sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
fa5dca0d24c5e49649732602128671ca267b80d9a9159d1ffb8be4e2f89b3999 | Python | 10,977 | 286 | import shutil
from pathlib import Path
from unittest.mock import patch
import holoviews as hv
import pytest
from guppy.frontend.visualization_dashboard import VisualizationDashboard
from guppy.testing.api import step1, step2, step3, step4, step5
from guppy.utils.utils import parse_run_name
from guppy_test_data import... |
7a2849e99d172967419b4e81d9e3ad09e91ec21756e7bb323da3f70faf3b4d97 | Python | 10,979 | 300 | """Utilities related to layer/model functionality.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from .conv_utils import convert_kernel
from .. import backend as K
import numpy as np
def count_params(weights):
"""Count the total number of scalars... |
0b8144061227e69efa13d0511abc2f40c417ea5f351f0ec74b2bb18a91098964 | Python | 10,980 | 351 | # -*- coding: utf-8 -*-
#
# burstiDAtor documentation build configuration file, created by
# sphinx-quickstart on Sat Jul 19 14:34:56 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.
#... |
722ed11b77efd5e1213bce99cfc01b52caaeb1c0b6d1e84e2d255bcd33fd3cb9 | Python | 10,997 | 325 | import numpy as np
from scipy.special import expit
import scipy
from cogmodels.bayesian_base import BayesianModel
from cogmodels.base import CogParam
class PCModel(BayesianModel):
"""
Debate: single subject fit, with one paramter sets, and multiple PC models
OR:
one fit for all subjects, and multiple... |
8ab7fe1f3f44f5ccb7f9f20f3032613d0d77683d6f490dcf87729b8529924e4b | Python | 11,004 | 320 | from __future__ import annotations
import os
import pickle
from typing import TYPE_CHECKING, Literal, get_args
import numpy as np
import pytest
from ase import Atoms
from ase.io.trajectory import Trajectory
from ase.md.npt import NPT
from ase.md.nptberendsen import Inhomogeneous_NPTBerendsen
from ase.md.nvtberendsen ... |
79dee7e641b38f298faad00c84790df0854380de4b70c7cc52d378ad4a2e19f7 | Python | 11,009 | 259 |
import torch
import numpy as np
import time
from collections import OrderedDict
def copy_state(model):
"""
Given a PyTorch module `model`, makes a copy of the state onto the CPU.
Parameters:
----------
model : torch.nn.Module
PyTorch module from which to copy the state dictionary.
Re... |
9547561f07403a7e6cb9d41cbb9a29fd7d9f2dec093147c906dbbc145a35c30e | Python | 11,012 | 243 | import os
import argparse
import torch
import torch.nn as nn
import torchvision.transforms as transforms
from torchvision.datasets import ImageFolder
from torch.utils.data import DataLoader
from torch.optim import Adam
from torchvision.utils import save_image
import numpy as np
# Parse input arguments
parser = argpars... |
66b691e96d6975c518c9a49b9566335376cd3b9eeafc2e2b5d6a36c06fd9a47e | Python | 11,024 | 323 |
"""
Generate the lowest-level Cython bindings to HDF5.
In order to translate HDF5 errors to exceptions, the raw HDF5 API is
wrapped with Cython "error wrappers". These are cdef functions with
the same names and signatures as their HDF5 equivalents, but implemented
in the h5py.defs extension modul... |
0b9fa4d5ea4cf1bfdb0f9784b4de63440544285ef4b7563083ab1391d71d4e76 | Python | 11,025 | 332 |
from typing import Dict, List, Optional, Tuple
import torch
from torch import nn, Tensor
from torch.autograd import grad
from torch_scatter import scatter_sum, scatter_mean
from torch_geometric.data import Data
from oa_reactdiff.model import EGNN
from oa_reactdiff.model.core import GatedMLP
from oa_reactdiff.utils i... |
61d1045633baa498c65a12caf379a0304f86af90cff7d44e66d29c287e99fcf4 | Python | 11,026 | 299 | import time
import logging
import threading
import sqlite3
from medperf.comms.auth.interface import Auth
from medperf.comms.auth.token_verifier import verify_token
from medperf.exceptions import CommunicationError, AuthenticationError
import requests
import medperf.config as config
from medperf.utils import log_respons... |
bef8d542d4b73c425db9a16d013723cd67a5690a965479ee8917dfc4d4a32b23 | Python | 11,036 | 182 | """Emodel generalisation package."""
# Copyright (c) 2022 EPFL-BBP, All rights reserved.
#
# THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
# PURPOSE ARE DISCL... |
c8229ca5a0ff21e68486328cb53e7ec864080231c669f08567dd3fbb16d53a57 | Python | 11,038 | 308 | """
Author : Alexis Lebrun (PhD student)
School : Université Laval (Qc, Canada)
This module provides functions for a variety of utilities.
"""
import numpy as np
from sklearn.model_selection import train_test_split
import logging
import pandas as pd
from io import BytesIO
from zipfile import ZipFile
from urllib.reque... |
0e701c3da96d9bd58111ff0041d79a499c517b331aff45ae5ebedf3492e145cc | Python | 11,044 | 276 | '''
Trains only an MLP on PCA-dimensionality-reduced features.
