sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
1d3a9e1412c2e394f9ee4d9ae9bb40ec81c1067b1c66b998a2ca8f81f963ebb9 | Python | 638 | 27 | """
This script tests StaticDecisionTree in staticDecisionTreeClasifier module
"""
# Authors: Taro Tezuka <tez@sings.jp>
from __future__ import division
import numpy as np
from staticDecisionTreeClassifier import StaticDecisionTreeClassifier
X_train = np.array([[3,2,5,1,1,1,3,2,5,4], [7,3,1,-2,6,5,-5,8,1,6], [2,5,... |
533b13b7753139afc929a97a92bb3f8ce5b00fe0f551fa333e64c08fa1100ac5 | Python | 638 | 27 | """
plot_optimization_history
=========================
.. autofunction:: optuna.visualization.matplotlib.plot_optimization_history
:no-index:
The following code snippet shows how to plot optimization history.
.. _visualization-plot-optimization-history-matplotlib-content:
"""
import optuna
def objective(tri... |
55b90416f11ab7cef42eb540a342aab2abb944664d80856f985d4b5d55312463 | Python | 639 | 17 | # Copyright 2007 Zachary Pincus
# This file is part of CellTool.
#
# CellTool is free software; you can redistribute it and/or modify
# it under the terms of version 2 of the GNU General Public License as
# published by the Free Software Foundation.
def configuration(parent_package='',top_path=None):
from numpy.d... |
a85323fe993e6c2194986b7edacc3600f238ca650e773dda17ca2f0880b764aa | Python | 641 | 23 | """Base class and type for numba distances."""
__author__ = ["chrisholder", "TonyBagnall"]
__all__ = [
"NumbaDistance",
"DistanceCallable",
"DistanceFactoryCallable",
"DistancePairwiseCallable",
"ValidCallableTypes",
"MetricInfo",
"DistanceAlignmentPathCallable",
"AlignmentPathReturn",
... |
b2fd560e95eb0216f29a324b4792441623f15b35c9372d7667136fa2bd110e6b | Python | 642 | 32 | """
plot_timeline
=============
.. autofunction:: optuna.visualization.matplotlib.plot_timeline
:no-index:
The following code snippet shows how to plot the timeline of a study.
.. _visualization-plot-timeline-matplotlib-content:
"""
import time
import optuna
def objective(trial):
x = trial.suggest_float... |
1252a372581f3b2f62d982490bfd1c9566fb75d528c8726afc13272c5d1a128b | Python | 643 | 26 | import datamol as dm
from rdkit.Chem import rdMolDescriptors
dm.disable_rdkit_log()
def smiles_to_fingerprint(smiles, fp_size, fp_radius):
mol = dm.to_mol(str(smiles), ordered=True)
fingerprint_function = rdMolDescriptors.GetMorganFingerprintAsBitVect
pars = {
"radius": fp_radius,
"nBit... |
19bb667d85d948815b3e2df6a4607e535f8eb35fe735a4cc5e16aa7b558d3b3b | Python | 643 | 17 | """utility functions for benchmarking module."""
import re
def _check_id_format(id_format: str, id: str) -> None:
"""Check if given input ID follows regex specified in id_format."""
if id_format is not None:
if not isinstance(id_format, str):
raise TypeError(f"id_format must be str but re... |
3aec6abf54ff61dd48532db606981c00d45aadb02ba1b7ec3e1dfc50c2bf36d0 | Python | 643 | 33 | #!/usr/bin/env python3
# tifffile/lsm2bin.py
"""Convert TZCYX LSM file to series of BIN files.
Usage: lsm2bin lsm_filename [bin_filename]
"""
import sys
try:
from .tifffile import lsm2bin
except ImportError:
try:
from tifffile.tifffile import lsm2bin
except ImportError:
from tifffile im... |
598adb4086091c96d5d45190702a88b73e4caf26f370d0c3a5760a17af9e3ec8 | Python | 643 | 27 | """
Cache test datasets before running tests / building docs.
Avoids race conditions that would arise from parallelization.
