sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
21b1ab533465d4e3245897d658d7554cb34435b30699749dcd7d242e8154eb4a | Python | 44,813 | 1,068 | import os
import cv2
import imgui
import numpy as np
import threading
import pyperclip
from typing import Optional, Tuple, Union
from .roi import ROIWidget
from .._renderer import CapturedException
from ..utils import EasyDict, LEFT_MOUSE_BUTTON, RIGHT_MOUSE_BUTTON
from ..gui import imgui_utils, gl_utils
import slide... |
7c8d8142099b21da47492483997d78a03992eddb12ce2aa46a6e9cd64bc08ade | Python | 45,015 | 1,164 | # Copyright 2026 The HuggingFace Team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicabl... |
e5c9d9ab8a93e26b8c62bbb121073607cc54cf9e69a1ca66bbf58dd0d082e956 | Python | 45,139 | 975 |
from matplotlib import pyplot as plt
import matplotlib as mpl
from matplotlib.gridspec import GridSpec
import numpy as np
import os
import pandas as pd
from scipy import stats as sp
from pathlib import Path
from connectivity import visualize as vis
from connectivity import nib_utils as nio
import connectivity.consta... |
5e570031034c79994271a35f2821cd55c161bc59ced2b4ee09c082959006b246 | Python | 45,234 | 1,237 | """
RDA Frequency Labeler: Label frequency for unlabeled LRDA/GRDA segments.
Targets segments with >=50% IIIC agreement that lack frequency labels.
Uses W05_DomOnly_IterRefine (Hilbert + iterative narrowband) for default
frequency estimate. Also runs Tautan et al. for comparison.
UI: EEG with narrowband overlay at se... |
a7f31a4f4ce928fb0bce7c92dd674fb18d05fd1acda39cbb21680d472145fda1 | Python | 45,261 | 1,143 | from typing import TYPE_CHECKING, Any, Dict, List, Optional, Tuple, Union
import os
import pickle
import numpy as np
import pandas as pd
import slideflow as sf
import warnings
from os.path import join, exists, isdir
from pandas.core.frame import DataFrame
from sklearn.cluster import KMeans
from slideflow import errors... |
63173ee1a44b2ebc82123e560e25deaa706f2ba3fab1f963e8a052f112c20af8 | Python | 45,328 | 1,113 | # Copyright 2020 The Facebook AI Research Team Authors and The HuggingFace Inc. team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Un... |
411e5c400731211c7558b129352e19bf8441aef4c469fc14cd6e7eee9b98db04 | Python | 45,412 | 1,231 | """Functions for extracting subgraphs.
The module only contains functions for extracting subgraphs deterministically.
For stochastic subgraph extraction, please see functions under :mod:`dgl.sampling`.
"""
from collections.abc import Mapping
from . import backend as F, graph_index, heterograph_index, utils
from ._ffi... |
d376ea7f253bc0464e2573a7ceb268d20ceaddec6dff25dc7962096654864e22 | Python | 45,484 | 1,393 | """Torch modules for graph global pooling."""
# pylint: disable= no-member, arguments-differ, invalid-name, W0235
import numpy as np
import torch as th
import torch.nn as nn
from ...backend import pytorch as F
from ...base import dgl_warning
from ...readout import (
broadcast_nodes,
max_nodes,
mean_nodes,
... |
8ad01442a04272196f9859705e0e1e6ccd0f331a5f30fca7621aaa7242f34613 | Python | 45,535 | 1,386 | """A set of graph services of getting subgraphs from DistGraph"""
import os
from collections import namedtuple
import numpy as np
import torch
from .. import backend as F, graphbolt as gb
from ..base import EID, ETYPE, NID
from ..convert import graph, heterograph
from ..sampling import (
sample_etype_neighbors ... |
d7d4a816b0256df55ef780dd6cfd8bfdd683ade386e86ea3cb68e463eec0015e | Python | 45,588 | 1,292 | """Provide concrete implementation for feature storage via HDF5."""
# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
# Federico Raimondo <f.raimondo@fz-juelich.de>
# License: AGPL
import io
from collections import defaultdict
from collections.abc import Sequence
from pathlib import Path
from typing import ... |
3a12ea1a9566c318441b8659cdd2b57945d82ea0581324757a74b776b0129a95 | Python | 45,676 | 1,177 | """
Tool Name: cxr_ett_tip_to_carina_report
========================================
Write final review artifacts for the CXR ETT tip-to-carina workflow.
