sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
c31bd30cdc6be9ca2df02f9ddbdac0ba06f4fc3e3fc3fe7c5906251b2fc9b519 | Python | 11,721 | 212 | import re
import sys
import os
import math
from scipy import stats
print("ALL_PPI_mutation_sites_mapping_with_allonco")
output = open(r'E:\OneDrive\学术\PPI article\data\mapped data\3. DNM_complex_mapping\ALL_Complex_PPI_mutation_sites_allonco.txt','w+')
with open(r'E:\OneDrive\学术\PPI article\data\mapped data\... |
cefc114578aef6880a684a07acfb429db54a699f8a267d84c019bb8db9c5c55d | Python | 11,729 | 329 | import torch
# import torch.fft
import torch.nn as nn
import torch.nn.functional as F
from cogdl.data import Graph
from cogdl.utils import row_normalization
from cogdl.utils.link_prediction_utils import GNNLinkPredict, sampling_edge_uniform, cal_mrr
from .. import BaseModel
# def ccorr(a, b):
# return torch.fft... |
4e437bdd277647391b073283ff29ed6fa740c9da5ba4a9d8502e9b7228c8907f | Python | 11,732 | 349 | from typing import Union, Tuple, Set
from .aabb_tree import AABB
import numpy as np
from copy import deepcopy
from functools import singledispatch, update_wrapper
def methdispatch(func):
dispatcher = singledispatch(func)
def wrapper(*args, **kw):
return dispatcher.dispatch(args[1].__class__)(*args, *... |
24309967f3cb112a888046d4f263f2a04b9f5b0a0e888ab2800d7bf906487b7b | Python | 11,733 | 396 | from . import idnadata
import bisect
import unicodedata
import re
import sys
from .intranges import intranges_contain
_virama_combining_class = 9
_alabel_prefix = b'xn--'
_unicode_dots_re = re.compile(u'[\u002e\u3002\uff0e\uff61]')
if sys.version_info[0] == 3:
unicode = str
unichr = chr
class IDNAError(Unico... |
632856c42d0a1186c07a36f4612e6d44bb26e9fc23e5221e953ebbca0e007c96 | Python | 11,733 | 223 | """
Created on May 2, 2025.
@author: voodoocode
"""
import numpy as np
import sklearn
import pyvista
import finnpy.src_rec.fwd_mdl # @UnresolvedImport
import copy
def plot_reg_avg(subj_to_fsavg_mdl, morphed_channels, color_data,
signal_type = None, rec_meta_info = None, coreg = None, ch_names = Non... |
633204add3b4df58e74f0ed77d1ea5be85624c4f3c931839500d4a76b64bd842 | Python | 11,733 | 337 | # rmf 3.25.2020, last modified 5.20.2021
# cleaned up 3.1.2022
import sys, re
import matplotlib as mpl
mpl.use('Agg')
from matplotlib import pyplot as plot
import numpy as np
# USAGE
usage = 'python ' + sys.argv[0] + ' <summary file> <p-value threshold> <asterisk threshold> <FDR annotation (True or False)>'
details =... |
b7ac1546dc77ce9c3a9f409a56b4253c8ec5a1a6eb63c73d64ae47ced4cff68a | Python | 11,734 | 354 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Mar 7 11:45:28 2024
@author: colin
"""
from dicom2bids import *
import os
from os.path import join as pjoin
from os.path import exists as pexists
import sys
import subprocess
import fcntl
import random
import shutil
import zipfile
import time
from pyd... |
838b40af86fb63312f5a9e6b5cdc6de9e038acde1423859c15bc43a95019190e | Python | 11,735 | 222 | #!/usr/bin/env python
#
# Copyright (c) 2017 10X Genomics, Inc. All rights reserved.
#
import cellranger.analysis.io as analysis_io
import cellranger.analysis.constants as analysis_constants
import cellranger.h5_constants as h5_constants
import cellranger.io as cr_io
import cellranger.analysis.stats as analysis_stats
... |
04d1311bb6622fbe92f3d5cee8d8298d7f909f38ed1e1534329b153b7de71a69 | Python | 11,737 | 323 | """Unit tests for the :mod:`networkx.algorithms.bipartite.matching` module."""
import itertools
import pytest
import networkx as nx
from networkx.algorithms.bipartite.matching import (
eppstein_matching,
hopcroft_karp_matching,
maximum_matching,
minimum_weight_full_matching,
to_vertex_cover,
)
... |
98a9ed4e141285d4f32079141ece5917ea1bd3dc37db9c36b94c4c06317b9eac | Python | 11,739 | 294 | import pathlib
from typing import Optional, Tuple, Union, Literal
import numpy as np
from skimage import measure, filters, morphology
from skimage.util import map_array
import pandas as pd
from alpineer import misc_utils, load_utils, image_utils, io_utils
from ark.segmentation.ez_seg.ez_seg_utils import log_creator
imp... |
f6f4f61b0399dd4c57c75f4c838c258b66e51044e7c046ef44cd50fcac1a75ef | Python | 11,741 | 265 | """
Unit tests of the `ConnectomeGlomerulusGranule` strategy
"""
import unittest
from os.path import abspath, dirname, join
import numpy as np
from bsb import (
Configuration,
ConfigurationError,
ConnectivityError,
Scaffold,
WorkflowError,
)
from bsb_test import NetworkFixture, NumpyTestCase, Rand... |
02a7e85dde609359cd0f2d8d94454042cfc0519943f6d8e0329003a02699aaee | Python | 11,756 | 388 | """
FlexSN Triton Kernel Templates.
