netcdf-c/ncdump/CMakeLists.txt

364 lines
13 KiB
CMake
Raw Normal View History

# Copyright 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014,
# 2015, 2016, 2017, 2018
# University Corporation for Atmospheric Research/Unidata.
# See netcdf-c/COPYRIGHT file for more info.
#IF(BUILD_SHARED_LIBS AND WIN32)
# remove_definitions(-DDLL_EXPORT)
# remove_definitions(-DDLL_NETCDF)
#ENDIF()
2012-08-07 00:57:29 +08:00
SET(RCMERGE OFF)
2012-08-22 04:08:53 +08:00
SET(ncdump_FILES ncdump.c vardata.c dumplib.c indent.c nctime0.c utils.c nciter.c)
SET(nccopy_FILES nccopy.c nciter.c chunkspec.c utils.c dimmap.c list.c)
2018-08-01 02:51:24 +08:00
SET(ocprint_FILES ocprint.c)
SET(ncvalidator_FILES ncvalidator.c)
SET(printfqn_FILES printfqn.c)
Add filter support to NCZarr 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'
2021-09-03 07:04:26 +08:00
SET(ncpathcvt_FILES ncpathcvt.c)
2012-09-14 04:41:54 +08:00
IF(USE_X_GETOPT)
SET(ncdump_FILES ${ncdump_FILES} XGetopt.c)
SET(nccopy_FILES ${nccopy_FILES} XGetopt.c)
2018-08-01 02:51:24 +08:00
SET(ocprint_FILES ${ocprint_FILES} XGetopt.c)
SET(ncvalidator_FILES ${ncvalidator_FILES} XGetopt.c)
Regularize the scoping of dimensions This is a follow-on to pull request ````https://github.com/Unidata/netcdf-c/pull/1959````, which fixed up type scoping. The primary changes are to _nc\_inq\_dimid()_ and to ncdump. The _nc\_inq\_dimid()_ function is supposed to allow the name to be and FQN, but this apparently never got implemented. So if was modified to support FQNs. The ncdump program is supposed to output fully qualified dimension names in its generated CDL file under certain conditions. Suppose ncdump has a netcdf-4 file F with variable V, and V's parent group is G. For each dimension id D referenced by V, ncdump needs to determine whether to print its name as a simple name or as a fully qualified name (FQN). The algorithm is as follows: 1. Search up the tree of ancestor groups. 2. If one of those ancestor groups contains the dimid, then call it dimgrp. 3. If one of those ancestor groups contains a dim with the same name as the dimid, but with a different dimid, then record that as duplicate=true. 4. If dimgrp is defined and duplicate == false, then we do not need an fqn. 5. If dimgrp is defined and duplicate == true, then we do need an fqn to avoid incorrectly using the duplicate. 6. If dimgrp is undefined, then do a preorder breadth-first search of all the groups looking for the dimid. 7. If found, then use the fqn of the first found such dimension location. 8. If not found, then fail. Test case ncdump/test_scope.sh was modified to test the proper operation of ncdump and _nc\_inq\_dimid()_. Misc. Other Changes: * Fix nc_inq_ncid (NC4_inq_ncid actually) to return root group id if the name argument is NULL. * Modify _ncdump/printfqn_ to print out a dimid FQN; this supports verification that the resulting .nc files were properly created.
2021-06-01 05:51:12 +08:00
SET(printfqn_FILES ${printfqn_FILES} XGetopt.c)
Add filter support to NCZarr 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'
2021-09-03 07:04:26 +08:00
SET(ncpathcvt_FILES ${ncpathcvt_FILES} XGetopt.c)
Regularize the scoping of dimensions This is a follow-on to pull request ````https://github.com/Unidata/netcdf-c/pull/1959````, which fixed up type scoping. The primary changes are to _nc\_inq\_dimid()_ and to ncdump. The _nc\_inq\_dimid()_ function is supposed to allow the name to be and FQN, but this apparently never got implemented. So if was modified to support FQNs. The ncdump program is supposed to output fully qualified dimension names in its generated CDL file under certain conditions. Suppose ncdump has a netcdf-4 file F with variable V, and V's parent group is G. For each dimension id D referenced by V, ncdump needs to determine whether to print its name as a simple name or as a fully qualified name (FQN). The algorithm is as follows: 1. Search up the tree of ancestor groups. 2. If one of those ancestor groups contains the dimid, then call it dimgrp. 3. If one of those ancestor groups contains a dim with the same name as the dimid, but with a different dimid, then record that as duplicate=true. 4. If dimgrp is defined and duplicate == false, then we do not need an fqn. 5. If dimgrp is defined and duplicate == true, then we do need an fqn to avoid incorrectly using the duplicate. 6. If dimgrp is undefined, then do a preorder breadth-first search of all the groups looking for the dimid. 7. If found, then use the fqn of the first found such dimension location. 8. If not found, then fail. Test case ncdump/test_scope.sh was modified to test the proper operation of ncdump and _nc\_inq\_dimid()_. Misc. Other Changes: * Fix nc_inq_ncid (NC4_inq_ncid actually) to return root group id if the name argument is NULL. * Modify _ncdump/printfqn_ to print out a dimid FQN; this supports verification that the resulting .nc files were properly created.