Produces one overlay PNG and one JSON per sample, plus a small dataset-level
CSV and HTML page rebuilt from the available per-sample JSON files.
"""
from __future__... |
8dfa9d80d969e4df814bdf1efd19e4b9fbff2f5bf97ee1632edfe6fd09dc915d | Python | 45,732 | 1,103 | # Copyright 2021 The Marian Team Authors and The HuggingFace Inc. team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0... |
fecb57047226597456e8badd6013dab622cdd3996a70cd442ea7eefe2b6aced4 | Python | 45,743 | 1,020 | # Copyright 2022 Meta Platforms, Inc. and The HuggingFace Inc. team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
... |
1f7c4e0090e9b23cfd9f39b844858f45d338bcb12f6c93fb4ce79e3cb59b6b55 | Python | 45,744 | 1,121 | # 🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨
# This file was automatically generated from src/transformers/models/clipseg/modular_clipseg.py.
# Do NOT edit this file manually as any edits will be overwritten by the generation o... |
634424649d28bb1df4a80af7f985eccb3f24bc83d48b969972b58514f83a50ea | Python | 45,746 | 1,013 | # Copyright 2025 Baidu Inc and The HuggingFace Inc. team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
888f9b604d89d55f78af92e9afa3e8ff43c661ae72046fe08ebc992edb8af6a2 | Python | 45,763 | 1,276 | """
prepare_fmap_intendedfor.py
---------------------------
For each sub/ses, populate the ``IntendedFor`` field in all fmap JSON sidecars.
How it works
------------
1. Read AcquisitionTime from every func JSON sidecar (bold + sbref).
2. Read AcquisitionTime from every fmap JSON sidecar (AP and PA epi).
3. Sort fmaps ... |
10ef83437e0b211200d99e6a05d882db6a78952277ba699e37a4c46a66634a62 | Python | 45,815 | 1,314 | # -----------------------------------------------------------------------------
# Copyright (c) Yongning Lei 2024-2025
# All rights reserved.
#
# This script is distributed under the Apache-2.0 license.
# You may use, distribute, and modify this code under the terms of the Apache-2.0 license.
# See the LICENSE file for... |
e11e39607b878fb3ba8bccde6126c188c449a407c700d5489cddf88fe3d47ee4 | Python | 45,980 | 1,189 | """Tools for evaluation MIL models."""
import os
import inspect
import pandas as pd
import slideflow as sf
import numpy as np
from rich.progress import Progress, track
from os.path import join, exists, dirname
from typing import Union, List, Optional, Callable, Tuple, Any, TYPE_CHECKING
from slideflow import Dataset,... |
72eee708425655cf8007ca1cfe308a9f55aae05333e6040db045c61c7f26b407 | Python | 46,057 | 1,018 | # Copyright 2026 Google Inc. HuggingFace Inc. team. All rights reserved.
#
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requir... |
e8157283bfccd7cb82160d318937f026083666df47fc2510cff9f2a4dbad32a4 | Python | 46,172 | 944 | # Copyright 2021 The HuggingFace Inc. team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed ... |
c9a982e59d582ee039abe3cf0b591164282d19febeef8c663ced0b0fcde541f3 | Python | 46,187 | 1,158 | # Copyright 2020 Microsoft and the Hugging Face Inc. team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable... |
68a6a052fe2e79309d0c03f0cdac12d6147ede8cac91a0386659c9156b2a6bce | Python | 46,213 | 951 | import time
import os
from os.path import dirname, abspath
import sys
import shutil
import warnings
import numpy as np
from collections import namedtuple
import json
import h5py
from tqdm import tqdm
import torch
from torch import optim
from torch.utils.data import SubsetRandomSampler, DataLoader
from torch.utils.tens... |
49a1d54cb6427bd9e4027de4fe1f3e906545339b84bc78a32fe6fa3454e92594 | Python | 46,232 | 1,202 | # Copyright 2024 HuggingFace Inc. team. All rights reserved.
