sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
45e6b13938eba728e1a8768d0c24e974a4d0018d54bb1cf677740b58c9205c81 | Python | 7,836 | 224 |
import json
import pickle
import dgl
import numpy as np
import torch
from scipy import sparse
from torch import nn
def get_noed_label():
NCI_set_path = "NCI_node_set_entrez.txt"
with open(NCI_set_path, 'r') as fin:
lines = fin.readlines()
# 获取每个node的set
node_entrez = []
... |
877e72f0175c6f8bf700aaed302bb7eb803c18c8bdb6c6edc68d345b165fe67b | Python | 7,837 | 202 | # Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
from typing import final
import numpy as np
import pandas as pd
import plotly.express as px
from ax.adapter.base import Adap... |
335284795ca47492af968a84d19413a53e4f01ddbf6816aeeb10399e79123002 | Python | 7,838 | 212 | import datetime
import logging
import math
from sqlalchemy import text
TMP_TABLE = "tmp_unused_history"
ASSOC_TABLES = (
"event",
"history_audit",
"history_tag_association",
"history_annotation_association",
"history_rating_association",
"history_user_share_association",
"default_history_... |
724535aa55fc10a936e019196417bbe2451f8fabe18095b4dd44d9a00fac904a | Python | 7,840 | 175 | # -*- coding: utf-8 -*-
import pandas as pd
import os
import re
import copy
import numpy as np
import time
def goDeeper(props,this_path,a,max_a,conditions,folders):
a += 1
for newFolder in os.listdir(this_path):
print(newFolder)
if conditions[a-1] != "":
if newFo... |
c182af5d915344e6e7e094a3f999a2fe9156365c0fa476a15a41e967a7289b5c | Python | 7,841 | 242 | # -*- coding: utf-8 -*-
"""PSF module
Generates an LSM point-spread function
"""
# Created on Thu Mar 21, 2020
# Contributions and Changelog accessed via a private git repository:
# https://github.com/philipwijesinghe/deep-learning-lsm.git
# philip.wijesinghe@gmail.com
# Copyright (c) 2020 Philip Wijesinghe@Univer... |
eea5ee7aecbc47bdd7100cf98f40825ce249684f5be1da662b40b6bd7abf0ce3 | Python | 7,841 | 184 | import numpy as np
import tensorflow as tf
from Dilationlayer import Dilationlayer,CNNlayer
from tensorflow.keras.layers import Input,GlobalAveragePooling2D,GlobalMaxPooling2D,SpatialDropout2D
import os
from InceptionA import InceptionA
from InceptionB import InceptionB
from InceptionC import InceptionC
from InceptionD... |
96c2a6ed6af17cc7b70473f4232ee7a809f0f0dd7ccea8864beec61503e94cd5 | Python | 7,843 | 188 | from __future__ import annotations
from dataclasses import dataclass
from typing import Literal, Optional
@dataclass(frozen=True)
class PrecisionConfig:
mode: Literal["fp32", "fp16", "bf16", "fp8"] = "fp32"
fp8_recipe: Literal["auto", "delayed", "current", "block", "mxfp8"] = "auto"
neuron_storage: Optio... |
9ff253b6e928d793080fa092052f29097224f5ddc665a490d99be6bf1fe15483 | Python | 7,844 | 224 |
import json
import pickle
import dgl
import numpy as np
import torch
from scipy import sparse
from torch import nn
def get_noed_label():
NCI_set_path = "Reactome_node_set_entrez.txt"
with open(NCI_set_path, 'r') as fin:
lines = fin.readlines()
# 获取每个node的set
node_entrez = [... |
c9765a1780207e8c067e39d4a5f1fc5269e478f0e24a1792894b36530357e379 | Python | 7,846 | 194 | # coding=utf-8
# Copyright (c) HISSL Contributors
try:
import h5py
except ImportError:
raise ValueError("You must have h5py installed to run this script: pip install h5py.")
