Merge branch 'v4.5.0-release-branch' into netrc.dmh

Author: WardF

CMakeLists.txt

@@ -757,6 +757,11 @@ IF(USE_HDF5 OR ENABLE_NETCDF_4)
 
 ENDIF(USE_HDF5 OR ENABLE_NETCDF_4)
 
+# Option to turn on CDF5 support.
+OPTION(ENABLE_CDF5 "Enable CDF5 Support." OFF)
+IF(ENABLE_CDF5)
+    SET(USE_CDF5 ON CACHE BOOL "")
+ENDIF(ENABLE_CDF5)
 
 # Option to Build DAP2+DAP4 Clients
 OPTION(ENABLE_DAP "Enable DAP2 and DAP4 Client." ON)
@@ -805,6 +810,12 @@ IF(ENABLE_DAP)
   #include <curl/curl.h>
   int main() {int x = CURLOPT_CHUNK_BGN_FUNCTION;}" HAVE_CURLOPT_CHUNK_BGN_FUNCTION)
 
+  # Check to see if CURLINFO_HTTP_CODE is defined.
+  # It showed up in curl 7.10.7.
+  CHECK_C_SOURCE_COMPILES("
+  #include <curl/curl.h>
+  int main() {int x = CURLINFO_HTTP_CODE;}" HAVE_CURLINFO_HTTP_CODE)
+
 ELSE()
   SET(ENABLE_DAP2 OFF)
   SET(ENABLE_DAP4 OFF)
@@ -1891,6 +1902,7 @@ is_enabled(USE_DISKLESS HAS_DISKLESS)
 is_enabled(USE_MMAP HAS_MMAP)
 is_enabled(JNA HAS_JNA)
 is_enabled(STATUS_RELAX_COORD_BOUND RELAX_COORD_BOUND)
+is_enabled(ENABLE_CDF5 HAS_CDF5)
 
 # Generate file from template.
 CONFIGURE_FILE("${CMAKE_CURRENT_SOURCE_DIR}/libnetcdf.settings.in"

RELEASE_NOTES.md

@@ -1,4 +1,4 @@
-Release Notes       {#RELEASE_NOTES}
+qRelease Notes       {#RELEASE_NOTES}
 =============
 
 \brief Release notes file for the netcdf-c package.
@@ -7,6 +7,10 @@ This file contains a high-level description of this package's evolution. Release
 
 ## 4.5.0 - TBD
 
+* [Bug] Corrected an issue where older versions of curl might fail. See [GitHub #487](https://github.com/Unidata/netcdf-c/issues/487) for more information.
+* [Enhancement] Added options to enable/disable `CDF5` support at configure time for autotools and cmake-based builds.  The options are `--enable/disable-cdf5` and `ENABLE_CDF5`, respectively.  See [Github #484](https://github.com/Unidata/netcdf-c/issues/484) for more information.
+* [Bug Fix] Corrected an issue when subsetting a netcdf3 file via `nccopy -v/-V`. See [Github #425](https://github.com/Unidata/netcdf-c/issues/425) and [Github #463](https://github.com/Unidata/netcdf-c/issues/463) for more information.
+* [Bug Fix] Corrected `--has-dap` and `--has-dap4` output for cmake-based builds. See [GitHub #473](https://github.com/Unidata/netcdf-c/pull/473) for more information.
 * [Bug Fix] Corrected an issue where `NC_64BIT_DATA` files were being read incorrectly by ncdump, despite the data having been written correctly.  See [GitHub #457](https://github.com/Unidata/netcdf-c/issues/457) for more information.
 * [Bug Fix] Corrected a potential stack buffer overflow.  See [GitHub #450](https://github.com/Unidata/netcdf-c/pull/450) for more information.
 

config.h.cmake.in

@@ -107,6 +107,10 @@ are set when opening a binary file on Windows. */
 /* set this only when building a DLL under MinGW */
 #cmakedefine DLL_NETCDF 1
 
+/* if true, enable CDF5 Support */
+#cmakedefine ENABLE_CDF5 1
+#cmakedefine USE_CDF5 1
+
 /* if true, build DAP2 and DAP4 Client */
 #cmakedefine ENABLE_DAP 1
 
@@ -147,6 +151,9 @@ are set when opening a binary file on Windows. */
 /* Is CURLINFO_RESPONSE_CODE defined */
 #cmakedefine HAVE_CURLINFO_RESPONSE_CODE 1
 
+/* Is CURLINFO_HTTP_CODE defined */
+#cmakedefine HAVE_CURLINFO_HTTP_CODE 1
+
 /* Is CURLOPT_CHUNK_BGN_FUNCTION defined */
 #cmakedefine HAVE_CURLOPT_CHUNK_BGN_FUNCTION 1
 

configure.ac

@@ -441,6 +441,22 @@ AC_MSG_RESULT([$enable_dap_long_tests])
 
 AM_CONDITIONAL(INTERNAL_OCLIB,[test "x" = "x"])
 
