sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 17k | content stringlengths 1 200k |
|---|---|---|---|---|
7737910cfb3596f272573e9778bbbfca73c31784841468e92212dd9883247fde | Python | 52,379 | 1,675 | """
==================================================
Laguerre Series (:mod:`numpy.polynomial.laguerre`)
==================================================
This module provides a number of objects (mostly functions) useful for
dealing with Laguerre series, including a `Laguerre` class that
encapsulates the usual arit... |
273f9e9b41831e37b187c16254461c700315e31079069f6441550c335b8135c6 | Python | 52,484 | 1,552 | """
C declarations, CPP macros, and C functions for f2py2e.
Only required declarations/macros/functions will be used.
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 Lice... |
459efb0279b3d9f39f67b2aeb62d7de7c9989d38344ec571207b476163c57ba6 | Python | 52,694 | 1,194 | """Independent Component Analysis by Entropy Bound Minimization (ICA-EBM).
This code is based on :cite:t:`Li2010A` and converted matlab versions provided by the
MLSP Lab at the University of Maryland, which is available here:
https://mlsp.umbc.edu/resources.html.
(:cite:t:`yang2025flexible`) H. Yang, T. Vu, Ehsan Ah... |
c6c6286b0bf32b8100d9021876d9392b2ac591409ee244ade703ad5c29bfbf5b | Python | 52,820 | 1,499 | """
Implementation of optimized einsum.
"""
import itertools
import operator
from numpy._core.multiarray import c_einsum
from numpy._core.numeric import asanyarray, tensordot
from numpy._core.overrides import array_function_dispatch
__all__ = ['einsum', 'einsum_path']
# importing string for string.ascii_letters wou... |
cdc142e4e15119903daf9de05ca985654415d28fd3d4191d4d72d9f2f1b460b0 | Python | 52,890 | 1,229 | import itertools
import pytest
import numpy as np
from numpy.testing import (
assert_, assert_equal, assert_array_equal, assert_almost_equal,
assert_raises, suppress_warnings, assert_raises_regex, assert_allclose
)
# Setup for optimize einsum
chars = 'abcdefghij'
sizes = np.array([2, 3, 4, 5, 4, 3, 2, 6,... |
cceec66063ab17d266fba34149e9a11907ba5ebbe0edbd50524e95bd478ccbdf | Python | 53,176 | 1,342 | #!/usr/bin/env python
"""
Segmentation Leakage Robustness Analysis for Cytocraft Algorithm
This script models a realistic tissue scenario where:
- Multiple cell types exist with DIFFERENT chromosome structures (e.g., epithelial,
fibroblast, immune cells each with distinct chromatin organization)
- Only Type 0 cells... |
37fdc3e527496a38cab129aa323de4d988977333cf55b8249333e542c6110658 | Python | 53,177 | 1,406 | """Tests for matrix-function spectral observables."""
import numpy as np
import pytest
from pytest_lazyfixture import lazy_fixture as lf
import tensorcircuit as tc
def _problem():
energies = np.array([-1.0, 0.2, 1.1])
hamiltonian = np.diag(energies).astype(np.complex64)
probes = np.eye(3, dtype=np.compl... |
3ef3f46cad052c40d08f5e2edf8d0726eee08734bfd96971846429274cdb3101 | Python | 53,254 | 1,517 | """Fortran/C symbolic expressions
References:
- J3/21-007: Draft Fortran 202x. https://j3-fortran.org/doc/year/21/21-007.pdf
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 Nu... |
88decbca5d059438e5136dddb92e984bf884a164523cff2dc9d40b76648c5ac2 | Python | 53,344 | 1,418 | import warnings
import pytest
import inspect
from functools import partial
import numpy as np
from numpy._core.numeric import normalize_axis_tuple
from numpy.exceptions import AxisError, ComplexWarning
from numpy.lib._nanfunctions_impl import _nan_mask, _replace_nan
from numpy.testing import (
assert_, assert_equa... |
d726a1b9d281f41b0e07fa5431cb5af9bafb5c0f26ae589a45d815dcd389ef37 | Python | 53,771 | 1,122 | # -*- coding: utf-8 -*-
# Time : 2023/4/19 14:58
# Author : Regulus
# FileName: main.py
# Explain:
# Software: PyCharm
import argparse
import time
import timm.models
import yaml
import os
import logging
from collections import OrderedDict
from contextlib import suppress
from datetime import datetime
from... |
bf18e7d5c38772520a24ac68ca206c41363ae461db919b5946e290d8054229ac | Python | 53,853 | 1,201 | """
pygments.lexers.python
~~~~~~~~~~~~~~~~~~~~~~
Lexers for Python and related languages.
