sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
7ea69a060d12140b41dd358273c636cca725b1b9e2818c6bfeb205a1dd6de0f5 | Python | 2,873 | 76 | ########################################################################
class Basic:
"""
Add the basic parameters for your trainer modality.
These parameters will be displayed on the Basic page of the GUI.
This file defines the parameter type and-or its possible values displayed on the GUI,
it... |
f834542e6ccd7905651dcc392a6ccbd71e7b471707e1803e7e9bf052fcaffb92 | Python | 2,874 | 91 | import os
import argparse
from tqdm import tqdm
import chromadb
def main(
documents_directory: str = "documents",
collection_name: str = "documents_collection",
persist_directory: str = ".",
) -> None:
# Read all files in the data directory
documents = []
metadatas = []
files = os.listdi... |
3ef2134e41ffc8092ecab51e9bf5227e9c0a0f94259c481880fe558c213a7b2b | Python | 2,875 | 86 | # Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... |
9e1f2bab26e01e07b5ff545c13686a84bc4c9c23a4ebf36874cbc7e2f229c206 | Python | 2,875 | 97 | """Test for the RDKit PMI descriptor
NOTE: This is a 3D descriptor and therefore the scoring component creates
a conformer. However, this is not deterministic meaning that the
generated 3D coordinates can vary depending on the flexibility of the
molecule and the quality of the conformer generator. ... |
c539da22900c6a1e5dddf1051e21d1f9a4d9ead1d48aa798cad9f9eea8b4736f | Python | 2,875 | 80 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
from typing import Union, List, Callable
import torch
import numpy as np
from numbers import Integral
from .. import AtomicDataDict
class AtomicDataset(torch.utils.data.Dataset):
"""Base class fo... |
b2830b5088a3c09b6b32bd5f0ac554daa5f1dd899f891ed5274e4835d8a97f7e | Python | 2,877 | 78 | # Generated by Django 4.1.1 on 2022-11-21 13:31
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('celsus', '0028_alter_project_cell_type_alter_project_curtain_and_more'),
]
operations = [
migrations.AlterField(
model_name='pro... |
586d9fd9c41a9f03375f4977d1e5de748e8e7d9320b1a61ec78bdf322c162f12 | Python | 2,878 | 88 | from pathlib import Path
import mne
from .. import io
from ... import logger
def set_montage(inst, montage, **kwargs):
"""
Set EEG sensor configuration and head digitization.
Parameters
----------
inst : mne.io.Raw | mne.io.RawArray | mne.Epochs | mne.Evoked
MNE instance of Raw | Epochs... |
2e5befa0c31b1203bf2b6faa89fed1cd90972814a296b8f7b65e756a50dd206c | Python | 2,879 | 95 | import numpy as np
import random
from scipy import stats
def alarm_evaluation(target, alarm):
idx_preictal = np.argwhere(target==1)
idx_alarms = np.argwhere(alarm==1)
true_alarm = 0
false_alarm = 0
for idx in idx_alarms:
if idx in idx_preictal:
tru... |
33a927aca03ed8463b435aef62b2f6fe90ce967abaf4f6c7b442f792732852e0 | Python | 2,879 | 76 | #!/usr/bin/env python3
import tensorflow as tf
class mae_ssim_loss(tf.keras.losses.Loss):
"""Combination of mean absolute error (MAE) and structural similarity index (SSIM).
Attributes
----------
max_val_ssim : float
Structural similarity index maximum value
alpha : float
Defines t... |
69876d9f57a3049df1f9e6803ef31af2163b413a37020fa01717d5aca954679a | Python | 2,881 | 83 | """Some EDA of the signals that compose the MODA database.
Ref:
Lacourse, K., Yetton, B., Mednick, S. et al.
Massive online data annotation, crowdsourcing to generate high quality sleep spindle annotations from EEG data.
Sci Data 7, 190 (2020).
https://doi.org/10.1038/s41597-020-0533-4
"""
from __future__ import abso... |
aab0cdc01713e578049961f0b9924ade8663afd272f2889f2ea3a6317010ce54 | Python | 2,881 | 125 | import numpy as np
import torch
import os, sys
sys.path.append(os.path.dirname(os.path.realpath(__file__)) + "/..")
from model import *
from train import *
from tasks.seqDS_lfp import seqDS
import time
print("cuda available = " + str(torch.cuda.is_available()))
# Set up the output dir where the output model will be s... |
1052443105faa063695e964172cdd24dbc3b50c8452f7bb1fe0d28c0c05c5868 | Python | 2,882 | 77 | """
Detect trigger times (i.e., state transition / local wavefronts onsets)
by applying a threshold to each channel signal.
"""
import neo
import numpy as np
import argparse
from utils.io_utils import load_neo, write_neo
from utils.neo_utils import remove_annotations
CLI = argparse.ArgumentParser()
CLI.add_argument(... |
3794838c7fd8b57b9cbaa622e1652c7a2beba5db47d29392f435be9857f2c8d4 | Python | 2,884 | 99 | # -*- coding: utf-8 -*-
import os
import requests
from math import ceil
import tqdm
import hashlib
def download_file(url, filename=None, chunk_size=1024, verbose=False,
md5sum=True):
"""
Download file with progressbar.
