sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
adfb6333dd91546e42d9875c019e6aad78e2b0f30193666c54fb33657014e519 | Python | 7,695 | 241 | #!/usr/bin/env python
# coding: utf-8
# # RNA Velocity analysis using velocyto, Seurat, and scVelo (Part 2: Analysis)
# ## For KNOCKOUT (ko) sample GLIA+NEURONS -- VERSION 1.1
# ### Kat Beigel (beigelk@chop.edu)
# #### 7/21/23
# See the following pages for guides on how to combine Seurat and velocyto data for scVelo ... |
4643049073368c0c3928606ec2e5f04b3ec4be51bf7d30e92dda777626cbe9fa | Python | 7,696 | 174 | import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
import os
from scipy.stats import ttest_rel # Using a paired t-test since we're comparing the same models
DATA_PATH = '../Extracted_Selectivity/VGG/PretrainedOnImageNet/NAPS/Tuning/'
emotion_FILE = '1002_BestModels0912_SI_byR... |
5f4fa2f4bccd995b7636559e7a88a5a1fc21bb8f50aa0c8e2182b5091411b401 | Python | 7,698 | 183 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
class TestGetIndexer:
def test_get_indexer(self):
index = pd.RangeIndex(start=0, stop=20, step=2)
target = pd.RangeIndex(10)
indexer = index.get_indexer(target)
expected = np.array([0, -1, 1, -1, 2, ... |
b316e00624fdd319de973f5ed5c168f4931d84697f084cdf5e8d40232421885f | Python | 7,698 | 234 | # -*- coding: utf-8 -*-
'''iCSD toolbox demonstration script'''
import matplotlib.pyplot as plt
import numpy as np
import icsd
from scipy import io
import neo
import quantities as pq
#patch quantities with the SI unit Siemens if it does not exist
for symbol, prefix, definition, u_symbol in zip(
['siemens', 'S', 'm... |
f185921128a6295bf9f611fe9f09d0040011d3dab023e4f343a63fbdc3ca1380 | Python | 7,701 | 220 | """This script produces a table summarising first level distributions."""
import os
from copy import deepcopy
import glmtools as glm
import h5py
import matplotlib.pyplot as plt
import mne
import numpy as np
import osl
import sails
import lemon_plotting
from glm_config import cfg
from lemon_support import (get_eeg_da... |
0ac8b2283695a56cf376cd794b6d04100837d8df0a01eb515a5c9af7e31adf67 | Python | 7,702 | 186 | import os
import torch
import torchvision
from torch import nn, optim
from torch.utils.data import DataLoader
from torchvision import transforms
# from matplotlib import pyplot as plt
import time
# from tqdm import *
from torch.utils.tensorboard import SummaryWriter
from torchvision.models import ViT_B_16_Weights
impo... |
c39ad9c3485fdaf05e1bfa48b75b844fca71fa21d317063892fb6a007bd727d2 | Python | 7,702 | 200 | from keras.callbacks import Callback
from keras import backend as K
import numpy as np
def clr_check_args(args):
req_keys = ['clr_mode','clr_base_lr','clr_max_lr','clr_gamma']
keys_present = True
for key in req_keys:
if key not in args.keys():
keys_present = False
return keys_prese... |
4529b3c87c39b18065b9c2ffdac6a5f5b5a2ca9e5ed5bc3a5b20ce1a26caaf38 | Python | 7,705 | 184 | import torch, random, os
import torch.nn as nn
import numpy as np
config = {
'hidden_unit': 64,
'fc_layer': 2,
'self_atten_layer': 2,
'attention_heads': 4,
'num_neighbor': 30,
'fc_dropout': 0.2,
'attention_dropout': 0,
'class_num': 1
}
class Self_Attention(nn.Module):
def __init_... |
5be12697e20c6591c2f7962c1ee458e4c5acb0d997946f43f4341a40e2341169 | Python | 7,705 | 191 | ## Script: determine_inv.py
## Description: Determine the status of inversion.
## Author: Kevin Lee
## Date: 2022.01.12
# NOTE: Criteria used to determine inversion form was revised (2022-02-22)
import argparse
from utils import InputStream
from utils import PathType
import sys,os
import numpy as np
impor... |
54f1f6567efdf55e554114f0b98eb195931aa14b28efe69db534e0c5ac5c8230 | Python | 7,711 | 252 | """
:func:`~pandas.eval` source string parsing functions
"""
from __future__ import annotations
from enum import Enum
from io import StringIO
from keyword import iskeyword
import token
import tokenize
from typing import TYPE_CHECKING
if TYPE_CHECKING:
from collections.abc import (
Hashable,
Itera... |
961758ae300a34a96351a22be1fafb1991821f58e7b7d98fc99f4161e566383c | Python | 7,711 | 239 | #!/usr/bin/env python
# coding: utf-8
# # RNA Velocity analysis using velocyto, Seurat, and scVelo (Part 2: Analysis)
# ## For WILD-TYPE (wt) sample GLIA+NEURONS -- VERSION 1.1
# ### Kat Beigel (beigelk@chop.edu)
# #### 7/21/23
# See the following pages for guides on how to combine Seurat and velocyto data for scVelo... |
c144bf5f55b203070c31391669bf428c84089fc24a6bfd7315bc15b802628ee0 | Python | 7,711 | 187 | # Copyright 2025 Xanadu Quantum Technologies Inc.
