Merge1 issue 839 PRs to hdf5 1 12 (#904)

* Fixes for a couple of trivial warnings (#676)

* Committing clang-format changes

* Trivial warning fixes:

* Removes an unused done target in H5Tbit.c
* Add (void) to quiet "ignored return value" warnings in the generators
  (which generally ignore errors)

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Removes alternative function enter/leave macro scheme (#678)

* Committing clang-format changes

* Converted BEGIN_FUNC, etc. macros to FUNC_ENTER

* Rips out the BEGIN_FUNC, etc. macros

* Removes 'end if', etc. comments from H5HL package

* Committing clang-format changes

* Fixes an H5EA iterate issue

* Fixes an issue in the H5FA iterator code

* Further cleanup in bin/trace after macro removal

* Iterator changes in H5EA and H5FA

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Various CMake changes (#679)

* Committing clang-format changes

* Several CMake updates:

* Removes unused HDF5_ENABLE_HSIZET
* Switches TEST_SHELL_SCRIPTS to ON
* Sets SH_PROGRAM to bash instead of sh

* Set default build type back to RelWithDebInfo

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* err_compat test cleanup (#681)

* Committing clang-format changes

* Cleans up err_compat test and output

* Formatted source

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* CMake fix for sporadic flush2 failures (#692)

* Committing clang-format changes

* Runs the flush1/flush2 tests in their own directory

Avoids file deletions by other tests.

* Revert "Runs the flush1/flush2 tests in their own directory"

This reverts commit 746c04882434cb502e4231de8f7dd5acb4949f54.

Also pulls the flush files from the clean list, which is a simpler fix.

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Ubsan fixes (#498)

* Fixed use of null pointer identified by UBSan

UBSan warned:
runtime error: member access within null pointer of type 'named_dt_t' (aka 'struct named_dt_t')

with these two tests:
H5REPACK-committed_dt_DFF
H5REPACK-committed_dt

Reformulated per @gnuoyd suggestion.

* Fixed undefined float -> unsigned char conversion in HL_test_image

* Removed dead skip_overflow_tests_g global

The global `skip_overflow_tests_g` was being set but never read.

* Don't treat 2d array as 1d array, fixing UBSan complaint in `CPP_testhdf5`

* Committing clang-format changes

* Remove extra ']' in line 730.

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>

* BUG: DataSet assignment operator is missing (#503)

* BUG: DataSet assignment operator is missing

* Some compilers complain if the copy constructor is given explicitly
  but the assignment operator is implicitly set to default.

* Explicitly defining the assignment operator allows us to properly
  handle reference counters for shared resources.

* BUG: DataSet assignment operator is missing.

* Mimicking code of H5DataType::operator() as suggested by @bmribler.

* Added test

Description:
    Added test for DataSet::operator= that Leengit added
Platform tested:
    Linux/64 (jelly)

* Removed Author field.

* Commit clang format changes.

* Entry for Leengit's github PR #503

* Removed lines left by mistake

Co-authored-by: Binh-Minh Ribler <bmribler@hdfgroup.org>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>

* Hdf5 merge pr7 (#516)

* Modify temporary rpath for testing in java example scripts.

* Update URL in source file Copyright headers for web copy of COPYING (license) file.

* Add release_docs/code-conventions.md file.

* Add script to test h5py.

* Fix script error.

* Add file h5pytest.yml.

* Test declaration of counter variables in for loops.

* Committing clang-format changes

* Committing clang-format changes

* Added [] to line 126 of H5LTanalyze.l.
Ran bin/genparser with flex v2.6.4 and Bison v3.0.4 on jelly.

* Revert "Added [] to line 126 of H5LTanalyze.l."

This reverts commit e4a9cee441efa75b16a8ee030c86189e186dd266.

* Revert extra commits to match canonical develop.

