sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
6e59fa68de0872cbb662e48e804cf7cc064754dafa3ec1047c1efbf0f7179e51 | Python | 3,477 | 123 | # coding=utf-8
# Copyright 2026 The Google Research 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 required by applicab... |
b94ddf7ed840279b59e8343ae0f4e8046ca717d14dafb6b228e66191cbeb2931 | Python | 3,477 | 109 | import os
import toml
import glob
import shutil
import logging
from ase.io import read
from ase.atoms import Atoms
from quacc import get_settings
from quacc import strip_decorator
from typing import List, Dict, Any
from quacc.recipes.newtonnet.ts import ts_job, irc_job, geodesic_job
def geodesic_ts_no_hess_irc_newton... |
d0a67637874b1d14016632550a8d320fa89ea421b4213b434dc8f641aee963d3 | Python | 3,477 | 118 | import numpy as np
import os
import matplotlib.pyplot as plt
import scipy.io as sio
from scipy import stats
import matplotlib.colors as mcolors
def load_dictionary(dict_filename):
"""
Helper function to load a dictionary file.
Args:
dict_filename (str): The filename of the dictionary to load.... |
3e6454d454787bd9faedbde7a04f34e356c9bb9283057f81e14e10af2a35f740 | Python | 3,478 | 94 | #
# MIT License
#
# Copyright (c) 2022 GT4SD team
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge,... |
ee1fc2d43341bc80b8236ec812054f1f211d3170de23e9d5fb360387eb4d8808 | Python | 3,479 | 93 | #! /usr/bin/env python3
import os
import subprocess
import logging
import APT_interface
class cd :
"""Context manager for changing the current working directory, and automagically changing back when done"""
def __init__(self, path):
self.path = path
def __enter__(self):
self.old_path = ... |
1e98b2e8dceb2764959ba478c7a91f9d74d22ac13cc5d19e417b6dc26c29bccf | Python | 3,481 | 108 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Mar 10 15:32:51 2021
@author: eveshalom
"""
import numpy as np
from scipy.integrate import cumtrapz as cumtrapz
from scipy.integrate import trapz as trapz
def modifiedToftsMurase(Cp, Ctiss, dt, datashape):
### Fit Modified Tofts (Linear from M... |
30703660f0198d93cc00a41ed814c1dcebfd3df22a0b0e1bb4602dac6e2c87fd | Python | 3,481 | 78 | import torch.nn as nn
import torch
import torch.nn.functional as F
class HANNA(nn.Module):
def __init__(self, Embedding_ChemBERT=384, nodes=96):
super(HANNA, self).__init__()
self.Embedding_ChemBERT = Embedding_ChemBERT # Pre-trained embeddings (E_i) from ChemBERTa-2
self.nodes = nodes # N... |
d1329d662c712d603ec70b40670e07729a899a3e17a6bc7566472dcb48134596 | Python | 3,481 | 120 | import functools
import os
import pathlib
import types
import warnings
from typing import Union, Iterable, ContextManager, BinaryIO, TextIO, Any
from . import _common
Package = Union[types.ModuleType, str]
Resource = str
def deprecated(func):
@functools.wraps(func)
def wrapper(*args, **kwargs):
war... |
d559c1c19d9fd935b74a0dfa2c1a37656126f9e105e1748a0bbf32cb21f2f113 | Python | 3,481 | 81 | # Copyright (c) 2021, Ko Sugawara
# 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 list of conditions and t... |
03ae5d67f4e9065ffb4c8550e11861438b415ebe614157b7c9fea835ca929fc8 | Python | 3,482 | 89 | # -*- coding: utf-8 -*-
import tensorflow as tf
from .. import _logging as logging
from .core import *
__all__ = [
'MultiplexerLayer',
]
class MultiplexerLayer(Layer):
"""
The :class:`MultiplexerLayer` selects inputs to be forwarded to output.
see `tutorial_mnist_multiplexer.py`.
Parameters
... |
2c7448ccce33ae5aba11bf70698fd590fa4b39a3a41d59a0a3f4a6c3df647dbd | Python | 3,482 | 95 | from collections import defaultdict
from unittest import TestCase
from codex.data.brain_regions import (
match_to_neuropil,
lookup_neuropil_set,
neuropil_description,
REGIONS,
REGION_CATEGORIES,
neuropil_hemisphere,
without_side_suffix,
)
class RegionsTest(TestCase):
def test_lookup_ne... |
2262e3273757a44dcb8ea01a4b91cb03b915ae307c57e12171c68f1d4a231cf6 | Python | 3,483 | 123 | # coding=utf-8
# Copyright 2026 The Google Research 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 required by applicab... |
49c3275e974ffb0da82e9520a913b4c080ad8720a1af8963b77ce8b3af988f16 | Python | 3,483 | 77 | import time
import os
os.environ["PATH"] = "E:\\Histology\\WSIs\\vips-dev-8.11\\bin" + ";" + os.environ["PATH"]
import pyvips as vips
import openslide
print("Pyips: ", vips.__version__)
print("Openslide: ", openslide.__version__)
from PIL import Image
from histolab.slide import Slide
from histolab.tiler import... |
75e8afd23e1106181402d25013fc809fae084bb5f49e2878b0ec066f541cea7f | Python | 3,483 | 66 | import pandas
import numpy
import connalysis
import conntility
from .network import filter_network
def create_dd_control_networks(M, Msmpl, Mnrn, cols_coords, model_name, cfg):
"""
Generates from a network a control model that preserves the original network's distance dependent
connection probability betw... |
21ede48557feea4c9da6875140f46571b49babbbfc43e251707326b3fc0e720c | Python | 3,484 | 96 | import numpy as np
import matplotlib.pyplot as plt
def add_wmaze_plot(ax, color="tab:orange"):
px = [0.5, 0.5, 7.5, 7.5, 6.5, 6.5, 4.5, 4.5, 3.5, 3.5, 1.5, 1.5, 0.5]
py = [0.5, 4.5, 4.5, 0.5, 0.5, 3.5, 3.5, 0.5, 0.5, 3.5, 3.5, 0.5, 0.5]
ax.text(1, 0.3, "L", ha="center", fontsize=10, color="black")
ax... |
36dec1148314265e25a2ea18498683338161efdeeea891fa19b98f581289bee1 | Python | 3,484 | 86 | # coding=utf-8
