Merge branch 'HDFGroup:develop' into develop

.codespellrc

@@ -1,6 +1,6 @@
 # Ref: https://github.com/codespell-project/codespell#using-a-config-file
 [codespell]
-skip = .git,*.svg,.codespellrc,./bin/trace,./hl/tools/h5watch/h5watch.c,./tools/test/h5jam/tellub.c,./config/sanitizer/LICENSE,./config/sanitizer/sanitizers.cmake,./tools/test/h5import/testfiles/*.conf,./tools/test/h5repack/testfiles/*.dat,./test/API/driver,./configure,./bin/ltmain.sh,./bin/depcomp,./bin/config.guess,./bin/config.sub,./autom4te.cache,./m4/libtool.m4,./c++/src/*.html,./HDF5Examples/depcomp
+skip = .git,*.svg,.codespellrc,./bin/trace,./hl/tools/h5watch/h5watch.c,./tools/test/h5jam/tellub.c,./config/sanitizer/LICENSE,./config/sanitizer/sanitizers.cmake,./tools/test/h5import/testfiles/*.conf,./tools/test/h5repack/testfiles/*.dat,./test/API/driver,./configure,./bin/ltmain.sh,./bin/depcomp,./bin/config.guess,./bin/config.sub,./autom4te.cache,./m4/libtool.m4,./c++/src/*.html,./HDF5Examples/depcomp,./release_docs/HISTORY-*.txt
 check-hidden = true
 # ignore-regex = 
-ignore-words-list = ot,isnt,inout,nd,parms,parm,ba,offsetP,ser,ois,had,fiter,fo,clude,refere,minnum,offsetp,creat,ans:,eiter,lastr,ans,isn't,ifset,sur,trun,dne,tthe,hda,filname,te,htmp,ake,gord,numer,ro,oce,msdos,TEXTIN
+ignore-words-list = ot,isnt,inout,nd,parms,parm,ba,offsetP,ser,ois,had,fiter,fo,clude,refere,minnum,offsetp,creat,ans:,eiter,lastr,ans,isn't,ifset,sur,trun,dne,tthe,hda,filname,te,htmp,ake,gord,numer,ro,oce,msdos,TEXTIN,indx,FLE

.devcontainer/Dockerfile

@@ -2,4 +2,4 @@ FROM mcr.microsoft.com/devcontainers/base:debian
 
 RUN apt-get update && apt-get -y install --no-install-recommends \
   build-essential cmake cmake-curses-gui doxygen git graphviz \
-  less libtool-bin libyajl-dev mpi-default-dev valgrind wget
+  less libtool-bin libyajl-dev mpi-default-dev ninja-build valgrind wget

.github/workflows/linkchecker.yml

@@ -42,6 +42,6 @@ jobs:
       - name: check
         run: |
           cd build/hdf5lib_docs/html
-          linkchecker --check-extern ./index.html
+          linkchecker --ignore-url=/doxygen.css --check-extern ./index.html
         continue-on-error: true
 

CMakeLists.txt

@@ -456,7 +456,7 @@ else ()
 endif ()
 set (HDF5_PACKAGE_STRING "${HDF5_PACKAGE_NAME} ${HDF5_PACKAGE_VERSION_STRING}")
 set (HDF5_PACKAGE_TARNAME "${HDF5_PACKAGE}${HDF_PACKAGE_EXT}")
-set (HDF5_PACKAGE_URL "http://www.hdfgroup.org")
+set (HDF5_PACKAGE_URL "https://www.hdfgroup.org")
 set (HDF5_PACKAGE_BUGREPORT "[email protected]")
 
 #-----------------------------------------------------------------------------

HDF5Examples/C/H5FLT/tfiles/h5ex_d_bshuf.ddl

@@ -11,7 +11,7 @@ GROUP "/" {
          USER_DEFINED_FILTER {
             FILTER_ID 32008
             COMMENT bitshuffle; see https://github.com/kiyo-masui/bitshuffle
-            PARAMS { 0 3 4 0 0 0 }
+            PARAMS { 0 4 4 0 0 0 }
          }
       }
       FILLVALUE {

c++/src/H5DataType.cpp

@@ -250,7 +250,7 @@ DataType::p_decode() const
     }
 
     // Call C function to decode the binary object description
-    hid_t encoded_dtype_id = H5Tdecode(encoded_buf);
+    hid_t encoded_dtype_id = H5Tdecode2(encoded_buf, buf_size);
 
     // If H5Tdecode fails, raise exception
     if (encoded_dtype_id < 0) {
@@ -924,7 +924,8 @@ DataType::close()
         // Free and reset buffer of encoded object description if it's been used
         if (encoded_buf != NULL) {
             delete[] encoded_buf;
-            buf_size = 0;
+            encoded_buf = NULL;
+            buf_size    = 0;
         }
     }
 }

config/cmake/cacheinit.cmake

@@ -94,7 +94,7 @@ set (BSHUF_GIT_URL "https://github.com/kiyo-masui/bitshuffle.git" CACHE STRING "
 set (BSHUF_GIT_BRANCH "master" CACHE STRING "" FORCE)
 
 set (BSHUF_TGZ_ORIGPATH "https://github.com/kiyo-masui/bitshuffle/archive/refs/tags" CACHE STRING "Use PLUGINS from original location" FORCE)
-set (BSHUF_TGZ_NAME "bitshuffle-0.5.1.tar.gz" CACHE STRING "Use BSHUF from compressed file" FORCE)
+set (BSHUF_TGZ_NAME "bitshuffle-0.5.2.tar.gz" CACHE STRING "Use BSHUF from compressed file" FORCE)
 
 set (BSHUF_PACKAGE_NAME "bshuf" CACHE STRING "Name of BSHUF package" FORCE)
 
