sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
4ac3e4fd07016bfb4bd777ddda92ac110f55c1eae92b6fe4a1e2b077c10b6319 | Python | 21,822 | 583 | """
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 ... |
fd1b93a3c8c35c9ba27d256d48ee028be2d19e5b2b23a7f7549affb79c9e5f75 | Python | 21,822 | 525 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.core.arrays.sparse import SparseArray
@pytest.fixture
def arr_data():
return np.array([np.nan, np.nan, 1, 2, 3, np.nan, 4, 5, np.nan, 6])
@pytest.fixture
def arr(arr_data):
return SparseArray(arr_data)
class Tes... |
29023143f4cc9ecc6e447601ad2b6ef420bdc53c04e3c420284fce9583de5809 | Python | 21,823 | 600 | from __future__ import annotations
from datetime import (
datetime,
time,
timedelta,
)
from decimal import Decimal
import re
import numpy as np
import pytest
from pandas.compat import (
pa_version_under18p0,
pa_version_under19p0,
)
from pandas.core.dtypes.dtypes import (
ArrowDtype,
)
impor... |
a95e46c5d5b5b6b8e52fc06af08eadf960925cac2a68c9f850dd5d5a21db4472 | Python | 21,844 | 844 | """Utility functions for the SAM algorithm.
This module provides helper functions for PCA, nearest neighbor computation,
gene correlation analysis, and other common operations.
"""
from __future__ import annotations
import errno
import os
from typing import TYPE_CHECKING, Any
import numpy as np
import scipy as sp
i... |
a0e2d8ca53fe16b7dc007c8cf462457c525acb37540a23b8687c6c01696b8441 | Python | 21,846 | 514 | """Test dali dataloading functionality."""
import os
import shutil
from unittest.mock import MagicMock, patch
import numpy as np
import pandas as pd
import pytest
import torch
pytest.importorskip('nvidia.dali', reason='nvidia-dali not installed')
from lightning_pose.data.video import dali as dali_module
from lightn... |
ab8c19f56ef1bf7748a55d64ca4fb33dc33c9a046fed1d8d170928323016ab7a | Python | 21,858 | 612 | # 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... |
f97426283c7df496d33e38c4e0ba83917158a2f46fd1c56353b45cb1760b1252 | Python | 21,874 | 641 | #!/usr/bin/env python3
#
# Copyright 2016 Google Inc. 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 requir... |
5ba5cb2db29dc19164cec5c3b8c18546ca622a7350956466bb9b15e43e1836c3 | Python | 21,880 | 642 | import numpy as np
import pytest
from pandas.compat import is_platform_arm
from pandas.errors import NumbaUtilError
import pandas.util._test_decorators as td
import pandas as pd
import pandas._testing as tm
from pandas.api.indexers import BaseIndexer
from pandas.util.version import Version
pytestmark = [pytest.mark.... |
d28cd4c834c49bc64128f1b4d6cff9f89fff4d00d2036e5b65591e9a3aaab9d0 | Python | 21,880 | 665 | from __future__ import annotations
from functools import wraps
from typing import (
TYPE_CHECKING,
Any,
Literal,
Self,
cast,
overload,
)
import numpy as np
from pandas._libs import lib
from pandas._libs.arrays import NDArrayBacked
from pandas._libs.tslibs import is_supported_dtype
from pandas... |
5f6674573ba4c0a0ec800efc0a0405c1da3cd66be228e9994fb79453af152503 | Python | 21,883 | 701 | from textwrap import dedent
import numpy as np
import pytest
from pandas.compat import is_platform_windows
from pandas.errors import Pandas4Warning
import pandas as pd
import pandas._testing as tm
from pandas.core.indexes.datetimes import date_range
@pytest.fixture
def test_frame():
return pd.DataFrame(
... |
d26ac7c14676fd2b0c8c79450b9ec3befdd1119b07c466f96b1829fcbfef4385 | Python | 21,891 | 572 | #! /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... |
345c3c23524838b606dd67f8b7f30fbb805ba39067f857b87ec850c97b262d47 | Python | 21,929 | 737 | """
missing types & inference
"""
from __future__ import annotations
from decimal import Decimal
from typing import (
TYPE_CHECKING,
TypeVar,
cast,
overload,
)
import warnings
import numpy as np
from pandas._libs import lib
import pandas._libs.missing as libmissing
from pandas._libs.tslibs import (
... |
47c1b4584a8dee172c79f35a5051f566977225225837451bead4aae47c4b99e2 | Python | 21,931 | 526 | from __future__ import print_function
from pymatch import *
import pymatch.functions as uf
class Matcher:
"""
Matcher Class -- Match data for an observational study.
Parameters
----------
test : pd.DataFrame
Data representing the test group
control : (pd.DataFrame)
Data represe... |
f25e4c8ffd7f8270349c01bb697f5ed0f1335f7509669c3c448d6ff4f8843523 | Python | 21,944 | 526 | from __future__ import print_function
from pymatch import *
import pymatch.functions as uf
class Matcher:
"""
Matcher Class -- Match data for an observational study.
