Most changes are to get plugins working.
libdispatchdreg.c went in in unidata/netcdf-c#2460,
after I'd done it here.
Summary of individual changes below.
BLD: Remove declspec(dllexport); in dreg.c.
By removing the explicit handling, the automatic handling
(equivalent to --export-all-symbols with recent GNU tools)
will be enabled again, so the generated library will have
more than one function exported.
BLD: Link plugins against libnetcdf on Cygwin.
BLD: Add AM_LDFLAGS to plugin _LDFLAGS to pass -no-undefined.
BLD: Link ncz*filters plugins against libnetcdf.
BLD: Add AM_LDFLAGS to test plugin _LDFLAGS.
Also move rpath from AM_LDFLAGS to test plugin _LDFLAGS.
TST: Don't run nczarr_test/run_specific_filters.sh on Cygwin.
It takes over half an hour to complete, where the others take a minute or less.
TST: Try to find the hanging Cygwin test.
re: Issue https://github.com/Unidata/netcdf-c/issues/2502
H/T Charlie Zender
* Fix NCZarr handling of endianness value NC_ENDIAN_NATIVE. This now matches how it is handled in libhdf5
* Fix NCZarr handling of char typed attribute with value "". This now matches how it is handled in libhdf5
* Add test for various char attribute values
* Change the mapping of NC_CHAR and NC_STRING to dtype; requires changing some test files also.
* Optimize the testing for NC_ENOTBUILT in NC_open.
* Turn off debugging left on accidentally
* Fix memory leak in tst_pnetcdf.c
* Fix blosc test
re: PR https://github.com/Unidata/netcdf-c/pull/2492
re: Issue https://github.com/Unidata/netcdf-c/issues/2494
This PR fixes some problems with the pull request https://github.com/Unidata/netcdf-c/pull/2492 in response to Issue https://github.com/Unidata/netcdf-c/issues/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"
* re: https://github.com/Unidata/netcdf-c/pull/2278
* re: https://github.com/Unidata/netcdf-c/issues/2485
* re: https://github.com/Unidata/netcdf-c/issues/2474
This PR subsumes PR https://github.com/Unidata/netcdf-c/pull/2278.
Actually is a bit an omnibus covering several issues.
## PR https://github.com/Unidata/netcdf-c/pull/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: https://github.com/Unidata/netcdf-c/issues/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: https://github.com/Unidata/netcdf-c/issues/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.
## Overwriting
I think I solved the file overwrite problem by doing light name
mangling of the shared library names. With this change the probabilty
is very small that installing our filter wrappers in a directory will
overwrite code produced by others.
## Default Install Location
I have setup the --with-plugin-dir option default to install in
the following locations in order of preference
1. If HDF5_PLUGIN_PATH is defined (at build time remember), then the last directory in that path will be where the filter wrapper shared libraries will be installed.
2. Otherwise the default is "/usr/local/hdf5/lib/plugin" (on *nix*) or "%ALLUSERSPROFILE%\\hdf5\\lib\\plugin" for Windows or Mingw.
Currently, --with-plugin-dir is disabled by default.
I should note that even if I enable it by default, installing
netcdf-c will still not run "out of the box" because the hypothetical
naive user will not know which compressor libraries need to be
pre-installed before netcdf is installed. Nor will that user have any
way to find out what needs to be installed.
re: https://github.com/Unidata/netcdf-c/issues/2338
re: https://github.com/Unidata/netcdf-c/issues/2294
In issue https://github.com/Unidata/netcdf-c/issues/2338,
Ed Hartnett suggested a better way to install filters to a user
defined location -- for Automake, anyway.
This PR implements that suggestion. It turns out to be more
complicated than it appears, so there are fair number of changes;
mostly to shell scripts. Most of the change is in plugins/Makefile.am.
NOTE: this PR still does NOT address the use of HDF5_PLUGIN_PATH
as the default; this turns out to be complex when dealing with NCZarr.
So this will be addressed in a subsequent post 4.9.0 PR.
## Misc. Changes
1. Record the occurrences of incomplete codecs in libnczarr so that
they can be included in _Codecs attribute correctly. This allows
users to see what missing filters are referenced in the Zarr file.
Primarily affects libnczarr/zfilter.[ch]. Also required creating a
new no-effect filter: H5Zunknown.c.
2. Move the unknown filter test to a separate test file.
3. Incorporates PR https://github.com/Unidata/netcdf-c/pull/2343
re: https://github.com/Unidata/netcdf-c/issues/2294
Ed Hartnett suggested that the netcdf library installation process
be extended to install the standard filters into a user specified
location. The user can then set HDF5_PLUGIN_PATH to that location.
This PR provides that capability using:
````
configure option: --with-plugin-dir=<absolute directory path>
cmake option: -DPLUGIN_INSTALL_DIR=<absolute directory path>
````
Currently, the following plugins are always installed, if
available: bzip2, zstd, blosc.
