sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
14abb79ff32aa890da357abb013e2f473056eb88029f41360444987506ffa742 | Python | 80,065 | 1,876 | #!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
Step S1: Autobinning and initial quality control for BASALT.
This module converts read formats, prepares paired-end tracking
information and runs multiple binners to generate initial binsets
and PE-based contig connection files.
"""
from lib2to3.fixes import fix_buff... |
2721f70d3d35508d606322c3cd51f2a92c6d82591d0517f7d61bd3a6f3dac2d0 | Python | 80,181 | 2,021 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Mar 23 15:37:03 2020
@author: reisertm
"""
import os
import tensorflow as tf
from timeit import default_timer as timer
from collections.abc import Iterable
import math
from .improc_utils import *
########## Cropmodel ################################... |
c889df209e1391fe4c6342258c2a4c9c83235103caa8abaac17df27c5aa08d8b | Python | 80,676 | 2,030 | import operator
from tokenize import TokenError
import numpy as np
import pytest
from pandas.errors import (
NumExprClobberingError,
UndefinedVariableError,
)
import pandas.util._test_decorators as td
import pandas as pd
import pandas._testing as tm
from pandas.core.computation.check import (
NUMEXPR_BLO... |
b64b2023d87f19a8a0cef3a62621250d4d0a1dd46e2d9ea3edafd42716777c86 | Python | 80,847 | 2,343 | from __future__ import annotations
from functools import cache
from typing import (
TYPE_CHECKING,
Any,
Literal,
Self,
cast,
overload,
)
import warnings
import numpy as np
from pandas._config import (
is_nan_na,
using_python_scalars,
)
from pandas._libs import (
algos as libalgos... |
b71c6036ea025a7b8923a17bf70c92b83be1d41ebc927f710611fabb38d5783b | Python | 81,256 | 2,027 | #! /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... |
db09f262b5cddc4f1b6efbc1808acb826883b1db1a6b181e6bdd194d0e95aa81 | Python | 81,576 | 2,414 | from __future__ import annotations
import abc
from collections import defaultdict
import functools
from functools import partial
import inspect
from typing import (
TYPE_CHECKING,
Any,
Literal,
TypeAlias,
cast,
)
import numpy as np
from pandas._libs.internals import BlockValuesRefs
from pandas.co... |
a38b4dc76a2bbb1157e369a700ab1e17c57b6b63385e237d7d6c141948408919 | Python | 82,071 | 2,418 | from __future__ import annotations
import abc
from collections import defaultdict
import functools
from functools import partial
import inspect
from typing import (
TYPE_CHECKING,
Any,
Literal,
TypeAlias,
cast,
)
import numpy as np
from pandas._libs.internals import BlockValuesRefs
from pandas.co... |
07fde8d837231c6ff9588689301fe7efd35a28038e215d0361f23a4430be7175 | Python | 82,415 | 1,212 | """
Core ScanOMetrics classes and methods
"""
import io
import pickle
import numpy as np
import os
from scanometrics import normative_models, processing, __version__
from scanometrics.utils import logging
from scanometrics.utils.zenodo_api import list_normative_models, download_file
from scanometrics.utils.stats import... |
e64a0984fefa977dec915c96ad498b759b5383f6acb5a5b117fd22324aa0ee1c | Python | 82,659 | 2,375 | # 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... |
494a4145cfa66c6d75a3e4d625d88084eeea7ba7b2cbaf1468fbc4dd99c68475 | Python | 82,764 | 2,397 | from datetime import datetime
from functools import partial
import zoneinfo
import numpy as np
import pytest
from pandas._libs.tslibs import Day
from pandas._typing import DatetimeNaTType
from pandas.compat import is_platform_windows
from pandas.compat.pyarrow import pa_version_under22p0
from pandas.errors import Pan... |
b7169ad291047c1206cb8e9f1c6cedb913811a93b92d3bfaa827879d943779c2 | Python | 82,938 | 1,125 | """
Wrapper for DL+DiReCT scripts to be run on <subjects_dir>/<subjid>. Includes pipeline template parameters as
proc_pipeline_name, and methods as run(), and proc2metric().
