Remove start/stop/step from AnalysisBase kwargs

package/CHANGELOG

@@ -86,6 +86,9 @@ Enhancements
   * Improve the distance search in water bridge analysis with capped_distance (PR #2480)
 
 Changes
+  * deprecated `start`, `stop`, and `step` keywords have been removed from `__init__` 
+    in :class:`AnalysisBase`. These should now be called in :meth:`AnalysisBase.run` 
+    (Issue #1463)
   * Standardize `select` keyword by removing `selection`, `atomselection`
     and `ref_select` (Issue #2461)
   * Removes support for setting `start`/`stop`/`step` trajecotry slicing

package/MDAnalysis/analysis/align.py

@@ -575,12 +575,6 @@ def __init__(self, mobile, reference, select='all', filename=None,
             exact methods
         force : bool (optional)
             Force overwrite of filename for rmsd-fitting
-        start : int (optional)
-            First frame of trajectory to analyse, Default: 0
-        stop : int (optional)
-            Last frame of trajectory to analyse, Default: -1
-        step : int (optional)
-            Step between frames to analyse, Default: 1
         in_memory : bool (optional)
             *Permanently* switch `mobile` to an in-memory trajectory
             so that alignment can be done in-place, which can improve
@@ -632,6 +626,10 @@ def __init__(self, mobile, reference, select='all', filename=None,
         .. versionchanged:: 0.17.0
            removed deprecated `mass_weighted` keyword
 
+        .. versionchanged:: 1.0.0
+           Support for the ``start``, ``stop``, and ``step`` keywords has been
+           removed. These should instead be passed to :meth:`AlignTraj.run`.
+
         """
         select = rms.process_selection(select)
         self.ref_atoms = reference.select_atoms(*select['reference'])
@@ -761,12 +759,6 @@ def __init__(self, mobile, reference=None, select='all', filename=None,
             exact methods
         force : bool (optional)
             Force overwrite of filename for rmsd-fitting
-        start : int (optional)
-            First frame of trajectory to analyse, Default: 0
-        stop : int (optional)
-            Last frame of trajectory to analyse, Default: -1
-        step : int (optional)
-            Step between frames to analyse, Default: 1
         in_memory : bool (optional)
             *Permanently* switch `mobile` to an in-memory trajectory
             so that alignment can be done in-place, which can improve
@@ -810,6 +802,11 @@ def __init__(self, mobile, reference=None, select='all', filename=None,
 
         .. versionadded:: 0.21.0
 
+        .. versionchanged:: 1.0.0
+           Support for the ``start``, ``stop``, and ``step`` keywords has been
+           removed. These should instead be passed
+           to :meth:`AverageStructure.run`.
+
         """
         if in_memory or isinstance(mobile.trajectory, MemoryReader):
             mobile.transfer_to_memory()

package/MDAnalysis/analysis/base.py

@@ -99,21 +99,14 @@ def __init__(self, trajectory, verbose=False, **kwargs):
             A trajectory Reader
         verbose : bool, optional
            Turn on more logging and debugging, default ``False``
+
+        .. versionchanged:: 1.0.0
+           Support for setting ``start``, ``stop``, and ``step`` has been
+           removed. These should now be directly passed to
+           :meth:`AnalysisBase.run`.
         """
         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):
         """
@@ -132,11 +125,6 @@ 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
@@ -236,6 +224,11 @@ def __init__(self, function, trajectory=None, *args, **kwargs):
         **kwargs : dict
             arguments for ``function`` and ``AnalysisBase``
 
+        .. versionchanged:: 1.0.0
+           Support for directly passing the ``start``, ``stop``, and ``step``
+           arguments has been removed. These should isntead be passed
+           to :meth:`AnalysisFromFunction.run`.
+
         """
         if (trajectory is not None) and (not isinstance(
                 trajectory, coordinates.base.ProtoReader)):
@@ -258,14 +251,9 @@ def __init__(self, function, trajectory=None, *args, **kwargs):
         self.function = function
         self.args = args
 
-        # 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)
+        super(AnalysisFromFunction, self).__init__(trajectory)
 
     def _prepare(self):
         self.results = []

package/MDAnalysis/analysis/contacts.py

@@ -464,8 +464,7 @@ def _new_selections(u_orig, selections, frame):
     return [u.select_atoms(s) for s in selections]
 
 
-def q1q2(u, select='all', radius=4.5,
-         start=None, stop=None, step=None):
+def q1q2(u, select='all', radius=4.5):
     """Perform a q1-q2 analysis.
 
