Merge branch 'HDFGroup:develop' into develop

hyoklee · Mar 15, 2024 · 7749911 · 7749911
2 parents 847aeb2 + 26837b4
commit 7749911
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diff --git a/fortran/src/CMakeLists.txt b/fortran/src/CMakeLists.txt
@@ -31,6 +31,12 @@ else ()
   set (CMAKE_H5_HAVE_MPI_F08 0)
 endif ()
 
+if (H5_HAVE_DARWIN) # Used in testing
+  set (CMAKE_H5_HAVE_DARWIN 1)
+else ()
+  set (CMAKE_H5_HAVE_DARWIN 0)
+endif ()
+
 # configure for Fortran preprocessor
 
 # Define Parallel variable for passing to H5config_f.inc.cmake

diff --git a/release_docs/NEWSLETTER.txt b/release_docs/NEWSLETTER.txt
@@ -1,25 +0,0 @@
-INTRODUCTION
-============
-
-This purpose of this document is to contain entries that can be used to quickly
-produce a release newsletter. When something is added to the library that is
-"newsletter worthy" (i.e., new feature, CVE fix, etc.) a summary note should
-be added here.
-
-The format should look like this:
-
-* SUMMARY OF NEWSLETTER-WORTHY THING
-
-    Here is where you describe the summary. Summarize the feature, fix, or
-    change in general language. Remember, RELEASE.txt is for communicating
-    technical specifics. Text entered here is more like advertising.
-
-    (GitHub #123, #125)
-
-The GitHub #s could be relevant issues or PRs. They will probably not appear
-in the final newsletter, but are so that the person writing the newsletter
-has easy access to context if they have questions.
-
-Every entry in RELEASE.txt does NOT require an entry here. The newsletter is
-for communicating major changes that are of interest to anyone. Minor bugfixes,
-memory leak fixes, etc. do not require entries.

diff --git a/release_docs/NEWSLETTER_README.txt b/release_docs/NEWSLETTER_README.txt
@@ -0,0 +1,25 @@
+INTRODUCTION
+============
+
+This purpose of this document is to contain entries that can be used to quickly
+produce a release newsletter. When something is added to the library that is
+"newsletter worthy" (i.e., new feature, CVE fix, etc.) a summary note should
+be added here.
+
+The format should look like this:
+
+* SUMMARY OF NEWSLETTER-WORTHY THING
+
+    Here is where you describe the summary. Summarize the feature, fix, or
+    change in general language. Remember, RELEASE.txt is for communicating
+    technical specifics. Text entered here is more like advertising.
+
+    (GitHub #123, #125)
+
+The GitHub #s could be relevant issues or PRs. They will probably not appear
+in the final newsletter, but are so that the person writing the newsletter
+has easy access to context if they have questions.
+
+Every entry in RELEASE.txt does NOT require an entry here. The newsletter is
+for communicating major changes that are of interest to anyone. Minor bugfixes,
+memory leak fixes, etc. do not require entries.
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
@@ -591,6 +591,13 @@ Bug Fixes since HDF5-1.14.0 release
 
     Library
     -------
+    - Fixed error when overwriting certain nested variable length types
+
+      Previously, when using a datatype that included a variable length type
+      within a compound or array within another variable length type, and
+      overwriting data with a shorter (top level) variable length sequence, an
+      error could occur. This has been fixed.
+
     - Fixed asserts raised by large values of H5Pset_est_link_info() parameters
 
       If large values for est_num_entries and/or est_name_len were passed
@@ -1545,6 +1552,9 @@ Known Problems
     in the HDF5 source. Please report any new problems found to
     help@hdfgroup.org.
 
+    File space may not be released when overwriting or deleting certain nested
+    variable length or reference types.
+
 