"""
import pathlib
import re
from seaborn import load_dataset
path = pathlib.Path(".")
py_files = path.rglob("*.py")
ipynb_files = path.rglob("*.ipynb")
datasets = []
for fname in py_files:
... |
cf02cd8c5466eb90a4cdcc217866a27270a47c9bc472313060055fb421565ca0 | Python | 644 | 22 | import scipy as sp
import numpy as np
def get_spearmanr(all_models, DataHandler):
predictions = []
test_input = [DataHandler['X_test'], DataHandler['dg_test']]
test_true_label = DataHandler['y_test']
for ind, model in enumerate(all_models):
test_prediction = model.predict(test_input)
... |
f46cf6eb4b86ee58ec04320515969786d94e6373943aea973c36cf8b86116efa | Python | 644 | 26 | import torch
import numpy as np
def gunpowder_balance(labels, mask=None, thresh=0.):
if mask is not None:
bmsk = (mask > 0)
nmsk = bmsk.sum().item()
assert(nmsk > 0)
else:
bmsk = torch.ones_like(labels, dtype=torch.uint8)
nmsk = np.prod(bmsk.size())
lpos = (torch.... |
afc520116c095d34477c5ef2577f0442b8eb578d4d26db4b2e92e257f6e9876b | Python | 646 | 21 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import numpy as np
from onnx.reference.op_run import OpRun
class InstanceNormalization(OpRun):
def _run(self, x, s, bias, epsilon=None):
dims_x = len(x.shape)
axis = tuple(range(2,... |
c9cb777183208050f0b96413e0b54076f2652f7cd06ed0d947bfdc8888fd7124 | Python | 648 | 33 | """
plot_rank
=========
.. autofunction:: optuna.visualization.plot_rank
:no-index:
The following code snippet shows how to plot the parameter relationship as a rank plot.
.. _visualization-plot-rank-plotly-content:
"""
import optuna
def objective(trial):
x = trial.suggest_float("x", -100, 100)
y = ... |
64eae3ed69edf1a1b2e116fcc45efa566f8006f7056727b7439f6e8ce437a38b | Python | 649 | 12 | """Regenerate every result and figure, then verify. Fixed seeds throughout."""
import subprocess, sys, os
HERE = os.path.dirname(os.path.abspath(__file__))
for script in ["t5_passk_crossover.py", "t2_t6.py", "t1_t3_t4_bridge.py",
"c6_correction.py", "t_star.py", "empirical.py",
"make_figur... |
8ecb50a5e05e6e7f7be17840bd320b19b81962936664ece7c999303d2bc460a9 | Python | 653 | 16 | # 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
#
# ... |
517504c9a584cbaa161929e7519fb24163d7c2b116ef81b1964abb8df3457aec | Python | 654 | 16 | # 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
#
# ... |
c35037b951d3e866709bc27bd4be4eab541c01675804da6c94c67b0e93e857a9 | Python | 654 | 23 | # 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 Mish(Base):
@staticmethod
def export() -> None:
node =... |
cf1a4e2861da90c9a2691d747406650558b780b05eafa47f177f8ca215fd69da | Python | 654 | 15 | # 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... |
0621ceb8d19f7ca46851af7b217026fc6ca6214a190321c375743101994710c6 | Python | 655 | 16 | # 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
#
# ... |
077ab23e695baad135d2dd360d3325e268c0d14de41a9748e210a58a920d702d | Python | 655 | 16 | # 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
#
# ... |
6ca1e67f5c6075b1d48d614a972c1b5d24e99e9a154e076414892264aa9e669a | Python | 655 | 16 | # 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
#
# ... |
511e0ce11851b452c2dc11cd52a3c1fbd247ce63a40b10b74c4e57f103c24b4e | Python | 657 | 16 | # 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
#
# ... |
8db1f903a58ad336a27e3952061888fe8c81b6e7376cbda890874e09be723bbd | Python | 657 | 30 | """
plot_param_importances
======================
.. autofunction:: optuna.visualization.plot_param_importances
:no-index:
The following code snippet shows how to plot hyperparameter importances.
