Commit Graph

23239 Commits

Author SHA1 Message Date
Dana Robinson
9a90122ef8
Header cleanup in C library (#4154)
* Ensure H5FL header is included everywhere

* Ensure H5SL header is included everywhere

* Ensure H5MM header is included everywhere
2024-03-16 11:42:32 -05:00
jhendersonHDF
1029e34fb9
Suppress H5Dmpio debugging output unless HDF5_DEBUG=d is set (#4155) 2024-03-16 11:42:01 -05:00
H. Joe Lee
4b0c6291f8
Remove HDF from Fortran 2003 configuration check message. (#4157) 2024-03-16 11:40:37 -05:00
Dana Robinson
6d85ea26ab
Remove H5O header and friend status from H5A.c (#4150) 2024-03-15 13:01:22 -07:00
Sergey Kosukhin
6635198d7f
Fix buffer size calculation in the deflate filter (#4147) 2024-03-15 13:01:03 -07:00
H. Joe Lee
3861c0c777
Remove at the end of list item. (#4151) 2024-03-15 13:00:47 -07:00
Dana Robinson
26837b4af8
Make the newsletter scheme work like HDF4 (#4149) 2024-03-15 10:36:18 -07:00
Scot Breitenfeld
e913eee81c
defined CMAKE_H5_HAVE_DARWIN (#4146) 2024-03-15 10:05:14 -07:00
Neil Fortner
40e1c6d078
Fix error when overwriting an indirectly nested vlen with a shorter sequence (#4140) 2024-03-15 09:26:56 -07:00
Dana Robinson
92d1463a02
Clean up some hbool_t/TRUE/FALSE stragglers (#4143)
It looks like most of these snuck in via selection I/O work
2024-03-15 08:54:08 -07:00
Dana Robinson
f3900f2f61
Remove useless headers (#4145)
Removes unnecessary headers from C library source files.
2024-03-15 08:49:59 -07:00
Allen Byrne
437f21549b
Fix doxygen link to example function usage (#4133) 2024-03-15 08:24:32 -07:00
Dana Robinson
c7c8b93d06
Fix Autotools -Werror cleanup (#4144)
The Autotools temporarily scrub -Werror(=whatever) from CFLAGS, etc.
  so configure checks don't trip over warnings generated by configure
  check programs. The sed line originally only scrubbed -Werror but not
  -Werror=something, which would cause errors when the '=something' was
  left behind in CFLAGS.

  The sed line has been updated to handle -Werror=something lines.

  Fixes one issue raised in #3872
2024-03-15 07:41:07 -05:00
Scot Breitenfeld
ece121b415
Fixed misc. H5E fortran failures due to previous PR (#4138)
* fixed promotion of integers and reals tests and check-passthrough-vol failure

* fixed cygwin issue
2024-03-15 07:37:22 -05:00
H. Joe Lee
78a5d8a70b
Capitalize option message for consistency. (#4141) 2024-03-15 05:33:20 -07:00
jhendersonHDF
ca9c942844
Skip part of dsets.c test for IBM long double type (#4136) 2024-03-15 00:12:50 -07:00
Dana Robinson
004ab16dbc
Remove ros3 and hdfs VFDs from Autotools VFD list (#4142)
These will never pass `make check` and would require a custom test
suite for more comprehensive testing.
2024-03-14 21:47:58 -07:00
Allen Byrne
112f445019
Add cygwin CI and update yaml files for consistency and accuracy (#4131)
* Add cygwin CI

* add cygwin packages

* Correct option names

* Cleanup yaml file and synch look and feel

* Synch CI look and feel and correct path issues

* Upgrade oneapi version

* pwsh needs env: for vars

* No continuation char for pwsh

* restore correct pwsh step

* Run subset of tests for cygwin workflow

* Remove space chars in regex

* restore full tests
2024-03-14 07:16:53 -07:00
bmribler
782c0e5a8c
Update URLs in RELEASE.txt (#4132) 2024-03-14 07:15:16 -07:00
mattjala
c3714b9f15
Fix segfault in vlen io API test (#4130) 2024-03-13 14:55:51 -05:00
Allen Byrne
c1f761bcbd
Remove invalid compile flag (#4129) 2024-03-13 10:10:38 -05:00
Jouke Witteveen
cfb1c798b9
Don't set the rpath when linking statically (#4125) 2024-03-13 08:03:21 -07:00
Allen Byrne
ca4db46c5a
Deprecate bin/cmakehdf5 (#4127)
* Deprecate bin/cmakehdf5

* Add reference text
2024-03-13 08:02:47 -07:00
Dana Robinson
8961016fe7
Update CMake comment about _POSIX_C_SOURCE (#4124)
Was missng the 2008 pread/write info
2024-03-12 17:35:41 -07:00
Dana Robinson
56f1092ddb
Overhaul CMake LFS support (#4122)
Externally visible:
* The HDF_ENABLE_LARGE_FILE option (advanced) has been removed
* We no longer run a test program to determine if LFS works, which
  will help with cross-compiling
* On Linux we now unilaterally set -D_LARGEFILE_SOURCE and
  -D_FILE_OFFSET_BITS=64, regardless of 32/64 bit system. CMake
  doesn't offer a nice equivalent to AC_SYS_LARGEFILE and since
  those options do nothing on 64-bit systems, this seems safe and
  covers all our bases. We don't set -D_LARGEFILE64_SOURCE since
  we don't use any of the POSIX 64-bit specific API calls like
  ftello64, as noted above.
* We didn't test for LFS support on non-Linux platforms. We've added
  comments for how LFS should probably be supported on AIX and Solaris,
  which seem to be alive, though uncommon. PRs would be appreciated if
  anyone wishes to test this.

Internal:
* Drops off64_t size checks since this is unused (as in Autotools)
* Remove HDF_EXTRA_FLAGS, which is now unused
* Remove hack around deprecated LINUX_LFS

Fixes #2395
2024-03-12 14:36:50 -07:00
Glenn Song
27f73183e2
Initialize selection type in chunk struct (#4087) 2024-03-12 12:01:23 -07:00
Dana Robinson
8123614b4d
Use AC_SYS_LARGEFILE on Autotools (#4119)
We previously used a hack introduced in 1.8.5 to paper over differences
in off_t and off64_t when determining the type sizes. We no longer explicitly
support off64_t in the library and AC_SYS_LARGEFILE works fine.
2024-03-12 11:30:24 -07:00
Allen Byrne
40cb71d4c2
Remove old cmake check (#4117) 2024-03-12 08:35:30 -07:00
jhendersonHDF
037c8b63d5
Handle IBM long double issues in dsets.c test_floattypes test (#4116)
* Handle IBM long double issues in dsets.c test_floattypes test
2024-03-12 07:49:41 -05:00
jhendersonHDF
4b297e986c
Implement ID creation optimization for container datatype conversions (#4113)
Makes the datatype conversion context object available during both the
initialization and conversion processes for a datatype conversion
function, allowing the compound, variable-length and array datatype
conversion functions to avoid creating IDs for the datatypes when they
aren't necessary

Adds internal H5CX_pushed routine to determine if an API context is
available to retrieve values from

Also adds error checking to several places in H5T.c and H5Tconv.c where
the code had previously assumed object close operations would succeed
2024-03-12 03:42:32 -07:00
Allen Byrne
fd280df53a
Adjust aocc workflow to fit the autotools/cmake pattern of other callable workflows. (#4115) 2024-03-12 03:39:45 -07:00
jhendersonHDF
4279c351f5
Fix up dsets test for some platforms with different long double format (#4114) 2024-03-11 14:39:13 -05:00
Allen Byrne
8340c4cb1f
long double tests has problems setting precision with offset (#4102)
* long double tests has problems setting precision with offset

* Disable long double until more development fixes issues
2024-03-11 07:58:35 -05:00
Dana Robinson
ac9541100f
Add Doxygen for HDFS VFD (#4106)
* Add Doxygen for HDFS VFD

* Fix Doxygen warning

* Update H5FDhdfs.h
2024-03-10 17:26:14 -07:00
Allen Byrne
50a6522322
Change compression tests reference files to use masking for compression ratios (#4083)
Rework TEST_FILTER tests to handle slightly different compression ratios
2024-03-10 16:43:37 -07:00
Dana Robinson
9bc6c20166
Remove lint comments (#4107) 2024-03-10 16:17:49 -07:00
Dana Robinson
7403f20757
Move common variables out of cache test blocks (#4108)
Fixes a stack size warning w/ XCode
2024-03-10 16:17:37 -07:00
Dana Robinson
700d1a24df
Convert H5B__assert to use error checks (#4109)
Switches assert() calls to HGOTO_ERROR in H5B__assert() so it can be
used in production mode. Also renames it to H5B__verify_structure()
to better reflect what it checks.
2024-03-10 16:16:41 -07:00
Dana Robinson
16b62825b3
Clean up a few things in H5T.c (#4105)
* remove (size_t) noise casts
* replace (hid_t)FAIL with H5I_INVALID_HID
2024-03-10 12:42:29 -07:00
Dana Robinson
f0ba8baa0d
Minimize use of abort() (#4110)
The abort() call is used at several places where it probably shouldn't.
2024-03-10 12:42:16 -07:00
jhendersonHDF
ef401a5f5e
Refactor datatype conversion code to use pointers rather than IDs (#4104)
The datatype conversion code previously used IDs for the source and
destination datatypes rather than pointers to the internal structures
for those datatypes. This was mostly due to the need for an ID for these
datatypes that can be passed to an application-registered datatype
conversion function or datatype conversion exception function. However,
using IDs internally caused a lot of unnecessary ID lookups and hurt
performance of datatype conversions in general. This was especially
problematic for compound datatype conversions, where the ID lookups were
occuring on every member of every compound element of a dataset. The
code has now been refactored to use pointers internally and only create
IDs for datatypes when necessary.

Fixed a test issue in dt_arith where a library datatype conversion
function was being cast to an application conversion function. Since the
two have different prototypes, this started failing after the parameters
for a library conversion function changed from hid_t to H5T_t * and an
extra parameter was added. This appears to have worked coincidentally in
the past since the only different between a library conversion function
and application conversion function was an extra DXPL parameter at the
end of an application conversion function

Fixed an issue where memory wasn't being freed in the h5fc_chk_idx test
program. Even though the program exits quickly after allocating the
memory, it still causes failures when testing with -fsanitize=address
2024-03-09 23:47:31 -08:00
Dana Robinson
28aaeb967c
Change how stats are printed in H5Z (#4097)
H5Z used the soon-to-be-removed HDEBUG macro to decide if stats
would be dumped and to what stream. This is now handled by a
DUMP_DEBUG_STATS_g variable and the output is always sent to
stdout.

This is an internal change, not normally visible to users.
2024-03-09 23:10:58 -08:00
Dana Robinson
6cb4b2f6d7
Remove printf debugging from H5Smpio.c (#4098) 2024-03-09 20:30:34 -08:00
Dana Robinson
08cf031588
Remove H5DEBUG() calls from H5Dmpio.c (#4103)
Just use stdout when a stream is needed.
2024-03-09 20:30:17 -08:00
Dana Robinson
fd7cf2a962
Remove a few H5O printf debugging statements (#4096)
These were in H5Oint.c, were protected by H5O_DEBUG, and only dumped
to stdout if the HDF5_DEBUG environment variable were set to do so.
2024-03-09 20:27:59 -08:00
Ben Boeckel
b1054b4ef3
msvc: don't declare HAVE_TIMEZONE for older MSVC (#3956)
It was introduced in MSVC 15 (Visual Studio 2017).
2024-03-09 10:25:40 -08:00
H. Joe Lee
c29a02d5e6
Remove leading / from relative path. (#4101) 2024-03-09 09:08:26 -08:00
Allen Byrne
cdef27d6ef
Correct missing change of source path for S3 build (#4100) 2024-03-09 09:07:08 -08:00
Dana Robinson
0ea1d7280b
Clean up off_t usage (#4095)
* Add comments to C++ and Fortran API calls that use off_t
* Remove noise casts for small integers
2024-03-09 09:06:10 -08:00
Dana Robinson
d4c84f8d0a
Fix the last C++ stack size warning (#4099) 2024-03-09 09:05:37 -08:00