Doxyfile

# Doxygen Configuration for CECE
# Generated for API documentation generation

PROJECT_NAME           = "CECE (Community Emissions Computing Engine)"
PROJECT_NUMBER         = "1.0"
PROJECT_BRIEF          = "High-performance emissions compute component for Earth System Models"
PROJECT_LOGO           =

OUTPUT_DIRECTORY       = ./docs/api
CREATE_SUBDIRS         = NO
ALLOW_UNICODE_NAMES    = YES

# Input files
INPUT                  = include/cece src/
INPUT_ENCODING         = UTF-8
FILE_PATTERNS          = *.hpp *.cpp *.h *.c
RECURSIVE              = YES

# Exclude patterns
EXCLUDE_PATTERNS       = */test* */.git* */build/*
EXCLUDE_SYMBOLS        = std::* boost::*

# Documentation options
EXTRACT_ALL            = NO
EXTRACT_PRIVATE        = NO
EXTRACT_PACKAGE        = NO
EXTRACT_STATIC         = YES
EXTRACT_LOCAL_CLASSES  = YES
EXTRACT_LOCAL_METHODS  = NO
EXTRACT_ANON_NSPCECE   = NO

# Build related options
CASE_SENSE_FILENAMES   = YES
HIDE_SCOPE_NAMES       = NO
HIDE_UNDOC_MEMBERS     = NO
HIDE_UNDOC_CLASSES     = NO
ALWAYS_DETAILED_SEC    = NO
INLINE_INHERITED_MEMB  = NO
INHERIT_DOCS           = YES
SEPARATE_MEMBER_PAGES  = NO
TAB_SIZE               = 4
ALIASES                =

# Output format
GENERATE_HTML          = YES
HTML_OUTPUT            = html
HTML_FILE_EXTENSION    = .html
HTML_HEADER            =
HTML_FOOTER            =
HTML_STYLESHEET        =
HTML_EXTRA_STYLESHEET  =
HTML_COLORSTYLE_HUE    = 220
HTML_COLORSTYLE_SAT    = 100
HTML_COLORSTYLE_GAMMA  = 80
HTML_TIMESTAMP         = YES
HTML_DYNAMIC_SECTIONS  = NO
HTML_INDEX_NUM_ENTRIES = 100

GENERATE_DOCSET        = NO
GENERATE_HTMLHELP      = NO
GENERATE_CHI           = NO
GENERATE_QHP           = NO
GENERATE_ECLIPSEHELP   = NO
GENERATE_LATEX         = NO
GENERATE_RTF           = NO
GENERATE_MAN           = NO
GENERATE_XML           = NO
GENERATE_DOCBOOK       = NO
GENERATE_AUTOGEN_DEF   = NO

# Diagram generation
HAVE_DOT               = YES
DOT_NUM_THREADS        = 4
DOT_FONTNAME           = Helvetica
DOT_FONTSIZE           = 10
DOT_GRAPH_MAX_NODES    = 50
MSCGEN_PATH            =
DIA_PATH               =

# Graph options
CLASS_GRAPH            = YES
COLLABORATION_GRAPH    = YES
GROUP_GRAPHS           = YES
UML_LOOK               = NO
UML_LIMIT_NUM_FIELDS   = 10
TEMPLATE_RELATIONS     = NO
INCLUDE_GRAPH          = YES
INCLUDED_BY_GRAPH      = YES
CALL_GRAPH             = YES
CALLER_GRAPH           = NO
GRAPHICAL_HIERARCHY    = YES
DIRECTORY_GRAPH        = YES
DOT_IMAGE_FORMAT       = png
INTERACTIVE_SVG        = NO
DOT_PATH               =
DOTFILE_DIRS           =
MSCFILE_DIRS           =

# Search engine
SEARCHENGINE           = YES
SERVER_BASED_SEARCH    = NO

# Preprocessing
ENABLE_PREPROCESSING   = YES
MACRO_EXPANSION        = NO
EXPAND_ONLY_PREDEF     = NO
SEARCH_INCLUDES        = YES
INCLUDE_PATH           = include/cece
INCLUDE_FILE_PATTERNS  = *.h *.hpp
PREDEFINED             = KOKKOS_LAMBDA=[] KOKKOS_FUNCTION= KOKKOS_INLINE_FUNCTION=inline
EXPAND_AS_DEFINED      =
SKIP_FUNCTION_MACROS   = YES

