Fix weights deprecations (#1356)

* deprecate mass_weighted in psa

* update CHANGELOG

Author: kain88-de

package/CHANGELOG

@@ -51,6 +51,8 @@ Fixes
 Changes
   * Enable various pylint warnings to increase python 3 compatibility
   * Change Mathjax cdn (Issue #1313)
+  * Change mass_weight to weights for PSA analysis
+  * Move mass_weights deprecation to version 0.18
   * Docs moved to http://docs.mdanalysis.org (Issue #1315)
     and made responsive (Alabaster theme with readable-sphinx CSS)
     (Issue #378)

package/MDAnalysis/analysis/psa.py

@@ -804,7 +804,7 @@ def __init__(self, universe, reference, ref_select='name CA',
 
     def fit_to_reference(self, filename=None, prefix='', postfix='_fit',
                          rmsdfile=None, targetdir=os.path.curdir,
-                         mass_weighted=False, tol_mass=0.1):
+                         mass_weighted=None, weights=None, tol_mass=0.1):
         """Align each trajectory frame to the reference structure
 
         Parameters
@@ -817,8 +817,10 @@ def fit_to_reference(self, filename=None, prefix='', postfix='_fit',
              prefix for auto-generating the new output filename
         rmsdfile : str (optional)
              file name for writing the RMSD time series [``None``]
-        mass_weighted : bool (optional)
-             do a mass-weighted RMSD fit, default is ``False``
+        mass_weighted : bool (deprecated)
+            do a mass-weighted RMSD fit
+        weights : str/array_like (optional)
+            choose weights. If 'str' uses masses as weights
         tol_mass : float (optional)
              Reject match if the atomic masses for matched atoms differ by more
              than `tol_mass` [0.1]
@@ -831,7 +833,18 @@ def fit_to_reference(self, filename=None, prefix='', postfix='_fit',
         Notes
         -----
         Uses :class:`MDAnalysis.analysis.align.AlignTraj` for the fitting.
+
+
+        .. deprecated:: 0.16.1
+           Instead of ``mass_weighted=True`` use new ``weights='mass'``;
+           refactored to fit with AnalysisBase API
         """
+        if mass_weighted is not None:
+            warnings.warn("mass weighted is deprecated argument. Please use "
+                          " 'weights=\"mass\" instead. Will be removed in 0.17.0",
+                          category=DeprecationWarning)
+            if mass_weighted:
+                weights = 'mass'
         head, tail = os.path.split(self.trj_name)
         oldname, ext = os.path.splitext(tail)
         filename = filename or oldname
@@ -842,7 +855,7 @@ def fit_to_reference(self, filename=None, prefix='', postfix='_fit',
                                                        select=self.ref_select,
                                                        filename=self.newtrj_name,
                                                        prefix=prefix,
-                                                       mass_weighted=mass_weighted,
+                                                       weights=weights,
                                                        tol_mass=tol_mass).run()
         if rmsdfile is not None:
             aligntrj.save(rmsdfile)
@@ -903,7 +916,7 @@ def to_path(self, fitted=False, select=None, flat=False):
 
 
     def run(self, align=False, filename=None, postfix='_fit', rmsdfile=None,
-            targetdir=os.path.curdir, mass_weighted=False, tol_mass=0.1,
+            targetdir=os.path.curdir, mass_weighted=None, weights=None, tol_mass=0.1,
             flat=False):
         r"""Generate a path from a trajectory and reference structure.
 
@@ -937,8 +950,10 @@ def run(self, align=False, filename=None, postfix='_fit', rmsdfile=None,
              prefix for auto-generating the new output filename
         rmsdfile : str (optional)
              file name for writing the RMSD time series [``None``]
-        mass_weighted : bool (optional)
-             do a mass-weighted RMSD fit
+        mass_weighted : bool (deprecated)
+            do a mass-weighted RMSD fit
+        weights : str/array_like (optional)
+            choose weights. If 'str' uses masses as weights
         tol_mass : float (optional)
              Reject match if the atomic masses for matched atoms differ by more
              than *tol_mass* [0.1]
@@ -951,12 +966,23 @@ def run(self, align=False, filename=None, postfix='_fit', rmsdfile=None,
         -------
         topology_trajectory : tuple
              A tuple of the topology name and new trajectory name.
+
+
+        .. deprecated:: 0.16.1
+           Instead of ``mass_weighted=True`` use new ``weights='mass'``;
+           refactored to fit with AnalysisBase API
         """
+        if mass_weighted is not None:
+            warnings.warn("mass weighted is deprecated argument. Please use "
+                          " 'weights=\"mass\" instead. Will be removed in 0.17.0",
+                          category=DeprecationWarning)
+            if mass_weighted:
+                weights = 'mass'
         if align:
-            self.u_fitted = self.fit_to_reference(                              \
-                                filename=filename, postfix=postfix,             \
-                                rmsdfile=rmsdfile, targetdir=targetdir,         \
-                                mass_weighted=False, tol_mass=0.1)
+            self.u_fitted = self.fit_to_reference(
+                                filename=filename, postfix=postfix,
+                                rmsdfile=rmsdfile, targetdir=targetdir,
+                                weights=weights, tol_mass=0.1)
         self.path = self.to_path(fitted=align, flat=flat)
         return self.top_name, self.newtrj_name
 
