From 305c1aa0f49a60dff1b5774c024233a3cbd4cf5f Mon Sep 17 00:00:00 2001
From: Niels Maeder <maedern@student.ethz.ch>
Date: Wed, 10 Dec 2025 15:13:49 +0100
Subject: [PATCH 1/2] add copyright statement

---
 serenityff/charge/__init__.py                               | 2 ++
 serenityff/charge/data/__init__.py                          | 2 ++
 serenityff/charge/dataset_preperation/MolMorganDataset.py   | 2 ++
 serenityff/charge/gnn/__init__.py                           | 2 ++
 serenityff/charge/gnn/attention_extraction/__init__.py      | 2 ++
 .../gnn/attention_extraction/bash_templates/__init__.py     | 2 ++
 .../gnn/attention_extraction/bash_templates/cleaner.py      | 2 ++
 .../gnn/attention_extraction/bash_templates/worker.py       | 2 ++
 serenityff/charge/gnn/attention_extraction/explainer.py     | 2 ++
 serenityff/charge/gnn/attention_extraction/extractor.py     | 2 ++
 serenityff/charge/gnn/training/__init__.py                  | 2 ++
 serenityff/charge/gnn/training/trainer.py                   | 2 ++
 serenityff/charge/gnn/utils/__init__.py                     | 2 ++
 serenityff/charge/gnn/utils/attentive_fp.py                 | 2 ++
 serenityff/charge/gnn/utils/custom_data.py                  | 2 ++
 serenityff/charge/gnn/utils/featurizer.py                   | 6 ++++--
 serenityff/charge/gnn/utils/model.py                        | 2 ++
 serenityff/charge/gnn/utils/rdkit_helper.py                 | 2 ++
 serenityff/charge/gnn/utils/split_utils.py                  | 2 ++
 serenityff/charge/tests/test_fundamental.py                 | 5 +++--
 serenityff/charge/tests/test_gnn_extraction.py              | 2 ++
 serenityff/charge/tests/test_gnn_training.py                | 2 ++
 serenityff/charge/tests/test_gnn_utils.py                   | 2 ++
 serenityff/charge/tests/test_off_plugin.py                  | 2 ++
 serenityff/charge/tree/atom_features.py                     | 2 ++
 serenityff/charge/tree/atom_features_reduced.py             | 2 ++
 serenityff/charge/tree/dash_tools.py                        | 2 ++
 serenityff/charge/tree/dash_tree.py                         | 2 ++
 serenityff/charge/tree/node.py                              | 2 ++
 serenityff/charge/tree/retrieve_data.py                     | 2 ++
 serenityff/charge/tree/tree_factory.py                      | 2 ++
 serenityff/charge/tree/tree_utils.py                        | 2 ++
 serenityff/charge/tree_develop/develop_node.py              | 2 ++
 serenityff/charge/tree_develop/tree_constructor.py          | 2 ++
 .../charge/tree_develop/tree_constructor_parallel_worker.py | 2 ++
 .../charge/tree_develop/tree_constructor_singleJB_worker.py | 2 ++
 serenityff/charge/utils/__init__.py                         | 4 +++-
 serenityff/charge/utils/exceptions.py                       | 2 ++
 serenityff/charge/utils/io.py                               | 2 ++
 serenityff/charge/utils/rdkit_typing.py                     | 5 ++++-
 serenityff/charge/utils/serenityff_charge_handler.py        | 2 ++
 tests/_testfiles/__init__.py                                | 2 ++
 tests/_utils.py                                             | 2 ++
 tests/conftest.py                                           | 2 ++
 tests/serenityff/charge/gnn/utils/test_rdkit_helper.py      | 2 ++
 tests/serenityff/charge/tree/test_retrieve_data.py          | 2 ++
 tests/serenityff/charge/tree/test_tree_factory.py           | 2 ++
 tests/serenityff/charge/utils/test_exceptions.py            | 2 ++
 tests/serenityff/charge/utils/test_io.py                    | 2 ++
 tests/serenityff/charge/utils/test_rdkit_typing.py          | 2 ++
 .../charge/utils/test_serenityff_charge_handler.py          | 2 ++
 51 files changed, 108 insertions(+), 6 deletions(-)