Parameters
----------
test : pd.DataFrame
Data representing the test group
control : (pd.DataFrame)
Data represe... |
3fae6a3e2c4c359f07fc6e299533460d0cd53ffd20ee6949f779856850445cb4 | Python | 21,946 | 594 | # Copyright 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 agre... |
6dae8a27b0e5b0eb69a8e592d0795b7be061cb63a3d730b070f959277f2cc26c | Python | 21,956 | 533 | # -------------------------------------------------------------------------------------------------------------------------------------
# Following code curated for GCPNet (https://github.com/BioinfoMachineLearning/GCPNet):
# ----------------------------------------------------------------------------------------------... |
99dd6405f419a01543210073ed364bd6eebd8eafe99652ce12ec519ae8224e41 | Python | 21,964 | 553 | # 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 agree... |
a52f5f6e71932b22ae735457dff3aea2c9338d66b3d5c0b8b1bb6197679c7737 | Python | 21,968 | 726 | from datetime import (
datetime,
timedelta,
)
import numpy as np
import pytest
from pandas._libs.tslibs.ccalendar import (
DAYS,
MONTHS,
)
from pandas._libs.tslibs.offsets import _get_offset
from pandas._libs.tslibs.period import INVALID_FREQ_ERR_MSG
from pandas.compat import is_platform_windows
from ... |
e5af6cc5a671d1c3db3fd6eca0d8de84ba8f0c216bb8fcd7e1c55cfb43458b26 | Python | 21,968 | 738 | """
missing types & inference
"""
from __future__ import annotations
from decimal import Decimal
from typing import (
TYPE_CHECKING,
Any,
TypeVar,
cast,
overload,
)
import warnings
import numpy as np
from pandas._libs import lib
import pandas._libs.missing as libmissing
from pandas._libs.tslibs ... |
03bb05d0f6d5000000bb8a27c8255415cd6a22f81eb0297ce39c0fbd74e39711 | Python | 22,006 | 637 | #!/usr/bin/env python
# Time-stamp: <2025-09-29 15:10:49 Tao Liu>
import io
import unittest
import pytest
from MACS3.IO.PeakIO import PeakIO
from MACS3.Signal.Region import Regions
class Test_Regions(unittest.TestCase):
def setUp(self):
self.test_regions1 = [(b"chrY", 0, 100),
... |
d1fa99e39663de2109dad09a9cf61567db9232e3c32eb42c275b82f2788e93e3 | Python | 22,026 | 621 | from itertools import chain
import operator
import numpy as np
import pytest
from pandas._libs.algos import (
Infinity,
NegInfinity,
)
import pandas.util._test_decorators as td
import pandas as pd
import pandas._testing as tm
from pandas.api.types import CategoricalDtype
@pytest.fixture
def ser():
retu... |
f12df4fcc5e3898b434fc6318fc2223b04274f6918721e075bfa81b18adf40f1 | Python | 22,063 | 611 | ''' copy_ppp_imagery.py
Rename and copy PPP PNGs
'''
import argparse
from glob import glob
from datetime import datetime, timezone
from io import BytesIO
import json
import os
from pathlib import Path
import re
import shutil
import sys
import colorlog
import boto3
from botocore.exceptions import ClientError
import... |
335038fa17aa43ed0315aaa6e4dc261b3581342dc2a662dd885bb00c1a085271 | Python | 22,102 | 456 | """Test the data factory module."""
import copy
import os
from unittest.mock import Mock
import numpy as np
import pytest
from omegaconf import OmegaConf
from omegaconf.errors import ValidationError
from PIL import Image
from lightning_pose.data import (
get_data_module,
get_dataset,
get_imgaug_transform... |
4ba59bc11b47e33c20809a3236426148d3878cf4de7fe6bf1fda8b42a2292598 | Python | 22,112 | 476 | """
These codes are from https://github.com/tctianchi/pyvenn/blob/master/venn.py
"""
# coding: utf-8
from itertools import chain
try:
# since python 3.10
from collections.abc import Iterable
except ImportError:
from collections import Iterable
import matplotlib.pyplot as plt
import matplotlib.patches as p... |
1b31f4e6e30ae4a385d2b18115d1884cda80169ec29b956b9371b2493bc74b64 | Python | 22,120 | 479 | import torch
import torch.nn as nn
import torch.nn.functional as F
from kornia.utils import create_meshgrid
from kornia.geometry.transform import warp_affine
from kornia.geometry.linalg import transform_points
import kornia
from typing import Tuple, Union
import ipdb
class TPS:
"""Most of the code for the Thin Pl... |
a8bd9bbc935dc5fcb1b31100c8c7cfb792c5fdf9d1c6749d26951d5f302d98e0 | Python | 22,121 | 573 | # 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... |
65218620dbda6432ac9f7daa394349398241f149b13252ceaf36c06cb5923a2b | Python | 22,122 | 696 | import os
import sys
import get_pdbinfo as pdbinfo
import chimera
from chimera import runCommand as rc
import fileinput
import copy
##### Part1 transfer Hg to Flag or Flag to Hg
def Hg2toFlag(filename):
"""
change Hg2+ ion atom name to be FLAG
"""
f = open("tmp","w")
for lines in fileinput.input(file... |
23b7466e9a71bbe98f426037e071c85e57b0039d200a22373c1ef8a9073e3866 | Python | 22,125 | 643 | import os
from datetime import datetime
import numpy as np
import pandas as pd
import torch
from scipy.special import softmax
from sklearn.metrics import (
accuracy_score,
precision_recall_fscore_support,
r2_score,
roc_auc_score,
)
from torch.nn import CrossEntropyLoss, L1Loss, MSELoss, NLLLoss
from to... |
4420a973269b764fe6b0fc8ad3a5386baf71af9c20f4ea1f2245326aca052bf0 | Python | 22,127 | 557 | # 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... |
662b7740d5ac0dd5279464a14c4ccbec6c9ce83759583942bcb2011f6447a148 | Python | 22,128 | 526 | """Tests for ModelConfig.validate() and its sub-validation methods."""
