diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index fba3dbd7a4..424a6e2dda 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -9,7 +9,7 @@ repos:
       - id: check-merge-conflict
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.22
+    rev: v0.16.0
     hooks:
       - id: ruff-check
         args: [--fix]
@@ -22,7 +22,7 @@ repos:
         args: [--mapping, '2', --sequence, '4', --offset, '2', --preserve-quotes]
 
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.5.0
+    rev: v2.5.5
     hooks:
       - id: biome-format
         types: [json]
diff --git a/documentation/source/development/debugging.md b/documentation/source/development/debugging.md
index aab5462a69..3d66db0375 100644
--- a/documentation/source/development/debugging.md
+++ b/documentation/source/development/debugging.md
@@ -8,6 +8,7 @@ breakpoint in the code, insert the following code where you want the code to bre
 
 ```python
 import pdb
+
 pdb.set_trace()
 ```
 
diff --git a/documentation/source/physics-models/plasma_beta/plasma_beta.md b/documentation/source/physics-models/plasma_beta/plasma_beta.md
index b8ffd0f58e..20e81f5a14 100644
--- a/documentation/source/physics-models/plasma_beta/plasma_beta.md
+++ b/documentation/source/physics-models/plasma_beta/plasma_beta.md
@@ -164,8 +164,6 @@ IN.DAT
 
 i_beta_norm_max = 0
 beta_norm_max = 3.0
-
-
 ```
 
 ---------
diff --git a/documentation/source/physics-models/plasma_current/plasma_current.md b/documentation/source/physics-models/plasma_current/plasma_current.md
index 1029b01d97..f7d31f95c9 100644
--- a/documentation/source/physics-models/plasma_current/plasma_current.md
+++ b/documentation/source/physics-models/plasma_current/plasma_current.md
@@ -557,8 +557,6 @@ IN.DAT
 
 i_alphaj = 0
 alphaj = 1.0
-
-
 ```
 
 -----------
diff --git a/documentation/source/physics-models/plasma_current/plasma_inductance.md b/documentation/source/physics-models/plasma_current/plasma_inductance.md
index 0d24f321ad..ea29832dd5 100644
--- a/documentation/source/physics-models/plasma_current/plasma_inductance.md
+++ b/documentation/source/physics-models/plasma_current/plasma_inductance.md
@@ -16,8 +16,6 @@ IN.DAT
 
 i_ind_plasma_internal_norm = 0
 ind_plasma_internal_norm = 1.0
-
-
 ```
 
 ----------
diff --git a/pyproject.toml b/pyproject.toml
index e4b044b744..6d716e1426 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -75,7 +75,7 @@ docs = [
   "mkdocs-gen-files",
   "mkdocs-literate-nav",
 ]
-lint = ["pre-commit>=2.16.0", "ruff==0.15.22", "ty"]
+lint = ["pre-commit>=2.16.0", "ruff==0.16.0", "ty"]
 all = ["process[test,docs,lint,examples,plotly]", "toml"]
 
 [project.scripts]
@@ -111,7 +111,7 @@ deploy = "mkdocs gh-deploy"
 
 [tool.hatch.envs.lint]
 detached     = true                           # Don't inherit from default (does not download project dependencies)
-dependencies = ["pre-commit", "ruff==0.15.22", "ty"]
+dependencies = ["pre-commit", "ruff==0.16.0", "ty"]
 
 [tool.hatch.envs.lint.scripts]
 fmt    = ["pre-commit run --all-files --hook-stage manual {args:}"]