sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
76003ad4ea3b850d8e4a8ee2b988cc6282ab549efdf055609494a75cedd8da87 | Python | 29,886 | 912 | from __future__ import annotations
from typing import TYPE_CHECKING
import numpy as np
import pytest
import tifffile
from cali.analysis._fov_metrics import (
create_stimulation_mask,
get_overlap_roi_with_stimulated_area,
)
if TYPE_CHECKING:
from pathlib import Path
def test_create_stimulation_mask_bin... |
c0bdcc16caeef272f1698d8a2e60857d9bdda6fb486072627b8e057fa57b7921 | Python | 29,886 | 843 | import calendar
from datetime import (
date,
datetime,
time,
)
import locale
import unicodedata
import numpy as np
import pytest
import pytz
from pandas._libs.tslibs.timezones import maybe_get_tz
from pandas.errors import SettingWithCopyError
from pandas.core.dtypes.common import (
is_integer_dtype,
... |
9a7c4f5f5c942d40b99761aae61b31297eea7e1f25359d4dfdcdc586cc1fdd2e | Python | 29,887 | 781 | """Interactive GUI to view the HRF in probe space after data has been processed.
Based on Homer3 v1.80.2 "PlotProbe2.m" (:cite:t:`Huppert2009`)
Boston University Neurophotonics Center
https://github.com/BUNPC/Homer3
Initial Contributors:
- Sung Ahn | ahnsm@bu.edu | 2024
"""
from __future__ import annotat... |
620d64872900a44ebb21052afae1247fd2b7b3ac1d5208e0cea9600eed2499e7 | Python | 29,952 | 819 | # flake8: noqa: G004
"""
This runner determinator is used to determine which set of runners to run a
GitHub job on. It uses the first comment of a GitHub issue (by default
https://github.com/pytorch/test-infra/issues/5132) to define the configuration
of which runners should be used to run which job.
The configuration... |
9fc68be92df174ec3b25e3068d30951e46abcc9027a712ad0c9d70d0570b8fd0 | Python | 29,982 | 676 | import torch
from torch.optim import Adam
import torch.nn.functional as F
from gym.spaces import Box, Discrete, MultiDiscrete
from multiagent.multi_discrete import MultiDiscrete
from utils.networks import MLPNetwork, SNNNetwork, LSTMClassifier
from utils.misc import soft_update, average_gradients, onehot_from_logits, g... |
a2beb884fcd94765eae1b9ebc7b349e6ee033421c47f668a2934904b5add0d42 | Python | 30,035 | 642 | import torch
from torch import nn
import torch.nn.functional as F
from torch_scatter import scatter
from torch_geometric.utils import degree
from e3nn.o3 import Irrep, Irreps, wigner_3j, matrix_to_angles, Linear, FullyConnectedTensorProduct, TensorProduct, SphericalHarmonics
from e3nn.nn import Extract
from .utils imp... |
ca218e7a9a5062f7cbbc6fc0953b34b44568fb060fa0ec00854a654755dd5199 | Python | 30,080 | 907 | """Utility functions for multi-well bar plots.
Common functions used across multiple plot types.
"""
from __future__ import annotations
import colorsys
from typing import TYPE_CHECKING, Callable, TypedDict
import numpy as np
import pyqtgraph as pg
from pyqtgraph import BarGraphItem
from sqlmodel import Session, col... |
15d77b5e2d5343f7ac657ab7d86bbe64f8928481c4d9544e49246dcdeb79d3db | Python | 30,103 | 952 | from __future__ import annotations
_shared_docs: dict[str, str] = {}
_shared_docs[
"aggregate"
] = """
Aggregate using one or more operations over the specified axis.
Parameters
----------
func : function, str, list or dict
Function to use for aggregating the data. If a function, must either
work when pa... |
0ccf984e2ea691be9dba9ef6b2b740e064c8c7a9f30e206842a2067f06b50508 | Python | 30,107 | 1,044 | """
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 datetime import datetime
from io import (
BytesIO,
StringIO,
)
from pathlib import Path
import numpy as np
import pytest
from pandas.errors import Empty... |
589a3285c609260695a5817b1e7a6e03bbcdd20734d205a7ebd8ab72dafbbcab | Python | 30,155 | 663 | import numpy as np
import random
import time
import math
import os
from copy import deepcopy
from scipy.spatial.distance import cdist
from torchvision.utils import save_image
import torch
# import pdb
from torch.nn import DataParallel
from torch.nn import functional as F
from torch import nn
from inclearn.convnet i... |
62e49700f52b5de91f401afc4c46f31ba6e0e404044c2eed6d8d44159559b846 | Python | 30,188 | 808 | import streamlit as st
import logging
from kani import ChatRole, ChatMessage
import asyncio
from upstash_redis import Redis
import base64
import dill
import hashlib
import urllib.parse
from kani_utils.utils import _seconds_to_days_hours, _sync_generator_from_kani_streammanager
import json
import datetime
class UIOnlyM... |
c163df883a5e8cb3815526c4d3cac69836a562e7158eb9559b8a6ef13b142441 | Python | 30,228 | 750 | import scipy.io as scio
import math
import random as rand
import copy
import os
import pandas as pd
import matplotlib.pyplot as plt
import numpy as np
from braincog.base.learningrule.STP import short_time
class six_layer_pfc():
"""
Define global parameters