from pathlib import Path
from unittest.mock import patch
import pytest
from omegaconf import OmegaConf
from lightning_pose.api.model_config import ModelConfig
# ---------------------------------------------------------------------------
# Helper... |
1351a94e11be0f7a189cea652476b45c97bf177139c16a3d25cdc8bc8518d7d9 | Python | 22,136 | 481 | import torch
import torch.nn as nn
import torch.nn.functional as F
from losses.modules import *
from losses.homography import *
class UnSupLoss(nn.Module):
def __init__(self):
super(UnSupLoss, self).__init__()
self.ssim = SSIM()
def forward(self, imgs, cams, depth, stage_idx):
# prin... |
4c2ba9bf88b9a7e36b5019745380eeb1f3d6c8fe3eb11e976bd85df3f9a9abf2 | Python | 22,137 | 574 | # Copyright 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 agre... |
59893dd779ff89a279c22014e129fce056460dfb804139abd9a7feab681943b4 | Python | 22,143 | 570 | import enum
from statistics import mean
import pytest
from pgen import models, esm_msa_sampler
from pgen import likelihood_esm_msa
from io import StringIO
from pgen.esm_msa_sampler import ESM_MSA_ALLOWED_AMINO_ACIDS
import tempfile
import pandas as pd
import torch
####### Fixtures #######
@pytest.fixture(scope="sessi... |
bb7d694eccece3bef50ee69c5dcd669454a9d1f13281449cd7ae5df97b78aed5 | Python | 22,161 | 712 | # -*- coding: utf-8 -*-
"""mtscomp tests."""
#------------------------------------------------------------------------------
# Imports
#------------------------------------------------------------------------------
from contextlib import redirect_stdout
import io
from itertools import product
import json
import has... |
29e634cb52f5c12497dca47ac278a827ce8dea9d7dda3f54b54862e87fe5c497 | Python | 22,237 | 573 | """Base classes for NiMARE."""
import gzip
import inspect
import logging
import multiprocessing as mp
import pickle
from abc import ABCMeta, abstractmethod
from collections import defaultdict
from hashlib import md5
import nibabel as nb
import numpy as np
from nilearn._utils.niimg_conversions import _check_same_fov
fr... |
bb6a32ab2beae30bcef24b3f84675f835aa0018b30898dfeef8692e81b7f3d79 | Python | 22,243 | 590 | from functools import partial
from itertools import pairwise
import re
import numpy as np
import pytest
import pandas.util._test_decorators as td
from pandas.core.dtypes.common import is_unsigned_integer_dtype
from pandas.core.dtypes.dtypes import IntervalDtype
import pandas as pd
import pandas._testing as tm
from ... |
30fe8d2ee9716000f5a532cc95a1e4b01a02066999a3ba20be3060c8bcc97049 | Python | 22,256 | 620 | import numpy as np
import pyqtgraph as pg
from kilosort.gui.logger import setup_logger
from kilosort.gui.palettes import COLORMAP_COLORS
from PyQt5 import QtCore, QtWidgets
logger = setup_logger(__name__)
class DataViewBox(QtWidgets.QGroupBox):
channelChanged = QtCore.pyqtSignal(int, int)
modeChanged = QtCor... |
330e9d8a193f0c05a0492e155b3acde14c916cbebf5615367843dc5321f95c0c | Python | 22,259 | 542 | # 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... |
17ce80e38a3154ad1d7db7baeb257669161cb478c0abd43f43fd5b454008d4c4 | Python | 22,264 | 656 | from typing import Dict, List, Optional, Tuple, Union
import numpy as np
import pandas as pd
import statsmodels.api as sm
from statsmodels.tools.sm_exceptions import MissingDataError as SmMissingDataError
from statsmodels.tsa.api import kpss
from statsmodels.tsa.stattools import adfuller
from pycaret.internal.logging... |
4c2f518ca8657e1b4879f452f4f29b4478629e6d11a92312a31b830769382858 | Python | 22,279 | 515 | import torch
import numpy
import matplotlib.pyplot as plt
import bionetwork
import plotting
import pandas
import time
import copy
class drugLayer(torch.nn.Module):
def __init__(self, nodeList, drugInName, drugNetwork):
super(drugLayer, self).__init__()
targetInName = numpy.unique(drugNetwork['targe... |
15a1cdb2a26b1b510dc329ee71df8107a09b4d76f6ccc6605c6d0eaa99dccd6b | Python | 22,292 | 581 | """CBMA methods from the activation likelihood estimation (ALE) family."""
