def test_persistent_offsets_readonly(self):
os.remove(XDR.offsets_filename(self.traj))
assert_equal(os.path.exists(
XDR.offsets_filename(self.trajectory.filename)), False)
os.chmod(self.tmpdir.name, 0o555)
self.trajectory._read_offsets(store=True)
assert_equal(os.path.exists(
XDR.offsets_filename(self.trajectory.filename)), False)
def test_persistent_offsets_readonly(self):
os.remove(XDR.offsets_filename(self.traj))
assert_equal(
os.path.exists(XDR.offsets_filename(self.trajectory.filename)),
False)
os.chmod(self.tmpdir.name, 0o555)
self.trajectory._read_offsets(store=True)
assert_equal(
os.path.exists(XDR.offsets_filename(self.trajectory.filename)),
False)
def test_offsets(self, trajectory, traj):
trajectory._read_offsets(store=True)
assert_almost_equal(
trajectory._xdr.offsets,
self.ref_offsets,
err_msg="wrong frame offsets")
outfile_offsets = XDR.offsets_filename(traj)
saved_offsets = XDR.read_numpy_offsets(outfile_offsets)
assert isinstance(saved_offsets, dict), \
"read_numpy_offsets did not return a dict"
assert_almost_equal(
trajectory._xdr.offsets,
saved_offsets['offsets'],
err_msg="error saving frame offsets")
assert_almost_equal(
self.ref_offsets,
saved_offsets['offsets'],
err_msg="saved frame offsets don't match "
"the known ones")
trajectory._load_offsets()
assert_almost_equal(
trajectory._xdr.offsets,
self.ref_offsets,
err_msg="error loading frame offsets")
assert_equal(saved_offsets['ctime'], os.path.getctime(traj))
assert_equal(saved_offsets['size'], os.path.getsize(traj))
def test_nonexistant_offsets_file(self, traj):
# assert that a nonexistant file returns False during read-in
outfile_offsets = XDR.offsets_filename(traj)
with patch.object(np, "load") as np_load_mock:
np_load_mock.side_effect = IOError
saved_offsets = XDR.read_numpy_offsets(outfile_offsets)
assert_equal(saved_offsets, False)
def test_offsets(self, trajectory, traj):
trajectory._read_offsets(store=True)
assert_almost_equal(
trajectory._xdr.offsets,
self.ref_offsets,
err_msg="wrong frame offsets")
outfile_offsets = XDR.offsets_filename(traj)
saved_offsets = XDR.read_numpy_offsets(outfile_offsets)
assert_almost_equal(
trajectory._xdr.offsets,
saved_offsets['offsets'],
err_msg="error saving frame offsets")
assert_almost_equal(
self.ref_offsets,
saved_offsets['offsets'],
err_msg="saved frame offsets don't match "
"the known ones")
trajectory._load_offsets()
assert_almost_equal(
trajectory._xdr.offsets,
self.ref_offsets,
err_msg="error loading frame offsets")
assert_equal(saved_offsets['ctime'], os.path.getctime(traj))
assert_equal(saved_offsets['size'], os.path.getsize(traj))
def test_persistent_offsets_readonly(self, tmpdir):
shutil.copy(self.filename, str(tmpdir))
os.chmod(str(tmpdir), 0o555)
filename = str(tmpdir.join(os.path.basename(self.filename)))
# try to write a offsets file
self._reader(filename)
assert_equal(os.path.exists(XDR.offsets_filename(filename)), False)
def test_persistent_offsets_natoms_mismatch(self, traj):
# check that stored offsets are not loaded when trajectory
# ctime differs from stored ctime
fname = XDR.offsets_filename(traj)
saved_offsets = XDR.read_numpy_offsets(fname)
saved_offsets['n_atoms'] += 1
np.savez(fname, **saved_offsets)
with pytest.warns(UserWarning, match="Reload offsets"):
self._reader(traj)
def test_persistent_offsets_natoms_mismatch(self, traj):
# check that stored offsets are not loaded when trajectory
# ctime differs from stored ctime
fname = XDR.offsets_filename(traj)
saved_offsets = XDR.read_numpy_offsets(fname)
