Merge branch 'master' into fix-find-ncxx-configs

CMakeLists.txt

@@ -26,13 +26,13 @@ set(PACKAGE "netCDF" CACHE STRING "")
 
 SET(NC_VERSION_MAJOR 4)
 SET(NC_VERSION_MINOR 5)
-SET(NC_VERSION_PATCH 0)
+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})
 SET(NC_VERSION ${netCDF_VERSION})
-SET(netCDF_LIB_VERSION 11.4.0)
+SET(netCDF_LIB_VERSION 13)
-SET(netCDF_SO_VERSION 11)
+SET(netCDF_SO_VERSION 13)
 SET(PACKAGE_VERSION ${VERSION})
 
 # Get system configuration, Use it to determine osname, os release, cpu. These

RELEASE_NOTES.md

@@ -5,24 +5,27 @@ Release Notes       {#RELEASE_NOTES}
 
 This file contains a high-level description of this package's evolution. Releases are in reverse chronological order (most recent first). Note that, as of netcdf 4.2, the `netcdf-c++` and `netcdf-fortran` libraries have been separated into their own libraries.
 
-## 4.5 - TBD
+## 4.5.0 - TBD
+
+### 4.5.0-rc1 - June 2, 2017
 
-* [Bug Fix] Corrected an issue where 'make check' would fail if 'make' or 'make all' had not run first.  See [Github #339](https://github.com/Unidata/netcdf-c/issues/339) for more information.
-* [Bug Fix] Corrected an issue on Windows with Large file tests. See [Github #385](https://github.com/Unidata/netcdf-c/issues/385]) for more information.
-* [Bug Fix] Corrected an issue with diskless file access, see [Pull Request #400](https://github.com/Unidata/netcdf-c/issues/400) and [Pull Request #403](https://github.com/Unidata/netcdf-c/issues/403) for more information.
 * [Enhancement] DAP4 is now included. Since dap2 is the default for urls, dap4 must be specified by
 (1) using "dap4:" as the url protocol, or
 (2) appending "#protocol=dap4" to the end of the url, or
 (3) appending "#dap4" to the end of the url
 Note that dap4 is enabled by default but remote-testing is
 disbled until the testserver situation is resolved.
-* [Enhancement] The remote testing server can now be specified with the '--with-testserver" option to ./configure.
+* [Enhancement] The remote testing server can now be specified with the `--with-testserver` option to ./configure.
+* [Enhancement] Modified netCDF4 to use ASCII for NC_CHAR.  See [Github Pull request #316](https://github.com/Unidata/netcdf-c/pull/316) for more information.
+* [Bug Fix] Corrected an error with how dimsizes might be read. See [Github #410](https://github.com/unidata/netcdf-c/issues/410) for more information.
+* [Bug Fix] Corrected an issue where 'make check' would fail if 'make' or 'make all' had not run first.  See [Github #339](https://github.com/Unidata/netcdf-c/issues/339) for more information.
+* [Bug Fix] Corrected an issue on Windows with Large file tests. See [Github #385](https://github.com/Unidata/netcdf-c/issues/385]) for more information.
+* [Bug Fix] Corrected an issue with diskless file access, see [Pull Request #400](https://github.com/Unidata/netcdf-c/issues/400) and [Pull Request #403](https://github.com/Unidata/netcdf-c/issues/403) for more information.
 * [Upgrade] The bash based test scripts have been upgraded to use a common test_common.sh include file that isolates build specific information.
 * [Upgrade] The bash based test scripts have been upgraded to use a common test_common.sh include file that isolates build specific information.
 * [Refactor] the oc2 library is no longer independent of the main netcdf-c library. For example, it now uses ncuri, nclist, and ncbytes instead of its homegrown equivalents.
 * [Bug Fix] `NC_EGLOBAL` is now properly returned when attempting to set a global `_FillValue` attribute. See [GitHub #388](https://github.com/Unidata/netcdf-c/issues/388) and [GitHub #389](https://github.com/Unidata/netcdf-c/issues/389) for more information.
 * [Bug Fix] Corrected an issue where data loss would occur when `_FillValue` was mistakenly allowed to be redefined.  See [Github #390](https://github.com/Unidata/netcdf-c/issues/390), [GitHub #387](https://github.com/Unidata/netcdf-c/pull/387) for more information.
-* [Enhancement] Modified netCDF4 to use ASCII for NC_CHAR.  See [Github Pull request #316](https://github.com/Unidata/netcdf-c/pull/316) for more information.
 * [Upgrade][Bug] Corrected an issue regarding how "orphaned" DAS attributes were handled. See [GitHub #376](https://github.com/Unidata/netcdf-c/pull/376) for more information.
 * [Upgrade] Update utf8proc.[ch] to use the version now maintained by the Julia Language project (https://github.com/JuliaLang/utf8proc/blob/master/LICENSE.md).
 * [Bug] Addressed conversion problem with Windows sscanf.  This primarily affected some OPeNDAP URLs on Windows.  See [GitHub #365](https://github.com/Unidata/netcdf-c/issues/365) and [GitHub #366](https://github.com/Unidata/netcdf-c/issues/366) for more information.

