Add support for Zarr string type to NCZarr #2492
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* re: Unidata#2278 * re: Unidata#2485 * re: Unidata#2474 This PR subsumes PR Unidata#2278. Actually is a bit an omnibus covering several issues. ## PR Unidata#2278 Add support for the Zarr string type. Zarr strings are restricted currently to be of fixed size. The primary issue to be addressed is to provide a way for user to specify the size of the fixed length strings. This is handled by providing the following new attributes special: 1. **_nczarr_default_maxstrlen** — This is an attribute of the root group. It specifies the default maximum string length for string types. If not specified, then it has the value of 64 characters. 2. **_nczarr_maxstrlen** — This is a per-variable attribute. It specifies the maximum string length for the string type associated with the variable. If not specified, then it is assigned the value of **_nczarr_default_maxstrlen**. This PR also requires some hacking to handle the existing netcdf-c NC_CHAR type, which does not exist in zarr. The goal was to choose numpy types for both the netcdf-c NC_STRING type and the netcdf-c NC_CHAR type such that if a pure zarr implementation read them, it would still work and an NC_CHAR type would be handled by zarr as a string of length 1. For writing variables and NCZarr attributes, the type mapping is as follows: * "|S1" for NC_CHAR. * ">S1" for NC_STRING && MAXSTRLEN==1 * ">Sn" for NC_STRING && MAXSTRLEN==n Note that it is a bit of a hack to use endianness, but it should be ok since for string/char, the endianness has no meaning. For reading attributes with pure zarr (i.e. with no nczarr atribute types defined), they will always be interpreted as of type NC_CHAR. ## Issue: Unidata#2474 This PR partly fixes this issue because it provided more comprehensive support for Zarr attributes that are JSON valued expressions. This PR still does not address the problem in that issue where the _ARRAY_DIMENSION attribute is incorrectly set. Than can only be fixed by the creator of the datasets. ## Issue: Unidata#2485 This PR also fixes the scalar failure shown in this issue. It generally cleans up scalar handling. It also adds a note to the documentation describing that NCZarr supports scalars while Zarr does not and also how scalar interoperability is achieved. ## Misc. Other Changes 1. Convert the nczarr special attributes and keys to be all lower case. So "_NCZARR_ATTR" now used "_nczarr_attr. Support back compatibility for the upper case names. 2. Cleanup my too-clever-by-half handling of scalars in libnczarr.
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This pull request introduces 1 alert and fixes 2 when merging 231ae96 into 9cc8831 - view on LGTM.com new alerts:
fixed alerts:
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This pull request introduces 1 alert and fixes 2 when merging c9205ae into 9cc8831 - view on LGTM.com new alerts:
fixed alerts:
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This pull request fixes 2 alerts when merging d0aff6a into 9cc8831 - view on LGTM.com fixed alerts:
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This was referenced Aug 28, 2022
dzenanz
reviewed
Aug 29, 2022
| * [Bug Fix] Provide a default enum const when fill value does not match any enum constant for the value zero. See [Github #2462](https://github.com/Unidata/netcdf-c/pull/2462). | ||
| * [Bug Fix] Fix the json submodule symbol conflicts between libnetcdf and the plugin specific netcdf_json.h. See [Github #2448](https://github.com/Unidata/netcdf-c/pull/2448). | ||
| * [Bug Fix] Fix quantize with CLASSIC_MODEL files. See [Github #2405](https://github.com/Unidata/netcdf-c/pull/2445). | ||
| * [Enhancement] Add `--disable-quantize` option to `configure`. | ||
| * [Bug Fix] Fix CMakeLists.txt to handle all acceptable boolean values for -DPLUGIN_INSTALL_DIR. See [Github #2430](https://github.com/Unidata/netcdf-c/pull/2430). | ||
| >>>>>>> master |
| @@ -27,8 +30,12 @@ This file contains a high-level description of this package's evolution. Release | |||
| * [Enhancement] Allow the read/write of JSON-valued Zarr attributes to allow | |||
| for domain specific info such as used by GDAL/Zarr. See [Github #2278](https://github.com/Unidata/netcdf-c/pull/2278). | |||
| * [Enhancement] Turn on the XArray convention for NCZarr files by default. WARNING, this means that the mode should explicitly specify "nczarr" or "zarr" even if "xarray" or "noxarray" is specified. See [Github #2257](https://github.com/Unidata/netcdf-c/pull/2257). | |||
| <<<<<<< HEAD | |||
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| * [Enhancement] Update the documentation to match the current filter capabilities. See [Github #2249](https://github.com/Unidata/netcdf-c/pull/2249). | ||
| >>>>>>> master |
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This pull request fixes 2 alerts when merging f4e181b into 9cc8831 - view on LGTM.com fixed alerts:
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DennisHeimbigner
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Sep 3, 2022
re: PR Unidata#2492 re: Issue Unidata#2494 This PR fixes some problems with the pull request Unidata#2492 in response to Issue Unidata#2494. * Found and fixed more scalar handling problems and add a test case for scalars. * Cleanup nczarr_test/run_string.sh test * Document *_nczarr_default_maxstrlen* and *_nczarr_maxstrlen*. * Support both "Nan" and *Nan* as being floating point constants for attributes. It is unclear from the Zarr V2 spec if unquoted *Nan* is legal or not, but support for reading. Write the quoted versions when writing an attribute. Similar for Infinity constants. So NCZarr supports the following constants for use in Attributes * *Nan*, "Nan", *-Nan*, "-Nan" * *Nanf*, "Nanf", *-Nanf*, "-Nanf" * *Infinity*, "Infinity", *-Infinity*, "-Infinity" * *Infinityf*, "Infinityf", *-Infinityf*, "-Infinityf"
clrpackages
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that referenced
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Feb 9, 2023
DWesl (26):
DEV: Add autools-generated files to .gitignore.
CI: Add Cygwin CI run.
CI, TST: Check that test plugins don't get installed with DESTDIR
BLD: Get netCDF4 build working on Windows.
DEV, TST: Move test plugins to check_LTLIBRARIES instead of tmp_LTLIBRARIES.
BLD: Try fixing the export-symbols problem on MinGW
CI, DBG: Upload MinGW test logs on failure.
TST: Add code for MinGW to findplugin.sh.
TST: Mark tst_filter.sh XFAIL on MinGW
CI: Try to skip failing NCZarr Plugin tests on MinGW
TST: Mark NCZarr plugins XFAIL on MinGW
TST: tst_h_strbug and tst_h_refs pass on Cygwin now
BLD: Use host platform instead of build platform for platform-specific checks.
CI: Prep Cygwin CI run for adding CMake build.
