[STY] run isort rules via ruff/pre-commit

.github/workflows/test-ci.yml

@@ -17,16 +17,8 @@ jobs:
       - name: Set up Python "3.10"
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
-      - name: Black setup
-        shell: bash
-        run: pip install black ruff
-      - name: Black Check
-        shell: bash
-        run: black . --diff --color
-      - name: ruff Check
-        shell: bash
-        run: ruff check src
+          python-version: "3.12"
+      - uses: pre-commit/[email protected]
 
   makedocs:
     name: build documentation
@@ -48,21 +40,9 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           python -m pip install .[optional,doc]
-
       - name: Build API documentation
         run: make -C docs html
 
-  codespell:
-    name: Check for spelling errors
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-      - name: Annotate locations with typos
-        uses: codespell-project/codespell-problem-matcher@v1
-      - name: Codespell
-        uses: codespell-project/actions-codespell@v2
 
   test-suite:
     runs-on: ${{ matrix.os }}

.github/workflows/update_precommit_hooks.yml

@@ -0,0 +1,49 @@
+---
+name: Update precommit hooks
+
+on:
+
+# Uses the cron schedule for github actions
+#
+# https://docs.github.com/en/free-pro-team@latest/actions/reference/events-that-trigger-workflows#scheduled-events
+#
+#            ┌───────────── minute (0 - 59)
+#            │ ┌───────────── hour (0 - 23)
+#            │ │ ┌───────────── day of the month (1 - 31)
+#            │ │ │ ┌───────────── month (1 - 12 or JAN-DEC)
+#            │ │ │ │ ┌───────────── day of the week (0 - 6 or SUN-SAT)
+#            │ │ │ │ │
+#            │ │ │ │ │
+#            │ │ │ │ │
+#            * * * * *
+    schedule:
+    # Run first day of the month at midnight UTC
+    -   cron: 0 0 1 * *
+
+  # Allows you to run this workflow manually from the Actions tab
+    workflow_dispatch:
+
+jobs:
+    update_precommit_hooks:
+
+        runs-on: ubuntu-latest
+        steps:
+        -   name: Checkout
+            uses: actions/checkout@v4
+        -   name: Set up Python
+            uses: actions/setup-python@v5
+            with:
+                python-version: '3.12'
+                allow-prereleases: false
+        -   name: Install pre-commit
+            run: pip install pre-commit
+        -   name: Update pre-commit hooks
+            run: pre-commit autoupdate
+        -   name: Create Pull Request
+            uses: peter-evans/create-pull-request@v7
+            with:
+                commit-message: pre-commit hooks auto-update
+                base: main
+                token: ${{ secrets.GITHUB_TOKEN }}
+                delete-branch: true
+                title: '[BOT] update pre-commit hooks'

.pre-commit-config.yaml

@@ -0,0 +1,28 @@
+---
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+
+repos:
+    # Checks for spelling errors
+-   repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+    -   id: codespell
+        args: [--toml, pyproject.toml]
+        additional_dependencies: [tomli]
+
+-   repo: https://github.com/psf/black
+    rev: 24.8.0
+    hooks:
+    -   id: black
+        args: [--config, pyproject.toml]
+
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.8
+    hooks:
+    # Run the linter.
+    -   id: ruff
+        # args: [--statistics]
+        args: [--fix, --show-fixes]
+    # Run the formatter.
+    -   id: ruff-format

docs/conf.py

@@ -5,6 +5,7 @@
 list see the documentation:
 https://www.sphinx-doc.org/en/master/usage/configuration.html
 """
+
 # -- Path setup --------------------------------------------------------------
 
 # If extensions (or modules to document with autodoc) are in another directory,
@@ -43,7 +44,7 @@
     "sphinx.ext.viewcode",
     "sphinx.ext.napoleon",
     # "sphinx_gallery.gen_gallery",
-    "sphinxarg.ext"
+    "sphinxarg.ext",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -75,9 +76,9 @@
 sphinx_gallery_conf = {
     "examples_dirs": ["../examples/"],
     "filename_pattern": "/example_",
-    'ignore_pattern': 'conftest.py',
-    'example_extensions': {'.py'},    
-    "gallery_dirs" : ["auto_examples"],
+    "ignore_pattern": "conftest.py",
+    "example_extensions": {".py"},
+    "gallery_dirs": ["auto_examples"],
     "reference_url": {
         "numpy": "http://docs.scipy.org/doc/numpy-1.9.1",
         "scipy": "http://docs.scipy.org/doc/scipy-0.17.0/reference",

examples/conftest.py

@@ -1,6 +1,8 @@
 """Configuration for testing the example scripts."""
-from pathlib import Path
+
 import runpy
+from pathlib import Path
+
 import pytest
 
 

examples/example_experimental_data.py

@@ -2,5 +2,3 @@
 Experimental Data denoising
 ===========================
 """
-
-

pyproject.toml

@@ -38,7 +38,7 @@ doc = [
   "sphinx",
 ]
 
