1.14 sync with develop #3660

jhendersonHDF · 2023-10-11T19:25:54Z

Please look over this and let me know if there's anything that shouldn't be merged into the 1.14 branch.

@byrnHDF it was easiest to sync everything from develop, including the gzip and szip changes. If those weren't supposed to come to 1.14, please let me know so I can revert whichever commits are relevant.

* Add workspace path * add debug * Make one job so workspace files are available * Put doxygen docs under docs folder in gh-pages

The compiler complains about using integers instead of size_t for some sizes.

Removes H5detect and H5make_libsettings from the build and replaces their functionality with things that don't affect cross-compiling. H5detect --> floating-point types are now detected on library load H5make_libsettings --> Moved functionality to a new H5build_settings.c template file

src/H5system.c:1293:13: warning: Dereference of null pointer [clang-analyzer-core.NullDereference] src/H5trace.c:4048:17: warning: Passed-by-value struct argument contains uninitialized data (e.g., via the field chain: 'initial.user') [clang-analyzer-core.CallAndMessage]

This script was used to ensure that all non-HDF5 calls were prefixed with 'HD'. We are removing this scheme so this script is no longer needed.

* Remove unused HD macros The library prefixes most C and POSIX API calls with 'HD'. We are going to start removing these so the code looks like normal C. This PR removes most of the unused HD markup macros. * Replace ntohl/ntohs

* Remove dead code * Replace mybzero with memset * Replace hbool_t/TRUE/FALSE with bool/true/false

* Revert "Remove long double conversion work-arounds (HDFGroup#3097)" This reverts commit 1e1dac1. * Update comments to reflect newer systems

* Add java options to build scripts Previously, cmakehdf5 turned on compiling of the java interface by default due to a value set in cacheinit.cmake. Now, consistent with how Fortran and CPP interfaces are handled, the script overwrites this default value to disable the libraries, fixing HDFGroup#2958. I also implemented the --enable-java/--disable java options for cmakehdf5, and -java for buildhdf5. Allen said these scripts should mention that compilers are to be specified in environment variables, but missing compilers causes errors at the CMake level, and CMake's error messages are already pretty informative (See the one in HDFGroup#2958 about JAVA_COMPILER).

These were last usefully modified in 2004

* Adds semicolons to function-like macros * Adds a do..while(0) loop to some macros * Removes semicolons when inappropriate, especially H5E_TRY_BEGIN/END

HDsocket(), etc. Only affects the mirror VFD and its test code.

Replaces with bool/true/false

- Added a cmake variable to the hdf5-config.cmake file which indicate if the library has been build with or without the read-only S3 functionality.

* Track s3 i/o when S3COMMS_DEBUG enabled

* Add upload url as artifact * Change doxygen path and comment log-url upload * zip doxygen files for upload * add workspace var

* chore: fix grammar

POSIX calls (HDstrndup, etc.) are unchanged

* Fixed various -Wmissing-variable-declarations by adding static keyword * In a few cases, renamed the variable suffix from _g to _s. * Fixed some -Wmissing-variable-declarations by using different declaration macros * Fixed various -Wconditional-uninitialized warnings by just initializing variable to zero * Fixed various -Wcomma warnings * Fixed clang -Wstrict-prototypes warnings * Fixed various -Wunused-variable warnings * Updated some casts to fix the only 3 -Wcast-qual warnings * Fixed the only -Wsometimes-uninitialized warning

jhendersonHDF · 2023-10-11T19:28:51Z

CMakePresets.json

- "HDF5_EXAMPLES_COMPRESSED_DIR": {"type": "STRING", "value": "${sourceParentDir}/temp"},
- "EXAMPLES_TGZ_ORIGPATH": {"type": "STRING", "value": "https://github.com/HDFGroup/hdf5-examples/archive/refs/tags/"},
- "EXAMPLES_TGZ_ORIGNAME": {"type": "STRING", "value": "2.0.4.tar.gz"}
+ "HDF5_EXAMPLES_COMPRESSED": {"type": "STRING", "value": "hdf5-examples-master.tar.gz"},


Some of these examples links seemed suspect going from 2.0.4 to master so I didn't know if this was correct or not for 1.14 as opposed to develop

This will be gone when examples is moved in

.github/workflows/h5py.yml

.github/workflows/autotools.yml

.github/workflows/main-cmake.yml

byrnHDF · 2023-10-11T19:40:23Z

.github/workflows/scorecard.yml

+ # To guarantee Maintained check is occasionally updated. See
+ # https://github.com/ossf/scorecard/blob/main/docs/checks.md#maintained
+ schedule:
+ - cron: '36 22 * * 4'


Should just remove the schedule item and leave the push?

yes I think that may have been how it was before. Will revert

byrnHDF · 2023-10-11T19:44:48Z

CMakeFilters.cmake

@@ -131,7 +119,7 @@ endif ()
 #-----------------------------------------------------------------------------
 # Option for SzLib support
 #-----------------------------------------------------------------------------
-option (HDF5_ENABLE_SZIP_SUPPORT "Use SZip Filter" OFF)
+option (HDF5_ENABLE_SZIP_SUPPORT "Use SZip Filter" ON)


This should probably remain as previously

Was this change part of other changes or by itself? I can revert the commit or make the individual change; just concerned about getting confused between the state of this between develop and 1.14

There were other changes

CMakePlugins.cmake

config/cmake/ConfigureChecks.cmake

byrnHDF · 2023-10-11T19:59:49Z

I'm not sure this is the way to do this - Reviewing will take a long time (it is slow on my computer!)
Maybe we should take it smaller bites?

jhendersonHDF · 2023-10-11T20:10:01Z

I'm not sure this is the way to do this - Reviewing will take a long time (it is slow on my computer!) Maybe we should take it smaller bites?

