sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
98760f6d6d2324e4bf525af46741ae122b578ec31eb5a27b713ed05aafad9116 | Python | 8,389 | 242 | # Note! This file is aimed specifically at pandas.io.formats.printing utility
# functions, not the general printing of pandas objects.
from collections.abc import Mapping
import string
import numpy as np
import pytest
import pandas._config.config as cf
import pandas as pd
from pandas.io.formats import printing
@p... |
46d62f9e7def8590852dbe48558de28bdf1dfee3c51258539d1009828d6aa1e1 | Python | 8,392 | 267 | # 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... |
0baa4a387edd71fa655cb6996d8c605878a1b532dbb4d7f7c7bc949d3b5c7948 | Python | 8,394 | 180 | from unittest import TestCase, mock
import numpy as np
import pandas as pd
import dynast.utils as utils
from tests import mixins
class TestUtils(mixins.TestMixin, TestCase):
def test_get_STAR_binary_path(self):
self.assertTrue(utils.get_STAR_binary_path().endswith('STAR'))
def test_get_STAR_versio... |
229f1b0ad38e36fefb59032aa05be7dc3909eac4e132fc3f78bcae003a65c622 | Python | 8,400 | 193 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Jan 28 14:07:17 2019
@author: vman
"""
import mne
import numpy as np
import multiprocessing
num_cores = multiprocessing.cpu_count()
from scipy.stats import entropy
from matplotlib import pyplot as plt
class Preprocess(object):
def __init_... |
9ae5d6386bcf9d684955105ec4198f60920d4f74356f8389c0aa3dc2dfce59f4 | Python | 8,401 | 252 | """
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 argparse import ArgumentParser
from DL_reconstruction import SSIMLoss
import torch
from data import transforms
from models import VarNe... |
6ebaa8b2a10acb816a5c93cc062cbe3c3a6fd08bf1708dda703234577de94482 | Python | 8,407 | 191 | # Copyright 2019 Image Analysis Lab, German Center for Neurodegenerative Diseases (DZNE), Bonn
#
# 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... |
03ff1f25d3b539b9d4c1262d3167bf3add12e23ba5a93702ef708aa229c58a31 | Python | 8,413 | 243 | import multiprocessing
import re
from collections import Counter
from functools import partial
from typing import Dict, List, Optional, Set, Tuple
import pysam
from .. import utils
from ..logging import logger
COVERAGE_PARSER = re.compile(
r'''^
(?P<contig>[^,]*),
(?P<genome_i>[^,]*),
(?P<coverage>[^... |
d6ca5447b429e996528a28f28f92652cb2bc9ba530baf7f4b8440e6053b93d3e | Python | 8,418 | 242 | ''' update_dynamodb_published_skeletons.py
Update a janelia-neuronbridge-skeletons DynamoDB table.
'''
import argparse
import json
import os
import sys
from types import SimpleNamespace
import boto3
import colorlog
import inquirer
from pymongo import MongoClient
import requests
from tqdm import tqdm
# pylint: dis... |
54a6a6e6c9120e9a4da100f2ae2bde129df9ba3d61101802b2a9fdfc0c3ac492 | Python | 8,421 | 246 | # 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... |
b6658aa46889e74376871af1c0946fee66bf0f0471bc4ca6966d627b987ae2d8 | Python | 8,421 | 231 | # -------------------------------------------------------------------------------------------------------------------------------------
# Following code curated for GCPNet (https://github.com/BioinfoMachineLearning/GCPNet):
# ----------------------------------------------------------------------------------------------... |
c7e926a5c499aaa03102d60c601d13a43a971cb84936bb7290e3bb1b661154b5 | Python | 8,421 | 218 | """Session 28 — god-class drain: unsupervised verbs.
``UnsupervisedExperiment.create_model`` and ``assign_model`` no longer
delegate to ``self._legacy.<verb>`` for clustering + anomaly. They run
the registry's sklearn / pyod estimator directly on
``self._legacy.X_transformed`` and return real sklearn Pipelines.
