diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index e526c254..98e0cef0 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -11,7 +11,7 @@ repos:
         types: [text]
         files: \.(json|ipynb)$
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.6
+    rev: v0.15.7
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]
@@ -22,6 +22,6 @@ repos:
       - id: ruff-format
         types_or: [python, jupyter]
   - repo: https://github.com/rbubley/mirrors-prettier # Update mirror as official mirror is deprecated
-    rev: v3.5.1
+    rev: v3.8.1
     hooks:
       - id: prettier
diff --git a/docs/paper/plotting_functions.py b/docs/paper/plotting_functions.py
index a11ea798..06009123 100644
--- a/docs/paper/plotting_functions.py
+++ b/docs/paper/plotting_functions.py
@@ -109,7 +109,7 @@ def plot_ctd(ds, ax, plot_variable, vmin, vmax, axes_labels=False):
     var_down = _ctd_descent_only(ctd_distance, MAP_VARNAMES[plot_variable])
 
     # 1d array of depth dimension (from deepest trajectory)
-    traj_idx, obs_idx = np.where(z_down == np.nanmin(z_down))
+    traj_idx, _ = np.where(z_down == np.nanmin(z_down))
     z1d = z_down.values[traj_idx[0], :]
 
     # distance as 1d array
diff --git a/src/virtualship/cli/_plan.py b/src/virtualship/cli/_plan.py
index 97dbc7d2..618906a3 100644
--- a/src/virtualship/cli/_plan.py
+++ b/src/virtualship/cli/_plan.py
@@ -1055,8 +1055,10 @@ def save_pressed(self) -> None:
             self.sync_ui_waypoints()  # call to ensure waypoint inputs are synced
 
             # verify schedule
-            wp_lats, wp_lons = _get_waypoint_latlons(
-                expedition_editor.expedition.schedule.waypoints
+            _wp_lats, _wp_lons = (
+                _get_waypoint_latlons(  # TODO: Remove these since they aren't used?
+                    expedition_editor.expedition.schedule.waypoints
+                )
             )
             instruments_config = expedition_editor.expedition.instruments_config