sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
ffe7db97468071e536aec16c8453e44d62d0b84b19fc9dad8a4cac66973564ba | Python | 39,490 | 951 | # Copyright 2026 Xanadu Quantum Technologies Inc.
# 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 agre... |
dd1387c6527c171650acd1344678d705915ca8499955e4019d9cf05375263fd5 | Python | 39,502 | 1,176 | """
Tests dtype specification during parsing
for all of the parsers defined in parsers.py
"""
from collections import defaultdict
from decimal import Decimal
from io import StringIO
import numpy as np
import pytest
from pandas._libs import lib
from pandas.compat.pyarrow import pa_version_under25p0
from pandas.errors... |
9d53261828f0ed0f78d48c7399c4ea6b6228bc2d68e4592a27828062039265d2 | Python | 39,542 | 1,102 | import csv
from datetime import (
UTC,
datetime,
)
import io
import os
import sys
from zipfile import ZipFile
import numpy as np
import pytest
from pandas.compat import is_platform_windows
import pandas.util._test_decorators as td
import pandas as pd
import pandas._testing as tm
from pandas.core.arrays impor... |
05735dbbd4936113c602a2031499c8760dd32c395dc3c2c3fe76fb56fb92e31b | Python | 39,568 | 1,027 | #----------------------------------------------------------------------------
# Functions and Classes
import struct
import sys
from numpy import loadtxt
import numpy as np
import copy
def initOnsetSpikes():
model.ncAMPAlist[0].event(data.st_onset * 1000)
def initSpikes():
if (len(data.etimes)>0):
for ... |
abd0b9024579c491dac4548496630c84d8c86c6e4244600480fca7f3ddb483c9 | Python | 39,608 | 997 | # Copyright 2018-2025 Xanadu Quantum Technologies Inc.
# 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... |
c6a5a2a307bf6fa43607b9d15d7a622a504eac2a919a289cb02b6980ad40fa7c | Python | 39,631 | 1,075 | """
This file contains a minimal set of tests for compliance with the extension
array interface test suite, and should contain no other tests.
The test suite for the full functionality of the array is located in
`pandas/tests/arrays/`.
The tests in this file are inherited from the BaseExtensionTests, and only
minimal t... |
b888bf857da850ae35e916a23aa7a143f6197401986497c08d0a4ab339a759c2 | Python | 39,652 | 1,105 | # cython: language_level=3
# Time-stamp: <2025-11-10 15:24:27 Tao Liu>
"""Module for FWTrack classes.
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD License (see the file LICENSE included with
the distribution).
"""
# ------------------------------------
# python modu... |
eddf20f59dee594bedb5ba5950ae53660670fd5f6e326581083bae8fad439dad | Python | 39,684 | 961 | # Copyright 2018-2021 Xanadu Quantum Technologies Inc.
# 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... |
a06cdbdfe9c2ef77ab493ab8e36d3c272f47c795e2b1d37882b94a00bef12229 | Python | 39,724 | 1,048 | # Copyright 2018-2021 Xanadu Quantum Technologies Inc.
# 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... |
b1860c88c18497305b3c224fc1be7b8d1c8c7bd03aeb394e5025240fa48e5f90 | Python | 39,749 | 1,196 | from datetime import datetime
from io import StringIO
import itertools
import re
import textwrap
import numpy as np
import pytest
import pandas.util._test_decorators as td
import pandas as pd
import pandas.io.formats.format as fmt
lorem_ipsum = (
"Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do... |
994b44e8de8a2ac498621f27bedb50528d79bb4bfdff0bad77b1d70b85caf68d | Python | 39,827 | 1,075 | import os
os.environ['ETS_TOOLKIT'] = 'qt4'
from pyface.qt import QtGui, QtCore
from model.scan import CT
from slice_viewer import SliceViewWidget
from mayavi.core.ui.api import MayaviScene, MlabSceneModel, \
SceneEditor
from mayavi import mlab
from traits.api import HasTraits, Instance, on_trait_change
from trai... |
a19e946cf1a5f9e5129b8879df24f3d5f6cfe3977afb74be1967b50fd6d92e22 | Python | 39,833 | 1,009 | #!/usr/bin/env python
"""Module Description: Test functions for pileup functions.
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD License (see the file LICENSE included with
the distribution).
"""
import unittest
import numpy as np
from pathlib import Path
from tempfile... |
92fa2a0992bc8c5acdfe0f0c5e7cc79f5e3ad3a6a5872086390fddaf70edc76c | Python | 39,854 | 1,076 | # Copyright 2018-2020 Xanadu Quantum Technologies Inc.