Insert a single-step kernel into a multi-step kernel template.
"""
from spikingjelly.logger import logger
try:
import triton
except (ImportError, OSError) as e:
from .. import triton_missing as dummy
logger.info("Optional Triton dependency unavailable: {}", e)
tr... |
e19c9e9148606626a122b030ca6a1866971857d9c1df43362781553d316b6726 | Python | 11,758 | 262 | """
Module for the configuration node of the Golgi to Glomerulus ConnectionStrategy
"""
import itertools
import numpy as np
from bsb import (
CfgReferenceError,
ConfigurationError,
ConnectionStrategy,
ConnectivityError,
config,
pool_cache,
refs,
)
from cerebellum.connectome.presyn_dist_st... |
53dff0ec9ae26fec3cb69018529a68227153cf17d2ade36155404192e9431f10 | Python | 11,781 | 379 | from __future__ import annotations
import string
from typing import cast
import numpy as np
import pandas as pd
import pytest
from anndata._core.xarray import Dataset2D
from anndata.compat import XDataArray, XDataset, XVariable
from anndata.tests.helpers import gen_typed_df
pytest.importorskip("xarray")
@pytest.f... |
4c717561f859806b85c1dd8109f959440129de9f20bb66e0da39eab236c19e9b | Python | 11,786 | 355 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Mar 11 13:56:08 2020
@author: amelie
"""
from brian2 import *
from scipy import signal
from FEF_full3_alternate import *
from LIP_full import *
from itertools import *
def generate_syn(source,target,syntype,connection_pattern,g_i,taur_i,taud_i,V... |
f29a97b6342494fa364f739f16b7972431fe5a806da0c78a11074ac229c3be92 | Python | 11,789 | 279 | from functools import partial
import numpy as np
import pytest
import scipy.linalg
import sklearn.linear_model
from himalaya.backend import ALL_BACKENDS, set_backend
from himalaya.kernel_ridge import KERNEL_RIDGE_SOLVERS, WEIGHTED_KERNEL_RIDGE_SOLVERS
from himalaya.kernel_ridge._solvers import _weighted_kernel_ridge_... |
259a9cddd84ca3121120734b96777c3b451fb2394503e599b7f3ec30c8cf6cc3 | Python | 11,793 | 337 | # 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... |
66ece56cd897daa6e58fdd05828d6e67587a3253b24e7ea2fa9cdfa8b7fb1fa8 | Python | 11,794 | 303 | import os
from dataclasses import dataclass
from typing import Sequence
import numpy as np
import tensorflow as tf
from tensorflow.keras.initializers import Initializer
import learnMSA.legacy.DirichletMixture as dm
from learnMSA.hmm.util.value_set import PHMMTransitionIndexSet, PHMMValueSet
class EmissionInitialize... |
5a21dbe573b2c38a6855e0419653267b912c3bc81debe97760db1a4536f88f6c | Python | 11,799 | 357 | # Copyright 2020 DeepMind Technologies Limited.
#
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agre... |
50d7a061235b1d924d288de0e51e1c27ca358c9aad70243f72a8309c76c26c7f | Python | 11,813 | 363 | """
Compiler for the intermediate representation of a Datalog program.
The :class:`DatalogProgram` class processes the
intermediate representation of a program and extracts
the extensional, intentional, and builtin
sets.
"""
import operator as op
from itertools import tee
from typing import AbstractSet, Any, Callable,... |
4820eb8e1d3ee7ae5b5640d47f30d9da4addeb3d4a4acfd198578006d39ae702 | Python | 11,815 | 240 |
##########################################################################################
#
# psim_parse.py
#
# - Utility functions for parsing text-based inputs to ProBioSim.
#
##########################################################################################
#
# ProBioSim
# Copyright (C) 2021 Matthew L... |
280a2a63e03076afbdd34cfdf2ba6d018cbebfcbc5b12e8af444dbccbc78d776 | Python | 11,816 | 355 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Mar 11 13:56:08 2020
@author: amelie
"""
from brian2 import *
from scipy import signal
from FEF_full3_altd import *
from LIP_full_altd import *
from itertools import *
def generate_syn(source,target,syntype,connection_pattern,g_i,taur_i,taud_i,V... |
3f7bde5e92c4573fbb3d6e6502bfdd13c30fe9af666327c740285f0545330a84 | Python | 11,818 | 290 | """
Error analysis agent for tool error diagnosis.
