def test_results_linearize(datadir, fs):
path = datadir / 'linearize' / 'linearize_dir1'
fs.create_dir('linearize_dir1')
fs.add_real_file(path / 'pheno_linbase.mod',
target_path='linearize_dir1/pheno_linbase.mod')
fs.add_real_file(path / 'pheno_linbase.ext',
target_path='linearize_dir1/pheno_linbase.ext')
fs.add_real_file(path / 'pheno_linbase.lst',
target_path='linearize_dir1/pheno_linbase.lst')
fs.add_real_file(path / 'pheno_linbase.phi',
target_path='linearize_dir1/pheno_linbase.phi')
fs.create_dir('linearize_dir1/scm_dir1')
fs.add_real_file(path / 'scm_dir1' / 'derivatives.mod',
target_path='linearize_dir1/scm_dir1/derivatives.mod')
fs.add_real_file(path / 'scm_dir1' / 'derivatives.ext',
target_path='linearize_dir1/scm_dir1/derivatives.ext')
fs.add_real_file(path / 'scm_dir1' / 'derivatives.lst',
target_path='linearize_dir1/scm_dir1/derivatives.lst')
fs.add_real_file(path / 'scm_dir1' / 'derivatives.phi',
target_path='linearize_dir1/scm_dir1/derivatives.phi')
args = ['results', 'linearize', 'linearize_dir1']
cli.main(args)
assert os.path.exists('linearize_dir1/results.json')
def test_add_iiv(datadir, fs, options):
fs.add_real_file(datadir / 'pheno_real.mod', target_path='run1.mod')
fs.add_real_file(datadir / 'pheno.dta', target_path='pheno.dta')
args = ['model', 'add_iiv', 'run1.mod', 'S1', 'exp'] + options
cli.main(args)
with open('run1.mod', 'r') as f_ori, open('run2.mod', 'r') as f_cov:
mod_ori = f_ori.read()
mod_cov = f_cov.read()
assert mod_ori != mod_cov
assert not re.search(r'EXP\(ETA\(3\)\)', mod_ori)
assert re.search(r'EXP\(ETA\(3\)\)', mod_cov)
def test_eta_transformation(datadir, fs, transformation, eta):
fs.add_real_file(datadir / 'pheno_real.mod', target_path='run1.mod')
fs.add_real_file(datadir / 'pheno.dta', target_path='pheno.dta')
args = ['model', transformation, 'run1.mod', '--etas', 'ETA(1)']
cli.main(args)
with open('run1.mod', 'r') as f_ori, open('run2.mod', 'r') as f_box:
mod_ori = f_ori.read()
mod_box = f_box.read()
assert mod_ori != mod_box
assert not re.search(eta, mod_ori)
assert re.search(eta, mod_box)
def test_model_sample(datadir, fs):
fs.add_real_file(datadir / 'pheno_real.mod', target_path='run1.mod')
fs.add_real_file(datadir / 'pheno_real.ext', target_path='run1.ext')
fs.add_real_file(datadir / 'pheno_real.lst', target_path='run1.lst')
fs.add_real_file(datadir / 'pheno_real.cov', target_path='run1.cov')
fs.add_real_file(datadir / 'pheno.dta', target_path='pheno.dta')
args = ['model', 'sample', 'run1.mod', '--seed=24']
cli.main(args)
with open('run1.mod', 'r') as f_ori, open('sample_1.mod', 'r') as f_cov:
mod_ori = f_ori.read()
mod_cov = f_cov.read()
assert mod_ori != mod_cov
def test_power_on_ruv(datadir, fs, epsilons_args):
fs.add_real_file(datadir / 'pheno_real.mod', target_path='run1.mod')
fs.add_real_file(datadir / 'pheno.dta', target_path='pheno.dta')
args = ['model', 'power_on_ruv', 'run1.mod'] + epsilons_args
cli.main(args)
with open('run1.mod', 'r') as f_ori, open('run2.mod', 'r') as f_cov:
mod_ori = f_ori.read()
mod_cov = f_cov.read()
assert mod_ori != mod_cov
assert not re.search(r'CIPREDI', mod_ori)
assert re.search(r'CIPREDI', mod_cov)
def test_remove_iiv(datadir, fs, to_remove):
fs.add_real_file(datadir / 'pheno.mod', target_path='run1.mod')
fs.add_real_file(datadir / 'pheno.dta', target_path='pheno.dta')
