Fixed Spelling Errors (#1166)

* 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

* switched from using MPI_count, to actual bytes written for H5FD_mpio_debug rw debugging

* Committing clang-format changes

* changed size_i in printf to reflect the I/O.

* Committing clang-format changes

* Fixed seg fault with xlf on BE with -qintsize=8

* fixed error function string

* spelling corrections via codespell, added new spell check github actions

* Committing clang-format changes

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* misc

* Committing clang-format changes

* misc

* misc

* misc

* misc

* misc

* misc

* Committing clang-format changes

* misc

* work around for codespell-project/codespell#2137

* misc

* added missing file

* misc

* misc.

* misc

* switch to using Codespell with GitHub Actions

* misc.

* misc.

* fixed more sp errors

* Fix new typos found by codespell.

* fixed proceed with precede

* fixed variable in fortran test

* fixed minnum

* updated spelling list

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

.github/workflows/codespell.yml

@@ -0,0 +1,15 @@
+# GitHub Action to automate the identification of common misspellings in text files
+# https://github.com/codespell-project/codespell
+# https://github.com/codespell-project/actions-codespell
+name: codespell
+on: [push, pull_request]
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: codespell-project/actions-codespell@master
+        with:
+          skip: ./bin/trace,./hl/tools/h5watch/h5watch.c,./tools/test/h5jam/tellub.c
+          ignore_words_list: 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,minnum

MANIFEST

@@ -39,6 +39,7 @@
 ./.github/workflows/clang-format-check.yml  _DO_NOT_DISTRIBUTE_
 ./.github/workflows/main.yml  _DO_NOT_DISTRIBUTE_
 ./.github/workflows/pr-check.yml  _DO_NOT_DISTRIBUTE_
+./.github/workflows/codespell.yml  _DO_NOT_DISTRIBUTE_
 
 ./m4/aclocal_fc.m4
 ./m4/aclocal_fc.f90

bin/bbrelease

@@ -48,7 +48,7 @@ USAGE()
 {
 cat << EOF
 Usage: $0 -d <dir> [--docver BRANCHNAME] [-h] [--nocheck] [--private] <methods> ...
-   -d DIR	The name of the directory where the releas(es) should be
+   -d DIR	The name of the directory where the release(s) should be
                 placed.
    --docver BRANCHNAME  This is added for 1.8 and beyond to get the correct
                         version of documentation files from the hdf5docs
@@ -103,7 +103,7 @@ EOF
 # Modifications
 #
 # Steps:
-# 1. untar the tarball in a temporay directory;
+# 1. untar the tarball in a temporary directory;
 #    Note: do this in a temporary directory to avoid changing
 #    the original source directory which maybe around.
 # 2. convert all its text files to DOS (LF-CR) style;
@@ -246,7 +246,7 @@ if [ "X$methods" = "X" ]; then
     methods="tar"
 fi
 
-# Create the temporay work directory.
+# Create the temporary work directory.
 if mkdir $tmpdir; then
     echo "temporary work directory for release.  "\
          "Can be deleted after release completes." > $tmpdir/README

bin/buildhdf5

@@ -178,7 +178,7 @@ LOCATE_SZLIB()
 	    esac
 	    ;;	# end of case ncsa
 	unknown)
-	    # Unknow domain. Give a shot at the some standard places.
+	    # Unknown domain. Give a shot at the some standard places.
 	    szlibpaths="/usr/local"
 	    ;;
     esac	# end of case $mydomain

bin/cmakehdf5

@@ -199,7 +199,7 @@ DUMP_LOGFILE()
 # Show a start time stamp
 TIMESTAMP
 
-# Initialize njobs if $AMKE is defined
+# Initialize njobs if $MAKE is defined
 if [ -n "$MAKE" ]; then
     # assume all arguments are for --jobs
     njobs=`echo $MAKE | cut -s -d' ' -f2-`
@@ -365,7 +365,7 @@ STEP "Test the library and tools..." "ctest . -C Release $njobs" $testlog
 #      7. Create an install image with this command:
 STEP "Create an install image..." "cpack -C Release CPackConfig.cmake" $packlog
 
