sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
fd276a58c8d395995317f22b0aaeb691a1a2ba7c9a2371a00a425e93bf3dc5f2 | Python | 18,498 | 489 | #!/usr/bin/env python
# Author: LiYang@cmt.tsinghua
# Date: 2021.04.08
# Descripution: This python code is designed for calculate the fermi energy
# and plot the band structure use the *.Band file.
# ::Input File::
# - *.Band
# ::Output File::
# - *... |
f48a1e84347ba8fb193880070dcb17e1e91a864794f0c124a5e60ca9bfdfc008 | Python | 18,502 | 643 | """
Tests dtype specification during parsing
for all of the parsers defined in parsers.py
"""
from collections import defaultdict
from io import StringIO
import numpy as np
import pytest
from pandas.errors import ParserWarning
import pandas as pd
from pandas import (
DataFrame,
Timestamp,
)
import pandas._te... |
1677ac7ea391fe904fa24b15e3eab22e172eea39677d7580988b74cbf4d7a211 | Python | 18,531 | 382 | import numpy as np
import torch
from scipy.sparse import issparse
from torch.autograd.functional import jacobian
import networkx as nx
import matplotlib.pyplot as plt
from .model import TNODE
from .utils import latent_data
import pandas as pd
from matplotlib.lines import Line2D
import scvelo as scv
from matplotlib.anim... |
df92b76edc6202909c4553c6e36f45640aaa5c82911cac786d573c4a0dc30a61 | Python | 18,553 | 523 | from collections import abc
import email
from email.parser import Parser
import numpy as np
import pytest
from pandas import (
CategoricalDtype,
DataFrame,
MultiIndex,
Series,
Timestamp,
date_range,
)
import pandas._testing as tm
class TestDataFrameToRecords:
def test_to_records_timeseri... |
16409d6166a436353645685f3bf32c6f2588226544f6a7a16e671bc83dd4ba68 | Python | 18,570 | 393 | # 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.
""" Contains the results class for each variant of clusterblast """
from collections import OrderedDict
import logging
import os
from typing import Any, Dict, List, Tupl... |
a93388bec9094137d377b218ef502a92c659b406319dea789c9c7f5261ca951c | Python | 18,570 | 522 | """Contains tests for the lcs module."""
# from python
import unittest
import random
import string
from pathlib import Path
# from other modules
import big_scape.comparison.record_pair
import big_scape.genbank as bs_genbank
import big_scape.hmm as bs_hmmer
import big_scape.comparison as bs_comparison
import big_scape... |
826c421972832cdfc066be1d436940e332ab53ce2e0edc1f16b74051d1730cd0 | Python | 18,573 | 521 | import re
import numpy as np
import pytest
from pandas._libs import lib
import pandas as pd
from pandas import (
DataFrame,
Index,
Series,
Timestamp,
date_range,
)
import pandas._testing as tm
from pandas.tests.groupby import get_groupby_method_args
class TestNumericOnly:
# make sure that w... |
d2252862981788baea9bf7560f8e42b353c527c7c700316d9413784e42cd350c | Python | 18,576 | 555 | """Tests for hermite module.
"""
from functools import reduce
import numpy as np
import numpy.polynomial.hermite as herm
from numpy.polynomial.polynomial import polyval
from numpy.testing import (
assert_almost_equal, assert_raises, assert_equal, assert_,
)
H0 = np.array([1])
H1 = np.array([0, 2])
H2 = np.ar... |
f0faa287bb3804cfab65f910a4b02d371c676fb54568634fad5d3d8996b50997 | Python | 18,580 | 527 | import MEArec as mr
import numpy as np
import scipy.optimize
import os
import sys
import re
import ast
import matplotlib.pyplot as plt
import pandas as pd
from collections import defaultdict
import spikeinterface as si
import spikeinterface.core as sc
import spikeinterface.extractors as se
import spikeinterface.sorter... |
6780b8d401ee17b619173b2a4d05c51205e651d00279479a91ff212d9110afe1 | Python | 18,581 | 566 | """Backing implementation for InstallRequirement's various constructors
The idea here is that these formed a major chunk of InstallRequirement's size
so, moving them and support code dedicated to them outside of that class
helps creates for better understandability for the rest of the code.
These are meant to be used... |
98400563cb1241d915034ac909365bf1caa3540b13bcbea65f3412117cb11207 | Python | 18,586 | 553 | import numpy as np
import pytest
import pandas as pd
from pandas import (
Index,
Series,
)
import pandas._testing as tm
class TestFloatNumericIndex:
@pytest.fixture(params=[np.float64, np.float32])
def dtype(self, request):
return request.param
@pytest.fixture
def simple_index(self, ... |
d637979d8e7e6ef0886979175f02cbfc19b5b9ee7bd2f304deb6dff2c22f0460 | Python | 18,588 | 421 | import torch
from torch import Tensor
from torch.autograd import Variable
from torch.optim import Adam
from MPE.utils.networks import MLPNetwork, RNN, SNNNetwork
from MPE.utils.misc import hard_update, gumbel_softmax, onehot_from_logits
from MPE.utils.noise import OUNoise
import time
class DDPGAgent(object):
"""
... |
6cd8be8aa123e0d3d9d34fa86feac7bf392f39bccdde5129830de0ea9692dd7c | Python | 18,590 | 561 | """
requests.cookies
~~~~~~~~~~~~~~~~
Compatibility code to be able to use `http.cookiejar.CookieJar` with requests.
requests.utils imports from here, so be careful with imports.