saved_offsets['n_atoms'] += 1
np.savez(fname, **saved_offsets)
with pytest.warns(UserWarning, match="Reload offsets"):
self._reader(traj)
def test_persistent_offsets_size_mismatch(self, traj):
# check that stored offsets are not loaded when trajectory
# size differs from stored size
fname = XDR.offsets_filename(traj)
saved_offsets = XDR.read_numpy_offsets(fname)
saved_offsets['size'] += 1
with open(fname, 'wb') as f:
np.savez(f, **saved_offsets)
with pytest.warns(UserWarning, match="Reload offsets"):
self._reader(traj)
def test_unsupported_format(self, traj):
fname = XDR.offsets_filename(traj)
saved_offsets = XDR.read_numpy_offsets(fname)
idx_frame = 3
saved_offsets.pop('n_atoms')
np.savez(fname, **saved_offsets)
# ok as long as this doesn't throw
reader = self._reader(traj)
reader[idx_frame]
def test_persistent_offsets_last_frame_wrong(self, traj):
fname = XDR.offsets_filename(traj)
saved_offsets = XDR.read_numpy_offsets(fname)
idx_frame = 3
saved_offsets['offsets'][idx_frame] += 42
np.savez(fname, **saved_offsets)
with pytest.warns(UserWarning, match="seek failed"):
reader = self._reader(traj)
reader[idx_frame]
def test_unsupported_format(self):
fname = XDR.offsets_filename(self.traj)
saved_offsets = XDR.read_numpy_offsets(fname)
idx_frame = 3
saved_offsets.pop('n_atoms')
np.savez(fname, **saved_offsets)
# ok as long as this doesn't throw
reader = self._reader(self.traj)
reader[idx_frame]
def test_persistent_offsets_size_mismatch(self, traj):
# check that stored offsets are not loaded when trajectory
# size differs from stored size
fname = XDR.offsets_filename(traj)
saved_offsets = XDR.read_numpy_offsets(fname)
saved_offsets['size'] += 1
with open(fname, 'wb') as f:
np.savez(f, **saved_offsets)
with pytest.warns(UserWarning, match="Reload offsets"):
self._reader(traj)
def test_persistent_offsets_last_frame_wrong(self, traj):
fname = XDR.offsets_filename(traj)
saved_offsets = XDR.read_numpy_offsets(fname)
idx_frame = 3
saved_offsets['offsets'][idx_frame] += 42
np.savez(fname, **saved_offsets)
with pytest.warns(UserWarning, match="seek failed"):
reader = self._reader(traj)
reader[idx_frame]
def test_persistent_offsets_natoms_mismatch(self):
# check that stored offsets are not loaded when trajectory
# ctime differs from stored ctime
fname = XDR.offsets_filename(self.traj)
saved_offsets = XDR.read_numpy_offsets(fname)
saved_offsets['n_atoms'] += 1
np.savez(fname, **saved_offsets)
with warnings.catch_warnings(record=True) as warn:
warnings.simplefilter('always')
self._reader(self.traj)
assert_equal(warn[0].message.args,
('Reload offsets from trajectory\n ctime or size or n_atoms did not match', ))
def test_persistent_offsets_last_frame_wrong(self, traj):
fname = XDR.offsets_filename(traj)
saved_offsets = XDR.read_numpy_offsets(fname)
assert isinstance(saved_offsets, dict), \
"read_numpy_offsets did not return a dict"
idx_frame = 3
saved_offsets['offsets'][idx_frame] += 42
np.savez(fname, **saved_offsets)
with pytest.warns(UserWarning, match="seek failed"):
reader = self._reader(traj)
reader[idx_frame]
def test_persistent_offsets_natoms_mismatch(self):
# check that stored offsets are not loaded when trajectory
# ctime differs from stored ctime
fname = XDR.offsets_filename(self.traj)
saved_offsets = XDR.read_numpy_offsets(fname)
saved_offsets['n_atoms'] += 1
np.savez(fname, **saved_offsets)
with warnings.catch_warnings(record=True) as warn:
warnings.simplefilter('always')
self._reader(self.traj)
assert_equal(warn[0].message.args, (
'Reload offsets from trajectory\n ctime or size or n_atoms did not match',