 CMake vs. Autotools installations
 =================================

diff --git a/src/H5A.c b/src/H5A.c
@@ -25,9 +25,7 @@
 #include "H5CXprivate.h" /* API Contexts                             */
 #include "H5Eprivate.h"  /* Error handling                           */
 #include "H5ESprivate.h" /* Event Sets                               */
-#include "H5FLprivate.h" /* Free Lists                               */
 #include "H5Iprivate.h"  /* IDs                                      */
-#include "H5MMprivate.h" /* Memory management                        */
 #include "H5Opkg.h"      /* Object headers                           */
 #include "H5Sprivate.h"  /* Dataspace functions                      */
 #include "H5VLprivate.h" /* Virtual Object Layer                     */

diff --git a/src/H5AC.c b/src/H5AC.c
@@ -40,7 +40,6 @@
 #include "H5CXprivate.h" /* API Contexts                             */
 #include "H5Eprivate.h"  /* Error handling                           */
 #include "H5Fpkg.h"      /* Files                                    */
-#include "H5Iprivate.h"  /* IDs                                      */
 #include "H5Pprivate.h"  /* Property lists                           */
 #include "H5SLprivate.h" /* Skip Lists                               */
 

diff --git a/src/H5Adeprec.c b/src/H5Adeprec.c
@@ -35,7 +35,6 @@
 #include "H5private.h"   /* Generic Functions                        */
 #include "H5Apkg.h"      /* Attributes                               */
 #include "H5CXprivate.h" /* API Contexts                             */
-#include "H5Dprivate.h"  /* Datasets                                 */
 #include "H5Eprivate.h"  /* Error handling                           */
 #include "H5Iprivate.h"  /* IDs                                      */
 #include "H5Opkg.h"      /* Object headers                           */

diff --git a/src/H5Aint.c b/src/H5Aint.c
@@ -31,8 +31,6 @@
 /***********/
 #include "H5private.h"   /* Generic Functions                        */
 #include "H5Apkg.h"      /* Attributes                               */
-#include "H5CXprivate.h" /* API Contexts                             */
-#include "H5Dprivate.h"  /* Datasets                                 */
 #include "H5Eprivate.h"  /* Error handling                           */
 #include "H5Iprivate.h"  /* IDs                                      */
 #include "H5MMprivate.h" /* Memory management                        */

diff --git a/src/H5Atest.c b/src/H5Atest.c
@@ -31,7 +31,6 @@
 /***********/
 #include "H5private.h"   /* Generic Functions                        */
 #include "H5Apkg.h"      /* Attributes                               */
-#include "H5ACprivate.h" /* Metadata cache                           */
 #include "H5CXprivate.h" /* API Contexts                             */
 #include "H5Eprivate.h"  /* Error handling                           */
 #include "H5Iprivate.h"  /* IDs                                      */

diff --git a/src/H5B.c b/src/H5B.c
@@ -101,10 +101,8 @@
 #include "H5Bpkg.h"      /* B-link trees				*/
 #include "H5CXprivate.h" /* API Contexts                         */
 #include "H5Eprivate.h"  /* Error handling		  	*/
-#include "H5Iprivate.h"  /* IDs			  		*/
 #include "H5MFprivate.h" /* File memory management		*/
 #include "H5MMprivate.h" /* Memory management			*/
-#include "H5Pprivate.h"  /* Property lists                       */
 
 /****************/
 /* Local Macros */

diff --git a/src/H5B2dbg.c b/src/H5B2dbg.c
@@ -28,10 +28,9 @@
 /***********/
 /* Headers */
 /***********/
-#include "H5private.h"   /* Generic Functions			*/
-#include "H5B2pkg.h"     /* v2 B-trees				*/
-#include "H5Eprivate.h"  /* Error handling		  	*/
-#include "H5FLprivate.h" /* Free Lists                           */
+#include "H5private.h"  /* Generic Functions			*/
+#include "H5B2pkg.h"    /* v2 B-trees				*/
+#include "H5Eprivate.h" /* Error handling		  	*/
 
 /****************/
 /* Local Macros */

diff --git a/src/H5CX.c b/src/H5CX.c
@@ -300,9 +300,9 @@ typedef struct H5CX_t {
     bool no_selection_io_cause_valid; /* Whether reason for not performing selection I/O is valid */
 
     uint32_t
-            actual_selection_io_mode; /* Actual selection I/O mode used (H5D_ACTUAL_SELECTION_IO_MODE_NAME) */
-    hbool_t actual_selection_io_mode_set;   /* Whether actual selection I/O mode is set */
-    hbool_t actual_selection_io_mode_valid; /* Whether actual selection I/O mode is valid */
+         actual_selection_io_mode; /* Actual selection I/O mode used (H5D_ACTUAL_SELECTION_IO_MODE_NAME) */
+    bool actual_selection_io_mode_set;   /* Whether actual selection I/O mode is set */
+    bool actual_selection_io_mode_valid; /* Whether actual selection I/O mode is valid */
 
     /* Cached LCPL properties */
     H5T_cset_t encoding;                 /* Link name character encoding */

diff --git a/src/H5Cimage.c b/src/H5Cimage.c
@@ -40,7 +40,6 @@
 #include "H5Fpkg.h"      /* Files				*/
 #include "H5FDprivate.h" /* File drivers				*/
 #include "H5FLprivate.h" /* Free Lists                           */
-#include "H5MFprivate.h" /* File memory management		*/
 #include "H5MMprivate.h" /* Memory management			*/
 
 /****************/

diff --git a/src/H5Ctag.c b/src/H5Ctag.c
@@ -37,7 +37,6 @@
 #include "H5Eprivate.h"  /* Error Handling                           */
 #include "H5Fpkg.h"      /* Files                                    */
 #include "H5FLprivate.h" /* Free Lists                               */
-#include "H5MMprivate.h" /* Memory management                        */
 
 /****************/
 /* Local Macros */

diff --git a/src/H5Dbtree.c b/src/H5Dbtree.c
@@ -31,7 +31,6 @@
 #include "H5Fprivate.h"  /* Files                                */
 #include "H5FDprivate.h" /* File drivers                         */
 #include "H5FLprivate.h" /* Free Lists                           */
-#include "H5Iprivate.h"  /* IDs                                  */
 #include "H5MFprivate.h" /* File space management                */
 #include "H5MMprivate.h" /* Memory management                    */
 #include "H5Oprivate.h"  /* Object headers                       */

diff --git a/src/H5Dcontig.c b/src/H5Dcontig.c
@@ -36,9 +36,7 @@
 #include "H5Iprivate.h"  /* IDs                          */
 #include "H5MFprivate.h" /* File memory management       */
 #include "H5MMprivate.h" /* Memory management			*/
-#include "H5FOprivate.h" /* File objects                 */
 #include "H5Oprivate.h"  /* Object headers               */
-#include "H5Pprivate.h"  /* Property lists               */
 #include "H5PBprivate.h" /* Page Buffer	                 */
 #include "H5VMprivate.h" /* Vector and array functions   */
 

diff --git a/src/H5Ddbg.c b/src/H5Ddbg.c
@@ -20,7 +20,6 @@
 /* Headers */
 /***********/
 #include "H5private.h"   /* Generic Functions                        */
-#include "H5CXprivate.h" /* API Contexts                             */
 #include "H5Dpkg.h"      /* Datasets                                 */
 #include "H5Eprivate.h"  /* Error handling                           */
 #include "H5Iprivate.h"  /* IDs                                      */

diff --git a/src/H5Dfill.c b/src/H5Dfill.c
@@ -29,11 +29,9 @@
 /* Headers */
 /***********/
 #include "H5private.h"   /* Generic Functions			*/
-#include "H5CXprivate.h" /* API Contexts                         */
 #include "H5Dpkg.h"      /* Dataset functions			*/
 #include "H5Eprivate.h"  /* Error handling		  	*/
 #include "H5FLprivate.h" /* Free Lists                           */
-#include "H5Iprivate.h"  /* IDs			  		*/
 #include "H5MMprivate.h" /* Memory management			*/
 #include "H5VMprivate.h" /* Vector and array functions		*/
 #include "H5WBprivate.h" /* Wrapped Buffers                      */

diff --git a/src/H5Dio.c b/src/H5Dio.c
@@ -24,12 +24,9 @@
 #include "H5Dpkg.h"      /* Dataset functions                        */
 #include "H5Eprivate.h"  /* Error handling                           */
 #include "H5FLprivate.h" /* Free Lists                               */
-#include "H5Iprivate.h"  /* IDs                                      */
 #include "H5MMprivate.h" /* Memory management                        */
 #include "H5Sprivate.h"  /* Dataspace                                */
 
