sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
2b98616c4d338f81991400078340f8546057f327ad8adc03051f3c206e4e63de | Python | 26,385 | 806 | """Sample size predictions based on a linear model."""
import numbers
from pkg_resources import resource_filename
import numpy as np
import xarray as xr
from sklearn.linear_model import LinearRegression
# from ..sample_analysis import analyze_model_parameters
from .interpolation import calc_n_required_all_metrics, ... |
3fd1b345f2d53fac58fc4e1383813a9e85acc4d4801576ce5d498bff1feb1ba5 | Python | 26,394 | 767 | """Product of manifolds.
Lead author: Nicolas Guigui, John Harvey.
"""
import math
import geomstats.backend as gs
import geomstats.errors
from geomstats.geometry.complex_manifold import ComplexManifold
from geomstats.geometry.complex_riemannian_metric import ComplexRiemannianMetric
from geomstats.geometry.manifold i... |
de082947e786e8014a1d006f500729d6dd48dd7f7ee564bb7ab04a0417c1626f | Python | 26,442 | 823 | import tensorflow as tf
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
from matplotlib import cm, gridspec
import scipy
import seaborn as sns
import random
import itertools
import keras
from scipy.sparse.linalg import lsmr
import statsmodels.api as sm
from scipy.stats import pearsonr, spearma... |
33dd2094e16f8b70d50a4fc3bc0357877774014c0f8981848415f23663e286e3 | Python | 26,471 | 667 | """Load an intracellular current-clamp NWB file into a SanPy ``bAnalysis``.
This standalone development script defines an NWB file-loader subclass and
injects it into ``bAnalysis`` without modifying SanPy's installed loader
registry. Edit ``NWB_PATH`` in the ``__main__`` block before running it.
run with:
uv run ... |
0e19022b1d251dde6c7b9533450dc27c33059359845023701caa2155055a7384 | Python | 26,477 | 693 | # Copyright (c) 2020 PaddlePaddle Authors. 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 appli... |
493e5504b21b6bfc6b2ee9a2ed4c5ba47a5a1026040a9c680b0c24e877e67a2d | Python | 26,480 | 815 | from typing import TYPE_CHECKING
from chromadb import (
CollectionMetadata,
Embeddings,
GetResult,
IDs,
Where,
WhereDocument,
Include,
Documents,
Metadatas,
QueryResult,
URIs,
)
from chromadb.api import ServerAPI
if TYPE_CHECKING:
from chromadb.api.models.AttachedFuncti... |
34bfc1a260e5abe28bf628d833fd6981409124f53f771d851513509f597e4347 | Python | 26,539 | 716 | # sys
import sys
import os
import shutil
import dill
import configparser
from pathlib import Path
# sci
import numpy as np
import pandas as pd
from sklearn.cluster import KMeans
from sklearn.decomposition import PCA
import quantities as pq
# ephys
import neo
import elephant as ele
# plotting
import matplotlib as mpl... |
012c98cb09ef5839738c6645f37fe266bc3f4d82cf0b534afaa8797e840b7007 | Python | 26,540 | 759 | # Script containing the modular version of the code
# so far we have only implemented the non_linear_embedding layer
# for simplicity we can just use dense layers for the merge operations
import numpy as np
# import matplotlib.pyplot as plt
import torch
import h5py
import torch.nn as nn
from torch.utils import data
... |
fe41cb2fe1e7e470ca8ca1700e03d7120a2c3e546f3927658ca23c0c5648f01a | Python | 26,559 | 875 | """
Session and experiment management
Author: Tal Eisenberg, 2021
Responsible for creating/continuing/deleting sessions and loading, running, and managing the
lifecycle of experiment modules.
"""
from datetime import datetime
import inspect
import re
import json
import shutil
import pandas as pd
from pathlib import ... |
1b72060cf028ea4f674b612c2cc45650fcfb0ffb7de328be7227ba91d945c7d4 | Python | 26,596 | 764 | # -*- coding: utf-8 -*-
#
#
# PyRates software framework for flexible implementation of neural
# network model_templates and simulations. See also:
# https://github.com/pyrates-neuroscience/PyRates
#
# Copyright (C) 2017-2018 the original authors (Richard Gast and
# Daniel Rose), the Max-Planck-Institute for Human Cogn... |
6cb705bfccd7ac836334d4726d39cc8789df9ad6259f432b5c23c0da2ed779d1 | Python | 26,617 | 705 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
"""
RoBERTa: A Robustly Optimized BERT Pretraining Approach.
"""
import logging
import torch
import torch.nn as nn
import torch.nn.functional... |
abffd3309025766fdc0eea28d9a6230ca534a502eea03c83927270fd409c81b9 | Python | 26,619 | 688 | from typing import Dict, Optional, Sequence, Tuple, TypedDict, Union, cast
from uuid import UUID
import json
import numpy as np
from numpy.typing import NDArray
import chromadb.proto.chroma_pb2 as chroma_pb
import chromadb.proto.query_executor_pb2 as query_pb
from chromadb.api.collection_configuration import (
co... |
a9731c5177425cf6c350b5d35fbe834a044ca8c33538212bfdb967e40e7e0a36 | Python | 26,698 | 691 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import logging
import os
import warnings
from argparse import Namespace
from typing import Any, Callable, Dict, List
import torch
from fairse... |
6331717b475e71a546c8540f90e4f535ed33c51186e595e6334815b2f0367f68 | Python | 26,704 | 581 | """Test suite for basic backend simulation functionalities.
