From 539e41d0ae08f6a1823b3b6fcf55da97c670e466 Mon Sep 17 00:00:00 2001 From: Michael Zingale Date: Sun, 5 Jan 2025 14:30:13 -0500 Subject: [PATCH 1/2] an attempt to get Doxygen working --- sphinx_docs/Doxyfile | 8 ++++---- sphinx_docs/Makefile | 2 +- sphinx_docs/source/index.rst | 8 ++++++++ 3 files changed, 13 insertions(+), 5 deletions(-) diff --git a/sphinx_docs/Doxyfile b/sphinx_docs/Doxyfile index c291cfa9a2..7d9f1fc2aa 100644 --- a/sphinx_docs/Doxyfile +++ b/sphinx_docs/Doxyfile @@ -425,7 +425,7 @@ LOOKUP_CACHE_SIZE = 0 # normally produced when WARNINGS is set to YES. # The default value is: NO. -EXTRACT_ALL = NO +EXTRACT_ALL = YES # If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will # be included in the documentation. @@ -443,7 +443,7 @@ EXTRACT_PACKAGE = NO # included in the documentation. # The default value is: NO. -EXTRACT_STATIC = NO +EXTRACT_STATIC = YES # If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined # locally in source files will be included in the documentation. If set to NO, @@ -780,7 +780,7 @@ WARN_LOGFILE = # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING # Note: If this tag is empty the current directory is searched. -INPUT = ../Source +INPUT = ../conductivity ../constants ../EOS ../integration ../interfaces ../networks ../neutrinos ../nse_solver ../nse_tabular ../opacity ../rates ../screening ../unit_test ../util # This tag can be used to specify the character encoding of the source files # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses @@ -839,7 +839,7 @@ EXCLUDE_SYMLINKS = NO # Note that the wildcards are matched against the file with absolute path, so to # exclude all test directories for example use the pattern */test/* -EXCLUDE_PATTERNS = +EXCLUDE_PATTERNS = util/autodiff/* util/gcem/* util/skynet/* */tmp_build_dir/* # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names # (namespaces, classes, functions, etc.) that should be excluded from the diff --git a/sphinx_docs/Makefile b/sphinx_docs/Makefile index cc4d477864..94f75db5cc 100644 --- a/sphinx_docs/Makefile +++ b/sphinx_docs/Makefile @@ -22,7 +22,7 @@ clean: html: ./rp.py > source/runtime_parameters.rst doxygen Doxyfile - breathe-apidoc --o source doxy_files/xml + breathe-apidoc --o source doxy_files/xml -g class,file @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) @if [ ! -d ../docs ]; then mkdir ../docs; fi diff --git a/sphinx_docs/source/index.rst b/sphinx_docs/source/index.rst index c0e9fc7623..5d90b49d77 100644 --- a/sphinx_docs/source/index.rst +++ b/sphinx_docs/source/index.rst @@ -80,6 +80,14 @@ of state routines. comprehensive_tests one_zone_tests +.. toctree:: + :maxdepth: 1 + :caption: API + + filelist + classlist +.. namespacelist + .. toctree:: :maxdepth: 1 :caption: References From b16843572e861e4de430bc764f3f1a1dd5cd9cc6 Mon Sep 17 00:00:00 2001 From: "Eric T. Johnson" Date: Thu, 16 Jan 2025 14:02:48 -0500 Subject: [PATCH 2/2] Fix breathe parsing errors --- sphinx_docs/Doxyfile | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/sphinx_docs/Doxyfile b/sphinx_docs/Doxyfile index 7d9f1fc2aa..51e9b29fac 100644 --- a/sphinx_docs/Doxyfile +++ b/sphinx_docs/Doxyfile @@ -839,7 +839,7 @@ EXCLUDE_SYMLINKS = NO # Note that the wildcards are matched against the file with absolute path, so to # exclude all test directories for example use the pattern */test/* -EXCLUDE_PATTERNS = util/autodiff/* util/gcem/* util/skynet/* */tmp_build_dir/* +EXCLUDE_PATTERNS = */util/autodiff/* */util/gcem/* */util/skynet/* */tmp_build_dir/* # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names # (namespaces, classes, functions, etc.) that should be excluded from the @@ -2009,7 +2009,7 @@ ENABLE_PREPROCESSING = YES # The default value is: NO. # This tag requires that the tag ENABLE_PREPROCESSING is set to YES. -MACRO_EXPANSION = NO +MACRO_EXPANSION = YES # If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then # the macro expansion is limited to the macros specified with the PREDEFINED and @@ -2017,7 +2017,7 @@ MACRO_EXPANSION = NO # The default value is: NO. # This tag requires that the tag ENABLE_PREPROCESSING is set to YES. -EXPAND_ONLY_PREDEF = NO +EXPAND_ONLY_PREDEF = YES # If the SEARCH_INCLUDES tag is set to YES, the include files in the # INCLUDE_PATH will be searched if a #include is found. @@ -2049,7 +2049,15 @@ INCLUDE_FILE_PATTERNS = # recursively expanded use the := operator instead of the = operator. # This tag requires that the tag ENABLE_PREPROCESSING is set to YES. -PREDEFINED = +# breathe barfs on these when trying to parse function definitions +# see https://github.com/breathe-doc/breathe/issues/905 +PREDEFINED = AMREX_GPU_DEVICE= \ + AMREX_GPU_HOST_DEVICE= \ + AMREX_GPU_MANAGED= \ + AMREX_INLINE= \ + AMREX_FORCE_INLINE= \ + AMREX_FLATTEN= \ + AUTODIFF_DEVICE_FUNC= # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this # tag can be used to specify a list of macro names that should be expanded. The