removed quiet in favour of verbose

updated usage of Analysis API, start/stop/step
now deprecated in __init__ and should be given in run method

made PCA setup respect start frame more,
if start is given then initial weights are from that frame
not frame 0

benchmarks/benchmarks/analysis/rms.py

@@ -96,13 +96,10 @@ def setup(self, n_atoms, step, weights):
         self.u = MDAnalysis.Universe(PSF, DCD)
         self.ag = self.u.atoms[:n_atoms]
         self.RMSF_inst = rms.RMSF(atomgroup=self.ag,
-                                  start=None,
-                                  stop=None,
-                                  step=step,
                                   weights=weights)
 
     def time_RMSF(self, n_atoms, step, weights):
         """Benchmark RMSF.run() method, which parses
         over the entire trajectory.
         """
-        self.RMSF_inst.run()
+        self.RMSF_inst.run(step=step)

package/CHANGELOG

@@ -78,7 +78,7 @@ Enhancements
     analysis module (PR #1997, PR #2033)
   * Added the analysis.data module for reference data used in analysis (PR #2033)
   * Added analysis.dihedrals with Ramachandran class to analysis module (PR #1997)
-  * Added augment functionality to create relevant images of particles 
+  * Added augment functionality to create relevant images of particles
   * Most functions in `MDanalysis.lib.distances` previously only accepting
     arrays of coordinates now also accept single coordinates as input (PR #2048,
     Issues #1262 #1938)
@@ -109,6 +109,8 @@ Fixes
   * Fixed SphericalLayer and SphericalZone selections with pbc=True.  Previously
     these shifted all atoms to inside the primary unit cell when calculating the
     center of the reference group (Issue #1795)
+  * PCA analysis now uses start frame as reference frame rather than 0th frame
+    (PR #2055)
 
 Changes
   * TopologyAttrs are now statically typed (Issue #1876)
@@ -130,8 +132,15 @@ Changes
     enforced to be of the form ``[lx, ly, lz, alpha, beta, gamma]`` as required
     by the docs (Issue #2046, PR #2048)
   * Added periodic keyword to select_atoms (#759)
+  * PCA.transform now requires that PCA.run() has already been called
+    otherwise a ValueError is raised (PR #2055)
+  * The quiet keyword has been removed and replaced with verbose (Issue #1975
+    PR #2055)
 
 Deprecations
+  * start/stop/step are deprecated in the initialization of Analysis classes.
+    These parameters should instead be given to the run() method of the class.
+    (Issue #1463 #1979 PR #2055)
   * Almost all "save()", "save_results()", "save_table()" methods in
     analysis classes were deprecated and will be removed in 1.0 (Issue
     #1972 and #1745)

package/MDAnalysis/analysis/base.py

@@ -32,11 +32,12 @@
 from six.moves import range, zip
 import inspect
 import logging
+import warnings
 
 import numpy as np
 from MDAnalysis import coordinates
 from MDAnalysis.core.groups import AtomGroup
-from MDAnalysis.lib.log import ProgressMeter, _set_verbose
+from MDAnalysis.lib.log import ProgressMeter
 
 logger = logging.getLogger(__name__)
 
@@ -84,30 +85,34 @@ def _conclude(self):
 
     .. code-block:: python
 
-       na = NewAnalysis(u.select_atoms('name CA'), 35).run()
+       na = NewAnalysis(u.select_atoms('name CA'), 35).run(start=10, stop=20)
        print(na.result)
 
     """
 
-    def __init__(self, trajectory, start=None,
-                 stop=None, step=None, verbose=None, quiet=None):
+    def __init__(self, trajectory, verbose=False, **kwargs):
         """
         Parameters
         ----------
         trajectory : mda.Reader
             A trajectory Reader
-        start : int, optional
-            start frame of analysis
-        stop : int, optional
-            stop frame of analysis
-        step : int, optional
-            number of frames to skip between each analysed frame
         verbose : bool, optional
-            Turn on verbosity
+           Turn on more logging and debugging, default ``False``
         """
-        self._verbose = _set_verbose(verbose, quiet, default=False)
-        self._quiet = not self._verbose
-        self._setup_frames(trajectory, start, stop, step)
+        self._trajectory = trajectory
+        self._verbose = verbose
+        # do deprecated kwargs
+        # remove in 1.0
+        deps = []
+        for arg in ['start', 'stop', 'step']:
+            if arg in kwargs and not kwargs[arg] is None:
+                deps.append(arg)
+                setattr(self, arg, kwargs[arg])
+        if deps:
+            warnings.warn('Setting the following kwargs should be '
+                          'done in the run() method: {}'.format(
+                              ', '.join(deps)),
+                          DeprecationWarning)
 
