================================== FAILURES ===================================
______________________ TestLeafLet.test_leaflet[n_jobs0] _______________________
self = <test_leaflet.TestLeafLet object at 0x7f0522a67080>
universe = <Universe with 43480 atoms>
correct_values = [array([36507, 36761, 37523, 37650, 38031, 38285]), array([36634]), array([36507, 36761, 38285, 39174]), array([36634]), array([36507, 36761, 37650, 38285, 39174, 39936]), array([36634]), ...]
n_jobs = MarkDecorator(mark=Mark(name='xfail', args=(-1,), kwargs={}))
@pytest.mark.parametrize('n_jobs', (pytest.mark.xfail(-1),
1,
pytest.mark.xfail(2)))
def test_leaflet(self, universe, correct_values, n_jobs):
lipid_heads = universe.select_atoms("name P and resname POPG")
universe.trajectory.rewind()
leaflets = leaflet.LeafletFinder(universe, lipid_heads)
> leaflets.run(n_jobs=n_jobs)
/home/travis/build/MDAnalysis/pmda/pmda/test/test_leaflet.py:49:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/home/travis/build/MDAnalysis/pmda/pmda/leaflet.py:301: in run
cutoff=cutoff)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <pmda.leaflet.LeafletFinder object at 0x7f0522075e48>
ts = < Timestep 0 with unit cell dimensions [102.844894 102.84479 132.1866 90. 90. 120. ] >
atomgroups = <AtomGroup with 55 atoms>
scheduler_kwargs = {'scheduler': 'single-threaded'}
n_jobs = MarkDecorator(mark=Mark(name='xfail', args=(-1,), kwargs={}))
cutoff = 15.0
def _single_frame(self, ts, atomgroups, scheduler_kwargs, n_jobs,
cutoff=15.0):
"""Perform computation on a single trajectory frame.
Must return computed values as a list. You can only **read**
from member variables stored in ``self``. Changing them during
a run will result in undefined behavior. `ts` and any of the
atomgroups can be changed (but changes will be overwritten
when the next time step is read).
Parameters
----------
scheduler_kwargs : Dask Scheduler parameters.
cutoff : float (optional)
head group-defining atoms within a distance of `cutoff`
Angstroms are deemed to be in the same leaflet [15.0]
Returns
-------
values : anything
The output from the computation over a single frame must
be returned. The `value` will be added to a list for each
block and the list of blocks is stored as :attr:`_results`
before :meth:`_conclude` is run. In order to simplify
processing, the `values` should be "simple" shallow data
structures such as arrays or lists of numbers.
"""
# Get positions of the atoms in the atomgroup and find their number.
atoms = ts.positions[atomgroups.indices]
matrix_size = atoms.shape[0]
arranged_coord = list()
> part_size = int(matrix_size / n_jobs)
E TypeError: unsupported operand type(s) for /: 'int' and 'MarkDecorator'
/home/travis/build/MDAnalysis/pmda/pmda/leaflet.py:192: TypeError
Expected behaviour
Tests pass as before.
Actual behaviour
Tests started failing in LEafletFinder with https://github.com/MDAnalysis/pmda/commit/f82e4c691801613b40f7785a7b87703d634ef15e which had nothing to do with this part of the code.
Full log snippet
See https://travis-ci.org/MDAnalysis/pmda/jobs/529478197