sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
f42e85c9dc88f9670e2d344cfa272519406ec139d35de146965b9bbab905b41b | Python | 1,528 | 56 | import random
import pytest
from geomstats.geometry.complex_matrices import ComplexMatrices
from geomstats.test.parametrizers import DataBasedParametrizer
from geomstats.test_cases.geometry.complex_matrices import ComplexMatricesTestCase
from geomstats.test_cases.geometry.hermitian import HermitianMetricTestCase
fro... |
16985ca7657c2cb8a7b899fd07209b162fd25e8b3a3f959e89f5cf052615d6b9 | Python | 1,529 | 74 |
from __future__ import print_function
from os import environ as env
URL = 'https://storage.yandexcloud.net'
class Progress:
def __init__(self):
self.size = 0
def show(self):
mb = self.size / 1024 / 1024
print('%.2fMB' % mb, end='\r')
def __call__(self, chunk):
self.si... |
537696065ce7998167d7e1283d4be41b19d22234370791e32402db663678cdcb | Python | 1,530 | 44 | from data.dataset import Brats184, Brats2021Train, Brats313, GanBratsFromFolder
from learning.train_from_folder_name import train_experiment
if __name__ == '__main__':
split_using_instances = True
base_dataset = 'Brats2021'
include_original = True
include_synthetic = False
single_channel = True
... |
087073cd4164fe1d7f2109e30aeaa5ee2610025c65a3bb83735d90b91b235a1d | Python | 1,534 | 37 | import json
import argparse
from rdkit import RDLogger
from dig.ggraph.method import GraphDF
from dig.ggraph.evaluation import PropOptEvaluator
RDLogger.DisableLog('rdApp.*')
parser = argparse.ArgumentParser()
parser.add_argument('--prop', type=str, default='plogp', choices=['plogp', 'qed'], help='property name')
par... |
5f6006ce9c3709286cf6d3d95eacec9267af2f5c251d7d72a1d4a43db6f60865 | Python | 1,534 | 63 |
from sleepy.processing.processor import Algorithm
from sleepy.processing.parameter import Parameter
import numpy as np
class Relative(Algorithm):
def __init__(self):
self.name = "Relative Amplitude"
self.durationLow = Parameter(
title = "Lower bound for duration interval [sec]",
fieldType = float,
de... |
a3d1ffac50dacda34da20162c374be5292a154ab77f77b0d1c9d30f03ae2ed57 | Python | 1,537 | 42 | """Tests for complete ABF extraction through the public PyABF API."""
from pathlib import Path
import numpy as np
import pyabf
from sanpy.io.zarr_export.pyabf_adapter import snapshot_abf
def test_snapshot_reads_every_sweep_and_adc_channel(small_abf: Path) -> None:
"""Read raw and command values for every sweep... |
4d524fd6e3363d1cf8036277c7d2851bd66b29d216a59687c4ed5cf6b88805d1 | Python | 1,538 | 60 | import pytest
from torch import nn
from reinvent.models.transformer.core.network.encode_decode.model import EncoderDecoder
from reinvent.models.transformer.core.vocabulary import build_vocabulary
from reinvent.models.transformer.libinvent.libinvent import LibinventModel
from reinvent.models import meta_data
from tests... |
9204bb2eace44064e08e21bb5b7ac1b9f9308ab5d8984277382ce22156184ac6 | Python | 1,539 | 48 | import numpy as np
import xarray as xr
from numpy.testing import assert_allclose, assert_raises
from gemmr.estimators import SVDPLS
from gemmr.data import generate_example_dataset
from gemmr.sample_analysis.macros import *
class MockEstr():
def fit(self, X, Y):
self.assocs_ = np.arange(2)
return... |
b621510163a47747647232f90ccb2232148837c3a51212dbfcad6c440814055e | Python | 1,539 | 45 | """
Calculate the number of triggers involved in each wave.
"""
import numpy as np
import argparse
from pathlib import Path
import pandas as pd
from utils.io_utils import load_neo, save_plot
from utils.parse import none_or_path
CLI = argparse.ArgumentParser()
CLI.add_argument("--data", nargs='?', type=Path, required=... |
574a7605a710699bb1847067bb2d1b230de79562098ecc204a6b5a9a7344a13d | Python | 1,540 | 44 | from dival import get_standard_dataset
from dival.measure import PSNR
from dival.reconstructors.tvadam_ct_reconstructor import TVAdamCTReconstructor
from dival.reference_reconstructors import (
check_for_params, download_params, get_params_path)
from dival.util.plot import plot_images
import matplotlib.pyplot as pl... |
ca827931bc09c3aa886e2e78386b0aee1aa5e19d93a05d0506c2f6c6324b7412 | Python | 1,540 | 48 | # Configuration file for the Sphinx documentation builder.
