sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
4017d1b425495b35dd0d630a7bfd40f0a3d17751a583a7f8befbb29201fce9c1 | Python | 37,750 | 1,012 | # tfmodisco.py
# Authors: Jacob Schreiber <jmschreiber91@gmail.com>
# adapted from code written by Avanti Shrikumar
import mmap
import pickle
import numba
import numpy as np
import scipy
import scipy.sparse
from collections import defaultdict
from concurrent.futures import ThreadPoolExecutor
from . import affinit... |
1893adc947e374157e16c3572db269cdb527b278b9c036878f0a05e018bf7611 | Python | 37,771 | 1,040 | import itertools as it
import pytest
import networkx as nx
from networkx.algorithms import isomorphism as iso
graph_classes = [nx.Graph, nx.DiGraph, nx.MultiGraph, nx.MultiDiGraph]
labels_same = ["blue"]
labels_many = [
"white",
"red",
"blue",
"green",
"orange",
"black",
"purple",
"y... |
9b1fa25844349f7e12a9261232189c7ecd65b46302cb3e63e833e49cae218dc8 | Python | 37,771 | 1,008 | from skimage import morphology, measure, io, util # For performing morphology operations (should maybe import more from skimage...)
from mpl_toolkits.mplot3d import Axes3D # Plotting in 3D
import matplotlib.pyplot as plt # To plot
from scipy.optimize import curve_fit
from pylab imp... |
b1806e55b2a4975d58aa29f1048c6ba3cfedc74190ff99f881bc7d1294b7c4dd | Python | 37,840 | 990 | """Routines related to PyPI, indexes"""
from __future__ import absolute_import
import cgi
import itertools
import logging
import mimetypes
import os
import posixpath
import re
import sys
from collections import namedtuple
from pip._vendor import html5lib, requests, six
from pip._vendor.distlib.compat import unescape
... |
c1f569d8535bad4e9510c83c77c006b05318f2a2f57aa29940cddc786b082bd4 | Python | 37,877 | 784 | # 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... |
407950b9f7e8e4b2e2c7805ae52b55318249fc41ba76e5be5845dc9604ddb58d | Python | 37,882 | 837 | """
TensorFlow implementations of the core MSA decoding operations.
These functions mirror :func:`AlignmentModel.decode_core` and
:func:`AlignmentModel.decode_flank` exactly but operate on ``tf.Tensor``
inputs so they can be JIT-compiled and executed on GPU.
Each function:
* accepts either a ``tf.Tensor`` or a ``np... |
b91dbf0932ab99461cb6ad86fbb5d37edd56ff9148e54cb52e77e11218f4dcb6 | Python | 37,901 | 1,093 | """
Mothur Metagenomics Datatypes
"""
import logging
import re
from typing import (
Optional,
)
from galaxy.datatypes.data import Text
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes.protocols import (
DatasetProtocol,
HasMetadata,
)
from galaxy.datatypes.sniff import (
bui... |
dbfb255bd217434b39ff1d1c42b2573f07395068dca14d7216397fbc0902b7bc | Python | 37,913 | 697 | # -*- coding: utf-8 -*-
"""
Generate docs/_generated/usecase_map.html — a "Global Reach" panel of published
SimBA use-cases, built from the public Google Sheet of citing studies.
Reuses the same vendored Chart.js as the download-stats page, so the styling
matches. The country and institution maps are the globe above i... |
6881b37c59c4ced1371e9c38adb9134d46bb1cf99171a196cd415ef333324db5 | Python | 37,966 | 810 | from meld_classifier.paths import NVERT
import meld_classifier.mesh_tools as mt
from meld_classifier.meld_cohort import MeldSubject
import meld_classifier.meld_plotting as mpt
from meld_classifier.dataset import load_combined_hemisphere_data
from meld_classifier.saliency import integrated_gradients, vanilla_backprop
i... |
c9c478399f6c8cfb76ef834e55322522baff7eef5543d47a5e2254fc451776dd | Python | 37,997 | 867 | """
Google Cloud Batch Job Runner
This runner submits Galaxy jobs to Google Cloud Batch for execution.
