sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
d1dc96a0c417760cb3902d8e79aa2641e93751f0a1337bbc855a3997c8c6c4c1 | Python | 22,059 | 566 |
''''
Main function for traininng DAG-GNN
'''
from __future__ import division
from __future__ import print_function
import time
import argparse
import pickle
import os
import datetime
# import torch
import torch.optim as optim
from torch.optim import lr_scheduler
import math
# import numpy as np
from utils import... |
7f0fc2e557ac61a95ce48caff078c2c5b8c61327d58971a39c733282dd968e32 | Python | 22,075 | 576 | """
GTN Search Library - Interface to the GTN SQLite database.
Provides search over Galaxy Training Network tutorials and FAQs
using SQLite FTS5 full-text search with BM25 ranking.
"""
import http.client
import logging
import os
import re
import shutil
import sqlite3
import urllib.request
from dataclasses import data... |
287b970c2e597557f64d60816e0bc8e94ee4f22197e142b80f080d500b8806db | Python | 22,090 | 520 | # -*- 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
# ... |
c844f086f79504853b8ba44e993a8a00432a335695622a7de20ef9d39b4e7c54 | Python | 22,092 | 579 | #!/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
"""Support functions for tests"""
import contextlib
import cProfile
import io
import linecache
import... |
9e98f8affcf44271d9ed411fa7e605bc12da16f6c93f8ef5504223a1cce70849 | Python | 22,103 | 504 | import pandas as pd
import os
def get_cluster_results(savepath_all_users_results_full):
path_to_users_groups = "../postprocess_all_products/"
path_to_results_all_users = savepath_all_users_results_full
dict_cluster_metrics = {'cluster': [],
'RF_F1_mean': [],
... |
45f730e2ff9432c8450396928da563a6af239fbe1982c4c81de99ac4413fa205 | Python | 22,106 | 655 | from abc import ABC, abstractmethod
from sklearn.base import BaseEstimator, RegressorMixin, MultiOutputMixin
from sklearn.utils.validation import check_is_fitted
from ._solvers import RIDGE_SOLVERS
from ._random_search import GROUP_RIDGE_SOLVERS
from ._random_search import solve_ridge_cv_svd
from ..validation import... |
a12637951ec41fa7c5eb9061cfd9bb8b44c614826971c7a1b1797ccc9dafb328 | Python | 22,124 | 489 | """
Job control via the DRMAA API.
"""
import json
import logging
import os
import shlex
import string
import time
from typing import (
TYPE_CHECKING,
TypeAlias,
Union,
)
from galaxy import model
from galaxy.jobs.handler import DEFAULT_JOB_RUNNER_FAILURE_MESSAGE
from galaxy.jobs.job_destination import Job... |
fc2548cf7793e31b391d714508d1a58fa250bf6d60b3899352e699657bb0821b | Python | 22,160 | 569 | #!/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 dataclasses
from unittest.mock import patch
import torch
f... |
c4575e63fe3e6e35c8e078fb18e6a736e5a41f3fd38eade4469015144f78d994 | Python | 22,168 | 620 | """
Unit tests for overall cell density computation
"""
import warnings
from pathlib import Path
import numpy as np
import pandas as pd
import pandas.testing as pdt
import pytest
from voxcell import RegionMap
import atlas_densities.densities.fitting as tested
from atlas_densities.densities import utils
from atlas_den... |
b074fe417624d7652253e7e65a4253d7ebc71b164aea893e556764f58c0bb5f2 | Python | 22,174 | 530 | # 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... |
ce9047ceca6d48a7de688714473b663dab949526d7cf9f0bcff3db763446318f | Python | 22,186 | 581 | # 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... |
ceea9feae04bf70264ad0901f01429ab7a9ae92d1712f9a114a7e4f0a86dbf3b | Python | 22,208 | 666 | from pathlib import Path
from nilearn import datasets
import numpy as np
import pytest
from numpy import random
import nibabel as nib
from ..aabb_tree import AABB
from ..CD_relations import (cardinal_relation,
cardinal_relation_prepare_regions,
direction_matrix,... |
209c7e6cce964daf97e260ace825063930edf9992a51d04f030d44a16c1c1cb2 | Python | 22,216 | 572 | from collections.abc import Sequence
import sys
if sys.version_info >= (3, 12):
from typing import override
else:
from typing_extensions import override
import numpy as np
import tensorflow as tf
from hidten.hmm import HMMConfig as HidtenHMMConfig
from hidten.prior import Prior
from hidten.tf.transitioner impo... |
5b5a360774a20ba10dc0e4753e7e650f06bc2384ce541f97f7fff5f8cf998c7a | Python | 22,217 | 429 | import torch
from torch.nn import functional as F
from models.fc.layers import fc_layer
from models.fc.nets import MLP
from models.conv.nets import ConvLayers
from models.cl.memory_buffer import MemoryBuffer
from models.cl.continual_learner import ContinualLearner
from models.utils import loss_functions as lf, modules
... |
518a3f2c982855770cd622cc5ecc0cda0e23bd4266bf1967ddee5b55f5f1435d | Python | 22,253 | 687 | """
Link prediction algorithms.