Based on
`<https://gist.github.com/ruxi/5d6803c116ec1130d484a4ab... |
fb467013c7bfd22ce86d26e808a0ddae7fd98ea3040c0b5a3a8145c5d5913f0f | Python | 2,884 | 97 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
import re
import requests
from urllib.parse import quote
from typing import Optional, NamedTuple
class ModelDownloadInfo(NamedTuple):
model_id: str
newer_version_id: Optional[str]
web_ur... |
b72271a078b3aef72c12aa62542547918a45b3fa206c55e71d03ebc959d31941 | Python | 2,885 | 89 | from typing import Optional, Dict
import torch
import torchvision
from ..encoding import Encoder, NullEncoder
def create_torchvision_dataset_wrapper(ds_type):
# language=rst
"""
Creates wrapper classes for datasets that output ``(image, label)`` from
``__getitem__``. This applies to all of the datas... |
cad9b8b613f4e06a103a0e457469ec7d88b041cedca230be237d390cb3bc8284 | Python | 2,885 | 62 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
"""
Model test classes composed from hierarchical test mixins.
The mixins are organized hierarchically:
BasicModelTestsMixin (base fixtures + basic tests)
└─ EnergyModelTestsMixin (adds energy-... |
cc1abc43b1cf03178cb795d94cd056509c3ab474c77d9217ce1eb47af37aa4cb | Python | 2,886 | 90 | """
Compute the maximum TM score against training set
"""
# NOTE this is a thin wrapper around function called in sample.py
import logging
import os, sys
import re
import json
from glob import glob
from pathlib import Path
import argparse
from typing import *
import multiprocessing as mp
from tqdm.auto import tqdm
f... |
92496175e386ae653b9b81f1e47bd049bdc3ce4f9b9e23744b32de2353d3c758 | Python | 2,887 | 84 | # Copyright (c) 2020 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... |
5491a209b0400c1a31762b27f38069ebd2ffd08ecfd70c4a9f04434cc7b4ff77 | Python | 2,888 | 105 | import argparse
import math
import os
from glob import glob
import numpy as np
import pandas as pd
def get_95_CI(metrics_list, n=10):
mean = np.nanmean(metrics_list)
std = np.nanstd(metrics_list, ddof=1)
lower_bound = mean - 1.96 * std / math.sqrt(n)
upper_bound = mean + 1.96 * std / math.sqrt(n)
... |
ba951376b26ee0ff50bf7fa5372a65297b7ea094671d8dc2c4e825b3f64b3cd2 | Python | 2,889 | 76 | import logging
import numpy as np
from idtrackerai import ListOfBlobs, conf
from idtrackerai.utils import track
class ModelArea:
"""Model of the individual blob area, used for a first discrimination
between blobs of single individuals and of multiple touching animals
(crossings).
The statistics are... |
32828f01e5f7987250192fce91b5ad21d51d9eb0b20c76f87a472bb198d705fa | Python | 2,890 | 92 | import geomstats.backend as gs
from geomstats.test.data import TestData
from .base import LevelSetTestData, MatrixVectorSpaceTestData
class LowerTriangularMatricesTestData(MatrixVectorSpaceTestData):
pass
class LowerTriangularMatrices2TestData(TestData):
def belongs_test_data(self):
data = [
... |
9df5f08983721ee91f379c80e957ff070df695c1c953099edbbcfc0b0a1a7ebd | Python | 2,890 | 111 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# FileName: main
# CreatedDate: 2017-11-20 14:05:59
#
import argparse
import os
from datetime import datetime
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
def main():
# setting option
parser = argparse.ArgumentParser(
descri... |
e3293727bf892bfd1cfcbd550874d4f6fe2fc43e9fee1d1d50fa1f3ee946bf31 | Python | 2,890 | 61 | import os.path
from common.experiment import experiment_run
from common.common import store_pickle
def run_experiments(config_dict_list):
all_experiments_results_summary_list = list()
all_experiments_items_summary_list = list()
for config_dict in config_dict_list:
single_experiment_results_summar... |
1cdaf086b4167d0b3b5c80bbe9d11e61c98d1465ca7788e0d8766002e4ad4e00 | Python | 2,891 | 78 | """
Detect trigger times (i.e., state transition / local wavefronts onsets)
by applying a threshold to each channel signal.
"""
import neo
import numpy as np
import argparse
from pathlib import Path
from utils.io_utils import load_neo, write_neo
from utils.neo_utils import remove_annotations
CLI = argparse.ArgumentPa... |
603cb73a8849c47bafa76ec8087d6a2a17bd046a6fd7a3617118cf208a88855a | Python | 2,891 | 89 | """Checkbox panel for turning named plot overlays on and off.
The widget draws the options. The owner decides what a checked name means.
"""
from qtpy import QtCore, QtWidgets
from sanpy.sanpyLogger import get_logger
logger = get_logger(__name__)
class PlotOptionsWidget(QtWidgets.QWidget):
"""Show named overl... |
c6ef64742bdeddcfd5a92b4641a1028ac377dda488b51dc8d3d656f760460dc2 | Python | 2,893 | 98 | import numpy as np
import torch
from torch_geometric.nn import to_hetero, SAGEConv
from torch.nn import Linear, Dropout, Tanh
import random
class GNNEncoder(torch.nn.Module):
def __init__(self, hidden_channels, out_channels, p=0.2):
super().__init__()
self.conv_in = SAGEConv((-1, -1), hidden_c... |
2818d4595d2db8ecbbbb387aa9622b8948dd8eeb9a0bc869c8f946b96d7a62f7 | Python | 2,896 | 98 | import numpy as np
import torch
from torch_geometric.nn import to_hetero, SAGEConv
from torch.nn import Linear, Dropout, Tanh
import random
class GNNEncoder(torch.nn.Module):
def __init__(self, hidden_channels, out_channels, p=0.2):
super().__init__()
self.conv_in = SAGEConv((-1, -1), hidden_c... |
19ef8312f1d08af9be917658ec221aaa409dc5bec022c6d020ac5544ad1e6a2e | Python | 2,897 | 84 | import numpy as np
import os
import numpy.random as rgn
from mpi4py import MPI
def input(path, t_synch_nb, dt):
"""
Simulate some random spike train input
:param path: the file for the configurations of the connection
:return:
"""
# Start communication channels
path_to_files = path
# F... |
d713a54c3f80cec8895f8b567062ed20e8b73e24134e1b7e4b420fdbd4d9d391 | Python | 2,898 | 115 | import functools
import inspect
from types import MethodType
import numpy as np
from scipy.interpolate import PPoly
import geomstats.backend as gs
def result_to_backend_type(result):
"""Convert np.array to gs.array within result object."""
