sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
bfd54fc68d3dde827615e9ea2ccbd0927fc52811fbdb34700acb34cbdcd5c70e | Python | 19,611 | 570 | import numpy as np
import scipy
import scipy.stats
import scipy.sparse
from sklearn.decomposition import PCA,TruncatedSVD
from sklearn.neighbors import NearestNeighbors
import time
########## PREPROCESSING PIPELINE
def print_optional(string, verbose=True):
if verbose:
print(string)
return
def pipeli... |
32a41183ee2bacadb014208ba53e80a858fa96e9f81826bc36ea66aa0c8b31b7 | Python | 19,634 | 531 | #!/usr/bin/env python3
import argparse
import gzip
import logging
import os
import subprocess
import sys
import shims
assert sys.version_info.major >= 3, 'Python 3 required'
version = shims.get_module_or_shim('utillib.version')
SCRIPT_DIR = os.path.dirname(os.path.realpath(__file__))
DESCRIPTION = """Run the entire Du... |
ab45bc07a9aff66d1eed12d57ed2297aeb7c2f317991a83bbc5d9e004cc8c05f | Python | 19,641 | 432 | # YOLOv5 🚀 by Ultralytics, GPL-3.0 license
"""
PyTorch utils
"""
import math
import os
import platform
import subprocess
import time
import warnings
from contextlib import contextmanager
from copy import deepcopy
from pathlib import Path
import torch
import torch.distributed as dist
import torch.nn as nn
import torc... |
abaad64dad3a1f3a5b1f0c4a136d6432a50ac6ed4c389bf0818aaaa811b56f9f | Python | 19,645 | 558 | # -*- coding: utf-8 -*-
"""
Created on Thu Mar 9 10:19:35 2023
@author: lindseyb
"""
import numpy as np
from sklearn.linear_model import LinearRegression
from sklearn.metrics import roc_auc_score
import matplotlib.pyplot as plt
import matplotlib
matplotlib.rcParams['pdf.fonttype'] = 42
matplotlib.rcParams['ps.fontty... |
77b13810494f800f296a07a7f7357f8da3c3c5ec6c40f50e8bb7b3ba7b3314dc | Python | 19,666 | 544 | import numpy as np
import pytest
from pytest_lazyfixture import lazy_fixture as lf
import tensorflow as tf
from scipy.linalg import expm
import tensorcircuit as tc
F = tc.fgs.FGSSimulator
FT = tc.fgs.FGSTestSimulator
@pytest.fixture
def requires_openfermion():
pytest.importorskip("openfermion")
@pytest.mark.p... |
d76daed86be1d317305b96f1d71c9d694c9fdea92039aec798a212d351b8eb03 | Python | 19,672 | 551 | """Integration tests for multi-well bar plots - verify actual plot data."""
from __future__ import annotations
from typing import TYPE_CHECKING
import pytest
from pyqtgraph import BarGraphItem
from qtpy.QtWidgets import QWidget
from sqlalchemy.exc import OperationalError
from sqlmodel import Session, create_engine, ... |
071621f5868b3e965caa5a93d1c4df73c5192f9625dba82f540a7e7a79645d17 | Python | 19,689 | 571 | import sys
import os
import numpy as np
import pytest
from pytest_lazyfixture import lazy_fixture as lf
from scipy.optimize import minimize
thisfile = os.path.abspath(__file__)
modulepath = os.path.dirname(os.path.dirname(thisfile))
sys.path.insert(0, modulepath)
import tensorcircuit as tc
from tensorcircuit.noisemod... |
549ed8d4d2fe5da5f21cfcf8a137fc2311d557bd9eb5782bbda3651192df4cbb | Python | 19,695 | 428 | import logging
import time
from pathlib import Path
import cv2
from PySide6.QtCore import QObject, QThread
from app.config.camera import CameraConfig
from app.config.grimace import GrimaceConfig
from app.config.pose_top import PoseTopConfig
from app.config.recording import RecordingConfig
from app.config.video_files ... |
24f9fc992a3b1524ee15a1f3a6210b8150704ecaa68c848b9c6a31968cba4a35 | Python | 19,699 | 573 | import re
import numpy as np
import pytest
import pandas.util._test_decorators as td
import pandas as pd
from pandas import (
Categorical,
CategoricalDtype,
CategoricalIndex,
DataFrame,
Index,
Interval,
Series,
Timedelta,
Timestamp,
option_context,
)
import pandas._testing as ... |
2b4610006846c9a2bf8f9b663fd21b431f333b9e880fd1a16d3693f6ffb74f53 | Python | 19,726 | 556 | from datetime import datetime
import numpy as np
import pytest
from pandas.core.dtypes.cast import find_common_type
from pandas.core.dtypes.common import is_dtype_equal
import pandas as pd
from pandas import (
DataFrame,
Index,
MultiIndex,
Series,
)
import pandas._testing as tm
class TestDataFrameC... |
85f71875abcd79e0db8988ef4c1a8303a3891f11f57ee34374cb536548b74598 | Python | 19,733 | 546 | import functools
import warnings
import operator
import types
import numpy as np
from . import numeric as _nx
from .numeric import result_type, nan, asanyarray, ndim
from numpy._core.multiarray import add_docstring
from numpy._core._multiarray_umath import _array_converter
from numpy._core import overrides
__all__ = ... |
5c32dc798ec16f158db1e1b46075fcbac87429cf5f8f7564ad579bf6c7b2bc25 | Python | 19,742 | 425 | """
Author: Bertrand Thirion, 2015
Modified by: Swetha Shankar, 2021
"""
import os
import glob
import numpy as np
import nibabel as nib
import matplotlib.pyplot as plt
from ibc_public.utils_data import get_subject_session
from joblib import Memory, Parallel, delayed
source_dir = '/storage/store2/data/ibc/sourcedata'
... |
a12060aa0df977c85033b850770ded55ae896299e1e567f627d098ab2e1cbbef | Python | 19,765 | 487 | #!/usr/bin/env python3
import argparse as arp
def make_parser():
prs = arp.ArgumentParser()
parser = arp.ArgumentParser()
subparsers = parser.add_subparsers(dest = 'command')
run_parser = subparsers.add_parser("run",
formatter_class=arp\
... |
4671d2dc7cf42d228c9bb8f8ffa096d8f0013065177e7b1f89e0aa7e665a5044 | Python | 19,814 | 585 | import torch
import torch.nn as nn
import copy
from protgps.models.abstract import AbstractModel
from protgps.utils.classes import set_protgps_type
from protgps.utils.registry import register_object, get_object
from torch.nn.utils.rnn import pad_sequence
import functools
@register_object("fair_esm", "model")
class Fa... |
75925861261e1a4b86adf74df54a09ee55927f7d375413324ec5c5deec9c5c46 | Python | 19,821 | 517 | ## ...........................................................................
