Merge pull request #1322 from Unidata/v4.6.2.1-dev.wif

Preparing Maintenance Release

RELEASE_NOTES.md

@@ -7,9 +7,15 @@ This file contains a high-level description of this package's evolution. Release
 
 ## 4.6.3 - TBD
 
+## 4.6.2.1 - February 15, 2019
+
+### Maintenance Release
+
 * Update the license from the home-brewed NetCDF license to the standard 3-Clause BSD License.  This change does not result in any new restrictions; it is merely the adoption of a standard, well-known and well-understood license in place of the historic NetCDF license written at Unidata.  This is part of a broader push by Unidata to adopt modern, standardized licensing.  
-
+* [BugFix] Corrected DAP-releated issues on big-endian machines. See [Github #1321](https://github.com/Unidata/netcdf-c/issues/1321), [Github #1302](https://github.com/Unidata/netcdf-c/issues/1302) for more information.
-
+* [BugFix][Enhancement]  Various and sundry bugfixes and performance enhancements, thanks to @edhartnett, @gsjaardema, @t-b, @wkliao, and all of our other contributors.
+* [Enhancement] Extended `nccopy -F` syntax to support multiple variables with a single invocation. See [Github #1311](https://github.com/Unidata/netcdf-c/issues/1311) for more information.
+* [BugFix] Corrected an issue where DAP2 was incorrectly converting signed bytes, resulting in an erroneous error message under some circumstances. See [GitHub #1317](https://github.com/Unidata/netcdf-c/issues/1317) for more information.  See [Github #1319](https://github.com/Unidata/netcdf-c/issues/1319) for related information.
 * [BugFix][Enhancement] Modified `nccopy` so that `_NCProperties` is not copied over verbatim but is instead generated based on the version of `libnetcdf` used when copying the file.  Additionally, `_NCProperties` are displayed if/when associated with a netcdf3 file, now. See [GitHub #803](https://github.com/Unidata/netcdf-c/issues/803) for more information.
 
 ## 4.6.2 - November 16, 2018

docs/DAP4.dox

@@ -46,11 +46,11 @@ format. The URL is composed of three parts.
    +  http://remotetest.unidata.ucar.edu/d4ts/test.01#protocol=dap4
    +  http://thredds.ucar.edu/thredds/dap4/...
 
- -  Constraints - these are suffixed to the URL and take the form
+-  Constraints - these are suffixed to the URL and take the form
     “?dap4.ce=\<expression\>”. The form of the constraint expression
     is somewhat complicated, and the specification should be consulted.
 
- - Client parameters - these may be specified in either of
+- Client parameters - these may be specified in either of
    two ways.  The older, deprecated form prefixes text to the
    front of the url and is of the the general form [\<name>]
    or [\<name>=value].  Examples include [show=fetch] or [noprefetch].
@@ -95,7 +95,7 @@ Parameter Name Legal Values Semantics
   for specially named elements in the DMR XML in order to
   achieve a better translation of the DAP4 meta-data to NetCDF enhanced
   metadata.
-- "opaquesize=<integer>" - This parameter causes the netCDF code to 
+- "opaquesize=<integer>" - This parameter causes the netCDF code to
   convert DAP4 variable size OPAQUE objects to netcdf-4 fixed size
   objects and forces all of them to be of the size specified.
 - "fillmismatch" - Unfortunately, a number of servers sometimes
@@ -152,79 +152,79 @@ Finally from the set so constructed, choose the first matching entry.
 Currently, the supported set of keys (with descriptions) are as
 follows.
 
--# HTTP.VERBOSE  
+-# HTTP.VERBOSE
-        Type: boolean ("1"/"0")  
+        Type: boolean ("1"/"0")
-        Description: Produce verbose output, especially using SSL.  
+        Description: Produce verbose output, especially using SSL.
-        Related CURL Flags: CURLOPT_VERBOSE  
+        Related CURL Flags: CURLOPT_VERBOSE
 
--# HTTP.DEFLATE  
+-# HTTP.DEFLATE
-        Type: boolean ("1"/"0")  
+        Type: boolean ("1"/"0")
-        Description: Allow use of compression by the server.  
+        Description: Allow use of compression by the server.
-        Related CURL Flags: CURLOPT_ENCODING  
+        Related CURL Flags: CURLOPT_ENCODING
 