:copyright: Copyright 2006-2025 by the Pygments team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
import keyword
from pip._vendor.pygments.lexer import DelegatingLexer, RegexLexer, include, \
... |
3d94b6adbbed9d84d88428c60eea857562e492da3c2115c07bf17e69bc63430f | Python | 53,937 | 1,493 | import logging
from typing import Dict, Optional, Union
import numpy as np
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 torch_sc... |
7ccb6a17a244c2e6ac05bc35d9d06fdc9647b511b89a87b487baf6cfcdd036c1 | Python | 53,980 | 1,174 | #!/usr/bin/env python3.7
"""Defines FiberSet 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 os... |
33a6e3717aff9ba7242ccd68a04415de55cf41e751883611138e198ea34cd389 | Python | 54,034 | 1,562 | from __future__ import annotations
from typing import TYPE_CHECKING, Literal
import numpy as np
import tifffile
from scipy.ndimage import gaussian_filter1d
from skimage import filters, morphology
from sqlmodel import Session, col, select
from cali.logger import cali_logger
from cali.sqlmodel import FOV, ROI, DataAna... |
30d03bd1488f17d062b17546a6f413b754a3653323efe279a7fe3705a67ee00a | Python | 54,256 | 1,733 | from datetime import datetime
import warnings
import numpy as np
import pytest
from pandas.core.dtypes.dtypes import CategoricalDtype
import pandas as pd
from pandas import (
DataFrame,
MultiIndex,
Series,
Timestamp,
date_range,
)
import pandas._testing as tm
from pandas.tests.frame.common import... |
d2e0c7bbd7521fd4cc34e3bf84f805ed05283d91e90e036f4ce26cda44325934 | Python | 54,326 | 1,128 | # New matplotlib colormaps by Nathaniel J. Smith, Stefan van der Walt,
# and (in the case of viridis) Eric Firing.
#
# This file and the colormaps in it are released under the CC0 license /
# public domain dedication. We would appreciate credit if you use or
# redistribute these colormaps, but do not impose any legal r... |
a756d7d7c2fe7d4c1616d9aed09e059da84107d7162c2b1458b91722d43bcc1d | Python | 54,466 | 1,740 | """
==============================================================
Hermite Series, "Physicists" (:mod:`numpy.polynomial.hermite`)
==============================================================
This module provides a number of objects (mostly functions) useful for
dealing with Hermite series, including a `Hermite` clas... |
6a1f2950b4c5f2e629bcbd20d82fd01e1ded8b727adbe2a44a6b5c86b6157cdf | Python | 54,654 | 1,564 | """
Built-in pipeline
"""
import time
import logging
import logging.config
import shutil
import os
import matplotlib
matplotlib.use('Agg')
# supress PCA unpickle userwarning
# Cat: TODO: this is dangersous, may wish to fix the problem in cluster.py
# import warnings
# warnings.filterwarnings("ignore", category=UserWa... |
d6995a216a6f460019e25ac5c8caf19d5eda6ddff6106e440cded2b67c4645e2 | Python | 54,823 | 1,642 | """Evoked experiment correlation and synchrony plots.
Sorted combined plots where stimulated ROIs are shown first, followed by
non-stimulated ROIs, to visualize network clustering.
"""
from __future__ import annotations
import contextlib
from typing import TYPE_CHECKING
import numpy as np
import pyqtgraph as pg
fro... |
cf49c22bd75b17cc30dd1a00dcc870657e7f044f9617c00017cebbd9ed989d5b | Python | 54,859 | 1,606 | from datetime import (
date,
datetime,
)
import numpy as np
import pytest
import pandas as pd
from pandas import (
DataFrame,
Index,
MultiIndex,
Series,
bdate_range,
)
import pandas._testing as tm
from pandas.tests.groupby import get_groupby_method_args
def test_apply_func_that_appends_g... |
b9dcc54ab8bed3b417815d2ffb11c9dc2c7cc0abc925aa02072c80c30220ea03 | Python | 54,899 | 1,511 | from datetime import (
date,
datetime,
timedelta,
)
from functools import partial
from io import BytesIO
import os
import re
import numpy as np
import pytest
from pandas.compat import is_platform_windows
from pandas.compat._constants import PY310
from pandas.compat._optional import import_optional_depende... |
3ded31374bf51f860fcf9e56219b39b7257acc9c1192b2da93fc75c571fa7414 | Python | 54,906 | 1,425 | import operator
import numpy as np
import pytest
from pandas.errors import (
NumExprClobberingError,
UndefinedVariableError,
)
import pandas.util._test_decorators as td
import pandas as pd
from pandas import (
DataFrame,
Index,
MultiIndex,
Series,
date_range,
)
import pandas._testing as t... |
f04350a435a233411287c1191275f3c3f5ed6d45221688ef162ecc399135e9d6 | Python | 55,181 | 1,747 | """
Generic data algorithms. This module is experimental at the moment and not
intended for public consumption
"""
from __future__ import annotations
import decimal
import operator
from textwrap import dedent
from typing import (
TYPE_CHECKING,
Literal,
cast,
)
import warnings
import numpy as np
from pan... |
3d0fc481df67f634a0b671906321782b98f69d8c21508ba584f9f28a691dafe9 | Python | 55,212 | 1,873 | """Built-in template filters used with the ``|`` operator."""
import math
import random
import re
import typing
import typing as t
from collections import abc
from inspect import getattr_static
from itertools import chain
from itertools import groupby
from markupsafe import escape
from markupsafe import Markup
from m... |
c632461eeede653fca5ff2c02fef14053153c6a17066825465eb5056b6e327b8 | Python | 55,297 | 1,444 | import sys
import warnings
import functools
import operator
import pytest
import numpy as np
from numpy._core._multiarray_tests import array_indexing
from itertools import product
from numpy.exceptions import ComplexWarning, VisibleDeprecationWarning
from numpy.testing import (
assert_, assert_equal, assert_raise... |
de754e70c03e20565df4d6390111110693dedfa9ce583245454ce0eacd9a7ea6 | Python | 55,350 | 1,702 | """Tests for correlation plot mouse event handlers.
