sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
b4964abb287df0549a1e2c44f558bc5d34cc1b5e6dc528b2c34e0a68db0fc3ef | Python | 16,527 | 518 | from __future__ import annotations
import re
import pytest
from pybind11_tests import ConstructorStats
from pybind11_tests import factory_constructors as m
from pybind11_tests.factory_constructors import tag
def test_init_factory_basic():
"""Tests py::init_factory() wrapper around various ways of returning the... |
e04749e9b50a99de7293d60d75291e50c53551d215dc54d9cdbd537ddff14fd9 | Python | 16,532 | 392 | """DO NOT EDIT.
This file was autogenerated. Do not edit it by hand,
since your modifications would be overwritten.
"""
from keras.src.export.tfsm_layer import TFSMLayer as TFSMLayer
from keras.src.layers import deserialize as deserialize
from keras.src.layers import serialize as serialize
from keras.src.layers.activ... |
4b3d3689b1e672a12dc4dfe25ec934e95c3fc8da37a78b4c87c96d2b1d333c30 | Python | 16,533 | 408 | """Compile advanced (opt-in) ``custom_filter`` forms into an evaluable predicate.
Pyrosm's default ``custom_filter`` is a plain dict of exact string values combined with
OR. Two richer forms are supported on top of that, and both are strictly opt-in:
1. **Regex values** inside a dict, e.g. ``{"ref": [re.compile(r"I[ ... |
c5b25787d16d3a3cf9503860e2f4513c94776f1f8748b070594d82531230bfa6 | Python | 16,534 | 361 | import glob
from copy import copy
import numpy as np
import argparse
import pandas
from tqdm import tqdm
from tqdm.contrib.concurrent import process_map
import pickle
from mp_dip.mark_structures import RawChannelStandin, create_tag
from mp_dip.utils.data_preprocessing_utils import convert_montage_channel_nr_to_raw
from... |
aa6f9136c44277577cfe325106a37c10eaa0f7eac29db553ae5311dcc4cf29b5 | Python | 16,552 | 442 | """Subspace selection producer: acceptance, provenance, and honesty gates.
Covers the producer-lane obligations: the producer returns a composable
``Selection``, the resolved mask is the basis SUPPORT SET (exact as a set,
verified against manually computed supports; a dense direction supports the
whole axis), basis PR... |
71c322dc270f3f77d5c6e1f591722527e80cfe0083c3891cbaa3e92b86f2495c | Python | 16,566 | 307 | import sys
import os
import gc
sys.path.append('../TM2_segmentation')
import SimpleITK as sitk
import numpy as np
import pandas as pd
import nibabel as nib
from skimage.transform import resize, rescale
from scipy.ndimage import rotate
from scipy import ndimage
import matplotlib.pyplot as plt
from numpy import median
i... |
58b3ae9c003bc258b863d14c7f44cf704760d3b97617a964600809402d158ef5 | Python | 16,569 | 460 | """Sparse runnable literal-grammar coverage for Python slice/index literals.
``x[:, 3:]``-style subscripting lowers ``__getitem__`` calls whose key argument is a
``slice`` (and, for multi-axis indexing, a tuple mixing ``slice``/``int``/``None``/
``Ellipsis``). These are inert value types -- no callables, no imports --... |
7f99996d8b0c74798befe785d4a0eecc4133c4c16996fdcf5bda7116ecdeaf12 | Python | 16,580 | 310 | from utils import *
DATADIR = (Path(os.getcwd()) / '..' / 'data').resolve()
RESULTDIR = (Path(os.getcwd()) / '..' / 'results').resolve()
CACHEDIR = (Path(os.getcwd()) / '..' / 'model_actv').resolve().as_posix()
from resources import source_layer_map
# Set random seed
import random
np.random.seed(0)
random.seed(0)
d... |
dbbf0e6dce49d29eafa5434360f668a49ede6e914b6f55bc3dbb66887b290b89 | Python | 16,581 | 392 | #!/usr/bin/env python3
"""
Diagnostic X — ridge-regularized HC-cov whitening + ROC sweep.
Three components:
1. Ridge-regularized HC-covariance whitening: Σ_c + λI before invsqrt.
Sweep λ ∈ {0.001, 0.01, 0.1, 0.3, 1.0, 3.0}; pick the value that
maximizes LOCO BA point estimate or that minimizes bootstrap CI
w... |
789973868c947b6d4a7e9740e39111a110bd9f6a709438872eb7dd064a76d604 | Python | 16,584 | 408 | # Copyright (c) 2023, Tri Dao.
import os
import time
from pathlib import Path
current_dir = Path(__file__).parent.absolute()
import pytest
import torch
from einops import rearrange
from flash_attn.models.falcon import falcon_config_to_gpt2_config, remap_state_dict_hf_falcon
from flash_attn.models.gpt import GPTLMHea... |
478bdf20f8c08afd5818ce9f140ae6aff11d8093362af1b4424840de996167ce | Python | 16,585 | 487 | """Helper functions and constants for GCP Batch runner."""