"""
import json
import logging
import os
import time
from typing import (
Any,
)
from google.api_core import exceptions as gcp_exceptions
from google.auth import default
from google.cloud import batch_v1
from ... |
9a3ef280b985ef7620837c0da1f79745ba442fb1688cfd43b72648b2837ea8c6 | Python | 38,089 | 850 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from __future__ import annotations
import ast
import json
import math
import unittest
from pathlib import Path
from types import SimpleNamespace
from unittest import mock
import datumaro as dm
import numpy as np
from attrs import evolve
from django... |
3745c4445fa4551e8183d27ba15af8676d3f0d58f2a6d65afce57340dbf95687 | Python | 38,107 | 1,032 | # -*- coding: utf-8 -*-
#
#
# Brainbow segmentation Python XTension
#
# <CustomTools>
# <Menu name = "Brainbow plugins">
# <Item name="Brainbow PCA segmentation (Three component selection)" icon="Python" tooltip="Brainbow segmentation based on PCA.">
# <Command>PythonXT::XTBB(%i)</Comma... |
29313ee6bcbb31eff4faefafc17ce6b0a0c6d73a026d5922d3e0692cf0d69a6b | Python | 38,127 | 918 | import matplotlib.pyplot as plt # To plot
from scipy.optimize import curve_fit
import numpy as np
import random
import math
import time
# Function for curve_fit
def costheta_exponential(s,P):
return np.exp(-s/P)
start_time = time.process_time()
arctest = False
# Max number of iterations in cur... |
6adbc9e30ecdca35947a2b73a273cadbf73ad2b54826b6fd62c88b5d484b37dc | Python | 38,270 | 1,009 | # 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
import numpy as np
import pandas as pd
from ax.analysis.plotly.utils import STALE_FAIL_REASON,... |
f98b277e0a2135746c3036afa6aa633ce5d40ac839b9898b946111c4b3ea5f6c | Python | 38,289 | 884 | import os.path
import warnings
from tqdm.auto import trange
import numpy as np
import tensorflow as tf
from . import feeder
from . import custom_layers
from .autoencoder import BaseAutoencoder
class AE_AR(BaseAutoencoder):
def __init__(self, *, rank=None, input_dim=None, inner_dim=None, nodes=None,
... |
6963692d38563cf562faa930f5ca54244424ba64becd5b98b852bc429344d86e | Python | 38,307 | 1,129 | """Graph diameter, radius, eccentricity and other properties."""
import math
import networkx as nx
from networkx.utils import not_implemented_for
__all__ = [
"eccentricity",
"diameter",
"harmonic_diameter",
"radius",
"periphery",
"center",
"centroid",
"barycenter",
"resistance_dis... |
c5f82d3329d867a20416d2a1034c54f2bbcb1415bbab924aebdf69758d2200f0 | Python | 38,495 | 822 | """
Different Objective Functions evaluating the probability of a certain partition
"""
# real non truncating division (same behaviour as in python 3)
from __future__ import division
import math
class ObjectiveFunction(object):
"""Measures the fitting of the SBM to the given graph"""
title = "Forgot to rep... |
6fcc703f3b032321dc9c8d4d2bc1e05bf0708336b7592e8d30ce6b08d53b2842 | Python | 38,531 | 1,140 | from __future__ import annotations
from contextlib import nullcontext
from copy import deepcopy
from functools import partial
from importlib.metadata import version
from importlib.util import find_spec
from typing import TYPE_CHECKING
import joblib
import numpy as np
import pandas as pd
import pytest
from dask.base i... |
177652877e101e7b032fb9f9156562b044001c7acda4d14eaaaf3897fd0cacb7 | Python | 38,541 | 1,259 | from spikingjelly.logger import logger
import math
import os
import shutil
import struct
from pathlib import Path
from typing import Callable, Optional, Union
import numpy as np
import torch
import torch.utils.data
import tqdm
from matplotlib import pyplot as plt
from torchvision import transforms
from .. import conf... |
8936de7ff9fe0d8060a9f4711c94de70b84809fc90ebbfb80fcbbf5ab5900dc2 | Python | 38,546 | 871 | import logging
from galaxy import util
from galaxy.tool_shed.util.container_util import (
generate_repository_dependencies_key_for_repository,
get_components_from_key,
)
from galaxy.tool_shed.util.repository_util import (
extract_components_from_tuple,
get_tool_shed_repository_by_id,
)
from galaxy.util... |
ddafa479e9a124e828cd4df88433ee2e13957dc302c08de79a0289f5ea6f0de5 | Python | 38,557 | 1,014 | """
File format detector
"""
import bz2
import gzip
import io
import logging
import os
import re
import shutil
import struct
import tempfile
import zipfile
from collections.abc import (
Callable,
Iterable,
)
from functools import partial
from typing import (
IO,
NamedTuple,
Optional,
TYPE_CHECK... |
168ee28b66b9e5bd99e74dbd55071f228a46eea27fcabb8aec47c6eeb40a5ffd | Python | 38,607 | 913 | import base64
import time
import unittest
from unittest.mock import MagicMock, patch
import jwt
import pytest
from django.test import override_settings
from io_storages.react_code_proxy import (
REACT_CODE_TOKEN_AUDIENCE,
REACT_CODE_TOKEN_TTL_DEFAULT,
REACT_CODE_TOKEN_TTL_MAX,
REACT_CODE_TOKEN_TTL_MIN,... |
9de4cbb203192c5a1049326a33ccda1486d29976a3cafce2e524d5bde345e37f | Python | 38,624 | 1,058 | # 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... |
3acceaef277ac9ad06dc732569acd275002d1f804bc044e302a6c541ccea876d | Python | 38,643 | 1,151 | # 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... |
0b1bab6c5f4a6ecfc7b8ad92f97be9975bebc138272dc55681e16f20b507585e | Python | 38,684 | 835 | #!/usr/bin/env python
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unle... |
b1f920caaa7e9b34814c83e33560abf08a7ea5045f05599a4da8007d99405307 | Python | 38,691 | 1,110 | from __future__ import annotations
import re
import warnings
import zipfile
from contextlib import contextmanager
from functools import partial
from importlib.util import find_spec
from pathlib import Path
from string import ascii_letters
from typing import TYPE_CHECKING
import h5py
import numpy as np
import pandas a... |
f47eff570a45bf4ee00e5705c775db0c947afaefc9b88e77682e36d9099f1aa3 | Python | 38,720 | 1,029 | from skimage import morphology, measure, io, util # For performing morphology operations (should maybe import more from skimage...)