#
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applic... |
87434c5b365d3a34db274992afa46c535a55c778bdf1c51f9f401448bcf0db66 | Python | 46,245 | 1,333 | # -----------------------------------------------------------------------------
# Copyright (c) Yongning Lei 2024-2025
# All rights reserved.
#
# This script is distributed under the Apache-2.0 license.
# You may use, distribute, and modify this code under the terms of the Apache-2.0 license.
# See the LICENSE file for... |
9f46a6a11be21f6c66005b9897bc986ac9fcd5b335651287789f8dea7cf255ef | Python | 46,399 | 1,338 | # -----------------------------------------------------------------------------
# Copyright (c) Yongning Lei 2024-2025
# All rights reserved.
#
# This script is distributed under the Apache-2.0 license.
# You may use, distribute, and modify this code under the terms of the Apache-2.0 license.
# See the LICENSE file for... |
bf4eaab3a17515b7ee9087a725dec2d0f3185448b1053b9f0fd2ddb2a16edaf6 | Python | 46,450 | 1,236 | # Copyright (c) 2026 ByteDance Ltd. and/or its affiliates
# SPDX-License-Identifier: Apache-2.0
# mypy: disable-error-code="attr-defined"
"""Source construction and distillation for the molecular LIT workflow."""
from __future__ import annotations
import logging
from dataclasses import replace
import jax
import num... |
f12d0e90c194b166b6d82e9fb36ac099c2f7c1d5d6ae10299116924ff28b4dcb | Python | 46,563 | 1,085 | # 🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨
# This file was automatically generated from src/transformers/models/bailing_hybrid/modular_bailing_hybrid.py.
# Do NOT edit this file manually as any edits will be overwritten by th... |
d5c70aec3646b86ed82354e7bfa674032ab16b71a59f2b95f42adbd0c84dd507 | Python | 46,586 | 844 | # Copyright 2026 The HuggingFace Inc. team
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed t... |
6940521448b4376c8bd00862bd39895193085600673642bff9e19f2637011c81 | Python | 46,604 | 1,025 | # Copyright 2025 The HuggingFace Team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicabl... |
43b2a208ed6bd36c48c10b20beed5c9f8058d9aec407d7906feae442e5d4f8bf | Python | 46,902 | 1,319 | # Copyright (c) 2026 ByteDance Ltd. and/or its affiliates
# SPDX-License-Identifier: Apache-2.0
# ruff: noqa: DOC201,DOC501
"""Direct NQS Lorentz integral transform for molecular dipole response.
This module follows the correction-vector formulation used in
arXiv:2504.20195: a full neural response wavefunction ``Psi_... |
d527490bb4aad958506cd63bd03096400503d242a66be49594abde8cf48b3283 | Python | 46,976 | 1,153 | # 🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨
# This file was automatically generated from src/transformers/models/beit/modular_beit.py.
# Do NOT edit this file manually as any edits will be overwritten by the generation of
# ... |
c09c6b42b1989ddcf40218ab17c5beddc7892a9d41cdca17b2f8cf9b99660429 | Python | 47,015 | 1,082 | # Copyright 2024 Meta Inc. and The HuggingFace Inc. team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless re... |
a560f205a74ac04e380cbda1cb3a6ff7e4ade3c723f5c6a102716a949783f815 | Python | 47,027 | 1,179 | # Copyright 2021 The I-BERT Authors (Sehoon Kim, Amir Gholami, Zhewei Yao,
# Michael Mahoney, Kurt Keutzer - UC Berkeley) and The HuggingFace Inc. team.
# Copyright (c) 2021, NVIDIA CORPORATION. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except ... |
ffcca6a8920b3d0d9836b1e10b94690945a96b7582d9a482ed44f939ea4c1434 | Python | 47,046 | 1,632 | """Provide tests for API functions."""
# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
# Leonard Sasse <l.sasse@fz-juelich.de>
# Synchon Mandal <s.mandal@fz-juelich.de>
# License: AGPL
import logging
import sys
import tempfile
from contextlib import AbstractContextManager, nullcontext
from c... |
4ac9f90d24f60b7bb3d4b7796fdceec67037e890086d539385bf40df6acb1b6c | Python | 47,123 | 1,122 | # 🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨
# This file was automatically generated from src/transformers/models/hubert/modular_hubert.py.
# Do NOT edit this file manually as any edits will be overwritten by the generation of
... |
1b197549e11ab1642f2567cb122dc08d483641497592b0f0554f7b83e612dded | Python | 47,280 | 2,102 | """This file defines the unified tensor framework interface required by DGL.
The principles of this interface:
* There should be as few interfaces as possible.
* The interface is used by DGL system so it is more important to have
clean definition rather than convenient usage.
* Default arguments should be avoided.