2021-06-01 05:51:12 +08:00
ENDIF(USE_X_GETOPT)
2012-09-14 02:27:23 +08:00
2012-08-04 06:24:29 +08:00
ADD_EXECUTABLE(ncdump ${ncdump_FILES})
ADD_EXECUTABLE(nccopy ${nccopy_FILES})
ADD_EXECUTABLE(ncvalidator ${ncvalidator_FILES})
Add filter support to NCZarr 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'
2021-09-03 07:04:26 +08:00
ADD_EXECUTABLE(ncpathcvt ${ncpathcvt_FILES})
IF(USE_HDF5)
ADD_EXECUTABLE(nc4print nc4print.c nc4printer.c)
ADD_EXECUTABLE(printfqn ${printfqn_FILES})
ENDIF(USE_HDF5)
IF(ENABLE_DAP)
ADD_EXECUTABLE(ocprint ${ocprint_FILES})
ENDIF(ENABLE_DAP)
2012-08-04 06:24:29 +08:00
2012-08-11 05:44:00 +08:00
TARGET_LINK_LIBRARIES(ncdump netcdf ${ALL_TLL_LIBS})
TARGET_LINK_LIBRARIES(nccopy netcdf ${ALL_TLL_LIBS})
TARGET_LINK_LIBRARIES(ncvalidator netcdf ${ALL_TLL_LIBS})
Add filter support to NCZarr 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'
2021-09-03 07:04:26 +08:00
TARGET_LINK_LIBRARIES(ncpathcvt netcdf ${ALL_TLL_LIBS})
IF(USE_HDF5)
TARGET_LINK_LIBRARIES(nc4print netcdf ${ALL_TLL_LIBS})
TARGET_LINK_LIBRARIES(printfqn netcdf ${ALL_TLL_LIBS})
ENDIF(USE_HDF5)
IF(ENABLE_DAP)
TARGET_LINK_LIBRARIES(ocprint netcdf ${ALL_TLL_LIBS})
ENDIF(ENABLE_DAP)
