Sync 2 develop changes October 2 to hdf5_1_16 (#4946)

* Correct publish path

* Update clang-format to 17 (#4931)

Also bump the clang-format GitHub actions to 17

* Committing clang-format changes

.github/workflows/clang-format-check.yml

@@ -18,6 +18,6 @@ jobs:
       with:
         source: '.'
         extensions: 'c,h,cpp,hpp,java'
-        clangFormatVersion: 13
+        clangFormatVersion: 17
         style: file
         exclude: './config ./hl/src/H5LTanalyze.c ./hl/src/H5LTparse.c ./hl/src/H5LTparse.h ./src/H5Epubgen.h ./src/H5Einit.h ./src/H5Eterm.h ./src/H5Edefin.h ./src/H5version.h ./src/H5overflow.h'

.github/workflows/clang-format-fix.yml

@@ -30,7 +30,7 @@ jobs:
       with:
         source: '.'
         extensions: 'c,h,cpp,hpp,java'
-        clangFormatVersion: 13
+        clangFormatVersion: 17
         inplace: True
         style: file
         exclude: './config ./hl/src/H5LTanalyze.c ./hl/src/H5LTparse.c ./hl/src/H5LTparse.h ./src/H5Epubgen.h ./src/H5Einit.h ./src/H5Eterm.h ./src/H5Edefin.h ./src/H5version.h ./src/H5overflow.h'

.github/workflows/publish-release.yml

@@ -58,3 +58,7 @@ jobs:
           run: |
                 aws s3 sync ./${{ inputs.file_name }}.doxygen s3://${{ secrets.AWS_S3_BUCKET }}/${{ vars.TARGET_PATH }}/${{ inputs.target_dir }}/documentation/doxygen --delete
 
+        - name: Sync userguide to latest S3 bucket
+          run: |
+                aws s3 sync ./${{ inputs.file_name }}.doxygen s3://${{ secrets.AWS_S3_BUCKET }}/documentation/hdf5/latest --delete
+

HDF5Examples/C/H5T/h5ex_t_objref.c

@@ -124,7 +124,7 @@ main(void)
 #if H5_VERSION_GE(1, 12, 0) && !defined(H5_USE_110_API) && !defined(H5_USE_18_API) && !defined(H5_USE_16_API)
     rdata = (H5R_ref_t *)malloc(dims[0] * sizeof(H5R_ref_t));
 #else
-    rdata  = (hobj_ref_t *)malloc(dims[0] * sizeof(hobj_ref_t));
+    rdata = (hobj_ref_t *)malloc(dims[0] * sizeof(hobj_ref_t));
 #endif
     /*
      * Read the data.

HDF5Examples/C/H5T/h5ex_t_objrefatt.c

@@ -136,7 +136,7 @@ main(void)
 #if H5_VERSION_GE(1, 12, 0) && !defined(H5_USE_110_API) && !defined(H5_USE_18_API) && !defined(H5_USE_16_API)
     rdata = (H5R_ref_t *)malloc(dims[0] * sizeof(H5R_ref_t));
 #else
-    rdata  = (hobj_ref_t *)malloc(dims[0] * sizeof(hobj_ref_t));
+    rdata = (hobj_ref_t *)malloc(dims[0] * sizeof(hobj_ref_t));
 #endif
     /*
      * Read the data.

HDF5Examples/C/H5T/h5ex_t_regref.c

@@ -154,7 +154,7 @@ main(void)
 #if H5_VERSION_GE(1, 12, 0) && !defined(H5_USE_110_API) && !defined(H5_USE_18_API) && !defined(H5_USE_16_API)
     rdata = (H5R_ref_t *)malloc(dims[0] * sizeof(H5R_ref_t));
 #else
-    rdata  = (hdset_reg_ref_t *)malloc(dims[0] * sizeof(hdset_reg_ref_t));
+    rdata = (hdset_reg_ref_t *)malloc(dims[0] * sizeof(hdset_reg_ref_t));
 #endif
 
     status = H5Sclose(space);

