From 94a036547cef465e388ff11cbecfbd6a2dbe2aed Mon Sep 17 00:00:00 2001 From: Matteo Di Giovinazzo Date: Sat, 27 Jun 2026 11:27:21 +0200 Subject: [PATCH 01/12] docs(java): fix javadoc error on H5Fcreate flags HTML list parsing --- java/hdf/hdf5lib/H5.java | 16 +++++----------- java/src-jni/hdf/hdf5lib/H5.java | 16 +++++----------- 2 files changed, 10 insertions(+), 22 deletions(-) diff --git a/java/hdf/hdf5lib/H5.java b/java/hdf/hdf5lib/H5.java index 628a543711c..deb709c780f 100644 --- a/java/hdf/hdf5lib/H5.java +++ b/java/hdf/hdf5lib/H5.java @@ -6714,17 +6714,11 @@ public static long H5Freopen(long file_id) throws HDF5LibraryException * @param flags * File access flags. Possible values include: * * * @param create_id diff --git a/java/src-jni/hdf/hdf5lib/H5.java b/java/src-jni/hdf/hdf5lib/H5.java index 069e80a0b94..38385589da2 100644 --- a/java/src-jni/hdf/hdf5lib/H5.java +++ b/java/src-jni/hdf/hdf5lib/H5.java @@ -4795,17 +4795,11 @@ public static long H5Freopen(long file_id) throws HDF5LibraryException * @param flags * File access flags. Possible values include: * * * @param create_id From f090f9b7e5d968f2cd338f516230233632bed9a5 Mon Sep 17 00:00:00 2001 From: Matteo Di Giovinazzo Date: Sat, 27 Jun 2026 11:27:19 +0200 Subject: [PATCH 02/12] docs(java): fix javadoc error on native signatures --- java/hdf/hdf5lib/H5.java | 5 ++--- java/src-jni/hdf/hdf5lib/H5.java | 13 +++++-------- 2 files changed, 7 insertions(+), 11 deletions(-) diff --git a/java/hdf/hdf5lib/H5.java b/java/hdf/hdf5lib/H5.java index deb709c780f..0522f0685a8 100644 --- a/java/hdf/hdf5lib/H5.java +++ b/java/hdf/hdf5lib/H5.java @@ -12461,8 +12461,7 @@ public static int H5Pget_filter(long plist, int filter_number, int[] flags, long * H5Pget_filter2 returns information about a filter, specified by its filter number, in a filter * pipeline, specified by the property list with which it is associated. * - * @see public static int H5Pget_filter(int plist, int filter_number, int[] flags, int[] cd_nelmts, int[] - * cd_values, int namelen, String[] name, int[] filter_config) + * @see #H5Pget_filter(long, int, int[], long[], int[], long, String[], int[]) * **/ private static int H5Pget_filter2(long plist, int filter_number, int[] flags, long[] cd_nelmts, @@ -18636,7 +18635,7 @@ public static int H5Rget_obj_type(long loc_id, int ref_type, byte ref[]) * * H5Rget_obj_type2 Retrieves the type of object that an object reference points to. * - * @see public static int H5Rget_obj_type(int loc_id, int ref_type, byte ref[]) + * @see #H5Rget_obj_type(long, int, byte[]) **/ private static int H5Rget_obj_type2(long loc_id, int ref_type, byte ref[], int[] obj_type) throws HDF5LibraryException, NullPointerException, HDF5FunctionArgumentException diff --git a/java/src-jni/hdf/hdf5lib/H5.java b/java/src-jni/hdf/hdf5lib/H5.java index 38385589da2..9ac6ddfcd47 100644 --- a/java/src-jni/hdf/hdf5lib/H5.java +++ b/java/src-jni/hdf/hdf5lib/H5.java @@ -733,8 +733,7 @@ public static long H5Acreate(long loc_id, String attr_name, long type_id, long s * * H5Acreate2 an attribute, attr_name, which is attached to the object specified by the identifier loc_id. * - * @see public static long H5Acreate( long loc_id, String attr_name, long type_id, long space_id, long - * acpl_id, long aapl_id ) + * @see #H5Acreate(long, String, long, long, long, long) **/ private synchronized static native long _H5Acreate2(long loc_id, String attr_name, long type_id, long space_id, long acpl_id, long aapl_id) @@ -2550,8 +2549,7 @@ public static long H5Dcreate(long loc_id, String name, long type_id, long space_ * * H5Dcreate2 creates a new dataset named name at the location specified by loc_id. * - * @see public static int H5Dcreate(int loc_id, String name, int type_id, int space_id, int lcpl_id, int - * dcpl_id, int dapl_id) + * @see #H5Dcreate(long, String, long, long, long, long, long) **/ private synchronized static native long _H5Dcreate2(long loc_id, String name, long type_id, long space_id, long lcpl_id, long dcpl_id, long dapl_id) @@ -2826,7 +2824,7 @@ public static long H5Dopen(long loc_id, String name, long dapl_id) * H5Dopen2 opens the existing dataset specified by a location identifier and name, loc_id and name, * respectively. * - * @see public static int H5Dopen(int loc_id, String name, int dapl_id) + * @see #H5Dopen(long, String, long) **/ private synchronized static native long _H5Dopen2(long loc_id, String name, long dapl_id) throws HDF5LibraryException, NullPointerException; @@ -8482,8 +8480,7 @@ public static int H5Pget_filter(long plist, int filter_number, int[] flags, long * H5Pget_filter2 returns information about a filter, specified by its filter number, in a filter * pipeline, specified by the property list with which it is associated. * - * @see public static int H5Pget_filter(int plist, int filter_number, int[] flags, int[] cd_nelmts, int[] - * cd_values, int namelen, String[] name, int[] filter_config) + * @see #H5Pget_filter(long, int, int[], long[], int[], long, String[], int[]) * **/ private synchronized static native int H5Pget_filter2(long plist, int filter_number, int[] flags, @@ -12222,7 +12219,7 @@ public synchronized static native int H5Rget_obj_type(long loc_id, int ref_type, * * H5Rget_obj_type2 Retrieves the type of object that an object reference points to. * - * @see public static int H5Rget_obj_type(int loc_id, int ref_type, byte ref[]) + * @see #H5Rget_obj_type(long, int, byte[]) **/ private synchronized static native int H5Rget_obj_type2(long loc_id, int ref_type, byte ref[], int[] obj_type) From 2e2e78bda0991c552d5f13890ac1b60a22f94bfc Mon Sep 17 00:00:00 2001 From: Matteo Di Giovinazzo Date: Fri, 3 Jul 2026 23:05:11 +0200 Subject: [PATCH 03/12] docs(java): fix javadoc error "@see" to "see also" --- java/hdf/hdf5lib/H5.java | 6 +++--- java/hdf/hdf5lib/package-info.java | 2 +- java/src-jni/hdf/hdf5lib/H5.java | 6 +++--- java/src-jni/hdf/hdf5lib/package-info.java | 2 +- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/java/hdf/hdf5lib/H5.java b/java/hdf/hdf5lib/H5.java index 0522f0685a8..eb201a77989 100644 --- a/java/hdf/hdf5lib/H5.java +++ b/java/hdf/hdf5lib/H5.java @@ -92,7 +92,7 @@ * This code is the called by Java programs to access the entry points of the HDF5 library. Each routine wraps * a single HDF5 entry point, generally with the arguments and return codes analogous to the C interface. *