--# HTTP.COOKIEJAR  
+-# HTTP.COOKIEJAR
-        Type: String representing file path  
+        Type: String representing file path
-        Description: Specify the name of file into which to store cookies. Defaults to in-memory storage.  
+        Description: Specify the name of file into which to store cookies. Defaults to in-memory storage.
-        Related CURL Flags:CURLOPT_COOKIEJAR  
+        Related CURL Flags:CURLOPT_COOKIEJAR
 
--# HTTP.CREDENTIALS.USER  
+-# HTTP.CREDENTIALS.USER
-        Type: String representing user name  
+        Type: String representing user name
-        Description: Specify the user name for Digest and Basic authentication.  
+        Description: Specify the user name for Digest and Basic authentication.
-        Related CURL Flags:  
+        Related CURL Flags:
-  
--# HTTP.CREDENTIALS.PASSWORD  
-        Type: String representing password  
-        Type: boolean ("1"/"0")  
-        Description: Specify the password for Digest and Basic authentication.  
-        Related CURL Flags:  
 
--# HTTP.SSL.CERTIFICATE  
+-# HTTP.CREDENTIALS.PASSWORD
-        Type: String representing file path  
+        Type: String representing password
-        Description: Path to a file containing a PEM cerficate.  
+        Type: boolean ("1"/"0")
-        Related CURL Flags: CURLOPT_CERT  
+        Description: Specify the password for Digest and Basic authentication.
+        Related CURL Flags:
 
--# HTTP.SSL.KEY  
+-# HTTP.SSL.CERTIFICATE
-        Type: String representing file path  
+        Type: String representing file path
-        Description: Same as HTTP.SSL.CERTIFICATE, and should usually have the same value.  
+        Description: Path to a file containing a PEM cerficate.
-        Related CURL Flags: CURLOPT_SSLKEY  
+        Related CURL Flags: CURLOPT_CERT
 
--# HTTP.SSL.KEYPASSWORD  
+-# HTTP.SSL.KEY
-        Type: String representing password  
+        Type: String representing file path
-        Description: Password for accessing the HTTP.SSL.KEY/HTTP.SSL.CERTIFICATE  
+        Description: Same as HTTP.SSL.CERTIFICATE, and should usually have the same value.
-        Related CURL Flags: CURLOPT_KEYPASSWORD  
+        Related CURL Flags: CURLOPT_SSLKEY
 
--# HTTP.SSL.CAPATH  
+-# HTTP.SSL.KEYPASSWORD
-        Type: String representing directory  
+        Type: String representing password
-        Description: Path to a directory containing trusted certificates for validating server certificates.  
+        Description: Password for accessing the HTTP.SSL.KEY/HTTP.SSL.CERTIFICATE
-        Related CURL Flags: CURLOPT_CAPATH  
+        Related CURL Flags: CURLOPT_KEYPASSWORD
 
--# HTTP.SSL.VALIDATE  
+-# HTTP.SSL.CAPATH
-        Type: boolean ("1"/"0")  
+        Type: String representing directory
-        Description: Cause the client to verify the server's presented certificate.  
+        Description: Path to a directory containing trusted certificates for validating server certificates.
-        Related CURL Flags: CURLOPT_SSL_VERIFYPEER, CURLOPT_SSL_VERIFYHOST  
+        Related CURL Flags: CURLOPT_CAPATH
 
--# HTTP.TIMEOUT  
+-# HTTP.SSL.VALIDATE
-        Type: String ("dddddd")  
+        Type: boolean ("1"/"0")
-        Description: Specify the maximum time in seconds that you allow the http transfer operation to take.  
+        Description: Cause the client to verify the server's presented certificate.
-        Related CURL Flags: CURLOPT_TIMEOUT, CURLOPT_NOSIGNAL  
+        Related CURL Flags: CURLOPT_SSL_VERIFYPEER, CURLOPT_SSL_VERIFYHOST
 
--# HTTP.PROXY_SERVER  
+-# HTTP.TIMEOUT
-        Type: String representing url to access the proxy: (e.g.http://[username:password@]host[:port])  
+        Type: String ("dddddd")
-        Description: Specify the needed information for accessing a proxy.  
+        Description: Specify the maximum time in seconds that you allow the http transfer operation to take.
-        Related CURL Flags: CURLOPT_PROXY, CURLOPT_PROXYHOST, CURLOPT_PROXYUSERPWD  
+        Related CURL Flags: CURLOPT_TIMEOUT, CURLOPT_NOSIGNAL
 