from pathlib import Path
# Idea of this script is to take the TCGA-CRCk or TCGA-BC features saved per tile in h5 format and output them
... |
11af216cb3853f66875fb37b3dc3637e4ff6afac0faddfc35d8d6734dea95ec8 | Python | 7,848 | 214 | import pytest
import sklearn.metrics
from himalaya.backend import set_backend
from himalaya.backend import ALL_BACKENDS
from himalaya.utils import assert_array_almost_equal
from himalaya.scoring import r2_score
from himalaya.scoring import l2_neg_loss
from himalaya.scoring import correlation_score
from himalaya.scori... |
dbebdd34012f62cec57964461c91c36e660d7e372146f1976112e614fc372605 | Python | 7,848 | 205 | # NICE
# Copyright (C) 2017 - Authors of NICE
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program ... |
9e9d55d9cb5ae11843a4a02fd0c7138fddba8dc421f3cec6974dae70926ab244 | Python | 7,850 | 212 | # Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
import re
from collections.abc import Sequence
from typing import final
from ax.adapter.base import Adapter
from ax.analysis... |
0c8476a53dcb3b3d774720e042d1ab0db58c6cba06db3828f37a73bd1e3bd4cc | Python | 7,851 | 184 | import tensorflow as tf
import numpy as np
import os
from data_reload import *
# REGULARIZER = 0.01
BATCH_SIZE = 10
def compute_accuracy(v_xs, v_ys):
global prediction
y_pre = sess.run(prediction, feed_dict={xs: v_xs, keep_prob: 1})
correct_prediction = tf.equal(tf.argmax(y_pre, 1), tf.argmax(v_ys, 1))
... |
307d65fbd4704588032b02ad95e4941fc14d9cffc08da61c3d446db91dc7565a | Python | 7,852 | 271 | from decimal import Decimal
import anndata
import numpy as np
import pandas as pd
import seaborn as sns
import xarray as xr
from sklearn.neighbors import LocalOutlierFactor
def _density_based_sample(data: pd.DataFrame, coords: list, portion=None, size=None, seed=None):
"""Down sample data based on density, to pr... |
8fdc434ea013bc74d217caaa5d473d10ebde59a9772c41d24f80016897d7a3a0 | Python | 7,858 | 232 | from typing import Mapping, Union
import numpy as np
from torch import optim
import torch
import logging
import anndata
from torch.utils.tensorboard import SummaryWriter
import torch
import torch.autograd as autograd
import torch.nn.functional as F
from scNTImpute.models import BaseCellModel, BatchClassifier
from scNT... |
cdf0a3a270680d98947e21f81861dddb85ad7aec5ad1106f137683eef740e388 | Python | 7,861 | 172 | """
Predict TF binding with a maxATAC model
"""
import logging
import os
import glob
import timeit
import pandas as pd
import multiprocessing
import pybedtools
from multiprocessing import Pool, Manager
from maxatac.utilities.system_tools import get_dir, Mute
with Mute():
from maxatac.utilities.genome_tools import ... |
f75ff5c5a336d1ff824b07ddaa5fff7c323c7776ace011de4cc02f1bb9d9d83c | Python | 7,861 | 174 | # -*- coding: utf-8 -*-
"""
Watch three external tool catalogues for entries that are not on the Related Software page yet:
* OpenBehavior (https://edspace.american.edu/openbehavior/) -- projects in its video-analysis and
home-cage categories, read from the site's public WordPress API;
* the Home Cage Monitoring Tec... |
746aad8200f5abc45535c7f96bfac1a6d943ed67a8d9db656ea2bac54aebc383 | Python | 7,864 | 280 | """Connected components."""
import networkx as nx
from networkx.utils.decorators import not_implemented_for
__all__ = [
"number_connected_components",
"connected_components",
"is_connected",
"node_connected_component",
]
@not_implemented_for("directed")
@nx._dispatchable
def connected_components(G):... |
9e9ec9b4eba0b418ea4ce47b5bbbb0a12b5e3101e46579966dcbb7bfd8b103ed | Python | 7,865 | 219 | import sys, os, time
from oct import *
import logging
from PyQt5.QtWidgets import QApplication
class processHandler():
""" Handles the argument cases for cmd line automated processing"""
def __init__(self):
self.directory = ''
self.state = ''
self.toggleRange = 1
self.startFram... |
42969387ffb36af181617116d008df0d0346a0a9729b49defab5ba6a07dce020 | Python | 7,866 | 202 | """
Created on Oct 13, 2022.
@author: voodoocode
"""
import numpy as np
import scipy.spatial
import finnpy.src_rec.utils # @UnresolvedImport
def _tessellate_sphere(vert, faces, level):
"""
Inflates the sphere.
Parameters
----------
vert : numpy.ndarray, shape(initial_vtx_cnt, 3)
... |
5fec1f12ec544df152fddf356750f56dcc4598b154d95c318ba79e585320021d | Python | 7,867 | 171 | import logging
from typing import TYPE_CHECKING
from galaxy import model
from galaxy.jobs.runners import JobState
from galaxy.util import now
from ._safe_eval import safe_eval
if TYPE_CHECKING:
from galaxy.app import GalaxyManagerApplication
from galaxy.jobs import ResubmitConfigDict
from galaxy.jobs.runn... |
240476b54abdfa03281d1f0ac8f0fd4376c11dbabfa305bea57a86166f470793 | Python | 7,869 | 251 | from __future__ import annotations
import importlib
import sys
import types
from contextlib import AbstractContextManager, nullcontext
from importlib.metadata import version
from typing import TYPE_CHECKING
import dask.array as da
import h5py
import numpy as np
import pandas as pd
import pytest
import zarr
from packa... |
515b8a056328610ecb4f7a363643917cb3d2c907fdb3092d273f78028cfdf6e4 | Python | 7,869 | 214 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
import datumaro as dm
from django.conf import settings
from django.db import transaction
from rest_framework import serializers
from cvat.apps.consensus.intersect_merge import IntersectMerge
from cvat.apps.consensus.models import ConsensusSettings
f... |
90108a8af6baf949ab03b278b872c8aac9b26b0aa576ceb13f7c868bab0a201a | Python | 7,869 | 216 | # -*- coding: utf-8 -*-
import ctypes
import os
import math
import numpy as np
import numpy.ctypeslib as ctl
import matplotlib.pyplot as plt
import sys
import tqdm
def debugPrint(msg):
sys.stdout.write(msg.decode("utf-8"))
return 1 # also print using OutputDebugString on C++ side
class NativeAPI:
def _... |
b05fa91be461ec885702070b12478c42fd8c8a26b06b3a6d0da9ca15cca00bb7 | Python | 7,871 | 218 | # Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
from __future__ import annotations
from abc import ABC, abstractmethod
from collections import ChainMap
from collections.abc... |
d0b0658bb1e5772eefc6de32ee14fb28ac582e58313ad4592576c2e23185ec20 | Python | 7,871 | 213 | #emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
#ex: set sts=4 ts=4 sw=4 et:
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
#
# See the COPYING file distributed along with the smile package for the
# copyright and license terms.
#
### ### ### ### ### ### ### ... |
702d9f11a9a62f468535470d6ad475827a5a6add358fb3614003b7da0bccada3 | Python | 7,879 | 187 | # 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... |
c83a7161ab7de5d43774912de9210e4d3797154c507f662ce6e7c327be07319d | Python | 7,880 | 238 | """Reusable helpers for migrating Custos authentication tokens into PSA format."""