If NCZarr is enabled, then additional plugins are installed:
fletcher32, shuffle, deflate, szip.
Additionally, the necessary codec support is installed
for each of the above filters that is installed.
## Changes:
1. Cleanup handling of built-in bzip2.
2. Add documentation to docs/filters.md
3. Re-factor the NCZarr codec libraries
4. Add a test, although it can only be exercised after
the library is installed, so it cannot be used during
normal testing.
5. Cleanup use of HDF5_PLUGIN_PATH in the filter test cases.
A number of other packages that read/write Zarr insert
attributes whose value is a dictionary containing specialized
information. An example is the GDAL Driver convention (see
https://gdal.org/drivers/raster/zarr.html).
In order to handle such attributes, this PR enforces a special
convention. It applies to both pure Zarr an NCZarr format as
written by the netdf-c library.
The convention is as follows:
## Reading
Suppose an attribute is read from *.zattrs* and it has a JSON
value that is a a dictionary. In this case, the JSON dictionary
is converted to a string value. It then appears in the netcdf-c
API as if it is a character valued attribute of the same name,
and whose value is the "stringified" dictionary.
# Writing
Suppose an attribute is of type character and its *value* *looks like*
a JSON dictionary. In this case, it is parsed to JSON
and written as the value of the attribute in the NCZarr file.
Here the *value* is the concatenation of all the characters
in the attributes netcdf-c value.
The term "looks like" means that the *value*'s first character is
"{", its last value is "}", and it can be successfully parsed
by a JSON parser.
A test case, *nczarr_test/run_jsonconventions.sh* was also added.
## Misc. Unrelated Changes
1. Fix an error in nc_test4/tst_broken_files.c
2. Modify the internal JSON parser API.
3. Modify the nczarr_test/zisjson program is modified to support
this convention.
re: https://github.com/pydata/xarray/issues/6374
As a result of a discussion about Xarray (see above issue),
I decided to turn on the xarray convention for NCZarr datasets
where possible so that xarray can read a larger set of nczarr
generated datasets.
This causes the following changes:
* If the user wants to generate a pure zarr file, then the mode "zarr" must be explicitly used; it is no longer the case that "mode=xarray" or mode="noxarray"
implies "mode=zarr".
* It is still the case that "mode=noxarray" will turn off the XArray convention.
The following conditions will cause ''_ARRAY_DIMENSIONS'' to not be written.
* The variable is not in the root group,
* Any dimension referenced by the variable is not in the root group.
re: Discussion https://github.com/Unidata/netcdf-c/discussions/2214
The primary change is to support so-called "standard filters".
A standard filter is one that is defined by the following
netcdf-c API:
````
int nc_def_var_XXX(int ncid, int varid, size_t nparams, unsigned* params);
int nc_inq_var_XXXX(int ncid, int varid, int* usefilterp, unsigned* params);
````
So for example, zstandard would be a standard filter by defining
the functions *nc_def_var_zstandard* and *nc_inq_var_zstandard*.
In order to define these functions, we need a new dispatch function:
````
int nc_inq_filter_avail(int ncid, unsigned filterid);
````
This function, combined with the existing filter API can be used
to implement arbitrary standard filters using a simple code pattern.
Note that I would have preferred that this function return a list
of all available filters, but HDF5 does not support that functionality.
So this PR implements the dispatch function and implements
the following standard functions:
+ bzip2
+ zstandard
+ blosc
Specific test cases are also provided for HDF5 and NCZarr.
Over time, other specific standard filters will be defined.
## Primary Changes
* Add nc_inq_filter_avail() to netcdf-c API.
* Add standard filter implementations to test use of *nc_inq_filter_avail*.
* Bump the dispatch table version number and add to all the relevant
dispatch tables (libsrc, libsrcp, etc).
* Create a program to invoke nc_inq_filter_avail so that it is accessible
to shell scripts.
* Cleanup szip support to properly support szip
when HDF5 is disabled. This involves detecting
libsz separately from testing if HDF5 supports szip.
* Integrate shuffle and fletcher32 into the existing
filter API. This means that, for example, nc_def_var_fletcher32
is now a wrapper around nc_def_var_filter.
* Extend the Codec defaulting to allow multiple default shared libraries.
## Misc. Changes
* Modify configure.ac/CMakeLists.txt to look for the relevant
libraries implementing standard filters.
* Modify libnetcdf.settings to list available standard filters
(including deflate and szip).
* Add CMake test modules to locate libbz2 and libzstd.
* Cleanup the HDF5 memory manager function use in the plugins.
* remove unused file include//ncfilter.h
* remove tests for the HDF5 memory operations e.g. H5allocate_memory.
