Commit Graph

21724 Commits

Author SHA1 Message Date
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
Sean McBride
c29e1b9fdf
Patches from vtk (#358)
* Drop the export attribute on forward declaration

They don't mean anything on forward declarations anyways.

* Fixed -Wunused-parameter warnings in some C++ files

Allowed all the attribute #defines to work in C++ also.

* Fixed -Wunused-variable warnings by removing dead code

* Fixed all -Wshorten-64-to-32 warnings by adjusting casts

There was no truncation in fact, since the unsigned result was upcast to size_t then implicitly downcast to uint32_t.

* Fixed all -Wcomma warnings by spliting statements onto own lines

* Fixed all -Wself-assign warnings with different unused param suppression

* Fixed all -Wextra-semi warnings

* Fixed all -Wswitch-enum warnings

Just added new explicit cases with the existing default case.

* Fixed all -Wmissing-prototypes warnings

Just made functions static. Moved them into an extern "C" block.

* Reformatted source with bin/format_source using clang version 10.0.1

Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
2021-02-25 12:15:02 -06:00
Sean McBride
c17b4b93d6
Fixed many -Wreserved-id-macro warnings by fixing header guard spelling (#361)
* Fixed many -Wreserved-id-macro warnings by fixing header guard spelling

Removed leading underscore(s) from header guard spelling.  Used 2 regexes:

` _H5(.*)_H`
` __H5(.*)_H`

Applied case-insensitively to only .h files.

* Modified scripts that generate header files to not use underscore prefix

Interestingly, there was already no leading underscore in the trailing comment at the end of the file

* Fixed remaining -Wreserved-id-macro warning not caught by regex
2021-02-22 22:29:56 -06:00
Sean McBride
5ed255a607
Fixed all -Wincompatible-pointer-types-discards-qualifiers warnings (#341)
* Fixed various -Wincompatible-pointer-types-discards-qualifiers warnings by adding const

* Fixed various -Wincompatible-pointer-types-discards-qualifiers warning by removing extraneous consts

There were casts with const, but the function parameter doesn't actaully take const, so just modified the casts.

In the other case, a local variable was const that should not have been, becuase its source wasn't const either.

* Fixed a -Wincompatible-pointer-types-discards-qualifiers warning by strdup-ing a string

Create a duplicate string instead of mutating a supposedly const one.
2021-02-22 11:37:12 -06:00
bmribler
99669024ff
Fixed HDFFV-11150 (#356)
Description
    Replaced an HDassert with a check for null pointer in H5O_dec_rc() to
    catch null pointer in corrupted data situation.
    As a result, removed the null check prior to H5O_dec_rc() calls.
Platforms tested:
    Linux/64 (jelly)
2021-02-19 13:01:44 -06:00
Sean McBride
5f015f4742
Fix undefined left shifting of negative numbers (#338)
Undefined Bahavior Sanitizer errored here about left shifting negative numbers.
2021-02-19 12:48:04 -06:00
Sean McBride
0a2a385acc
Fixed uninitialized warnings (#360)
* Fixed all -Wsometimes-uninitialized warnings by initializing variables

* Fixed all -Wconditional-uninitialized warnings by initializing variables

* Commit alignment changes from running bin/format_source with clang
version 10.0.1.

Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
2021-02-19 11:25:44 -06:00
Sean McBride
a6f1b6ce53
Fixed various clang -Wformat-security warnings (#340) 2021-02-19 09:18:30 -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
Larry Knox
4819f89d3f
Update license url (#332)
* Modify temporary rpath for testing in java example scripts.

* Update URL in source file Copyright headers for web copy of COPYING
file - src and test directories.
2021-02-17 08:52:04 -06:00
jhendersonHDF
afdb7903c6
Fix for HDFFV-11109 - Copy MPI comm and info object into output FAPL from H5F_get_access_plist (#342)
* Avoid freeing MPI_COMM_WORLD in H5_mpi_comm_free

* Copy MPI Comm and Info to new FAPL in H5F_get_access_plist
2021-02-17 06:37:23 -06:00
Sean
2359a9b020
Fix clang unknown pragma warnings (#337)
Although clang defines __GNUC__ and supports most gcc warnings, it doesn't support all, and will in fact even warn about an unknown pragma.