--# HTTP.READ.BUFFERSIZE  
+-# HTTP.PROXY_SERVER
-        Type: String ("dddddd")  
+        Type: String representing url to access the proxy: (e.g.http://[username:password@]host[:port])
-        Description: Specify the the internal buffer size for curl reads.  
+        Description: Specify the needed information for accessing a proxy.
-        Related CURL Flags: CURLOPT_BUFFERSIZE, CURL_MAX_WRITE_SIZE (16kB),  
+        Related CURL Flags: CURLOPT_PROXY, CURLOPT_PROXYHOST, CURLOPT_PROXYUSERPWD
-                            CURL_MAX_READ_SIZE (512kB).  
+
+-# HTTP.READ.BUFFERSIZE
+        Type: String ("dddddd")
+        Description: Specify the the internal buffer size for curl reads.
+        Related CURL Flags: CURLOPT_BUFFERSIZE, CURL_MAX_WRITE_SIZE (16kB),
+                            CURL_MAX_READ_SIZE (512kB).
+
+-# HTTP.KEEPALIVE
+        Type: String ("on|n/m")
+        Description: Specify that TCP KEEPALIVE should be enabled and that the associated idle wait time is n and that the associated repeat interval is m. If the value is of the form is the string "on", then turn on keepalive, but do not set idle or interval.
+        Related CURL Flags: CURLOPT_TCP_KEEPALIVE, CURLOPT_TCP_KEEPIDLE,
+                            CURLOPT_TCP_KEEPINTVL.
 
--# HTTP.KEEPALIVE  
-        Type: String ("on|n/m")  
-        Description: Specify that TCP KEEPALIVE should be enabled and that the associated idle wait time is n and that the associated repeat interval is m. If the value is of the form is the string "on", then turn on keepalive, but do not set idle or interval.  
-        Related CURL Flags: CURLOPT_TCP_KEEPALIVE, CURLOPT_TCP_KEEPIDLE,  
-                            CURLOPT_TCP_KEEPINTVL.  
-  
 The related curl flags line indicates the curl flags modified by this
 key. See the libcurl documentation of the _curl_easy_setopt()_ function
 for more detail (http://curl.haxx.se/libcurl/c/curl_easy_setopt.html).

docs/guide.dox

@@ -88,12 +88,8 @@ were written.
 
 Unidata supports the netCDF interfaces for C (see <a
 href="http://www.unidata.ucar.edu/netcdf/docs/" >NetCDF-C User's
-Guide</a>), FORTRAN 77 (see <a
+Guide</a>), Fortran (see <a href="http://www.unidata.ucar.edu/netcdf/fortran/docs/" >NetCDF-Fortran User's Guide</a>)
-href="http://www.unidata.ucar.edu/netcdf/documentation/historic/netcdf-f77/index.html#Top"
+and C++ (see <a href="http://www.unidata.ucar.edu/netcdf/documentation/historic/cxx4/index.html"
->NetCDF Fortran 77 Interface Guide</a>), FORTRAN 90 (see <a
-href="http://www.unidata.ucar.edu/netcdf/documentation/historic/netcdf-f90/index.html"
->NetCDF Fortran 90 Interface Guide</a>), and C++ (see <a
-href="http://www.unidata.ucar.edu/netcdf/documentation/historic/cxx4/index.html"
 >NetCDF C++ Interface Guide</a>).
 
 The netCDF library is supported for various UNIX operating systems. A

docs/mainpage.dox

@@ -9,6 +9,12 @@ NetCDF is a set of software libraries and self-describing, machine-independent d
 
 The NetCDF homepage may be found at <a href="http://www.unidata.ucar.edu/software/netcdf/">http://www.unidata.ucar.edu/software/netcdf/</a>.  The NetCDF source-code is hosted at <a href="http://github.com">GitHub</a>, and may be found directly at <a href="http://github.com/Unidata/netcdf-c">http://github.com/Unidata/netcdf-c</a>.
 