- * For details of the HDF5 library, @see @ref RM + * For details of the HDF5 library, see also @ref RM *

*

* Mapping of arguments for Java @@ -147,7 +147,7 @@ * rather than just return int as in the C. Functions that return a value are declared * equivalent to the C function. * However, in most cases the Java method will raise an exception instead of returning an error code. - * @see @ref ERRORS. + * See also @ref ERRORS. *

* Java does not support pass by reference of arguments, so arguments that are returned through OUT * parameters must be wrapped in an object or array. The Java API for HDF consistently wraps arguments in @@ -263,7 +263,7 @@ * @ref ERRORS hdf.hdf5lib.HDF5Exception
* HDF5 * - * For details of the HDF5 library, @see @ref RM + * For details of the HDF5 library, see also @ref RM */ /** diff --git a/java/hdf/hdf5lib/package-info.java b/java/hdf/hdf5lib/package-info.java index bf0a8137bd4..1c5779fcdad 100644 --- a/java/hdf/hdf5lib/package-info.java +++ b/java/hdf/hdf5lib/package-info.java @@ -76,7 +76,7 @@ * in the C. Functions that return a value or else FAIL are declared the equivalent to the C function. * However, in most * cases the Java method will raise an exception instead of returning an error code. - * @see @ref ERRORS. + * See also @ref ERRORS. *

* Java does not support pass by reference of arguments, so arguments that are returned through OUT * parameters diff --git a/java/src-jni/hdf/hdf5lib/H5.java b/java/src-jni/hdf/hdf5lib/H5.java index 9ac6ddfcd47..e0c9b1170fb 100644 --- a/java/src-jni/hdf/hdf5lib/H5.java +++ b/java/src-jni/hdf/hdf5lib/H5.java @@ -67,7 +67,7 @@ * This code is the called by Java programs to access the entry points of the HDF5 library. Each routine wraps * a single HDF5 entry point, generally with the arguments and return codes analogous to the C interface. *

- * For details of the HDF5 library, @see @ref RM + * For details of the HDF5 library, see also @ref RM *

*

* Mapping of arguments for Java @@ -122,7 +122,7 @@ * rather than just return int as in the C. Functions that return a value are declared * equivalent to the C function. * However, in most cases the Java method will raise an exception instead of returning an error code. - * @see @ref ERRORS. + * See also @ref ERRORS. *

* Java does not support pass by reference of arguments, so arguments that are returned through OUT * parameters must be wrapped in an object or array. The Java API for HDF consistently wraps arguments in @@ -238,7 +238,7 @@ * @ref ERRORS hdf.hdf5lib.HDF5Exception
* HDF5 * - * For details of the HDF5 library, @see @ref RM + * For details of the HDF5 library, see also @ref RM */ /** diff --git a/java/src-jni/hdf/hdf5lib/package-info.java b/java/src-jni/hdf/hdf5lib/package-info.java index bf0a8137bd4..1c5779fcdad 100644 --- a/java/src-jni/hdf/hdf5lib/package-info.java +++ b/java/src-jni/hdf/hdf5lib/package-info.java @@ -76,7 +76,7 @@ * in the C. Functions that return a value or else FAIL are declared the equivalent to the C function. * However, in most * cases the Java method will raise an exception instead of returning an error code. - * @see @ref ERRORS. + * See also @ref ERRORS. *

* Java does not support pass by reference of arguments, so arguments that are returned through OUT * parameters From 868f2e9560d64da3c529bce3b2ed23378b3d2221 Mon Sep 17 00:00:00 2001 From: Matteo Di Giovinazzo Date: Fri, 3 Jul 2026 23:09:02 +0200 Subject: [PATCH 04/12] docs(java): fix javadoc error @see wrapping bold @ref H5E --- java/hdf/hdf5lib/exceptions/HDF5LibraryException.java | 2 +- java/src-jni/hdf/hdf5lib/exceptions/HDF5LibraryException.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/java/hdf/hdf5lib/exceptions/HDF5LibraryException.java b/java/hdf/hdf5lib/exceptions/HDF5LibraryException.java index 496e6136133..ca221167871 100644 --- a/java/hdf/hdf5lib/exceptions/HDF5LibraryException.java +++ b/java/hdf/hdf5lib/exceptions/HDF5LibraryException.java @@ -37,7 +37,7 @@ * this class, and by default the 'detailedMessage' is set according to the * minor error code from the HDF5 Library. *

- * For major and minor error codes, @see @ref H5E in the HDF5 library. + * For major and minor error codes, see @ref H5E in the HDF5 library. * * @defgroup JERRLIB HDF5 Library JNI Exception Interface * diff --git a/java/src-jni/hdf/hdf5lib/exceptions/HDF5LibraryException.java b/java/src-jni/hdf/hdf5lib/exceptions/HDF5LibraryException.java index 442867c09c8..5ee90ab0442 100644 --- a/java/src-jni/hdf/hdf5lib/exceptions/HDF5LibraryException.java +++ b/java/src-jni/hdf/hdf5lib/exceptions/HDF5LibraryException.java @@ -23,7 +23,7 @@ * this class, and by default the 'detailedMessage' is set according to the * minor error code from the HDF5 Library. *

