sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
094a42d47db5fcee31b4002e26f84bb4fdd0a1cc02f9bd1de60ea3313f0cc930 | Python | 59,526 | 1,688 | from __future__ import annotations
from collections.abc import Callable
from collections.abc import Container
from collections.abc import Iterable
from collections.abc import Mapping
from collections.abc import Sequence
import copy
from numbers import Integral
from numbers import Real
import threading
from typing impo... |
7b997d2c876e97aab9ad290c65f8a834ab588b2f391276e526ad250eb2989f53 | Python | 59,609 | 2,077 | # tifffile/tifffile_geodb.py
"""GeoTIFF GeoKey Database.
Adapted from http://gis.ess.washington.edu/data/raster/drg/docs/geotiff.txt
"""
import enum
class Proj(enum.IntEnum):
"""Projection Codes."""
Undefined = 0
User_Defined = 32767
Alabama_CS27_East = 10101
Alabama_CS27_West = 10102
Ala... |
f1f901af9c8012d4d1f6fda01bbb27d71623faf5c4c36a2dd2d6c17fb6a65125 | Python | 59,623 | 1,397 | """Search space transformation and encoding/decoding classes"""
from __future__ import absolute_import, division, print_function
import numpy as np
from numpy import array, isfinite, log
import warnings as _warnings
from .utilities.utils import rglen, print_warning, is_one, SolutionDict as _SolutionDict
from .utiliti... |
c1f49c8c930fd1dc5b50b3d3998c3aca794b97652a66758052f331cc8bf299d4 | Python | 59,837 | 1,307 | import csv
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
from sklearn.metrics import roc_curve, auc
from scipy import interp
import pickle
from scipy import stats
from sklearn.metrics import roc_auc_score
from itertools import cycle
from itertools import *
impo... |
e009f56c6ac20b97ed00d65c9d2935939fdbbadebda25ed6e3455955fa967ce9 | Python | 60,464 | 1,449 | # SPDX-License-Identifier: LGPL-3.0-or-later
import contextlib
import datetime
import functools
import logging
import time
from copy import (
deepcopy,
)
from pathlib import (
Path,
)
from typing import (
Any,
)
import numpy as np
import paddle
import paddle.distributed as dist
from paddle.distributed impo... |
bc5129e62222ef5cecd59f2cb1cec7987b31a7bcd99ee133b8da908587c0dc1e | Python | 60,615 | 1,303 | # ----------------------------------------------------------------------------
# Copyright (c) 2017-2026, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------------... |
a12468490fe79ed3f3e871d06757545799c9db8d234a116cb0bb9307dc100b01 | Python | 61,467 | 1,567 | from __future__ import print_function
import weakref
import numpy as np
import scipy.optimize
from collections import OrderedDict
import neuron
from neuron import h
from ..util import nstomho, mho2ns
from ..util import custom_init
from .. import synapses
from .. import data
from .. import morphology
from .. import deco... |
c8f8fe1b551c275c51e78fa54e0a4b4f85205c36311141faebd681d0d309d286 | Python | 61,975 | 1,086 | """
Script to plot paper figure panels from main analysis file generated via rwave_build_main.py
"""
import argparse
import os
from os import path
from typing import Any, List
import h5py
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as pl
from matplotlib_venn import venn2
import seaborn as sns
... |
951537f9402e6b200bcd2ed0d52e466927d341afd2bdf3a5be5c69c159cfa43c | Python | 62,322 | 1,759 | from __future__ import division
from itertools import product
from textwrap import dedent
from distutils.version import LooseVersion
import numpy as np
import pandas as pd
import matplotlib as mpl
import matplotlib.pyplot as plt
from .external.six import string_types
from . import utils
from .utils import (categoric... |
b589d5add050aa17ed7c933f5296d77e63c886d913d160787348e82a8834ceda | Python | 62,551 | 1,585 | import os
import time
import torch
import numpy as np
from os.path import join as pjoin
from scipy.stats import pearsonr
from functools import partial
from PIL import Image
from torch import nn
from torch.utils.data import DataLoader
from torchvision import transforms
from torchvision import models as tv_models
from d... |
2d2ffccc9093572fd4a2a90c2d53124503631440a7753ba4fc8d6625fc03fd88 | Python | 62,642 | 1,962 | # Copyright 2026 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
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
b04fa2f539417dcc06b57fd657a2cf22223e71cec5595e745da1f75df707d50c | Python | 62,699 | 1,208 | import os
import numpy as np
import pickle as pkl
import pandas as pd
import src.models.kernel_regression as kernel_regression
import src.visualization.vizregression as vizregression
import src.data.process_ephys_data as pephys
import src.data.analyse_spikes as anaspikes
import sklearn.model_selection as sklselection
... |
f27e197ee91c6479ad3e92251e8f57a6b77cc7dc35a1197f9951909cf3815ad7 | Python | 62,856 | 1,650 | import abc
import cv2
import time
import copy
import torch
import numpy as np
from os import remove
from os.path import join as pjoin
from PIL import Image
from scipy.ndimage.filters import gaussian_filter
from torch.optim import Adam
import torch.nn as nn
from torch.nn.functional import interpolate
from matplotlib im... |
898a9f63b21edd88738ea9ad8293d4e6d03f24edae24075cc8bf85a00b62ec96 | Python | 63,035 | 1,878 | import numpy as np
import pandas as pd
import matplotlib as mpl
import matplotlib.pyplot as plt
import pytest
import numpy.testing as npt
from numpy.testing import assert_array_equal, assert_array_almost_equal
import pandas.testing as tm
from seaborn._base import categorical_order
from seaborn import rcmod
from seabo... |
0e20db43a5b2511b60d9df6f9c6af17caf9bdea99efe32e75e49938cfbaa17ce | Python | 63,165 | 1,861 | from itertools import product
import warnings
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
from matplotlib.colors import same_color, to_rgba
import pytest
from numpy.testing import assert_array_equal, assert_array_almost_equal
from seaborn.palettes import color_palette
from seaborn._ba... |
e8f23f6935324b0f57c983fc2bef5658ea96e29e098d1e5f0156a7ccea267b12 | Python | 63,316 | 1,556 | # Copyright 2019-2021 The AmpliGraph Authors. All Rights Reserved.
