build: migrate to uv, add ruff/ty, format all files

.github/workflows/python-app.yml

@@ -19,22 +19,19 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
     - name: Set up Python 3.12
-      uses: actions/setup-python@v3
-      with:
-        python-version: "3.12"
+      run: uv python install 3.12
     - name: Install dependencies
+      run: uv sync
+    - name: Lint with ruff
       run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest
-        pip install .
-        pip install -r requirements-pytest.txt
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        uv run ruff check .
+        uv run ruff format --check .
+    - name: Type check with ty
+      continue-on-error: true
+      run: uv run ty check
     - name: Test with pytest
       run: |
-        pytest
+        uv run pytest

.gitignore

@@ -3,6 +3,8 @@ __pycache__/
 *.py[cod]
 *$py.class
 
+AGENTS.md
+
 # C extensions
 *.so
 
@@ -143,6 +145,9 @@ venv.bak/
 .dmypy.json
 dmypy.json
 
+# ruff
+.ruff_cache/
+
 # Pyre type checker
 .pyre/
 
@@ -165,6 +170,9 @@ cython_debug/
 # Nextflow files
 .nextflow/
 *.nextflow.log*
+
+# Standalone tools (separate git repos)
+tools/
 workflows/work/
 *work/
 
@@ -184,3 +192,8 @@ workflows/work/
 
 # Temp code file
 draft.py
+
+# Exculde subject data folders (symlinks)
+sub-*
+
+.python-version

.pre-commit-config.yaml

@@ -0,0 +1,19 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.8
+    hooks:
+      - id: ruff-format
+      - id: ruff
+        args: [--fix]
+  - repo: local
+    hooks:
+      - id: ty
+        name: ty (type check)
+        entry: bash -c 'uv run --frozen ty check || true'
+        language: system
+        types: [python]
+        files: ^linumpy/
+        pass_filenames: false
+        # Non-blocking (advisory) until the existing error baseline is resolved.
+        # Switch entry to just "uv run ty check" once errors reach zero.
+        verbose: true

Dockerfile

@@ -1,5 +1,7 @@
 FROM python:3.12
 
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/
+
 WORKDIR /linumpy/
 
 ENV PYTHONDONTWRITEBYTECODE=1
@@ -14,11 +16,8 @@ RUN apt-get update && apt-get install -y \
     zip \
     && rm -rf /var/lib/apt/lists/*
 
-# Upgrade pip, setuptools and wheel
-RUN pip install --upgrade pip setuptools wheel build
-
-# Install with verbose output
+# Install with uv
 COPY linumpy ./linumpy
 COPY scripts ./scripts
-COPY pyproject.toml requirements.txt README.md setup.py ./
-RUN pip install --no-cache-dir -v -e .
+COPY pyproject.toml uv.lock README.md .python-version ./
+RUN uv sync --frozen --no-dev

linumpy/__init__.py

@@ -1,19 +1,19 @@
 # Configure thread limits FIRST, before any numerical libraries are imported
-import os as _os
-
 from linumpy._thread_config import (
-    configure_thread_limits,
     apply_threadpool_limits,
     configure_all_libraries,
     configure_sitk,
+    configure_thread_limits,
 )
 
+import os as _os
+
 
 def get_home():
-    """ Set a user-writeable file-system location to put files. """
-    if 'LINUMPY_HOME' in _os.environ:
-        return _os.environ['LINUMPY_HOME']
-    return _os.path.join(_os.path.expanduser('~'), '.linumpy')
+    """Set a user-writeable file-system location to put files."""
+    if "LINUMPY_HOME" in _os.environ:
+        return _os.environ["LINUMPY_HOME"]
+    return _os.path.join(_os.path.expanduser("~"), ".linumpy")
 
 
 def get_root():