This module tests that:
1. Hover handlers accept pg.Point directly (not via event.scenePos())
2. Click handlers accept MouseClickEvent with ev.scenePos() method
3. All correlation plots emit roiSelected signal on click
4. Handlers are properly connected/disconnected
... |
806accc82a7d61a699ea6fe14ed9b514d2ba60af2607412ba51f23f9602a0809 | Python | 55,369 | 1,257 | import numpy as np
import contextlib
import os
import inspect
import pandas as pd
import warnings
from typing import Literal
from causarray.DR_estimation import AIPW_mean, cross_fitting
from causarray.gcate_glm import loess_fit, ls_fit
import causarray.gcate_glm as _gcate_glm # for _backend_override
from causarray.DR_... |
e7af4963b3e3978e778973ffb71ae592d5725321f5091ff7ebbeddb9edac7f05 | Python | 55,511 | 1,567 | # Arithmetic tests for DataFrame/Series/Index/Array classes that should
# behave identically.
# Specifically for numeric dtypes
from __future__ import annotations
from collections import abc
from datetime import timedelta
from decimal import Decimal
import operator
import numpy as np
import pytest
import pandas as p... |
e12e8f10abd1824d142d2a339f7edc3ac87aa219c41d9df2692184a740e687d9 | Python | 55,554 | 1,672 | """
test .agg behavior / note that .apply is tested generally in test_groupby.py
"""
import datetime
import functools
from functools import partial
import re
import numpy as np
import pytest
from pandas.errors import SpecificationError
from pandas.core.dtypes.common import is_integer_dtype
import pandas as pd
from ... |
fee0f40f4955c99e0e4d90e6cb535e64ccf021f251c655dbae96589d27b81902 | Python | 55,584 | 1,220 | # YOLOv5 🚀 by Ultralytics, GPL-3.0 license
"""
Dataloaders and dataset utils
"""
import contextlib
import glob
import hashlib
import json
import math
import os
import random
import shutil
import time
from itertools import repeat
from multiprocessing.pool import Pool, ThreadPool
from pathlib import Path
from threading... |
052746ab0181f04210a4b99368fe47f42e1e3f5200466cb8a9b1370eb8b19f21 | Python | 55,621 | 1,316 | import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
import pandas as pd
import os
import re
from pathlib import Path
import scipy.stats as sts
from statsmodels.stats.multitest import multipletests
from collections.abc import Iterable
from scipy.optimize import curve_fit
from matplotlib.ticker impor... |
815269c68884698e6471af2e980911b7a033d8bd062b77dfc2307adc42c6eb63 | Python | 55,634 | 1,650 | from __future__ import annotations
from typing import (
TYPE_CHECKING,
Any,
Callable,
Literal,
overload,
)
import warnings
import numpy as np
from pandas._libs import (
lib,
missing as libmissing,
)
from pandas._libs.tslibs import is_supported_dtype
from pandas._typing import (
ArrayL... |
8f663326268c5867cfd486d1e5d8d0c803df5324417ea2cf4dd75bc14fb31180 | Python | 55,739 | 1,476 | """
SMI: Standard Model Imaging class
"""
import os
import sys
from math import comb
import numpy as np
import itertools
import scipy.ndimage as snd
import scipy.cluster.hierarchy as sch
import scipy.special as scp
import scipy.linalg as scl
import scipy.io as sio
import scipy.optimize as sco
import warnings
class S... |
9de3504e38104048b8e8dcc1e16aa1849c4c556658a264c8751495d7e7d97df0 | Python | 55,890 | 1,307 | import os
import warnings
import random
import torchvision.datasets
import braincog.datasets.ucf101_dvs
try:
import tonic
from tonic import DiskCachedDataset
except:
warnings.warn("tonic should be installed, 'pip install git+https://github.com/FloyedShen/tonic.git'")
import torch
import torch.nn.function... |
57b8f3ffa1969221e4fa9d6a363e175fe7fee1b259337436efc68f472d6ad7d0 | Python | 56,015 | 1,754 | from typing import Any
import numpy as np
import pytest
from pytest_lazyfixture import lazy_fixture as lf
import sympy
import tensornetwork as tn
import tensorcircuit as tc
from tensorcircuit.simplify import _full_light_cone_cancel
from tensorcircuit.symbolgates import (
sym_cphase,
sym_cr,
sym_crx,
s... |
3ee0dddecef0febe7807620b5ca421785314c649729473cdfaf1d5abf9868e4f | Python | 56,064 | 1,416 | """Tests for the array padding functions.
