sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
54465e7026702c2aaee1a2fb521ca63ffd84ecd338fb5d9482df8cb093bb08bd | Python | 12,882 | 239 | """ Dataloader for all datasets. """
import os.path as osp
import os,json
from PIL import Image
import numpy as np
import pdb
import pandas as pd
import torch
from torch.utils.data import Dataset
from torchvision import transforms
import torch.nn.functional as F
from .augmentation_pool import RandAugmentMC,RandAugmentP... |
7241666b41c2dc2136fdba92dce15e47f8c1e996986b9c4f612ddaae7384d69a | Python | 12,904 | 439 | #!/usr/bin/env python3
########################################################################
#
# Copyright (c) 2021 by the contributors (see AUTHORS file)
#
# This file is part of the CRISPRon
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General ... |
b792efce0614a3660ff733eac101438ee8ce7e08dda9a703169eb3ead620f15d | Python | 12,910 | 326 | # coding = utf-8
# Copyright (C) 2022. Huawei Technologies Co., Ltd. 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
#
... |
0a6a850d2c02d18a4d2545a10929c7461a9860f6036ff40b6ba5afa3341e6693 | Python | 12,913 | 802 | # type specimen identifier mapping
# keys http://api.brain-map.org/api/v2/data/Specimen/
# values http://uri.interlex.org/npo/uris/neurons/
ts_mapping = {
566728192: 116,
523729022: 117,
483099796: 118,
486560376: 119,
483061182: 120,
483018019: 121,
502808270: 122,
486235288: 123,
484509440: 124,
486175203: 125,
4... |
ccb7e9952b8900083d17f2d3e97933e142d344b9633b77452b16c4a08d4f97a5 | Python | 12,915 | 277 | from mprl.utility_services.lock_server.protobuf.lock_server_pb2 import LockRequest, LockConfirmation, LockWorkerPing, LockList
from mprl.utility_services.lock_server.protobuf.lock_server_pb2_grpc import LockServerServicer, \
add_LockServerServicer_to_server
import logging
import threading
import os
from socket imp... |
1cbcfcfdecb2bd070e7633172d65de91fdaa0c75bef56d43754aa045b33e8426 | Python | 12,918 | 371 | # copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
# Ported from skchange (BSD-3-Clause), original authors: Tveten
"""Circular binary segmentation algorithm for segment anomaly detection."""
__author__ = ["Tveten"]
__all__ = ["CircularBinarySegmentation"]
import numpy as np
import pandas as pd
f... |
e338b494dacf28a220b3770276f978a058ef05918e735d7be9373086a1b3330a | Python | 12,918 | 378 | # Copyright 2019 DeepMind Technologies Ltd. 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... |
8843350a84e38df8be01b00f0fd3f3256e56bad070c8cc2f0a033b5ee1f8ee03 | Python | 12,925 | 269 | import os
import numpy as np
import torch
import cv2
from scipy.ndimage.measurements import label
import random
import custom_utils.transforms as T
def get_valid_filenames(dir_, masks=False):
"""Function to get all valid image and mask filenames in a directory"""
all_filenames = [f for f in os.listdir(dir_) ... |
17bff13836456ae62b7fdf2fcfb9b7027b83e11beec875be565a6485864ab224 | Python | 12,927 | 302 | import os
import importlib
import json
import glob
from jsonschema import validate
from datetime import datetime
from pathlib import Path
from time import time
import pickle
import numpy as np
import pandas as pd
from sklearn.pipeline import make_pipeline
from timeflux.core.node import Node
from timeflux.core.excepti... |
fa2c70e3b60eae01652a431de37793d2d0c7baf59c9de411fcaff2016cfbd41c | Python | 12,945 | 429 | from pathlib import Path
from utils.argparse_utils import get_bool, get_device, get_dtype
from utils.argparse_utils import (
parse_model_settings,
parse_plot_settings,
parse_covariance_test_settings,
parse_data_settings,
)
from utils.utils import create_model_folder, get_compression_rate
from utils.util... |
e8f6c9f8521e269eedd037b77a0936eeaedc30e216cb09fa23514d84f4da1f46 | Python | 12,951 | 370 | """
plot_conflict_shav.py
Produce circular scatter plots showing the change in bearing
between rolls three and four of the data generated by
conflict_shav.py.
Note that the same -s option can be specified here, in which
case the routine will load any data which was generated using
the adjusted reliability weighting m... |
13103506e85ae36f9340b6a7f58c4378b6a84c09ac0f6b0d604ed0355cbcc461 | Python | 12,978 | 312 | # Copyright 2019 DeepMind Technologies Limited
#
# 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 agr... |
f09a95ca7b1d73d53649b7e79cb6d57cd308feba04c445a9743c45ffba000347 | Python | 13,006 | 409 | """Module to parse and transform the different output files generated by VASP.
