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Merge branch '6153' into blob

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Brings the CI fixes: the H5FC_DLL declarations for the H5Zf.c Fortran
helpers, and the clang-format pass over this series.

Conflict resolution: only the H5Z_modify signature line, where the two
branches wrapped the argument list differently. Kept 6153's, which is
what clang-format 17 produces.

Also formats src/H5Opline.c and src/H5Zscaleoffset.c. Those two carry
formatting drift that predates this merge -- they are clean on 6153 but
were not on this branch, so the clang-format job would have flagged
them here regardless. A whole-tree run using CI's source path and
exclusion list now passes.

Full build clean; ctest 3458/3459, the one failure being the
pre-existing ph5_f90_filtered_writes_no_sel example bug fixed upstream
in HDFGroup/hdf5#6633.
This commit is contained in:
Scot Breitenfeld
2026-08-21 09:42:51 -05:00
parent cbd0bce545 fc12e0b6c1
commit b50f870d8a
13 changed files with 39 additions and 44 deletions
Download Patch File Download Diff File Expand all files Collapse all files
fortran/src/H5f90proto.h
+4
View File
@@ -588,6 +588,10 @@ H5FC_DLL int_f h5dont_atexit_c(void);
H5FC_DLL herr_t H5Pappend_filter_str_c(hid_t plist, H5Z_filter_t id, unsigned flags, const char *params);
H5FC_DLL herr_t H5Pappend_filter_raw_c(hid_t plist, H5Z_filter_t id, unsigned flags, size_t cd_nelmts,
const unsigned *cd_values);
H5FC_DLL herr_t H5Pmodify_filter_by_idx_str_c(hid_t plist, unsigned filter_idx, unsigned flags,
const char *params);
H5FC_DLL herr_t H5Pmodify_filter_by_idx_raw_c(hid_t plist, unsigned filter_idx, unsigned flags,
size_t cd_nelmts, const unsigned *cd_values);
/*
* Functions from H5Lf.c
java/hdf/hdf5lib/H5.java
+5 -6
View File
@@ -12531,7 +12531,7 @@ public class H5 implements java.io.Serializable {
params_struct.set(ValueLayout.JAVA_INT, 0, H5Z_PARAMS_STRING);
params_struct.set(ValueLayout.ADDRESS, 8, str_seg);
retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pmodify_filter_by_idx(plist_id, filter_idx, flags,
params_struct);
params_struct);
}
catch (HDF5LibraryException e) {
throw e;
@@ -12576,18 +12576,17 @@ public class H5 implements java.io.Serializable {
* addresses an entry by filter ID and resolves to the first match, whereas
* this API addresses by pipeline index. The struct is built explicitly. */
final int H5Z_PARAMS_CDVALUES = 0;
int[] values = (cd_values != null) ? cd_values : new int[0];
int[] values = (cd_values != null) ? cd_values : new int[0];
try (Arena arena = Arena.ofConfined()) {
MemorySegment vals_seg = (values.length > 0)
? arena.allocateFrom(ValueLayout.JAVA_INT, values)
: MemorySegment.NULL;
MemorySegment vals_seg =
(values.length > 0) ? arena.allocateFrom(ValueLayout.JAVA_INT, values) : MemorySegment.NULL;
MemorySegment params_struct = arena.allocate(24, 8);
params_struct.set(ValueLayout.JAVA_INT, 0, H5Z_PARAMS_CDVALUES);
/* union { struct { size_t cd_nelmts; const unsigned *cd_values; } raw; ... } */
params_struct.set(ValueLayout.JAVA_LONG, 8, (long)values.length);
params_struct.set(ValueLayout.ADDRESS, 16, vals_seg);
retVal = org.hdfgroup.javahdf5.hdf5_h.H5Pmodify_filter_by_idx(plist_id, filter_idx, flags,
params_struct);
params_struct);
}
catch (HDF5LibraryException e) {
throw e;
java/src-jni/hdf/hdf5lib/H5.java
+2 -2
View File
@@ -8521,7 +8521,7 @@ public class H5 implements java.io.Serializable {
* Error from the HDF5 Library.
**/
public synchronized static int H5Pmodify_filter_by_idx(long plist_id, int filter_idx, int flags,
String params) throws HDF5LibraryException
String params) throws HDF5LibraryException
{
return H5Pmodify_filter_by_idx_str(plist_id, filter_idx, flags, params);
}
@@ -8552,7 +8552,7 @@ public class H5 implements java.io.Serializable {
* Error from the HDF5 Library.
