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Deprecation of _reformat_hb in hbonds/hbond_analysis.py for v1.0 #2492

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IAlibay opened this issue Feb 2, 2020 · 4 comments · Fixed by #2494
Closed

Deprecation of _reformat_hb in hbonds/hbond_analysis.py for v1.0 #2492

IAlibay opened this issue Feb 2, 2020 · 4 comments · Fixed by #2494

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@IAlibay
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IAlibay commented Feb 2, 2020

Currently going through and doing the required removals/deprecations for #1745 and I noticed that _reformat_hb was set for deprecation as part of #1339

        .. deprecated:: 1.0
           This is a compatibility layer so that we can provide the same output
           in timeseries as before. However, for 1.0 we should make timeseries
           just return _timeseries, i.e., change the format of timeseries to
           the un-ambiguous representation provided in _timeseries.

It seems like some change is required here prior to v1.0.0, but it's unclear to me as to what.

@IAlibay
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IAlibay commented Feb 2, 2020

pinging @orbeckst as the author of #1339

@orbeckst
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orbeckst commented Feb 2, 2020

As this is in the old hbond code, which we will just keep for legacy reasons in 1.0 I would say, just remove the deprecation notice and we freeze it as it is, warts and all.

For 2.0 we should consider removing the whole old hbond thing and just use the new hydrogenbond analysis but I don't know what else would need to be updated for this to work.

@IAlibay
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IAlibay commented Feb 2, 2020

Ok thanks, I'll update #2494 accordingly.

@orbeckst
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orbeckst commented Feb 3, 2020

Closing because nothing needs to be done. (Except removing the note)

@orbeckst orbeckst closed this as completed Feb 3, 2020
@IAlibay IAlibay mentioned this issue Feb 4, 2020
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orbeckst pushed a commit that referenced this issue Feb 6, 2020
* Partly addresses #1745 (completes save() removal with PR #2487 and PR #2486 )
* removes save methods
  - removes save method from psa.py
  - also minor change to test_hbonds.py
* deprecates hbond_analysis
  - close #2492
* updates changelog
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2 participants