Merge branch 'master' into bigend.dmh

WardF · web-flow · commit 3a14251dd956 · 2019-02-07T14:28:39.000-07:00
diff --git a/CMakeInstallation.cmake b/CMakeInstallation.cmake
@@ -38,6 +38,7 @@ SET(CPACK_SOURCE_IGNORE_FILES "${CPACK_SOURCE_IGNORE_FILES}"
   "/obsolete/"
   "/unknown/"
   ".*~"
+  ".git/"
   )
 
 ###
@@ -56,9 +57,9 @@ IF(WIN32)
   SET(CPACK_NSIS_CONTACT "support-netcdf@unidata.ucar.edu")
   SET(CPACK_NSIS_ENABLE_UNINSTALL_BEFORE_INSTALL ON)
   SET(CPACK_NSIS_MENU_LINKS
-	"http://www.unidata.ucar.edu/netcdf" "Unidata Website"
-	"http://www.unidata.ucar.edu/netcdf/docs" "NetCDF Stable Documentation"
-	"http://www.unidata.ucar.edu/netcdf/docs_rc" "NetCDF Unstable Documentation")
+	"http://www.unidata.ucar.edu/software/netcdf" "Unidata Website"
+	"http://www.unidata.ucar.edu/software/netcdf/docs" "NetCDF Stable Documentation"
+	"http://www.unidata.ucar.edu/software/netcdf/docs_rc" "NetCDF Unstable Documentation")
 
 ENDIF()
 
@@ -103,7 +104,7 @@ ENDIF()
 
 IF(APPLE)
   SET(CPACK_SOURCE_GENERATOR "TGZ")
-  SET(CPACK_GENERATOR "PackageMaker" "STGZ" "TBZ2" "TGZ" "ZIP")
+  SET(CPACK_GENERATOR "productbuild" "STGZ" "TBZ2" "TGZ" "ZIP")
 ENDIF()
 
 ##
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -82,7 +82,7 @@ IF(MSVC)
 ENDIF()
 
 #Add custom CMake Module
-SET(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/modules/"
+SET(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake/modules/"
   CACHE INTERNAL "Location of our custom CMake modules.")
 
 # auto-configure style checks, other CMake modules.
diff --git a/include/hdf5internal.h b/include/hdf5internal.h
@@ -135,7 +135,14 @@ int nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *coord_var, NC_DIM_IN
 extern hid_t NC4_image_init(NC_FILE_INFO_T* h5);
 extern void NC4_image_finalize(void*);
 
-/* These functions are internal to the libhdf5 directory. */
+/* Create HDF5 dataset for dim without a coord var. */
+extern int nc4_create_dim_wo_var(NC_DIM_INFO_T *dim);
+
+/* Give a var a secret HDF5 name, for use when there is a dim of this
+ * name, but the var is not a coord var of that dim. */
+extern int nc4_give_var_secret_name(NC_VAR_INFO_T *var);
+
+/* Get the fill value for a var. */
 int nc4_get_fill_value(NC_FILE_INFO_T *h5, NC_VAR_INFO_T *var, void **fillp);
 
 
diff --git a/include/nc4internal.h b/include/nc4internal.h
@@ -153,7 +153,7 @@ typedef struct NC_VAR_INFO
    nc_bool_t created;           /* Variable has already been created (_not_ that it was just created) */
    nc_bool_t written_to;        /* True if variable has data written to it */
    struct NC_TYPE_INFO *type_info;
-   int atts_not_read;           /* If true, the atts have not yet been read. */
+   int atts_read;               /* If true, the atts have been read. */
    nc_bool_t meta_read;         /* True if this vars metadata has been completely read. */
    nc_bool_t coords_read;       /* True if this var has hidden coordinates att, and it has been read. */
    NCindex *att; 		/* NCindex<NC_ATT_INFO_T*> */
@@ -229,7 +229,7 @@ typedef struct NC_GRP_INFO
    void *format_grp_info;
    struct NC_FILE_INFO *nc4_info;
    struct NC_GRP_INFO *parent;
-   int atts_not_read;
+   int atts_read;               /* True if atts have been read for this group. */
    NCindex* children;		/* NCindex<struct NC_GRP_INFO*> */
    NCindex* dim;		/* NCindex<NC_DIM_INFO_T> * */
    NCindex* att;		/* NCindex<NC_ATT_INFO_T> * */
diff --git a/include/ncconfigure.h b/include/ncconfigure.h
@@ -89,4 +89,8 @@ typedef unsigned short ushort;
 typedef unsigned int uint;
 #endif
 
