sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
f2b9feb6d57fd794a1204d7f33f63114376d872bc5118312272a3defdc20ac65 | Python | 26,957 | 776 | """Hardening tests for the technical-preview MLX backend."""
from __future__ import annotations
import os
import sys
from pathlib import Path
from typing import Any
import numpy as np
import pytest
if sys.platform != "darwin" and os.environ.get("TORCHLENS_RUN_UNSTABLE_MLX_TESTS") != "1":
pytest.skip(
"M... |
8f0e2d843cb901a604d17dbccde1dee5409644090f2d25ca36638c1f036c21d4 | Python | 26,965 | 784 | from __future__ import annotations
import numpy as np
import pytest
from larvaworld.portal.canvas_widgets.environment_canvas import (
DEFAULT_LARVA_COLOR,
EnvironmentCanvas,
STATIC_LARVA_GROUP_MEMBER_HALF_LENGTH,
)
from larvaworld.portal.canvas_widgets.environment_models import (
CanvasArena,
Canv... |
d76c22623f9080c2992021d4074c6a3f766fe1c8f9922fad10a4d5743f6a9462 | Python | 26,998 | 644 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created in December 2018
@author: Quentin Lutz <qlutz@enst.fr>
@author: Nathan de Lara <nathan.delara@polytechnique.org>
@author: Thomas Bonald <bonald@enst.fr>
"""
from csv import reader
from typing import Dict, List, Tuple, Union, Optional
from xml.etree import Elem... |
da960c5792daf2f1cef8c14113d9c95c8ce389a9689abb395fe867f4054d0ba1 | Python | 27,017 | 692 | from __future__ import annotations
import os
import typing as t
from collections import defaultdict
from functools import update_wrapper
from .. import typing as ft
from .scaffold import _endpoint_from_view_func
from .scaffold import _sentinel
from .scaffold import Scaffold
from .scaffold import setupmethod
if t.TYP... |
8b692d2aecbefb9e2dbf96f35c8d1b4dad1fdb7ef89320459ef76a9c6f434ed3 | Python | 27,031 | 529 | # Created by: Pieter Barkema
# Date: February, 2022
# Description:
# This file creates a GUI for uploading and processing neuroimaging data
# with normative modelling. The backend computes results and returns them to
# users accessing from all over the world.
# It is hosted as a website from a remote gunico... |
c2ae6f248d251f2177047ae162a0654d2a5328171ef6a0a0e48ffbce5dc6445f | Python | 27,031 | 753 | # -*- coding: utf-8 -*-
"""Benchmark Results
Updated: 13.02.2023
------------------------------------------------------------------------------------------
| Model | Batch Size | Epochs | KNN Test Accuracy | Time | Peak GPU Usage |
-----------------------------------------------------------------------... |
9942072af35170b70f1ced884c76538aadd5cb906e37a52158940a51fc6d9bc5 | Python | 27,035 | 654 | #!/usr/bin/env python3
"""
Dx AK — all-cohorts epoch-count sensitivity.
Extension of Dx AJ from a single-cohort variation (figshare) to
all-cohorts simultaneous variation. For each cohort we re-extract
per-epoch 5D features and per-epoch CAR data, then aggregate to
K in {2, 3, 5, 7, 10}; for each K we plug the K-epoch... |
5dd53cc52fd2ee94828daaab221e0a3754f8f85cd3964f55c4fb2aafc3472cc0 | Python | 27,041 | 639 | import math
import time
import ipdb
import torch
import numpy as np
from pandas import read_csv
import os
from torch.utils.data import DataLoader, Dataset
from tqdm import tqdm
import torch.utils.data as dat
import matplotlib.pyplot as plt
from ourmodel import TransferLoss
#A为原始列表，a为左移位数
def list_move_left(A,a):
... |
77745ef5eb7cb1a36ce084764a51b22b025fcb474f8664c80eb290c4251bb5c9 | Python | 27,049 | 745 | import awkward as ak
import numpy as np
import pytest
from seqpro.rag._core import Ragged
from seqpro.rag._layout import RaggedLayout, RecordLayout, validate_layout
from seqpro.rag._utils import OFFSET_TYPE, lengths_to_offsets
def _two_field_record():
shared = lengths_to_offsets(np.array([2, 1, 3], dtype=np.uint3... |
32caa7c1bb50e42cbc7b244161f955eac6aaa8f721f5105c400a2edb235d7302 | Python | 27,059 | 671 | from contextlib import contextmanager
from unittest.mock import MagicMock, Mock, patch
import pytest
from celery import Celery, signals
from celery.concurrency.thread import TaskPool as ThreadTaskPool
from celery.fixups.django import DjangoFixup, DjangoWorkerFixup, FixupWarning, _maybe_close_fd, fixup
from celery.loc... |
8c86f39a4cbfdce98a3e041463c8a417060fdceeebb0c69eb818c775b62f7a23 | Python | 27,060 | 811 | """ Functions for Multiscale vision model implementation """
#import itertools as itt
import numpy as np
from scipy import ndimage
from . import atrous, mmt
from .utils import threshold_w, simple_rec, simple_rec_iterative
from imfun.cluster import metrics
from imfun.core import deco
from imfun.core import array_han... |
2bfa56bc5ebe59df2fd98ad66ad5be367ddedd884e2a6489d03fe2afd861ddc8 | Python | 27,064 | 756 | from ..utils import constants, utils
import folium
from folium.plugins import HeatMap
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import shapely
from geojson import LineString
import geopandas as gpd
import json
import warnings
# COLOR = {
# 0: '#FF0000', # Red
# 1: '#008000', # G... |
98b07dbde2e25c98bac9d162db41eca23a417ce9cb4bc6bfaba726429525730b | Python | 27,065 | 679 | ## ----------------------------------------
# this script was taken from the rslds package: https://github.com/davidzoltowski/ssmdm
# and modified by Elaheh Imani
# You need to clone the main version of the code from
# the above repository and replace this file with the originial one
##
import autograd.numpy as np
imp... |
9d5cbe50e411fc2b9d8a01d37b4f3c85a961229c9b5fc7b82147ebb6cde21402 | Python | 27,086 | 658 | """P4 amendment lane: dual-leg reducer, watermark transport, lifecycle.