:param SizeHistOutput: Set the peak value of the... |
21dc1e9e6231302a7871fa2bd3f72881514f898efb0ed751aa2d3b25d36a1817 | Python | 30,238 | 609 | # Copyright 2024 RADar-AZDelta
# SPDX-License-Identifier: gpl3+
import logging
from abc import ABC, abstractmethod
from pathlib import Path
from typing import Any
import dash_bootstrap_components as dbc
import polars as pl
from dash import Dash, Input, Output, dash_table, dcc, html
from .etl_base import EtlBase
cl... |
ee5d5b26b9b1ec6410b9c2e6c32193690caa68cbf4e6418443628e977401474e | Python | 30,246 | 847 | # -*- coding: utf-8 -*-
from __future__ import division
from string import ascii_letters
import torch
import math
import cv2
import numpy as np
import random
import numbers
import collections
Sequence = collections.abc.Sequence
Iterable = collections.abc.Iterable
INTER_MODE = {'NEAREST': cv2.INTER_NEAREST, 'BILINEAR'... |
579cd67bed982b0254f7183fa83a19ac64898b02fad891c0e2a72c8658bd296b | Python | 30,277 | 891 | """
Backend magic inherited from tensornetwork: pytorch backend
"""
# pylint: disable=invalid-name
import logging
from typing import Any, Callable, Optional, Sequence, Tuple, Union
from operator import mul
from functools import reduce, partial
from scipy.sparse import coo_matrix
import tensornetwork
from tensornetwo... |
abac0ce18e1a60c18637f2e2b6c8f73d82a9052dd9beeb74c610e6a4110715da | Python | 30,387 | 792 | from __future__ import annotations
import importlib.util
import os
import pathlib
import sys
import typing as t
from collections import defaultdict
from functools import update_wrapper
from jinja2 import BaseLoader
from jinja2 import FileSystemLoader
from werkzeug.exceptions import default_exceptions
from werkzeug.ex... |
a5dc60d75cf872c03258352d2c04ca3536770835b38def56c577ee2334bb8af9 | Python | 30,421 | 600 | # ------------------------------------------------------------------------------
# functions.py
# Author: Dr. Timo Hofsähs
#
# Description:
# This Python script is part of the code accompanying the scientific publication:
# The Virtual Brain links transcranial magnetic stimulation evoked potentials and
# neurotransmi... |
a149524fb630a1eb8013a2335a8924664f0871c4a3dfd1d3d32a5004e3e3d9f3 | Python | 30,472 | 803 | from __future__ import annotations
import errno
import json
import operator
import os
import shutil
import site
from optparse import SUPPRESS_HELP, Values
from pathlib import Path
from pip._vendor.packaging.utils import canonicalize_name
from pip._vendor.requests.exceptions import InvalidProxyURL
from pip._vendor.ric... |
0a5d5da449ce7f0af3ccf6e4bbe7a67a935e37846dff4ff9f08cb6c7e2464e6f | Python | 30,503 | 831 | """
requests.sessions
~~~~~~~~~~~~~~~~~
This module provides a Session object to manage and persist settings across
requests (cookies, auth, proxies).
"""
import os
import sys
import time
from collections import OrderedDict
from datetime import timedelta
from ._internal_utils import to_native_string
from .adapters im... |
2e57133f2946fe74ca075d07480088ef1d44cd28476ee1674b1f60e6550af80c | Python | 30,560 | 712 | import logging
import os
import unicodedata
from typing import Any, Dict, List, Optional
import requests
from dotenv import load_dotenv
from kani import AIParam, ai_function
from kani_utils.base_kanis import StreamlitKani
from requests.exceptions import HTTPError, RequestException
from typing_extensions import Annotat... |
18664c0180b7031b68f01f9610f64dbd3ba7d7d01d1138ea95a15561927cff88 | Python | 30,571 | 882 | # -*- coding: utf-8 -*-
#
# sampler.py
#
# Copyright 2020 Amazon.com, Inc. or its affiliates. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.or... |
fcf56a76e9a1917d8743d01d93f7b5f420611464c37ecc61f15f0a619bdcd3c6 | Python | 30,582 | 786 | """Multiple functions to import the behavioral data.
Some other functions to transform the data are included.
"""
import os
import glob
import re
import ipdb
import pandas as pd
import numpy as np
import utils
DIR = os.path.dirname(os.path.abspath(__file__))
DATA_FOLDER = os.path.abspath('../source_data/')
SPEED_T... |
b4bae74b8a04543c236f1ef87c7ca2f6be37c8013427b9896557dd787be54898 | Python | 30,601 | 822 | import pytest
import numpy as np
from numpy._core.multiarray import _vec_string
from numpy.testing import (
assert_, assert_equal, assert_array_equal, assert_raises,
assert_raises_regex
)
kw_unicode_true = {'unicode': True} # make 2to3 work properly
kw_unicode_false = {'unicode': False}
class TestBasic:... |
3131e359449306781566dc942dd05ed50c401aaf48af1355f0eb61ba328aaf4c | Python | 30,607 | 821 | """
Copyright 1999 -- 2011 Pearu Peterson all rights reserved.
Copyright 2011 -- present NumPy Developers.
Permission to use, modify, and distribute this software is given under the
terms of the NumPy License.
NO WARRANTY IS EXPRESSED OR IMPLIED. USE AT YOUR OWN RISK.