))
def test_persistent_offsets_readonly(self, tmpdir):
shutil.copy(self.filename, str(tmpdir))
if os.name == 'nt':
# Windows platform has a unique way to deny write access
subprocess.call("icacls {fname} /deny Users:W".format(fname=tmpdir),
shell=True)
else:
os.chmod(str(tmpdir), 0o555)
filename = str(tmpdir.join(os.path.basename(self.filename)))
# try to write a offsets file
self._reader(filename)
assert_equal(os.path.exists(XDR.offsets_filename(filename)), False)
def test_persistent_offsets_readonly(self, tmpdir):
shutil.copy(self.filename, str(tmpdir))
if os.name == 'nt':
# Windows platform has a unique way to deny write access
subprocess.call("icacls {fname} /deny Users:W".format(fname=tmpdir),
shell=True)
else:
os.chmod(str(tmpdir), 0o555)
filename = str(tmpdir.join(os.path.basename(self.filename)))
# try to write a offsets file
self._reader(filename)
assert_equal(os.path.exists(XDR.offsets_filename(filename)), False)
def test_unsupported_format(self, traj):
fname = XDR.offsets_filename(traj)
saved_offsets = XDR.read_numpy_offsets(fname)
assert isinstance(saved_offsets, dict), \
"read_numpy_offsets did not return a dict"
idx_frame = 3
saved_offsets.pop('n_atoms')
np.savez(fname, **saved_offsets)
# ok as long as this doesn't throw
reader = self._reader(traj)
reader[idx_frame]
def test_persistent_offsets_last_frame_wrong(self):
fname = XDR.offsets_filename(self.traj)
saved_offsets = XDR.read_numpy_offsets(fname)
idx_frame = 3
saved_offsets['offsets'][idx_frame] += 42
np.savez(fname, **saved_offsets)
with warnings.catch_warnings(record=True) as warn:
warnings.simplefilter('always')
reader = self._reader(self.traj)
reader[idx_frame]
assert_equal(warn[0].message.args[0],
'seek failed, recalculating offsets and retrying')
def test_persistent_offsets_last_frame_wrong(self):
fname = XDR.offsets_filename(self.traj)
saved_offsets = XDR.read_numpy_offsets(fname)
idx_frame = 3
saved_offsets['offsets'][idx_frame] += 42
np.savez(fname, **saved_offsets)
with warnings.catch_warnings(record=True) as warn:
warnings.simplefilter('always')
reader = self._reader(self.traj)
reader[idx_frame]
assert_equal(warn[0].message.args[0],
'seek failed, recalculating offsets and retrying')
def test_persistent_offsets_ctime_mismatch(self, traj):
# check that stored offsets are not loaded when trajectory
# ctime differs from stored ctime
fname = XDR.offsets_filename(traj)
saved_offsets = XDR.read_numpy_offsets(fname)
assert isinstance(saved_offsets, dict), \
"read_numpy_offsets did not return a dict"
saved_offsets['ctime'] += 1
with open(fname, 'wb') as f:
np.savez(f, **saved_offsets)
with pytest.warns(UserWarning, match="Reload offsets"):
self._reader(traj)
def test_offsets(self):
self.trajectory._read_offsets(store=True)
assert_array_almost_equal(self.trajectory._xdr.offsets,
self.ref_offsets,
err_msg="wrong frame offsets")
outfile_offsets = XDR.offsets_filename(self.traj)
saved_offsets = XDR.read_numpy_offsets(outfile_offsets)
assert_array_almost_equal(self.trajectory._xdr.offsets,
saved_offsets['offsets'],
err_msg="error saving frame offsets")
assert_array_almost_equal(self.ref_offsets,
saved_offsets['offsets'],
err_msg="saved frame offsets don't match "
"the known ones")
self.trajectory._load_offsets()
assert_array_almost_equal(self.trajectory._xdr.offsets,
self.ref_offsets,
err_msg="error loading frame offsets")
assert_equal(saved_offsets['ctime'], os.path.getctime(self.traj))
assert_equal(saved_offsets['size'], os.path.getsize(self.traj))