def test_sample_parameters(self):
numpy.random.seed(1)
n = Network(edges=[
self.second_order_deg, self.first_order_transition,
self.zero_order_prod
])
params = sorted([i for i in n.parameter_sampling().values()])
vals = sorted(
[-0.331911981189704, 0.8812979737686324, -1.9995425007306205])
self.assertListEqual(params, vals)
def test_infer_nodes2(self):
n = Network(edges=[
self.first_order_deg, self.zero_order_prod,
self.second_order_transition
])
nodes = ['A', 'B', 'C', 'D']
self.assertListEqual(sorted([i for i in n.nodes.keys()]), nodes)
def test_zero_order_deg_eq(self):
n = Network(edges=self.first_order_deg)
self.assertEqual(n.nodes['A'].equation, '-k0*A')
def test_zero_order_prod_eq(self):
n = Network(edges=self.zero_order_prod)
self.assertEqual(n.nodes['B'].equation, '+k0')
def test_first_order_transition_eq(self):
n = Network(edges=self.first_order_transition)
self.assertEqual(n.nodes['A'].equation, '-k0*A')
def test_infer_nodes(self):
n = Network(edges=[self.first_order_deg, self.zero_order_prod])
nodes = ['A', 'B']
self.assertListEqual(sorted([i for i in n.nodes.keys()]), nodes)
def test_zeroth_order(self):
n = Network(self.tsg)
out = n.zeroth_order('parameter1')
self.assertTrue(str(out) == 'parameter1')
def test_second_order_transition_eq4(self):
n = Network(edges=self.second_order_transition)
self.assertEqual(n.nodes['D'].equation, '+k0*A*B')
def test_parameter_list(self):
n = Network(edges=[self.second_order_deg, self.first_order_transition])
self.assertEqual(n.parameter_list, 'k0 k1'.split())
def test_edge4(self):
n = Network(self.tsg)
# print(n.new_innovation())
n.random_edge(0)
def test_node_factory(self):
n = Network(self.tsg)
self.assertTrue(n.node_factory() == 'N3')
def test_parameter_factory(self):
n = Network(self.tsg)
self.assertTrue(n.parameter_factory() == 'k1')
def test_select_node(self):
n = Network(self.tsg)
nodes = sorted(n.select_node(2))
self.assertTrue(nodes == [0, 1])
def test_second_order(self):
n = Network(self.tsg)
out = n.second_order('parameter1', 'species1', 'species2')
self.assertTrue(str(out) == 'parameter1*species1*species2')
def test_first_order(self):
n = Network(self.tsg)
out = n.first_order('parameter1', 'species1')
self.assertTrue(str(out) == 'parameter1*species1')
def test_complex_break_eq3(self):
n = Network(edges=self.complex_break)
self.assertEqual(n.nodes['C'].equation, '+k0*A')
def test_complex_form_eq3(self):
n = Network(edges=self.complex_form)
self.assertEqual(n.nodes['C'].equation, '+k0*A*B')
def test_solve(self):
n = Network(edges=[self.first_order_transition])
print(n.ode)
ic = {'A': 10, 'B': 0}
params = {'k0': 0.1}
n.solve(ic, params)
def test_second_order_deg_eq1(self):
n = Network(edges=self.second_order_deg)
self.assertEqual(n.nodes['A'].equation, '-k0*A*B')
def test_select_sign(self):
n = Network(self.tsg)
sign = n.select_sign()
self.assertTrue(sign in ['-', '+'])