# Source browsing
SOURCE_BROWSER         = YES
INLINE_SOURCES         = NO
STRIP_CODE_COMMENTS    = NO
REFERENCED_BY_RELATION = NO
REFERENCES_RELATION    = NO
REFERENCES_LINK_SOURCE = YES
SOURCE_TOOLTIPS        = YES
USE_HTAGS              = NO
VERBATIM_HEADERS       = YES

# Index
GENERATE_TREEVIEW      = YES
TREEVIEW_WIDTH         = 250
EXT_LINKS_IN_WINDOW    = NO
FORMULA_FONTSIZE       = 10
FORMULA_TRANSPARENT    = YES
USE_MATHJAX            = NO
MATHJAX_FORMAT         = HTML-CSS
MATHJAX_RELPATH        = https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/
MATHJAX_EXTENSIONS    = TeX/AMSmath TeX/AMSsymbols
MATHJAX_CODEFILE       =

# LaTeX output
LATEX_OUTPUT           = latex
LATEX_CMD_NAME         = latex
MAKEINDEX_CMD_NAME     = makeindex
LATEX_MAKEINDEX_CMD    = makeindex
COMPACT_LATEX          = NO
LATEX_HYPERLINK        = YES
PDF_HYPERLINKS         = YES
USE_PDFLATEX           = YES
LATEX_BATCHMODE        = NO
LATEX_HIDE_INDICES     = NO
LATEX_SOURCE_CODE      = NO
LATEX_BIB_STYLE        = plain

# RTF output
RTF_OUTPUT             = rtf
COMPACT_RTF            = NO
RTF_HYPERLINKS         = NO
RTF_STYLESHEET_FILE    =
RTF_EXTENSIONS_FILE    =

# Man page output
MAN_OUTPUT             = man
MAN_EXTENSION          = .3
MAN_SUBDIR             =
MAN_LINKS              = NO

# XML output
XML_OUTPUT             = xml
XML_SCHEMA             =
XML_DTD                =
XML_PROGRAMLISTING     = YES

# Docbook output
DOCBOOK_OUTPUT         = docbook
DOCBOOK_PROGRAMLISTING = NO

# AutoGen definitions
GENERATE_AUTOGEN_DEF   = NO

# Perl module output
GENERATE_PERLMOD       = NO
PERLMOD_LATEX          = NO
PERLMOD_PRETTY         = YES
PERLMOD_MAKEVAR_PREFIX =

# Messaging
QUIET                  = NO
WARNINGS               = YES
WARN_IF_UNDOCUMENTED   = YES
WARN_IF_DOC_LACKED     = YES
WARN_NO_PARAMDOC       = NO
WARN_AS_ERROR          = NO
WARN_FORMAT            = "$file:$line: $text"
WARN_LOGFILE           =

# Filtering
FILTER_PATTERNS        =
FILTER_SOURCE_FILES    = NO
FILTER_SOURCE_PATTERNS =

# Custom commands
ALIASES                =

# Sorting
SORT_MEMBER_DOCS       = YES
SORT_BRIEF_DOCS        = NO
SORT_MEMBERS_CTORS_1ST = NO
SORT_GROUP_NAMES       = NO
SORT_BY_SCOPE_NAME     = NO

# Misc options
GENERATE_BUGLIST       = YES
GENERATE_DEPRECATEDLIST= YES
GENERATE_TODOLIST      = YES
GENERATE_TESTLIST      = YES
GENERATE_BUGLIST       = YES
MAX_INITIALIZERS       = 30
SHOW_USED_FILES        = YES
SHOW_FILES             = YES
SHOW_NAMESPCECE        = YES
FILE_VERSION_FILTER    =

# Configuration options related to the alphabetical index
ALPHABETICAL_INDEX     = YES
COLS_IN_ALPHA_INDEX    = 5
IGNORE_PREFIX          =

# Configuration options related to the HTML output
HTML_DYNAMIC_SECTIONS  = NO
CHM_FILE               =
HHC_LOCATION           =
GENERATE_CHI           = NO
CHM_INDEX_ENCODING     =
BINARY_TOC             = NO
TOC_EXPAND             = NO
DISABLE_INDEX          = NO
ENUM_VALUES_PER_LINE   = 4
TREEVIEW_WIDTH         = 250
EXT_LINKS_IN_WINDOW    = NO
FORMULA_FONTSIZE       = 10
FORMULA_TRANSPARENT    = YES
USE_MATHJAX            = NO
SEARCHENGINE           = YES
SERVER_BASED_SEARCH    = NO
EXTERNAL_SEARCH        = NO
EXTERNAL_SEARCH_ID     =
EXTRA_SEARCH_MAPPINGS  =