Merge pull request #355 from bgilbert/prek

pre-commit: switch to Ruff and prek

Author: bgilbert

.github/maintainer/README.md

@@ -3,4 +3,4 @@
 ## Maintainer issue templates
 
 - [Release checklist](https://github.com/openslide/openslide-python/issues/new?title=Release+X.Y.Z&body=%23+OpenSlide+Python+release+process%0A%0A-+%5B+%5D+Update+%60CHANGELOG.md%60+and+version+in+%60openslide%2F_version.py%60%0A-+%5B+%5D+Create+and+push+signed+tag%0A-+%5B+%5D+Find+the+%5Bworkflow+run%5D%28https%3A%2F%2Fgithub.com%2Fopenslide%2Fopenslide-python%2Factions%2Fworkflows%2Fpython.yml%29+for+the+tag%0A++-+%5B+%5D+Once+the+build+finishes%2C+approve+deployment+to+PyPI%0A++-+%5B+%5D+Download+the+docs+artifact%0A-+%5B+%5D+Verify+that+the+workflow+created+a+%5BPyPI+release%5D%28https%3A%2F%2Fpypi.org%2Fp%2Fopenslide-python%29+with+a+description%2C+source+tarball%2C+and+wheels%0A-+%5B+%5D+Verify+that+the+workflow+created+a+%5BGitHub+release%5D%28https%3A%2F%2Fgithub.com%2Fopenslide%2Fopenslide-python%2Freleases%29+with+release+notes%2C+source+tarballs%2C+and+wheels%0A-+%5B+%5D+%60cd%60+into+website+checkout%3B+%60rm+-r+api%2Fpython+%26%26+unzip+%2Fpath%2Fto%2Fdownloaded%2Fopenslide-python-docs.zip+%26%26+mv+openslide-python-docs-%2A+api%2Fpython%60%0A-+%5B+%5D+Update+website%3A+%60_data%2Freleases.yaml%60%2C+%60_includes%2Fnews.md%60%0A-+%5B+%5D+Start+a+%5BCI+build%5D%28https%3A%2F%2Fgithub.com%2Fopenslide%2Fopenslide.github.io%2Factions%2Fworkflows%2Fretile.yml%29+of+the+demo+site%0A-+%5B+%5D+Update+Ubuntu+PPA%0A-+%5B+%5D+Update+Fedora+and+possibly+EPEL+packages%0A-+%5B+%5D+Check+that+%5BCopr+package%5D%28https%3A%2F%2Fcopr.fedorainfracloud.org%2Fcoprs%2Fg%2Fopenslide%2Fopenslide%2Fbuilds%2F%29+built+successfully%0A-+%5B+%5D+Send+mail+to+-announce+and+-users%0A-+%5B+%5D+Post+to+%5Bforum.image.sc%5D%28https%3A%2F%2Fforum.image.sc%2Fc%2Fannouncements%2F10%29%0A-+%5B+%5D+Update+MacPorts+package&labels=release)
-- [Update checklist for a Python minor release](https://github.com/openslide/openslide-python/issues/new?title=Add+Python+X.Y&body=%23+Adding+a+new+Python+release%0A%0A-+Update+Git+main%0A++-+%5B+%5D+%60git+checkout+main%60%0A++-+%5B+%5D+In+%60pyproject.toml%60%2C+add+classifier+for+new+Python+version+and+update+%60tool.black.target-version%60%0A++-+%5B+%5D+In+%60.github%2Fworkflows%2Fpython.yml%60%2C+update+hardcoded+Python+versions+and+add+new+version+to+lists%0A++-+%5B+%5D+Commit+and+open+a+PR%0A++-+%5B+%5D+Merge+the+PR+when+CI+passes%0A++-+%5B+%5D+Add+new+Python+jobs+to+%5Bbranch+protection+required+checks%5D%28https%3A%2F%2Fgithub.com%2Fopenslide%2Fopenslide-python%2Fsettings%2Fbranches%29%0A-+%5B+%5D+Update+MacPorts+package%0A-+%5B+%5D+Update+website%3A+Python+3+versions+in+%60download%2Findex.md%60&labels=release)
+- [Update checklist for a Python minor release](https://github.com/openslide/openslide-python/issues/new?title=Add+Python+X.Y&body=%23+Adding+a+new+Python+release%0A%0A-+Update+Git+main%0A++-+%5B+%5D+%60git+checkout+main%60%0A++-+%5B+%5D+In+%60pyproject.toml%60%2C+add+classifier+for+new+Python+version%0A++-+%5B+%5D+In+%60.github%2Fworkflows%2Fpython.yml%60%2C+update+hardcoded+Python+versions+and+add+new+version+to+lists%0A++-+%5B+%5D+Commit+and+open+a+PR%0A++-+%5B+%5D+Merge+the+PR+when+CI+passes%0A++-+%5B+%5D+Add+new+Python+jobs+to+%5Bbranch+protection+required+checks%5D%28https%3A%2F%2Fgithub.com%2Fopenslide%2Fopenslide-python%2Fsettings%2Fbranches%29%0A-+%5B+%5D+Update+MacPorts+package%0A-+%5B+%5D+Update+website%3A+Python+3+versions+in+%60download%2Findex.md%60&labels=release)

