Merge branch 'main' into updatedocs.dmh

Author: WardF

.github/workflows/run_tests_osx.yml

@@ -7,7 +7,7 @@
 name: Run macOS-based netCDF Tests
 
 
-on: [pull_request,push]
+on: [pull_request]
 
 jobs:
 

.github/workflows/run_tests_ubuntu.yml

@@ -4,7 +4,7 @@
 
 name: Run Ubuntu/Linux netCDF Tests
 
-on: [ pull_request ]
+on: [pull_request]
 
 jobs:
 
@@ -82,7 +82,7 @@ jobs:
           key: hdf5-parallel-${{ runner.os }}-${{ matrix.hdf5 }}
 
 
-      - name: Build libhdf5-${{ matrix.hdf5 }}
+      - name: Build libhdf5-${{ matrix.hdf5 }}-pnetcdf-1.12.3
         if: steps.cache-hdf5.outputs.cache-hit != 'true'
         run: |
           set -x
@@ -100,6 +100,13 @@ jobs:
           make -j
           make install -j
           popd
+          wget https://parallel-netcdf.github.io/Release/pnetcdf-1.12.3.tar.gz
+          tar -zxf pnetcdf-1.12.3.tar.gz
+          pushd pnetcdf-1.12.3
+          CC=mpicc ./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }} 
+          make -j
+          make install -j
+          popd
           
   #####
   # One-Off Autotools-based tests.
@@ -233,7 +240,7 @@ jobs:
 
       - name: Configure
         shell: bash -l {0}
-        run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} CC=mpicc ./configure --enable-hdf4 --enable-hdf5 --enable-dap --disable-dap-remote-tests
+        run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} CC=mpicc ./configure --enable-hdf4 --enable-hdf5 --enable-dap --disable-dap-remote-tests --enable-parallel-tests --enable-pnetcdf
         if: ${{ success() }}
 
       - name: Look at config.log if error

CMakeLists.txt

@@ -623,26 +623,6 @@ ENDIF(ENABLE_STRICT_NULL_BYTE_HEADER_PADDING)
 # 3. is nczarr enabled?
 # We need separate flags for cases 1 and 2
 
-# We need to determine if libsz is available both for HDF5 and NCZarr
-# If user has specified the `SZIP_LIBRARY`, use it; otherwise try to find...
-IF(NOT SZIP_LIBRARY)
-  FIND_LIBRARY(SZIP PATH NAMES szip sz sz2)
-  IF(SZIP)
-    SET(SZIP_LIBRARY ${SZIP})
-  ELSE()
-    UNSET(SZIP_LIBRARY)
-    UNSET(SZIP)
-  ENDIF()
-ENDIF()
-
-IF(SZIP_LIBRARY)
-  SET(SZIP_FOUND yes)
-  SET(HAVE_SZ yes)
-ELSE()
-  SET(SZIP_FOUND no)
-  SET(HAVE_SZ no)
-ENDIF()
-
 ##
 # Option to Enable HDF5
 #
@@ -905,15 +885,6 @@ IF(USE_HDF5)
    int x = 1;}" USE_HDF5_SZIP)
   IF(USE_HDF5_SZIP)
     SET(HAVE_H5Z_SZIP yes)
-    # If user has specified the `SZIP_LIBRARY`, use it; otherwise try to find...
-    IF(SZIP_FOUND)
-      SET(CMAKE_REQUIRED_LIBRARIES ${SZIP_LIBRARY} ${CMAKE_REQUIRED_LIBRARIES})
-      MESSAGE(STATUS "HDF5 has szip.")
-    ELSE()
-        MESSAGE(FATAL_ERROR "HDF5 Requires SZIP, but cannot find libszip or libsz.")
-    ENDIF()
-  ELSE()
-    SET(HAVE_H5Z_SZIP no)  
   ENDIF()
 
   ####
@@ -1114,25 +1085,53 @@ string(TOLOWER "${filter}" downfilter)
 IF(${filter}_FOUND)
   INCLUDE_DIRECTORIES(${filter}_INCLUDE_DIRS})
   SET(ENABLE_${upfilter} TRUE)
-  SET(STD_FILTERS "${STD_FILTERS},${downfilter}")
+  SET(HAVE_${upfilter} ON)
+  SET(STD_FILTERS "${STD_FILTERS} ${downfilter}")
+  MESSAGE(">>> Standard Filter: ${downfilter}")
 ELSE()
   SET(ENABLE_${upfilter} FALSE)
+  SET(HAVE_${upfilter} OFF)
 ENDIF()
 endmacro(set_std_filter)
 