"""
import logging
import re
from functools import partial
from pathlib import Path
from typing import (
Any,
Optional,
)
import anyio
from pydantic import BaseModel
from pydantic_ai import Agent
from galaxy.schema.agents import ConfidenceLevel
from .base im... |
143555c1585859be266fc2211f89f38108a3d8daccfb9accd20b6aaafa48a922 | Python | 11,820 | 339 | import copy
from types import SimpleNamespace
import pytest
import torch
try:
import transformers
except ImportError:
transformers = None
from spikingjelly.activation_based import functional
from spikingjelly.activation_based.ann2snn import (
ModuleConverter,
Qwen2SNNCalibration,
Qwen2SNNConfig,
... |
0f9055e4ca53ae55bbffbd6a56c85d52aa489d6e6d8ed769146a35d4ed169f75 | Python | 11,824 | 311 | # 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 unittest.mock import patch
from ax.adapter.registry import Generators
from ax.adapter.torch import TorchAdapter
from ax... |
7a6d2ff6b63a997f4de7c1c8ac149f1fabc39e38c7378a62c8620d60d765ea6f | Python | 11,825 | 348 | import copy
import math
import pytest
import torch
import torch.nn as nn
import torch.nn.functional as F
from spikingjelly.activation_based import functional, layer, neuron
def test_delay_step_matches_sequence_delay_and_gradients():
x_seq = torch.randn(5, 2, 3, requires_grad=True)
queue = ()
outputs = [... |
21b2416e385d8daf7b96a4f1618a46812c232c40137b2427089d906fe14862ce | Python | 11,835 | 351 | '''
The baseline model implementation is from:
https://github.com/MilesCranmer/symbolic_deep_learning/blob/master/models.py (MIT license)
'''
import numpy as np
import torch
from torch import nn
from torch.functional import F
from torch.optim import Adam
from torch_geometric.nn import MetaLayer, MessagePassing
from ... |
ce27d00be7780265f64c1474582ff203069cca67c1d12119b3d65f5dd87c07ac | Python | 11,838 | 356 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Mar 11 13:56:08 2020
@author: amelie
"""
from brian2 import *
from scipy import signal
from FEF_full3 import *
from LIP_full_alternate import *
from itertools import *
def generate_syn(source,target,syntype,connection_pattern,g_i,taur_i,taud_i,V... |
b601a9fbe363c5d299bb1e8d1af81327e64d3d36e6755baf829704e1aeac8933 | Python | 11,841 | 282 | # 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 enum import Enum, unique
from math import ceil, floor
from typing import Any
from ax... |
8ca45199cebff6c4fe11d17fc7d53cab46e775f5e7485ee69fd6c782add66e73 | Python | 11,842 | 281 | """
Manager and Serializers for Quotas.
For more information about quotas: https://galaxyproject.org/admin/disk-quotas/
"""
import logging
from typing import (
cast,
Optional,
Union,
)
from sqlalchemy import (
and_,
select,
)
from galaxy import (
model,
util,
)
from galaxy.exceptions imp... |
434fc14f421aefbdd1876ab668ec5d71200a5b7d1ea3e6e4f212085493a33d5a | Python | 11,846 | 337 | #!/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
import numpy as np
import pandas as pd
from ax.early_stopping.simulation import (
_check_patience... |
6dad645d0faa349d5737412397dca5d9ae3e05a5e67af3a847e7d39dbc0ef0bc | Python | 11,847 | 323 | # Adapted from
# https://github.com/funkelab/scikit-image/blob/fix_clahe/skimage/exposure/_adapthist.py
"""
Adapted code from "Contrast Limited Adaptive Histogram Equalization" by Karel
Zuiderveld <karel@cv.ruu.nl>, Graphics Gems IV, Academic Press, 1994.
http://tog.acm.org/resources/GraphicsGems/
The Graphics Gems ... |
682267df8343888119b30bd5a558cb08793890c89515d3ac1de686f5a311d7ba | Python | 11,855 | 316 | """Progress updates and stale-job detection for ProjectImport / ProjectReimport."""
import logging
import django_rq
import rq
from core.redis import redis_connected
from django.conf import settings
from django.db.models import Q
from django.utils import timezone
from rq.job import Job
logger = logging.getLogger(__na... |
6fcbecb653f25556a27eb661072db37634dab5a888fd5cdcc978569f3fcfa2f6 | Python | 11,864 | 297 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sun Jan 30 22:07:08 2022
@author: wirrbel
"""
# We begin by adding the current path to sys.path to make sure that the imports work correctly
import sys
sys.path.append('../brainrender/')
import os
import pandas as pd
import numpy as np
from shutil import co... |
2e1cc05d21c508f436906feb3e05dbd3a60a769a4eedbb80a64b020b8188e30f | Python | 11,878 | 338 | """
Label propagation community detection algorithms.
"""
from collections import Counter, defaultdict, deque
import networkx as nx
from networkx.utils import groups, not_implemented_for, py_random_state
__all__ = [
"label_propagation_communities",
"asyn_lpa_communities",
"fast_label_propagation_communit... |
e6e825391a519971d63ad52699803137bd52c401b9222b51a961224ae75bd655 | Python | 11,878 | 293 | #!/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
from collections.abc import Callable, Mapping, Sequence
from datac... |
df2a3348fc97f9e82226daa38609706245a575bfaea14bc83bc55f8a47a08581 | Python | 11,880 | 398 | import functools
import math
import typing
import numpy as np
from .. import config
from ..config import refs, types
from ..rng import RngConsumer
if typing.TYPE_CHECKING: # pragma: nocover
from ..cell_types import CellType
from .cell import CellModel
def _target_name(targetting) -> str:
"""Name a tar... |
e25f4b2fedce3b1c9639571bed5c0339ef24e97069f73171ea98e547c89c8d1a | Python | 11,881 | 325 | from typing import Optional
import torch
from .. import functional, surrogate
from .base_node import BaseNode, NonSpikingBaseNode, SimpleBaseNode
__all__ = ["SimpleLIFNode", "LIFNode", "NonSpikingLIFNode"]
class SimpleLIFNode(SimpleBaseNode):
def __init__(
self,
tau: float,
decay_input... |
425e2b967ddb2ced067f51d87626596c0faed3bb03b13b75be74573027739909 | Python | 11,883 | 367 | from __future__ import annotations
from string import ascii_letters
import numpy as np
import pandas as pd
import pytest
from scipy import sparse
import anndata as ad
from anndata.compat import CupyArray, CupyCSRMatrix, DaskArray
from anndata.tests.helpers import (
BASE_MATRIX_PARAMS,
CUPY_MATRIX_PARAMS,
... |
d7d48dcb863e4ac266ed604fe64274de0acaf6cdcce00de6c106abb8fa576cf4 | Python | 11,888 | 329 | """ """
import hashlib
import logging
import os
import threading
import time
from math import inf
from typing import (
List,
Tuple,
)
from uuid import UUID
from typing_extensions import NamedTuple
from galaxy.util import (
nice_size,
string_as_bool,
)
from galaxy.util.sleeper import Sleeper
log = lo... |
eb76723ed2a63c346f5d0644da2b6490b67993c20380252be0e5d137747d441c | Python | 11,890 | 377 | import pytest
import networkx as nx
def test_random_partition_graph():
G = nx.random_partition_graph([3, 3, 3], 1, 0, seed=42)
C = G.graph["partition"]
assert C == [{0, 1, 2}, {3, 4, 5}, {6, 7, 8}]
assert len(G) == 9
assert len(list(G.edges())) == 9
G = nx.random_partition_graph([3, 3, 3], 0... |
203f58f8e26ff46a40a9763efec90f686ed4516858b40f3aead9231218bbc46c | Python | 11,894 | 303 | #!/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 itertools import product
from typing import Any
from unittest.mock import MagicMock
import numpy... |
ac023cb54e1c54d312fd508d7a7e9055bfc341f2512bf35143d65879c09b1fb5 | Python | 11,897 | 290 | #!/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 collections.abc import Iterable
from dataclasses import dataclass
from heapq import nsmallest
im... |
4b0874e4f608f86fd5c0d68718ffa0183e2455cefae8e6413c96eda2873b3472 | Python | 11,902 | 369 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Mar 12 16:23:57 2020
@author: amelie
"""
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Mar 11 13:56:08 2020
@author: amelie
"""
from brian2 import *
from scipy import signal
from FEF_full import *
from LIP_full import *
from mdP... |
54e0fbcea76620acf08aae3ed6e9c75af67880e77faae9d6167d4b8d52bea524 | Python | 11,903 | 375 | # -*- coding: utf-8 -*-
"""
Plot
====
Plotting routines for overlaying labels, tilings, and sectioning of 3d data sets
Supported functionality:
* plot volumetric data as a sequence of tiles via :func:`plotTiling`
* overlay points on images via :func:`overlayPoints` and
:func:`plotOverlayPoints`
* ... |
4554074e5e322291353594c40e7d7811a2418534557b11bbab3077f8a40e8026 | Python | 11,904 | 356 | """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... |
434f3a5c2079aa76ec56549e728f3ea889b6b4c46f7fa757d0c485789ed5a2cf | Python | 11,918 | 280 | # 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... |
10d5db8c6547432bf690520cc0f7e751ae65b107475ea1643f36230a77bc5db9 | Python | 11,927 | 272 | import os, sys, argparse, time
