Released version 1.0

.gitignore

@@ -0,0 +1,4 @@
+# Ignore dirs
+build
+nauty
+nauty27b11

README.md

@@ -0,0 +1,37 @@
+# Pynauty
+*by Sam Morley-Short*
+
+This is a fork of `pynauty`--a Python extension of the C module `nauty`--to add extra features needed for exploring LC classes of quantum graph states.
+
+It was made entirely for use by my other Graph State Compass (gsc) module, which can be found [here](https://github.com/sammorley-short/gsc).
+
+It is redistributed under the GPL v3 copyleft lisence WITHOUT ANY WARRANTY.
+
+To install, follow the instructions provided [here](https://web.cs.dal.ca/~peter/software/pynauty/html/install.html).
+
+Loosely, this requires:
+
+1. Downloading nauty, (working as of version 27b11, found [here](http://users.cecs.anu.edu.au/~bdm/nauty/nauty27b11.tar.gz)),
+2. Unzipping it and placing it in `/pynauty-hack`,
+3. Symbolic link the nauty directory to `/nauty` (for the above case on Mac OS X this means running `ln -s nauty27b11 nauty` from the command line),
+4. Installing pynauty (`make user-ins` can be used to install globally).
+
+## Original warranty
+
+pynauty  --  isomorphism testing and automorphism groups of graphs
+version: 0.6
+
+Copyright (c) 2015 Peter Dobsan
+
+This is the source distribution of pynauty, a Python/C extension module.
+It can be used to compare graphs for isomorphism and to determine their
+automorphism group. It is based on the Nauty C procedures.
+
+pynauty is compatible both Python-2 and Python-3.
+
+pynauty is distributed under the terms GPL v3 WITHOUT ANY WARRANTY.
+For exact details on licencing see the file COPYING.
+
+For documentations, including instructions for  installation, API and
+User's Guide see the docs/ directory.
+

src/graph.py

@@ -6,7 +6,7 @@
 '''
 from __future__ import absolute_import
 
-__LICENSE__     = '''
+__LICENSE__ = '''
 Copyright (c) 2015 Peter Dobsan
 
 This program is free software; you can redistribute it and/or modify it
@@ -23,6 +23,7 @@
     'autgrp',
     'isomorphic',
     'certificate',
+    'canon_label',
     'delete_random_edge',
 ]
 
@@ -67,8 +68,8 @@ def _check_vertices(self, vs):
         for v in vs:
             if not (0 <= v and v < self.number_of_vertices):
                 raise ValueError(
-                'vertex %d conflicts with number_of_vertices=%d' %
-                                 (v, self.number_of_vertices))
+                    'vertex %d conflicts with number_of_vertices=%d' %
+                    (v, self.number_of_vertices))
 
     def _get_adjacency_dict(self):
         return self._adjacency_dict
@@ -141,9 +142,9 @@ def __repr__(self):
         s = ['Graph(number_of_vertices=%d, directed=%s,' %
              (self.number_of_vertices, self.directed)]
         s.append(' adjacency_dict = {')
-        for k,v in self._adjacency_dict.items():
+        for k, v in self._adjacency_dict.items():
             v.sort()
-            s.append('  %d: %s,' % (k,v))
+            s.append('  %d: %s,' % (k, v))
         s.append(' },')
         s.append(' vertex_coloring = [')
         for x in self._vertex_coloring:
@@ -184,6 +185,21 @@ def certificate(g):
     return nautywrap.graph_cert(g)
 
 
+def canon_label(g):
+    '''
+    Finds the canonical labeling of vertices.
+
+    *g*
+        A Graph object.
+
+    return ->
+        A list with each node relabelled.
+    '''
+    if not isinstance(g, Graph):
+        raise TypeError
+    return nautywrap.graph_canonlab(g)
+
+
 def isomorphic(a, b):
     '''
     Determine if two graphs are isomorphic.
@@ -214,7 +230,7 @@ def delete_random_edge(g):
     '''
     if g.adjacency_dict:
         # pick a random vertex 'x' which is connected
-        x = random.sample(list(g.adjacency_dict),1)[0]
+        x = random.sample(list(g.adjacency_dict), 1)[0]
         # remove a random edge connected to 'x'
         xs = g.adjacency_dict[x]
         y = xs.pop(random.randrange(len(xs)))
@@ -229,4 +245,3 @@ def delete_random_edge(g):
         # the graph has no edges
         x, y = None, None
     return (x, y)
-

src/nautywrap.c

@@ -103,7 +103,7 @@ void destroy_nygraph(NyGraph *g)
 NyGraph * create_nygraph(int no_vertices)
 //
 // Allocate a data structure to hold all data structures used by Nauty
-// 
+//
 {
     NyGraph *g;
     int i, *p;
@@ -127,7 +127,7 @@ NyGraph * create_nygraph(int no_vertices)
     g->no_setwords = (no_vertices + WORDSIZE - 1) / WORDSIZE;
     nauty_check(WORDSIZE, g->no_setwords, g->no_vertices, NAUTYVERSIONID);
 
-    if ((g->matrix = malloc((size_t) g->no_setwords * 
+    if ((g->matrix = malloc((size_t) g->no_setwords *
                     (size_t) (no_vertices * sizeof(setword)))) == NULL) {
         destroy_nygraph(g);
         return NULL;
@@ -546,11 +546,55 @@ graph_cert(PyObject *self, PyObject *args)
     return pyret;
 }
 
+// SMS EDIT: New function graph_canonlab
+static char graph_canonlab_docs[] =
+"graph_canonlab(g): \n\
+    Return the canonical relabelling of NyGraph 'g'.\n";
+
+static PyObject*
+graph_canonlab(PyObject *self, PyObject *args)
+{
+    int i;
+    PyObject *py_graph;
+    NyGraph * g;
+    PyObject *pyret;
+
+    if (!PyArg_ParseTuple(args, "O", &py_graph)) {
+        PyErr_SetString(PyExc_TypeError, "Missing argument.");
+        return NULL;
+    }
+    g = _make_nygraph(py_graph);
+    if (g == NULL) return NULL;
+
+    // produce graph certificate by computing canonical labeling
+    g->options->getcanon = TRUE;
+    if (extend_canonical(g) == NULL) {
+        PyErr_SetString(PyExc_MemoryError,
+                "Allocating canonical matrix failed");
+        return NULL;
+    }
+    // the produced generators are ignored
+    g->options->userautomproc = NULL;
+
+    // *** nauty ***
+    nauty(g->matrix, g->lab, g->ptn, NULL, g->orbits,
+            g->options, g->stats,  g->workspace, g->worksize,
+            g->no_setwords, g->no_vertices, g->cmatrix);
+
+    pyret = PyList_New(g->no_vertices);
+    for (i=0; i < g->no_vertices; i++) {
+        PyList_SET_ITEM(pyret, i, Py_BuildValue("i", g->lab[i]));
+    }
+
+    destroy_nygraph(g);
+    return pyret;
+}
 
 //  Python module initialization  =============================================
 
 static PyMethodDef nautywrap_methods[] = {
     {"graph_cert", graph_cert, METH_VARARGS, graph_cert_docs},
+    {"graph_canonlab", graph_canonlab, METH_VARARGS, graph_canonlab_docs},
     {"graph_autgrp", graph_autgrp, METH_VARARGS, graph_autgrp_docs},
     {"make_nygraph", make_nygraph, METH_VARARGS, make_nygraph_docs},
     {"delete_nygraph", delete_nygraph, METH_VARARGS, delete_nygraph_docs},