if gs.__name__.endswith("numpy") or gs.__name__.endswith("autograd")... |
3a768367352f6e028a2ef1182182556ecebb79a349e348bebfc3426fb7d5d04a | Python | 2,900 | 78 | """
Detect trigger times (i.e., state transition / local wavefronts onsets)
by applying a threshold to each channel signal.
"""
import neo
import numpy as np
import argparse
from pathlib import Path
from utils.io_utils import load_neo, write_neo
from utils.neo_utils import remove_annotations
CLI = argparse.ArgumentP... |
5e0c65f8e8a87ac9686a9f39203254315d4b14fd06b57663b061af5ddb59816b | Python | 2,900 | 60 | import pandas as pd, matplotlib.pyplot as plt, seaborn as sns, matplotlib as mpl
mpl.rcParams['pdf.fonttype'] = 42
# ==========================================
# 1. LOAD DATA (synchronized with re-run: Fig 6 accuracy + clean T4 latency)
# ==========================================
data = {
'Model': ['YOLOv8-Nano',... |
1718948e2f05c192259873e56baf8f5824092a5c97f3276755eed21b6ee9e95d | Python | 2,901 | 87 | # Copyright (C) 2020-2025 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""You may copy this file as the starting point of your own model."""
from keras.models import model_from_json
from keras_contrib.layers import InstanceNormalization
from openfl.federated import KerasTaskRunner
from keras import backen... |
1a337b6057ccec100caa1e8b802b4431d35eafab8f7b2e2a07251b0bf809c4f3 | Python | 2,902 | 76 | # -*- coding: utf-8 -*-
"""
Created on Thu Aug 27 11:17:18 2020
@author: Tom
"""
from tensorflow.keras.preprocessing.image import ImageDataGenerator
import warnings
from data_frame_iterator_pat import DataFrameIteratorPat
class ImageDataGeneratorPat(ImageDataGenerator):
def flow_from_dataframe(self,
... |
891353d7d19510c3f1e29e2f37e98d3b96fcde847fa2ec5860331d5067e82b75 | Python | 2,902 | 88 | import xgboost as xgb
from openfl.federated.data.loader import DataLoader
class XGBoostDataLoader(DataLoader):
"""A class used to represent a Data Loader for XGBoost models.
Attributes:
batch_size (int): Size of batches used for all data loaders.
X_train (np.array): Training features.
... |
d6276e7f77dfeedbe6870d614026a580cc65d16676ecd6d78ae4ffb9dd9517a3 | Python | 2,902 | 101 | import random
import pytest
from geomstats.geometry.hyperboloid import Hyperboloid
from geomstats.geometry.open_hemisphere import (
OpenHemisphere,
OpenHemispheresProduct,
OpenHemisphereToHyperboloidDiffeo,
)
from geomstats.test.parametrizers import DataBasedParametrizer
from geomstats.test.random import ... |
69250991dbe2cf5b4ed48eb9347df5087da2759105c2939b8779e280ec5c866f | Python | 2,903 | 74 | """Unit tests for the pure-numpy GNC backend helpers.
No scanner data, no FSL/TORTOISE binaries, no scratch dir - just numpy/nibabel.
"""
import numpy as np
import nibabel as nib
import pytest
from lib.gnc.backends import _sanitize_graddev_matrix
from lib.gnc.backends.tortoise import _lps_disp_to_fsl_rel, resolve_is... |
6eb41af8f84f80048f430a2b034a5a298463cf0aea9e5eb6dd9618f6a3061e39 | Python | 2,903 | 86 | # Copyright (c) 2020 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... |
dffded4a129ecf747781d8b65b090e4a3286f6775f7c9a4ce9b26097176f3e14 | Python | 2,903 | 68 | import torch
from typing import Union, Sequence, Dict
from math import sqrt
from nequip.data import AtomicDataDict
class AvgNumNeighborsNorm(torch.nn.Module):
def __init__(
self,
type_names: Sequence[str],
avg_num_neighbors: Union[float, Dict[str, float]],
) -> None:
"""
... |
d4a2e0ba3c37c7432e3aa63b63257e2506ef8fae8cc2d71511d44fc8aabce5c2 | Python | 2,904 | 84 | import experiment as exp
from experiment import session_state
import arena
import functools
class StackedFeeders(exp.Experiment):
default_params = {
"feeders": {
"Left Feeders": ["Bottom Left Feeder", "Top Left Feeder"],
"Right Feeders": ["Bottom Right Feeder", "Top Right Feeder"],... |
2291505cbf2ee1dff08d6b0bf885ea9bb5df013b40e6d5d54a45ec94a1ff36de | Python | 2,905 | 97 | """Protect the import boundary between SanPy's backend and Qt interface."""
