Allow indpendent execution of doxygen (i.e. outside of build.sh) and …

…tweak formatting

Doxyfile

@@ -655,7 +655,7 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories
 # with spaces.
 
-INPUT                  = gpstk_sources
+INPUT                  = core/lib ext/lib
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
@@ -1732,7 +1732,7 @@ INTERACTIVE_SVG        = NO
 # The tag DOT_PATH can be used to specify the path where the dot tool can be
 # found. If left blank, it is assumed the dot tool can be found in the path.
 
-DOT_PATH               = /usr/bin
+DOT_PATH               = 
 
 # The DOTFILE_DIRS tag can be used to specify one or more directories that
 # contain dot files that are included in the documentation (see the

DoxygenLayout.xml

@@ -0,0 +1,189 @@
+<doxygenlayout version="1.0">
+  <!-- Generated by doxygen 1.8.8 -->
+  <!-- Navigation index tabs for HTML output -->
+  <navindex>
+    <tab type="mainpage" visible="yes" title=""/>
+    <tab type="pages" visible="yes" title="" intro=""/>
+    <tab type="modules" visible="yes" title="" intro=""/>
+    <tab type="namespaces" visible="yes" title="">
+      <tab type="namespacelist" visible="yes" title="" intro=""/>
+      <tab type="namespacemembers" visible="yes" title="" intro=""/>
+    </tab>
+    <tab type="classes" visible="yes" title="">
+      <tab type="classlist" visible="yes" title="" intro=""/>
+      <tab type="classindex" visible="$ALPHABETICAL_INDEX" title=""/> 
+      <tab type="hierarchy" visible="yes" title="" intro=""/>
+      <tab type="classmembers" visible="yes" title="" intro=""/>
+    </tab>
+    <tab type="files" visible="yes" title="">
+      <tab type="filelist" visible="yes" title="" intro=""/>
+      <tab type="globals" visible="yes" title="" intro=""/>
+    </tab>
+    <tab type="examples" visible="yes" title="" intro=""/>  
+  </navindex>
+
+  <!-- Layout definition for a class page -->
+  <class>
+    <detaileddescription title=""/>
+    <includes visible="$SHOW_INCLUDE_FILES"/>
+    <inheritancegraph visible="$CLASS_GRAPH"/>
+    <collaborationgraph visible="$COLLABORATION_GRAPH"/>
+    <memberdecl>
+      <nestedclasses visible="yes" title=""/>
+      <publictypes title=""/>
+      <services title=""/>
+      <interfaces title=""/>
+      <publicslots title=""/>
+      <signals title=""/>
+      <publicmethods title=""/>
+      <publicstaticmethods title=""/>
+      <publicattributes title=""/>
+      <publicstaticattributes title=""/>
+      <protectedtypes title=""/>
+      <protectedslots title=""/>
+      <protectedmethods title=""/>
+      <protectedstaticmethods title=""/>
+      <protectedattributes title=""/>
+      <protectedstaticattributes title=""/>
+      <packagetypes title=""/>
+      <packagemethods title=""/>
+      <packagestaticmethods title=""/>
+      <packageattributes title=""/>
+      <packagestaticattributes title=""/>
+      <properties title=""/>
+      <events title=""/>
+      <privatetypes title=""/>
+      <privateslots title=""/>
+      <privatemethods title=""/>
+      <privatestaticmethods title=""/>
+      <privateattributes title=""/>
+      <privatestaticattributes title=""/>
+      <friends title=""/>
+      <related title="" subtitle=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <memberdef>
+      <inlineclasses title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <services title=""/>
+      <interfaces title=""/>
+      <constructors title=""/>
+      <functions title=""/>
+      <related title=""/>
+      <variables title=""/>
+      <properties title=""/>
+      <events title=""/>
+    </memberdef>
+    <allmemberslink visible="yes"/>
+    <usedfiles visible="$SHOW_USED_FILES"/>
+    <authorsection visible="yes"/>
+  </class>
+
+  <!-- Layout definition for a namespace page -->
+  <namespace>
+    <detaileddescription title=""/>
+    <memberdecl>
+      <nestednamespaces visible="yes" title=""/>
+      <constantgroups visible="yes" title=""/>
+      <classes visible="yes" title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <memberdef>
+      <inlineclasses title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+    </memberdef>
+    <authorsection visible="yes"/>
+  </namespace>
+
+  <!-- Layout definition for a file page -->
+  <file>
+    <detaileddescription title=""/>
+    <includes visible="$SHOW_INCLUDE_FILES"/>
+    <includegraph visible="$INCLUDE_GRAPH"/>
+    <includedbygraph visible="$INCLUDED_BY_GRAPH"/>
+    <sourcelink visible="yes"/>
+    <memberdecl>
+      <classes visible="yes" title=""/>
+      <namespaces visible="yes" title=""/>
+      <constantgroups visible="yes" title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <memberdef>
+      <inlineclasses title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <functions title=""/>
+      <variables title=""/>
+    </memberdef>
+    <authorsection/>
+  </file>
+
+  <!-- Layout definition for a group page -->
+  <group>
+    <detaileddescription title=""/>
+    <groupgraph visible="$GROUP_GRAPHS"/>
+    <memberdecl>
+      <nestedgroups visible="yes" title=""/>
+      <dirs visible="yes" title=""/>
+      <files visible="yes" title=""/>
+      <namespaces visible="yes" title=""/>
+      <classes visible="yes" title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <enumvalues title=""/>
+      <functions title=""/>
+      <variables title=""/>
+      <signals title=""/>
+      <publicslots title=""/>
+      <protectedslots title=""/>
+      <privateslots title=""/>
+      <events title=""/>
+      <properties title=""/>
+      <friends title=""/>
+      <membergroups visible="yes"/>
+    </memberdecl>
+    <memberdef>
+      <pagedocs/>
+      <inlineclasses title=""/>
+      <defines title=""/>
+      <typedefs title=""/>
+      <enums title=""/>
+      <enumvalues title=""/>
+      <functions title=""/>
+      <variables title=""/>
+      <signals title=""/>
+      <publicslots title=""/>
+      <protectedslots title=""/>
+      <privateslots title=""/>
+      <events title=""/>
+      <properties title=""/>
+      <friends title=""/>
+    </memberdef>
+    <authorsection visible="yes"/>
+  </group>
+
+  <!-- Layout definition for a directory page -->
+  <directory>
+    <detaileddescription title=""/>
+    <directorygraph visible="yes"/>
+    <memberdecl>
+      <dirs visible="yes"/>
+      <files visible="yes"/>
+    </memberdecl>
+  </directory>
+</doxygenlayout>

