sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
5cf9caee512d427d088139ee9c924065ec298029ac24318f8c6d0c7d34a26f91 | Python | 9,240 | 173 | """The episode declaration dataclass for ``tl.trace(..., episode=...)``.
Split from :mod:`torchlens.options` along the episode option-family seam
(R43 file-size ratchet); the public spelling stays
``tl.options.EpisodeSpec`` (re-exported there). Semantics are pinned by the
ratified S2/S6/S7 contracts; the doc of record... |
ebe3e895f932580c6e28032732b7e0d43ac7273d6e6be4238e9b7d6095a2862d | Python | 9,240 | 260 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created in March 2020
@author: Quentin Lutz <qlutz@enst.fr>
@author: Thomas Bonald <tbonald@enst.fr>
"""
from typing import Optional, Union
import numpy as np
from scipy import sparse
from sknetwork.clustering.louvain import Louvain
from sknetwork.hierarchy.base impo... |
8e617c5a15875d664db47ae1df3bd40f06b3de87839352e10da0f028e3e7c62d | Python | 9,241 | 244 | # -*- coding: utf-8 -*-
# Copyright (c) 2016-2018 Braintech Sp. z o.o. [Ltd.] <http://www.braintech.pl>
# All rights reserved.
"""Mixin for readmanager to create MNE.Raw objects."""
import json
import time
from datetime import datetime, timezone
from typing import Union
from copy import copy, deepcopy
import numpy
i... |
808381c4ff0e6268533e24a34a4344d59a9fbb150fed66bb6d868649c0cddd6a | Python | 9,242 | 317 | """
Base classes shared by the behavioural effector modules.
Defines the effector interface, its stepwise and oscillatory specializations,
and the adapter that lets an effector be driven by a Nengo network.
"""
from __future__ import annotations
from typing import Any
import numpy as np
import param
from ...param i... |
0e0d607d96aa9da850ceb9b148459f3e055a618397fee440955fd6e9b39e03b3 | Python | 9,246 | 214 | import numpy as np
import torch
from models.Estimator import Estimator
from models.Transformer import Transformer
class Distiller:
"""
A class to use for distillation.
"""
def __init__(self, estimator=Estimator, model=Transformer,
model_parameters=None, fit_parameters=None, device='... |
37a6e0675c9975ec4c00f284f124f763f790353c55b0cd18f280a01b64e4a3b4 | Python | 9,247 | 253 | from collections import defaultdict
import torchhd
from torch.utils.data import DataLoader, Dataset
from transformers import AutoTokenizer, AutoModelForCausalLM
from tqdm import tqdm
import torch
from torch.autograd import grad
from dict_hash import sha256
from os.path import join
import transformers
import joblib
impo... |
3df8d7721e0eaa4c564fcaeb690639e5f1b3c7b8b205b077ebe15160dbcc5586 | Python | 9,247 | 299 | import torch
from torch.utils.data import Dataset, DataLoader, RandomSampler, SequentialSampler
import torch.optim as optim
from models.attention_model import Attention_MB
from learning.logger import EarlyStopping, Accuracy_Logger
import os
import numpy as np
class MIL_Dataset(Dataset):
""" Dataset for DataLoad... |
4afbe691ff9f4e22b0f0a37a88fd4e3d9b76532611a55790c5b544472e99cbbc | Python | 9,247 | 203 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
from pathlib import Path
from typing import Any
import torch
from torch.nn import functional as F
from ultralytics.data import YOLOConcatDataset, build_dataloader, build_yolo_dataset
from ultralytics.data.augment ... |
04ea1714b919461e4c4a137f25197f4957032c7fa1e8a753f977199eb28a4e4f | Python | 9,248 | 321 | import json
import pickle
import numpy as np
import pandas as pd
from modular_splicing.utils.construct import construct
from shelved.full_gtex_dataset.pipeline import (
produce_datasets_from_datafile,
)
from modular_splicing.data_pipeline.create_datafile import produce_datafiles
from modular_splicing.gtex_data.a... |
735b9cf4a0aa390f7b79413e5548ab3163929449d776f5d2006813c29ef7a994 | Python | 9,248 | 242 | #!/usr/bin/env python3
# encoding: utf-8
from __future__ import (absolute_import, division,
print_function, unicode_literals)
import os, sys, re
import logging
import argparse
import collections
import numpy
import time
logging.basicConfig(stream=sys.stderr, level=logging.INFO)
logger = loggi... |
a87eb85c085b653219b96c9826d506c565618450c367675f04999074088180c4 | Python | 9,248 | 173 | # Written by Seonwoo Min, Seoul National University (mswzeus@gmail.com)
# PLUS
import os
import sys
import argparse
import torch
import plus.config as config
from plus.data.alphabets import Protein
import plus.data.fluorescence as fluorescence
import plus.data.dataset as dataset
import plus.model.plus_rnn as plus_rn... |
03907c04472f154704f6f511891ff41edb36c2a69f240dae2000ae3abee27d1c | Python | 9,250 | 234 | #################################################################################################################################################################
####################### Training MulitRBP ####################################################################################################################... |
b4c3240b5669f14d5b06327d5568169cc978217b0a771ac788c7f2cfb1f838c4 | Python | 9,250 | 223 | # FIXME: check the rpc-interface.js version and warn if incompatible
# support python 2.7+ and 3
from __future__ import unicode_literals
from IPython.display import display, Javascript, clear_output
from json import dumps as json_encode, loads as json_decode
# the base64 library produces clean output without newlines
... |
e2c9f0125b26a4912a24336007383045924cddd969d284f8eb86318cf189146d | Python | 9,251 | 191 | # -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function
from collections import Counter
from functools import partial
import numpy as np
import tensorflow as tf
from tensorflow.python.ops import gen_audio_ops as contrib_audio
from .config import Config
from .text import text_to_char... |
7d4d6426d53ee4102c5f74420323031253675e2962e1c268609321a4b39d8ec3 | Python | 9,252 | 205 | """
History agent for understanding and answering questions about Galaxy histories.