import logging
import multiprocessing as mp
import numpy as np
import pandas as pd
from tqdm.auto import tqdm
from ... import references
from ...due import due
from ...stats import null_to_p, nullhist_to_p
from ...transforms import p_to_z
from... |
ea4227327dc211938cfcff09952ed0a315d0c557e4394845a6c97f886e6345b5 | Python | 22,321 | 418 | import torch
import torch.nn as nn
import torch.nn.functional as F
from .modules import *
from typing import List, Tuple, Dict, Callable, Any, Union
from collections import OrderedDict
Align_Corners_Range = False
class ListModule(nn.Module):
def __init__(self, modules: Union[List, OrderedDict]):
super(Li... |
12518d0ec30aa81fdf0078c83bb82ccfc84821aab0ea038b82f908ce4be7a714 | Python | 22,323 | 356 | import torch
from torch import nn
import torch.nn.functional as F
from torch.nn import MSELoss
def initialize_weights(m):
if isinstance(m, nn.Linear):
# nn.init.trunc_normal_(m.weight.data, std=0.1, a=-0.2, b=+0.2)
nn.init.kaiming_normal_(m.weight.data, nonlinearity='relu')
nn.init.constant... |
4b987ed3c0b2f64010207a0bb48a84399cb37c54d18f0999e94dd087a8b500e2 | Python | 22,334 | 706 | from __future__ import annotations
from typing import (
TYPE_CHECKING,
Any,
Literal,
Self,
cast,
)
import numpy as np
from pandas._libs import lib
from pandas._libs.tslibs import is_supported_dtype
from pandas.compat.numpy import function as nv
from pandas.errors import LossySetitemError
from pan... |
1b5aa752a2c84e42622462fc42f332ad939ca672cf964ce7b1f1576f70b23495 | Python | 22,354 | 504 | import pandas as pd
import numpy as np
from sklearn.model_selection import train_test_split
from scipy import stats
from Bio.PDB.PDBParser import PDBParser
from Bio import BiopythonWarning
import json
import os
import sys
import urllib.request
import pickle
import warnings
warnings.filterwarnings("ignore")
from colle... |
795a5f57e717823ffcf0ed31c7f16fb8bdd17b567224dd1f323d156cd610b6dc | Python | 22,369 | 743 | """Widely useful utility methods.
"""
from collections import OrderedDict
from collections.abc import Iterable, Sequence
from datetime import datetime
import errno
import functools
import logging
import math
from numbers import Number
import time
from atropos import AtroposError
# TODO: the nucleotide table should be ... |
8b50fe032fcfa06d3839688f00284ba5ebd82e2db70780ab7aeea0f4698a30f3 | Python | 22,386 | 601 | import warnings
from warnings import warn
import numpy as np
import scipy.linalg
import scipy.sparse
import scipy.sparse.csgraph
from sklearn.decomposition import TruncatedSVD
from sklearn.manifold import SpectralEmbedding
from sklearn.metrics import pairwise_distances
from sklearn.metrics.pairwise import _VALID_MET... |
615d4a6535eedf304bf7d82214eb984be78eb5b58e36c128ec9596781ab51b9e | Python | 22,392 | 531 | #!/usr/bin/env python
"""Module Description: Test functions of the refinepeak subcommand
(MACS3/Commands/refinepeak_cmd.py), called directly and through
``macs3 refinepeak``.