# 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 law or agre... |
7fb300fc3b626bd425b249f32c02e71a06169b1d389c2aa9c6cd871b76315b6b | Python | 7,712 | 181 | #%%
# -*- coding: utf-8 -*-
import os
import numpy as np
import pickle as pkl
from scipy.optimize import minimize
from scipy.interpolate import interp2d
import matplotlib
import matplotlib.pyplot as plt
from matplotlib.patches import Polygon as matplotlib_polygon
import imageio
factor1 = 15 #1e+5 #1e+10 ... |
3eb77eaaab1661900fcdeca05a437a83d4d8b822f92187d94ffac22dcec7a95b | Python | 7,716 | 225 | """Test data export"""
import pathlib
import tempfile
from unittest import mock
import dclab
import numpy as np
from PyQt6 import QtCore, QtWidgets
import pytest
from shapeout2.gui.main import ShapeOut2
from shapeout2.gui import export
from shapeout2 import session
data_path = pathlib.Path(__file__).parent / "data"
... |
70e0a5a94d10273bcb7349d4daf418a6a12c6217a9c142f5e74789f580c416a1 | Python | 7,717 | 240 | """
Copyright (c) Facebook, 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
from collections import deque
from pathlib import Path
from typing import Deque, Optional
import ase
import torch
from torch_... |
7b16f5880e558695569392738a37b2980671a19e652a2019d31b346a994d15b1 | Python | 7,717 | 205 | # Copyright 2018-2021 Xanadu Quantum Technologies Inc.
# 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 law or... |
4f475d0212e26c38e9b0d3c9e1525df84d7888c24afb13893b1772995d57d627 | Python | 7,718 | 222 | """Hermetic checks for Clock Explorer generation and committed artifacts.
The generator test uses temporary input and output paths; committed-artifact
checks validate docs/_static without network access.
"""
import csv
import importlib.util
import json
import os
import sys
from unittest.mock import Mock
import torch... |
d30835705780af1d5a12ccf83836a8c4cff62500bb118aac31f301ac7de956b5 | Python | 7,719 | 134 | #! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this wo... |
2e0bb969d035e837253151b6434551097b74f7b0c5085c29077d4021f5d36411 | Python | 7,721 | 228 | # MOFTransformer version 2.2.0
import torch
from torch.optim import AdamW
from transformers import (
get_polynomial_decay_schedule_with_warmup,
get_cosine_schedule_with_warmup,
get_constant_schedule,
get_constant_schedule_with_warmup,
)
from moftransformer.gadgets.my_metrics import Accuracy... |
8c787b4101e3ed1c0c3ea1d54c2f607396d6f55a3d6a317db6d2bc75ce1c8ba1 | Python | 7,721 | 279 | import gc
import numpy as np
from pandas import (
DatetimeIndex,
Index,
IntervalIndex,
MultiIndex,
RangeIndex,
Series,
date_range,
)
class SetOperations:
params = (
["monotonic", "non_monotonic"],
["datetime", "date_string", "int", "strings", "ea_int"],
["inte... |
c181aad0d8ad338f5714883e8d11698dd4acd5b2219bbbf7f71f4e3c1f2116ba | Python | 7,721 | 193 | import torch
from torch import Tensor
import torch.nn.functional as F
from torch.nn import Sequential, Linear, BatchNorm1d
import torch_geometric
from torch_geometric.nn import (
Set2Set,
global_mean_pool,
global_add_pool,
global_max_pool,
CGConv,
DiffGroupNorm
)
from torch_scatter ... |
e585c72f5d1d89a08cfa340ef21d6c32569b0e050827c26620834ec281989c4d | Python | 7,721 | 212 | import os.path
from torch.utils.data import DataLoader
import torch
from torch.utils.data import Dataset
from tqdm import tqdm
import re
import pytorch_lightning as pl
class SCARTransformerDataset(Dataset):
def __init__(self, consults, labels, tokenizer, max_len):
self.tokenizer = tokenizer
self.c... |
34c7406896ec6be92c648fe1de05ec4efc8816849492b4e83aa37ca5c3f1773d | Python | 7,722 | 195 | from typing import (
Any,
final,
)
import pytest
import pandas as pd
import pandas._testing as tm
class BaseReduceTests:
"""
Reduction specific tests. Generally these only
make sense for numeric/boolean operations.
"""
def _supports_reduction(self, ser: pd.Series, op_name: str) -> bool:... |
2315dab415a86c782ff1c0915d74c51cff0e76b7513b047b3e0404949883f604 | Python | 7,723 | 199 | import numpy as np
import pytest
import pandas as pd
def test_is_monotonic_increasing_lexsorted(lexsorted_two_level_string_multiindex):
# string ordering
mi = lexsorted_two_level_string_multiindex
assert mi.is_monotonic_increasing is False
assert pd.Index(mi.values).is_monotonic_increasing is False
... |
fe6b442765dd7204d59091cfb33c0bbe75f70664b8e356c1d5725fdf515ab2c8 | Python | 7,723 | 213 | ''' update_dynamodb_published_skeletons.py
Update a janelia-neuronbridge-skeletons DynamoDB table.