import logging
import math
import re
from typing import (
Any,
TypedDict,
)
from humanfriendly import parse_timespan
log = logging.getLogger(__name__)
class VolumeDict(TypedDict):
server: str # NFS server hostname/IP
remote_path: str # pa... |
59ac881720d857298450b21fc7acd836bc76ebbf6d6c70b39989554977bffd2b | Python | 16,593 | 472 | import math
from keras.src.utils import backend_utils
SUPPORTED_FORMATS = (
"xyxy",
"yxyx",
"xywh",
"center_xywh",
"center_yxhw",
"rel_xyxy",
"rel_yxyx",
"rel_xywh",
"rel_center_xywh",
)
class BoundingBox:
def __init__(self):
self.backend = backend_utils.DynamicBacken... |
d0d49f2b93a25931d972ed016ee4b6308e7b53563f448e8e483e352f913225e3 | Python | 16,593 | 650 | #Written by Maryam Mahootiha
#Import Libraries
# In[]:
import time
import os
import shutil
import tempfile
import matplotlib.pyplot as plt
from PIL import Image
import torch
import numpy as np
from sklearn.metrics import classification_report
import pandas as pd
from sklearn.model_selection import KFold
import random... |
513cc193959ef7e47cee0db4e2cf0a06ee654416df955861ab85879494f968a0 | Python | 16,594 | 348 | # Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... |
b39b51302bfe3e3ad1cb389598c1db5ebdfd974b90fa22bdf2fe632cc765b1c2 | Python | 16,594 | 475 | import inspect
import os
import re
import textwrap
import typing
import warnings
from collections import OrderedDict
from rpy2.robjects.robject import RObjectMixin
import rpy2.rinterface as rinterface
import rpy2.rinterface_lib.sexp
from rpy2.robjects import help
from rpy2.robjects import conversion
from rpy2.robjects.... |
aa6357ab88520907dc2357d0fe50baf2749e3f566634e64f99411195814aeb56 | Python | 16,600 | 422 | # Copyright (c) 2023, Tri Dao.
import json
import math
import os
import re
from collections import OrderedDict
from pathlib import Path
from typing import Dict, List, Union
import torch
import torch.nn.functional as F
from sentencepiece import SentencePieceProcessor
from transformers import GPT2Config, LlamaConfig
f... |
7f5d24a78852dcd29f3abd516a3c69cbb34e82286c4ee5131049036334df9d9f | Python | 16,602 | 355 | """RCNN Model."""
from __future__ import absolute_import
import warnings
import mxnet as mx
from mxnet import gluon
from mxnet.gluon import nn
from ...nn.coder import NormalizedBoxCenterDecoder, MultiPerClassDecoder
from ...nn.feature import FPNFeatureExpander
class RCNN(gluon.HybridBlock):
"""RCNN network.
... |
d268636b284b540c7a5cf2d13d85bb8b243bdacd9d7e319a401a0a4930c1a3c0 | Python | 16,607 | 403 | """
Visualization Tools: A Tour of PyCoBi's Plot Methods
====================================================
PyCoBi exposes five visualization methods on top of matplotlib, each
suited to a different aspect of a bifurcation analysis:
* :meth:`ODESystem.plot_continuation` — the 1D / 2D bifurcation
diagram. Stable ... |
ca6a908d9285628000520b072975664a50fb5abe76fe9932e90948048d7c43c9 | Python | 16,614 | 395 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
import sys
from collections import OrderedDict
from pathlib import Path
from types import SimpleNamespace
from unittest import mock
import pytest
import torch
from tests import MODEL, SOURCE, TASK_MODEL_DATA
from ultralytics import YOLO
from ultraly... |
5b9c445837d221d4271bfea923448028c80c949eec25fbd0927e2e81a3a3b2ea | Python | 16,618 | 417 | '''
The setup of the adjacency matrices, atomic feature vectors, and reaction feature vectors.
BE SURE TO BE USING NETWORKX VER. 1.11!!
If using Fukui indices as input, import fukui_utils and uncomment out line 17 & line 343.
'''
import os
import numpy as np
import networkx as nx
import torch
from rdkit import Chem
... |
51c675a96a76efe56fdaeb306200be73837383665d5b42df661033d8d47d005d | Python | 16,622 | 428 | """
ROI Template system for external configuration of ROI definitions.
This module provides the ROITemplate class that allows loading ROI configurations
from external JSON files, replacing hardcoded parameters in ROI builders.
"""
import json
import os
from typing import Any
import numpy as np
from ethoscope.core.r... |
760ee820064024f7b56cf55365d3a64a355cf7c58109423e3ef935fa6c6b36ed | Python | 16,622 | 418 | from ovseg.HPO.SHA import SHA
from ovseg.model.SegmentationModel import SegmentationModel
from ovseg.model.SegmentationEnsemble import SegmentationEnsemble
from ovseg.utils.io import load_pkl
from os import environ, listdir, makedirs
from os.path import join, exists
from time import sleep
import numpy as np
import sys
... |
c5f95a490dbec404a4cf2ae0634916cfa0d20199d28ad3713a38b713e6a33795 | Python | 16,622 | 404 | """Predictors that map a history of embeddings and optional actions to the future.
