Hdf5 merge issue 537 v112 (#538)

* Snapshot version 1.12 release 1-3.  Update  version to 1.12.1-4.

* First cut of the H5 public API documentation. (#80)

* First cut of the H5 public API documentation.

* Added H5Z "bonus track."

* Applied Quincey's patch.

* Added the missing patches from Quincey's original patch.

* H5PL (complete) and basic H5VL API documentation.

* Added H5I API docs.

* Added H5L API docs.

* First installment from Elena's H5T batch.

* Second installment of Elena's H5T batch.

* Final installment of Elena's H5T batch.

* Full set of current H5F documentation. (#105)

* First cut of the H5 public API documentation.

* Added H5Z "bonus track."

* Applied Quincey's patch.

* Added the missing patches from Quincey's original patch.

* H5PL (complete) and basic H5VL API documentation.

* Added H5I API docs.

* Added H5L API docs.

* First installment from Elena's H5T batch.

* Second installment of Elena's H5T batch.

* Final installment of Elena's H5T batch.

* Migrated documentation for SWMR functions.

* Catching up on MDC functions.

* Integrated the H5F MDC function documentation.

* Added MDC and parallel H5F functions.

* Slightly updated main page.

* Added doxygen/dox/H5AC_cache_config_t.dox to MANIFEST.

* Doxygen - added (mostly) beginner functions (#112)

* Doxygen - added (mostly) beginner functions

* Removed duplicate H5Pset_szip function

* Add src/H5module.h to MANIFEST.

* close #195. (#196)

* Update HDF5PluginMacros.cmake

* Update HDF5PluginMacros.cmake

* Avoid aligned access for references by decoding into temporary buffer and then copying the result into the actual buffer.   Update test to be more thorough with using compound datatype fields everywhere. (#206)

* Modify temporary rpath for testing in java example scripts. (#230)

* Fix undefined left shifting of negative numbers (#338)

Undefined Bahavior Sanitizer errored here about left shifting negative numbers.

* Fixes various warnings noticed on Windows (#425)

* Fixes various warnings noticed on Windows

- Adds a prototype for our implementation of vasprintf
- Return type of H5_get_utf16_str() is now non-const
- Fixes possible uninitialized return type in Wremove_utf8
- Better isolation of fork() code in accum.c:test_swmr_write_big()
- Better isolation of non-zlib code in dsets.c:test_filter_delete()
- Removed unused variable in trefer.c:test_reference_cmpnd_obj()

* Fixes clang-format issues

* Applied clang-tidy readability-non-const-parameter warning fixes auto… (#429)

* Automatically applied clang-tidy readability-avoid-const-params-in-decls fixes

Removes useless const declarations.

* Fixed most readability-non-const-parameter warnings

These changes were made automatically by clang-tidy, but I manually reverted the changes related to the H5Z_func_t signature.

* Reformat source with clang v10.0.1.

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

* Added C++11 override keyword where appropriate (#433)

Added H5_OVERRIDE macro for compatibility with both C++11 and older.

* Various clang tidy warning fixes (#448)

* Fixed clang-tidy bugprone-reserved-identifier warnings

* Fixed clang-tidy bugprone-assert-side-effect warnings

* Fixed clang-tidy bugprone-copy-constructor-init warning

* Fixed clang-tidy readability-redundant-preprocessor warning

For error_test.c the removed code was already dead, because it was in the else of an `#if H5_USE_16_API` block.

Based on H5Location.h, I think p_get_ref_obj_type was meant to be in `#ifndef DOXYGEN_SHOULD_SKIP_THIS` and an `#endif` was missing.  Similarly, in the header, getObjTypeByIdx is only in H5_NO_DEPRECATED_SYMBOLS, not DOXYGEN_SHOULD_SKIP_THIS.

* Fixed clang-tidy readability-redundant-string-init warnings

* Fixed some clang-tidy performance-type-promotion-in-math-fn warnings

* Fixed clang-tidy performance-unnecessary-value-param warnings

* Reformat source with clang v10.0.1.

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

* Removed checks/workarounds for pre-C++89 compatibility (#449)

After 30+ years, just assume that the following exist:
- extension-less includes
- namespaces
- std::
- static_cast
- bool

* Fixed all clang-tidy bugprone-suspicious-string-compare warnings (#451)

* Fixed all clang-tidy bugprone-suspicious-string-compare warnings

This change was generated entirely by clang-tidy itself.