BLD: Get CMake build compiling on Cygwin.
BUG: Robustify nulldup definition.
TST: Mark nczarr s3 cleanup test XFAIL on Cygwin instead of skipping.
CI: Disable CMake tests on Cygwin and MinGW.
CI: Revert Windows CI run on push.
BLD: Fix syntax in configure.ac.
BLD: Avoid specifying -version-info and -avoid-version
BLD: Specify -avoid-version on MinGW and Cygwin; -version-info otherwise
STY: Move nulldup backup definition from cp_win32.c to ncconfigure.h
FIX: ifndef requires no parentheses.
BLD: Declare nulldup backup definition static not extern
CI: Change autotools CI build to out-of-tree build.
Dan Ibanez (1):
Rename variable to avoid function name conflict
Dennis Heimbigner (65):
Fix nc_def_var_fletcher32 operation
Update release notes
Use env variable USERPROFILE instead of HOME for windows and mingw.
Update release notes
restart github
Make public a limited API for programmatic access to internal .rc tables
Update Release Notes
Fix errors:
Use env variable USERPROFILE instead of HOME for windows and mingw.
Cleanup szip handling some more
Update release notes
fix RELEASENOTES
undebug
Minimal changes to RELEASENOTES to get a working patch
force rebuild
Fix way CMake handle -DPLUGIN_INSTALL_DIR
Update Release notes
debug1
Ensure that netcdf_json.h does not interfere with ncjson.
Update RELEASENOTES.md
Fix bad cmake install location
Fix some bugs in the blosc filter wrapper
Update release notes
Update blosc testing
Provide a default enum const when fill value does not match any enum const.
Update release notes
debug1
Fix support for reading arrays of HDF5 fixed size strings
Windows specific blosc fixed
debug1
nodebug
Add option to control accessing external servers
Add support for Zarr string type to NCZarr
Update release notes"
update release notes
Fix LGTM alert: too few args
Update nczarr documentation
update file permission
Fix some problems with PR Unidata/netcdf-c#2492
Update release notes
Update Release Notes
Fix missing files
Catch Xarray dimension inconsistencies
Fix some addtional errors in NCZarr
Update release notes
update file permission
Cleanup built test sources in nczarr_test
restore
Move construction of VERSION file to end of the build
Turn off extraneous debug output
test
test
test2
merged
Fix race condition in ncdump (and other) tests.
Update RELEASE notes
test3
Restore DAP4 functionality and testing
test4
ckp
Suppress nczarr_test/tst_unknown filter test (and its nczarr_test equivalen)
Update Release Notes
retry
Fix infinite loop in file inferencing
Fix Memory Leak
Dženan Zukić (1):
Fix AWS SDK linking errors
Edward Hartnett (37):
checking doxygen version
updated Doxyfile.in
turned on WARN_AS_ERROR and added documentation build to CI
fixed case of --enable-doxygen but doxygen not found
installing doxygen in CI when needed
installing doxygen in CI when needed
installing doxygen in CI when needed
installing doxygen in CI when needed
installing doxygen in CI when needed
change to trigger CI
updated release notes
change to rerun CI
change to trigger CI
change to trigger CI
fixed RELEASE_NOTES.md
fixed missing quote
fixed missing quote
changed backslash to and
change to trigger CI
change to trigger CI
moved quantize error documentation
fix and test quantize mode for NC_CLASSIC_MODEL
documentation
code and documentation cleanup
code and documentation cleanup
adding pre-processor constant NC_MAX_FILENAME to nc_tests.h
more quantize testing
more quantize testing
more quantize testing
more quantize testing
more testing of quantize
more testing of quantize
more testing of quantize
more testing of quantize
more testing of quantize
more testing of quantize
more testing of quantize
Greg Sjaardema (2):
Minor update to doxygen function documentation
For loop initial declarations are only allowed in C99 mode
James Edwards (1):
make UDF0 not require NC_NETCDF4
Jim Edwards (3):
add udf2 fix magic
remove whitespace changes
fix syntax error
Magnus Ulimoen (3):
Prevent cmake writing to source dir
fix musl build
Use int64_t instead of __int64
Stephen Herbener (3):
Added an ncdump -t calendars test using variable length string
Modifications to enable the use of variable length string attributes for both
Moved the new ncdump_tst_calendars_nc4 test to the "USE_HDF5" section.
Ward Fisher (103):
Add manual GitHub actions triggers for the tests.
Added a check for xml2-config as a test for the libxml2-dev header files.
Add libxml2 install to mingw GitHub actions.
Generate nc_test/run_pnetcdf_tests.sh when using cmake, in support of Unidata/netcdf-c#2435
Fixing cmake-based run_pnetcdf_tests.sh
Building test programs invoked by run_pnetcdf_tests.sh
Fix cache check.
Run one-off tests first.
Fix a typo.
Fix a typo.
Make pnetcdf tests run in serial fashion when using cmake
Work in a one-line change as originally suggested in Unidata/netcdf-c#2426.
Updated CMakeLists to avoid the error described in Unidata/netcdf-c#2271
configure.ac logic for disabling quantize.
Update release notes.
Guard _declspec(dllexport) in support of Unidata/netcdf-c#2446
Changed attribute case in documentation in support of Unidata/netcdf-c#2481
Address jump-misses-init issue.
Remove stray conflict markers that made their way into the branch.
Adding all-error-codes.md back in to distribution documentation.
Remove obsolete tags from Doxyfile.
Updating doxygen files.
Doxygen update, reorganizing.
Update hdf5 version in github actions.
Added an additional check for zstd.h in configure.ac
Clean up (on linux) an issue with uintptr_t
Add a check for stdint.h in order to fix a weird issue where libzstd-dev, when present, was masking a missing data type declaration.
Adding additional flags to nc-config to indicate presence of newer functionality, and plugin directory location.
Added plugin directory to nc-config
Add various newer options to nc-config
Updated release notes.
Updated release notes.
Adding NC_HAS_BLOSC and NC_HAS_BZ2 to netcdf_meta.h in support of Unidata/netcdf-c#2511
Update cmakelists.txt in support of Unidata/netcdf-c#2511
Updated release notes.
Updated test logic in nc-config.in file.
Corrected an error.
Correct nccopy4 dependency on tst_fillbug.
Added a dependency to tst_nans to nccopy4
Added additional dependencies.
Add LDFLAGS for two plugins, nczstdfilters and nczhdf5filters, in support of Unidata/netcdf-c#2478
Add prepreqs to ncdump/tst_nccopy4, revising some race condition related errors.
Add blank filter quickstart guide file.
Updated release notes.