# 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... |
a1f28a65ffec563e67ec6156d6910a35e9e295535a35fdda0c71e1e1ee76f305 | Python | 39,859 | 1,135 | import numpy as np
import pytest
from pandas.errors import Pandas4Warning
import pandas as pd
import pandas._testing as tm
class TestDataFrameSortIndex:
def test_sort_index_and_reconstruction_doc_example(self):
# doc example
df = pd.DataFrame(
{"value": [1, 2, 3, 4]},
ind... |
d8d3d0a91105b8257048e1bb847533a7f7dc0fc238a4018b2c582fff21b4745f | Python | 39,893 | 1,096 | # Copyright 2018-2023 Xanadu Quantum Technologies Inc.
# 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... |
e3ee73e3a9e484ddefc83a17fcf632bfb73123dd73c5e67ac05e9df69e8604fe | Python | 39,900 | 1,080 | # Copyright 2018-2022 Xanadu Quantum Technologies Inc.
# 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... |
0b963f5476eb1b3f3a40f1e4e273a9d98a91e66c34b79198d94c3b0c024c3808 | Python | 39,914 | 1,078 | # Copyright 2018-2020 Xanadu Quantum Technologies Inc.
# 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... |
7618b5a17310933a25fce494ead613e0dcec3af0dd770b4785a563de3de9f22f | Python | 39,959 | 1,154 | # Copyright 2018-2021 Xanadu Quantum Technologies Inc.
# 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... |
1d213bfa762b0799233a9d532e8261ec2f9892aaf11dccef7580213755d8991c | Python | 40,037 | 1,018 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.core.arrays.sparse import SparseArray
class TestReductions:
@pytest.mark.parametrize(
"data,pos,neg",
[
([True, True, True], True, False),
([1, 2, 1], 1, 0),
([1.0, 2.... |
eb591c2e7fb07bbbfd8cbdcd7879d1602f13135a519c645711b96d991c859ccb | Python | 40,053 | 1,176 | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import ast
import collections
import copy
import importlib
import itertools
import json
import logging
import os
import sys
import time
from ... |
1dc8bb4ad90978e4943302506564eb8dc969a45ae9ad61e7f93d3769cb63a5fd | Python | 40,203 | 1,256 | from math import ceil
from typing import Any, Dict, List, Optional, Tuple, Union
# matplotlib removed from core deps in 4.0.0a1 (time-series plots use
# plotly primarily; matplotlib paths are residual).
try:
import matplotlib
import matplotlib.pyplot as plt
except ImportError: # pragma: no cover
matplotli... |
4fc83ead090ddbefb950aa3d338aa0b140a3717ece317d61bfe774919be563eb | Python | 40,366 | 1,027 | # Copyright 2025 Xanadu Quantum Technologies Inc.
# 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 agre... |
b3381b284ba63ce8543b55e819a89bc9371f3613214e4307dd7401a2594f0432 | Python | 40,368 | 1,121 | from collections import (
abc,
deque,
)
from collections.abc import Iterator
from datetime import datetime
from decimal import Decimal
import itertools
import numpy as np
import pytest
from pandas.errors import (
InvalidIndexError,
Pandas4Warning,
)
import pandas as pd
import pandas._testing as tm
fr... |
7c68abb40516ebe2f23fd9a155f6a550410e86ae1437b551cf66e93470d69395 | Python | 40,426 | 1,253 | """
:mod:`pandas.io.html` is a module containing functionality for dealing with
HTML IO.
"""
from __future__ import annotations
from collections import abc
import numbers
import re
from re import Pattern
from typing import (
TYPE_CHECKING,
Literal,
cast,
)
from pandas._libs import lib
from pandas.compat... |
699b785b45c959f3bacc41c50ca25cfbbe088f73672031beafa90761b476961c | Python | 40,440 | 1,059 | #!/usr/bin/env python
import argparse
import gzip
import logging
import os
import re
import signal
import subprocess
import sys
import time
from collections import defaultdict
logging.basicConfig(
format='[%(asctime)s %(levelname)s] %(message)s', stream=sys.stdout
)
log = logging.getLogger(__na... |
e138b931902ee79e115ee04fa5198c0e256d0fc6ae45e324de696efd1c3488d0 | Python | 40,495 | 1,026 | # Copyright 2018-2021 Xanadu Quantum Technologies Inc.
# 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... |
1fff27773669ea69308c6a83aa82d1414e97a93e2b20b44ef952b7d34a80acf1 | Python | 40,509 | 1,288 | from __future__ import annotations
from datetime import (
datetime,
timedelta,
)
from typing import (
TYPE_CHECKING,
Literal,
overload,
)
import warnings
from dateutil.relativedelta import (
FR,
MO,
SA,
SU,
TH,
TU,
WE,
)
import numpy as np
from pandas._libs.tslibs.offs... |
abcc7ce225a82b5b517b5c0fc184af75a352193981bd5c4c9b7634bf5c2985a9 | Python | 40,512 | 953 | #!/usr/bin/env python
"""
Step S9 (CheckM branch): Short-read-based reassembly of bins.
