NetCDF operators (NCO) version 4.7.3

Version 4.7.3 of the netCDF Operators (NCO) has been released. NCO is an Open Source package that consists of a dozen standalone, command-line programs that take netCDF files as input, then operate (e.g., derive new data, average, print, hyperslab, manipulate metadata) and output the results to screen or files in text, binary, or netCDF formats.

The NCO project is coordinated by Professor Charlie Zender of the Department of Earth System Science, University of California, Irvine. More information about the project, along with binary and source downloads, are available on the SourceForge project page .

From the release message:

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.

New Features
  1. 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.
  2. 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 -m
  3. 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 -i . -o /tmp
  4. 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/
    will print up to five significant digits, and no more. This allows users to round numbers before printing them.
  5. 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
    Synonyms are --fl_prn, --prn_fl, --file_print, and --print_file.
  6. 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.

Additional details are available in the ChangeLog.


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