Working towards writing the quick start for plugins and integrating it into doxygen.
Roughed in initial quickstart
Working on filter quickstart document.
Continuing to flesh out the quick-start guide.
Further editing.
Updated SO version.
Updated for next release cycle.
Manually bump version in diff-compare to get RC1 out the door, this will need to be automatically excluded from the test at some point otherwise we will see this test fail every time the VERSION string changes.
Copy zmap reference files for cmake-based tests.
Update release notes.
Add generated files to distclean.
Correct an issue with 'make distcheck' where out-of-source tests were failing.
Working on another make distcheck failure.
Correct an issue observed in out-of-source builds.
Updated RELEASE_NOTES
Updated the relees notes.
Correct a typo in support of Unidata/netcdf-c#2534
Make dap4 reference dap instead of hard-wired to be disabled.
Add a check for HAVE_DECL_ISINF and HAVE_DECL_ISNAN in support of Unidata/netcdf-c#2132
Fix mismatched arguments warning in CMakeLists.txt
Restore release date for 4.9.1 RC1 in release notes.
Added target release date for RC2.
Supported headers for hdf4 are not installed in actions, and there does not appear (currently) to be an easy way to reinstall these.
Update release date.
DAP4 is back on for cmake-based builds.
Add an old static file.
Added another old static html page in preparation for updating.
Fix a logic error re: DAP4 tests, when DAP4 is specified, but hdf5/netcdf4 support is disabled.
Added S3 status to libnetcdf.settings, turned byterange on by default.
Cleaning up NCZARR_S3 summary, turning on byterange by default.
Add libcurl-dev to cygwin github actions
Correct libcurl development package.
Add libiconv-devel to cygwin CI
Correct version string change that should not have ended up in this branch.
Correct logic for running DAP4 tests when HDF5 is not enabled.
Update whitespace.
Correct lingering merge issue.
Merging Unidata/netcdf-c#2583 manually into the v4.9.1 wellspring branch.
Fix a doxygen warning-treated-as-error
Add new test, tst_calendars_nc4.sh, to automake-based builds.
Fix an issue I introduced with make distcheck
Remove internal flag from byterange documentation.
Update additional documentation infrastructure.
Update github action configuration scripts.
Small tweak.
Updating filter documentation with a quickstart guide.
Remove dangling file.
A bit of doxygen cleanup.
re-added quickstart filters document.
Clean up some garbled output from Doxygen.
Change in support of Unidata/netcdf-c#2599
Update release notes with v4.9.1 release date.
Updating for v4.9.1 release.
Updating in preparation for 4.9.1
Updating in prep for the v4.9.1 release.
Updated .gitignore.
Added autoconf generated files for a stand-alone release.
Added generated manfile for a stand-alone release.
Update Release Notes with proper release date.
Yuriy Chernyshov (1):
Fix typo in CMakeLists.txt
wkliao (3):
use malloc to increase read chunk size from 1 KB to 4 MB
typo fix
replace 4194304 with READ_BLOCK_SIZE
netbsd-srcmastr
pushed a commit
to NetBSD/pkgsrc
that referenced
this pull request
Jun 3, 2023
Release Notes {#RELEASE_NOTES}
=============
\brief Release notes file for the netcdf-c package.
This file contains a high-level description of this package's
evolution. Releases are in reverse chronological order (most recent
first). Note that, as of netcdf 4.2, the `netcdf-c++` and
`netcdf-fortran` libraries have been separated into their own
libraries.
## 4.9.3 - TBD
## 4.9.2 - March 14, 2023
This is the maintenance release which adds support for HDF5 version
1.14.0, in addition to a handful of other changes and bugfixes.
* Fix 'make distcheck' error in run_interop.sh. See [Github
#????](https://github.com/Unidata/netcdf-c/pull/????).
* Update `nc-config` to remove inclusion from automatically-detected
`nf-config` and `ncxx-config` files, as the wrong files could be
included in the output. This is in support of [GitHub
#2274](Unidata/netcdf-c#2274).
* Update H5FDhttp.[ch] to work with HDF5 version 1.13.2 and later. See
[Github #2635](Unidata/netcdf-c#2635).
* [Bug Fix] Update DAP code to enable CURLOPT_ACCEPT_ENCODING by
default. See [Github
#2630](Unidata/netcdf-c#2630).
* [Bug Fix] Fix byterange failures for certain URLs. See [Github
#2649](Unidata/netcdf-c#2649).
* [Bug Fix] Fix 'make distcheck' error in run_interop.sh. See [Github
#2631](Unidata/netcdf-c#2631).
* [Enhancement] Update `nc-config` to remove inclusion from
automatically-detected `nf-config` and `ncxx-config` files, as the
wrong files could be included in the output. This is in support of
[GitHub #2274](Unidata/netcdf-c#2274).
* [Enhancement] Update H5FDhttp.[ch] to work with HDF5 version
1.14.0. See [Github
#2615](Unidata/netcdf-c#2615).
## 4.9.1 - February 2, 2023
## Known Issues
* A test in the `main` branch of `netcdf-cxx4` is broken by this rc; this will
bear further investigation, but not being treated as a roadblock for the
release candidate.
* The new document, `netcdf-c/docs/filter_quickstart.md` is in
rough-draft form.