##
## PIMMS (Polymer Interactions in Multicomponent Mixtures)
## Alex Holehouse, Pappu Lab, Holehouse Lab
## Copyright 2015 - 2026
## ...........................................................................
import numpy as np
import c... |
4570fae168a31f407b66086b39ad14f26a9d40c016626939277fe4ef44fe5796 | Python | 19,831 | 637 | """
QAOA portfolio selection with fund NAV data fetched by xalpha.
The example chooses one representative fund for each requested exposure:
- 110020: 易方达沪深300ETF联接A
- 090010: 大成中证红利指数A
- 110026: 易方达创业板ETF联接A
- 000307: 易方达黄金ETF联接A
- 270042: 广发纳斯达克100ETF联接人民币(QDII)A
"""
from __future__ import annotations
import argpa... |
727d053de878a0a469234a34d6d171db854ea0d42bf7418288a20ca3c701684d | Python | 19,840 | 589 | import numpy as np
import pytest
from pandas.errors import SettingWithCopyError
import pandas.util._test_decorators as td
import pandas as pd
from pandas import (
DataFrame,
MultiIndex,
Series,
date_range,
isna,
notna,
)
import pandas._testing as tm
def assert_equal(a, b):
assert a == b
... |
8aadf82118fdc23877d65b90157ee8b66a99960b00f7ff3865416164f2f86a42 | Python | 19,852 | 469 | """Networks_ide.py - Model and module class for EfficientNet.
They are built to mirror those in the official TensorFlow implementation.
"""
# Author: lukemelas (github username)
# Github repo: https://github.com/lukemelas/EfficientNet-PyTorch
# With adjustments and added comments by workingcoder (github username).
... |
4c70970e5446ec09dc5f9c33465a7dc3544dad80346d3a569b312b3157d3d3ec | Python | 19,853 | 535 | from functools import partial
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
from pandas import (
Categorical,
CategoricalDtype,
CategoricalIndex,
Index,
... |
fa71632943581bffa027a46965b5a7c7f4c996691101a800ec09d569ff5825f2 | Python | 19,855 | 493 | # pylint: disable-msg=W0611, W0612, W0511,R0201
"""Tests suite for mrecords.
:author: Pierre Gerard-Marchant
:contact: pierregm_at_uga_dot_edu
"""
import pickle
import numpy as np
import numpy.ma as ma
from numpy.ma import masked, nomask
from numpy.testing import temppath
from numpy._core.records import (
recarr... |
0ac8444d589b674febc1b36ad32eec3e4cd28275e9c08ec552dbc08fc79f53a4 | Python | 19,861 | 639 | from __future__ import annotations
import mmap
from typing import (
TYPE_CHECKING,
Any,
cast,
)
import numpy as np
from pandas.compat._optional import import_optional_dependency
from pandas.util._decorators import doc
from pandas.core.shared_docs import _shared_docs
from pandas.io.excel._base import (
... |
13197cd48a321863d8b75373da2a4943bf5c0d7aa55599c9b85842b887cab794 | Python | 19,878 | 604 | from datetime import (
datetime,
timezone,
)
import numpy as np
import pytest
from pandas._libs.tslibs import iNaT
from pandas.compat import (
is_ci_environment,
is_platform_windows,
)
from pandas.compat.numpy import np_version_lt1p23
import pandas as pd
import pandas._testing as tm
from pandas.core.... |
22fcb71ba316e377cb318c169fd41d13dc174712eba45f0816852907e4e99427 | Python | 19,879 | 501 | import re
import numpy as np
import pytest
from pandas.compat import PY311
from pandas import (
Categorical,
CategoricalIndex,
DataFrame,
Index,
Series,
StringDtype,
)
import pandas._testing as tm
from pandas.core.arrays.categorical import recode_for_categories
class TestCategoricalAPI:
... |
536af5fe0ff5cd28ec8e251d00449cda200c7378b8ae2fd2f0f60fea4439cf52 | Python | 19,919 | 482 | """
Spinners are from:
* cli-spinners:
MIT License
Copyright (c) Sindre Sorhus <sindresorhus@gmail.com> (sindresorhus.com)
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 withou... |
56116f76d7ed957ea0e9aa01e1bcbdf57aaf7ee1daa250f5fbc96153ae0db055 | Python | 19,938 | 597 | import json
from pathlib import Path
from unittest.mock import patch
import numpy as np
import pytest
import tensorstore as ts
import tifffile
import useq
import zarr
from useq import MDASequence, WellPlatePlan
from cali.readers._ome_zarr_reader import OMEZarrReader
from cali.readers._tensorstore_zarr_reader import T... |
e27fbb04ade27371aa798da1a47ed4c4adc2bec629ef46dfa968c1e0734f8297 | Python | 19,944 | 450 | import warnings
import os
import torch
from torch import nn
import torch.nn.functional as F
from torch_scatter import scatter
from e3nn.nn import Gate
from e3nn.o3 import Irreps, Linear, SphericalHarmonics, FullyConnectedTensorProduct
from .from_nequip.cutoffs import PolynomialCutoff
from .from_nequip.radial_basis impo... |
b2974fda4999155d1589305448802e844073320e58238f286a6dfe5fc4ac15c1 | Python | 19,945 | 589 | import warnings
from collections import Counter
from typing import Dict, Literal, Optional
import numpy as np
import pandas as pd
from scipy.sparse import coo_matrix, issparse
from anndata import AnnData
from scanpy import Neighbors