**/
public synchronized static int H5Pmodify_filter_by_idx(long plist_id, int filter_idx, int flags,
int[] cd_values) throws HDF5LibraryException
int[] cd_values) throws HDF5LibraryException
{
return H5Pmodify_filter_by_idx_raw(plist_id, filter_idx, flags, cd_values);
}
java/src-jni/jni/h5pDCPLImp.c
+4 -4
View File
@@ -1464,8 +1464,8 @@ done:
* Signature: (JIILjava/lang/String;)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pmodify_1filter_1by_1idx_1str(JNIEnv *env, jclass clss, jlong plist_id,
jint filter_idx, jint flags, jstring params)
Java_hdf_hdf5lib_H5_H5Pmodify_1filter_1by_1idx_1str(JNIEnv *env, jclass clss, jlong plist_id, jint filter_idx,
jint flags, jstring params)
{
H5Z_params_t p;
const char *c_params = NULL;
@@ -1497,8 +1497,8 @@ done:
* Signature: (JII[I)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Pmodify_1filter_1by_1idx_1raw(JNIEnv *env, jclass clss, jlong plist_id,
jint filter_idx, jint flags, jintArray cd_values)
Java_hdf_hdf5lib_H5_H5Pmodify_1filter_1by_1idx_1raw(JNIEnv *env, jclass clss, jlong plist_id, jint filter_idx,
jint flags, jintArray cd_values)
{
H5Z_params_t p;
jint *c_cd_values = NULL;
java/src-jni/jni/h5pDCPLImp.h
+2 -2
View File
@@ -161,7 +161,7 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Pappend_1filter_1raw(JNIEnv *, jcla
* Signature: (JIILjava/lang/String;)I
*/
JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Pmodify_1filter_1by_1idx_1str(JNIEnv *, jclass, jlong, jint,
jint, jstring);
jint, jstring);
/*
* Class: hdf_hdf5lib_H5
@@ -169,7 +169,7 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Pmodify_1filter_1by_1idx_1str(JNIEn
* Signature: (JII[I)I
*/
JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Pmodify_1filter_1by_1idx_1raw(JNIEnv *, jclass, jlong, jint,
jint, jintArray);
jint, jintArray);
/*
* Class: hdf_hdf5lib_H5
java/test/TestH5Z.java
+5 -6
View File
@@ -267,8 +267,7 @@ public class TestH5Z {
ret = H5.H5Pget_filter_params_by_idx(dcpl_id, 0, params);
assertTrue("H5Pget_filter_params_by_idx", ret >= 0);
assertNotNull("params[0] is non-null", params[0]);
assertTrue("stored string reflects the modify: " + params[0],
params[0].contains("level=9"));
assertTrue("stored string reflects the modify: " + params[0], params[0].contains("level=9"));
}
}
catch (Throwable err) {
@@ -305,10 +304,10 @@ public class TestH5Z {
assertEquals("nfilters after H5Pmodify_filter_by_idx", 1, nfilters);
// cd_values were replaced.
int[] cd_out = new int[1];
int[] flags_out = new int[1];
long[] cd_nelmts = new long[] {1};
String[] name_out = new String[] {""};
int[] cd_out = new int[1];
int[] flags_out = new int[1];
long[] cd_nelmts = new long[] {1};
String[] name_out = new String[] {""};
int filter_id =
H5.H5Pget_filter(dcpl_id, 0, flags_out, cd_nelmts, cd_out, 256, name_out, new int[1]);
assertEquals("filter id unchanged by modify", HDF5Constants.H5Z_FILTER_DEFLATE, filter_id);
src/H5Opline.c
+2 -4
View File
@@ -263,8 +263,7 @@ H5O__pline_decode(H5F_t *f, H5O_t H5_ATTR_UNUSED *open_oh, unsigned H5_ATTR_UNUS
uint32_t ext_length;
if (H5_IS_BUFFER_OVERFLOW(p, H5O_PLINE_EXT_HDR_SIZE, p_end))
HGOTO_ERROR(H5E_OHDR, H5E_OVERFLOW, NULL,
"ran off end of input buffer while decoding");
HGOTO_ERROR(H5E_OHDR, H5E_OVERFLOW, NULL, "ran off end of input buffer while decoding");
UINT16DECODE(p, ext_type);
ext_flags = *p++;
ext_reserved = *p++;
@@ -285,8 +284,7 @@ H5O__pline_decode(H5F_t *f, H5O_t H5_ATTR_UNUSED *open_oh, unsigned H5_ATTR_UNUS
prev_type = ext_type;
if (H5_IS_BUFFER_OVERFLOW(p, ext_length, p_end))
HGOTO_ERROR(H5E_OHDR, H5E_OVERFLOW, NULL,
"ran off end of input buffer while decoding");
HGOTO_ERROR(H5E_OHDR, H5E_OVERFLOW, NULL, "ran off end of input buffer while decoding");
switch (ext_type) {
case H5O_PLINE_EXT_CONFIG:
src/H5Pocpl.c
+2 -4
View File
@@ -2009,8 +2009,7 @@ H5Pappend_filter(hid_t plist_id, H5Z_filter_t filter, unsigned int flags, const
* An empty input stores nothing. */
if (!empty_input) {
if (NULL == (canon_config = H5Z_canonicalize_params(param_str)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL,
"can't canonicalize filter parameter string");
