sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
230d976f1931333d4259b2fe9839681336fabfcb921d2d12e9704e30cb36613b | Python | 12,694 | 383 | """Test estimator, kerneltransformer, and multiple comparisons corrector performance."""
import os
from contextlib import ExitStack as does_not_raise
import numpy as np
import pytest
from ..correct import FDRCorrector, FWECorrector
from ..generate import create_coordinate_dataset
from ..meta import ale, kernel, mkda
... |
91e00e18a381aea97c0990b1252105d855a843c44fce349a123e0d05cf80bb87 | Python | 12,696 | 325 | #! /usr/bin/env python3
# Usage:
# techtree.py <depfile>
#
# Where input <depfile> is created in Easel directory by clang preprocessing:
# for cfile in esl_*.c easel.c; do clang -MM -c -I. -DeslENABLE_AVX -DeslENABLE_AVX512 -DeslENABLE_VMX -DeslENABLE_NEON -DeslENABLE_SSE -DHAVE_MPI ${cfile} >> easel.dep; done ... |
c148b6dc118df9c34460bb74a6f90c8da8b6e27b1a6394bc20fa585d73c4295b | Python | 12,699 | 412 | """Performs power analysis on pre-processed data.
METHODS
-------
morlet_analysis
- Takes a coh_signal.Signal object of pre-processed data and performs Morlet
wavelet power analysis.
fooof_analysis
- Takes a coh_signal.PowerMorlet object of power data and performs FOOOF power
analysis.
"""
import os
impo... |
a86bcccd3f041ac81a1d6f349d537ee1049c6afa4d799b9293b410da4409f038 | Python | 12,707 | 392 | from collections.abc import Callable
import copy
from datetime import datetime
import operator
import re
import numpy as np
import pytest
from pandas._libs.properties import cache_readonly
import pandas as pd
import pandas._testing as tm
from pandas.api.typing import Expression
from pandas.tests.test_register_access... |
383b695d9745632e354dd03f99a3c11700098535cd7928116fd1cb68da5eb87c | Python | 12,709 | 282 | """Tests for the hot-loop performance batch: replay/experience buffer pinning
removal, disabled GradScaler under bf16 autocast, SAC submodule compilation,
and batched score-observer updates."""
import numpy as np
import pytest
import torch
from types import SimpleNamespace
from rl_games.algos_torch import torch_ext
f... |
63f6ee8305a09ae26b46ac2433b8753a946bb9e21074f276df7da1eb6601e078 | Python | 12,712 | 263 |
"""
Call variant based on a list of SAMMPileUpRecord where list[i] is the record of i-th position
Most of the code follows Juliet's code at
https://github.com/PacificBiosciences/minorseq/blob/develop/src/AminoAcidCaller.cpp
"""
import os, sys
import scipy.stats as stats
from collections import Counter, namedtuple
B... |
be39345db535f38acd711d596223b5af14478fc24aec316942b2a77783cf3258 | Python | 12,724 | 355 | """Color routines."""
# ------------------------------------------------------------------------------
# Imports
# ------------------------------------------------------------------------------
import logging
import colorcet as cc
import numpy as np
from matplotlib.colors import hsv_to_rgb, rgb_to_hsv
from numpy.ran... |
f17cc95126740216a2d978aa2c3f41aca3f548a5603cd4a2f592b222dcf78a86 | Python | 12,726 | 444 | """
Additional tests for NumpyExtensionArray that aren't covered by
the interface tests.
"""
import numpy as np
import pytest
from pandas.errors import Pandas4Warning
from pandas.core.dtypes.dtypes import NumpyEADtype
import pandas as pd
import pandas._testing as tm
from pandas.arrays import NumpyExtensionArray
@... |
2ca1097dda4103ea646f571f0fa222a50e6762955a2f0c59a1619d224c8df811 | Python | 12,731 | 383 | """Test estimator, kerneltransformer, and multiple comparisons corrector performance."""
import os
from contextlib import ExitStack as does_not_raise
import numpy as np
import pytest
from nimare.correct import FDRCorrector, FWECorrector
from nimare.generate import create_coordinate_dataset
from nimare.meta import ale... |
8f47867f0a611ad277bd494cb46f7aea824f02b986e4716bc96d0088e22cc412 | Python | 12,738 | 324 | # Copyright (c) 2018-2023, NVIDIA Corporation
# 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 condit... |
c4bebe124f70bf7d10409c8493bbad6bc6050d64b1b1b638a410ac4dde41fb83 | Python | 12,747 | 393 | from collections.abc import Callable
import copy
from datetime import datetime
import operator
import re
from typing import Any
import numpy as np
import pytest
from pandas._libs.properties import cache_readonly
import pandas as pd
import pandas._testing as tm
from pandas.api.typing import Expression
from pandas.tes... |
bd5d3de2ad008fa4451d09df577c50abbf5695770ddfda9722f6068c6d5386d4 | Python | 12,750 | 363 | """
Tests for 2D compatibility.
