$Header$ -*-text-*-

The netCDF Operators NCO version 4.7.1 have escaped.

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

What's new?
Version 4.7.1 contains mostly minor fixes and few new features.
One major improvement, long in development, is a Conda Windows port. 
Most NCO functionality is now easily available to Windows users
through the Conda distribution. 

Pedro Vicente turned his Windows scripts into a CMake implementation. 
Building on Pedro's CMake contribution, a team of about six volunteers
used, refined, or implemented Windows ports for the full NCO software
stack. Filipe Fernandez coordinated the Conda work, added AppVeyor
support, and brought in extra help and testing. Pedro and Isuru
Fernando tracked down bugs and improved the build matrix.
No one person could have accomplished this.
The power of Open Source development is awesome.

Work on NCO 4.7.1 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. NCO Conda package for Windows: All NCO binaries are thought
   to work correctly, although the regression test script itself
   (which is written in Perl) has not yet been run on Windows.
   Windows' idiosyncratic quoting rules can interfere with ncap2
   (try running from Powershell to use UNIXy quotes).
   The two scripted operators, ncclimo and ncremap, are problematic.
   As sophisticated Bash scripts, these do not work on Windows.
   Volunteers to port them to a Windows-friendly language (e.g.,
   Python) are welcome! 
   Within a few days of release, try this Windows install command:
   conda install -c conda-forge nco   
   http://nco.sf.net/nco.html#conda
   
B. ncclimo in daily mode now handles stdin input more cleverly.
   Piping or redirecting filename lists to ncclimo --clm_md=dly
   is the easiest way to feed huge lists of filenames to ncclimo.
   However, these lists are often dominated in size by the path
   component of the filename, rather than the filename itself.
   Now ncclimo allows specification of the path with -i drc_in,
   and it will prepend that path to the standard input names.
   Previously it prepended the current working directory.
   This functionality allows easy retention of the full
   provenance of the input files, without requiring repetitive
   inclusion of long pathnames in the filenames.
   ls *.clm2.h0.* | ncclimo -c caseid -C dly -s 1960 -e 2005 -i data
   http://nco.sf.net/nco.html#ncclimo

C. JSON printing of netCDF3 strings, i.e., character arrays,
   has changed. Previously ncks printed square brackets around
   the string, as with numeric arrays. However this was somewhat
   redundant since the quotation marks around a JSON string already
   indicate an array of characters. Now ncks omits the inner-most
   (i.e., most rapidly varying) set of brackets from the printing of
   character arrays: 
   ncks --jsn_fmt=2 -C -H -v char_var_2D_arr ~/nco/data/in.nc
   {
     "dimensions": {
         "lat": 2,
         "lon": 4
      },
      "variables": {
         "char_var_2D_arr": {
         "shape": ["lat", "lon"],
         "type": "char",
         "data": ["one", "two"]
    ...

   This is instead of "data": [["one"], ["two"]]
   in the last line. 
   http://nco.sf.net/nco.html#json

BUG FIXES:

A. Fix bug where ncclimo --clm_md=dly/ann expected a season list.
   This bug was inadvertently introduced with season code in 4.6.8.
   The workaround is to use NCO <= 4.6.7 or upgrade to 4.7.1.

B. ncks in JSON, CDL, and XML modes now prints a single NUL as "".
   Previously a scalar NUL printed as "0", as in ncdump's CDL.
   However, we think this is a bug in ncdump since NUL is not zero.

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 4.7.1 built/tested under
   MacOS 10.13.2 with netCDF 4.4.1.1 on HDF5 1.10.1 and with
   Linux with netCDF 4.5.1-development (20171220) 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

