sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
1734143fbfd5c8261fe94317bb1da1a013e6d101352b744592125eb051558617 | Python | 34,202 | 806 | import logging
import os
from collections.abc import Callable
from datetime import datetime
from enum import Enum
from typing import (
Any,
Optional,
)
from sqlalchemy import (
Boolean,
Column,
DateTime,
ForeignKey,
Integer,
String,
TEXT,
)
from sqlalchemy.orm import (
Declarati... |
9664bb6e3f9b2fb543d59dcfb626e003f064b768c4fd57539600827666a22a96 | Python | 34,216 | 985 | import pytest
import torch
from spikingjelly.activation_based import functional, neuron, surrogate
def _table(scale=1.0):
return neuron.FewSpikeTable(
theta=torch.tensor([0.25, 0.5, 0.75]) * scale,
h=torch.tensor([0.2, 0.3, 0.4]) * scale,
d=torch.tensor([1.0, 2.0, 4.0]) * scale,
)
d... |
db9396df9687d3da11de6f745c786aea7c4a4815fd3bcbe1f1ac304385ef78b6 | Python | 34,221 | 513 | import torch
import time
from torch.nn import ReLU
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from matplotlib.colors import Normalize, ListedColormap
from sklearn.decomposition import PCA
import pandas as pd
import seaborn as sns
ReLu = ReLU()
########################################... |
71109226c72d3aad037d5c2e5190d407d900f09e2bbaaf2189a0d97ea9a9acb0 | Python | 34,228 | 1,034 | """
Algorithms for finding optimum branchings and spanning arborescences.
This implementation is based on:
J. Edmonds, Optimum branchings, J. Res. Natl. Bur. Standards 71B (1967),
233–240. URL: http://archive.org/details/jresv71Bn4p233
"""
# TODO: Implement method from Gabow, Galil, Spence and Tarjan:
#
# @... |
eacfb7ee202a5d5a6dabccfb53f2e81ffa5b20fac24149bf67c42e206136f50d | Python | 34,275 | 953 | # -*- coding: utf-8 -*-
"""
requests.models
~~~~~~~~~~~~~~~
This module contains the primary objects that power Requests.
"""
import datetime
import sys
# Import encoding now, to avoid implicit import later.
# Implicit import within threads may cause LookupError when standard library is in a ZIP,
# such as in Embed... |
1ff3de983326458ad12b8dd829a853bdd4397cafce7573fc028f2d4b23534c54 | Python | 34,287 | 771 | """
Plot of the potential using Mayavi mlab
=======================================
.. currentmodule:: mlab_potential
:platform: Linux
:synopsis: module for plotting and simulating the amplitude equation and its potential
.. moduleauthor:: Jose M. Esnaola-Acebes <josemesnaola@gmail.com>
This module contains an... |
3a0192aa0c723d9482c1c21669e005a630e892ba26ed1042b10155d73df4f367 | Python | 34,313 | 797 | import matplotlib
#
import sys
sys.path.append("/home/cat/code/widefield/") # Adds higher directory to python modules path.
import h5py
import numpy as np
import scipy.io as sio
import matplotlib.pyplot as plt
from sklearn.cross_decomposition import CCA
import torch
import time
import warnings
warnings.filterwarnings... |
6ad2685ca6192df2db69fe4d9c1215b43857629204f12cc8f99be5d58ac2d04c | Python | 34,330 | 1,058 | import plotly.graph_objects as go
from plotly.subplots import make_subplots
from .networks import all_depth_first_branches, get_branch_points, reduce_branch
import numpy as np, math, functools
from .morphologies import Compartment
from contextlib import contextmanager
import random, types
from .reporting import warn
... |
8c7d9e4e17d3824b52eca5f84b483e1e1067ce9e9707a4e889f2fac26221fe40 | Python | 34,368 | 554 | # -*- coding: utf-8 -*-
"""
Generate the Related Software page's tool table and its plain-text index:
* docs/_generated/related_tools_table.html -- one searchable, filterable table of every tool;
* docs/_generated/related_tools_index.rst -- the same tools as a plain A-Z list, so the docs search
(which indexes RST t... |
d7108e69aca377c56d9c177f36e70ef112f4e9a580b9533490c198e89eacff81 | Python | 34,410 | 1,017 | import copy
import gc
import pickle
import platform
import weakref
import pytest
import networkx as nx
from networkx.utils import edges_equal, graphs_equal, nodes_equal
def test_degree_node_not_found_exception_message():
"""See gh-7740"""
G = nx.path_graph(5)
with pytest.raises(nx.NetworkXError, match="... |
d22fe8667deed2b1381d4918d8a346846be78b88fc8208426a6ec29e79b54143 | Python | 34,424 | 816 | # 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... |
4214b796c391b86f68ed8ef7f695d972009f3506d30a58ac40db463b2a2ffbd7 | Python | 34,447 | 631 | import argparse
from utils import NumpyEncoder