#
# This file is Licensed under the Apache License, Version 2.0.
# A copy of the Licence is available in LICENCE, or at:
#
# http://www.apache.org/licenses/LICENSE-2.0
#
from collections.abc import Iterable
from itertools import product, islice
imp... |
3e29f3243ce2f6b6b7c04ac5e94a4afe22928abe147d2e252dbd33c0e18fe5e9 | Python | 63,765 | 1,696 | """Machine type checkers for Series scitype.
Exports checkers for Series scitype:
check_dict: dict indexed by pairs of str
1st element = mtype - str
2nd element = scitype - str
elements are checker/validation functions for mtype
Function signature of all elements
check_dict[(mtype, scitype)]
Parameters
--------... |
37895010e1df33be2c4db15539761b5156ed1bba1bbc88d9e932d5e7b8350863 | Python | 63,862 | 2,051 | # roifile.py
# Copyright (c) 2020-2026, Christoph Gohlke
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this li... |
6b8ad4295ee7a523d563b1dbb4a644e2f1a2606771ebe01d1710a9849843200d | Python | 64,101 | 91 | ## For Calculating Psilocybin Concentration in the ECS
from numba import jit
import numpy as np
#import matplotlib.pyplot as plt
from scipy import interpolate
import time
begin = time.time()
h=0.01 # In minutes -- time step size
g=0.01 # In Centimeter -- spatial step size
print("h=",h)
print("g=",g)
#... |
8b628375ef5c34a7e7dd2582450ce4e4fc0ba1821dd75fedabf3d0a8004df3f3 | Python | 64,638 | 1,062 | from bert_serving.server.helper import get_args_parser
from bert_serving.server import BertServer
from bert_serving.server.helper import get_shutdown_parser
import pandas as pd
import os
from tqdm import tqdm
import re
import pickle
import sys
import numpy as np
from nltk.tokenize import RegexpTokenizer #... |
cd361deb10e584f988945b382609ac133810c59d5326cd5ad7c7af2d392e3744 | Python | 65,092 | 1,386 | import pdb
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
import sciplotlib.style as splstyle
import xarray as xr
import pandas as pd
import scipy.signal as ssignal
import scipy.stats as sstats
import sklearn as skl
import src.data.process_facecam as pface
import src.data.analyse_2p as ana... |
9a29f2e388a17cf08f26eb9748354436c8392f5d0c3066755b3fceb6531b5574 | Python | 65,488 | 1,602 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import os
import pathlib
import shutil
import uuid
import warnings
from typing import TYPE_CHECKING, Any
import numpy as np
import pytest
import onnx
from onnx import (
ModelProto,
NodeProto,
... |
50ae7733d2e5ad8d70401e5c1719df8ecc0eac0f44f16967ed337a46b0a3779f | Python | 65,489 | 1,522 | import matplotlib.pyplot as plt
from matplotlib.colors import Normalize
import numpy as np
from ipywidgets import widgets
from CGAL.CGAL_Polyhedron_3 import Polyhedron_3
from typing import List, Tuple, Dict, Set, Iterable, Callable
from spine_fitter import SpineGrouping
from spine_segmentation import point_2_list, list... |
8a96509352c78b06420c27e5f97cc9900f8d9b655edf43aafc1906e98d35c648 | Python | 65,598 | 1,752 | """Utilities for loading datasets."""
__author__ = [
"mloning",
"sajaysurya",
"big-o",
"SebasKoel",
"Emiliathewolf",
"TonyBagnall",
"yairbeer",
"patrickZIB",
"aiwalter",
"jasonlines",
"achieveordie",
"ciaran-g",
"jonathanbechtel",
]
__all__ = [
"load_airline",
... |
269f35bd625a535033ae229b50dc318a27e15da82a51eaecb6f5fe8be6728e81 | Python | 65,918 | 1,764 | from __future__ import annotations
import warnings
import itertools
from copy import copy
from collections import UserString
from collections.abc import Iterable, Sequence, Mapping
from numbers import Number
from datetime import datetime
import numpy as np
import pandas as pd
import matplotlib as mpl
from seaborn._co... |
f209b5441c841725b417bb24af50edfd428fdb9bab142b01f72418db9f0cb4c0 | Python | 66,038 | 1,586 | from matplotlib import colors
from seaborn._compat import register_colormap
_rocket_lut = [
[ 0.01060815, 0.01808215, 0.10018654],
[ 0.01428972, 0.02048237, 0.10374486],
[ 0.01831941, 0.0229766 , 0.10738511],
[ 0.02275049, 0.02554464, 0.11108639],
[ 0.02759119, 0.02818316, 0.11483751],
[ 0.032... |
18c6adaa6e1d260851826cc116da42f0f125e22ee711b4b1525a5898f7deeb72 | Python | 66,065 | 1,189 | import argparse
import logging
import math
import os
import random
import time
import traceback
from collections import defaultdict
from functools import partial
from pathlib import Path
from typing import Dict, List, Optional, Tuple, Union
import numpy as np
import pandas as pd
import torch
import torch.distributed a... |
441b0fcbd77051239e3a9f725cefe0866540ab2c4068b275ee1aa15c7afb49cd | Python | 68,231 | 1,824 | """The classes for specifying and compiling a declarative visualization."""