config.h.cmake.in

@@ -3,6 +3,18 @@
 
 #ifdef _MSC_VER
 
+/* Prevent an issue where there is a circular inclusion
+   of winsock.h/windows.h.  This weird state occurs with
+   libdap4 and hdf4 support. The solution comes from the
+   following URL, found after a bit of research.
+
+   Added in support of the 4.5.0-rc1.  Hello, future generations.
+
+   * https://stackoverflow.com/questions/1372480/c-redefinition-header-files-winsock2-h
+
+   */
+   #define _WINSOCKAPI_
+
    #if _MSC_VER>=1900
      #define STDC99
    #endif

configure.ac

@@ -15,7 +15,7 @@ AC_REVISION([$Id: configure.ac,v 1.450 2010/05/28 19:42:47 dmh Exp $])
 AC_PREREQ([2.59])
 
 # Initialize with name, version, and support email address.
-AC_INIT([netCDF], [4.5.0-development], [support-netcdf@unidata.ucar.edu])
+AC_INIT([netCDF], [4.5.1-development], [support-netcdf@unidata.ucar.edu])
 
 ##
 # Prefer an empty CFLAGS variable instead of the default -g -O2.
@@ -26,7 +26,7 @@ AC_INIT([netCDF], [4.5.0-development], [support-netcdf@unidata.ucar.edu])
 
 AC_SUBST([NC_VERSION_MAJOR]) NC_VERSION_MAJOR=4
 AC_SUBST([NC_VERSION_MINOR]) NC_VERSION_MINOR=5
-AC_SUBST([NC_VERSION_PATCH]) NC_VERSION_PATCH=0
+AC_SUBST([NC_VERSION_PATCH]) NC_VERSION_PATCH=1
 AC_SUBST([NC_VERSION_NOTE]) NC_VERSION_NOTE="-development"
 
 #####
@@ -71,6 +71,9 @@ AC_CONFIG_LINKS([nc_test4/ref_hdf5_compat1.nc:nc_test4/ref_hdf5_compat1.nc])
 AC_CONFIG_LINKS([nc_test4/ref_hdf5_compat2.nc:nc_test4/ref_hdf5_compat2.nc])
 AC_CONFIG_LINKS([nc_test4/ref_hdf5_compat3.nc:nc_test4/ref_hdf5_compat3.nc])
 
+AC_CONFIG_LINKS([nc_test4/ref_chunked.hdf4:nc_test4/ref_chunked.hdf4])
+AC_CONFIG_LINKS([nc_test4/ref_contiguous.hdf4:nc_test4/ref_contiguous.hdf4])
+
 # This call is required by automake.
 AM_INIT_AUTOMAKE([foreign dist-zip subdir-objects])
 
