sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
19d02994c706dfd812118bf730e3075cf9c24368af85036b898ce0df17fc4ce1 | Python | 11,685 | 354 | """Interface layer for pykube library shared between Galaxy and Pulsar."""
import logging
import os
import re
from pathlib import PurePath
try:
from pykube.config import KubeConfig
from pykube.exceptions import (
HTTPError,
ObjectDoesNotExist,
)
from pykube.http import HTTPClient
f... |
f13f9a030c7a7d4be8dd4a1fb337fe604ef107fd700a2d0b3476525073095efb | Python | 11,685 | 242 | import json
import numpy as np
import os, sys
from collections import Counter
from sklearn import preprocessing
from sklearn.metrics import f1_score
from sklearn.metrics import confusion_matrix
import torch
import torch.nn as nn
import torch.nn.utils.rnn as rnn_utils
import torch.nn.functional as F
from torch.utils.dat... |
2fa8c1ed7740216d1af10a705c5d7b65dc37741e42097edfcdaf8fd4670fe4c1 | Python | 11,686 | 335 | import numpy as np
from numpy.testing import (
assert_array_almost_equal,
assert_array_equal,
assert_raises,
)
import pytest
from pyriemann.estimation import (
Covariances,
ERPCovariances,
XdawnCovariances,
CospCovariances,
HankelCovariances,
Coherences,
Shrinkage,
BlockCova... |
d94708e420ece1b8fb3e43a5aaf3eccdea1fcc7a6fc5d654e7ef73a3110385ec | Python | 11,690 | 263 | #!/usr/bin/env python
# =============================================================================
# MODULE DOCSTRING
# =============================================================================
"""
Transformation that constrains the (weighted) centroid of the DOFs.
"""
# ====================================... |
6170dcee425d74e2b536b4eacc61be86b9bd6d363320d5d5d09b396fe1f1092d | Python | 11,691 | 371 | import os
import json
import morphio
import numpy as np
from numpy.testing import assert_equal
from numpy.testing import assert_raises
from numpy.testing import assert_allclose
from numpy.testing import assert_array_equal
from numpy.testing import assert_almost_equal
from tns.utils import TNSError
from tns.generate.so... |
470c9a961968606e19fd6e3439c82931261b07124477594e5eb772eb0b596110 | Python | 11,692 | 202 | import glob
import json
import os
import socket
import sys
import argparse
from functools import partial
from multiprocessing import cpu_count
import numpy as np
from mne.datasets import fetch_fsaverage
from tqdm import tqdm
from tqdm.contrib.concurrent import process_map
from mp_dip.obci_readmanager.signal_processi... |
fc098d728f894afb1a135654dff9394430573476045b880ba00838becc972aad | Python | 11,693 | 412 | '''
File: draw_curve copy.py
Project: error_analysis
Created Date: 2023-10-04 15:24:24
Author: chenkaixu
-----
Comment:
This script used to analysis the experiment results, especially for the the error classification.
Across 5 fold cross validation and then print the metrics.
Meanwhile can print the CM.
Have a good c... |
1c61dd74df29f3ce9e2aae623a1724981f014f1a8060aa22a97851f581ed62f9 | Python | 11,694 | 309 | from conftest import get_metrics
import pytest
import numpy as np
from numpy.testing import assert_array_equal
from pyriemann.spatialfilters import Xdawn, CSP, SPoC, BilinearFilter, AJDC
@pytest.mark.parametrize("spfilt", [Xdawn, CSP, SPoC, BilinearFilter, AJDC])
@pytest.mark.parametrize("n_channels", [3, 5, 7])
@py... |
634eb781987f21b5cfb2a901bd31f93cb2e5d55f59efd839570c50de87252dba | Python | 11,695 | 333 | '''
The code here is modified from https://github.com/charlesq34/pointnet under MIT License
'''
if __name__ == '__main__' and __package__ is None:
from os import sys
sys.path.append('../')
import torch
import torch.nn as nn
import torch.nn.parallel
import torch.utils.data
from torch.autograd import Variable
i... |
d109d033d7dcb1abc6722f68f830f7f974d9dfdd1a320b429c2191c1a35b339c | Python | 11,696 | 313 | """RG vision scenarios on real ResNet-18 weights (testing memo 5.2; F36 E2).
RG01 trace, RG10 extraction, RG11 RDM/CKA, RG12 runnable roundtrip, RG13
render floors, RG16 training step, RG20 receptive fields -- each with an
INDEPENDENT oracle (assertion-ladder rung 1), on the pinned
``r1-resnet18-imagenet1k-v1`` regist... |
5e1caf80cf6061c84b053aa203c99799b3e97e49956794c6c35a0718743760a7 | Python | 11,698 | 223 | import argparse
import csv
import datetime
import logging
import os
import SimpleITK as sitk
import pytorch_lightning as pl
import torch
import torch.utils.data
from pytorch_lightning.loggers import TensorBoardLogger
from datasets import get_dataset
from models import get_model
from strategies import get_strategy
fro... |
37cbb7691860efe781f637ebf7190a05e78688c32cf4038812aea318dd1ca634 | Python | 11,700 | 251 | # Based on: https://medium.com/analytics-vidhya/implementing-srresnet-srgan-super-resolution-with-tensorflow-89900d2ec9b2
# Paper: https://arxiv.org/pdf/1609.04802.pdf (SRGAN)
# Pytorch Impl: https://github.com/Lornatang/SRGAN-PyTorch/blob/main/model.py
import os
import tensorflow as tf
import keras
import model_build... |
4d54530bbf919a41d831d8b2d77cd49d965bbf3305f0e08e0db17d5665f75dc9 | Python | 11,700 | 322 | """Import and construction tripwires for runnable contract scaffolding."""
from __future__ import annotations
import inspect
from dataclasses import fields
import pytest
from torchlens.errors import ReattachError, RunnableTLSPECError, StateBindingError
from torchlens.runnable import (
CANONICAL_INITIALIZER_BY_R... |
2080fd6ce43b39d4e721378b09460bb4dc84cde322edc6b3cda47fd175e71d87 | Python | 11,704 | 297 | """Prefork execution pool.
