sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
cab2308a3e3537d3dd255c0ae4fd2e3cd68c2b77bed3619d3ccd1e62c713162a | Python | 37,712 | 988 | ## ...........................................................................
##
## PIMMS (Polymer Interactions in Multicomponent Mixtures)
## Alex Holehouse, Pappu Lab, Holehouse Lab
## Copyright 2015 - 2026
## ...........................................................................
###
###
###
## Set of tool... |
b4b1a1970c7fd074e38d0b2710e1346d5d56fa19c1d1998cb5174c101cdcacd0 | Python | 37,773 | 932 | """FOOOF - Fitting Oscillations & One-Over F.
Notes
-----
- Methods without defined docstrings import docs at runtime, from aliased external functions.
- Private attributes of the FOOOF method, not publicly exposed, are documented below.
Attributes (private)
----------
_spectrum_flat : 1d array
Flattened power sp... |
870ccd4790f86d84c353ce3a8f4b8aa139d1b19936da398ce4a797662b64be65 | Python | 37,798 | 1,414 | """
This module contains a set of functions for vectorized string
operations and methods.
.. note::
The `chararray` class exists for backwards compatibility with
Numarray, it is not recommended for new development. Starting from numpy
1.4, if one needs arrays of strings, it is recommended to use arrays of
... |
7938bc6f5e89ba669cf16231f0b2dfffd65e173038bb59e2a47314a1ce7e9723 | Python | 37,830 | 1,185 | from __future__ import annotations
from datetime import timedelta
import operator
from typing import (
TYPE_CHECKING,
cast,
)
import numpy as np
from pandas._libs import (
lib,
tslibs,
)
from pandas._libs.tslibs import (
NaT,
NaTType,
Tick,
Timedelta,
astype_overflowsafe,
get_... |
dba79baed27f9fcdfe91729ee8fd0c30b44341d05bed5a7c273d886fc0665a28 | Python | 37,847 | 905 | #!/usr/bin/env python3.7
"""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 json
import os
import re
import shuti... |
da2e45a3565109238e7668aa2370d3e6ee4d35101d972f54fe82311b78b41379 | Python | 37,893 | 891 | import os
import sys
import pickle
import shutil
import configparser
from pathlib import Path
import numpy as np
from PySide6.QtCore import Slot, QThread, Qt
from PySide6.QtWidgets import QApplication, QMainWindow, QButtonGroup, QFileDialog, QMessageBox, QProgressDialog, \
QInputDialog
from PySide6.QtGui import QSt... |
639b12d752b9af828670f6991f139aa015090d902371f745eea4afc6957276aa | Python | 38,023 | 1,000 | """Test functions for 1D array set operations.
"""
import numpy as np
from numpy import (
ediff1d, intersect1d, setxor1d, union1d, setdiff1d, unique, isin
)
from numpy.exceptions import AxisError
from numpy.testing import (assert_array_equal, assert_equal,
assert_raises, assert_rais... |
5a3f4d546b624758ef919f6048577dd6eb1494cf07d20d3a68f573dac321e1bc | Python | 38,116 | 964 | from __future__ import annotations
import logging
import os
import sys
import typing as t
from datetime import timedelta
from itertools import chain
from werkzeug.exceptions import Aborter
from werkzeug.exceptions import BadRequest
from werkzeug.exceptions import BadRequestKeyError
from werkzeug.routing import BuildE... |
637a0e8188d82715001e7fcf896d9e587af3d6d58d56e357b4971fdd1244d8f6 | Python | 38,125 | 1,099 | from datetime import datetime
from hypothesis import given
import numpy as np
import pytest
from pandas.core.dtypes.common import is_scalar
import pandas as pd
from pandas import (
DataFrame,
DatetimeIndex,
Index,
Series,
StringDtype,
Timestamp,
date_range,
isna,
)
import pandas._test... |
1e7d5515c9d5a397c5e38f3f6fcbdde26e646cb80c40cfcee5b11ed43d0c3377 | Python | 38,133 | 1,224 | """
Declarations of single-qubit and two-qubit gates and their corresponding matrix.
"""
import builtins
import sys
import warnings
from copy import deepcopy
from functools import reduce, partial
from typing import Any, Callable, Optional, Sequence, List, Union, Tuple
from operator import mul
import numpy as np
try:... |
9984dd2b8a24c0c8ad58f3e1df7e4b637c33cb98579dc1173e7c4b7755eb0d70 | Python | 38,156 | 1,183 | """
Tests for scalar Timedelta arithmetic ops
"""
from datetime import (
datetime,
timedelta,
)
import operator
import numpy as np
import pytest
from pandas.errors import OutOfBoundsTimedelta
import pandas as pd
from pandas import (
NaT,
Timedelta,
Timestamp,
offsets,
)
import pandas._testing... |
efd75d38546c1288fb82545835cabe2fbacf079cb78c5c6e3859c20f99505bea | Python | 38,190 | 1,136 | """ define the IntervalIndex """
from __future__ import annotations
from operator import (
le,
lt,
)
import textwrap
from typing import (
TYPE_CHECKING,
Any,
Literal,
)
import numpy as np
from pandas._libs import lib
from pandas._libs.interval import (
Interval,
IntervalMixin,
Interva... |
a993f3a6cf27e7febbfc5706a41c8cf46e0f16aafb7f83d67307f9d8eb35eae2 | Python | 38,234 | 1,208 | """
Provide classes to perform the groupby aggregate operations.
