sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
b5fdb7763c4c954a31bac942b5128953ae6f792cdb84ddd82900a8646e76d7bb | Python | 2,599 | 84 | import logging
from typing import Any
from flair.trainers.plugins.base import TrainerPlugin
log = logging.getLogger("flair")
class WandbLoggingHandler(logging.Handler):
def __init__(self, wandb, *args, **kwargs) -> None:
super().__init__(*args, **kwargs)
self.wandb = wandb
def emit(self, r... |
2f70d39a7a69f3802f5dfc4d34faa830d40d94a3f2dc96bf88ec1b2811868d9b | Python | 2,600 | 60 | from __future__ import print_function
import sys
from os import listdir
import pickle
import string
import random
from functools import reduce
from parameterSetup import ParameterSetup
from classifierTrainer import connectSamplesAndTrain
from fileManagement import fileIDs2triplets
from tester import test_by_classifierI... |
31cd0b7ae2634ae102ba1ff45c9dd3c30947bd90cb83e4bbb6f7277ad41cfae6 | Python | 2,600 | 78 | # 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
#
# ... |
dbe503741ae1c298fa5bc2a3364aebf40191f08a9016a0a805cb6f8a922f68bf | Python | 2,600 | 81 | # 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... |
ecc4e95aea717a65848ae7cde722e667b8ead23bf90d3c7beb77296a6de01322 | Python | 2,600 | 78 | # 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... |
332f9366d50e20ebb9621c81164c4ee98c928e93b6da45e850812ca6454f5ce1 | Python | 2,601 | 86 | import sys
import numpy as np
import nengo
import time
import pickle
import matplotlib.pyplot as plt
from sns_toolbox.neurons import NonSpikingNeuron
from sns_toolbox.connections import NonSpikingSynapse
from sns_toolbox.networks import Network
class SpikingNeuronsWithSynapticInput(nengo.Process):
def __init__(se... |
933bf7159e211476829f6d90c09eaa0397d64a1e06d3d8e30d7cb0e9aca42fbc | Python | 2,603 | 62 | """
Train models on synthetic data, with angle regularization.
"""
import os
import numpy as np
from six.moves import cPickle
from tensorflow import keras
from gradient_correction import helper, model_zoo, regul
#------------------------------------------------------------------------
num_trials = 20
... |
5395a7a9039c3d5f84fc9491e52a3d21d053e7f7f72a3aee130447544446fd85 | Python | 2,604 | 73 | # Copyright (c) ONNX Project Contributors
#
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import numpy as np
import onnx
from onnx.backend.test.case.base import Base
from onnx.backend.test.case.node import expect
class Sub(Base):
@staticmethod
def export() -> None:
node = ... |
a5bf75496021c2cbcdc1b695bd13a5728da4a2baed557d91baf6c22d395a6517 | Python | 2,604 | 72 | # -*- coding: utf-8 -*-
from __future__ import print_function
import click
import os
import re
import face_recognition.api as face_recognition
import multiprocessing
import sys
import itertools
def print_result(filename, location):
top, right, bottom, left = location
print("{},{},{},{},{}".format(filename, to... |
4b2b98c29800197fa9ae9ba09c7a4380e7bbc0d6965427e0b9a22b367d009051 | Python | 2,607 | 57 | #!/usr/bin/env python3
from pyontutils.config import auth
__doc__ = f""" Create nginx configs for resolver.
Usage:
make_config [options]
Options:
-l --git-local=LBASE local git folder [default: {auth.get_path('git-local-base')}]
-d --debug call IPython embed when done
"... |
7df5bcdda1dea0bc20bcfba2fbd9e0b8815e52dbf1152c05e2a79cca52f8419d | Python | 2,607 | 66 | #!/usr/bin/env python3
"""Check that a Linux release binary is portable.
packaging/linux/check_binary.py <bin/baysor>
Fails unless
* every NEEDED entry is a glibc library,
* no required GLIBC_ symbol version is newer than GLIBC_FLOOR (the glibc of
the manylinux_2_28 build image),
* no libstdc++/libgcc s... |
8daea1def0a846bd611828ac2bc200470cf8c97cd45ccc1c8f3e82c4f0c23f38 | Python | 2,607 | 78 | # -*- coding: utf-8 -*-
"""
Created on Thu December 10 11:41:02 2022
@author: Pawan Panwar, Quanpeng Yang, Ashlie Martini
PyL3dMD: Python LAMMPS 3D Molecular Dynamics/Descriptors
Copyright (C) 2022 Pawan Panwar, Quanpeng Yang, Ashlie Martini
This file is part of PyL3dMD.
PyL3dMD is free software: you ... |
ae7b3a3d3ec984d95c5d5abc2fe1dc75c242c57e6e16da697accc08c0c93bf31 | Python | 2,607 | 70 | # Copyright (c) OpenMMLab. All rights reserved.
import os.path as osp
import mmcv
import numpy as np
from ..builder import PIPELINES
@PIPELINES.register_module()
class LoadImageFromFile(object):
"""Load an image from file.
