def test_program_warn(self, tmpdir, mutation):
params = self.gen_params(keypair=mutation, restart=False)
with tmpdir.as_cwd():
self.create_ncdf(params)
with pytest.warns(UserWarning) as record:
NCDFReader(params['filename'])
assert len(record) == 1
wmsg = ("NCDF trajectory test.nc may not fully adhere to AMBER "
"standards as either the `program` or `programVersion` "
"attributes are missing")
assert str(record[0].message.args[0]) == wmsg
def test_conventionversion_warn(self, tmpdir):
mutation = {'ConventionVersion': '2.0'}
params = self.gen_params(keypair=mutation, restart=False)
with tmpdir.as_cwd():
self.create_ncdf(params)
with pytest.warns(UserWarning) as record:
NCDFReader(params['filename'])
assert len(record) == 1
wmsg = ("NCDF trajectory format is 2.0 but the reader "
"implements format 1.0")
assert str(record[0].message.args[0]) == wmsg
def test_degrees_warn(self, tmpdir):
"""Checks that plural degrees throws an user deprecation warning
TODO: remove in MDAnalysis version 1.0 (Issue #2327)"""
mutation = {'cell_angles': 'degrees'}
params = self.gen_params(keypair=mutation, restart=False)
with tmpdir.as_cwd():
self.create_ncdf(params)
with pytest.warns(DeprecationWarning) as record:
NCDFReader(params['filename'])
assert len(record) == 1
wmsg = ("DEPRECATED (1.0): NCDF trajectory {0} uses units of "
"`degrees` for the `cell_angles` variable instead of "
"`degree`. Support for non-AMBER convention units is "
"now deprecated and will end in MDAnalysis version 1.0. "
"Afterwards, reading this file will raise an error.")
assert str(record[0].message.args[0]) == wmsg
def test_import_netcdfreader(self):
# do it here because netcdf isn't required
from MDAnalysis.coordinates.TRJ import NCDFReader
# Check the error meessage that we're giving out
try:
rd = NCDFReader('myfile.ncdf', n_atoms=100)
except ImportError as e:
assert_('netCDF4 package missing' in e.args[0])
assert_('See installation instructions at' in e.args[0])
else:
# fail if we don't get importerror
raise AssertionError
finally:
try:
os.unlink('myfile.ncdf')
except OSError:
pass
def test_verify_units_errors(self, evaluate, expected):
"""Directly tests expected failures of _verify_units"""
with pytest.raises(NotImplementedError):
NCDFReader._verify_units(evaluate.encode('utf-8'), expected)
def test_notimplemented_errors(self, tmpdir, mutation):
params = self.gen_params(keypair=mutation, restart=False)
with tmpdir.as_cwd():
self.create_ncdf(params)
with pytest.raises(NotImplementedError):
NCDFReader(params['filename'])