Covers DoR 4.3-4.6 plus the binding reviewer notes:
* append-only op lane with lane-local amendment seq (Tier-F event ``seq``
facts never shift when an amendment lands),
* canonical reducer fold (amendment order, last-wins per path, absent-face... |
bbef30fb92b1ec9133ec5a042ea06beeaa1713982705fce32b13da76979cce43 | Python | 27,107 | 567 | from __future__ import annotations
import builtins
import logging
from typing import (
TYPE_CHECKING,
TypedDict,
)
import jwt as pyjwt
from social_core.exceptions import (
AuthAlreadyAssociated,
AuthCanceled,
AuthForbidden,
AuthTokenError,
)
from social_core.utils import module_member
from ga... |
585adf41681eeb1c607d50ea1079b83d2468eeed03c07a8a29b53d420acce9ec | Python | 27,110 | 749 | from threading import Thread
import urllib.request, urllib.error, urllib.parse
import os
import datetime
import json
import time
import logging
import traceback
from functools import wraps
import socket
from zeroconf import ServiceBrowser, Zeroconf
from ethoscope_node.utils.etho_db import ExperimentalDB
class ScanEx... |
b79fd8874f37170b61a92d670b3220df23beae77a7c8e913eb8d7ac4b111564d | Python | 27,115 | 494 | #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Written by Yuichiro Yada
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
################################################
# A code for Supplementary Figure 3
################################################
import numpy as np
import pandas as pd
import seaborn as ... |
9a7a8607efadb27ba46addc5a1a01d42b8d4985c4ba583cf2eb44d9d55ca1479 | Python | 27,122 | 659 | #!/usr/bin/env python3
"""
File: bryois_ct_eqtl_replication.py
Created: 2022/10/25
Last Changed:
Author: M.Vochteloo
Copyright (C) 2020 University Medical Center Groningen.
A copy of the BSD 3-Clause "New" or "Revised" License can be found in the
LICENSE file in the root directory of this source t... |
4e2dec0da7ec48bc0820835c4630f6d72bb80cd9f0a1f030efdf7b49d3cfc370 | Python | 27,130 | 685 | import json
import logging
import os
import pickle
import warnings
from copy import deepcopy
from typing import Union
import numpy as np
import pandas as pd
from sklearn.decomposition import PCA
from scipy.io import loadmat
from scipy.signal import savgol_filter
# global variables, double check these ma... |
82cacd5d12166acc318c87a8527f43bda5408080bf40e04ddf2f43d810a6fc5b | Python | 27,132 | 666 | import pytorch_lightning as pl
import torch
from monai.networks.blocks import UnetOutBlock, UnetrBasicBlock,\
UnetrUpBlock, UnetrPrUpBlock
from monai.losses import DiceLoss
from survival_plus_x.models.vit import ViT3D
from survival_plus_x.models.multitask import MultitaskHead,\
multitask_metrics_from_step_out... |
ca73773fe32c2ee6a5fcb4074f1803e7ff1e9c4a0b078e923e304d96f3f34195 | Python | 27,137 | 686 | from math import ceil, floor, log, log2, sqrt, inf
import random
from numpy import pi
from numpy.lib.type_check import iscomplex
import numpy as np
from minimize import minimize
def TAFKAP_decode(samples=None, p={}):
def fun_negLL_norm(params, getder=True):
if getder:
minll, minder = fun_LL_... |
baa740d10328c98c16b7f6deb934dc3218bd480d2dafc30ab757ca2ec40cb5e6 | Python | 27,142 | 594 | #!/usr/bin/env python3
"""
File: calculate_explained_variance.py
Created: 2022/01/18
Last Changed: 2022/07/25
Author: M.Vochteloo
Copyright (C) 2020 University Medical Center Groningen.
A copy of the BSD 3-Clause "New" or "Revised" License can be found in the
LICENSE file in the root directory of ... |
558a7547aeb82358c9b4eae1324c3232051d0d4ebb4b6b442c76789d561ad88d | Python | 27,146 | 762 | import torch
import torch.nn as nn
import torch.nn.functional as F
from ..base import _layers as layers
from ..base import _blocks as blocks
from ..base import _towers as towers
from typing import Union, Callable, Optional, Any, Tuple, List
class FCN(nn.Module):
"""Basic fully connected network
Instantiate a... |
3b56689ec70ffc0c21e503674cc1eb016f72ccff4d56c4c7b8fc0e27120661fb | Python | 27,150 | 724 | """
Unit tests for Tunnel Utils API endpoints.
Tests tunnel configuration, service management, and URL generation.
"""
import json
import os
import unittest
from unittest.mock import Mock, mock_open, patch
from ethoscope_node.api.tunnel_utils import TunnelUtils
class TestTunnelUtils(unittest.TestCase):
"""Test... |
ad015404b32fbb00955b5b9ce1bdf4ba4cdec43ff71caad13c934976bd736b16 | Python | 27,151 | 759 | # adapted from https://github.com/facebookresearch/detectron2/blob/master/detectron2/data/detection_utils.py
"""
Common data processing utilities that are used in a
typical object detection data pipeline.
