changeset 33:5064f618ec1c

remove munkres dependency

--- a/assignment_of_optimal_breeding_pairs.xml	Fri Sep 20 13:54:23 2013 -0400
+++ b/assignment_of_optimal_breeding_pairs.xml	Fri Sep 20 14:01:30 2013 -0400
@@ -14,9 +14,11 @@
     <data name="output" format="txt" />
   </outputs>
 
+  <!--
   <requirements>
     <requirement type="package" version="1.0.5.4">munkres</requirement>
   </requirements>
+  -->
 
   <!--
   <tests>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/munkres.py	Fri Sep 20 14:01:30 2013 -0400
@@ -0,0 +1,791 @@
+#!/usr/bin/env python
+# -*- coding: iso-8859-1 -*-
+
+# Documentation is intended to be processed by Epydoc.
+
+"""
+Introduction
+============
+
+The Munkres module provides an implementation of the Munkres algorithm
+(also called the Hungarian algorithm or the Kuhn-Munkres algorithm),
+useful for solving the Assignment Problem.
+
+Assignment Problem
+==================
+
+Let *C* be an *n*\ x\ *n* matrix representing the costs of each of *n* workers
+to perform any of *n* jobs. The assignment problem is to assign jobs to
+workers in a way that minimizes the total cost. Since each worker can perform
+only one job and each job can be assigned to only one worker the assignments
+represent an independent set of the matrix *C*.
+
+One way to generate the optimal set is to create all permutations of
+the indexes necessary to traverse the matrix so that no row and column
+are used more than once. For instance, given this matrix (expressed in
+Python)::
+
+    matrix = [[5, 9, 1],
+              [10, 3, 2],
+              [8, 7, 4]]
+
+You could use this code to generate the traversal indexes::
+
+    def permute(a, results):
+        if len(a) == 1:
+            results.insert(len(results), a)
+
+        else:
+            for i in range(0, len(a)):
+                element = a[i]
+                a_copy = [a[j] for j in range(0, len(a)) if j != i]
+                subresults = []
+                permute(a_copy, subresults)
+                for subresult in subresults:
+                    result = [element] + subresult
+                    results.insert(len(results), result)
+
+    results = []
+    permute(range(len(matrix)), results) # [0, 1, 2] for a 3x3 matrix
+
+After the call to permute(), the results matrix would look like this::
+
+    [[0, 1, 2],
+     [0, 2, 1],
+     [1, 0, 2],
+     [1, 2, 0],
+     [2, 0, 1],
+     [2, 1, 0]]
+
+You could then use that index matrix to loop over the original cost matrix
+and calculate the smallest cost of the combinations::
+
+    n = len(matrix)
+    minval = sys.maxint
+    for row in range(n):
+        cost = 0
+        for col in range(n):
+            cost += matrix[row][col]
+        minval = min(cost, minval)
+
+    print minval
+
+While this approach works fine for small matrices, it does not scale. It
+executes in O(*n*!) time: Calculating the permutations for an *n*\ x\ *n*
+matrix requires *n*! operations. For a 12x12 matrix, that's 479,001,600
+traversals. Even if you could manage to perform each traversal in just one
+millisecond, it would still take more than 133 hours to perform the entire
+traversal. A 20x20 matrix would take 2,432,902,008,176,640,000 operations. At
+an optimistic millisecond per operation, that's more than 77 million years.
+
+The Munkres algorithm runs in O(*n*\ ^3) time, rather than O(*n*!). This
+package provides an implementation of that algorithm.
+
+This version is based on
+http://www.public.iastate.edu/~ddoty/HungarianAlgorithm.html.
+
+This version was written for Python by Brian Clapper from the (Ada) algorithm
+at the above web site. (The ``Algorithm::Munkres`` Perl version, in CPAN, was
+clearly adapted from the same web site.)
