docs(medcat): Add Medcat Tutorials into public documentation page

.devcontainer/devcontainer.json

@@ -3,7 +3,7 @@
 {
 	"name": "Python 3",
 	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
-	"image": "mcr.microsoft.com/devcontainers/python:1-3.12-bullseye",
+	"image": "mcr.microsoft.com/devcontainers/python:3.13-bookworm",
 	"features": {
 		"ghcr.io/devcontainers/features/docker-outside-of-docker:1": {},
 		"ghcr.io/va-h/devcontainers-features/uv:1": {

medcat-v2-tutorials/README.md

@@ -2,35 +2,27 @@
 
 The MedCAT Tutorials provide an interactive learning path for using MedCAT.
 
-NOTE: These tutorials are aimed at developers and / or people creating their own models.
-For every day usage (e.g inference) the [medcat-scripts](../medcat-scripts) portion would probably be more useful.
+See the cogstack documentation site to view these tutorials and all the documentation on [docs.cogstack.org](https://docs.cogstack.org)
 
-## Introductory tutorials
+## Developer Readme
+The following readmes are around the setup of the tutorials themselves aimed at a tutorial author.
 
-### Migration of v1 models
+### Documentation Build
 
-| Part | Title                                                                       |
-| ---- |-----------------------------------------------------------------------------|
-| 1.   |  [Migrate a v1 model to v2](notebooks/introductory/migration/1._Migrate_v1_model_to_v2.ipynb)                                    |
+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.
 
-### Basic (regex-tokenizer) tutorials
+In `medcat-v2/mkdocs.yml` the `Tutorials` section is wired in via an include:
 
-| Part | Title                                                                       |
-| ---- |-----------------------------------------------------------------------------|
-| 1.   |  [Building a Concept Database and a Vocab](notebooks/introductory/basic/1._Build_a_Concept_Database_and_a_Vocabulary.ipynb)                                    |
-| 2.   | [Unsupervised training on model](notebooks/introductory/basic/2._Unsupervised_training_on_model.ipynb) |
-| 3.   | [Supervised training on model](notebooks/introductory/basic/3._Supervised_training_on_model.ipynb) |
-| 4.   | [Evaluating perfromance on dataset](notebooks/introductory/basic/4._Evaluating_performance_on_dataset.ipynb) |
+```yaml
+nav:
+  - Tutorials: '!include ../medcat-v2-tutorials/mkdocs.yml'
+```
 
-### MetaCAT (meta-annotation) tutorials
+#### Run the docs locally (rendered site)
 
-| Part | Title                                                                       |
-| ---- |-----------------------------------------------------------------------------|
-| 1.   |  [Add a MetaCAT to a Model](notebooks/introductory/meta/1._Add_a_MetaCat_to_a_Model.ipynb)                                    |
+To preview the rendered docs site locally:
 
-## Advanced tutorials
-
-| Part | Title                                                                       |
-| ---- |-----------------------------------------------------------------------------|
-| 1.   |  [Creating and using a custom tokenizer](notebooks/advanced/1._Creating_and_using_a_custom_tokenizer.ipynb)                               |
-| 2.   |  [Create and use component](notebooks/advanced/2._Create_and_use_component.ipynb)                                    |
+```bash
+cd cogstack-nlp/medcat-v2-tutorials
+uv run mkdocs serve
+```