"""
from math import log
import networkx as nx
from networkx.utils import not_implemented_for
__all__ = [
"resource_allocation_index",
"jaccard_coefficient",
"adamic_adar_index",
"preferential_attachment",
"cn_soundarajan_hopcroft",
"ra_index_soundarajan_hopcro... |
c3d8c9baf46f489a97370cd84c0138e20c2bc82d8d9a20c81df57c4b8153c864 | Python | 22,261 | 517 | """
Copyright (c) 2019 10x Genomics, Inc. All rights reserved.
Consume multiple fastq files and spit out a pooled fastq file with targeted adapters removed from the ends of the reads.
"""
from __future__ import division
import itertools
import json
import random
from subprocess import PIPE
from barcodes import load_... |
441cb79e0eb27de80564c854b897162bfc1d531f3c4ae34995110451b67d44b5 | Python | 22,265 | 725 | import itertools
import math
import operator
import re
import warnings
import numpy
import pytest
from nl_core.datalog.basic_representation import DatalogProgram
from nl_expr.exceptions import UnsupportedProgramError
from nl_expr.expressions import Constant, Symbol
from nl_expr.logic import Conjunction, Implication
f... |
a5959d1703c3c3aac63bbd0d7573d017c00498c22a1352f5fb19c7e94cf2b77c | Python | 22,284 | 562 | # 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 datetime import datetime
from unittest.mock import patch
import pandas as pd
from ax.adapter.base import Adapter
from ... |
0616f8e0c5bba5ac02310828d69e9163966925c699ca6b185cc39350e6874141 | Python | 22,289 | 598 | # -*- coding:utf-8 -*-
import collections
import copy
import hashlib
import time
from functools import partial
import numpy as np
import pandas as pd
from sklearn.compose import ColumnTransformer
from sklearn.pipeline import make_pipeline
from hypernets.tabular import sklearn_ex as skex, get_tool_box, is_dask_instal... |
e07a5b8633384b54233f01e6771fede9c28dbf6782ebfe98c1ca3d9f6b1cf751 | Python | 22,295 | 564 | # 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 logging
import unittest
from copy import deepcopy
from unittest import mock
import numpy as np
import numpy.typing a... |
5e3a3fe8a8e24d58fb23607e03496766caf7645910279f0566a11cc555ad2234 | Python | 22,298 | 550 | import logging
import re
from typing import (
Optional,
TYPE_CHECKING,
Union,
)
from sqlalchemy.dialects.postgresql import insert as postgresql_insert
from sqlalchemy.dialects.sqlite import insert as sqlite_insert
from sqlalchemy.exc import IntegrityError
from sqlalchemy.orm import (
scoped_session,
... |
4e22428ba1ed6f29cf7ea48d8781ca63d6d3fba6b45863f1b6833a993bc6f163 | Python | 22,303 | 657 | from __future__ import annotations
import warnings
import weakref
from collections import defaultdict
from typing import Any, Callable
import torch
import torch.nn as nn
from torch.overrides import resolve_name
from ..neuron.base_node import BaseNode
from ._sparse_memory import active_element_count, dense_bytes, is_... |
9222f4492cac648549b647405cf0b2a544e24dd1d01ebde735311eefd70a580f | Python | 22,311 | 567 | import warnings
import ipywidgets as widgets
import matplotlib.patheffects as path_effects
import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns
from IPython.display import display
from scipy.cluster.hierarchy import dendrogram
from scipy.stats import zscore
from .colormap_helper import distinct_cm... |
138d9e5338fd6962a112d36c1a724a5febf9a3a52a046b9bdad7cc5d59f84499 | Python | 22,315 | 586 | # 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 import OrderedDict
from unittest import TestCase
from unittest.mock impo... |
91c995d4db0fc54b440a4f1e7f5f51794534339340c5c19a3e44015a96e77a47 | Python | 22,330 | 379 | # -*- coding: utf-8 -*-
"""
Created on Fri Jul 5 10:13:28 2019
@author: schelskim
"""
import os
import numpy as np
import pandas as pd
from skimage import io
import copy
import math
from skimage.draw import line_aa
import re
class Analyzers():
@staticmethod
def analyzeIntensities(dat... |
314dcc4b1286fb72c62fec84250e3eafe4bfeb55cde8df553990c7ad0f2f2951 | Python | 22,335 | 431 | import torch
from torch.nn import functional as F
from models.fc.layers import fc_layer
from models.fc.nets import MLP
from models.conv.nets import ConvLayers
from models.cl.memory_buffer import MemoryBuffer
from models.cl.continual_learner import ContinualLearner
from models.utils import loss_functions as lf, modules
... |
e9474e2277297006c43acd7d5889d59a3b52bd29df2c1ad95fd21ca91fc43235 | Python | 22,337 | 707 | """Optimisers rewriting and pushing selections."""