"""
import calendar
import copy
import time
from ._internal_utils import to_native_string
from .compat import Morsel, MutableMapping, coo... |
3ba3700992b9c1af70f5af0e9ba2c703691648b7d37ab6a4923ae061718921aa | Python | 18,601 | 505 | from collections.abc import Iterator
from datetime import datetime
from decimal import Decimal
import numpy as np
import pytest
import pytz
from pandas._config import using_pyarrow_string_dtype
from pandas.compat import is_platform_little_endian
from pandas import (
CategoricalIndex,
DataFrame,
Index,
... |
5c415e3750a963743db1c1884d0ab06ab1f78c8eb5dac459af14ecdf3067f909 | Python | 18,607 | 520 | # Copyright 2021 The NetKet Authors - 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.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
42fa7be84f49737220c98b9b9e9a88f5f4bb7ac78639ee058e97952aa2adf48c | Python | 18,612 | 447 | # -*- coding: utf-8 -*-
#
# Copyright (C) 2013-2023 Vinay Sajip.
# Licensed to the Python Software Foundation under a contributor agreement.
# See LICENSE.txt and CONTRIBUTORS.txt.
#
from io import BytesIO
import logging
import os
import re
import struct
import sys
import time
from zipfile import ZipInfo
from .compat ... |
e0a98e7dcff5ca864f2e79d1b9e2b08a8b1bdf659875d0dc70a3d3d6bee210a1 | Python | 18,615 | 339 | #!/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
import sys
import timeit
def isoprop_plot(db, exp, outPrefix):
conn=sqlite3.connect(db)
c=conn.cursor()
exp_f... |
62e44d141aefc62750409f0a4a7dbeaf1da5cbb67e9ac1fbe9ba1b981a275649 | Python | 18,624 | 494 |
from numpy import argmax
import random, time, pygame, sys
import pygame
pygame.init()
from pygame.locals import *
import os
os.environ["SDL_VIDEODRIVER"] = "dummy"
from rulebasedpolicy.world_model import *
from rulebasedpolicy.statedata_pre import *
from rulebasedpolicy.Find_a_way import *
import numpy as np
from uti... |
4d1d1d5c419cbd66fd128dda6901171a19ef352dc51781f841cb8b9ef02f628e | Python | 18,636 | 603 | import os
import re
import typing as t
from gettext import gettext as _
from .core import Argument
from .core import BaseCommand
from .core import Context
from .core import MultiCommand
from .core import Option
from .core import Parameter
from .core import ParameterSource
from .parser import split_arg_string
from .uti... |
04428db3bad416777f71967bc10cf4026289ed4fbb2ac108e95dde0296f5721c | Python | 18,640 | 535 | from collections import (
OrderedDict,
defaultdict,
)
from datetime import datetime
import numpy as np
import pytest
import pytz
from pandas import (
NA,
DataFrame,
Index,
Interval,
MultiIndex,
Period,
Series,
Timedelta,
Timestamp,
)
import pandas._testing as tm
class Tes... |
ce0821a720da435b606084f596a1fd35e783c70e8c39745cdc5b947dbc088d97 | Python | 18,660 | 593 | """
Benchmark TFIM VQE value and gradient evaluation.
The TensorCircuit-NG paths mirror ``benchmark_mq_vs_tc_vqe.py``: JAX backend,
TFIM Hamiltonian, ``depth=10`` by default, ``complex64`` by default, initial
``|+>^n``, nearest-neighbor ``RZZ`` gates, and single-qubit ``RX`` gates.
Backends:
- ``tc-jax-scan``: scan ... |
6a1e65ca40a2adbf73f8c7f2c10e0b5532a24205bb235f93075e84d9cb64bae5 | Python | 18,661 | 528 | #!/usr/bin/env python3
"""Extract libtorch package from a PyTorch wheel.
Creates a libtorch zip from a pre-built wheel by copying the C++ libraries,
headers, and CMake files. On Linux, optionally splits debug symbols from
libtorch_cpu.so into a separate debug zip.
Usage:
python extract_libtorch_from_wheel.py \
... |
7ed49bea741cfc407ece570f7de5cb388124750ac6baf18708596789349cf062 | Python | 18,662 | 461 | from causarray.gcate_likelihood import *
from causarray.utils import *
import causarray.gcate_glm as _gcate_glm # module-qualified so _USE_FAST_BACKEND changes take effect at call time
import scipy as sp
from scipy.sparse.linalg import svds
from joblib import Parallel, delayed
from collections import defaultdict
@nj... |
4e449043de702c73ef06fd73dc23b12308f1dc4814ac37aa05e168f30559c482 | Python | 18,671 | 506 | """Batch GLM fitting for causarray, backed by crispyx.
causarray's designs are always ``[covariates | one-hot treatments]``: a few
dense columns (intercept, covariates, latent factors) beside one indicator
column per perturbation, at most one of which is set for any cell. crispyx
solves exactly that shape with :class... |
716349dcabb8c176f2c16829f22ccd45943d2989937026c880524a9d6b4b1679 | Python | 18,671 | 568 | import torch
import torch.nn as nn
from timm.models.layers import to_2tuple, trunc_normal_, DropPath
from timm.models.registry import register_model
from timm.models.vision_transformer import _cfg
import torch.nn.functional as F
from braincog.model_zoo.base_module import BaseModule
from braincog.base.node.node import *... |
e005ebc2bc42428439708325609a472670226a290b7ef94bf93e5363bcfd9b3a | Python | 18,672 | 568 | """Tests for legendre module.
