Add Doxygen Github action for CCPP SciDoc display

.github/workflows/doxygen.yml

@@ -0,0 +1,107 @@
+name: Doxygen GitHub Pages Deploy Action
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pages: write
+      id-token: write
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    steps:
+
+    - name: Checkout current ccpp-physics code
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Store remote-URL for current ccpp-physics code
+      run: echo "GIT_REMOTE_URL=`git remote get-url origin`" >> $GITHUB_ENV
+
+    - name: Store branch name for current ccpp-physics code
+      run: echo "GIT_REMOTE_BRANCH=`git rev-parse --abbrev-ref HEAD`" >> $GITHUB_ENV
+
+    - name: Store hash for HEAD of current ccpp-physics code
+      run: echo "GIT_REMOTE_HASH=`git rev-parse HEAD`" >> $GITHUB_ENV
+
+    - name: Checkout latest ccpp-physics code
+      run: git clone https://github.com/NCAR/ccpp-physics.git
+
+    - name: Initialize submodules
+      run: |
+        cd /home/runner/work/ccpp-physics/ccpp-physics/ccpp-physics
+        git submodule update --init --recursive
+
+    - name: Update ccpp-physics hash 
+      if: github.event.pull_request == false
+      run: |
+        cd /home/runner/work/ccpp-physics/ccpp-physics/ccpp-physics/physics
+        echo $GIT_REMOTE_URL
+        echo $GIT_REMOTE_BRANCH
+        echo ${{github.repository}}
+        echo ${{ github.event.pull_request.head.sha }}
+        echo $GITHUB_SHA
+        git remote add remote_local $GIT_REMOTE_URL
+        git fetch remote_local $GIT_REMOTE_BRANCH
+        git checkout remote_local/$GIT_REMOTE_BRANCH
+
+
+#    - name: Set up and run Doxygen
+#      #uses: DenverCoder1/doxygen-github-pages-action@v2.0.0
+#      #with:
+#      #  config_file: ./physics/docs/ccpp_doxyfile
+#      #  folder: ./
+#      uses: mattnotmitt/doxygen-action@v1.12.0
+#      with:
+#        working-directory: '.'
+#        doxyfile-path: './physics/docs/ccpp_doxyfile'
+#        enable-latex: true
+
+    - name: Install Doxygen + Graphviz + LaTeX
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y doxygen graphviz perl texlive-latex-base texlive-latex-extra texlive-fonts-recommended texlive-bibtex-extra
+
+    - name: Verify Perl installation
+      run: which perl
+
+    - name: Verify bibtex installation
+      run: which bibtex
+
+    - name: Verify Doxygen version
+      run: doxygen --version
+
+    - name: update doxyfile
+      run: |
+        cd physics/docs
+        doxygen -u ccpp_doxyfile
+
+    - name: Run Doxygen
+      run: |
+        cd physics/docs
+        doxygen ccpp_doxyfile
+
+    - name: Find html output
+      run: find . -type d -name html
+
+    - name: Setup Pages
+      uses: actions/configure-pages@v5
+    - name: Upload artifact
+      uses: actions/upload-pages-artifact@v3
+      with:
+        path: physics/docs/doc/html
+    - name: list files
+      run: ls -la physics/docs/doc/html/
+
+    - name: Deploy to GitHub Pages
+      id: deployment
+      uses: actions/deploy-pages@v4.0.5
+

physics/docs/ccpp_doxyfile

@@ -42,7 +42,7 @@ DOXYFILE_ENCODING      = UTF-8
 # title of most generated pages and in a few other places.
 # The default value is: My Project.
 
-PROJECT_NAME           = "CCPP SciDoc v7.0.0"
+PROJECT_NAME           = "CCPP SciDoc v7.0.x"
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number. This
 # could be handy for archiving the generated documentation or if some version
@@ -814,7 +814,7 @@ FILE_VERSION_FILTER    =
 # DoxygenLayout.xml, Doxygen will parse it automatically even if the LAYOUT_FILE
 # tag is left empty.
 
-LAYOUT_FILE            = ccpp_dox_layout.xml
+LAYOUT_FILE            = /home/runner/work/ccpp-physics/ccpp-physics/physics/docs/ccpp_dox_layout.xml
 
 # The CITE_BIB_FILES tag can be used to specify one or more bib files containing
 # the reference definitions. This must be a list of .bib files. The .bib
@@ -824,7 +824,7 @@ LAYOUT_FILE            = ccpp_dox_layout.xml
 # LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
 # search path. See also \cite for info how to create references.
 
-CITE_BIB_FILES         = library.bib
+CITE_BIB_FILES         = /home/runner/work/ccpp-physics/ccpp-physics/physics/docs/library.bib
 
 # The EXTERNAL_TOOL_PATH tag can be used to extend the search path (PATH
 # environment variable) so that external tools such as latex and gs can be
@@ -840,7 +840,7 @@ CITE_BIB_FILES         = library.bib
 # launching external tools will then become
 # PATH=/Library/TeX/texbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin
 
-EXTERNAL_TOOL_PATH     =
+EXTERNAL_TOOL_PATH     = /usr/bin
 
 #---------------------------------------------------------------------------
 # Configuration options related to warning and progress messages
@@ -1127,7 +1127,7 @@ EXCLUDE_SYMBOLS        =
 # command).
 
 EXAMPLE_PATH           = pdftxt/RE7 \
-                         doc/html
+                         pdftxt
 
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the
 # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
@@ -1173,7 +1173,7 @@ IMAGE_PATH             = img
 # need to set EXTENSION_MAPPING for the extension otherwise the files are not
 # properly processed by Doxygen.
 
-INPUT_FILTER           =
+INPUT_FILTER           = 
 
 # The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
 # basis. Doxygen will compare the file name with each pattern and apply the
@@ -1186,7 +1186,7 @@ INPUT_FILTER           =
 # need to set EXTENSION_MAPPING for the extension otherwise the files are not
 # properly processed by Doxygen.
 
-FILTER_PATTERNS        =
+FILTER_PATTERNS        = 
 
 # If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
 # INPUT_FILTER) will also be used to filter the input files that are used for
@@ -2809,7 +2809,7 @@ INTERACTIVE_SVG        = YES
 # found. If left blank, it is assumed the dot tool can be found in the path.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-DOT_PATH               = /opt/homebrew/bin
+DOT_PATH               = 
 
 # The DOTFILE_DIRS tag can be used to specify one or more directories that
 # contain dot files that are included in the documentation (see the \dotfile

physics/docs/pdftxt/GFS_v16_suite.txt

@@ -22,14 +22,14 @@ The GFS_v16 suite uses the parameterizations in the following order:
  - \ref GFDL_cloud
 
 \section sdf_gfsv16b Suite Definition File 
-\include  suite_FV3_GFS_v16.xml
+\include  suite_SCM_GFS_v16.xml
 
 
 \section gfs16_nml_opt_des Namelist 
 \ref GFDL_cloud namelist options 
-\snippet RE300/FV3_GFS_v16_input.nml GFDL_CLOUD_MICROPHYSICS_NML
+\snippet RE7/input_GFS_v16.nml GFDL_CLOUD_MICROPHYSICS_NML
 Other namelist options
-\snippet RE300/FV3_GFS_v16_input.nml GFS_PHYSICS_NML
+\snippet RE7/input_GFS_v16.nml GFS_PHYSICS_NML
 
 - nstf_name = \f$[2,0,0,0,0]^1 [2,1,0,0,0]^2\f$
  - \f$^1\f$ NSST is on and coupled with spin up off