import os
import json
import logging
import time
from statistics import mean, stdev
from typing import List
from collections import defaultdict
from sklearn import metrics
from operator import add
import copy
from select_diverse_models import select_diverse_models
import d... |
4a433c8084d90b2e86e476938bd688e2f53c12c379dcde0ff40c42780b75f47b | Python | 34,495 | 964 | from abc import abstractmethod
import torch
import torch.nn as nn
import torch.nn.functional as F
from . import base, functional, neuron, surrogate
def _population_parameters(obs_dim, pop_dim, mean_range, std):
mean = torch.linspace(mean_range[0], mean_range[1], pop_dim)
mean = mean.expand(1, obs_dim, pop_d... |
fc029772533d81a869e656235ec8982cec2e03ce2e444c746779ee1fd0acead1 | Python | 34,527 | 658 | from ipywidgets import interact, Layout, Label
import ipywidgets as widgets
import os
import pybel
import sys
from IPython.display import display, clear_output, Javascript
from rdkit import Chem
from rdkit.Chem.Draw import IPythonConsole
import os.path
import csv
import pandas as pd
from collections import Counter
sty... |
2a842f31dd0e7de3149fe5a2fefd9ef7d8f192e7bfcca9311411e28900d2dd9d | Python | 34,696 | 971 | from __future__ import absolute_import
import cgi
import email.utils
import getpass
import json
import logging
import mimetypes
import os
import platform
import re
import shutil
import sys
from pip._vendor import requests, six, urllib3
from pip._vendor.cachecontrol import CacheControlAdapter
from pip._vendor.cachecon... |
f3cbf467ca45bdbdfdc3997eceb3abfe533fc90091bfa32d16590ba50f236a8d | Python | 34,709 | 1,074 | # -*- coding: utf-8 -*-
"""
Vasculature
===========
Expert vasculature image processing pipeline.
This module provides the basic routines for processing vasculature data.
The routines are used in the :mod:`ClearMap.Scripts.TubeMap` pipeline.
"""
__author__ = 'Christoph Kirst <christoph.kirst.ck@gmail.com>'
__licen... |
33a9e49df1a53474711833ee3d54ff847193899e042e129b602217931d0ef576 | Python | 34,710 | 1,054 | """
Implementation of the weighted model counting approach through knowledge
compilation.
"""
import logging
import operator as op
from typing import AbstractSet
import numpy as np
import pandas as pd
from nl_expr.config import config
from ..datalog.expression_processing import (
UnifyExistentialVariableE... |
51978400a5b10b174944e1b83b1e2e5b9905a6303df6e3f725d091ee2b06ee74 | Python | 34,738 | 820 | import os
import tempfile
from copy import deepcopy
import feather
import numpy as np
import pandas as pd
import pytest
from alpineer import io_utils, misc_utils
import ark.phenotyping.cluster_helpers as cluster_helpers
import ark.phenotyping.pixel_cluster_utils as pixel_cluster_utils
import ark.phenotyping.pixel_met... |
4a0b6668717eb57c80a4ee541dfac5f65250f514d247372c09b1b8f232aa611e | Python | 34,753 | 815 | import random
import torch
import os
import torch
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
from torch.utils.data import RandomSampler, BatchSampler, SequentialSampler
from .utils import calculate_accuracy, Cutout, calculate_accuracy_by_labels, calculate_FP, calculate_FP_Max
from .newtra... |
c00b73fac4594a6b182d914c4626e66f39ee4b01a841c0f01180c4f3e2d0dcba | Python | 34,799 | 982 | import random
from itertools import chain, islice, tee
from math import inf
import pytest
import networkx as nx
from networkx.algorithms.traversal.edgedfs import FORWARD, REVERSE
def check_independent(basis):
if len(basis) == 0:
return
np = pytest.importorskip("numpy")
sp = pytest.importorskip(... |
294f11666134655177b4ca5bb82e4b4d98ad92c73a01d6c02ed36caf5204a61c | Python | 34,805 | 1,067 | """Generators for classes of graphs used in studying social networks."""
import itertools
import math
import networkx as nx
from networkx.utils import py_random_state
__all__ = [
"caveman_graph",
"connected_caveman_graph",
"relaxed_caveman_graph",
"random_partition_graph",
"planted_partition_grap... |
86f63e0392a91da8ca97b1fc5a222273b5e675ad347539167271e1deab0d8aac | Python | 34,871 | 932 | #!/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 unittest.mock import Mock, patch, PropertyMock
import numpy as np
import pandas as pd
from ax.co... |
ef886df5da1de41c730de5d37169496964b6897ed63a5c8ada69983dc0781ed2 | Python | 35,041 | 875 | """Stitching of tile-cut cells flagged by :func:`~squidpy.experimental.tl.calculate_tiling_qc`.