from scanpy.preprocessing import pca
from scvelo import logging as logg
from scvelo ... |
09edb040770d577dea9e47876ce4638be496e794671d0daf51d1972b56152419 | Python | 19,956 | 580 | import os
from os.path import join
import sys
import numpy as np
from numpy.testing import (assert_equal, assert_allclose, assert_array_equal,
assert_raises)
import pytest
from numpy.random import (
Generator, MT19937, PCG64, PCG64DXSM, Philox, RandomState, SeedSequence,
SFC64, defa... |
2cc0f488b13a9431029f7986d344208b9c399047cbddc039710bde2646630b21 | Python | 19,956 | 499 | import datetime
import logging
import pathlib
import base64
import time
import streamlit as st
from utils.auth_utils import login_user, register_user, get_user_details, logout, forgot_password
from utils.account_utils import update_user_query_limits, update_user_openai_key_api
import kani_utils.kani_streamlit... |
a5484d354c4b06fe3f0fe976b6c1c8085893e6bb838ef963db8a0490d6727319 | Python | 19,972 | 709 | from datetime import (
datetime,
timedelta,
)
import operator
import numpy as np
import pytest
import pytz
from pandas._libs.tslibs import iNaT
from pandas.compat.numpy import np_version_gte1p24p3
from pandas import (
DatetimeIndex,
DatetimeTZDtype,
Index,
NaT,
Period,
Series,
Tim... |
bed0e56dd1613b443fc52a3f090c09401713617593816594cdd8e1732094ab59 | Python | 19,976 | 533 | import math
import torch
import torch.nn as nn
from torch import einsum
import torch.nn.functional as F
import matplotlib.pyplot as plt
from einops import rearrange, repeat, reduce
from einops.layers.torch import Rearrange
from dropout import *
def init_weights(m):
#print(m)
if m is not None and isinstance(m,... |
2e6d260aca47949f26230df3707ee976d7e4ade6ee98d782d3c138aa640abafe | Python | 19,983 | 575 | ## ...........................................................................
##
## PIMMS (Polymer Interactions in Multicomponent Mixtures)
## Alex Holehouse, Pappu Lab, Holehouse Lab
## Copyright 2015 - 2026
## ...........................................................................
# Functions for creating and... |
e5e1212f4109f143928203b9da8836bb4c0d8c9d4c0aa9c58ab6bb34bdc9bad7 | Python | 19,985 | 372 | ##Sulcal phenotype measurement functions that require brainvisa's python distribution
##Note that trimesh must be installed by entering into BrainVISA's bash distribution
##(e.g., `bv bash`) and using `pip install trimesh`
#load in relevant modules
from soma import aims, aimsalgo
import numpy as np
import pandas as pd... |
696ca15d1b4d3b82549c249556a29329077c1174ef526d5537da60b366dc38da | Python | 19,990 | 540 | from __future__ import absolute_import
import collections
import functools
import logging
from ._collections import HTTPHeaderDict, RecentlyUsedContainer
from .connectionpool import HTTPConnectionPool, HTTPSConnectionPool, port_by_scheme
from .exceptions import (
LocationValueError,
MaxRetryError,
ProxySc... |
0a7dfc37ee48c564b68deb2285581bfff3dab8a2d3ab6067bbd771ded70e3204 | Python | 20,040 | 394 | import collections
import itertools
import os
import json
import warnings
import torch
from torch_geometric.data import Data, Batch
import numpy as np
import h5py
from .from_pymatgen.lattice import find_neighbors, _one_to_three, _compute_cube_index, _three_to_one
from .utils import flt2cplx
class Collater:
def ... |
857dbc87718ab849bee6b6ff0f15ee7d9d9b94424c4192155070a778fadd56c5 | Python | 20,043 | 505 | #!/usr/bin/env python3.7
"""Defines Waveform class.
The copyrights of this software are owned by Duke University. Please
refer to the LICENSE and README.md files for licensing instructions. The
source code can be found on the following GitHub repository:
https://github.com/wmglab-duke/ascent
"""
import csv
import ma... |
24132b9928b6c968ce5f4c00ee88805d96ca2def54fc36225ff14e480452556c | Python | 20,044 | 506 | #!/usr/bin/env python3.7
"""Defines Waveform class.
The copyrights of this software are owned by Duke University. Please
refer to the LICENSE and README.md files for licensing instructions. The
source code can be found on the following GitHub repository:
https://github.com/wmglab-duke/ascent
"""
import csv
import ma... |
84bd9f1de654a02afbfb6b5a114fc62102ca53254a080441b1aca0649d16b651 | Python | 20,045 | 377 | import os
from collections import namedtuple
from typing import List, Tuple, Optional, Union
import numpy as np
import torch
import torchmetrics
from torchmetrics.classification import Accuracy
from pytorch_lightning import LightningModule
import src.audio_transforms as at
import src.audio_attention_transforms as aat... |
9d06c37021f5200b40e651c3e6b904c7eb71064165204d54f6002f1367effe09 | Python | 20,118 | 475 | """
Script used to perform retinotopic analysis based on the IBC low-level visual
protocol.
