Commit Graph

22214 Commits

Author SHA1 Message Date
Dana Robinson
3015e3d7ab
Quiets Automake rules in src directory (#2051)
* Quiets Automake rules in src directory

* Fix whitespace
2022-08-22 06:25:17 -07:00
Dana Robinson
10eb43d0c2
Removes ST from the list of debug packages (Autotools only) (#2045)
* Removes ST from the list of debug packages

The ST package (ternary search trees) was removed from the library a while ago

* Replaced B2 package

I did some crude timing with and without the B2 debug code enabled
and it doesn't seem to make much of a difference.
2022-08-22 04:12:12 -07:00
Dana Robinson
3e38a001a1
Simplify the CODEOWNERS file (#2049)
Simplify the CODEOWNERS file
2022-08-22 03:01:00 -07:00
jhendersonHDF
2b786ffe5a
[WIP] 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
2022-08-19 17:18:30 -07:00
jhendersonHDF
281db5876e
Cleanup some warnings in Java JNI code (#2034) 2022-08-19 09:05:43 -07:00
Dana Robinson
7f6261a677
Removes cmake_ext_mod (files moved to cmake) (#2041)
At one time this content was a git submodule shared between several
projects but that time has long passed.
2022-08-19 07:54:42 -07:00
Dana Robinson
de46019a86
Removes bin/deploy, which just calls h5redeploy under the hood (#2027) 2022-08-19 09:11:22 -05:00
Dana Robinson
8cd97c4793
Updates the warnist script to report gfortran generic warnings (#2040)
These are not associated with a file and line number, like specifying
a non-existant include directory on the compile line.
2022-08-19 09:09:59 -05:00
Larry Knox
9dfcca0bbb
Release updates (#2033)
* Update HISTORy-1_13.txt and clean RELEASE.txt entries after 1.13.2 release.
2022-08-18 08:35:21 -05:00
Neil Fortner
a3fd350483
Add note to RELEASE.txt for GitHub #2016 (#2030)
* Fix bug in attribute type conversion where the background buffer would
not be initialized with the destination contents when necessary.  Other
minor simplification.

* Committing clang-format changes

* Fix warnings.

* Address review comments.

* Add RELEASE.txt note for PR #2016

* Add GitHub number to release note

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-08-17 22:08:43 -05:00
Dana Robinson
e6f16c0ec2
Fixes codespell issues (#2032)
* Fixes codespell issues

* Fixed another typo
2022-08-17 16:31:54 -07:00
Neil Fortner
9304f277e8
Add note to RELEASE.txt for HDFFV-11308 (#2029)
* Add note to RELEASE.txt for HDFFV-11308

* Fix formatting error in RELEASE.txt
2022-08-17 13:35:48 -07:00
Dana Robinson
cf482563cc
Remove unused dependency files (#2025) 2022-08-17 11:21:03 -07:00
Dana Robinson
d201907a4b
Update bin/README.md
Correct missing space after # and ##
2022-08-17 10:46:21 -07:00
Dana Robinson
e4de06057a
Adds a TODO section to bin/README.md (#2028)
Mainly to address the semi-broken state of chkcopyright
2022-08-17 10:45:05 -07:00
jhendersonHDF
07efecd9f4
Adjustments to t_bigio.c for >2GiB I/O test (#1992) 2022-08-17 10:44:00 -07:00
Dana Robinson
ecc9bbe4b6
Adds a README.md file to bin that indicates script usage (#2024)
* Adds a README.md file to bin that indicates script usage

