Deprecate Timestep as argument for writers

[orbeckst]

As discussed in #206 we want to streamline the trajectory writer interface so that

Writer.write(arg)

only accepts AtomGroup or Universe as arg but not Timestep anymore. (We can't think of a good reason when we would have a Timestep but not an AG.)

• deprecate the part of base.Writer.write()

  mdanalysis/package/MDAnalysis/coordinates/base.py

  Line 2146 in 388346d

  if isinstance(obj, Timestep):

  that can directly take a Timestep
• check all specific Writers that we don't override
• add comments that in 1.0 supplying a Timestep will raise a TypeError
• add tests for all writers that check for the deprecation warning (and can later be turned into tests that check for TypeError)
• check docs and replace deprecated usage

[orbeckst]

I am adding this to 0.19.0 – but this can be targeted to a 0.19.x later.

[orbeckst]

We might have missed the boat on deprecating to get rid of 1.0.

So I think we should deprecate in 1.0 and remove in 2.0.

[orbeckst]

@richardjgowers @IAlibay what is left over after merge of PR #2110?

Close or re-target to later milestone.

[IAlibay]

I think #2110 should have fixed all this now. I'll close.