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_solvent_unset():
rxn = Reaction()
rxn.solvent = 'w'
assert len(rxn) == 1
rxn.solvent = None
assert len(rxn) == 0
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_iter_sorting_solvent():
as_list = lambda rxn: [x.name for x in rxn]
rxn = Reaction()
rxn.solvent = 'w'
rxn['x']
assert as_list(rxn) == ['w', 'x']
rxn = Reaction()
rxn.solvent = 'w'
rxn['w']
rxn['x']
assert as_list(rxn) == ['w', 'x']
rxn = Reaction()
rxn.solvent = 'w'
rxn['x']
rxn['w']
assert as_list(rxn) == ['x', 'w']
rxn = Reaction()
rxn.solvent = 'w'
rxn['x'].order = 2
rxn['w'].order = 1
assert as_list(rxn) == ['w', 'x']
rxn = Reaction()
rxn.solvent = 'w'
rxn['w'].order = 2
rxn['x'].order = 1
assert as_list(rxn) == ['x', 'w']
def test_reaction_iter_non_solvent():
as_list = lambda rxn: [x.name for x in rxn]
rxn = Reaction()
rxn.solvent = None
assert as_list(rxn.iter_non_solvent_reagents()) == []
rxn.solvent = 'w'
assert as_list(rxn.iter_non_solvent_reagents()) == []
rxn['x']
assert as_list(rxn.iter_non_solvent_reagents()) == ['x']
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_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_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_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_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_iter_by_flag():
as_list = lambda rxn: [x.name for x in rxn]
rxn = Reaction()
rxn.solvent = None
assert as_list(rxn.iter_reagents_by_flag('a')) == []
rxn.solvent = 'w'
assert as_list(rxn.iter_reagents_by_flag('a')) == []
rxn['w'].flags.add('a')
assert as_list(rxn.iter_reagents_by_flag('a')) == ['w']
rxn['w'].flags.remove('a')
assert as_list(rxn.iter_reagents_by_flag('a')) == []
rxn['x']
assert as_list(rxn.iter_reagents_by_flag('a')) == []
rxn['x'].flags.add('a')
assert as_list(rxn.iter_reagents_by_flag('a')) == ['x']
rxn['x'].flags.remove('a')
assert as_list(rxn.iter_reagents_by_flag('a')) == []
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_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_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_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_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_solvent_repr():
rxn = Reaction()
rxn.solvent = 'w'
assert re.match(r"Solvent\(reaction=\d{4}, name='w'\)", repr(rxn['w']))