+\subsection mainpage_learn_more_fortran Looking for NetCDF-Fortran Documentation?
+
+You can find the documentation for netCDF-Fortran here:
+
+- <a href="http://www.unidata.ucar.edu/software/netcdf/fortran/docs"> The NetCDF-Fortran Developer's Guide</a>
+
 \section this_release Learn more about the current NetCDF-C Release
 
 - \subpage RELEASE_NOTES
@@ -23,6 +29,7 @@ The NetCDF homepage may be found at <a href="http://www.unidata.ucar.edu/softwar
 
 \subsubsection NetCDF-Fortran
 
+
 - <A href="http://cdash.unidata.ucar.edu/index.php?project=netcdf-fortran">The netCDF-Fortran Nightly and Continuous Integration Dashboard</A>
 - <A href="https://travis-ci.org/Unidata/netcdf-c">NetCDF-Fortran at Travis-CI</A>
 

include/ncconfigure.h

@@ -41,7 +41,10 @@ typedef SSIZE_T ssize_t;
   in its headers.*/
 #ifndef _WIN32
 #if __STDC__ == 1 /*supposed to be same as -ansi flag */
+
+#ifndef strdup
 extern char* strdup(const char*);
+#endif
 
 #ifndef strlcat
 extern size_t strlcat(char*,const char*,size_t);
@@ -58,8 +61,10 @@ extern unsigned long long int strtoull(const char*, char**, int);
 #endif
 
 #ifdef _WIN32
+#ifndef strlcat
 #define strlcat(d,s,n) strcat_s((d),(n),(s))
 #endif
+#endif
 
 /* handle null arguments */
 #ifndef nulldup

include/netcdf_mem.h

@@ -12,6 +12,20 @@
 #ifndef NETCDF_MEM_H
 #define NETCDF_MEM_H 1
 
+/* Declaration modifiers for DLL support (MSC et al) */
+#if defined(DLL_NETCDF) /* define when library is a DLL */
+#  if defined(DLL_EXPORT) /* define when building the library */
+#   define MSC_EXTRA __declspec(dllexport)
+#  else
+#   define MSC_EXTRA __declspec(dllimport)
+#  endif
+#  include <io.h>
+#else
+#define MSC_EXTRA  /**< Needed for DLL build. */
+#endif  /* defined(DLL_NETCDF) */
+
+#define EXTERNL MSC_EXTRA extern /**< Needed for DLL build. */
+
 typedef struct NC_memio {
     size_t size;
     void* memory;

nc_test4/CMakeLists.txt

@@ -16,7 +16,7 @@ SET(NC4_TESTS tst_dims tst_dims2 tst_dims3 tst_files tst_files4
   tst_files6 tst_sync tst_h_strbug tst_h_refs tst_h_scalar tst_rename
   tst_rename2 tst_rename3 tst_h5_endians tst_atts_string_rewrite tst_put_vars_two_unlim_dim
   tst_hdf5_file_compat tst_fill_attr_vanish tst_rehash tst_types tst_bug324
-  tst_filterparser tst_atts3 tst_put_vars tst_elatefill tst_udf)
+  tst_atts3 tst_put_vars tst_elatefill tst_udf)
 
 # Note, renamegroup needs to be compiled before run_grp_rename
 
@@ -29,6 +29,7 @@ IF(ENABLE_FILTER_TESTING)
   build_bin_test(test_filter)
   build_bin_test(test_filter_misc)
   ADD_SH_TEST(nc_test4 tst_filter)
+  SET(NC4_TESTS ${NC4_TESTS} tst_filterparser)
 ENDIF(ENABLE_FILTER_TESTING)
 
 ENDIF(BUILD_UTILITIES)

plugins/CMakeLists.txt

@@ -8,7 +8,7 @@ SET(CMAKE_BUILD_TYPE "")
 
 SET(libbzip2_SOURCES blocksort.c huffman.c crctable.c randtable.c compress.c decompress.c bzlib.c H5Zbzip2.c)
 
-SET(libmisc_SOURCES H5Zmisc.c)
+SET(libmisc_SOURCES H5Zmisc.c H5Zutil.c h5misc.h)
 
 IF(ENABLE_FILTER_TESTING)
 IF(BUILD_UTILITIES)

plugins/H5Zutil.c

@@ -48,9 +48,10 @@ byteswap4(unsigned char* mem)
 void
 NC_filterfix8(void* mem0, int decode)
 {
+
+unsigned char* mem = mem0;
 #ifdef WORDS_BIGENDIAN
-    unsigned char* mem = mem0;    
+ if(decode) { /* Apply inverse of the encode case */
-    if(decode) { /* Apply inverse of the encode case */
 	byteswap4(mem); /* step 1: byte-swap each piece */
 	byteswap4(mem+4);
 	byteswap8(mem); /* step 2: convert to little endian format */
@@ -60,6 +61,8 @@ NC_filterfix8(void* mem0, int decode)
 	byteswap4(mem+4);
     }
 #else /* Little endian */
+
+
     /* No action is necessary */
-#endif	    
+#endif
 }