Apply linting to entire codebase & add CI workflow to check linting

.github/workflows/format.yml

@@ -0,0 +1,61 @@
+name: pre-commit (PR only on changed files)
+
+on:
+  pull_request:
+    types: [opened, synchronize, reopened]
+
+jobs:
+  detect_changes:
+    runs-on: ubuntu-latest
+    outputs:
+      changed: ${{ steps.changed_files.outputs.changed }}
+
+    steps:
+      - name: Checkout full history
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Detect changed files
+        id: changed_files
+        run: |
+          git fetch origin ${{ github.base_ref }}
+          CHANGED_FILES=$(git diff --name-only origin/${{ github.base_ref }}...HEAD)
+
+          {
+            echo "changed<<EOF"
+            echo "$CHANGED_FILES"
+            echo "EOF"
+          } >> "$GITHUB_OUTPUT"
+
+      - name: Show changed files
+        run: |
+          echo "Changed files:"
+          echo "${{ steps.changed_files.outputs.changed }}"
+
+  precommit:
+    needs: detect_changes
+    runs-on: ubuntu-latest
+    if: ${{ needs.detect_changes.outputs.changed != '' }}
+
+    steps:
+      - name: Checkout PR branch
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          ref: ${{ github.head_ref }}
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install pre-commit
+        run: pip install pre-commit
+
+      - name: Run pre-commit (CI check-only stage) on changed files
+        env:
+          CHANGED_FILES: ${{ needs.detect_changes.outputs.changed }}
+        run: |
+          mapfile -t files <<< "$CHANGED_FILES"
+          pre-commit run --hook-stage manual --files "${files[@]}" --show-diff-on-failure

.pre-commit-config.yaml

@@ -2,21 +2,28 @@ repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:
-      - id: check-docstring-first
+      - id: check-added-large-files
+      - id: check-yaml
+      - id: check-toml
       - id: end-of-file-fixer
+      - id: name-tests-test
       - id: trailing-whitespace
-  - repo: https://github.com/asottile/setup-cfg-fmt
-    rev: v3.2.0
-    hooks:
-      - id: setup-cfg-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.10
+    rev: v0.15.4
     hooks:
       # Run the formatter.
       - id: ruff-format
       # Run the linter.
       - id: ruff-check
         args: [--fix,--unsafe-fixes]
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: v2.16.2
+    hooks:
+      - id: pyproject-fmt
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.25
+    hooks:
+      - id: validate-pyproject
   - repo: https://github.com/tlambert03/napari-plugin-checks
     rev: v0.3.0
     hooks:

pyproject.toml

@@ -1,19 +1,99 @@
 [build-system]
-requires = ["setuptools", "wheel", "setuptools_scm"]
 build-backend = "setuptools.build_meta"
+requires = [ "setuptools>=77", "setuptools-scm[toml]>=7", "wheel" ]
 
-[tool.ruff]
-lint.select = ["E", "F", "B", "I", "UP"]
-lint.ignore = ["E741"]
-target-version = "py310"
-fix = true
-line-length = 120
+[project]
+name = "napari-deeplabcut"
+description = "napari + DeepLabCut annotation tool"
+readme = { file = "README.md", content-type = "text/markdown" }
+license = "LGPL-3.0-only"
+license-files = [ "LICENSE" ]
+requires-python = ">=3.10"
+classifiers = [
+  "Development Status :: 2 - Pre-Alpha",
+  "Framework :: napari",
+  "Intended Audience :: Developers",
+  "Operating System :: OS Independent",
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Topic :: Scientific/Engineering :: Artificial Intelligence",
+  "Topic :: Scientific/Engineering :: Image Processing",
+  "Topic :: Scientific/Engineering :: Visualization",
+]
+# Using setuptools-scm -> version is derived from git tags
+dynamic = [ "version" ]
+dependencies = [
+  "dask-image",
+  "matplotlib>=3.3",
+  "napari==0.6.6",
+  "natsort",
+  "numpy>=1.18.5,<2",
+  "opencv-python-headless",
+  "pandas",
+  "pyside6>=6.4.2",
+  "pyyaml",
+  "qtpy>=2.4",
+  "scikit-image",
+  "scipy",
+  "tables",
+]
+[[project.authors]]
+name = "Team DeepLabCut, led by Jessy Lauer"
+email = "admin@deeplabcut.org"
+[project.entry-points."napari.manifest"]
+napari-deeplabcut = "napari_deeplabcut:napari.yaml"
+[project.optional-dependencies]
+testing = [
+  "pillow",
+  "pytest",
+  "pytest-cov",
+  "pytest-qt",
+  "tox",
+]
+[project.urls]
+"Bug Tracker" = "https://github.com/DeepLabCut/napari-deeplabcut/issues"
+Documentation = "https://github.com/DeepLabCut/napari-deeplabcut#README.md"
+"Source Code" = "https://github.com/DeepLabCut/napari-deeplabcut"
+"User Support" = "https://github.com/DeepLabCut/napari-deeplabcut/issues"
 