"""
from functools import reduce
import numpy as np
import numpy.polynomial.legendre as leg
from numpy.polynomial.polynomial import polyval
from numpy.testing import (
assert_almost_equal, assert_raises, assert_equal, assert_,
)
L0 = np.array([1])
L1 = np.array([0, 1])
L2 = np.a... |
2247477a607cd0dfbf806fa9644a544437aa516c54bca7acca4307ae06f3972e | Python | 18,676 | 568 | import torch
import torch.nn as nn
from timm.models.layers import to_2tuple, trunc_normal_, DropPath
from timm.models.registry import register_model
from timm.models.vision_transformer import _cfg
import torch.nn.functional as F
from braincog.model_zoo.base_module import BaseModule
from braincog.base.node.node import *... |
0f9d901a43bff8196c9ca1e0731042d11a73aabab8bf9cd3220a6401b83842c1 | Python | 18,684 | 522 | """
Benchmark explicit ready-wave batching on one fixed OMECO contraction tree.
The script builds a circuit expectation tensor network with ``reuse=False``,
searches a single contraction tree with ``omeco.TreeSA``, and then replays the
same path in two ways:
- plain sequential pairwise contractions
- ready-wave batch... |
5805f6018536a6a4474dc26bfed15a3cdfc16a0591ed1e26aa8c77c816a18727 | Python | 18,712 | 574 | """Test CaliGui database-only loading mode (no raw imaging data)."""
from pathlib import Path
from unittest.mock import MagicMock, patch
import pytest
from pytestqt.qtbot import QtBot
from qtpy.QtCore import Qt
from cali.gui import CaliGui
from cali.gui._init_dialog import InputDialogData, _InputDialog
from cali.gui... |
ad138ec21362730faeecaba0974a050c09bae3d3216c859bd0aee9602bcf9a11 | Python | 18,714 | 548 | import numpy as np
np.random.seed(1)
import tkinter as tk
import time
from PIL import ImageGrab
UNIT = 40 # pixels
MAZE_H = 9 # grid height
MAZE_W = 4 # grid width
class Maze(tk.Tk, object):
def __init__(self):
super(Maze, self).__init__()
self.action_space = ['u', 'd', 'l', 'r']
self.... |
2062a1fc9e5075f2842e2b6745f4c61e779e8d6c680b0fcd5fdb5f31b75c837c | Python | 18,730 | 623 | import codecs
import io
import os
import re
import sys
import typing as t
from weakref import WeakKeyDictionary
CYGWIN = sys.platform.startswith("cygwin")
WIN = sys.platform.startswith("win")
auto_wrap_for_ansi: t.Optional[t.Callable[[t.TextIO], t.TextIO]] = None
_ansi_re = re.compile(r"\033\[[;?0-9]*[a-zA-Z]")
def ... |
19c5b872e8e69cb59ec62441e8db4d76be783f2116b3cfc280a2c99e487b7eec | Python | 18,731 | 508 | import glob
import json
import logging
import os
import sys
from pathlib import Path
logger = logging.getLogger(__name__)
FILE = Path(__file__).resolve()
ROOT = FILE.parents[3] # YOLOv5 root directory
if str(ROOT) not in sys.path:
sys.path.append(str(ROOT)) # add ROOT to PATH
try:
import comet_ml
# Pr... |
cd2c909a45bf012bc77e259b779d7651658a3223f7ccb33a3cdfd52d0a1b0c9c | Python | 18,752 | 509 | """
Created on Jun 17, 2024
@author: mning
"""
from typing import List
from typing import Union
import numpy as np
import pandas as pd
## TODO: pick one of the two functions and clean up code for consistency.
def getPairs(this_df: pd.DataFrame) -> tuple[pd.DataFrame, pd.DataFrame]:
# return 2 lists, one for V1... |
2d34c3aefbb390ee4834b9b1ba7af8687b502e179cfc23749330747c79ba62fd | Python | 18,753 | 578 | import datetime
import re
import numpy as np
import pytest
from pandas._libs.tslibs import Timestamp
from pandas.compat import is_platform_windows
import pandas as pd
from pandas import (
DataFrame,
DatetimeIndex,
Index,
Series,
_testing as tm,
bdate_range,
date_range,
read_hdf,
)
fro... |
3a52d112b510f41dd4fa438a4479b38c0f749d412e7ec2c9588d2c4f3b603ae7 | Python | 18,759 | 537 | """Temporal basis functions for the GLM."""
from __future__ import annotations
from abc import ABC, abstractmethod
import numpy as np
import pint
import xarray as xr
import cedalion.typing as cdt
import cedalion.dataclasses as cdc
from cedalion import cite, Quantity, units
from cedalion.sigproc.frequency import samp... |
f8683bd03ac9ab7c2be7a359984262407eefd84632e659f3956cb0e893f1c18f | Python | 18,775 | 413 | import numpy as np
from tkinter import messagebox
from scipy.optimize import curve_fit
from core.calculate_baseline import calculate_baseline
def rise_function(t, tau, y0_baseline):
"""
Exponential growth: y = y0 x e^{t/tau}
REF: https://www.graphpad.com/guides/prism/latest/curve-fitting/reg_exponential_gr... |
e36b633265cae3a7b004ba5af46aa532ae37417fe76536f62b93566f3c82f132 | Python | 18,783 | 440 | import pandas as pd
from sklearn.neighbors import KDTree
import numpy as np
from tqdm import tqdm
from sklearn.linear_model import LinearRegression
from math import sqrt, atan2, pi
from scipy.optimize import linear_sum_assignment
from collections import Counter
class Predictor:
def __init__(self, min_sampling_cou... |
f317e6f88a4515232ee1d0cb1a50a439e060013d29794cbc762a17f49892ea0b | Python | 18,813 | 581 | """
2008-04-11, C. Schmidt-Hieber
Batch analysis of Na IVs
"""
import numpy as np
from scipy.io import write_array
def dens_batch( nFunc = 0 ):
"""Fits activation and inactivation of 15 iv pulses
using a biexponential funtion with a delay, creates a
table showing the results.