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 ... |
9c0ec754fcb161c2f88de4b110c6c322bc2d823b8780792e0c5f2ad123ea8f07 | Python | 22,406 | 686 | from __future__ import annotations
import re
from typing import (
TYPE_CHECKING,
Any,
)
import numpy as np
from pandas.util._decorators import set_module
from pandas.core.dtypes.common import (
is_iterator,
is_list_like,
)
from pandas.core.dtypes.concat import concat_compat
from pandas.core.dtypes.m... |
c1d7f730639ec398315b5367a2d1c257fa8189df1bda56a7ac13b34531008dad | Python | 22,407 | 621 | from __future__ import annotations
import functools
from typing import (
TYPE_CHECKING,
cast,
overload,
)
import warnings
import numpy as np
from pandas._libs import (
algos as libalgos,
lib,
)
from pandas.errors import Pandas4Warning
from pandas.util._exceptions import find_stack_level
from pan... |
a7c12b9fd2cd256df96c33db2a42767c2965b08d22610b3201401d2e2a182210 | Python | 22,414 | 476 | # 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... |
7ac92aec641bf0ef1170b1323f842e0f392a738c3e2721f5025ca86a399b5f80 | Python | 22,423 | 464 | import os
import glob
import json
import logging
import torch
import numpy as np
from pybullet_utils import transformations
from rsl_rl.utils import utils
from rsl_rl.datasets import pose3d
from rsl_rl.datasets import motion_util
from legged_gym.utils.torch_jit_utils import *
from legged_gym.utils.math import *
cla... |
7d13e10059bb075032d1681ceabb19599019740c254aa0e8b9a99d0ee1aaea3b | Python | 22,431 | 581 | from __future__ import absolute_import
import collections
import gzip
import logging
import os
import sys
import multiprocessing
import threading
import argparse
try:
import configparser
except ImportError:
import ConfigParser as configparser
import numpy as np
import pandas as pd
from itertools import cycle... |
4b7a613ddc1008860787d6c2d0c5266bde0f53bb4e4da5968d9bb47084c1e37e | Python | 22,449 | 617 | from typing import Tuple
import torch
from torch import nn
from torch.nn import functional as F
class EfficientSelfAtten(nn.Module):
def __init__(self, dim, head, reduction_ratio):
super().__init__()
self.head = head
self.reduction_ratio = reduction_ratio
self.scale = ... |
48268a718f24c0205df3a9f938d99e83a5446842a498f7f981973647f0725279 | Python | 22,450 | 421 | import sys
import os
import argparse
import numpy as np
import pandas as pd
import matplotlib
matplotlib.use('Agg')
from matplotlib import pyplot as plt
from cdr.config import Config
from cdr.signif import permutation_test
from cdr.util import filter_models, get_partition_list, nested, stderr, extract_cdr_prediction_d... |
e306f8f36222d0dbf92c76b1bb66b64c09abd37f63a9762f6ccccccee9dc160e | Python | 22,456 | 637 | import inspect
import os
import warnings
import pytest
import pandas._config.config as cf
from pandas._config.config import OptionError
from pandas.errors import Pandas4Warning
import pandas as pd
import pandas._testing as tm
class TestConfig:
@pytest.fixture(autouse=True)
def clean_config(self, monkeypat... |
049c5774af3ee8ee98de92f8d8a3683e5042f236190e6e8a89b3bf9552f1051a | Python | 22,468 | 413 | #!/usr/bin/env python
# -*- coding: UTF-8 -*-
#coding=utf-8
from Bio import SeqIO
import os, copy, math
import os, threading
from multiprocessing import Pool
def cat_contigs(bin_folder, pwd):
bin_length, bin_contigs_n, bin_contigs_5k, bin_avg_length, bin_n50_length, bin_contigs_position_list={}, {}, {}, {}, {}, {... |
69ad64b869059fa3b0a7e90af243535ff5c79c88adcf3ec609cfc4e27974726f | Python | 22,489 | 709 | from __future__ import annotations
from typing import (
TYPE_CHECKING,
Any,
Literal,
Self,
cast,
)
import numpy as np
from pandas._libs import lib
from pandas._libs.tslibs import is_supported_dtype
from pandas.compat.numpy import function as nv
from pandas.errors import LossySetitemError
from pan... |
66a81d6cb7ddef5c2b6133cb1d1d7bd0e692f3b490b7aa43e4fdcc0ec8dab7c4 | Python | 22,498 | 500 | #! /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... |
41038950c7c67929b876ff8bf60347f175588eb18280203500735d7f0a61c669 | Python | 22,518 | 504 | # Copyright (c) 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 conditions ... |
4d4353d36bcfbcbfaf6d3ce5d4544f94ae7e3ba606ab45f9110f1ca3a4338044 | Python | 22,528 | 539 | #!/usr/bin/env python3
"""Regression tests for us_mpi_analysis.
Each case builds an HPC job archive (synthetic data written by
us_mpi_testdata plus an hpcrequest XML in the format the LIMS writes), runs
us_mpi_analysis under mpirun and reduces the result archive to a JSON summary
of every fitted model (RMSD and solute... |
fc2896005a22cef99a3c67b4542405eea573e2759c8b6195296480dfb2be0b7a | Python | 22,548 | 769 | """
Tests that apply specifically to the Python parser. Unless specifically
stated as a Python-specific issue, the goal is to eventually move as many of
these tests out of this module as soon as the C parser can accept further
arguments when parsing.
"""
from __future__ import annotations
import csv
from io import (
... |
07ccb08a75ad362fb46cbe97e1d1693848590ffaeb1b1fd3f5753df7c7a1cc2f | Python | 22,577 | 647 | # -*- coding: utf-8 -*-
"""
Copyright I3S CNRS UCA
This code is an implementation of the statistical evaluation of the autoencoder described in the article :
Learning a confidence score and the latent space of a new Supervised Autoencoder for diagnosis and prognosis in clinical metabolomic studies.