from __future__ import annotations
import ast
from pathlib import Path
import subprocess
import sys
import sanpy
SANPY_PACKAGE_DIR = Path(__file__).resolve().parents[1] / "sanpy"
FORBIDDEN_BACKEND_IMPORTS = (
"PyQt5",
"PyQt6",
... |
86be0b4e55909975480ab615c6801350fbc00be1f5be7e69c98aca0db62a1762 | Python | 2,910 | 126 | import analysis_utils as au
import torch
import matplotlib
acf2gain = {
'nn.Sigmoid()': 1,
'nn.Tanh()': 1.6666666666666667,
'nn.ReLU()': 1.4142135623730951,
'nn.LeakyReLU()': 0.9999000099990001,
'pc.NoneModule()': 1.0,
}
def plot_mean(df, id='test'):
df = au.nature_pre(df)
# input(df.lo... |
0646b4ad4036e753e6107cafc4f3fd513e348c262314d32ff35d78a7503454fb | Python | 2,911 | 97 | '''
the preprocessing code refers to the work(Yin, B., Corradi, F. & Bohté, S. M. Accurate and efficient time-domain classification with adaptive spiking recurrent neural
networks. Nat. Mach. Intell. 3, 905–913 (2021)).
'''
import os
import urllib.request
import gzip, shutil
# from keras.utils import get_file
import ma... |
7490f8e2ee6d0402a29b63f11a87d5dc75db71cf5de91edd142c7065ab0beabc | Python | 2,911 | 75 | """
Downsample the input data by combining and averaging neighboring channels.
"""
import numpy as np
import matplotlib.pyplot as plt
import argparse
from pathlib import Path
import os
import neo
from skimage import measure
from utils.io_utils import load_neo, write_neo, save_plot
from utils.parse import none_or_path
... |
81b922ad651d878ca5a974da4a232b495c8bc43ef1f3552aa624cf326aaed9a8 | Python | 2,912 | 81 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Dec 12 15:25:17 2018
@author: ngritti
"""
from csbdeep.models import CARE
import time, os, glob
from tqdm import tqdm
import numpy as np
from skimage.io import imread, imsave
os.environ['CUDA_VISIBLE_DEVICES']='1'
#%%
'''
register images and save them ... |
a255c24c5ec01bdd64e49165ad89dd900647dead80019687f9d9c3c6b07bf1ee | Python | 2,912 | 94 | #
# For licensing see accompanying LICENSE file.
# Copyright (C) 2022 Apple Inc. All Rights Reserved.
#
import os
import importlib
import argparse
COLLATE_FN_REGISTRY = {}
def register_collate_fn(name):
def register_collate_fn_method(f):
if name in COLLATE_FN_REGISTRY:
raise ValueError(
... |
fbc467fabc9598d8c9287473a1c3dbb9e77d1601f4786b6b224fb18d24cdd1b2 | Python | 2,914 | 97 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Dec 12 15:25:17 2018
@author: ngritti
"""
from csbdeep.models import CARE
import time, os, glob
from tqdm import tqdm
import numpy as np
from skimage.io import imsave
#os.environ['CUDA_VISIBLE_DEVICES']='1'
#%%
'''
register images and save them in the ... |
0c63ff799baedba77f3c07e394dd6b06e31226aa89281c19c2438e9f27db1945 | Python | 2,915 | 71 | import pytest
import unittest
import numpy as np
import numpy.testing as npt
import torch
import torch.utils.data as tud
from reinvent.models import Mol2MolAdapter
from reinvent.models.transformer.core.dataset.dataset import Dataset
from reinvent.models.transformer.core.enums.sampling_mode_enum import SamplingModesEn... |
914c25683c601f82a9ea2431b3ccab7a1f42357e220761c5a6cb6c1589dca3f9 | Python | 2,915 | 77 |
import torch.nn.functional as F
import torch
class gru(torch.nn.Module):
def __init__(self, classes, arch=[45, 7, 5, 20, 0.23128823035454756, 71]):
super(gru, self).__init__()
self.input_size = 1
self.num_layers = 3
self.bidirectional = True
self.arch = arch
... |
b1401fd130143c466c118dc7df486613a1e8f9f2488cbbc9cd7f8bf7ae245aa4 | Python | 2,915 | 101 | import math
import geomstats.backend as gs
from geomstats.test.data import TestData
from .euclidean import EuclideanMetricTestData
class MinkowskiTestData(TestData):
def basis_cardinality_test_data(self):
return None
class MinkowskiMetricTestData(EuclideanMetricTestData):
fail_for_autodiff_excepti... |
db5a684a12023fa09a34ba7fcffff5ab72c8fd3498850d1b2dc837fe29555616 | Python | 2,916 | 89 | import random
import pytest
from geomstats.geometry.general_linear import GeneralLinear
from geomstats.geometry.group_action import (
CongruenceAction,
PermutationAction,
RowPermutationAction,
permutation_matrix_from_vector,
)
from geomstats.geometry.matrices import Matrices
from geomstats.geometry.sp... |
b3cce7e21ae98d661035be4f9a89f8639a4ab23a3b33c7e01d230258a13684dd | Python | 2,917 | 96 | #
