Merge branch 'main' into killdebugdir.dmh

.github/workflows/run_tests.yml

@@ -199,9 +199,9 @@ jobs:
         if: matrix.use_dap == 'dap_off'
       - run: echo "ENABLE_DAP=ON" >> $GITHUB_ENV
         if: matrix.use_dap == 'dap_on'
-      - run: echo "ENABLE_NCZARR=--disable-nczarr" >> $GITHUB_ENV
+      - run: echo "ENABLE_NCZARR=OFF" >> $GITHUB_ENV
         if: matrix.use_nczarr == 'nczarr_off'
-      - run: echo "ENABLE_NCZARR=--enable-nczarr" >> $GITHUB_ENV
+      - run: echo "ENABLE_NCZARR=ON" >> $GITHUB_ENV
         if: matrix.use_nczarr == 'nczarr_on'
       - run: echo "CTEST_OUTPUT_ON_FAILURE=1" >> $GITHUB_ENV
 

CMakeLists.txt

@@ -26,7 +26,7 @@ set(PACKAGE "netCDF" CACHE STRING "")
 
 SET(NC_VERSION_MAJOR 4)
 SET(NC_VERSION_MINOR 8)
-SET(NC_VERSION_PATCH 2)
+SET(NC_VERSION_PATCH 1)
 SET(NC_VERSION_NOTE "-development")
 SET(netCDF_VERSION ${NC_VERSION_MAJOR}.${NC_VERSION_MINOR}.${NC_VERSION_PATCH}${NC_VERSION_NOTE})
 SET(VERSION ${netCDF_VERSION})
@@ -118,6 +118,11 @@ MACRO(CHECK_C_LINKER_FLAG M_FLAG M_RESULT)
   SET(CMAKE_REQUIRED_FLAGS "${T_REQ_FLAG}")
 ENDMACRO()
 
+# Enable 'dist and distcheck'.
+# File adapted from http://ensc.de/cmake/FindMakeDist.cmake
+FIND_PACKAGE(MakeDist)
+# End 'enable dist and distcheck'
+
 # Set the build type.
 IF(NOT CMAKE_BUILD_TYPE)
   SET(CMAKE_BUILD_TYPE DEBUG CACHE STRING "Choose the type of build, options are: None, Debug, Release."
@@ -194,15 +199,6 @@ ENDIF()
 
 OPTION(NC_FIND_SHARED_LIBS "Find dynamically-built versions of dependent libraries" ${BUILD_SHARED_LIBS})
 
-##
-# Check to see if C compiler supports -fno-strict-aliasing, in support of
-# https://github.com/Unidata/netcdf-c/issues/1983
-##
-CHECK_C_COMPILER_FLAG(-fno-strict-aliasing CC_SUPPORTS_NO_STRICT_ALIASING)
-IF(CC_SUPPORTS_NO_STRICT_ALIASING)
-  SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fno-strict-aliasing")
-ENDIF(CC_SUPPORTS_NO_STRICT_ALIASING)
-
 ##
 # We've had a request to allow for non-versioned shared libraries.
 # This seems reasonable enough to accommodate.  See
@@ -773,10 +769,6 @@ IF(USE_HDF5)
       # are a hot mess between versions.
       ####
 
-      IF(HDF5_hdf5_LIBRARY AND NOT HDF5_C_LIBRARY)
-        SET(HDF5_C_LIBRARY ${HDF5_hdf5_LIBRARY})
-      ENDIF()
-
       # Depending on the install, either HDF5_hdf_library or
       # HDF5_C_LIBRARIES may be defined.  We must check for either.
       IF(HDF5_C_LIBRARIES AND NOT HDF5_hdf5_LIBRARY)
@@ -933,7 +925,7 @@ int main() {
 }" HAVE_LIBCURL_766)
 
 IF (HAVE_LIBCURL_766)
-  # If libcurl version is >= 7.66, then can skip tests
+  # If libcurl version is >= 7.66, then can skip tests 
   # for these symbols which were added in an earlier version
   set(HAVE_CURLOPT_USERNAME TRUE)
   set(HAVE_CURLOPT_PASSWORD TRUE)
@@ -1016,17 +1008,63 @@ OPTION(ENABLE_DAP_LONG_TESTS "Enable DAP long tests." OFF)
 OPTION(ENABLE_DAP_REMOTE_TESTS "Enable DAP remote tests." ON)
 SET(REMOTETESTSERVERS "remotetest.unidata.ucar.edu" CACHE STRING "test servers to use for remote test")
 
