Commit Graph

211 Commits

Author SHA1 Message Date
Allen Byrne
8dc72928b8
Develop java newrefs fixes for obj ref datasets (#1354)
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
2022-01-18 14:02:53 -06:00
Allen Byrne
2f34c433dc
Update the java slf4j logging jars to latest 1.7.33 (#1369) 2022-01-18 07:44:11 -06:00
Allen Byrne
03217eca81
Add tests for H5Ocopy of new object refs (#1338)
* Add tests for H5Ocopy of new object refs

* Correct class name

* Skip test because of issue with debug assertions

* Update reference file

* Fix object examples for new refs
2022-01-08 08:19:52 -06:00
Scot Breitenfeld
f859cb732b
Fixed Spelling Errors (#1166)
* fixed missed closing of a dataset

* fixed missed closing of a dataset

* fixed typo in error return

* Committing clang-format changes

* minor edits

* code format

* Committing clang-format changes

* code format

* minor edit

* switched from using MPI_count, to actual bytes written for H5FD_mpio_debug rw debugging

* Committing clang-format changes

* changed size_i in printf to reflect the I/O.

* Committing clang-format changes

* Fixed seg fault with xlf on BE with -qintsize=8

* fixed error function string

* spelling corrections via codespell, added new spell check github actions

* Committing clang-format changes

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* Committing clang-format changes

* misc

* misc

* misc

* misc

* misc

* misc

* Committing clang-format changes

* misc

* work around for https://github.com/codespell-project/codespell/issues/2137

* misc

* added missing file

* misc

* misc.

* misc

* switch to using Codespell with GitHub Actions

* misc.

* misc.

* fixed more sp errors

* Fix new typos found by codespell.

* fixed proceed with precede

* fixed variable in fortran test

* fixed minnum

* updated spelling list

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
2021-12-07 08:27:29 -06:00
Larry Knox
89ad105b1c
Update version to 1.13.1-1 after creation of branch for 1.13.0 release. (#1236) 2021-11-30 12:53:45 -06:00
Allen Byrne
81b9d71a24
Fix Java VOL tests (#1158) 2021-11-03 07:28:30 -05:00
Allen Byrne
1c892fb41f
Fix java warnings (#1005) 2021-09-15 08:26:25 -05:00
Allen Byrne
af7989e858
Correct dataset close in java test (#919)
* Correct dataset close

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2021-08-18 11:02:29 -05:00
Allen Byrne
0262a49f9c
Java and fortran cmake changes (#694)
* 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

* Add "option" command for clang options

* Rework CMake add_custom to use the BYPRODUCTS argument

* Add stamp files to BYPRODUCTS

* Only one copy of file exists

* Fix custom cmmand depends targets

* Fix fortran custom command DEPENDS

* Add LD_LIBRARY_PATH to tests

* Add custom target for DEPENDS

* Add h5detect conditionaly to generated target DEPENDS

* Correct DEPENDS targets

* Parallel builds need the mpi compiler for pkgconfig scripts.

* install only if MPI build

* Fortran target depends

* Remove incorrect source attribute

* doxygen adjustments

* doxygen build updates

* Correct version

* Correct function version - function has been merged to 1.12

* Correct version string for map functions

* Cleanup warnings for tools debug builds

* TRILAB-227 - fix indexing for h5diff selections

* Correct location of pos to index function call

* TRILAB-227 Enable test

* Quote subset args

* Use MATCHES because of AppleClang

* if blocks needed for build modes

* Update list of DT platforms

* VS2019 correctly displays float values

* revert VS2019 change

* Issue #669 remove version from pkgcfg filename

* remove version from h5cc script

* Java reference functions updated

enabled fortran in cmake gcc action yaml file
java reference test changed to correctly test refs
jni reference functions that create ids changed to use jni id logging

* Correct BYPRODUCTS argument

* Correct more genereated files BYPRODUCTS

* BYPRODUCTS must have unique locations

* Fix typo

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2021-05-28 21:56:29 -05:00
Allen Byrne
e21f7aaac4
Tools long double updates (#522)
* 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

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2021-04-15 07:59:01 -05:00
Allen Byrne
748da20bbc
develop JNI export references and java updates (#467)
* 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

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2021-03-12 07:47:47 -06:00
Allen Byrne
216bff5778
#386 copyright corrections for java folder (#389)
* 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
2021-02-26 09:27:15 -06:00
Allen Byrne
c7ffe683e5
Primary change is HDFFV-11212 - new refs and JNI (#372)
* 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
2021-02-25 15:12:57 -06:00
Larry Knox
2ea165efd0
Update license url part2 (#333)
* Modify temporary rpath for testing in java example scripts.

