sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
78fd796a0ea73e3001df3b29d4a6fa97f89088101a4d5c42aaf995e4c9a671a0 | Python | 29,796 | 1,026 | """
Tests the 'read_fwf' function in parsers.py. This
test suite is independent of the others because the
engine is set to 'python-fwf' internally.
"""
from io import (
BytesIO,
StringIO,
)
import numpy as np
import pytest
from pandas.errors import EmptyDataError
import pandas as pd
import pandas._testing a... |
9524b7ad7e906a4684017c310cd9e66a9ebb631aaca3129d62cccdbf19e80f35 | Python | 29,816 | 665 | # 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... |
94f33662dfb2765b062620d00f43cf9777a3cd078d810d843a62e6767136920a | Python | 29,823 | 763 | """Methods for decoding subsets of voxels or experiments into text."""
import numpy as np
import pandas as pd
from nilearn._utils import load_niimg
from scipy import special
from scipy.stats import binom
from statsmodels.sandbox.stats.multicomp import multipletests
from .. import references
from ..base import Decoder
... |
f1c7034e7988d5244933f2e4f9917f5143b5c6810b23f7a7cf34417804c3f0fc | Python | 29,835 | 663 | # My library
from molgraph.dataset import *
from molgraph.graphmodel import *
from molgraph.training import *
from molgraph.testing import *
from molgraph.visualize import *
from molgraph.experiment import *
from molgraph.interpret import *
from molgraph.fragmentation import *
# General library
import argparse
import n... |
3728fd1890aca5df2aaa482c91550f5431a59b4f0f7339e2683a09f3ff156722 | Python | 29,875 | 868 | # 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... |
10eac1acb66ee86fa63d9be04d3d1ce153f95b2ce491052a2e811a7303db99e5 | Python | 29,879 | 979 | # 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... |
337cf8d694cd65d2f3f87843c86717f2ef466ca55690b7c00747ceb3a18f5ad2 | Python | 29,903 | 908 | # 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... |
32ec5704943a6572568eeddda4ad8af1a66f3f0ab00568de1ffd8aa84f66a10a | Python | 29,906 | 898 | """
Constructor functions intended to be shared by pd.array, Series.__init__,
and Index.__new__.
These should not depend on core.internals.
"""
from __future__ import annotations
from typing import (
TYPE_CHECKING,
Any,
cast,
overload,
)
import numpy as np
from numpy import ma
from pandas._config i... |
d4435c046a877026810fc3347d3d41cf86f7cac8601bfc4e978ea5cf8a00edcf | Python | 29,958 | 810 | """Unit testing of conversion functions for parity transform"""
import pytest
import pennylane as qp
from pennylane.fermi.conversion import parity_transform
from pennylane.fermi.fermionic import FermiSentence, FermiWord
from pennylane.ops import Identity, SProd
from pennylane.pauli import PauliSentence, PauliWord
fro... |
ea2d8d24965fd1accf251f8ad3794e3001deef298f879258df4efd7b04191027 | Python | 29,966 | 678 | """Test pynvvc dataloading functionality."""
import logging
import os
import shutil
import sys
from unittest.mock import MagicMock, patch
import pandas as pd
import pytest
import torch
import lightning_pose as lp
from lightning_pose.data import _IMAGENET_MEAN, _IMAGENET_STD
from lightning_pose.data.video import utils... |
d31592c49642a29b8c08f6b3788d63570de4db2bfd43a41ff3fbd03b007a95d4 | Python | 29,967 | 601 | import numpy.linalg as LA
import numpy as np
from .bfgs import bfgs
from . import gaussianDiffeons as gd
from . import conjugateGradient as cg, kernelFunctions as kfun, surfaces
from . import pointEvolution as evol
from . import surfaceMatching
from .surfaceMatching import Direction
from .affineBasis import AffineBasis... |
caa60d7261c8ac82898d57dfbe57779add3df10773e7c1534ad28e255351a3c1 | Python | 29,982 | 893 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
class TestDataFrameSubclassing:
def test_no_warning_on_mgr(self):
# GH#57032
df = tm.SubclassedDataFrame(
{"X": [1, 2, 3], "Y": [1, 2, 3]}, index=["a", "b", "c"]
)
with tm.assert_produces... |
7d1660cf879a5786f82e7d3c9171c39e6e00b6217ad5be27996d94037186ce44 | Python | 30,014 | 789 | from datetime import datetime
import re
import numpy as np
import pytest
from pandas.errors import OutOfBoundsDatetime
import pandas.util._test_decorators as td
import pandas as pd
import pandas._testing as tm
from pandas.core.arrays import IntervalArray
class TestSeriesReplace:
def test_replace_explicit_none(... |
24de3cdc3f7c0dee3f7287bd9d00a818e39e4a15ca60c4109a43cbf6aa975986 | Python | 30,048 | 923 | """Helper functions for accessing data."""
