Unidata / netcdf-c

• [Windows] Bumped packaged HDF5 to 1.10.6, HDF4 to 4.2.14, and libcurl to 7.60.0.
• [Enhancement] Support has been added for HDF5-1.12.0. See [https://github.com//issues/1528].
• [Bug Fix] Correct behavior for the command line utilities when directly accessing a directory using utf8 characters. See Github #1669, Github #1668 and Github #1666 for more information.
• [Bug Fix] Attempts to set filters or chunked storage on scalar vars will now return NC_EINVAL. Scalar vars cannot be chunked, and only chunked vars can have filters. Previously the library ignored these attempts, and always storing scalars as contiguous storage. See [https://github.com//issues/1644].
• [Enhancement] Support has been added for multiple filters per variable. See [https://github.com//issues/1584].
• [Enhancement] Now nc_inq_var_szip retuns 0 for parameter values if szip is not in use for var. See [https://github.com//issues/1618].
• [Enhancement] Now allow parallel I/O with filters, for HDF5-1.10.3 and later. See [https://github.com//issues/1473].
• [Enhancement] Increased default size of cache buffer to 16 MB, from 4 MB. Increased number of slots to 4133. See [https://github.com//issues/1541].
• [Enhancement] Allow zlib compression to be used with parallel I/O writes, if HDF5 version is 1.10.3 or greater. See [https://github.com//issues/1580].
• [Enhancement] Restore use of szip compression when writing data (including writing in parallel if HDF5 version is 1.10.3 or greater). See [https://github.com//issues/1546].
• [Enhancement] Enable use of compact storage option for small vars in netCDF/HDF5 files. See [https://github.com//issues/1570].
• [Enhancement] Updated benchmarking program bm_file.c to better handle very large files. See [https://github.com//issues/1555].
• [Enhancement] Added version number to dispatch table, and now check version with nc_def_user_format(). See [https://github.com//issues/1599].
• [Bug Fix] Fixed user setting of MPI launcher for parallel I/O HDF5 test in h5_test. See [https://github.com//issues/1626].
• [Bug Fix] Fixed problem of growing memory when netCDF-4 files were opened and closed. See [https://github.com//issues/1575 and https://github.com//issues/1571].
• [Enhancement] Increased size of maximum allowed name in HDF4 files to NC_MAX_NAME. See [https://github.com//issues/1631].

• [Bug Fix]Fixed an issue where installs from tarballs will not properly compile in parallel environments.
• [Bug Fix] Library was modified so that rewriting the same attribute happens without deleting the attribute, to avoid a limit on how many times this may be done in HDF5. This fix was thought to be in 4.6.2 but was not. See [https://github.com//issues/350].
• [Enhancement] Add a dispatch version number to netcdf_meta.h and libnetcdf.settings, in case we decide to change dispatch table in future. See [https://github.com//issues/1469].
• [Bug Fix] Now testing that endianness can only be set on atomic ints and floats. See [https://github.com//issues/1479].
• [Bug Fix] Fix for subtle error involving var and unlimited dim of the same name, but unrelated, in netCDF-4. See [https://github.com//issues/1496].
• [Enhancement] Update for attribute documentation. See [https://github.com//issues/1512].
• [Bug Fix][Enhancement] Corrected assignment of anonymous (a.k.a. phony) dimensions in an HDF5 file. Now when a dataset uses multiple dimensions of the same size, netcdf assumes they are different dimensions. See GitHub #1484 for more information.

• [OSX][Bug Fix][Enhancement] Corrected an issue where protected memory was being written to with some pointer slight-of-hand. This has been in the code for a while, but appears to be caught by the compiler on OSX, under circumstances yet to be completely nailed down. See GitHub #1486 for more information.
• [Enhancement] [Parallel IO] Added support for parallel functions in MSVC. See Github #1492 for more information.
• [Enhancement] Added a function for changing the ncid of an open file. This function should only be used if you know what you are doing, and is meant to be used primarily with PIO integration. See GitHub #1483 and GitHub #1487 for more information.
• [Bug Fix][Enhancement] Various bug fixes and enhancements.

• [Enhancement] Added unit_test directory, which contains unit tests
  for the libdispatch and libsrc4 code (and any other directories that
  want to put unit tests there). Use --disable-unit-tests to run without
  unit tests (ex. for code coverage analysis).
  See GitHub #1458

• [Bug Fix] Remove obsolete _CRAYMPP and LOCKNUMREC macros from
  code. Also brought documentation up to date in man page. These macros
  were used in ancient times, before modern parallel I/O systems were
  developed. Programmers interested in parallel I/O should see
  nc_open_par() and nc_create_par().
  See GitHub #1459

• [Enhancement] Remove obsolete and deprecated functions
  nc_set_base_pe() and nc_inq_base_pe() from the dispatch table. (Both
  functions are still supported in the library, this is an internal
  change only.)
  See GitHub #1468

• [Bug Fix] Reverted nccopy behavior so that if no -c parameters
  are given, then any default chunking is left to the netcdf-c library
  to decide.
  See GitHub #1436

• Various other bugfixes and enhancements.