"""
from shutil import rmtree, copyfile, which
from importlib.metadata import version, PackageNotFoundError
import subprocess
import numpy as np... |
bc4662170e0e86031318c6254ff90927901c7db7984ff091b526e6863e7ff2e5 | Python | 83,021 | 1,941 | # pipelines.py
from initialization.initialization import *
from initialization.config import *
from data_processing.cell_identifier import *
from data_processing.cleaning_formatting_filtering import *
from data_processing.clustering import *
from data_processing.data_wrangling import *
from data_processing.dimensiona... |
1ee7a40a62a9f77ce72c333c3d0c4119204fc256d700f4b57a4461559b16f574 | Python | 83,024 | 2,395 | import torch
import numpy as np
from matplotlib import pyplot as plt
import pandas as pd
import time
from sklearn.model_selection import KFold
from scipy import stats
import matplotlib as mpl
from torch import nn
from tqdm import tqdm
from sklearn.decomposition import PCA
from sklearn.manifold import TSNE
try:
... |
3147858b097072a03311d68b1f658196cb37132de62cb3776a8d33f31f7e9b4a | Python | 83,095 | 1,689 | # 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... |
2f0dd4daa9b86dead6ac1c263cc27e0544d0c35faf5c8f81b1408c24b639fd0b | Python | 83,192 | 1,720 | # -*- coding: utf-8 -*-
"""
Created on Wed Feb 16 07:52:09 2022
@author: tpisano
#can set anaconda ipython console path to C:\ProgramData\Anaconda3\envs\sleap\python.exe
#conda create -y -n sleap -c sleap -c sleap/label/dev -c nvidia -c conda-forge sleap=1.2.0a6
conda create -y -n sleap -c sleap -c nvid... |
fa599fef23f08b8a5e0771da55cc36ee58e1d15abfcacc4bef8787228b3b4117 | Python | 83,620 | 2,498 | # 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... |
fcef8510db859b153e4883dd283dcee95e5eae15bd7d9dad9efa1c0a7d225757 | Python | 84,004 | 1,993 | #!/usr/bin/env python
"""Module Description: Test the `macs3 hmmratac` command and the public
output functions in MACS3.Commands.hmmratac_cmd.
Most command-line runs use a small synthetic ATAC-seq-like BEDPE file
(open regions full of short fragments, flanked by positioned
nucleosomes, over a sparse background of mon... |
c7b6b7e52415f414b7a5d0520b0feb5e9360ce066c098b7a1520449a3a90a84e | Python | 84,393 | 2,240 | import copy
import matplotlib.pyplot as plt
from matplotlib.patches import Rectangle
import numpy as np
import os
from scipy.stats import pearsonr
import torch
import windseer.data as data
import windseer.utils as utils
import windseer.nn as nn
import windseer.plotting as plotting
def load_wind_data(config, detect_l... |
2a112841f42850aa58561809e5a4974bcf45ac7ff139d14012f5174d006e38d5 | Python | 84,563 | 2,114 | from __future__ import division
import numpy as np
import torch
import torch.nn as nn
import torch.optim as optim
from sklearn.decomposition import PCA
import time
import task_train_test as tk
### PCA ###################################################
def PCA_Calc(Data, Reference_TT):
# Data: RNN activat... |
f9e7ef7b4f2287641fbaa840a4096140ace62295a57bcc5cd17844a957889ea0 | Python | 85,018 | 2,411 | from __future__ import annotations
from abc import (
ABC,
abstractmethod,
)
from collections.abc import (
Hashable,
Iterable,
Iterator,
Sequence,
)
from decimal import Decimal
from functools import partial
from typing import (
TYPE_CHECKING,
Any,
Literal,
cast,
final,
)
impo... |
d5a15b4e1cee65cdf185a2e05d9acc2f800647d1e8afc2fe1b5eefe1acb3b490 | Python | 85,327 | 2,346 | from __future__ import annotations
from itertools import product
from types import MappingProxyType
import numpy as np
import pytest
from pandas.compat import (
PY312,
PY314,
)
from pandas.compat._optional import import_optional_dependency
from pandas.errors import (
NumExprClobberingError,
Pandas4Wa... |
c7494f8a77f9dc66b4211895fb624d54399a2947da7614a8a2c5c342df545042 | Python | 85,570 | 2,140 | #! /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... |
e3b3d955d5f6274e924a19fd6b880221439f33348d1528ac2ac11e18dd138895 | Python | 85,717 | 2,584 | """
Define extension dtypes.
"""
from __future__ import annotations
from datetime import (
date,
datetime,
time,
timedelta,
)
from decimal import Decimal
import re
from typing import (
TYPE_CHECKING,
Any,
Self,
cast,
)
import warnings
import zoneinfo
import numpy as np
from pandas._c... |
df74379d5493fa4682d4be0118288f0155fff6c82729b0eed093c3837f419d63 | Python | 85,791 | 2,239 | # 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... |
a0df109559cd2c35342126cd516060cde8ff4fbc767362a44f6f1fc5130a8005 | Python | 86,051 | 2,591 | """
Define extension dtypes.
