## 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:
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/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.
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'
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
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.
2. modified ncdap_tests to remove <cr>
from generated output before comparison
to expected. This is a hack because
my other attempts to force windows to use
binary mode have not worked.
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