These are not exposed to the user and provide implementations of the grouping
operations, primarily in cython. These classes (BaseGrouper and BinGrouper)
are contained *in* the SeriesGroupBy and DataFrameGroupBy objects.
"""
from __future__ import annota... |
ef5b4ffe436d6f956065d69fcbf387d6c59d64e03a3da4fb709a97eed2a067e9 | Python | 38,261 | 1,008 | from __future__ import annotations
import os
import types
import typing as t
import warnings
from weakref import WeakKeyDictionary
import sqlalchemy as sa
import sqlalchemy.event as sa_event
import sqlalchemy.exc as sa_exc
import sqlalchemy.orm as sa_orm
from flask import abort
from flask import current_app
from flas... |
06015268503a3b5f17c8c6c7ef6830fd0f62645cf3764ff8801978c888daab39 | Python | 38,289 | 853 | #!/usr/bin/env python3.7
"""Defines Simulation 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 copy
import... |
6f40798f91c6b618c62f2e052ec310b633cf8e5799107f1a80859f2d59def6fd | Python | 38,327 | 1,127 | from __future__ import annotations
import datetime as dt
import operator
from typing import TYPE_CHECKING
import warnings
import numpy as np
import pytz
from pandas._libs import (
NaT,
Period,
Timestamp,
index as libindex,
lib,
)
from pandas._libs.tslibs import (
Resolution,
Tick,
Tim... |
171052f63a6fe8d3c1ab04c5d1586fc6bfae5364adf133b26eb4b9c7c54d43a4 | Python | 38,402 | 879 | import pandas, openpyxl, io, boto3, datetime, sys
from awsglue.transforms import *
from awsglue.utils import getResolvedOptions
from awsglue.context import GlueContext
from awsglue.job import Job
from awsglue.dynamicframe import DynamicFrame
from pyspark.context import SparkContext
from pyspark.sql.window impo... |
11b6ac027a4e2a1c30f9b2d544be36fc733b45f3afd506cab1ee79456c8eafc2 | Python | 38,427 | 886 | #!/usr/bin/env python
# https://github.com/FoxoTech/methylprep/blob/master/methylprep/files/idat.py#L228
# https://github.com/HenrikBengtsson/illuminaio/blob/develop/R/readIDAT_nonenc.R
# https://github.com/bioinformed/glu-genetics/blob/dcbbbf67a308d35e157b20a9c76373530510379a/glu/lib/illumina.py#L44-L61
import idatt... |
75b9a0df9cf01703d289847ee4eb9203bf74b2504472df0de82d639045dc841b | Python | 38,445 | 828 | import pytest
from pandas._libs.tslibs.period import INVALID_FREQ_ERR_MSG
from pandas.errors import OutOfBoundsDatetime
from pandas import (
Period,
Timestamp,
offsets,
)
import pandas._testing as tm
bday_msg = "Period with BDay freq is deprecated"
class TestFreqConversion:
"""Test frequency conver... |
dfc0e81d28f102c2b13b6ab150a33495fa41364107736c5905a39152c283919d | Python | 38,649 | 895 | #!/usr/bin/env python3
import json
import os
import subprocess
import tempfile
from typing import Any
from unittest import main, mock, TestCase
import yaml
from filter_test_configs import (
filter,
filter_selected_test_configs,
get_ghstack_below_count,
get_labels,
get_reenabled_issues,
mark_un... |
64a1ec14008826194d26a53c9cd0691be3a31d9dae13fc3387de0e381ba3f222 | Python | 38,656 | 1,177 | """
:mod:``pandas.io.xml`` is a module for reading XML.
"""
from __future__ import annotations
import io
from os import PathLike
from typing import (
TYPE_CHECKING,
Any,
Callable,
)
import warnings
from pandas._libs import lib
from pandas.compat._optional import import_optional_dependency
from pandas.err... |
badc72512eccfac4d86a259e93db916886801c79b48da4db22a0d7f868c41d81 | Python | 38,672 | 1,102 | """
Provide user facing operators for doing the split part of the
split-apply-combine paradigm.
"""
from __future__ import annotations
from typing import (
TYPE_CHECKING,
final,
)
import warnings
import numpy as np
from pandas._config import (
using_copy_on_write,
warn_copy_on_write,
)
from pandas._... |
7a56ca41232f57ca77a9610554503f9e77928dd5e5e37d906039616b5706546c | Python | 38,699 | 1,177 | from datetime import datetime
from io import StringIO
import itertools
import re
import textwrap
import numpy as np
import pytest
import pandas as pd
from pandas import (
DataFrame,
Index,
MultiIndex,
get_option,
option_context,
)
import pandas._testing as tm
import pandas.io.formats.format as fm... |
972af3073dff5c8238ec07f9a271ea9bcc78b70561fb2bbf7079b2bfd3cfd821 | Python | 38,707 | 1,018 | """
SymbolCircuit: symbolic parameterized quantum circuit.
Gate parameters are sympy Symbols (or expressions). Amplitude and expectation
values are computed via tensor network contraction of numpy object arrays,
producing sympy expressions. The class also supports translation to a Qiskit
QuantumCircuit with Parameter ... |
2f0ffd2df33f67ba8179fddba1a987e4bb4beea893d748292325b2f548fa953a | Python | 38,762 | 1,090 | """
Histogram-related functions
"""
import contextlib
import functools
import operator
import warnings
import numpy as np
from numpy._core import overrides
__all__ = ['histogram', 'histogramdd', 'histogram_bin_edges']
array_function_dispatch = functools.partial(
overrides.array_function_dispatch, module='numpy')... |
ba33d9d4ac07ded507bb8741c32e0f3b9b62e3f31b5e405fedbceecb763b2a01 | Python | 38,775 | 1,023 | """Forward model for simulating light transport in the head.