"""
import pytest
import numpy as np
from numpy.testing import assert_array_equal, assert_allclose, assert_equal
from numpy.lib._arraypad_impl import _as_pairs
_numeric_dtypes = (
np._core.sctypes["uint"]
+ np._core.sctypes["int"]
+ np._core.sctypes["float"]
... |
5b157155d5cbd568a741dc6e2a9dd905bd853ecac778cdf0cebdd0605620b87c | Python | 56,211 | 1,621 | """
Methods for abstract circuits independent of nodes, edges and contractions
"""
# pylint: disable=invalid-name
import json
import logging
from copy import deepcopy
from functools import reduce
from operator import add
from typing import (
Any,
Callable,
Dict,
List,
Optional,
Sequence,
T... |
062b28098fe2ffa30b075987c45a2fd5b121cddc9792a11addec469b1ed2f79e | Python | 56,693 | 1,461 | from __future__ import division
import torch
import math
import random
import numpy as np
import numbers
import collections
import warnings
import PIL
from . import functional as F
Sequence = collections.abc.Sequence
Iterable = collections.abc.Iterable
__all__ = [
"Compose", "ToTensor", "ToCVImage", "Normalize",... |
998f3eb668b96ea067817c217d3352db1ff57f09dc2cfde2a344f01f04fe9f99 | Python | 56,862 | 1,657 | from collections.abc import Iterator
from functools import partial
from io import (
BytesIO,
StringIO,
)
import os
from pathlib import Path
import re
import threading
from urllib.error import URLError
import numpy as np
import pytest
from pandas.compat import is_platform_windows
import pandas.util._test_decor... |
d2b1b9fcb99af0c108b3f97f192f20d1e0e100bb24e7fc28920f48bb346f491b | Python | 57,218 | 1,702 | """ test with the .transform """
import numpy as np
import pytest
from pandas._libs import lib
from pandas.core.dtypes.common import ensure_platform_int
import pandas as pd
from pandas import (
Categorical,
DataFrame,
Index,
MultiIndex,
Series,
Timestamp,
concat,
date_range,
)
import ... |
6d6993d179198a1cad890d55f3e5cde2d9649af190c3f9c176f552c0a24dbc94 | Python | 57,249 | 609 | {
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "9f14ea5c",
"metadata": {},
"outputs": [],
"source": [
"import math\n",
"import random\n",
"import h5py\n",
"import copy\n",
"import os \n",
"import numpy as np\n",
"import keras\n",
"import tensorflow a... |
c0fe12b6106b2a14ffc3ad9032efddbd8e48eccd0020120ad03da582b9b1a855 | Python | 57,271 | 1,277 | 7# -*- coding: utf-8 -*-
"""
All the main models and architectures used as classes. This code is planned for NEST 3.2
"""
import nest
import numpy as np
import pandas as pd
import os, sys
import time
sys.path.append(os.path.dirname(__file__))
import tools
nest.Install('mymodule3')
# nest.Install('mymoduleSOM')
class... |
b43a772e7aca8cbdb0b3e2700126eccf990a00070d6afef45ec7104a0b30cee7 | Python | 57,394 | 1,825 | import concurrent.futures
import itertools
import os
import pickle
import string
import sys
import tempfile
import numpy as np
import pytest
from numpy.dtypes import StringDType
from numpy._core.tests._natype import pd_NA
from numpy.testing import assert_array_equal, IS_WASM, IS_PYPY
@pytest.fixture
def string_list... |
cbfd2e8d8257e078b17c772aa094b63754461e4501b5d762eeb46b7bf86173c4 | Python | 57,395 | 1,782 | """module containing integration tests for the distance generatio/comparison workflows"""
# from python
from unittest import TestCase
from unittest.mock import MagicMock
from click.globals import push_context
from pathlib import Path
from itertools import combinations
# from dependencies
from Bio.SeqFeature import Se... |
2828e79f3be795ae88cac2a56ef50ef1b5d2677871c6a7ec91cf42c1e0ddd623 | Python | 57,446 | 1,673 | from datetime import (
datetime,
timedelta,
)
from decimal import Decimal
import numpy as np
import pytest
import pandas as pd
from pandas import (
Categorical,
DataFrame,
DatetimeIndex,
Index,
NaT,
Period,
PeriodIndex,
RangeIndex,
Series,
Timedelta,
TimedeltaIndex,... |
0c2a5e5fef7633a81423182c67cc7cf2109155f8eb18eb548b394dfdfc4630ae | Python | 57,450 | 1,348 | import os
import warnings
import random
import torchvision.datasets
import braincog.datasets.ucf101_dvs
try:
import tonic
from tonic import DiskCachedDataset
except:
warnings.warn("tonic should be installed, 'pip install git+https://github.com/FloyedShen/tonic.git'")
import torch
import torch.nn.function... |
52679f6435217478d6b516d6715c2745aec91772f8f8de0d4b13b8214ef08a8b | Python | 57,475 | 1,444 | """
Physics-facing density-of-states, thermal, and response estimators.
The module separates physical quantities from the numerical reductions in
``tensorcircuit.matrixfunc``. A reader can therefore start from a Hamiltonian,
an observable, and a few probes without choosing a recurrence implementation.
The lower-level ... |
0b4e32916de65b35bea0435febfac5c3f0da084f0aa1247cb7ef9199588a19d6 | Python | 57,498 | 1,450 | import os
import numpy as np
import matplotlib.patches as mpatches
import matplotlib.pyplot as plt
import tqdm
import parmap
import scipy
import networkx as nx
import logging
import datetime as dt
from statsmodels import robust
from scipy.signal import argrelmin
from sklearn.discriminant_analysis import LinearDiscrimi... |
d98984c1fc9774ddc7718054b60f56b2cacf76ac099b3c769a1250b481276c18 | Python | 57,710 | 1,494 | """Various hierarchical models for hand movements."""
from itertools import product
import numpy as np
from scipy.integrate import solve_ivp
from src import utils
from src.model import single
def get_crho(num_neurons, seq_length, clusters):
"""Set the values for the interneuron connections.
The sequences ... |
c7bafcfa786761d89fc3f3e3a294f46b8b7df4c4c6ce5381bfe837f07387c629 | Python | 58,095 | 1,588 | import contextlib
import copy
import re
from textwrap import dedent
import numpy as np
import pytest
from pandas import (
DataFrame,
IndexSlice,
MultiIndex,
Series,
option_context,
)
import pandas._testing as tm
jinja2 = pytest.importorskip("jinja2")
from pandas.io.formats.style import ( # isort... |
d0fed9047291d26234b5ab72a83087c277dec04122438f1dc2bcd52f63d0024d | Python | 58,137 | 1,754 | """
Create the numpy._core.multiarray namespace for backward compatibility.