"""
# external _imports
from typing import Union
import numpy as np
import pytest
# pyrates internal _imports
from pyrates import integrate
# meta infos
__author__ = "Richard Gast, Daniel Rose"
__status__ = "Development"
###########
# Utility #
###########... |
93533821541143e14e89f91f42e38ba27eb51805b6961666ccaaa3e46f01d103 | Python | 26,717 | 671 | import seaborn as sns
import numpy as np
import scanpy as sc
import squidpy as sq
from scipy.spatial import distance_matrix
from scipy.spatial.distance import *
import time
import anndata as ad
from sklearn.metrics import *
from sklearn.ensemble import RandomForestRegressor,RandomForestClassifier
from sklearn.multioutp... |
ea79bb94fa50526d533339d0e0ef4c9e22759886737bc881d5525a6e3e7a5d32 | Python | 26,724 | 748 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import contextlib
import copy
import logging
import math
import re
from argparse import Namespace
from dataclasses import dataclass, field
fro... |
f981cccab721432ccf535c298a576678823fa674795e4d23f374df242edfc0c2 | Python | 26,727 | 673 | from PymoNNto.NetworkCore.Network import *
import numpy as np
import matplotlib.pylab as plt
from collections import Counter
import scipy.sparse as sp
class Reconstruct_Analyze_Label_Network():
def __init__(self, network):
self.network = network
def get_network_responses(self, pattern_group, target_... |
33d2a0ddcc398812022e3b78d8054982dfa1be6817202a9ce0fb84b0b6a4991f | Python | 26,793 | 796 | #import matplotlib
#matplotlib.use('Qt5Agg')
from PyQt5 import QtCore
from PyQt5.QtGui import *
from PyQt5.QtWidgets import *
import pyqtgraph as pg
import numpy as np
#from Exploration.Visualization.Visualization_Helper import *
from PyQt5.QtWidgets import QTabWidget
from PyQt5.QtCore import Qt, QPoint, QMimeData
fr... |
53778db36c080681f8d3d56e0e77e84fda81ee0d5e01a11892a38b57eeebe327 | Python | 26,793 | 523 | import numpy as np
# import tensorflow as tf
import tensorflow.compat.v1 as tf
tf.disable_v2_behavior()
import os
import sys
import time
import NALSM_GEN_SUPPORT as sup
import NALSM_PARALLEL_SAVE as parasaver
import NALSM_CONSTRUCTOR_MNIST as construct
import NALSM_SIM_SUPPORT as runSupport
class run_sim:
... |
a8b27b0152a33811d37e8605b3541047395cac587d8651750418cbdf4a1a3a8d | Python | 26,798 | 557 | # %%
import os
import sys
import math
import numpy as np
import time
import h5py
import pyfftw
from scipy import sparse
from scipy import signal
from scipy import special
from scipy.optimize import linear_sum_assignment
from scipy.io import savemat, loadmat
import multiprocessing as mp
from suns.Online.par_online impo... |
90b24000fc1e773200625db55772345c2669d60fc36cd96ab4f0df04d12962db | Python | 26,804 | 604 | """ROC (Receiver Operating Characteristic) analysis for single-interval classification.
These tools provide the ability to quickly run receiver operating characteristic
analyses on the output of machine-learning models applied to imaging data.
"""
import numpy as np
from nltools.plotting import _plot_roc
from scipy.s... |
bfd17de5cb587f788e74fe2a6efae6d420a144ec78dac2a67624e90a7144ead3 | Python | 26,821 | 788 | """
Descriptive statistical functions
"""
from __future__ import absolute_import
from functools import wraps
import itertools
from decorator import decorator
import numpy as np
from scipy import stats
import warnings
from . import CI
from .iterators import nd_bootstrap
from .decorators import mod2pi, swap2zeroaxis
... |
7aee3fa029a670a68d29eb2f238c9f0548849e1ea989775060935fc6a8238d73 | Python | 26,844 | 870 | """
This module is responsible for creating visualizations for images, videos, statistical plots and notebook widgets.
Documented more loosely than the other modules, as it's less important
Authors: Tal Eisenberg, Itai Turkenish, 2020
"""
import os
import numpy as np
import cv2 as cv
import matplotlib.pyplot as plt
f... |
c7f03e780618209acce7e38ecb69d944b00fa2b9b2be2343cd5b80126835fb25 | Python | 26,854 | 948 | """Module exposing the `Matrices` and `MatricesMetric` class."""