from __future__ import annotations
import json
from collections.abc import Collection, Sequence
from importlib.util import find_spec
from typing import TYPE_CHECKING, TypedDict, overload
import numpy as np
import pandas as pd
from anndata import AnnData
from numpy.typing im... |
f04414d55972cdefa6d67786d4d62f17181a29360bab1ae4da99157caba63169 | Python | 30,053 | 712 | import copy
import numpy as np
import twixtools
from twixtools.recon_helpers import (
remove_oversampling, calc_regrid_traj, perform_regrid
)
# define categories in which the twix data should be sorted based on MDH flags
# that must or must not be set (True/False)
# only one 'any' per category allowed (... |
4a4762359eb22ee68f1dd85af4255ecf66bb1656c202aa3a9c485fc34a2fe934 | Python | 30,059 | 689 | # Copyright (c) 2012-2021, NECOTIS
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification,
# are permitted provided that the following conditions are met:
#
# - Redistributions of source code must retain the above copyright notice,
# this list of conditions and th... |
c819888c5b348b3eabb1e0835e2d08c5b382396428d7999b0764aacae24e7f43 | Python | 30,063 | 969 | from initialization.config import *
from initialization.initialization import *
from data_processing.cleaning_formatting_filtering import *
from data_processing.shape_calculations import *
from data_processing.statistics import *
from data_processing.time_calculations import *
from visualization.trajectory_visualizat... |
6814353ebac947284f7f2ec10d6fe2d3f24dbfebc5f44ab52f045480455077ef | Python | 30,064 | 774 | from datetime import (
datetime,
timedelta,
)
from importlib import reload
import string
import sys
import numpy as np
import pytest
from pandas._libs.tslibs import iNaT
from pandas.errors import Pandas4Warning
import pandas.util._test_decorators as td
import pandas as pd
import pandas._testing as tm
def r... |
f233cab9154856f9408e65549ee9c82197dc874e0bc821606ba36201c01cf5e3 | Python | 30,099 | 803 | """
Visualization of mutation effects
Authors:
Thomas A. Hopf
Anna G. Green (mutation_pymol_script generalization)
"""
from math import isnan
from copy import deepcopy
import numpy as np
import pandas as pd
import matplotlib as mpl
import matplotlib.pyplot as plt
from bokeh import plotting as bp
from bokeh.core.... |
41a0c619da4bd7bb1cb6d1fedf6959ddeddbc372e8d0d4b02b974dd74645ebe9 | Python | 30,104 | 710 | # 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... |
3935507981f0e50bca375ca8966d69f63121ce47418827e82705a0bcd6cb1646 | Python | 30,158 | 675 | import torch
import torch.nn.functional as F
import dgl
import dgl.function as fn
from dgl.nn.pytorch import edge_softmax
from dgl.nn.pytorch import WeightAndSum
import itertools
import torch.nn as nn
import numpy as np
import pandas as pd
#All possible graphs (can't handle peptides longer than length 30 or shorter th... |
c87cbef318c82655c63470beba5d54dda1f51b9150b995efa1055d512796f1a0 | Python | 30,177 | 790 | import re
import unicodedata
import numpy as np
import pytest
import pandas.util._test_decorators as td
from pandas.core.dtypes.common import is_integer_dtype
import pandas as pd
import pandas._testing as tm
from pandas.core.arrays.sparse import SparseArray
try:
import pyarrow as pa
except ImportError:
pa ... |
