Commit Graph
323 Commits
Author SHA1 Message Date
Allen Byrne 5e69b25d84 Correct dimensions in java test (#3483) 2023-09-01 10:53:16 -07:00
Allen Byrne 1dec26ca32 Sync Java changes - particularly VL handling (#3442) 2023-08-29 14:28:52 -07:00
Allen Byrne bfe867c4cb sync cmake and examples changes (#3438)
* sync cmake and examples changes

* Add java lib changes

* Update jave log files

* Update java logger version

* More logger version changes
2023-08-28 08:10:30 -07:00
Allen Byrne d31a017e6c Various merges from develop (#3135)
* Merges from develop/1.14
* Fix doxygen warnings
* Fix spelling
* Fix doxygen ref
* Add braces
* Fix format
* Remove unused file
2023-06-18 22:21:40 -07:00
Larry Knox bc2517b33d Update HDF5 version after 1.10.10 release. (#2681)
* Update HDF5 version after 1.10.10 release.
Update so numbers to match 1.10.10 release so numbers.
Update HISTORY-1_10.txt.
Clean RELEASE.txt entries.

* Missed one version change.
2023-04-07 07:49:26 -05:00
Allen Byrneandgithub-actions 278102ae79 Revert the removal of HDF5GroupInfo class and deprecate. (#2636)
* Revert the removal of HDF5GroupInfo class and deprecate.

* revert H5_QUARTER_HADDR_MAX removal

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2023-03-27 15:47:06 -05:00
Allen Byrne 7b4387df43 Merge CMake cleanup process from develop (#2622)
* Merge CMake cleanup process from develop

* Update test script files
2023-03-22 17:37:04 -07:00
Allen Byrne f1e7081cc2 Add Option to not build gif tools and remove javadoc option (#2611)
* Add Option to not build gif tools and remove javadoc option

* Remove old option

* Fix CMake command format
2023-03-20 15:41:53 -07:00
jhendersonHDF fd5d0944e2 [1.10 Merge] Add Developer build mode to CMake (#2617)
* Add Developer build mode to CMake (#1659)

* Add Developer build mode to CMake

* Set a few CMake variables for Developer build modes

* Refactor enabling of debug and developer-level compile definitions

* Convert cache debugging macros to normal ifdef style

Normal ifdef-style instead of if-style allows build system to define macros
without warning about redefining macros with different values (0 vs. 1)

* Add HDF5 Developer compile definitions to testing files

* Temporarily disable -fanalyzer flag for GCC 12+ Developer builds

* Fix Java tests for Developer build modes (#2079)

* Minor adjustment of Developer build mode changes for 1.10 branch
2023-03-20 15:39:21 -07:00
Allen Byrne 1ffaa38174 Gather latest CMake changes from develop (#2609)
Add HDF5_SRC_INCLUDE_DIRS variable
cleanup cmake comments and documentation
2023-03-20 11:00:00 -07:00
Dana Robinson 6d881fe775 Unify cmake and cmake_ext_mod like develop (#2596) 2023-03-19 21:23:50 -07:00
Larry Knox f723c1df42 Update copyright headers. (#2527) 2023-03-09 22:33:12 -06:00
Allen Byrne af9659d847 1.10: Add spelling check to CI and fix errors. (#2442)
* Update CI and support files to match latest from 1.14

* Correct spelling

* More spelling corrections

* spelling fixes in testpar

* Fix spelling errors in tools

* More tools spelling fixes

* Spelling fixes for rest of tools and some src

* Fix spelling errors in src files, pt 2

* Fix spelling in src pt3

* Fix spelling errors pt4

* Fix spelling errors pt5

* Spelling fix pt6

* fix spelling error examples

* fix spelling in tests

* fix spelling errors in test pt2

* Fix spelling errors in test pt3

* fix spelling in test pt4

* Fix spelling errors in hl

* fix spelling errors in c++

* Spelling fixes for fortran

* spelling fixes for bin and java

* Add relative path

* Change spelling action to use a file for list of ignore words

* Fix spelling ignore list

* remove unused file
2023-02-16 07:23:09 -06:00
Allen Byrne e1673be0ef 1.10 Merge HDFGroup#2175 Implement option for using CMake GNUInstallDirs (#2222) 2022-11-05 14:47:02 -05:00
Allen Byrne 0ca9e2bfad 1.10 Fix some Java warnings (#2147)
* Fix some Java warnings

* fix formatting
2022-10-06 16:40:45 -07:00
jhendersonHDF 7a2dc4b860 Cleanup some warnings in Java JNI code (#2034) (#2099) 2022-09-15 19:29:00 -05:00
Allen Byrne c28fb80cf6 Main Getting Started page and the three HDF Resources have pages. (#2092)
HDFView is still under construction, but mostly there.

