re: Issue https://github.com/Unidata/netcdf-c/issues/1936
The algorithm controlling interaction of -d 0 -F and -c / options
is incorrect.
The fix:
1. make -d 0 => no deflation
2. make -F properly use the filter specs to decide.
Also added a test case to ncdump/tst_nccopy4.sh.
re: https://github.com/Unidata/netcdf-c/issues/1642
Modify ncdump, nccopy, and ncgen to support the NC_COMPACT storage option.
Added test cases and added description to the man pages for the utilities.
1. ncdump: For compact storage variable, print special attribute __Storage_ as
````
<var>: _Storage = "compact";
````
2. ncgen: parse and implement
````
<var>: _Storage = "compact";
````
in a .cdl file
3. nccopy: Extend the chunk specification (-c flag) to support
compact using the forms
````
nccopy ... -c <var>:compact
and
nccopy ... -c <var>:contiguous
````
Misc. other changes
1. cleanup the copy_chunking function in ncdump/nccopy.c
re: issue https://github.com/Unidata/netcdf-c/issues/1436
It used to be that when no -c parameters were specified
(and the input was some variant of netcdf-3) that nccopy
let the netcdf-c library decide on any default chunking.
Now, it attempts to do it itself and is not doing it
correctly when unlimited dimensions are involved.
So fix is to revert to previous behavior.
Note: The chunking rules are getting too complicated; consider revising.
A user suggested that the nccopy -F option
syntax should be extended to support specification
of multiple (or all) variables in a single -F option.
The new syntax allows:
1. '*' as the name of the variable; this means apply the
filter to all variables in the data set.
2. *var1|var2|...* as the variable name to indicate that the filter
should be applied to the multiple specified variables.
re: https://github.com/Unidata/netcdf-c/issues/1183
Changes:
1. fix typo in nccopy.1 man page
2. fix chunkspec parsing for -c so that "-c var:"
(with no chunkspec arguments) disables chunking
on the specified variable
3. Add test case to ncdump/tst_nccopy5.sh
re: issue https://github.com/Unidata/netcdf-c/issues/1151
Modify DAP2 and DAP4 code to handle case when _FillValue type is not
same as the parent variable type.
Specifically:
1. Define a parameter [fillmismatch] to allow this mismatch;
default is to disallow.
2. If allowed, forcibly change the type of the _FillValue to match
the parent variable.
3. If allowed Convert the values to match new type
4. Generate a log message
5. if not allowed, then fail
Implementing this required some changes to ncdap_test/dapcvt.c
Also added test cases.
Minor Unrelated Changes:
1. There were a number of warnings about e.g.
assigning a const char* to a char*. Fix these
2. In nccopy.1, replace .NP with .IP "n"
(re PR https://github.com/Unidata/netcdf-c/pull/1144)
3. fix minor error in ncdump/ocprint
stored in the _NCProperties attribute to allow two things:
1. capture of additional library dependencies (over and above
hdf5)
2. Recognition of non-netcdf libraries that create netcdf-4 format
files.
To this end, the _NCProperties format has been extended to be
and arbitrary set of key=value pairs separated by commas.
This new format has version = 2, and uses commas as the pair separator.
Thus the general form is:
_NCProperties = "version=2,key1=value,key2=value2..." ;
This new version is accompanied by a new ./configure option of the form
--with-ncproperties="key1=value1,key2=value2..."
that specifies pairs to add to the _NCProperties attribute for all
files created with that netcdf library.
At this point, what is missing is some programmatic way to
specify either all the pairs or additional pairs
to the _NCProperties attribute. Not sure of the best way
to do this.
Builders using non-netcdf libraries can specify
whatever they want in the key value pairs (as long
as the version=2 is specified first).
By convention, the primary library is expected to be the
the first pair after the leading version=2 pair, but this
is convention only and is neither required nor enforced.
Related changes:
1. Fixed the tests that check _NCProperties to properly operate with version=2.
2. When reading a version 1 _NCProperties attribute, convert it to look
like a version 2 attribute.
2. Added some version 2 tests to ncdump/tst_fileinfo.c and
ncdump/tst_fileinfo.sh
Misc Changes:
1. Fix minor problem in ncdap_test/testurl.sh where a parameter to
buildurl needed to be quoted.
2. Minor fix to ncgen to swap switches -H and -h to be consistent
with other utilities.
3. Document the -M flag in nccopy usage() and the nccopy man page.
4. Modify a test case to use the nccopy -M flag.
After a long discussion, I implemented the rules at the end of that issue.
They are documented in nccopy.1.
Additionally, I added a new, per-variable, -c flag that allows
for the direct setting of the chunking parameters for a variable.
The form is
-c var:c1,c2,...ck
where var is the name of the variable (possibly a fully qualified name)
and the ci are the chunksizes for that variable. It must be the case
that the rank of the variable is k. If the new form is used as well
as the old form, then the new form overrides the old form for the
specified variable. Note that multiple occurrences of the new form
-c flag may be specified.
Misc. Other fixes
1. Added -M <size> option to nccopy to specify the minimum
allowable chunksize.
2. Removed the unused variables from bigmeta.c
(Issue https://github.com/Unidata/netcdf-c/issues/1079)
3. Fixed failure of nc_test4/tst_filter.sh by using the new -M
flag (#1) to allow filter test on a small chunk size.
1. Allow nccopy to apply filters, especially on the output file.
This provides a third way to do this other than using ncgen or
programatically
2. Make sure that even if the filter code is not available, it is
possible to see the filter id and parameters for variables using
e.g ncdump -hs.
3. Fix bug in nccopy so that the input file does
not necessarily have to be netcdf-4.
4. At last minute decided to change to using a
single "_Filter" attribute for ncgen
5. Added a test to tst_filter.sh to generate C code using ncgen.
by an HDF5 configure option, not a netCDF-4 configure option.
- Fixed bug in HDF5 strings test code.
- Minor fixes to nccopy man page documentation.
- Minor fixes to Fortran-90 texinfo docs, since we don't have doxygen
docs for Fortran yet: just using "Fortran" instead of "fortran" or
"FORTRAN".