 # Locate some compressors
+FIND_PACKAGE(Szip)
 FIND_PACKAGE(Bz2)
 FIND_PACKAGE(Blosc)
 FIND_PACKAGE(Zstd)
 
 # Accumulate standard filters
-set(STD_FILTERS "deflate") # Always have deflate */
-set_std_filter(SZIP)
+set(STD_FILTERS "deflate") # Always have deflate*/
+set_std_filter(Szip)
+  SET(HAVE_SZ ${Szip_FOUND})
 set_std_filter(Blosc)
 set_std_filter(Zstd)
-set_std_filter(Bz2)
-IF(NOT Bz2_FOUND)
-set(STD_FILTERS "${STD_FILTERS},bzip2") # Always have bzip2 */
+IF(Bz2_FOUND)
+  set_std_filter(Bz2)
+ELSE()
+  # The reason we use a local version is to support a more comples test case
+  MESSAGE(WARNING "libbz2 not found using built-in version")
+  SET(HAVE_LOCAL_BZ2 ON)
+  SET(HAVE_BZ2 ON)
+  set(STD_FILTERS "${STD_FILTERS} bz2")
+ENDIF()
+
+
+# If user wants, then install selected plugins
+SET(PLUGIN_INSTALL_DIR "" CACHE STRING "Whether and where we should install plugins")
+SET(ENABLE_PLUGIN_INSTALL OFF)
+if(DEFINED PLUGIN_INSTALL_DIR OR DEFINED CACHE{PLUGIN_INSTALL_DIR})
+  IF(PLUGIN_INSTALL_DIR STREQUAL "")
+    MESSAGE(WARNING "No plugin directory value specified; option ignored.")  
+    UNSET(PLUGIN_INSTALL_DIR)
+    UNSET(PLUGIN_INSTALL_DIR CACHE)
+    SET(PLUGIN_INSTALL_DIR_SETTING "N.A.")
+  ELSE()
+      SET(PLUGIN_INSTALL_DIR_SETTING "${PLUGIN_INSTALL_DIR}")
+      SET(ENABLE_PLUGIN_INSTALL ON)
+  ENDIF()
+ELSE()
+    SET(PLUGIN_INSTALL_DIR_SETTING "N.A.")
 ENDIF()
 
 # See if we have libzip
@@ -2442,6 +2441,7 @@ is_enabled(ENABLE_V2_API HAS_NC2)
 is_enabled(ENABLE_NETCDF_4 HAS_NC4)
 is_enabled(ENABLE_HDF4 HAS_HDF4)
 is_enabled(USE_HDF5 HAS_HDF5)
+is_enabled(OFF HAS_BENCHMARKS)
 is_enabled(STATUS_PNETCDF HAS_PNETCDF)
 is_enabled(STATUS_PARALLEL HAS_PARALLEL)
 is_enabled(ENABLE_PARALLEL4 HAS_PARALLEL4)
@@ -2465,6 +2465,7 @@ is_enabled(ENABLE_LOGGING HAS_LOGGING)
 is_enabled(ENABLE_FILTER_TESTING DO_FILTER_TESTS)
 is_enabled(HAVE_SZ HAS_SZIP)
 is_enabled(HAVE_SZ HAS_SZLIB_WRITE)
+is_enabled(HAVE_ZSTD HAS_ZSTD)
 
 # Generate file from template.
 CONFIGURE_FILE("${CMAKE_CURRENT_SOURCE_DIR}/libnetcdf.settings.in"
@@ -2520,6 +2521,10 @@ IF(ENABLE_NCZARR)
 configure_file(${CMAKE_CURRENT_SOURCE_DIR}/nc_test4/findplugin.in ${CMAKE_CURRENT_BINARY_DIR}/nczarr_test/findplugin.sh @ONLY NEWLINE_STYLE LF)
 ENDIF()
 