'''
import argparse
import collections
from operator import attrgetter
import sys
import boto3
import inquirer
from inquirer.themes import BlueComposure
from tqdm import tqdm
import jrc_common.jrc_common as JRC
# py... |
e445c21a07719ea08a257bf15fed9e3088b3afb13de4f3c4e6d1763ae14af705 | Python | 7,728 | 194 | # Copyright 2022 Xanadu Quantum Technologies Inc.
# 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 law or agre... |
df0c2d194ee967840ac0191b1933dba7bc4ac3c16bcf80d24f1f581bb64c6394 | Python | 7,730 | 206 | import numpy as np
import os
from kcsd import csd_profile as CSD
from kcsd import KCSD2D
from scipy.integrate import simps
from scipy.interpolate import griddata
from figure_properties import *
import matplotlib.pyplot as plt
import matplotlib.cm as cm
import matplotlib.gridspec as gridspec
def integrate_2d(csd_at, t... |
2f6cc6aa6daac8e6af61c2d1e9aa97b698062dad5528c1038290b0812c3470d5 | Python | 7,732 | 235 | from typing import *
import numpy as np
import pytorch_lightning as pl
import torch
from pytorch_tabnet.tab_network import (EmbeddingGenerator, RandomObfuscator,
TabNetDecoder, TabNetEncoder)
# ALL THIS IS FLATTENING THE API FROM https://github.com/dreamquark-ai/tabnet
class N... |
340a26f20d9bec790c075b01c8ccca1292d707b768b0f36a80d041186755eedf | Python | 7,733 | 221 | import operator
import re
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
class TestDataFrameLogicalOperators:
# &, |, ^
@pytest.mark.parametrize(
"left, right, op, expected",
[
(
[True, False, np.nan],
[True, Fal... |
7a448a8f06dbba3ce83533519214f96d01658c612464143724de227ebb7a167b | Python | 7,736 | 251 | import h5py
import numpy as np
import os
import pandas as pd
import sys
from .summarydata import SummaryData
from . import preprocessing
from . import metrics
from . import utils
from cellex import ES_METRICS
class ESObject(object):
"""A class that integrates the CELLEX workflow to compute ES
Workflow: filte... |
ac19989299c9f6f405894bf0883ded591795a3325aa54e52a8887b853aab5f49 | Python | 7,737 | 206 | """Bounded BED/BEDPE EOF regressions for #804 / #757 item 7."""
import gzip
import subprocess
import sys
import pytest
from conftest import macs3_env
from MACS3.Utilities.Constants import READ_BUFFER_SIZE
SCRIPT = r'''
import sys
from MACS3.IO.Parser import BEDParser, BEDPEParser, StrandFormatError
from MACS3.Sign... |
cca062ff50cc9752db4b14980cf3993d377b11c77642cf6ee366386c3b42bcac | Python | 7,739 | 230 | from io import BytesIO
import os
import pathlib
import tarfile
import zipfile
import numpy as np
import pytest
from pandas.compat.pyarrow import pa_version_under17p0
from pandas.errors import Pandas4Warning
import pandas as pd
import pandas._testing as tm
from pandas.util import _test_decorators as td
@pytest.fixt... |
56110a2a71fbd16a032c470780b73ad543721f5a353b7c3466a6ff2e5f82ae5e | Python | 7,741 | 265 | import numpy as np
import matplotlib.pyplot as plt
import matplotlib as mpl
# increase the figure size
plt.rcParams["figure.figsize"] = [12, 10]
# remove the top and right spines from plot in the global plt setting
plt.rcParams["axes.spines.top"] = False
plt.rcParams["axes.spines.right"] = False
# change the linewidt... |
617a4ac7d62a10bcefd123785768b52d1f59323cb14db15e6d0514f35cff8207 | Python | 7,744 | 200 | # Copyright 2018-2021 Xanadu Quantum Technologies Inc.
# 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 law or... |
a2570686bc305357cfa0972b4f6687df79b68a1d4b8dc4e9a684a6aa83bbd78c | Python | 7,744 | 182 | """EnvPool vectorized environment wrapper for rl_games.
Uses envpool's native gymnasium API. Requires envpool >= 1.2.6 on Python
3.12+ (randomized MyoSuite resets; wheels start at cp312) with an envpool
1.2.5 fallback on Python 3.11 — both verified against numpy 2.x: 1.2.6 +
numpy 2.4.4 (CartPole, HalfCheetah and the ... |
5843cd1c8d0690a99d9ec83f5a74c6cccaab91fe0135b7a0a221d07058733dbe | Python | 7,750 | 205 | import socket
import serial
import time
import schedule
import smtplib
import threading
import queue
from datetime import datetime
from email.mime.text import MIMEText
gmail_user = ''
gmail_password = ''
arduino_timeout_s = 1500
mailing_list = [''] # ['me@gmail.com', 'bill@gmail.com']
mail_q = queue.Q... |
980fbf6a5bf87e9ef816a986979484ae36202986044b401d7f0aa733338296e5 | Python | 7,751 | 269 | import inspect
import linecache
import pathlib
import warnings
from functools import cache, cached_property, partial
from itertools import chain
from typing import *
import anndata as an
import numpy as np
import pandas as pd
import torch
from scipy.sparse import issparse
from sklearn.model_selection import train_test... |
d6b9a379499909043cfa740f7f8370ae6f0ecd5630bf0e18d797b44288570a89 | Python | 7,758 | 239 | import re
import numpy as np
import pytest
from pandas.errors import Pandas4Warning
import pandas as pd
import pandas._testing as tm
@pytest.fixture
def left():
return pd.DataFrame({"key": ["a", "c", "e"], "lvalue": [1, 2.0, 3]})
@pytest.fixture
def right():
return pd.DataFrame({"key": ["b", "c", "d", "f... |
54dee2b085c308332f9f5831ef905c09fadbbb64f7118cfe902cb0a9a591d254 | Python | 7,759 | 207 | """
Utility functions for other submodules
"""
import warnings
import itertools
import logging
import numpy as np
from bids.layout import BIDSLayout
mod_logger = logging.getLogger(__name__)
def is_hemispherical(vecs):
"""Test whether all points on a unit sphere lie in the same hemisphere.