* Add cmake variable HDF5_LIB_INFIX (#7)

* Add cmake variable HDF5_LIB_INFIX

This infix is added to all library names after 'hdf5'.
e.g. the infix '_openmpi' results in the library name 'libhdf5_openmpi.so'
This name is used in packages on debian based systems.
(see https://packages.debian.org/jessie/amd64/libhdf5-openmpi-8/filelist)

This option is useful when testing projects on debian based systems with
custom builds of hdf5 while trying to minimize differences between the
custom setup and the environment created by installing system packages.

* Added RELEASE.txt entry for HDF5_LIB_INFIX.

Co-authored-by: Larry Knox <lrknox@hdfgroup.org>

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Raphael Grimm <barcode@users.noreply.github.com>

* Fixes a segfault when H5Pset_mdc_log_options is called multiple times on a fapl (#601)

* Committing clang-format changes

* Fixes a segfault when H5Pset_mdc_log_options() is called multiple times

An internal string is incorrectly freed when the API call is invoked
multiple times on a property list, which will usually cause a segfault
to occur. On the first call the log location is NULL so the problem
doesn't occur.

Fixes HDFFV-11239

* Fixes typos

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fix for a segfault when H5Pset_fapl_log is passed an invalid fapl ID (#607)

* Committing clang-format changes

* Fixes an issue where H5Pset_fapl_log sefaults when passed an invalid
fapl ID

This was due to a pointer-containing struct being memset after the first
internal API call. If the first call failed, the error condition would
check if the pointer was not NULL and then attempt to free it if not.
This would lead to the freeing of a wild pointer if an invalid fapl ID
were passed in.

This was fixed by reordering the memset and adding a test to ensure the
problem stays fixed.

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fixes crashes when size_hint > UINT32_MAX is passed to H5Gcreate1 (#611)

* Committing clang-format changes

* Fixes incorrect size_hint handling in H5Gcreate1

* Updates the size hint type for group creation

* Updates the RELEASE.txt note

* Revert "Updates the RELEASE.txt note"

This reverts commit 3df386acca806d652bbe2209f7c4503b30f068ff.

* Reverts previous behavior to use a uint32_t struct field

* Updates RELEASE.txt

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Sean McBride <sean@rogue-research.com>
Co-authored-by: Lee Newberg <35611400+Leengit@users.noreply.github.com>
Co-authored-by: Binh-Minh Ribler <bmribler@hdfgroup.org>
Co-authored-by: Raphael Grimm <barcode@users.noreply.github.com>

4 files changed, 25 insertions, 27 deletions

diff --git a/tools/lib/h5tools_error.h b/tools/lib/h5tools_error.h
index 8fd33bb..5840a98 100644
--- a/tools/lib/h5tools_error.h
+++ b/tools/lib/h5tools_error.h
@@ -220,22 +220,22 @@ H5TOOLS_DLLVAR hid_t H5E_tools_min_dbg_id_g;
 /* Macro for "catching" flow of control when an error occurs.  Note that the
  *      H5_LEAVE macro won't jump back here once it's past this point.
  */
-/* #define CATCH catch_except:; past_catch = TRUE; defined in H5Eprivate.h */
+#define CATCH                                                                                                \
+catch_except:;                                                                                               \
+    past_catch = TRUE;
 
 /*
- * H5_LEAVE macro, used to facilitate control flow between a
- * BEGIN_FUNC() and an END_FUNC() within a function body.  The argument is
- * the return value.
- * The return value is assigned to a variable `ret_value' and control branches
- * to the `catch_except' label, if we're not already past it.
+ * H5_LEAVE macro, used to facilitate control flow in a function. The argument
+ * is the return value. The return value is assigned to a variable `ret_value'
+ * and control branches to the `catch_except' label, if we're not already past
+ * it.
  */
-/*
- *  #define H5_LEAVE(v) {                           \
- *   ret_value = v;                              \
- *   if(!past_catch)                             \
- *        goto catch_except;                      \
- * }
- * defined in H5Eprivate.h */
+#define H5_LEAVE(v)                                                                                          \
+    {                                                                                                        \
+        ret_value = v;                                                                                       \
+        if (!past_catch)                                                                                     \
+            goto catch_except;                                                                               \
+    }
 
