Commit Graph
255 Commits
Author SHA1 Message Date
Allen Byrne 63803d7115 allow better CMake version testing (#5727)
* add cmake latest workflow with lukka/get-cmake@latest
* Upgrade minimum CMake version to 3.26
2025-08-23 06:43:20 -05:00
Allen Byrne 497b65ad0f Add file header comments to CMake files (#5688) 2025-08-13 07:19:57 -05:00
Aleksandar Jelenak 104bd625ab Change default dataset chunk cache size to 8 MiB (#5558)
* Change default dataset chunk cache size to 8 MiB

* Fix 2 Java tests for chunk cache size

* Add release note about chunk cache size change
2025-08-08 15:05:27 -04:00
Allen Byrne 637c5fd2f7 Correct tools test files ref paths (#5607) 2025-06-19 08:06:58 -05:00
Matt L 6beb04760d Move tool testfiles to shared folder (#5597)
* Maintain tool testfile division in build folders
* Add h5dump reference files to shared folder
* Fix testfile path for java
* Remove unused filter
2025-06-17 06:54:19 -05:00
Allen Byrne 4cc7161fc2 refactor run scripts to a single macros with includes (#5538)
* Refactor the CMake scripts into a single script
* Adjust args to do grep testing
2025-05-24 16:26:46 -05:00
Allen Byrne af34892134 Update java test jars (#5385) 2025-03-18 11:09:10 -05:00
Allen Byrne 1602e1fbfe Remove autotools files and docs (#5358) 2025-03-14 13:28:44 -05:00
jhendersonHDF 90429f5e7d Implement support for complex number datatypes (#4630)
* Implement support for complex number datatypes

Adds the new datatype class H5T_COMPLEX

Adds the new API function H5Tcomplex_create which creates a complex
number datatype from an ID of a base floating-point datatype

Adds the new feature check macros H5_HAVE_COMPLEX_NUMBERS and
H5_HAVE_C99_COMPLEX_NUMBERS

Adds the new datatype size macros H5_SIZEOF_FLOAT_COMPLEX,
H5_SIZEOF_DOUBLE_COMPLEX and H5_SIZEOF_LONG_DOUBLE_COMPLEX

Adds the new datatype ID macros H5T_NATIVE_FLOAT_COMPLEX,
H5T_NATIVE_DOUBLE_COMPLEX, H5T_NATIVE_LDOUBLE_COMPLEX,
H5T_CPLX_IEEE_F16LE, H5T_CPLX_IEEE_F16BE,
H5T_CPLX_IEEE_F32LE, H5T_CPLX_IEEE_F32BE,
H5T_CPLX_IEEE_F64LE and H5T_CPLX_IEEE_F64BE

Adds hard and soft datatype conversion paths between complex number
datatypes and all the integer and floating-point datatypes, as well as
between other complex number datatypes

Adds a special conversion path between complex number datatypes and
array or compound datatypes where the in-memory layout of data is the
same between the datatypes and data can be converted directly

Adds support for complex number datatypes to the h5dump, h5ls and
h5diff/ph5diff tools. Allows h5dump '-m' option to change floating-point
printing format for float complex and double complex datatypes, as well
as long double complex if it has the same size as double complex

Adds minimal support to the h5watch and h5import tools

Adds support for the predefined complex number datatypes and
H5Tcomplex_create function to the Java wrappers. Also adds initial,
untested support to the JNI for future use with HDFView

Adds support for just the H5T_COMPLEX datatype class to the Fortran
wrappers

Adds support for the predefined complex number datatypes and
H5Tcomplex_create function to the high level library H5LT interface
for use with the H5LTtext_to_dtype and H5LTdtype_to_text functions

Changes some usages of "complex" in the library since it conflicts with
the "complex" keyword from the complex.h header. Also changes various
usages of the word "complex" throughout the library to distinguish
compound datatypes from complex datatypes.
2024-10-31 13:54:25 -07:00
Allen Byrne 5425a571e0 Convert develop to v2.0.0 (#5006)
Switches previous 1.16/17/18 values to 2.0
2024-10-27 21:51:07 -07:00
Dana Robinson 7f1e49206d Renamed COPYING to LICENSE (#4978)
This is where most people will expect to find license information. The
COPYING_LBNL_HDF5 file has also been renamed to LICENSE_LBNL_HDF5.
The licenses are unchanged.
2024-10-18 21:13:04 -07:00
Dana Robinson 54f8f12ed9 Update clang-format to 17 (#4931)
Also bump the clang-format GitHub actions to 17
2024-10-04 19:49:35 -07:00
Quincey Koziol 767282f68a VOL refactor and cleanup (#4856)
Cleanup and prepare for thread-safety changes.

