Avoid breathe

.github/workflows/docs.yml

@@ -26,17 +26,14 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y --no-install-recommends doxygen graphviz
           python3 -m pip install --upgrade pip
-          pip3 install sphinx sphinx_rtd_theme
+          pip3 install sphinx sphinx_rtd_theme sphinxcontrib-bibtex
       - name: Build
         # execute from top-level nalu-wind directory
         run: |
+          mkdir -p ./build_docs/doxygen
+          doxygen ./docs/doxygen/Doxyfile
           echo "::add-matcher::.github/problem-matchers/sphinx.json"
           sphinx-build -M html ./docs/sphinx ./build_docs/manual -W --keep-going -n 2>&1 | tee -a build-output.txt
-          # Doxygen output gets parsed wrong by the sphinx problem matcher so unregister it
-          echo "::remove-matcher owner=sphinx-problem-matcher-loose-no-severity::"
-          echo "::remove-matcher owner=sphinx-problem-matcher-loose::"
-          echo "::remove-matcher owner=sphinx-problem-matcher::"
-          doxygen ./docs/doxygen/Doxyfile
           mv ./build_docs/manual/html ./documentation
           mv ./build_docs/doxygen/html ./documentation/api_docs
           touch ./documentation/.nojekyll
@@ -46,7 +43,7 @@ jobs:
           egrep "WARNING:" build-output.txt | sort | uniq | \
             awk 'BEGIN{i=0}{print $0}{i++}END{print "Warnings: "i}' > build-output-warnings.txt
           cat build-output-warnings.txt
-          #exit $(tail -n 1 build-output-warnings.txt | awk '{print $2}')
+          exit $(tail -n 1 build-output-warnings.txt | awk '{print $2}')
       - name: Deploy
         if: github.event_name == 'push'
         uses: JamesIves/github-pages-deploy-action@releases/v3

docs/doxygen/Doxyfile

@@ -38,7 +38,7 @@ PROJECT_NAME           = "Nalu-Wind"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = v0.1.0
+PROJECT_NUMBER         = v1.2.0
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
@@ -778,7 +778,7 @@ WARNINGS               = YES
 # will automatically be disabled.
 # The default value is: YES.
 
-WARN_IF_UNDOCUMENTED   = YES
+WARN_IF_UNDOCUMENTED   = NO
 
 # If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
 # potential errors in the documentation, such as not documenting some parameters
@@ -829,8 +829,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = ./src \
-                         ./docs/doxygen/main_page.md
+INPUT                  = ./include ./src
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -861,6 +860,7 @@ FILE_PATTERNS          = *.c \
                          *.cc \
                          *.cxx \
                          *.cpp \
+                         *.C \
                          *.c++ \
                          *.H \
                          *.h \
@@ -2133,7 +2133,7 @@ INCLUDE_FILE_PATTERNS  =
 # recursively expanded use the := operator instead of the = operator.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-PREDEFINED             =
+PREDEFINED             = 
 
 # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
 # tag can be used to specify a list of macro names that should be expanded. The

docs/sphinx/conf.py

@@ -15,10 +15,8 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-# import os
+import os
 import sys
-# sys.path.insert(0, os.path.abspath('.'))
-#sys.path.append("../breathe")
 
 # -- General configuration ------------------------------------------------
 
@@ -29,15 +27,22 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = [ 'sphinx.ext.mathjax']
-
-
+extensions = [
+              'sphinx.ext.autodoc',
+              'sphinx.ext.autosummary',
+              'sphinx.ext.mathjax',
+              'sphinx.ext.intersphinx',
+              'sphinxcontrib.bibtex',
+             ]
+bibtex_bibfiles = ['references/references.bib']
+autodoc_default_flags = ['members','show-inheritance','undoc-members']
+autoclass_content = 'both'
+mathjax_path = 'https://cdn.jsdelivr.net/npm/mathjax@2/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
+numfig = True
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
-#breathe_projects = {"Nalu-Wind": "../doxygen_output/xml/"}
-#breathe_default_project = "Nalu-Wind"
 
-fortran_src ='../../src/'
+#fortran_src ='../../src/'
 #fortran_ext =[' 'F90']
 
 # The suffix(es) of source filenames.
@@ -347,10 +352,9 @@
 #
 # texinfo_no_detailmenu = False
 
+primary_domain = "cpp"
+
 def setup(app):
-    app.add_object_type("cmakeval", "cmakeval",
-                        objname="CMake configuration value",
-                        indextemplate="pair: %s; CMake configuration")
-    app.add_object_type("input_param", "input_param",
-                        objname="Nalu-Wind input parameter",
-                        indextemplate="pair: %s; Nalu-Wind input parameter")
+    app.add_object_type("inpfile", "inpfile",
+                        objname="Nalu-Wind Input File Parameter",
+                        indextemplate="pair: %s; Nalu-Wind Input File Parameter")