*... |
a3185dce6e297ad23194d26f24effc92e7223a9a7a3ff991770879798967c3ef | Python | 47,431 | 1,166 | # Copyright 2022 Intel Labs, OpenMMLab and The HuggingFace Inc. team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#... |
286630321893f37b69446e71c2b07feba4d20d8b21ef33155871a9b083c2acf5 | Python | 47,482 | 1,125 | # 🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨
# This file was automatically generated from src/transformers/models/aria/modular_aria.py.
# Do NOT edit this file manually as any edits will be overwritten by the generation of
# ... |
cb7c386d5de19228284fc100fc3e205955a8362313057ff701cfc816eda5eb16 | Python | 47,562 | 792 | # Copyright 2026 The HuggingFace Inc. team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed ... |
09feff890e0c38cc6a468c05aadea56139bf7a500f6e36b83906039a96f2f19e | Python | 47,645 | 1,325 | from copy import deepcopy
from heapq import heapify, heappop, heappush, nsmallest
import dgl
import numpy as np
# We use lapjv implementation (https://github.com/src-d/lapjv) to solve assignment problem, because of its scalability
# Also see https://github.com/berhane/LAP-solvers for benchmarking of LAP solvers
from ... |
b8edee2da6c4aced5f7e030958f43409783025a56a281308013fdf4f242b52a2 | Python | 47,748 | 1,170 | # 🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨
# This file was automatically generated from src/transformers/models/metaclip_2/modular_metaclip_2.py.
# Do NOT edit this file manually as any edits will be overwritten by the genera... |
b6eab4c2170101f2b045affa855504ce504aa23a3fed6cfada5f174086673a02 | Python | 47,798 | 1,259 | """
Phase 2: Retrain ChannelPD-Net with balanced LPD/GPD data and a
heteroscedastic uncertainty head for frequency estimation.
Key changes from V1/V3:
- freq_head split into freq_head_mu + freq_head_logvar (uncertainty)
- Heteroscedastic NLL loss instead of MSE for frequency
- GPD frequency examples upweighted 3... |
e1b3ce0b5ce2eedcdf5bf6b0417676b25b8673bb0e14eb25f50623e954008c8f | Python | 47,861 | 1,477 | """DGL sparse matrix module."""
# pylint: disable= invalid-name
from typing import Optional, Tuple
import torch
class SparseMatrix:
r"""Class for sparse matrix."""
def __init__(self, c_sparse_matrix: torch.ScriptObject):
self.c_sparse_matrix = c_sparse_matrix
def __repr__(self):
return ... |
b17eff257f7bb060ffff47c7fdd560abc36b6845e444d75082efc51b917173b8 | Python | 47,974 | 1,183 | # 🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨
# This file was automatically generated from src/transformers/models/data2vec/modular_data2vec_text.py.
# Do NOT edit this file manually as any edits will be overwritten by the gener... |
4e04c9b30978909ee31e06aeed2ebc94ad3d90f738b1f532ede07a1345f4d721 | Python | 48,047 | 1,607 | """Module for heterogeneous graph index class definition."""
from __future__ import absolute_import
import itertools
import sys
import numpy as np
import scipy
from . import backend as F, utils
from ._ffi.function import _init_api
from ._ffi.object import ObjectBase, register_object
from ._ffi.streams import to_dgl_... |
4d504cd1ea42676f03e3720601e986084a3f8b8cc882db068f1732d413cd1a96 | Python | 48,581 | 1,231 | """Libvips slide-reading backend.
Requires: libvips (https://libvips.github.io/libvips/)
"""
import re
import cv2
import numpy as np
import slideflow as sf
import xml.etree.ElementTree as ET
from types import SimpleNamespace
from PIL import Image, UnidentifiedImageError
from typing import (Any, Dict, List, Optional, ... |
c549d2af26f30fc7bcda9d716b997b341cf895d318d3eb1c8b52886776788c09 | Python | 48,642 | 1,114 | # Copyright 2024 the HuggingFace Inc. team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... |
068e5bc6886be9970ea96dfeb83d24133f8101d978e97d7bc9fb71d94a7b2d20 | Python | 48,656 | 1,117 | # 🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨
# This file was automatically generated from src/transformers/models/gemma3/modular_gemma3.py.
# Do NOT edit this file manually as any edits will be overwritten by the generation of
... |
0c0a4930c817a9fd2434d10ea82206fc02310998fa5f34ada1a4466c9358e552 | Python | 48,704 | 1,005 | # Copyright 2022 The HuggingFace Inc. team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed ... |
e87ea019b47b70dc75a269e135d86657438c805f77c04256dc5aec36ca977210 | Python | 48,744 | 1,362 | """PipelineCreator class."""
# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
# Sami Hamdan <s.hamdan@fz-juelich.de>
# License: AGPL
import typing
from dataclasses import dataclass, field
from typing import Any
import sklearn
from scipy import stats
from sklearn.ensemble import AdaBoostClassifier, Ad... |
93ba4270e4ea9be82a0e9b90c21ae1b0539d2c75c3c191ba86f595e745cd180e | Python | 48,785 | 1,277 | #!/usr/bin/env python3
"""
Check Analysis Integrity (Generic Engine)
==========================================
Validates completeness of neuroimaging analysis folders.
All analysis-specific knowledge (file lists, folder structure, timing logic)
lives in analysis_checker/. This file contains only:
- AnalysisSpec AB... |
f368ee43d646fa72a31130eaf0bf7f6484f9ba52ebdd0684cdb82dc5f2b49fdc | Python | 48,791 | 1,128 | # Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with
# the License. You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by... |
c18e5f3e447dfcafb089ae542f538d42fc30459b3f735b6d33d69c1ed4c8a61e | Python | 48,993 | 1,119 | # Copyright 2024 The HuggingFace Inc. team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... |
59e2cae203b822378e0b6c9efba98a3fe26c3f59e3c42ee58943316f54a674df | Python | 49,104 | 1,158 | # Copyright 2022 Microsoft Research and The HuggingFace Inc. team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ap... |
5642ab84815cbaae1794a2e615237b5ca6c26c109fbfbf314bfaec984ad07ada | Python | 49,309 | 1,145 | # Copyright 2024 The HuggingFace Inc. team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... |
6d2d50fc6db756211a1f6ff0119fcf7e9116ff80ba314562376ed06a7fc76837 | Python | 49,410 | 1,139 | # Copyright 2022 The HuggingFace Inc. team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed ... |
ae257dfde3fd36410d6af9dfc2661ac2837724bd33aa1774b8b5ba37c87cb47e | Python | 49,485 | 1,176 | # Copyright 2025 HuggingFace Inc. team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
5b0e8c8be47436f43bd569ebbb5f1535ed62f12b0d5a02bcaae465107b9c420c | Python | 49,799 | 1,111 | """V4 Unified Methods Round 2 — 25 methods targeting AUC>0.814 AND Freq ρ>0.667.
All methods process hemispheres independently, outputting:
left_score, right_score — for lateralization + classification
extras.freq — frequency estimate from dominant hemisphere
"""
import numpy as np
from scipy.signal import wel... |
dedf404dbc353961aa6ff23aa6b068a623821f9f2a18bee46e00e96dba923234 | Python | 49,815 | 1,394 | """
Runtime support: replay reuse
=================================
Description:
Helper functions used by run_plan.py to compare a current plan against
prior blackboard run_start records and decide whether tool outputs can be
reused.
Arguments:
- replay_plan_id: run to be replayed
- re... |
d68de1e50c186b5135aa67fec9ee2c3a9841e06beb62f41fd2a8c7cc5135f583 | Python | 49,943 | 1,439 | import os
import sys
import logging
import copy
import math
from abc import ABCMeta, abstractmethod
import mne
import numpy as np
# from scipy.fftpack import rfft, rfftfreq
from scipy.signal import welch, decimate
from scipy.signal import decimate, welch
from cycler import cycler
import matplotlib
from matplotlib imp... |
a1266ed90c378718f41e84d4eab28c0e4b131e12e915af2fd210f5950a49fe7a | Python | 49,974 | 1,076 | # 🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨
# This file was automatically generated from src/transformers/models/csm/modular_csm.py.
# Do NOT edit this file manually as any edits will be overwritten by the generation of
# ... |
4206cd351e54ca8acb65c57a6df8d9ddcea6541af444687d182450fd01d42f2a | Python | 50,143 | 1,142 | """
=====================================================
:mod:`benchmarks` -- Benchmark optimization functions
=====================================================
This module provides a set of benchmark problems for global optimization.
