WenjieDu · WenjieDu · May 4, 2026 · May 4, 2026 · May 4, 2026 · May 4, 2026
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -7,10 +7,11 @@ on:
             - dev
     pull_request:
         branches:
+            - main
             - dev
 
 jobs:
-    flake8-linting:
+    ruff-linting:
         runs-on: ubuntu-latest
 
         steps:
@@ -19,12 +20,12 @@ jobs:
             - name: Set up Python
               uses: actions/setup-python@v6
               with:
-                  python-version: "3.10"
+                  python-version: "3.13"
 
-            - name: Install Flake8
+            - name: Install Ruff
               run: |
-                pip install flake8 flake8-pyproject
+                pip install ruff
 
             - name: Run linting
               run: |
-                flake8 .
+                ruff check .
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -8,19 +8,10 @@ repos:
             -   id: check-yaml
 
     # hooks for linting code
-    -   repo: https://github.com/psf/black
-        rev: 24.8.0
+    -   repo: local
         hooks:
-            -   id: black
-                args: [
-                    --line-length=120, # refer to pyproject.toml
-                ]
-
-    -   repo: https://github.com/PyCQA/flake8
-        rev: 7.1.1
-        hooks:
-            -   id: flake8
-                args: [
-                    --max-line-length=120, # refer to pyproject.toml
-                    --extend-ignore=E203,E231
-                ]
+            -   id: ruff
+                name: ruff
+                entry: ruff check --config pyproject.toml --force-exclude
+                language: unsupported
+                types_or: [python, pyi]
diff --git a/README.md b/README.md
@@ -51,8 +51,8 @@
     <a href="https://deepwiki.com/WenjieDu/PyPOTS">
         <img alt="Ask DeepWiki" src="https://deepwiki.com/badge.svg">
     </a>
-    <a href="https://github.com/psf/black">
-        <img alt="Code Style" src="https://img.shields.io/badge/Code_Style-black-000000">
+    <a href="https://github.com/astral-sh/ruff">
+        <img alt="Code Style" src="https://img.shields.io/badge/Code_Style-Ruff-D7FF64?logo=ruff">
     </a>
     <a href="https://anaconda.org/conda-forge/pypots">
         <img alt="Conda downloads" src="https://pypots.com/figs/downloads_badges/conda_pypots_downloads.svg">
@@ -268,8 +268,8 @@ conda update  conda-forge::pypots  # update pypots to the latest version
 # via docker
 docker run -it --name pypots wenjiedu/pypots  # docker will auto pull our built image and run a instance for you
 # after things settled, you can run python in the container to access the well-configured environment for running pypots
-# if you'd like to detach from the container, press ctrl-P + ctrl-Q 
-# run `docker attach pypots` to enter the container again. 
+# if you'd like to detach from the container, press ctrl-P + ctrl-Q
+# run `docker attach pypots` to enter the container again.
 ```
 
 ## ❖ Usage
@@ -295,15 +295,15 @@ data = preprocess_physionet2012(subset='set-a',rate=0.1) # Our ecosystem libs wi
 train_X, val_X, test_X = data["train_X"], data["val_X"], data["test_X"]
 print(train_X.shape)  # (n_samples, n_steps, n_features)
 print(val_X.shape)  # samples (n_samples) in train set and val set are different, but they have the same sequence len (n_steps) and feature dim (n_features)
-print(f"We have {calc_missing_rate(train_X):.1%} values missing in train_X")  
+print(f"We have {calc_missing_rate(train_X):.1%} values missing in train_X")
 train_set = {"X": train_X}  # in training set, simply put the incomplete time series into it
 val_set = {
     "X": val_X,
     "X_ori": data["val_X_ori"],  # in validation set, we need ground truth for evaluation and picking the best model checkpoint
 }
 test_set = {"X": test_X}  # in test set, only give the testing incomplete time series for model to impute
 test_X_ori = data["test_X_ori"]  # test_X_ori bears ground truth for evaluation
-indicating_mask = np.isnan(test_X) ^ np.isnan(test_X_ori)  # mask indicates the values that are missing in X but not in X_ori, i.e. where the gt values are 
+indicating_mask = np.isnan(test_X) ^ np.isnan(test_X_ori)  # mask indicates the values that are missing in X but not in X_ori, i.e. where the gt values are
 
 from pypots.imputation import SAITS  # import the model you want to use
 from pypots.nn.functional import calc_mae
@@ -522,7 +522,7 @@ Fröhlich, H. (2019).
 [An empirical evaluation of generic convolutional and recurrent networks for sequence modeling](https://arxiv.org/abs/1803.01271).
 *arXiv 2018*.
 [^36]: Project Gungnir, the world 1st LLM for time-series multitask modeling, will meet you soon. 🚀 Missing values and
-variable lengths in your datasets? Hard to perform multitask learning with your time series? Not problems no longer. 
+variable lengths in your datasets? Hard to perform multitask learning with your time series? Not problems no longer.
 Join our waitlist right now to receive the latest news and be the first to try it when it's released!
 <a href="https://time-series.ai"><img src="https://pypots.com/figs/timeseriesai/logo.png" width="20px">Time-Series.AI</a>
 [^37]: Wang, S., Wu, H., Shi, X., Hu, T., Luo, H., Ma, L., ... & ZHOU, J. (2024).
@@ -579,4 +579,4 @@ Join our waitlist right now to receive the latest news and be the first to try i
 *arXiv 2024*.
 [^55]: Zhang, F., Du, W., Zhang, H., Yu, K., & Qu, S. (2026).
 [HELIX: Hybrid Encoding with Learnable Identity and Cross-dimensional Synthesis for Time Series Imputation](https://openreview.net/forum?id=FN20iuPnEU).
-*ICML 2026*.
+*ICML 2026*.
diff --git a/README_zh.md b/README_zh.md
@@ -51,8 +51,8 @@
     <a href="https://deepwiki.com/WenjieDu/PyPOTS">
         <img alt="Ask DeepWiki" src="https://deepwiki.com/badge.svg">
     </a>
-    <a href="https://github.com/psf/black">
-        <img alt="Code Style" src="https://img.shields.io/badge/Code_Style-black-000000">
+    <a href="https://github.com/astral-sh/ruff">
+        <img alt="Code Style" src="https://img.shields.io/badge/Code_Style-Ruff-D7FF64?logo=ruff">
     </a>
     <a href="https://anaconda.org/conda-forge/pypots">
         <img alt="Conda downloads" src="https://pypots.com/figs/downloads_badges/conda_pypots_downloads.svg">
@@ -258,7 +258,7 @@ conda update  conda-forge::pypots  # 更新为最新版本
 # via docker
 docker run -it --name pypots wenjiedu/pypots  # docker会自动拉取我们构建好的镜像并为你运行一个实例
 # 运行结束后, 你可以在该容器中运行python即可使用我们为运行pypots配置好的环境
-# 如果你想退出该容器, 先按ctrl-P然后按ctrl-Q即可退出 
+# 如果你想退出该容器, 先按ctrl-P然后按ctrl-Q即可退出
 # 运行命令`docker attach pypots`可以重新进入该容器
 ```
 
