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Cleanup CMake code for doxygen and perl shell scripts #552

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Apr 19, 2021
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23e0df3
OESS-98 convert plugin option to FetchContent, add tests
byrnHDF Dec 10, 2020
84293f5
Fixes for pkcfg files because of plugin option
byrnHDF Dec 11, 2020
544bd61
OESS-98 fix tools test for plugins
byrnHDF Dec 15, 2020
ffb182f
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Jan 8, 2021
2561b6b
Keep doxygen comments under 100 chars long - format hint
byrnHDF Jan 8, 2021
1c73615
Whitespace
byrnHDF Jan 8, 2021
b71a853
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Jan 11, 2021
b68973c
HDFFV-11144 - Reclassify CMake messages
byrnHDF Jan 11, 2021
f64497d
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Jan 13, 2021
c854ffe
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Jan 14, 2021
0f90d26
HDFFV-11099/11100 added help text
byrnHDF Jan 14, 2021
20757d6
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Jan 15, 2021
d161733
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Jan 20, 2021
f03b095
Reworked switch statement to compare string instead
byrnHDF Jan 22, 2021
bd52065
Fix typo
byrnHDF Jan 22, 2021
238c060
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Jan 25, 2021
f12b2ae
Update CDash mode
byrnHDF Jan 26, 2021
673aac8
Correct name of threadsafe
byrnHDF Jan 26, 2021
97df6db
Correct option name
byrnHDF Jan 26, 2021
e48f758
Undo accidental commit
byrnHDF Jan 26, 2021
2f364d8
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Jan 27, 2021
f42f02b
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Jan 27, 2021
5b48b33
Note LLVM 10 to 11 format default changes
byrnHDF Jan 27, 2021
9927372
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Jan 28, 2021
ad61d57
Update format plugin
byrnHDF Jan 28, 2021
613bc7a
Undo clang-format version 11 changes
byrnHDF Jan 28, 2021
0114098
One more correction
byrnHDF Jan 28, 2021
a685efa
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Jan 29, 2021
78f25ac
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Feb 1, 2021
1899ba6
Update supported platforms
byrnHDF Feb 2, 2021
28d6d63
Revert whitespace changes
byrnHDF Feb 2, 2021
f1a0239
Correct whitespace
byrnHDF Feb 2, 2021
b656722
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Feb 3, 2021
1c9eaf4
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Feb 4, 2021
f85f7da
Changes from PR#3
byrnHDF Feb 4, 2021
464d08e
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Feb 5, 2021
34ad32c
HDFFV-11213 added option to control gcc10 warnings diagnostics
byrnHDF Feb 5, 2021
d6db05b
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into
byrnHDF Feb 8, 2021
264caff
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Feb 9, 2021
9b42150
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Feb 10, 2021
4569d39
HDFFV-11212 Use the new references correctly in JNI utility and tests
byrnHDF Feb 11, 2021
4a2865c
format source
byrnHDF Feb 11, 2021
1a2dc75
Fix typo
byrnHDF Feb 11, 2021
23679fa
Add new test file
byrnHDF Feb 11, 2021
232426b
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Feb 16, 2021
020a40c
HDFFV-11212 - update test and remove unused arg
byrnHDF Feb 16, 2021
2352972
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Feb 17, 2021
5806658
Minor non-space formatting changes
byrnHDF Feb 18, 2021
83b619f
Use H5I_INVALID_ID instead of "-1"
byrnHDF Feb 19, 2021
fbf97be
source formatting
byrnHDF Feb 19, 2021
ea94075
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Feb 19, 2021
797a6c2
add missing testfile, update jni function
byrnHDF Feb 19, 2021
32d6ee9
Undo commit of debug code
byrnHDF Feb 19, 2021
71c4557
remove mislocated file
byrnHDF Feb 19, 2021
2c6df43
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Feb 19, 2021
66d54a9
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Feb 19, 2021
08c7738
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Feb 19, 2021
46c620f
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Feb 22, 2021
a4132c8
Fix h5repack test for handling of fapls and id close
byrnHDF Feb 22, 2021
498d7ec
Update h5diff test files usage text
byrnHDF Feb 22, 2021
82ff537
HDFFV-11212 add new ref tests for JNI export dataset
byrnHDF Feb 22, 2021
7e81307
src format update
byrnHDF Feb 22, 2021
4bda56f
Remove blank line typo
byrnHDF Feb 22, 2021
25884a6
src format typo
byrnHDF Feb 22, 2021
07d8cf2
long double requires %Lg
byrnHDF Feb 22, 2021
8735c2a
Another long double foramt specifer S.B. %Lg
byrnHDF Feb 22, 2021
140aca0
issue with t128bit test
byrnHDF Feb 22, 2021
c790f17
Windows issue with h5dump and type.
byrnHDF Feb 22, 2021
eb3f7cc
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Feb 23, 2021
76d4fba
Fix review issues
byrnHDF Feb 23, 2021
7b96c23
refactor function nesting and fix error checks
byrnHDF Feb 23, 2021
90bb747
format fixes
byrnHDF Feb 23, 2021
321b926
Remove untested functions and javadoc quiet comments
byrnHDF Feb 23, 2021
2d40134
Restore TRY block.
byrnHDF Feb 24, 2021
b8cda57
Change string append errors to memory exception
byrnHDF Feb 24, 2021
ec3c879
revert to H5_JNI_FATAL_ERROR - support functions need work
byrnHDF Feb 24, 2021
0a56190
Add assertion error for h5util functions
byrnHDF Feb 24, 2021
282ac70
remove duplicate function
byrnHDF Feb 24, 2021
9eae4f5
format fix
byrnHDF Feb 24, 2021
a3d7f13
Revert HD function error handling
byrnHDF Feb 24, 2021
3ea3719
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Feb 25, 2021
2a71393
Update copyright comments