# For licensing see accompanying LICENSE file.
# Copyright (C) 2022 Apple Inc. All Rights Reserved.
#
import argparse
import os
import importlib, inspect
from .base_layer import BaseLayer
from .conv_layer import (
ConvLayer,
NormActLayer,
TransposeConvLayer,
ConvLayer3d,
SeparableConv,
)
from .l... |
1e36b384affd2a994fec65b3299fc8bbeac968ed738a978e53a82984dd9a036f | Python | 2,918 | 109 | import glob
import os
from model_angelo.utils.grid import (
apply_bfactor_to_map,
crop_center_along_z,
get_auto_mask,
load_mrc,
make_model_angelo_grid,
save_mrc,
)
def standardize_mrc(args):
if not os.path.isfile(args.input_path):
input_files = glob.glob(os.path.join(args.input_pa... |
6373f95076eff7a8f016d4d7eee74c68c5ebe85b2051306b82be2da1f2eab7f3 | Python | 2,918 | 82 | import os
import pandas as pd
import sys
import numpy as np
#Read in the intersected narrowPeak file derived from liftover
#cutoff is the argument that determines the degree of overlap required between two peaks for them to be considered partners.
y = sys.argv[1]
cutoff = float(sys.argv[2])
m = pd.read_csv(sy... |
681ba3d7dbed1cd53d8ddc2166f79a221c8708669bb73153c9df030e8f5d52b8 | Python | 2,920 | 82 | from qtpy.QtGui import QKeyEvent
from qtpy.QtWidgets import QLabel, QListWidget, QVBoxLayout, QWidget
from superqt import QToggleSwitch
from idtrackerai import Blob, Fragment
from idtrackerai.GUI_tools import GUIBase, key_event_modifier
class CustomListWidget(QListWidget):
"""List widget that remaps W/S to Up/Do... |
40622131444d8d5382cd6a3ed3b2f9b4f4451acb4d17e7bf07913bf88afac8bf | Python | 2,922 | 86 | import logging
import tempfile
import numpy as np
import torch
import torch.nn.functional
from torch import nn, optim
from mace.tools import (
AtomicNumberTable,
CheckpointHandler,
CheckpointState,
atomic_numbers_to_indices,
)
def test_atomic_number_table():
table = AtomicNumberTable(zs=[1, 8])
... |
e4722a5c1eaa86e615a43c65c3404223f087e3ee496a890b26cd8f8ec3d63d79 | Python | 2,924 | 86 | import json
import logging
import os
import pathlib
import shlex
import shutil
import stat
import tempfile
import yaml
from reinvent_plugins.components.run_program import run_command
from reinvent_plugins.components.synthsense.aizynthfinder_config import (
ensure_custom_stock_is_inchikey,
prepare_config,
)
fr... |
bd0e2c12ded33bf9bfad3ddcd95fb59dcf25b6da0118ceced4ea3ed7a9403693 | Python | 2,927 | 94 | from video_stream import ImageObserver
import numpy as np
import video_system
import data_log
import experiment as exp
class YOLOv4ImageObserver(ImageObserver):
default_params = {
**ImageObserver.default_params,
"cfg_path": None,
"weights_path": None,
"meta_path": "image_observers/... |
164a9d34a7d4be57695720e71f5ea32c6f4ef6c36f52c236ed0a40ec27bcc084 | Python | 2,929 | 87 | """Test for the integrators."""
import pytest
import geomstats.backend as gs
import geomstats.integrator as integrator
from geomstats.geometry.euclidean import Euclidean
from geomstats.geometry.matrices import Matrices
from geomstats.test.test_case import TestCase
class TestIntegrator(TestCase):
def setup_metho... |
649a7f6af8c1fbf9dbb2cea547d6af7517f6b8244e574b8065b24799cd129133 | Python | 2,930 | 105 | """
Neurodecode's logger.
TODO: Add file handler.
"""
import sys
import logging
# log level options provided by neurodecode
LOG_LEVELS = {
'DEBUG': logging.DEBUG,
'INFO': logging.INFO,
'WARNING': logging.WARNING,
'ERROR': logging.ERROR
}
def init_logger(logger, verbosity='INFO'):
"""
Initiali... |
31eff75f71ccc4a9b2a43ba57cc04a9eecf464f00660192002ae042acf9f73b2 | Python | 2,931 | 102 | #
# For licensing see accompanying LICENSE file.
# Copyright (C) 2022 Apple Inc. All Rights Reserved.
#
import os
import importlib
import argparse
SUPPORTED_NORM_FNS = []
def register_norm_fn(name):
def register_fn(fn):
if name in SUPPORTED_NORM_FNS:
raise ValueError(
"Cannot... |
acdf9725db369862d929f3d457af9ac94c9c9e089d8afe5f1c63e6e88f840853 | Python | 2,934 | 96 | """Tests for the standalone plot options checkbox panel."""
