From 1d852b5c71fd95d71cce09b09e488fb8985e69f5 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 16:33:05 +0100 Subject: [PATCH 01/56] Rename medcat-v2 folder to medcat --- {medcat-v2 => medcat}/.gitignore | 0 {medcat-v2 => medcat}/.readthedocs.yaml | 0 {medcat-v2 => medcat}/.release/README.md | 0 .../.release/install_bundle_readme.md | 0 .../.release/prepare_minor_release.sh | 0 .../.release/prepare_patch_release.sh | 0 {medcat-v2 => medcat}/.release/prepare_release.sh | 0 {medcat-v2 => medcat}/MANIFEST.in | 0 {medcat-v2 => medcat}/README.md | 0 {medcat-v2 => medcat}/docs/_static/img/cat-logo.png | Bin {medcat-v2 => medcat}/docs/_static/img/cat-logo.svg | 0 {medcat-v2 => medcat}/docs/architecture.md | 0 {medcat-v2 => medcat}/docs/breaking_changes.md | 0 {medcat-v2 => medcat}/docs/index.md | 0 {medcat-v2 => medcat}/docs/migration_guide_v2.md | 0 {medcat-v2 => medcat}/docs/pyproject.toml | 0 {medcat-v2 => medcat}/docs/uv.lock | 0 {medcat-v2 => medcat}/docs/v1_news.md | 0 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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 From 121de42ba3722e70921f9989e85b6b4fd2473cea Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 16:37:03 +0100 Subject: [PATCH 03/56] Add README in old folder to point to new foldeR --- medcat-v2/README.md | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 medcat-v2/README.md diff --git a/medcat-v2/README.md b/medcat-v2/README.md new file mode 100644 index 000000000..ca7afa66b --- /dev/null +++ b/medcat-v2/README.md @@ -0,0 +1,3 @@ +# MedCAT v2 + +MedCAT v2 is now simply in at (../medcat)[./medcat]. \ No newline at end of file From 7110a66c59c14a07cbd5041d15010f268afc8116 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 16:38:28 +0100 Subject: [PATCH 04/56] Move main workflow to correct folder --- .github/workflows/medcat-v2_main.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) 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 From 2f1bb7b647d3e23dd5cb6ed64114df8f45ca1761 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 16:40:37 +0100 Subject: [PATCH 05/56] Move release workflow to correct folder --- .github/workflows/medcat-v2_release.yml | 30 ++++++++++++------------- 1 file changed, 15 insertions(+), 15 deletions(-) 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: From fc596eac8e5d1dfd08587bc6e7e6c05a68526ad6 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 16:41:17 +0100 Subject: [PATCH 06/56] Move lib stability workflow to correct folder --- .github/workflows/medcat-v2-lib-stability.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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: From 304433dcbc02354dd468991de88397d40fef9422 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 16:42:03 +0100 Subject: [PATCH 07/56] Move tutorials workflow to use correct folder --- .github/workflows/medcat-v2-tutorials_main.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/medcat-v2-tutorials_main.yml b/.github/workflows/medcat-v2-tutorials_main.yml index 86aa03a38..b43615d4c 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**' 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: | From a7455de277199b287c87059d648bb7fab9b60f65 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 16:44:27 +0100 Subject: [PATCH 08/56] Fix some v1 links / references (that used v1 paths) --- v1/medcat-trainer/docs/installation.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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| From b06fcf0b2f6a5d9390b0bef647c42725fab33aab Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 16:44:59 +0100 Subject: [PATCH 09/56] Fix some v1 links / references (that used v1 paths) --- v1/medcat-trainer/docs/project_admin.