.. _visualization-plot-param-importances-plotly-content:
"""
import optuna
def objective(trial):
x = trial.s... |
53c1f533937bf30044e6bfc385f8adab21809a76e0f78162700ac0c4788934ae | Python | 658 | 42 | # SPDX-License-Identifier: LGPL-3.0-or-later
from .charge import (
GridDensityLoss,
)
from .dens import (
DeNSLoss,
)
from .dos import (
DOSLoss,
)
from .ener import (
EnergyHessianStdLoss,
EnergyStdLoss,
)
from .ener_spin import (
EnergySpinLoss,
)
from .loss import (
TaskLoss,
)
from .popu... |
5db02ced90724a7967b78953b3c42f42c884848ad32c41bab56425d112d259db | Python | 658 | 16 | # 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... |
7595628eaf0094b4ab630f4729dd6703adb937847c15961e7db876d967b7fac3 | Python | 658 | 16 | # 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
#
# ... |
f07fd32840890b90b1544954f819bfeef42eda9e11264ef3ae76c7460fb246d6 | Python | 658 | 32 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Aug 2 13:59:29 2022
@author: sam
"""
import h5py
import glob
import matplotlib.pyplot as plt
import os
dirname='/home/sam/bucket/octopus/8k/oct_456'
file = dirname + '/htFlip.csv'
af = sorted(glob.glob(dirname + '/' + '*.reg'))
#df = pd.DataFrame(dat... |
0ef4f1b6ecad6254488320d63d39d7594758a8ab221f25252c77a379c63e0cc6 | Python | 659 | 15 | import os
import torch
import torchvision
class ImageFolderWithPaths(torchvision.datasets.ImageFolder):
"""Custom dataset that includes image file paths. Extends torchvision.datasets.ImageFolder"""
# override the __getitem__ method. this is the method that dataloader calls
def __getitem__(self, index):
... |
659f515a8282bc3d5cde1c982a20a386359414c3990d1e0b778ffef0c44ddfff | Python | 659 | 22 | #!/usr/bin/env python
"""Django's command-line utility for administrative tasks."""
import os
import sys
def main():
"""Run administrative tasks."""
os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'web.settings')
try:
from django.core.management import execute_from_command_line
except ImportEr... |
78a8bc8d54bfe16c67753221f7fb71a3445882e23ed9ef774a0c2fc4fe10de64 | Python | 659 | 22 | import numpy as np
import pandas as pd
import seaborn as sns
from graspologic.simulations import sbm
def sample_toy_networks(seed=888888, ns=None, B=None):
np.random.seed(seed)
if ns is None:
ns = [5, 6, 7]
if B is None:
B = np.array([[0.8, 0.2, 0.05], [0.05, 0.9, 0.2], [0.05, 0.05, 0.7]])... |
f71299fedd0ce3158bb774be5e7b995b6f35bc2c724f13c46cccdcc8fe16406b | Python | 659 | 21 | """Concrete catalgue classes for forecasting experiments."""
from sktime.catalogues.forecasting.dummy import DummyForecastingCatalogue
from sktime.catalogues.forecasting.M4 import (
M4CompetitionCatalogueDaily,
M4CompetitionCatalogueHourly,
M4CompetitionCatalogueMonthly,
M4CompetitionCatalogueQuarterly... |
9b69b8f28fc3614c90ac6745c45bb798d3e547a6d45dd7f96b2fd0d52e2c0c24 | Python | 660 | 15 | # 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... |
283c47b148738549b802b7ed2acd7e0b9a21599428bdde325004f4c89be30c36 | Python | 661 | 23 | from sciunit.models.backends import Backend
import os
class storage(Backend):
name = 'storage'
def _backend_run(self):
try:
data = self.model.load()
except Exception as e:
print(e)
raise NotImplementedError('Hint: the model class must define a '
... |
f20df4abeddad84352a1dbdc86f1e366ac3b5d8ebf2c0bea42c82e7f604173a1 | Python | 661 | 29 | """
plot_parallel_coordinate
========================
.. autofunction:: optuna.visualization.plot_parallel_coordinate
:no-index:
The following code snippet shows how to plot the high-dimensional parameter relationships.
.. _visualization-plot-parallel-coordinate-plotly-content:
"""
import optuna
def objecti... |
931ab8932d6d7e9f5a8ad1540eea5fec52a0d7ce7374b0ba41efd1940d6d9514 | Python | 662 | 21 | import os
import torch.nn.functional as F
import torch
from torch_geometric.nn import GCNConv
from collections import Counter
class Net(torch.nn.Module):
def __init__(self, in_size=16, hid_size=8, out_size=2):
super(Net, self).__init__()
self.conv1 = GCNConv(in_size, hid_size)
self.conv2 = ... |
48c37e43e02e84bf472e037a7ecc825c84442aa0906a53d588ef9b0a1b667e50 | Python | 663 | 24 | class Solution():
#structure of the solution
def __init__(self):
self.num_features = None
self.num_agents = None
self.max_iter = None
self.obj_function = None
self.execution_time = None
self.convergence_curve = {}
self.best_agent = None
self.b... |
2b32f29b42f15799cc67494858c0d435e857022af3dbd4a7bc13867a9eeddfec | Python | 664 | 32 | """
plot_rank
=========
.. autofunction:: optuna.visualization.matplotlib.plot_rank
:no-index:
The following code snippet shows how to plot the parameter relationship as a rank plot.