+# See if we have zlib
+FIND_PACKAGE(ZLIB)
+
+# Define a test flag for have zlib library
+IF(ZLIB_FOUND)
+  INCLUDE_DIRECTORIES(${ZLIB_INCLUDE_DIRS})
+  SET(ENABLE_ZLIB TRUE)
+ELSE()
+  SET(ENABLE_ZLIB FALSE)
+ENDIF()
+
+# See if we have libblosc
+IF(!MSVC)
+FIND_PACKAGE(Blosc)
+ENDIF()
+# Define a test flag for have blosc library
+IF(Blosc_FOUND)
+  INCLUDE_DIRECTORIES(${Blosc_INCLUDE_DIRS})
+  SET(ENABLE_BLOSC TRUE)
+ELSE()
+  SET(ENABLE_BLOSC FALSE)
+ENDIF()
+
+# See if we have libszip
+IF(!MSVC)
+#FIND_PACKAGE(SZIP)
+#FIND_LIBRARY(SZIP PATH NAMES szip sz)
+SET(SZIP_LIBRARY ${SZIP})
+ENDIF()
+message("xxx: ${SZIP_FOUND} ; ${SZIP}")
+# Define a test flag for have szip library
+IF(SZIP_FOUND)
+  INCLUDE_DIRECTORIES(${SZIP_INCLUDE_DIRS})
+  SET(ENABLE_SZIP TRUE)
+ELSE()
+  SET(ENABLE_SZIP FALSE)
+ENDIF()
+
 # See if we have libzip
 FIND_PACKAGE(Zip)
 
-# Define a test flag for have curl library
+# Define a test flag for have zip library
 IF(Zip_FOUND)
   INCLUDE_DIRECTORIES(${Zip_INCLUDE_DIRS})
   SET(ENABLE_NCZARR_ZIP TRUE)
 ELSE()
   SET(ENABLE_NCZARR_ZIP FALSE)
 ENDIF()
 
+# libdl is always available; built-in in Windows and OSX
+SET(ENABLE_PLUGINS TRUE)
+IF(NOT WIN32)
+  IF(HAVE_DLFCN_H)
+    INCLUDE_DIRECTORIES("dlfcn.h")
+  ENDIF()
+ENDIF()
+
 # Enable some developer-only tests
 OPTION(ENABLE_EXTRA_TESTS "Enable Extra tests. Some may not work because of known issues. Developers only." OFF)
 IF(ENABLE_EXTRA_TESTS)
@@ -1049,9 +1087,9 @@ IF(MSVC)
     FILE(COPY ${netCDF_SOURCE_DIR}/libsrc/XGetopt.c
          DESTINATION ${netCDF_BINARY_DIR}/ncdump/)
     FILE(COPY ${netCDF_SOURCE_DIR}/libsrc/XGetopt.c
-         DESTINATION ${netCDF_BINARY_DIR}/nczarr_test/)
+         DESTINATION ${netCDF_BINARY_DIR}/nczarr_test/) 
     FILE(COPY ${netCDF_SOURCE_DIR}/libsrc/XGetopt.c
-         DESTINATION ${netCDF_BINARY_DIR}/ncdap_test/)
+         DESTINATION ${netCDF_BINARY_DIR}/ncdap_test/) 
   ENDIF()
 ENDIF()
 
@@ -1386,20 +1424,21 @@ IF (ENABLE_PARALLEL_TESTS AND NOT USE_PARALLEL)
 ENDIF()
 
 # Enable special filter test; experimental when using cmake.
-OPTION(ENABLE_FILTER_TESTING "Enable filter testing. Ignored if shared libraries or netCDF4 are not enabled" ${ENABLE_HDF5})
-IF(ENABLE_FILTER_TESTING AND NOT ENABLE_HDF5)
-  MESSAGE(WARNING "ENABLE_FILTER_TESTING requires HDF5. Disabling.")
-  SET(ENABLE_FILTER_TESTING OFF)
+OPTION(ENABLE_FILTER_TESTING "Enable filter testing. Ignored if shared libraries or netCDF4 are not enabled" yes)
+
+IF(ENABLE_FILTER_TESTING)
+  if(NOT ENABLE_HDF5 AND NOT ENABLE_NCZARR)
+    MESSAGE(WARNING "ENABLE_FILTER_TESTING requires HDF5 and/or NCZarr. Disabling.")
+    SET(ENABLE_FILTER_TESTING OFF CACHE BOOL "Enable Filter Testing" FORCE)
+  ENDIF()
 ENDIF()
+
 IF(NOT BUILD_SHARED_LIBS)
   MESSAGE(WARNING "ENABLE_FILTER_TESTING requires shared libraries. Disabling.")
   SET(ENABLE_FILTER_TESTING OFF)
 ENDIF()
-OPTION(ENABLE_CLIENTSIDE_FILTERS "Enable client-side filter registration." OFF)
-IF(NOT ENABLE_FILTER_TESTING)
-SET(ENABLE_CLIENTSIDE_FILTERS OFF)
-ENDIF()
 