+# Check whether we want to enable CDF5 support.
+AC_MSG_CHECKING([whether CDF5 support should be enabled (default off)])
+AC_ARG_ENABLE([cdf5],
+              [AS_HELP_STRING([--enable-cdf5],
+                              [build with CDF5 support.])])
+test "x$enable_cdf5" = xyes || enable_cdf5=no
+AC_MSG_RESULT($enable_cdf5)
+
+if test "x$enable_cdf5" = xyes; then
+   AC_DEFINE([USE_CDF5], [1], [if true, enable CDF5 Support])
+   AC_DEFINE([ENABLE_CDF5], [1], [if true, enable CDF5 Support])
+fi
+
+AM_CONDITIONAL(USE_CDF5, [test x$enable_cdf5 = xyes ])
+AM_CONDITIONAL(ENABLE_CDF5, [test x$enable_cdf5 = xyes ])
+
 # Does the user want to do some extra tests?
 AC_MSG_CHECKING([whether netCDF extra tests should be run (developers only)])
 AC_ARG_ENABLE([extra-tests],
@@ -1000,11 +1016,15 @@ if test "x$enable_netcdf_4" = xyes; then
    fi
 
    # The user may have built HDF5 with the SZLIB library.
+   enable_szlib=no
    if test "x$ac_cv_func_H5Z_SZIP" = xyes; then
-    AC_SEARCH_LIBS([SZ_Compress], [szip sz], [], [])
+    enable_szlib=yes
+    AC_SEARCH_LIBS([ SZ_Compress], [szip sz], [], [])
   	AC_DEFINE([USE_SZIP], [1], [if true, compile in szip compression in netCDF-4 variables])
    fi
 
+
+
    if test "x$ac_cv_func_H5free_memory" = xyes; then
       AC_DEFINE([HDF5_HAS_H5FREE], [1], [if true, H5free_memory() will be used to free hdf5-allocated memory in nc4file.])
    fi
@@ -1249,7 +1269,7 @@ AM_CONDITIONAL(USE_DAP, [test "x$enable_dap" = xyes]) # Alias
 # Provide protocol specific flags
 AM_CONDITIONAL(ENABLE_DAP, [test "x$enable_dap" = xyes])
 AM_CONDITIONAL(ENABLE_DAP4, [test "x$enable_dap4" = xyes])
-
+AM_CONDITIONAL(ENABLE_CDF5, [test "x$enable_cdf5" = xyes])
 AM_CONDITIONAL(ENABLE_DAP_REMOTE_TESTS, [test "x$enable_dap_remote_tests" = xyes])
 AM_CONDITIONAL(ENABLE_DAP_AUTH_TESTS, [test "x$enable_dap_auth_tests" = xyes])
 AM_CONDITIONAL(ENABLE_DAP_LONG_TESTS, [test "x$enable_dap_long_tests" = xyes])
@@ -1362,11 +1382,12 @@ AC_SUBST(HAS_DAP,[$enable_dap])
 AC_SUBST(HAS_DAP4,[$enable_dap4])
 AC_SUBST(HAS_NC2,[$nc_build_v2])
 AC_SUBST(HAS_NC4,[$enable_netcdf_4])
+AC_SUBST(HAS_CDF5,[$enable_cdf5])
 AC_SUBST(HAS_HDF4,[$enable_hdf4])
 AC_SUBST(HAS_PNETCDF,[$enable_pnetcdf])
 AC_SUBST(HAS_HDF5,[$enable_netcdf_4])
 AC_SUBST(HAS_LOGGING, [$enable_logging])
-AC_SUBST(HAS_SZLIB,[$ac_cv_func_H4Z_SZIP])
+AC_SUBST(HAS_SZLIB,[$enable_szlib])
 AC_SUBST(HAS_PARALLEL,[$enable_parallel])
 AC_SUBST(HAS_PARALLEL4,[$enable_parallel4])
 AC_SUBST(HAS_DISKLESS,[$enable_diskless])

docs/attribute_conventions.md

@@ -25,11 +25,14 @@ It is strongly recommended that applicable conventions be followed unless there
 
 <p>
 
-> It is not necessary to define your own _FillValue attribute for a variable if the default fill value for the type of the variable is adequate. However, use of the default fill value for data type byte is not recommended. Note that if you change the value of this attribute, the changed value applies only to subsequent writes; previously written data are not changed.
+> If _FillValue is undefined, it is assumed that there are no unwritten data-values. Generic applications needing to write a value to represent undefined or missing values may use either `_FillValue` or `missing_value` for this purpose. It is legal (but not recommended) for the fill value to be within the valid range of the data.
 
