Update docstrings

src/scirpy/ir_dist/__init__.py

@@ -1,4 +1,5 @@
 """Compute distances between immune receptor sequences"""
+
 import itertools
 from collections.abc import Sequence
 from typing import Literal, Optional, Union
@@ -114,7 +115,7 @@ def _ir_dist(
     sequence: Literal["aa", "nt"] = "nt",
     key_added: Union[str, None] = None,
     inplace: bool = True,
-    n_jobs: Union[int, None] = -1,
+    n_jobs: int = -1,
     airr_mod: str = "airr",
     airr_key: str = "airr",
     chain_idx_key: str = "chain_indices",
@@ -247,7 +248,7 @@ def sequence_dist(
     *,
     metric: MetricType = "identity",
     cutoff: Union[None, int] = None,
-    n_jobs: Union[None, int] = -1,
+    n_jobs: int = -1,
     **kwargs,
 ) -> csr_matrix:
     """

src/scirpy/ir_dist/_clonotype_neighbors.py

@@ -28,7 +28,7 @@ def __init__(
         match_columns: Union[None, Sequence[str]] = None,
         distance_key: str,
         sequence_key: str,
-        n_jobs: Union[int, None] = None,
+        n_jobs: int,
         chunksize: int = 2000,
     ):
         """Computes pairwise distances between cells with identical

src/scirpy/ir_dist/metrics.py

@@ -115,7 +115,7 @@ def __init__(
         self,
         cutoff: int,
         *,
-        n_jobs: Optional[int] = -1,
+        n_jobs: int = -1,
         block_size: Optional[int] = None,
     ):
         super().__init__(cutoff)
@@ -444,7 +444,7 @@ def __init__(
         self,
         cutoff: int = 10,
         *,
-        n_jobs: Union[int, None] = -1,
+        n_jobs: int = -1,
         block_size: Optional[int] = None,
         subst_mat: str = "blosum62",
         gap_open: int = 11,
@@ -580,7 +580,7 @@ def __init__(
         self,
         cutoff: int = 10,
         *,
-        n_jobs: Union[int, None] = None,
+        n_jobs: int = -1,
         block_size: Optional[int] = None,
         subst_mat: str = "blosum62",
         gap_open: int = 11,

src/scirpy/tests/test_ir_dist.py

@@ -25,7 +25,7 @@ def adata_cdr3_mock_distance_calculator():
     """Mock distances for the adata_cdr3 fixture"""
 
     class MockDistanceCalculator(DistanceCalculator):
-        def __init__(self, n_jobs=None):
+        def __init__(self, n_jobs=-1):
             pass
 
         def calc_dist_mat(self, seqs, seqs2=None):

src/scirpy/tl/_clonotypes.py

@@ -204,7 +204,7 @@ def define_clonotype_clusters(
     n_iterations: int = 5,
     distance_key: Union[str, None] = None,
     inplace: bool = True,
-    n_jobs: Union[int, None] = None,
+    n_jobs: int = -1,
     chunksize: int = 2000,
     airr_mod="airr",
     airr_key="airr",

src/scirpy/tl/_ir_query.py

@@ -90,7 +90,7 @@ def ir_query(
     key_added: Optional[str] = None,
     distance_key: Optional[str] = None,
     inplace: bool = True,
-    n_jobs: Optional[int] = -1,
+    n_jobs: int = -1,
     chunksize: int = 2000,
     airr_mod: str = "airr",
     airr_key: str = "airr",