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netcdf-c/nczarr_test
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Dennis Heimbigner 11fe00ea05 Add filter support to NCZarr 
Filter support has three goals:

1. Use the existing HDF5 filter implementations,
2. Allow filter metadata to be stored in the NumCodecs metadata format used by Zarr,
3. Allow filters to be used even when HDF5 is disabled

Detailed usage directions are define in docs/filters.md.

For now, the existing filter API is left in place. So filters
are defined using ''nc_def_var_filter'' using the HDF5 style
where the id and parameters are unsigned integers.

This is a big change since filters affect many parts of the code.

In the following, the terms "compressor" and "filter" and "codec" are generally
used synonomously.

### Filter-Related Changes:
* In order to support dynamic loading of shared filter libraries, a new library was added in the libncpoco directory; it helps to isolate dynamic loading across multiple platforms.
* Provide a json parsing library for use by plugins; this is created by merging libdispatch/ncjson.c with include/ncjson.h.
* Add a new _Codecs attribute to allow clients to see what codecs are being used; let ncdump -s print it out.
* Provide special headers to help support compilation of HDF5 filters when HDF5 is not enabled: netcdf_filter_hdf5_build.h and netcdf_filter_build.h.
* Add a number of new test to test the new nczarr filters.
* Let ncgen parse _Codecs attribute, although it is ignored.

### Plugin directory changes:
* Add support for the Blosc compressor; this is essential because it is the most common compressor used in Zarr datasets. This also necessitated adding a CMake FindBlosc.cmake file
* Add NCZarr support for the big-four filters provided by HDF5: shuffle, fletcher32, deflate (zlib), and szip
* Add a Codec defaulter (see docs/filters.md) for the big four filters.
* Make plugins work with windows by properly adding __declspec declaration.

