "Demner-Fushman, Dina and + Ananiadou, Sophia and + Roberts, Kirk and + Tsujii, Junichi", + booktitle = "{B}io{NLP} 2026", + month = jul, + year = "2026", + address = "San Diego, California", + publisher = "Association for Computational Linguistics", + url = "https://aclanthology.org/2026.bionlp-1.17/", + doi = "10.18653/v1/2026.bionlp-1.17", + pages = "191--198", + ISBN = "979-8-89176-434-7", + abstract = "MedCAT is an open-source framework for clinical named entity recognition and linking (NER+L) widely used in research and healthcare settings. We present MedCAT v2, a re-engineered version designed to improve modularity, extensibility, and maintainability while preserving the core functionality and performance of previous releases. The new architecture introduces a registry-based component system and a flexible pipeline that enables easy substitution of components, integration of alternative methods, and future expansion, including support for pre-trained components across the full NER+L and contextualisation workflow. This enables systematic exploration of clinical NER+L design trade-offs by evaluating different components in the pipeline. Evaluation across multiple public datasets shows equivalent or improved performance compared to earlier versions, with reduced integration overhead and improved runtime flexibility. The framework also supports optional extensions such as meta-annotation, relation extraction, providing a unified and reproducible environment for clinical NLP in real-world settings." +} +``` +
+MedCAT v1 citation + +``` +@ARTICLE{Kraljevic2021-ln, + title="Multi-domain clinical natural language processing with {MedCAT}: The Medical Concept Annotation Toolkit", + author="Kraljevic, Zeljko and Searle, Thomas and Shek, Anthony and Roguski, Lukasz and Noor, Kawsar and Bean, Daniel and Mascio, Aurelie and Zhu, Leilei and Folarin, Amos A and Roberts, Angus and Bendayan, Rebecca and Richardson, Mark P and Stewart, Robert and Shah, Anoop D and Wong, Wai Keong and Ibrahim, Zina and Teo, James T and Dobson, Richard J B", + journal="Artif. Intell. Med.", + volume=117, + pages="102083", + month=jul, + year=2021, + issn="0933-3657", + doi="10.1016/j.artmed.2021.102083" +} +
+``` diff --git a/medcat-v2/docs/_static/img/cat-logo.png b/medcat/docs/_static/img/cat-logo.png similarity index 100% rename from medcat-v2/docs/_static/img/cat-logo.png rename to medcat/docs/_static/img/cat-logo.png diff --git a/medcat-v2/docs/_static/img/cat-logo.svg b/medcat/docs/_static/img/cat-logo.svg similarity index 100% rename from medcat-v2/docs/_static/img/cat-logo.svg rename to medcat/docs/_static/img/cat-logo.svg diff --git a/medcat-v2/docs/architecture.md b/medcat/docs/architecture.md similarity index 100% rename from medcat-v2/docs/architecture.md rename to medcat/docs/architecture.md diff --git a/medcat-v2/docs/breaking_changes.md b/medcat/docs/breaking_changes.md similarity index 100% rename from medcat-v2/docs/breaking_changes.md rename to medcat/docs/breaking_changes.md diff --git a/medcat/docs/hooks.py b/medcat/docs/hooks.py new file mode 100644 index 000000000..f5533829c --- /dev/null +++ b/medcat/docs/hooks.py @@ -0,0 +1,16 @@ +import re +from pathlib import Path + + +def on_page_markdown(markdown, page, config, files): + if page.file.src_uri == "index.md": + snippet_pattern = r'--8<--\s*["\']README\.md["\']' + if re.search(snippet_pattern, markdown): + readme_path = Path(config["config_file_path"]).parent / "README.md" + if readme_path.exists(): + readme_content = readme_path.read_text(encoding="utf-8") + # Rewrite [text](docs/page.md) -> [text](page.md) + # Also handles anchors like [text](docs/page.md#section) -> [text](page.md#section) + rewritten = re.sub(r'\]\(docs/([^\)]+\.md(?:#[^\)]*)?)\)', r'](\1)', readme_content) + markdown = re.sub(snippet_pattern, rewritten, markdown) + return markdown diff --git a/medcat-v2/docs/index.md b/medcat/docs/index.md similarity index 100% rename from medcat-v2/docs/index.md rename to medcat/docs/index.md diff --git a/medcat-v2/docs/migration_guide_v2.md b/medcat/docs/migration_guide_v2.md similarity index 99% rename from medcat-v2/docs/migration_guide_v2.md rename to medcat/docs/migration_guide_v2.md index 9101709a5..36a463542 100644 --- a/medcat-v2/docs/migration_guide_v2.md +++ b/medcat/docs/migration_guide_v2.md @@ -121,7 +121,7 @@ We recommend re-saving v1 models using `cat.save_model_pack` in v2 format to mit All v2 tutorials have been completely redone. They do not go as far into detail in everything as the v1 tutorials did. But they should hopefully cover most of the use cases -The v2 tutorials are available [here](https://github.com/CogStack/cogstack-nlp/tree/main/medcat-v2-tutorials). +The v2 tutorials are available [here](https://github.com/CogStack/cogstack-nlp/tree/main/medcat-tutorials). ## Updated `working_with_cogstack` scripts diff --git a/medcat-v2/docs/pyproject.toml b/medcat/docs/pyproject.toml similarity index 100% rename from medcat-v2/docs/pyproject.toml rename to medcat/docs/pyproject.toml diff --git a/medcat-v2/docs/uv.lock b/medcat/docs/uv.lock similarity index 100% rename from medcat-v2/docs/uv.lock rename to medcat/docs/uv.lock diff --git a/medcat/docs/v1_conversion.md b/medcat/docs/v1_conversion.md new file mode 100644 index 000000000..7f9428c7e --- /dev/null +++ b/medcat/docs/v1_conversion.md @@ -0,0 +1,20 @@ +# Converting a v1 model to v2 format + +While we encourage you use MedCAT v2 and the models in that native format, if you download an older version MedCAT v2 will be able to load it and covnert it to the format it knows. However, the loading process will be considerably longer in those cases. + +If you wish you can also convert the v1 models into the v2 format (see [tutorial](../../medcat-tutorials/notebooks/introductory/migration/1._Migrate_v1_model_to_v2.ipynb)). + +```python +from medcat.utils.legacy import legacy_converter +from medcat.storage.serialisers import AvailableSerialisers +old_model = '' +new_model_dir = '' +legacy_converter.do_conversion(old_model_path, new_model_dir, AvailableSerialisers.dill) +``` +OR +```bash +model_path = "models/medcat1_model_pack.zip" +new_model_folder = "models" # file in this folder +! python -m medcat.utils.legacy.legacy_converter $model_path $new_model_folder --verbose +``` + diff --git a/medcat/docs/v1_info.md b/medcat/docs/v1_info.md new file mode 100644 index 000000000..e62e1032f --- /dev/null +++ b/medcat/docs/v1_info.md @@ -0,0 +1,9 @@ +## Why MedCAT v2? + +MedCAT v2 is a comprehensive refactor designed to improve modularity, flexibility, and maintainability. The core library is now lightweight, with optional extras (spaCy tokenization, MetaCAT, DeID, RelCAT$ + +**There's a number of breaking changes in MedCAT v2 compared to v1.** +When moving from v1 to v2, please refer to the [migration guide](migration_guide_v2.md). +Details on breaking are outlined [here](breaking_changes.md). + +Legacy model conversion is addressed [here](v1_conversion.md). diff --git a/medcat-v2/docs/v1_news.md b/medcat/docs/v1_news.md similarity index 99% rename from medcat-v2/docs/v1_news.md rename to medcat/docs/v1_news.md index 70f02a55c..8a3e9c9db 100644 --- a/medcat-v2/docs/v1_news.md +++ b/medcat/docs/v1_news.md @@ -12,4 +12,4 @@ branch and will still be supported until 1. July 2021 (with respect to potential bug fixes), after it will still be available but not updated anymore. - **Paper**: [What’s in a Summary? Laying the Groundwork for Advances in Hospital-Course Summarization](https://www.aclweb.org/anthology/2021.naacl-main.382.pdf) -- ([more...](https://github.com/CogStack/cogstack-nlp/blob/main/medcat-v2/media/news.md)) \ No newline at end of file +- ([more...](https://github.com/CogStack/cogstack-nlp/blob/main/medcat/media/news.md)) diff --git a/medcat-v2/medcat/__init__.py b/medcat/medcat/__init__.py similarity index 100% rename from medcat-v2/medcat/__init__.py rename to medcat/medcat/__init__.py diff --git a/medcat-v2/medcat/__main__.py b/medcat/medcat/__main__.py similarity index 100% rename from medcat-v2/medcat/__main__.py rename to medcat/medcat/__main__.py diff --git a/medcat-v2/medcat/cat.py b/medcat/medcat/cat.py similarity index 100% rename from medcat-v2/medcat/cat.py rename to medcat/medcat/cat.py diff --git a/medcat-v2/medcat/cdb/__init__.py b/medcat/medcat/cdb/__init__.py