NOTE: Cedalion currently supports two ways to compute fluence:
1) via monte-carlo simulation using the MonteCarloXtreme (MCX) package, and
2) via the finite element method (FEM) using the NIRFASTer package.
While MCX is automatically installed using pip, NIR... |
c63b1fb5307624896c09dc68ac3227a1e709e9a7ecd4ed25b2a520e04c5c5c8d | Python | 38,835 | 1,059 | """Routines related to PyPI, indexes"""
from __future__ import annotations
import enum
import functools
import itertools
import logging
import re
from collections.abc import Iterable
from dataclasses import dataclass
from typing import (
TYPE_CHECKING,
Optional,
Union,
)
from pip._vendor.packaging import... |
bea13fc06677deff58f8867c998273df67042fe86fe87e72591c1f81f9924ba3 | Python | 38,920 | 1,177 | import numpy as np
import pytest
from pytest_lazyfixture import lazy_fixture as lf
import tensorcircuit as tc
# We will implement this soon
from tensorcircuit.u1circuit import U1Circuit
@pytest.mark.parametrize("backend", [lf("npb"), lf("tfb"), lf("jaxb")])
def test_u1circuit_correctness(backend):
# n=4, k=2, fi... |
ac95fcde5b8b3d59b8d7a0eae1b3af5770c86831a9d2c8e9845b563b1839017a | Python | 38,997 | 1,114 | import collections.abc as cabc
import random
from inspect import signature
import numpy as np
import matplotlib.pyplot as pl
from matplotlib import rcParams
from matplotlib.path import get_path_collection_extents
from scvelo import logging as logg
from scvelo import settings
from scvelo.tools.paga import get_igraph_... |
fd7f7cd40d56a2420221e76902647b7ccb26c89c4a8a0115952d8dd073c25564 | Python | 39,021 | 836 | """
lib to load formatted neural data from mat and pickle files.
"""
import mat73
from scipy.io import loadmat
import pickle
from easydict import EasyDict as edict
import os
import re
import glob
from pathlib import Path
import numpy as np
import os.path
from os.path import join
from collections import OrderedDict
... |
d960d8a3b60e23fae36676cf475735ac4eaba11db43dadc4af932100753aeeda | Python | 39,168 | 1,114 | """Registrating optodes to scalp surfaces."""
from dataclasses import dataclass
import numpy as np
from numpy.linalg import pinv
from scipy.optimize import linear_sum_assignment, minimize
from scipy.spatial import KDTree
import xarray as xr
import warnings
import pandas as pd
import cedalion
import cedalion.dataclass... |
a7589ed70fc7e71f831b44bd97fc1d819eacdd91201c75fb4c944f53a712983d | Python | 39,174 | 1,132 | import logging
import os
import random
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
import wandb
from pnet i... |
dde9f234ef3eb1d1d258cb1cb50a06955570d75975b9075ab1d5f5c46e1c2915 | Python | 39,194 | 895 | #!/usr/bin/env python3
"""
Adaptive CNN for Influenza Antigen Prediction
PyTorch implementation with automatic architecture adaptation
DETERMINISTIC MODE:
- All seeds (torch, cuda, numpy, random) are fixed for reproducibility
- torch.backends.cudnn.deterministic = True
- torch.backends.cudnn.benchmark = False
... |
8e388c6e73007b9e9642938d7e682506d579ddcb9194974a855557798ab90060 | Python | 39,298 | 908 | import os
import sys
import time
from copy import deepcopy
from enum import Enum
from pathlib import Path, PurePath
from typing import Optional, Dict, List
import cv2
import torch
from PySide6.QtCore import QObject, Signal, QTimer, QThread
from ultralytics import YOLO
from app.config.camera import CameraConfig
from a... |
0810e81b67d6cf1d0e2136d910a9450f9594a3d1d046a9acc1ea0c3ad1ca423b | Python | 39,309 | 1,215 | """
Set operations for arrays based on sorting.
Notes
-----
For floating point arrays, inaccurate results may appear due to usual round-off
and floating point comparison issues.
Speed could be gained in some operations by an implementation of
`numpy.sort`, that can provide directly the permutation vectors, thus avoi... |
0076d73e9e2c1f48042604b233403dce098cf4cc26ea347fa79a56b545dea95f | Python | 39,353 | 1,294 | import functools
import warnings
import numpy._core.numeric as _nx
from numpy._core.numeric import asarray, zeros, zeros_like, array, asanyarray
from numpy._core.fromnumeric import reshape, transpose
from numpy._core.multiarray import normalize_axis_index
from numpy._core._multiarray_umath import _array_converter
from... |
6827133858f074b41b119dc92c4be55324a282963e3381a9f2957cb9ef92d088 | Python | 39,371 | 1,216 | from datetime import (
datetime,
timedelta,
)
from io import StringIO
import re
import sys
from textwrap import dedent
import numpy as np
import pytest
from pandas._config import using_pyarrow_string_dtype
from pandas import (
CategoricalIndex,
DataFrame,
Index,
NaT,
Series,
Timestamp... |
361abe8757ca4bf01114f77a051ab26b58113a6a80d0a5f5fde18e37903262cc | Python | 39,451 | 1,197 | """
Abstract base class for the various polynomial Classes.
