From 170af4c9ac22fdbf5614c0477a3900187fc5e35c Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 29 Oct 2024 00:27:45 +0000 Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/asottile/reorder-python-imports: v3.12.0 → v3.14.0](https://github.com/asottile/reorder-python-imports/compare/v3.12.0...v3.14.0) - [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v5.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.5.0...v5.0.0) - [github.com/asottile/pyupgrade: v3.15.0 → v3.19.0](https://github.com/asottile/pyupgrade/compare/v3.15.0...v3.19.0) - [github.com/psf/black: 23.12.1 → 24.10.0](https://github.com/psf/black/compare/23.12.1...24.10.0) --- .pre-commit-config.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 654cfa6..d7b2e4e 100644 --- a/.pre-commit-config.yaml +++ b/.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"] From 1640ec3718d713b214e66be95d5d4304b3a5bb44 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 29 Oct 2024 00:27:52 +0000 Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- geneplexus/__init__.py | 1 + geneplexus/_config/__init__.py | 1 + geneplexus/_config/config.py | 1 + geneplexus/_config/logger_util.py | 1 + geneplexus/cli.py | 1 + geneplexus/download.py | 1 + geneplexus/geneplexus.py | 1 + geneplexus/util.py | 1 + 8 files changed, 8 insertions(+) diff --git a/geneplexus/__init__.py b/geneplexus/__init__.py index ae58500..7ba5bb5 100644 --- a/geneplexus/__init__.py +++ b/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 diff --git a/geneplexus/_config/__init__.py b/geneplexus/_config/__init__.py index eeb3ffe..add5578 100644 --- a/geneplexus/_config/__init__.py +++ b/geneplexus/_config/__init__.py @@ -1,4 +1,5 @@ """Basic configurations.""" + from . import config from .logger_util import make_logger diff --git a/geneplexus/_config/config.py b/geneplexus/_config/config.py index 67dd677..b697c35 100644 --- a/geneplexus/_config/config.py +++ b/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 diff --git a/geneplexus/_config/logger_util.py b/geneplexus/_config/logger_util.py index 8c5933f..074a080 100644 --- a/geneplexus/_config/logger_util.py +++ b/geneplexus/_config/logger_util.py @@ -1,4 +1,5 @@ """Logger utilities.""" + import logging from contextlib import contextmanager from typing import Optional diff --git a/geneplexus/cli.py b/geneplexus/cli.py index 25116d9..9fe89ea 100644 --- a/geneplexus/cli.py +++ b/geneplexus/cli.py @@ -1,4 +1,5 @@ """Command line interface for the GenePlexus pipeline.""" + import argparse import atexit import os diff --git a/geneplexus/download.py b/geneplexus/download.py index 4bf4fa4..9d2c8ba 100755 --- a/geneplexus/download.py +++ b/geneplexus/download.py @@ -1,4 +1,5 @@ """Data download module.""" + import io import os import os.path as osp diff --git a/geneplexus/geneplexus.py b/geneplexus/geneplexus.py index 85fef23..0b42ca8 100755 --- a/geneplexus/geneplexus.py +++ b/geneplexus/geneplexus.py @@ -1,4 +1,5 @@ """GenePlexus API.""" + import os import os.path as osp import warnings diff --git a/geneplexus/util.py b/geneplexus/util.py index 5b108b5..f1289e9 100755 --- a/geneplexus/util.py +++ b/geneplexus/util.py @@ -1,4 +1,5 @@ """Utilities including file and path handling.""" + import functools import json import os