Provides tools to explore histories, datasets, jobs, and tool usage. Can answer
general questions about history contents, interpret results, generate methods
sections, and summarize analyses.
"""
import logging
from pathlib import Pat... |
c96040cc1f954fa55959c6ea557e853f0b9713aa1650a9af99636b6b005691ea | Python | 9,252 | 301 | """MLX object-module hierarchy tests."""
from __future__ import annotations
from pathlib import Path
import numpy as np
import pytest
pytestmark = pytest.mark.backend_mlx
mlx = pytest.importorskip("mlx")
import mlx.core as mx # noqa: E402
import mlx.nn as nn # noqa: E402
import torchlens as tl # noqa: E402
fro... |
e3bf4146d7c5f1350f2e9d4d48fb28d479079ea174cd618ae7127b297e7b8b23 | Python | 9,252 | 158 | """
Network Initialization
======================
`RectiPy` models are generally initialized via the :code:`rectipy.Network` class. The method `Network.from_yaml` serves
as the main user interface for network model initialization.
It allows the user to define the dynamic equations and default parameters of the units o... |
f5b87e8a0529daa5576d525b00daabb71ca227fd2a1d33a4ef1d63ef400ca291 | Python | 9,252 | 158 | """
Network Initialization
======================
`RectiPy` models are generally initialized via the :code:`rectipy.Network` class. The method `Network.from_yaml` serves
as the main user interface for network model initialization.
It allows the user to define the dynamic equations and default parameters of the units o... |
94588d80adce2b02d207765031a2dfac1f5aa34172515b12ca4461803eb1e73c | Python | 9,256 | 245 | """
Convert online server json to hf3 input/json
"""
import logging
import dataclasses
from typing import Optional, List
import copy
import itertools
from helixfold.common import residue_constants
from infer_scripts.rdkit_utils import SMILESParseError, ConformerGenerationError
from infer_scripts.rdkit_utils import... |
c363e494d0b64de9a327c2ab739ad70a828eea6dc6298a3b9010757a635f33b8 | Python | 9,256 | 216 | from __future__ import absolute_import, division
from tqdm.auto import tqdm
import torch
import torch.nn.functional as F
from trainingUtils import MultipleOptimizer, MultipleScheduler, compute_kernel, compute_mmd
from models import Decoder, SimpleEncoder,LocalDiscriminator,PriorDiscriminator,Classifier,SpeciesCovariate... |
c10e149be634163f414384adac23d1cee00dfaf4ccbef9487f454e8a0833f560 | Python | 9,257 | 251 | from keras.src import backend
from keras.src.api_export import keras_export
from keras.src.optimizers import optimizer
@keras_export(["keras.optimizers.Adafactor"])
class Adafactor(optimizer.Optimizer):
"""Optimizer that implements the Adafactor algorithm.
Adafactor is commonly used in NLP tasks, and has the... |
23687e6b060f133a123c0317802849b23bf33febecc0467c7a7e50e9a64d4295 | Python | 9,259 | 229 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
@author: pramod
- Modify lines 19-27 to point to the locations of the input files and cell type.
- Modify lines 120, 123, 126, 129, 134, 140, 143,146, 147
to point to the dir where the output files are to be written.
"""
import pandas as pd
import networkx as n... |
453be7819ff018bee4c400cb098a74178cb4cc0802e050f29e124168e5525022 | Python | 9,261 | 186 | import pandas as pd
import random
holidaysfile = 'src/random_holidays_EPobjects_list.csv'
def add_ddy_objects(command1 ,command2 ,idf1,ddy_data):
"""
#Add Sizing:DesignDay object from .ddy file to IDF
command1 is a boolean to add the ddy objects or not
if command1 is True and command... |
6881ef0390fb5dac6cb46c444e07f6b4511ff553b0f68c0c76078998c471266a | Python | 9,261 | 299 | import json
import os
from textwrap import dedent
import pytest
from caper.caper_workflow_opts import CaperWorkflowOpts
from caper.cromwell_backend import BACKEND_AWS, BACKEND_GCP
def test_create_file(tmp_path):
"""Test without docker/singularity."""