# Copyright 2020 Mesh TensorFlow authors, T5 Authors and HuggingFace Inc. team.
#
# 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... |
579674c2dfb60753aea677e51867820c837153ae175ce79523e484eb651fbdb5 | Python | 3,484 | 116 |
import torch
import lightning.pytorch as pl
import numpy as np
from lib.human_legnet.trainer import LitModel
from lib.human_legnet.training_config import TrainingConfig
from torch.utils.data import DataLoader, Dataset
class TrainSeqDatasetProb(Dataset):
"""np.array dataset"""
def __init__(self,
... |
cede07f407102fba859f8f33385f4d85f091b637eba2dabeb5b0c17fbf1a6d2d | Python | 3,484 | 100 | # coding=utf-8
# Copyright 2026 The Google Research 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 required by applicab... |
3d39c7b64cdb73bb6a87bbb5943322f004e1ff6a836662590f9589cbbac8865d | Python | 3,485 | 115 | #!/usr/bin/env python
# This work is licensed under the terms of the MIT license.
# For a copy, see <https://opensource.org/licenses/MIT>.
"""
This module provides the base class for all autonomous agents
"""
from __future__ import print_function
import carla
from srunner.autoagents.sensor_interface import SensorI... |
8e94612576fa381b93a08f593ee4b29f85474f82bac75fb821cc0c368186bc9e | Python | 3,487 | 136 | """Score a directory of PDBs with BERTScore"""
import argparse
from eudockscore.equiformer_v2_resi.model_v2_new import EuBERT
from torch_geometric.loader import DataLoader
from transformers import BertTokenizer
import torch
import torch.nn as nn
import os
import pandas as pd
from atom3d.datasets import LMDBDataset
fro... |
b4ba823075afc33eb131279e4bbc11f152f3971b741de2e8e8ac2c515a0cfb97 | Python | 3,487 | 93 | import os
import pandas as pd
import numpy as np
from tqdm import tqdm
from joblib import Parallel, delayed
import joblib
import contextlib
@contextlib.contextmanager
def tqdm_joblib(tqdm_object):
"""Context manager to patch joblib to report into tqdm progress bar given as argument"""
class TqdmBatchCompletion... |
077937fa6db4ef1d641e9658583873bf31166ffe80516a09a322fc96d4e3448d | Python | 3,488 | 112 | import numpy as np
import pandas as pd
import os, re
import matplotlib.pyplot as plt
import matplotlib as mpl
from os.path import join as pjoin
import matplotlib.font_manager as font_manager
import h5py
# define path and params
dataset_path = ''
fmriprep_path = pjoin(dataset_path, ' ', ' ')
support_path ... |
cfc9d547660144be422c046e58d0dfae8c240622a10ac445451460d60b8c8fee | Python | 3,489 | 126 | # Node group "XPBD Solve Hook" (GeometryNodeTree), dumped by nodebpy.assets.dump_library.
# Rebuild the library with nodebpy.assets.build_library (nodebpy build).
# Shared by several assets, which import it; not an asset itself.
# _build_group() is the source of truth: the docstring, __init__ and accessors are regenera... |
80852c325d43b94e3b0b33d3ce403322f10383c84e2637eb9de4f5bc42ba4bc1 | Python | 3,490 | 110 | from typing import List
import numpy as np
from lifelines.utils import concordance_index
from pycox.models.loss import CoxPHLoss
import torch.nn as nn
from pytorch_lightning.utilities import rank_zero_warn
from torch import Tensor
import torch
from torchmetrics import Metric
from wsilearn.dl.torch_utils import to_nump... |
171193c45ca19f07221b3c37ccb8e96af455002ac78a3bb6ac542cd2eeca2a2e | Python | 3,491 | 83 | import numpy as np
import pytest
from regtools.geometry_registration.pipeline import (
_pad_border,
_to_rgb_uint8,
_translate_registration_error,
)
from regtools.geometry_registration.types import RunParams
def test_runparams_border_default():
assert RunParams(tiff_path="x", ccf_index=0).... |
59073c8e6ffa36b45ed64727423e96b151122b56b87a88ae7ce5471497cd4fba | Python | 3,491 | 129 | import warnings
from abc import ABC
from typing import Literal
import bpy
from .render import enable_optimal_gpu
_CyclesDeviceTypes = Literal["CPU", "GPU"]
class RenderEngine(ABC):
"""
Configuration for a render engine.
