Merge pull request #495 from datamol-io/headers

Copyright headers.
datamol-io · Dec 22, 2023 · 45f5016 · 45f5016
2 parents 23dd5ca + 2829821
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diff --git a/LICENSE b/LICENSE
@@ -186,7 +186,20 @@
       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
+
+   Various Academic groups have also contributed to this software under
+   the given license. These include, but are not limited, to the following
+
+   1. University of Montreal
+   2. McGill University
+   3. Mila - Institut Quebecois d'intelligence artificielle
+   4. HEC Montreal
+   5. CIFAR AI Chair
+   6. New Jersey Institute of Technology
+   7. RWTH Aachen University
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.

diff --git a/cleanup_files.sh b/cleanup_files.sh
@@ -1,3 +1,17 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals and Graphcore Limited.
+
+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 Graphcore Limited 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/*

diff --git a/docs/api/graphium.visualization.md b/docs/api/graphium.visualization.md
diff --git a/docs/design.md b/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

diff --git a/enable_ipu.sh b/enable_ipu.sh
@@ -1,3 +1,17 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Graphcore Limited.
+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

diff --git a/graphium/config/_load.py b/graphium/config/_load.py
@@ -1,3 +1,16 @@
+"""
+--------------------------------------------------------------------------------
+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

diff --git a/graphium/config/_loader.py b/graphium/config/_loader.py
@@ -1,3 +1,17 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals and Graphcore Limited.
+
+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 Graphcore Limited 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

diff --git a/graphium/config/config_convert.py b/graphium/config/config_convert.py
@@ -1,3 +1,17 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals and Graphcore Limited.
+
+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 Graphcore Limited are not liable for any damages arising from its use.
+Refer to the LICENSE file for the full terms and conditions.
+--------------------------------------------------------------------------------
+"""
+
+
 import omegaconf
 
 

diff --git a/graphium/data/collate.py b/graphium/data/collate.py
@@ -1,3 +1,17 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals and Graphcore.
+
+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 Graphcore 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

diff --git a/graphium/data/datamodule.py b/graphium/data/datamodule.py
@@ -1,3 +1,17 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals and Graphcore Limited.
+
+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 Graphcore Limited 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

diff --git a/graphium/data/dataset.py b/graphium/data/dataset.py
@@ -1,3 +1,17 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals and Graphcore Limited.
+
+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 Graphcore Limited 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

diff --git a/graphium/data/multilevel_utils.py b/graphium/data/multilevel_utils.py
@@ -1,3 +1,17 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals and Graphcore Limited.
+
+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 Graphcore Limited 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

diff --git a/graphium/data/normalization.py b/graphium/data/normalization.py
@@ -1,3 +1,17 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals and Graphcore Limited.
+
+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 Graphcore Limited 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

diff --git a/graphium/data/sampler.py b/graphium/data/sampler.py
@@ -1,3 +1,17 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals and Graphcore Limited.
+
+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 Graphcore Limited 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
 

diff --git a/graphium/data/sdf2csv.py b/graphium/data/sdf2csv.py
@@ -1,3 +1,16 @@
+"""
+--------------------------------------------------------------------------------
+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 and Recursion Pharmaceuticals 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

diff --git a/graphium/data/smiles_transform.py b/graphium/data/smiles_transform.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 and Recursion Pharmaceuticals 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

diff --git a/graphium/data/utils.py b/graphium/data/utils.py
@@ -1,3 +1,17 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals and Graphcore Limited.
+
+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 Graphcore Limited 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

diff --git a/graphium/features/commute.py b/graphium/features/commute.py
@@ -1,3 +1,17 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals and Graphcore Limited.
+
+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 Graphcore Limited 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

diff --git a/graphium/features/electrostatic.py b/graphium/features/electrostatic.py
@@ -1,3 +1,17 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals and Graphcore Limited.
+
+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 Graphcore Limited 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

diff --git a/graphium/features/featurizer.py b/graphium/features/featurizer.py
@@ -1,3 +1,17 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals and Graphcore Limited.
+
+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 Graphcore Limited 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

diff --git a/graphium/features/graphormer.py b/graphium/features/graphormer.py
@@ -1,3 +1,17 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals and Graphcore Limited.
+
+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 Graphcore Limited 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

diff --git a/graphium/features/nmp.py b/graphium/features/nmp.py
@@ -1,3 +1,17 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals and Graphcore Limited.
+
+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 Graphcore Limited 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

diff --git a/graphium/features/positional_encoding.py b/graphium/features/positional_encoding.py
@@ -1,3 +1,17 @@
+"""
+--------------------------------------------------------------------------------
+Copyright (c) 2023 Valence Labs, Recursion Pharmaceuticals and Graphcore Limited.
+
+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 Graphcore Limited 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, Optional, Dict, Any, OrderedDict
 from copy import deepcopy
 import numpy as np