fix mkdocs error

Author: NetZissou

.github/workflows/docs.yml

@@ -3,62 +3,31 @@ name: Deploy MkDocs to GitHub Pages
 on:
   push:
     branches: [ main, master, feature/doc_use_case ]
-  pull_request:
-    branches: [ main, master ]
   workflow_dispatch:
 
-permissions:
-  contents: read
-  pages: write
-  id-token: write
-
-concurrency:
-  group: "pages"
-  cancel-in-progress: false
-
 jobs:
-  build:
+  deploy:
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout
+      - name: Checkout code
         uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
 
-      - name: Setup Python
-        uses: actions/setup-python@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
         with:
           python-version: '3.11'
 
-      - name: Install uv
-        uses: astral-sh/setup-uv@v3
-
       - name: Install dependencies
         run: |
-          uv pip install -r docs-requirements.txt --system
+          python -m pip install --upgrade pip
+          pip install -r docs-requirements.txt
 
-      - name: Build documentation
+      - name: Build MkDocs site
         run: |
           mkdocs build --clean --strict
 
-      - name: Setup Pages
-        if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master'
-        uses: actions/configure-pages@v3
-
-      - name: Upload artifact
-        if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master'
-        uses: actions/upload-pages-artifact@v2
-        with:
-          path: ./site
-
-  deploy:
-    if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master'
-    environment:
-      name: github-pages
-      url: ${{ steps.deployment.outputs.page_url }}
-    runs-on: ubuntu-latest
-    needs: build
-    steps:
       - name: Deploy to GitHub Pages
-        id: deployment
-        uses: actions/deploy-pages@v2
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./site

mkdocs.yml

@@ -1,5 +1,6 @@
 site_name: HPC-Inference
 site_description: Batch inference solution for large-scale image datasets on HPC
+site_author: Imageomics Institute
 site_url: https://imageomics.github.io/hpc-inference
 repo_url: https://github.com/Imageomics/hpc-inference
 repo_name: Imageomics/hpc-inference
@@ -14,26 +15,35 @@ nav:
 
 theme:
   name: material
+  logo: docs/imgs/Imageomics_logo_butterfly.png
+  favicon: docs/imgs/Imageomics_logo_butterfly.png
   palette:
-    - scheme: default
-      primary: teal
-      accent: cyan
+    # Palette toggle for automatic mode
+    - media: "(prefers-color-scheme)"
+      toggle:
+        icon: material/brightness-auto
+        name: Switch to light mode
+    # Palette toggle for light mode
+    - media: "(prefers-color-scheme: light)"
+      scheme: default
       toggle:
         icon: material/brightness-7
         name: Switch to dark mode
-    - scheme: slate
-      primary: teal
-      accent: cyan
+    # Palette toggle for dark mode
+    - media: "(prefers-color-scheme: dark)"
+      scheme: slate
       toggle:
         icon: material/brightness-4
-        name: Switch to light mode
+        name: Switch to system preference
   features:
+    - content.action.view
+    - content.code.copy
     - navigation.tabs
+    - navigation.tabs.sticky
     - navigation.sections
     - navigation.expand
     - navigation.top
     - search.highlight
-    - content.code.copy
 
 markdown_extensions:
   - admonition
@@ -58,3 +68,46 @@ plugins:
       handlers:
         python:
           paths: [src]
+
+extra:
+  social:
+    - icon: fontawesome/brands/github
+      link: https://github.com/Imageomics
+    - icon: simple/huggingface
+      link: https://huggingface.co/imageomics
+    - icon: fontawesome/brands/linkedin
+      link: https://www.linkedin.com/company/imageomics-institute
+    - icon: fontawesome/brands/bluesky
+      link: https://bsky.app/profile/imageomics.bsky.social
+    - icon: fontawesome/brands/x-twitter
+      link: https://twitter.com/imageomics
+    - icon: fontawesome/brands/instagram
+      link: https://www.instagram.com/imageomics/
+    - icon: fontawesome/brands/youtube
+      link: https://www.youtube.com/@ImageomicsInstitute/videos
+    - icon: octicons/link-16
+      link: https://imageomics.org
+
+copyright: >
+  This work was supported by both the <a
+  href="https://imageomics.org" target="_blank"><u>Imageomics Institute</u></a> and the <a
+  href="http://abcresearchcenter.org/" target="_blank"><u>AI and Biodiversity Change (ABC) Global
+  Center</u></a>. 
+  
+  The Imageomics Institute is funded by the US National
+  Science Foundation's Harnessing the Data Revolution (HDR) program under <a
+  href="https://www.nsf.gov/awardsearch/showAward?AWD_ID=2118240" target="_blank"><u>Award
+  #2118240</u></a> (Imageomics: A New Frontier of Biological Information Powered by
+  Knowledge-Guided Machine Learning).
+  
+  The ABC Global Center is funded by the US
+  National Science Foundation under <a
+  href="https://www.nsf.gov/awardsearch/showAward?AWD_ID=2330423&HistoricalAwards=false" target="_blank"><u>Award No.
+  2330423</u></a> and the Natural Sciences and Engineering Research Council of Canada
+  under <a
+  href="https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=782440" target="_blank"><u>Award No. 585136</u></a>.
+  
+  Any opinions, findings,
+  conclusions, or recommendations expressed in this material are those of the
+  author(s) and do not necessarily reflect the views of the National Science
+  Foundation or the Natural Sciences and Engineering Research Council of Canada.