"""
from pyRDTP import geomio
from io import IOBase
import numpy as np
import xml.etree.ElementTree
class Frequencies:
"""Frequencies readed from OUTCAR file
Attributes:
freqs (lst of obj:`Freq`): List containing the diffe... |
0770cbcfd43b1cd1c0f9f73eb6e8b7cce971a86c8b1e38c353972b83d64a40ff | Python | 13,019 | 329 | # Copyright (c) ONNX Project Contributors
#
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import os
import tarfile
from collections import deque
from typing import TYPE_CHECKING
import onnx.checker
import onnx.helper
import onnx.shape_inference
if TYPE_CHECKING:
from onnx.onnx_pb impor... |
be9607bc8ef252f1386733966f7844df017d4aa0f4ee30894540f6f9452c8a53 | Python | 13,030 | 373 | #!/usr/bin/env python3 -u
# copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Implements base class for time series forests."""
__author__ = ["mloning", "AyushmaanSeth"]
__all__ = ["BaseTimeSeriesForest"]
from abc import abstractmethod
from warnings import catch_warnings, simplefilter
import n... |
5f7060ad4678e977160be841835e73cd77cbcd7d62fd20f9a3d9956ea26ffb5c | Python | 13,031 | 161 | # the original step3: train and test the phenotype confirmation model for rare disease entity linking filtering.
# updated with functions and for parameter tuning
# the program uses the output of mention_disamb_data files generated by step1_tr_data_creat_ment_disamb.py
from sent_bert_emb_viz_util import load_data,... |
6c09a68f59072033316bdb9a3c7f8ea269cee29e5c9fc445c956ac5aebdd475c | Python | 13,048 | 404 | # Copyright (c) OpenMMLab. All rights reserved.
import os.path as osp
import tempfile
from copy import deepcopy
import numpy as np
import pytest
import torch
from mmcv import ConfigDict
from mmcv.runner.base_module import BaseModule
from mmcls.models import CLASSIFIERS
from mmcls.models.classifiers import ImageClassi... |
535e95d757ebd924cb0526e27cb3fdd972e645578287d242e3a336f2dffda975 | Python | 13,059 | 368 | # Copyright (c) OpenMMLab. All rights reserved.
from copy import deepcopy
from typing import Sequence
import numpy as np
import torch
import torch.nn as nn
from mmcv.cnn import build_norm_layer
from mmcv.cnn.bricks.transformer import FFN
from mmcv.cnn.utils.weight_init import trunc_normal_
from mmcv.runner.base_module... |
2cb6208f2a8abdf958d994c87d8f985d2a86edefed5a5ad79e05dc6b885478ec | Python | 13,063 | 395 | """Forecasting benchmarks tests."""
import numpy as np
import pandas as pd
import pytest
from sklearn.model_selection import KFold
from sktime.benchmarking.benchmarks import _coerce_estimator_and_id
from sktime.benchmarking.forecasting import ForecastingBenchmark
from sktime.datasets import (
ForecastingData,
... |
8d9d306b1a582cd52405a6e9c66dccdde62e266aa78ddc9f020383d8f73355b3 | Python | 13,067 | 395 | # SPDX-License-Identifier: LGPL-3.0-or-later
import logging
from copy import (
deepcopy,
)
import pytest
from deepmd.utils import (
finetune,
)
def _model_config(
type_map: list[str],
*,
descriptor_sel: list[int] | None = None,
fitting_neuron: list[int] | None = None,
trainable: bool = T... |
8cd020e0c3b3017d7466927a9cd49598e82c077eab794076d557b49d8d1da0f5 | Python | 13,094 | 375 | # coding=utf-8
# Copyright (C) 2021. Huawei Technologies Co., Ltd. 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
#
# ... |
ae392246e3cb4d3be4cf79e90cdae023564802cebbd6f8e093e1558bdd71953e | Python | 13,099 | 333 | """Functions for reading time series data from .tsf files."""
__author__ = ["rakshitha123"]
__all__ = ["load_tsf_to_dataframe"]
from datetime import datetime
import pandas as pd
from sktime.datasets._readers_writers.utils import get_path
from sktime.datatypes import MTYPE_LIST_HIERARCHICAL, convert
from sktime.uti... |
fd6e54ad30457f45213f7fe994bb07473ecac29d660453ce1d3366cd06676a99 | Python | 13,100 | 158 | """
VS data
Vector strength for models with SAM tones, different input configurations.
9 Oct 2020 version.
Results are printout from DataTablesVCN after selecting the data runs.
