Copyright headers.

LICENSE

@@ -186,7 +186,10 @@
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-   Copyright 2021 Valence
+   Copyright 2023 Valence Labs
+   Copyright 2023 Recursion Pharmaceuticals
+   Copyright 2023 Graphcore Limited
+   Copyright 2023 --- various academic groups have also contributed to the code and detain copyright.
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.

cleanup_files.sh

@@ -1,3 +1,18 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals, Graphcore Limited and Academic Collaborators.
+
+This software is part of a collaboration between industrial and academic institutions.
+Use of this software is subject to the terms and conditions outlined in the LICENSE file.
+Unauthorized modification, distribution, or use is prohibited. Provided 'as is' without
+warranties of any kind.
+
+Valence Labs, Recursion Pharmaceuticals, Graphcore Limited, and its collaborators are not liable
+for any damages arising from its use. Refer to the LICENSE file for the full terms and conditions.
+--------------------------------------------------------------------------------
+"""
+
+
 # Delete saved files like wandb, checkpoints, profiling etc.
 # Usage: bash cleanup_files.sh
 rm -rf wandb/*

docs/design.md

@@ -46,7 +46,6 @@ Below are a list of directory and their respective documentations:
 - [nn](https://github.com/datamol-io/graphium/tree/main/graphium/nn/README.md)
 - [trainer](https://github.com/datamol-io/graphium/tree/main/graphium/trainer/README.md)
 - [utils](https://github.com/datamol-io/graphium/tree/main/graphium/features/README.md)
-- [visualization](https://github.com/datamol-io/graphium/tree/main/graphium/visualization/README.md)
 
 
 ## Structure of the configs

enable_ipu.sh

@@ -1,3 +1,17 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Graphcore Limited and Academic Collaborators.
+
+Use of this software is subject to the terms and conditions outlined in the LICENSE file.
+Unauthorized modification, distribution, or use is prohibited. Provided 'as is' without
+warranties of any kind.
+
+Graphcore Limited is not liable
+for any damages arising from its use. Refer to the LICENSE file for the full terms and conditions.
+--------------------------------------------------------------------------------
+"""
+
+
 #!/bin/bash
 
 # Default location for the virtual environment

graphium/config/_load.py

@@ -1,3 +1,17 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals.
+
+Use of this software is subject to the terms and conditions outlined in the LICENSE file.
+Unauthorized modification, distribution, or use is prohibited. Provided 'as is' without
+warranties of any kind.
+
+Valence Labs, Recursion Pharmaceuticals are not liable
+for any damages arising from its use. Refer to the LICENSE file for the full terms and conditions.
+--------------------------------------------------------------------------------
+"""
+
+
 import importlib.resources
 
 import omegaconf

graphium/config/_loader.py

@@ -1,3 +1,18 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals, Graphcore Limited and Academic Collaborators.
+
+This software is part of a collaboration between industrial and academic institutions.
+Use of this software is subject to the terms and conditions outlined in the LICENSE file.
+Unauthorized modification, distribution, or use is prohibited. Provided 'as is' without
+warranties of any kind.
+
+Valence Labs, Recursion Pharmaceuticals, Graphcore Limited, and its collaborators are not liable
+for any damages arising from its use. Refer to the LICENSE file for the full terms and conditions.
+--------------------------------------------------------------------------------
+"""
+
+
 # Misc
 import os
 from copy import deepcopy

graphium/config/config_convert.py

@@ -1,3 +1,18 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals, Graphcore Limited and Academic Collaborators.
+
+This software is part of a collaboration between industrial and academic institutions.
+Use of this software is subject to the terms and conditions outlined in the LICENSE file.
+Unauthorized modification, distribution, or use is prohibited. Provided 'as is' without
+warranties of any kind.
+
+Valence Labs, Recursion Pharmaceuticals, Graphcore Limited, and its collaborators are not liable
+for any damages arising from its use. Refer to the LICENSE file for the full terms and conditions.
+--------------------------------------------------------------------------------
+"""
+
+
 import omegaconf
 
 

graphium/data/collate.py

@@ -1,3 +1,18 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals, Graphcore and Academic Collaborators.
+
+This software is part of a collaboration between industrial and academic institutions.
+Use of this software is subject to the terms and conditions outlined in the LICENSE file.
+Unauthorized modification, distribution, or use is prohibited. Provided 'as is' without
+warranties of any kind.
+
+Valence Labs, Recursion Pharmaceuticals, Graphcore, and its collaborators are not liable
+for any damages arising from its use. Refer to the LICENSE file for the full terms and conditions.
+--------------------------------------------------------------------------------
+"""
+
+
 from collections.abc import Mapping, Sequence
 