diff --git a/serenityff/charge/__init__.py b/serenityff/charge/__init__.py
index 413dfd6..e988d7c 100644
--- a/serenityff/charge/__init__.py
+++ b/serenityff/charge/__init__.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2022-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 # from serenityff.charge.gnn import ChargeCorrectedNodeWiseAttentiveFP, NodeWiseAttentiveFP, Extractor, Trainer
 
 # from . import _version
diff --git a/serenityff/charge/data/__init__.py b/serenityff/charge/data/__init__.py
index 85f8187..cda3e83 100644
--- a/serenityff/charge/data/__init__.py
+++ b/serenityff/charge/data/__init__.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2022-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 from pathlib import Path
 
 default_dash_tree_path = Path(__file__).parent / "default_dash_tree"
diff --git a/serenityff/charge/dataset_preperation/MolMorganDataset.py b/serenityff/charge/dataset_preperation/MolMorganDataset.py
index e184931..1e18f2b 100644
--- a/serenityff/charge/dataset_preperation/MolMorganDataset.py
+++ b/serenityff/charge/dataset_preperation/MolMorganDataset.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2022-2025 ETH Zurich, Jakob Teetz and other DASH contributors.
+
 import os
 import numpy
 import pickle
diff --git a/serenityff/charge/gnn/__init__.py b/serenityff/charge/gnn/__init__.py
index fb5a751..0d1d60b 100644
--- a/serenityff/charge/gnn/__init__.py
+++ b/serenityff/charge/gnn/__init__.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2022-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 # from .attention_extraction import Extractor
 # from .training import Trainer
 # from .utils import ChargeCorrectedNodeWiseAttentiveFP, NodeWiseAttentiveFP, MolGraphConvFeaturizer, get_graph_from_mol
diff --git a/serenityff/charge/gnn/attention_extraction/__init__.py b/serenityff/charge/gnn/attention_extraction/__init__.py
index 7cd5d7c..1aaa5c7 100644
--- a/serenityff/charge/gnn/attention_extraction/__init__.py
+++ b/serenityff/charge/gnn/attention_extraction/__init__.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2022-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 from .explainer import Explainer
 from .extractor import Extractor
 
diff --git a/serenityff/charge/gnn/attention_extraction/bash_templates/__init__.py b/serenityff/charge/gnn/attention_extraction/bash_templates/__init__.py
index 07e9f16..6977e45 100644
--- a/serenityff/charge/gnn/attention_extraction/bash_templates/__init__.py
+++ b/serenityff/charge/gnn/attention_extraction/bash_templates/__init__.py
@@ -1,2 +1,4 @@
+# Copyright (C) 2024-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 from .cleaner import CLEANER_CONTENT
 from .worker import get_lsf_worker_content, get_slurm_worker_content
diff --git a/serenityff/charge/gnn/attention_extraction/bash_templates/cleaner.py b/serenityff/charge/gnn/attention_extraction/bash_templates/cleaner.py
index 993f7a9..4123af9 100644
--- a/serenityff/charge/gnn/attention_extraction/bash_templates/cleaner.py
+++ b/serenityff/charge/gnn/attention_extraction/bash_templates/cleaner.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2024-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 CLEANER_CONTENT = """
 #! /bin/bash
 
diff --git a/serenityff/charge/gnn/attention_extraction/bash_templates/worker.py b/serenityff/charge/gnn/attention_extraction/bash_templates/worker.py
index 1f51400..2ec8cbf 100644
--- a/serenityff/charge/gnn/attention_extraction/bash_templates/worker.py
+++ b/serenityff/charge/gnn/attention_extraction/bash_templates/worker.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2024-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 worker_template = """
 #! /bin/bash
 