Author: Hanna M. Tolle
Date: 2025-02-17
License: BSD 3-Clause
'''
import sys
sys.path.append('graphTRIP/')
from sacred import Experiment
from experiments.ingredients.data_ingredient import *
from experiments.ingredients.mlp_ingredient import *
import ... |
53bcfd5dd8964d7487178d76690da0a61335e49385c087981c5fb9653b8c49a3 | Python | 11,044 | 203 |
"""
In cases where a BOLD file exists but the corresponding events.tsv file is missing,
there are several scenarios to consider:
1. Incomplete Behavioral Data with TEMP Files Available:
TEMP files, which are trial-by-trial backups that don't rely on a final "save,"
may exist even if the behavioral data wasn't fully... |
b5acf79c363188449e7c86e5b3d38a70bac55bc7516d54322b133f6696cfe12d | Python | 11,044 | 322 | import json
from importlib.metadata import version
from pathlib import Path
import pytest
from guppy.orchestration.save_parameters import (
read_artifact_provenance,
save_parameters,
)
# Derived provenance, recorded by the preprocessing steps rather than taken from the form.
ARTIFACT_PROVENANCE_KEYS = {
... |
18282d7577719b2264fbd2d6d276e0867b9f3b4cce4357e8f096339b94016629 | Python | 11,049 | 332 | import torch
import torch.nn as nn
from typing import Tuple, Union, Optional
from torch_sparse import SparseTensor
import numpy as np
class AdjToEdge:
"""
Convert adjacency matrix to edge indices and weights for graph decoders.
Parameters
----------
threshold : float, optional ... |
8b7953873740e687743cb9e71b6c7f2e957ce14ea4f17296ba3f1bc6604f3f45 | Python | 11,049 | 283 | import numpy as np
import os
import subprocess
import glob
def train_val_test_split(files, nr_val_datasets, nr_train_datasets):
"""
Custom dataset split based on exclusion criteria.
Parameters
----------
files : list of str
List of file names.
nr_val_datasets : int
Number of d... |
5f10a22daec4c5fb4b89f3217a03916ee95d2b3a27fa17053255ae615d8f7f24 | Python | 11,050 | 364 | # 20180625
import importlib
import pickle
import mne
import numpy as np
import pandas as pd
import h5py
import os
import re
import sys
import yaml
import multiprocessing
import gc
#from scipy.io import loadmat
from glob import glob
from progressbar import Bar, ETA, Percentage, ProgressBar
from joblib import Paralle... |
29af5f88243b03d2e825dbe8d2841908cf32fba2de44ae68723888e46fd84d4a | Python | 11,051 | 243 | import matplotlib.pyplot as plt
import sys, os, struct
import pysam
import numpy as np
from statistics import median, stdev
import pyarrow as pa
import pyarrow.parquet as pq
import time
"""
python /private/groups/brookslab/cafelton/fusions-code/pod5kmersignal/plotSignalInRegion.py chr13:52310695-52310705
can_m... |
49c5bfeb07d81242d2794860af1fab50800617ec72580e3f60c70bf6435d4375 | Python | 11,055 | 251 | # this file is used to evalaute the performance of the ev2gym environment with various stable baselines algorithms.
from stable_baselines3 import PPO, A2C, DDPG, SAC, TD3, DQN
from stable_baselines3.common.callbacks import BaseCallback
from stable_baselines3.common.callbacks import EvalCallback
from sb3_contrib import... |
8c58e64a5d23938a89ad4fabdad602bb55bdf4424ab0e8238c893cee8cff2b01 | Python | 11,075 | 256 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://w... |
a1656cea56173b0f431bb8c16519fa5f6fd1eadf43cfb310ddd6b270c295de12 | Python | 11,078 | 300 | import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import scipy as sp
import seaborn as sns
from statsmodels.stats.anova import AnovaRM
condition_map = {
'early_appetitive': 'Early',
'late_appetitive': 'Late',
'threat': 'Threat',
'post_threat': 'Post-threat'
}
def get_traces(sessi... |
b7b79e5d1fc08fc3ffda358f330b3337c2cac0497b471712a264a2715b57a217 | Python | 11,078 | 344 | """Tests for Figures REST API endpoints."""