In v1.16 the multiarray and umath c-extension modules were merged into
a single _multiarray_umath extension module. So we replicate the old
namespace by importing from the extension module.
"""
import functools
from . import overrides
from . ... |
826aa63e8304e7f0e2e3c36ddbcfc26bec1a6e3325b488e906ed2091595b744a | Python | 58,726 | 1,504 | """
Fermion Gaussian state simulator
"""
from typing import Any, Dict, List, Optional, Sequence, Tuple, Union
import numpy as np
try:
import openfermion
except ModuleNotFoundError:
pass
from .cons import backend, dtypestr, rdtypestr, get_backend
from .circuit import Circuit
from . import quantum
Tensor = A... |
093f9f3d99455108f4173c9012c6261c69c3db86b895b3017e437226de05cf3f | Python | 58,788 | 1,156 | #SCENIC+ PIPELINE from current Seurat+Singac processed datasets (using un-paired data)
export LD_LIBRARY_PATH="/opt/R/3.5.2/lib64/R/lib:$LD_LIBRARY_PATH"
import os
os.environ['R_HOME'] = "/opt/R/3.5.2/lib64/R/"
#Quality control - required for later run SCENIC+
import pybiomart as pbm
dataset = pbm.Dataset(name='hsapi... |
ee494377289c92c401fd7825fb7500981c33098a2bd40219aa4948713e9d1fff | Python | 58,796 | 1,613 | # -*- coding: utf-8 -*-
"""
This module offers a generic date/time string parser which is able to parse
most known formats to represent a date and/or time.
This module attempts to be forgiving with regards to unlikely input formats,
returning a datetime object even for dates which are ambiguous. If an element
of a dat... |
4ee68078680c36f3e334b625cb4c2b56007808349f9f4badb4efb4f8d874c033 | Python | 58,824 | 1,740 | from pathlib import Path
from typing import Any
from unittest.mock import MagicMock, Mock, patch
import pytest
import useq
from pytestqt.qtbot import QtBot
from qtpy.QtCore import Qt
from qtpy.QtGui import QStandardItemModel
from qtpy.QtWidgets import QApplication, QMessageBox
from sqlmodel import Session, create_engi... |
9f298c8f533d61eb5016923c7ae56cdc73428f9daff61ae6cefa47e1db68a9bb | Python | 58,972 | 1,217 | import numpy as np
from pathlib import Path
import os
from collections import defaultdict
import matplotlib.pyplot as plt
import pandas as pd
import csv
import re
import librosa
from running_mean import RunningStatsArray
class CrossCorrelationProcessor:
"""Class to process cross-correlation data for statistical an... |
b44041e66dcb70bf191efeb62afec6e1497d30496bd97f09ae45ef69dca9cc2e | Python | 59,073 | 1,659 | from __future__ import annotations
from collections.abc import (
Hashable,
Iterable,
Mapping,
Sequence,
)
import datetime
from functools import partial
from io import BytesIO
import os
from textwrap import fill
from typing import (
IO,
TYPE_CHECKING,
Any,
Callable,
Generic,
Lite... |
3ff0518e744a42fcbda7cc1ebeab8049e11fce612771d78249030e56bab16300 | Python | 59,158 | 1,627 | # pylint: disable=invalid-name
import itertools
import importlib
import os
import sys
from functools import partial
import numpy as np
import pytest
import tensornetwork as tn
from pytest_lazyfixture import lazy_fixture as lf
thisfile = os.path.abspath(__file__)
modulepath = os.path.dirname(os.path.dirname(thisfile)... |
bb1764acf22930cec15942a6c25a15882104d49b4eb3191728275fc4b43a1350 | Python | 59,617 | 1,675 | # Arithmetic tests for DataFrame/Series/Index/Array classes that should
# behave identically.
# Specifically for Period dtype
import operator
import numpy as np
import pytest
from pandas._libs.tslibs import (
IncompatibleFrequency,
Period,
Timestamp,
to_offset,
)
from pandas.errors import PerformanceW... |
e5f6e0d1a32e0db80ea5f6260d307286534a65680d902543740f01438cd95f30 | Python | 59,654 | 1,685 | """
Collection of utilities to manipulate structured arrays.
Most of these functions were initially implemented by John Hunter for
matplotlib. They have been rewritten and extended for convenience.