import logging
import math
from functools import reduce
import geomstats.backend as gs
import geomstats.errors
from geomstats.algebra_utils import flip_determinant, from_vector_to_diagonal_matrix
from geomstats.geometry.base import MatrixVectorSpace
fro... |
43f3ad422fe10996e66c0bb80d8269b9cab0c810f10256143fd8d4979fff663b | Python | 26,873 | 842 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import argparse
import collections
import contextlib
import copy
import importlib
import logging
import os
import sys
import warnings
from ite... |
f5044ccdd389b47c4e9b22982ec57470e015e25a36edaa876ffd3548ef8f845b | Python | 26,894 | 652 | import logging
import os
import pickle
import coloredlogs
import numpy as np
import torch
import torch.nn.functional as F
from einops import rearrange
from torch import nn
from adni.models.network import make_network
from common.adni.utils import CATEGORICAL_COLS, NUMERICAL_COLS, CATEGORY2CLASSNUM, IMAGING_COLS, remo... |
53b92729825fa2e95148671125ca3538e73b989e604803c732f92c2d9962e417 | Python | 26,922 | 747 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import copy
import logging
from typing import Dict, List, Optional, Tuple
import numpy as np
import torch
import torch.nn as nn
from torch im... |
4b795613af2a04058c5b19a4f66ce4c7049266d6380fbbb86655baa22f8a5199 | Python | 26,923 | 720 | # Copyright (c) 2023 PaddlePaddle Authors. 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 appli... |
f5b077dce7aac75b2250d1f13ffe894a030fb8833d0ee671a89c458cbeb22203 | Python | 26,926 | 749 | # copyright (c) 2022 PaddlePaddle Authors. All Rights Reserve.
# 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... |
73aad30520402f62da0b18e9d1df3c90f95f674f5b4db2d738faf5d5dcfa4db9 | Python | 26,929 | 588 | """The release comparison, on fixtures small enough to reason about.
The comparison is the acceptance gate for every later phase, so its own failure modes matter more
than most: one that under-reports would wave a regression through, and one that over-reports would
be switched off.
"""
from __future__ import annotatio... |
9915c7afa4ebeecd8b8ef86e2320a8a1710baf20fe84d2f1fb0ab7c9d344f54f | Python | 26,949 | 811 | import torch
import numpy as np
import matplotlib.pyplot as plt
import matplotlib
from matplotlib import cm
from matplotlib.axes import Axes
from matplotlib.image import AxesImage
from torch.nn.modules.utils import _pair
from matplotlib.collections import PathCollection
from mpl_toolkits.axes_grid1 import make_axes_lo... |
6a690d12df79cbca1fd37d172d279bdc1abe9974698240436a32b242e3437caa | Python | 26,954 | 723 | """MACE TorchSim model interface."""
from __future__ import annotations
import logging
from pathlib import Path
from typing import Any, Callable, Dict, Optional, Union
import torch
from mace.modules.extensions import PolarMACE
from mace.tools import atomic_numbers_to_indices, utils
log = logging.getLogger(__name__... |
dd90a78aefbdd3d3d1739fdce8130f11a126731d04d33fed1e0e0bf5224db459 | Python | 26,968 | 524 | import numpy as np
# import tensorflow as tf
import tensorflow.compat.v1 as tf
tf.disable_v2_behavior()
import os
import sys
import time
import NALSM_CONSTRUCTOR_MNIST as construct
import NALSM_GEN_SUPPORT as sup
import NALSM_PARALLEL_SAVE as parasaver
import NALSM_SIM_SUPPORT as runSupport
class run_sim... |
0679d8dfd96124d1cf5b51032d237fdb2226b18e02d4278e09fb43e07e2c47f5 | Python | 27,040 | 604 | # Copyright 2020-2024 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""Experimental Aggregator module."""
import asyncio
import inspect
import queue
import time
from copy import deepcopy
from logging import getLogger
from threading import Event
from typing import Any, Callable, Dict, List, Tuple
import di... |
0a91f0d3b73111e7b1a38d0dfb1f60fcfdbbf36582fc2799c6e17c100007a622 | Python | 27,049 | 884 | import itertools
import numpy as np
import numba as nb
from scipy import linalg, signal
# -----------------------------------------------------------------------------
# trajectory functions
class LazyTrajectories:
"""Load trajectories lazily from disk.
