sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
56401d56036a87062af2ff2cfa60ac31855a969931e79447b64d24174339654a | Python | 78,600 | 2,220 | # Copyright 2001-2019 by Vinay Sajip. All Rights Reserved.
#
# Permission to use, copy, modify, and distribute this software and its
# documentation for any purpose and without fee is hereby granted,
# provided that the above copyright notice appear in all copies and that
# both that copyright notice and this permissio... |
4d5f565d5853e7bf55d9e7c3a2a7952fcfdc2987e8032b88639929e8bf202c45 | Python | 78,612 | 2,284 | # Copyright 2017 Google LLC.
#
# 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 list of conditions and the following disclaimer.
#
#... |
3bf2b0bb840f4ebaaa0a0815d820d51f4d96e3aa55eb056edf4c4f219afc9ca2 | Python | 78,661 | 2,146 | """Read/write support for Maildir, mbox, MH, Babyl, and MMDF mailboxes."""
# Notes for authors of new mailbox subclasses:
#
# Remember to fsync() changes to disk before closing a modified file
# or returning from a flush() method. See functions _sync_flush() and
# _sync_close().
import os
import time
import calendar... |
6d190e855b5a2173a74f2a8da1f76d1486416ab0b962465e3bddfdb16dbec3c5 | Python | 78,670 | 2,204 | # Copyright 2017 Google LLC.
#
# 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 list of conditions and the following disclaimer.
#
#... |
6457893f0d08f9448c17168de2166f4986126343d27f1dd4a9e4458090f65f5a | Python | 78,685 | 2,055 | """
TIFF overlay generation for detection, pairing, and tracking.
Creates multi-channel TIFF stacks with original data and overlays
for quality control and visualization.
"""
from __future__ import annotations
from pathlib import Path
from typing import Optional, List, Tuple, Dict
import warnings
import numpy as np... |
00e2b719add427557c8b00b817c14a7d5b8dde7f6d914d96852e9a8fa8168874 | Python | 78,689 | 1,973 | # Copyright (c) Microsoft Corporation.
# Licensed under the MIT License.
import abc
import logging
import os
import warnings
from collections.abc import Callable
import numpy as np
import torch
import torch.nn as nn
from torch._prims_common import DeviceLikeType
from tqdm import tqdm
from .sde_lib import SDE, _broadc... |
6e763574daac72927d478cb6c288d0921b6937a05663370c95648a69899db7d6 | Python | 78,782 | 1,769 | __author__ = 'Carlos Ventura'
__email__ = ['carlosventura@stonybrook.edu']
#!/usr/bin/python
import os
import subprocess
import shutil
import glob
import sys
import ast
from pathlib import Path
import importlib
import gzip
import pickle
import logging
current_dir = Path(__file__).resolve().parent
package_dir = curre... |
e695a76d936f009d926e50eae09e34e1256ceee86ffb5b5825748e98f9080036 | Python | 78,794 | 2,151 | """Read/write support for Maildir, mbox, MH, Babyl, and MMDF mailboxes."""
# Notes for authors of new mailbox subclasses:
#
# Remember to fsync() changes to disk before closing a modified file
# or returning from a flush() method. See functions _sync_flush() and
# _sync_close().
import os
import time
import calendar... |
fe2df8b4092506850959468d347601fe867d43aef0f617e70e87cb942441410e | Python | 78,958 | 1,999 | """Various cluster quality metrics.
Some of then come from or the old implementation:
* https://github.com/AllenInstitute/ecephys_spike_sorting/tree/master/ecephys_spike_sorting/modules/quality_metrics
* https://github.com/SpikeInterface/spikemetrics
Implementations here have been refactored to support the multi-segm... |
06191ecf6a60f3532df4190fb7dd181059ddbc83a5356b58bd510044821b454e | Python | 79,070 | 2,224 | # -*- coding: utf-8 -*-
"""This module defines functions for signature dynamics (SignDy), analyzing normal modes obtained
for conformations in an ensemble."""
import time
from numbers import Integral
from numpy import ndarray
import numpy as np
import warnings
from prody import LOGGER, SETTINGS
from prody.utilities ... |
b55833e467eff207122dd43b17d6f13bc4d284558a9acc8ee9ef5da11ef682d1 | Python | 79,354 | 2,019 | # Mancy Chen 29/01/2025
########################################################################################################################
# Visualize Schaefer atlas
import sys
sys.path.append('/.../miniconda3/lib/python3.10/site-packages')
# Import necessary libraries
from nilearn import datasets, plotting, i... |
14f7b204d739be08ffb9d7b49f95242cd483c167fae15fc0823cc105e310e178 | Python | 79,760 | 2,288 | """
Test the parallel module.