args = ['model', 'remove_iiv', 'run1.mod'] + to_remove
cli.main(args)
with open('run1.mod', 'r') as f_ori, open('run2.mod', 'r') as f_cov:
mod_ori = f_ori.read()
mod_cov = f_cov.read()
assert mod_ori != mod_cov
assert re.search(r'EXP\(ETA\(2\)\)', mod_ori)
assert not re.search(r'EXP\(ETA\(2\)\)', mod_cov)
def test_create_rv_block(datadir, fs, eta_args):
fs.add_real_file(datadir / 'pheno_real.mod', target_path='run1.mod')
fs.add_real_file(datadir / 'pheno.dta', target_path='pheno.dta')
args = ['model', 'create_rv_block', 'run1.mod'] + eta_args
cli.main(args)
with open('run1.mod', 'r') as f_ori, open('run2.mod', 'r') as f_cov:
mod_ori = f_ori.read()
mod_cov = f_cov.read()
assert mod_ori != mod_cov
assert not re.search(r'BLOCK\(2\)', mod_ori)
assert re.search(r'BLOCK\(2\)', mod_cov)
def test_add_iov(datadir, fs, options):
fs.add_real_file(datadir / 'pheno_real.mod', target_path='run1.mod')
fs.add_real_file(datadir / 'pheno.dta', target_path='pheno.dta')
args = ['model', 'add_iov', 'run1.mod', 'FA1', '--etas', 'ETA(1)'
] + options
cli.main(args)
with open('run1.mod', 'r') as f_ori, open('run2.mod', 'r') as f_cov:
mod_ori = f_ori.read()
mod_cov = f_cov.read()
assert mod_ori != mod_cov
assert not re.search(r'ETAI1', mod_ori)
assert re.search(r'ETAI1', mod_cov)
def test_add_covariate_effect(datadir, fs, operation):
fs.add_real_file(datadir / 'pheno_real.mod', target_path='run1.mod')
fs.add_real_file(datadir / 'pheno.dta', target_path='pheno.dta')
args = [
'model', 'add_cov_effect', 'run1.mod', 'CL', 'WGT', 'exp',
'--operation', operation
]
cli.main(args)
with open('run1.mod', 'r') as f_ori, open('run2.mod', 'r') as f_cov:
mod_ori = f_ori.read()
mod_cov = f_cov.read()
assert mod_ori != mod_cov
assert not re.search('CLWGT', mod_ori)
assert re.search('CLWGT', mod_cov)
def test_remove_iov(datadir, fs):
fs.add_real_file(datadir / 'qa/iov.mod', target_path='run1.mod')
fs.add_real_file(datadir / 'pheno.dta', target_path='pheno.dta')
args = ['model', 'remove_iov', 'run1.mod']
cli.main(args)
with open('run1.mod', 'r') as f_ori, open('run2.mod', 'r') as f_cov:
mod_ori = f_ori.read()
mod_cov = f_cov.read()
assert mod_ori != mod_cov
assert re.search('SAME', mod_ori)
assert not re.search('SAME', mod_cov)
assert re.search(r'ETA\(3\)', mod_ori)
assert not re.search(r'ETA\(3\)', mod_cov)
def test_update_inits(datadir, fs, force_args, file_exists):
fs.add_real_file(datadir / 'pheno_real.mod', target_path='run1.mod')
fs.add_real_file(datadir / 'pheno_real.ext', target_path='run1.ext')
fs.add_real_file(datadir / 'pheno_real.phi', target_path='run1.phi')
fs.add_real_file(datadir / 'pheno.dta', target_path='pheno.dta')
args = ['model', 'update_inits', 'run1.mod'] + force_args
cli.main(args)
with open('run1.mod', 'r') as f_ori, open('run2.mod', 'r') as f_cov:
mod_ori = f_ori.read()
mod_cov = f_cov.read()
assert mod_ori != mod_cov
assert not re.search(r'\$ETAS FILE=run2_input.phi', mod_ori)
assert bool(re.search(r'\$ETAS FILE=run2_input.phi',
mod_cov)) is file_exists
assert (os.path.isfile('run2_input.phi')) is file_exists
def test_usage():
f = io.StringIO()
with redirect_stdout(f):
cli.main([])
out = f.getvalue()
assert 'usage:' in out
def test_model_print(datadir, capsys):
args = ['model', 'print', str(datadir / 'pheno.mod')]
cli.main(args)
captured = capsys.readouterr()
assert 'ETA(1)' in captured.out