Switch from mkdocs to Jupyter Book v2

Remove mkdocs.yml, add myst.yml for Jupyter Book v2 / MyST-MD.
Update docs.yml workflow to use jupyter-book>=2 with Node.js.
Add jupyter-book ^2.0.0 as docs dependency in pyproject.toml.
Add TMS credentials example to _toc.yml.

Author: kks32

.github/workflows/docs.yml

@@ -26,19 +26,24 @@ jobs:
         with:
           python-version: "3.12"
 
+      - name: Set up Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: "22"
+
       - name: Install dependencies
         run: |
-          pip install "jupyter-book<1"
+          pip install "jupyter-book>=2"
           pip install .
 
       - name: Build the book
         run: |
-          jupyter-book build . --path-output out
+          jupyter-book build --html
 
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v3
         with:
-          path: ./out/_build/html
+          path: ./_build/html
 
   deploy:
     environment:

_toc.yml

@@ -20,6 +20,7 @@ parts:
       - file: docs/examples/mpm
       - file: docs/examples/opensees
       - file: docs/examples/openfoam
+      - file: docs/examples/tms_credentials
       - file: docs/examples/database
   - caption: API Reference
     chapters:

mkdocs.yml

@@ -0,0 +1,57 @@
+version: 1
+project:
+  title: DAPI - DesignSafe API
+  authors:
+    - name: Krishna Kumar
+      email: krishnak@utexas.edu
+    - name: Pedro Arduino
+      email: parduino@uw.edu
+    - name: Scott Brandenberg
+      email: sjbrandenberg@ucla.edu
+  copyright: "2024"
+  github: https://github.com/DesignSafe-CI/dapi
+  license: MIT
+  toc:
+    - file: docs/index.md
+    - title: Getting Started
+      children:
+        - file: docs/installation.md
+        - file: docs/authentication.md
+        - file: docs/quickstart.md
+    - title: User Guide
+      children:
+        - file: docs/jobs.md
+        - file: docs/database.md
+    - title: Examples
+      children:
+        - file: docs/examples.md
+        - file: docs/examples/apps.md
+        - file: docs/examples/mpm.md
+        - file: docs/examples/opensees.md
+        - file: docs/examples/openfoam.md
+        - file: docs/examples/tms_credentials.md
+        - file: docs/examples/database.md
+    - title: API Reference
+      children:
+        - file: docs/api/index.md
+        - file: docs/api/client.md
+        - file: docs/api/jobs.md
+        - file: docs/api/files.md
+        - file: docs/api/apps.md
+        - file: docs/api/systems.md
+        - file: docs/api/database.md
+        - file: docs/api/auth.md
+        - file: docs/api/exceptions.md
+  exclude:
+    - _build/**
+    - out/**
+    - "**.ipynb_checkpoints"
+    - examples/**
+    - README.md
+    - AUTHORS.md
+    - LICENSE.md
+site:
+  template: book-theme
+  options:
+    logo: docs/nheri.png
+    favicon: docs/favicon.ico