@@ -560,4 +560,4 @@ test recently ;-) Follow us, and stay tuned!
 *arXiv 2024*.
 [^55]: Zhang, F., Du, W., Zhang, H., Yu, K., & Qu, S. (2026).
 [HELIX: Hybrid Encoding with Learnable Identity and Cross-dimensional Synthesis for Time Series Imputation](https://openreview.net/forum?id=FN20iuPnEU).
-*ICML 2026*.
+*ICML 2026*.
diff --git a/docs/index.rst b/docs/index.rst
@@ -66,9 +66,9 @@ Welcome to PyPOTS docs!
    :alt: Ask DeepWiki
    :target: https://deepwiki.com/WenjieDu/PyPOTS
 
-.. image:: https://img.shields.io/badge/Code_Style-black-000000
+.. image:: https://img.shields.io/badge/Code_Style-ruff-D7FF64
    :alt: Code Style
-   :target: https://github.com/psf/black
+   :target: https://github.com/astral-sh/ruff
 
 .. image:: https://pypots.com/figs/downloads_badges/conda_pypots_downloads.svg
    :alt: Conda downloads

diff --git a/pypots/anomaly_detection/autoformer/__init__.py b/pypots/anomaly_detection/autoformer/__init__.py
@@ -16,7 +16,6 @@
 # Created by Wenjie Du <wenjay.du@gmail.com>
 # License: BSD-3-Clause
 
-
 from .model import Autoformer
 
 __all__ = [

diff --git a/pypots/anomaly_detection/autoformer/model.py b/pypots/anomaly_detection/autoformer/model.py
@@ -6,7 +6,6 @@
 # Created by Wenjie Du <wenjay.du@gmail.com>
 # License: BSD-3-Clause
 
-
 from typing import Union, Optional
 
 import torch

diff --git a/pypots/anomaly_detection/base.py b/pypots/anomaly_detection/base.py
@@ -5,7 +5,6 @@
 # Created by Wenjie Du <wenjay.du@gmail.com>
 # License: BSD-3-Clause
 