2012-08-04 06:24:29 +08:00
####
# We have to do a little tweaking
# to remove the Release/ and Debug/ directories
# in MSVC builds. This is required to get
# test scripts to work.
####
IF(MSVC)
SET_TARGET_PROPERTIES(ncdump PROPERTIES RUNTIME_OUTPUT_DIRECTORY
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(ncdump PROPERTIES RUNTIME_OUTPUT_DIRECTORY_DEBUG
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(ncdump PROPERTIES RUNTIME_OUTPUT_DIRECTORY_RELEASE
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(nccopy PROPERTIES RUNTIME_OUTPUT_DIRECTORY
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(nccopy PROPERTIES RUNTIME_OUTPUT_DIRECTORY_DEBUG
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(nccopy PROPERTIES RUNTIME_OUTPUT_DIRECTORY_RELEASE
${CMAKE_CURRENT_BINARY_DIR})
2018-08-01 02:51:24 +08:00
SET_TARGET_PROPERTIES(ncvalidator PROPERTIES RUNTIME_OUTPUT_DIRECTORY
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(ncvalidator PROPERTIES RUNTIME_OUTPUT_DIRECTORY_DEBUG
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(ncvalidator PROPERTIES RUNTIME_OUTPUT_DIRECTORY_RELEASE
${CMAKE_CURRENT_BINARY_DIR})
Add filter support to NCZarr 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'
2021-09-03 07:04:26 +08:00
SET_TARGET_PROPERTIES(ncpathcvt PROPERTIES RUNTIME_OUTPUT_DIRECTORY
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(ncpathcvt PROPERTIES RUNTIME_OUTPUT_DIRECTORY_DEBUG
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(ncpathcvt PROPERTIES RUNTIME_OUTPUT_DIRECTORY_RELEASE
${CMAKE_CURRENT_BINARY_DIR})
Add filter support to NCZarr 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'
2021-09-03 07:04:26 +08:00
IF(USE_HDF5)
SET_TARGET_PROPERTIES(printfqn PROPERTIES RUNTIME_OUTPUT_DIRECTORY
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(printfqn PROPERTIES RUNTIME_OUTPUT_DIRECTORY_DEBUG
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(printfqn PROPERTIES RUNTIME_OUTPUT_DIRECTORY_RELEASE
${CMAKE_CURRENT_BINARY_DIR})
ENDIF(USE_HDF5)
IF(ENABLE_DAP)
2018-08-01 02:51:24 +08:00
SET_TARGET_PROPERTIES(ocprint PROPERTIES RUNTIME_OUTPUT_DIRECTORY
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(ocprint PROPERTIES RUNTIME_OUTPUT_DIRECTORY_DEBUG
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(ocprint PROPERTIES RUNTIME_OUTPUT_DIRECTORY_RELEASE
${CMAKE_CURRENT_BINARY_DIR})
ENDIF(ENABLE_DAP)
ENDIF()
IF(ENABLE_TESTS)
ADD_EXECUTABLE(rewrite-scalar rewrite-scalar.c)
ADD_EXECUTABLE(bom bom.c)
2016-01-06 13:26:20 +08:00
ADD_EXECUTABLE(tst_dimsizes tst_dimsizes.c)
Primary change: add dap4 support 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
2017-03-09 08:01:10 +08:00
ADD_EXECUTABLE(nctrunc nctrunc.c)
if(RCMERGE)
Upgrade the nczarr code to match Zarr V2 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
2021-04-25 09:48:15 +08:00
ADD_EXECUTABLE(tst_rcmerge tst_rcmerge.c)
endif()
TARGET_LINK_LIBRARIES(rewrite-scalar netcdf)
TARGET_LINK_LIBRARIES(bom netcdf)
2016-01-06 13:26:20 +08:00
TARGET_LINK_LIBRARIES(tst_dimsizes netcdf)
Upgrade the nczarr code to match Zarr V2 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
2021-04-25 09:48:15 +08:00
TARGET_LINK_LIBRARIES(nctrunc netcdf)
if(RCMERGE)
Upgrade the nczarr code to match Zarr V2 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
2021-04-25 09:48:15 +08:00
TARGET_LINK_LIBRARIES(tst_rcmerge netcdf)
endif()
IF(USE_HDF5)
ADD_EXECUTABLE(tst_fileinfo tst_fileinfo.c)
TARGET_LINK_LIBRARIES(tst_fileinfo netcdf)
ENDIF()
IF(MSVC)
SET_TARGET_PROPERTIES(rewrite-scalar PROPERTIES RUNTIME_OUTPUT_DIRECTORY
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(rewrite-scalar PROPERTIES RUNTIME_OUTPUT_DIRECTORY_DEBUG
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(rewrite-scalar PROPERTIES RUNTIME_OUTPUT_DIRECTORY_RELEASE
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(bom PROPERTIES RUNTIME_OUTPUT_DIRECTORY
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(bom PROPERTIES RUNTIME_OUTPUT_DIRECTORY_DEBUG
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(bom PROPERTIES RUNTIME_OUTPUT_DIRECTORY_RELEASE
${CMAKE_CURRENT_BINARY_DIR})
2016-01-06 13:26:20 +08:00
SET_TARGET_PROPERTIES(tst_dimsizes PROPERTIES RUNTIME_OUTPUT_DIRECTORY
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(tst_dimsizes PROPERTIES RUNTIME_OUTPUT_DIRECTORY_DEBUG
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(tst_dimsizes PROPERTIES RUNTIME_OUTPUT_DIRECTORY_RELEASE
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(nctrunc PROPERTIES RUNTIME_OUTPUT_DIRECTORY
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(nctrunc PROPERTIES RUNTIME_OUTPUT_DIRECTORY_DEBUG
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(nctrunc PROPERTIES RUNTIME_OUTPUT_DIRECTORY_RELEASE
${CMAKE_CURRENT_BINARY_DIR})
IF(RCMERGE)
SET_TARGET_PROPERTIES(tst_rcmerge PROPERTIES RUNTIME_OUTPUT_DIRECTORY
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(tst_rcmerge PROPERTIES RUNTIME_OUTPUT_DIRECTORY_DEBUG
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(tst_rcmerge PROPERTIES RUNTIME_OUTPUT_DIRECTORY_RELEASE ${CMAKE_CURRENT_BINARY_DIR})
endif()
Upgrade the nczarr code to match Zarr V2 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
2021-04-25 09:48:15 +08:00
IF(USE_HDF5)
SET_TARGET_PROPERTIES(tst_fileinfo PROPERTIES RUNTIME_OUTPUT_DIRECTORY
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(tst_fileinfo PROPERTIES RUNTIME_OUTPUT_DIRECTORY_DEBUG
${CMAKE_CURRENT_BINARY_DIR})
SET_TARGET_PROPERTIES(tst_fileinfo PROPERTIES RUNTIME_OUTPUT_DIRECTORY_RELEASE
${CMAKE_CURRENT_BINARY_DIR})
Codify cross-platform file paths 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.