build.sh

@@ -182,8 +182,9 @@ if ((verbose>3)); then
     exit
 fi
 
-cd "$build_root"
-
+# Doxygen should be run in the top level directory so it picks up
+# formatting files
+cd "$repo"
 if [ $build_docs ]; then
     log "Pre-build documentation processing ..."
     # Dynamically configure the Doxyfile with the source and destination paths
@@ -192,7 +193,8 @@ if [ $build_docs ]; then
         sources+=" $repo/ext/lib"
     fi
     log "Generating Doxygen files from C/C++ source ..."
-    sed -e "s#gpstk_sources#$sources#g" -e "s#gpstk_doc_dir#$build_root/doc#g" $repo/Doxyfile | doxygen - >"$build_root"/Doxygen.log
+    sed -e "s#^INPUT *=.*#INPUT = $sources#" -e "s#gpstk_sources#$sources#g" -e "s#gpstk_doc_dir#$build_root/doc#g" $repo/Doxyfile >$repo/doxyfoo
+    sed -e "s#^INPUT *=.*#INPUT = $sources#" -e "s#gpstk_sources#$sources#g" -e "s#gpstk_doc_dir#$build_root/doc#g" $repo/Doxyfile | doxygen - >"$build_root"/Doxygen.log
     tar -czf gpstk_doc_cpp.tgz -C doc/html .
 
     if [[ -z $exclude_python && $build_ext ]] ; then
@@ -201,6 +203,8 @@ if [ $build_docs ]; then
     fi
 fi
 
+cd "$build_root"
+
 # setup the cmake command
 args=$@
 if [ $exclude_python ]; then