     def _setup_frames(self, trajectory, start=None, stop=None, step=None):
         """
@@ -126,6 +131,11 @@ def _setup_frames(self, trajectory, start=None, stop=None, step=None):
             number of frames to skip between each analysed frame
         """
         self._trajectory = trajectory
+        # TODO: Remove once start/stop/step are deprecated from init
+        # See if these have been set as class attributes, and use that
+        start = getattr(self, 'start', start)
+        stop = getattr(self, 'stop', stop)
+        step = getattr(self, 'step', step)
         start, stop, step = trajectory.check_slice_indices(start, stop, step)
         self.start = start
         self.stop = stop
@@ -135,21 +145,9 @@ def _setup_frames(self, trajectory, start=None, stop=None, step=None):
         if interval == 0:
             interval = 1
 
-        # ensure _verbose is set when __init__ wasn't called, this is to not
-        # break pre 0.16.0 API usage of AnalysisBase
-        if not hasattr(self, '_verbose'):
-            if hasattr(self, '_quiet'):
-                # Here, we are in the odd case where a children class defined
-                # self._quiet without going through AnalysisBase.__init__.
-                warnings.warn("The *_quiet* attribute of analyses is "
-                              "deprecated (from 0.16)use *_verbose* instead.",
-                              DeprecationWarning)
-                self._verbose = not self._quiet
-            else:
-                self._verbose = True
-                self._quiet = not self._verbose
+        verbose = getattr(self, '_verbose', False)
         self._pm = ProgressMeter(self.n_frames if self.n_frames else 1,
-                                 interval=interval, verbose=self._verbose)
+                                 interval=interval, verbose=verbose)
 
     def _single_frame(self):
         """Calculate data from a single frame of trajectory
@@ -169,8 +167,25 @@ def _conclude(self):
         """
         pass
 
-    def run(self):
-        """Perform the calculation"""
+    def run(self, start=None, stop=None, step=None, verbose=None):
+        """Perform the calculation
+
+        Parameters
+        ----------
+        start : int, optional
+            start frame of analysis
+        stop : int, optional
+            stop frame of analysis
+        step : int, optional
+            number of frames to skip between each analysed frame
+        verbose : bool, optional
+            Turn on verbosity
+        """
+        logger.info("Choosing frames to analyze")
+        # if verbose unchanged, use class default
+        verbose = getattr(self, '_verbose', False) if verbose is None else verbose
+
+        self._setup_frames(self._trajectory, start, stop, step)
         logger.info("Starting preparation")
         self._prepare()
         for i, ts in enumerate(
@@ -241,10 +256,15 @@ def __init__(self, function, trajectory=None, *args, **kwargs):
 
         self.function = function
         self.args = args
-        base_kwargs, self.kwargs = _filter_baseanalysis_kwargs(self.function,
-                                                               kwargs)
 
-        super(AnalysisFromFunction, self).__init__(trajectory, **base_kwargs)
+        # TODO: Remove in 1.0
+        my_kwargs = {}
+        for depped_arg in ['start', 'stop', 'step']:
+            if depped_arg in kwargs:
+                my_kwargs[depped_arg] = kwargs.pop(depped_arg)
+        self.kwargs = kwargs
+
+        super(AnalysisFromFunction, self).__init__(trajectory, **my_kwargs)
 
     def _prepare(self):
         self.results = []
@@ -272,7 +292,7 @@ def analysis_class(function):
     >>> def RotationMatrix(mobile, ref):
     >>>     return mda.analysis.align.rotation_matrix(mobile, ref)[0]
 
-    >>> rot = RotationMatrix(u.trajectory, mobile, ref, step=2).run()
+    >>> rot = RotationMatrix(u.trajectory, mobile, ref).run(step=2)
     >>> print(rot.results)
     """
 

package/MDAnalysis/analysis/contacts.py

@@ -388,14 +388,6 @@ def __init__(self, u, selection, refgroup, method="hard_cut", radius=4.5,
         kwargs : dict, optional
             dictionary of additional kwargs passed to `method`. Check
             respective functions for reasonable values.
-        start : int, optional
-            First frame of trajectory to analyse, Default: None becomes 0.
-        stop : int, optional
-            Frame index to stop analysis. Default: None becomes
-            n_frames. Iteration stops *before* this frame number,
-            which means that the trajectory would be read until the end.
-        step : int, optional
-            Step between frames to analyse, Default: None becomes 1.
         verbose : bool (optional)
              Show detailed progress of the calculation if set to ``True``; the
              default is ``False``.