"""
from . import __version__
f2py_version = __ve... |
47af567f5db4a146cc691c94cb62de94a1c87af55d63060b34e764b326d563f5 | Python | 30,623 | 876 | """Tests for database to CSV export functionality."""
from __future__ import annotations
from typing import TYPE_CHECKING
import pytest
from sqlmodel import Session, create_engine
from cali._constants import (
CALCIUM_DEN_DFF_CORRELATION,
CALCIUM_DFF_CORRELATION,
DFF_TRACES,
NEUROPIL_CORRECTED_TRACE... |
7e60c9005906ef5b854e7fac5524e1d88c345a6717418aa46d18e286fc018d4f | Python | 30,641 | 879 | from __future__ import absolute_import
import io
import logging
import sys
import warnings
import zlib
from contextlib import contextmanager
from socket import error as SocketError
from socket import timeout as SocketTimeout
brotli = None
from . import util
from ._collections import HTTPHeaderDict
from .connection i... |
956092aba1d936a3e98df7de8df92a73d24a8e144f51456e2cf5b2593c970c6e | Python | 30,676 | 873 | """Tests for Table Schema integration."""
from collections import OrderedDict
from io import StringIO
import json
import numpy as np
import pytest
from pandas.core.dtypes.dtypes import (
CategoricalDtype,
DatetimeTZDtype,
PeriodDtype,
)
import pandas as pd
from pandas import DataFrame
import pandas._test... |
3459a6318281b411f1accddde270711b465c935fa7fae110b1b00378fb806e5d | Python | 30,705 | 783 | from datetime import (
date,
datetime,
)
import numpy as np
import pytest
from pandas._config import using_pyarrow_string_dtype
from pandas.core.dtypes.common import (
is_float_dtype,
is_integer_dtype,
)
from pandas.core.dtypes.dtypes import CategoricalDtype
import pandas as pd
from pandas import (
... |
fc53ea200339c996d84a5727756b9a22d355920b37ca52843dbfa8eb7411cc41 | Python | 30,750 | 923 | from contextlib import nullcontext
from datetime import datetime
from decimal import Decimal
import numpy as np
import pytest
from pandas._config import config as cf
from pandas._libs import missing as libmissing
from pandas._libs.tslibs import iNaT
from pandas.compat.numpy import np_version_gte1p25
from pandas.cor... |
f41f272b23bd452b8333e05b1304397a0172a7a106fda5d00a7be307f37b54d4 | Python | 30,751 | 809 | """Tests for save and load settings functionality in CaliGui."""
from __future__ import annotations
import json
from typing import TYPE_CHECKING, Any
import pytest
if TYPE_CHECKING:
from collections.abc import Generator
from pathlib import Path
from pytestqt.qtbot import QtBot
@pytest.fixture
def set... |
046577a15710f7cfa0cea32cdd6342d3ec7be9f99f6864bfd9b0e72c11cf87dd | Python | 30,800 | 1,118 | __all__ = ['matrix', 'bmat', 'asmatrix']
import sys
import warnings
import ast
from .._utils import set_module
import numpy._core.numeric as N
from numpy._core.numeric import concatenate, isscalar
# While not in __all__, matrix_power used to be defined here, so we import
# it for backward compatibility.
from numpy.li... |
78e4282500468c0a8572cc1d3418a91e818c18180b8b02c5348cd3b99e574a42 | Python | 30,816 | 907 | import json
import numpy as np
import pytest
from pandas import (
DataFrame,
Index,
Series,
json_normalize,
)
import pandas._testing as tm
from pandas.io.json._normalize import nested_to_record
@pytest.fixture
def deep_nested():
# deeply nested data
return [
{
"country":... |
ed174cf4187bd509a97f66e450fbb63221c3c1d51bd8d248c26c4ade0d501017 | Python | 30,872 | 979 | """
Tests that work on both the Python and C engines but do not have a
specific classification into the other test modules.
"""
from datetime import datetime
from inspect import signature
from io import StringIO
import os
from pathlib import Path
import sys
import numpy as np
import pytest
from pandas.errors import (... |
8d905d06fc25840b54d820fc63603d9713b8047d7271f7e8894d609d7ead1bdc | Python | 30,933 | 753 | """Adaptation / eccentricity analysis utilities."""
import os
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from matplotlib.colors import LinearSegmentedColormap
import seaborn as sns
from sklearn.cluster import KMeans, DBSCAN, SpectralClustering, AgglomerativeClustering
from sklearn.metrics i... |
98c87178606df93f29ae35a93619ffc6f6428fabba3965a69acbca3fabdb339c | Python | 30,941 | 899 | """A collection of functions designed to help I/O with ascii files.
"""
__docformat__ = "restructuredtext en"
import numpy as np
import numpy._core.numeric as nx
from numpy._utils import asbytes, asunicode
def _decode_line(line, encoding=None):
"""Decode bytes from binary input streams.