The predictor is the part that a latent world model has. It reads the embeddings
of the past frames and, optionally, the actions that were taken, and it returns
embeddings of future frames. It never sees pixels, so an encoder trained
al... |
dfd8b3117c1f31fcdae090d2e944e4f316995e6c32ff8a9dae63f2307fd19a9d | Python | 16,623 | 445 | import numpy as np
import torch
from ..preprocess._preprocess import decode_seq, decode_seqs, ohe_seq, reverse_complement_seqs
from ..preprocess._helpers import _get_vocab
def perturb_seq(seq):
"""Numpy version of perturbations"""
n_choices, seq_len = seq.shape
idxs = seq.argmax(axis=0)
n = seq_len * ... |
51bf32097a4c6fdba5b744e4ce78ac1beb6ed81a1ce04010ea179d7027ef0bb3 | Python | 16,625 | 323 | #!/usr/bin/env python
# encoding: utf-8
from __future__ import (absolute_import, division, print_function, unicode_literals)
import argparse
import math
import string
import os
class fasta_input(object):
def __init__(self, seq):
super(fasta_input, self).__init__()
self.buffer_size = os.stat(seq).... |
8bbe9a64fe9f5e0d72bb36331d431857c07348ab6d75f779657fab827843c705 | Python | 16,636 | 495 | """Module for downsampling numpy arrays via various methods.
See the :class:`~ome_zarr.scale.Scaler` class for details.
"""
import inspect
import logging
import warnings
from collections.abc import Callable, Iterator, Sequence
from dataclasses import dataclass
from enum import Enum
from typing import Any, Union, cast... |
f0d86dcc781dae266ca6cc7ca846032339dc26a01f89c35cdb389c96697990a2 | Python | 16,647 | 426 | """Group model object and associated code for fitting the model to 2D groups of power spectra.
Notes
-----
Methods without defined docstrings import docs at runtime, from aliased external functions.
"""
import numpy as np
from specparam.models import SpectralModel
from specparam.data.data import Data2D
from specpara... |
98e40221ee7e9f61a9e2328277074347deeddfb66e32af67e5a569a58623e967 | Python | 16,663 | 418 | """
Page assistant agent for Galaxy History Pages.
Reads history contents via tools, proposes markdown edits with structured output
(FullReplacementEdit or SectionPatchEdit), and supports conversational responses.
"""
import logging
from pathlib import Path
from typing import (
Any,
Literal,
)
from pydantic ... |
f7c101164d0dbda15a2647a88cf736c120e56c933a0304846510e3c7442173b0 | Python | 16,665 | 425 | """This script is largely borrowed from https://github.com/open-mmlab/mmaction.
"""
import argparse
import sys
import os
import os.path as osp
import glob
import fnmatch
import random
import zipfile
from pipes import quote
from multiprocessing import Pool, current_process
import csv
def dump_frames(vid_item):
fr... |
0e54cd6e06552cf898fd28ebfac2e0c911593e59e8153c99cd49650c15f52020 | Python | 16,668 | 349 | import torch
import torch.nn.functional as F
from torch.distributions import NegativeBinomial
from torch.distributions.gamma import Gamma
import math
import numpy as np
import pandas as pd
from sklearn.model_selection import train_test_split,cross_validate,KFold
from sklearn.neighbors import KNeighborsClassifier
from s... |
d3f018667613b5e80d377b11a5b1d7c6d973bcc41e64b5c354fec395d8ba33d6 | Python | 16,673 | 505 | """Functional-style utilities."""
import inspect
import operator
import sys
from collections import UserList
from functools import partial
from itertools import islice, tee, zip_longest
from typing import Any, Callable
from kombu.utils.functional import LRUCache, dictfilter, is_list, lazy, maybe_evaluate, maybe_list, ... |
3457defc75f4b631b217edf454492f3bf7de666def9938ffd9ca8024e71dce1a | Python | 16,681 | 440 | """Round-3 RNG monitor closures: uuid1's C funnel, raw ``_thread`` spawns,
and bounded ``uncertain_detail`` growth.
Three hunt-b8 findings on ``utils/rng.py``:
* ``uuid.uuid1()`` escaped the seal completely on Linux -- the libuuid
``uuid._generate_time_safe`` C path (wall clock + clock-seq entropy + node)
touches... |
0776ff7634206568e8797a6619558885e609a5dbe28f28387ebd40aed30d2ff5 | Python | 16,685 | 508 | """Selector-valued ``layers=``: resolve on batch zero, freeze, attest (D12).
``layers=`` accepts capture's selector/predicate algebra plus extraction's
string lookups and selector-valued mappings. Batch zero resolves in
EXECUTION order and is harvested from the same trace; the ordered
structural site keys and pass-qua... |
e0568e8da469c0bb9f71b9e73240e0a8c0658d1bd321394df00f58f9f669ee67 | Python | 16,685 | 361 | #!/usr/bin/env python
import os
import numpy as np
import cv2
import math
import rospy
import tf2_ros
from utils import decoder
from utils import transforms
from std_msgs.msg import String
from geometry_msgs.msg import Transform, PoseStamped, Twist
from sensor_msgs.msg import Image, CompressedImage, CameraInfo
from ... |
f1a6954df8d9ed9d8063814de7b5ccaeacf23b532250ec05c6b0bd9c2c988d95 | Python | 16,686 | 349 | #!/usr/bin/python3
##########################################################################
## ##
## Copyright (c) 2019 Philipp Lösel. All rights reserved. ##
## ##
#... |
726232633ea667ae177e1495598be95ccb5f2bc4507ac11695ff94ad3aaecb12 | Python | 16,687 | 459 | """Brute-force phase oracles for per-unit receptive-field queries."""
