def test_solvent_key():
rxn = Reaction()
rxn.solvent = 'w'
rxn['x']
w = rxn['w']
rxn['y']
assert w.key == 'w'
# Set the key without changing it. This shouldn't cause problems:
rxn.solvent = 'w'
# Re-key the solvent via the reaction:
rxn.solvent = 'w2'
assert 'w' not in rxn
assert 'w2' in rxn
assert rxn['w2'] is w
assert rxn['w2'].key == 'w2'
# Re-key the solvent via itself:
w.key = 'w3'
assert 'w' not in rxn
assert 'w2' not in rxn
assert 'w3' in rxn
assert rxn['w3'] is w
assert rxn['w3'].key == 'w3'
def test_reaction_len_contains():
rxn = Reaction()
rxn.solvent = None
assert len(rxn) == 0
assert 'x' not in rxn
assert 'y' not in rxn
assert 'w' not in rxn
rxn['x']
assert len(rxn) == 1
assert 'x' in rxn
assert 'y' not in rxn
assert 'w' not in rxn
rxn['y']
assert len(rxn) == 2
assert 'x' in rxn
assert 'y' in rxn
assert 'w' not in rxn
rxn.solvent = 'w'
assert len(rxn) == 3
assert 'x' in rxn
assert 'y' in rxn
assert 'w' in rxn
rxn['w']
assert len(rxn) == 3
assert 'x' in rxn
assert 'y' in rxn
assert 'w' in rxn
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_solvent_unset():
rxn = Reaction()
rxn.solvent = 'w'
assert len(rxn) == 1
rxn.solvent = None
assert len(rxn) == 0
def test_reaction_iter_sorting(x, y, solvent, expected):
as_list = lambda rxn: [x.name for x in rxn]
rxn = Reaction()
rxn.solvent = solvent
rxn['x'].order = x
rxn['y'].order = y
assert as_list(rxn) == 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(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_reaction_getitem():
rxn = Reaction()
assert isinstance(rxn['x'], Reagent)
assert rxn['x'] is rxn['x']
assert rxn['x'].name == 'x'
rxn.solvent = 'w'
assert isinstance(rxn['w'], Solvent)
assert rxn['w'] is rxn['w']
assert rxn['w'].name == rxn.solvent == 'w'
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_solvent():
rxn = Reaction()
rxn.solvent = 'w'
assert rxn['w'].master_mix == True
assert rxn['w'].order == None
rxn['w'].master_mix = False
rxn['w'].order = 1
assert rxn['w'].master_mix == False
assert rxn['w'].order == 1
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_delitem():
rxn = Reaction()
rxn.solvent = 'w'
rxn['x']
assert 'x' in rxn
assert 'w' in rxn
del rxn['x']
assert 'x' not in rxn
del rxn['w']
assert 'w' not in rxn
assert rxn.solvent == None
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_volume(given, expected):
rxn = Reaction()
x = Reagent(rxn, 'x')
assert x.volume == None
x.volume = given
assert x.volume == expected
def test_reagent_order():
rxn = Reaction()
x = Reagent(rxn, 'x')
assert x.order == None
x.order = 1
assert x.order == 1
def test_reagent_stock_conc(given, expected):
rxn = Reaction()
x = Reagent(rxn, 'x')
assert x.stock_conc == None
x.stock_conc = given
assert x.stock_conc == expected
def test_reaction_repr():
rxn = Reaction()
rxn.solvent = None
assert repr(rxn) == "Reaction()"
rxn.solvent = 'w'
assert repr(rxn) == "Reaction('w')"
rxn['x']
assert repr(rxn) == "Reaction('w', 'x')"
rxn['y']
assert repr(rxn) == "Reaction('w', 'x', 'y')"
rxn['w']
assert repr(rxn) == "Reaction('x', 'y', 'w')"
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_solvent_name():
rxn = Reaction()
rxn.solvent = 'w'
w = rxn['w']
assert w.key == 'w'
assert w.name == 'w'
assert 'w' in rxn
assert 'w2' not in rxn
w.name = 'w2'
assert w.key == 'w'
assert w.name == 'w2'
assert 'w' in rxn
assert 'w2' not in rxn
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_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_reaction_iter():
as_list = lambda rxn: [x.name for x in rxn]
rxn = Reaction()
rxn.solvent = None
assert as_list(rxn) == []
rxn.solvent = 'w'
assert as_list(rxn) == ['w']
rxn['x']
assert as_list(rxn) == ['w', 'x']
rxn['y']
assert as_list(rxn) == ['w', 'x', 'y']
rxn['w']
assert as_list(rxn) == ['x', 'y', 'w']
def test_reaction_from_text_catalog_num():
rxn = Reaction.from_text("""\
Reagent Stock Volume MM? Cat
======= ===== ======= === ===
w to 8 µL yes
x 2x 3 µL no 101
""")
assert rxn['w'].catalog_num == ''
assert rxn['x'].catalog_num == '101'
def test_reaction_from_text_flags():
rxn = Reaction.from_text("""\
Reagent Stock Volume MM? Flags
======= ===== ======= === =====
w to 8 µL yes a
x 2x 3 µL no a,b
""")
assert rxn['w'].flags == {'a'}
assert rxn['x'].flags == {'a', 'b'}
def test_reagent_master_mix():
rxn = Reaction()
x = Reagent(rxn, 'x')
assert not x.master_mix
x.master_mix = True
assert x.master_mix
x.master_mix = False
assert not x.master_mix
def test_reaction_from_text(text, volume, reagents):
rxn = Reaction.from_text(text)
assert len(rxn) == len(reagents)
assert rxn.volume == volume
for name, expected in reagents.items():
volume, stock_conc, master_mix = expected
if volume != ...: assert rxn[name].volume == volume
if stock_conc != ...: assert rxn[name].stock_conc == stock_conc
if master_mix != ...: assert rxn[name].master_mix == master_mix
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_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_reagent_key():
rxn = Reaction()
x = Reagent(rxn, 'x')
assert x.key == 'x'
assert 'x' in rxn
assert 'y' not in rxn
x.key = 'y'
assert x.key == 'y'
assert 'x' not in rxn
assert 'y' in rxn