+#ifndef NC_UNUSED
+#define NC_UNUSED(var) (void)var
+#endif
+
 #endif /* NCCONFIGURE_H */
diff --git a/libdispatch/dparallel.c b/libdispatch/dparallel.c
@@ -102,6 +102,11 @@ int nc_create_par(const char *path, int cmode, MPI_Comm comm,
                   MPI_Info info, int *ncidp)
 {
 #ifndef USE_PARALLEL
+    NC_UNUSED(path);
+    NC_UNUSED(cmode);
+    NC_UNUSED(comm);
+    NC_UNUSED(info);
+    NC_UNUSED(ncidp);
     return NC_ENOPAR;
 #else
     NC_MPI_INFO data;
@@ -201,6 +206,11 @@ nc_open_par(const char *path, int omode, MPI_Comm comm,
             MPI_Info info, int *ncidp)
 {
 #ifndef USE_PARALLEL
+    NC_UNUSED(path);
+    NC_UNUSED(omode);
+    NC_UNUSED(comm);
+    NC_UNUSED(info);
+    NC_UNUSED(ncidp);
     return NC_ENOPAR;
 #else
     NC_MPI_INFO mpi_data;
@@ -249,6 +259,11 @@ nc_open_par_fortran(const char *path, int omode, int comm,
                     int info, int *ncidp)
 {
 #ifndef USE_PARALLEL
+    NC_UNUSED(path);
+    NC_UNUSED(omode);
+    NC_UNUSED(comm);
+    NC_UNUSED(info);
+    NC_UNUSED(ncidp);
     return NC_ENOPAR;
 #else
     MPI_Comm comm_c;
@@ -348,6 +363,9 @@ int
 nc_var_par_access(int ncid, int varid, int par_access)
 {
 #ifndef USE_PARALLEL
+    NC_UNUSED(ncid);
+    NC_UNUSED(varid);
+    NC_UNUSED(par_access);
     return NC_ENOPAR;
 #else
     int stat = NC_NOERR;
@@ -403,6 +421,11 @@ nc_create_par_fortran(const char *path, int cmode, int comm,
                       int info, int *ncidp)
 {
 #ifndef USE_PARALLEL
+    NC_UNUSED(path);
+    NC_UNUSED(cmode);
+    NC_UNUSED(comm);
+    NC_UNUSED(info);
+    NC_UNUSED(ncidp);
     return NC_ENOPAR;
 #else
     MPI_Comm comm_c;
diff --git a/libdispatch/drc.c b/libdispatch/drc.c
@@ -396,8 +396,8 @@ rcsearch(const char* prefix, const char* rcname, char** pathp)
 {
     char* path = NULL;
     FILE* f = NULL;
-    int plen = strlen(prefix);
-    int rclen = strlen(rcname);
+    size_t plen = strlen(prefix);
+    size_t rclen = strlen(rcname);
     int ret = NC_NOERR;
 
     size_t pathlen = plen+rclen+1; /*+1 for '/' */
diff --git a/libdispatch/dutil.c b/libdispatch/dutil.c
@@ -210,7 +210,7 @@ NC_mktmp(const char* base)
 	    char spid[7];
 	    if(rno < 0) rno = -rno;
             snprintf(spid,sizeof(spid),"%06d",rno);
-            strncat(tmp,spid,sizeof(tmp));
+            strncat(tmp,spid,sizeof(tmp) - strlen(tmp) - 1);
 	}
 #endif /* HAVE_MKTEMP */
 #ifdef _MSC_VER
diff --git a/libdispatch/nclog.c b/libdispatch/nclog.c
@@ -213,6 +213,7 @@ Each line will be sent using nclog with the specified tag.
 void
 nclogtextn(int tag, const char* text, size_t count)
 {
+    NC_UNUSED(tag);
     if(!nclogging || nclogstream == NULL) return;
     fwrite(text,1,count,nclogstream);
     fflush(nclogstream);
diff --git a/libdispatch/nctime.c b/libdispatch/nctime.c
@@ -23,6 +23,7 @@
 #include <string.h>
 #include <stdarg.h>
 #include <assert.h>
+#include "ncconfigure.h"
 #include "nctime.h"
 