+
+Usage
+=====
+
+Construct a Munkres object::
+
+    from munkres import Munkres
+
+    m = Munkres()
+
+Then use it to compute the lowest cost assignment from a cost matrix. Here's
+a sample program::
+
+    from munkres import Munkres, print_matrix
+
+    matrix = [[5, 9, 1],
+              [10, 3, 2],
+              [8, 7, 4]]
+    m = Munkres()
+    indexes = m.compute(matrix)
+    print_matrix(matrix, msg='Lowest cost through this matrix:')
+    total = 0
+    for row, column in indexes:
+        value = matrix[row][column]
+        total += value
+        print '(%d, %d) -> %d' % (row, column, value)
+    print 'total cost: %d' % total
+
+Running that program produces::
+
+    Lowest cost through this matrix:
+    [5, 9, 1]
+    [10, 3, 2]
+    [8, 7, 4]
+    (0, 0) -> 5
+    (1, 1) -> 3
+    (2, 2) -> 4
+    total cost=12
+
+The instantiated Munkres object can be used multiple times on different
+matrices.
+
+Non-square Cost Matrices
+========================
+
+The Munkres algorithm assumes that the cost matrix is square. However, it's
+possible to use a rectangular matrix if you first pad it with 0 values to make
+it square. This module automatically pads rectangular cost matrices to make
+them square.
+
+Notes:
+
+- The module operates on a *copy* of the caller's matrix, so any padding will
+  not be seen by the caller.
+- The cost matrix must be rectangular or square. An irregular matrix will
+  *not* work.
+
+Calculating Profit, Rather than Cost
+====================================
+
+The cost matrix is just that: A cost matrix. The Munkres algorithm finds
+the combination of elements (one from each row and column) that results in
+the smallest cost. It's also possible to use the algorithm to maximize
+profit. To do that, however, you have to convert your profit matrix to a
+cost matrix. The simplest way to do that is to subtract all elements from a
+large value. For example::
+
+    from munkres import Munkres, print_matrix
+
+    matrix = [[5, 9, 1],
+              [10, 3, 2],
+              [8, 7, 4]]
+    cost_matrix = []
+    for row in matrix:
+        cost_row = []
+        for col in row:
+            cost_row += [sys.maxint - col]
+        cost_matrix += [cost_row]
+
+    m = Munkres()
+    indexes = m.compute(cost_matrix)
+    print_matrix(matrix, msg='Highest profit through this matrix:')
+    total = 0
+    for row, column in indexes:
+        value = matrix[row][column]
+        total += value
+        print '(%d, %d) -> %d' % (row, column, value)
+
+    print 'total profit=%d' % total
+
+Running that program produces::
+
+    Highest profit through this matrix:
+    [5, 9, 1]
+    [10, 3, 2]
+    [8, 7, 4]
+    (0, 1) -> 9
+    (1, 0) -> 10
+    (2, 2) -> 4
+    total profit=23
+
+The ``munkres`` module provides a convenience method for creating a cost
+matrix from a profit matrix. Since it doesn't know whether the matrix contains
+floating point numbers, decimals, or integers, you have to provide the
+conversion function; but the convenience method takes care of the actual
+creation of the cost matrix::
+
+    import munkres
+
+    cost_matrix = munkres.make_cost_matrix(matrix,
+                                           lambda cost: sys.maxint - cost)
+
+So, the above profit-calculation program can be recast as::
+
+    from munkres import Munkres, print_matrix, make_cost_matrix
+
+    matrix = [[5, 9, 1],
+              [10, 3, 2],
+              [8, 7, 4]]
+    cost_matrix = make_cost_matrix(matrix, lambda cost: sys.maxint - cost)
+    m = Munkres()
+    indexes = m.compute(cost_matrix)
+    print_matrix(matrix, msg='Lowest cost through this matrix:')
+    total = 0
+    for row, column in indexes:
+        value = matrix[row][column]
+        total += value
+        print '(%d, %d) -> %d' % (row, column, value)
+    print 'total profit=%d' % total
+
+References
+==========
+
+1. http://www.public.iastate.edu/~ddoty/HungarianAlgorithm.html
+
+2. Harold W. Kuhn. The Hungarian Method for the assignment problem.
+   *Naval Research Logistics Quarterly*, 2:83-97, 1955.