"""
# Author: Gael Varoquaux <gael dot varoquaux at normalesup dot org>
# Copyright (c) 2010-2011 Gael Varoquaux
# License: BSD Style, 3 clauses.
import mmap
import os
import re
import sys
import threading
import time
import warnings
import weakref
from contextlib import nullcontext
from... |
4af1cb70c313e0caf1f30a1d8fce8aa3b5c96b9396c0a118b8ddd066be1917f3 | Python | 79,801 | 2,377 | from tkinter import *
from tkinter import ttk
from matplotlib.figure import Figure
from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
import numpy as np
from matplotlib import rcParams
import os
import pickle
def precalculate_all_acgs(
clus_info, param, save_path=None, bin_size=0.001, max_lag=0.05
):... |
03eec53cff45fe43d2f8af6754a4542db609202c27605b4548b55d9cb3e2fd86 | Python | 79,836 | 2,012 | #!/usr/bin/env python3
# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the BSD-style license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
import typing
import warnings
from typing import (
Any,
Callable,
cast,
Dict,
... |
fb4466bab237d5780068ddb45828b4ceb72ea1ab7dd27340ef4ffac86971d8f5 | Python | 79,875 | 2,420 | # Copyright 2007 Google Inc.
# Licensed to PSF under a Contributor Agreement.
"""A fast, lightweight IPv4/IPv6 manipulation library in Python.
This library is used to create/poke/manipulate IPv4 and IPv6 addresses
and networks.
"""
from __future__ import unicode_literals
import itertools
import struct
__version... |
0d36e136eabdfec486d46449999e8d711b1d2478334917c01fcc6a06ce835624 | Python | 79,983 | 1,449 | import pandas as pd
import numpy as np
from matplotlib import cm
import matplotlib as mpl
import config
import theories_rois
from pathlib import Path
import matplotlib.pyplot as plt
from general_utilities import load_fsaverage_coord
from matplotlib import font_manager
import os
selectivity_colors = {
"face": [1, 1... |
b91e94a7f783c397bb1f49aff7e77ed11ef900ae2cdd5fa9f9336bdac16009bf | Python | 80,023 | 1,540 | """program "PAW_protein_grouper.py"
Produces quantitative protein and peptide results tables.
This is a protein grouping step in the PAW analysis pipeline for Comet
searches of large data sets where spectral count or TMT quantitation is being
performed. The program combines similar proteins into "families" (homology
g... |
56b4f0170836e7706d39e59993fd1aa91357d6a18c9a0326086f12a77c9d0648 | Python | 80,158 | 1,636 | import copy
import logging
from functools import partial
from typing import (TYPE_CHECKING, Any, Callable, Dict, List, Optional,
Sequence, Tuple, Union)
import numpy as np
import pandas as pd
import shap
import shap.utils._legacy as shap_utils
from scipy import sparse
from scipy.special import expi... |
30163ab69d3836d3bc3dfdca6bc73d8d89ed6784ef1e87e796591fd46af19bb2 | Python | 80,557 | 1,714 | from __future__ import annotations
from re import T
"""class_unet_fan_nosplit.py – Training UNet on fan-label maps (angle units)
with the same nosplit dataset strategy as grid version.
"""
import os
import random
import json
import shutil
import argparse
from collections import Counter, defaultdict
from typing import ... |
63bde22975010462d974706e451c2f6b517a0772b7f27f475316f65e76994abd | Python | 80,695 | 2,104 | #!/usr/bin/env python
"""
gui/localize
~~~~~~~~~~~~~~~~~~~~
Graphical user interface for localizing single molecules
:authors: Joerg Schnitzbauer, Maximilian Thomas Strauss, 2015-2019
:copyright: Copyright (c) 2015-2019 Jungmann Lab, MPI of Biochemistry
"""
import os.path
import sys
import yaml
f... |
a64d8807ccc36ae62cdfa8e86d536202defb82ad542993532061e1e7d0af9991 | Python | 80,717 | 1,900 | # Documentation style guide:
## - Class init docstrings should be in the class definition docstring.
## - Use a style guide similar to Google's Python style guide except that argument definitions should start on a new indented line after the argument name.
## - If there is more than one argument, use multiple lines for... |
40f0558f0974d467ed24df802ca7d7a8db20e2d1b7b5bdc1bae3046b28786c40 | Python | 80,873 | 2,174 | import math
import os
import numpy as np
import pytest
from absl.testing import parameterized
from keras.src import backend
from keras.src import constraints
from keras.src import export
from keras.src import layers
from keras.src import models
from keras.src import ops
from keras.src import optimizers
from keras.src... |
d649519f4ec66872cd58369c84d1c680ed03be4992ab3b33157d69fbb7b44294 | Python | 80,899 | 1,868 | import functools
import importlib
import inspect
import json
import logging
import math
import threading
from contextvars import ContextVar, copy_context
from dataclasses import asdict, dataclass, fields
from enum import Enum
from typing import Any, Callable, ClassVar, Literal, TypeAlias, TypeVar, overload
from pydant... |
4ba7bf1e009ae818bb71af40097338d9a074a28819a2cea5191bdb965b2eda62 | Python | 80,974 | 1,560 | import ctypes
import sys
from abc import ABC, abstractmethod # abstract class
import torch
import torch.nn as nn
import numpy as np
import os
from deprecated import deprecated
import ailoc.common
class VectorPSF(ABC):
"""
Abstract base class for vector psf simulators
"""
@abstractmethod
def sim... |
06a8d3eca34069d7342afc45e4fd49a63e737c905e7e1540345b90cd0a2665cf | Python | 81,128 | 1,929 | from __future__ import annotations
import argparse
import csv
import gzip
import json
import math
import re
from dataclasses import dataclass
from pathlib import Path
from statistics import mean, median
from typing import Any, Callable
import matplotlib
import numpy as np
from scipy import signal as sp_signal
matplo... |
3ffd8e26deac4ba3d6117eeb0bf7227d65abd90e1bfc5df0fe7732df3cd7790e | Python | 81,167 | 1,800 | """Provide JIDT estimators."""
from pkg_resources import resource_filename
import numpy as np
from abc import abstractmethod
from idtxl.estimator import Estimator
from . import idtxl_exceptions as ex
from . import idtxl_utils as utils
try:
import jpype as jp
except ImportError as err:
ex.package_missing(err, 'J... |
185096bb24ce355bb7b1bf9f9c9e60a37ebb6a0a2b3904158750077624da9302 | Python | 81,181 | 2,141 |
# Version: 0.22
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/python-versioneer/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible with: Python 3.6, 3.7, 3.8, 3.9, 3.10 and pypy3
* [![Latest Versio... |
3068f9759a091c34289cfdffbc4a869e672c2311bc028890b9e5c54a5e561b7a | Python | 81,237 | 1,811 | import inspect
import json
import keyword
import logging
import os
import pathlib
import signal
import urllib.parse
from abc import ABCMeta, abstractmethod
from contextlib import contextmanager, nullcontext
from dataclasses import dataclass
from inspect import Parameter, Signature
from types import FunctionType
from ty... |
93e0d80d0cf47f2e062ecf1d7a91e8f2624597d2943d1c5c395dddea1507fe7c | Python | 81,271 | 1,624 | """The gallery-tier suite: one case per expectation in the gallery, which every member proves.
This module builds the suite's collection-time parameterization -- the (case, data source) product
that turns the declarative case table in `gallery_expectation_case_table.py` into parametrized test
items --
and the measurem... |
042cd3e8619ff0cb1aa6581c343bf97c058f046bd7dc05211b1e14d4740e0bbf | Python | 81,352 | 1,879 | """The ants module provides basic functions for interfacing with ants
functions.
"""
import os
from ...utils.filemanip import ensure_list
from ..base import TraitedSpec, File, Str, traits, InputMultiPath, isdefined, Tuple
from .base import ANTSCommand, ANTSCommandInputSpec, LOCAL_DEFAULT_NUMBER_OF_THREADS
class ANT... |
6a52384509da439408f87bbbeb0aa35caf269ac431742b0740372481207cafe7 | Python | 81,479 | 2,035 | # Author: Nicolas Legrand <nicolas.legrand@cas.au.dk>
# Author: Aleksandrs Baskakovs <aleks@cas.au.dk>
"""Vectorised belief propagation step for deep predictive coding networks."""
from __future__ import annotations
import dataclasses
from typing import Optional
import equinox as eqx
import jax
import jax.numpy as ... |
549a50dd19e7336bd89ed2ac11ea7351ffb0f1b0f61048f2c62acfbc0c3d7cce | Python | 81,571 | 2,005 | '''
'Mag' usually refers to the magnetic resin that contains magnetic and fluorescent particles of different wavelengths
'''
#########################################################
### Start of config example for NikonPeter microscope ###
#########################################################
mic = 'NikonPeter'
mi... |
41ae017646e071539a5454ae6292bcafc129f172270ad7351672483023f68369 | Python | 81,985 | 2,378 | # Copyright 2017 Google LLC.
#
# 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 list of conditions and the following disclaimer.
#
#... |
16983b1e732657cbaffd49e46b25a9762c9706c404128c73f8fb34f9059dfb34 | Python | 82,126 | 1,727 | """
This file regroups several custom keras layers used in the generation model:
- RandomSpatialDeformation,
- RandomCrop,
- RandomFlip,
- SampleConditionalGMM,
- SampleResolution,
- GaussianBlur,
- DynamicGaussianBlur,
- MimicAcquisition,
- BiasFieldCorruption,
- IntensityAugmen... |
a0180a708c318f20938fd9c3a76b9e3cb01590da485358eeffc87d1f85305230 | Python | 82,145 | 1,643 | # -*- coding: utf-8 -*-
'''
Class to extract sequences from neural firing and calculate relevant variables
Use:
(1) call init with Spikes, position, and method to generate Sequences object
(2) call init with name to load object for further processing
'''
# standard libraries
from os.path import exists, getsize... |
189452d5618e833eb205a5222b3b905c6742dfb2d64ee656a6eeee52f3ce18de | Python | 82,327 | 1,931 | from __future__ import annotations
import argparse
import csv
import json
import math
from dataclasses import dataclass
from pathlib import Path
from typing import Any
import mne
import numpy as np
import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
from eeg_units import ensure_eeg_data_in_volts
... |
00dc0dc4b1e941c555756b0958cb185fc1020412c2e883eed6fdbbe193843ffa | Python | 82,442 | 1,878 | # -*- coding: utf-8 -*-
"""The ants module provides basic functions for interfacing with ants
functions.
"""
import os
from ...utils.filemanip import ensure_list
from ..base import TraitedSpec, File, Str, traits, InputMultiPath, isdefined
from .base import ANTSCommand, ANTSCommandInputSpec, LOCAL_DEFAULT_NUMBER_OF_... |
4043d6eadc7c4ac1a9cae8e32a4045ca2261051b0e372b94de2a31da3d715262 | Python | 82,464 | 1,829 | """ Topic Model
References
----------
Blei, David M., Andrew Y. Ng, and Michael I. Jordan. "Latent Dirichlet
Allocation." Journal of Machine Learning Research 3 (2003): 993–1022.
