diff options
| -rw-r--r-- | gn3/computations/correlations2.py | 37 | ||||
| -rw-r--r-- | gn3/computations/slink.py | 84 | ||||
| -rw-r--r-- | tests/unit/computations/test_correlation.py | 32 | ||||
| -rw-r--r-- | tests/unit/computations/test_slink.py | 401 |
4 files changed, 335 insertions, 219 deletions
diff --git a/gn3/computations/correlations2.py b/gn3/computations/correlations2.py index 6c456db..93db3fa 100644 --- a/gn3/computations/correlations2.py +++ b/gn3/computations/correlations2.py @@ -1,15 +1,25 @@ +""" +DESCRIPTION: + TODO: Add a description for the module + +FUNCTIONS: +compute_correlation: + TODO: Describe what the function does...""" + from math import sqrt from functools import reduce ## From GN1: mostly for clustering and heatmap generation -def items_with_values(dbdata, userdata): +def __items_with_values(dbdata, userdata): """Retains only corresponding items in the data items that are not `None` values. -This should probably be renamed to something sensible""" + This should probably be renamed to something sensible""" def both_not_none(item1, item2): + """Check that both items are not the value `None`.""" if (item1 is not None) and (item2 is not None): return (item1, item2) return None def split_lists(accumulator, item): + """Separate the 'x' and 'y' items.""" return [accumulator[0] + [item[0]], accumulator[1] + [item[1]]] return reduce( split_lists, @@ -17,19 +27,24 @@ This should probably be renamed to something sensible""" [[], []]) def compute_correlation(dbdata, userdata): - x, y = items_with_values(dbdata, userdata) - if len(x) < 6: - return (0.0, len(x)) - meanx = sum(x)/len(x) - meany = sum(y)/len(y) + """Compute some form of correlation. + + This is extracted from + https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/utility/webqtlUtil.py#L622-L647 + """ + x_items, y_items = __items_with_values(dbdata, userdata) + if len(x_items) < 6: + return (0.0, len(x_items)) + meanx = sum(x_items)/len(x_items) + meany = sum(y_items)/len(y_items) def cal_corr_vals(acc, item): xitem, yitem = item return [ acc[0] + ((xitem - meanx) * (yitem - meany)), acc[1] + ((xitem - meanx) * (xitem - meanx)), acc[2] + ((yitem - meany) * (yitem - meany))] - xyd, sxd, syd = reduce(cal_corr_vals, zip(x, y), [0.0, 0.0, 0.0]) + xyd, sxd, syd = reduce(cal_corr_vals, zip(x_items, y_items), [0.0, 0.0, 0.0]) try: - return ((xyd/(sqrt(sxd)*sqrt(syd))), len(x)) - except ZeroDivisionError as zde: - return(0, len(x)) + return ((xyd/(sqrt(sxd)*sqrt(syd))), len(x_items)) + except ZeroDivisionError: + return(0, len(x_items)) diff --git a/gn3/computations/slink.py b/gn3/computations/slink.py index 8d51f29..4aac6b3 100644 --- a/gn3/computations/slink.py +++ b/gn3/computations/slink.py @@ -7,13 +7,14 @@ slink: TODO: Describe what the function does... """ import logging -from functools import partial class LengthError(BaseException): - pass + """Raised whenever child lists/tuples are not the same length as the parent + list of tuple.""" class MirrorError(BaseException): - pass + """Raised if the distance from child A to child B is not the same as the + distance from child B to child A.""" def __is_list_or_tuple(item): return type(item) in [list, tuple] @@ -50,19 +51,20 @@ def __raise_valueerror_if_child_list_distance_from_itself_is_not_zero(lists): def __raise_mirrorerror_of_distances_one_way_are_not_same_other_way(lists): """Check that the distance from A to B, is the same as the distance from B to A. If the two distances are different, throw an exception.""" - for i in range(len(lists)): - for j in range(len(lists)): - if lists[i][j] != lists[j][i]: - raise MirrorError( - ("Distance from one child({}) to the other ({}) " - "should be the same in both directions.").format( - lists[i][j], lists[j][i])) + inner_coords = range(len(lists)) + coords = ((i, j) for i in inner_coords for j in inner_coords) + def __is_same_reversed(coord): + return lists[coord[0]][coord[1]] == lists[coord[1]][coord[0]] + if not all(map(__is_same_reversed, coords)): + raise MirrorError(( + "Distance from one child to the other should be the same in both " + "directions.")) def __raise_valueerror_on_negative_distances(lists): """Check that distances between 'somethings' are all positive, otherwise, raise an exception.""" def zero_or_positive(val): - return val >= 0; + return val >= 0 # flatten lists flattened = __flatten_list_of_lists(lists) if not all(map(zero_or_positive, flattened)): @@ -76,7 +78,8 @@ def nearest(lists, i, j): Computes shortest distance between member(s) in `i` and member(s) in `j`. Description: - This is 'copied' over from genenetwork1, from https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L42-L64. + This is 'copied' over from genenetwork1, from + https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L42-L64. This description should be updated to better describe what 'member' means in the context where the function is used. @@ -108,18 +111,20 @@ def nearest(lists, i, j): __raise_mirrorerror_of_distances_one_way_are_not_same_other_way(lists) __raise_valueerror_on_negative_distances(lists) #### END: Guard Functions #### - if type(i) == int and type(j) == int: # From member i to member j + if isinstance(i, int) and isinstance(j, int): # From member i to member j return lists[i][j] - elif type(i) == int and __is_list_or_tuple(j): + + if isinstance(i, int) and __is_list_or_tuple(j): return min(map(lambda j_new: nearest(lists, i, j_new), j[:-1])) - elif type(j) == int and __is_list_or_tuple(i): + if isinstance(j, int) and __is_list_or_tuple(i): return min(map(lambda i_new: nearest(lists, i_new, j), i[:-1])) - elif __is_list_or_tuple(i) and __is_list_or_tuple(j): + + if __is_list_or_tuple(i) and __is_list_or_tuple(j): coordinate_pairs = __flatten_list_of_lists( [[(itemi, itemj) for itemj in j[:-1]] for itemi in i[:-1]]) return min(map(lambda x: nearest(lists, x[0], x[1]), coordinate_pairs)) - else: - raise ValueError("member values (i or j) should be lists/tuples of integers or integers") + + raise ValueError("member values (i or j) should be lists/tuples of integers or integers") def slink(lists): """ @@ -144,36 +149,39 @@ def slink(lists): """ try: size = len(lists) - listindex = range(size) listindexcopy = list(range(size)) - listscopy = [[item for item in child] for child in lists] - initSize = size + listscopy = [child[:] for child in lists] + init_size = size candidate = [] - while initSize >2: + while init_size > 2: mindist = 1e10 - for i in range(initSize): - for j in range(i+1,initSize): + for i in range(init_size): + for j in range(i+1, init_size): if listscopy[i][j] < mindist: - mindist = listscopy[i][j] - candidate=[[i,j]] + mindist = listscopy[i][j] + candidate = [[i, j]] elif listscopy[i][j] == mindist: - mindist = listscopy[i][j] - candidate.append([i,j]) + mindist = listscopy[i][j] + candidate.append([i, j]) else: pass - newmem = (listindexcopy[candidate[0][0]],listindexcopy[candidate[0][1]],mindist) + newmem = ( + listindexcopy[candidate[0][0]], listindexcopy[candidate[0][1]], + mindist) listindexcopy.pop(candidate[0][1]) listindexcopy[candidate[0][0]] = newmem - initSize -= 1 - for i in range(initSize): - for j in range(i+1,initSize): - listscopy[i][j] = nearest(lists,listindexcopy[i],listindexcopy[j]) + init_size -= 1 + for i in range(init_size): + for j in range(i+1, init_size): + listscopy[i][j] = nearest( + lists, listindexcopy[i], listindexcopy[j]) listscopy[j][i] = listscopy[i][j] - listindexcopy.append(nearest(lists,listindexcopy[0],listindexcopy[1])) + listindexcopy.append( + nearest(lists, listindexcopy[0], listindexcopy[1])) return listindexcopy - except Exception as e: - # TODO: Look into making the logging log output to the system's - # configured logger(s) - logging.warning("Exception: {}, {}".format(type(e), e)) + except (LengthError, MirrorError, TypeError, IndexError) as exc: + # Look into making the logging log output to the system's + # configured logger(s) + logging.warning("Exception: %s, %s", type(exc), exc) return [] diff --git a/tests/unit/computations/test_correlation.py b/tests/unit/computations/test_correlation.py index 6153c8a..9450094 100644 --- a/tests/unit/computations/test_correlation.py +++ b/tests/unit/computations/test_correlation.py @@ -467,26 +467,28 @@ class TestCorrelation(TestCase): self.assertEqual(results, [expected_results]) def test_compute_correlation(self): - for dbdata,userdata,expected in [ - [[None,None,None,None,None,None,None,None,None,None], - [None,None,None,None,None,None,None,None,None,None], + """Test that the new correlation function works the same as the original + from genenetwork1.""" + for dbdata, userdata, expected in [ + [[None, None, None, None, None, None, None, None, None, None], + [None, None, None, None, None, None, None, None, None, None], (0.0, 0)], - [[None,None,None,None,None,None,None,None,None,0], - [None,None,None,None,None,None,None,None,None,None], + [[None, None, None, None, None, None, None, None, None, 0], + [None, None, None, None, None, None, None, None, None, None], (0.0, 