Parameters
... |
1f31650bb8345ae852da1bf522f92d402b5b1607aef493fd39ca52685b023454 | Python | 7,761 | 261 | """Test views."""
# ------------------------------------------------------------------------------
# Imports
# ------------------------------------------------------------------------------
import numpy as np
from numpy.testing import assert_allclose as ac
from phylib.io.mock import artificial_waveforms
from phylib.u... |
6ba676e3a21206291c2c80132e4755bb58c9ca9e2498665d3eeaba70e39829c8 | Python | 7,765 | 223 | # Copyright 2026 Xanadu Quantum Technologies Inc.
# 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 law or agre... |
24e3123b918caa11336c55b5bb50ab43db9e36b58f4d87a932b8798f0fefb28e | Python | 7,772 | 238 | # -*- coding: utf-8 -*-
# @File name: plot_waveforms_from_pkls.py
# @Author: Alicia Garrido-Peña
# @Date: 2023-08-10 22:38:38
# @Contact: alicia.garrido@uam.es
# "Copyright (c) 2023 Alicia Garrido-Peña. All Rights Reserved."
# Use of this source code is govern by GPL-3.0 license that
# can be found in the LICENSE f... |
c9e4c618e85b02e16f47545d8bcbc971f0c62993edfa370919779732d1c9f1e3 | Python | 7,774 | 260 | """
Tests for offsets.BDay
"""
from __future__ import annotations
from datetime import (
date,
datetime,
timedelta,
)
import numpy as np
import pytest
from pandas._libs.tslibs import iNaT
from pandas._libs.tslibs.offsets import BDay
import pandas as pd
import pandas._testing as tm
from pandas.tests.tse... |
4be2c7c580fae39c72dc732f4de9e5932bd61baa77a1d2d6e1138234d44db6f2 | Python | 7,783 | 202 | import numpy as np
import pytest
from pandas.errors import Pandas4Warning
import pandas as pd
import pandas._testing as tm
from pandas.io.sas.sas_xport import (
XportReader,
_parse_float_vec,
)
from pandas.io.sas.sasreader import read_sas
# CSV versions of test xpt files were obtained using the R foreign li... |
7ee3dd9c9dd70bff27b3ebea3e2121edfcf19951e16fd7289d67bfa8a949dac5 | Python | 7,786 | 138 | #!/usr/bin/env python
# -*- coding: UTF-8 -*-
# Created by Roberto Preste
HEADERS_MAIN = (
("Locus", "locus", "Locus to which the variant belongs"),
("FunctionalLocus", "func_locus",
"Functional locus to which the variant belongs"),
("CodonPosition", "codon_position", "Codon position of the variant"),... |
c791556db149e82bf506e4ac920bdb473ea565063d9cb935e58ff61fc47b2751 | Python | 7,786 | 123 | # MIT License
#
# Copyright 2026 Broad Institute
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, ... |
807f0cdedfde398109e5208570d8527611104e0a3499478e55280d151b948115 | Python | 7,788 | 211 | # Copyright 2018-2025 Xanadu Quantum Technologies Inc.
# 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 law or... |
0d15dce17dbf6789712a0a993a564f6f7ea3997eb62d3739d96d534947f8ef0d | Python | 7,789 | 217 | #!/usr/bin/env python
import os, sys, numpy, math, argparse
from argparse import RawTextHelpFormatter
###################################################
### 0. script description and parsing arguments ###
###################################################
synopsis1 = "\
report number of nodes in OrthNets that ... |
6d1b4887d58d5130f05321bdd3c188f41c33f3f296a08cb679a406077a00ba47 | Python | 7,789 | 186 | import os
import sys
from botocore.client import Config
import ibm_boto3
import pandas as pd
from pathlib import Path
from shutil import rmtree
import numpy as np
import json
import re
import nda_helper as ndh
sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
sys.path.append(os.path.abspath(o... |
c85bdb69b4f027d4f1c708735c8cfebfb495bef4a6caea21a48c2429c6480e89 | Python | 7,794 | 183 | # Copyright 2026 Xanadu Quantum Technologies Inc.
# 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 law or agre... |
ffd80adb6e59d25c78607a9dcf4f771152c7e4d85a25b096aebf44467034c19e | Python | 7,794 | 230 | """Classes for formatting and writing trimmed reads to output.