from datetime import datetime
from typing import (
cast,
Optional,
)
import jwt
from sqlalchemy import (
Column,
DateTime,
Integer,
MetaData,
select,
String,
Table,
Text,
)
from sqlalchemy.engine... |
daa2d6ee2457b075b256f7cf6a875fc9d403b55d8267c3c71d91ae73b851a0f1 | Python | 7,880 | 192 | import os
import numpy as np
import pandas as pd
import nibabel as nb
from glob import glob
from nilearn.image import smooth_img, new_img_like
from nilearn.plotting import plot_stat_map
from nistats.design_matrix import make_first_level_design_matrix
from nistats.reporting import plot_contrast_matrix, plot_design_matri... |
6455797d2f60e753a7fdf07902345c3f33379b19b77494858c8881a51a013cb4 | Python | 7,890 | 229 | import pathlib
from typing import Union
from matplotlib.axes import Axes
from skimage.io import imread
from skimage import feature, color, filters
from skimage.util import img_as_ubyte
import numpy as np
import matplotlib.pyplot as plt
import os
from matplotlib.figure import Figure
from matplotlib import gridspec
from ... |
aa6f025fc6af3ec1c63ceb6cb3e646f509d2944aeada9a26b76f3010cda2ab66 | Python | 7,894 | 231 | # -*- coding: utf-8 -*-
"""
MeasureRadius
=============
Measures intensity decays at spcified points in the data.
"""
__author__ = 'Christoph Kirst <christoph.kirst.ck@gmail.com>'
__license__ = 'GPLv3 - GNU General Pulic License v3 (see LICENSE.txt)'
__copyright__ = 'Copyright © 2020 by Christoph Kirst'
__webpage... |
82ef6e632e250fd76e114b23814dfd2baf271002d2daff12fca9be8e2e099c73 | Python | 7,897 | 195 | # % Statistical test for kernel conditional independence of X and Y given Z with
# % incomplete Cholesky factorization for low rank approximation of Gram matrices
# %
# % Arguments:
# % X n x p vector of data points
# % Y n x m vector of data points
# % Z n x r vector of data points
# % alph... |
6c9c5e5927bead374c38cd997676b2a0457d9d415519dbe25587e09e30765433 | Python | 7,898 | 236 | #!/usr/bin/env python3
# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
from __future__ import annotations
import json
from copy import deepcopy
from logging import Logger
... |
f40eeffaec05ea2334932d0e706406acef5e9f0fad353bea13d6226245ffda56 | Python | 7,898 | 199 | import pytest
import numpy as np
import sklearn.linear_model
import sklearn.model_selection
import scipy.linalg
from himalaya.backend import set_backend
from himalaya.backend import ALL_BACKENDS
from himalaya.utils import assert_array_almost_equal
from himalaya.scoring import r2_score
from himalaya.kernel_ridge impo... |
1c02c147bd2fecd400ef9032a097c10dd337e7bbc1171cd3b297e8b85bb633ce | Python | 7,899 | 240 | # -*- coding: utf-8 -*-
"""
Created on Fri Nov 22 08:38:28 2019
@author: Amelie Aussel
"""
from brian2 import *
defaultclock.dt = 0.01*ms
prefs.codegen.target = 'numpy'
eq_TC_mdPul='''
dV/dt=(-INa-IK-IL-IKL-IH-ITLT-J-Isyn-Iapp-Itheta)/Cm_TC : volt
J : amp * meter ** -2
Itheta = amptheta * int(... |
d54cbc31ef90f0b94708412ca9a8886b0ab24df50090f271275c4d45efb60b7d | Python | 7,906 | 168 | import abc
import torch
from torch import nn
from torch.nn import functional as F
import numpy as np
def reservoir_sampling(samples_so_far, budget):
'''Reservoir sampling algorithm to decide whether an new sample should be stored in the buffer or not.'''
# If buffer is not yet full, simply add the new sample... |
82da1b4deec142a0807001b49142952181cd9eac72da7947af6278d565f65e57 | Python | 7,908 | 252 | # -*- coding: utf-8 -*-
"""
Created on Wed Dec 4 11:35:36 2019
@author: aaussel
"""
from cells.RE_mdPul import *
from cells.TC_mdPul import *
from scipy import signal
prefs.codegen.target = 'numpy'
defaultclock.dt = 0.01*ms
runtime=3*second
start_scope()
def create_mdPul(N_TC,N_RE):
HTC_A=NeuronGroup(N_TC,... |
887ced3b16275895400c9b507c1d223ce67788939b33fd916b8c881d0bf25a29 | Python | 7,915 | 380 | from typing import AbstractSet
import pytest
import numpy as np
from nl_expr.exceptions import ForbiddenUnstratifiedAggregation
from nl_expr.expression_walker import ExpressionBasicEvaluator
from nl_expr.expressions import (
Constant,
ExpressionBlock,
NeuroLangException,
Symbol,
)
from nl_expr.type_s... |
513cecc02d656a66443d2cee04ca69fbc58b562b912af41ee1e0a985c25493c9 | Python | 7,916 | 199 | """Unit tests for the :mod:`networkx.algorithms.structuralholes` module."""
import math
import pytest
import networkx as nx
from networkx.classes.tests import dispatch_interface
class TestStructuralHolesNoScipy:
"""Unit tests for computing measures of structural holes.