0)], - [[None,None,None,None,None,None,None,None,None,0], - [None,None,None,None,None,None,None,None,None,0], + [[None, None, None, None, None, None, None, None, None, 0], + [None, None, None, None, None, None, None, None, None, 0], (0.0, 1)], - [[0,0,0,0,0,0,0,0,0,0],[0,0,0,0,0,0,0,0,0,0], + [[0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], (0, 10)], - [[9.87,9.87,9.87,9.87,9.87,9.87,9.87,9.87,9.87,9.87], - [9.87,9.87,9.87,9.87,9.87,9.87,9.87,9.87,9.87,9.87], + [[9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87], + [9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87, 9.87], (0.9999999999999998, 10)], - [[9.3,2.2,5.4,7.2,6.4,7.6,3.8,1.8,8.4,0.2], - [0.6,3.97,5.82,8.21,1.65,4.55,6.72,9.5,7.33,2.34], + [[9.3, 2.2, 5.4, 7.2, 6.4, 7.6, 3.8, 1.8, 8.4, 0.2], + [0.6, 3.97, 5.82, 8.21, 1.65, 4.55, 6.72, 9.5, 7.33, 2.34], (-0.12720361919462056, 10)], - [[0,1,2,3,4,5,6,7,8,9], - [None,None,None,None,2,None,None,3,None,None], + [[0, 1, 2, 3, 4, 5, 6, 7, 8, 9], + [None, None, None, None, 2, None, None, 3, None, None], (0.0, 2)]]: with self.subTest(dbdata=dbdata, userdata=userdata): - self.assertEqual(compute_correlation(dbdata,userdata), expected) + self.assertEqual(compute_correlation(dbdata, userdata), expected) diff --git a/tests/unit/computations/test_slink.py b/tests/unit/computations/test_slink.py index 5627767..995393b 100644 --- a/tests/unit/computations/test_slink.py +++ b/tests/unit/computations/test_slink.py @@ -1,5 +1,4 @@ """Module contains tests for slink""" -import unittest from unittest import TestCase from gn3.computations.slink import slink @@ -11,210 +10,302 @@ class TestSlink(TestCase): """Class for testing slink functions""" def test_nearest_expects_list_of_lists(self): + """Test that function only accepts a list of lists.""" # This might be better handled with type-hints and mypy for item in [9, "some string", 5.432, - [1,2,3], ["test", 7.4]]: + [1, 2, 3], ["test", 7.4]]: with self.subTest(item=item): with self.assertRaises(ValueError, msg="Expected list or tuple"): nearest(item, 1, 1) def test_nearest_does_not_allow_empty_lists(self): + """Test that function does not accept an empty list, or any of the child + lists to be empty.""" for lst in [[], - [[],[]], - [[],[],[]], - [[0, 1, 2],[],[1, 2, 0]]]: + [[], []], + [[], [], []], + [[0, 1, 2], [], [1, 2, 0]]]: with self.subTest(lst=lst): with self.assertRaises(ValueError): nearest(lst, 1, 1) - def test_nearest_expects_exception_if_all_child_lists_are_not_of_equal_length_to_length_of_parent_list(self): - for lst in [[[0,1]], - [[0,1,2],[3,4,5]], - [[0,1,2,3],[4,5,6],[7,8,9,0]], - [[0,1,2,3,4],[5,6,7,8,9],[1,2,3,4,5],[2,3],[3,4,5,6,7]]]: + def test_nearest_expects_children_are_same_length_as_parent(self): + """Test that children lists are same length as parent list.""" + for lst in [[[0, 1]], + [[0, 1, 2], [3, 4, 5]], + [[0, 1, 2, 3], [4, 5, 6], [7, 8, 9, 0]], + [[0, 1, 2, 3, 4], [5, 6, 7, 8, 9], [1, 2, 3, 4, 5], [2, 3], + [3, 4, 5, 6, 7]]]: with self.subTest(lst=lst): with self.assertRaises(LengthError): nearest(lst, 1, 1) - def test_nearest_expects_exception_if_distance_of_child_from_itself_is_not_zero(self): + def test_nearest_expects_member_is_zero_distance_from_itself(self): + """Test that distance of a member from itself is zero""" for lst in [[[1]], - [[1,2],[3,4]], - [1,0,0],[0,0,5],[0,3,4], - [0,0,0,0],[0,0,3,3],[0,1,2,3],[0,3,2,0]]: + [[1, 2], [3, 4]], + [1, 0, 0], [0, 0, 5], [0, 3, 4], + [0, 0, 0, 0], [0, 0, 3, 3], [0, 1, 2, 3], [0, 3, 2, 0]]: with self.subTest(lst=lst): with self.assertRaises(ValueError): nearest(lst, 1, 1) - def test_nearest_expects_exception_if_distance_from_child_a_to_child_b_is_not_distance_from_child_b_to_child_a(self): - for lst in [[[0,1],[2,0]], - [[0,1,2],[1,0,3],[9,7,0]], - [[0,1,2,3],[7,0,2,3],[2,3,0,1],[8,9,5,0]]]: + def test_nearest_expects_distance_atob_is_equal_to_distance_btoa(self): + """Test that the distance from member A to member B is the same as that + from member B to member A.""" + for lst in [[[0, 1], [2, 0]], + [[0, 1, 2], [1, 0, 3], [9, 7, 0]], + [[0, 1, 2, 3], [7, 0, 2, 3], [2, 3, 0, 1], [8, 9, 5, 0]]]: with self.subTest(lst=lst): with self.assertRaises(MirrorError): nearest(lst, 1, 1) def test_nearest_expects_zero_or_positive_distances(self): + """Test that all distances are either zero, or greater than zero.""" # Based on: # https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L87-L89 - for lst in [[[0,-1,2,3],[-1,0,3,4],[2,3,0,5],[3,4,5,0]], - [[0,1,-2,3],[1,0,3,4],[-2,3,0,5],[3,4,5,0]], - [[0,1,2,3],[1,0,-3,4],[2,-3,0,5],[3,4,5,0]], - [[0,1,2,-3],[1,0,3,4],[2,3,0,5],[-3,4,5,0]], - [[0,1,2,3],[1,0,3,-4],[2,3,0,5],[3,-4,5,0]], - [[0,1,2,3],[1,0,3,4],[2,3,0,-5],[3,4,-5,0]]]: + for lst in [[[0, -1, 2, 3], [-1, 0, 3, 4], [2, 3, 0, 5], [3, 4, 5, 0]], + [[0, 1, -2, 3], [1, 0, 3, 4], [-2, 3, 0, 5], [3, 4, 5, 0]], + [[0, 1, 2, 3], [1, 0, -3, 4], [2, -3, 0, 5], [3, 4, 5, 0]], + [[0, 1, 2, -3], [1, 0, 3, 4], [2, 3, 0, 5], [-3, 4, 5, 0]], + [[0, 1, 2, 3], [1, 0, 3, -4], [2, 3, 0, 5], [3, -4, 5, 0]], + [[0, 1, 2, 3], [1, 0, 3, 4], [2, 3, 0, -5], [3, 4, -5, 0]]]: with self.subTest(lst=lst): with self.assertRaises(ValueError, msg="Distances should be positive."): nearest(lst, 1, 1) def test_nearest_returns_shortest_distance_given_coordinates_to_both_group_members(self): + """Test that the shortest distance is returned.""" # This test is named wrong - at least I think it is, from the expected results # This tests distance when both `i`, and `j` are integers # We still need to add tests for when (either one/both) (is/are) not (an) integer(s) # https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L39-L40 - for lst, i, j, expected in [[[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - 0,0,0], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - 0,1,9], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - 0,2,3], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - 0,3,6], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - 0,4,11], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - 1,0,9], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - 1,1,0], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - 1,2,7], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - 1,3,5], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - 1,4,10], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - 2,0,3], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - 2,1,7], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - 2,2,0], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - 2,3,9], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - 2,4,2], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - 3,0,6], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - 3,1,5], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - 3,2,9], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - 3,3,0], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - 3,4,8], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - 4,0,11], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - 4,1,10], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - 4,2,2], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - 4,3,8], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - 4,4,0], - [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], - 0,0,0], - [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], - 0,1,9], - [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], - 0,2,5.5], - [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], - 0,3,6], - [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], - 0,4,11], - [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], - 1,0,9], - [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], - 1,1,0], - [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], - 1,2,7], - [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], - 1,3,5], - [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], - 1,4,10], - [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], - 2,0,5.5], - [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], - 2,1,7], - [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], - 2,2,0], - [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], - 2,3,9], - [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], - 2,4,2], - [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], - 3,0,6], - [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], - 3,1,5], - [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], - 3,2,9], - [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], - 3,3,0], - [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], - 3,4,3], - [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], - 4,0,11], - [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], - 4,1,10], - [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], - 4,2,2], - [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], - 4,3,3], - [[[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]], - 4,4,0]]: + for lst, i, j, expected in [ + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + 0, 0, 0], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + 0, 1, 9], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + 0, 2, 3], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + 0, 3, 6], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + 0, 4, 11], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + 1, 0, 9], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + 1, 1, 0], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + 1, 2, 7], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + 1, 3, 5], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + 1, 4, 10], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + 2, 0, 3], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + 2, 1, 7], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + 2, 2, 0], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + 2, 3, 9], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + 2, 4, 2], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + 3, 0, 6], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + 3, 1, 5], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + 3, 2, 9], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + 3, 3, 0], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + 3, 4, 8], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + 4, 0, 11], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + 4, 1, 10], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + 4, 2, 2], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + 4, 3, 8], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + 4, 4, 0], + [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2], + [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]], + 0, 0, 0], + [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2], + [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]], + 0, 1, 9], + [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2], + [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]], + 0, 2, 5.5], + [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2], + [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]], + 0, 3, 6], + [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2], + [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]], + 0, 4, 11], + [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2], + [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]], + 1, 0, 9], + [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2], + [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]], + 1, 1, 0], + [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2], + [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]], + 1, 2, 7], + [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2], + [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]], + 1, 3, 5], + [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2], + [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]], + 1, 4, 10], + [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2], + [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]], + 2, 0, 5.5], + [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2], + [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]], + 2, 1, 7], + [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2], + [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]], + 2, 2, 0], + [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2], + [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]], + 2, 3, 9], + [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2], + [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]], + 2, 4, 2], + [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2], + [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]], + 3, 0, 6], + [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2], + [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]], + 3, 1, 5], + [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2], + [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]], + 3, 2, 9], + [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2], + [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]], + 3, 3, 0], + [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2], + [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]], + 3, 4, 3], + [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2], + [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]], + 4, 0, 11], + [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2], + [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]], + 4, 1, 