"""
import sys
from atropos.io import STDOUT, xopen, open_output
from atropos.io.compression import splitext_compressed
from atropos.io.seqio import create_seq_formatter
from .filters import NoFilter
class Writers(object):
"""Manages writing to one or ... |
c241e6d78c168c326eabc97e0b3f2575615f7c029624b9d5af5e583c5532e532 | Python | 7,795 | 223 | """Test the recommend CLI command argument parsing."""
import argparse
from unittest.mock import patch
import pytest
from lightning_pose.cli.commands.recommend import (
_resolve_output_path,
get_parser,
handle,
)
class TestGetParser:
"""Test the get_parser function."""
def test_returns_argumen... |
96992a616b766f405b695de53e4b7150b80cc4fc727ead167c31841880c3c9c4 | Python | 7,796 | 270 | # -*- coding: utf-8 -*-
"""
Created on Tue Jan 31 14:57:55 2023
@author: jeanbaptiste
"""
import json
import matplotlib.pyplot as plt
import numpy as np
import deepcellcontrol as dcc
# Optogenetic input sequence
# light_sequence = [0]*24 + [1]*180 + [0, 1]*180 + [0] * 180 + [0, 1] * 180
light_sequence = [0]*4*12 + ... |
fd8c47b5ec31d59cb6b8f6fe0275241de11779c9f1d0f83271286d2a32324a61 | Python | 7,796 | 218 | #!/usr/bin/env python
import os, sys, subprocess, math, numpy, argparse
from argparse import RawTextHelpFormatter
###################################################
### 0. script description and parsing arguments ###
###################################################
synopsis1 = "\
combine CLfinder results for... |
981c6f57a056bd175206edf6f365c36f1f1b7cdb3ed890ae1907fb4c5f61dded | Python | 7,797 | 188 | import numpy as np, matplotlib.pyplot as plt, sys
import pumpprobe as pp, wormdatamodel as wormdm
from scipy.optimize import curve_fit
import matplotlib.ticker as ticker
ds_list = "/projects/LEIFER/francesco/funatlas_list.txt"
ds_tags = None
ds_exclude_tags = "mutant"
ds_exclude_i = []
inclall_occ = "--inclall-occ" in... |
4948dad82db51d3241903a0bf0c516e8e9fbb08adf631842d1675fd275ad28ec | Python | 7,798 | 204 | '''
Methods for fast binning of synapse activation dask dataframe.
Exemplary use:
groupby = ['EI']
values = synapse_activation_postprocess_dask(mdb['synapse_activation'], groupby = groupby, prefun = prefun, applyfun = applyfun, postfun = postfun)
values = values.compute(get = c.get)
print 'save'
... |
01c5d12e7549dc4a8ffae94998c24c81e49ef92880e76b4219d58484beb3a3de | Python | 7,799 | 177 | """Regressions for #799 / #757: pileups after sampling empties a chromosome."""
from pathlib import Path
import random
import subprocess
import sys
import textwrap
import MACS3
import pytest
from conftest import macs3_env, no_core_dumps
def run_probe(tmp_path, source):
script = tmp_path / "probe.py"
script... |
1d671abc60bae7e6774a4584ba27fc929be63edf4b04bd711f57721e0064337d | Python | 7,803 | 202 | """
Copied (and improved) from:
https://github.com/fadel/pytorch_ema/blob/master/torch_ema/ema.py (MIT license)
"""
from __future__ import division, unicode_literals
import copy
import weakref
from typing import Iterable, Optional
import torch
# Partially based on:
# https://github.com/tensorflow/tensorflow/blob/r... |
796de4ece1a1a49a9ae7668c556dc504e93edebe6ea071bd135eacd6573ad936 | Python | 7,810 | 186 | """Original-author oracle regressions for PCBrainAge and PCGrimAge proxies."""
import importlib
import importlib.util
import pytest
import torch
MODEL_NAMES = [
"PCBrainAge",
"PCGrimAgePackYrs",
"PCGrimAgeADM",
"PCGrimAgeB2M",
"PCGrimAgeCystatinC",
"PCGrimAgeGDF15",
"PCGrimAgeLeptin",
... |
94a731dac8081e7c8ed401c8a7736314f3f1e98d053f3f38113c68d176df4102 | Python | 7,814 | 209 | import glob
import numpy as np
import os
import tifffile
import pathlib
from image_registration.czi import get_image
from image_registration.registration import get_tiffiles, get_aligned_images, get_aligned_tiffiles, final_image, pyramidal_final_image
from sys import getsizeof
import gc
import pandas as pd
from datetim... |
eb258d74bbf2eace4c29ddad39f7181574aafef55653002ab837a9719396d766 | Python | 7,814 | 232 | """
Atropos version {}
usage: atropos [--config <config file>] <command> [options]
commands
--------
{}
optional arguments:
-h, --help show this help message and exit
--config <config file> provide options in a config file
Use "atropos <command> --help" to see all options for a specific comman... |
7e8e984e5265e93f6d40d1cdb196533fe820af51de3f6a94ffbd5528f3a40b83 | Python | 7,815 | 193 | # Copyright 2018-2024 Xanadu Quantum Technologies Inc.