d9bbff7db93731a45b336e9a3ee2b07a9558110a2a40f1dd700c33840a7392ed | Python | 30,204 | 853 | # Copyright 2020-2023 Xupeng Chen, Ran Wang
#
# 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 agreed to ... |
240ade47eccd548caea2b925903f542ff60bc335a40243876c39a322e32e511b | Python | 30,247 | 939 | # 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... |
01890947533c91cf15dd64242fd53e64c1e79ee6ad9e87a9219bd87674602731 | Python | 30,288 | 902 | # Copyright 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 agre... |
7a4f8737b44bfa2a9b2761b250f793c135b33ea955a80eb5c058634bf7d62069 | Python | 30,299 | 482 | #! /usr/bin/env python
import argparse
import os
import pysam
import pandas as pd
import numpy as np
from scipy.optimize import nnls
import scipy.sparse
import multiprocessing as mp
from hashed_read_genome_array import HashedReadBAMGenomeArray, ReadKeyMapFactory, read_length_nmis, get_hashed_counts
from plastid.genomi... |
6e0be2b035a1889fb4a0dbf9731e170a20de399d5a34575a1488b586f106d07d | Python | 30,324 | 587 | import logging
import time
import gc
import matplotlib.pyplot as plt
import statsmodels.api as sm
import numpy as np
import torch
import torch.nn as nn
import torch.utils.data as data
from scipy.stats import ttest_rel
from tqdm import tqdm
from ema import EMA
from model import *
from pretraining.dcg import DCG as Aux... |
2c4972503f320d6720515c94a5123f693ed8729d198dec19079529aa97a4f98a | Python | 30,331 | 1,217 | #funcsboot.py
from placerg.funcs import *
from placerg.funcsrg import *
from placerg.funcsall import *
from placerg.objects import *
from scipy.optimize import curve_fit
def bootfunc(a, env):
rate=[]
coeff=[]
eigspec=[]
var=[]
psil=[]
actmom=[]
autocorr=[]
tau=[]
... |
e2fc4bb4966e9859e14b64f76115e71e8192144d2bf76cbf6a86da70bdb9ac0e | Python | 30,355 | 780 | import nibabel as nib
import numpy as np
from traits.api import HasTraits , CArray, Instance,on_trait_change
from collections import OrderedDict
import logging
import json
import interpolator
import re
log = logging.getLogger()
class PylocModelException(Exception):
pass
class Scan(object):
def __init__(sel... |
9206b9be093e2c9ddb6cd9a9010e05bc66b3208b50a5b50afde3369f8ef9bee2 | Python | 30,420 | 663 | #migration_calculations.py
from initialization.config import *
from initialization.initialization import *
import os
import numpy as np
import pandas as pd
from tqdm import tqdm
def cell_delta_calcs(cell_tarray, t_window=MIG_T_WIND, debug=False):
'''
Calculate delta x, delta y, delta z, and directionality i... |
8a3fbf9b25ca47d2f6cf8ed6e23d747fa2b43a5f194c0ef7d4f91808f9254b19 | Python | 30,421 | 1,005 | import decimal
import re
import numpy as np
from numpy import iinfo
import pytest
import pandas.util._test_decorators as td
import pandas as pd
import pandas._testing as tm
@pytest.fixture(params=[None, "raise", "coerce"])
def errors(request):
return request.param
@pytest.fixture(params=[True, False])
def si... |
c9f44495c87940b84808713c27ec00f5e5a30569b80f6eca03e0721dd214e2c1 | Python | 30,434 | 692 | # 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... |
f8df6250305890ef7b0de67707eb12322c641549c34d59bc4669fc9b505bb3ff | Python | 30,440 | 864 | # cython: language_level=3
# Time-stamp: <2024-10-07 16:09:06 Tao Liu>
"""Utilities for reading BAM files and their BAI indexes in MACS3.
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).