from __future__ import annotations
import io
import os
import re
import inspect
import itertools
import textwrap
from contextlib import contextmanager
from collections import abc
from collections.abc import Callable, Generator, Mapping
from ty... |
82a08a51b443759b0b9ac8bff4ca45a1093f542c07496c268690013b761ca2ce | Python | 68,238 | 1,947 | from __future__ import annotations
from collections.abc import Callable
from concurrent.futures import as_completed
from concurrent.futures import ProcessPoolExecutor
from concurrent.futures import ThreadPoolExecutor
import copy
import multiprocessing
import pickle
import threading
import time
from typing import Any
f... |
2e84ea29943d30c6f9bfb96bb27bacbd6a8f96a421b67f8f7d7af41925c2847a | Python | 68,318 | 1,648 | import hashlib
import logging
import re
import tempfile
from collections import Counter
from pathlib import Path
from typing import Any, Optional, Union
import numpy as np
import torch
from deprecated.sphinx import deprecated
from sentencepiece import SentencePieceProcessor
from torch import nn
import flair
from flai... |
b90196d295ad6986dd97a5afc98f79254d1bacfd36ef25e299e94c18ae7d8f52 | Python | 68,696 | 1,568 | #!/usr/bin/env python3
""" run neurondm related exports and conversions
Usage:
neurondm-build release [options]
neurondm-build all [options]
neurondm-build [indicators phenotypes] [options]
neurondm-build [models bridge old dep dev] [options]
neurondm-build [sheets] [options]
Options:
-h --help... |
503dd6b1ad18ffec0ece888b3817198267579a1b152757af493ad6a47f20396e | Python | 68,859 | 1,696 | import logging
import re
from pathlib import Path
from typing import Optional, Union
import flair
from flair.data import Corpus, FlairDataset, Sentence, Token
from flair.datasets.base import find_train_dev_test_files
from flair.file_utils import cached_path
log = logging.getLogger("flair")
class UniversalDependenci... |
4c1a09e79bcf3497bf8f060bf477f33ee287bfbab73e604c5613b5e879a9afba | Python | 68,887 | 1,551 | import inspect
import os
import random
import re
import tempfile
import warnings
import zipfile
from abc import abstractmethod
from io import BytesIO
from pathlib import Path
from typing import Any, Callable, Dict, Literal, Optional, Union, cast
import torch
import transformers
from packaging.version import Version
fr... |
14e46978790d86a138ea372c925679785d2accbd671346bd0ce6b6650a0a2821 | Python | 69,486 | 1,644 | import numpy as np
import os
import matplotlib
import tkinter as tk
import tkinter.messagebox
# Set the matplotlib backend to tk figures.
# If imported, cannot plot to regular matplotlib figures!
from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
from matplotlib.figure import Figure
from seas.signalanaly... |
bdb365301f815ab8df19c10ab035ffa8773fad8307bfc8ca432d01bd180890a2 | Python | 69,766 | 1,915 | # Copyright 2019-2026 The AmpliGraph Authors. All Rights Reserved.
#
# This file is Licensed under the Apache License, Version 2.0.
# A copy of the Licence is available in LICENCE, or at:
#
# http://www.apache.org/licenses/LICENSE-2.0
#
import json
import logging
import os
from collections import namedtuple
from a... |
c42c7f63b21d157e4533bf7897bdf630339e702fa39e02ba63d4fe4d6fa067e3 | Python | 70,517 | 2,168 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""BBOB noiseless testbed.
The optimisation test functions are represented as classes `F1` to
`F24` (and `F101` to `F130`).
This module implements the class `BBOBFunction` and
sub-classes:
* class `BBOBNfreeFunction` which have all the methods common to the
classes `F... |
75545f1263c5df9392c84ca10b0671155ef3dcfae5da41f25791cca0fecd6ab8 | Python | 71,185 | 2,307 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
from typing import ClassVar
import automatic_conversion_test_base
import numpy as np
import pytest
import onnx
from onnx import TensorProto, helper
####################################################... |
2376dcce95f2e5be9524c09ac91ff78fcdf481ee6ca8ff582e03b7942fa848dc | Python | 72,081 | 1,976 | """Atoms and Molecules module.