The ABCPolyBase class provides the methods needed to implement the common API
for the various polynomial classes. It operates as a mixin, but uses the
abc module from the stdlib, hence it is only available for Python >= 2.6.
"""
import os
import abc
import n... |
a82d192cd4fbec10e7050d5ab7104ddb4006d3a9a2d74babf3ee013fdcc42838 | Python | 39,486 | 1,068 | import calendar
from datetime import (
date,
datetime,
timedelta,
timezone,
)
import zoneinfo
import dateutil.tz
from dateutil.tz import (
gettz,
tzoffset,
tzutc,
)
import numpy as np
import pytest
import pytz
from pandas._libs.tslibs.dtypes import NpyDatetimeUnit
from pandas.compat import... |
aade484b66dab639ce1def7450ae63112ee9661825a695bffb5c2278b959cac0 | Python | 39,511 | 1,187 | from __future__ import annotations
from collections.abc import (
Hashable,
Iterator,
)
from datetime import timedelta
import operator
from sys import getsizeof
from typing import (
TYPE_CHECKING,
Any,
Callable,
Literal,
cast,
overload,
)
import numpy as np
from pandas._libs import (
... |
138add653e8355c31149e0da71e06c3295ab73e03d68012f179b1b5b80ecb488 | Python | 39,546 | 1,259 | """
:mod:`pandas.io.html` is a module containing functionality for dealing with
HTML IO.
"""
from __future__ import annotations
from collections import abc
import numbers
import re
from re import Pattern
from typing import (
TYPE_CHECKING,
Literal,
cast,
)
import warnings
from pandas._libs import lib
fr... |
1c113e6e15db1f2746fd6c29f3f54d27f38f8b9bde8ef9b51ba900af145e8ead | Python | 39,803 | 1,114 | """
Linear Discriminant Analysis and Quadratic Discriminant Analysis
"""
# Authors: Clemens Brunner
# Martin Billinger
# Matthieu Perrot
# Mathieu Blondel
# Matthew Ning <mhn@bu.edu>
# License: BSD 3-Clause
import warnings
from numbers import Integral
from numbers import Real
import... |
bcec9bdb07dbd51140ff05c04737ece14a68680e4436806a0e459f65b8ea4a82 | Python | 39,818 | 1,045 | """Contains tests for extension of comparable regions with record pairs"""
# from python
import unittest
import random
import string
import big_scape.comparison.record_pair
# from other modules
import big_scape.genbank as bs_genbank
import big_scape.hmm as bs_hmmer
import big_scape.comparison as bs_comp
import big_sc... |
171f65915db729f8a36528fc12f4c7b0fac7fe4853c1162ed5f4433894564842 | Python | 39,819 | 1,009 | """Set of functions for visualization of mean waveform if action potentials."""
import numpy as np
import os
import matplotlib.pyplot as plt
import parmap
from scipy.spatial.transform import Rotation
from scipy.spatial.distance import cdist, pdist, squareform
from scipy.signal import argrelmin
from tqdm import tqdm
... |
e4a9e9a6f6903c29c4d38ed15d3d6a4249694e01a9dd195a90530669d9965a55 | Python | 39,847 | 1,124 | """Test for cancellation during mid-position extraction (partial ROI processing).
This test verifies that when cancellation happens while processing ROIs within
a single position, the position is NOT marked as complete in the database.
"""
from __future__ import annotations
from typing import TYPE_CHECKING, Any
from... |
f1ac0c12c8c187b47ff2cfb0e6ba00abe999ae197ff4dad640e53c955f0260fb | Python | 39,874 | 1,241 | """
these are systematically testing all of the args to value_counts
with different size combinations. This is to ensure stability of the sorting
and proper parameter handling
"""
import numpy as np
import pytest
import pandas.util._test_decorators as td
from pandas import (
Categorical,
CategoricalIndex,
... |
d80d4eedfa535dc7de0f9215e075ab2281175e482ae64f2df5a5ab8f1f74567c | Python | 39,886 | 1,119 | """PyPI and direct package downloading"""
import sys
import os
import re
import io
import shutil
import socket
import base64
import hashlib
import itertools
import warnings
import configparser
import html
import http.client
import urllib.parse
import urllib.request
import urllib.error
from functools import wraps
impor... |
3677cde166fe51af62d569626e2341aec688ebe6022e2efad144498c92490f44 | Python | 39,926 | 1,061 | from __future__ import annotations
from datetime import datetime
import weakref
import numpy as np
import pytest
from pandas._config import using_pyarrow_string_dtype
from pandas._libs.tslibs import Timestamp
from pandas.core.dtypes.common import (
is_integer_dtype,
is_numeric_dtype,
)
from pandas.core.dty... |
6b70a159481269dfbbc97aef454e30afa958e4eaaddb8df4f19fe4324a85c718 | Python | 40,042 | 1,157 | """ test fancy indexing & misc """
import array
from datetime import datetime
import re
import weakref
import numpy as np
import pytest
from pandas._config import using_pyarrow_string_dtype
from pandas.errors import IndexingError
from pandas.core.dtypes.common import (
is_float_dtype,
is_integer_dtype,
... |
6664fb57b30c08e60ac3b4c663d4992f26037fa25d33e5957f4ec5755b958532 | Python | 40,049 | 1,006 | from dataclasses import dataclass, field, replace
from typing import (
TYPE_CHECKING,
Dict,
Iterable,
List,
NamedTuple,
Optional,
Sequence,
Tuple,
Union,
)
from . import box, errors
from ._loop import loop_first_last, loop_last
from ._pick import pick_bool
from ._ratio import ratio_... |
186d703cd31c2f47cc24eebcbc5e77c0a31dc277de84371a23eafd3694df8a50 | Python | 40,074 | 1,020 | # This file is dual licensed under the terms of the Apache License, Version