"""
from __future__ import annotations
from datetime import (
date,
datetime,
time,
timedelta,
)
from decimal import Decimal
import re
from typing import (
TYPE_CHECKING,
Any,
Self,
cast,
)
import warnings
import zoneinfo
import numpy as np
from pandas._c... |
426c1f8933c8484cbc190375e7f10929df08823e38b539a91fd3899d0ed75a25 | Python | 86,053 | 2,481 | from datetime import datetime
from functools import partial
import zoneinfo
import numpy as np
import pytest
from pandas._libs.tslibs import Day
from pandas._typing import DatetimeNaTType
from pandas.compat import is_platform_windows
from pandas.compat.pyarrow import pa_version_under22p0
from pandas.errors import Pan... |
05323e17820fd402f78e052cf69f0d8d9391ee5be7cef2b5f807b8fa9b904c35 | Python | 86,181 | 2,484 | from collections import deque
from datetime import (
UTC,
datetime,
)
from enum import Enum
import functools
import operator
import re
import numpy as np
import pytest
from pandas.compat._optional import import_optional_dependency
from pandas.errors import Pandas4Warning
import pandas as pd
import pandas._te... |
50d999cf844c67b893e761cdc7636db812085d610fcc631b7ee2e30d04c99e41 | Python | 86,238 | 2,454 | # 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... |
119ad2f44850e2472962a428e711ba8395dc335e80377ca3f7d2ca483dceff1b | Python | 86,522 | 2,494 | from collections import deque
from datetime import (
UTC,
datetime,
)
from enum import Enum
import functools
import operator
import re
import numpy as np
import pytest
from pandas.compat._optional import import_optional_dependency
from pandas.errors import Pandas4Warning
import pandas as pd
import pandas._te... |
cb80a5676a38b94bcc2507eb4296d22ca4f0de4578bebf6ac8614def325ea40f | Python | 86,607 | 2,447 | from __future__ import annotations
from abc import (
ABC,
abstractmethod,
)
from collections.abc import (
Hashable,
Iterable,
Iterator,
Sequence,
)
from decimal import Decimal
from functools import partial
from typing import (
TYPE_CHECKING,
Any,
Literal,
cast,
final,
)
impo... |
72bb20cd69ff73f000f1f9f98949abb800c0cbb1b7317738b58aca50f02c144b | Python | 86,793 | 2,377 | # 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... |
a40a452cc2cbfe32c8ae7291f82bf3c65dbfa485a91412c7ddd4ea22853676da | Python | 86,910 | 2,218 | #import matplotlib
import os
import numpy as np
from numba import jit, int64
import scipy as sp
import scipy.linalg as LA
from scipy.sparse import csr_matrix
from scipy.sparse.csgraph import connected_components
from skimage import measure
try:
from vtk import vtkCellArray, vtkPoints, vtkPolyData, vtkVersion,\
... |
1dc06ad583e8701906342e7e84bd910647e2d45cdab926eeaae42b88b6e01fbc | Python | 87,332 | 2,515 | """Test GUI component."""
# ------------------------------------------------------------------------------
# Imports
# ------------------------------------------------------------------------------
# from contextlib import contextmanager
import sys
from timeit import default_timer
import numpy as np
from numpy.test... |
1bd793bf833922b1e3209e9d6e37fb37804d65d85427b88666dfd2f9ebf79558 | Python | 87,461 | 2,453 | # 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... |
6d16f266986ddfecc044e50750fce17cb38a98144fa55ad6062c07daadf9dda1 | Python | 88,071 | 2,799 | # 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... |
eb674b5bc57df237f545a55d902bf3a30890b7bcf99cdd9591b4660a30d6fcaf | Python | 88,392 | 1,424 | # Created on Monday November 12 14:23:00 2022
# @author: Andres
# Takes sematically segmented images of axon/myelin,
# postprocesses the segmentation, labels individual axons and
# associated myelin, and calculates the morphometrics of those
# fibers.
import os
from pathlib import Path
from tqdm import tqdm
import num... |
aa7b2a58ca29cd8dbadf1bf79152177558d3306fc275f3d6b0efe7d43e075964 | Python | 88,485 | 983 | # -*- coding: utf-8 -*-
import numpy as np
import sys
import os
import pickle
import argparse
import math
import time
import torch
import torch.nn as nn
import torch.backends.cudnn as cudnn
import torchvision.transforms as trn
import torchvision.datasets as dset
import torch.nn.functional as F
from torch.autograd impor... |
4f2e4e4985787b9a7589a934be1b04b7bc9eb50b5d25c38e2c58de2fb8ba80ec | Python | 88,691 | 2,463 | # 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... |
3f6c548349604194c3c9cca64b597f7a02f7f19646a53236195707db06ae65ee | Python | 89,436 | 2,197 | """A pytorch implementation of scipy.spatial.transform.Rotation.
