Fix license headers to apache. (#350)

## Summary
Fixing all headers to be Apache license, ahead of open source release.

## Details
Should not affect any executed code.

bionemo/data/equidock/__init__.py

@@ -13,17 +13,4 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
-#!/bin/bash
-
-# SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
-# SPDX-License-Identifier: LicenseRef-NvidiaProprietary
-#
-# NVIDIA CORPORATION, its affiliates and licensors retain all intellectual
-# property and proprietary rights in and to this material, related
-# documentation and any modifications thereto. Any use, reproduction,
-# disclosure or distribution of this material and related documentation
-# without an express license agreement from NVIDIA CORPORATION or
-# its affiliates is strictly prohibited.
-
 from .data_manager import DataManager

bionemo/data/equidock/data_manager.py

@@ -13,19 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
-#!/bin/bash
-
-# SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
-# SPDX-License-Identifier: LicenseRef-NvidiaProprietary
-#
-# NVIDIA CORPORATION, its affiliates and licensors retain all intellectual
-# property and proprietary rights in and to this material, related
-# documentation and any modifications thereto. Any use, reproduction,
-# disclosure or distribution of this material and related documentation
-# without an express license agreement from NVIDIA CORPORATION or
-# its affiliates is strictly prohibited.
-
 from bionemo.data.equidock.db5_data import nemo_get_dataset
 
 

bionemo/data/equidock/db5_data.py

@@ -13,19 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
-#!/bin/bash
-
-# SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
-# SPDX-License-Identifier: LicenseRef-NvidiaProprietary
-#
-# NVIDIA CORPORATION, its affiliates and licensors retain all intellectual
-# property and proprietary rights in and to this material, related
-# documentation and any modifications thereto. Any use, reproduction,
-# disclosure or distribution of this material and related documentation
-# without an express license agreement from NVIDIA CORPORATION or
-# its affiliates is strictly prohibited.
-
 import os
 import pickle
 

bionemo/data/equidock/preprocess.py

@@ -13,19 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
-#!/bin/bash
-
-# SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
-# SPDX-License-Identifier: LicenseRef-NvidiaProprietary
-#
-# NVIDIA CORPORATION, its affiliates and licensors retain all intellectual
-# property and proprietary rights in and to this material, related
-# documentation and any modifications thereto. Any use, reproduction,
-# disclosure or distribution of this material and related documentation
-# without an express license agreement from NVIDIA CORPORATION or
-# its affiliates is strictly prohibited.
-
 import os
 import pickle
 import random

bionemo/data/equidock/protein_featurizers.py

@@ -13,19 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
-#!/bin/bash
-
-# SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
-# SPDX-License-Identifier: LicenseRef-NvidiaProprietary
-#
-# NVIDIA CORPORATION, its affiliates and licensors retain all intellectual
-# property and proprietary rights in and to this material, related
-# documentation and any modifications thereto. Any use, reproduction,
-# disclosure or distribution of this material and related documentation
-# without an express license agreement from NVIDIA CORPORATION or
-# its affiliates is strictly prohibited.
-
 from dgllife.utils import one_hot_encoding
 from nemo.utils import logging
 

bionemo/data/equidock/protein_utils.py

@@ -13,19 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
-#!/bin/bash
-
-# SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
-# SPDX-License-Identifier: LicenseRef-NvidiaProprietary
-#
-# NVIDIA CORPORATION, its affiliates and licensors retain all intellectual
-# property and proprietary rights in and to this material, related
-# documentation and any modifications thereto. Any use, reproduction,
-# disclosure or distribution of this material and related documentation
-# without an express license agreement from NVIDIA CORPORATION or
-# its affiliates is strictly prohibited.
-
 import math
 from zipfile import ZipFile
 

bionemo/model/protein/equidock/__init__.py

@@ -12,16 +12,3 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
-
-#!/bin/bash
-
-# SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
-# SPDX-License-Identifier: LicenseRef-NvidiaProprietary
-#
-# NVIDIA CORPORATION, its affiliates and licensors retain all intellectual
-# property and proprietary rights in and to this material, related
-# documentation and any modifications thereto. Any use, reproduction,
-# disclosure or distribution of this material and related documentation
-# without an express license agreement from NVIDIA CORPORATION or
-# its affiliates is strictly prohibited.

