fix docs and default parameters

package/MDAnalysis/analysis/align.py

@@ -362,10 +362,10 @@ def alignto(mobile, reference, select="all", mass_weighted=None, weights=None,
        When using 2. or 3. with *sel1* and *sel2* then these selections can
        also each be a list of selection strings (to generate a AtomGroup with
        defined atom order as described under :ref:`ordered-selections-label`).
-    mass_weighted : boolean, optional, deprecated
+    mass_weighted : boolean, optional (deprecated)
        ``True`` uses the masses :meth:`reference.masses` as weights for the
        RMSD fit.
-    weights : str/array_like (optional)
+    weights : str/array_like, optional
        weights to be used for fit. Can be either 'mass' or an array_like
     tol_mass: float, optional
        Reject match if the atomic masses for matched atoms differ by more than
@@ -395,6 +395,7 @@ def alignto(mobile, reference, select="all", mass_weighted=None, weights=None,
     old_rmsd
         RMSD before spatial alignment
     new_rmsd
+        RMSD after spatial alignment
 
     See Also
     --------
@@ -411,7 +412,7 @@ def alignto(mobile, reference, select="all", mass_weighted=None, weights=None,
        the old behavior was the equivalent of *strict* = ``True``.
 
     .. versionchanged:: 0.16.0
-       new general 'weights' kwarg replace mass_weights
+       new general 'weights' kwarg replace mass_weights, deprecated 'mass_weights'
     """
     if select in ('all', None):
         # keep the EXACT order in the input AtomGroups; select_atoms('all')

package/MDAnalysis/analysis/encore/covariance.py

@@ -173,7 +173,7 @@ def shrinkage_covariance_estimator( coordinates,
 def covariance_matrix(ensemble,
                       selection="name CA",
                       estimator=shrinkage_covariance_estimator,
-                      weights=None,
+                      weights='mass',
                       reference=None):
     """
     Calculates (optionally mass weighted) covariance matrix
@@ -190,7 +190,7 @@ def covariance_matrix(ensemble,
         of frames and M the number of atoms). See ml_covariance_estimator and
         shrinkage_covariance_estimator for reference.
     weights : str/array_like (optional)
-        specify optional weights. If ``mass`` then chose masses of ensemble atoms
+        specify weights. If ``'mass'`` then chose masses of ensemble atoms, if ``None`` chose uniform weights
     reference : MDAnalysis.Universe object (optional)
         Use the distances to a specific reference structure rather than the
         distance to the mean.

package/MDAnalysis/analysis/rms.py

@@ -199,8 +199,8 @@ def rmsd(a, b, weights=None, center=False, superposition=False):
     if center or superposition:
         # make copies (do not change the user data!)
         # weights=None is equivalent to all weights 1
-        a = a - np.average(a, axis=0, weights=weights)
-        b = b - np.average(b, axis=0, weights=weights)
+        a -= np.average(a, axis=0, weights=weights)
+        b -= np.average(b, axis=0, weights=weights)
 
     if weights is not None:
         if len(weights) != len(a):
@@ -328,9 +328,9 @@ def __init__(self, atomgroup, reference=None, select='all',
             .. Note:: Experimental feature. Only limited error checking
                       implemented.
 
-        filename : str (optional)
+        filename : str, optional
             write RSMD into file file :meth:`RMSD.save`
-        mass_weighted : bool deprecated
+        mass_weighted : bool (deprecated)
              do a mass-weighted RMSD fit
         weights : str/array_like (optional)
              choose weights. If 'str' uses masses as weights