Required keys are "img_prefix" and "img_info" (a dict that must contain the
key ... |
8326087b69a5bd4c8b2a6ead6272deb953fa3fffa9f8836324a3f5aa3a491df3 | Python | 2,608 | 76 | # Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If ex... |
409a3d0d4524bef851c21ebd552fef08b11f99e1ef646c21273698d3ddf5b2c6 | Python | 2,609 | 58 | # Copyright 2023 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... |
2b841b7f4ce3361da6be1822f9929a73c363dfd3cbe794d4411c9733fb6aa995 | Python | 2,610 | 70 | import time
import numpy as np
from fig import Config as C
class SingleThreadedClientSim(object):
def __init__(self, client_config):
"""Creates a new detection source that implements the `poll` function.
Detections are for the MOT16 dataset, sourced from a Faster RCNN model.
The MOTClient ... |
e7a148bcb35ce26f2175b4039957c79cd234e2859875bd80c4607138b3643a9b | Python | 2,612 | 67 | import pytest
from vp_suite.measure import METRIC_CLASSES, LOSS_CLASSES
import torch
"""
These tests are prob. useless since they check the metric axioms on single instances
"""
AVAILABLE_MEASURES = {**METRIC_CLASSES, **LOSS_CLASSES}
measure_names = list(AVAILABLE_MEASURES.keys())
measure_classes = list(AVAILABLE_... |
70aaaa5a1599a1a8d8506805a510b0be214baadfb921c5883c0bc73a33a8a6fd | Python | 2,615 | 75 | import os
import shutil
from glob import glob
import numpy as np
from ray import tune
def uniform(min_bound, max_bound):
""" returns a uniform sampling function for `hyperparam_mutations` """
return lambda: float(np.random.uniform(min_bound, max_bound))
def loguniform(min_bound, max_bound, base=10):
""... |
d3814ec29fe8c55b87e1a3c30fa497724cac2785b0f54a058caa43ac8f09ff5d | Python | 2,616 | 64 | #!/usr/bin/env python
# arima_mapping 0.0.1
# Generated by dx-app-wizard.
#
# Basic execution pattern: Your app will run on a single machine from
# beginning to end.
#
# See https://wiki.dnanexus.com/Developer-Portal for documentation and
# tutorials on how to modify this file.
#
# DNAnexus Python Bindings (dxpy) docum... |
6a6edf1ad57e6d9bf1d54700da48a6a0ced1df6fc0705b81099681bdb9943f9b | Python | 2,618 | 88 | """
Provides basic spike detection, spike shape analysis, and IV analysis if
appropriate. We use readmodel (ReadModel) to read the pickled data file into
acq4 format, then we can use the ephys analysis tools to analyze the data
This module is part of *vcnmodel*.
Support::
NIH grants:
DC R01 DC015901 (Spirou,... |
bc11497f58a6fff11fc0c7201ffd40de45489acac4302fc71d51c5f477868ce5 | Python | 2,619 | 102 | from __future__ import annotations
import io
from typing import IO, TYPE_CHECKING
from .binary import decode_bin, encode_bin
if TYPE_CHECKING:
from typing import Self
from typing_extensions import Buffer # 3.12+
class BitStream(io.RawIOBase, IO[bytes]):
__slots__ = ("substream",)
def __init__(s... |
de5a8e2a1fc25ef465c9f24d734f3295270117bd36a852abef2f7e80f925d7c7 | Python | 2,619 | 79 | import torch
import torch.nn as nn
import torch.nn.init as init
import torch.nn.functional as F
def initialize_weights(net_l, scale=1):
if not isinstance(net_l, list):
net_l = [net_l]
for net in net_l:
for m in net.modules():
if isinstance(m, nn.Conv2d):
init.kaimin... |
2217f3a4dd7533b62521ff7f49ef667cce0e539b8100e629f59efb14816a359f | Python | 2,622 | 75 | __author__ = ["chrisholder", "TonyBagnall"]
"""Factory module that adds 3D vectorization to all exported distances.
Applies pairwise_distance to all distances exported by module, so exported distances
function with 1D, 2D and 3D input.
"""
import numpy as np
from sktime.dists_kernels._numba_distances._distance i... |
75ca8366ee08b8b8c6fbb3fe3dd12ba3d7bdaf0157d77db828c488f64a46c2d2 | Python | 2,623 | 87 | # dncnn.py