@@ -1439,6 +1442,7 @@ abs_top_builddir=`pwd`
 cd $srcdir
 abs_top_srcdir=`pwd`
 cd $abs_top_builddir
+#AC_CONFIG_FILES(test_common.sh.in)
 rm -f ${abs_top_builddir}/test_common.sh
 sed -e "s|@TOPSRCDIR@|${abs_top_srcdir}|" -e "s|@TOPBUILDDIR@|${abs_top_builddir}|" <${abs_top_srcdir}/test_common.in >${abs_top_builddir}/test_common.sh
 
@@ -1485,4 +1489,6 @@ AC_CONFIG_FILES([Makefile
                  [test -f  nc-config && chmod 755 nc-config])
 AC_OUTPUT()
 
+    mv -f ${abs_top_srcdir}/test_common.sh ${abs_top_builddir}/test_common.sh
+
 cat libnetcdf.settings

dap4_test/test_raw.sh

@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 
 if test "x$srcdir" = x ; then srcdir=`pwd`; fi
 . ../test_common.sh

docs/Doxyfile.developer

@@ -38,7 +38,7 @@ PROJECT_NAME           = netCDF-C
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 4.4.1-development
+PROJECT_NUMBER         = 4.5.1-development
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

gdb-branch.txt

@@ -1,18 +0,0 @@
-set breakpoint pending yes
-break test_nc_redef
-commands
-break util.c:888 if i == 6
-end
-
-#break util.c:903 if i == 6
-#break util.c:1020
-#break util.c:1014 if i == 6 && j == 0
-#break util.c:1016 if i == 6 && j == 0
-#commands
-#break putget.c:10948
-#end
-
-#break test_write.c:216
-#commands
-#break ncx_put_int_double
-#end

gdb-master.txt

@@ -1,12 +0,0 @@
-set breakpoint pending yes
-break test_nc_redef
-commands
-break util.c:835 if i == 6
-end
-
-#break test_write.c:139
-#break util.c:961 if i == 6 && j == 0
-#break util.c:963 if i == 6 && j == 0
-#commands
-#break putget.c:10414
-#end

gh319 Notes.md

@@ -1,10 +0,0 @@
-# Notes related to bug gh319
-
-## NNotes
-
-## Results and Debugging Table
-
-Variable  | Master | GH319
-----------        |--------|------
-expect            |  127   | 255
-value / value[0]  |  127   | -1

liblib/Makefile.am

@@ -18,7 +18,7 @@ lib_LTLIBRARIES = libnetcdf.la
 # for information regarding incrementing `-version-info`.
 ##
 
-libnetcdf_la_LDFLAGS = -version-info 11:4:0 ${NOUNDEFINED}
+libnetcdf_la_LDFLAGS = -version-info 12:0:1
 
 libnetcdf_la_CPPFLAGS = ${AM_CPPFLAGS}
 libnetcdf_la_LIBADD =

libsrc/ncx.m4

@@ -2196,9 +2196,9 @@ APIPrefix`x_get_size_t'(const void **xpp,  size_t *ulp)
 	/* similar to get_ix_int */
 	const uchar *cp = (const uchar *) *xpp;
 
-	*ulp  = (size_t)(*cp++ << 24);
+	*ulp  = (unsigned)(*cp++ << 24);
-	*ulp |= (size_t)(*cp++ << 16);
+	*ulp |= (*cp++ << 16);
-	*ulp |= (size_t)(*cp++ << 8);
+	*ulp |= (*cp++ << 8);
 	*ulp |= *cp;
 
 	*xpp = (const void *)((const char *)(*xpp) + X_SIZEOF_SIZE_T);

nc_test4/CMakeLists.txt

@@ -28,8 +28,6 @@ ENDIF(BUILD_UTILITIES)
 BUILD_BIN_TEST(tst_empty_vlen_unlim)
 ADD_SH_TEST(nc_test4 run_empty_vlen_test)
 
-
-
 IF(NOT MSVC)
   SET(NC4_TESTS ${NC4_TESTS} tst_interops5 tst_camrun)
 ENDIF()
@@ -63,7 +61,7 @@ IF(BUILD_BENCHMARKS)
 ENDIF()
 