HDF5Examples/C/H5T/h5ex_t_regrefatt.c

@@ -169,7 +169,7 @@ main(void)
 #if H5_VERSION_GE(1, 12, 0) && !defined(H5_USE_110_API) && !defined(H5_USE_18_API) && !defined(H5_USE_16_API)
     rdata = (H5R_ref_t *)malloc(dims[0] * sizeof(H5R_ref_t));
 #else
-    rdata  = (hdset_reg_ref_t *)malloc(dims[0] * sizeof(hdset_reg_ref_t));
+    rdata = (hdset_reg_ref_t *)malloc(dims[0] * sizeof(hdset_reg_ref_t));
 #endif
 
     status = H5Sclose(space);

HDF5Examples/C/TUTR/h5_extend.c

@@ -36,8 +36,8 @@ main(void)
     herr_t  status;
     hsize_t chunk_dims[2] = {2, 5};
     int     data[3][3]    = {{1, 1, 1}, /* data to write */
-                      {1, 1, 1},
-                      {1, 1, 1}};
+                             {1, 1, 1},
+                             {1, 1, 1}};
 
     /* Variables used in extending and writing to the extended portion of dataset */
     hsize_t size[2];

HDF5Examples/CXX/TUTR/h5tutr_extend.cpp

@@ -33,8 +33,8 @@ main(void)
     hsize_t maxdims[2]    = {H5S_UNLIMITED, H5S_UNLIMITED};
     hsize_t chunk_dims[2] = {2, 5};
     int     data[3][3]    = {{1, 1, 1}, // data to write
-                      {1, 1, 1},
-                      {1, 1, 1}};
+                             {1, 1, 1},
+                             {1, 1, 1}};
 
     // Variables used in extending and writing to the extended portion of dataset
 

HDF5Examples/JAVA/H5T/H5Ex_T_Commit.java

@@ -73,7 +73,7 @@ private static class Sensor_Datatype {
 
         String[] memberNames       = {"Serial number", "Location", "Temperature (F)", "Pressure (inHg)"};
         long[] memberFileTypes     = {HDF5Constants.H5T_STD_I32BE, HDF5Constants.H5T_C_S1,
-                                  HDF5Constants.H5T_IEEE_F64BE, HDF5Constants.H5T_IEEE_F64BE};
+                                      HDF5Constants.H5T_IEEE_F64BE, HDF5Constants.H5T_IEEE_F64BE};
         static int[] memberStorage = {INTEGERSIZE, MAXSTRINGSIZE, DOUBLESIZE, DOUBLESIZE};
 
         // Data size is the storage size for the members not the object.

HDF5Examples/JAVA/H5T/H5Ex_T_Compound.java

@@ -43,7 +43,7 @@ static class Sensor_Datatype {
 
         static String[] memberNames   = {"Serial number", "Location", "Temperature (F)", "Pressure (inHg)"};
         static long[] memberMemTypes  = {HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5T_C_S1,
-                                        HDF5Constants.H5T_NATIVE_DOUBLE, HDF5Constants.H5T_NATIVE_DOUBLE};
+                                         HDF5Constants.H5T_NATIVE_DOUBLE, HDF5Constants.H5T_NATIVE_DOUBLE};
         static long[] memberFileTypes = {HDF5Constants.H5T_STD_I32BE, HDF5Constants.H5T_C_S1,
                                          HDF5Constants.H5T_IEEE_F64BE, HDF5Constants.H5T_IEEE_F64BE};
         static int[] memberStorage    = {INTEGERSIZE, MAXSTRINGSIZE, DOUBLESIZE, DOUBLESIZE};

HDF5Examples/JAVA/H5T/H5Ex_T_CompoundAttribute.java

@@ -44,7 +44,7 @@ static class Sensor_Datatype {
 
         static String[] memberNames   = {"Serial number", "Location", "Temperature (F)", "Pressure (inHg)"};
         static long[] memberMemTypes  = {HDF5Constants.H5T_NATIVE_INT, HDF5Constants.H5T_C_S1,
-                                        HDF5Constants.H5T_NATIVE_DOUBLE, HDF5Constants.H5T_NATIVE_DOUBLE};
+                                         HDF5Constants.H5T_NATIVE_DOUBLE, HDF5Constants.H5T_NATIVE_DOUBLE};
         static long[] memberFileTypes = {HDF5Constants.H5T_STD_I32BE, HDF5Constants.H5T_C_S1,
                                          HDF5Constants.H5T_IEEE_F64BE, HDF5Constants.H5T_IEEE_F64BE};
         static int[] memberStorage    = {INTEGERSIZE, MAXSTRINGSIZE, DOUBLESIZE, DOUBLESIZE};

