sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
b11e8d9bbce6b8fb166dab6cabd3c12200d7aecdb64c4ccba8c69effc1470a8c | Python | 39,426 | 1,125 | # 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 os
import sys
from dataclasses import _MISSING_TYPE, dataclass, field
from typing import Any, List, Optional
import torch
from omegaco... |
fd68746ace82a3883cc2aefe8b782c5e846faceb1b162447bbbf93e16a5f5035 | Python | 39,499 | 952 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import os
import sys
import warnings
from pathlib import Path
import numpy as np
import matplotlib as mplb
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec, GridSpecFromSubplotSpec
from matplotlib import font_manager as fm
from matplotlib import ... |
1ffb620948d238bd139223bdb203af8ccd8dbc9e8f59bfd2fc0700d8b8609f41 | Python | 39,819 | 1,153 | import argparse
import json
import os
import sys
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from matplotlib.ticker import MultipleLocator
sys.path.append(os.path.dirname(os.path.abspath(__file__)))
from helper_functions import ( # pyright: ignore[reportMissingImports... |
8ba6a27a7a0a415a3dea1268c45cf9e69f4e230886404b81d8003905d8321f73 | Python | 39,908 | 1,222 | """Tests for SanPy application, window, and plugin shutdown behavior."""
import gc
from functools import partial
from pathlib import Path
from types import SimpleNamespace
from typing import Any
from unittest.mock import Mock
import pytest
import pyqtgraph as pg
from matplotlib.backends.backend_qtagg import Navigatio... |
7aee6c2dba14d6d4ef45390a8ae2b3549983677d24f53d8585feaade4c695283 | Python | 40,258 | 834 | 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... |
739f53fd6b2a24900903ef311f7c0d85966acbb81339ddc916fc508920269482 | Python | 40,274 | 1,134 | import hashlib
import hypothesis
import hypothesis.strategies as st
from typing import Any, Optional, List, Dict, Union, cast, Tuple
from typing_extensions import TypedDict
import uuid
import numpy as np
import numpy.typing as npt
import chromadb.api.types as types
import re
from hypothesis.strategies._internal.strateg... |
0c88e24199e9a64c4f30f957bcf563a9fa896d7e21f95c80cc488c2b98f8652a | Python | 40,288 | 953 | # 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... |
4a7694c8390f19621ced903629922e986d3881f887f4dce9c3d99c222b3b7037 | Python | 40,288 | 1,020 | # 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... |
b6f14e8fa2a95de4d38218fef31380c6a70de770f585107e209ff83075c307ef | Python | 40,302 | 794 | # Copyright (c) 2021, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
#
# NVIDIA CORPORATION and its licensors retain all intellectual property
# and proprietary rights in and to this software, related documentation
# and any modifications thereto. Any use, reproduction, disclosure or
# distribution of this sof... |
f1f6827af1e0a54f28fde70b045cb0bcc60f46d496fca057516fffa789c89cf2 | Python | 40,455 | 1,014 | # 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 math
import sys
from typing import Dict, List, Optional
import torch
import torch.nn as nn
from torch import Tensor
from fairseq impo... |
23e01bdbdd4f6c44f44081a7e983c92aa01dc00021a3a3ad56227312c5f141e6 | Python | 40,528 | 625 | #!/usr/bin/env python3
#
# Sniffles2
# A fast structural variant caller for long-read sequencing data
#
# Created: 18.10.2021
# Author: Moritz Smolka
# Maintainer: Hermann Romanek
# Contact: sniffles@romanek.at
#
import os
import sys
import datetime
import argparse
import tempfile
from collections import... |
b2e075985a79df08f4474c6d640ac94ab0a0ce6e3ebc749a408afb38642b4045 | Python | 40,551 | 998 | # -*- coding: utf-8 -*-
import numpy as np
from scipy import stats
import copy
import functions.prediction
from sklearn.preprocessing import MinMaxScaler
from scipy.ndimage.measurements import center_of_mass
import functions.transient
import functions.time_functions as tf
def tst_v_baseline_selectivity_r... |
cefaf611604fd9426c03c802c9be1d057237abf9c74ace16b6493933a455e328 | Python | 40,559 | 991 | # 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... |
c3539679d4257608d9762e09d1052ca80ff0897508f78b00a30c47fd3e90577f | Python | 40,855 | 1,025 | """
Modelling
"""
import os
import re
import shutil
import time
import glob
from pathlib import Path
import json
import inspect
import logging
import math
import functools
from typing import *
import torch
from torch import nn
from torch.nn import functional as F
import pytorch_lightning as pl
from transformers impo... |
a802b7864b31ffe95a4764faad0a3d7766d1aa5aa0552ae4bc72535b0c07b4ac | Python | 40,860 | 1,186 | # Author: Robert H Cudmore
# Date: 20190722
import os, sys
import numpy as np
import scipy.signal
from PyQt5 import QtWidgets, QtGui, QtCore
import matplotlib
import matplotlib.figure
from matplotlib.backends import backend_qtagg
import matplotlib.pyplot as plt # abb 202012 added to set theme
import matplotlib.ticker... |
878bc7bad719e6a72d5440e8abb738bda56f8cc0b41a9d54c421894fe5997979 | Python | 40,911 | 1,145 | """Network model functions."""