import operator
from nl_expr import expression_walker as ew
from nl_expr.expressions import Constant, FunctionApplication
from ..relational_algebra import (
Column,
ColumnInt,
ColumnStr,
EquiJoin,
ExtendedProjection,
FullOuterNaturalJoin,
... |
b2c6d5fba48c3f04c7d1bc1532124ae12dcec8ca4f801b58bc4e35ef794df198 | Python | 22,374 | 517 | # 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... |
d20af360a3ad68c37735c1bac1f919d654ac244725fd696ef98773c123e03a17 | Python | 22,397 | 574 | # 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... |
eaac472d67081c01e4b69e2729a169eb23948fb258b2e283d3b4569f86b6a2ea | Python | 22,411 | 617 | # -*- coding: utf-8 -*-
"""
Created on Mon Dec 2 14:28:44 2019
@author: aaussel
"""
#import matplotlib
#matplotlib.use('Agg')
from brian2 import *
start_scope()
from scipy import signal
from cells.RS_LIP_alte import *
from cells.FS_LIP_alte import *
from cells.SI_LIP import *
from cells.IB_soma_LIP import *
from c... |
9d55016ed4de2d21ec82d4ac16604d0bfae9fcd13e97d626496ddd43b0e82c6e | Python | 22,418 | 534 | # 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... |
86dd63c4adb8a5b4e285ae6bd0ee1762cf25b4a7773819861aed0ada90e9cdf9 | Python | 22,432 | 525 | import warnings
import numbers
import numpy as np
from ..backend import get_backend
from ..backend._utils import _dtype_to_str
from ..progress_bar import bar
from ..scoring import l2_neg_loss
from ..validation import check_random_state
from ..validation import check_cv
from ..kernel_ridge import generate_dirichlet_sa... |
53db8d22c7c0e416c7ef9cb370e648b19235c7fc5c349a2e1ba49640293c4a93 | Python | 22,437 | 533 | import hashlib
import json
import logging
import pathlib
import shutil
from datetime import datetime
from functools import reduce
from core.redis import redis_connected, start_job_async_or_sync
from core.utils.common import batch
from core.utils.io import (
get_all_dirs_from_dir,
get_all_files_from_dir,
ge... |
dd81db2e3ea23c5c9b7df12d8b6f313f64542dccb8860d972ecc1edc52df76b0 | Python | 22,440 | 554 | import os
import tempfile
from copy import deepcopy
import feather
import numpy as np
import pandas as pd
import pytest
import ark.phenotyping.cell_cluster_utils as cell_cluster_utils
import ark.phenotyping.cluster_helpers as cluster_helpers
import ark.phenotyping.weighted_channel_comp as weighted_channel_comp
def ... |
a9a2098158f6dbc46e6f17e421b3646f0c8e10d546385eab92422de93b944684 | Python | 22,446 | 638 | import numpy as np
from matplotlib import pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
import os
import glob
from scipy.stats import zscore
import importlib
import zipfile
import math
import utils
import scipy as sp
from scipy import io
import scipy.signal
from scipy.sparse.linalg import eigsh
import csv
impor... |
e38ebd963743cf94a03d204ebe90acb75cdc8fccd4c05668616f09098e728827 | Python | 22,465 | 579 | # 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... |
c68e01ef750f09b3302f0eff2f2974c0d091e2a5dba0da5b9dc0f23b69f454cb | Python | 22,470 | 618 | """Optimisers flattening, simplifying and reordering joins and products."""
from functools import reduce
from itertools import combinations
from nl_expr import expression_walker as ew
from nl_expr.expressions import Constant
from ..relational_algebra import (
NameColumns,
NaturalJoin,
NaryNaturalJoin,
... |
19727414589d7e6d0edbb2462a5946be5d129b57acfae48d1d592fd026be5c1d | Python | 22,479 | 488 | # This file is now part of the Galaxy Project, but due to historical reasons
# reflecting time developed outside of the Galaxy Project, this file is under
# the MIT license.
#
# The MIT License (MIT)
# Copyright (c) 2012,2013,2014,2015,2016 Peter Cock
# Copyright (c) 2012 Edward Kirton
# Copyright (c) 2013 Nicola Soran... |
4a0d57ee275d3967d841688d75abf677fceaf7341c6bec63478822a532e8a2b7 | Python | 22,483 | 589 | import numpy as np
class PHMMTransitionIndexSet:
""" Indices for accessing groups of values in a PHMM transition matrix.
Uses the state order\\
M1 ... ML I1 ... IL-1 D1 ... DL LF B E C RF T\\
if not folded, and otherwise\\
M1 ... ML I1 ... IL-1 LF C RF T.
Attributes:
L: Number of matc... |
77fb17852b8dc66d0f6511d771032b53902be718c009333e82eb2a08c8f64dc1 | Python | 22,520 | 507 | import numpy as np
from astropy.convolution import Gaussian2DKernel,AiryDisk2DKernel
import cv2
import scipy
import copy
from collections import namedtuple
import tensorflow as tf
import tensorflow_addons as tfa
class Kernel():
def __init__(self):
self.px_size = 100
seed = 42 # switch seed
... |
76106ff0e467048ad2697130c036fe59cfb85bd53752251707c971064449318f | Python | 22,530 | 557 | # 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... |
6c8be69c528fc69f3a831dc4b4f3448e9b7b9d533567d9975b738295d2ccadb4 | Python | 22,541 | 585 | """Galaxy job runners to use Amazon AWS native compute resources, such as AWS Batch."""
import bisect
import hashlib
import json
import logging
import os
import re
from typing import (
Any,
TYPE_CHECKING,
Union,
)
from galaxy import model
from galaxy.job_execution.output_collect import default_exit_code_f... |
ee10327fa691b3ac9438eccb4b5751b4ece016d42eccb1678ef0e138bc81e5d8 | Python | 22,547 | 647 | from __future__ import annotations
from collections.abc import Iterable, Sequence
from enum import Enum
from functools import singledispatch, wraps
from itertools import repeat
from types import EllipsisType
from typing import TYPE_CHECKING, Literal, NamedTuple, cast, overload
import h5py
import numpy as np
import pa... |
6475cfdb945d75b1e82adbcca17b98b6ff84f0d0a1c40531b7f302954941f0de | Python | 22,576 | 521 | # 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... |
3aa2f26c1c13855d0846ad31c2796c10d58107dfa1c3c0dcbf9a543e0e50b4ac | Python | 22,580 | 566 | from __future__ import absolute_import
import errno
import logging
import operator
import os
import shutil
from optparse import SUPPRESS_HELP
from pip._vendor import pkg_resources
from pip._internal.cache import WheelCache
from pip._internal.cli import cmdoptions
from pip._internal.cli.base_command import Requiremen... |
f9a864cba22bcdc82cea3f33f0f5b41e3a236269ba2cc7d58446353537d066b4 | Python | 22,588 | 704 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from __future__ import annotations
from collections.abc import Sequence
from dataclasses import dataclass
from enum import Enum
from functools import cached_property
from typing import TYPE_CHECKING, Any
from django.conf import settings
from django... |
61887934e566dba4f0da598b5378e85898b8c83b8f36638b741d7178dc78aa17 | Python | 22,592 | 668 | from __future__ import annotations
from abc import ABC, abstractmethod
from collections.abc import MutableMapping
from copy import copy
from dataclasses import dataclass, field
from itertools import chain
from typing import TYPE_CHECKING, cast, overload
import h5py
import numpy as np
import pandas as pd
import zarr
f... |
9f6753f9901e6a193df67f1c2188821d4fe90f2327ce4947260b81c2b9909db6 | Python | 22,593 | 581 | """
Tests for Group Centrality Measures
"""
import itertools
from functools import partial
import pytest
import networkx as nx
class TestGroupBetweennessCentrality:
def test_group_betweenness_single_node(self):
"""
Group betweenness centrality for single node group
"""
G = nx.pa... |
698be01c72d1aa9cbd48f13e1fd980287b2a2c13a266284ed5e3b3386737ea17 | Python | 22,617 | 701 | #!/usr/bin/env python
#
# Copyright (c) 2016 10X Genomics, Inc. All rights reserved.
#
#
# Determine the locations of the cell barcode, cDNA sequence, UMI, sample index.
#
from collections import OrderedDict
import copy
import tenkit.constants as tk_constants
import tenkit.fasta as tk_fasta
import tenkit.stats as tk_st... |
e9cd92f1134bb42c5a5f19840a9333aab45b74b05e4ec7bfd3acf0f38981b071 | Python | 22,644 | 539 | from brian2 import Synapses, ms
import re
import numpy as np
from .parameter_checks import *
from .constants import synapse_sign_mode
class LoihiSynapses(Synapses):
"""
The LoihiSynapses extends the Synapses class from Brian2.
This class provides Loihi parameters for delay and pre- and post-synaptic
t... |
4fc9f557fc7e3f963beb8fac19d00b81fe2d3ea2d0c1d8c3bf8b825631e75a47 | Python | 22,656 | 486 | # 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.
#
# ## ### ### ### ### ### ... |
7bf1612e4956a420cff2e4c9d6ea23ca31833f368428fc84714bb1cea27a72c8 | Python | 22,673 | 619 | #!/usr/bin/env python3
# -*- 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 Licen... |
a7f8ea7df262bfdca1eccf4ef75aff797a692ac9e91c04a788d582e6e89f8259 | Python | 22,680 | 583 | # 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"... |
53a120aa7805b85d321ad6fb4b677b12b4265fea7ae7e87d962d08e693cc78a4 | Python | 22,699 | 683 | """
This module contains all classes and functions required to run the scaffold
from the command line.