"""
import itertools
import numpy as np
import numpy.ma as ma
import numpy.ma.mrecords as mrec
from numpy._core.overri... |
f42c82b448bef5b1e6a7958d15b5d495279ff5f45fcc9b00d06feee0be614d83 | Python | 59,759 | 1,502 | # encoding: utf-8
# Author : Floyed<Floyed_Shen@outlook.com>
# Datetime : 2022/4/10 18:46
# User : Floyed
# Product : PyCharm
# Project : braincog
# File : node.py
# explain : 神经元节点类型
import abc
import math
from abc import ABC
import numpy as np
import random
import torch
from torch import nn
from ... |
0dd6928ea217d2c4dcfb35c5bf775bbaad0a45cab8a9cc4971911b96076d2328 | Python | 60,265 | 1,855 | from datetime import (
date,
datetime,
)
from decimal import Decimal
import os
import numpy as np
import pytest
from pandas.compat.numpy import (
np_version_gt2,
np_version_gte1p24,
)
from pandas.errors import IndexingError
from pandas.core.dtypes.common import is_list_like
from pandas import (
... |
09473696453e5f9f6655d19f8cc0819197a218f2f7bb174e36384d245d93ef06 | Python | 60,408 | 1,715 | from __future__ import annotations
import io
import typing
import warnings
from abc import ABC, abstractmethod
from collections import deque
from dataclasses import dataclass, field
from datetime import timedelta
from io import RawIOBase, UnsupportedOperation
from math import ceil
from mmap import mmap
from operator i... |
4defaba61f1ba3d83d957b1c084b157ac693e9262ed8e07ff23201395b123794 | Python | 60,624 | 1,737 | from collections import defaultdict
from datetime import datetime
from functools import partial
import math
import operator
import re
import numpy as np
import pytest
from pandas.compat import IS64
from pandas.errors import InvalidIndexError
import pandas.util._test_decorators as td
from pandas.core.dtypes.common im... |
bee55edde249d7f7c1a093600e82dd4d80a2a9784c9921f9a871ac7774fb2360 | Python | 61,257 | 2,097 | from __future__ import annotations
from io import (
BytesIO,
StringIO,
)
from lzma import LZMAError
import os
from tarfile import ReadError
from urllib.error import HTTPError
from xml.etree.ElementTree import ParseError
from zipfile import BadZipFile
import numpy as np
import pytest
from pandas.compat._optio... |
d821021fc7ce6143fb2f1caa95e8441d599eda848de19bc49778631fcb7e4c36 | Python | 61,363 | 1,721 | """
test date_range, bdate_range construction from the convenience range functions
"""
from datetime import (
datetime,
time,
timedelta,
)
import re
import numpy as np
import pytest
import pytz
from pytz import timezone
from pandas._libs.tslibs import timezones
from pandas._libs.tslibs.offsets import (
... |
f6786b3fb0a1f8d6c65f4d30bf2af8cb2fae84d1ead8e09ceb48201ab9e2fdf9 | Python | 61,513 | 1,672 | """Classes for managing templates and their runtime and compile time
options.
"""
import os
import typing
import typing as t
import weakref
from collections import ChainMap
from functools import lru_cache
from functools import partial
from functools import reduce
from types import CodeType
from markupsafe import Mark... |
184ed0384fcdf531c38eeccac7481423d685e212e1d31c010daee12d5b23cbea | Python | 61,725 | 1,536 | from __future__ import annotations
import collections.abc as cabc
import os
import sys
import typing as t
import weakref
from datetime import timedelta
from inspect import iscoroutinefunction
from itertools import chain
from types import TracebackType
from urllib.parse import quote as _url_quote
import click
from wer... |
50917a7a929819f1aaf5096b47d62e03b10afe623c010da8b1d038521b21d66b | Python | 61,824 | 1,497 | from __future__ import annotations
from typing import Any
import numpy as np
SEED_NONE = None
SEED_INT = 4579435749574957634658964293569
SEED_ARR: np.ndarray[Any, np.dtype[np.int64]] = np.array([1, 2, 3, 4], dtype=np.int64)
SEED_ARRLIKE: list[int] = [1, 2, 3, 4]
SEED_SEED_SEQ: np.random.SeedSequence = np.random.SeedS... |
9de08511eaacd9de84227e114090e279b4f37544998385d4d2a31dbf15f46579 | Python | 62,034 | 1,698 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from smac.env.multiagentenv import MultiAgentEnv
from smac.env.starcraft2.maps import get_map_params
import atexit
from warnings import warn
from operator import attrgetter
from copy import deepcopy
import num... |
dc09a42fc8dd1450415730e33f7ce8dbbce2de48d72ad06970afa3eb59711d15 | Python | 62,146 | 1,843 | import os
from collections import abc
from cycler import Cycler, cycler
import numpy as np
import pandas as pd
from pandas import Index
from scipy import stats
from scipy.sparse import issparse
import matplotlib.pyplot as pl
import matplotlib.transforms as tx
from matplotlib import patheffects, rcParams
from matplot... |
527cbd79a643d631917d69a1ea9ebfeb91d27af98d9b5eaf3f406f4f3bc7e614 | Python | 62,164 | 1,970 | """
Routines for casting.
"""
from __future__ import annotations
import datetime as dt
import functools
from typing import (
TYPE_CHECKING,
Any,
Literal,
TypeVar,
cast,
overload,
)
import warnings
import numpy as np
from pandas._config import using_pyarrow_string_dtype
from pandas._libs imp... |
53c3e5d2bf65dc057deb121299a0e36fe6ef6c2553eb5ae6ef35a24f92fcff08 | Python | 62,165 | 2,003 | """
====================================================
Chebyshev Series (:mod:`numpy.polynomial.chebyshev`)
====================================================
This module provides a number of objects (mostly functions) useful for
dealing with Chebyshev series, including a `Chebyshev` class that
encapsulates the us... |
db794b7bdbc7b48c6aab5ac7fba119eaaa8875c27b340b35f7b1e8a88600373e | Python | 62,259 | 1,951 | import marimo
__generated_with = "0.18.2"
app = marimo.App()
@app.cell
def _():
# Load the files
import numpy as np
# Load the data files
PV_mTCOff = np.load("PV_mTCOff.npy", allow_pickle=True)
PV_mTCOn = np.load("PV_mTCOn.npy", allow_pickle=True)
SST_mTCOff = np.load("SST_mTCOff.npy", allow... |
428cede225607195e9f314af8bf6ac4cc67862e7feef64a9eb3eade5ff95657a | Python | 62,553 | 1,918 | import warnings
import numpy as np
import pandas as pd
from scipy.sparse import issparse
from scipy.stats.distributions import chi2, norm
import matplotlib as mpl
import matplotlib.pyplot as pl
from matplotlib import gridspec, rcParams
from scvelo import logging as logg
from scvelo.core import clipped_log, invert, S... |
6331c22cd9126bb49a1197221f2604969122a3081083c56fcbf71a70681699fa | Python | 62,639 | 1,813 | """Solver for the image reconstruction problem."""