Parameters
----------
filenames : list of str... |
ee07ced3abb874bd672b5b16d6ae8752187001fe1f033da8d0ff0e2eae93da29 | Python | 27,063 | 842 | from __future__ import print_function
import os
import subprocess
import glob
import copy
import pprint
import torch
import numpy as np
import matplotlib.pyplot as plt
import utils
import analysis_utils
from dataset_learning_trainable import DatasetLearningTrainable
import torch.nn as nn
import torch.nn.functional ... |
9d409e0fc5c6b69a931455e43ca6559c8bf78f7313af84916e807758414e4bd1 | Python | 27,079 | 865 | # Authors: Carolina Fernandez <cxf418@miami.edu>
# Nick Tolley <nicholas_tolley@brown.edu>
# Ryan Thorpe <ryan_thorpe@brown.edu>
# Mainak Jas <mjas@mgh.harvard.edu>
import pickle
from hnn_core import simulate_dipole
from hnn_core.dipole import _rmse
from hnn_core.optimization import Optimiz... |
572334c3cb64309261bc921b0f02daac6cdfe4f7e4519081674a7f5b40ff20cf | Python | 27,126 | 638 | # Copyright (c) 2021 PaddlePaddle Authors. 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 appli... |
47635ecd549c00e5f67fddebd705adaa8516ea762121818445639961687e5ad0 | Python | 27,172 | 868 | from __future__ import absolute_import, division, print_function
from builtins import range
import os
import numpy as np
import pickle
import gzip
import math
import random
import pymatgen as mg
import rdkit
from rdkit import DataStructs
from rdkit.Chem import AllChem as Chem
from rdkit.Chem import Crippen, MolFromSmil... |
71bd1f016e2e204f39f244ed5bbef28ad51bbfc506f345c36c74e1025dd45aa6 | Python | 27,186 | 528 | import numpy as np
# import tensorflow as tf
import tensorflow.compat.v1 as tf
tf.disable_v2_behavior()
import os
import sys
import time
import LSM_STDP_CONSTRUCTOR_MNIST as construct
import NALSM_PARALLEL_SAVE as parasaver
import NALSM_SIM_SUPPORT as runSupport
import NALSM_GEN_SUPPORT as sup
class run_... |
8f142e4f8b0a0a6172ea49286cdf5c3cfa2a85ecd145f353a65e0442bb1cdc55 | Python | 27,209 | 678 | import scipy.io
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.colors import to_rgba
import os
import pandas as pd
# =============================================================================
# path configuration <- edit this section before running
# ===================================... |
f2d5c262bde718952173ffec686aa6e8f664dc84c196a03b24b29cf9d3727858 | Python | 27,227 | 546 | import numpy as np
# import tensorflow as tf
import tensorflow.compat.v1 as tf
tf.disable_v2_behavior()
import os
import sys
import time
import LSM_APSTDP_CONSTRUCTOR_N_MNIST as construct
import NALSM_PARALLEL_SAVE as parasaver
import NALSM_SIM_SUPPORT as runSupport
import NALSM_GEN_SUPPORT as sup
class ... |
416aade3af5ae445bd996fef6efbc68f46204dc93204a5fee41f5a7339f24fef | Python | 27,238 | 666 | import logging
import os
import pickle
import coloredlogs
import numpy as np
import torch
import torch.nn.functional as F
from einops import rearrange
from torch import nn
from adni.models.network import make_network
from common.adni.utils import CATEGORICAL_COLS, NUMERICAL_COLS, CATEGORY2CLASSNUM, IMAGING_COLS, remo... |
44bcc13462a55d227998a055f59d3e1afa071ebd5646ee8d1dac6ca5f14d8d3d | Python | 27,273 | 823 | #!/usr/bin/env python
# coding: latin-1
""" Shared Response Model (SRM)
===========================
The implementations are based on the following publications:
Chen, P. H. C., Chen, J., Yeshurun, Y., Hasson, U., Haxby, J., & Ramadge,
P. J. (2015). A reduced-dimension fMRI shared response model. In A... |
d3f2cc0ee763cecb26d0aac0f0769355db3466da063190cb4d65dee79e654553 | Python | 27,274 | 648 | """pfl3_stim.py
Analysis and plotting functions for PFL3_LAL_stimulation.ipynb
"""
import os
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
import scipy as sc
import matplotlib as mpl
import read_data as rd
import analysis_plot as ap
import functions as fc
import plotti... |
8d4a62f703b7f2e6bef63aab7e0900b3db18cb86d7afaa2eb57c3aa3b16990eb | Python | 27,290 | 800 | # Copyright 2020-2024 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""openfl.experimental.workflow.utilities.metaflow_utils module."""
from __future__ import annotations
import ast
import fcntl
import hashlib
import os
import tempfile
from datetime import datetime
from pathlib import Path
# getsource on... |
457db7b5211788f140d6016d1d7f9fe0799aadbf865456e2645078cad487f2d4 | Python | 27,326 | 518 | # Copyright 2025 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
from hashlib import sha256, sha384
import json
from unittest.mock import MagicMock, patch
from openfl.federated.data.sources.azure_blob_data_source import AzureBlobDataSource
from openfl.federated.data.sources.local_data_source import LocalDataSo... |
0cbf933acdbeb02f05721902b231a34ec2fb97bbcbe0889cfa2982a401b165c6 | Python | 27,335 | 712 | """
Created on Sat September 17 21:15:06 2023
Description: Datasets class implementation for
Paper url: https://www.biorxiv.org/content/10.1101/2023.09.11.557230v2
@author: Ekaterina Kuzmina, ekaterina.kuzmina@skoltech.ru
@author: Dmitrii Kriukov, dmitrii.kriukov@skoltech.ru
"""
import mat73
import numpy as np
impor... |
8a5a8e8066c1997550c3e4c00a2ac6aae289a16fb0a28fa9535bb639a1c1ab05 | Python | 27,369 | 595 | # Copyright 2025 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
import json
import os
from pathlib import Path
from typing import List, Tuple
from unittest.mock import MagicMock, patch