.. _visualization-plot-rank-matplotlib-content:
"""
import optuna
def objective(trial):
x = trial.suggest_float("x", -100... |
6da0cf58cb92ee9f3eebc2f50e96321cbde5f96cac57be245d75cbf72b2408a2 | Python | 664 | 16 | # 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
#
# ... |
3be1886072b8bb647d90fbec01d8a637d044663a717d4a2f341d4510e6aa611a | Python | 665 | 16 | # 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
#
# ... |
6dad9e5d36d7cdb21b65fbb5b8a57f562ed992568aad3009f4f795b05a13e79f | Python | 665 | 16 | # 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
#
# ... |
edd7cf90de8200801baadb6e08eba0623c5c0f712e34547c5d28e0f3f4a3e368 | Python | 665 | 18 | # 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
#
"""AmpliGraph is a library for relational learning on knowledge graphs."""
impo... |
e3ab847346d41539e5171290b261dda01bbbf23d95ec85bbb4baf216e5d520f8 | Python | 666 | 16 | # 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
#
# ... |
6ed739bb366fb94d563530a0ba6edf9b8f3c3ead313e235077739cf741f980c8 | Python | 668 | 24 | """
These are the plotting functions used by many ODP programs
"""
import matplotlib
def format_matplotlib():
"""format the fonts and print options for the plots"""
font = {'family' : 'sans-serif',
'sans-serif' : 'Helvetica',
'weight' : 'normal',
'size' : 12}
matplot... |
3c8d445540fb91dd885708439085f5bb8e018a6218691deff45bd405bec6d9d1 | Python | 669 | 26 | # roifile/tests/conftest.py
"""Pytest configuration."""
import os
import sys
if os.environ.get('VSCODE_CWD'):
# work around pytest not using PYTHONPATH in VSCode
sys.path.insert(
0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
)
def pytest_report_header(config: object) -> str:... |
93ac1f9eb46800448ebfadd9021ea3c4dc7516e69b70f40650b63a23ba8d1d87 | Python | 669 | 16 | # 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
#
# ... |
0d62d14c9189df95bd98822e2edcad6443cb3ae91eba9b5627c545103de4904c | Python | 670 | 9 | #=======================================================================================================================
#Copyright
#=======================================================================================================================
# Copyright (C) 2021 Matvey Safroshkin, Grigory Arutyunov, Patrick ... |
2fe2970be5629f77fbf34b9f91e65786b20c7f3b24429f6d051ffc38ac18532b | Python | 670 | 20 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import numpy as np
from onnx.reference.ops._op_common_window import _CommonWindow
class HannWindow(_CommonWindow):
r"""Returns :math:`\\omega_n = \\sin^2\\left( \\frac{\\pi n}{N-1} \\right)` where... |
9b41c79dd31fc13002255e0a8bdbbdb7ce2132b35a7da33cb9a0ac941081019e | Python | 670 | 16 | # 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
#
# ... |
d38e8a29cbed15bd2eee5a27aaea291f3ee2bf6d40a1427ad11a428453798fa6 | Python | 671 | 20 | import ontquery as oq
from pyontutils.core import OntTerm
import os
TEST = 'https://test3.scicrunch.org/api/1/'
PRODUCTION = 'https://scicrunch.org/api/1/'
InterLexRemote = oq.plugin.get('InterLex')
interlex_remote_production = InterLexRemote(
# When ready, should be changed to 'https://scicrunch.org/api/1/' for ... |
f9f013342a36d379cef35b1bdfabbb976c313de028c88e8afeb5b450fdc465f5 | Python | 671 | 16 | # 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
#
# ... |
907db71da62e0c6da4c804d0168594dd0712ceb84694dc2b4aff320360c2898b | Python | 673 | 29 | """
plot_param_importances
======================
.. autofunction:: optuna.visualization.matplotlib.plot_param_importances
:no-index:
The following code snippet shows how to plot hyperparameter importances.