from mpl_toolkits.mplot3d import Axes3D # Plotting in 3D
import matplotlib.pyplot as plt # To plot
from scipy.optimize import curve_fit
from pylab imp... |
e180ecc4352f3adeb6f5c34e5010d38824bbeb835bcd3db711dba2f12920b283 | Python | 38,807 | 828 | from __future__ import print_function, unicode_literals, absolute_import, division
from statistics import mean
import numpy as np
import sys
import warnings
import math
from tqdm import tqdm
from collections import namedtuple
from pathlib import Path
from csbdeep.models.base_model import BaseModel
from csbdeep.utils.... |
7d8dfcbf909ccf4276916cd892e80de283a1af3433598a06fb793b2a69d25b88 | Python | 38,819 | 1,279 | from operator import eq
from typing import AbstractSet
import pytest
from ...datalog.translate_to_named_ra import TranslateToNamedRA
from nl_expr.config import config
from nl_expr.exceptions import (
NonLiftableException,
NotInFONegE,
UnsupportedSolverError,
)
from nl_expr.expressions import Constant, Sym... |
d1e81b8c994e80616451733d9c08d846817f7dd46393f7b959e29fc36f5b9f45 | Python | 38,831 | 1,008 | # 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... |
c1b87da752d64ac9ede482161f8fc524dfe0786e60e31b526da1efef1ebad4aa | Python | 38,849 | 1,053 | from skimage import morphology, measure, io, util # For performing morphology operations (should maybe import more from skimage...)
from mpl_toolkits.mplot3d import Axes3D # Plotting in 3D
import matplotlib.pyplot as plt # To plot
from scipy.optimize import curve_fit
from pylab import ... |
3f74895ff329e1b7006597361e5399f3fef5eedb7fa87466ecce70ffa05cf6e3 | Python | 38,878 | 1,062 | """
Shared operations layer for AI agents (MCP and internal pydantic-ai).
Delegates to the Galaxy service layer for validation, permission checks, and pagination.
"""
import logging
from typing import (
Any,
Optional,
)
from sqlalchemy import select
from galaxy.agents import iwc
from galaxy.managers.context... |
436965de91021587a8f0e884a8f00d1236d5bba7d47f2db90d9fae8eb5b6dc5d | Python | 38,886 | 903 | """
Manager and Serializer for Users.
"""
import hashlib
import logging
import random
import string
import time
from typing import (
Any,
Optional,
)
from markupsafe import escape
from sqlalchemy import (
and_,
exc,
select,
true,
)
from sqlalchemy.exc import NoResultFound
from galaxy import (... |
4ba2771d2d7ac4e13ab319df755494ee69b464579eefcf4dcc24758eea6efd7c | Python | 38,898 | 779 | # 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... |
7df432b6dc28e8bcfe252ab667511923602027b1202857e48926027df193b17f | Python | 38,937 | 1,091 | import copy
from contextlib import contextmanager, nullcontext
import sys
import types
import pytest
import torch
from spikingjelly.activation_based import layer, neuron
from spikingjelly.activation_based.layer.attention import SpikingSelfAttention
from spikingjelly.activation_based.model import Spikformer
from spiki... |
2b93e9f9bfda2d96aebefc3db1d605c1f5d878feab05df9071a335022be7c021 | Python | 38,992 | 774 |
##########################################################################################
#
# psim_model.py
#
# - Class for creating and manipulating ProBioSim models, along with related functions.
#
##########################################################################################
#
# ProBioSim
# Copyrigh... |
f40fce0bb84be32e588f5aac98187ea060c1e6d03a581edba3feb2be8e3d0cb8 | Python | 39,064 | 1,028 | # 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... |
36c43e5b638d284b9228ce6667fdbccd01b2e36434471a8727ba7a22d35286fa | Python | 39,117 | 1,236 | from ..exceptions import NotInFONegE
from ..expression_walker import (
ChainedWalker,
ExpressionWalker,
IdentityWalker,
PatternWalker,
ReplaceExpressionWalker,
ReplaceSymbolWalker,
add_match
)
from ..logic.expression_processing import (
ExtractFreeVariablesWalker,
WalkLogicProgramAgg... |
2d0c89a773d4416d6ecd33309c701f06d2f0c3b950653c141b3364c21f7eb6d0 | Python | 39,139 | 820 | from ..utils import nextPowerOf2, closestDividableNumber, checkForCupy
import logging
from oct.utils.psUtils import stokes, unweaveInputPolarizations
from ..load.metadata import Metadata
cp, np, convolve, gpuAvailable, freeMemory, e = checkForCupy()
class Tomogram:
""" Tomogram reconstruction for OCT """
def ... |
8a8a16b0ad9a71773d8caa90af673575bd760702530f4a6244a928486e9fa60a | Python | 39,166 | 904 | # -*- coding:utf-8 -*-
"""Training and inference for tabular datasets using neural nets."""