+IF(ENABLE_PLUGINS)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/nc_test4/findplugin.in ${CMAKE_CURRENT_BINARY_DIR}/plugins/findplugin.sh @ONLY NEWLINE_STYLE LF)
+ENDIF()
+
 IF(ENABLE_EXAMPLES)
 configure_file(${CMAKE_CURRENT_SOURCE_DIR}/nc_test4/findplugin.in ${CMAKE_CURRENT_BINARY_DIR}/examples/C/findplugin.sh @ONLY NEWLINE_STYLE LF)
 ENDIF()

RELEASE_NOTES.md

@@ -8,6 +8,7 @@ This file contains a high-level description of this package's evolution. Release
 ## 4.8.2 - TBD
 
 * [Enhancement] Update the documentation to match the current filter capabilities  See [Github #2249](https://github.com/Unidata/netcdf-c/pull/2249).
+* [Enhancement] Support installation of pre-built standard filters into user-specified location. See [Github #2318](https://github.com/Unidata/netcdf-c/pull/2318).
 * [Enhancement] Improve filter support. More specifically (1) add nc_inq_filter_avail to check if a filter is available, (2) add the notion of standard filters, (3) cleanup szip support to fix interaction with NCZarr. See [Github #2245](https://github.com/Unidata/netcdf-c/pull/2245).
 * [Enhancement] Switch to tinyxml2 as the default xml parser implementation. See [Github #2170](https://github.com/Unidata/netcdf-c/pull/2170).
 * [Bug Fix] Require that the type of the variable in nc_def_var_filter is not variable length. See [Github #/2231](https://github.com/Unidata/netcdf-c/pull/2231).
@@ -68,7 +69,7 @@ This file contains a high-level description of this package's evolution. Release
 * [Enhancement] Add some optimizations to NCZarr, dosome cleanup of code cruft, add some NCZarr test cases, add a performance test to NCZarr. See [Github #1908](https://github.com/Unidata/netcdf-c/pull/1908) for more information.
 * [Bug Fix] Implement a better chunk cache system for NCZarr. The cache now uses extendible hashing plus a linked list for provide a combination of expandibility, fast access, and LRU behavior. See [Github #1887](https://github.com/Unidata/netcdf-c/pull/1887) for more information.
 * [Enhancement] Provide .rc fields for S3 authentication: HTTP.S3.ACCESSID and HTTP.S3.SECRETKEY.
-* [Enhancement] Give the client control over what parts of a DAP2 URL are URL encoded (i.e. %xx). This is to support the different decoding rules that servers apply to incoming URLS. See [Github #1884](https://github.com/Unidata/netcdf-c/pull/1844) for more information.
+* [Enhancement] Give the client control over what parts of a DAP2 URL are URL encoded (i.e. %xx). This is to support the different decoding rules that servers apply to incoming URLS. See [Github #1884](https://github.com/Unidata/netcdf-c/pull/1884) for more information.
 * [Bug Fix] Fix incorrect time offsets from `ncdump -t`, in some cases when the time `units` attribute contains both a **non-zero** time-of-day, and a time zone suffix containing the letter "T", such as "UTC".  See [Github #1866](https://github.com/Unidata/netcdf-c/pull/1866) for more information.
 * [Bug Fix] Cleanup the NCZarr S3 build options. See [Github #1869](https://github.com/Unidata/netcdf-c/pull/1869) for more information.
 * [Bug Fix] Support aligned access for selected ARM processors.  See [Github #1871](https://github.com/Unidata/netcdf-c/pull/1871) for more information.