Constructing an engine stores the requested settings without touching the
scene;... |
8496e3670e9637ac3457ca069236aa8224a575d772305e422239aba6966c1f4b | Python | 3,492 | 95 | from torch.utils.data import Dataset
from torch import nn
import torch
class InceptionBlock(nn.Module):
def __init__(self, input_channels, num_filters=16):
super(InceptionBlock, self).__init__()
self.conv1x1 = nn.Conv1d(input_channels, num_filters, kernel_size=1)
self.conv3x3_1 = nn.Conv1d(... |
37dcae070fc0b3cf05d25278e456d67692290cb975012f48a726aeda0392a8bc | Python | 3,493 | 128 | # 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, software
# distributed under th... |
6666fe04e8342a592011254fa5d268a74ace309b4b16b64df4a0985756bef82e | Python | 3,493 | 101 | import os
import pandas as pd
from calvados.cfg import Config, Job, Components
import subprocess
import numpy as np
from argparse import ArgumentParser
parser = ArgumentParser()
parser.add_argument('--name_1',nargs='?',required=True,type=str)
parser.add_argument('--name_2',nargs='?',required=True,type=str)
args = pars... |
b1b59f6c2470715236ab5fc9c3b0290844b33d2f5515d4bbe2e184289dd858c2 | Python | 3,493 | 89 | #! /usr/bin/env python3
import os
import subprocess
import logging
import APT_interface
class cd :
"""Context manager for changing the current working directory, and automagically changing back when done"""
def __init__(self, path):
self.path = path
def __enter__(self):
self.old_path = ... |
e406f7cdf5c13701e782ba835703d71e919631e3a807273d66e450f2707d404e | Python | 3,493 | 114 | """Nox sessions for cog Python SDK testing."""
import glob
import platform
import nox
# Use uv for venv creation and Python management (uv auto-downloads Python if needed)
nox.options.default_venv_backend = "uv"
PYTHON_VERSIONS = ["3.10", "3.11", "3.12", "3.13"]
PYTHON_DEFAULT = "3.13"
TRACING_DEPS = [
"opente... |
58259c222d7540aa2b59e951f2e6d5642e657cbae24aef9acc763e2df6acd27e | Python | 3,494 | 70 | """DOOR_AND_FIRE.py 2026-09-30. Pre-registration: 04-NOTES/PREREG-2026-09-30u-DOOR-AND-FIRE.md
With the antennal lobe repaired but il3LN6 left excitatory, does the right-side sugar input still explode?
usage: python DOOR_AND_FIRE.py run | analyse"""
import sys, os, time, hashlib
sys.path.insert(0, os.path.dirname(os.pa... |
9e2886b0718987cff7b2d7fcc3a9768f7f12653375a3f2ed3acc7a62ed2fa454 | Python | 3,494 | 98 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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
#
# ht... |
13a225ef808820d0918da91751c5aa4968df0bfb1da7842da1dd01c39cbf34d4 | Python | 3,495 | 109 | """distutils.spawn
Provides the 'spawn()' function, a front-end to various platform-
specific functions for launching another program in a sub-process.
Also provides the 'find_executable()' to search the path for a given
executable name.
"""
import sys
import os
import subprocess
from .errors import DistutilsExecErr... |
26c586534d61ee41f1f88ba54b8b1fc0a5a8bcbcf4df4ced045ac4f5c6e68651 | Python | 3,495 | 75 | #! /usr/bin/env python3
import os
import subprocess
import logging
import APT_interface
class cd :
"""Context manager for changing the current working directory, and automagically changing back when done"""
def __init__(self, path):
self.path = path
def __enter__(self):
self.old_path = ... |
b199ef0f3ce7bae935721a38044d704f7a2c383a1971302ee0d3005688e63120 | Python | 3,495 | 60 |
from sklearn.linear_model import LinearRegression
#from ..tools import regression
import numpy as np
def multregconn(activity_matrix, target_ts=None, parcelstoexclude_bytarget=None, conn_mask=None):
"""
activity_matrix: Activity matrix should be nodes X time
target_ts: Optional, used when o... |
6d73a1434b8639b6c2d208c73c7b1fbb443f61174268166f414336c939782907 | Python | 3,496 | 97 | # coding=utf-8