+SET(ENABLE_CLIENTSIDE_FILTERS OFF)
 
 # Determine whether or not to generate documentation.
 OPTION(ENABLE_DOXYGEN "Enable generation of doxygen-based documentation." OFF)
@@ -1533,6 +1572,7 @@ CHECK_INCLUDE_FILE("libgen.h" HAVE_LIBGEN_H)
 CHECK_INCLUDE_FILE("execinfo.h" HAVE_EXECINFO_H)
 CHECK_INCLUDE_FILE("dirent.h" HAVE_DIRENT_H)
 CHECK_INCLUDE_FILE("time.h" HAVE_TIME_H)
+CHECK_INCLUDE_FILE("dlfcn.h" HAVE_DLFCN_H)
 
 # Symbol Exists
 CHECK_SYMBOL_EXISTS(isfinite "math.h" HAVE_DECL_ISFINITE)
@@ -1931,7 +1971,7 @@ ENDIF(ENABLE_BASH_SCRIPT_TESTING)
 
 MACRO(add_sh_test prefix F)
   IF(HAVE_BASH)
-    ADD_TEST(${prefix}_${F} bash "-c" "export srcdir=${CMAKE_CURRENT_SOURCE_DIR};export TOPSRCDIR=${CMAKE_SOURCE_DIR};${CMAKE_CURRENT_BINARY_DIR}/${F}.sh ${ARGN}")
+    ADD_TEST(${prefix}_${F} bash "-c" "export srcdir=${CMAKE_CURRENT_SOURCE_DIR};export TOPSRCDIR=${CMAKE_SOURCE_DIR};${CMAKE_CURRENT_BINARY_DIR}/${F}.sh ${F}.sh ${ARGN}")
   ENDIF()
 ENDMACRO()
 
@@ -2018,17 +2058,31 @@ IF(ENABLE_DAP4)
   ADD_SUBDIRECTORY(libdap4)
 ENDIF()
 
+IF(ENABLE_PLUGINS)
+  ADD_SUBDIRECTORY(libncpoco)
+ENDIF()
+
 IF(ENABLE_NCZARR)
   ADD_SUBDIRECTORY(libnczarr)
   FILE(COPY ${netCDF_SOURCE_DIR}/unit_test/timer_utils.h
        DESTINATION ${netCDF_BINARY_DIR}/nczarr_test/)
   FILE(COPY ${netCDF_SOURCE_DIR}/unit_test/timer_utils.c
        DESTINATION ${netCDF_BINARY_DIR}/nczarr_test/)
+  FILE(COPY ${netCDF_SOURCE_DIR}/nc_test4/test_filter.c
+       DESTINATION ${netCDF_BINARY_DIR}/nczarr_test/)
+  FILE(COPY ${netCDF_SOURCE_DIR}/nc_test4/test_filter_misc.c
+       DESTINATION ${netCDF_BINARY_DIR}/nczarr_test/)
+  FILE(COPY ${netCDF_SOURCE_DIR}/nc_test4/test_filter_repeat.c
+       DESTINATION ${netCDF_BINARY_DIR}/nczarr_test/)
+  FILE(COPY ${netCDF_SOURCE_DIR}/nc_test4/test_filter_order.c
+       DESTINATION ${netCDF_BINARY_DIR}/nczarr_test/)
+  FILE(COPY ${netCDF_SOURCE_DIR}/nc_test4/tst_multifilter.c
+       DESTINATION ${netCDF_BINARY_DIR}/nczarr_test/)
 ENDIF()
 
 add_subdirectory(liblib)
 
-IF(ENABLE_FILTER_TESTING)
+IF(ENABLE_PLUGINS)
   add_subdirectory(plugins)
 ENDIF()
 
@@ -2194,6 +2248,9 @@ INSTALL(PROGRAMS ${netCDF_BINARY_DIR}/nc-config
 ##
 print_conf_summary()
 
