$Header$ -*-text-*-

The netCDF Operators NCO version 4.7.3 have hatched.

http://nco.sf.net (Homepage, Mailing lists, Help)
http://github.com/nco (Source Code, Issues, Releases, Developers)

What's new?
Version 4.7.3 contains little features and fixes.
A new security whitelist could break some workflows, and the
other features offer better support for TempestRemap, MPAS, and
heavy users of NCO print features in CDL, JSON, and XML.

Work on NCO 4.7.4 has commenced. Planned changes include
better diagnosis and workarounds for the netCDF CDF5 bug,
parallel weight generation by ncremap, and possibly workarounds for 
using quotation marks with ncap2 in Windows.

Enjoy,
Charlie

NEW FEATURES (full details always in ChangeLog):

A. Filename character whitelist:
   NCO manipulates files, sometimes with shell calls.
   We have never received a report of a security issue due to NCO.
   Nevertheless, to pre-emptively reduce potential vulnerabilities, we 
   instituted in 4.7.3 a whitelist of allowed filename characters:
   abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890_-.@ :%\/
   The implied blacklist includes ;|<>[](),*
   If you want a character(s) added to the whitelist, please send us
   the rationale and a real-world use-case.
   http://nco.sf.net/nco.html#whitelist

B. ncremap implements E3SM-recommended Tempest remapping algorithms. 
   It has done so since 4.7.2, but that version omitted a switch that
   only a user can provide, and is necessary to indicate to
   TempestRemap to generate mapping weights from a source grid that
   has more coverage than the destination grid, i.e., the destination
   grid is a subset of the source. The switch is --a2o, or --atm2ocn,
   or numerous synonyms (b2l, big2ltl, l2s, lrg2sml).
   When computing the intersection of two meshes, TempestRemap uses an
   algorithm (an executable named GenerateOverlapMesh) that expects
   the mesh with less coverage to be the first grid, and the grid with
   greater coverage to be the second, regardless of mapping direction.
   By default, ncremap supplies the source grid first and the
   destination second, and this order causes GenerateOverlapMesh to
   fail when the source grid covers regions not in the destination
   grid. For example, a global atmosphere grid has more coverage than
   a global ocean grid, so that remapping from atmosphere-to-ocean
   would require invoking the --atm2ocn switch:
   ncremap --a2o -a se2fv_flx --src_grd=ne30.g --dst_grd=fv.nc -m map.nc
   http://nco.sf.net/nco.html#a2o
   http://nco.sf.net/nco.html#ncremap
   
C. ncclimo supports two more dataset filename template regular
   expressions: prefix.YYYY-MM.suffix, and prefix.YYYY-MM-01.suffix.
   When such a name is the argument to --caseid, the prefix and suffix
   will be automatically abstracted and used to template and generate
   all monthly filenames based on the specified yr_srt and yr_end.
   Please tell us any dataset filename regular expressions that you
   would like added to ncclimo rx database. 
   ncclimo -s 300 -e 400 --caseid=foo.0300-01-01.nc -i . -o /tmp
   http://nco.sf.net/nco.html#caseid

D. printf() format option for printed output (CDL, XML, JSON, TRD).  
   Formerly ncks would always print variable values with the default
   format specification for the given output type. This meant that,
   single and double-precision values would print ~7 and ~15 digits,
   respectively. The new --fmt_val option causes ncks to use the
   supplied printf() format string to print floating point values:
   ncks --fmt_val %.5f ~/nco/data/in.nc   
   will print up to five significant digits, and no more.
   This allows users to round numbers before printing them.
   http://nco.sf.net/nco.html#fmt_val

E. ncks now accepts a --print_file=file option to print directly to
   the named file rather than to stdout. Previously one could
   achieve the same result by redirecting stdout to a named file.
   However, it is slightly faster to print formatted output directly
   to a file than to stdout. 
   ncks --print_file=foo.txt --jsn in.nc
   Synonyms are --fl_prn, --prn_fl, --file_print, and --print_file.
   http://nco.sf.net/nco.html#prn_fl

F. ncap, the predecessor to ncap2, has been completely eliminated.
   This simplifies the build procedure by eliminating Bison/Yacc.
   (Flex/Lex is still needed for other operators (notably ncwa)).
   Old files may cause local NCO repositories to fail to build.
   If this occurs, simply delete then re-check-out the repository.

BUG FIXES:

A. Those who build NCO from source will notice that most or all of
   the compiler warnings from building ncap2 have been eliminated.

Full release statement at http://nco.sf.net/ANNOUNCE

KNOWN PROBLEMS DUE TO NCO:

   This section of ANNOUNCE reports and reminds users of the
   existence and severity of known, not yet fixed, problems. 
   These problems occur with NCO 4.7.3 built/tested under
   MacOS 10.13.2 with netCDF 4.4.1.1 on HDF5 1.10.1 and with
   Linux with netCDF 4.6.1-development (20180110) on HDF5 1.8.19.

A. NOT YET FIXED (NCO problem)
   Correctly read arrays of NC_STRING with embedded delimiters in ncatted arguments

   Demonstration:
   ncatted -D 5 -O -a new_string_att,att_var,c,sng,"list","of","str,ings" ~/nco/data/in_4.nc ~/foo.nc
   ncks -m -C -v att_var ~/foo.nc

   20130724: Verified problem still exists
   TODO nco1102
   Cause: NCO parsing of ncatted arguments is not sophisticated
   enough to handle arrays of NC_STRINGS with embedded delimiters.