import pytest
from helpers import (
MockSioServer,
auth_header,
create_test_room,
create_test_user_in_db,
)
from httpx import AsyncClient
from sqlalchemy.ext.asyncio import AsyncSession
from zndraw.exceptions import FigureNotFound
from zndraw.models import R... |
dbfc8026d6a1252644089d205c1bdc47a57b66c301be9ae2dfbee3eefafc79fd | Python | 11,081 | 330 | import glob
import time
import numpy as np
import matplotlib.pyplot as plt
from skimage import draw
from random import shuffle
import matplotlib.image as mpimg
from torch.utils.data import Dataset
import itertools
import torch
from inspect import currentframe, getframeinfo
from PIL import Image
class ... |
d6471716881876eb977aa200c6c6c12511a91ad4263e22661c4ec9c60395491e | Python | 11,085 | 352 | """
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 torch
from .atom_update_block import AtomUpdateBlock
from .base_layers import Dense, ResidualLayer
from .ef... |
af16fe286df41ff3cd4b5d9777c83400566124954e39069825dc11ec5021099e | Python | 11,087 | 262 | #!/usr/bin/env python
"""
# Author: ChangXu
# Created Time : Mon 23 Apr 2021 08:26:32 PM CST
# File Name: STMAP_train.py
# Description:`
"""
"""
test:
from cal_graph import graph
import scanpy as sc
from GCN import STMAP_model
from STMAP_main import train
data_path = "/home/xuchang/Project/STMAP/Human_br... |
be460de771b7e41fab07ab49a3d6843a4f4ed1aec8bc07d7d02b1c9538e63d8d | Python | 11,090 | 335 | import json
from pathlib import Path
from typing import Any
from schema_salad.utils import convert_to_dict
from cwltool.context import LoadingContext
from cwltool.load_tool import load_tool
from cwltool.subgraph import get_step, get_subgraph
from cwltool.workflow import Workflow, default_make_tool
from .util import ... |
05c28797a2f9f82e32374d8bdbbfc6032525f40b5e3723f0a445a9d240b5ba91 | Python | 11,092 | 309 | from .mixin import scviMixin, adjMixin
from .GODEVAE import GODEVAE_r
from .utils_ODE import get_step_size
import torch
import torch.nn.functional as F
from torch_geometric.data import Data
import numpy as np
from typing import List, Tuple, Optional
from torchdiffeq import odeint
class GODEVAE_Train... |
a4b06b585cb100c01aca96e3e22801b6bb70aa6dd3cc3bc7d393f3b6129d72ad | Python | 11,094 | 228 | #!/usr/bin/env python2.7
import os, sys
os.environ["OMP_NUM_THREADS"] = "1"
os.environ["OPENBLAS_NUM_THREADS"] = "1"
os.environ["MKL_NUM_THREADS"] = "1"
os.environ["VECLIB_MAXIMUM_THREADS"] = "1"
os.environ["NUMEXPR_NUM_THREADS"] = "1"
import argparse
import chisel
src = os.path.dirname(chisel.__file__)
from ..Ut... |
22c7a265238bb336235f45d6ea431d669986f425f928fef2958161006ef9c1a6 | Python | 11,099 | 221 | import msgpack
import psycopg2
import ujson
from django.core.management.base import BaseCommand, CommandError
from django.conf import settings
from django.db import connection
from catmaid.control.node import (_node_list_tuples_query, update_cache,
Postgis2dNodeProvider, ORIENTATIONS, update_node_query_cache,... |
b5b2cb1ce727233fa28ac58ff0b53e5596203e174fd113bf81c289495d130fc7 | Python | 11,117 | 280 | # Linux/cgroup memory diagnostics used by the DuckDB exporter and report rules.
# All functions are best-effort: they degrade to None/``unknown`` off Linux or when
# the relevant /proc and /sys/fs/cgroup files are absent, and they never raise.
import os.path
import resource
import sys
from src.util import get_logger
... |
b81a29f254cd66d4d15f007496b6128033d59b512c50e9804eac1755e8c48d36 | Python | 11,119 | 295 | from medperf.comms.entity_resources import resources
from medperf.exceptions import InvalidArgumentError, MedperfException
from medperf.utils import remove_path, run_command, tmp_path_for_file_decryption
from .utils import (
check_allowed_run_args,
add_medperf_run_args,
add_user_defined_run_args,
add_me... |
3e16d786ce2024a5244afe6c358a96093129bf05d3aef40cd86a56f9302a452b | Python | 11,121 | 352 | """
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 torch
from torch_geometric.nn import SchNet
from torch_scatter import scatter
from ocpmodels.common.registry import registry
from ocp... |
48f5c7a9dee5ee8025284c6c39589b408496cd6acbbde5457509ca542ce4d1a9 | Python | 11,123 | 309 | #!/usr/bin/env python
from __future__ import annotations
import argparse
import json
import os
import re
import shutil
import subprocess
import sys
from multiprocessing import Pool, cpu_count
from time import time
def call(args: list[str]) -> tuple[int, int, str, list[str]]:
"""Subprocess run wrapper."""
com... |
c0dee7c00b18446c8a6ed99adcb176bec7ce84e8d26b9773f4a374117dcf337d | Python | 11,126 | 339 | """
classifier_builder.py - Build a random forest classification model from raw data.
"""
# imports
from sklearn.ensemble import RandomForestClassifier
from sklearn.feature_selection import SelectKBest
from sklearn.model_selection import train_test_split, cross_val_score, KFold
from sklearn.metrics import roc_curve, a... |
d58db04d71bb5a4ac1e24bde7b1d2f8dbbc02b33be4343eb25ca7118f3e55b31 | Python | 11,132 | 183 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://w... |
3e99ebf3d090772a52252672ecb4379b0fc9c8f7c29b291d0898583c8afe2f98 | Python | 11,136 | 325 | import argparse
import os
from collections import OrderedDict
import nearl.data
import numpy as np
import nearl
def parser():
parser = argparse.ArgumentParser(description="Featurize the misato trajectories")
# Input and output settings
parser.add_argument(
"-f",
"--pdbcodes",
typ... |
b1d1c611aa273ff6448d788c4c2ddc40e26e176009942d188f4e680fdf7654c6 | Python | 11,136 | 273 | from __future__ import print_function, division
import csv
import functools
import json
import os
import random
import warnings
import numpy as np
import torch
from pymatgen.core.structure import Structure
from torch.utils.data import Dataset, DataLoader
from torch.utils.data.dataloader import default_collate
from to... |
08e150a9a732aa02fb5fea2a1361d1ca2a480ded114b7bc4f553658ae308cb25 | Python | 11,139 | 279 | #!/bin/env python
# Author: Qiyuan Zhao (zhaoqy1996@gmail.com)
import subprocess
import os
import time
from ReactBench.utils.parsers import xyz_parse
class PYGS... |
1be27c99542696c097a3ef03b07eacdd9163f8bb9de83757aec0b1dccfe25ad0 | Python | 11,159 | 253 | import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
from matplotlib.lines import Line2D
from glob import glob
import scienceplots
import matplotlib.gridspec as gridspec
import scipy.stats as st
from matplotlib.colors import LinearSegmentedColormap
import matplotlib.colors as col... |
4edea989f8c7f8ba894206980c4ebda10bf1395fe3438526562416dc28260807 | Python | 11,159 | 339 | """
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 torch
from torch_geometric.nn import SchNet
from torch_scatter import scatter
from ocpmodels.common.registry import registry
from ocp... |
4777a850f2be0f0225fdb5375ebd8827988b7446ee50da1cf35dfc9d62745918 | Python | 11,160 | 337 | # This file is part of h5py, a Python interface to the HDF5 library.