* Add flag to ncdump to force use of _Filter instead of _Deflate
or _Shuffle or _Fletcher32. Used for testing.
re: https://github.com/Unidata/netcdf-c/issues/2189
Compression of a variable whose type is variable length
fails for all current filters. This is because at some point,
the compression buffer will contain pointers to data instead
of the actual data. Compression of pointers of course is meaningless.
The PR changes the behavior of nc_def_var_filter so that it will
fail with error NC_EFILTER if an attempt is made to add a filter
to a variable whose type is variable-length.
A variable is variable-length if it is of type string or VLEN
or transitively (via a compound type) contains a string or VLEN.
Also added a test case for this.
## Misc Changes
1. Turn off a number of debugging statements
re: Issue https://github.com/Unidata/netcdf-c/issues/2190
The primary purpose of this PR is to improve the utf8 support
for windows. This is persuant to a change in Windows that
supports utf8 natively (almost). The almost means that it is
still utf16 internally and the set of characters representable
by utf8 is larger than those representable by utf16.
This leaves open the question in the Issue about handling
the Windows 1252 character set.
This required the following changes:
1. Test the Windows build and major version in order to see if
native utf8 is supported.
2. If native utf8 is supported, Modify dpathmgr.c to call the 8-bit
version of the windows fopen() and open() functions.
3. In support of this, programs that use XGetOpt (Windows versions)
need to get the command line as utf8 and then parse to
arc+argv as utf8. This requires using a homegrown command line parser
named XCommandLineToArgvA.
4. Add a utility program called "acpget" that prints out the
current Windows code page and locale.
Additionally, some technical debt was cleaned up as follows:
1. Unify all the places which attempt to read all or a part
of a file into the dutil.c#NC_readfile code.
2. Similary unify all the code that creates temp files into
dutil.c#NC_mktmp code.
3. Convert almost all remaining calls to fopen() and open()
to NCfopen() and NCopen3(). This is to ensure that path management
is used consistently. This touches a number of files.
4. extern->EXTERNL as needed to get it to work under Windows.
re: https://github.com/Unidata/netcdf-c/issues/2177
re: https://github.com/Unidata/netcdf-c/pull/2178
Provide get/set functions to store global data alignment
information and apply it when a file is created.
The api is as follows:
````
int nc_set_alignment(int threshold, int alignment);
int nc_get_alignment(int* thresholdp, int* alignmentp);
````
If defined, then for every file created opened after the call to
nc_set_alignment, for every new variable added to the file, the
most recently set threshold and alignment values will be applied
to that variable.
The nc_get_alignment function return the last values set by
nc_set_alignment. If nc_set_alignment has not been called, then
it returns the value 0 for both threshold and alignment.
The alignment parameters are stored in the NCglobalstate object
(see below) for use as needed. Repeated calls to nc_set_alignment
will overwrite any existing values in NCglobalstate.
The alignment parameters are applied in libhdf5/hdf5create.c
and libhdf5/hdf5open.c
The set/get alignment functions are defined in libsrc4/nc4internal.c.
A test program was added as nc_test4/tst_alignment.c.
## Misc. Changes Unrelated to Alignment
* The NCRCglobalstate type was renamed to NCglobalstate to
indicate that it represented more general global state than
just .rc data. It was also moved to nc4internal.h. This led
to a large number of small changes: mostly renaming. The
global state management functions were moved to nc4internal.c.
* The global chunk cache variables have been moved into
NCglobalstate. As warranted, other global state will be moved
as well.
* Some misc. problems with the nczarr performance tests were corrected.
re: PR https://github.com/Unidata/netcdf-c/pull/2088
re: PR https://github.com/Unidata/netcdf-c/pull/2130
replaces: https://github.com/Unidata/netcdf-c/pull/2140
Changes:
* Add NCZarr-specific quantize functions to the dispatch table.
* Copy (modified) quantize code from libhdf5 to NCZarr
* Add quantize invocation to zvar.c
* Add support for _QuantizeBitgroomNumberOfSignificantDigits
and _QuantizeGranularBitgroomNumberOfSignificantDigits to ncgen.
* Modify nc_test4/tst_quantize.c to allow it to be used both for hdf5
and for nczarr.
* Make dap4 properly handle quantize functions in dispatch table.
* Add quantize attribute support to ncgen.
Other changes:
* Caught and fixed some S3 problems
* Fixed some nczarr fillvalue problems.
* Fixed some nczarr cache problems.
* Cleanup some flaws in libdispatch/dinfermodel.c
* Allow byterange requests to S3 be readable by dinfermodel.c/check_file_type
* Remove the libnczarr ztracedispatch code (big change).
re:
The current netcdf-c release has some problems with the mingw platform
on windows. Mostly they are path issues.
Changes to support mingw+msys2:
-------------------------------
* Enable option of looking into the windows registry to find
the mingw root path. In aid of proper path handling.