.. Copyright 2012 Aaron Garrett
.. Permission is here... |
669f99cf24035c71e9fca14ddcca47edc82ee2b65e22911147a9042114cc7a87 | Python | 50,335 | 1,152 | # Copyright 2025 The ZhipuAI Inc. team and HuggingFace Inc. team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... |
baabca31a84e136ffee8bdef3ee838faf3a61b8061db64672c3cfee68e5ca656 | Python | 50,363 | 1,338 | """
HemiCET Optimization — Experiments E5, E6, E7 (E4 skipped — too slow)
Runs sequentially:
E5: HemiCET with 10 channels (8 hemisphere + Fz-Cz idx16 + Cz-Pz idx17)
E6: Multi-segment training (up to 5 segments per patient, standard 8ch)
E7: Gold-standard freq oracle test (how much room from better freq estimatio... |
f2dbc27819c3c8346396aaa0d8f0f4510df3a491b4822aca497af6bf95e6c9d8 | Python | 50,431 | 1,126 | # 🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨
# This file was automatically generated from src/transformers/models/conditional_detr/modular_conditional_detr.py.
# Do NOT edit this file manually as any edits will be overwritten b... |
e283c187560eee847193e96cbd2d24ec088d48b268fa16608275e52d813559a8 | Python | 50,462 | 1,129 | # Copyright 2018 The OpenAI Team Authors and HuggingFace Inc. team.
# Copyright (c) 2018, NVIDIA CORPORATION. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# htt... |
b4e2180d8262518271a1e3c7f11533e251cb6ce952b990b91efd197ff700ab9e | Python | 50,525 | 1,205 | # 🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨
# This file was automatically generated from src/transformers/models/falcon_h1/modular_falcon_h1.py.
# Do NOT edit this file manually as any edits will be overwritten by the generati... |
189f436a268fe79c691820aa3365513267d34a22e784a7cd8dce4ff9e649a6de | Python | 50,553 | 1,604 | """Define distributed kvstore"""
import os
import numpy as np
from .. import backend as F, utils
from .._ffi.ndarray import empty_shared_mem
from . import rpc
from .graph_partition_book import EdgePartitionPolicy, NodePartitionPolicy
from .standalone_kvstore import KVClient as SA_KVClient
#########################... |
27e0d41ee846b5aa98acf27303ef0404007a6c2500d89c1712e50517fee4f068 | Python | 50,605 | 1,289 | # Copyright 2022 The Salesforce Team Authors and The HuggingFace Team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
... |
cf97cfc6595271873c5f6a6c254cbcbbe6173ce8bcd991ff1743e438cd979930 | Python | 50,868 | 1,136 | """
Generate IRR comparison figure: expert-expert vs expert-algorithm reliability.
Computes ICC(3,1), Percentage Agreement, and MAE for frequency and spatial extent.
Compares 4 expert raters (LB, PH, SZ, MW) with PDProfiler (W05) and Tautan et al.
Layout: 2x4 subplot
Row 1: RDA (LRDA + GRDA)
Row 2: PD (LPD + GPD)... |
50dd0aa3424a4f7becfda482b92647226a7f7f176eb331bcb3e8e83f1564d91c | Python | 50,873 | 1,148 | # 🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨
# This file was automatically generated from src/transformers/models/conditional_detr/modular_conditional_detr.py.
# Do NOT edit this file manually as any edits will be overwritten b... |
50475379016bd421b991289c82f97063e52dcf61dc7ae852df2759aef5125fe9 | Python | 51,201 | 1,362 | #!/usr/bin/env python
"""
Collection of plotting functions and utilities for Hi-C analysis
Part of ChromaWalker package
"""
import numpy as np
import os
import sys
#import matplotlib as mpl
#mpl.use('Agg')
import matplotlib.pyplot as plt
import random
import copy
import matplotlib.gridspec as gridspec
from time impo... |
6aed8324961c1d48eea18073e34eee37e54c9c232707e940b8c0f2b1899713d6 | Python | 51,205 | 1,250 | #!/usr/bin/python
from __future__ import division
__author__ = "Donghoon Lee"
__copyright__ = "Copyright 2019, Gerstein Lab"
__credits__ = ["Donghoon Lee", "Mark Gerstein"]
__license__ = "GPL"
__version__ = "1.0.0"
__maintainer__ = "Donghoon Lee"
__email__ = "donghoon.lee@yale.edu"
import numpy as np
import pandas as... |
4c5f04d5b13b39da1829810a5f7ff2f1138482d7cc0b41029ff6c2f8043b8795 | Python | 51,317 | 1,411 | """
LRDA Labeling Tool — frequency, laterality, and wave morphology annotation.