"""
# pylint: disable=pointless-string-statement
import os
import logging
import numpy as np
from PIL import Image
... |
9257747e90f623063be266a73ef289b111e2032ed0f0dd1aa2b3630277cd80d3 | Python | 27,152 | 860 | """
Methods for dataset evaluation/comparison
"""
from __future__ import annotations
from typing import Any, Dict, List, Optional, Sequence
import numpy as np
import pandas as pd
import param
from scipy.stats import ks_2samp
from sklearn.preprocessing import MinMaxScaler, StandardScaler
from .. import reg, util
from... |
b58e7963851c91434eeb96442f6ff7ac09a23f6c11f33d27e36fe9e52d70b408 | Python | 27,160 | 671 | import hashlib
import importlib.resources
import io
import logging
import os
import pathlib
import time
import traceback
import afmformats.errors
import nanite
import nanite.fit as nfit
import numpy as np
from PyQt6 import uic, QtCore, QtGui, QtWidgets
from .. import colormap
from ..head.custom_widgets import show_wa... |
253b667ae31293810eb986bc519e78e22449b6ae74f5e6b6840efb0b8cb9cbd6 | Python | 27,190 | 494 | '''
Copyright 2023 Douglas Feitosa Tomé
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hop... |
ce7446e8634e92b8f103ef98773bc0fed04a3b261687eb9274f25e159e6e572f | Python | 27,197 | 524 | """
Ensemble inference
Copyright (c) 2023 Polytechnique Montreal <www.neuro.polymtl.ca>
License: see the file LICENSE
"""
import logging
import os
import shutil
import time
from pathlib import Path
import glob
import multiprocessing as mp
from ivadomed import inference as imed_inference
from totalspineseg.inference ... |
92caf2151aa136833abb7f6d6c705a09f2e34cb78be664262730974aa03d7336 | Python | 27,200 | 552 | '''
Date: 23/09/22
@author: Kaan Karas & TMSi
Counts the events and at the end save them to a txt document.
TMSiSDK: Real-time filter that can be applied to incoming data
Copyright 2021 Twente Medical Systems international B.V., Oldenzaal The Netherlands
Licensed under the Apache License, Version 2.0 (the "License");
... |
8d2b7afe0be450b6dea56763382e724b3cf24d04844065f15eea2f7b5a3f7db0 | Python | 27,210 | 634 | from __future__ import annotations
from dataclasses import asdict
from PySide6.QtCore import QSignalBlocker, Qt
from PySide6.QtWidgets import (
QCheckBox,
QComboBox,
QDoubleSpinBox,
QFormLayout,
QFrame,
QHBoxLayout,
QHeaderView,
QLabel,
QLineEdit,
QMessageBox,
QPushButton,
... |
e040d9fe4727bd83ad6ea58184c53c0a8ad4b08a89568d6ae72b58d9b141f26a | Python | 27,217 | 686 | from copy import copy
from math import sqrt
from typing import Optional
import numpy as np
import torch
from tqdm import tqdm
import networkx as nx
from torch_geometric.nn import MessagePassing
from torch_geometric.data import Data
import matplotlib.pyplot as plt
from torch_geometric.utils import k_hop_subgraph, to_ne... |
23e2b56fc28dcbf1e9a02cc283e51fc3a975a228bd1a50a0dd76e6317022574a | Python | 27,254 | 555 | '''
Date: 08/09/22
@author: Kaan Karas & TMSi
TMSiSDK: Real-time filter that can be applied to incoming data
'''
import os
import sys
from .. import sample_data_server
from ..device import ChannelType
import numpy as np
import queue
from copy import deepcopy
import threading
import time
from datetime import datetim... |
a36de76069992fc3ffab470df2202e229d1113c8b6c64063eb5f980f7b260df3 | Python | 27,274 | 620 | """Live input sites and metadata contract checks."""
from __future__ import annotations
from collections.abc import Callable, Mapping, Sequence
from typing import TYPE_CHECKING, Any, cast
import torch
from .errors import (
ReattachError,
RunCapabilityUnavailableError,
RunPreconditionError,
)
from .runna... |
f31922a9ecb817923038db3addcd83a9486a8bfba2b0d74be6ee23f42256e704 | Python | 27,276 | 575 | # Copyright (c) 2025, Jay Shah, Ganesh Bikshandi, Ying Zhang, Vijay Thakkar, Pradeep Ramani, Tri Dao.
# A reimplementation of https://github.com/Dao-AILab/flash-attention/blob/main/hopper/flash_bwd_preprocess_kernel.h
# from Cutlass C++ to Cute-DSL.
#
# Computes D_i = (dO_i * O_i).sum(dim=-1), optionally adjusted for L... |
a9372b8db97d5cf65f51a02b8d3d1c0236cf4561e2920eb9db2293e9d31b1ba8 | Python | 27,278 | 864 | # -*- coding: utf-8 -*-
import numpy as np
from matplotlib import pyplot as plt
import random
import sklearn
import seaborn as sns
import scipy as sp
from matplotlib import rc
import matplotlib.ticker as mtick
import matplotlib as mpl
from scipy import signal
from sklearn.linear_model import LinearRegressi... |
0be30cda9099b8f4198aa26e7fea14a777869e20b874074e2d280e9a2e1c6f1e | Python | 27,279 | 800 | import torch
from torch.nn import Linear
from torch.functional import F
from torch_geometric.nn import GCNConv, GraphConv, MetaLayer, MessagePassing
from torch_geometric.nn import GINConv, GINEConv
from torch_geometric.nn import global_mean_pool, global_add_pool, global_max_pool
from torch_geometric.nn import SGConv
fr... |
4835822ea89ddb30430f07b7543ae78019536369f4b38268d5ecae5d0fc457fe | Python | 27,289 | 557 | '''
Date: 23/09/22
@author: Kaan Karas & TMSi
Counts the events and at the end save them to a txt document.