Defaults to decodin... |
bbda33621cccf95d0620d622d388d878db23883ed7b6cb2b0f6f7384555a380d | Python | 30,982 | 860 | import pytest
import numpy as np
from numpy._core import (
array, arange, atleast_1d, atleast_2d, atleast_3d, block, vstack, hstack,
newaxis, concatenate, stack
)
from numpy.exceptions import AxisError
from numpy._core.shape_base import (_block_dispatcher, _block_setup,
_b... |
daf39dc884ba363cf27064f989dc4ac713ac7f0e93811e370917b6952b5860bd | Python | 31,025 | 1,110 | """
shared options and groups
The principle here is to define options once, but *not* instantiate them
globally. One reason being that options with action='append' can carry state
between parses. pip parses general options twice internally, and shouldn't
pass on state. To be consistent, all options will follow this de... |
734661220911abd25fa688678b1b4cfa7d9faedc85d9f476a675058c5111f1f6 | Python | 31,042 | 928 | """ test the scalar Timestamp """
import calendar
from datetime import (
datetime,
timedelta,
timezone,
)
import locale
import time
import unicodedata
from dateutil.tz import (
tzlocal,
tzutc,
)
from hypothesis import (
given,
strategies as st,
)
import numpy as np
import pytest
import pyt... |
0fa2135f3ca367e4f16f93b13e2d800b1a9abe86cad04ad84e1a080ba9cc85f1 | Python | 31,114 | 852 | import threading
from collections.abc import Mapping
from pathlib import Path
import numpy as np
import tifffile
from sqlalchemy.engine import Engine
from sqlmodel import Session, create_engine, select
from tqdm import tqdm
from cali._constants import OZ, TS
from cali.logger import cali_logger
from cali.readers impor... |
915e6d50234096327bf083cdae169e0d7f40c8ab4dd8a745f19a4d313783cb36 | Python | 31,130 | 934 | import numpy as np
import pytest
import pandas.util._test_decorators as td
import pandas as pd
from pandas import (
DataFrame,
Index,
MultiIndex,
RangeIndex,
Series,
Timestamp,
option_context,
)
import pandas._testing as tm
from pandas.core.reshape.concat import concat
from pandas.core.res... |
288ad31e83dca9353721f0f65b28163195b0e013c51876a618410d19fcbe8025 | Python | 31,146 | 661 | import numpy as np
import librosa
from pathlib import Path
import os
import re
import soundfile as sf
import pandas as pd
import scipy.signal as sig
import matplotlib.pyplot as plt
from collections.abc import Iterable
from plot_stimulus_correlations import stimuli_correlation
from butterworth_filter import butter_filte... |
b31b277dcf0a06c9ec4af23ef2c28828da36280daebebaef5b4598642ab28f29 | Python | 31,178 | 773 | """ Build swig and f2py sources.
"""
import os
import re
import sys
import shlex
import copy
from distutils.command import build_ext
from distutils.dep_util import newer_group, newer
from distutils.util import get_platform
from distutils.errors import DistutilsError, DistutilsSetupError
# this import can't be done h... |
c0842ebc2a41cb850cb496a483b8042befc614e331fac9e9b25ee9016e633d00 | Python | 31,207 | 779 | from typing import Dict, Union
import torch
from torch.nn.modules.loss import _Loss
from torch_geometric.data import Data
from torch_cluster import radius_graph
import torch.nn as nn
import os
from e3nn import o3
from e3nn.math import soft_one_hot_linspace
from e3nn.nn import Gate, Dropout, BatchNorm, FullyConnectedNe... |
2168df2c9227d8ef2bba8faafc2914b7197de2676202f5ce9d59d4db0de75ecf | Python | 31,230 | 802 | """
Functional dense MPS state data and contractions.
"""
from dataclasses import dataclass
from typing import Any, Iterable, Iterator, Sequence, Tuple
import jax
import jax.numpy as jnp
import numpy as np
from ..backends.jax_ops import adaware_qr, adaware_svd
from .layout import MPSSpec, block_bucket_plan
Array = ... |
befe5c6ecdcfe607f8ddeff5bfbda0c1243637f0ffaa9b1fb973b27ab3210ee2 | Python | 31,273 | 828 | from __future__ import annotations
import functools
import logging
import os
import shutil
import sys
import uuid
import zipfile
from collections.abc import Collection, Iterable
from optparse import Values
from pathlib import Path
from typing import Any
from pip._vendor.packaging.markers import Marker
from pip._vendo... |
bf9a234d95934a6f05a484f2fe2039f393aacedff883242695cd3b349b682737 | Python | 31,354 | 849 | """
Created on Jun 24, 2024
@author: mning
"""
"""
Created on May 22, 2023
@author: mning
"""
"""
Created on May 10, 2023
@author: mning
Note: all must accept same input arguments and yield same output types
"""
import logging
import numpy as np
from sklearn.covariance import LedoitWolf
from sklearn.covariance imp... |
128685f2beb822bec8e27a4af3c67dadfca2b8e05d3d216f999b387c2f93de18 | Python | 31,371 | 815 | """Behaviour analyses for the motor adaptation task."""
from __future__ import annotations
import os
from typing import Optional, Tuple
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
from scipy.stats import pearsonr
import pingouin as pg
from matplotlib.colors import Lis... |
257e0d7d5bcbd518573e89aaafe3e4e34191b784994c3a493ee37925b90ee226 | Python | 31,381 | 1,005 | """Tests for connectivity plot functionality."""
from __future__ import annotations
from typing import TYPE_CHECKING
from unittest.mock import MagicMock, Mock
import numpy as np
import pyqtgraph as pg
import pytest
from PyQt6.QtWidgets import QWidget
from cali.sqlmodel import FOVAnalysis
if TYPE_CHECKING:
from... |
3bccdda0a33bb6d9c286703414a0a543ce989a9f9797b2571aec992d1236d7a6 | Python | 31,524 | 863 | #!/usr/bin/env python3
"""Source space construction for combined cerebral and cerebellar MEG/EEG analysis.
Provides functions to set up cerebellar surface source spaces, register them
to individual subject anatomy via ANTs diffeomorphic registration, and merge
them with MNE-Python cortical source spaces.