import hashlib
import logging
from abc import ABC, abstractmethod
from pathlib import Path
from typing import Literal
import h5py
import numpy as np
import pint
import scipy.stats
import xarray as xr
from scipy.sparse import csr_array
from scipy.spatial import KDTree... |
43a2798a75f5d283c1b57fa56e53e5604c6ecf2728bc6afe2c5313ed061ef697 | Python | 62,692 | 1,687 | """
Discrete Fourier Transforms
Routines in this module:
fft(a, n=None, axis=-1, norm="backward")
ifft(a, n=None, axis=-1, norm="backward")
rfft(a, n=None, axis=-1, norm="backward")
irfft(a, n=None, axis=-1, norm="backward")
hfft(a, n=None, axis=-1, norm="backward")
ihfft(a, n=None, axis=-1, norm="backward")
fftn(a, ... |
1149c474c7de4e15e263a978b21f7205a6d9eb7fcf3b3cb4d734ac87db619f5a | Python | 62,855 | 1,849 | # -*- coding: utf-8 -*-
"""
This module offers timezone implementations subclassing the abstract
:py:class:`datetime.tzinfo` type. There are classes to handle tzfile format
files (usually are in :file:`/etc/localtime`, :file:`/usr/share/zoneinfo`,
etc), TZ environment string (in all known formats), given ranges (with h... |
942dd0718141b738ef990ca0638dc18549a7370e4e9eb697596c363b4eeaa8c0 | Python | 62,905 | 1,514 | import os, warnings
import torchvision.datasets
try:
import tonic
from tonic import DiskCachedDataset
except:
warnings.warn("tonic should be installed, 'pip install git+https://github.com/BrainCog-X/tonic_braincog.git'")
import torch
import torch.nn.functional as F
import torch.utils
import torchvision.data... |
121393a85637334517e5d40696d8739050b46fe4799c2561e124f8b69d2c9856 | Python | 62,938 | 1,578 | """
Rules for building C/API module with f2py2e.
Here is a skeleton of a new wrapper function (13Dec2001):
wrapper_function(args)
declarations
get_python_arguments, say, `a' and `b'
get_a_from_python
if (successful) {
get_b_from_python
if (successful) {
callfortran
if (successful) {
... |
5a18050b04b1ef3ae84bdad4a03271c22aedf0bec0411dff0ee56a248ae3d129 | Python | 63,170 | 1,340 | #!/usr/bin/env python3.7
"""Defines FiberSet 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 mat... |
ae8fd63dc53397158a8e87062e012c7847258db0489e3ceb97cc8f382b7cec6d | Python | 63,176 | 1,917 | from __future__ import annotations
import operator
from operator import (
le,
lt,
)
import textwrap
from typing import (
TYPE_CHECKING,
Literal,
Union,
overload,
)
import warnings
import numpy as np
from pandas._libs import lib
from pandas._libs.interval import (
VALID_CLOSED,
Interva... |
427f0be3584a74eff6c64a533418b67aaa54c7438057705fa9e50aa123a7d1a3 | Python | 63,198 | 1,751 | from __future__ import annotations
from datetime import (
datetime,
time,
)
from functools import partial
from io import BytesIO
import os
from pathlib import Path
import platform
import re
from urllib.error import URLError
from zipfile import BadZipFile
import numpy as np
import pytest
from pandas._config i... |
6a5fbfac17a646e1af8a7b2b33a6ad36c1d3989e8351bc36e2ad8ed91bb57017 | Python | 63,208 | 153 | """
pygments.unistring
~~~~~~~~~~~~~~~~~~
Strings of all Unicode characters of a certain category.
Used for matching in Unicode-aware languages. Run to regenerate.
Inspired by chartypes_create.py from the MoinMoin project.
:copyright: Copyright 2006-2025 by the Pygments team, see AUTHORS.
... |
bd99e0f2bd0f5ad2956fbe23734365122a56cae7afaae7915ad3a102df31eb10 | Python | 63,884 | 1,929 | """
SparseArray data structure
"""
from __future__ import annotations
from collections import abc
import numbers
import operator
from typing import (
TYPE_CHECKING,
Any,
Callable,
Literal,
cast,
overload,
)
import warnings
import numpy as np
from pandas._libs import lib
import pandas._libs.sp... |
f6755d3992a5ae6f2c99545b7c739c99d89e5054b9f10871eb79fb36f9497a33 | Python | 64,742 | 2,060 | """Tests for _RunsPanel — runs list, saved-segmentations, and keep-detection flows."""
from __future__ import annotations
import gc
from pathlib import Path
from typing import TYPE_CHECKING
import pytest
from qtpy.QtCore import QEvent, QPointF, Qt
from qtpy.QtGui import QMouseEvent
from qtpy.QtWidgets import QDialog... |
b3994c2efdd6cbf7dade10753aa51a33887525af5207f5fedf3024416d53bb81 | Python | 64,812 | 1,756 | """Array printing function
$Id: arrayprint.py,v 1.9 2005/09/13 13:58:44 teoliphant Exp $
"""
__all__ = ["array2string", "array_str", "array_repr",
"set_printoptions", "get_printoptions", "printoptions",
"format_float_positional", "format_float_scientific"]
__docformat__ = 'restructuredtext'
#
#... |
216d0ccb59c00c50a96e48cc14b59f5d3dfa3716dcb3d9bb1528a4b121cce237 | Python | 64,846 | 1,726 | from __future__ import annotations
from datetime import datetime
import re
import numpy as np
import pytest
from pandas._config import using_pyarrow_string_dtype
import pandas as pd
from pandas import (
DataFrame,
Index,
Series,
Timestamp,
date_range,
)
import pandas._testing as tm
@pytest.fix... |
0b58a5fa6d33b799ec709a9ad1fd0d93a55c1eb5caddf2eb0755dee79325c7ee | Python | 65,326 | 1,526 | """Takes segmented nerve/fascicle, preprocesses the images,
creates the perineurium, generates a connectivity map, and creates fibersets."""