+
+3. Harold W. Kuhn. Variants of the Hungarian method for assignment
+   problems. *Naval Research Logistics Quarterly*, 3: 253-258, 1956.
+
+4. Munkres, J. Algorithms for the Assignment and Transportation Problems.
+   *Journal of the Society of Industrial and Applied Mathematics*,
+   5(1):32-38, March, 1957.
+
+5. http://en.wikipedia.org/wiki/Hungarian_algorithm
+
+Copyright and License
+=====================
+
+This software is released under a BSD license, adapted from
+<http://opensource.org/licenses/bsd-license.php>
+
+Copyright (c) 2008 Brian M. Clapper
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice,
+  this list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name "clapper.org" nor the names of its contributors may be
+  used to endorse or promote products derived from this software without
+  specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.
+"""
+
+__docformat__ = 'restructuredtext'
+
+# ---------------------------------------------------------------------------
+# Imports
+# ---------------------------------------------------------------------------
+
+import sys
+
+# ---------------------------------------------------------------------------
+# Exports
+# ---------------------------------------------------------------------------
+
+__all__     = ['Munkres', 'make_cost_matrix']
+
+# ---------------------------------------------------------------------------
+# Globals
+# ---------------------------------------------------------------------------
+
+# Info about the module
+__version__   = "1.0.5.4"
+__author__    = "Brian Clapper, [e-mail]"
+__url__       = "http://bmc.github.com/munkres/"
+__copyright__ = "(c) 2008 Brian M. Clapper"
+__license__   = "BSD-style license"
+
+# ---------------------------------------------------------------------------
+# Classes
+# ---------------------------------------------------------------------------
+
+class Munkres:
+    """
+    Calculate the Munkres solution to the classical assignment problem.
+    See the module documentation for usage.
+    """
+
+    def __init__(self):
+        """Create a new instance"""
+        self.C = None
+        self.row_covered = []
+        self.col_covered = []
+        self.n = 0
+        self.Z0_r = 0
+        self.Z0_c = 0
+        self.marked = None
+        self.path = None
+
+    def make_cost_matrix(profit_matrix, inversion_function):
+        """
+        **DEPRECATED**
+
+        Please use the module function ``make_cost_matrix()``.
+        """
+        import munkres
+        return munkres.make_cost_matrix(profit_matrix, inversion_function)
+
+    make_cost_matrix = staticmethod(make_cost_matrix)
+
+    def pad_matrix(self, matrix, pad_value=0):
+        """
+        Pad a possibly non-square matrix to make it square.
+
+        :Parameters:
+            matrix : list of lists
+                matrix to pad
+
+            pad_value : int
+                value to use to pad the matrix
+
+        :rtype: list of lists
+        :return: a new, possibly padded, matrix
+        """
+        max_columns = 0
+        total_rows = len(matrix)
+
+        for row in matrix:
+            max_columns = max(max_columns, len(row))
+
+        total_rows = max(max_columns, total_rows)
+
+        new_matrix = []
+        for row in matrix:
+            row_len = len(row)
+            new_row = row[:]
+            if total_rows > row_len:
+                # Row too short. Pad it.
+                new_row += [0] * (total_rows - row_len)
+            new_matrix += [new_row]
+
+        while len(new_matrix) < total_rows:
+            new_matrix += [[0] * total_rows]
+
+        return new_matrix
+
+    def compute(self, cost_matrix):
+        """
+        Compute the indexes for the lowest-cost pairings between rows and
+        columns in the database. Returns a list of (row, column) tuples
+        that can be used to traverse the matrix.
+
+        :Parameters:
+            cost_matrix : list of lists
+                The cost matrix. If this cost matrix is not square, it
+                will be padded with zeros, via a call to ``pad_matrix()``.
+                (This method does *not* modify the caller's matrix. It
+                operates on a copy of the matrix.)
+
+                **WARNING**: This code handles square and rectangular
+                matrices. It does *not* handle irregular matrices.