pbm
"""
data="""Cell,Configuration,frequency,dmod,dB,VectorStrength,SpikeCount,phase,phasesd,Rayleigh,RayleighP,ANVS,maxArea,ninputs,
2,al... |
21b0f1a5f5cd2f28912b94bbb1a1bc0daa6bd49272f091ee2096fc2a9bce970e | Python | 13,105 | 316 | # Copyright 2019 DeepMind Technologies Ltd. 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... |
084fcb5e4953e405d7c242cdf19c7d8ea82d034b2e4cb1b33755cb2cd0d47e1a | Python | 13,111 | 334 | from __future__ import print_function
import numpy as np
import random
from copy import deepcopy
# for the replication of the same simulation data, uncomment next line
# np.random.seed(2020)
""" Function to generate simulation data with two modalities """
def multi_modal_simulator(n_clusters,
... |
7bbf1b7604922be9339684a921cf5acd90a68ff7318400e1114b6bfa7276787d | Python | 13,119 | 445 | # coding=utf-8
# Copyright (C) 2021. Huawei Technologies Co., Ltd. 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
#
# ... |
46ab3c2e3859a3dc1b9484052fdd898e2ccba6801559e4ab7c293fb29b80f77d | Python | 13,120 | 278 | #!/usr/bin/env python3
import rdflib
from pathlib import Path
from lxml import etree
from pyontutils.core import makeGraph, createOntology, OntGraph
from pyontutils.config import auth
from pyontutils.scigraph import Vocabulary
from pyontutils.namespaces import makePrefixes
try:
breakpoint
except NameError:
fro... |
3d3cba7dd96030e177be367ed1d43c1828d97fbed8010a04c53499d0c3908a96 | Python | 13,121 | 268 | from neuron import h
from math import exp
import numpy as np
import json
import neuron_cls as n
import spine as sp
import parameters as p
mod = "./mod/"
params = "./params_dMSN.json"
morphology = "./morphology/MSN_morphology_D1.swc"
h.load_file('stdlib.hoc')
h.load_file('import3d.hoc')
h.nrn_load_dll(mod + 'x... |
9196fe8c3d2b8ca90417625b676f9b17e3ab01515e7952e0d028512693e4f43c | Python | 13,123 | 336 | # Copyright 2022 DeepMind Technologies Limited
#
# 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 agr... |
6a28d1aad004849b8981160ca417367fcadb22daf2371e27da8973bbf21bcd07 | Python | 13,125 | 317 | # Copyright 2019 DeepMind Technologies Limited
#
# 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 agr... |
e6224abf18bf97c92672cfffb5de416b930525ba2afe78b02a7f09bca928d11b | Python | 13,130 | 330 | """Predefined ParaDime routines for existing DR techniques.
The :mod:`paradime.routines` module implements parametric versions of existing
dimensionality reduction techniques using the :class:`paradime.dr.ParametricDR`
interface.
"""
from typing import Optional, Union
import torch
import sklearn.decomposition
import... |
f4a805f57c9e35b35f3f57bf98a27e717ddeb9bca77050fa3d1880df03213979 | Python | 13,131 | 447 | """
This document contains methods to visualize compositional data that was imported into scCODA's data format.
:authors: Johannes Ostner
"""
# Setup
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
from matplotlib import cm, rcParams
from matplotlib.colors import ListedCo... |
0edd90556a6dec444a2e2335290aff876f606e354eb74cdd0d56106b6e423860 | Python | 13,142 | 386 | # Copyright 2019 DeepMind Technologies Ltd. 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... |
5c79e1244c0f5c7ea360a77fa4139c08a36ccc5aaf994447558fa82bb2f1b81d | Python | 13,159 | 365 | # Copyright 2026 DeepMind Technologies Limited
#
# 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 agr... |
7201f52ba80f42bf5a2d4cd6d46d8f10565814928d9593f8a70b90a38696c93c | Python | 13,161 | 340 | # =============================================================================
# IMPORTS
# =============================================================================
import torch.nn as nn
import pandas as pd
import torch
import numpy as np
from tqdm import tqdm
bar_format = "{percentage:3.0f}%|{bar:20}{r_bar}"
# =... |
1e934c2a4ee457f446514483d5a160aa292dc8ed9849d2d4e017a42ad4f2c042 | Python | 13,182 | 286 | """
These are all the runs for the SAM tone data
Run with the 0.7686 ASA density
Cells 2 and 5 with "standardized axon"
15 dB SPL
3 December 2021 to 8 December 2021
Manual copy from DataTableVCN using selection of runs and "print" function
Built: 9 December 2021
"""
samdata = {
2: [
"runANPSTH-all-2021... |
3490a0858a49747fca465d138b3e4a25a6810b5c5c709a0af6e07cd1f39ef3d3 | Python | 13,183 | 310 | """This script is used to run GAME-Net on the web server."""
import argparse
import os
import sys
import time
from multiprocessing import Pool
import resource
sys.path.insert(0, "../src")
sys.path.insert(0, "./adsurf")
import dockonsurf.dockonsurf as dos
import ase
from ase.constraints import FixAtoms
from ase.db imp... |
4dda3a9792f76f1249bcfe7eb29957a9d6bd7492b77f296539e2ed2f5972393f | Python | 13,187 | 298 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
"""Guards against defining an operator schema without registering it.