When segmentation is run tile-by-tile (Cellpose, Stardist, Mesmer, ...) cells
that straddle tile boundaries get cut into 2-4 pieces with characteristic
straight, axis-aligned cut edges. :func:`~squidpy.experimental.tl.calc... |
ae073fdc3d15b03e550f1af82b3cc0f0f95e7b44667ab9b958a6fbd457315aef | Python | 35,097 | 896 | from __future__ import absolute_import
import errno
import logging
import sys
import warnings
from socket import error as SocketError, timeout as SocketTimeout
import socket
from .exceptions import (
ClosedPoolError,
ProtocolError,
EmptyPoolError,
HeaderParsingError,
HostChangedError,
Locatio... |
2f4829a7c9ed417764ba6586063839af360f976f2c1715e4b647200f613d94fc | Python | 35,140 | 1,057 | """Accessor classes for AnnData interface."""
from __future__ import annotations
import abc
import sys
from collections.abc import Hashable
from dataclasses import KW_ONLY, dataclass, field
from functools import cached_property
from typing import TYPE_CHECKING, ClassVar, Protocol, overload, runtime_checkable
if sys.... |
099eb38da9d2ea53b616413dce900185bc5ee9a8e2bd6ccc52c255d223768954 | Python | 35,147 | 940 | #!/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 abc import ABC, abstractmethod
from collections.abc import Ca... |
8576ccb875fe10abce9dd40127df5f3c23a5a5af69f088a6c643624062eacf83 | Python | 35,191 | 635 | import torch
from torch import optim
from torch.utils.data.dataloader import DataLoader
from torch.utils.data import ConcatDataset
import numpy as np
import tqdm
import copy
from utils import get_data_loader,checkattr
from data.manipulate import SubDataset, MemorySetDataset
from models.cl.continual_learner import Conti... |
8e20adb6024b7e185fba6c631f35073827b8038adcc1f850ed062e8534704918 | Python | 35,203 | 882 | import torch
import torch.nn as nn
import torch.nn.utils.rnn as tn
from torch.autograd import Variable
import os
import torch.nn.functional as F
import numpy as np
import scipy
import time
import copy
import random
from .utils import init
from sklearn.neural_network import MLPClassifier
from sklearn.model_selection imp... |
f26f45b7d80559741bcfdd54fb252bf4e840838a86efe4633824509e2bd716cf | Python | 35,233 | 794 | from numpy import *
from numpy.linalg import LinAlgError
from numpy.random import randint
from six import iteritems
from six.moves import range
import hashlib
from random import shuffle
from .logger import log_message
from .mask_starts import mask_starts
from .linear_algebra import BlockPlusDiagonalMatrix
from .defau... |
cb38e9d2ddbc0d3d6a76e3dfa009237fe8ae5210e9ecd349a634942d05aba02a | Python | 35,234 | 945 | 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... |
86aeca04700bc25e59b87fdfae80d8a370774c897b75c795f75fc756555af839 | Python | 35,257 | 755 | 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... |
a71b0f1308b9558d3cbd5465d2f6d089868215941bf531f749a7c6860871ab90 | Python | 35,292 | 985 | """
Provide basic convenience data types.
Most classes are based on pytables and hdf5 dictionaries,
allowing on-disk storage and therefore processing of large
files. Other features include indexing and querying.
"""
from __future__ import division
from fanc.config import config
import tables as t
from tables.nodes im... |
b5107658b6cec2998e6326a6227517412269b5f01652d59fb8f83d1ee253c724 | Python | 35,319 | 924 | # stdlib imports
import os, getpass, datetime, pathlib, tempfile, functools, glob
# non-stdlib core dependencies
import numpy as np
import scipy
import cellpose.io
import cellpose.models
import tifffile
import imagecodecs
# distributed dependencies
import dask
import distributed
import dask_image.ndmeasure
import yam... |
13fa35ce2cdac35f17f212a7e073384ce1b390a1f1e0c444dc93eef823db56aa | Python | 35,328 | 694 | # 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... |
06949c082f2cad826027a0744ee29682924e0015d41eaf629c1aade7e1be84da | Python | 35,351 | 997 | import numpy as np
import math
import matplotlib.pyplot as plt
import power_law
import matplotlib as mpl
from cycler import cycler
from tqdm import tqdm
mpl.rcParams['axes.prop_cycle'] = cycler(color='bgrcmyk')
def gabor_features_no_phase(theta_stim, theta_pr, sigma, thresh, a = 1.3):
th_diff = np.outer(theta_st... |
0f6b33a50e2b13dd327c92125ccb3e2fd5450c2a78396aadc4c346cbc2aaed65 | Python | 35,356 | 1,051 | # 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... |
999b1aa240ea7d3b86087ab9ced489e9336e0eaebe1178b46509a784b08106e5 | Python | 35,378 | 994 | import torch
from nidn.utils.global_constants import PI
from .constants import *
from .utils.fft_funs import Epsilon_fft, get_ifft
from .utils.kbloch import Lattice_Reciprocate, Lattice_getG, Lattice_SetKs
from .utils.torch_functions import torch_transpose, torch_dot, torch_eye, torch_zeros
class TRCWA:
def __... |
1bbfef1430bcc8a4353e2ba68de07a9a3942886b81538e26c26d6a9978146fbb | Python | 35,433 | 912 | import unittest
from time import sleep
import numpy as np
from bsb_test import (
NetworkFixture,
NumpyTestCase,
RandomStorageFixture,
get_test_config,
skip_parallel,
)
from bsb import (
MPI,
BootError,
CellType,
Chunk,
Configuration,
IndicatorError,
PackingWarning,
... |
77332db3b63598c52ecf8cc4cf869d12a6143685e2f4131ffa8cb343404c1b7b | Python | 35,502 | 983 | import pytest
import networkx as nx
from networkx.utils import pairwise
def validate_path(G, s, t, soln_len, path, weight="weight"):
assert path[0] == s
assert path[-1] == t
if callable(weight):
weight_f = weight
else:
if G.is_multigraph():
def weight_f(u, v, d):
... |
3b6e29e2190871434e428a685a41961cdd5082c5497a457860943d7c6ac67cf0 | Python | 35,593 | 1,040 | # 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.