-# The implementation of installation is imcomplete (only works for linux).
+# The implementation of installation is incomplete (only works for linux).
 # Screen it out for now till it is completed.
 if false; then
 #      8. Install with this command:

bin/genparser

@@ -27,7 +27,7 @@
 # IMPORTANT OS X NOTE
 #
 # If you are using OS X, you will probably not have flex or bison
-# installed. In addtion, even if you do have bison installed, the bison
+# installed. In addition, even if you do have bison installed, the bison
 # version you have installed may also have a bug that makes it unable to
 # process our input files.
 #

bin/h5cc.in

@@ -40,7 +40,7 @@ HL="@HL@"
 ##    $CLINKER $H5BLD_CPPFLAGS $CPPFLAGS $H5BLD_CFLAGS $CFLAGS $LDFLAGS   ##
 ##    $LIBS $clibpath $link_objs $link_args $shared_link                  ##
 ##                                                                        ##
-## These settings can be overriden by setting HDF5_CFLAGS,                ##
+## These settings can be overridden by setting HDF5_CFLAGS,                ##
 ## HDF5_CPPFLAGS, HDF5_LDFLAGS, or HDF5_LIBS in the environment.          ##
 ##                                                                        ##
 ############################################################################
@@ -144,7 +144,7 @@ usage() {
   echo "                                           shared libraries]"
   echo " "
   echo " You can also add or change paths and flags to the compile line using"
-  echo " the following environment varibles or by assigning them to their counterparts"
+  echo " the following environment variables or by assigning them to their counterparts"
   echo " in the 'Things You Can Modify to Override...'" section of $prog_name
   echo " "
   echo "  Variable              Current value to be replaced"
@@ -318,7 +318,7 @@ fi
 
 if test "x$do_link" = "xyes"; then
   shared_link=""
-# conditionnaly link with the hl library
+# conditionally link with the hl library
   if test "X$HL" = "Xhl"; then
    libraries=" $libraries -lhdf5_hl -lhdf5 "
   else

bin/newer

@@ -19,7 +19,7 @@
 # Created Date: 2005/07/06
 # Modification:
 #    Albert Cheng 2005/8/30
-#    Changed from two arguments to mulitple arguments.
+#    Changed from two arguments to multiple arguments.
 
 if test $# -lt 2; then
     exit 1

bin/release

@@ -39,7 +39,7 @@ USAGE()
 {
 cat << EOF
 Usage: $0 -d <dir> [--docver BRANCHNAME] [-h] [--nocheck] [--private] <methods> ...
-   -d DIR   The name of the directory where the releas(es) should be
+   -d DIR   The name of the directory where the release(es) should be
                 placed.
    --docver BRANCHNAME  This is added for 1.8 and beyond to get the correct
                         version of documentation files from the hdf5docs
@@ -60,7 +60,7 @@ for compressing the resulting tar archive (if none are given then
     cmake-tgz   -- create a tar file using the gzip default level with a build-unix.sh
                    command file and all other CMake files needed to build HDF5 source
                    using CMake on unix machines.
-    cmake-zip   -- convert all text files to DOS style and create a zip file inluding cmake
+    cmake-zip   -- convert all text files to DOS style and create a zip file including cmake
                    scripts and .bat files to build HDF5 source using CMake on Windows.
     hpc-cmake-tgz
                 -- create a tar file using the gzip default level with a build-unix.sh
@@ -512,7 +512,7 @@ if [ "X$methods" = "X" ]; then
     methods="tar"
 fi
 
