integrate doxygen with sphinx using breathe

analysis/FlowAdaptor.h

@@ -15,7 +15,6 @@
 
 /**
  * \class FlowAdaptor
- *
  * @brief 
  * The FlowAdaptor class operates on a lattice Boltzmann model to alter the flow conditions
  * 

docs/README.md

@@ -6,14 +6,20 @@ pip install Sphinx
 # foamatting requires sphinx read-the-docs-theme
 pip install sphinx-rtd-theme
 
+# support for doxygen requires breathe
+pip install breathe
+
 # equation rendering requires latex and dvipng command
 sudo apt-get install dvipng
 sudo apt-get install texlive texstudio
 sudo apt-get install texlive-latex-recommended texlive-pictures texlive-latex-extra
 
-
 # To build the docs
 Step 1) install dependencies listed above
-Step 2) type 'make html' from the docs/ directory
+Step 2) build LBPM with doxygen support enabled in CMake
-Step 3) point your browser at ~/local/doc/build/html/index.html
+Step 3) From the build directory run the command 'make doc' to build html and xml from doxygen
+Step 4) modify source/conf.py so that the breathe directory specifies the full path to the xml
+        documentation built in Step 3
+Step 5) type 'make html' from the docs/ directory (the same directory that contains this README file)
+Step 6) point your browser at ~/local/doc/build/html/index.html
 # 

docs/source/conf.py

@@ -31,7 +31,8 @@ release = '1.0'
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.imgmath'
+    'sphinx.ext.imgmath',
+    'breathe'
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -55,7 +56,6 @@ html_theme = 'alabaster'
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
 
-
 ## Read the docs style:
 if os.environ.get('READTHEDOCS') != 'True':
     try:
@@ -68,3 +68,12 @@ if os.environ.get('READTHEDOCS') != 'True':
     
 #def setup(app):
 #    app.add_stylesheet("fix_rtd.css")
+
+
+# -- Breathe configuration -------------------------------------------------
+
+breathe_projects = {
+	"LBPM Doxygen": "/home/mcclurej/local/dev/LBPM/doc/xml/"
+}
+breathe_default_project = "LBPM Doxygen"
+breathe_default_members = ('members', 'undoc-members')

docs/source/developerGuide/doxygen/Analysis.rst

@@ -0,0 +1,9 @@
+###############################################################################
+Analysis methods
+###############################################################################
+
+.. toctree::
+   :glob:
+   :maxdepth: 2
+   
+   analysis/*

docs/source/developerGuide/doxygen/Models.rst

@@ -0,0 +1,10 @@
+###############################################################################
+Models
+###############################################################################
+
+.. toctree::
+   :glob:
+   :maxdepth: 2
+
+   models/*
+   

docs/source/developerGuide/doxygen/ScaLBL.rst

@@ -0,0 +1,5 @@
+============================================
+Scalable Lattice Boltzmann Library (ScalBL)
+============================================
+.. doxygenfile:: ScaLBL.h
+   :project: LBPM Doxygen

docs/source/developerGuide/doxygen/analysis/DCEL.rst

@@ -0,0 +1,5 @@
+============================================
+DCEL
+============================================
+.. doxygenfile:: dcel.h
+   :project: LBPM Doxygen

docs/source/developerGuide/doxygen/analysis/FlowAdaptor.rst

@@ -0,0 +1,5 @@
+============================================
+FlowAdaptor
+============================================
+.. doxygenfile:: FlowAdaptor.h
+   :project: LBPM Doxygen

docs/source/developerGuide/doxygen/analysis/Minkowski.rst

@@ -0,0 +1,5 @@
+============================================
+Minkowski
+============================================
+.. doxygenfile:: Minkowski.h
+   :project: LBPM Doxygen

docs/source/developerGuide/doxygen/analysis/SubPhase.rst

@@ -0,0 +1,5 @@
+============================================
+SubPhase analysis 
+============================================
+.. doxygenfile:: SubPhase.h
+   :project: LBPM Doxygen

docs/source/developerGuide/doxygen/models/ColorModel.rst

@@ -0,0 +1,5 @@
+============================================
+Color Model 
+============================================
+.. doxygenfile:: ColorModel.h
+   :project: LBPM Doxygen

docs/source/developerGuide/doxygen/models/FreeEnergyModel.rst

@@ -0,0 +1,5 @@
+============================================
+Free Energy Model
+============================================
+.. doxygenfile:: FreeLeeModel.h
+   :project: LBPM Doxygen

docs/source/developerGuide/doxygen/models/GreyscaleModel.rst

@@ -0,0 +1,5 @@
+============================================
+Greyscale Model 
+============================================
+.. doxygenfile:: GreyscaleModel.h
+   :project: LBPM Doxygen

docs/source/developerGuide/doxygen/models/MRTModel.rst

@@ -0,0 +1,5 @@
+============================================
+Multi-relaxation time (MRT) Model 
+============================================
+.. doxygenfile:: MRTModel.h
+   :project: LBPM Doxygen

docs/source/developerGuide/doxygen/models/NernstPlanckModel.rst

@@ -0,0 +1,5 @@
+============================================
+Ion Model 
+============================================
+.. doxygenfile:: IonModel.h
+   :project: LBPM Doxygen

docs/source/developerGuide/doxygen/models/PoissonModel.rst

@@ -0,0 +1,5 @@
+============================================
+Poisson Model 
+============================================
+.. doxygenfile:: PoissonSolver.h
+   :project: LBPM Doxygen

docs/source/developerGuide/index.rst

@@ -15,4 +15,8 @@ into the framework.
 
    testingModels/*
 
- 
+   doxygen/ScaLBL.rst
+
+   doxygen/Models.rst
+
+   doxygen/Analysis.rst

doxygen/Doxyfile.in

@@ -25,13 +25,13 @@ DOXYFILE_ENCODING      = UTF-8
 # The PROJECT_NAME tag is a single word (or a sequence of words surrounded 
 # by quotes) that should identify the project.
 
-PROJECT_NAME           = "@PROJECT_NAME@"
+PROJECT_NAME           = "LBPM Doxygen"
 
 # 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 control system is used.
 
-PROJECT_NUMBER         = "@PROJECT_VERSION@"
+PROJECT_NUMBER         = "9.12.2021"
 
 # 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