PendingDeprecationWarning instead of DeprecationWarning

[RMeli]

I was looking at #2472 and found out that there are two sub-packages for hydrogen bond analysis: MDAnalysis/analysis/hbond and MDAnalysis/analysis/hydrogenbonds. In MDAnalysis/analysis/hbond there is this warning:

warnings.warn(
            "This module will be deprecated in version 1.0."
            "Please use MDAnalysis.analysis.hydrogenbonds.hbond_analysis instead.",
            category=DeprecationWarning
        )

I think a PendingDeprecationWarning is more appropriate in this case.

[IAlibay]

This is code that is in progress of getting removed as part of #2443 , but I believe all previous cases of deprecations have been calling DeprecationWarning. A change might not be a bad idea though.

[RMeli]

Should it be removed? The message says that it will be deprecated in version 1.0, not removed...

[IAlibay]

That is a very good point, I hadn't read it properly it seems.

Maybe one of the coredevs can clarify here, I'm glad I hadn't pushed part 2 of my removals yet 😅

[RMeli]

I think if we are going for 0.21 it should be changed to PendingDeprecationWarning, while if we are going for 1.0 we should simply change the error message to something like this:

warnings.warn(
            "This module is deprecated."
            "Please use MDAnalysis.analysis.hydrogenbonds.hbond_analysis instead.",
            category=DeprecationWarning
        )

But removing code is always good, so maybe it can be removed directly in 1.0 since a DeprecationWarning was already in place?

[IAlibay]

Yes, I agree, I'll add the change assuming v1.0 as part of the removal changes.

(the alternative code seems like it was added in v0.21 so it probably is best to just go for a proper deprecation).

[orbeckst]

In this case PendingDeprecationWarning seems more appropriate than DeprecationWarning. Is this an existing warning in 2 and 3?

1.0 will contain both hbonds modules as we want to make it easy for users to keep the last 2-capable version of MDA for their projects.

For 2.0 we would want to remove hbonds — if we can.

[RMeli]

Yes, PendingDeprecationWarning is also available in Python 2.7. I can change it to PendingDeprecationWarning if there is a version 0.21; otherwise I'll live it as it is for 1.0.

I checked other deprecation warnings and this is the only one where "pending" is more appropriate.

[orbeckst]

Thanks for checking. It seems that we’re heading for 1.0 so leave it.