def test_read_sg_005_edges(self):
"""Just a edge"""
g = SizeGraph.readsg(sio("""4
MS
0.1
0.2
0.3
0.4
1
0 1
"""))
self.assertEqual(4, len(g.nodes))
C = g.get_connections()
self.assertEqual(1, len(C))
c = C.pop()
self._assert_connection(c, 0.1, 0.2)
g = SizeGraph.readsg(sio("""4
1
0 1
"""),ms=[.1,.2,.3,.4])
self.assertEqual(4, len(g.nodes))
C = g.get_connections()
self.assertEqual(1, len(C))
c = C.pop()
self._assert_connection(c, 0.1, 0.2)
"""More edges"""
g = SizeGraph.readsg(sio("""4
MS
0.1
0.2
0.3
0.4
4
0 1
1 2
2 3
3 0
"""))
self.assertEqual(4, len(g.nodes))
C = g.get_connections()
self.assertEqual(4, len(C))
ii=[.1,.2,.3,.4,.1]
for i in xrange(4):
self._assert_in_connection(C, ii[i],ii[i+1])
g = SizeGraph.readsg(sio("""4
4
0 1
1 2
2 3
3 0
"""),ms=[.1,.2,.3,.4])
self.assertEqual(4, len(g.nodes))
C = g.get_connections()
self.assertEqual(4, len(C))
ii=[.1,.2,.3,.4,.1]
for i in xrange(4):
self._assert_in_connection(C, ii[i],ii[i+1])
def _get_graph(fg, fms):
if fms is None:
ms = None
else:
ms = []
l = fms.readline()
while l:
ms.append(float(l))
l = fms.readline()
return SizeGraph.readsg(fg, ms)
def _get_graph(fg,fms):
if fms is None:
ms = None
else:
ms = []
l=fms.readline()
while l:
ms.append(float(l))
l=fms.readline()
return SizeGraph.readsg(fg, ms)
def test_xxx_dump_read_sg_dual(self):
g = SG()
N = [g.add_node(.1), g.add_node(.2), g.add_node(.3), g.add_node(.4) ]
N[0].connect(N[1])
N[0].connect(N[2])
N[1].connect(N[3])
f = sio()
g.dump(f)
f.seek(0)
self.assertSameGraph(g, SizeGraph.readsg(f))
print f.getvalue()
def _read_and_compute(fg, fms, fout):
if fms is None:
ms = None
else:
ms = []
l = fms.readline()
while l:
ms.append(float(l))
l = fms.readline()
g = SizeGraph.readsg(fg, ms)
h = H0Tree.compute_H0Tree(g)
sf = h.get_sf()
sf.dump(fout)
def test_xxx_dump_options(self):
g = SG()
N = [g.add_node(.1), g.add_node(.2), g.add_node(.3), g.add_node(.4) ]
N[0].connect(N[1])
N[0].connect(N[2])
N[1].connect(N[3])
f = sio()
g.dump(f,legacy=True)
f.seek(0)
print """LEGACY ########################
""" + f.getvalue()
self.assertSameGraph(g, SizeGraph.readsg(f,ms=[.1,.2,.3,.4]))
self.assertNotIn("#", f.getvalue())
self.assertNotIn("MS", f.getvalue())
f = sio()
g.dump(f,comments=False)
f.seek(0)
print """COMMENTS ########################
""" + f.getvalue()
self.assertSameGraph(g, SizeGraph.readsg(f))
self.assertNotIn("#", f.getvalue())
self.assertIn("MS", f.getvalue())
def test_read_sg_x00_from_file_real_file(self):
p = tempfile.mktemp()
f = file(p, "w")
try:
f.write("""1
MS
1.1
""")
f.close()
g = SG()
g.add_node(1.1)
self.assertSameGraph(g, SizeGraph.readsg(p))
finally:
os.unlink(p)
def test_read_sg_000_nodes(self):
g = SizeGraph.readsg(sio())
self.assertIsInstance(g, SG)
"""Just a Node"""
g = SizeGraph.readsg(sio("1"))
self.assertEqual(1, len(g.nodes))
g = SizeGraph.readsg(sio("""1"""),[0.2])
self.assertEqual(1, len(g.nodes))