#
# DnCNN model from Zhang et al., 2016 for denoising diffusion MRI data in DeepDTI from Tian et al., 2020.
#
# (c) Qiyuan Tian, Harvard, 2021
from keras.models import Model
from keras.layers import Input, Conv3D, BatchNormalization, Activation, concatenate
from keras.utils import plot_model
def dncnn_mo... |
2ecf74d72af96f51af747d36e005a5f20e95119de2a21cab78e2690415890ebe | Python | 2,624 | 89 | # Hack to avoid circular imports
from lgn.g_lib import g_tau, g_tensor, g_torch
from lgn.g_lib import g_scalar, g_wigner_d
GTau = g_tau.GTau
GTensor = g_tensor.GTensor
GScalar = g_scalar.GScalar
GWignerD = g_wigner_d.GWignerD
class GVec(GTensor):
"""
Core class for creating and tracking G Vectors (aka G repr... |
757f333a22359883132f5fb5dff9ecb15517c34dc12117cfdfe81fc9b2258d82 | Python | 2,624 | 78 | import numpy as np
from keras.models import *
from keras.optimizers import *
from sklearn.metrics import mean_squared_error, r2_score
import scipy as sp
from scripts import models_util
def scheduler(epoch, lr):
learning_rate = 0.01 # initial learning rate
decay_rate = 0.03
lrate = learning_rate ... |
85babfc18c40a5705de65066543ee213f680ac13bfb89215841ca0e8e7f80a47 | Python | 2,625 | 88 | import matplotlib.pyplot as plt
import numpy as np
from Historia.ep import solver as solep
from Historia.shared.plot_utils import get_col, interp_col
def main():
# ---------------------------------------------------------------
# Electrophysiology
rat = "sham"
hz = 6
nbeats = 1
E = solep.EPS... |
12d182e6877b0a4a6a16801db5a91da3c9dc9ddb9d67aeb19458e25e29a0215b | Python | 2,626 | 54 | from tensorflow.keras.models import Model
from tensorflow.keras.layers import Dense, Activation, Permute, Dropout
from tensorflow.keras.layers import Conv2D, MaxPooling2D, AveragePooling2D, Convolution2D
from tensorflow.keras.layers import SeparableConv2D, DepthwiseConv2D
from tensorflow.keras.layers import BatchNormal... |
ce75b8a001edd6e1a3765cf34cca08ecf2ff5233c9293d2f9b73ebda62600e8b | Python | 2,627 | 82 | # SPDX-License-Identifier: LGPL-3.0-or-later
from typing import (
Any,
)
from torch.utils.data import (
Dataset,
)
from deepmd.pt.modifier import (
BaseModifier,
)
from deepmd.pt.utils.env import (
NUM_WORKERS,
)
from deepmd.utils.data import (
DataRequirementItem,
DeepmdData,
)
class Deep... |
f1c460de47646cda23135cb9173a87e1b9e787e9b8485922324f62f5353c7b35 | Python | 2,628 | 74 | #!/usr/bin/env python
#-------------------------------------------------------------------------------
# test/run_examples_test.py
#
# Run the examples and compare their output to a reference
#
# Seva Alekseyev (sevaa@sprynet.com)
# This code is in the public domain
#
# This runs and times in-memory firehose DWARF pars... |
dd69ad0065b8999baa30fb05497e1a758f9505f7a6df9d7e75f73d4e51aa1a1d | Python | 2,629 | 78 | #!/usr/bin/env python3
""" Script for deploying files from github to the nifstd ftp. Must be run from the root of the ontology directory so we can glob files. NOTE: you can shoot yourself in the foot with this.
Usage:
deploy [--branch=BRANCH] <path>...
deploy [--commit=COMMIT] <path>...
deploy <path>...
Opt... |
46c29e03aa7491cd946cf52e436e34e4e791bab36e099236d8189591d5261b6c | Python | 2,630 | 65 | from sklearn.metrics import accuracy_score, precision_score, recall_score, f1_score, roc_auc_score
import tensorflow as tf
from tensorflow.keras.layers import Input, Conv2D, MaxPooling2D, UpSampling2D, concatenate, Dense, Flatten, Dropout
from tensorflow.keras.models import Model
from tensorflow.keras.applications impo... |
15beae6cd24dd69b4bf2dea03544d961d5904fe5616dd34e31ae1f45ffa17a8d | Python | 2,632 | 104 | import random
import torch
import torch.nn as nn
import torch.nn.functional as F
import torchvision.transforms as TvT
from torch.autograd import Variable
from spikingjelly.clock_driven import functional
from spikingjelly.clock_driven import neuron
from network_3d.poolingNet_cat_1res import NeuronPool_... |
1e097eed029c76c65ffe47d037e75b40b4b985975d3bb54f62199b9e70028446 | Python | 2,632 | 72 | import pickle
import numpy as np
from ksstatistics import StatisticalTester
from fileManagement import readStandardMice, getFileIDs
from parameterSetup import ParameterSetup
eegFilePrefix = 'eegAndStage'
params = ParameterSetup()
pickledDir = params.pickledDir
standardMiceData, standardMiceFileFullNames = readStandard... |
b7894f9830e728f837554fba1305583a56204881ad07dce22f6439cbe4fe4e75 | Python | 2,633 | 65 | """Base module for statistical transformations."""
