* 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>
* 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>
* More warning fixes (#400)
* Fixed -Wunused-local-typedef warning
* Fixed -Wformat warnings
In one case also removed a `z` character. There was a `z%d` that I think was supposed to be `%zd`
* Fixed -Wshorten-64-to-32 warnings
* Fixed -Wself-assign warnings
* Fixed -Wreserved-id-macro warnings
* Commit format changes from clang-format, clang version 10.0.1.
* Fixed -Wself-assign warnings
* Fixed -Wunused-local-typedef warning
* Fixed -Wformat warnings
In two cases also removed a `z` character. There was a `z%d` that was supposed to be `%zd`.
* Fixed -Wshorten-64-to-32 warnings
* Fixed -Wreserved-id-macro warnings
* Fixed -Wself-assign warnings
* Format source.
* Remove blank lines to pass format check.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Changes found during merge to 1.12 (#414)
* 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
* File locks now work on Windows (#480)
* File locks now work on Windows
Uses LockFileEx() and UnlockFileEx(). Fixes HDFFV-10191 (partial).
* Committing clang-format changes
* Committing clang-format changes
* Fixes commenting in h5repack
* Reworks H5Fis_accessible()
H5Fis_accessible() created a new file handle and attempted to read
through it, which will fail when a file has been opened with an
exclusive lock on operating systems that have mandatory locks.
This change uses the same scheme we use in H5Fopen() to check if
the file is already open and only tries to read the file signature
if the file has not already been opened.
Also adds a test for this behavior.
* Committing clang-format changes
* Trivial change to force github to run actions
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* small edits (#481)
* 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
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Adds an implementation for nanosleep on Windows (#483)
* Adds an implementation for nanosleep on Windows
* Committing clang-format changes
* Fix insane formatter issue
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Updates HSYS_GOTO_ERROR to emit GetLastError() values on Win32 (#492)
* Committing clang-format changes
* Updates H5SYS_GOTO_ERROR to emit Win32's GetLastError()
* Committing clang-format changes
* Format source changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Updates that allow accum SWMR tests to work on Windows (#493)
* Committing clang-format changes
* Updates the accum test to work on Windows
Uses CreateProcess() on Windows
* Source formatting
* Fix for Unix child result
* Fixes process return code bug on Windows
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Disable long double tests and remove CMake flag groups (#494)
* 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
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Misc warning fixes (#495)
* Committing clang-format changes
* Misc warning fixes from Visual Studio
* Committing clang-format changes
* Fixes warnings in swmr.c test
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
* Correct merge errors.
* Committing clang-format changes
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>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
* 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>
* Purge the buffer used in type conversion. (#263)
Some of the uniniitialized bits in the buffer may get carried through
all the way to disk, creating a risk for leaks.
We observed an msan error during the floating point output conversion.
Due to the encoding certain bits could remain untouched during the conversion.
In this draft we zero initialize the dbuf used by every convertor.
* Fixed HDFFV-10480 (CVE-2018-11206) and HDFFV-11159 (CVE-2018-14033) (#405)
* Fixed HDFFV-10480 (CVE-2018-11206) and HDFFV-11159 (CVE-2018-14033)
Description
Checked against buffer size to prevent segfault, in case of data corruption.
+ HDFFV-11159 CVE-2018-14033 Buffer over-read in H5O_layout_decode
+ HDFFV-10480 CVE-2018-11206 Buffer over-read in H5O_fill_new[/old]_decode
Platforms tested:
Linux/64 (jelly)
* Accidentally left in another occurrence of the previous patch from user
after a more correct fix was applied, that is the check now accounted
for the previous advance of the buffer pointer. Removed it.
* Typo
* Fixed format issues.
* Added test.
* Changed arguments to ADD_H5_TEST
* Fixing arguments to ADD_H5_TEST again.
* Fixing arguments again.
* Took out the CMake changes until Allen can help.
* Added files:
tCVE_2018_11206_fill_old.h5
tCVE_2018_11206_fill_new.h5
* Revert "Took out the CMake changes until Allen can help."
This reverts commit c21324d6e0.
* Revert "Fixing arguments again."
This reverts commit 5832a70674.
* Revert "Fixing arguments to ADD_H5_TEST again."
This reverts commit b45de823c2.
* Revert "Changed arguments to ADD_H5_TEST"
This reverts commit 16719824f5.
* Added first argument to ADD_H5_TEST for HDFFV-10480 fix.
* Changed argument 0 to 1
* Revert "Changed argument 0 to 1"
This reverts commit b343d6613b.
* Revert "Added first argument to ADD_H5_TEST for HDFFV-10480 fix."
This reverts commit b8a0f9a9e8.
* Added first argument and corrected the second.
* Updated fixes for HDFFV-10480 and HDFFV-11159/HDFFV-11049
* Improved error messages.
* Added description of the current HDF5 branches; added a draft of contribution policy. (#445)
* Added description of the current HDF5 branches.
* Removed capitalization in from Develop, Release, Feature to reflect the real naming schema
* Added a draft of contributions guidance document.
* Fixed typos.
* Fixed section title.
* Fixed typo.
* Fixed typos and formatting.
* Fixed many typos and simplified the text (e.g., removed testing instructions and left pointers to where to find them, etc.)
* Fixed a typo.
Please enter the commit message for your changes. Lines starting
* Added contributing.md file and rearranged doc entries in alphabetical order.
* ddressed Gerd's review comments; found and fixed more typos.
* Addressed comments from Larry and Scot.
* Fix CMake error message location. (#478)
Print error message if Perl is not found.
* Committing clang-format changes
* Update MANIFEST.
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>
Co-authored-by: Yu Feng <rainwoodman@gmail.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
Co-authored-by: epourmal <epourmal@hdfgroup.org>
* 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>
* 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.
* Fixed clang-tidy readability-misleading-indentation warnings (#427)
* Fixed clang-tidy readability-misleading-indentation warnings
* Reformatted src/H5Zscaleoffset.c with clang v10.0.1.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Fixed clang-tidy readability-redundant-control-flow warnings (#428)
* Fixed clang-tidy readability-redundant-control-flow warnings
Just removed useless trailing return statements.
* Removed blank lines from h5diffgentest.c with clang-format v10.0.1.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* Removed bad function pointer casts (#434)
* Removed bad function pointer casts
In one case fixed the actual function signature to be correct.
* Reformat source with clang v10.0.1.
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
* fix block coordinate printing example (#437)
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: Sean McBride <sean@rogue-research.com>
Co-authored-by: Mike Smith <grimbough@gmail.com>
* 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>
1) Check for valid object header version for a refcount messge
2) Check for invalid fill value size
3) Check for invalid dimension size in a layout message
4) Add --enable-error-stack option to h5stat
5) Add error checks to h5stat.c
6) Add tests to h5stat and h5dump