"""
# --------------... |
20385952f22a8f43a344272b482e1ca7555c4b136270b3edfd6649e57da825a9 | Python | 30,453 | 825 | from datetime import (
date,
datetime,
time,
timedelta,
)
import numpy as np
import pytest
from pandas.errors import Pandas4Warning
import pandas.util._test_decorators as td
import pandas as pd
import pandas._testing as tm
from pandas.tseries.frequencies import to_offset
START, END = datetime(2009,... |
ad876f3a639dc4ca167d667b1a7e7bb84011ece4509a079673a70cf5cbfbb4c1 | Python | 30,463 | 875 | # 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... |
e716cba53aa38eb7fcac69a84db6ee7304a8bfd0785484ee69f6640a12c1584f | Python | 30,476 | 780 | import multiprocessing
import os
import shutil
import tempfile
from collections import Counter
from functools import partial
from typing import List, Optional, Set, Tuple, Union
import ngs_tools as ngs
import numpy as np
import pandas as pd
import pysam
from typing_extensions import Literal
from .. import config, uti... |
a71ec4b0c556c37b975a4441f8e99c19346a703e63212f8332bcb2c092d05653 | Python | 30,487 | 814 | # 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 ... |
565243c14e7724d7bde6cb8f884378d796aa9200db8a5e014476ab339441c22e | Python | 30,498 | 755 | # 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... |
6d38c06a140801dc7b0f356b439bdd52c9fa8efd645eed104283de34281a9dd5 | Python | 30,506 | 710 | # -*- coding: utf-8 -*-
"""
Created on Sun Apr 16 18:11:11 2023
@author: lonya
"""
#%% Load Data
import tkinter as tk
import tkinter.filedialog as fd
import numpy as np
import os
import matplotlib.pyplot as plt
import pandas as pd
import my_funcs as mf
import seaborn as sns
from scipy.stats import sem
from scipy.stats ... |
6cfdc27d25e43cbfcc39867cd7d31e63291ef4305a94abccf49b18aa83ce5347 | Python | 30,546 | 834 | """
Tests for the pandas.io.common functionalities
"""
import codecs
import contextlib
import errno
from functools import partial
from io import (
BytesIO,
IOBase,
StringIO,
)
import mmap
import os
from pathlib import Path
import pickle
import re
import sqlite3
import tempfile
import numpy as np
import py... |
0363e68309d55b8663009622be3d662fdd81e9d9bbd2fae456e4ea8cfd62232a | Python | 30,583 | 826 | """test the scalar Timedelta"""
from datetime import timedelta
import numpy as np
import pytest
from pandas._libs import lib
from pandas._libs.missing import NA
from pandas._libs.tslibs import (
NaT,
iNaT,
)
from pandas._libs.tslibs.dtypes import NpyDatetimeUnit
from pandas.compat import WASM
from pandas.com... |
7f0aa142cb350908417243a6f5a92024cad0626f20ab4b061fd7091ebb134b59 | Python | 30,598 | 734 | '''
Created on Aug 15, 2016
@author: arco
'''
from __future__ import absolute_import
import os, random, string, threading
import contextlib
import shutil
import tempfile
import datetime
import cloudpickle as pickle
import yaml
if 'ISF_MDB_CONFIG' in os.environ:
config_path = os.environ['ISF_MDB_CONFIG']
wit... |
42cdd6e533a54ae5d0481ed188181f1c78bedd566cfd92b24d885b45eea6e126 | Python | 30,630 | 1,014 | """
Inference of evolutionary couplings
from sequence alignments using
mean field approximation.
Authors:
Sophia F. Mersmann
"""
import numpy as np
import numba
from copy import deepcopy
from evcouplings.align import parse_header
from evcouplings.couplings import CouplingsModel
# arbitrary value that is written
#... |
f47df32b5bf33092d6f19be137b798381c251c76e52958eb06c3af0cea245c75 | Python | 30,636 | 806 | # 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... |
7a8eb2a451bccd53f8691d8c8b49e19f221f551b5a33f10b2ca8c3c723351585 | Python | 30,639 | 661 | #! /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... |
460fff1be85e84017189aa35ce2d926b55d890eb970b83b7991843f308b485a6 | Python | 30,641 | 765 | #!/usr/bin/env python
# Time-stamp: <2025-09-29 14:18:42 Tao Liu>
import re
import struct
import unittest
from collections import Counter
import pytest
from MACS3.IO.BAM import BAIFile, BAMaccessor
from MACS3.IO.BAM import (StrandFormatError,
MDTagMissingError)
class Test_BAIFile(unittest... |
c07e2347d06afbf6c8ae53223814d5590a5c1d8e910a48a1e563e9eec6bc31f5 | Python | 30,664 | 803 | """Functions for predicting keypoints on labeled datasets and unlabeled videos."""
from __future__ import annotations
import datetime
import gc
import logging
import os
from pathlib import Path
from typing import TYPE_CHECKING, Any, Literal, cast, overload
import cv2
import lightning.pytorch as pl
import matplotlib.... |
aef83dcbc69080127c05dbcfd7ff4aff82cf071791036b4d2459b5a030417932 | Python | 30,707 | 732 | #! /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... |
98abb1af5756fd7fcbb8388aba50851fc65092561fc907bb6ec0bcf74c894e0c | Python | 30,777 | 1,056 | """
Tests the 'read_fwf' function in parsers.py. This
test suite is independent of the others because the
engine is set to 'python-fwf' internally.