Merge the Fortran doxygen changes from develop PR, updated RM index.
Adjusted references to UG and created some TODOs for missing UG modules
Some may just need a reference back to a section of the user guide. Made
some Fortran doxygen changes for overall consistency.
2022-09-08 20:33:47 -05:00
Allen Byrneandgithub-actions 2672e64bf4 Update java code with doxygen tags, add menu files. (#1972)
* Update java code with doxygen tags, add menu files.

* Add -Xdoclint:none to autotools javadoc command

* Committing clang-format changes

* Add fortran RM list descriptions

* delete empty file

* doc tag location changes

* Spelling corrections

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-08-09 16:09:42 -07:00
Allen Byrne 40fc2cca16 1.10 clang 13 format #1933 (#1940)
* clang 13 format #1933

* Correct workflow
2022-07-29 08:36:40 -05:00
Allen Byrneandgithub-actions 2c966f1e55 1 10 Add utility JNI function for 1.10 style references (#1890)
* Add utility JNI function for 1.10 style references

* Clarify text

* Correct signature

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-07-18 06:19:13 -07:00
Allen Byrne ddb0c502ed 1 10 HDFFV-11310 implement JNI VL support for primitive types (#1858)
* HDFFV-11310 - implement vlen read/write for atomic types.

* HDFFV-11310 - VL read/write function for primitive types

* Add read/write VL option

* fix function name typo

* remove debugging prints

* Remove more debugging code

* Correct note to match change in code.

* HDFFV-11318 add VL references as byte arrays

* Fix unreleased allocations, fix debug

* Fix format

* Fix formatting

* Correct typo
2022-07-12 08:47:06 -07:00
Allen Byrne 5e3017f31c Add datasets UG chapter, plus fix doxygen refs (#1841)
* Add datasets UG chapter, plus fix doxygen refs

* Remove duplicates
2022-07-05 09:08:56 -07:00
Allen Byrne 0311d4c00a Hdf5 1 10 sync (#1795)
* Branch sync updates and spelling

* Revert format of getenv
2022-06-09 16:29:04 -05:00
Larry Knox b2794b474a Update version to 1.10.10-1 (#1783)
Update so numbers to match 1.10.9 release.
Clear 1.10.9 entries from RELEASE.txt.
2022-05-19 18:35:50 -05:00
Allen Byrne 4d2b244e73 Add H5P doxygen chapter (#1762) 2022-05-13 23:25:07 -05:00
Allen Byrne 02a5508e50 Reinstate java API removed in 1.10.8 (#1697)
* Revert java API removal with JNI private function

* Fix name typo

* Correct format
2022-04-28 22:46:21 -05:00
Allen Byrne 41a36efde1 Add java to format source (#1690) 2022-04-25 20:32:50 -05:00
jhendersonHDF 3961f6500d Hdf5 1 10 merges (#1633) 2022-04-14 09:05:40 -05:00
Allen Byrne 407c52f397 Merge various cleanup java test, test files, comments (#1364)
Plus some spelling corrections
2022-01-19 17:30:19 -06:00
Allen Byrne 240108c2d7 Merge Update the java slf4j logging jars to latest 1.7.33 (#1371) 2022-01-14 17:27:45 -06:00
Allen Byrne e7f11d487c 1.10 Merge Add javadoc to packages - HDFFV-11285 (#1199)
* Merge Add javadoc to packages - HDFFV-11285

* Correct list
2021-11-20 08:34:03 -06:00
Allen Byrne a931934fa7 Merge Correct java exception declarations #1121 (#1123) 2021-10-25 09:28:18 -05:00
Allen Byrne 8299373d41 1.10 Merge Add missing dataset reference text #1081 (#1083)
* Merge Add missing dataset reference text #1081

* Only print name if not printing data
2021-10-09 09:23:49 -05:00
Larry Knox 0e9960a401 Update version to 1.10.9-1. (#1069)
Clear 1.10.8 entries out of RELEASE.txt.
2021-10-03 13:24:21 -05:00
Allen Byrne 3d085ed2db Fix javadoc and java warnings (#1011) 2021-09-16 08:48:12 -05:00
Larry Knoxandgithub-actions 440cb48268 Update copyright headers with reproduction notice in 5 files (#993) (#1002)
* Update copyright headers with reproduction notice in 5 files that did
not match terms in COPYING file
.