- * For major and minor error codes, @see @ref H5E in the HDF5 library. + * For major and minor error codes, see @ref H5E in the HDF5 library. * * @defgroup JERRLIB HDF5 Library JNI Exception Interface * From d3f478c45eb57f9b93bd12f4250854d828c0146d Mon Sep 17 00:00:00 2001 From: Matteo Di Giovinazzo Date: Fri, 3 Jul 2026 23:31:19 +0200 Subject: [PATCH 05/12] docs(java): fix javadoc error @see before "H5x_UG, User Guide" references --- java/hdf/hdf5lib/H5.java | 34 ++++++++++++++++---------------- java/src-jni/hdf/hdf5lib/H5.java | 34 ++++++++++++++++---------------- 2 files changed, 34 insertions(+), 34 deletions(-) diff --git a/java/hdf/hdf5lib/H5.java b/java/hdf/hdf5lib/H5.java index eb201a77989..cba34e1bab7 100644 --- a/java/hdf/hdf5lib/H5.java +++ b/java/hdf/hdf5lib/H5.java @@ -276,7 +276,7 @@ * * @see H5, C-API * - * @see @ref H5_UG, User Guide + * @ref H5_UG, User Guide * */ public class H5 implements java.io.Serializable { @@ -834,7 +834,7 @@ private static String extractStringFromCharArray(MemorySegment charArray) * * @see H5A, C-API * - * @see @ref H5A_UG, User Guide + * @ref H5A_UG, User Guide **/ /** @@ -3531,7 +3531,7 @@ public static int H5Aiterate_by_name(long loc_id, String obj_name, int idx_type, * * @see H5D, C-API * - * @see @ref H5D_UG, User Guide + * @ref H5D_UG, User Guide **/ /** @@ -5966,7 +5966,7 @@ public static void H5Drefresh(long dataset_id) throws HDF5LibraryException * * @see H5E, C-API * - * @see @ref H5E_UG, User Guide + * @ref H5E_UG, User Guide */ /** @@ -6580,7 +6580,7 @@ public static void H5Ewalk2(long stack_id, long direction, hdf.hdf5lib.callbacks * * @see H5ES, C-API * - * @see @ref H5ES_UG, User Guide + * @ref H5ES_UG, User Guide */ // /////// unimplemented //////// @@ -6610,7 +6610,7 @@ public static void H5Ewalk2(long stack_id, long direction, hdf.hdf5lib.callbacks * * @see H5F, C-API * - * @see @ref H5F_UG, User Guide + * @ref H5F_UG, User Guide */ /** @@ -7638,7 +7638,7 @@ public static void H5Fset_libver_bounds(long file_id, int low, int high) throws * * @see H5G, C-API * - * @see @ref H5G_UG, User Guide + * @ref H5G_UG, User Guide **/ /** @@ -8636,7 +8636,7 @@ public static void H5Grefresh(long group_id) throws HDF5LibraryException * * @see H5I, C-API * - * @see @ref H5I_UG, User Guide + * @ref H5I_UG, User Guide **/ /** @@ -9039,7 +9039,7 @@ public static void H5Idestroy_type(int type_id) throws HDF5LibraryException * * @see H5L, C-API * - * @see @ref H5L_UG, User Guide + * @ref H5L_UG, User Guide **/ /** @@ -10001,7 +10001,7 @@ public static void H5Lunregister(int link_cls_id) throws HDF5LibraryException * * @see H5O, C-API * - * @see @ref H5O_UG, User Guide + * @ref H5O_UG, User Guide **/ /** @@ -11310,7 +11310,7 @@ public static hdf.hdf5lib.structs.H5O_native_info_t H5Oget_native_info_by_name(l * * @see H5P, C-API * - * @see @ref H5P_UG, User Guide + * @ref H5P_UG, User Guide **/ /** @@ -18065,7 +18065,7 @@ public static hdf.hdf5lib.structs.H5FD_ros3_fapl_t H5Pget_fapl_ros3(long fapl_id * * @see H5PL, C-API * - * @see @ref H5PL_UG, User Guide + * @ref H5PL_UG, User Guide **/ /** @@ -18355,7 +18355,7 @@ public static int H5PLsize() throws HDF5LibraryException * * @see H5R, C-API * - * @see @ref H5R_UG, User Guide + * @ref H5R_UG, User Guide * @deprecated As of HDF5 1.12.0 in favor of H5Rcreate_object(), H5Rcreate_region() and H5Rcreate_attr() **/ @Deprecated @@ -19302,7 +19302,7 @@ public static String H5Rget_attr_name(byte[] ref_ptr) * * @see H5S, C-API * - * @see @ref H5S_UG, User Guide + * @ref H5S_UG, User Guide **/ /** @@ -20776,7 +20776,7 @@ public static long H5Sselect_project_intersection(long src_space_id, long dst_sp * * @see H5T, C-API * - * @see @ref H5T_UG, User Guide + * @ref H5T_UG, User Guide **/ /** @@ -23222,7 +23222,7 @@ public static void H5Trefresh(long dtype_id) throws HDF5LibraryException * * @see H5VL, C-API * - * @see @ref H5VL_UG, User Guide + * @ref H5VL_UG, User Guide **/ /** @@ -23561,7 +23561,7 @@ public static boolean H5VLcmp_connector_cls(long conn_id1, long conn_id2) throws * * @see H5Z, C-API * - * @see @ref H5Z_UG, User Guide + * @ref H5Z_UG, User Guide **/ /** diff --git a/java/src-jni/hdf/hdf5lib/H5.java b/java/src-jni/hdf/hdf5lib/H5.java index e0c9b1170fb..6e1db2aacf0 100644 --- a/java/src-jni/hdf/hdf5lib/H5.java +++ b/java/src-jni/hdf/hdf5lib/H5.java @@ -251,7 +251,7 @@ * * @see H5, C-API * - * @see @ref H5_UG, User Guide + * @ref H5_UG, User Guide * */ public class H5 implements java.io.Serializable { @@ -644,7 +644,7 @@ public synchronized static native void H5export_attribute(String file_export_nam * * @see H5A, C-API * - * @see @ref H5A_UG, User Guide + * @ref H5A_UG, User Guide **/ /** @@ -2459,7 +2459,7 @@ public synchronized static native int H5Aiterate_by_name(long loc_id, String obj * * @see H5D, C-API * - * @see @ref H5D_UG, User Guide + * @ref H5D_UG, User Guide **/ /** @@ -4242,7 +4242,7 @@ public synchronized static native int H5Dwrite_VLStrings(long dataset_id, long m * * @see H5E, C-API * - * @see @ref H5E_UG, User Guide + * @ref H5E_UG, User Guide */ /** @@ -4664,7 +4664,7 @@ public synchronized static native void H5Ewalk2(long stack_id, long direction, H * * @see H5ES, C-API * - * @see @ref H5ES_UG, User Guide + * @ref H5ES_UG, User Guide */ // /////// unimplemented //////// @@ -4694,7 +4694,7 @@ public synchronized static native void H5Ewalk2(long stack_id, long direction, H * * @see H5F, C-API * - * @see @ref H5F_UG, User Guide + * @ref H5F_UG, User Guide */ /** @@ -5436,7 +5436,7 @@ public synchronized static native void H5Fset_libver_bounds(long file_id, int lo * * @see H5G, C-API * - * @see @ref H5G_UG, User Guide + * @ref H5G_UG, User Guide **/ /** @@ -6051,7 +6051,7 @@ private synchronized static native long _H5Gopen2(long loc_id, String name, long * * @see H5I, C-API * - * @see @ref H5I_UG, User Guide + * @ref H5I_UG, User Guide **/ /** @@ -6320,7 +6320,7 @@ public synchronized static native void H5Iclear_type(int type_id, boolean force) * * @see H5L, C-API * - * @see @ref H5L_UG, User Guide + * @ref H5L_UG, User Guide **/ /** @@ -6859,7 +6859,7 @@ public synchronized static native int H5Lvisit_by_name(long loc_id, String group * * @see H5O, C-API * - * @see @ref H5O_UG, User Guide + * @ref H5O_UG, User Guide **/ /** @@ -7732,7 +7732,7 @@ public synchronized static native H5O_native_info_t H5Oget_native_info_by_name(l * * @see H5P, C-API * - * @see @ref H5P_UG, User Guide + * @ref H5P_UG, User Guide **/ /** @@ -11891,7 +11891,7 @@ public synchronized static native H5FD_ros3_fapl_t H5Pget_fapl_ros3(long fapl_id * * @see H5PL, C-API * - * @see @ref H5PL_UG, User Guide + * @ref H5PL_UG, User Guide **/ /** @@ -12048,7 +12048,7 @@ public synchronized static native void H5PLinsert(String plugin_path, int index) * * @see H5R, C-API * - * @see @ref H5R_UG, User Guide + * @ref H5R_UG, User Guide **/ private synchronized static native int H5Rcreate(byte[] ref, long loc_id, String name, int ref_type, @@ -12654,7 +12654,7 @@ public synchronized static native String H5Rget_attr_name(byte[] ref_ptr) * * @see H5S, C-API * - * @see @ref H5S_UG, User Guide + * @ref H5S_UG, User Guide **/ /** @@ -13644,7 +13644,7 @@ public synchronized static native int H5Sget_select_hyper_blocklist(long spaceid * * @see H5T, C-API * - * @see @ref H5T_UG, User Guide + * @ref H5T_UG, User Guide **/ /** @@ -15413,7 +15413,7 @@ public static long H5Tvlen_create(long base_id) throws HDF5LibraryException * * @see H5VL, C-API * - * @see @ref H5VL_UG, User Guide + * @ref H5VL_UG, User Guide **/ /** @@ -15605,7 +15605,7 @@ public synchronized static native boolean H5VLcmp_connector_cls(long conn_id1, l * * @see H5Z, C-API * - * @see @ref H5Z_UG, User Guide + * @ref H5Z_UG, User Guide **/ /** From 00bbb348c3b4cc4e428f488be3706dd5e4b507c3 Mon Sep 17 00:00:00 2001 From: Matteo Di Giovinazzo Date: Fri, 3 Jul 2026 23:34:50 +0200 Subject: [PATCH 06/12] docs(java): fix javadoc error @see before "H5x, C-API" references --- java/hdf/hdf5lib/H5.java | 26 ++++++++++++------------ java/src-jni/hdf/hdf5lib/H5.java | 34 ++++++++++++++++---------------- 2 files changed, 30 insertions(+), 30 deletions(-) diff --git a/java/hdf/hdf5lib/H5.java b/java/hdf/hdf5lib/H5.java