CheckM-specific reassembly workflow using short-read data on
CheckM-filtered binsets.
"""
from Bio import SeqIO
import sys, os, threading, copy, math
from multiprocessing import Pool
def mod_bin(binset_folder):
"""
Crea... |
f2985010f8ce6892b48d9b85f9765e56a1dd85d6b3bfbbcafff1ec67decead08 | Python | 40,653 | 884 | """Tests for the KData class."""
import datetime
import io
import re
import shutil
from collections.abc import Sequence
from types import EllipsisType
from typing import Literal
from xml.etree import ElementTree as ET
import h5py
import ismrmrd
import pytest
import torch
from einops import repeat
from ismrmrd.seriali... |
808fe2dc58351f0a7c88ebb1f3d4266f0080b78be16ae5e8578d406d514e2447 | Python | 40,683 | 1,071 | #!/usr/bin/env python3
"""
Build an interactive SVG visualization of a chaining problem using D3.js.
Usage: build-chain-viz.py <data_directory> <chain_number> <output.svg>
"""
import sys
import os
import glob
import json
import gzip
import base64
from collections import defaultdict, Counter
def parse_seeds_file(fil... |
768a93ecf4461356269c2c7bd7c3dabd51405c98da078650b32b29a41eba35b5 | Python | 40,726 | 1,264 | """
:mod:`pandas.io.html` is a module containing functionality for dealing with
HTML IO.
"""
from __future__ import annotations
from collections import abc
import numbers
import re
from re import Pattern
from typing import (
TYPE_CHECKING,
Any,
Literal,
cast,
)
from pandas._libs import lib
from pand... |
2f8e38ba921c90557e4be5418d337ef217c0d52d8ba1ccfc4fd4587fd4598164 | Python | 40,737 | 1,099 | # Copyright 2018-2025 Xanadu Quantum Technologies Inc.
# 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... |
e0c827b2a25afc317f343b2b4cc97a36e49615cd290bf2d134128646dd08ffad | Python | 40,748 | 872 | # Copyright 2018-2022 Xanadu Quantum Technologies Inc.
# 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... |
d7d7971b4061f01d78679bcea450642013762221bd0958c4e1af3f99d9718a64 | Python | 40,761 | 946 | """High-level Model class for loading trained checkpoints and running inference."""
from __future__ import annotations
import copy
from pathlib import Path
from typing import Any, Literal, cast, get_args
import cv2
import numpy as np
import pandas as pd
import torch
from omegaconf import DictConfig, ListConfig, Omeg... |
4b804b228deee5bceb30f80dfdf62e6c47bd41fa666a4bc6f01b86b730778f6a | Python | 40,782 | 923 | import argparse
import json
import logging
import os
import platform
import re
import sh
from sh import git
import signal
import subprocess
import sys
import time
import traceback
from datetime import datetime
import coloredlogs
import redis
import yaml
from redis import Redis
from .exceptions import (GraphError, Nod... |
6e5741b18a227c142080918d2eb1cdec5d49969f682cab621fe5727c645cfd56 | Python | 40,821 | 1,119 | """Test of Quick View set functionalities"""
import pathlib
import shutil
import dclab
import h5py
import numpy as np
import pytest
from PyQt6 import QtCore, QtWidgets
from shapeout2 import session
from shapeout2.gui.main import ShapeOut2
datapath = pathlib.Path(__file__).parent / "data"
@pytest.fixture(autouse=Tr... |
9bddf0228c43a43757d3049edaff08bea1ad677a7c2193d77f68acc6ae83e2fb | Python | 40,857 | 942 | """
.. module:: main
:platform: Linux, Windows
:synopsis: GUI for interactive volume segmentation
.. moduleauthor:: Fredrik Nysjo
"""
import cmd_manager
import cmd_volume
import gfx_mpr
import gfx_manager
import gfx_shaders
import gfx_utils
import image_dicom
import image_manager
import image_nifti
import image... |
84867c385d3ea273709c162f103e284602bfce34a2a7f6a98b6dec9b216d12d3 | Python | 40,924 | 986 | # Copyright 2018-2023 Xanadu Quantum Technologies Inc.
# 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... |
2e6e6320b2ca97e6d4cb4cc1fb6fd2f2c0bd16f4f376c7798a873fa5d8659820 | Python | 40,956 | 1,070 | # Copyright 2026 Xanadu Quantum Technologies Inc.
