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adding sort shortest to longest and vice versa #41

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adding sort shortest to longest and vice versa #41

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42539cf
longest/shortest pathways and 100% testing pa
nuclearkatie Jan 14, 2022
051602e
linting
nuclearkatie Jan 14, 2022
6905e44
re-added missing comma
nuclearkatie Jan 14, 2022
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170 changes: 115 additions & 55 deletions tests/test_pathway_analysis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,8 +26,8 @@ def test_ndp():


@pytest.mark.parametrize("source,target", [('import', 'heu_pu_collector'),
('mine', 'export'),
('import', 'export')])
('mine', 'export'),
('import', 'export')])
def test_ndp_raise_exception(source, target):
G = nx.DiGraph()
edges = [('mine', 'civ_enrich'), ('mine', 'mil_enrich'),
Expand All @@ -36,7 +36,7 @@ def test_ndp_raise_exception(source, target):
('mil_enrich', 'heu_pu_collector')]
G.add_edges_from(edges)

with pytest.raises(ValueError) as excinfo:
with pytest.raises(ValueError) as excinfo:
obj = pa.find_node_disjoint_paths(G, source, target)
assert 'Source and/or target not in graph G!' in str(excinfo.value)

Expand Down Expand Up @@ -101,7 +101,7 @@ def test_has_multiedges_not_multigraph():
exp = None
G = nx.DiGraph()
G.add_edge('a', 'b')

obs = pa.has_multiedges(G)
assert obs == exp

Expand All @@ -119,6 +119,17 @@ def test_transform_to_digraph():
assert obs == exp


def test_transform_to_digraph_has_multiedges():
G = nx.MultiDiGraph()
G.add_edge('a', 'b')
G.add_edge('a', 'b')
exp = False

(obs_H, obs_safe) = pa.transform_to_digraph(G)

assert obs_safe == exp


@pytest.mark.parametrize("G", [(nx.Graph()), (nx.MultiGraph())])
def test_transform_to_digraph_unsafe(G):
exp = False
Expand All @@ -130,7 +141,7 @@ def test_transform_to_digraph_unsafe(G):
assert obs_safe == exp


@pytest.mark.parametrize("G,exp", [(nx.Graph(), None),
@pytest.mark.parametrize("G,exp", [(nx.Graph(), None),
(nx.MultiGraph(), None)])
def test_transform_to_digraph_formats(G, exp):
G.add_edge('a', 'b')
Expand All @@ -139,7 +150,7 @@ def test_transform_to_digraph_formats(G, exp):
assert obs_H == exp


@pytest.mark.parametrize("G,exp", [(nx.Graph(), False),
@pytest.mark.parametrize("G,exp", [(nx.Graph(), False),
(nx.DiGraph(), True),
(nx.MultiGraph(), False),
(nx.MultiDiGraph(), True)])
Expand Down Expand Up @@ -176,7 +187,7 @@ def test_maximum_flow_several_paths():


def test_maximum_flow_multigraph():
'''NetworkX retains only the most recently added edge if multiple edges
'''NetworkX retains only the most recently added edge if multiple edges
exit and a MultiGraph is converted into a DiGraph'''
exp = 1
G = nx.DiGraph()
Expand All @@ -190,7 +201,7 @@ def test_maximum_flow_multigraph():


def test_maximum_flow_multigraph_order_flipped():
'''NetworkX retains only the most recently added edge if multiple edges
'''NetworkX retains only the most recently added edge if multiple edges
exit and a MultiGraph is converted into a DiGraph'''
exp = 2
G = nx.DiGraph()
Expand Down Expand Up @@ -221,8 +232,8 @@ def test_maximum_flow_directed_only():
def test_maximum_flow_not_directed_or_multi():
exp = None
G = nx.Graph()
G.add_edge('a', 'b', capacity = 2)
G.add_edge('b', 'c', capacity = 5)
G.add_edge('a', 'b', capacity=2)
G.add_edge('b', 'c', capacity=5)