The expected values for these functi... |
c76236364709d552bce4888809b929d24f240d47c982ccf9cb63234ca396cfba | Python | 7,916 | 188 | import ipaddress
import logging
import os
import socket
import tempfile
from typing import Optional
from urllib.parse import urlparse
from galaxy.exceptions import (
AdminRequiredException,
ConfigDoesNotAllowException,
RequestParameterInvalidException,
)
from galaxy.files import (
ConfiguredFileSources... |
e052b6c6bc6fe46f0e8d76a6b1f9086e3ff046f2610c2f392a1c81a90cbd14d0 | Python | 7,920 | 225 | '''
Tools for monitoring KK as it runs
MonitoringServer and MonitoringClient are lightly adapted from Brian (briansimulator.org).
'''
try:
import multiprocessing
from multiprocessing.connection import Listener, Client
except ImportError:
multiprocessing = None
import select
import inspect
from six import ... |
b2757b647a95f8d861b97c8d9e30184f509d910bc44da033a5907ca0d6e44db2 | Python | 7,925 | 257 | # ----------------------------------------------------------------------------
# build_region_matrix.py
# Author: Antoine Beauchamp
# Created: January 31st, 2022
"""
Build a gene-by-region expression matrix
Description
-----------
This script imports a gene-by-voxel expression matrix from a CSV file
and aggregates th... |
0292b4319566cd9733a8e667fd28a34d5c17c9e7b147b71b04ca0461e60947d2 | Python | 7,926 | 172 | """
Copyright (c) 2019 10x Genomics, Inc. All rights reserved.
"""
import os
os.environ["MKL_NUM_THREADS"] = "1"
os.environ["NUMEXPR_NUM_THREADS"] = "1"
os.environ["OMP_NUM_THREADS"] = "1"
import numpy as np
import cellranger.analysis.constants as analysis_constants
import cellranger.analysis.diffexp as cr_diffexp
i... |
f7029666ec0b3d9ac700cf59c50af8cb4a43bef501f269ad15432de8c56c99df | Python | 7,928 | 361 | #!/usr/bin/env python
# coding: utf-8
# # Data analysis for our study on the transparency and open science standards in the policies of medical and health science journals
# The protocol and details of our study is openly availble via the OSF [here](https://osf.io/h2xud/).
# In[1]:
# import libraries required for ... |
174421f8a66b1611b7ce584e4578756300fb08e369ae9451f5d2062eca2f2fac | Python | 7,931 | 281 | """
Tools for quickly creating a simple websummary, with embedded figures.
Copyright (c) 2019 10x Genomics, Inc. All rights reserved.
"""
import os
import base64
from StringIO import StringIO
CSS = """
/* Style the metric tables */
table {
border-collapse: collapse;
}
th, td {
padding: 15px;
}
tr:nth-child(e... |
f4b072704a7abea66ad57013da99da92c58cd3d1b5e8561591b64a93769d9d72 | Python | 7,933 | 239 | # MIT License
#
# Copyright (c) 2019-2024 The PyQMC Developers
#
# 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 the rights
# to use, copy, m... |
78c90934960ebd74d5ad60e704a3daf57c1547008302758279552b45b5ad6b82 | Python | 7,940 | 256 | import matplotlib as mpl
import seaborn as sns
from matplotlib.cm import get_cmap
from matplotlib.colors import Normalize
from scipy.cluster.hierarchy import dendrogram as _dendrogram
def straight_branch(ax, a, b, plot_kws):
"""Draw link line between a and b."""
a_x, ay = a
bx, by = b
branch_x = [a_x,... |
8adfd6c308b4601034cddf5cc9a9b52242845d2ccba909d5e83f43b47bb55420 | Python | 7,940 | 184 | import numpy as np
import csv
from ..strategy import ConnectionStrategy
from ...reporting import report, warn
class ConnectomeDcnGlyGolgi(ConnectionStrategy):
"""
Implementation for the connections between mossy fibers and glomeruli.
