Convert doc folder files to doxygen (HDFGroup#5216)

.codespellrc

@@ -3,4 +3,4 @@
 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
 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,FLE

.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

@@ -454,7 +454,7 @@ 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]")
 
 #-----------------------------------------------------------------------------

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>"