package/MDAnalysis/analysis/density.py

@@ -552,7 +552,7 @@ def density_from_Universe(universe, delta=1.0, atomselection='name OH2',
                           start=None, stop=None, step=None,
                           metadata=None, padding=2.0, cutoff=0, soluteselection=None,
                           use_kdtree=True, update_selection=False,
-                          verbose=None, interval=1, quiet=None,
+                          verbose=False, interval=1, quiet=None,
                           parameters=None,
                           gridcenter=None, xdim=None, ydim=None, zdim=None):
     """Create a density grid from a :class:`MDAnalysis.Universe` object.
@@ -751,7 +751,7 @@ def current_coordinates():
     h = grid.copy()
 
     pm = ProgressMeter(u.trajectory.n_frames, interval=interval,
-                       verbose=verbose, quiet=quiet,
+                       verbose=verbose,
                        format="Histogramming %(n_atoms)6d atoms in frame "
                        "%(step)5d/%(numsteps)d  [%(percentage)5.1f%%]\r")
     start, stop, step = u.trajectory.check_slice_indices(start, stop, step)

package/MDAnalysis/analysis/diffusionmap.py

@@ -198,8 +198,7 @@ class DistanceMatrix(AnalysisBase):
 
     """
     def __init__(self, u, select='all', metric=rmsd, cutoff=1E0-5,
-                 weights=None, start=None, stop=None, step=None,
-                 **kwargs):
+                 weights=None, **kwargs):
         """
         Parameters
         ----------
@@ -226,14 +225,6 @@ def __init__(self, u, select='all', metric=rmsd, cutoff=1E0-5,
             Default: 1EO-5
         weights : array, optional
             Weights to be given to coordinates for metric calculation
-        start : int, optional
-            First frame of trajectory to analyse, Default: None becomes 0.
-        stop : int, optional
-            Frame index to stop analysis. Default: None becomes
-            n_frames. Iteration stops *before* this frame number,
-            which means that the trajectory would be read until the end.
-        step : int, optional
-            Step between frames to analyse, Default: None becomes 1.
         verbose : bool (optional)
              Show detailed progress of the calculation if set to ``True``; the
              default is ``False``.
@@ -242,8 +233,7 @@ def __init__(self, u, select='all', metric=rmsd, cutoff=1E0-5,
         traj = self._u.trajectory
 
         # remember that this must be called before referencing self.n_frames
-        super(DistanceMatrix, self).__init__(self._u.trajectory,
-                                           start=start, stop=stop, step=step, **kwargs)
+        super(DistanceMatrix, self).__init__(self._u.trajectory, **kwargs)
 
         self.atoms = self._u.select_atoms(select)
         self._metric = metric
@@ -325,7 +315,7 @@ def __init__(self, u, epsilon=1, **kwargs):
         **kwargs
             Parameters to be passed for the initialization of a
             :class:`DistanceMatrix`.
-            """
+        """
         if isinstance(u, Universe):
             self._dist_matrix = DistanceMatrix(u, **kwargs)
         elif isinstance(u, DistanceMatrix):
@@ -334,20 +324,32 @@ def __init__(self, u, epsilon=1, **kwargs):
             raise ValueError("U is not a Universe or DistanceMatrix and"
                              " so the DiffusionMap has no data to work with.")
         self._epsilon = epsilon
+
+    def run(self, start=None, stop=None, step=None):
+        """ Create and decompose the diffusion matrix in preparation
+        for a diffusion map.
+
+        Parameters
+        ----------
+        start : int, optional
+            start frame of analysis
+        stop : int, optional
+            stop frame of analysis
+        step : int, optional
+            number of frames to skip between each analysed frame
+
+        .. versionchanged:: 0.19.0
+           Added start/stop/step kwargs
+        """
+        # run only if distance matrix not already calculated
+        if not self._dist_matrix._calculated:
+            self._dist_matrix.run(start=start, stop=stop, step=step)
         # important for transform function and length of .run() method
         self._n_frames = self._dist_matrix.n_frames
         if self._n_frames > 5000:
             warnings.warn("The distance matrix is very large, and can "
                           "be very slow to compute. Consider picking a larger "
                           "step size in distance matrix initialization.")
-
-
-    def run(self):
-        """ Create and decompose the diffusion matrix in preparation
-        for a diffusion map."""
-        # run only if distance matrix not already calculated
-        if not self._dist_matrix._calculated:
-            self._dist_matrix.run()
         self._scaled_matrix = (self._dist_matrix.dist_matrix ** 2 /
                                self._epsilon)
         # take negative exponent of scaled matrix to create Isotropic kernel