from __future__ import annotations
from collections.abc import Iterable
from dataclasses import dataclass
from typing import ClassVar, Any
import warnings
from typing import TYPE_CHECKING
if TYPE_CHECKING:
from pandas import DataFrame
from seaborn._core.groupb... |
ca7eefe4f95afa9ba18c564977a8e2b97613c9845f976c11dda69e97bfeae746 | Python | 2,634 | 77 | # 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... |
e1e513c88fb2c2cf6f57435d69652a6c1654c76563f76436203d568cd6b3c3fa | Python | 2,634 | 91 | import numpy as np
from sklearn.linear_model import LinearRegression
from sklearn.gaussian_process import GaussianProcessRegressor
from sklearn.preprocessing import PolynomialFeatures
from scipy.spatial.distance import pdist, squareform
def BIC_input_graph(X, g, reg_type='LR', score_type='BIC'):
"""cal BIC score ... |
8dd547375d555fdf1c3fc071a9809647bbabed1d0d9e01db571bea74b2cdfcc8 | Python | 2,639 | 86 | """Tests for tabular-to-panel distance aggregation/reduction."""
import numpy as np
import pytest
from sktime.datatypes import convert_to
from sktime.dists_kernels.compose_tab_to_panel import AggrDist
from sktime.dists_kernels.scipy_dist import ScipyDist
from sktime.registry import all_estimators
from sktime.tests.te... |
555bbbcced95febe6cc3a875c5bdb051f59ab1b9f2d9c170dc4c93d9f0a22f30 | Python | 2,641 | 66 | # Copyright 2018-2025
# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
# 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/LICE... |
2f9f6eaa529819e413a10362da4b8cd1d8d6dbeb26a6e074eb36f1f23658a0cd | Python | 2,642 | 64 | import torch
from collections import OrderedDict
from torch import nn
class IntermediateLayerGetter(nn.ModuleDict):
"""
IntermediateLayerGetter is the direct copy of torchvision.models.segmentation/_utils/IntermediateLayerGetter.
We had to copy here as it is a protected class.
Module wrapper that ret... |
9a46055c09c968a1ba83473dc7c691bad27977c0892d2f82a69bac2568b80fcb | Python | 2,644 | 82 | from __future__ import annotations
import numpy as np
import matplotlib as mpl
from seaborn.utils import _version_predates
def norm_from_scale(scale, norm):
"""Produce a Normalize object given a Scale and min/max domain limits."""
# This is an internal maplotlib function that simplifies things to access
... |
b31fc5bb7bc9f785a5cc976f975a9a90cbd542763af59ddf4aba8ae7a3a124fc | Python | 2,645 | 57 | # Copyright 2019-2020 The ASReview 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 appl... |
c82b1cee83e74b1014d937e13ca9c22fd4ce08474fd647ecdeb11849ce523c81 | Python | 2,645 | 77 | #!/usr/bin/env python
# encoding: utf-8
"""
expfitting.py
Provide single or double exponential fits to data.
"""
import lmfit
import numpy as np
import scipy.optimize
class ExpFitting:
"""
Parameters
----------
nexp : int
1 or 2 for single or double exponential fit
initpars : dict
... |
6c34f811c061d7b219e1abceaf1d616440d5cd30d5b56b980e84493643dfe8b0 | Python | 2,646 | 73 | from networkunit.tests.two_sample_test import two_sample_test
from networkunit.capabilities.ProducesSpikeTrains import ProducesSpikeTrains
from networkunit.utils import use_cache, filter_valid_params, parallelize
from elephant.statistics import time_histogram
from elephant.spectral import welch_psd
from elephant.signal... |
f5090a78bdd5620d66dc791a899bbf64839a498e23ec7dd99eeb9d7b983d5705 | Python | 2,646 | 83 | import pytest
import numpy as np
import pandas as pd
import scanpy as sc
from scipy.sparse import csr_matrix
from palantir.utils import run_magic_imputation
@pytest.fixture
def mock_dm_res():
rng = np.random.default_rng()
return {"T": csr_matrix(rng.random((50, 50)))}
# Test with numpy ndarray
def test_run... |
4da5e000520adc3d2b5140ca11c34186102c6f1ee4b8a77a5de6c9bae90fb381 | Python | 2,647 | 91 | # Data Technqiues
str_default = "default"
str_atacseq = "atacseq"
str_dbitseq = "dbitseq"
str_dlpfc = "dlpfc"
str_patchseq = "patchseq"
# Model Configs
str_input = "input"
str_output = "output"
str_hiddens = "hiddens"
str_use_biases = "use_biases"
str_dropouts = "dropouts"
str_use_batch_norms = "use_batch_norms"
str_u... |
a0f98741d22212d43585b25f46d9bbc25895452de141ca5a28fa3af291248c78 | Python | 2,647 | 84 | # Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If ex... |
b62938209e9828431ea80639218ae749cb9b2fc3f5fcf18473fc6c2734455c33 | Python | 2,647 | 78 | #Copyright (C) 2021. Huawei Technologies Co., Ltd. All rights reserved.
#This program is free software;
#you can redistribute it and/or modify
#it under the terms of the MIT License.
