From: Michael R. Crusoe <michael.crusoe@gmail.com>
Subject: Fix Bio.Cluster._cluster doctests
--- python-biopython.orig/Bio/Cluster/clustermodule.c
+++ python-biopython/Bio/Cluster/clustermodule.c
@@ -1438,16 +1438,17 @@
 "\n"
 "   Examples are:\n"
 "\n"
+"       >>> from numpy import array\n"
 "       >>> distance = array([[0.0, 1.1, 2.3],\n"
 "       ...                   [1.1, 0.0, 4.5],\n"
 "       ...                   [2.3, 4.5, 0.0]])\n"
-"       (option #1)\n"
+"       >>> # (option #1)\n"
 "       >>> distance = array([1.1, 2.3, 4.5])\n"
-"       (option #2)\n"
+"       >>> # (option #2)\n"
 "       >>> distance = [array([]),\n"
 "       ...             array([1.1]),\n"
 "       ...             array([2.3, 4.5])]\n"
-"       (option #3)\n"
+"       >>> # (option #3)\n"
 "\n"
 "   These three correspond to the same distance matrix.\n"
 "\n"
@@ -1596,16 +1597,17 @@
 "\n"
 "   Examples are:\n"
 "\n"
+"       >>> from numpy import array\n"
 "       >>> distance = array([[0.0, 1.1, 2.3],\n"
 "       ...                   [1.1, 0.0, 4.5],\n"
 "       ...                   [2.3, 4.5, 0.0]])\n"
-"       # option 1.\n"
+"       >>> # option 1.\n"
 "       >>> distance = array([1.1, 2.3, 4.5])\n"
-"       # option 2.\n"
+"       >>> # option 2.\n"
 "       >>> distance = [array([]),\n"
 "       ...             array([1.1]),\n"
 "       ...             array([2.3, 4.5])]\n"
-"       # option 3.\n"
+"       >>> # option 3.\n"
 "\n"
 "   These three correspond to the same distance matrix.\n"
 "\n"
@@ -2318,7 +2320,7 @@
 "Adding the column means to the dot product of the coordinates and the\n"
 "principal components, i.e.\n"
 "\n"
-"    >>> columnmean + dot(coordinates, pc)\n"
+"   'columnmean + dot(coordinates, pc)'\n"
 "\n"
 "recreates the data matrix.\n";
 