-[tool.uv]
-package = true
+# ----------------------------
+# setuptools configuration
+# ----------------------------
+[tool.setuptools]
+include-package-data = true
+[tool.setuptools.package-data]
+napari_deeplabcut = [ "napari.yaml" ]
+[tool.setuptools.package-dir]
+"" = "src"
+[tool.setuptools.packages.find]
+where = [ "src" ]
 
 [tool.setuptools_scm]
 write_to = "src/napari_deeplabcut/_version.py"
 
+[tool.uv]
+package = true
+
+# ----------------------------
+# existing tool configuration
+# ----------------------------
+[tool.ruff]
+target-version = "py310"
+line-length = 120
+fix = true
+[tool.ruff.lint]
+select = [ "E", "F", "B", "I", "UP" ]
+ignore = [ "E741" ]
+[tool.ruff.lint.pydocstyle]
+convention = "google"
+
+[tool.pyproject-fmt]
+max_supported_python = "3.12"
+generate_python_version_classifiers = true
+# Avoid collapsing tables to field.key = value format (less readable)
+table_format = "long"
+
 [tool.pytest.ini_options]
 qt_api = "pyside6"

src/napari_deeplabcut/__init__.py

@@ -40,7 +40,8 @@
 # FIXME: Circumvent the need to access window.qt_viewer
 warnings.filterwarnings("ignore", category=FutureWarning)
 
-import re
+import re  # noqa: E402
+
 # Suppress RuntimeWarnings caused by NaN values in dataframe
 # (encountered during model-predicted labels refinement stage)
 warnings.filterwarnings(
@@ -49,6 +50,7 @@
     message=re.escape("invalid value encountered in cast"),
 )
 
+
 class VispyWarningFilter(logging.Filter):
     def filter(self, record: logging.LogRecord) -> bool:
         ignore_messages = (

src/napari_deeplabcut/_tests/test_reader.py

@@ -374,7 +374,7 @@ def test_lazy_imread_grayscale_and_rgba(tmp_path):
     gray = (np.random.rand(10, 10) * 255).astype(np.uint8)
     rgba = (np.random.rand(10, 10, 4) * 255).astype(np.uint8)
     p1, p2 = tmp_path / "g.png", tmp_path / "r.png"
-    cv2.imwrite(str(p1), gray)  # cv2 writes grayscale as-is; color images are written as BGR 
+    cv2.imwrite(str(p1), gray)  # cv2 writes grayscale as-is; color images are written as BGR
     cv2.imwrite(str(p2), cv2.cvtColor(rgba, cv2.COLOR_RGBA2BGRA))
     res = _reader._lazy_imread([p1, p2], use_dask=False, stack=False)
     assert all(img.shape[-1] == 3 for img in res)

src/napari_deeplabcut/assets/superanimal_quadruped.json

@@ -155,4 +155,4 @@
         707.5655627887081,
         375.0788206592507
     ]
-}
+}

src/napari_deeplabcut/assets/superanimal_topviewmouse.json

@@ -107,4 +107,4 @@
         117.41024099594408,
         252.35239163633167
     ]
-}
+}

src/napari_deeplabcut/styles/dark.mplstyle

@@ -9,4 +9,4 @@ axes.labelcolor     : f0f1f2
 axes.facecolor      : none
 axes.edgecolor      : 414851
 xtick.color         : f0f1f2
-ytick.color         : f0f1f2
+ytick.color         : f0f1f2

src/napari_deeplabcut/styles/light.mplstyle

@@ -9,4 +9,4 @@ axes.labelcolor     : 3b3a39
 axes.facecolor      : none
 axes.edgecolor      : d6d0ce
 xtick.color         : 3b3a39
-ytick.color         : 3b3a39
+ytick.color         : 3b3a39