# 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 agre... |
6ffc25adfc71a9034731f009582661fe83228c79b1fef948c1f717b1154f8529 | Python | 40,972 | 732 | # Copyright (c) 2018-2023, NVIDIA Corporation
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
# list of condit... |
93f51b72aadc1c1ce1c7e514fb7fb29f564418dc56b23ab4aa0fc574d229f108 | Python | 40,989 | 1,172 | # Copyright 2018-2023 Xanadu Quantum Technologies Inc.
# 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... |
1889e73c61cbfea06ea787fda7df2427f92bf3bcded21b18fdedd8724306e243 | Python | 40,998 | 887 | import os
import time
import numpy as np
from datetime import datetime
import torch
import torch.nn as nn
from torch import optim
from torch.utils.tensorboard import SummaryWriter
from rl_games.algos_torch import model_builder, torch_ext
from rl_games.common import vecenv, schedulers, experience
from rl_games.common.... |
f668f52bdea2c4f578af5b0748cb56bd489b534b56f2fa38fae1b8ea2b03bfc7 | Python | 41,011 | 1,012 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Pattern exploration and detection
Explore and detect patterns (loops, borders, centromeres, etc.) in Hi-C contact
maps with pattern matching.
Usage:
chromosight detect [--kernel-config=FILE] [--pattern=loops]
[--pearson=auto] [--win-size=a... |
ba5ed9578f7f17733070776ba7061c0424d1cf8b6040c70063318090e0e89d4b | Python | 41,019 | 1,042 | import numpy as np
import pytest
from pandas.errors import Pandas4Warning
import pandas as pd
import pandas._testing as tm
from pandas.core.arrays.sparse import SparseArray
class TestReductions:
@pytest.mark.parametrize(
"data,pos,neg",
[
([True, True, True], True, False),
... |
c96a1b7bd7d0442bb1aec777974084dd7ef882423c90e473fdb2dfaa7f724ea4 | Python | 41,032 | 1,243 | # -*- coding: utf-8 -*-
'''icsd testing suite'''
import os
import numpy as np
import numpy.testing as nt
import quantities as pq
import scipy.integrate as si
from scipy.interpolate import interp1d
import icsd
import unittest
#patch quantities with the SI unit Siemens if it does not exist
for symbol, prefix, definitio... |
328cfb2312e584307ea6bd0505d908c079bcd6f03ccc7cc6f4aea80dca14c872 | Python | 41,035 | 749 | from __future__ import print_function
import argparse
import HTSeq
import os
import pyfaidx
import regex
from statsmodels.distributions.empirical_distribution import ECDF
import sys
import numpy as np
""" Tabulate merged start positions.
Identify genomic coordinates for reads mapping across 151/152 bp position.
... |
21fff92cc3f8791000c3d69116d4e927415af9682070da0f4d18a4de8910311d | Python | 41,106 | 1,034 | # Copyright 2018-2021 Xanadu Quantum Technologies Inc.
# 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... |
2ab892f9ea2c8b2d9a788657058ce5ec56f8aecb6328735a972efcb3a219da72 | Python | 41,124 | 1,205 | from __future__ import annotations
import datetime
from functools import partial
from typing import (
TYPE_CHECKING,
cast,
)
import numpy as np
from pandas._libs.tslibs import Timedelta
import pandas._libs.window.aggregations as window_aggregations
from pandas.util._decorators import set_module
from pandas.... |
8ce6c487717c6b5b4a51ac66c9ca7d61feff9380759006fb89d0596fb41992f2 | Python | 41,165 | 1,089 | import scipy.io
import pandas as pd
import numpy as np
import h5py
import sys
import os
import math
import pickle
from tensorflow import keras
from keras.models import Sequential
from keras import layers, optimizers
from keras.initializers import GlorotUniform, Orthogonal
from xgboost import XGBClassifier
from imblearn... |
fce816a16cb3f12e6547085db9ce47a01636a1baa668becae4419c97cc142f4b | Python | 41,220 | 1,231 | # -*- coding: utf-8 -*-
"""
Script for evaluation of ODE-based forecasting. Specifically, Fig. S7, S8 are
plotted here.