When using this... |
82b773e6bd374e570efe38990154e839bca341d02b1e03d2a1ac57721875029e | Python | 22,593 | 769 | """
Tests that apply specifically to the Python parser. Unless specifically
stated as a Python-specific issue, the goal is to eventually move as many of
these tests out of this module as soon as the C parser can accept further
arguments when parsing.
"""
from __future__ import annotations
import csv
from io import (
... |
67e3c57407702d3a0fc214b6ad74a2783795205bc141273ddc7603b20d81bc68 | Python | 22,599 | 475 | from tensorflow.python.keras.models import model_from_json
from ImSetNorm import Normalize
from scipy.stats import sem
import tensorflow.python.keras as keras
import pandas as pd
import glob
import cv2
import numpy as np
import os
import scipy
import matplotlib.pyplot as plt
import matplotlib
class Anal... |
ebd3882f3b80653167e91de8a023042d321b28f81c5cc7df2f6622eaf84d2947 | Python | 22,615 | 593 | from datetime import datetime
import numpy as np
from pandas.errors import Pandas4Warning
from pandas.core.dtypes.dtypes import CategoricalDtype
import pandas as pd
import pandas._testing as tm
class TestCategoricalConcat:
def test_categorical_concat(self, sort):
# See GH 10177
df1 = pd.DataFr... |
2101435ad9ff2e909d6f8eff3deda6d04eacbb5160552121250d6b15aec71545 | Python | 22,621 | 690 | from __future__ import annotations
import re
from typing import (
TYPE_CHECKING,
Any,
)
import numpy as np
from pandas.util._decorators import set_module
from pandas.core.dtypes.common import (
is_iterator,
is_list_like,
)
from pandas.core.dtypes.concat import concat_compat
from pandas.core.dtypes.m... |
4424b706cb1e698886f92a4749647ee794d8be0e190127534f77bc65169df6f4 | Python | 22,639 | 561 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sat Nov 6 23:23:38 2021
This script is used primarily to retrieve useful information from PPMI for the
XLS database. Together with *imaging_file_prunning.py*, it provides all
necessary code to have PPMI ready to be uploaded to the cloud.
Another part of t... |
d847aa98b426daf9c818f5b1a16c497080341e144046bc06d0f03f8adfbc8db0 | Python | 22,642 | 613 | # 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... |
13a0dfc71af0f643166c88ff59f604bc309898220e02d65932d29fcd51e43d4e | Python | 22,651 | 528 | import os
import numpy as np
import torch
import torchvision.transforms as trn
import torchvision.transforms.functional as trn_F
import cv2
from PIL import Image as PILImage
import skimage.color as skcolor
from skimage.util import random_noise
from wand.image import Image as WandImage
from wand.api import library as wa... |
b81011ea62548c4fd904c0e9dfac65266646f6c9504aeaed01c00ca41a14ad19 | Python | 22,664 | 605 | #!/usr/bin/env python
"""Module Description: Test functions in HMMR_Signal_Processing that
split ATAC-seq fragments into short, mono-, di- and tri-nucleosomal
signals and extract binned signals for the HMMRATAC Hidden Markov
Model.
This code is free software; you can redistribute it and/or modify it
under the terms o... |
be4a866c9e981ae332f524754c43859f0a25d0eceba8e3648b0ea0112a789445 | Python | 22,676 | 590 | import re
import numpy as np
import pytest
from pandas.errors import Pandas4Warning
import pandas as pd
import pandas._testing as tm
@pytest.mark.parametrize(
"msg,labels,level",
[
(r"labels \[4\] not found in level", 4, "a"),
(r"labels \[7\] not found in level", 7, "b"),
],
)
def test_... |
80b145ec850976628bb3a0be166757ae5629c68edf1ee5a0259756c2f7cba8ea | Python | 22,685 | 674 | """Indexer objects for computing start/end window bounds for rolling operations"""
from __future__ import annotations
from datetime import timedelta
from typing import TYPE_CHECKING
import numpy as np
from pandas._libs.tslibs import BaseOffset
from pandas._libs.window.indexers import calculate_variable_window_bound... |
13aac69b463c8f0db0409801989be342fb16e83318aa03bf81cb3df52e54ca72 | Python | 22,708 | 638 | # 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... |
8ebd2efa9248f889d2967d1fca120ccdf8851d09145483b54670bc34e3dddeb7 | Python | 22,715 | 692 | import numpy as np
import pytest
from pandas.errors import Pandas4Warning
import pandas.util._test_decorators as td
from pandas.core.dtypes.missing import na_value_for_dtype
import pandas as pd
import pandas._testing as tm
from pandas.tests.groupby import get_groupby_method_args
@pytest.mark.parametrize(
"drop... |
d6c8201b295ed74249d2ab8e498e2e4a9ed3b157a7e76decbef8b030436db15f | Python | 22,722 | 593 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.core.algorithms import safe_sort
@pytest.fixture(
params=[
pd.DataFrame([[2, 4], [1, 2], [5, 2], [8, 1]], columns=[1, 0]),
pd.DataFrame([[2, 4], [1, 2], [5, 2], [8, 1]], columns=[1, 1]),
pd.DataF... |
36bfc1beff4d0ba7f9fed4e18efa36425a962e8c67374ad2ee7924d92fae2459 | Python | 22,727 | 556 | import argparse
import os
import shutil
import sys
import time
import warnings
from random import sample
import numpy as np
import torch
import torch.nn as nn
import torch.optim as optim
from sklearn import metrics
from torch.autograd import Variable
from torch.optim.lr_scheduler import MultiStepLR
from cgcnn.data im... |
c405b68aa476c2899cbe8ad7265aac2501e3b77c5fb80235ec7185f002d53f3f | Python | 22,749 | 535 | import numpy as np
import random
import gymnasium as gym
import torch
from rl_games.common.segment_tree import SumSegmentTree, MinSegmentTree
from rl_games.algos_torch.torch_ext import numpy_to_torch_dtype_dict
class ReplayBuffer(object):
"""
Replay buffer for storing and sampling transitions.