import argparse
import io
import json
import os
import re
import shutil
import subprocess
import uuid
from pathlib import Path
import mdfor... |
4b3e2ba2481b946fa61399ca10866488c06c997c758b22dfb108368a3ed82d25 | Python | 35,618 | 949 | import matplotlib.pyplot as plt # To plot
from scipy.optimize import curve_fit
from pylab import *
import numpy as np
import data_treatment as datr
import random
import math
import time
import os
import glob
import copy
def rmsd(x,y):
Nx = len(x)
Ny = len(y)
if Nx!=Ny:
... |
60785ef786c8115acec0ba01e9df1d9ad9ac46e31408802b9dac065916feadf9 | Python | 35,635 | 944 | # -*- coding: utf-8 -*-
#
# Copyright (c) 2013 Egor Zindy <egor.zindy@manchester.ac.uk>
#
# * ArrayElementVar and ArrayVar based on Bryan Oakley's code from
# http://stackoverflow.com/questions/3876229/how-to-run-a-code-whenever-a-tkinter-widget-value-changes
# * clean() lambda from
# https://stackoverfl... |
8b5ca2aa2e89316d50ef61148a23d1dd73943d2c560e14f0c139fa4d03d81458 | Python | 35,652 | 955 | """Analyze one single-host Nsight Systems SQLite export without a GPU."""
from __future__ import annotations
import argparse
import csv
import json
import re
import sqlite3
import statistics
from collections import Counter, defaultdict
from pathlib import Path
if __package__:
from .plot_nsys_snn import render
el... |
27ab9da4e57b11a96bda8c1d2d1b50f0bdb33fd42e5eb3973158c8c83aba21e4 | Python | 35,689 | 1,014 | import atexit
import tempfile
import unittest
from numbers import Integral
import numpy as np
import pytest
from numcodecs import Adler32, Zlib
from numpy.testing import assert_array_equal
import zarr
from zarr.convenience import (
consolidate_metadata,
copy,
copy_store,
load,
open,
open_conso... |
c4963e5e320f40da811b0f3ba5618d7c0c9187715e13fdaef9153e5c28dffa84 | Python | 35,732 | 821 | """ Script to build the action space for decorating crystal structures
in the RL search. Action space:
Action space:
1. Choose the elements desired for the battery material
i.e., conducting ion, framework cation(s), and anion(s)
2. For a given combination of elements, randomly select a composition
from one... |
09e084c0df9dd33314164dd12b460162b7e8210df506ff035f1c4f0015372877 | Python | 35,743 | 964 | 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... |
d7e2dfa07d66d8458c1700aa02a078de523163c7a8374011cb05e5ae8fa56d12 | Python | 35,761 | 878 | # Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
from __future__ import annotations
from abc import abstractmethod
from typing import TYPE_CHECKING
from ax.core import Mult... |
135b82c99abf1506b3b2cf710ae505f16f6cc84d09a656f987d89cb3d1025fb5 | Python | 35,878 | 1,133 | import logging
import numbers
import operator
import typing
import warnings
from typing import AbstractSet
import pandas
from nl_core.datalog.expression_processing import UnifyVariableEqualitiesMixin
from nl_expr.exceptions import UnsupportedProgramError
from nl_expr.expression_pattern_matching import add_match
from ... |
ac525c36988a6f500f14b0fa68f6b3dc0c9e27f4bc25561600f0a96b55254055 | Python | 35,884 | 657 | """
Constants that are used by all code are placed here for easy access.
These include:
1. ACCEPTED_RES
2. RES_3_TO_1
3. TARGET_ATOMS
4. RANDOM_COIL_TBL
5. RANDOM_COIL_AVG
6. RANDOM_COIL_STD
7. ONEHOT (code: 10)
8. BLOSUM (code: 45, 50, 62, 80, 90)
"""
from numpy import rad2deg as np_r... |
f15fa5fa88a9616c59a4a6982fa72dbaae06766eabf27e8041536fbe001a6ca2 | Python | 35,918 | 967 | import matplotlib
#
import numpy as np
import matplotlib.pyplot as plt
import os
#########################################
########### HELPER FUNCTIONS ############
#########################################
def load_data_PCA(fname_whole_stack,
fname_lever_times,
fname_blue_light):
... |
3f5eaac2f853dc4765a155816796500933dd6bcf24e29a2e284f326f960ec488 | Python | 35,944 | 1,031 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
# =============================================================================
# Final code for NNMF brain tumor anatomy project
# =============================================================================
# @author: J. M. Kernbach (NAILA, Neurosurgical Artificia... |
470485cb352d3be0792f91982f686d5be91e5b7e84f920759483f4c8f787649a | Python | 36,023 | 852 | # 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 copy
from unittest import mock
from unittest.mock import Mock, patch
import numpy as np
import pandas as pd
import to... |
6ce5dbaa931556e45789ba41d2dacd0025f823ccbddf9398a9c1b3d063677957 | Python | 36,141 | 769 | 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,... |
e1e4df14770ceeff8c0cec774b7b15b53b09f689faf13314f11ca1cc4411d498 | Python | 36,215 | 593 | """
Class encapsulating the management of repository dependencies installed or being installed
into Galaxy from the Tool Shed.
