Added support for the __index__ protocol.

PyNIO now works with __index__, so that numpy integers can be used as indexes. Also fixed issues in setup.py that were
causing opendap and netcdf4 to not be linked properly. Fixes NCAR#15.

build_py2.sh

@@ -0,0 +1,31 @@
+#!/bin/sh
+
+export HAS_NETCDF4=1
+export HAS_HDFEOS=1
+export HAS_HDFEOS5=1
+export HAS_GDAL=1
+export HAS_GRIB2=1
+export NETCDF_PREFIX=${CONDA_PREFIX}
+export F2CLIBS=gfortran
+export HAS_SZIP=0
+export HAS_HDF4=1
+export HAS_HDF5=1
+export HAS_GDAL=1
+
+export CXXFLAGS="-fPIC $CXXFLAGS"
+export LDFLAGS="-L$CONDA_PREFIX/lib $LDFLAGS"
+export CPPFLAGS="-I$CONDA_PREFIX/include $CPPFLAGS"
+export CFLAGS="-D_BSD_SOURCE -D_XOPEN_SOURCE -I$PREFIX/include $CFLAGS"
+
+if [[ $(uname) == Darwin ]]; then
+  export CC=gcc
+  export CXX=g++
+  export MACOSX_DEPLOYMENT_TARGET="10.9"
+  export CXXFLAGS="-stdlib=libc++ $CXXFLAGS"
+  export CXXFLAGS="$CXXFLAGS -stdlib=libc++"
+  export LDFLAGS="-headerpad_max_install_names $LDFLAGS"
+fi
+
+python setup.py build
+pip install .
+

build_py3.sh

@@ -0,0 +1,34 @@
+#!/bin/sh
+
+export HAS_NETCDF4=1
+export HAS_HDFEOS=1
+export HAS_HDFEOS5=1
+export HAS_GDAL=1
+export HAS_GRIB2=1
+export NETCDF_PREFIX=${CONDA_PREFIX}
+export F2CLIBS=gfortran
+export HAS_SZIP=0
+export HAS_HDF4=1
+export HAS_HDF5=1
+export HAS_GDAL=1
+
+export CXXFLAGS="-g -O0 -fPIC $CXXFLAGS"
+export LDFLAGS="-L$CONDA_PREFIX/lib $LDFLAGS"
+export CPPFLAGS="-I$CONDA_PREFIX/include $CPPFLAGS"
+export CFLAGS="-D_BSD_SOURCE -D_XOPEN_SOURCE -I$CONDA_PREFIX/include $CFLAGS"
+
+if [[ $(uname) == Darwin ]]; then
+  export CC=gcc
+  export CXX=g++
+  export MACOSX_DEPLOYMENT_TARGET="10.9"
+  export CXXFLAGS="-stdlib=libc++ $CXXFLAGS"
+  export CXXFLAGS="$CXXFLAGS -stdlib=libc++"
+  export LDFLAGS="-headerpad_max_install_names $LDFLAGS"
+fi
+
+env
+
+ python setup.py build
+
+pip install .
+