"""
def... |
70dc128aab9e41b5858d3c6e38bc80dcd9c39f34a4d63a83e975d904a55dfb50 | Python | 22,751 | 532 | import os
import numpy as np
import torch
import torchvision.transforms as trn
import torchvision.transforms.functional as trn_F
import cv2
from PIL import Image as PILImage
import skimage.color as skcolor
from skimage.util import random_noise
from wand.image import Image as WandImage
from wand.api import library as wa... |
51c20eee679980b1503f32b630ab7195fe997d5b8d8d8c9d8ee250b54c0ad639 | Python | 22,777 | 536 | import os
import sys
from subprocess import call
import shutil
import argparse
from fiber_bundle_filters import matrix_dist_filtering, Consistency,ConsistencyValsFiltering, ConvexHullFiltering,distance_matrix_Dend, distance_matrix_SSPD
import numpy as np
import read_write_bundle as bt
import time
from joblib import Par... |
d7b225fe86fba7c6bcf68913e7bc1616747eb53451f88b618999d0702b2ff6f4 | Python | 22,779 | 461 | import argparse
import os
import sys
import re
import pickle
import numpy as np
import pandas as pd
from sklearn.metrics import f1_score
pd.options.mode.chained_assignment = None
from cdr.config import Config
from cdr.io import read_tabular_data
from cdr.formula import Formula
from cdr.data import add_responses, filt... |
37b9c834cea6e0c9dc404fd630462b30b6dfc88e85c6eaed47952ec11a1a384f | Python | 22,782 | 489 | #!/usr/bin/env python3
# MIT License
#
# Copyright 2026 Broad Institute
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use... |
3b02657e320c059e366c68ae5242c65f27542820905218b1adfae5cb4c63c7d0 | Python | 22,787 | 656 | """Data-source CRUD + CSV upload route.
Mounted under ``/api/v1/workspaces/{workspace_id}/data-sources`` for listing
and creation; ``/api/v1/data-sources/{id}`` for fetch + delete. CSV uploads
land in ``${PYCARET_ARTIFACT_DIR}/data-sources/<uuid>.csv`` and the resulting
``DataSource`` row carries ``kind="csv_upload"``... |
1a85035eb1655368f243e43517107fff7f24c4bb57828eae5d4dedacd4a4ddc8 | Python | 22,793 | 637 | ######################
### Import Library ###
######################
# my library
from molgraph.utilsonehot import *
from molgraph.utilsmol import *
from molgraph.utilsgraph import *
# standard
import numpy as np
import copy as copy
from tqdm import tqdm
# rdkit
from rdkit import Chem
from rdkit.Chem import rdDepictor... |
e8a52b005be8289ab252d06aa59675ac6e77776166c6e13338a7ea38a3e39b89 | Python | 22,801 | 507 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Jan 10 10:28:02 2022
@author: wirrbel
"""
import pandas as pd
import os
import glob
import re
import tifffile
import shutil
import multiprocessing as mp
import numpy as np
import more_itertools
import subprocess
import datetime
def atlas_align(mBrain... |
69f5978f0994a02974721aeb327466d69eda23d5320ae12effbdcb2aa6c4f744 | Python | 22,854 | 604 | # 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... |
a872eacb69aa55839074b312d18054c8a8351eb1430a608b61c4e20a02050474 | Python | 22,883 | 715 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.tests.apply.common import series_transform_kernels
@pytest.fixture(params=[False, "compat"])
def by_row(request):
return request.param
def test_series_map_box_timedelta(by_row):
# GH#11349
ser = pd.Series(pd.t... |
07ffe00a7211d568ff9c94938bb619eb75200143a51a8abf1489f80f21c289d7 | Python | 22,902 | 533 | import os
import numpy as np
import torch
import torchvision.transforms as trn
import torchvision.transforms.functional as trn_F
import cv2
from PIL import Image as PILImage
import skimage.color as skcolor
from skimage.util import random_noise
from wand.image import Image as WandImage
from wand.api import library as wa... |
75cc7813ecc5b8754852466222bfb6971ebdc37c544358ae908ab139dec01050 | Python | 22,911 | 632 | import copy
import warnings
import dclab
import numpy as np
from ..idiom import SLOPING_FEATURES
from .dataslot import Dataslot
from .filter import Filter
from .filter_ray import FilterRay
from .plot import Plot
class EmptyDatasetWarning(UserWarning):
pass
class MissingFeatureWarning(UserWarning):