For each LRDA segment, pre-computes NVO (Narrowband Variance Optimization)
across a grid of candidate frequencies. The HTML viewer lets MW:
1. Pick a frequency (buttons or slider) — see per-channel VE heatmap update
2. Label lateralit... |
7f3c28b102ec3696ffa21e1307277ae3ee8fe4de5235b51ab13722986af97ce3 | Python | 51,544 | 1,232 | # 🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨
# This file was automatically generated from src/transformers/models/data2vec/modular_data2vec_audio.py.
# Do NOT edit this file manually as any edits will be overwritten by the gene... |
b1393dd524193e987c340b2cf5131250e640a49f84fd784ce06f16ceb31a35d7 | Python | 51,868 | 1,451 | """
Spatial Labeling Viewer for PD and RDA EEG Segments.
Generates HTML viewers where MW can review and correct model-predicted
spatial localization (which brain regions are involved with periodic/rhythmic
discharges).
For LPD/GPD: uses PDProfiler for channel_probs and region_scores.
For LRDA/GRDA: uses PLV-based sco... |
7945c4d657cfcbedfba08cefd9c6b848cc089e91ccca83eff9a8f03143753c89 | Python | 52,122 | 1,252 | # 🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨
# This file was automatically generated from src/transformers/models/camembert/modular_camembert.py.
# Do NOT edit this file manually as any edits will be overwritten by the generati... |
65e3997c4a0a43115411eed711786dbaa65593c43791a5838f66e588f0f0db18 | Python | 52,134 | 1,372 | #!/usr/bin/env python
"""
Collection of target set optimization functions and utilities for Hi-C analysis
Part of ChromaWalker package
"""
import numpy as np
import os
import sys
import matplotlib.pyplot as plt
import random
import copy
from time import time
import hicutils as hcu
import plotutils as plu
import hicF... |
1e393190959104efe283e8eae1073e608fa635a85847978f8f1c720fec183761 | Python | 52,201 | 1,474 | """
PD Frequency + Timing Labeler (LPD / GPD).
For each segment missing frequency+timing labels:
1. Runs PDProfiler for default frequency/laterality prediction
2. Precomputes HPP discharge times at each frequency button
3. Generates an HTML viewer where MW can:
- Select frequency via up/down arrows (or clic... |
d5b96b4f32452fc66b125d53849a8e6dfcf85b14f9ea3702ff4fc47c681252c0 | Python | 52,297 | 1,269 | # Copyright 2025 The HuggingFace Team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicabl... |
a1e7cb015a9bb8f57bf8af86ab674d8bd03f14f6b19375d622c1654b6e77a022 | Python | 52,480 | 1,204 | # Copyright 2022 Meta Platforms and The HuggingFace Inc. team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unle... |
b2fe6d1ac7a4af363efdab06c6c6e5b2708741994a5c024a70c51897268f84cf | Python | 52,936 | 1,157 | # Copyright 2022 Microsoft Research Asia and The HuggingFace Inc. team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0... |
c7297dfb28324e89bbfc4ad74e3db8a443854de7ddf384d2019781aca99b5494 | Python | 52,955 | 1,446 | import pandas as pd
import numpy as np
import math
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
from torch.autograd import Variable
from torch.distributions import NegativeBinomial, Normal, Distribution, Gamma, Poisson, constraints
from torch.distributions import kl_di... |
ea13e4a46a403f7a0d2f211f6d34b9b3d5cccfd39f39d7a546b5cf337e9822f9 | Python | 53,187 | 1,286 | # Copyright 2025 the HuggingFace Team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicabl... |
3e997324b91fbfea396c1bc2f0013d94fa3e4febfa1cdb244af0d936ef9399d1 | Python | 53,476 | 1,237 |
forceserial = False
import os
if forceserial:
os.environ['MKL_NUM_THREADS'] = '1'
os.environ['NUMEXPR_NUM_THREADS'] = '1'
os.environ['OMP_NUM_THREADS'] = '1'
import numpy as np
import matplotlib.pyplot as plt
import sys
import copy
import cPickle as pickle
from scipy.ndimage.filters import gaussian_fi... |
4a82c41e467f6aee9cb858b34a2fff4dfb29976028026626fb221d46a825870a | Python | 53,492 | 1,271 | # Copyright 2026 The HuggingFace Team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicabl... |
0575af98a7d087357cd356f17dc2e4c2ed607276860a9a66dcd4b330b07e3443 | Python | 53,714 | 1,342 | #!/usr/bin/env python
"""
Collection of data-file handling functions and utilities for Hi-C analysis
Part of ChromaWalker package
"""
import numpy as np
import os
import sys
import copy
from time import sleep
import cPickle as pickle
import hicFileIO as hfio
import msmBasics as mb
import msmTPT as mt
import matplotl... |
70b724009bbe95e9336ec8ad11289c87fc3a116a0da17b06fc6a9ff55284b70c | Python | 53,781 | 1,165 | # Copyright 2026 the HuggingFace Team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicabl... |
0401b12f5c3f4c8fc425e2eabfcb6c15a6ae1e7f8de5691ae6ffd6bdb1ea0eb1 | Python | 53,812 | 1,328 | # Copyright 2020 Microsoft and the Hugging Face Inc. team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable... |
405792c8ebd70504d8eb556fd2754e079ab91d819b8a25f36e87731ee9613ea7 | Python | 53,967 | 1,331 | # Copyright 2022 NVIDIA and The HuggingFace Team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required b... |
56e3dedc5e1eb99af92b3c316f32efcdc1f3fad1939b364b1bb3a9aa8ca68aef | Python | 54,332 | 1,311 | # Copyright 2021 The Fairseq Authors and The HuggingFace Inc. team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
#... |
deb68dcf652538a886893af36a159c9ae88bdd6dec19c79ddbf506e6311f34e2 | Python | 54,364 | 1,369 | # Copyright 2018 The Google AI Language Team Authors and The HuggingFace Inc. team.