from __future__ import annotations
from collections.abc import Iterator, Sequence
from fractions import Fraction
from functools import partial
import pytest
import torch
import torch.nn.functional as functional
from support.rf_isolation import pre... |
38bb82a742866fb84a72f6d57b92a052d4adc16de66508a59820f45e97dfcc28 | Python | 16,689 | 529 | from plotly.express._core import build_dataframe
from plotly.express._doc import make_docstring
from plotly.express._chart_types import choropleth_map, scatter_map
import narwhals.stable.v1 as nw
import numpy as np
def _project_latlon_to_wgs84(lat, lon):
"""
Projects lat and lon to WGS84, used to get regular ... |
3754a708c7e6f91ec790affa64f312bf7f1dd321ae8ea3b0979998fec5d5556f | Python | 16,697 | 309 | import json, os, random
import torch
import numpy as np
import h5py
from torch.utils.data import Dataset
import dareblopy as db
import torch.utils
import torch.utils.data
cpu = torch.device('cpu')
class ECoGDataset(Dataset):
"""docstring for ECoGDataset"""
def __init__(self, cfg,ReqSubjDict, mode = '... |
b82f08011428008253e04831a8cb8679e0bd4b7a2b069e3e4c85404f729e3422 | Python | 16,700 | 393 | """DO NOT EDIT.
This file was autogenerated. Do not edit it by hand,
since your modifications would be overwritten.
"""
from keras.src.export.tfsm_layer import TFSMLayer as TFSMLayer
from keras.src.layers import deserialize as deserialize
from keras.src.layers import serialize as serialize
from keras.src.layers.activ... |
5a47c342217bef967ff531988783608df0457d4195c1ae44b7e234acdfd527c5 | Python | 16,702 | 549 | """Distances between SPD/HPD matrices."""
import numpy as np
from scipy.linalg import eigvalsh, solve
from .base import logm, sqrtm, invsqrtm
def _check_inputs(A, B):
if not isinstance(A, np.ndarray) or not isinstance(B, np.ndarray):
raise ValueError("Inputs must be ndarrays")
if not A.shape == B.sh... |
21c31a2496e7797724e053382192975fcd706090dfd74f9b9062df354317d2fd | Python | 16,704 | 313 | import argparse
import template
parser = argparse.ArgumentParser(description='EDSR and MDSR')
parser.add_argument('--debug', action='store_true',
help='Enables debug mode')
parser.add_argument('--template', default='.',
help='You can set various templates in option.py')
# Hard... |
5e488d29181f9e1fde20d5df1df4bacea9cfdaece0621848e7f73b0b4bae9e2a | Python | 16,707 | 411 | """Round-47 hon2_1 immunizer -- cross-thread captured-operand consumption over the FULL op surface.
r45 hon2_1 ceilinged a runnable capture to UNVERIFIABLE when a NON-owner thread consumed a captured
tensor as an operand -- but ONLY through the global torch-FUNCTION wrapper. The entire
``torch.ops.*`` (aten / higher-o... |
8d6575bcdb82b0a7a4886affa00b3b736fb77e5c7607384ef2752858572d9ae4 | Python | 16,707 | 384 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Feb 25 11:43:54 2021
This script containts the functions implementing the learning dynamics and connectivity analyses (Fig. 4 in the
manuscript).
@author: emilia
"""
import pickle
import torch
import numpy as np
import matplotlib.pyplot as plt
from sci... |
ce7c5787eec179954156eef7cdc6b9e939b03378e4ba35afea80d917fc2279ee | Python | 16,716 | 542 | import pandas as pd
import numpy as np
import Code_General_utility_spikes_pickling as util
import os
import matplotlib.pyplot as plt
import matplotlib as mpl
import matplotlib.colors as mcolors
import warnings
import logging
logging.getLogger('matplotlib.font_manager').disabled = True
warnings.filterwarni... |
8c1b91afb4a225f6a4eb8a05c077172cdc99e30e17198e8b0cfe6ba219d14d51 | Python | 16,719 | 543 | import pandas as pd
import numpy as np
import Code_General_utility_spikes_pickling as util
import os
import matplotlib.pyplot as plt
import matplotlib as mpl
import matplotlib.colors as mcolors
import warnings
import logging
logging.getLogger('matplotlib.font_manager').disabled = True
warnings.filterwarni... |
963eefa3484bf98343f40810e0be444bb95bbb950de5ecea43b1774b25fdb243 | Python | 16,721 | 442 | """
ResNet code gently borrowed from
https://github.com/pytorch/vision/blob/master/torchvision/models/resnet.py
"""
from __future__ import print_function, division, absolute_import
from collections import OrderedDict
import math
import torch.nn as nn
from torch.utils import model_zoo
__all__ = ['SENet', 'senet154', '... |
378cbac9b473e5b70a3575c134941b5937b482dc1934ecbdac0e82804a4c93fc | Python | 16,722 | 475 | """
Timeseries plotting
"""
from __future__ import annotations
from typing import Any, Optional, Sequence, Tuple
import numpy as np
from .. import plot, reg, util, funcs
__all__: list[str] = [
"plot_ethogram",
"plot_nengo_network",
"timeplot",
"timeplots",
"plot_navigation_index",
"plot_path... |
cb3eda44d7d4eec964cfa13e9cd81f98e803bb17019127d87c347b90ccb82a70 | Python | 16,727 | 445 | """
Example end-to-end pipelines for running the ``face_rhythm`` package.
Each pipeline accepts a ``params`` dictionary that must contain all fields
required by the steps it executes.
