Backwards-compat breaking changes

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

• merge sparse pca
• 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
• replace default pca solver with 'arpack'
• change default solver in logreg solver in rank_genes_groups to lbfgs
• merge #621
• Transition away from positional APIs: #464 (actually backwards compatible through decorator!)

done in #3653

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

anndata:

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

This issue is a historical checklist rather than a single task, with several completed items and remaining entries referring to #572, #446, #464, and a neighbors/init.py location. Review the unchecked changes and their linked issues first; there is no single entry point or completion criterion for the issue as a whole.