 static int cuErrOpts;			     /* Error options */
@@ -309,7 +310,7 @@ cdParseRelunits(cdCalenType timetype, char* relunits, cdUnitTime* unit, cdCompTi
 	char charunits[CD_MAX_RELUNITS];
 	char basetime_1[CD_MAX_CHARTIME];
 	char basetime_2[CD_MAX_CHARTIME];
-	char basetime[CD_MAX_CHARTIME];
+	char basetime[2 * CD_MAX_CHARTIME + 1];
 	int nconv1, nconv2, nconv;
 
 					     /* Parse the relunits */
@@ -659,6 +660,7 @@ Cdh2e(CdTime *htime, double *etime)
 static int
 cdValidateTime(cdCalenType timetype, cdCompTime comptime)
 {
+	NC_UNUSED(timetype);
 	if(comptime.month<1 || comptime.month>12){
 		cdError("Error on time conversion: invalid month = %hd\n",comptime.month);
 		return 1;
diff --git a/libdispatch/ncuri.c b/libdispatch/ncuri.c
@@ -67,7 +67,7 @@ static char* queryallow =
 static char* userpwdallow =
 "0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ!$&'()*+,-.;=_~?#/";
 
-#ifndef HAVE_STRNCMP
+#ifndef HAVE_STRNDUP
 #define strndup ncstrndup
 /* Not all systems have strndup, so provide one*/
 char*
@@ -258,7 +258,7 @@ ncuriparse(const char* uri0, NCURI** durip)
 
     isfile = (strcmp(tmp.protocol,"file")==0);
     if(isfile) {
-	int l = strlen(p); /* to test if we have enough characters */
+	size_t l = strlen(p); /* to test if we have enough characters */
 	hashost = 0; /* always */
 	if(l >= 2 && p[1] == ':' && strchr(DRIVELETTERS,p[0]) != NULL) { /* case 1 */
 	    ; /* p points to the start of the path */
diff --git a/libhdf4/hdf4file.c b/libhdf4/hdf4file.c
@@ -415,6 +415,7 @@ nc4_var_list_add_full(NC_GRP_INFO_T* grp, const char* name, int ndims, nc_type x
    (*var)->created = NC_TRUE;
    (*var)->written_to = NC_TRUE;
    (*var)->format_var_info = format_var_info;
+   (*var)->atts_read = 1;
 
    /* Fill special type_info struct for variable type information. */
    if ((retval = nc4_set_var_type(xtype, endianness, type_size, type_name,
@@ -630,6 +631,7 @@ NC_HDF4_open(const char *path, int mode, int basepe, size_t *chunksizehintp,
    assert(nc4_info && nc4_info->root_grp);
    h5 = nc4_info;
    h5->no_write = NC_TRUE;
+   h5->root_grp->atts_read = 1;
 
    /* Allocate data to hold HDF4 specific file data. */
    if (!(hdf4_file = malloc(sizeof(NC_HDF4_FILE_INFO_T))))
diff --git a/libhdf5/hdf5attr.c b/libhdf5/hdf5attr.c
@@ -27,13 +27,14 @@ static int
 getattlist(NC_GRP_INFO_T *grp, int varid, NC_VAR_INFO_T **varp,
             NCindex **attlist)
 {
-   NC_VAR_INFO_T* var;
    int retval;
 
+   assert(grp && attlist);
+
    if (varid == NC_GLOBAL)
    {
       /* Do we need to read the atts? */
-      if (grp->atts_not_read)
+      if (!grp->atts_read)
          if ((retval = nc4_read_atts(grp, NULL)))
             return retval;
 