# edit to use threedmodel TODO max importance
# also may need to move over cuff models from 3D? to see #TODO
import argparse
import gc
import glob
import json
import math
import ... |
69694f16a0e4d06d537ce939f845989d4f94e76459c647fd7ae687dcdef3e2be | Python | 65,433 | 1,469 | ## ...........................................................................
##
## PIMMS (Polymer Interactions in Multicomponent Mixtures)
## Alex Holehouse, Pappu Lab, Holehouse Lab
## Copyright 2015 - 2026
## ...........................................................................
"""
Regression tests for the c... |
e40e6139b7fbb52bf6dc4d9edf5215845e04d02db60965310cd9337ded43271d | Python | 65,614 | 1,445 | #!/usr/bin/env python3.7
"""Defines Query 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 cProfile
import f... |
3c402156deba134b13e1bc92f555982b9db5e5570e8c4f8c0897f5ff10c4fbc7 | Python | 65,891 | 1,461 | import numpy as np
import sys, os, math
import datetime as dt
import scipy, scipy.signal
import parmap
from scipy.interpolate import splrep, splev, make_interp_spline, splder, sproot
from tqdm import tqdm
# doing imports inside module until travis is fixed
# Cat: TODO: move these to the top once Peter's workstation wo... |
14f78a5b85004a338b07e37bdc77d565656f8aa51b0cfa01a152c24318492631 | Python | 66,127 | 2,058 | """
Internal module for formatting output data in csv, html, xml,
and latex files. This module also applies to display formatting.
"""
from __future__ import annotations
from collections.abc import (
Generator,
Hashable,
Mapping,
Sequence,
)
from contextlib import contextmanager
from csv import QUOTE_N... |
688750eac063f2a5c483de2e5ceee260e830936a8a5b0784ef32b4018f1292d3 | Python | 66,450 | 1,463 | """Analysis GUI for configuring analysis settings."""
from __future__ import annotations
import os
from dataclasses import dataclass
from datetime import datetime
from typing import TYPE_CHECKING, cast
from qtpy.QtCore import Qt
from qtpy.QtWidgets import (
QCheckBox,
QComboBox,
QDoubleSpinBox,
QGrid... |
26fb2a76faff48aaddce0458c284e5349792fcd58c4930f5f37b1017e950300b | Python | 66,544 | 1,760 | """ 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._libs.tslibs.dtypes import freq_to_period_freqstr
... |
289cca95a09dd6311bbb8037f1996db256a801487d9d26dd6ce15d8e9ef429ec | Python | 66,557 | 1,737 | # -*- coding: utf-8 -*-
"""
The rrule module offers a small, complete, and very fast, implementation of
the recurrence rules documented in the
`iCalendar RFC <https://tools.ietf.org/html/rfc5545>`_,
including support for caching of results.
"""
import calendar
import datetime
import heapq
import itertools
import re
imp... |
04b2330eb45c6830d80695e3f277f0dda21769ba2ce989703e3a277589a1e882 | Python | 66,558 | 1,946 | from __future__ import annotations
import importlib
from typing import (
TYPE_CHECKING,
Callable,
Literal,
)
from pandas._config import get_option
from pandas.util._decorators import (
Appender,
Substitution,
)
from pandas.core.dtypes.common import (
is_integer,
is_list_like,
)
from pand... |
bcc3c6bec4b88fd845e98f64dd3ca89b569a1cb6f4ac5999004cb378075e97dc | Python | 66,682 | 1,984 | #
# Copyright (C) 2012-2023 The Python Software Foundation.
# See LICENSE.txt and CONTRIBUTORS.txt.
#
import codecs
from collections import deque
import contextlib
import csv
from glob import iglob as std_iglob
import io
import json
import logging
import os
import py_compile
import re
import socket
try:
import ssl
... |
2edbc31b2f065819a5c17f79afdb07a673f16dc46b5d338ee580a84c750e687a | Python | 66,696 | 1,863 | # pylint: disable=invalid-name
import sys
import os
from functools import partial
os.environ["TF_FORCE_GPU_ALLOW_GROWTH"] = "true"
import numpy as np
import pytest
from pytest_lazyfixture import lazy_fixture as lf
import scipy
import tensorflow as tf
thisfile = os.path.abspath(__file__)
modulepath = os.path.dirname... |
4dec5994c0e9f8b9b194245e42e1c1e20fe308cf821ca0fe351f45cbf7793547 | Python | 67,345 | 2,062 | from __future__ import annotations
import abc
from collections import defaultdict
import functools
from functools import partial
import inspect
from typing import (
TYPE_CHECKING,
Any,
Callable,
Literal,
cast,
)
import warnings
import numpy as np
from pandas._config import option_context
from pa... |
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