# 2.0, and the BSD License. See the LICENSE file in the root of this repository
# for complete details.
"""
.. testsetup::
from packaging.specifiers import Specifier, SpecifierSet, InvalidSpecifier
from packaging.version import Version... |
d415c987938747714e39413ac1dcb2ed08096ccef34384cfbc165e0e76213293 | Python | 40,076 | 750 | from torch.utils.data import DataLoader
import numpy as np
import torch
import torch.nn as nn
from utils import InfoNCE
from tqdm import tqdm
import torch.nn.functional as F
from torch.optim import Adam
from utils import DualBranchContrast
from pl_bolts.optimizers import LinearWarmupCosineAnnealingLR
from model_scripts... |
c9cf43fccc9c2449b052966f72cd4e64bf477e23459b2c3445969e1d134790fc | Python | 40,079 | 1,019 | # This file is dual licensed under the terms of the Apache License, Version
# 2.0, and the BSD License. See the LICENSE file in the root of this repository
# for complete details.
"""
.. testsetup::
from pip._vendor.packaging.specifiers import Specifier, SpecifierSet, InvalidSpecifier
from pip._vendor.packagin... |
ce31d1553c8f791ef2d9280c9f552c50cd4cdfb11f4f5932a683eeaa3c6c1462 | Python | 40,121 | 1,154 | from datetime import (
date,
datetime,
timedelta,
)
import re
import numpy as np
import pytest
from pandas._libs.tslibs import iNaT
from pandas._libs.tslibs.ccalendar import (
DAYS,
MONTHS,
)
from pandas._libs.tslibs.np_datetime import OutOfBoundsDatetime
from pandas._libs.tslibs.parsing import Da... |
877460e0dc380617d693e0ca28cad3703b8012c704c670b19bebe60985b59b17 | Python | 40,131 | 929 | #!/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... |
a40c0851e873b4029773d7ce9c1245958a566c9d046216fc13d1df64f541e185 | Python | 40,181 | 1,128 | """
Circuit object translation in different packages
"""
import logging
from copy import deepcopy
from typing import Any, Dict, List, Optional, Sequence, Tuple, Union
import numpy as np
logger = logging.getLogger(__name__)
try:
import qiskit.quantum_info as qi
from qiskit import QuantumCircuit
from qis... |
94b385cb7b0498773921a1074621f5b1056721dda6a14433872789653b5d637d | Python | 40,383 | 1,049 | """Parse tokens from the lexer into nodes for the compiler."""
import typing
import typing as t
from . import nodes
from .exceptions import TemplateAssertionError
from .exceptions import TemplateSyntaxError
from .lexer import describe_token
from .lexer import describe_token_expr
if t.TYPE_CHECKING:
import typing... |
e14e23b40d17de23fcdee42707df9323e1c34b0f04f32f333181dad148db6da2 | Python | 40,392 | 940 | """
pygments.filters
~~~~~~~~~~~~~~~~
Module containing filter lookup functions and default
filters.
:copyright: Copyright 2006-2025 by the Pygments team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
import re
from pip._vendor.pygments.token import String, Comment, Keyword, Name,... |
7145e83b42c0c2bb07f5c2ea7430309ef016780b432124b517dfcb594b62b95a | Python | 40,401 | 1,064 | """
Quantum circuit: the state simulator.
Supports qubit (dim=2) and qudit (3 <= dim <= 36) systems.
For string-encoded samples/counts, digits use 0-9A-Z where A=10, ..., Z=35.
"""
# pylint: disable=invalid-name
from typing import Any, Callable, Dict, List, Optional, Sequence, Tuple
from functools import reduce
from ... |
7b67a203035b14d08ac63e1bc0328d2bec3b1c8752cf73a633153f4c8b7e7af4 | Python | 40,408 | 1,140 | from __future__ import absolute_import
import errno
import logging
import re
import socket
import sys
import warnings
from socket import error as SocketError
from socket import timeout as SocketTimeout
from ._collections import HTTPHeaderDict
from .connection import (
BaseSSLError,
BrokenPipeError,
DummyC... |
b8fd122115290464b8ad947b897b700ec7f5be909993fd5fdbd36f61c722ef7f | Python | 40,522 | 1,100 | """
Tests specific to `np.loadtxt` added during the move of loadtxt to be backed
by C code.
These tests complement those found in `test_io.py`.
