def test_component_in_bond(self):
# see issues 85
c = new('C')
se = new('Se')
r = new('R')
one = new('1')
bg = new()
bg.add(c, se, r, one)
bonds = [(c, one.non_inverting),
(se, one),
(one, r)]
for bond in bonds:
connect(*bond)
comps = [{c, one}, {se, one}, {one, r}]
all_comps = {c, se, r, one}
for i, bond in enumerate(bg.bonds):
for component in all_comps:
if component in comps[i]:
assert component in bond
else:
assert component not in bond
def test_compare(self):
from BondGraphTools.base import Bond
from BondGraphTools.actions import new
c = new('C')
one = new('1')
b_1 = Bond(head=(c, 0), tail=(one, 0))
assert b_1 == ((one, 0), (c, 0))
def test_get_exposed_port(self):
from BondGraphTools.actions import new, expose
model = new()
port = new('SS')
model.add(port)
expose(port, label='port_1')
port = model.get_port()
assert port.index == 0
assert port.name == "port_1"
def test_cmp(self):
from BondGraphTools.base import Port
from BondGraphTools.actions import new
c = new("C")
one = new("1")
port_c = Port(c, 0)
port_one = Port(one, 0)
assert port_c is not port_one
assert port_c != port_one
def test_in(self):
from BondGraphTools.base import Port
from BondGraphTools.actions import new
c = new("C")
one = new("1")
port_c = Port(c, 0)
assert c in port_c
assert c is not port_c
assert one is not port_c
assert one not in port_c
def test_create(self):
from BondGraphTools.base import Bond
from BondGraphTools.actions import new
c = new('C')
one = new('1')
b_1 = Bond(head=(c, 0), tail=(one, 0))
assert c in b_1
assert one in b_1
assert (c, 0) in b_1
assert (one, 0) in b_1
assert (one, 1) not in b_1
def test_connection_feedback(self):
from BondGraphTools import new, connect, add
from BondGraphTools.exceptions import InvalidPortException
model = new()
c1 = new('C')
c2 = new('C')
c3 = new('C')
add(model, c1, c2, c3)
connect(c1, (c2, 0))
with pytest.raises(InvalidPortException) as ex:
connect((c2, 0), c3)
assert "Port is already connected: " in str(ex)
def test_failstate(self):
# see issue 110
from BondGraphTools import new, expose, connect
from BondGraphTools.exceptions import InvalidPortException
model = new()
port = new('SS')
model.add(port)
expose(port, label='port_1')
test_model = new()
component = new("0") ## could be anything
test_model.add(component, model)
target_port = (model, 'port_') # typo in port name
with pytest.raises(InvalidPortException):
connect(component, target_port)
def test_one_port(self):
c = new('C')
se = new('Se')
r = new('R')
one = new('1')
bg = new()
bg.add(c, se, r, one)
connect(c, one.non_inverting)
connect(se, one)
connect(one, r)
p0, p1, p2 = tuple(one.ports)
assert p0.weight == 1
assert p1.weight == 1
assert p2.weight == -1
def _build_reactions(self, system, species_anchors, normalised):
if normalised:
param_dict = {"R": 1, "T": 1}
else:
param_dict = {"R": R, "T": self._T}
for reaction_name, (bck_sto, fwd_sto, _, _) in self._reactions.items():
reaction = new("Re", library=LIBRARY,
name=reaction_name, value=param_dict)
system.add(reaction)
fwd_name = "".join(
list(fwd_sto.keys())
)
bck_name = "".join(
list(bck_sto.keys())
)
if len(bck_sto) == 1 and list(bck_sto.values())[0] == 1:
species = list(bck_sto.keys()).pop()
connect(species_anchors[species], reaction)
else:
reverse_complex = new("1", name=bck_name)
system.add(reverse_complex)
connect(reverse_complex.inverting, reaction)
self._connect_complex(
system, species_anchors, reverse_complex,
bck_sto, is_reversed=True
)
if len(fwd_sto) == 1 and list(fwd_sto.values())[0] == 1:
species = list(fwd_sto.keys()).pop()
connect(reaction, species_anchors[species])
else:
forward_complex = new("1", name=fwd_name)
system.add(forward_complex)
connect(reaction, forward_complex.inverting)
self._connect_complex(
system, species_anchors, forward_complex,
fwd_sto, is_reversed=False
)
def _build_species(self, system, normalised):
if normalised:
param_dict = {"R": 1, "T": 1}
else:
param_dict = {"R": R, "T": self._T}
species_anchors = {}
for species, n_reactions in self._species.items():
# edit: create new component for chemostat
if species in self._chemostats:
this_species = new(
"Se", name=species, value=self._chemostats[species]
)
n_reactions = n_reactions - 1
else:
this_species = new(
"Ce", library=LIBRARY, name=species, value=param_dict
)
system.add(this_species)
if n_reactions == 1:
species_anchors[species] = this_species
else:
anchor = new("0", name=species)
system.add(anchor)
connect(anchor, this_species)
species_anchors[species] = anchor
if species in self._flowstats:
flowstat = new(
"Sf", value=self._flowstats[species], name=species
)
system.add(flowstat)
connect(flowstat, species_anchors[species])
return species_anchors
def as_network_model(self, normalised: bool = False):
"""Produces a bond graph :obj:`BondGraph.BondGraph` model of the system
Args:
normalised: If true, sets pressure and temperature to 1
Returns:
A new instance of :obj:`BondGraphTools.BondGraph` representing
this reaction system.
"""
system = new(name=self.name)
species_anchor = self._build_species(system, normalised)
self._build_reactions(system, species_anchor, normalised)
return system
def _connect_complex(system, species_anchors, junct, stoichiometry,
is_reversed=False):
for i, (species, qty) in enumerate(stoichiometry.items()):
if qty == 1:
if is_reversed:
connect(species_anchors[species], junct.non_inverting)
else:
connect(junct.non_inverting, species_anchors[species])
else:
tf = new("TF", value=qty)
system.add(tf)
if is_reversed:
connect((tf, 1), junct.non_inverting)
connect(species_anchors[species], (tf, 0))
else:
connect(junct.non_inverting, (tf, 1))
connect((tf, 0), species_anchors[species])