This module contains a series of tools and functions in order to create and
handle molecules in a different ways
Attributes:
DIM_DICT (:obj`dict`): translation dict for cartesian coordinate system
"""
import warnings
from itertools import product
from collections import OrderedDict,... |
628c1047b555d21fce1f0d317f3bcf8655f5c224559005d0b2f1c7d16aded1b6 | Python | 72,340 | 1,730 | # SPDX-License-Identifier: LGPL-3.0-or-later
import math
import types
from typing import (
Any,
)
import torch
from torch.fx.experimental.proxy_tensor import (
make_fx,
)
from deepmd.dpmodel import (
get_hessian_name,
)
from deepmd.dpmodel.atomic_model.base_atomic_model import (
BaseAtomicModel,
)
fro... |
ad8a549ca09c4627f0ff61c16115ab757cbe25a928ae9a2f44047c9edd70f2be | Python | 72,538 | 6,951 | """
@file: plane_policy_representation.py
Created on 18.04.19
@project: CrazyAra
@author: Moritz Willig and later updated by queensgambit
Functionality for representing all possible moves in the policy feature maps.
Note, most of the entries in the policy feature map are unusable because the represent illegal moves
wh... |
1bf2215d7ec811f5ead42b8556b70b26803df3e656f0bb79bd8d83339877ab7a | Python | 72,645 | 1,645 | """
These are functions that are shared by odp, odp_trio, and other scripts
"""
# this is all needed to load our custom fasta parser
import gzip
import os
import sys
snakefile_path = os.path.dirname(os.path.abspath(__file__))
dependencies_path = os.path.join(snakefile_path, "../dependencies")
sys.path.insert(1, depend... |
78f0700ffb036fcdf46a133d2fbc0806027505a3cc4654452c3ab48e5064fb4a | Python | 72,674 | 1,689 | #!/usr/bin/env python3
""" run neurondm related exports and conversions
Usage:
neurondm-build release [options]
neurondm-build all [options]
neurondm-build [indicators phenotypes] [options]
neurondm-build [models bridge old dep dev neurdf] [options]
neurondm-build [sheets] [options]
Options:
-h... |
905428c63ba0eb7f0e4a8cfbcbf11fbee4dc0b03db6f4d03a15a8e7fb67d859a | Python | 73,128 | 2,031 | # Copyright 2026 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
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
965a673dd7c738718ed8c03a1d3dc2f175ce51e9ac5186630f5929c82437823d | Python | 73,422 | 1,913 | # Copyright 2019-2026 The AmpliGraph Authors. All Rights Reserved.
#
# This file is Licensed under the Apache License, Version 2.0.
# A copy of the Licence is available in LICENCE, or at:
#
# http://www.apache.org/licenses/LICENSE-2.0
#
"""Data indexer.
This module provides a class that maps raw data to indexes an... |
fd7fae4a76849c44677401649e87f08e40425ab6bbb9c36b0c1a1fc5d32e7435 | Python | 73,774 | 1,773 | # coding=utf-8
# Copyright 2018 The Google AI Language Team Authors.
#
# 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 req... |
c910d331fc21fd8a5748a2840fc72da05839e86c0014eeafe5dc7df15a79a73a | Python | 73,880 | 1,950 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""CauKer V2 generation and pre-generated KernelSynth Arrow readers.
The offline KernelSynth shard generator is intentionally not part of this
repository. ArrowSyntheticIterableDataset consumes shards produced ahead of
training and does not generate those shards itself.
""... |
2751653cd7f101378e0c42b53e432a8a9d46c0ae008e01aa3bf4e003486e8e87 | Python | 73,883 | 1,777 | # coding=utf-8
# Copyright 2018 The Google AI Language Team Authors.
#
# 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 req... |
7d54251268e61d11999b0c7f640c7a24863ce879025b10c077c00f635d7ee2db | Python | 74,309 | 1,695 | import pytest
import unittest
import subprocess
import pprint
from pathlib import Path
from collections import Counter
import rdflib
import ttlser
from pyontutils.core import yield_recursive, OntGraph, bnNone, OntResIri
from pyontutils.identity_bnode import bnodes, IdentityBNode as IdentityBNodeBase, idf, it as ibn_it
... |
b3d994e93ff2e530176714a7373aa341c26e7bf1b337bade7cb6a5e837b90666 | Python | 75,034 | 1,860 | # Copyright 2018-2026
# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
# 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/LICE... |
b0695a4574225e459bc530653417f8368b6237d58f93a6496baefaed982a2f15 | Python | 75,151 | 1,843 | #!/usr/bin/env python3
# SPDX-License-Identifier: LGPL-3.0-or-later
import bisect
import copy
import functools
import hashlib
import logging
from collections.abc import (
Iterable,
Iterator,
)
from concurrent.futures import (
ThreadPoolExecutor,
as_completed,
)
from pathlib import (
Path,
)
from ty... |
dd14fc50a1a0ac74aae785cbf6d1d2c6834a6c48931de35f503a218be7959233 | Python | 75,240 | 1,421 | # uncompyle6 version 3.7.5.dev0
# Python bytecode 3.7 (3394)
# Decompiled from: Python 2.7.17 (default, Feb 27 2021, 15:10:58)
# [GCC 7.5.0]
# Warning: this version of Python has problems handling the Python 3 "byte" type in constants properly.
# Embedded file name: /home/timsit/multisensory-integration/src/models/de... |
bac9c40a8bff889efe99c2345536c549a1c95e74d3b47e9138334221aa7fe24b | Python | 75,872 | 2,398 | """
Unfinished. Attempting to create a more object-oriented extensible version of
Foraging.
Goals:
- Runs with or without stimuli of any kind.
- Add foraging objects (lick sensors, encoders, stimulus objects, etc)
a la carte.
"""
import time
import datetime
import numpy as np
impor... |
34903d3e4213b24b6d8d6565ec45b9a33c9317f2803745c558a9a1d097a1ba15 | Python | 76,966 | 2,329 | import io
import xml
import functools
import itertools
import warnings
import numpy as np
import pandas as pd
import matplotlib as mpl
import matplotlib.pyplot as plt
from PIL import Image
import pytest
from pandas.testing import assert_frame_equal, assert_series_equal
from numpy.testing import assert_array_equal, as... |
c4bd52a3fc9c943bded7b00dd5ea959245ba78803d32730ae10c4e0256672420 | Python | 76,996 | 2,036 | # SPDX-License-Identifier: LGPL-3.0-or-later
import dataclasses
import math
from typing import (
Any,
)
from unittest import (
mock,
)
import numpy as np
import pytest
from deepmd.dpmodel.descriptor.dpa4c import (
DescrptDPA4C,
)
from deepmd.dpmodel.descriptor.dpa4c_nn import (
build_angular_basis,
... |
286bcfeff92297dbcf9f795f34317e64e53db091f1c4ed6acf029bfb43fa3e29 | Python | 79,865 | 2,491 | import itertools
import warnings
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
from matplotlib.colors import to_rgb, to_rgba
import pytest
from numpy.testing import assert_array_equal, assert_array_almost_equal
from seaborn import distributions as dist
from seaborn.palettes import (
... |
e004179e547ddf8a254cd1689843cc2093c3027b88c9becdef3cadd0b0a048b3 | Python | 80,189 | 1,630 | import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from matplotlib.colors import to_rgba
import seaborn as sns
import multiprocessing
import os
sns.set()
sns.set_style("whitegrid", {'axes.grid' : False})
from functools import reduce
from sklearn.neighbors import KernelDensity
from sklearn... |
00a72ff2abff51483d7cdf16d56fec116ebc3dd86cf59d5d98fcdc7d82fcce22 | Python | 80,634 | 1,614 | # Copyright 2007 Zachary Pincus
# This file is part of CellTool.
#
# CellTool is free software; you can redistribute it and/or modify
# it under the terms of version 2 of the GNU General Public License as
# published by the Free Software Foundation.
"""Classes for dealing with data organized as 2D point clouds and con... |
e38d1fe34e012872d7997fa1dab35e00459c855c5dc16212c8bab16fbdbd23ec | Python | 81,584 | 1,662 | """
This is an implementation of the LDDMM algorithm with modifications, written by Devin Crowley and based on
"Diffeomorphic registration with intensity transformation and missing data: Application to 3D digital pathology of Alzheimer's disease."
This paper extends on an older LDDMM paper,
"Computing large deformat... |
31970764b3020746b3f106c98cafa585225237fc0641957db63fd337b3ff20ea | Python | 81,946 | 1,933 | import copy
import io
import logging.config
import os
import shutil
import git
import h5py
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import tensorflow as tf
import tensorflow_probability as tfp
import yaml
from lfads_tf2.defaults import get_cfg_defaults
from lfads_tf2.initializers import v... |
3e0190c770a986d48ddb9981757124c83e8824d8e5b89201973f446ecb12ca86 | Python | 82,441 | 1,787 | import os
import random
import itertools as it
import numpy as np
import skimage as ski
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
import torchvision.models as models
import torchvision.transforms.functional as TF
import torchvision.transforms.v2 as transfo... |
37eb7ed538f119e20f32ce3d85337e70fb0f8edfb095a9293b705f33c24873a9 | Python | 83,878 | 1,751 | # 4. function that gives a loaded model
# 4. function that takes in the model and some sequences and gives embeddings
# 3. give file and columns (for cdr3/TCR seqs, and delimiter)
from torch.nn import LayerNorm
import logging
import datetime
# from transformers import AutoTokenizer, AutoModel, pipeline
import pickle
i... |
0aa94596b1cd24e5c924c83600f6e453b864c27b059b1af146f5fc53ee81a0ec | Python | 85,159 | 2,351 | from __future__ import division
from itertools import product
from distutils.version import LooseVersion
import warnings
from textwrap import dedent
import numpy as np
import pandas as pd
from scipy import stats
import matplotlib as mpl
import matplotlib.pyplot as plt
from . import utils
from .palettes import color_p... |
b4837492172a3bf8a7633066287cd99f072cf1c687569bc7645af43194e7b821 | Python | 86,026 | 2,201 | # SPDX-License-Identifier: LGPL-3.0-or-later
r"""Compact and Compressible degree-wise DPA4 descriptor.
DPA4C is the compact and compressible degree-wise member of the DPA4 family, a
graph-native local descriptor for lightweight training and for distillation
from DPA4. It reuses the DPA4 radial basis, bias-free radial ... |
d728a66ff77981fa7090a5c5dcf93830560687e257800efb3ed208538199c4c8 | Python | 86,239 | 636 | regs_per_section ={1 : ['OV', 'E', 'GrO', 'IPI', 'Mi', 'EPI', 'Gl'],
2 : ['OV', 'E', 'GrO', 'IPI', 'Mi', 'EPI', 'Gl', 'GrA', 'aci'],
3 : ['OV', 'E', 'GrO', 'IPI', 'Mi', 'EPI', 'Gl', 'GrA', 'aci', 'EPlA', 'MiA', 'dlo', 'AOL', 'AOE', 'unname', 'lo'],
4 : ['OV', 'E', 'GrO', 'IPI', 'Mi', 'EPI', 'Gl', 'GrA', 'aci', 'EPlA', ... |
652813e7d96864659fc5fd30ae9bb612c547e58b5b888ccf0016889fbdc37e4d | Python | 86,864 | 2,532 | """Plotting functions for visualizing distributions."""