"""
import json
import logging
import os
from typing import TYPE_CHECKING
from urllib.error import HTTPError
from urllib.parse import (
urlencode,
urlparse,
)
from urllib.request impor... |
3633139d683f2501a0016787b5383fba367a99b156c90a7589110feaa9381d7b | Python | 36,269 | 925 | #!/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 logging
from collections.abc import Mapping
from datetime import datetime
from math import ceil... |
3c5290780d776529d71cfd17adf8a7a6cbd87627a468ee029a8cdb0131c14496 | Python | 36,277 | 1,064 | import random
import pytest
import networkx as nx
from networkx.utils import edges_equal, nodes_equal
def test_degree_histogram_empty():
G = nx.Graph()
assert nx.degree_histogram(G) == []
class TestFunction:
def setup_method(self):
self.G = nx.Graph({0: [1, 2, 3], 1: [1, 2, 0], 4: []}, name="T... |
9240fe9148d47badca8b54554ebac70a6cc115dc1d9a2bc30c362cd01afbe19c | Python | 36,300 | 989 | """Functions for building graphs from spatial coordinates."""
from __future__ import annotations
import warnings
from typing import Any, Literal, NamedTuple
import geopandas as gpd
import numpy as np
import pandas as pd
from anndata import AnnData
from anndata.utils import make_index_unique
from numba import njit
fr... |
58a65f5b6f311b3ece90abe8a73956610bcbb2a69636aa6c68450aedbf1d9ee8 | Python | 36,311 | 1,039 | from __future__ import annotations
import itertools
from collections.abc import Mapping, Sequence
from copy import copy
from functools import partial
from numbers import Number
from types import MappingProxyType
from typing import Any, Literal, NamedTuple
import dask.array as da
import numpy as np
import pandas as pd... |
a348bd083100a66c473f337f00095b12a386dd6e7548c67f45a850d41b48a912 | Python | 36,314 | 812 | """
Heterogenous lists/contents are difficult to query properly since unions are
not easily made.
"""
import json
import logging
from typing import (
Any,
Optional,
)
from sqlalchemy import (
asc,
cast,
desc,
false,
func,
Integer,
literal,
null,
nullsfirst,
nullslast,
... |
dee390f7176ec778bfcc51b184397e7511b39d910e4abd0ee4c395c5147dfc9e | Python | 36,399 | 713 | import matplotlib.pyplot as plt
import matplotlib
import itertools
import statistics
import pickle
import numpy as np
import pandas as pd
import scipy.stats
from stats.Stats import *
import seaborn as sns
from pprint import pprint
from utils.Utils import *
from utils.ColorUtils import *
import os
import fnmatch
from sy... |
874965f319ead76988f4fb90f5077f221b6dd3c4a9f0bd09aa11bd298f15ca39 | Python | 36,411 | 977 | """Fallback pure Python implementation of msgpack"""
import sys
import struct
import warnings
if sys.version_info[0] == 3:
PY3 = True
int_types = int
Unicode = str
xrange = range
def dict_iteritems(d):
return d.items()
else:
PY3 = False
int_types = (int, long)
Unicode = unicode... |
3174e5e8dbc2f64f9a1d0aebc20a456668eb7ab7c220b8d3b1bcbb6b61a6faa1 | Python | 36,521 | 1,070 | """Functions for generating trees.
The functions sampling trees at random in this module come
in two variants: labeled and unlabeled. The labeled variants
sample from every possible tree with the given number of nodes
uniformly at random. The unlabeled variants sample from every
possible *isomorphism class* of trees w... |
04fd61d1d144e01ce9c0edd220ab81c35b1727f3159990725fdfc3a39533dc9d | Python | 36,524 | 1,022 | # 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... |
9fba55cc58225cd8e1df28bf6c6410ace2630d0b019ff2f9db47884776dfb532 | Python | 36,532 | 930 | #!/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 itertools
import math
from bisect import bisect_right
from ... |
3cca471aa30fb03e8a71edb3966f47f0b1299fa9b1592d2cfaffca42958531be | Python | 36,556 | 888 | from genomic_regions import GenomicRegion, Bedpe
from collections import defaultdict
import numpy as np
from ..tools.general import RareUpdateProgressBar
from ..general import FileGroup
from skimage.transform import resize
import warnings
import tables
import logging
logger = logging.getLogger(__name__)
class Aggre... |
f3a3d94f3b0d67c2556dff6579911b1aab0ea3acad59dd6ac8a624030fdbf267 | Python | 36,630 | 1,152 | """Model the behavioral data."""