Pool implementation using :mod:`multiprocessing`.
"""
import os
import threading
import time
from billiard import forking_enable, get_start_method, set_start_method
from billiard.common import REMAP_SIGTERM, TERM_SIGNAME
from billiard.pool import CLOSE, RUN
from billiard.pool import Pool as... |
55658e9fc7d6c9e6de6d55386afd6c94ac08edc41dcba4f6129537f3408504ce | Python | 11,704 | 338 | import warnings
from pathlib import Path
from typing import List, Literal, Optional, Union, cast
import pandera.polars as pa
import polars as pl
import xarray as xr
import zarr
from pybedtools import BedTool
from seqdata._io.utils import _df_to_xr_zarr
from seqdata.types import PathType
BED_COLS = [
"chrom",
... |
f630bfb83c51d6b371b20ecc9de6eb6baeaaaa1640be5c78544579fffe160a36 | Python | 11,704 | 319 | """Golden tests for the receptive-field geometric engine."""
from __future__ import annotations
from collections.abc import Iterator
from fractions import Fraction
import pytest
import torch
from support.rf_isolation import preserved_rf_registry
from torch import nn
import torchlens as tl
from torchlens._io import ... |
237c73539c49f06da94c5d5e4fb93bec4464aa8e47dea515b99a153724332183 | Python | 11,708 | 336 | # 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.
import datetime
import functools
import os
import subprocess
import sys
import time
from collections import defaultdict, d... |
23cc6f49fdbd729eda603e8764c7d0e043af5e39878acf33dca0bedced5232ba | Python | 11,711 | 347 | import json
from typing import List, Tuple, Dict
from datetime import timedelta, datetime
from scipy.sparse import csr_matrix, coo_matrix, hstack
import pandas as pd
import numpy as np
import sparse
from sklearn.model_selection import train_test_split
from omop_learn.data.common import ConceptTokenizer
from omop_lear... |
478c67b321e51bb15c4522667d1fa25e13f51214e2fc562b711a23aba2910ec7 | Python | 11,711 | 305 | # SOURCE: vendored from Audio-WestlakeU/RVAE-EM @ 3398d13ca903
# https://raw.githubusercontent.com/Audio-WestlakeU/RVAE-EM/3398d13ca903/model/RVAE.py
# https://raw.githubusercontent.com/Audio-WestlakeU/RVAE-EM/3398d13ca903/model/module.py
#
# RVAE-EM (Pengyu Wang et al., "RVAE-EM: Generative Speech Dereverberation Base... |
8dcf147dd6e3a540b90e989de5ccfc7abebc0a8137fb4e58eb9b4cd9d8141e2e | Python | 11,711 | 313 | import numpy as np
from utils import Recorder, Q_nak
from mitochondria import Mito
from steady_state import get_steady_state
from lifcell import LIFCell
from gates import ros_inf, get_ros
import figure_properties as fp
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
from matplotlib.collections ... |
9f8e156fbaac27b7acda3c1b09359b3b365357daf02649cc2443eb230fc72cd4 | Python | 11,711 | 351 | # 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... |
118801a84b122373bf5f509ee38686422e02f8637a9fe4fee41438c1017f88d1 | Python | 11,712 | 316 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torchvision import models
try:
from torchvision.models.utils import load_state_dict_from_url
except ImportError:
from torch.utils.model_zoo import load_url as load_state_dict_from_url
# Inception weights ported to Pytorch from
# http://do... |
9c129fe9da6d4361d9d1008e5a6c26d28a24c9502a293a2d45a9c9c04d6b93e3 | Python | 11,713 | 299 | """SM100 backward with the query heads of a KV head packed into the Q tile
(FLASH_ATTENTION_BWD_PACK_GQA=1) against the per-head path (FLASH_ATTENTION_BWD_PACK_GQA=0) and
against FP64 eager.