import pytest
import boto3
from moto import mock_aws
import torch
from torchvision.transforms import ToTensor
import io
fro... |
65fb539ca1501b9b209e13d182edb26549f34d64ae9aa031d14da3c81752e35f | Python | 27,372 | 903 | import asyncio
import os
from typing import Any, Dict, List, Optional, Union
from uuid import uuid4
import numpy as np
import pytest
from chromadb.api import ClientAPI
from chromadb.api.client import Client as ClientCreator
from chromadb.api.conditional_http import ConditionalHttpTransaction
from chromadb.api.models.... |
deb1a3507dce17b510cd755f2a73817ea1ead5c49b2ab33b8323f4df0dcd117e | Python | 27,456 | 688 | """
metrics for the neuron project
If you use this code, please cite the following, and read function docs for further info/citations
Dalca AV, Guttag J, Sabuncu MR
Anatomical Priors in Convolutional Networks for Unsupervised Biomedical Segmentation,
CVPR 2018. https://arxiv.org/abs/1903.03148
Copyright 2020 Adrian... |
1de7f4112036481de1c629f7568a1e94b5a91fa09929aa00ac021a3d15be0bb0 | Python | 27,480 | 678 | #!/usr/bin/env python3
#
# Sniffles2
# A fast structural variant caller for long-read sequencing data
#
# Created: 28.05.2021
# Author: Moritz Smolka
# Maintainer: Hermann Romanek
# Contact: sniffles@romanek.at
#
import logging
import time
from dataclasses import dataclass
from typing import Optional, Ite... |
dfbcd138db1c17c31a73e4178eb95b5fadad6130ab0ccf180ce5fb2c4f6038cf | Python | 27,484 | 768 | from PymoNNto.Exploration.UI_Base import *
from PyQt5 import QtCore, QtGui, QtWidgets
from PyQt5 import QtCore
from PyQt5.QtGui import *
from PyQt5.QtWidgets import *
import pyqtgraph as pg
import copy
import sys
import traceback
from PymoNNto.NetworkCore.Neuron_Group import *
from PymoNNto.NetworkCore.Synapse_Group im... |
f239fb9d06b044662167fc175780217a1aff7ebad1f2b558328d8906131f264a | Python | 27,524 | 558 | import numpy as np
import math
import statistics
# If we are given a diagonal matrix D = (d1, ..., d_n) and want to compute the eigenvalues
# of D + u u^T, these are up to deflation of trivial eigenvalues given by the solutions of the
# so-called secular equation, given by
# 1 + \sum_{i = 1}^n u_i^2 / (d_i + \lambda... |
17e57cde92654d39f7343a287596719da93786b727be435b248996f1b1f0e4a6 | Python | 27,557 | 660 | # Copyright (c) 2024 PaddlePaddle Authors. 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 appli... |
bb2088a1e1895294d51f217fb821319acda40a422c5edfbd14d8ff9b5f9f82f5 | Python | 27,579 | 690 | import torch
import numpy as np
from ase import Atoms
import ase.build
from nequip.data import AtomicDataDict, from_dict, from_ase
from nequip.data.transforms import (
VirialToStressTransform,
StressSignFlipTransform,
NeighborListTransform,
SortedNeighborListTransform,
ChemicalSpeciesToAtomTypeMap... |
163ab876c383b33028a3fb27c6377472d0140235fe6b1d97ce86853c0ea9fb1d | Python | 27,592 | 766 | import sys
import time
from pathlib import Path
import h5py
import numpy as np
import pandas as pd
from scipy import signal
import Analyses.spatial_functions as spatial_funcs
import Utils.filter_functions as filt_funcs
import Pre_Processing.pre_process_functions as pp_funcs
import matplotlib.pyplot as plt
from shape... |
3183a6fd46efcf36460dc95ef5b7ad01d315eb00449aece5ad51c054a8f2f2c5 | Python | 27,599 | 540 | import numpy as np
# import tensorflow as tf
import tensorflow.compat.v1 as tf
tf.disable_v2_behavior()
import os
import sys
import time
import LSM_APSTDP_CONSTRUCTOR_MNIST as construct
import NALSM_PARALLEL_SAVE as parasaver
import NALSM_SIM_SUPPORT as runSupport
import NALSM_GEN_SUPPORT as sup
class ru... |
f8a434b6f851967c11c2fc28ee15a653b20de4d53684b091cbcd1a705fd9fe66 | Python | 27,631 | 711 | import numpy as np
import statsmodels.api as sm
import pandas as pd
import statsmodels.formula.api as smf
import scipy.stats as stats
import ipywidgets as widgets
from ipywidgets import interact, fixed, interact_manual
from IPython.display import display
import warnings
from statsmodels.tools.sm_exceptions import Con... |
181ae68a7a8c1c89cfd503a520d76c42f847ababb4adf178d13216159c8e3f80 | Python | 27,666 | 765 | """utils.py: Module for general data eeg data operations."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import math
import os
import numpy as np
from scipy.interpolate import interp1d
from scipy.signal import (
resample_poly,
butter,
filtf... |
3a3c8c3941798e0da325eb853531017901c32bc3a69fa03edb1aa7ffede8741f | Python | 27,694 | 587 | import io
import json
from datetime import datetime, timedelta
import django_rq
import pandas as pd
from asgiref.sync import async_to_sync
from channels.layers import get_channel_layer
from django.db.models import Count
from django.db.models.functions import TruncDate, TruncDay, TruncWeek
from request.models import Re... |
f869ebd45ac3f15f78391284811b79d8084aa5f8dac4c5d36b361c35864afdb6 | Python | 27,718 | 760 | # Copyright 2020-2024 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""Plan module."""
from functools import partial
from hashlib import sha384
from importlib import import_module
from logging import getLogger
from os.path import splitext
from pathlib import Path
from yaml import SafeDumper, dump, safe_lo... |
066514a0b3f75ea589d1ec167b4f27e22bb5aa8f6db138e704a41e5980b3131e | Python | 27,730 | 803 | """Utilities for converting Snakemake apps to BIDS apps."""