Griffiths, Thomas L., and Mark Steyvers. "Finding Scientific Topics."
Proceedings of the National Academy of Sciences 101 (2004): 5228–5235.... |
17b27a457f1120705240654868ff36d377c9ffb508e62ca9ed9b0800275aaece | Python | 82,563 | 1,943 | """This file and its contents are licensed under the Apache License 2.0. Please see the included NOTICE for copyright information and LICENSE for a copy of the license."""
import json
import logging
from typing import Any, Mapping, Optional
from annoying.fields import AutoOneToOneField
from core.current_request impor... |
71adc65b2ac0e19a3372bb54cfa7266457bc965b5d7189bee378e93eb0c47b90 | Python | 82,603 | 2,045 | """Functions for creation of an HTML report that plots and explains output."""
import datetime
import logging
import os
import shutil
import subprocess
import warnings
from typing import Any, Dict
import matplotlib.pyplot as plt
import numpy as np
import scipy.sparse as sp
import scipy.stats
import torch
from IPython... |
d2f73c7128a3931f74411b46352146ba85322a8dc8f12a721d4801dc43d9766e | Python | 82,644 | 2,080 | # subprocess - Subprocesses with accessible I/O streams
#
# For more information about this module, see PEP 324.
#
# Copyright (c) 2003-2005 by Peter Astrand <astrand@lysator.liu.se>
#
# Licensed to PSF under a Contributor Agreement.
# See http://www.python.org/2.4/license for licensing details.
r"""Subprocesses with ... |
99732cf0d6ac2d74ba38eb8d589cb7325807919c741d2b71235d6e64dcb07822 | Python | 82,796 | 1,803 | __author__ = "Simon Nilsson; sronilsson@gmail.com"
from typing import List, Optional, Tuple
import numpy as np
from numba import float32, float64, int64, jit, njit, prange, typed, types
from simba.utils.checks import check_float, check_valid_array
from simba.utils.data import get_mode
from simba.utils.enums import F... |
61fc1c5e8f36e03e0e833efbccdeaaa4945c6d5281e9f452ab2c3aa209f43c21 | Python | 82,868 | 2,344 | """Tests for the fn-14 non-LD filtering trail."""
from __future__ import annotations
import itertools
import logging
import operator
import warnings
from collections.abc import Callable
from functools import reduce
from pathlib import Path
from typing import Any
import numpy as np
import pandas as pd
import pytest
... |
2b894402921b38a2a1ee4cc52447816358b13b95f99fa61dca16804472989657 | Python | 82,977 | 2,433 | # -*- coding: utf-8 -*-
r"""This module defines a class for selecting subsets of atoms. You can read
this page in interactive sessions using ``help(select)``.
ProDy offers a fast and powerful atom selection class, :class:`.Select`.
Selection features, grammar, and keywords are similar to those of VMD.
Small differenc... |
ae98f73d60de485c8e5b339e9fb0438ebb926e0d8b4ee2a5beeda4b9c23d3adc | Python | 83,493 | 1,788 | from mimetypes import init
import torch
import torch.nn as nn
import torch.nn.functional as F
from functools import partial
import math
import modeling.unet
from .utils import freeze, log_ftr_map_histograms, flag_pretrain, is_pretrain
from timm.models.layers import DropPath, trunc_normal_
from .vision_transformer impo... |
e2599958bb443d12e797c3737ed3a861325da3a8e978cb4fe9da900b483f6d64 | Python | 83,518 | 2,947 | from __future__ import absolute_import, division, unicode_literals
import string
EOF = None
E = {
"null-character":
"Null character in input stream, replaced with U+FFFD.",
"invalid-codepoint":
"Invalid codepoint in stream.",
"incorrectly-placed-solidus":
"Solidus (/) incorrectly ... |
1b34cab0ef5502267a203a91d6d1f07665425abef4416d09f559de2ef2dfbf11 | Python | 83,718 | 1,800 | # -*- coding: utf-8 -*-
"""
Created on Mon Feb 19 02:54:48 2024
@author: staslist
"""
import re
import csv
import unittest
import numpy as np
import os
#import time
from scipy.stats import hypergeom
from datetime import datetime
from numba import jit
# Bi-Clustering Algorithm Code
# Assume I have... |
cf52484a1a512187e709e30c37fd2f5d976b35049ff775ab47c5b81c654137fd | Python | 83,798 | 2,593 | # Copyright (c) 2025 Bytedance Ltd. and/or its affiliates
# 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... |
6889e659235773422a944335780fce472cc59dbdd0ccb861bf3b92d5c931ae42 | Python | 84,058 | 2,086 | """
Module difflib -- helpers for computing deltas between objects.
Function get_close_matches(word, possibilities, n=3, cutoff=0.6):
Use SequenceMatcher to return list of the best "good enough" matches.
Function context_diff(a, b):
For two lists of strings, return a delta in context diff format.
