Friendly request to `@deprecate` API changes via semver

[dehann]

Hi BioAlignments,

Just wanted to put in a friendly request for API changes to follow Julia's @deprecate pattern for API changes please, so for example in package v0.1.x:

# src/AwesomeCode.jl
oldsignature(x::Int) = # does thing

Then the API change goes into v0.2.0 along with the deprecation

# src/AwesomeCode.jl
newsignature(x::Float64) = # does similar thing

# src/Deprecated.jl
@deprecate oldsignature(x::Int) newsignature(float(x))

This will give users a chance to update their scripts with a useful auto-generated warning, which tells them how to replace old calls with new ones.

Then remove the deprecation in v0.3

# src/AwesomeCode.jl
newsignature(x::Float64) = # does similar thing

Also consider listing breaking changes in a NEWS.md. Based on a quick search it looks like the @deprecate feature is not used here much.

Thanks for the great package!

[dehann]

Oh, there is also overwriting the Base.getproperty(obj::MyType, f::Symbol) when deprecating fields in a struct. And then inside that use Base.getfield to avoid stack overflows.

Can close this issue on comment received :-)

[kescobo]

Yeah, we definitely should do this throughout BioJulia, especially after packages have reached v1.0. Apologies for the failure to do so in the past. In principle, we could even do patch-releases on previous versions retroactively, though I'm not sure how much effort that's worth.

Unfortunately, developer time in this ecosystem is pretty limited - I suspect this is why it wasn't done in the past. As an aside, if you want to make a PR for this purpose, I think it would be very warmly received :-)