#
# http://www.h5py.org
#
# Copyright 2008-2013 Andrew Collette and contributors
#
# License: Standard 3-clause BSD; see "license.txt" for full license terms
# and contributor agreement.
"""
Tests the h5py.File object.
"""
import h5py... |
d1314d3a587d2e46d6139eb93940a9c0970cff48e34f0b595bbc5b2acc2b90c5 | Python | 11,160 | 367 | from scipy import special, stats as sstats
from sklearn.neighbors import KernelDensity
import numpy as np
from joblib import Parallel, delayed
from scipy.spatial.distance import correlation
from netneurotools import stats
from neuromaps.stats import compare_images
def compare_maps(src, trg, metric='pearsonr', ignore_z... |
b140c3f78652dfb1ef7e7ae71d2a612e5df7974c6539bb886b06ffa37307ac6d | Python | 11,164 | 318 | import math
import random
from abc import ABC, abstractmethod
from collections import defaultdict, namedtuple
from dataclasses import dataclass, field
from typing import Any, Set, Optional, Dict, List
import keras
import numpy as np
from dante.obj_functions import ObjectiveFunction, BuiltInSyntheticFuncti... |
069d7dec0f18a108037e98ab9bcb9af23e10df992ef98c8dccaecfee341b9a3c | Python | 11,166 | 324 | """Utilities related to metrics."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from enum import Enum
from .. import backend as K
from . import losses_utils
NEG_INF = -1e10
class Reduction(object):
"""Types of metrics reduction.
Contains th... |
c57a9929c55ac4e85d344a8432862ff4004b0b873c4535237b6460db654898df | Python | 11,174 | 314 | """
Caffe network visualization: draw the NetParameter protobuffer.
.. note::
This requires pydot>=1.0.2, which is not included in requirements.txt since
it requires graphviz and other prerequisites outside the scope of the
Caffe.
"""
from caffe.proto import caffe_pb2
"""
pydot is not supported under p... |
0d2e9ed86c723b0890eb27e9cbb44b037ab097629b5bdd79f3ccba957c4a05c6 | Python | 11,182 | 291 | import math
from typing import Callable, Optional
from torch.utils.data import Dataset
import torch
import numpy as np
import os
from scipy.linalg import eigh
import tonic
import torch.utils.data
from torch.utils.data import DataLoader
import pytorch_lightning as pl
from datasets.utils.pad_tensors import PadTensors
... |
6b75d6c94f35e822d2988950715d3eb4d09592af212f09b4e0c44161ca199295 | Python | 11,182 | 287 | import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import os, json
import pickle
from . import util
def to_csv(df, path):
"""
https://stackoverflow.com/questions/50047237/how-to-preserve-dtypes-of-dataframes-when-using-to-csv
"""
# Prepend dtypes to the top of df
df2 = df.copy(... |
7393f440abf91d23c154a2feab8724977e6914fa0614ca39012b55f986fe56a5 | Python | 11,193 | 347 | """Test the 1.3 loop feature."""
import json
from collections.abc import MutableMapping, MutableSequence
from io import StringIO
from cwltool.main import main
from .util import get_data
def test_validate_loop() -> None:
"""Affirm that a loop workflow validates with --enable-dev."""
params = [
"--en... |
af09d258e9b5b0385637842f8e77956d7e1dda6df984497febee2fd535defcf8 | Python | 11,198 | 345 | # Author: Huaxu Yu
"""
classifier_builder.py - Build a random forest classification model from raw data.
"""
# imports
from sklearn.ensemble import RandomForestClassifier
from sklearn.feature_selection import SelectKBest
from sklearn.model_selection import train_test_split, cross_val_score, KFold
from sklearn.metrics... |
0c38b17934c8f091ae9e8a628ad7c737dfc959bbc78686727aae81b000aa2786 | Python | 11,203 | 347 | import torch
import torch.cuda
import glob
import os
import pandas as pd
import json
from collections import *
import random
import diskcache
from torch.utils.data import Dataset
from torch.utils.data import DataLoader
import numpy as np
import cv2
import torchvision.transforms.functional as fn
import Utils.config as ... |
2df6b12baafa552a9e54ba2c895084f9c58a7b7ab0b5736aa7363feea530f7f1 | Python | 11,219 | 308 | """
Qt dialog for manual labeling of an image
Copyright (c) 2017 Polytechnique Montreal <www.neuro.polymtl.ca>
License: see the file LICENSE
"""
import logging
import sys
import numpy as np
from PyQt5 import QtCore, QtWidgets, QtGui
from spinalcordtoolbox.gui import base
from spinalcordtoolbox.gui import widgets
fr... |
c4a45757383e87172b4475edd3b32efbe3da1bccb9a36a859a94ca62f1e659a1 | Python | 11,225 | 187 | import cv2
from create_dataset import *
from utils import *
from PDFN import PDFN
from options import *
from saver import Saver, resume
from time import time
from tqdm import tqdm
from optimizer import Optimizer
import datetime
import torch.utils.data
import torch
timestamp = datetime.datetime.now().strftim... |
ab4423e0571953c545bed05d151500750756b3af255ef625df25b66f41f7f02d | Python | 11,227 | 361 | """
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 Optional
import torch
from ocpmodels.common import gp_utils
from ocpmodels.modules.scaling import ScaleFacto... |
2da262e47f5a297944497562946ebf7fee29891d9ce402e4526b0c4237ce8a71 | Python | 11,230 | 256 | """Contract and mode-table tests for PyPhotometryRecordingExtractor."""
import json
from pathlib import Path
import numpy as np
import pytest
from guppy.extractors.pyphotometry_recording_extractor import (
PyPhotometryRecordingExtractor,
)
from guppy_test_data import STUBBED_TESTING_DATA
from .recording_extract... |
6d63fb92476bdd4608c0b0bab797d68fd32e64ff44ecf0c9b4e8b844c4095279 | Python | 11,234 | 286 | import re
import pandas as pd
from pathlib import Path
import json
import subprocess
# Constants
DATALAD_DIR = Path('/Users/h/Documents/projects_local/1076_spacetop')
SCANNOTES_FNAME = Path('/Users/h/Documents/projects_local/cue_expectancy/resources/spacetop_scannotes/ST_Participants - scan_info_08-10-2022.csv')
# Ta... |
f319fcbb2a1de466a7ea67cbba78f1262e2aaa22a44573779e921c76f7004b75 | Python | 11,244 | 296 | import concurrent.futures
import sqlite3
from pathlib import Path
import numpy as np
import pandas as pd
import torch
from rdkit import Chem, DataStructs
from rdkit.Chem import QED, rdFingerprintGenerator
from torch_pca import PCA
from tqdm import tqdm
from DiastereomericResolutions.main.molecule_db import MoleculeDa... |
566b1f321786cbf26acb297479e94a2f9d0df227e395b63a2683226bb164da87 | Python | 11,247 | 308 | """Reformat a CWL document and all its references to be a single stream."""
import copy
import urllib
from collections.abc import Callable, MutableMapping, MutableSequence
from typing import Any, Optional, Union, cast
from cwl_utils.types import CWLObjectType, CWLOutputType
from ruamel.yaml.comments import CommentedM... |
c216478175f68ca597c4b15e9b5bd808aacf723e73821fc0544acd9231eebc46 | Python | 11,248 | 305 | """Sequential model class.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import warnings
import copy
from . import network
from .training import Model
from .base_layer import Layer
from .input_layer import Input
from .input_layer import InputLayer
fro... |
5c792c892034472d3dfa98e94444f9feba3ca3d057829f0d5303ea81a78cffa6 | Python | 11,258 | 224 | # Description: Implementation of the Local Optimal Linear Estimator (LOLE) algorithm.
import numpy as np
from sklearn.linear_model import MultiTaskLasso, LinearRegression, LogisticRegression
from grid_cell.manifold_fitter import label_mesh
from sklearn.metrics import mean_squared_error
from grid_cell.util import permut... |
9c55d9615528494c627216cf375feebacdba693248c870d6ca2302c8b8fafb4e | Python | 11,265 | 359 | import numpy as np
from scipy.special import expit
import scipy
from cogmodels.base import CogParam
from cogmodels.rl import RL_4p
from cogmodels.utils import regularize
PRECISION = 15
TOL = 1e-15
class Pearce_Hall(RL_4p):
"""
Adapted from Li et al. 2011:
Q_{t+1} = Q_t + alpha * alpha_nu_t * rpe_t
al... |
5a5ec382b2298bb4da1611a87912b738c715356a754c2d39c0ff68bb65154040 | Python | 11,276 | 225 | # -*- coding: utf-8 -*-
# Generated by Django 1.9.13 on 2017-04-16 23:06
from django.conf import settings
from django.db import migrations, models
import django.db.models.deletion
import django.utils.timezone
class Migration(migrations.Migration):
dependencies = [
migrations.swappable_dependency(setting... |
403c742eb3c0d634e9701345f410819af29d4132af572f4c9dfa1ca9eb900762 | Python | 11,279 | 312 | """TDD tests for analysis extensions.
Tests for Distance, DihedralAngle, Properties1D, Properties2D.
Calls extension.run(vis) directly against a real server to verify
that analysis extensions create correct Plotly figures.