"""
# -------... |
8ae44d9efca2561b411e99c4ac4cc23b9a95639bf04dc26c5f66790c12fddb45 | Python | 31,534 | 810 | #!/usr/bin/env python3.7
"""Defines Trace 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 random
from cop... |
db7228296e49f58f88651446e31fce7d879d24ee1b5d40be4623084203a13872 | Python | 31,551 | 652 | # YOLOv5 🚀 by Ultralytics, GPL-3.0 license
"""
Export a YOLOv5 PyTorch model to other formats. TensorFlow exports authored by https://github.com/zldrobit
Format | `export.py --include` | Model
--- | --- | ---
PyTorch | ... |
2a0c69a29b83eaca9ea742ecba6307d798e85a287455d6e75e9626f844cd8e81 | Python | 31,612 | 755 | """distutils.command.build_ext
Implements the Distutils 'build_ext' command, for building extension
modules (currently limited to C extensions, should accommodate C++
extensions ASAP)."""
import contextlib
import os
import re
import sys
from distutils.core import Command
from distutils.errors import *
from distutils.... |
857e24b185d10be4377c4bcbac03481bdee6ab7b703ba67090c85f00d34add88 | Python | 31,683 | 757 | """distutils.command.build_ext
Implements the Distutils 'build_ext' command, for building extension
modules (currently limited to C extensions, should accommodate C++
extensions ASAP)."""
import contextlib
import os
import re
import sys
from distutils.core import Command
from distutils.errors import *
from distutils.... |
f3b0b87dc22eda08710b11e1b4ad003ca4c9827c20b230a4d4390dd7df65075f | Python | 31,751 | 650 | """
Some utils too deal with peculiar protocols or peculiar ways of handling them
Author: Bertrand Thirion, Ana Luisa Grilo Pinho, 2015
"""
import numpy as np
from pandas import read_csv, concat
rsvp_language = ['consonant_strings', 'word_list', 'pseudoword_list',
'jabberwocky', 'simple_sentence', '... |
322d786538048794a08525f8961611071fd1290b42b302081ff1cc063d790651 | Python | 31,775 | 586 | # standard
from pathlib import Path
import numpy as np
import torch
import time
import matplotlib.pyplot as plt
from tqdm import tqdm
import argparse
# lRomul
import argus
from src.data import get_mouse_data
from src.predictors import Predictor
from src import constants
# mine
import utils_reconstruction.image_simil... |
e33befdfedc15f241ad70a99910f37447859d3c5814aeb36424fe37795dbcdcf | Python | 31,810 | 946 | import numpy as np
import logging
import os
from tqdm import tqdm
import parmap
import torch
import torch.multiprocessing as mp
from sklearn.decomposition import PCA
from scipy.signal import argrelmin
#from numba import jit
from yass.util import absolute_path_to_asset
from yass.empty import empty
from yass.geometry i... |
e4f1797877e1f265c02315c71d1076c576d7a218bca44de71d23b16baeae4bb1 | Python | 31,875 | 870 | """Extension API for adding custom tags and behavior."""
import pprint
import re
import typing as t
from markupsafe import Markup
from . import defaults
from . import nodes
from .environment import Environment
from .exceptions import TemplateAssertionError
from .exceptions import TemplateSyntaxError
from .runtime im... |
21e698de2542a0e5035e41cdce07a1887cd7e800ff1b8ee88ce4529103549308 | Python | 31,997 | 817 | import logging
import math
from typing import Dict, List, Optional
import pytorch_lightning as pl
import torch
import torch.nn as nn
from torch.optim import Optimizer
from torch.optim.lr_scheduler import LRScheduler
from torch_geometric.data import Data
from torch_geometric.nn import radius_graph
from nablaDFT.gemnet... |
1b5b752483c078d9063cb0d61025b5d7550ef3295ad0d2d748d4829498dd7397 | Python | 32,037 | 928 | """Tests for PCA and UMAP scatter plot functions.
Covers:
- plot_pca_scatter renders ScatterPlotItem objects per condition
- plot_umap_scatter works when umap-learn is installed, gracefully fails otherwise
- Empty database → no crash
- Feature matrix building returns expected columns
"""
from __future__ import annota... |
948163d16a90bc4655112a9839f3fc7e556ab8ca15118a75b9b24661a0992604 | Python | 32,102 | 911 | import re
import numpy as np
import pytest
import pandas.util._test_decorators as td
import pandas as pd
from pandas import (
Categorical,
CategoricalDtype,
DataFrame,
DatetimeTZDtype,
Index,
Interval,
IntervalDtype,
NaT,
Series,
Timedelta,
Timestamp,
concat,
date_... |
9e9b6efb1ff8b0a0b6954cc1d16f1b193e8983dcf7ae00400bb7d7da8fbdb020 | Python | 32,179 | 845 | ## ...........................................................................
##
## PIMMS (Polymer Interactions in Multicomponent Mixtures)
## Alex Holehouse, Pappu Lab, Holehouse Lab
## Copyright 2015 - 2026
## ...........................................................................
import random
import numpy a... |
d768868e36a4de188c7f09e1e7347626a03bf3ea2bfaef4fd604c609c8c90f41 | Python | 32,179 | 1,069 | import functools
import sys
import math
import warnings
import numpy as np
from .._utils import set_module
import numpy._core.numeric as _nx
from numpy._core.numeric import ScalarType, array
from numpy._core.numerictypes import issubdtype
import numpy.matrixlib as matrixlib
from numpy._core.multiarray import ravel_mu... |
4a430fc8f21886c199371392bcc37115420eb74ecb4f8cda73655e920af7014d | Python | 32,212 | 829 | import torch
import torch.nn as nn
import torch.optim as optim
import torch.nn.functional as F
import pytorch_lightning as pl
from torch.optim import AdamW,SGD
from collections import OrderedDict, defaultdict
from torch.optim.lr_scheduler import ReduceLROnPlateau,StepLR
from pytorch_lightning.utilities import CombinedL... |
b6a70accaff043bb63a111a0cbfb75866b597793a24e9751c10aa848e0fb03f6 | Python | 32,226 | 758 | #!/usr/bin/env python3
from __future__ import annotations
from datetime import datetime, timedelta, timezone
from typing import Any
from unittest import main, mock, TestCase
import greenlight_guard
from greenlight_guard import (
DEAD_REVIEW_AGE,
evaluate_greenlight_guard,
GREENLIGHT_LOGIN,
Greenlight... |
c66f0f92e9edec300a016be7c9212ca166e332f72664bf8e0bba9ef8b41aaee4 | Python | 32,326 | 891 | """
The arraypad module contains a group of functions to pad values onto the edges
of an n-dimensional array.