A container for proper and improper Rotations, that can be created from quaternions, euler angles, rotation vectors,
rotation matrices, etc, can be applied to torch.Tensors and SpatialDimensions, multiplied, and can be converted
to quaternions, euler ang... |
60ae41648c465692f5ff71ebaf388354b8680073fe47c7b63b784ecb2106ea19 | Python | 89,453 | 2,167 | # 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... |
0194f34a9ee8fb572c05f7955a41796f290b81d010acb62d5d0d5e44acc66ccd | Python | 89,468 | 1,986 | import os
import glob
import matplotlib
matplotlib.use("TKAgg")
import scipy.linalg as la
import scipy.optimize as sopt
from . import curves
from . import conjugateGradient as cg, grid, matchingParam, pointEvolution as evol, loggingUtils, bfgs
from .affineBasis import *
import matplotlib.pyplot as plt
import matplotlib... |
93fc578fc593b82c5139cf450c1a82ff35cb694febcdb7534142ff012739118d | Python | 90,023 | 2,348 | from collections import OrderedDict
from collections.abc import Iterator
from datetime import (
datetime,
timedelta,
)
from dateutil.tz import tzoffset
import numpy as np
from numpy import ma
import pytest
from pandas._libs import (
iNaT,
lib,
)
from pandas.compat import HAS_PYARROW
from pandas.errors... |
a766cc5394c7440ffcc0abea53e551d36c9595acebafe27cb68d57c78bafd612 | Python | 90,046 | 2,331 | # 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... |
8926e9ada582a044df2ca781795874e2505c7da9049f93252e97430ffc137a45 | Python | 90,414 | 2,419 | """
Tests for the file pandas.io.formats.format, *not* tests for general formatting
of pandas objects.
"""
from datetime import datetime
from io import StringIO
import re
from shutil import get_terminal_size
import numpy as np
import pytest
import pandas as pd
from pandas.io.formats import printing
import pandas.io... |
cf711b560aec5571a9ee1a3454470e75d888d47d34214b5b624dd8c62b15f56f | Python | 90,589 | 2,594 | from __future__ import annotations
import inspect
import re
from typing import (
TYPE_CHECKING,
Any,
Literal,
Self,
cast,
final,
)
import warnings
import numpy as np
from pandas._libs import (
NaT,
algos as libalgos,
internals as libinternals,
lib,
)
from pandas._libs.internal... |
e309596004ca2effa3268063dc999e3c86df68468257376368e9ffb85a7755d4 | Python | 90,694 | 2,295 | from datetime import (
datetime,
timedelta,
)
import operator
from tokenize import TokenError
import numpy as np
import pytest
from pandas.errors import (
NumExprClobberingError,
UndefinedVariableError,
)
import pandas.util._test_decorators as td
import pandas as pd
import pandas._testing as tm
from ... |
fa95767fa3b5427448c2e22032c56f2aed6dfed679c7cb4b6503fb69e739c3f5 | Python | 90,810 | 2,553 | # 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... |
97e05315c41f53e58029c943c097ada6380dafb5487ea0830f7ca2277f82cd28 | Python | 90,986 | 2,608 | from __future__ import annotations
import itertools
from typing import (
TYPE_CHECKING,
Any,
Literal,
NoReturn,
Self,
cast,
final,
)
import warnings
import numpy as np
from pandas._config.config import _global_config as config
from pandas._libs import (
algos as libalgos,
interna... |
fadcb71c8d2100e12ea0ca9a5a8c98674bb8eccc7dfa324b495a01fec586523f | Python | 91,555 | 2,308 | """Test cases for time series specific (freq conversion, etc)"""
from datetime import (
date,
datetime,
time,
timedelta,
)
import pickle
import numpy as np
import pytest
from pandas._libs.tslibs import (
BaseOffset,
to_offset,
)
from pandas.core.dtypes.dtypes import PeriodDtype
import panda... |
1f0c03d16427df77597979efd2a86dcb448e6c9f0faa7d877388bce2037af8dc | Python | 91,691 | 2,548 | from __future__ import annotations
import importlib
from typing import (
TYPE_CHECKING,
Literal,
)
from pandas._config.config import _global_config as config
from pandas.util._decorators import set_module
from pandas.core.dtypes.common import (
is_integer,
is_list_like,
)
from pandas.core.dtypes.gen... |
ef20d98d61702bade62635e768b3b315a01694be8984ebda2b6fedf350cf46dd | Python | 91,894 | 2,369 | from datetime import datetime
import struct
import numpy as np
import pytest
from pandas._libs import (
algos as libalgos,
hashtable as ht,
)
from pandas.core.dtypes.common import (
is_bool_dtype,
is_complex_dtype,
is_float_dtype,
is_integer_dtype,
is_object_dtype,
)
from pandas.core.dtyp... |
a29b0085bcee0ab2f89571480f0e07a30727342ff44c5b6504b1fe0a55cce84e | Python | 91,895 | 1,965 | #!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
Step S8 (CheckM2 branch): OLC-based reassembly of selected bins.
This module performs overlap-layout-consensus (OLC) reassembly of
bins using selected contigs to improve continuity and assembly
quality.