Function nd... |
4ed5bb9a20b3e26a34a1c1e54cfec5ba296480185e56683f5190b2437b7a79f1 | Python | 84,200 | 2,155 | import argparse
import csv
import json
import math
from dataclasses import dataclass
from pathlib import Path
from typing import Dict, List, Optional, Tuple
DEFAULT_METRIC_KEYS = (
"test_loss_mean",
"eval_loss_mean",
"loss_mean",
"accuracy_mean",
"mcc_mean",
"f1_mean",
"roc_auc_mean",
... |
2f05640f5ae64243bf33522b7a349bc23c2c54703341fe9b456bddd31769ab5e | Python | 84,304 | 1,897 | __author__ = "Simon Nilsson; sronilsson@gmail.com"
import math
from itertools import combinations
from typing import Optional, Tuple, Union
from simba.utils.printing import SimbaTimer
try:
from typing import Literal
except:
from typing_extensions import Literal
import numpy as np
from numba import cuda
fro... |
a4de88ef5361c2434c4440e9354d0238cb20b1307c4386125d31dea3ea6465d1 | Python | 84,346 | 2,096 | """
Module difflib -- helpers for computing deltas between objects.
Function get_close_matches(word, possibilities, n=3, cutoff=0.6):
Use SequenceMatcher to return list of the best "good enough" matches.
Function context_diff(a, b):
For two lists of strings, return a delta in context diff format.
Function nd... |
9f79d3c27ee9483a43cc3358596ddf3efc30532c0b550f35523433a8b9ad90e9 | Python | 84,836 | 2,082 | import base64
import datetime as dt
import decimal
import importlib
import json
import logging
import os
import re
import shutil
import sys
import tempfile
import uuid
from contextlib import contextmanager
from copy import deepcopy
from pathlib import Path
from typing import Any, Dict, List, Union
import numpy as np
i... |
eee545e602db54bf0aea0c6523f4cbf55b4906dfeb57f831de4840254632c0fe | Python | 84,931 | 2,331 | """ MaxVit and CoAtNet Vision Transformer - CNN Hybrids in PyTorch
This is a from-scratch implementation of both CoAtNet and MaxVit in PyTorch.
99% of the implementation was done from papers, however last minute some adjustments were made
based on the (as yet unfinished?) public code release https://github.com/google... |
cfe2d2e3e7f9d7d482025673e9c645f2dc2328c0844fa8a8d3959315c86d8581 | Python | 85,135 | 2,109 | from __future__ import annotations
import math
import csv
import dataclasses
import sys
import copy
from dataclasses import dataclass, field
from typing import List, Tuple, Optional, Dict, Callable
import time
import numpy as np
# 可选依赖：matplotlib（更稳的 backend 选择 + 交互绘图）
try:
import os
import m... |
6c991d22c15fc2c4d9fc50a25ba533c7c24b460d4edd840ce0900c91a5e3fd5e | Python | 85,279 | 1,705 | import numpy as np
import utils.ipt_util as utility
import torch
from tqdm import tqdm
from help_func import print_var_detail
import time
from utils.evaluation_utils import calc_nmse_tensor, calc_psnr_tensor, calc_ssim_tensor, binaryMaskIOU
import copy
from utils.dice_score import dice_loss, multiclass_dice_coeff, d... |
68d276d539ca3eee49c76ff7d356335ba8bc7899312ea7e8110588dfde6e5f84 | Python | 85,341 | 2,290 | """
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ https://setuptools.readthedocs.io/en/latest/deprecated/easy_install.html
"""
from glo... |
5529d3ce0b8fa3e8db793b834434ee2ff16b2b61df3c21b9403706c7a205c99a | Python | 85,405 | 1,873 | from pathlib import Path
from typing import List, Optional, Literal, Dict, BinaryIO
import sys
import warnings
import importlib.util
import numpy as np
from spikeinterface import get_global_tmp_folder
from spikeinterface.core import BaseRecording, BaseRecordingSegment, BaseSorting, BaseSortingSegment
from spikeinterf... |
a76fb695e0e96d03b6434b1bf317f777bb88370b561cc81c85b21b0ebe9631b8 | Python | 85,673 | 1,862 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Probe designer GUI
@author: amandaschott
"""
import sys
import os
import re
import numpy as np
import pandas as pd
import seaborn as sns
import matplotlib
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.backends.backend... |
ef63fa19da93442119677c4489a6c0dfc425e2c64873ad9a25b7b35c93ca235f | Python | 85,727 | 1,349 | # ───── Version and SCRIPT_VERSION ───────────────────────────────────────────
SCRIPT_VERSION = "1.4.3" # Incremented version
# CHANGELOG removed as per user request
import logging
from pathlib import Path
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
import os
import tor... |
ff26c105cad52c03d6d47565299bea7f9a2a5e88600bd25dea2d66a2a8acede8 | Python | 85,786 | 2,245 | """ Bring-Your-Own-Blocks Network
A flexible network w/ dataclass based config for stacking those NN blocks.
This model is currently used to implement the following networks:
GPU Efficient (ResNets) - gernet_l/m/s (original versions called genet, but this was already used (by SENet author)).
Paper: `Neural Architect... |
c7b9fc2034e12474ca864be98543aae3dcbf2f6667ddb73a9453f19ff4dbe017 | Python | 85,792 | 2,275 | """Functions related to the plotting of the e-models."""