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2021-09-09 13:59:28 -05:00
Allen Byrneandgithub-actions e367c80b39 1.10 merge clang tidy of examples and hl (#966)
* Merge of clang tidy of examples and hl from 1.12

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2021-08-25 18:21:03 -05:00
Allen Byrne cde9951d8e Correct dataset close in java test #919 (#921) 2021-08-19 13:19:41 -05:00
Allen Byrneandgithub-actions 27198d814a Hdf5 1 10 merge of printf specifiers and VS2015 min changes (#612)
* HDFFV-10865 - merge from dev, HDFArray perf fix.

* Remove duplicate setting

* Whitespace changes after clang format

* Undo version 11 clang format changes

* Merge CMake changes from develop

* test testing script merge from develop

* Update supported platforms

* PR#3 merge from develop

* Merge gcc 10 diagnostics option from develop

* Merge #318 OSX changes from develop

* Merge small changes from develop

* Minor non-space formatting changes

* #386 copyright corrections for java folder

* Merges from develop

#358 patches from vtk
#361 fix header guard spelling

* Merge updates

#358 patches from vtk
#361 fix header guard spelling

* format fix

* Fix missing underscore and make H5public.h closer to dev

* Merges from develop

#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
header guard underscore cleanup
JNI cleanup

* format alignment

* Add missing test ref file

* Merge #380 from develop

* Finish java merges from develop

* Fix java issues with tests and javadoc

* Correct use of attribute access plist

* Remove debug code

* Remove unused variable

* Change file access to read only for java tests

* Split clang format operations.

* More javadoc comments

* Remove pre-split setting

* format source

* Change windows TS to use older VS.

* Mostly all javadoc fixes, one argument rename.

* synch file

* Merge of long double fix and compiler flags

* HDFFV-11229 merge changes from develop

* HDFFV-11229 correct test script

* HDFFV-11229 update autotools test script for two ref files

* HDFFV-11229 merge dev changes for long double display in tools

* Committing clang-format changes

* minor whitespace

* remove unneeded macro

* Committing clang-format changes

* Add "option" command for clang options

* Rework CMake add_custom to use the BYPRODUCTS argument

Update pkgconfig scripts for parallel builds.
Fix install COPYING file reference.
Remove unused round defines.
Change CMake default setting of BUILD_CPP to off.

* Fortran target depends

* Remove incorrect source attribute

* Revert define removal

* printf specifiers and VS2015 min changes

* Committing clang-format changes

* Add time struct

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2021-04-30 11:07:50 -05:00
d29e11cdb6 110 copying update (#564)
* close #195. (#196)

* Update HDF5PluginMacros.cmake

* Update HDF5PluginMacros.cmake

* Modify temporary rpath for testing in java example scripts. (#230)

* Fix undefined left shifting of negative numbers (#338)

Undefined Bahavior Sanitizer errored here about left shifting negative numbers.

* 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.

* Cleans up a couple of MSVC warnings in testhdf5 (#475)
* Fixes a few testhdf5 warnings raised in Visual Studio

Visual Studio is grumpier about treating pointers like integers than
gcc.

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fix typos and grammar errors. (#476)

* Suppresses the tcheck_version test's abort dialog on Windows (#477)

* Suppresses the tcheck_version test's abort dialog on Windows

Windows raises a modal abort/retry/ignore dialog box when CRT
calls abort(). This change installs a report hook that suppresses
the dialog so that the CMake tests don't time out waiting for a
nonexistent user to click a dialog box.

* Committing clang-format changes

* Removes __cdecl from callback

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Update top-level COPYING file and remove COPYING files from
subdirectories.

* Update top-level COPYING file and remove COPYING files from subdirectories (#561)

* Modify temporary rpath for testing in java example scripts.

* Update URL in source file Copyright headers for web copy of COPYING (license) file.

* Add release_docs/code-conventions.md file.

* Add script to test h5py.

* Fix script error.

* Add file h5pytest.yml.

* Test declaration of counter variables in for loops.

