sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
14c0cd4d15d40df0cc6f6a904d845d4a78560b005ea50912229673dac5a2e40d | Python | 24,975 | 672 | import struct
import sys
import types
import unittest
from unittest import mock
from codecarbon.core import windows_emi
from codecarbon.core.units import Time
from codecarbon.core.windows_emi import (
EMI_VERSION_V1,
EMI_VERSION_V2,
WindowsEMI,
clear_emi_cache,
find_mirrored_channels,
is_emi_av... |
914e179abf83026d580ba139bc15195407d334b4987068dab904ff56d1588ba9 | Python | 24,987 | 833 | """
Building blocks shared by the configuration widgets.
Turns ``param`` objects into form sections -- nested class attributes,
class dictionaries, collapsible families and documentation panes -- so that the
individual widgets compose these rather than laying out fields by hand.
"""
from __future__ import annotations... |
ad39321ff8cea561e0608d8eb2c1630a7be72c3637c8428cabff907b7437868a | Python | 24,989 | 508 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
import glob
import math
import os
import random
import shutil
from copy import copy, deepcopy
from multiprocessing.pool import ThreadPool
from pathlib import Path
from typing import Any
import cv2
import numpy as n... |
8f8c6c628618c36441d4f2d86719487e8952ce98dc8c7bedd93694cdc41dd205 | Python | 24,998 | 498 | '''
Date: 09/09/22
@author: Kaan Karas & TMSi
TMSiSDK: Real-time filter that can be applied to incoming data
'''
import sys
import os
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 datetime... |
ad4e8fb5235cc845791d5c510b4a17fa21a5684f313a4eeb730a3e37f34345b1 | Python | 24,999 | 663 | #!/usr/bin/env python
from itertools import repeat
import multiprocessing
import istarmap
import tqdm
import time
import tempfile
import subprocess
import statsmodels.formula.api as smf
import statsmodels.api as sm
import scikits.bootstrap as boot
import pysam
import pandas as pd
import os
import numpy as np
import mat... |
d958f612b1daf184a9798e7e4d6e7360293362cfe85385686f047667247a0bf2 | Python | 25,005 | 659 | import json
import logging
import os
import shutil
import sys
import tarfile
import numpy as np
from qtpy import QtCore
import llspy
import llspy.gui.exceptions as err
from llspy.gui.helpers import byteArrayToString, newWorkerThread, shortname
logger = logging.getLogger(__name__) # set root logger
try:
_CUDAB... |
9b6a2d229034ccfe32fe386e6bbd66440cdeda89462a64753574a85e8f053874 | Python | 25,007 | 629 | """
sess_data_util.py
This module contains functions for processing data generated by the Allen
Institute OpenScope experiments for the Credit Assignment Project.
Authors: Colleen Gillon
Date: August, 2018
Note: this code uses python 3.7.
"""
import copy
import numpy as np
from util import data_util, gen_util,... |
e60e552febba4ddb4266d2069688b93ef643d0796862849b5860b11891dd2234 | Python | 25,007 | 704 | import logging
import os
import shutil
import signal
import sys
import tempfile
import time
import traceback
import bottle
from ethoscope_node.api import (
AuthAPI,
BackupAPI,
BugReportAPI,
DatabaseAPI,
DeviceAPI,
FileAPI,
NodeAPI,
ROITemplateAPI,
SensorAPI,
SetupAPI,
Tunne... |
0654e254a57b885c7908d161faded16011d9828de621a579ff7eaaec404894d1 | Python | 25,017 | 645 | """Shared capture-honesty facts and preamble for report/export surfaces.
ONE source of truth for the honesty facts every human report, machine dump,
tabular export, and file export must carry: the settled capture outcome, the
verification ceiling, the rescue disclosure, structure-only hypothesis status,
sparse-run poi... |
f0ef62199c4f007ba8114280d3309be31ba6b1c9a4157f9c37cfb06630e02e61 | Python | 25,048 | 640 | #!/usr/bin/env python
"""
Unit tests for the email notification service.
"""
import datetime
import smtplib
import time
from email.mime.application import MIMEApplication
from email.mime.multipart import MIMEMultipart
from email.mime.text import MIMEText
from unittest.mock import MagicMock, Mock, call, patch
import ... |
21c61f99fdec573fc456855249ba9a7d35f7fcb1c2d9a4480ed1d7c48d71d186 | Python | 25,050 | 463 | """
Runs audio metamer generation on all of the layers specified in build_network.py
Removes additional layers from saving to reduce the file size
You can either make a copy of this file into the directory with the build_network.py file
and run it from there directly, or specify the model directory containing the buil... |
0451df97e6ee82d254b842bdc7e1a1953bf7b987b91dbe9a214e472db2bf4e8d | Python | 25,054 | 524 | import numpy as np
import os
import sys
import time
import tensorflow as tf
import tensorflow.keras
from tensorflow.keras.models import Sequential
import random
import pandas as pd
#import matplotlib.pyplot as plt
import matplotlib.ticker as ticker
import matplotlib
matplotlib.use('Agg') # Must be before importing mat... |
b820c2a503210d69071e1400c7d1a79915c3a96424fd93e645e2ff051ddc2209 | Python | 25,059 | 720 | from types import SimpleNamespace
from unittest.mock import MagicMock, patch
import pytest
from codecarbon.core.resource_tracker import MODE_CPU_LOAD, ResourceTracker
def make_tracker(**overrides):
tracker = SimpleNamespace(
_force_ram_power=None,
_tracking_mode="machine",
_conf={"cpu_ph... |
97ea93378e036b6a5b0a09b933139462bb6c93ccea8dcdfbcbb2ad4853823942 | Python | 25,060 | 573 | #!/usr/bin/env python3
"""
File: fast_eqtl_mapper.py
Created: 2023/05/19
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 tree.