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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. From 62cc4939068c94440f0d880d2fb125389f9cd1e1 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 16:47:15 +0100 Subject: [PATCH 10/56] Fix reference in scripts README --- medcat-scripts/README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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 +``` From d04ba6133a3d469961f83ff4e3b2efd5bb3726e3 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 16:47:46 +0100 Subject: [PATCH 11/56] Fix notebook patch install path for tutorials --- medcat-tutorials/.ci/patch_notebook_installs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/medcat-tutorials/.ci/patch_notebook_installs.py b/medcat-tutorials/.ci/patch_notebook_installs.py index 4a201fd60..545751192 100644 --- a/medcat-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: From fb1de39142f0a46a7a2ea4a498088ae178fe1676 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 16:49:09 +0100 Subject: [PATCH 12/56] Update medcat tutorials README --- medcat-tutorials/README.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/medcat-tutorials/README.md b/medcat-tutorials/README.md index 771b05229..bdbfe4306 100644 --- a/medcat-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 ``` From e69fafc7ae5b6c4014fd87c2ceae2107020e36f9 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 16:49:39 +0100 Subject: [PATCH 13/56] Fix notebooks documentation --- medcat-tutorials/notebooks/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/medcat-tutorials/notebooks/index.md b/medcat-tutorials/notebooks/index.md index 426bbedf9..8ba932c06 100644 --- a/medcat-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 From c2f01f12bdc1c324b85497d4236fbb276eb6c291 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 16:59:17 +0100 Subject: [PATCH 14/56] Fix paths in paper speed script --- .../paper/scripts/speed/get_load_speed_for_multiple_v2.sh | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/medcat/paper/scripts/speed/get_load_speed_for_multiple_v2.sh b/medcat/paper/scripts/speed/get_load_speed_for_multiple_v2.sh index e1e22a857..44e91e4b7 100644 --- a/medcat/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" ]] From 120c60a863f532bfeab6a8c00e1ec52b69db6064 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 16:59:56 +0100 Subject: [PATCH 15/56] Fix paths in paper unsup train speed script --- .../scripts/speed/get_unsup_train_speed_for_multiple_v2.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/medcat/paper/scripts/speed/get_unsup_train_speed_for_multiple_v2.sh b/medcat/paper/scripts/speed/get_unsup_train_speed_for_multiple_v2.sh index 0eb6e083b..9ea2bbac8 100644 --- a/medcat/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" From 7933264bdd60c16bff31a99c89ca0c9301dcaea1 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 17:02:32 +0100 Subject: [PATCH 16/56] Fix medcat-v2 paths in get inference speed script in paper --- .../scripts/speed/get_inference_speed_for_multiple_v2.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/medcat/paper/scripts/speed/get_inference_speed_for_multiple_v2.sh b/medcat/paper/scripts/speed/get_inference_speed_for_multiple_v2.sh index 62b21bee9..8e2dde407 100644 --- a/medcat/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" From f95ba09051a7af1a3a3cc59a217e78e1565f594a Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 17:03:10 +0100 Subject: [PATCH 17/56] Fix get all performance script paths in paper --- medcat/paper/scripts/performance/get_performance_all.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/medcat/paper/scripts/performance/get_performance_all.sh b/medcat/paper/scripts/performance/get_performance_all.sh index 7ac6d4408..d9bdf7f09 100644 --- a/medcat/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" From fac95eade4451af204bb87afb20a9b6952429379 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 17:03:44 +0100 Subject: [PATCH 18/56] Fix get regression script paths in paper --- medcat/paper/scripts/performance/get_regression_all.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/medcat/paper/scripts/performance/get_regression_all.sh b/medcat/paper/scripts/performance/get_regression_all.sh index c8dbd3ed7..de7ef85e5 100644 --- a/medcat/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" From 7643cd70f48f03df4abfe1ce01d8cf9b96448343 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 17:04:12 +0100 Subject: [PATCH 19/56] Fix paths in mkdocs for medcat --- medcat/mkdocs.