An operator schema is *defined* with one of the ONNX_..._OPERATOR_SET_SCHEMA
macros in an onnx/defs/**/*.cc file, but it is only actually placed in
the schema registry ... |
597ebd36ddefd3a3f375ed05816cee8355b64d5d0319f4766f47cca587639361 | Python | 13,193 | 408 | # Copyright 2022 DeepMind Technologies Limited
#
# 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 agr... |
1a7942efff298a3de11a99ebea4fc83d8578d0a5ff1c2e5b81cf61bd05c3e78c | Python | 13,201 | 274 | from neuron import h
from math import exp
import numpy as np
import json
import neuron_cls as n
import spine as sp
import parameters as p
mod = "./mod/"
params = "./params_iMSN.json"
morphology = "./morphology/WT-iMSN_P270-09_1.01_SGA2-m1.swc"
h.load_file('stdlib.hoc')
h.load_file('import3d.hoc')
h.nrn_load_d... |
a694762118379e3e31dec973fc0822617c6783bc5466240fa293c0be07d543ea | Python | 13,217 | 374 | # Copyright 2026 DeepMind Technologies Limited
#
# 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 agr... |
975e40e26197b319fcf5fa54cd2964dea6cdbc6b059fb3adf6137732f25f532f | Python | 13,248 | 338 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""Compact LMDB restart state through the real pt_expt data adapter."""
import copy
import json
from contextlib import (
ExitStack,
closing,
)
from unittest.mock import (
patch,
)
import lmdb
import msgpack
import pytest
from deepmd.dpmodel.utils import lmdb_d... |
3a8c40397140d895080812d470d456ecc2178a4c00c0a2a8b2434db05304a0d1 | Python | 13,252 | 321 | # Copyright 2019 DeepMind Technologies Ltd. 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... |
e3a70bb08293b5c43269a77e07184e57f3a8183a572499209114478b2e48e2e9 | Python | 13,252 | 496 | # SPDX-License-Identifier: LGPL-3.0-or-later
import itertools
import os
from abc import (
ABC,
abstractmethod,
)
from functools import (
lru_cache,
)
from pathlib import (
Path,
)
from typing import (
Any,
ClassVar,
)
import h5py
import numpy as np
from typing_extensions import (
Self,
)
fr... |
bd629747bd7ef9911869411c6d985136dcf336900aeb8dfa4bfe619c46ed0773 | Python | 13,271 | 371 | import os.path as osp
import argparse
import logging
from pathlib import Path
import torch
import numpy as np
from utils.argparse_utils import get_bool, get_device, get_dtype
from utils.argparse_utils import (
parse_model_settings,
parse_plot_settings,
parse_covariance_test_settings,
parse_data_settings... |
3bbc98153eec596c1fbfc42b9bf5cbc9ddf16683bec042c54c73d68267b69b22 | Python | 13,295 | 386 | """Functions for plotting EEG processing results.
"""
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
import sklearn.metrics as skm
import seaborn as sns
import pandas as pd
import pywt
import scipy.signal
import sklearn.decomposition
fro... |
ce53ac2b94629f5c8197cf17a74098227ef637bab770e28d051baadaa192aaa3 | Python | 13,302 | 378 | """Synthetic data generating functions."""
import numpy as np
import numpy.typing as npt
from sklearn.utils.validation import check_random_state
def piecewise_normal_multivariate(
means: npt.ArrayLike,
lengths: npt.ArrayLike,
variances: npt.ArrayLike | float = 1.0,
covariances: npt.ArrayLike = None,
... |
73f5a7946192e848b2df52b5905cbd57e2743a1e08d09f1bbd394657f3f6123b | Python | 13,304 | 280 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import tensorflow as tf
from tensorflow.python.distribute import distribution_strategy_context
from tensorflow.python.eager import context
from tensorflow.python.framework import dtypes
from tensorflow.... |
a0dd58b2b2bceef2c9a6f978ec419c1bdbb01454962ea7d7ca2c941e83c272a3 | Python | 13,305 | 350 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# This prog... |
a5d380ee01e5d20e1d32ca5409eba073063b63420d8819165781bea73970f1cf | Python | 13,322 | 350 | import torch
import torch.nn as nn
from torchvision import datasets
from torchvision import transforms
import numpy as np
import torch.nn.functional as F
import torch.optim as optim
import sys
"""
Maps the values of the model predictions back into a square contact matrix
"""
def generate_image(pred):
pred = np.s... |
bedd1f5c2f08c3e3ec336c5b67bbc68a9c157faf61aecce43e7e4ff829103ff5 | Python | 13,327 | 371 | from __future__ import annotations
from typing import TYPE_CHECKING
import numpy as np
from optuna._experimental import experimental_func
from optuna._imports import try_import
from optuna.visualization._contour import _AxisInfo
from optuna.visualization._contour import _ContourInfo
from optuna.visualization._contou... |
44c264136795dc5688c696a532668ceeff29e617808e1c17267e1e232a2c5dda | Python | 13,329 | 392 | import os
import sys
import yaml
import tempfile
from pathlib import Path
from tempfile import gettempdir
from functools import wraps
import orthauth as oa
from pyontutils.utils_fast import TermColors as tc, log
from pyontutils.utils_fast import get_working_dir
oa.utils.log.removeHandler(oa.utils.log.handlers[0])
oa.u... |
e6411e359b82aea8390d285bcc5dc8ca3500d848bd74096cd1909608314f10a9 | Python | 13,333 | 339 | import asyncio
import os
from fhirpy import AsyncFHIRClient
from fhirpy import SyncFHIRClient
import datetime
import random
from .loinc_lookup import *
import pandas as pd
import numpy as np
import joblib
import shap
import matplotlib.pyplot as plt
def datetime_to_str(timestamp):
return timestamp.strftime("%Y-%m-%... |
fcc6c76f94149b8e9336a13514ecacc2aa733209bc2c9dc88571bd733305b43d | Python | 13,333 | 371 | from argparse import Namespace
from typing import Iterable, Optional, Tuple, Union
from .utils import get_jet_name
from utils.utils import make_dir
import os.path as osp
import numpy as np
import matplotlib.pyplot as plt
from .utils import NUM_BINS, PLOT_FONT_SIZE
FIGSIZE = (12, 4)
LABELS_CARTESIAN_ABS_COORD = (r"$p_x... |
0bd396d6b7ac1b6f92b80908aba646508b103daee61cc2e51f3b9a93de095629 | Python | 13,341 | 338 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""The Uni-Mol v1 molecular-pretraining objective.