.. _visualization-plot-param-importances-matplotlib-content:
"""
import optuna
def objective(trial):
... |
0182a285f3084d930e9da5e93b1af1daa50a4bde10356ca70b8914901801dedc | Python | 674 | 32 | #!/usr/bin/env python
import unittest
from hbip.tests.test_example import TestExample
from hbip.tests.test_load_test_data import TestLoadTestData
from hbip.tests.test_main import TestMain
class CountSuite(object):
def __init__(self):
self.count = 0
self.s = unittest.TestSuite()
def add(self,... |
f65b6234135bcd0c268357afa4e32e73e75d43d4cf5eb47f6d9199b4daac6bfa | Python | 674 | 21 | """Tests for bycycle.utils.timeseries."""
import numpy as np
from bycycle.utils.timeseries import *
###################################################################################################
###################################################################################################
def test_limit_s... |
c9caa8cbd6cede06d19b79942d3cb6286153d2c1d9d732bfcd34fde4847e4703 | Python | 675 | 15 | # 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... |
04067f6de6c0c66f3d852f2bf52526db4b898523c7862fd162a511cee58411ce | Python | 677 | 28 | """
plot_parallel_coordinate
========================
.. autofunction:: optuna.visualization.matplotlib.plot_parallel_coordinate
:no-index:
The following code snippet shows how to plot the high-dimensional parameter relationships.
.. _visualization-plot-parallel-coordinate-matplotlib-content:
"""
import optun... |
31ae999022bf9444a5ea43406b34bfad41f9ad0da93b6a148a9d351feb222a62 | Python | 679 | 23 | import torch
import torch.nn as nn
import torch.nn.functional as F
from .resnet import resnet18ori
import pdb
class FeatureNet(nn.Module):
def __init__(self, args, n_class=2):
super(FeatureNet,self).__init__()
self.args = args
self.n_class = n_class
self.encoder = resnet18... |
63b198a74ab3cd0d76cb4020ca185befe13d07117737b34fbf4ddc729ccfb44e | Python | 679 | 27 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
from onnx.helper import np_dtype_to_tensor_dtype
from onnx.reference.op_run import OpRun
from onnx.reference.ops.op_cast import cast_to
def _cast_like(x, y, saturate: bool):
return (cast_to(x, np_d... |
8363d283c7e9f87995fcecffcfb138a18c0dbe9bfebd5e33e95085f69aa98ff9 | Python | 679 | 20 | import inspect
def list_classes_from_module(module, parent_class=None):
"""
Parse user defined module to get all model service classes in it.
:param module:
:param parent_class:
:return: List of model service class definitions
"""
# Parsing the module to get all defined classes
class... |
8cce2865f1b881719f5352b70d1f9c66e8b38961438dcd64854134944cc85865 | Python | 679 | 27 | # -*- coding: utf-8 -*-
"""
Created on Wed Jan 23 18:55:32 2019
@author: daniel
"""
class Synapse(object):
"""Generic synapse class."""
def __init__(self):
self.type = None
self.sec = None
self.pos = None
self.spinepos = None
self.obj = None
self.source = None
... |
7750664f6d488b90551d0ec72b5aeacaa4eb18f02a7570438350fbdc7193f3ae | Python | 680 | 27 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import numpy as np
from onnx.reference.ops._op import OpRunUnaryNum
def sigmoid(x: np.ndarray) -> np.ndarray:
"""Numerically stable sigmoid implementation that supports scalars and nd-arrays."""
... |
96e394cf03c5568116f30228d25372ef671ea0c137043cb7b0cee5e1650faa6e | Python | 680 | 26 | from setuptools import find_packages, setup
setup(
name="lfads_tf2",
version="0.1.0",
packages=find_packages(),
install_requires=[
"tensorflow-gpu==2.0.0",
"tensorflow-probability==0.8.0",
"tensorflow-addons==0.6",
"tensorboard==2.0.2",
"yacs==0.1.6",
"Py... |
1a92041dee5e2e117d9ed1e9a14ff5f425dd2e27f91cad6fa6ad3b0b5e7a95b3 | Python | 682 | 13 | import torch.nn as nn
class VPModelBlock(nn.Module):
r"""
This class implements the base class for many model blocks used by this package's prediction models.
The named constants exposed in this base class provide convenient ways to implement model blocks that match
official implementations.
"""
... |
3b139140a3df24576be3d913aa4c9df320dfaa6a627f91a2d69f3cdc83b26bc5 | Python | 682 | 23 | from torchvision import datasets, transforms
from src.base import BaseDataLoader
class DataLoader(BaseDataLoader):
"""
Something interesting.