"""
import sys
import os
import pytest
from tempfile import NamedTemporaryFile, mkstemp
from io import StringIO
import numpy as np
from numpy.ma.testutils import assert_equal... |
243e9df381981181bc01771cf076d4aa8063f8866db762f110c439683af46a79 | Python | 40,580 | 978 | # -*- coding: utf-8 -*-
#
# ke_model.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.o... |
86c8c1a5973c8bd3bf68a3290a6b34b6e4368c0a9b915ccb5e750a234d5355c5 | Python | 40,615 | 1,267 | """Common IO api utilities"""
from __future__ import annotations
from abc import (
ABC,
abstractmethod,
)
import codecs
from collections import defaultdict
from collections.abc import (
Hashable,
Mapping,
Sequence,
)
import dataclasses
import functools
import gzip
from io import (
BufferedIOBas... |
0ea7da88a1956a0385b8bd2fdd56716599119d65af972d3f9581ee2e36994c1a | Python | 40,625 | 1,035 | """numpy.distutils.fcompiler
Contains FCompiler, an abstract base class that defines the interface
for the numpy.distutils Fortran compiler abstraction model.
Terminology:
To be consistent, where the term 'executable' is used, it means the single
file, like 'gcc', that is executed, and should be a string. In contras... |
3e6dd1072ba9c5e66d3200164343adaf4cf766817e1e403bf797e2e97cb15b03 | Python | 40,698 | 984 | """ demixed Principal Component Analysis
"""
# Author: Wieland Brendel <wieland.brendel@neuro.fchampalimaud.org>
#
# License: BSD 3 clause
from __future__ import print_function
import numpy as np
from collections import OrderedDict
from itertools import combinations, chain
from scipy.sparse.linalg import svds
from s... |
33470b15b1419ffc83f7dcbf910f1863835631a1f59d5772c017f9e82ae98899 | Python | 40,756 | 1,313 | from __future__ import annotations
from datetime import timedelta
import operator
from typing import (
TYPE_CHECKING,
Any,
Callable,
Literal,
TypeVar,
cast,
overload,
)
import warnings
import numpy as np
from pandas._libs import (
algos as libalgos,
lib,
)
from pandas._libs.arrays... |
e26b042242db15ab41a5f7d857dc0d8ac26ef13109f1337c4869889f680a3b4f | Python | 40,808 | 1,202 | #!/usr/bin/env python
# coding: utf-8
try:
get_ipython # type: ignore
except NameError:
def get_ipython():
class _DummyShell:
def run_line_magic(self, *args, **kwargs):
pass
def run_cell_magic(self, *args, **kwargs):
pass
def magic(s... |
a5b221b57dc4d3b314f46377d1facbfbe28a316de2626d5e15a4e2c0fab7f4c5 | Python | 40,911 | 1,026 | # doctest
r''' Test the .npy file format.
Set up:
>>> import sys
>>> from io import BytesIO
>>> from numpy.lib import format
>>>
>>> scalars = [
... np.uint8,
... np.int8,
... np.uint16,
... np.int16,
... np.uint32,
... np.int32,
... np.uint6... |
b6f5e6b15ae57e173e06bddb69ee472a2b9096628f58bf6d4556e2ecc861669c | Python | 40,940 | 1,391 | """
Base and utility classes for pandas objects.
"""
from __future__ import annotations
import textwrap
from typing import (
TYPE_CHECKING,
Any,
Generic,
Literal,
cast,
final,
overload,
)
import warnings
import numpy as np
from pandas._config import using_copy_on_write
from pandas._libs... |
7e33ab1cb5cf764f2d4d17c9bc64fa41bb94a737e6663710f4ce98af8773c229 | Python | 41,011 | 1,049 | """Set of functions for visualization of mean waveform if action potentials."""
import numpy as np
import os
import matplotlib.pyplot as plt
from matplotlib.lines import Line2D
from scipy.spatial.transform import Rotation
from scipy.spatial.distance import cdist, pdist, squareform
from tqdm import tqdm
class Geome... |
c23966226a204cb1c9b018bc169be51898f718d2d174002073093988ec6dae19 | Python | 41,070 | 1,059 | """Panel widget for displaying analysis and detection runs."""
from __future__ import annotations
from pathlib import Path
from typing import TYPE_CHECKING, Any, NamedTuple
from qtpy.QtCore import QEvent, QObject, Qt, Signal
from qtpy.QtWidgets import (
QCheckBox,
QDialog,
QDialogButtonBox,
QGroupBox... |
2649ce77835177829d157ce350a29800dd17bf25f566629b9454363028decd1a | Python | 41,210 | 995 | # coding: utf-8
import math
import os
from argparse import Namespace
from collections import defaultdict
import numpy as np
import torch
import torch.nn as nn
from .modules import (
BernsteinRadialBasisFunctions,
ClebschGordan,
EnergyLayer,
ExponentialBernsteinRadialBasisFunctions,
ExponentialGau... |
57970f48a27187962d7f672684681ea42f22d5d9bddff0376669fe317330bf5f | Python | 41,328 | 986 | import torch
import torch.nn as nn
import torch.optim as optim
import pytorch_lightning as pl
from torch.optim import AdamW
from collections import OrderedDict
from torch.optim.lr_scheduler import ReduceLROnPlateau
from torch.utils.data import DataLoader, TensorDataset, random_split, Subset, ConcatDataset
from pytorch_... |
02a84174f8c21e8f64ced0e98161abe9e5fb82695c90406061a0209af6d878ae | Python | 41,334 | 1,082 | """
##############################################################################
ShinGLMCC.ShinGLMCC.py
This module primarily contains functions
related to the connectivity estimation algorithms
ShinGLMCC and GLMCC.