The connectivity is somatotopic and
"""
def validate(self):
... |
b784e0da316f5a18c2ed77821faa2bd9a0098ad13f2225b1afbcfb524a9621d6 | Python | 7,941 | 344 | from ...expressions import Symbol
from .. import (
FALSE,
TRUE,
Conjunction,
Disjunction,
ExistentialPredicate,
Negation,
UniversalPredicate
)
from ..transformations import (
AbsorbAssertedConjuncts,
AbsorbAssertedConjunctsInNegations,
LogicExpressionWalker,
PushExistentialsD... |
0f4a67bb0711605847df249d38e0209da873a528de6bf58db2f2f88895c8f3c7 | Python | 7,942 | 271 | import tensorflow as tf
from tensorflow import keras
from keras import optimizers
from tensorflow.keras import layers
import numpy as np
np.set_printoptions(precision=5)
import matplotlib.pyplot as plt
import pandas as pd
pd.options.display.float_format = '{:,.5f}'.format
import scipy as sp
from scipy import stats
imp... |
edce9d2f83930c7e064f3fb25a742805388d71016a374f3d018528553e8b76dd | Python | 7,943 | 205 | from warnings import warn
import igraph as ig
import leidenalg as la
import networkx as nx
import numpy as np
import pandas as pd
def sdi(data):
"""
Calculate the Shannon Diversity Index (SDI) for a categorical data series.
Higher SDI indicates higher diversity.
"""
if len(data) == 0:
re... |
72a67ddd7875b7dd401cda9863681cad0870ace81c65018b53f19faaeaf71754 | Python | 7,948 | 182 | #!/usr/bin/env python3
# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
from __future__ import annotations
import math
from typing import TYPE_CHECKING
import numpy as np
f... |
8edf25f557022d0ca1f9d480b7cf9e5d6d33b4fbcc4d54d9b6a8d8ea4606ebde | Python | 7,956 | 230 | import random
import time
import numpy as np
import scipy.sparse as sp
import torch
import torch.nn.functional as F
from ..base import InjectionAttack
from cogdl.utils.grb_utils import eval_acc, feat_preprocess, adj_preprocess, getGraph, getGRBGraph
class RAND(InjectionAttack):
r"""
Description
--------... |
4b47852f9aa257846e916a6b87f8f0be95d5f51b7bbf141b9aec032c9848c4ea | Python | 7,957 | 176 |
# -*- coding: utf-8 -*-
'''
Created on 2020.05.19
@author: Jiahua Rao, Weiming Li, Hui Yang, Jiancong Xie
CUDA_VISIBLE_DEVICES=2 python Training_Experiments.py --config_file ../MolRep/Configs/config_CMPNN.yml \
--dataset_name ogbg-molbbbp \
... |
914e5f2752b01ada35c9f68bfffe57463a651e2e74375278c5167df56496ab95 | Python | 7,957 | 293 | import operator
from typing import AbstractSet
from pytest import fixture
from ...datalog.expression_processing import extract_logic_atoms
from ...datalog.translate_to_named_ra import TranslateToNamedRA
from ...datalog.wrapped_collections import WrappedRelationalAlgebraSet
from nl_expr.expressions import Constant, Sy... |
a1f5cd8d26ddc7294720491d4b7b3caaffac5aa90b4996217ad3dc22d8095aeb | Python | 7,960 | 193 | """
Methods for doing peakcalling.
Copyright (c) 2019 10x Genomics, Inc. All rights reserved.
"""
from __future__ import division, print_function, absolute_import
from collections import namedtuple
import numpy as np
from scipy import stats
from analysis.em_fitting import (
MLE_dispersion, MLE_geometric_parameter... |
f132054c20e60052339cd79f94df1e96207097c2e12e361dc68dc4b30932cb32 | Python | 7,960 | 266 | from enum import Enum
from typing import (
Literal,
Optional,
)
from pydantic import (
Field,
RootModel,
)
from galaxy.schema.fields import (
EncodedDatabaseIdField,
ModelClassField,
)
from galaxy.schema.schema import (
GroupModel,
Model,
UserModel,
WithModelClass,
)
QUOTA = L... |
c1e93874bf967eda0f376a58812e218e446249d947421639a140e44dc6ac9dbf | Python | 7,961 | 211 | """
Shared model and mapping code between Galaxy and Tool Shed, trying to
generalize to generic database connections.
"""
import logging
import os
import threading
from contextvars import ContextVar
from inspect import (
getmembers,
isclass,
)
from types import ModuleType
from typing import (
TYPE_CHECKING... |
29fb515142648f7b00f144b14d7923ab0052ff7447855a91d8df89095c5d9c3c | Python | 7,964 | 271 | """General utilities"""
import os
import glob
import subprocess
from datetime import datetime
import natsort
import numpy as np
import pandas as pd
import pingouin as pg
import nibabel as nib
from brainspace.mesh.mesh_io import read_surface
import bct
from neuromaps import images
from adaptman.config import Config
... |
65d73737bcee366d8208eaa48cddaaabb455d2bc6bf58c3eccc27b4fefda8b49 | Python | 7,973 | 211 | """
Regression tests for all NIST SP 800-22 test modules.
Two categories:
- Regression tests: run each module against the deterministic binary
expansion of e (data/data.e, 1 000 000 bits) and verify p-values
match known-good results to 6 significant figures.