c++/src/H5DataType.cpp

@@ -91,8 +91,8 @@ DataType::DataType(const H5T_class_t type_class, size_t size)
 ///\exception   H5::ReferenceException
 //--------------------------------------------------------------------------
 DataType::DataType(const H5Location &loc, const void *ref, H5R_type_t ref_type, const PropList &plist)
-    : H5Object(), id{H5Location::p_dereference(loc.getId(), ref, ref_type, plist,
-                                               "constructor - by dereference")},
+    : H5Object(),
+      id{H5Location::p_dereference(loc.getId(), ref, ref_type, plist, "constructor - by dereference")},
       encoded_buf(NULL), buf_size(0)
 {
 }

c++/test/titerate.cpp

@@ -30,17 +30,17 @@ using namespace H5;
 #define NDATASETS 50
 
 /* Number of attributes for attribute iteration test */
-//#define NATTR 50
+// #define NATTR 50
 
 /* Number of groups for second group iteration test */
-//#define ITER_NGROUPS 150
+// #define ITER_NGROUPS 150
 
 /* General maximum length of names used */
 #define NAMELEN 80
 
 /* 1-D dataset with fixed dimensions */
-//#define SPACE1_RANK     1
-//#define SPACE1_DIM1     4
+// #define SPACE1_RANK     1
+// #define SPACE1_DIM1     4
 
 const H5std_string FILE_ITERATE("titerate.h5");
 const H5std_string GROUP1("Top Group");

fortran/src/H5_f.c

@@ -568,17 +568,17 @@ h5init_flags_c(int_f *h5d_flags, size_t_f *h5d_size_flags, int_f *h5e_flags, hid
     h5fd_flags[20] = (int_f)SELECT_IOC_TOTAL;
     h5fd_flags[21] = (int_f)ioc_selection_options;
 #else
-    h5fd_flags[11]    = 0;
-    h5fd_flags[12]    = 0;
-    h5fd_flags[13]    = 0;
-    h5fd_flags[14]    = 0;
-    h5fd_flags[15]    = 0;
-    h5fd_flags[16]    = 0;
-    h5fd_flags[17]    = 0;
-    h5fd_flags[18]    = 0;
-    h5fd_flags[19]    = 0;
-    h5fd_flags[20]    = 0;
-    h5fd_flags[21]    = 0;
+    h5fd_flags[11] = 0;
+    h5fd_flags[12] = 0;
+    h5fd_flags[13] = 0;
+    h5fd_flags[14] = 0;
+    h5fd_flags[15] = 0;
+    h5fd_flags[16] = 0;
+    h5fd_flags[17] = 0;
+    h5fd_flags[18] = 0;
+    h5fd_flags[19] = 0;
+    h5fd_flags[20] = 0;
+    h5fd_flags[21] = 0;
 #endif
 
     /*

hl/examples/ex_table_03.c

@@ -47,7 +47,7 @@ main(void)
 
     Particle p                  = {"zero", 0, 0, 0.0F, 0.0};
     size_t   dst_sizes[NFIELDS] = {sizeof(p.name), sizeof(p.lati), sizeof(p.longi), sizeof(p.pressure),
-                                 sizeof(p.temperature)};
+                                   sizeof(p.temperature)};
 