#This program is distributed in the hope that it will be useful,
#but WITHOUT ANY WARRANTY; without even the implied warranty of
#MERCHA... |
b390b64df64cda628c3d504a6dbd8224c83eec2ed2abfb762c1796bbd05cf43c | Python | 2,648 | 81 | import argparse
import torch
import onmt
import onmt.model_builder
import onmt.inputters as inputters
import onmt.opts
from onmt.utils.misc import use_gpu
from onmt.utils.logging import init_logger, logger
parser = argparse.ArgumentParser(description='translate.py')
parser.add_argument('-model', required=True,
... |
7c191352e8d41dd71fcc5d643ef313578c78d552573d42792dba6bfe0e06c583 | Python | 2,649 | 89 | # Copyright 2018-2025
# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
# 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/LICE... |
b82c8ce1b4e3bb3fd974eab018db7167998db4c0bb947c5ce800b3c8666430aa | Python | 2,649 | 64 | import unittest
import os
import pandas as pd
from ddt import ddt
import shutil
import site
import SPHARM.lib.vrml_parse as vr
@ddt
class TestVRML(unittest.TestCase):
def test_extract_node_names(self):
path = site.getsitepackages()[0] + '/SPHARM/tests/'
vr.extract_node_names(path + 'data/test_v... |
d5ea60c6dd1088933de1cdeab71b0078f35ebe892813ccf73f4530f5e75fb7ef | Python | 2,649 | 97 | """
An implementation of sparsemax (Martins & Astudillo, 2016). See
:cite:`DBLP:journals/corr/MartinsA16` for detailed description.
By Ben Peters and Vlad Niculae
"""
import torch
from torch.autograd import Function
import torch.nn as nn
def _make_ix_like(input, dim=0):
d = input.size(dim)
rho = torch.arang... |
2183782af27cae4731a04a6f89fde5040965c274f9c15aa42363845978c02f92 | Python | 2,650 | 92 | import numpy as np
from brian2 import *
# import matplotlib.pyplot as plt
import time
import pickle
# Personal stuff to send an email once data collection is finished
import sys
sys.path.extend(['/home/will'])
from email_utils import send_email
"""
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%... |
f9150c8c07939f49c0310854307d1fbf95a7b6f2de14afdd02427fa2f4cb1eac | Python | 2,650 | 70 | import time
import numpy as np
class MOTClient(object):
def __init__(self, client_config):
"""Creates a new detection source that implements the `poll` function.
Detections are for the MOT16 dataset, sourced from a Faster RCNN model.
The MOTClient object implements a configurable latency, ... |
0bbdc25eeda379c7ebd8bbd7776b75cc7fd18ffae861b3a34afc7b077191081e | Python | 2,654 | 96 | from typing import Sequence
from itertools import chain
import torch
import torch.nn as nn
from torchvision import models
from .utils import normalize_activation
def get_network(net_type: str):
if net_type == 'alex':
return AlexNet()
elif net_type == 'squeeze':
return SqueezeNet()
elif ... |
5bbd51491ffbc27c2ef54ddb5d298e24c71f5fa2f8feb13db7ed6fb07f00c881 | Python | 2,655 | 93 | # SPDX-License-Identifier: LGPL-3.0-or-later
import numpy as np
_RANDOM_GENERATOR = np.random.RandomState()
def choice(
a: np.ndarray | int,
size: int | tuple[int, ...] | None = None,
replace: bool = True,
p: np.ndarray | None = None,
) -> np.ndarray | int:
"""Generates a random sample from a gi... |
c66d57ca839196eafe14c4d1428d48ca150da25eef723c467abcc17d5ba5791e | Python | 2,656 | 72 | # 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... |
9d355e91b7f8c01e209f85b22ace1f641865f96be7b65af7fcf3814d7284e829 | Python | 2,657 | 54 | # 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
#
from ampligraph.latent_features.layers.scoring import DistMult
import pytest
... |
200ea0131f769ccfa3ebb08a7972a9ed7daa4e8ede796c6a0cab4ed6f0cf6edd | Python | 2,659 | 53 | from __future__ import print_function
import numpy as np
from freqAnalysisTools import band
from featureExtractor import FeatureExtractor
class FeatureExtractorClassical(FeatureExtractor):
def __init__(self, params):
self.params = params
self.extractorType = 'classical'
def getFeatures(self, ... |
727d203a2834ca06b681246fae9f8ded10e06e6e0d0e4fd2852c4d2925687e00 | Python | 2,659 | 92 | # Copyright (c) ONNX Project Contributors
#
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import numpy as np
import onnx
from onnx.backend.test.case.base import Base
from onnx.backend.test.case.node import expect
def hardmax(x: np.ndarray, axis: int = -1) -> np.ndarray:
x_argmax = np.... |
693ebcd88a2c89819102351807e1f62dd30e57d2c67fe69962c829265396cb92 | Python | 2,662 | 96 | # SPDX-License-Identifier: LGPL-3.0-or-later
from copy import (
deepcopy,
)
from typing import (
Any,
)
import torch
from deepmd.pt.model.atomic_model import (
DPDensityAtomicModel,
)
from deepmd.pt.model.model.model import (
BaseModel,
)
from .dp_model import (
DPModelCommon,
)
from .make_densit... |
6ca19e9fb4023650249c2a54f80892e6fa83e072bf143a7440f85965542d168c | Python | 2,662 | 86 | # 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... |
dfea03cb203657687791cfdc08a6fa721764c9b769ebcf8b3abb3e211acc0810 | Python | 2,662 | 90 | __all__ = [
"convert_dict",
]
