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Remove velovi #1274

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Sep 30, 2024
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Remove velovi #1274

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176ac20
Remove VELOVI from code base
WeilerP Sep 30, 2024
334c994
Remove veloVI from docs
WeilerP Sep 30, 2024
7de37d1
Update `pyproject.toml`
WeilerP Sep 30, 2024
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18 changes: 0 additions & 18 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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1 change: 0 additions & 1 deletion docs/source/api.rst
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Expand Up @@ -76,7 +76,6 @@ Tools (tl)

tl.recover_dynamics
tl.differential_kinetic_test
tl.VELOVI

**Dynamical genes**

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19 changes: 0 additions & 19 deletions docs/source/index.rst
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Expand Up @@ -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
Expand Down
9 changes: 3 additions & 6 deletions pyproject.toml
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Expand Up @@ -53,9 +53,6 @@ dependencies = [
]

[project.optional-dependencies]
vi = [
"scvi-tools>=0.20.1",
]
louvain = [
"igraph",
"louvain"
Expand Down Expand Up @@ -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"
]

Expand Down Expand Up @@ -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
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10 changes: 0 additions & 10 deletions scvelo/tools/__init__.py
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@@ -1,5 +1,3 @@
import contextlib

from scanpy.tools import diffmap, dpt, louvain, tsne, umap

from ._em_model import ExpectationMaximizationModel
Expand All @@ -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",
Expand Down Expand Up @@ -60,7 +54,3 @@
"SecondOrderSteadyStateModel",
"ExpectationMaximizationModel",
]
if "VELOVI" in locals():
__all__ += ["VELOVI"]

del contextlib
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