* Race conditions exist in some of the tests when run concurrently with large
numbers of processors
## What's Changed from v4.9.0 (automatically generated)
* Fix nc_def_var_fletcher32 operation by \@DennisHeimbigner in
Unidata/netcdf-c#2403
* Merge relevant info updates back into `main` by \@WardF in
Unidata/netcdf-c#2387
* Add manual GitHub actions triggers for the tests. by \@WardF in
Unidata/netcdf-c#2404
* Use env variable USERPROFILE instead of HOME for windows and mingw. by
\@DennisHeimbigner in Unidata/netcdf-c#2405
* Make public a limited API for programmatic access to internal .rc tables by
\@DennisHeimbigner in Unidata/netcdf-c#2408
* Fix typo in CMakeLists.txt by \@georgthegreat in
Unidata/netcdf-c#2412
* Fix choice of HOME dir by \@DennisHeimbigner in
Unidata/netcdf-c#2416
* Check for libxml2 development files by \@WardF in
Unidata/netcdf-c#2417
* Updating Doxyfile.in with doxygen-1.8.17, turned on WARN_AS_ERROR, added
doxygen build to CI run by \@edwardhartnett in
Unidata/netcdf-c#2377
* updated release notes by \@edwardhartnett in
Unidata/netcdf-c#2392
* increase read block size from 1 KB to 4 MB by \@wkliao in
Unidata/netcdf-c#2319
* fixed RELEASE_NOTES.md by \@edwardhartnett in
Unidata/netcdf-c#2423
* Fix pnetcdf tests in cmake by \@WardF in
Unidata/netcdf-c#2437
* Updated CMakeLists to avoid corner case cmake error by \@WardF in
Unidata/netcdf-c#2438
* Add `--disable-quantize` to configure by \@WardF in
Unidata/netcdf-c#2439
* Fix the way CMake handles -DPLUGIN_INSTALL_DIR by \@DennisHeimbigner in
Unidata/netcdf-c#2430
* fix and test quantize mode for NC_CLASSIC_MODEL by \@edwardhartnett in
Unidata/netcdf-c#2445
* Guard _declspec(dllexport) in support of #2446 by \@WardF in
Unidata/netcdf-c#2460
* Ensure that netcdf_json.h does not interfere with ncjson. by
\@DennisHeimbigner in Unidata/netcdf-c#2448
* Prevent cmake writing to source dir by \@magnusuMET in
Unidata/netcdf-c#2463
* more quantize testing and adding pre-processor constant NC_MAX_FILENAME to
nc_tests.h by \@edwardhartnett in
Unidata/netcdf-c#2457
* Provide a default enum const when fill value does not match any enum
constant by \@DennisHeimbigner in
Unidata/netcdf-c#2462
* Fix support for reading arrays of HDF5 fixed size strings by
\@DennisHeimbigner in Unidata/netcdf-c#2466
* fix musl build by \@magnusuMET in
Unidata/netcdf-c#1701
* Fix AWS SDK linking errors by \@dzenanz in
Unidata/netcdf-c#2470
* Address jump-misses-init issue. by \@WardF in
Unidata/netcdf-c#2488
* Remove stray merge conflict markers by \@WardF in
Unidata/netcdf-c#2493
* Add support for Zarr string type to NCZarr by \@DennisHeimbigner in
Unidata/netcdf-c#2492
* Fix some problems with PR 2492 by \@DennisHeimbigner in
Unidata/netcdf-c#2497
* Fix some bugs in the blosc filter wrapper by \@DennisHeimbigner in
Unidata/netcdf-c#2461
* Add option to control accessing external servers by \@DennisHeimbigner in
Unidata/netcdf-c#2491
* Changed attribute case in documentation by \@WardF in
Unidata/netcdf-c#2482
* Adding all-error-codes.md back in to distribution documentation. by \@WardF in
Unidata/netcdf-c#2501
* Update hdf5 version in github actions. by \@WardF in
Unidata/netcdf-c#2504
* Minor update to doxygen function documentation by \@gsjaardema in
Unidata/netcdf-c#2451
* Fix some addtional errors in NCZarr by \@DennisHeimbigner in
Unidata/netcdf-c#2503
* Cleanup szip handling some more by \@DennisHeimbigner in
Unidata/netcdf-c#2421
* Check for zstd development headers in autotools by \@WardF in
Unidata/netcdf-c#2507
* Add new options to nc-config by \@WardF in
Unidata/netcdf-c#2509
* Cleanup built test sources in nczarr_test by \@DennisHeimbigner in
Unidata/netcdf-c#2508
* Fix inconsistency in netcdf_meta.h by \@WardF in
Unidata/netcdf-c#2512
* Small fix in nc-config.in by \@WardF in
Unidata/netcdf-c#2513
* For loop initial declarations are only allowed in C99 mode by \@gsjaardema in
Unidata/netcdf-c#2517
* Fix some dependencies in tst_nccopy3 by \@WardF in
Unidata/netcdf-c#2518
* Update plugins/Makefile.am by \@WardF in
Unidata/netcdf-c#2519
* Fix prereqs in ncdump/tst_nccopy4 in order to avoid race conditions. by
\@WardF in Unidata/netcdf-c#2520
* Move construction of VERSION file to end of the build by \@DennisHeimbigner in
Unidata/netcdf-c#2527
* Add draft filter quickstart guide by \@WardF in
Unidata/netcdf-c#2531
* Turn off extraneous debug output by \@DennisHeimbigner in
Unidata/netcdf-c#2537
* typo fix by \@wkliao in Unidata/netcdf-c#2538
* replace 4194304 with READ_BLOCK_SIZE by \@wkliao in
Unidata/netcdf-c#2539
* Rename variable to avoid function name conflict by \@ibaned in
Unidata/netcdf-c#2550
* Add Cygwin CI and stop installing unwanted plugins by \@DWesl in
Unidata/netcdf-c#2529
* Merge subset of v4.9.1 files back into main development branch by \@WardF in
Unidata/netcdf-c#2530
* Add a Filter quickstart guide document by \@WardF in
Unidata/netcdf-c#2524
* Fix race condition in ncdump (and other) tests. by \@DennisHeimbigner in
Unidata/netcdf-c#2552
* Make dap4 reference dap instead of hard-wired to be disabled. by \@WardF in
Unidata/netcdf-c#2553
* Suppress nczarr_test/tst_unknown filter test by \@DennisHeimbigner in
Unidata/netcdf-c#2557
* Add fenceposting for HAVE_DECL_ISINF and HAVE_DECL_ISNAN by \@WardF in
Unidata/netcdf-c#2559
* Add an old static file. by \@WardF in
Unidata/netcdf-c#2575
* Fix infinite loop in file inferencing by \@DennisHeimbigner in
Unidata/netcdf-c#2574
* Merge Wellspring back into development branch by \@WardF in
Unidata/netcdf-c#2560
* Allow ncdump -t to handle variable length string attributes by \@srherbener in
Unidata/netcdf-c#2584
* Fix an issue I introduced with make distcheck by \@WardF in
Unidata/netcdf-c#2590
* make UDF0 not require NC_NETCDF4 by \@jedwards4b in
Unidata/netcdf-c#2586
* Expose user-facing documentation related to byterange DAP functionality. by
\@WardF in Unidata/netcdf-c#2596
* Fix Memory Leak by \@DennisHeimbigner in
Unidata/netcdf-c#2598
* CI: Change autotools CI build to out-of-tree build. by \@DWesl in
Unidata/netcdf-c#2577
* Update github action configuration scripts. by \@WardF in
Unidata/netcdf-c#2600
* Update the filter quickstart guide. by \@WardF in
Unidata/netcdf-c#2602
* Fix symbol export on Windows by \@WardF in
Unidata/netcdf-c#2604
## New Contributors
* \@georgthegreat made their first contribution in Unidata/netcdf-c#2412
* \@dzenanz made their first contribution in Unidata/netcdf-c#2470
* \@DWesl made their first contribution in Unidata/netcdf-c#2529
* \@srherbener made their first contribution in Unidata/netcdf-c#2584
* \@jedwards4b made their first contribution in Unidata/netcdf-c#2586
**Full Changelog**: Unidata/netcdf-c@v4.9.0...v4.9.1
### 4.9.1 - Release Candidate 2 - November 21, 2022
#### Known Issues
* A test in the `main` branch of `netcdf-cxx4` is broken by this rc;
this will bear further investigation, but not being treated as a
roadblock for the release candidate.