* Committing clang-format changes

* Committing clang-format changes

* Added [] to line 126 of H5LTanalyze.l.
Ran bin/genparser with flex v2.6.4 and Bison v3.0.4 on jelly.

* Revert "Added [] to line 126 of H5LTanalyze.l."

This reverts commit e4a9cee441.

* Revert extra commits to match canonical develop.

* Update top-level COPYING file and remove COPYING files from
subdirectories.

* Remove subdirectory COPYING files from MANIFEST.

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: Sean McBride <sean@rogue-research.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2021-04-26 14:08:31 -05:00
Allen Byrneandgithub-actions c9caf426a8 1 10 Merge of long double fix and compiler flags (#531)
* HDFFV-10865 - merge from dev, HDFArray perf fix.

* Remove duplicate setting

* Whitespace changes after clang format

* Undo version 11 clang format changes

* Merge CMake changes from develop

* test testing script merge from develop

* Update supported platforms

* PR#3 merge from develop

* Merge gcc 10 diagnostics option from develop

* Merge #318 OSX changes from develop

* Merge small changes from develop

* Minor non-space formatting changes

* #386 copyright corrections for java folder

* Merges from develop

#358 patches from vtk
#361 fix header guard spelling

* Merge updates

#358 patches from vtk
#361 fix header guard spelling

* format fix

* Fix missing underscore and make H5public.h closer to dev

* Merges from develop

#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
header guard underscore cleanup
JNI cleanup

* format alignment

* Add missing test ref file

* Merge #380 from develop

* Finish java merges from develop

* Fix java issues with tests and javadoc

* Correct use of attribute access plist

* Remove debug code

* Remove unused variable

* Change file access to read only for java tests

* Split clang format operations.

* More javadoc comments

* Remove pre-split setting

* format source

* Change windows TS to use older VS.

* Mostly all javadoc fixes, one argument rename.

* synch file

* Merge of long double fix and compiler flags

* HDFFV-11229 merge changes from develop

* HDFFV-11229 correct test script

* HDFFV-11229 update autotools test script for two ref files

* HDFFV-11229 merge dev changes for long double display in tools

* Committing clang-format changes

* minor whitespace

* remove unneeded macro

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2021-04-19 17:19:58 -05:00
87d18137ce Hdf5 merge issue 487 v110 (#533)
* Cleans up a couple of MSVC warnings in testhdf5 (#475)
* Fixes a few testhdf5 warnings raised in Visual Studio

Visual Studio is grumpier about treating pointers like integers than
gcc.

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fix typos and grammar errors. (#476)

* Suppresses the tcheck_version test's abort dialog on Windows (#477)

* Suppresses the tcheck_version test's abort dialog on Windows

Windows raises a modal abort/retry/ignore dialog box when CRT
calls abort(). This change installs a report hook that suppresses
the dialog so that the CMake tests don't time out waiting for a
nonexistent user to click a dialog box.

* Committing clang-format changes

* Removes __cdecl from callback

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Committing clang-format changes

Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
2021-04-01 15:14:21 -05:00
Allen Byrneandgithub-actions 05b0f6745c 1 10 - Mostly all javadoc warning fixes (#508)
* HDFFV-10865 - merge from dev, HDFArray perf fix.

* Remove duplicate setting

* Whitespace changes after clang format

* Undo version 11 clang format changes

* Merge CMake changes from develop

* test testing script merge from develop

* Update supported platforms

* PR#3 merge from develop

* Merge gcc 10 diagnostics option from develop

* Merge #318 OSX changes from develop

* Merge small changes from develop

* Minor non-space formatting changes

* #386 copyright corrections for java folder

* Merges from develop

#358 patches from vtk
#361 fix header guard spelling

* Merge updates

#358 patches from vtk
#361 fix header guard spelling

* format fix

* Fix missing underscore and make H5public.h closer to dev

* Merges from develop

#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
header guard underscore cleanup
JNI cleanup

* format alignment

* Add missing test ref file

* Merge #380 from develop

* Finish java merges from develop

* Fix java issues with tests and javadoc

* Correct use of attribute access plist

* Remove debug code

* Remove unused variable

* Change file access to read only for java tests

* Split clang format operations.

* More javadoc comments

* Remove pre-split setting

* format source

* Change windows TS to use older VS.

* Mostly all javadoc fixes, one argument rename.

