def hole(self, universe, tmpdir):
with tmpdir.as_cwd():
h = hole2.HoleAnalysis(universe)
h.run(start=self.start,
stop=self.stop,
random_seed=self.random_seed)
return h
def test_output_level(self, tmpdir, universe):
with tmpdir.as_cwd():
with pytest.warns(UserWarning, match="needs to be < 3"):
h = hole2.HoleAnalysis(universe, output_level=100)
h.run(start=self.start,
stop=self.stop,
random_seed=self.random_seed)
# no profiles
assert len(h.profiles) == 0
def test_output_level(self, tmpdir, universe):
with tmpdir.as_cwd():
with pytest.warns(UserWarning) as rec:
h = hole2.HoleAnalysis(universe, output_level=100)
h.run(start=self.start,
stop=self.stop,
random_seed=self.random_seed)
assert len(rec) == 1
assert 'needs to be < 3' in rec[0].message.args[0]
# no profiles
assert len(h.profiles) == 0
def test_hole_module_fd_closure(self, universe, tmpdir):
"""test open file descriptors are closed (MDAnalysisTests.analysis.test_hole.TestHoleModule): Issue 129"""
# If Issue 129 isn't resolved, this function will produce an OSError on
# the system, and cause many other tests to fail as well.
#
# Successful test takes ~10 s, failure ~2 s.
# Hasten failure by setting "ulimit -n 64" (can't go too low because of open modules etc...)
import resource
# ----- temporary hack -----
# on Mac OS X (on Travis) we run out of open file descriptors
# before even starting this test (see
# https://github.com/MDAnalysis/mdanalysis/pull/901#issuecomment-231938093);
# if this issue is solved by #363 then revert the following
# hack:
#
import platform
if platform.platform() == "Darwin":
max_open_files = 512
else:
max_open_files = 64
#
# --------------------------
resource.setrlimit(resource.RLIMIT_NOFILE,
(max_open_files, self.hard_max_open_files))
with tmpdir.as_cwd():
try:
H = hole2.HoleAnalysis(universe, cvect=[0, 1, 0], sample=20.0)
finally:
self._restore_rlimits()
# pretty unlikely that the code will get through 2 rounds if the MDA
# issue 129 isn't fixed, although this depends on the file descriptor
# open limit for the machine in question
try:
for i in range(2):
# will typically get an OSError for too many files being open after
# about 2 seconds if issue 129 isn't resolved
H.run()
except OSError as err:
if err.errno == errno.EMFILE:
raise pytest.fail(
"hole2.HoleAnalysis does not close file descriptors (Issue 129)"
)
raise
finally:
# make sure to restore open file limit !!
self._restore_rlimits()
def test_output_level(self, tmpdir, universe):
with tmpdir.as_cwd():
with pytest.warns(UserWarning) as rec:
h = hole2.HoleAnalysis(universe, output_level=100)
h.run(start=self.start,
stop=self.stop,
random_seed=self.random_seed)
assert len(rec) == 5
assert any('needs to be < 3' in r.message.args[0] for r in rec)
assert any('has no dt information' in r.message.args[0]
for r in rec) # 2x
assert any('Unit cell dimensions not found.' in r.message.args[0]
for r in rec) # 2x
# no profiles
assert len(h.profiles) == 0
def test_cpoint_geometry(self, tmpdir, universe):
protein = universe.select_atoms('protein')
cogs = [protein.center_of_geometry() for ts in universe.trajectory]
with tmpdir.as_cwd():
h = hole2.HoleAnalysis(universe,
select='protein',
cpoint='center_of_geometry',
write_input_files=True)
h.run(start=self.start,
stop=self.stop,
random_seed=self.random_seed)
infiles = sorted(glob.glob(str(tmpdir.join('hole*.inp'))))
for file, cog in zip(infiles, cogs[self.start:self.stop]):
with open(file, 'r') as f:
line = f.read().split('CPOINT')[1].split('\n')[0]
arr = np.array(list(map(float, line.split())))
assert_almost_equal(arr, cog)
def test_context_manager(self, universe, tmpdir):
with tmpdir.as_cwd():
with hole2.HoleAnalysis(universe) as h:
h.run()
h.run() # run again for *.old files
h.create_vmd_surface(filename='hole.vmd')
sphpdbs = tmpdir.join('*.sph')
assert len(glob.glob(str(sphpdbs))) == 0
outfiles = tmpdir.join('*.out')
assert len(glob.glob(str(outfiles))) == 0
vdwradii = tmpdir.join('simple2.rad')
assert len(glob.glob(str(vdwradii))) == 0
pdbfiles = tmpdir.join('*.pdb')
assert len(glob.glob(str(pdbfiles))) == 0
oldfiles = tmpdir.join('*.old')
assert len(glob.glob(str(oldfiles))) == 0
vmd_file = tmpdir.join('hole.vmd')
assert len(glob.glob(str(vmd_file))) == 1