 # from pprint import pprint

graphium/data/datamodule.py

@@ -1,3 +1,18 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals, Graphcore Limited and Academic Collaborators.
+
+This software is part of a collaboration between industrial and academic institutions.
+Use of this software is subject to the terms and conditions outlined in the LICENSE file.
+Unauthorized modification, distribution, or use is prohibited. Provided 'as is' without
+warranties of any kind.
+
+Valence Labs, Recursion Pharmaceuticals, Graphcore Limited, and its collaborators are not liable
+for any damages arising from its use. Refer to the LICENSE file for the full terms and conditions.
+--------------------------------------------------------------------------------
+"""
+
+
 import tempfile
 from contextlib import redirect_stderr, redirect_stdout
 from typing import Type, List, Dict, Union, Any, Callable, Optional, Tuple, Iterable, Literal

graphium/data/dataset.py

@@ -1,3 +1,18 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals, Graphcore Limited and Academic Collaborators.
+
+This software is part of a collaboration between industrial and academic institutions.
+Use of this software is subject to the terms and conditions outlined in the LICENSE file.
+Unauthorized modification, distribution, or use is prohibited. Provided 'as is' without
+warranties of any kind.
+
+Valence Labs, Recursion Pharmaceuticals, Graphcore Limited, and its collaborators are not liable
+for any damages arising from its use. Refer to the LICENSE file for the full terms and conditions.
+--------------------------------------------------------------------------------
+"""
+
+
 import os
 from copy import deepcopy
 from functools import lru_cache

graphium/data/multilevel_utils.py

@@ -1,3 +1,18 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals, Graphcore Limited and Academic Collaborators.
+
+This software is part of a collaboration between industrial and academic institutions.
+Use of this software is subject to the terms and conditions outlined in the LICENSE file.
+Unauthorized modification, distribution, or use is prohibited. Provided 'as is' without
+warranties of any kind.
+
+Valence Labs, Recursion Pharmaceuticals, Graphcore Limited, and its collaborators are not liable
+for any damages arising from its use. Refer to the LICENSE file for the full terms and conditions.
+--------------------------------------------------------------------------------
+"""
+
+
 import pandas as pd
 import ast
 import numpy as np

graphium/data/normalization.py

@@ -1,3 +1,18 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals, Graphcore Limited and Academic Collaborators.
+
+This software is part of a collaboration between industrial and academic institutions.
+Use of this software is subject to the terms and conditions outlined in the LICENSE file.
+Unauthorized modification, distribution, or use is prohibited. Provided 'as is' without
+warranties of any kind.
+
+Valence Labs, Recursion Pharmaceuticals, Graphcore Limited, and its collaborators are not liable
+for any damages arising from its use. Refer to the LICENSE file for the full terms and conditions.
+--------------------------------------------------------------------------------
+"""
+
+
 from typing import Optional
 from loguru import logger
 import numpy as np

graphium/data/sampler.py

@@ -1,3 +1,18 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals, Graphcore Limited and Academic Collaborators.
+
+This software is part of a collaboration between industrial and academic institutions.
+Use of this software is subject to the terms and conditions outlined in the LICENSE file.
+Unauthorized modification, distribution, or use is prohibited. Provided 'as is' without
+warranties of any kind.
+
+Valence Labs, Recursion Pharmaceuticals, Graphcore Limited, and its collaborators are not liable
+for any damages arising from its use. Refer to the LICENSE file for the full terms and conditions.
+--------------------------------------------------------------------------------
+"""
+
+
 from typing import Dict, Optional
 from torch.utils.data.dataloader import Dataset
 

graphium/data/sdf2csv.py

@@ -1,3 +1,17 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals.
+
+This software is part of a collaboration between industrial and academic institutions.
+Use of this software is subject to the terms and conditions outlined in the LICENSE file.
+Unauthorized modification, distribution, or use is prohibited. Provided 'as is' without
+warranties of any kind.
+
+Valence Labs, Recursion Pharmaceuticals, and its collaborators are not liable
+for any damages arising from its use. Refer to the LICENSE file for the full terms and conditions.
+--------------------------------------------------------------------------------
+"""
+
 import datamol as dm
 import zipfile
 import pandas as pd