     /* Define field information */
     const char *field_names[NFIELDS] = {"Name", "Latitude", "Longitude", "Pressure", "Temperature"};

hl/examples/ex_table_04.c

@@ -56,7 +56,7 @@ main(void)
     size_t dst_offset[NFIELDS] = {HOFFSET(Particle, name), HOFFSET(Particle, lati), HOFFSET(Particle, longi),
                                   HOFFSET(Particle, pressure), HOFFSET(Particle, temperature)};
     size_t dst_sizes[NFIELDS]  = {sizeof(dst_buf[0].name), sizeof(dst_buf[0].lati), sizeof(dst_buf[0].longi),
-                                 sizeof(dst_buf[0].pressure), sizeof(dst_buf[0].temperature)};
+                                  sizeof(dst_buf[0].pressure), sizeof(dst_buf[0].temperature)};
     size_t field_offset_pos[2] = {HOFFSET(Position, lati), HOFFSET(Position, longi)};
     const char *field_names[NFIELDS] = /* Define field information */
         {"Name", "Latitude", "Longitude", "Pressure", "Temperature"};

hl/examples/ex_table_05.c

@@ -50,7 +50,7 @@ main(void)
     size_t dst_offset[NFIELDS] = {HOFFSET(Particle, name), HOFFSET(Particle, lati), HOFFSET(Particle, longi),
                                   HOFFSET(Particle, pressure), HOFFSET(Particle, temperature)};
     size_t dst_sizes[NFIELDS]  = {sizeof(dst_buf[0].name), sizeof(dst_buf[0].lati), sizeof(dst_buf[0].longi),
-                                 sizeof(dst_buf[0].pressure), sizeof(dst_buf[0].temperature)};
+                                  sizeof(dst_buf[0].pressure), sizeof(dst_buf[0].temperature)};
 
     size_t field_offset_pos[2] = {HOFFSET(Position, lati), HOFFSET(Position, longi)};
 

hl/examples/ex_table_08.c

@@ -50,7 +50,7 @@ main(void)
     size_t dst_offset[NFIELDS] = {HOFFSET(Particle, name), HOFFSET(Particle, lati), HOFFSET(Particle, longi),
                                   HOFFSET(Particle, pressure), HOFFSET(Particle, temperature)};
     size_t dst_sizes[NFIELDS]  = {sizeof(p_data[0].name), sizeof(p_data[0].lati), sizeof(p_data[0].longi),
-                                 sizeof(p_data[0].pressure), sizeof(p_data[0].temperature)};
+                                  sizeof(p_data[0].pressure), sizeof(p_data[0].temperature)};
 
     /* Define an array of Particles to insert */
     Particle p_data_insert[NRECORDS_INS] = {{"new", 30, 30, 3.0F, 30.0}, {"new", 40, 40, 4.0F, 40.0}};

hl/examples/ex_table_09.c

@@ -45,7 +45,7 @@ main(void)
     size_t dst_offset[NFIELDS] = {HOFFSET(Particle, name), HOFFSET(Particle, lati), HOFFSET(Particle, longi),
                                   HOFFSET(Particle, pressure), HOFFSET(Particle, temperature)};
     size_t dst_sizes[NFIELDS]  = {sizeof(dst_buf[0].name), sizeof(dst_buf[0].lati), sizeof(dst_buf[0].longi),
-                                 sizeof(dst_buf[0].pressure), sizeof(dst_buf[0].temperature)};
+                                  sizeof(dst_buf[0].pressure), sizeof(dst_buf[0].temperature)};
 
     /* Define an array of Particles */
     Particle p_data[NRECORDS] = {{"zero", 0, 0, 0.0F, 0.0},    {"one", 10, 10, 1.0F, 10.0},

hl/examples/ex_table_10.c

@@ -50,7 +50,7 @@ main(void)
     size_t dst_offset[NFIELDS] = {HOFFSET(Particle, name), HOFFSET(Particle, lati), HOFFSET(Particle, longi),
                                   HOFFSET(Particle, pressure), HOFFSET(Particle, temperature)};
     size_t dst_sizes[NFIELDS]  = {sizeof(dst_buf[0].name), sizeof(dst_buf[0].lati), sizeof(dst_buf[0].longi),
-                                 sizeof(dst_buf[0].pressure), sizeof(dst_buf[0].temperature)};
+                                  sizeof(dst_buf[0].pressure), sizeof(dst_buf[0].temperature)};
 
