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update analysis.base.AnalysisBase to conform to API #1463

@orbeckst

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@orbeckst

In #719 we decided on the details of the analysis interface ("Bauhaus" style). The description for implementation is on the wiki MDAnalysis.analysis user interface but we also decided to change a few additional things that are directly defined in the base class and automatically apply to all analysis code: The following needs to be changed in AnalysisBase:

  1. start, stop, step are kwargs of AnalysisBase.run() but not of __init__().
  2. verbose is a kwarg of __init__ where it sets the default; verbose is also a kwarg of run() where it overrides the default value for the duration of run (this allows the user to mute the frame-by-frame calculation but still have verbose output during pre- and post-processing).

Because 1 changes the API, we need to deprecate start, stop, step in __init__ and remove them in 1.0.0. Until then it needs to be possible to set the iteration range in __init__ and kwargs in run() will override the __init__ values.

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    APIComponent-AnalysisdeprecationDeprecated functionality to give advance warning for API changes.

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