-#include "H5VLnative_private.h" /* Native VOL connector                     */
-
 /****************/
 /* Local Macros */
 /****************/

diff --git a/src/H5Dmpio.c b/src/H5Dmpio.c
@@ -30,7 +30,6 @@
 #include "H5Fprivate.h"  /* File access       */
 #include "H5FDprivate.h" /* File drivers      */
 #include "H5FLprivate.h" /* Free Lists        */
-#include "H5Iprivate.h"  /* IDs               */
 #include "H5MMprivate.h" /* Memory management */
 #include "H5Oprivate.h"  /* Object headers    */
 #include "H5Pprivate.h"  /* Property lists    */

diff --git a/src/H5Dnone.c b/src/H5Dnone.c
@@ -34,7 +34,6 @@
 #include "H5private.h"   /* Generic Functions                    */
 #include "H5Dpkg.h"      /* Datasets                             */
 #include "H5Eprivate.h"  /* Error handling                       */
-#include "H5FLprivate.h" /* Free Lists                           */
 #include "H5MFprivate.h" /* File space management                */
 #include "H5VMprivate.h" /* Vector functions                     */
 

diff --git a/src/H5Dscatgath.c b/src/H5Dscatgath.c
@@ -24,7 +24,6 @@
 #include "H5Dpkg.h"      /* Dataset functions			*/
 #include "H5Eprivate.h"  /* Error handling		  	*/
 #include "H5FLprivate.h" /* Free Lists                           */
-#include "H5Iprivate.h"  /* IDs                                  */
 #include "H5MMprivate.h" /* Memory management			*/
 
 /****************/

diff --git a/src/H5Dsingle.c b/src/H5Dsingle.c
@@ -30,9 +30,7 @@
 #include "H5private.h"   /* Generic Functions                    */
 #include "H5Dpkg.h"      /* Datasets                             */
 #include "H5Eprivate.h"  /* Error handling                       */
-#include "H5FLprivate.h" /* Free Lists                           */
 #include "H5MFprivate.h" /* File space management                */
-#include "H5VMprivate.h" /* Vector functions                     */
 
 /****************/
 /* Local Macros */

diff --git a/src/H5EAcache.c b/src/H5EAcache.c
@@ -35,10 +35,7 @@
 #include "H5private.h"   /* Generic Functions			*/
 #include "H5Eprivate.h"  /* Error handling		  	*/
 #include "H5EApkg.h"     /* Extensible Arrays			*/
-#include "H5MFprivate.h" /* File memory management		*/
 #include "H5MMprivate.h" /* Memory management			*/
-#include "H5VMprivate.h" /* Vectors and arrays 			*/
-#include "H5WBprivate.h" /* Wrapped Buffers                      */
 
 /****************/
 /* Local Macros */

diff --git a/src/H5EAdblkpage.c b/src/H5EAdblkpage.c
@@ -36,7 +36,6 @@
 #include "H5Eprivate.h"  /* Error handling		  	*/
 #include "H5EApkg.h"     /* Extensible Arrays			*/
 #include "H5FLprivate.h" /* Free Lists                           */
-#include "H5VMprivate.h" /* Vectors and arrays 			*/
 
 /****************/
 /* Local Macros */

diff --git a/src/H5EApkg.h b/src/H5EApkg.h
@@ -27,6 +27,7 @@
 
 /* Other private headers needed by this file */
 #include "H5FLprivate.h" /* Free Lists                           */
+#include "H5VMprivate.h" /* Vectors and arrays 			*/
 
 /**************************/
 /* Package Private Macros */

diff --git a/src/H5ES.c b/src/H5ES.c
@@ -35,7 +35,6 @@
 #include "H5private.h"   /* Generic Functions			 */
 #include "H5Eprivate.h"  /* Error handling		  	 */
 #include "H5ESpkg.h"     /* Event Sets                           */
-#include "H5FLprivate.h" /* Free Lists                           */
 #include "H5Iprivate.h"  /* IDs                                  */
 #include "H5MMprivate.h" /* Memory management                    */
 

diff --git a/src/H5ESlist.c b/src/H5ESlist.c
@@ -32,10 +32,9 @@
 /***********/
 /* Headers */
 /***********/
-#include "H5private.h"   /* Generic Functions			 */
-#include "H5Eprivate.h"  /* Error handling		  	 */
-#include "H5ESpkg.h"     /* Event Sets                           */
-#include "H5FLprivate.h" /* Free Lists                           */
+#include "H5private.h"  /* Generic Functions			 */
+#include "H5Eprivate.h" /* Error handling		  	 */
+#include "H5ESpkg.h"    /* Event Sets                           */
 