diff --git a/serenityff/charge/gnn/attention_extraction/explainer.py b/serenityff/charge/gnn/attention_extraction/explainer.py
index 50910a0..39c58cb 100644
--- a/serenityff/charge/gnn/attention_extraction/explainer.py
+++ b/serenityff/charge/gnn/attention_extraction/explainer.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2022-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 from typing import List, Optional, Tuple
 
 from torch import Tensor
diff --git a/serenityff/charge/gnn/attention_extraction/extractor.py b/serenityff/charge/gnn/attention_extraction/extractor.py
index 91badb2..b21b678 100644
--- a/serenityff/charge/gnn/attention_extraction/extractor.py
+++ b/serenityff/charge/gnn/attention_extraction/extractor.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2022-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 import argparse
 import os
 from math import ceil
diff --git a/serenityff/charge/gnn/training/__init__.py b/serenityff/charge/gnn/training/__init__.py
index e5e22dd..6493fa1 100644
--- a/serenityff/charge/gnn/training/__init__.py
+++ b/serenityff/charge/gnn/training/__init__.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2022-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 from .trainer import Trainer
 
 __all__ = [Trainer]
diff --git a/serenityff/charge/gnn/training/trainer.py b/serenityff/charge/gnn/training/trainer.py
index 0d3e821..5fe2a31 100644
--- a/serenityff/charge/gnn/training/trainer.py
+++ b/serenityff/charge/gnn/training/trainer.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2022-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 import contextlib
 import os
 from typing import Callable, List, Optional, OrderedDict, Sequence, Tuple, Union
diff --git a/serenityff/charge/gnn/utils/__init__.py b/serenityff/charge/gnn/utils/__init__.py
index c38e02f..f51264e 100644
--- a/serenityff/charge/gnn/utils/__init__.py
+++ b/serenityff/charge/gnn/utils/__init__.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2022-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 from .custom_data import CustomData
 from .featurizer import MolGraphConvFeaturizer
 from .model import ChargeCorrectedNodeWiseAttentiveFP, NodeWiseAttentiveFP
diff --git a/serenityff/charge/gnn/utils/attentive_fp.py b/serenityff/charge/gnn/utils/attentive_fp.py
index cd60f58..ae0f7db 100644
--- a/serenityff/charge/gnn/utils/attentive_fp.py
+++ b/serenityff/charge/gnn/utils/attentive_fp.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2023-2025 ETH Zurich, Marc Lehner and other DASH contributors.
+
 from typing import Optional, Any
 import math
 
diff --git a/serenityff/charge/gnn/utils/custom_data.py b/serenityff/charge/gnn/utils/custom_data.py
index 8e0e0d9..53a5c44 100644
--- a/serenityff/charge/gnn/utils/custom_data.py
+++ b/serenityff/charge/gnn/utils/custom_data.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2022-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 from typing import Any, Optional, Union
 
 import numpy as np
diff --git a/serenityff/charge/gnn/utils/featurizer.py b/serenityff/charge/gnn/utils/featurizer.py
index 6cddd78..ff40a19 100644
--- a/serenityff/charge/gnn/utils/featurizer.py
+++ b/serenityff/charge/gnn/utils/featurizer.py
@@ -1,5 +1,7 @@
-"""_
-This file is necessary to eliminate the packages dependecy on deepchem.
+# Copyright (C) 2022-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
+"""Necessary to eliminate the packages dependecy on deepchem.
+
 Most of the functionality is adapted from deepchem.
 https://github.com/deepchem/deepchem/tree/master/deepchem/feat
 """
diff --git a/serenityff/charge/gnn/utils/model.py b/serenityff/charge/gnn/utils/model.py
index 331bc5c..5e64c7c 100644
--- a/serenityff/charge/gnn/utils/model.py
+++ b/serenityff/charge/gnn/utils/model.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2022-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 from typing import Optional
 