2021-03-05 04:41:31 +08:00
ENDIF(USE_HDF5)
ENDIF(MSVC)
# Build support programs
build_bin_test_no_prefix(tst_utf8)
build_bin_test_no_prefix(tst_fillbug)
IF(USE_HDF5)
build_bin_test_no_prefix(tst_h_rdc0)
build_bin_test_no_prefix(tst_unicode)
add_bin_test_no_prefix(tst_create_files)
add_bin_test_no_prefix(tst_opaque_data)
add_bin_test_no_prefix(tst_string_data)
add_bin_test_no_prefix(tst_vlen_data)
add_bin_test_no_prefix(tst_comp2)
add_bin_test_no_prefix(tst_nans)
add_bin_test_no_prefix(tst_h_scalar)
add_bin_test_no_prefix(tst_compress)
add_bin_test_no_prefix(tst_chunking)
add_bin_test_no_prefix(tst_group_data)
add_bin_test_no_prefix(tst_enum_data)
add_bin_test_no_prefix(tst_comp)
# Add this test by hand, as it is also called from a script.
# Editing the script would break autotools compatibility.
add_bin_test_no_prefix(tst_special_atts)
ENDIF(USE_HDF5)
# Base tests
# The tests are set up as a combination of shell scripts and executables that
# must be run in a particular order. It is painful but will use macros to help
# keep it from being too bad.
IF(HAVE_BASH)
## Start adding tests in the appropriate order
2017-11-17 08:54:30 +08:00
add_bin_test_no_prefix(ref_ctest)
add_bin_test_no_prefix(ref_ctest64)
add_sh_test(ncdump run_tests)
add_sh_test(ncdump tst_64bit)
add_sh_test(ncdump tst_lengths)
add_sh_test(ncdump tst_calendars)
add_sh_test(ncdump run_utf8_tests)
add_sh_test(ncdump tst_nccopy3_subset)
add_sh_test(ncdump tst_charfill)
add_sh_test(ncdump tst_formatx3)
add_sh_test(ncdump tst_bom)
add_sh_test(ncdump tst_dimsizes)
add_sh_test(ncdump tst_inmemory_nc3)
add_sh_test(ncdump tst_nccopy_w3)
add_sh_test(ncdump run_ncgen_tests)
add_sh_test(ncdump tst_inttags)
add_sh_test(ncdump test_radix)
add_sh_test(ncdump tst_ctests)
add_sh_test(ncdump tst_null_byte_padding)
IF(USE_STRICT_NULL_BYTE_HEADER_PADDING)
SET_TESTS_PROPERTIES(ncdump_tst_null_byte_padding PROPERTIES WILL_FAIL TRUE)
ENDIF(USE_STRICT_NULL_BYTE_HEADER_PADDING)
2017-11-21 04:52:06 +08:00
IF(NOT MSVC AND NOT MINGW)
add_sh_test(ncdump tst_output)
add_sh_test(ncdump tst_nccopy3)