-# Create the temporay work directory.
+# Create the temporary work directory.
 if mkdir $tmpdir; then
     echo "temporary work directory for release.  "\
          "Can be deleted after release completes." > $tmpdir/README

bin/runtest

@@ -630,7 +630,7 @@ while [ $# -gt 0 ]; do
 	    # setup the directory structure for snapshot test.
 	    CMD=setup
 	    ;;
-	-*) # Unknow option
+	-*) # Unknown option
 	    PRINT "Unknown option ($1)"
 	    USAGE
 	    exit 1
@@ -830,7 +830,7 @@ if [ -z "$NOCVS" ]; then
 else
     # make sure the cvs update, if done by another host, has completed.
     # First wait for the presence of $CVSLOG which signals some host
-    # has started the cvs update.  Then wait for the absense of $CVSLOG_LOCK
+    # has started the cvs update.  Then wait for the absence of $CVSLOG_LOCK
     # which signals the host has completed the cvs update.
     WAITFOR $CVSLOG 90
     if [ $WAIT_STATUS -ne 0 ]; then
@@ -911,7 +911,7 @@ if [ -n "$TESTHOST" -a $HOSTNAME != "$TESTHOST" ]; then
 		PRINT $h is not reachable  "(`date`)"
 		;;
 	    *)
-		PRINT "CHECK_RSH for $h returned unknow result ($RSH)"
+		PRINT "CHECK_RSH for $h returned unknown result ($RSH)"
 		;;
 	esac >> $TMP_OUTPUT 2>&1
     done

bin/snapshot

@@ -156,7 +156,7 @@ Usage: $PROGNAME [all] [checkout] [ftp <URL> [diff] [test] [srcdir] [release] [h
               "snapshot srcdir" is equivalent to "snapshot srcdir all"
               "snapshot srcdir checkout" is equivalent to "snapshot checkout"
     srcdirname <dir>:
-              Use <dir> as the srcdir testing directory if srcdir is choosen.
+              Use <dir> as the srcdir testing directory if srcdir is chosen.
               If <dir> starts with '-', it is append to the default name
               E.g., "snapshot srcdir srcdirname -xx" uses hostname-xx
               [Default is hostname]
@@ -422,7 +422,7 @@ while [ $# -gt 0 ] ; do
 	    fi
 	    cmd=""
             EXEC_CMD_ARG="$@"
-	    # exit the parsing while loop since all arguments have been consummed.
+	    # exit the parsing while loop since all arguments have been consumed.
 	    break
             ;;
 	check-vfd)
@@ -455,7 +455,7 @@ while [ $# -gt 0 ] ; do
 	    OP_CONFIGURE="$OP_CONFIGURE $1"
 	    ;;
 	*)
-	    echo "Unkown option $1"
+	    echo "Unknown option $1"
 	    errcode=1
 	    cmd="help"
 	    break
@@ -623,7 +623,7 @@ if [ "$cmd" = "all" -o -n "$cmdtest" -o -n "$cmddiff" ]; then
 	fi
     fi
 
-    # if diff is choosen, exit 0 if no significant differences are found.
+    # if diff is chosen, exit 0 if no significant differences are found.
     # otherwise, exit 1.  This includes cases of other failures.
     if [ -n "$cmddiff" ]; then
 	if [ $snapshot = no ]; then
@@ -799,7 +799,7 @@ if [ "$cmd" = "all" -o -n "$cmdrel" ]; then
     # Replace the previous version with the current version.
     # Should check if the errcode of the release process but there
     # are other failures after release was done (e.g. h5vers or git failures)
-    # that should allow the replacement to occure.
+    # that should allow the replacement to occur.
     rm -rf ${PREVIOUS}
     mv ${CURRENT} ${PREVIOUS}
 fi #Release snapshot

bin/trace

@@ -381,9 +381,9 @@ sub rewrite_func ($$$$$) {
 
       # Wrap lines that will be longer than the limit
       if ($len_if_added > $max_trace_macro_line_len) {
-        # Wrap line, with indention
+        # Wrap line, with indentation
         $trace .= ",\n             ";
-        $len = 13;              # Set to 13, for indention
+        $len = 13;              # Set to 13, for indentation
 