 import torch
diff --git a/serenityff/charge/gnn/utils/rdkit_helper.py b/serenityff/charge/gnn/utils/rdkit_helper.py
index 1a56c6b..83f4509 100644
--- a/serenityff/charge/gnn/utils/rdkit_helper.py
+++ b/serenityff/charge/gnn/utils/rdkit_helper.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2022-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 from typing import List, Optional, Sequence
 
 import numpy as np
diff --git a/serenityff/charge/gnn/utils/split_utils.py b/serenityff/charge/gnn/utils/split_utils.py
index b5acaf2..fe507e8 100644
--- a/serenityff/charge/gnn/utils/split_utils.py
+++ b/serenityff/charge/gnn/utils/split_utils.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2022-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 from math import ceil
 from typing import List, Optional, Sequence, Tuple
 
diff --git a/serenityff/charge/tests/test_fundamental.py b/serenityff/charge/tests/test_fundamental.py
index 2022a2c..4a81442 100644
--- a/serenityff/charge/tests/test_fundamental.py
+++ b/serenityff/charge/tests/test_fundamental.py
@@ -1,5 +1,6 @@
-"""
-Unit and regression dev for the serenityff package.
+# Copyright (C) 2022-2025 ETH Zurich, Marc Lehner and other DASH contributors.
+
+"""Unit and regression dev for the serenityff package.
 
 Test most fundamental functionality of package
 """
diff --git a/serenityff/charge/tests/test_gnn_extraction.py b/serenityff/charge/tests/test_gnn_extraction.py
index fe12711..24438ef 100644
--- a/serenityff/charge/tests/test_gnn_extraction.py
+++ b/serenityff/charge/tests/test_gnn_extraction.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2022-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 import os
 from shutil import rmtree
 from typing import OrderedDict, Sequence
diff --git a/serenityff/charge/tests/test_gnn_training.py b/serenityff/charge/tests/test_gnn_training.py
index 94bee20..e25177f 100644
--- a/serenityff/charge/tests/test_gnn_training.py
+++ b/serenityff/charge/tests/test_gnn_training.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2022-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 import os
 from typing import OrderedDict
 
diff --git a/serenityff/charge/tests/test_gnn_utils.py b/serenityff/charge/tests/test_gnn_utils.py
index 18ccbd4..20bfe41 100644
--- a/serenityff/charge/tests/test_gnn_utils.py
+++ b/serenityff/charge/tests/test_gnn_utils.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2022-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 from typing import List, Sequence
 
 import numpy as np
diff --git a/serenityff/charge/tests/test_off_plugin.py b/serenityff/charge/tests/test_off_plugin.py
index 9d45479..4d919a0 100644
--- a/serenityff/charge/tests/test_off_plugin.py
+++ b/serenityff/charge/tests/test_off_plugin.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2022-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 import os
 
 import pytest
diff --git a/serenityff/charge/tree/atom_features.py b/serenityff/charge/tree/atom_features.py
index 6581dad..39d5c29 100644
--- a/serenityff/charge/tree/atom_features.py
+++ b/serenityff/charge/tree/atom_features.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2022-2025 ETH Zurich, Marc Lehner and other DASH contributors.
+
 from typing import Any, Tuple
 import numpy as np
 from rdkit import Chem
diff --git a/serenityff/charge/tree/atom_features_reduced.py b/serenityff/charge/tree/atom_features_reduced.py
index ab17319..6d67a6d 100644
--- a/serenityff/charge/tree/atom_features_reduced.py
+++ b/serenityff/charge/tree/atom_features_reduced.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2024-2025 ETH Zurich, Marc Lehner and other DASH contributors.
+
 from serenityff.charge.tree.atom_features import (
     AtomFeatures,
     get_connection_info_bond_type,
diff --git a/serenityff/charge/tree/dash_tools.py b/serenityff/charge/tree/dash_tools.py
index 0084dfc..60ebb30 100644
--- a/serenityff/charge/tree/dash_tools.py
+++ b/serenityff/charge/tree/dash_tools.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2023-2025 ETH Zurich, Marc Lehner and other DASH contributors.
+
 from rdkit import Chem
 