"""
def __init__(self, data_dir, batch_size, shuffle, validation_split, num_workers, training=True):
trsfm = transforms.Compose([
transform... |
dc07357ed51eebc4eb6dcb1fd1f29c58976491e78ea767f504b5265265ec70a4 | Python | 682 | 24 | import pytest
import sys
import os
sys.path.insert(0, os.path.join(os.path.dirname(__file__), 'helpers'))
def pytest_addoption(parser):
parser.addoption(
"--runslow", action="store_true", default=False, help="run slow tests"
)
def pytest_configure(config):
config.addinivalue_line("markers", "slo... |
9b4148b2b9c7c172a00c2fb1ecbac815bfa6aa1cb4c14b70b00243492709c9da | Python | 686 | 16 | # 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
#
# ... |
5f30bf90447ef62fefffa1682f936acb067700517ee242c8229c6041f22c4bee | Python | 689 | 28 | """Import commonly used libraries"""
import time
import logging
import glob
import os
import numpy as np
import pandas as pd
import collections
# from natsort import natsorted
# matplotlib
import matplotlib as mpl
import matplotlib.pyplot as plt
mpl.rcParams['pdf.fonttype'] = 42 # editable text in matplotlib
mpl.rcPa... |
bc3064801541c2edb256ad381c01520ccd016043fbe78afeee5b5a07acf5f417 | Python | 689 | 32 | """
plot_hypervolume_history
========================
.. autofunction:: optuna.visualization.plot_hypervolume_history
:no-index:
The following code snippet shows how to plot optimization history.
.. _visualization-plot-hypervolume-history-plotly-content:
"""
import optuna
def objective(trial):
x = trial... |
0dc13a5fb77cd90121fd4b684ec3985095c77090a42b51e7ade3c0d81d71b3ae | Python | 690 | 20 | # 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... |
53dd8042c36de5cb4816673767fd8889cb7c222a9292d66eebdfa77aa3f592aa | Python | 691 | 16 | # 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
#
# ... |
e2bc1b7242d833f4e62106b24e17fb93e9049e40890399f56504794118c68c98 | Python | 692 | 31 | import cv2
import numpy as np
def main():
img = cv2.imread("Boom_LO350.jpg", cv2.IMREAD_COLOR)
assert img.shape[2] == 3, img.shape[2]
n = 581.0/1200
time_for_conv = np.ones(shape=(1, 1, 224, 224), dtype=np.float32) * n
time_for_fc = np.ones(shape=(1,1), dtype=np.float32) * n
... |
21cf06eba32f03b99c1fa887f5f47d5a2e8e186e797c988c63d10e1af91f0363 | Python | 693 | 27 | # Copyright (c) ONNX Project Contributors
#
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import argparse
from onnx import NodeProto, checker, load
def check_model() -> None:
parser = argparse.ArgumentParser("check-model")
parser.add_argument("model_pb", type=argparse.FileType("rb... |
658f3f97fc54090b018685a57e8fb42f86c62bca3c02dcc4853132fd86dfb24f | Python | 695 | 14 | """ Modules for translation """
from onmt.translate.translator import Translator
from onmt.translate.translation import Translation, TranslationBuilder
from onmt.translate.beam_search import BeamSearch, GNMTGlobalScorer
from onmt.translate.decode_strategy import DecodeStrategy
from onmt.translate.greedy_search import G... |
89ccee241da3512f7bfe9802f46d99b7e0ca2cede2019cc4609d15ab265af7ce | Python | 696 | 26 | """
Joint and marginal histograms
=============================
_thumb: .52, .505
"""
import seaborn as sns
sns.set_theme(style="ticks")
# Load the planets dataset and initialize the figure
planets = sns.load_dataset("planets")
g = sns.JointGrid(data=planets, x="year", y="distance", marginal_ticks=True)
# Set a log... |
0970c65af58e3685f8e2ea7a921768f9042b47336f844d60624d8c0712039bee | Python | 697 | 16 | """Module defining encoders."""
from onmt.encoders.encoder import EncoderBase
from onmt.encoders.transformer import TransformerEncoder
from onmt.encoders.rnn_encoder import RNNEncoder
from onmt.encoders.cnn_encoder import CNNEncoder
from onmt.encoders.mean_encoder import MeanEncoder
from onmt.encoders.audio_encoder imp... |
536aee258f75c2528c244f6161a038dcd619ff2542108a91c825b93a059c3bb8 | Python | 697 | 37 | from Cython.Build import cythonize
from setuptools import setup, Extension, find_packages
requirements = [
'numpy',
'scipy',
'Cython',
]
extensions = [
Extension(
'augmentor.warping._warping',
sources = ['augmentor/warping/*.pyx']
),
]
setup(
# Metadata
name='augmentor'... |
93f93c5a6919f3d3fa0b99cc8a8914c95c02dbefe42c3bc5e5ee228459a8defa | Python | 698 | 16 | # Copyright 2019-2021 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... |
ab8995a0d573f4f476b2424ded133ed0a2d3b6444e4f1fc71810b9b72060ba91 | Python | 698 | 18 | import sys
from typing import NewType
import numpy as np
import numpy.typing as npt
if sys.version_info >= (3, 10):
from typing import TypeAlias
Distribution: TypeAlias = npt.NDArray[np.float64]
