fix sphinx and update doxygen (#29)

CMakeLists.txt

@@ -38,7 +38,10 @@ add_compile_options("$<$<AND:$<CONFIG:Debug>,$<COMPILE_LANGUAGE:Fortran>,$<Fortr
 add_compile_options("$<$<AND:$<CONFIG:Debug>,$<COMPILE_LANGUAGE:C>,$<C_COMPILER_ID:GNU>>:-Wall;-Wextra>")
 add_compile_options("$<$<AND:$<CONFIG:Debug>,$<COMPILE_LANGUAGE:CXX>,$<CXX_COMPILER_ID:GNU>>:-Wall;-Wextra>")
 
-project(ALL)
+project(ALL
+    VERSION "0.1.0"
+    DESCRIPTION "A Loadbalacing Library"
+    HOMEPAGE_URL "localhost")
 
 # add custom find-scripts to module path
 set(CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})

docs/CMakeLists.txt

 message("Generating ALL Documentation:")
 find_package(Doxygen REQUIRED)
+find_package(Python3 REQUIRED)
+message(DEBUG "Python3 version: ${PYTHON3_VERSION}")
 find_package(Sphinx REQUIRED)
+#find breathe
+# todo(s.schulz): The following does not seem to work. It returns non zero even
+# though the package is installed and the correct Python interpreter is found.
+# The python interpreter is in a non standard path and included using
+# environment variables and the module was installed in the users directory
+# (pip3 install --user breathe).
+#execute_process(
+#	COMMAND Python3::Interpreter -c "import breathe"
+#	RESULT_VARIABLE BREATHE_NOT_FOUND
+#	OUTPUT_QUIET
+#	)
+#if(NOT ${BREATHE_NOT_FOUND} EQUAL 0)
+#	message( FATAL_ERROR "Python \"breathe\" package not found")
+#endif()
+#do we need to make sure sphinx_rtd_theme is installed?
 
 # Find all public headers
 get_target_property(ALL_PUBLIC_HEADER_DIR ALL INTERFACE_INCLUDE_DIRECTORIES)
 file(GLOB_RECURSE ALL_PUBLIC_HEADERS ${ALL_PUBLIC_HEADER_DIR})
 
 # setup configuring of doxygen
-set(DOXYGEN_INPUT_DIR ${PROJECT_SOURCE_DIR}/include)
+# Caveat(s.schulz): Make sure there are not spaces within the paths.
+set(DOXYGEN_INPUT_DIR ${PROJECT_SOURCE_DIR}/include ${PROJECT_SOURCE_DIR}/src ${PROJECT_SOURCE_DIR}/example)
+string(REPLACE ";" "\" \"" DOXYGEN_INPUT_DIR "${DOXYGEN_INPUT_DIR}")
 set(DOXYGEN_OUTPUT_DIR ${CMAKE_CURRENT_BINARY_DIR}/doc/doxygen)
 set(DOXYGEN_INDEX_FILE ${DOXYGEN_OUTPUT_DIR}/xml/index.xml)
 set(DOXYFILE_IN ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in)
 set(DOXYFILE_OUT ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile)
+set(DOXYGEN_INTERNAL_DOCS NO)
+set(DOXYGEN_EXAMPLE_PATH ${PROJECT_SOURCE_DIR}/example)
+set(DOXYGEN_USE_MDFILE_AS_MAINPAGE ${PROJECT_SOURCE_DIR}/README.md)
 
 # configure doxygen config file
 configure_file(${DOXYFILE_IN} ${DOXYFILE_OUT} @ONLY)

docs/Doxyfile.in

@@ -32,19 +32,19 @@ DOXYFILE_ENCODING      = UTF-8
 # title of most generated pages and in a few other places.
 # The default value is: My Project.
 
-PROJECT_NAME           = "MPCD"
+PROJECT_NAME           = "@PROJECT_NAME@"
 
 # 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_NUMBER         = "@PROJECT_VERSION_MAJOR@.@PROJECT_VERSION_MINOR@.@PROJECT_VERSION_PATCH@"
 
 # 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
 # quick idea about the purpose of the project. Keep the description short.
 
