From 73477cd50d839851e74538f33c3790f79269bae9 Mon Sep 17 00:00:00 2001 From: "ligia.bernardet" Date: Sun, 1 Sep 2019 16:19:11 -0600 Subject: [PATCH 1/3] Added file ccpp_doxyfile, which is a new doxygen configuration file identical to ccppv3_doxyfile, except that it is not specific to the V3 release and contains information about where to find the HTML files containing the metadata tables created from the .meta files (new metadata format). --- physics/docs/ccpp_doxyfile | 441 +++++++++++++++++++++++++++++++++++++ 1 file changed, 441 insertions(+) create mode 100644 physics/docs/ccpp_doxyfile diff --git a/physics/docs/ccpp_doxyfile b/physics/docs/ccpp_doxyfile new file mode 100644 index 000000000..1a11e9e99 --- /dev/null +++ b/physics/docs/ccpp_doxyfile @@ -0,0 +1,441 @@ +# Doxyfile 1.8.11 +DOXYFILE_ENCODING = UTF-8 +PROJECT_NAME = "Common Community Physics Package (CCPP) Scientific Documentation" +PROJECT_NUMBER = "Version 3.0" +PROJECT_BRIEF = " " +PROJECT_LOGO = img/dtc_logo.png +OUTPUT_DIRECTORY = doc +CREATE_SUBDIRS = NO +ALLOW_UNICODE_NAMES = NO +OUTPUT_LANGUAGE = English +BRIEF_MEMBER_DESC = YES +REPEAT_BRIEF = NO +ABBREVIATE_BRIEF = +ALWAYS_DETAILED_SEC = NO +INLINE_INHERITED_MEMB = NO +FULL_PATH_NAMES = NO +STRIP_FROM_PATH = +STRIP_FROM_INC_PATH = +SHORT_NAMES = NO +JAVADOC_AUTOBRIEF = NO +QT_AUTOBRIEF = NO +MULTILINE_CPP_IS_BRIEF = NO +INHERIT_DOCS = YES +SEPARATE_MEMBER_PAGES = YES +TAB_SIZE = 4 +ALIASES = +TCL_SUBST = +OPTIMIZE_OUTPUT_FOR_C = NO +OPTIMIZE_OUTPUT_JAVA = NO +OPTIMIZE_FOR_FORTRAN = YES +OPTIMIZE_OUTPUT_VHDL = NO +EXTENSION_MAPPING = .f=FortranFree \ + .F90=FortranFree \ + .f90=FortranFree +MARKDOWN_SUPPORT = YES +AUTOLINK_SUPPORT = YES +BUILTIN_STL_SUPPORT = NO +CPP_CLI_SUPPORT = NO +SIP_SUPPORT = NO +IDL_PROPERTY_SUPPORT = YES +DISTRIBUTE_GROUP_DOC = YES +GROUP_NESTED_COMPOUNDS = NO +SUBGROUPING = YES +INLINE_GROUPED_CLASSES = NO +INLINE_SIMPLE_STRUCTS = NO +TYPEDEF_HIDES_STRUCT = YES +LOOKUP_CACHE_SIZE = 0 +EXTRACT_ALL = YES +EXTRACT_PRIVATE = YES +EXTRACT_PACKAGE = YES +EXTRACT_STATIC = YES +EXTRACT_LOCAL_CLASSES = YES +EXTRACT_LOCAL_METHODS = YES +EXTRACT_ANON_NSPACES = YES +HIDE_UNDOC_MEMBERS = NO +HIDE_UNDOC_CLASSES = NO +HIDE_FRIEND_COMPOUNDS = NO +HIDE_IN_BODY_DOCS = NO +INTERNAL_DOCS = YES + +CASE_SENSE_NAMES = NO + +HIDE_SCOPE_NAMES = NO + +HIDE_COMPOUND_REFERENCE= NO + +SHOW_INCLUDE_FILES = NO + +SHOW_GROUPED_MEMB_INC = NO + +FORCE_LOCAL_INCLUDES = NO + +INLINE_INFO = YES + +SORT_MEMBER_DOCS = NO + +SORT_BRIEF_DOCS = NO +SORT_MEMBERS_CTORS_1ST = NO +SORT_GROUP_NAMES = NO +SORT_BY_SCOPE_NAME = NO +STRICT_PROTO_MATCHING = NO +GENERATE_TODOLIST = YES +GENERATE_TESTLIST = YES +GENERATE_BUGLIST = YES +GENERATE_DEPRECATEDLIST= YES +ENABLED_SECTIONS = YES +MAX_INITIALIZER_LINES = 30 +SHOW_USED_FILES = YES +SHOW_FILES = YES +SHOW_NAMESPACES = YES +FILE_VERSION_FILTER = +LAYOUT_FILE = ccpp_dox_layout.xml +CITE_BIB_FILES = library.bib +QUIET = NO +WARNINGS = YES +WARN_IF_UNDOCUMENTED = NO +WARN_IF_DOC_ERROR = YES +WARN_NO_PARAMDOC = NO +WARN_AS_ERROR = NO +WARN_FORMAT = +WARN_LOGFILE = +INPUT = pdftxt/mainpage.txt \ + pdftxt/all_shemes_list.txt \ + pdftxt/GFSv15_suite.txt \ + pdftxt/GFSv15_suite_TKEEDMF.txt \ + pdftxt/CPT_adv_suite.txt \ + pdftxt/GSD_adv_suite.txt \ + pdftxt/GFS_RRTMG.txt \ + pdftxt/GFS_SFCLYR.txt \ + pdftxt/GFS_NSST.txt \ + pdftxt/GFS_NOAH.txt \ + pdftxt/GFS_SFCSICE.txt \ + pdftxt/GFS_HEDMF.txt \ + pdftxt/GFS_SATMEDMF.txt \ + pdftxt/GFS_GWDPS.txt \ + pdftxt/GFS_OZPHYS.txt \ + pdftxt/GFS_H2OPHYS.txt \ + pdftxt/GFS_RAYLEIGH.txt \ + pdftxt/GFS_SAMF.txt \ + pdftxt/GFS_SAMFdeep.txt \ + pdftxt/GFS_GWDC.txt \ + pdftxt/GFS_SAMFshal.txt \ + pdftxt/GFDL_cloud.txt \ +### pdftxt/GFS_SURFACE_PERT.txt \ + pdftxt/GFS_CALPRECIPTYPE.txt \ +### pdftxt/rad_cld.txt \ + pdftxt/CPT_CSAW.txt \ + pdftxt/CPT_MG3.txt \ + pdftxt/GSD_MYNN_EDMF.txt \ + pdftxt/GSD_CU_GF_deep.txt \ + pdftxt/GSD_RUCLSM.txt \ + pdftxt/GSD_THOMPSON.txt \ +### pdftxt/GFSphys_namelist.txt \ +### pdftxt/GFS_STOCHY_PHYS.txt \ + pdftxt/suite_input.nml.txt \ +### in-core MP + ../gfdl_fv_sat_adj.F90 \ +### time_vary + ../GFS_phys_time_vary.fv3.F90 \ + ../GFS_rad_time_vary.fv3.F90 \ + ../ozne_def.f \ + ../ozinterp.f90 \ + ../h2o_def.f \ + ../h2ointerp.f90 \ + ../aerclm_def.F \ + ../aerinterp.F90 \ + ../iccn_def.F \ + ../iccninterp.F90 \ + ../sfcsub.F \ + ../gcycle.F90 \ +### Radiation + ../radlw_main.f \ + ../radsw_main.f \ + ../radiation_aerosols.f \ + ../radiation_astronomy.f \ + ../radiation_clouds.f \ + ../radiation_gases.f \ + ../radiation_surface.f \ + ../radlw_param.f \ + ../radlw_datatb.f \ + ../radsw_param.f \ + ../radsw_datatb.f \ + ../dcyc2.f \ +### Land Surface + ../sfc_diff.f \ + ../sfc_nst.f \ + ../module_nst_model.f90 \ + ../module_nst_parameters.f90 \ + ../module_nst_water_prop.f90 \ + ../sfc_drv.f \ + ../sflx.f \ + ../namelist_soilveg.f \ + ../set_soilveg.f \ +### Sea Ice Surface + ../sfc_sice.f \ +### PBL + ../moninedmf.f \ + ../mfpbl.f \ + ../tridi.f \ +### satmedmf + ../satmedmfvdif.F \ + ../mfpblt.f \ + ../mfscu.f \ + ../tridi.f \ +### Orographic Gravity Wave + ../gwdps.f \ +### Rayleigh Dampling + ../rayleigh_damp.f \ +### Prognostic Ozone + ../ozphys_2015.f \ +### ../ozphys.f \ +### stratospheric h2o + ../h2ophys.f \ +### Deep Convection + ../samfdeepcnv.f \ +### Convective Gravity Wave + ../gwdc.f \ +### Shallow Convection + ../samfshalcnv.f \ + ../cnvc90.f \ +### Microphysics +### ../gscond.f \ +### ../precpd.f \ + ../module_bfmicrophysics.f \ +### GFDL cloud MP + ../gfdl_cloud_microphys.F90 \ + ../module_gfdl_cloud_microphys.F90 \ +### + ../GFS_MP_generic.F90 \ + ../calpreciptype.f90 \ +### stochy +### ../GFS_stochastics.F90 \ +### ../surface_perturbation.F90 \ +### ../../stochastic_physics/stochastic_physics.F90 \ +### CPT + ../m_micro.F90 \ +### ../micro_mg2_0.F90 \ + ../micro_mg3_0.F90 \ + ../micro_mg_utils.F90 \ + ../cldmacro.F \ + ../aer_cloud.F \ + ../cldwat2m_micro.F \ + ../wv_saturation.F \ + ../cs_conv_aw_adj.F90 \ + ../cs_conv.F90 \ +### GSD + ../cu_gf_driver.F90 \ + ../cu_gf_deep.F90 \ + ../cu_gf_sh.F90 \ + ../module_MYNNrad_pre.F90 \ + ../module_MYNNrad_post.F90 \ + ../module_MYNNPBL_wrapper.F90 \ + ../module_bl_mynn.F90 \ +### ../module_MYNNSFC_wrapper.F90 \ +### ../module_sf_mynn.F90 \ + ../sfc_drv_ruc.F90 \ + ../module_sf_ruclsm.F90 \ + ../namelist_soilveg_ruc.F90 \ + ../set_soilveg_ruc.F90 \ + ../module_soil_pre.F90 \ + ../mp_thompson_pre.F90 \ + ../module_mp_thompson_make_number_concentrations.F90 \ + ../mp_thompson.F90 \ + ../module_mp_thompson.F90 \ + ../module_mp_radar.F90 \ + ../mp_thompson_post.F90 \ +### utils + ../funcphys.f90 \ + ../physparam.f \ + ../physcons.F90 \ + ../radcons.f90 \ + ../mersenne_twister.f \ + compns_stochy.F90 + + +INPUT_ENCODING = UTF-8 +FILE_PATTERNS = *.f \ + *.F90 \ + *.f90 \ + *.nml \ + *.txt +RECURSIVE = YES +EXCLUDE = +EXCLUDE_SYMLINKS = NO +EXCLUDE_PATTERNS = +EXCLUDE_SYMBOLS = +EXAMPLE_PATH = ./ +EXAMPLE_PATTERNS = +EXAMPLE_RECURSIVE = NO +IMAGE_PATH = img +INPUT_FILTER = +FILTER_PATTERNS = +FILTER_SOURCE_FILES = NO +FILTER_SOURCE_PATTERNS = +USE_MDFILE_AS_MAINPAGE = +SOURCE_BROWSER = NO +INLINE_SOURCES = NO +STRIP_CODE_COMMENTS = YES +REFERENCED_BY_RELATION = YES +REFERENCES_RELATION = YES +REFERENCES_LINK_SOURCE = YES +SOURCE_TOOLTIPS = YES +USE_HTAGS = NO +VERBATIM_HEADERS = YES +#CLANG_ASSISTED_PARSING = NO +#CLANG_OPTIONS = +ALPHABETICAL_INDEX = NO +COLS_IN_ALPHA_INDEX = 5 +IGNORE_PREFIX = +GENERATE_HTML = YES +HTML_OUTPUT = html +HTML_FILE_EXTENSION = .html +HTML_HEADER = +HTML_FOOTER = +HTML_STYLESHEET = +HTML_EXTRA_STYLESHEET = ccpp_dox_extra_style.css +HTML_EXTRA_FILES = +HTML_COLORSTYLE_HUE = 220 +HTML_COLORSTYLE_SAT = 100 +HTML_COLORSTYLE_GAMMA = 80 +HTML_TIMESTAMP = NO +HTML_DYNAMIC_SECTIONS = NO +HTML_INDEX_NUM_ENTRIES = 100 +GENERATE_DOCSET = NO +DOCSET_FEEDNAME = "Doxygen generated docs" +DOCSET_BUNDLE_ID = org.doxygen.Project +DOCSET_PUBLISHER_ID = org.doxygen.Publisher +DOCSET_PUBLISHER_NAME = Publisher +GENERATE_HTMLHELP = NO +CHM_FILE = +HHC_LOCATION = +GENERATE_CHI = NO +CHM_INDEX_ENCODING = +BINARY_TOC = NO +TOC_EXPAND = NO +GENERATE_QHP = NO +QCH_FILE = +QHP_NAMESPACE = org.doxygen.Project +QHP_VIRTUAL_FOLDER = doc +QHP_CUST_FILTER_NAME = +QHP_CUST_FILTER_ATTRS = +QHP_SECT_FILTER_ATTRS = +QHG_LOCATION = +GENERATE_ECLIPSEHELP = NO +ECLIPSE_DOC_ID = org.doxygen.Project +DISABLE_INDEX = YES +GENERATE_TREEVIEW = YES +ENUM_VALUES_PER_LINE = 4 +TREEVIEW_WIDTH = 250 +EXT_LINKS_IN_WINDOW = NO +FORMULA_FONTSIZE = 10 +FORMULA_TRANSPARENT = YES +USE_MATHJAX = YES +MATHJAX_FORMAT = HTML-CSS +MATHJAX_RELPATH = https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.2 +MATHJAX_EXTENSIONS = +MATHJAX_CODEFILE = +SEARCHENGINE = YES +SERVER_BASED_SEARCH = NO +EXTERNAL_SEARCH = NO +SEARCHENGINE_URL = +SEARCHDATA_FILE = searchdata.xml +EXTERNAL_SEARCH_ID = +EXTRA_SEARCH_MAPPINGS = +GENERATE_LATEX = YES +LATEX_OUTPUT = latex +LATEX_CMD_NAME = latex +MAKEINDEX_CMD_NAME = makeindex +COMPACT_LATEX = YES +PAPER_TYPE = a4 +EXTRA_PACKAGES = amsmath +LATEX_HEADER = +LATEX_FOOTER = +LATEX_EXTRA_STYLESHEET = +LATEX_EXTRA_FILES = +PDF_HYPERLINKS = YES +USE_PDFLATEX = YES +LATEX_BATCHMODE = NO +LATEX_HIDE_INDICES = YES +LATEX_SOURCE_CODE = NO + +LATEX_BIB_STYLE = plainnat + +LATEX_TIMESTAMP = NO + +GENERATE_RTF = NO + +RTF_OUTPUT = rtf +COMPACT_RTF = NO +RTF_HYPERLINKS = NO +RTF_STYLESHEET_FILE = +RTF_EXTENSIONS_FILE = +RTF_SOURCE_CODE = NO +GENERATE_MAN = NO +MAN_OUTPUT = man +MAN_EXTENSION = .3 +MAN_SUBDIR = +MAN_LINKS = NO +GENERATE_XML = NO +XML_OUTPUT = xml +XML_PROGRAMLISTING = YES +GENERATE_DOCBOOK = NO +DOCBOOK_OUTPUT = docbook +DOCBOOK_PROGRAMLISTING = NO +GENERATE_AUTOGEN_DEF = NO +GENERATE_PERLMOD = NO +PERLMOD_LATEX = NO +PERLMOD_PRETTY = YES +PERLMOD_MAKEVAR_PREFIX = +ENABLE_PREPROCESSING = NO +MACRO_EXPANSION = NO +EXPAND_ONLY_PREDEF = NO +SEARCH_INCLUDES = YES +INCLUDE_PATH = +INCLUDE_FILE_PATTERNS = +PREDEFINED = CCPP \ + MULTI_GASES \ + 0 +EXPAND_AS_DEFINED = +SKIP_FUNCTION_MACROS = YES +TAGFILES = +GENERATE_TAGFILE = +ALLEXTERNALS = NO +EXTERNAL_GROUPS = YES +EXTERNAL_PAGES = YES +PERL_PATH = /usr/bin/perl +CLASS_DIAGRAMS = YES +MSCGEN_PATH = +DIA_PATH = +HIDE_UNDOC_RELATIONS = NO +HAVE_DOT = YES +DOT_NUM_THREADS = 0 +DOT_FONTNAME = Helvetica +DOT_FONTSIZE = 10 +DOT_FONTPATH = +CLASS_GRAPH = NO +COLLABORATION_GRAPH = NO +GROUP_GRAPHS = YES +UML_LOOK = YES +UML_LIMIT_NUM_FIELDS = 10 +TEMPLATE_RELATIONS = NO +INCLUDE_GRAPH = YES +INCLUDED_BY_GRAPH = NO +CALL_GRAPH = YES +CALLER_GRAPH = NO +GRAPHICAL_HIERARCHY = YES +DIRECTORY_GRAPH = YES +DOT_IMAGE_FORMAT = svg +INTERACTIVE_SVG = NO +DOT_PATH = +DOTFILE_DIRS = +MSCFILE_DIRS = +DIAFILE_DIRS = +PLANTUML_JAR_PATH = +PLANTUML_INCLUDE_PATH = +DOT_GRAPH_MAX_NODES = 200 +MAX_DOT_GRAPH_DEPTH = 0 +DOT_TRANSPARENT = NO +DOT_MULTI_TARGETS = YES +GENERATE_LEGEND = YES +DOT_CLEANUP = YES From cd8f28091aa5206dc3ab9b3ebe0a3ffdbc3f52a9 Mon Sep 17 00:00:00 2001 From: "ligia.bernardet" Date: Wed, 4 Sep 2019 10:53:33 -0600 Subject: [PATCH 2/3] Address reviewer comment regarding patterns for files that need to be documented (added .F). Remove mention of V3 release so documentation is generic. --- physics/docs/ccpp_doxyfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/physics/docs/ccpp_doxyfile b/physics/docs/ccpp_doxyfile index 1a11e9e99..351dc022f 100644 --- a/physics/docs/ccpp_doxyfile +++ b/physics/docs/ccpp_doxyfile @@ -1,7 +1,7 @@ # Doxyfile 1.8.11 DOXYFILE_ENCODING = UTF-8 PROJECT_NAME = "Common Community Physics Package (CCPP) Scientific Documentation" -PROJECT_NUMBER = "Version 3.0" +PROJECT_NUMBER = "" PROJECT_BRIEF = " " PROJECT_LOGO = img/dtc_logo.png OUTPUT_DIRECTORY = doc @@ -255,6 +255,7 @@ INPUT = pdftxt/mainpage.txt \ INPUT_ENCODING = UTF-8 FILE_PATTERNS = *.f \ + *.F \ *.F90 \ *.f90 \ *.nml \ From 7d11d9ce511701a17a5feda12a0adfd385d0d085 Mon Sep 17 00:00:00 2001 From: "ligia.bernardet" Date: Thu, 5 Sep 2019 10:18:57 -0600 Subject: [PATCH 3/3] Address review comment with changes in EXTENSION_MAPPING. No changes in derived HTML output. --- physics/docs/ccpp_doxyfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/physics/docs/ccpp_doxyfile b/physics/docs/ccpp_doxyfile index 351dc022f..91c80c221 100644 --- a/physics/docs/ccpp_doxyfile +++ b/physics/docs/ccpp_doxyfile @@ -29,7 +29,8 @@ OPTIMIZE_OUTPUT_FOR_C = NO OPTIMIZE_OUTPUT_JAVA = NO OPTIMIZE_FOR_FORTRAN = YES OPTIMIZE_OUTPUT_VHDL = NO -EXTENSION_MAPPING = .f=FortranFree \ +EXTENSION_MAPPING = .f=Fortranfixed \ + .F=Fortranfixed \ .F90=FortranFree \ .f90=FortranFree MARKDOWN_SUPPORT = YES