# 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 law or... |
6c629310112e06f278d50f5b116e4cad885f5b8fe31d1273dedc2b33f4689d2a | Python | 7,822 | 191 | import torch
from torch import Tensor
import torch.nn.functional as F
from torch.nn import Sequential, Linear, BatchNorm1d
import torch_geometric
from torch_geometric.nn import (
Set2Set,
global_mean_pool,
global_add_pool,
global_max_pool,
DiffGroupNorm
)
from torch_scatter import scatte... |
de005123a3374fccf0cb1c1e038677ecd71c96be38fe2e3dbde7d92c4c8216b6 | Python | 7,822 | 197 | from typing import (
Any,
final,
)
import pytest
import pandas as pd
import pandas._testing as tm
class BaseReduceTests:
"""
Reduction specific tests. Generally these only
make sense for numeric/boolean operations.
"""
def _supports_reduction(self, ser: pd.Series, op_name: str) -> bool:... |
96da9727879e9c888f04d16324019d15dddd2e7267612b769e3f9440be074a50 | Python | 7,826 | 177 | from tensorflow.keras.layers import BatchNormalization, Layer, InputSpec
from tensorflow.keras import initializers, regularizers, constraints
from tensorflow.keras import backend as K
import tensorflow as tf
from tensorflow.python.keras.backend import _regular_normalize_batch_in_training
class BatchNormalizationF16(L... |
9ba9942806e3f2cebee3ac8fa1bfca6d195ffbb32f6d0499af2ab9c7924099b5 | Python | 7,827 | 227 | """Global attention modules (Luong / Bahdanau)"""
import torch
import torch.nn as nn
import torch.nn.functional as F
from onmt.modules.sparse_activations import sparsemax
from onmt.utils.misc import aeq, sequence_mask
# This class is mainly used by decoder.py for RNNs but also
# by the CNN / transformer decoder when ... |
81247b7a48604d2e7f88cfbc7f0be0aa6574104d27959b971170e197bc8abc79 | Python | 7,829 | 232 | """
Tests that comments are properly handled during parsing
for all of the parsers defined in parsers.py
"""
from io import StringIO
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
@pytest.mark.parametrize("na_values", [None, ["NaN"]])
def test_comment(all_parsers, na_values):
... |
6078b9e6edec2da97d3e94e814fed3f80d308ba6766c7a84a651a4d6161c3edd | Python | 7,832 | 211 | # -*- coding: utf-8 -*-
import torch
from itertools import accumulate
from onmt.constants import SubwordMarker
def make_batch_align_matrix(index_tensor, size=None, normalize=False):
"""
Convert a sparse index_tensor into a batch of alignment matrix,
with row normalize to the sum of 1 if set normalize.
... |
f829364a2a2fc35660f62bb0b767cfd4277e67ea05f2ddd4ae2b14c83c89a96f | Python | 7,832 | 221 | """Scatter view."""
# -----------------------------------------------------------------------------
# Imports
# -----------------------------------------------------------------------------
import logging
import numpy as np
from phylib.io.array import _index_of
from phylib.utils import emit
from phy.plot.visuals i... |
41952cd2b2e5705d7d74a68d52e15bcf8f1cbf2df9038e62345ddb32599f882b | Python | 7,833 | 249 | """Chromosight's plotting submodule contains utilities to visualize the pileup
of detected patterns or the input matrix. It also implements an interactive map
recording the coordinates of double clicks."""
import os
import sys
import numpy as np
from matplotlib import pyplot as plt
def pileup_plot(pileup_pattern, ou... |
1691755cdcc20bf7646c66836e88f8a05f10358e429da78ed116c588e0cff19e | Python | 7,836 | 185 | import subprocess
from pathlib import Path
import numpy as np
import nibabel as nib
from multiprocessing import Pool
import pandas as pd
import re
def nda_s3_download_single_file(pkg_id, s3_path, out_dir, username, passwd):
cmd = (f'downloadcmd --package {pkg_id} {s3_path} -u {username} '
f'-p {passwd} ... |
c0f9a1016bccbf750711c0247d2b047eb5e5326b7e70404e16b9804cafc6b89b | Python | 7,845 | 240 | import h5py
import numpy as np
import sigpy as sp
import torchvision.transforms as T
from sigpy.mri import app, muse, retro, sms
import os
DIR = os.path.dirname(os.path.realpath(__file__))
print('> current directory: ', DIR)
HOME_DIR = DIR.rsplit('/', 1)[0].rsplit('/', 1)[0]
DAT_DIR = HOME_DIR + '/data'
print('> da... |
7a5fdf5c2009ba17ebb87df4707ddf55eba51a5fb6d66227470b04fd9ef8ac9a | Python | 7,852 | 215 | # cython: language_level=3
"""Internal, caller-owned pileup storage; no scoring or caller imports.
The parent owns the directory until destroy(). Forked workers inherit its path
and write private copies of the chromosome-file mapping. Returned paths are
registered by the parent; directory-wide cleanup also finds unret... |
63d829304ff0188a96d7f5ef5dd4b922d168588a855e6e269f7e05182ec02cb6 | Python | 7,855 | 242 | #
# File to train networks built from the hnn.py class.
#
# This file establishes the clebsch gordan coefficients, sets up an hnn with given parameters,
# loads holograms from .npy files, and then tests the network via a function call.
#
from argparse import ArgumentParser
import logging
import os
import sys
import k... |
a217ac4e9fec965c288d9d74f57d8ab610f53eb9652d36b22e197ecfba03ffb1 | Python | 7,859 | 206 | import math
import random
import numpy as np
import os
import json
from tqdm import tqdm
from math import ceil, floor, sqrt
from .readPDB import readPDB, readPDB2Pd
def resize_data(xyz, content, edge_length, relaxed=True):
if relaxed:
chainAchar = 'A'
chainBchar = 'B'
else:
chainAcha... |
6be53b65456a7d681d53fc1e0d402c61e6e0463b0142e08221beaaccef7caa9f | Python | 7,861 | 259 | import random
import re
def gen_headers(cv_file):
"""Generate the headers that will be used in the ANOVA.
