Switch linter from flake8 to ruff

Ruff is 10-100x faster, supports auto-fix, and replaces flake8 plus
plugins in a single tool. Translated .flake8 config to ruff.toml,
auto-fixed all existing lint errors, and made CI lint step blocking.

Author: Barthelemy-Drabczuk

.github/workflows/ci.yml

@@ -35,9 +35,8 @@ jobs:
       - name: Install dependencies
         run: pixi run install-all
 
-      - name: Flake8 (non-blocking)
-        continue-on-error: true
-        run: pixi run flake8 src/ tests/
+      - name: Ruff lint
+        run: pixi run lint
 
       - name: Pytest
         run: pixi run test

pixi.lock

@@ -14,7 +14,6 @@ morphologist = ">=0.0.29"
 disco = ">=6.0"
 pip = ">=25.3,<26"
 setuptools = ">=65.0,<81"
-flake8 = ">=7.3.0,<8"
 pytest = ">=7.0"
 pytest-cov = ">=4.0"
 pytest-mock = ">=3.10"
@@ -24,6 +23,7 @@ dracopy = ">=1.4.2"
 huggingface-hub = ">=0.20.0"
 transformers = ">=4.36.0"
 datasets = ">=2.16.0"
+ruff = ">=0.9.0"
 
 [tasks]
 # Initialize submodules
@@ -92,6 +92,11 @@ uninstall-all = """
   echo "Uninstallation of Pixi-managed dependencies complete."
 """
 
+# Linting tasks
+lint = "ruff check src/ tests/"
+lint-fix = "ruff check --fix src/ tests/"
+format = "ruff format src/ tests/"
+
 # Testing tasks
 test = "pytest tests/ -v"
 test-unit = "pytest tests/ -v -m unit"

pixi.toml

@@ -0,0 +1,8 @@
+line-length = 120
+exclude = [".pixi", "__pycache__", "external", "*.pyc"]
+
+[lint]
+extend-ignore = ["E203"]
+
+[lint.per-file-ignores]
+"__init__.py" = ["F401"]