 from serenityff.charge.tree.atom_features import AtomFeatures
diff --git a/serenityff/charge/tree/dash_tree.py b/serenityff/charge/tree/dash_tree.py
index 13afdd0..353b088 100644
--- a/serenityff/charge/tree/dash_tree.py
+++ b/serenityff/charge/tree/dash_tree.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2023-2025 ETH Zurich, Marc Lehner and other DASH contributors.
+
 import gzip
 import io
 import os
diff --git a/serenityff/charge/tree/node.py b/serenityff/charge/tree/node.py
index 2fd3be1..063fd19 100644
--- a/serenityff/charge/tree/node.py
+++ b/serenityff/charge/tree/node.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2022-2025 ETH Zurich, Marc Lehner and other DASH contributors.
+
 from __future__ import annotations
 
 from typing import Dict, List
diff --git a/serenityff/charge/tree/retrieve_data.py b/serenityff/charge/tree/retrieve_data.py
index e0938f6..b9b1da0 100644
--- a/serenityff/charge/tree/retrieve_data.py
+++ b/serenityff/charge/tree/retrieve_data.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2024-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 """Functionality to obtain the DASH properties data from ETH research archive."""
 import zipfile
 from enum import Enum, auto
diff --git a/serenityff/charge/tree/tree_factory.py b/serenityff/charge/tree/tree_factory.py
index 655ec1a..6650474 100644
--- a/serenityff/charge/tree/tree_factory.py
+++ b/serenityff/charge/tree/tree_factory.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2024-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 """Factory for dash Trees with different properties loaded."""
 from serenityff.charge.data import dash_props_tree_path
 from serenityff.charge.tree.dash_tree import DASHTree, TreeType
diff --git a/serenityff/charge/tree/tree_utils.py b/serenityff/charge/tree/tree_utils.py
index 380019f..c15e7d1 100644
--- a/serenityff/charge/tree/tree_utils.py
+++ b/serenityff/charge/tree/tree_utils.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2022-2025 ETH Zurich, Marc Lehner and other DASH contributors.
+
 from typing import Tuple, Union
 
 import numpy as np
diff --git a/serenityff/charge/tree_develop/develop_node.py b/serenityff/charge/tree_develop/develop_node.py
index fc5517c..c30128e 100644
--- a/serenityff/charge/tree_develop/develop_node.py
+++ b/serenityff/charge/tree_develop/develop_node.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2022-2025 ETH Zurich, Marc Lehner and other DASH contributors.
+
 from typing import Sequence, Tuple, Union
 
 import numpy as np
diff --git a/serenityff/charge/tree_develop/tree_constructor.py b/serenityff/charge/tree_develop/tree_constructor.py
index cdd9146..1b70710 100644
--- a/serenityff/charge/tree_develop/tree_constructor.py
+++ b/serenityff/charge/tree_develop/tree_constructor.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2022-2025 ETH Zurich, Marc Lehner and other DASH contributors.
+
 import datetime
 import pickle
 import random
diff --git a/serenityff/charge/tree_develop/tree_constructor_parallel_worker.py b/serenityff/charge/tree_develop/tree_constructor_parallel_worker.py
index 7f15e70..086291d 100644
--- a/serenityff/charge/tree_develop/tree_constructor_parallel_worker.py
+++ b/serenityff/charge/tree_develop/tree_constructor_parallel_worker.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2023-2025 ETH Zurich, Marc Lehner and other DASH contributors.
+
 import traceback
 from typing import List
 import numpy as np
diff --git a/serenityff/charge/tree_develop/tree_constructor_singleJB_worker.py b/serenityff/charge/tree_develop/tree_constructor_singleJB_worker.py
index 27bc4a0..3c97636 100644
--- a/serenityff/charge/tree_develop/tree_constructor_singleJB_worker.py
+++ b/serenityff/charge/tree_develop/tree_constructor_singleJB_worker.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2023-2025 ETH Zurich, Marc Lehner and other DASH contributors.
+
 import pickle
 import os
 from typing import Sequence
diff --git a/serenityff/charge/utils/__init__.py b/serenityff/charge/utils/__init__.py
index 47df51b..20d31af 100644
--- a/serenityff/charge/utils/__init__.py
+++ b/serenityff/charge/utils/__init__.py
@@ -1,4 +1,6 @@
-# Classes and functions used by different submodules.
+# Copyright (C) 2022-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
+"""Classes and functions used by different submodules."""
 