### Misc. Non-Filter Changes
* Replace most uses of USE_NETCDF4 (deprecated) with USE_HDF5.
* Improve support for caching
* More fixes for path conversion code
* Fix misc. memory leaks
* Add new utility -- ncdump/ncpathcvt -- that does more or less the same thing as cygpath.
* Add a number of new test to test the non-filter fixes.
* Update the parsers
* Convert most instances of '#ifdef _MSC_VER' to '#ifdef _WIN32'
2021-09-02 17:04:26 -06:00
..
refs
bm_chunks3.c Additional Fixes to NCZarr 2020-12-16 20:48:02 -07:00
bm_timer.h Add missing files so --enable-benchmarks works again. 2021-08-07 21:19:40 -06:00
bm_utils.c Add missing files so --enable-benchmarks works again. 2021-08-07 21:19:40 -06:00
bm_utils.h Add missing files so --enable-benchmarks works again. 2021-08-07 21:19:40 -06:00
CMakeLists.txt Add filter support to NCZarr 2021-09-02 17:04:26 -06:00
Makefile.am Add filter support to NCZarr 2021-09-02 17:04:26 -06:00
ncdumpchunks.c Merge branch 'master' into eliminate_need_for_hdf5-1.6-API 2021-05-28 07:11:13 -06:00
ref_any.cdl Add filter support to NCZarr 2021-09-02 17:04:26 -06:00
ref_avail1.cdl More NCZarr optimizations 2021-01-06 13:35:59 -07:00
ref_avail1.dmp More NCZarr optimizations 2021-01-06 13:35:59 -07:00
ref_avail1.txt More NCZarr optimizations 2021-01-06 13:35:59 -07:00
ref_blosc_zmap.txt Add filter support to NCZarr 2021-09-02 17:04:26 -06:00
ref_byte_fill_value_null.cdl Add filter support to NCZarr 2021-09-02 17:04:26 -06:00
ref_byte_fill_value_null.zarr.zip Add filter support to NCZarr 2021-09-02 17:04:26 -06:00
ref_byte.cdl Add test cases 2021-08-10 14:15:24 -06:00
ref_byte.zarr.zip Add test cases 2021-08-10 14:15:24 -06:00
ref_bzip2.cdl Add filter support to NCZarr 2021-09-02 17:04:26 -06:00
ref_fillonly.cdl Fix error where not converting fill data 2020-09-12 14:49:59 -06:00
ref_filtered.cdl Add filter support to NCZarr 2021-09-02 17:04:26 -06:00
ref_groups_regular.cdl Add test cases 2021-08-10 14:15:24 -06:00
ref_groups.h5 Add test cases 2021-08-10 14:15:24 -06:00
ref_misc1.cdl Fix some additional edges cases for mapping slices to chunks 2020-12-19 21:17:46 -07:00
ref_misc1.dmp More NCZarr optimizations 2021-01-06 13:35:59 -07:00
ref_misc2.cdl Add filter support to NCZarr 2021-09-02 17:04:26 -06:00
ref_multi.cdl Add filter support to NCZarr 2021-09-02 17:04:26 -06:00
ref_nczarr2zarr.cdl Add filter support to NCZarr 2021-09-02 17:04:26 -06:00
ref_ndims.cdl Fix some additional edges cases for mapping slices to chunks 2020-12-19 21:17:46 -07:00
ref_ndims.dmp More NCZarr optimizations 2021-01-06 13:35:59 -07:00
ref_newformatpure.cdl Add filter support to NCZarr 2021-09-02 17:04:26 -06:00
ref_oldformat.cdl Move to Version 2 NCZarr Extended Meta-Data 2021-07-17 16:55:30 -06:00
ref_oldformat.zip Fix bad chunkpath calculation 2021-07-18 16:20:22 -06:00
ref_perdimspecs.cdl Provide a Number of fixes/improvements to NCZarr 2020-11-19 17:01:04 -07:00
ref_power_901_constants.cdl Fix JSON quoted string processing in libnczarr 2021-05-06 16:39:44 -06:00
ref_power_901_constants.zip Fix JSON quoted string processing in libnczarr 2021-05-06 16:39:44 -06:00
ref_purezarr_base.cdl Add support for the XArray Zarr _ARRAY_DIMENSIONS attribute 2021-02-24 13:46:11 -07:00
ref_purezarr.cdl Add filter support to NCZarr 2021-09-02 17:04:26 -06:00
ref_quotes.cdl Fix JSON quoted string processing in libnczarr 2021-05-06 16:39:44 -06:00
ref_quotes.zip Fix JSON quoted string processing in libnczarr 2021-05-06 16:39:44 -06:00
ref_rem.cdl Fix some additional edges cases for mapping slices to chunks 2020-12-19 21:17:46 -07:00
ref_rem.dmp More NCZarr optimizations 2021-01-06 13:35:59 -07:00
ref_skip.cdl Additional Fixes to NCZarr 2020-12-16 20:48:02 -07:00
ref_skip.txt More NCZarr optimizations 2021-01-06 13:35:59 -07:00
ref_skipw.cdl Fix some additional edges cases for mapping slices to chunks 2020-12-19 21:17:46 -07:00
ref_t_meta_dim1.cdl
ref_t_meta_var1.cdl
ref_ut_json_build.txt
ref_ut_json_parse.txt
ref_ut_map_create.cdl Add zip file support 2021-01-28 20:11:01 -07:00
ref_ut_map_readdata_nz4.txt
ref_ut_map_readmeta2.txt Add support for the XArray Zarr _ARRAY_DIMENSIONS attribute 2021-02-24 13:46:11 -07:00
ref_ut_map_readmeta_nz4.txt
ref_ut_map_readmeta_nzf.txt
ref_ut_map_readmeta.txt Add zip file support 2021-01-28 20:11:01 -07:00
ref_ut_map_search_nz4.txt Revert "Revert "Fix nczarr-experimental: improve build support, disengage hdf5 vs netcdf4 flags, and find AWS libraries"" 2020-08-17 19:15:47 -06:00
ref_ut_map_search_nzf.txt Revert "Revert "Fix nczarr-experimental: improve build support, disengage hdf5 vs netcdf4 flags, and find AWS libraries"" 2020-08-17 19:15:47 -06:00
ref_ut_map_search.txt Add support for the XArray Zarr _ARRAY_DIMENSIONS attribute 2021-02-24 13:46:11 -07:00
ref_ut_map_writedata.cdl Add support for the XArray Zarr _ARRAY_DIMENSIONS attribute 2021-02-24 13:46:11 -07:00