niomodule.c

@@ -1854,6 +1854,9 @@ NioFileObject_new_dimension(NioFileObject *self, PyObject *args) {
 #endif
 	else if (PyLong_Check(size_ob))
 		size = (Py_ssize_t) PyLong_AsSsize_t(size_ob);
+	else if (PyIndex_Check(size_ob)) {
+		size = PyNumber_AsSsize_t(size_ob, PyExc_OverflowError);
+	}
 	else {
 		PyErr_SetString(PyExc_TypeError, "size must be None or integer");
 		return NULL;
@@ -1933,6 +1936,9 @@ static PyObject *NioFileObject_new_chunk_dimension(NioFileObject *self,
 #endif
 	else if (PyLong_Check(size_ob))
 		size = (Py_ssize_t) PyLong_AsSsize_t(size_ob);
+	else if (PyIndex_Check(size_ob)) {
+		size = PyNumber_AsSsize_t(size_ob, PyExc_OverflowError);
+	}
 	else {
 		PyErr_SetString(PyExc_TypeError, "size must be None or integer");
 		return NULL;
@@ -2884,6 +2890,9 @@ static PyObject *NioFileObject_new_compound_type(NioFileObject *self,
 				memb_sizes[i] = (int) PyInt_AsLong(item2);
 			}
 #endif
+			else if (PyIndex_Check(item2)) {
+				memb_sizes[i] = (int) PyNumber_AsSsize_t(item2, PyExc_OverflowError);
+			}
 			else if (is_string_type(item2)) {
 				typestr = as_utf8_char(item2);
 				sscanf(typestr, "%d", &(memb_sizes[i]));
@@ -3069,6 +3078,9 @@ static PyObject *NioFileObject_new_compound(NioFileObject *self, PyObject *args)
 				memb_sizes[i] = (int) PyInt_AsLong(item2);
 			}
 #endif
+			else if (PyIndex_Check(item2)) {
+				memb_sizes[i] = (int) PyNumber_AsSsize_t(item2, PyExc_OverflowError);
+			}
 			else if (is_string_type(item2)) {
 				typestr = as_utf8_char(item2);
 				sscanf(typestr, "%d", &(memb_sizes[i]));
@@ -6376,6 +6388,11 @@ NioVariableObject_subscript(NioVariableObject *self, PyObject *index) {
 		return NioVariableObject_item(self, i);
 	}
 #endif
+	else if (PyIndex_Check(index)) {
+		Py_ssize_t i = PyNumber_AsSsize_t(index, PyExc_OverflowError);
+		return NioVariableObject_item(self, i);
+	}
+
 	if (self->nd == 0) {
 		PyErr_SetString(PyExc_TypeError, "Not a sequence");
 		return NULL;
@@ -6442,6 +6459,21 @@ NioVariableObject_subscript(NioVariableObject *self, PyObject *index) {
 						d++;
 					}
 #endif
+					else if (PyIndex_Check(subscript)) {
+						Py_ssize_t n = PyNumber_AsSsize_t(subscript, PyExc_OverflowError);
+						if (n >= self->dimensions[d]
+								|| n < -self->dimensions[d]) {
+							PyErr_Format(PyExc_IndexError,
+									"index %d is out of bounds for axis %d with size %ld",
+									(int) n, d, self->dimensions[d]);
+							free(indices);
+							return NULL;
+						}
+						indices[d].start = n;
+						indices[d].stop = n + 1;
+						indices[d].item = 1;
+						d++;
+					}
 					else if (PySlice_Check(subscript)) {
 						Py_ssize_t slicelen;
 						PySliceObject *slice = (PySliceObject *) subscript;
@@ -6547,6 +6579,11 @@ static int NioVariableObject_ass_subscript(NioVariableObject *self,
 		return NioVariableObject_ass_item(self, i, value);
 	}
 #endif
+	else if (PyIndex_Check(index)) {
+		Py_ssize_t i = PyNumber_AsSsize_t(index, PyExc_OverflowError);
+		return NioVariableObject_ass_item(self, i, value);
+	}
+
 	if (value == NULL) {
 		PyErr_SetString(PyExc_ValueError, "Can't delete elements.");
 		return -1;
@@ -6563,7 +6600,7 @@ static int NioVariableObject_ass_subscript(NioVariableObject *self,
 #if PY_MAJOR_VERSION < 3
 			if (PySlice_GetIndicesEx((PySliceObject *) index,
 #else
-					if (PySlice_GetIndicesEx(index,
+		    if (PySlice_GetIndicesEx(index,
 #endif
 					self->dimensions[0], &indices->start, &indices->stop,
 					&indices->stride, &slicelen) < 0) {
@@ -6585,6 +6622,9 @@ static int NioVariableObject_ass_subscript(NioVariableObject *self,
 					indices->start = PyInt_AsLong(slice->start);
 				}
 #endif
+				else if (PyIndex_Check(slice->start)) {
+					indices->start = PyNumber_AsSsize_t(slice->start, PyExc_OverflowError);
+				}
 				if (indices->start < PY_SSIZE_T_MIN * 100)
 					indices->no_start = 1;
 			}
@@ -6595,10 +6635,14 @@ static int NioVariableObject_ass_subscript(NioVariableObject *self,
 					indices->stop = PyLong_AsLong(slice->stop);
 				}
 #if PY_MAJOR_VERSION < 3
-				if (PyInt_Check(slice->stop)) {
+				else if (PyInt_Check(slice->stop)) {
 					indices->stop = PyInt_AsLong(slice->stop);
 				}
 #endif
+				else if (PyIndex_Check(slice->stop)) {
+					indices->stop = PyNumber_AsSsize_t(slice->stop, PyExc_OverflowError);
+				}
+
 				if (indices->stop > PY_SSIZE_T_MAX / 100)
 					indices->no_stop = 1;
 			}
@@ -6627,13 +6671,20 @@ static int NioVariableObject_ass_subscript(NioVariableObject *self,
 						d++;
 					}
 #endif
+					else if (PyIndex_Check(subscript)) {
+						Py_ssize_t n = PyNumber_AsSsize_t(subscript, PyExc_OverflowError);
+						indices[d].start = n;
+						indices[d].stop = n + 1;
+						indices[d].item = 1;
+						d++;
+					}
 					else if (PySlice_Check(subscript)) {
 						Py_ssize_t slicelen;
 						PySliceObject *slice = (PySliceObject *) subscript;
 #if PY_MAJOR_VERSION < 3
 						if (PySlice_GetIndicesEx((PySliceObject *) subscript,
 #else
-								if (PySlice_GetIndicesEx(subscript,
+						if (PySlice_GetIndicesEx(subscript,
 #endif
 								self->dimensions[d], &indices[d].start,
 								&indices[d].stop, &indices[d].stride, &slicelen)
@@ -6653,10 +6704,13 @@ static int NioVariableObject_ass_subscript(NioVariableObject *self,
 								indices[d].start = PyLong_AsLong(slice->start);
 							}
 #if PY_MAJOR_VERSION < 3
-							if (PyInt_Check(slice->start)) {
+							else if (PyInt_Check(slice->start)) {
 								indices[d].start = PyInt_AsLong(slice->start);
 							}
 #endif
+							else if (PyIndex_Check(slice->start)) {
+								indices[d].start = PyNumber_AsSsize_t(slice->start, PyExc_OverflowError);
+							}
 						}
 						if (slice->stop == Py_None)
 							indices[d].no_stop = 1;
@@ -6669,6 +6723,9 @@ static int NioVariableObject_ass_subscript(NioVariableObject *self,
 								indices[d].stop = PyInt_AsLong(slice->stop);
 							}
 #endif
+							else if (PyIndex_Check(slice->stop)) {
+								indices[d].stop = PyNumber_AsSsize_t(slice->stop, PyExc_OverflowError);
+							}
 						}
 						d++;
 					} else if (subscript == Py_Ellipsis) {
@@ -7295,6 +7352,14 @@ void SetNioOptions(NrmQuark extq, int mode, PyObject *options,
 			/* printf("%s %ld\n",keystr,PyLong_AsLong(value));*/
 		}
 #endif
+		else if (PyIndex_Check(value)) {
+			int* ival = (int *) malloc(sizeof(int));
+			*ival = (int) PyNumber_AsSsize_t(value, PyExc_OverflowError);
+			md = _NclCreateMultiDVal(NULL, NULL, Ncl_MultiDValData, 0,
+					(void*) ival, NULL, 1, &len_dims, TEMPORARY, NULL,
+					(NclTypeClass) nclTypeintClass);
+			/* printf("%s %ld\n",keystr,PyLong_AsLong(value));*/
+		}
 		else if (PyFloat_Check(value)) {
 			float *fval = (float *) malloc(sizeof(float));
 			*fval = (float) PyFloat_AsDouble(value);