#
# For the full list of built-in configuration values, see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Project information -----------------------------------------------------
# https://www.sphinx-doc.org/en/master... |
110712aa4113368a4d45cf02019c47588f949ab6a331a2acb48b8290dcf82600 | Python | 1,541 | 67 | import torch.nn as nn
from . import base
from . import functional as F
from ..base.modules import Activation
class JaccardLoss(base.Loss):
def __init__(self, eps=1.0, activation=None, ignore_channels=None, **kwargs):
super().__init__(**kwargs)
self.eps = eps
self.activation = Activation(a... |
850683f105ea140c8fb1b1bb1f4799f79cf45b66e98ad98e0f6f433e7ac73ae0 | Python | 1,542 | 45 | # Copyright (c) 2019, NVIDIA CORPORATION. All rights reserved.
#
# This work is licensed under the Creative Commons Attribution-NonCommercial
# 4.0 International License. To view a copy of this license, visit
# http://creativecommons.org/licenses/by-nc/4.0/ or send a letter to
# Creative Commons, PO Box 1866, Mountain ... |
c43028eae6443e48887c42bd2641e6a2684dddda4650686a7b893a68dac5d8bd | Python | 1,542 | 49 | """Statistical Manifold of categorical distributions with the Fisher metric.
Lead author: Alice Le Brigant.
"""
from geomstats.information_geometry.multinomial import (
MultinomialDistributions,
MultinomialMetric,
)
class CategoricalDistributions(MultinomialDistributions):
r"""Class for the manifold of ... |
0508d2159ca29f52a87cd429c2622aeb7fc80758f7866b9fccd2fc90756a6e8f | Python | 1,544 | 40 | from rdkit import Chem
from reinvent.chemistry.library_design import bond_maker, attachment_points
from reinvent.chemistry.library_design.reaction_filters import ReactionFiltersEnum
from tests.chemistry.fixtures.test_data import (
SCAFFOLD_SUZUKI,
DECORATION_SUZUKI,
SCAFFOLD_NO_SUZUKI,
DECORATION_NO_SU... |
cad1d38278ae7560ccb37a36e303a581d6b7db861889842ae5a4e7d70af9dc09 | Python | 1,544 | 62 | import os
import numpy as np
import scipy.signal as sig
import matplotlib.pyplot as plt
# Parameters
T = 10
ms = 1e-3
dt = 0.1*ms
fs = int(1/dt)
tv = np.arange(0, T, dt)
# file path
datadir = 'results_PRC_new/None/22-06-2022 12H35M46S/data'
datadir = '/home/nikos/Documents/projects/Python/memstim-hh/results/new_test/... |
cc965fcdf56eb9344e8f0555acb34dd246715c0cbcb80e1f3777eca75cce9bec | Python | 1,545 | 37 | from deeprank_gnn.GraphGenMP import GraphHDF5
from deeprank_gnn.NeuralNet import NeuralNet
from deeprank_gnn.ginet import GINet
from deeprank_gnn.tools.CustomizeGraph import add_target
import glob
#path to the docking models in pdb format
pdb_path = '../DC/pdb/'
#path to the pssm files
pssm_path = '../DC/pssm/'
#pat... |
111875b7976c78d2264e47a186c9bacc5adf21877a1b7f570298fecbf1426386 | Python | 1,546 | 40 | """Neighbour queries own one OpenMP allocation and restore the caller's pools."""
