How to handle legacy software tools?

[mlocardpaulet]

Some tools are implemented in ProteoBench but not maintained anymore, this is the case for AlphaPept in the DDA quant LFQ module.
Two solutions were proposed to handle this:

• remove the tool
• have some sort of marker for legacy tools (e.g. tools that haven’t been updated in a year)

I personally prefer the second option, specially because some of these tools may still be available and used within the community, so I would rather not remove them. What do you think?

[bittremieux]

I agree with option 2. There are many tools that end up in a stable status or only get updates sporadically. So imo this is not a problem, and an official marker isn't even really necessary (unless the tool has been officially deprecated).

[enryH]

I guess people will just stop submitting with an archived tools and it fill be less highlighted after a while.

[mlocardpaulet]

what do you mean by "less highlighted"? Currently, we do not highlight the most recent submission.

[enryH]

ok. but the tool will also not improve. then I also opt for option 2.

[JuliaS92]

I would also agree with option 2. Even if the tool is officially archived it is still openly available and might still be used.

[mlocardpaulet]

Hi, we now have a mention "(legacy tool)" next to the tool name in the main plot legend. It is also mentioned in the documentation for this tool (we did it for AlphaPept in the DDA Precursor quantification (QExactive) module).