import os
import pickle
import time
import numpy as np
import pandas as pd
from joblib import Parallel, delayed
from sklearn.metrics import roc_auc_score
from sklearn.model_selection import KFold, StratifiedKFold
from keras.ap... |
11e3f8e45b7afd3999add561b62ed9dc4dd57b4e5e77a32f4ef1a1c459938d31 | Python | 39,180 | 931 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Mar 5 19:01:33 2018
@author: jacobrosenstein
"""
from chemcpupy import MixtureList,CompoundList
#from chemcpupy.tools.misc import *
import numpy as np
import copy
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
import pandas as ... |
4792d0f6a9bc783b746282a4da71a15ae9cc1b62c396d9b97119f34b518c6e3e | Python | 39,264 | 829 | import ray
def val_pc_gauss(data_trans,alpha):
from timeawarepc.pcalg_ray_1 import estimate_skeleton, estimate_cpdag, causaleff_ida, ci_test_gauss
import networkx as nx
(g, sep_set) = estimate_skeleton(indep_test_func=ci_test_gauss,
data_matrix=data_trans,
... |
11aaaa7970fa5cfe15f67aae34b8acabffc8a8a526bffe428c119d5ce5f3574f | Python | 39,308 | 1,063 | """
***************
VF2++ Algorithm
***************
An implementation of the VF2++ algorithm [1]_ for Graph Isomorphism testing.
The simplest interface to use this module is to call:
`vf2pp_is_isomorphic`: check whether two graphs are isomorphic.
`vf2pp_isomorphism`: obtain the node isomorphism mapping between two g... |
0bad1ddfd246148d50d443b373ec0b7499038823397a7cbc883b915d7ff73930 | Python | 39,314 | 740 | # 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.
#
### ### ### ### ### ### ##... |
6059c6811992d484aea6e08be72540d94a869c29310dad05690de357c7f1a9a7 | Python | 39,318 | 577 | # -*- coding: utf-8 -*-
"""
Generate docs/_generated/usecase_globe.html, an interactive globe.gl view of the published SimBA
studies (top of the published-studies page) with three views:
* Countries - countries raised & coloured by number of studies (log scale). Default.
* Institutions - one bar per institution... |
92f76a8e1edc778de8cb620d72eee776c7a96fe60717ab8d4ae3764a8f31747f | Python | 39,330 | 818 | """Functions to create volumetric neuron densities for the following inhibitory neuron types of
the mouse brain:
- PV+
- SST+
- VIP+
- GAD67+ (a superset of the union of the previous three)
The algorithm is presented in "Atlas of inhibitory neurons in the mouse brain" by D. Rodarie et
al., to appear in <journal>.
Thi... |
8345de0c1cc2288cc2fd971da130c30c0620c81507bfb6807664d3259e93815f | Python | 39,372 | 893 | # 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 itertools import product
from unittest.mock import Mock
import numpy as np
import numpy.typin... |
5037326c3285845ca1f825aea36cd8e555f7bb4cd0408e91012fc19869d157a5 | Python | 39,418 | 1,029 | """
This module handles all configuration of the scaffold.
"""
import os, sys, site
from inspect import isclass
from .models import CellType, Layer
from .morphologies import Representation
from .connectivity import ConnectionStrategy, FiberTransform
from .placement import PlacementStrategy
from .output import Outp... |
fcaa315945526a272815c4b436211ff459284e09e88799f3675f0e6c30d14f61 | Python | 39,474 | 1,127 | import os
import pathlib
import shutil
import subprocess
import warnings
from concurrent.futures import ProcessPoolExecutor, as_completed
import dask
import joblib
import numpy as np
import pandas as pd
import pybedtools
import pyBigWig
import xarray as xr
import yaml
from pybedtools import BedTool
from ALLCools.util... |
b143cd4d7603c88c529a03b8591272bbdad51bac505f4f6cb11902be6db8f9a3 | Python | 39,477 | 1,037 | """Generators for geometric graphs."""
import math
from bisect import bisect_left
from itertools import accumulate, combinations, product
import networkx as nx
from networkx.utils import py_random_state
__all__ = [
"geometric_edges",
"geographical_threshold_graph",
"navigable_small_world_graph",
"ran... |
63caa5a9fda10910a026ebf2e5de08394fa446d32493c177ef2b267e3a58ba89 | Python | 39,496 | 798 | import os
os.environ["CUDA_DEVICE_ORDER"]="PCI_BUS_ID"
os.environ["CUDA_VISIBLE_DEVICES"] = "0"
import numpy as np
import torch
from torch.autograd import Variable
from matplotlib import pyplot as plt
import pickle as pkl
from torch_geometric.data import Data, DataLoader
from tqdm import tqdm
import math
import random... |
8178450c679e680872d4eb6af1ca100fa117d69b0ce91d80d2c6386b05d9164e | Python | 39,581 | 798 | import os
os.environ["CUDA_DEVICE_ORDER"]="PCI_BUS_ID"
os.environ["CUDA_VISIBLE_DEVICES"] = "0"
import numpy as np
import torch
from torch.autograd import Variable
from matplotlib import pyplot as plt
import pickle as pkl
from torch_geometric.data import Data, DataLoader
from tqdm import tqdm
import math
import random... |
790db9fe1ead876d8fff343131d57522ff10fcfac370b25eeea8c98c76471fc5 | Python | 39,612 | 715 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon May 25 14:31:34 2020
This is the main script for processing scRNA-Seq Data through ScanPy.
@author: smith
"""
#%%
import os
os.chdir('/d1/software/scanpy/')
import scanpy as sc
import scanpy.external as sce
import numpy as np
import pandas as pd
from s... |
b327068977dea21c0bc05d4461e8a2edf9fd62880d016fe8c317515b75bef5ce | Python | 39,648 | 986 | # 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
"""
Module for benchmarking Ax algorithms.
Key terms used:
* Replication: 1 run of an optimization loop; (BenchmarkProblem,... |
1fd0f63ceb712fcdeffa1ad62af721f0df43ae984f88f3817d358700bbd33f80 | Python | 39,651 | 868 | # 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 collections.abc import Mapping, Sequence
from logging import Logger
... |
bd51e0f2b665f957082ece7d41f62a267fa134cf3b7a1c169a46cc3a95c0fd8e | Python | 39,680 | 834 | def val_pc_gauss(data_trans,alpha):
from timeawarepc.pcalg_ray import estimate_skeleton, estimate_cpdag, causaleff_ida, ci_test_gauss
import networkx as nx
(g, sep_set) = estimate_skeleton(indep_test_func=ci_test_gauss,
data_matrix=data_trans,
... |
9c10792567d3f47d0ffea46717e73643853e694e02dbe89591b4edf4f87305d1 | Python | 39,781 | 788 | # 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... |
815e772831bb0606f1b1d78a8e70136cfe3b81310944dca5708784d531629f5a | Python | 39,880 | 988 | # -*- coding: utf-8 -*-
#
# Copyright (C) 2013-2017 Vinay Sajip.
# Licensed to the Python Software Foundation under a contributor agreement.
# See LICENSE.txt and CONTRIBUTORS.txt.
#
from __future__ import unicode_literals
import base64
import codecs
import datetime
import distutils.util
from email import message_from... |
60d20148759b2aa822f57536f1fd27443a2c1aca3d811c8fca08cd08e5b2617f | Python | 39,893 | 840 | def val_pc_gauss(data_trans,alpha):
from timeawarepc.pcalg_ray import estimate_skeleton, estimate_cpdag, causaleff_ida, ci_test_gauss
import networkx as nx
(g, sep_set) = estimate_skeleton(indep_test_func=ci_test_gauss,
data_matrix=data_trans,
... |
6cff9e0a089fca3dc61bdcdad83712364d0c4d6305f7308b374b59a0921769b3 | Python | 39,947 | 1,121 | from skimage import morphology, measure, io, util # For performing morphology operations (should maybe import more from skimage...)
from mpl_toolkits.mplot3d import Axes3D # Plotting in 3D
import matplotlib.pyplot as plt # To plot
from scipy.optimize import curve_fit
from pylab import ... |
057ae9722471ebf021d4e7de60742dffc04a520a51a6044fa8e4f42e86ccb03f | Python | 39,955 | 1,021 | from __future__ import absolute_import
import logging
import os
import shutil
import sys
import sysconfig
import zipfile
from distutils.util import change_root
from pip._vendor import pkg_resources, six
from pip._vendor.packaging.requirements import Requirement
from pip._vendor.packaging.utils import canonicalize_nam... |
e617a41f93fcd329b6c9e9de5466073dbf7bc679039dc6b4ff4c7fb3a83d82cb | Python | 39,959 | 875 | # 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... |
ed8051120a918b53ac5e4cbbdbf05b1fe412189e47ad8a2925cab9c12f386ae4 | Python | 40,001 | 953 | """Job control via the HTCondor DRM using the htcondor2 Python API.
See the Galaxy cluster documentation (doc/source/admin/cluster.md) for
configuration, architecture details, and testing instructions.