B. NOT YET FIXED (NCO problem?)
   ncra/ncrcat (not ncks) hyperslabbing can fail on variables with multiple record dimensions

   Demonstration:
   ncrcat -O -d time,0 ~/nco/data/mrd.nc ~/foo.nc

   20140826: Verified problem still exists
   20140619: Problem reported by rmla
   Cause: Unsure. Maybe ncra.c loop structure not amenable to MRD?
   Workaround: Convert to fixed dimensions then hyperslab

KNOWN PROBLEMS DUE TO BASE LIBRARIES/PROTOCOLS:

A. NOT YET FIXED (netCDF4 or HDF5 problem?)
   Specifying strided hyperslab on large netCDF4 datasets leads
   to slowdown or failure with recent netCDF versions.

   Demonstration with NCO <= 4.4.5:
   time ncks -O -d time,0,,12 ~/ET_2000-01_2001-12.nc ~/foo.nc
   Demonstration with NCL:
   time ncl < ~/nco/data/ncl.ncl   
   20140718: Problem reported by Parker Norton
   20140826: Verified problem still exists
   20140930: Finish NCO workaround for problem
   Cause: Slow algorithm in nc_var_gets()?
   Workaround #1: Use NCO 4.4.6 or later (avoids nc_var_gets())
   Workaround #2: Convert file to netCDF3 first, then use stride

B. NOT YET FIXED (netCDF4 library bug)
   Simultaneously renaming multiple dimensions in netCDF4 file can corrupt output

   Demonstration:
   ncrename -O -d lev,z -d lat,y -d lon,x ~/nco/data/in_grp.nc ~/foo.nc # Completes but file is unreadable
   ncks -v one ~/foo.nc

   20150922: Confirmed problem reported by Isabelle Dast, reported to Unidata
   20150924: Unidata confirmed problem
   20160212: Verified problem still exists in netCDF library
   20160512: Ditto
   20161028: Verified problem still exists with netCDF 4.4.1
   20170323: Verified problem still exists with netCDF 4.4.2-development
   20170323: https://github.com/Unidata/netcdf-c/issues/381
   20171102: Verified problem still exists with netCDF 4.5.1-development
   20171107: https://github.com/Unidata/netcdf-c/issues/597
   Bug tracking: https://www.unidata.ucar.edu/jira/browse/fxm
   More details: http://nco.sf.net/nco.html#ncrename_crd

C. NOT YET FIXED (netCDF4 library bug)
   Renaming a non-coordinate variable to a coordinate variable fails in netCDF4

   Demonstration:
   ncrename -O -v non_coord,coord ~/nco/data/in_grp.nc ~/foo.nc # Fails (HDF error)

   20170323: Confirmed problem reported by Paolo Oliveri, reported to Unidata
   20170323: https://github.com/Unidata/netcdf-c/issues/381
   20171102: Verified problem still exists with netCDF 4.5.1-development
   20171107: https://github.com/Unidata/netcdf-c/issues/597

   Bug tracking: https://www.unidata.ucar.edu/jira/browse/fxm
   More details: http://nco.sf.net/nco.html#ncrename_crd

D. FIXED in netCDF Development branch as of 20161116 and in maintenance release 4.4.1.1
   nc-config/nf-config produce erroneous switches that cause NCO builds to fail
   This problem affects netCDF 4.4.1 on all operating systems.
   Some pre-compiled netCDF packages may have patched the problem.
   Hence it does not affect my MacPorts install of netCDF 4.4.1.

   Demonstration:
   % nc-config --cflags # Produces extraneous text that confuses make
   Using nf-config: /usr/local/bin/nf-config
   -I/usr/local/include -I/usr/local/include -I/usr/include/hdf

   If your nc-config output contains the "Using ..." line, you are
   affected by this issue. 

   20161029: Reported problem to Unidata
   20161101: Unidata confirmed reproducibility, attributed to netCDF 4.4.1 changes
   20161116: Unidata patch is in tree for netCDF 4.4.2 release
   20161123: Fixed in maintenance release netCDF 4.4.1.1

E. NOT YET FIXED (would require DAP protocol change?)
   Unable to retrieve contents of variables including period '.' in name
   Periods are legal characters in netCDF variable names.
   Metadata are returned successfully, data are not.
   DAP non-transparency: Works locally, fails through DAP server.

   Demonstration:
   ncks -O -C -D 3 -v var_nm.dot -p http://thredds-test.ucar.edu/thredds/dodsC/testdods in.nc # Fails to find variable

   20130724: Verified problem still exists. 
   Stopped testing because inclusion of var_nm.dot broke all test scripts.
   NB: Hard to fix since DAP interprets '.' as structure delimiter in HTTP query string.

   Bug tracking: https://www.unidata.ucar.edu/jira/browse/NCF-47

F. NOT YET FIXED (would require DAP protocol change)
   Correctly read scalar characters over DAP.
   DAP non-transparency: Works locally, fails through DAP server.
   Problem, IMHO, is with DAP definition/protocol

   Demonstration:
   ncks -O -D 1 -H -C -m --md5_dgs -v md5_a -p http://thredds-test.ucar.edu/thredds/dodsC/testdods in.nc

   20120801: Verified problem still exists
   Bug report not filed
   Cause: DAP translates scalar characters into 64-element (this
   dimension is user-configurable, but still...), NUL-terminated
   strings so MD5 agreement fails 

"Sticky" reminders:

A. Reminder that NCO works on most HDF4 and HDF5 datasets, e.g., 
   HDF4: AMSR MERRA MODIS ...
   HDF5: GLAS ICESat Mabel SBUV ...
   HDF-EOS5: AURA HIRDLS OMI ...

B. Pre-built executables for many OS's at:
   http://nco.sf.net#bnr

