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genotoul-bioinfo
jflow
Commits
80259313
Commit
80259313
authored
Sep 23, 2015
by
Jerome Mariette
Browse files
from python2 to python3 > ok from command line
parent
f1028f5b
Changes
7
Hide whitespace changes
Inline
Side-by-side
src/pygraph/__init__.py
View file @
80259313
...
...
@@ -60,4 +60,4 @@ A quick introductory example:
{'A': 'B', 'C': 'A', 'B': 'Y', 'Y': 'X', 'X': None, 'Z': 'X'}
"""
__import__
(
'pkg_resources'
).
declare_namespace
(
__name__
)
#
__import__('pkg_resources').declare_namespace(__name__)
src/pygraph/algorithms/generators.py
View file @
80259313
...
...
@@ -63,7 +63,7 @@ def generate(num_nodes, num_edges, directed=False, weight_range=(1, 1)):
random_graph
=
graph
()
# Nodes
nodes
=
range
(
num_nodes
)
nodes
=
list
(
range
(
num_nodes
)
)
random_graph
.
add_nodes
(
nodes
)
# Build a list of all possible edges
...
...
src/pygraph/algorithms/minmax.py
View file @
80259313
...
...
@@ -429,7 +429,7 @@ def cut_value(graph, flow, cut):
#max flow/min cut value calculation
S
=
[]
T
=
[]
for
node
in
cut
.
keys
():
for
node
in
list
(
cut
.
keys
()
)
:
if
cut
[
node
]
==
0
:
S
.
append
(
node
)
elif
cut
[
node
]
==
1
:
...
...
@@ -481,7 +481,7 @@ def cut_tree(igraph, caps = None):
N
=
N
+
1
#predecessor function
p
=
{}.
fromkeys
(
range
(
N
),
0
)
p
=
{}.
fromkeys
(
list
(
range
(
N
)
)
,
0
)
p
[
0
]
=
None
for
s
in
range
(
1
,
N
):
...
...
src/pygraph/algorithms/searching.py
View file @
80259313
...
...
@@ -64,7 +64,7 @@ def depth_first_search(graph, root=None, filter=null()):
pre
.
append
(
node
)
# Explore recursively the connected component
for
each
in
graph
[
node
]:
if
(
each
not
in
visited
and
filter
(
each
,
node
)):
if
(
each
not
in
visited
and
list
(
filter
(
each
,
node
))
)
:
spanning_tree
[
each
]
=
node
dfs
(
each
)
post
.
append
(
node
)
...
...
@@ -77,7 +77,7 @@ def depth_first_search(graph, root=None, filter=null()):
# DFS from one node only
if
(
root
is
not
None
):
if
filter
(
root
,
None
):
if
list
(
filter
(
root
,
None
)
)
:
spanning_tree
[
root
]
=
None
dfs
(
root
)
setrecursionlimit
(
recursionlimit
)
...
...
@@ -86,7 +86,7 @@ def depth_first_search(graph, root=None, filter=null()):
# Algorithm loop
for
each
in
graph
:
# Select a non-visited node
if
(
each
not
in
visited
and
filter
(
each
,
None
)):
if
(
each
not
in
visited
and
list
(
filter
(
each
,
None
))
)
:
spanning_tree
[
each
]
=
None
# Explore node's connected component
dfs
(
each
)
...
...
@@ -122,7 +122,7 @@ def breadth_first_search(graph, root=None, filter=null()):
node
=
queue
.
pop
(
0
)
for
other
in
graph
[
node
]:
if
(
other
not
in
spanning_tree
and
filter
(
other
,
node
)):
if
(
other
not
in
spanning_tree
and
list
(
filter
(
other
,
node
))
)
:
queue
.
append
(
other
)
ordering
.
append
(
other
)
spanning_tree
[
other
]
=
node
...
...
@@ -134,7 +134,7 @@ def breadth_first_search(graph, root=None, filter=null()):
# BFS from one node only
if
(
root
is
not
None
):
if
filter
(
root
,
None
):
if
list
(
filter
(
root
,
None
)
)
:
queue
.
append
(
root
)
ordering
.
append
(
root
)
spanning_tree
[
root
]
=
None
...
...
@@ -144,7 +144,7 @@ def breadth_first_search(graph, root=None, filter=null()):
# Algorithm
for
each
in
graph
:
if
(
each
not
in
spanning_tree
):
if
filter
(
each
,
None
):
if
list
(
filter
(
each
,
None
)
)
:
queue
.
append
(
each
)
ordering
.
append
(
each
)
spanning_tree
[
each
]
=
None
...
...
src/pygraph/classes/digraph.py
View file @
80259313
...
...
@@ -101,7 +101,7 @@ class digraph (basegraph, common, labeling):
return
[
a
for
a
in
self
.
_edges
()
]
def
_edges
(
self
):
for
n
,
neighbors
in
self
.
node_neighbors
.
items
():
for
n
,
neighbors
in
list
(
self
.
node_neighbors
.
items
()
)
:
for
neighbor
in
neighbors
:
yield
(
n
,
neighbor
)
...
...
src/pygraph/classes/graph.py
View file @
80259313
...
...
@@ -87,7 +87,7 @@ class graph(basegraph, common, labeling):
@rtype: list
@return: List of all edges in the graph.
"""
return
[
a
for
a
in
self
.
edge_properties
.
keys
()
]
return
[
a
for
a
in
list
(
self
.
edge_properties
.
keys
()
)
]
def
has_node
(
self
,
node
):
"""
...
...
src/pygraph/mixins/__init__.py
View file @
80259313
...
...
@@ -30,4 +30,4 @@ Base classes used to compose the the graph classes.
The classes in this namespace should not be used directly.
"""
__import__
(
'pkg_resources'
).
declare_namespace
(
__name__
)
#
__import__('pkg_resources').declare_namespace(__name__)
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