"""
import sys, os
import configparser
import builtins
import argparse
import traceback
from types import ModuleType
##
## This is the package entry point API and REPL.
##
def scaffold_cli():
"""
c... |
9c55505ffd0c6b15193bf1b50b42b126d6dfe66331d8e148c86c1f198773aa6d | Python | 22,719 | 656 | # 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... |
f240f28e7c0897f12d1cad6f9c88353af590645465156c8bf9533652780ea6c2 | Python | 22,748 | 568 | """Test the find_noisy_channels module."""
# Authors: The PyPREP developers
# SPDX-License-Identifier: MIT
import logging
import numpy as np
import pytest
from pyprep.find_noisy_channels import NoisyChannels
from pyprep.ransac import find_bad_by_ransac
from pyprep.removeTrend import removeTrend
# Set a fixed rando... |
de8be2d291f4312114ed8e75fd33a650cf53cc5da1e07de417ff9b72e0cbf93e | Python | 22,763 | 570 | # Copyright 2010-2015 by Haibao Tang. All rights reserved.
#
# This code is part of the goatools distribution and goverend by its
# license. Please see the LICENSE file included with goatools.
"""Read and store Gene Ontology's obo file."""
# -*- coding: UTF-8 -*-
from __future__ import print_function
import sys
impor... |
c987662e4d4370fbaeca2245154663833a1b841ac42235dd68ff9b4fab696e69 | Python | 22,784 | 476 | """
Created on Feb 22, 2024.
@author: voodoocode
"""
import os
import shutil
import mne
import numpy as np
import nibabel.freesurfer
import warnings
import matplotlib.pyplot as plt
import finnpy.misc.external_calls as ex_c # @UnresolvedImport
def init_paths(freesurfer_path, anatomy_path,
fastsurfer_... |
4f84b686d4a625c632a04771e923571c6c05d95e1cdf8a764fe7272770fb5469 | Python | 22,787 | 576 | """ Module Docstring """
# Standard Imports
from time import time
# Third Party Imports
import torch
import numpy as np
from scipy import spatial
from sklearn.utils.extmath import randomized_svd
# Custom Module Imports
from .video import RegionMetadata
from .video import LowRankVideo
from .demix import HalsNMF
from .... |
6e59c5be022e8198a3c4f01391f023f7781f0db2efce0a03ba54aa56cff464b1 | Python | 22,817 | 625 | """
Copyright © 2025 Howard Hughes Medical Institute, Authored by Carsen Stringer , Michael Rariden and Marius Pachitariu.
"""
import os, gc
import numpy as np
import cv2
import fastremap
from ..io import imread, imread_2D, imread_3D, imsave, outlines_to_text, add_model, remove_model, save_rois
from ..models import no... |
1eda473544e9a022f44c94c9339817f8210a06dcf502e5e4db52539d632e6353 | Python | 22,837 | 610 | import hashlib
import logging
import os
import shutil
from typing import Optional
try:
import rucio.common
from rucio.client import Client
from rucio.client.downloadclient import DownloadClient
from rucio.client.uploadclient import UploadClient
from .rucio_extra_clients import (
DeleteClie... |
26680a14fff063bdfa8e234b234a3cc117ea7f9bf563101e7d6d64d94a3083ea | Python | 22,841 | 560 | # -*- coding: utf-8 -*-
"""
Created on 2020.05.19
@author: Jiahua Rao, Weiming Li, Hui Yang, Jiancong Xie
Code based on:
Yang et al "Analyzing Learned Molecular Representations for Property Prediction" & "A Deep Learning Approach to Antibiotic Discovery" -> https://github.com/chemprop/chemprop
Song et al "Communicati... |
1555dcce30dd68a62163d71ab4c50c06004b66cfcca64794ba7da7dd491367a0 | Python | 22,898 | 682 | # 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... |
46b5f6efe93c7dd1bccd60574415aa4f6a69dc00095ac50985a26e060ed0b762 | Python | 22,902 | 563 | #!/usr/bin/env python