TMSiSDK: Real-time filter that can be applied to incoming data
Copyright 2021 Twente Medical Systems international B.V., Oldenzaal The Netherlands
Licensed under the Apache License, Version 2.0 (the "License");
... |
8676b732ce83752a854a49acfe19a93e93689827576a5a3ba2ca1d34c6756a65 | Python | 27,299 | 589 | """r61 whole-class immunizer -- allocation projection completeness (free_1 + corr_2 close).
r57/r59 bounded per-op allocation via a ``FakeTensorMode`` projection, but GATED it on
``_has_numeric_literal``: a call with no int/float literal skipped the projection on the
premise "sizes coming only from live tensor shapes ... |
01da3b6d208ce48b970c7666de86f37ed07cc9942d17981ce43b81d690084a22 | Python | 27,301 | 601 | # Copyright (c) 2024 PaddleHelix Authors. All Rights Reserved.
#
# Licensed under Creative Commons Attribution-NonCommercial-ShareAlike 4.0
# International License (the "License"); you may not use this file except
# in compliance with the License. You may obtain a copy of the License at
#
# http://creativecommo... |
ba0759191097b8e4c2deaffa7c467393698f5a4ace61c81380cd4ba5299b867a | Python | 27,309 | 678 | #!/usr/bin/env python
"""
Unit tests for the Mattermost notification service.
"""
import datetime
import json
import time
from unittest.mock import MagicMock, Mock, call, patch
import pytest
from ethoscope_node.notifications.mattermost import MattermostNotificationService
class TestMattermostNotificationService:
... |
632aed5608681ae63ba62d75c6d49b32c13cc02954809a4f75507af0e7685942 | Python | 27,311 | 726 | import sys
from datetime import datetime, timedelta
from datetime import timezone as _timezone
from datetime import tzinfo
from unittest.mock import Mock, patch
import pytest
from dateutil import tz as dateutil_tz
if sys.version_info >= (3, 9):
from zoneinfo import ZoneInfo
else:
from backports.zoneinfo impor... |
78c1a33423c90e30ea7a3de25f3dab4761ec091dfaacb5c7cd161dd1c607d547 | Python | 27,328 | 669 | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import itertools
import logging as log
import matplotlib.pyplot as plt
import numpy as np
import slowfast.utils.logging as logging
import torch
from detectron2.utils.visualizer import Visualizer
from slowfast.utils.misc imp... |
6d2b356ded360cda7e5687dcaf61c1466118772df8f2389234bd6527aade7d7a | Python | 27,330 | 806 | from typing import Callable, Optional
import random
import math
import cutlass
import cutlass.cute as cute
import torch
from flash_attn.cute import utils
from flash_attn.cute.block_sparsity import fast_sampling
# =============================================================================
# CuTe mask_mod function... |
f28c987632bfff18dbca4bfc3b992f1b0de70de4b504e8621855e55b8d152a94 | Python | 27,331 | 695 | """ Optimizers class """
import torch
import torch.optim as optim
from torch.nn.utils import clip_grad_norm_
import operator
import functools
from copy import copy
from math import sqrt
import types
import importlib
from bioseq2seq.utils.misc import fn_args
def build_torch_optimizer(model, opt):
"""Builds the PyT... |
5b88dc60cf1039c9f40d1363760037d13bd96978303a790e881874ea539bf3a3 | Python | 27,340 | 579 | import matplotlib.pyplot as plt
from sklearn.linear_model import LogisticRegression
from sklearn.manifold import TSNE
from scipy import stats
from sklearn.decomposition import PCA
from sklearn.model_selection import KFold
from sklearn import svm
import os
from utils_analysis import make_piechart, plot_sorted_averaged_r... |
2001577ee5c459126a827b3dad20872cf25b1f2ac0afe26d22bc1d29edae1b8d | Python | 27,350 | 700 | import copy
import collections
import math
import numpy as np
import paddle
from paddle.nn.layer.common import Linear, Dropout
from paddle.nn.layer.norm import LayerNorm
from paddle.nn import functional as F
from paddle import tensor
from paddle.fluid import layers
from paddle.fluid.dygraph import Layer, LayerList
fro... |
22b8583ffae57410a441453c5380d0c731033a6c140d2dcba980dbff0eb9aa43 | Python | 27,352 | 765 | """
Module to manage datasets and loaders
"""
import os
import re
import cv2
import numpy as np
import pandas as pd
import torch
from torch.utils.data import Dataset, DataLoader
import pytorch_lightning as pl
import albumentations as A
from albumentations.pytorch import ToTensorV2
import matplotlib.pyplot as plt
impor... |
ca28ce8a9e971f7d98b91c0791e115b6713f98dec0ef646410247b533a17fb2b | Python | 27,367 | 617 | name = "ptltSNEcv"
# Loading necessary libraries
libnames = [('mdtraj', 'md'), ('numpy', 'np'), ('tensorflow', 'tf'), ('keras', 'krs'), ('argparse', 'arg'), ('datetime', 'dt')]
for (name, short) in libnames:
try:
lib = __import__(name)
except ImportError:
print("Library %s is not installed or not working ... |
ecbfdae6b48b1358ccaa84308ea05846b6871fc057bc0a021e8a84ba9e5da6d6 | Python | 27,370 | 735 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Marker(_BaseTraceHierarchyType):
_parent_path_str = "scatter3d"
_path_str... |
dfe4826a14fbbd642568fc134f1dbdb779a38dae6f89fbd453c3a0b10ec3de9a | Python | 27,392 | 679 | import torch
import torch.nn as nn
class LSTMCNN(nn.Module):
def __init__(self, input_size: int = 1280, dropout_input=0.25, n_filters=32, filter_size=3, hidden_size=64, num_lstm_layers=1, dropout_conv1=0.15, n_tissues=0):
'''
bidirectional LSTM - CNN model to process sequence data. returns output... |
03fede1e5579f6fca3f2e52a00aea57b6fbe729ca6e6a46ddc4af1c1c91b9bf2 | Python | 27,394 | 519 | """Faster RCNN Estimator."""
