Remove velovi (#1274)

* Remove VELOVI from code base * Remove veloVI from docs * Update `pyproject.toml` - Remove optional vi dependency - Remove redundant packages from isort settings
theislab · Sep 30, 2024 · e624ca9 · e624ca9
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diff --git a/README.md b/README.md
@@ -55,24 +55,6 @@ If you use the _EM_ (_dynamical_) or _steady-state model_, cite
 }
 ```
 
-### veloVI
-
-If you use _veloVI_ (_VI model_), cite
-
-```bibtex
-@article{Gayoso2023,
-  title = {Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells},
-  ISSN = {1548-7105},
-  url = {http://dx.doi.org/10.1038/s41592-023-01994-w},
-  DOI = {10.1038/s41592-023-01994-w},
-  journal = {Nature Methods},
-  publisher = {Springer Science and Business Media LLC},
-  author = {Gayoso, Adam and Weiler, Philipp and Lotfollahi, Mohammad and Klein, Dominik and Hong, Justin and Streets, Aaron and Theis, Fabian J. and Yosef, Nir},
-  year = {2023},
-  month = sep
-}
-```
-
 ### RNA velocity inference through metabolic labeling information
 
 If you use the implemented method for estimating RNA velocity from metabolic labeling

diff --git a/docs/source/api.rst b/docs/source/api.rst
@@ -76,7 +76,6 @@ Tools (tl)
 
    tl.recover_dynamics
    tl.differential_kinetic_test
-   tl.VELOVI
 
 **Dynamical genes**
 

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -52,25 +52,6 @@ If you use the *EM* (*dynamical*) or *steady-state model*, cite
         pages = {1408–1414}
     }
 
-
-**veloVI**
-
-If you use *veloVI* (*VI model*), cite
-
-.. code-block:: bibtex
-
-    @article{Gayoso2023,
-        title = {Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells},
-        ISSN = {1548-7105},
-        url = {http://dx.doi.org/10.1038/s41592-023-01994-w},
-        DOI = {10.1038/s41592-023-01994-w},
-        journal = {Nature Methods},
-        publisher = {Springer Science and Business Media LLC},
-        author = {Gayoso, Adam and Weiler, Philipp and Lotfollahi, Mohammad and Klein, Dominik and Hong, Justin and Streets, Aaron and Theis, Fabian J. and Yosef, Nir},
-        year = {2023},
-        month = sep
-    }
-
 **RNA velocity inference through metabolic labeling information**
 
 If you use the implemented method for estimating RNA velocity from metabolic labeling

diff --git a/pyproject.toml b/pyproject.toml
@@ -53,9 +53,6 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-vi = [
-    "scvi-tools>=0.20.1",
-]
 louvain = [
     "igraph",
     "louvain"
@@ -93,7 +90,7 @@ docs = [
     "Jinja2<3.1",
     # converting notebooks to html
     "ipykernel",
-    "sphinx>=1.7,<4.0",
+    "sphinx>=1.7",
     "nbsphinx>=0.7,<0.8.7"
 ]
 
@@ -142,9 +139,9 @@ exclude = '''
 [tool.isort]
 profile = "black"
 use_parentheses = true
-known_num = "networkx,numpy,pandas,scipy,sklearn,statmodels,torch"
+known_num = "networkx,numpy,pandas,scipy,sklearn,statmodels"
 known_plot = "matplotlib,mpl_toolkits,seaborn"
-known_bio = "anndata,scanpy,scvi"
+known_bio = "anndata,scanpy"
 sections = "FUTURE,STDLIB,THIRDPARTY,NUM,PLOT,BIO,FIRSTPARTY,LOCALFOLDER"
 no_lines_before = "LOCALFOLDER"
 balanced_wrapping = true

diff --git a/scvelo/tools/__init__.py b/scvelo/tools/__init__.py
@@ -1,5 +1,3 @@
-import contextlib
-
 from scanpy.tools import diffmap, dpt, louvain, tsne, umap
 
 from ._em_model import ExpectationMaximizationModel
@@ -24,10 +22,6 @@
 from .velocity_graph import velocity_graph
 from .velocity_pseudotime import velocity_map, velocity_pseudotime
 
-with contextlib.suppress(ImportError):
-    from ._vi_model import VELOVI
-
-
 __all__ = [
     "align_dynamics",
     "differential_kinetic_test",
@@ -60,7 +54,3 @@
     "SecondOrderSteadyStateModel",
     "ExpectationMaximizationModel",
 ]
-if "VELOVI" in locals():
-    __all__ += ["VELOVI"]
-
-del contextlib