Merge pull request #175 from DeepLabCut/cy/feature-refactor-2026

Plugin refactor : full version

User patch notes available [here(#195).

Author: C-Achard

.github/workflows/format.yml

@@ -12,7 +12,7 @@ jobs:
 
     steps:
       - name: Checkout full history
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
@@ -40,13 +40,13 @@ jobs:
 
     steps:
       - name: Checkout PR branch
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
           ref: ${{ github.head_ref }}
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.12"
 

.github/workflows/test_and_deploy.yml

@@ -7,13 +7,11 @@ on:
   push:
     branches:
       - main
-      - npe2
     tags:
       - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
   pull_request:
     branches:
       - main
-      - npe2
   workflow_dispatch:
     inputs:
       force_deploy:
@@ -33,10 +31,10 @@ jobs:
         python-version: ["3.10", "3.11", "3.12"]
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -69,7 +67,7 @@ jobs:
           PLATFORM: ${{ matrix.platform }}
 
       - name: Coverage
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v6
 
   deploy:
     # this will run when you have tagged a commit, starting with "v*"
@@ -78,24 +76,28 @@ jobs:
     needs: [test]
     runs-on: ubuntu-latest
     if: |
-      always() &&
-      inputs.force_deploy ||
-      (contains(github.ref, 'tags') && contains(needs.test.result, 'success'))
+      always() && (
+        (github.event_name == 'workflow_dispatch' && inputs.force_deploy) ||
+        (startsWith(github.ref, 'refs/tags/v') && needs.test.result == 'success')
+      )
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v6
         with:
           python-version: "3.x"
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install -U setuptools setuptools_scm wheel twine build
-      - name: Build and publish
+      - name: Build package
+        run: python -m build .
+      - name: Check metadata
+        run: twine check --strict dist/*
+      - name: Publish to PyPI
         env:
           TWINE_USERNAME: __token__
           TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
         run: |
           git tag
-          python -m build .
           twine upload dist/*

.gitignore

@@ -82,3 +82,6 @@ venv/
 
 # written by setuptools_scm
 **/_version.py
+
+# Package managers
+uv.lock

.pre-commit-config.yaml

@@ -1,38 +1,65 @@
+default_stages: [pre-commit]
+
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:
+      # These are safe to run in both local & CI (they don't require "fix vs check" split)
       - id: check-added-large-files
+        stages: [pre-commit, manual]
         args: ['--maxkb=1024']
       - id: check-yaml
+        stages: [pre-commit, manual]
       - id: check-toml
-      - id: end-of-file-fixer
+        stages: [pre-commit, manual]
+      - id: check-merge-conflict
+        stages: [pre-commit, manual]
       - id: name-tests-test
-        args: ['--pytest-test-first']
+        stages: [pre-commit, manual]
+        args: ["--pytest-test-first"]
+
+      # These modify files. Run locally only (pre-commit stage).
+      - id: end-of-file-fixer
+        stages: [pre-commit]
       - id: trailing-whitespace
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.4
-    hooks:
-      # Run the formatter.
-      - id: ruff-format
-      # Run the linter.
-      - id: ruff-check
-        args: [--fix,--unsafe-fixes]
+        stages: [pre-commit]
+
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.16.2
+    rev: v2.21.1
     hooks:
       - id: pyproject-fmt
+        stages: [pre-commit]    # modifies -> local only
+
   - 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
+        stages: [pre-commit, manual]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.12
     hooks:
-      - id: napari-plugin-checks
-  # https://mypy.readthedocs.io/en/stable/introduction.html
-  # you may wish to add this as well!
-  # - repo: https://github.com/pre-commit/mirrors-mypy
-  #   rev: v0.910-1
-  #   hooks:
-  #     - id: mypy
+      # --------------------------
+      # LOCAL AUTOFIX (developers)
+      # --------------------------
+      - id: ruff-check
+        name: ruff-check (fix)
+        args: [--fix, --unsafe-fixes]
+        stages: [pre-commit]
+
+      - id: ruff-format
+        name: ruff-format (write)
+        stages: [pre-commit]
+
+      # --------------------------
+      # CI CHECK-ONLY (no writes)
+      # --------------------------
+      - id: ruff-check
+        name: ruff-check (ci)
+        args: [--output-format=github]
+        stages: [manual]
+
+      - id: ruff-format
+        name: ruff-format (ci)
+        args: [--check, --diff]
+        stages: [manual]