# A DistanceMatrix is a square symmetric matrix with zeros along the diagonal
# and nonnegative entries.
DistanceMatrix... |
6f8ebe374a3bf8eacae2627e33e5cd0f562102803b7b3eef66e6eca237659cf5 | Python | 699 | 14 | from setuptools import setup
setup(name='prediction',
version='1.0',
description='Python package for CRISPR/Cas9 single guide RNA on- and off-target activities prediction',
url='https://github.com/Peppags/CRISPRont-CRISPRofft',
author='Guishan Zhang',
author_email='gszhang@stu.edu.... |
f67718c0144d4790be8dcbd9c517b6ac279a1660dbfda211a3d2fe5fbd291759 | Python | 699 | 19 | #!/usr/bin/env python3
import rdflib
from pyontutils.core import makeGraph
from pyontutils.namespaces import makePrefixes
def main():
PREFIXES = makePrefixes('NIFGA', 'NIFSTD', 'owl')
g = rdflib.Graph()
g.parse('http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-nifstd.owl', format='xml')
... |
389759a1523b9e0c4af6015c4f5de64f4ab9ede7f4dba1fcb998321e72912059 | Python | 702 | 21 | # Copyright 2019-2026 The AmpliGraph Authors. All Rights Reserved.
#
# This file is Licensed under the Apache License, Version 2.0.0.
# A copy of the Licence is available in LICENCE, or at:
#
# http://www.apache.org/licenses/LICENSE-2.0
#
"""AmpliGraph is a library for relational learning on knowledge graphs."""
im... |
3ad6a5e18ada6ec8ddab33c96ac3839b84cdf31e7da09a73131ca1335c43fd80 | Python | 703 | 29 | # 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
#
"""This module contains utility functions for neural knowledge graph
embeddi... |
1deb0d14177d261c4259013338c93b90499a859454a3212c559d20ffae1ffea3 | Python | 705 | 26 | import numpy as np
import hashlib, struct
_current_seed = 0
def set_seed(seed):
"""
Set the random seed to be used globally. If a string is supplied, it
will be converted to int using hash().
This immediately seeds the numpy RNG. Any other RNGs must be seeded using
current_seed()
"""
... |
e76eaaaeaf35f6290f280ef1f501bdbac02f4bc626bd444b1a7ce0d7caf84383 | Python | 705 | 21 | import numpy as np
import pandas as pd
import os
deg_files = [i for i in os.listdir('time_samplegroup_celltype_KO') if (i.startswith('d') and i.endswith('.txt'))]
df_combined = pd.DataFrame()
for deg_file in deg_files:
timepoint = deg_file.split('_')[0]
cell_type = deg_file.split('_')[1]
source = deg_fil... |
5e9c8c9ae031fba03e23d246a0bd8f03c07ad1c9064280c3177fb7f17c187e78 | Python | 706 | 16 | # 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
#
# ... |
6c7f24237f95b2143e379889abce6565deb54d08338c72ee1cee6472a1a446bb | Python | 706 | 22 | import rpy2.robjects.packages as rpackages
utils = rpackages.importr('utils')
pck_names = ['Matrix', 'mgcv', 'codetools', 'rpart', 'glmnet', 'mboost', 'CAM']
for pck_name in pck_names:
if rpackages.isinstalled(pck_name):
continue
if pck_name != 'CAM':
utils.install_packages(pck_name)
else... |
3a2f98b4b1c4786b170e03fac847cd9a48bd63a4f87e9ee3aede4516c72e4852 | Python | 708 | 23 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import numpy as np
from onnx.reference.op_run import OpRun
_acceptable_str_dtypes = ("U", "O")
class StringConcat(OpRun):
def _run(self, x, y):
if (
x.dtype.kind not in _accep... |
e338ae4376d7f5d668286556e66ac7d901861330a990b83c23c38d0d23a49086 | Python | 708 | 23 | import argparse
import logging
import yaml
from mprl.utility_services.manager.manager import ManagerServer
from mprl.utility_services.utils import pretty_print
logger = logging.getLogger(__name__)
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument("-c", "--config", help="path ... |
13d5b9925244b113aede999fccced935c6d2ac4713742bceb03ad04d6171ca84 | Python | 709 | 22 | #!/usr/bin/python