- Guard tests: verify that each module returns t... |
93181af9248743df86f2653116cd7dfef266c9d3dd829530e65ca8feac1a9426 | Python | 7,974 | 254 | import numpy as np
import torch
from .base import FactorCollection
from .base import VideoWrapper
from .factor import TensorFactor
class Video(VideoWrapper):
""" Manages Unrolled Tensor and multiplication with a Full Video """
def __init__(self,
video_shape,
device='cuda'):
... |
ef024d266589a0bf9f1b5d6029ddde5768b8b17dff47824cf23702e6a8f4a4b2 | Python | 7,975 | 223 | import os
from nipype.interfaces.utility import Function, IdentityInterface
import nipype.pipeline.engine as pe
from .utils import get_scrub_vector_node, logical_or_across_lists, expand_scrub_dict
from .image_workflows import (
build_image_postprocessing_workflow,
STEP_CONFOUND_REGRESSION,
STEP_SCRUB_TIME... |
5e1a4468b840cd2092ba337b0216516a134539aa62c42100121f7d7ccae3654f | Python | 7,977 | 231 | from __future__ import division
import numpy as np
from fanc.regions import Chromosome, Genome, RegionsTable
from genomic_regions import GenomicRegion
import pytest
import os.path
import tables as t
class TestChromosome:
@classmethod
def setup_method(self, method):
self.chromosome = Chromosome(name=... |
9551355a76a6fc25778efe7bd39d613b7681cf7b3484b928b8a25f025cb25c33 | Python | 7,983 | 254 | import numpy as np
import torch
from .base import FactorCollection
from .base import VideoWrapper
from .factor import TensorFactor
class Video(VideoWrapper):
""" Manages Unrolled Tensor and multiplication with a Full Video """
def __init__(self,
video_shape,
device='cuda'):
... |
a20fba511052adfc16640cd09e79abcc9d8773a8c264ffd429d532d194a5c82e | Python | 7,983 | 197 | # Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
import pandas as pd
from ax.analysis.healthcheck.baseline_improvement import BaselineImprovementAnalysis
from ax.analysis.he... |
20789d144bfb308efcd73b1d93b5d3f38f2b2ef2f00e4db004ad458cbf8246fe | Python | 7,985 | 241 | from itertools import chain, combinations
import pytest
import networkx as nx
def test_directed_not_supported():
with pytest.raises(nx.NetworkXNotImplemented):
# not supported for directed graphs
test = nx.DiGraph()
test.add_edge("a", "b")
test.add_edge("a", "c")
test.add... |
6280fe3e0b9866211f40ed2f7f1817d76e6360d2813f9305f1722b56a9250a9b | Python | 7,985 | 200 | # Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
from typing import final
import pandas as pd
from ax.adapter.base import Adapter
from ax.adapter.random import RandomAdapter... |
94d184238ee23c5e517bd5b024bc11c71213eccce9c3826cedb459061dcb21dd | Python | 7,985 | 264 | import shutil
from pathlib import Path
import click
from . import _manager, _mpi
from ._fs import clear_cache, get_cache_path, get_local_pkg_path
from ._local import create_local_package
from .assets import ModName
from .exceptions import *
from .packaging import PackageManager
@click.group()
def glia():
pass
... |
037a3a61f9c575c66bf117dd566e227ac49675dddc1e3bc52c8b3fbb7e960011 | Python | 7,986 | 260 | # 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... |
e64713a670ff8c6561902a72b12a59cf7a202248d0f385c33189c0ebec31b4b6 | Python | 7,989 | 186 | # coding: utf-8
# 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"... |
87e8f2b4565de90032d9d738097beb438bbb4c54a54e566ac41138c0027615e8 | Python | 7,997 | 238 | import torch
import sys
import torch.nn.functional as F
from torch.cuda import amp
from spikingjelly.activation_based import functional, surrogate, neuron
from spikingjelly.activation_based.model import parametric_lif_net
from spikingjelly.datasets.dvs128_gesture import DVS128Gesture
from torch.utils.tensorboard import... |
97e7d8313b0d64522157e731fc5065cc48ead37b3701219e0e0ed0c9d77c313c | Python | 8,006 | 207 | import pandas as pd
from tensorflow.keras.models import Model
import numpy as np
from sklearn.model_selection import train_test_split, KFold
from sklearn.metrics import accuracy_score
from tensorflow.keras.optimizers import Adam, SGD
import os
import random
from sklearn.model_selection import train_test_split... |
f21e524df25bc62a0c0b90b5ea64c75030dfce969d9ee8a1432aef84bff26c88 | Python | 8,008 | 248 | '''
Created on Aug 5, 2020
@author: voodoocode
'''
import finnpy.misc.timed_pool as tp
import time
import numpy as np
import multiprocessing
import psutil
import joblib
import matplotlib.pyplot as plt
import finnpy.filters.frequency as ff
import finnpy.data.paths as paths
def demo_fnct2(data):
data2 = ff.f... |
52c4f10c885070cc51524e7e9646baf05806e64d46cb6c793e4d4b7f79f21d10 | Python | 8,010 | 196 | """Correlation of each synthetic test EEG data features (EEG_channels x
EEG_time_points) with the corresponding biological test EEG data features
(across the 200 test image conditions), and noise ceiling calculation.
