Commit Graph

23384 Commits

Author SHA1 Message Date
Dana Robinson
7b8fe54c1a
Remove noise comment from H5DO.c (#4342) 2024-04-08 07:56:56 -07:00
Dana Robinson
7349023339
Remove the getting started guide (#4339)
This was moved to the wiki
2024-04-07 17:24:03 -05:00
Dana Robinson
a99d620172
Clean up random number generator code (#4338)
* Clean up random number generator code

Depending on the platform, we use a mix of random, rand, and rand_r
to generate pseudo-random numbers, along with a messy set of ifdefs
in H5private.h. We are not a cryptographic library, only use random
numbers in our test code, and have no need for anything more than the
C standard's (s)rand(). There's no point dithering about using rand()
vs random() when we're also doing bad things like using mod to
restrict the range, which introduces bias.

Also removes CMake/configure checks for rand_r and random

* Remove random/rand_r checks from build system

* Fix missed HDrandom after GitHub merge
2024-04-07 15:15:25 -07:00
bmribler
8def3f61bd
Add VDS and SWMR to documentation (#4336) 2024-04-07 17:01:45 -05:00
Dana Robinson
f776a348fc
Remove HD prefix from toupper/tolower (#4340) 2024-04-07 14:51:58 -07:00
Dana Robinson
0de523bc42
Remove HD macros for C time functions (#4337)
* HDasctime
* HDclock
* HDctime
* HDdifftime
* HDgmtime
* HDlocaltime
* HDmktime
* HDtime
* HDtzset

HDgettimeofday will be done later
2024-04-07 14:09:23 -07:00
H. Joe Lee
a6d689a1d6
Fix grammar and content in HDF5Examples (#4333) 2024-04-06 07:21:18 -05:00
bmribler
ded34c53f4
Revert "Fixed dead links in docs (#4334)" (#4335)
This reverts commit 408fc66002.
2024-04-06 07:00:53 -05:00
bmribler
408fc66002
Fixed dead links in docs (#4334) 2024-04-05 11:13:46 -05:00
mattjala
88b640a1ac
Remove unnecessary step from REST VOL workflow (#4331) 2024-04-04 19:56:09 -05:00
jhendersonHDF
90a1baede9
Revise _Float16 configure checks (#4323)
Run configure checks with and without CFLAGS/CMAKE_C_FLAGS since some
compilers work in one case while not working in the other case

Sync CMake configure checks with Autotools
2024-04-04 09:59:25 -05:00
jhendersonHDF
3db69574f0
Fix h5py testing failure due to invalid datatype IDs (#4321)
Fixes an issue where invalid datatype IDs are passed to application conversion
functions in the case where the top-level conversion function is a library-internal
function that operates on a container-like datatype, but one or more of the
base datatype members are converted with an application conversion function.
2024-04-04 09:55:20 -05:00
jhendersonHDF
3424bc9756
Fix issues with empty or uninitialized link names (#4322)
Converts an assertion in H5G_loc_find into a normal error
check that checks for empty link names

Initializes H5O_link_t structure early in H5G__ent_to_link
to avoid trying to free potentially uninitialized memory

Checks for an empty link name after H5MM_strndup in
H5G__ent_to_link

Fixes GitHub #4307
2024-04-04 07:34:05 -05:00
jhendersonHDF
a37a049ceb
Simply check for datatypes with unusual number of unused bits (#4309)
Avoids potential undefined behavior in H5T_is_numeric_with_unusual_unused_bits
2024-04-03 15:40:15 -07:00
H. Joe Lee
c22b801c9d
Remove VS ptable error from Known Problems (#4317) 2024-04-03 10:48:27 -05:00
jhendersonHDF
c4544543a2
Remove old wait_H5Tinit.cmake file (#4314) 2024-04-03 02:29:25 -07:00
jhendersonHDF
fa0c3ca3db
Fix README badges (#4313) 2024-04-03 02:28:53 -07:00
H. Joe Lee
c6e26a1da9
Fix typo - differetly (#4311) 2024-04-02 14:55:12 -07:00
Allen Byrne
2f4e9b1392
PR merge workflows (#4303)
* Merge the Test Express workflows into the PR CI