from multiprocessing import Pool
from tqdm import tqdm
from lib.common.util import is_dir, is_file, read_option_file, makedir_if_not_exists
# from lib.complex_alignment_generation.geno_dist import Geno_interact
# from lib.complex_alignment_generation.pdb_interact import PDB_interact
from ... |
77dec13f2c43a092fc0f54dd8705df5008c82218f492fc94bd1438a0c081459e | Python | 11,929 | 328 | # 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... |
7cf27f83f4ba14717d7c5e01245abe16394c0fb85da0dc4fb94b51da0f4d6464 | Python | 11,954 | 287 | """
Pipeline to prepare data from new patients :
1) combat harmonise (make sure you have computed the combat harmonisation parameters for your site prior)
2) inter & intra normalisation
3) Save data in the "combat" hdf5 matrix
"""
## To run : python run_script_preprocessing.py -site <site_code> -ids <text_file_with_s... |
b126e0a49b9da44f3b9382ca6a8dff4306cc2b547e5f12785acead882d7403b6 | Python | 11,968 | 255 | import errno
import logging
import os
from typing import (
Any,
Optional,
)
from galaxy.tool_shed.galaxy_install.client import (
DataManagerInterface,
INSTALLATION_RELOAD_TIMEOUT,
InstallationTarget,
)
from galaxy.util import (
Element,
etree,
parse_xml_string,
xml_to_string,
)
from... |
9e12ca3041266b7e939d2ab29283db9bdf1b67e069aca4202a91cad06287ae07 | Python | 11,971 | 316 | import logging
import os.path
from collections.abc import Sequence
from typing import (
Optional,
Union,
)
from sqlalchemy import (
false,
null,
select,
)
from sqlalchemy.orm import (
aliased,
Session,
)
from galaxy.exceptions import RequestParameterInvalidException
from galaxy.model impor... |
a414c8e47fd53b812eecae01db79c9a03d52a913f0a3b339e73b18d0532a00cd | Python | 11,976 | 353 | import os.path as osp
import numpy as np
import torch
from cogdl.data import Graph, Dataset
from cogdl.utils import download_url
class BidirectionalOneShotIterator(object):
def __init__(self, dataloader_head, dataloader_tail):
self.iterator_head = self.one_shot_iterator(dataloader_head)
self.i... |
9ab81f82373da5e47345c301ec1acaf43cc8f3a132b76a985f6eff87de84f469 | Python | 11,985 | 322 | """
NeuroSynth engine initialization.
Registers the following predicates:
* ``peak_reported(i, j, k, study_id)`` — reported activation peaks
converted to voxel coordinates, the Talairach ones converted to MNI
(see :func:`process_peaks` for those of ``UNKNOWN`` space).
* ``peak_mni(x, y, z, study_id)`` — the same ... |
ade7f4474fb47f9a81196da643001d62b4293fe46fd8675acfaf0dfc3246ebd1 | Python | 11,992 | 320 | # 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 collections.abc import Callable, Iterable, Mapping, Sequence
from dataclasses import dataclass, field, InitVar
from func... |
875ddda1ffb2a7d361289a5f45824713ab86e611e51ec4ec42654b70f24a4dc0 | Python | 11,999 | 393 | import logging
import nipype.pipeline.engine as pe
from pathlib import Path
import os
from typing import List
DEFAULT_GRAPH_STYLE = "colored"
def find_sub_list(sl, l):
results = []
sll = len(sl)
for ind in (i for i, e in enumerate(l) if e == sl[0]):
if l[ind : ind + sll] == sl:
resu... |
a601daf6f4854c0776ad3b0fe7e2ebe50a9ad7d6810c7d76b8acdd00893f4a6a | Python | 12,008 | 302 | #!/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
from collections.abc import Callable, Iterable
from logging import... |
1708e292cb66ba82eb30bf28fbebf670e52890384ee784e918b420a968300820 | Python | 12,009 | 260 | import os
import tempfile
import timeit
import numpy as np
import pytest
import test_utils
import xarray as xr
import pandas as pd
import ark.settings as settings
import ark.spLDA.processing as pros
from ark.analysis import visualize
import test_utils as ark_test_utils
def test_draw_heatmap():
# Create random Z... |
63f0691a9209bf8672bfd17afbebbc24d24e2c56afa488d9bdb1f36f4855e759 | Python | 12,009 | 320 | # 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... |
5a4aa4c75bd0f9b6eb000c5c4a316a3358747c71def84348c3742eeba276fb61 | Python | 12,013 | 334 | """Tests for mibidata.segmentation
Copyright (C) 2021 Ionpath, Inc. All rights reserved."""