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't canonicalize filter parameter string");
retain_config = canon_config;
}
@@ -2275,8 +2274,7 @@ H5Pmodify_filter_by_idx(hid_t plist_id, unsigned filter_idx, unsigned flags, con
}
if (retain_config) {
if (NULL == (staged_config = (char *)H5MM_strdup(retain_config)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL,
"memory allocation failed for filter config string");
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for filter config string");
}
/* ---- Commit: nothing below can fail. ---- */
src/H5Pprivate.h
+1 -2
View File
@@ -198,8 +198,7 @@ H5_DLL int H5P_fill_value_cmp(const void *value1, const void *value2, size_t
/* keep_config: see H5Z_modify() in H5Zprivate.h. set_local callbacks pass
* true; a caller replacing cd_values directly passes false. */
H5_DLL herr_t H5P_modify_filter(H5P_genplist_t *plist, H5Z_filter_t filter, unsigned flags, size_t cd_nelmts,
bool keep_config,
const unsigned cd_values[]);
bool keep_config, const unsigned cd_values[]);
H5_DLL herr_t H5P_get_filter_by_id(H5P_genplist_t *plist, H5Z_filter_t id, unsigned int *flags,
size_t *cd_nelmts, unsigned cd_values[], size_t namelen, char name[],
unsigned *filter_config);
src/H5Z.c
+1 -2
View File
@@ -1304,8 +1304,7 @@ done:
*-------------------------------------------------------------------------
*/
herr_t
H5Z_modify(const H5O_pline_t *pline, H5Z_filter_t filter, unsigned flags, size_t cd_nelmts,
bool keep_config,
H5Z_modify(const H5O_pline_t *pline, H5Z_filter_t filter, unsigned flags, size_t cd_nelmts, bool keep_config,
const unsigned int cd_values[/*cd_nelmts*/])
{
size_t idx; /* Index of filter in pipeline */
src/H5Zprivate.h
+1 -1
View File
@@ -144,7 +144,7 @@ H5_DLL herr_t H5Z_get_filter_info(H5Z_filter_t filter, unsigned int
/* Normalise a parameter string into the form persisted in pipeline v3:
* outer braces stripped and hex-float literals rewritten to %.17e decimal,
* so the stored bytes are valid TOML v1.0.0. Caller frees with H5MM_xfree(). */
H5_DLL char *H5Z_canonicalize_params(const char *params);
H5_DLL char *H5Z_canonicalize_params(const char *params);
/* Filter blob storage (in-file large binary configuration) */
struct H5F_t; /*forward decl*/
src/H5Zscaleoffset.c
+1 -2
View File
@@ -1217,8 +1217,7 @@ H5Z__set_local_scaleoffset(hid_t dcpl_id, hid_t type_id, hid_t space_id)
/* set_local specialises cd_values for this dataset; keep the stored
* configuration string (keep_config = true). */
if (H5P_modify_filter(dcpl_plist, H5Z_FILTER_SCALEOFFSET, flags, (size_t)H5Z_SCALEOFFSET_TOTAL_NPARMS,
true,
cd_values) < 0)
true, cd_values) < 0)
HGOTO_ERROR(H5E_PLINE, H5E_CANTSET, FAIL, "can't set local scaleoffset parameters");
done:
test/tfilter2.c
+9 -9
View File
@@ -4196,8 +4196,8 @@ error:
#define CANON_FILTER_ID 532
static herr_t
canon_set_config(const char *params, unsigned H5_ATTR_UNUSED *flags, size_t *cd_nelmts,
unsigned cd_values[], size_t cd_values_size)
canon_set_config(const char *params, unsigned H5_ATTR_UNUSED *flags, size_t *cd_nelmts, unsigned cd_values[],
size_t cd_values_size)
{
double rate = 0.0;
@@ -4492,8 +4492,8 @@ test_set_local_keeps_config(hid_t fapl)
hsize_t dims[2] = {8, 8}, chunk[2] = {4, 4};
char filename[1024];
char pbuf[H5Z_CONFIG_STRING_MAX + 1];
size_t plen = 0;
const char *compact = "scale_type=\"int\",scale_factor=8";
size_t plen = 0;
const char *compact = "scale_type=\"int\",scale_factor=8";
H5Z_params_t p;
TESTING("set_local preserves the stored configuration string");
@@ -4572,8 +4572,8 @@ test_modify_filter_by_idx(hid_t fapl)
hsize_t dims[2] = {8, 8};
char filename[1024];
char pbuf[H5Z_CONFIG_STRING_MAX + 1];
size_t plen = 0;
double got = 0.0;
size_t plen = 0;
double got = 0.0;
unsigned flags_out = 0;
unsigned cd[8];
size_t cd_nelmts = 8;
@@ -4637,9 +4637,9 @@ test_modify_filter_by_idx(hid_t fapl)
unsigned raw[2] = {0, 0};
memcpy(raw, &v, sizeof(v));
p.type = H5Z_PARAMS_CDVALUES;
p.u.raw.cd_nelmts = 2;
p.u.raw.cd_values = raw;
p.type = H5Z_PARAMS_CDVALUES;
p.u.raw.cd_nelmts = 2;
p.u.raw.cd_values = raw;
if (H5Pmodify_filter_by_idx(dcpl, 0, H5Z_FLAG_MANDATORY, &p) < 0)
TEST_ERROR;
}