* Reformat code with clang v10.0.1.

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

* Remove 2 functions incorrectly merged from develop in a cherry-pick merge of PR #451.

* More warning fixes (#400)

* Fixed -Wunused-local-typedef warning

* Fixed -Wformat warnings

In one case also removed a `z` character. There was a `z%d` that I think was supposed to be `%zd`

* Fixed -Wshorten-64-to-32 warnings

* Fixed -Wself-assign warnings

* Fixed -Wreserved-id-macro warnings

* Commit format changes from clang-format, clang version 10.0.1.

* Fixed -Wself-assign warnings

* Fixed -Wunused-local-typedef warning

* Fixed -Wformat warnings

In two cases also removed a `z` character. There was a `z%d` that was supposed to be `%zd`.

* Fixed -Wshorten-64-to-32 warnings

* Fixed -Wreserved-id-macro warnings

* Fixed -Wself-assign warnings

* Format source.

* Remove blank lines to pass format check.

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

* Changes found during merge to 1.12 (#414)

* OESS-98 convert plugin option to FetchContent, add tests

* Fixes for pkcfg files because of plugin option

* OESS-98 fix tools test for plugins

* Keep doxygen comments under 100 chars long - format hint

* Whitespace

* HDFFV-11144 - Reclassify CMake messages

* HDFFV-11099/11100 added help text

* Reworked switch statement to compare string instead

* Fix typo

* Update CDash mode

* Correct name of threadsafe

* Correct option name

* Undo accidental commit

* Note LLVM 10 to 11 format default changes

* Update format plugin

* Undo clang-format version 11 changes

* One more correction

* Update supported platforms

* Revert whitespace changes

* Correct whitespace

* Changes from PR#3

* HDFFV-11213 added option to control gcc10 warnings diagnostics

* HDFFV-11212 Use the new references correctly in JNI utility and tests

* format source

* Fix typo

* Add new test file

* HDFFV-11212 - update test and remove unused arg

* Minor non-space formatting changes

* Use H5I_INVALID_ID instead of "-1"

* source formatting

* add missing testfile, update jni function

* Undo commit of debug code

* remove mislocated file

* Fix h5repack test for handling of fapls and id close

* Update h5diff test files usage text

* HDFFV-11212 add new ref tests for JNI export dataset

* src format update

* Remove blank line typo

* src format typo

* long double requires %Lg

* Another long double foramt specifer S.B. %Lg

* issue with t128bit test

* Windows issue with h5dump and type.

* Fix review issues

* refactor function nesting and fix error checks

* format fixes

* Remove untested functions and javadoc quiet comments

* Restore TRY block.

* Change string append errors to memory exception

* revert to H5_JNI_FATAL_ERROR - support functions need work

* Add assertion error for h5util functions

* remove duplicate function

* format fix

* Revert HD function error handling

* Update copyright comments

* GH #386 java folder copyright corrections

* Whitespace

* GH #359 implement and fix tools 1.6 API usage

* remove excessive comments

* Flip inits to correct ifdef section

* rework ifdef to be simpler

* format issue

* Reformat ifdef inits

* remove static attribute

* format compliance

* Update names

* Revert because logic relies on float not being int

* Changes noticed from creating merge of #412

* Double underscore change

* Correct compiler version variable used

* Remove header guard underscores

* Whitespace cleanup

* Align with "parallel fence" changes (#479)

* Small code updates and simplifications

* Committing clang-format changes

* Fix 'make installcheck' for parallel builds

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

* File locks now work on Windows (#480)

* File locks now work on Windows

Uses LockFileEx() and UnlockFileEx(). Fixes HDFFV-10191 (partial).

* Committing clang-format changes

* Committing clang-format changes

* Fixes commenting in h5repack

* Reworks H5Fis_accessible()

H5Fis_accessible() created a new file handle and attempted to read
through it, which will fail when a file has been opened with an
exclusive lock on operating systems that have mandatory locks.

This change uses the same scheme we use in H5Fopen() to check if
the file is already open and only tries to read the file signature
if the file has not already been opened.

Also adds a test for this behavior.