"""
from io import (
BytesIO,
StringIO,
)
import numpy as np
import pytest
from pandas.errors import EmptyDataError
import pandas as pd
import pandas._testing a... |
d03c585d9ac4493fc213ea0204ed8dc5f6b517ffd8604c989f38245da174bae3 | Python | 30,787 | 811 | from initialization.initialization import *
from initialization.config import *
from data_processing.cleaning_formatting_filtering import *
from data_processing.migration_calculations import *
from data_processing.load_trackmate import *
# from data_processing.shape_calculations import * # rah
import os
import numpy ... |
c26155306a299a689fddfd45160f46a8c3e15457a0c43b8584a3d732d508a526 | Python | 30,804 | 433 | """
Module for implementation of developmental models
"""
import abc
import os
import numpy as np
from glob import glob1
from scanometrics import __version__
from scanometrics.utils import logging
from scipy.stats.mstats import mquantiles
from scipy.stats import norm
from scipy.stats import f as fstat
from scipy.sta... |
6dee0f9f93607c5692f19c0f3d43ee9695030cb77292a434cf63d2ba101b6835 | Python | 30,810 | 739 | # Copyright 2018-2026 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... |
f66dfb0d71ff8959c3d0da29a660afb32aad725e3dd22af99e5190fc37c8ed79 | Python | 30,816 | 922 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.api.types import CategoricalDtype
import pandas.core.reshape.tile as tmod
def test_simple():
data = np.ones(5, dtype="int64")
result = pd.cut(data, 4, labels=False)
expected = np.array([1, 1, 1, 1, 1])
tm.a... |
eba07c9cd299838fb16f30673346eda3936560f103a8d17514f4e7b1a1dc3e68 | Python | 30,819 | 601 | ######################
### Import Library ###
######################
# my library
from molgraph.graphmodel import *
# from molgraph.graphmodel_star import *
# from molgraph.graphmodel_signed import *
from molgraph.dataset import *
from molgraph.experiment import *
# general
import math as math
from tqdm.notebook impor... |
51e1d9061e20a0a4d367aeb7e262ffcfbda251e5e609bee233f7ef3d58ab97d9 | Python | 30,849 | 819 | import re
import numpy as np
import pytest
from pandas.errors import InvalidIndexError
import pandas as pd
import pandas._testing as tm
class TestGetItem:
def test_getitem(self, closed):
idx = pd.IntervalIndex.from_arrays(
(0, 1, np.nan), (1, 2, np.nan), closed=closed
)
asse... |
5d6882d83f70f39e5e247a82ada9928746b154de9942eda4acbfa8ddef7038f7 | Python | 30,856 | 899 | # 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... |
6582d0a19a6fbca2dc72d417f870ea6bce2b8a4c9ea70fa346d58811f4eb01fc | Python | 30,875 | 786 | """Test cases for DataFrame.plot"""
import string
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.tests.plotting.common import (
_check_axes_shape,
_check_box_return_type,
_check_legend_labels,
_check_ticks_props,
_check_visible,
_flatten_visible,... |
385c3514f2854df032f89477610a8658336630842230af8bc2891d78e300f618 | Python | 30,876 | 855 | # 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... |
04bc9daf839bd666267735e181728ae40398d08cdacebe4ecd8f56d6e4a4cc27 | Python | 30,878 | 867 | """
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.
