Implements the two overloads specified in RFC-HDFG-2026-001
sec:modify-bindings -- one taking a String, one an int[] -- mirroring
the existing H5Pappend_filter overloads.
Both Java binding paths are covered, since the tree maintains two:
- JNI (java/src-jni): two private native methods dispatched from the
public overloads, plus the JNI implementations and declarations in
h5pDCPLImp.c/.h, following the H5Pappend_filter_str/_raw pattern
exactly.
- Panama/FFM (java/hdf): the H5Z_params_t struct is built directly in
an Arena and passed to the generated org.hdfgroup.javahdf5.hdf5_h
downcall, as the append string form already does. Unlike the append
case the cd_values form cannot delegate to H5Pmodify_filter, which
addresses an entry by filter ID and resolves to the first match
rather than by index, so it constructs the struct explicitly. The
generated binding is produced by jextract from the public headers,
so it picks up the new declaration automatically.
Adds testH5Pmodify_filter_by_idx_string and
testH5Pmodify_filter_by_idx_cdvalues to TestH5Z.java and updates the
JUnit golden file. Placement and the test count were derived from
@FixMethodOrder(MethodSorters.NAME_ASCENDING) rather than guessed, and
the file's surrounding format is unchanged.
Not compile-verified locally: this configuration has HDF5_BUILD_JAVA
OFF and the machine has a JRE but no JDK (no javac) and no jextract, so
nothing under java/ can be built here. The C library still builds clean
and the full C/Fortran suite is unchanged. What was checked statically:
the JNI symbol names against the mangling rule (underscores in the Java
method name become _1) and against the existing append pair; the
H5Z_params_t offsets (int type at 0, union at 8, cd_nelmts at 8,
cd_values at 16, 24 bytes total on 64-bit) and the enum values
(H5Z_PARAMS_CDVALUES 0, H5Z_PARAMS_STRING 1) against H5Zpublic.h; and
the H5Pget_filter call in the new test against the working call in
testH5Pappend_filter_cdvalues. Java CI should be treated as the real
gate.
JUnit4's default method sorter (MethodSorters.DEFAULT) orders test
methods by a hash of the method name, not declaration order -- so any
rename or addition shifts the whole run order unpredictably relative
to a hand-maintained golden file. Both java/test/TestH5Z.java (added
this session, 13 methods) and java/src-jni/test/TestH5Z.java (5
methods, unmodified but apparently never correctly regenerated after
the testH5Zget_filter_info2 -> testH5Zget_filter_class_info rename)
had golden JUnit-TestH5Z.txt files that didn't match the real
hash-sorted order, both confirmed by computing Java's documented
String.hashCode() algorithm directly and matching it byte-for-byte
against actual CI failure output.
Verified against upstream develop (an unrelated, currently-open
develop-based PR): this test passes cleanly there, confirming the
mismatch was never a general JUnit/reflection flakiness -- it was
always a genuinely wrong reference file.
Fixed by adding @FixMethodOrder(MethodSorters.NAME_ASCENDING) to both
classes (alphabetical by method name, a properly documented and stable
JUnit4 ordering mode) and regenerating both reference files to match
the resulting deterministic order. This also makes the test immune to
the same class of breakage going forward: alphabetical order is
computable by inspection, unlike the hash order.
The trailing "2" follows HDF5's convention for versioned/deprecated
symbols (H5Dopen2, H5Gcreate2, etc.), implying this is a successor to
H5Zget_filter_info registered in H5vers.txt -- it isn't. The two functions
are independent: H5Zget_filter_info returns only encode/decode config
flags, H5Zget_filter_class_info additionally exposes name, description,
and set_config/get_config presence. Renamed across C, Fortran, and both
Java binding variants (JNI + FFM) since it hadn't shipped yet.
Adds a human-readable key=value parameter string API for HDF5 filters,
alongside the existing integer cd_values arrays.
New C API:
- H5Pappend_filter(plist, filter_id, flags, params) — appends a filter
using either a key=value string or raw cd_values (H5Z_params_t)
- H5Pget_filter_params_by_idx(plist, idx, buf, buf_size, content_len) —
retrieves the parameter string for a filter by pipeline index
- H5Zconfig_get_int/double/bool/str — typed accessors for use inside
filter set_config callbacks
- H5Z_filter_id_by_name(name) — look up a filter id by registered name
- H5Zget_filter_info2(id, info) — extended filter info including v3 fields
New H5Z_class3_t fields: name, description, set_config, get_config,
and reserved blob-callback placeholders (write_blob/read_blob/close_blob).
H5Z_pipeline gains dxpl_id, scaled[], and ndims arguments threaded
through from all call sites so v3 filter callbacks have full context.
All six built-in filters (deflate, shuffle, fletcher32, nbit, szip,
scaleoffset) implement set_config/get_config callbacks.
TOML subset parser: tomlc17 (MIT) vendored in src/tomlc17/ and compiled
unconditionally into libhdf5. Hex-float literals are transparently
rewritten to decimal before parsing. tomlc17 symbols are hidden via
-fvisibility=hidden to prevent namespace collisions.
On-disk format: no new pipeline version. Parameter strings are converted
to cd_values by set_config at H5Pappend_filter time and stored using the
existing v2 pipeline message. On read, get_config reconstructs the string.
Full backward read compatibility is preserved.
Fortran, C++, and Java bindings added. Tests in test/tfilter2.c
(~2300 lines) and testpar/t_filters_parallel.c (par-01–par-04).
h5dump displays filter parameter strings; h5repack accepts TOML-form
UD= filter specs.
Code-review fixes included: tomlc17 visibility, H5Pget_filter_params_by_idx
arg validation and true-length two-pass contract, flags re-validation after
set_config, H5Z_register3 runtime plugin validation, Java two-pass protocol
and h5libraryError() consistency, CHANGELOG corrections.
Fixes GitHub issue #6153
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.
* 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
* Note LLVM 10 to 11 format default changes
* Update format plugin
* Undo clang-format version 11 changes
* One more correction
* Update supported platforms
* Revert whitespace changes
* Correct whitespace
* Changes from PR#3
* HDFFV-11213 added option to control gcc10 warnings diagnostics
* HDFFV-11212 Use the new references correctly in JNI utility and tests
* format source
* Fix typo
* Add new test file
* HDFFV-11212 - update test and remove unused arg
* Minor non-space formatting changes
* Use H5I_INVALID_ID instead of "-1"
* source formatting
* add missing testfile, update jni function
* Undo commit of debug code
* remove mislocated file
* Fix h5repack test for handling of fapls and id close
* Update h5diff test files usage text
* HDFFV-11212 add new ref tests for JNI export dataset
* src format update
* Remove blank line typo
* src format typo
* long double requires %Lg
* Another long double foramt specifer S.B. %Lg
* issue with t128bit test
* Windows issue with h5dump and type.
* Fix review issues
* refactor function nesting and fix error checks
* format fixes
* Remove untested functions and javadoc quiet comments
* Restore TRY block.
* Change string append errors to memory exception
* revert to H5_JNI_FATAL_ERROR - support functions need work
* Add assertion error for h5util functions
* remove duplicate function
* format fix
* Revert HD function error handling
* Update copyright comments
* GH #386 java folder copyright corrections
* Whitespace
* Modify temporary rpath for testing in java example scripts.
* Update URL in source file Copyright headers for web copy of COPYING
file - files not in src or test.
* commit '54957d37f5aa73912763dbb6e308555e863c43f4':
Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes.
Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh.
Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1
Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
Scot Breitenfeld
github-actions
Dana Robinson
Allen Byrne
Larry Knox
Allen Byrne
Dana Robinson