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2021-03-25 07:35:24 -05:00
Allen Byrne dd5b8a8747 1 10 Fix java data export functions (#450)
* HDFFV-10865 - merge from dev, HDFArray perf fix.

* Remove duplicate setting

* Whitespace changes after clang format

* Undo version 11 clang format changes

* Merge CMake changes from develop

* test testing script merge from develop

* Update supported platforms

* PR#3 merge from develop

* Merge gcc 10 diagnostics option from develop

* Merge #318 OSX changes from develop

* Merge small changes from develop

* Minor non-space formatting changes

* #386 copyright corrections for java folder

* Merges from develop

#358 patches from vtk
#361 fix header guard spelling

* Merge updates

#358 patches from vtk
#361 fix header guard spelling

* format fix

* Fix missing underscore and make H5public.h closer to dev

* Merges from develop

#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
header guard underscore cleanup
JNI cleanup

* format alignment

* Add missing test ref file

* Merge #380 from develop

* Finish java merges from develop

* Fix java issues with tests and javadoc

* Correct use of attribute access plist

* Remove debug code

* Remove unused variable

* Change file access to read only for java tests

* Split clang format operations.

* More javadoc comments

* Remove pre-split setting

* format source
2021-03-10 07:41:14 -06:00
Allen Byrne 583e9d5c32 1 10 Merges from develop (#424)
* HDFFV-10865 - merge from dev, HDFArray perf fix.

* Remove duplicate setting

* Whitespace changes after clang format

* Undo version 11 clang format changes

* Merge CMake changes from develop

* test testing script merge from develop

* Update supported platforms

* PR#3 merge from develop

* Merge gcc 10 diagnostics option from develop

* Merge #318 OSX changes from develop

* Merge small changes from develop

* Minor non-space formatting changes

* #386 copyright corrections for java folder

* Merges from develop

#358 patches from vtk
#361 fix header guard spelling

* Merge updates

#358 patches from vtk
#361 fix header guard spelling

* format fix

* Fix missing underscore and make H5public.h closer to dev

* Merges from develop

#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
header guard underscore cleanup
JNI cleanup

* format alignment

* Add missing test ref file
2021-03-04 16:06:47 -06:00
Allen Byrne c14fa9cebf 1 10 merge java copyright header changes (#392)
* HDFFV-10865 - merge from dev, HDFArray perf fix.

* Remove duplicate setting

* Whitespace changes after clang format

* Undo version 11 clang format changes

* Merge CMake changes from develop

* test testing script merge from develop

* Update supported platforms

* PR#3 merge from develop

* Merge gcc 10 diagnostics option from develop

* Merge #318 OSX changes from develop

* Merge small changes from develop

* Minor non-space formatting changes

* #386 copyright corrections for java folder
2021-03-01 12:33:35 -06:00
dea591a353 Hdf5 1 10 update license url part2 (#404)
* close #195. (#196)

* Update HDF5PluginMacros.cmake

* Update HDF5PluginMacros.cmake

* Modify temporary rpath for testing in java example scripts. (#230)

* Fix undefined left shifting of negative numbers (#338)

Undefined Bahavior Sanitizer errored here about left shifting negative numbers.

* 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.

* 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.

* Update URL in source file Copyright headers for web.

Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: Sean McBride <sean@rogue-research.com>
2021-03-01 10:35:51 -06:00
Allen Byrne 8cfcf0e394 1 10 merges from develop (#298)
* HDFFV-10865 - merge from dev, HDFArray perf fix.

* Remove duplicate setting

* Whitespace changes after clang format

* Undo version 11 clang format changes

* Merge CMake changes from develop

* test testing script merge from develop

* Update supported platforms
2021-02-04 08:20:25 -06:00
Allen Byrne 674e1f02a3 1 10 Whitespace changes after clang-format run (#287)
* HDFFV-10865 - merge from dev, HDFArray perf fix.

* Remove duplicate setting

* Whitespace changes after clang format

* Undo version 11 clang format changes
2021-01-29 06:59:33 -06:00
Larry KnoxandH. Joe Lee 0a7296663b Hdf5 1 10 - Modify temporary rpath for testing in java example scripts (#243)
* close #195. (#196)

* Update HDF5PluginMacros.cmake

* Update HDF5PluginMacros.cmake

* Modify temporary rpath for testing in java example scripts. (#230)

Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
2021-01-06 08:13:59 -06:00