* Add mingw+msys as a specific platform in configure.ac and move testing
of the platform to the front so it is available early.
* Handle mingw X libncpoco (dynamic loader) properly even though
mingw does not yet support it.
* Handle mingw X plugins properly even though mingw does not yet support it.
* Alias pwd='pwd -W' to better handle paths in shell scripts.
* Plus a number of other minor compile irritations.
* Disallow the use of multiple nc_open's on the same file for windows
(and mingw) because windows does not seem to handle these properly.
Not sure why we did not catch this earlier.
* Add mountpoint info to dpathmgr.c to help support mingw.
* Cleanup dpathmgr conversions.
Known problems:
---------------
* I have not been able to get shared libraries to work, so
plugins/filters must be disabled.
* There is some kind of problem with libcurl that I have not solved,
so all uses of libcurl (currently DAP+Byterange) must be disabled.
Misc. other fixes:
------------------
* Cleanup the relationship between ENABLE_PLUGINS and various other flags
in CMakeLists.txt and configure.ac.
* Re-arrange the TESTDIRS order in Makefile.am.
* Add pseudo-breakpoint to nclog.[ch] for debugging.
* Improve the documentation of the path manager code in ncpathmgr.h
* Add better support for relative paths in dpathmgr.c
* Default the mode args to NCfopen to include "b" (binary) for windows.
* Add optional debugging output in various places.
* Make sure that everything builds with plugins disabled.
* Fix numerous (s)printf inconsistencies betweenb the format spec
and the arguments.
re: https://github.com/Unidata/netcdf-c/issues/2151
The of a non-aws appliance broke during the switch to testing
against Amazon S3.
So make necessary changes to get non-aws appliances work correctly.
re: https://github.com/Unidata/netcdf-c/issues/2119
H/T to [Egbert Eich](https://github.com/e4t) and [Bas Couwenberg](https://github.com/sebastic) for this PR.
It is undesirable to make netcdf be dependent on the availability
of libxml2, but it is desirable to allow its use if available.
In order to do this, a wrapper API (include/ncxml.h) was constructed
that supports either ezxml or libxml2 as the implementation.
Additionally, the xml support code was moved to a new directory
netcdf-c/libncxml.
Primary changes:
* Create a new sub-directory named netcdf-c/libncxml to hold all the xml implementation code.
* Move ezxml.c and ezxml.h to libncxml
* Create a wrapper API -- include/ncxml.h
* Create an implementation, ncxml_ezxml.c to support use of ezxml.
* Create an implementation, ncxml_xml2.c to support use of libxml2.
* Add a check for libxml2 in configure.ac and CMakeLists.txt
* Modify libdap to use the wrapper API instead of ezxml directly.
Misc. Other Changes:
* Change include/netcdf_json.h from built source to be part of the distribution.
re: https://github.com/Unidata/netcdf-c/issues/2117
re: https://github.com/Unidata/netcdf-c/issues/2119
* Modify libsrc to allow byte-range reading of netcdf-3 files in private S3 buckets; this required using the aws sdk. Also add a test case.
* The aws sdk can sometimes cause problems if the Awd::ShutdownAPI function is not called. So at optional atexit() support to ensure it is called. This is disabled for Windows.
* Add documentation to nczarr.md on how to build and use the aws sdk under windows. Currently it builds, but testing fails.
* Switch testing from stratus to the Unidata bucket on S3.
* Improve support for the s3: url protocol.
* Add a s3 specific utility code file: ds3util.c
* Modify NC_infermodel to attempt to read the magic number of byte-ranged files in S3.
## Misc.
* Move and rename the core S3 SDK wrapper code (libnczarr/zs3sdk.cpp) to libdispatch since it now used in libsrc as well as libnczarr.
* Add calls to nc_finalize in the utilities in case atexit is disabled.
* Add header only json parser to the distribution rather than as a built source.
## S3 Related Fixes
* Add comprehensive support for specifying AWS profiles to provide access credentials.
* Parse the files "~/.aws/config" and "~/.aws/credentials to provide credentials for the HDF5 ROS3 driver and to locate default region.
* Add a function to obtain the currently active S3 credentials. The search rules are defined in docs/nczarr.md.
* Provide documentation for the new features.
* Modify the struct NCauth (in include/ncauth.h) to replace specific S3 credentials with a profile name.
* Add a unit test to test the operation of profile and credentials management.
* Add support for URLS of the form "s3://<bucket>/<key>"; this requires obtaining a default region.
* Allows the specification of profile and/or region in a URL of the form "#mode=nczarr,...&aws.region=...&aws.profile=..."
## Misc. Fixes
* Move the ezxml code to libdispatch so that it can be used both by DAP4 and nczarr.
* Modify nclist to provide a deep clone operation.
* Modify ncuri to provide a deep clone operation.