* Forgot header row
2022-08-17 09:34:45 -07:00
Dana Robinson
b54d01fcb5
Removes bin/chkconfigure (#2023)
We check autoconf in configure.ac and can check for anything else in
autogen.sh
2022-08-17 09:22:39 -07:00
Dana Robinson
1483eeef34
Removes bin/format_source_patch (#2022)
This differs only trivially from bin/format_source
2022-08-17 09:22:13 -07:00
Dana Robinson
dc9562ee77
Removes the bin/gcov_script file (#2021)
We don't need fragile scripts to run basic profiling programs
2022-08-17 09:21:38 -07:00
Dana Robinson
afc54d75a1
Replaces bin/newer with -nt comparison in Makefiles (#2020) 2022-08-17 09:21:24 -07:00
Dana Robinson
2bba853375
Removes the bin/yodconfigure script which appears unused (#2019) 2022-08-17 08:03:14 -07:00
Dana Robinson
d6927e49c0
Replaced bin/mkdirs w/ mkdir -p -m 755, which is POSIX (#2018) 2022-08-17 08:02:39 -07:00
Dana Robinson
191c27c0a9
Removes the broken bin/errors script (#2017) 2022-08-16 15:42:55 -07:00
bmribler
951566a4ad
Fix cpp comment (#2011)
* Fix test failure

Description:
    - Added two H5File constructors to open file with non-default fapl
    - Added non-default fapl to test functions
    - Commented certain renaming attribute tests because of the unexpected
      behavior in renaming an attribute (HDFFV-11327)

Platform tested:
    Linux/64 (jelly)

* Committing clang-format changes

* Update H5File.cpp

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-08-16 14:06:55 -07:00
Neil Fortner
75f4d9b042
Fix bug in attribute type conversion wiith compound types (#2016)
* Fix bug in attribute type conversion where the background buffer would
not be initialized with the destination contents when necessary.  Other
minor simplification.

* Committing clang-format changes

* Fix warnings.

* Address review comments.

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-08-16 14:04:48 -07:00
bmribler
10e4dd4ef1
Fix c++ test failure (#2005)
* Fix test failure

Description:
    - Added two H5File constructors to open file with non-default fapl
    - Added non-default fapl to test functions
    - Commented certain renaming attribute tests because of the unexpected
      behavior in renaming an attribute (HDFFV-11327)

Platform tested:
    Linux/64 (jelly)

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-08-12 13:33:30 -05:00
Larry Knox
25ef534039
Update version to 1.13.3-1 after creating hdf5_1_13_2 branch for 1.13.2 (#2004)
release.
Added new version to exceptions in line 75 of src/H5.c.
2022-08-12 08:17:25 -05:00
Larry Knox
029cde6111 Revert "Increment version to 1.13.3-1 after creating hdf5_1_13_2 branch for release"
This reverts commit c58558e872.

H5TEST-tcheck_version-release failed.
2022-08-11 22:45:43 -05:00
Larry Knox
c58558e872 Increment version to 1.13.3-1 after creating hdf5_1_13_2 branch for release
of HDF5 1.13.2.
2022-08-11 22:15:46 -05:00
Allen Byrne
8d5fcbcdce
Correct target name for szaec lib (#2000) 2022-08-11 15:35:14 -07:00
jhendersonHDF
b745b54a09
Only use Subfiling VFD in tools if MPI was initialized previously (#1998) 2022-08-11 15:52:25 -05:00
Allen Byrne
ec5100bf26
Fix Cmake depends prop (#1995) 2022-08-11 09:23:16 -07:00
Allen Byrne
29c8937f60
Remove misnamed java vol clear test (#1990) 2022-08-10 14:20:41 -07:00
jhendersonHDF
a3e37c587b
Only include and run Subfiling example when Subfiling is enabled (#1991) 2022-08-10 14:20:28 -07:00
luzpaz
174505ca3c
Fix typos found in the rest of the hdf5 code-base (#1985)
* Fix typos found in the rest of the hdf5 code-base

* Typo in tool.cmake

* Revert "Typo in tool.cmake"

This reverts commit 06b8403d99.