with pytest.raises(TypeError) as excinfo:
(obs_path, obs) = pa.find_maximum_flow(G, 'a', 'c')
Expand All @@ -232,14 +243,14 @@ def test_maximum_flow_not_directed_or_multi():
def test_find_pathway_flow():
G = nx.DiGraph()
edges = [(0, 1, {'capacity': 3}),
(1, 2, {'capacity': 5}),
(2, 3, {'capacity': 3}),
(3, 4, {'capacity': 4}),
(0, 5, {'capacity': 2}),
(5, 6, {'capacity': 3}),
(6, 3, {'capacity': 2}),
(3, 7, {'capacity': 1}),
(7, 4, {'capacity': 2})]
(1, 2, {'capacity': 5}),
(2, 3, {'capacity': 3}),
(3, 4, {'capacity': 4}),
(0, 5, {'capacity': 2}),
(5, 6, {'capacity': 3}),
(6, 3, {'capacity': 2}),
(3, 7, {'capacity': 1}),
(7, 4, {'capacity': 2})]
G.add_edges_from(edges)
path = (0, 5, 6, 3, 7)

Expand All @@ -248,15 +259,16 @@ def test_find_pathway_flow():

assert obs == exp


def test_find_pathway_flow_no_capacity():
G = nx.DiGraph()
edges = [(0,1), (1,2), (2,3)]
edges = [(0, 1), (1, 2), (2, 3)]
G.add_edges_from(edges)
path = (0, 1, 2, 3)

with pytest.raises(nx.exception.NetworkXUnbounded) as excinfo:
obj = pa.find_pathway_flow(G, path)
assert 'Infinite capacity path, flow unbounded above.' in str(excinfo.value)
with pytest.raises(nx.exception.NetworkXUnbounded) as excinfo:
obj = pa.find_pathway_flow(G, path)
assert 'Infinite capacity path' in str(excinfo.value)


def test_find_pathway_flow_single_infinite():
Expand All @@ -281,14 +293,14 @@ def test_find_pathway_flow_all_infinite():
G.add_edges_from(edges)
path = (0, 1, 2, 3)

with pytest.raises(nx.exception.NetworkXUnbounded) as excinfo:
obj = pa.find_pathway_flow(G, path)
assert 'Infinite capacity path, flow unbounded above.' in str(excinfo.value)
with pytest.raises(nx.exception.NetworkXUnbounded) as excinfo:
obj = pa.find_pathway_flow(G, path)
assert 'Infinite capacity path' in str(excinfo.value)


def test_find_pathway_flow_multiedges():
G = nx.MultiDiGraph()
edges = [(0,1), (1,2), (1,2), (2,3)]
edges = [(0, 1), (1, 2), (1, 2), (2, 3)]
G.add_edges_from(edges)
pathway = (0, 1, 2, 3)

Expand All @@ -299,7 +311,7 @@ def test_find_pathway_flow_multiedges():

def test_find_pathway_flow_other_type():
G = nx.Graph()
edges = [(0,1), (1,2), (2,3)]
edges = [(0, 1), (1, 2), (2, 3)]
G.add_edges_from(edges)
pathway = (0, 1, 2, 3)

Expand All @@ -310,7 +322,15 @@ def test_find_pathway_flow_other_type():

@pytest.mark.parametrize("steps,exp", [(('FacilityA', 'FacilityB'), 1),
(('FacilityA', 'Sink'), -1)])
def test_check_if_sublist(steps,exp):
def test_check_if_sublist(steps, exp):
path = ('Source', 'FacilityA', 'FacilityB', 'Sink')
pos = pa.check_if_sublist(path, steps)
assert pos == exp


