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'
The netcdf-c code has to deal with a variety of platforms:
Windows, OSX, Linux, Cygwin, MSYS, etc. These platforms differ
significantly in the kind of file paths that they accept. So in
order to handle this, I have created a set of replacements for
the most common file system operations such as _open_ or _fopen_
or _access_ to manage the file path differences correctly.
A more limited version of this idea was already implemented via
the ncwinpath.h and dwinpath.c code. So this can be viewed as a
replacement for that code. And in path in many cases, the only
change that was required was to replace '#include <ncwinpath.h>'
with '#include <ncpathmgt.h>' and then replace file operation
calls with the NCxxx equivalent from ncpathmgr.h Note that
recently, the ncwinpath.h was renamed ncpathmgmt.h, so this pull
request should not require dealing with winpath.
The heart of the change is include/ncpathmgmt.h, which provides
alternate operations such as NCfopen or NCaccess and which properly
parse and rebuild path arguments to work for the platform on which
the code is executing. This mostly matters for Windows because of the
way that it uses backslash and drive letters, as compared to *nix*.
One important feature is that the user can do string manipulations
on a file path without having to worry too much about the platform
because the path management code will properly handle most mixed cases.
So one can for example concatenate a path suffix that uses forward
slashes to a Windows path and have it work correctly.
The conversion code is in libdispatch/dpathmgr.c, and the
important function there is NCpathcvt which does the proper
conversions to the local path format.
As a rule, most code should just replace their file operations with
the corresponding NCxxx ones defined in include/ncpathmgmt.h. These
NCxxx functions all call NCpathcvt on their path arguments before
executing the actual file operation.
In some rare cases, the client may need to directly use NCpathcvt,
but this should be avoided as much as possible. If there is a need
for supporting a new file operation not already in ncpathmgmt.h, then
use the code in dpathmgr.c as a template. Also please notify Unidata
so we can include it as a formal part or our supported operations.
Also, if you see an operation in the library that is not using the
NCxxx form, then please submit an issue so we can fix it.
Misc. Changes:
* Clean up the utf8 testing code; it is impossible to get some
tests to work under windows using shell scripts; the args do
not pass as utf8 but as some other encoding.
* Added an extra utf8 test case: test_unicode_path.sh
* Add a true test for HDF5 1.10.6 or later because as noted in
PR https://github.com/Unidata/netcdf-c/pull/1794,
HDF5 changed its Windows file path handling.
The primary change is to support the use of a zip file as a
storage format. Simultaneously the .nz4 support is made obsolete
Use of zip requires the libzip support library, so a number of
changes to the build files (Makefile.am, CMakeLists.txt) are
necessary to locate and incorporate libzip. The nczarr_tests
tests are also changed to add zip testing.
Other changes:
* Make sure distcheck leaves no files around.
* Add some functions to netcdf_aux to export some functions of libnetcdf.
* Add a new error NC_EFOUND as the complement of NC_EEMPTY.
* Add tracing support to nclog and use it in libnczarr.
* Modify the zmap interface to support the writeonce semantics of zip.
* Create a new s3util.c to support a variety of S3 auxilliary functions.
* EXTERNL'ize a number of functions so they can be used in s3util.
* Add support for the S3 ListObjects CommonPrefixes mechanism
to improve search.
* Add experimental support for running nczarr X s3 tests against
the actual Amazon S3 cloud.
There were some irregularities in the flags for handling NCZarr S3 support.
The primary change is to regularize the flags controlling this to the following.
1. Automake: --enable-nczarr-s3 and CMake: ENABLE_NCZARR_S3
2. Automake: --enable-nczarr-s3-tests and CMake: ENABLE_NCZARR_S3_TESTS
Flag 1 indicates that NCZarr should be built with S3 support enabled.
Flag 2 indicates that the NCZarr S3 tests should be run
These two flags are separate because running the NCZarr S3 tests
requires access to protected S3 resources. Currently, running
these tests is restricted to Unidata personnel. However, users
may want to enable S3 support even if they cannot run the tests.
It is, of course, an error to specify 2 without specifying 1.
Additionally, if the AWS S3 SDK library is not found, then the NCZARR S3
support and testing must be disabled. Otherwise an error is signaled
during the build.
Some of these NCZarr and S3 changes are propagated to nc-config.
Misc. Other Changes:
1. Allow testing for CYGWIN or MSVC in shell scripts.
2. Add specific test for HDF5 library version 1.10.6.
This is encoded as "HDF5_UTF8_PATHS" because that is the first
version where HDF5 properly supports it under Windows. This is used
in hdf5internal/nc4_ndf5_ansi_to_utf8.
3. Add a AM Conditional -- AX_IGNORE -- for use in testing
when it is desirable to temporarily suppress Makefile code.