Keyword argument:
... |
35a21e081f70ee233f3ed6a6c782282cc470206f5e510c6c4c9a54d9c041e72d | Python | 18,819 | 543 | from collections.abc import Iterator
from io import StringIO
from pathlib import Path
import numpy as np
import pytest
import pandas as pd
from pandas import (
DataFrame,
read_json,
)
import pandas._testing as tm
from pandas.io.json._json import JsonReader
pytestmark = pytest.mark.filterwarnings(
"ignor... |
9bc051201fec6cc0d3c9854d8697388bf9d6bb01bb8c4385c456277e2f81a46d | Python | 18,835 | 421 | import numpy as np
try:
from skimage.transform import resize, rescale
except:
print("Warning: skimage.transform is not available. Will use scipy.misc.imresize instead.")
from PIL import Image
def resize(img, size):
return np.array(Image.fromarray(img).resize(size, Image.Resampling(2)))
import ma... |
0218155538581e37cc11c7274837c7d81de9b8753a6633f0c4f708b854a7cd10 | Python | 18,836 | 602 | """
============================
``ctypes`` Utility Functions
============================
See Also
--------
load_library : Load a C library.
ndpointer : Array restype/argtype with verification.
as_ctypes : Create a ctypes array from an ndarray.
as_array : Create an ndarray from a ctypes array.
References
----------
... |
965fbbd9186a088b483c1f7b9ce5a11fb1f6f768789d5217ff0d6da0a4cf3148 | Python | 18,841 | 541 | """Test functions for matrix module
"""
from numpy.testing import (
assert_equal, assert_array_equal, assert_array_max_ulp,
assert_array_almost_equal, assert_raises, assert_
)
from numpy import (
arange, add, fliplr, flipud, zeros, ones, eye, array, diag, histogram2d,
tri, mask_indices, triu_indices, t... |
7091334c4b562f1cb1bcc97b1e8bf11cbc2585d348d772c1ef123f7d09768a9a | Python | 18,848 | 530 | import numpy as np
import torch,os,sys
from torch import nn
from torch.nn import Parameter
import abc
import math
from abc import ABC
import numpy as np
import torch
from torch import nn
from torch.nn import Parameter
import torch.nn.functional as F
import matplotlib.pyplot as plt
from braincog.base.strat... |
72c73ea62e929d0751cf042c77fadc127e63768c1f7de331aeb227d6a9d8e7c7 | Python | 18,848 | 454 | """Defines plotting functions used for analyzing data.
See ``examples/analysis`` for examples of how to use.
"""
import json
import os
import warnings
from typing import List
import matplotlib.colorbar as cbar
import matplotlib.colors as mplcolors
import matplotlib.pyplot as plt
import matplotlib.ticker as tick
impo... |
3297ef27af3e286d77b04c4446f33c680c360c414d5fdc09d20c5ac038b3cdc0 | Python | 18,857 | 386 | from torch.utils.data import DataLoader
import numpy as np
import torch
from utils import InfoNCE
from tqdm import tqdm
from torch.optim import Adam
from utils import DualBranchContrast
from pl_bolts.optimizers import LinearWarmupCosineAnnealingLR
from model_scripts.VarCoNet import VarCoNet
from utils import ABIDEDatas... |
b760ef791561b59519dd065f641bb783a10b3510f4f0fc44dab944ccd7cb5376 | Python | 18,859 | 524 | #!/usr/bin/env python3
"""GPU/toolchain environment setup (runs once before any wheel is built).
The manywheel builder image (.ci/docker/manywheel/Dockerfile_2_28) is
expected to ship the heavy build dependencies (CUDA, cuDNN, NCCL, MAGMA,
cuSPARSELt, MKL, plus the standard OS package set). This script:
* Installs ... |
fc0de8840592e075eb406d3a4bc2f8edd226759193c18a2c0979e8cb0ecbe39a | Python | 18,911 | 556 | """Tests for hermite_e module.
