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";