gcp_zones = ['us-west-1', 'us-west-2']
slurm_partitio... |
a70ba7ccc65066bbadbbfbc3f764898cd8ff45a45f84e03271e0f036db2de132 | Python | 9,261 | 286 | # -*- coding: utf-8 -*-
#
# Asteroid Impact documentation build configuration file, created by
# sphinx-quickstart on Wed Oct 14 19:17:31 2015.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated fil... |
5598e5b3dac85ec2d1b006233130dfb25bb115ea2bee53287e15cff6e7e92729 | Python | 9,262 | 273 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import numpy as np
import tensorflow as tf
import pandas as pd
import argparse
import os
import sys
import pwd
import pdb
import grp
INPUT_PATH = "SimBoost/data/davis_cv_nmlzd.csv"
LOG_DIR = "logs/"
uid = pwd... |
2dcb26265b6398a6f9fdefb2d9c9b199d0e78df3b1c7ddbe0150d9b0f0609bb5 | Python | 9,263 | 231 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# h264_to_mp4.py
#
# Copyright 2020 Giorgio Gilestro <giorgio@gilest.ro>
#
# 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 2 o... |
2151c4e68462e817c9358372485d6d554f7141a92949874a68e472c0fb7cc39b | Python | 9,265 | 223 | """Regression tests for final Trace field ownership."""
from __future__ import annotations
import torch
from torch import nn
import torchlens as tl
from torchlens.constants import MODEL_LOG_FIELD_ORDER
def test_trace_field_set_subset_of_user_facing() -> None:
"""Assert final Trace objects carry no capture-only... |
7a4acbe19022cc34b971bf4e75eea29c43c438c9db4184ff6653ee4c5a52cf89 | Python | 9,265 | 277 | """Functions and utilities for transforming power spectra."""
import numpy as np
from specparam.sim.params import update_sim_ap_params
###################################################################################################
##################################################################################... |
5bd2cf6b67b3d8f3f00287eb87aa0a53f309a7e1ada413d4fb26f439555db4dc | Python | 9,267 | 246 | # -*- coding: utf-8 -*-
from enum import Enum
import numpy as np
class DetectionType(Enum):
EDGES = 1
WHITENESS = 2
class CircleDetector:
"""Contains functions which returns circles found at given positions in a
given pixel array.
"""
# pylint: disable=bad-whitespace
__directions = [
... |
0b9d75752b8b2b2c210215c57790fc2718d2122aebba3f06652a48a98f4c8756 | Python | 9,270 | 192 | # Copyright (c) ByteDance, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
from pprint import pformat
from typing import List
import sys
import torch
import torch.nn as nn
from timm.data import IM... |
7472e42f85094ba71c040f8633c776049530daac065de024abe19f1745776d9e | Python | 9,270 | 233 | """
Train on CIFAR-10 with Mixup
============================
"""
from __future__ import division
import matplotlib
matplotlib.use('Agg')
import argparse, time, logging, random, math
import numpy as np
import mxnet as mx
from mxnet import gluon, nd
from mxnet import autograd as ag
from mxnet.gluon import nn
from ... |
9adddd5ddf2486963ffe1d62e64ae752fb8689e1643c7df97fa05264be53b7a2 | Python | 9,271 | 296 | """Evaluation helper functions."""
import argparse
import json
import os
from typing import List, Optional, Tuple
from scalabel.common.parallel import NPROC
from scalabel.eval.boundary import evaluate_boundary
from scalabel.eval.detect import evaluate_det
from scalabel.eval.ins_seg import evaluate_ins_seg as sc_eval_... |
d4a0fec7b68ebfe09eba29afc1f5ea71e623e8bac9c09f85f9234e5aa914a9a6 | Python | 9,272 | 174 | # Written by Seonwoo Min, Seoul National University (mswzeus@gmail.com)
# PLUS
import os
import sys
import argparse
import torch
import plus.config as config
from plus.data.alphabets import Protein
import plus.data.secstr as secstr
import plus.data.dataset as dataset
import plus.model.plus_rnn as plus_rnn
import plu... |
6f5c8930acf98a7cda146a5c584f5150131c616c6de22f23eb64c886a80749e9 | Python | 9,276 | 260 | '''DNN Feature decoding - decoders test (prediction) script'''
from __future__ import print_function
import glob
from itertools import product
import os
from time import time
import argparse
import bdpy
from bdpy.dataform import Features, load_array, save_array
from bdpy.distcomp import DistComp
from bdpy.ml import... |
685905eb2d10da2aa34e58667cc5c7502dc2c2924211fa65891951655421d75f | Python | 9,277 | 239 | import argparse
import os
import numpy as np
import math
import h5py
import scipy
import torchvision.transforms as transforms
from torchvision.utils import save_image
from torch.utils.data import DataLoader
from torchvision import datasets
from torch.autograd import Variable
import torch.nn as n... |
7670cc675b11b0979035165a1ff246654f2468f900c0a3adec3a01f19f10c572 | Python | 9,278 | 200 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
figio.py — 图的落盘出口：一次调用同时写出位图 PNG 与矢量 PDF
------------------------------------------------------------------
为什么需要：GeroScience 规定「**Figures should be submitted separately** …
only **PDF and TIFF** files will be allowed for publication」。本仓库此前只写
PNG（170–180 dpi），按满栏 174 mm... |
db3ca480e1801bd73e13b910cb0b3cb875bc6fe3d3ceac075e88a04cd0272578 | Python | 9,278 | 263 | """Segment boxes may only group siblings that are adjacent in execution order.