-PROJECT_BRIEF          =
+PROJECT_BRIEF          = "@PROJECT_DESCRIPTION@"
 
 # With the PROJECT_LOGO tag one can specify a logo or an icon that is included
 # in the documentation. The maximum height of the logo should not exceed 55
@@ -226,7 +226,7 @@ SEPARATE_MEMBER_PAGES  = NO
 # uses this value to replace tabs by spaces in code fragments.
 # Minimum value: 1, maximum value: 16, default value: 4.
 
-TAB_SIZE               = 4
+TAB_SIZE               = 2
 
 # This tag can be used to specify a number of aliases that act as commands in
 # the documentation. An alias has the form:
@@ -328,7 +328,7 @@ AUTOLINK_SUPPORT       = YES
 # diagrams that involve STL classes more complete and accurate.
 # The default value is: NO.
 
-BUILTIN_STL_SUPPORT    = NO
+BUILTIN_STL_SUPPORT    = YES
 
 # If you use Microsoft's C++/CLI language, you should set this option to YES to
 # enable parsing support.
@@ -397,7 +397,7 @@ INLINE_GROUPED_CLASSES = NO
 # Man pages) or section (for LaTeX and RTF).
 # The default value is: NO.
 
-INLINE_SIMPLE_STRUCTS  = NO
+INLINE_SIMPLE_STRUCTS  = YES
 
 # When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
 # enum is documented as struct, union, or enum with the name of the typedef. So
@@ -515,7 +515,7 @@ HIDE_IN_BODY_DOCS      = NO
 # will be excluded. Set it to YES to include the internal documentation.
 # The default value is: NO.
 
-INTERNAL_DOCS          = NO
+INTERNAL_DOCS          = @DOXYGEN_INTERNAL_DOCS@
 
 # If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file
 # names in lower-case letters. If set to YES, upper-case letters are also
@@ -578,7 +578,7 @@ SORT_MEMBER_DOCS       = YES
 # this will also influence the order of the classes in the class list.
 # The default value is: NO.
 
-SORT_BRIEF_DOCS        = NO
+SORT_BRIEF_DOCS        = YES
 
 # If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
 # (brief and detailed) documentation of class members so that constructors and
@@ -590,7 +590,7 @@ SORT_BRIEF_DOCS        = NO
 # detailed member documentation.
 # The default value is: NO.
 
-SORT_MEMBERS_CTORS_1ST = NO
+SORT_MEMBERS_CTORS_1ST = YES
 
 # If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
 # of group names into alphabetical order. If set to NO the group names will
@@ -623,7 +623,7 @@ STRICT_PROTO_MATCHING  = NO
 # list. This list is created by putting \todo commands in the documentation.
 # The default value is: YES.
 
-GENERATE_TODOLIST      = YES
+GENERATE_TODOLIST      = NO
 
 # The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test
 # list. This list is created by putting \test commands in the documentation.
@@ -820,45 +820,24 @@ FILE_PATTERNS          = *.c \
                          *.cxx \
                          *.cpp \
                          *.c++ \
-                         *.java \
-                         *.ii \
-                         *.ixx \
-                         *.ipp \
-                         *.i++ \
-                         *.inl \
-                         *.idl \
-                         *.ddl \
-                         *.odl \
                          *.h \
                          *.hh \
                          *.hxx \
                          *.hpp \
                          *.h++ \
-                         *.cs \
-                         *.d \
-                         *.php \
-                         *.php4 \
-                         *.php5 \
-                         *.phtml \
                          *.inc \
-                         *.m \
                          *.markdown \
                          *.md \
-                         *.mm \
                          *.dox \
                          *.py \
                          *.pyw \
                          *.f90 \
+                         *.F90 \
                          *.f95 \
                          *.f03 \
                          *.f08 \
                          *.f \
-                         *.for \
-                         *.tcl \
-                         *.vhd \
-                         *.vhdl \
-                         *.ucf \
-                         *.qsf
+                         *.for
 
 # The RECURSIVE tag can be used to specify whether or not subdirectories should
 # be searched for input files as well.
@@ -906,7 +885,7 @@ EXCLUDE_SYMBOLS        =
 # that contain example code fragments that are included (see the \include
 # command).
 
-EXAMPLE_PATH           =
+EXAMPLE_PATH           = "@DOXYGEN_EXAMPLE_PATH@"
 
 # 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
@@ -982,7 +961,7 @@ FILTER_SOURCE_PATTERNS =
 # (index.html). This can be useful if you have a project on for instance GitHub
 # and want to reuse the introduction page also for the doxygen output.
 
