Commit Graph

23049 Commits

Author SHA1 Message Date
Scot Breitenfeld
2c3d23d1e6
corrected warning: implicit conversion changes signedness (#3982) 2024-02-02 08:11:16 -06:00
Scot Breitenfeld
6e42618f53
Fixed spacing issues in example tests. (#3979)
* The space difference in the Fortran examples must be fixed to match the expected output for compression filter examples.
2024-02-01 23:42:58 -06:00
H. Joe Lee
0843a8c1be
Add h5dump tests that require subfiling VFD (#3879) 2024-02-01 09:02:47 -08:00
Stefano Probst
5bdd685311
Create CITATION.cff (#3927)
Add citation source based on http://web.archive.org/web/20230610185232/https://portal.hdfgroup.org/display/knowledge/How+do+I+properly+cite+HDF5%2C+HDFView%2C+and+HSDS+in+a+paper. Created with https://citation-file-format.github.io/cff-initializer-javascript/
2024-02-01 08:28:17 -08:00
Scot Breitenfeld
9c327bc616
append '-WF,' when passing C preprocessor directives to the xlf compiler (#3976)
* append '-WF,' when passing C preprocessor directives to the xlf compiler

* strip path from compiler name
2024-01-31 23:04:43 -06:00
mattjala
d1ed02d49f
Clarify vlen string datatype message (#3950) 2024-01-31 16:16:49 -06:00
Larry Knox
bca1dc10a3
Replace 'T2' with ' ' to avoid failure to match expected output due to (#3975)
system tab difference.
2024-01-31 15:49:25 -06:00
Allen Byrne
595b5099ea
Add binary testing to CI testing (#3971)
* Add binary test job

* Correct names of jobs

* Add build mode to binary names

* Limit packaging execution

* Make mac DragNDrop optional

* Format if checks

* fix checks for TS

* Allow examples to be packaged

* Correct if NOT format

* Correct configure and workflow call

* Separate out CMake/Autotools Parallel job

* Correct binary examples path

* Correct dir path for windows test

* Correct paths and add extlibs

* Windows binaries do not have a share folder
2024-01-31 08:13:15 -06:00
Allen Byrne
45ac12e6b6
Explicitly use PROJECT_BINARY_DIR in target copy location (#3974) 2024-01-30 16:21:21 -06:00
Scot Breitenfeld
3a3501df2d
h5 compiler wrappers now pass all arguments passed to it to the compile line (#3954)
* The issue was that the "allargs" variable was not being used in the final command of the compiler wrapper. Any entries containing an escaped quote (\", \') or other non-matching argument (*) would not be passed to the compile line. I have fixed this problem by ensuring all arguments passed to the compiler wrapper are now included in the compile line.

* added testing for compiler wrappers
2024-01-30 12:20:58 -06:00
Scot Breitenfeld
791915e92a
Fixed XL and gfortran errors (#3968)
* fixed XL and Gfortran errors

* fixed data type len array
2024-01-30 09:05:20 -08:00
Gerd Heber
1e511d4092
Added a GitHub Codespaces configuration. (#3966) 2024-01-30 09:04:27 -08:00
Scot Breitenfeld
d79667eb0c
Add API support for Fortran MPI_F08 module definitions. (#3959)
* revert to using c-stub for _F08 MPI APIs

* use mpi compiler wrappers for cmake and nvhpc
2024-01-29 13:13:33 -06:00
Allen Byrne
365e23340c
Fix doxygen errors (#3962)
* Switch warnings as errors to default OFF

* Enable mac docs

* Add doxygen action uses step

* Use html div around snippet

* Allow preset name to be an argument to cmake-ctest.yml
2024-01-29 07:38:54 -06:00
mattjala
1bea9e6100
Document that fileno is same for all handles (#3963) 2024-01-26 12:30:12 -08:00
jhendersonHDF
a1d3e486e6
Add RELEASE.txt note for the fix for issue #1256 (#3955) 2024-01-26 07:59:48 -08:00
Yaroslav Halchenko
487d5f0813
RF: move codespell configuration into .codespellrc so could be used locally as well (#3958)
ATM configuration was embedded within the CI workflow but that makes impossible
to use  codespell  locally since the tool would not find those settings. I moved them
into .codespellrc  but then also removed codespell.yml workflow from skips, added .git and
in general makde it look for .dotfiles too
2024-01-26 07:59:25 -08:00
Dana Robinson
70ce646c22
Change 'extensible' to 'fixed' in H5FA code (#3964) 2024-01-26 07:58:58 -08:00
mattjala
853a7c6c9c
Fix potential infinite loop in API test (#3960) 2024-01-25 08:57:31 -08:00
Scot Breitenfeld
424f3803ea
fixed BIND name (#3957)
* update H5Ssel_iter_reset_f test
2024-01-24 10:19:47 -06:00
jhendersonHDF
f86fe61c7f
Remove cached datatype conversion path table entries on file close (#3942)
Remove cached datatype conversion path table entries on file close

When performing datatype conversions during I/O, the library
checks to see whether it can re-use a cached datatype conversion
pathway by performing comparisons between the source and destination
datatypes of the current operation and the source and destination
datatypes associated with each cached datatype conversion pathway.
For variable-length and reference datatypes, a comparison is made
between the VOL object for the file associated with these datatypes,
which may change as a file is closed and reopened. In workflows
involving a loop that opens a file, performs I/O on an object with a
variable-length or reference datatype and then closes the file, this
can lead to constant memory usage growth as the library compares the
file VOL objects between the datatypes as different and adds a new
cached conversion pathway entry on each iteration during I/O. This is
now fixed by clearing out any cached conversion pathway entries for
variable-length or reference datatypes associated with a particular
file when that file is closed.
2024-01-23 08:21:59 -08:00
vchoi-hdfgroup
7e48d4f767
Add the user test program in HDFFV-9174 for committed types. (#3937)
Add the user test program for committed types in HDFFV-9174
2024-01-23 08:11:33 -08:00
Scot Breitenfeld
54fb809382
Fortran API work. (#3941)
* - Added Fortran APIs:
      H5FGET_INTENT_F, H5SSELECT_ITER_CREATE_F, H5SSEL_ITER_GET_SEQ_LIST_F,
      H5SSELECT_ITER_CLOSE_F, H5S_mp_H5SSELECT_ITER_RESET_F

    - Added Fortran Parameters:
      H5S_SEL_ITER_GET_SEQ_LIST_SORTED_F, H5S_SEL_ITER_SHARE_WITH_DATASPACE_F

    - Added tests for new APIs
    - Removed H5F C wrapper stubs
    - Documentation misc. cleanup.
2024-01-23 07:59:10 -08:00
mattjala
51f150a945
Update H5Fget_obj_count/ids docs to reflect dtype behavior (#3932)
* Update H5Fget_obj_count/ids to reflect dtype behavior

* Clarify comments on H5Fget_obj_ids
2024-01-19 21:11:06 -06:00
Glenn Song
3d1fc2c38a
Fix chid_t to hid_t (#3948)
Co-authored-by: Glenn Song <gsong@hdfgroup.org>
2024-01-19 21:08:19 -06:00
Dana Robinson
ab11e076bf
Replace off_t with HDoff_t internally (#3944)
off_t is a 32-bit signed value on Windows, so we should use HDoff_t
(which is __int64 on Windows) internally instead.

Also defines HDftell on Windows to be _ftelli64().
2024-01-18 09:03:59 -08:00
Dana Robinson
5ae4ecc1f2
Clean up Doxygen for szip functions and constants (#3943) 2024-01-18 09:03:43 -08:00
Satish Balay
b72cc4f7f4
autogen.sh: check directly for libtoolize instead of libtool [as libtool is not used here] (#3886)
* autogen.sh: check directly for libtoolize instead of libtool [as libtool is not used here]

* autogen.sh: simplify (g)libtoolize check - look for glibtoolize first - and then libtoolize
2024-01-12 17:43:40 -08:00
Allen Byrne
5f5f5f030e
Remove incorrect include of sz header (#3939) 2024-01-10 16:32:31 -06:00
Allen Byrne
efe7cb72ba
Add binary build for linux S3 (#3936)
* Reorg and update options for doc and cmake config

* Correct subfiling depends

* Add linux S3 binaries to GH published files

* Correct path

* Try reducing parallel jobs in tests

* Change examples jobs for test from 8 to 4
2024-01-09 09:47:55 -08:00
Allen Byrne
c12932865d
Reorg and update options for doc and cmake config (#3934)
* Reorg and update options for doc and cmake config
* Correct subfiling depends
2024-01-09 09:42:45 -08:00
H. Joe Lee
6a5dd86315
Remove check for MPI initialization in tools library when using parallel VFDs
The tools library no longer checks for whether MPI is initialized when attempting to use a parallel VFD, such as the MPI I/O VFD or Subfiling VFD. This requires that parallel VFDs check for this situation and initialize MPI on their own if need be, but also allows parallel VFDs to be used with non-parallel HDF5 tools, such as h5dump.
2024-01-09 10:38:35 -06:00
Allen Byrne
d001379f68
Update upload- artifact to match download version (#3929)
* Update upload- artifact to match download version