"""
Copyright 2023-2024 Blue Brain Project / EPFL
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/LICENS... |
5ef6f4faa9b82b3c627a0476778963b9bc332260685a59bba37101c9f441e449 | Python | 86,292 | 2,421 | import os
import sys
import re
import pprint
from typing import Optional, Dict, List
import yaml
import napari
from napari.layers import Labels
from napari.layers import Labels, Image
from napari.types import LayerDataTuple
from napari.viewer import Viewer
from magicgui import magicgui
from pathlib import Path
impor... |
17034d5081f864ea0347cc74ee6d0dbd199491b041d5f8c886150545e04e8f1d | Python | 86,449 | 2,023 | #!/usr/bin/env python3
"""
═══════════════════════════════════════════════════════════════════════════════
MS3 SIGMA DIVERGENCE DEFINITIVE PIPELINE — Google Colab (12GB RAM)
═══════════════════════════════════════════════════════════════════════════════
MANUSCRIPT: "Sigma-1 and Sigma-2 Receptors Exhibit Divergent Geno... |
0ae13da21bbccd38a90bd81da5549f64e8238e9fcacc8701ce78d5d188fc5f7d | Python | 86,507 | 1,795 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
HEPPy Streamlit UI
"""
from __future__ import annotations
from pathlib import Path
from types import SimpleNamespace
import json
import re
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import streamlit as st
import mne
import neurokit2 as nk
... |
eb179de8356ee9945fae1fa744c93eaf1dd8cf1fd49e4b021300c312e5888763 | Python | 86,535 | 2,275 | """
picasso.simulate-gui
~~~~~~~~~~~~~~~~
GUI for Simulate :
Simulate single molcule fluorescence data
:author: Maximilian Thomas Strauss, 2016
:copyright: Copyright (c) 2016 Jungmann Lab, MPI of Biochemistry
"""
import csv
import glob as _glob
import os
import sys
import time
import importli... |
e131787e6d88f2a6c9e268394d381e0d407ceea42c5fa5e5a7fe9426146ed708 | Python | 86,813 | 1,565 | import os
import re
import logging
import random
import pickle as pkl
import time
import tracemalloc
import torch
import pandas as pd
from sklearn.preprocessing import MinMaxScaler, StandardScaler
from sklearn.model_selection import KFold
from sklearn.linear_model import Lasso, LinearRegression
import numpy as np
from... |
4f577fdee4052eeafaa8dacdb448a2455ce57840af1c17bd7adafba37226aaec | Python | 86,924 | 2,339 | """
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ https://setuptools.readthedocs.io/en/latest/easy_install.html
"""
from glob import gl... |
f9d35af2458b77b3647749dafa0b8158bbed122daf6d63c3be933ff6905aad01 | Python | 87,100 | 2,771 | from pathlib import Path
import os
import sys
from zipfile import ZipFile
import tarfile
from collections import namedtuple
import time
import re
import warnings
from json import loads, dumps
from io import StringIO
from itertools import zip_longest
from collections.abc import Iterable
import numpy as np
import pandas... |
df6e2da67a3394a47ed57cfbd44298109d26f71ea22948a8840b6b56b0f6189d | Python | 87,278 | 2,428 | """
Read and write ZIP files.
XXX references to utf-8 need further investigation.
"""
import binascii
import importlib.util
import io
import itertools
import os
import posixpath
import shutil
import stat
import struct
import sys
import threading
import time
import contextlib
try:
import zlib # We may need its com... |
168f05e8c73b02149915d353ed366b473704d752f99b3c28b5ac0980f22fd37b | Python | 87,608 | 2,026 | """
This package (`biapy.models`) is responsible for building and managing deep learning models within the BiaPy framework.
It provides functionalities to:
1. **Dynamically build models**: Select and instantiate various neural network architectures
(e.g., U-Net, ResUNet, ViT, ConvNeXt variants, etc.) based on co... |
128296054c9f506907bfb4336ddf9837397dcb71e047dfffd5323d06687922d2 | Python | 87,657 | 2,354 | """
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ https://setuptools.readthedocs.io/en/latest/easy_install.html
"""
from glob import gl... |
9586dffd04fb9b7f2df7bdd98dd033a6898c84c334752cfa4d8657a2231f56fe | Python | 87,719 | 1,943 | import torch
import torch.nn as nn
import torch.nn.functional as F
import torch
# import os
import pandas as pd
import numpy as np
# import json
from fastNLP.core.metrics import MetricBase,seq_len_to_mask
from fastNLP.core.losses import LossBase
from preprocess import NPPeptidePipe,PPeptidePipe
from torch.nn import Cos... |
ac29ed5e746df106226580ea460fb7345b34153637e868dfb6a7ab66e09cd17b | Python | 87,728 | 2,441 | """
Read and write ZIP files.
XXX references to utf-8 need further investigation.
"""
import binascii
import functools
import importlib.util
import io
import itertools
import os
import posixpath
import shutil
import stat
import struct
import sys
import threading
import time
import contextlib
try:
import zlib # We... |
431586528ca1a069cd96a960f10c424a82bedb1a7eacd3c239e9165611a2e44f | Python | 87,898 | 2,101 | """
Helpers for embarrassingly parallel code.