"""
import json
import logging
import os
import select
import shlex
import subprocess
import sys
import threading
fr... |
542d4710108eda02a3bb73cc95c7ffc9af8a10953d02988d956f09572d107953 | Python | 40,113 | 1,116 | from skimage import morphology, measure, io, util # For performing morphology operations (should maybe import more from skimage...)
from mpl_toolkits.mplot3d import Axes3D # Plotting in 3D
import matplotlib.pyplot as plt # To plot
from scipy.optimize import curve_fit
from pylab import ... |
380f9acfbd0071458ab3d369a2fd86995b87164bac0ccfa54c5c243801694014 | Python | 40,139 | 1,054 | """
Some code are adapted from https://github.com/liyaguang/DCRNN
and https://github.com/xlwang233/pytorch-DCRNN, which are
licensed under the MIT License.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import numpy as np
import random
import torch
im... |
04d0a7a517c556c97265ca2caf8be713f61b9116f74cdc57b64ed3ac3b3325d7 | Python | 40,172 | 1,094 | # -*- coding: utf-8 -*-
#
# Copyright (C) 2012 The Python Software Foundation.
# See LICENSE.txt and CONTRIBUTORS.txt.
#
"""Implementation of the Metadata for Python packages PEPs.
Supports all metadata formats (1.0, 1.1, 1.2, and 2.0 experimental).
"""
from __future__ import unicode_literals
import codecs
from email... |
f8f0bc53e09456157a7eec9d15067d555b2c18fcf8898a09c73f6f256a6f5924 | Python | 40,183 | 953 | """
Galaxy FilesSource implementation for eLabFTW.
This module implements a FilesSource that interacts with an eLabFTW [1] instance. eLabFTW revolves around the concepts
of *experiment* [2] and *resource* [3]. Experiments and resources can have files attached to them. To get a quick
overview, try out the live demo [4]... |
cccb3b057c9a19ff7ac98a74eb4cde5ed9814910627a2900855fcb50e1efd9f5 | Python | 40,229 | 1,036 | """Functions for measuring the quality of a partition (into
communities).
"""
from collections import defaultdict
from itertools import combinations
from math import isfinite, log2
import networkx as nx
from networkx.algorithms.community.community_utils import is_cover, is_partition
from networkx.utils.decorators im... |
cc788a3a4b63a24f73cbc4c6f8a324648c2307918b09e26e27d19eec38061727 | Python | 40,291 | 858 | import fnmatch
import logging
import time
import os
from oct import *
cp, np, convolve, gpuAvailable, freeMemory, e = checkForCupy()
class Post:
"""
A post-processing object for managing pipeline of OCT processing after acquisition
Notes:
The post processing object will not run without a populat... |
5ec8f813b87ba668b968ea9ec2e174ec2e4019e81301c5a847fdd1417962c244 | Python | 40,317 | 1,180 | import os
import numpy as np
from fanc.compatibility.cooler import to_cooler
from genomic_regions import GenomicRegion
from fanc.matrix import Edge, RegionPairsTable, RegionMatrixTable, RegionMatrix
from fanc.hic import Hic, _get_overlap_map, _edge_overlap_split_rao, kr_balancing, ice_balancing
from fanc.regions import... |
afd5ffaf42f1eaf96bbda09336e9a8761cd0f06c294d7b6b17bcab9fd9b0a59f | Python | 40,396 | 913 | """
Copyright © 2025 Howard Hughes Medical Institute, Authored by Carsen Stringer , Michael Rariden and Marius Pachitariu.
"""
import logging
import cv2
import numpy as np
import torch
from scipy.ndimage import gaussian_filter1d
from torch.fft import fft2, fftshift, ifft2
from torchvision.transforms import functional ... |
7a5f87f383e8adaef189b8e9a9970241d6f3925298bd625dd3d7353caac2d4b9 | Python | 40,464 | 831 | import math
import random as rd
import unittest as ut
import networkx as nx
from pysbm.sbm import PeixotoInference
from pysbm.sbm.nxpartitiongraphbased import NxPartitionGraphBased
from pysbm.sbm.partition import NxPartition
from pysbm.sbm.objective_function_newman_group_size import *
from pysbm.sbm.objective_functio... |
1e2461430c107f98fc8d9e7b4c9637b976b1670d4f0c007ac632418907732afa | Python | 40,595 | 1,047 | """Tests for engine initialization modules."""
import numbers
import tempfile
from pathlib import Path
import numpy as np
import pandas as pd
import pytest
from unittest.mock import MagicMock, patch
from neurolang.frontend.neurosynth_utils import StudyID
# Where the engines keep their cache: a directory of the run,... |
7f681547d97ecc5b7f4749fbfa98b165a38aa3f957a9b9c491eaae03dc290b6e | Python | 40,617 | 1,095 | """
*******
GraphML
*******
Read and write graphs in GraphML format.
.. warning::
This parser uses the standard xml library present in Python, which is
insecure - see :external+python:mod:`xml` for additional information.
Only parse GraphML files you trust.
This implementation does not support mixed grap... |
0067b057d45bf1608b664a449d2766b8ff36689aabe685f1a7d0af7006df2333 | Python | 40,628 | 1,328 | import abc
import functools
import typing
from pathlib import Path
import numpy as np
from .. import config, plugins
from .._util import immutable, obj_str_insert
from ..trees import BoxTree
from ._chunks import Chunk
if typing.TYPE_CHECKING: # pragma: nocover
from ..cell_types import CellType
@config.pluggab... |
4ed40a2af0d765424695e55343a367268438bbe49d9087d3edbd52a8f6c5ac4d | Python | 40,660 | 1,029 | """
This module performs iterative mapping of reads in FASTQ files to a reference genome.