* The new document, `netcdf-c/docs/filter_quickstart.md` is in rough-draft form.
#### Changes
* [Bug Fix] Fix a race condition when testing missing filters. See
[Github #2557](Unidata/netcdf-c#2557).
* [Bug Fix] Fix some race conditions due to use of a common file in multiple
shell scripts . See [Github
#2552](Unidata/netcdf-c#2552).
### 4.9.1 - Release Candidate 1 - October 24, 2022
* [Enhancement][Documentation] Add Plugins Quick Start Guide. See
[GitHub #2524](Unidata/netcdf-c#2524) for
more information.
* [Enhancement] Add new entries in `netcdf_meta.h`, `NC_HAS_BLOSC` and
`NC_HAS_BZ2`. See [Github
#2511](Unidata/netcdf-c#2511) and [Github
#2512](Unidata/netcdf-c#2512) for more
information.
* [Enhancement] Add new options to `nc-config`: `--has-multifilters`,
`--has-stdfilters`, `--has-quantize`, `--plugindir`. See [Github
#2509](Unidata/netcdf-c#2509) for more
information.
* [Bug Fix] Fix some errors detected in PR 2497. [PR
#2497](Unidata/netcdf-c#2497) . See [Github
#2503](Unidata/netcdf-c#2503).
* [Bug Fix] Split the remote tests into two parts: one for the
remotetest server and one for all other external servers. Also add a
configure option to enable the latter set. See [Github
#2491](Unidata/netcdf-c#2491).
* [Bug Fix] Fix blosc plugin errors. See [Github
#2461](Unidata/netcdf-c#2461).
* [Bug Fix] Fix support for reading arrays of HDF5 fixed size
strings. See [Github
#2466](Unidata/netcdf-c#2466).
* [Bug Fix] Fix some errors detected in [PR
#2492](Unidata/netcdf-c#2492) . See [Github
#2497](Unidata/netcdf-c#2497).
* [Enhancement] Add support for Zarr (fixed length) string type in
nczarr. See [Github
#2492](Unidata/netcdf-c#2492).
* [Bug Fix] Split the remote tests into two parts: one for the
remotetest server and one for all other external servers. Also add a
configure option to enable the latter set. See [Github
#2491](Unidata/netcdf-c#2491).
* [Bug Fix] Fix support for reading arrays of HDF5 fixed size
strings. See [Github
#2462](Unidata/netcdf-c#2466).
* [Bug Fix] Provide a default enum const when fill value does not
match any enum constant for the value zero. See [Github
#2462](Unidata/netcdf-c#2462).
* [Bug Fix] Fix the json submodule symbol conflicts between libnetcdf
and the plugin specific netcdf_json.h. See [Github
#2448](Unidata/netcdf-c#2448).
* [Bug Fix] Fix quantize with CLASSIC_MODEL files. See [Github
#2405](Unidata/netcdf-c#2445).
* [Enhancement] Add `--disable-quantize` option to `configure`.
* [Bug Fix] Fix CMakeLists.txt to handle all acceptable boolean values
for -DPLUGIN_INSTALL_DIR. See [Github
#2430](Unidata/netcdf-c#2430).
* [Bug Fix] Fix tst_vars3.c to use the proper szip flag. See [Github
#2421](Unidata/netcdf-c#2421).
* [Enhancement] Provide a simple API to allow user access to the
internal .rc file table: supports get/set/overwrite of entries of
the form "key=value". See [Github
#2408](Unidata/netcdf-c#2408).
* [Bug Fix] Use env variable USERPROFILE instead of HOME for windows
and mingw. See [Github
#2405](Unidata/netcdf-c#2405).
* [Bug Fix] Fix the nc_def_var_fletcher32 code in hdf5 to properly
test value of the fletcher32 argument. See [Github
#2403](Unidata/netcdf-c#2403).
## 4.9.0 - June 10, 2022
* [Enhancement] Add quantize functions nc_def_var_quantize() and
nc_inq_var_quantize() to enable lossy compression. See [Github
#1548](Unidata/netcdf-c#1548).
* [Enhancement] Add zstandard compression functions nc_def_var_zstandard() and
nc_inq_var_zstandard(). See [Github
#2173](Unidata/netcdf-c#2173).
* [Enhancement] Have netCDF-4 logging output one file per processor when used
with parallel I/O. See [Github
#1762](Unidata/netcdf-c#1762).
* [Enhancement] Improve filter installation process to avoid use of an extra
shell script. See [Github
#2348](Unidata/netcdf-c#2348).
* [Bug Fix] Get "make distcheck" to work See [Github
#2343](Unidata/netcdf-c#2343).
* [Enhancement] Allow the read/write of JSON-valued Zarr attributes to allow for
domain specific info such as used by GDAL/Zarr. See [Github
#2278](Unidata/netcdf-c#2278).
* [Enhancement] Turn on the XArray convention for NCZarr files by
default. WARNING, this means that the mode should explicitly specify "nczarr"
or "zarr" even if "xarray" or "noxarray" is specified. See [Github
#2257](Unidata/netcdf-c#2257).
* [Enhancement] Update the documentation to match the current filter
capabilities See [Github
#2249](Unidata/netcdf-c#2249).
* [Enhancement] Update the documentation to match the current filter
capabilities. See [Github
#2249](Unidata/netcdf-c#2249).
* [Enhancement] Support installation of pre-built standard filters into
user-specified location. See [Github
#2318](Unidata/netcdf-c#2318).
* [Enhancement] Improve filter support. More specifically (1) add
nc_inq_filter_avail to check if a filter is available, (2) add the notion of
standard filters, (3) cleanup szip support to fix interaction with NCZarr. See
[Github #2245](Unidata/netcdf-c#2245).
* [Enhancement] Switch to tinyxml2 as the default xml parser implementation. See
[Github #2170](Unidata/netcdf-c#2170).
* [Bug Fix] Require that the type of the variable in nc_def_var_filter is not
variable length. See [Github
#/2231](Unidata/netcdf-c#2231).
* [File Change] Apply HDF5 v1.8 format compatibility when writing to previous
files, as well as when creating new files. The superblock version remains at
2 for newly created files. Full backward read/write compatibility for
netCDF-4 is maintained in all cases. See [Github
#2176](Unidata/netcdf-c#2176).
