Merge pull request #966 from Unidata/issue964

fix detection of parallel HDF5 support in netcdf-c 4.6.1

Changelog

@@ -10,6 +10,7 @@
  * remove newlines from string representation (pull request #960).
  * fix for issue #957 (size of scalar var is a float since numpy.prod(())=1.0).
  * make sure Variable.setncattr fails to set _FillValue (issue #959).
+ * fix detection of parallel HDF5 support with netcdf-c 4.6.1 (issue #964).
 
  version 1.5.1.2 (tag v1.5.1.2rel)
 ==================================

netCDF4/_netCDF4.pyx

@@ -3094,8 +3094,10 @@ this `netCDF4.Dataset` or `netCDF4.Group`, as well as for all
 variables in all its subgroups.
 
 **`True_or_False`**: Boolean determining if automatic conversion of
-masked arrays with no missing values to regular ararys shall be
-applied for all variables.
+masked arrays with no missing values to regular numpy arrays shall be
+applied for all variables. Default True. Set to False to restore the default behaviour
+in versions prior to 1.4.1 (numpy array returned unless missing values are present,
+otherwise masked array returned).
 
 ***Note***: Calling this function only affects existing
 variables. Variables created after calling this function will follow
@@ -5135,12 +5137,11 @@ The default value of `mask` is `True`
 turn on or off conversion of data without missing values to regular
 numpy arrays.
 
-If `always_mask` is set to `True` then a masked array with no missing
-values is converted to a regular numpy array.
-
-The default value of `always_mask` is `True` (conversions to regular
-numpy arrays are not performed).
-
+`always_mask` is a Boolean determining if automatic conversion of
+masked arrays with no missing values to regular numpy arrays shall be
+applied. Default is True. Set to False to restore the default behaviour
+in versions prior to 1.4.1 (numpy array returned unless missing values are present,
+otherwise masked array returned).
         """
         self.always_mask = bool(always_mask)
 

setup.py

@@ -49,13 +49,14 @@ def check_ifnetcdf4(netcdf4_includedir):
     return isnetcdf4
 
 
-def check_api(inc_dirs):
+def check_api(inc_dirs,netcdf_lib_version):
     has_rename_grp = False
     has_nc_inq_path = False
     has_nc_inq_format_extended = False
     has_cdf5_format = False
     has_nc_open_mem = False
     has_nc_create_mem = False
+    has_parallel_support = False
     has_parallel4_support = False
     has_pnetcdf_support = False
 
@@ -91,10 +92,20 @@ def check_api(inc_dirs):
             for line in open(ncmetapath):
                 if line.startswith('#define NC_HAS_CDF5'):
                     has_cdf5_format = bool(int(line.split()[2]))
-                elif line.startswith('#define NC_HAS_PARALLEL4'):
+                if line.startswith('#define NC_HAS_PARALLEL'):
+                    has_parallel_support = bool(int(line.split()[2]))
+                if line.startswith('#define NC_HAS_PARALLEL4'):
                     has_parallel4_support = bool(int(line.split()[2]))
-                elif line.startswith('#define NC_HAS_PNETCDF'):
+                if line.startswith('#define NC_HAS_PNETCDF'):
                     has_pnetcdf_support = bool(int(line.split()[2]))
+        # NC_HAS_PARALLEL4 missing in 4.6.1 (issue #964)
+        if not has_parallel4_support and has_parallel_support and not has_pnetcdf_support:
+            has_parallel4_support = True
+        # for 4.6.1, if NC_HAS_PARALLEL=NC_HAS_PNETCDF=1, guess that
+        # parallel HDF5 is enabled (must guess since there is no
+        # NC_HAS_PARALLEL4)
+        elif netcdf_lib_version == "4.6.1" and not has_parallel4_support and has_parallel_support:
+            has_parallel4_support = True
         break
 
     return has_rename_grp, has_nc_inq_path, has_nc_inq_format_extended, \
@@ -182,7 +193,7 @@ def getnetcdfvers(libdirs):
 use_ncconfig = None
 if USE_SETUPCFG and os.path.exists(setup_cfg):
     sys.stdout.write('reading from setup.cfg...\n')
-    config = configparser.SafeConfigParser()
+    config = configparser.ConfigParser()
     config.read(setup_cfg)
     try:
         HDF5_dir = config.get("directories", "HDF5_dir")
@@ -494,7 +505,8 @@ def _populate_hdf5_info(dirstosearch, inc_dirs, libs, lib_dirs):
     # this determines whether renameGroup and filepath methods will work.
     has_rename_grp, has_nc_inq_path, has_nc_inq_format_extended, \
     has_cdf5_format, has_nc_open_mem, has_nc_create_mem, \
-    has_parallel4_support, has_pnetcdf_support = check_api(inc_dirs)
+    has_parallel4_support, has_pnetcdf_support = \
+    check_api(inc_dirs,netcdf_lib_version)
     # for netcdf 4.4.x CDF5 format is always enabled.
     if netcdf_lib_version is not None and\
        (netcdf_lib_version > "4.4" and netcdf_lib_version < "4.5"):