1 10 Merge of long double fix and compiler flags (#531)

* HDFFV-10865 - merge from dev, HDFArray perf fix.

* Remove duplicate setting

* Whitespace changes after clang format

* Undo version 11 clang format changes

* Merge CMake changes from develop

* test testing script merge from develop

* Update supported platforms

* PR#3 merge from develop

* Merge gcc 10 diagnostics option from develop

* Merge #318 OSX changes from develop

* Merge small changes from develop

* Minor non-space formatting changes

* #386 copyright corrections for java folder

* Merges from develop

#358 patches from vtk
#361 fix header guard spelling

* Merge updates

#358 patches from vtk
#361 fix header guard spelling

* format fix

* Fix missing underscore and make H5public.h closer to dev

* Merges from develop

#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
header guard underscore cleanup
JNI cleanup

* format alignment

* Add missing test ref file

* Merge #380 from develop

* Finish java merges from develop

* Fix java issues with tests and javadoc

* Correct use of attribute access plist

* Remove debug code

* Remove unused variable

* Change file access to read only for java tests

* Split clang format operations.

* More javadoc comments

* Remove pre-split setting

* format source

* Change windows TS to use older VS.

* Mostly all javadoc fixes, one argument rename.

* synch file

* Merge of long double fix and compiler flags

* HDFFV-11229 merge changes from develop

* HDFFV-11229 correct test script

* HDFFV-11229 update autotools test script for two ref files

* HDFFV-11229 merge dev changes for long double display in tools

* Committing clang-format changes

* minor whitespace

* remove unneeded macro

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

1 files changed, 26 insertions, 18 deletions

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 329a2dc..7b70e67 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -924,8 +924,7 @@ set (H5_PUBLIC_GENERATED_HEADERS
 option (HDF5_GENERATE_HEADERS "Rebuild Generated Files" ON)
 if (HDF5_GENERATE_HEADERS)
   set_source_files_properties(${H5_GENERATED_HEADERS} PROPERTIES GENERATED TRUE)
-  find_package (Perl)
-  if (PERL_FOUND)
+  if (H5_PERL_FOUND)
     execute_process (
         COMMAND ${PERL_EXECUTABLE} ${HDF5_SOURCE_DIR}/bin/make_err ${HDF5_SRC_DIR}/H5err.txt OUTPUT_VARIABLE SCRIPT_OUTPUT
     )
@@ -1302,34 +1301,43 @@ endif ()
 if (DOXYGEN_FOUND)
   set (DOXYGEN_PACKAGE ${HDF5_PACKAGE})
   set (DOXYGEN_VERSION_STRING ${HDF5_VERSION_STRING})
-  set (DOXYGEN_INCLUDE_ALIASES ${HDF5_DOXYGEN_DIR}/aliases)
+  set (DOXYGEN_INCLUDE_ALIASES_PATH ${HDF5_DOXYGEN_DIR})
+  set (DOXYGEN_INCLUDE_ALIASES aliases)
+  set (DOXYGEN_VERBATIM_VARS DOXYGEN_INCLUDE_ALIASES)
   set (DOXYGEN_PROJECT_LOGO ${HDF5_DOXYGEN_DIR}/img/HDFG-logo.png)
   set (DOXYGEN_PROJECT_BRIEF "C-API Reference")
-  set (DOXYGEN_INPUT_DIRECTORY ${HDF5_SRC_DIR} ${HDF5_DOXYGEN_DIR}/dox ${HDF5_GENERATED_SOURCE_DIR}/shared)
+  set (DOXYGEN_INPUT_DIRECTORY "${HDF5_SRC_DIR} ${HDF5_DOXYGEN_DIR}/dox ${HDF5_GENERATED_SOURCE_DIR}/shared")
   set (DOXYGEN_OPTIMIZE_OUTPUT_FOR_C YES)
   set (DOXYGEN_MACRO_EXPANSION YES)
   set (DOXYGEN_OUTPUT_DIRECTORY ${HDF5_BINARY_DIR}/hdf5lib_docs)
 
+# This configure and custom target work together
   # Replace variables inside @@ with the current values
-  configure_file(${HDF5_DOXYGEN_DIR}/Doxyfile.in Doxyfile @ONLY)
-
-  doxygen_add_docs(hdf5lib_doc
-#      ${common_SRCS} ${shared_gen_SRCS} ${H5_PUBLIC_HEADERS} ${H5_PRIVATE_HEADERS} ${H5_GENERATED_HEADERS} ${HDF5_DOXYGEN_DIR}/dox
-      ${DOXYGEN_INPUT_DIRECTORY}
-      ALL
-      WORKING_DIRECTORY ${HDF5_SRC_DIR}
-      COMMENT "Generating HDF5 library Source Documentation"
-  )
-  install(
+  configure_file (${HDF5_DOXYGEN_DIR}/Doxyfile.in ${HDF5_BINARY_DIR}/Doxyfile @ONLY)
+  add_custom_target (hdf5lib_doc ALL
+        COMMAND ${DOXYGEN_EXECUTABLE} ${HDF5_BINARY_DIR}/Doxyfile
+        WORKING_DIRECTORY ${HDF5_SRC_DIR}
+        COMMENT "Generating HDF5 library Source API documentation with Doxygen"
+        VERBATIM )
+# This cmake function requires that the non-default doxyfile settings are provided with set (DOXYGEN_xxx) commands
+# In addition the doxyfile aliases @INCLUDE option is not supported and would need to be provided in a set (DOXYGEN_ALIASES) command.
+#  doxygen_add_docs (hdf5lib_doc
+##      ${common_SRCS} ${shared_gen_SRCS} ${H5_PUBLIC_HEADERS} ${H5_PRIVATE_HEADERS} ${H5_GENERATED_HEADERS} ${HDF5_DOXYGEN_DIR}/dox
+#      ${DOXYGEN_INPUT_DIRECTORY}
+#      ALL
+#      WORKING_DIRECTORY ${HDF5_SRC_DIR}
+#      COMMENT "Generating HDF5 library Source Documentation"
+#  )
+  install (
       DIRECTORY ${HDF5_BINARY_DIR}/hdf5lib_docs/html
       DESTINATION ${HDF5_INSTALL_DATA_DIR}
       COMPONENT Documents
   )
 
-  if(NOT TARGET doxygen)
-    add_custom_target(doxygen)
-  endif()
+  if (NOT TARGET doxygen)
+    add_custom_target (doxygen)
+  endif ()
 
-  add_dependencies(doxygen hdf5lib_doc)
+  add_dependencies (doxygen hdf5lib_doc)
 
 endif ()