similarity index 100% rename from medcat-v2/medcat/cdb/__init__.py rename to medcat/medcat/cdb/__init__.py diff --git a/medcat-v2/medcat/cdb/cdb.py b/medcat/medcat/cdb/cdb.py similarity index 100% rename from medcat-v2/medcat/cdb/cdb.py rename to medcat/medcat/cdb/cdb.py diff --git a/medcat-v2/medcat/cdb/concepts.py b/medcat/medcat/cdb/concepts.py similarity index 100% rename from medcat-v2/medcat/cdb/concepts.py rename to medcat/medcat/cdb/concepts.py diff --git a/medcat-v2/medcat/components/__init__.py b/medcat/medcat/components/__init__.py similarity index 100% rename from medcat-v2/medcat/components/__init__.py rename to medcat/medcat/components/__init__.py diff --git a/medcat-v2/medcat/components/addons/__init__.py b/medcat/medcat/components/addons/__init__.py similarity index 100% rename from medcat-v2/medcat/components/addons/__init__.py rename to medcat/medcat/components/addons/__init__.py diff --git a/medcat-v2/medcat/components/addons/addons.py b/medcat/medcat/components/addons/addons.py similarity index 100% rename from medcat-v2/medcat/components/addons/addons.py rename to medcat/medcat/components/addons/addons.py diff --git a/medcat-v2/medcat/components/addons/meta_cat/__init__.py b/medcat/medcat/components/addons/meta_cat/__init__.py similarity index 100% rename from medcat-v2/medcat/components/addons/meta_cat/__init__.py rename to medcat/medcat/components/addons/meta_cat/__init__.py diff --git a/medcat-v2/medcat/components/addons/meta_cat/data_utils.py b/medcat/medcat/components/addons/meta_cat/data_utils.py similarity index 100% rename from medcat-v2/medcat/components/addons/meta_cat/data_utils.py rename to medcat/medcat/components/addons/meta_cat/data_utils.py diff --git a/medcat-v2/medcat/components/addons/meta_cat/mctokenizers/__init__.py b/medcat/medcat/components/addons/meta_cat/mctokenizers/__init__.py similarity index 100% rename from medcat-v2/medcat/components/addons/meta_cat/mctokenizers/__init__.py rename to medcat/medcat/components/addons/meta_cat/mctokenizers/__init__.py diff --git a/medcat-v2/medcat/components/addons/meta_cat/mctokenizers/bert_tokenizer.py b/medcat/medcat/components/addons/meta_cat/mctokenizers/bert_tokenizer.py similarity index 100% rename from medcat-v2/medcat/components/addons/meta_cat/mctokenizers/bert_tokenizer.py rename to medcat/medcat/components/addons/meta_cat/mctokenizers/bert_tokenizer.py diff --git a/medcat-v2/medcat/components/addons/meta_cat/mctokenizers/bpe_tokenizer.py b/medcat/medcat/components/addons/meta_cat/mctokenizers/bpe_tokenizer.py similarity index 100% rename from medcat-v2/medcat/components/addons/meta_cat/mctokenizers/bpe_tokenizer.py rename to medcat/medcat/components/addons/meta_cat/mctokenizers/bpe_tokenizer.py diff --git a/medcat-v2/medcat/components/addons/meta_cat/mctokenizers/tokenizers.py b/medcat/medcat/components/addons/meta_cat/mctokenizers/tokenizers.py similarity index 100% rename from medcat-v2/medcat/components/addons/meta_cat/mctokenizers/tokenizers.py rename to medcat/medcat/components/addons/meta_cat/mctokenizers/tokenizers.py diff --git a/medcat-v2/medcat/components/addons/meta_cat/meta_cat.py b/medcat/medcat/components/addons/meta_cat/meta_cat.py similarity index 100% rename from medcat-v2/medcat/components/addons/meta_cat/meta_cat.py rename to medcat/medcat/components/addons/meta_cat/meta_cat.py diff --git a/medcat-v2/medcat/components/addons/meta_cat/ml_utils.py b/medcat/medcat/components/addons/meta_cat/ml_utils.py similarity index 100% rename from medcat-v2/medcat/components/addons/meta_cat/ml_utils.py rename to medcat/medcat/components/addons/meta_cat/ml_utils.py diff --git a/medcat-v2/medcat/components/addons/meta_cat/models.py b/medcat/medcat/components/addons/meta_cat/models.py similarity index 100% rename from medcat-v2/medcat/components/addons/meta_cat/models.py rename to medcat/medcat/components/addons/meta_cat/models.py diff --git a/medcat-v2/medcat/components/addons/relation_extraction/__init__.py 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b/medcat/medcat/tokenizing/tokens.py similarity index 100% rename from medcat-v2/medcat/tokenizing/tokens.py rename to medcat/medcat/tokenizing/tokens.py diff --git a/medcat-v2/medcat/trainer.py b/medcat/medcat/trainer.py similarity index 100% rename from medcat-v2/medcat/trainer.py rename to medcat/medcat/trainer.py diff --git a/medcat-v2/medcat/utils/__init__.py b/medcat/medcat/utils/__init__.py similarity index 100% rename from medcat-v2/medcat/utils/__init__.py rename to medcat/medcat/utils/__init__.py diff --git a/medcat-v2/medcat/utils/cdb_state.py b/medcat/medcat/utils/cdb_state.py similarity index 100% rename from medcat-v2/medcat/utils/cdb_state.py rename to medcat/medcat/utils/cdb_state.py diff --git a/medcat-v2/medcat/utils/cdb_utils.py b/medcat/medcat/utils/cdb_utils.py similarity index 100% rename from medcat-v2/medcat/utils/cdb_utils.py rename to medcat/medcat/utils/cdb_utils.py diff --git a/medcat-v2/medcat/utils/check_for_updates.py b/medcat/medcat/utils/check_for_updates.py similarity index 100% rename from medcat-v2/medcat/utils/check_for_updates.py rename to medcat/medcat/utils/check_for_updates.py diff --git a/medcat-v2/medcat/utils/config_utils.py b/medcat/medcat/utils/config_utils.py similarity index 100% rename from medcat-v2/medcat/utils/config_utils.py rename to medcat/medcat/utils/config_utils.py diff --git a/medcat-v2/medcat/utils/data_utils.py b/medcat/medcat/utils/data_utils.py similarity index 100% rename from medcat-v2/medcat/utils/data_utils.py rename to medcat/medcat/utils/data_utils.py diff --git a/medcat-v2/medcat/utils/defaults.py b/medcat/medcat/utils/defaults.py similarity index 100% rename from medcat-v2/medcat/utils/defaults.py rename to medcat/medcat/utils/defaults.py diff --git a/medcat-v2/medcat/utils/download_scripts.py b/medcat/medcat/utils/download_scripts.py similarity index 100% rename from medcat-v2/medcat/utils/download_scripts.py rename to medcat/medcat/utils/download_scripts.py diff --git a/medcat-v2/medcat/utils/envsnapshot.py b/medcat/medcat/utils/envsnapshot.py similarity index 100% rename from medcat-v2/medcat/utils/envsnapshot.py rename to medcat/medcat/utils/envsnapshot.py diff --git a/medcat-v2/medcat/utils/exceptions.py b/medcat/medcat/utils/exceptions.py similarity index 100% rename from medcat-v2/medcat/utils/exceptions.py rename to medcat/medcat/utils/exceptions.py diff --git a/medcat-v2/medcat/utils/fileutils.py b/medcat/medcat/utils/fileutils.py similarity index 100% rename from medcat-v2/medcat/utils/fileutils.py rename to medcat/medcat/utils/fileutils.py diff --git a/medcat-v2/medcat/utils/filters.py b/medcat/medcat/utils/filters.py similarity index 100% rename from medcat-v2/medcat/utils/filters.py rename to medcat/medcat/utils/filters.py diff --git a/medcat-v2/medcat/utils/hasher.py b/medcat/medcat/utils/hasher.py similarity index 100% rename from medcat-v2/medcat/utils/hasher.py rename to medcat/medcat/utils/hasher.py diff --git a/medcat-v2/medcat/utils/import_utils.py b/medcat/medcat/utils/import_utils.py similarity index 100% rename from medcat-v2/medcat/utils/import_utils.py rename to medcat/medcat/utils/import_utils.py diff --git a/medcat-v2/medcat/utils/iterutils.py b/medcat/medcat/utils/iterutils.py similarity index 100% rename from medcat-v2/medcat/utils/iterutils.py rename to medcat/medcat/utils/iterutils.py diff --git a/medcat-v2/medcat/utils/legacy/__init__.py b/medcat/medcat/utils/legacy/__init__.py similarity index 100% rename from medcat-v2/medcat/utils/legacy/__init__.py rename to medcat/medcat/utils/legacy/__init__.py diff --git a/medcat-v2/medcat/utils/legacy/conversion_all.py b/medcat/medcat/utils/legacy/conversion_all.py similarity index 100% rename from medcat-v2/medcat/utils/legacy/conversion_all.py rename to medcat/medcat/utils/legacy/conversion_all.py diff --git a/medcat-v2/medcat/utils/legacy/convert_cdb.py b/medcat/medcat/utils/legacy/convert_cdb.py similarity index 100% rename from medcat-v2/medcat/utils/legacy/convert_cdb.py rename to medcat/medcat/utils/legacy/convert_cdb.py diff --git a/medcat-v2/medcat/utils/legacy/convert_config.py b/medcat/medcat/utils/legacy/convert_config.py similarity index 100% rename from medcat-v2/medcat/utils/legacy/convert_config.py rename to medcat/medcat/utils/legacy/convert_config.py diff --git a/medcat-v2/medcat/utils/legacy/convert_deid.py