Update to Bioc3.18 and reduce merge memory #269
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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. |
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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.Rwhere I changed a fewpurrrfunctions 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 usestopifnotrather than separateifstatements 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!