Ported from Uni-Mol (https://github.com/deepmodeling/Uni-Mol) at commit 90f52c4,
MIT licensed:
Copyright (c) DP Technology
This source code is licensed under the MIT license found in the LICENSE
file in the roo... |
ef3485170947c4a6166e4698e1351335a46a0a6832e190eac024a3803af14213 | Python | 13,347 | 355 | import argparse
import functools
import random
from pathlib import Path
from typing import Dict, List, Optional
import numpy as np
import networkx as nx
from joblib import Parallel, delayed
from tqdm.auto import tqdm
import cupy as cp
from gluonts.dataset.arrow import ArrowWriter
from sklearn.gaussian_process.kernels ... |
741e608371748a23e7835596549bd7cc24aa64f62ef174059e7e55aa449385bb | Python | 13,354 | 278 | # Copyright 2019-2021 The AmpliGraph Authors. All Rights Reserved.
#
# This file is Licensed under the Apache License, Version 2.0.
# A copy of the Licence is available in LICENCE, or at:
#
# http://www.apache.org/licenses/LICENSE-2.0
#
from .ComplEx import ComplEx, register_model
from ampligraph.latent_features im... |
4b636a17bd3534e82d5d1e4e75dcb52e6d343eef097555de76edc761eeb23e8d | Python | 13,360 | 337 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""Test the LAMMPS ``charge_spin`` keyword through ``pair_style deepspin``.
The sibling ``test_lammps_chg_spin_pt2.py`` exercises the keyword through
``pair_style deepmd`` (DPA3, non-spin); the DeepSpin ingestion seam is a
SEPARATE code path (``pair_deepspin.cpp``'s own ``c... |
d2420590a76e98a641592d7d28642103fd4d8b90d41d75d1c217d60d34d04a78 | Python | 13,372 | 346 | import os
import re
import logging
import argparse
import csv
from dendrogram_tools import dend_json_2_nodes_n_edges
from template_generation_utils import read_tsv, index_dendrogram, read_csv_to_dict
from nomenclature_tools import nomenclature_2_nodes_n_edges
from abc import ABC, abstractmethod, ABCMeta
from os.path i... |
72bd1c591b7f0a98e2b253d3b9a5ce2544b8caab5af7ed0456bd9afd329e43f1 | Python | 13,373 | 340 | import torch
import torch.nn as nn
import torch.nn.functional as F
import pytorch_lightning as pl
import numpy as np
from fft_utils import *
from misc_utils import *
import copy
from pathlib import Path
from optimizer import IIPG
DEFAULT_OPTS = {'kernel_size':11,
'features_in':1,
'featu... |
f333d7732d65cfa732b0334305887839b40c5101346a362b75a4e8feae0b961e | Python | 13,378 | 334 | # !/usr/bin/env python3 -u
# copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Implements adapter for statsmodels forecasters to be used in sktime framework."""
__author__ = ["mloning", "ciaran-g"]
__all__ = ["_StatsModelsAdapter"]
import inspect
import numpy as np
import pandas as pd
from sk... |
f237a4f4725bdbe644b5877c637d32b99633922b24a73b03ebaef66277e4d30c | Python | 13,401 | 461 | """Extract reference documentation from the pypa/packaging source tree.
In the process of copying, some unused methods / classes were removed.
These include:
- parse()
- anything involving LegacyVersion
This software is made available under the terms of *either* of the licenses
found in LICENSE.APACHE or LICENSE.BSD... |
5b9c53d7092426336693fa9546fca55ed0790c5ba23c6a756d516ce9fdfd0a77 | Python | 13,402 | 286 | """
These are all the runs for the SAM tone data
Run with the 0.7686 ASA density
Cells 2 and 5 with "standardized axon"
30 dB SPL
11Aug2021 to 16Aug2021
Manual copy from DataTableVCN using selection of runs and "print" function
"""
samdata = {
2: [
"runANPSTH-largestonly-2021-08-15.16-02-05",
"... |
9bd841bee2d9237d9aad6c083da38767a1323e9352ead3e69c8b97fe40bbe8c2 | Python | 13,403 | 298 | """
This plots figure 6e of the paper.