* Split merge request triggers into autotools vs cmake
2024-04-02 14:22:04 -05:00
Scot Breitenfeld
8b5644a0cd
Report build options of VFDs (#4304)
* changed to if string contains instead

* return status of VFDs in libhdf5.settings

* use *_ENABLE_* settings instead to report the state

* added map state

* updated resetting status if cmake option fails
2024-04-02 13:24:02 -05:00
Allen Byrne
9148f7c563
Prepend MPI_TEST_ to parallel example test names (#4306) 2024-04-02 13:01:02 -05:00
H. Joe Lee
f2cf0be9cb
Fix typo - glueing (#4299) 2024-04-02 07:12:17 -07:00
dependabot[bot]
16b2bc57b7
Bump the github-actions group with 3 updates (#4300)
Bumps the github-actions group with 3 updates: [actions/download-artifact](https://github.com/actions/download-artifact), [softprops/action-gh-release](https://github.com/softprops/action-gh-release) and [github/codeql-action](https://github.com/github/codeql-action).


Updates `actions/download-artifact` from 4.1.1 to 4.1.4
- [Release notes](https://github.com/actions/download-artifact/releases)
- [Commits](https://github.com/actions/download-artifact/compare/v4.1.1...c850b930e6ba138125429b7e5c93fc707a7f8427)

Updates `softprops/action-gh-release` from 1 to 2
- [Release notes](https://github.com/softprops/action-gh-release/releases)
- [Changelog](https://github.com/softprops/action-gh-release/blob/master/CHANGELOG.md)
- [Commits](de2c0eb89a...9d7c94cfd0)

Updates `github/codeql-action` from 3.24.6 to 3.24.9
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](8a470fddaf...1b1aada464)

---
updated-dependencies:
- dependency-name: actions/download-artifact
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: github-actions
- dependency-name: softprops/action-gh-release
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: github-actions
- dependency-name: github/codeql-action
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: github-actions
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2024-04-02 07:11:56 -07:00
H. Joe Lee
1042ed4d49
Fix typo - Cnversion (#4301) 2024-04-02 07:11:21 -07:00
Dana Robinson
a314a7a497
Fix divide-by-zero when page buf page size is 0 (#4296)
If a corrupt file sets the page buffer size in the superblock to zero,
the library could attempt to divide by zero when allocating space in
the file. The library now checks for valid page buffer sizes when
reading the superblock message.

Fixes oss-fuzz issue 58762
2024-04-01 12:26:48 -07:00
H. Joe Lee
ff7f5861cb
Fix Figure 9. table format in HDF5 Groups User Guide (#4295) 2024-04-01 12:02:14 -05:00
Allen Byrne
a7a4fc2445
Synch workflows and require apt-get update (#4294) 2024-04-01 11:04:55 -05:00
Neil Fortner
589f5238fe
Fix problems with background buffers and array datatypes (#4218)
* Fix bug in array conversion with strided background buffer. Convert some
memmove calls to non-overlapping buffers to memcpy.

* Revert inappropriate use of mempy to memmove in H5T__conv_array

* Add testing

* Add RELEASE.txt note and overwrite test case.
2024-03-31 22:49:45 -05:00
H. Joe Lee
23b78f6721
Use AOCC 4.2 and OpenMPI 4.1.6 (#4290) 2024-03-31 22:47:56 -05:00
bmribler
f24e8113a3
Add documentation (H5FD) (#4269) 2024-03-31 22:47:14 -05:00
jhendersonHDF
dc69e39f65
Add configure options for disabling extension features (#4277)
Add configure option to enable or disable extension features in general

Add configure option to enable or disable _Float16 support

Add new config options to various settings files
2024-03-31 22:45:50 -05:00
jhendersonHDF
ce53bc020d
Fixes for file format security issues (#4283) 2024-03-31 22:44:18 -05:00
Allen Byrne
875fb3e70a
Add missing foreach for VFD and Pasthrough runs (#4292) 2024-03-31 22:43:36 -05:00
Dana Robinson
80fc8558b0
Fix off_t straggers (#4291)
Convert off_t to HDoff_t (mainly for Windows):