from numbers import Number
from functools import partial
import math
import textwrap
import warnings
import numpy as np
import pandas as pd
import matplotlib as mpl
import matplotlib.pyplot as plt
import matplotlib.transforms as tx
from matplotlib.cbook import no... |
476308c37379612ccfec9c813b906830e6a70c5dd3e4331d239c5246a2be9b91 | Python | 87,369 | 635 | regs_per_section ={1 : ['OV', 'E', 'GrO', 'IPI', 'Mi', 'EPI', 'Gl'],
2 : ['OV', 'E', 'GrO', 'IPI', 'Mi', 'EPI', 'Gl', 'GrA', 'aci'],
3 : ['OV', 'E', 'GrO', 'IPI', 'Mi', 'EPI', 'Gl', 'GrA', 'aci', 'EPlA', 'MiA', 'dlo', 'AOL', 'AOE', 'unname', 'lo'],
4 : ['OV', 'E', 'GrO', 'IPI', 'Mi', 'EPI', 'Gl', 'GrA', 'aci', 'EPlA', ... |
a5508a5ed2a4a4db0684ff71b39146231243b6f7d7f616988acb9b4a2341b47b | Python | 87,560 | 2,401 | from __future__ import annotations
from itertools import product
from inspect import signature
import warnings
from textwrap import dedent
import numpy as np
import pandas as pd
import matplotlib as mpl
import matplotlib.pyplot as plt
from ._base import VectorPlotter, variable_type, categorical_order
from ._core.data... |
9726a0ea147c4653e6e55396ebe594c06fdad13f44143259b8a16aaff861740c | Python | 87,789 | 2,362 | # Author: Steven J. Bethard <steven.bethard@gmail.com>.
"""Command-line parsing library
This module is an optparse-inspired command-line parsing library that:
- handles both optional and positional arguments
- produces highly informative usage messages
- supports parsers that dispatch to sub-parsers
The... |
158a17e5af9e118ce4821415c1fa39b4103c7a87190d03a804029f67bb272d36 | Python | 87,916 | 2,353 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
# mypy: ignore-errors
from __future__ import annotations
import importlib
import itertools
import os
import numpy as np
import pytest
from numpy.testing import assert_allclose
import onnx
from onnx import ONNX_ML, TensorProto, TypeProto... |
a3efc04affa842f7396028482c7f017c42b8642204245fa4ddec1a2b7f8e1cd6 | Python | 88,464 | 2,504 | # -*- coding: utf-8 -*-
import numpy as np
import scipy.stats as ss
import itertools as it
from statsmodels.sandbox.stats.multicomp import multipletests
from statsmodels.stats.multicomp import pairwise_tukeyhsd
from statsmodels.stats.libqsturng import psturng
from pandas import DataFrame, Categorical, Series
def __co... |
df09ec0f342964e6fc553597613fd960fb6747e2e51fc6a87085f5ebe7169ad2 | Python | 89,339 | 1,635 | import warnings
warnings.filterwarnings('ignore', category=FutureWarning)
import pandas as pd
from pandas import DataFrame
from bs4 import BeautifulSoup, SoupStrainer
import urllib.request
import numpy as np
import os
import itertools
pd.options.mode.chained_assignment = None
from rdkit.Chem.Descriptors3D import Asphe... |
ee8b64f2d81f043b83f42673792157ea8ef8a907409ad277c809d22047e1bc7c | Python | 90,038 | 2,080 | # Copyright 2019 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
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
7ba7931600f5632eef44a2d57bf554be92df8110b5f77e5afcd72be4bcb16c79 | Python | 90,550 | 6,959 | """
@file: constants
Created on 26.09.19
@project: CrazyAra
@author: queensgambit
Definition of all constants for the variants:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Available MODES (active MODE is defined in main_config.py):
+ MODE_CRAZYHOUSE:
-- Input and output constant... |
23db8600b8dfd08d30d36cc807771943aafc00b65d35d23c14d62b4f69120b6e | Python | 90,780 | 2,186 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import os
import tempfile
from typing import TYPE_CHECKING
import numpy as np
import pytest
import onnx.defs
import onnx.parser
from onnx import (
GraphProto,
ModelProto,
SparseTensorProto,... |
e33ab59d2e90a6e8c529b34ac1896a6746bcc895734f0cd05ca63e70955c8a7b | Python | 90,984 | 2,210 | # copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Implements pipelines for forecasting."""