from typing import Any
import pytest
from qtpy import QtWidgets
from sanpy.interface.plot_options_widget import PlotOptionsWidget
def _checkbox_grid(
widget: PlotOptionsWidget,
) -> list[tuple[int, int, str, bool]]:
"""Return checkbox row, column,... |
a3037c81b497d136d094b982ea83c01bfdb8c8d72dea77ebb865516ce140689f | Python | 2,935 | 88 | import numpy as np
from numpy.linalg import norm
from skimage.measure import label, regionprops
def colour_deconvolution(image, stains):
# same as my MATLAB function, but not as efficient (ca. factor 10)
if stains == 'HE':
# Color deconvolution of H&E stains
# RGB OD matrix for hematoxyli... |
64fd8ca534d843e9e362da864053eb266e83eaa1961b427ce287bd2dc49c072a | Python | 2,936 | 97 | from abc import abstractmethod
import os
from typing import ClassVar, Dict, Any
import uuid
import chromadb
from chromadb.config import Component
from pathlib import Path
from enum import Enum
TELEMETRY_WHITELISTED_SETTINGS = [
"chroma_api_impl",
"is_persistent",
"chroma_server_ssl_enabled",
"chroma_se... |
218d0350e356ff244a61d7d29c1a87f246366d63d32d4b9ecf10c43e752e7f19 | Python | 2,939 | 113 | from numba import njit, jit, objmode
from numba.experimental import jitclass
from numba import int32, int64, float32, float64, boolean
from numba import typed, types
from numba.types import pyobject
import numpy as np
from scipy.io import loadmat, savemat
spec = [
('nil', int32),
('capac... |
e62f33d375c04e8a7fed2f66d2ad0a08a02a5d45da569da4a97c652be485599e | Python | 2,939 | 114 | #!/usr/bin/env python
#
# Installer for REINVENT4
#
# Simple script to compute the command line parameters for pip. PyTorch
# controls the version for the processor type via setting the right URL. Some
# packages are optional and may need a URL of their own.
#
import subprocess as sp
import argparse
OPTIONAL_DEPENDE... |
b3c2f4fcb469e50ff2f9a64b1160c90effa4aa2aa0afdc16512b659dfd04a80e | Python | 2,941 | 94 | # Copyright 2020-2024 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""openfl.experimental.workflow.runtime module Runtime class."""
from typing import Callable, List
from openfl.experimental.workflow.interface.fl_spec import FLSpec
from openfl.experimental.workflow.interface.participants import Aggregato... |
91907377255b95576a90cfc3e721be3dd07362611321abf8f6e693ca067937cf | Python | 2,942 | 91 | """Tanimoto similarity and Jaccard distance"""
from __future__ import annotations
__all__ = ["TanimotoSimilarity", "TanimotoDistance"]
import warnings
from typing import List
import numpy as np
from pydantic.dataclasses import dataclass
from reinvent.chemistry import conversions
from reinvent.chemistry.similarity ... |
0342fb07c69b172b355ff416cd8641a16272a51488102fa1bd097ea125ad701f | Python | 2,943 | 105 | # This tests a very minimal of test_add in test_add.py as a example based test
# instead of a property based test. We can use the delta to get the property
# test working and then enable
import random
import time
from chromadb.api import ClientAPI
from chromadb.test.conftest import (
multi_region_test,
reset,
... |
161c26e464da9fd1e6245d7fd35c3ecd7eaf96ce00b016d97a21ea15040d9227 | Python | 2,947 | 79 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Dec 12 15:25:17 2018
@author: ngritti
"""
from csbdeep.models import CARE
import time, os, glob
# from keras import backend as K
# import tensorflow as tf
import numpy as np
from skimage.io import imread, imsave
# time.sleep(60*60*6)
#%%
'''
register... |
c675682bd29333b2f86852b3f9e1bfdb87772000602bc3ea852ae73269d4444f | Python | 2,949 | 108 | """
Randomly sample angles in the test set to construct a baselines for scTM scores
We sample angles by
"""
import os
from pathlib import Path
import json
import logging
import argparse
from tqdm.auto import tqdm
import numpy as np
import pandas as pd
import torch
from sample import build_datasets, create_new_chain... |
97a6cabea7992a5031c56e0c9483f50211c867f7a0f44fae2299934d0d34efe7 | Python | 2,951 | 89 | # Copyright (c) 2021 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... |
3c94308bf1963f026a3ff8e24ca81cdac9fa7f02933dcbb43b9b0a2f932cc17d | Python | 2,955 | 108 | import random
import pytest
from geomstats.geometry.euclidean import Euclidean
from geomstats.geometry.hypersphere import Hypersphere
from geomstats.geometry.spd_matrices import SPDMatrices
from geomstats.learning.frechet_mean import FrechetMean
from geomstats.learning.kmeans import RiemannianKMeans
from geomstats.te... |
e82562f014eed5f3e67797618d45232437a7e1652cf2c06cc696e88ea311c067 | Python | 2,960 | 104 | """Module containing utils"""
from numpy.polynomial.legendre import Legendre
import numpy as np
import scipy.linalg as la
def compute_tsnr(data, confounds):
"""Compute tSNR on data by first regressing out the following nuisance
regressors:
- six motion parameters and their derivatives
- global signal... |
90990438a16f54350c8b4d938d91331dc320d4e4aa841e4695ca408ee4853c68 | Python | 2,961 | 107 | """Compute various scores with RDKit"""
from typing import List, Callable
import numpy as np
from rdkit.Chem import AllChem as Chem, Crippen, Descriptors, Lipinski
from ..component_results import ComponentResults
from reinvent_plugins.mol_cache import molcache
def compute_scores(mols: List[Chem.Mol], func: Callabl... |
025b3e6e31a80de96b4151c362949f13daa461705737480042df30139f72699a | Python | 2,962 | 90 | # Copyright (C) 2025 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
import pandas as pd
from sklearn.datasets import load_iris
from openfl.federated.data.loader import DataLoader
class IRISInMemory(DataLoader):
"""Data Loader for IRIS Dataset."""