Big ideas:

* Wrap H5VL_class_t with H5VL_connector_t, so use of the class can be refcounted within the H5VL package, instead of relying on storing an ID within the H5VL_t struct and incrementing & decrementing the ID's refcount.
* Register H5VL_connector_t* for VOL connector IDs, instead of the H5VL_class_t*
* Stop other packages from rummaging around inside H5VL_connector_t and H5VL_object_t data structures, so that the H5VL package can change implementation details without coupled changes throughout the library

Small things:

* Simplified the coding for creating links
* Moved some routines into more logical locations
2024-10-03 12:19:33 -07:00
Larry Knox 698ee8e439 Set develop branch version to 1.17.0. (#4912) 2024-10-02 12:28:19 -05:00
Allen Byrne f17ca5689e Update for blosc2 in plugins and prefix hdf5 cmake varnames (#4468) 2024-05-10 13:01:28 -05:00
Quincey Koziol 0ce1a96b4e Don't print thread ID when the library isn't multithreaded. (#4428)
Corresponding changes to make error output for regression tests agnostic
to thread setting.

Signed-off-by: Quincey Koziol <quincey@koziol.cc>
2024-04-24 08:32:28 -07:00
Allen Byrne 6b22af7c43 Add abi-complience check and upload to releases (#3996) 2024-02-08 07:58:08 -06:00
Allen Byrne 3ea21ccb3e Add HDF5_DISABLE_TESTS_REGEX option to skip tests (#3859) 2023-11-22 07:51:30 -06:00
Dana Robinson 29b27b7761 Clean Java test files on Autotools (#3740)
Removes generated HDF5 and text output files when running `make clean`.
2023-10-21 11:44:16 -07:00
Allen Byrne 1529ec0ab3 Develop tools move (#3580)
Reorganizes the tools files to support the VOL tests
2023-09-26 13:46:55 -07:00
Allen Byrne 80fe48f2d3 Correct java test dimension (#3482) 2023-09-01 10:52:24 -07:00
Allen Byrne e94071fe53 Change name of test file to avoid conflict (#2701) 2023-04-12 12:50:46 -07:00
Allen Byrne fa388e6ba4 Update java logger version (#2643) 2023-04-03 14:36:23 -07:00
Allen Byrne 9f5cf0a457 H5F_LIBVER_LATEST changes for move to 1.15 (#2288)
* H5F_LIBVER_LATEST changes for move to 1.15

* Add new default api check

* Format fixes

* Fix default configure

* fix lib version tests

* Fix another version variable

* Add 1.14 doc link
2022-12-21 10:07:25 -08:00
Allen Byrne 2376723d4a Develop jni trans (#2266)
* Add compound and refactor out atomic types

* Add Array String tests back

* Convert Attribute version of compound example

* Update transfer atom8ic read to return object
2022-12-05 22:29:42 -06:00
Allen Byrne 719d800499 Refactor JNI translate functions to a recursive switch on datatype (#2232) 2022-11-15 22:44:33 -06:00
Larry Knox 0173706826 Update develop branch version to 1.13.4-1 (#2189)
* Updated version to 1.13.4-1 after creating hdf5_1_13_3 branch for 1.13.3
release.
Added new version to exceptions in lines 74-5 of src/H5.c
2022-10-26 11:07:17 -05:00
Allen Byrne 9c61f7b1e1 JNI: Improve varlen datatype handling in H5A/H5D read/write functions (#2156)
* Improve JNI VL datatype read/write to handle complex combinations

* Implement VL of VL JNI writes and reads

* Add Java VLofVL test for attributtes

* Changes to address review issues

* Fix H5Aread vl blocks
2022-10-25 23:33:30 -05:00
Allen Byrne c114bd64b0 Fix mostly java warnings, and cpp cast (#2134) 2022-10-03 13:31:32 -05:00
Allen Byrne 45178c87a3 develop Merge doxygen from 1.12 branch (#2095) 2022-09-14 15:44:24 -05:00
Allen Byrne c8fdd92cd4 Update CMake code to 3.18 minimum version (#2080)
* Update CMake code to 3.18 minimum version