         # Indent an extra space to account for extra digit in 'H5TRACE' macro
         if (scalar(@arg_str) >= 10) {

bin/warnhist

@@ -78,7 +78,7 @@ sub do_help {
     print "\t-S <file string list>\tDisplay warnings for files which contain a string, <file string list>\n";
     print "\t\t<file string list> is a comma separated list, with no spaces\n";
     print "\t\tFor example: 'H5Fint' or 'H5Fint,H5Gnode'\n";
-    print "\t-l\tDisplay line nunbers for file/warning\n";
+    print "\t-l\tDisplay line numbers for file/warning\n";
     print "\t-u\tLeave 'unique' types in warnings, instead of genericizing them\n";
     print "\t-i <name list>\tIgnore named files, <name list>\n";
     print "\t\t<name list> is a comma separated list, with no spaces\n";

c++/src/H5Attribute.cpp

@@ -562,7 +562,7 @@ Attribute::p_read_variable_len(const DataType &mem_type, H5std_string &strg) con
 ///\exception   H5::IdComponentException when the attempt to close the HDF5
 ///             object fails
 // Description:
-//              The underlaying reference counting in the C library ensures
+//              The underlying reference counting in the C library ensures
 //              that the current valid id of this object is properly closed.
 //              Then the object's id is reset to the new id.
 // Programmer   Binh-Minh Ribler - 2000

c++/src/H5DataSet.cpp

@@ -769,7 +769,7 @@ DataSet::p_read_variable_len(const hid_t mem_type_id, const hid_t mem_space_id,
 ///\exception   H5::IdComponentException when the attempt to close the HDF5
 ///             object fails
 // Description:
-//              The underlaying reference counting in the C library ensures
+//              The underlying reference counting in the C library ensures
 //              that the current valid id of this object is properly closed.
 //              Then the object's id is reset to the new id.
 //--------------------------------------------------------------------------

c++/src/H5DataSpace.cpp

@@ -629,7 +629,7 @@ DataSpace::getId() const
 ///\exception   H5::IdComponentException when the attempt to close the HDF5
 ///             object fails
 // Description:
-//              The underlaying reference counting in the C library ensures
+//              The underlying reference counting in the C library ensures
 //              that the current valid id of this object is properly closed.
 //              Then the object's id is reset to the new id.
 // Programmer   Binh-Minh Ribler - 2000

c++/src/H5DataType.cpp

@@ -927,7 +927,7 @@ DataType::p_opentype(const H5Location &loc, const char *dtype_name) const
 ///\exception   H5::IdComponentException when the attempt to close the HDF5
 ///             object fails
 // Description:
-//              The underlaying reference counting in the C library ensures
+//              The underlying reference counting in the C library ensures
 //              that the current valid id of this object is properly closed.
 //              Then the object's id is reset to the new id.
 // Programmer   Binh-Minh Ribler - 2000
@@ -983,7 +983,7 @@ DataType::close()
 //              - Replaced decRefCount with close() to let the C library
 //                handle the reference counting - BMR, Jun 1, 2006
 //              - Added the use of H5CPP_EXITED to terminate the HDF5 library
-//                and elimiate previous memory leaks.  See comments in the
+//                and eliminate previous memory leaks.  See comments in the
 //                header file "H5PredType.h" for details. - BMR, Mar 30, 2012
 //              - Major re-implementation of the global constants was done
 //                to avoid relying on the order of the creation and deletion

c++/src/H5DcreatProp.cpp

@@ -552,7 +552,7 @@ DSetCreatPropList::setShuffle() const
 ///\exception   H5::PropListIException
 ///\par Description
 ///             The values of space allocation time can be one of the
-///             followings:
+///             following:
 ///             \li \c H5D_ALLOC_TIME_DEFAULT
 ///             \li \c H5D_ALLOC_TIME_EARLY
 ///             \li \c H5D_ALLOC_TIME_LATE

c++/src/H5File.cpp

@@ -665,7 +665,7 @@ H5File::getLocId() const
 ///\exception   H5::IdComponentException when the attempt to close the HDF5
 ///             object fails
 // Description
-//              The underlaying reference counting in the C library ensures
+//              The underlying reference counting in the C library ensures
 //              that the current valid id of this object is properly closed.
 //              Then the object's id is reset to the new id.
 // December 2000

c++/src/H5Group.cpp

@@ -208,7 +208,7 @@ Group::getId() const
 ///\exception   H5::IdComponentException when the attempt to close the HDF5
 ///             object fails
 // Description:
-//              The underlaying reference counting in the C library ensures
+//              The underlying reference counting in the C library ensures
 //              that the current valid id of this object is properly closed.
 //              Then the object's id is reset to the new id.
 // Programmer   Binh-Minh Ribler - 2000