* Modify the .rc file format to allow the specification of a path to be tested when looking for an entry in the .rc file.
* Ensure that the NC_rcload function is called.
* Modify nchttp to support setting request headers.
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'
re: https://github.com/zarr-developers/zarr-specs/issues/41
After discussions with the Zarr community, it was decided to
convert to a new representation of the NCZarr meta-data extensions: version 2.
These extensions store information necessary to mapping the Zarr data model
to the netcdf-4 data model.
The basic change is to remove the NCZarr specific objects: .nczarr, .nczgroup, .nczarray, and .nczattr.
The contents of these objects is moved into the corresponding existing Zarr objects as special keys. The mapping is as follows:
* ''.nczarr'' => ''/.zgroup/_NCZARR_SUPERBLOCK_''
* ''.nczgroup => ''.zgroup/_NCZARR_GROUP_''
* ''.nczarray => ''.zarray/_NCZARR_ARRAY_''
* ''.nczattr => ''.zattr/_NCZARR_ATTR_''
Backward compatibility is maintained by looking for the object ''/.nczarr''
and if found, then assuming that the dataset is in the older version 1 format.
This compatibility only supports reading of such version 1 datasets.
Documentation and test cases are also added.
Misc. Other Changes:
1. The json parsing code was added to the general library instead of nczarr only (ncjson.c, ncjson.h).
2. Improved support for different platform paths by allowing conversion
to a single common path representation.
3. Add some new error codes.
4. Modify nccopy usage to mention the new chunking specification.
re: https://github.com/Unidata/netcdf-c/pull/2003#issuecomment-847637871
Turns out that mingw defines both _WIN32 and also defines getopt.
This means that this test:
````
#ifdef _WIN32
#include "XGetopt.h"
#endif
````
fails on this error:
````
../include/XGetopt.h:38:24: error: conflicting types for 'getopt'
````
Fix is to replace
````
#ifdef _WIN32
with
#if defined(_WIN32) && !defined(__MINGW32__)
````
re: Issue https://github.com/Unidata/netcdf-c/issues/1999
NCclosedir code is incorrect. Fix.
Note that this issue crops up when using a non-VisualStudio windows build
such as Mingw because Mingq defines dirent.h, but Visual Studio does not.
Addendum:
Fix some mingw bugs:
1. Modify XGetopt.h to be conditional on _WIN32 instead of _MSC_VER.
2. Make sure sys/stat.h is included in ncpathmgr.h
re: github issue https://github.com/Unidata/netcdf-c/issues/1982
The problem was that the libnczarr/zsjon.c handling of strings with
embedded double quotes was wrong; a one line fix.
Also added a test case.
Misc. other changes:
1. I Discovered, en passant, that the handling of 64 bit constants
had an error that was fixed.
2. cleanup of the constant conversion code to recurse on arrays of values.
Re: https://github.com/zarr-developers/zarr-python/pull/716
The Zarr version 2 spec has been extended to include the ability
to choose the dimension separator in chunk name keys. The legal
separators has been extended from {'.'} to {'.' '/'}. So now it
is possible to use a key like "0/1/2/0" for chunk names.
This PR implements this for NCZarr. The V2 spec now says that
this separator can be set on a per-variable basis. For now, I
have chosen to allow this be set only globally by adding a key
named "ZARR.DIMENSION_SEPARATOR=<char>" in the
.daprc/.dodsrc/ncrc file. Currently, the only legal separator
characters are '.' (the default) and '/'. On writing, this key
will only be written if its value is different than the default.
This change caused problems because supporting a separator of '/'
is difficult to parse when keys/paths use '/' as the path separator.
A test case was added for this.
Additionally, make nczarr be enabled default by default. This required
some additional changes so that if zip and/or AWS S3 sdk are unavailable,
then they are disabled for NCZarr.
In addition the following unrelated changes were made.
1. Tested that pure-zarr mode could read an nczarr formatted store.
1. The .rc file handling now merges all known .rc files (.ncrc,.daprc, and .dodsrc) in that order and using those in HOME first, then in current directory. For duplicate entries, the later ones override the earlier ones. This change is to remove some of the conflicts inherent in the current .rc file load process. A set of test cases was also added.
1. Re-order tests in configure.ac and CMakeLists.txt so that if libcurl
is not found then the other options that depend upon it properly
are disabled.
1. I decided that xarray support should be enabled by default for pure
zarr. In order to allow disabling, I added a new mode flag "noxarray".
1. Certain test in nczarr_test depend on use of .dodsrc. In order for these
to work when testing in parallel, some inter-test dependencies needed to
be added.
1. Improved authorization testing to use changes in thredds.ucar.edu
re: https://github.com/Unidata/netcdf-c/issues/1988
There was an issue with certain shell programs (bash notably).
