diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 75eef4e..9c700f3 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: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-added-large-files
       - id: check-case-conflict
@@ -14,7 +14,7 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v18.1.8
+    rev: v19.1.1
     hooks:
       - id: clang-format
 
@@ -25,7 +25,7 @@ repos:
         additional_dependencies: [pyyaml]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.7
+    rev: v0.6.9
     hooks:
       - id: ruff
         args: ["--fix", "--show-fixes"]
diff --git a/examples/signals.ipynb b/examples/signals.ipynb
index 74db9a5..c97aa77 100644
--- a/examples/signals.ipynb
+++ b/examples/signals.ipynb
@@ -1,5 +1,5 @@
 {
-    "cells" : [
+    "cells": [
         {
             "cell_type": "code",
             "execution_count": 245,
@@ -277,25 +277,25 @@
             "source": []
         }
     ],
-              "metadata" : {
-                  "kernelspec": {
-                      "display_name": "Python 3",
-                      "language": "python",
-                      "name": "python3"
-                  },
-                  "language_info": {
-                      "codemirror_mode": {
-                          "name": "ipython",
-                          "version": 2
-                      },
-                      "file_extension": ".py",
-                      "mimetype": "text/x-python",
-                      "name": "python",
-                      "nbconvert_exporter": "python",
-                      "pygments_lexer": "ipython2",
-                      "version": "2.7.6"
-                  }
-              },
-                           "nbformat" : 4,
-                           "nbformat_minor" : 5
+    "metadata": {
+        "kernelspec": {
+            "display_name": "Python 3",
+            "language": "python",
+            "name": "python3"
+        },
+        "language_info": {
+            "codemirror_mode": {
+                "name": "ipython",
+                "version": 2
+            },
+            "file_extension": ".py",
+            "mimetype": "text/x-python",
+            "name": "python",
+            "nbconvert_exporter": "python",
+            "pygments_lexer": "ipython2",
+            "version": "2.7.6"
+        }
+    },
+    "nbformat": 4,
+    "nbformat_minor": 5
 }
diff --git a/viewer/feminos-viewer.py b/viewer/feminos-viewer.py
index 6bb3748..ab8f2c7 100755
--- a/viewer/feminos-viewer.py
+++ b/viewer/feminos-viewer.py
@@ -1609,7 +1609,7 @@ def white_to_jet(n):
 
 
 def amplitude_to_color(
-        amplitude, min_amplitude=0, max_amplitude=4095, cmap_name="jet", log_scale=True
+    amplitude, min_amplitude=0, max_amplitude=4095, cmap_name="jet", log_scale=True
 ):
     amplitude = max(amplitude, min_amplitude)
 
@@ -1625,7 +1625,7 @@ def amplitude_to_color(
     else:
         # Linear scaling
         normalized_amplitude = (amplitude - min_amplitude) / (
-                max_amplitude - min_amplitude
+            max_amplitude - min_amplitude
         )
 
     # Normalize the value to be between 0 and 1
@@ -1675,9 +1675,9 @@ def get_event(tree: uproot.TTree, entry: int):
 
 @njit
 def compute_energy_estimate(
-        event: ak.highlevel.Record,
-        signal_ids_allowed: set[int],
-        baseline_range: float = 0.2,
+    event: ak.highlevel.Record,
+    signal_ids_allowed: set[int],
+    baseline_range: float = 0.2,
 ) -> float:
     energy = 0.0
     baseline_factor = int(baseline_range * len(event.signals.values[0]))
@@ -1697,7 +1697,7 @@ def compute_energy_estimate(
 
 @njit
 def compute_energy_of_waveform(
-        waveform: np.ndarray, baseline_range: float = 0.2
+    waveform: np.ndarray, baseline_range: float = 0.2
 ) -> float:
     baseline_factor = int(baseline_range * len(waveform))
     return np.max(waveform) - np.mean(waveform[:baseline_factor])
@@ -1770,7 +1770,7 @@ def __init__(self, _root):
         self.readout_menu.pack(side=tk.LEFT, padx=20, pady=5)
         self.selected_readout.set("IAXO-D1")
         assert (
-                self.selected_readout.get() in readouts
+            self.selected_readout.get() in readouts
         ), f"Invalid readout {self.selected_readout.get()}. Available readouts are {readouts.keys()}"
         self.readout_signal_ids = set(readouts[self.readout]["mapping"].keys())
 
@@ -2065,7 +2065,9 @@ def load_file(self):
 
     def open_local_file(self, filename: str | None = None):
         if filename is None:
-            self.filepath = filedialog.askopenfilename(filetypes=[("ROOT files", "*.root")])
+            self.filepath = filedialog.askopenfilename(
+                filetypes=[("ROOT files", "*.root")]
+            )
             if not self.filepath:
                 return
         else:
@@ -2314,7 +2316,7 @@ def plot_event_time(self):
 
             signal_type = readouts[self.readout]["mapping"][int(signal_id)][0]
             assert (
-                    len(values) == 512
+                len(values) == 512
             ), f"Signal {signal_id} has {len(values)} bins, not 512"
             for i in range(len(values)):
                 value = values[i]
@@ -2379,8 +2381,8 @@ def plot_readout_observables(self):
             energy_estimate_quantile = 0.99
 
             observable_energy_estimate = self.observable_energy_estimate[
-                                         : int(len(self.observable_energy_estimate) * energy_estimate_quantile)
-                                         ]
+                : int(len(self.observable_energy_estimate) * energy_estimate_quantile)
+            ]
 
             self.ax_left.hist(
                 observable_energy_estimate,
@@ -2445,13 +2447,13 @@ def plot_readout_activity_x_y(self):
                 signal_id
                 for signal_id in self.observable_channel_activity.keys()
                 if signal_id in self.readout_signal_ids
-                   and readouts[self.readout]["mapping"][signal_id][0] == "X"
+                and readouts[self.readout]["mapping"][signal_id][0] == "X"
             ]
             signal_ids_y = [
                 signal_id
                 for signal_id in self.observable_channel_activity.keys()
                 if signal_id in self.readout_signal_ids
-                   and readouts[self.readout]["mapping"][signal_id][0] == "Y"
+                and readouts[self.readout]["mapping"][signal_id][0] == "Y"
             ]
 
             positions_x = [