 /*
  * H5TOOLS_THROW macro, used to facilitate error reporting within a function body.
diff --git a/tools/src/h5repack/h5repack.c b/tools/src/h5repack/h5repack.c
index 7bcca8f..7cad36b 100644
--- a/tools/src/h5repack/h5repack.c
+++ b/tools/src/h5repack/h5repack.c
@@ -225,9 +225,9 @@ hid_t
 copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, trav_table_t *travt,
                     pack_opt_t *options)
 {
-    named_dt_t *dt     = *named_dt_head_p; /* Stack pointer */
-    named_dt_t *dt_ret = NULL;             /* Datatype to return */
-    H5O_info2_t oinfo;                     /* Object info of input dtype */
+    named_dt_t *dt     = NULL; /* Stack pointer */
+    named_dt_t *dt_ret = NULL; /* Datatype to return */
+    H5O_info2_t oinfo;         /* Object info of input dtype */
     int         token_cmp;
     hid_t       ret_value = H5I_INVALID_HID;
 
@@ -235,15 +235,13 @@ copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, t
         H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "H5Oget_info failed");
 
     if (*named_dt_head_p) {
-        if (H5Otoken_cmp(type_in, &dt->obj_token, &oinfo.token, &token_cmp) < 0)
-            H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "failed to compare object tokens");
-
-        /* Stack already exists, search for the datatype */
-        while (dt && token_cmp) {
-            dt = dt->next;
-
+        /* Search the stack for the datatype. */
+        for (dt = *named_dt_head_p; dt != NULL; dt = dt->next) {
             if (H5Otoken_cmp(type_in, &dt->obj_token, &oinfo.token, &token_cmp) < 0)
                 H5TOOLS_GOTO_ERROR(H5I_INVALID_HID, "failed to compare object tokens");
+
+            if (token_cmp == 0)
+                break; // found it!
         }
 
         dt_ret = dt;
diff --git a/tools/test/h5jam/h5jamgentest.c b/tools/test/h5jam/h5jamgentest.c
index 45ff0b0..1da6b63 100644
--- a/tools/test/h5jam/h5jamgentest.c
+++ b/tools/test/h5jam/h5jamgentest.c
@@ -277,7 +277,7 @@ gent_ub(const char *filename, size_t ub_size, size_t ub_fill)
         for (u = 0; u < ub_fill; u++)
             *bp++ = pattern[u % 10];
 
-        HDwrite(fd, buf, ub_size);
+        (void)HDwrite(fd, buf, ub_size);
 
         HDclose(fd);
     }
@@ -301,7 +301,7 @@ create_textfile(const char *name, size_t size)
     for (i = 0; i < size; i++)
         *bp++ = pattern[i % 10];
 
-    HDwrite(fd, buf, size);
+    (void)HDwrite(fd, buf, size);
 
     HDfree(buf);
 
@@ -329,7 +329,7 @@ create_binfile(char *name, off_t size)
     for (i = 0; i < size; i++)
         *bp++ = (char)i & 0xff;
 
-    HDwrite(fd, buf, size);
+    (void)HDwrite(fd, buf, size);
 
     HDclose(fd);
 }
diff --git a/tools/test/h5stat/h5stat_gentest.c b/tools/test/h5stat/h5stat_gentest.c
index b55cd06..a9813e7 100644
--- a/tools/test/h5stat/h5stat_gentest.c
+++ b/tools/test/h5stat/h5stat_gentest.c
@@ -497,7 +497,7 @@ gen_err_refcount(const char *fname)
            attribute message */
     if ((fd = HDopen(fname, O_RDWR, 0633)) >= 0) {
         HDlseek(fd, 4520 + 24, SEEK_SET);
-        HDwrite(fd, &val, 2);
+        (void)HDwrite(fd, &val, 2);
         HDclose(fd);
     }