See NOTE [bwd pack_gqa] in pack_gqa.py: one tile per KV head iterates over the packed
rows of all its query heads, dK / dV stay ... |
6d6717493030517f20d00b2a563a8b108fa67af45852cdd40e9b6429f62cdf1c | Python | 11,716 | 364 | #
# Galaxy documentation build configuration file, created by
# sphinx-quickstart on Tue Mar 6 10:44:44 2012.
#
# 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 file.
#
# All configuration values hav... |
b1a254963fb9a5c0db5b8c8f7bdb94d40fde10dbadff35c1a1bdf3c9a6629016 | Python | 11,716 | 275 | import warnings
import numpy as np
import pandas as pd
from typing import Any
from mirp._data_import.dicom_file import ImageDicomFile
from mirp._data_import.generic_file import MaskFile
from mirp._data_import.generic_file_stack import ImageFileStack, MaskFileStack
from mirp._data_import.utilities import get_pydicom_me... |
2b02ef2c7abf60d563ce1c9ec1576130b133028f99c9203948b2a1ab941b0c3b | Python | 11,720 | 283 | import torch
from icecream import ic
import random
import numpy as np
from kinematics import get_init_xyz
import torch.nn as nn
from util_module import ComputeAllAtomCoords
from util import *
from inpainting_util import MSAFeaturize_fixbb, TemplFeaturizeFixbb, lddt_unbin
from kinematics import xyz_to_t2d
def mask_in... |
57f3772cbd2e3becd4ecdb23c9f956653a9c0f3ee528d0303d14114c2765d69e | Python | 11,721 | 286 | import os
import math
import logging
import numpy as np
import scipy
from scipy.signal import fftconvolve
from .TqdmLoggingHandler import TqdmLoggingHandler
logger = logging.getLogger(__name__)
logger.setLevel(logging.WARN)
logger.addHandler(TqdmLoggingHandler())
# We thank Eli Horn for providing this code, used wit... |
17d0eee2a1d3e5fdbc31947a6faaf4a4ffd1caa3608f54e6be3031685776b10f | Python | 11,727 | 304 | """r55 CLASS 3 immunizer -- the op-execution allocation-bomb seam r53 free_1 missed.
r54 ``free_1`` (HIGH): a taken-path op whose output size is a literal integer
(``torch.arange(n)``/``zeros(n)``/...) let an attacker edit one plaintext
``manifest.json`` integer to drive an ~8 TB allocation on the default
``tl.load(pa... |
7ae56b43c097140e41d7362cce6816e3a36ff248a844b7663be1b732d630b3ec | Python | 11,729 | 280 | import sys
from random import choice, randint
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from scipy import signal
from scipy.stats import truncnorm
def plot_df_acf(df, cat1, name):
# from statsmodels.graphics.tsaplots import plot_acf
# from scipy import signal
df = np.array(df)
u1 = s... |
beee7a01ee8e463fd933fdc3533f6e5dbd62548ce6d0119837cc902f8ac05bf1 | Python | 11,729 | 373 | import pytest
from pyrosm import get_data
@pytest.fixture
def test_pbf():
pbf_path = get_data("test_pbf")
return pbf_path
@pytest.fixture
def helsinki_pbf():
pbf_path = get_data("helsinki_pbf")
return pbf_path
@pytest.fixture
def test_output_dir():
import os, tempfile
return os.path.join(t... |
402979172d38e4be2766e395403daa4223258b08f270f885b6d8bd0666b95701 | Python | 11,730 | 307 | import sys
try:
import dash
import dash_bootstrap_components as dbc
except ImportError:
print(
"\n❌ Error: Carbonboard requires additional dependencies that are not installed.\n"
"\nTo install them, run:\n"
" pip install codecarbon[carbonboard]\n"
"\nOr if using uv:\n"
... |
459c33c3153979314a0d236c8cf192e2f076b34a21b7fc133e574220739f5b08 | Python | 11,732 | 257 | #!/usr/bin/env python3
'''
This script will generate the lines for a new types file with the iterative poses generated from counterexample_generation_jobs.py
!!WARNING!!
Part of this process is to determine which newly generated poses are NOT REDUNDANT with the previously generated ones.
This requires an O(n^2) calcu... |
6b74d82ecad8119e407c04eb7a0e0f7dbb530582411c7728cfe6d4970f8915e5 | Python | 11,734 | 289 | """MS COCO object detection dataset."""
from __future__ import absolute_import
from __future__ import division
import os
import numpy as np
from PIL import Image
import mxnet as mx
from .utils import try_import_pycocotools
from ..base import VisionDataset
from ...utils import try_import_dali
from ...utils.bbox impor... |
0758e8f1ad6ad94fbfe69526639bd951ee41fb03df631feb8d328d35a95140fd | Python | 11,735 | 359 | import numpy as np
from keras.src.backend.common import dtypes
from keras.src.backend.common import standardize_dtype
from keras.src.backend.jax.ops.math import fft as jax_fft
from keras.src.backend.jax.ops.math import fft2 as jax_fft2
from keras.src.backend.numpy.ops.core import convert_to_tensor
from keras.src.utils... |
5caed0e92376060e3c5ae9493e9e7b41cbaa165fb2e69062a1562032da5c9b3b | Python | 11,744 | 262 | """Functions for simulating power spectra."""
