Update black to v21 (#265)

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/ambv/black
-    rev: 20.8b1
+    rev: 21.4b1
     hooks:
     - id: black
-      language_version: python3.7
+      language_version: python3.8

scirpy/_plotting/_cdr_convergence.py

@@ -24,7 +24,7 @@ def cdr_convergence(
     sizeprofile: Union[Literal["small"], None] = None,
     no_singles: bool = False,
     fraction: Union[None, str, bool] = None,
-    **kwds
+    **kwds,
 ) -> Union[List[plt.Axes], AnnData]:
     """how many nucleotide versions a single CDR3 amino acid sequence typically has in a given group
     cells belong to each clonotype within a certain sample.

scirpy/_plotting/_diversity.py

@@ -14,7 +14,7 @@ def alpha_diversity(
     *,
     target_col: str = "clone_id",
     vistype: Literal["bar"] = "bar",
-    **kwargs
+    **kwargs,
 ) -> plt.Axes:
     """Plot the alpha diversity per group.
 

scirpy/_tools/_convergence.py

@@ -13,7 +13,7 @@ def clonotype_convergence(
     key_coarse: str,
     key_fine: str,
     key_added: str = "is_convergent",
-    inplace=True
+    inplace=True,
 ) -> Optional[Categorical]:
     """
     Finds evidence for :term:`Convergent evolution of clonotypes`.

scirpy/_tools/_diversity.py

@@ -13,7 +13,7 @@ def alpha_diversity(
     *,
     target_col: str = "clone_id",
     inplace: bool = True,
-    key_added: Union[None, str] = None
+    key_added: Union[None, str] = None,
 ) -> pd.DataFrame:
     """Computes the alpha diversity of clonotypes within a group.
 

scirpy/io/_datastructures.py

@@ -77,12 +77,12 @@ def __repr__(self):
 
     @property
     def cell_id(self) -> str:
-        """Unique identifier (barcode) of the cell. """
+        """Unique identifier (barcode) of the cell."""
         return self["cell_id"]
 
     @property
     def chains(self) -> List[dict]:
-        """List of chain-dictionaries added to the cell. """
+        """List of chain-dictionaries added to the cell."""
         return self._chains
 
     @property

scirpy/io/_io.py

@@ -142,7 +142,7 @@ def _read_10x_vdj_json(path: Union[str, Path], filtered: bool = True) -> AnnData
 
 
 def _read_10x_vdj_csv(path: Union[str, Path], filtered: bool = True) -> AnnData:
-    """Read IR data from a 10x genomics `_contig_annotations.csv` file """
+    """Read IR data from a 10x genomics `_contig_annotations.csv` file"""
     logger = _IOLogger()
     df = pd.read_csv(path)
 

scirpy/ir_dist/_clonotype_neighbors.py

@@ -68,7 +68,7 @@ def _prepare(self, adata: AnnData):
         logging.hint("Done initializing lookup tables.", time=start)
 
     def _make_clonotype_table(self, adata):
-        """Define 'preliminary' clonotypes based identical IR features. """
+        """Define 'preliminary' clonotypes based identical IR features."""
         if not adata.obs_names.is_unique:
             raise ValueError("Obs names need to be unique!")
 

scirpy/ir_dist/_util.py

@@ -11,7 +11,7 @@
 
 
 def merge_coo_matrices(mats):
-    """Fast sum of coo_matrices. Equivalent to builtin function `sum()`, but faster. """
+    """Fast sum of coo_matrices. Equivalent to builtin function `sum()`, but faster."""
     mats = list(mats)
 
     # special case: empty list - sum returns 0

scirpy/tests/test_ir_dist.py

@@ -616,7 +616,7 @@ def test_compute_distances11(adata_cdr3, adata_cdr3_mock_distance_calculator, n_
 
 
 def test_compute_distances12(adata_cdr3, adata_cdr3_mock_distance_calculator):
-    """Test for #174. Gracefully handle the case when there are no distances. """
+    """Test for #174. Gracefully handle the case when there are no distances."""
     adata_cdr3.obs["IR_VJ_1_junction_aa"] = np.nan
     adata_cdr3.obs["IR_VDJ_1_junction_aa"] = np.nan
     # test both receptor arms, primary chain only
@@ -642,7 +642,7 @@ def test_compute_distances12(adata_cdr3, adata_cdr3_mock_distance_calculator):
 
 
 def test_compute_distances13(adata_cdr3, adata_cdr3_mock_distance_calculator):
-    """Test for #174. Gracefully handle the case when there are IR. """
+    """Test for #174. Gracefully handle the case when there are IR."""
     adata_cdr3.obs["IR_VJ_1_junction_aa"] = np.nan
     adata_cdr3.obs["IR_VDJ_1_junction_aa"] = np.nan
     adata_cdr3.obs["has_ir"] = "False"