 <p>
 
-> Generic applications often need to write a value to represent undefined or missing values. The fill value provides an appropriate value for this purpose because it is normally outside the valid range and therefore treated as missing when read by generic applications. It is legal (but not recommended) for the fill value to be within the valid range.
+> Generic applications often need to write a value to represent undefined or missing values. The fill value provides an appropriate value for this purpose because it is normally outside the valid range and therefore treated as missing when read by generic applications. It is legal (but not recommended) for the fill value to be within the valid range.		
+
+> **Note that if you change the value of this attribute, the changed value applies only to subsequent writes; previously written data are not changed.**
+
 
 `missing_value`
 
@@ -183,4 +186,3 @@ Using the following API calls will fail.
 > The type of this attribute is NC_INT.
 
 > This attribute is computed by using the HDF5 API to walk the file to look for attributes specific to netcdf-4.  False negatives are possible for a small subset of netcdf-4 files, especially those not containing dimensions. False positives are only possible by deliberate modifications to an existing HDF5 file thru the HDF5 API. For files with the _NCProperties attribute, this attribute is redundant. For files created prior to the introduction of the _NCProperties attribute, this may be a useful indicator of the provenance of the file.
-

docs/types.dox

@@ -22,9 +22,10 @@ The atomic external types supported by the netCDF interface are:
 - ::NC_UINT64 	64-bit unsigned integer *
 - ::NC_FLOAT 	32-bit floating point
 - ::NC_DOUBLE 	64-bit floating point
-- ::NC_STRING 	variable length character string *
+- ::NC_STRING 	variable length character string +
 
-\remark{* These types are available only for CDF5 (NC_CDF5) and netCDF-4 format (NC_NETCDF4) files. All the unsigned ints (except \ref NC_CHAR), the 64-bit ints, and string type are for CDF5 or netCDF-4 files only.}
+\remark * These types are available only for CDF5 (NC_CDF5) and netCDF-4 format (NC_NETCDF4) files. All the unsigned ints (except \ref NC_CHAR) and the 64-bit ints are for CDF5 or netCDF-4 files only.
+\remark + These types are available only for netCDF-4 (NC_NETCDF4) files.
 
 These types were chosen to provide a reasonably wide range of
 trade-offs between data precision and number of bits required for each

include/nctestserver.h

@@ -9,6 +9,10 @@
 #define TIMEOUT 10 /*seconds*/
 #define BUFSIZE 8192 /*bytes*/
 
+#ifndef HAVE_CURLINFO_RESPONSE_CODE
+#define CURLINFO_RESPONSE_CODE CURLINFO_HTTP_CODE
+#endif
+
 static int ping(const char* url);
 
 static char**

libdap4/d4curlflags.c

@@ -11,7 +11,9 @@ struct CURLFLAG curlopts[] = {
 {"CURLOPT_PROXYUSERPWD",CURLOPT_PROXYUSERPWD,10006,CF_STRING},
 {"CURLOPT_SSLCERT",CURLOPT_SSLCERT,10025,CF_STRING},
 {"CURLOPT_SSLKEY",CURLOPT_SSLKEY,10087,CF_STRING},
+#ifdef HAVE_CURLOPT_KEYPASSWD
 {"CURLOPT_SSLKEYPASSWD",CURLOPT_SSLKEYPASSWD,CURLOPT_KEYPASSWD,CF_STRING},
+#endif
 {"CURLOPT_SSL_VERIFYHOST",CURLOPT_SSL_VERIFYHOST,81,CF_LONG},
 {"CURLOPT_SSL_VERIFYPEER",CURLOPT_SSL_VERIFYPEER,64,CF_LONG},
 {"CURLOPT_TIMEOUT",CURLOPT_TIMEOUT,13,CF_LONG},

libdap4/d4curlfunctions.h

@@ -6,6 +6,14 @@
 #ifndef D4CURLFUNCTIONS_H
 #define D4CURLFUNCTIONS_H
 
+/* Aliases to older names */
+#ifndef HAVE_CURLOPT_KEYPASSWD
+#define CURLOPT_KEYPASSWD CURLOPT_SSLKEYPASSWD
+#endif
+#ifndef HAVE_CURLINFO_RESPONSE_CODE
+#define CURLINFO_RESPONSE_CODE CURLINFO_HTTP_CODE
+#endif
+
 enum CURLFLAGTYPE {CF_UNKNOWN=0,CF_OTHER=1,CF_STRING=2,CF_LONG=3};
 struct CURLFLAG {
     const char* name;

libdap4/d4rc.c

@@ -103,9 +103,11 @@ rcorder(NClist* rc)
 	nclistpush(newrc,ti);
     }
 #ifdef D4DEBUG
+
     storedump("reorder:",newrc);
 #endif
     return newrc;
+
 }
 
 /* Create a triple store from a file */
@@ -540,7 +542,9 @@ storedump(char* msg, NClist* triples)
     for(i=0;i<nclistlength(triples);i++) {
 	NCD4triple* t = (NCD4triple*)nclistget(triples,i);
         fprintf(stderr,"\t%s\t%s\t%s\n",
+
                 ((t->host == NULL || strlen(t->host)==0)?"--":t->host),t->key,t->value);
+
     }
     fflush(stderr);
 }