def test_add_parameters(pheno_path, param_new, init_expected, buf_new):
model = Model(pheno_path)
pset = model.parameters
assert len(pset) == 6
pset.append(param_new)
model.parameters = pset
model.update_source()
assert len(pset) == 7
assert model.parameters[param_new.name].init == init_expected
parser = NMTranParser()
stream = parser.parse(str(model))
assert str(model.control_stream) == str(stream)
rec_ref = (
f'$THETA (0,0.00469307) ; PTVCL\n'
f'$THETA (0,1.00916) ; PTVV\n'
f'$THETA (-.99,.1)\n'
f'{buf_new}\n'
)
rec_mod = ''
for rec in model.control_stream.get_records('THETA'):
rec_mod += str(rec)
assert rec_ref == rec_mod
def test_round_trip(pheno_path):
parser = NMTranParser()
with open(pheno_path, 'r') as fh:
content = fh.read()
model = parser.parse(content)
assert str(model) == content
def test_statements_setter(pheno_path, buf_new, len_expected):
model = Model(pheno_path)
parser = NMTranParser()
statements_new = parser.parse(f'$PRED\n{buf_new}').records[0].statements
assert len(model.statements) == 15
assert len(statements_new) == len_expected
model.statements = statements_new
assert len(model.statements) == len_expected
assert model.statements == statements_new
def test_remove_iov(testdata):
model = Model(testdata / 'nonmem/pheno_block.mod')
model_str = str(model)
model_with_iov = re.sub(
r'\$OMEGA 0.031128 ; IVV\n\$OMEGA 0.1',
r'$OMEGA BLOCK(1)\n0.1\n$OMEGA BLOCK(1) SAME\n',
model_str,
)
model.control_stream = NMTranParser().parse(model_with_iov)
remove_iov(model)
model.update_source()
assert (str(model.get_pred_pk_record()) == '$PK\n'
'CL=THETA(1)*EXP(ETA(1))\n'
'V = THETA(2)\n'
'S1 = ETA(2) + ETA(3) + V\n\n')
rec_omega = ''.join(
str(rec) for rec in model.control_stream.get_records('OMEGA'))
assert (rec_omega == '$OMEGA 0.0309626 ; IVCL\n'
'$OMEGA BLOCK(2)\n'
'0.0309626\n'
'0.0005 0.031128\n')
model = Model(testdata / 'nonmem/pheno_block.mod')
with pytest.warns(UserWarning):
remove_iov(model)
def test_iiv_on_ruv(pheno_path, epsilons, same_eta, err_ref, omega_ref):
model = Model(pheno_path)
model_str = str(model)
model_more_eps = re.sub('IPRED=F\nIRES=DV-IPRED',
'IPRED=F+EPS(2)\nIRES=DV-IPRED+EPS(3)', model_str)
model_sigma = re.sub(r'\$SIGMA 0.013241',
'$SIGMA 0.013241\n$SIGMA 0.1\n$SIGMA 0.1',
model_more_eps)
model.control_stream = NMTranParser().parse(model_sigma)
iiv_on_ruv(model, epsilons, same_eta)
model.update_source()
err_rec = model.control_stream.get_records('ERROR')[0]
assert str(
err_rec) == f'$ERROR\n' f'W=F\n' f'{err_ref}' f'IWRES=IRES/W\n\n'
omega_rec = ''.join(
str(rec) for rec in model.control_stream.get_records('OMEGA'))
assert omega_rec == (f'$OMEGA DIAGONAL(2)\n'
f' 0.0309626 ; IVCL\n'
f' 0.031128 ; IVV\n\n'
f'{omega_ref}\n')
def test_simple_parse():
parser = NMTranParser()
model = parser.parse('$PROBLEM MYPROB\n')
assert len(model.records) == 1
assert type(model.records[0]).__name__ == 'ProblemRecord'
assert str(model) == '$PROBLEM MYPROB\n'
model2_str = ';Comment\n $PROBLEM TW2\n'
model2 = parser.parse(model2_str)
assert len(model2.records) == 2
assert type(model2.records[0]).__name__ == 'RawRecord'
assert type(model2.records[1]).__name__ == 'ProblemRecord'
assert str(model2) == model2_str
def test_add_statements(pheno_path, statement_new, buf_new):
model = Model(pheno_path)
sset = model.statements
assert len(sset) == 15
# Insert new statement before ODE system.
new_sset = ModelStatements()
for s in sset:
if isinstance(s, ODESystem):
new_sset.append(statement_new)
new_sset.append(s)
model.statements = new_sset
model.update_source()
assert len(model.statements) == 16
parser = NMTranParser()
stream = parser.parse(str(model))
assert str(model.control_stream) == str(stream)
rec_ref = (
f'$PK\n'
f'IF(AMT.GT.0) BTIME=TIME\n'
f'TAD=TIME-BTIME\n'
f'TVCL=THETA(1)*WGT\n'
f'TVV=THETA(2)*WGT\n'
f'IF(APGR.LT.5) TVV=TVV*(1+THETA(3))\n'
f'CL=TVCL*EXP(ETA(1))\n'
f'V=TVV*EXP(ETA(2))\n'
f'S1=V\n'
f'{buf_new}\n\n'
)
rec_mod = str(model.control_stream.get_records('PK')[0])
assert rec_ref == rec_mod
def test_parse_illegal_record_name():
parser = NMTranParser()
with pytest.raises(ModelSyntaxError):
parser.parse('$PROBLEM MYPROB\n$1REC\n')