     /* Define field information */
     const char *field_names[NFIELDS] = {"Name", "Latitude", "Longitude", "Pressure", "Temperature"};

hl/test/gen_test_ds.c

@@ -136,9 +136,9 @@ create_long_dataset(hid_t fid, const char *name, const char *dsidx)
     int     rankds                = 1;
     hsize_t dims[4]               = {DIM1_SIZE, DIM2_SIZE, DIM3_SIZE, DIM4_SIZE};
     long    buf[DIM_DATA * 3 * 2] = {1, 2, 3, 4,  5,  6,  7, 8, 9, 10, 11, 12, 1, 2, 3, 4,  5,  6,
-                                  7, 8, 9, 10, 11, 12, 1, 2, 3, 4,  5,  6,  7, 8, 9, 10, 11, 12,
-                                  1, 2, 3, 4,  5,  6,  7, 8, 9, 10, 11, 12, 1, 2, 3, 4,  5,  6,
-                                  7, 8, 9, 10, 11, 12, 1, 2, 3, 4,  5,  6,  7, 8, 9, 10, 11, 12};
+                                     7, 8, 9, 10, 11, 12, 1, 2, 3, 4,  5,  6,  7, 8, 9, 10, 11, 12,
+                                     1, 2, 3, 4,  5,  6,  7, 8, 9, 10, 11, 12, 1, 2, 3, 4,  5,  6,
+                                     7, 8, 9, 10, 11, 12, 1, 2, 3, 4,  5,  6,  7, 8, 9, 10, 11, 12};
     hsize_t s1_dim[1]             = {DIM1_SIZE};
     hsize_t s2_dim[1]             = {DIM2_SIZE};
     hsize_t s3_dim[1]             = {DIM3_SIZE};

hl/test/test_table.c

@@ -236,13 +236,13 @@ test_table(hid_t fid, int do_write)
                                      0.0,
                                      0,
                                  },
-                                 {"one", 10, 1.0F, 10.0, 10},
-                                 {"two", 20, 2.0F, 20.0, 20},
-                                 {"three", 30, 3.0F, 30.0, 30},
-                                 {"four", 40, 4.0F, 40.0, 40},
-                                 {"five", 50, 5.0F, 50.0, 50},
-                                 {"six", 60, 6.0F, 60.0, 60},
-                                 {"seven", 70, 7.0F, 70.0, 70}};
+                                  {"one", 10, 1.0F, 10.0, 10},
+                                  {"two", 20, 2.0F, 20.0, 20},
+                                  {"three", 30, 3.0F, 30.0, 30},
+                                  {"four", 40, 4.0F, 40.0, 40},
+                                  {"five", 50, 5.0F, 50.0, 50},
+                                  {"six", 60, 6.0F, 60.0, 60},
+                                  {"seven", 70, 7.0F, 70.0, 70}};
     /* buffers for the field "Pressure" and "New_field" */
     float pressure_in[NRECORDS] = {0.0F, 1.0F, 2.0F, 3.0F, 4.0F, 5.0F, 6.0F, 7.0F};
     float pressure_out[NRECORDS];
@@ -302,8 +302,8 @@ test_table(hid_t fid, int do_write)
                                        HOFFSET(particle2_t, pressure), HOFFSET(particle2_t, temperature),
                                        HOFFSET(particle2_t, lati),     HOFFSET(particle2_t, new_field)};
     size_t dst_sizes2[NFIELDS + 1]  = {sizeof(rbuf2[0].name),     sizeof(rbuf2[0].longi),
-                                      sizeof(rbuf2[0].pressure), sizeof(rbuf2[0].temperature),
-                                      sizeof(rbuf2[0].lati),     sizeof(rbuf2[0].new_field)};
+                                       sizeof(rbuf2[0].pressure), sizeof(rbuf2[0].temperature),
+                                       sizeof(rbuf2[0].lati),     sizeof(rbuf2[0].new_field)};
     /*-------------------------------------------------------------------------
      * initialize table parameters
      * size and the offsets of struct members in memory
@@ -353,7 +353,7 @@ test_table(hid_t fid, int do_write)
                                     HOFFSET(particle_t, pressure), HOFFSET(particle_t, temperature),
                                     HOFFSET(particle_t, lati)};
     size_t field_size[NFIELDS]   = {sizeof(rbuf[0].name), sizeof(rbuf[0].longi), sizeof(rbuf[0].pressure),
-                                  sizeof(rbuf[0].temperature), sizeof(rbuf[0].lati)};
+                                    sizeof(rbuf[0].temperature), sizeof(rbuf[0].lati)};
 