def __init__(self, batch_size=32, data_path=None, **... |
1c5f821d9eedb13e720315d64533dc37b0b3a417cb9d53851220d8c6eb37d128 | Python | 2,962 | 74 | import torch
from torch_geometric.nn import global_mean_pool, global_max_pool
import torch.nn.functional as F
from torch_geometric.nn import SAGEConv, GENConv, GraphConv, JumpingKnowledge, GATv2Conv, GINConv
from torch.nn import Linear, BatchNorm1d, ReLU, Dropout
class Net(torch.nn.Module):
def __init__(s... |
5d04ddfadc777e80f6d6ca65aaf873a130cbf6888161fa24e11da9fd15cd109f | Python | 2,964 | 101 | # -*- coding: utf-8 -*-
# -*- coding: utf-8 -*-
import os
pwd = os.path.join(os.path.abspath('.'), 'src/data')
import sys
sys.path.insert(0, pwd)
from data_functions import load_data
from simulate_dros import parameters_df, normalize, writeTbsFile
import glob
import argparse
import logging
import numpy as np
impo... |
4f82b612603ec389caedfdb868bae0e8279115ed45b96305b54d62972100555d | Python | 2,965 | 73 | from rest_framework.permissions import BasePermission, SAFE_METHODS
from rest_framework_simplejwt.exceptions import TokenError
from rest_framework_simplejwt.tokens import AccessToken
from celsus.models import CurtainAccessToken
from celsusdjango import settings
class IsOwnerOrReadOnly(BasePermission):
def has_ob... |
adeb37ab19a4d1db2213bb6df5efa45b49b4f7232be45c97b77bae729634de8d | Python | 2,968 | 66 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
import torch
from nequip.data import AtomicDataDict
class VirialToStressTransform(torch.nn.Module):
r"""Converts virials to stress and adds the stress to the ``AtomicDataDict``.
Specifically ... |
80880f72bca01a38e8289f885e1ff88d2c18bc654944020d87c113d628040cec | Python | 2,972 | 92 | import torch
import numpy as np
def get_topic_diversity(beta, topk):
num_topics = beta.shape[0]
list_w = np.zeros((num_topics, topk))
for k in range(num_topics):
idx = beta[k,:].argsort()[-topk:][::-1]
list_w[k,:] = idx
n_unique = len(np.unique(list_w))
TD = n_unique / (topk * num_... |
5597244f9732edef5d6a760ae8b277318159048117d54a8aafa16e2827e7c81b | Python | 2,979 | 85 | import numpy as np
import scipy.stats
DATA_DIR = '/media/O_o/UB/research/dataset/20newsgroups/CoEmbedding/'
vocab_pt = DATA_DIR + 'vocab.txt'
#embedding_pt = 'D:/UB/research/dataset/20newsgroups/CoEmbedding/results/Embeddings_K50_iter19.npz'
embedding_pt = DATA_DIR + 'results_parallel/Embeddings_K50_iter19.npz... |
6b88ba11b65614d5eb447e791ba0489dc945ea78d95648670093ddf4ca3afbc1 | Python | 2,979 | 122 | # -*- coding: utf-8 -*-
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Feb 1 16:21:13 2022
@author: kilgoretrout
"""
# -*- coding: utf-8 -*-
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import numpy as np
import logging
import argparse
import os
import torch
import h5... |
694109ee6ce3dd41265d5ab5a5d5da98f70537e6d2a09412aaaebed4b8df6fe0 | Python | 2,980 | 87 | # coding=utf-8
import torch
import torch.nn.utils.rnn as tnnur
import torch.utils.data as tud
class Dataset(tud.Dataset):
"""Dataset that takes a list of SMILES only."""
def __init__(self, smiles_list, vocabulary, tokenizer):
"""
Instantiates a Dataset.
:param smiles_list: A list with... |
f8a51242e47103804c811a1a95008c9694bf17ee28add5efac460ffddf1ac3bc | Python | 2,981 | 104 | from __future__ import annotations
import textwrap
from typing import TYPE_CHECKING
from snakebids.utils.utils import entity_to_wildcard
if TYPE_CHECKING:
from snakebids.paths._utils import BidsPathSpec, BidsPathSpecFile
TEMPLATE = '''
def {spec}(subject_dir: bool = True, session_dir: bool = True) -> BidsPathSp... |
3471686dadf39b4e8c094203da7397930bb8c599dde4a0739c72f2276e094573 | Python | 2,982 | 45 | #*----------------------------------------------------------------------------*
#* Copyright (C) 2024 ETH Zurich, Switzerland *
#* SPDX-License-Identifier: Apache-2.0 *
#* *
... |
b357f946471911d7679fb8fcc363d5433f37a5b2ab0a06d7436efa33ba249158 | Python | 2,983 | 116 | """
Get synapse info: presynaptic cell and size
"""
import argparse
from sys import argv
import numpy as np
import pandas as pd
import tifffile as tif
from cloudvolume import CloudVolume
from utils import load_volume
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument("--syn_seg", ... |
b9eed1ffde7cf09316e1322f4dc13d9f06881d81432f71c7e3cfd9a11efbced3 | Python | 2,984 | 94 | from unittest import TestCase
import torch.nn as nn
import torchvision.transforms.functional as FT
from smithers.ml.models.vgg import VGG
default_cfg = [
64, 64, 'M', 128, 128, 'M', 256, 256, 256, 'M', 512, 512, 512, 'M', 512,
512, 512, 'M'
] #vgg16
vgg19_cfg = [
64, 64, 'M', 128, 128, 'M', 256, 256, 256... |
8ba74319d7a1bc47b7da1d385c03c8a01f0a0b2a6e8f71a06417b6493bfa6c34 | Python | 2,986 | 97 | from threading import Lock
from typing import Dict, List, Sequence
from uuid import UUID, uuid4
from overrides import override
from chromadb.config import System
from chromadb.db.system import SysDB
from chromadb.segment import (
SegmentImplementation,
SegmentManager,
SegmentType,
)
from chromadb.segment.... |
5d1da393211f0c05fbf2ca86808d2571c1566a278e06ac6add634da96bcd6bd9 | Python | 2,987 | 108 | import pytest
from corgie.boundingcube import BoundingCube
from corgie.stack import Stack
from corgie.layers.base import BaseLayerType
from corgie.block import Block, partition, get_blocks
@pytest.mark.parametrize(
"xrange, sz, overlap, skip, result",
[
(range(4), 2, 0, [], [range(0, 2), range(2, 4)])... |
07e5410e351b01a5233a7372b0fdcf2083c08fce58a53615627b8fac8ad2b175 | Python | 2,988 | 102 | # Copyright (C) 2020-2023 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""CustomAssigner tests."""