     Compares native contacts between the starting structure and final structure
@@ -479,29 +478,21 @@ def q1q2(u, select='all', radius=4.5,
         atoms to do analysis on
     radius : float, optional
         distance at which contact is formed
-    start : int, optional
-        First frame of trajectory to analyse, Default: 0
-    stop : int, optional
-        Last frame of trajectory to analyse, Default: -1
-    step : int, optional
-        Step between frames to analyse, Default: 1
 
     Returns
     -------
     contacts : :class:`Contacts`
         Contact Analysis that is set up for a q1-q2 analysis
 
-    Notes
-    -----
 
     .. versionchanged:: 1.0.0
        Changed `selection` keyword to `select`
-
+       Support for setting ``start``, ``stop``, and ``step`` has been removed.
+       These should now be directly passed to :meth:`Contacts.run`.
     """
     selection = (select, select)
     first_frame_refs = _new_selections(u, selection, 0)
     last_frame_refs = _new_selections(u, selection, -1)
     return Contacts(u, selection,
                     (first_frame_refs, last_frame_refs),
-                    radius=radius, method='radius_cut',
-                    start=start, stop=stop, step=step)
+                    radius=radius, method='radius_cut')

package/MDAnalysis/analysis/diffusionmap.py

@@ -211,7 +211,7 @@ def __init__(self, u, select='all', metric=rmsd, cutoff=1E0-5,
             computational cost of eigenvalue decomposition
             scales at O(N^3) where N is the number of frames.
             Cost can be reduced by increasing step interval or specifying a
-            start and stop.
+            start and stop value when calling :meth:`DistanceMatrix.run`.
         select: str, optional
             Any valid selection string for
             :meth:`~MDAnalysis.core.groups.AtomGroup.select_atoms`

package/MDAnalysis/analysis/lineardensity.py

@@ -50,12 +50,6 @@ class LinearDensity(AnalysisBase):
           Bin width in Angstrom used to build linear density
           histograms. Defines the resolution of the resulting density
           profile (smaller --> higher resolution) [0.25]
-    start : int
-          The frame to start at [0]
-    stop : int
-          The frame to end at [-1]
-    step : int
-          The step size through the trajectory in frames [0]
     verbose : bool (optional)
           Show detailed progress of the calculation if set to ``True``; the
           default is ``False``.
@@ -80,10 +74,11 @@ class LinearDensity(AnalysisBase):
     .. versionadded:: 0.14.0
 
     .. versionchanged:: 1.0.0
-       ``save()`` method was removed, you can use ``np.savetxt()`` or
+       Support for the ``start``, ``stop``, and ``step`` keywords has been
+       removed. These should instead be passed to :meth:`LinearDensity.run`.
+       The ``save()`` method was also removed, you can use ``np.savetxt()`` or
        ``np.save()`` on the :attr:`LinearDensity.results` dictionary contents
        instead.
-
     """
 
     def __init__(self, selection, grouping='atoms', binsize=0.25, **kwargs):

package/MDAnalysis/analysis/rdf.py

@@ -132,13 +132,6 @@ class InterRDF(AnalysisBase):
     exclusion_block : tuple (optional)
           A tuple representing the tile to exclude from the distance
           array. [None]
-    start : int (optional)
-          The frame to start at (default is first)
-    stop : int (optional)
-          The frame to end at (default is last)
-    step : int (optional)
-          The step size through the trajectory in frames (default is
-          every frame)
     verbose : bool (optional)
           Show detailed progress of the calculation if set to ``True``; the
           default is ``False``.
@@ -164,6 +157,10 @@ class InterRDF(AnalysisBase):
 