 from .exceptions import ExtractionError, NotInitializedError
 from .io import command_to_shell_file
diff --git a/serenityff/charge/utils/exceptions.py b/serenityff/charge/utils/exceptions.py
index d48642c..97b36de 100644
--- a/serenityff/charge/utils/exceptions.py
+++ b/serenityff/charge/utils/exceptions.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2022-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 class ExtractionError(Exception):
     """
     Error thrown if Feature extraction did not work properly.
diff --git a/serenityff/charge/utils/io.py b/serenityff/charge/utils/io.py
index 34807a9..96c0c2b 100644
--- a/serenityff/charge/utils/io.py
+++ b/serenityff/charge/utils/io.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2022-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 def command_to_shell_file(command: str, filename: str) -> None:
     """
     Writes a string to a .sh file
diff --git a/serenityff/charge/utils/rdkit_typing.py b/serenityff/charge/utils/rdkit_typing.py
index d4d1378..af14838 100644
--- a/serenityff/charge/utils/rdkit_typing.py
+++ b/serenityff/charge/utils/rdkit_typing.py
@@ -1,4 +1,7 @@
-# typing tools for the use of rdkit
+# Copyright (C) 2022-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
+"""Typing tools for the use of rdkit."""
+
 from rdkit import Chem
 
 Molecule = Chem.rdchem.Mol
diff --git a/serenityff/charge/utils/serenityff_charge_handler.py b/serenityff/charge/utils/serenityff_charge_handler.py
index 7ce019b..77c7e2b 100644
--- a/serenityff/charge/utils/serenityff_charge_handler.py
+++ b/serenityff/charge/utils/serenityff_charge_handler.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2022-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 from typing import List
 import numpy as np
 
diff --git a/tests/_testfiles/__init__.py b/tests/_testfiles/__init__.py
index 5da47b3..3d3fb2c 100644
--- a/tests/_testfiles/__init__.py
+++ b/tests/_testfiles/__init__.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2024-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 from pathlib import Path
 
 _this = Path(__file__).parent
diff --git a/tests/_utils.py b/tests/_utils.py
index ac23a80..be39d8d 100644
--- a/tests/_utils.py
+++ b/tests/_utils.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2024-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+ 
 """Utilitary functions for running the pytests."""
 import json
 import os
diff --git a/tests/conftest.py b/tests/conftest.py
index b656d05..cc1d77b 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2024-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 """Pytest configuration file."""
 
 from collections.abc import Sequence
diff --git a/tests/serenityff/charge/gnn/utils/test_rdkit_helper.py b/tests/serenityff/charge/gnn/utils/test_rdkit_helper.py
index 624fbd5..91ab425 100644
--- a/tests/serenityff/charge/gnn/utils/test_rdkit_helper.py
+++ b/tests/serenityff/charge/gnn/utils/test_rdkit_helper.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 import numpy as np
 import pytest
 import torch as pt
diff --git a/tests/serenityff/charge/tree/test_retrieve_data.py b/tests/serenityff/charge/tree/test_retrieve_data.py
index ef5c44e..1c71f8f 100644
--- a/tests/serenityff/charge/tree/test_retrieve_data.py
+++ b/tests/serenityff/charge/tree/test_retrieve_data.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2024-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 from pathlib import Path
 from typing import Any, Union
 