index cba34e1bab7..25421c4b803 100644 --- a/java/hdf/hdf5lib/H5.java +++ b/java/hdf/hdf5lib/H5.java @@ -274,7 +274,7 @@ * This code is the called by Java programs to access the entry points of the HDF5 library. Each routine wraps * a single HDF5 entry point, generally with the arguments and return codes analogous to the C interface. * - * @see H5, C-API + * @ref H5, C-API * * @ref H5_UG, User Guide * @@ -832,7 +832,7 @@ private static String extractStringFromCharArray(MemorySegment charArray) * An HDF5 attribute is a small metadata object describing the nature and/or intended usage of a primary *data object. A primary data object may be a dataset, group, or committed datatype. * - * @see H5A, C-API + * @ref H5A, C-API * * @ref H5A_UG, User Guide **/ @@ -3529,7 +3529,7 @@ public static int H5Aiterate_by_name(long loc_id, String obj_name, int idx_type, /** * @defgroup JH5D Java Datasets (H5D) Interface * - * @see H5D, C-API + * @ref H5D, C-API * * @ref H5D_UG, User Guide **/ @@ -5964,7 +5964,7 @@ public static void H5Drefresh(long dataset_id) throws HDF5LibraryException * * @defgroup JH5E Java Error (H5E) Interface * - * @see H5E, C-API + * @ref H5E, C-API * * @ref H5E_UG, User Guide */ @@ -6578,7 +6578,7 @@ public static void H5Ewalk2(long stack_id, long direction, hdf.hdf5lib.callbacks * * @defgroup JH5ES Java Event Set (H5ES) Interface * - * @see H5ES, C-API + * @ref H5ES, C-API * * @ref H5ES_UG, User Guide */ @@ -6608,7 +6608,7 @@ public static void H5Ewalk2(long stack_id, long direction, hdf.hdf5lib.callbacks * * @defgroup JH5F Java File (H5F) Interface * - * @see H5F, C-API + * @ref H5F, C-API * * @ref H5F_UG, User Guide */ @@ -7636,7 +7636,7 @@ public static void H5Fset_libver_bounds(long file_id, int low, int high) throws /** * @defgroup JH5G Java Group (H5G) Interface * - * @see H5G, C-API + * @ref H5G, C-API * * @ref H5G_UG, User Guide **/ @@ -8634,7 +8634,7 @@ public static void H5Grefresh(long group_id) throws HDF5LibraryException /** * @defgroup JH5I Java Identifier (H5I) Interface * - * @see H5I, C-API + * @ref H5I, C-API * * @ref H5I_UG, User Guide **/ @@ -9037,7 +9037,7 @@ public static void H5Idestroy_type(int type_id) throws HDF5LibraryException /** * @defgroup JH5L Java Link (H5L) Interface * - * @see H5L, C-API + * @ref H5L, C-API * * @ref H5L_UG, User Guide **/ @@ -9999,7 +9999,7 @@ public static void H5Lunregister(int link_cls_id) throws HDF5LibraryException /** * @defgroup JH5O Java Object (H5O) Interface * - * @see H5O, C-API + * @ref H5O, C-API * * @ref H5O_UG, User Guide **/ @@ -11308,7 +11308,7 @@ public static hdf.hdf5lib.structs.H5O_native_info_t H5Oget_native_info_by_name(l /** * @defgroup JH5P Java Property List (H5P) Interface * - * @see H5P, C-API + * @ref H5P, C-API * * @ref H5P_UG, User Guide **/ @@ -18063,7 +18063,7 @@ public static hdf.hdf5lib.structs.H5FD_ros3_fapl_t H5Pget_fapl_ros3(long fapl_id /** * @defgroup JH5PL Java Plugin (H5PL) Interface * - * @see H5PL, C-API + * @ref H5PL, C-API * * @ref H5PL_UG, User Guide **/ @@ -18353,7 +18353,7 @@ public static int H5PLsize() throws HDF5LibraryException /** * @defgroup JH5R Java Reference (H5R) Interface * - * @see H5R, C-API + * @ref H5R, C-API * * @ref H5R_UG, User Guide * @deprecated As of HDF5 1.12.0 in favor of H5Rcreate_object(), H5Rcreate_region() and H5Rcreate_attr() diff --git a/java/src-jni/hdf/hdf5lib/H5.java b/java/src-jni/hdf/hdf5lib/H5.java index 6e1db2aacf0..f47fcd954ae 100644 --- a/java/src-jni/hdf/hdf5lib/H5.java +++ b/java/src-jni/hdf/hdf5lib/H5.java @@ -249,7 +249,7 @@ * This code is the called by Java programs to access the entry points of the HDF5 library. Each routine wraps * a single HDF5 entry point, generally with the arguments and return codes analogous to the C interface. * - * @see H5, C-API + * @ref H5, C-API * * @ref H5_UG, User Guide * @@ -642,7 +642,7 @@ public synchronized static native void H5export_attribute(String file_export_nam * An HDF5 attribute is a small metadata object describing the nature and/or intended usage of a primary *data object. A primary data object may be a dataset, group, or committed datatype. * - * @see H5A, C-API + * @ref H5A, C-API * * @ref H5A_UG, User Guide **/ @@ -2457,7 +2457,7 @@ public synchronized static native int H5Aiterate_by_name(long loc_id, String obj /** * @defgroup JH5D Java Datasets (H5D) Interface * - * @see H5D, C-API + * @ref H5D, C-API * * @ref H5D_UG, User Guide **/ @@ -4240,7 +4240,7 @@ public synchronized static native int H5Dwrite_VLStrings(long dataset_id, long m * * @defgroup JH5E Java Error (H5E) Interface * - * @see H5E, C-API + * @ref H5E, C-API * * @ref H5E_UG, User Guide */ @@ -4662,7 +4662,7 @@ public synchronized static native void H5Ewalk2(long stack_id, long direction, H * * @defgroup JH5ES Java Event Set (H5ES) Interface * - * @see H5ES, C-API + * @ref H5ES, C-API * * @ref H5ES_UG, User Guide */ @@ -4692,7 +4692,7 @@ public synchronized static native void H5Ewalk2(long stack_id, long direction, H * * @defgroup JH5F Java File (H5F) Interface * - * @see H5F, C-API + * @ref H5F, C-API * * @ref H5F_UG, User Guide */ @@ -5434,7 +5434,7 @@ public synchronized static native void H5Fset_libver_bounds(long file_id, int lo /** * @defgroup JH5G Java Group (H5G) Interface * - * @see H5G, C-API + * @ref H5G, C-API * * @ref H5G_UG, User Guide **/ @@ -6049,7 +6049,7 @@ private synchronized static native long _H5Gopen2(long loc_id, String name, long /** * @defgroup JH5I Java Identifier (H5I) Interface * - * @see H5I, C-API + * @ref H5I, C-API * * @ref H5I_UG, User Guide **/ @@ -6318,7 +6318,7 @@ public synchronized static native void H5Iclear_type(int type_id, boolean force) /** * @defgroup JH5L Java Link (H5L) Interface * - * @see H5L, C-API + * @ref H5L, C-API * * @ref H5L_UG, User Guide **/ @@ -6857,7 +6857,7 @@ public synchronized static native int H5Lvisit_by_name(long loc_id, String group /** * @defgroup JH5O Java Object (H5O) Interface * - * @see H5O, C-API + * @ref H5O, C-API * * @ref H5O_UG, User Guide **/ @@ -7730,7 +7730,7 @@ public synchronized static native H5O_native_info_t H5Oget_native_info_by_name(l /** * @defgroup JH5P Java Property List (H5P) Interface * - * @see H5P, C-API + * @ref H5P, C-API * * @ref H5P_UG, User Guide **/ @@ -11889,7 +11889,7 @@ public synchronized static native H5FD_ros3_fapl_t H5Pget_fapl_ros3(long fapl_id /** * @defgroup JH5PL Java Plugin (H5PL) Interface * - * @see H5PL, C-API + * @ref H5PL, C-API * * @ref H5PL_UG, User Guide **/ @@ -12046,7 +12046,7 @@ public synchronized static native void H5PLinsert(String plugin_path, int index) /** * @defgroup JH5R Java Reference (H5R) Interface * - * @see H5R, C-API + * @ref H5R, C-API * * @ref H5R_UG, User Guide **/ @@ -12652,7 +12652,7 @@ public synchronized static native String H5Rget_attr_name(byte[] ref_ptr) /** * @defgroup JH5S Java Dataspace (H5S) Interface * - * @see H5S, C-API + * @ref H5S, C-API * * @ref H5S_UG, User Guide **/ @@ -13642,7 +13642,7 @@ public synchronized static native int H5Sget_select_hyper_blocklist(long spaceid /** * @defgroup JH5T Java Datatype (H5T) Interface * - * @see H5T, C-API + * @ref H5T, C-API * * @ref H5T_UG, User Guide **/ @@ -15411,7 +15411,7 @@ public static long H5Tvlen_create(long base_id) throws HDF5LibraryException /** * @defgroup JH5VL Java VOL Connector (H5VL) Interface * - * @see H5VL, C-API + * @ref H5VL, C-API * * @ref H5VL_UG, User Guide **/ @@ -15603,7 +15603,7 @@ public synchronized static native boolean H5VLcmp_connector_cls(long conn_id1, l /** * @defgroup JH5Z Java Filter (H5Z) Interface * - * @see H5Z, C-API + * @ref H5Z, C-API * * @ref H5Z_UG, User Guide **/ From a2dc04187110c3ce94146532875810f1254b377a Mon Sep 17 00:00:00 2001 From: Matteo Di Giovinazzo Date: Fri, 3 Jul 2026 23:39:12 +0200 Subject: [PATCH 07/12] docs(java): fix javadoc error @see before HDF5LIB --- java/hdf/hdf5lib/HDF5Constants.java | 2 +- java/src-jni/hdf/hdf5lib/HDF5Constants.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/java/hdf/hdf5lib/HDF5Constants.java b/java/hdf/hdf5lib/HDF5Constants.java index 6c444399fed..7061c7789ac 100644 --- a/java/hdf/hdf5lib/HDF5Constants.java +++ b/java/hdf/hdf5lib/HDF5Constants.java @@ -33,7 +33,7 @@ *