from unittest import mock
import pytest
from openfl.interface.aggregation_functions import GeometricMedian
from openfl.interface.aggregation_functions import WeightedAverage
from openfl.component.assigner.cu... |
02666d168e77ee8c86294f215c13d0e29f5e01a36ca24a9b7864842f2d8d57d4 | Python | 2,989 | 89 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import paddle
import paddle.nn as nn
import paddle.nn.functional as F
from ppdet.core.workspace import load_config, merge_config, create
from ppdet.utils.checkpoint import load_weight, load_pretrain_weight
fro... |
c2f375f8f4ced805b2b7432962a614f8e64152eb9e429ec2b52f8fa80432c5fc | Python | 2,992 | 74 | import subprocess
import pandas as pd
import numpy as np
import concurrent.futures
from Bio import SeqIO
from typing import List
def blast_search(seq, database_path, blast_executable, species):
blast_cmd = [blast_executable, "-db", database_path, "-query", "-", "-outfmt", "6 qseqid sseqid pident length mismatch g... |
695faaae300063d30124387f65ee31cc69c565faac650a27ad942d253625bf4c | Python | 2,993 | 111 | import six
from filters.schema import base_query_params_schema
from filters.validations import DatetimeWithTZ, IntegerLike, CSVofIntegers, Alphanumeric, GenericSeparatedValidator
organism_query_schema = base_query_params_schema.extend(
{
"id": IntegerLike(),
"created": DatetimeWithTZ(),
"n... |
6f1c0f1c830ed44a71397eba2a0bf338314aea88a7c23b9b5368e61155c4267f | Python | 2,996 | 79 | #!/usr/bin/python
# -*- coding: utf-8 -*-
#####################################
# File name : gpu_mem.py
# Create date : 2019-06-02 16:56
# Modified date : 2019-06-02 16:59
# Author : DARREN
# Describe : not set
# Email : lzygzh@126.com
#####################################
from __future__ import division
fr... |
029e02a9ea6ac6d694e5b89e3645ce49892fd75f2562a4ed2bc664a33b602915 | Python | 2,998 | 88 | # Copyright 2020-2025 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
import logging
from openfl.experimental.workflow.interface.fl_spec import FLSpec
from openfl.experimental.workflow.interface.participants import Aggregator, Collaborator
from openfl.experimental.workflow.runtime import LocalRuntime
from open... |
b244622bef2843964901b34baf6fba60b3715742435aa69ebe1a1b6709a04cb0 | Python | 3,000 | 91 | from typing import Dict, List, Union
import pytest
from snakebids.core.filtering import filter_list
@pytest.mark.parametrize(
("zip_list", "filters", "output"),
[
(
{
"dir": ["AP", "PA", "AP", "PA", "AP", "PA", "AP", "PA"],
"acq": ["98", "98", "98", "98", ... |
b93093913f3fcc4900ae88aca3717bde963bacc3eb3c33455c817e57f637a30a | Python | 3,002 | 73 | #!/usr/bin/env python
import sys
import subprocess
import os
from pprint import pprint
from time import gmtime, strftime
if __name__ == '__main__':
if len(sys.argv) != 5:
print( \
"Error expecting: " + \
"starting_fov " + \
"num_fovs " + \
"b... |
7d00adb118afd0da30118e1226484a86fd0488c336b4111c0635b7c2a81ab9ee | Python | 3,006 | 96 | # ##############################################################
# This file is received from
# - https://github.com/czbiohub/noise2self/blob/master/mask.py
# It is masking mechanisim implementation from noise2self paper.
# The code is licenced under MIT licence
# https://github.com/czbiohub/noise2self/blob/master/LICE... |
9fc714a234ad80fd5c8e6c6d97cee3e0245ef6936f9b6f6ac0328ad7882e81e0 | Python | 3,009 | 84 | from PymoNNto.Exploration.Network_UI.Network_UI import *
from PymoNNto.Exploration.Network_UI.TabBase import *
from PymoNNto.Exploration.Visualization.Analysis_Plots import *
class Analysis_Module_tab(TabBase):
def __init__(self, title='Modules'):
super().__init__(title)
def add_execute_btn(self, Net... |
a55ae36deeb9716fe882efd018046755872bf4782f84e1e2ae63084388c4429f | Python | 3,009 | 89 | from . import register_scheduler
from .base_scheduler import BaseLRScheduler
import argparse
import math
@register_scheduler("multi_step")
class MultiStepLRScheduler(BaseLRScheduler):
"""
Multi-step learning rate scheduler with optional linear warm-up strategy
"""
def __init__(self, opts, **kwargs) -... |
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