@@ -43,12 +44,14 @@ getattlist(NC_GRP_INFO_T *grp, int varid, NC_VAR_INFO_T **varp,
    }
    else
    {
+      NC_VAR_INFO_T *var;
+
       if (!(var = (NC_VAR_INFO_T *)ncindexith(grp->vars, varid)))
          return NC_ENOTVAR;
       assert(var->hdr.id == varid);
 
       /* Do we need to read the atts? */
-      if (var->atts_not_read)
+      if (!var->atts_read)
          if ((retval = nc4_read_atts(grp, var)))
             return retval;
 
diff --git a/libhdf5/hdf5create.c b/libhdf5/hdf5create.c
@@ -66,6 +66,7 @@ nc4_create_file(const char *path, int cmode, size_t initialsz,
       BAIL(retval);
    nc4_info = NC4_DATA(nc);
    assert(nc4_info && nc4_info->root_grp);
+   nc4_info->root_grp->atts_read = 1;
 
    /* Add struct to hold HDF5-specific file metadata. */
    if (!(nc4_info->format_file_info = calloc(1, sizeof(NC_HDF5_FILE_INFO_T))))
diff --git a/libhdf5/hdf5file.c b/libhdf5/hdf5file.c
@@ -727,7 +727,7 @@ NC4_inq(int ncid, int *ndimsp, int *nvarsp, int *nattsp, int *unlimdimidp)
    if (nattsp)
    {
       /* Do we need to read the atts? */
-      if (grp->atts_not_read)
+      if (!grp->atts_read)
          if ((retval = nc4_read_atts(grp, NULL)))
             return retval;
 
diff --git a/libhdf5/hdf5grp.c b/libhdf5/hdf5grp.c
@@ -67,6 +67,11 @@ NC4_def_grp(int parent_ncid, const char *name, int *new_ncid)
       return retval;
    if (!(g->format_grp_info = calloc(1, sizeof(NC_HDF5_GRP_INFO_T))))
       return NC_ENOMEM;
+
+   /* For new groups, there are no atts to read from file. */
+   g->atts_read = 1;
+
+   /* Return the ncid to the user. */
    if (new_ncid)
       *new_ncid = grp->nc4_info->controller->ext_ncid | g->hdr.id;
 
diff --git a/libhdf5/hdf5internal.c b/libhdf5/hdf5internal.c
diff --git a/libhdf5/hdf5open.c b/libhdf5/hdf5open.c
diff --git a/libhdf5/hdf5var.c b/libhdf5/hdf5var.c
diff --git a/libhdf5/nc4hdf.c b/libhdf5/nc4hdf.c
diff --git a/libsrc/posixio.c b/libsrc/posixio.c
diff --git a/libsrc4/nc4var.c b/libsrc4/nc4var.c
diff --git a/nc_test4/Makefile.am b/nc_test4/Makefile.am
diff --git a/nc_test4/tst_rename2.c b/nc_test4/tst_rename2.c

Original file line number	Diff line number	Diff line change
`@@ -210,7 +210,7 @@ NC_mktmp(const char* base)`
`210`	`210`	`char spid[7];`
`211`	`211`	`if(rno < 0) rno = -rno;`
`212`	`212`	`snprintf(spid,sizeof(spid),"%06d",rno);`
`213`		`- strncat(tmp,spid,sizeof(tmp));`
	`213`	`+ strncat(tmp,spid,sizeof(tmp) - strlen(tmp) - 1);`
`214`	`214`	`}`
`215`	`215`	`#endif /* HAVE_MKTEMP */`
`216`	`216`	`#ifdef _MSC_VER`
Original file line number	Diff line number	Diff line change
`@@ -213,6 +213,7 @@ Each line will be sent using nclog with the specified tag.`
`213`	`213`	`void`
`214`	`214`	`nclogtextn(int tag, const char* text, size_t count)`
`215`	`215`	`{`
	`216`	`+ NC_UNUSED(tag);`
`216`	`217`	`if(!nclogging \|\| nclogstream == NULL) return;`
`217`	`218`	`fwrite(text,1,count,nclogstream);`
`218`	`219`	`fflush(nclogstream);`