# Copyright 2018 The Google AI Language Team Authors and The HuggingFace Inc. team.
# Copyright (c) 2018, NVIDIA CORPORATION. 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 cop... |
90af762bde961ba4080b14aa742262670d6624c9d97da3464a8d4411bfa9e1ae | Python | 3,496 | 106 | # coding=utf-8
# Copyright 2026 The Google Research 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 required by applicab... |
6df8795ee10995d3c24f619390b45e942e87bc2fdbb1f85c2eafe540300aec99 | Python | 3,497 | 92 | #
# MIT License
#
# Copyright (c) 2022 GT4SD team
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge,... |
cabc1219faf486abf8286f4161f55d15a044a30fa9ab09331a8953317076aee6 | Python | 3,497 | 104 | from __future__ import print_function
from unittest import TestCase
import numpy as np
import matplotlib.pyplot as plt
from soundsig.discrete_process import DiscreteProcessEstimator
from soundsig.colormaps import magma
class DiscreteProcessTest(TestCase):
def setUp(self):
pass
def tearDown(self)... |
e9d3ccedb420ed61b2fac08547f33d86733f787d869f53f8808e84c1152abd36 | Python | 3,498 | 129 | import sys
from scipy.io import wavfile
from scipy.signal import stft, spectrogram
from scipy.ndimage.filters import gaussian_filter
import os
import numpy as np
from librosa import feature as libfeature
def get_spec_min_max(wav_path, start_s=0, stop_s=-1):
"""
Automatically calculate the 'spec_min_val... |
05c540b024ca2f86eb350fe6a6d1b7fb111f1c1a151756439ac2317cc5b21a85 | Python | 3,499 | 92 | import os
import pytest
import numpy as np
from oxasl import Workspace, AslImage, preproc
def test_preproc_none():
wsp = Workspace()
d = np.random.rand(5, 5, 5, 6)
wsp.asldata = AslImage(d, name="asldata", tis=[1.5], iaf="tc", order="lrt")
preproc.preprocess(wsp)
assert wsp.asldata.ntis == wsp.as... |
0f3529e9f0f0f6996c8364bbe92ea05d2b5ee3385bf61f0a0c5df2e79a4ebdb8 | Python | 3,499 | 107 | # Node group ".MN_select_attribute" (GeometryNodeTree), dumped by nodebpy.assets.dump_library.
# Rebuild the library with nodebpy.assets.build_library (nodebpy build).
# Shared by several assets, which import it; not an asset itself.
# _build_group() is the source of truth: the docstring, __init__ and accessors are reg... |
431c06a821d9e6429e20c9b696ea4ad43db8ada1eef0c34de74b40437287270d | Python | 3,499 | 78 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
from downward import suites
from lab.reports import Attribute, gm
from common_setup import IssueConfig, IssueExperiment
#from relativescatter import RelativeScatterPlotReport
def main(revisions=None):
suite=suites.suite_optimal_strips()
suite.extend(suites.suite... |
4f80116369d3294200570408a30b3611d37b165dee997b71d337d38875c28aae | Python | 3,499 | 63 | """Golden regression: the 'are you a fly?' exchange must reproduce token for token.
Reference token arrays are copied verbatim from publication/habr-fly-question/capture.json
(captured on CUDA, RTX 3070 Ti, float16) into tests/fixtures/fly_question_golden.json.
Verified on 2026-10-10: CUDA float16 and CPU float32 (AMD... |
a33cf38ec625ae70a2466f4be5e5816e4d7862d467661e64407fb2787f600a99 | Python | 3,499 | 103 | import click
import numpy as np
import pandas as pd
import random
import os
#from set_seed import set_global_determinism
SEED = 0
def set_seeds(seed=SEED):
np.random.seed(seed)
os.environ['PYTHONHASHSEED'] = str(seed)
random.seed(seed)
def set_global_determinism(seed=SEED):
set_seeds(seed=seed)
# op... |
03c9daa2d604647b2805d839ba094fb0cac69d75a248db6ef75027cd7ab95444 | Python | 3,500 | 129 | import operator as op
import autograd.numpy as np
import autograd.numpy.random as npr
from autograd import dict as ag_dict
from autograd import grad
from autograd import isinstance as ag_isinstance
from autograd.test_util import check_grads
npr.seed(0)
def test_getter():
def fun(input_dict):
A = np.sum(... |
256f6a6dcf3a97a480370ffc4b254c0a73758333b1559a640286d911946c4ca8 | Python | 3,503 | 88 | from collections.abc import Sequence
import torch
from torch import nn
from torchdrug import core, layers
from torchdrug.core import Registry as R
@R.register("models.GAT")
class GraphAttentionNetwork(nn.Module, core.Configurable):
"""
Graph Attention Network proposed in `Graph Attention Networks`_.
..... |
6dda2856ddc0dcdd2c8f2352cdafd65250366ec3f463ad3a1d6d5c8b84f0aadf | Python | 3,503 | 116 | """
Given two x,y curves this gives intersection points.
Based on: http://uk.mathworks.com/matlabcentral/fileexchange/11837-fast-and-robust-curve-intersections
Source: https://github.com/sukhbinder/intersection
Copyright 5 April 2017 Sukhbinder
Permission is hereby granted, free of charge, to any person obtaining a... |
786f6893873a61d42d197ad8759d4f252a473b32794ddd466cbe888631ac9ddc | Python | 3,503 | 124 | #!/usr/bin/env python
"""
Visualize Schaefer IS-RSA results on glass brains.
This script reads the IS-RSA R output files and visualizes thresholded
t-statistic maps for the Features_Post effect for each movie.
