search

AlexsLemonade / scpcaTools

BSD 3-Clause "New" or "Revised" License
1 stars 0 forks source link

Update to Bioc3.18 and reduce merge memory #269

Closed jashapiro closed 7 months ago

jashapiro commented 7 months ago

This PR started as a couple small changes to reduce the merge memory footprint, but then I had to update some packages, so that ended up sneaking in.

The main changes worth a full look are in merge_sce_list.R where I changed a few purrr functions to prevent having to create copies of the sce_list. Some of these resulted in slightly more aggressive refactoring.

The other changes are mostly linting updates, now that we have pre-commit in here and some things were being rebuilt. Many of these are changes from single to double &, as is now required more aggressively. The changes cascaded a bit, with the most significant change being a place where I converted a bunch of tests to use stopifnot rather than separate if statements because that reduced the "cyclomatic complexity" by a good degree.

A lot of this is really in prep for #265, but I didn't want to put that in here so as not to end up bloating too much!

jashapiro commented 7 months ago

I realized that this update also updates zellkonverter, so there is a chance it would allow merged anndata export to work on bigger files. Anndata itself has been updated as well (though I did not change it in requirements here... I think that will happen in #265 where I am changing the way we manage that file.