Batch EJH Pull requests

CMakeLists.txt

@@ -1265,6 +1265,7 @@ CHECK_INCLUDE_FILE("memory.h"  HAVE_MEMORY_H)
 CHECK_INCLUDE_FILE("string.h"  HAVE_STRING_H)
 CHECK_INCLUDE_FILE("winsock2.h" HAVE_WINSOCK2_H)
 CHECK_INCLUDE_FILE("ftw.h"  HAVE_FTW_H)
+CHECK_INCLUDE_FILE("libgen.h" HAVE_LIBGEN_H)
 
 CHECK_INCLUDE_FILES("time.h;sys/time.h" TIME_WITH_SYS_TIME)
 

Makefile.am

@@ -1,9 +1,10 @@
 ## This is a automake file, part of Unidata's netCDF package.
-# Copyright 2005-2013, see the COPYRIGHT file for more information.
+# Copyright 2005-2018, see the COPYRIGHT file for more information.
 
 # This is the main automake file for netCDF. It builds the different
 # netcdf directories. Not all directories are built, depending on the
 # options selected during configure.
+
 # Ed Hartnett, Ward Fisher
 
 # This directory stores libtool macros, put there by aclocal.
@@ -17,14 +18,9 @@ RELEASE_NOTES.md CTestCustom.cmake CTestConfig.cmake.in			\
 libnetcdf.settings.in netCDFConfig.cmake.in CMakeInstallation.cmake	\
 test-driver-verbose test_common.in
 
-pkgconfigdir=$(libdir)/pkgconfig
+pkgconfigdir = $(libdir)/pkgconfig
 pkgconfig_DATA = netcdf.pc
 
-# We need a way to automatically generate INSTALL from
-# docs/install.doc, now that we've switched from texinfo to doxygen.
-# INSTALL:
-#	non-existent-doxygen-to-text-utility <  docs/install.doc > INSTALL
-
 # Does the user want to build the V2 API?
 if BUILD_V2
 V2_TEST = nctest
@@ -68,7 +64,8 @@ endif
 
 # Define Test directories
 if BUILD_TESTSETS
-TESTDIRS = $(V2_TEST) nc_test $(NC_TEST4) $(NCDAP2TESTDIR) $(NCDAP4TESTDIR)
+TESTDIRS = $(V2_TEST) nc_test $(NC_TEST4) $(NCDAP2TESTDIR)	\
+$(NCDAP4TESTDIR)
 endif
 
 # This is the list of subdirs for which Makefiles will be constructed
@@ -85,21 +82,6 @@ test_common.sh
 # The nc-config script helps the user build programs with netCDF.
 bin_SCRIPTS = nc-config
 
-# What needs to go in the binrary dist?
-BINFILES = README_BINARIES.txt
-BINFILES += include/netcdf.h share/man/man3/netcdf.3 lib/libnetcdf.a
-BINFILES += libnetcdf.settings
-ZIPBINFILES = ${prefix}/include/netcdf.h			\
-${prefix}/share/man/man3/netcdf.3 ${prefix}/lib/libnetcdf.a
-
-if BUILD_UTILITIES
-BINFILES += bin/ncgen3$(EXEEXT) bin/ncgen$(EXEEXT) bin/ncdump$(EXEEXT)	\
-share/man/man1/ncgen.1 share/man/man1/ncdump.1
-ZIPBINFILES += ${prefix}/bin/ncgen3$(EXEEXT)				\
-${prefix}/bin/ncgen$(EXEEXT) ${prefix}/bin/ncdump$(EXEEXT)		\
-${prefix}/share/man/man1/ncgen.1 ${prefix}/share/man/man1/ncdump.1
-endif
-
 # install libnetcdf.settings in lib directory.
 settingsdir = $(libdir)
 settings_DATA = libnetcdf.settings
@@ -118,7 +100,6 @@ mm4::
 	  b=`basename $$m` ; d=`dirname $$m`;\
 	  pushd $$d; m4 -s $${b}.m4 > $${b}.c ; popd; done
 
-
 #####
 # If ENABLE_FORTRAN was turned on,
 # we have new make targets, build-netcdf-fortran and

config.h.cmake.in

@@ -379,6 +379,9 @@ are set when opening a binary file on Windows. */
 /* Define to 1 if you have the <ftw.h> header file. */
 #cmakedefine HAVE_FTW_H 1
 
+/* Define to 1 if you have the <libgen.h> header file. */
+#cmakedefine HAVE_LIBGEN_H 1
+
 /* Define to 1 if you have the `strlcat' function. */
 #cmakedefine HAVE_STRLCAT 1
 

configure.ac

@@ -745,6 +745,7 @@ AC_CHECK_HEADER(stdlib.h, ,AC_DEFINE([NO_STDLIB_H], [], [no stdlib.h]))
 AC_CHECK_HEADER(sys/types.h, ,AC_DEFINE([NO_SYS_TYPES_H], [], [no sys_types.h]))
 AC_CHECK_HEADERS([sys/dir.h])
 AC_CHECK_HEADERS([sys/param.h])
+AC_CHECK_HEADERS([libgen.h])
 #AC_CHECK_HEADERS([locale.h])
 AC_HEADER_DIRENT
 AC_HEADER_STDC

examples/C/filter_example.c

@@ -214,7 +214,7 @@ test_bzip2(void)
     /* Show chunking */ 
     printf("show chunks:");
     for(i=0;i<actualdims;i++)
-	printf("%s%d",(i==0?" chunks=":","),chunks[i]);
+	printf("%s%ld",(i==0?" chunks=":","),chunks[i]);
     printf("\n");
 