The collapse reference promises that a dashed segment box asserts adjacency: its
members are one consecutive run of siblings joined member to member. A segment
that groups non-adjacent siblings (``b1, b2, b3`` around ``t1, t2``) or hides a
... |
8bfc2e1a61fbc07938ae12facd8bc57d82618af9b5268c379711153fcbdeaa85 | Python | 9,280 | 235 | """
Validation tests for essay_conf.py configurations.
Tests essay configuration validation and error handling.
Focuses on branch coverage for validation logic.
Target: essay_conf.py: 11% → 65% (+200+ lines)
"""
import pytest
from unittest.mock import patch
from larvaworld.lib.reg.stored_confs import essay_conf
@p... |
213e932f3c0f71ea1c792bb727c4b128622770aa2613cc2138e3eb491fd8d894 | Python | 9,281 | 218 | # Copyright 2025 Google.
#
# 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 agreed to in writing, soft... |
2434b1adcd1ed099b7bcbe02afae1f0dd45de50b83acb0d06411ca97ca441a9d | Python | 9,282 | 231 | """Model-input METADATA-PREDICATE witness contract for sparse runnable execution (r27-H2).
These tests lock the honesty rule that a sparse runnable ``run`` may never report
``VERIFIED``/``ATTESTED`` after silently replaying the recorded taken path for a
runtime input that differs on a metadata predicate the captured f... |
6832f55777ad6f45be4483e4416eefba84c9ac8e25c27de93a57555faeffed0e | Python | 9,284 | 249 | """Regression tests for the cert6 (round-6) intervention hardening fixes.
Each test pins a specific silent-corruption / silent-empty-result bug found by the
cert5 inspector that previously lacked coverage:
* BLOCKER-1 -- differentiable-replay shallow fork aliased nested annotation dicts,
so mutating the fork silent... |
f07a4683fe10e574310702a2e5b5fc268ef4b63d78b3652d3a9e0be58b2280ea | Python | 9,288 | 199 | import pandas as pd
from tqdm import tqdm
import torch
from omegaconf import OmegaConf
import os
import sys
script_dir = os.path.dirname(os.path.realpath(__file__))
sys.path.append(os.path.dirname(script_dir))
from datasets import MegaScaleDataset, ddgBenchDataset, FireProtDataset, Mutation
from protein_mpnn_utils imp... |
ffd03ef7db1f82557effc542f8f4ebfc721ac74f0a33328fdd4d1345c21f038d | Python | 9,288 | 178 | #This program is distributed WITHOUT ANY WARRANTY; without even the implied
#warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
#
#
#This file contains a Python version of Carl Rasmussen's Matlab-function
#minimize.m
#
#minimize.m is copyright (C) 1999 - 2006, Carl Edward Rasmussen.
#Python adaptation ... |
105a5c068bdb454aec506e40fcb94e51d187b09f62db09b99fc1f3d4780f841e | Python | 9,289 | 226 | from typing import Optional, Tuple, Union
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch import Tensor
from torch.nn import Parameter
from torch_geometric.nn.conv import MessagePassing
from torch_geometric.nn.dense.linear import Linear
from torch_geometric.typing import Adj, NoneType, Op... |
dbdab09459f33312a9feed5ff09317dc2e783e058619fe91e90bb91d42808610 | Python | 9,289 | 226 | import os
import time
import math
import argparse
import random
import numpy as np
import paddle
import paddle.nn.functional as F
from dataloader import DualDataLoader as Dataloader
from dataset import Molecule2DView, Molecule3DView
from model import GeomMPNN
from utils import split_dataset, rmse
from sklearn.metrics ... |
538a596f5257b669bb1078aa75283b4073dbcd049ec2cda53d3e86d6df26b4c2 | Python | 9,292 | 286 | # Dependencies
import numpy as np
import yaml
import nest
import sys
# Accept and assign variables
scriptpath = sys.argv[1] # Path to Scripts
scriptpath += "/"
Experiment = sys.argv[2] # Experiment defining file
# Load Parameters and unpack
yaml_files = ["network.yaml", "simulation.yaml", Experiment]
for file in y... |
08b64bb2da62ff5e8f9004ab4f3d6561cac3115f1ade07baf60d9e6f4e535f1e | Python | 9,294 | 295 | # SOURCE: vendored from kuielab/mdx-net @ main
# https://github.com/kuielab/mdx-net/blob/main/src/models/mdxnet.py
# https://github.com/kuielab/mdx-net/blob/main/src/models/modules.py
#
# The original AbstractMDXNet/ConvTDFNet classes subclass pytorch_lightning.LightningModule
# purely for training-loop plumbing (train... |
584ecdb203ff1dbd9f4606a3bf1251913bd87fe8b5f3586fbeba68906d1c6ece | Python | 9,294 | 231 | from . import InvertibleModule
import torch
import torch.nn as nn
import numpy as np
def _fast_h(v, stride=2):
"""
Fast product of a series of Householder matrices. This implementation is oriented to the one introducesd in:
https://invertibleworkshop.github.io/accepted_papers/pdfs/10.pdf
This makes us... |
a0388f94f16c46511e2b3cda70a110f330e4b4c48834bad4ebbe08de0f7008ab | Python | 9,294 | 242 | import os
import XML_Parse as parse
import Euclidean_Distance as ed
import pandas as pd
import numpy as np
import plotly.graph_objects as go
import matplotlib.pyplot as plt
#######################################################################################################################
# Data Management and Or... |
0211196c8c5a578fe62c33e58e22d28bf107655339d577b60148982da020f36c | Python | 9,295 | 268 | ######################################################################################
# cell2location tutorial code (to use as template)
# adapted from:
# https://cell2location.readthedocs.io/en/latest/notebooks/cell2location_tutorial.html
###############################################################################... |
0392b4cf6a238d8294ae4622bc50771208101360c2941a633a3cda83b0da9bb9 | Python | 9,298 | 243 | """
Maze generation for the 2D robot simulation.