This ... |
98ea67469533fd8a12ab674490a79ceb286230e606553576ff6678d51016221a | Python | 8,426 | 258 | import os
import numpy as np
import scipy as sp
import plotly.graph_objects as go
import streamlit as st
import pandas as pd
from math import floor
from sonpy import lib as sonp
import io
from scipy.signal import find_peaks
@st.cache
def filename_list(sidebar_path):
smr_files = []
for file in os.listdir(s... |
b04e75e967c16be3ae8113dc77c4854a5151f3f0557741b29fca93d61126617e | Python | 8,426 | 190 | import os
import torch.nn as nn
import pytorch_lightning as pl
from transformers import LongformerModel, AdamW, get_linear_schedule_with_warmup
from torchmetrics import Accuracy
import torch
from evaluators.calculate_metrics import calculate_metrics
class Longformer(pl.LightningModule):
# Set up the classifier
... |
1cfa7934f6e73c153b7ecdf073631b0f1896aaea5293814ec8e590ff3fdf08d0 | Python | 8,427 | 304 | """
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 typing import Any, List
import torch
from torch import distributed as dist
"""
Functions to support graph parallel training... |
2a39f6a672a44d49018674e2e46e2586a8ca5316453592db44231984da72627d | Python | 8,429 | 221 | import pprint
import torch
import numpy as np
import time
import yacs.config
from torch.utils.data import DataLoader
from torchvision import transforms
from typing import Union
import VINNA.utils.logging as logging_u
from VINNA.models.networks import build_model
from VINNA.data_processing.augmentation.augmentation imp... |
4653845f7f53936cc25c4b1777a3c561a042165f563ec9d60a7d037c83051c8f | Python | 8,429 | 332 | from __future__ import annotations
from collections.abc import (
Callable,
Hashable,
Iterable,
MutableMapping,
Sequence,
)
from typing import (
TYPE_CHECKING,
Any,
Literal,
TypeGuard,
TypeVar,
overload,
)
from pandas.compat._optional import import_optional_dependency
from ... |
8525f5e3234c0d9dfe0438be3f9f78bbac9519e65d33f84a92d66f0d8830c5ff | Python | 8,431 | 272 | import numpy as np
import pytest
from pandas.errors import SpecificationError
import pandas as pd
import pandas._testing as tm
from pandas.tests.apply.common import frame_transform_kernels
from pandas.tests.frame.common import zip_frames
def unpack_obj(obj, klass, axis):
"""
Helper to ensure we have the rig... |
af42afff82cabee5bf55e3835199624c84ed6f3828a692245ff2284de506fb87 | Python | 8,432 | 220 | #
# File to train networks built from the hnn.py class.
#
# This file establishes the clebsch gordan coefficients, sets up an hnn with given parameters,
# loads holograms from .npy files, and then tests the network via a function call.
#
from argparse import ArgumentParser
import logging
import os
import sys
import ... |
a80b5fbee2c34e761bb5c3ce13b13c419819dd71349f69a2afedd32972a8d131 | Python | 8,435 | 268 | # 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... |
69a3776f2e3b0eafa6714fe2d9fa5569f0f4d2deac360a2c9b4ba584c23d7b49 | Python | 8,436 | 253 | """
Created on Aug 6, 2022.
data_provider_UKA.py
@author: Soroosh Tayebi Arasteh <soroosh.arasteh@rwth-aachen.de>
https://github.com/tayebiarasteh/
"""
import os
import torch
import pandas as pd
import numpy as np
from torch.utils.data import Dataset
from torchvision import transforms
import cv2
from config.serde i... |
58a59e16ba8a53fb22e7c3a4a110ab12998561e66e69e92d3217cef208cc6ce1 | Python | 8,444 | 198 | # Copyright 2015 Google, Inc. 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 applicable law or ... |
e89393551dce704fc5be2d5607a46951e497d62e4de07e66bddd3616b4676da8 | Python | 8,445 | 221 | """
=========================================================================
Compute SESAME inverse solution on simulated data in the frequency domain
=========================================================================
In the present example we shall devise a synthetic scenario in which
two dipolar sources are ... |
7efaaa63dd2d8078b890598a32bbaa44c7cb6b67e6e0e7022986ba633d9854df | Python | 8,446 | 267 | # -*- coding: utf-8 -*-
#
# atropos documentation build configuration file, created by
# sphinx-quickstart on Fri Sep 12 09:11:16 2014.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# A... |
95c8b1f1af20fd0ae179bc18481e33211838cc18cdb80c80f0150bf830684abb | Python | 8,449 | 263 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
def test_group_shift_with_null_key():
# This test is designed to replicate the segfault in issue #13813.
n_rows = 1200
# Generate a moderately large dataframe with occasional missing
# values in column `B`, and then gr... |
93356c552980a7145677fc23c307cf5da9de5c863dcbec8bc9c2384a42bae608 | Python | 8,450 | 238 | # 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... |
9220be89ad9f2ae7eca681f8412e42e4ef5d8910948c3fb6e611cf3d71a7cf4c | Python | 8,451 | 253 | # 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... |
db32bf09eb87f2fab8efb1d63130f113e2cf02e3ac87078dcc9a28b6cea9b7c0 | Python | 8,457 | 218 | import numpy as np
import matplotlib.pyplot as plt
from matplotlib import colors
import matplotlib.cm as cm
from neuron import h
def rotate(x,z,theta):
x2 = x * np.cos(theta) + z * np.sin(theta)
z2 = z * np.cos(theta) - x * np.sin(theta)
return [x2, z2]
def plot_syns(data, model, plotInh=False, iB=[]):... |
16e82ceb99ec20f6efd2008a63eaef133b9c2e6301fd7481f8bf4231c3f86afa | Python | 8,458 | 255 | # 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... |
42e26222f3c25e5e4165b7bc00aecf4b2bea03c94911ef1695f426b69da1885a | Python | 8,459 | 188 | import torch
import torch.nn as nn
import torch.nn.functional as F
import math
from torch.autograd import Variable
from torch.nn import Sequential as Seq, Linear
torch.set_default_dtype(torch.float64)
class SiLU(nn.Module):
# from https://pytorch.org/docs/stable/_modules/torch/nn/modules/activation.html#SiLU... |
51d82319f43e8d3822b756ed94137fb6c89c6452ece643ccf565983d926e502b | Python | 8,459 | 183 | """Test the video reader factory (backend resolution + construction dispatch)."""
