The NETCDF_ENABLE_SET_LOG_LEVEL_FUNC option is apparently not used, but
is effectively used to set NETCDF_ENABLE_SET_LOG_LEVEL.
This is not clear from the build files CMakeLists.txt and configure.ac.
So this PR cleanups the code to make it more clear what is going on.
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.
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.
error occurs after an "exit:" label.
Corrected a dozen Coverity errors (mainly allocation issues, along with a few
other things):
711711, 711802, 711803, 711905, 970825, 996123, 996124, 1025787,
1047274, 1130013, 1130014, 1139538
Refactored internal fill-value code to correctly handle string types, and
especially to allow NULL pointers and null strings (ie. "") to be
distinguished. The code now avoids partially aliasing the two together
(which only happened on the 'write' side of things and wasn't reflected on
the 'read' side, adding to the previous confusion).
Probably still weak on handling fill-values of variable-length and compound
datatypes.
Refactored the recursive metadata reads a bit more, to process HDF5 named
datatypes and datasets immediately, avoiding chewing up memory for those
types of objects, etc.
Finished uncommenting and updating the nc_test4/tst_fills2.c code (as I'm
proceeding alphabetically through the nc_test4 code files).