Author: Bertrand Thirion, 2015--2017
"""
import os
import glob
from os.path import join as pjoin
import numpy as np
from nilearn.image import mean_img, math_img
from ibc_public.utils_retino import phase_maps
import nibabel as n... |
7a7944afc85a33f86abfe76cca6347a4872a8c6db052902d12dde31ec706e172 | Python | 20,120 | 573 | """Utility functions for xarray objects."""
import warnings
import numpy as np
import pint
import xarray as xr
import scipy.sparse
def pinv(array: xr.DataArray) -> xr.DataArray:
"""Calculate the pseudoinverse of a 2D xr.DataArray.
FIXME: handles unitless and quantified DataArrays but not
DataArr... |
f00eeac6c220560742f7e3ff582964bc859b44e6c17786b0d877fbf1e972c787 | Python | 20,120 | 548 | import numpy as np
import pytest
from pandas._config import using_pyarrow_string_dtype
from pandas.errors import ChainedAssignmentError
import pandas.util._test_decorators as td
from pandas import (
DataFrame,
NaT,
Series,
date_range,
)
import pandas._testing as tm
class TestDataFrameInterpolate:
... |
b3250d72c0be025385a1fa01c31508d557fa14245ec81bd9fc01f2be9b8659ab | Python | 20,130 | 619 | """
Requirements file parsing
"""
from __future__ import annotations
import codecs
import locale
import logging
import optparse
import os
import re
import shlex
import sys
import urllib.parse
from collections.abc import Generator, Iterable
from dataclasses import dataclass
from optparse import Values
from typing impo... |
4c2d807fa800e0e9112310d35b2ff98e61cd22b82ca961a639517bd3bc0e9fc3 | Python | 20,152 | 514 | import operator
import numpy as np
import pytest
import pandas as pd
from pandas import SparseDtype
import pandas._testing as tm
from pandas.core.arrays.sparse import SparseArray
@pytest.fixture(params=["integer", "block"])
def kind(request):
"""kind kwarg to pass to SparseArray"""
return request.param
@p... |
9651c92a0565393b0e56f560e489dd73b7c8978922c8ab299e05376c9a1ce420 | Python | 20,167 | 658 | import hashlib
import importlib.util
import re
import shutil
import subprocess
import sys
from pathlib import Path
from tempfile import mktemp
import click
import spin
# tomllib is built in on Python 3.11+, and spin depends on tomli for older versions.
if sys.version_info >= (3, 11):
import tomllib
else:
imp... |
31c103683c69d04603fe24afa70ead481e84c2badc509c41f8b11e0c0d346a4b | Python | 20,202 | 502 | """FOV-level analysis functions for computing correlation and synchrony matrices.
This module provides functions to compute pairwise correlation and synchrony
matrices across all active ROIs in a FOV, as well as population-level burst
detection. These metrics are computed once during analysis and stored in the
FOVAnal... |
21811f4c6894784011b9c5f5ef49707d9f6c41e372e589f351b9067c55649594 | Python | 20,217 | 521 | """Unit tests for nb_glm_fast.py and the gcate_glm backend toggle."""
from __future__ import annotations
import math
import warnings
from unittest.mock import patch, MagicMock
import numpy as np
import pytest
import scipy.sparse as sp
import causarray.gcate_glm as gcate_glm
from causarray.nb_glm_fast import (
_m... |
2a23fb9a52a9555ef5c31525aa376a4b259abf127cd1861fe929ffa28ebe027a | Python | 20,237 | 465 | import os
import time
import pickle
import numpy as np
import torch
import nrrd
import pandas as pd
import wandb
from tqdm import tqdm
from scipy.spatial import cKDTree
from monai.data import decollate_batch, MetaTensor
from monai.metrics import DiceMetric, CumulativeAverage
from monai.inferers import sliding_window... |
99cdbcfc9f034064682cc965564b66971353d66795a0738865c9ef54bc2db37f | Python | 20,240 | 492 | """Various plots, candidates and helpers for paper figures."""