from skbase.utils.dependencies import _check_soft_dependencies
from sktime.datatypes._convert_utils._coerce import _coerce_df_dtypes
from sktime.datatypes._convert_utils._convert import _extend_conversions
# this needs to be refactored with the convert module
MTYPE_LIST_HIERARCHICAL... |
3b9ef7f972f5b63b8e30c88fabe06d0acd465a7d75d8c39feb3c78effc46f1e3 | Python | 2,664 | 73 | import unittest
import os
import pandas as pd
from ddt import ddt
import shutil
import site
from SPHARM.lib import spharm
import SPHARM.lib.parallel as prl
@ddt
class TestSPHARM(unittest.TestCase):
def test_spharm_batch(self):
path = site.getsitepackages()[0] + '/SPHARM/tests/'
prl.run_parallel... |
580beba4cf422c61661246a8d20e0eb7dc82b9281b5fc42113311a56d235928e | Python | 2,665 | 82 | import numpy as np
from cnmodel.util import sound
def test_conversions():
pa = np.array([3990.5, 20, 0.3639, 2e-5])
db = np.array([ 166, 120, 85.2, 0])
assert np.allclose(sound.pa_to_dbspl(pa), db, atol=0.1, rtol=0.002)
assert np.allclose(sound.dbspl_to_pa(db), pa, atol=0.1, rtol=0.002)
... |
c7b869c387ab0a8bbe0dd446fc0e06732981d2c004da9cc080ef25c4ab9c460a | Python | 2,667 | 73 | import os, sys
import numpy as np
import torch
import pytorch_lightning as pl
from six.moves import cPickle
from evoaug import evoaug
sys.path.append('../../evoaug_analysis')
import utils
from model_zoo import DeepSTARR
device = torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')
# load data
expt_name = '... |
a6c30830a4c10193b012fee4eb01ffaaa90354fac06eef46d45966807fdbca57 | Python | 2,668 | 84 | # 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... |
cf53506d82e1f990e4e41597bc1f3befc319cc8a3eea45f6dc943df8208b8a3f | Python | 2,669 | 92 | # Copyright (c) ONNX Project Contributors
#
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import numpy as np
import onnx
from onnx.backend.test.case.base import Base
from onnx.backend.test.case.node import expect
# The below GatherElements' numpy implementation is from https://stackoverfl... |
b5c34e81cf7b69225fbbc6cf92529632a1eba09b8e3e7bda5e88da61f977e036 | Python | 2,672 | 76 | """
@file: rl_config.py
Created on 01.04.2021
@project: CrazyAra
@author: queensgambit, maxalexger
Configuration file for Reinforcement Learning
"""
from dataclasses import dataclass
@dataclass
class RLConfig:
"""Dataclass storing the options (except UCI options) for executing reinforcement learning."""
# Ho... |
8944ef27f57e01a327bc6fa0c68b65f1f91fc9a78d617d85d059690eaf80c72d | Python | 2,673 | 103 | #!/usr/bin/env python
__doc__ = """
Sample Specification
Nicholas Turner <nturner@cs.princeton.edu>, 2017
"""
class SampleSpec(object):
"""
Class specifying the purpose of each volume within a dataset sample
The three possible classes are: input, label, mask
Links each label to a mask if it exists
... |
cab9a0f97245fba0fdc786e88ff4c1eba462aba7add87153be69381847bf4db7 | Python | 2,674 | 84 | # 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... |
e4af67a8219857f9a71dd04c1c2cc30aba8ae748358277d9e608cb1df3994399 | Python | 2,675 | 49 | {'config-search-paths': ['{:user-config-path}/pyontutils/config.yaml',],
'auth-variables':
{'curies': ['../nifstd/scigraph/curie_map.yaml', # git
'{:cwd}/share/pyontutils/curie_map.yaml', # ebuild testing
'{:user-config-path}/pyontutils/curie_map.yaml', # config
'{:user-data-... |
5c263fb825f9be22b36ac2fb8b3edc794cb5060dd10b7a7671aa8cf9652e77e9 | Python | 2,682 | 66 | import sys
sys.path.insert(0, "../src")
from pymatgen.core.periodic_table import Element
from pymatgen.core.structure import Structure
from pymatgen.analysis.adsorption import AdsorbateSiteFinder
from gnn_eads.functions import get_voronoi_neighbourlist
from pymatgen.io.ase import AseAtomsAdaptor
def get_act_sites(meta... |
0fd7f1f9b87caf11b7d836c037680132fea1ed6c7c0e7d730e7a231b8f122f81 | Python | 2,684 | 89 | from __future__ import absolute_import, print_function
import time
import numpy as np
import pandas as pd
from tqdm import tqdm
def get_data_df(fpath='data_processed.csv'):
return pd.read_csv(fpath)
def split_data_df(data, val_frac=0.1, test_frac=0.1, shuffle=False, seed=None):
# Define shuffling
if sh... |
45ada0b6f145a1d17c4481afd10c61a115f0993d1687b67ea46178287905fbb9 | Python | 2,684 | 75 | # Copyright 2019-2020 The ASReview 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 appl... |
f052a41e3f75e8b8f397cb14cd9562a6ca3e9d847477663e1bbff19d3b990d3b | Python | 2,686 | 91 | # Copyright (c) ONNX Project Contributors
#
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import numpy as np
import onnx
from onnx.backend.test.case.base import Base
from onnx.backend.test.case.node import expect
def softmax(x: np.ndarray, axis: int = -1) -> np.ndarray:
x_max = np.max... |
a935fe9a3dcbdf20bfe331370909b924de8dcad2577195389bbd6bd9349fbff5 | Python | 2,687 | 92 | from __future__ import print_function
import numpy as np
from .augment import Augment, Compose
__all__ = ['Flip', 'Transpose', 'FlipRotate']
class Flip(Augment):
"""Random flip.