import numpy as np
import pytest
from threadpoolctl import threadpool_info, threadpool_limits
from vdjdb.motifs import tcremp
@pytest.mark.parametrize('operation', ['radius', 'dbscan'])
def test_neighbour_queries_own_allocation_and_res... |
1f91e99f2c81eb6ba50d05d1b24be6ff41b36554b1a54dcbfdfcec650d467fdf | Python | 1,546 | 49 | import geomstats.backend as gs
from geomstats.test.data import TestData
from .base import ComplexVectorSpaceTestData
from .complex_riemannian_metric import ComplexRiemannianMetricTestData
from .mixins import GroupExpMixinsTestData
class HermitianTestData(GroupExpMixinsTestData, ComplexVectorSpaceTestData):
def e... |
224d5a2ff07bd2ba3e95c4995a6b843c51468dd53aa782f02d1d8e085a7b3d0f | Python | 1,546 | 52 | import numpy as np
from sleeprnn.common import constants
from sleeprnn.data import utils
def get_inta_eeg_names(signal_names):
result = []
for single_name in signal_names:
if len(single_name) == 5 and single_name[2] == "-":
result.append(single_name)
return result
def get_inta_eog_e... |
378426a912b5806c71484af4d15d42b80a69dd19841ff97b0e0ea0db8079d223 | Python | 1,546 | 75 |
from tempfile import NamedTemporaryFile
import numpy as np
import pytest
from navec import Navec
from navec.meta import Meta
from navec.vocab import Vocab
from navec.pq import PQ
@pytest.fixture
def emb():
meta = Meta(
id='test_1B_3k_6d_2q'
)
pq = PQ(
vectors=3,
dim=6,
q... |
c32f1331a6cfb0cd2d54f9be01aa51ff9632228215e76b4d1ac65747564be7e4 | Python | 1,546 | 37 | import anndata as ad
import pandas as pd
import scanpy as sc
from scETM import scETM, UnsupervisedTrainer, evaluate, prepare_for_transfer
sc.set_figure_params(dpi=120, dpi_save=250, fontsize=10, figsize=(10, 10), facecolor="white")
data_raw=pd.read_csv("Adult-Brain_Lake_dge.txt",sep=",",index_col=0,header=0)
df... |
7079946f2a331fe24ab693c2777b3df66d4d3a434d2bb8a65dfb779e655c2463 | Python | 1,552 | 55 | # -*- coding: utf-8 -*-
import os
import argparse
import logging
import numpy as np
# use this format to tell the parsers
# where to insert certain parts of the script
# ${imports}
def parse_args():
# Argument Parser
parser = argparse.ArgumentParser()
# my args
parser.add_argument("--verbose", action... |
9ab60955ebfe465db0e1df3edb17ee1b1f56e266b174ec1b7e411ca598eb8d99 | Python | 1,554 | 35 | """Build, proofread and release the VDJdb T-cell receptor specificity database.
Layout mirrors the pipeline stages; see ``ROADMAP.md`` for which are implemented.
schema/ the column registry every output format projects from
io/ chunk reading, release bundling
qc/ chunk validation
cura... |
9b1bd0f496174c80c05dd5d2923db1a910cdb700d19448468b8cd52de23faf86 | Python | 1,555 | 28 | # Author: Youzhi Luo (yzluo@tamu.edu)
# Updated by: Anmol Anand (aanand@tamu.edu)
import argparse
from examples.auggraph.GraphAug.conf.generator_conf import generator_conf
from examples.auggraph.GraphAug.conf.reward_gen_conf import reward_gen_conf
from dig.auggraph.method.GraphAug.runner_generator import RunnerGenerat... |
9e7ef9ad63125143897f8eb8dc26207b05d5f4007866325a48cd557f1265d4bf | Python | 1,555 | 132 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
"""
Relevant chunk from ASE
https://gitlab.com/ase/ase/-/blob/master/ase/data/__init__.py
to reduce dependencies for nn modules
"""
chemical_symbols = [
"X",
"H",
"He",
"Li",
"Be",
... |
c288eb9777f0546d57ba9b80109d66c39645146fcbeea58ce29bf03f08426aca | Python | 1,556 | 59 | """Benchmark metric logarithm."""
from importlib import import_module
import pandas as pd
import pytest
def read_benchmark_log_data():
"""Read benchmark parameters from file benchmark_params.pkl."""