The main function is :func:`~iterative_mapping`, which requires an input FASTQ file,
an output SAM file, and a suitable mapper. Mapper options are :class:`~Bowtie2Mapper`
and :class:`~BwaMapper` for the time being, but by subclas... |
44d8e3289e0c17b24118bdbccbe8d49d383a3edc0e4b8b6ce79a6ce659c2115f | Python | 40,668 | 1,118 | from skimage import morphology, measure, io, util # For performing morphology operations (should maybe import more from skimage...)
from mpl_toolkits.mplot3d import Axes3D # Plotting in 3D
import matplotlib.pyplot as plt # To plot
from scipy.optimize import curve_fit
from pylab import ... |
0b97717bedc193c2e42788c36e7031b7df0269374ba3a1d2cc80bccaad0f0af6 | Python | 40,798 | 1,200 | """
Tests that each element in an anndata is written correctly
"""
from __future__ import annotations
import re
from contextlib import ExitStack, nullcontext
from dataclasses import dataclass
from importlib.metadata import version
from pathlib import Path
from types import SimpleNamespace
from typing import TYPE_CHEC... |
1e4c7950e9d04cc57aaac8d4d8be105143143afbfc92b0248fe74fdc2686ceac | Python | 40,829 | 1,464 | from operator import add, eq, lt, mul, pow, sub, truediv
import pytest
from nl_expr.logic import Disjunction, ExistentialPredicate
from nl_core.datalog import Conjunction, Fact, Implication, Negation, Union
from nl_expr.expressions import (
Command,
Constant,
FunctionApplication,
Lambda,
Query,
... |
82cbd8a2650f1df908af3f7b58a6803a888141e69587ef15b3ee3e9bc72871b5 | Python | 40,873 | 997 | #!/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 warnings
from collections import OrderedDict
from collections.abc import Mapping, Sequence
from... |
e811822510a12d4bb4d2a79222e396c21103f8f5b9a621ded57884796c57a6d1 | Python | 40,895 | 906 | import itertools
import numpy as np
from brian2.parsing.bast import brian_dtype_from_dtype
from brian2.parsing.rendering import NumpyNodeRenderer
from brian2.core.functions import DEFAULT_FUNCTIONS, timestep
from brian2.core.variables import Constant, ArrayVariable
from brian2.utils.stringtools import get_identifiers... |
1d768f170ebf600274aa9a4008fbb460b0142ed46cdd0a2f44cfc20991c6758d | Python | 40,899 | 1,979 | # This file is automatically generated by tools/idna-data
__version__ = "11.0.0"
scripts = {
'Greek': (
0x37000000374,
0x37500000378,
0x37a0000037e,
0x37f00000380,
0x38400000385,
0x38600000387,
0x3880000038b,
0x38c0000038d,
0x38e000003a2,
... |
6bd3b0d5b279d6171f66c56986b821382d7afc5b305dfafad271f5d0e1382e15 | Python | 40,960 | 1,034 | import numba as nb
import itertools
import os
import pathlib
import re
from typing import List, Literal, Union, Sequence
from numpy.typing import ArrayLike, DTypeLike
from numpy import ma
import feather
import natsort as ns
import numpy as np
import pandas as pd
import skimage.io as io
from alpineer import data_utils,... |
1048b4d22daff660251de3b6cb0b6110211d8e047121217e60553baff0bf49f4 | Python | 40,996 | 1,057 | from __future__ import annotations
import functools
import importlib
import inspect
import json
import os
import random
import time
from collections.abc import Callable
from concurrent.futures import Future
from contextlib import ExitStack
from dataclasses import asdict
from pathlib import Path
from typing import Any,... |
d75d1dfbc0b8b20fd19991f0f9b5403ef1e202217d4c0859257a3db6f3753c89 | Python | 41,001 | 1,095 | """
Support for installing and building the "wheel" binary package format.
