Phase 4: add MkDocs + ReadTheDocs documentation infrastructure

- mkdocs.yml: Material theme site with mkdocstrings (Google style, show_source)
  and full nav covering all sub-packages
- .readthedocs.yml: ReadTheDocs v2 config pointing to mkdocs.yml, Python 3.12,
  installs package with docs extras
- .github/workflows/docs.yml: CI job that builds docs on every push/PR to main
- docs/: landing page, getting-started guide, and 12 API reference pages
  (one per sub-package) using mkdocstrings ::: directives

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: Hendrik-code

.github/workflows/docs.yml

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+name: Docs
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install package and docs dependencies
+        run: |
+          pip install -e .
+          pip install mkdocs mkdocs-material "mkdocstrings[python]" mkdocs-gen-files mkdocs-literate-nav
+
+      - name: Build docs
+        run: mkdocs build

.readthedocs.yml

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+version: 2
+
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.12"
+
+mkdocs:
+  configuration: mkdocs.yml
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

CLAUDE.md

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+# BIDS Files
+
+Classes for navigating BIDS-compliant datasets, parsing filenames into structured entities,
+and filtering/querying files across subjects and sessions.
+
+## BIDS_Global_info
+
+::: TPTBox.core.bids_files.BIDS_Global_info
+    options:
+      show_source: true
+      members_order: source
+
+## Subject_Container
+
+::: TPTBox.core.bids_files.Subject_Container
+    options:
+      show_source: true
+
+## BIDS_FILE
+
+::: TPTBox.core.bids_files.BIDS_FILE
+    options:
+      show_source: true
+
+## Searchquery
+
+::: TPTBox.core.bids_files.Searchquery
+    options:
+      show_source: true
+
+## BIDS_Family
+
+::: TPTBox.core.bids_files.BIDS_Family
+    options:
+      show_source: true

docs/api/bids.md

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+# Logger
+
+Structured, consistent logging for long-running medical image processing pipelines.
+
+## Logger
+
+::: TPTBox.logger.log_file.Logger
+    options:
+      show_source: true
+
+## Logger_Interface
+
+::: TPTBox.logger.log_file.Logger_Interface
+    options:
+      show_source: true
+
+## No_Logger
+
+::: TPTBox.logger.log_file.No_Logger
+    options:
+      show_source: true
+
+## String_Logger
+
+::: TPTBox.logger.log_file.String_Logger
+    options:
+      show_source: true
+
+## Log_Type
+
+::: TPTBox.logger.log_constants.Log_Type
+    options:
+      show_source: true

docs/api/logger.md

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+# Mesh 3D
+
+3D surface mesh generation from segmentation volumes and snapshot rendering.
+
+## Snapshot 3D
+
+::: TPTBox.mesh3D.snapshot3D
+    options:
+      show_source: true
+      filters: ["!^_"]
+
+## Mesh
+
+::: TPTBox.mesh3D.mesh
+    options:
+      show_source: true
+      filters: ["!^_"]
+
+## Mesh Colors
+
+::: TPTBox.mesh3D.mesh_colors
+    options:
+      show_source: true
+      filters: ["!^_"]
+
+## HTML Preview
+
+::: TPTBox.mesh3D.html_preview
+    options:
+      show_source: true
+      filters: ["!^_"]

docs/api/mesh3d.md

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+# NII — NIfTI Image Wrapper
+
+The [`NII`][TPTBox.core.nii_wrapper.NII] class is the central image abstraction in TPTBox.
+It wraps a nibabel `Nifti1Image` and exposes reorientation, resampling, masking, arithmetic,
+and I/O operations through a consistent interface.
+
+## NII
+
+::: TPTBox.core.nii_wrapper.NII
+    options:
+      show_source: true
+      members_order: source

docs/api/nii.md

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+# NumPy Utilities
+
+Low-level array helpers used throughout TPTBox for label extraction, morphological operations,
+connected components, centre-of-mass computation, and more.
+
+::: TPTBox.core.np_utils
+    options:
+      show_source: true
+      members_order: source
+      filters:
+        - "!^_"

docs/api/np_utils.md

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+# POI — Points of Interest
+
+[`POI`][TPTBox.core.poi.POI] maps `(vertebra_id, subregion_id)` tuples to 3D coordinates and
+provides save/load, coordinate-space conversion, and iteration helpers.
+
+## POI
+
+::: TPTBox.core.poi.POI
+    options:
+      show_source: true
+      members_order: source
+
+## POI_Global
+
+::: TPTBox.core.poi_fun.poi_global.POI_Global
+    options:
+      show_source: true
+
+## Helper functions
+
+::: TPTBox.core.poi
+    options:
+      show_source: true
+      members:
+        - calc_centroids
+        - calc_poi_from_subreg_vert
+        - calc_poi_from_two_segs

docs/api/poi.md

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+# POI Strategies
+
+Internal modules that implement the various strategies for computing Points of Interest
+from segmentation volumes.
+
+## Ray Casting
+
+::: TPTBox.core.poi_fun.ray_casting
+    options:
+      show_source: true
+      filters: ["!^_"]
+
+## Vertebra Direction
+
+::: TPTBox.core.poi_fun.vertebra_direction
+    options:
+      show_source: true
+      filters: ["!^_"]
+
+## Vertebra Non-Centroid POIs
+
+::: TPTBox.core.poi_fun.vertebra_pois_non_centroids
+    options:
+      show_source: true
+      filters: ["!^_"]
+
+## Pixel-Based Point Finder
+
+::: TPTBox.core.poi_fun.pixel_based_point_finder
+    options:
+      show_source: true
+      filters: ["!^_"]
+
+## Strategies
+
+::: TPTBox.core.poi_fun.strategies
+    options:
+      show_source: true
+      filters: ["!^_"]
+
+## Save / Load
+
+::: TPTBox.core.poi_fun.save_load
+    options:
+      show_source: true
+      filters: ["!^_"]