Builds a randomized maze out of wall segments, used as an obstacle course for
the robot agents.
"""
from __future__ import annotations
from typing import Any, List
import random
from shapely.geometry import LineString
__all__: list[str] = [
"Cell",
"Maze",
]
... |
63c4fd1f74b09d3a709db658c465b59dd4c61ece2ea9339100b8db94d195cce8 | Python | 9,298 | 265 | import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
import argparse
import xlsxwriter
from models import GraphConv, AE, LP
from utils import *
from sklearn.metrics import roc_curve, auc, roc_auc_score, precision_score, recall_score, f1_score, accuracy_score
parser = argparse.Argument... |
15335b846aefd860785063898a74d8057573bdf4b9eeffd6ec8bacb26bbf0ff9 | Python | 9,299 | 219 | # pylint: disable=line-too-long
"""
Utility functions for video action recognition task
"""
import os
import logging
import time
import numpy as np
import torch
from ..utils import AverageMeter, accuracy
logger = logging.getLogger(__name__)
def train_classification(base_iter,
model,
... |
e5bec01075e4e6112bc732db7f4f7bedf320e5f129e9c92505ed0cf3ce16f7d8 | Python | 9,300 | 318 | """Celery error types.
Error Hierarchy
===============
- :exc:`Exception`
- :exc:`celery.exceptions.CeleryError`
- :exc:`~celery.exceptions.ImproperlyConfigured`
- :exc:`~celery.exceptions.SecurityError`
- :exc:`~celery.exceptions.TaskPredicate`
- :exc:`~celery.exceptions.Ignor... |
34e9f19d4f8d0fd95ae66d252048f838936ca357f716f114bd7a36a9a6253364 | Python | 9,301 | 268 | import torch
import numpy as np
import pytorch_lightning as pl
from collections import defaultdict
from torch import nn
from torch.nn import functional as F
from torch_geometric.utils import to_dense_batch
from dimenet import DimeNetPlusPlus
from reporting import get_metrics
def swish(x):
return x * x.sigmoid()... |
2a986ab3c7f2329ba92b012743a808f1d6b2ab3aeb296e555f2c8f7525b40df7 | Python | 9,302 | 267 | """
Code here relates to text parsing and creation of HTML and markdown files
to display the ABF header in a neat and organized way.
"""
import tempfile
import webbrowser
import time
import glob
import os
import datetime
import numpy as np
np.set_printoptions(precision=4, suppress=True, threshold=5)
import pyabf.wave... |
e841e1602266e2b1b56c859b9e48fef935f8ede406934a7993789abcf37128f5 | Python | 9,302 | 186 | # MIT License
# Copyright (c) 2018 Adrian Wolny (https://github.com/wolny/pytorch-3dunet)
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation t... |
4204a19db127d3c62fbeebb74fc8d6a4e7ad164c9c56b804994aec1604bc0de3 | Python | 9,304 | 240 | """
metadata *.txt is CSV with double quotes: "Symbol";"Value";"Unit";
"""
import os.path
import json
ISO_only=True
fasteners_only=True
popup_processed=False # will be set in the first download
download_folder="/home/qxia/Downloads/" # Permission denied
nb_file_per_subcategory = 2
# need to be backup each time, r... |
825eb41ee5a5c67fbd17261fa9438192b9189fce4db328723e3a18d0a247e55c | Python | 9,304 | 273 | import torch as ch
import shutil
import dill
import os
from subprocess import Popen, PIPE
import pandas as pd
from PIL import Image
from . import constants
from robustness.audio_functions import audio_transforms
def has_attr(obj, k):
"""Checks both that obj.k exists and is not equal to None"""
try:
re... |
057416717ebdc37ddd079480d725d199b39355840a514d59502b88606f4bc2c0 | Python | 9,307 | 289 | # --- 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 Line(_BaseTraceHierarchyType):
_parent_path_str = "scatter"
_path_str = "... |
4720c486fb7c523087453ce0aa9dac37e163532d153ceb72fd50609fe9ba45f1 | Python | 9,309 | 292 | #!/usr/bin/env python3
"""
Test script for validating the new backup format functionality.
This script tests the updated backup system with the new nested databases structure.
