#
# Note: all relative paths are relative to package/doc!
#
@INCLUDE_PATH          = $(TRILINOS_HOME)/packages
@INCLUDE=common/Doxyfile
@INCLUDE=thyra/doc/TagFiles # Requires @INCLUDE_PAH=$(TRILINOS_HOME)/packages
TAGFILES += \
  $(TRILINOS_HOME)/packages/common/tag_files/epetra.tag=$(TRILINOS_HOME)/packages/epetra/doc/html \
  $(TRILINOS_HOME)/packages/common/tag_files/EpetraThyra.tag=$(TRILINOS_HOME)/packages/epetra/thyra/doc/html \
  $(TRILINOS_HOME)/packages/common/tag_files/epetraext.tag=$(TRILINOS_HOME)/packages/epetraext/doc/html \
  $(TRILINOS_HOME)/packages/common/tag_files/EpetraExtThyra.tag=$(TRILINOS_HOME)/packages/epetraext/thyra/doc/html \
  $(TRILINOS_HOME)/packages/common/tag_files/stratimikos.tag=$(TRILINOS_HOME)/packages/stratimikos/doc/html \
  $(TRILINOS_HOME)/packages/common/tag_files/nox.tag=$(TRILINOS_HOME)/packages/nox/doc/html \
  $(TRILINOS_HOME)/packages/common/tag_files/MoochoUtilities.tag=$(TRILINOS_HOME)/packages/moocho/src/MoochoUtilities/doc/html \
  $(TRILINOS_HOME)/packages/common/tag_files/IterationPack.tag=$(TRILINOS_HOME)/packages/moocho/src/IterationPack/doc/html \
  $(TRILINOS_HOME)/packages/common/tag_files/RTOpPack.tag=$(TRILINOS_HOME)/packages/moocho/src/RTOpPack/doc/html \
  $(TRILINOS_HOME)/packages/common/tag_files/DenseLinAlgPack.tag=$(TRILINOS_HOME)/packages/moocho/src/DenseLinAlgPack/doc/html \
  $(TRILINOS_HOME)/packages/common/tag_files/AbstractLinAlgPack.tag=$(TRILINOS_HOME)/packages/moocho/src/AbstractLinAlgPack/doc/html \
  $(TRILINOS_HOME)/packages/common/tag_files/NLPInterfacePack.tag=$(TRILINOS_HOME)/packages/moocho/src/NLPInterfacePack/doc/html \
  $(TRILINOS_HOME)/packages/common/tag_files/ConstrainedOptPack.tag=$(TRILINOS_HOME)/packages/moocho/src/ConstrainedOptPack/doc/html \
  $(TRILINOS_HOME)/packages/common/tag_files/MoochoPack.tag=$(TRILINOS_HOME)/packages/moocho/src/MoochoPack/doc/html
#
# Package options
#
PROJECT_NAME           = "Rythmos - Transient Integration for Differential Equations"
PROJECT_NUMBER         = "Version of the Day"
OUTPUT_DIRECTORY       = .
OUTPUT_LANGUAGE        = English


#
# What and how documentation is extracted
#
EXTRACT_ALL            = YES
#EXTRACT_ALL            = NO
EXTRACT_PRIVATE        = YES
EXTRACT_STATIC         = YES
HIDE_UNDOC_MEMBERS     = YES
HIDE_UNDOC_CLASSES     = YES
BRIEF_MEMBER_DESC      = YES
REPEAT_BRIEF           = YES
ALWAYS_DETAILED_SEC    = YES
FULL_PATH_NAMES        = NO
STRIP_FROM_PATH        = 
INTERNAL_DOCS          = NO
CLASS_DIAGRAMS         = YES
SOURCE_BROWSER         = YES
INLINE_SOURCES         = NO
STRIP_CODE_COMMENTS    = YES
REFERENCED_BY_RELATION = NO
REFERENCES_RELATION    = NO
CASE_SENSE_NAMES       = YES
HIDE_SCOPE_NAMES       = NO
VERBATIM_HEADERS       = YES
SHOW_INCLUDE_FILES     = YES
#JAVADOC_AUTOBRIEF      = YES
INHERIT_DOCS           = YES
INLINE_INFO            = YES
SORT_MEMBER_DOCS       = NO
TAB_SIZE               = 2
ENABLED_SECTIONS       = 
GENERATE_TODOLIST      = YES
GENERATE_TESTLIST      = YES
QUIET                  = NO
WARNINGS               = YES
WARN_IF_UNDOCUMENTED   = YES
WARN_FORMAT            = "$file:$line: $text"
INPUT                  = index.doc \
                         ../src \
                         ../example/diagonalTransient/diagonalTransientMain.cpp \
                         ../../epetraext/example/model_evaluator/DiagonalTransient/EpetraExt_DiagonalTransientModel.hpp \
                         ../../epetraext/example/model_evaluator/DiagonalTransient/EpetraExt_DiagonalTransientModel.cpp
#                         ../example/epetra/1Dfem/ExampleApplication1Dfem.hpp \
#                         ../example/epetra/1Dfem/ExampleApplication1Dfem.cpp \
#                         ../example/epetra/1Dfem/1DfemInterface.H \
#                         ../example/epetra/1Dfem/1DfemInterface.C \
#                         ../example/epetra/1Dfem/1DfemTransient.H \
#                         ../example/epetra/1Dfem/cxx_main.cpp 
FILE_PATTERNS          = *.hpp *.cpp
RECURSIVE              = YES
EXCLUDE                = 
EXCLUDE_PATTERNS       = *.x *.o *.out
EXAMPLE_PATH           =  ../example/basicExample
EXAMPLE_PATTERNS       = *.cpp *.hpp
IMAGE_PATH             = 
INPUT_FILTER           = 
ALPHABETICAL_INDEX     = YES
COLS_IN_ALPHA_INDEX    = 4
IGNORE_PREFIX          = 
#
# What diagrams are created
#
CLASS_GRAPH            = YES
COLLABORATION_GRAPH    = YES
INCLUDE_GRAPH          = YES
INCLUDED_BY_GRAPH      = YES
GRAPHICAL_HIERARCHY    = YES
#
# Preprocessing
#
ENABLE_PREPROCESSING   = YES
MACRO_EXPANSION        = YES
EXPAND_ONLY_PREDEF     = YES
SEARCH_INCLUDES        = YES
INCLUDE_FILE_PATTERNS  = 
PREDEFINED             = DOXYGEN_COMPILE DOXYGEN_SHOULD_SKIP_THIS EPETRA_MPI
INCLUDE_PATH           = ../../teuchos/src
EXPAND_AS_DEFINED      = STANDARD_MEMBER_COMPOSITION_MEMBERS
#
GENERATE_TAGFILE       = ../../common/tag_files/rythmos.tag
ALLEXTERNALS           = NO
EXTERNAL_GROUPS        = NO
#
# Environment
#
PERL_PATH              = /usr/bin/perl
HAVE_DOT               = YES
DOT_PATH               = 
MAX_DOT_GRAPH_WIDTH    = 1024
MAX_DOT_GRAPH_HEIGHT   = 1024
#
# What kind of documentation is generated
#
GENERATE_HTML          = YES
GENERATE_HTMLHELP      = NO
DISABLE_INDEX          = NO
GENERATE_LATEX         = NO
GENERATE_RTF           = NO
GENERATE_MAN           = NO
GENERATE_XML           = NO