Created on Fri Apr 28 16:50:03 2023
@author: jeanbaptiste
"""
import time
import json
import pickle
import copy
from scipy.integrate import solve_ivp
from scipy.linalg import inv
import numpy as np... |
ea31ca8fb43dc465ca6f9bb4e28d34e8598cd547a3a54359656e7df36f03ad1f | Python | 41,259 | 894 | """
Original Author Ernesto P. Adorio, Ph.D
Original Source: http://my-other-life-as-programmer.blogspot.com/2012/02/python-finding-nearest-matching-color.html
Modifed By: JDiscar
This class maps an RGB value to the nearest color name it can find. Code is modified to include
ImageMagick names and WebColor names. ... |
dacd26d6b060ca16a89c6dda66d292936c8cd0d8f6012fa7d557a264aecca29b | Python | 41,306 | 1,111 | # Copyright 2022 Xanadu Quantum Technologies Inc.
# 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 agre... |
017552a2aac4f2d37595509bac460f7c452e03d648da4745eac6eb98e1ba8e1e | Python | 41,345 | 1,118 | # Copyright 2018-2021 Xanadu Quantum Technologies Inc.
# 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... |
9217264cd5d5bb7e57184feaa2e408498728f8d89f8ee5676f796c166f5f677e | Python | 41,369 | 1,290 | ##General imports
import csv
import os
import time
from datetime import datetime
import shutil
import copy
import numpy as np
from functools import partial
import platform
##Torch imports
import torch.nn.functional as F
import torch
from torch_geometric.data import DataLoader, Dataset
from torch_geometric.nn import Da... |
d12b378067e9c7643683eb005f73c60b85db7c27556293f5a0334adc4b571645 | Python | 41,395 | 1,173 | # Copyright 2022 Xanadu Quantum Technologies Inc.
# 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 agre... |
6f4c953a18e407135289f0a0bae97ee7e0f92c1a40d5db8d022b017da5d6b15b | Python | 41,418 | 1,144 | from collections import (
abc,
deque,
)
from collections.abc import Iterator
from datetime import datetime
from decimal import Decimal
import itertools
import numpy as np
import pytest
from pandas.errors import (
InvalidIndexError,
Pandas4Warning,
)
import pandas as pd
import pandas._testing as tm
fr... |
f63b9ea5319a7bc26173096784d499734472947ff3df7954ac714aa74ae690e8 | Python | 41,449 | 1,189 | from datetime import datetime
import numpy as np
import pytest
import pandas.util._test_decorators as td
import pandas as pd
import pandas._testing as tm
def get_test_data(ngroups=8, n=50):
unique_groups = list(range(ngroups))
arr = np.asarray(np.tile(unique_groups, n // ngroups))
if len(arr) < n:
... |
2497cd4aaf8ac548843d6851675fbe235458edc12a425fe46704bd68671c841b | Python | 41,456 | 1,121 | # Copyright 2023 Xanadu Quantum Technologies Inc.
# 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 agre... |
8ce679872c8a152a726dd42538a1b50247200510e0261fec341d38600c66db6b | Python | 41,522 | 1,293 | ##General imports
import csv
import os
import time
from datetime import datetime
import shutil
import copy
import numpy as np
from functools import partial
import platform
##Torch imports
import torch.nn.functional as F
import torch
from torch_geometric.data import DataLoader, Dataset
from torch_geometric.nn import Da... |
557838eeeda166ca9ec2acdddf69a6bb296a79eef2d5c33591f7675f1c176429 | Python | 41,647 | 1,255 | from datetime import (
datetime,
timedelta,
)
from io import StringIO
import re
import sys
from textwrap import dedent
import numpy as np
import pytest
from pandas._config import using_string_dtype
from pandas.errors import Pandas4Warning
import pandas as pd
import pandas._testing as tm
def _three_digit_e... |
0b6d2c784caec9389a66dd7bbf172ec5b931f5c96b848eba2b6215d7efe8eb89 | Python | 41,698 | 921 | # Copyright 2026 Xanadu Quantum Technologies Inc.
# 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 agre... |
f093d5554dbfbd307377e96189febb72608852a01a3072ea521f0a251083886c | Python | 41,702 | 1,049 | # Copyright 2021 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... |
ab13e6d355855f1f5374ef1f6abbfb8cda2d772ec647162f538289501a428493 | Python | 41,706 | 1,241 | import contextlib
import datetime as dt
import hashlib
import re
import tempfile
import time
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.api.types import (
CategoricalDtype,
)
from pandas.util.version import Version
from pandas.io.pytables import (
HDFStore,
... |
6e73a32c7052db2944c022adacb2eb1044ef2384a2bb23a6e4f53fef4e18ac72 | Python | 41,741 | 1,130 | # cython: language_level=3
# Time-stamp: <2024-10-15 10:20:32 Tao Liu>
"""Module Description: Build shifting model
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD License (see the file LICENSE included with
the distribution).