Guard appropriately.
2021-02-15 15:32:08 -06:00
Sean
5c1ddd2d49
Fix cmake syntax error with regex escaping (#336)
Fixes:

   Syntax error in cmake code at

     /some/path/hdf5/CMakeLists.txt:240

   when parsing string

     .*#define[ \t]+H5_VERS_SUBRELEASE[ \t]+\"([0-9A-Za-z._\-]*)\".*$

   Invalid escape sequence \-
2021-02-15 15:26:48 -06:00
Sean
ca6a26225d
Detect correct long double size with universal binaires (#335)
On macOS on x86_64, long double is 16 bytes; on macOS on arm64, it's 8 bytes.

Use the same existing technique used to properly detect other sizes to now also properly detect the size of long double.

For bug #311.
2021-02-15 15:23:43 -06:00
jhendersonHDF
52ac74689a
Check for wrap context before unwrapping file VOL object in H5F__dest (#325) 2021-02-09 18:41:49 -06:00
Allen Byrne
bccf5b5c08
Add option to control gcc 10 warnings diagnostics (#321)
* 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
2021-02-08 17:23:09 -06:00
Sean
aa95b70f6d
Remove prohibition against building Universal Binaries on macOS (#318)
Fixes github issue #311.
2021-02-08 14:16:41 -06:00
jhendersonHDF
2b4b8e8423
Unwrap file VOL object when destroying file (#308) 2021-02-06 08:20:49 -06:00
Allen Byrne
b3934e99eb
Changes for sanitize=address (#312)
* 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
2021-02-05 10:35:05 -06:00
Scot Breitenfeld
a06693be21
Fix DS examples (#307)
* fixed missed closing of a dataset

* fixed missed closing of a dataset
2021-02-04 07:17:49 -06:00
jhendersonHDF
c55ac8ab71
Ensure processes always synchronize in t_shapesame test setup (#306) 2021-02-03 11:08:19 -06:00
Dana Robinson
eac05994c7
Fixes bin/trace so it doesn't dirty the repo when autogen runs (#295)
* Fixes bin/trace so it doesn't dirty the repo when autogen runs

* Put the trace max back to 110 and comment off H5O.c line
2021-02-03 08:19:58 -06:00
Allen Byrne
ab2c31bc87
Update supported platforms (#303)
* 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
2021-02-03 07:57:04 -06:00
Neil Fortner
ddd799282f
Modify VDS code to always open source files with H5F_CLOSE_WEAK close (#291)
degree.  Add test cases to VDS test for this, and reduce the amount of
output from that test.
2021-01-30 16:47:23 -06:00
Dana Robinson
4869307bd6
Remove unused AC_REVISION macro from configure.ac (#292)
* Fixes a wayward parenthesis in H5TS.c

* Removes unmaintained AC_REVISION macro from configure.ac
2021-01-29 22:40:43 -06:00
Allen Byrne
6db183590f
develop revert source to clang-format version 11 (#293)
* 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
2021-01-29 06:55:18 -06:00
Allen Byrne
5a812bf519
develop clang-format comments (#286)
* 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
2021-01-27 17:51:59 -06:00
Allen Byrne
9524dc494f
Jan ws changes (#282)
* 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

* Whitespace fixes except for H5Tprivate.h typo fix
2021-01-27 08:15:34 -06:00
Allen Byrne
799ec0fde4
Small fixes (#285)
* 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

* Small changes plus merge of tools arg parse from 1.12
2021-01-27 07:56:28 -06:00
Allen Byrne
d7bce33123
Java replace switch on string (#273)
* 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
2021-01-26 22:27:10 -06:00
Quincey Koziol
b516921b7d
Add H5ESpublic.h to main hdf5.h header (#278) 2021-01-22 20:40:40 -06:00
Neil Fortner
a8ee85971b
Fix problems with vlens and refs inside compound using H5VLget_file_type() (#274)
* Fixed problems with vlens and refs inside compound using H5VLget_file_type()

* Fix date in RELEASE.txt

* Add assertions

* Move some manipulation of H5VL_object_t struct fields into the H5VL
package.
2021-01-22 15:05:39 -06:00
Dana Robinson
672892cc0e
Fixes a wayward parenthesis in H5TS.c (#262) 2021-01-19 18:42:38 -06:00
Neil Fortner
a5ffedb8c6
Improve performance of multiple calls to H5Sget_select_elem_pointlist (#270)
* Cache the pointer to the next point to process after the last call to
H5S__get_select_elem_pointlist.  This allows the normal process of
iterating over the points in batches to be much more efficient, as the
library does not need to traverse the entirety of the preceding points
every time the funciton is re-entered.