import sys
from unittest.mock import MagicMock, patch
import pandas as pd
import pytest
from lightning_pose.data.video.factory import build_video_reader
def _fake_dali_module(prepare_dali: MagicMock) -> MagicMock:
"""A stand-in fo... |
84411c3a5793a5c9009ac343975bab6632acd3b47c2f0093e1e28608e4b9fa2c | Python | 8,460 | 242 | # 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... |
c9d5e0ac276bd9341ef44d2befe7a7e45f78d6af363a78c58703b6535ad04af6 | Python | 8,464 | 142 | import pytest
from pgen import utils
import io
import tempfile
####### Fixtures #######
@pytest.fixture(scope="function")
def a2m_file():
f = io.StringIO(
"""
>seq_1
mdgtrtsldieeysdtevqknqvlTLEEWQDKWVNGKTAFHQEQGHQLLKKHLDTflKGKSGLRVFFPLCGKAVEMKWFADRGHSVVGVEISELGIQEFFTEQNLSYSeep*
>seq_2
........................TLEEW... |
0e8523b24ae5fa7d9f444fe37407ba5093456df52e1da010fdc76babe510b0a6 | Python | 8,474 | 312 | """
Abstract base class for regression models in the PCNToolkit.
This module provides the base class for all regression models, defining the common
interface and shared functionality that all regression implementations must follow.
Notes
-----
All regression model implementations should inherit from this base class a... |
ad8629efc894c79965a5740bf0b52d2d22e631b275d0dd6d50b3ea4cc0a8eb6c | Python | 8,474 | 231 | #python buildDundeeTokFixns.py origFile eyeFile eventFile
import sys
import re
textfileix = 1
textfixfileix = 2
eventfileix = 3
#########################
#
# Load Text File
#
#########################
#NB: startofsentence and endofsentence measures aren't accurate here, so we shouldn't include them here
corpus = [... |
477f10426902f1463b89604ef2a9e41284e9cb07c2b5fea16cbdcf8da6c1a8bd | Python | 8,476 | 229 | """Multiple comparisons correction methods."""
import inspect
import logging
from abc import ABCMeta, abstractmethod, abstractproperty
import numpy as np
import statsmodels.stats.multitest as mc
from .results import MetaResult
from .transforms import p_to_z
LGR = logging.getLogger(__name__)
class Corrector(metacla... |
a7b45825aba9afe2c174f12084b38ce9712f334a7799ad651c847f9686df2c63 | Python | 8,480 | 227 | # 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... |
19e135df3edc2568350f7d040ff237f05d7f393333f108eb8bb4e13d37aeb4e5 | Python | 8,481 | 214 | # 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... |
d74b869cfe8b07f4dfc38c5fb37c146ebad2c4433d838e426e0f53e7bbbfcb9b | Python | 8,481 | 252 | """
CNN-based discriminator models for pg-gan.
Author: Sara Mathieson, Zhanpeng Wang, Jiaping Wang
Date: 2/4/21
"""
# python imports
import tensorflow as tf
from tensorflow.keras.layers import Dense, Flatten, Conv1D, Conv2D, \
MaxPooling2D, AveragePooling1D, Dropout, Concatenate
from tensorflow.keras import Model... |
369de5a6fba71b25741faa12b7541f0d963eb7e424f455daf7ff7e63de43a961 | Python | 8,482 | 270 | import os
import csv
import re
import argparse
def file_delim(file_path):
"""
Determine the delimiter based on the file extension.
Parameters:
file_path (str): The path to the file.
Returns:
str: The delimiter to use (either '\t' for TSV or ',' for CSV).
"""
file_ext = os.path.splite... |
ad4aff39619418276d66092e20e7ddcff7464502f68e6079e2ab50a8337bcf97 | Python | 8,483 | 205 | #!/usr/bin/env python
# coding: utf-8
### Author: federica.magnabosco@mrc-cbu.cam.ac.uk
### Fit decoding model SDvsSD individual ROIs and save accuracy
# Import some relevant packages.
import numpy as np
import pandas as pd
import pickle
import random
from itertools import combinations
from sklearn.pipeline import ... |
7885ddda4e0e1e8aee223866a456db1572037737ec3ad6d7095114b7102d1624 | Python | 8,484 | 266 | """Session 33 — Notebook runtime hardening.