"""
# ------------------------------------
#... |
3a8eef2eb278a6d9a6417c5cfdb3287a3a361866893fd2d910602a9ac7100901 | Python | 41,790 | 1,166 | import csv
from datetime import (
UTC,
datetime,
)
import io
import os
import sys
from zipfile import ZipFile
import numpy as np
import pytest
from pandas.compat import is_platform_windows
import pandas.util._test_decorators as td
import pandas as pd
import pandas._testing as tm
from pandas.core.arrays impor... |
2b7f46b00a6cd4672e6083cfb13d06c106785f4c01cffb7c52a2e7acee1fa2ef | Python | 41,875 | 956 | # Copyright 2025 Xanadu Quantum Technologies Inc.
# 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 agre... |
5228d820ad9ef073890dffa3477d5f288c5f560290fadc0635c2e7a418512744 | Python | 41,927 | 1,115 | # Copyright 2018-2025 Xanadu Quantum Technologies Inc.
# 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... |
fae695c3e3706db294f90716ca2c95ba82694fff07f706a94a92a3560e1eafc5 | Python | 41,987 | 1,066 | from __future__ import absolute_import
import numpy as np
import pandas as pd
## Adding conditional import for compatibility between
## sklearn versions
## The second commented line corresponds to a more recent version
#from sklearn.preprocessing import Imputer
#from sklearn.impute import SimpleImputer
try:
from ... |
a2fc69ffdc83d555f1957d7673558028d20f05378a8df927cc891a6c53653805 | Python | 42,025 | 1,112 | # Copyright 2022 Xanadu Quantum Technologies Inc.
# 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 agre... |
c79530cd86805f5ce953d1c52992a4b1dd8a7be62f095afc782910637cba4346 | Python | 42,134 | 1,260 | import contextlib
import datetime as dt
import hashlib
import re
import tempfile
import time
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.api.types import (
CategoricalDtype,
)
from pandas.util.version import Version
from pandas.io.pytables import (
HDFStore,
... |
74762fc80e65263871786a55ce1a70fb42983d5d17dfbbffb5f7ad1cdac01dfb | Python | 42,183 | 1,145 | #!/usr/bin/env python
"""Module Description: Test the option validators in
MACS3/Utilities/OptValidator.py.
Options are built with the real ``bin/macs3`` argument parser and then
passed to the validator, as ``bin/macs3`` does. Where a branch can only
be reached with a value that argparse rejects (a format outside the... |
998cbc7f3b5ed0c90a537a8736cbec67083ed76be3b6b23799239d76e70cba0a | Python | 42,257 | 1,199 | #!/usr/bin/env python
""" Translator Class and builder """
import codecs
import os
import time
import re
import numpy as np
from itertools import count, zip_longest
import torch
from onmt.constants import DefaultTokens
import onmt.model_builder
import onmt.inputters as inputters
import onmt.decoders.ensemble
from onm... |
a7967422f0b77768874f14d308687450086d19c6bff9779f2fb06bb483fbf889 | Python | 42,276 | 1,088 | # Copyright 2018-2024 Xanadu Quantum Technologies Inc.
# 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... |
ffc5d79015fe80ef556f21d103d4a55ae0c19bae46d7175929f5762332c23e11 | Python | 42,314 | 1,061 | # Copyright 2018-2024 Xanadu Quantum Technologies Inc.
# 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... |
c2325f187b205f02c82af94be5f1a00f90fc0d8ad5f062821b868978dbc27e51 | Python | 42,324 | 1,219 | """
:mod:``pandas.io.xml`` is a module for reading XML.