"""
... |
900c37dcd5ef1bf177bcc58cc4c1d831557dace32dbaaccf5c04216aca7a74b4 | Python | 25,077 | 646 | import locale
locale.setlocale( locale.LC_ALL, 'en_US.UTF-8' )
import re
import pandas as pd
import camelot
import pdfminer
from pdfminer.high_level import extract_pages
import pdb
try:
from local_extractor.utils import common_utils
except ImportError:
import sys, os, pathlib
path = pathlib.Path(__file__... |
5e3607278d3ba2dba5cf4cd25ffe41237a16b8bbb3a73eebecb46cc7d89765d5 | Python | 25,080 | 491 | #!/usr/bin/env python3
"""Журнал протокола B («Когда выгодно учиться»): статистика и HTML-секция.
Читает runs/daily/protocol_b.jsonl (суточный прогон runs/daily_b.py),
считает по всему накопленному то, что объявлено в PREREGISTRATION_B.md,
и отдаёт машинное состояние (docs/journal_b.json) плюс HTML-фрагмент,
который r... |
d9c4a7f5ae409c35cee644aa4499ce8732e86705c2fd40dca2dbf3bf5959c14d | Python | 25,086 | 718 | """
An R frontend
"""
import os, sys
import pygtk
pygtk.require('2.0')
import gtk
import rpy2
import rpy2.robjects as robjects
import itertools
import gobject
class FunctionPanel(gtk.VBox):
_as_list = robjects.r['as.list']
def __init__(self, rfunction):
super(FunctionPanel, self).__init__()
... |
8eb490161b8b04d4875a0e31b31d29e6ef540547cd5e349d75785bb6d6d05e29 | Python | 25,094 | 824 | """
misc_analys.py
This script contains miscellaneous analysis functions.
Authors: Colleen Gillon
Date: January, 2021
Note: this code uses python 3.7.
"""
import warnings
import numpy as np
import pandas as pd
import scipy.stats as scist
from util import gen_util, math_util
from sess_util import sess_ntuple_util... |
9b02297c8e827f71c3b4d53e60260edde0d2d1ecb8e9f76021ede3f9dac316f1 | Python | 25,096 | 524 | import numpy as np
import os
import sys
import time
import tensorflow as tf
import tensorflow.keras
from tensorflow.keras.models import Sequential
import random
import pandas as pd
#import matplotlib.pyplot as plt
import matplotlib.ticker as ticker
import matplotlib
matplotlib.use('Agg') # Must be before importing mat... |
98a275b9a43aeb39259e7a1429d3cb000d4bae1a81a87fa79c978d46b9e5a722 | Python | 25,109 | 582 | import pickle
import torch
import torch.nn.functional as F
from trainingUtils import NBLoss,_convert_mean_disp_to_counts_logits #,MultipleOptimizer, MultipleScheduler, compute_kernel, compute_mmd
from models import Encoder,Decoder,GaussianDecoder,VAE,CellStateEncoder,\
CellStateDecoder, CellStateVAE,... |
a96b310d16adf31de3ad44c48766b11b16961564b446f9eb08ac7cc7ee6c8e0d | Python | 25,131 | 642 | import os
import csv
import copy
import datetime as dt
from pyoperant.behavior import base, shape
from pyoperant.errors import EndSession, EndBlock
from pyoperant import components, utils, reinf, queues
# New trial class that allows for early responses
# Saves the response, time, and whether it was correct
# Most chan... |
af9d8e9410d2ca7e975619f7cc51ecb51bb471a9c0f55d58f894fe98f5d7b372 | Python | 25,135 | 719 | import numpy as np
import torch
from scipy.special import softmax
import logging
from tqdm import tqdm
import matplotlib.pyplot as plt
from itertools import combinations
def calc_KS(strat_obj, dataframe, which_highest, network_name, temperature=1):
nb_parties = 1000
arr_proba = np.zeros((nb_parties))
arr_... |
f496ac0ab20fe8bc64399221539d479a58292ba27e18c57c5e70f992ac0f3f32 | Python | 25,149 | 529 | #!/usr/bin/env python3
"""
File: cluster_pic_eqtl_genes.py
Created: 2022/02/23
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 tree.... |
f72f33f9b02b2542a5f3d8ca3c393ae7e9a11af238e4080289f6d4e09b07b27d | Python | 25,154 | 595 | """Tier-(b) collective boundary capture: gloo sims.
Single-process pins for boundary-node shape, C0 payload content, nesting
suppression, tensorless journaling, and typed refusals; then 2-rank
``spawn`` gloo sims proving rank-local graph completeness and cross-rank
correlation-key agreement (merge-ranks tier (b), scop... |
8b26685463bf2cf39f2364d06f1d7874167be12b2bd30704b8aa8812bf490c0b | Python | 25,164 | 604 | # pylint: disable=arguments-differ,unused-argument,line-too-long
"""R2Plus1D, implemented in Gluon. https://arxiv.org/abs/1711.11248.
Code adapted from https://github.com/pytorch/vision/blob/master/torchvision/models/video/resnet.py."""
