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.
## Improvements to S3 Documentation
* Create a new document *quickstart_paths.md* that give a summary of the legal path formats used by netcdf-c. This includes both file paths and URL paths.
* Modify *nczarr.md* to remove most of the S3 related text.
* Move the S3 text from *nczarr.md* to a new document *cloud.md*.
* Add some S3-related text to the *byterange.md* document.
Hopefully, this will make it easier for users to find the information they want.
## Rebuild NCZarr Testing
In order to avoid problems with running make check in parallel, two changes were made:
1. The *nczarr_test* test system was rebuilt. Now, for each test.
any generated files are kept in a test-specific directory, isolated
from all other test executions.
2. Similarly, since the S3 test bucket is shared, any generated S3 objects
are isolated using a test-specific key path.
## Other S3 Related Changes
* Add code to ensure that files created on S3 are reclaimed at end of testing.
* Used the bash "trap" command to ensure S3 cleanup even if the test fails.
* Cleanup the S3 related configure.ac flag set since S3 is used in several places. So now one should use the option *--enable-s3* instead of *--enable-nczarr-s3*, although the latter is still kept as a deprecated alias for the former.
* Get some of the github actions yml to work with S3; required fixing various test scripts adding a secret to access the Unidata S3 bucket.
* Cleanup S3 portion of libnetcdf.settings.in and netcdf_meta.h.in and test_common.in.
* Merge partial S3 support into dhttp.c.
* Create an experimental s3 access library especially for use with Windows. It is enabled by using the options *--enable-s3-internal* (automake) or *-DENABLE_S3_INTERNAL=ON* (CMake). Also add a unit-test for it.
* Move some definitions from ncrc.h to ncs3sdk.h
## Other Changes
* Provide a default implementation of strlcpy and move this and similar defaults into *dmissing.c*.
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.
* 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
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.
re: https://github.com/Unidata/netcdf-c/issues/1373 (partial)
* Mark some global constants be const to indicate to make them easier to track.
* Hide direct access to the ncrc_globalstate behind a function call.
* Convert dispatch tables to constants (except the user defined ones)
This has some consequences in terms of function arguments needing to be marked
as const also.
* Remove some no longer needed global fields
* Aggregate all the globals in nclog.c
* Uniformly replace nc_sizevector{0,1} with NC_coord_{zero,one}
* Uniformly replace nc_ptrdffvector1 with NC_stride_one
* Remove some obsolete code
re: issue https://github.com/Unidata/netcdf-c/issues/1151
Modify DAP2 and DAP4 code to handle case when _FillValue type is not
same as the parent variable type.
Specifically:
1. Define a parameter [fillmismatch] to allow this mismatch;
default is to disallow.
2. If allowed, forcibly change the type of the _FillValue to match
the parent variable.
3. If allowed Convert the values to match new type
4. Generate a log message
5. if not allowed, then fail
Implementing this required some changes to ncdap_test/dapcvt.c
Also added test cases.
Minor Unrelated Changes:
1. There were a number of warnings about e.g.
assigning a const char* to a char*. Fix these
2. In nccopy.1, replace .NP with .IP "n"
(re PR https://github.com/Unidata/netcdf-c/pull/1144)
3. fix minor error in ncdump/ocprint
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