"""
import ase
import numpy as np
import plotly.graph_objects as go
import pytest
from zndraw ... |
d4ff1e48d31529734a5124e734399bb67126fc03177cc6a2ac832bad45c60b13 | Python | 11,280 | 341 | from itertools import product
from typing import Any, Dict
import numpy as np
import pytest
from hypothesis import given, note, settings, strategies
import xgboost as xgb
from xgboost import testing as tm
from xgboost.testing.params import (
cat_parameter_strategy,
exact_parameter_strategy,
hist_cache_str... |
247ff85dec7f202f1ed66e047ead948481b36ae35249cf962ba265a98b232365 | Python | 11,282 | 371 | import torch
import torch.cuda
import glob
import os
from collections import namedtuple
import pandas as pd
import json
from collections import *
import random
import diskcache
from torch.utils.data import Dataset
from torch.utils.data import DataLoader
import numpy as np
import cv2
import torchvision.transforms.functi... |
aa5ce299fb3c5ac31190e9e2a63b06ea1df8ba633a18a61f903d0cd55aa8106f | Python | 11,283 | 276 | # -*- coding: utf-8 -*-
import logging
import os
import re
import functools
from selenium import webdriver
from selenium.webdriver.common.by import By
from selenium.webdriver.common.keys import Keys
from selenium.webdriver.support.ui import WebDriverWait
import selenium.webdriver.support.expected_conditions as EC
fr... |
8ddd8181a103b8194be771a077226fade4f443bef54d6c892c94efe310535cbd | Python | 11,299 | 263 | import numpy as np
import pytest
from guppy.analysis.z_score import compute_z_score, deltaFF, z_score_computation
# ── deltaFF ───────────────────────────────────────────────────────────────────
def test_delta_ff_equal_signal_and_control_returns_zeros():
signal = np.array([1.0, 2.0, 3.0])
control = np.array... |
9a7cf6a007727e1b6e14331e77ea250386d4cc50b91b38708f60a7fc84ebe451 | Python | 11,304 | 372 | """Test ephys model objects"""
import os
import tempfile
import contextlib
import pytest
import numpy
from bluepyopt import ephys
sim = ephys.simulators.NrnSimulator()
TESTDATA_DIR = os.path.join(
os.path.dirname(
os.path.abspath(__file__)),
'testdata')
simple_morphology_path = os.path.join(TESTDAT... |
8a70643d027e3d049cf70fb25864cb9989551851883937724101209a4a1839d1 | Python | 11,312 | 188 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://w... |
7040051fc65f21e327ea9096b3222bc3962b490c5c9b25a3c75d986dc00cb95a | Python | 11,316 | 296 | # Copyright (c) 2021 EleutherAI
# This file is based on code by the authors denoted below and has been modified from its original version.
#
# Copyright (c) 2020, NVIDIA CORPORATION. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in complianc... |
f012d43e05b3540c32cac66e4890d8d819a794df981a2846d2344283c8683a4d | Python | 11,318 | 376 | import os
import sys
import numpy as np
import pathlib as pl
import subprocess as sp
from decimal import Decimal
from scipy.stats import pearsonr
from scipy import stats
from scipy.interpolate import Akima1DInterpolator
def smooth(a, window_size=5, window_type='hanning', axis=1):
"""
Smooth array by convolving... |
7f17019d934e2e95f72440f5a1f983e40b76f01949631f7fc7369fc0a7c5b863 | Python | 11,319 | 259 | print("It works!")
import pandas as pd
import scanpy as sc
import numpy as np
import os
import json
import anndata as ad
import scipy
import h5py
### reading the data that we want to apply the clock to
adata = ad.read('./external_data/frohlich_control_lognorm_2024-12-19.h5ad', backed='r')
with h5py.File("external_da... |
bbe19d5110f8aec5df6a5a20bfd9bc9cdd4af236b46af08482c67a6a19b9f1db | Python | 11,319 | 333 | """
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 numpy as np
import sympy as sym
import torch
from scipy import special as sp
from scipy.optimize import brentq
def Jn(r:... |
c5e0fbb98eda876e2efc6897330cde86081a973874f40c8940c6be4b79ddff55 | Python | 11,322 | 269 | # -*- coding: utf-8 -*-
from collections import defaultdict
from functools import partial
from itertools import combinations, chain
import json
import math
import networkx as nx
from rest_framework.decorators import api_view
from typing import Any, DefaultDict, Dict, Iterator, List, Optional, Set, Tuple, Union
from ... |
643cf0ff1301f67ec63ab0e2868d34023e626504a5a79ed49c3e4c2ecba7ebf4 | Python | 11,323 | 302 | #!/usr/bin/env python
#
# Warp template and atlas to a given volume (DTI, MT, etc.).
#
# Copyright (c) 2013 Polytechnique Montreal <www.neuro.polymtl.ca>
# License: see the file LICENSE
import sys
import os
from typing import Sequence
import spinalcordtoolbox.metadata
from spinalcordtoolbox.reports.qc import generate... |
d4f05c2aaa06d71d8f183163ae28068aebbcbadfe3445827ae4a366b21c9e57e | Python | 11,323 | 289 | # Cluster measurement.
