Remove doc warnings (#1313)

.github/workflows/docs.yml

@@ -40,7 +40,7 @@ jobs:
       - name: Report
         run: |
           echo "::add-matcher::.github/problem-matchers/sphinx.json"
-          egrep "WARNING:" build-output.txt | sort | uniq | \
+          egrep "WARNING:|Warning:|ERROR:|Error:" 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}')

docs/sphinx/conf.py

@@ -15,8 +15,10 @@
 # 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 sys
+# import os
+#import sys
+# sys.path.insert(0, os.path.abspath('.'))
+#sys.path.append("../breathe")
 
 # -- General configuration ------------------------------------------------
 
@@ -27,20 +29,14 @@
 # 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.autodoc',
-              'sphinx.ext.autosummary',
-              'sphinx.ext.mathjax',
-              'sphinx.ext.intersphinx',
-              'sphinxcontrib.bibtex',
-             ]
+extensions = ['sphinx.ext.mathjax', '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_ext =[' 'F90']
@@ -352,9 +348,7 @@
 #
 # texinfo_no_detailmenu = False
 
-primary_domain = "cpp"
-
 def setup(app):
     app.add_object_type("inpfile", "inpfile",
-                        objname="Nalu-Wind Input File Parameter",
-                        indextemplate="pair: %s; Nalu-Wind Input File Parameter")
+                        objname="Nalu-Wind input parameter",
+                        indextemplate="pair: %s; Nalu-Wind input parameter")

docs/sphinx/source/developer/write_developer_doc.rst

@@ -18,12 +18,3 @@ copy of the file.
 .. literalinclude:: dox_example/example.h
    :language: c++
    :caption: Sample C++ header file showing inline documentation using specially formatted comments.
-
-Once processed by Doxygen and embedded in Sphinx, the resulting documentation of
-the class looks as shown below:
-
-.. doxygenclass:: ExampleClass
-   :project: example_cpp
-   :members:
-   :private-members:
-   :protected-members:

docs/sphinx/source/theory/windEnergy.rst

@@ -329,7 +329,7 @@ Initial conditions
 
 Nalu-Wind has the ability to initialize the internal flow fields to uniform
 conditions for all pressure, velocity, temperature, and TKE (:math:`k`) in the
-:inpfile:`input file <initial_conditions.constant>`. Nalu-Wind also provides a *user
+`input file <initial_conditions.constant>`. Nalu-Wind also provides a *user
 function* to add perturbations to the velocity field to trigger turbulence
 generation during precursor simulations. To specify more complex flow field
 conditions, a temperature profile with a capping inversion for example, users