This is the psychometric fit of the behaviour output of the naive model.
Internal notes:
This is from notebook 21.25
Note that it currently requires xarray == 0.16.2
TODO: there are some pickle files that should be converted to something more readable and independent of xarray v... |
a42d42ef49361969a3b8d1265b260e3c733762a760b700d00b8b2888651ff077 | Python | 13,406 | 405 | #!/usr/bin/env python
import argparse
from functools import partial
from multiprocessing import Pool, cpu_count
from numpy import isnan
import os
import re
import shutil
import subprocess
import sys
from urllib.request import urlretrieve
from __init__ import ENCODE, ParseUtils
usage_msg = """
usage: %s --genome STR ... |
8b5b381e3f5f6691c294f60e49e35ead1b30a2cd2c3a28115f443fb861385d4d | Python | 13,407 | 321 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import numpy as np
from numpy.testing import assert_allclose
import onnx
from onnx import TensorProto, helper, numpy_helper
from onnx.defs import onnx_opset_version
from onnx.reference import ReferenceE... |
f326fa14775f4e77de7aca537f19439975f51a79d4ca8aae43a0601a463ab9bc | Python | 13,408 | 366 | import numpy as np
from scipy import signal
from numba import njit
import colorednoise as cn
class ConfigGenerator:
names = [
"betas",
"gammas",
"beta_sharpness",
"phase",
"pac",
"cross_pac",
"phase_shift",
"burst_length",
]
def __init__(sel... |
c5432768aead2225f1bb7f9bd06c974a30beae80a889d3201daa167639e5a8fe | Python | 13,413 | 405 | # SPDX-License-Identifier: LGPL-3.0-or-later
from __future__ import (
annotations,
)
import warnings
from contextlib import (
contextmanager,
)
from typing import (
TYPE_CHECKING,
overload,
)
if TYPE_CHECKING:
from collections.abc import Generator
from deepmd.pd.model.network.init import (
... |
ce9fc116705d83dd3f00e0093964d976e71b5734e00f98c3c836eca6f0433116 | Python | 13,414 | 332 | import copy
import logging
import os
from collections import defaultdict, deque, namedtuple
import numpy as np
from ray.tune.schedulers import FIFOScheduler, TrialScheduler
from ray.tune.suggest.variant_generator import format_vars
from ray.tune.trial import Checkpoint, Trial
from tune_tf2.defaults import EXPLOIT_CSV,... |
88b17da70e7811f8c83857b3b7e2e4d15c1a64a3cd8ba34d21c51b1c4a51486e | Python | 13,420 | 422 | import pandas as pd
def convert_pandas_to_listDataset(pd_dataframe: pd.DataFrame):
"""Convert a given pandas DataFrame to a gluonTS ListDataset.
Parameters
----------
pd_dataframe : pd.DataFrame
A valid pandas DataFrame
Returns
-------
list_dataset: list
A list of dict wh... |
1e88b85db49f5bd91d8595de7cb741317df58bc4f2e7f613ac875be319a5e805 | Python | 13,423 | 392 | # copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
# Ported from skchange (BSD-3-Clause), original authors: johannvk
"""CROPS algorithm for path solutions to the PELT algorithm."""
__author__ = ["johannvk"]
__all__ = ["CROPS"]
import warnings
import numpy as np
import pandas as pd
from sktime.d... |
00997b8ddfee97881da500dc9647a7327909040c9ab40a2e2c065d88906a6833 | Python | 13,448 | 336 | # Copyright 2026 DeepMind Technologies Limited
#
# 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 agr... |
948accafbb6c83c0f4735263692985a87034a30514ede0057339b934250891e7 | Python | 13,455 | 386 | # -*- coding: utf-8 -*-