* Update URL in source file Copyright headers for web copy of COPYING
    file - files not in src or test.
2021-02-17 08:52:36 -06:00
Dana Robinson
f6dce729e8
Moves the lists of VOL connectors and VFDs in Autotools builds (#162)
The VOL_LIST variable used in the Autotools was duplicated in many
subdirectories. It's been moved to config/conclude.am to avoid
duplication. VFD_LIST was also moved to conclude.am.
2020-12-12 09:25:54 -06:00
Michel Zou
0db1fe81d5 CMake: MINGW implies WIN32 2020-10-30 16:09:28 +01:00
Allen Byrne
f8b3f576ce HDFFV-10868 - add H5Sselect API java wrappers.
Also added javadoc comments to H5E and H5s constants.
2020-10-27 16:48:02 -05:00
Dana Robinson
bc1bed2c55 Squash merge of file locking fixes 2020-08-03 09:11:27 -07:00
Dana Robinson
e4603ff8a1 Updated the Java tests to deal with H5Sset_extent_none changes 2020-07-28 08:28:38 -07:00
Larry Knox
da607fe463 Change load path in libhdf5_java.dylib to unversioned libhdf5.dylib for
junit tests on Macs.
2020-07-07 10:52:58 -05:00
Larry Knox
fc69de0e8a Lib files needed are now copied to a subdirectory in the java/test
directory, and on Macs the loader path for libhdf5.xxxs.so is changed
in the temporary copy of libhdf5_java.dylib.
Fix for HDFFV-11063
2020-07-02 11:29:12 -05:00
Larry Knox
32c483cb86 Copy lib files for junit.sh to temporary subdirectory of <build
directory>/java/test instead of to the prefix/lib directory.  Fix for
HDFFV-11063.
2020-06-27 15:39:53 -05:00
Allen Byrne
c1565d2b57 Correct test 2020-05-06 09:38:59 -05:00
Quincey Koziol
9e5dbf6906 Trim trailing whitespace 2020-04-20 18:12:00 -05:00
Allen Byrne
666205a55f TRILAB-142 Change minimum CMake version to 3.12 2020-02-21 16:16:06 -06:00
Allen Byrne
00d68851fc HDFFV-10996 - add java vol tests 2020-02-03 13:45:14 -06:00
Jordan Henderson
e41f671d2f Introduce new H5VL _by_value routines 2020-01-28 18:18:38 -06:00
Dana Robinson
a92c735c9b Squashed commit of the token_refactoring branch: 2020-01-16 13:29:34 -08:00
Allen Byrne
7022a3380c HDFFV-11001 need to qualify all by parallel or serial types 2020-01-15 12:28:53 -06:00
Allen Byrne
b73c0aeaa9 HDFFV-10995 - Update all time instances 2020-01-08 12:48:48 -06:00
Allen Byrne
59ab02a6c5 HDFFV-10995 adjust testing to tolerate non-US locale 2020-01-08 12:44:48 -06:00
Allen Byrne
c087ef41b6 Add H5Rdestroy calls to cleanup 2019-12-08 14:43:06 -06:00
Allen Byrne
1cde6b2fba Remove problem tests for now 2019-12-08 14:03:05 -06:00
Allen Byrne
1d3186ad45 HDFFV-10876 ignore old reference API tests 2019-12-07 15:05:08 -06:00
Allen Byrne
e8ad5f6d1a HDFFV-10876 Update dump to match DDL spec 2019-12-05 17:21:02 -06:00
Allen Byrne
cc2407257a Update create calls 2019-12-04 12:35:48 -06:00
Allen Byrne
ba8f2f1174 Update reference calls 2019-12-04 12:24:53 -06:00
Allen Byrne
6b927a773c HDFFV-10876 Update h5dump and h5ls for new ref api. 2019-11-07 09:49:11 -06:00
Jordan Henderson
93f509a2f2 Fix various Java issues when deprecated symbols are disabled 2019-10-10 13:37:18 -05:00
Larry Knox
b04e1ad058 Update develop branch version to 1.13.0 after creation of hdf5_1_12
branch.
2019-09-25 16:21:23 -05:00
Allen Byrne
cf9eff93e0 Remove obsolete symbol 2019-09-20 09:30:36 -05:00
Allen Byrne
aa8c7b31d7 small syntax changes 2019-09-19 16:32:40 -05:00
Allen Byrne
b477f9bcc7 HDFFV-10901 add missing config options 2019-09-13 11:34:00 -05:00
Allen Byrne
dcab85c83b Add back missing java implementation 2019-09-05 14:35:33 -05:00
Allen Byrne
935f27c1b8 HDFFV-10887 Implement requested functions 2019-08-19 11:58:52 -05:00
Larry Knox
c234479258 Update junit.sh.in to copy lib files to $prefix/lib.
Correct checking for s3 and hdfs options.
2019-08-02 09:58:48 -05:00
Allen Byrne
44e2ddac97 Merge cleanup mostly whitespace 2019-07-30 12:39:20 -05:00
Allen Byrne
517cadac26 Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)
* commit 'f97e11e7635a0cd8728d4604ca5dceb3925ba44c':
  Update comment and check for strtoumax.
  Modify CMakeLists.txt file for renamed h5tools_test_utils files.
  Add HD to string functions. Switched strtoul to strtoumax in H5FDs3comms.c. Removed unused functions and variables in s3 and hdfs TestH5Pfapl*.java. Update Copyright headers.
  Squashed commit of the following:
2019-07-29 16:10:45 -05:00
Allen Byrne
da2ec6163d Update libvers usage 2019-07-28 14:41:52 -05:00
Larry Knox
094f14ef38 Add HD to string functions.
Switched strtoul to strtoumax in H5FDs3comms.c.
Removed unused functions and variables in s3 and hdfs TestH5Pfapl*.java.
Update Copyright headers.
2019-07-26 11:56:03 -05:00