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/medcat/mkdocs.yml b/medcat/mkdocs.yml index 974e795db..c6356337b 100644 --- a/medcat/mkdocs.yml +++ b/medcat/mkdocs.yml @@ -34,7 +34,7 @@ docs_dir: docs nav: - Home: index.md - Architecture: architecture.md - - Tutorials: '!include ../medcat-v2-tutorials/mkdocs.yml' + - Tutorials: '!include ../medcat-tutorials/mkdocs.yml' - Upgrading: - Migration guide (v2): migration_guide_v2.md - Breaking changes: breaking_changes.md @@ -80,4 +80,4 @@ 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 From 27cc0aeffe9442f9b17cf15541ea87022082464a Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 17:05:07 +0100 Subject: [PATCH 20/56] Fic paths in install bundle readme --- medcat/.release/install_bundle_readme.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/medcat/.release/install_bundle_readme.md b/medcat/.release/install_bundle_readme.md index e9f69a575..4340d0b10 100644 --- a/medcat/.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). From bca818e80ca9c6e4a95db2f9b8d4f4d49b9edeb1 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 17:05:32 +0100 Subject: [PATCH 21/56] Fix resource fetch doc string path --- medcat/tests/resource_fetch.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/medcat/tests/resource_fetch.py b/medcat/tests/resource_fetch.py index 6ac710958..63630d5ba 100644 --- a/medcat/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. # From 9e7c788467b91380fb3957e8470282781724ab25 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 17:06:13 +0100 Subject: [PATCH 22/56] Fix v2 link in v1 news docs --- medcat/docs/v1_news.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/medcat/docs/v1_news.md b/medcat/docs/v1_news.md index 70f02a55c..8a3e9c9db 100644 --- a/medcat/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)) From 504b0acabc7a4d4dec438e38869cf1049b314d8e Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 17:06:38 +0100 Subject: [PATCH 23/56] Fix path in migration guide --- medcat/docs/migration_guide_v2.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/medcat/docs/migration_guide_v2.md b/medcat/docs/migration_guide_v2.md index 9101709a5..36a463542 100644 --- a/medcat/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 From 1e3fd76e0a176e4604c27a42b5902b57a80fa0cc Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 17:07:10 +0100 Subject: [PATCH 24/56] Fix hard link in medcat README --- medcat/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/medcat/README.md b/medcat/README.md index 26557ef2d..b3ef3b122 100644 --- a/medcat/README.md +++ b/medcat/README.md @@ -32,7 +32,7 @@ To download any of these models, please [follow this link](https://medcat.sites. 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)). +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 e7c5bf50af732e4e1bc5be9cd37ad91af92d4878 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 17:07:59 +0100 Subject: [PATCH 25/56] Fix paths in read the docs config --- medcat/.readthedocs.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/medcat/.readthedocs.yaml b/medcat/.readthedocs.yaml index 97683321c..15491d72c 100644 --- a/medcat/.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 From 218e2e5e18d700cdfeec8101da18ed2fc4469a7d Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 17:08:36 +0100 Subject: [PATCH 26/56] Fix core lib path in service docker file --- medcat-service/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From 4fb0b5eba8b5c99f1fe4bc9988f0479de275c04d Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 17:09:21 +0100 Subject: [PATCH 27/56] Fix link in medcat service setup configuration --- medcat-service/docs/setup/configuration.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From 65ad1bddcea1169ef0f0171fc8beb7229770ba68 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 17:09:57 +0100 Subject: [PATCH 28/56] Fix link in medcat service docs index --- medcat-service/docs/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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! From 2723d8a89607f4845fed6fe42a0270f2d39fab93 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 17:10:36 +0100 Subject: [PATCH 29/56] Fix paths in medcat service readme --- medcat-service/README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) 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 +``` From f2f08efc7104558aebea0b76ae8dbe76f93c24db Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 17:11:01 +0100 Subject: [PATCH 30/56] Fix medcat service gpu-dockerfile --- medcat-service/Dockerfile_gpu | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From 9d44930cbc5ca20250d9625f983988194dd89c7e Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 17:12:39 +0100 Subject: [PATCH 31/56] Fix paths in overal README --- README.