"""
import numpy as np
import pytest
from pandas._libs.missing import is_matching_na
from pandas.core.dtypes.common import (
is_bool_dtype,
is_integer_dtype,
)
import pandas as pd
import pandas._testing as tm
from pandas.core.arrays.integer import NUMPY_INT_TO_DTYPE
class D... |
4cbbc9f9e93417aa911c4cfdda257ebfc52e6f3f7c4d67c495f90dc7bb4e29c5 | Python | 12,765 | 376 | ''' load_codex_to_mongo.py
This program update emBody and emDataSet in MongoDB from the classification.csv
data from Codex (https://codex.flywire.ai/api/download)
'''
__version__ = '0.0.1'
import argparse
import csv
from datetime import datetime
from operator import attrgetter
import socket
import sys
import t... |
51c303a0a4a7e72b22667ed0043d1454155e440d9a0b87cc98743190a5e57569 | Python | 12,770 | 380 | import math
import warnings
import numpy as np
import SimpleITK as sitk
import torch
from scipy import interpolate
TABULAR_NAMES = [
"AVA",
"Age",
"Aortic_regurgitation",
"BMI",
"Creatinine",
"Glomerular_filtration_rate",
"Hemoglobin",
"LVEF",
"Mean_transaortic_pressure_gradient",... |
bd702b59d679808bc5c8c0a3ce4f5f4fc67c70a420fcf6fcbb0587a19c1312b3 | Python | 12,770 | 183 | from pathlib import Path
from botocore.client import Config
import ibm_boto3
import os
import pandas as pd
import sys
sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..")))
from load_db.AIBL import extract_sympt... |
36d7acba718e947edaa1befbd906395368c0feb83ac263f603005175b6321cd6 | Python | 12,772 | 402 | # -*- encoding: utf-8 -*-
# last change: 2015-07-27, dynamic ylim in plots
# JN 2015-04-15
"""
reads out all clusters from sessions and puts them into one file
for final grouping
"""
from __future__ import print_function, division, absolute_import
import os
import logging
import numpy as np
# pylint: disable=E1101
im... |
c15be04f5830b25e84be70110e957fee1a0a5e442b27d2057fee36cab4356d6c | Python | 12,773 | 339 | # Copyright 2018-2023 Xanadu Quantum Technologies Inc.
# 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... |
84536ba89e41b37f0acbb827cde6dbf8c04734fe7d7bed342ceb9085aab309a9 | Python | 12,779 | 288 | from spycon.spycon_inference import SpikeConnectivityInference
# Import classes
from idtxl.estimators_jidt import JidtDiscreteTE
from itertools import repeat
import multiprocessing
import numpy
from scipy.stats import norm
from tqdm import tqdm
class TE_IDTXL(SpikeConnectivityInference):
"""
Transfer entrop... |
6991cf882d504e7dbb2bd7e5251c070421441ec34a689bf83934fbb5da3f9cf8 | Python | 12,792 | 258 | from botocore.client import Config
import ibm_boto3
import os
import pandas as pd
import numpy as np
import sys
import json
import logging
sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..")))
from config.global... |
58c7edb2daccbb813c20ef95e5e9c10c4d7e9fe2d79d2dc8ca1ea04833010ba7 | Python | 12,793 | 377 | import math
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
import pandas.core.common as com
class TestCategoricalIndexingWithFactor:
def test_getitem(self):
factor = pd.Categorical(["a", "b", "b", "a", "a", "c", "c", "c"], ordered=True)
assert factor[0] == "a"
... |
cd68d34de73d0cd5f6babbe605d977f924ba94301bf75208c65192847039b918 | Python | 12,793 | 341 | # Copyright 2024 Xanadu Quantum Technologies Inc.
# 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 agre... |
7658938eec6538e4d8722677e5399f7dd1b35e0bb370299b842fb920576d7be9 | Python | 12,797 | 314 | import re
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.utils.checkpoint as cp
from collections import OrderedDict
from torchvision._internally_replaced_utils import load_state_dict_from_url
from torch import Tensor
from typing import Any, List, Tuple
__all__ = ['DenseNet', 'densenet... |
d71d19cd65f8a0f73d12ffd7e6b36a62e06d7bc88e3213d1e946e5435e1f4efb | Python | 12,797 | 322 | # Copyright 2018-2024 Xanadu Quantum Technologies Inc.
# 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... |
d170dbae5c3a262e4ad6ad58537628789d7dee9273adbd5e57b6ef71eed03ec2 | Python | 12,798 | 359 | # -*- coding: utf-8 -*-
"""
Created on Tue Feb 14 11:11:06 2023
Figure 3. Dorsal striatal neurons encoding single-limb phase angle, body speed,
and start/stop of walking.
