samsrabin · Oct 14, 2026 · Oct 14, 2026 · Oct 14, 2026 · Oct 14, 2026 · Oct 14, 2026
diff --git a/.github/workflows/gh-page_builder.yml b/.github/workflows/gh-page_builder.yml
@@ -26,7 +26,7 @@ jobs:
         PATH="${PATH}:${HOME}/.local/bin"
     - name: Build book HTML
       run: |
-        jupyter-book build .
+        jupyter-book build -W --keep-going .
     - name: Push _build/html to gh-pages
       # The below condition allows publication on pushes to main (including PR merges) as well as workflow_dispatch from main.
       if: github.ref == 'refs/heads/main'

diff --git a/_config.yml b/_config.yml
@@ -5,9 +5,17 @@ title: CLM Tutorial
 author: NCAR/CGD Staff
 logo: images/ncar_logo.png
 
-# Removing CESM2 Porting for 2026 tutorial (need to update to CESM3 in future)
 exclude_patterns:
+  - notebooks/diagnostics/additional/cvdp.ipynb
+  - notebooks/intro/cesm_expts/**
+  - notebooks/intro/community_experiments.ipynb
+  - notebooks/modifications/xml.ipynb
+  - notebooks/modifications/xml/**
+  - notebooks/namelist/**
+  - notebooks/resources/ncar_hpc_login.ipynb
   - notebooks/resources/porting.ipynb
+  - notebooks/resources/profile.ipynb
+  - notebooks/resources/tutorial_specific.ipynb
 
 sphinx:
   config:

diff --git a/_toc.yml b/_toc.yml
@@ -15,6 +15,8 @@ chapters:
     - file: notebooks/intro/project
     - file: notebooks/intro/getting_involved
     - file: notebooks/intro/getting_help
+  # IF UNCOMMENTING THE BELOW, MAKE SURE TO REMOVE THEIR ENTRIES
+  # FROM exclude_patterns IN _config.yml.
   #- file: notebooks/intro/community_experiments
   #  sections:
   #  - file: notebooks/intro/cesm_expts/clim_data_guide
@@ -49,6 +51,8 @@ chapters:
     - file: notebooks/basics/exercises/extra
     - file: notebooks/basics/exercises/review_questions
 
+# IF UNCOMMENTING THE BELOW, MAKE SURE TO REMOVE THEIR ENTRIES
+# FROM exclude_patterns IN _config.yml.
 #- file: notebooks/modifications/xml
 #  sections:
 #  - file: notebooks/modifications/xml/overview
@@ -71,6 +75,8 @@ chapters:
 #    - file: notebooks/modifications/xml/exercises/xml_runtype_exercise
 #    - file: notebooks/modifications/xml/exercises/xml_timestep_exercise
 
+# IF UNCOMMENTING THE BELOW, MAKE SURE TO REMOVE THEIR ENTRIES
+# FROM exclude_patterns IN _config.yml.
 #- file: notebooks/namelist/namelist
 #  sections:
 #  - file: notebooks/namelist/overview
@@ -145,6 +151,8 @@ chapters:
   - file: notebooks/resources/github
   - file: notebooks/resources/fortran
   - file: notebooks/resources/netcdf
+  # IF UNCOMMENTING THE BELOW, MAKE SURE TO REMOVE ITS ENTRY
+  # FROM exclude_patterns IN _config.yml.
   # - file: notebooks/resources/porting
 
 
diff --git a/notebooks/challenge/clm_ctsm/clm_ctsm.ipynb b/notebooks/challenge/clm_ctsm/clm_ctsm.ipynb
@@ -127,23 +127,11 @@
    "metadata": {},
    "source": [
     "As explained earlier, you can get information on compsets by using \"query_config in the cime/scripts directory under your CESM checkout.\n",
-    "\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "06a6c211",
-   "metadata": {
-    "vscode": {
-     "languageId": "shellscript"
-    }
-   },
-   "outputs": [],
-   "source": [
+    "\n",
+    "```bash\n",
     "cd /glade/u/home/$USER/code/my_cesm_code\n",
     "cime/scripts/query_config --compsets clm | grep \"I2000Clm60Sp \"\n",
-    "\n"
+    "```"
    ]
   },
   {

diff --git a/notebooks/challenge/clm_ctsm/clm_exercise_2.ipynb b/notebooks/challenge/clm_ctsm/clm_exercise_2.ipynb
@@ -22,23 +22,11 @@
    "metadata": {},
    "source": [
     "Using query_config again we learn more about this compset:\n",
-    "\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "b4513705",
-   "metadata": {
-    "vscode": {
-     "languageId": "shellscript"
-    }
-   },
-   "outputs": [],
-   "source": [
+    "\n",
+    "```bash\n",
     "cd /glade/u/home/$USER/code/my_clm_code\n",
     "cime/scripts/query_config --compsets clm | grep \"I2000Clm60Sp \"\n",
-    "\n"
+    "```"
    ]
   },
   {

diff --git a/notebooks/challenge/clm_ctsm/clm_exercise_3.ipynb b/notebooks/challenge/clm_ctsm/clm_exercise_3.ipynb
@@ -56,23 +56,11 @@
     "We will be running FATES in Satellite Phenology mode. This can be done by either choosing an SP compset (e.g. ) or manually setting this via the `user_nl_clm` file, with the parameters `use_fates_sp`, `use_fates_nocomp`, `use_fates_fixed_biogeog`. Check out the <a href=\"https://fates-users-guide.readthedocs.io/en/latest/user/namelist-options.html\">online documentation</a>  for more information on these parameters.\n",
     "\n",
     "Using query_config again we learn more about the FATES compset we will use:\n",
-    "\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "286afe86",
-   "metadata": {
-    "vscode": {
-     "languageId": "shellscript"
-    }
-   },
-   "outputs": [],
-   "source": [
+    "\n",
+    "```bash\n",
     "cd /glade/u/home/$USER/code/my_clm_code\n",
     "cime/scripts/query_config --compsets clm | grep \"I2000Clm60FatesSpCrujraRsGs \"\n",
-    "\n"
+    "```"
    ]
   },
   {