The changes from 4.6.3 include but are not limited to:

• [Enhancement] A plethora of bug fixes and performance improvements.

• [Enhancement] Updated behavior of pkgconfig and nc-config to allow the use of the --static flags, e.g. nc-config --libs --static, which will show information for linking against libnetcdf statically. See Github #1360 and Github #1257 for more information.

• [Enhancement] Provide byte-range reading of remote datasets. This allows
  read-only access to, for example, Amazon S3 objects and also Thredds Server
  datasets via the HTTPService access method.
  See GitHub #1251.

• Update the license from the home-brewed NetCDF license to the standard 3-Clause BSD License. This change does not result in any new restrictions; it is merely the adoption of a standard, well-known and well-understood license in place of the historic NetCDF license written at Unidata. This is part of a broader push by Unidata to adopt modern, standardized licensing.

The changes from 4.6.2 include but are not limited to:

• [Bug Fix] Correctly generated netcdf.pc generated either by configure or cmake. If linking against a static netcdf, you would need to pass the --static argument to pkg-config in order to list all of the downstream dependencies. See Github #1324 for more information.
• Now always write hidden coordinates attribute, which allows faster file opens when present. See Github #1262 for more information.
• Some fixes for rename, including fix for renumbering of varids after a rename (#1307), renaming var to dim without coordinate var. See Github #1297.
• Fix of NULL parameter causing segfaults in put_vars functions. See Github #1265 for more information.
• Fix of --enable-benchmark benchmark tests Github #1211
• Update the license from the home-brewed NetCDF license to the standard 3-Clause BSD License. This change does not result in any new restrictions; it is merely the adoption of a standard, well-known and well-understood license in place of the historic NetCDF license written at Unidata. This is part of a broader push by Unidata to adopt modern, standardized licensing.
• [BugFix] Corrected DAP-releated issues on big-endian machines. See Github #1321, Github #1302 for more information.
• [BugFix][Enhancement] Various and sundry bugfixes and performance enhancements, thanks to @edhartnett, @gsjaardema, @t-b, @wkliao, and all of our other contributors.
• [Enhancement] Extended nccopy -F syntax to support multiple variables with a single invocation. See Github #1311 for more information.
• [BugFix] Corrected an issue where DAP2 was incorrectly converting signed bytes, resulting in an erroneous error message under some circumstances. See GitHub #1317 for more information. See Github #1319 for related information.
• [BugFix][Enhancement] Modified nccopy so that _NCProperties is not copied over verbatim but is instead generated based on the version of libnetcdf used when copying the file. Additionally, _NCProperties are displayed if/when associated with a netcdf3 file, now. See GitHub #803 for more information.

The changes from version 4.6.1 include (but are not limited to):

• [Enhancement] Lazy att read - only read atts when user requests one of them. See GitHub #857.
• [Enhancement] Fast global att read - when global atts are read, they are read much more quickly. See GitHub #857.
• [Enhancement] Add nccopy command options for per-variable chunk sizing, and minimum chunk size. See GitHub #1087.
• [Bug Fix] Fix nccopy handling of user specified chunk sizes. See GitHub #725,#1087.
• [Bug Fix] Avoid limit on number of times a netCDF4 attribute can be updated. Not a complete fix for the HDF5 "maximum creation order" problem, but should greatly reduce occurrences in many real-world cases. See GitHub #350.
• [Bug Fix] The use of NC_DISKLESS has been modified to make it cleaner. This adds a new flag called NC_PERSIST that takes over the now obsolete NC_MPIPOSIX.
• [Obsolete] Obsolete the MPIPOSIX flag.
• [Bug Fix] When using filters with HDF5 1.10.x or later, it is necessary to utilize the HDF5 replacements for malloc, realloc, and free in the filter code.
• [Enhancement] Create a new version of _NCProperties provenance attribute. This version (version 2) supports arbitrary key-value pairs. It is the default when new files are created. Version 1 continues to be accepted.
• [Enhancement] Allow user to set http read buffersize for DAP2 and DAP4 using the tag HTTP.READ.BUFFERSIZE in the .daprc file.
• [Enhancement] Allow user to set http keepalive for DAP2 and DAP4 using the tag HTTP.KEEPALIVE in the .daprc file (see the OPeNDAP documentation for details).
• [Enhancement] Support DAP4 remote tests using a new remote test server locatedon the Unidata JetStream project.
• [Enhancement] Improved the performance of the nc_get/put_vars operations by using the equivalent slab capabilities of hdf5. Result is a significant speedup of these operations. See GitHub #1001 for more information.
• [Enhancement] Expanded the capabilities of NC_INMEMORY to support writing and accessing the final modified memory. See GitHub #879 for more information.
• [Enhancement] Made CDF5 support enabled by default. See Github #931 for more information.
• [Bug Fix] Corrected a number of memory issues identified in ncgen. See GitHub #558 for more information.