+# Enable Makedist files.
+ADD_MAKEDIST()
+ENABLE_MAKEDIST(README.md COPYRIGHT RELEASE_NOTES.md INSTALL INSTALL.cmake test_prog.c lib_flags.am cmake CMakeLists.txt COMPILE.cmake.txt config.h.cmake.in cmake_uninstall.cmake.in netcdf-config-version.cmake.in netcdf-config.cmake.in FixBundle.cmake.in nc-config.cmake.in configure configure.ac install-sh config.h.in config.sub CTestConfig.cmake.in)
 
 #####
 # Configure and print the libnetcdf.settings file.
@@ -2245,6 +2302,8 @@ is_enabled(ENABLE_NCZARR_S3_TESTS DO_NCZARR_S3_TESTS)
 is_enabled(ENABLE_MULTIFILTERS HAS_MULTIFILTERS)
 is_enabled(ENABLE_NCZARR_ZIP DO_NCZARR_ZIP_TESTS)
 is_enabled(ENABLE_LOGGING HAS_LOGGING)
+is_enabled(ENABLE_FILTER_TESTING DO_FILTER_TESTS)
+is_enabled(ENABLE_BLOSC HAS_BLOSC)
 
 # Generate file from template.
 CONFIGURE_FILE("${CMAKE_CURRENT_SOURCE_DIR}/libnetcdf.settings.in"
@@ -2302,6 +2361,10 @@ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/test_common.in ${CMAKE_CURRENT_BINARY
 #####
 configure_file(${CMAKE_CURRENT_SOURCE_DIR}/nc_test4/findplugin.in ${CMAKE_CURRENT_BINARY_DIR}/nc_test4/findplugin.sh @ONLY NEWLINE_STYLE LF)
 
+IF(ENABLE_NCZARR)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/nc_test4/findplugin.in ${CMAKE_CURRENT_BINARY_DIR}/nczarr_test/findplugin.sh @ONLY NEWLINE_STYLE LF)
+ENDIF()
+
 IF(ENABLE_EXAMPLES)
 configure_file(${CMAKE_CURRENT_SOURCE_DIR}/nc_test4/findplugin.in ${CMAKE_CURRENT_BINARY_DIR}/examples/C/findplugin.sh @ONLY NEWLINE_STYLE LF)
 ENDIF()

Makefile.am

@@ -81,13 +81,18 @@ HDF4_TEST_DIR = hdf4_test
 LIBHDF4 = libhdf4
 endif
 
+# Build Plugin support
+if ENABLE_PLUGINS
+NCPOCO = libncpoco
+endif
+
 # Build Cloud Storage if desired.
 if ENABLE_NCZARR
 ZARR_TEST_DIR = nczarr_test
-ZARR = libnczarr
+ZARR = libnczarr 
 endif
 
-# Optionally build plugins
+# Optionally build test plugins
 if ENABLE_FILTER_TESTING
 PLUGIN_DIR = plugins
 endif
@@ -108,7 +113,7 @@ endif
 # and run. ncgen must come before ncdump, because their tests
 # depend on it.
 SUBDIRS = include $(H5_TEST_DIR) libdispatch libsrc $(LIBSRC4_DIR)	\
-$(LIBSRCP) $(LIBHDF4) $(LIBHDF5) $(OCLIB) $(DAP2) ${DAP4} ${ZARR} liblib \
+$(LIBSRCP) $(LIBHDF4) $(LIBHDF5) $(OCLIB) $(DAP2) ${DAP4} ${NCPOCO} ${ZARR} liblib \
 $(NCGEN3) $(NCGEN) $(NCDUMP) ${PLUGIN_DIR} $(TESTDIRS) docs		\
 $(EXAMPLES)
 

RELEASE_NOTES.md

@@ -8,6 +8,7 @@ This file contains a high-level description of this package's evolution. Release
 ## 4.8.2 - TBD
 
 * [Bug Fix] Ensure that internal Fortran APIs are always defined. See [Github #2098](https://github.com/Unidata/netcdf-c/pull/2098).
+* [Enhancement] Support filters for NCZarr. See [Github #2101](https://github.com/Unidata/netcdf-c/pull/2101)
 * [Bug Fix] Make PR 2075 long file name be idempotent. See [Github #2094](https://github.com/Unidata/netcdf-c/pull/2094).
 