@@ -1263,8 +1289,6 @@ def __init__(self, universes, reference=None, ref_select='name CA',
              can also each be a list of selection strings (to generate an
              AtomGroup with defined atom order as described under
              :ref:`ordered-selections-label`).
-        mass_weighted : bool
-             do a mass-weighted RMSD fit [``False``]
         tol_mass : float
              Reject match if the atomic masses for matched atoms differ by more
              than *tol_mass* [0.1]
@@ -1350,7 +1374,8 @@ def __init__(self, universes, reference=None, ref_select='name CA',
         self._psa_pairs = None # (distance vector order) list of all PSAPairs
 
 
-    def generate_paths(self, **kwargs):
+    def generate_paths(self, align=False, filename='fitted', infix='', mass_weighted=None, weights=None,
+                       tol_mass=False, ref_frame=None, flat=False, save=True, store=True):
         """Generate paths, aligning each to reference structure if necessary.
 
         Parameters
@@ -1364,8 +1389,10 @@ def generate_paths(self, **kwargs):
         infix : str
              additional tag string that is inserted into the output filename of
              the fitted trajectory files ['']
-        mass_weighted : bool
-             do a mass-weighted RMSD fit
+        mass_weighted : bool (deprecated)
+            do a mass-weighted RMSD fit
+        weights : str/array_like (optional)
+            choose weights. If 'str' uses masses as weights
         tol_mass : float
              Reject match if the atomic masses for matched atoms differ by more
              than *tol_mass*
@@ -1393,28 +1420,31 @@ def generate_paths(self, **kwargs):
         persistence and can be accessed as the attribute
         :attr:`PSAnalysis.paths`.
 
+
+        .. deprecated:: 0.16.1
+           Instead of ``mass_weighted=True`` use new ``weights='mass'``;
+           refactored to fit with AnalysisBase API
         """
-        align = kwargs.pop('align', False)
-        filename = kwargs.pop('filename', 'fitted')
-        infix = kwargs.pop('infix', '')
-        mass_weighted = kwargs.pop('mass_weighted', False)
-        tol_mass = kwargs.pop('tol_mass', False)
-        ref_frame = kwargs.pop('ref_frame', self.ref_frame)
-        flat = kwargs.pop('flat', False)
-        save = kwargs.pop('save', True)
-        store = kwargs.pop('store', False)
+        if mass_weighted is not None:
+            warnings.warn("mass weighted is deprecated argument. Please use "
+                          " 'weights=\"mass\" instead. Will be removed in 0.17.0",
+                          category=DeprecationWarning)
+            if mass_weighted:
+                weights = 'mass'
+        if ref_frame is None:
+            ref_frame = self.ref_frame
 
         paths = []
         fit_trj_names = []
         for i, u in enumerate(self.universes):
-            p = Path(u, self.u_reference, ref_select=self.ref_select,           \
+            p = Path(u, self.u_reference, ref_select=self.ref_select,
                      path_select=self.path_select, ref_frame=ref_frame)
             trj_dir = self.targetdir + self.datadirs['fitted_trajs']
             postfix = '{0}{1}{2:03n}'.format(infix, '_psa', i+1)
-            top_name, fit_trj_name = p.run(align=align, filename=filename,      \
-                                           postfix=postfix,                     \
-                                           targetdir=trj_dir,                   \
-                                           mass_weighted=mass_weighted,         \
+            top_name, fit_trj_name = p.run(align=align, filename=filename,
+                                           postfix=postfix,
+                                           targetdir=trj_dir,
+                                           weights=weights,
                                            tol_mass=tol_mass, flat=flat)
             paths.append(p.path)
             fit_trj_names.append(fit_trj_name)
@@ -1426,7 +1456,6 @@ def generate_paths(self, **kwargs):
             with open(self._fit_trjs_pkl, 'wb') as output:
                 cPickle.dump(self.fit_trj_names, output)
         if store:
-            filename = kwargs.pop('filename', None)
             self.save_paths(filename=filename)