* Do not edit this file! * - * @see @ref HDF5LIB + * @ref HDF5LIB */ public class HDF5Constants { diff --git a/java/src-jni/hdf/hdf5lib/HDF5Constants.java b/java/src-jni/hdf/hdf5lib/HDF5Constants.java index 1c83276018d..263ffdef8b8 100644 --- a/java/src-jni/hdf/hdf5lib/HDF5Constants.java +++ b/java/src-jni/hdf/hdf5lib/HDF5Constants.java @@ -23,7 +23,7 @@ *

* Do not edit this file! * - * @see @ref HDF5LIB + * @ref HDF5LIB */ public class HDF5Constants { static { H5.loadH5Lib(); } From 6fcc2f864b2b69a88289a23f4e8e66ac0ba615d2 Mon Sep 17 00:00:00 2001 From: Matteo Di Giovinazzo Date: Fri, 3 Jul 2026 23:39:36 +0200 Subject: [PATCH 08/12] docs(java): fix javadoc error @see before HDFARRAY --- java/hdf/hdf5lib/HDFNativeData.java | 2 +- java/src-jni/hdf/hdf5lib/HDFNativeData.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/java/hdf/hdf5lib/HDFNativeData.java b/java/hdf/hdf5lib/HDFNativeData.java index 9a4b8395c3b..2e57403da76 100644 --- a/java/hdf/hdf5lib/HDFNativeData.java +++ b/java/hdf/hdf5lib/HDFNativeData.java @@ -30,7 +30,7 @@ * Variant interfaces convert a section of an array, and also can convert to * sub-classes of Java Number. *