* Fix clang-format styling
2022-08-10 13:57:26 -07:00
Allen Byrne
e794dc5ec4
Fix CMake macro code commands (#1989) 2022-08-10 12:20:16 -07:00
luzpaz
f04312a792
Fix bug in cppcheck in tool.cmake (#1988)
Ref: https://github.com/HDFGroup/hdf5/pull/1985#issuecomment-1211046328
2022-08-10 12:19:26 -07:00
Gerd Heber
4c73c284e0
Fix4 readme (#1986)
* Update README.md

* Update README.md
2022-08-10 11:17:56 -07:00
Dana Robinson
9777d05848
Move VFD SWMR release version to 1.13.3 in README.md (#1987) 2022-08-10 11:17:43 -07:00
luzpaz
36ae75fb93
Fix typos found in src/ subdirectory (#1983)
Found via `codespell -q 3 -S ./release_docs,./bin/trace,./hl/tools/h5watch/h5watch.c,./tools/test/h5jam/tellub.c -L isnt,inout,nd,parms,parm,ba,offsetP,ser,ois,had,fiter,fo,clude,refere,minnum,offsetp,creat,ans:,eiter,lastr,ans,isn\'t,ifset,sur,trun,dne,tthe,hda,filname,te,htmp,minnum,ake,gord,numer,ro,oce`
2022-08-10 09:03:22 -07:00
jhendersonHDF
6c5b5e0759
Remove usage of libgen.h (#1984) 2022-08-10 09:00:45 -07:00
jhendersonHDF
95ceec786a
Add documentation for parallel compression feature (#1981) 2022-08-09 16:08:13 -07:00
jhendersonHDF
ef33ac8bac
Subfiling VFD - tidying up and fixing a few new testing failures (#1977)
* Rename Subfiling IOC "thread_pool_count" field to "thread_pool_size"

* Add simple HDF5 example for Subfiling VFD

* Subfiling VFD - never cache app topology as it may change

* Subfiling VFD - cleanup unused funtionality and tidy up some TODOs

* Subfiling VFD - tidy up subfiling error handling in H5subfiling_common.c

* Subfiling VFD - show number of failed I/O requests on close

* Subfiling VFD - Update file cmp callback after switching to MPI I/O VFD

* Amend RELEASE.txt with info about h5fuse.sh and Subfiling limitations

* Subfiling VFD - switch to using H5_basename and H5_dirname
2022-08-09 16:05:37 -07:00
Allen Byrne
b84241e57a
Remove stray files, incorrect vds and mpi clean files (#1979) 2022-08-09 08:29:58 -07:00
Allen Byrne
60ba2356de
Revert for older cmake versions (#1974)
* Revert for older cmake versions

* Remove unneeded clear/clean tests because of changes to test macro
2022-08-08 13:01:06 -07:00
Dana Robinson
5d63aca604
Turns off clang optimizations on a couple of onion VFD functions (#1976)
Ancient clang (7.7.3 on OS X) emits problematic code with -O2 or -O3
2022-08-08 12:04:01 -07:00
Dana Robinson
57926d549e
Fixes some badness in the onion VFD revision comment code (#1975)
* Fixes some badness in the revision comment code

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-08-08 11:00:13 -07:00
Allen Byrne
956282fa6f
Develop cmake clean (#1971) 2022-08-06 23:59:31 -05:00
Mark Kittisopikul
7127d8912c
H5Dchunk_iter now passes offsets in units of dataset elements, fix #1419 (#1969)
* H5Dchunk_iter now passes chunk dimension scaled offsets, fix #1419

* Update docs for H5Dchunk_iter, H5Dget_chunk_info*

Modified description for `H5Dchunk_iter`, `H5Dget_chunk_info`, and `H5Dget_chunk_info_by_coord` to the following

 * offset          Logical position of the chunk’s first element in units of dataset elements
 * filter_mask  Bitmask indicating the filters used when the chunk was written
 * size             Chunk size in bytes, 0 if the chunk does not exist
2022-08-06 23:57:41 -05:00