medcat-v2-tutorials/mkdocs.yml

@@ -0,0 +1,74 @@
+# yaml-language-server: $schema=https://squidfunk.github.io/mkdocs-material/schema.json
+site_name: MedCAT Tutorials
+site_url: https://docs.cogstack.org/
+
+theme:
+  name: material
+  favicon: _static/img/cat-logo.svg
+  logo: _static/img/cat-logo.svg
+  icon:
+    logo:  _static/img/cat-logo.svg
+  palette:
+    primary: white
+
+  features:
+    - navigation.tabs
+    - navigation.sections
+    - navigation.top
+    - navigation.indexes
+    - navigation.tracking
+    - navigation.footer
+    - header.autohide
+    - content.tooltips
+    - search.highlight
+    - search.share
+    - search.suggest
+    - toc.follow
+    - attr_list
+
+repo_url: https://github.com/CogStack/cogstack-nlp
+repo_name: cogstack-nlp
+
+docs_dir: notebooks
+
+nav:
+  - Home: index.md
+  - Introductory Tutorials:
+    - Basic:
+      - README: introductory/basic/README.md
+      - 1. Build a Concept Database and a Vocabulary: introductory/basic/1._Build_a_Concept_Database_and_a_Vocabulary.ipynb
+      - 2. Unsupervised training on model: introductory/basic/2._Unsupervised_training_on_model.ipynb
+      - 3. Supervised training on model: introductory/basic/3._Supervised_training_on_model.ipynb
+      - 4. Evaluating performance on dataset: introductory/basic/4._Evaluating_performance_on_dataset.ipynb
+    - MetaCAT:
+      - README: introductory/meta/README.md
+      - 1. Add a MetaCat to a Model: introductory/meta/1._Add_a_MetaCat_to_a_Model.ipynb
+    - RelCAT:
+      - 1. Supervised Training Relation Extraction: introductory/relcat/1._Supervised_Training_Relation_Extraction.ipynb
+      - 2. Infering relations from annotations with Relation toolkit: introductory/relcat/2._Infering_relations_from_annotations_with_Relation_toolkit.ipynb
+
+  - Advanced Tutorials:
+    - 1. Creating and using a custom tokenizer: advanced/1._Creating_and_using_a_custom_tokenizer.ipynb
+    - 2. Create and use component: advanced/2._Create_and_use_component.ipynb
+    - Custom Components:
+      - README: introductory/custom/README.md
+      - 1. Create Modelpack with 2step linker: introductory/custom/1._Create_Modelpack_with_2step_linker.ipynb
+    - Migration:
+      - README: introductory/migration/README.md
+      - 1. Migrate v1 model to v2: introductory/migration/1._Migrate_v1_model_to_v2.ipynb
+
+plugins:
+  - search
+  - termynal
+  - autorefs  # Resolves cross-refs from mkdocstrings so type links work across pages
+  - mkdocs-jupyter:
+      ignore_h1_titles: True
+
+markdown_extensions:
+  - admonition
+  - attr_list
+  - pymdownx.details
+  - pymdownx.superfences
+  - pymdownx.emoji:
+      emoji_index: !!python/name:material.extensions.emoji.twemoji
+      emoji_generator: !!python/name:material.extensions.emoji.to_svg

medcat-v2-tutorials/notebooks/index.md

@@ -0,0 +1,32 @@
+# MedCAT Tutorials
+
+The MedCAT Tutorials provide an interactive learning path for using MedCAT.
+
+These tutorials are aimed at developers and / or people creating their own models.
+For every day usage (e.g inference) the [medcat-scripts](https://github.com/CogStack/cogstack-nlp/tree/main/medcat-scripts) portion would probably be more useful.
+
+## Learning Path
+
+Get started by going to the [basic tutorials](introductory/basic/). Here you will learn about Concept Databases, Vocabularies, and perform supervised and unsupervised training.
+
+After that you can continue to see the other features of medcat, such as configuring MetaCAT and RelCAT.
+
+Finally you can look at advanced tutorials where you will dig into the internals of MedCAT.
+
+## Interactive Usage
+
+!!! tip
+
+    These tutorials are written as real, executable code in jupyter notebooks. The version on docs.cogstack.org is read only, but you could instead choose to follow along and run the code as you go.
+
+To get set up to run the tutorials interactively, clone the repo and install the tutorial dependencies.
+
+```bash
+git clone https://github.com/CogStack/cogstack-nlp.git
+cd cogstack-nlp/medcat-v2-tutorials
+
+python -m venv .venv
+source .venv/bin/activate
+pip install -r requirements.txt
+```
+You can now open the notebook in vscode and run the tutorials. Alternatively you could use `pip install jupyter` and run `jupyter lab` to do this on the command line. 

medcat-v2-tutorials/pyproject.toml

@@ -0,0 +1,20 @@
+[project]
+name = "medcat-v2-documentation"
+version = "0.1.0"
+description = "MedCAT v2 Documentation"
+requires-python = ">=3.10"
+dependencies = [
+    "mkdocs-api-autonav>=0.4.0",
+    "mkdocs-material>=9.7.0",
+    "mkdocstrings-python>=2.0.3",
+    "termynal>=0.13.1",
+    "mkdocs-jupyter>=0.26.1",
+]
+
+[project.optional-dependencies]
+dev = [
+    "ruff>=0.12.11",
+]
+
+[tool.ruff]
+line-length = 120