"""
import numpy as np
from numpy._core.overrides import array_function_dispatch
from numpy.lib._index_tricks_impl import ndindex
__all__ = ['pad']
#########################################################... |
152d85f0cd0f48fd248ac3076340959525e271935fe56996b8ce8ef369962774 | Python | 32,327 | 910 | """Test FOV-level analysis measurements for correlation and synchrony.
This module tests the 6 different metrics computed in compute_fov_analysis:
- Calcium: zero-lag correlation, jitter synchrony, max lag correlation
- Spikes: zero-lag correlation, max lag correlation, jitter synchrony
"""
from __future__ import ann... |
0f418be0f71bc52f7390d1b68c19108bd2756c401ed249aaef83c0e5c40bfda4 | Python | 32,344 | 770 | # -*- coding: utf-8 -*-
import gc
import warnings
import numpy as np
from sklearn.utils.validation import check_random_state
from . import compute, structures, utils
def gen_permsamp(groups, n_cond, n_perm, seed=None, verbose=True):
"""
Generates permutation arrays for PLS permutation testing
Parameters... |
d2056505616a591679da39a2e662510b7877550851a2d1a19f0b34cb473207da | Python | 32,367 | 823 | #!/public/EM/anaconda3/envs/relion-5.0/bin/python
import argparse
import math
import sys, os
from pathlib import Path
import numpy as np
import pandas as pd
import starfile
import torch
import torch.nn as nn
import torch.nn.functional as F
import mrcfile
import matplotlib
matplotlib.use("Agg") # non-GUI backend, no... |
d20d4fce9d2fb66044989e70f45decffe24c55444ff114b81b571ce5345a02c2 | Python | 32,390 | 929 | """Fallback pure Python implementation of msgpack"""
import struct
import sys
from datetime import datetime as _DateTime
if hasattr(sys, "pypy_version_info"):
from __pypy__ import newlist_hint
from __pypy__.builders import BytesBuilder
_USING_STRINGBUILDER = True
class BytesIO:
def __init__(... |
2223c3f2d3d6f5c5653733bebae90d5f87c6a68355d2a12960841e5dd576c957 | Python | 32,407 | 915 | import os
import numpy as np
import tqdm
import parmap
import scipy
import logging
from diptest import diptest as dp
from sklearn.discriminant_analysis import LinearDiscriminantAnalysis as LDA
from sklearn.metrics import pairwise_distances
import networkx as nx
from scipy.spatial.distance import pdist, squareform
from... |
bb28bb8ecca2f22db67286a3d3e43360140104ead2bd66f9c98460241dcf90be | Python | 32,420 | 1,077 | """
Some common noise quantum channels.
"""
import sys
from typing import Any, Sequence, Union, Optional, Dict
from functools import partial
import numpy as np
from . import cons
from . import interfaces
from .cons import backend, dtypestr
from . import gates
from .gates import array_to_tensor
thismodule = sys.modu... |
b466c6827a2d604e5724bb74706f43fc57f38927e56fda0dce57eac9e65b34be | Python | 32,440 | 912 | from collections import (
abc,
deque,
)
from collections.abc import Iterator
from datetime import datetime
from decimal import Decimal
import numpy as np
import pytest
from pandas.errors import InvalidIndexError
import pandas.util._test_decorators as td
import pandas as pd
from pandas import (
DataFrame,... |
e6965035f16a34a893b21098c19dc04f1fbb1d35ebf9f03580b1f7ba60cf7555 | Python | 32,511 | 557 | from __future__ import annotations
from abc import ABC, abstractmethod
from typing import Dict, List
import re
import logging
class ESCARGOTPrompter:
"""
ALZKBPrompter provides the generation of prompts specific to the
ALZKB example for the language models.