Args:
axis (int):
prob (float, optional):
"""
def __init__(self, axis, prob=0.5):
self.axis = ax... |
a96d8468c681a8f9683f99358593a2dd5f3c729c621bf991cd3e2bf5d1e9aed6 | Python | 2,688 | 78 | """precipitation_lightning.py"""
"""
Author: Yimin Yang
Last revision date: Jan 18, 2022
Function: Essential TransUnet_base for using pytorch_lightning
Ref: https://github.com/HansBambel/SmaAt-UNet
"""
from torch import nn, optim
import torch.nn.functional
import pytorch_lightning as pl
class AA_TransUnet_base(pl.L... |
d69e2414f097a2ba490057e1236ad546958b877538f07bb09cc72675d28e9569 | Python | 2,688 | 87 | # 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... |
16c8b012e2da63cdcd5584e9d45e281a55d9b294856eb5a30efa40f293cfef2c | Python | 2,691 | 83 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import sys
sys.path.append("/public/siwenbin/DLQSM_YH/")
#
# Description:
# Testing code of QSMnet
#
# Copyright @ Yanqiu Feng
# Laboratory for Medical Imaging and Diagnostic Technology
# Southern Medical University
# email: foree@163.com
#
from utils import *
from ca... |
2a28ba8dc8e96c6b1a1ed068c3286f5efc1e954401cfc7ccaf6d008fb3c5aa7a | Python | 2,691 | 55 | from expert.src.evaluator import Evaluator
import pandas as pd
import os
from expert.src.utils import get_dmax
from tqdm import trange
import numpy as np
from joblib import Parallel
def evaluate(cfg, args):
layers = [os.path.join(args.input, i) for i in sorted(os.listdir(args.input), key=lambda x: int(x... |
0827020ac57c92699ee910bed7add393fb23212da3bb3c8fb91a31e8bf2a602d | Python | 2,692 | 63 | from tqdm import tqdm
import torch
def update_bn(loader, model, device=None, tune_bert=False):
r"""Updates BatchNorm running_mean, running_var buffers in the model.
It performs one pass over data in `loader` to estimate the activation
statistics for BatchNorm layers in the model.
Arguments:
loa... |
706228d63b8317537e06b239c337f94bf7f1939ed66409c7cfd355dadba15e0a | Python | 2,692 | 66 | import torch
import torch.nn as nn
class CNN3D(nn.Module):
"""Base 3D convolutional neural network architecture for molecular data, consisting of six layers of 3D convolutions, each followed by batch normalization, ReLU activation, and optionally dropout.
This network uses strided convolutions to downsample t... |
b3514d2bd71cf36e61d845591902c245bb0477f9d5ab20493dc2a07a88ced0e6 | Python | 2,693 | 87 | import sciunit
import quantities as pq
from networkunit.capabilities.ProducesSpikeTrains import ProducesSpikeTrains
class nest_simulation(sciunit.models.RunnableModel, ProducesSpikeTrains):
# ToDo: How to use attrs?
nest_instance = None
def __init__(self, name, nest_instance=None, attrs=None, model_param... |
0bae0b0e44e34abe378b04c0938e0b7f16e46167bf0b7dff2c0dd87faa322ec8 | Python | 2,696 | 67 | # -*- coding: utf-8 -*-
