TODO: Backwards-compat breaking changes

[falexwolf]

A list for keeping track of things that we might change when breaking backwards compat at some point:

• [x] merge sparse pca
• [x] merge https://github.com/theislab/scanpy/pull/1111
• [ ] merge #572
• [ ] set the cachdir default to user_cache_dir(…), ~/.scanpy/cache/ or ~/.cache/
• [ ] stationary states in DPT: https://github.com/theislab/scanpy/blob/b11b4abe5e16053c010e57b2dd3a27396a4b0cf2/scanpy/neighbors/init.py#L853-L857 thanks to @Marius1311 for pointing it out!
• [ ] rename log2fc or similarly: #446
• [ ] add inplace functionality where easily possible, that's not a simple renaming; a function that has inplace in it, should only return the annotation if inplace=False; the copy functions return the whole adata, which we don't want...
• [ ] rename n_comps to n_components everywhere
• [x] replace default pca solver with 'arpack'
• [ ] change default solver in logreg solver in rank_genes_groups to lbfgs
• [x] merge #621
• [x] Transition away from positional APIs: #464 (actually backwards compatible through decorator!)

done in #3653

• [x] make t-test or wilxocon the default of tl.rank_genes_groups
• [x] make pp.highly_variable_genes return a df instead of a recarray...

anndata:

• [x] merge https://github.com/theislab/anndata/pull/130 and fix Scanpy tests

[ivirshup]

Could this issue include the previously discussed (https://github.com/theislab/scanpy/pull/316#issuecomment-436380459) change from copy to inplace?

[flying-sheep]

sure. could you please edit your comment to contain a link to said discussion?

[ivirshup]

I've edited my comment. I'd also be very in favor of the differential expression API getting reworked (#61). It's possible diffxpy should cover this, but I'm not really sure what the state of its development is.

[falexwolf]

Completely agreed, @ivirshup!

The inplace and copy change is not just about renaming. See my edit of the check box list above.