Parameters
----------
sub : int
Used subject.
encoding_type : str
Whether to analyze the 'linearizin... |
ea831e3940f1523e39128c86d830a8b75aab61357bde444112fb62ddd02c2eb3 | Python | 8,013 | 225 | """Tests of the resampling of a probabilistic choice, ``RESAMPLE``."""
import numpy as np
import pytest
from nl_expr.exceptions import ForbiddenExpressionError
from neurolang.frontend import NeurolangPDL
from neurolang.frontend.resampling import resampling_ratios
STUDIES = [f"s{i:02d}" for i in range(12)]
RNG = np.ra... |
41933c27070f11af349cc74769fd2e4a86e3a72df0ee31f8f0f75138117ad28d | Python | 8,020 | 217 | # 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... |
10e806105d63d8860827841e8aaea0d498a1520b1dce20a697a05a83f71d2e7a | Python | 8,023 | 206 | # -*- coding:utf-8 -*-
import time
import pytest
import tensorflow as tf
from sklearn.model_selection import train_test_split
from keras import backend as K
from keras import layers
import keras
from deeptables.datasets import dsutils
from deeptables.models import deepnets
from deeptables.models import deeptable
from... |
46c60880b88644d65ba8832582b0983701a630f6fb6c6a16e8551c69b3df8ee3 | Python | 8,023 | 157 |
import torch.nn as nn
import math
import torch.utils.model_zoo as model_zoo
import torch.nn.functional as F
from .basic_conv import *
class Inception2d(nn.Module):
def __init__(self, in_channels, pool_features):
super(Inception2d, self).__init__()
self.branchA = BasicConv2d(in_channels, pool_feat... |
9b7c3185f957b1ec9021974a6fa2ece0e6a6c5e76d719be5534039f78e7fa0c2 | Python | 8,023 | 167 | from __future__ import print_function
import os
import sys
import pdb
import copy
import sklearn
import tensorflow as tf
import pandas as pd
import PIL
import numpy as np
import keras
from keras.models import load_model
import function as func
import function_dl as func_dl
def cnn_prediction(cnv_file, model_file, use_... |
9c8634ffe4797b4948277a69ca599cd6e3f37d8bedca937c56c092e9e423dda6 | Python | 8,024 | 212 | import tensorflow as tf
from learnMSA.legacy.Utility import deserialize
class Bidirectional(tf.keras.layers.Layer):
"""Simple bidirectional wrapper for forward and backward RNNs with shared state.
Args:
layer: `keras.layers.RNN` instance.
merge_mode: Mode by which outputs of the forward and b... |
7852c9188a26287f79016880db4e9d7f9001d8c8f9a662b35282b93a1688fe54 | Python | 8,026 | 218 | import os
import csv
import shutil
import torch
import torch.nn as nn
from torch.optim.lr_scheduler import LambdaLR
from torch.utils.data import DataLoader
from torch.optim import Adam
from dataset.e_piano import create_epiano_datasets, compute_epiano_accuracy
from model.music_transformer import MusicTransformer
from... |
8b883498a69a43d45aa36addb583987fa67396d88a20408fea527cdc57cb61db | Python | 8,030 | 178 | from typing import TYPE_CHECKING
from sqlalchemy import (
literal,
union,
)
from sqlalchemy.sql import (
expression,
select,
)
from galaxy import model
from galaxy.managers.base import get_class
if TYPE_CHECKING:
from sqlalchemy.orm import scoped_session
class JobConnectionsManager:
"""Get ... |
1d608b47f71ee3580c199ebb0ac682530e2191077aa4709daf1d0c0195634e0a | Python | 8,035 | 168 | """
Functionality for dealing with dbkeys.
"""
import logging
import os.path
import re
from json import loads
from typing import (
Optional,
)
from sqlalchemy import select
from galaxy.model import HistoryDatasetAssociation
from galaxy.model.scoped_session import galaxy_scoped_session
from galaxy.util import (
... |
6c82b8ce47db3006f022fd66a0c2809257162f178dd960f634d72bbe3349d071 | Python | 8,040 | 206 | # Copyright (c) MONAI Consortium
# 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, so... |
c35e29c168404069032f294c18c9e72f1010aeae0a020cc74f759ae5449df2d0 | Python | 8,042 | 203 | # %% import
import sys, os, platform
from src.pipelines import ComputeMinimumControlEnergy
from src.plotting import my_bsci_pair_plot
from src.utils import rank_int, get_null_p, get_fdr_p
from src.utils import get_bootstrap_indices
from brainsmash.mapgen.base import Base
from tqdm import tqdm
# %% import workspace
os... |
e2c311d1bd796a35865614a71432ba413a5622cdc9404259ef4a9f90cfed5ed8 | Python | 8,043 | 206 | import pandas as pd
from keras.models import Model
import numpy as np
from sklearn.model_selection import train_test_split, KFold
from sklearn.metrics import accuracy_score
from keras import optimizers
import os
import random
from sklearn.model_selection import train_test_split, KFold
from sklearn import metri... |
4923b96887df2ffa191f800a2e73a1c637d3975965efe0740e9ea8bb53cf5a9e | Python | 8,048 | 279 | from qtpy.QtWidgets import (
QMainWindow,
QLabel,
QVBoxLayout,
QPushButton,
QWidget,
QListWidget,
QHBoxLayout,
QLineEdit,
QTreeView,
QSplitter,
)
from qtpy.QtCore import Qt
from qtpy import QtGui
from qtpy.QtGui import QStandardItemModel
from pkg_resources import resource_filenam... |
53b4e6c0d8b4e0591dc25481789c2308eed29c0cb022a79b3a37f76e3f7845e6 | Python | 8,049 | 193 | from __future__ import division
import fanc
from fanc.data.network import RaoPeakCaller, RaoPeakInfo
from fanc.data.genomic import Hic, RegionMatrix, GenomicRegion
from fanc.tools.general import pairwise
import numpy as np
import math
import pickle
import os.path
class TestRaoPeakCaller:
def setup_method(self, m... |
78999632fb505c7be836473f79b14737a08125dda389c3fe6e46b3e39e494df4 | Python | 8,051 | 178 | # -*- coding: utf-8 -*-
import pandas as pd
import os
import seaborn as sb
from matplotlib import pyplot as plt
from matplotlib import image as mpimg
import numpy as np
from skimage import io
from scipy import ndimage
from scipy.ndimage import morphology
def calculate_length_from_kymograph(path_kymograph, b... |
9186e4894c4838a61eca5e4c14930200a8342d05bfc84bad3a00e70399905e74 | Python | 8,051 | 171 | """
Copyright (c) 2019 10x Genomics, Inc. All rights reserved.