"""
import os
import pandas as pd
import matplotlib.pyplot as plt
from nltools.data import Brain_Data
from ... |
132cb940e2cea63b2955c541a6a647b2dd3bba37b4acf51efca4c4207413039f | Python | 3,504 | 94 | #!/bin/usr/python3
# Use example 1: python preprocessing_test2.py /home/melanie/data_test data_test_information.csv /home/melanie/data_test/transforms
# Use example 2: python preprocessing_test2.py data/train4/BIDS_data_brain Test2_algo_train1.csv test2_algo_train1_preprocessed
## Import libraries
import os
import s... |
23297ff62f162b28496e2b6172ace1e85579caca60311221bb3215928a973a8e | Python | 3,505 | 100 | import pandas as pd
import argparse
import os
def arg_parser():
parser = argparse.ArgumentParser(description="Refine cell counts")
parser.add_argument("--csv", type=str, help="path to csv file")
parser.add_argument("--out", type=str, default="", help="output_dir")
parser.add_argument("--level... |
b8a74d02b24f3763cc4953c46a678bacfcca1dd1ae5a567b9574a464953ee9ff | Python | 3,505 | 119 | """Phonon recipes for MLPs."""
from __future__ import annotations
from importlib.util import find_spec
from typing import TYPE_CHECKING
from monty.dev import requires
from quacc import flow
from quacc.recipes.common.phonons import phonon_subflow
from quacc.recipes.mlp.core import static_job
from quacc.wflow_tools.c... |
2095b97690b72c2bfafe7e0820089f4fa219fa34f120f865e9193b6bf8e3abb5 | Python | 3,506 | 92 | import numpy as np
import torch
import torch.nn as nn
class FocalLoss(nn.Module):
"""
copy from: https://github.com/Hsuxu/Loss_ToolBox-PyTorch/blob/master/FocalLoss/FocalLoss.py
This is a implementation of Focal Loss with smooth label cross entropy supported which is proposed in
'Focal Loss for Dense ... |
d1628e9614f736a86c21c6456de38f54a74be5cdbc8249b8f216f590ed3d56d0 | Python | 3,506 | 85 | import os
import argparse
def generate_slurm_script(input_dir, output_dir, output_filename, read_group_prefix):
# Ensure output directory exists
os.makedirs(output_dir, exist_ok=True)
# Find all .fq.gz files in the input directory
fq_files = sorted([f for f in os.listdir(input_dir) if f.endswith('.fq.... |
aeffae0f4f760f8fb54145171b6100c4cd84e1816da0a93314f117ff6d8570b5 | Python | 3,507 | 127 | """Various general utilities for working with PDB files"""
from Bio import PDB
import logging
import numpy as np
from scipy.spatial import KDTree, distance_matrix
import warnings
logging.disable(logging.WARNING)
warnings.filterwarnings("ignore", category=DeprecationWarning)
def load_pdb_file(pdb_path: str) -> PDB.Mo... |
cc856d07a725abaaf952b617f770d1392ac5a4b6169ba03a45932f53ceb81786 | Python | 3,507 | 108 | # Node-group asset "Residue Mask" (GeometryNodeTree), dumped by nodebpy.assets.dump_library.
# Rebuild the library with nodebpy.assets.build_library (nodebpy build).
# _build_group() is the source of truth: the docstring, __init__ and accessors are regenerated from it on the next dump.
from typing import TYPE_CHECKING
... |
bf37282fd711914aeb22187ff9a9c5e45cf3560ee189a29d98a7abd1af5df3bb | Python | 3,508 | 99 | import importlib
import os
import sys
from PyQt5 import QtWidgets
import globals.global_style as gs
FILE_PATH, FILE_FULL_NAME = os.path.split(os.path.realpath(__file__))
FILE_NAME, FILE_EXT = os.path.splitext(FILE_FULL_NAME)
sys.path.append(FILE_PATH + r'\panels')
class ProgPanel(QtWidgets.QWidget):
... |
c2798eaae5a82891a5df6b154ba691a1cdbb8f61540cc33e94a43cdd2d1e7b6e | Python | 3,510 | 85 | import torch
from torch.optim.optimizer import Optimizer, required
import math
class Adaptive_HB(Optimizer):
def __init__(self, params, lr=required, betas=(0.9, 0.99), epsilon=1e-8, weight_decay=0.0, momentum_init=0.9):
if lr is not required and lr < 0.0:
raise ValueError(f"Invalid learning rat... |
19baab28094f5e08f1d6b1cc99fe6260c59b35e10e0851e227d563d7ed4cdcea | Python | 3,511 | 114 | # Node-group asset "Separate First Point" (GeometryNodeTree), dumped by nodebpy.assets.dump_library.
# Rebuild the library with nodebpy.assets.build_library (nodebpy build).
# _build_group() is the source of truth: the docstring, __init__ and accessors are regenerated from it on the next dump.
from typing import TYPE_C... |
20a1ea20f48e7b3325a27ed5ab733107ac4729177f6d52a2e542b0393edb1ad9 | Python | 3,512 | 95 | import sys
if sys.version_info.major > 2:
import urllib.request as url_lib
else:
import urllib as url_lib
sys.path.append('..')
import tempfile
import os
import APT_interface as apt
import ast
import glob
import re
import numpy as np
import PoseTools
import apt_expts
import os
os.environ['CUDA_VISIBLE_DEVICES']... |
d9598d66b4b6612e8b9f63adf75c96496d28473e76ea9be3c516f38629ef7480 | Python | 3,513 | 125 | # coding=utf-8
# Copyright 2026 The Google Research 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 required by applicab... |
fb364745d28baf3f7af673f7f9322bd41d7e44ed869f7a223291c353250a6d1f | Python | 3,513 | 95 | import torch
import torch.nn as nn
import pytorch_lightning as pl
from torchmetrics import Accuracy
class PilotCareTransNet(pl.LightningModule):
def __init__(self, input_dim: int, num_labels: int, learning_rate: float = 1e-4):
super(PilotCareTransNet, self).__init__()
# Transformer mode... |
c85d19ea9665d7bfc76c9f1d42d4e0ce05c71c133f2af598113b947dd9bd79ab | Python | 3,514 | 71 | from pddlstream.language.constants import get_prefix, get_args
from pddlstream.language.exogenous import replace_literals
from pddlstream.language.external import get_domain_predicates
from pddlstream.language.stream import Stream
from pddlstream.utils import find_unique, get_mapping
def get_predicate_map(state_strea... |
d23d08685e024c545b87686ca2e64091bad12bc1d25ea0dfdcb529d41cecdaa4 | Python | 3,514 | 92 | from collections.abc import Callable
from elasticai.creator.arithmetic import FxpConverter, FxpParams
from elasticai.creator.file_generation.savable import Path
from elasticai.creator.file_generation.template import (
InProjectTemplate,
module_to_package,
)
from elasticai.creator.vhdl.auto_wire_protocols.port_... |
141b24fa9984ea60aefb0f688847a75fbc3fe09415337a7db61289b8f0c156c2 | Python | 3,515 | 112 | """
Optuna example that optimizes multi-layer perceptrons using skorch.
In this example, we optimize the validation accuracy of hand-written digit recognition
using skorch and MNIST. We optimize the neural network architecture. As it is too time
consuming to use the whole MNIST dataset, we here use a small subset of i... |
7a0072d7f23525df178d5411df4916862f22ad83544cb38b808205ab5474c0b6 | Python | 3,515 | 109 | #!/usr/bin/env python3
"""
pdbfixer_cleaning.py
Given a PDB ID, this script will:
1. Create a folder ./<pdbid>/
2. Download the PDB file into that folder.
3. Strip out all heterogens except water.
4. Build any missing residues/atoms.
5. Add all hydrogens at pH 7.0.
6. Write out <pdbid>_cleaned.pdb in that folder... |
c5971beb4b7b629935178121c369b53c8b9a66c069b101db34d65b3ea2f6eb9e | Python | 3,515 | 114 | import numpy.matlib
import numpy as np
from scipy.sparse import *
from sklearn.metrics.pairwise import rbf_kernel
from numpy import linalg as LA
def spec(X, **kwargs):
"""
This function implements the SPEC feature selection
Input
-----
X: {numpy array}, shape (n_samples, n_features)
input... |
4141e3df72ff00e7b173b3b9e4a2bc632a83b4d7f0bac5b4db00ecb7a64d1426 | Python | 3,516 | 89 | # Librairies
import os
import sys
code_path = os.path.split(os.path.split(os.getcwd())[0])[0]
sys.path.append(code_path)
import numpy as np
import argparse
from setting import *
from loader import *
from XAI_method import *
from XAI_interpret import *
from utils import *
# Arguments
argParser = argparse.ArgumentParse... |
2f66e298bc1a8b274727b9bb8256aa4542bc41745c811d97023cd11565423376 | Python | 3,517 | 122 | import matplotlib.pylab as plt
import numpy as np
import tensorflow as tf
def lin_interpolate(input_matrix, baseline=False, steps=50):
'''
input: numpy array of the sample to explain
params:
- baseline: reference to use for linear interpolation; zero by default
- steps: number of steps to tak... |
9f7a488f6ffe2836cb67c5dce288719986744d108286cbd5adee8a61d91635ca | Python | 3,517 | 95 | import sys
import logging
import os
import copy
import shutil
import gzip
import numpy as np
import pandas as pd
from typing import Optional, List, TypedDict, Any, NamedTuple
from collections import defaultdict
from tqdm import tqdm
from glob import glob
import torch
def nio_patchpath_to_coord(patch_name: str):
"... |
7d695a7b0f951b5d59495bb2eb2986c212359007e3889894ae7f893513414079 | Python | 3,518 | 96 | """Example for loading the optimal HMM runs and calculating model inferences
"""
# Set up dependencies
import os
import pickle
import numpy as np
from sys import argv
from osl_dynamics import data
from osl_dynamics.inference import tf_ops
from osl_dynamics.models.hmm import Model
if __name__ == "__main__":
# --... |
4d6bd828fffec4ed9c8466bc00a758f57905458ef9fc61c0de6529529f1672cc | Python | 3,519 | 115 | # Node-group asset "Backbone Vector List" (GeometryNodeTree), dumped by nodebpy.assets.dump_library.