graphium/data/smiles_transform.py

@@ -1,3 +1,18 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals.
+
+This software is part of a collaboration between industrial and academic institutions.
+Use of this software is subject to the terms and conditions outlined in the LICENSE file.
+Unauthorized modification, distribution, or use is prohibited. Provided 'as is' without
+warranties of any kind.
+
+Valence Labs, Recursion Pharmaceuticals, and its collaborators are not liable
+for any damages arising from its use. Refer to the LICENSE file for the full terms and conditions.
+--------------------------------------------------------------------------------
+"""
+
+
 from typing import Type, List, Dict, Union, Any, Callable, Optional, Tuple, Iterable
 
 import os

graphium/data/utils.py

@@ -1,3 +1,18 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals, Graphcore Limited and Academic Collaborators.
+
+This software is part of a collaboration between industrial and academic institutions.
+Use of this software is subject to the terms and conditions outlined in the LICENSE file.
+Unauthorized modification, distribution, or use is prohibited. Provided 'as is' without
+warranties of any kind.
+
+Valence Labs, Recursion Pharmaceuticals, Graphcore Limited, and its collaborators are not liable
+for any damages arising from its use. Refer to the LICENSE file for the full terms and conditions.
+--------------------------------------------------------------------------------
+"""
+
+
 from typing import Union, List, Callable, Dict, Tuple, Any, Optional
 
 import importlib.resources

graphium/features/commute.py

@@ -1,3 +1,18 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals, Graphcore Limited and Academic Collaborators.
+
+This software is part of a collaboration between industrial and academic institutions.
+Use of this software is subject to the terms and conditions outlined in the LICENSE file.
+Unauthorized modification, distribution, or use is prohibited. Provided 'as is' without
+warranties of any kind.
+
+Valence Labs, Recursion Pharmaceuticals, Graphcore Limited, and its collaborators are not liable
+for any damages arising from its use. Refer to the LICENSE file for the full terms and conditions.
+--------------------------------------------------------------------------------
+"""
+
+
 from typing import Tuple, Union, Dict, Any
 
 import numpy as np

graphium/features/electrostatic.py

@@ -1,3 +1,18 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals, Graphcore Limited and Academic Collaborators.
+
+This software is part of a collaboration between industrial and academic institutions.
+Use of this software is subject to the terms and conditions outlined in the LICENSE file.
+Unauthorized modification, distribution, or use is prohibited. Provided 'as is' without
+warranties of any kind.
+
+Valence Labs, Recursion Pharmaceuticals, Graphcore Limited, and its collaborators are not liable
+for any damages arising from its use. Refer to the LICENSE file for the full terms and conditions.
+--------------------------------------------------------------------------------
+"""
+
+
 from typing import Tuple, Union, Dict, Any
 
 import numpy as np

graphium/features/featurizer.py

@@ -1,3 +1,18 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals, Graphcore Limited and Academic Collaborators.
+
+This software is part of a collaboration between industrial and academic institutions.
+Use of this software is subject to the terms and conditions outlined in the LICENSE file.
+Unauthorized modification, distribution, or use is prohibited. Provided 'as is' without
+warranties of any kind.
+
+Valence Labs, Recursion Pharmaceuticals, Graphcore Limited, and its collaborators are not liable
+for any damages arising from its use. Refer to the LICENSE file for the full terms and conditions.
+--------------------------------------------------------------------------------
+"""
+
+
 from typing import Union, List, Callable, Dict, Tuple, Any, Optional
 
 import inspect

graphium/features/graphormer.py

@@ -1,3 +1,18 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals, Graphcore Limited and Academic Collaborators.
+
+This software is part of a collaboration between industrial and academic institutions.
+Use of this software is subject to the terms and conditions outlined in the LICENSE file.
+Unauthorized modification, distribution, or use is prohibited. Provided 'as is' without
+warranties of any kind.
+
+Valence Labs, Recursion Pharmaceuticals, Graphcore Limited, and its collaborators are not liable
+for any damages arising from its use. Refer to the LICENSE file for the full terms and conditions.
+--------------------------------------------------------------------------------
+"""
+
+
 from typing import Tuple, Union, Dict, Any
 
 import numpy as np

graphium/features/nmp.py

@@ -1,3 +1,18 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals, Graphcore Limited and Academic Collaborators.
+
+This software is part of a collaboration between industrial and academic institutions.
+Use of this software is subject to the terms and conditions outlined in the LICENSE file.
+Unauthorized modification, distribution, or use is prohibited. Provided 'as is' without
+warranties of any kind.
+
+Valence Labs, Recursion Pharmaceuticals, Graphcore Limited, and its collaborators are not liable
+for any damages arising from its use. Refer to the LICENSE file for the full terms and conditions.
+--------------------------------------------------------------------------------
+"""
+
+
 from typing import Tuple, Optional, Dict, Union
 import importlib.resources
 from copy import deepcopy