"""
from Bio import SeqIO
from Bio.Seq import Seq
try:
from ... |
80c499c3739d29fe981e27ff8576b3b30f6e7ffc795e9a3a3712a768f0e6a1a8 | Python | 92,181 | 2,633 | from __future__ import annotations
import itertools
from typing import (
TYPE_CHECKING,
Any,
Literal,
NoReturn,
Self,
cast,
final,
)
import warnings
import numpy as np
from pandas._config import using_python_scalars
from pandas._config.config import _global_config as config
from pandas._... |
5419b6bf1a22e3ea2543da57a1184aaea6b2119c4c931f9c947cd17cb80120ce | Python | 92,269 | 1,904 | #!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
Step S6 (CheckM2 branch): Contig retrieval from PE-supported connections.
This module retrieves additional contigs for each bin based on
paired-end connectivity and coverage patterns.
"""
import pandas as pd
# import seaborn as sns
# import matplotlib.pyplot as plt
f... |
847add1b50d79e6a0e99c5e11f7b1307097e31bec68bdd05b8e2d1022c3ff461 | Python | 92,305 | 1,074 | # -*- coding: utf-8 -*-
import numpy as np
import sys
import os
import pickle
import argparse
import math
import time
import torch
import torch.nn as nn
import torch.backends.cudnn as cudnn
import torchvision.transforms as trn
import torchvision.datasets as dset
import torch.nn.functional as F
from torch.autograd impor... |
38c07ab87a421f3c8b138be1e690c3e09e6a70786492062ef63cddad599ff630 | Python | 92,317 | 2,310 | # 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... |
a3a0ac37b1d019875dd79a0ae8065fc5561966aa765bb6fea8cdd88503396c83 | Python | 92,367 | 2,558 | from __future__ import annotations
from datetime import (
datetime,
timedelta,
)
from functools import wraps
import operator
from typing import (
TYPE_CHECKING,
Any,
Literal,
Self,
TypeAlias,
cast,
final,
overload,
)
import warnings
import numpy as np
from pandas._config impor... |
3f08fc9cbf5a5544ea23e6749ca23a1ae8d9961253c6044c210515c69c7f1a79 | Python | 92,441 | 2,391 | from datetime import datetime
import struct
import numpy as np
import pytest
from pandas._libs import (
algos as libalgos,
hashtable as ht,
)
from pandas.core.dtypes.common import (
is_bool_dtype,
is_complex_dtype,
is_float_dtype,
is_integer_dtype,
is_object_dtype,
)
from pandas.core.dtyp... |
a0c7c00825ed97600c4e7c07ea4f2849d7fc0414e43aa4f096918bc3dadcb214 | Python | 92,553 | 2,655 | """Plotting functions for AnnData."""
from __future__ import annotations
from collections import OrderedDict
from collections.abc import Collection, Mapping, Sequence
from itertools import pairwise, product
from types import NoneType
from typing import TYPE_CHECKING, NamedTuple, TypedDict, cast
import numpy as np
im... |
dd012048a4a37d4c4fa243dd314d89c4b8340f6d0917c3b1eeff2d35b5a287b4 | Python | 92,763 | 2,640 | from __future__ import annotations
import inspect
import re
from typing import (
TYPE_CHECKING,
Any,
Literal,
Self,
cast,
final,
)
import warnings
import numpy as np
from pandas._libs import (
NaT,
algos as libalgos,
internals as libinternals,
lib,
)
from pandas._libs.internal... |
27a3c4b4b7905fb685f03bf8297b265e679f098f7bd30586461097de9a5ae286 | Python | 93,294 | 1,986 | import copy
import os
import warnings
from rl_games.common import vecenv
from rl_games.algos_torch.moving_mean_std import GeneralizedMovingStats
from rl_games.algos_torch.self_play_manager import SelfPlayManager
from rl_games.algos_torch import torch_ext
from rl_games.common import schedulers
from rl_games.common.exp... |
8d3104d9a24c65c596f9a52de4686ca968a91bf6d9d3442f5966d5e6542430aa | Python | 93,400 | 2,526 | """test positional based indexing with iloc"""
from array import array as std_array
from collections import deque
from datetime import datetime
import re
import numpy as np
import pytest
from pandas.errors import IndexingError
import pandas.util._test_decorators as td
import pandas as pd
import pandas._testing as t... |
042a0b84e7c151b717003123d771d79fa305d9960fcad433ea066076626a41b2 | Python | 93,517 | 2,586 | from __future__ import annotations
from datetime import (
datetime,
timedelta,
)
from functools import wraps
import operator
from typing import (
TYPE_CHECKING,
Any,
Literal,
Self,
TypeAlias,
cast,
final,
overload,
)
import warnings
import numpy as np
from pandas._config impor... |
3e6b08df20723f8b909904fd8d9ebc1543e9c6683c139572259eea6096345aa8 | Python | 93,627 | 1,936 | # !/usr/bin/env python
'''
PyBehaviour
(c) 2015 Lloyd Russell
v2019.09.06
'''
import warnings
warnings.filterwarnings('ignore')
import matplotlib
matplotlib.use('Qt5Agg', force=True)
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.backends.backend_pdf im... |
2dda0f7be901aaf775f37a715008966327a43384159f9f41bba62278f78f1c76 | Python | 93,820 | 2,501 | """
Tests for the file pandas.io.formats.format, *not* tests for general formatting
of pandas objects.
