From b2c78e15cf2e78221c0f04fa47107f9ce94393fe Mon Sep 17 00:00:00 2001
From: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Date: Mon, 19 Apr 2021 07:28:32 -0500
Subject: Cleanup CMake code for doxygen and perl shell scripts (#552)

* OESS-98 convert plugin option to FetchContent, add tests

* Fixes for pkcfg files because of plugin option

* OESS-98 fix tools test for plugins

* Keep doxygen comments under 100 chars long - format hint

* Whitespace

* HDFFV-11144 - Reclassify CMake messages

* HDFFV-11099/11100 added help text

* Reworked switch statement to compare string instead

* Fix typo

* Update CDash mode

* Correct name of threadsafe

* Correct option name

* Undo accidental commit

* Note LLVM 10 to 11 format default changes

* Update format plugin

* Undo clang-format version 11 changes

* One more correction

* Update supported platforms

* Revert whitespace changes

* Correct whitespace

* Changes from PR#3

* HDFFV-11213 added option to control gcc10 warnings diagnostics

* HDFFV-11212 Use the new references correctly in JNI utility and tests

* format source

* Fix typo

* Add new test file

* HDFFV-11212 - update test and remove unused arg

* Minor non-space formatting changes

* Use H5I_INVALID_ID instead of "-1"

* source formatting

* add missing testfile, update jni function

* Undo commit of debug code

* remove mislocated file

* Fix h5repack test for handling of fapls and id close

* Update h5diff test files usage text

* HDFFV-11212 add new ref tests for JNI export dataset

* src format update

* Remove blank line typo

* src format typo

* long double requires %Lg

* Another long double foramt specifer S.B. %Lg

* issue with t128bit test

* Windows issue with h5dump and type.

* Fix review issues

* refactor function nesting and fix error checks

* format fixes

* Remove untested functions and javadoc quiet comments

* Restore TRY block.

* Change string append errors to memory exception

* revert to H5_JNI_FATAL_ERROR - support functions need work

* Add assertion error for h5util functions

* remove duplicate function

* format fix

* Revert HD function error handling

* Update copyright comments

* GH #386 java folder copyright corrections

* Whitespace

* GH #359 implement and fix tools 1.6 API usage

* remove excessive comments

* Flip inits to correct ifdef section

* rework ifdef to be simpler

* format issue

* Reformat ifdef inits

* remove static attribute

* format compliance

* Update names

* Revert because logic relies on float not being int

* Changes noticed from creating merge of #412

* Double underscore change

* Correct compiler version variable used

* Remove header guard underscores

* Whitespace cleanup

* Split format source and commit changes on repo push

* remove pre-split setting

* Change windows TS to use older VS.

* correct window os name

* HDFFV-11212 JNI export util and Javadoc

* Suggested review changes

* Another change found

* Committing clang-format changes

* HDFFV-11113 long double in tools

* HDFFV-11113 add note

* Disable long double tests for now

* HDFFV-11228 remove arbitrary CMake warning groups.

* Make each flag a string

* Some Javadoc warning fixes

* Updated javadoc fixes

* # WARNING: head commit changed in the meantime

HDFFV-11229 Fix long double usage in tools and java

Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.

* Committing clang-format changes

* HDFFV-11229 Add release note

* HDFFV-11229 windows testfile needed

* fix typo

* Remove non supported message text

* HDFFV-11229 - change ldouble test to check both native and general

* HDFFV-11229 add second file compare

* HDFFV-11229 fix reference file

* HDFFV-11229 autotools check two refs

* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output

* Committing clang-format changes

* Update release note

* Update attribute type of ref file

* Change source of ninja for macs

* try port instead of brew

* Recommended is to use brew.

* Undo non long double changes

* remove unneeded file

* Fix perl and doxygen CMake code

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
---
 CMakeLists.txt        |  8 ++++++++
 doxygen/Doxyfile.in   |  1 +
 src/CMakeLists.txt    | 44 ++++++++++++++++++++++++++------------------
 test/CMakeTests.cmake |  3 +--
 test/ShellTests.cmake |  3 +--
 5 files changed, 37 insertions(+), 22 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 99dc035..0771ac6 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -508,6 +508,14 @@ else ()
 endif ()
 
 #-----------------------------------------------------------------------------
+# perl is used in some optional src and tests, check availability
+find_package (Perl)
+if (PERL_FOUND)
+  set (H5_PERL_FOUND YES)
+endif ()
+#-----------------------------------------------------------------------------
+
+#-----------------------------------------------------------------------------
 # Option to Build Static executables
 #-----------------------------------------------------------------------------
 option (BUILD_STATIC_EXECS "Build Static Executables" OFF)
diff --git a/doxygen/Doxyfile.in b/doxygen/Doxyfile.in
index 24fc4ba..2395d6c 100644
--- a/doxygen/Doxyfile.in
+++ b/doxygen/Doxyfile.in
@@ -263,6 +263,7 @@ TAB_SIZE               = 4
 
 ALIASES                =
 
+@INCLUDE_PATH          = @DOXYGEN_INCLUDE_ALIASES_PATH@
 @INCLUDE               = @DOXYGEN_INCLUDE_ALIASES@
 
 # Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 06b0c8c..a07122d 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -991,8 +991,7 @@ 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
     )
@@ -1369,34 +1368,43 @@ 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 ()
diff --git a/test/CMakeTests.cmake b/test/CMakeTests.cmake
index 242c918..d3e0788 100644
--- a/test/CMakeTests.cmake
+++ b/test/CMakeTests.cmake
@@ -889,8 +889,7 @@ if (ENABLE_EXTENDED_TESTS)
 
 #-- Adding test for flushrefresh
   file (MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/H5TEST/flushrefresh_test")
-  find_package (Perl)
-  if (PERL_FOUND)
+  if (H5_PERL_FOUND)
     add_test (
         NAME H5TEST-testflushrefresh-clear-objects
         COMMAND ${CMAKE_COMMAND} -E remove flushrefresh.h5
diff --git a/test/ShellTests.cmake b/test/ShellTests.cmake
index 4676184..4d23de3 100644
--- a/test/ShellTests.cmake
+++ b/test/ShellTests.cmake
@@ -23,8 +23,7 @@ if (UNIX)
     ##############################################################################
     #  configure scripts to test dir
     ##############################################################################
-    find_package (Perl)
-    if (PERL_FOUND)
+    if (H5_PERL_FOUND)
       configure_file(${HDF5_TEST_SOURCE_DIR}/testflushrefresh.sh.in ${HDF5_TEST_BINARY_DIR}/H5TEST/testflushrefresh.sh @ONLY)
     endif ()
     configure_file(${HDF5_TEST_SOURCE_DIR}/test_usecases.sh.in ${HDF5_TEST_BINARY_DIR}/H5TEST/test_usecases.sh @ONLY)
-- 
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