import numpy as np
from specparam.utils.checks import check_iter
from specparam.sim.params import collect_sim_params
from specparam.sim.gen import gen_freqs, gen_power_vals, gen_rotated_power_vals
from specparam.sim.transform import compute_rotation_offset
from specparam.... |
95547a20a24e732034e85370a2e9207d0d4c9313333b38462efd424dc4ca9258 | Python | 11,744 | 289 | import numpy as np
import torch
from torch import nn
import networkx as nx
from typing import *
from functools import partial
def circDist1Sq(phi: torch.Tensor, psi: torch.Tensor):
return (torch.pi - (torch.pi - (phi - psi).abs()).abs()).square().sum(dim=-1)
def entropyLogAm(x: torch.Tensor, m: int):
return m... |
21f67cdb3960a222cb358b41240a4d4e6df3d392525b5a407fc261642f4a7a94 | Python | 11,745 | 241 | import numpy as np
from brian2.only import *
import deepdish as dd
from readout import load_results
from digest import conds
import spatial
out_fname = 'distance.h5'
def get_bspikes(res, episode):
b = np.zeros(np.asarray(res['raw_dynamics']['v'].shape)[[0,2,3]], bool)
for itrial, (i, spike_t) in enumerate(z... |
f1c4c0bce8bc6e2320a8dace00f932004957b165f4e2f198b1a6fd14fc0e9da2 | Python | 11,745 | 354 | """
Utility functions for COOT model
"""
import ctypes
import datetime
import logging
import multiprocessing as mp
import os
from pathlib import Path
import random
import sys
from typing import Tuple, Dict
import numpy as np
import torch
import torch.backends.cudnn as cudnn
from torch import cuda
import torch.nn.funct... |
16ca1c350bebfddcb3c4e7123bb55213fbcf1b04a6cfc58e98bc24b0e239d747 | Python | 11,747 | 336 | #!/usr/bin/env python
#
# device_listener.py
#
# Copyright 2022 Giorgio F. Gilestro <gg@jenner>
#
# 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 of the License, or
# (at ... |
a8c2442bb735eb1246505fc591f7db629fa3e406a57cc2a34d22cec90b64ad0c | Python | 11,748 | 327 | import json
import pathlib
import warnings
import errno
import numpy as np
from .structure import StructureComposite, StructureCompositeStack
from .data import DataSource
from .formats import get_signature
from .util import equal_states
from ._version import version
class ImposeDataFileNotFoundError(FileNotFoundErr... |
b28d09cb2ee13aacc5ad3be26688685373719a511ff1c4efeac006093d892834 | Python | 11,748 | 326 | """
Tabular data prediction using TabPFN
"""
import argparse
import time
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from sklearn.metrics import (
accuracy_score,
average_precision_score,
balanced_accuracy_score,
f1_score,
precision_recall_curve,
r2_score,
root_m... |
be236fe0a2c6ad005983656d6505b80d179a9e09d8efc8bf1b606de2745e0ebd | Python | 11,754 | 402 | """
Functions to shuffle timestamps to create surrogate datasets.
"""
import warnings
import numpy as np
from .. import core as nap
def shift_timestamps(data, min_shift=0.0, max_shift=None, mode="drop"):
"""
Shifts all the time stamps of a random amount between a minimum and maximum shift, wrapping the
... |
012737afc49e6e4401f6d00fda49934998c9e191c5cc0670fc4d3010fca2502c | Python | 11,756 | 374 |
import os
def to_head( projectpath ):
pathlayers = os.path.join( projectpath, 'layers/' ).replace('\\', '/')
return r"""
\documentclass[border=8pt, multi, tikz]{standalone}
\usepackage{import}
\usepackage{bm}
\usepackage{transparent}
\subimport{"""+ pathlayers + r"""}{init}
\usetikzlibrary{positioning}
\useti... |
c061946c218cf2fcb202dd0fe98a40a41fff0b3315dde0b8591b8897bc701555 | Python | 11,757 | 299 | """A-BUNDLE-OUTCOME proofs: Bundle declares outcome authority (foldB D9 + D8).
Bundle is the THIRD instance of the "two answers for one product"
outcome-authority disease (PartialTrace: ``_OUTCOME_DELEGATE_FIELD``;
Recording: ``_OUTCOME_SELF_AUTHORITY``): ``outcome_for(bundle)`` returned
``None`` while every member wa... |
6fd182c9acb781df16abe6760a7e9a667dc419febdbe87f626ab9087877a7c88 | Python | 11,759 | 336 | # 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... |
a0cfa842df9fa9cf864e497b6ef791d67437e1962a565f772e568b6124b047dc | Python | 11,763 | 233 | 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... |
2442c364bf3c39e4898612debf7294b0660cbd36b57c63e9d61acdbb228907af | Python | 11,764 | 320 | from keras.src.api_export import keras_export
from keras.src.quantizers import strategy_registry
from keras.src.saving import serialization_lib
@keras_export("keras.quantizers.QuantizationConfig")
class QuantizationConfig:
"""Base class for quantization configs.