-dev = ["black", "isort", "ruff"]
+dev = ["black", "ruff"]
 
 [project.scripts]
 patch-denoise = "patch_denoise.bindings.cli:main"
@@ -68,14 +68,16 @@ src = ["src", "tests"]
 [tool.ruff.lint]
 ignore = ["B905"]
 exclude = ["examples/", "tests/"]
-select = ["E", "F", "B", "Q", "UP", "D"]
+select = ["E", "F", "B", "Q", "UP", "D", "I"]
+
+[tool.ruff.lint.per-file-ignores]
+"**/{tests}/*" = ["D100", "D103", "D104", "D205", "F841", "E501", "E402", "F401"]
+"**/{examples}/*" = ["D400", "D205", "E501"]
+
 
 [tool.ruff.lint.pydocstyle]
 convention="numpy"
 
-[tool.isort]
-profile="black"
-
 [tool.pytest.ini_options]
 minversion = "6.0"
 addopts = [

src/patch_denoise/__init__.py

@@ -1,13 +1,13 @@
 """Collection of patch-based denoising methods."""
+
 from patch_denoise.denoise import (
-    mp_pca,
+    adaptive_thresholding,
     hybrid_pca,
+    mp_pca,
+    nordic,
     optimal_thresholding,
-    adaptive_thresholding,
     raw_svt,
-    nordic,
 )
-
 from patch_denoise.space_time.lowrank import (
     AdaptiveDenoiser,
     HybridPCADenoiser,
@@ -39,9 +39,10 @@
 except ImportError:
     # -- Source mode --
     # use setuptools_scm to get the current version from src using git
-    from setuptools_scm import get_version as _gv
     from os import path as _path
 
+    from setuptools_scm import get_version as _gv
+
     try:
         __version__ = _gv(_path.join(_path.dirname(__file__), _path.pardir))
     except LookupError:

src/patch_denoise/_docs.py

@@ -10,7 +10,6 @@
 import inspect
 from string import Template
 
-
 docdict = dict(
     patch_config="""
 patch_shape: tuple

src/patch_denoise/bindings/cli.py

@@ -8,16 +8,16 @@
 
 import numpy as np
 
+from patch_denoise import __version__
+
 from .utils import (
     DENOISER_MAP,
     DenoiseParameters,
     compute_mask,
     load_as_array,
-    save_array,
     load_complex_nifti,
+    save_array,
 )
-from patch_denoise import __version__
-
 
 DENOISER_NAMES = ", ".join(d for d in DENOISER_MAP if d)
 

src/patch_denoise/bindings/nipype.py

@@ -14,8 +14,8 @@
 )
 from nipype.utils.filemanip import split_filename
 
-from .utils import DENOISER_MAP, DenoiseParameters
 from ..space_time.utils import estimate_noise
+from .utils import DENOISER_MAP, DenoiseParameters
 
 
 class PatchDenoiseInputSpec(BaseInterfaceInputSpec):

src/patch_denoise/bindings/utils.py

@@ -8,15 +8,14 @@
 import numpy as np
 
 from patch_denoise.denoise import (
+    adaptive_thresholding,
     hybrid_pca,
     mp_pca,
     nordic,
     optimal_thresholding,
     raw_svt,
-    adaptive_thresholding,
 )
 
-
 DENOISER_MAP = {
     None: None,
     "mp-pca": mp_pca,

src/patch_denoise/denoise.py

@@ -1,4 +1,5 @@
 """Provides a functional entry point for denoising methods."""
+
 from ._docs import fill_doc
 from .space_time.lowrank import (
     AdaptiveDenoiser,

src/patch_denoise/simulation/noise.py

@@ -1,4 +1,5 @@
 """Functions to add different source of temporal noise to data."""
+
 import numpy as np
 from numpy.random import default_rng
 

src/patch_denoise/space_time/__init__.py

@@ -1,4 +1,5 @@
 """Denoising Operator working on space-time dimension."""
+
 from .base import BaseSpaceTimeDenoiser
 from .lowrank import (
     HybridPCADenoiser,

src/patch_denoise/space_time/base.py

@@ -53,17 +53,21 @@ def __init__(
 
         # Calculate the shape and strides of the sliding view
         grid_shape = tuple(
-            ((self._arr.shape[i] - self._ps[i]) // step[i] + 1)
-            if self._ps[i] < self._arr.shape[i]
-            else 1
+            (
+                ((self._arr.shape[i] - self._ps[i]) // step[i] + 1)
+                if self._ps[i] < self._arr.shape[i]
+                else 1
+            )
             for i in range(dimensions)
         )
         shape = grid_shape + tuple(self._ps)
         strides = (
             tuple(
-                self._arr.strides[i] * step[i]
-                if self._ps[i] < self._arr.shape[i]
-                else 0
+                (
+                    self._arr.strides[i] * step[i]
+                    if self._ps[i] < self._arr.shape[i]
+                    else 0
+                )
                 for i in range(dimensions)
             )
             + self._arr.strides