@author: lonya
"""
#%% Load Data
import tkinter as tk
import tkinter.filedialog as fd
import numpy as np
import os
import matplotlib... |
f9b1db94cb2d6e18654ad7f960410b040c3dc197bb37ec1dec67ea0df7f5496a | Python | 12,800 | 440 | #!/usr/bin/env python
# _*_ coding: utf-8 _*_
import socket
import threading
import math
import numpy as np
from collections import deque
from scipy import signal
from loguru import logger
from sklearn.utils import resample
from .NeuroScanMessage import NeuroScanMessage
class NeuroScanEEGThread(threadi... |
3ceb17cd0fe831a32e05088d9b061d821cf8a4478ae5af2bd167be5a7e8e8c04 | Python | 12,801 | 358 | # Copyright 2018-2020 Xanadu Quantum Technologies Inc.
# 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... |
bd534afb61bd032ecfd5b1d4d08fa0bafd3c257638364243409045e87d540950 | Python | 12,805 | 245 | import sys
sys.path.append('.')
from sklearn.metrics import mean_squared_error, r2_score, mean_absolute_error
from scipy.stats import pearsonr
import torch
import torch.nn as nn
import torch.optim as opt
import torch.cuda.amp as amp
import datetime
from torch.utils.tensorboard import SummaryWriter
from model.drp_model.... |
0261c5b5d536c11f3747561b3359a5bb6742d966a349eabf5e28288494212634 | Python | 12,807 | 350 | # Copyright 2018-2025 Xanadu Quantum Technologies Inc.
# 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... |
6c3fcdb11e00c262e79477ccf68dfaf9f1417d2367c87afbae671742bf559ef9 | Python | 12,810 | 320 | """Compiled public API and CLI regressions for invocation CPU budgets."""
import json
import os
from pathlib import Path
import signal
import subprocess
import sys
from types import SimpleNamespace
import pytest
from conftest import macs3_env
from test_Parser_bam_truncation import HEADER, record, write_bam
from test... |
c0eb6d8f1df58a9205df35a6ac064ff8804cb74190c58dbd8d8876dd75d234bb | Python | 12,812 | 370 | # MOFTransformer version 2.0.0
""" Vision Transformer (ViT) in PyTorch
A PyTorch implement of Vision Transformers as described in
'An Image Is Worth 16 x 16 Words: Transformers for Image Recognition at Scale' - https://arxiv.org/abs/2010.11929
The official jax code is released and available at https://github.co... |
72aeca9165713a0995103b68d428a0f480256960296e3c68941831e30842cdf4 | Python | 12,813 | 251 |
"""
module containing functions for calculating the choice probability of recorded neurons
1/19/2018
Eric Finkel
"""
import time
import math
import scipy as sp
import scipy.io
import scipy.stats
import os
import numpy as np
import pandas as pd
import glob
import csv
import random as rand
from sklearn.metrics import ro... |
a36f2af5541950e71ec5b24c1a8004082dbf92b06b05b0e79f634a3281bace06 | Python | 12,813 | 326 | import torch, numpy as np
from torch import Tensor
import torch.nn as nn
import torch.nn.functional as F
from torch.nn import Sequential, Linear, BatchNorm1d, Dropout, Parameter
from torch_geometric.nn.conv import MessagePassing
from torch_geometric.utils import softmax as tg_softmax
from torch_geometric.nn.inits i... |
500f75ebf3e5e4cc2ddbeae6346960d8ae70b3b93876eff291b04ed7f5fb711d | Python | 12,816 | 415 | """
Mapping indices for complexes / multi-domain sequences to
internal model numbering.
Authors:
Thomas A. Hopf
Anna G. Green (MultiSegmentCouplingsModel)
"""
from collections.abc import Iterable
from copy import deepcopy
from evcouplings.couplings.model import CouplingsModel
import pandas as pd
import numpy as n... |
5f9145421d5e6498d61266aad4aa18cbceadc7fe8c60a05657e10a23d7e66355 | Python | 12,818 | 417 | # Module: internal.distributions
# Author: Antoni Baum (Yard1) <antoni.baum@protonmail.com>
# License: MIT
from typing import Dict, Optional
from scipy.stats import loguniform, randint, uniform
try:
from collections.abc import Hashable
except Exception:
from collections import Hashable
from copy import copy... |
35390b4fc064c9d0c3f85f680d91dc22cf8c820a37f919d594fb18dd724dc361 | Python | 12,820 | 369 | # ----------------------------------------------------------------------------
# Copyright (c) 2016-2026, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------------... |
c7b62e6794cb011e054682dcbc8fcdb6f1bf7def57b0babcbf40721ff66041ee | Python | 12,820 | 332 | # Copyright 2026 Xanadu Quantum Technologies Inc.
# 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 agre... |
7d334a11e8a41b518a889a3ffd3f340453a2f2c57b3831134a041f3366b61230 | Python | 12,822 | 378 | # Copyright 2018-2021 Xanadu Quantum Technologies Inc.
# 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... |
1514fb7e5cd69f5adff5abac249848ff6d0a02b4ee39741c5ec34f32d6ae71f5 | Python | 12,823 | 168 | """Final figure set: readable at journal width, with explicit sensitivity.