ref_ut_map_writemeta2.cdl Add support for the XArray Zarr _ARRAY_DIMENSIONS attribute 2021-02-24 13:46:11 -07:00
ref_ut_map_writemeta.cdl Add zip file support 2021-01-28 20:11:01 -07:00
ref_ut_mapapi_create.cdl Add zip file support 2021-01-28 20:11:01 -07:00
ref_ut_mapapi_data.cdl Add zip file support 2021-01-28 20:11:01 -07:00
ref_ut_mapapi_meta.cdl Add zip file support 2021-01-28 20:11:01 -07:00
ref_ut_mapapi_search_nz4.txt Revert "Revert "Fix nczarr-experimental: improve build support, disengage hdf5 vs netcdf4 flags, and find AWS libraries"" 2020-08-17 19:15:47 -06:00
ref_ut_mapapi_search_nzf.txt Revert "Revert "Fix nczarr-experimental: improve build support, disengage hdf5 vs netcdf4 flags, and find AWS libraries"" 2020-08-17 19:15:47 -06:00
ref_ut_mapapi_search_s3.txt
ref_ut_mapapi_search.txt Add zip file support 2021-01-28 20:11:01 -07:00
ref_ut_proj.txt More NCZarr optimizations 2021-01-06 13:35:59 -07:00
ref_ut_testmap_create.cdl Add zip file support 2021-01-28 20:11:01 -07:00
ref_whole.cdl More NCZarr optimizations 2021-01-06 13:35:59 -07:00
ref_whole.txt More NCZarr optimizations 2021-01-06 13:35:59 -07:00
ref_xarray.cdl Add filter support to NCZarr 2021-09-02 17:04:26 -06:00
run_chunkcases.sh Upgrade the nczarr code to match Zarr V2 2021-04-24 19:48:15 -06:00
run_fillonlyz.sh Add zip file support 2021-01-28 20:11:01 -07:00
run_filter.sh Add filter support to NCZarr 2021-09-02 17:04:26 -06:00
run_interop.sh Fix JSON quoted string processing in libnczarr 2021-05-06 16:39:44 -06:00
run_it_chunks1.sh Add zip file support 2021-01-28 20:11:01 -07:00
run_misc.sh Add test cases 2021-08-10 14:15:24 -06:00
run_nccopyz.sh More modification in support of #1940 2021-03-09 10:49:30 -07:00
run_ncgen4.sh Add filter support to NCZarr 2021-09-02 17:04:26 -06:00
run_nczarr_fill.sh Add test cases 2021-08-10 14:15:24 -06:00
run_newformat.sh Move to Version 2 NCZarr Extended Meta-Data 2021-07-17 16:55:30 -06:00
run_perf_chunks1.sh Add zip file support 2021-01-28 20:11:01 -07:00
run_purezarr.sh Upgrade the nczarr code to match Zarr V2 2021-04-24 19:48:15 -06:00
run_s3_cleanup.sh Add zip file support 2021-01-28 20:11:01 -07:00
run_specific_filters.sh Add filter support to NCZarr 2021-09-02 17:04:26 -06:00
run_ut_chunk.sh Revert "Revert "Fix nczarr-experimental: improve build support, disengage hdf5 vs netcdf4 flags, and find AWS libraries"" 2020-08-17 19:15:47 -06:00
run_ut_map.sh Add zip file support 2021-01-28 20:11:01 -07:00
run_ut_mapapi.sh Add filter support to NCZarr 2021-09-02 17:04:26 -06:00
run_ut_misc.sh Revert "Revert "Fix nczarr-experimental: improve build support, disengage hdf5 vs netcdf4 flags, and find AWS libraries"" 2020-08-17 19:15:47 -06:00
s3util.c Fix Mingw versus XGetopt (again) 2021-05-26 14:27:27 -06:00
test_nczarr_utils.h Add filter support to NCZarr 2021-09-02 17:04:26 -06:00
test_nczarr.sh Add filter support to NCZarr 2021-09-02 17:04:26 -06:00
testfilter_misc.c Add filter support to NCZarr 2021-09-02 17:04:26 -06:00
testfilter_multi.c Add filter support to NCZarr 2021-09-02 17:04:26 -06:00
testfilter_order.c Add filter support to NCZarr 2021-09-02 17:04:26 -06:00
testfilter_repeat.c Add filter support to NCZarr 2021-09-02 17:04:26 -06:00
testfilter.c Add filter support to NCZarr 2021-09-02 17:04:26 -06:00
tst_chunkcases.c Add zip file support 2021-01-28 20:11:01 -07:00
tst_fillonlyz.c Add zip file support 2021-01-28 20:11:01 -07:00
tst_nczfilter.c Add filter support to NCZarr 2021-09-02 17:04:26 -06:00
tst_utils.c Merge branch 'master' into eliminate_need_for_hdf5-1.6-API 2021-05-28 07:11:13 -06:00
tst_utils.h Add zip file support 2021-01-28 20:11:01 -07:00
tst_zchunks2.c Additional Fixes to NCZarr 2020-12-16 20:48:02 -07:00
tst_zchunks3.c Add zip file support 2021-01-28 20:11:01 -07:00
tst_zchunks.c Additional Fixes to NCZarr 2020-12-16 20:48:02 -07:00
ut_chunking.c Fix some additional edges cases for mapping slices to chunks 2020-12-19 21:17:46 -07:00
ut_includes.h Fix bad chunkpath calculation 2021-07-18 16:20:22 -06:00
ut_json.c Add filter support to NCZarr 2021-09-02 17:04:26 -06:00
ut_map.c Move to Version 2 NCZarr Extended Meta-Data 2021-07-17 16:55:30 -06:00
ut_mapapi.c Move to Version 2 NCZarr Extended Meta-Data 2021-07-17 16:55:30 -06:00
ut_projections.c Fix some additional edges cases for mapping slices to chunks 2020-12-19 21:17:46 -07:00
ut_projtest.h
ut_test.c Fix Mingw versus XGetopt (again) 2021-05-26 14:27:27 -06:00
ut_test.h Provide a Number of fixes/improvements to NCZarr 2020-11-19 17:01:04 -07:00
ut_util.c Add zip file support 2021-01-28 20:11:01 -07:00
ut_util.h Fix some additional edges cases for mapping slices to chunks 2020-12-19 21:17:46 -07:00
z4dump.c
zhex.c Add zip file support 2021-01-28 20:11:01 -07:00
zisjson.c Move to Version 2 NCZarr Extended Meta-Data 2021-07-17 16:55:30 -06:00
zmapio.c Move to Version 2 NCZarr Extended Meta-Data 2021-07-17 16:55:30 -06:00
zs3parse.c Fix Mingw versus XGetopt (again) 2021-05-26 14:27:27 -06:00