__all__ = ["TransformedTargetForecaster", "ForecastingPipeline", "ForecastX"]
import pandas as pd
from sktime.base import _HeterogenousMetaEstimator
from sktime.datatypes import ALL_TIME_SERIES_MTYPES... |
ed14a224ceb66d424f3783692054662727ae94a04d452fcc7c8552b7c66e0a56 | Python | 91,582 | 6,983 | """
@file: constants
Created on 26.09.19
@project: CrazyAra
@author: queensgambit
Definition of all constants for the variants:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Available MODES (active MODE is defined in main_config.py):
+ MODE_CRAZYHOUSE:
-- Input and output constant... |
d2037f166ee486d898ede605c03aec55b04b41a5073bf389cffd75d13fa37234 | Python | 91,700 | 1,747 | # -*- coding: utf-8 -*-
"""
Created on Wed Feb 24 22:07:30 2016
@author: tpisano
"""
import os, sys, cv2, time, re, warnings, shutil, mmap, collections, random, numpy as np, SimpleITK as sitk, multiprocessing as mp
import scipy.stats, pickle, scipy.ndimage
from skimage.external import tifffile
from tools.imageproces... |
0c38666041a364592f9514e5f129ca6688fac0d4a8ec29a6f9f40e8f731119e7 | Python | 91,740 | 2,182 | import csv
import json
import logging
import os
import tarfile
from pathlib import Path
from typing import Optional, Union
import flair
from flair.data import (
Corpus,
DataPair,
FlairDataset,
Sentence,
Tokenizer,
_iter_dataset,
)
from flair.datasets.base import find_train_dev_test_files
from f... |
81a0cee06f45a448b84c75c0164efb92a15a336d18eff0e7b288fa22cf93f991 | Python | 92,329 | 2,007 | from sklearn.pipeline import Pipeline
from sklearn import svm
from sklearn import dummy
import sklearn as skl
import sklearn.model_selection as sklselection
from sklearn.model_selection import cross_val_score
from sklearn.model_selection import RepeatedStratifiedKFold
from sklearn.model_selection import RepeatedKFold
... |
7887df9299904128c794e20c3ced5ae8e912557deab83d9330b264826e4046b0 | Python | 92,563 | 2,007 | #!/usr/bin/env python
#-------------------------------------------------------------------------------
# scripts/readelf.py
#
# A clone of 'readelf' in Python, based on the pyelftools library
#
# Eli Bendersky (eliben@gmail.com)
# This code is in the public domain
#------------------------------------------------------... |
fe23bd4574dea469220a048ed6153313fa7dab66cfd3715a4cdf3a4410b5eb5a | Python | 92,756 | 2,509 | from typing import Union, Optional, List, Tuple, Dict, Literal, Sequence, Callable, Any
import collections.abc as cabc
import warnings
from copy import copy
from cycler import Cycler
import numpy as np
import pandas as pd
from sklearn.preprocessing import StandardScaler
from scipy.stats import gaussian_kde
import scanp... |
f8276ed52aa2a0ce38d90746f38fb4ab5fad4af8b2cbaad478f79b09aeaf40b4 | Python | 93,473 | 2,670 | # SPDX-License-Identifier: LGPL-3.0-or-later
r"""Bindings and immutable artifacts for compressed degree-wise DPA4C.
The CUDA operator evaluates the complete DPA4C graph descriptor: the tabulated
radial branch and its shared mode profiles, the ordered PairFiLM amplitude, one
destination reduction that produces both env... |
5bbf1099d19901586089a8e935c1231733c51bbd9f657092fbcd9efb360f795d | Python | 93,965 | 2,422 | __author__ = ["chrisholder", "TonyBagnall"]
from collections.abc import Callable
from typing import Any
import numpy as np
from sktime.dists_kernels._numba_distances._ddtw import _DdtwDistance
from sktime.dists_kernels._numba_distances._dtw import _DtwDistance
from sktime.dists_kernels._numba_distances._edr import _... |
530fe6c1824f0a037381c28d01cfe46a98e49d69b5ec5498c9bff2743a9a803a | Python | 94,050 | 2,694 | import numpy as np
import pandas as pd
import scipy
from scipy import stats, spatial
import matplotlib as mpl
import matplotlib.pyplot as plt
from matplotlib.colors import rgb2hex
from distutils.version import LooseVersion
import pytest
import nose.tools as nt
import numpy.testing as npt
from numpy.testing.decorators... |
4d7d61760080a6837778348aa695cff82a850705fc38a6b622c5f6d106c23f10 | Python | 95,482 | 2,603 | # tifffile/zarr.py
# Copyright (c) 2008-2026, Christoph Gohlke
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# t... |
06046e1c5a3c682fa4c506d6b3b57f58d6b6a2013224feeefb8965a2b9c0081b | Python | 96,083 | 2,306 | # Copyright 2019-2026 The AmpliGraph Authors. All Rights Reserved.
#
# This file is Licensed under the Apache License, Version 2.0.
# A copy of the Licence is available in LICENCE, or at:
#
# http://www.apache.org/licenses/LICENSE-2.0
#
import tensorflow as tf
import copy
import shelve
import pickle
import numpy as... |
74975ac34332e261be030fdfe4abfccf432c48db2ec382bbf68556156ff8bbe5 | Python | 96,099 | 2,442 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Tabby-Pretrain mixed-data training entry point.
