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deprecate scvi #1703

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Merged
ivirshup merged 5 commits into from
Mar 9, 2021
Merged

deprecate scvi #1703

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79af8ce
deprecate scvi
Mar 2, 2021
80e641e
Update .azure-pipelines.yml
mjayasur Mar 7, 2021
4667f5a
remove :func: links to scvi in release notes
mjayasur Mar 7, 2021
2e0e737
remove tildes in front of scvi in release notes
mjayasur Mar 8, 2021
684a627
Update docs/release-notes/1.5.0.rst
ivirshup Mar 9, 2021
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4 changes: 2 additions & 2 deletions docs/release-notes/1.5.0.rst
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Expand Up @@ -12,12 +12,12 @@ The `1.5.0` release adds a lot of new functionality, much of which takes advanta

.. rubric:: New functionality

- Many functions, like :func:`~scanpy.pp.neighbors` and :func:`~scanpy.tl.umap`, now store cell-by-cell graphs in :attr:`~anndata.AnnData.obsp` :pr:`1118` :smaller:`S Rybakov`
- Many functions, like :func:`scanpy.pp.neighbors` and :func:`~scanpy.tl.umap`, now store cell-by-cell graphs in :attr:`~anndata.AnnData.obsp` :pr:`1118` :smaller:`S Rybakov`
- :func:`~scanpy.pp.scale` and :func:`~scanpy.pp.log1p` can be used on any element in :attr:`~anndata.AnnData.layers` or :attr:`~anndata.AnnData.obsm` :pr:`1173` :smaller:`I Virshup`

.. rubric:: External tools

- `~scanpy.external.pp.scvi` for preprocessing with scVI :pr:`1085` :smaller:`G Xing`
- `scanpy.external.pp.scvi` for preprocessing with scVI :pr:`1085` :smaller:`G Xing`
- Guide for using :ref:`Scanpy in R <conversion_to_r>` :pr:`1186` :smaller:`L Zappia`

.. rubric:: Performance
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2 changes: 1 addition & 1 deletion docs/release-notes/1.7.0.rst
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Expand Up @@ -27,7 +27,7 @@
- Updates for :func:`~scanpy.external.tl.palantir` and :func:`~scanpy.external.tl.palantir_results` :pr:`1245` :smaller:`A Mousa`
- Fixes to :func:`~scanpy.external.tl.harmony_timeseries` docs :pr:`1248` :smaller:`A Mousa`
- Support for `leiden` clustering by :func:`scanpy.external.tl.phenograph` :pr:`1080` :smaller:`A Mousa`
- Deprecate `~scanpy.external.pp.scvi` :pr:`1554` :smaller:`G Xing`
- Deprecate `scanpy.external.pp.scvi` :pr:`1554` :smaller:`G Xing`
- Updated default params of :func:`~scanpy.external.tl.sam` to work with larger data :pr:`1540` :smaller:`A Tarashansky`

.. rubric:: Documentation
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