Smoke tests for:
- ``LocalManager``: start / is_alive / stop on the dev-stub backend.
(Docker backend tests require a daemon and are skipped in CI; see
``test_docker_manager_*`` below.)
- ``GET /notebooks/{id}/content`` returns the default starter when no
bytes are pe... |
110a4c249dc8d57301c59947389451c3499507c14db56f70fbe5194c52b20996 | Python | 8,487 | 217 | ##################################################################################################################
# Obtained from https://github.com/vgsatorras/egnn/blob/main/models/egnn_clean/egnn_clean.py
# Credit: 'E(n) Equivariant Graph Neural Networks' by Victor Garcia Satorras, Emiel Hogeboom, Max Welling
# ... |
3d99c5986b46b3ca4cab3ec935d24417ff29e4a762ee7c090b51a80afef90cd7 | Python | 8,487 | 259 | """
@author: mkowalska
"""
import os
from os.path import expanduser
import numpy as np
from numpy.linalg import LinAlgError
import matplotlib.pyplot as plt
from figure_properties import *
import matplotlib.gridspec as gridspec
import datetime
import time
from kcsd import KCSD1D
import targeted_basis as tb
__abs_file_... |
6faa70e0e6788dc350c9bdf1ab2937a076bb67c170da437aa5105ec23a2d1fa9 | Python | 8,487 | 276 | # -*- coding: utf-8 -*-
import os
from itertools import product
from os.path import join
import numpy as np
import pytest
from emcee import EnsembleSampler, State, backends
from emcee.backends.hdf import does_hdf5_support_longdouble
try:
import h5py
except ImportError:
h5py = None
__all__ = ["test_backend"... |
4f0edcc5cdb8adc116e28511fb3df1ec28cee3e28f027ab771815cce85ca01e4 | Python | 8,489 | 190 | import torch
import torch.nn as nn
from collections import OrderedDict
import dgl
from dgl.nn.functional import edge_softmax
class MLP(nn.Module):
def __init__(self, inp_dim, hidden_dim, num_layers,batch_norm=True, dropout=0.):
super(MLP, self).__init__()
layer_list = OrderedDict()
in_dim =... |
243c456a5f5cb3877717f4ed9803a40aded24e7a293da07bbe3f2bf23f026b00 | Python | 8,490 | 214 | """Internal, invocation-owned peak-caller scheduling and pool lifetime.
No scoring types are imported here. The caller passes typed worker adapters
and the pool initializer; only children bind a caller in that initializer.
Each PeakExecution owns a workload snapshot and an immutable ExecutionPolicy,
but never retains ... |
c052bf881e2cff786452b8b609ba0bc7e9f79a40b7568586b72ed2de6011a59b | Python | 8,492 | 216 | # 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... |
533d928f578e21d2ad0b58ab7767303a7321b4f2769c7d331376cae695af6a6c | Python | 8,493 | 229 | import torch
from torch import nn
import torch.nn.functional as F
from common import device
norm_dict = dict(instance=nn.LazyInstanceNorm1d, batch=nn.LazyBatchNorm1d)
ONEBYONECHANNELS = 4
class AlexNetBasicBlock(nn.Module):
def __init__(self, in_channels, out_channels, kern_size=3,
dropRate=0.0... |
491b91249ae7cb6c83775e2311194ae9b10f0376c1d710578caf688673f6a2ba | Python | 8,494 | 214 | # MIT License
#
# Copyright (c) 2024 EPFL Biorobotics Laboratory (BioRob).
#
# 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
# ... |
b2bd213027ec52728ab3c27a6bcee7fc3c1e03893d588f71122ef8db4caf84a1 | Python | 8,494 | 242 | """Sample / bundled CSV datasets.
The PyCaret repo ships a catalog of small public datasets under
``<repo>/datasets/`` with an ``index.csv`` describing each one. They're
the same files the 3.x ``get_data(name)`` helper has always served.
This module exposes:
- ``GET /sample-datasets`` — list of bundled samples with ... |
448be19d0d476219840a824c5919fc89902ae741adcee7643006665ef2c54619 | Python | 8,496 | 256 | import sys
sys.path.append('/gscratch/stf/mpun/software/PyRosetta4.Release.python38.linux.release-317/')
import pyrosetta
from pyrosetta.rosetta import core, protocols, numeric, basic, utility
from protein_holography.coordinates.get_structural_info import get_padded_structural_info as c_struct
from protein_holography.c... |
6be7931826c9e2514ea150dfdc10553e0dae1aea71238cd16454a6a7f62d61ad | Python | 8,497 | 253 | """
@author: mkowalska
"""
from builtins import range
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from scipy.interpolate import griddata
from matplotlib import gridspec
from kcsd import csd_profile as CSD
from kcsd import ValidateKCSD2D
from figure_properties import *
def set_axis(... |
2dc0889991e240bd5ad62bf9c7b0fac084e236bea25031a04b10d72890b0d5df | Python | 8,501 | 271 | """
Tests of the groupby API, including internal consistency and with other pandas objects.
Tests in this file should only check the existence, names, and arguments of groupby
methods. It should not test the results of any groupby operation.
"""
import inspect
import pytest
import pandas as pd
from pandas.core.grou... |
ed91d87618d43a44d840517d65d090f8c4128e0894b129c7270e1d8bd9c5ea68 | Python | 8,503 | 256 | # 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... |
3f477864c9c7e8362230fcabf54dae0d4f8bf782676157cff0c62e635f4f8fe8 | Python | 8,509 | 271 | import numpy as np
import matplotlib.pyplot as plt
# increase the figure size
plt.rcParams["figure.figsize"] = [12, 10]
# remove the top and right spines from plot in the global plt setting
plt.rcParams["axes.spines.top"] = False
plt.rcParams["axes.spines.right"] = False
# change the linewidth of the axes and spines
... |
8ae049e8c8c55ac0f781623753b5b062a914873190229173bdc9b6d5fa83c4a9 | Python | 8,514 | 215 | # 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... |
e3d12c4e73ffcc82a49ce187ee727ca1670af58537a6bdc40033dcfaaf6de816 | Python | 8,514 | 176 |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Wed Nov 20 00:42:56 2019
@author: Mehmood Ali Khan
"""
import time
from DataPreprocessing import DataPreprocessing
from DataReader import DataReader
from LSTMModel import LSTMModel
if __name__=='__main__':
objReader = DataReader()
... |
30f6832c1a3c3f9fb11f4c751412a45942aa386c35c03b5a5563e1d5f006a1da | Python | 8,518 | 210 | import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation
import wormdatamodel as wormdm
import wormbrain as wormb
import pumpprobe as pp
import mistofrutta as mf
import sys
import os
import subprocess
# Parse inputs and make destination folder
folder=sys.argv[1]
if folder[-1]!="/":fo... |
9b4e54a77118dae8a4e48210330926b0a5c41aa12475bb6901f9cca8e5cf7d0d | Python | 8,518 | 171 | """Build Healthspan Proteomic Score from the pinned original Kuo lab R release.
Run ``uv run python clocks/build_hps.py`` from the repository root. Fitted
numerical parameters are extracted directly from the author release; neither
Biolearn nor MethylCYPHER is used as a source.
"""
import argparse
import hashlib
impo... |
87a70ee1029fb2ea657b992cda9a5a7470074b3662e701a28e01760530f3c48f | Python | 8,519 | 317 | # -*- coding: utf-8 -*-
"""
Code to train an RNN on audiovisual action recognition using the feature
embeddings of the AVMIT dataset.
"""
import os
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
import datetime
import tensorflow as tf
from pathlib import Path
import pandas as pd
import yaml
from functools import partial
i... |
04d28ec1fd26061f18b191d1cae002a9e8c6ea38a962226e35220567b0007f7f | Python | 8,522 | 269 | ######################
### Import Library ###
######################
# my library
from molgraph.molgraph import *
from molgraph.utilsonehot import *
from molgraph.utilsmol import *
from molgraph.utilsgraph import *
# standard
import os as os
import copy as copy
import random as random
# plotting
import matplotlib.pypl... |
77b5bcfdeacd03c4afe307c6a05b7941cb1c4aa720f903bfa24f57e7c0966c28 | Python | 8,524 | 324 | import numpy as np
import pytest
import umap.distances as dist
def numerical_gradient(f, x, eps=1e-6, forward_only=False):
"""
Finite-difference gradient of scalar function f at x.
Parameters
----------
f : callable
Scalar function f(x).
x : ndarray
Point at which to evaluate... |
3da7063ba9a86ad14c3266a40c5639bdaf8524368256c52d7bcf8a9261a6ae29 | Python | 8,526 | 265 | """
Tests that work on both the Python and C engines but do not have a
specific classification into the other test modules.
"""
from io import StringIO
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
xfail_pyarrow = pytest.mark.usefixtures("pyarrow_xfail")
skip_pyarrow = pytest.mar... |
2813e38b4a7e0590299a1d460e327fcf15b07ad942f8dd298913506b1eb2ceb4 | Python | 8,528 | 219 | """Session 44 — phase 5c (cont.): drain ``TimeSeriesExperiment.finalize_model``.