"""
def pipeline_basic(params):
"""
Runs the basic ``face_rhythm`` pipeline, mirroring
``notebooks/interactive_pipeline_ba... |
e9c51639fc1e50be3bfe5c9b5b3e04fbfbd6770d8bac34fbeb686ad01bf711f8 | Python | 16,727 | 355 | import torch.nn as nn
import torch.nn.functional as F
import torch.nn.init as init
from bioseq2seq.models import NMTModel
from bioseq2seq.encoders import TransformerEncoder, CNNEncoder, FourierEncoder, GlobalFilterEncoderLayer,\
LocalFilterEncoderLayer,FNetEncoderLayer,AFNOEncoderLayer
from bioseq2seq.decoders... |
5b11ef6c94c9e65844acc7818fd785e5ec517c9341be2b7481a39938321e5b49 | Python | 16,729 | 456 | #!/usr/bin/env python
# =============================================================================
# MODULE DOCSTRING
# =============================================================================
"""
Affine transformer for autoregressive normalizing flows.
"""
# ===============================================... |
6922f1353b14afdc617060d220ed4a05604338defc743f0e3175f747e5df9f21 | Python | 16,730 | 369 | import argparse, time, logging, os
import mxnet as mx
from mxnet import gluon, nd
from mxnet import autograd as ag
from mxnet.gluon import nn
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.loss import MixSoftmaxCross... |
c4b08d2153c4981c6b4e2f1f0f8f1d5d35971d3faa936905f6bcc40a60ff6b91 | Python | 16,732 | 401 | """Model object, which defines the power spectrum model.
Code Notes
----------
Methods without defined docstrings import docs at runtime, from aliased external functions.
"""
import numpy as np
from specparam.models.base import BaseModel
from specparam.data.data import Data
from specparam.data.conversions import mod... |
22d610a0f260e24fceb8073a50d1c64dea1085d14f65abf43ad71d4b94ee900e | Python | 16,735 | 498 | """Extraction v2 engine rows: the D13 store pipeline end to end (lane F18).
Covers the manifested pipeline order on real (toy-scale) runs: input-derived
row truth (T-ROWCOUNT), pool numerics against manual oracles, dtype routing
with byte-exact bf16/fp8 storage (T-FP8-BF16), the D4 ragged gate
(T-WIDTH / T-DRIFT-PREFI... |
7677c981bc5c9f997f8e1a82eacb2e4498ba55a6c6acccdb96196ec2c24ae193 | Python | 16,735 | 434 | # Benchmark FP8 attention for FA4 (CuTe-DSL) on SM100.
#
# Run (recommended):
# python -m flash_attn.cute.benchmark_flash_attention_fp8
#
# Notes:
# - This is intended to be used while bringing up FP8 support for SM100.
# - FP8 correctness depends on descales + max-offset scaling being implemented in the SM100 kernel... |
39148f6a1eb828e56b2a8f889cc337ce04b91d0a9b9794cb1c59c4fcbc6cb6af | Python | 16,737 | 460 | from __future__ import absolute_import
import csv
import functools
import logging
import os
import sys
import sysconfig
from pip._vendor import pkg_resources
from pip._internal.exceptions import UninstallationError
from pip._internal.locations import bin_py, bin_user
from pip._internal.utils.compat import WINDOWS, c... |
d1343292123f6fe3d8929424ec6f683c7f2a5cfccbdc15f7f93ed36109dd3353 | Python | 16,743 | 454 | """Reachable-surface walk and the 4-way classification (oracles D2/D3).
The enumeration root is what a user can actually reach: every non-underscore
attribute of the ``torchlens`` module (module layer) and every non-underscore
member of every class object reachable there (class layer). ``__all__`` is a
CLAIM gated aga... |
4a8eebd040905a15c63af1f683aa501f9f482cd0c4854ec36dfc8665fb7b6d21 | Python | 16,746 | 382 | #!/usr/bin/env python
# =============================================================================
# MODULE DOCSTRING
# =============================================================================
"""
Test objects and function in the module ``tfep.io.log``.
"""
# ===============================================... |
e51f99688793c7d6a21d9a0df0420c7fe2a89760d90e6ad1cc29532fcc7e73fc | Python | 16,757 | 441 | """Round-45 hon2_1 immunizer -- cross-thread captured-OPERAND consumption ceiling.
r43 closed the DIRECT / owner-derived cross-thread escape rings: a non-owner thread's
tensor->host escape ceilings only when the escaped tensor's OBJECT IDENTITY is captured or
owner-registered. r44 hon2_1 found the WORKER-DERIVED sibli... |
23fa91ad623dc9f832db1dddf470da689be852e67edeb886f2c42b1866e565dc | Python | 16,763 | 453 | """
Unit tests for sensor_scanner module.
This module tests Sensor-specific scanner functionality including
CSV data logging, sensor data retrieval, and remote configuration.
"""
import csv
import json
import os
import tempfile
import time
import urllib.parse
import urllib.request
from unittest.mock import MagicMock,... |
e0352d592930ba0debaf011be40168a6c22c7fab6c9d341516d84468777897b0 | Python | 16,768 | 390 | """
Infers fine-scale recombination maps from data.
Functions:
optimize: Builds and optimizes an objective functon.
Run on the command line with pyrho optimzie -h or --help to see
a list of options and their description.