b/medcat/medcat/utils/legacy/convert_deid.py similarity index 100% rename from medcat-v2/medcat/utils/legacy/convert_deid.py rename to medcat/medcat/utils/legacy/convert_deid.py diff --git a/medcat-v2/medcat/utils/legacy/convert_meta_cat.py b/medcat/medcat/utils/legacy/convert_meta_cat.py similarity index 100% rename from medcat-v2/medcat/utils/legacy/convert_meta_cat.py rename to medcat/medcat/utils/legacy/convert_meta_cat.py diff --git a/medcat-v2/medcat/utils/legacy/convert_rel_cat.py b/medcat/medcat/utils/legacy/convert_rel_cat.py similarity index 100% rename from medcat-v2/medcat/utils/legacy/convert_rel_cat.py rename to medcat/medcat/utils/legacy/convert_rel_cat.py diff --git a/medcat-v2/medcat/utils/legacy/convert_vocab.py b/medcat/medcat/utils/legacy/convert_vocab.py similarity index 100% rename from medcat-v2/medcat/utils/legacy/convert_vocab.py rename to medcat/medcat/utils/legacy/convert_vocab.py diff --git a/medcat-v2/medcat/utils/legacy/fixes.py b/medcat/medcat/utils/legacy/fixes.py similarity index 100% rename from medcat-v2/medcat/utils/legacy/fixes.py rename to medcat/medcat/utils/legacy/fixes.py diff --git a/medcat-v2/medcat/utils/legacy/helpers.py b/medcat/medcat/utils/legacy/helpers.py similarity index 100% rename from medcat-v2/medcat/utils/legacy/helpers.py rename to medcat/medcat/utils/legacy/helpers.py diff --git a/medcat-v2/medcat/utils/legacy/identifier.py b/medcat/medcat/utils/legacy/identifier.py similarity index 100% rename from medcat-v2/medcat/utils/legacy/identifier.py rename to medcat/medcat/utils/legacy/identifier.py diff --git a/medcat-v2/medcat/utils/legacy/legacy_converter.py b/medcat/medcat/utils/legacy/legacy_converter.py similarity index 100% rename from medcat-v2/medcat/utils/legacy/legacy_converter.py rename to medcat/medcat/utils/legacy/legacy_converter.py diff --git a/medcat-v2/medcat/utils/legacy/v2_beta.py b/medcat/medcat/utils/legacy/v2_beta.py similarity index 100% rename from medcat-v2/medcat/utils/legacy/v2_beta.py rename to medcat/medcat/utils/legacy/v2_beta.py diff --git a/medcat-v2/medcat/utils/matutils.py b/medcat/medcat/utils/matutils.py similarity index 100% rename from medcat-v2/medcat/utils/matutils.py rename to medcat/medcat/utils/matutils.py diff --git a/medcat-v2/medcat/utils/ner/__init__.py b/medcat/medcat/utils/ner/__init__.py similarity index 100% rename from medcat-v2/medcat/utils/ner/__init__.py rename to medcat/medcat/utils/ner/__init__.py diff --git a/medcat-v2/medcat/utils/ner/data_collator.py b/medcat/medcat/utils/ner/data_collator.py similarity index 100% rename from medcat-v2/medcat/utils/ner/data_collator.py rename to medcat/medcat/utils/ner/data_collator.py diff --git a/medcat-v2/medcat/utils/ner/metrics.py b/medcat/medcat/utils/ner/metrics.py similarity index 100% rename from medcat-v2/medcat/utils/ner/metrics.py rename to medcat/medcat/utils/ner/metrics.py diff --git a/medcat-v2/medcat/utils/ner/transformers_ner.py b/medcat/medcat/utils/ner/transformers_ner.py similarity index 100% rename from medcat-v2/medcat/utils/ner/transformers_ner.py rename to medcat/medcat/utils/ner/transformers_ner.py diff --git a/medcat-v2/medcat/utils/postprocessing.py b/medcat/medcat/utils/postprocessing.py similarity index 100% rename from medcat-v2/medcat/utils/postprocessing.py rename to medcat/medcat/utils/postprocessing.py diff --git a/medcat-v2/medcat/utils/registry.py b/medcat/medcat/utils/registry.py similarity index 100% rename from medcat-v2/medcat/utils/registry.py rename to medcat/medcat/utils/registry.py diff --git a/medcat-v2/medcat/utils/regression/__init__.py b/medcat/medcat/utils/regression/__init__.py similarity index 100% rename from medcat-v2/medcat/utils/regression/__init__.py rename to medcat/medcat/utils/regression/__init__.py diff --git a/medcat-v2/medcat/utils/regression/checking.py b/medcat/medcat/utils/regression/checking.py similarity index 100% rename from medcat-v2/medcat/utils/regression/checking.py rename to medcat/medcat/utils/regression/checking.py diff --git a/medcat-v2/medcat/utils/regression/regression_checker.py b/medcat/medcat/utils/regression/regression_checker.py similarity index 100% rename from medcat-v2/medcat/utils/regression/regression_checker.py rename to medcat/medcat/utils/regression/regression_checker.py diff --git a/medcat-v2/medcat/utils/regression/results.py b/medcat/medcat/utils/regression/results.py similarity index 100% rename from medcat-v2/medcat/utils/regression/results.py rename to medcat/medcat/utils/regression/results.py diff --git a/medcat-v2/medcat/utils/regression/targeting.py b/medcat/medcat/utils/regression/targeting.py similarity index 100% rename from medcat-v2/medcat/utils/regression/targeting.py rename to medcat/medcat/utils/regression/targeting.py diff --git a/medcat-v2/medcat/utils/regression/utils.py b/medcat/medcat/utils/regression/utils.py similarity index 100% rename from medcat-v2/medcat/utils/regression/utils.py rename to medcat/medcat/utils/regression/utils.py diff --git a/medcat-v2/medcat/utils/training_utils.py b/medcat/medcat/utils/training_utils.py similarity index 100% rename from medcat-v2/medcat/utils/training_utils.py rename to medcat/medcat/utils/training_utils.py diff --git a/medcat-v2/medcat/utils/usage_monitoring.py b/medcat/medcat/utils/usage_monitoring.py similarity index 100% rename from medcat-v2/medcat/utils/usage_monitoring.py rename to medcat/medcat/utils/usage_monitoring.py diff --git a/medcat-v2/medcat/utils/vocab_utils.py b/medcat/medcat/utils/vocab_utils.py similarity index 100% rename from medcat-v2/medcat/utils/vocab_utils.py rename to medcat/medcat/utils/vocab_utils.py diff --git a/medcat-v2/medcat/version.py b/medcat/medcat/version.py similarity index 100% rename from medcat-v2/medcat/version.py rename to medcat/medcat/version.py diff --git a/medcat-v2/medcat/vocab.py b/medcat/medcat/vocab.py similarity index 100% rename from medcat-v2/medcat/vocab.py rename to medcat/medcat/vocab.py diff --git a/medcat-v2/mkdocs.yml b/medcat/mkdocs.yml similarity index 82% rename from medcat-v2/mkdocs.yml rename to medcat/mkdocs.yml index 974e795db..99ccf5df4 100644 --- a/medcat-v2/mkdocs.yml +++ b/medcat/mkdocs.yml @@ -1,4 +1,4 @@ -w# yaml-language-server: $schema=https://squidfunk.github.io/mkdocs-material/schema.json +# yaml-language-server: $schema=https://squidfunk.github.io/mkdocs-material/schema.json site_name: MedCAT Documentation site_url: https://docs.cogstack.org/ @@ -34,10 +34,18 @@ docs_dir: docs nav: - Home: index.md - Architecture: architecture.md - - Tutorials: '!include ../medcat-v2-tutorials/mkdocs.yml' + - Tutorials: '!include ../medcat-tutorials/mkdocs.yml' - Upgrading: + - Information for users coming from MedCAT v1: v1_info.md - Migration guide (v2): migration_guide_v2.md - Breaking changes: breaking_changes.md + +# to fix medcat folder and medcat/medcat folder confusion +# within mkdocs-monorepo-plugin that caused relative +# links in README.md not properly work when it was pulled +# into docs/index.md +hooks: + - docs/hooks.py plugins: - search @@ -80,4 +88,4 @@ markdown_extensions: emoji_generator: !!python/name:material.extensions.emoji.to_svg - pymdownx.snippets: # NOTE: looks like this starts from project root rather than mkdocs location - base_path: ['medcat-v2'] # so "README.md" resolves to ../README.md + base_path: ['medcat'] # so "README.md" resolves to ../README.md diff --git a/medcat-v2/mypy.ini b/medcat/mypy.ini similarity index 100% rename from medcat-v2/mypy.ini rename to medcat/mypy.ini diff --git a/medcat-v2/paper/README.md b/medcat/paper/README.md similarity index 100% rename from medcat-v2/paper/README.md rename to medcat/paper/README.md diff --git a/medcat-v2/paper/data/supervised/MDACE/raw/README.md b/medcat/paper/data/supervised/MDACE/raw/README.md similarity index 100% rename from medcat-v2/paper/data/supervised/MDACE/raw/README.md rename to medcat/paper/data/supervised/MDACE/raw/README.md diff --git a/medcat-v2/paper/data/supervised/MDACE/raw/convert_to_mct_export.py b/medcat/paper/data/supervised/MDACE/raw/convert_to_mct_export.py similarity index 100% rename from medcat-v2/paper/data/supervised/MDACE/raw/convert_to_mct_export.py rename to medcat/paper/data/supervised/MDACE/raw/convert_to_mct_export.py diff --git a/medcat-v2/paper/data/supervised/MDACE/raw/map_from_icd_to_snomed.py