diff --git a/tests/serenityff/charge/tree/test_tree_factory.py b/tests/serenityff/charge/tree/test_tree_factory.py
index 56c1d19..475e849 100644
--- a/tests/serenityff/charge/tree/test_tree_factory.py
+++ b/tests/serenityff/charge/tree/test_tree_factory.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2024-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 from collections.abc import Callable, Sequence
 
 import numpy as np
diff --git a/tests/serenityff/charge/utils/test_exceptions.py b/tests/serenityff/charge/utils/test_exceptions.py
index 25e8b87..d86daf0 100644
--- a/tests/serenityff/charge/utils/test_exceptions.py
+++ b/tests/serenityff/charge/utils/test_exceptions.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2024-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 """Test `serenityff.charge.utils.exceptions`."""
 
 import pytest
diff --git a/tests/serenityff/charge/utils/test_io.py b/tests/serenityff/charge/utils/test_io.py
index b95b8b0..8772678 100644
--- a/tests/serenityff/charge/utils/test_io.py
+++ b/tests/serenityff/charge/utils/test_io.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2024-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 """Testing `serenityff.charge.utils.io`."""
 
 from pathlib import Path
diff --git a/tests/serenityff/charge/utils/test_rdkit_typing.py b/tests/serenityff/charge/utils/test_rdkit_typing.py
index 0ccf406..5ef1471 100644
--- a/tests/serenityff/charge/utils/test_rdkit_typing.py
+++ b/tests/serenityff/charge/utils/test_rdkit_typing.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2024-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 """Test `serenityff.charge.utils.rdkit_typing`."""
 
 import pytest
diff --git a/tests/serenityff/charge/utils/test_serenityff_charge_handler.py b/tests/serenityff/charge/utils/test_serenityff_charge_handler.py
index d4c7684..d5d3526 100644
--- a/tests/serenityff/charge/utils/test_serenityff_charge_handler.py
+++ b/tests/serenityff/charge/utils/test_serenityff_charge_handler.py
@@ -1,3 +1,5 @@
+# Copyright (C) 2024-2025 ETH Zurich, Niels Maeder and other DASH contributors.
+
 """Test serenityff.charge.utils.serenityff_charge_handler.py."""
 from pathlib import Path
 

From 5a6990712d7ff587c7817c4000b042b69583d279 Mon Sep 17 00:00:00 2001
From: Niels Maeder <maedern@student.ethz.ch>
Date: Wed, 10 Dec 2025 15:24:45 +0100
Subject: [PATCH 2/2] run pre-commit

---
 serenityff/charge/utils/exceptions.py | 1 +
 serenityff/charge/utils/io.py         | 1 +
 tests/_utils.py                       | 2 +-
 3 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/serenityff/charge/utils/exceptions.py b/serenityff/charge/utils/exceptions.py
index 97b36de..51b14d8 100644
--- a/serenityff/charge/utils/exceptions.py
+++ b/serenityff/charge/utils/exceptions.py
@@ -1,5 +1,6 @@
 # Copyright (C) 2022-2025 ETH Zurich, Niels Maeder and other DASH contributors.
 
+
 class ExtractionError(Exception):
     """
     Error thrown if Feature extraction did not work properly.
diff --git a/serenityff/charge/utils/io.py b/serenityff/charge/utils/io.py
index 96c0c2b..05d93f1 100644
--- a/serenityff/charge/utils/io.py
+++ b/serenityff/charge/utils/io.py
@@ -1,5 +1,6 @@
 # Copyright (C) 2022-2025 ETH Zurich, Niels Maeder and other DASH contributors.
 
+
 def command_to_shell_file(command: str, filename: str) -> None:
     """
     Writes a string to a .sh file
diff --git a/tests/_utils.py b/tests/_utils.py
index be39d8d..0650a7a 100644
--- a/tests/_utils.py
+++ b/tests/_utils.py
@@ -1,5 +1,5 @@
 # Copyright (C) 2024-2025 ETH Zurich, Niels Maeder and other DASH contributors.
- 
+
 """Utilitary functions for running the pytests."""
 import json
 import os