# Rebuild the library with nodebpy.assets.build_library (nodebpy build).
# _build_group() is the source of truth: the docstring, __init__ and accessors are regenerated from it on the next dump.
from typing import TYPE_C... |
8f4a229f47e91911dc0850b111ca4f090a0512f03e0cc2d42ca7463fc36fefaa | Python | 3,519 | 112 | import logging
from typing import List, Optional, Tuple
from pip._internal.utils.misc import HiddenText, display_path
from pip._internal.utils.subprocess import make_command
from pip._internal.utils.urls import path_to_url
from pip._internal.vcs.versioncontrol import (
AuthInfo,
RemoteNotFoundError,
RevOpt... |
ec50579f6f7bd58dedf6f24ffd119bc88e7338fe04c2c458892e6f0305dde553 | Python | 3,519 | 98 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue May 9 16:28:29 2023
@author: Felipe
"""
import numpy as np
import sys
import os
sys.path.append(os.path.abspath('../../'))
import analysis.frequency as frequency
import analysis.synchronization as synchronization
import scipy.io as sio
import scipy.si... |
fedfe50b10d7fced48948ee9afc68d194fea81b52553063661fa75b4582a39ff | Python | 3,519 | 77 | import torch.nn as nn
from ..utils import _triple_same
class BaseConverter(object):
"""
base class for converters
"""
converter_attributes = []
target_conv = None
def __init__(self, model):
""" Convert the model to its corresponding counterparts and deal with original weights if necess... |
050b093200bcda2bc3f170d9e8458f257f81ac13455a20d0a807fcdeddf737de | Python | 3,520 | 96 | import numpy as np
from scipy.io import FortranFile
from .utils import KGData, VKBGData, tqdm_mpi_tofile, one_by_one, set_range, is_master
'''
This module contains functions for reading BerkeleyGW related files
'''
class bgw_vsc:
'''
VSC file: stores the FT of total effective local potential
'''
def ... |
21cbf937304a2396c2b6498b9e27d30ba76ff38618834ca34d386079f4fa45e3 | Python | 3,520 | 105 | # coding=utf-8
# Copyright 2026 The Google Research 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 required by applicab... |
5c79eab2d93de7bd7502b63d6ad249fa47f4be1f7e8d0618ea4ca7d31c538c58 | Python | 3,520 | 99 | from dreamcoder.domains.arc.arcPrimitivesIC2 import *
import dreamcoder.domains.arc.arcPrimitivesIC2 as p
from dreamcoder.domains.arc.arcInput import load_task, num_to_id
import arckit
# def train_examples(task_dict):
# # examples = [((Input(ex["input"], task_dict["train"]),),
# # Grid(ex["output"])) for ... |
b2ed2828427ff6506245c9b0039e84e35bc6df4c4a756980c88b73c5750a46eb | Python | 3,521 | 124 | import os
import dash_bootstrap_components as dbc
import flask
from dash import Dash, html, page_registry, page_container, Output, Input, State
os.environ['LOGURU_LEVEL'] = 'WARNING'
BAR_STYLE = {
"zIndex": "1",
}
def get_navbar(nav_links: list[dbc.NavLink], navbar_id="pvis_navbar"):
bar = dbc.Row(
... |
c1b483f6d7a1b45ffc4981cf4abf8e3eb54583b7e01fa3ddf34f58462390d604 | Python | 3,521 | 87 | from typing import Tuple, Union
import pathlib
import torch
import torchvision
import yacs.config
from torch.utils.data import Dataset
from pytorch_image_classification import create_transform
class SubsetDataset(Dataset):
def __init__(self, subset_dataset, transform=None):
self.subset_dataset = subse... |
9136de9f15a91314db647b87d4feb84ca799640eb1c04d0b12ce296e3e09dc52 | Python | 3,522 | 92 | #!/usr/bin/env python
import boto3
import base64
from datetime import datetime
def get_user_data():
# my bash code to execute
user_data = """#!/bin/bash
apt-get update
#apt-get install -y nfs-common
#mkfs -t ext4 /dev/xvdca
#mount /dev/xvdca /tmp
eval "$(aws ecr get-login --no-include-email)"
nvidia-docker r... |
4d8b8bdcb823bd455f9753a414c7c6a5fa12f4d970b0cf4f007d693564a506d0 | Python | 3,523 | 81 | """PyNEST Mesocircuit: Run Mesocircuit
--------------------------------------
Main example script to run a simulation of the mesocircuit with NEST and
subsequently analyze and plot the results.
The simulation of the spiking neural network can be followed by an LFP
simulation and the corresponding postprocessing and p... |
8fa2b8021f0cc5980ccc3a4625a9ea43e444a105a4797c5f3cc5a94c97a6ad88 | Python | 3,523 | 86 |
import numpy as np
from scipy import sparse
import random
import itertools
import torch
from torch.utils.data import DataLoader
from cobolt.utils.data import MultiData
class MultiomicDataset(torch.utils.data.Dataset):
def __init__(self, dt: MultiData):
self.dt = dt.get_data()
self.omic = list(sel... |
a3c462872f857ea27801b4f4700c46e577fea4996ca076581820ce75c01fbaa8 | Python | 3,523 | 106 | """
Optuna example that optimizes convolutional neural network and data augmentation using fastai V2.
In this example, we optimize the hyperparameters of a convolutional neural network and
data augmentation for hand-written digit recognition in terms of validation accuracy.
The network is implemented by fastai and
eva... |
ecd9b0009ac01a5aa4155b944b8d2c30c496aa0183e85d89791611151c3bed39 | Python | 3,523 | 113 | # Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If ex... |
17bf69febbe20c5a55a3b483b99a6f6f63e6c2a12942a98ed2fcd1cbd5f2b8fe | Python | 3,525 | 110 | # -*- coding: utf-8 -*-
from __future__ import print_function
import sys
"""
We document Fast Downward exit codes at
http://www.fast-downward.org/ExitCodes. Please update this documentation when
making changes below.
