def test_reagent_hold_stock_conc_in_place():
rxn = Reaction()
rxn.volume = '10 µL'
x = Reagent(rxn, 'x')
x.volume = '1 µL'
x.stock_conc = '10 ng/µL'
assert x.conc == '1 ng/µL'
x.hold_stock_conc.volume += '1 µL'
assert x.conc == '2 ng/µL'
x.hold_stock_conc.volume -= '1 µL'
assert x.conc == '1 ng/µL'
x.hold_stock_conc.volume *= 2
assert x.conc == '2 ng/µL'
x.hold_stock_conc.volume /= 2
assert x.conc == '1 ng/µL'
x.hold_stock_conc.conc += '1 ng/µL'
assert x.volume == '2 µL'
x.hold_stock_conc.conc -= '1 ng/µL'
assert x.volume == '1 µL'
x.hold_stock_conc.conc *= 2
assert x.volume == '2 µL'
x.hold_stock_conc.conc /= 2
assert x.volume == '1 µL'
def test_reagent_conc(volume, stock_conc, rxn_volume, expected):
rxn = Reaction()
rxn.volume = rxn_volume
x = Reagent(rxn, 'x')
x.volume = volume
x.stock_conc = stock_conc
assert x.conc == expected
def test_reagent_volume_implicit_solvent():
# When iterating through the reagents of a reaction, new solvent objects
# can get created on the fly. This can break code that assumes the
# reaction will always return the exact same solvent instance.
rxn = Reaction()
rxn.volume = '10 µL'
for reagent in rxn:
assert reagent.volume == '10 µL'
def test_reagent_conc_raises(volume, stock_conc, rxn_volume, err):
rxn = Reaction()
x = Reagent(rxn, 'Reagent Name')
if rxn_volume: rxn.volume = rxn_volume
if volume: x.volume = volume
if stock_conc: x.stock_conc = stock_conc
with pytest.raises(ValueError, match=err):
x.conc
def test_reaction_hold_ratios(v1, r1, v2, r2):
rxn = Reaction()
rxn.volume = v1
for k, v in r1.items():
rxn[k].volume = v
# Set the volume without scaling the reagents:
rxn.volume = v2
assert rxn.volume == v2
assert rxn.hold_ratios.volume == v2
for k, v in r1.items():
assert rxn[k].volume == v
# Set the volume and scale the reagents:
rxn.volume = v1
rxn.hold_ratios.volume = v2
assert rxn.volume == v2
assert rxn.hold_ratios.volume == v2
for k, v in r2.items():
assert rxn[k].volume == v
def test_reaction_volume_no_solvent():
rxn = Reaction()
del rxn.solvent
assert rxn.volume == 0
rxn['x'].volume = '2 µL'
assert rxn.volume == '2 µL'
rxn['y'].volume = '1 µL'
assert rxn.volume == '3 µL'
with pytest.raises(ValueError, match="no solvent specified"):
rxn.volume = '4 µL'
def test_reaction_hold_ratios_no_solvent():
rxn = Reaction()
del rxn.solvent
rxn['x'].volume = '1 µL'
rxn['y'].volume = '2 µL'
assert rxn.volume == '3 µL'
with pytest.raises(ValueError, match="no solvent"):
rxn.volume = '6 µL'
rxn.hold_ratios.volume = '6 µL'
assert rxn.volume == '6 µL'
assert rxn['x'].volume == '2 µL'
assert rxn['y'].volume == '4 µL'
def test_reagent_hold_stock_conc(rxn_volume, s1, v1, c1, v2, c2):
rxn = Reaction()
x = Reagent(rxn, 'x')
y = Reagent(rxn, 'y')
# Set volume:
x.hold_stock_conc.volume = v2
assert x.volume == v2
# Set concentration:
rxn.volume = rxn_volume
y.stock_conc = s1
y.hold_stock_conc.conc = c2
assert y.volume == v2
assert y.stock_conc == s1
assert y.conc == c2
def test_fix_volumes(solvent, donor_before, acceptor_before, donor_after, acceptor_after):
rxn = Reaction()
rxn.solvent = solvent
rxn.add_reagent('donor')
rxn.add_reagent('acceptor')
if solvent != 'donor':
rxn['donor'].volume = donor_before, 'µL'
if solvent != 'acceptor':
rxn['acceptor'].volume = acceptor_before, 'µL'
if solvent != 'water':
rxn.volume = donor_before + acceptor_before, 'µL'
rxn.fix_volumes('donor', 'acceptor')
assert rxn['donor'].volume == (donor_after, 'µL')
assert rxn['acceptor'].volume == (acceptor_after, 'µL')
def test_solvent_volume():
rxn = Reaction()
rxn.solvent = 'w'
rxn.volume = '10 µL'
rxn['x'].volume = '1 µL'
assert rxn['w'].volume == '9 µL'
rxn['x'].volume = '2 µL'
assert rxn['w'].volume == '8 µL'
rxn['y'].volume = '1 µL'
assert rxn['w'].volume == '7 µL'
rxn['x'].volume = None
with pytest.raises(ValueError):
rxn['w'].volume
def test_reagent_hold_volume(rxn_volume, v1, s1, c1, s2, c2):
rxn = Reaction()
x = Reagent(rxn, 'x')
y = Reagent(rxn, 'y')
# Set stock concentration:
x.hold_volume.stock_conc = s2
assert x.stock_conc == s2
# Set concentration:
rxn.volume = rxn_volume
y.volume = v1
y.hold_volume.conc = c2
assert y.volume == v1
assert y.stock_conc == s2
assert y.conc == c2
def test_reaction_free_volume():
rxn = Reaction()
rxn.solvent = 'w'
rxn.volume = '4 µL'
assert rxn.free_volume == '4 µL'
rxn['x'].volume = '1 µL'
assert rxn.free_volume == '3 µL'
assert rxn.get_free_volume_excluding('x') == '4 µL'
rxn['y'].volume = '2 µL'
assert rxn.free_volume == '1 µL'
assert rxn.get_free_volume_excluding('x') == '2 µL'
assert rxn.get_free_volume_excluding('y') == '3 µL'
assert rxn.get_free_volume_excluding('x', 'y') == '4 µL'
rxn['z'].volume = '1 µL'
assert rxn.free_volume == '0 µL'
def test_reaction_hold_ratios_in_place():
rxn = Reaction()
rxn.volume = '10 µL'
rxn['x'].volume = '2 µL'
rxn.hold_ratios.volume += '5 µL'
assert rxn.volume == '15 µL'
assert rxn['x'].volume == '3 µL'
rxn.hold_ratios.volume -= '5 µL'
assert rxn.volume == '10 µL'
assert rxn['x'].volume == '2 µL'
rxn.hold_ratios.volume *= 2
assert rxn.volume == '20 µL'
assert rxn['x'].volume == '4 µL'
rxn.hold_ratios.volume /= 2
assert rxn.volume == '10 µL'
assert rxn['x'].volume == '2 µL'
def test_reaction_volume(given, expected):
rxn = Reaction()
assert rxn.volume == None
rxn.volume = given
assert rxn.volume == expected