diff --git a/notebooks/challenge/clm_ctsm/clm_exercise_4.ipynb b/notebooks/challenge/clm_ctsm/clm_exercise_4.ipynb
@@ -397,7 +397,7 @@
     "<details>\n",
     "<summary><font face=\"Times New Roman\">Click here for the solution</font></summary><br>\n",
     "\n",
-    "![plot example](\"../../../images/challenge/fates_vcmax_diff.png\")\n",
+    "![plot example](../../../images/challenge/fates_vcmax_diff.png)\n",
     "\n",
     "*<p style=\"text-align: left;\"> Figure: Plotting solution comparing the two FATES simulations. </p>*\n",
     "    \n",
@@ -603,7 +603,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "#### Questions:\n",
+    "### Questions:\n",
     "- What is the primary difference in GPP between the IHIST BGC case and the I2000 SP case?\n",
     "- Why might this be occuring? "
    ]

diff --git a/notebooks/challenge/clm_ctsm/clm_exercise_5.ipynb b/notebooks/challenge/clm_ctsm/clm_exercise_5.ipynb
@@ -348,7 +348,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "#### Questions: \n",
+    "### Questions: \n",
     "\n",
     " - How do GPP and LAI track each other through the year? Which leads the other in spring, and does that make physical sense?\n",
     " - Does LAI fall all the way to zero in winter? What does the residual tell you about the mix of plant functional types at this site? (think back to which PFTs grow at BART.)"

diff --git a/notebooks/resources/ncar_hpc_module.ipynb b/notebooks/resources/ncar_hpc_module.ipynb
@@ -49,7 +49,7 @@
    "id": "33d4014c-bc0f-4ab0-aaf3-cf6cf7572f22",
    "metadata": {},
    "source": [
-    "### Checking what modules are loaded in your environment\n",
+    "## Checking what modules are loaded in your environment\n",
     "\n",
     "To check what modules you have loaded in your environment, use the following at the command line:"
    ]
@@ -69,7 +69,7 @@
    "id": "2a5ec941-4f4a-4a99-a3a0-6e514c448805",
    "metadata": {},
    "source": [
-    "### Checking what modules are available\n",
+    "## Checking what modules are available\n",
     "\n",
     "You can see which modules are available on the HPC resources by using the following at the command line:"
    ]
@@ -119,7 +119,7 @@
    "id": "65848ac8-1cad-47bf-b680-8b129ce4e25d",
    "metadata": {},
    "source": [
-    "### Loading a new module to your environment\n",
+    "## Loading a new module to your environment\n",
     "\n",
     "You can load one of the available modules (here we show loading ncview) using the following at the command line: "
    ]

diff --git a/notebooks/resources/text_editors.ipynb b/notebooks/resources/text_editors.ipynb
@@ -21,16 +21,8 @@
    "id": "69a56d2b-7508-4df0-9dc1-33f1f0887127",
    "metadata": {},
    "source": [
-    "## Emacs"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "14daecd3-2958-4925-bc37-e8748db4937b",
-   "metadata": {},
-   "outputs": [],
-   "source": [
+    "## Emacs\n",
+    "\n",
     "Emacs is an extensible, customizable, and self-documenting editor. Emacs opens a GUI to your computer and requires X11 forwarding. Once open, it can be used similar to a normal document including scrolling.\n",
     "\n",
     "**NOTE:** `emacs` **does not need to be loaded in your environment to be used. While it will work from the terminal command line, it does not work in the Jupyter environment.**"

diff --git a/notebooks/resources/tutorial_queue_account.ipynb b/notebooks/resources/tutorial_queue_account.ipynb
@@ -13,7 +13,7 @@
    "id": "4a6f76fe-9658-443c-89a7-9ede364803e5",
    "metadata": {},
    "source": [
-    "### Tutorial Project Account\n",
+    "## Tutorial Project Account\n",
     "\n",
     "<div class=\"alert alert-warning\">\n",
     "You should have access to project account <strong>UESM0016</strong> and use this for your simulations.\n",
@@ -30,7 +30,7 @@
    "id": "9db9d54e-ef78-44ef-a003-4ddd8a416317",
    "metadata": {},
    "source": [
-    "### Special Queues\n",
+    "## Special Queues\n",
     "\n",
     "<div class=\"alert alert-warning\">\n",
     "\n",
@@ -60,7 +60,7 @@
    "id": "d312e6e0-f48b-4f86-a97b-96c255d35d26",
    "metadata": {},
    "source": [
-    "### Compiling in the Special Queue"
+    "## Compiling in the Special Queue"
    ]
   },
   {

diff --git a/notebooks/singlepoint/exercises/FATESsp_NEON.ipynb b/notebooks/singlepoint/exercises/FATESsp_NEON.ipynb
@@ -701,7 +701,7 @@
     "\n",
     "***\n",
     "\n",
-    "### **./create_clone**\n",
+    "## **./create_clone**\n",
     "\n",
     "<div class=\"alert alert-block alert-info\">\n",
     "\n",