Merge pull request #665 from Unidata/encoding

recognize _Encoding attribute for char and string arrays

Changelog

@@ -6,6 +6,20 @@
    (pull request #652, issues #406 and #295).
  * fix for negative times in num2date (issue #659).
  * fix for failing tests in numpy 1.13 due to changes in numpy.ma (issue #662).
+ * Checking for _Encoding attribute for NC_STRING variables, otherwise use
+   'utf-8'. 'utf-8' is used everywhere else, 'default_encoding' global module
+   variable is no longer used.  getncattr method now takes optional kwarg
+   'encoding' (default 'utf-8') so encoding of attributes can be specified
+   if desired. If _Encoding is specified for an NC_CHAR ('S1') variable,
+   the chartostring utility function is used to convert the array of
+   characters to an array of strings with one less dimension (the last
+   dimension is interpreted as the length of each string) when reading the
+   data. When writing the data, stringtochar is used to convert a numpy 
+   array of fixed length strings to an array of characters with one more
+   dimension. chartostring and stringtochar now also have an 'encoding' kwarg.
+   Automatic conversion to/from character to string arrays can be turned off
+   via a new set_auto_chartostring Dataset and Variable method (default
+   is True).
 
  version 1.2.7 (tag v1.2.7rel)
 ==============================

conda.recipe/run_test.py

@@ -1,14 +1,8 @@
 import os
 import netCDF4
 
-# Check OPeNDAP functionality.
-url = 'http://geoport-dev.whoi.edu/thredds/dodsC/estofs/atlantic'
-nc = netCDF4.Dataset(url)
-
-# Check if it was compiled with cython.
-assert nc.filepath() == url
-
-# Run the unittests.
+# Run the unittests, skipping the opendap test.
 test_dir = os.path.join('test')
 os.chdir(test_dir)
+os.environ['NO_NET']='1'
 os.system('python run_all.py')

include/netCDF4.pxi

@@ -250,7 +250,6 @@ cdef extern from "netcdf.h":
     int nc_create(char *path, int cmode, int *ncidp)
     int nc__create(char *path, int cmode, size_t initialsz, size_t *chunksizehintp, int *ncidp)
     int nc_open(char *path, int mode, int *ncidp)
-    int nc_open_mem(const char *path, int mode, size_t size, void* memory, int *ncidp)
     int nc__open(char *path, int mode, size_t *chunksizehintp, int *ncidp)
     int nc_inq_path(int ncid, size_t *pathlen, char *path) nogil
     int nc_inq_format_extended(int ncid, int *formatp, int* modep) nogil
@@ -718,6 +717,11 @@ cdef extern from "netcdf.h":
 
     int nc_inq_enum_ident(int ncid, nc_type xtype, long long value, char *identifier) nogil
 
+
+IF HAS_NC_OPEN_MEM:
+    cdef extern from "netcdf_mem.h":
+        int nc_open_mem(const char *path, int mode, size_t size, void* memory, int *ncidp)
+
 # taken from numpy.pxi in numpy 1.0rc2.
 cdef extern from "numpy/arrayobject.h":
     ctypedef int npy_intp