* Updated release note
2022-09-02 17:31:29 -07:00
jhendersonHDF 5719187a34 Fix Java tests for Developer build modes (#2079) 2022-08-29 09:00:42 -07:00
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 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
Allen Byrne 956282fa6f Develop cmake clean (#1971) 2022-08-06 23:59:31 -05:00
Allen Byrne ae414872f5 Develop clang 13 format (#1933)
* Update format source to clang 13

* More format changes
2022-07-26 14:45:46 -07:00
Allen Byrneandgithub-actions b9d1d66ab8 Develop HDFFV-11310 (#1811)
* Rework java vl check in read/write. Handle old refs in h5dump

* Committing clang-format changes

* Java changes allow default VL reads

* Fix JNI utility for old refs

* HDFFV-11310 - implement vlen read/write for atomic types.

* format check fix

* Mostly format fixes

* More format issues

* Two format changes

* Use JNI names for sizeof

* format change

* fix size typo

* Change to older method to initialize list

* remove unused var

* format fix

* switch writeVL functions to use datatype instead of java type

* Add VL option to generic read/write check

* Correct function name typo

* Add JIRA issue

* Correct note to match change in code.

* HDFFV-11318 add VL references as byte arrays

* Add release note and format changes

* Another format update

* Fix unreleased allocations

* Fix format

* format correction

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2022-07-11 13:59:52 -07:00
Quincey Koziol c8b87fa320 Improve handling of copying of dynamic libraries and clean them up after (#1681)
test finishes.
2022-04-24 09:59:12 -05:00
Allen Byrne 03c3a54695 Develop clang format java (#1653) 2022-04-19 13:08:09 -05:00
Larry Knox 94d01f5377 Update version to 1.13.2-1 after 1.13.1 release; add new Makefile.in files to MANIFEST (#1460) 2022-03-01 14:20:34 -06:00
Allen Byrne ebf89bb231 Fix install config and java test name conflict (#1467) 2022-03-01 14:19:43 -06:00
8dc72928b8 Develop java newrefs fixes for obj ref datasets (#1354)
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
2022-01-18 14:02:53 -06:00
Allen Byrne 2f34c433dc Update the java slf4j logging jars to latest 1.7.33 (#1369) 2022-01-18 07:44:11 -06:00
Allen Byrne 03217eca81 Add tests for H5Ocopy of new object refs (#1338)
* Add tests for H5Ocopy of new object refs

* Correct class name

* Skip test because of issue with debug assertions

* Update reference file

* Fix object examples for new refs
2022-01-08 08:19:52 -06:00
f859cb732b Fixed Spelling Errors (#1166)
* fixed missed closing of a dataset

* fixed missed closing of a dataset

* fixed typo in error return

* Committing clang-format changes

* minor edits

* code format

* Committing clang-format changes

* code format

* minor edit

* switched from using MPI_count, to actual bytes written for H5FD_mpio_debug rw debugging

* Committing clang-format changes

* changed size_i in printf to reflect the I/O.

* Committing clang-format changes

* Fixed seg fault with xlf on BE with -qintsize=8

* fixed error function string

* spelling corrections via codespell, added new spell check github actions

* Committing clang-format changes

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* Committing clang-format changes

* misc

* misc

* misc

* misc

* misc

* misc

* Committing clang-format changes

* misc

* work around for https://github.com/codespell-project/codespell/issues/2137

* misc

* added missing file

* misc

* misc.

* misc

* switch to using Codespell with GitHub Actions

* misc.

* misc.

* fixed more sp errors

* Fix new typos found by codespell.

* fixed proceed with precede

* fixed variable in fortran test

* fixed minnum

* updated spelling list

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
2021-12-07 08:27:29 -06:00
Larry Knox 89ad105b1c Update version to 1.13.1-1 after creation of branch for 1.13.0 release. (#1236) 2021-11-30 12:53:45 -06:00
Allen Byrne 81b9d71a24 Fix Java VOL tests (#1158) 2021-11-03 07:28:30 -05:00