# Generated by the protocol buffer compiler. DO NOT EDIT!
# source: lock_server.proto
from google.protobuf import descriptor as _descriptor
from google.protobuf import message as _message
from google.protobuf import reflection as _reflection
from google.protobuf import symbol_database as _symb... |
5d164d3233c159d794f704864bc791cc551032620a868e131ffa77e244ec691c | Python | 13,458 | 362 | import math
import numpy as np
import torch
from functools import reduce
from scipy.special import factorial
from torch import nn as nn
from vp_suite.base import VPModelBlock
from vp_suite.model_blocks.conv_lstm_ndrplz import ConvLSTMCell
from vp_suite.model_blocks.conv import DCGANConv, DCGANConvTranspose
class Phy... |
633416e0597ff0b5942c5770b5d1e3292f4a63e10eaef1a6daba8d61ce9349d3 | Python | 13,458 | 416 | # Copyright 2026 DeepMind Technologies Limited
#
# 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 agr... |
633e56c9916dca4a643b9b212424835d4dcda0cc90d5072f0ff7c80d6f10e5e2 | Python | 13,459 | 367 | # SPDX-License-Identifier: LGPL-3.0-or-later
import logging
import os
from abc import (
ABC,
abstractmethod,
)
from collections.abc import (
Callable,
)
from typing import (
Any,
)
import array_api_compat
from deepmd.utils.errors import (
OutOfMemoryError,
)
log = logging.getLogger(__name__)
cl... |
8731866b504db657d6703d3d7e3c96068c4e0f91f747bbc6919d5ba85e96d3da | Python | 13,471 | 410 | #!/usr/bin/env python
# coding: utf-8
# In[1]:
import pandas as pd
import matplotlib.pyplot as plt
import cv2 as cv
import numpy as np
from dataclasses import dataclass
import os
import random
# from numba import njit, jit
import shutil
from sklearn.utils import shuffle
# In[2]:
## read csv files that has been g... |
6406074bb7df35856d80d19abbb04bbd46e2cc0830276fd2519c0f38e0b1aadc | Python | 13,477 | 303 | # copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Extension template for unsupervised sequence aligners.
Purpose of this implementation template:
quick implementation of new estimators following the template
NOT a concrete class to import! This is NOT a base class or concrete class!
... |
81220fa3bd4bb183428926b538166a915030f1470605fff8b429c9f66f6df6d5 | Python | 13,481 | 438 | import torch
import torch.nn.functional as F
from src.constants import *
import random
import numpy as np
class BaseLoss:
eps = 1e-9
def __init__(self, model):
self.n_output = len(list(model.clusters[0].parameters())[0])
self.weight = 1
@staticmethod
def compute_distance(is_binary... |
b9087f8445f3990abdb8097ccf16234d9c90f5d3d6f4be50a3522d2480d5e969 | Python | 13,490 | 375 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""Edge-vector neighbor-list helpers for SeZM-style models.
LEGACY: serves only the deprecated pt-backend edge_vec .pt2 schema;
scheduled for removal with that rail.
"""
from __future__ import (
annotations,
)
import torch
from deepmd.dpmodel.utils.neighbor_list impo... |
c17d6129e28367fa3bcfbe195cbdf9935e1dda32735d7f544e73adbf2f005d21 | Python | 13,501 | 292 | #=======================================================================================================================
#Copyright
#=======================================================================================================================
# Copyright (C) 2021 Matvey Safroshkin, Grigory Arutyunov, Patrick ... |
00dad86cb5803c6ed7d2ea336d02371e9dd2cdc2de02e6c5a96e413082a3f7f4 | Python | 13,509 | 438 | """
Figure data: a dict of which simulations are in which figures
The dictionaries all should have the same basic structure: top level keys are
the cell number/ID. Second level keys relate to the experimental conditions. The
data in the second level key is either the name of the directory that holds the
simulation dat... |
62882bad03e90190341cd55cdbeb8215bc7f4e94f434babcb7929cfb3c6c4a86 | Python | 13,516 | 347 | # Copyright 2026 DeepMind Technologies Limited
#
# 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 agr... |
a573fb7488c07009d04059b8e131ddeb8235d116a9b97b6c57bdb32c489dd978 | Python | 13,524 | 345 | #!/usr/bin/env python3 -u
# copyright: sktime developers, BSD-3-Clause License (see LICENSE file).
"""
Implements the FallbackForecaster.
The FallbackForecaster works with a list of forecasters and tries to fit them in order.
If the active forecaster fails during prediction, it proceeds to the next. This ensures
a rob... |
2616f08c554a2e8ad47e3d0b886bdcab452ec2dc2362ee4f3b555bcc15d461d0 | Python | 13,541 | 385 | """Utilities for working with the local dataset cache. Copied from AllenNLP."""
import base64
import functools
import io
import logging
import mmap
import os
import re
import shutil
import tempfile
import typing
import warnings
import zipfile
from collections.abc import Sequence
from pathlib import Path
from typing im... |
8dca2a55b990c7243ba4bf9110a514deb437876ae0a2e1064bf12618789396dc | Python | 13,542 | 378 | import os.path as osp
import argparse
import logging
from pathlib import Path
import torch
import numpy as np
from utils.argparse_utils import get_bool, get_device, get_dtype
from utils.argparse_utils import (
parse_model_settings,
parse_plot_settings,
parse_covariance_test_settings,
parse_data_settings... |
b15fedf7a97b129d84b165d004a5a06a7aff25b1effe817274d372a505681f5d | Python | 13,549 | 386 | # Copyright 2019 DeepMind Technologies Limited
#
# 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 agr... |
7c2624b56cfc2f993092ed54ec68db5e0549d40e66583ac8657c175ab9c0ddbe | Python | 13,554 | 292 | # copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Extension template for forecasters, SIMPLE version.
Contains only bare minimum of implementation requirements for a functional forecaster.