"""
from __future__ import annotations
from functools import partial
import io
from os import PathLike
from typing import (
TYPE_CHECKING,
Any,
)
from pandas._libs import lib
from pandas.compat._optional import import_optional_dependency
from pandas.err... |
33f82d7aa1dbb7bf8d70cf9007c61a0800960e7bc11d97eecfdbde6d0c9ba35c | Python | 42,327 | 1,244 | from __future__ import annotations
import contextlib
import datetime as pydt
from datetime import (
datetime,
tzinfo,
)
import functools
from itertools import chain
from typing import (
TYPE_CHECKING,
Any,
cast,
)
import matplotlib as mpl
import matplotlib.dates as mdates
import matplotlib.units a... |
b2d4f6c975cd58126cfa8849fa1c61ef3531e135e8b60c40c380d6f9a2d75503 | Python | 42,329 | 952 | '''
Created on Mar 8, 2012
@author: regger, abast
abast:
february 2019: deprecated scaleFunc keyword, added support to specify cell_modify_functions
within the parameters
'''
import warnings
from neuron import h
import numpy as np
import math
from . import reader
from .cell import PySection, Cell
from . import cel... |
50e9fc4306f1be1abd1708da171a217c48e50e7f37c1a4cd59d4afcd2097a550 | Python | 42,342 | 1,413 | # -*- coding: utf-8 -*-
"""
Created on Mon Sep 13 16:06:38 2021
@author: jeanbaptiste
"""
import time
import warnings
from typing import cast, Tuple, List, Optional, Union, Any, Dict
import copy
import numpy as np
import matplotlib.pyplot as plt
from .. import config as cfg
from .processors import AbstractControlle... |
29099dc152dc1f760941e946fa729b325088e226fd7b3037b1d46f905f66495c | Python | 42,350 | 1,583 | # Author: Leland McInnes <leland.mcinnes@gmail.com>
#
# License: BSD 3 clause
import numba
import numpy as np
import scipy.stats
from sklearn.metrics import pairwise_distances
_mock_identity = np.eye(2, dtype=np.float64)
_mock_cost = 1.0 - _mock_identity
_mock_ones = np.ones(2, dtype=np.float64)
@numba.njit()
def si... |
6efbb77fff65b26e15f2dae0819e0550a5d6248d3a4c72cc89cfdfb8b0420f7a | Python | 42,458 | 904 | #! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this wo... |
a82cd0237c037e0d88104beada748a8c9351d3c5a90293403fd39c7015a65b84 | Python | 42,475 | 1,138 | # coding: utf-8
"""This module implements all the read modifications that atropos supports.
A modifier must be callable. It is implemented as a function if no parameters
need to be stored, and as a class with a __call__ method if there are parameters
(or statistics).
"""
from collections import OrderedDict
import copy
... |
a0c2a013d51fab10c39ae0305b4cadd07de649bac50fd7084bd42c5b6d80c397 | Python | 42,508 | 998 | # Copyright 2026 Xanadu Quantum Technologies Inc.
# 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 agre... |
4988b1383724e849ee320b1fe719165554128a82b99143ddb77d69b3dfa94227 | Python | 42,510 | 1,175 | """File that contains PES object data generated via functions in vibrant."""
# pylint: skip-file
import numpy as np
# Reference copied from vibrant HDF5 files
# mol = H2S
# coords =[[0.0, -1.0, -1.0], [0.0, 1.0, -1.0], [0.0, 0.0, 0.0]]
# localize = True
taylor_1D = np.array(
[
[1.01030577e-05, -4.474054... |
9688024d8243b3539ac921f48a08c80e4b532070af294f1adbaf04e539578c9f | Python | 42,524 | 1,225 | """
:mod:``pandas.io.xml`` is a module for reading XML.
"""
from __future__ import annotations
from functools import partial
import io
from os import PathLike
from typing import (
TYPE_CHECKING,
Any,
)
from pandas._libs import lib
from pandas.compat._optional import import_optional_dependency
from pandas.err... |
f204ed799abbcc04776e690699531df66102925c76e74f7e138020801c1ab47f | Python | 42,578 | 1,130 | #
# pandas documentation build configuration file, created by
#
# This file is execfile()d with the current directory set to its containing
# dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# se... |
7a02feb48b39c22071f47a93e8d361ec085bd59b8cc551b8751ef1d7d3a0f55f | Python | 42,618 | 932 | # -*- coding: utf-8 -*-
# Authors: Gianvittorio Luria <luria@dima.unige.it>
# Sara Sommariva <sommariva@dima.unige.it>
# Alberto Sorrentino <sorrentino@dima.unige.it>
#
# License: BSD (3-clause)
import os
os.environ['SCIPY_ARRAY_API'] = '1'
import itertools
import time
import copy
import numpy as np... |
6422cfc7892cb5d076194354b05fe91fe40a49cee28548e62c4e211f32cfa050 | Python | 42,716 | 1,253 | """
Class to store parameters of undirected graphical model of
sequences and perform calculations using the model
(statistical energies, coupling scores).
Authors:
Thomas A. Hopf
"""
from collections.abc import Iterable
from copy import deepcopy
from numba import jit
import numpy as np
import pandas as pd
# Consta... |
89c8ccc1f2bfff4afbafc3748b0aaaccf868dd4eab343659c9fd6733c7ad4e55 | Python | 42,718 | 1,033 | #SphericalCoordCalculation.py
# interface module for accessing pdb files
#
import imp
import os
import Bio.PDB as pdb
import Bio.PDB.mmtf
import numpy as np
import protein_holography.coordinates.COA_ref_frame as COA
from protein_holography.coordinates.geo import cartesian_to_spherical
import protein_holography.holog... |
165a91b521386457a62c760cf2b585f9c5ecfbe197b29ab64546383f173921b6 | Python | 42,784 | 1,247 | """
Tests date parsing functionality for all of the
parsers defined in parsers.py
"""
from datetime import (
datetime,
timedelta,
timezone,
)
from io import (
BytesIO,
StringIO,
)
import numpy as np
import pytest
from pandas._config import using_string_dtype
from pandas._libs import lib
from pan... |
ff1136ef48cb97397ebe7a8d6b7052ed51e162ce801fdccd792d239076bbb06f | Python | 42,821 | 930 | """Topic modeling with generalized correspondence latent Dirichlet allocation."""
