sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
5658e9431520575aa204377cfc5b1dfdda1b746dd73f9af7511637c68dad0250 | Python | 16,742 | 361 | # script to sample from proteinMPNN for defined positions
# this code is adapted from https://github.com/dauparas/ProteinMPNN
import sys
import importlib
sys.path.append('../ProteinMPNN/')
sys.path.append('../ProteinMPNN/vanilla_proteinmpnn')
sys.path.append('../../../../src/')
from regressionTools import hamming
... |
cc1a63762a3f5f60307697317910d7418d58b4e98678d49dfbf1b80fa8a6f9ab | Python | 16,761 | 478 | # copyright (c) 2020 PaddlePaddle Authors. All Rights Reserve.
#
# 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... |
f81d71ec14b38de059d46ba7f354ca0ccde4f3988c6d851538612ef06b624fc8 | Python | 16,768 | 477 | import numpy as np
# import matplotlib.pyplot as plt
import torch
import h5py
import torch.nn as nn
from torch.utils import data
import itertools
import json
import sys
from os import path
import gc
gc.collect()
nameScript = sys.argv[0].split('/')[-1]
# we are going to give all the arguments using a Json file
nameJso... |
63c24e67abd3a91f5442068431be53032510a16cab13651d5bc5d35affb597c4 | Python | 16,774 | 508 | # coding: utf8
# Copyright (c) 2023 PaddlePaddle Authors. All Rights Reserve.
#
# 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 requ... |
45e18b439746310f68f15bd5a1d2d76bf87912d8cd77fe254a93039254e2ac8b | Python | 16,780 | 412 | # Copyright (c) 2021 PaddlePaddle 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 appli... |
7a65c6ecbf0e9b19abfb6b9bca93a63fc37309e90b3f2638da220d8cf4f42d1c | Python | 16,790 | 432 | from collections.abc import Sequence
from pathlib import Path
import cv2
import numpy as np
from qtpy.QtCore import QRect, Qt
from qtpy.QtGui import QIcon, QImage, QPixmap
from qtpy.QtWidgets import (
QApplication,
QFileDialog,
QHBoxLayout,
QLabel,
QMessageBox,
QProgressDialog,
QPushButton,... |
e814b81560c51be17dd7d745e152b6ca4e9f41ca31080f87c9ae5bd9885ffda4 | Python | 16,802 | 415 | """Test suite for CircuitTemplate.get_jacobian_func."""
import numpy as np
import pytest
from pyrates import CircuitTemplate, OperatorTemplate, clear
from pyrates.ir.node import clear_ir_caches
def setup_module():
print("\n")
print("================================")
print("| Test Suite: Jacobian Functio... |
47b7e51bb80c8911c5e064ff1c9650291862db99c4b913faff6c68ec0f1b6b4d | Python | 16,804 | 362 | """
ManifestHandler
"""
import os
from python.glassfunc import locate
SOURCE_FASTQ_TYPE = "FASTQ"
SOURCE_BAM_TYPE = "uBAM"
ALIGNED_BAM_TYPE = "aligned BAM"
class ManifestHandler:
"""
Class that defines the GLASS manifest
It should not be implemented directly, but either as a JSONManifest using
JSON ... |
0da0bfe17af583d176267d1588050f047c2447f68cf4c3a186f97d0ef054f87b | Python | 16,822 | 441 | # -*- coding: utf-8 -*-
"""
SimilarityAssessment class
functions to assess similarity between dFC results
Created on Jun 29 2023
@author: Mohammad Torabi
"""
from copy import deepcopy
import numpy as np
from joblib import Parallel, delayed
from scipy import stats
from ..dfc_utils import (
TR_intersection,
c... |
ef5dc97f1d4095e210ddd862c43389e9ecd1831421e605a68b1849a9202a96e1 | Python | 16,850 | 473 | """
This is an implementation of ProNet model
"""
from torch_geometric.nn import inits, MessagePassing
from torch_geometric.nn import radius_graph
from .features import d_angle_emb, d_theta_phi_emb
from torch_scatter import scatter
from torch_sparse import matmul
import torch
from torch import nn
from torch.nn imp... |
8bdf81be7510c9d364c2e8afa561ccd683b7ae1507eccf426c3c9c1252ddb3ca | Python | 16,855 | 395 | import os
import itertools
import collections
import numpy as np
from numpy.random import default_rng
import librosa
from pydub import AudioSegment
from common import normalise
from common.tfrecord_creator import TFRecordCreator
from common.data_sample import Sample
def make_tfrecords(data_folder,
... |
271268d61d84e9de305286698c7d0652fa29e7d946c4d316b58fcb759c4679e6 | Python | 16,919 | 468 | import numpy as np
import pytest
from reinvent.scoring.pumas_support import have_pumas
from reinvent.scoring.scorer import Scorer
from numpy.testing import assert_array_almost_equal
USE_PUMAS = [
pytest.param(
True,
marks=pytest.mark.skipif(not have_pumas, reason="optional 'pumas' package not insta... |
1c397491d23cda454c474f386c656a3ff12ccc37973b034f8b28f6e0310bf30a | Python | 16,938 | 433 | # Copyright (c) 2020 PaddlePaddle 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 appli... |
fb69f5f6d8482813d0778e8190afab317cb11fd149d2c43889d21f4abe138aaf | Python | 16,952 | 434 | import pytest
import renderapi
from test_data import (
render_params,
rough_parameters)
from bigfeta import bigfeta, utils
from marshmallow import ValidationError
import json
import os
import copy
import numpy as np
dname = os.path.dirname(os.path.abspath(__file__))
FILE_ROUGH_TILES = os.path.join(
... |
e0d8126d30632432cf67385cd74cec36faad74f0ffdde74c8caa4f40bb99c82d | Python | 16,970 | 421 | # -*- coding: utf-8 -*-
"""
Created on Fr Sep 30 11:30 2022
@author: Jacqueline Cornean
Here are the functions used in the expansion microscopy analysis.