cmake/modules/FindBzip2.cmake

@@ -0,0 +1,64 @@
+# Searches for an installation of the bzip2 library. On success, it sets the following variables:
+#
+#   Bzip2_FOUND              Set to true to indicate the bzip2 library was found
+#   Bzip2_INCLUDE_DIRS       The directory containing the header file bzip2/bzip2.h
+#   Bzip2_LIBRARIES          The libraries needed to use the bzip2 library
+#
+# To specify an additional directory to search, set Bzip2_ROOT.
+#
+# Author: Siddhartha Chaudhuri, 2009
+#
+
+# Look for the header, first in the user-specified location and then in the system locations
+SET(Bzip2_INCLUDE_DOC "The directory containing the header file bzip2.h")
+FIND_PATH(Bzip2_INCLUDE_DIRS NAMES bzip2.h bzip2/bzip2.h PATHS ${Bzip2_ROOT} ${Bzip2_ROOT}/include DOC ${Bzip2_INCLUDE_DOC} NO_DEFAULT_PATH)
+IF(NOT Bzip2_INCLUDE_DIRS)  # now look in system locations
+  FIND_PATH(Bzip2_INCLUDE_DIRS NAMES bzlib.h DOC ${Bzip2_INCLUDE_DOC})
+ENDIF(NOT Bzip2_INCLUDE_DIRS)
+
+SET(Bzip2_FOUND FALSE)
+
+IF(Bzip2_INCLUDE_DIRS)
+  SET(Bzip2_LIBRARY_DIRS ${Bzip2_INCLUDE_DIRS})
+
+  IF("${Bzip2_LIBRARY_DIRS}" MATCHES "/include$")
+    # Strip off the trailing "/include" in the path.
+    GET_FILENAME_COMPONENT(Bzip2_LIBRARY_DIRS ${Bzip2_LIBRARY_DIRS} PATH)
+  ENDIF("${Bzip2_LIBRARY_DIRS}" MATCHES "/include$")
+
+  IF(EXISTS "${Bzip2_LIBRARY_DIRS}/lib")
+    SET(Bzip2_LIBRARY_DIRS ${Bzip2_LIBRARY_DIRS}/lib)
+  ENDIF(EXISTS "${Bzip2_LIBRARY_DIRS}/lib")
+
+  # Find Bzip2 libraries
+  FIND_LIBRARY(Bzip2_DEBUG_LIBRARY NAMES bzip2d bzip2_d libbzip2d libbzip2_d libbzip2
+               PATH_SUFFIXES Debug ${CMAKE_LIBRARY_ARCHITECTURE} ${CMAKE_LIBRARY_ARCHITECTURE}/Debug
+               PATHS ${Bzip2_LIBRARY_DIRS} NO_DEFAULT_PATH)
+  FIND_LIBRARY(Bzip2_RELEASE_LIBRARY NAMES bzip2 libbzip2
+               PATH_SUFFIXES Release ${CMAKE_LIBRARY_ARCHITECTURE} ${CMAKE_LIBRARY_ARCHITECTURE}/Release
+               PATHS ${Bzip2_LIBRARY_DIRS} NO_DEFAULT_PATH)
+
+  SET(Bzip2_LIBRARIES )
+  IF(Bzip2_DEBUG_LIBRARY AND Bzip2_RELEASE_LIBRARY)
+    SET(Bzip2_LIBRARIES debug ${Bzip2_DEBUG_LIBRARY} optimized ${Bzip2_RELEASE_LIBRARY})
+  ELSEIF(Bzip2_DEBUG_LIBRARY)
+    SET(Bzip2_LIBRARIES ${Bzip2_DEBUG_LIBRARY})
+  ELSEIF(Bzip2_RELEASE_LIBRARY)
+    SET(Bzip2_LIBRARIES ${Bzip2_RELEASE_LIBRARY})
+  ENDIF(Bzip2_DEBUG_LIBRARY AND Bzip2_RELEASE_LIBRARY)
+
+  IF(Bzip2_LIBRARIES)
+    SET(Bzip2_FOUND TRUE)
+  ENDIF(Bzip2_LIBRARIES)
+ENDIF(Bzip2_INCLUDE_DIRS)
+
+IF(Bzip2_FOUND)
+#  IF(NOT Bzip2_FIND_QUIETLY)
+    MESSAGE(STATUS "Found Bzip2: headers at ${Bzip2_INCLUDE_DIRS}, libraries at ${Bzip2_LIBRARY_DIRS}")
+    MESSAGE(STATUS "	library is ${Bzip2_LIBRARIES}")    
+#  ENDIF(NOT Bzip2_FIND_QUIETLY)
+ELSE(Bzip2_FOUND)
+  IF(Bzip2_FIND_REQUIRED)
+    MESSAGE(FATAL_ERROR "Bzip2 library not found")
+  ENDIF(Bzip2_FIND_REQUIRED)
+ENDIF(Bzip2_FOUND)