Run after 05_make_figures.py and 15_strengthen_inference.py. Panel letters are
the only titles; interpretation and study windows belong in DOCX captions.
"""
from figure_style import *
from matplotlib.lines import Line2D
import calendar
C=pd.r... |
0f1309eaf168ac344664c928277743ed83fd1c600875de6870c3b04655a42bb6 | Python | 12,835 | 274 | from Environment_ui import *
from PySide2.QtWidgets import QWidget, QFileDialog, QTextBrowser, QPushButton, QProgressBar, QMessageBox
from PySide2.QtUiTools import QUiLoader
from PySide2.QtCore import Signal, QObject
from threading import Thread
from pages.Analysis.seg3d_to_2d import seg3d_to_2d
from math import ceil,f... |
067762fdde446566ab32ab0392d0e51a2904d91546f5d72c6aa3f49ddf337553 | Python | 12,837 | 232 | # Copyright 2026 Xanadu Quantum Technologies Inc.
# 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 agre... |
a9667843ae4bf14c6c79b218d7f8a9ddc100200cbc4699b13211f6012ac92421 | Python | 12,839 | 380 | """Session 22 — control plane progress: secrets encryption + prediction logs + trials.
Three concerns wired in this slice:
1. ``pycaret_server.crypto`` — Fernet round-trip + legacy plaintext fallback
+ encryption is applied when LLM provider settings are written.
2. ``PredictionLog`` — every ``/deployments/{slug}/... |
d8631444bf84d562b407809413019cb4d06ae3754de64a45785b3523dca6e3f5 | Python | 12,843 | 324 | import math
from itertools import permutations
import numpy as np
from scipy import spatial, stats
class MantelResult:
"""
Object representing the result of a Mantel test. Specific properties can
be queried by dot notation (e.g. `result.correlations`, `result.r`,
`result.p`, etc.) or the result object... |
ef1b4ad8ac2b88f69d5105fa1ddbaa2c091c90c902e0d90a5da487b4a664f1ed | Python | 12,845 | 406 | # Copyright 2018-2025 Xanadu Quantum Technologies Inc.
# 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... |
59a2aed4226113c4e401d22e9008ae78055bff3e799be882ce5a56c4cf1aa9e8 | Python | 12,850 | 360 | from tensorflow.keras.layers import Input, Conv1D, MaxPooling1D, Dropout, BatchNormalization, Activation, Add, Flatten, Dense
from tensorflow import keras
from tensorflow.keras.initializers import lecun_normal
import tensorflow as tf
from tensorflow.keras.callbacks import ModelCheckpoint, CSVLogger
import pandas as pd
... |
d9d71088cd5bd2272d6f0242a09ede131086f672ebff46b8018cfc3b363ea1c2 | Python | 12,857 | 286 | import argparse
import numpy as np
import os
import sys
import tqdm
import torch
import torchinfo
import logging
import torch.nn as nn
from pathlib import Path
from collections import defaultdict
from torch.utils.data import DataLoader
from torch.utils.tensorboard import SummaryWriter
from local.training import Sequent... |
008703de0a2e770bd6166d2774c743e6433cc4a9a642662fc84be736dc3a0173 | Python | 12,859 | 406 | # Copyright 2024 Xanadu Quantum Technologies Inc.
# 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 agre... |
b041d3873f15196e167f26e6214d3515934d386a6861b54cf610e2821207aace | Python | 12,876 | 269 | """Bounded subprocess driver exercising compiled public execution paths."""
import ctypes
import hashlib
import io
import json
import os
from pathlib import Path
import sys
import threading
from types import SimpleNamespace
from unittest.mock import patch
import numpy as np
from MACS3.IO.Parser import BAMParser, BAMP... |
cf4a4eff56db8615deddd3c47125e4f719f65d8176a7560a64059f4f9f75ef31 | Python | 12,876 | 356 | import os
from typing import Dict,Tuple
import io
# import pandas as pd
from pathlib import Path
import uuid
import subprocess
import numpy as np
import string
import random
import argparse
import tempfile
import os
import sys
from Bio import SearchIO
class RawAndDefaultsFormatter(argparse.ArgumentDefaultsHelpFormatt... |
76da522dc28e438b9c759df011936d99e9a187fabcc660357a7bdbe52f408cfa | Python | 12,882 | 472 | import argparse
import os
import sys
import torch
from sklearn.model_selection import train_test_split as split
from roost.roost.data import CompositionData, collate_batch
from roost.roost.model import Roost
from roost.utils import results_multitask, train_ensemble
def main(
data_path,
fea_path,
targets... |
8e3b279e4459adf17c58f2e674b96c883e1deca4b3354ffb02ad18f85ae74218 | Python | 12,884 | 341 | # Copyright 2018-2024 Xanadu Quantum Technologies Inc.
# 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... |
4fe011e92604a5b90823066b3c5bc4e73951ff9d534be7a25476d3f715c01548 | Python | 12,889 | 331 | """
@author: mkowalska
"""
import os
import numpy as np
from figure_properties import *
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
import targeted_basis as tb
__abs_file__ = os.path.abspath(__file__)
def set_axis(ax, letter=None):
"""
Formats the plot's caption.
