marvinDoc config changes

marvinDoc

@@ -58,7 +58,7 @@ PROJECT_LOGO           =
 # entered, it will be relative to the location where doxygen was started. If
 # left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       = \doc
+OUTPUT_DIRECTORY       = doc
 
 # If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
 # directories (in 2 levels) under the output directory of each output format and
@@ -829,7 +829,8 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = /marvin/
+INPUT                  = 
+#run doxygen from root marvin folder, current directory
 
 # 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
@@ -840,6 +841,8 @@ INPUT                  = /marvin/
 
 INPUT_ENCODING         = ISO-8859-1
 
+#UTF-8 - md files is not yet converted to UTF-8
+
 # If the value of the INPUT tag contains directories, you can use the
 # FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
 # *.h) to filter out the source-files in the directories.
@@ -931,7 +934,7 @@ 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       = */README.md
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the
@@ -968,7 +971,7 @@ EXAMPLE_RECURSIVE      = NO
 # that contain images that are to be included in the documentation (see the
 # \image command).
 
-IMAGE_PATH             = marvin42-dacapo-docs/Marvin42-dacapo-docs/images
+IMAGE_PATH             = marvin42-dacapo-docs/images
 
 # The INPUT_FILTER tag can be used to specify a program that doxygen should
 # invoke to filter for each input file. Doxygen will invoke the filter program
@@ -1121,15 +1124,15 @@ VERBATIM_HEADERS       = YES
 # generated with the -Duse_libclang=ON option for CMake.
 # The default value is: NO.
 
-CLANG_ASSISTED_PARSING = NO
+#CLANG_ASSISTED_PARSING = NO
 
 # If clang assisted parsing is enabled you can provide the compiler with command
 # line options that you would normally use when invoking the compiler. Note that
 # the include paths will already be set by doxygen for the files and directories
 # specified with INPUT and INCLUDE_PATH.
 # This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES.
 
-CLANG_OPTIONS          =
+#CLANG_OPTIONS          =
 
 # If clang assisted parsing is enabled you can provide the clang parser with the
 # path to the compilation database (see:
@@ -1139,7 +1142,7 @@ CLANG_OPTIONS          =
 # Note: The availability of this option depends on whether or not doxygen was
 # generated with the -Duse_libclang=ON option for CMake.
 
-CLANG_DATABASE_PATH    =
+#CLANG_DATABASE_PATH    =
 
 #---------------------------------------------------------------------------
 # Configuration options related to the alphabetical class index