- * @see @ref HDFARRAY. + * @ref HDFARRAY. */ public class HDFNativeData { diff --git a/java/src-jni/hdf/hdf5lib/HDFNativeData.java b/java/src-jni/hdf/hdf5lib/HDFNativeData.java index 9a4b8395c3b..2e57403da76 100644 --- a/java/src-jni/hdf/hdf5lib/HDFNativeData.java +++ b/java/src-jni/hdf/hdf5lib/HDFNativeData.java @@ -30,7 +30,7 @@ * Variant interfaces convert a section of an array, and also can convert to * sub-classes of Java Number. *

- * @see @ref HDFARRAY. + * @ref HDFARRAY. */ public class HDFNativeData { From 563b96a879f467738eeda8072d503eff22eb430b Mon Sep 17 00:00:00 2001 From: Matteo Di Giovinazzo Date: Sat, 27 Jun 2026 11:27:23 +0200 Subject: [PATCH 09/12] docs(java): fix javadoc error package-info HTML and comment formatting --- java/hdf/hdf5lib/package-info.java | 6 ++---- java/src-jni/hdf/hdf5lib/package-info.java | 6 ++---- 2 files changed, 4 insertions(+), 8 deletions(-) diff --git a/java/hdf/hdf5lib/package-info.java b/java/hdf/hdf5lib/package-info.java index 1c5779fcdad..e13fb4c9c9b 100644 --- a/java/hdf/hdf5lib/package-info.java +++ b/java/hdf/hdf5lib/package-info.java @@ -11,7 +11,7 @@ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /** - \page HDF5LIB_UG HDF5 Java Package + * \page HDF5LIB_UG HDF5 Java Package * This package is the Java interface for the HDF5 library. *

* This code is the called by Java programs to access the entry points of the HDF5 library. @@ -20,7 +20,6 @@ *

* For details of the HDF5 library, see the HDF5 Documentation at: * https://support.hdfgroup.org/documentation/ - *

*

* Mapping of arguments for Java * @@ -192,11 +191,10 @@ * in the HDF5 C API @ref H5Eprint(). This may be * used by Java * exception handlers to print out the HDF5 error stack. - *

* * @ref HDF5LIB * - * @see: HDF5" + * HDF5 * */ package hdf.hdf5lib; diff --git a/java/src-jni/hdf/hdf5lib/package-info.java b/java/src-jni/hdf/hdf5lib/package-info.java index 1c5779fcdad..e13fb4c9c9b 100644 --- a/java/src-jni/hdf/hdf5lib/package-info.java +++ b/java/src-jni/hdf/hdf5lib/package-info.java @@ -11,7 +11,7 @@ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ /** - \page HDF5LIB_UG HDF5 Java Package + * \page HDF5LIB_UG HDF5 Java Package * This package is the Java interface for the HDF5 library. *