from __future__ import annotations
import json
import logging
import os
import re
import warnings
from collections import defaultdict
from pathlib import Path
from typing import (
Any,
Iterable,
Literal,
overload,
)
import more_itertools as ... |
fd20c6fa9c5e55352b550d38147a7a447396afa06b4ed02866842d07c68a9732 | Python | 27,777 | 592 | import json
import coloredlogs
import hydra
import pandas as pd
from omegaconf import OmegaConf
from omegaconf.listconfig import ListConfig
from sklearn.metrics import f1_score, roc_auc_score, average_precision_score, balanced_accuracy_score, \
mean_squared_error, accuracy_score, mean_absolute_error
from tqdm impo... |
50d5e1a2ce062a4c1b8d1cb7d478e473626d5b8dfa8b68ec478c045be91b7d4d | Python | 27,782 | 767 | ###########################################################################################
# Long Range Blocks
# Authors: Will Baldwin, Ilyes Batatia
# This program is distributed under the MIT License (see MIT.md)
###########################################################################################
from __futu... |
680015acae0f857c969a7fe5ea46271e8166c81677dcb8fa21ad8c10bf29480c | Python | 27,794 | 797 | #
# For licensing see accompanying LICENSE file.
# Copyright (C) 2022 Apple Inc. All Rights Reserved.
#
import torch
from torch import nn, Tensor
from typing import Optional, Union, Tuple
import argparse
from utils import logger
from .base_layer import BaseLayer
from .normalization_layers import get_normalization_la... |
58a7ab12141d82f68e0ca91b172a5445be8d88d8f4135008d22475cb23b5fbab | Python | 27,855 | 728 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
from typing import Dict, List, Optional
import torch
import torch.nn as nn
from torch import Tensor
from fairseq import utils
from fairseq.m... |
b78eff9d027cfc2a3ea078a3862406cdfb0f6afc6ee4e3b537d8dcf31131c5ef | Python | 27,856 | 691 | """Model fitting, contrasts, and statistical tests for `BrainData`.
GLM and ridge fitting (with cross-validation), contrast computation, one- and
two-sample t-tests, and the design-matrix diagnostics `fit` runs before a GLM.
`BrainData` methods delegate here.
"""
import dataclasses
import warnings
from collections.ab... |
9943d46e1f9de50e60301f330d3f524adf84584a2b363fd9a1263596d2e618b6 | Python | 27,865 | 662 | from typing import Any, Sequence
import jax
from jax import vmap
from jax import numpy as jnp
from .jax_utils import val_and_jacrev, val_and_jacfwd
from flax import linen as nn
Dtype = Any
class HelmholtzModel(nn.Module):
"""
Helmholtz free energy model based on artificial neural networks for the Mie fluid
... |
a88cc69b6c283f02ab0ec8d66ff2aa05c86d7629798719f905400f5cbed7f496 | Python | 27,902 | 503 | from models.rnn import *
from models.schnet import *
from utils import *
from torch import optim
import time
from sklearn.metrics import r2_score
class ReactionCLModel:
def __init__(self, args=None):
self.args = args
multi = 2 if args.rnn_use_bidirectional else 1
self.Projector = MLP(input... |
f31f882a0458aa7194a351cbaa2e87fe6393e0dee5f5a59be2d619d056f35f9a | Python | 27,923 | 964 | import os
import re
import openpyxl
import csv
import pronto
import distutils
import distutils.util
import urllib.request
import json
import re
import requests
import traceback
BCIOVOCAB_API = "https://api.bciosearch.org/"
GET_TERMS_BY_LABEL = "terms?label={}&page={}&itemsPerPage={}"
GET_TERMS = "terms/{}"
POST_TERM... |
fc1b129195e22436379092752093657300326996e0673e59bdb5f952df3026ad | Python | 27,928 | 745 | from __future__ import absolute_import
import torch
import numpy as np
import pandas as pd
import scipy
import copy
from pysurvival import HAS_GPU
from pysurvival import utils
from pysurvival.utils import neural_networks as nn
from pysurvival.utils import optimization as opt
from pysurvival.models import BaseModel
from... |
b31d7984f211aad941195e92091cd08591ed6ee4a34c18883d1361f28a7624d7 | Python | 27,944 | 669 | from pathlib import Path
from os import environ
import io
import itertools
import re
from contextlib import redirect_stdout
from importlib.metadata import PackageNotFoundError, distribution
from threading import Thread, Event
from time import sleep
from urllib.request import urlretrieve
import numpy as np
from numpy i... |
f82148080b8ba512015f0a530554ca793ce10d0b8236b2768971bb3e5787d05a | Python | 27,972 | 663 | # Copyright (c) 2025 PaddlePaddle Authors. 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 appli... |