"""
# Author: Gael Varoquaux < gael dot varoquaux at normalesup dot org >
# Copyright: 2010, Gael Varoquaux
# License: BSD 3 clause
from __future__ import division
import collections
import functools
import itertools
import os
import queue
import sys
import threading
impo... |
a533ccd0627fd3164523ea63dcc5e86f05e0717e20c3d260f178b8134f22e702 | Python | 87,923 | 1,945 | import torch
import torch.nn as nn
import torch.nn.functional as F
import torch
# import os
import pandas as pd
import numpy as np
# import json
from fastNLP.core.metrics import MetricBase,seq_len_to_mask
from fastNLP.core.losses import LossBase
from preprocess import NPPeptidePipe,PPeptidePipe
from torch.nn import Cos... |
de58b977b2627a813eb42ad29766b55e7526e288ed80e51edfe33a5f000c7af2 | Python | 87,959 | 1,980 | """
Base data generator for paired image and mask data in BiaPy.
This module provides the PairBaseDataGenerator class, which supports flexible
data loading, augmentation, and normalization for deep learning workflows.
It includes a wide range of augmentation options for both 2D and 3D data,
and is designed to work wit... |
02cf704e95bc28eefcd960574754e2ec8b8dea972342bf82c272203270797a2c | Python | 88,125 | 2,106 | """
Helpers for embarrassingly parallel code.
"""
# Author: Gael Varoquaux < gael dot varoquaux at normalesup dot org >
# Copyright: 2010, Gael Varoquaux
# License: BSD 3 clause
from __future__ import division
import collections
import functools
import itertools
import os
import queue
import sys
import threading
impo... |
61790d91c7b7ff8ab454d405abd52d989e852bae24443a5758fcdf04730b7630 | Python | 88,248 | 2,836 | # -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""The fsl module provides classes for interfacing with the `FSL
<http://www.fmrib.ox.ac.uk/fsl/index.html>`_ command line tools. This
was written to work with FSL version 4.1.4.
E... |
05c2c329698f60b68eb213670b88c112b0a18be97a7d61b9835c54d18e3617d2 | Python | 88,287 | 2,520 | """Concrete date/time and related types.
See http://www.iana.org/time-zones/repository/tz-link.html for
time zone and DST data sources.
"""
import time as _time
import math as _math
import sys
def _cmp(x, y):
return 0 if x == y else 1 if x > y else -1
MINYEAR = 1
MAXYEAR = 9999
_MAXORDINAL = 3652059 # date.max... |
2cec3f91b5453e33735b000011a890ec5a229e8bae4e1919d1adfd3ce1da79d7 | Python | 88,317 | 1,927 | # doing simple morpghological operations might be easier than WEKA ...
# What do I want exactly ?
# approximate locations are ok
# CCs are ok, simply need to fine tune a bit more
# make a double CC on the two channels, and use a weight a.BF + (1-a).Fluo
# --preprocess correctly at the beginning
# --blend the ... |
240e5561ed02a609626e8026936e65c5ff7cae53051d31020e5936b962b8f9a0 | Python | 88,378 | 2,324 | # -*- coding: utf-8 -*-
"""
functions.py - Miscellaneous functions with no other home
Copyright 2010 Luke Campagnola
Distributed under MIT/X11 license. See license.txt for more infomation.
"""
from __future__ import division
import warnings
import numpy as np
import decimal, re
import ctypes
import sys, struct
from ... |
76bbb5d5885fe8db5d23011da8d31923c2fea251f4783a26b9c0d5f19d5ccf9d | Python | 88,393 | 1,935 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# mitoMutantAccTimes
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"""
Here we read the synthetic data generated by replViaTranscription.jar ... |
78c734b4ba10f6f3f0f73024151d87592f5f82eb65ce19282454dce7052c53e3 | Python | 88,425 | 1,617 | import os
import shelve
import numpy as np
import prody as pr
import pandas as pd
from tqdm import tqdm
from typing import Tuple, Dict, Optional, List
from collections import defaultdict
from sklearn.model_selection import train_test_split
import torch
from torch_cluster import knn_graph, radius_graph
from torch_scatt... |
13904f0c7492a0edf24bcab33e8094b73ef9c574459360181856d4ab943b8529 | Python | 88,498 | 2,235 | """Layer is an Operation with state.
Takes care of:
- Weights / variables (and tracking thereof)
- deferred build
- trainable argument value inference
- masking
- autocasting
And some more magic:
- add_loss
- metric tracking
- RNG seed tracking
- activity regularization
"""
import collections
import functools
impo... |
bb09d32c38d948f93967b6ef022ec81a69d9c81ae9610c38e0c8de04bee8ad09 | Python | 88,887 | 2,514 | """
picasso/rotation
~~~~~~~~~~~~~~~~~~~~
Rotation window classes and functions.
Extension of Picasso: Render to visualize 3D data.
Many functions are copied from gui.render.View to avoid circular import
:author: Rafal Kowalewski, 2021-2022
:copyright: Copyright (c) 2021 Jungmann Lab, MPI ... |
cc0da8c335b5059a5c072c729b7a684be1b67307473569d6777ec849802e7845 | Python | 88,985 | 1,652 | #!/usr/bin/env python3
# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the BSD-style license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
import threading
import warnings
from collections import defaultdict
from typing import (
A... |
0b7d2c2b8258a5d6d6aa430a48501de8dfae03da1db9dc89dec75863f1161d74 | Python | 89,093 | 1,946 | import sys
import os
import math
import torch
import numpy as np
import logging
from time import time
from argparse import ArgumentParser, SUPPRESS
from threading import Thread
from math import log, e
from collections import namedtuple
from clair3.task.gt21 import (
GT21_Type, gt21_enum_from_label,
HOMO_SNP_GT... |
8d50a3a6920ae7ed0a835140974315aeae3e0a495bd24f644e3feceee1b53233 | Python | 89,150 | 2,555 | """Concrete date/time and related types.