* This code is the called by Java programs to access the entry points of the HDF5 library. @@ -20,7 +20,6 @@ *

* For details of the HDF5 library, see the HDF5 Documentation at: * https://support.hdfgroup.org/documentation/ - *

*

* Mapping of arguments for Java * @@ -192,11 +191,10 @@ * in the HDF5 C API @ref H5Eprint(). This may be * used by Java * exception handlers to print out the HDF5 error stack. - *

* * @ref HDF5LIB * - * @see: HDF5" + * HDF5 * */ package hdf.hdf5lib; From 2fb089c7763d308521b3e928c7f06e87f1078d43 Mon Sep 17 00:00:00 2001 From: Matteo Di Giovinazzo Date: Fri, 3 Jul 2026 23:50:30 +0200 Subject: [PATCH 10/12] docs(java): fix doxygen @ref HDFNATIVE --- java/hdf/hdf5lib/HDFArray.java | 8 +++++--- java/src-jni/hdf/hdf5lib/HDFArray.java | 7 ++++--- 2 files changed, 9 insertions(+), 6 deletions(-) diff --git a/java/hdf/hdf5lib/HDFArray.java b/java/hdf/hdf5lib/HDFArray.java index e339e5852b9..6e2777ed5e6 100644 --- a/java/hdf/hdf5lib/HDFArray.java +++ b/java/hdf/hdf5lib/HDFArray.java @@ -25,14 +25,16 @@ import hdf.hdf5lib.exceptions.HDF5JavaException; /** - * \page HDFARRAY Java Array Conversion This is a class for handling multidimensional arrays for HDF. + * \page HDFARRAY Java Array Conversion + * This is a class for handling multidimensional arrays for HDF. *

* The purpose is to allow the storage and retrieval of arbitrary array types containing scientific data. *

* The methods support the conversion of an array to and from Java to a one-dimensional array of bytes - * suitable for I/O by the C library.

This class heavily uses the + * suitable for I/O by the C library.

This class heavily uses the HDFNativeData class to convert between + * Java and C representations. * - * @ref HDFNATIVE class to convert between Java and C representations. + * See also @ref HDFNATIVE */ public class HDFArray { diff --git a/java/src-jni/hdf/hdf5lib/HDFArray.java b/java/src-jni/hdf/hdf5lib/HDFArray.java index 888e0641fc5..c810998ae67 100644 --- a/java/src-jni/hdf/hdf5lib/HDFArray.java +++ b/java/src-jni/hdf/hdf5lib/HDFArray.java @@ -24,9 +24,10 @@ * The purpose is to allow the storage and retrieval of arbitrary array types containing scientific data. *

* The methods support the conversion of an array to and from Java to a one-dimensional array of bytes - * suitable for I/O by the C library.

This class heavily uses the - * @ref HDFNATIVE - * class to convert between Java and C representations. + * suitable for I/O by the C library.