__all__ = ['R2Plus1D', 'r2plus1d_resnet18_kinetics400',
'r2plus1d_resn... |
c51539cebf1e2f449e740b55c08e549515aee456cc451d375a08b4544e456130 | Python | 25,172 | 655 | #!/usr/bin/env python
# =============================================================================
# MODULE DOCSTRING
# =============================================================================
"""
Train the normalizing flow potential.
"""
# ==================================================================... |
a2119841c7c1742db0aca1b0f8c282df07a7e60d6cd450fdb38fc3bce29e830d | Python | 25,176 | 535 | import numpy as np
import os
import sys
import time
import tensorflow as tf
import tensorflow.keras
from tensorflow.keras.models import Sequential
import random
import pandas as pd
#import matplotlib.pyplot as plt
import matplotlib.ticker as ticker
import matplotlib
matplotlib.use('Agg') # Must be before importing mat... |
da44ffc68a620271a902eea8560d70c417f4afa1961f56660b4fc9f3e15d5890 | Python | 25,176 | 535 | import numpy as np
import os
import sys
import time
import tensorflow as tf
import tensorflow.keras
from tensorflow.keras.models import Sequential
import random
import pandas as pd
#import matplotlib.pyplot as plt
import matplotlib.ticker as ticker
import matplotlib
matplotlib.use('Agg') # Must be before importing mat... |
d1020108c356036b00d4eab254e4b1736f0c355762cc8763a0740ad9ee9d4579 | Python | 25,183 | 647 | """Lane F01 regions checkpoint: derived admissibility on the existing verbs.
Surgery memo 3.4 / foldA D12: a region is a user-selected contiguous chunk of
the executed graph treated as ONE unit. Covered here: derived complete exits
(user list leak refusal), convexity (``between(R, R) <= R`` with an offending
path prin... |
253214004b1fe70cf62537f7899aeaa86d529b4e3c3e70b339181877f12e4a7e | Python | 25,186 | 756 | #!/usr/bin/env python
# Created on: August 2, 2013
__author__ = "Sven Kreiss, Kyle Cranmer"
__version__ = "0.1"
import ROOT
from PyROOTUtils import interpolate
from scipy.optimize import minimize
import math
from pprint import pprint
container = []
import re, pickle
import numpy
from multiprocessing import Poo... |
48aa57ba24ebf64e0c34ec8a753c553f417b8d6f829a96b6ea7890d552d355a8 | Python | 25,192 | 595 | from typing import Optional
import mujoco
import numpy as np
from gymnasium import utils
from scipy.spatial import transform
import angorapy.tasks.utils
from angorapy.common.const import N_SUBSTEPS
from angorapy.common.senses import Sensation
from angorapy.tasks.envs.dexterity.consts import DEFAULT_INITIAL_QPOS
from ... |
109bd94fcb8fa275b3f532fd99bb72510a396afaf39283d34fe6da0afd3c500d | Python | 25,199 | 561 | import torch
import torch.nn as nn
import torch.nn.functional as F
from functools import partial
from timm.models.layers import DropPath, to_2tuple, trunc_normal_
from timm.models.registry import register_model
from timm.models.vision_transformer import _cfg
import math
from model import common
from model import acb
... |
0d1351fd859d9166f81270230a8256693b605beed919b9bf60799cc830478209 | Python | 25,220 | 522 | #!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
@author: Pramod Bharadwaj Chandrashekar, Li Liu
@email: pchandrashe3@wisc.edu, liliu@asu.edu
"""
import sys
import tensorflow as tf
from tensorflow.contrib import rnn
class CnnBilstm(object):
"""
A CNN for gene expression prediction.
Uses a convolution la... |
c68a39e0ebdf9817c68fd3a778aba5a663cba28829af64f7d0f28a069c083466 | Python | 25,230 | 602 | # -*- coding: utf-8 -*-
import matplotlib.pyplot as plt
import numpy as np
__all__ = [
'Task'
]
class Task(object):
def __init__(self,
trial_type='DMS',
dt=100, # ms
tau=100, # ms
batch_size=1024):
self.dt = dt
self.dt_sec = dt / 1000
se... |
149085ca36d8ac64b530a5aa4a98cda0de1015caab3f734b17d697546a5d9853 | Python | 25,234 | 498 | """CziMsem.py
Implements full affine and optimally constrained affine fitting with the
same interface as required by scikit-learn.
Copyright (C) 2018-2026 Max Planck Institute for Neurobiology of Behavior
This program is free software: you can redistribute it and/or modify it under
the terms of the GNU General Pub... |
896732d30789956a71b4270ae96b5d64f12258ae065b07f9cc0a3c43414da381 | Python | 25,245 | 488 | """Predefined Mask RCNN Model."""
from __future__ import absolute_import
import mxnet as mx
from mxnet.gluon import nn
from mxnet.gluon.contrib.nn import SyncBatchNorm
from ..mask_rcnn import get_mask_rcnn
from ....nn.feature import FPNFeatureExpander
__all__ = ['mask_rcnn_resnet50_v1b_coco',
'mask_rcnn_f... |
ae5c14d126553ee8a6450466e7fc8ef942c9ba63e6cbccbc16ef8b724a09fbef | Python | 25,246 | 881 | """Generate formatted strings for printing out information in report format."""
import numpy as np
from specparam.utils.select import list_insert
from specparam.utils.array import compute_arr_desc
from specparam.utils.properties import compute_presence
from specparam.version import __version__ as MODULE_VERSION
from ... |
2d2c7e726ace80e1522b91809e8ddb34acfa6e40bf863074ec14df3fc76badd5 | Python | 25,249 | 836 | """Means of SPD/HPD matrices."""