b/medcat/paper/data/supervised/MDACE/raw/map_from_icd_to_snomed.py similarity index 100% rename from medcat-v2/paper/data/supervised/MDACE/raw/map_from_icd_to_snomed.py rename to medcat/paper/data/supervised/MDACE/raw/map_from_icd_to_snomed.py diff --git a/medcat-v2/paper/data/supervised/cometa/raw/README.md b/medcat/paper/data/supervised/cometa/raw/README.md similarity index 100% rename from medcat-v2/paper/data/supervised/cometa/raw/README.md rename to medcat/paper/data/supervised/cometa/raw/README.md diff --git a/medcat-v2/paper/data/supervised/cometa/raw/conversion/converter.py b/medcat/paper/data/supervised/cometa/raw/conversion/converter.py similarity index 100% rename from medcat-v2/paper/data/supervised/cometa/raw/conversion/converter.py rename to medcat/paper/data/supervised/cometa/raw/conversion/converter.py diff --git a/medcat-v2/paper/data/supervised/distemist/raw/README.md b/medcat/paper/data/supervised/distemist/raw/README.md similarity index 100% rename from medcat-v2/paper/data/supervised/distemist/raw/README.md rename to medcat/paper/data/supervised/distemist/raw/README.md diff --git a/medcat-v2/paper/data/supervised/distemist/raw/convert_to_mct_export.py b/medcat/paper/data/supervised/distemist/raw/convert_to_mct_export.py similarity index 100% rename from medcat-v2/paper/data/supervised/distemist/raw/convert_to_mct_export.py rename to medcat/paper/data/supervised/distemist/raw/convert_to_mct_export.py diff --git a/medcat-v2/paper/data/supervised/linking_challenge/raw/README.md b/medcat/paper/data/supervised/linking_challenge/raw/README.md similarity index 100% rename from medcat-v2/paper/data/supervised/linking_challenge/raw/README.md rename to medcat/paper/data/supervised/linking_challenge/raw/README.md diff --git a/medcat-v2/paper/data/supervised/linking_challenge/raw/convert_to_mct_export.py b/medcat/paper/data/supervised/linking_challenge/raw/convert_to_mct_export.py similarity index 100% rename from medcat-v2/paper/data/supervised/linking_challenge/raw/convert_to_mct_export.py rename to medcat/paper/data/supervised/linking_challenge/raw/convert_to_mct_export.py diff --git a/medcat-v2/paper/data/supervised/medmentions/raw/README.md b/medcat/paper/data/supervised/medmentions/raw/README.md similarity index 100% rename from medcat-v2/paper/data/supervised/medmentions/raw/README.md rename to medcat/paper/data/supervised/medmentions/raw/README.md diff --git a/medcat-v2/paper/data/supervised/medmentions/raw/src/conversion_mapper.py b/medcat/paper/data/supervised/medmentions/raw/src/conversion_mapper.py similarity index 100% rename from medcat-v2/paper/data/supervised/medmentions/raw/src/conversion_mapper.py rename to medcat/paper/data/supervised/medmentions/raw/src/conversion_mapper.py diff --git a/medcat-v2/paper/data/supervised/medmentions/raw/src/medmen_umls2snomed_converter.py b/medcat/paper/data/supervised/medmentions/raw/src/medmen_umls2snomed_converter.py similarity index 100% rename from medcat-v2/paper/data/supervised/medmentions/raw/src/medmen_umls2snomed_converter.py rename to medcat/paper/data/supervised/medmentions/raw/src/medmen_umls2snomed_converter.py diff --git a/medcat-v2/paper/data/supervised/medmentions/raw/src/medmentions_converter.py b/medcat/paper/data/supervised/medmentions/raw/src/medmentions_converter.py similarity index 100% rename from medcat-v2/paper/data/supervised/medmentions/raw/src/medmentions_converter.py rename to medcat/paper/data/supervised/medmentions/raw/src/medmentions_converter.py diff --git a/medcat-v2/paper/data/unsupervised/.keep b/medcat/paper/data/unsupervised/.keep similarity index 100% rename from medcat-v2/paper/data/unsupervised/.keep rename to medcat/paper/data/unsupervised/.keep diff --git a/medcat-v2/paper/out/.keep b/medcat/paper/out/.keep similarity index 100% rename from medcat-v2/paper/out/.keep rename to medcat/paper/out/.keep diff --git a/medcat-v2/paper/out/inference_speed/.keep b/medcat/paper/out/inference_speed/.keep similarity index 100% rename from medcat-v2/paper/out/inference_speed/.keep rename to medcat/paper/out/inference_speed/.keep diff --git a/medcat-v2/paper/out/load_speed/.keep b/medcat/paper/out/load_speed/.keep similarity index 100% rename from medcat-v2/paper/out/load_speed/.keep rename to medcat/paper/out/load_speed/.keep diff --git a/medcat-v2/paper/out/performance/.keep b/medcat/paper/out/performance/.keep similarity index 100% rename from medcat-v2/paper/out/performance/.keep rename to medcat/paper/out/performance/.keep diff --git a/medcat-v2/paper/out/unsup_train_speed/.keep b/medcat/paper/out/unsup_train_speed/.keep similarity index 100% rename from medcat-v2/paper/out/unsup_train_speed/.keep rename to medcat/paper/out/unsup_train_speed/.keep diff --git a/medcat-v2/paper/scripts/performance/common_pref.py b/medcat/paper/scripts/performance/common_pref.py similarity index 100% rename from medcat-v2/paper/scripts/performance/common_pref.py rename to medcat/paper/scripts/performance/common_pref.py diff --git a/medcat-v2/paper/scripts/performance/get_performance_all.sh b/medcat/paper/scripts/performance/get_performance_all.sh similarity index 81% rename from medcat-v2/paper/scripts/performance/get_performance_all.sh rename to medcat/paper/scripts/performance/get_performance_all.sh index 7ac6d4408..d9bdf7f09 100644 --- a/medcat-v2/paper/scripts/performance/get_performance_all.sh +++ b/medcat/paper/scripts/performance/get_performance_all.sh @@ -2,9 +2,9 @@ a script_path="scripts/performance/get_performance_for_model_and_ds.py" v1_model_pack="/Users/martratas/Documents/CogStack/MedCAT/MedCAT/models/20230227__kch_gstt_trained_model_no_mc_d84c313f24311484.zip" -v2_model_pack="/Users/martratas/Documents/CogStack/MedCAT/monorepo-nlp/medcat-v2/.temp/CONVERT_2023_model_no_mc_234dda1597f635e3.zip" +v2_model_pack="/Users/martratas/Documents/CogStack/MedCAT/monorepo-nlp/medcat/.temp/CONVERT_2023_model_no_mc_234dda1597f635e3.zip" # v1_model_pack="/Users/martratas/Documents/CogStack/MedCAT/medcat-snomed-model-creation/.creation_cache/out_snomed_2025/final_model_Snomed2025-07-11_de7cbec4a786e418.zip" -# v2_model_pack="/Users/martratas/Documents/CogStack/MedCAT/monorepo-nlp/medcat-v2/.temp/2025_11_19_issue228_add_meta_cat_to_other/models/v2_Snomed2025_MIMIC_IV_bbe806e192df009f.zip" +# v2_model_pack="/Users/martratas/Documents/CogStack/MedCAT/monorepo-nlp/medcat/.temp/2025_11_19_issue228_add_meta_cat_to_other/models/v2_Snomed2025_MIMIC_IV_bbe806e192df009f.zip" echo "*****************" echo "running v1 stuff" diff --git a/medcat-v2/paper/scripts/performance/get_performance_for_model_and_ds.py b/medcat/paper/scripts/performance/get_performance_for_model_and_ds.py similarity index 100% rename from medcat-v2/paper/scripts/performance/get_performance_for_model_and_ds.py rename to medcat/paper/scripts/performance/get_performance_for_model_and_ds.py diff --git a/medcat-v2/paper/scripts/performance/get_regression_all.sh b/medcat/paper/scripts/performance/get_regression_all.sh similarity index 90% rename from medcat-v2/paper/scripts/performance/get_regression_all.sh rename to medcat/paper/scripts/performance/get_regression_all.sh index c8dbd3ed7..de7ef85e5 100644 --- a/medcat-v2/paper/scripts/performance/get_regression_all.sh +++ b/medcat/paper/scripts/performance/get_regression_all.sh @@ -2,7 +2,7 @@ script_path="scripts/performance/regression_perf.py" v1_model_pack="/Users/martratas/Documents/CogStack/MedCAT/MedCAT/models/20230227__kch_gstt_trained_model_no_mc_d84c313f24311484.zip" -v2_model_pack="/Users/martratas/Documents/CogStack/MedCAT/monorepo-nlp/medcat-v2/.temp/CONVERT_2023_model_no_mc_234dda1597f635e3.zip" +v2_model_pack="/Users/martratas/Documents/CogStack/MedCAT/monorepo-nlp/medcat/.temp/CONVERT_2023_model_no_mc_234dda1597f635e3.zip" v1_out_file="out/performance/v1_regression.csv" v2_out_file="out/performance/v2_regression.csv" diff --git a/medcat-v2/paper/scripts/performance/my_stats.py b/medcat/paper/scripts/performance/my_stats.py similarity index 100% rename from medcat-v2/paper/scripts/performance/my_stats.py rename to medcat/paper/scripts/performance/my_stats.py diff --git a/medcat-v2/paper/scripts/performance/regression_perf.py b/medcat/paper/scripts/performance/regression_perf.py similarity index 100% rename from medcat-v2/paper/scripts/performance/regression_perf.py rename to medcat/paper/scripts/performance/regression_perf.py