import unittest
import numpy as np
from numpy.testing import assert_array_equal
import pandas as pd
import pandas.testing as pdt
from mibidata import mibi_image as mi, segmentation
class TestSegmentation(unittest.TestCase... |
9f47d9e9723bffd71b90b77a47f6a2df07238d3291f5cb65bdf30647e47d4cff | Python | 12,015 | 346 | # 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 ... |
9828676df40496ae9c23c02d0868e49f65650310aad35b0e581447ad4f8fe164 | Python | 12,034 | 319 | # -*- coding: utf-8 -*-
"""
Created on Fri Jul 5 13:08:06 2019
@author: schelskim
"""
from scipy.spatial import distance
import numpy as np
import cv2
from skimage import morphology as morph
from scipy import ndimage
import copy
from skimage.morphology import disk
from matplotlib import pyplot as plt
#import pyopen... |
a61c74c22a760e09534f75f054ed7342d7a175b38c675695151b596576e467b6 | Python | 12,040 | 259 | import errno
import logging
import os
from time import sleep
from typing import TYPE_CHECKING
from galaxy import model
from galaxy.jobs import (
JobWrapper,
TaskWrapper,
)
from galaxy.jobs.runners import BaseJobRunner
if TYPE_CHECKING:
from galaxy.app import GalaxyManagerApplication
from galaxy.jobs i... |
87937db09f13df1bfab8b4c2987a332159a9b596ee5edfed4799a38129713cf8 | Python | 12,041 | 275 | import itertools
import math
import os
import pathlib
import random
import tempfile
from typing import Generator
import numpy as np
import pandas as pd
import pytest
from alpineer import io_utils, test_utils, misc_utils
from pytest_mock import MockerFixture
import ark.settings as settings
from ark.segmentation import... |
1420cab022ab28a62867753e8dc55dee0b1f96bb2329679da2d84ac217e136d5 | Python | 12,053 | 319 | """
===========================
Creating annotated heatmaps
===========================
It is often desirable to show data which depends on two independent
variables as a color coded image plot. This is often referred to as a
heatmap. If the data is categorical, this would be called a categorical
heatmap.
Matplotlib'... |
a888878ca4d06dcacd79b12f20564971f82a57ce84336fc053ec8630db359d85 | Python | 12,061 | 286 | #!/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 copy import deepcopy
from ax.adapter.base import DataLoaderConfig
from ax.adapter.data_utils imp... |
ef0a032df91609489f479ebdf32357f902c9f3d9c2b60bba1829021b97aa8122 | Python | 12,072 | 216 | import re
import sys
import os
import math
from scipy import stats
print("ALL_PPI_mutation_sites_mapping_with_allonco")
output = open(r'E:\OneDrive\学术\PPI article\data\mapped data\4. DNM_MIPPI_mapping\ALL_MIPPI_psymukb_mapping.txt','w+')
with open(r'E:\OneDrive\学术\PPI article\data\mapped data\0.data filter\I... |
76c65534d16e3a7996fa03152f8bab796619bcd5ba0c72ed15a10e2a98c3aa45 | Python | 12,087 | 287 | #!/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 typing import Any
import torch
from ax.adapter.registry import Generators
from ax.api.utils.str... |
bdcead01cd2667eb630e774903b6b4fbd401750f53959528452cf0fbfb4332e4 | Python | 12,089 | 325 | import logging
from functools import wraps
from core.feature_flags import flag_set
from core.redis import start_job_async_or_sync
from core.utils.common import load_func
from core.utils.io import ssrf_safe_post
from django.conf import settings
from django.db.models import F, Q
from django.db.models.functions import Co... |
9348bc44c26c5096a79011c75b2ecef6a27493b9f463f58f01923181f2c83edf | Python | 12,094 | 470 | # -*- coding: utf-8 -*-
"""
TIF module provides interface to read and write tif image files.
Note
----
This modules relies onf the tifffile library.
"""
__author__ = 'Christoph Kirst <christoph.kirst.ck@gmail.com>'
__license__ = 'GPLv3 - GNU General Pulic License v3 (see LICENSE.txt)'
__copyright__ = 'Copyright ©... |
a149b94b3e75bd24b24134c4c89248dca0a1efc993a05cdd8f70a2f0355076a3 | Python | 12,095 | 315 | # ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
#
# See the COPYING file distributed along with the smile package for the
# copyright and license terms.
#
# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
from .video import WidgetState
from kivy.uix.wid... |
821d466b4ca25a092ba4ee30bc16b9600c1a2cc4de5b723112de003fc386fd8d | Python | 12,098 | 352 | import os
import h5py
import pandas
import shutil
import tempfile
import logomaker
from matplotlib import pyplot as plt
import numpy as np
import pandas as pd
from pathlib import Path
from typing import List, Union
from memelite import tomtom
from memelite.io import read_meme
pd.options.display.max_colwidth = 500... |
9ba9ede139a0643dceb0e123baeed49a744fbd89c14217338f8d3f86244e53e6 | Python | 12,105 | 332 | """
Object Store plugin for the Microsoft Azure Block Blob Storage system
"""
import logging
import os
from datetime import timedelta
try:
from azure.core.exceptions import HttpResponseError
from azure.storage.blob import (
BlobSasPermissions,
BlobServiceClient,
generate_blob_sas,
... |
b6d0db78d67af1e5608b04d000e73f1e92637605401a06a15d04b27b43fe04fd | Python | 12,110 | 352 | import rdkit
import random
import itertools
from rdkit import Chem
from rdkit.Chem import rdFMCS
from collections import defaultdict, deque
from MolRep.Explainer.Attribution.utils.fuseprop.vocab import MAX_VALENCE
lg = rdkit.RDLogger.logger()
lg.setLevel(rdkit.RDLogger.CRITICAL)
def set_atommap(mol, num=0):
for ... |
ab3768cf358af2f2da83e08052aad700cd82659c0c14de6f32ee9376bc1d7fe1 | Python | 12,128 | 362 | import pickle
import pytest
import networkx as nx
class TestAtlasView:
# node->data
def setup_method(self):
self.d = {0: {"color": "blue", "weight": 1.2}, 1: {}, 2: {"color": 1}}
self.av = nx.classes.coreviews.AtlasView(self.d)
def test_pickle(self):
view = self.av
pview... |
76cb697f8f096891fa847f6a017536e344dd074b30db7169a65eea2721f9f1ce | Python | 12,132 | 295 | """
Identifies likely barcode multiplets.