# Copyright (c) 2018, NVIDIA CORPORATION. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the Licens... |
a2864630f1d1793a09e70b615c2f8c04b8ef6c08fbbafefb0538ade916e666b1 | Python | 54,425 | 1,222 | # Copyright 2023 the Falcon authors and HuggingFace Inc. team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unl... |
f3561090b834b94d9ad8f6a0e24ba9a1832518c715ace22d8cd696f00d40a744 | Python | 54,496 | 1,211 | # 🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨
# This file was automatically generated from src/transformers/models/eomt/modular_eomt.py.
# Do NOT edit this file manually as any edits will be overwritten by the generation of
# ... |
994a7ae2094ba7527ac6210f4d0ff92b845ae68bff3447be505144ed3a43e4fa | Python | 54,881 | 1,019 | '''
Pymol script for quantifying peptide-receptor models.
Author: Xiaozhe Ding
Email: xding@caltech.edu, dingxiaozhe@gmail.com
'''
import platform
import sys
import argparse
import glob
import os
import csv
from datetime import datetime
import numpy as np
import numpy.linalg as LA
from itertools import groupby
from... |
2f47baaf930fc4c1d562d70316c7cfae440cd390b540fd3d57c4f590d91f11b9 | Python | 54,900 | 1,266 | # Copyright 2022 EleutherAI and the HuggingFace Inc. team. All rights reserved.
#
# This code is based on EleutherAI's GPT-NeoX library and the GPT-NeoX
# and OPT implementations in this library. It has been modified from its
# original forms to accommodate minor architectural differences compared
# to GPT-NeoX and OPT... |
7a8fa98d08fccad6b5e3328a15fe84f2444fd0e36ada392e9b3996a5cb7a218f | Python | 54,947 | 1,295 | # 🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨🚨
# This file was automatically generated from src/transformers/models/granitemoehybrid/modular_granitemoehybrid.py.
# Do NOT edit this file manually as any edits will be overwritten b... |
6ca524d7a1aa57bb4ece08a23f8ca78cdaff8d25494264e6cf29e6b906827a96 | Python | 55,006 | 970 | # -*- coding: utf-8 -*-
"""
Functions for Cb Stellate model
"""
__author__ = "Nils A. Koch"
__copyright__ = "Copyright 2022, Nils A. Koch"
__license__ = "MIT"
import h5py
import gc
import scipy
import json
import copy
import os
import numpy as np
from numba import types, njit
from numba.typed import Dict
from scipy ... |
a801ec166e37523ee6b1c0805c9b8dcad7b32e68e15b1dc4c2dd99e4f0212da3 | Python | 55,243 | 1,222 | # Copyright 2026 The HuggingFace Inc. team. All rights reserved.
# Modifications Copyright (C) 2025, Advanced Micro Devices, Inc. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the Lic... |
1f545081a3a829fc02dc8d1905658e1ab4ec511e7f15582fa395a3e846c66cc3 | Python | 55,285 | 1,516 | # Copyright (c) 2026 ByteDance Ltd. and/or its affiliates
# SPDX-License-Identifier: Apache-2.0
# mypy: disable-error-code="attr-defined"
"""Frequency optimization and estimators for the molecular LIT workflow."""
from __future__ import annotations
import hashlib
import logging
import jax
import numpy as np
from ja... |
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