# Known failure on MSVC; the number of 0's padding
# is different, but the result is actually correct.
if(USE_HDF5)
add_sh_test(ncdump tst_netcdf4)
endif()
SET_TESTS_PROPERTIES(ncdump_tst_nccopy3 PROPERTIES DEPENDS
"ncdump_tst_calendars;ncdump_run_utf8_tests;ncdump_tst_output;ncdump_tst_64bit;ncdump_run_tests;ncdump_tst_lengths")
ENDIF()
IF(USE_HDF5)
add_sh_test(ncdump tst_formatx4)
add_sh_test(ncdump_sh tst_fillbug)
add_sh_test(ncdump_shell tst_h_scalar)
add_sh_test(ncdump tst_mud)
add_sh_test(ncdump tst_grp_spec)
add_sh_test(ncdump tst_nccopy5)
add_sh_test(ncdump tst_inttags4)
add_sh_test(ncdump run_utf8_nc4_tests)
add_sh_test(ncdump tst_fileinfo)
add_sh_test(ncdump tst_hdf5_offset)
add_sh_test(ncdump tst_inmemory_nc4)
add_sh_test(ncdump tst_nccopy_w4)
add_sh_test(ncdump run_ncgen_nc4_tests)
add_sh_test(ncdump tst_ncgen4)
add_sh_test(ncdump tst_netcdf4_4)
add_sh_test(ncdump tst_nccopy4)
SET_TESTS_PROPERTIES(ncdump_tst_nccopy4 PROPERTIES DEPENDS "ncdump_run_ncgen_tests;ncdump_tst_output;ncdump_tst_ncgen4;ncdump_tst_fillbug;ncdump_tst_netcdf4_4;ncdump_tst_h_scalar;tst_comp;tst_comp2")
SET_TESTS_PROPERTIES(ncdump_tst_nccopy5 PROPERTIES DEPENDS "ncdump_tst_nccopy4")
ENDIF(USE_HDF5)
# The following test script invokes
# gcc directly.
IF(CMAKE_COMPILER_IS_GNUCC OR APPLE)
IF(ENABLE_LARGE_FILE_TESTS)
add_sh_test(ncdump tst_iter)
ENDIF(ENABLE_LARGE_FILE_TESTS)
ENDIF(CMAKE_COMPILER_IS_GNUCC OR APPLE)
###
# This test fails on Visual Studio builds with bash.
# It passes, but technically fails because the scientific
# formatting omits a 0.
###
IF(EXTRA_TESTS)
IF(USE_HDF5)
IF(NOT MSVC AND NOT MINGW)
add_sh_test(ncdump run_back_comp_tests)
ENDIF()
ENDIF()
ENDIF(EXTRA_TESTS)
2019-11-04 03:03:13 +08:00
This PR adds EXPERIMENTAL support for accessing data in the 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.
2020-06-29 08:02:47 +08:00
IF(ENABLE_UNFIXED_MEMORY_LEAKS)
SET_TESTS_PROPERTIES(ncdump_run_ncgen_nc4_tests.sh ncdump_tst_nccopy4.sh ncdump_tst_ncgen_shared.sh ncdump_tst_netcdf4.sh
PROPERTIES ENVIRONMENT NC_VLEN_NOTEST=1)
ENDIF()
Codify cross-platform file paths 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.
2021-03-05 04:41:31 +08:00
# The unicode tests are complicated
IF(USE_HDF5)
IF(NOT MSVC AND NOT MINGW)
Codify cross-platform file paths 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.
2021-03-05 04:41:31 +08:00
# These tests do not work under windows
add_sh_test(ncdump test_unicode_directory)
add_sh_test(ncdump test_unicode_path)
ENDIF()
Codify cross-platform file paths 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.
2021-03-05 04:41:31 +08:00
ENDIF(USE_HDF5)
IF(USE_CDF5)
add_sh_test(ncdump test_keywords)
ENDIF()
2020-12-08 03:18:30 +08:00
2021-03-09 05:27:56 +08:00
IF(USE_HDF5)
add_sh_test(ncdump test_scope)
ENDIF()
if(RCMERGE)
add_sh_test(ncdump test_rcmerge)
endif()
ENDIF(HAVE_BASH)
Add filter support to NCZarr 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'
2021-09-03 07:04:26 +08:00
Codify cross-platform file paths 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.