"""
import json
import os
import sys
import tempfile
from pathlib import Path
# Add the src directory to Python path
sys.path.insert(0, os.pa... |
bccb40827005887f41175bc7b23557da1e203fe915a5488fb3d47bd5ac39376f | Python | 9,310 | 494 | """
Color scales and sequences from the colorbrewer 2 project
Learn more at http://colorbrewer2.org
colorbrewer is made available under an Apache license: http://colorbrewer2.org/export/LICENSE.txt
"""
from ._swatches import _swatches
def swatches(template=None):
return _swatches(__name__, globals(), template)... |
6773fdb5e1855db36d5c420e1fc48c85f15367cecd4c69089cba5af23eafab07 | Python | 9,311 | 259 | #!/usr/bin/env python3
import argparse
import csv
import os
import re
import subprocess
import unicodedata
import zipfile
from glob import glob
from multiprocessing import Pool
import progressbar
import sox
from deepspeech_training.util.downloader import SIMPLE_BAR, maybe_download
from deepspeech_training.util.import... |
c4b409b81ad8adc70d16b1d51b812899de6602ddebc0e6cceac7143e0aafd620 | Python | 9,311 | 223 | import pytest
import torch
from pytest_mock import MockerFixture
from lightly.utils import dependency
if not dependency.timm_vit_available():
# We do not use pytest.importorskip on module level because it makes mypy unhappy.
pytest.skip("TIMM vision transformer is not available", allow_module_level=True)
fro... |
21c2b95516a39263379c936299bad9b759d1c5ac7dd9134ba3765c24ed492978 | Python | 9,314 | 219 | import sys
from sys import argv
from pybedtools import BedTool
if len(argv) != 9:
sys.exit("Usage: python NN_model_prep.py parse-train.tsv cluster-train.tsv gtruth_400-train.bed exclude_region-train.bed "
"parse-test.tsv cluster-test.tsv gtruth_400-test.bed exclude_region-test.bed")
# Obt... |
93063beafc945160f48e7551c709bef2f2c4593bc27b643011260dcbc978281f | Python | 9,315 | 232 | """Functions to refine staining and RNA alignments.
"""
import math
from typing import List, Optional, Union
import cv2
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from anndata import AnnData
from kornia.geometry.transform import thin_plate_spline as tps
from tqdm import tqdm
... |
c1e9f1866d60672b9f8e4e15622f1d8b0dd67627077675f250cfadc2112a1eb5 | Python | 9,316 | 204 | # 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... |
a38d82f67bba832a4ca31de772cb03fc0d4b06008be9133a3e6c384ede395977 | Python | 9,317 | 213 | """6. Reproducing SoTA on Pascal VOC Dataset
=========================================
This is a semantic segmentation tutorial for reproducing state-of-the-art results
on Pascal VOC dataset using Gluon CV toolkit.
Start Training Now
~~~~~~~~~~~~~~~~~~
.. hint::
Feel free to skip the tutorial because the traini... |
ba651229e5741b857aac477b625b923210f7d05bb79eb0b0f39730dd50eec371 | Python | 9,318 | 211 | import pandas as pd
import os
import json
from display import figure_counter
def data_counter(overview_df, session, bids, bids_root, results, verbose=False):
"""
Counts available data and makes a heatmap representation of the availability
:param overview_df: [Pandas DataFrame] Overview dataframe of all s... |
138db9ca606f0fab3d0e86d21e854453dab63fc20720b915c20452c9478d17a3 | Python | 9,319 | 300 | """
Keymap/shortcuts for interactive pygame visualization of simulations.
"""
from __future__ import annotations
from typing import Any, Dict
import json
import string
from ... import CONF_DIR
from ...lib import util
__all__: list[str] = [
"ControlRegistry",
"build_pygame_keys",
"default_controls",
... |
2fce663fda0cd0013365c38de5a1f8c52f57a3161a8c889c8939cb59be4df969 | Python | 9,319 | 212 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
import os
from pathlib import Path
import numpy as np
from PIL import Image
from ultralytics.data.utils import IMG_FORMATS
from ultralytics.utils import LOGGER, TORCH_VERSION
from ultralytics.utils.checks import c... |
51c7ad5a1f4100607b1b712f9156d5e0e0fea124db882fa29c6bf3067d9d2d5b | Python | 9,319 | 257 | #!/usr/bin/env python3
"""
File: plot_vertex_distribution.py
Created: 2021/04/08
Last Changed: 2021/07/07
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... |
bb072d1204de54889bf515a08afd13851f018c7ac8b3f7de16887e358cc439b8 | Python | 9,319 | 229 | """r32-abc Fix A pins: saved-tensors pack/unpack hooks must not corrupt capture.
Round-34 Finding A (MED, pre-existing at e7f036fe): a torch op executed inside a
``torch.autograd.graph.saved_tensors_hooks`` PACK hook fires DURING the producing
user op's dispatch, before that op is logged. Two graph corruptions followe... |
dd8eb58770b406858623bd36d60f2724c6166bd1275b30cad7ab6849cac3c7b8 | Python | 9,319 | 282 | import logging
import signal
import time
from subprocess import PIPE, Popen
from threading import Thread
logger = logging.getLogger(__name__)
interrupted = False
terminated = False
def sigterm_handler(signo, frame):
global terminated
logger.info('Received SIGTERM.')
terminated = True
def sigint_handler... |
163e17cd9c6072de3d747ad1e4d2ca00019c04482e6289e0f8073f3b2e16a42d | Python | 9,320 | 175 | # Written by Seonwoo Min, Seoul National University (mswzeus@gmail.com)
# PLUS
import os
import sys
import argparse
import torch
import plus.config as config
from plus.data.alphabets import Protein
import plus.data.transmembrane as transmembrane
import plus.data.dataset as dataset
import plus.model.plus_rnn as plus_... |
654bffa79e54b21d464903d529a7fbbf2b7a2a3c8e55d879c7703cbca0a7dcd3 | Python | 9,320 | 305 | # LICENSE
#
# _This file is Copyright 2018 by the Image Processing and Analysis Group (BioImage Suite Team). Dept. of Radiology & Biomedical Imaging, Yale School of Medicine._
#
# BioImage Suite Web is licensed under the Apache License, Version 2.0 (the "License");
#
# - you may not use this software except in complian... |
6fb2f948f42f09b8ae2350ed8e412d18221a5b535c8f316c0ca4349cd43a8347 | Python | 9,322 | 189 | """
Creates a null distribution for a model created with a build_network.py file from robust audio.