---
MIT License
Copyright (c) 2021 www.compscience.org
Permission is hereby granted, free of charge, to any person obtaining a copy
of this so... |
ca80f9a3234b05c99e0cc0a0d5527f2012e1635b62a8e0f81da2505858471f58 | Python | 30,878 | 559 | # -------------------------------------------------------------------------------------------------------------------------------------
# Following code curated for GCPNet (https://github.com/BioinfoMachineLearning/GCPNet):
# ----------------------------------------------------------------------------------------------... |
56d53ca8b147b449068dec27d504c053d3f40dcc88260f1c194b07a95b96909c | Python | 30,897 | 924 | from __future__ import annotations
import numpy as np
import pytest
from pandas.compat import HAS_PYARROW
from pandas.errors import Pandas4Warning
import pandas.util._test_decorators as td
from pandas.core.dtypes.astype import astype_array
import pandas.core.dtypes.common as com
from pandas.core.dtypes.dtypes import... |
405a4e3e3c45bb9114a70ebbbb85bfc2e2fbc7964886527b8e10d95bb967dba1 | Python | 30,899 | 786 | """Test cases for DataFrame.plot"""
import string
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.tests.plotting.common import (
_check_axes_shape,
_check_box_return_type,
_check_legend_labels,
_check_ticks_props,
_check_visible,
_flatten_visible,... |
3bad897fbf675da2d1e7a26bf343100a17d26f4e797c70c40c5c9ce4d706bbf3 | Python | 30,932 | 832 | """
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 datetime
import errno
import logging
import os
import random
import subprocess
from abc import ABC, abstractmethod
from collections imp... |
b09582a9cfae66c07b483e321350c33e3d0fa4c13d03c5f04998a75718a86008 | Python | 30,935 | 824 | # 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... |
c38de9cd811a6986723ba25558589107fc057a7ee983b1e20f0ae2a5e0b17603 | Python | 30,936 | 926 | from __future__ import annotations
from typing import Any
import numpy as np
import pytest
from pandas.compat import HAS_PYARROW
from pandas.errors import Pandas4Warning
import pandas.util._test_decorators as td
from pandas.core.dtypes.astype import astype_array
import pandas.core.dtypes.common as com
from pandas.c... |
3ad65d6faf7b9bde06973e66ec311648fb45a6dad4ed9ff64eb48ff46aa3b3bb | Python | 30,961 | 664 | # 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... |
15db26eb68074c3798ffcff4d5a82ef8eef373411fa68fed952163f43980fc7d | Python | 30,968 | 932 | # 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... |
4a6dcff3173acb4129bd38106c09348a5f35c9bf48c2e7b2b468972abf45e71d | Python | 30,975 | 897 | from collections import namedtuple
from collections.abc import Generator
from contextlib import contextmanager
import re
import struct
import tracemalloc
import weakref
import numpy as np
import pytest
from pandas._libs import hashtable as ht
import pandas as pd
import pandas._testing as tm
from pandas.core.algorith... |
e4f352a05d56d8c2e12bda529bd61c144be621ec80db9a360a360bc8d303c21b | Python | 30,985 | 701 | # 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... |
0fc95e3155ea69a51543467115d0ad87e3d595cfb2fd51994020b4a4cf71597f | Python | 30,986 | 873 | # 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... |
0428adb463607ebb339f48f8c67e9e9b935de2150fc7ba791a7ef624c6ef2eec | Python | 30,998 | 659 | import json
import pickle, gzip
import numpy as np
import matplotlib.patches as mpatches
import matplotlib as mpl
from matplotlib import pyplot as plt, cm
from scipy.optimize import curve_fit
from neuron import h, gui
from scipy.stats import f_oneway, tukey_hsd, ttest_ind_from_stats
plt.style.use('seaborn-colorblind')... |
8c3dbbf8dcb94b1605e75bab04c21d7e83d9bf012f951d86a28591b2f63ef6ab | Python | 31,028 | 738 | # Fast protein structure searching using structure graph embeddings
# faiss and biopython imported in functions
import torch
from torch.nn import Dropout, Identity, Linear, Sequential, SiLU
from torch.nn.functional import normalize
from torch.utils.data import Dataset
from torch_scatter import scatter
from torch_geome... |
50ec892e682df989ec8360ce36cd2c9ebec6fbf14c741b0aa410d63852e7c2a3 | Python | 31,092 | 483 | #! /usr/bin/env python
import argparse
from Bio import SeqIO
from plastid.genomics.roitools import Transcript, SegmentChain
import re
from collections import defaultdict
import pandas as pd
import numpy as np
import multiprocessing as mp
import subprocess as sp
import os
import sys
from time import strftime
parser = ... |
803d05ec5073dc29ed086e26982695a015ed6093635ee56264e11eab6b398c47 | Python | 31,097 | 678 | #!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
Step S2 (CheckM2 branch): Bin abundance estimation and PE connections.
This module computes coverage-based abundance information and paired-end
connections across bins using multiprocessing, preparing inputs for
downstream dereplication and comparison steps.