"""
from datetime import datetime
from io import StringIO
import re
from shutil import get_terminal_size
import numpy as np
import pytest
import pandas as pd
from pandas.io.formats import printing
import pandas.io... |
770de9bc18523591daab696b646044527354802aeac4ee247a86957792d25a7d | Python | 94,991 | 2,575 | """test positional based indexing with iloc"""
from array import array as std_array
from collections import deque
from datetime import datetime
import re
import numpy as np
import pytest
from pandas.errors import IndexingError
import pandas.util._test_decorators as td
import pandas as pd
import pandas._testing as t... |
63fa71a9e2e12851029964662d58e98edbc9ea274de738e40aaf661404f1baeb | Python | 95,883 | 2,298 | # 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... |
f16675a143781be75d692757eea8f71c1178a0dd1c4d9ee40a8c453390a00f2a | Python | 95,967 | 2,580 | # 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... |
574736093622f971326297ad0429514f854f460322be04ea20a9a3e03a6faf3f | Python | 96,540 | 2,683 | # 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... |
1f0eb81cc9f9b6f3462bf4ed11e4d976bdb6811aa7aadbe512cd5fc5fd63f1d4 | Python | 97,124 | 1,982 | #!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
Step S10 (CheckM branch): OLC-based refinement after reassembly.
CheckM-specific implementation of the post-reassembly OLC elongation
and comparison step, using CheckM-informed bin quality as guidance.
"""
from Bio import SeqIO
from Bio.Seq import Seq
try:
from B... |
a96e4c887c431d432b0c9385f754e92a97131dc166a6a79fffd3b0453a4fd46c | Python | 97,284 | 2,256 | """
Tests for the parallel read_csv implementation (C engine, large local files).
The parallel path is enabled automatically when:
- reading from a local uncompressed file path
- using the C engine (the default)
- not in iterator / chunked mode
- file size >= _PARALLEL_READ_MIN_BYTES
We test correctness (para... |
afddee3662dc0266c67601c095aaefe5719a8af38b17d67575480d7c5e39d778 | Python | 97,878 | 2,648 | # cython: language_level=3
# Time-stamp: <2024-10-15 16:18:23 Tao Liu>
"""Module for BedGraph data class.
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 ... |
5d5285937c73e43f5a9b11b3170c22f6f99d5557e0b36738d4bf570d8a134a85 | Python | 98,025 | 3,061 | from datetime import datetime
import decimal
from decimal import Decimal
import re
import numpy as np
import pytest
from pandas.errors import (
Pandas4Warning,
SpecificationError,
)
import pandas as pd
import pandas._testing as tm
from pandas.core.arrays import BooleanArray
import pandas.core.common as com
... |
215f2da960dcb3f725687b4345e57a3b1327a017eac2b9748518297481de9f45 | Python | 98,318 | 2,629 | # Arithmetic tests for DataFrame/Series/Index/Array classes that should
# behave identically.
from datetime import (
datetime,
timedelta,
)
import operator
import numpy as np
import pytest
from pandas._libs.tslibs import (
iNaT,
timezones,
)
from pandas.compat import WASM
from pandas.errors import (
... |
d9b427c90256b5e9462cfa31ac1a59791e3cfd2eb01631408b13bf9b7d6b26d7 | Python | 98,357 | 2,452 | """The PyCaret 4.0 `Experiment` base class — a real sklearn-compatible object.
Design rationale in `docs/revamp/ARCHITECTURE.md`.
Two concrete guarantees this class delivers:
1. **It's a `BaseEstimator`.** `get_params`, `set_params`, `__sklearn_tags__`,
`__sklearn_is_fitted__`, HTML repr, `clone` — all work.
2. *... |
2fbfe173e3211d54dafad22cc5f10082a4393e9f80e65c9eedb801c9bd89b78d | Python | 98,464 | 2,301 | # 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... |
67832da1459b698c2367ad322206216aa697e658a006776252ccfddfa1373b5f | Python | 98,951 | 1,928 | # -------------------------------------------------------------------------------------------------------------------------------------
# Following code curated for GCPNet (https://github.com/BioinfoMachineLearning/GCPNet):
# ----------------------------------------------------------------------------------------------... |
8da8bce86b8cb4a575592d774756a86b48d5ef0fd144478495326c1ddd209236 | Python | 98,989 | 2,512 | """Classes for plotting results.
