Remove support for ts as an input to the ParmedConverter

[IAlibay]

Context

As discussed in #3029 (comment) the ParmedConverter currently takes either an atomgroup/universe or timestep as an input. However as of #2754, support for passing timestep objects to writers was removed.

Given this, it might make sense to remove support for ts?

Maybe we should deprecate for 1.0.x and remove for 2.0?

[avitomar12]

Hey @IAlibay Is it possible to give reference to the code for this issue?

[IAlibay]

@avitomar12 we are referring to:

mdanalysis/package/MDAnalysis/coordinates/ParmEd.py

Line 137 in 6282385

class ParmEdConverter(base.ConverterBase):

Particularly the class' ability to take timestep objects as an input.

@lilyminium should we try to get the deprecation warning through in 1.1.0 for this?

[lilyminium]

I don't know how many people actually use this code instead of just the convert_to function. Did we have a deprecation warning when we removed ts from the other writers?

[IAlibay]

Yup:

mdanalysis/package/MDAnalysis/coordinates/base.py

Lines 2225 to 2230 in 4365f3b

	if isinstance(obj, Timestep):
	warnings.warn(
	'Passing a Timestep to write is deprecated, '
	'and will be removed in 2.0; '
	'use either an AtomGroup or Universe',
	DeprecationWarning)

[lilyminium]

Okies, sounds good. I'll do that and the chainID deprecation.

Edit: I think a PR for this issue would be for 2.0 though right

[kitsiosvas]

Hi, @IAlibay is this issue taken? I would like to work on this if not.

[IAlibay]

@kitsiosvas as far as I am aware there are no PRs open on for this issue. Whilst @avitomar12 indicated they may want to work on it ten days ago, MDAnalysis has decided to take a PR-first approach (i.e. the first PR open is the one we will review, see: https://github.com/MDAnalysis/mdanalysis/wiki/GSoC-FAQ#can-i-claim-an-issue-to-work-on). So please do feel free to open a PR addressing the issue.

[IAlibay]

This was taken care of for 1.1. Needs forward porting.

[kitsiosvas]

@IAlibay Apologies for my delay on working for this issue. I want to inform you that I will not be able to work on this. If anyone else wants to take it, I haven't opened a PR yet so it's free. Again, apologies.

[IAlibay]

@IAlibay Apologies for my delay on working for this issue. I want to inform you that I will not be able to work on this. If anyone else wants to take it, I haven't opened a PR yet so it's free. Again, apologies.

No worries, thanks for letting us know :)