"""
from __future__ import division
import time
import logging
import sys
from itertools impo... |
c3b8ba7cacc4e37772a2c4032f13871a5789ebf324600ac8b398aa463bd3b42a | Python | 16,774 | 467 | 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
try:
from local_extractor.utils import common_utils
except ImportError:
import sys, os, pathlib
path = pathlib.Path(__file__).absolute(... |
2a65a6d136442c2673b11a0a8973ac55d2c8bc163613ceecc64560f669305bc4 | Python | 16,775 | 418 | '''
Functions related to the extraction of signal from the frames, coded as numpy
slicing and eventual weighting.
Imports
-------
numpy
'''
import numpy as np
def _generate_box_indices(Centers, box_size=(1,3,3), Box=np.array([]),
shape=[None,None,None]):
'''
Generate indices for sl... |
6d67501a2d22b7d7375b7509ff44bb4efa957c7922cdc7be801c672e60c7c4ed | Python | 16,777 | 456 | from functools import lru_cache
from typing import Generator
import numpy as np
import pandas as pd
from mirp._images.generic_image import GenericImage
from mirp._masks.base_mask import BaseMask
from mirp._features.histogram import HistogramDerivedFeature
from mirp.settings.feature_parameters import FeatureExtractio... |
8033d9e3cfd5b7af70abc9e72ec220b537035f219150b02e4c66a670d14b89ab | Python | 16,778 | 374 | """
Traces_extraction.py
Marthe Priouret, priouretmarthe@orange.fr
Script to extract spatio-temporal components of firing neurons from Ca-imaging recordings.
This pipeline is based on Caiman, and requires prior installation of the Caiman environment before running.
See documentation here: https://github.com/flatiro... |
32f59d645cfc43765945ad1c9cd3c287c7739e5465f31074a60a30578ca3d394 | Python | 16,783 | 397 | from typing import List
import numpy as np
from sklearn.metrics import accuracy_score
from sklearn.linear_model import LogisticRegression, RidgeClassifier
import imodels
from sklearn.base import BaseEstimator, ClassifierMixin, RegressorMixin
import imodelsx.augtree.data
import imodelsx.augtree.llm
import imodelsx.augtr... |
12addb8d255c454e0ab9f43b5ffc428d533e135a06a1e3e6c81c13f4f9259f38 | Python | 16,786 | 395 | import locale
locale.setlocale( locale.LC_ALL, 'en_US.UTF-8' )
import re
import json
import pandas as pd
import camelot
import pdfminer
from pdfminer.high_level import extract_pages
try:
from local_extractor.utils import common_utils
from local_extractor.states.state_utils import UK_utils
except ImportError:... |
d6866ae159b7414bb3cc40ead26410cd4d41bf03c134377203d747e771dc125b | Python | 16,802 | 413 | #!/usr/bin/env python3
"""
File: compare_simulated_vs_observed.py
Created: 2023/06/29
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 sourc... |
d01ec0e19b753e37ba1591d2ce6243d26d1f08c152cf33cead4ae6fb3331f3ca | Python | 16,804 | 448 | """Custom fsspec filesystem implementation for Aspera ascp transfers.
This module provides an fsspec-compatible filesystem wrapper around the Aspera ascp
command-line tool for high-speed file transfers. It is designed to be extensible
for future enhancements such as ENA-specific handling, retry logic, and fallback mec... |
979a0c2faaec0afd4d8d7e555f47fd6208440d5a3fec46c889d3cbcb02a98e21 | Python | 16,809 | 464 | import numpy as np
from scipy.stats import zscore, spearmanr
from scipy.optimize import curve_fit
from sklearn.decomposition import PCA
from netneurotools import datasets
import pandas as pd
import seaborn as sns
sns.set_style("ticks")
import matplotlib.pyplot as plt
plt.rcParams['svg.fonttype'] = 'none'
import plot... |
9e504823cb4adf93f43abe3dce7dc82375cabae59147ec1cc3759e92565d65e5 | Python | 16,814 | 465 | """classic Acrobot task"""
from typing import Optional
import numpy as np
from numpy import cos, pi, sin
from gym import core, logger, spaces
from gym.error import DependencyNotInstalled
__copyright__ = "Copyright 2013, RLPy http://acl.mit.edu/RLPy"
__credits__ = [
"Alborz Geramifard",
"Robert H. Klein",
... |
e2221fbcbf0eef679b0616bd6b2bd1cac8eeda275ef81e69a2f7b62f7cb82b86 | Python | 16,820 | 463 | # Copyright 2023 DeepMind Technologies Limited
#
# 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 agree... |
9b8cee22efa64b9293d4717e0349cff3e80df38126024a45d16a79f8f2c6716d | Python | 16,833 | 461 | # -*- coding: utf-8 -*-
"""
Created on Sun Aug 3 15:18:38 2014
@author: Dan Denman and Josh Siegle
Loads .continuous, .events, and .spikes files saved from the Open Ephys GUI
Usage:
import OpenEphys
data = OpenEphys.load(pathToFile) # returns a dict with data, timestamps, etc.