# Author: David Young, 2019
"""Clustering measurements."""
import os
import numpy as np
import pandas as pd
try:
from sklearn import cluster
from sklearn import neighbors
except ImportError:
cluster = None
neighbors = None
from magmap.cv import chunking, detector
from magmap.se... |
22a46482d2808454c44aa016b270186d6fdb96b08ee5ddc1a4638f4f3c11ac38 | Python | 11,334 | 398 | """Validate alignment of histological sections to structural reference volume."""
import os
from multiprocessing import cpu_count
from typing import Callable, Tuple
import matplotlib.pyplot as plt
import nibabel as nib
import numpy as np
import pandas as pd
from brainbuilder.utils import utils
from joblib import Paral... |
9f39f115bbddb1cee5586230be72dc7903e2b7391b2a86b9973ce5d22bdea67a | Python | 11,341 | 357 | import torch
import torch.nn as nn
from nnunet_mednext.network_architecture.custom_modules.custom_networks.TransBTS.Transformer import TransformerModel
from nnunet_mednext.network_architecture.custom_modules.custom_networks.TransBTS.PositionalEncoding import FixedPositionalEncoding,LearnedPositionalEncoding
from nnunet... |
2d227f3cf332301ce87e1a595e3fc1c6fe796189962fe9fbe5aeb3eec4c129f0 | Python | 11,344 | 300 | # Extract faces from videos on nas and store them
import os
import platform
import re
import shutil
import time
import pandas as pd
from pathlib import Path
# from moviepy.video.io.ffmpeg_tools import ffmpeg_extract_subclip
PATH_TO_NAS = Path('/nas/student/SimonPistrosch') if platform.system() == 'Linux' else Path('/... |
44df7e2d86bb601678aced8a687c78c462b188b787922e2ae9e419b2531db310 | Python | 11,344 | 290 | #%%
# This script produces the results shown in Figure 1 in Wolff and Rademaker (2024)
# It loads the simulation data obtained from Fig1_run_first_GFM_simulations.m and performs the decoding analysis
# precomputed simulation data and decoding results are available at https://osf.io/bdf74/
import scipy.io as sio
impor... |
22b3a6b5bf2df0eb259cad8eb8925ee043720b7d3fcb21f965a5bc117b10bc51 | Python | 11,349 | 271 | import logging
import shutil
from pathlib import Path
from typing import Any
import numpy as np
import pandas as pd
from guppy.extractors import BaseRecordingExtractor
from guppy.extractors.detect_acquisition_formats import _classify_csv_file
from guppy.utils._hdf5_io import write_hdf5
logger = logging.getLogger(__n... |
cd00db27141e0180a525643a8a3c2bf09b7f3a87f43c400f8948c9172aa83c99 | Python | 11,349 | 270 | #!/usr/bin/env python
import argparse
import os
import sys
import datetime
from parse_config import parse_json_config, print_config
from parse_gene_anno import parse_gff_tree
from sc_longread import blocks_to_junctions, remove_similar_tr, get_gene_flat, get_gene_blocks, group_bam2isoform
from gff3_to_fa import get_tra... |
83149fe402e89e764cd8caa7db6b92d846be157ec4cab8c40ac8ab1d4607655d | Python | 11,356 | 448 | #!/usr/bin/env python
#
# Copyright 2009 Neal Norwitz All Rights Reserved.
# Portions Copyright 2009 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
#
# ... |
00efbd9a26ecfad00eace1bd3769d1b68196227754a3952e00a68223cfd15897 | Python | 11,360 | 254 | from pytorch_lightning import LightningModule
from pytorch_lightning.strategies import DeepSpeedStrategy
from deepspeed.ops.adam import DeepSpeedCPUAdam, FusedAdam
from transformers.optimization import AdamW, TYPE_TO_SCHEDULER_FUNCTION
from torch.optim import Optimizer
from torch.optim.lr_scheduler import _LRScheduler
... |
be565b149701a61f02cbebc0e640ab0eb64a820a88abc9148ba2ea4ad2b037ca | Python | 11,364 | 381 | """Genereal utils."""
import itertools
import os
from collections import deque
from datetime import datetime
from pathlib import Path
from typing import Iterable, Optional
import cv2
import cv2 as cv
import numpy as np
from numpy.typing import NDArray
from omegaconf import OmegaConf
from PIL import Image
from soccertr... |
fb3dee896eeb9fbd20a0aa5be2665c87c0086bc700849b612fd555e3713881e1 | Python | 11,366 | 310 | #!/usr/bin/env python
# coding=utf-8
# Copyright 2023 Statistics and Machine Learning Research Group at HKUST. All rights reserved.
"""A simple shell to inference the input data.
"""
from cmath import e
from dataclasses import dataclass, field
import logging
import json
import numpy as np
import requests
from PIL impor... |
4b2348b541a576e78f86cdbe51f9531d26851341b07803400c418160d19443bd | Python | 11,372 | 267 | # SPDX-License-Identifier: Apache-2.0
# This file is cloned from microsoft/onnxruntime/tools/python and updated L57 by adding default dim value 1
# onnxruntime commit id: fdce4fa6af437b0b822958ab47b3b8f77f9e14ae
import glob
import os
import shutil
import numpy as np
import onnx
import onnx_test_data_utils
from onnx ... |
c1c2d766b90c0f5772e574b29b0516749fd9e3c1091eaf21429a2fd391ed43e1 | Python | 11,383 | 410 | import pytest
from kgx.graph.nx_graph import NxGraph
from kgx.graph_operations import (
remove_singleton_nodes,
fold_predicate,
unfold_node_property,
remap_edge_property,
remap_node_property,
remap_node_identifier,
)
def get_graphs1():
"""
Returns instances of defined graphs.