bionemo/model/protein/equidock/equidock_model.py

@@ -13,19 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
-#!/bin/bash
-
-# SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
-# SPDX-License-Identifier: LicenseRef-NvidiaProprietary
-#
-# NVIDIA CORPORATION, its affiliates and licensors retain all intellectual
-# property and proprietary rights in and to this material, related
-# documentation and any modifications thereto. Any use, reproduction,
-# disclosure or distribution of this material and related documentation
-# without an express license agreement from NVIDIA CORPORATION or
-# its affiliates is strictly prohibited.
-
 import random
 from functools import partial
 from typing import List, Tuple

bionemo/model/protein/equidock/loss_metrics/__init__.py

@@ -12,16 +12,3 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
-
-#!/bin/bash
-
-# SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
-# SPDX-License-Identifier: LicenseRef-NvidiaProprietary
-#
-# NVIDIA CORPORATION, its affiliates and licensors retain all intellectual
-# property and proprietary rights in and to this material, related
-# documentation and any modifications thereto. Any use, reproduction,
-# disclosure or distribution of this material and related documentation
-# without an express license agreement from NVIDIA CORPORATION or
-# its affiliates is strictly prohibited.

bionemo/model/protein/equidock/loss_metrics/eval.py

@@ -13,19 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
-#!/bin/bash
-
-# SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
-# SPDX-License-Identifier: LicenseRef-NvidiaProprietary
-#
-# NVIDIA CORPORATION, its affiliates and licensors retain all intellectual
-# property and proprietary rights in and to this material, related
-# documentation and any modifications thereto. Any use, reproduction,
-# disclosure or distribution of this material and related documentation
-# without an express license agreement from NVIDIA CORPORATION or
-# its affiliates is strictly prohibited.
-
 from typing import List
 
 import numpy as np

bionemo/model/protein/equidock/loss_metrics/intersection_loss.py

@@ -13,19 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
-#!/bin/bash
-
-# SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
-# SPDX-License-Identifier: LicenseRef-NvidiaProprietary
-#
-# NVIDIA CORPORATION, its affiliates and licensors retain all intellectual
-# property and proprietary rights in and to this material, related
-# documentation and any modifications thereto. Any use, reproduction,
-# disclosure or distribution of this material and related documentation
-# without an express license agreement from NVIDIA CORPORATION or
-# its affiliates is strictly prohibited.
-
 import torch
 
 

bionemo/model/protein/equidock/loss_metrics/ot_utils.py

@@ -13,19 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
-#!/bin/bash
-
-# SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
-# SPDX-License-Identifier: LicenseRef-NvidiaProprietary
-#
-# NVIDIA CORPORATION, its affiliates and licensors retain all intellectual
-# property and proprietary rights in and to this material, related
-# documentation and any modifications thereto. Any use, reproduction,
-# disclosure or distribution of this material and related documentation
-# without an express license agreement from NVIDIA CORPORATION or
-# its affiliates is strictly prohibited.
-
 import numpy as np
 import ot
 import torch

bionemo/model/protein/equidock/model/__init__.py

@@ -13,17 +13,4 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
-#!/bin/bash
-
-# SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
-# SPDX-License-Identifier: LicenseRef-NvidiaProprietary
-#
-# NVIDIA CORPORATION, its affiliates and licensors retain all intellectual
-# property and proprietary rights in and to this material, related
-# documentation and any modifications thereto. Any use, reproduction,
-# disclosure or distribution of this material and related documentation
-# without an express license agreement from NVIDIA CORPORATION or
-# its affiliates is strictly prohibited.
-
 from .rigid_docking_model import Rigid_Body_Docking_Net

bionemo/model/protein/equidock/model/block.py

@@ -13,19 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
-#!/bin/bash
-
-# SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
-# SPDX-License-Identifier: LicenseRef-NvidiaProprietary
-#
-# NVIDIA CORPORATION, its affiliates and licensors retain all intellectual
-# property and proprietary rights in and to this material, related
-# documentation and any modifications thereto. Any use, reproduction,
-# disclosure or distribution of this material and related documentation
-# without an express license agreement from NVIDIA CORPORATION or
-# its affiliates is strictly prohibited.
-
 import math
 import sys
 import warnings

bionemo/model/protein/equidock/model/graph_norm.py

@@ -13,19 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
-#!/bin/bash
-
-# SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
-# SPDX-License-Identifier: LicenseRef-NvidiaProprietary
-#
-# NVIDIA CORPORATION, its affiliates and licensors retain all intellectual
-# property and proprietary rights in and to this material, related
-# documentation and any modifications thereto. Any use, reproduction,
-# disclosure or distribution of this material and related documentation
-# without an express license agreement from NVIDIA CORPORATION or
-# its affiliates is strictly prohibited.
-
 import torch
 import torch.nn as nn
 

bionemo/model/protein/equidock/model/layers.py

@@ -13,19 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
-#!/bin/bash
-
-# SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
-# SPDX-License-Identifier: LicenseRef-NvidiaProprietary
-#
-# NVIDIA CORPORATION, its affiliates and licensors retain all intellectual
-# property and proprietary rights in and to this material, related
-# documentation and any modifications thereto. Any use, reproduction,
-# disclosure or distribution of this material and related documentation
-# without an express license agreement from NVIDIA CORPORATION or
-# its affiliates is strictly prohibited.
-
 import math
 
 import torch

bionemo/model/protein/equidock/model/rigid_docking_model.py

@@ -13,19 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
-#!/bin/bash
-
-# SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
-# SPDX-License-Identifier: LicenseRef-NvidiaProprietary
-#
-# NVIDIA CORPORATION, its affiliates and licensors retain all intellectual
-# property and proprietary rights in and to this material, related
-# documentation and any modifications thereto. Any use, reproduction,
-# disclosure or distribution of this material and related documentation
-# without an express license agreement from NVIDIA CORPORATION or
-# its affiliates is strictly prohibited.
-
 import dgl
 import torch
 from nemo.core import NeuralModule

bionemo/model/protein/equidock/model/utils.py

@@ -13,19 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
-#!/bin/bash
-
-# SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
-# SPDX-License-Identifier: LicenseRef-NvidiaProprietary
-#
-# NVIDIA CORPORATION, its affiliates and licensors retain all intellectual
-# property and proprietary rights in and to this material, related
-# documentation and any modifications thereto. Any use, reproduction,
-# disclosure or distribution of this material and related documentation
-# without an express license agreement from NVIDIA CORPORATION or
-# its affiliates is strictly prohibited.
-
 import torch
 from torch import nn
 from torch.nn import functional as F

bionemo/model/protein/equidock/utils/__init__.py

@@ -12,16 +12,3 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-
-
-#!/bin/bash
-
-# SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
-# SPDX-License-Identifier: LicenseRef-NvidiaProprietary
-#
-# NVIDIA CORPORATION, its affiliates and licensors retain all intellectual
-# property and proprietary rights in and to this material, related
-# documentation and any modifications thereto. Any use, reproduction,
-# disclosure or distribution of this material and related documentation
-# without an express license agreement from NVIDIA CORPORATION or
-# its affiliates is strictly prohibited.

bionemo/model/protein/equidock/utils/train_utils.py

@@ -13,19 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-
-#!/bin/bash
-
-# SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
-# SPDX-License-Identifier: LicenseRef-NvidiaProprietary
-#
-# NVIDIA CORPORATION, its affiliates and licensors retain all intellectual
-# property and proprietary rights in and to this material, related
-# documentation and any modifications thereto. Any use, reproduction,
-# disclosure or distribution of this material and related documentation
-# without an express license agreement from NVIDIA CORPORATION or
-# its affiliates is strictly prohibited.
-
 import warnings
 
 import dgl