"""
from functools import reduce
import numpy as np
import numpy.polynomial.hermite_e as herme
from numpy.polynomial.polynomial import polyval
from numpy.testing import (
assert_almost_equal, assert_raises, assert_equal, assert_,
)
He0 = np.array([1])
He1 = np.array([0, 1])
He2... |
0fe92c4b439a6c00f1f9861161fb2bcdeafe2005e110824129f86f3b072a43de | Python | 18,914 | 379 | import pickle
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
from tools.Tools import save_fig, get_data_path
# np.random.seed(0)
class MazeTurnEnvVec:
"""Vectorized RL T-Maze environment written in pure Numpy. We require an efficient environment since we need to evaluate
... |
eede85f905a8c2d2e1e85ffa97ee18578638c8d4dca85404bbd8b7ef3233ebcb | Python | 18,925 | 562 | import inspect
import types
import typing as t
from functools import update_wrapper
from gettext import gettext as _
from .core import Argument
from .core import Command
from .core import Context
from .core import Group
from .core import Option
from .core import Parameter
from .globals import get_current_context
from ... |
ac2659bd3c7141aa88960b4c55fcf184cccb2ab0dbca96164750f493133bd94d | Python | 18,934 | 397 | from Client_config import (
VENDOR_ID,
PRODUCT_ID,
USB_PREAMBLE,
TEST_SERVER,
WORD_LENGTH_IN_BYTES,
MAX_PKG_ID,
ZMQ_USBCOM_ENDPOINT,
connect_to_zmq,
drain_zmq_queue,
)
import usb.core
import usb.util
import time
import numpy as np
import multiprocessing as mp
import mu... |
f8b25a570c07bce29d71efe0d39e822f6c00f9eefe38086c93dde4b9c830b42d | Python | 18,966 | 525 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
The collection of helper functions for the DCBC calculation
Created on Fri Sep 27 11:55:06 2024
Author: dzhi
"""
import os, warnings, scipy
import numpy as np
import nibabel as nb
import matplotlib.pyplot as plt
# Check if torch is available
try:
import torch as ... |
6ca941b7949fb77b97ef88f848dfcdb42ca5b3a78792cfac1ed827c0baa84569 | Python | 18,969 | 541 | import numpy as np
np.random.seed(1)
import tkinter as tk
import time
from PIL import ImageGrab
UNIT = 40 # pixels
MAZE_H = 11 # grid height
MAZE_W = 5 # grid width
class Maze2(tk.Tk, object):
def __init__(self,lamda=0):
super(Maze2, self).__init__()
self.action_space = ['u', 'd', 'l', 'r']
... |
04de215e6d7a864cfa6c5439e8182fa116f461f74afb80a359be0571844505f9 | Python | 18,970 | 570 | from __future__ import annotations
from collections import defaultdict
from collections.abc import (
Hashable,
Iterable,
)
import itertools
from typing import (
TYPE_CHECKING,
cast,
)
import numpy as np
from pandas._libs.sparse import IntIndex
from pandas.core.dtypes.common import (
is_integer_d... |
a2187b278dc2815d628f19fda333613b9570bb4935fb7c9444859359e34f4608 | Python | 18,978 | 614 | from __future__ import annotations
from datetime import (
datetime,
timedelta,
)
from typing import TYPE_CHECKING
import warnings
import numpy as np
from pandas._libs import index as libindex
from pandas._libs.tslibs import (
BaseOffset,
NaT,
Period,
Resolution,
Tick,
)
from pandas._libs.... |
a19f2f27e93b3eed84edaccf7b7d241c3480301a0a68ce1a764361fafef4c0b8 | Python | 18,992 | 503 |
from numpy import argmax
import random, time, pygame, sys
import pygame
pygame.init()
from pygame.locals import *
import os
# os.environ['SDL_AUDIODRIVER'] = 'dsp'
# os.environ['SDL_VIDEODRIVER']='windib'
os.environ["SDL_VIDEODRIVER"] = "dummy"
# os.environ['DISPLAY'] = "localhost:13.0"
from rulebasedpolicy.world_mod... |
9219a4283bb487d6ebb020518632decf55eafa7cb3d70028fbd10a4f4c25e93c | Python | 19,007 | 540 | import os
import tempfile
import numpy as np
import pytest
import warnings as _warnings
from scipy.sparse import find
import sys
import xarray as xr
import cedalion.data
import cedalion.dot as cdot
import cedalion.dot.forward_model as fw
import cedalion.dataclasses as cdc
import cedalion.nirs
import cedalion.xrutils
... |
a763b3f7d2cc761b8cb84919bacac9563da0df6c7943f24bc3aad4ba7dab9275 | Python | 19,026 | 418 | import os
import escargot.language_models as language_models
import logging
import io
import threading
import time
from escargot import operations
import escargot.controller as controller
import escargot.memory as memory
#vectorized knowledge
from escargot.vector_db.weaviate import WeaviateClient
from escargot.parser... |
91467c32dc0438d21c64101db7ead5e5a7b80c7422137d6b4ae7acde87812e76 | Python | 19,029 | 516 | #!/usr/bin/env python3.7
"""Defines Slide 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 itertools
import ... |
7a64f8af8b987bc82a1b53e88f6e19d5b938a3f25adc0ead07b6d18257b50aff | Python | 19,067 | 467 | import h5py
import numpy as np
import os
import pandas as pd
import pathlib
from pathlib import Path
import pickle
import scipy.stats as stats
import soxr
#! change below to spatial_attn_lighting if want to use with modular
import src.spatial_attn_lightning as attn_tracking_lightning
import src.audio_transforms as at
... |
878b2775ca45e4e1eb65037cbc3f0859be4e072bd6ec005b8514e8c68beba92f | Python | 19,067 | 531 | """
This module started out as largely a copy paste from the stdlib's
optparse module with the features removed that we do not need from
optparse because we implement them in Click on a higher level (for
instance type handling, help formatting and a lot more).
The plan is to remove more and more from here over time.
... |
c65d61e055c1451712e7db471754683685829339991e9d0a6ea924f45ea21dfb | Python | 19,067 | 488 | #!/usr/bin/env python
# Author: LiYang@cmt.tsinghua
# Date: 2021.04.08
# Descripution: This python code is designed for calculate the fermi energy
# and plot the band structure use the *.Band file.
# ::Input File::
# - *.Band
# ::Output File::
# ... |
42105ccf0ca41ecf148722066c2fb8ebc52f4a1415e4e3538aacd5e275c042d9 | Python | 19,073 | 464 | from __future__ import annotations
import importlib.util
import re
from collections import defaultdict
from pathlib import Path
from typing import TYPE_CHECKING, Any, cast
from pymmcore_plus.mda.handlers import (
ImageSequenceWriter,
OMETiffWriter,
OMEZarrWriter,
TensorStoreHandler,
)
from pymmcore_wi... |
50835847347bebe28ed618568141f6289adfdfaea9a645bc739d05ac540479ea | Python | 19,079 | 564 | from unittest.mock import MagicMock, patch
import numpy as np
from cali.analysis._fov_metrics import (
_compute_jitter_synchrony_matrix_numba,
_detect_spike_onsets,
_get_calcium_peaks_event_correlations_matrix,
_get_calcium_peaks_event_synchrony,
_get_calcium_peaks_events_from_rois,
)
from cali.pl... |
c0d57b44bf8766807f23ad58945e67b24a47fb84710369f73ff823df58b5f053 | Python | 19,079 | 604 | """
Functions for arithmetic and comparison operations on NumPy arrays and
ExtensionArrays.
