diff --git a/.github/workflows/tox-workflow.yaml b/.github/workflows/tox-workflow.yaml
index a2ac22a4..d35b9b64 100644
--- a/.github/workflows/tox-workflow.yaml
+++ b/.github/workflows/tox-workflow.yaml
@@ -22,6 +22,8 @@ jobs:
       - name: Install Tox
         run: python -m pip install tox
       - name: Run Tox
+        env:
+          RUFF_OUTPUT_FORMAT: github
         run: |
           eval "$(/home/linuxbrew/.linuxbrew/bin/brew shellenv)"
           tox run -e ${{ matrix.tox_env }}
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 9732eee5..3406db50 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
     -   id: trailing-whitespace
         exclude: '^\.gitignore$'
@@ -26,23 +26,23 @@ repos:
     -   id: rst-directive-colons
     -   id: rst-inline-touching-normal
 -   repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.27.3
+    rev: 0.28.2
     hooks:
     -   id: check-dependabot
     -   id: check-github-workflows
     -   id: check-readthedocs
 -   repo: https://github.com/Lucas-C/pre-commit-hooks
-    rev: v1.5.4
+    rev: v1.5.5
     hooks:
     -   id: forbid-crlf
         exclude: '^\.gitignore$'
     -   id: forbid-tabs
         types: [python]
 -   repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 23.12.1
+    rev: 24.4.2
     hooks:
     -   id: black-jupyter
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.9
+    rev: v0.4.3
     hooks:
     -   id: ruff
diff --git a/pyproject.toml b/pyproject.toml
index a9a8dadc..6410bed6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -178,9 +178,12 @@ extend-exclude = [
 ]
 # Group violations by containing file.
 output-format = "grouped"
+line-length = 120
+target-version = "py39"
+
+[tool.ruff.lint]
 ignore = ["C408"]
 ignore-init-module-imports = true
-line-length = 120
 select = [
     "C4",
     "C9",
@@ -190,15 +193,14 @@ select = [
     "PT",
     "W",
 ]
-target-version = "py39"
 
-[tool.ruff.flake8-pytest-style]
+[tool.ruff.lint.flake8-pytest-style]
 parametrize-names-type = "csv"
 
-[tool.ruff.mccabe]
+[tool.ruff.lint.mccabe]
 max-complexity = 10
 
-[tool.ruff.isort]
+[tool.ruff.lint.isort]
 force-sort-within-sections = true
 known-first-party = ["sksurv"]
 
diff --git a/tox.ini b/tox.ini
index d15ec115..3a3ba749 100644
--- a/tox.ini
+++ b/tox.ini
@@ -11,8 +11,9 @@ deps =
 description = Run linters
 skip_install = true
 deps =
-    ruff~=0.1.0
+    ruff~=0.4.3
 commands = ruff check sksurv/ tests/ setup.py
+pass_env = RUFF_*
 
 # Documentation
 [testenv:docs]