from copy import deepcopy
import numpy as np
import warnings
from .ajd import ajd_pham
from .base import sqrtm, invsqrtm, logm, expm, powm
from .distance import distance_riemann
from .geodesic import geodesic_riemann
from .utils import check_weights
def mean_ale(covmats, tol=10e-7, ... |
f53d09b4fb36fd243119465fb5132098013c68681888aaf1a04b5c3ae916d35a | Python | 25,249 | 558 |
import os
import re
import math
import random
import resampy
import numpy as np
from multiprocessing import Queue, Process
from .audio import gain_db_to_ratio, max_dbfs, normalize_audio, AUDIO_TYPE_NP, AUDIO_TYPE_PCM, AUDIO_TYPE_OPUS
from .helpers import LimitingPool, int_range, float_range, pick_value_from_range, tf... |
339ed51934d42f3a0b4e5538267553f3eb42a9877f4638b6be5098919d1c360b | Python | 25,252 | 706 | """Tests for serialization_lib."""
import json
import numpy as np
import keras
from keras.src import ops
from keras.src import random
from keras.src import testing
from keras.src.saving import deserialize_keras_object
from keras.src.saving import object_registration
from keras.src.saving import serialization_lib
d... |
8e1b85f15ed1db1bafdb5a09718da2c9d294a526071bb2e658039717eba23a7a | Python | 25,253 | 636 | #!/usr/bin/env python
# -*- coding: UTF-8 -*-
__author__ = "Bjoern Gruening"
__version__ = "0.1"
__date__ = ""
__license__ = "GLP3+"
"""
These script converts a Blast XML Output to the NCBI Feature Table format,
required for submission of Serquence data.
http://www.ncbi.nlm.nih.gov/WebSub/index.cgi?tool=genbank
TODO:... |
5829adc4a93d279415e69c337053eb099a19c4896eee1ca4593aad78fdbdf358 | Python | 25,265 | 618 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
from collections.abc import Callable
from types import SimpleNamespace
from typing import Any
import cv2
import numpy as np
from ultralytics.utils import LOGGER, RANK, TESTS_RUNNING, env_bool, ops
from ultralytics... |
9e9914ad8a536e77c3d7e21037a9c653dfde03d2d6114697fcb5e14347574b3e | Python | 25,282 | 548 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
20_analysis.py — 路线 A 主分析
==================================================================
在完全公开的纵向人血浆蛋白组数据上，复现英矽智能 rentosertib 研究
（Nature Biotechnology 2026, DOI 10.1038/s41587-026-03286-y）的分析链：
药物干预前后配对血样 → Olink 蛋白质组 → 蛋白质组衰老时钟 → 预测年龄位移
数据集：GSE169148（GEO, 完全公... |
ac0f339d7d337d98622b802bab2cb4fa5754a69b97757262193e3759bb49352d | Python | 25,290 | 693 | """Artifact detection."""
import numpy as np
from scipy.stats import combine_pvalues, norm
from sklearn.base import BaseEstimator, TransformerMixin
from .classification import MDM
from .geometry.geodesic import geodesic
from .geometry.mean import gmean
from .utils._base import SpdClassifMixin
from .utils._check import... |
4b2eaca03e20cfa800740049dbad46d395bbef7007f596c18f55cb4360676345 | Python | 25,291 | 688 | '''
This code provides with an easy way to avoid boilerplate for training and validating results.
author: obanmarcos
'''
'''
This code provides with an easy way to avoid boilerplate for training and validating results.
author: obanmarcos
'''
import sys
sys.path.append('~/DeepOPT/')
import torch
from . import modl
impo... |
3b99f3c79f5881db4d9cedb948c914830d38cc751cdbd5cf05ca8de44126befc | Python | 25,300 | 659 | """r65 Cluster Y: input-boundary walker container parity (single-sourced dispatch).
The three input-boundary walkers -- W1 (capture literal-leaf), W2 (capture
metadata-read-site), W3 (runtime literal-path) -- witness the SAME physical input
tree for different fact families, so a container kind handled by one walker bu... |
5b40dac1ba212e788063d30d8b753d2d00549d6059c9cfd85d45b9879348c21e | Python | 25,310 | 693 | import numpy as np
import scipy
import brian2.only as br
from tqdm import tqdm
import matplotlib as mpl
import matplotlib.pyplot as plt
import pandas as pd
import seaborn as sns
import network
import analysis
import fig2
from functools import partial
from multiprocessing import Manager, Pool
import sys... |
e4def0fc93af8776b34714e181318d364bf078b6a864efd8342cb25accbb1bae | Python | 25,317 | 509 | import argparse, time, logging, os, math
import numpy as np
import mxnet as mx
from mxnet import gluon, nd
from mxnet import autograd as ag
from mxnet.gluon.data.vision import transforms
import gluoncv as gcv
gcv.utils.check_version('0.6.0')
from gluoncv.data import imagenet
from gluoncv.model_zoo import get_model
fr... |
1dcb000bcc89e9ee1bb6accae43a36b7488652bb137a3ff97e38e1bd1dcdea3c | Python | 25,330 | 773 | """
Reusable groups of related configuration parameters.
Each class bundles the parameters that belong together -- framerate, spatial
resolution, simulation timing, runtime paths and output options -- so that the
datasets, simulations and portal apps share one definition of them.