Arguments
---------
cv_file : str
File containing the results of the resumed CV analysis.
Raises
------
TypeError
If cv_vile is not a resumed CV file.
Returns
... |
bab1cc18a0cedd2862c47908455ea3e945d7574684f168eacc20dc13437c314c | Python | 7,864 | 248 | # Copyright 2018-2024 Xanadu Quantum Technologies Inc.
# 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 law or... |
88262246d2b5b927cdc83894a5a0fcacae94a43dad10e64f20fc8db1e3fed4c8 | Python | 7,866 | 212 | # Copyright 2026 Xanadu Quantum Technologies Inc.
# 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 law or agre... |
c257a76f0b646c7e09092b6c0e71eef3250ab17f5a1ee17453d5c5b4d603e80a | Python | 7,869 | 265 | from collections import defaultdict
from datetime import datetime
import pandas as pd
import yaml
from bokeh.embed import components
from bokeh.layouts import row
from bokeh.models import (
ColumnDataSource,
CrosshairTool,
HoverTool,
PanTool,
Range1d,
ResetTool,
SaveTool,
)
from bokeh.palet... |
7323d23968bc491aca47dd62e7f7633da163eff1b42501e9f2d637b7b34717e0 | Python | 7,871 | 238 | """
Tests for DatetimeIndex timezone-related methods
"""
from datetime import (
UTC,
datetime,
timedelta,
tzinfo,
)
import zoneinfo
from dateutil.tz import gettz
import numpy as np
import pytest
from pandas._libs.tslibs import (
conversion,
timezones,
)
import pandas as pd
import pandas._tes... |
7898d0f96204f9e8c441a30affc2a98655f6b0fa10862514a249e2bce86c8687 | Python | 7,871 | 252 | # ----------------------------------------------------------------------------
# Simulation general parameters
data.dt = 0.2
lb.h.dt = data.dt
lb.h.steps_per_ms = 1.0 / lb.h.dt
data.recordDend = True
data.recordGDend = False
if data.actType == 'passive': data.recordGDend = False
if data.actType == 'aSoma': data.recordG... |
0268147e8a0ef9d43d12229fb8e92a74b22c5cedef84df019d0383e283d8510b | Python | 7,873 | 192 | """Session 39 — native setup() phase 5a: time-series accessor parity.
The supervised + unsupervised tabular tasks landed full native setup
in phases 1-4 (s35-s38). Phase 5 is the time-series drain — the most
involved because TS uses sktime, has its own data shape (univariate
Series with PeriodIndex / DatetimeIndex), i... |
9048402ec4b4493b351e0e53af08c7468872892bd3ee82d3897ffe94ff42946e | Python | 7,877 | 191 | # Copyright 2024 Xanadu Quantum Technologies Inc.
# 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 law or agre... |
a00afa9480044fa932c9ef65715e2ac0e52b99556d5e007019cfd15ff060ad06 | Python | 7,878 | 186 | """Conjugate Gradient for linear systems with self-adjoint positive semidefinite linear operator."""
from collections.abc import Callable, Sequence
import torch
from typing_extensions import Unpack, overload
from mrpro.algorithms.optimizers.OptimizerStatus import OptimizerStatus
from mrpro.operators.LinearOperator i... |
8c998c15c398f24edca65ae4330c6f467e9c132296046f1f508aa7a2314c3c41 | Python | 7,880 | 219 | """Sync per-clock Hugging Face repositories under the pyaging organization.
Each clock gets its own model repo (``pyaging/<clock_name>``) containing the
weight file, a ``config.json`` with the audited clock metadata (also the file
the Hub counts as a download), and a generated model card. A clock whose
preprocessing n... |
95cbf55563defc08e2fd732da3f8c5283bcef1dc15e6e527870dffda55d322fc | Python | 7,887 | 203 | import numpy as np
import scipy as sp
import scipy.linalg as la
from base.curves import Curve, remesh
from base import kernelFunctions as kff, pointEvolution as evol
import matplotlib.pyplot as plt
Npts = 200
def diffusion(c0, t1, K, dt = 0.1, iso_par = 1., area_par=1., peri_par = 1.0, stdev=1.,
K2=Non... |
ea2b3c78f83a7f03264339c6daeab1e041c571c64653c340418edaa02a99babc | Python | 7,887 | 236 | from pathlib import Path
import shutil
import os
import pytest
import torch
from kilosort import io
from kilosort.utils import download_probes, DOWNLOADS_DIR
@pytest.fixture(scope='session')
def gpu(request):
return request.config.getoption('--gpu')
@pytest.fixture(scope='session')
def download(request):
r... |
c264acea79981f53c822273f7735169326bb913e34af762bfc18e5519797261f | Python | 7,894 | 218 | import logging
import socket
import struct
import socket
import numpy as np
import gadgetron
from modules import parser, socketmaker, structmaker
class MLCImageArrayParser(parser.Parser):
"""
Child class for extract relevant meta data from the acquisition/connection that needs
to be sent... |
9455e91f0aa5a99b358556c59e48764e6e739d8bf7eeebc8cabd9e866c8cb394 | Python | 7,895 | 209 | # Copyright 2018-2021 Xanadu Quantum Technologies Inc.