 /****************/
 /* Local Macros */

diff --git a/src/H5FAcache.c b/src/H5FAcache.c
@@ -35,10 +35,7 @@
 #include "H5private.h"   /* Generic Functions			*/
 #include "H5Eprivate.h"  /* Error handling		  	*/
 #include "H5FApkg.h"     /* Fixed Arrays				*/
-#include "H5MFprivate.h" /* File memory management		*/
 #include "H5MMprivate.h" /* Memory management			*/
-#include "H5VMprivate.h" /* Vectors and arrays 			*/
-#include "H5WBprivate.h" /* Wrapped Buffers                      */
 
 /****************/
 /* Local Macros */

diff --git a/src/H5FAdbg.c b/src/H5FAdbg.c
@@ -35,7 +35,6 @@
 #include "H5private.h"   /* Generic Functions			*/
 #include "H5Eprivate.h"  /* Error handling		  	*/
 #include "H5FApkg.h"     /* Fixed Arrays				*/
-#include "H5Oprivate.h"  /* Object Header 			*/
 #include "H5VMprivate.h" /* Vector functions                     */
 
 /****************/

diff --git a/src/H5FD.c b/src/H5FD.c
@@ -30,7 +30,6 @@
 /***********/
 #include "H5private.h"   /* Generic Functions                        */
 #include "H5CXprivate.h" /* API Contexts                             */
-#include "H5Dprivate.h"  /* Datasets                                 */
 #include "H5Eprivate.h"  /* Error handling                           */
 #include "H5Fpkg.h"      /* File access                              */
 #include "H5FDpkg.h"     /* File Drivers                             */

diff --git a/src/H5FDfamily.c b/src/H5FDfamily.c
@@ -31,7 +31,6 @@
 #include "H5FDdrvr_module.h" /* This source code file is part of the H5FD driver module */
 
 #include "H5private.h"   /* Generic Functions            */
-#include "H5CXprivate.h" /* API Contexts                         */
 #include "H5Eprivate.h"  /* Error handling              */
 #include "H5Fprivate.h"  /* File access                */
 #include "H5FDprivate.h" /* File drivers                */

diff --git a/src/H5FDint.c b/src/H5FDint.c
@@ -376,7 +376,7 @@ H5FD_read_vector(H5FD_t *file, uint32_t count, H5FD_mem_t types[], haddr_t addrs
     size_t     size      = 0;
     H5FD_mem_t type      = H5FD_MEM_DEFAULT;
     hid_t      dxpl_id   = H5I_INVALID_HID; /* DXPL for operation */
-    hbool_t    is_raw    = FALSE;           /* Does this include raw data */
+    bool       is_raw    = false;           /* Does this include raw data */
     herr_t     ret_value = SUCCEED;         /* Return value */
 
     FUNC_ENTER_NOAPI(FAIL)
@@ -461,7 +461,7 @@ H5FD_read_vector(H5FD_t *file, uint32_t count, H5FD_mem_t types[], haddr_t addrs
 
                     /* Check for raw data operation */
                     if (type == H5FD_MEM_DRAW)
-                        is_raw = TRUE;
+                        is_raw = true;
                 }
             }
 
@@ -618,7 +618,7 @@ H5FD_write_vector(H5FD_t *file, uint32_t count, H5FD_mem_t types[], haddr_t addr
     H5FD_mem_t type = H5FD_MEM_DEFAULT;
     hid_t      dxpl_id;                 /* DXPL for operation */
     haddr_t    eoa       = HADDR_UNDEF; /* EOA for file */
-    hbool_t    is_raw    = FALSE;       /* Does this include raw data */
+    bool       is_raw    = false;       /* Does this include raw data */
     herr_t     ret_value = SUCCEED;     /* Return value */
 
     FUNC_ENTER_NOAPI(FAIL)

diff --git a/src/H5FDmpi.c b/src/H5FDmpi.c
@@ -15,12 +15,9 @@
  */
 
 #include "H5private.h"   /* Generic Functions			*/
-#include "H5CXprivate.h" /* API Contexts                         */
 #include "H5Eprivate.h"  /* Error handling		  	*/
-#include "H5Fprivate.h"  /* File access				*/
 #include "H5FDprivate.h" /* File drivers				*/
 #include "H5FDmpi.h"     /* Common MPI file driver		*/
-#include "H5Pprivate.h"  /* Property lists			*/
 
 #ifdef H5_HAVE_PARALLEL