from itertools import product
import numpy as np
from matplotlib import pyplot as plt
from matplotlib import gridspec as gs
import seaborn as sns
import pandas as pd
from src import simulations as sims
from src import utils
from src import analyses as ana... |
20e924e4c8823976d05a7afaff12918a2634caeb7d328a14c916de667cfd0042 | Python | 20,277 | 536 | from typing import Dict, List
import numpy as np
import pytorch_lightning as pl
import torch
from e3nn import o3
from e3nn.o3 import Linear
from torch import nn
from torch.optim import Optimizer
from torch.optim.lr_scheduler import LRScheduler
from torch_cluster import radius_graph
from torch_geometric.data import Dat... |
23ab71edf8e11d30b181d51e9e3a746d1a158da87813e7e206673117fba443b3 | Python | 20,282 | 406 | # YOLOv5 🚀 by Ultralytics, GPL-3.0 license
"""
Validate a trained YOLOv5 detection model on a detection dataset
Usage:
$ python val.py --weights yolov5s.pt --data coco128.yaml --img 640
Usage - formats:
$ python val.py --weights yolov5s.pt # PyTorch
yolov5s.torch... |
0865a8396a154fa4d35c3e8c99152bfb38eacef5b0a6ae8709967adbdd0131cb | Python | 20,295 | 641 | try:
import vtk
VTK_INSTALLED = 1
except ImportError as e:
VTK_INSTALLED = 0
import numpy as np
from scipy.sparse.linalg import cg # ,spilu,LinearOperator
from scipy.sparse import eye, spdiags, csc_matrix, vstack # , diags
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.tri as mtri
import matpl... |
b6d200f74f41adb4d4cf092a11efd3cd9561e0938e8fb83ad58b1e8b69abc068 | Python | 20,314 | 572 | from __future__ import absolute_import
import datetime
import logging
import os
import re
import socket
import warnings
from socket import error as SocketError
from socket import timeout as SocketTimeout
from .packages import six
from .packages.six.moves.http_client import HTTPConnection as _HTTPConnection
from .pack... |
49820b17ad502bd038e34c5d0fd710a1d8fb858bdf6450a78ea1fce03ae6f4c9 | Python | 20,326 | 548 | import torch.nn as nn
import torchvision.models as models
import numpy as np
import os
from sklearn.utils import shuffle
import torch
import torch.nn.functional as F
class Appr(object):
""" Class implementing the TALL """
def __init__(self, pretrained_feat_extractor, num_task, torc,device='cuda', args=None):
... |
a8d49417edad9ff283a224dc24cb80860e190739974363e50a72ec702f69e81e | Python | 20,328 | 419 | # -*- coding: utf-8 -*-
import os
import csv
import numpy as np
import dirfiles
from confparser import load_config
from score import calc_score
import expyriment
from expyriment import design, control, stimuli, io, misc
def protocol(protocol_ini, exp, island):
# %%
# ======================== LOAD CONFIG.IN... |
71ef88acef6294823be8b1a4537e78a4e7476dea4cf147ed7cd1fb49f314ff6f | Python | 20,330 | 624 | import os
import re
import sys
import typing as t
from functools import update_wrapper
from types import ModuleType
from types import TracebackType
from ._compat import _default_text_stderr
from ._compat import _default_text_stdout
from ._compat import _find_binary_writer
from ._compat import auto_wrap_for_ansi
from .... |
0ef923ffeece928002cf27047a199a6e0bdbaa9a7e82e0d6861163a2adc81b28 | Python | 20,353 | 548 | import numpy as np
import pytest
from pimms import lattice_utils
from pimms.latticeExceptions import (
ChainConnectivityError,
ChainDeletionFailure,
ChainInsertionFailure,
ClusterSizeThresholdException,
LatticeUtilsException,
ResidueAugmentException,
RotationException,
)
class _DummyChain... |
e35453983facb906c29d98e915c1b9e95948c7564ff91782fa3e58221a49dd60 | Python | 20,362 | 546 | import re
import numpy as np
import pytest
from pandas.errors import PerformanceWarning
import pandas as pd
from pandas import (
DataFrame,
DatetimeIndex,
Index,
MultiIndex,
Series,
Timestamp,
)
import pandas._testing as tm
@pytest.mark.parametrize(
"msg,labels,level",
[
(r"... |
6692acbdddcfde9da1c1f8fab0794bfe5cac269d487af02833a01da5e4c0c7c3 | Python | 20,368 | 553 | import pytest
import numpy as np
from numpy.testing import (
assert_, assert_equal, assert_array_equal, assert_almost_equal,
assert_array_almost_equal, assert_raises, assert_raises_regex,
)
from numpy.lib._index_tricks_impl import (
mgrid, ogrid, ndenumerate, fill_diagonal, diag_indices, diag_indices_f... |
b4ac44f4c84ce0a70eee8d69f02fd96cc21523cb623491c699ac0d8b1e1c0887 | Python | 20,368 | 450 | parent_path = r'/.../baselines'
import sys
sys.path.append(parent_path)
from torch.utils.data import DataLoader
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from tqdm import tqdm
from torch.optim import SGD
from torch.optim.lr_scheduler import MultiStepLR
from utils import ABIDE... |
8406ffc7dd6b1836d84906b28e6c29816e1c0187e8102cfce48ffb5befd06ca6 | Python | 20,399 | 468 | import sys
import os
import re
import time
import random
import math
import numpy as np
import copy
from boundslist import *
from network import *
from parseinputs import *
from deephuntermutators import *
def get_covprop_helper(grid):
#recursive: for each elem in grid, if it is a number then check 1 or 0, otherw... |
d02566f6f87488ba38d6289901e8a6922e7c0d7a99958655c22c391c850bc54f | Python | 20,407 | 458 | import time
from .util import get_data, normalize_index
from .psenacutil import extend_phyche_index, get_phyche_index, make_pseknc_vector, make_old_pseknc_vector
def check_psenac(lamada, w, k):
"""Check the validation of parameter lamada, w and k.
"""
try:
if not isinstance(lamada, int) o... |
2c8f3a494f1853fa1c7a7ed87f063d72d3c29a133d8bd3d89782cf2118aa6917 | Python | 20,415 | 457 | import numpy as np
import pandas
import matplotlib.pyplot as pl
import math
import matplotlib as mpl
from matplotlib import cm
from sklearn.discriminant_analysis import LinearDiscriminantAnalysis
from sklearn.metrics import accuracy_score
from sklearn.model_selection import train_test_split
from sklearn.decomposition ... |
768fe005319110076bb7415646ecfb8d46a6121c7b3f7660abbc69222b0cff70 | Python | 20,451 | 509 | """Tools for resampling data."""
from __future__ import annotations
import warnings
from itertools import zip_longest
from typing import TYPE_CHECKING, Callable, Union
import numpy as np
import pandas as pd
from tqdm import tqdm
if TYPE_CHECKING:
import numpy.typing as npt
from ..tools._arcos4py_deprecation im... |
d71e3c972f1d3fcf9b47fc4597aaa6b7c2c3fa91a5b7591382c66de30b795584 | Python | 20,453 | 513 | #!/usr/bin/env python3.7
"""Defines Waveform class.
