Port contact_matrix_no_pbc to cython

Simple Cython implementation. Instead of the other functions in
distances.pyx I have used pure cython for clarity. The loop is converted
to pure C except for saving the sparse matrix element.

package/MDAnalysis/analysis/distances.py

@@ -36,6 +36,7 @@
 from scipy.weave import converters
 
 from MDAnalysis.lib.distances import distance_array, self_distance_array
+from MDAnalysis.lib._distances import contact_matrix_no_pbc
 from MDAnalysis.lib.KDTree.NeighborSearch import AtomNeighborSearch
 
 import logging
@@ -150,51 +151,6 @@ def contact_matrix_pbc(coord, sparse_contacts, box, cutoff, progress_meter_freq,
                  type_converters=converters.blitz)
 
 
-def contact_matrix_no_pbc(coord, sparse_contacts, cutoff, progress_meter_freq, quiet):
-    """Contact matrix calculation without periodic boundary conditions.
-
-    You don't have to call this function explicitly; just set *box* =
-    ``None`` when calling :func:`contact_matrix`, which will then call
-    this function.
-
-    This function uses  `python.weave`_.
-
-    ..  _`python.weave`: http://github.com/scipy/scipy/tree/master/scipy/weave/examples
-    """
-    _quiet = 1 if quiet else 0  # weave does not like Python True/False and does not convert to bool
-
-    c_code = """
-    #include <math.h>
-    int rows = Ncoord[0];
-    float cutoff2 = powf(cutoff, 2.);
-    py::tuple args(2);
-    bool b = 1;
-    args[1] = b;
-    for (int i=0; i < rows; i++) {
-        // Print progress meter
-        if (! _quiet && (i % progress_meter_freq == 0)) {
-            printf("%.1f percent done \\n", (100.0 * i / rows));
-        }
-        for (int j=0; j < rows; j++) {
-            float x = coord(i,0) - coord(j,0);
-            float y = coord(i,1) - coord(j,1);
-            float z = coord(i,2) - coord(j,2);
-
-            float dist = powf(x, 2.) + powf(y, 2.) + powf(z, 2.);
-            if (dist != 0.0 && dist < cutoff2) {
-                py::tuple idx(2);
-                idx[0] = i;
-                idx[1] = j;
-                args[0] = idx;
-                sparse_contacts.mcall("__setitem__",args);
-            }
-        }
-    }
-    """
-    weave.inline(c_code, ['coord', 'sparse_contacts', 'cutoff', 'progress_meter_freq', '_quiet'],
-                 type_converters=converters.blitz)
-
-
 def dist(A, B, offset=0):
     """Return distance between atoms in two atom groups.