Pools single-cell analyses from other stages and calculates bulk metrics from the pooled dataset.
"""
from __future__ import division
import json
import pandas as pd
import numpy as np
from tenkit.stats import robust_divide
from tools import ReferenceMan... |
d2be1d9efd67ba3483e3a6a33dc88680e79cb5a69c621e7b8d451dd5181587f1 | Python | 8,051 | 273 | import tensorflow as tf
from tensorflow import keras
from keras import optimizers
from tensorflow.keras import layers
import numpy as np
np.set_printoptions(precision=5)
import matplotlib.pyplot as plt
import pandas as pd
pd.options.display.float_format = '{:,.5f}'.format
import scipy as sp
from scipy import stats
imp... |
31a3bde28110dcc51e21841779f8eb38258f4716d0104ab3d581a1d6c83cda18 | Python | 8,055 | 315 | """
==========================
Bipartite Graph Algorithms
==========================
"""
import networkx as nx
from networkx.algorithms.components import connected_components
__all__ = [
"is_bipartite",
"is_bipartite_node_set",
"color",
"sets",
"density",
"degrees",
]
@nx._dispatchable
def c... |
3fc2e80935377e91e618e3dceb1fc90ba49d138a5815bb96a3fcb5b2f255bf2b | Python | 8,058 | 234 | # -*- coding: utf-8 -*-
"""
Created on 2022.06.20
@author: Jiahua Rao
"""
import os
import json
import numpy as np
import pandas as pd
from rdkit import Chem
from pathlib import Path
from sklearn.model_selection import train_test_split
from itertools import repeat, product
import torch
from torch_geometric.data i... |
7706b14841afb455781bab96d5d34b6dfa55f716cf0417436c7b2547514dee37 | Python | 8,064 | 197 | from __future__ import absolute_import
import logging
from collections import OrderedDict
from pip._internal.exceptions import InstallationError
from pip._internal.utils.logging import indent_log
from pip._internal.utils.typing import MYPY_CHECK_RUNNING
from pip._internal.wheel import Wheel
if MYPY_CHECK_RUNNING:
... |
a4c5e7124bc350239e19d349d55c4b0d4b6fc08dab1c60091116ac8c33884ebe | Python | 8,067 | 223 | """Current-flow betweenness centrality measures for subsets of nodes."""
import networkx as nx
from networkx.algorithms.centrality.flow_matrix import flow_matrix_row
from networkx.utils import not_implemented_for, reverse_cuthill_mckee_ordering
__all__ = [
"current_flow_betweenness_centrality_subset",
"edge_c... |
7ef20e3531002c73fb32a5137bc310679a74cff2d0d5b2c7b9514a6e89dd0f53 | Python | 8,074 | 199 | # Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
import pandas as pd
from ax.analysis.healthcheck.healthcheck_analysis import HealthcheckStatus
from ax.analysis.healthcheck.... |
0395db76a505b0e9f7a03e2682f528f8e684075ef8eca79a3a1a0ff4dc0f2fde | Python | 8,076 | 221 | """
Tracing the requests the assistant sends to its model, and its replies.
:class:`TracingClient` wraps a chat client and reports each request and
reply as an event, a dict whose ``event`` key is:
* ``request``: the ``call`` number, the ``messages`` added to the
conversation since the previous request (from index ... |
4da24bdda152c6c5e6a309924e44ee4fa44e8707a7f78101b826704855f7e33a | Python | 8,079 | 247 | import logging
import os
import shutil
import json
from fibsem_tools.io import read
import dask.array as da
import numpy as np
from numcodecs import Zlib
import incasem as fos
logger = logging.getLogger(__name__)
logger.setLevel(logging.INFO)
def make_config_janelia_crops(zarr_ds: str,
... |
c47a331b7bc5429703194e7e6166896fdb6e2df9140c06376ffa018a8ddff307 | Python | 8,079 | 207 | from nl_expr.exceptions import NeuroLangException
from nl_expr.expression_pattern_matching import add_match
from nl_expr.expression_walker import ExpressionWalker, ReplaceSymbolWalker
from nl_expr.expressions import FunctionApplication, Symbol
from nl_expr.logic import Conjunction, ExistentialPredicate
from nl_core.pro... |
90bb5b066d95674a4bf9425b7f07ab10bb5af4460fbad5e3d758dc12ffd46576 | Python | 8,081 | 208 | """Combines a folder of single-channel TIFFs into a multiplexed MIBItiff.
Copyright (C) 2021 Ionpath, Inc. All rights reserved."""
import argparse
import datetime
import os
import re
import numpy as np
from skimage import io as skio
from mibidata import mibi_image as mi, panels, runs, tiff
def _load_single_chann... |
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