For certain platforms and when given a url that had an escaped
'#' character (e.g. \\#) bash would not remove the backslash. So I
had to add a hack for this. Unfortunately I overdid it and it
removed all '' characters. This is ok for non-windows platforms,
but obviously fails for windows.
The fix is this.
1. In a utility program (ncgen, ncdump, nccopy, etc) there is probably a call (or calls) to NC_backslashUnescape(xxx) where xxx is a path argument from the command line.
2. Replace each such call with NC_shellUnescape(xxx).
The NC_shellUnescape function was added and searched only for occurrences of "\#" and replaces them with "#".
interoperability fixed. We were given a Zarr format dataset
stored as a directory+file tree. This dataset uses the XArray
conventions and was generated by some non-Unidata Zarr implementation.
In attempting to process it with NCZarr, several interoperability
problems were discovered and fixed. This gives us more confidence
that NCZarr -- using pure zarr -- can interoperate with other
Zarr implementations.
Specific changes:
* Add test nczarr_test/run_interop.sh
* Support attributes with single value not enclosed in JSON array tags.
* Add mode inferencing and use it in nczarr_test/run_purezarr.sh
* Reduce size of tst_err_enddef.nc because it is more than 3 GB.
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 XArray implementation that uses Zarr for storage
provides a mechanism to simulate named dimensions.
It does this by adding a per-variable attribute called
_ARRAY_DIMENSIONS. This attribute contains a list of names
to be matched against the shape values of the variable.
In effect a named dimension is created with the name
_ARRAY_DIMENSIONS(i) and length shape(i) for all i
in range 0..rank(variable).
Both read and write support is provided.
This XArray support is only invoked if the mode value
of "xarray" is defined. So for example, as in this URL.
````
https://s3.us-west-1.amazonaws.com/bucket/dataset#mode=nczarr,xarray,s3
````
Note that the "xarray" mode flag also implies mode flag "zarr", so the above
is equivalent to this URL.
````
https://s3.us-west-1.amazonaws.com/bucket/dataset#mode=nczarr,zarr,xarray,s3
````
The primary change to implement this was to unify the handling
of dimension references in libnczarr/zsync.
A test for this and other pure-zarr features was added as
nczarr_test/run_purezarr.sh
Other changes:
* Make sure distcheck leaves no files around.
* Change the special attribute flag DIMSCALEFLAG to HIDDENATTRFLAG
to support the xarray attribute.
* Annotate the zmap implementations with feature flags such as
WRITEONCE (for zip files).
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.
* Replace wholevar with more useful wholechunk optimization
* Add optimization to read multiple values at one time
* Replace NCDEFAULT_get/put_vars with native nczarr versions.
* Clarify chunk projection computations
* zdebdispatch.h
* Add more chunking test cases and re-enable run_chunkcases
* If !szip, then suppress deflate interference test
* Make H5Znoop(1) filter produce more information
* cleanup bzlib.c API
* Turn back on the DAP2 remote tests, but leave DAP4 remote tests disabled.
* Turn on selected non-remote DAP4 tests
* Replace d4crc32 with the equivalents in libdispatch
re: https://github.com/Unidata/netcdf-c/issues/1923
re: https://github.com/Unidata/netcdf-c/issues/1921
The issue was raised about the order of returned filter ids
for nc_inq_var_filter_ids() when creating a file as opposed
to later reading the file.
For creation, the order is the same as the order in which the
calls to nc_def_var_filter() occur.
However, after the file is closed and then reopened for reading,
the question was raised if the returned order is the same or the reverse.
In fact the order is the same in both cases.
This PR extends the existing filter order testcase to check the create
versus read orders. This also required changing the H5Znoop(1) filters
in the plugins directory.
Misc. Unrelated Changes
1. fix calls to fdopen under windows
2. Temporarily suppres the nczarr_tests/run_chunkcases test
since it seems to be causing problems with github actions.
Primary Fixes:
* Add a whole variable optimization -- used in the rare case that nc_get/put_vara covers the whole of a variable and the variable has a single chunk.
* Fix chunking error when stride causes whole chunks to be skipped.
* Fix some memory leaks
* Add test cases
* Add one performance test to nczarr_test/. This uses the timer utils from unit_test: timer_utils.[ch].
* Move ncdumpchunks utility from ncdump to nczarr_test
Misc. Other Changes:
* Make check for aws libraries conditional on --enable-nczarr-s3
* Remove all but one bm tests from nczarr_test until they are working.
* Remove another dependency on HDF5 from supposedly non-HDF5 specific code; specifically hdf5_log_hdf5.
* Make the BAIL2 macro be hdf5 specific and replace elsewhere with an HDF5 independent equivalent.
* Move hdf5cache.c to libsrc4/nc4cache.c because it is used by nczarr.
* Modify unit_tests so that some of them are run even if using Windows.
* Misc. small bug fixes and refactors and memory leaks.
