Merge remote-tracking branch 'origin/pre-commit-ci-update-config' int…

…o template-update-icbi-lab-infercnvpy-v0.4.0

.pre-commit-config.yaml

@@ -13,15 +13,15 @@ repos:
         # doesn't work in combination with jupytext hook yet. See https://github.com/mwouts/jupytext/issues/580
         exclude: "docs/notebooks/.*\\.md"
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.4
+    rev: v0.4.8
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
         types_or: [python, pyi, jupyter]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: detect-private-key
       - id: check-ast

src/infercnvpy/tl/__init__.py

@@ -41,24 +41,24 @@ def pca(
 ) -> Union[np.ndarray, None]:
     """Compute the PCA on the result of :func:`infercnvpy.tl.infercnv`.
 
-    Thin wrapper around :func:`scanpy.tl.pca`.
+    Thin wrapper around :func:`scanpy.pp.pca`.
 
     Parameters
     ----------
     adata
         annotated data matrix
     svd_solver
-        See :func:`scanpy.tl.pca`.
+        See :func:`scanpy.pp.pca`.
     zero_center
-        See :func:`scanpy.tl.pca`.
+        See :func:`scanpy.pp.pca`.
     inplace
         If True, store the result in adata.obsm. Otherwise return the PCA matrix.
     use_rep
         Key under which the result of infercnv is stored in adata
     key_added
         Key under which the result will be stored in adata.obsm if `inplace=True`.
     **kwargs
-        Additional arguments passed to :func:`scanpy.tl.pca`.
+        Additional arguments passed to :func:`scanpy.pp.pca`.
     """
     if f"X_{use_rep}" not in adata.obsm:
         raise KeyError(f"X_{use_rep} is not in adata.obsm. Did you run `tl.infercnv`?")