-
 from abc import abstractmethod
 from typing import Union, Optional
 

diff --git a/pypots/anomaly_detection/crossformer/__init__.py b/pypots/anomaly_detection/crossformer/__init__.py
@@ -16,7 +16,6 @@
 # Created by Yiyuan Yang <yyy1997sjz@gmail.com>
 # License: BSD-3-Clause
 
-
 from .model import Crossformer
 
 __all__ = [

diff --git a/pypots/anomaly_detection/dlinear/__init__.py b/pypots/anomaly_detection/dlinear/__init__.py
@@ -16,7 +16,6 @@
 # Created by Wenjie Du <wenjay.du@gmail.com>
 # License: BSD-3-Clause
 
-
 from .model import DLinear
 
 __all__ = [

diff --git a/pypots/anomaly_detection/dlinear/model.py b/pypots/anomaly_detection/dlinear/model.py
@@ -6,7 +6,6 @@
 # Created by Wenjie Du <wenjay.du@gmail.com>
 # License: BSD-3-Clause
 
-
 from typing import Union, Optional
 
 import torch

diff --git a/pypots/anomaly_detection/etsformer/__init__.py b/pypots/anomaly_detection/etsformer/__init__.py
@@ -16,7 +16,6 @@
 # Created by Yiyuan Yang <yyy1997sjz@gmail.com>
 # License: BSD-3-Clause
 
-
 from .model import ETSformer
 
 __all__ = [

diff --git a/pypots/anomaly_detection/fedformer/__init__.py b/pypots/anomaly_detection/fedformer/__init__.py
@@ -16,7 +16,6 @@
 # Created by Yiyuan Yang <yyy1997sjz@gmail.com>
 # License: BSD-3-Clause
 
-
 from .model import FEDformer
 
 __all__ = [

diff --git a/pypots/anomaly_detection/film/__init__.py b/pypots/anomaly_detection/film/__init__.py
@@ -16,7 +16,6 @@
 # Created by Yiyuan Yang <yyy1997sjz@gmail.com>
 # License: BSD-3-Clause
 
-
 from .model import FiLM
 
 __all__ = [

diff --git a/pypots/anomaly_detection/imputeformer/__init__.py b/pypots/anomaly_detection/imputeformer/__init__.py
@@ -16,7 +16,6 @@
 # Created by Wenjie Du <wenjay.du@gmail.com>
 # License: BSD-3-Clause
 
-
 from .model import ImputeFormer
 
 __all__ = [

diff --git a/pypots/anomaly_detection/imputeformer/model.py b/pypots/anomaly_detection/imputeformer/model.py
@@ -6,7 +6,6 @@
 # Created by Wenjie Du <wenjay.du@gmail.com>
 # License: BSD-3-Clause
 
-
 from typing import Union, Optional
 
 import torch

diff --git a/pypots/anomaly_detection/informer/__init__.py b/pypots/anomaly_detection/informer/__init__.py
@@ -16,7 +16,6 @@
 # Created by Yiyuan Yang <yyy1997sjz@gmail.com>
 # License: BSD-3-Clause
 
-
 from .model import Informer
 
 __all__ = [

diff --git a/pypots/anomaly_detection/nonstationary_transformer/__init__.py b/pypots/anomaly_detection/nonstationary_transformer/__init__.py
@@ -16,7 +16,6 @@
 # Created by Yiyuan Yang <yyy1997sjz@gmail.com>
 # License: BSD-3-Clause
 
-
 from .model import NonstationaryTransformer
 
 __all__ = [

diff --git a/pypots/anomaly_detection/patchtst/__init__.py b/pypots/anomaly_detection/patchtst/__init__.py
@@ -16,7 +16,6 @@
 # Created by Wenjie Du <wenjay.du@gmail.com>
 # License: BSD-3-Clause
 
-
 from .model import PatchTST
 
 __all__ = [

diff --git a/pypots/anomaly_detection/patchtst/model.py b/pypots/anomaly_detection/patchtst/model.py
@@ -6,7 +6,6 @@
 # Created by Wenjie Du <wenjay.du@gmail.com>
 # License: BSD-3-Clause
 
-
 from typing import Union, Optional
 
 import torch

diff --git a/pypots/anomaly_detection/pyraformer/__init__.py b/pypots/anomaly_detection/pyraformer/__init__.py
@@ -16,7 +16,6 @@
 # Created by Yiyuan Yang <yyy1997sjz@gmail.com>
 # License: BSD-3-Clause
 
-
 from .model import Pyraformer
 
 __all__ = [

diff --git a/pypots/anomaly_detection/reformer/__init__.py b/pypots/anomaly_detection/reformer/__init__.py
@@ -17,7 +17,6 @@
 # Created by Wenjie Du <wenjay.du@gmail.com>
 # License: BSD-3-Clause
 