Works for both image and audio clips, using the dataset and augmentations that are specified in the build_network.py file.
"""
import torch
from robustness.tools.distance_measures import *
from matplotlib import py... |
c170b5baabdaaa615311abd96f882dfe70ccc57080dfb45dee32851d95160bd0 | Python | 9,322 | 275 | #!/usr/bin/env python3
"""
File: plot_ieqtl_barplot2.py
Created: 2022/07/05
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.
""... |
f3d446284d857c47ab7e78780d84467b99bc97a566bdd0f614ead45a2add3671 | Python | 9,323 | 238 | """F26: sink protocol, JSONL artifact, TB duck-writer path, transfer oracle."""
from __future__ import annotations
import json
import pytest
import torch
import torchlens.trackers as trk
from torchlens.trackers._errors import SinkDeliveryError, SinkProtocolError, TrackersError
class _DuckWriter:
"""A dependen... |
1709512dd9a2abe8564e14ea0df8f0b25e8ee73ad70fad6e66d4a0dde8a8bbaa | Python | 9,324 | 189 | #!/usr/bin/env python
# Dan Blankenberg
import sys
import bx.intervals.io
def force_bed_field_count(fields, region_count: int, force_num_columns: int):
if force_num_columns >= 4 and len(fields) < 4:
fields.append(f"region_{region_count}")
if force_num_columns >= 5 and len(fields) < 5:
fields... |
84173c74f6122e147f068f802af343fbfbeb75fc3da1fcbd3240d83c6ac97b30 | Python | 9,324 | 271 | #!/usr/bin/env python
__author__ = "Bjoern Gruening"
__version__ = "0.1"
__date__ = ""
__license__ = "GLP3+"
"""
Housten we have a problem. NCBI does not accept sequences with gaps in it.
Scaffold on the other hands can have large amounts of N-runs in it.
These script, remove all N-runs and creates an add... |
a851805eed7af0fc4527c57660bfeb83759602990a8ef557ddbfec0cade12d21 | Python | 9,324 | 304 | """
Turner modules generating lateral bending.
Provides the turner interface and its alternative implementations, from a
constant or sinusoidal torque to a neural oscillator whose intrinsic dynamics
produce the alternating head casts.
"""
from __future__ import annotations
from typing import Any
import random
impor... |
c0790e24ad06549ae194b3d7da13cc14bdeedba669ee1072acfaf6c3e79bfbaa | Python | 9,324 | 244 | import math
from typing import Optional, Tuple, Union
import numpy as np
import pyvista as pv
from pyvista import MultiBlock, PolyData, UnstructuredGrid
try:
from typing import Literal
except ImportError:
from typing_extensions import Literal
from ...logging import logger_manager as lm
from ..models import c... |
dba7ed101e3dba0569f49511c0e962d5b2379d70fc861450b621790eec008769 | Python | 9,325 | 262 | """Tests that the `env_checker` runs as expects and all errors are possible."""
import re
import warnings
from typing import Tuple, Union
import numpy as np
import pytest
import gym
from gym import spaces
from gym.core import ObsType
from gym.utils.env_checker import (
check_env,
check_reset_options,
chec... |
877d6e25b62fb765d40e94e90c5ea06d2a6066931060e214f8394cdc871f97b1 | Python | 9,326 | 223 | import pandas as pd
from sklearn.metrics import auc, precision_recall_fscore_support,confusion_matrix,matthews_corrcoef, accuracy_score,roc_auc_score,average_precision_score,precision_recall_curve
import sys
import seaborn as sns
import matplotlib.pyplot as plt
from utils import parse_config,build_output_dir,setup_font... |
10f26f07ce93956cb119cf0d44e7dd6b6e554233b72b9126b0e85264aee3fe65 | Python | 9,329 | 162 | # -*- coding: utf-8 -*-
"""
Created on Tue Feb 21 01:42:19 2023
@author: Caterina Brighi
"""
#%% Import functions
import matplotlib.pyplot as plt
import matplotlib as mpl
import SimpleITK as sitk
import numpy as np
import pandas as pd
import datetime
import os
import glob
import gzip
import shutil... |
dff0f9460fc3cc84beb5e019ca9ff4f1ee689374e795237f11aad00236d04171 | Python | 9,330 | 239 | import argparse
import os
import numpy as np
import math
import h5py
import scipy
import torchvision.transforms as transforms
from torchvision.utils import save_image
from torch.utils.data import DataLoader
from torchvision import datasets
from torch.autograd import Variable
import torch.nn as n... |
3ffd39fa130af487e921509bf5f6ec41bf2175fd6487f09f193329636b724eb0 | Python | 9,332 | 233 | import numpy as np
import pandas as pd
import re
import math
import subprocess
import os
import shutil
# ------------------------------------------------------
# -- 3d distance
def distance3d(a, b):
d = math.sqrt(math.pow(a[0] - b[0], 2) + math.pow(a[1] - b[1], 2) + math.pow(a[2] - b[2], 2) * 1.0)
return d
... |
984bad997de13f2e5b594c364471b09df810fe10f9685f2b4193062df950a3a9 | Python | 9,332 | 173 | import numpy as np
from gym import utils
from gym.envs.mujoco import MujocoEnv
from gym.spaces import Box
class InvertedDoublePendulumEnv(MujocoEnv, utils.EzPickle):
"""
### Description
This environment originates from control theory and builds on the cartpole
environment based on the work done by B... |
b774a8fcda3a49e8b58dc921c136564351143045f112cd061095dbeddb414afa | Python | 9,333 | 293 | # SOURCE: vendored from https://github.com/saikatchatt/danse-jrnl @ main
# Vendored files: src/danse.py (DANSE class, dropping training-only methods not part
# of the nn.Module forward graph -- push_model/save_model/train_danse/
# compute_predictions/compute_logprob_batch) and src/rnn.py (RNN_model class). The
# ... |
56261eb8267c8bd11698821ffe206bbf926835d46be66d1ad10db89af8e0a426 | Python | 9,334 | 242 | """Gradient receptive-field oracle tests."""
