1.4.5 :small:`2019-12-30`
Please install scanpy==1.4.5.post3 instead of scanpy==1.4.5.
New functionality
- :func:`~scanpy.tl.ingest` maps labels and embeddings of reference data to new data :tutorial:`integrating-data-using-ingest` :pr:`651` :smaller:`S Rybakov, A Wolf`
- :mod:`~scanpy.queries` recieved many updates including enrichment through gprofiler and more advanced biomart queries :pr:`467` :smaller:`I Virshup`
- :func:`~scanpy.set_figure_params` allows setting figsize and accepts facecolor='white', useful for working in dark mode :smaller:`A Wolf`
Code design
- :mod:`~scanpy.pp.downsample_counts` now always preserves the dtype of it's input, instead of converting floats to ints :pr:`865` :smaller:`I Virshup`
- allow specifying a base for :func:`~scanpy.pp.log1p` :pr:`931` :smaller:`G Eraslan`
- run neighbors on a GPU using rapids :pr:`830` :smaller:`T White`
- param docs from typed params :smaller:`P Angerer`
- :func:`~scanpy.tl.embedding_density` now only takes one positional argument; similar for :func:`~scanpy.pl.embedding_density`, which gains a param groupby :pr:`965` :smaller:`A Wolf`
- webpage overhaul, ecosystem page, release notes, tutorials overhaul :pr:`960` :pr:`966` :smaller:`A Wolf`
Warning
- changed default solver in :func:`~scanpy.tl.pca` from auto to arpack
- changed default use_raw in :func:`~scanpy.tl.score_genes` from False to None