rename count_file in internal API to counts_file (#944)

Co-authored-by: Tim Treis <[email protected]>

Author: flying-sheep

src/squidpy/read/_read.py

@@ -4,10 +4,7 @@
 import os
 import re
 from pathlib import Path
-from typing import (
-    Any,
-    Union,  # noqa: F401
-)
+from typing import Any
 
 import numpy as np
 import pandas as pd
@@ -64,7 +61,7 @@ def visium(
         - :attr:`anndata.AnnData.uns` ``['spatial']['{library_id}']['metadata']`` - various metadata.
     """  # noqa: E501
     path = Path(path)
-    adata, library_id = _read_counts(path, count_file=counts_file, library_id=library_id, **kwargs)
+    adata, library_id = _read_counts(path, counts_file=counts_file, library_id=library_id, **kwargs)
 
     if not load_images:
         return adata
@@ -149,7 +146,7 @@ def vizgen(
     """
     path = Path(path)
     adata, library_id = _read_counts(
-        path=path, count_file=counts_file, library_id=library_id, delimiter=",", first_column_names=True, **kwargs
+        path=path, counts_file=counts_file, library_id=library_id, delimiter=",", first_column_names=True, **kwargs
     )
     blank_genes = np.array(["Blank" in v for v in adata.var_names])
     adata.obsm["blank_genes"] = pd.DataFrame(

src/squidpy/read/_utils.py

@@ -16,14 +16,14 @@
 
 def _read_counts(
     path: str | Path,
-    count_file: str,
+    counts_file: str,
     library_id: str | None = None,
     **kwargs: Any,
 ) -> tuple[AnnData, str]:
     path = Path(path)
-    if count_file.endswith(".h5"):
-        adata: AnnData = read_10x_h5(path / count_file, **kwargs)
-        with File(path / count_file, mode="r") as f:
+    if counts_file.endswith(".h5"):
+        adata: AnnData = read_10x_h5(path / counts_file, **kwargs)
+        with File(path / counts_file, mode="r") as f:
             attrs = dict(f.attrs)
             if library_id is None:
                 try:
@@ -46,9 +46,9 @@ def _read_counts(
     if library_id is None:
         raise ValueError("Please explicitly specify library id.")
 
-    if count_file.endswith((".csv", ".txt")):
-        adata = read_text(path / count_file, **kwargs)
-    elif count_file.endswith(".mtx.gz"):
+    if counts_file.endswith((".csv", ".txt")):
+        adata = read_text(path / counts_file, **kwargs)
+    elif counts_file.endswith(".mtx.gz"):
         adata = read_10x_mtx(path, **kwargs)
     else:
         raise NotImplementedError("TODO")