# pylint: disable=logging-not-lazy,abstract-method,unused-variable,logging-format-interpolation,arguments-differ
import os
import math
import time
import warnings
from PIL import Image
import pandas as pd
import numpy as np
import mxnet as mx
from mxnet import gluon
from ....data.batchify... |
4ebedc2a5be09855c73e3f8594a75260cdf93e590128da74ad93b897880e0c87 | Python | 27,410 | 987 | """
Composite grid-structured figure
"""
from __future__ import annotations
from typing import Any, Dict, List, Optional, Sequence, Tuple
import os
import numpy as np
from matplotlib.gridspec import GridSpec
from .. import plot, reg, util, funcs
__all__: list[str] = [
"calibration_plot",
"model_summary",
... |
b4485233bfc3946ec79dc4f955d8ee5e43f3f676fbe65dd2bcb8ee558eb72bd6 | Python | 27,412 | 623 | import pandas as pd
import geopandas as gpd
from ..utils import constants, utils, plot
import numpy as np
from warnings import warn
from ..tessellation.tilers import tiler
from shapely.geometry import Point, Polygon
class FlowSeries(pd.Series):
@property
def _constructor(self):
return FlowSeries
... |
71335912ce88cfd785df82942fbf040f886c640dbb719063535d144b430fbd3e | Python | 27,426 | 562 | from bdb import set_trace
from typing import Any, Sequence, Tuple, List
import torch
from torch.utils.data import Dataset
import torch.nn.functional as F
import os
import pandas as pd
from hashlib import md5
import numpy as np
def make_hashes(names: List[str]) -> List[str]:
hashes = []
for name in names:
... |
38199282f8b06c0ab736c066f94bce3efba46a95556b4ee157a296f15d7efd2a | Python | 27,427 | 700 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""The primary workflows for xcp_d."""
import os
import sys
from copy import deepcopy
from pathlib import Path
import bids
import matplotlib as mpl
import nibabel as nb
import nilearn
import numpy as np
i... |
939aaaf39d71ad5394c5806ae7d7157c5e6b8df1449ab1b1e08d68100b1fd251 | Python | 27,430 | 711 | # AUTOGENERATED! DO NOT EDIT! File to edit: nbs/Importing.ipynb (unless otherwise specified).
__all__ = ['read_file', 'extract_rawfile_unique_values', 'import_spectronaut_data', 'import_maxquant_data',
'convert_ap_mq_mod', 'import_alphapept_data', 'convert_diann_mq_mod', 'import_diann_data',
'con... |
51fc8afe452a42a1c45a1214ec529154e5ab8da85115641e7cdb375f4e61c96c | Python | 27,435 | 650 | import pandas as pd
import numpy as np
import os
import random
import json, pickle
from collections import OrderedDict
from rdkit import Chem
from rdkit.Chem import MolFromSmiles
import networkx as nx
from sklearn.utils import resample
from utils import *
import random,ast
#Setting the protein and ligand properties f... |
1887e167e1693e7518326efaf05b649100a2e0c314e76eacf68d4bad763c29a4 | Python | 27,438 | 770 | #!/usr/bin/env python
"""
Unit tests for the notification base analyzer.
"""
import datetime
import json
import time
from unittest.mock import MagicMock, Mock, patch
import pytest
from ethoscope_node.notifications.base import NotificationAnalyzer
class TestNotificationAnalyzer:
"""Test cases for NotificationA... |
3450b8d929d8b226d6e97842c1ce5b2f73b63e73a09c7601987d42bf2163d0ba | Python | 27,452 | 846 | """Code adapted from https://github.com/open-mmlab/mmaction
and https://github.com/bryanyzhu/two-stream-pytorch"""
import random
from PIL import Image, ImageOps
import numpy as np
import numbers
import math
import cv2
import collections
import PIL
class Transform:
def __call__(self, data):
raise NotImpl... |
dd963e7e657b29e1a0138e29f9daa16f9a45c56026a1fc0f8c54f50c2407ad92 | Python | 27,454 | 568 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
from pathlib import Path
from typing import Any
import numpy as np
import torch
from ultralytics.cfg import _handle_deprecation, get_cfg
from ultralytics.data.build import load_inference_source
from ultralytics.en... |
2e6b57280a7ffa9b939c44cadff7d115255cc6352de743314d451de8e97d7db5 | Python | 27,471 | 769 | import contextlib
import inspect
import math as python_math
import jax
import jax.experimental.sparse as jax_sparse
import jax.numpy as jnp
import ml_dtypes
import numpy as np
from jax import export as jax_export
from keras.src import tree
from keras.src.backend import config
from keras.src.backend.common import Kera... |
fc9d54d238477369ad67fe6b1f13180d95898815d2f4db36d95ac6dada675ebe | Python | 27,475 | 808 | """
corr_plots.py
This script contains functions for plotting USI correlation analyses.