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) 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 From acab7b68c1449d8d8d89d1fbca49c1c54264abe6 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 21:55:09 +0100 Subject: [PATCH 32/56] Fix anoncat demo app readme path --- anoncat-demo-app/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From f39f0c072d1f9b0e4fb96b6835318d4ea6888b79 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 21:55:32 +0100 Subject: [PATCH 33/56] Fix install path in transformers NER CI --- .github/workflows/medcat-transformer-ner-ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From 6157aacf1d7547ff5a69319be9d757cf8b95a25e Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 21:57:01 +0100 Subject: [PATCH 34/56] Fix tutorials path in deps update workflow --- .github/workflows/medcat-deps-update.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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" From 561d59b7bf0f5c4ee50d68090d80ba1631b0b323 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 21:58:28 +0100 Subject: [PATCH 35/56] Fix path in medcat service compose file --- .github/workflows/medcat-service_docker.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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 From d1b309f8c6f2481f5b670f6adfb07e13edca666d Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 21:59:03 +0100 Subject: [PATCH 36/56] Fix install path for embedding linker workflow --- .github/workflows/medcat-embedding-linker_ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From 2994a4380c1a24d4f4333147a058f4cbfceeb5e8 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 21:59:34 +0100 Subject: [PATCH 37/56] Fix paths in v2 tutotirals CI --- .github/workflows/medcat-v2-tutorials_main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/medcat-v2-tutorials_main.yml b/.github/workflows/medcat-v2-tutorials_main.yml index b43615d4c..b16c132c8 100644 --- a/.github/workflows/medcat-v2-tutorials_main.yml +++ b/.github/workflows/medcat-v2-tutorials_main.yml @@ -8,7 +8,7 @@ on: - 'medcat/**' - 'medcat-tutorials/**' - '.github/workflows/medcat-v2**' - - '.github/workflows/medcat-v2-tutorials**' + - '.github/workflows/medcat-tutorials**' defaults: run: working-directory: ./medcat-tutorials From a7be11ff12a94904a2802b8cf92610dcbb45ed92 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 22:00:03 +0100 Subject: [PATCH 38/56] Fix paths in trainer workflow --- .github/workflows/medcat-trainer_ci.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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: From 13dd5a53c14a587a4b5110615a3864e27128d833 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 22:00:40 +0100 Subject: [PATCH 39/56] Fix path in medcat-service CI / workflow --- .github/workflows/medcat-service_run-tests.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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: | From e1a0dc55ec9a926cdaa875f08f1c8a37251bcc11 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 22:01:01 +0100 Subject: [PATCH 40/56] Fix path in medcat model distributor CI --- .github/workflows/medcat-model-distributor_build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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: From 57412c14325369ddf4d37c3f40073a52b104577a Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 22:01:33 +0100 Subject: [PATCH 41/56] Fix local install path for medcat den workflow --- .github/workflows/medcat-den_main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From afe835b63632d61d5243840e08d46f0f3561129a Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 22:01:55 +0100 Subject: [PATCH 42/56] Fix local install path for medcat-scripts workflow --- .github/workflows/medcat-scripts_main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From 595d35591d218da9d28f8a944d6871fc6f062f3f Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 22:02:38 +0100 Subject: [PATCH 43/56] Fix local paths for model distributor test-compose --- medcat-model-distributor/docker-compose-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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: From 2eb0d998dfca06d7ecc5d7c91ff4b05553f6b016 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 22:03:10 +0100 Subject: [PATCH 44/56] Fix note regarding path in resource fetcher --- medcat-den/tests/resource_fetch.