The best way of course would be to keep the two branches in sync regularly. Since there are apparently 540 commits not merged from develop, I don't know the best way to go about this. Smaller batches may help, but there are still a ton of changes. Cherry picking out the tools move PR may help, but that will make it harder to do a regular merge of the other files.

jhendersonHDF · 2023-10-11T20:39:32Z

git merge-base shows that the last common commit between develop and the 1.14 branch is b9f4c001ade4c230f8325080f3dd8181648324ab from December 9. I could start there and pick up things in batches of a hundred commits or so, but the PRs that capture the tools move change and the FALSE -> false, hbool_t -> bool changes will still be huge.

byrnHDF and others added 30 commits June 12, 2023 20:05

Rework tools.cmake and add C flags (HDFGroup#3110)

1891387

Fix gh pages so that the doxygen files are uploaded (HDFGroup#3102)

281dbf4

* Add workspace path * add debug * Make one job so workspace files are available * Put doxygen docs under docs folder in gh-pages

Fix a misc warning in test/vol.c (HDFGroup#3112)

9e7e2f8

The compiler complains about using integers instead of size_t for some sizes.

Add note for issue 3056 (HDFGroup#3117)

75bcd68

Use 1.14 toolchain (HDFGroup#3116)

340c376

Remove the checkposix script (HDFGroup#3122)

ce794d6

This script was used to ensure that all non-HDF5 calls were prefixed with 'HD'. We are removing this scheme so this script is no longer needed.

Remove unused HD macros (HDFGroup#3120)

d1ef48e

* Remove unused HD macros The library prefixes most C and POSIX API calls with 'HD'. We are going to start removing these so the code looks like normal C. This PR removes most of the unused HD markup macros. * Replace ntohl/ntohs

Adds an optional version arg to bin/format_source (HDFGroup#3119)

61d43eb

Clean up mirror VFD code in utils dir (HDFGroup#3121)

69e8c8f

* Remove dead code * Replace mybzero with memset * Replace hbool_t/TRUE/FALSE with bool/true/false

Fix spelling issues flagged by codespell (HDFGroup#3130)

b571da1

Make autogen.sh output message consistent (HDFGroup#3128)

3c12247

Add Python for HDF-EOS zoo description (HDFGroup#3129)

fcadfca

Fix function name in comment in ros3 VFD (HDFGroup#3131)

9a8c581

Revert long double checks (HDFGroup#3133)

fcdd0ab

* Revert "Remove long double conversion work-arounds (HDFGroup#3097)" This reverts commit 1e1dac1. * Update comments to reflect newer systems

Removed .lnt linter files (HDFGroup#3143)

de2cbcf

These were last usefully modified in 2004

Fix path to libhdf5.settings in cmakehdf5 (HDFGroup#3140)

10093f7

Many clang -Wextra-semi-stmt fixes (HDFGroup#2537)

68eba3d

* Adds semicolons to function-like macros * Adds a do..while(0) loop to some macros * Removes semicolons when inappropriate, especially H5E_TRY_BEGIN/END

Remove HD prefix from network calls (HDFGroup#3142)

546d79d

HDsocket(), etc. Only affects the mirror VFD and its test code.

Remove hbool_t/TRUE/FALSE from java (HDFGroup#3145)

41b474b

Replaces with bool/true/false

CMake: (feature) ROS3 and cmake config file. (HDFGroup#3146)

8135cc2

- Added a cmake variable to the hdf5-config.cmake file which indicate if the library has been build with or without the read-only S3 functionality.

Define minimal permissions for new GitHub workflows (HDFGroup#3147)

5e8a230

Track s3 i/o when S3COMMS_DEBUG enabled (HDFGroup#3139)

cef648e

* Track s3 i/o when S3COMMS_DEBUG enabled

Fix the snapshots workflow (HDFGroup#3148)

0f2cb0f

* Add upload url as artifact * Change doxygen path and comment log-url upload * zip doxygen files for upload * add workspace var

chore: fix grammar (HDFGroup#3150)

a37795d

* chore: fix grammar

Removes the HD prefix from java C99 calls (HDFGroup#3149)

560110d

POSIX calls (HDstrndup, etc.) are unchanged

Correct the zip usage (HDFGroup#3153)

1f20354

jhendersonHDF requested review from brtnfld, epourmal, lrknox, fortnern, qkoziol, vchoi-hdfgroup, bmribler, glennsong09 and mattjala as code owners October 11, 2023 19:25

jhendersonHDF commented Oct 11, 2023

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byrnHDF reviewed Oct 11, 2023

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brtnfld added this to the 1.14.3 milestone Oct 11, 2023

jhendersonHDF force-pushed the 1_14_dev_sync branch 5 times, most recently from edfbf5f to a377a27 Compare October 12, 2023 01:04

Adjust 1.14 files after merging

a377a27

lrknox approved these changes Oct 12, 2023

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lrknox merged commit ea3f926 into HDFGroup:hdf5_1_14 Oct 12, 2023
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jhendersonHDF deleted the 1_14_dev_sync branch October 18, 2023 01:59

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1.14 sync with develop #3660

1.14 sync with develop #3660

jhendersonHDF commented Oct 11, 2023

jhendersonHDF Oct 11, 2023

byrnHDF Oct 11, 2023

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jhendersonHDF commented Oct 11, 2023

1.14 sync with develop #3660

1.14 sync with develop #3660

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