     .. versionadded:: 0.13.0
 
+    .. versionchanged:: 1.0.0
+       Support for the ``start``, ``stop``, and ``step`` keywords has been
+       removed. These should instead be passed to :meth:`InterRDF.run`.
+
     """
     def __init__(self, g1, g2,
                  nbins=75, range=(0.0, 15.0), exclusion_block=None,
@@ -248,13 +245,6 @@ class InterRDF_s(AnalysisBase):
           Number of bins in the histogram [75]
     range : tuple or list (optional)
           The size of the RDF [0.0, 15.0]
-    start : int (optional)
-          The frame to start at (default is first)
-    stop : int (optional)
-          The frame to end at (default is last)
-    step : int (optional)
-          The step size through the trajectory in frames (default is
-          every frame)
 
     Example
     -------
@@ -297,6 +287,10 @@ class InterRDF_s(AnalysisBase):
 
     .. versionadded:: 0.19.0
 
+    .. versionchanged:: 1.0.0
+       Support for the ``start``, ``stop``, and ``step`` keywords has been
+       removed. These should instead be passed to :meth:`InterRDF_s.run`.
+
     """
     def __init__(self, u, ags,
                  nbins=75, range=(0.0, 15.0), density=True, **kwargs):

package/MDAnalysis/analysis/rms.py

@@ -666,14 +666,6 @@ def __init__(self, atomgroup, **kwargs):
         ----------
         atomgroup : AtomGroup
             Atoms for which RMSF is calculated
-        start : int (optional)
-            starting frame, 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, default None becomes 1.
         verbose : bool (optional)
              Show detailed progress of the calculation if set to ``True``; the
              default is ``False``.
@@ -775,6 +767,9 @@ def __init__(self, atomgroup, **kwargs):
            the keyword argument `quiet` is deprecated in favor of `verbose`.
         .. versionchanged:: 0.17.0
            removed unused keyword `weights`
+        .. versionchanged:: 1.0.0
+           Support for the ``start``, ``stop``, and ``step`` keywords has been
+           removed. These should instead be passed to :meth:`RMSF.run`.
 
         """
         super(RMSF, self).__init__(atomgroup.universe.trajectory, **kwargs)

testsuite/MDAnalysisTests/analysis/test_base.py

@@ -133,20 +133,31 @@ def simple_function(mobile):
     return mobile.center_of_geometry()
 
 
-def test_AnalysisFromFunction():
-    u = mda.Universe(PSF, DCD)
-    step = 2
-    ana1 = base.AnalysisFromFunction(
-        simple_function, mobile=u.atoms).run(step=step)
-    ana2 = base.AnalysisFromFunction(simple_function, u.atoms).run(step=step)
-    ana3 = base.AnalysisFromFunction(
-        simple_function, u.trajectory, u.atoms).run(step=step)
+@pytest.mark.parametrize('start, stop, step, nframes', [
+        (None, None, 2, 49),
+        (None, 50, 2, 25),
+        (20, 50, 2, 15),
+        (20, 50, None, 30)
+    ])
+def test_AnalysisFromFunction(u, start, stop, step, nframes):
+    ana1 = base.AnalysisFromFunction(simple_function, mobile=u.atoms)
+    ana1.run(start=start, stop=stop, step=step)
+
+    ana2 = base.AnalysisFromFunction(simple_function, u.atoms)
+    ana2.run(start=start, stop=stop, step=step)
+
+    ana3 = base.AnalysisFromFunction(simple_function, u.trajectory, u.atoms)
+    ana3.run(start=start, stop=stop, step=step)
 
     results = []
-    for ts in u.trajectory[::step]:
+
+    for ts in u.trajectory[start:stop:step]:
         results.append(simple_function(u.atoms))
+
     results = np.asarray(results)
 
+    assert np.size(results, 0) == nframes
+
     for ana in (ana1, ana2, ana3):
         assert_equal(results, ana.results)
 
@@ -183,16 +194,3 @@ def distance(a, b):
 
     with no_deprecated_call():
         d = Distances(u.atoms[:10], u.atoms[10:20]).run()
-
-@pytest.mark.parametrize('param', ['start', 'stop', 'step'])
-def test_runargs_deprecation(param):
-    u = mda.Universe(PSF, DCD)
-
-    class NothingAnalysis(base.AnalysisBase):
-        def _single_frame(self):
-            self.results = []
-
-    with pytest.warns(DeprecationWarning):
-        ana = NothingAnalysis(u.trajectory, **{param: 10})
-
-    ana.run()