Authors: Colleen Gillon
Date: January, 2021
Note: this code uses python 3.7.
"""
from matplotlib import pyplot as plt
import numpy as np
from util import logger_util, math_util, plot_util
from sess_util import sess_plot_util
f... |
933c4e09141c4686e736878251353dff5092b13bc5b6ad1d347889ba8bc8db5f | Python | 27,478 | 821 | """Panel UI layer for the Parameter Database popup: the draggable popup
shell, the table + sidebar, database-wide actions (Remove confirmation),
and the top-level dropdown/standalone-page wiring. Single-parameter popup
content (Inspect, Add) lives in `parameter_popups.py`.
"""
from __future__ import annotations
impor... |
40aa0999419a2d8bf26b0559f5759523286785ede57d741ffea235203ec43bfa | Python | 27,481 | 678 | # Copyright (c) 2024 PaddleHelix Authors. All Rights Reserved.
#
# Licensed under Creative Commons Attribution-NonCommercial-ShareAlike 4.0
# International License (the "License"); you may not use this file except
# in compliance with the License. You may obtain a copy of the License at
#
# http://creativecommo... |
d87bea6d95af4a30c59e75f5026fb3ff3e94f8d5972054485715f7ea7b0c53d3 | Python | 27,485 | 684 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
import json
import logging
import plistlib
import shutil
import subprocess
import sys
import threading
import time
from datetime import datetime
from pathlib import Path
from ultralytics.utils import LINUX, LOGGER, MACOS, RANK, WINDOWS
class Consol... |
971fdb84fd0089aea2ecf06ae202d8da575b1bc1c90133baa925b0b126e50435 | Python | 27,488 | 645 | """Wrap-state identity shims: torch-internal ``x is F.y`` checks stay truthful.
TorchLens wrapping replaces public torch callables with wrapper functions, so
a torch-internal identity check whose two operands were read at different wrap
epochs (a class-def-time default or a protocol-passed original on one side, a
post... |
3e9e95517cb6b3a9e0a13f45a616e95545c643837a503aa325707f828c3876dd | Python | 27,511 | 652 | import pandas as pd
import numpy as np
import os
import random
import json, pickle
from collections import OrderedDict
from rdkit import Chem
from rdkit.Chem import MolFromSmiles
import networkx as nx
from sklearn.utils import resample
from utils import *
import random,ast
#Setting the protein and ligand properties f... |
f22cc9a6c2abed380515c6115a2ef9fa5492a936470d607a43f4b67daf08d332 | Python | 27,511 | 711 | """Seed, RNG, attestation, and fork utilities."""
from __future__ import annotations
import dataclasses
from collections.abc import Mapping, Sequence
from typing import TYPE_CHECKING, Any
import torch
from . import _state
from ._io._torch_symbols import torch_attr
from ._runnable_state import (
PreparedRunnable... |
3ba9b7abf7d11ac662eb6b3f95f6d25a976323df4b218d3291e197357f1f4b0c | Python | 27,529 | 755 | #!/usr/bin/env python3
"""
Unit tests for backup helper functions including file-based cache system.
Tests the enhanced backup functionality with video file caching,
rsync integration, and device backup information extraction.
"""
import json
import os
import pickle
import shutil
import sys
import tempfile
import tim... |
85961de70323fbf7d5b98d6204837472d5bccdaac586f9e03d9789efc4dfeff3 | Python | 27,535 | 791 | """Tensor kwargs must be extracted as op parents (bug ARG-KWARGS-MISSING).
``extract_tensors_and_params()`` consults static ``ArgSpec`` table entries
whose ``tensor_kwargs`` tuples were empty (or wrongly named) for several
common functions, so tensors passed as KEYWORD arguments were silently
dropped from parent/param... |
367db6145a1529834f24471465e2b7c86c43ab0a12cc1a6e6f4a694f027bd2b1 | Python | 27,539 | 750 | from __future__ import absolute_import
import torch
from torch import nn
import torch.nn.functional as F
import math
from transformers import BertConfig
from transformers.modeling_outputs import BaseModelOutputWithPooling, BaseModelOutput
from LRP.layers_ours import *
from transformers import (
BertPreTr... |
0e1d502b24e72c52d7ed791e90771e3c9168de5996ea93cffe03ad69a9ca99b0 | Python | 27,547 | 730 | import pandas as pd
import Code_General_utility_spikes_pickling as util
import numpy as np
import matplotlib.pyplot as plt
import os
import scipy.stats as stats
_RES_DPI = 48
_SAVEDATA = False
_X_MARKER_SIZE = 50
_show_excluded = False
ID_trunk = [0,1,2,3,4] # IDs of trunk dendrites (add 7 to ID to return linear i... |
5d7ca98a4f04d83a78567984a5e75a0539db5463cc99d18fcb58247c6a8a9334 | Python | 27,547 | 810 | """
Keyboard shortcut configuration for the simulation display.
Lets the user inspect and rebind the keys the running simulation responds to.