.github/maintainer/mkmaintainer.py

@@ -23,5 +23,5 @@
                 'labels': ','.join(info.get('labels', [])),
             }
         )
-        url = f"https://github.com/{info['repo']}/issues/new?{args}"
-        fh.write(f"- [{info['link-text']}]({url})\n")
+        url = f'https://github.com/{info["repo"]}/issues/new?{args}'
+        fh.write(f'- [{info["link-text"]}]({url})\n')

.github/maintainer/update-python.md

@@ -9,7 +9,7 @@ labels: [release]
 
 - Update Git main
   - [ ] `git checkout main`
-  - [ ] In `pyproject.toml`, add classifier for new Python version and update `tool.black.target-version`
+  - [ ] In `pyproject.toml`, add classifier for new Python version
   - [ ] In `.github/workflows/python.yml`, update hardcoded Python versions and add new version to lists
   - [ ] Commit and open a PR
   - [ ] Merge the PR when CI passes

.github/workflows/python.yml

@@ -28,14 +28,14 @@ jobs:
       with:
         python-version: '3.14'
     - name: Install dependencies
-      run: python -m pip install pre-commit
+      run: python -m pip install prek uv
     - name: Cache pre-commit environments
       uses: actions/cache@v5
       with:
-        path: ~/.cache/pre-commit
-        key: pre-commit|${{ env.pythonLocation }}|${{ hashFiles('.pre-commit-config.yaml') }}
+        path: ~/.cache/prek
+        key: prek|${{ env.pythonLocation }}|${{ hashFiles('.pre-commit-config.yaml') }}
     - name: Run pre-commit hooks
-      run: pre-commit run -a --show-diff-on-failure --color=always
+      run: prek run -a --show-diff-on-failure --color=always
     - name: Define artifact paths
       id: paths
       run: |

.pre-commit-config.yaml

@@ -1,3 +1,8 @@
+# priorities:
+# 0    - read-only
+# 1000 - mutually non-conflicting fixers
+# none - other fixers
+
 # exclude vendored files
 exclude: '^(COPYING\.LESSER|examples/deepzoom/static/.*\.js)$'
 
@@ -6,58 +11,34 @@ repos:
     rev: v6.0.0
     hooks:
       - id: check-added-large-files
+        priority: 0
       - id: check-merge-conflict
+        priority: 0
       - id: check-toml
+        priority: 0
       - id: check-vcs-permalinks
+        priority: 0
       - id: check-yaml
+        priority: 0
       - id: end-of-file-fixer
       - id: fix-byte-order-marker
       - id: mixed-line-ending
       - id: trailing-whitespace
 
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.21.2
-    hooks:
-      - id: pyupgrade
-        name: Modernize python code
-        args: ["--py310-plus"]
-
-  - repo: https://github.com/PyCQA/isort
-    rev: 8.0.1
-    hooks:
-      - id: isort
-        name: Reorder python imports with isort
-
-  - repo: https://github.com/psf/black
-    rev: 26.3.1
-    hooks:
-      - id: black
-        name: Format python code with black
-
-  - repo: https://github.com/asottile/blacken-docs
-    rev: 1.20.0
-    hooks:
-      - id: blacken-docs
-        name: Format python code in documentation
-
-  - repo: https://github.com/asottile/yesqa
-    rev: v1.5.0
-    hooks:
-      - id: yesqa
-        additional_dependencies: [flake8-bugbear, Flake8-pyproject]
-
-  - repo: https://github.com/PyCQA/flake8
-    rev: 7.3.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.10
     hooks:
-      - id: flake8
-        name: Lint python code with flake8
-        additional_dependencies: [flake8-bugbear, Flake8-pyproject]
+      - id: ruff-check
+        types_or: [python, pyi, pyproject]
+        args: [--fix]
+      - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.20.0
     hooks:
       - id: mypy
         name: Check Python types
+        priority: 0
         # Pillow is ignored in dependabot.yml
         additional_dependencies: [flask, openslide-bin, pillow >= 12.1.0, types-PyYAML, types-setuptools]
 
@@ -66,32 +47,38 @@ repos:
     hooks:
       - id: rstcheck
         name: Validate reStructuredText syntax
+        priority: 0
         additional_dependencies: [sphinx, toml]
 