"""
from... |
d18b731da015306968e1a558aeb487943384b232b77aa4764438b9533ce33af1 | Python | 31,125 | 742 | # 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... |
75373d2c23fcb0987fa8b4a6381023d3de775d5d023a3fde9916d4e8773be8e7 | Python | 31,138 | 549 | # Copyright 2019 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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://w... |
38f4c679549fe1f4ef66870894806390c43fdebf0fbeda3519551ee85d31744d | Python | 31,142 | 799 | # 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... |
2cd25f2eaa8fd317842dccbbc6eb1cddbd922a7775e5dd1e38b12cf071867d38 | Python | 31,160 | 876 | # 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... |
0a141bf9945cdc86876a4d2b7e4f26fe563a1e8cdbd4a48a1f5977cf54f5bae0 | Python | 31,171 | 869 | from collections import deque
from datetime import (
date,
datetime,
time,
timedelta,
)
import re
import string
import numpy as np
import pytest
from pandas.errors import Pandas4Warning
import pandas.util._test_decorators as td
import pandas as pd
import pandas._testing as tm
from pandas.arrays impor... |
cd6f1728970d26828342110fdd23d2bf12ee07012551e1f0aeb2f474df967c3d | Python | 31,185 | 938 | """Utility functions for NiMARE."""
import datetime
import inspect
import logging
import os
import os.path as op
import re
from functools import wraps
from tempfile import mkstemp
import nibabel as nib
import numpy as np
import pandas as pd
from nilearn.input_data import NiftiMasker
from . import references
from .due... |
299c8524411dd271e039c3cae9418a4342f99502d90d34e007eb1c8a4232bb17 | Python | 31,196 | 675 | """Tests the Spatial class."""
import pytest
import torch
from mrpro.data import SpatialDimension
from mrpro.utils import RandomGenerator
from typing_extensions import Any, assert_type
def test_spatial_dimension_from_xyz_int() -> None:
"""Test creation from an object with x, y, z attributes"""
class XYZint:... |
4b48d20ce5a99a33be245a220556e7c3e64410b9ef55ac4238053c388dd1751a | Python | 31,258 | 856 | from datetime import datetime
from itertools import product
import numpy as np
import pytest
from pandas.errors import Pandas4Warning
from pandas.core.dtypes.common import (
is_float_dtype,
is_integer_dtype,
)
import pandas as pd
import pandas._testing as tm
@pytest.fixture
def multiindex_df():
levels... |
c10a70704bef9582e800ef8b8bc7c432cf846ee836b62f1dc742133c1ab8ab5f | Python | 31,264 | 832 | # 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... |
4fed9f6b4821b247ca814ebf3646fb364a99e5f02a2b3a394bd51eb2d5a40b4a | Python | 31,293 | 817 | # 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... |
2857600957e1b4e704a78b61efc5deb32e07d379930243c0f501b4b79ef38fb7 | Python | 31,299 | 819 | """Implementation of the 'trim' command.
"""
from collections import defaultdict
from collections.abc import Sequence
import logging
import sys
import textwrap
from atropos.commands.base import (
BaseCommandRunner,
Summary,
Pipeline,
SingleEndPipelineMixin,
PairedEndPipelineMixin,
)
from atropos.com... |
882edf070211d23318ea0ca3e5701c79686d14e07636dfed63cdd39cf8230bb9 | Python | 31,302 | 900 | from __future__ import annotations
from datetime import (
datetime,
timedelta,
)
import numpy as np
import pytest
from pandas.compat import (
IS64,
is_platform_windows,
)
from pandas.errors import Pandas4Warning
import pandas as pd
import pandas._testing as tm
######################################... |
40909abedf412caf1f58876ba9b04e1a129c7e9e5dd69cfc73be407940cd6c5c | Python | 31,308 | 637 |
import argparse, os, sys, time, gc, datetime
from torch.functional import norm
import torch
import torch.nn as nn
import torch.nn.parallel
import torch.backends.cudnn as cudnn
import torch.optim as optim
import torch.distributed as dist
from torch.utils.data import DataLoader
from torch.utils.tensorboard import Summa... |
b8db96d14a7ac7845dff648a67a468fd86d82ebd82fbd40f0cf41a65117b67a7 | Python | 31,311 | 660 | # -*- coding: utf-8 -*-
import torch
import numpy as np
from collections import defaultdict
from sdna.sim import *
BASE_REPRESENTATION = {(-1.0, -1.0): 'A',
(-1.0, 1.0): 'G',
( 1.0, -1.0): 'T',
( 1.0, 1.0): 'C'}
NUMBER_REPRESENTATION = {'A': (-1... |
0329aa47ca03076b43726a6f06c20b00089eabc91162f89a5f993c573152b222 | Python | 31,323 | 796 | import os
from copy import deepcopy
from numbers import Integral
import anndata
import numpy as np
import torch
from scipy import sparse
try:
import cupy as cp
CUPY_AVAILABLE = cp.cuda.is_available()
except Exception:
CUPY_AVAILABLE = False
import gc
from ..models._base_models import pyagingModel
from ... |
4fc71f65163e907257485ddfb267a52e1b44ed329ca94c9534c19e522c983d5c | Python | 31,329 | 938 | """
Constructor functions intended to be shared by pd.array, Series.__init__,
and Index.__new__.