* Update RELEASE.txt for point selection iteration performance fix.
2021-01-19 18:42:14 -06:00
Allen Byrne
9578160cef
11099 Add help text line (#259)
* 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
2021-01-15 17:38:03 -06:00
Dana Robinson
a1091585ad
Fixes naked pthread usage in H5TS code added for async (#260) 2021-01-14 13:44:28 -06:00
Dana Robinson
0d8529055d
Removes lock/unlock callbacks from ros3 and hdfs VFDs (#258)
* Removes no-op callback stubs from read-only VFDs

Also changes VFD registration to allow read-only VFDs with no
write callback to be registered.

* Adds a RELEASE.txt note for HDFFV-11205

For the read-only VFD registration change

* Revert "Removes no-op callback stubs from read-only VFDs"

This reverts commit a7a9549730.

* Removes lock callbacks from ros3 and hdfs VFDs
2021-01-14 08:19:48 -06:00
Allen Byrne
b1eb47ac4d
Reclassify CMake messages - HDFFV-11144 (#253)
* 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
2021-01-13 08:29:15 -06:00
Dana Robinson
b84f48f929
Allow read-only VFD registration (#257)
* Removes no-op callback stubs from read-only VFDs

Also changes VFD registration to allow read-only VFDs with no
write callback to be registered.

* Adds a RELEASE.txt note for HDFFV-11205

For the read-only VFD registration change
2021-01-12 22:12:51 -06:00
Allen Byrne
0e09b0b636
Keep doxygen comment length under 100 char line length (#247)
* 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
2021-01-08 12:02:44 -06:00
Dana Robinson
9e1739f76f
Fixes Autotools detection of the st_blocks field in stat (#246)
* Fixes Autotools detection of the st_blocks field in stat

The Autotools and CMake will now both correctly determine if the
stat struct has the st_blocks field and set H5_HAVE_STAT_ST_BLOCKS
appropriately.

* Fixes a typo in configure.ac
2021-01-08 06:52:08 -06:00
Quincey Koziol
e3b7d68826
Reformat source (#244) 2021-01-07 16:16:00 -06:00
Neil Fortner
3ae45182b5
Fix error is H5Mclose_async. (#240) 2021-01-05 10:02:03 -06:00
Allen Byrne
4b733b2926
Remove duplicate setting (#236)
* OESS-98 convert plugin option to FetchContent, add tests

* Fixes for pkcfg files because of plugin option

* OESS-98 fix tools test for plugins

* Remove duplicate setting
2021-01-05 08:08:54 -06:00
Larry Knox
f50fd0cc07
Modify temporary rpath for testing in java example scripts. (#230) 2020-12-29 15:43:49 -06:00
Dana Robinson
a6386824c7
Switch bool/true/false to hbool_t/TRUE/FALSE in a few places (#229) 2020-12-24 09:12:01 -06:00
bljhdf
5c9d08a964
Doxygen: Added more H5P RM entries (#226)
* Doxygen - RM entries for H5A, H5S, and H5P APIs

* fix issues on ubuntu

* added missing H5F_fspace_strategy_t_snip

* Doxygen: Add more H5P functions

Co-authored-by: hdfhelp <hdfhelp@jelly.ad.hdfgroup.org>
2020-12-23 22:13:14 -06:00
bmribler
5af00191b5
RM blocks for H5R (#219)
* Transferred RM blocks in H5D and H5G to develop

* Added RM blocks to H5R and added new aliases.

Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
2020-12-23 00:01:46 -06:00
Allen Byrne
8183284f09
dev -Update pkgconfig settings with version - #218 (#220)
* OESS-98 convert plugin option to FetchContent, add tests

* Fixes for pkcfg files because of plugin option

* OESS-98 fix tools test for plugins

* Pkgconfig fix - #218

* Update all pkgconfig settings with version
2020-12-22 14:43:58 -06:00
Quincey Koziol
71440cef1c
Add compiler flags for GCC 10, along with updating warnhist script to accommodate them. (#217) 2020-12-21 12:57:18 -06:00