-
 from .model import Reformer
 
 __all__ = [

diff --git a/pypots/anomaly_detection/reformer/model.py b/pypots/anomaly_detection/reformer/model.py
@@ -6,7 +6,6 @@
 # Created by Wenjie Du <wenjay.du@gmail.com>
 # License: BSD-3-Clause
 
-
 from typing import Union, Optional
 
 import torch

diff --git a/pypots/anomaly_detection/saits/__init__.py b/pypots/anomaly_detection/saits/__init__.py
@@ -16,7 +16,6 @@
 # Created by Wenjie Du <wenjay.du@gmail.com>
 # License: BSD-3-Clause
 
-
 from .model import SAITS
 
 __all__ = [

diff --git a/pypots/anomaly_detection/saits/model.py b/pypots/anomaly_detection/saits/model.py
@@ -6,7 +6,6 @@
 # Created by Wenjie Du <wenjay.du@gmail.com>
 # License: BSD-3-Clause
 
-
 from typing import Union, Optional
 
 import torch

diff --git a/pypots/anomaly_detection/scinet/__init__.py b/pypots/anomaly_detection/scinet/__init__.py
@@ -16,7 +16,6 @@
 # Created by Wenjie Du <wenjay.du@gmail.com>
 # License: BSD-3-Clause
 
-
 from .model import SCINet
 
 __all__ = [

diff --git a/pypots/anomaly_detection/scinet/model.py b/pypots/anomaly_detection/scinet/model.py
@@ -6,7 +6,6 @@
 # Created by Wenjie Du <wenjay.du@gmail.com>
 # License: BSD-3-Clause
 
-
 from typing import Union, Optional
 
 import torch

diff --git a/pypots/anomaly_detection/segrnn/__init__.py b/pypots/anomaly_detection/segrnn/__init__.py
@@ -16,7 +16,6 @@
 # Created by Wenjie Du <wenjay.du@gmail.com>
 # License: BSD-3-Clause
 
-
 from .model import SegRNN
 
 __all__ = [

diff --git a/pypots/anomaly_detection/segrnn/model.py b/pypots/anomaly_detection/segrnn/model.py
@@ -6,7 +6,6 @@
 # Created by Wenjie Du <wenjay.du@gmail.com>
 # License: BSD-3-Clause
 
-
 from typing import Union, Optional
 
 import torch

diff --git a/pypots/anomaly_detection/tefn/__init__.py b/pypots/anomaly_detection/tefn/__init__.py
@@ -16,7 +16,6 @@
 # Created by Wenjie Du <wenjay.du@gmail.com>
 # License: BSD-3-Clause
 
-
 from .model import TEFN
 
 __all__ = [

diff --git a/pypots/anomaly_detection/tefn/model.py b/pypots/anomaly_detection/tefn/model.py
@@ -6,7 +6,6 @@
 # Created by Wenjie Du <wenjay.du@gmail.com>
 # License: BSD-3-Clause
 
-
 import logging
 from typing import Union, Optional
 

diff --git a/pypots/anomaly_detection/timemixer/__init__.py b/pypots/anomaly_detection/timemixer/__init__.py
@@ -16,7 +16,6 @@
 # Created by Yiyuan Yang <yyy1997sjz@gmail.com>
 # License: BSD-3-Clause
 
-
 from .model import TimeMixer
 
 __all__ = [

diff --git a/pypots/anomaly_detection/timemixerpp/__init__.py b/pypots/anomaly_detection/timemixerpp/__init__.py
@@ -17,7 +17,6 @@
 # Created by Wenjie Du <wenjay.du@gmail.com>
 # License: BSD-3-Clause
 
-
 from .model import TimeMixerPP
 
 __all__ = [

diff --git a/pypots/anomaly_detection/timemixerpp/model.py b/pypots/anomaly_detection/timemixerpp/model.py
@@ -6,7 +6,6 @@
 # Created by Wenjie Du <wenjay.du@gmail.com>
 # License: BSD-3-Clause
 
-
 from typing import Union, Optional
 
 import torch

diff --git a/pypots/anomaly_detection/timesnet/__init__.py b/pypots/anomaly_detection/timesnet/__init__.py
@@ -16,7 +16,6 @@
 # Created by Yiyuan Yang <yyy1997sjz@gmail.com>
 # License: BSD-3-Clause
 
-
 from .model import TimesNet
 
 __all__ = [

diff --git a/pypots/anomaly_detection/transformer/__init__.py b/pypots/anomaly_detection/transformer/__init__.py
@@ -21,7 +21,6 @@
 # Created by Yiyuan Yang <yyy1997sjz@gmail.com>
 # License: BSD-3-Clause
 
-
 from .model import Transformer
 
 __all__ = [