"""
from __future__ import annotations
import datetime
from functools import partial
import operator
from typing import (
TYPE_CHECKING,
Any,
)
import warnings
import numpy as np
from pandas._libs import (
NaT,
... |
f3601c10e0703c2860a61382a2896280d3fb44d01390f7f0770697161cc5aa86 | Python | 19,085 | 535 | import pysam
from sinto import utils
from scipy import sparse
import numpy as np
from collections import Counter, defaultdict
from multiprocessing import Pool
import functools
import re
import gc
import tempfile
import os
import math
def writeFragments(fragments, filepath):
"""Write fragments to file
Paramet... |
7699db336b2aef8adbe9c33b1b585abe69d602dc5a560cf6de2c3cd414ad7e98 | Python | 19,087 | 527 | """Virtual zarr-like reader for collections of TIFF files.
This module provides a reader that maps TIFF files to a plate/well/FOV structure
and provides lazy array-like access without loading everything into memory.
"""
from __future__ import annotations
import json
from dataclasses import dataclass
from datetime im... |
62a0b8137471845347f96e0b3aacb546dc5c1d1cbd851c98343f766523571307 | Python | 19,095 | 653 | #
# This file is part of gunicorn released under the MIT license.
# See the NOTICE for more information.
import ast
import email.utils
import errno
import fcntl
import html
import importlib
import inspect
import io
import logging
import os
import pwd
import random
import re
import socket
import sys
import textwrap
impo... |
731d0797cc4b66052e5eecbbf068a1f406230adaaeae6623549c72038c96b7bc | Python | 19,101 | 511 | # SPDX-FileCopyrightText: 2015 Eric Larson
#
# SPDX-License-Identifier: Apache-2.0
"""
The httplib2 algorithms ported for use with requests.
"""
from __future__ import annotations
import calendar
import logging
import re
import time
import weakref
from email.utils import parsedate_tz
from typing import TYPE_CHECKING... |
b1e1beab741233cd5b3cd106b92a18198f434249ad57c98f0c78cb2800bf7719 | Python | 19,118 | 441 | parent_path = r'/.../baselines'
import sys
sys.path.append(parent_path)
from torch.utils.data import DataLoader
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from tqdm import tqdm
from utils import ABIDEDataset
import os
import pickle
from sklearn.metrics import roc_auc_score
fro... |
4290eebd75dcc09178f65501707e418924f8e91cfdc121bb556fe9ecdff4dbb3 | Python | 19,132 | 512 | from __future__ import annotations
import collections.abc as c
import sys
import typing as t
import weakref
from collections import defaultdict
from contextlib import contextmanager
from functools import cached_property
from inspect import iscoroutinefunction
from ._utilities import make_id
from ._utilities import ma... |
d8c141489ccf3865538586e19c60e5e88a5750a53f84f20fd8e6b02ee85a738f | Python | 19,139 | 530 | import numpy as np
import torch
from utils.utils import *
import os
from dataset_modules.dataset_generic import save_splits
from models.model_mil import MIL_fc, MIL_fc_mc
from models.model_clam import CLAM_MB, CLAM_SB
from sklearn.preprocessing import label_binarize
from sklearn.metrics import roc_auc_score, roc_curve
... |
4d37aa0eecd2fbf04548db944ad556984da7183a4abaf521041264fc20905d5d | Python | 19,144 | 571 | from __future__ import annotations
import logging
import os.path
import pathlib
import re
import urllib.parse
import urllib.request
from dataclasses import replace
from typing import Any
from pip._internal.exceptions import BadCommand, InstallationError
from pip._internal.utils.misc import HiddenText, display_path, h... |
fe02d0793d0aa8a3de72467103350dedb4aea7e570dfdae596de2c841efbba4e | Python | 19,147 | 613 | import marimo
__generated_with = "0.18.0"
app = marimo.App(width="medium")
with app.setup:
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
import matplotlib.ticker as ticker
import cmasher as cmr
import pandas as pd
import seaborn as sns
from scipy.stats imp... |
43f3271c8292301bc8bc0e83a4c36472c412bfc694f438af527d66940ffdcc4b | Python | 19,151 | 598 | from __future__ import annotations
from typing import (
TYPE_CHECKING,
cast,
)
import warnings
import numpy as np
from pandas._libs import (
NaT,
algos as libalgos,
internals as libinternals,
lib,
)
from pandas._libs.missing import NA
from pandas.util._decorators import cache_readonly
from pa... |
31d3fcccd95241e794ee9b0e5f0194750d7ef172b360297998a30872930288df | Python | 19,152 | 643 | """
datetimelike delegation
"""
from __future__ import annotations
from typing import (
TYPE_CHECKING,
cast,
)
import warnings
import numpy as np
from pandas._libs import lib
from pandas.util._exceptions import find_stack_level
from pandas.core.dtypes.common import (
is_integer_dtype,
is_list_like,
... |
bda565d00d39369a80c526c877029ac5604c0a1e0fc10dcf0b99350939fe4ad0 | Python | 19,158 | 596 | import math
import os
import shutil
import subprocess
import sys
from typing import List, Tuple
from AIMD import arguments
from Calculators.device_strategy import DeviceStrategy
from utils.pdb import reorder_atoms, standardise_pdb, translate_coord_pdb, reorder_coord_amber2tinker
from utils.system import get_physical_c... |
df37c1fbd952dadd0f267ef416aae4e9134f75cb46296a3c00327490564a607d | Python | 19,166 | 603 | from matplotlib import pyplot as plt
import scipy.stats
from scipy.sparse import spmatrix, issparse, csr_matrix
from scipy.stats import multivariate_normal
from anndata import AnnData
from typing import Optional, Union
from shapely.geometry import Point, MultiPoint
from numpy.linalg import svd, solve, lstsq
from numpy.... |
784f9550824653d61e79a572eed540bcc4568a032ccae00ca7192395ba6d6e3a | Python | 19,188 | 528 | """PipSession and supporting code, containing all pip-specific
network request configuration and behavior.
"""
from __future__ import annotations
import email.utils
import functools
import io
import ipaddress
import json
import logging
import mimetypes
import os
import platform
import shutil
import subprocess
import ... |
14343e819d10363a030ecf3901c8e6f3f1edba9c2c8ab9da9fc7385a3e8da89c | Python | 19,210 | 508 | import logging # noqa: I001
import os
import pandas as pd
from pnet.data_processing import (
utils,
data_manipulation,
) # for manipulating the germline VCFs, filtering, etc
logger = logging.getLogger(__name__)
##############################
# Prostate project data loading
##############################... |
0eff5aed0091d5ba811e85e00a398fac611ec06d6fd8106d13ff157dc178c925 | Python | 19,220 | 699 | """Automatically adapted for numpy Sep 19, 2005 by convertcode.py
"""
import functools
__all__ = ['iscomplexobj', 'isrealobj', 'imag', 'iscomplex',
'isreal', 'nan_to_num', 'real', 'real_if_close',
'typename', 'mintypecode',
'common_type']
from .._utils import set_module
import numpy.... |
00c266da4f6011aebce6dcf2a01a2b79008db2b65612338b838f33ff055894d6 | Python | 19,227 | 278 | #!/usr/bin/env python3
from lib.designer_input_utils import *
from lib.designer_func_wrappers import *
def usage(cmdline): #pylint: disable=unused-variable
from mrtrix3 import app #pylint: disable=no-name-in-module, import-outside-toplevel
cmdline.set_copyright("""Copyright (c) 2016 New York University.\n\n
... |
6d91c5a59ebfd6d2a0007cc29c9c6a50d145366ff785557587209fa01b2ee2ed | Python | 19,258 | 496 | import torch,os
from random import randint
import torch
from torch import nn
from braincog.base.strategy.surrogate import *
from braincog.model_zoo.bdmsnn import BDMSNN
import pygame
from pygame.locals import *
from collections import deque
from random import randint
import numpy as np
import matplotlib.py... |
16fa7c606480bb1f028d727a9690a7f32e0ff6f0ff0ab7d8e79b2dacc4f859cc | Python | 19,274 | 504 | import torch
import os
from braincog.model_zoo.bdmsnn import BDMSNN
import pygame
from pygame.locals import *
from collections import deque
from random import randint
import numpy as np
try:
pygame.display.init()
except:
os.environ["SDL_VIDEODRIVER"] = "dummy"
def load_images():
"""
... |
fe17ebdfab7e8e6f903a123d1b06ddeac41923969558c322c4763e3983aa2ae3 | Python | 19,293 | 551 | import operator
import numpy as np
import pytest
import pandas._libs.sparse as splib
import pandas.util._test_decorators as td
from pandas import Series
import pandas._testing as tm
from pandas.core.arrays.sparse import (
BlockIndex,
IntIndex,
make_sparse_index,
)
@pytest.fixture
def test_length():
... |
737573c6d86e79b96406e67c551909760fae9abddce22d4908e396e4dc5b3bdc | Python | 19,308 | 586 | # module.py
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.distributions import Normal
from typing import Tuple, Union, Literal, Optional
from .mixin import NODEMixin
class Encoder(nn.Module):
"""
Variational encoder mapping input states to latent distributions.
Suppor... |
6b86e501ef1b41d57267ef199ee93b3a3ee029f8d152f3c203a9b8783d193105 | Python | 19,311 | 410 | ## ...........................................................................
##
## PIMMS (Polymer Interactions in Multicomponent Mixtures)
## Alex Holehouse, Pappu Lab, Holehouse Lab
## Copyright 2015 - 2026
## ...........................................................................
import random
import numpy a... |
4c2b990e945df193d91fa491c0865c5990b76a819cd7c46597a15871ac12eaa6 | Python | 19,317 | 469 | """ Modified version of build_clib that handles fortran source files.