CLASSES
-------
Plotting : Abstract Base Class
- Abstract class for plotting results.
LinePlot : subclass of Plotting
- Class for plotting results on line plots.
BoxPlot : subclass of Plotting
- Class for plotting results on box plots.
"""
from abc import ABC, abstractmethod
f... |
4ae7f9be9657f716c85448e8f0238802b17a5dcb2b48fb5c0a6ef03747231f33 | Python | 99,119 | 2,096 | #!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
Step S10 (CheckM2 branch): OLC-based refinement after reassembly.
This module performs an additional round of overlap-layout-consensus
based elongation and comparison on bins generated by previous steps,
further improving contiguity and resolving ambiguous contigs.
""... |
542ee5cbe49e05257f17afbfaacc6596c8a1a8fa394a64369fd0dadb21a3539a | Python | 99,120 | 2,953 | # Written by i3s
import os
import numpy as np
from sklearn.preprocessing import OneHotEncoder
import pandas as pd
import seaborn as sns
import time
from sklearn.model_selection import KFold
from matplotlib import pyplot as plt
from sklearn.svm import SVC
from sklearn.ensemble import RandomForestClassifier, AdaBoostC... |
3c1fe2923f5032a612b3d466e9d4e5c655547d6c4fa41da5709e838611d55b1b | Python | 99,688 | 2,839 | # 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... |
827615a54230692258a79bb02c921e0a97a99c1f20aa72b48d91e33118c50166 | Python | 101,152 | 3,148 | from datetime import datetime
import decimal
from decimal import Decimal
import re
import numpy as np
import pytest
from pandas.errors import (
Pandas4Warning,
SpecificationError,
)
import pandas as pd
import pandas._testing as tm
from pandas.core.arrays import BooleanArray
import pandas.core.common as com
f... |
8a8d424663ecfdada1b429daa2ecf80532f9e408697824818b1854f8189df015 | Python | 101,187 | 1,922 | # -*- coding: utf-8 -*-
"""
Created on Tue May 10 15:16:26 2022
@author: s mellor
"""
import matplotlib.pyplot as plt
import numpy as np
import scipy.io
import scipy.spatial.distance
from scipy.optimize import curve_fit
import seaborn as sns
import pandas as pd
from mpl_toolkits.axes_grid1.inset_locator import inset_... |
c17bce76b181ee6ed1de6453227b55d0902c9274648407708b3975ea9eb9d706 | Python | 101,196 | 2,732 | from __future__ import annotations
from collections import defaultdict
from collections.abc import (
Callable,
Mapping,
Sequence,
)
from functools import partial
import pathlib
import re
from typing import (
TYPE_CHECKING,
Any,
TypeAlias,
TypedDict,
)
from uuid import uuid4
import numpy as... |
53d6a65bd3452684e7cccb6c74246829231cbceaa487b3a8a01f8d3ec7ea5fa4 | Python | 101,201 | 2,708 | import os
import torch
import torchaudio
from torch import nn
from torch.nn import functional as F
from torch.nn.parameter import Parameter
import numpy as np
import utils.lreq as ln
import utils.lreq_causal as ln_c
from utils.registry import *
from modules.Swin3D_blocks import *
device = 'cuda' if torch.cuda.is_avail... |
c0a9225c9d6e4bf5269768e3c2bad51c1035bd71598f005929b5f94e351eeb14 | Python | 101,338 | 2,700 | # Arithmetic tests for DataFrame/Series/Index/Array classes that should
# behave identically.
# Specifically for datetime64 and datetime64tz dtypes
from datetime import (
UTC,
datetime,
time,
timedelta,
)
from itertools import (
product,
)
import operator
import numpy as np
import pytest
from pand... |
e36121a4fca45982828da24d09ad1a4b7427e32035fdd5689335afd0c5fdb3a7 | Python | 101,496 | 2,563 | """Base controller to make clustering GUIs."""
# ------------------------------------------------------------------------------
# Imports
# ------------------------------------------------------------------------------
import inspect
import logging
import os
import shutil
from functools import partial
from pathlib i... |
a9f34fc86f1b99ec9f8d11ac89ed58fe058f097e86c0e02786458d9bf3e8aaf2 | Python | 102,307 | 1,347 | """
Wrapper for freesurfer scripts to be run on <subjects_dir>/<subjid>. Includes pipeline template parameters as
proc_pipeline_name, and methods as run(), and proc2metric().