# Written (W) 2008-2012 Christian Widmer
# Written (W) 2008-2010 Cheng Soon Ong
# Written (W) 2012-2014 Daniel Blanchard, dblanchard@ets.org
# Copyright (C) 2008-2012 Max-Planck-Society, 2012-2014 ETS
# This file is part of GridMap.
# GridMap is free software: you can redistribute it and/or m... |
fcb80570ee676feef619c684d256d022698a46f16512120adcd727f6793bd60a | Python | 2,696 | 82 | import unittest
from pathlib import Path
import pytest
from pyontutils.utils import get_working_dir
from pyontutils.config import auth
from pyontutils.integration_test_helper import _TestScriptsBase, Folders, Repo
import neurondm
class TestScripts(Folders, _TestScriptsBase):
""" woo! """
only = tuple()
lasts =... |
08dd4e782b168adf2fa6ec7f7ab411db98aafc127fad4bb5e54c6fda6f8c095c | Python | 2,697 | 91 | from torch import nn
import torch
class Compressor(nn.Module):
def __init__(self, n_channels: int, amp: float = 0.0):
super().__init__()
self.slope = nn.Parameter(amp * torch.randn(1, n_channels, 1))
def forward(self, x):
eps = 1e-8
slope_ = torch.exp(self.slope)
ret... |
3f012b4d180d01044d35b1327b358c4e8f8db672b9043f688fcfe510a13346b8 | Python | 2,698 | 92 | # Copyright (c) OpenMMLab. All rights reserved.
from copy import deepcopy
import pytest
import torch
from torch.nn.modules import GroupNorm
from torch.nn.modules.batchnorm import _BatchNorm
from mmcls.models.backbones import Conformer
def is_norm(modules):
"""Check if is one of the norms."""
if isinstance(m... |
1f232d95ce57499a1fa217efa8c2e856eaf326c6f6139611fab6e9c3dd549c05 | Python | 2,699 | 82 | # 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... |
3302d87d349a7ebd7c3d4fa051715bdd84537cf2ed9525c8c497b49e7d98b6fa | Python | 2,699 | 77 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
from typing import TYPE_CHECKING
from onnx.reference.op_run import OpRun
if TYPE_CHECKING:
import numpy as np
class If(OpRun):
def __init__(self, onnx_node, run_params):
OpRun.__init... |
3a5decef171adafd272ee3d93c34d1fef54ee188593cfb6fef6f51648180108a | Python | 2,699 | 97 | # -*- coding: utf-8 -*-
"""! @file util.py
@brief Utility functions for gammacal, hopefully temporary.
@author Perry Hargrave
@date 2016-05-05
A temporary file while re-factoring old gammacal code bits.
"""
from datetime import datetime
import logging
from matplotlib import pyplot as plt
import numpy a... |
c4df2c675bf7144d2ea4015a5e5810a158b3e8ee8f40c0dcfabc47d64a14bed3 | Python | 2,699 | 63 | # 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... |
8883982b60462fdd1bd32a7e20f63becbd072d6c4aee571253d434ec6a9888e6 | Python | 2,700 | 64 | # Copyright 2023 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... |
5846c6ad0258221c96aa192940304ebff241e8bd8388379b935587609a9591bb | Python | 2,701 | 53 | import numpy as np
from Bio import SeqIO
import pickle
def create_test_file(filename):
# these lsit below contains actual sequences from SignalP 6.0 dataset. Please process your files with e.g. biopython
# for fasta files, pickle for binaries, pandas for CSV/excel files; After you find a suitable way to extr... |
9eb45d42cd861acf51721ee02430086b59c9d0719ebde798c1391584a89746d5 | Python | 2,702 | 60 | # Copyright 2019 The TensorFlow 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 applica... |
1881f6dfbf31e4792b991074f3c038806c4a376672db50f67b46c1ec52f49f21 | Python | 2,705 | 72 | import torch.nn as nn
import torch
import torch.nn.functional as F
from torch.distributions import Bernoulli
from torch.autograd import Variable
from scipy.special import gamma
import numpy as np
import math
import pdb
from .ResNetFeat import create_feature_extractor
class FeatureNet(nn.Module):
def __init__(sel... |
be7c31b7cce15de534967a354c6ecc5f959c36e6bb3837ea1a714eb7316678cc | Python | 2,705 | 87 | # 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... |
0b56fb503068a053d714015b556e9f7075f681fb25699026259858a1d19056e3 | Python | 2,706 | 89 | import ast
import unittest
from datetime import datetime, date
from pyontutils import utils
from pyontutils.utils import injective_dict, Async, deferred, listIn, asStr
class TestInjectiveDict(unittest.TestCase):
def setUp(self):
self.test_funcs = (
lambda d: injective_dict(d),
lamb... |
a1a1fbb731cecadb908ba41d817b1de3d8cb0c61a1e1705281ad2335a7d8efae | Python | 2,706 | 86 | import setuptools
import sys
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration(None, parent_package, top_path)
config.set_options(
ignore_setup_xxx_py=True,
assume_default_configuration=True,
delegat... |
4d7d03ac36ccc14d1d13cedab53cf288e705dc80b07402ecb7e0e9ca9613487f | Python | 2,707 | 67 | """precipitation_lightning_base.py"""
"""
Author: Yimin Yang
Last revision date: Jan 18, 2022
Function: precipitation maps dataloader for training sets, test sets and validation sets
Ref: https://github.com/HansBambel/SmaAt-UNet
"""
import torch
from torch.utils.data import SubsetRandomSampler
import numpy as np
from... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.