"""
... |
e6e5993522b7823e8b0b7cf3c973732e2119e0c2abc29cfd865cb2252f5b2ba8 | Python | 11,386 | 239 | #!/usr/bin/env python
# Import required modules
from __future__ import print_function
from future import standard_library
standard_library.install_aliases()
from builtins import str
import os
import argparse
import subprocess
import ICA_AROMA_functions as aromafunc
import shutil
# Change to script directory
cwd = os.... |
fe402d6d65eb7172fef8eb42664548bcd746df4de1210c69b851ef755cf5e9ae | Python | 11,389 | 238 | import numpy as np
from collections import Counter, defaultdict
from time import time
import re
from glob import glob
from sklearn.base import clone as CLONE
import warnings
from sklearn.exceptions import ConvergenceWarning
import sklearn.metrics as metrics
# Imputation
from sklearn.experimental import enable_iterativ... |
a9006e48e817a024f2cf1660f0fe0632f515df822d5f0d32a435c5df57ca3a06 | Python | 11,394 | 386 | import os
import json
import tempfile
import gzip
from kgx.source import TrapiSource
from kgx.transformer import Transformer
from tests import RESOURCE_DIR, TARGET_DIR
def test_read_trapi_json1():
"""
Read from a JSON using TrapiSource.
"""
t = Transformer()
s = TrapiSource(t)
g = s.parse(os... |
7a9ff920e585ce2da750f1388b143040bbc5c41e85792895d0a1ff2e5b5e1002 | Python | 11,396 | 250 | # encoding=utf-8
import torch, math
import torch.nn.functional as F
def top_k_logits(logits, top_k=0, top_p=0.0, filter_value=-float('Inf')):
# This function has been mostly taken from huggingface conversational ai code at
# https://medium.com/huggingface/how-to-build-a-state-of-the-art-conversational-ai-with... |
f89f96d591e651a9f4abb558332cc36919103ac7427330556b0804b20fe43da5 | Python | 11,399 | 270 | # -*- coding: utf-8 -*-
import json
from datetime import datetime
from catmaid.control.annotation import _annotate_entities
from catmaid.control.annotation import create_annotation_query
from .common import CatmaidApiTestCase
class AnnotationsApiTests(CatmaidApiTestCase):
def test_annotation_creation(self):
... |
7881e7bbf98814905e12c8afea66c2b7c53ca808ca40d863195232501ff2c026 | Python | 11,400 | 319 | from statistics import mean
import numpy as np
import math
np.seterr(divide='ignore', invalid='ignore')
def find_plane_equation(plane):
"""
Finds the plane equation of a plane
:param plane: the plane to find the equation of
:type plane: :any:`numpy.ndarray`
:returns: the normal vector of the pla... |
f1e93b60165794cf81843c906b264057cef0903dac920b585069cea935cff980 | Python | 11,400 | 317 | from statistics import mean
import numpy as np
import math
np.seterr(divide="ignore", invalid="ignore")
def find_plane_equation(plane):
"""
Finds the plane equation of a plane
:param plane: the plane to find the equation of
:type plane: :any:`numpy.ndarray`
:returns: the normal vector of the pla... |
cb0f3d95d41ae70fb968a455d8eb1fd2d546c666e81d916012801940cd04baa8 | Python | 11,403 | 274 | import pymonetdb
import uuid
from prov.model import ProvDocument
from prov.dot import prov_to_dot
import os
import sys
import json
import argparse
import re
from provdbconnector import ProvDb
from provdbconnector import Neo4jAdapter
from neo4j import GraphDatabase
# Environment variables for Neo4j credentials and con... |
d9c74cc3e553929d60e9d2496ea8dcd57950b243375183d6413c111b48c2f5e7 | Python | 11,403 | 352 | # tests/test_serve.py
"""Tests for JobManager auto-serve: claim loop, lifecycle wrapping, wait()."""
import threading
import uuid
from typing import Any, ClassVar
from unittest.mock import MagicMock
from zndraw_joblib.client import (
Category,
ClaimedTask,
Extension,
JobManager,
)
from zndraw_joblib.e... |
7ea9ac5720a950ccbfce6a6f99d372717c1b0f6adef00c4406be7d60d6b336a8 | Python | 11,411 | 393 | #!/usr/bin/env python
# coding=utf-8
# Copyright 2023 Statistics and Machine Learning Research Group at HKUST. All rights reserved.
"""A simple Multimodal chatbot implemented with lmflow APIs.
"""
import logging
import json
import time
from PIL import Image
from lmflow.pipeline.inferencer import Inferencer
import num... |
847c7777412235c16f0f9776574c0064e234aca5280f3f69e8c8cd4c4ea2acfd | Python | 11,417 | 275 | #!/bin/env python
# Author: Qiyuan Zhao (zhaoqy1996@gmail.com)
import os,sys
from glob import glob
import yaml
import logging
import time
import pyjokes
import multiprocessing as mp
from logging.handlers import QueueHandler
from joblib import Parallel, delayed
# Add the parent directory to Python path to enable Reac... |
6690b9b31233d4f8800ae0d45b959ff203deb5f1f90bf62cd36db24045a43d84 | Python | 11,425 | 285 | # load Modules
from PyQt5 import QtGui, QtWidgets, QtCore
import pyqtgraph as pg
import numpy as np
import math
from util.conf import cs_roi_params
from util import colors
from features.Feature import Feature
from view.ImageView import ImageView
from model.Object import Object
class CellSelection(Feature):
def _... |
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