Upgrade doc generator to JupyterBook 2

.github/workflows/docs.yml

@@ -29,6 +29,13 @@ jobs:
           python-version: 3.12
           cache: 'pip'
 
+      - name: Install Ubuntu dependencies
+        uses: awalsh128/cache-apt-pkgs-action@latest
+        with:
+          packages: nodejs npm
+          version: 1.0
+          execute_install_scripts: true
+
       - name: Install pip packages
         run:  pip install -r ${GITHUB_WORKSPACE}/docs/requirements.txt
 
@@ -65,4 +72,4 @@ jobs:
       id: deployment
       uses: actions/deploy-pages@v4
       with:
-        artifact_name: eCLM_docs
+        artifact_name: eCLM_docs

docs/Makefile

@@ -2,7 +2,7 @@ BUILD_DIR = ./_build
 SRC_DIR = ../src
 
 docs:
-	jupyter-book build -W -n --keep-going .
+	myst build --html
 
 src-browser:
 	ford -d $(SRC_DIR) -o $(BUILD_DIR)/html/src FORD_options.md
@@ -12,4 +12,4 @@ all: docs src-browser
 .PHONY: clean
 
 clean:
-	jupyter-book clean .
+	myst clean -ay

docs/myst.yml

@@ -0,0 +1,53 @@
+# See docs at: https://mystmd.org/guide/frontmatter
+version: 1
+project:
+  id: 0cb7f824-8ccf-46a1-9ffe-0e41f6058eff
+  title: eCLM Documentation
+  description: eCLM Documentation
+  # keywords: []
+  # authors: []
+  github: https://github.com/HPSCTerrSys/eCLM
+  # To autogenerate a Table of Contents, run "myst init --write-toc"
+  toc:
+    # Auto-generated by `myst init --write-toc`
+    - file: INDEX.md
+    - title: Introduction
+      children:
+        - file: users_guide/installation/README.md
+        - file: users_guide/introduction/introduction.md
+    - title: User's Guide
+      children:
+        - file: users_guide/case_examples/README.md
+          children:
+            - file: users_guide/case_examples/Wuestebach.md
+            - file: users_guide/case_examples/NRW.md
+            - file: users_guide/case_examples/EURO-CORDEX.md
+        - file: users_guide/running_cases/case_customization.md
+        - file: users_guide/analyzing_model_output.md
+        - file: users_guide/case_creation/README.md
+          children:
+            - file: users_guide/case_creation/1_create_grid_file.md
+            - file: users_guide/case_creation/2_create_mapping_file.md
+            - file: users_guide/case_creation/3_create_domain_file.md
+            - file: users_guide/case_creation/4_create_surface_file.md
+            - file: users_guide/case_creation/5_modifications_surface_domain_file.md
+            - file: users_guide/case_creation/6_create_atm_forcings.md
+    - title: Developer's Guide
+      children:
+        - file: users_guide/installation/source_installation.md
+        - title: eCLM Source Code Browser
+          url: https://hpscterrsys.github.io/eCLM/src
+    - title: Reference
+      children:
+        - title: CLM5 Technical Note
+          url: https://escomp.github.io/CTSM/release-clm5.0/tech_note/index.html
+        - title: eCLM static file generator
+          url: https://github.com/HPSCTerrSys/eCLM_static-file-generator/blob/main/README.md
+        - title: TSMP2 Workflow Engine
+          url: https://hpscterrsys.github.io/TSMP2_workflow-engine
+
+site:
+  template: book-theme
+  # options:
+  #   favicon: favicon.ico
+  #   logo: site_logo.png

docs/requirements.txt

@@ -1,4 +1,4 @@
-jupyter-book
+mystmd
 matplotlib
 numpy
 ghp-import