from __future__ import annotations
from collections.abc import Iterator
import pytest
import torch
from support.rf_isolation import preserved_rf_registry
from torch import nn
import torchlens as tl
from torchlens.receptive_field import _rules
from torchlens.receptive_fie... |
8a7021378f1a097bab85c1bba6d0681dd0c75e4f5dff8e016954a9299ce0878d | Python | 9,334 | 243 | # -*- coding: utf-8 -*-
# Copyright (c) 2016-2018 Braintech Sp. z o.o. [Ltd.] <http://www.braintech.pl>
# All rights reserved.
"""
Module provides single :class 'ReadManager' responsible for reading OpenBCI file format.
Author:
Mateusz Kruszyński <mateusz.kruszynski@gmail.com>
"""
import copy
import os.path
from... |
fce64f0200d9f09c510b0fb7639a08997150957f1565dd05ca705617ed7b123c | Python | 9,334 | 291 | # %% Plot spm glm results
import numpy as np
from nilearn import plotting
import nibabel as nib
import matplotlib.pyplot as plt
import sys
sys.path.insert(0, '..')
from functions.data_helpers import get_computer
# Ensure MNI152NLin2009cAsym template is available
# can be downloaded from https://www.templateflow.org/... |
bb9c9f8a34bd9982ca2dd811928974d16f06864f84b22688a77fdf3f63dc9b95 | Python | 9,335 | 212 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Jan 29 18:04:08 2021
This is the configuration file for Experiment 1, the AI vs learning speed analysis. It different from the main
Experiment 1 configuration file in 2 aspects: it is set to train more (N=100) models, and it uses a different
convergence... |
082c72dabccdc24c58cf011a1bdc5c5d462e0ca7368f54231075cfa1a20d566e | Python | 9,338 | 280 | """Phase 5a tests for consolidated validation."""
from __future__ import annotations
from typing import Any
from unittest import mock
import pytest
import torch
import torchlens as tl
import torchlens.validation.consolidated as consolidated_validation
from torchlens.validation.consolidated import InterventionValida... |
3da5752b3f7206db916f559fdf379983c8964be3472d0e96f4dcfd6f93c549e2 | Python | 9,338 | 264 | # -*- coding: utf-8 -*-
import argparse
import os
import sys
import time
import brainpy as bp
import brainpy.math as bm
import brainpy_datasets as bd
import jax
import jax.numpy as jnp
from jax import lax
bm.set_environment(mode=bm.training_mode, dt=1.)
class ConvLIF(bp.DynamicalSystem):
def __init__(self, n_tim... |
af7fa068dc1998564ca160bfd91728723c7c1201d6444ed75ec388de2f7daf4e | Python | 9,338 | 265 | import os
import torch
import sys
import numpy as np
class Trainer:
r"""Class to train a model.
This contains an internal training loop which takes care of validation and can be
extended with custom functionality using hooks.
Args:
model_path (str): path to the model directory.
model (... |
09f695e6d1fcdd864c4d13bd1a603a3c8b654c11509f9d7b378da724f272f4ff | Python | 9,339 | 295 | import sys
from typing import TYPE_CHECKING
if TYPE_CHECKING:
from ._bar import Bar
from ._barpolar import Barpolar
from ._box import Box
from ._candlestick import Candlestick
from ._carpet import Carpet
from ._choropleth import Choropleth
from ._choroplethmap import Choroplethmap
from ... |
5cd434492aeb924bcfca8cb093428108d5f196f63bfff11d87fc5842dafb263b | Python | 9,341 | 221 | import time
import math
from matplotlib.pyplot import title
import numpy as np
import torch
import os
import torch.nn as nn
import torch.utils.data
import torch.utils.data as Data
import torch.optim as optim
import torch.optim.lr_scheduler as lr_scheduler
import tqdm
from sklearn.manifold import TSNE
from torch.nn.mo... |
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