# %%
# Imports
import itertools
import json
import sys
import warnings
from functools import partial
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import pingouin
import scipy.stats
import seaborn as sns
import statsmodels.stats.multitest
from scipy.optimize im... |
fa5bb7c6f58ec470e4a1ab3e2154db620846675b6e74455d178445988d59f783 | Python | 36,769 | 906 | """
Source files for genome annotation. Each variable is a dictionary in which
keys are supported genome versions
GTF_SOURCE: GENCODE basic CHR gtf file
DHS_SOURCE: Master Peak List ENCODE3 human and mouse DNase-seq October 2015
BLACKLIST_SOURCE: ENCODE black list for ChIP-seq, DNase-sea and ATAC-seq
... |
1dd53e45703c53a8e4bcc7d5492b26983c2dc43781c9edddf07dccf52288ac8d | Python | 36,778 | 1,018 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Feb 16 10:58:44 2024
@author: colin
"""
import asyncio
import asyncssh
import contextvars
import functools
import paramiko
import threading
import os
from os.path import join as pjoin
from os.path import exists as pexists
import sys
import subprocess
# ... |
229c189d1d45756387a79bf2c4cb7b4609a306baf644e8b58140bef822f12679 | Python | 36,796 | 995 | import matplotlib.pyplot as plt # To plot
from scipy.optimize import curve_fit
from pylab import *
import data_treatment as datr
import numpy as np
import random
import math
import time
import os
import glob
import copy
def rmsd(x,y):
Nx = len(x)
Ny = len(y)
if Nx!=Ny:
... |
c6f6e26aee86a84d68c2c0585cfd16546e67fd78f4e2bc98a03ba41de780475f | Python | 36,841 | 937 | from unittest.mock import patch
from organizations.tests.factories import OrganizationFactory
from projects.models import Project
from projects.tests.factories import ProjectFactory
from rest_framework.test import APITestCase
from tasks.models import Annotation, AnnotationDraft, Task
from tasks.tests.factories import ... |
0547c89a5261759cc6762a78ed17379c348261f0aec119ea7221143e174c35e7 | Python | 36,884 | 915 | """Tests for backend system and cross-backend numerical equivalence.
These tests verify that:
1. The backend switching mechanism works correctly
2. NumPy and PyTorch backends produce numerically equivalent results
3. All core computational functions work with all backends
4. torch_cuda and torch_mps backends (when ava... |
121f6eb5b7b44c916ad85f423b7b1c905226c93bd4d79b00115d96fbbeffc6a7 | Python | 36,885 | 866 | """Functions to estimate average cell densities of various cell types in brain regions based
on measurements from the scientific literature.
Known density values are used to perform a linear fitting for each cell type of interest in
the following three groups:
- isocortex
- cerebellum
- the rest
The cerebellum was s... |
22391ca9a4b1931a356e11430e88e3d1a5ff1e14f5a2bc4667d1d58384f4dde0 | Python | 36,893 | 839 | import sys
import copy
import math
from PyQt5 import QtGui
from PyQt5 import QtCore
from PyQt5 import QtWidgets
import inspect
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.backends.backend_qt5agg import \
NavigationToolbar2QT as NavigationToolbar
from matplotlib.... |
0c0d75a10868c75a3fa8673dfbfa320509988080333f624ed212a30fe3ae52f4 | Python | 36,894 | 870 | import os
import numpy as np
import importlib
from jinja2 import FileSystemLoader, Environment
from lava.magma.core.run_configs import Loihi2SimCfg
from lava.magma.core.run_conditions import RunSteps
# Import Brian2 modules
# from brian2.units.allunits import second
# from brian2.core.functions import Function
# from... |
951f2acbc5990b42d2417a380ee12c861111af4cf1f7352e1ce3b1aaac8a4654 | Python | 36,961 | 976 | """Base class for MultiDiGraph."""
from copy import deepcopy
from functools import cached_property
import networkx as nx
from networkx import convert
from networkx.classes.coreviews import MultiAdjacencyView
from networkx.classes.digraph import DiGraph
from networkx.classes.multigraph import MultiGraph
from networkx.... |
37db89f100df95c3a1f563a21b4f48d505f5ae8df64770b92c84b22580b92a91 | Python | 36,967 | 977 | import numbers
from typing import Optional, Union
import torch
from .. import base, functional, surrogate
from .base_node import BaseNode, NonSpikingBaseNode, SimpleBaseNode
__all__ = [
"SimpleIFNode",
"IFNode",
"HalfThresholdIFNode",
"ActivationAwareIFNode",
"NonSpikingIFNode",
]
class SimpleI... |
a7eb30da1a6db197024cb13b6dc7dd398cb9baa49631059877ee923413b446a0 | Python | 36,990 | 911 | # -*- coding: utf-8 -*-
# Imports
import pandas as pd
import numpy as np
import dill
from gpytorch.priors import GammaPrior
from .models import GP_Model
from .base_models import fast_computation
from .init_scheme import Init
from .objective import objective
from .acq_func import acquisition
from .plot_utils import... |
db1b1d37252b0aa8d7305625365eedf2dca321a5ef94e93a38b93926bb8b599d | Python | 37,058 | 922 | #!/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 Adapter
from ax.adapter.data_utils import (
... |
27b80505c0e7720517217f1296e2f97b88fe34c1e6d6f5c6defffc7c30447232 | Python | 37,090 | 917 | import logging
from collections.abc import Callable
from datetime import datetime
from enum import Enum
from typing import (
cast,
NamedTuple,
Optional,
Union,
)
from urllib.parse import urlparse
from pydantic import (
BaseModel,
ValidationError,
)
from sqlalchemy import (
and_,
delete,... |
cc1826cc8613e9a01cb6e30846615a2e7cc2de2cf81b1ee3e4d8f899d62a47e0 | Python | 37,111 | 1,291 | # -*- coding: utf-8 -*-
"""
FileList
========
Module to handle sources distributed over a list of files.