The released 165K recipe uses BLAST, pre-generated KernelSynth Arrow shards,
and online CauKer V2 samples. The optional GIFT loader is retained only for
backward compatibility and is disabled by default; it was not used to... |
0905fd0be818a575e3e32409c4f98619c9d29b90c422c4b7f41891881e02e3f1 | Python | 96,141 | 1,581 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file '.\design\GUI.ui'
#
# Created by: PyQt5 UI code generator 5.15.6
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
from PyQt5 import QtCore,... |
b608d65a29216a7c867eb6002d099366178fcba41195b99c6ec35e031f545e7e | Python | 97,279 | 662 | regs_per_section ={1 : ['OV', 'E', 'GrO', 'IPI', 'Mi', 'EPI', 'Gl'],
2 : ['OV', 'E', 'GrO', 'IPI', 'Mi', 'EPI', 'Gl', 'GrA', 'aci'],
3 : ['OV', 'E', 'GrO', 'IPI', 'Mi', 'EPI', 'Gl', 'GrA', 'aci', 'EPlA', 'MiA', 'dlo', 'AOL', 'AOE', 'unname', 'lo'],
4 : ['OV', 'E', 'GrO', 'IPI', 'Mi', 'EPI', 'Gl', 'GrA', 'aci', 'EPlA', ... |
719bf6fffa79bf2a3ee454f25509744638ba1e65887341921002d56063cb21c3 | Python | 98,783 | 1,652 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file '.\design\GUI.ui'
#
# Created by: PyQt5 UI code generator 5.15.6
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
from PyQt5 import QtCore,... |
5494c6226a6421be891bd2b07f8c2754fbdc51df770d407a2c77b3e5e1877712 | Python | 99,646 | 2,788 | # Copyright 2026 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
#
# Unless required by applica... |
3a4f4160db12cb0d78c86ffbf5d9f62df4b30659900ed64acad27f6bbace6f24 | Python | 100,665 | 2,403 | # This files contains all funtions and classes needed for running the code in test_notebook.ipynb
import os
import errno
from tabnanny import verbose
import numpy as np
import pandas as pd
from sklearn.model_selection import train_test_split
from sklearn.preprocessing import StandardScaler, MinMaxScaler, QuantileTran... |
d91c7af351b6e5776c865cdd0632f9bd247a802aae36ff9111835f781ec9e152 | Python | 102,216 | 2,133 | # Copyright 2019-2021 The AmpliGraph Authors. All Rights Reserved.
#
# This file is Licensed under the Apache License, Version 2.0.
# A copy of the Licence is available in LICENCE, or at:
#
# http://www.apache.org/licenses/LICENSE-2.0
#
import numpy as np
#import tensorflow as tf
import tensorflow.compat.v1 as tf
t... |
fc5e7a25a6fb9d849f4c44b19e15bf1bf0ad6155e9c1bb93176603ef052a77b1 | Python | 104,466 | 2,349 | import voxelmorph as vxm
from classification_models_3D.keras import Classifiers
from voxelmorph import layers as vxm_layers
from voxelmorph.tf.modelio import LoadableModel, store_config_args
from NetworkBasis.densenet import DenseBlocks
from NetworkBasis.layers import *
from NetworkBasis.swin import *
from Net... |
5a344afeccc4d174be5cca9e711a50c1e52df69b79fcc3b1abdff596b4d36c88 | Python | 106,465 | 2,545 | # SPDX-License-Identifier: LGPL-3.0-or-later
import functools
import json
import logging
import time
from collections.abc import (
Callable,
Generator,
Iterable,
Mapping,
)
from contextlib import (
nullcontext,
)
from copy import (
deepcopy,
)
from pathlib import (
Path,
)
from typing import... |
7fc0913cb5dda6f3faedaa38b89ead1fb81148863717b9920bf5b149c1306587 | Python | 109,658 | 2,089 | import sys
import hashlib
from collections import defaultdict
import rdflib
from enum import Enum
from .utils_fast import log as _log
log = _log.getChild('ibnode')
bnNone = rdflib.BNode() # BNode to use in cases where subject would be None
#_session_only_token = rdflib.BNode() # ensure raw bnode identities cannot ... |
54d138ed2a36b0cec2f83bbf8b7d0207a7db42fc7e3897fdb532fd79705f9f14 | Python | 109,659 | 1,995 | """
Simulation backends for synthetic nervous system networks. Each of these are python-based, and are constructed using a
Network. They can then be run for a step, with the inputs being a vector of neural states and applied currents and the
output being the next step of neural states.
"""
"""
%%%%%%%%%%%%%%%%%%%%%%%%... |
48c3b8c9325a2a127a06ea9b4db561272721f226cfddc7eb5fa41e5f01400644 | Python | 110,630 | 2,724 | """ model_run2.py - main simulation control.
Run a model based on a hoc cell structure, decorating the structure with ion channels and synapses.
Requires:
1. Python 3.7, 3.8 or 3.9 (anaconda distribution or a local environment - preferred).
2. Neuron7.7 - 8.0 (neuron.yale.edu)
3. pyqtgraph (Luke Campagn... |
cf21dca8e44a1aeacaceb8225cb18ce63f7d75c8d118f8eba803eeb6119797e4 | Python | 112,935 | 2,449 | from sns_toolbox.backends import SNS_Numpy, SNS_Torch, SNS_Sparse, SNS_Iterative
from sns_toolbox.neurons import SpikingNeuron, NonSpikingNeuronWithGatedChannels
import numpy as np
import torch
import sys
import warnings
def __compile_numpy__(network, dt=0.01, debug=False) -> SNS_Numpy:
if debug:
print('-... |
537eb0bf0ed640e9ebe1d1300d456d0c40b65a70f955eb8ee2de1ab127d405eb | Python | 113,123 | 2,646 | import abc
import bisect
import csv
import logging
import os
import re
from collections.abc import Iterable, Iterator
from pathlib import Path
from typing import Any, Optional, Union
import requests
from bioc import biocxml, pubtator
import flair
from flair.data import Corpus, EntityCandidate, MultiCorpus, Sentence, ... |
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