"""
from __future__ import annotation... |
0ef31880a9f0d0c2665798e26507c874abf63789ca5ffd2393e0b0dfe29f22cf | Python | 25,333 | 629 | # -*- coding: utf-8 -*-
import os
import io
import csv
import json
import tarfile
from pathlib import Path
from functools import partial
from .helpers import KILOBYTE, MEGABYTE, GIGABYTE, Interleaved, LenMap
from .audio import (
Sample,
AUDIO_TYPE_PCM,
AUDIO_TYPE_OPUS,
SERIALIZABLE_AUDIO_TYPES,
ge... |
b89b314070e46c629b0fa6fa6559440ed1d4cf37062b2d98683c5a8059968f59 | Python | 25,345 | 657 | import numpy as np
import pandas as pd
import nibabel as nib
from scipy.io import loadmat
from os.path import join as pjoin
from magicbox.io.io import CiftiReader
proj_dir = '/nfs/z1/userhome/ChenXiaYu/workingdir/study/visual_dev'
meas2color = {
'Myelination': 'cornflowerblue', 'Thickness': 'limegreen',
'PC1... |
7efc382c277bae206997d2442d8dffd8c78cde4e3bd4139034aaf7879df09e63 | Python | 25,361 | 590 | import argparse
import random
from mxnet import gluon, image,autograd
from mxnet.gluon.data.vision import transforms
from mxnet.base import numeric_types
import gluoncv as gcv
gcv.utils.check_version('0.6.0')
from gluoncv import utils as gutils
from mxnet.gluon.data import DataLoader
from mxnet.gluon import nn
import m... |
2f5738abb6580ac2d719594817c32017fa112e49f107706a7beff3cefb4451d3 | Python | 25,366 | 649 | import os
import shutil
import sys
import tempfile
from argparse import (
ArgumentParser,
Namespace,
)
from collections.abc import Callable
from io import StringIO
from pathlib import Path
from textwrap import TextWrapper
from typing import (
Any,
NamedTuple,
)
import yaml
from boltons.iterutils import... |
7d18d2da916d6a28ac6c5703d8148e015a5b16265ac38b24cc7acb6a533c5030 | Python | 25,374 | 591 | """Numeric attestation and nondeterminism checks."""
from __future__ import annotations
from collections.abc import Iterable, Mapping, Sequence
from typing import TYPE_CHECKING, Any
import torch
from .runnable import (
ActivationPayloadLayerDescriptor,
ActivationPayloadMember,
ControlWitnessKind,
Ru... |
3c1ecf1e11be5ff85c8beeb8f205e1afbb60049d7c5d391eacd7bac2f12047e3 | Python | 25,384 | 665 | """Tigramite causal discovery for time series."""
# Author: Jakob Runge <jakob@jakob-runge.com>
#
# License: GNU General Public License v3.0
from __future__ import print_function
from scipy import special, spatial, stats
import numpy as np
from numba import jit
import warnings
from tigramite.independence_tests.indep... |
3db898e5df4d7437c7945569ab45dec067d856389ad9142ac30d9ca76efe8f2e | Python | 25,392 | 688 | """
FlashAttention benchmarking script with Flex Attention-style
mask mod support and varlen sequences.
"""
from dataclasses import dataclass
import math
from typing import Any, Dict, Optional, Tuple
import cuda.bindings.driver as cuda
import cutlass
import cutlass.cute as cute
from cutlass.cute.runtime import from_d... |
66eaa917e7d2c89960a4b76421b942e50ac489381850256d1ba67748cbf3aaa7 | Python | 25,398 | 649 | #!/usr/bin/env python3
"""Shared extra-feature extraction library for paper7_ad_cross_cohort Diagnostic F."""
from __future__ import annotations
import numpy as np
FS_TARGET = 100
EPOCH_SEC = 30
EPOCH_SAMPLES_RS = EPOCH_SEC * FS_TARGET # 3000
MAX_EPOCHS_PER_SUBJECT = 10
def fft_resample(data, fs_orig, fs_target):
... |
a8f0af9694926a45779560305a5fd092edda3720a8471e213b57574a9c2bc45f | Python | 25,410 | 653 | """Comparative selection producers: acceptance and honesty gates.
Covers the comparative-producer lane obligations: differential producers
(``changed`` / ``top_changed``) compare the SUBJECT (resolution trace)
against ONE explicit reference with a directional float64 delta, masks are
exact AS SETS against manually com... |
853497760fd3e56ef2445849bd5c9cbe1ffcba030cbfdfc9bb63870b468b2845 | Python | 25,456 | 664 | """Tests for Module, ModuleCall, and ModuleAccessor."""
import example_models
import pytest
import torch
import torch.nn as nn
import torchlens as tl
from torchlens import trace as trace_fn
from torchlens.data_classes import ModuleAccessor, ParamAccessor
from torchlens.types import Module, ModuleCall
# -------------... |
7cc1f938c7179ed182358d17fedaafd836ce60a8f07fcdb650de776a31358c3c | Python | 25,474 | 594 | """r67 C3+C6 -- ONE atomic storage-accessor disposition surface with ACTUAL-READ gating.
corr1-4 / free-F4 / free-F5 / r66b-R3 root causes, closed structurally:
* Handle ACQUISITION (``untyped_storage`` / ``storage`` / ``_typed_storage``) records
origin/watch ONLY -- a discarded handle is not an observation (the le... |
d2e5e07e5ada484757830ffa940df05c1b33a15465ed480c4f5f524f089ff757 | Python | 25,482 | 714 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceType as _BaseTraceType
import copy as _copy
class Table(_BaseTraceType):
_parent_path_str = ""
_path_str = "table"
_valid_props = {
... |
dcdcb90570be4a23439cd8ddfdcb05b66c312083ba960a308e4285ae7a15425b | Python | 25,497 | 577 | """Governance for the mutation driver's known-red DESELECT ledger.