diff --git a/medcat-v2/paper/scripts/performance/v1_helper.py b/medcat/paper/scripts/performance/v1_helper.py similarity index 100% rename from medcat-v2/paper/scripts/performance/v1_helper.py rename to medcat/paper/scripts/performance/v1_helper.py diff --git a/medcat-v2/paper/scripts/run_all_at_once.sh b/medcat/paper/scripts/run_all_at_once.sh similarity index 100% rename from medcat-v2/paper/scripts/run_all_at_once.sh rename to medcat/paper/scripts/run_all_at_once.sh diff --git a/medcat-v2/paper/scripts/speed/common.py b/medcat/paper/scripts/speed/common.py similarity index 100% rename from medcat-v2/paper/scripts/speed/common.py rename to medcat/paper/scripts/speed/common.py diff --git a/medcat-v2/paper/scripts/speed/common4subproc.py b/medcat/paper/scripts/speed/common4subproc.py similarity index 100% rename from medcat-v2/paper/scripts/speed/common4subproc.py rename to medcat/paper/scripts/speed/common4subproc.py diff --git a/medcat-v2/paper/scripts/speed/get_inference_speed.py b/medcat/paper/scripts/speed/get_inference_speed.py similarity index 100% rename from medcat-v2/paper/scripts/speed/get_inference_speed.py rename to medcat/paper/scripts/speed/get_inference_speed.py diff --git a/medcat-v2/paper/scripts/speed/get_inference_speed_all.py b/medcat/paper/scripts/speed/get_inference_speed_all.py similarity index 100% rename from medcat-v2/paper/scripts/speed/get_inference_speed_all.py rename to medcat/paper/scripts/speed/get_inference_speed_all.py diff --git a/medcat-v2/paper/scripts/speed/get_inference_speed_for_multiple.sh b/medcat/paper/scripts/speed/get_inference_speed_for_multiple.sh similarity index 100% rename from medcat-v2/paper/scripts/speed/get_inference_speed_for_multiple.sh rename to medcat/paper/scripts/speed/get_inference_speed_for_multiple.sh diff --git a/medcat-v2/paper/scripts/speed/get_inference_speed_for_multiple_v1.sh b/medcat/paper/scripts/speed/get_inference_speed_for_multiple_v1.sh similarity index 100% rename from medcat-v2/paper/scripts/speed/get_inference_speed_for_multiple_v1.sh rename to medcat/paper/scripts/speed/get_inference_speed_for_multiple_v1.sh diff --git a/medcat-v2/paper/scripts/speed/get_inference_speed_for_multiple_v2.sh b/medcat/paper/scripts/speed/get_inference_speed_for_multiple_v2.sh similarity index 76% rename from medcat-v2/paper/scripts/speed/get_inference_speed_for_multiple_v2.sh rename to medcat/paper/scripts/speed/get_inference_speed_for_multiple_v2.sh index 62b21bee9..8e2dde407 100644 --- a/medcat-v2/paper/scripts/speed/get_inference_speed_for_multiple_v2.sh +++ b/medcat/paper/scripts/speed/get_inference_speed_for_multiple_v2.sh @@ -1,7 +1,7 @@ ner1="2023_NER_no_MetaCAT" -ner_model_path_no_mc="/Users/martratas/Documents/CogStack/MedCAT/monorepo-nlp/medcat-v2/.temp/CONVERT_2023_model_no_mc_234dda1597f635e3.zip" +ner_model_path_no_mc="/Users/martratas/Documents/CogStack/MedCAT/monorepo-nlp/medcat/.temp/CONVERT_2023_model_no_mc_234dda1597f635e3.zip" ner2="2023_NER_w_MetaCAT" -ner_model_path_w_mc="/Users/martratas/Documents/CogStack/MedCAT/monorepo-nlp/medcat-v2/.temp/20230227__kch_gstt_trained_model_f76d2121b77c3e9a.zip" +ner_model_path_w_mc="/Users/martratas/Documents/CogStack/MedCAT/monorepo-nlp/medcat/.temp/20230227__kch_gstt_trained_model_f76d2121b77c3e9a.zip" csv_path="data/unsupervised/mimic_iv_discharge_head20.csv" out_prefix="out/inference_speed/v2" diff --git a/medcat-v2/paper/scripts/speed/get_load_speed.py b/medcat/paper/scripts/speed/get_load_speed.py similarity index 100% rename from medcat-v2/paper/scripts/speed/get_load_speed.py rename to medcat/paper/scripts/speed/get_load_speed.py diff --git a/medcat-v2/paper/scripts/speed/get_load_speed_all.py b/medcat/paper/scripts/speed/get_load_speed_all.py similarity index 100% rename from medcat-v2/paper/scripts/speed/get_load_speed_all.py rename to medcat/paper/scripts/speed/get_load_speed_all.py diff --git a/medcat-v2/paper/scripts/speed/get_load_speed_for_multiple.sh b/medcat/paper/scripts/speed/get_load_speed_for_multiple.sh similarity index 100% rename from medcat-v2/paper/scripts/speed/get_load_speed_for_multiple.sh rename to medcat/paper/scripts/speed/get_load_speed_for_multiple.sh diff --git a/medcat-v2/paper/scripts/speed/get_load_speed_for_multiple_v1.sh b/medcat/paper/scripts/speed/get_load_speed_for_multiple_v1.sh similarity index 100% rename from medcat-v2/paper/scripts/speed/get_load_speed_for_multiple_v1.sh rename to medcat/paper/scripts/speed/get_load_speed_for_multiple_v1.sh diff --git a/medcat-v2/paper/scripts/speed/get_load_speed_for_multiple_v2.sh b/medcat/paper/scripts/speed/get_load_speed_for_multiple_v2.sh similarity index 69% rename from medcat-v2/paper/scripts/speed/get_load_speed_for_multiple_v2.sh rename to medcat/paper/scripts/speed/get_load_speed_for_multiple_v2.sh index e1e22a857..44e91e4b7 100644 --- a/medcat-v2/paper/scripts/speed/get_load_speed_for_multiple_v2.sh +++ b/medcat/paper/scripts/speed/get_load_speed_for_multiple_v2.sh @@ -1,9 +1,9 @@ ner1="2023_NER_no_MetaCAT" -ner_model_path_no_mc="/Users/martratas/Documents/CogStack/MedCAT/monorepo-nlp/medcat-v2/.temp/CONVERT_2023_model_no_mc_234dda1597f635e3.zip" +ner_model_path_no_mc="/Users/martratas/Documents/CogStack/MedCAT/monorepo-nlp/medcat2/.temp/CONVERT_2023_model_no_mc_234dda1597f635e3.zip" ner2="2023_NER_w_MetaCAT" -ner_model_path_w_mc="/Users/martratas/Documents/CogStack/MedCAT/monorepo-nlp/medcat-v2/.temp/20230227__kch_gstt_trained_model_f76d2121b77c3e9a.zip" +ner_model_path_w_mc="/Users/martratas/Documents/CogStack/MedCAT/monorepo-nlp/medcat/.temp/20230227__kch_gstt_trained_model_f76d2121b77c3e9a.zip" deid="n2c2_DeID" -deid_model_path="/Users/martratas/Documents/CogStack/MedCAT/monorepo-nlp/medcat-v2/.temp/CONVERT_deid_model_af31d2a9c5ccbe4d.zip.zip" +deid_model_path="/Users/martratas/Documents/CogStack/MedCAT/monorepo-nlp/medcat/.temp/CONVERT_deid_model_af31d2a9c5ccbe4d.zip.zip" out_prefix="out/load_speed/v2" if [[ ! -z "$1" ]] diff --git a/medcat-v2/paper/scripts/speed/get_unsup_train_speed.py b/medcat/paper/scripts/speed/get_unsup_train_speed.py similarity index 100% rename from medcat-v2/paper/scripts/speed/get_unsup_train_speed.py rename to medcat/paper/scripts/speed/get_unsup_train_speed.py diff --git a/medcat-v2/paper/scripts/speed/get_unsup_train_speed_all.py b/medcat/paper/scripts/speed/get_unsup_train_speed_all.py similarity index 100% rename from medcat-v2/paper/scripts/speed/get_unsup_train_speed_all.py rename to medcat/paper/scripts/speed/get_unsup_train_speed_all.py diff --git a/medcat-v2/paper/scripts/speed/get_unsup_train_speed_for_multiple.sh b/medcat/paper/scripts/speed/get_unsup_train_speed_for_multiple.sh similarity index 100% rename from medcat-v2/paper/scripts/speed/get_unsup_train_speed_for_multiple.sh rename to medcat/paper/scripts/speed/get_unsup_train_speed_for_multiple.sh diff --git a/medcat-v2/paper/scripts/speed/get_unsup_train_speed_for_multiple_v1.sh b/medcat/paper/scripts/speed/get_unsup_train_speed_for_multiple_v1.sh similarity index 100% rename from medcat-v2/paper/scripts/speed/get_unsup_train_speed_for_multiple_v1.sh rename to medcat/paper/scripts/speed/get_unsup_train_speed_for_multiple_v1.sh diff --git a/medcat-v2/paper/scripts/speed/get_unsup_train_speed_for_multiple_v2.sh b/medcat/paper/scripts/speed/get_unsup_train_speed_for_multiple_v2.sh similarity index 76% rename from medcat-v2/paper/scripts/speed/get_unsup_train_speed_for_multiple_v2.sh rename to medcat/paper/scripts/speed/get_unsup_train_speed_for_multiple_v2.sh index 0eb6e083b..9ea2bbac8 100644 --- a/medcat-v2/paper/scripts/speed/get_unsup_train_speed_for_multiple_v2.sh +++ b/medcat/paper/scripts/speed/get_unsup_train_speed_for_multiple_v2.sh @@ -1,7 +1,7 @@ ner1="2023_NER_no_MetaCAT" -ner_model_path_no_mc="/Users/martratas/Documents/CogStack/MedCAT/monorepo-nlp/medcat-v2/.temp/CONVERT_2023_model_no_mc_234dda1597f635e3.zip" +ner_model_path_no_mc="/Users/martratas/Documents/CogStack/MedCAT/monorepo-nlp/medcat/.temp/CONVERT_2023_model_no_mc_234dda1597f635e3.zip" ner2="2023_NER_w_MetaCAT" -ner_model_path_w_mc="/Users/martratas/Documents/CogStack/MedCAT/monorepo-nlp/medcat-v2/.temp/20230227__kch_gstt_trained_model_f76d2121b77c3e9a.zip" +ner_model_path_w_mc="/Users/martratas/Documents/CogStack/MedCAT/monorepo-nlp/medcat/.temp/20230227__kch_gstt_trained_model_f76d2121b77c3e9a.zip" csv_path="data/unsupervised/mimic_iv_discharge_head20.csv" out_prefix="out/unsup_train_speed/v2" diff --git a/medcat-v2/paper/scripts/speed/run_all_speed_scripts.sh b/medcat/paper/scripts/speed/run_all_speed_scripts.sh similarity index 100% rename from medcat-v2/paper/scripts/speed/run_all_speed_scripts.sh rename to medcat/paper/scripts/speed/run_all_speed_scripts.sh diff --git a/medcat-v2/paper/scripts/speed/run_all_speed_scripts_for_version.sh b/medcat/paper/scripts/speed/run_all_speed_scripts_for_version.sh similarity index 100% rename from medcat-v2/paper/scripts/speed/run_all_speed_scripts_for_version.sh rename to medcat/paper/scripts/speed/run_all_speed_scripts_for_version.sh diff --git a/medcat-v2/paper/scripts/speed/summarise_speeds.py b/medcat/paper/scripts/speed/summarise_speeds.py similarity index 100% rename from medcat-v2/paper/scripts/speed/summarise_speeds.py rename to medcat/paper/scripts/speed/summarise_speeds.py diff --git a/medcat-v2/paper/scripts/variance/convert_to_embed_linker.py b/medcat/paper/scripts/variance/convert_to_embed_linker.py similarity index 100% rename from medcat-v2/paper/scripts/variance/convert_to_embed_linker.py rename to medcat/paper/scripts/variance/convert_to_embed_linker.py diff --git a/medcat-v2/paper/scripts/variance/get_variance_with_linker_and_tokenizer.py b/medcat/paper/scripts/variance/get_variance_with_linker_and_tokenizer.py similarity index 100% rename from medcat-v2/paper/scripts/variance/get_variance_with_linker_and_tokenizer.py rename to medcat/paper/scripts/variance/get_variance_with_linker_and_tokenizer.py diff --git a/medcat-v2/paper/scripts/variance/get_variance_with_linker_and_tokenizer_all.sh b/medcat/paper/scripts/variance/get_variance_with_linker_and_tokenizer_all.sh similarity index 100% rename from medcat-v2/paper/scripts/variance/get_variance_with_linker_and_tokenizer_all.sh rename to medcat/paper/scripts/variance/get_variance_with_linker_and_tokenizer_all.sh diff --git a/medcat-v2/paper/scripts/variance/plot_variance.py b/medcat/paper/scripts/variance/plot_variance.py similarity index 100% rename from medcat-v2/paper/scripts/variance/plot_variance.py rename to medcat/paper/scripts/variance/plot_variance.py diff --git a/medcat-v2/pyproject.toml b/medcat/pyproject.toml similarity index 100% rename from medcat-v2/pyproject.toml rename to medcat/pyproject.toml diff --git a/medcat-v2/tests/__init__.py b/medcat/tests/__init__.py similarity index 100% rename from medcat-v2/tests/__init__.py rename to medcat/tests/__init__.py diff --git a/medcat-v2/tests/backwards_compatibility/check_backwards_compatibility.sh b/medcat/tests/backwards_compatibility/check_backwards_compatibility.sh similarity index 100% rename from medcat-v2/tests/backwards_compatibility/check_backwards_compatibility.sh rename to medcat/tests/backwards_compatibility/check_backwards_compatibility.sh diff --git a/medcat-v2/tests/backwards_compatibility/creation/cat_creation.py b/medcat/tests/backwards_compatibility/creation/cat_creation.py similarity index 100% rename from medcat-v2/tests/backwards_compatibility/creation/cat_creation.py rename to medcat/tests/backwards_compatibility/creation/cat_creation.py diff --git a/medcat-v2/tests/backwards_compatibility/creation/preprocessed4cdb.txt b/medcat/tests/backwards_compatibility/creation/preprocessed4cdb.txt similarity index 100% rename from medcat-v2/tests/backwards_compatibility/creation/preprocessed4cdb.txt rename to medcat/tests/backwards_compatibility/creation/preprocessed4cdb.txt diff --git a/medcat-v2/tests/backwards_compatibility/creation/selfsupervised_data.txt b/medcat/tests/backwards_compatibility/creation/selfsupervised_data.txt similarity index 100% rename from medcat-v2/tests/backwards_compatibility/creation/selfsupervised_data.txt rename to 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medcat-v2/tests/components/linking/__init__.py rename to medcat/tests/components/linking/__init__.py diff --git a/medcat-v2/tests/components/linking/test_context_based_linker.py b/medcat/tests/components/linking/test_context_based_linker.py similarity index 100% rename from medcat-v2/tests/components/linking/test_context_based_linker.py rename to medcat/tests/components/linking/test_context_based_linker.py diff --git a/medcat-v2/tests/components/linking/test_primary_name_only_linker.py b/medcat/tests/components/linking/test_primary_name_only_linker.py similarity index 100% rename from medcat-v2/tests/components/linking/test_primary_name_only_linker.py rename to medcat/tests/components/linking/test_primary_name_only_linker.py diff --git a/medcat-v2/tests/components/ner/__init__.py b/medcat/tests/components/ner/__init__.py similarity index 100% rename from medcat-v2/tests/components/ner/__init__.py rename to medcat/tests/components/ner/__init__.py diff --git a/medcat-v2/tests/components/ner/test_vocab_based_annotator.py b/medcat/tests/components/ner/test_vocab_based_annotator.py similarity index 100% rename from medcat-v2/tests/components/ner/test_vocab_based_annotator.py rename to medcat/tests/components/ner/test_vocab_based_annotator.py diff --git a/medcat-v2/tests/components/ner/test_vocab_based_ner.py b/medcat/tests/components/ner/test_vocab_based_ner.py similarity index 100% rename from medcat-v2/tests/components/ner/test_vocab_based_ner.py rename to medcat/tests/components/ner/test_vocab_based_ner.py diff --git a/medcat-v2/tests/components/ner/trf/__init__.py b/medcat/tests/components/ner/trf/__init__.py similarity index 100% rename from medcat-v2/tests/components/ner/trf/__init__.py rename to medcat/tests/components/ner/trf/__init__.py diff --git a/medcat-v2/tests/components/ner/trf/test_transformers_ner.py b/medcat/tests/components/ner/trf/test_transformers_ner.py similarity index 100% rename from medcat-v2/tests/components/ner/trf/test_transformers_ner.py rename to medcat/tests/components/ner/trf/test_transformers_ner.py diff --git a/medcat-v2/tests/components/normalizing/__init__.py b/medcat/tests/components/normalizing/__init__.py similarity index 100% rename from medcat-v2/tests/components/normalizing/__init__.py rename to medcat/tests/components/normalizing/__init__.py diff --git a/medcat-v2/tests/components/normalizing/test_normalizer.py b/medcat/tests/components/normalizing/test_normalizer.py similarity index 100% rename from medcat-v2/tests/components/normalizing/test_normalizer.py rename to medcat/tests/components/normalizing/test_normalizer.py diff --git a/medcat-v2/tests/components/tagging/__init__.py b/medcat/tests/components/tagging/__init__.py similarity index 100% rename from medcat-v2/tests/components/tagging/__init__.py rename to medcat/tests/components/tagging/__init__.py diff --git a/medcat-v2/tests/components/tagging/test_tagger.py b/medcat/tests/components/tagging/test_tagger.py similarity index 100% rename from medcat-v2/tests/components/tagging/test_tagger.py rename to medcat/tests/components/tagging/test_tagger.py diff --git a/medcat-v2/tests/components/test_registration.py b/medcat/tests/components/test_registration.py similarity index 100% rename from medcat-v2/tests/components/test_registration.py rename to medcat/tests/components/test_registration.py diff --git a/medcat-v2/tests/components/test_types.py b/medcat/tests/components/test_types.py similarity index 100% rename from medcat-v2/tests/components/test_types.py rename to medcat/tests/components/test_types.py diff --git a/medcat-v2/tests/config/__init__.py b/medcat/tests/config/__init__.py similarity index 100% rename from medcat-v2/tests/config/__init__.py rename to medcat/tests/config/__init__.py diff --git a/medcat-v2/tests/config/test_config.py b/medcat/tests/config/test_config.py similarity index 100% rename from medcat-v2/tests/config/test_config.py rename to medcat/tests/config/test_config.py diff --git a/medcat-v2/tests/config/test_config_env_at_import_time.py b/medcat/tests/config/test_config_env_at_import_time.py similarity index 100% rename from medcat-v2/tests/config/test_config_env_at_import_time.py rename to medcat/tests/config/test_config_env_at_import_time.py diff --git a/medcat-v2/tests/config/test_config_import_no_warnings.py b/medcat/tests/config/test_config_import_no_warnings.py similarity index 100% rename from medcat-v2/tests/config/test_config_import_no_warnings.py rename to medcat/tests/config/test_config_import_no_warnings.py diff --git a/medcat-v2/tests/config/test_config_serialisation.py b/medcat/tests/config/test_config_serialisation.py similarity index 100% rename from medcat-v2/tests/config/test_config_serialisation.py rename to medcat/tests/config/test_config_serialisation.py diff --git a/medcat-v2/tests/data/__init__.py b/medcat/tests/data/__init__.py similarity index 100% rename from medcat-v2/tests/data/__init__.py rename to medcat/tests/data/__init__.py diff --git a/medcat-v2/tests/data/test_mctexport.py b/medcat/tests/data/test_mctexport.py similarity index 100% rename from medcat-v2/tests/data/test_mctexport.py rename to medcat/tests/data/test_mctexport.py diff --git a/medcat-v2/tests/model_creation/__init__.py b/medcat/tests/model_creation/__init__.py similarity index 100% rename from medcat-v2/tests/model_creation/__init__.py rename to medcat/tests/model_creation/__init__.py diff --git a/medcat-v2/tests/model_creation/test_cdb_maker.py b/medcat/tests/model_creation/test_cdb_maker.py similarity index 100% rename from medcat-v2/tests/model_creation/test_cdb_maker.py rename to medcat/tests/model_creation/test_cdb_maker.py diff --git a/medcat-v2/tests/other/check_base_install_can_import_all.py b/medcat/tests/other/check_base_install_can_import_all.py similarity index 100% rename from medcat-v2/tests/other/check_base_install_can_import_all.py rename to medcat/tests/other/check_base_install_can_import_all.py diff --git a/medcat-v2/tests/other/download_all_transformers_models.py b/medcat/tests/other/download_all_transformers_models.py similarity index 100% rename from medcat-v2/tests/other/download_all_transformers_models.py rename to medcat/tests/other/download_all_transformers_models.py diff --git a/medcat-v2/tests/pipeline/__init__.py b/medcat/tests/pipeline/__init__.py similarity index 100% rename from medcat-v2/tests/pipeline/__init__.py rename to medcat/tests/pipeline/__init__.py diff --git a/medcat-v2/tests/pipeline/test_pipeline.py b/medcat/tests/pipeline/test_pipeline.py similarity index 100% rename from medcat-v2/tests/pipeline/test_pipeline.py rename to medcat/tests/pipeline/test_pipeline.py diff --git a/medcat-v2/tests/pipeline/test_speed_utils.py b/medcat/tests/pipeline/test_speed_utils.py similarity index 100% rename from medcat-v2/tests/pipeline/test_speed_utils.py rename to medcat/tests/pipeline/test_speed_utils.py diff --git a/medcat-v2/tests/plugins/__init__.py b/medcat/tests/plugins/__init__.py similarity index 100% rename from medcat-v2/tests/plugins/__init__.py rename to medcat/tests/plugins/__init__.py diff --git a/medcat-v2/tests/plugins/test_catalog.py b/medcat/tests/plugins/test_catalog.py similarity index 100% rename from medcat-v2/tests/plugins/test_catalog.py rename to medcat/tests/plugins/test_catalog.py diff --git a/medcat-v2/tests/plugins/test_cli.py b/medcat/tests/plugins/test_cli.py similarity index 100% rename from medcat-v2/tests/plugins/test_cli.py rename to medcat/tests/plugins/test_cli.py diff --git a/medcat-v2/tests/plugins/test_downloadable.py b/medcat/tests/plugins/test_downloadable.py similarity index 100% rename from medcat-v2/tests/plugins/test_downloadable.py rename to medcat/tests/plugins/test_downloadable.py diff --git a/medcat-v2/tests/plugins/test_installer.py b/medcat/tests/plugins/test_installer.py similarity index 100% rename from medcat-v2/tests/plugins/test_installer.py rename to medcat/tests/plugins/test_installer.py diff --git a/medcat-v2/tests/plugins/test_loader.py b/medcat/tests/plugins/test_loader.py similarity index 100% rename from medcat-v2/tests/plugins/test_loader.py rename to medcat/tests/plugins/test_loader.py diff --git a/medcat-v2/tests/preprocessors/__init__.py b/medcat/tests/preprocessors/__init__.py similarity index 100% rename from medcat-v2/tests/preprocessors/__init__.py rename to medcat/tests/preprocessors/__init__.py diff --git a/medcat-v2/tests/preprocessors/test_cleaners.py b/medcat/tests/preprocessors/test_cleaners.py similarity index 100% rename from medcat-v2/tests/preprocessors/test_cleaners.py rename to medcat/tests/preprocessors/test_cleaners.py diff --git a/medcat-v2/tests/resource_fetch.py b/medcat/tests/resource_fetch.py similarity index 98% rename from medcat-v2/tests/resource_fetch.py rename to medcat/tests/resource_fetch.py index 6ac710958..63630d5ba 100644 --- a/medcat-v2/tests/resource_fetch.py +++ b/medcat/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. # diff --git a/medcat-v2/tests/resources/cdb_example.csv b/medcat/tests/resources/cdb_example.csv similarity index 100% rename from medcat-v2/tests/resources/cdb_example.csv rename to medcat/tests/resources/cdb_example.csv diff --git a/medcat-v2/tests/resources/cdb_meta.csv b/medcat/tests/resources/cdb_meta.csv similarity index 100% rename from medcat-v2/tests/resources/cdb_meta.csv rename to medcat/tests/resources/cdb_meta.csv diff --git a/medcat-v2/tests/resources/cdb_meta.zip b/medcat/tests/resources/cdb_meta.zip similarity index 100% rename from medcat-v2/tests/resources/cdb_meta.zip rename to medcat/tests/resources/cdb_meta.zip diff --git a/medcat-v2/tests/resources/default_regression_tests.yml b/medcat/tests/resources/default_regression_tests.yml similarity index 100% rename from medcat-v2/tests/resources/default_regression_tests.yml rename to medcat/tests/resources/default_regression_tests.yml diff --git a/medcat-v2/tests/resources/deid_test_data.json b/medcat/tests/resources/deid_test_data.json similarity index 100% rename from medcat-v2/tests/resources/deid_test_data.json rename to medcat/tests/resources/deid_test_data.json diff --git a/medcat-v2/tests/resources/deid_train_data.json b/medcat/tests/resources/deid_train_data.json similarity index 100% rename from medcat-v2/tests/resources/deid_train_data.json rename to medcat/tests/resources/deid_train_data.json diff --git a/medcat-v2/tests/resources/mct2_cdb.zip b/medcat/tests/resources/mct2_cdb.zip similarity index 100% rename from medcat-v2/tests/resources/mct2_cdb.zip rename to medcat/tests/resources/mct2_cdb.zip diff --git a/medcat-v2/tests/resources/mct2_cdb/.schema.json b/medcat/tests/resources/mct2_cdb/.schema.json similarity index 100% rename from medcat-v2/tests/resources/mct2_cdb/.schema.json rename to medcat/tests/resources/mct2_cdb/.schema.json diff --git a/medcat-v2/tests/resources/mct2_cdb/.serialised_by b/medcat/tests/resources/mct2_cdb/.serialised_by similarity index 100% rename from medcat-v2/tests/resources/mct2_cdb/.serialised_by rename to medcat/tests/resources/mct2_cdb/.serialised_by diff --git a/medcat-v2/tests/resources/mct2_cdb/config/.schema.json b/medcat/tests/resources/mct2_cdb/config/.schema.json similarity index 100% rename from medcat-v2/tests/resources/mct2_cdb/config/.schema.json rename to medcat/tests/resources/mct2_cdb/config/.schema.json diff --git a/medcat-v2/tests/resources/mct2_cdb/config/.serialised_by b/medcat/tests/resources/mct2_cdb/config/.serialised_by similarity index 100% rename from medcat-v2/tests/resources/mct2_cdb/config/.serialised_by rename to medcat/tests/resources/mct2_cdb/config/.serialised_by diff --git a/medcat-v2/tests/resources/mct2_cdb/config/annotation_output/.schema.json b/medcat/tests/resources/mct2_cdb/config/annotation_output/.schema.json similarity index 100% rename from medcat-v2/tests/resources/mct2_cdb/config/annotation_output/.schema.json rename to medcat/tests/resources/mct2_cdb/config/annotation_output/.schema.json diff --git a/medcat-v2/tests/resources/mct2_cdb/config/annotation_output/.serialised_by b/medcat/tests/resources/mct2_cdb/config/annotation_output/.serialised_by similarity index 100% rename from medcat-v2/tests/resources/mct2_cdb/config/annotation_output/.serialised_by rename to medcat/tests/resources/mct2_cdb/config/annotation_output/.serialised_by diff --git a/medcat-v2/tests/resources/mct2_cdb/config/cdb_maker/.schema.json b/medcat/tests/resources/mct2_cdb/config/cdb_maker/.schema.json similarity index 100% rename from medcat-v2/tests/resources/mct2_cdb/config/cdb_maker/.schema.json rename to medcat/tests/resources/mct2_cdb/config/cdb_maker/.schema.json diff --git a/medcat-v2/tests/resources/mct2_cdb/config/cdb_maker/.serialised_by b/medcat/tests/resources/mct2_cdb/config/cdb_maker/.serialised_by similarity index 100% rename from medcat-v2/tests/resources/mct2_cdb/config/cdb_maker/.serialised_by rename to