* Committing clang-format changes

* Trivial change to force github to run actions

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

* small edits (#481)

* fixed missed closing of a dataset

* fixed missed closing of a dataset

* fixed typo in error return

* Committing clang-format changes

* minor edits

* code format

* Committing clang-format changes

* code format

* minor edit

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

* Adds an implementation for nanosleep on Windows (#483)

* Adds an implementation for nanosleep on Windows

* Committing clang-format changes

* Fix insane formatter issue

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

* Updates HSYS_GOTO_ERROR to emit GetLastError() values on Win32 (#492)

* Committing clang-format changes

* Updates H5SYS_GOTO_ERROR to emit Win32's GetLastError()

* Committing clang-format changes

* Format source changes

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

* Updates that allow accum SWMR tests to work on Windows (#493)

* Committing clang-format changes

* Updates the accum test to work on Windows

Uses CreateProcess() on Windows

* Source formatting

* Fix for Unix child result

* Fixes process return code bug on Windows

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

* Disable long double tests and remove CMake flag groups (#494)

* OESS-98 convert plugin option to FetchContent, add tests

* Fixes for pkcfg files because of plugin option

* OESS-98 fix tools test for plugins

* Keep doxygen comments under 100 chars long - format hint

* Whitespace

* HDFFV-11144 - Reclassify CMake messages

* HDFFV-11099/11100 added help text

* Reworked switch statement to compare string instead

* Fix typo

* Update CDash mode

* Correct name of threadsafe

* Correct option name

* Undo accidental commit

* Note LLVM 10 to 11 format default changes

* Update format plugin

* Undo clang-format version 11 changes

* One more correction

* Update supported platforms

* Revert whitespace changes

* Correct whitespace

* Changes from PR#3

* HDFFV-11213 added option to control gcc10 warnings diagnostics

* HDFFV-11212 Use the new references correctly in JNI utility and tests

* format source

* Fix typo

* Add new test file

* HDFFV-11212 - update test and remove unused arg

* Minor non-space formatting changes

* Use H5I_INVALID_ID instead of "-1"

* source formatting

* add missing testfile, update jni function

* Undo commit of debug code

* remove mislocated file

* Fix h5repack test for handling of fapls and id close

* Update h5diff test files usage text

* HDFFV-11212 add new ref tests for JNI export dataset

* src format update

* Remove blank line typo

* src format typo

* long double requires %Lg

* Another long double foramt specifer S.B. %Lg

* issue with t128bit test

* Windows issue with h5dump and type.

* Fix review issues

* refactor function nesting and fix error checks

* format fixes

* Remove untested functions and javadoc quiet comments

* Restore TRY block.

* Change string append errors to memory exception

* revert to H5_JNI_FATAL_ERROR - support functions need work

* Add assertion error for h5util functions

* remove duplicate function

* format fix

* Revert HD function error handling

* Update copyright comments

* GH #386 java folder copyright corrections

* Whitespace

* GH #359 implement and fix tools 1.6 API usage

* remove excessive comments

* Flip inits to correct ifdef section

* rework ifdef to be simpler

* format issue

* Reformat ifdef inits

* remove static attribute

* format compliance

* Update names

* Revert because logic relies on float not being int

* Changes noticed from creating merge of #412

* Double underscore change

* Correct compiler version variable used

* Remove header guard underscores

* Whitespace cleanup

* Split format source and commit changes on repo push

* remove pre-split setting

* Change windows TS to use older VS.

* correct window os name

* HDFFV-11212 JNI export util and Javadoc

* Suggested review changes

* Another change found

* Committing clang-format changes

* HDFFV-11113 long double in tools

* HDFFV-11113 add note

* Disable long double tests for now

* HDFFV-11228 remove arbitrary CMake warning groups.

* Make each flag a string

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

* Misc warning fixes (#495)

* Committing clang-format changes

* Misc warning fixes from Visual Studio

* Committing clang-format changes

* Fixes warnings in swmr.c test

* Committing clang-format changes

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

* Removes support for pre-2015 Visual Studio (#496)

* Committing clang-format changes

* Removes work-around code for pre-2015 Visual Studio

HDF5 no longer provides an implementation for:

* <inttypes.h>
* snprintf and vsnprintf
* llround(f), lround(f), round(f)
* strtoll and strtoull
* va_copy
* struct timespec

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

* Remove extra parameter from merge.

* Resolve missed merge conflict.