Parameters
... |
0eacc0e43c9e47a8761482e9ce0e32137b344dae259882c0dd8efdf80ab0498a | Python | 12,890 | 367 | from datetime import (
UTC,
datetime,
)
from decimal import Decimal
import numpy as np
import pytest
from pandas.errors import (
InvalidIndexError,
Pandas4Warning,
)
import pandas as pd
import pandas._testing as tm
def test_at_dateoffset_columns():
# GH#20948 - .at with DateOffset columns
o... |
e75990551d7c45a2c066fe10d69f8e093d2efd98527dacfeb2984fe82a065873 | Python | 12,890 | 391 | import numpy as np
import pytest
from pandas.compat import HAS_PYARROW
from pandas.errors import Pandas4Warning
import pandas as pd
import pandas._testing as tm
@pytest.mark.parametrize("operation, expected", [("min", "a"), ("max", "b")])
def test_reductions_series_strings(operation, expected):
# GH#31746
s... |
14c7bca709184c3884651e075e5b6e65d452b5648d68a2ea5b9a6ef2669c31b1 | Python | 12,897 | 316 | """
Utility functions for link prediction
Most code is adapted from authors' implementation of RGCN link prediction:
https://github.com/MichSchli/RelationPrediction
"""
import numpy as np
import torch
import dgl
#######################################################################
#
# Utility function for building... |
49548c3a2874c57f21c7a98558abd94624062f1439f19755ad62875d3c672e70 | Python | 12,901 | 251 | #!/usr/bin/env python3
# MIT License
#
# Copyright 2024 Broad Institute
#
# 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 u... |
7891f3b0c9689df5eb05434b5d6b853ad4d3b519b1052fea1aa83b7883d53b37 | Python | 12,901 | 389 | from datetime import (
date,
datetime,
)
import subprocess
import sys
import numpy as np
import pytest
import pandas._config.config as cf
from pandas._libs.tslibs import to_offset
import pandas as pd
import pandas._testing as tm
from pandas.plotting import (
deregister_matplotlib_converters,
regist... |
a271b9f5f792d984381b13caf94e8f7459e704fd662022d8e171b1f2d9578cae | Python | 12,904 | 305 | # Copyright 2018-2022 Xanadu Quantum Technologies Inc.
# 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... |
228b167d398a9fabf760f9c61302fe3c4cc46d9c3cf7800b611225c18716dd88 | Python | 12,912 | 473 | import argparse
import os
import sys
import torch
from sklearn.model_selection import train_test_split as split
from roost.roost.data import CompositionData, collate_batch
from roost.roost.model import Roost
from roost.utils import results_multitask, train_ensemble
def main(
data_path,
fea_path,
targets... |
8cd7945245c2e593dddf09a1e96f1d300805fd7ca6a01c343d6f419ea738d038 | Python | 12,915 | 520 | """basic inference routines"""
from __future__ import annotations
from collections import abc
from numbers import Number
import re
from re import Pattern
from typing import (
TYPE_CHECKING,
Any,
TypeGuard,
)
import numpy as np
from pandas._libs import lib
from pandas.util._decorators import set_module
... |
2306ad08b235e8f80650f9bcaacb9b76215e16b613a4c220b31e772824a1c01c | Python | 12,923 | 216 | #! /usr/bin/env python
import argparse
import os
import pandas as pd
import numpy as np
from sklearn.ensemble import RandomForestClassifier
from sklearn.model_selection import GridSearchCV, cross_val_score, StratifiedKFold
from multiisotonic.multiisotonic import MultiIsotonicRegressor
import sys
from time import strft... |
9dfd05cf6dbee7deebebb76b5c939107f7c8b73fadfdc4c2e6de80ec3e857b0f | Python | 12,933 | 288 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.core.arrays.sparse import SparseArray
@pytest.fixture(params=[0, np.nan])
def fill_value(request):
return request.param
@pytest.fixture
def sparse_df(fill_value):
"""DataFrame with sparse int columns and a dense g... |
b512bb2807be84b62626b8892e1a62585ed39eb3b8c3e7ec2e4f007fb49250c6 | Python | 12,933 | 378 | import datetime
import numpy as np
import pytest
from pandas.errors import Pandas4Warning
import pandas as pd
import pandas._testing as tm
class TestMultiLevel:
def test_reindex_level(self, multiindex_year_month_day_dataframe_random_data):
# axis=0
ymd = multiindex_year_month_day_dataframe_rand... |
eb5a37b061f1fa420dba54dbffaa16ba0ed8fc0899e5e42f0dc86292647a0fd9 | Python | 12,937 | 362 | """Shared fixtures for the MACS3 test suite.
The existing test files open data with paths relative to the repository
root (``test/tiny.bed.gz``), so ``pytest`` is expected to run from the
repository root. New tests use the absolute paths given by the
``test_dir`` and ``data_dir`` fixtures and run from anywhere.