medcat/tests/resources/mct2_cdb/config/cdb_maker/.serialised_by diff --git a/medcat-v2/tests/resources/mct2_cdb/config/components/.schema.json b/medcat/tests/resources/mct2_cdb/config/components/.schema.json similarity index 100% rename from medcat-v2/tests/resources/mct2_cdb/config/components/.schema.json rename to medcat/tests/resources/mct2_cdb/config/components/.schema.json diff --git a/medcat-v2/tests/resources/mct2_cdb/config/components/.serialised_by b/medcat/tests/resources/mct2_cdb/config/components/.serialised_by similarity index 100% rename from medcat-v2/tests/resources/mct2_cdb/config/components/.serialised_by rename to medcat/tests/resources/mct2_cdb/config/components/.serialised_by diff --git a/medcat-v2/tests/resources/mct2_cdb/config/components/linking/.schema.json b/medcat/tests/resources/mct2_cdb/config/components/linking/.schema.json similarity index 100% rename from medcat-v2/tests/resources/mct2_cdb/config/components/linking/.schema.json rename to medcat/tests/resources/mct2_cdb/config/components/linking/.schema.json diff --git a/medcat-v2/tests/resources/mct2_cdb/config/components/linking/.serialised_by b/medcat/tests/resources/mct2_cdb/config/components/linking/.serialised_by similarity index 100% rename from medcat-v2/tests/resources/mct2_cdb/config/components/linking/.serialised_by rename to medcat/tests/resources/mct2_cdb/config/components/linking/.serialised_by diff --git a/medcat-v2/tests/resources/mct2_cdb/config/components/linking/filters/.schema.json b/medcat/tests/resources/mct2_cdb/config/components/linking/filters/.schema.json similarity index 100% rename from medcat-v2/tests/resources/mct2_cdb/config/components/linking/filters/.schema.json rename to medcat/tests/resources/mct2_cdb/config/components/linking/filters/.schema.json diff --git a/medcat-v2/tests/resources/mct2_cdb/config/components/linking/filters/.serialised_by b/medcat/tests/resources/mct2_cdb/config/components/linking/filters/.serialised_by similarity index 100% rename from medcat-v2/tests/resources/mct2_cdb/config/components/linking/filters/.serialised_by rename to medcat/tests/resources/mct2_cdb/config/components/linking/filters/.serialised_by diff --git a/medcat-v2/tests/resources/mct2_cdb/config/components/ner/.schema.json b/medcat/tests/resources/mct2_cdb/config/components/ner/.schema.json similarity index 100% rename from medcat-v2/tests/resources/mct2_cdb/config/components/ner/.schema.json rename to medcat/tests/resources/mct2_cdb/config/components/ner/.schema.json diff --git a/medcat-v2/tests/resources/mct2_cdb/config/components/ner/.serialised_by b/medcat/tests/resources/mct2_cdb/config/components/ner/.serialised_by similarity index 100% rename from medcat-v2/tests/resources/mct2_cdb/config/components/ner/.serialised_by rename to medcat/tests/resources/mct2_cdb/config/components/ner/.serialised_by diff --git a/medcat-v2/tests/resources/mct2_cdb/config/components/tagging/.schema.json b/medcat/tests/resources/mct2_cdb/config/components/tagging/.schema.json similarity index 100% rename from medcat-v2/tests/resources/mct2_cdb/config/components/tagging/.schema.json rename to medcat/tests/resources/mct2_cdb/config/components/tagging/.schema.json diff --git a/medcat-v2/tests/resources/mct2_cdb/config/components/tagging/.serialised_by b/medcat/tests/resources/mct2_cdb/config/components/tagging/.serialised_by similarity index 100% rename from medcat-v2/tests/resources/mct2_cdb/config/components/tagging/.serialised_by rename to medcat/tests/resources/mct2_cdb/config/components/tagging/.serialised_by diff --git a/medcat-v2/tests/resources/mct2_cdb/config/components/token_normalizing/.schema.json b/medcat/tests/resources/mct2_cdb/config/components/token_normalizing/.schema.json similarity index 100% rename from medcat-v2/tests/resources/mct2_cdb/config/components/token_normalizing/.schema.json rename to medcat/tests/resources/mct2_cdb/config/components/token_normalizing/.schema.json diff --git a/medcat-v2/tests/resources/mct2_cdb/config/components/token_normalizing/.serialised_by b/medcat/tests/resources/mct2_cdb/config/components/token_normalizing/.serialised_by similarity index 100% rename from medcat-v2/tests/resources/mct2_cdb/config/components/token_normalizing/.serialised_by rename to medcat/tests/resources/mct2_cdb/config/components/token_normalizing/.serialised_by diff --git a/medcat-v2/tests/resources/mct2_cdb/config/general/.schema.json b/medcat/tests/resources/mct2_cdb/config/general/.schema.json similarity index 100% rename from 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medcat/tests/resources/mct2_vocab.zip diff --git a/medcat-v2/tests/resources/mct_export_for_kfold.json b/medcat/tests/resources/mct_export_for_kfold.json similarity index 100% rename from medcat-v2/tests/resources/mct_export_for_kfold.json rename to medcat/tests/resources/mct_export_for_kfold.json diff --git a/medcat-v2/tests/resources/mct_export_for_meta_cat_full_text.json b/medcat/tests/resources/mct_export_for_meta_cat_full_text.json similarity index 100% rename from medcat-v2/tests/resources/mct_export_for_meta_cat_full_text.json rename to medcat/tests/resources/mct_export_for_meta_cat_full_text.json diff --git a/medcat-v2/tests/resources/mct_export_for_meta_cat_test.json b/medcat/tests/resources/mct_export_for_meta_cat_test.json similarity index 100% rename from medcat-v2/tests/resources/mct_export_for_meta_cat_test.json rename to medcat/tests/resources/mct_export_for_meta_cat_test.json diff --git a/medcat-v2/tests/resources/mct_export_for_test_exp_perfect.json 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b/medcat/tests/utils/test_training_utils.py similarity index 100% rename from medcat-v2/tests/utils/test_training_utils.py rename to medcat/tests/utils/test_training_utils.py diff --git a/medcat-v2/tests/utils/test_usage_monitoring.py b/medcat/tests/utils/test_usage_monitoring.py similarity index 100% rename from medcat-v2/tests/utils/test_usage_monitoring.py rename to medcat/tests/utils/test_usage_monitoring.py diff --git a/medcat-v2/tests/utils/test_vocab_utils.py b/medcat/tests/utils/test_vocab_utils.py similarity index 100% rename from medcat-v2/tests/utils/test_vocab_utils.py rename to medcat/tests/utils/test_vocab_utils.py diff --git a/medcat-v2/uv.lock b/medcat/uv.lock similarity index 100% rename from medcat-v2/uv.lock rename to medcat/uv.lock diff --git a/v1/medcat-trainer/docs/installation.md b/v1/medcat-trainer/docs/installation.md index f9b0738e7..cd711b053 100644 --- a/v1/medcat-trainer/docs/installation.md +++ b/v1/medcat-trainer/docs/installation.md @@ -61,7 +61,7 @@ Environment variables are used to configure the app: |Parameter|Description| |---------|-----------| -|MEDCAT_CONFIG_FILE|MedCAT config file as described [here](https://github.com/CogStack/cogstack-nlp/blob/main/medcat-v2/medcat/config/config.py)| +|MEDCAT_CONFIG_FILE|MedCAT config file as described [here](https://github.com/CogStack/cogstack-nlp/blob/main/v1/medcat/medcat/config/config.py)| |BEHIND_RP| If you're running MedCATtrainer, use 1, otherwise this defaults to 0 i.e. False| |MCTRAINER_PORT|The port to run the trainer app on| |EMAIL_USER|Email address which will be used to send users emails regarding password resets| diff --git a/v1/medcat-trainer/docs/project_admin.md b/v1/medcat-trainer/docs/project_admin.md index 19f1e30ab..11b43e784 100644 --- a/v1/medcat-trainer/docs/project_admin.md +++ b/v1/medcat-trainer/docs/project_admin.md @@ -69,7 +69,7 @@ Admin users have extra options on the home screen: 3. Save Model - Write the in memory model to disk - to save the current in memory model state. This option is generally not advised as full model training should be done outside the trainer instance ideally. ### Notes -- Example Concept and Vocab databses are freely available on MedCAT [github](https://github.com/CogStack/cogstack-nlp/tree/main/medcat-v2). +- Example Concept and Vocab databses are freely available on MedCAT [github](https://github.com/CogStack/cogstack-nlp/tree/main/medcat). Note. UMLS and SNOMED-CT are licensed products so only these smaller trained concept / vocab databases are made available currently. - More documentation on the creation of UMLS / SNOMED-CT CDBs from respective source data will be released soon. - Tasks allow for the creation of meta-annotations and their associated set of values an annotator can use.