Copyright (c) 2019 10x Genomics, Inc. All rights reserved.
"""
from __future__ import absolute_import, division, print_function
from barcodes import query_barcode_subsequences, split_barcode, merge_barcode
from tools import ReferenceManager, grouped_fragments_from_contig
impo... |
fa47c2cbf07781d0fa10ec9a93eddd4a2d8545b6cf4c8f1ee12f7978c3449283 | Python | 12,142 | 252 | # -*- coding: utf-8 -*-
from figureflow import figure
import seaborn as sb
import numpy as np
import os
import importlib
importlib.reload(figure)
Figure = figure.Figure
input_folder = os.path.dirname(os.path.abspath(__file__))
figure = Figure(input_folder,number="S16",dpi=600,width=4.75)
figure.... |
6e75dce055aaa3d4a3199ca5863c15afcfc408078e8d9520d0c4694c2106efce | Python | 12,144 | 259 | # 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... |
48c2d77bc0ce4e00320957ef959fe5baad6264c5eadb88c5025820e6ca856c82 | Python | 12,150 | 334 | #!/usr/bin/env python3
import sys
import os
import numpy as np
# -expand module search path to parent directory
sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
# -custom-written code
import main
import utils
from utils import checkattr
from params.param_stamp import get_param_stamp_from_... |
a43054370080d938b1c39c297841d75e9039e8784be71c8c102483bf3b2d4fa5 | Python | 12,153 | 315 | #!/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
from unittest.mock import patch
import torch
from ax.exceptions.c... |
2b251e6e1968f78cffcd67bda2210571bcd8fbe0c18a445e299e1d325f021329 | Python | 12,157 | 312 | #!/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 collections.abc import Mapping, Sequence
import numpy as np
from ax.adapter.adapter_utils impor... |
526cb9bbedd9f79ec68ab75aa6789c5d53a91da338c5d39900126e2717da7890 | Python | 12,162 | 346 | """
Low-level helpers for the SecureTransport bindings.
These are Python functions that are not directly related to the high-level APIs
but are necessary to get them to work. They include a whole bunch of low-level
CoreFoundation messing about and memory management. The concerns in this module
are almost entirely abou... |
2219908ef9fe45f973af0339860c391e8a52df9c524c7884756b2546e895b7e0 | Python | 12,165 | 306 | #!/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 warnings
from copy import deepcopy
from logging import Logge... |
28f8c5beca2647bfe5c4856db169301ab9597adec12d8637d3ef7b2a4c585ede | Python | 12,167 | 285 | import logging
import mimetypes
import posixpath
import uuid
from datetime import timedelta
from urllib.parse import unquote
import jwt
from django.conf import settings
from django.contrib.auth import get_user_model
from django.http import HttpResponse
from django.utils import timezone
from drf_spectacular.utils impor... |
408fd6931e818510cd4e1226bb7cc90da381156468db0ff108984112293dd76b | Python | 12,168 | 353 | from dataclasses import dataclass
import torch
from spikingjelly.logger import logger
from .layout import _layout_args
from .triton_runtime import (
is_fp8_dtype,
normalize_cuda_device,
normalize_triton_compute_dtype_name,
normalize_triton_storage_dtype,
resolve_triton_compute_dtype,
tl,
... |
927ff6fc3a10dc5c53ee3c952d9b945e662d43af1261a2027f58e3684e5e7e2c | Python | 12,170 | 318 | from datasets import ScanpathLoadDatasets
from torchvision import transforms
import torch
import os
import scipy.io as sio
from numpy import asarray
import scipy.io as spio
import numpy as np
import random
from PIL import Image
print(' Computing Model ')
entro_folder = 'x'
#train scanpath prediction
# Applying Tran... |
3b08c0683748e27b0c73e0e1479fa9d925d0241ee6f5a709f83b26a6415c923a | Python | 12,173 | 323 | """This file and its contents are licensed under the Apache License 2.0. Please see the included NOTICE for copyright information and LICENSE for a copy of the license."""
import logging
from django.conf import settings
from django.core.exceptions import ValidationError
from django.db import models
from django.db.mod... |
4853955f2e61f44c30693ac7332379a24758cd3bcdaeb08d4ec841a82642e10d | Python | 12,173 | 303 | # -- Extend metaDataTags to support addition of new unspecified datasets ------
class MetaDataTags(MetaDataTags):
def add(self, name, value):
"""Add a new tag to the list.