* [Enhancement] Add ability to set dataset alignment for netcdf-4/HDF5
files. See [Github #2206](Unidata/netcdf-c#2206).
* [Bug Fix] Improve UTF8 support on windows so that it can use utf8
natively. See [Github #2222](Unidata/netcdf-c#2222).
* [Enhancement] Add complete bitgroom support to NCZarr. See [Github
#2197](Unidata/netcdf-c#2197).
* [Bug Fix] Clean up the handling of deeply nested VLEN types. Marks
nc_free_vlen() and nc_free_string as deprecated in favor of
ncaux_reclaim_data(). See [Github
#2179](Unidata/netcdf-c#2179).
* [Bug Fix] Make sure that netcdf.h accurately defines the flags in the
open/create mode flags. See [Github
#2183](Unidata/netcdf-c#2183).
* [Enhancement] Improve support for msys2+mingw platform. See [Github
#2171](Unidata/netcdf-c#2171).
* [Bug Fix] Clean up the various inter-test dependencies in ncdump for
CMake. See [Github #2168](Unidata/netcdf-c#2168).
* [Bug Fix] Fix use of non-aws appliances. See [Github
#2152](Unidata/netcdf-c#2152).
* [Enhancement] Added options to suppress the new behavior from [Github
#2135](Unidata/netcdf-c#2135). The options for
`cmake` and `configure` are, respectively `-DENABLE_LIBXML2` and
`--(enable/disable)-libxml2`. Both of these options defaul to 'on/enabled'.
When disabled, the bundled `ezxml` XML interpreter is used regardless of
whether `libxml2` is present on the system.
* [Enhancement] Support optional use of libxml2, otherwise default to ezxml. See
[Github #2135](Unidata/netcdf-c#2135) -- H/T to
[Egbert Eich](https://github.com/e4t).
* [Bug Fix] Fix several os related errors. See [Github
#2138](Unidata/netcdf-c#2138).
* [Enhancement] Support byte-range reading of netcdf-3 files stored in private
buckets in S3. See [Github
#2134](Unidata/netcdf-c#2134)
* [Enhancement] Support Amazon S3 access for NCZarr. Also support use of the
existing Amazon SDK credentials system. See [Github
#2114](Unidata/netcdf-c#2114)
* [Bug Fix] Fix string allocation error in H5FDhttp.c. See [Github
#2127](Unidata/netcdf-c#2127).
* [Bug Fix] Apply patches for ezxml and for selected oss-fuzz detected
errors. See [Github #2125](Unidata/netcdf-c#2125).
* [Bug Fix] Ensure that internal Fortran APIs are always defined. See [Github
#2098](Unidata/netcdf-c#2098).
* [Enhancement] Support filters for NCZarr. See [Github
#2101](Unidata/netcdf-c#2101)
* [Bug Fix] Make PR 2075 long file name be idempotent. See [Github
#2094](Unidata/netcdf-c#2094).
## 4.8.1 - August 18, 2021
* [Bug Fix] Fix multiple bugs in libnczarr. See [Github
#2066](Unidata/netcdf-c#2066).
* [Enhancement] Support windows network paths (e.g. \\svc\...). See [Github
#2065](Unidata/netcdf-c#2065).
* [Enhancement] Convert to a new representation of the NCZarr meta-data
extensions: version 2. Read-only backward compatibility is provided. See
[Github #2032](Unidata/netcdf-c#2032).
* [Bug Fix] Fix dimension_separator bug in libnczarr. See [Github
#2035](Unidata/netcdf-c#2035).
* [Bug Fix] Fix bugs in libdap4. See [Github
#2005](Unidata/netcdf-c#2005).
* [Bug Fix] Store NCZarr fillvalue as a singleton instead of a 1-element
array. See [Github #2017](Unidata/netcdf-c#2017).
* [Bug Fixes] The netcdf-c library was incorrectly determining the scope of
dimension; similar to the type scope problem. See [Github
#2012](Unidata/netcdf-c#2012) for more information.
* [Bug Fix] Re-enable DAP2 authorization testing. See [Github
#2011](Unidata/netcdf-c#2011).
* [Bug Fix] Fix bug with windows version of mkstemp that causes failure to
create more than 26 temp files. See [Github
#1998](Unidata/netcdf-c#1998).
* [Bug Fix] Fix ncdump bug when printing VLENs with basetype char. See [Github
#1986](Unidata/netcdf-c#1986).
* [Bug Fixes] The netcdf-c library was incorrectly determining the scope of
types referred to by nc_inq_type_equal. See [Github
#1959](Unidata/netcdf-c#1959) for more information.
* [Bug Fix] Fix bug in use of XGetopt when building under Mingw. See [Github
#2009](Unidata/netcdf-c#2009).
* [Enhancement] Improve the error reporting when attempting to use a filter for
which no implementation can be found in HDF5_PLUGIN_PATH. See [Github
#2000](Unidata/netcdf-c#2000) for more information.
* [Bug Fix] Fix `make distcheck` issue in `nczarr_test/` directory. See [Github
#2007](Unidata/netcdf-c#2007).
* [Bug Fix] Fix bug in NCclosedir in dpathmgr.c. See [Github
#2003](Unidata/netcdf-c#2003).
* [Bug Fix] Fix bug in ncdump that assumes that there is a relationship between
the total number of dimensions and the max dimension id. See [Github
#2004](Unidata/netcdf-c#2004).
* [Bug Fix] Fix bug in JSON processing of strings with embedded quotes. See
[Github #1993](Unidata/netcdf-c#1993).
* [Enhancement] Add support for the new "dimension_separator" enhancement to
Zarr v2. See [Github #1990](Unidata/netcdf-c#1990) for
more information.
* [Bug Fix] Fix hack for handling failure of shell programs to properly handle
escape characters. See [Github
#1989](Unidata/netcdf-c#1989).
* [Bug Fix] Allow some primitive type names to be used as identifiers depending
on the file format. See [Github
#1984](Unidata/netcdf-c#1984).
* [Enhancement] Add support for reading/writing pure Zarr storage format that
supports the XArray _ARRAY_DIMENSIONS attribute. See [Github
#1952](Unidata/netcdf-c#1952) for more information.
* [Update] Updated version of bzip2 used in filter testing/functionality, in
support of [Github #1969](Unidata/netcdf-c#1969).
* [Bug Fix] Corrected HDF5 version detection logic as described in [Github
#1962](Unidata/netcdf-c#1962).
