# Description
Remove various obsolete build options. Also do some code movement.
## Specific Changes
* The remotetest server is sometimes unstable, so provide a mechanism
to force disabling calls to remotetest.unidata.ucar.edu.
This is enabled by adding a repository variable named
REMOTETESTDOWN with the value "yes".
* Fix CMakeLists.txt to use the uname command as an alternate
to using the hostname command (which does not work under cygwin).
* Remove the JNA stuff as obsolete
* Remove the ENABLE_CLIENTSIDE_FILTERS options since it has been
disabled for a while.
* Fix bad option flag in some github action .yml files: change --disable-xml2 to --disable-libxml2
* Collect globalstate definitions into nc4internal.h
* Remove ENABLE_NCZARR_FILTERS_TESTING option as obsolete and replace
with ENABLE_NCZARR_FILTERS
* Move some dispatcher independent functions from libsrc4/nc4internal.c to libdispatch/ddispatch.c
* As a long term goal, and because it is now the case that --enable-nczarr
=> USE_NETCDF4, make the external options --enable-netcdf-4 and
--enable-netcdf4 obsolete in favor of --enable-hdf5
We will do the following for one more release cycle.
1. Make --enable-netcdf-4 be an alias for --enable-netcdf4.
2. Make --enable-netcdf4 an alias for --enable-hdf5.
3. Internally, convert most uses of USE_NETCDF_4 ad USE_NETCDF4 to USE_HDF5
After the next release, --enable-netcdf-4 and --enable-netcdf4 will
be removed.
# Primary Change
In order to conform to the cmake overhaul, occurrences of
ENABLE_XXX options in the nczarr code have been changed to
NETCDF_ENABLE_XXX.
# Misc. Other changes
* Fix use of rand_s in libdispatch/ncrandom.c
* Fix some bugs in the mingw gitub action.
* Fix signature bug in libncpoco/cp_win32.c
* Make some NCZarr fixes to config.h.cmake.in
Argument 'count' in NetCDF is not exactly the same as the 'count' in
H5Sselect_hyperslabs(space_id, op, start, stride, count, block).
When the argument 'stride' is NULL, NetCDF's 'count' should be used in
argument 'block', for example,
H5Sselect_hyperslabs(space_id, op, start, NULL, ones, count);
where 'one' is an array of all 1s. Although using NULL 'block' below
H5Sselect_hyperslabs(space_id, op, start, NULL, count, NULL);
has the same effect, HDF5 internally stores the space of a subarray as a
list of single elements, instead of a "block", which can affect the
performance.
NOTE: it is important that this fix gets into 4.9.3
re: Issue https://github.com/Unidata/netcdf-c/issues/2798
## Modifications
* This PR includes PR https://github.com/Unidata/netcdf-c/pull/2813
* Support the following AWS environment variables in the internal S3 library
(they are already supported by aws-sdk-cpp).
- AWS_REGION
- AWS_DEFAULT_REGION
- AWS_ACCESS_KEY_ID
- AWS_CONFIG_FILE
- AWS_PROFILE
- AWS_SECRET_ACCESS_KEY
- (source https://docs.aws.amazon.com/cli/latest/userguide/cli-configure-envvars.html).
* Support an empty region when specifying s3.amazonaws.com as the host.
* Move some S3/AWS related functions to ds3util.c
* Add a test case to test empty region and AWS_[DEFAULT]_REGION.
Mostly just add an explicit cast when calling `malloc` and its
variants. Sometimes instead change the type of a local variable if
this would silence multiple warnings.
re: Issue https://github.com/Unidata/netcdf-c/issues/2748
This PR fixes a number of issues and bugs.
## s3cleanup fixes
* Delete extraneous s3cleanup.sh related files.
* Remove duplicate s3cleanup.uids entries.
## Support the Google S3 API
* Add code to recognize "storage.gooleapis.com"
* Add extra code to track the kind of server being accessed: unknown, Amazon, Google.
* Add a new mode flag "gs3" (analog to "s3") to support this api.
* Modify the S3 URL code to support this case.
* Modify the listobjects result parsing because Google returns some non-standard XML elements.
* Change signature and calls for NC_s3urlrebuild.
## Handle corrupt Zarr files where shape is empty for a variable.
Modify behavior when a variable's "shape" dictionary entry.
Previously it returned an error, but now it suppresses such a variable.
This change makes it possible to read non-corrupt data from the file.
Also added a test case.
## Misc. Other Changes
* Fix the nclog level handling to suppress output by default.
* Fix de-duplicates code in ncuri.c
* Restore testing of iridl.ldeo.columbia.edu.
* Fix bug in define_vars() which did not always do a proper reclaim between variables.
This PR started as an attempt to add unlimited dimensions to NCZarr.
It did that, but this exposed significant problems with test interference.
So this PR is mostly about fixing -- well mitigating anyway -- test
interference.
The problem of test interference is now documented in the document docs/internal.md.
The solutions implemented here are also describe in that document.
The solution is somewhat fragile but multiple cleanup mechanisms
are provided. Note that this feature requires that the
AWS command line utility must be installed.
## Unlimited Dimensions.
The existing NCZarr extensions to Zarr are modified to support unlimited dimensions.
NCzarr extends the Zarr meta-data for the ".zgroup" object to include netcdf-4 model extensions. This information is stored in ".zgroup" as dictionary named "_nczarr_group".
Inside "_nczarr_group", there is a key named "dims" that stores information about netcdf-4 named dimensions. The value of "dims" is a dictionary whose keys are the named dimensions. The value associated with each dimension name has one of two forms
Form 1 is a special case of form 2, and is kept for backward compatibility. Whenever a new file is written, it uses format 1 if possible, otherwise format 2.
* Form 1: An integer representing the size of the dimension, which is used for simple named dimensions.
* Form 2: A dictionary with the following keys and values"
- "size" with an integer value representing the (current) size of the dimension.
- "unlimited" with a value of either "1" or "0" to indicate if this dimension is an unlimited dimension.
For Unlimited dimensions, the size is initially zero, and as variables extend the length of that dimension, the size value for the dimension increases.
That dimension size is shared by all arrays referencing that dimension, so if one array extends an unlimited dimension, it is implicitly extended for all other arrays that reference that dimension.
This is the standard semantics for unlimited dimensions.
Adding unlimited dimensions required a number of other changes to the NCZarr code-base. These included the following.
* Did a partial refactor of the slice handling code in zwalk.c to clean it up.
* Added a number of tests for unlimited dimensions derived from the same test in nc_test4.
* Added several NCZarr specific unlimited tests; more are needed.
* Add test of endianness.
## Misc. Other Changes
* Modify libdispatch/ncs3sdk_aws.cpp to optionally support use of the
AWS Transfer Utility mechanism. This is controlled by the
```#define TRANSFER```` command in that file. It defaults to being disabled.
* Parameterize both the standard Unidata S3 bucket (S3TESTBUCKET) and the netcdf-c test data prefix (S3TESTSUBTREE).
* Fixed an obscure memory leak in ncdump.
* Removed some obsolete unit testing code and test cases.
* Uncovered a bug in the netcdf-c handling of big-endian floats and doubles. Have not fixed yet. See tst_h5_endians.c.
* Renamed some nczarr_tests testcases to avoid name conflicts with nc_test4.
* Modify the semantics of zmap\#ncsmap_write to only allow total rewrite of objects.
* Modify the semantics of zodom to properly handle stride > 1.
* Add a truncate operation to the libnczarr zmap code.