by Yasuhiro Tsubo
modified ver. 2023.10.23
##########################################... |
83277e941fc06aed83421d6a4e1385de76b7ce7663d999e5b645bb62e1bf16e3 | Python | 41,465 | 860 | # YOLOv5 🚀 by Ultralytics, GPL-3.0 license
"""
Common modules
"""
import ast
import contextlib
import json
import math
import platform
import warnings
import zipfile
from collections import OrderedDict, namedtuple
from copy import copy
from pathlib import Path
from urllib.parse import urlparse
import cv2
import nump... |
da34528d1238a3ebe55de4cad8108621486473a7bd646852b1a711339a2c793c | Python | 41,467 | 1,137 | # -*- coding: utf-8 -*-
#
# Copyright (C) 2013-2017 Vinay Sajip.
# Licensed to the Python Software Foundation under a contributor agreement.
# See LICENSE.txt and CONTRIBUTORS.txt.
#
from __future__ import absolute_import
import os
import re
import shutil
import sys
try:
import ssl
except ImportError: # pragma: ... |
4b3a33ccf3fb686e72db2e0c51026795f63b4087dedd478fb8b2229965dbacd6 | Python | 41,514 | 1,159 | """Copyright (c) Meta, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import logging
import time
from typing import Dict, List
import pytorch_lightning as pl
import torch
import torch.nn as nn
from torch.optim impor... |
536f673a9033175cde23788de7a599fc93234ddee8c27531d010f28695c067a9 | Python | 41,557 | 957 | # model
import torch
import torch_geometric as tg
import os
# data pre-processing
import numpy as np
import pandas as pd
import pickle as pkl
from sklearn.model_selection import train_test_split
from scipy.stats import gaussian_kde
import math
import seaborn as sns
# data visualization
import matplotlib as mpl
impor... |
5abd12268f4e671d9f9d2c6f332e5f28aa0b475cc739d89307f8541575637fc3 | Python | 41,564 | 1,006 | #!/usr/bin/env python3.7
"""Defines Sample 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 copy
import math... |
91af243b16bb74b3f7c107fb6f87461cb34ff6573a4c8d4c09ea6c2d27d8a134 | Python | 41,660 | 1,425 | import codecs
from datetime import datetime
from textwrap import dedent
import pytest
import pandas as pd
from pandas import (
DataFrame,
Series,
)
import pandas._testing as tm
pytest.importorskip("jinja2")
def _dedent(string):
"""Dedent without new line in the beginning.
Built-in textwrap.dedent ... |
4f70f5970eae027844fa4121927b858ae662210583259fe49ea1a4e381cedd8b | Python | 41,739 | 922 | # 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.
""" Implements a more readable and efficient version of biopython's SeqRecord.
Most attributes are wrapped, with the record features being secmet features
and acc... |
32a72d44cd8fc3df32260c32d094da7c5ce42ee338a2e0f57c03b6c786817cc4 | Python | 41,872 | 1,176 | """PyPI and direct package downloading"""
import sys
import subprocess
import os
import re
import io
import shutil
import socket
import base64
import hashlib
import itertools
import warnings
import configparser
import html
import http.client
import urllib.parse
import urllib.request
import urllib.error
from functools i... |
90f64c65318c3894b4cf2627abc08ced9c2c809a5919a1b9d31988528da372da | Python | 41,878 | 1,255 | import os
import h5py
import json
import argparse
import warnings
import numpy as np
import spglib, seekpath
from typing import Callable, Union
from mendeleev import element
from scipy.optimize import minimize_scalar
from scipy.special import erf
import matplotlib.pyplot as plt
from matplotlib.lines import Line2D
impo... |
943d285fd384198559e67639dc8569570fa230d6079a03a4f4c3d2b3a593418b | Python | 41,880 | 1,087 | """
##############################################################################
ShinGLMCC.ShinGLMCC2.py
This module primarily contains functions
related to the connectivity estimation algorithms
ShinGLMCC and GLMCC.
by Yasuhiro Tsubo
modified ver. 2024.5.14
##########################################... |
18193eef191041a9644bac7a0e8eb3c39c3d1dc33967341b014db672e0cae197 | Python | 41,884 | 1,006 | import torch
from torch.nn import functional as F
from e3nn import o3, nn
from abc import abstractmethod
from e3nn.util.jit import compile_mode
from typing import Callable, List, Optional, Tuple, Union
from .from_mfn.blocks import (RealAgnosticResidualInteractionBlockUp, RealAgnosticResidualInteractionBlock,
... |
e0d5aaa356bc2403c524fbadb5b0664f8763b3e34bccb59926758a89d72be5e4 | Python | 41,885 | 776 | '''
Several notes:
1. There are two kinds of input files - (a) user data and (b) system data. The former has three files - (a) expression profile, (b) lncRNA target
prediction, (c) TF target prediction. LncRNAs' targets are predicted using LongTarget (or the more rapid version Farsim); TFs' targets are
pre... |
6ef3c51cb8ebc57b40549738bc3821dbe7a326a268063b7b6486f4ef002de53d | Python | 41,930 | 1,019 | #!/usr/bin/env python3
import re
import os
import sys
import errno
import random
import logging
import argparse
import collections
# sys.path hack to access lib package in root directory.
sys.path.insert(0, os.path.dirname(sys.path[0]))