Phases 5b/5c (s40-s43) drained ``create_model``, ``predict_model``,
``compare_models``, and ``tune_model``. This session drains the fifth
TS verb. ``exp.finalize_model(forecaster)`` no longer touches
``self._legacy.finalize_model`` — refi... |
0af51cd1896142a83a89fd696744c6f7d5af90dce38f6eff3260a6d8aa383414 | Python | 8,529 | 189 | #! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this wo... |
57c8d2713d27199bdcc14b205be4ae50067d272dc7eb1667b29b547b1fb0b5f9 | Python | 8,530 | 202 | import pandas as pd
from rdkit import Chem
def check_if_identical(tree_df,query_smi,weight,supporting_compounds):
"""
function that checks if an identical substr is already in tree_df, only the one with higher summed weight is kept
input: original tree_df, query_smi (str), weight(float): summed... |
6b066ce797252fb5c021cef36c107be54b11fc381a3dcb8c7109beb833ec32a4 | Python | 8,531 | 338 | # -*- coding: utf-8 -*-
"""
Created on Sun May 1 17:33:44 2022
@author: jeanbaptiste
"""
import os
import json
import pycromanager_tessie as pmt
from pycromanager_tessie.acquisitions import experiment
# Start platform:
platform = pmt.microscope.platform.Platform(load_synchronizer=True)
# Set LED ring
platform.neop... |
07390fa03e78c46d5fd9f639a6040e03fa18d2345cfc2894dd6dd64e0b8877ef | Python | 8,533 | 261 | import torch, os
from kilosort import preprocessing
dev = torch.device('cuda:0')
import numpy as np
from torch.fft import fft, ifft, fftshift
from scipy.interpolate import interp1d
from tqdm import trange
def get_drift_matrix(ops, dshift):
""" for a given dshift drift, computes the linear drift matrix for interpol... |
85ebea1779d39c08aa6decdabc2dc68e61ca3a6f54442948cdc971147878efa7 | Python | 8,533 | 223 | #
# File to train networks built from the hnn.py class.
#
# This file establishes the clebsch gordan coefficients, sets up an hnn with given parameters,
# loads holograms from .npy files, and then tests the network via a function call.
#
from argparse import ArgumentParser
import logging
import os
import sys
import ... |
9ed0515c3284e8731bf4716e0481edf459e09f69f7fbdba052be228a47042b10 | Python | 8,535 | 334 | # import os
import numpy as np
from typing import Tuple
from tifffile import imread, imwrite
import imageio.v3 as iio
from scipy.signal import fftconvolve
def read_tiff(path: str) -> np.ndarray:
"""read a .tiff image into a numpy array
Args:
path (str): path to the image
Returns:
np.nda... |
f5a43780a9b5e7fc6c11f9f37885826bc24bb0a79b4e14b06f3ff96672f663e3 | Python | 8,537 | 213 | # 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... |
bc18c031bd9b88629d7ad9e182abe9f193b11f99d8c768923fdfbf27b338fcea | Python | 8,540 | 296 | # 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... |
db163fd268ee8ccdcc5c967223a6fb87e6016ca845cf38866e5ea0cf7235b3dd | Python | 8,540 | 216 | import sys, configparser, torch, re, os
from collections import Counter
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
import numpy as np
def eprint(*args, **kwargs):
print(*args, file=sys.stderr, **kwargs)
def prepare_data():
data = [line.strip() for line in sys.stdin]
... |
f3c9b06ce9487c5c23d24dbd43768de5e6289284df5ca5a1da1e76aca058cf64 | Python | 8,545 | 233 | # 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... |
f3414acc2242325e092eb2aebdede66c40d6dae0e5a9cc9ec29b71326035ca6e | Python | 8,553 | 223 | from wordfreq import (
word_frequency, available_languages, cB_to_freq,
top_n_list, random_words, random_ascii_words, tokenize, lossy_tokenize
)
import pytest
def test_freq_examples():
# Stopwords are most common in the correct language
assert word_frequency('the', 'en') > word_frequency('de', 'en')
... |
d0389b0ca4b8b96c7c1ee172f96373df7b00433ce0a5960e453db9c7c6fda7ea | Python | 8,556 | 223 | import kCSD2D_reconstruction_from_npx as npx
import matplotlib.pyplot as plt
import matplotlib.cm as cm
import scipy
import numpy as np
from numpy.linalg import LinAlgError
from scipy.signal import filtfilt, butter
def set_axis(ax, x, y, letter=None):
ax.text(
x,
y,
letter,
fontsiz... |
9c49d63bad93dd602dca90b72162f9dbcb1a5f8c951430008b2e0ea278a66096 | Python | 8,559 | 243 | import numpy as np
import pytest
from pandas._libs import index as libindex
import pandas as pd
import pandas._testing as tm
class TestIntervalIndex:
@pytest.fixture
def series_with_interval_index(self):
return pd.Series(np.arange(5), pd.IntervalIndex.from_breaks(np.arange(6)))
def test_getitem... |
caff0824e597686597518b24adbbf9c5d2f910e31fdaf332f37e67b7c91eab1a | Python | 8,559 | 196 | """Public benchmark CLI gates, using the same compiled build as pytest.