pass
... |
bfb93117ce5c0c919d00468f4b031affb73fa12af91647505d68e666ec49a205 | Python | 22,921 | 617 | from __future__ import annotations
from datetime import (
date,
time,
)
from decimal import Decimal
import re
import numpy as np
import pytest
from pandas.core.dtypes.dtypes import (
ArrowDtype,
)
import pandas as pd
import pandas._testing as tm
pa = pytest.importorskip("pyarrow")
from pandas.core.arr... |
c1c31be7c60c682cc2bf03bb534b3ce0f9cb30eb255584b88b768ccc5216704f | Python | 22,934 | 682 | from datetime import datetime
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
def test_rank_unordered_categorical_typeerror():
# GH#51034 should be TypeError, not NotImplementedError
cat = pd.Categorical([], ordered=False)
ser = pd.Series(cat)
df = ser.to_frame()
... |
39e3e8b2b5666f56b549f4bf5a63a6a1e79e1eb835a9f8494b94b9d8d03f256b | Python | 22,969 | 565 | # -*- coding: utf-8 -*-
'''
SEGNASTIC_CLI
COMMAND LINE (CLI) VERSION FOR SPATIOTEMPORAL INDEXING CLUSTERING OF MOLECULAR TRAJECTORY SEGMENT DATA
Design and coding: Tristan Wallis
Additional coding: Kyle Young, Alex McCann
Debugging: Sophie Huiyi Hou, Kye Kudo, Alex McCann
Queensland Brain Institute
The University of Q... |
80c5c81b514ab6aa6afea420b8e51ad759c588d483a9fef3fa7968f3609ecbe0 | Python | 22,977 | 504 | """Class for 3D->2D Projection Operator."""
import itertools
import warnings
from collections.abc import Callable, Sequence
from typing import Literal, TypeAlias, cast
import einops
import numpy as np
import torch
from torch import Tensor
from mrpro.data.Rotation import Rotation
from mrpro.data.SpatialDimension impo... |
1bf55f9d6a2322a31d67081592d02b54c9c894789d92672a18f56c8e33b4fdfe | Python | 22,982 | 669 | # 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... |
b80a894ed7e47eb5a65c438498e48f95f49b98a20533ae323ba814de11c00e7b | Python | 22,982 | 700 | import numpy as np
import pytest
from pandas.errors import Pandas4Warning
import pandas.util._test_decorators as td
from pandas.core.dtypes.missing import na_value_for_dtype
import pandas as pd
import pandas._testing as tm
from pandas.tests.groupby import get_groupby_method_args
@pytest.mark.parametrize(
"drop... |
496202006c9b975e349cd9b98122b14a0bfdaa01e9750fa60cb731453d9844ab | Python | 23,008 | 729 | from __future__ import annotations
from typing import TYPE_CHECKING
import warnings
import numpy as np
from pandas._config import using_infer_freq_offset
from pandas._libs import lib
from pandas._libs.algos import unique_deltas
from pandas._libs.tslibs import (
Timestamp,
get_unit_from_dtype,
periods_pe... |
c99e44db70da7b2053e05dc79d14aba9de1458187d4416bd6811b767a0525706 | Python | 23,024 | 504 | import argparse
import os
import torch
import torch.nn as nn
import torch.nn.parallel
import torch.backends.cudnn as cudnn
import torch.optim as optim
from torch.utils.data import DataLoader
from torch.autograd import Variable
import torch.nn.functional as F
import numpy as np
import time
import sys
import cv2
from ply... |
26d527bdcd909bdd2be58055dbabc74548483788926ba0142de39bed78527aba | Python | 23,030 | 601 | from collections.abc import Iterator
from datetime import (
UTC,
datetime,
)
from decimal import Decimal
import numpy as np
import pytest
from pandas._config import using_string_dtype
from pandas.compat import is_platform_little_endian
from pandas.errors import Pandas4Warning
import pandas as pd
import pand... |
6b8a05804ffccaa399b7417aa09a69daddab7f53247ffb732d8a06a3392bd174 | Python | 23,060 | 611 | import numpy as np
import numba
from sklearn.base import BaseEstimator
from sklearn.utils import check_array
from umap.sparse import arr_intersect as intersect1d
from umap.sparse import arr_union as union1d
from umap.umap_ import UMAP, make_epochs_per_sample
from umap.spectral import spectral_layout
from umap.layouts ... |
c34eb76e76dae09db06a1917b64ff0b8ee71235a7873a7a361e80c4291016ed2 | Python | 23,069 | 451 | # Copyright (c) 2021-2023, 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... |
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