 # Copy some test files from current source dir to out-of-tree build dir.
-FILE(GLOB COPY_FILES ${CMAKE_CURRENT_SOURCE_DIR}/*.nc ${CMAKE_CURRENT_SOURCE_DIR}/*.sh)
+FILE(GLOB COPY_FILES ${CMAKE_CURRENT_SOURCE_DIR}/*.nc ${CMAKE_CURRENT_SOURCE_DIR}/*.sh ${CMAKE_CURRENT_SOURCE_DIR}/*.hdf4)
 FILE(COPY ${COPY_FILES} DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 IF(MSVC)
   FILE(COPY ${COPY_FILES} DESTINATION ${RUNTIME_OUTPUT_DIRECTORY}/)

nc_test4/Makefile.am

@@ -25,7 +25,7 @@ tst_h_scalar tst_rename tst_h5_endians tst_atts_string_rewrite 		\
 tst_hdf5_file_compat tst_fill_attr_vanish tst_rehash
 
 # Temporary I hope
-if !ISCYGWIN 
+if !ISCYGWIN
 NC4_TESTS += tst_h_strbug tst_h_refs
 endif
 
@@ -131,12 +131,11 @@ run_get_hdf4_files.sh run_valgrind_tests.sh run_valgrind_tests2.sh	\
 run_bm_ar4.sh ref_tst_compounds.nc run_hdf4_valgrind_tests.sh		\
 ref_tst_xplatform2_1.nc ref_tst_xplatform2_2.nc ref_tst_dims.nc		\
 ref_tst_interops4.nc run_get_knmi_files.sh CMakeLists.txt               \
-run_grp_rename.sh tst_formatx_hdf4.sh                                   \
+run_grp_rename.sh tst_formatx_hdf4.sh run_chunk_hdf4.sh \
-run_chunk_hdf4.sh contiguous.hdf4 chunked.hdf4 \
 tst_h5_endians.c tst_h4_lendian.c tst_atts_string_rewrite.c \
 tst_put_vars_two_unlim_dim.c tst_empty_vlen_unlim.c run_empty_vlen_test.sh \
 ref_hdf5_compat1.nc ref_hdf5_compat2.nc ref_hdf5_compat3.nc tst_misc.sh \
-tdset.h5 tst_hdf4_read_var.sh
+tdset.h5 tst_hdf4_read_var.sh ref_contiguous.hdf4 ref_chunked.hdf4
 
 
 CLEANFILES = tst_mpi_parallel.bin cdm_sea_soundings.nc bm_chunking.nc	\
@@ -157,4 +156,6 @@ AMSR_E_L3_DailyLand_V06_20020619.hdf			\
 MYD29.A2009152.0000.005.2009153124331.hdf		\
 MYD29.A2002185.0000.005.2007160150627.hdf		\
 MOD29.A2000055.0005.005.2006267200024.hdf
+
+
 endif # HDF4_FILE_TESTS

nc_test4/run_chunk_hdf4.sh

@@ -1,37 +1,26 @@
 #!/bin/sh
-# Run test_chunk_hdf4 passing ${src_dir}
+# Run test_chunk_hdf4 passing ${srcdir}
+
+
 
 if test "x$srcdir" = x ; then srcdir=`pwd`; fi
 . ../test_common.sh
 
-CHUNKED=chunked.hdf4
+set -e
-CONTIG=contiguous.hdf4
 
 echo ""
 echo "*** Testing hdf4 chunking..."
 
-if test "x${src_dir}" = "x" ; then
+if test "x${srcdir}" = "x" ; then
-src_dir="."
+srcdir="."
-fi
-
-# Move the data sets into place
-ISDISTCHECK=0
-if test -f ./${CHUNKED} ; then
-ISDISTCHECK=0
-else
-ISDISTCHECK=1
-cp ${src_dir}/${CHUNKED} .
-cp ${src_dir}/${CONTIG} .
 fi
 
 if ./tst_chunk_hdf4 ; then
   echo "***SUCCESS!! tst_chunk_hdf4"
 else
+  RES=$?
   echo "***FAIL: tst_chunk_hdf4"
-fi
+  exit $RES
-
-if test "x${ISDISTCHECK}" = "x1" ; then
-echo rm -f ./${CHUNKED} ./${CONTIG}
 fi
 
 exit 0

nc_test4/tst_chunk_hdf4.c

@@ -11,10 +11,10 @@
 #include <H5DSpublic.h>
 #include <mfhdf.h>
 
-#define CHUNKEDFILE "chunked.hdf4"
+#define CHUNKEDFILE "ref_chunked.hdf4"
 #define CHUNKEDVAR "LandWater"
 