* Correct form of action call
2024-01-08 06:06:40 -08:00
mattjala
3d39b85952
Add H5Dread/write_multi to API tests (#3919) 2024-01-05 20:44:27 -06:00
Scot Breitenfeld
9d1fe2c166
renamed defined H5_VERS* to avoid conflicts (#3926) 2024-01-05 06:55:54 -06:00
Allen Byrne
a00d62f77a
Use props for includes and remove global includes (#3921) 2024-01-04 12:06:36 -06:00
mattjala
de3ee47a44
Fix building VOLs under library with CMake <3.24 (#3920)
* Fix building VOLs under library with CMake <3.24

* Handle CMake version through override variable
2024-01-04 12:03:50 -06:00
Allen Byrne
772276ea1f
Remove examples that have been moved to HDF5Examples folder (#3917) 2024-01-03 14:17:46 -06:00
Scot Breitenfeld
8f1a93f1a2
New Fortran Examples added (#3916)
* added subfiling example

* Added filtered writes with no selection example
2024-01-03 10:55:17 -06:00
dependabot[bot]
812be1a3bd
Bump the github-actions group with 3 updates (#3913)
(https://github.com/ilammy/msvc-dev-cmd), [actions/download-artifact](https://github.com/actions/download-artifact) and [github/codeql-action](https://github.com/github/codeql-action).
2024-01-02 07:38:37 -06:00
Scot Breitenfeld
2fc140079b
Added H5Fdelete_f with test (#3912) 2023-12-30 17:33:31 -06:00
Quincey Koziol
3a21ee0877
Add 'warning density' computation to the warnhist script (#3910)
* Add 'warning density' computation to the warnhist script, along with several
cleanups to it.   Add "--enable-show-all-warnings" configure (and CMake)
option to disable compiler diagnostic suppression (and therefore show all the
otherwise suppressed compiler diagnostics), disabled by default.  Clean up
a buncn of misc. warnings.

Signed-off-by: Quincey Koziol <qkoziol@amazon.com>
2023-12-29 08:42:35 -06:00
jhendersonHDF
6ffc55c6d9
Implement optimized support for vector I/O in Subfiling VFD (#3896)
Vector I/O requests are now processed within a single
set of I/O call batches, rather than each I/O vector
entry (tuple constructed from the types, addrs, sizes
and bufs arrays) being processed individually. This allows I/O to be
more efficiently parallelized among the I/O concentrator processes
during large I/O requests.

* Fixed some calculations and add test cases for issues spotted from review

* Removed a variable that was compensating for previous miscalculations
2023-12-27 16:28:41 -06:00
Scot Breitenfeld
695efa94df
Added new H5G Fortran HDF5examples (#3908)
* updated traverse example

* added H5PAR success statement

* skipping H5_f90_h5ex_g_traverse
2023-12-22 15:57:16 -06:00
Allen Byrne
366f2d94a3
Add CMake api checks to test the new Examples folder. (#3907)
* Fix missing build-mode value

* Use 110 version file only for the 1.10 library

* Fix H5_LIBVER_DIR variable

* Disable 1.6 API tests for now.
2023-12-22 15:17:05 -06:00
H. Joe Lee
11e15aeed1
Change Trouble Shooting to Troubleshooting (#3905) 2023-12-22 09:02:09 -08:00
Gerd Heber
37124bc1c1
Doc versions (#3903)
* Added missing \since tags to H5D.

* Committing clang-format changes

* Fixed H5T version info.

* Committing clang-format changes

* Added missing version info to H5E.

* Committing clang-format changes

* Added version info to H5F public APIs.

* Committing clang-format changes

* Added missing H5Z public API version info.

* Added missing version info to H5G public APIs

* Added missing version info to H5I public API.

* Added missing version info to H5 public APIs

* Committing clang-format changes

* Added missing version info to H5P public APIs

* Added missing version info to H5R public APIs

* Fix comment error.

* Committing clang-format changes

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2023-12-21 14:51:58 -06:00
H. Joe Lee
2149744b35
Move Glossary to the end of docs navigation menu (#3902) 2023-12-21 10:01:33 -06:00
Allen Byrne
aa734a5d7e
Add VDS examples and fix non-standalone build (#3898)
* Choose a size for rdata dimension

* Fix platform naming conflicts

* Fix doxygen references to point within library repo
2023-12-21 09:53:24 -06:00
Allen Byrne
773245a084
Disable doxygen as errors for netcdf (#3900)
* disable building doxygen for netcdf test
2023-12-20 09:56:32 -06:00