Comma... |
4cb4687c5ee766b1eb4ad7e5aee0d07696736b0a5f616ecfb028fe4c8afe0429 | Python | 12,939 | 414 | """
Tests for the following offsets:
- CustomBusinessMonthBase
- CustomBusinessMonthBegin
- CustomBusinessMonthEnd
"""
from __future__ import annotations
from datetime import (
date,
datetime,
timedelta,
)
import numpy as np
import pytest
from pandas._libs.tslibs.offsets import (
CBMonthBegin,
C... |
f722b75da214e9cf762ba1be203035cfd75d36b20c6a67176435ac2187ed8cbb | Python | 12,940 | 338 | import sys
import os
from numpy import nan
import pandas as pd
import argparse
#sys.stdin.reconfigure(encoding='latin-1',errors='replace') #'utf-8',errors='replace') #'ignore')
if __name__ == '__main__':
argparser = argparse.ArgumentParser('''
Extract eye-tracking time series from Dundee eye-trackin... |
8f06d7556497b2caf55396907147ee90102d40125261a291a5acaa6f3fd62986 | Python | 12,942 | 364 | import numpy as np
from numba import jit, prange
@jit(nopython=True, parallel=True)
def interpolate_3d(f, w, num_points1, num_points2, num_points3,
indexx, indexy, indexz, dx1, dx2, dx3):
dim1 = indexx.shape[0]
dim2 = indexx.shape[1]
dim3 = indexx.shape[2]
f_out = np.zeros((dim1, dim2, dim3)... |
b8b92b714d3b889a7bc284115d16419cd4b8b041b7af8b43058d4105b722df28 | Python | 12,947 | 360 | from tensorflow.keras.layers import Input, Conv1D, MaxPooling1D, Dropout, BatchNormalization, Activation, Add, Flatten, Dense
from tensorflow import keras
from tensorflow.keras.initializers import lecun_normal
import tensorflow as tf
from tensorflow.keras.callbacks import ModelCheckpoint, CSVLogger
import pandas as pd
... |
765c2be9f54a3c619aa52e1aad48d8f1bcffe92fba43407859a589f9a2c2229b | Python | 12,951 | 386 | from itertools import product
import re
import numpy as np
import pytest
from pandas._libs import hashtable
import pandas as pd
import pandas._testing as tm
@pytest.fixture
def idx_dup():
# compare tests/indexes/multi/conftest.py
major_axis = pd.Index(["foo", "bar", "baz", "qux"])
minor_axis = pd.Index... |
4ef17c89fc47fabe181061850614259ea46b698f366834b3d4892e6e78bc81f2 | Python | 12,957 | 202 | """Publication cartography at 180 mm with native, unsmoothed raster support."""
from figure_style import *
from matplotlib.ticker import LogFormatterMathtext
import matplotlib.text
from PIL import Image
from pyproj import Transformer
from shapely.ops import transform as reproject
from matplotlib.patches import Polygon ... |
1bc760f39b683c013a3f20ef74f156ec2ed5f3906d98f7d7f4490bfb4cbc44a3 | Python | 12,960 | 412 | #%%
#Imports
import numpy as np
import os
from pathlib import Path
import matplotlib.pyplot as plt
import matplotlib.animation as animation
from matplotlib.gridspec import GridSpec
import matplotlib.backends.backend_pdf
import matplotlib
# plt.style.use('seaborn-talk')
# style specs
matplotlib.rcParams['lines.linewidth... |
fac991728d5885a6da61042d9b1e2e7e93bb972a784977dbca84331770626341 | Python | 12,963 | 418 | """Functions for normalising data.
METHODS
-------
find_exclusion_indices
- Finds the indices of the frequencies to exclude from the normalisation
calculation.
find_inclusion_indices
- Finds the indices of the frequencies to include in the normalisation
calculation.
sort_data_dims
- Sorts the dimension... |
f3ed77400f6eaa14015dd5f93bab2fad88156517024f0e69796e49d0d4d7acd9 | Python | 12,964 | 270 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Aug 15 17:33:34 2022
@author: ecastrow
"""
from botocore.client import Config
import ibm_boto3
import os
import pandas as pd
import numpy as np
import sys
import json
import logging
sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file_... |
5d01f908b0d2ebc128170623d12dca9d8cc001830f6ae8c745208514a0dc2d70 | Python | 12,973 | 332 | # basics
import os
import numpy as np
import nibabel as nib
from path import Path
from tqdm import tqdm
from skimage.util import view_as_windows
import time
import datetime
# dl
import torch
import monai
from monai.networks.nets import BasicUNet
from .sliding_window_inferer import SlidingWindowInferer
from monai.tra... |
b4a4df2947f5baa6a3fe25f7c6d5007e0a2febdffa7e5dba7e0bb1441483054d | Python | 12,979 | 389 | """
file_tools.py - File handling utilities for cptools2
This module extends cptools2 with capabilities for post-processing analysis
results generated by CellProfiler pipelines. The main functionality involves
automatically joining CSV output files based on patterns specified in the
configuration YAML file, with autom... |
e77eead9ce365697eed0832338a1fc3f1c5ba898ed55d15adacbe05fb22de530 | Python | 12,979 | 405 | # Copyright 2018-2020 Xanadu Quantum Technologies Inc.
