deprecate scvi (#1703)

* deprecate scvi

* Update .azure-pipelines.yml

Co-authored-by: Isaac Virshup <[email protected]>

* remove :func: links to scvi in release notes

* remove tildes in front of scvi in release notes

* Update docs/release-notes/1.5.0.rst

Co-authored-by: Michael Jayasuriya <[email protected]>
Co-authored-by: Isaac Virshup <[email protected]>

Author: 3 people

.azure-pipelines.yml

@@ -43,7 +43,7 @@ jobs:
   - script: |
       python -m pip install --upgrade pip
       pip install pytest-cov wheel
-      pip install .[dev,doc,test,louvain,leiden,magic,scvi,harmony,scrublet,scanorama]
+      pip install .[dev,doc,test,louvain,leiden,magic,harmony,scrublet,scanorama,skmisc]
     displayName: 'Install dependencies'
 
   - script: |

.travis.yml

@@ -18,7 +18,7 @@ matrix:
   - name: "anndata dev"
     python: "3.7"
     install:
-    - pip install .[dev,test,louvain,leiden,magic,scvi,harmony,skmisc,scrublet,scanorama]
+    - pip install .[dev,test,louvain,leiden,magic,harmony,skmisc,scrublet,scanorama]
     - pip install git+https://github.com/theislab/anndata
 python:
 - '3.6'
@@ -29,7 +29,7 @@ cache:
 - directories:
   - data
 install:
-- pip install .[dev,test,louvain,leiden,magic,scvi,harmony,skmisc,scrublet,scanorama]
+- pip install .[dev,test,louvain,leiden,magic,harmony,skmisc,scrublet,scanorama]
 env:
 - MPLBACKEND=Agg
 script:

docs/release-notes/1.5.0.rst

@@ -17,7 +17,7 @@ The `1.5.0` release adds a lot of new functionality, much of which takes advanta
 
 .. rubric:: External tools
 
-- :func:`~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
@@ -48,4 +48,3 @@ The `1.5.0` release adds a lot of new functionality, much of which takes advanta
 - :func:`~scanpy.tl.louvain` for Louvain `0.6` :pr:`1197` :smaller:`I Virshup`
 - :func:`~scanpy.pp.highly_variable_genes` which could lead to incorrect results when the `batch_key` argument was used :pr:`1180` :smaller:`G Eraslan`
 - :func:`~scanpy.tl.ingest` where an inconsistent number of neighbors was used :pr:`1111` :smaller:`S Rybakov`
-

docs/release-notes/1.7.0.rst

@@ -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 :func:`~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

pyproject.toml

@@ -71,7 +71,6 @@ requires = [
 louvain = ['python-igraph', 'louvain>=0.6,!=0.6.2']
 leiden = ['python-igraph', 'leidenalg']
 bbknn = ['bbknn']
-scvi = ['scvi==0.6.7']
 rapids = ['cudf>=0.9', 'cuml>=0.9', 'cugraph>=0.9']
 magic = ['magic-impute>=2.0']
 skmisc = ['scikit-misc>=0.1.3']

scanpy/external/__init__.py

@@ -58,7 +58,6 @@
 
    pp.dca
    pp.magic
-   pp.scvi
 
 
 Tools: TL

scanpy/external/pp/__init__.py

@@ -4,6 +4,5 @@
 from ._harmony_integrate import harmony_integrate
 from ._magic import magic
 from ._scanorama_integrate import scanorama_integrate
-from ._scvi import scvi
 from ._hashsolo import hashsolo
 from ._scrublet import scrublet, scrublet_simulate_doublets