2021-03-05 04:41:31 +08:00
ENDIF(ENABLE_TESTS)
#IF(MSVC)
# SET_TARGET_PROPERTIES(ncdump
# PROPERTIES LINK_FLAGS_DEBUG " /NODEFAULTLIB:MSVCRT"
# )
# SET_TARGET_PROPERTIES(nccopy
# PROPERTIES LINK_FLAGS_DEBUG " /NODEFAULTLIB:MSVCRT"
# )
# SET_TARGET_PROPERTIES(ncvalidator
# PROPERTIES LINK_FLAGS_DEBUG " /NODEFAULTLIB:MSVCRT"
# )
# IF(ENABLE_DAP)
# SET_TARGET_PROPERTIES(ocprint
# PROPERTIES LINK_FLAGS_DEBUG " /NODEFAULTLIB:MSVCRT"
# )
# ENDIF(ENABLE_DAP)
#ENDIF()
2012-09-20 05:32:28 +08:00
INSTALL(TARGETS ncdump RUNTIME DESTINATION bin COMPONENT utilities)
INSTALL(TARGETS nccopy RUNTIME DESTINATION bin COMPONENT utilities)
2012-10-18 05:14:30 +08:00
SET(MAN_FILES nccopy.1 ncdump.1)
# Note, the L512.bin file is file containing exactly 512 bytes each of value 0.
re e-support UBS-599337 re pull request https://github.com/Unidata/netcdf-c/pull/405 re pull request https://github.com/Unidata/netcdf-c/pull/446 Notes: 1. This branch is a cleanup of the magic.dmh branch. 2. magic.dmh was originally merged, but caused problems with parallel IO. It was re-issued as pull request https://github.com/Unidata/netcdf-c/pull/446. 3. This branch + pull request replace any previous pull requests and magic.dmh branch. Given an otherwise valid netCDF file that has a corrupted header, the netcdf library currently crashes. Instead, it should return NC_ENOTNC. Additionally, the NC_check_file_type code does not do the forward search required by hdf5 files. It currently only looks at file position 0 instead of 512, 1024, 2048,... Also, it turns out that the HDF4 magic number is assumed to always be at the beginning of the file (unlike HDF5). The change is localized to libdispatch/dfile.c See https://support.hdfgroup.org/release4/doc/DSpec_html/DS.pdf Also, it turns out that the code in NC_check_file_type is duplicated (mostly) in the function libsrc4/nc4file.c#nc_check_for_hdf. This branch does the following. 1. Make NC_check_file_type return NC_ENOTNC instead of crashing. 2. Remove nc_check_for_hdf and centralize all file format checking NC_check_file_type. 3. Add proper forward search for HDF5 files (but not HDF4 files) to look for the magic number at offsets of 0, 512, 1024... 4. Add test tst_hdf5_offset.sh. This tests that hdf5 files with an offset are properly recognized. It does so by prefixing a legal file with some number of zero bytes: 512, 1024, etc. 5. Off-topic: Added -N flag to ncdump to force a specific output dataset name.
2017-10-25 06:25:09 +08:00
# It is used for creating hdf5 files with varying offsets for testing.
Add filter support to NCZarr 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'
2021-09-03 07:04:26 +08:00
FILE(GLOB COPY_FILES ${CMAKE_BINARY_DIR}/ncgen/*.nc ${CMAKE_BINARY_DIR}/nc_test4/*.nc ${CMAKE_CURRENT_SOURCE_DIR}/*.ncml ${CMAKE_CURRENT_SOURCE_DIR}/*.nc ${CMAKE_CURRENT_SOURCE_DIR}/*.cdl ${CMAKE_CURRENT_SOURCE_DIR}/*.sh ${CMAKE_CURRENT_SOURCE_DIR}/*.1 ${CMAKE_CURRENT_SOURCE_DIR}/L512.bin ${CMAKE_CURRENT_SOURCE_DIR}/ref_ctest*.c )
FILE(COPY ${COPY_FILES} DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/ FILE_PERMISSIONS OWNER_WRITE OWNER_READ OWNER_EXECUTE)
ADD_SUBDIRECTORY(cdl)
ADD_SUBDIRECTORY(expected)
2012-08-28 05:49:09 +08:00
SET_DIRECTORY_PROPERTIES(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "${CLEANFILES}")
IF(NOT MSVC)
INSTALL(FILES ${MAN_FILES} DESTINATION "share/man/man1" COMPONENT documentation)
ENDIF()