@pytest.mark.parametrize("path,steps,exp", [(('Source', 'Sink'), (), -1),
((), ('Sink'), -1)])
def test_check_if_sublist_len_zero(path, steps, exp):
path = ('Source', 'FacilityA', 'FacilityB', 'Sink')
pos = pa.check_if_sublist(path, steps)
assert pos == exp
Expand All @@ -331,7 +351,7 @@ def test_roll_cycle(cycle, exp):
def test_insert_cycle_single():
path = (0, 1, 3, 4, 7, 8)
rolled_cycles = {(7, 3, 4)}

exp = (0, 1, 3, 4, (7, 3, 4), 7, 8)
obs = pa.insert_cycles(path, rolled_cycles)
assert obs == exp
Expand All @@ -340,7 +360,7 @@ def test_insert_cycle_single():
def test_insert_cycle_loop():
path = (0, 1, 3, 4, 7, 8)
rolled_cycles = {(7,)}

exp = (0, 1, 3, 4, (7,), 7, 8)
obs = pa.insert_cycles(path, rolled_cycles)
assert obs == exp
Expand All @@ -356,10 +376,10 @@ def test_insert_cycle_multiple():


def test_insert_cycle_multiple_same_index():
path = ('Source' , 'A', 'B', 'C', 'Sink')
path = ('Source', 'A', 'B', 'C', 'Sink')
rolled_cycles = (('C', 'D', 'B'), ('C', 'D', 'E', 'A', 'B'))
exp = ('Source' , 'A', 'B', ('C', 'D', 'B'), ('C', 'D', 'E', 'A', 'B'),

exp = ('Source', 'A', 'B', ('C', 'D', 'B'), ('C', 'D', 'E', 'A', 'B'),
'C', 'Sink')
obs = pa.insert_cycles(path, rolled_cycles)
assert obs == exp
Expand Down Expand Up @@ -393,7 +413,7 @@ def test_get_pathways_with_cycles_multiple():
(0, 2, (6, 5), 6, (7, 3, 4), 7, 8)}

obs = pa.get_pathways_with_cycles(pathways, sc)
#assert all(x in obs for x in exp)
# assert all(x in obs for x in exp)
assert obs == exp


Expand Down Expand Up @@ -422,10 +442,10 @@ def data():

@pytest.mark.parametrize("source,exp", [("SourceA",
{("SourceA", "Facility", "SinkA"),
("SourceA", "Facility", "SinkB")}),
("SourceA", "Facility", "SinkB")}),
("SourceC", set()),
("Facility", set())])
def test_find_paths_with_source(source,exp):
def test_find_paths_with_source(source, exp):
pathways = testdata[2][4]

obs_subset = pa.find_paths_with_source(pathways, source)
Expand All @@ -441,10 +461,10 @@ def test_find_paths_with_source_none():

@pytest.mark.parametrize("sink,exp", [("SinkB",
{("SourceA", "Facility", "SinkB"),
("SourceB", "Facility", "SinkB")}),
("SourceB", "Facility", "SinkB")}),
("SinkC", set()),
("SourceA", set())])
def test_find_paths_with_sink(sink,exp):
def test_find_paths_with_sink(sink, exp):
pathways = testdata[2][4]

obs_subset = pa.find_paths_with_sink(pathways, sink)
Expand All @@ -458,9 +478,9 @@ def test_find_paths_with_sink_none():
assert obs == set()


@pytest.mark.parametrize("contain,exp", [("SourceB",
@pytest.mark.parametrize("contain,exp", [("SourceB",
{("SourceB", "Facility", "SinkA"),
("SourceB", "Facility", "SinkB")}),
("SourceB", "Facility", "SinkB")}),
(["SourceB", "SinkB"],
{("SourceB", "Facility", "SinkB")}),
(["SourceB", "SourceA"], set()),
Expand All @@ -472,17 +492,18 @@ def test_find_paths_containing_all(contain, exp):
assert obs == exp


@pytest.mark.parametrize("contain,exp", [(5, {(0,1,5,6,4)}),
([5], {(0,1,5,6,4)}),
([1, 5], {(0,1,5,6,4)}),
([0, 3], {(0,1,2,3,4), (0,2,3,4)}),
@pytest.mark.parametrize("contain,exp", [(5, {(0, 1, 5, 6, 4)}),
([5], {(0, 1, 5, 6, 4)}),
([1, 5], {(0, 1, 5, 6, 4)}),
([0, 3], {(0, 1, 2, 3, 4),
(0, 2, 3, 4)}),
([5, 7], set()),
([8], set()),
([7,8], set()),
([7, 8], set()),
([], set())])
def test_find_paths_containing_all_int(contain, exp):
pathways = {(0,1,2,3,4), (0,2,3,4), (0,1,5,6,4), (0,1,7,4)}
pathways = {(0, 1, 2, 3, 4), (0, 2, 3, 4), (0, 1, 5, 6, 4), (0, 1, 7, 4)}

obs = pa.find_paths_containing_all(pathways, contain)
assert obs == exp

Expand All @@ -496,11 +517,11 @@ def test_find_paths_containing_all_none():