#
# Copyright (c) 2015 10X Genomics, Inc. All rights reserved.
#
import collections
import itertools
import json
import numpy as np
import os
import re
import sys
import tenkit.constants as tk_constants
import tenkit.fasta as tk_fasta
import tenkit.safe_json as tk_safe_json
import tenkit.seq as tk... |
ab2f0d7779389a99b71b8bfa25bec657dc12c101a24243dce50be94d09c0708e | Python | 22,910 | 699 | from typing import (
Annotated,
Any,
Literal,
Optional,
Union,
)
from pydantic import (
Field,
model_validator,
RootModel,
)
from galaxy.util.config_templates import (
ConfiguredOAuth2Sources,
EnvironmentDict,
expand_raw_config,
get_oauth2_config_from,
ImplicitConfi... |
a86fc39216512e193b1e5df80f402c01ec14fa77c876ade5dc000ec8d90c5bc8 | Python | 22,925 | 726 | import operator
from typing import AbstractSet
import numpy as np
import pytest
from nl_expr.expressions import Constant, Symbol
from nl_expr.exceptions import RelationalAlgebraError
from ..probabilistic.cplogic import testing
from ..relational_algebra import (
ColumnInt,
ColumnStr,
NaturalJoin,
Produ... |
13ca4802cc31c077e81b9b813a1193b0234c0a2a4d6946de375c326d7fb185eb | Python | 22,932 | 659 | import numpy as np
import pytest
import tensorflow as tf
from pathlib import Path
import learnMSA.model.training_util as training_util
import tests.hmm.ref as ref
from learnMSA.config import Configuration, TrainingConfig, TreeConfig
from learnMSA.config.hmm import PHMMPriorConfig
from learnMSA.model.tf.model import Le... |
ab47eb051e2cc0fb2f888ac286d1ac9d888462467a0c610a9242122f4548f602 | Python | 22,943 | 589 | import os.path as op
import pickle
import sys
from pathlib import Path
# Need this to make sure that ants.registration is available for mocking in tests
import ants.registration # ruff: ignore[F401]
import mne
import nibabel as nib
import numpy as np
import pytest
from mne.datasets import sample
from nibabel import N... |
6c39de2541991c43479ebea3686e8f3c43d92b567b2230cfa4d5cf81e1be998c | Python | 22,950 | 582 | """
A server collecting the answers of the query assistant and their ratings.
The assistants that share their answers (``feedback`` in the LLM
configuration, see :mod:`.feedback`) post them here; people rate them
correct, incorrect or unsure and correct their query, from the REPL
(``.rate``, ``.refine``) or the review... |
47c874884190b5c2316dd3535d221ee30b01b034d36c6556225a8109809291e9 | Python | 22,953 | 555 | import os
import os.path
import resource
import shutil
import subprocess
import sys
import pysam
import pandas as pd
import numpy as np
import tenkit.log_subprocess as tk_subproc
import tools.regions as regtools
from collections import namedtuple, Counter
from cellranger.h5_constants import GZIP_SUFFIX, LZ4_SUFFIX
fro... |
ded3380337a837515245a66fa9101e047f6473076c340b10d733c88a88c8498b | Python | 22,980 | 655 | r"""
.. codeauthor:: Yanqi Chen <chyq@pku.edu.cn>, Ismail Khalfaoui Hassani <ismail.khalfaoui-hassani@univ-tlse3.fr>
A reproduction of the paper `Technical report: supervised training of convolutional spiking neural networks with PyTorch <https://arxiv.org/pdf/1911.10124.pdf>`_\ .
This code reproduces an audio recogn... |
4bbe5878f74c4e52aff7900946ec506f82997d1fc2c7fd87dade469001717582 | Python | 22,999 | 562 | from __future__ import division
import math
import random as rd
import networkx as nx
import numpy as np
# from pysbm import sbm
from MolRep.Interactions.link_models.CFLP.pysbm import sbm
class NetworkSuppplier(object):
""" Create different types of graphs"""
STANDARD_SEED = 42
def __init__(self):
... |
3f9be04df034be98bce3e0975411e9bfd3b8d32424a7d6b41bd86e7b55eb87c7 | Python | 23,008 | 582 | import numpy as np
import warnings
import math
from tqdm import tqdm
from skimage.measure import regionprops
from skimage.draw import polygon
from csbdeep.utils import _raise, axes_check_and_normalize, axes_dict
from itertools import product
from .geometry import polygons_to_label
OBJECT_KEYS = set(('prob', 'points... |
7d9fb26bb33419b03dcb8fa52eb3a8e24783503091002a1983945bded52434e1 | Python | 23,020 | 582 | import numpy as np
import warnings
import math
from tqdm import tqdm
from skimage.measure import regionprops
from skimage.draw import polygon
from csbdeep.utils import _raise, axes_check_and_normalize, axes_dict
from itertools import product
from .geometry import polygons_to_label
OBJECT_KEYS = set(('prob', 'points... |
8c5be97d7ad3021088d0e5ec7da27ecf1e2bb918a08d834a201febe4d345552e | Python | 23,074 | 593 | import imageio
import numpy as np
from hidten.visualize import Figure, SubFigure, plot_emissions, plot_transition_graph
from matplotlib import pyplot as plt
from matplotlib.gridspec import GridSpec, GridSpecFromSubplotSpec
from learnMSA.util import SequenceDataset
from learnMSA.hmm.tf.layer import PHMMLayer
def phmm... |
e84cca6c33df12d7235c5a9386f738d8819361460e5cd94048e6919afade86e2 | Python | 23,085 | 561 | #!/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 contextlib import ExitStack
from copy import deepcopy
from unittest import mock
from unittest.moc... |
5d9bf2cbf42a05c1404cc72f121ea94ff466a2075f112c7144457b5248a14f8d | Python | 23,103 | 613 | # 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
from logging import Logger
from typing import Any, final
import numpy as np
im... |
7af55a106332545a68eb2b4452cdb94a9a4688d8c16e8b86e9b5b936e795b7ee | Python | 23,110 | 584 | #!/usr/bin/python3
"""
Implementation of the grammatical evolution
Author: Leonardo Lucio Custode
Creation Date: 04-04-2020
Last modified: mer 6 mag 2020, 16:30:41
"""
import re
import os
import sys
import deap
import random
from deap.algorithms import varAnd
os.environ['OPENBLAS_NUM_THREADS'] = '1'
import numpy as np... |
6efea2f136a2d55b93466949a47f8a914a666b5ffd26846420bc79f5d20b821f | Python | 23,122 | 559 | import json
import errr
import numpy as np
from bsb import CellType, Chunk, DatasetNotFoundError, chunklist
from bsb import ConnectivitySet as IConnectivitySet
from .resource import (
HANDLED,
Resource,
handles_class_handles,
handles_handles,
handles_static_handles,
)
_root = "/connectivity/"
c... |
3aebde829bf38b9cce7f63cd5246eef2bc48bc762877316c713b819ac8f17e3b | Python | 23,136 | 677 | import numpy as np
import warnings
import numbers
import scipy
import matplotlib.pyplot as plt
from abc import ABC, abstractmethod
from sklearn.neighbors import NearestNeighbors
class YourCustomKNN(ABC):
""" Template class helper for custom knn """
def __init__(self, your_custom_param):
self.your_cus... |
2c1b9b98c69805829e342962ff6fe05ea9dddcf14974d5441db1acdc27443e20 | Python | 23,141 | 548 | """GTN Training Agent - searches Galaxy Training Network tutorials and FAQs."""
import json
import logging
import re
from pathlib import Path
from typing import (
Any,
Optional,
)
from pydantic import (
BaseModel,
Field,
)
from pydantic_ai import (
Agent,
RunContext,
)
from galaxy.schema.agen... |
d53d72598f0ca269b634cbbcac13c7f199c09663d6ab5707a64119be1e96923c | Python | 23,141 | 554 | from typing import (
Any,
cast,
Dict,
List,
Optional,
TYPE_CHECKING,
Union,
)
from typing_extensions import TypedDict
from galaxy.tool_util.parser.interface import (
InputSource,
PageSource,
PagesSource,
ToolSource,
)
from galaxy.tool_util.parser.parameter_validators import... |
f60f0a1146b3eb66b87d1801f90070b19a616257835d0539519a46203ac205b6 | Python | 23,141 | 561 | """
Graph summarization finds smaller representations of graphs resulting in faster
runtime of algorithms, reduced storage needs, and noise reduction.
Summarization has applications in areas such as visualization, pattern mining,
clustering and community detection, and more. Core graph summarization
techniques are gro... |
1eaefd97f713d04190cfbc0de615e74a5855acc9f991fa4ea970af3a21f0f167 | Python | 23,142 | 735 | import pytest
from seqeval.scheme import (BILOU, IOB1, IOB2, IOBES, IOE1, IOE2, Entities,
Entity, Prefix, Token, Tokens, auto_detect)
def test_entity_repr():
data = (0, 0, 0, 0)
entity = Entity(*data)
assert str(data) == str(entity)
@pytest.mark.parametrize(
'data1, data... |
0c893ff417b71f4f559b31e60b6c1ceb56beb89e6bc0b71952749c4a421ce938 | Python | 23,147 | 448 | import function as func
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import matplotlib.ticker as mtick
import seaborn as sns
import pdb
import os
import re
import math
import vcf
import pysam
import sys
import lockfile
import datetime
from time import sleep
from os.path import exists
## Varia... |
dd32dd1ec8fdd1e75197386ea42ab691daea7ddcfcc01bc888a539bbe3474fef | Python | 23,147 | 503 | # real non truncating division (same behaviour as in python 3)
from __future__ import division
import math
from .peixotos_hierarchical_sbm_tools import log_binom
# from pysbm import sbm
from MolRep.Interactions.link_models.CFLP.pysbm import sbm
import networkx as nx
def minimum_description_length_peixoto_first(par... |
eebe58dc0fadacb86658bed8c471c922a64bcaecedcb39482f7bbd7a35fed238 | Python | 23,173 | 564 | #!/usr/bin/env python
# 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
# "L... |
88ab0fff79946f298ea58b464b7cce3f4528bd6f367eb0f24f5ee0d813a31ee7 | Python | 23,180 | 546 | import torch
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
import pandas as pd
import random
import pickle
import math
from Model.DRPreter import DRPreter
from torch.utils.data import Dataset, DataLoader
from torch_geometric.data import Batch
from sklearn.model_selection import tra... |
389b66f2e5110fbbac1274b91c28506e23a4502aa775fc0233194e743074b08b | Python | 23,189 | 645 | from collections import namedtuple
from itertools import chain, tee
import logging
from nl_expr.logic import Union
from operator import contains, eq
from typing import Iterable, List, Tuple, Type
from nl_expr.exceptions import (
NeuroLangException,
NoValidChaseClassForStratumException,
)
from nl_expr.expressio... |
2429d10fe3422d7d3645468d01727fc79a615621143da942fd42f35b3851c002 | Python | 23,200 | 635 | """Tests of the LLM query assistant in the REPL: ``.ask`` and ``.llm``."""