Inherits from the Prompter class and implem... |
7c94eaae3560e39614a7c68f09ca60473acd1285e26d9200cfc4e6cf671333b9 | Python | 32,578 | 886 | import numpy as np
import pytest
import pandas as pd
from pandas import (
CategoricalDtype,
CategoricalIndex,
DataFrame,
Index,
MultiIndex,
Series,
crosstab,
)
import pandas._testing as tm
@pytest.fixture
def df():
df = DataFrame(
{
"A": [
"foo",
... |
37e7092ad4dfa0e7b9af36cf41b20a1cd0a0073b624a10e3a04e1e39d673380d | Python | 32,599 | 855 | """
readout error mitigation functionalities
"""
# Part of the code in this file is from mthree: https://github.com/Qiskit-Partners/mthree (Apache2)
# https://journals.aps.org/prxquantum/pdf/10.1103/PRXQuantum.2.040326
from typing import Any, Callable, List, Sequence, Optional, Union, Dict
import warnings
from time i... |
85e0a6e1f9503ef34c356eb379ccff5d4adf5793beff359da5a9bf764dd5d937 | Python | 32,621 | 1,101 | from __future__ import annotations
from abc import (
ABC,
abstractmethod,
)
import sys
from textwrap import dedent
from typing import TYPE_CHECKING
from pandas._config import get_option
from pandas.io.formats import format as fmt
from pandas.io.formats.printing import pprint_thing
if TYPE_CHECKING:
from... |
47179e9c86855cb4fd6cf0c49d5ef37e970fbf9502e503158e9fa16f4220bfd8 | Python | 32,629 | 940 | from __future__ import annotations
from datetime import (
datetime,
timedelta,
)
import itertools
import numpy as np
import pytest
from pandas._config import using_pyarrow_string_dtype
from pandas.compat import (
IS64,
is_platform_windows,
)
from pandas.compat.numpy import np_version_gt2
import pan... |
affe69ccddab1826e4ae821108b7bf061aead4d0cb08bce3f3934ef1c4d9750f | Python | 32,683 | 902 | import sys, boto3, os, io, pandas, datetime
from itertools import chain
from awsglue.transforms import *
from awsglue.utils import getResolvedOptions
from pyspark.context import SparkContext
from awsglue.context import GlueContext
from awsglue.job import Job
from pyspark.sql import SQLContext
from awsglue.dynamicframe... |
16f5b4661e94f0290e2a8d0f96fcfc5beb9d3a0b1cce0f6a6b0c95abec732aa7 | Python | 32,702 | 1,009 | from textwrap import (
dedent,
indent,
)
import numpy as np
import pytest
from pandas import (
DataFrame,
MultiIndex,
option_context,
)
jinja2 = pytest.importorskip("jinja2")
from pandas.io.formats.style import Styler
@pytest.fixture
def env():
loader = jinja2.PackageLoader("pandas", "io/fo... |
f389720c3bed845a56a186e054444a90d1c2db08a6c4542721f45280cc746b77 | Python | 32,712 | 867 | """
Analog time evolution engines
"""
from typing import Any, Tuple, Optional, Callable, Sequence, Dict
from functools import partial
import math
import warnings
import numpy as np
from .cons import backend, dtypestr, rdtypestr, contractor
from .gates import Gate
from . import matrixfunc
from .quantum import aslinea... |
798b4c0dc6c8eeef0883e288475966e084ff38c02198d7c356e705e169d93c59 | Python | 32,727 | 635 | #!/usr/bin/env python
import sqlite3
import csv
import numpy as np
import pandas as pd
import datetime
import argparse
import plotly.graph_objects as go
import plotly.io as pio
import plotly.express as px
fig = go.Figure()
pio.full_figure_for_development(fig,warn=False)
import sys
import timeit
import subprocess
impor... |
056d35ff89bcc19707bc0919f052230e615fbac9e380598655b472a9b583d34d | Python | 32,753 | 876 | from functools import reduce
import pickle
import pytest
import numpy as np
import numpy._core.umath as umath
import numpy._core.fromnumeric as fromnumeric
from numpy.testing import (
assert_, assert_raises, assert_equal,
)
from numpy.ma import (
MaskType, MaskedArray, absolute, add, all, allclose, allequ... |
b7ad29e15d342e9e0b3d57eec074d7e0ed6c27cd5f40db61d22e954e3553e082 | Python | 32,775 | 720 | # Copyright 2024 RADar-AZDelta
# SPDX-License-Identifier: gpl3+
import logging
from datetime import date
from pathlib import Path
from threading import Lock
from typing import Any, Optional
from polars import Config as pl_Config
from polars import col, from_dicts
from ..etl import Etl
from .ctes import extract_ctes
... |
7e95b4f48fe05afde72e027b7427bfdd7892f0dd54d9360b784576ba8aeb9e12 | Python | 32,792 | 849 | import streamlit as st
def show_about_page():
st.markdown(f"""
<style>
@import url('https://fonts.googleapis.com/css2?family=Inter:wght@400;500;600;700&display=swap');
:root {{
--primary:#0f4c81;
--accent:#1f8ef1;
--text:#1f2d3a;
--muted:#6e7c95;
--c... |
695bc41c82ef252edc62134a1246bf42226511c3e29bbeacdbd15094d6c5611c | Python | 32,795 | 992 | import numpy as np
import pytest
from pandas.errors import (
IndexingError,
PerformanceWarning,
)
import pandas as pd
from pandas import (
DataFrame,
Index,
MultiIndex,
Series,
)
import pandas._testing as tm
@pytest.fixture
def single_level_multiindex():
"""single level MultiIndex"""
... |
0542b553a2cd9a73358ea7c3bd1e789926706918d05be4c18be8c556fe33bf96 | Python | 32,881 | 860 | """Utilities for converting fNIRS datasets to the BIDS standard.
Provides functions to organise raw SNIRF files into a BIDS directory tree,
generate BIDS-compliant filenames, create required sidecar files
(``dataset_description.json``, ``participants.tsv``/``.json``,
``_scans.tsv``, ``_sessions.tsv``), and read/write ... |
08adcbadc7d62a70a1a24526d5e1d8b0be3743b0f9a8fabb4310cfb9860c9c05 | Python | 32,883 | 1,004 | __all__ = ['atleast_1d', 'atleast_2d', 'atleast_3d', 'block', 'hstack',
'stack', 'unstack', 'vstack']
import functools
import itertools
import operator
from . import numeric as _nx
from . import overrides
from .multiarray import array, asanyarray, normalize_axis_index
from . import fromnumeric as _from_nx
... |
d2aeec6be59f7ab264f6b8ccf4bcfe2786d64da7373bc58aff261df4e5763bf5 | Python | 32,938 | 959 | """
The tests in this package are to ensure the proper resultant dtypes of
set operations.
