search

OSCA-source / OSCA.basic

Basics of the OSCA book
10 stars 11 forks source link

Cell-annotation fix for AUCell #6

Closed alanocallaghan closed 2 years ago

alanocallaghan commented 2 years ago

So a) sorry for the unintended pushes to master; I thought I'd added my fork as a remote but I'd actually just added osca-source twice.

Should we assume that AUCell aren't going to accept this PR after ~6 months? https://github.com/aertslab/AUCell/issues/28

Obviously a breaking change for no reason is not good; maybe it'd be better to try removing it as a dependency and finding an alternative?

hpages commented 2 years ago

Should we assume that AUCell aren't going to accept this PR after ~6 months? aertslab/AUCell#28

Just to be clear, this is a link to an issue that discusses the unnecessary breaking changes that the AUCell developers have introduced to their package in BioC 3.16. AFAIK, no PR was submitted to their package to address that.

But I agree that after 6 months we can assume that they're not interested in fixing the problem they've introduced :disappointed:

maybe it'd be better to try removing it as a dependency and finding an alternative?

Absolutely! Especially if the stability of the OSCA book is a concern. Also, as an educational tool, the book should only pick state of the art tools that adhere to good software engineering practices. I don't think a function like AUCell_buildRankings() falls in that category.

Thanks for dealing with this.

H.

alanocallaghan commented 2 years ago

Ah true, I was reading the proposed changes as a diff somehow.

The alternative then would be to make a PR, but I don't see that being hugely useful; in my experience a PR is likely to sit for months as well.

I'll have a look at what buildrankings does at the weekend