## 4.8.0 - March 30, 2021
* [Enhancement] Bump the NC_DISPATCH_VERSION from 2 to 3, and as a side effect,
unify the definition of NC_DISPATCH_VERSION so it only needs to be defined in
CMakeLists.txt and configure.ac. See [Github
#1945](Unidata/netcdf-c#1945) for more information.
* [Enhancement] Provide better cross platform path name management. This
converts paths for various platforms (e.g. Windows, MSYS, etc.) so that they
are in the proper format for the executing platform. See [Github
#1958](Unidata/netcdf-c#1958) for more information.
* [Bug Fixes] The nccopy program was treating -d0 as turning deflation on rather
than interpreting it as "turn off deflation". See [Github
#1944](Unidata/netcdf-c#1944) for more information.
* [Enhancement] Add support for storing NCZarr data in zip files. See [Github
#1942](Unidata/netcdf-c#1942) for more information.
* [Bug Fixes] Make fillmismatch the default for DAP2 and DAP4; too many servers
ignore this requirement.
* [Bug Fixes] Fix some memory leaks in NCZarr, fix a bug with long strides in
NCZarr. See [Github #1913](Unidata/netcdf-c#1913) for
more information.
* [Enhancement] Add some optimizations to NCZarr, dosome cleanup of code cruft,
add some NCZarr test cases, add a performance test to NCZarr. See [Github
#1908](Unidata/netcdf-c#1908) for more information.
* [Bug Fix] Implement a better chunk cache system for NCZarr. The cache now uses
extendible hashing plus a linked list for provide a combination of
expandibility, fast access, and LRU behavior. See [Github
#1887](Unidata/netcdf-c#1887) for more information.
* [Enhancement] Provide .rc fields for S3 authentication: HTTP.S3.ACCESSID and
HTTP.S3.SECRETKEY.
* [Enhancement] Give the client control over what parts of a DAP2 URL are URL
encoded (i.e. %xx). This is to support the different decoding rules that
servers apply to incoming URLS. See [Github
#1884](Unidata/netcdf-c#1884) for more information.
* [Bug Fix] Fix incorrect time offsets from `ncdump -t`, in some cases when the
time `units` attribute contains both a **non-zero** time-of-day, and a time
zone suffix containing the letter "T", such as "UTC". See [Github
#1866](Unidata/netcdf-c#1866) for more information.
* [Bug Fix] Cleanup the NCZarr S3 build options. See [Github
#1869](Unidata/netcdf-c#1869) for more information.
* [Bug Fix] Support aligned access for selected ARM processors. See [Github
#1871](Unidata/netcdf-c#1871) for more information.
* [Documentation] Migrated the documents in the NUG/ directory to the dedicated
NUG repository found at https://github.com/Unidata/netcdf
* [Bug Fix] Revert the internal filter code to simplify it. From the user's
point of view, the only visible change should be that (1) the functions that
convert text to filter specs have had their signature reverted and renamed and
have been moved to netcdf_aux.h, and (2) Some filter API functions now return
NC_ENOFILTER when inquiry is made about some filter. Internally, the dispatch
table has been modified to get rid of the complex structures.
* [Bug Fix] If the HDF5 byte-range Virtual File Driver is available )HDf5 1.10.6
or later) then use it because it has better performance than the one currently
built into the netcdf library.
* [Bug Fix] Fixed byte-range support with cURL > 7.69. See
[Unidata/netcdf-c#1798].
* [Enhancement] Added new test for using compression with parallel I/O:
nc_test4/tst_h_par_compress.c. See
[Unidata/netcdf-c#1784].
* [Bug Fix] Don't return error for extra calls to nc_redef() for netCDF/HDF5
files, unless classic model is in use. See
[Unidata/netcdf-c#1779].
* [Enhancement] Added new parallel I/O benchmark program to mimic NOAA UFS data
writes, built when --enable-benchmarks is in configure. See
[Unidata/netcdf-c#1777].
* [Bug Fix] Now allow szip to be used on variables with unlimited dimension
[Unidata/netcdf-c#1774].
* [Enhancement] Add support for cloud storage using a variant of the Zarr
storage format. Warning: this feature is highly experimental and is subject to
rapid evolution
[https://www.unidata.ucar.edu/blogs/developer/en/entry/overview-of-zarr-support-in].
* [Bug Fix] Fix nccopy to properly set default chunking parameters when not
otherwise specified. This can significantly improve performance in selected
cases. Note that if seeing slow performance with nccopy, then, as a
work-around, specifically set the chunking
parameters. [Unidata/netcdf-c#1763].
* [Bug Fix] Fix some protocol bugs/differences between the netcdf-c library and
the OPeNDAP Hyrax server. Also cleanup checksum handling
[https://github.com/Unidata/netcdf-c/issues/1712].* [Bug Fix] IMPORTANT: Ncgen
was not properly handling large data sections. The problem manifests as
incorrect ordering of data in the created file. Aside from examining the file
with ncdump, the error can be detected by running ncgen with the -lc flag (to
produce a C file). Examine the file to see if any variable is written in pieces
as opposed to a single call to nc_put_vara. If multiple calls to nc_put_vara are
used to write a variable, then it is probable that the data order is
incorrect. Such multiple writes can occur for large variables and especially
when one of the dimensions is unlimited.
* [Bug Fix] Add necessary __declspec declarations to allow compilation of netcdf
library without causing errors or (_declspec related) warnings
[Unidata/netcdf-c#1725].
* [Enhancement] When a filter is applied twice with different
parameters, then the second set is used for writing the dataset
[Unidata/netcdf-c#1713].
* [Bug Fix] Now larger cache settings are used for sequential HDF5 file creates/opens on parallel I/O capable builds; see [Github #1716](Unidata/netcdf-c#1716) for more information.
* [Bug Fix] Add functions to libdispatch/dnotnc4.c to support
dispatch table operations that should work for any dispatch
table, even if they do not do anything; functions such as
nc_inq_var_filter [Unidata/netcdf-c#1693].
* [Bug Fix] Fixed a scalar annotation error when scalar == 0; see [Github
#1707](Unidata/netcdf-c#1707) for more information.
* [Bug Fix] Use proper CURLOPT values for VERIFYHOST and VERIFYPEER; the
semantics for VERIFYHOST in particular changed. Documented in NUG/DAP2.md. See
[Unidata/netcdf-c#1684].
* [Bug Fix][cmake] Correct an issue with parallel filter test logic in
CMake-based builds.
* [Bug Fix] Now allow nc_inq_var_deflate()/nc_inq_var_szip() to be called for
all formats, not just HDF5. Non-HDF5 files return NC_NOERR and report no
compression in use. This reverts behavior that was changed in the 4.7.4
release. See [Unidata/netcdf-c#1691].