   - repo: https://github.com/codespell-project/codespell
     rev: v2.4.2
     hooks:
       - id: codespell
         name: Check spelling with codespell
+        priority: 0
         additional_dependencies:
           - tomli  # Python < 3.11
 
   - repo: meta
     hooks:
       - id: check-hooks-apply
+        priority: 0
       - id: check-useless-excludes
+        priority: 0
 
   - repo: local
     hooks:
       - id: mkmaintainer
         name: Sync maintainer issue templates
+        priority: 1000
         entry: .github/maintainer/mkmaintainer.py
         files: .github/maintainer/
         language: python
         additional_dependencies: [PyYAML]
 
       - id: annotations
         name: Require "from __future__ import annotations"
+        priority: 0
         language: pygrep
         types: [python]
         # exclude config-like files

doc/jekyll_fix.py

@@ -38,7 +38,7 @@
 }
 FILES = {
     # Added in Sphinx 5.0.0, scheduled to be removed in Sphinx 6
-    'static/_sphinx_javascript_frameworks_compat.js': 'static/sphinx_javascript_frameworks_compat.js',  # noqa: E501
+    'static/_sphinx_javascript_frameworks_compat.js': 'static/sphinx_javascript_frameworks_compat.js',
 }
 REWRITE_EXTENSIONS = {'.html', '.js'}
 

examples/deepzoom/deepzoom_multiserver.py

@@ -31,8 +31,8 @@
 from typing import TYPE_CHECKING, Any, Literal
 import zlib
 
-from PIL import Image, ImageCms
 from flask import Flask, Response, abort, make_response, render_template, url_for
+from PIL import Image, ImageCms
 
 if TYPE_CHECKING:
     # Python 3.10+
@@ -41,7 +41,7 @@
 if os.name == 'nt':
     _dll_path = os.getenv('OPENSLIDE_PATH')
     if _dll_path is not None:
-        with os.add_dll_directory(_dll_path):  # type: ignore[attr-defined,unused-ignore]  # noqa: E501
+        with os.add_dll_directory(_dll_path):  # type: ignore[attr-defined,unused-ignore]
             import openslide
     else:
         import openslide
@@ -192,7 +192,7 @@ def tile(path: str, level: int, col: int, row: int, format: str) -> Response:
             icc_profile=tile.info.get('icc_profile'),
         )
         resp = make_response(buf.getvalue())
-        resp.mimetype = 'image/%s' % format
+        resp.mimetype = f'image/{format}'
         return resp
 
     return app

examples/deepzoom/deepzoom_server.py

@@ -31,8 +31,8 @@
 from unicodedata import normalize
 import zlib
 
-from PIL import Image, ImageCms
 from flask import Flask, Response, abort, make_response, render_template, url_for
+from PIL import Image, ImageCms
 
 if TYPE_CHECKING:
     # Python 3.10+
@@ -41,7 +41,7 @@
 if os.name == 'nt':
     _dll_path = os.getenv('OPENSLIDE_PATH')
     if _dll_path is not None:
-        with os.add_dll_directory(_dll_path):  # type: ignore[attr-defined,unused-ignore]  # noqa: E501
+        with os.add_dll_directory(_dll_path):  # type: ignore[attr-defined,unused-ignore]
             import openslide
     else:
         import openslide
@@ -193,7 +193,7 @@ def tile(slug: str, level: int, col: int, row: int, format: str) -> Response:
             icc_profile=tile.info.get('icc_profile'),
         )
         resp = make_response(buf.getvalue())
-        resp.mimetype = 'image/%s' % format
+        resp.mimetype = f'image/{format}'
         return resp
 
     return app

examples/deepzoom/deepzoom_tile.py

@@ -47,7 +47,7 @@
 if os.name == 'nt':
     _dll_path = os.getenv('OPENSLIDE_PATH')
     if _dll_path is not None:
-        with os.add_dll_directory(_dll_path):  # type: ignore[attr-defined,unused-ignore]  # noqa: E501
+        with os.add_dll_directory(_dll_path):  # type: ignore[attr-defined,unused-ignore]
             import openslide
     else:
         import openslide
@@ -231,8 +231,7 @@ def _tile_done(self) -> None:
         count, total = self._processed, self._dz.tile_count
         if count % 100 == 0 or count == total:
             print(
-                "Tiling %s: wrote %d/%d tiles"
-                % (self._associated or 'slide', count, total),
+                f'Tiling {self._associated or "slide"}: wrote {count}/{total} tiles',
                 end='\r',
                 file=sys.stderr,
             )
@@ -320,7 +319,7 @@ def _url_for(self, associated: str | None) -> str:
             base = VIEWER_SLIDE_NAME
         else:
             base = self._slugify(associated)
-        return '%s.dzi' % base
+        return f'{base}.dzi'
 