b9-opus R71r3-F1 (part 2): for the second consecutive hunt pass, the driver's
``DESELECT`` list carried entries whose tests had gone GREEN on tip — each
stale entry silently deletes the margin of whatever mutants its tests would
have killed, and the dr... |
7d4a16b926e43c2c9c5a65e250839c6c3eb0c2c81c82f7febb3cbc995dc7d32d | Python | 25,502 | 549 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
import sys
from typing import Any
import numpy as np
from ..utils import LOGGER
from ..utils.ops import xywh2ltwh
from .basetrack import BaseTrack, TrackState
from .utils import matching
from .utils.kalman_filter ... |
87e7d3795e2e9523eb38276786858cae544113e69324db81ca1436b5e6030e16 | Python | 25,502 | 786 | # TODO: make it cffi-buildable with conditional function definition
# (Python if ABI, C if API)
import abc
import enum
import inspect
import logging
from typing import Tuple
import typing
import warnings
from rpy2.rinterface_lib import ffi_proxy
from rpy2.rinterface_lib import openrlib
from rpy2.rinterface_lib import c... |
785e1b142164b3367c44ff128941ab9394befb8c7857c49f6a206d22b4c64cc9 | Python | 25,503 | 665 | import logging
import os
import threading
import time
from collections.abc import Callable
from dataclasses import dataclass
from typing import (
Any,
cast,
TypeVar,
)
from pydantic import (
BaseModel,
UUID4,
)
from typing_extensions import TypedDict
from galaxy.exceptions import (
Inconsisten... |
fc1ed81237942efbffab84f16ddde8c0b85b87ec8017087d1ed36b0ba8464114 | Python | 25,523 | 575 | """
This code plots the figures in Results.
"""
import os
import os.path as op
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from mne.channels import find_ch_adjacency
from mne.stats import spatio_temporal_cluster_test, ttest_ind_no_p
from scipy.signal import butter, fi... |
aa82a360dc09655750a3e106c60b4c3c29e754e49a2c6a40b485e7701a23bdef | Python | 25,534 | 790 | """Compact dependency-gated reimplementations for REIMPL2 shard 7.
Sources checked: scvi-tools model docs for scVI/scANVI/totalVI/MultiVI/PeakVI/
DestVI/veloVI, Fuchs et al. 2020 SE(3)-Transformer, Kirillov et al. 2023 SAM,
and Linsley et al. 2018 hGRU. These models are small random-init PyTorch
reconstructions that ... |
cc062f685b9f6ef6ebf353371d0f8fbca0b0623b3fb2711d108c2bddadfbc98b | Python | 25,539 | 706 | """Erik Linder-Noren's PyTorch-GAN reference generators (and a couple discriminators).
Source: https://github.com/eriklindernoren/PyTorch-GAN
A widely-used educational collection of compact, faithful PyTorch ports of classic
GAN papers. Each generator below reproduces the *distinctive* architecture of its
paper at sma... |
f9dca622eeaa209f43ed464cc1a94b8adc7d0b7072168072aa16404d870eef0b | Python | 25,542 | 684 | import hypothesis.strategies as st
import numpy as np
import pytest
import seqpro as sp
from Bio.Seq import translate
from hypothesis import given
from numpy.typing import NDArray
from pytest_cases import parametrize_with_cases
from seqpro._numba import (
_nb_drop_unknown_codons,
gufunc_translate,
gufunc_tr... |
9c3b635618abb370cac4ac36ca6d8d7bbe6e5d0ac0fc4091b9bd33d3392e5bc3 | Python | 25,565 | 649 | import numbers
import numpy as np
import shapely
from shapely import ops
from shapely.geometry import (
LinearRing,
LineString,
MultiLineString,
MultiPolygon,
Polygon,
box,
)
from pyrosm.exceptions import PBFNotImplemented
import functools
import inspect
import os
from pathlib import Path
impor... |
b9e75ce95593b4ac6df6d9acc8857b94cd728cce9d9859bfa9bf932dd37c7e88 | Python | 25,578 | 707 | """
Base classes shared by every larva agent.
Defines the common interface of the simulated, replayed and offline larvae:
their body geometry, their pose, and the accessors that the analysis and
rendering layers read.
"""
from __future__ import annotations
from typing import Any
import math
from copy import deepcopy... |
d1efd35eb31fa5af271933bb1a625c9a93c2316ce58998bacedf5a31c865ba67 | Python | 25,578 | 717 | """setuptools.command.egg_info
Create a distribution's .egg-info directory and contents"""
from distutils.filelist import FileList as _FileList
from distutils.errors import DistutilsInternalError
from distutils.util import convert_path
from distutils import log
import distutils.errors
import distutils.filelist
import... |
59297b718936cb768f8ddfd8448d1b60f1d0f0299c4d353af5f4d8eb761a4523 | Python | 25,592 | 697 | # Copyright (c) 2021 PaddlePaddle 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 app... |
996a5da2d5b0f66b63ab36f298c295eeb36463f5cc63de7d80cbc21df76a9899 | Python | 25,600 | 629 | #!/usr/bin/env python
"""
run_run_analysis.py
This script runs running analyses using a Session object with data generated
by the Allen Institute OpenScope experiments for the Credit Assignment Project.
Authors: Colleen Gillon
Date: October, 2018
Note: this code uses python 3.7.
