Merge branch 'master' of https://github.com/lhqing/ALLCools

Author: lhqing

.pre-commit-config.yaml

@@ -7,19 +7,19 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
     - repo: https://github.com/psf/black
-      rev: 23.3.0
+      rev: 24.3.0
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v3.0.0-alpha.9-for-vscode
+      rev: v4.0.0-alpha.8
       hooks:
           - id: prettier
     - repo: https://github.com/asottile/blacken-docs
-      rev: 1.14.0
+      rev: 1.16.0
       hooks:
           - id: blacken-docs
     - repo: https://github.com/PyCQA/isort
-      rev: 5.12.0
+      rev: 5.13.2
       hooks:
           - id: isort
     - repo: https://github.com/asottile/yesqa
@@ -34,7 +34,7 @@ repos:
                 - flake8-bugbear
                 - flake8-blind-except
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.4.0
+      rev: v4.6.0
       hooks:
           - id: detect-private-key
           - id: check-ast
@@ -44,7 +44,7 @@ repos:
           - id: trailing-whitespace
           - id: check-case-conflict
     - repo: https://github.com/PyCQA/autoflake
-      rev: v2.2.0
+      rev: v2.3.1
       hooks:
           - id: autoflake
             args:
@@ -53,7 +53,7 @@ repos:
                 - --remove-unused-variable
                 - --ignore-init-module-imports
     - repo: https://github.com/PyCQA/flake8
-      rev: 6.0.0
+      rev: 7.0.0
       hooks:
           - id: flake8
             additional_dependencies:
@@ -64,7 +64,7 @@ repos:
                 - flake8-bugbear
                 - flake8-blind-except
     - repo: https://github.com/asottile/pyupgrade
-      rev: v3.7.0
+      rev: v3.15.2
       hooks:
           - id: pyupgrade
             args: [--py3-plus, --py38-plus, --keep-runtime-typing]

ALLCools/_open.py

@@ -30,6 +30,7 @@
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 THE SOFTWARE.
 """
+
 import codecs
 import gzip
 import os

ALLCools/clustering/balanced_pca.py

@@ -3,6 +3,7 @@
 
 A class allow user provide fitted model and just transform MCDS to adata with PCs.
 """
+
 import anndata
 import joblib
 import numpy as np

ALLCools/clustering/doublets/coverage_doublets.py

@@ -12,7 +12,6 @@
 
 """
 
-
 import json
 import pathlib
 from collections import defaultdict

ALLCools/mcds/mcds.py

@@ -293,7 +293,7 @@ def open(
             ds = xr.open_dataset(
                 _final_paths[0],
                 engine=engine,
-                **kwargs
+                **kwargs,
                 # chunks=chunks  # do not apply chunks parameter here, apply in the end
             )
         else: