[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -1,13 +1,13 @@
 repos:
 -   repo: https://github.com/asottile/reorder-python-imports
-    rev: v3.12.0
+    rev: v3.14.0
     hooks:
     -   id: reorder-python-imports
         args: ["--py38-plus"]
         exclude: ^docs/
 
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
@@ -19,12 +19,12 @@ repos:
     -   id: add-trailing-comma
 
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
+    rev: v3.19.0
     hooks:
     -   id: pyupgrade
 
 -   repo: https://github.com/psf/black
-    rev: 23.12.1
+    rev: 24.10.0
     hooks:
     -   id: black
         args: ["--safe", "-l120"]

geneplexus/__init__.py

@@ -125,6 +125,7 @@
 analysis *cannot* be done due to the lack to pretrained models.
 
 """
+
 from ._config import config  # noreorder
 from . import download
 from . import util

geneplexus/_config/__init__.py

@@ -1,4 +1,5 @@
 """Basic configurations."""
+
 from . import config
 from .logger_util import make_logger
 

geneplexus/_config/config.py

@@ -1,4 +1,5 @@
 """Global variables used by the GenePlexus library."""
+
 import os.path as osp
 import pathlib
 from typing import Any

geneplexus/_config/logger_util.py

@@ -1,4 +1,5 @@
 """Logger utilities."""
+
 import logging
 from contextlib import contextmanager
 from typing import Optional

geneplexus/cli.py

@@ -1,4 +1,5 @@
 """Command line interface for the GenePlexus pipeline."""
+
 import argparse
 import atexit
 import os

geneplexus/download.py

@@ -1,4 +1,5 @@
 """Data download module."""
+
 import io
 import os
 import os.path as osp

geneplexus/geneplexus.py

@@ -1,4 +1,5 @@
 """GenePlexus API."""
+
 import os
 import os.path as osp
 import warnings

geneplexus/util.py

@@ -1,4 +1,5 @@
 """Utilities including file and path handling."""
+
 import functools
 import json
 import os