+
+        :rtype: list
+        :return: A list of ``(row, column)`` tuples that describe the lowest
+                 cost path through the matrix
+
+        """
+        self.C = self.pad_matrix(cost_matrix)
+        self.n = len(self.C)
+        self.original_length = len(cost_matrix)
+        self.original_width = len(cost_matrix[0])
+        self.row_covered = [False for i in range(self.n)]
+        self.col_covered = [False for i in range(self.n)]
+        self.Z0_r = 0
+        self.Z0_c = 0
+        self.path = self.__make_matrix(self.n * 2, 0)
+        self.marked = self.__make_matrix(self.n, 0)
+
+        done = False
+        step = 1
+
+        steps = { 1 : self.__step1,
+                  2 : self.__step2,
+                  3 : self.__step3,
+                  4 : self.__step4,
+                  5 : self.__step5,
+                  6 : self.__step6 }
+
+        while not done:
+            try:
+                func = steps[step]
+                step = func()
+            except KeyError:
+                done = True
+
+        # Look for the starred columns
+        results = []
+        for i in range(self.original_length):
+            for j in range(self.original_width):
+                if self.marked[i][j] == 1:
+                    results += [(i, j)]
+
+        return results
+
+    def __copy_matrix(self, matrix):
+        """Return an exact copy of the supplied matrix"""
+        return copy.deepcopy(matrix)
+
+    def __make_matrix(self, n, val):
+        """Create an *n*x*n* matrix, populating it with the specific value."""
+        matrix = []
+        for i in range(n):
+            matrix += [[val for j in range(n)]]
+        return matrix
+
+    def __step1(self):
+        """
+        For each row of the matrix, find the smallest element and
+        subtract it from every element in its row. Go to Step 2.
+        """
+        C = self.C
+        n = self.n
+        for i in range(n):
+            minval = min(self.C[i])
+            # Find the minimum value for this row and subtract that minimum
+            # from every element in the row.
+            for j in range(n):
+                self.C[i][j] -= minval
+
+        return 2
+
+    def __step2(self):
+        """
+        Find a zero (Z) in the resulting matrix. If there is no starred
+        zero in its row or column, star Z. Repeat for each element in the
+        matrix. Go to Step 3.
+        """
+        n = self.n
+        for i in range(n):
+            for j in range(n):
+                if (self.C[i][j] == 0) and \
+                   (not self.col_covered[j]) and \
+                   (not self.row_covered[i]):
+                    self.marked[i][j] = 1
+                    self.col_covered[j] = True
+                    self.row_covered[i] = True
+
+        self.__clear_covers()
+        return 3
+
+    def __step3(self):
+        """
+        Cover each column containing a starred zero. If K columns are
+        covered, the starred zeros describe a complete set of unique
+        assignments. In this case, Go to DONE, otherwise, Go to Step 4.
+        """
+        n = self.n
+        count = 0
+        for i in range(n):
+            for j in range(n):
+                if self.marked[i][j] == 1:
+                    self.col_covered[j] = True
+                    count += 1
+
+        if count >= n:
+            step = 7 # done
+        else:
+            step = 4
+
+        return step
+
+    def __step4(self):
+        """
+        Find a noncovered zero and prime it. If there is no starred zero
+        in the row containing this primed zero, Go to Step 5. Otherwise,
+        cover this row and uncover the column containing the starred
+        zero. Continue in this manner until there are no uncovered zeros
+        left. Save the smallest uncovered value and Go to Step 6.
+        """
+        step = 0
+        done = False
+        row = -1
+        col = -1
+        star_col = -1
+        while not done:
+            (row, col) = self.__find_a_zero()
+            if row < 0:
+                done = True
+                step = 6
+            else:
+                self.marked[row][col] = 2
+                star_col = self.__find_star_in_row(row)
+                if star_col >= 0:
+                    col = star_col
+                    self.row_covered[row] = True
+                    self.col_covered[col] = False
+                else:
+                    done = True
+                    self.Z0_r = row
+                    self.Z0_c = col
+                    step = 5
+
+        return step
+
+    def __step5(self):
+        """
+        Construct a series of alternating primed and starred zeros as
+        follows. Let Z0 represent the uncovered primed zero found in Step 4.