The end-to-end case takes ~10 s and <200 MiB on macOS. Fixtures are tiny;
the full 64 MiB log-cache probe deliberately exercises the production cap.
"""
import json
import os
from pathlib import Path
import subprocess
import sys
from types import... |
f71aa2cf2a566172baa10a958040feeca530611ec2844c062ef33d6caa0c103f | Python | 8,559 | 275 | """
Module providing entry points for fitting and predicting with normative models from the command line.
"""
import argparse
import cloudpickle as pickle # noqa: F401
import numpy as np
from pcntoolkit.dataio import fileio
from pcntoolkit.dataio.norm_data import NormData
from pcntoolkit.normative_model import Norm... |
b4e2ecb7e68d05f048c4a2508a7da711518057657da5391b778f73f9a5cbd18e | Python | 8,561 | 196 | import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
import os
from scipy.stats import ttest_rel # Using a paired t-test since we're comparing the same models
DATA_PATH = '../Extracted_Selectivity/VGG/PretrainedOnImageNet/IAPS/Tuning/'
emotion_FILE = '1001_Lesion_BestModels0912... |
23b1f6cc44747a9d1ae0dd0b1a3a31ff3f3b6497a6bda776a03b2eb8bb8ffe31 | Python | 8,562 | 295 | from __future__ import annotations
import itertools
from typing import (
TYPE_CHECKING,
cast,
overload,
)
import warnings
import matplotlib as mpl
import matplotlib.colors
import numpy as np
from pandas.util._exceptions import find_stack_level
from pandas.core.dtypes.common import is_list_like
if TYPE_... |
12141a1e06a51b5f9ae90ef189fda71dce4a591a1dad85a90b8b354015f4c5d2 | Python | 8,565 | 202 | '''
Compares two CONLL-formatted coreference files for 1. anaphoricity recall/precision and 2. among correctly recalled mentions, what is precision of correct antecedent choice?
Usage:
python <script-name> key.conll preds.conll parsed.tokdecs
'''
import sys
import pdb
DELIM = "\t"
TOKDECDELIM = " "
PRONOUNS = [... |
50a9f5c9995b7f1a4b2d56aacb87e2bff8bfeefde66251427496cd7a2229f4ca | Python | 8,565 | 237 | # 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... |
b14c984eb827797a397c524d59a53194eeb31424a97c9e9efbe5c426c5aec4b1 | Python | 8,565 | 297 | from datetime import timedelta
import dateutil
import numpy as np
from pandas import (
DataFrame,
Series,
date_range,
period_range,
timedelta_range,
)
from pandas.tseries.frequencies import infer_freq
try:
from pandas.plotting._matplotlib.converter import DatetimeConverter
except ImportError... |
c1aa38204458eb08cc4d5ff52bb9c34287377b83f6eed99978c8107aeec05b3c | Python | 8,569 | 176 | import pandas as pd
import numpy as np
import torch
from rdkit import Chem
from rdkit.Chem import AllChem, PandasTools
from pytorch_classes_and_functions import DNN
from helper_functions import get_fp_matrix, create_df_activations, get_bit_comp_df
from fca_functions import fca_lattice_from_df, extract_substr_fro... |
ba9c66b4bc7d339ed0b658886f2a3d4ee4612176b62d2a96dd62de11e275266b | Python | 8,571 | 229 | import tensorflow as tf
from tensorflow.keras import backend as K
from tensorflow.keras.models import Model
from tensorflow.keras.layers import Conv3D, MaxPooling3D, BatchNormalization, Conv3DTranspose, concatenate, \
Cropping3D, Input
from tensorflow.keras.optimizers import Adam
# from keras.callbacks import Reduc... |
0b13e29fa2a8198a3da6e8520cb6187d388adef022f260d71c2ab21e765bebaf | Python | 8,572 | 252 | """Tests for KTrajectory Calculator classes."""
import pytest
import torch
from einops import rearrange
from mrpro.data import KData, SpatialDimension
from mrpro.data.traj_calculators import (
KTrajectoryCartesian,
KTrajectoryIsmrmrd,
KTrajectoryPulseq,
KTrajectoryRadial2D,
KTrajectoryRpe,
KTra... |
d5a788d2e2c5b2ea22407c41dfaae40c27891b97e6143423548fea60f4fc7c49 | Python | 8,573 | 218 | import itertools
from logging import Logger
from typing import Any, Iterable, Mapping, Optional, Sequence, Union, cast
import numpy as np
import pandas as pd
from ..chem.gpep.sort import GlycanComparer
from .scorer import GlycoPeptideStructScorer
from ..speclib.gpep.spec import GlycoPeptideMS2SpectrumProto
from ..util... |
479fd9f5f7dbbca3fb57b3b2feeaa3e31d6a6bb0da75df4a7d93e843bcfa893b | Python | 8,591 | 203 | from __future__ import print_function
import math
import os
import random
import copy
import scipy
import imageio
import string
import numpy as np
from skimage.transform import resize
try: # SciPy >= 0.19
from scipy.special import comb
except ImportError:
from scipy.misc import comb
def bernstein_poly(i, n, t... |
6c3fd4fed3652946bc3d200e8b8d84f2938603e4d822c20c64eb86bbd68e7ae8 | Python | 8,593 | 253 | #!/usr/bin/env python