c++/src/H5Location.cpp

@@ -1745,7 +1745,7 @@ H5Location::getObjinfo(const H5std_string &name, hbool_t follow_link, H5G_stat_t
 // Function:    H5Location::getObjinfo
 ///\brief       This is an overloaded member function, provided for convenience.
 ///             It differs from the above functions in that it doesn't have
-///             the paramemter \a follow_link.
+///             the parameter \a follow_link.
 // Nov, 2005
 //--------------------------------------------------------------------------
 void

c++/src/H5Location.h

@@ -15,7 +15,7 @@
 #ifndef H5Location_H
 #define H5Location_H
 
-#include "H5Classes.h" // constains forward class declarations
+#include "H5Classes.h" // contains forward class declarations
 
 namespace H5 {
 

c++/src/H5PredType.cpp

@@ -790,7 +790,7 @@ September 2015:
         classes, such as PropList, PredType, DataSpace, etc...  Previously,
         these global constants were declared statically and the C++ library used
         a constant, called PredType::AtExit, to detect when all the global
-        contants are destroyed then close the C library (H5close).  This method
+        constants are destroyed then close the C library (H5close).  This method
         relied on the order of the constants being created and destroyed and
         that PredType constants be the last to be destroyed.  In September
         2015, it was recognized that the order in which the global constants were

c++/src/H5PropList.cpp

@@ -301,7 +301,7 @@ PropList::getId() const
 ///\exception   H5::IdComponentException when the attempt to close the HDF5
 ///             object fails
 // Description:
-//              The underlaying reference counting in the C library ensures
+//              The underlying reference counting in the C library ensures
 //              that the current valid id of this object is properly closed.
 //              Then the object's id is reset to the new id.
 // Programmer   Binh-Minh Ribler - 2000

c++/test/tobject.cpp

@@ -740,7 +740,7 @@ test_object()
     MESSAGE(5, ("Testing Object Functions\n"));
 
     test_get_objname();             // Test get object name from groups/datasets
-    test_existance();               // Test check for object existance
+    test_existance();               // Test check for object existence
     test_get_objname_ontypes();     // Test get object name from types
     test_get_objtype();             // Test get object type
     test_open_object_header();      // Test object header functions (H5O)

c++/test/ttypes.cpp

@@ -28,7 +28,7 @@ using namespace H5;
 #include "h5cpputil.h" // C++ utilility header file
 
 /*
- * Offset from alinged memory returned by malloc().  This can be used to test
+ * Offset from aligned memory returned by malloc().  This can be used to test
  * that type conversions handle non-aligned buffers correctly.
  */
 #define ALIGNMENT 1

config/BlankForm

@@ -61,7 +61,7 @@ fi
 #
 # PROD_CFLAGS		Flags to pass to the compiler to create a
 # PROD_CPPFLAGS		production version of the library.  These
-#			usualy exclude symbolic debugging switches
+#			usually exclude symbolic debugging switches
 #			(like `-g') and include optimization switches
 #			(like `-O').
 #
@@ -84,7 +84,7 @@ fi
 #			compiler or a descendent of gcc such as EGCS or PGCC.
 #
 # AM_CFLAGS             Flags added directly into this variable will
-#                       be propogated to the compiler wrapper scripts (h5cc,
+#                       be propagated to the compiler wrapper scripts (h5cc,
 #                       h5c++, et cetera) in addition to being used to compile 
 #                       the library.
 #

config/cmake/ConfigureChecks.cmake

@@ -30,7 +30,7 @@ MARK_AS_ADVANCED (HDF5_STRICT_FORMAT_CHECKS)
 
 # ----------------------------------------------------------------------
 # Decide whether the data accuracy has higher priority during data
-# conversions.  If not, some hard conversions will still be prefered even
+# conversions.  If not, some hard conversions will still be preferred even
 # though the data may be wrong (for example, some compilers don't
 # support denormalized floating values) to maximize speed.
 #-----------------------------------------------------------------------------