* [Bug Fix] Compiling on a big-endian machine exposes some missing forward
delcarations in dfilter.c.
* [File Change] Change from HDF5 v1.6 format compatibility, back to v1.8
compatibility, for newly created files. The superblock changes from version 0
back to version 2. An exception is when using libhdf5 deprecated versions
1.10.0 and 1.10.1, which can only create v1.6 compatible format. Full
backward read/write compatibility for netCDF-4 is maintained in all cases.
See [Github #951](Unidata/netcdf-c#951).
## 4.7.4 - March 27, 2020
* [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
[Unidata/netcdf-c#1528].
* [Bug Fix] Correct behavior for the command line utilities when directly
accessing a directory using utf8 characters. See
[Github #1669] (Unidata/netcdf-c#1669),
[Github #1668] (Unidata/netcdf-c#1668) and
[Github #1666] (Unidata/netcdf-c#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
[Unidata/netcdf-c#1644].
* [Enhancement] Support has been added for multiple filters per variable. See
[Unidata/netcdf-c#1584].
* [Enhancement] Now nc_inq_var_szip retuns 0 for parameter values if szip is not
in use for var. See [Unidata/netcdf-c#1618].
* [Enhancement] Now allow parallel I/O with filters, for HDF5-1.10.3 and
later. See [Unidata/netcdf-c#1473].
* [Enhancement] Increased default size of cache buffer to 16 MB, from 4
MB. Increased number of slots to 4133. See
[Unidata/netcdf-c#1541].
* [Enhancement] Allow zlib compression to be used with parallel I/O writes, if
HDF5 version is 1.10.3 or greater. See
[Unidata/netcdf-c#1580].
* [Enhancement] Restore use of szip compression when writing data (including
writing in parallel if HDF5 version is 1.10.3 or greater). See
[Unidata/netcdf-c#1546].
* [Enhancement] Enable use of compact storage option for small vars in
netCDF/HDF5 files. See [Unidata/netcdf-c#1570].
* [Enhancement] Updated benchmarking program bm_file.c to better handle very
large files. See [Unidata/netcdf-c#1555].
* [Enhancement] Added version number to dispatch table, and now check version
with nc_def_user_format(). See
[Unidata/netcdf-c#1599].
* [Bug Fix] Fixed user setting of MPI launcher for parallel I/O HDF5 test in
h5_test. See [Unidata/netcdf-c#1626].
* [Bug Fix] Fixed problem of growing memory when netCDF-4 files were opened and
closed. See [Unidata/netcdf-c#1575 and
Unidata/netcdf-c#1571].
* [Enhancement] Increased size of maximum allowed name in HDF4 files to
NC_MAX_NAME. See [Unidata/netcdf-c#1631].
## 4.7.3 - November 20, 2019
* [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
[Unidata/netcdf-c#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
[Unidata/netcdf-c#1469].
* [Bug Fix] Now testing that endianness can only be set on atomic ints and
floats. See [Unidata/netcdf-c#1479].
* [Bug Fix] Fix for subtle error involving var and unlimited dim of the same
name, but unrelated, in netCDF-4. See
[Unidata/netcdf-c#1496].
* [Enhancement] Update for attribute documentation. See
[Unidata/netcdf-c#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](Unidata/netcdf-c#1484) for more information.
## 4.7.2 - October 22, 2019
* [Bug Fix][Enhancement] Various bug fixes and enhancements.
* [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] (Unidata/netcdf-c#1486) for more information.
* [Enhancement] [Parallel IO] Added support for parallel functions in MSVC. See
[Github #1492](Unidata/netcdf-c#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] (Unidata/netcdf-c#1483) and
[GitHub #1487] (Unidata/netcdf-c#1487) for more information.
## 4.7.1 - August 27, 2019
* [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] (Unidata/netcdf-c#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](Unidata/netcdf-c#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](Unidata/netcdf-c#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](Unidata/netcdf-c#1436).
## 4.7.0 - April 29, 2019
* [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] (Unidata/netcdf-c#1360) and
[Github #1257] (Unidata/netcdf-c#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] (Unidata/netcdf-c#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.
## 4.6.3 - February 28, 2019
* [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](Unidata/netcdf-c#1324) for more information.
* Now always write hidden coordinates attribute, which allows faster file opens
when present. See
[Github #1262](Unidata/netcdf-c#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] (Unidata/netcdf-c#1297).
* Fix of NULL parameter causing segfaults in put_vars functions. See
[Github #1265] (Unidata/netcdf-c#1265) for more information.
* Fix of --enable-benchmark benchmark tests
[Github #1211] (Unidata/netcdf-c#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-related issues on big-endian machines. See
[Github #1321] (Unidata/netcdf-c#1321),
[Github #1302] (Unidata/netcdf-c#1302) for more information.
* [BugFix][Enhancement] Various and sundry bugfixes and performance
enhancements, thanks to \@edhartnett, \@gsjarrdema, \@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](Unidata/netcdf-c#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] (Unidata/netcdf-c#1317) for more
information. See
[Github #1319] (Unidata/netcdf-c#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] (Unidata/netcdf-c#803) for more information.
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This PR subsumes PR #2278.
Actually is a bit an omnibus covering several issues.
PR #2278
Add support for the Zarr string type.
Zarr strings are restricted currently to be of fixed size.
The primary issue to be addressed is to provide a way for user to
specify the size of the fixed length strings. This is handled by providing
the following new attributes special:
This PR also requires some hacking to handle the existing netcdf-c NC_CHAR
type, which does not exist in zarr. The goal was to choose numpy types for
both the netcdf-c NC_STRING type and the netcdf-c NC_CHAR type such that
if a pure zarr implementation reads them, it would still work and an
NC_CHAR type would be handled by zarr as a string of length 1.
For writing variables and NCZarr attributes, the type mapping is as follows:
Note that it is a bit of a hack to use endianness, but it should be ok since for string/char, the endianness has no meaning.
For reading attributes with pure zarr (i.e. with no nczarr
atribute types defined), they will always be interpreted as of
type NC_CHAR.
Issue: #2474
This PR partly fixes this issue because it provided more
comprehensive support for Zarr attributes that are JSON valued expressions.
This PR still does not address the problem in that issue where the
_ARRAY_DIMENSION attribute is incorrectly set. Than can only be
fixed by the creator of the datasets.
Issue: #2485
This PR also fixes the scalar failure shown in this issue.
It generally cleans up scalar handling.
It also adds a note to the documentation describing that
NCZarr supports scalars while Zarr does not and also how
scalar interoperability is achieved.
Misc. Other Changes