Subclasses must implement the `mode` property ... |
6e6deabf24ea50b8c41f2fcbfea1241b68771e8e25673c4eae807de8be7573b3 | Python | 11,767 | 252 | import numpy as np
import logging
from cuteSV.cuteSV_genotype import overlap_cover, assign_gt
import pickle
def resolution_INV(path, chr, svtype, read_count, max_cluster_bias, sv_size,
bam_path, action, MaxSize, gt_round, sigs_index):
'''
cluster INV
***************************************************... |
08aceb5f06f9873eede502f1bdeffba40f6a61c3b4cd7081386715f03e777c8f | Python | 11,770 | 325 | from sklearn.metrics import roc_curve, auc, roc_auc_score, brier_score_loss, precision_recall_curve, f1_score, precision_score, recall_score
from math import sqrt
from collections import OrderedDict
from imblearn.over_sampling import RandomOverSampler, SMOTE, BorderlineSMOTE, SVMSMOTE, ADASYN
from imblearn.under_... |
cf10dc526c4700652dba00762e7b5686e975dee96935e9ad8fb0b572936fdc2c | Python | 11,774 | 302 | import html
import json
import posixpath
import re
import tarfile
from contextlib import contextmanager
from typing import (
Annotated,
)
from pydantic import Field
from galaxy.exceptions import (
MessageException,
ObjectNotFound,
)
from galaxy.files.models import (
AnyRemoteEntry,
BaseFileSourceC... |
9e6e07dc69842a99c4cbd420b917ce4832765e0483dccf12215be577078ebaf1 | Python | 11,775 | 295 | import sys,re,os
import subprocess
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio import AlignIO
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
from utils import getLongestORF,parse_config, setup_fonts, build_output_dir,palette_by... |
94abc110082e456019d06656011b6385b2a8f9011d75d71ae09a2b3dd1f37765 | Python | 11,776 | 338 | '''
load the RBNS data
'''
import csv
import re
import h5py
import urllib3
import urllib
import gzip
from io import StringIO
import requests
import numpy as np
import time
from utils_rbns import create_datapoints
rbns_data = 'metadata_rbns.csv'
encode_dir = 'encode/'
data_dir = 'data_large/' # 'data/'
protein_idx_ma... |
96344869dcd59b9dddf66b4c9a6ddc0428d55b10b90920e822c743f3e21e81d7 | Python | 11,776 | 325 | # -*- coding: utf-8 -*-
"""
Transformerに必要な基本的なlayer群を記載
tf2.1.0で動作させることを想定して実装
"""
import tensorflow as tf
import numpy as np
from tensorflow.python.keras import constraints
from tensorflow.python.keras import initializers
from tensorflow.python.keras import regularizers
## padding_mask ##
def create_padding_mask... |
648dac10616530371ba15292c831871cd6a6867064d50dc2084aa7e4c61ae411 | Python | 11,777 | 326 | from typing import Any
import numpy as np
import pandas as pd
import copy
from warnings import warn
from mirp._images.generic_image import GenericImage
from mirp._imagefilters.utilities import FilterSet2D, FilterSet3D
from mirp._images.transformed_image import TransformedImage
from mirp.settings.generic import Setti... |
be534b9bcf3caae0e70061975bfdf5149b70e020930579bec450d386709a3404 | Python | 11,777 | 359 | import pysam
import os
import re
import copy
import gzip
from TestUtils import load_and_convert, make_data_files, TABIX_DATADIR
def setUpModule():
make_data_files(TABIX_DATADIR)
class TestBED:
filename = os.path.join(TABIX_DATADIR, "fivecolumns.bed.gz")
def setup_method(self):
self.tabix = pys... |
d88206bf430c05f2339f7decd8c88cbaf6af01f87b6cb09f1741e5d90eb89aff | Python | 11,777 | 226 | import argparse
import os
# os.environ["CUDA_DEVICE_ORDER"] = "PCI_BUS_ID"
# os.environ["CUDA_VISIBLE_DEVICES"] = "0" # specify which GPU(s) to be used
import time
import numpy as np
import torch
from torch.utils.data import DataLoader
from external_src.group_free_3D.models import parse_predictions
from external_src... |
802fc7439427951e78edc9f72fb264e544f4ccf14f23086482ce50c9a8bf041e | Python | 11,779 | 326 | """Functions for shuffling data."""
from functools import wraps
import numpy as np
from spiketools.measures.spikes import compute_isis, compute_firing_rate
from spiketools.measures.conversions import (convert_times_to_train, convert_isis_to_times,
convert_train_to_times)
... |
8fc91d732b9b8c1704e482aa51be92374f2751fc143196d55e50978642aec962 | Python | 11,784 | 287 | #!/usr/bin/env python3
"""
File: prepare_bios_eqtl_file.py
Created: 2021/11/11
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.... |
67292ab67456992d634b23d26b88ecd786d7926a55d1dabf5d8f11ec14330d90 | Python | 11,786 | 326 | """Functions to analyze and investigate model fit results - periodic components."""
import numpy as np
###################################################################################################
###################################################################################################
def get_band_p... |
b74cfa9193180149dd78f8e0dfb09fdd9b58350e94eb3ef6cb440619fbfe3796 | Python | 11,786 | 253 | from pyabf.abfReader import AbfReader
import datetime
import os # TODO: replace with pathutil
class HeaderV1(AbfReader):
"""
The first several bytes of an ABF1 file contain variables
located at specific byte positions from the start of the file.
All ABF1 header values are read in this single block.
... |
39c7be02d516a7a22dd864748fb27da0b13072acc40b89ce45e7e5d225426522 | Python | 11,790 | 525 | """Static Paddle wrapper inventory snapshot tests."""
from __future__ import annotations
from collections.abc import Iterator
from contextlib import contextmanager
import pytest
from torchlens.backends.paddle import wrappers as paddle_wrappers
from torchlens.backends.paddle.wrappers import PaddleInventory, _PaddleW... |
a6a1213f0da1328a94cfde9dec98d376aee779872ff44a4d3bd491958e0ff30b | Python | 11,790 | 307 | """IO functions for NanoString CosMx technology.
"""
import glob
import os
import re
import warnings
from typing import List, NamedTuple, Optional, Union
import numpy as np
import pandas as pd
with warnings.catch_warnings():
warnings.simplefilter("ignore")
import skimage.io
from anndata import AnnData
from s... |
04ee8006e77e685a7f5aa558e7935de42442546b3be36a15c034e41554f992ca | Python | 11,791 | 351 | """
Load, save, delete and reset actions for a stored configuration.