# coding: utf-8
### Author: federica.magnabosco@mrc-cbu.cam.ac.uk
### Fit decoding model LDvsSD individual ROIs and save accuracy
# Import some relevant packages.
import numpy as np
import pandas as pd
import pickle
import seaborn as sns
import matplotlib.pyplot as plt
from scipy.stats import se... |
60b4ae6c8e87118318f9e1109a75742fcf577c6f48ca1379370b146e6e8fc812 | Python | 8,596 | 294 | """
Testing that we work in the downstream packages
"""
import array
from functools import partial
import importlib
import subprocess
import sys
import numpy as np
import pytest
from pandas.errors import IntCastingNaNError
import pandas as pd
import pandas._testing as tm
from pandas.util.version import Version
@p... |
800155d0bfa14158276fe50120feafac9125c9843adc9cc28d985de16791a9ae | Python | 8,599 | 267 | # MOFTransformer version 2.2.0
import torch
import torch.nn as nn
import torch.nn.functional as F
from torchmetrics.functional import mean_absolute_error
def init_weights(module):
if isinstance(module, (nn.Linear, nn.Embedding)):
module.weight.data.normal_(mean=0.0, std=0.02)
elif isinstance... |
01654ba620b8afba6281e0216afb88306c877f4ab19c1b9b09d747274bfa3550 | Python | 8,604 | 219 | # train.py
# Script to train policies in Isaac Gym
#
# 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... |
4693b69124a04e9cafcaf84fb644b41d23b4e268a3e1c0ea6f03660459c82033 | Python | 8,606 | 220 | import numpy as np
import pytest
from pandas.compat import PY315
import pandas as pd
import pandas._testing as tm
class TestPeriodIndex:
def test_getitem_periodindex_duplicates_string_slice(self):
# monotonic
idx = pd.PeriodIndex(["2000", "2007", "2007", "2009", "2009"], freq="Y-JUN")
ts... |
faf25d8e8994f409c22b25e033000567337a5edcf7ee314e497a8279dd51a4be | Python | 8,608 | 243 | # This module is mostly borrowed from Olivecrona original implementation
# (https://github.com/MarcusOlivecrona/REINVENT).
# We adjusted some functions for this project.
#
import numpy as np
import random
import re
import pickle
from rdkit import Chem
import sys
import time
import torch
from torch.utils.data import D... |
10c2d595b4ef266761e5b6f302d24d91a44cbd6f21cf96bae7ead66679f9b7a5 | Python | 8,613 | 260 | import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
import seaborn as sns
from fmriprep_denoise.features.derivatives import get_qc_criteria
from fmriprep_denoise.visualization import utils
strategy_order = list(utils.GRID_LOCATION.values())
def load_data(path_root, datasets, criteria_name, fmripre... |
7c5d1cf04f8fda61653904b85d83138eb9246a509c02fd5928ef90d07ab5282b | Python | 8,614 | 256 | # MOFTransformer version 2.1.0
import sys
import os
import copy
import warnings
import json
from pathlib import Path
import pytorch_lightning as pl
from moftransformer.config import ex
from moftransformer.config import config as _config
from moftransformer.datamodules.datamodule import Datamodule
from mo... |
2c4c171b6c65c3081ae45bd78e22af4a05d6276be23630f7e9febfe8f72718bd | Python | 8,618 | 264 | """Session 23 — Model Library + admin/users routes.
- ``/workspaces/{id}/model-library`` lazily seeds from the engine's
``list_models`` on first read; subsequent reads serve DB rows.
- ``/admin/users`` is gated on ``user.is_superuser``; non-superusers get 403.
- Patching ``is_superuser`` / ``is_active`` works, with ... |
c16c823abf6acd356e29bcf606fff7cd976c758a776852a93c55e6103163f061 | Python | 8,618 | 256 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Mar 6 16:17:10 2023
@author: hklumpe
"""
import sys
import os
import time
import json
sys.path.insert(0,'/project/dunlop/shared_python_packages/')
import qsub
# Make sure the proper package is used:
sys.path.insert(0,'./../')
import deepcellcontrol ... |
b7e67f84ac85b071b0258b14aeda4633afd91ce73d4db44cddab2c750b711e8c | Python | 8,619 | 240 | #! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this wo... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.