This class heavily uses the HDFNativeData class to convert between + * Java and C representations. + * + * See also @ref HDFNATIVE */ public class HDFArray { From 6a5ff145cd48b6a8a8e924471316de4e54a5d8cc Mon Sep 17 00:00:00 2001 From: Matteo Di Giovinazzo Date: Sat, 4 Jul 2026 11:41:57 +0200 Subject: [PATCH 11/12] docs(java): fix javadoc error self-closing element not allowed --- java/hdf/hdf5lib/H5.java | 2 +- java/hdf/hdf5lib/package-info.java | 2 +- java/src-jni/hdf/hdf5lib/H5.java | 2 +- java/src-jni/hdf/hdf5lib/package-info.java | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/java/hdf/hdf5lib/H5.java b/java/hdf/hdf5lib/H5.java index 25421c4b803..55ac3cbb723 100644 --- a/java/hdf/hdf5lib/H5.java +++ b/java/hdf/hdf5lib/H5.java @@ -132,7 +132,7 @@ * java.lang.String * * - * void *
+ * void *
* (i.e., pointer to Any) * Special -- see @ref HDFARRAY * diff --git a/java/hdf/hdf5lib/package-info.java b/java/hdf/hdf5lib/package-info.java index e13fb4c9c9b..978dfe29566 100644 --- a/java/hdf/hdf5lib/package-info.java +++ b/java/hdf/hdf5lib/package-info.java @@ -58,7 +58,7 @@ * java.lang.String * * - * void *
+ * void *
* (i.e., pointer to `Any') * Special -- see HDFArray * diff --git a/java/src-jni/hdf/hdf5lib/H5.java b/java/src-jni/hdf/hdf5lib/H5.java index f47fcd954ae..756161b1cda 100644 --- a/java/src-jni/hdf/hdf5lib/H5.java +++ b/java/src-jni/hdf/hdf5lib/H5.java @@ -107,7 +107,7 @@ * java.lang.String * * - * void *
+ * void *
* (i.e., pointer to `Any`) * Special -- see @ref HDFARRAY * diff --git a/java/src-jni/hdf/hdf5lib/package-info.java b/java/src-jni/hdf/hdf5lib/package-info.java index e13fb4c9c9b..978dfe29566 100644 --- a/java/src-jni/hdf/hdf5lib/package-info.java +++ b/java/src-jni/hdf/hdf5lib/package-info.java @@ -58,7 +58,7 @@ * java.lang.String * * - * void *
+ * void *
* (i.e., pointer to `Any') * Special -- see HDFArray * From 7b94f19e880ef240d08638d4a2ed50b81f43e3ba Mon Sep 17 00:00:00 2001 From: Matteo Di Giovinazzo Date: Sat, 4 Jul 2026 12:24:18 +0200 Subject: [PATCH 12/12] docs(java): align FFM javadoc @param names with method signatures Update callback interface and struct constructor documentation to match FFM apply() parameter names after the bindings were regenerated from jextract. Co-authored-by: Cursor --- java/hdf/hdf5lib/callbacks/H5A_iterate_cb.java | 6 +++--- java/hdf/hdf5lib/callbacks/H5D_iterate_cb.java | 10 +++++----- java/hdf/hdf5lib/callbacks/H5E_walk_cb.java | 6 +++--- java/hdf/hdf5lib/callbacks/H5L_iterate_t.java | 2 +- java/hdf/hdf5lib/callbacks/H5O_iterate_t.java | 2 +- java/hdf/hdf5lib/callbacks/H5P_iterate_cb.java | 6 +++--- java/hdf/hdf5lib/structs/H5F_info2_t.java | 2 +- 7 files changed, 17 insertions(+), 17 deletions(-) diff --git a/java/hdf/hdf5lib/callbacks/H5A_iterate_cb.java b/java/hdf/hdf5lib/callbacks/H5A_iterate_cb.java index f2bc4e13e72..662412f1294 100644 --- a/java/hdf/hdf5lib/callbacks/H5A_iterate_cb.java +++ b/java/hdf/hdf5lib/callbacks/H5A_iterate_cb.java @@ -28,9 +28,9 @@ public interface H5A_iterate_cb extends org.hdfgroup.javahdf5.H5A_operator2_t.Fu * * application callback for each attribute * - * @param loc_id the ID for the group or dataset being iterated over - * @param name the name of the current attribute about the object - * @param info the attribute's "info" struct + * @param location_id the ID for the group or dataset being iterated over + * @param attr_name the name of the current attribute about the object + * @param ainfo the attribute's "info" struct * @param op_data the operator data passed in to H5Aiterate * * @return operation status diff --git a/java/hdf/hdf5lib/callbacks/H5D_iterate_cb.java b/java/hdf/hdf5lib/callbacks/H5D_iterate_cb.java index 6fbb9b772c1..865e9b9a40d 100644 --- a/java/hdf/hdf5lib/callbacks/H5D_iterate_cb.java +++ b/java/hdf/hdf5lib/callbacks/H5D_iterate_cb.java @@ -28,11 +28,11 @@ public interface H5D_iterate_cb extends org.hdfgroup.javahdf5.H5D_operator_t.Fun * * application callback for each dataset element * - * @param elem the pointer to the element in memory containing the current point - * @param elem_type the datatype ID for the elements stored in elem - * @param ndim the number of dimensions for POINT array - * @param point the array containing the location of the element within the original dataspace - * @param op_data the operator data passed in to H5Diterate + * @param elem the pointer to the element in memory containing the current point + * @param type_id the datatype ID for the elements stored in elem + * @param ndim the number of dimensions for POINT array + * @param point the array containing the location of the element within the original dataspace + * @param operator_data the operator data passed in to H5Diterate * * @return operation status * A. Zero causes the iterator to continue, returning zero when all diff --git a/java/hdf/hdf5lib/callbacks/H5E_walk_cb.java b/java/hdf/hdf5lib/callbacks/H5E_walk_cb.java index c964ecd6a2f..557ae91f1b8 100644 --- a/java/hdf/hdf5lib/callbacks/H5E_walk_cb.java +++ b/java/hdf/hdf5lib/callbacks/H5E_walk_cb.java @@ -28,9 +28,9 @@ public interface H5E_walk_cb extends H5E_walk2_t.Function { * * application callback for each error stack element * - * @param nidx the index of the current error stack element - * @param info the error stack "info" struct - * @param op_data the operator data passed in to H5Ewalk + * @param n the index of the current error stack element + * @param err_desc the error stack "info" struct + * @param client_data the operator data passed in to H5Ewalk * * @return operation status * A. Zero causes the iterator to continue, returning zero when all diff --git a/java/hdf/hdf5lib/callbacks/H5L_iterate_t.java b/java/hdf/hdf5lib/callbacks/H5L_iterate_t.java index 21bc0ed2470..d0d23dfbd61 100644 --- a/java/hdf/hdf5lib/callbacks/H5L_iterate_t.java +++ b/java/hdf/hdf5lib/callbacks/H5L_iterate_t.java @@ -28,7 +28,7 @@ public interface H5L_iterate_t extends H5L_iterate2_t.Function { * * application callback for each group * - * @param loc_id the ID for the group being iterated over + * @param group the ID for the group being iterated over * @param name the name of the current link * @param info the link's "info" struct * @param op_data the operator data passed in to H5Literate diff --git a/java/hdf/hdf5lib/callbacks/H5O_iterate_t.java b/java/hdf/hdf5lib/callbacks/H5O_iterate_t.java index ce5973188c5..c591e5bb133 100644 --- a/java/hdf/hdf5lib/callbacks/H5O_iterate_t.java +++ b/java/hdf/hdf5lib/callbacks/H5O_iterate_t.java @@ -28,7 +28,7 @@ public interface H5O_iterate_t extends H5O_iterate2_t.Function { * * application callback for each group * - * @param loc_id the ID for the group or dataset being iterated over + * @param obj the ID for the group or dataset being iterated over * @param name the name of the current object * @param info the object's "info" struct * @param op_data the operator data passed in to H5Oiterate diff --git a/java/hdf/hdf5lib/callbacks/H5P_iterate_cb.java b/java/hdf/hdf5lib/callbacks/H5P_iterate_cb.java index bfc9a048a91..a7391151ad3 100644 --- a/java/hdf/hdf5lib/callbacks/H5P_iterate_cb.java +++ b/java/hdf/hdf5lib/callbacks/H5P_iterate_cb.java @@ -28,9 +28,9 @@ public interface H5P_iterate_cb extends org.hdfgroup.javahdf5.H5P_iterate_t.Func * * application callback for each property list * - * @param plist the ID for the property list being iterated over - * @param name the name of the current property list - * @param op_data the operator data passed in to H5Piterate + * @param id the ID for the property list being iterated over + * @param name the name of the current property list + * @param iter_data the operator data passed in to H5Piterate * * @return operation status * A. Zero causes the iterator to continue, returning zero when all diff --git a/java/hdf/hdf5lib/structs/H5F_info2_t.java b/java/hdf/hdf5lib/structs/H5F_info2_t.java index 5102f451c51..e7cc7887e94 100644 --- a/java/hdf/hdf5lib/structs/H5F_info2_t.java +++ b/java/hdf/hdf5lib/structs/H5F_info2_t.java @@ -77,7 +77,7 @@ public H5F_info2_t(int super_version, long super_size, long super_ext_size, int } /** * Constructor for current "global" information about file - * @param info_segment: Memory segment for H5F_info2_t + * @param finfo_segment Memory segment for H5F_info2_t */ public H5F_info2_t(MemorySegment finfo_segment) {