"""
from __future__ import annotations
import json
from dataclasses import dataclass
from pathlib import Path
from typing import Any
import panel as pn
import param
from lar... |
10b4a0d5b7c2a1d4a7da728e35143fff4112ec0b8325d15b21383ff7d40434f7 | Python | 27,548 | 791 | from functools import partial
import warnings
from joblib import Parallel, delayed
import numpy as np
from scipy.stats import multivariate_normal
from sklearn.base import BaseEstimator
from sklearn.utils import check_random_state
from ..geometry._docs import deprecated
from ..geometry.base import ctranspose, sqrtm
fr... |
f5d34b4afbf1e399b8095235a7edcaff8e0626d30a27f5dbc3fef5f665819eb3 | Python | 27,572 | 873 | import torch
import cutlass
import cutlass.cute as cute
from cutlass._mlir.dialects import math as mlir_math
import operator
# =============================================================================
# Score_mod functions that don't use global indices
# All use signature: (tSrS_ssa, b_idx, h_idx, q_idx, kv_idx, s... |
c68f8fa4b1ff2dd24dd7fb169af79e4c29ded16bbd10862a5ae9754ee765ec8c | Python | 27,578 | 720 |
"""
Rewrite of liquid time-constant network from https://github.com/rtqichen/time-series-datasets
"""
import numpy as np
import os
import argparse
from _datasets import *
import brainpy as bp
import brainpy.math as bm
from enum import Enum
bm.set_environment(bm.training_mode)
if any(
[
not os.path.exi... |
da3c7b80a374b6fa0f4c74ffb028d2a238c02fb54b8556e202d89777c1576a25 | Python | 27,593 | 881 | """
Copyright (c) 2022 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE BLUE BRAIN PROJE... |
022e0959964f9b45c2b88617ffb9c589de1ceb8c5977c078dbd167c71f907b61 | Python | 27,596 | 783 | # SPDX-License-Identifier: LGPL-2.1-or-later
from __future__ import print_function, division, absolute_import
import os
import unittest
import numpy as np
from pyEcoHAB import incohort_sociability as ics
from pyEcoHAB.utils import general as utils
from pyEcoHAB import data_path, sample_data
from pyEcoHAB import Loader... |
0d7bae89d87ba125ed7cf440a5345384298e1bf9f330ea333462dedbb32e4769 | Python | 27,604 | 906 | """Single-cell subprocess runner for TorchLens performance benchmarks."""
from __future__ import annotations
import argparse
import json
import os
import platform
import random
import resource
import statistics
import subprocess
import sys
import tempfile
import threading
import time
from collections import Counter
f... |
fffd8caa2b89b36a6eeeb94d01ec9824a4acbfa1c4fed40b95a189a8c5e9897c | Python | 27,608 | 684 | """An async vector environment."""
import multiprocessing as mp
import sys
import time
from copy import deepcopy
from enum import Enum
from typing import List, Optional, Sequence, Tuple, Union
import numpy as np
import gym
from gym import logger
from gym.core import ObsType
from gym.error import (
AlreadyPendingC... |
d9aa680638bc04427ccc643b9b00453a3a678ea4ebe32a3989793977eb0c16d3 | Python | 27,622 | 770 | """Clustering functions."""
import numpy as np
from scipy.stats import norm, chi2
from sklearn.base import (BaseEstimator, ClassifierMixin, TransformerMixin,
ClusterMixin, clone)
try:
from sklearn.cluster._kmeans import _init_centroids
except ImportError:
# Workaround for scikit-learn... |
dd69c8b9e45f86f2517a0e64ba5fb98c0c48813d5e88208626ab34bb5589725c | Python | 27,636 | 854 | #!/usr/bin/python
import time
import os
import subprocess
import sys
import re
import pandas as pd
import numpy as np
import tabix
import glob
import ConfigParser
from bisect import bisect_left
##### initialize parameters #####
class getParams:
def __init__(self, filedir, cfg, param_cfg):
leadSNPs = param_cfg.get('... |
a0192008918380bfc1fd824809cfe7a078ab28cc24e26ae296cbbd6fda2d961f | Python | 27,643 | 817 | import argparse
import json
import os
import sys
import warnings
import imblearn
import joblib
import numpy as np
import pandas as pd
import skrebate
from galaxy_ml import __version__ as galaxy_ml_version
from galaxy_ml.binarize_target import IRAPSClassifier
from galaxy_ml.model_persist import dump_model_to_h5, load_m... |
c4bc410b9d891c1d3ccc752859e96439bd5d1c1736a5a645be7fcf008c52bd1d | Python | 27,700 | 795 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
"""Plot uniform time-series of one variable."""
from typing import Any, Callable, Dict, Sequence, Tuple, Union
import matplotlib.axes
import matplotlib.colors
import matplotlib.patches
import numpy as np
from .._colorspaces import oneway_colors, to_rgba
from ..... |
bf68634022008a2f6cdab0e5495794d7e11e3c233b5ce4f1ff3173873cd6ffe2 | Python | 27,707 | 739 | # noinspection PyPackageRequirements
import cv2
import numpy as np
import time
import datetime
import warnings
import logging
from PyQt5 import QtCore
from .global_defs import DeviceState as State
from score_behavior.video_control import VideoControlWidget
from score_behavior.score_config import get_config_section
l... |
cc2026f955ba653223b66136f916485c2cab5ec674c354ad41bbb88acf9bdb5b | Python | 27,719 | 864 | """
Copyright (c) 2022 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE BLUE BRAIN PROJE... |
20299e53a2c4ba51f74ea45425b5ee88cf0b248019a3402c6cd64cb84a07dc21 | Python | 27,728 | 887 | from typing import (
Annotated,
Any,
Literal,
)
from pydantic import (
Field,
field_validator,
model_validator,
RootModel,
)
from galaxy.util.config_templates import (
ConfiguredOAuth2Sources,
EnvironmentDict,
expand_raw_config,
get_oauth2_config_from,
ImplicitConfigura... |
55ff0a8a4a68509031a67ed5f489f8a89ef1dc680f5af19eebf5502f9c6b5e84 | Python | 27,732 | 703 | """P2 settlement proofs: every termination path settles through the authority.
