Commit Graph

1993 Commits

Author SHA1 Message Date
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
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
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
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
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
Dana Robinson
a6b76a45b2
Adds h5delete tool (#187)
* Adds h5delete tool

* Fixed MANIFEST

* Added RELEASE.txt note

* Fix typo in RELEASE.txt
2020-12-16 13:50:30 -06:00
Allen Byrne
faf3a2fae0
OESS-98 convert plugin option to FetchContent, add tests (#155)
* OESS-98 convert plugin option to FetchContent, add tests

* Fixes for pkcfg files because of plugin option

* Update other test machines

* OESS-98 fix tools test for plugins

* HDFFV-10865 performance improvement for java array
2020-12-16 11:59:51 -06:00
Dana Robinson
c256612e09
Replace H5E_ATOM major error category with H5E_ID (#121)
* Renames H5I_ATOM to H5I_ID, among other related changes

* Java has been updated.
* Fortran is failing on my VM, even though I don't touch that.

* Adds a RELEASE.txt note for H5E_ATOM to H5E_ID changes

* Fixes typos in comments
2020-11-30 06:50:39 -06:00
Dana Robinson
a6e3d22604
FreeBSD autotools changes (#142)
* Updates to allow autotools builds on recent FreeBSD

* Switches the default C compiler to cc from gcc
  (this may need a version string check if we want to support
  FreeBSD 9 and earlier. FreeBSD 10 was released in 2014)
* Makes the default C++ compiler c++ (no previous setting)
* Both of these resolve to Clang on FreeBSD 10+
* Added a note about flang being unsuitable on FreeBSD
  (the port uses an ancient build of flang that lacks Fortran
  2003 support)
* Autotools only - CMake appears to use different CPP flags
  which cause compilation errors

* Adds a RELEASE.txt note for new FreeBSD autotools changes
2020-11-29 22:44:47 -06:00
Dana Robinson
ffcb354237
Minor/solaris gcc fix (#126)
* Adds gnu99 as the standard when building with gcc on Solaris

* Adds a note to RELEASE.txt and improves comments

For Solaris + gcc fix (HDFFV-11191)
2020-11-25 09:26:35 -06:00
Dana Robinson
7b9c5e124b
Adds a configure/CMake option to control -Werror behavior (#119)
* Works in both Autotools and CMake
* OFF by default
* Reverts "always on" -Werror behavior released in 1.10.7
2020-11-24 21:57:48 -06:00
Allen Byrne
ecbcb4356c
Update release text files (#109)
* Update release text files

* spelling correction

* Update list
2020-11-23 12:04:49 -06:00
Allen Byrne
4e6b6781ee Set doxygen default to normally disabled. 2020-11-09 07:55:52 -06:00
Allen Byrne
014af41c9e Doxygen correct typos 2020-11-04 07:55:41 -06:00
Allen Byrne
d6c92bde00 Doxygen add new files and update docs 2020-11-03 12:23:06 -06:00
Michel Zou
7259b5eb7a CMake: Add an option to opt-out static libgcc
With sjlj exception model, statically link to libgcc/libstdc++
prevents exceptions to be caught from other dynamic libraries.
2020-10-31 10:31:38 +01:00
Michel Zou
de4ccdfd63 CMake: Add an option to opt-out MSVC naming convention
We might want to keep the default mingw import name, see:
https://github.com/msys2/MINGW-packages/blob/master/mingw-w64-hdf5/hdf5-default-import-suffix.patch
2020-10-30 13:19:18 +01:00
Allen Byrne
ba00760d7a HDFFV-10868 - add note 2020-10-28 07:06:01 -05:00
Allen Byrne
c849825c9d Correct SZ options for building plugins 2020-10-21 15:40:42 -05:00
Allen Byrne
4a88f0c8d7 URL and options corrections 2020-10-19 16:21:57 -05:00
Allen Byrne
176eef2737 Whitespace and url correction 2020-10-19 09:42:09 -05:00
Larry Knox
4ad5597525 Correct entries related to --enable-build-mode and --enable-profiling in
INSTALL file, and remove obsolete SZIP paragraph from COPYING file.
2020-10-03 15:32:57 -05:00
Allen Byrne
088014bef4 More info for building plugins with library 2020-09-28 09:41:43 -05:00
Allen Byrne
9941e4b1ae OESS-98 add release note for option 2020-09-27 11:46:58 -05:00
Allen Byrne
aa08db839e Merge pull request #2882 in HDFFV/hdf5 from ~BYRN/hdf5_adb:feature/cmakeV2-clang-format to develop
* commit '571a5e9250ca69adb54ef956361a5cf77059f67c':
  Add h5ls test plugin format target
  Fix manifest
  Add code owners file
  Update actions - split push/pull-request commits
  Change to executable
  Change to based on LLVM format
  Fix comment formatting due to tabs conversion
  Disable formatting for file
  File changes to affect formatting
  CMake and script changes for clang-format
2020-09-25 16:11:52 -05:00
Jordan Henderson
9b3a3445db Add release note for new H5Ssel_iter_reset function 2020-09-18 13:31:50 -05:00
Allen Byrne
30c7264c2c CMake and script changes for clang-format 2020-09-04 16:36:52 -05:00
Dana Robinson
49e01e594e Adds RELEASE.txt note about HDFS VFD stubs being removed 2020-08-27 10:54:14 -07:00
Binh-Minh Ribler
24c23c79d8 Merge pull request #2771 in HDFFV/hdf5 from ~BMRIBLER/hdf5_bmr:hdf5_bmr_HDFFV-10933 to develop
Fixed HDFFV-10933