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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. # From 722ff5c191d3ca1421987fb2850dadc7dd25f86b Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 22:03:37 +0100 Subject: [PATCH 45/56] Fix link/reference in security docs --- SECURITY.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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. From c1d0bfa511af0d949dc60ca2a471da7e1c79c1a6 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 22:07:18 +0100 Subject: [PATCH 46/56] Remove (most of) v1-specific references from README --- medcat/README.md | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/medcat/README.md b/medcat/README.md index b3ef3b122..ee74b373a 100644 --- a/medcat/README.md +++ b/medcat/README.md @@ -1,15 +1,9 @@ -# Medical oncept Annotation Tool (version 2) +# 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). -## 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). +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) From cc38906dff4f5dbc63a8e71f44a6524de74d0d61 Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 22:07:55 +0100 Subject: [PATCH 47/56] Add back v1 info to a separate docs page --- medcat/docs/v1_info.md | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 medcat/docs/v1_info.md diff --git a/medcat/docs/v1_info.md b/medcat/docs/v1_info.md new file mode 100644 index 000000000..227190744 --- /dev/null +++ b/medcat/docs/v1_info.md @@ -0,0 +1,8 @@ +## 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). + From 8463811c691d24e3407523e839f38e37c12e185f Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 22:26:32 +0100 Subject: [PATCH 48/56] Move legacy conversion to a separate document --- medcat/README.md | 22 ++-------------------- medcat/docs/v1_conversion.md | 20 ++++++++++++++++++++ 2 files changed, 22 insertions(+), 20 deletions(-) create mode 100644 medcat/docs/v1_conversion.md diff --git a/medcat/README.md b/medcat/README.md index ee74b373a..ad59df66c 100644 --- a/medcat/README.md +++ b/medcat/README.md @@ -16,32 +16,14 @@ Coming from MedCAT v1? See [here](docs/v1_info.md) for more info. ## Available Models -We have 2 public v2 models available: +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 MedCAT v1 models available that can automatically be converted if required. +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. -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-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. diff --git a/medcat/docs/v1_conversion.md b/medcat/docs/v1_conversion.md new file mode 100644 index 000000000..7d3c0bb32 --- /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 +``` + From 5606e03f10f6606d7e6ab8eac6dfc0eb16b0ad1e Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 22:27:17 +0100 Subject: [PATCH 49/56] Add link to legacy conversion docs to v1 info docs --- medcat/docs/v1_info.md | 1 + 1 file changed, 1 insertion(+) diff --git a/medcat/docs/v1_info.md b/medcat/docs/v1_info.md index 227190744..e62e1032f 100644 --- a/medcat/docs/v1_info.md +++ b/medcat/docs/v1_info.md @@ -6,3 +6,4 @@ MedCAT v2 is a comprehensive refactor designed to improve modularity, flexibilit 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). From 5bce16cf7e1091576a6dd19fef4eff7dbae22b8a Mon Sep 17 00:00:00 2001 From: mart-r Date: Tue, 18 Aug 2026 22:31:11 +0100 Subject: [PATCH 50/56] Add v1 info page to docs --- medcat/mkdocs.