setup.py

@@ -3,6 +3,7 @@
 # may be required. See the following comments.
 #
 from __future__ import print_function
+from sys import version_info
 import os
 import sys
 import subprocess
@@ -88,12 +89,14 @@
 def set_curl_libs():
   #curl_libs = commands.getstatusoutput('curl-config --libs')
 
-  p = subprocess.Popen(["curl-config ", "--libs"], stdout=PIPE, stderr=STDOUT)
+  p = subprocess.Popen(["curl-config", "--libs"], stdout=subprocess.PIPE, 
+                       stderr=subprocess.STDOUT)
   output, _ = p.communicate()
 
   if p.returncode == 0:
-
-    output = output.decode("utf-8")
+
+    if version_info >= (3,): 
+        output = output.decode("utf-8")
 #
 # Split into individual lines so we can loop through each one.
 #
@@ -102,9 +105,9 @@ def set_curl_libs():
 # Check if this is a -L or -l string and do the appropriate thing.
 #
     for clibstr in clibs:
-      if bytes(clibstr[0:2]) == "-L":
+      if clibstr[0:2] == "-L":
         LIB_DIRS.append(clibstr.split("-L")[1])
-      elif bytes(clibstr[0:2]) == "-l":
+      elif clibstr[0:2] == "-l":
         LIBRARIES.append(clibstr.split("-l")[1])
   else:
 #
@@ -482,9 +485,6 @@ def configuration(parent_package='',top_path=None):
     for file in LIB_EXCLUDE_SOURCES: 
       sources.remove(file)
     sources = [ join('libsrc', file) for file in sources ]
-    #print (len(sources))
-    #print (sources)
-    #raise RuntimeError("out")
     config.add_library('nio',sources,
                        include_dirs=INC_DIRS,
                        macros=LIB_MACROS,

version

@@ -1 +1 @@
-1.5.0
+1.5.1