Backport PR #2637 on branch 1.2.x (chore(external): remove velovi pre…

…process functions) (#2638)

Backport PR #2637: chore(external): remove velovi preprocess functions

Co-authored-by: Martin Kim <46072231+martinkim0@users.noreply.github.com>

pyproject.toml

@@ -99,9 +99,8 @@ pymde = ["pymde"]  # scvi.model.utils.mde dependencies
 regseq = ["biopython>=1.81", "genomepy"]  # scvi.data.add_dna_sequence
 loompy = ["loompy>=3.0.6"]  # read loom
 scanpy = ["scanpy>=1.6"]  # scvi.criticism and read 10x
-velovi = ["scvelo>=0.3.0"]  # scvi.external.velovi
 optional = [
-    "scvi-tools[autotune,aws,criticism,hub,loompy,pymde,regseq,scanpy,velovi]"
+    "scvi-tools[autotune,aws,criticism,hub,loompy,pymde,regseq,scanpy]"
 ]  # all optional user functionality
 
 tutorials = [

scvi/external/velovi/__init__.py

@@ -1,5 +1,4 @@
 from ._model import VELOVI
 from ._module import VELOVAE
-from ._utils import get_permutation_scores, preprocess_data
 
-__all__ = ["VELOVI", "VELOVAE", "get_permutation_scores", "preprocess_data"]
+__all__ = ["VELOVI", "VELOVAE"]

tests/external/velovi/test_velovi.py

@@ -1,20 +1,7 @@
-import scvelo as scv
-
 from scvi.data import synthetic_iid
 from scvi.external.velovi import VELOVI
 
 
-def test_preprocess_data():
-    adata = synthetic_iid()
-    adata.layers["spliced"] = adata.X.copy()
-    adata.layers["unspliced"] = adata.X.copy()
-    scv.pp.normalize_per_cell(adata)
-    scv.pp.log1p(adata)
-    scv.pp.moments(adata, n_pcs=30, n_neighbors=30)
-    # TODO(adamgayoso): use real data for this test
-    # preprocess_data(adata)
-
-
 def test_velovi():
     n_latent = 5
     adata = synthetic_iid()