"""
SUCCESS = 0
SEARCH_PLAN_FOUND_AND_OUT_OF_MEMORY = 1
SEARCH_PLAN_FOUND_AND_OUT_OF_TIME = 2
SEARC... |
4d828dc14a4b3d18220007b89e51f72e3b938a005d0d98cf9cf805d9aadec3c5 | Python | 3,525 | 114 | # coding=utf-8
# Copyright 2026 The Google Research 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 required by applicab... |
abd9a1ef907088a9241178a6ec5fea6a1c1045070c7b933671741adaec447d88 | Python | 3,525 | 89 | from __future__ import annotations
from ase.build import molecule
from numpy.testing import assert_array_equal
from quacc.recipes.gaussian.core import relax_job, static_job
def test_static_job(tmp_path, monkeypatch):
monkeypatch.chdir(tmp_path)
atoms = molecule("H2")
output = static_job(atoms, 0, 1)
... |
baecd3846226f92e72de04daf17913484023e42fb8585580edac570db14ef63a | Python | 3,526 | 115 | # coding=utf-8
# Copyright 2026 The Google Research 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 required by applicab... |
d98b632904e45a9b1fd658488d7c7d7d1f2555456f2534af1677db52fbebc292 | Python | 3,526 | 111 |
import torch
import torch.nn as nn
from torch import Generator
from typing import Any
from .coreblock import CoreBlock
from .final_layers_block import FinalLayersBlock
from .first_layers_block import FirstLayersBlock
class PrixFixeNet(nn.Module):
"""
Main model
Can contain up to three blocks:
1. Fir... |
4d66f77eccd83eeb2fb654e2d4aaa61b421ce2709c525ab80dd8a08c0097a4af | Python | 3,527 | 81 | from argparse import ArgumentParser, Namespace, FileType
from Bio.PDB import PDBParser,PDBIO
import torch,os,copy
import pandas as pd
from utils.visualise import save_protein
parser = ArgumentParser()
parser.add_argument('--results_path', type=str, default='results/user_inference', help='Directory where the outputs wi... |
ca4d1ebca4dbd9006365cd3c670cf87ef8c396094769b2c6061b603fee73b02d | Python | 3,527 | 84 | """Write the per-run output artifacts for a geometry-registration result."""
from __future__ import annotations
import json
import os
from typing import Optional
import imageio.v2 as imageio
import numpy as np
from .types import RunResult
def _overlay(registered: np.ndarray, edge_atlas: np.ndarray) ... |
af3ced4526e5e181a03c76f465c8bc061244123aa5a3a69aa05a130f8cc52c45 | Python | 3,528 | 91 | """Edit-summary panel tests."""
import pytest
@pytest.fixture
def qapp():
from PySide6.QtWidgets import QApplication
app = QApplication.instance() or QApplication([])
yield app
def _two_region_volumes(tmp_path, shape=(3, 20, 30)):
import nibabel as nib
import numpy as np
... |
b5477b5363f83b3bf06a7f23a0d871c8eecbca04ea1b0f8fe0432d5f64f524fe | Python | 3,528 | 106 | #!/usr/bin/env python
# ----------------------------------------------------------------------
# Copyright (C) 2014-2015, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This program is free software: you ca... |
cff4dbebc19932cffd6a8b1f9530f140e0a3c0eef5f6c4d473d3ccf61ee69750 | Python | 3,528 | 56 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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
#
# ht... |
d5c1f742e8ed2aaac5512b3669b20022ca6fb14c216b03a61a29d1d90ac064e6 | Python | 3,529 | 84 | """
em_fetch.py — read 2-D cut-outs of the public FlyWire EM volume (gs://flywire_em/aligned/v1, 8x8x40 nm)
without any account: neuroglancer 'uint64_sharded_v1' format read with HTTP range requests.
Coordinates: FlyWire nm (the same space as the synister synapse positions).
"""
import gzip, json, urllib.request
import... |
169862ad569a76620eec7fbafef4f820a415712bd54761127f873b397dd67559 | Python | 3,530 | 106 | # coding=utf-8
# Copyright 2026 The Google Research 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 required by applicab... |
32f5e3487ba2d53c14a397b197fb07b33dd76016ab117971854094c2e5241e90 | Python | 3,530 | 95 | from pathlib import Path
from typing import cast
import bpy
from nodebpy.builder import TreeBuilder
from ... import blender as bl
from ... import material
from ...nodes import geometry
from ..utilities import create_object
from .base import Ensemble, EntityType
from .reader import CellPackReader
class CellPack(Ensemb... |
004a845a9e01c60af746c04f060acb6f72dd2c7a9f1b3af0e6d82543b5af94c1 | Python | 3,531 | 124 | from collections.abc import Sequence
from elasticai.creator.vhdl.design.signal import Signal
def _sorted_dict(items: dict[str, str]) -> dict[str, str]:
return dict((key, items[key]) for key in sorted(items))
def create_instance(
*,
name: str,
entity: str,
signal_mapping: dict[str, str],
lib... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.