"""
import os
from glob import glob
import shutil
from distutils.command.build_clib import build_clib as old_build_clib
from distutils.errors import DistutilsSetupError, DistutilsError, \
DistutilsFileError
from numpy.distutils import log
from d... |
66e4a3ce725864ad193e9c92a78053e764549ba14d81ecc0e6c1e0dc0b846152 | Python | 19,347 | 512 | from typing import List
import pytest
import numpy as np
from scipy.sparse import csr_matrix, issparse
from anndata import AnnData
from scvelo.preprocessing.moments import (
get_moments,
moments,
second_order_moments,
second_order_moments_u,
)
class TestGetMoments:
@pytest.mark.parametrize("da... |
84e68e051f2a2a7a2373aab5c510b72e626aa3b11a9d54f5ec9e35ddbe570eed | Python | 19,359 | 369 | import torch
import os
import re
import sys
import json
import numpy as np
import torch.nn as nn
from collections import OrderedDict
from src.layers import conv2d_same
from src.layers import padding as pad_utils
from src.custom_modules import HannPooling2d
class SimpleAttentionalGain(nn.Module):
def __init__(se... |
e451a87b5571266899f90e29dbcd5146c0e11abe1992a3807acf29aedb91f904 | Python | 19,380 | 408 | '''
Related Figures:s5
'''
import os
import torch
import scipy.io
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
from sklearn.linear_model import LinearRegression
class WaveletConvolution(nn.Module):
"""
A wrapper around two Conv1d layers, one (feat / hpf)which returns the
interme... |
bed5fbef0ca2ff6abc28efbecf66fd4d02fbbe01c32c9187ab336f236ffc2b47 | Python | 19,383 | 340 | import numpy as np
from utils.util import get_dim_from_space
from utils.segment_tree import SumSegmentTree, MinSegmentTree
def _cast(x):
return x.transpose(1, 0, 2)
class MlpReplayBuffer(object):
def __init__(self, policy_info, policy_agents, buffer_size, use_same_share_obs, use_avail_acts,
... |
9da97924c91a7f4949a69449a3b0f70051ee793f9d4ec5d8e7ce42cb6f963871 | Python | 19,385 | 266 | #!/usr/bin/env python
# coding: utf-8
# # AdEx double pool SDE system
# In[4]:
#export
# Initialization
import numpy as np
# ## Derivatives of transfer functions with respect to firing rates
# In[5]:
#export
def diff_fe(TF, fe, fi ,XX, df=1e-5):
return (TF(fe+df/2., fi,XX)-TF(fe-df/2.,fi,XX))/df ... |
5e585918f390e6928bd0cab6c5005ab1585ccd2b634946948ad40675b85c47ba | Python | 19,410 | 600 | """
Backend magic inherited from tensornetwork: numpy backend
"""
# pylint: disable=invalid-name
import logging
from typing import Any, Callable, Optional, Sequence, Tuple, Union
import numpy as np
import tensornetwork
from scipy.linalg import expm, solve, schur
from scipy.special import softmax, expit, ive, jv
fro... |
cb8ac7e4f916f1db073ed61c2cefa0d4b8d1081b006c990a65d561f41b968f2c | Python | 19,452 | 448 | """
Additional filtering: germline-specific factors (e.g. MAF <0.01)
Enable filter to a subset of variants likely to be high impact and biologically relevant.
Modified from this notebook: https://app.terra.bio/#workspaces/vanallen-firecloud-nih/Germline_pipeline_components/analysis/launch/Jan2023_PathogenicVariantFilt... |
f3682030da63912603bb84e4def992d334f09fc019dd5a828be3244133f6a5a0 | Python | 19,459 | 567 | from __future__ import annotations
import decimal
import operator
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.tests.extension import base
from pandas.tests.extension.decimal.array import (
DecimalArray,
DecimalDtype,
make_data,
to_decimal,
)
@pytest... |
2c730cc3f71eb4d3da96a1b5b2e46c3d906a82968e4110996da092fec8611f41 | Python | 19,472 | 759 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sun Sep 1 18:04:35 2019
@author: charleshen
@note: this code derived from PybioMed<https://github.com/gadsbyfly/PyBioMed>, with a major modified
"""
from rdkit import Chem
from rdkit.Chem import rdPartialCharges as GMCharge
import numpy
############... |
9e3977f0fc6617f3e6d3529e8e6f60b37c7aa1af2a0ee06bb0416020dc9f6fc8 | Python | 19,473 | 541 | import os
os.environ["TF_CPP_MIN_LOG_LEVEL"] = "3"
import typing
import numpy as np
from tensorflow.keras.models import Model
import plotly.graph_objects as go
from plotly.subplots import make_subplots
from plotly.colors import n_colors
from .data import tokenize_sequence
from .constants import *
def get_determine... |
bfac366c54ad022b89a617c5cb117d196002560934a36eebed7478b5cca062ab | Python | 19,521 | 481 | import time
import numpy as np
import multiprocessing as mp
import sys
from PyQt6 import QtWidgets, QtGui
from PyQt6.QtWidgets import QApplication, QWidget
from pyqtgraph.Qt import QtCore
from datetime import datetime
import os
from GUI import App
import zmq
import struct
import socket
from ctypes import *
from Clien... |
5e173d0d0fe806ab1c2819499bb0096b9eaa34186dd3337fbd977ec548f008b5 | Python | 19,550 | 535 | """Widget for creating TiffCollectionReader configurations via a dialog interface."""
from __future__ import annotations
from pathlib import Path
from typing import TYPE_CHECKING, cast
from pymmcore_widgets.useq_widgets import WellPlateWidget
from pymmcore_widgets.useq_widgets._well_plate_widget import (
DATA_PO... |
26491126fd1ffc15e407ece7549180027f344bd923bc0718651a074707538876 | Python | 19,610 | 593 | import numpy as np
import pytest
import tensorcircuit as tc
from tensorcircuit.pauliprop import (
PauliPropagationEngine,
SPARSE_WORD_QUBITS,
SparsePauliPropagationEngine,
pauli_propagation,
)
@pytest.mark.parametrize("backend", ["npb", "jaxb"])
def test_initialization(request, backend):
request.g... |
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