"""
from tqdm.notebook import tqdm
from scipy.spatial.distance import cdist
import pandas as pd
import numpy as np
from skimage.feature import mat... |
2cba448a5adebab6b91b9caaccc9e95c2270f403c6fae73dea0b7275cb50f0ca | Python | 16,990 | 509 | """Loading toy datasets.
Refer to notebook: `geomstats/notebooks/01_data_on_manifolds.ipynb`
to visualize these datasets.
Lead author: Nina Miolane.
"""
import csv
import json
import os
import zipfile
import numpy as np
import pandas as pd
import geomstats.backend as gs
from geomstats.datasets._base import Figshar... |
e0e70233a77d6dee5b2fdf1f5328dba6f8363a9babc2beb226d5dce353dae058 | Python | 16,997 | 353 | # Copyright (c) 2021 PaddlePaddle 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 ... |
dd3961a8a8c199bc556c265308d7c82ffc517a2d3e14674913b63f20e8386c41 | Python | 17,006 | 426 | #!/usr/bin/env python3
#
# Sniffles2
# A fast structural variant caller for long-read sequencing data
#
# Created: 27.08.2021
# Author: Moritz Smolka
# Contact: moritz.g.smolka@gmail.com
#
from dataclasses import dataclass
import collections
from sniffles import sv
from sniffles import util
from sniffles import con... |
dcd87ea38a2e25083933b5ccabca4d486d45f797dc9f38880a210e292dc65099 | Python | 17,008 | 337 | import numpy as np
import pandas as pd
import pytorch_lightning as pl
import torch
from torch.utils.data import random_split, DataLoader
import sklearn
from modules.dataset import RealFlashPatterns
class FireflyDataModule(pl.LightningDataModule):
def __init__(self, data_dir, augmentations, class_limit, batch_siz... |
7f9efa809c420611b8caff9d5ca246126e5590f0c974c3e20b601a9662b3a6e7 | Python | 17,053 | 485 | #!/usr/bin/env python3
import math
import torch
import torch.nn as nn
from fairseq.data.data_utils import compute_mask_indices
from fairseq.models import FairseqEncoder
from fairseq.models.wav2vec import ConvFeatureExtractionModel
from fairseq.modules import GradMultiply, LayerNorm, SamePad, TransformerEncoderLayer
... |
eb1786362d4e802a1e9d83bd6d3dc18db0478545016575a587e03f3c171b4506 | Python | 17,067 | 398 | import torch
import torch.nn.functional as F
import torch.nn as nn
import ISNetFunctions
import LRPDenseNet
import pytorch_lightning as pl
import warnings
from collections import OrderedDict
import numpy as np
from torch.autograd import Variable
import torch.autograd as ag
import torchvision
import torch.multiprocessi... |
337bdf51630900432b21096e16b1ad89042696e097bb9f93970371f51f956d0e | Python | 17,090 | 459 | """Cluster reports — peak/cluster geometry plus atlas labels.
The peak/sub-peak geometry comes from `get_clusters_table`;
the cluster masks and mass-weighted labels are computed locally so we can
attribute every voxel of every cluster to one or more atlases.
"""
from collections.abc import Sequence
from dataclasses i... |
2431ab787b5797dc68144d943777d6349987da39a2bc8e8598909476e4701957 | Python | 17,141 | 430 | # Copyright (c) 2021 PaddlePaddle 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 appli... |
20c552dffef10f6abaf6198d463fce5dfcc90f3b9188427a678c463795d56fa7 | Python | 17,164 | 520 | """Classes for the pullback metric.
Lead author: Nina Miolane.
"""
import geomstats.backend as gs
from geomstats.geometry.riemannian_metric import RiemannianMetric
from geomstats.numerics.geodesic import ExpODESolver, LogShootingSolver
from geomstats.numerics.ivp import GSIVPIntegrator
from geomstats.vectorization im... |
b54a84d5fb8494cd0c1ff5720073e4c76ad2b02fc7f31e69105431a43a86e21d | Python | 17,197 | 551 | #!/opt/conda/bin/python
import argparse
import dask.dataframe as dd
import json
import matplotlib.pyplot as plt
import numpy as np
import os
import os.path as op
import pandas as pd
import re
import s3fs
import seaborn as sns
from matplotlib.lines import Line2D
from matplotlib.markers import MarkerStyle
from plot_for... |
0ac49dca35840dc074a4444e87fe7771a68b0906366418ebf3807fad82aea5ca | Python | 17,207 | 489 | """
Created on Mon October 23 11:05:36 2023
Description: Visualization functions for
Paper url: https://www.biorxiv.org/content/10.1101/2023.09.11.557230v2
@author: Ekaterina Kuzmina, ekaterina.kuzmina@skoltech.ru
@author: Dmitrii Kriukov, dmitrii.kriukov@skoltech.ru
"""
import matplotlib.pyplot as plt
import numpy ... |
67d883756eb06a5e9de07f468bfc5127a60d0b5a0b31af2c1518cdb5be6f2822 | Python | 17,207 | 551 | # Copyright (c) 2021 PaddlePaddle 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 appli... |
0ebc0f8f8776f274bc67073ce43720a59eda14e5b6ee564c13c7ee28175070c8 | Python | 17,216 | 315 | # Copyright (c) 2018, NVIDIA CORPORATION. All rights reserved.
#
# This work is licensed under the Creative Commons Attribution-NonCommercial
# 4.0 International License. To view a copy of this license, visit
# http://creativecommons.org/licenses/by-nc/4.0/ or send a letter to
# Creative Commons, PO Box 1866, Mountain ... |
8a5a2a7192c174fcf8b31e4d22b7bac657e615bf92db5d8820e3d838df0c6f0b | Python | 17,228 | 494 | # Copyright (c) 2019 PaddlePaddle 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 appli... |
6b048200086824d608c9bb7fc9ff126b7353deaee97aa48a42f5e97c893c5fcd | Python | 17,238 | 514 | # in this script to fellow fairly closely Zou et al
# but the create a equivariant descriptor for each type
# of tree topology from the beggining
# We use a an embedding "across sequences" instead to
# within sequences.
# this is an optimized version of the lstm network
import numpy as np
# added random seed for re... |
b5c675be78ee099942356cfeacff58e572a4c9b244e21370801e48458021fb3f | Python | 17,238 | 399 | import numpy as np
# import tensorflow as tf
import tensorflow.compat.v1 as tf
tf.disable_v2_behavior()
import os
import sys
import time
import LSM_STDP_CONSTRUCTOR_N_MNIST as construct
import NALSM_PARALLEL_SAVE as parasaver
import NALSM_SIM_SUPPORT as runSupport
import NALSM_GEN_SUPPORT as sup
class ru... |
c27f40145e384efc8d52ee5dd83a814c92950f242bdba836ae46fa471677442a | Python | 17,256 | 365 | # -*- coding: utf-8 -*-
"""
"""
import scipy.stats as stats
import matplotlib.pyplot as plt
from scipy.io import loadmat, savemat
from statsmodels.stats import multitest as mtest
import pickle
import numpy as np
import pdb
import os
from plotting_functions import figure_layout, set_size
from library_plot import im_ma... |
0fcb2fecd07e39f97d52eb871018d273df08d6eab0fb7fd9dc7bd41b106f57f0 | Python | 17,274 | 406 | import os
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.nn.utils.rnn as rnn_utils
from torch.utils.data import Dataset, DataLoader
import numpy as np
import dgl
import shutil
import random
import logging
import argparse
from typing import List, Union
from rdkit import Chem
from rdkit i... |
06d4f53527243e2158c2b3842d30b828a070164d815dcaf6f22259efdf329ad4 | Python | 17,300 | 709 | """Pytorch based computation backend."""
from collections.abc import Iterable as _Iterable
import numpy as _np
import torch as _torch
from torch import (
arange,
argmin,
asarray,
clip,
complex64,
complex128,
conj,
empty,
empty_like,
erf,
eye,
flatten,
float32,
f... |
abffbf39b80dda4855441fcfa883bf4bd5ba7ea2c1605e54635a8a4542359367 | Python | 17,307 | 482 | import rdkit
import rdkit.Chem as Chem
from scipy.sparse import csr_matrix
from scipy.sparse.csgraph import minimum_spanning_tree
from collections import defaultdict
from rdkit.Chem.EnumerateStereoisomers import EnumerateStereoisomers, StereoEnumerationOptions
from .vocab import Vocab
MST_MAX_WEIGHT = 100
MAX_NCAND = ... |
ffcac6e40c630c7334dc3a3ba8e54668744c288800fddc8a267d454816c817ec | Python | 17,337 | 484 | # Author: Guoqing Bao
# School of Computer Science, The University of Sydney
# Date: 2019-12-12
# GitHub Project Link: https://github.com/guoqingbao/Pathofusion
# Please cite our work if you found it is useful for your research or clinical practice
# from IPython import get_ipython
# %%
import os
# os.environ["CUDA_V... |
c92247b1251f093189e644a19c1b4e3e1dc59d8926f313629d1aff0facb4abd5 | Python | 17,340 | 458 | import torch
from torch.autograd import Variable
import torch.nn.functional as F
from torch.utils import data
from torch.utils.data import SequentialSampler
from torch import nn
from tqdm import tqdm
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from time import time
from sklearn.metrics impor... |
f261f14b994db96d3068c57232ed4ce2fcaa1c823d42fdafec19a4a43f455cef | Python | 17,354 | 367 | import tensorflow as tf
from variational.layers import DenseReparameterisation
def dice_sorensen_coefficient(x_avg, x):
dsc = 2 * tf.divide(tf.multiply(x_avg, x), (tf.pow(x_avg, 2.0) + tf.pow(x, 2.0)))
return dsc
class AdaPool2D(tf.keras.layers.Layer):
def __init__(self,
pool_size,
... |
85f5597dda8e44bdda1168f3cc23b61f9e26797d7c182f0078cfd3322d8a0284 | Python | 17,366 | 331 | """The spellings this repository's ASE calculators use for their results.
The golden harness is deliberately framework-agnostic: it knows what a
channel *is* -- its shape and its unit -- but not what any particular
implementation calls it. That knowledge lives here (for the calculator
surface) and in ``model_keys`` (f... |
223e50eb3eac23be87c8012208040a462985bef502251812bbf1d20b15e69c3e | Python | 17,373 | 452 | """Structural and cross-resource validation for SanPy Zarr collections."""
from __future__ import annotations
import json
from datetime import datetime
from importlib.resources import files
from pathlib import Path
from typing import Any
import pandas as pd
import numpy as np
import zarr
from jsonschema import Draft... |
ee0e8a68e2db5011814765b48b9f329ee84ce049f153f5a5dfab7a6c12ec4e67 | Python | 17,385 | 523 | r"""Geodesic Regression.
Lead author: Nicolas Guigui.
The generative model of the data is:
:math:`Z = Exp_{\beta_0}(\beta_1.X)` and :math:`Y = Exp_Z(\epsilon)`
where:
- :math:`Exp` denotes the Riemannian exponential,
- :math:`\beta_0` is called the intercept,
and is a point on the manifold,
- :math:`\beta_1` is ca... |
eab0dad618c601925e032e45ff316b2a3addefebc662d38cc400a7d6ac792d3f | Python | 17,393 | 426 | import os
import re
import collections
import numpy as np
import pydub
from pydub import AudioSegment
from pydub.utils import mediainfo
import librosa
import osa.configuration as configuration
from common.data_sample import Sample
def get_features_and_stats(waveform, orig_sr=48000, verbose=False):
waveform = li... |
e6697a77bcf9c047c5f4e2bcdeb200dd4fb68ec196caeff043167f5b08b91965 | Python | 17,401 | 488 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import csv
import io
import logging
import re
from collections import defaultdict
from dataclasses import dataclass
from pathlib import Path
f... |
f4631cd847107fcc296fdc6b916f77286c97a8be0782d4edfb0a723fda510d18 | Python | 17,411 | 377 | r"""
This is an official implementation of `FlowX: Towards Explainable Graph Neural Networks via Message Flows
<https://arxiv.org/abs/2206.12987>`_.
"""
from itertools import combinations
from typing import List, Tuple, Union, Dict
import torch
import torch.nn as nn
from torch import Tensor
from torch.nn.functional i... |
8f9c23b14f371cf609bfcea05d42bbbd0c5571c57dc7ac4ead0aea513b41ff66 | Python | 17,424 | 519 | import logging
from collections.abc import Callable, Sequence
from io import BytesIO
from multiprocessing import Pool
from pathlib import Path
import cv2
import h5py
import numpy as np
from idtrackerai import Blob, Session
from idtrackerai.start.arg_parser import pair_of_ints
from idtrackerai.utils import (
LOGGI... |
787b0dc73a4ab952f42bf8e63ec43890e635390fc3c3b36e03212a3f0eff7c73 | Python | 17,435 | 390 | # -*- coding: utf-8 -*-
#
#
# PyRates software framework for flexible implementation of neural
# network model_templates and simulations. See also:
# https://github.com/pyrates-neuroscience/PyRates
#
# Copyright (C) 2017-2018 the original authors (Richard Gast and
# Daniel Rose), the Max-Planck-Institute for Human Cogn... |
d7d1dc8f6f7f98159ab7315f7e3e90c6440335ff017000b0e1063326eb135d93 | Python | 17,440 | 384 | """Structural result records returned by fitting, decoding and resampling."""
from __future__ import annotations
from copy import deepcopy
from dataclasses import asdict as dataclass_asdict
from dataclasses import dataclass, field
from typing import TYPE_CHECKING, Any, Generic
import numpy as np
from nltools.models... |
9b07fda867112276fc3c96c699c186826fd981563034ca0123799becd5951728 | Python | 17,449 | 282 | # -*- coding: utf-8 -*-
"""
Created on Tue Aug 6 12:23:53 2019
@author: danilo
"""
import matplotlib.pyplot as plt
import numpy as np
import os
from plotting_functions import figure_layout, set_size
def table_plot(str_all, filename_tosave='example', pwd_tosave=None, hem_sep=True, mouse_name=None):
###############... |
065615e54cea1d48aac9de7e79075340e0b5e712da18177ca39a3acfcb37fbc8 | Python | 17,452 | 480 | # Copyright (c) 2022 PaddlePaddle 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 appli... |
aa2938d842c104882aa4ca52fc016c9fb510086f3ff37d70b85e42f8ad76e544 | Python | 17,459 | 565 | import numpy as np
import cv2
import copy
def decode_image(img_path):
with open(img_path, 'rb') as f:
im_read = f.read()
data = np.frombuffer(im_read, dtype='uint8')
im = cv2.imdecode(data, 1) # BGR mode, but need RGB mode
im = cv2.cvtColor(im, cv2.COLOR_BGR2RGB)
img_info = {
"im_... |
a46e78e0296578c16dd8f9e945154b2b408bed9118da81890320bec089421b0e | Python | 17,465 | 293 | """CDR3 markup and repair, via ``arda.cdr3fix``.
Replaces the k-mer scanner vendored from the Groovy-era build
(``annotate/_legacy_fixer/``). ``arda`` aligns the germline-templated run with a semi-global
Needleman-Wunsch anchored at [FW]118 with free end gaps, where the legacy used a longest-hit k-mer
scan, so it exte... |
4692993cfab51ac39f1a8739b0d2b2b0be600b53a15bb628bd1aca21c15e4aac | Python | 17,485 | 510 | from __future__ import annotations
import argparse
import copy
import tempfile
from pathlib import Path
from typing import Any, Mapping, Sequence
import pytest
from hypothesis import given
from hypothesis import strategies as st
from pytest_mock import MockerFixture
from pytest_mock.plugin import MockType
from snake... |
9971acff773c4a5ffba51e3aa671731aa8dbc011fce46f340f0dcb306cd4a21e | Python | 17,560 | 403 | import numpy as np
# import tensorflow as tf
import tensorflow.compat.v1 as tf
tf.disable_v2_behavior()
import os
import sys
import time
import NALSM_CONSTRUCTOR_N_MNIST_NOISE as construct
import NALSM_PARALLEL_SAVE as parasaver
import NALSM_SIM_SUPPORT as runSupport
import NALSM_GEN_SUPPORT as sup
class... |
cffbd3414c297ef3f1ab77e698d2dd0c1930d9cf2ebfae1f0fd44c3e88e22370 | Python | 17,561 | 467 | # -*- coding: utf-8 -*-
"""
Created on Sun Aug 3 15:18:38 2014
@author: Dan Denman and Josh Siegle
Loads .continuous, .events, and .spikes files saved from the Open Ephys GUI
Usage:
import OpenEphys
data = OpenEphys.load(pathToFile) # returns a dict with data, timestamps, etc.
"""
import os
import numpy a... |
39ae6fd597dd51b09fdafbebda06b80e0e3787ee0cf64d8a569576f4d1fc91a2 | Python | 17,567 | 481 | ###########################################################################################
# Script for evaluating configurations contained in an xyz file with a trained model
# Authors: Ilyes Batatia, Gregor Simm
# This program is distributed under the MIT License (see MIT.md)
########################################... |
d9bb95a76a99e4f036d92808fde95764f30ba78cecd7f262218f606d794ed8fb | Python | 17,568 | 422 | import time
import os
import torch
import torch.nn.functional as F
from torch.optim import Adam
from torch_geometric.data import DataLoader
from metric import compute_cla_metric, compute_reg_metric
import numpy as np
from libauc.losses import APLoss_SH, AUCMLoss
from libauc.optimizers import SOAP_ADAM, PESG
from libauc... |
e87e39955249b4c3a858e95616c3c1a65961f97017aa21f29bbe45d6c22e2d0a | Python | 17,575 | 322 | # Copyright (c) 2019, NVIDIA CORPORATION. All rights reserved.
#
# This work is licensed under the Creative Commons Attribution-NonCommercial
# 4.0 International License. To view a copy of this license, visit
# http://creativecommons.org/licenses/by-nc/4.0/ or send a letter to
# Creative Commons, PO Box 1866, Mountain ... |
b0495954e3a28a952707adc6237b358c9332745307f7393d517e66ef4a94b9da | Python | 17,580 | 537 | # %%
"""
#### ## ## ######## ####### ######## ######## ######
## ### ### ## ## ## ## ## ## ## ## ##
## #### #### ## ## ## ## ## ## ## ##
## ## ### ## ######## ## ## ######## ## ######
## ## ## ## ## ## ## ## ... |
b25cb10ff7dd8e52cb30c26279e98c949f2d53b0c3890cb8605a2f82041c6f57 | Python | 17,592 | 422 | """Intersubject correlation, functional connectivity, and phase synchrony."""
import numpy as np
import polars as pl
from scipy.signal import hilbert
from .isc import _isc_permutation_test
from .matrix import _compute_cross_correlation
from .utils import _maybe_tqdm
from ..signal import (
_butter_bandpass_filter... |
5a3db2cf740e0f14bf86a549d172be0f189b6738cfc0c8f8e3495aa419820660 | Python | 17,652 | 443 | ################################################################################
# Import, Set up MPI Variables, Load Necessary Files
################################################################################
import os
from os.path import join
import sys
import matplotlib
import matplotlib.pyplot as plt
from matp... |
9a5e869d68d9f261866be4ace055a3397563235257ec70d973e1af591e8860b5 | Python | 17,656 | 443 | import io
import multiprocessing as mp
import os
import queue
import tarfile
import time
from multiprocessing.shared_memory import SharedMemory
from os import PathLike
from pathlib import Path
from typing import Optional, TypedDict
import warnings
import numpy as np
from PIL import Image
from ppafm.ocl.field import El... |
07107d1b7ec81ad28672e4f90c639b90d5231cede2bd7e7a563ce8d671a73cc0 | Python | 17,667 | 463 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
# OS stuff
import os
import sys
import warnings
from pathlib import Path
# Computational stuff
import numpy as np
import matplotlib as mplb
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec, GridSpecFromSubplotSpec
from matplotlib import font_manag... |
7d357a60a618b41d3cbc14f68edd9568141429d8767450dbf3cb0ed33a2abc23 | Python | 17,667 | 502 | # Copyright (c) 2021 PaddlePaddle 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 appli... |
202445a680891688656ba86abd325b465ee3d8c42a892863e00d0510291d5dbc | Python | 17,681 | 462 | import argparse
import json
import os
import sys
import time
import numpy as np
import psutil
from .history import History
from .optimizer import Optimizer, make_optimizer
g_log_file = sys.stderr # File used by printlog()
g_log_echo = False # True if printlog() should print to stderr.
def assert_equal(first, sec... |
6d226b12af4211653fb5a19fb447c8f03f08274aa4cfa51a1a4e99e498637063 | Python | 17,684 | 459 | import pytest
from geomstats.test.vectorization import generate_vectorization_data
from geomstats.test_cases.geometry.riemannian_metric import RiemannianMetricTestCase
from geomstats.vectorization import repeat_point
# TODO: more random tests (e.g. inner product)
# TODO: add lie algebra related tests
class _Invari... |
09a7a874b9be7d95db2b1fb57dd28cff5f0fca6c3d0c7ef96fa198c79b75c82d | Python | 17,690 | 363 | import numpy as np
import os
import sys
import NALSM_GEN_SUPPORT as sup
import GEN_NET_LIF as cLIF
class create_network:
def __init__(self,seed_IN):
self.main_Path = os.getcwd()
self.codePath = self.main_Path
self.dataPath = self.main_Path + '/networks'
np.random.seed... |
3071c96b57c31652b4cc04b66f55ac3d48ac40e543d458df61749af69d37c07d | Python | 17,691 | 480 | """Shared helpers for BrainData submodules.
These are internal utilities used by the facade and submodules — not part of the
public API.
"""
import gc
import os
import threading
from contextlib import contextmanager
import numpy as np
from numpy.typing import ArrayLike
from ..ownership import _copy_graph
#: Guard... |
36dc22e4ed873b1acd69c523e53ce0234b2b840370c672ab842b911b3728a39e | Python | 17,706 | 489 | """
Integration test for the Collection statistics wrapper methods
"""
import json
import time
from typing import Any
import pytest
from chromadb.api.client import Client as ClientCreator
from chromadb.base_types import SparseVector
from chromadb.config import System
from chromadb.test.conftest import skip_if_not_cl... |
db51d84dc30180532e24b3a201aa2f22cb7f5684aa2b74c797edfd1fbec5f34d | Python | 17,708 | 435 | # Copyright (c) 2023 PaddlePaddle 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 appli... |
3c4d94816ad89cfc627cb5b9d3a0680ceab31cccc7e72e63a2cc678631da0eae | Python | 17,719 | 461 | # Method signatures differ between Qt bindings, so overrides can't match them all
# pyright: reportIncompatibleMethodOverride=false
import logging
from collections.abc import Iterable, Sequence
from contextlib import suppress
from pathlib import Path
import numpy as np
import toml
from qtpy.QtCore import Signal # typ... |
aa59a832187b0ef8fa0758f464e00c32a0464ddbb86fb3044a91a1582109ca1b | Python | 17,720 | 467 | # Copyright (c) 2023 PaddlePaddle 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 appli... |
f0dbc619a2b79de8b9ee0fb97723385e2410fed481b78c7947b1596f8a980411 | Python | 17,749 | 443 | ################################################################################
# Import, Set up MPI Variables, Load Necessary Files
################################################################################
import os
from os.path import join
import sys
import matplotlib
import matplotlib.pyplot as plt
from matp... |
e9f3a55822aca01eca2b76fe60ee9d006a7bebe595f724af5dfc8efa3dc9d3aa | Python | 17,760 | 450 | # Method signatures differ between Qt bindings, so overrides can't match them all
# pyright: reportIncompatibleMethodOverride=false
import logging
from collections.abc import Sequence
from pathlib import Path
from typing import Any
import cv2
import toml
from qtpy.QtCore import Qt, QTimer
from qtpy.QtGui import QKeyEv... |
2ded00f9971360aafee73ecc87c41a3ac4a2d57bf484cfe35620c8c316da15e5 | Python | 17,761 | 475 | import logging
import os
import warnings
import json
from pathlib import Path
from datetime import datetime
import numpy as np
from ScanImageTiffReader import ScanImageTiffReader
with warnings.catch_warnings():
warnings.simplefilter('ignore', category=FutureWarning)
import caiman as cm
from caiman.source_... |
939bca5bbd623287fb44d329aa9c103df13e64e916a76aabd5982006839e7335 | Python | 17,765 | 516 | """CCA and PLS estimators.
"""
import warnings
import numpy as np
from scipy.linalg import svd
from scipy.stats import pearsonr
from scipy.spatial.distance import cdist
from sklearn.base import BaseEstimator
from sklearn.utils import check_array, check_consistent_length
from sklearn.utils.validation import check_is_... |
485fa83a9e373c5a96fe4382f23630e438d4dc061fe091f155cbb93ae3bc0446 | Python | 17,777 | 318 | import haiku as hk
import jax
from jax import numpy as jnp
from deeperwin.configuration import MLPConfig, TransferableAtomicOrbitalsConfig, OrbFeatureDenseGNNConfig
from deeperwin.model import MLP, antisymmetrize, symmetrize, DiffAndDistances, Embeddings
from deeperwin.model.mlp import get_rbf_features
from deeperwin.m... |
62c8d5bbbb9ce67130a30e830ab2f678bfb08131499329baa3d4eed7cd58a8ef | Python | 17,794 | 485 | #!/usr/bin/env python3
import collections.abc
import math
import warnings
from itertools import repeat
from typing import List, Optional, Tuple
import torch
import torch.nn as nn
import torch.nn.functional as F
try:
from torch import _assert
except ImportError:
def _assert(condition: bool, message: str):
... |
55da8850bf4e19dcb85bae994a9c8bdc4bcc5516f64e2a777bb776bf7eb8a1f4 | Python | 17,830 | 334 | """Small discrete Bayesian evidence classifier with exact missing-value inference.
Install the ``confidence`` extra for fitting. Missing fields are marginalized at prediction;
no evidence returns the fitted network prior. Fitted artifacts contain no receptor identities.
"""
from __future__ import annotations
import m... |
528464b2c04a6a3ed06c828a93fa879b2956fe9b14807621a0d06b97e5c83a1d | Python | 17,839 | 426 | import os
import torch
from tqdm import trange
import torch.nn as nn
from torch_geometric.data import Batch, Data
from dig.sslgraph.method.contrastive.objectives import NCE_loss, JSE_loss
class Contrastive(nn.Module):
r"""
Base class for creating contrastive learning models for either graph-level or
node... |
2f023c467bec24f15b92eaa19a037db07f71546ea78064876c3b8570f12aec09 | Python | 17,846 | 485 | from configparser import ConfigParser
import numpy as np
import zipfile
import time
from subprocess import call
import os
import pickle
import imageio
import sys
import shutil
import glob
#import matplotlib.pylab as plt
#storage_manager_folder = '../../Data/StorageManager/'
def create_folder_if_not_exist(path):
... |
9606d455557c003985cb91141c7bf630a379b18699a09ec2a1ff7e94831d3a52 | Python | 17,851 | 449 | '''
Description:
Author: voicebeer
Date: 2020-09-09 00:06:57
LastEditTime: 2021-03-25 03:27:41
'''
import torch.nn as nn
import torch.nn.functional as F
import torch
import numpy as np
import utils
class CFE(nn.Module):
def __init__(self):
super(CFE, self).__init__()
self.module = nn.Sequential... |
d5579d44bb02a76a2840ce17a12114fa765d0f8b3a3721d5dfd14a7d51858fcf | Python | 17,878 | 460 | # -*- coding: utf-8 -*-
import os
from warnings import warn
from importlib import import_module
import requests
from dival import get_standard_dataset
from dival.reconstructors import LearnedReconstructor
from dival.config import CONFIG
from dival.util.input import input_yes_no
from dival.util.download import download_... |
4fe215f1bea138c6d75b28734f3b520191b5fe895527510d19ffe190072aafb5 | Python | 17,887 | 358 | import numpy as np
from orientation_reconstruction_utilities import *
import statistics
import matplotlib.pyplot as plt
import matplotlib as mpl
import pickle
from matplotlib.lines import Line2D
#################################
# input data
#################################
eeg_lf = np.load('data/V5_eeg_lf.npy')
meg... |
b855d053e4d41406dbaef3cfcc1db09fc5ba3ce1fd066773cbb6aaeb1a223aae | Python | 17,899 | 425 | # Copyright (c) 2022 PaddlePaddle 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 appli... |
3414ed967fbbfbf3cb6a5983d6a55681a17f67e0f189f568e0d9bbc86df4152b | Python | 17,924 | 381 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
import torch
from .. import AtomicDataDict
from nequip.utils.logger import RankedLogger
import lightning
from omegaconf import OmegaConf, DictConfig, ListConfig
from hydra.utils import instantiate
impo... |
be1b575d8f33371e1e7ab3dab6ec345cb46db749273f977fe4bb75176249b43d | Python | 17,938 | 497 | # Copyright (c) Facebook, Inc. and its 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
import itertools
import json
import logging
import os
from typing import Optional
from argparse impor... |
e9c429ac3ae0bc195f65c12337ee99708dd7b273595b8fe3f267dfb23f101250 | Python | 17,947 | 400 | import numpy as np
# import tensorflow as tf
import tensorflow.compat.v1 as tf
tf.disable_v2_behavior()
import os
import sys
import time
import LSM_STDP_CONSTRUCTOR_MNIST as construct
import NALSM_PARALLEL_SAVE as parasaver
import NALSM_SIM_SUPPORT as runSupport
import NALSM_GEN_SUPPORT as sup
class run_... |
d365af19ff2e8d6cfa71843caf526ecd6dca0b1316b33090ac47a0c2ee72aa2f | Python | 17,971 | 514 | import sys
import json
from tqdm import tqdm
import pickle
sys.path.append('../')
from utils import *
from processing import *
import numpy as np
import random
from sklearn.utils.extmath import randomized_svd
from sklearn.decomposition import TruncatedSVD
from joblib import Parallel, delayed
class Subs... |
3ac3a7c1ff6ce0da480c4c7625da5daf6645d1b71fdbf0660c1569877d09579a | Python | 17,982 | 481 | # Copyright (c) 2021 PaddlePaddle 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
#
# Unl... |
3efba631859e5f411a09b77c8524ac17dd8829e74bc803c7b82066fd305afd3d | Python | 17,992 | 503 | import torch
from torch.autograd import Variable
import torch.nn.functional as F
from torch.utils import data
from torch.utils.data import SequentialSampler
from torch import nn
from tqdm import tqdm
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from time import time
from sklearn.metrics impo... |
dde96f1646839a75fb077ebd453bfe6c28575d5500fe69c973d3c97e92efbff9 | Python | 17,993 | 574 | import lightning as L
import numpy as np
import torch
from lightning.pytorch.callbacks import ModelCheckpoint
from lightning.pytorch.callbacks.early_stopping import EarlyStopping
from .linear import LinearIVAC, LinearVAC
class NonlinearIVAC:
"""Solve nonlinear IVAC using a neural network basis.
Parameters
... |
ffe2dcf26f396881fde1eab51012d8465b0fe9a0ceee3fb5df0f1e04db446043 | Python | 18,022 | 550 | "Saving and loading of trajectory files in all supported formats and versions"
import json
import logging
import pickle
from argparse import ArgumentParser
from collections.abc import Iterable
from contextlib import suppress
from pathlib import Path
from typing import Literal
import numpy as np
from h5py import Datas... |
1aa44f1afef6e8e7c3950089cc9201f8ffd3f792d90b6f41963d993f23178da2 | Python | 18,040 | 457 | import sys
import os
sys.path.append(os.path.abspath(''))
sys.path.append(os.path.abspath('..'))
import time
import datetime
import torch.nn as nn
from torchnet import meter
import pickle
import argparse
from torch_geometric.loader import DataLoader
from data_io_guassian import NeighResidue3DPoint
from GN_model_guass... |
0713d463be05835cfa83a2e80626474cd817722cbc05a134e3e515c319e4f089 | Python | 18,041 | 358 | """The interactive dashboard: one self-contained HTML file, served from GitHub Pages.
An **additive** artifact. The R document stays the shipped dashboard - `vdjdb-web` injects its
fragment into `/overview` and `summary/check_summary.py` gates it - and nothing here feeds that path.
This is the version you can interrog... |
37e2a8fde9c3e461d8a58300776d943614ef1ed0e4d11dd94fce576fcafa0f9f | Python | 18,047 | 468 | '''
Utilities for the construction of the reduced version of a
Neural Network.
'''
import torch
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
from sklearn import decomposition
from scipy import linalg
if torch.cuda.is_available():
device = torch.device('cuda')
else:
device = torch... |
4c50606bdbb34392f66fabf879413da6337d5da5c252320e7fd218d1e921de16 | Python | 18,091 | 485 | import argparse
import json
import os
import sys
import matplotlib.pyplot as plt
import nibabel as nib
import numpy as np
import pandas as pd
import seaborn as sns
from matplotlib.colors import to_rgba
from nilearn import datasets, plotting
from pydfc import data_loader
from pydfc.ml_utils import find_available_subje... |
cce198bd3b6c90c126a86707479e255dfc0f3d7cf8cb3603b373f3807565dc5f | Python | 18,131 | 454 | import numpy as np
import polars as pl
import pytest
from nltools.data import BrainData, Adjacency
class TestBrainDataCore:
"""Test BrainData dunders, properties, arithmetic, stats, indexing, append, copy, and distance."""
# ==================== Properties & Statistics ====================
def test_sha... |
7c1109752706096e33c20e8daac995014a020b6a41d1a655edead7b20fc28ccb | Python | 18,165 | 462 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import contextlib
import logging
import os
from collections import OrderedDict
from argparse import ArgumentError
import torch
from fairseq i... |
7f2e509580c7bba5da93b5d8537184d389761b6ebad8f872a3ef13e986d68434 | Python | 18,193 | 567 | #! /usr/bin/env python3
# igraph library
# Copyright (C) 2005-2021 The igraph development team
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
#... |
28b3175f7a2499e56066f4dab87e63e3f0257c35fa751468b33e5da6171e414f | Python | 18,219 | 405 | import numpy as np
# import tensorflow as tf
import tensorflow.compat.v1 as tf
tf.disable_v2_behavior()
import os
import sys
import time
import NALSM_CONSTRUCTOR_MNIST_NOISE as construct
import NALSM_PARALLEL_SAVE as parasaver
import NALSM_SIM_SUPPORT as runSupport
import NALSM_GEN_SUPPORT as sup
class r... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.