Merge branch 'master' into pyup-pin-codecov-2.1.13

pytim/interface.py

@@ -90,6 +90,7 @@ def _assign_layers(self):
 
     @property
     def atoms(self):
+        if len(self._layers) == 0: return self._layers # an empty atom group
         return self._layers[:].sum()
 
     @property

pytim/observables/profile.py

@@ -187,6 +187,8 @@ def _sample_random_distribution(self, group):
         rnd *= self.interface.universe.dimensions[:3]
         rnd_pos = IntrinsicDistance(
             self.interface, symmetry=self.symmetry).compute(rnd)
+        # the interpolator can return NaNs in some cases
+        rnd_pos = rnd_pos[np.isfinite(rnd_pos)]
         rnd_accum, bins, _ = stats.binned_statistic(
             rnd_pos,
             np.ones(len(rnd_pos)),
@@ -221,6 +223,9 @@ def sample(self, group, **kargs):
                 rnd_accum, bins = self._sample_random_distribution(group)
 
         values = self.observable.compute(group, **kargs)
+        # the interpolator can return NaNs in some cases
+        cond = np.isfinite(pos)
+        values, pos = values[cond], pos[cond]
         accum, bins, _ = stats.binned_statistic(
             pos,
             values,

pytim/willard_chandler.py

@@ -27,6 +27,7 @@
 
 class WillardChandler(Interface):
     """ Identifies the dividing surface using the Willard-Chandler method
+        NOTE that this method does *not* identify surface atoms
 
         *(Willard, A. P.; Chandler, D. J. Phys. Chem. B 2010, 114, 1954–1958)*
 
@@ -83,9 +84,20 @@ class WillardChandler(Interface):
     @property
     def layers(self):
         """ The method does not identify layers.
+
+        Example:
+
+        >>> import MDAnalysis as mda
+        >>> import pytim
+        >>> from pytim.datafiles import *
+        >>>
+        >>> u = mda.Universe(MICELLE_PDB)
+        >>> g = u.select_atoms('resname DPC')
+        >>> inter= pytim.WillardChandler(u, group=g, alpha=3.0, fast=True)
+        >>> inter.layers
+        <AtomGroup with 0 atoms>
         """
-        self.layers = None
-        return None
+        return self._layers
 
     def _sanity_checks(self):
         """ Basic checks to be performed after the initialization.

requirements.testing.txt

@@ -1,4 +1,4 @@
 mdtraj
-pytest==7.2.1
+pytest==8.1.1
 codecov==2.1.13
-pytest-cov 
+pytest-cov==5.0.0