# 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 law or... |
e24c4e212e7d41ef10b8c2604b934897d09fb6bfb38ed352e65bb65b0d6f15df | Python | 7,896 | 224 | # -*- coding: utf-8 -*-
from functools import partial
import torch
from torchtext.data import Field, RawField
from onmt.constants import DefaultTokens
from onmt.inputters.datareader_base import DataReaderBase
class TextDataReader(DataReaderBase):
def read(self, sequences, side, features={}):
"""Read tex... |
5c0dfd976798437612b4f9810ef079c730391bacaea74ee4e7cee43dce750ef4 | Python | 7,901 | 204 | import tensorflow as tf
import subprocess
import sys
import numpy as np
from halo import Halo
from const import SIZE, LABELS, FILTERED_LABELS, LABEL_MAP, FREQ_LIST, FREQ_PROP
from dataset import load_all_datasets
def model(img, labels, dims):
init = tf.contrib.layers.xavier_initializer()
training = tf.plac... |
7b3f13fd4c02a79eed42ec3d4364e218afd676bcb070e8e82893893de4c54177 | Python | 7,902 | 243 | """
Simulate data for training or testing using msprime.
Author: Sara Matheison, Zhanpeng Wang, Jiaping Wang, Rebecca Riley
Date: 9/27/22
"""
# python imports
import math
import msprime
# our imports
import global_vars
import util
################################################################################
# SIM... |
f50b4595dbcf8f07b2ba8df78b60f5181c698b8497e9e07a64e9ffc567a4c054 | Python | 7,902 | 236 | import functools
import os
import numpy as np
import pandas as pd
import torch
from pymatgen.core.composition import Composition
from torch.utils.data import Dataset
from roost.core import Featurizer
import pickle
class CompositionData(Dataset):
"""
The CompositionData dataset is a wrapper for a dataset data... |
a27b2cb6768f8a0a0feec8b8b79aac96d0e0443c602faa3f03d50adf377e3a1f | Python | 7,905 | 223 | import datetime
import numpy as np
import pytest
from pandas.errors import DataError
from pandas.core.dtypes.common import pandas_dtype
import pandas as pd
import pandas._testing as tm
# gh-12373 : rolling functions error on float32 data
# make sure rolling functions works for different dtypes
#
# further note tha... |
9df6b57eef1c9b9321a4faab5be57ce2256c2ed8043e74cb2859cc7fb15e5eab | Python | 7,907 | 144 | import sys as sys
import numpy as np
import itertools
from scipy.spatial.distance import cdist
from scipy.stats import multivariate_normal
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
import numpy as np
import time
from MM2SF.basics.functions import *
def angular_selector(trjname=None, rcut=... |
da172545145d4af046e9523e702f82becd32046e903bfb0ee33161ee97711e27 | Python | 7,907 | 179 | """Build PCBrainAge and eight PCGrimAge proxies from author-derived coefficients.
Normal deterministic rebuild (no R or network required)::
uv run python clocks/build_pc_extensions.py
Regenerate the compact coefficients and independent R oracle first::
uv run python clocks/build_pc_extensions.py --source-di... |
9aac07d8289f6ac88ea9ae7a404b50389f294668b6210e255ce49f19a098205f | Python | 7,911 | 245 | """Computation of the dissimilarity representation of a set of objects
(streamlines) from a set of prototypes (streamlines) given a distance
function. Some prototype selection algorithms are available.
See Olivetti E., Nguyen T.B., Garyfallidis, E., The Approximation of
the Dissimilarity Projection, http://dx.doi.org/... |
ab7bf85bf4f1016530a59e67e9e89b196c0da3b69961bb24d52adf284e8c31be | Python | 7,916 | 223 | import torch
import torch.nn as nn
import time
import numpy as np
from tqdm import tqdm
def to_np(x):
return x.cpu().detach().numpy()
def to_torch(x, device):
return torch.from_numpy(x).to(device, torch.float32)
class Tanh(nn.Module):
def forward(self, inp):
return torch.tanh(inp)
def deri... |
49dc14dd6019261a3cc6e629988d7758c4ef34e732700207886a9bb97086e2a6 | Python | 7,919 | 195 | # %%
# Imports
from sklearn.preprocessing import StandardScaler
from sklearn.decomposition import PCA
from scipy.stats import gaussian_kde
import numpy as np
import os
from pathlib import Path
import matplotlib.pyplot as plt
import matplotlib.backends.backend_pdf
# plt.style.use('seaborn-talk')
matplotlib.rc... |
c3886e689efe79a7d5d66c68d38d33d92873e11f1d16f44180ad2981b37b45ce | Python | 7,920 | 256 | # Copyright 2023 Xanadu Quantum Technologies Inc.
# 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 law or agre... |
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