"""
import argparse
import copy
... |
a30a78062eae8ba78d88a54e099b2cac8ddd943c124e1d9fd76b36e59d610777 | Python | 25,602 | 714 | #!/usr/bin/env python3
import copy
import csv
import json
import logging
import os
import re
import sys
from autouri import GCSURI, AutoURI
from . import __version__ as version
from .caper_args import ResourceAnalysisReductionMethod, get_parser_and_defaults
from .caper_client import CaperClient, CaperClientSubmit
fro... |
9e5ede628e95fc616905be8f52f5f59a2b1b5d8961ef5114d9fa768b2030dc81 | Python | 25,603 | 558 | import math
import os
import time
import torch
import torch.nn as nn
import numpy as np;
from torch.autograd import Variable
import scipy
import matplotlib.pyplot as plt
import scipy.io as sio
from sklearn.preprocessing import normalize
from sklearn.cluster import KMeans
from sklearn.metrics import normalized_mutual_in... |
9399f514a621942b5b35231829e03a0f1bead6f5e2f4f92883c3fd766a5896e9 | Python | 25,619 | 612 | import logging
import os
import subprocess
import traceback
from git import GitCommandError, Remote, Repo
class DeviceUpdateError(Exception):
"""Custom exception raised when device updates fail."""
pass
class DeviceUpdater:
"""
A class to manage and update a device's Git repository.
It handle... |
a3078191cc2cd24db0a58f02d5b68bdc37859364bdbd9b33f768eb02f30b020a | Python | 25,619 | 642 | import hashlib
import io
import os
import pathlib
import pkg_resources
import time
import afmformats.errors
import nanite
import nanite.fit as nfit
import numpy as np
from PyQt5 import uic, QtCore, QtGui, QtWidgets
from .. import colormap
from ..head.custom_widgets import show_wait_cursor
from .. import units
from .... |
dd651a74877f88cfefa6a0188188f97b7e7663223760220dc859465346678866 | Python | 25,625 | 585 | """Round-43 security regression: INVERT the CLASS 1 pure-forward-callable gate on the
internal-builtin torch roots ``torch`` / ``torch._C`` / ``torch._tensor`` from a growing
denylist-of-verbs to a positive STRUCTURAL recognized-operator predicate (findings
secE-r42-1/2/3).
The pre-r43 gate admitted any callable whose... |
403c275e7eabe8ecf089c1bfcda9dfde8152d52a6558b806d3a85b58a5e62101 | Python | 25,637 | 682 | #!/usr/bin/env python
# Created on: September 30, 2013
__author__ = "Sven Kreiss, Kyle Cranmer"
__version__ = "0.1"
__description__ = """
Creates a counting model using HistFactory for the H2ph, HZZ4l and HWWlvlv
channels in ATLAS.
The numbers are taken from these papers and conf notes:
- http://arxiv.org/pdf/130... |
6cb169a300cee3ddff917dbab7d4db97fcd45cdbcb3042c15456bf383f1aae3d | Python | 25,637 | 738 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceType as _BaseTraceType
import copy as _copy
class Indicator(_BaseTraceType):
_parent_path_str = ""
_path_str = "indicator"
_valid_props =... |
1de72fa3881ce91c55c0eba35b45a7f87c3b13b30304d00130b04aa1742d834b | Python | 25,639 | 409 | import sys
import tensorflow as tf
from tensorflow.keras import datasets
from time import perf_counter
import numpy as np
from pdb import set_trace
import sys
ENABLE_MEMORY_GROWTH = True # https://stackoverflow.com/questions/36927607/how-can-i-solve-ran-out-of-gpu-memory-in-tensorflow
DEBUG_CONV = False
TEST_KERAS... |
6de74d1e0ce41e1022390874f49ce3be9a956b0c42239b937ed855758260107c | Python | 25,640 | 832 | """
Tomographic Reconstruction Utilities Using TwIST, ADMM, and TV Denoising.
This module provides a collection of iterative reconstruction algorithms and
image-processing utilities for tomographic imaging, including implementations of:
* TwIST (Two-Step Iterative Soft Thresholding) reconstruction
* ADMM-based regu... |
29a3b9e812aa51cfe79b5ea391cb0df9bf276fe3a2653ab628a474dacb4630e1 | Python | 25,650 | 739 | """Run simple cell optimization"""
"""
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... |
a8f777244a6d02cabd84c16900d5ee08e7f2f20d8ad13dbb6326394412da8a9f | Python | 25,659 | 731 | import numpy as np
from sklearn.utils.validation import check_random_state
from ..geometry._docs import deprecated
from ..geometry.base import (
_symmetrize, ctranspose, invsqrtm, powm, sqrtm, expm
)
from ..geometry.distance import distance_riemann
from ..geometry.mean import mean_riemann
from ..transfer import en... |
85b20d3b41c0e89b0aa540e0d7a8865848887eee20ad48901fd14692f04c862c | Python | 25,675 | 730 | """In-memory representation of cluster state.
This module implements a data-structure used to keep
track of the state of a cluster of workers and the tasks
it is working on (by consuming events).