"""
from datetime import datetime
import operator
import numpy as np
import pytest
from pandas._libs import lib
from pandas.core.dtypes.cast import find_common_type
from pandas import (
CategoricalDtype,
CategoricalIn... |
35398686f9bf7e573a83376d39e00e5ec3b76a2e8ade97b21f8efa4a3faa7cb0 | Python | 32,982 | 940 | import numpy as np
import pytest
import pandas as pd
from pandas import (
Categorical,
DataFrame,
NaT,
Timestamp,
date_range,
)
import pandas._testing as tm
from pandas.util.version import Version
class TestDataFrameSortValues:
@pytest.mark.parametrize("dtype", [np.uint8, bool])
def test_... |
51cc86f0a2b2adde6fd6ceaa0dd284933c0bc26a0c95f1c0f3ddcb8fe38e825d | Python | 32,983 | 752 | """ Modified version of build_ext that handles fortran source files.
"""
import os
import subprocess
from glob import glob
from distutils.dep_util import newer_group
from distutils.command.build_ext import build_ext as old_build_ext
from distutils.errors import DistutilsFileError, DistutilsSetupError,\
DistutilsE... |
bd6e7f3e28b88bfc2ffd5355474c27fbb205c1d81fdadcd13a8af87938553baf | Python | 32,994 | 962 | """
Utilities for conversion to writer-agnostic Excel representation.
"""
from __future__ import annotations
from collections.abc import (
Hashable,
Iterable,
Mapping,
Sequence,
)
import functools
import itertools
import re
from typing import (
TYPE_CHECKING,
Any,
Callable,
cast,
)
impo... |
11bb010a5b89fb67952d2c571e02e8e94bace95b27adbcea3bdb18691b9ec20b | Python | 33,008 | 1,090 | from textwrap import dedent
import numpy as np
import pytest
from pandas import (
DataFrame,
MultiIndex,
Series,
option_context,
)
pytest.importorskip("jinja2")
from pandas.io.formats.style import Styler
from pandas.io.formats.style_render import (
_parse_latex_cell_styles,
_parse_latex_css_c... |
77b5c3560b985744636e244655cf4719a95a895b8080aa2ac4060adab5a58246 | Python | 33,027 | 926 | """Gaussian-copula mutual information estimation.
The estimators in this module follow the historical MATLAB implementation in
this repository, but are packaged for modern Python use.
"""
from __future__ import annotations
import math
import os
import warnings
from numbers import Integral
import numpy as np
from sc... |
00ffd7ece91df261193f1f8724621f96dd7a10cdb87ea5285088a94c0fa7c5d4 | Python | 33,085 | 830 | # License: GNU Affero General Public License v3 or later
# A copy of GNU AGPL v3 should have been included in this software package in LICENSE.txt.
""" Shared functions across variants of clusterblast """
from collections import defaultdict, OrderedDict
import logging
import os
import struct
from tempfile import Name... |
c5c50041343816e93f36c562c3eb0bef92dfe4b96b5179fe081a2999bbacb71a | Python | 33,102 | 988 | """
Backend magic inherited from tensornetwork: jax backend
"""
# pylint: disable=invalid-name
import logging
from functools import partial
from typing import Any, Callable, Optional, Sequence, Tuple, Union
import numpy as np
import tensornetwork
from scipy.sparse import coo_matrix
from tensornetwork.backends.jax i... |
95b385220d9a5c50db67a216a6e6d14d99b599bf92582273c07206c78eb7fb41 | Python | 33,104 | 941 | """Provides pipeline for segmenting the cerebellum."""
# ---------------------------------------------------------------------------
# Authors: John G Samuelson <johnsam@mit.edu>
# Christoph Dinh <christoph.dinh@brain-link.de>
# Teemu Taivainen
# Created: September, 2021 (Modified: July, 2026)
# Licen... |
3fa66e6d7f70ff21cffac5bf6f97da65d070ce72633f59c80307a4cb88942da7 | Python | 33,154 | 983 | ## ...........................................................................
##
## PIMMS (Polymer Interactions in Multicomponent Mixtures)
## Alex Holehouse, Pappu Lab, Holehouse Lab
## Copyright 2015 - 2026
## ...........................................................................
#
##
## analysis_general
##... |
83d0569a48bcae1a12823ea9104abf6ae772396805bdc689d949b699abcec17f | Python | 33,156 | 855 | #!/usr/bin/env python3.7
"""Submits NEURON fiber simulations.
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 arg... |
fa3fefea531a1b4fc2730fdc81f07640cc2d25ec14a5123c56d482cf98dbdbd7 | Python | 33,202 | 767 | # License: GNU Affero General Public License v3 or later
# A copy of GNU AGPL v3 should have been included in this software package in LICENSE.txt.
# for test files, silence irrelevant and noisy pylint warnings
# pylint: disable=no-self-use,protected-access,missing-docstring
from collections import defaultdict
import... |
b002d2822437dedb774d3ea790bd3379da2d607b62570b4daf9ebeb6a9caafa2 | Python | 33,216 | 1,025 | # -*- coding: utf-8 -*-
"""
##########################################################################################
This module is used for computing the Autocorrelation descriptors based different
properties of AADs.You can also input your properties of AADs, then it can help you
to compute Autocorrelat... |
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