#
# Synapse definitions for models.
#
# This file includes a number of different synapse definitions and default conductances
# for point models. Most are models from the lab for neurons of the cochlear nucleus.
# the synaptic receptor models are gleaned from the literature and sometimes fitted to the... |
29c6b106c6d45e63deee8ffba725303959edcd5cbafa92dde9872f866b21bbb5 | Python | 709 | 19 | import numpy as np
import atom3d.util.results as res
import atom3d.util.metrics as met
cutoff='06'
maxnumat='600'
for id_split in ['30','60']:
name = 'lba-id'+id_split+'_cutoff-'+cutoff+'_maxnumat-'+maxnumat
print(name)
rloader = res.ResultsENN(name, reps=[1,2,3])
results = rloader.get_all_predictions... |
d9041c978581f46c88860b673a7443bc6706f2da92a4f1f04f1783bc3df38bae | Python | 709 | 17 | # 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
#
# ... |
105f9e27ab81f0bf1b8a07559c9ec9bbb81e77b064e593ce3686b24158837edf | Python | 710 | 27 | """ Environment-specific commands """
import os
import socket
from cuneify_interface import FileCuneiformCache
if not "mws" in socket.gethostname().lower():
raise RuntimeError(
"Unrecognised environment: {}".format(socket.gethostname().lower())
)
MY_URL = "http://cuneifyplus.arch.cam.ac.uk"
def ... |
a91788e3a352731afde9810bffa9c7ec43dda70840509f5c62a6ec3b5a4b5497 | Python | 710 | 21 | # copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Change score functions for change point detection."""
from sktime.detection._change_scores._continuous_linear_trend_score import (
ContinuousLinearTrendScore,
)
from sktime.detection._change_scores._cusum import CUSUM
from sktime.detection.... |
b5ca1459af631e8c650a28edb614473663570de5bdaac94026dec2d013fa962a | Python | 711 | 17 | from pathlib import Path
from vcnmodel.util.parse_hoc import ParseHoc
import toml
config = toml.load("wheres_my_data.toml")
import re
from pathlib import Path
pathn = Path(config['disk'], config['cellDataDirectory'])
cellname = 'VCN_c08'
refpts = {'VCN_c11': 'first', 'VCN_c08': 'first', 'VCN_c09': 'last', 'VCN_c14': '... |
1b2de9b6e8bf54a9b214ddb586bf13de71543ebd3d3e43bbede04b8890df1f2d | Python | 712 | 24 | # Copyright (c) OpenMMLab. All rights reserved.
from collections import abc
import numpy as np
import torch
def cast_tensor_type(inputs, src_type, dst_type):
if isinstance(inputs, torch.Tensor):
return inputs.to(dst_type)
elif isinstance(inputs, str):
return inputs
elif isinstance(inputs,... |
7d4993c45d296665f381f74e6eaec383901d9a26aba95a2d3b44b28548ce0bd5 | Python | 712 | 16 | # Copyright 2026 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... |
9a7b94206a58a929dec709eb4f74420622f259ef5b8c2c012f7635745f8a3b15 | Python | 712 | 27 | """lesion_features — BIDS-compatible lesion and disconnectome feature extraction."""
from bcblib.tools.lesion_features._bids import (
parse_bids_entities,
build_lf_csv_path,
build_lf_tsv_path,
build_prep_path,
iter_bids_lesions,
)
from bcblib.tools.lesion_features._constants import EBRAINS_ATLAS_SP... |
2e9b9295e8a41ab2567bcfb53e8f0037be95dbc637bcf53de4c6fa918eb4d667 | Python | 713 | 28 | # 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 Tan(Base):
@staticmethod
def export() -> None:
node = ... |
5518ce09dd6fb341426344acf50ae75e9cea3184d0f2bcbb568a92480c3bbf69 | Python | 713 | 28 | # 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 Cos(Base):
@staticmethod
def export() -> None:
node = ... |
cad40b0eac67891e8131ca354d29cb40c09d633bb6a4aebcdf27c267f8c9f099 | Python | 713 | 28 | # 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 Sin(Base):
@staticmethod
def export() -> None:
node = ... |
6905930766301aee5f90e60b2cb3ac30a3df535c5d7592d4ed3ce9c65825b471 | Python | 714 | 16 | # 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... |
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