# Authors: Nick Tolley <nicholas_tolley@brown.edu>
from pathlib import Path
from copy import deepcopy
import warnings
import hnn_core
from hnn_core import read_params
from .network import Network, _create_cell_coords
from .params import _short_name
from .cells_default import (
baske... |
628de5320dbdac9320627eae1e0794b525c19eb0a131cd440a70cfbb6add485c | Python | 41,177 | 708 | import torch
import torch.nn as nn
import numpy as np
from rdkit import Chem
from dig.ggraph.utils import check_chemical_validity, check_valency, calculate_min_plogp, qed
from dig.ggraph.utils import convert_radical_electrons_to_hydrogens, steric_strain_filter, zinc_molecule_filter
from .disgraphaf import DisGraphAF
... |
561fe6b15f17970bac48e9a8da675b3c4b5b275052c4be83ea100ec5629da2df | Python | 41,182 | 863 | # 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 ... |
668698e81b2474a42bb107a271cde8ce263f08704efbb0ee345a3d3187d48ed7 | Python | 41,237 | 1,081 | """Backend abstraction for CPU/GPU operations.
Supports NumPy (CPU-only) and PyTorch (CPU/CUDA/MPS) backends for linear algebra
operations, so algorithms are written once against NumPy semantics and run on a
GPU when one is available.
This module is also the package's single GPU execution layer: memory budgets
(`_dev... |
83f9b072b0d1927f7c845346a4174c2728b9467226f27ff862f33de9643c37ec | Python | 41,352 | 1,422 | import os
from copy import deepcopy
from pathlib import Path
import matplotlib.pyplot as plt
import numpy as np
# sys.path.append('./BIC_codes/')
from functions.dFC_funcs import *
from functions.post_analysis_funcs import *
print(" VISUALIZATION IN PROGRESS ... ")
################################# LOAD RESULTS ####... |
ac27b79ae7c1723308b0ad2e756c52ae280ed82a819365e63ac7534b1dc7765d | Python | 41,358 | 1,537 | import math
import glob
import logging
import os
import re
import smtplib
import ssl
import subprocess
import time
import copy
import collections
import json
import matplotlib
import matplotlib.pyplot as plt
from matplotlib.backends.backend_agg import FigureCanvasAgg
import numpy as np
import pandas as pd
import requ... |
24d56a1e2220ff567d749f1c409acc8e804da7a8c9b90b402666585a730a03d8 | Python | 41,550 | 1,092 | """Loading, resampling, writing, and uploading for `BrainData`.
Functions that resolve a mask, load data (from files, lists, URLs, HDF5, or other
`BrainData` objects), resample to a target grid, write NIfTI/HDF5, and upload to
NeuroVault. `BrainData` methods delegate here.
"""
import os
import shutil
import tempfile
... |
4b4bb16cc3e6bfd552f0e9d191a61f24b00beb2a371c5f7e443c61cb1a9e2777 | Python | 41,772 | 1,158 | """The n-dimensional hypersphere.
The n-dimensional hypersphere embedded in (n+1)-dimensional
Euclidean space.
Lead author: Nina Miolane.
"""
import logging
import math
from scipy.stats import beta
import geomstats.algebra_utils as utils
import geomstats.backend as gs
from geomstats.geometry.base import LevelSet
f... |
f83af3bfafc2cf3ebc07f96a57fd2b2dc5eeb77efc905afefbbaf736d5820e6a | Python | 41,820 | 1,203 | """
Integration test for Chroma's Task API
Tests the task creation, execution, and removal functionality
for automatically processing collections.
"""
import functools
import io
import json
import pytest
import time
import urllib.parse
import uuid
from typing import Any, Optional, cast
from chromadb.api.client import... |
821aa12328f6fd201f5c0d7dffd6b1b27f2c520a86ffa20438b1ef654f18b965 | Python | 41,879 | 1,375 | import argparse
from collections import namedtuple
from itertools import product
from typing import List, Tuple
import einops
import matplotlib.pylab as plt
import mrcfile as mrc
import numpy as np
import scipy
import torch
import torch.nn.functional as F
from numpy.typing import ArrayLike
from scipy.ndimage import co... |
18a91af8d4bb64a01b17ce2ed8eb478794c778dd3819de02328a298fee31d56a | Python | 41,937 | 1,044 | #
# For licensing see accompanying LICENSE file.
# Copyright (C) 2022 Apple Inc. All Rights Reserved.
#
import sys
import traceback
import torch
import copy
import gc
import time
import shutil
from typing import Dict
from torch.cuda.amp import autocast
from torch.nn import functional as F
import random
from typing im... |
f0a26ef602a190083af9a21ff3feef30d0c5377c9a76c410e4b6aa71df9d7fa8 | Python | 41,974 | 1,205 | # Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
# SPDX-License-Identifier: MIT-0
from typing import List, Tuple, Union
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch import Tensor
from .gvp import GVP, GVPConvLayer, LayerNorm
import dgl
INTER_PHYS_KEYS = [
"int... |
764f19b5bb4d2978cf9cc28b06cd398a88d5529e1b94e55bc440ac4afb6513f7 | Python | 42,023 | 1,005 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
import dataclasses
import torch
from torchmetrics import Metric
from nequip.data import AtomicDataDict, BaseModifier, PerAtomModifier
from .metrics import (
MeanSquaredError,
MeanAbsoluteError,
... |
9c27b73e13ea6c1592a9902056066c7424e08a4f718a9fc1949bb9dec05196b4 | Python | 42,065 | 1,118 | # Copyright (C) 2023: Max F. K. Wills & Ian C. Eperon
# FluoroTensor: identification and tracking of colocalised molecules and their stoichiometries in multi-colour single molecule imaging via deep learning
# Max F.K. Wills, Carlos Bueno Alejo, Nikolas Hundt, Andrew J. Hudson, Ian C. Eperon
# bioRxiv 2023.11.21.567874... |
b8da1d2c6664ceeed0020d0d2d3b61470a978454fadc68a2b26f71c490e1d720 | Python | 42,130 | 1,184 | import torch
import numpy as np
import pytorch_lightning as pl
from collections import defaultdict
from torch import nn
from torch.nn import functional as F
from torch.nn import Linear, ReLU
import torch_geometric
from torch_geometric.nn import (
GCNConv,
PNAConv,
VGAE,
global_mean_pool,
global_add... |
15df8fd8f450acf40c2c07c902839a0c88dc2256962bf4292eae7b32942b87b3 | Python | 42,163 | 1,230 | from typing import TYPE_CHECKING
from tenacity import retry, stop_after_attempt, retry_if_exception, wait_fixed
from chromadb.api import ServerAPI
if TYPE_CHECKING:
from chromadb.api.models.AttachedFunction import AttachedFunction
from chromadb.api.collection_configuration import (
CreateCollectionConfigurati... |
8859d0b4a1eeda5ce98fc0827e926c627f265dc08c2cb575c21aa576e1a9de2d | Python | 42,174 | 967 | import json
import logging
import os
import uuid
from datetime import timedelta
from django.core.files.base import File as djangoFile
from django.contrib.auth.models import User, AnonymousUser
from django.db.models import Q, Count
from django.utils.decorators import method_decorator
from django.views.decorators.cache ... |
95b9df11cc8da008657284f21ea61b57082191aaa0b6484e9171d8a84f57b101 | Python | 42,520 | 1,120 | """Example from pytest documentation
https://pytest.org/en/stable/example/simple.html#incremental-testing-test-steps
"""
from typing import Dict, Tuple
import copy
import pytest
import pickle
from pathlib import Path
import hnn_core
from hnn_core import (
read_params,
calcium_model,
duecker_ET_model,
... |
c94e63cb8736dead3cc412ec749529910d76bb3da8e20fc163d1f81576ee7da2 | Python | 42,529 | 1,245 | import multiprocessing
import os
import socket
import subprocess
import tempfile
import time
from typing import (
Any,
Generator,
Iterator,
List,
Optional,
Sequence,
Tuple,
Callable,
cast,
)
from uuid import UUID
import hypothesis
import pytest
import uvicorn
from httpx import Conne... |
a5fa8afbabddb7712c252118560754f4f850adaf3249e4ae57167a683026d48c | Python | 42,636 | 1,149 | """
Author: Arnaud Desvachez --<arnaud.desvachez@gmail.com>
Purpose: Defines the path search class.
It is required due to the dynamic loading of parameters/widgets.
One cannot connect the clicked of the button to write in the QLineEdit
Created: 4/09/2019
"""
import os
import pickle
from glob import glob
... |
54d34ccf9f7b8e20c40d30a0ab7a450b9b1c72b5cfedb71f6f3a80d4fe23dde8 | Python | 42,755 | 1,056 | """pfl3_im.py
Analysis and plotting functions for PFL3_LAL_imaging.ipynb
"""
import os
import numpy as np
import pandas as pd
import matplotlib as mpl
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
import scipy as sc
from scipy.interpolate import interp1d
import analysis_plot as ap
import fun... |
4776325da2290072f8c561a7678751cb6966bee2d3000615912312ed5eb5dce9 | Python | 42,798 | 1,181 | """Establish class def for general cell features."""
# Authors: Mainak Jas <mjas@mgh.harvard.edu>
# Sam Neymotin <samnemo@gmail.com>
from copy import deepcopy
import numpy as np
from numpy.linalg import norm
from neuron import h, nrn
from .viz import plot_cell_morphology
from .externals.mne import _valida... |
f5756a1b86ca10d45b9078795c33697578a9b801151edd461739ab523ca5dc62 | Python | 42,878 | 1,193 | from abc import ABC
from typing import Union, Optional, Sequence
import torch
from torch import optim
import numpy as np
from ..network.nodes import SRM0Nodes
from ..network.topology import (
AbstractConnection,
Connection,
Conv2dConnection,
LocalConnection,
)
from ..utils import im2col_indices
clas... |
073a3251ddbc52ffad47c3028993e7299e2063df1f54d8d1f409d117ca4e41a6 | Python | 42,882 | 1,161 | """analysis_plot.py
Common analyses and plotting functions
"""
import numpy as np
import matplotlib.gridspec as gridspec
import matplotlib.pyplot as plt
import pandas as pd
from simplification.cutil import simplify_coords_idx
from scipy import stats, ndimage
from scipy.signal import find_peaks
import sqlite3
import... |
0564867e45d5880190b6f59c2b3806068920b223460a9d88ed2e3ed3091a43c5 | Python | 42,968 | 1,075 | import json
import logging
from collections.abc import Iterable, Sequence
from datetime import datetime
from importlib import metadata
from itertools import count, pairwise
from math import sqrt
from os import cpu_count
from pathlib import Path
from statistics import fmean
from typing import Any, Literal
import cv2
im... |
11d6d737badb553c4c4c0519bc4bc08fb076eb7ec1e70e6c04825950dcc8bde0 | Python | 43,011 | 1,133 | import logging
import sys
from collections.abc import Sequence
from datetime import datetime
from enum import Enum
from pathlib import Path
from time import sleep
import numpy as np
import toml
from qtpy.QtCore import Signal # type: ignore[reportPrivateImportUsage]
from qtpy.QtCore import Qt, QThread
from qtpy.QtGui ... |
51167692951babe4a848893d3a41e0cdd2acc94b4b2a7d12de30af2c6cf916c3 | Python | 43,133 | 796 | """TCREMP: cluster CDR3s by where they land in a prototype-distance embedding.
The second motif method, run beside :mod:`vdjdb.motifs.tcrnet` rather than instead of it. TCRNET
asks whether a clonotype has more neighbours than a background repertoire explains, which only sees
sequences that are literally one substituti... |
76175a1fc386a52302c454e1917cfc1bedbd6444331be7b31d6636e387358bae | Python | 43,164 | 1,042 | """Polars-based design matrix for neuroimaging analysis.
`DesignMatrix` wraps a Polars DataFrame with neuroimaging metadata (sampling
frequency, which columns are HRF-convolved, which are confounds) and offers
HRF convolution, resampling, polynomial and cosine drift regressors, multi-run
concatenation, and collinearit... |
06cf687238fb55bf06225123682f48540e9b0b9c958feea921bf64bab0261007 | Python | 43,173 | 1,352 | """The manifold of full-rank correlation matrices.
Lead authors: Yann Thanwerdas and Olivier Bisson.
References
----------
.. [T2022] Yann Thanwerdas. Riemannian and stratified
geometries on covariance and correlation matrices. Differential
Geometry [math.DG]. Université Côte d'Azur, 2022.
"""
import logging... |
bfc3e23eb832be0c79551c51afeb4a27a82659d69ce343e7be64ca6bbcade593 | Python | 43,189 | 1,456 | ###########################################################################################
# Parsing functionalities
# Authors: Ilyes Batatia, Gregor Simm, David Kovacs
# This program is distributed under the MIT License (see MIT.md)
#####################################################################################... |
0be6d12a0c52d27b8f6650739884281cb462860eda75d79d5e702e6d66c2968a | Python | 43,259 | 1,029 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
"""
Basic and energy-specific model test mixins.
These mixins provide core functionality tests and energy model-specific tests.
They can be composed with other test mixins (compilation, integrations) a... |
a45e7dd9df9b576f92465396a456d1a0f8cebebb3f6050f01efd275cd3bd997c | Python | 43,321 | 1,348 | import keras
from keras.preprocessing.text import Tokenizer
from keras.preprocessing.sequence import pad_sequences
from keras.layers import Dense, Dropout, Merge, Input
from keras.callbacks import ModelCheckpoint, EarlyStopping
from sklearn import metrics
from keras import optimizers
from gensim.models import Word2Vec
... |
9cf640b9b7f8c8a4d892087644aa315b6e2b8d0aba690488642f6ce5672f9b47 | Python | 43,350 | 1,043 | #!/usr/bin/env python3
import typing
import warnings
from typing import Any, Callable, List, Tuple, Union, cast
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch import Tensor
from torch.nn import Module
from torch.utils.hooks import RemovableHandle
from captum.attr._uti... |
072b82d10f9f083b1b87be9c3af182800de70b7d05f7e6b41fa4305966953717 | Python | 43,411 | 964 | # 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... |
670b9c3fc5ba5fdc98c7e6dc6b505e36884a4542203fcae58a16df0a20e3d467 | Python | 43,443 | 1,044 | import os
import typing
import warnings
import tqdm
import copy
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
import torch
import torch.nn as nn
import torch.optim as optim
from . import utils
from . import pc_layer
class PCTrainer(object):
"""A trainer for predict... |
a97951fc1c48fd02f8ed2eb32b7215bfcce14b8f82a31e59382c06f12505b959 | Python | 43,514 | 1,284 | # 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 math
from dataclasses import dataclass, field
from typing import List, Tuple
import numpy as np
import torch
import torch.nn as nn
imp... |
69b867da8eea2433cb475f27f4a6035595f1b094e0bec717a7bd8335081f8d05 | Python | 43,550 | 1,039 | import json
import logging
from abc import abstractmethod
from dataclasses import field
from functools import cached_property
from typing import Literal, Optional, Union
from typing_extensions import Annotated, override
import numpy as np
import pydantic
from pydantic import ConfigDict, Field
from pydantic.dataclasses... |
1b9c9de2ee73461b42331a9803e685e1989b898903e34500133aacad4c00b9b7 | Python | 43,769 | 1,362 | import math
import enum
# Error if we use 'from functools import partial'
# Error shows up in sanpy.bPlugin when it tries to grab <plugin>.myHumanName ???
import functools
from typing import Union, Dict, List, Tuple, Optional, Optional
from matplotlib.backends import backend_qtagg
import matplotlib as mpl
import mat... |
12153d079a7a6bcd11bc159234d3de058b270ca447f3b3048b82a6a438ea612e | Python | 44,214 | 1,527 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Feb 8 2023
@author: mte
"""
import math
import os
import sys
import warnings
from copy import deepcopy
from math import ceil
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import scipy.cluster.hierarchy... |
3c88cd468c5a89da2d28c3b59f508020e552e27e157b58b757563abed08fad35 | Python | 44,309 | 1,232 | """Class for the BHV Tree Space.
Lead author: Jonas Lueg
References
----------
.. [BHV01] Billera, L. J., S. P. Holmes, K. Vogtmann.
"Geometry of the Space of Phylogenetic Trees."
Advances in Applied Mathematics,
volume 27, issue 4, pages 733-767, 2001.
https://doi.org/10.1006%2Faama.2001.0759
.. [OP1... |
6bf64bd6005bec828e2f6fee35f79831353119cd13908065802df3595a663c0b | Python | 44,342 | 1,144 | """Tests for BrainData.predict() — kwargs API returning PredictResult dataclass."""
import inspect
import numpy as np
import pytest
from sklearn.base import BaseEstimator
from sklearn.model_selection import (
LeaveOneGroupOut,
StratifiedKFold,
)
from nltools.data import PredictResult
from nltools.data.braind... |
ce51255098cde92a8613d42362d14e07edcce77b3715572249a3cf75273ba1e2 | Python | 44,686 | 817 | """IMGT segment nomenclature (#389), driven by the authority table rather than a hand-written map.
``proofreading/imgt_alleles.tsv.gz`` is the authority: 5,342 alleles across the species VDJdb
covers. This module reads it.
Nothing is invented and nothing is guessed between two candidates. A call that IMGT already kno... |
8172395745ad26654eb39883143b5805eff2be12dd03ea62e27b8ac26e6f79ef | Python | 44,718 | 933 | # -*- coding: utf-8 -*-
"""Tools for the evaluation of reconstruction methods.
"""
import sys
from warnings import warn
from itertools import product
from math import ceil
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from tqdm import tqdm
from dival.util.odl_utility import CallbackStoreAfter
f... |
d1ad3a6d4ea9a47ab7867df6d602434195c7516bf3bd3df9a6b0ef488a8f557a | Python | 44,790 | 1,219 | """
Contains source code for loading in data and creating requisite PyTorch
data loader object
"""
import json
import pickle
import hashlib
import functools
import multiprocessing
import os
import glob
import logging
from pathlib import Path
from typing import *
from matplotlib import pyplot as plt
import numpy as np... |
6516eede1138b91ef49709fabb77e60d6488dfaf811545a5c7149c658caca0de | Python | 44,964 | 1,129 | # import os.path as op
# import tempfile
from unittest.mock import patch
import matplotlib
from matplotlib import backend_bases
import matplotlib.pyplot as plt
from matplotlib.colorbar import Colorbar
import numpy as np
from numpy.testing import assert_allclose
import pytest
# from hnn_core import read_spikes
from hn... |
bad9c5dab5cac00f7f98a9a04866ca72a4274cd1922ecba11073b5eb30557cc8 | Python | 44,990 | 1,213 | from brian2 import *
from mpl3d import glm # https://github.com/rougier/matplotlib-3d
from mpl3d.camera import Camera
# -----------
import numpy as np
import matplotlib as mplb
from scipy import signal as sig
from matplotlib import ticker
from matplotlib import colors
from matplotlib import font_manager... |
7f725baed395e07ffb4b0e4ec97d1ed8f357945100e51e184e520f7b5f3fb7ee | Python | 45,052 | 880 | #!/usr/bin/env python3
import os
import logging
import json
from logging import StreamHandler, FileHandler
from lib.designer_input_utils import get_input_info, convert_input_data, create_shell_table, assert_inputs
from lib.designer_fit_wrappers import refit_or_smooth, save_params
from lib.io import load_mrtrix
from mr... |
46280159aa7e71cd1cec658088ac20cbb052f8b1f9f47ca4bedf8e13fdcedd40 | Python | 45,129 | 1,283 | from pathlib import Path
import numpy as np
import pytest
import torch
import torch.nn.functional
from ase.build import molecule
from e3nn import o3
from e3nn.util import jit
from scipy.spatial.transform import Rotation as R
from mace import data, modules, tools
from tests.helpers import REPO_ROOT
from mace.calculato... |
1b3265263b91004c268a15bdf7d9571c1cfdff274c8ed9995f39c0bfbad762c9 | Python | 45,474 | 979 | import pickle
import pandas as pd
import numpy as np
import os
import warnings
import sys
import shutil
from tqdm import tqdm, trange
import random
import torch
from torch_geometric.data import InMemoryDataset, Data
import prettytable as pt
import math
import argparse
warnings.simplefilter(action='ignore', category=Fu... |
dab827c32b49ad7e20f8e1c33d0538397cc6937bee85f01acf6318f15e934da1 | Python | 45,868 | 772 | import os
import numpy as np
import torch
import torch.nn as nn
from rdkit import Chem
from dig.ggraph.utils import check_chemical_validity, check_valency, calculate_min_plogp, qed
from dig.ggraph.utils import convert_radical_electrons_to_hydrogens, steric_strain_filter, zinc_molecule_filter
from .graphaf import Masked... |
09ff9ee370ff9e49e081f820e502effcc524ae4a25b74cdbea167a7c2da29620 | Python | 46,015 | 1,313 | import torch
import torch.nn as nn
import globals
from collections import OrderedDict
from typing import Dict, Callable
Detached=True
def GlobalWeightedRankPooling(x,d=0.9):
x,_=torch.sort(x.view(x.shape[0],x.shape[1],x.shape[2],
x.shape[3]*x.shape[4]),
... |
5074f476d84adb76c17dde168f808a83df996e4ef8195ef8a362938407fc2cf0 | Python | 46,296 | 1,255 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
from brian2 import *
import brian2cuda
from scipy.spatial import distance as dst
from scipy.spatial.transform import Rotation as R
# from tqdm import tqdm
from random import sample as smplf
import os
import time
import sys
from shutil import copyfile
import argparse
impo... |
37faf7227461a1ee62c155b4cdec2fd73c4a346ccf08647fa03d271c3fc71b33 | Python | 46,767 | 1,376 | """The special Euclidean group SE(n).
i.e. the Lie group of rigid transformations in n dimensions.
Lead authors: Nicolas Guigui and Nina Miolane.
"""
import math
import geomstats.algebra_utils as utils
import geomstats.backend as gs
from geomstats.geometry.base import LevelSet
from geomstats.geometry.euclidean impo... |
d560716d6c33db2cc59111c4b993d16b8ada8309662e6b9d4c12d82b9020365d | Python | 46,849 | 1,105 | '''
Utilities for the transformations needed inside a CNN and performing
object detection
'''
import random
import torch
import torch.nn.functional as F
import torchvision.transforms.functional as FT
import numpy as np
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
def decimate(tensor, m):
... |
741388d2bd6621b2538d39ccf4f819a9891e46a31f37b4aa3f8e11bfd0c14d8b | Python | 46,925 | 976 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
"""
Train a YOLOv5 model on a custom dataset. Models and datasets download automatically from the latest YOLOv5 release.
Usage - Single-GPU training:
$ python train.py --data coco128.yaml --weights yolov5s.pt --img 640 # from pretrained (recommen... |
bd45cc4c769709101877c17f86f6bb80b3ff2d8a691934e2287a08732193446d | Python | 47,023 | 930 | """Comparison of a candidate build against a released bundle.
``vdjdb diff <reference> <candidate>`` compares a released bundle against a freshly built one in
three passes:
1. **file set** -- exact names and count;
2. **two digests per file** -- raw sha256 and *canonical* sha256 (data rows sorted). Canonical
equal... |
fa99a8326a494eeba8cc50b059317daa98c4a2bf5c42557cca5932dbca5c1bad | Python | 47,065 | 1,202 | """The CLI-observable contract of the legacy stack.
These tests are written once and re-used verbatim: the rewrite may change the
syntax of the command line, but the semantics pinned here are the user
contract it has to honour, and the live parity run re-executes this file with
the engine switched rather than porting ... |
52669a93b032497c0fa920ee81a67d9523db72d75d9f00abc31806d5cffae254 | Python | 47,468 | 1,336 | """Default cell models."""
# Authors: Mainak Jas <mjas@mgh.harvard.edu>
# Sam Neymotin <samnemo@gmail.com>
import numpy as np
from functools import partial
from .cell import Cell, Section
from .params import compare_dictionaries
from .params_default import (
get_L2Pyr_params_default,
get_L5Pyr_param... |
9b3193d91d617a6c9e6ef49896dc8612cbcbb67c146d0a76ce16bf2b64dac86f | Python | 47,810 | 1,080 | # 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
#
# Unle... |
fc7e2f16c7fd08c60d50317b8264afb439dbc70c85c89b5ab7d799463323bc4e | Python | 48,050 | 1,210 | # +
from copy import deepcopy
def flatten_list(nested_list):
"""Flatten an arbitrarily nested list, without recursion (to avoid
stack overflows). Returns a new list, the original list is unchanged.
>> list(flatten_list([1, 2, 3, [4], [], [[[[[[[[[5]]]]]]]]]]))
[1, 2, 3, 4, 5]
>> list(flatten_list([... |
60136e5093246362e26fc4c9df35ab1185d7061400407adc482e9cb9605ac39c | Python | 48,178 | 936 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Sep 16 12:41:34 2019
@author: mmolina
"""
import os
import numpy as np
import torch
import torch.utils.data
from PIL import Image, ImageFile
import torch
from collections import OrderedDict
import torchvision_05
from torchvision_05.models.detection.rp... |
4eb582d3765ba49c9ba86bd97930eeb1d113dd936006caec53901e39e204c8a7 | Python | 48,211 | 974 | import numpy as np
from .SharedTrees import cstr, get_fmt, Description, AmplifierState_v9, LockInParams_v9, UserParamDescrType
from .SharedTrees import \
get_segment_class, \
get_data_kind, \
get_seg_store_type, \
get_leak_comp_type, \
get_break_type, \
get_leak_hold_type, \
get_lea... |
bf142575108192d575d0b66eea4afa45b2595b1bbbef651c1ffb7f97c6fae938 | Python | 48,271 | 918 | # %%
import sys
import os
import cv2
import math
import numpy as np
import time
import h5py
import pyfftw
from scipy import sparse
from scipy.io import savemat, loadmat
import multiprocessing as mp
# sys.path.insert(1, '../..') # the path containing "suns" folder
os.environ['KERAS_BACKEND'] = 'tensorflow'
# os.enviro... |
6568df9bfbb187f88594a38dcc2c13281635ef17f1089ce523120ffc06e3da0c | Python | 48,511 | 1,270 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
from brian2 import *
from scipy.spatial import distance as dst
from scipy.spatial.transform import Rotation as R
from random import sample as smplf
import os
import time
import sys
from shutil import copyfile
import argparse
import parameters
import re # regular expressi... |
e36ee9077f71fd4accee7b77a065ffa3fdcf0764edb77323dce8765d531846bb | Python | 48,852 | 1,038 |
import os, sys, argparse
import serial, datetime, time
from transitions import Machine
from transitions.extensions.states import add_state_features, Timeout, State
import random, copy
import numpy as np
from collections import Counter
# #gpio.setmode(gpio.BOARD)
# GPIOChans = [33,35,36,37,38,40]
# IRD_GPIOChan_Map = ... |
d1644dc5bfff7123bc622a5070fce27bc9fb6d6420622d8a59257591f57e31fb | Python | 48,861 | 1,180 | #!/usr/bin/env python3
"""Chain co-occurrence graph for the four-donor Immudex dCODE matrices.
A node is one chain (locus + V + J + CDR3). An edge is two chains in the same
cell barcode, carrying both UMI counts. A cell carries one beta and up to two
alphas; any further chain is the contamination slot. The ambient rat... |
8b665918c408506862e88741d8b893753ca8ab536ccf729847d22be75ba18f06 | Python | 48,862 | 1,198 | # 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... |
1b7ed40d88143a18aeae04aac69633e47fed5da6d0a35272dba271575e7fcad0 | Python | 48,942 | 1,413 | import numpy as np
from sklearn.decomposition import PCA
import matplotlib.pyplot as plt
from sklearn import mixture
import torch
from matplotlib import colors
import os, sys
file_dir = os.path.dirname(__file__)
sys.path.append(file_dir)
from model import *
sys.path.append(os.path.dirname(os.path.realpath(__file__)) + ... |
c5d4cf0521528ff63a92c39af03a16830c091f90b0c21f2b58e650a7059613e2 | Python | 49,289 | 1,271 | # +
from copy import deepcopy
def flatten_list(nested_list):
"""Flatten an arbitrarily nested list, without recursion (to avoid
stack overflows). Returns a new list, the original list is unchanged.
>> list(flatten_list([1, 2, 3, [4], [], [[[[[[[[[5]]]]]]]]]]))
[1, 2, 3, 4, 5]
>> list(flatten_list([... |
8868e80b9b3d99ce96ab9de7186e8194fa6e0fa98744d5859253218b69b9d4a0 | Python | 49,389 | 1,327 | """Left- and right- invariant metrics that exist on Lie groups.
Lead authors: Nicolas Guigui and Nina Miolane.
"""
import geomstats.backend as gs
from geomstats.geometry.matrices import Matrices
from geomstats.geometry.riemannian_metric import RiemannianMetric
from geomstats.integrator import integrate
from geomstats... |
b2706de826abf0177942fbf85b8173e1d0d91f93c614835edbf840ef95792c78 | Python | 49,459 | 1,294 | """Add-ons for sample analyzers.
"""
import warnings
from functools import partial
import numpy as np
import xarray as xr
from scipy.spatial.distance import cosine as cos_dist, cdist
from scipy.stats import spearmanr, pearsonr
from sklearn.decomposition import PCA
from sklearn.model_selection import cross_validate
... |
dcf5e6e6a89574f55168f2b4d5e7280db4fb80da2f5cf03b3def70686ffcb794 | Python | 49,823 | 1,373 | """
tensorflow/keras utilities for the neuron project
If you use this code, please cite
Dalca AV, Guttag J, Sabuncu MR
Anatomical Priors in Convolutional Networks for Unsupervised Biomedical Segmentation,
CVPR 2018
or for the transformation/interpolation related functions:
Unsupervised Learning for Fast ... |
68a21198f984b202d825081e300c759d01e74930f7c2d6801b55c27f43c07613 | Python | 49,901 | 1,266 | """BrainData prediction — timeseries (encoding) and MVPA (decoding).
Single entry point: `predict`. It resolves exactly one mode, validates every
argument for that mode, and returns either a new `BrainData` (fitted-model
prediction) or a frozen `PredictResult` record (MVPA). Nothing is attached to the
source object.
"... |
3fc7f49dc93d47dded6bb7c36cba9f73c0600e1570b4d5838cbe9648dd637744 | Python | 50,056 | 1,582 | """Exposes the `SpecialOrthogonal` group class.
Lead authors: Nicolas Guigui and Nina Miolane.
"""
import geomstats.algebra_utils as utils
import geomstats.backend as gs
from geomstats.geometry.base import LevelSet
from geomstats.geometry.general_linear import GeneralLinear
from geomstats.geometry.hermitian_matrices ... |
fa6fd94d6a3d44a223538ccb7c585380823264685046d3167c2d5be968d814c6 | Python | 50,100 | 1,201 | # 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... |
71db078407cf6402abf37cbacd8b2283ce16a24b35cedcc0e5532dee3bf99635 | Python | 50,547 | 1,000 | ################################################################################
# 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... |
9bbe5abc45403d0309a8b4203cc75fc2bed807c6e1bb28811be68a9590c75ccf | Python | 50,662 | 1,228 | ###########################################################################################
# Training utils
# Authors: David Kovacs, Ilyes Batatia
# This program is distributed under the MIT License (see MIT.md)
###########################################################################################
import argpars... |
f46647c92f3e6d72c7dc38945c07755893ed68de8216c9946b6f96203aa78087 | Python | 50,889 | 1,216 | """Module that defines losses to train a model."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import numpy as np
import tensorflow as tf
from sleeprnn.common import constants
def get_border_weights_quad(labels, amplitude, half_width):
print(
... |
85f22c20dbc33a7c666ced3985b7049a446b3349152c0825ab8e353f1a6751c1 | Python | 51,381 | 1,360 | # 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 app... |
5b6fc6c97c04ee4e3bf8f61231e8659ac10990307c78eff1e3c4cb72b3ebb634 | Python | 51,408 | 1,278 | # 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... |
aeb8de1d9dfa35a919a9572c2c7b425a05f81f7501994b9485d5c9dbcb343267 | Python | 51,423 | 1,161 | # 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
#
# Un... |
7215a0e3ee5b8d231fa4b4c30418ec4841acdf42bbe55228c6413d11dd39fda2 | Python | 51,612 | 1,537 | """The MACE v1.0 disposition table: every surface v1 removes or replaces.
Generated from the rewrite's feature inventory, which carries a KEEP / MERGE /
DROP disposition and a reason for every enumerable surface of this package. Only
the non-KEEP rows are reproduced here, because those are the ones a 0.3.x user has
to... |
9021c71f8d61d496de7077e344988a6260cf779ac7e4e036029b38e7c2a10fa3 | Python | 51,626 | 1,192 | # 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... |
6c2148b4644d3b08a2bec92e0633e6426ccbc2f80a90272cc0d44072e7bf7f1b | Python | 51,636 | 1,501 | """Manage folder-backed collections of SanPy recording analyses."""
# Acknowledgements:
# Author: Robert H Cudmore
# Date: 20210603
import os
import time
import copy # For copy.deepcopy() of bAnalysis
# import uuid # to generate unique key on bAnalysis spike detect
import pathlib # ned to use this (introduced in P... |
82858d5833df54c6d3b93bc01fa095c1d6d97b97ac043431f78d366e27bc8bde | Python | 51,783 | 1,458 | """Discrete Surfaces with Elastic metrics.
Lead authors: Emmanuel Hartman, Adele Myers.
References
----------
.. [HSKCB2022] Emmanuel Hartman, Yashil Sukurdeep, Eric Klassen,
Nicolas Charon, and Martin Bauer.
"Elastic shape analysis of surfaces with second-order Sobolev metrics:
a comprehensive numerical ... |
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