byrnHDF Feb 25, 2021
68d7443
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Feb 25, 2021
dab6971
GH #386 java folder copyright corrections
byrnHDF Feb 26, 2021
bfa3508
Whitespace
byrnHDF Feb 26, 2021
b42646f
GH #359 implement and fix tools 1.6 API usage
byrnHDF Feb 26, 2021
f10a3a1
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Feb 26, 2021
6d17d6f
remove excessive comments
byrnHDF Feb 26, 2021
a9bd5ba
Flip inits to correct ifdef section
byrnHDF Feb 26, 2021
7037609
rework ifdef to be simpler
byrnHDF Feb 26, 2021
9e7b3d7
format issue
byrnHDF Feb 26, 2021
d76e848
Reformat ifdef inits
byrnHDF Feb 26, 2021
49e5203
remove static attribute
byrnHDF Feb 26, 2021
53a1528
format compliance
byrnHDF Feb 26, 2021
bb01c7b
Update names
byrnHDF Feb 28, 2021
70a7b81
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Mar 1, 2021
97ed2a4
Revert because logic relies on float not being int
byrnHDF Mar 1, 2021
f19f7d6
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Mar 1, 2021
2998e91
Changes noticed from creating merge of #412
byrnHDF Mar 2, 2021
5b6e1af
Double underscore change
byrnHDF Mar 2, 2021
e478961
Correct compiler version variable used
byrnHDF Mar 3, 2021
f00ce36
Remove header guard underscores
byrnHDF Mar 3, 2021
24db13a
Whitespace cleanup
byrnHDF Mar 3, 2021
1309524
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Mar 4, 2021
0b04714
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Mar 5, 2021
e460b2b
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Mar 5, 2021
c7115cd
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Mar 8, 2021
746ab82
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Mar 10, 2021
d429b3f
Split format source and commit changes on repo push
byrnHDF Mar 10, 2021
9029a70
remove pre-split setting
byrnHDF Mar 10, 2021
04284c1
Change windows TS to use older VS.
byrnHDF Mar 10, 2021
33f8693
correct window os name
byrnHDF Mar 10, 2021
723aa6d
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Mar 10, 2021
49f92f0
HDFFV-11212 JNI export util and Javadoc
byrnHDF Mar 11, 2021
b6d4127
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Mar 11, 2021
e555eb6
Suggested review changes
byrnHDF Mar 11, 2021
720c393
Another change found
byrnHDF Mar 11, 2021
c3bd691
Committing clang-format changes
github-actions[bot] Mar 11, 2021
a57c9b7
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Mar 12, 2021
cadc876
HDFFV-11113 long double in tools
byrnHDF Mar 12, 2021
fdd4a51
HDFFV-11113 add note
byrnHDF Mar 12, 2021
efe338b
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Mar 15, 2021
421ab67
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Mar 17, 2021
d67f8d3
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Mar 18, 2021
e6972f2
Disable long double tests for now
byrnHDF Mar 22, 2021
866da1a
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Mar 22, 2021
ef237e4
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Mar 22, 2021
3691b55
HDFFV-11228 remove arbitrary CMake warning groups.
byrnHDF Mar 22, 2021
fdd06ab
Make each flag a string
byrnHDF Mar 22, 2021
fd83148
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Mar 22, 2021
f1cd80f
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Mar 23, 2021
742a7e3
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Mar 24, 2021
d3f4392
Some Javadoc warning fixes
byrnHDF Mar 24, 2021
9c3becc
Updated javadoc fixes
byrnHDF Mar 24, 2021
bb93f4d
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Mar 25, 2021
04568ab
# WARNING: head commit changed in the meantime
byrnHDF Mar 25, 2021
23aaf37
Committing clang-format changes
github-actions[bot] Mar 25, 2021
511bf0e
HDFFV-11229 Add release note
byrnHDF Mar 25, 2021
e8d97c9
HDFFV-11229 windows testfile needed
byrnHDF Mar 25, 2021
69e1491
fix typo
byrnHDF Mar 25, 2021
e3de592
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Mar 26, 2021
3d88c6a
Remove non supported message text
byrnHDF Mar 26, 2021
fe9d07c
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Mar 26, 2021
452b890
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Mar 29, 2021
f4e1413
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Mar 30, 2021
8c6e61f
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Mar 31, 2021
ab3ae07
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Mar 31, 2021
c9a8d50
HDFFV-11229 - change ldouble test to check both native and general
byrnHDF Apr 5, 2021
72fd93d
HDFFV-11229 add second file compare
byrnHDF Apr 5, 2021
dff390e
HDFFV-11229 fix reference file
byrnHDF Apr 5, 2021
362beb3
HDFFV-11229 autotools check two refs
byrnHDF Apr 5, 2021
2385150
HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
byrnHDF Apr 7, 2021
c17ca54
Committing clang-format changes
github-actions[bot] Apr 7, 2021
f05c84e
Update release note
byrnHDF Apr 7, 2021
1e6224c
Update attribute type of ref file
byrnHDF Apr 7, 2021
baf0fd3
Change source of ninja for macs
byrnHDF Apr 12, 2021
6d780f6
try port instead of brew
byrnHDF Apr 12, 2021
c2cf490
Recommended is to use brew.
byrnHDF Apr 12, 2021
2e0f725
Undo non long double changes
byrnHDF Apr 13, 2021
e97e2e8
remove unneeded file
byrnHDF Apr 13, 2021
3756724
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Apr 15, 2021
292a651
Fix perl and doxygen CMake code
byrnHDF Apr 15, 2021
b34207a
Merge branch 'develop' of https://github.com/HDFGroup/hdf5.git into d…
byrnHDF Apr 19, 2021
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8 changes: 8 additions & 0 deletions CMakeLists.txt
Original file line number Diff line number Diff line change
Expand Up @@ -507,6 +507,14 @@ else ()
set (tgt_file_ext "-shared")
endif ()