# sys.path hack to allow overriding installed pyBamParser.
for key in 'PYBAMPATH', ... |
347552aa7c25f7083513edf45c3e034461245c2066e4b9f837a635021bdf3b69 | Python | 41,973 | 969 | import numpy as np
import glob
import pandas as pd
import librosa
import matplotlib.pyplot as plt
import os
import csv
from pathlib import Path
from cross_correlation import cross_corr
from butterworth_filter import filterA, butter_filter
class ExperimentEvaluator:
"""Class to preprocess the recordings of the DPOA... |
e831aed7453270114155923bbe27fe01a550acf9ba5da15c7a053a5be7d8cc71 | Python | 41,998 | 1,381 | from fractions import Fraction
import random
import pytest
import numpy as np
import jax.numpy as jnp
import pyzx_param as pyzx
from pytest_lazyfixture import lazy_fixture as lf
import tensorcircuit as tc
from tensorcircuit.zx.stabilizertcircuit import StabilizerTCircuit
from tensorcircuit.zx.scalar_graph import (
... |
9b2a091752446d76a69a8fe30bc4a8c5f58148c0d4a326ee018ca579eac4949d | Python | 42,211 | 1,252 | import re
import numpy as np
import pytest
import pandas as pd
from pandas import (
DataFrame,
Index,
date_range,
lreshape,
melt,
wide_to_long,
)
import pandas._testing as tm
@pytest.fixture
def df():
res = DataFrame(
np.random.default_rng(2).standard_normal((10, 4)),
col... |
13a8cd530e4bbab0d87e995a2abed50d4bf65ca3f4fd8b28cd2cdd186057b9df | Python | 42,227 | 1,174 | """
Backend magic inherited from tensornetwork: tensorflow backend
"""
# pylint: disable=invalid-name
import os
import re
from functools import reduce, partial
from operator import mul
from typing import Any, Callable, Optional, Sequence, Tuple, Union
from scipy.sparse import coo_matrix
import tensornetwork
from ten... |
d704fb772bde46e902b160c5f16599b42c58bc695fe787a8b606b6f37ee2becb | Python | 42,232 | 1,103 | """
##############################################################################
ShinGLMCC.ShinGLMCC.py
This module primarily contains functions
related to the connectivity estimation algorithms
ShinGLMCC and GLMCC.
by Yasuhiro Tsubo
modified ver 1.0 2023.10.23
ver 2.0 2024.08.28 (add find... |
1af675466e9dfbc59462fa93a51df838cf895690f7b0e6a17a14edab3255d2c7 | Python | 42,367 | 950 | """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.
"""
import numpy as np
import cedalion.data
from cedal... |
1c1e5dfcdca6df860371844171d07a096bc155c7c87cc097420c69413c923cf8 | Python | 42,374 | 1,084 | # Standard library imports
import os
import json
import math
import random
import re
import pickle
import warnings
from datetime import datetime
from collections import defaultdict, Counter
from itertools import permutations
from pathlib import Path
# Third-party imports
import numpy as np
import pandas... |
e1697fdea65d7e17a86beecd900acf88ee6b1d9ebecd39dfcf60853287dcd620 | Python | 42,737 | 871 | # -*- coding: utf-8 -*-
# Time : 2023/2/14 11:52
# Author : Regulus
# FileName: main_visual_losslandscape.py
# Explain:
# Software: PyCharm
import sys
import tqdm
from loss_landscape.plot_surface import *
from Pytorch_Grad_Cam.cam import *
import argparse
import math
import time
import CKA
import numpy
... |
e0e506adc80c1e56a2de9eed42dd2c5e8a4d613ac674415251a55fe92ed9cf22 | Python | 42,980 | 1,266 | import numpy as np
import pytest
from pandas.errors import SettingWithCopyWarning
from pandas.core.dtypes.common import is_float_dtype
import pandas as pd
from pandas import (
DataFrame,
Series,
)
import pandas._testing as tm
from pandas.tests.copy_view.util import get_array
@pytest.fixture(params=["numpy"... |
b931035be91f192d5914c4e4201c2ff60c5154d96325e60dff9efbac4cfe5d9f | Python | 42,991 | 1,113 | """Utilities for Pearson correlation statistical analysis."""
import re
import warnings
from pathlib import Path
from typing import TypedDict, cast
import h5py as h5
import nibabel as nib
import numpy as np
import numpy.typing as npt
import statsmodels.api as sm
from joblib import Parallel, delayed
from nilearn impor... |
0de506062295f67120f73044976d5f07b65bb656f48472af291b7cc2fddefc1d | Python | 43,061 | 1,397 | # -------------------------
# Plotting utilities
# -------------------------
import contextlib
import logging
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from matplotlib.gridspec import GridSpec
from matplotlib.lines import Line2D
from mpl_toolkits.axes_grid1.inset_loca... |
ce5682b4dd0823bc4083dfac1c3a3a1dd30d261ae68422d56d259ee103d9911f | Python | 43,093 | 1,100 | from datetime import datetime
import warnings
import dateutil
import numpy as np
import pytest
import pytz
from pandas._libs.tslibs.ccalendar import (
DAYS,
MONTHS,
)
from pandas._libs.tslibs.period import IncompatibleFrequency
from pandas.errors import InvalidIndexError
import pandas as pd
from pandas impor... |
ef7bad7e5d0d1d0fd77e9e66dfec256e8ed8680df54bf76495e8793f71932b0b | Python | 43,162 | 1,156 | # -*- coding: utf-8 -*-
__all__ = ['Distribution']
import io
import sys
import re
import os
import warnings
import numbers
import distutils.log
import distutils.core
import distutils.cmd
import distutils.dist
import distutils.command
from distutils.util import strtobool
from distutils.debug import DEBUG
from distutils... |
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