* Rename some conflicting tests for cmake.
* Attempted to make nc_perf work with cmake and failed.
Re: GH Issue https://github.com/Unidata/netcdf-c/issues/1900
Apparently the clock_gettime() function is not always available.
It is used in unit_test/tst_exhash.c and unit_test/tst_xcache.c.
To solve this, a number of things were changed:
* Move the timing code to a new file unit_tests/timer_utils.[ch]
* Modify the timing code to choose one of several timing methods
depending on availability. The prioritized order is as follows:
1. If Windows, use the QueryPerformanceCounter mechanism else
2. Use clock_gettime if available else
3. Use gettimeofday if available else
4. Use getrusage if available
Note that the resolution of 3 and 4 is less than 1 or 2.
Misc. Other Changes:
* Move the test in CMakeLists.txt that disables unit tests for WIN32 to unit_test/CMakeLists.txt since some unit tests actually work under Visual Studio.
* Fix some of the unit tests to work under visual studio
* Fix problem with using remove() in zmap_nzf.c
* Remove some warning about use of EXTERNL
Primary changes:
* Add an improved cache system to speed up performance.
* Fix NCZarr to properly handle scalar variables.
Misc. Related Changes:
* Added unit tests for extendible hash and for the generic cache.
* Add config parameter to set size of the NCZarr cache.
* Add initial performance tests but leave them unused.
* Add CRC64 support.
* Move location of ncdumpchunks utility from /ncgen to /ncdump.
* Refactor auth support.
Misc. Unrelated Changes:
* More cleanup of the S3 support
* Add support for S3 authentication in .rc files: HTTP.S3.ACCESSID and HTTP.S3.SECRETKEY.
* Remove the hashkey from the struct OBJHDR since it is never used.
re: https://github.com/Unidata/netcdf-c/issues/1836
Revert the internal filter code to simplify it. From the user's
point of view, the only visible changes should be:
1. The functions that convert text to filter specs have had their signature reverted and have been moved to netcdf_aux.h
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 filter_actions
entry and associated complex structures. It has been replaced with
inq_var_filter_ids and inq_var_filter_info entries and the dispatch table
version has been bumped to 3. Corresponding NOOP and NOTNC4 functions
were added to libdispatch/dnotnc4.c. Also, the filter_action entries
in dispatch tables were replaced for all dispatch code bases (HDF5, DAP2,
etc). This should only impact UDF users.
In the process, it became clear that the form of the filters
field in NC_VAR_INFO_T was format dependent, so I converted it to
be of type void* and pushed its management into the various dispatch
code bases. Specifically libhdf5 and libnczarr now manage the filters
field in their own way.
The auxilliary functions for parsing textual filter specifications
were moved to netcdf_aux.h and were renamed to the following:
* ncaux_h5filterspec_parse
* ncaux_h5filterspec_parselist
* ncaux_h5filterspec_free
* ncaux_h5filter_fix8
Misc. Other Changes:
1. Document NUG/filters.md updated to reflect the changes above.
2. All the old data types (structs and enums)
used by filter_actions actions were deleted.
The exception is the NC_H5_Filterspec because it is needed
by ncaux_h5filterspec_parselist.
3. Clientside filters were removed -- another enhancement
for which no-one ever asked.
4. The ability to remove filters was itself removed.
5. Some functionality needed by nczarr was moved from libhdf5
to libsrc4 e.g. nc4_find_default_chunksizes
6. All the filterx code was removed
7. ncfilter.h and nc4filter.c no longer used
Misc. Unrelated Changes:
1. The nczarr_test makefile clean was leaving some directories; so
add clean-local to take care of them.
re: Github Issue https://github.com/Unidata/netcdf-c/issues/1826
It turns out that the common get code (NC4_get_vars) in libhdf5
(and libnczarr) has an optimization where it does not attempt to
read from the file if the file is all fill values. Rather it
just fills the output buffer with the fill value. The problem
is that -- in that case -- it forgets that conversion might still be
needed. So the conversion never occurs and the raw bits of
the fill data are stored directly into the memory space.
Solution: move some code around to properly do the
conversion no matter how the data was obtained.
Added a test cases nc_test4/test_fillonly.sh and
nczarr_test/test_fillonlyz.sh
As it was, nccopy -c dim/x was sometimes being ignored. So
modify nccopy to properly take into account. This also required
a change to the nczarr code because it was not applying default
chunking in the same way as libhdf5.
Modify ncdump/tst_nccopy4.sh to test this feature properly.
Also add a similar test to nczarr_test.
Additionally, fix some other things that were causing Visual
Studio builds with testing to not work.
* fix curl testing under CMake to properly handle case
where DAP is disabled, but byterange support is enabled.
* properly test and/or define uintptr_t
* Convert _O_XXX to O_XXX flags used by open();
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.
The primary fix is to improve CMake build support.