The product-constructor inventory (design section 4): each reachable path
stamps a typed ``CaptureOutcome`` as its final settling act, failure phases
attribute exactly (FORWARD / FINALIZE / POSTPROCESS / TEARDOWN), secondary
failures keep e... |
71ecb0f110ef0ac2fbe72cf0538bf5e1101ad67a406a1d88684dbc11eb776fe4 | Python | 27,733 | 776 | import logging
from webbrowser import get
#from matplotlib import test
import numpy as np
from tqdm import tqdm
import torch
from sklearn.model_selection import KFold
from graphmae.utils import (
build_args,
create_optimizer,
mask_edge,
set_random_seed,
TBLogger,
get_current_lr,
load_best_c... |
ff726010171e328b2de8c9413e16747ba34b8f4abb2da7c8518a897f6129577e | Python | 27,792 | 683 | """
Developmental Data Demo
=======================
An example analysis applied to developmental data, demonstrating best practices.
"""
###################################################################################################
# Spectral Parameterization for studying neurodevelopment
# ---------------------... |
9ff53ca4d57db1cc2fdc0ae55ae40fff5a679691dd9abf0385035f336f4efac0 | Python | 27,800 | 609 | """State contracts and captured execution contexts."""
from __future__ import annotations
import sys
from collections.abc import Mapping
from contextlib import contextmanager, nullcontext
from functools import lru_cache
from typing import TYPE_CHECKING, Any, cast
import torch
from ._io._torch_symbols import torch_a... |
925d7ca960d8b657018846c2c0718cc934f3965314e2bc224eda7bae65534c97 | Python | 27,803 | 684 | from unittest import mock
import numpy as np
import pytest
from absl.testing import parameterized
from keras.src import backend
from keras.src import dtype_policies
from keras.src import layers
from keras.src import models
from keras.src import ops
from keras.src import testing
from keras.src.backend.common import Au... |
d0fcb6abd53dfc84bf3e88a4beab3cb976a833197bc7a59299514d16c8eb1450 | Python | 27,822 | 762 | """StudioGAN: A library implementing many GAN variants with common training infrastructure.
Kang et al., "StudioGAN: A Taxonomy and Benchmark of GANs for Image Synthesis",
IEEE TPAMI 2023. arXiv:2206.09479.
Source: https://github.com/POSTECH-CVLab/StudioGAN
Each entry here shows the SIGNATURE OP of a distinct GAN var... |
4ec1dbfdd6cc9a871e16500f5d36c1369382ee0717f97f9a05ea26d7ba9f0a11 | Python | 27,835 | 777 | import hashlib
import numpy as np
import pandas as pd
import copy
from mirp._images.generic_image import GenericImage
from mirp._masks.base_mask import BaseMask
from mirp.utilities.utilities import zero_if_close
class Data3DMesh(object):
def __init__(self):
# Mesh faces
self.mesh_faces: np.nda... |
cc75e7c1e743b9e24507c04dd01566089d5f303b41d6835374519875bc07ceaf | Python | 27,859 | 556 | #!/usr/bin/env python
import normalize_plot_and_summarize as nps
from flattener import write_tab_for_all
import argparse
import csv
import datetime
import errno
import os
import subprocess
import tables
import logging
import sys
import abc
import collections
import numpy
from time import time
from os.path import ... |
4ad556c747bd4f4351198c9b23a163975717794c1b288546fe47253a44154ae1 | Python | 27,883 | 1,050 | from __future__ import annotations
import contextlib
import sys
import types
import pytest
import env
from pybind11_tests import detailed_error_messages_enabled
from pybind11_tests import pytypes as m
def test_obj_class_name():
assert m.obj_class_name(None) == "NoneType"
assert m.obj_class_name(list) == "l... |
6ba6bb134d3ef006dd80195e7ac877660e7fe01c2896374b2b042fc9e442fe96 | Python | 27,885 | 709 | import random
import numpy as np
import ot
import torch
from anndata import AnnData
try:
from typing import Any, Dict, List, Literal, Optional, Tuple, Union
except ImportError:
from typing_extensions import Literal
from typing import List, Optional, Tuple, Union
import pandas as pd
from spateo.logging impo... |
c0e92462764831abd9b98db353ee16fa576770670bb2f0c59071d6d5faaf3a0b | Python | 27,905 | 591 | """Input structure, literal, and metadata witness helpers."""
from __future__ import annotations
import struct
from typing import TYPE_CHECKING, Any
import torch
from . import _state
from ._runnable_state import (
RunResourceCeiling,
_guarded_defensive_materialize,
)
from .errors import (
PathDivergence... |
4c4555ff71c5ae16c8cd153d240d2db952de92d35ebf8dede6408de5c0d5f4ad | Python | 27,908 | 697 | from __future__ import print_function, division, absolute_import
import torch
import torch.nn as nn
from torch.autograd import Variable
from functools import reduce
class LambdaBase(nn.Sequential):
def __init__(self, *args):
super(LambdaBase, self).__init__(*args)
def forward_prepare(self, input):
... |
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