diff --git a/.gitignore b/.gitignore
index 2b67e22..d06d632 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,7 +4,6 @@
 !.github
 !.gitlab-ci.yml
 !.readthedocs.yaml
-!.flake8
 
 # Byte / compiled / optimized
 *.py[cod]
diff --git a/pyproject.toml b/pyproject.toml
index 8d3b473..5682476 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -30,8 +30,14 @@ Issues = "https://github.com/ewoks-kit/ewoksgalaxy/issues"
 Changelog = "https://github.com/ewoks-kit/ewoksgalaxy/blob/main/CHANGELOG.md"
 
 [project.optional-dependencies]
-test = ["pytest >=7", "ewoks"]
-dev = ["ewoksgalaxy[test]", "ruff"]
+test = [
+    "pytest >=7",
+    "ewoks"
+]
+dev = [
+    "ewoksgalaxy[test]",
+    "ruff>=0.16.0"
+]
 doc = [
     "ewoksgalaxy[test]",
     "sphinx >=4.5",
@@ -56,15 +62,24 @@ namespaces = false
 omit = ["*/tests/*"]
 
 [tool.ruff.lint]
-select = ["E", "F", "I", "S"]
-ignore = ["E203", "E501", "E701"]
+select = [
+    "E", # pycodestyle errors
+    "F", # pyflakes
+    "I", # isort
+    "S", # flake8-bandit
+]
+ignore = [
+    "E501", # line too long
+]
 
 [tool.ruff.lint.per-file-ignores]
-# Ignore `S101` (assert used violations) in all test files
-"*/test_*.py" = ["S101", "S603"]
+"*/test_*.py" = [
+    "S101"  # allow asserts
+]
 
 [tool.ruff.lint.isort]
 force-single-line = true
+known-first-party = ["ewoksgalaxy"]
 
 [project.entry-points."ewoks.engines"]
 "gxwf" = "ewoksgalaxy.engine:GalaxyWorkflowEngine"
diff --git a/src/ewoksgalaxy/tests/test_engine.py b/src/ewoksgalaxy/tests/test_engine.py
index bc35f28..c61cb08 100644
--- a/src/ewoksgalaxy/tests/test_engine.py
+++ b/src/ewoksgalaxy/tests/test_engine.py
@@ -10,7 +10,7 @@ def test_convert(ewoks_workflow: dict, tmpdir: Path):
         json.dump(ewoks_workflow, f)
 
     output_path = tmpdir / "workflow.yaml"
-    subprocess.run(
+    subprocess.run(  # noqa: S603
         [
             sys.executable,
             "-m",
@@ -25,7 +25,7 @@ def test_convert(ewoks_workflow: dict, tmpdir: Path):
     )
     assert output_path.exists()
 
-    subprocess.run(
+    subprocess.run(  # noqa: S603
         [sys.executable, "-m", "gxformat2.lint", str(output_path)],
         check=True,
     )