22bcd99b85942b14bb010d70d4dadfc4ca3c303f978053fe60aaa6155984bcf4 | Python | 28,015 | 660 | # python function
import numpy as np
# import matplotlib.pyplot as plt
import torch
import math
import random
from sklearn import svm
import itertools
import os
import copy
from sklearn.model_selection import StratifiedKFold
from sklearn.model_selection import ShuffleSplit
from sklearn.metrics import mean_squared_error... |
7c128e539637925ec04415e26fdbb0dbd19379126e837f90f68e0b7c54ed61e7 | Python | 28,031 | 687 | # Copyright (c) 2020 PaddlePaddle Authors. 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 app... |
319b0c678c78a9da8db9d5a261f253614dffed81b1f5fe92a0a69dd78c67ae9c | Python | 28,049 | 723 | # import pdb
import numpy as np
import torch
import torch.nn as nn
class SampleCNNGA(nn.Module):
def __init__(self, n_classes=2, in_channels=42):
super(SampleCNNGA, self).__init__()
self.in_channels = in_channels
# 300 x 42
self.conv1 = nn.Sequential(
nn.Conv1d(in_cha... |
f400d848c4961d63bc9f51993905f047a2d41ae4ae2c6c409557882595c2b47d | Python | 28,049 | 715 | # -*- coding: utf-8 -*-
"""
Created on Tue Jun 13 09:49:46 2023
@author: Em
"""
from .utils import get_device
from .core import core
from torch import (is_tensor,
tensor,
arange,
manual_seed,
randperm,
zeros,
... |
96f9e2eb1919fac1698b08793f7e323afb5e1de7226d63d8f1baa081d802130b | Python | 28,056 | 752 | # Copyright (c) 2021 PaddlePaddle Authors. 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 appli... |
5e2233bf8f83b4ca216914b2c90b493177f5c03d1b46d33a0f8cdbf0eba9f1df | Python | 28,116 | 645 | """The differentiable physics glue, characterized against finite differences.
**These docstrings are normative.** CORE-3 copies the three sign conventions
below verbatim into the rewrite's units module, and every one of them is
asserted by a test in this file rather than assumed:
* **forces** = -dE/d(positions), in e... |
7bbe2c63a820bfd1e2929a3761989ff32d3d4624e489fdb787aa354ad5df9436 | Python | 28,117 | 778 | import os
import sys
from pathlib import Path
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
import sssio
import sssort.functions as sf
import sssort.plotters as sp
from functions_post_processing import *
import configparser
from sssort import sssio
logger = sssio.get_logger() # FIXME
plt.r... |
c5d6227c54d03f5971b7be842ce4e37a0f5d764c7811a1e3a7b13f1f78efd058 | Python | 28,187 | 862 | # -*- coding: utf-8 -*-
"""
Functions to facilitate task-based validation.
Created on Oct 25 2023
@author: Mohammad Torabi
"""
import warnings
import matplotlib.pyplot as plt
import numpy as np
from nilearn import glm
from scipy import signal
from sklearn.mixture import GaussianMixture
from statsmodels.tsa.stattools... |
0c632f7767b15dbbed3d00f0d141a8f65efe28dd095c2335eb9599d23cdbd16f | Python | 28,195 | 930 | """Estimate statistics on a grid using DGA with memory."""
import numpy as np
import scipy as sp
__all__ = [
"stationary_distribution",
"stationary_distribution_matrices",
"stationary_distribution_projection",
"stationary_distribution_solution",
"forecast",
"forecast_matrices",
"forecast_p... |
31f3326b4639b14a1656bd9815699f118d5879acb08f4c28463c2812bb00cbb1 | Python | 28,211 | 645 | import numpy as np
import os
# import tensorflow as tf
import tensorflow.compat.v1 as tf
tf.disable_v2_behavior()
import NALSM_GEN_SUPPORT as sup
class run_support:
def __init__(self,number_of_networks_IN):
self.main_Path = os.getcwd()
self.dataPath_TRAIN = self.main_Path + '/train_data... |
6907f645504910b16071ae5f222b0fad16c5ac6b0047dba2f5acae472eac86a6 | Python | 28,231 | 739 | # Copyright 2020-2024 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""PyTorchTaskRunner module."""
import logging
import os
from copy import deepcopy
from typing import Iterator, Tuple
import numpy as np
import torch
import torch.nn as nn
import tqdm
from openfl.federated.task.runner import TaskRunner
f... |
62d13ec3c24e4c47251ad69e518249a5c8667fdc4092bdc43902f43706379a10 | Python | 28,234 | 677 | # -*- coding: utf-8 -*-
"""Provides the abstract reconstructor base class."""
import os
from inspect import signature, Parameter
import json
from warnings import warn
from copy import deepcopy
class _ReconstructorMeta(type):
def __init__(cls, name, bases, dct):
def get_fget(k):
def fget(self):... |
92677d309e48ddd94cff3e78536030d34baa2fecb4dc450830ffc011059bd53d | Python | 28,256 | 657 | """The tiny magnetic anchor reproduces its committed reference.