# 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... |
fa5d5367361ada51b2e3dee3c77029a1ed282ab559db4ac7827b31d13c00a589 | Python | 12,982 | 390 | from datetime import (
date,
datetime,
)
import subprocess
import sys
import numpy as np
import pytest
import pandas._config.config as cf
from pandas._libs.tslibs import to_offset
import pandas as pd
import pandas._testing as tm
from pandas.plotting import (
deregister_matplotlib_converters,
regist... |
662ea66bc0f3d8df650fed2b1b922328369a163bf3f0a9d8d9cea8b20115569a | Python | 12,989 | 351 | #!/usr/bin/env python3
"""Download and validate the trained BASALT model weights."""
from __future__ import annotations
import argparse
import hashlib
import os
import sys
from pathlib import Path
from typing import Optional
from zipfile import BadZipFile, ZipFile
HUGGING_FACE_REPO = "PKU-EMBL/BASALT_WEIGHT"
HUGGI... |
3d87f85a77b7ba9d2418902afe67ac442a6be0801bf26d6a21e7734ad808ea93 | Python | 12,997 | 283 | import sys
import os
import re
import numpy as np
import pandas as pd
import yaml
try:
from yaml import CLoader as Loader, CDumper as Dumper
except ImportError:
from yaml import Loader, Dumper
from statsmodels.stats.multitest import fdrcorrection
import argparse
delimiters = [
'_v_',
'_vs_',
' vs '... |
d8cf9c9da53071268cd03543c885e4bebd7d68135df6976416a28b22c9ebd93a | Python | 13,001 | 347 | # Copyright 2018-2021 Xanadu Quantum Technologies Inc.
# 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... |
7c4758749b8bfd438879a57d7dd14014df8b417f23da81e2948cf363bff8b226 | Python | 13,007 | 334 | import numpy as np
from random import shuffle
import pdb
import random
import copy
codon_to_aa_dict = {
'ATA': 'I', 'ATC': 'I', 'ATT': 'I', 'ATG': 'M',
'ACA': 'T', 'ACC': 'T', 'ACG': 'T', 'ACT': 'T', # M = start codon
'AAC': 'N', 'AAT': 'N', 'AAA': 'K', 'AAG': 'K', # Z = stop codon
'AGC': 'S', 'AGT'... |
ccc44f1635346360b5ebc72d7ff1c1f5f31a853a0437ac45bcf0a7019e438cd1 | Python | 13,007 | 340 | """Session 23 — god-class drain: ``predict_model``.
``Experiment.predict_model`` no longer delegates to
``self._legacy.predict_model``. It now calls ``estimator.predict`` and
(for classifiers) ``estimator.predict_proba`` directly, on the assumption
that the estimator is a fitted sklearn Pipeline with preprocessing bak... |
cb7efac54663ac4c5df339cae76889025c77bab67522c59fd5fc46d9845e4c0b | Python | 13,009 | 362 | # Copyright 2018-2021 Xanadu Quantum Technologies Inc.
# 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... |
89945973470501e24ee0e066b3bab783ea5b2f1314f3345e447f7b82ccc24645 | Python | 13,012 | 380 | """
Utility functions and classes (including default parameters).
Author: Sara Mathieson, Rebecca Riley
Date: 9/27/22
"""
# python imports
import numpy as np
import optparse
import sys
# our imports
import generator
import global_vars
import param_set
import real_data_random
import simulation
from slim_iterator impor... |
a2e2d2a229768dea6fe6fa9b0cda6718a61102177f7e439b8031784572b38b40 | Python | 13,012 | 376 | import io
import numpy as np
import pytest
import pandas as pd
pytest.importorskip("jinja2")
def bar_grad(a=None, b=None, c=None, d=None):
"""Used in multiple tests to simplify formatting of expected result"""
ret = [("width", "10em")]
if all(x is None for x in [a, b, c, d]):
return ret
ret... |
f72e593b921f34b8982542a35e0679349efe5c50f61587b50e244f9fd619a19f | Python | 13,022 | 304 | import os
import sys
import random
import time
import numpy
import scipy.io
import matplotlib.pyplot as plt
import collections
import kornia
import torch
import torch.nn as nn
import torch.nn.parallel
import torch.optim as optim
import torch.utils.data
import torch.utils.data.distributed
import torchvision.transforms ... |
b376c46e79a720f551d519b55755bbbf353cc013d279183028de30d2d3cd0a63 | Python | 13,024 | 399 | #!/usr/bin/env python3
"""
Python script for building documentation.
To build the docs you must have all optional dependencies for pandas
installed. See the installation instructions for a list of these.