     const char *field_names4[NFIELDS + 1] = {"F1", "F2", "F3", "F4", "F5", "F6"};
     hid_t       field_type4[NFIELDS + 1];

java/test/TestAll.java

@@ -28,5 +28,4 @@
                      TestH5Obasic.class,    TestH5Ocopy.class,    TestH5Ocreate.class,   TestH5PL.class,
                      TestH5Z.class})
 
-public class TestAll {
-}
+public class TestAll {}

java/test/TestH5D.java

@@ -939,8 +939,8 @@ public int callback(byte[] elem_buf, long elem_id, int ndim, long[] point, H5D_i
     public void testH5Dvlen_get_buf_size()
     {
         String[] str_data   = {"Parting", "is such", "sweet", "sorrow.", "Testing",  "one", "two",   "three.",
-                             "Dog,",    "man's",   "best",  "friend.", "Diamonds", "are", "a",     "girls!",
-                             "S A",     "T U R",   "D A Y", "night",   "That's",   "all", "folks", "!!!"};
+                               "Dog,",    "man's",   "best",  "friend.", "Diamonds", "are", "a",     "girls!",
+                               "S A",     "T U R",   "D A Y", "night",   "That's",   "all", "folks", "!!!"};
         long vl_size        = -1; /* Number of bytes used */
         long str_data_bytes = 0;
         for (int idx = 0; idx < str_data.length; idx++)

java/test/TestH5F.java

@@ -45,8 +45,8 @@ public class TestH5F {
     private static final int[] OBJ_COUNTS = {COUNT_OBJ_FILE,     COUNT_OBJ_DATASET, COUNT_OBJ_GROUP,
                                              COUNT_OBJ_DATATYPE, COUNT_OBJ_ATTR,    COUNT_OBJ_ALL};
     private static final int[] OBJ_TYPES  = {HDF5Constants.H5F_OBJ_FILE,  HDF5Constants.H5F_OBJ_DATASET,
-                                            HDF5Constants.H5F_OBJ_GROUP, HDF5Constants.H5F_OBJ_DATATYPE,
-                                            HDF5Constants.H5F_OBJ_ATTR,  HDF5Constants.H5F_OBJ_ALL};
+                                             HDF5Constants.H5F_OBJ_GROUP, HDF5Constants.H5F_OBJ_DATATYPE,
+                                             HDF5Constants.H5F_OBJ_ATTR,  HDF5Constants.H5F_OBJ_ALL};
     long H5fid                            = HDF5Constants.H5I_INVALID_HID;
 
     private final void _deleteFile(String filename)

java/test/TestH5G.java

@@ -37,7 +37,7 @@ public class TestH5G {
     private static final String H5_FILE   = "testG.h5";
     private static final String H5_FILE2  = "testG2.h5";
     private static final String[] GROUPS  = {"/G1",          "/G1/G11",      "/G1/G12",     "/G1/G11/G111",
-                                            "/G1/G11/G112", "/G1/G11/G113", "/G1/G11/G114"};
+                                             "/G1/G11/G112", "/G1/G11/G113", "/G1/G11/G114"};
     private static final String[] GROUPS2 = {"/G1", "/G1/G14", "/G1/G12", "/G1/G13", "/G1/G11"};
     long H5fid                            = HDF5Constants.H5I_INVALID_HID;
     long H5fid2                           = HDF5Constants.H5I_INVALID_HID;

java/test/TestH5Plist.java

@@ -73,7 +73,7 @@ public class TestH5Plist {
 
     private static final String PROP3_NAME = "Property 3";
     private static final char[] prop3_def  = {'T', 'e', 'n', ' ', 'c',
-                                             'h', 'a', 'r', 's', ' '}; // Property 3 default value
+                                              'h', 'a', 'r', 's', ' '}; // Property 3 default value
     private static final int PROP3_SIZE    = 10;
 
     private static final String PROP4_NAME = "Property 4";