* commit '16349c5fddce8a74644e18d01d7ea8186aaaa255':
  Fixed HDFFV-10933
2020-08-16 15:34:18 -05:00
Binh-Minh Ribler
16349c5fdd Fixed HDFFV-10933
Description:
    Updated the original fix by Kent Y. in commit
        200a77d8c3
    - used internal functions instead of public API
    - moved some code into the subroutine for a cleaner look.
    - added test to dsets.c
Platforms tested:
    Linux/64 (jelly)
2020-08-14 14:49:42 -05:00
Allen Byrne
500d87fd1f HDFFV-9984 Add options to merge/prune external links during repack 2020-08-14 12:16:58 -05:00
Elena Pourmal
6b347a8d97 Merge pull request #2753 in HDFFV/hdf5 from ~EPOURMAL/hdf5_ep:develop to develop
* commit 'c6248cfb6975a6ecadf0259390247ce05dc13c4b':
  Addresseda Dana's comments from the pull request.
  Fixed several typos in the comments found by Larry during the review.
  The H5DSis_scale function was updated to return "not a dimension scale" (0) instead of failing (-1), when CLASS or DIMENSION_SCALE attributes are not written according to Dimension Scales Specification (HDFFV-10436).
2020-08-14 07:29:40 -05:00
Allen Byrne
747fde00fe spelling 2020-08-13 06:22:50 -05:00
Allen Byrne
cecaed97f7 HDFFV-11127 - force RTLD_LOCAL in dlopen 2020-08-12 16:14:44 -05:00
Elena
768f8abb18 The H5DSis_scale function was updated to return "not a dimension scale" (0)
instead of failing (-1), when CLASS or DIMENSION_SCALE attributes are
not written according to Dimension Scales Specification (HDFFV-10436).
2020-08-12 08:40:11 -05:00
Dana Robinson
47ad0ac723 Renames BEST-EFFORT to BEST_EFFORT for file locking env var 2020-08-06 15:09:59 -07:00
Dana Robinson
bc1bed2c55 Squash merge of file locking fixes 2020-08-03 09:11:27 -07:00
Binh-Minh Ribler
cf4e78b3c9 Merge pull request #2711 in HDFFV/hdf5 from bmr-HDFFV-11120 to develop
Fix HDFFV-11120 and HDFFV-11121 (CVE-2018-13870 and CVE-2018-13869)

* commit '707e30c6be1954c0027374124207e46caae68cbc':
  Fixed typos in error messages.
  Fix HDFFV-11120 and HDFFV-11121 (CVE-2018-13870 and CVE-2018-13869)
2020-07-28 19:08:19 -05:00
Dana Robinson
b201a78b33 Merge pull request #2714 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:h5s_set_extent_none to develop
* commit 'e4603ff8a171e82de6373ba6eddcf59d5eeab5aa':
  Updated the Java tests to deal with H5Sset_extent_none changes
  Fixed additional typos in tselect.c comments.
  Fixes typo in tselect.c
  Updates H5Sset_extent_none() to set H5S_NULL
2020-07-28 11:29:04 -05:00
Dana Robinson
91f5320ff0 Updates H5Sset_extent_none() to set H5S_NULL
The API call used to set the internal H5S_NO_CLASS value which
produced errors when such a dataspace was passed to many other API
calls.

Fixes HDFFV-11027
2020-07-27 17:32:01 -07:00
Binh-Minh Ribler
88e458ac43 Fix HDFFV-11120 and HDFFV-11121 (CVE-2018-13870 and CVE-2018-13869)
Description:
    When a buffer overflow occurred because a name length was corrupted
    and became very large, h5dump produced a segfault on one file and a
    memcpy parameter overlap on another file.  This commit added checks
    that detect a read pass the end of the buffer to prevent these error
    conditions.
Platforms tested:
    Linux/64 (jelly)
    SunOS 5.11 (emu)
2020-07-22 16:13:26 -05:00
Allen Byrne
bae8107621 Add release notes for tools 2020-07-20 10:26:17 -05:00
vchoi
4bc49d8b2b Fix for jira issue HDFFV-11080:
(1) Patch up the file pointer when reading attribute of variable length datatype
(2) Test to verify the fix when doing multiple threads
2020-07-14 10:56:33 -05:00
Allen Byrne
07a52ecb2f HDFFV-11116 Add option for install location of Fortran MOD files 2020-07-09 13:03:58 -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
Binh-Minh Ribler
7c006fd761 - added comment to explain a kluge
- added the associated entry to release notes
2020-06-29 14:16:35 -05:00
Binh-Minh Ribler
7d58d11507 Added note for HDFFV-10591. 2020-06-19 16:08:37 -05:00