-USE_MDFILE_AS_MAINPAGE =
+USE_MDFILE_AS_MAINPAGE = "@DOXYGEN_USE_MDFILE_AS_MAINPAGE@"
 
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing
@@ -995,7 +974,7 @@ USE_MDFILE_AS_MAINPAGE =
 # also VERBATIM_HEADERS is set to NO.
 # The default value is: NO.
 
-SOURCE_BROWSER         = NO
+SOURCE_BROWSER         = YES
 
 # Setting the INLINE_SOURCES tag to YES will include the body of functions,
 # classes and enums directly into the documentation.
@@ -1249,7 +1228,7 @@ HTML_TIMESTAMP         = NO
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_DYNAMIC_SECTIONS  = NO
+HTML_DYNAMIC_SECTIONS  = YES
 
 # With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
 # shown in the various tree structured indices initially; the user can expand
@@ -1478,7 +1457,7 @@ DISABLE_INDEX          = NO
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-GENERATE_TREEVIEW      = NO
+GENERATE_TREEVIEW      = YES
 
 # The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
 # doxygen will group on one line in the generated HTML documentation.
@@ -1666,7 +1645,7 @@ EXTRA_SEARCH_MAPPINGS  =
 # If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
 # The default value is: YES.
 
-GENERATE_LATEX         = YES
+GENERATE_LATEX         = NO
 
 # The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
 # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
@@ -2099,7 +2078,7 @@ 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             = ALL_VORONOI_ACTIVE ALL_VTK_OUTPUT
 
 # 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
@@ -2331,7 +2310,7 @@ INCLUDED_BY_GRAPH      = YES
 # The default value is: NO.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-CALL_GRAPH             = NO
+CALL_GRAPH             = YES
 
 # If the CALLER_GRAPH tag is set to YES then doxygen will generate a caller
 # dependency graph for every global function or class method.
@@ -2343,7 +2322,7 @@ CALL_GRAPH             = NO
 # The default value is: NO.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-CALLER_GRAPH           = NO
+CALLER_GRAPH           = YES
 
 # If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical
 # hierarchy of all classes instead of a textual one.

docs/classes/ALL.rst

@@ -2,7 +2,7 @@
 ALL
 ===
 
-.. doxygenclass:: ALL
+.. doxygenclass:: ALL::ALL
    :members:
    :protected-members:
    :private-members:

docs/classes/ALL_Functions.rst

@@ -2,6 +2,6 @@
 ALL_Functions overview
 ======================
 
-.. doxygennamespace:: ALL_Functions
+.. doxygennamespace:: ALL::Functions
    :project: ALL
 

docs/classes/ALL_Histogram.rst

@@ -2,7 +2,7 @@
 ALL_Histogram
 =============
 
-.. doxygenclass:: ALL_Histogram_LB
+.. doxygenclass:: ALL::Histogram_LB
    :members:
    :protected-members:
    :private-members:

docs/classes/ALL_LB.rst

@@ -2,7 +2,7 @@
 ALL_LB
 =============
 
-.. doxygenclass:: ALL_LB
+.. doxygenclass:: ALL::LB
    :members:
    :protected-members:
    :private-members:

docs/classes/ALL_Point.rst

@@ -2,7 +2,7 @@
 ALL_Point
 =============
 
-.. doxygenclass:: ALL_Point
+.. doxygenclass:: ALL::Point
    :members:
    :protected-members:
    :private-members:

docs/classes/ALL_Staggered.rst

@@ -2,7 +2,7 @@
 ALL_Staggered
 =============
 
-.. doxygenclass:: ALL_Staggered_LB
+.. doxygenclass:: ALL::Staggered_LB
    :members:
    :protected-members:
    :private-members:

docs/classes/ALL_Tensor.rst

@@ -2,7 +2,7 @@
 ALL_Tensor
 ==========
 
-.. doxygenclass:: ALL_Tensor_LB
+.. doxygenclass:: ALL::Tensor_LB
    :members:
    :private-members:
    :protected-members:

docs/classes/ALL_Voronoi.rst

+===========
+ALL_Voronoi
+===========
+
+.. doxygenclass:: ALL::Voronoi_LB
+   :members:
+   :private-members:
+   :protected-members:
+   :undoc-members: