sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
7ce43697cadab0e6a589c38c56437523e30a8aad57cd9922590da61a83dd1815 | Python | 5,000 | 132 | from rest_framework import serializers
from django.utils import timezone
from training.models import TrainingExperiment
from dataset.models import Dataset
from .models import ExperimentDataset
from utils.associations import (
validate_approval_status_on_creation,
validate_approval_status_on_update,
)
def is_... |
f77be4075ab67747abfed7b4fbb9a7d70be0bb1f81103aacb3b04712ceab6fbd | Python | 5,000 | 135 | """Smoke tests for the pyoxigraph API surface used across all Babel datahandlers.
These tests exercise Store.bulk_load() and RdfFormat.* directly, which are bypassed
when other tests inject a pre-built store via ClassName.__new__().
"""
import io
import pyoxigraph
import pytest
def _store_from_bytes(data: bytes, f... |
2acfd3d98afcaad1553a98e040420c1500526f5d2746c7691a829fad5ce0267d | Python | 5,004 | 146 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import argparse
import os
import shutil
import itertools
from multiprocessing import Pool
import numpy as np
from dmriqcpy.analysis.stats import stats_mask_volume
from dmriqcpy.io.report import Report
from dmriqcpy.io.utils import (add_online_arg, add_overwrite_arg,
... |
39f68b9c42fa140c59fd76335e49e468aca4febf651cddbbfd1aaddf086d9c4d | Python | 5,004 | 146 | #!/usr/bin/env python3
"""Offline self-test: emapper over every --itype against the downloadable
mini dataset, diffed against committed golden annotations.
Requires the ``test_datasets/data`` + ``test_datasets/fixtures`` +
``test_datasets/golden`` directories (produced by ``make_test_dataset.py`` and
``gen_golden.py``... |
9a5dc3316bf6bdc5999cc04033cf361f8394f345f3f1a4014be6f2a5c4c31481 | Python | 5,004 | 85 | import os
import pandas as pd
import shutil
import json
def format_filenames(source_dir, target_dir):
if not os.path.isdir(target_dir):
os.makedirs(target_dir)
subject_info = dict()
file_info = []
for dir1 in os.listdir(source_dir):
if dir1.startswith('S'):
space_idx = dir... |
8298c50fed7ab8792cd2f0598a5a6263a4f6bd4ab7ada7ffa9df1e6c160472d4 | Python | 5,005 | 173 | """
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 ..initializers import he_orthogonal_init
class EfficientInteractionDownProjection(torch.nn.Module):
"""
Down pro... |
bbe669f29315b8cbf5e6067e53e1e3abbc17741709c7e32b79c0be018f4e4cc5 | Python | 5,005 | 96 | # -*- coding: utf-8 -*-
from django.db.models import Count
from django_migration_testcase import MigrationTest
class Migration0018Tests(MigrationTest):
app_name = 'catmaid'
before = '0017_update_edge_indices'
after = '0018_add_stack_mirrors_and_groups'
def migrate_kwargs(self):
return {
... |
25e08bacf0e1265ac8e38d833937dcd90a3b0709434863d8036fd0b2167a35fc | Python | 5,007 | 135 | import os
import medperf.config as config
from medperf.enums import AutoApprovalMode
from medperf.exceptions import InvalidArgumentError, MedperfException
from medperf.utils import sanitize_path, validate_and_normalize_emails
class UpdateAssociationsPolicy:
@classmethod
def run(
cls,
benchmar... |
7a5fb17435b3e1783ea6ce997da11fc74511538d740fe103e057040959e69d9d | Python | 5,008 | 136 | """Test singularity{,-ce} & apptainer versions."""
import pytest
from packaging.version import Version
import cwltool.singularity
from cwltool.singularity import (
get_version,
is_apptainer_1_or_newer,
is_version_2_6,
is_version_3_1_or_newer,
is_version_3_4_or_newer,
is_version_3_or_newer,
)
... |
065942d96f44b02e8c5cb0f8379ccbd0085e00995d3bf49bd1a0bcd623521d64 | Python | 5,011 | 146 | """
Benchmark the data throughput of the Data Extraction from the HDF5 dataset.
"""
import argparse
import json
import os
import time
from nearl.io.dataset import Dataset
def benchmark_dataset_method(dset, exit_point=None, **kwargs):
st = time.perf_counter()
st_total = time.perf_counter()
print("Started... |
96dee99579ad7589528918dba86a1f7c31d1b91b93ddfc1bea296a07a366ea5a | Python | 5,018 | 141 | # Copyright (c) OpenMMLab. All rights reserved.
import torch
import torch.nn as nn
import torch.nn.functional as F
from mmcv.cnn import ConvModule, build_activation_layer, build_norm_layer
from mmseg.registry import MODELS
from .decode_head import BaseDecodeHead
class DCM(nn.Module):
"""Dynamic Convolutional Mod... |
8383f59872bd1e48cb92972ef2a6583ada212c936807b250daa4cda347a0f688 | Python | 5,019 | 137 | #!/usr/bin/env python3
#
# Copyright 2015, Daehwan Kim <infphilo@gmail.com>
#
# This file is part of HISAT 2.
#
# HISAT 2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# ... |
87b59fb71fa5bdee9abea4b396534a5afebe4ad4132a8e440061fd4898c0b2e8 | Python | 5,027 | 124 | import os.path
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
SIGNAL_PATH = r'8.csv' # Please set this PATH to the signal waveform CSV file.
CLUSTER_RESULTS_PATH = r'DBSCAN_f8.csv' #Please set this PATH to the CSV file generated by DBSCAN.py.
tInc = 4.000000e-06
SENSOR_PAD = [2,1,4,... |
8b22c41d609e27eefd01f822102a7b2bedbf4252a797b6b87a7a055fea901340 | Python | 5,027 | 153 | import numpy as np
import pytest
from keras.utils.test_utils import layer_test
from keras.layers import pooling
from keras.layers import Masking
from keras.layers import convolutional
from keras.models import Sequential
@pytest.mark.parametrize(
'padding,stride,data_format',
[(padding, stride, data_format)
... |
ba0e517cff757bda21acb8b9ea5a4e941966523ae812ad67011886f4892d906b | Python | 5,029 | 111 | """
Preprocess the motion curves into adequate length and format to be loaded in
the motion simulation pipeline.
- run this script (from iml-dl/.) with:
python -u ./projects/motion-simulation/preprocessing/motion_curves.py
--input_dir folder_with_motion_data --output_dir output_folder
--output_dir_s... |
bf3aa1e590e70b93e52c4122785f5538ec99d8f07d46d7eb084c488fc1a6c9ce | Python | 5,031 | 88 |
# %% libraries
import os, glob, re
import shutil
import gzip
from os.path import join
from nilearn import image, plotting, masking
import numpy as np
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import itertools
import pathlib
import argparse
epi01_fname = '/Users/h/Documents/projects_local/... |
bf5fddbc5c6e4941e0c105bb8a6a9740f8d6a70808f1d8565e63727f60ba14b7 | Python | 5,034 | 130 | import time
import numpy as np
from Nearl import data_io, log, models
from scipy import stats
from sklearn.metrics import mean_squared_error, r2_score
from sklearn.model_selection import train_test_split
st = time.perf_counter()
log("Loading data...")
input_files = [
"/MieT5/Nearl/data/trainingdata/misato_trains... |
ece02cc01c14004c24842c020f28b617393811b6d7711bc8ba2d8116cc2e3d64 | Python | 5,035 | 181 | """
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 typing import Optional
import numpy as np
import torch
from .base_layers import Dense
from torch_geometric.nn.models.schnet import Gau... |
1c889a632be6531d0d157e2d6ab86dacc58a9099babd7b4bdc73bcc1fde84df7 | Python | 5,037 | 145 | #!/usr/bin/python
import logging
import os
import re
import shutil
import sys
from collections import defaultdict
from isorefiner.common import get_version, run_command, func_with_log
logger = logging.getLogger(__name__)
def main(args):
try:
# Set variables
raw_reads_files = [os.path.abs... |
29b637da97684e2504d27f1424354caa047442502139a62bb5ea082a923c8b42 | Python | 5,043 | 154 | import sys
import pandas as pd
import numpy as np
import diffrax
import jax.numpy as jnp
import jax
import optax
import argparse
jax.config.update("jax_enable_x64", True)
from jaxkineticmodel.parameter_estimation.training import (
create_log_params_means_centered_loss_func,
log_transform_parameters,
expone... |
f895df1ad67df2b55850649f51ca0d0ca4a32b3f36ada58a0219ec9bc26ae656 | Python | 5,045 | 186 | # pylint: disable=missing-function-docstring
"""Global configuration for XGBoost"""
import ctypes
import json
from contextlib import contextmanager
from functools import wraps
from typing import Any, Callable, Dict, Iterator, Optional, cast
from ._typing import _F
from .core import _LIB, _check_call, c_str, py_str
d... |
87cd4c8d04addc85e7deef83628afb390360ef985b91c64f82fdc4e5c627c9b1 | Python | 5,049 | 143 | """
Functions dealing with 2d and 3d curve fitting
Copyright (c) 2019 Polytechnique Montreal <www.neuro.polymtl.ca>
License: see the file LICENSE
"""
# TODO: implement robust fitting, i.e., detection and removal of outliers. See:
# https://github.com/spinalcordtoolbox/spinalcordtoolbox/blob/24ec6668d623be00194b21038... |
a559a4671e85fa2255f77bdad64838aa44d18e2c08d31d6f8f524e0bf8d83f08 | Python | 5,050 | 1 | # -*- coding: utf-8 -*-
"""
Generates simulated (matching) GRFs on the surface of fsaverage5 with a
specified correlation for use in "ground truth" testing of spatial null models.
"""
from pathlib import Path
import os
from joblib import Parallel, delayed
import nibabel as nib
import numpy as np
import pandas as pd
... |
4dc8096afbd1a530b5cb2cbe7fb3b91e254d84b6821695571ce5fbb0a30eada9 | Python | 5,051 | 147 | import torch
import torch.nn as nn
import torch.nn.functional as F
class SE_block(nn.Module):
def __init__(self,inchannels,reduction = 16 ):
super(SE_block,self).__init__()
self.GAP = nn.AdaptiveAvgPool3d((1,1,1))
self.FC1 = nn.Linear(inchannels,inchannels//reduction)
self.... |
9ca49a33def161d2cafa56ddef744178fa56d3219242bd8b69909904c2e63dff | Python | 5,051 | 174 | # Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
import os
from setuptools import find_packages, setup
# Package metadata
NAME = "SAM-2"
VERSION = "1.0"
DESCRIPTION = "SA... |
398037728ccdce78cdb8a7d3e49153a6e1cb9c1dd74263a1b3ae413591e8a15e | Python | 5,056 | 153 | import random
from typing import Optional, Sequence
from pathlib import Path
import hydra
import numpy as np
import omegaconf
import pytorch_lightning as pl
import torch
from omegaconf import DictConfig
from torch.utils.data import Dataset
from torch_geometric.data import DataLoader
from ccdvaeplus.commo... |
020e4aee90541cee81bef7373b89175aed9c5f9dd621fb784f9b08c9859c2e57 | Python | 5,057 | 165 | import ase
import numpy as np
from DiastereomericResolutions.Representation.molecular_representation import (
MolecularRepresentation,
)
from ..Helper_funs.mopac_funs import (
compute_partial_charges,
pm7_compute_bonds,
)
from . import PERIODIC_TABLE_PROPS
from .weighted_rdf import gen_weighted_rdf
np.se... |
2a515e4e2254182325edd0d07147b72cdfa49adc0409d970c692d1f3c9ed14e6 | Python | 5,057 | 140 | import torch
from torch import nn
import numpy as np
from torch.autograd import Variable
from torch.nn import init
from ccdvaeplus.pl_modules.condition_block import ScalarEmbedding, comp_embedding
class Generator(nn.Module):
def __init__(self, dim=[256, 128, 50], condition_prop=False, condition_formula=T... |
40a934ba4fff7a69dd310a59a742553857cd066eeb3727b1e260f4d63c2762e4 | Python | 5,059 | 156 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# -----------------------------------
# @File : dataset.py
# @Time : 2024/03/13 14:22:36
# @Author: Zhang, Zehong
# @Email : zhang@fmp-berlin.de
# @Desc : None
# -----------------------------------
import os
import math
import numpy as np
import pandas as pd
import tor... |
4689f522afd5bcb269aeeaf2626be7c595af266b9323c5a37cc70fd96dff1b10 | Python | 5,061 | 167 | """CLI login (device-code flow) router."""
import logging
import secrets
import string
import uuid
from datetime import UTC, datetime, timedelta
from typing import Annotated
import jwt as pyjwt
from fastapi import APIRouter, Depends, HTTPException, Query, Response
from sqlmodel import select
from zndraw_auth.db impo... |
8dda2da8b874800fb3da041b763b5e1f932b7bf477b140b1d8692a1137703990 | Python | 5,061 | 129 | import ItClust as ic
import scanpy.api as sc
import os
from numpy.random import seed
from tensorflow import set_random_seed
import numpy as np
import warnings
import sys
import metrics as M
os.environ["CUDA_VISIBLE_DEVICES"]="1"
warnings.filterwarnings("ignore")
#import sys
#!{sys.executable} -m pip install 'scanpy==... |
2ba3ebddc54413a3099ae388b763f93b8ca6114da376237b169ee5b8e9aebadf | Python | 5,063 | 174 | """
Filtering criteria (predicates)
"""
from abc import ABC, abstractmethod
from .qualtrim import expected_errors
from .modifiers import ModificationInfo
class Predicate(ABC):
@abstractmethod
def test(self, read, info: ModificationInfo) -> bool:
"""
Return True if the filtering criterion mat... |
eaac2f86140d8c17d86e55692e48e914d90da37db0b2bd5e3001bd76964065fa | Python | 5,063 | 202 | import pytest
from cutadapt.cli import main
from utils import assert_files_equal, datapath, cutpath
# pytest.mark.timeout will not fail even if pytest-timeout is not installed
try:
import pytest_timeout as _unused
except ImportError: # pragma: no cover
raise ImportError("pytest_timeout needs to be installed"... |
7b13863b1ebf820b539bf32bc1b64d734a2ff2b1f478984aa6b87bd7a980a43e | Python | 5,064 | 122 | #! /bin/python3
import subprocess
from subprocess import PIPE
import time
from .bcolors import Bcolors
import os
def run_instruction(cmd, fun, dry_run, fun_module, name, logfile, slurm = None, modules = None):
with open(logfile, "a") as log:
if slurm != None:
cmd = ' '.join(cmd)
job... |
4e4b158d701f843f8c7098bb21d9cb95470f99cec63224deea6be48e997034fa | Python | 5,067 | 115 | import json
import shutil
from pathlib import Path
import numpy as np
import pytest
from guppy.analysis.io_utils import read_hdf5
from guppy.testing.api import locate_run_folder, step1, step2, step3
from guppy_test_data import STUBBED_TESTING_DATA
SESSION_SUBDIR = "csv/sample_data_csv_1"
STORE_ID_TO_STORE_LABEL = {
... |
b4a457ece1d5cca8bec309773ce30aeed2c6890c3c9b3c4b33781c7d351dd960 | Python | 5,067 | 142 | ## ECCV-2018-Image Super-Resolution Using Very Deep Residual Channel Attention Networks
## https://arxiv.org/abs/1807.02758
from model import common
import torch.nn as nn
def make_model(args, parent=False):
return RCAN(args)
## Channel Attention (CA) Layer
class CALayer(nn.Module):
def __init__(self, channel... |
d93fd96a54594f84af9dcdeb6f61ced22e562954982475dab33d4b8059a0306f | Python | 5,072 | 154 | # -*- coding: utf-8 -*-
# tests/test_angles.py
################################################################################
# EncoderMap: A python library for dimensionality reduction.
#
# Copyright 2019-2024 University of Konstanz and the Authors
#
# Authors:
# Kevin Sawade, Tobias Lemke
#
# Encodermap is free sof... |
ae02690c31e17bd63063f56faac66f1d1044a8e25a85f5e5cf8015b7fd50aa0d | Python | 5,073 | 146 | import os
import sys
from pdb import set_trace as bp
import infomap
import matplotlib
import networkx as nx
import numpy as np
from nilearn.input_data import NiftiMasker
from nilearn.masking import unmask
from sklearn.cluster import KMeans
from sklearn.metrics import pairwise_distances
# from sklearn.metrics.pairwise... |
580660e703f718bc48d43f346fa00853802360f828b59050baae56f4109d218a | Python | 5,074 | 138 | import pickle
import numpy as np
from pathlib import Path
def model_values_path():
"""Returns the location of the cas9 cleavage model values.
Returns
-------
os.pathlike
Path to the pickle containing the cleavage values.
"""
THIS_DIR = Path(__file__).parent
path_to_model_values = P... |
a02bfb652e808b1f261b9705038d4dc18fa8c3af87a5ff60a3eca8b2aa145f9a | Python | 5,077 | 158 | #!/usr/bin/env python
# 2023 Jamie McGowan <jamie.mcgowan@earlham.ac.uk>
#
# Reports how many species a BUSCO family was found to be single-copy in
# Only looks at single-copies, ignores if present as multi copy or fragmented
# Usage: python count_buscos.py -d BUSCO_runs
import argparse, os, sys
from os import chdi... |
41a694aa7975ec7473594266424952a72df2fc1b6746d5ac732c5d15e0c9bd08 | Python | 5,078 | 131 | # Copyright (c) OpenMMLab. All rights reserved.
import torch
import torch.nn as nn
from mmcv.cnn import ConvModule, DepthwiseSeparableConvModule
from mmengine.model import BaseModule
from mmseg.registry import MODELS
from ..utils import resize
@MODELS.register_module()
class JPU(BaseModule):
"""FastFCN: Rethinki... |
bae7b52d75243479201f76a64dd8e175911432f796aeeee1a6bef636aea4b58b | Python | 5,079 | 121 | import time
import numpy as np
from sklearn.ensemble import RandomForestRegressor as randomforest
from sklearn.metrics import mean_squared_error, r2_score
from sklearn.model_selection import train_test_split
from scipy import stats
from Nearl import utils, data_io, models, printit
st = time.perf_counter()
printit... |
de833cec365f718929fde072163c1a0a4fe06a77639fa313b9e99b957edbf619 | Python | 5,080 | 164 | """Compute the efeatures generated by the released l5pc model"""
"""
Copyright (c) 2016-2022, EPFL/Blue Brain Project
This file is part of BluePyOpt <https://github.com/BlueBrain/BluePyOpt>
This library is free software; you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public Lic... |
b6dec7c5ecaee764140a234f694ad75f6d642b8fc863438728709e14615a8003 | Python | 5,081 | 90 | from gpflow.kernels import SharedIndependent
from grid_cell.gaussian_wishart.src.likelihoods.WishartProcessLikelihood import *
from grid_cell.gaussian_wishart.src.likelihoods.FactorizedWishartLikelihood import *
from grid_cell.gaussian_wishart.src.models.WishartProcess import *
from grid_cell.gaussian_wishart.src.model... |
00baff70f6a66ef4f960f3e6e8773ac1a09751abf34efce1fae4841848e5eeaf | Python | 5,083 | 154 | import os
import math
from decimal import Decimal
import utility
import torch
import torch.nn.utils as utils
from tqdm import tqdm
class Trainer():
def __init__(self, args, loader, my_model, my_loss, ckp):
self.args = args
self.scale = args.scale
self.ckp = ckp
self.loader_train ... |
0418f764fe03b63e312a49f5a2b1e08eb77b118c0d51fc09247b632bf0895908 | Python | 5,087 | 89 | # 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... |
ea50bf74ba1e38a13e0781f250edf8488aecb16eb907473ad579b0ef4311e0b6 | Python | 5,090 | 126 | import sys
from pathlib import Path
import pandas as pd
import cv2
import time
from joblib import Parallel, delayed
import os
import shutil
import numpy as np
def save_frames_as_images(src, dst, starts, ends):
dst = Path(dst)
dst.mkdir(exist_ok=True, parents=True)
cap = cv2.VideoCapture(str(src))
for ... |
9a94f1e2e2fd9644e299a30ad17df90f043a2fec95a2415acb084fc859d1f64a | Python | 5,091 | 137 | #!/usr/bin/env python3 -u
# 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 argparse
import pathlib
import torch
from esm import Alphabet, FastaBatchedDataset, ProteinBertModel, pretr... |
e9fa5550118d84ab2d778d79cdfcd6d775c759651c501be05e673efa7a7491e1 | Python | 5,092 | 129 | # Copyright (c) OpenMMLab. All rights reserved.
import os.path as osp
import warnings
from typing import Optional, Sequence
import mmcv
from mmengine.fileio import get
from mmengine.hooks import Hook
from mmengine.runner import Runner
from mmengine.visualization import Visualizer
from mmseg.registry import HOOKS
from... |
4b568646375fa26b904c038012f04a720bf44e5ce510f86f75d6a98afe56267c | Python | 5,094 | 164 | """Compute the efeatures generated by the released l5pc model"""
"""
Copyright (c) 2016-2022, EPFL/Blue Brain Project
This file is part of BluePyOpt <https://github.com/BlueBrain/BluePyOpt>
This library is free software; you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public Lic... |
6f02820beb11294311925236d9b4eadbbfee1591ae385939db1b74883514b292 | Python | 5,094 | 174 | """
Shared graph model error reporting code currently used in
the validator, summarize_graph and meta_knowledge_graph modules
"""
from enum import Enum
from json import dump as json_dump
from sys import stderr
from typing import Dict, List, Optional, TextIO
class ErrorType(Enum):
"""
Validation error types
... |
5edb188d121e9e4e14905b6aee8d6dfb7b666441a17aa3a3e17bdc51c7de532a | Python | 5,099 | 133 | #!/usr/bin/env python
## ----------------------------------------
## scikit-ribo
## ----------------------------------------
## Run RNAfold in parallel
## ----------------------------------------
## author: Han Fang
## contact: hanfang.cshl@gmail.com
## website: hanfang.github.io
## date: 12/28/2016
## ---------------... |
f4c2edb4b7ed919886428141e7a3479a5114405a457a1f982f8eabbb49764b00 | Python | 5,100 | 127 | import torch
import math
from dl_utils.config_utils import set_seed
from mr_utils.parameter_fitting import T2StarFit, CalcSusceptibilityGradient
from projects.moco_t2star.utils import *
set_seed(2109)
config = {
'out_folder': './results/MRM/',
'data_params': {'path': './data/links_to_data/recon_test_motion/',... |
73475311c7cc562a794c111b89dee2739aa17ceb158c94337616a53c3be61a00 | Python | 5,101 | 140 | """Unit tests for BaseRecordingExtractor contract."""
import h5py
import numpy as np
import pytest
from guppy.extractors.base_recording_extractor import (
BaseRecordingExtractor,
read_and_save_events_for_extractor,
)
from guppy.testing.mock_recording_extractor import (
_MOCK_DURATION_IN_SECONDS,
_MOCK... |
a21b879a8ee8a08e1d69750f28b056e0aeec65f3ec307fabaa709d8c41ebd9e7 | Python | 5,104 | 127 | import numpy as np
from scipy.signal.windows import gaussian
from scipy.interpolate import CubicSpline
from zigzeg import event_finder, find_runs
from zigzeg.events import find_events_threshold
from scipy.signal import find_peaks
from sklearn.neighbors import KernelDensity
def find_events_peaks(x, thresh, distance=10... |
af0590fc540ea192a3c8bc987a29cda7658c9f4d7833aae0a2280b130ba7ae72 | Python | 5,104 | 131 | # -*- coding: utf-8 -*-
import json
from django.urls import reverse
from django.conf import settings
from django.http import HttpResponseRedirect
from django.views.generic import TemplateView
from django.contrib import messages
from django.contrib.auth import get_user_model
from django.contrib.auth.models import Grou... |
736b12a7a16dad977d121e020c8f478a8234c2b88c6b79966cb1b66a8ce20c71 | Python | 5,105 | 153 | import concurrent.futures as cf
import datetime
import logging
import socket
import subprocess
import sys
import time
from typer import Argument, Typer
from DiastereomericResolutions.Helper_funs.db_utils import _get_needed_pairs_from_file
from DiastereomericResolutions.Helper_funs.job_db import (
complete_job,
... |
03c63c317d8e06f468115862f9cf16e1d5d1e74cda70e25d21281bfc1b12b1a4 | Python | 5,106 | 109 | # coding=utf-8
# Copyright 2022 EleutherAI and The HuggingFace Inc. team. 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... |
9e23c24a76da06a03df531dc15c69601eeab45c8d04e1b10ac37acd5136e5f9d | Python | 5,106 | 169 | """Stores Research Object including provenance."""
import hashlib
import os
import pwd
import re
import uuid
from collections.abc import Callable
from getpass import getuser
from typing import IO, Any, Optional, TypedDict, Union
def _whoami() -> tuple[str, str]:
"""Return the current operating system account as ... |
bc105e31a58bb16f05b6ea0a094bf89f5597e325a7e02441ea2a5ddaf1ea0ddf | Python | 5,108 | 156 | """Seed the server database with demo entries for integration tests or tutorials.
Tokens to access the local server are either from the local JWT factory provided
in the repository root, or from the auth provider. The later case is to do
integration tests with the auth provider. For simplicity, the auth provider
tokens... |
adb8d86aff43edd146f939ecfd10ee3f6e01e9bc11f342ceff6776350622861f | Python | 5,109 | 181 | # 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.
"""
Implements support for HDF5 dimension scales... |
b7bb55a7ec7dd7079813cd1460a2b4b49bd0056bf2aa6a78f6d3ea603fb97c92 | Python | 5,109 | 138 | """
Functions dealing with centerline detection and manipulation
Copyright (c) 2017 Polytechnique Montreal <www.neuro.polymtl.ca>
License: see the file LICENSE
"""
import os
import datetime
import logging
import numpy as np
from spinalcordtoolbox.image import Image
from spinalcordtoolbox.utils.sys import sct_dir_lo... |
fb6823a582397bed9e30b23eb8da47c19cde9e7bb965d1a884f3a911180f4479 | Python | 5,110 | 95 | NEO4J_TEST_CONNECTION = """MATCH (n) RETURN count(n) as count"""
# create
NEO4J_CREATE_DOCUMENT_NODE_RETURN_ID = """
CYPHER 3.5
CREATE (node { }) RETURN ID(node) as ID"""
NEO4J_CREATE_NODE_SET_PART = "SET node.`{attr_name}` = {{`{attr_name}`}}"
NEO4J_CREATE_NODE_SET_PART_MERGE_ATTR = "SET node.`{attr_name}` = (CASE WH... |
f44061fd6cae94e21b8d98747d2a706f29c4e663d1576edde5d4cb1b0a9a4cd2 | Python | 5,113 | 113 | # # measure the localling decoding performance on different data. Run generate_processed_exp_data.py first. Requires run lca_upper_bound.py and generate_processed_exp_data.py first
import numpy as np
import matplotlib.pyplot as plt
import hickle as hkl
import os
from sklearn.linear_model import LogisticRegression
from ... |
b59e620848b39d916cf0411f8046503caf4b762de10b2a3ad374967fc27dbd79 | Python | 5,114 | 128 | # Copyright (c) OpenMMLab. All rights reserved.
from typing import List, Optional, Union
import numpy as np
import torch
import torch.nn.functional as F
from .typing_utils import SampleList
def add_prefix(inputs, prefix):
"""Add prefix for dict.
Args:
inputs (dict): The input dict with str keys.
... |
072711f88ee556b2492601eab95776cfffd9fe4ca79c8977410fa3b5f7f8daa5 | Python | 5,115 | 116 | #!/usr/bin/env python2.7
import os
import argparse
import subprocess as sp
import multiprocessing as mp
import shlex
import datetime
import re
import chisel
src = os.path.dirname(chisel.__file__)
from ..Utils import *
def parse_args():
description = "CHISEL command to re-run the inference of allele- and haplot... |
96d23b519c37edb5275b135d0d86ec4bf104039737a7fa7f2d4f4a4123146c61 | Python | 5,117 | 143 | # Copyright (c) OpenMMLab. All rights reserved.
import argparse
import datetime
import json
import os
import os.path as osp
from collections import OrderedDict
from utils import load_config
# automatically collect all the results
# The structure of the directory:
# ├── work-dir
# │ ├── config_1
# │ │... |
913137914bfd5d2816bd79f1470ad5f953e8abde9db582114ba29862e7cee15c | Python | 5,119 | 168 | #!/usr/bin/env python3
#
# Figure 2: All data, sorted from low to high, no correlations
#
import sys
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
import base
# Sigma multiplier to get 90-th percentile
s90 = 1.6448536269514729
# Include Oocytes or not
nooocytes = True
# Gather data
print('Ga... |
6a48e6caa655c3545eca53bb468826f752c9096625cedc5815ecd8c2fa06fdee | Python | 5,122 | 116 | """Tabulate MONDO's ``oboInOwl:hasDbXref`` target namespaces against what Babel actually ingests.
Babel builds MONDO's concords from ``skos:exactMatch``/``closeMatch`` only, with one deliberate
exception (``MONDO_GARD``). This script regenerates the evidence table in
``docs/sources/MONDO/README.md``: for every namespa... |
c49a51d4ce21a4ae38e142f683bef39ea62c9959321e32abab9dbae70bfe225f | Python | 5,122 | 155 | # Copyright (c) OpenMMLab. All rights reserved.
import argparse
import os.path as osp
import nibabel as nib
import numpy as np
from mmengine.utils import mkdir_or_exist
from PIL import Image
def read_files_from_txt(txt_path):
with open(txt_path) as f:
files = f.readlines()
files = [file.strip() for f... |
08e32444e5c3b6bc9bd6422ccf63d50591e947784d2f51cbba69d6a223513950 | Python | 5,123 | 155 | import os
import tempfile
import threading
import unittest
from sqlmodel import Session, create_engine, select
from DiastereomericResolutions.Helper_funs.job_db import (
Job,
complete_job,
create_md_db,
get_job,
register_worker,
)
from DiastereomericResolutions.Molecular_dynamics.md_config import ... |
314b10d53348d2055a663fabefb7e2dde5accccb78599a3dee8fbf14dfd91940 | Python | 5,124 | 172 | import typer
from typing import Optional
import medperf.config as config
from medperf.decorators import clean_except
from medperf.commands.view import EntityView
from medperf.entities.execution import Execution
from medperf.commands.list import EntityList
from medperf.commands.execution.create import BenchmarkExecutio... |
9b5a4192d030c0b5ccb8ac3de6f572b03cef219f5ed49e76f01fd87851b111a7 | Python | 5,124 | 145 | from itertools import product
import os
import itertools
from bdpy.dataform import Features, DecodedFeatures
from bdpy.evals.metrics import profile_correlation, pattern_correlation
import hdf5storage
import numpy as np
import pandas as pd
# Main #######################################################################
... |
bbd05f25ad9812c445995d2797f5b3287f3522b2a30ebc309a73c8336353ff84 | Python | 5,124 | 152 | import torch
import torch.nn as nn
def mask_zero(mask, value):
return torch.where(mask, value, torch.zeros_like(value))
class DistanceToBins(nn.Module):
def __init__(self, dist_min=0.0, dist_max=20.0, num_bins=64, use_onehot=False):
super().__init__()
self.dist_min = dist_min
self.d... |
ccc71619fdc48574cd994a3c01ef24c35051f388f8f797bda8cb9715406143f2 | Python | 5,130 | 173 | """
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 ..initializers import he_orthogonal_init
class EfficientInteractionDownProjection(torch.nn.Module):
"""... |
03686393f4828ff4e51ffc38b16f9325e400b8fbb6c8c05ad004058df3aed794 | Python | 5,131 | 198 | # Author: Huaxu Yu
# Evaluate feature quality by chromatographic peak shapes, mz errors, rt errors, etc.
# imports
import numpy as np
from numpy import dot
"""
Functions
------------------------------------------------------------------------------------------------------------------------
"""
def calculate_gaussia... |
44bda2091f19a443b4338e3a08918551cc94db6048ac31a4d2c8333a30cc6925 | Python | 5,144 | 149 | # -*- coding: utf-8 -*-
# tests/test_non_backbone_atoms.py
################################################################################
# EncoderMap: A python library for dimensionality reduction.
#
# Copyright 2019-2024 University of Konstanz and the Authors
#
# Authors:
# Kevin Sawade, Tobias Lemke
#
# Encodermap... |
f6d507c5f5a14559a2d30981cbd0d2dfeadde25ed0fb90fd02cb37114173fefd | Python | 5,148 | 103 | import statistics
import surrogateTraining
from surrogateParams import surrParams
import weightAnalysis
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec
import numpy as np
def makeMultiHiddenSpikePlot(x_spikes, y_spikes, indices, tag, fileName = 'hiddenDataSpikes.png', plotdir='.', dim=(3,5)):
... |
08aa3243d6ac81049945419734b54000826da3c77467b6770aab29c36b26e66e | Python | 5,151 | 91 | from src.circuit import create_exc_neurons,create_inh_connections
from src.stimulus import create_experimental_stimulus
from pyrates.frontend import CircuitTemplate
import argparse
def main(args):
# Print parameters
params = vars(args)
f = open(f'{args.outdir}/parameters.txt','w')
for p in params.keys():
line =... |
980c4fda57bd6ab9eac8f358712eea432e133415d3c33a4f1267dd35c4c2c9bf | Python | 5,151 | 150 | """
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 typing import TYPE_CHECKING, Optional, Union
import numpy as np
import pytest
from syrupy.extensions.amber import AmberSnapshotExtensio... |
a474b27ce5b5e3210f5eed9041b3c1ebf360d0d2556de97ad1d2f92fddc565b9 | Python | 5,154 | 155 | from typing import List
import numpy as np
import pandas as pd
import pytest
from xgboost import testing as tm
pytestmark = [pytest.mark.skipif(**tm.no_spark())]
from xgboost import DMatrix, QuantileDMatrix
from xgboost.spark.data import (
_read_csr_matrix_from_unwrapped_spark_vec,
alias,
create_dmatrix... |
d9ff92180c213b3571cec57d235d5a1766b0db83ef8fc5aef152b010ef2231b5 | Python | 5,154 | 133 | import sys
import typer
import logging
import logging.handlers
from medperf import __version__
import medperf.config as config
from medperf.decorators import clean_except, add_inline_parameters
from medperf.commands.execution import execution
from medperf.commands.execution.create import BenchmarkExecution
from medper... |
ea69dc025ba1e2d71f853e07db9c94f37fa5be12beb298f5a7594fb89ef27ce9 | Python | 5,155 | 159 | import logging
import os
import ase.io as ase_io
import numpy as np
import torch
from simgen.element_swapping import SwappingAtomicNumberTable
from simgen.generation_utils import calculate_restorative_force_strength
from simgen.integrators import IntegrationParameters
from simgen.manifolds import MultivariateGaussian... |
197ffa30b819d6b35feae930fa52495ed98d775c77a671638e302ecd77869365 | Python | 5,158 | 142 | import warnings
from typing import Iterator, List, Optional
import torch
from torch.utils.data import Dataset, RandomSampler
from torch.utils.data.sampler import Sampler, BatchSampler
from torch.utils.data.distributed import DistributedSampler
class DynamicBatchSampler(Sampler):
r"""Dynamically adds samples to ... |
0eacbadb5100658043e2d23220e3e370d21bd63b0ffe4edc8d31b418153be285 | Python | 5,161 | 167 | #!/usr/bin/env python
"""
MetaWIBELE: combine_gene_sequences module
Combine genes sequences from different samples
Copyright (c) 2019 Harvard School of Public Health
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to d... |
eb1c1fff7b82a18c2b7e0b06d525d1997c1bf7ae12cc54072f1b6ce9c8807075 | Python | 5,162 | 123 | from PyQt5 import QtCore, QtWidgets, QtGui
import quantities as pq
import numpy as np
class ABFLoaderDialog(QtWidgets.QDialog):
def __init__(self, parent, abf):
QtWidgets.QDialog.__init__(self, parent, flags = QtCore.Qt.WindowTitleHint | QtCore.Qt.WindowCloseButtonHint)
self.setWindowT... |
4da15e292de8b34738c028ab56c276facc38fb982f2518f61d85423e29f166d3 | Python | 5,164 | 149 | """MLCube handler file"""
import typer
from collaborator import start_collaborator, check_connectivity
from aggregator import start_aggregator
from plan import generate_plan
from hooks import (
aggregator_pre_training_hook,
aggregator_post_training_hook,
collaborator_pre_training_hook,
collaborator_pos... |
dd38d536fff6d8a2405c030eebe118a87c34faf6c5c140b4e99c503617e163fb | Python | 5,164 | 129 | ## The following code contains work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105.
## Additionally, we waive copyright and related rights in the utilized code worldwide through the CC0 1.0 Universal public domain dedication.
from ipaddress import IPv4Address, ip_... |
2b91a6aedf8f372516f0357c85940b2fcab352bd2eadbfcde2687d14fd53f9a1 | Python | 5,165 | 137 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
R5-Helicon Neural Simulation
This script runs simulations of coupled R5 and Helicon neuron populations
under different time-of-day conditions (morning and night).
"""
import argparse
import os
import numpy as np
from brian2 import *
# Import local modules
from R5_He... |
67a5c1dc15b4d023aba4a83b1c1473b6c74f563b744d8ae7ade9edb5e6e25228 | Python | 5,166 | 131 | import bitsandbytes as bnb
import torch
from transformers import AutoModelForCausalLM, AutoTokenizer, BitsAndBytesConfig
import random
import sys
import json
# sys.path.append("/home/aoboyang/local/captum")
from captum.attr import (
FeatureAblation,
ShapleyValues,
LayerIntegratedGradients,
LLMAttribu... |
6112b93cda6e14a36021450da1f4717ab73724f723b677e0bac73eefbe90f612 | Python | 5,167 | 120 | import os
from json import JSONDecodeError
from string import Template
from time import sleep
from urllib.error import HTTPError
from SPARQLWrapper import JSON, POST, POSTDIRECTLY, SPARQLWrapper2
from src.babel_utils import get_user_agent
from src.util import get_config, get_logger
logger = get_logger(__name__)
cl... |
a78d36b2c5c2dec3dc5e480b5f2c64f1af234cbe67d4610147fb658521bd0e06 | Python | 5,168 | 147 | #!/usr/bin/env python
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from utils import Variable
device = torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')
class MultiGRU(nn.Module):
""" Implements a three layer GRU cell including an embedding layer
and... |
640dd681b749f4eab29305a3a0cfec52285abaec9355768bd7eb635989416b8c | Python | 5,173 | 147 | """MLCube handler file"""
import typer
from collaborator import start_collaborator, check_connectivity
from aggregator import start_aggregator
from plan import generate_plan
from hooks import (
aggregator_pre_training_hook,
aggregator_post_training_hook,
collaborator_pre_training_hook,
collaborator_pos... |
9735596237d6245506a1fa29c55ab703772ee68b1f1d79a5453fce4419a15d84 | Python | 5,173 | 191 | import sys
import re
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
import deepxde as dde
from pathlib import Path
from parameters import N, beta, sigma, S0, I0, R0
sns.set_theme(style="whitegrid")
def dinn(
data_observed,
parameters,
hyperparameters,
e... |
6179eebc285889f1e226dcc4249767ba86460dd4653f5fa4458a03f8ea39028a | Python | 5,177 | 155 | from tqdm import tqdm
import pandas as pd
import argparse
from rdkit import Chem
# suppress rdkit warning
from rdkit import RDLogger
RDLogger.DisableLog('rdApp.*')
from rdkit.Chem import AllChem
from rdkit.Chem.Draw import rdDepictor
'''
preprocess:
1. remove the invalid 3d conformer
2. remove the molecules with... |
703a399a7b693403858fc481ef6669dd501b29c6a58832e9b9252bdc8a5806bb | Python | 5,177 | 155 | # MagellanMapper logging
"""Logging utilities."""
import logging
from logging import handlers
import pathlib
class LogWriter:
"""File-like object to write standard output to logging functions.
Attributes:
fn_logging (func): Logging function
buffer (list[str]): String buffer.
"""... |
80bfedc5f0a279126d9e98031ca6781682db7b12e606e5d85dfad01ed44e1181 | Python | 5,179 | 147 | #!/usr/bin/env python
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from MCMG_utils.utils import Variable
device = torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')
class MultiGRU(nn.Module):
""" Implements a three layer GRU cell including an embedding layer... |
6bb0e95914032ae5bef40fa22822308bfd056951e99f9252731d0e33a1e276c7 | Python | 5,181 | 125 | # coding=utf-8
# 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 compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless re... |
2e7d13103b12ba546657dc8776706b99c69b7f923675e02553394dc6622b7264 | Python | 5,182 | 192 | # 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 complian... |
3b1e9c5ca9f68be29e4952b2cd94aa78bb68f387a0bdf359d91b8e0f92ab4bfe | Python | 5,183 | 164 | import csv
from functools import partial
from pathlib import Path
import tensorflow as tf
from tensorflow.keras.applications.resnet import preprocess_input
from tensorflow.keras.layers.experimental.preprocessing import Resizing
AUTOTUNE = tf.data.experimental.AUTOTUNE
@tf.function
def preprocess_input_fn(data, prep... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.