 ## 4.8.1 - August 18, 2021

cmake/modules/FindBlosc.cmake

@@ -0,0 +1,64 @@
+# Searches for an installation of the blosc library. On success, it sets the following variables:
+#
+#   Blosc_FOUND              Set to true to indicate the blosc library was found
+#   Blosc_INCLUDE_DIRS       The directory containing the header file blosc/blosc.h
+#   Blosc_LIBRARIES          The libraries needed to use the blosc library
+#
+# To specify an additional directory to search, set Blosc_ROOT.
+#
+# Author: Siddhartha Chaudhuri, 2009
+#
+
+# Look for the header, first in the user-specified location and then in the system locations
+SET(Blosc_INCLUDE_DOC "The directory containing the header file blosc.h")
+FIND_PATH(Blosc_INCLUDE_DIRS NAMES blosc.h blosc/blosc.h PATHS ${Blosc_ROOT} ${Blosc_ROOT}/include DOC ${Blosc_INCLUDE_DOC} NO_DEFAULT_PATH)
+IF(NOT Blosc_INCLUDE_DIRS)  # now look in system locations
+  FIND_PATH(Blosc_INCLUDE_DIRS NAMES blosc.h blosc/blosc.h DOC ${Blosc_INCLUDE_DOC})
+ENDIF(NOT Blosc_INCLUDE_DIRS)
+
+SET(Blosc_FOUND FALSE)
+
+IF(Blosc_INCLUDE_DIRS)
+  SET(Blosc_LIBRARY_DIRS ${Blosc_INCLUDE_DIRS})
+
+  IF("${Blosc_LIBRARY_DIRS}" MATCHES "/include$")
+    # Strip off the trailing "/include" in the path.
+    GET_FILENAME_COMPONENT(Blosc_LIBRARY_DIRS ${Blosc_LIBRARY_DIRS} PATH)
+  ENDIF("${Blosc_LIBRARY_DIRS}" MATCHES "/include$")
+
+  IF(EXISTS "${Blosc_LIBRARY_DIRS}/lib")
+    SET(Blosc_LIBRARY_DIRS ${Blosc_LIBRARY_DIRS}/lib)
+  ENDIF(EXISTS "${Blosc_LIBRARY_DIRS}/lib")
+
+  # Find Blosc libraries
+  FIND_LIBRARY(Blosc_DEBUG_LIBRARY NAMES bloscd blosc_d libbloscd libblosc_d libblosc
+               PATH_SUFFIXES Debug ${CMAKE_LIBRARY_ARCHITECTURE} ${CMAKE_LIBRARY_ARCHITECTURE}/Debug
+               PATHS ${Blosc_LIBRARY_DIRS} NO_DEFAULT_PATH)
+  FIND_LIBRARY(Blosc_RELEASE_LIBRARY NAMES blosc libblosc
+               PATH_SUFFIXES Release ${CMAKE_LIBRARY_ARCHITECTURE} ${CMAKE_LIBRARY_ARCHITECTURE}/Release
+               PATHS ${Blosc_LIBRARY_DIRS} NO_DEFAULT_PATH)
+
+  SET(Blosc_LIBRARIES )
+  IF(Blosc_DEBUG_LIBRARY AND Blosc_RELEASE_LIBRARY)
+    SET(Blosc_LIBRARIES debug ${Blosc_DEBUG_LIBRARY} optimized ${Blosc_RELEASE_LIBRARY})
+  ELSEIF(Blosc_DEBUG_LIBRARY)
+    SET(Blosc_LIBRARIES ${Blosc_DEBUG_LIBRARY})
+  ELSEIF(Blosc_RELEASE_LIBRARY)
+    SET(Blosc_LIBRARIES ${Blosc_RELEASE_LIBRARY})
+  ENDIF(Blosc_DEBUG_LIBRARY AND Blosc_RELEASE_LIBRARY)
+
+  IF(Blosc_LIBRARIES)
+    SET(Blosc_FOUND TRUE)
+  ENDIF(Blosc_LIBRARIES)
+ENDIF(Blosc_INCLUDE_DIRS)
+
+IF(Blosc_FOUND)
+#  IF(NOT Blosc_FIND_QUIETLY)
+    MESSAGE(STATUS "Found Blosc: headers at ${Blosc_INCLUDE_DIRS}, libraries at ${Blosc_LIBRARY_DIRS}")
+    MESSAGE(STATUS "	library is ${Blosc_LIBRARIES}")    
+#  ENDIF(NOT Blosc_FIND_QUIETLY)
+ELSE(Blosc_FOUND)
+  IF(Blosc_FIND_REQUIRED)
+    MESSAGE(FATAL_ERROR "Blosc library not found")
+  ENDIF(Blosc_FIND_REQUIRED)
+ENDIF(Blosc_FOUND)