This is the numerical reference the magnetic family did not have. The
behavioural suite next door (``tests/extensions/magnetic``, 39 tests) covers
rotation equivariance, inversion parity, parameter registration, calculator
backends and dtype scoping -- pr... |
5cb3fe8ad0f95eeab5b3329e0b9378849640ecc5297cceb160843db29c235755 | Python | 28,329 | 875 | from typing import Optional, Sequence
from types import TracebackType
from uuid import UUID
from overrides import override
import httpx
from chromadb.api import AdminAPI, ClientAPI, ServerAPI
from chromadb.api.collection_configuration import (
CreateCollectionConfiguration,
UpdateCollectionConfiguration,
v... |
fa211b159f64182854deeb4bfd7e52694aead0df013b6d66071662634dd4effb | Python | 28,351 | 839 | from typing import Any, Dict, List, Optional, cast
import uuid
from hypothesis import example, given, settings, HealthCheck
import pytest
from typing import cast
from chromadb.api import ClientAPI
from chromadb.test.property import invariants
from chromadb.api.types import (
Document,
Documents,
Embedding,
... |
f1315e3b4e88306063db3e2bd8fb2cb874f83811909c91f6d9bdaf5725e0e8b4 | Python | 28,363 | 635 | # OS stuff
import os
import sys
import warnings
from pathlib import Path
# Computational stuff
import numpy as np
import matplotlib as mplb
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpecFromSubplotSpec
from matplotlib import ticker
# TensorPAC
from tensorpac import Pac, PreferredPhase
from t... |
068a9fec461d626af92e91f2626678bf620d7105d88dc1f22b58eae3b8d6c432 | Python | 28,387 | 846 | # Copyright (c) 2021 PaddlePaddle Authors. 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
#
# Un... |
88501b890c8e64c380195e41a8f06699f07d68f7fcf2fb6d6e50f8f18bcb1a7d | Python | 28,453 | 657 | import torch
import torch.nn.functional as F
import torch.nn as nn
import ISNetLayersZe as ISNetLayers
import ISNetFunctionsZe as ISNetFunctions
import LRPDenseNetZe as LRPDenseNet
import globalsZe as globals
import pytorch_lightning as pl
import warnings
from collections import OrderedDict
import numpy as np
from torc... |
8c44c61886aa1c48c2619252c7b2cbcb4c27de7f756ade38269814941d3e84f5 | Python | 28,495 | 615 | import time
import os
import copy
import torch
from torch.optim import Adam
from tqdm import tqdm
from rdkit import Chem
from dig.ggraph.method import Generator
from dig.ggraph.utils import gen_mol_from_one_shot_tensor
from dig.ggraph.utils import qed, calculate_min_plogp, reward_target_molecule_similarity
from .en... |
1432352df6c03a4b2d356e562894cd7e24d89c0d17569aa9300ee611175d7226 | Python | 28,502 | 840 | """
NeuroLearn Plotting Tools
=========================
Numerous functions to plot data
"""
__all__ = [
"dist_from_hyperplane_plot",
"scatterplot",
"probability_plot",
"roc_plot",
"plot_stacked_adjacency",
"plot_mean_label_distance",
"plot_between_label_distance",
"plot_silhouette",
... |
6c7a2beff053c2607b39b7b2700f24287e7df8371e82664b09a19ad52c0f80b4 | Python | 28,510 | 855 | # Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
# SPDX-License-Identifier: MIT-0
"""
Train and evaluate EGGNet models
"""
from rdkit import Chem
from transformers import T5Tokenizer, T5EncoderModel
import pytorch_lightning as pl
from pytorch_lightning.callbacks.early_stopping import EarlyStopping
f... |
643894bcd22f8e5e15404777baa50d593664c7adbd0d589dce9d4e097727030b | Python | 28,541 | 685 | import logging
from pathlib import Path
from typing import Literal
import numpy as np
from idtrackerai import (
Fragment,
GlobalFragment,
ListOfFragments,
ListOfGlobalFragments,
conf,
)
from ..network import IdentifierBase, get_predictions
AccStrategy = Literal["global", "partial"]
rng = np.ra... |
8508e6cdd364c6c5f89960893dc3df6a596201acd481c9f087234818782d049a | Python | 28,560 | 773 | """Tests for bootstrap inference utilities."""
import tracemalloc
import numpy as np
import pytest
from nltools.algorithms.backends import check_gpu_available
from nltools.algorithms.inference.bootstrap import (
_BootstrapAccumulator,
_bootstrap_ridge_predict_cpu_parallel,
_bootstrap_ridge_weights_cpu_pa... |
d77279a8bfa0e2b2baf9c653c69d355dd868c14f6daa40753d8f6feff94e4590 | Python | 28,602 | 787 | import argparse
import inspect
import json
import os
from pathlib import Path
from typing import Any, Dict, List, Optional, Sequence, Tuple
import numpy as np
import pandas as pd
from pydfc.ml_utils import (
dFC_feature_extraction_subj_lvl,
find_available_subjects,
load_dFC,
load_task_data,
)
def st... |
28a6df7bd55513aa904d0f1f3df2c2ec1dafe4f89362935ab0ddc35aae148292 | Python | 28,618 | 682 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import contextlib
import json
import logging
import math
import os
from argparse import Namespace
from collections import OrderedDict, default... |
5a128d7bf399efc21fba7165dbd3a11ec6d5718c227d497aae2df04dc8caf1b6 | Python | 28,709 | 686 | # -*- coding: utf-8 -*-
"""Provides the dataset base classes.
"""
from itertools import islice
from math import ceil
import numpy as np
from dival.data import DataPairs
from dival.util.odl_utility import NoiseOperator
class Dataset():
"""Dataset base class.
Subclasses must either implement :meth:`generator` ... |
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