Specific changes include:
* CMake: Provide a better soln to locating the AWS SDK
libraries; the new way is the preferred method as described in
the aws-cpp-sdk documentation.
* CMake (and Automake): allow -DENABLE_S3_SDK (default off) to suppress
looking for AWS libraries.
* CMake: add the complete set of nczarr tests
* CMake: add EXTERNL as needed to various .h files.
* Improve support for windows drive letters in paths.
* Add nczarr and s3 flags to nc-config
* For VisualStudio X nczarr, cleanup the NAN+INFINITY handling
* Convert _MSC_VER -> _WIN32 and vice versa as needed
* NCZarr - support multiple platform paths including windows, cygwin.
mingw, etc.
* NCZarr - sort the test outputs because different platforms
produce directory contents in different orders.
One big change concerns netcdf-c/CMakeLists.txt and netcdf-c/configure.ac.
In the current versions, it was the case that --disable-hdf5
disabled netcdf-4 (libsrc4). With nczarr, this can no longer
be the case because nczarr requires libsrc4 even if libhdf5
is disabled. So, I modified the above files to move the
format options (HDF5, NCZarr, HDF4, etc) to a single place
near the front of the files. Now it is the case that:
* Enabling any of the formats that require libsrc4
also does an implicit --enable-netcdf4.
* --disable-netcdf4 | --disable-netcdf-4 now becomes
and alias for --disable-hdf5.
There are probably some bugs in this change in terms of
dependencies between format options.
Problems:
* CMake S3 support is still not working for Visual Studio
* A recent issue points out that there is work to do on handling
UTF8 filenames, but that will be addressed in a separate fix.
Notes:
* Consider converting all of our includes/.h files to use EXTERNL
They rely on access to the unidata S3 bucket on stratus,
so only Unidata NetCDF personnel can execute them,
To enable them, one needs to do this at command level:
export NETCDF_S3_TESTS=1
cloud using a variant of the Zarr protocol and storage
format. This enhancement is generically referred to as "NCZarr".
The data model supported by NCZarr is netcdf-4 minus the user-defined
types and the String type. In this sense it is similar to the CDF-5
data model.
More detailed information about enabling and using NCZarr is
described in the document NUG/nczarr.md and in a
[Unidata Developer's blog entry](https://www.unidata.ucar.edu/blogs/developer/en/entry/overview-of-zarr-support-in).
WARNING: this code has had limited testing, so do use this version
for production work. Also, performance improvements are ongoing.
Note especially the following platform matrix of successful tests:
Platform | Build System | S3 support
------------------------------------
Linux+gcc | Automake | yes
Linux+gcc | CMake | yes
Visual Studio | CMake | no
Additionally, and as a consequence of the addition of NCZarr,
major changes have been made to the Filter API. NOTE: NCZarr
does not yet support filters, but these changes are enablers for
that support in the future. Note that it is possible
(probable?) that there will be some accidental reversions if the
changes here did not correctly mimic the existing filter testing.
In any case, previously filter ids and parameters were of type
unsigned int. In order to support the more general zarr filter
model, this was all converted to char*. The old HDF5-specific,
unsigned int operations are still supported but they are
wrappers around the new, char* based nc_filterx_XXX functions.
This entailed at least the following changes:
1. Added the files libdispatch/dfilterx.c and include/ncfilter.h
2. Some filterx utilities have been moved to libdispatch/daux.c
3. A new entry, "filter_actions" was added to the NCDispatch table
and the version bumped.
4. An overly complex set of structs was created to support funnelling
all of the filterx operations thru a single dispatch
"filter_actions" entry.
5. Move common code to from libhdf5 to libsrc4 so that it is accessible
to nczarr.
Changes directly related to Zarr:
1. Modified CMakeList.txt and configure.ac to support both C and C++
-- this is in support of S3 support via the awd-sdk libraries.
2. Define a size64_t type to support nczarr.
3. More reworking of libdispatch/dinfermodel.c to
support zarr and to regularize the structure of the fragments
section of a URL.
Changes not directly related to Zarr:
1. Make client-side filter registration be conditional, with default off.
2. Hack include/nc4internal.h to make some flags added by Ed be unique:
e.g. NC_CREAT, NC_INDEF, etc.
3. cleanup include/nchttp.h and libdispatch/dhttp.c.
4. Misc. changes to support compiling under Visual Studio including:
* Better testing under windows for dirent.h and opendir and closedir.
5. Misc. changes to the oc2 code to support various libcurl CURLOPT flags
and to centralize error reporting.
6. By default, suppress the vlen tests that have unfixed memory leaks; add option to enable them.
7. Make part of the nc_test/test_byterange.sh test be contingent on remotetest.unidata.ucar.edu being accessible.
Changes Left TO-DO:
1. fix provenance code, it is too HDF5 specific.