10], + [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2], + [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]], + 4, 2, 2], + [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2], + [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]], + 4, 3, 3], + [[[0, 9, 5.5, 6, 11], [9, 0, 7, 5, 10], [5.5, 7, 0, 9, 2], + [6, 5, 9, 0, 3], [11, 10, 2, 3, 0]], + 4, 4, 0]]: with self.subTest(lst=lst): self.assertEqual(nearest(lst, i, j), expected) - def test_given_a_list_or_tuple_of_members_distances_and_a_coordinate_find_closest_member_to_member_at_coordinate(self): - for md, ml, mc, ed in [ - [[[0,9,3],[9,0,7],[3,7,0]],(0,2,3),1,7], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],[0,1,2,3,4],3,0], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],[0,1,2,4],3,5], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],[0,2,4],3,6], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]],[2,4],3,9]]: + def test_nearest_gives_shortest_distance_between_list_of_members_and_member(self): + """Test that the shortest distance is returned.""" + for members_distances, members_list, member_coordinate, expected_distance in [ + [[[0, 9, 3], [9, 0, 7], [3, 7, 0]], (0, 2, 3), 1, 7], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], [0, 1, 2, 3, 4], 3, 0], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], [0, 1, 2, 4], 3, 5], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], [0, 2, 4], 3, 6], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], [2, 4], 3, 9]]: with self.subTest( - members_distances=md, members_list=ml, member_coordinate=mc, - expected_distance=ed): - self.assertEqual(nearest(md, ml, mc), ed) - self.assertEqual(nearest(md, mc, ml), ed) + members_distances=members_distances, + members_list=members_list, + member_coordinate=member_coordinate, + expected_distance=expected_distance): + self.assertEqual( + nearest( + members_distances, members_list, member_coordinate), + expected_distance) + self.assertEqual( + nearest( + members_distances, member_coordinate, members_list), + expected_distance) - def test_given_2_lists_or_tuples_of_members_distances_nearest_returns_shortest_distance(self): - for md, ml, mc, ed in [ - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - [0,1,2,3,4],[0,1,2,3,4],0], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - [0,1],[3,4],6], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - [0,1],[2,3,4],3], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]], - [0,2],[3,4],6]]: + def test_nearest_returns_shortest_distance_given_two_lists_of_members(self): + """Test that the shortest distance is returned.""" + for members_distances, members_list, member_list2, expected_distance in [ + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + [0, 1, 2, 3, 4], [0, 1, 2, 3, 4], 0], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + [0, 1], [3, 4], 6], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + [0, 1], [2, 3, 4], 3], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], [11, 10, 2, 8, 0]], + [0, 2], [3, 4], 6]]: with self.subTest( - members_distances=md, members_list=ml, member_coordinate=mc, - expected_distance=ed): - self.assertEqual(nearest(md, ml, mc), ed) - self.assertEqual(nearest(md, mc, ml), ed) + members_distances=members_distances, + members_list=members_list, + member_list2=member_list2, + expected_distance=expected_distance): + self.assertEqual( + nearest( + members_distances, members_list, member_list2), + expected_distance) + self.assertEqual( + nearest( + members_distances, member_list2, members_list), + expected_distance) def test_slink_wrong_data_returns_empty_list(self): + """Test that empty list is returned for wrong data.""" for data in [1, "test", [], 2.945, nearest, [0]]: with self.subTest(data=data): self.assertEqual(slink(data), []) def test_slink_with_data(self): + """Test slink with example data, and expected results for each data + sample.""" for data, expected in [ - [[[0,9],[9,0]],[0,1,9]], - [[[0,9,3],[9,0,7],[3,7,0]],[(0,2,3),1,7]], - [[[0,9,3,6],[9,0,7,5],[3,7,0,9],[6,5,9,0]],[(0,2,3),(1,3,5),6]], - [[[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8], - [11,10,2,8,0]], - [(0,(2,4,2),3),(1,3,5),6]]]: + [[[0, 9], [9, 0]], [0, 1, 9]], + [[[0, 9, 3], [9, 0, 7], [3, 7, 0]], [(0, 2, 3), 1, 7]], + [[[0, 9, 3, 6], [9, 0, 7, 5], [3, 7, 0, 9], [6, 5, 9, 0]], + [(0, 2, 3), (1, 3, 5), 6]], + [[[0, 9, 3, 6, 11], [9, 0, 7, 5, 10], [3, 7, 0, 9, 2], + [6, 5, 9, 0, 8], + [11, 10, 2, 8, 0]], + [(0, (2, 4, 2), 3), (1, 3, 5), 6]]]: with self.subTest(data=data): self.assertEqual(slink(data), expected) |