def test_recursive(model_file):
""" check the whole chain has been printed"""
from pyemma.util.contexts import Capturing
with Capturing() as out:
main(['--recursive', model_file])
assert out
all_out = '\n'.join(out)
assert_('FeatureReader' in all_out)
assert_('TICA' in all_out)
assert_('Kmeans' in all_out)
def test_with_pg_data_not_in_memory(self):
import pkg_resources
import pyemma
path = pkg_resources.resource_filename('pyemma.coordinates.tests', 'data') + os.path.sep
pdb_file = os.path.join(path, 'bpti_ca.pdb')
traj_files = [
os.path.join(path, 'bpti_001-033.xtc'),
os.path.join(path, 'bpti_034-066.xtc'),
os.path.join(path, 'bpti_067-100.xtc')
]
reader = pyemma.coordinates.source(traj_files, top=pdb_file)
with settings(show_progress_bars=True), Capturing(which='stderr') as out:
cluster_kmeans(reader)
self.assertIn('creating data array', '\n'.join(out))
def test_with_pg(self):
with settings(show_progress_bars=True), Capturing(
which='stderr') as output:
cluster_kmeans(np.random.rand(100, 3))
self.assertNotIn('creating data array', '\n'.join(output))