The copyrights of this software are owned by Duke University. Please
refer to the LICENSE and README.md files for licensing instructions. The
source code can be found on the following GitHub repository:
https://github.com/wmglab-duke/ascent
"""
import csv
import ma... |
e7400dec17c1fa909f1266ca365159497b5d0b40bc9acd70689ac5d9aae49d01 | Python | 20,454 | 591 | from __future__ import annotations
import logging
import sys
from collections.abc import Iterable
from typing import TYPE_CHECKING, Any, Union, cast
from pip._vendor.packaging.requirements import InvalidRequirement
from pip._vendor.packaging.utils import NormalizedName, canonicalize_name
from pip._vendor.packaging.ve... |
0de817ce0289244cd97dbb20dd9f92fab38be446e7f5cf3d4dd97b2de5ecc8c6 | Python | 20,477 | 542 | import h5py
import parmap
import numpy as np
import scipy.io as sio
import os
from tqdm import tqdm
import scipy
import scipy.io
import scipy.optimize as opt
from scipy.spatial.distance import cdist
from scipy.ndimage import gaussian_filter
import networkx as nx
from pkg_resources import resource_filename
from yass im... |
45c62ddac23f2a9148d08849e2a5f9494a6ca7764ad0aa4c1a8e9ede53d4ac25 | Python | 20,485 | 616 | """
Customized ops for ML framework
"""
# pylint: disable=invalid-name
# pylint: disable=unused-variable
from typing import Any, Tuple, Sequence, Callable, Optional, Union
from functools import partial
import jax
import jax.numpy as jnp
import jax.scipy as jsp
Array = Any # jnp.array
@jax.custom_vjp
def adaware... |
13fdc0d785ec835e8f63dbd4562312cf5aa6d69bb457b96c34a6c3943eb656e8 | Python | 20,487 | 550 | import warnings
import numpy as np
from scvelo import logging as logg
from scvelo import settings
from scvelo.core import LinearRegression
from scvelo.preprocessing.moments import moments, second_order_moments
from .optimization import leastsq_generalized, maximum_likelihood
from .utils import groups_to_bool, make_de... |
6a0f2ffe9a7e7d8a433ca26c56635a17037adb56f5305400c5ec344f529d13f6 | Python | 20,502 | 555 | import re
import os
import sys
import warnings
import platform
import tempfile
import hashlib
import base64
import subprocess
from subprocess import Popen, PIPE, STDOUT
from numpy.distutils.exec_command import filepath_from_subprocess_output
from numpy.distutils.fcompiler import FCompiler
from distutils.version import ... |
9d994b90e9accd413483aaf2470055198e423b33f2b9d72c889b4359aacce4b4 | Python | 20,503 | 571 | import contextlib
import ctypes
import platform
import ssl
import typing
from ctypes import (
CDLL,
POINTER,
c_bool,
c_char_p,
c_int32,
c_long,
c_uint32,
c_ulong,
c_void_p,
)
from ctypes.util import find_library
from ._ssl_constants import _set_ssl_context_verify_mode
_mac_version ... |
c69ddc7b6676d7d94aa78545708f8008b9cd0abffde7a4e768f5ad9f71f1523b | Python | 20,505 | 658 | """
Variational Quantum Eigensolver (VQE) for the Toric Code Model
This module implements VQE optimization for finding ground states of the
generalized 2D toric code Hamiltonian with open boundary conditions and provides comparison
among different ansätze: FLDC, GLDC, and FDC.
Reference:
- [arXiv:2311.01393](https://... |
3d75f302623b54a85466f4ee347939b391d4b83f4453f0a149db730fa7973a15 | Python | 20,513 | 536 | import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
import matplotlib.colors as mpc
from matplotlib.transforms import ScaledTranslation
from nilearn.plotting import plot_surf
from neuromaps.datasets import fetch_atlas
from neuromaps.parcellate import Parcellater
from neuromaps.images import dlabel_... |
44d3ecc3bef9146a6bf6f4f9e3d9e198c3f57b365b5dfdcd5b5a42454d280a6a | Python | 20,517 | 656 | """Implements the graph convolutional neural network for shift simulation and DP5 probaility estimation"""
from dp5.neural_net.nfp.preprocessing import GraphSequence
from dp5.neural_net.nfp.models import GraphModel
from dp5.neural_net.nfp.layers import (
Squeeze,
ReduceBondToAtom,
GatherAtomToBond,
Red... |
ead32c14fd61ecaf197fbda634eb5ae93bf9dbf7d54e55e49ec7ae7df8f4f347 | Python | 20,522 | 619 | """Tests for chebyshev module.
"""
from functools import reduce
import numpy as np
import numpy.polynomial.chebyshev as cheb
from numpy.polynomial.polynomial import polyval
from numpy.testing import (
assert_almost_equal, assert_raises, assert_equal, assert_,
)
def trim(x):
return cheb.chebtrim(x, tol=1... |
7b20c96fea20968861816e1be2c6707beff53c006190cf7fedaf6a5379fba005 | Python | 20,534 | 540 | import collections.abc
import textwrap
from io import BytesIO
from os import path
from pathlib import Path
import pickle
import pytest
import numpy as np
from numpy.testing import (
assert_, assert_equal, assert_array_equal, assert_array_almost_equal,
assert_raises, temppath,
)
class TestFromrecords:
... |
a9235b3266989501b875d7b37b3f0791c16d484b47f010a72fb50cd45c0035b5 | Python | 20,534 | 643 | """
Tests that apply specifically to the CParser. Unless specifically stated
as a CParser-specific issue, the goal is to eventually move as many of
these tests out of this module as soon as the Python parser can accept
further arguments when parsing.