@pytest.mark.parametrize("contain,exp", [("SourceA",
{("SourceA", "Facility", "SinkA"),
("SourceA", "Facility", "SinkB")}),
("SourceA", "Facility", "SinkB")}),
(["SourceA", "SinkA"],
{("SourceA", "Facility", "SinkA"),
("SourceA", "Facility", "SinkB"),
("SourceB", "Facility", "SinkA")}),
("SourceA", "Facility", "SinkB"),
("SourceB", "Facility", "SinkA")}),
(["SourceC"], set()),
([], set())])
def test_find_paths_containing_one_of(contain, exp):
Expand All @@ -510,15 +531,16 @@ def test_find_paths_containing_one_of(contain, exp):
assert obs == exp


@pytest.mark.parametrize("contain,exp", [(5, {(0,1,5,6,4)}),
([5], {(0,1,5,6,4)}),
([5, 7], {(0,1,5,6,4),(0,1,7,4)}),
@pytest.mark.parametrize("contain,exp", [(5, {(0, 1, 5, 6, 4)}),
([5], {(0, 1, 5, 6, 4)}),
([5, 7], {(0, 1, 5, 6, 4),
(0, 1, 7, 4)}),
(8, set()),
([8], set()),
([7,8], {(0,1,7,4)}),
([7, 8], {(0, 1, 7, 4)}),
([], set())])
def test_find_paths_containing_one_of_int(contain, exp):
pathways = {(0,1,2,3,4), (0,2,3,4),(0,1,5,6,4), (0,1,7,4)}
pathways = {(0, 1, 2, 3, 4), (0, 2, 3, 4), (0, 1, 5, 6, 4), (0, 1, 7, 4)}

obs = pa.find_paths_containing_one_of(pathways, contain)
assert obs == exp
Expand Down Expand Up @@ -552,3 +574,41 @@ def test_get_longest_paths(name, short, long, edges, paths, sc):
exp = {path for path in paths if len(path) == long}
obs = pa.get_longest_path(paths)
assert obs == exp


def test_sort_shortest():
pathways = {(2, 3), (3, 4, 7, 4, 3, 32, 3), (10000, 10000, 0)}
exp = [(2, 3), (10000, 10000, 0), (3, 4, 7, 4, 3, 32, 3)]

obs = pa.sort_by_shortest(pathways)
assert obs == exp


def test_sort_longest():
pathways = {(2, 3), (3, 4, 7, 4, 3, 32, 3), (10000, 10000, 0)}
exp = [(3, 4, 7, 4, 3, 32, 3), (10000, 10000, 0), (2, 3)]

obs = pa.sort_by_longest(pathways)
assert obs == exp


@pytest.mark.parametrize("pathways", [{("a", "b")},
{("a", "b"), (1, "b")},
{(1, 4)},
{(4, 5), (6, 5.9)},
{(6.3, "a")}])
def test_check_for_invalid_pathways(pathways):
obs = pa.check_for_invalid_pathways(pathways)
assert obs is None
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Does it make more sense to some how test that there is no exception?



@pytest.mark.parametrize("pathways", [{("a")},
{("a", "b"), "c"},
{(1)},
{(4, 5), 6},
{(6.3, "a"), 4.6},
{(5.3)}])
def test_check_for_invalid_pathways_type_error(pathways):
with pytest.raises(TypeError) as excinfo:
obj = pa.sort_by_longest(pathways)
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why not just call check_for_invalid_pathways here?

assert 'pathways contains' in str(excinfo.value)
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