#
# Taken from Thyra Doxyfile.options
#

# 2007/06/09: rabartl: ToDo: I need to clean these option up!



#
# What and how documentation is extracted
#
SUBGROUPING            = NO
EXTRACT_ALL            = NO
EXTRACT_PRIVATE        = NO
EXTRACT_STATIC         = YES
EXTRACT_LOCAL_CLASSES  = NO
HIDE_UNDOC_MEMBERS     = YES
HIDE_UNDOC_CLASSES     = YES
BRIEF_MEMBER_DESC      = YES
REPEAT_BRIEF           = YES
ALWAYS_DETAILED_SEC    = YES
#DETAILS_AT_TOP         = YES
DETAILS_AT_TOP         = NO
FULL_PATH_NAMES        = NO
STRIP_FROM_PATH        = 
SHOW_DIRECTORIES       = YES
INTERNAL_DOCS          = NO
CLASS_DIAGRAMS         = YES
SOURCE_BROWSER         = YES
INLINE_SOURCES         = NO
STRIP_CODE_COMMENTS    = YES
REFERENCED_BY_RELATION = NO
REFERENCES_RELATION    = NO
CASE_SENSE_NAMES       = YES
HIDE_SCOPE_NAMES       = NO
VERBATIM_HEADERS       = YES
SHOW_INCLUDE_FILES     = YES
JAVADOC_AUTOBRIEF      = NO
INHERIT_DOCS           = YES
INLINE_INFO            = YES
SORT_MEMBER_DOCS       = NO
TAB_SIZE               = 2
ENABLED_SECTIONS       = 
GENERATE_TODOLIST      = YES
GENERATE_TESTLIST      = YES
QUIET                  = NO
WARNINGS               = YES
WARN_IF_UNDOCUMENTED   = YES
WARN_FORMAT            = "$file:$line: $text"
ALPHABETICAL_INDEX     = YES
COLS_IN_ALPHA_INDEX    = 4
#
# What diagrams are created
#
CLASS_GRAPH            = YES
COLLABORATION_GRAPH    = NO
INCLUDE_GRAPH          = YES
INCLUDED_BY_GRAPH      = YES
GRAPHICAL_HIERARCHY    = YES
#UML_LOOK               = YES
TEMPLATE_RELATIONS     = YES
#TEMPLATE_RELATIONS     = NO
#MAX_DOT_GRAPH_WIDTH    = 500
HIDE_UNDOC_RELATIONS   = YES
#
# Preprocessing
#
ENABLE_PREPROCESSING   = YES
MACRO_EXPANSION        = YES
EXPAND_ONLY_PREDEF     = YES
SEARCH_INCLUDES        = YES
INCLUDE_FILE_PATTERNS  = 
PREDEFINED             += DOXYGEN_COMPILE EPETRA_MPI __sun
INCLUDE_PATH           += ../../../../Trilinos/packages/teuchos/src
EXPAND_AS_DEFINED      += STANDARD_MEMBER_COMPOSITION_MEMBERS STANDARD_COMPOSITION_MEMBERS \
                         STANDARD_NONCONST_COMPOSITION_MEMBERS STANDARD_CONST_COMPOSITION_MEMBERS
#
# What kind of documentation is generated
#
GENERATE_HTMLHELP      = NO
DISABLE_INDEX          = NO
GENERATE_LATEX         = NO
GENERATE_RTF           = NO
GENERATE_MAN           = NO
GENERATE_XML           = NO