Also assumes *no composition*, i.e., no forecaster or other estimator components.
For advanced cases (pro... |
17970b0d1b897f5d1881602526ffc5a7f2017a73c28fa5ad2d2387407700619b | Python | 13,556 | 303 | import ast
import itertools
import math
import os
import pickle
from collections import defaultdict
import cv2
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from PIL import Image
from allensdk.core.mouse_connectivity_cache import MouseConnectivityCache
from matplotlib.collect... |
b7b3c6afcb983ef2e2bfd616155d4ef3c34a26dbc30443d5f26455d69a160ee8 | Python | 13,557 | 404 | # Copyright 2026 DeepMind Technologies Limited
#
# 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 agr... |
62730a4f8d5acb65c78937b2d8861d2370c5bdbc46a838428a6935dff4565c41 | Python | 13,567 | 383 | # Copyright 2019 DeepMind Technologies Limited
#
# 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 agr... |
828daf8746df19706af834d7f0c2373b854488b02fe0b78b2a83c3a60520362b | Python | 13,568 | 349 | #!/usr/bin/env python3
import os
import json
from glob import glob
from hashlib import md5
from functools import wraps
import robobrowser
import rdflib
from pyontutils.core import makeGraph
from pyontutils.scigraph import Vocabulary
from pyontutils.namespaces import makePrefixes
# ilx api implementation (will change)... |
9f18276d9144bf33d0b11a4078b46da7caa12417881484623fc9055e11300643 | Python | 13,573 | 398 | # Copyright (c) ONNX Project Contributors
#
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import itertools
import numpy as np
import onnx
from onnx import TensorProto
from onnx.backend.test.case.base import Base
from onnx.backend.test.case.node import expect
from onnx.helper import (
m... |
63a368a4eac91fad546cd76567a364514ded1b0d562b4909519c5649c1a73d8c | Python | 13,583 | 398 | """A module which implements the time frequency estimation.
Authors : Hari Bharadwaj <hari@nmr.mgh.harvard.edu>
License : BSD 3-clause
Multitaper wavelet method
"""
import warnings
from math import sqrt
import numpy as np
from scipy import linalg
from scipy.fftpack import fftn, ifftn
from .utils import logger, ver... |
bd712b051e64758202ea6fef786a90a70e70f048ac5e731fecb30658015ae3b0 | Python | 13,608 | 356 | # copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Machine type converters for scitypes.
Exports
-------
convert_to(obj, to_type: str, as_scitype: str, store=None)
converts object "obj" to type "to_type", considered as "as_scitype"
convert(obj, from_type: str, to_type: str, as_scitype: str... |
11e49ee6dd57c79b0c2581786ee4234676e73076bcb6b98f4e1af75db95cb9ca | Python | 13,611 | 341 | # SPDX-License-Identifier: LGPL-3.0-or-later
import json
import os
import tempfile
import unittest
from pathlib import (
Path,
)
import numpy as np
from deepmd.utils.finetune import (
get_index_between_two_maps,
)
from deepmd.utils.preset_out_bias import (
bundled_preset_out_bias_tables,
load_preset_o... |
24befa6c90be53b5d804a97bba6f780ee1e2b293bb76bb01b79cb0881b8a0674 | Python | 13,633 | 208 | #!/usr/bin/env python3
from neurondm import *
__all__ = ['Test',
'Layers',
'PaxRatLayers',
'Regions',
'PaxRatRegions',
'Species',
'BBP',
'CUT']
Config() # explicitly load the core graph TODO need a lighter weight way to do this
class Tes... |
860a4a360a3811beeff87a469c5d69c05b12e37a444b94c74c3e5d98c9abe6f4 | Python | 13,633 | 363 | # Copyright 2019-2026 The AmpliGraph Authors. All Rights Reserved.
#
# This file is Licensed under the Apache License, Version 2.0.
# A copy of the Licence is available in LICENCE, or at:
#
# http://www.apache.org/licenses/LICENSE-2.0
#
import tensorflow as tf
import numpy as np
class EmbeddingLookupLayer(tf.kera... |
2ae0dfbdfd7a976dcc38ee12fcab82dee1d509ad997b01959c8e3926e350ae1f | Python | 13,643 | 411 |
import numpy as np
import matplotlib as mpl
from matplotlib.colors import same_color, to_rgba
from numpy.testing import assert_array_equal, assert_array_almost_equal
from seaborn._core.plot import Plot
from seaborn._core.moves import Dodge
from seaborn._marks.line import Dash, Line, Path, Lines, Paths, Range
class... |
76aea30541346999d874bcc155122ef34a3cfc7670161b100b68c719ec92a8f9 | Python | 13,645 | 384 | """Orchestration pipelines for preprocessing and feature extraction."""
import time
import warnings
from pathlib import Path
from typing import Dict, List, Optional
from bcblib.tools.lesion_features._constants import EBRAINS_ATLAS_SPECS, LF_SUBDIR, TARGET_SPACE
from bcblib.tools.lesion_features._bids import (
bui... |
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