"""
from shutil import rmtree, which
from glob import glob
import subprocess
import numpy as np
import os
import re
from scanometrics.utils imp... |
dd64d102700b05441c336ed1061ea8f4f7d28b04442ff6138f71803b049a480e | Python | 102,504 | 3,277 | import math
import torch
import torch.nn as nn
# ``predict/_pred_utils`` imports ``..models`` in turn, so these two lines close a cycle.
# It holds because ``_pred_utils`` only takes names ``models/__init__`` has already bound
# from ``_base_models`` by the time this module runs; importing a name defined here would
#... |
45ae2f3c23cb94ceca315b9fb5db78763308482aa45df363589e388267af09ad | Python | 102,848 | 2,446 | # 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... |
57c843b4eb8a0a46add62e0f042bf3a0c56a2b63983539b681f5704fc73e5c6c | Python | 103,229 | 1,979 | import os
import traceback
import warnings
import sys
import settings
import matplotlib.pylab as plt
import matplotlib.ticker as ticker
import pandas as pd
from scipy import stats
from scipy import signal
from astropy.timeseries import LombScargle
from astropy.convolution import convolve, Gaussian1DKernel
from astro... |
e84bfa6574cc5dfc2e1d3aeb3b22f323a263c244735099255c9a97e1dfefbee8 | Python | 103,473 | 1,448 | # 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... |
edfac934748a37eb1ac663cc43359f17153b8b6aa958aa4aa8f81e48a69bc7b1 | Python | 103,559 | 2,790 | from __future__ import annotations
from collections import defaultdict
from collections.abc import (
Callable,
Mapping,
Sequence,
)
from functools import partial
import pathlib
import re
from typing import (
TYPE_CHECKING,
Any,
TypeAlias,
TypedDict,
)
from uuid import uuid4
import numpy as... |
bbc3a1cc1383c4e108f116b990d94817d6319541ba5334bae67239c4f1306ab4 | Python | 103,609 | 2,697 | """Test cases for DataFrame.plot"""
from datetime import (
date,
datetime,
)
from decimal import Decimal
import itertools
import re
import string
import numpy as np
import pytest
import pandas.util._test_decorators as td
from pandas.core.dtypes.api import is_list_like
import pandas as pd
import pandas._tes... |
0ee3940973566a2fe15823866808f6615af510cc9a8e56471abe692b2ec096eb | Python | 104,025 | 1,289 | import sys
import re
import copy
import tree
import lex
## Flags mutable by command-line arguments...
VERBOSE = False ## print debugging info.
ANAPH = True ## apply anaphor expansions.
SKIPS = [] ## skip articles.
ONLY = -1 ## print debugging info only for certain articles.
## Process comman... |
975865a336f2d08b786c9ddb9a9eb70c3dc6c3e89b92fdba370626902b020632 | Python | 104,370 | 2,751 | import datetime
from datetime import timedelta
import errno
from io import (
BytesIO,
StringIO,
)
import json
import os
from pathlib import Path
import re
import sys
from urllib.error import HTTPError
import uuid
import numpy as np
import pytest
from pandas._config import using_string_dtype
from pandas.compa... |
d03eda4bf7b8b245300dbfdae584650ad34a84762896ba64486d24293461b8dd | Python | 104,629 | 2,618 | """Test cases for time series specific (freq conversion, etc)"""
from datetime import (
date,
datetime,
time,
timedelta,
)
import pickle
import numpy as np
import pytest
from pandas._libs.tslibs import (
BaseOffset,
to_offset,
)
from pandas.core.dtypes.dtypes import PeriodDtype
import panda... |
66dc0c9c78bfd59a1f8ae0302758595d0f96b8b749fe217ab99332002d3e25ca | Python | 105,529 | 3,243 | from __future__ import annotations
import copy
from typing import (
TYPE_CHECKING,
Concatenate,
Literal,
Self,
cast,
final,
no_type_check,
overload,
)
import warnings
import numpy as np
from pandas._libs import lib
from pandas._libs.tslibs import (
BaseOffset,
IncompatibleFreq... |
2e5f1e79d11680c718040933e8eb33a4bcf2109d70298973b8978eba1ac0b3bf | Python | 105,794 | 2,912 | from __future__ import annotations
import datetime as dt
import operator
from typing import (
TYPE_CHECKING,
Self,
)
import warnings
import numpy as np
from pandas._libs import (
NaT,
Period,
Timestamp,
index as libindex,
lib,
)
from pandas._libs.tslibs import (
Resolution,
Tick,
... |
7cd1687beca70acbed0328ea2470062fd2a555b47c1b36652ee4bbd45f5bdc2a | Python | 105,858 | 2,913 | from __future__ import annotations
import datetime as dt
import operator
from typing import (
TYPE_CHECKING,
Self,
)
import warnings
import numpy as np
from pandas._libs import (
NaT,
Period,
Timestamp,
index as libindex,
lib,
)
from pandas._libs.tslibs import (
Resolution,
Tick,
... |
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