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/medcat/mkdocs.yml b/medcat/mkdocs.yml index c6356337b..fb79f6c3c 100644 --- a/medcat/mkdocs.yml +++ b/medcat/mkdocs.yml @@ -36,6 +36,7 @@ nav: - Architecture: architecture.md - 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 From 498cefc50759c94d8708c2a032932b0a9e9cb9ea Mon Sep 17 00:00:00 2001 From: mart-r Date: Wed, 19 Aug 2026 10:39:48 +0100 Subject: [PATCH 51/56] Fix minor issue in the preamble of mkdocs --- medcat/mkdocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/medcat/mkdocs.yml b/medcat/mkdocs.yml index fb79f6c3c..cc4ca561a 100644 --- a/medcat/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/ From 80034c460e64053dd804be9edfe5a0c5467b1eef Mon Sep 17 00:00:00 2001 From: mart-r Date: Wed, 19 Aug 2026 11:09:06 +0100 Subject: [PATCH 52/56] Fix relative link to migration tutorial --- medcat/docs/v1_conversion.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/medcat/docs/v1_conversion.md b/medcat/docs/v1_conversion.md index 7d3c0bb32..7f9428c7e 100644 --- a/medcat/docs/v1_conversion.md +++ b/medcat/docs/v1_conversion.md @@ -2,7 +2,7 @@ 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)). +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 d6c60a8e6479944a00604ec959116ca96c39c013 Mon Sep 17 00:00:00 2001 From: mart-r Date: Wed, 19 Aug 2026 11:45:26 +0100 Subject: [PATCH 53/56] Add a hook to fix issue with relative links in README --- medcat/docs/hooks.py | 9 +++++++++ medcat/mkdocs.yml | 7 +++++++ 2 files changed, 16 insertions(+) create mode 100644 medcat/docs/hooks.py diff --git a/medcat/docs/hooks.py b/medcat/docs/hooks.py new file mode 100644 index 000000000..d8dfc0ca8 --- /dev/null +++ b/medcat/docs/hooks.py @@ -0,0 +1,9 @@ +import re + +def on_page_markdown(markdown, page, config, files): + # Only rewrite relative links on the home/index page where README is embedded + if page.file.src_uri == "index.md": + # Rewrites [text](docs/page.md) -> [text](page.md) + return re.sub(r'\]\(docs/([^\)]+\.md)\)', r'](\1)', markdown) + return markdown + diff --git a/medcat/mkdocs.yml b/medcat/mkdocs.yml index cc4ca561a..99ccf5df4 100644 --- a/medcat/mkdocs.yml +++ b/medcat/mkdocs.yml @@ -39,6 +39,13 @@ nav: - 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 From ae3eef584df4c1daec98d06e59c9b9bb71542009 Mon Sep 17 00:00:00 2001 From: mart-r Date: Wed, 19 Aug 2026 12:03:10 +0100 Subject: [PATCH 54/56] Fix docs hook --- medcat/docs/hooks.py | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/medcat/docs/hooks.py b/medcat/docs/hooks.py index d8dfc0ca8..45f70eeba 100644 --- a/medcat/docs/hooks.py +++ b/medcat/docs/hooks.py @@ -1,9 +1,10 @@ import re -def on_page_markdown(markdown, page, config, files): - # Only rewrite relative links on the home/index page where README is embedded - if page.file.src_uri == "index.md": - # Rewrites [text](docs/page.md) -> [text](page.md) - return re.sub(r'\]\(docs/([^\)]+\.md)\)', r'](\1)', markdown) - return markdown +def on_page_content(html, page, config, files): + if page.file.src_uri == "index.md": + # Rewrites (or ) to + # Handles .md extensions or already-rendered clean URLs + html = re.sub(r'href="docs/([^"#\?]+)\.md([#\?][^"]*)?"', r'href="../\1/\2"', html) + html = re.sub(r'href="docs/([^"#\?]+)/([#\?][^"]*)?"', r'href="../\1/\2"', html) + return html From a1ec2ffcfbb5db6d5c6ecbceee55aab17a80e2a9 Mon Sep 17 00:00:00 2001 From: mart-r Date: Wed, 19 Aug 2026 12:09:46 +0100 Subject: [PATCH 55/56] Fix docs hook for the (hopefully) final time --- medcat/docs/hooks.py | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/medcat/docs/hooks.py b/medcat/docs/hooks.py index 45f70eeba..781057a93 100644 --- a/medcat/docs/hooks.py +++ b/medcat/docs/hooks.py @@ -1,10 +1,15 @@ import re -def on_page_content(html, page, config, files): +def on_page_markdown(markdown, page, config, files): if page.file.src_uri == "index.md": - # Rewrites (or ) to - # Handles .md extensions or already-rendered clean URLs - html = re.sub(r'href="docs/([^"#\?]+)\.md([#\?][^"]*)?"', r'href="../\1/\2"', html) - html = re.sub(r'href="docs/([^"#\?]+)/([#\?][^"]*)?"', r'href="../\1/\2"', html) - return html + 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 From c9605da92fe901b68f82a1b3cc7f077a85dc1e8f Mon Sep 17 00:00:00 2001 From: mart-r Date: Wed, 19 Aug 2026 12:12:01 +0100 Subject: [PATCH 56/56] Fix import in hook --- medcat/docs/hooks.py | 1 + 1 file changed, 1 insertion(+) diff --git a/medcat/docs/hooks.py b/medcat/docs/hooks.py index 781057a93..f5533829c 100644 --- a/medcat/docs/hooks.py +++ b/medcat/docs/hooks.py @@ -1,4 +1,5 @@ import re +from pathlib import Path def on_page_markdown(markdown, page, config, files):