Doxygen documentation improvement

1 files changed, 22 insertions, 22 deletions

diff --git a/src/Doxyfile.in b/src/Doxyfile.in
index 49e781bd..4784b915 100644
--- a/src/Doxyfile.in
+++ b/src/Doxyfile.in
@@ -32,7 +32,7 @@ DOXYFILE_ENCODING      = UTF-8
 # title of most generated pages and in a few other places.
 # The default value is: My Project.
 
-PROJECT_NAME           = "GUDHI"
+PROJECT_NAME           = "@CMAKE_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
@@ -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       =
 
 # 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
@@ -672,9 +672,9 @@ LAYOUT_FILE            =
 # search path. Do not use file names with spaces, bibtex cannot handle them. See
 # also \cite for info how to create references.
 
-CITE_BIB_FILES         = biblio/bibliography.bib \
-                        biblio/how_to_cite_cgal.bib \
-                        biblio/how_to_cite_gudhi.bib
+CITE_BIB_FILES         = @CMAKE_SOURCE_DIR@/biblio/bibliography.bib \
+                         @CMAKE_SOURCE_DIR@/biblio/how_to_cite_cgal.bib \
+                         @CMAKE_SOURCE_DIR@/biblio/how_to_cite_gudhi.bib
 
 #---------------------------------------------------------------------------
 # Configuration options related to warning and progress messages
@@ -745,7 +745,7 @@ WARN_LOGFILE           =
 # spaces.
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  =
+INPUT                  = @CMAKE_SOURCE_DIR@
 
 # 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
@@ -780,13 +780,14 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                = data/                   \
-	                     example/                \
-	                     GudhUI/                 \
-                         cmake/                  \
-                         python/                 \
-                         ext/                    \
-                         README.md
+EXCLUDE                = @CMAKE_SOURCE_DIR@/data/     \
+                         @CMAKE_SOURCE_DIR@/ext/      \
+                         @CMAKE_SOURCE_DIR@/README.md \
+                         @CMAKE_SOURCE_DIR@/.github \
+                         @CMAKE_CURRENT_BINARY_DIR@/new_gudhi_version_creation.md \
+                         @GUDHI_DOXYGEN_SOURCE_PREFIX@/GudhUI/ \
+                         @GUDHI_DOXYGEN_SOURCE_PREFIX@/cmake/  \
+                         @GUDHI_DOXYGEN_SOURCE_PREFIX@/python/ \
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
@@ -802,7 +803,7 @@ 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       = */utilities/*/*.md
+EXCLUDE_PATTERNS       = @GUDHI_DOXYGEN_SOURCE_PREFIX@/@GUDHI_DOXYGEN_UTILS_PATH@/*.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
@@ -819,10 +820,9 @@ EXCLUDE_SYMBOLS        =
 # that contain example code fragments that are included (see the \include
 # command).
 
-EXAMPLE_PATH           = biblio/    \
-	                     example/   \
-	                     utilities/   \
-	                     data/
+EXAMPLE_PATH           = @CMAKE_SOURCE_DIR@/biblio/ \
+                         @CMAKE_SOURCE_DIR@/data/   \
+                         @GUDHI_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
@@ -890,7 +890,7 @@ 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 = doc/common/main_page.md
+USE_MDFILE_AS_MAINPAGE = @GUDHI_DOXYGEN_COMMON_DOC_PATH@/main_page.md
 
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing
@@ -1046,7 +1046,7 @@ HTML_FILE_EXTENSION    = .html
 # of the possible markers and block names see the documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_HEADER            = doc/common/header.html
+HTML_HEADER            = @GUDHI_DOXYGEN_COMMON_DOC_PATH@/header.html
 
 # The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
 # generated HTML page. If the tag is left blank doxygen will generate a standard
@@ -1056,7 +1056,7 @@ HTML_HEADER            = doc/common/header.html
 # that doxygen normally uses.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_FOOTER            = doc/common/footer.html
+HTML_FOOTER            = @GUDHI_DOXYGEN_COMMON_DOC_PATH@/footer.html
 
 # The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
 # sheet that is used by each HTML page. It can be used to fine-tune the look of
@@ -1068,7 +1068,7 @@ HTML_FOOTER            = doc/common/footer.html
 # obsolete.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_STYLESHEET        = doc/common/stylesheet.css
+HTML_STYLESHEET        = @GUDHI_DOXYGEN_COMMON_DOC_PATH@/stylesheet.css
 
 # The HTML_EXTRA_STYLESHEET tag can be used to specify an additional user-
 # defined cascading style sheet that is included after the standard style sheets