[WIP] try to get doxygen working

Docs/Doxyfile

@@ -425,7 +425,7 @@ LOOKUP_CACHE_SIZE      = 0
 # normally produced when WARNINGS is set to YES.
 # The default value is: NO.
 
-EXTRACT_ALL            = NO
+EXTRACT_ALL            = YES
 
 # If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
 # be included in the documentation.
@@ -443,7 +443,7 @@ EXTRACT_PACKAGE        = NO
 # included in the documentation.
 # The default value is: NO.
 
-EXTRACT_STATIC         = NO
+EXTRACT_STATIC         = YES
 
 # If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
 # locally in source files will be included in the documentation. If set to NO,
@@ -780,7 +780,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = ../Source
+INPUT                  = ../conductivity ../constants ../EOS ../integration ../interfaces ../networks ../neutrinos ../nse_solver ../nse_tabular ../opacity ../rates ../screening ../unit_test ../util
 
 # 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
@@ -839,7 +839,7 @@ EXCLUDE_SYMLINKS       = NO
 # Note that the wildcards are matched against the file with absolute path, so to
 # exclude all test directories for example use the pattern */test/*
 
-EXCLUDE_PATTERNS       =
+EXCLUDE_PATTERNS       = */util/autodiff/* */util/gcem/* */util/skynet/* */tmp_build_dir/*
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the
@@ -2009,15 +2009,15 @@ ENABLE_PREPROCESSING   = YES
 # The default value is: NO.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-MACRO_EXPANSION        = NO
+MACRO_EXPANSION        = YES
 
 # If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
 # the macro expansion is limited to the macros specified with the PREDEFINED and
 # EXPAND_AS_DEFINED tags.
 # The default value is: NO.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-EXPAND_ONLY_PREDEF     = NO
+EXPAND_ONLY_PREDEF     = YES
 
 # If the SEARCH_INCLUDES tag is set to YES, the include files in the
 # INCLUDE_PATH will be searched if a #include is found.
@@ -2049,7 +2049,15 @@ 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             =
+# breathe barfs on these when trying to parse function definitions
+# see https://github.com/breathe-doc/breathe/issues/905
+PREDEFINED             = AMREX_GPU_DEVICE= \
+                         AMREX_GPU_HOST_DEVICE= \
+                         AMREX_GPU_MANAGED= \
+                         AMREX_INLINE= \
+                         AMREX_FORCE_INLINE= \
+                         AMREX_FLATTEN= \
+                         AUTODIFF_DEVICE_FUNC=
 
 # 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/Makefile

@@ -22,7 +22,7 @@ clean:
 html:
 	./rp.py > source/runtime_parameters.rst
 	doxygen Doxyfile
-	breathe-apidoc --o source doxy_files/xml
+	breathe-apidoc --o source doxy_files/xml -g class,file
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 	@if [ ! -d ../docs ]; then mkdir ../docs; fi
 

Docs/source/index.rst

@@ -90,6 +90,14 @@ of state routines.
    comprehensive_tests
    one_zone_tests
 
+.. toctree::
+   :maxdepth: 1
+   :caption: API
+
+   filelist
+   classlist
+.. namespacelist
+
 .. toctree::
    :maxdepth: 1
    :caption: References