rinikerlab · nmaeder · Dec 10, 2025 · Dec 10, 2025 · Dec 10, 2025
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -1,3 +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
@@ -1,3 +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/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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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