+        Let Z1 denote the starred zero in the column of Z0 (if any).
+        Let Z2 denote the primed zero in the row of Z1 (there will always
+        be one). Continue until the series terminates at a primed zero
+        that has no starred zero in its column. Unstar each starred zero
+        of the series, star each primed zero of the series, erase all
+        primes and uncover every line in the matrix. Return to Step 3
+        """
+        count = 0
+        path = self.path
+        path[count][0] = self.Z0_r
+        path[count][1] = self.Z0_c
+        done = False
+        while not done:
+            row = self.__find_star_in_col(path[count][1])
+            if row >= 0:
+                count += 1
+                path[count][0] = row
+                path[count][1] = path[count-1][1]
+            else:
+                done = True
+
+            if not done:
+                col = self.__find_prime_in_row(path[count][0])
+                count += 1
+                path[count][0] = path[count-1][0]
+                path[count][1] = col
+
+        self.__convert_path(path, count)
+        self.__clear_covers()
+        self.__erase_primes()
+        return 3
+
+    def __step6(self):
+        """
+        Add the value found in Step 4 to every element of each covered
+        row, and subtract it from every element of each uncovered column.
+        Return to Step 4 without altering any stars, primes, or covered
+        lines.
+        """
+        minval = self.__find_smallest()
+        for i in range(self.n):
+            for j in range(self.n):
+                if self.row_covered[i]:
+                    self.C[i][j] += minval
+                if not self.col_covered[j]:
+                    self.C[i][j] -= minval
+        return 4
+
+    def __find_smallest(self):
+        """Find the smallest uncovered value in the matrix."""
+        minval = sys.maxint
+        for i in range(self.n):
+            for j in range(self.n):
+                if (not self.row_covered[i]) and (not self.col_covered[j]):
+                    if minval > self.C[i][j]:
+                        minval = self.C[i][j]
+        return minval
+
+    def __find_a_zero(self):
+        """Find the first uncovered element with value 0"""
+        row = -1
+        col = -1
+        i = 0
+        n = self.n
+        done = False
+
+        while not done:
+            j = 0
+            while True:
+                if (self.C[i][j] == 0) and \
+                   (not self.row_covered[i]) and \
+                   (not self.col_covered[j]):
+                    row = i
+                    col = j
+                    done = True
+                j += 1
+                if j >= n:
+                    break
+            i += 1
+            if i >= n:
+                done = True
+
+        return (row, col)
+
+    def __find_star_in_row(self, row):
+        """
+        Find the first starred element in the specified row. Returns
+        the column index, or -1 if no starred element was found.
+        """
+        col = -1
+        for j in range(self.n):
+            if self.marked[row][j] == 1:
+                col = j
+                break
+
+        return col
+
+    def __find_star_in_col(self, col):
+        """
+        Find the first starred element in the specified row. Returns
+        the row index, or -1 if no starred element was found.
+        """
+        row = -1
+        for i in range(self.n):
+            if self.marked[i][col] == 1:
+                row = i
+                break
+
+        return row
+
+    def __find_prime_in_row(self, row):
+        """
+        Find the first prime element in the specified row. Returns
+        the column index, or -1 if no starred element was found.
+        """
+        col = -1
+        for j in range(self.n):
+            if self.marked[row][j] == 2:
+                col = j
+                break
+
+        return col
+
+    def __convert_path(self, path, count):
+        for i in range(count+1):
+            if self.marked[path[i][0]][path[i][1]] == 1:
+                self.marked[path[i][0]][path[i][1]] = 0
+            else:
+                self.marked[path[i][0]][path[i][1]] = 1
+
+    def __clear_covers(self):
+        """Clear all covered matrix cells"""
+        for i in range(self.n):
+            self.row_covered[i] = False
+            self.col_covered[i] = False
+
+    def __erase_primes(self):
+        """Erase all prime markings"""
+        for i in range(self.n):
+            for j in range(self.n):
+                if self.marked[i][j] == 2:
+                    self.marked[i][j] = 0
+
+# ---------------------------------------------------------------------------
+# Functions
+# ---------------------------------------------------------------------------
+
+def make_cost_matrix(profit_matrix, inversion_function):
+    """
+    Create a cost matrix from a profit matrix by calling
+    'inversion_function' to invert each value. The inversion
+    function must take one numeric argument (of any type) and return
+    another numeric argument which is presumed to be the cost inverse
+    of the original profit.
+
+    This is a static method. Call it like this:
+
+    .. python::
+
+        cost_matrix = Munkres.make_cost_matrix(matrix, inversion_func)
+
+    For example:
+
+    .. python::
+
+        cost_matrix = Munkres.make_cost_matrix(matrix, lambda x : sys.maxint - x)
+
+    :Parameters:
+        profit_matrix : list of lists
+            The matrix to convert from a profit to a cost matrix
+
+        inversion_function : function
+            The function to use to invert each entry in the profit matrix
+
+    :rtype: list of lists
+    :return: The converted matrix
+    """
+    cost_matrix = []
+    for row in profit_matrix:
+        cost_matrix.append([inversion_function(value) for value in row])
+    return cost_matrix
+
+def print_matrix(matrix, msg=None):
+    """
+    Convenience function: Displays the contents of a matrix of integers.
+
+    :Parameters:
+        matrix : list of lists
+            Matrix to print
+
+        msg : str
+            Optional message to print before displaying the matrix
+    """
+    import math
+
+    if msg is not None:
+        print msg
+
+    # Calculate the appropriate format width.
+    width = 0
+    for row in matrix:
+        for val in row:
+            width = max(width, int(math.log10(val)) + 1)
+
+    # Make the format string
+    format = '%%%dd' % width
+
+    # Print the matrix
+    for row in matrix:
+        sep = '['
+        for val in row:
+            sys.stdout.write(sep + format % val)
+            sep = ', '
+        sys.stdout.write(']\n')
+
+# ---------------------------------------------------------------------------
+# Main
+# ---------------------------------------------------------------------------
+
+if __name__ == '__main__':
+
+
+    matrices = [
+                # Square
+                ([[400, 150, 400],
+                  [400, 450, 600],
+                  [300, 225, 300]],
+                 850 # expected cost
+                ),
+
+                # Rectangular variant
+                ([[400, 150, 400, 1],
+                  [400, 450, 600, 2],
+                  [300, 225, 300, 3]],
+                 452 # expected cost
+                ),
+
+                # Square
+                ([[10, 10,  8],
+                  [ 9,  8,  1],
+                  [ 9,  7,  4]],
+                 18
+                ),
+
+                # Rectangular variant
+                ([[10, 10,  8, 11],
+                  [ 9,  8,  1, 1],
+                  [ 9,  7,  4, 10]],
+                 15
+                ),
+               ]
+
+    m = Munkres()
+    for cost_matrix, expected_total in matrices:
+        print_matrix(cost_matrix, msg='cost matrix')
+        indexes = m.compute(cost_matrix)
+        total_cost = 0
+        for r, c in indexes:
+            x = cost_matrix[r][c]
+            total_cost += x
+            print '(%d, %d) -> %d' % (r, c, x)
+        print 'lowest cost=%d' % total_cost
+        assert expected_total == total_cost
+

--- a/tool_dependencies.xml	Fri Sep 20 13:54:23 2013 -0400
+++ b/tool_dependencies.xml	Fri Sep 20 14:01:30 2013 -0400
@@ -20,9 +20,11 @@
   <package name="mechanize" version="0.2.5">
     <repository prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu/" owner="miller-lab" name="package_mechanize_0_2_5" changeset_revision="59801857421b" />
   </package>
+  <!--
   <package name="munkres" version="1.0.5.4">
     <repository prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu/" owner="miller-lab" name="package_munkres_1_0_5_4" changeset_revision="613b89b28767" />
   </package>
+  -->
   <package name="networkx" version="1.8.1">
     <repository prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu/" owner="miller-lab" name="package_networkx_1_8_1" changeset_revision="43c20433f2d6" />
   </package>