-#define CONTIGFILE "contiguous.hdf4"
+#define CONTIGFILE "ref_contiguous.hdf4"
 #define CONTIGVAR "pres"
 
 #define LAT_LEN 3

ncdump/tst_dimsizes.c

@@ -30,12 +30,12 @@ main(int argc, char **argv)
     size_t dimsize;
     int dimid;
     int stat = NC_NOERR;
-
+    nc_set_log_level(5);
     printf("\n*** Testing Max Dimension Sizes\n");
 
     printf("\n|size_t|=%lu\n",(unsigned long)sizeof(size_t));
 
-    printf("\n*** Writing Max Dimension Size For NC_CLASSIC\n");
+    printf("\n*** Writing Max Dimension Size (%d) For NC_CLASSIC\n",DIMMAXCLASSIC);
     if ((stat=nc_create(FILECLASSIC, NC_CLOBBER, &ncid))) ERRSTAT(stat);
     dimsize = DIMMAXCLASSIC;
     if ((stat=nc_def_dim(ncid, "testdim", dimsize, &dimid))) ERRSTAT(stat);
@@ -48,10 +48,11 @@ main(int argc, char **argv)
     if(dimsize != DIMMAXCLASSIC) ERR;
     if ((stat=nc_close(ncid))) ERRSTAT(stat);
 
-    printf("\n*** Writing Max Dimension Size For NC_64BIT_OFFSET\n");
+    printf("\n*** Writing Max Dimension Size (%u) For NC_64BIT_OFFSET\n",DIMMAX64OFFSET);
     if ((stat=nc_create(FILE64OFFSET, NC_CLOBBER | NC_64BIT_OFFSET, &ncid))) ERRSTAT(stat);
     dimsize = DIMMAX64OFFSET;
     if ((stat=nc_def_dim(ncid, "testdim", dimsize, &dimid))) ERRSTAT(stat);
+    if ((stat=nc_enddef(ncid))) ERRSTAT(stat);
     if ((stat=nc_close(ncid))) ERRSTAT(stat);
 
     printf("\n*** Reading Max Dimension Size For NC_64BIT_OFFSET\n");
@@ -62,7 +63,7 @@ main(int argc, char **argv)
     if ((stat=nc_close(ncid))) ERRSTAT(stat);
 
     if(sizeof(size_t) == 8) {
-        printf("\n*** Writing Max Dimension Size For NC_64BIT_DATA\n");
+      printf("\n*** Writing Max Dimension Size (%llu) For NC_64BIT_DATA\n",DIMMAX64DATA);
         if ((stat=nc_create(FILE64DATA, NC_CLOBBER | NC_64BIT_DATA, &ncid))) ERRSTAT(stat);
         dimsize = (size_t)DIMMAX64DATA;
         if ((stat=nc_def_dim(ncid, "testdim", dimsize, &dimid))) ERRSTAT(stat);

ncdump/tst_dimsizes.sh

@@ -1,6 +1,8 @@
 #!/bin/sh
 
-if test "x$srcdir" = x ; then srcdir=`pwd`; fi 
+#set -e
+
+if test "x$srcdir" = x ; then srcdir=`pwd`; fi
 . ../test_common.sh
 
 echo "*** Test Maximum dimension sizes X mode"
@@ -48,4 +50,3 @@ fi
 rm -f tmp tst_dimsize_classic.nc tst_dimsize_64offset.nc tst_dimsize_64data.nc
 
 exit $RETURN
-

test_common.in

@@ -1,3 +1,5 @@
+set -e
+
 TOPSRCDIR=@TOPSRCDIR@
 TOPBUILDDIR=@TOPBUILDDIR@