These should not depend on core.internals.
"""
from __future__ import annotations
from typing import (
TYPE_CHECKING,
Any,
cast,
overload,
)
import warnings
import numpy as np
from numpy import ma
from ... |
5cbe8aaa40edee8563d8cdefd0d1170957133c31ca2b72991431719c3070f57e | Python | 31,330 | 901 | from __future__ import annotations
from datetime import (
datetime,
timedelta,
)
from typing import Any
import numpy as np
import pytest
from pandas.compat import (
IS64,
is_platform_windows,
)
from pandas.errors import Pandas4Warning
import pandas as pd
import pandas._testing as tm
###############... |
b2ba34c2dd706337f1e7169cacc4932904fb648fc8de23108a2b33d098d5caca | Python | 31,376 | 873 | """
Tests dtype specification during parsing
for all of the parsers defined in parsers.py
"""
import csv
from io import StringIO
import numpy as np
import pytest
from pandas._config import using_string_dtype
from pandas._libs import parsers as libparsers
from pandas.errors import Pandas4Warning
from pandas.core.dt... |
3fbd3762c208ecbd3865f6dc835f63eda8d395a81ba42c240d8cdd65b4be8581 | Python | 31,384 | 532 | import sys
import matplotlib.pyplot as plt
import matplotlib.colors as colors
from eLife_Grid_anchoring_2024.vr_grid_cells import *
from eLife_Grid_anchoring_2024.Helpers.array_manipulations import *
import eLife_Grid_anchoring_2024.Helpers.plot_utility as plot_utility
warnings.filterwarnings('ignore')
def min_max_n... |
643968c7c0502c6d6adfc82a7cfa6728c6195a85bf6c1b4ef58e7a0b0509d0d5 | Python | 31,392 | 656 | #!/usr/bin/env python
from __future__ import (
print_function,
division,
unicode_literals,
absolute_import,
)
from builtins import str
import os
import os.path as op
import numpy as np
import nibabel as nb
import warnings
from nipype.interfaces.base import traits, TraitedSpec, InputMultiPath, File,... |
1dc8cd7af79452fe6803525cadf91169628c26d90a032872fcca2982df8fd216 | Python | 31,404 | 569 | # Copyright 2018-2026 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... |
44577a35ad1d4c8c5c127b3b315cd9719d8f2a12d48b37207fae90b944d0833b | Python | 31,406 | 798 | """Test cases for .boxplot method"""
from __future__ import annotations
import itertools
import string
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.tests.plotting.common import (
_check_axes_shape,
_check_box_return_type,
_check_plot_works,
_check_tic... |
70f572618891e21b6e6f6176a8a508b54f666d082025a011400aac41c5955e60 | Python | 31,419 | 699 | import torch
import torch.nn as nn
from torch.nn import init
import functools
from torch.optim import lr_scheduler
import os
import numpy as np
import scipy.io as sio
###############################################################################
# Helper Functions
####################################################... |
313e2dc1dd7347b0da9673d9bccf9e017d4ca91dd6317d60aba5cbb18a9b99fd | Python | 31,444 | 853 | """
Tools for working with AQuA event features
Designed to accompany the paper "Network-level encoding of local
neurotransmitters in cortical astrocytes" (DOI: TODO)
"""
## ------------------------------------------------------------------------ ##
## Imports
## ------------------------------------------------------... |
744ae919f2de06f636129edc8c3f5bd3c1edff67fb608e423613b60c5e340150 | Python | 31,453 | 680 | import codecs
from contextlib import closing
import requests
import csv
import itertools
import statistics
import random
import collections
import copy
import math
import pprint as pp
import seaborn as sns
import matplotlib.pyplot as plt
from matplotlib.colors import ListedColormap
import numpy as np
imp... |
ae10e50535847ed0dfa551488c8926bbead881df1d3f1ace50ae0180b70ba88e | Python | 31,462 | 858 | """Detect adapter sequences directly from reads based on kmer frequency.
"""
from collections import defaultdict
import logging
import math
import re
from atropos.align import Aligner, SEMIGLOBAL
from atropos.commands.base import (
BaseCommandRunner, Pipeline, SingleEndPipelineMixin, PairedEndPipelineMixin)
from at... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.