Merge branch 'bug-endianness', which really had to do with nccopy -d0

and chunking issues.

man4/guide.dox

@@ -3348,12 +3348,15 @@ Note that \b nccopy requires all variables to be compressed using the
 same compression level, but the API has no such restriction.  With a
 program you can customize compression for each variable independently.
 
-\par -s
-For netCDF-4 output, including netCDF-4 classic model,
-specify shuffling of variable data bytes before compression or after
-decompression.  This option is ignored unless a non-zero deflation
-level is specified.  Turning shuffling on sometimes improves
-compression.
+\par -s For netCDF-4 output, including netCDF-4 classic model, specify
+shuffling of variable data bytes before compression or after
+decompression.  Shuffling refers to interlacing of bytes in a chunk so
+that the first bytes of all values are contiguous in storage, followed
+by all the second bytes, and so on, which often improves compression.
+This option is ignored unless a non-zero deflation level is specified.
+Using -d0 to specify no deflation on input data that has been
+compressed and shuffled turns off both compression and shuffling in
+the output.
 
 \par -u
 Convert any unlimited size dimensions in the input to fixed size
@@ -3384,8 +3387,9 @@ The chunkspec argument is a string of comma-separated associations,
 each specifying a dimension name, a '/' character, and optionally the
 corresponding chunk length for that dimension.  No blanks should
 appear in the chunkspec string, except possibly escaped blanks that
-are part of a dimension name.  A chunkspec must name at least one
-dimension, and may omit dimensions which are not to be chunked or for
+are part of a dimension name.  A chunkspec names dimensions along
+which chunking is to take place, and omits dimensions which are 
+not to be chunked or for
 which the default chunk length is desired.  If a dimension name is
 followed by a '/' character but no subsequent chunk length, the actual
 dimension length is assumed.  If copying a classic model file to a
@@ -3393,7 +3397,13 @@ netCDF-4 output file and not naming all dimensions in the chunkspec,
 unnamed dimensions will also use the actual dimension length for the
 chunk length.  An example of a chunkspec for variables that use
 'm' and 'n' dimensions might be 'm/100,n/200' to specify 100 by 200
-chunks.  To see the chunking resulting from copying with a chunkspec,
+chunks.  
+
+\par
+The chunkspec '/' that omits all dimension names and
+corresponding chunk lengths specifies that no chunking is to occur in
+the output, so can be used to unchunk all the chunked variables.
+To see the chunking resulting from copying with a chunkspec,
 use the '-s' option of ncdump on the output file.
 
 \par

ncdump/nccopy.c

@@ -823,7 +823,6 @@ copy_var(int igrp, int varid, int ogrp)
 
     /* define the output variable */
     NC_CHECK(nc_def_var(ogrp, name, o_typeid, ndims, odimids, &o_varid));
-
     /* attach the variable attributes to the output variable */
     NC_CHECK(copy_atts(igrp, varid, ogrp, o_varid));
 #ifdef USE_NETCDF4    

ncdump/tst_nccopy4.sh

@@ -44,7 +44,16 @@ echo "*** Test nccopy -d1 -s can compress a netCDF-4 file even more ..."
 if test `wc -c < tmp.nc` -ge  `wc -c < tst_inflated4.nc`; then
     exit 1
 fi
-rm tst_deflated.nc tst_inflated.nc tst_inflated4.nc tmp.nc 
+echo "*** Test nccopy -d0 turns off compression, shuffling of compressed, shuffled file ..."
+./nccopy -d0 tst_inflated4.nc tmp.nc
+./ncdump -sh tmp.nc > tmp.cdl
+if fgrep '_DeflateLevel' < tmp.cdl ; then
+    exit 1
+fi
+if fgrep '_Shuffle' < tmp.cdl ; then
+    exit 1
+fi
+rm tst_deflated.nc tst_inflated.nc tst_inflated4.nc tmp.nc tmp.cdl
 
 echo "*** Testing nccopy -d1 -s on ncdump/*.nc files"
 for i in $TESTFILES ; do
@@ -66,6 +75,9 @@ diff tmp.cdl tmp-chunked.cdl
 ./nccopy -c dim0/,dim1/,dim2/,dim3/,dim4/,dim5/,dim6/ tmp-chunked.nc tmp-unchunked.nc
 ./ncdump -n tmp tmp-unchunked.nc > tmp-unchunked.cdl
 diff tmp.cdl tmp-unchunked.cdl
+./nccopy -c / tmp-chunked.nc tmp-unchunked.nc
+./ncdump -n tmp tmp-unchunked.nc > tmp-unchunked.cdl
+diff tmp.cdl tmp-unchunked.cdl
 # echo "*** Test that nccopy compression with chunking can improve compression"
 rm tst_chunking.nc tmp.nc tmp.cdl tmp-chunked.nc tmp-chunked.cdl tmp-unchunked.nc tmp-unchunked.cdl