docs: try out docs publishing workflow

Author: okunator

.github/workflows/docs.yml

@@ -0,0 +1,39 @@
+name: Deploy Docs
+
+on:
+  push:
+    branches:
+      - main
+  release:
+    types: [published]
+    branches: [main]
+  workflow_dispatch:
+
+jobs:
+  build-and-publish:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout sources
+        uses: actions/checkout@v2
+
+
+      - name: "Set up Python"
+        uses: actions/setup-python@v5
+        with:
+            python-version: "3.10"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+        # Step 4: Install dependencies using UV
+      - name: Install deps
+        run: uv sync --locked --all-extras --dev
+
+      - name: Deploy Docs
+        run: |
+          source .venv/bin/activate
+          uv run mkdocs gh-deploy --force

README.md

@@ -4,7 +4,7 @@
 
 **A Python library for scalable panoptic spatial analysis of histological WSIs**
 
-[![Github Test](https://img.shields.io/github/actions/workflow/status/okunator/cellseg_gsontools/tests.yml?label=tests)](https://github.com/HautaniemiLab/histolytics/blob/main/.github/workflows/tests.yml)[![Generic badge](https://img.shields.io/github/license/okunator/cellseg_gsontools)](https://github.com/okunator/cellseg_gsontools/blob/master/LICENSE) [![Python - Version](https://img.shields.io/pypi/pyversions/cellseg_gsontools)](https://www.python.org/)
+[![Github Test](https://img.shields.io/github/actions/workflow/status/HautaniemiLab/histolytics/tests.yml?label=tests)](https://github.com/HautaniemiLab/histolytics/blob/main/.github/workflows/tests.yml)[![Generic badge](https://img.shields.io/github/license/okunator/cellseg_gsontools)](https://github.com/okunator/cellseg_gsontools/blob/master/LICENSE) [![Python - Version](https://img.shields.io/pypi/pyversions/cellseg_gsontools)](https://www.python.org/)
 
 </div>
 

mkdocs.yml

@@ -54,11 +54,17 @@ nav:
   - Home: index.md
   - Getting Started: getting_started.md
   - User Guide:
-    - Installation: user_guide/installation.md
+    - Model Fine-tuning: user_guide/fine_tuning.md
     - WSI Segmentation: user_guide/wsi_segmentation.md
+    - Data Wrangling: user_guide/data_wrangling.md
+  - Analysis Tutorials:
+    - Nuclear Morphology: analysis_tutorials/nuclear_morphology.md
+    - Chromatin Patterns: analysis_tutorials/chromatin_patterns.md
+    - Collagen Fibers: analysis_tutorials/collagen_fibers.md
+    - Stromal Morphology: analysis_tutorials/stromal_features.md
+    - Spatial Neighborhoods: analysis_tutorials/neighborhood_analysis.md
+    - Spatial Clustering: analysis_tutorials/clustering.md
   - API Reference:
     - WSI Segmenter: api/wsi_segmenter.md
     - Slide Reader: api/slide_reader.md
-  - Tutorials:
-    - Basic Usage: tutorials/basic_usage.md
   - Contributing: contributing.md