File lists ar specified using a :mod:`~ClearMap.Utils.TagExpression`.
"""
__author__ = 'Christoph Kirst <christoph.kirst.ck@gmail.com>'
__license__ = 'GPLv3 - GNU General Pulic License v3 (see LICENSE.txt)'
_... |
6a3bfe3e3d277fea94fc791201e9b10e1db20d84053afc319d421733191edd56 | Python | 37,132 | 1,044 | from __future__ import annotations
from collections.abc import Mapping
from functools import reduce
from itertools import chain, pairwise
from typing import TYPE_CHECKING, cast
import numpy as np
import pandas as pd
from h5py import Dataset
from testing.anndata._doctest import doctest_filterwarnings
from ..._core.a... |
e99a03b18c6b3de75b7a634b16ffb1d56d4be0175c4d4478b30320573f5cefd1 | Python | 37,242 | 998 | from __future__ import print_function
import matplotlib as mpl
mpl.use('TkAgg')
from mpl_toolkits.mplot3d import Axes3D
import BBStaticDialog as BBDialog
import Tkinter as tk
import tkFileDialog
import ttk
from Tkinter import TclError
from tkColorChooser import askcolor
import matplotlib.pyplot as plt... |
1f9c06cbbc289b527b56e0d8e04671e8c3f6ab06ef837d3eaaf91c3e91e927cf | Python | 37,250 | 942 | import os
import pathlib
import random
import shutil
import tempfile
from shutil import rmtree
from typing import Generator, Iterator, List, Tuple
import anndata.tests.helpers
import feather
import numpy as np
import pandas as pd
import pytest
import skimage.io as io
import xarray as xr
import numba as nb
import test_... |
39638f278546638de7b1aeaeeb31e05ca8ce1a60e62f8d8afac641c2515a0835 | Python | 37,315 | 992 | """
Base classes for Galaxy AI agents.
"""
import asyncio
import fnmatch
import logging
import os
import random
from abc import (
ABC,
abstractmethod,
)
from collections.abc import (
Callable,
Sequence,
)
from dataclasses import (
dataclass,
field,
)
from typing import (
Any,
Literal,
... |
e409399d0c3d2f0fe781ea5ec3a54b35f30a3351f311bb25a85959b4d31245f7 | Python | 37,333 | 1,019 | """
Provide basic convenience data types.
Most classes are based on PyTables and HDF5 dictionaries,
allowing on-disk storage and therefore processing of large
files. Other features include indexing and querying.
"""
from __future__ import division
import logging
import os
import shutil
import tempfile
import warning... |
49429e7d3f09e5c5d1a7b2b3ad1d2085d85a092fb79b928a81a188b37f14e452 | Python | 37,334 | 1,236 | from typing import Optional
import torch
from spikingjelly.activation_based import surrogate
from spikingjelly.logger import logger
from ..layout import _empty_like
from ..surrogate_dispatch import resolve_sg_triton_id_and_alpha, sg_triton
from ..triton_layout import (
_block_minor,
_check_mp_cuda_inputs,
... |
ddc9f1bbab5f0606c877f5a48c0899b294036be1fab3642433d900a5a45fff09 | Python | 37,349 | 1,018 | import datetime
import json
from collections.abc import Callable
from concurrent.futures import TimeoutError
from functools import lru_cache
from pathlib import Path
from typing import (
Any,
Optional,
)
from urllib.parse import urlparse
from celery import current_task
from sqlalchemy import (
and_,
cr... |
81d5a0dddedf0989958798aad506da9dd2f5f6d106a8c3eb20e19c8c40095cb4 | Python | 37,370 | 1,150 | """
Proteomics Datatypes
"""
import logging
import re
from typing import (
IO,
Optional,
)
from galaxy.datatypes import data
from galaxy.datatypes.binary import Binary
from galaxy.datatypes.data import Text
from galaxy.datatypes.protocols import (
DatasetHasHidProtocol,
DatasetProtocol,
HasExtraFi... |
b7275ae4fd63205f5864cdefdef6a54d63265bd141e217e5deefec93299662c4 | Python | 37,380 | 866 | #!/usr/bin/env python