"""
from __future__ import absolute_import
import collections
import compileall
import csv
import hashlib
import logging
import os.path
import re
import shutil
import stat
import sys
import warnings
from base64 import urlsafe_b64encode
from ema... |
ac32622685215ad4bb267c787d614edf6c232906b926273895a6d43172ce159c | Python | 41,145 | 978 | import matplotlib.pyplot as plt
from scipy.optimize import curve_fit
from pylab import *
import numpy as np
import random
import math
import time
import os
import glob
# change the default font family
plt.rcParams.update({'font.family':'Arial'})
def myexponential(x,A,l):
return A*np.exp(-x/l)+1
... |
974daae8f327c1e9e0f047d49ba674ca8afe532fb377a58dd139b6f25877a415 | Python | 41,248 | 1,158 | import pytest
import networkx as nx
from networkx.algorithms.similarity import (
graph_edit_distance,
optimal_edit_paths,
optimize_graph_edit_distance,
)
from networkx.generators.classic import (
circular_ladder_graph,
cycle_graph,
path_graph,
wheel_graph,
)
@pytest.mark.parametrize("sour... |
4975cf9bb2d1b347f5f2a5f0d48a58fefeee732c313c68860f62fe1f6baf398c | Python | 41,306 | 1,041 | # 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... |
04c58a324713944d721fc2d207915563459ce420a4bdf466718a77d4f7f09843 | Python | 41,316 | 882 | import os
import scipy.io
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
import logging
from mpl_toolkits.mplot3d import Axes3D, art3d # Import 3D plotting toolkit
from scipy import stats
import re
from sklearn.preprocessing import MinMaxScaler
class MUSIC_TUS_DataAnalyze... |
bc595273fec70e663d5d21759736f60a81ee65acae31c7bca5951fc1bfdc064a | Python | 41,353 | 1,116 | from skimage import morphology, measure, io, util # For performing morphology operations (should maybe import more from skimage...)
from mpl_toolkits.mplot3d import Axes3D # Plotting in 3D
import matplotlib.pyplot as plt # To plot
from scipy.optimize import curve_fit
from pylab imp... |
786092798e0477ee482944c8670306da73f9c1a3d79eb6c5d3037ad1b1471c18 | Python | 41,404 | 921 | # 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... |
30aa4fc54979ecd1c483aeb7572bc8dcae06c651caa3debe4a67c9605b795356 | Python | 41,429 | 1,098 | from __future__ import print_function, unicode_literals, absolute_import, division
import numpy as np
import sys
import warnings
import math
from tqdm import tqdm
from collections import namedtuple
from pathlib import Path
from csbdeep.models.base_model import BaseModel
from csbdeep.utils.tf import export_SavedModel,... |
bc2bcf223089e92393f96a6f4fc477c3583294078b36e56ba7670610437f8486 | Python | 41,450 | 1,086 | # 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... |
d2eeb395250408bef7e4e78ae64cf78923b16b482024a561f4a1492aaf962669 | Python | 41,514 | 967 | import copy
import os
import tempfile
import numpy as np
import pytest
import skimage.morphology as morph
import test_utils
import xarray as xr
from alpineer import image_utils, misc_utils
from alpineer.test_utils import (create_paired_xarray_fovs, gen_fov_chan_names,
make_images_xarra... |
e21b1adfdef18de00a0611325c552974423137d6a3c5ff7de9d74e19c4dccb85 | Python | 41,578 | 1,209 | """Workflow Builder Functions.
Contains a collection of image processing workflow builders used to create a
postprocessing pipeline.
"""
import os
from math import sqrt, log
from pathlib import Path
import pkg_resources
import pandas as pd
# TODO: import these without specifying, to help with code readability
from ... |
0bd805af3a294ad8d707bf75a819f030fc91e7df0a433747cb8a7e6eec4df45b | Python | 41,626 | 1,212 | """Workflow Builder Functions.
Contains a collection of image processing workflow builders used to create a
postprocessing pipeline.
"""
import os
from math import sqrt, log
from pathlib import Path
import pkg_resources
import pandas as pd
# TODO: import these without specifying, to help with code readability
from ... |
1856b2063062072932e231ce07ed63b366c7e9777e44c36470edb8ffebdf0211 | Python | 41,757 | 1,148 | import copy
import os
import shutil
import tempfile
import types
import unittest
import warnings
import numpy as np
from bsb_arbor import ArborSimulation, SpikeRecorder
from bsb_test import FixedPosConfigFixture, NumpyTestCase, RandomStorageFixture
from neo import io
from bsb import (
MPI,
AfterPrepareHook,
... |
d7a1bddeb18f1fbabbd1e4716d41dd7bfcda193b541b4fec9979e793bd794737 | Python | 41,760 | 747 | import numpy as np
import math
import torch
from torch import nn
from torch.nn import functional as F
from models.fc.layers import fc_layer,fc_layer_split,fc_layer_fixed_gates
from models.fc.nets import MLP,MLP_gates
from models.conv.nets import ConvLayers,DeconvLayers
from models.cl.continual_learner import ContinualL... |
7a5f02614d0e9a02448a9d0a9e3430b6743f980845546df251b964c6edc11d15 | Python | 42,037 | 1,050 | #!/usr/bin/env python
#
# Copyright (c) 2018 10X Genomics, Inc. All rights reserved.
#
from collections import OrderedDict
import copy
import h5py as h5
import itertools
import json
import numpy as np
import scipy.io as sp_io
import os
import pandas as pd
pd.set_option("compute.use_numexpr", False)
import shutil
import... |
3e69b77eea726fd8ac8dd72399ad595f6b0b293e3811d1f738c0e8f939a2901d | Python | 42,133 | 1,124 | from __future__ import annotations
import argparse
from contextlib import nullcontext, suppress
import json
import os
import platform
import signal
import statistics
import subprocess
import sys
import time
from dataclasses import asdict
from datetime import datetime, timezone
from pathlib import Path
from typing impo... |
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