import logging
import os.path as op
import nibabel as nib
import numpy as np
import pandas as pd
from nilearn._utils import load_niimg
from scipy.stats import multivariate_normal
from nimare import references
from nimare.base import NiM... |
e4a919b99531152c01e9847a1b48462203c978b30a794928932742234123e4c1 | Python | 42,824 | 1,054 | #!/usr/bin/env python
"""Module Description: Test MACS3.Commands.callvar_cmd and the
``macs3 callvar`` command: check_names, run, call_variants_at_range,
every command-line option and the option validation.
Inputs are small sorted and indexed BAM files written with pysam whose
reads carry MD tags computed against a d... |
841ad35e57d1701b01e67a6e68ad8a6c0211af3fd9a7f9d8708a93f39ef20d19 | Python | 42,829 | 1,139 | # Copyright 2022 Xanadu Quantum Technologies Inc.
# 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 agre... |
175ef1a32c477a919bb7095fe9605865fe61981f8526ad564703975eccd5e6ef | Python | 42,858 | 996 | import warnings
warnings.simplefilter(action='ignore', category=FutureWarning)
import altair as alt
import numpy as np
import pandas as pd
import os.path as op
import os
from math import ceil, floor
from pymatch.Matcher import Matcher
from tqdm import tqdm
import scipy.stats as st
from scipy.optimize import linear_su... |
ed79311f689ab2f4e0719d8f0da1f4d2da910038f91157c267694359d45ba1e5 | Python | 42,871 | 1,245 | from datetime import datetime
import numpy as np
import pytest
import pandas.util._test_decorators as td
from pandas.core.dtypes.common import is_scalar
import pandas as pd
import pandas._testing as tm
@pytest.fixture(params=["default", "float_string", "mixed_float", "mixed_int"])
def where_frame(request, float_s... |
4b8c5892b29b0614870cca86937b7ee09714b9671df7052e4ce638abda5fc618 | Python | 42,907 | 1,159 | from __future__ import annotations
import itertools
from typing import (
TYPE_CHECKING,
cast,
overload,
)
import warnings
import numpy as np
from pandas._config.config import _global_config as config
from pandas._libs import lib
import pandas._libs.reshape as libreshape
from pandas.errors import (
P... |
bd90a611eeea24c56f8daa5d6c40150cffc43954ed6dee610ff6f19dbf8c6fc2 | Python | 42,915 | 1,235 | """
This file contains code for some utility functions, such as code for saving CSV logs.
vivian added codes for loading datasets
Code credits to Xifeng Guo: `https://github.com/XifengGuo/CapsNet-Keras`
"""
import numpy as np
from matplotlib import pyplot as plt
import csv
import math
import numpy as np
from tensorf... |
062b4de6b7f9eb7897ec41ad7518e3c95b86dab590dd3413f62100d8a92ac264 | Python | 42,933 | 1,230 | from collections import deque
from datetime import (
UTC,
date,
timedelta,
)
from decimal import Decimal
from enum import (
Enum,
auto,
)
import operator
import numpy as np
import pytest
from pandas._libs import lib
from pandas.errors import Pandas4Warning
import pandas as pd
import pandas._testi... |
781351164af790bc29c916b634f4d184806650370391761a1bc3774b5ab7bd66 | Python | 42,943 | 1,158 | from __future__ import annotations
import itertools
from typing import (
TYPE_CHECKING,
cast,
overload,
)
import warnings
import numpy as np
from pandas._config.config import _global_config as config
from pandas._libs import lib
import pandas._libs.reshape as libreshape
from pandas.errors import (
P... |
41595fba101a9adfd716755de36302981c17ab7bce9ea6d1f4ce5cf6eb6e5437 | Python | 42,969 | 969 | #!/usr/bin/env python
"""Module Description: Test functions of the pileup subcommand
(MACS3/Commands/pileup_cmd.py), called directly and through
``macs3 pileup``.
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD License (see the file LICENSE included with
the distribution... |
62cc753f57c8fd38d37e722c54dac2e5fa2364a8ca591f1320856e59769e75de | Python | 42,993 | 1,224 | # Copyright 2025 Xanadu Quantum Technologies Inc.
# 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 agre... |
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