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APIComponent-AnalysisdeprecationDeprecated functionality to give advance warning for API changes.Deprecated functionality to give advance warning for API changes.
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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:
start,stop,stepare kwargs ofAnalysisBase.run()but not of__init__().verboseis a kwarg of__init__where it sets the default;verboseis also a kwarg ofrun()where it overrides the default value for the duration ofrun(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.Deprecated functionality to give advance warning for API changes.