"""
from decimal import Decimal
from io import (
BytesIO,
Str... |
df06720f9f64c7db0ad69900283e1ba4bd3de255336cc24fe27f1031e51fae44 | Python | 20,565 | 692 | """Tests for plot legend functionality in burst and evoked plots.
This module tests that legends are properly displayed and contain
the expected items for plots that use the widget's shared legend.
"""
from __future__ import annotations
from typing import TYPE_CHECKING
from unittest.mock import MagicMock
import num... |
19eadeaa8ab95297ecf8dd797b0f7f903b41c6035567ab1b68c7e472c05559bb | Python | 20,567 | 493 | '''大数据纤维工具脚本'''
import os, json
import shutil
from os.path import join
import numpy as np
'''基础函数'''
# '''Swc多树拆分'''
def SplitSwcData(swcData):
indLs = np.where(swcData[:, -1] == -1)[0].tolist() + [swcData.shape[0]]
swcDataLs = []
for i in range(len(indLs) - 1):
data = swcData[indLs[i]: indLs[i +... |
286fd3fcf38811ce679d52fb662f334b06a685a85b7e3531058ac2de29519442 | Python | 20,603 | 689 | import numpy as np
import pytest
from pandas import (
DataFrame,
Index,
RangeIndex,
Series,
date_range,
period_range,
timedelta_range,
)
import pandas._testing as tm
def gen_obj(klass, index):
if klass is Series:
obj = Series(np.arange(len(index)), index=index)
else:
... |
06f35a16d8023117f2f28beef0682ca056f1f66469696ca38cc53346fb686983 | Python | 20,633 | 571 |
import matplotlib.pyplot as plt
plt.switch_backend('agg')
from rdkit.Chem import MolFromSmiles
from rdkit.Chem import Draw
import numpy as np
import rdkit
from rdkit import Chem
from rdkit.Chem import AllChem
import os
from AttentiveFP.Featurizer import *
import pickle
import time
from rdkit.Chem import rdDepictor
fr... |
506c687d4605a37b6abbed9f81a360992f0afaec21c2fed7dedbbb3eeef27904 | Python | 20,635 | 423 | """ Test printing of scalar types.
"""
import code
import platform
import pytest
import sys
from tempfile import TemporaryFile
import numpy as np
from numpy.testing import (
assert_, assert_equal, assert_raises, assert_raises_regex, IS_MUSL)
class TestRealScalars:
def test_str(self):
svals = [0.0, -0... |
31710ad092f03988b5c210e53e4eafa4fa5e00f48d160392ab58c54533a12be7 | Python | 20,644 | 567 | import matplotlib.pyplot as plt
plt.switch_backend('agg')
from rdkit.Chem import MolFromSmiles
from rdkit.Chem import Draw
import numpy as np
import rdkit
from rdkit import Chem
from rdkit.Chem import AllChem
import os
from AttentiveFP.Featurizer_aromaticity_rm import *
import pickle
import time
from rdkit.Chem import... |
b7aa7acf753b2a5987c11118ad47a93c5bbfe28f39eca9e797516b687f7d739e | Python | 20,648 | 439 | import os
import numpy as np
import torch
import matplotlib
matplotlib.use('Agg') # 设置后端为Agg，不需要图形界面
import matplotlib.pyplot as plt
from torchvision.utils import save_image
from tqdm import tqdm
import argparse
from skimage.metrics import peak_signal_noise_ratio, structural_similarity
import json
from date... |
d2fec1ea722c0173f5d40ef1a92e850ba94501d688ab3c73fc2f9ab7868c720b | Python | 20,655 | 548 | """distutils.util
Miscellaneous utility functions -- anything that doesn't fit into
one of the other *util.py modules.
"""
import os
import re
import importlib.util
import string
import sys
from distutils.errors import DistutilsPlatformError
from distutils.dep_util import newer
from distutils.spawn import spawn
from ... |
2c0b929bfb631d0969ff4a1e90d735e0d09b8f681e8b8451f63a308dbfeeeb9a | Python | 20,669 | 675 | """
test all other .agg behavior
"""
import datetime as dt
from functools import partial
import numpy as np
import pytest
from pandas.errors import SpecificationError
import pandas as pd
from pandas import (
DataFrame,
Index,
MultiIndex,
PeriodIndex,
Series,
date_range,
period_range,
)
i... |
7ad242049bac5e9fb2ccfa1d6670815b43498313cd86ff85453a27eae57beb51 | Python | 20,670 | 516 | # Added Fortran compiler support to config. Currently useful only for
# try_compile call. try_run works but is untested for most of Fortran
# compilers (they must define linker_exe first).
# Pearu Peterson
import os
import signal
import subprocess
import sys
import textwrap
import warnings
from distutils.command.confi... |
b80c1118062756d80d4999b81cc0b704c00292003b92ee26f30ba9897e8ba4af | Python | 20,681 | 564 | """Network Authentication Helpers
Contains interface (MultiDomainBasicAuth) and associated glue code for
providing credentials in the context of network requests.