     def _write_html(self) -> None:
         import jinja2

openslide/__init__.py

@@ -35,16 +35,12 @@
 from openslide import lowlevel
 
 # Re-exports for the benefit of library users
-from openslide._version import (  # noqa: F401  module-imported-but-unused
-    __version__ as __version__,
-)
+from openslide._version import __version__ as __version__
+from openslide.lowlevel import OpenSlideError as OpenSlideError
 from openslide.lowlevel import (
     OpenSlideUnsupportedFormatError as OpenSlideUnsupportedFormatError,
 )
-from openslide.lowlevel import (  # noqa: F401  module-imported-but-unused
-    OpenSlideVersionError as OpenSlideVersionError,
-)
-from openslide.lowlevel import OpenSlideError as OpenSlideError
+from openslide.lowlevel import OpenSlideVersionError as OpenSlideVersionError
 
 __library_version__ = lowlevel.get_version()
 
@@ -173,7 +169,9 @@ def get_thumbnail(self, size: tuple[int, int]) -> Image.Image:
         """Return a PIL.Image containing an RGB thumbnail of the image.
 
         size:     the maximum size of the thumbnail."""
-        downsample = max(dim / thumb for dim, thumb in zip(self.dimensions, size))
+        downsample = max(
+            dim / thumb for dim, thumb in zip(self.dimensions, size, strict=True)
+        )
         level = self.get_best_level_for_downsample(downsample)
         tile = self.read_region((0, 0), level, self.level_dimensions[level])
         # Apply on solid background
@@ -457,27 +455,32 @@ def read_region(
         if self._image is None:
             raise ValueError('Cannot read from a closed slide')
         if level != 0:
-            raise OpenSlideError("Invalid level")
+            raise OpenSlideError('Invalid level')
         if ['fail' for s in size if s < 0]:
-            raise OpenSlideError(f"Size {size} must be non-negative")
+            raise OpenSlideError(f'Size {size} must be non-negative')
         # Any corner of the requested region may be outside the bounds of
         # the image.  Create a transparent tile of the correct size and
         # paste the valid part of the region into the correct location.
         image_topleft = [
-            max(0, min(l, limit - 1)) for l, limit in zip(location, self._image.size)
+            max(0, min(l, limit - 1))
+            for l, limit in zip(location, self._image.size, strict=True)
         ]
         image_bottomright = [
             max(0, min(l + s - 1, limit - 1))
-            for l, s, limit in zip(location, size, self._image.size)
+            for l, s, limit in zip(location, size, self._image.size, strict=True)
         ]
-        tile = Image.new("RGBA", size, (0,) * 4)
+        tile = Image.new('RGBA', size, (0,) * 4)
         if not [
-            'fail' for tl, br in zip(image_topleft, image_bottomright) if br - tl < 0
+            'fail'
+            for tl, br in zip(image_topleft, image_bottomright, strict=True)
+            if br - tl < 0
         ]:  # "< 0" not a typo
             # Crop size is greater than zero in both dimensions.
             # PIL thinks the bottom right is the first *excluded* pixel
             crop_box = tuple(image_topleft + [d + 1 for d in image_bottomright])
-            tile_offset = tuple(il - l for il, l in zip(image_topleft, location))
+            tile_offset = tuple(
+                il - l for il, l in zip(image_topleft, location, strict=True)
+            )
             assert len(crop_box) == 4 and len(tile_offset) == 2
             crop = self._image.crop(crop_box)
             tile.paste(crop, tile_offset)
@@ -500,12 +503,12 @@ def open_slide(filename: lowlevel.Filename) -> OpenSlide | ImageSlide:
 if __name__ == '__main__':
     import sys
 
-    print("OpenSlide vendor:", OpenSlide.detect_format(sys.argv[1]))
-    print("PIL format:", ImageSlide.detect_format(sys.argv[1]))
+    print('OpenSlide vendor:', OpenSlide.detect_format(sys.argv[1]))
+    print('PIL format:', ImageSlide.detect_format(sys.argv[1]))
     with open_slide(sys.argv[1]) as _slide:
-        print("Dimensions:", _slide.dimensions)
-        print("Levels:", _slide.level_count)
-        print("Level dimensions:", _slide.level_dimensions)
-        print("Level downsamples:", _slide.level_downsamples)
-        print("Properties:", _slide.properties)
-        print("Associated images:", _slide.associated_images)
+        print('Dimensions:', _slide.dimensions)
+        print('Levels:', _slide.level_count)
+        print('Level dimensions:', _slide.level_dimensions)
+        print('Level downsamples:', _slide.level_downsamples)
+        print('Properties:', _slide.properties)
+        print('Associated images:', _slide.associated_images)