"""
"""
@Modification by Zh... |
9846c866f3211e4acacd6b89c418bc956376f63fa0c75c11abd00d358ad6653d | Python | 16,839 | 449 | import logging
import time
import traceback
import mysql.connector
from .base import BaseAsyncSQLWriter, BaseResultWriter
# Character encoding for MariaDB/MySQL connections
SQL_CHARSET = "latin1"
class AsyncMySQLWriter(BaseAsyncSQLWriter):
"""
Asynchronous MySQL/MariaDB database writer that runs in a separ... |
f0d2c52d815b35d044c2498073993f4ddcaa5e1420e8e2234d432c8093fbdb81 | Python | 16,845 | 416 | """Transforms relate to noising from BART: based on code of fairseq."""
import math
import numpy as np
import torch
from typing import Sequence, Callable
from bioseq2seq.constants import DefaultTokens, SubwordMarker
from bioseq2seq.transforms import register_transform
from .transform import Transform
def _subword_st... |
cd06e7efe130cfcecf9ba5dad2736f110951737b4b1e8927c0c1f1b39f07b969 | Python | 16,851 | 376 | from __future__ import annotations
from collections import defaultdict
from dataclasses import dataclass, field
from typing import Dict, Mapping, Optional, Sequence, Tuple
import numpy as np
import torch
import torch.nn.functional as F
from .config import TrainingConfig
from .data import DomainBatch, DomainTensorDat... |
68436b899385e93eefe56f0528a0953aaed3cc692c440f179859aa485f80071c | Python | 16,853 | 421 | """This script is for preprocessing HMDB51 dataset.
"""
import argparse
import sys
import os
import os.path as osp
import glob
import fnmatch
import random
from pipes import quote
from multiprocessing import Pool, current_process
def dump_frames(vid_item):
from gluoncv.utils.filesystem import try_import_mmcv
... |
9d81761e587796adcd95e5823c4356e2d4463dacdbc32ac2a895966a2feab1a2 | Python | 16,854 | 434 | """Render the user-defined tool authoring help into a Sphinx page.
The content lives in ``client/src/components/Tool/authoringHelp.yml`` so the
tool editor's help panel and this page stay the same text. See that file for
the authoring conventions; this script only reshapes it into MyST markdown.
"""
from __future__ i... |
d0c2bcaa2c7b56b40e6d5479ca18da4776f46da88114a0611c9e67f8ea7074f6 | Python | 16,855 | 480 | # -*- coding: utf-8 -*-
"""
Functionality for connectivity matrix
"""
import os
import numpy as np
import warnings
from scipy.linalg import eigh
from bct import get_components, distance_bin, reference
from conn2res import utils
PROJ_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
DATA_DIR = os.path... |
3f32768eae76a0240fc94a422915d6b4c5edbf3e1ca7adcfe81d71a5d249c102 | Python | 16,863 | 364 | ##########################################################################
## ##
## Copyright (c) 2019-2024 Philipp Lösel. All rights reserved. ##
## ##
## This file is par... |
92e8feed10c1051d16b849b7bbff5e210cb96895981aa63b00be842f5b5b5ecc | Python | 16,863 | 445 | # -*- coding: utf-8 -*-
import tensorflow as tf
## ResNet base model ##
class ResNet(tf.keras.models.Model):
def __init__(self, stacks, version, use_bias, classes, bn_ep=1.001e-5):
super(ResNet, self).__init__()
self.version = version
self.stacks = stacks
# initial layers
... |
ecda71b9c68c58406eab0ade29b683ca1a7f80b2f9587cc6a4a0bdb83b16ab39 | Python | 16,866 | 505 | """
This module is currently primarily intended to be used as a script.
It will print information about the rpy2's environment (Python version,
R version, rpy2 version, etc...).
"""
import argparse
import enum
import locale
import logging
import os
import shlex
import subprocess
import sys
from typing import Optional
... |
65e6e51955d5f5471a77635b5e1c5d81c278f36899483dc01d539ede9b6a613c | Python | 16,872 | 454 | # SPDX-License-Identifier: LGPL-2.1-or-later
#!/usr/bin/env python
#-*- coding: utf-8 -*-
import os
import numpy as np
from .utils import general as utils
def make_header_for_activity(phases, delimiter):
header = 'mouse%s\"time [h]\"' % delimiter
for phase in phases:
header += delimiter + '\"' + phase... |
86cc45d27857beaf447c2f2dacf6d3a80b42e84abcf29325e73fe616268b9a44 | Python | 16,878 | 509 | from plotly import exceptions, optional_imports
import plotly.colors as clrs
from plotly.graph_objs import graph_objs
np = optional_imports.get_module("numpy")
def map_face2color(face, colormap, scale, vmin, vmax):
"""
Normalize facecolor values by vmin/vmax and return rgb-color strings
This function ta... |
07fba5202f2c8bd8275c1583e9b9c09ca23a6937ea54dfd45635d920f90448e1 | Python | 16,879 | 363 | import os
import torch
import numpy as np
import pickle
def get_model_params_2d_segmentation(n_fg_classes=1,
fp32=False):
model_parameters = {}
# we're doing no preprocessing parameters here as they can be loaded
# from the preprocessed folder
# Let's jump straigh... |
2dd58a14583a473e40c5b42d358cfab7205ca722ec763d3bd21715cdc7e7ef79 | Python | 16,881 | 475 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Workflows for post-processing NIfTI-format BOLD data."""
from nipype import logging
from nipype.interfaces import utility as niu
from nipype.pipeline import engine as pe
from niworkflows.engine.workflow... |
12267075575047ade2e8355389a3bba934bfcdedcc972f1105474392008a2a5f | Python | 16,885 | 432 | 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,... |
04ad4c6078a1a23a5abcd0ad4ce0e771e865265e744c8ad27aaea5c2406ce596 | Python | 16,893 | 517 | # Copyright (c) 2022 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... |
1142d822d72a7118103eda0f862c59d6276f2c5d2b334377a8fe9888adc7e2ef | Python | 16,894 | 432 | """S5 escaping test pack (E1-E6): the precondition for any HTML-label ship.