Provides the bare registry-CRUD buttons, meant to pair with a caller-supplied
selector rather than carrying a catalog of their own.
"""
from __future__ import annotations
from collections.abc import Callable
from typing import Any
import panel as ... |
160a8219ea30462e7da441c7f87c4b1552712561ca25c36f0d4d05eeff02f22a | Python | 11,797 | 302 | from keras.src import backend
from keras.src import ops
from keras.src.backend.common import get_keras_mask
from keras.src.backend.common import set_keras_mask
from keras.src.backend.common.keras_tensor import KerasTensor
from keras.src.layers.layer import Layer
class Merge(Layer):
"""Generic merge layer for elem... |
3bdbe78f8f50c3585166ee78de227e74631071f43dcb9d6b9256f595ec1fff3d | Python | 11,799 | 245 | """
This code contains additional analysis suggested by reviewers.
"""
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.s... |
7cedf36f547a056dff60dc40d843987bd9669eda6cb84075db801e2d55546d73 | Python | 11,805 | 325 | #!/usr/bin/env python3
"""
File: create_upsetplot2.py
Created: 2023/07/20
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.
"""
... |
c6a7fb94a5827962961eae3e418de093e9d6b7410d0165f8ee4ba0c4660c8e65 | Python | 11,805 | 300 | import ssm
import ssm.extensions.mp_srslds.emissions_ext as mp_emission
import ssm.extensions.mp_srslds.transitions_ext_2 as mp_transition
import ssm.init_state_distns as isd
import scipy.io
from matplotlib import pyplot as plt
import numpy as np
import autograd.numpy.random as npr
import seaborn as sns
from ssm.plots ... |
ca9f3b55518998b7f089b0a7ba2515bbe4bf3414f990680233c7b3e5e64ee101 | Python | 11,810 | 296 | """
Topographical Analyses with MNE
===============================
Parameterizing neural power spectra with MNE, doing a topographical analysis.
This tutorial requires that you have `MNE <https://mne.tools/>`_
installed. This tutorial needs mne >= 1.2.
If you don't already have MNE, you can follow instructions to g... |
2910bac2ad8e7dbf15e22276b6132e8f25432b2e7fbf753ceda45d2e6694f664 | Python | 11,817 | 261 | from __future__ import division
import argparse, time, logging, os, math
from tqdm import tqdm
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 mxnet.gluon.data.vision import transforms
import gluoncv as gcv
gcv.utils.check_version('0.... |
fbae76cc2b555ca8ac1cb6e9118279d283750a8ece84d81e57a659073ff8f58a | Python | 11,817 | 316 | """
Multi-stimulator system for sequential stimulator activation.
Allows multiple stimulators with individual date/time ranges within a single experiment.
"""
__author__ = "giorgio"
import logging
from ethoscope.hardware.interfaces.interfaces import DefaultInterface
from ethoscope.stimulators.stimulators import Base... |
01b386bd5cdb378402a1ed1471358fa363aca8cc0a3e046ccf37d3a3871fc23c | Python | 11,819 | 321 | """Implementation of EM algorithm to identify parameter estimates for a
Negative Binomial mixture model.
https://iopscience.iop.org/article/10.1088/1742-6596/1324/1/012093/meta
Written by @HailinPan, optimized by @Lioscro.
"""
from functools import partial
from typing import Dict, Optional, Tuple, Union
import numpy... |
4b4349d5dc42ea49f353be132c8ff9026c3c8deed5535123968d8f252a95265e | Python | 11,819 | 263 | #!/usr/bin/env python3
"""
Dx BN — Training-pool-derived τ + out-of-sample Platt scaling
==============================================================
Reviewer item: τ in §3.1 was selected on the held-out figshare ROC,
making sens/spec/PPV in-sample-optimized. Re-derive max-BA τ from
training-pool LOCO scores (proper... |
13f6a1a634e4b574eeca3e57c913579a669388da8bd4d75d5bd59b3dd63a991b | Python | 11,820 | 287 | import os
import pickle
import matplotlib.pyplot as plt
import tensorflow as tf
import tensorflow.keras.backend as K
from sklearn.metrics import confusion_matrix
from tensorflow.keras import Input, layers, models, optimizers, callbacks
from tensorflow.keras.layers import Layer
def create_input_layers(xshapes):
i... |
5a99392b497013c9901d5fb2dbba6e9304903a149ab2fddd7559fba1de4099c4 | Python | 11,822 | 359 | """Key-value store."""
from typing import List, Tuple, Union, Optional
import os
import sqlite3
from pathlib import Path
import numpy as np
_array_t = np.ndarray
_path_t = Union[str, Path]
class BaseKeyValueStore(object):
"""Base class for key-value store."""
def get(self, **kwargs) -> _array_t:
... |
6e22428fe5c26ca9d05cd777a44f8d96d0e247f866910e186969904dcff9ff6d | Python | 11,822 | 326 | import os
import time
import numpy as np
import pandas as pd
import nibabel as nib
from os.path import join as pjoin
from scipy.signal import detrend
from scipy.fft import fft, fftfreq
from magicbox.io.io import CiftiReader, save2cifti
from cxy_visual_dev.lib.predefine import proj_dir, All_count_32k
anal_dir = pjoin(p... |
19a0722d77b4fe60f53c71bf4b85b0cbe30d4e8bb76aa0ea1be60c8f613f2e05 | Python | 11,826 | 342 | """Phase 3a capture-unification regression tests."""
from __future__ import annotations
from collections.abc import Callable
import pytest
import torch
from torch import nn
import torchlens as tl
from torchlens.fastlog import RecordContext
class PredicateToy(nn.Module):
"""Small model with mixed operation typ... |
2d932d3121925ae2005ac1d34b9cb0d5dceecb0f984ab176fee90c9e5d2ccb6b | Python | 11,826 | 326 | '''
Late Stage Functionalization predictions after the NMR Pretraining.