Co-authored-by: Gerd Heber <gheber@hdfgroup.org>
Co-authored-by: bljhdf <58825073+bljhdf@users.noreply.github.com>
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: Quincey Koziol <quincey@koziol.cc>
Co-authored-by: Sean McBride <sean@rogue-research.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: Quincey Koziol <koziol@lbl.gov>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>

1 files changed, 46 insertions, 21 deletions

diff --git a/tools/src/h5repack/h5repack_copy.c b/tools/src/h5repack/h5repack_copy.c
index 7e05a5a..536de69 100644
--- a/tools/src/h5repack/h5repack_copy.c
+++ b/tools/src/h5repack/h5repack_copy.c
@@ -305,14 +305,6 @@ copy_objects(const char *fnamein, const char *fnameout, pack_opt_t *options)
         H5TOOLS_GOTO_ERROR((-1), "H5Fcreate could not create file <%s>:", fnameout);
 
     /*-------------------------------------------------------------------------
-     * write a new user block if requested
-     *-------------------------------------------------------------------------
-     */
-    if (options->ublock_size > 0)
-        if (copy_user_block(options->ublock_filename, fnameout, options->ublock_size) < 0)
-            H5TOOLS_GOTO_ERROR((-1), "Could not copy user block. Exiting...");
-
-    /*-------------------------------------------------------------------------
      * get list of objects
      *-------------------------------------------------------------------------
      */
@@ -346,27 +338,60 @@ copy_objects(const char *fnamein, const char *fnameout, pack_opt_t *options)
     }
 
     /*-------------------------------------------------------------------------
-     * write only the input file user block if there is no user block file input
+     * Close the file and everything in it so the lock is removed
+     *-------------------------------------------------------------------------
+     */
+    if (H5Pclose(fcpl) < 0)
+        H5TOOLS_GOTO_ERROR((-1), "could not close fcpl");
+    if (H5Pclose(options->fout_fapl) < 0)
+        H5TOOLS_GOTO_ERROR((-1), "could not close fcpl");
+    options->fout_fapl = H5P_DEFAULT;
+    if (H5Pclose(gcpl_in) < 0)
+        H5TOOLS_GOTO_ERROR((-1), "could not close fcpl");
+    if (H5Gclose(grp_in) < 0)
+        H5TOOLS_GOTO_ERROR((-1), "could not close fcpl");
+    if (H5Fclose(fidout) < 0)
+        H5TOOLS_GOTO_ERROR((-1), "could not close fcpl");
+    if (H5Fclose(fidin) < 0)
+        H5TOOLS_GOTO_ERROR((-1), "could not close fcpl");
+
+    /*-------------------------------------------------------------------------
+     * NOTE: The userblock MUST be written out AFTER the file is closed or
+     * the file locking will cause failures on Windows, where file locks
+     * are mandatory, not advisory.
+     *-------------------------------------------------------------------------
+     */
+
+    /*-------------------------------------------------------------------------
+     * Write a new user block if requested, using the input file user block if
+     * there is no separate user block file input
      *-------------------------------------------------------------------------
      */
 
-    if (ub_size > 0 && options->ublock_size == 0)
+    if (options->ublock_size > 0) {
+        if (copy_user_block(options->ublock_filename, fnameout, options->ublock_size) < 0)
+            H5TOOLS_GOTO_ERROR((-1), "Could not copy user block. Exiting...");
+    }
+    else if (ub_size > 0 && options->ublock_size == 0) {
         if (copy_user_block(fnamein, fnameout, ub_size) < 0)
             H5TOOLS_GOTO_ERROR((-1), "Could not copy user block. Exiting...");
+    }
 
 done:
-    H5E_BEGIN_TRY
-    {
-        H5Pclose(fcpl);
-        H5Pclose(options->fout_fapl);
-        options->fout_fapl = H5P_DEFAULT;
-        H5Pclose(gcpl_in);
-        H5Gclose(grp_in);
-        H5Pclose(fcpl_in);
-        H5Fclose(fidout);
-        H5Fclose(fidin);
+    if (-1 == ret_value) {
+        H5E_BEGIN_TRY
+        {
+            H5Pclose(fcpl);
+            H5Pclose(options->fout_fapl);
+            options->fout_fapl = H5P_DEFAULT;
+            H5Pclose(gcpl_in);
+            H5Gclose(grp_in);
+            H5Pclose(fcpl_in);
+            H5Fclose(fidout);
+            H5Fclose(fidin);
+        }
+        H5E_END_TRY;
     }
-    H5E_END_TRY;
     if (travt)
         trav_table_free(travt);