#-----------------------------------------------------------------------------
# perl is used in some optional src and tests, check availability
find_package (Perl)
if (PERL_FOUND)
set (H5_PERL_FOUND YES)
endif ()
#-----------------------------------------------------------------------------

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Why can't we just use PERL_FOUND directly?

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@byrnHDF note this change is also in the PRs #523, 531, and 548 to merge long double changes to 1.12, 1.10, and 1.8, so I'm waiting for this answer to merge those, too.

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Why can't we just use PERL_FOUND directly?

There seemed to be a variable visibility issue, which these changes solved. I did not do any further investigating.

#-----------------------------------------------------------------------------
# Option to Build Static executables
#-----------------------------------------------------------------------------
Expand Down
1 change: 1 addition & 0 deletions doxygen/Doxyfile.in
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
44 changes: 26 additions & 18 deletions src/CMakeLists.txt
Original file line number Diff line number Diff line change
Expand Up @@ -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
)
Expand Down Expand Up @@ -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 ()
3 changes: 1 addition & 2 deletions test/CMakeTests.cmake
Original file line number Diff line number Diff line change
Expand Up @@ -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 ${CMAKE_COMMAND} -E remove flushrefresh.h5
Expand Down
3 changes: 1 addition & 2 deletions test/ShellTests.cmake
Original file line number Diff line number Diff line change
Expand Up @@ -23,8 +23,7 @@ if (UNIX)
##############################################################################
# configure scripts to test dir
##############################################################################
find_package (Perl)
if (PERL_FOUND)
if (H5_PERL_FOUND)
configure_file(${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)
Expand Down