     /* prepare to write */

include/nc_tests.h

@@ -41,6 +41,7 @@
 #define ONE_TWENTY_EIGHT_MEG (SIXTEEN_MEG * 8)
 #define TEST_VAL_42 42
 #define BAD_NAME "dd//d/  "
+#define NUM_CLASSIC_TYPES 6
 #define NUM_NETCDF_TYPES 12
 /** \} */
 

libdispatch/dvar.c

@@ -1,8 +1,8 @@
-/*! \file
-Functions for defining and inquiring about variables.
-
-Copyright 2010 University Corporation for Atmospheric
-Research/Unidata. See COPYRIGHT file for more info.
+/* Copyright 2010-2018 University Corporation for Atmospheric
+   Research/Unidata. See COPYRIGHT file for more info. */
+/**
+ * @file
+ * Functions for defining and inquiring about variables.
 */
 
 #include "ncdispatch.h"
@@ -239,6 +239,10 @@ For classic format, 64-bit offset format, and netCDF-4/HDF5 with
 classic mode, if the new name is longer than the old name, the netCDF
 dataset must be in define mode.
 
+For netCDF-4/HDF5 files, renaming the variable changes the order of
+the variables in the file. The renamed variable becomes the last
+variable in the file.
+
 @param ncid NetCDF or group ID, from a previous call to nc_open(),
 nc_create(), nc_def_grp(), or associated inquiry functions such as
 nc_inq_ncid().
@@ -279,7 +283,7 @@ rel_hum in an existing netCDF dataset named foo.nc:
      status = nc_enddef(ncid);
      if (status != NC_NOERR) handle_error(status);
 @endcode
-
+@author Glenn Davis, Ed Hartnett, Dennis Heimbigner
 */
 int
 nc_rename_var(int ncid, int varid, const char *name)
@@ -416,13 +420,16 @@ NC_inq_recvar(int ncid, int varid, int* nrecdimsp, int *is_recdim)
    entirely.
 */
 
-/** \internal
-\ingroup variables
-Find the length of a type. This is how much space is required by the user, as in
-\code
-vals = malloc(nel * nctypelen(var.type));
-ncvarget(cdfid, varid, cor, edg, vals);
-\endcode
+/**
+ * @internal
+ * @ingroup variables
+ * Find the length of a type. This is how much space is required by
+ * the in memory to hold one element of this type.
+ *
+ * @parm type A netCDF atomic type.
+ *
+ * @return Length of the type in bytes, or -1 if type not found.
+ * @author Ed Hartnett
  */
 int
 nctypelen(nc_type type)
@@ -761,11 +768,22 @@ nc_free_string(size_t len, char **data)
  * This function must be called after nc_def_var and before nc_enddef
  * or any functions which writes data to the file.
  *
+ * Deflation and shuffline require chunked data. If this function is
+ * called on a variable with contigious data, then the data is changed
+ * to chunked data, with default chunksizes. Use nc_def_var_chunking()
+ * to tune performance with user-defined chunksizes.
+ *
+ * If this function is called on a scalar variable, it is ignored.
+ *
  * @param ncid NetCDF or group ID, from a previous call to nc_open(),
  * nc_create(), nc_def_grp(), or associated inquiry functions such as
  * nc_inq_ncid().
  * @param varid Variable ID
- * @param shuffle True to turn on the shuffle filter.
+ * @param shuffle True to turn on the shuffle filter. The shuffle
+ * filter can assist with the compression of integer data by changing
+ * the byte order in the data stream. It makes no sense to use the
+ * shuffle filter without setting a deflate level, or to use shuffle
+ * on non-integer data.
  * @param deflate True to turn on deflation for this variable.
  * @param deflate_level A number between 0 (no compression) and 9
  * (maximum compression).
@@ -833,6 +851,7 @@ filter and compression.
       ERR(retval);
         ...
 @endcode
+* @author Ed Hartnett, Dennis Heimbigner
 */
 int
 nc_def_var_deflate(int ncid, int varid, int shuffle, int deflate, int deflate_level)
@@ -851,6 +870,11 @@ nc_def_var_deflate(int ncid, int varid, int shuffle, int deflate, int deflate_le
  * This function must be called after nc_def_var and before nc_enddef
  * or any functions which writes data to the file.
  *
+ * Checksums require chunked data. If this function is called on a
+ * variable with contigious data, then the data is changed to chunked
+ * data, with default chunksizes. Use nc_def_var_chunking() to tune
+ * performance with user-defined chunksizes.
+ *
  * @param ncid NetCDF or group ID, from a previous call to nc_open(),
  * nc_create(), nc_def_grp(), or associated inquiry functions such as
  * nc_inq_ncid().
@@ -867,6 +891,7 @@ not netCDF-4/HDF5.
 netcdf-4 file.
  * @returns ::NC_ELATEDEF Too late to change settings for this variable.
  * @returns ::NC_EINVAL Invalid input
+ * @author Ed Hartnett, Dennis Heimbigner
 */
 int
 nc_def_var_fletcher32(int ncid, int varid, int fletcher32)
@@ -1066,6 +1091,7 @@ nc_def_var_endian(int ncid, int varid, int endian)
  * @param parms Filter parameters.
  *
  * @return ::NC_NOERR No error.
+ * @return ::NC_EBADID Bad ID.
  * @author Dennis Heimbigner
  */
 int