self.assertEqual(0.2,g.nodes.pop().phy)
g = SizeGraph.readsg(sio("""1
MS
0.5"""))
self.assertEqual(1, len(g.nodes))
self.assertEqual(0.5,g.nodes.pop().phy)
"""Just a Nodes"""
g = SizeGraph.readsg(sio("4"))
self.assertEqual(4, len(g.nodes))
g = SizeGraph.readsg(sio("""4"""),[1,2,3,4])
self.assertEqual(4, len(g.nodes))
for i in xrange(1,5):
self.assertIn(i,[n.phy for n in g.nodes])
g = SizeGraph.readsg(sio("""4
MS
0.1
0.2
0.3
0.4"""))
self.assertEqual(4, len(g.nodes))
for i in range(1,5):
self.assertIn(i/10.0,[n.phy for n in g.nodes])
"""ms instead file value"""
g = SizeGraph.readsg(sio("""4
MS
0.1
0.2
0.3
0.4"""),[1,2,3,4])
self.assertEqual(4, len(g.nodes))
for i in range(1,5):
self.assertIn(i,[n.phy for n in g.nodes])
def test_read_sg_050_asserts(self):
"""Pass wrong ms"""
self.assertRaises(ValueError, SizeGraph.readsg,
f=sio("""2"""),ms=[1])
"""Sanity check"""
SizeGraph.readsg(f=sio("""2"""),ms=[1,2,3])
"""Invalid formats"""
self.assertRaises(ValueError, SizeGraph.readsg,
f=sio("""1.2"""))
self.assertRaises(ValueError, SizeGraph.readsg,
f=sio("""1.2"""))
self.assertRaises(ValueError, SizeGraph.readsg,
f=sio("""1
paperino"""))
self.assertRaises(ValueError, SizeGraph.readsg,
f=sio("""1
1.3"""))
self.assertRaises(ValueError, SizeGraph.readsg,
f=sio("""1
MS
qqq"""))
self.assertRaises(ValueError, SizeGraph.readsg,
f=sio("""1
MS
1.2
2.2
"""))
self.assertRaises(ValueError, SizeGraph.readsg,
f=sio("""1
MS
1.2
pippo
"""))
self.assertRaises(ValueError, SizeGraph.readsg,
f=sio("""2
MS
1.2
2.3
1
a 2
"""))
self.assertRaises(ValueError, SizeGraph.readsg,
f=sio("""2
MS
1.2
2.3
1
1 a
"""))
self.assertRaises(ValueError, SizeGraph.readsg,
f=sio("""2
MS
1.2
2.3
1
paperino
"""))
self.assertRaises(ValueError, SizeGraph.readsg,
f=sio("""2
MS
1.2
2.3
1
0.2 1.1
"""))
def test_read_sg_010_comments_and_empty_lines(self):
"""Empty graph"""
g = SizeGraph.readsg(sio("""
"""))
self.assertEqual(0, len(g.nodes))
g = SizeGraph.readsg(sio("""# comment
#c
# o
#mme
# nt
"""))
self.assertEqual(0, len(g.nodes))
"""Just a node"""
g = SizeGraph.readsg(sio("""
1
"""))
self.assertEqual(1, len(g.nodes))
g = SizeGraph.readsg(sio("""# comment
#c
# o
1
#mme
# nt
"""))
self.assertEqual(1, len(g.nodes))
"""Some Nodes"""
g = SizeGraph.readsg(sio("""
4
"""))
self.assertEqual(4, len(g.nodes))
g = SizeGraph.readsg(sio("""# comment
#c
# o
5
#mme
# nt
"""))
self.assertEqual(5, len(g.nodes))
g = SizeGraph.readsg(sio("""
4
MS
1
# www
2
3
# ha
# ha
4
"""))
self.assertEqual(4, len(g.nodes))
for i in xrange(1,5):
self.assertIn(i, [n.phy for n in g.nodes])
"""Edges"""
g = SizeGraph.readsg(sio("""# dddd
4
#co
MS
#mments
0.1
#
0.2
0.3
0.4
#
4
#more com
0 1
1 2
# ments
2 3
3 0
"""))
self.assertEqual(4, len(g.nodes))
C = g.get_connections()
self.assertEqual(4, len(C))
ii=[.1,.2,.3,.4,.1]
for i in xrange(4):
self._assert_in_connection(C, ii[i],ii[i+1])