4. Add MULTIFILTER flag to CMakeLists.txt
disengagement of enable-netcdf4 from enable-hdf5.
That is, with the advent of nczarr, it is possible
to turn off hdf5 but still need netcdf-4 enabled
because nczarr uses libsrc4, but not libhdf5.
This change involves a bunch of things:
1. Modify configure.ac and CMakelist to make enable_hdf5
control if hdf5 support is provided. For back compatibility,
disable-netcdf4 is treated as disable-hdf5. But internally,
netcdf4 support is controlled only by the enabling of formats
that require it.
2. In support of #1, modify .travis.yml to use enable/disable-hdf5
instead of enable/disable-netcdf4.
3. test_common.in is modified to track selected features,
including enable-hdf5 and enable-s3-tests. This is used in
selected tests that mix netcdf-3 and netcdf4 tests.
4. The conflation of USE_HDF5 and USE_NETCDF4 is common in
code, tests, and build files, so all of those had to be weeded out.
5. It turns out that some of the NC4_dim functions really are HDF5 specific,
but are not treated as such. So they are moved from nc4dim.c to
hdf5dim.c or hdf5dispatch.c
6. Some generic functions in libhdf5 can be (and were) moved to libsrc4.
2. Fixed plugin building (nc_test4/hdf5plugins)
to be done properly by cmake and automake.
4. Duplicated part of the nc_test4 filter test code
in examples/C
An incomplete and untested set of hooks exist
for OS-X in nc_test4/findplugins.in. They need testing.
The problem was that for opendap, it is possible to use keywords
as identifiers
when there is no ambiguity. However, the DAP2
parser lost the case of the identifier used the lower case version.
Fix is to use the actual text of the symbol when it is used as an identifier.
Also added a test case for this (kwcase.*).
Additionally cleaned up some misc. dap2 testing problems.
1. ncdap_test/tst_ncdap3.sh was using an empty test set.
restored the testing of datasets.
2. as a consequence of #1, some tests needed to be updated with minor
tweeks.
3. fix dapmerge to handle multiple DODS_EXTRAS attributes.
4. modify buildattribute to suppress nul characters and terminate
the name at the first nul.
5. clean up various test scripts to remove residual, unused
references to obsolete netcdf-4 translation.
6. export e.g. NCDUMP from test_common.in so that non-top-level
shell scripts can access it.
1. Cleanup test_common.sh to expunge (mostly) the use of the VS
path value. This has the effect of being unable to use the
Visual Studio C compiler for shell tests.
2. There is a missing case in CMakeLists.txt so add
defaulting for HDF5_C_LIBRARY_hdf5 using HDF5_C_LIBRARY.
Ward should probably examine this to get it fixed correctly.
3. Put back ref to esg.md in docs/Doxyfile.in
4. Fix minor warning in dut8proc.h
1. When running under windows (as opposed to cygwin)
we need to make sure to not user /cygdrive/ file paths.
This was ocurring in libdap4/d4read.c, but may occur
elsewhere.
2. Shell scripts in the git repo are not being checked-out
with the executable mode set. Had core.filemode set to false.
Was a major hassle to fix.
Specific changes:
1. Add dap4 code: libdap4 and dap4_test.
Note that until the d4ts server problem is solved, dap4 is turned off.
2. Modify various files to support dap4 flags:
configure.ac, Makefile.am, CMakeLists.txt, etc.
3. Add nc_test/test_common.sh. This centralizes
the handling of the locations of various
things in the build tree: e.g. where is
ncgen.exe located. See nc_test/test_common.sh
for details.
4. Modify .sh files to use test_common.sh
5. Obsolete separate oc2 by moving it to be part of
netcdf-c. This means replacing code with netcdf-c
equivalents.
5. Add --with-testserver to configure.ac to allow
override of the servers to be used for --enable-dap-remote-tests.
6. There were multiple versions of nctypealignment code. Try to
centralize in libdispatch/doffset.c and include/ncoffsets.h
7. Add a unit test for the ncuri code because of its complexity.
8. Move the findserver code out of libdispatch and into
a separate, self contained program in ncdap_test and dap4_test.
9. Move the dispatch header files (nc{3,4}dispatch.h) to
.../include because they are now shared by modules.
10. Revamp the handling of TOPSRCDIR and TOPBUILDDIR for shell scripts.
11. Make use of MREMAP if available
12. Misc. minor changes e.g.
- #include <config.h> -> #include "config.h"
- Add some no-install headers to /include
- extern -> EXTERNL and vice versa as needed
- misc header cleanup
- clean up checking for misc. unix vs microsoft functions
13. Change copyright decls in some files to point to LICENSE file.
14. Add notes to RELEASENOTES.md