@@ -126,7 +126,7 @@ set (BLOSC2_GIT_URL "https://github.com/Blosc/c-blosc2.git" CACHE STRING "Use BL
 set (BLOSC2_GIT_BRANCH "main" CACHE STRING "" FORCE)
 
 set (BLOSC2_TGZ_ORIGPATH "https://github.com/Blosc/c-blosc2/archive/refs/tags" CACHE STRING "Use PLUGINS from original location" FORCE)
-set (BLOSC2_TGZ_NAME "c-blosc2-2.15.1.tar.gz" CACHE STRING "Use BLOSC2 from compressed file" FORCE)
+set (BLOSC2_TGZ_NAME "c-blosc2-2.15.2.tar.gz" CACHE STRING "Use BLOSC2 from compressed file" FORCE)
 
 set (BLOSC2_PACKAGE_NAME "blosc2" CACHE STRING "Name of BLOSC2 package" FORCE)
 

doxygen/aliases

@@ -5,8 +5,8 @@ ALIASES += THG="The HDF Group"
 ################################################################################
 # Default URL for HDF Group Files
 ALIASES += HDFURL="support.hdfgroup.org"
-# URL for archived files
-ALIASES += ARCURL="\HDFURL/archive/support/HDF5/doc"
+# URL for archived files - not currently used as all docs referenced are in doxygen
+# ALIASES += ARCURL="\HDFURL/archive/support/HDF5/doc"
 # URL for release files
 ALIASES += RELURL="\HDFURL/releases/hdf5"
 # URL for documentation
@@ -21,7 +21,7 @@ ALIASES += DOXURL="hdfgroup.github.io/hdf5/develop"
 #branch name (develop, hdf5_1_14)
 ALIASES += SRCURL="github.com/HDFGroup/hdf5/blob/develop"
 #Other projects that contribute to HDF5
-ALIASES += PRJURL="\HDFURL/projects"
+ALIASES += PRJURL="\HDFURL/archive/support/projects"
 ALIASES += HVURL="github.com/HDFGroup/hdfview/blob/master"
 ALIASES += PLURL="github.com/HDFGroup/hdf5_plugins/blob/master"
 ################################################################################
@@ -257,14 +257,20 @@ ALIASES += callback_note="\attention \Bold{Leaving callback functions:}\n The ca
 ALIASES += par_compr_note="\attention If you are planning to use compression with parallel HDF5, ensure that calls to H5Dwrite() occur in collective mode. In other words, all MPI ranks (in the relevant communicator) call H5Dwrite() and pass a dataset transfer property list with the MPI-IO collective option property set to #H5FD_MPIO_COLLECTIVE_IO.\n Note that data transformations are currently \Bold{not} supported when writing to datasets in parallel and with compression enabled."
 ALIASES += sa_metadata_ops="\sa \li H5Pget_all_coll_metadata_ops() \li H5Pget_coll_metadata_write() \li H5Pset_all_coll_metadata_ops() \li H5Pset_coll_metadata_write() \li \ref maybe_metadata_reads"
 
+################################################################################
+# Specifications
+################################################################################
+
+ALIASES += ref_spec_fileformat="\ref FMT3"
+ALIASES += ref_spec_fileformat_btrees_v1="\ref subsubsec_fmt3_infra_btrees_v1"
+
 ################################################################################
 # References
 ################################################################################
 
 ALIASES += ref_cons_semantics="<a href=\"https://\RFCURL/RFC%20PHDF5%20Consistency%20Semantics%20MC%20120328.docx.pdf\">Enabling a Strict Consistency Semantics Model in Parallel HDF5</a>"
 ALIASES += ref_filter_pipe="<a href=\"https://\DOCURL/advanced_topics/data_flow_pline_H5Dread.md\">Data Flow Pipeline for H5Dread()</a>"
 ALIASES += ref_group_impls="<a href=\"https://\DOXURL/group___h5_g.html\">Group implementations in HDF5</a>"
-ALIASES += ref_h5lib_relver="<a href=\"https://\ARCURL/TechNotes/Version.html\">HDF5 Library Release Version Numbers</a>"
 ALIASES += ref_mdc_in_hdf5="<a href=\"https://\DOCURL/advanced_topics/FineTuningMetadataCache.md\">Metadata Caching in HDF5</a>"
 ALIASES += ref_mdc_logging="<a href=\"https://\RFCURL/Design-MetadataCache-Logging-THG20140224-v4.pdf\">Metadata Cache Logging</a>"
 ALIASES += ref_news_112="<a href=\"https://\DOCURL/release_specifics/new_features_1_12.md\">New Features in HDF5 Release 1.12</a>"