#
# Copyright (c) 2015 10X Genomics, Inc. All rights reserved.
#
from collections import defaultdict, OrderedDict, namedtuple
import cPickle
import h5py
import tables
import itertools
import json
import math
import random
import numpy as np
from cellranger.feature_ref import FeatureReference, Feat... |
704134bb91d8cbf6a88d12b73779467ebe19915464da308a449e11a5fb10eb68 | Python | 37,384 | 914 | import copy
from collections import Counter, defaultdict
from itertools import combinations
import os
import pickle
import numpy as np
import pandas as pd
from scipy.stats import spearmanr, pearsonr
from scipy.special import softmax
from scipy.optimize import minimize
from sklearn.impute import KNNImputer
from sklearn.... |
c74fd3f8d9fc29b5b1ffb6a8696c4dc0ba4234d4bd4aaf0e3b940348bc547ea5 | Python | 37,384 | 814 | import os
import re
import torch
import numpy as np
from .dual_position_bert_model import DualPositionBertForPreTrainingPreLN
from .utils import colored, OAG_TOKEN_TYPE_NAMES, stringLenCJK, stringRjustCJK
from transformers import BertTokenizer
import sentencepiece as spm
class OAGMetaInfoBertModel(DualPositionBertFor... |
e190bc5caa1a738d8b127d673af78c61a3753e4b38e4775bc1c60967a617d6e5 | Python | 37,396 | 962 | from . import __version__
from .reporting import warn
from .helpers import ConfigurableClass, get_qualified_class_name
from .morphologies import Morphology, Compartment, Branch
from .helpers import suppress_stdout
from contextlib import contextmanager
from abc import abstractmethod, ABC
import h5py, os, time, pickle, r... |
14ed6143550621134e6a3c7b362a60472aee52bd63f8fef072953030a294e06a | Python | 37,431 | 1,359 | import pytest
from unittest.mock import patch
import operator
from nl_expr.exceptions import NeuroLangException
from nl_expr.expressions import (
Symbol,
Constant,
FunctionApplication,
ExpressionBlock,
)
from nl_expr.logic.unification import most_general_unifier
from nl_expr.logic import (
Implicat... |
6c46e73025c6afa3c94392d6d24a50b99be0d330ef4098b1347c2dc4d0a49c70 | Python | 37,453 | 1,188 | from typing import Optional
import torch
from spikingjelly.activation_based import surrogate
from spikingjelly.logger import logger
from ..layout import _empty_like
from ..surrogate_dispatch import resolve_sg_triton_id_and_alpha, sg_triton
from ..triton_layout import (
_block_minor,
_check_mp_cuda_inputs,
... |
4ac543533387c807f3257f4ec6482e2b92c5fbe7556b1a72534d04bf24576a1e | Python | 37,460 | 1,002 | 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... |
bbf68839ba89f5d7110ec56c20b10c3635911dd61e45f9fa4b9792bf92c6bb6d | Python | 37,549 | 756 | import random as rd
import unittest as ut
import networkx as nx
from pysbm.sbm.inference import PeixotoInference
from pysbm.sbm.nxpartitiongraphbased import NxPartitionGraphBased
from pysbm.sbm.objective_function_iclex import *
from pysbm.sbm.objective_functions import TraditionalUnnormalizedLogLikelyhood
def gener... |
f5d782bd300e5c7ad91aa1a695cf0907c9cca67e801dbeb4b03c656a508b333f | Python | 37,598 | 931 | """
Modified from pygenometracks.
LICENSE: https://github.com/deeptools/pyGenomeTracks/blob/master/LICENSE
"""
import logging
import os
import pathlib
import time
import warnings
from collections import OrderedDict
from configparser import ConfigParser
import matplotlib
import matplotlib.cm
import matplotlib.colors
... |
f5d89b6ea02cae8023f05ba2937c93f665567b01f2e2c9e63a6812e07e8e507e | Python | 37,614 | 952 | """
Created on Jun 12, 2018.
This module implements generalized linear mixed model via encapsulating R.
@author: voodoocode
"""
import numpy as np
import warnings
import gc
import rpy2.robjects as ro
import rpy2.robjects.numpy2ri
import rpy2.rinterface_lib.embedded
import rpy2.robjects.conversion as conv
def che... |
2bd30388f6c272980c1955c9c81ce7e673f1ece9dfbb85387ca7479e088da4f8 | Python | 37,643 | 1,060 | # -*- coding: utf-8 -*-
"""
Resampling
==========
This module provides methods to resample and reorient data.
Resampling the data is usually necessary as the first step to match the
resolution and orientation of the reference object.
"""
__author__ = 'Christoph Kirst <christoph.kirst.ck@gmail.com>'
__license__ ... |
2b7031fc1e87364396d714beda85a24465786358672afe0726e56b8765073bed | Python | 37,725 | 1,225 | from copy import deepcopy
from dataclasses import dataclass
from typing import ClassVar, Optional
import torch
import torch.distributed as dist
import torch.nn as nn
from torch.distributed import ProcessGroup
from .. import functional, layer, memopt, neuron
from ..distributed.tensor_parallel import (
ChannelShard... |
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