"""
from __future__ import annotations
import logging
import os
import shutil
import subprocess
import sysconfig
import typing
import urllib.parse
from ab... |
51b93159588e4716807079fafee45fb04df2e5f31e32847cf8e982d6fd23acd4 | Python | 20,688 | 401 | from datasets import load_dataset
import numpy as np
import pandas as pd
import re
from PIL import Image
import napari
from time import time
from scribbles_creator import create_even_scribbles
from napari_convpaint.conv_paint_utils import compute_image_stats, normalize_image
from scribbles_testing.image_analysis_helpe... |
b4e7252fa6ec61b74ab67dcbf0d743391b3c850974c8bedc743e99f8d910dedb | Python | 20,722 | 500 | import logging
import os
import numpy as np
import torch
from tqdm import tqdm
from sklearn.decomposition import PCA
from sklearn.mixture import GaussianMixture
from diptest import diptest as dp
import yass
from yass import read_config
from yass.reader import READER
from yass.residual.residual_gpu import RESIDUAL_GPU... |
d7e8955da1402cfc4cd62a3e399cca2b651b2d6b5d0f3789f6d5b18fcd40ef7e | Python | 20,728 | 607 | from __future__ import annotations
import contextlib
from typing import TYPE_CHECKING
import numpy as np
import pyqtgraph as pg
from sqlalchemy.exc import OperationalError
from sqlmodel import Session, col, select
from cali.logger import cali_logger
from cali.plot._util import add_colorbar_to_widget, disconnect_hove... |
50ca1f1893b57d09afbe9fe416def3930c37ce8c9db3e4ef2eef4662934e1f27 | Python | 20,734 | 545 | #!/usr/bin/env python3
import logging
import math
import multiprocessing
import time
from datetime import datetime
import numpy as np
import torch
from nn import NeuralNetwork
from tensorboardX import SummaryWriter
from torch.nn.functional import softplus
from training import (
ExponentialMovingAverage,
Looka... |
41428fb84c680f7495d9243d18e30a3e6ea204480b90376f7015a92ef12161d7 | Python | 20,744 | 513 | import os
import captum
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import pytorch_lightning as pl
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
from torch.optim.lr_scheduler import StepLR
from pnet import ReactomeNetworkOG, pnet_loader, util... |
efe2f6199e3769634a1ba873fa3f1184bf0120418012fa588baad7e99b2f9bfe | Python | 20,745 | 666 | """ manage PyTables query interface via Expressions """
from __future__ import annotations
import ast
from decimal import (
Decimal,
InvalidOperation,
)
from functools import partial
from typing import (
TYPE_CHECKING,
Any,
ClassVar,
)
import numpy as np
from pandas._libs.tslibs import (
Time... |
7bf7fc0af5ee20077d711dd4c9b3412efb16a403a7c460f36daa562788e8f535 | Python | 20,749 | 525 | """Tests for fit_gcate_batch and gcate_lfc_batch."""
import gc
import numpy as np
import pandas as pd
import pytest
from causarray.utils import subsample_ctrl_cells, subsample_pert_cells
from causarray.gcate import fit_gcate_batch
from causarray.DR_learner import gcate_lfc_batch, LFC_batch
# ------------------------... |
078760b37116226f2a2aea10327e8535a1867ffa809bf1009b89765f77070cc3 | Python | 20,755 | 530 | """
These test the method maybe_promote from core/dtypes/cast.py
"""
import datetime
from decimal import Decimal
import numpy as np
import pytest
from pandas._libs.tslibs import NaT
from pandas.core.dtypes.cast import maybe_promote
from pandas.core.dtypes.common import is_scalar
from pandas.core.dtypes.dtypes impor... |
798ed3235a159515eef5f008269884d2283b1fa6d10be2f660438936a223875e | Python | 20,755 | 652 | """
manage legacy pickle tests
How to add pickle tests:
1. Install pandas version intended to output the pickle.
2. Execute "generate_legacy_storage_files.py" to create the pickle.
$ python generate_legacy_storage_files.py <output_dir> pickle
3. Move the created pickle to "data/legacy_pickle/<version>" directory.
"... |
0d1ecd43b1b7d2ca7b3ca892c73df4c1889b8d8c70a522ae285a50a8a42ecee3 | Python | 20,779 | 548 | # -*- coding: utf-8 -*-
"""
Functions for statistical analysis. Functions are built on top of
MNE Python, numpy, pinguoin, and scipy.
Written by Joshua Kosnoff
jkosnoff@andrew.cmu.edu
"""
import scipy
import numpy as np
import pingouin as pg
import pandas as pd
import warnings
from statsmodels.tsa.api i... |
2deee13d1e7eecd7e49e5b2f33b4dcac40ca1ff8c13ed6dcc89de47bf55601bb | Python | 20,813 | 494 | """Defines Model class.
The copyrights of this software are owned by Duke University. Please
refer to the LICENSE and README.md files for licensing instructions. The
source code can be found on the following GitHub repository:
https://github.com/wmglab-duke/ascent
"""
import os
from copy import deepcopy
import numpy ... |
043af9ab163f5545122cad7ca4fbe5b480be192290e50772f1926abebc51d7bb | Python | 20,814 | 650 | """Connectivity graph plotting for calcium imaging analysis."""
from __future__ import annotations
from typing import TYPE_CHECKING, Any
import numpy as np
import pyqtgraph as pg
from sqlmodel import Session, col, select
from cali.plot._util import disconnect_hover_handlers
if TYPE_CHECKING:
from collections.a... |
9ffa639fd994ed0409efb4855e8804739a1fa0ca9180d6e48a6c1716e9f3efd3 | Python | 20,815 | 594 | from __future__ import annotations
import functools
from typing import (
TYPE_CHECKING,
cast,
overload,
)
import numpy as np
from pandas._libs import (
algos as libalgos,
lib,
)
from pandas.core.dtypes.cast import maybe_promote
from pandas.core.dtypes.common import (
ensure_platform_int,
... |
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