For every event consumed the state is updated,
so the state represents the state of the cluster
at the time of the last ev... |
4e46dc189d6a818fd48fa35e7d3165047987338a9db5d1d2df3b03a22b5ae25a | Python | 25,731 | 802 | """
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... |
664743469d0c50945884fe42d572b4859307d0b302226417babddf57e9056371 | Python | 25,735 | 685 | from __future__ import annotations
from itertools import product
from pathlib import Path
from typing import TYPE_CHECKING, Any
import matplotlib.pyplot as plt
import numpy as np
from gymnasium import Wrapper
from natsort import natsorted
from neurogym import _SB3_INSTALLED
from neurogym.config.base import LOCAL_DIR... |
61fa70633e00e84938636b8c488c24e2c9412b5a33177aa6d566075ab96dc0a5 | Python | 25,737 | 598 | #################################################################
# Code written by Edward Choi (mp2893@gatech.edu)
# For bug report, please contact author using the email address
#################################################################
import sys, random
import numpy as np
import cPickle as pickle
from colle... |
47511fa14be1910ff7827e09c8a7f1e539d62b4c4ee0db5f65cb42bf285816ff | Python | 25,739 | 727 | #!/usr/bin/env python
import datetime
from typing import Any
import requests
from ..utils.configuration import EthoscopeConfiguration
from ..utils.etho_db import ExperimentalDB
from .base import NotificationAnalyzer
class SlackNotificationService(NotificationAnalyzer):
"""
Slack notification service for Et... |
1af81c7231e126891a8403d90fc6f3a8f248605eb28a3b77b6e0e26e2979168f | Python | 25,741 | 612 | """Quiet-box A/B capture-overhead and fast-tier harness with re-baselined gates.
This is the durable home of the ad-hoc ``/tmp/perf_ab.py`` A/B harness (D14
ruling: the ~20-30% small-capture fixed overhead is ACCEPTED for the feature
sprint; the scheduled post-features perf pass owns optimizing it, and the
harness is ... |
643f959f1ff5066dfcb40c4593f80ab609f8864ae0cfbd5f552b5aa35952b599 | Python | 25,741 | 698 | """Buffer-rung full parity with the param rung (r81, r80 free/hon1/review HIGHs).
Round 80 demonstrated TWO HIGH false-VERIFIEDs sharing ONE root: the
buffer/tensor-meta provenance rung trusted a STATIC buffer stamp
(``TensorMeta.address``, and the sibling ``label_raw``/``buffer_source``
components) with NO verificati... |
339f347f5bfbb63a3c576460950efc559841dc12a22705638f49e5d4f9c1e36e | Python | 25,743 | 570 | ##########################################################################
## ##
## Copyright (c) 2019 Philipp Lösel. All rights reserved. ##
## ##
## This file is par... |
376740cadaafe923ad673db681430f09ae0adcae3e852438b18475b84bdbba21 | Python | 25,744 | 757 | import os
import warnings
import time
import shutil
import numpy as np
import torch
import pandas as pd
from torch.utils.tensorboard import SummaryWriter
from tensorboard.backend.event_processing.event_accumulator import EventAccumulator
import wandb
import matplotlib.pyplot as plt
import psutil
from tqdm.auto import ... |
7ecd731a8c47dccf86f6bb7e53424491029100c8dceed97f3caf6576f5adf868 | Python | 25,747 | 565 | """Functions for building the input features (reference ccd features) for the HelixFold model."""
import collections
import os
import time
from typing import Any, KeysView, Mapping, MutableMapping, Optional, Sequence, Union, List
from absl import logging
from helixfold.common import residue_constants
from helixfold.da... |
f3bd923dbfb97db3e2db0d51ec65322e6083cd520e1e8f560384743c2ea267b3 | Python | 25,748 | 460 |
__author__ = 'Aaron Gudmundson'
__email__ = 'agudmun2@jhmi.edu'
__date__ = '2022/08/01'
__version__ = '01.0.0'
__status__ = 'beta'
from scipy.optimize import minimize, curve_fit
import matplotlib.patches as mpatches # Figure Legends
import matplotlib.pyplot a... |
8569846fe4a27434d31470a5cf347d5b628a6a7ab09bd6a821253be507650c1b | Python | 25,753 | 686 | """Tests for pynapple.io.interface_neurosuite module."""
import xml.etree.ElementTree as ET
from pathlib import Path
import numpy as np
import pytest
import pynapple as nap
from pynapple.io.interface_neurosuite import (
NeuroSuiteIO,
_build_events,
_pair_start_stop,
parse_neuroscope_xml,
)
# -------... |
22dabc07c30eab0d1c2984befff9889a4cfc64be1e3a576b1b037f3bdac8186c | Python | 25,762 | 745 | import io
import os
import re
import numpy as np
from rdkit.Chem import AllChem
from rdkit import RDLogger
from scipy.optimize import differential_evolution
RDLogger.DisableLog("rdApp.*")
from rdkit.Chem import rdMolTransforms
import copy
import lmdb
import pickle
import pandas as pd
import torch
from multiprocessing... |
8efe5902949776d7c2e16212b7128016bf0e817dd5a0f3e27156a377bce8591f | Python | 25,775 | 364 | '''
K-Folding script
author: obanmarcos
'''
import os
import os, sys
from config import *
import wandb
sys.path.append(where_am_i())
import lightning as pl
import argparse
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
from utilities import dataloading_utilities as dlutils
from utilities.fold... |
7d219324ddc1ac2fa430dd5a2f7456420d7ffa12af1097913a3fb7555d2c6046 | Python | 25,782 | 521 | import numpy
from voxcell import VoxelData
from parcellation_project.analyses import flatmaps as fm_analyses
from sklearn.cluster import KMeans
from sklearn import svm
from scipy.cluster.hierarchy import linkage, fcluster
import scipy
from scipy.spatial.distance import pdist
from sklearn.metrics import confusion_matrix... |
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