Args:
name (str): The name of the tag to add (will be added as an attribute of this `MetaDataTags` in... |
a19b706ff87cc11132471a92f014d4e601b9e2910ffb9326009efbc149304212 | Python | 12,174 | 385 | from vedo import Plotter
from vedo import settings as vsettings
import numpy as np
from datetime import datetime
from rich import print
from pathlib import Path
from myterial import orange, amber, deep_purple_light, teal
from rich.syntax import Syntax
from loguru import logger
from brainrender import settings
from bra... |
05d6504beaac59b11b457b9600dbc7d9e5c4bfb9b200acae95db50cc78fa9f86 | Python | 12,190 | 451 | import pytest
import networkx as nx
from networkx.utils import edges_equal
def test_union_attributes():
g = nx.Graph()
g.add_node(0, x=4)
g.add_node(1, x=5)
g.add_edge(0, 1, size=5)
g.graph["name"] = "g"
h = g.copy()
h.graph["name"] = "h"
h.graph["attr"] = "attr"
h.nodes[0]["x"] ... |
373f3ef125fb7265bfbda0f1aedb771f2fb7780446d9f9c02cb96194a59aa142 | Python | 12,193 | 348 | """ Base processing tasks for cloud workflows """
import time
from .. import seg_utils
from . import seg
from . import edge
from . import overlap
from . import anchor
from . import hashing
from . import utils
from . import colnames as cn
def timed(fn_desc, fn, *args, **kwargs):
""" Measures the execution time ... |
f7d4a73e7a944b52699f45a8a80665cde8cf4f4049f37920c1e704711d4ed8b7 | Python | 12,194 | 304 | import sys, os, platform
from src.utils import get_p_val_string, get_exact_p
import numpy as np
import pandas as pd
import scipy as sp
import nibabel as nib
import math
from scipy import stats
import seaborn as sns
import pkg_resources
import matplotlib as mpl
import matplotlib.pyplot as plt
def set_plotting_params... |
4564dadc1636e6c35825cb729cc126dc91166ae5f3778a9076c458eca1a94fff | Python | 12,197 | 368 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Mar 11 13:56:08 2020
@author: amelie
"""
from brian2 import *
from scipy import signal
from FEF_full3_alternate3 import *
from LIP_full_alternate3 import *
from itertools import *
def generate_syn(source,target,syntype,connection_pattern,g_i,tau... |
3a8d9cf4a771a322b8e1ae2904896b0db0f70bbb9f9f6cec282695ddfb1de7c9 | Python | 12,204 | 204 | """
06_cohort_stats.py - Cohort statistics for the tDCS conductivity-model study (the main group deliverable).
Concatenates per-subject ROI E-field CSVs; computes paired MD-dMRI-vs-DTI/ISO (Wilcoxon), PD-vs-HC, and
partial age correlation per ROI per montage, with BH-FDR within each (montage, test-family).
PD-vs-HC PR... |
a8e6001d1ae2fc1cac67189440fc599a8559171e0cea32b41dce47ea7e2ed5bb | Python | 12,204 | 304 | # 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... |
3c2d5334d28a5a23b2d48f5bcfe5f4d74c8eebd444083856022cfca247fd686a | Python | 12,205 | 331 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Example usage:
python -m utils.benchmark 2 scrna/visium_brain_sagittal/data/visium_brain_sagittal_J2000.h5ad
Fit a model to a dataset and save the results.
Inputs:
* integer row ID (from slurm job array), pulls out one set of params from csv
* parent directory o... |
b094c758e8e6213ddd5d773f1c1a5532b4f6423afd0a02c4fc6a6c81cb5b7c80 | Python | 12,210 | 353 | """Functions for splitting a network into two communities (finding a bipartition)."""
import random
from copy import deepcopy
import networkx as nx
__all__ = [
"kernighan_lin_bisection",
"spectral_modularity_bipartition",
"greedy_node_swap_bipartition",
]
def _kernighan_lin_sweep(edge_info, side):
... |
b608eb29858ae06c27cc114e30ff54c6393503fe191ced32b8109abba13a89b8 | Python | 12,218 | 355 | # 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 collections.abc import Mapping
from enum import StrEnum
from logging import Logger
from typing import Protocol
import n... |
d4fd83f4d314dcc0eb4a61cbc1a492a6a109d50514e7cfac5aa607d8018d1bff | Python | 12,223 | 334 | import os
import matplotlib
matplotlib.use("agg")
import numpy as np
import nibabel as nib
import scipy.io as sio
import matplotlib.pyplot as plt
from bids.layout import BIDSLayout, parse_file_entities
from scipy import stats, signal
from scipy.sparse import lil_matrix
from rsHRF import (
spm_dep,
processing,
... |
97f6b50d090dbe40a2852bbe7a955ced36d4e5873d35b4ec626bda06a06a31ac | Python | 12,230 | 263 | from torch.utils.data import Dataset
import pandas as pd
import os
from typing import List, Tuple, Iterable
import numpy as np
from tqdm import tqdm
from torch.utils.data import DataLoader
import torch
from sklearn.model_selection import StratifiedShuffleSplit
class CovidData:
def __init__(self, csvs_dir: str, st... |
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