NOTE: WE ARE USING THE ALL ATOM GRU 2 LINEAR LAYER SETUP FOR THIS COMMIT!
'''
import os
import argparse
import pandas as pd
import numpy as np
import torch
import logging
from collections import Counter
from neural_nets.LSF_Finetune_Net import L... |
81d21cfdc2e0d4a2c4c8fe8aa840e20aa381ff470212fd948ed2185df59fc8b7 | Python | 11,826 | 275 | """grouping= knob entry legality + the grouping_policy_v1 stamp: writer
content, loader coherence rules C1-C8, tamper degradation, the canonical
degraded settlement's monotonic round trip, and the G-gates for the stamp
family (S3 switch discipline).
All stamp vocabulary and refusal spellings are PROVISIONAL pending th... |
a4a4840dec6040e78170224649e5c54ced73b84d6f788ca5dd9fc4e3f274054b | Python | 11,827 | 312 | """
Matplotlib Exporter
===================
This submodule contains tools for crawling a matplotlib figure and exporting
relevant pieces to a renderer.
"""
import warnings
import io
from . import utils
import matplotlib
from matplotlib import transforms
from matplotlib.backends.backend_agg import FigureCanvasAgg
cl... |
c42cac0cb59b7b4db45716afab103985a44dc9ea7102894c079edba989b9103a | Python | 11,831 | 292 | import torch
import torch.nn as nn
from dgl.ops import edge_softmax
import dgl.function as fn
from dgl.utils import expand_as_pair
from graphmae.utils import create_activation
class GAT(nn.Module):
def __init__(self,
in_dim,
num_hidden,
out_dim,
... |
f2a7173831372c4d3d8a438318b7007dfa1a4d27ffb6e6ba4ab2ffe2cae70891 | Python | 11,831 | 314 | # 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... |
e6100fdd7a9c01f016b56034ffb8d920ff1d4de947a13088e0ada52a593e9e42 | Python | 11,833 | 240 | """
Advanced test cases - with plots of computed alpha-relative density ratios.
"""
from .context import densratio
from scipy.stats import norm, cauchy, uniform, bernoulli, multivariate_normal
import numpy as np
import unittest
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
class AdvancedTes... |
998fa9f098e261aa69b2863a642fc6453d7d1a11022b991dcdf122f6c61127e7 | Python | 11,835 | 302 | #==========================================================================
#
# Copyright NumFOCUS
#
# 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/l... |
11af226551ec99af086c48fcbcebea1bdbe82efd8a5e3f5afa361d5e316543fc | Python | 11,840 | 318 | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import json
import os
import random
from itertools import chain as chain
import numpy as np
import slowfast.utils.logging as logging
import torch
import torch.utils.data
from slowfast.utils.env import pathmgr
from . import... |
909a9adcc3776c9c5c6337fc1a3800853bc7d2ef790976e54e6dd6531e57335a | Python | 11,841 | 331 | """tvscope B4/B5 + composition rows 2-3: the manifest block + the input path.
Every new artifact carries the schema-versioned ``input_preprocessing``
block (allowed to say unknown); legacy/pre-block artifacts read as unknown;
resume never grafts new provenance; the input-transform identity joins the
resume signature s... |
f5e848f10e02be012e9c995af3c4788159b8fdfabdd489eeae64e115cef40e02 | Python | 11,846 | 349 |
import math
from typing import Dict, Optional
import torch
from torch import Tensor, nn
import torch.nn.functional as F
from transformers.activations import ACT2FN
def softmax_dropout(input, dropout_prob, is_training=True, mask=None, bias=None, inplace=True):
"""softmax dropout, and mask, bias are optional.
... |
a8a374ae5560b7e962f03e168f370b5b13b32f084330773f0d9c6c95117bc6f7 | Python | 11,847 | 304 | # --- 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 Colorscale(_BaseTraceHierarchyType):
_parent_path_str = "sankey.link"
_pa... |
741b98569b30409d6f616e6225f17148cfe204146782e842fb557f07cc7b44a2 | Python | 11,849 | 310 | """
module for custom functions used for evaluation and validation of trained models
"""
import logging, logging.config
from lib.models import BoneAgeModel
logger = logging.getLogger(__name__)
import os
import matplotlib.pyplot as plt
import numpy as np
from numpy import linalg as la
from scipy import s... |
87f75d077edc2a3ad409c6a04a003c2d92b1529b17d7986e9efee23b50d02e95 | Python | 11,852 | 313 | import pandas as pd
import numpy as np
import pre_process
import entropy_opt
import modeling
from seqtools import SequenceTools
from Bio.Seq import Seq
from tensorflow import keras
def aa_probs_from_nuc_probs(nuc_probs):
"""
Calculates amino acid probabilities given nucleotide probabilities.
