Test PR to Fix Doc CI Fail - Do Not Merge

.readthedocs.yaml

@@ -4,10 +4,13 @@
 
 # Required
 version: 2
-build: 
-  os: ubuntu-20.04
-  tools: 
-    python: "3.9"
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+  jobs:
+    post_create_environment:
+      - python -m pip install --upgrade "pip" "setuptools<81"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

doc/UsersGuide/requirements.in

@@ -1,4 +1,5 @@
-sphinx==7.4.7
-sphinx_rtd_theme
-sphinxcontrib-bibtex
-requests==2.32.2
+sphinx>=8.0.0
+sphinx_rtd_theme>=3.0.0
+sphinxcontrib-bibtex>=2.6.4
+requests>=2.32.2
+setuptools<81.0.0

doc/UsersGuide/requirements.txt

@@ -2,7 +2,7 @@
 # This file is autogenerated by pip-compile with Python 3.13
 # by the following command:
 #
-#    pip-compile requirements.in
+#    pip-compile --allow-unsafe --strip-extras requirements.in
 #
 alabaster==0.7.16
     # via sphinx
@@ -50,17 +50,17 @@ six==1.16.0
     #   pybtex
 snowballstemmer==2.2.0
     # via sphinx
-sphinx==7.4.7
+sphinx==8.0.2
     # via
     #   -r requirements.in
     #   sphinx-rtd-theme
     #   sphinxcontrib-bibtex
     #   sphinxcontrib-jquery
-sphinx-rtd-theme==2.0.0
+sphinx-rtd-theme==3.1.0
     # via -r requirements.in
 sphinxcontrib-applehelp==1.0.8
     # via sphinx
-sphinxcontrib-bibtex==2.6.2
+sphinxcontrib-bibtex==2.6.4
     # via -r requirements.in
 sphinxcontrib-devhelp==1.0.6
     # via sphinx
@@ -76,3 +76,9 @@ sphinxcontrib-serializinghtml==1.1.10
     # via sphinx
 urllib3==2.2.2
     # via requests
+
+# The following packages are considered to be unsafe in a requirements file:
+setuptools==80.10.2
+    # via
+    #   -r requirements.in
+    #   sphinxcontrib-bibtex

doc/UsersGuide/source/Glossary.rst

@@ -22,7 +22,7 @@ Glossary
       The `Air Quality Model <https://github.com/NOAA-EMC/AQM>`_ (AQM) is a UFS Application that dynamically couples the Community Multiscale Air Quality (:term:`CMAQ`) model with the UFS Weather Model through the :term:`NUOPC` Layer to simulate temporal and spatial variations of atmospheric compositions (e.g., ozone and aerosol compositions). The CMAQ, treated as a column chemistry model, updates concentrations of chemical species (e.g., ozone and aerosol compositions) at each integration time step. The transport terms (e.g., :term:`advection` and diffusion) of all chemical species are handled by the UFS Weather Model as :term:`tracers<tracer>`.
 
    CCPP
-      The `Common Community Physics Package <https://dtcenter.org/community-code/common-community-physics-package-ccpp>`_ is a forecast-model agnostic, vetted collection of code containing atmospheric physical parameterizations and suites of parameterizations for use in Numerical Weather Prediction (:term:`NWP`) along with a framework that connects the physics to the host forecast model.
+      The `Common Community Physics Package <https://dtcenter.org/software-tools/common-community-physics-package-ccpp>`_ is a forecast-model agnostic, vetted collection of code containing atmospheric physical parameterizations and suites of parameterizations for use in Numerical Weather Prediction (:term:`NWP`) along with a framework that connects the physics to the host forecast model.
 
    CCPP-Framework
      The infrastructure that connects physics schemes with a host model; also refers to a software

doc/UsersGuide/source/InputsOutputs.rst

@@ -28,7 +28,7 @@ mediator). Currently, supported configurations include:
    * - ATMAERO
      - :term:`ATM` coupled to :term:`GOCART`
    * - ATMAQ
-     - :term:`ATM` coupled to :term:`CMAQ`
+     - :term:`ATM` coupled to :term:`AQM`
    * - ATML
      - :term:`ATM` coupled to :term:`NOAHMP`
    * - ATMF
@@ -1078,7 +1078,7 @@ The aerosol initial input currently read by GOCART is the same format as the UFS
 .. _aqm-in:
 
 --------------
-AQM (CMAQ)
+UFS AQM
 --------------
 
 .. _aqm-fix-files:
@@ -1110,20 +1110,20 @@ AQM inputs defined in ``aqm.rc`` are listed and described in :numref:`Table %s <
 
    * - Filename
      - Description
-   * - AE_cb6r3_ae6_aq.nml 
-     - AE Matrix NML
-   * - GC_cb6r3_ae6_aq.nml 
-     - GC Matrix NML
-   * - NR_cb6r3_ae6_aq.nml 
-     - NR Matrix NML
+   * - AE_cb6r5_ae7_aq.nml 
+     - AE Matrix NML - Specifies chemical species, emissions mapping, and related settings for CMAQ's CB6r5 (Revision 5 of the Carbon Bond 6 Mechanism) chemical mechanism.
+   * - GC_cb6r5_ae7_aq.nml 
+     - GC Matrix NML - Configures CMAQ's gas-phase chemistry controls.
+   * - NR_cb6r5_ae7_aq.nml 
+     - NR Matrix NML - Non-reactive, gas-phase chemical species configuration for CMAQ.
    * - Species_Table_TR_0.nml 
-     - TR Matrix NML
-   * - CSQY_DATA_cb6r3_ae6_aq
-     - CSQY Data
+     - TR Matrix NML - CMAQ species transport definitions. Empty in the UFS as CMAQ is used as a column model with tracer transport using FV3.
+   * - CSQY_DATA_cb6r5_ae7_aq
+     - CSQY Data - CMAQ's chemical stoichiometric yield data table used by the solver for numerical calculations.
    * - PHOT_OPTICS.dat
      - Optics Data
    * - omi_cmaq_2015_361X179.dat
-     - OMI data
+     - OMI data - Ozone Monitoring Instrument (OMI) profile mappings used in establishing CMAQ boundary conditions.
    * - NEXUS/NEXUS_Expt.nc
      - Emissions File
    * - BEIS_RRFScmaq_C775.ncf
@@ -1133,6 +1133,17 @@ AQM inputs defined in ``aqm.rc`` are listed and described in :numref:`Table %s <
    * - Hourly_Emissions_regrid_rrfs_13km_20190801_t12z_h72.nc
      - File Emissions File 
 
+
+The most recent AQM input data files can be found in the `Weather Model S3 bucket <https://noaa-ufs-regtests-pds.s3.amazonaws.com/index.html>`_ in the input-data-202XXXXX/AQM directory for the most recent date. Below are the data subdirectories that exist in ``input-data-202XXXXX/AQM/v8``.
+
+   * - ``fix``
+     - Fix files are static, climatological, and topographical datasets required for model initialization and running. These files include terrain, land use, vegetation, and soil data.
+   * - ``NEXUS``
+     - "NEXUS" (NOAA Emission and eXchange Unified System) files are specialized input files used for air quality modeling to incorporate pollutant emissions data. 
+   * - ``INPUT``
+     - This directory contains pre-processing, initial conditions, grid-dependent, and namelist files.
+
+
 .. _lnd-in:
 
 --------------