PROJECT_NAME           = @CMAKE_PROJECT_NAME@
@INCLUDE               = Doxyfile-version
LAYOUT_FILE            = @CMAKE_CURRENT_SOURCE_DIR@/DoxygenLayout.xml
INPUT                  = @CMAKE_CURRENT_SOURCE_DIR@ \
                         @CMAKE_SOURCE_DIR@/src \
                         @CMAKE_SOURCE_DIR@/share/template
FILE_PATTERNS          = *.c *.cpp *.h *.md
# CUDA files could be included like this, but currently produce a lot of
# warnings.
# FILE_PATTERNS         += *.cu *.cuh
EXAMPLE_PATH           = @CMAKE_SOURCE_DIR@
RECURSIVE              = YES
EXCLUDE                = @CMAKE_CURRENT_SOURCE_DIR@/examples \
                         @CMAKE_SOURCE_DIR@/src/contrib \
                         @CMAKE_SOURCE_DIR@/src/external \
                         @CMAKE_SOURCE_DIR@/src/gromacs/selection/parser.cpp \
                         @CMAKE_SOURCE_DIR@/src/gromacs/selection/parser.h \
                         @CMAKE_SOURCE_DIR@/src/gromacs/selection/scanner.cpp @NB_KERNEL_DIRS_TO_IGNORE_IN_DOXYGEN@
EXCLUDE_SYMBOLS        = YY* yy* _gmx_sel_yy*
EXCLUDE_SYMBOLS       += __STDC*
EXCLUDE_SYMBOLS       += TEST TEST_F TEST_P TYPED_TEST_CASE TYPED_TEST INSTANTIATE_TEST_CASE_P
EXCLUDE_SYMBOLS       += MOCK_METHOD* MOCK_CONST_METHOD*
FULL_PATH_NAMES        = YES
STRIP_FROM_PATH        = @CMAKE_SOURCE_DIR@
STRIP_FROM_INC_PATH    = @CMAKE_SOURCE_DIR@/src
INCLUDE_PATH           = @CMAKE_SOURCE_DIR@/src
HAVE_DOT               = @DOXYGEN_DOT_FOUND@
DOT_PATH               = @DOXYGEN_DOT_PATH@
MSCGEN_PATH            = @DOXYGEN_MSCGEN_PATH@
DOTFILE_DIRS           = @DEPGRAPH_DIR@
@DOXYGEN_EXTRA_SETTINGS@

ENABLED_SECTIONS       = @DOXYGEN_SECTIONS@

MACRO_EXPANSION        = YES
# Extract documentation also for code in headers within #ifdef __cplusplus
PREDEFINED             = __cplusplus
# This is for cases where \cond does not work, so that #ifndef can also be used.
# thread_mpi also uses this, but it is now excluded from the documentation.
PREDEFINED            += DOXYGEN
# This makes 'static gmx_inline' functions appear better in the documentation.
PREDEFINED            += gmx_inline=inline
# This is for parser.cpp to make it produce code that Doxygen understands
# and that does not have unnecessary function declarations.
PREDEFINED            += __STDC__ YYMALLOC=malloc YYFREE=free

JAVADOC_AUTOBRIEF      = YES
BUILTIN_STL_SUPPORT    = YES
INLINE_INHERITED_MEMB  = YES
SORT_BY_SCOPE_NAME     = YES
ALPHABETICAL_INDEX     = YES
HTML_DYNAMIC_SECTIONS  = YES
GENERATE_LATEX         = NO
# Setting this to NO has a side effect to hide undocumented headers from the
# file list, which makes it generally look nicer.
VERBATIM_HEADERS       = NO
STRIP_CODE_COMMENTS    = NO

EXTRACT_LOCAL_CLASSES  = NO
# This includes 'static inline' functions from headers in the documentation.
EXTRACT_STATIC         = YES

ALIASES               += Gromacs=GROMACS

DOT_IMAGE_FORMAT       = svg
DOT_MULTI_TARGETS      = YES
# According to Doxygen docs, this is required for svg support on IE
HTML_FILE_EXTENSION    = .xhtml

OUTPUT_DIRECTORY       = @HTML_OUTPUT_DIR@/doxygen