"""
l_nuc... |
b061c4f54e51368e7f49f7e06c116c1940710cf5a55881d676be44c040bbd943 | Python | 11,854 | 291 | from typing import Any
import numpy as np
import pandas as pd
import copy
from mirp._images.generic_image import GenericImage
from mirp._images.transformed_image import TransformedImage
from mirp.settings.generic import SettingsClass
from mirp._imagefilters.generic import GenericFilter
from mirp._imagefilters.utiliti... |
6974e2bb20a027e2ddd98df06c1cc0bc109777dd6f85ad162aecb0533daca63d | Python | 11,855 | 292 | from keras.src import tree
from keras.src.api_export import keras_export
from keras.src.backend.common import standardize_dtype
from keras.src.backend.common import standardize_shape
@keras_export(["keras.InputSpec", "keras.layers.InputSpec"])
class InputSpec:
"""Specifies the rank, dtype and shape of every input... |
012fb2f73929f1ab51131a2ed97558cbb0a031abb0369d97dbea06ab9ee24e63 | Python | 11,857 | 251 | import torch
import numpy as np
from typing import Callable, Union
import torch.nn.functional as F
from monai.data.utils import compute_importance_map, dense_patch_slices, get_valid_patch_size
from monai.utils import BlendMode, PytorchPadMode, fall_back_tuple
# def pad_patient_3D(patient, shape_must_be_divisible_by=1... |
3dcf1566fb51f1a5b4458e4d0770d9bd168a9e31bf0ed5c8cfe3b8b3531ceeae | Python | 11,857 | 256 | '''
This file contains all model components.
Pasted from
crf_models.py
lstm_cnn.py
'''
import torch
import torch.nn as nn
from crf import CRF
class LSTMCNN(nn.Module):
def __init__(self, input_size: int = 1280, dropout_input=0.25, n_filters=32, filter_size=3, hidden_size=64, num_lstm_layers=1, dropout_conv1=0... |
bd7da045a7aac573a3d5d3cf4627a75c4697c235d5c6f2cd550d18909e53eeff | Python | 11,857 | 350 | # -*- coding: utf-8 -*-
"""
Created on Wed Aug 31 11:53:02 2022
@author: LABadmin
"""
def AlignStim(signal, time, eventTimes, window,timeUnit=1,timeLimit=1):
aligned = [];
t = [];
dt = np.median(np.diff(time,axis=0))
if (timeUnit==1):
w = np.rint(window / dt).astype(int)
else:
w =... |
4337eea547151a032fb825e910d018396df82487fafae29736e94cf2cb42ce5a | Python | 11,865 | 243 | import os
from pyexpat import model
import torch
import torch.nn as nn
import argparse
import time
import datetime
import numpy as np
import math
import tifffile as tiff
from torch.autograd import Variable
from torch.utils.data import DataLoader
from utils import save_yaml_test
from skimage import io
fr... |
0cfc8eac411ce8b36532c7c333176be08f3a25ec5fd14c3fe07bf4381ec77753 | Python | 11,868 | 301 | """Lane F22 neuro.datasets handoff contract (neuro MEMO 4.1, rows T7/T10/T14).
Pins:
- Default sweeps cover only STIMULUS-INDEXED saved sites through the core
gate (buffer overwrites skipped with ONE summarized disclosure); explicit
ineligible requests refuse actionably.
- Descriptors are the product: site, reque... |
de4d28c65e08f2ce93f9e9f22bc036edd756090075336dc2e82b056343b4c5d2 | Python | 11,871 | 359 | """Container visualization and UI tests."""
from __future__ import annotations
from pathlib import Path
from typing import Any
import pytest
import torch
from torch import nn
import torchlens as tl
from torchlens.experimental import dagua
class DictOutputModel(nn.Module):
"""Return a two-leaf dictionary outpu... |
dabdc2a05f31cfa8cb3b1920187bfa44c413d735e554ac9eb87b07017704bf85 | Python | 11,874 | 312 | from typing import List
import numpy as np
import pytest
import seqpro as sp
from hypothesis import given, note
from seqpro.rag import Ragged
from hypothesis import strategies as st
seq = st.text(
alphabet=st.characters(codec="ascii", min_codepoint=32, max_codepoint=126),
min_size=1,
)
seqs = st.lists(seq, mi... |
45c9c81b25aebb7d1e8d29c7ed53666457ca58aeab46cb84d539a9c469d8a2da | Python | 11,878 | 248 | import os.path as osp
import torch
import torch_geometric
from torch_geometric.data import Dataset, Data
from pathlib import Path
from helpers.configurations import TAKE_SPLIT, OR_4D_DATA_ROOT_PATH
from role_prediction.graphormer.role_prediction_configs import USE_GT, USE_IMAGES
import json
import numpy as np
from pyv... |
2701b4cbf74d168c137ae0166eb202790c47b874618e29ea954c17a25953de48 | Python | 11,880 | 281 | # FAITHFUL PORT of debbiemarkslab/DeepSequence @ master (original framework: Theano)
# DeepSequence/model.py (class VariationalAutoencoder)
# The real repo is written in Theano (`theano.tensor`, `theano.shared`) and cannot run
# in the base torch env. This ports the "Doubly Variational Autoencoder" (Riesselman,
# Ing... |
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