The S5 contract (L5 design memo sec 1.4) requires this pack to land BEFORE any
encoding channel, suppression, or summary-row work ships. Scope: (1) node
labels through the ONE HTML choke point ``render_lines_to_html`` and (2)
graph-proper labe... |
14bd5068af6c3c34268411fd6f573b8ca538395815436d8db879d6d08a40d2e1 | Python | 16,897 | 324 | import torch
import itertools
from util.image_pool import ImagePool
from .base_model import BaseModel
from data import aux_dataset
from . import networks
class AttnCycleGANV2Model(BaseModel):
"""
This class implements the CycleGAN model, for learning image-to-image translation without paired data.
The mo... |
598f2e8781c1156ef2cf21603cd35e090c4e168a0e2b64d04ccae9682270778f | Python | 16,899 | 500 | """eFEL Python API functions.
This module provides the user-facing Python API of eFEL.
The convenience functions defined here call the underlying 'cppcore' library
to hide the lower level API from the user.
Copyright (c) 2015, EPFL/Blue Brain Project
This file is part of eFEL <https://github.com/BlueBrain/eFEL>
... |
2010a21fec85a0193e1895126d02707c64644146800c5b173bd91d830f871bbe | Python | 16,903 | 513 | import math
from functools import partial
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from enum import Enum
seed = 1234
torch.cuda.manual_seed(seed)
#torch.cuda.manual_seed_all(seed)
torch.manual_seed(seed)
np.random.seed(seed)
#torch.manual_seed_all(seed)
class SelfAttention... |
b46ad16f36f96423ed0ed62f1c5d1d73c5fe24dd2faf05b5985fc1f79cffc280 | Python | 16,906 | 510 | """Informational capture-path performance benchmark matrix."""
from __future__ import annotations
import gc
import importlib.util
import math
import os
import resource
import statistics
import tempfile
import time
from collections.abc import Callable, Iterable, Iterator
from dataclasses import dataclass
from pathlib ... |
7b55c063a2f31473bca53e7959cacb72befbbddcf1b378779e637b0ff557052a | Python | 16,922 | 543 | # SOURCE: vendored from claritychallenge/clarity @ baf2b2c99f2e799ba5b0e24d0ad8a9f7ca0370d6
# https://raw.githubusercontent.com/claritychallenge/clarity/main/clarity/enhancer/dnn/mc_conv_tasnet.py
#
# Spatial Conv-TasNet ("mc_conv_tasnet" / multi-channel Conv-TasNet, itself adapted by
# the Clarity Challenge team from ... |
cad3dbba27d7a0da543cb90f96c9e6359865de8ea961a94cb0694fd4b0344b8b | Python | 16,923 | 491 | '''
Created on Dec 21, 2010
Mpl examples:
http://matplotlib.sourceforge.net/examples/user_interfaces/index.html
'''
from logging import getLogger
import tempfile
import numpy as np
from matplotlib.backends.backend_wx import NavigationToolbar2Wx
from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg
from ma... |
10363cd6289bb0d89339fc39ad5684f5f8a1709e9fd464cd6e37c0606e4e4b63 | Python | 16,924 | 584 | #from tkinter import Image
import utils.helper as helper
from albumentations import (RandomCrop, Normalize, Compose)
class ImageProperty(object):
""" Class to store parameters of one WholeSlideImage type to use
Attributes
----------
staining : string
staining to use same as in WSI file name
... |
0f51c0b4b56fcbeaea68f6fc50ac64741ecc7ed8d548f7131b77d41cc272e346 | Python | 16,927 | 502 | from __future__ import annotations
"""Python implementation of features"""
"""
Copyright (c) 2015, Blue Brain Project/EPFL
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source co... |
ae714ad5d7139507639de77e25b9d8e51a377f8caaf6bbe063d83d3e6f684e4d | Python | 16,933 | 472 | ##########################################################################
## ##
## Copyright (c) 2019 Philipp Lösel. All rights reserved. ##
## ##
## This file is par... |
01fc2a878afee892ff24760e498f3a36008cdda59b192ad53ecd935d35d773e1 | Python | 16,937 | 570 | """
Matplotlib interface with the UI. Handles plotting of the traces in the base UI.
SimplyFire - Customizable analysis of electrophysiology data
Copyright (C) 2022 Megumi Mori
This program comes with ABSOLUTELY NO WARRANTY
This program is free software: you can redistribute it and/or modify
it under the term... |
3f955956af5a2c82442d4547accb8149cb623f788c12bc787de26a3901f80b5a | Python | 16,938 | 451 | """Input/output-tree container contract honesty for sparse runnable execution.
Round-5 hardening. The round-4 fix covered opaque *values*, but the input/output
tree contract still mishandled whole classes of container shapes:
* F1 -- non-tensor input leaves under non-``str``/``int`` mapping keys (tuple, bool,
float... |
bd1fd788d1d30871533f0e744d06a03f5c3809f3f1e674c7604731582eba9972 | Python | 16,941 | 405 | """r58 A3a: ``trace(..., cache=True)`` must never unpickle unauthenticated bytes.
The capture cache stored a whole pickled ``Trace`` and read it back with a BARE
``pickle.load`` from a directory named by ``TORCHLENS_CACHE_DIR``. Point that variable
at any path a second principal can write -- a CI cache mount, a contai... |
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