* h5jam
* h5unjam
* chunk_info test
2024-03-31 12:12:26 -07:00
Allen Byrne
203a95abb5
Add autotools ExpressTest=0 (#4289) 2024-03-30 22:33:19 -07:00
Allen Byrne
530effbbc1
Fix example ref files path (#4285) 2024-03-30 06:45:57 -05:00
Scot Breitenfeld
54a42fc9d9
changed to if string contains instead (#4286) 2024-03-29 15:40:56 -07:00
H. Joe Lee
2d970ecba4
chore: improve error message (#4287)
close #192
2024-03-29 15:39:33 -07:00
Allen Byrne
6596c3edc3
Add TestExpress=0 workflow (#4281)
* Add TestExpress=0 CI
2024-03-29 14:19:58 -05:00
Dana Robinson
855b95b34b
Relaxed behavior of H5Pset_page_buffer_size() when opening files (#4280)
This API call sets the size of a file's page buffer cache. This call
was extremely strict about matching its parameters to the file strategy
and page size used to create the file, requiring a separate open of the
file to obtain these parameters.

These requirements have been relaxed when using the fapl to open
a previously-created file:

* When opening a file that does not use the H5F_FSPACE_STRATEGY_PAGE
  strategy, the setting is ignored and the file will be opened, but
  without a page buffer cache. This was previously an error.

* When opening a file that has a page size larger than the desired
  page buffer cache size, the page buffer cache size will be increased
  to the file's page size. This was previously an error.

The behavior when creating a file using H5Pset_page_buffer_size() is
unchanged.

Fixes GitHub issue #3382
2024-03-29 11:46:31 -07:00
Larry Knox
64f86353d1
Remove CRLF from NEWSLETTER.txt. (#4282) 2024-03-29 09:34:46 -07:00
jhendersonHDF
50d30bd4f0
Fix potential buffer read overflows in H5PB_read (#4279)
H5PB_read previously did not account for the fact that the size of the
read it's performing could overflow the page buffer pointer, depending
on the calculated offset for the read. This has been fixed by adjusting
the size of the read if it's determined that it would overflow the page.
2024-03-29 07:43:59 -05:00
jhendersonHDF
98c19af7c8
Fix range check in H5_addr_overlap (#4278)
When the H5_addr_overlap macro was updated to use H5_RANGE_OVERLAP,
it failed to take into account that H5_RANGE_OVERLAP expects the
range to be inclusive. This lead to an assertion failure in
H5MM_memcpy due to a memcpy operation on overlapping memory.
This has been fixed by subtracting 1 from the calculated high
bound values passed to H5_RANGE_OVERLAP
2024-03-29 07:41:42 -05:00
Allen Byrne
16ba713e31
Merge julia workflows into standard ci format (#4273) 2024-03-28 15:29:22 -07:00
Scot Breitenfeld
f6ae241032
Addresses configuration fortran testing flags (#4276)
* turn warnings to errors in fortran configure test

* Intel fortran test fix
2024-03-28 16:55:32 -05:00
H. Joe Lee
6c54122042
Update Cygwin installation guide (#4265) 2024-03-28 14:40:28 -05:00
Dana Robinson
e908accadf
Add release note for CVE-2017-17507 (#4275) 2024-03-28 12:08:05 -07:00
Dana Robinson
c3d1c7c0ab
CHECK --> CHECK_PTR in tmisc.c (#4274) 2024-03-28 12:07:52 -07:00
jhendersonHDF
03b6575b1b
Minor fixes after merge of file format security fixes (#4263)
* Update H5_IS_BUFFER_OVERFLOW to account for 'size' of 0

* Invert a few checks to avoid function call
2024-03-28 11:49:50 -07:00
jhendersonHDF
372381c530
Prevent stack overflows in H5E__push_stack (#4264) 2024-03-28 11:12:19 -07:00