See http://www.iana.org/time-zones/repository/tz-link.html for
time zone and DST data sources.
"""
__all__ = ("date", "datetime", "time", "timedelta", "timezone", "tzinfo",
"MINYEAR", "MAXYEAR")
import time as _time
import math as _math
import sys
def _cmp(x, y):... |
80f6146141f45eb3bd503922dcb1ee7d51f678835fab36e741393bd92663137f | Python | 89,229 | 2,741 | #!/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.
from dataclasses import dataclass, field
from typing import Any, Dict, List, Optional
from hydra.core.config_store im... |
ccb93da19a85fa2c59132f6588983c52b8cd54b6f7071adf02396dfefccbc4d6 | Python | 89,440 | 2,068 | # Author: Nicolas Legrand <nicolas.legrand@cas.au.dk>
# Author: Aleksandrs Baskakovs <aleks@cas.au.dk>
"""Vectorised deep predictive coding network.
This module provides a vectorised implementation of deep HGF networks that uses layer-
wise matrix operations instead of per-node updates.
"""
from __future__ import an... |
a8f9dcda037b19524a8c450f40559098675e7d1a9c26eb998edce0a4dcf8fbb6 | Python | 89,675 | 2,391 | # -*- coding: utf-8 -*-
"""ML Coconut Fiber 1.ipynb
Automatically generated by Colab.
Original file is located at
https://colab.research.google.com/drive/1cm1GzhRTH-QRb4NhIyNmJS3yfRSV-KHo
# **Optimized and Explainable Machine Learning for Coconut Fiber Concrete Strength Using SHAP, PDP, and ICE**
**Frequency Hi... |
05377a95a4ebbc72fd7222838e24f621f4af3b1c92ad96454dde6bb4c0b54c79 | Python | 89,865 | 1,669 | """ This script contains all helper function for the preprocessing pipeline
authors: Alex Lepauvre and Katarina Bendtz
alex.lepauvre@ae.mpg.de
katarina.bendtz@tch.harvard.edu
Dec 2020
"""
import os
from pathlib import Path
import numpy as np
import math
import mne
from mne.viz import plot_alignment, s... |
b66ac2aa9ac82070dff32ff4392f4b2858f58c015c8e299ff59645e9c7939477 | Python | 89,934 | 2,912 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""The fsl module provides classes for interfacing with the `FSL
<http://www.fmrib.ox.ac.uk/fsl/index.html>`_ command line tools. This
was written to work with FSL version 4.1.4.
Examples
--------
See the... |
e6a28545e38f1fc036bc91a8bedd07ba55ddfc8a6e711ad16d004dc9edcf1d02 | Python | 90,406 | 2,554 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""The fsl module provides classes for interfacing with the `FSL
<http://www.fmrib.ox.ac.uk/fsl/index.html>`_ command line tools. This
was written to work with FSL version 4.1.4.
"""
import os
from glob i... |
3e70661f01329a67191e6755ab9f97ed174d3958411f7bc2f4e05fe72d756672 | Python | 90,779 | 2,574 | # -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""The fsl module provides classes for interfacing with the `FSL
<http://www.fmrib.ox.ac.uk/fsl/index.html>`_ command line tools. This
was written to work with FSL version 4.1.4.
""... |
fed02494aa96b8dbd75a6ccf1334dfa2c2a7bd4949c781386944a6981ced1c3e | Python | 91,111 | 1,868 | # SPDX-License-Identifier: Apache-2.0
"""
Classes to get, save and load (static or time dependent) connection matrices and sample submatrices from them
authors: Michael Reimann, András Ecker
last modified: 01.2022
"""
import h5py
import numpy as np
import pandas as pd
from scipy import sparse, stats
from .circuit_mod... |
b957d735f008150fedde725c7bf0772ea5f3e37d02bd7ded25a47cf8010d4988 | Python | 91,132 | 2,053 | # coding=utf-8
# Copyright 2022 Microsoft Research and The HuggingFace Inc. team.
# 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... |
511d20d989028551b549d8d31cd0aa116b834574c0c9e4157b2a551f172fbcef | Python | 91,337 | 1,906 | # -*- coding: utf-8 -*-
"""
Created on Fri Apr 9 17:04:19 2021
@author: user
"""
import os
import numpy as np
import scipy as sp
#from scipy import stats
import pandas as pd
import skimage
#import subprocess
#from statsmodels.stats.multitest import multipletests
import gc
#import sys
#import h5py
i... |
f3e2771652245d728453d774f8c90d11278932c4c8b3e7e7fba73167ec6454e7 | Python | 91,363 | 1,749 | import numpy as np
import utils.ipt_util as utility
import torch
from tqdm import tqdm
from help_func import print_var_detail
import time
from utils.evaluation_utils import calc_nmse_tensor, calc_psnr_tensor, calc_ssim_tensor, binaryMaskIOU
import copy
from utils.dice_score import dice_loss, multiclass_dice_coeff, d... |
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