Usage
-----
$ python make.py clean
$ python make.py html
$ python make.py latex
"""
import argparse
i... |
511d54cde5e7c3fc46a3c0de14c5f0eaa26989a81a7c653cdf498ad474e5ec06 | Python | 13,025 | 318 | # Copyright 2025 Xanadu Quantum Technologies Inc.
# 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 agre... |
576e710501250bd26ab9fddc64767c1b522c5986cb29986a4c04860d8f0338ea | Python | 13,025 | 333 | # Copyright 2024 Xanadu Quantum Technologies Inc.
# 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 agre... |
7a93d12f23d9b2b39d6325025403611ecb187cadfe953e9b1acb36fbc2c11f4d | Python | 13,031 | 406 | # Copyright 2019 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
#
# http://w... |
d028fd953dc5bc69f4363c0c934c1ee2498833e5a8fb2cf677d0ee97725e4592 | Python | 13,036 | 366 | """
Tests for Series cumulative operations.
See also
--------
tests.frame.test_cumulative
"""
import re
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
methods = {
"cumsum": np.cumsum,
"cumprod": np.cumprod,
"cummin": np.minimum.accumulate,
"cummax": np.maximum.acc... |
c38572ea33150c202126f5b422f4cb8f48038b15099ddba67ed1bbb5153da31c | Python | 13,037 | 444 | #!/usr/bin/env python
# _*_ coding: utf-8 _*_
import socket
import threading
import math
import numpy as np
from collections import deque
from scipy import signal
from loguru import logger
from sklearn.utils import resample
from .NeuroScanMessage import NeuroScanMessage
class NeuroScanEEGThread(threadi... |
dfd83bc9c0e4d4e50ec5e4351ed62d716c92687c117dcffb47fe0bb4978675f5 | Python | 13,044 | 362 | # Copyright 2018-2021 Xanadu Quantum Technologies Inc.
# 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... |
060c5876d805b55bc924f0a4ff4ff022f97d79fb1443b3fd9029ffd1bb98a647 | Python | 13,047 | 386 | """Tests for thriveline utilities, VelocityModel.compute_thrivelines, and
plot_thrivelines."""
from __future__ import annotations
import math
import warnings
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import pytest
from scipy.stats import norm
from pcntoolkit.longitudinal.correlation_mat... |
29208d8c1423630768cc7215b8feb57eb116b1e9a8a8a3353d3619ffb1776506 | Python | 13,053 | 351 | # Copyright 2026 Xanadu Quantum Technologies Inc.
# 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 agre... |
d3787cde0626ca256ba2dbbeab3d8d9e41d5eee6742f1cca4cb28e79282a6c8d | Python | 13,053 | 441 | # Module: containers.models.anomaly
# Author: Moez Ali <moez.ali@queensu.ca> and Antoni Baum (Yard1) <antoni.baum@protonmail.com>
# License: MIT
# The purpose of this module is to serve as a central repository of anomaly models. The `anomaly` module will
# call `get_all_model_containers()`, which will return instances... |
daccda0851fc30b731270a8f83513bc9e28c25b104f43bc3ddd36033d6cf1a14 | Python | 13,061 | 340 | from statistics import mean
import pytest
import torch
from pgen import models, esm_sampler
from pgen.esm_sampler import generate_step, ESM_ALLOWED_AMINO_ACIDS
####### Fixtures #######
@pytest.fixture
def esm6(scope="session"):
return models.ESM6()
@pytest.fixture
def esm_sampler_fixture(esm6, scope="session")... |
8df96863cf5790052240119b2c935fd981c4e99db011313aefe1a8976ad2ad3b | Python | 13,071 | 453 | """
Additional tests for NumpyExtensionArray that aren't covered by
the interface tests.
"""
import numpy as np
import pytest
from pandas.errors import Pandas4Warning
from pandas.core.dtypes.dtypes import NumpyEADtype
import pandas as pd
import pandas._testing as tm
from pandas.arrays import NumpyExtensionArray
@... |
04ac6a1a7fb85a032318e75770b11a3ae629b3cd4af6e44ad334cc1d54f75a1e | Python | 13,100 | 377 | # Copyright 2018-2020 Xanadu Quantum Technologies Inc.
# 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... |
5dab128524582ed8e2a2af6ff8dad69fbab4a7bd29cdb55d8b0354f723523f05 | Python | 13,100 | 311 | import matplotlib.pyplot as plt
import numpy as np
import os
import pandas as pd
import re
import scipy as sp
import scikit_posthocs as posthoc
import seaborn as sns
sns.set(font_scale=1.5)
data_dir = os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))), 'data')
logs_dir = os.path.join(data_dir, '... |
4d0f4f06d478076fc9830f1c837a478fab0d56babc691e42fd02c429875e935c | Python | 13,104 | 390 | import sys, os, time
import warnings
import six
from six.moves.cPickle import PicklingError # this import format has potential issues (see six documentation) -rieke
import cloudpickle
import contextlib
import io
import dask.dataframe as dd
import dask
import pandas as pd
import numpy as np
import distributed
import six... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.