import io
import json
import pytest
pytest.importorskip("prompt_toolkit")
pytest.importorskip("rich")
pytest.importorskip("httpx")
from rich.console import Console # noqa: E402
from neurolang_apps.utils.llm.config import parse_config # no... |
472bbbb4b4ce0520fa2678b69c0ad43a99d60dc2a70f0d35ca0fc1e33427cdfc | Python | 23,214 | 565 | # 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
from functools import partial
from typing import final
import pandas as pd
fr... |
f986494b6453ae10ee61566c0323f15d23f7c2c2e2f3264a7a12359598a5a3d5 | Python | 23,226 | 597 | # 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 inspect
from collections import Counter
from datetime import datetime
from typing import Any, get_type_hints
from ax.... |
579d4b0c48f6e2cb99b49fef1f051c719867276e295a6959757f983608f07cd3 | Python | 23,249 | 596 | """Betweenness centrality measures."""
import math
from collections import deque
from heapq import heappop, heappush
from itertools import count
import networkx as nx
from networkx.algorithms.shortest_paths.weighted import _weight_function
from networkx.utils import py_random_state
from networkx.utils.decorators impo... |
1d6005b6df3e6cb0ce2b486c5efcaa1bb31b7174dddb27614c601c2fa8471068 | Python | 23,262 | 658 | from warnings import warn
import numpy as np
from numcodecs.registry import codec_registry
from zarr._storage.store import DEFAULT_ZARR_VERSION
from zarr.core import Array
from zarr.errors import (
ArrayNotFoundError,
ContainsArrayError,
ContainsGroupError,
)
from zarr.storage import (contains_array, cont... |
32d57bfd38d6a5bda92efbb47b808db0a8fbdc1d334d83dd20ae69aa88a1d194 | Python | 23,268 | 614 | """Tests for lazy loading annotations feature (FIT-720).
This module tests the AnnotationStubSerializer and the annotations_stub
query parameter for the TaskAPI endpoint.
"""
from organizations.tests.factories import OrganizationFactory
from projects.tests.factories import ProjectFactory
from rest_framework.test impo... |
966e4dc47c7c6970873d9a022069b09b58b11ab1d5fcefd2cb6e171225e60aac | Python | 23,292 | 573 | import itertools
import os
import pathlib
from typing import Dict, Optional, Union
import matplotlib.pyplot as plt
from matplotlib import colormaps
import natsort as ns
import numpy as np
import pandas as pd
import scipy.ndimage as ndi
import skimage.io as io
from alpineer import image_utils, io_utils, load_utils, mis... |
2a3aecad9bf1388863b28ad6d836434957686ba4c6aa118f238fc1949bc7d5e9 | Python | 23,301 | 623 | # -*- coding: utf-8 -*-
"""
Created on Mon Dec 2 14:28:44 2019
@author: aaussel
"""
#import matplotlib
#matplotlib.use('Agg')
from brian2 import *
start_scope()
from scipy import signal
from cells.RS_LIP import *
from cells.FS_LIP import *
from cells.SI_LIP import *
from cells.IB_soma_LIP import *
from cells.IB_ax... |
167e19f16c7b213f6ad6b5777fc8240cda971d61aac820d1f6849aeed879022d | Python | 23,307 | 660 | import math
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.nn.modules.module import Module
from torch.nn.parameter import Parameter
from .. import BaseModel
from cogdl.utils import spmm
class GraphConvolutionBS(Module):
"""
GCN Layer with BN, Self-loop and Res connection.
... |
fc512ec0a5fa2657b1957738d2c0f049df3c5f510c97cf6e0581f5654e1c8de8 | Python | 23,307 | 459 | # 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... |
d5d3b2efecb2e839cb6e1deae3d724a4b89e871f97ca566385e952f7c507b726 | Python | 23,316 | 624 | # -*- coding: utf-8 -*-
"""
Created on Mon Dec 2 14:28:44 2019
@author: aaussel
"""
#import matplotlib
#matplotlib.use('Agg')
from brian2 import *
start_scope()
from scipy import signal
from cells.RS_LIP import *
from cells.FS_LIP import *
#from cells.SI_LIP import *
from cells.SI_LIP_alt import *
from cells.IB_so... |
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