data = []
ids = []
df = pd.read_pickle("benchmark_params.pkl")
params = list(df.itertuples(index=... |
676a883695012ffddc1f77477a35e0aeae67e1c4f0911a7f689a89055380f978 | Python | 1,557 | 49 | import numpy as np
import nibabel as nib
import pandas as pd
def get_atlas_rois_from_mask(mask, atlas):
mask_data = mask.get_fdata()
atlas_data = atlas.get_fdata()
mask_rois = (np.setdiff1d(np.unique(atlas_data[mask_data == 1]), 0)).astype(int)
return mask_rois
def get_module_vol(atlas, rois, value=... |
025d47f62a64407f4b5a40d99ffa4bc29c58fce8c1880ad94aa030b7804e74f7 | Python | 1,558 | 50 | # 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
#
# Un... |
6a2920e2ac2460cbd437c035e2eb83231140e32412b816d67e31bba1f81445b7 | Python | 1,558 | 40 | """WebLabelling URL Configuration
The `urlpatterns` list routes URLs to views. For more information please see:
https://docs.djangoproject.com/en/2.1/topics/http/urls/
Examples:
Function views
1. Add an import: from my_app import views
2. Add a URL to urlpatterns: path('', views.home, name='home')
Class-... |
0d77699bd35adf3d8f626c0b9c5efdd07cbf225a59f0bcf286b9c556e981cf3b | Python | 1,559 | 59 | #!/usr/bin/env python3
# ruff: noqa W291
import os
text = """<!--- DO NOT EDIT THIS FILE. Generated by [[GEN]]-->
# Inferring conductivity from temperature
"""
def add_subdir(subdir, title, cmd, img=True):
global text
text += f"""
### {title}
```
{cmd}
```
Output directory `{subdir}`:
* [`train.log`]([... |
804539f206fe7f3738f337f402b60b796afb88ee9d6c17ad12c8374bbb64b09b | Python | 1,560 | 73 | import os
import argparse
import numpy as np
from bindsnet.environment import GymEnvironment
parser = argparse.ArgumentParser()
parser.add_argument("-n", type=int, default=1000000)
parser.add_argument("--render", dest="render", action="store_true")
parser.set_defaults(render=False)
args = parser.parse_args()
n = ar... |
d392c3ca02e34214acec5819250cb5c9538d9796900ab3188ea6a37ee5511621 | Python | 1,560 | 48 |
import numpy as np
class DataSource:
"""A :class:`DataSet` loads the data initially and converts it into a
useable form. It further creates a dictionary of dataSources, the epochs
of the data. Each epoch contains information about the sampling-rate,
the interval of the epoch and maintains an in... |
e7322355b84319870e9781f2aaa56f609c16456acc3edeb960bdaf1a3a6c6e98 | Python | 1,561 | 38 | import argparse
from data.dataset import GanBrats, get_brats_diff
from learning.train import train_experiment
if __name__ == '__main__':
split_using_instances = False
parser = argparse.ArgumentParser(description='Train BRATS 2D segmentations model.')
parser.add_argument('fraction', type=float, nargs=1, ... |
ed1f95dffe07ff009be0c0763a1381dd55ae3408bdbda891a0d3b50def2d7abc | Python | 1,561 | 48 | import os
os.environ['OPENBLAS_NUM_THREADS'] = '1'
import pandas as pd
import sys
import numpy as np
#Retains the lowest q-value associated with a peak (max log value).
a = sys.argv[1]
prev = []
qs = []
o = []
z = pd.read_csv(a, sep = "\t", header=None)
#z = z.sort_values([0,1])
merged_peaks = []
print... |
5479c78487f0ce382a785f28ec9816cfc708531f799c57e9c5a3e08d386dd794 | Python | 1,562 | 37 | import json
import argparse
from rdkit import RDLogger
from dig.ggraph.method import GraphAF
from dig.ggraph.evaluation import PropOptEvaluator
RDLogger.DisableLog('rdApp.*')
parser = argparse.ArgumentParser()
parser.add_argument('--prop', type=str, default='plogp', choices=['plogp', 'qed'], help='property name')
par... |
d967bf0d7ecefbd40c137b7e5fafc53c30f4fecf7ac9e59260a4bcbe58efe059 | Python | 1,562 | 39 | """Built chains are complete, and incomplete input stops publication."""
import polars as pl
import pytest
from vdjdb.assemble.master import FIX_FIELDS, assert_complete_chains
def master():
row = {'record_id': 'r1'}
for gene in ('alpha', 'beta'):
row.update({f'cdr3.{gene}': 'CASSF' if gene == 'beta' ... |
6fad418cbbebf175623d5f28cd9f3b5a9e61f168ff48e9342c5facf3e4a1fb80 | Python | 1,563 | 71 | import numba as nb
import numpy as np
import pytest
@nb.njit
def ou_process(n, dt):
"""Simulate an OU process.
Simulates the OU process
.. math::
dX_t = -X_t dt + \sqrt{2} dW_t
Parameters
----------
n : int
Length of trajectory.
dt : float
Sampling time.
Re... |
a2f00f223c1635343458a0bf52db517637fc602b1a306ec4678235e019ab5104 | Python | 1,563 | 28 | # Author: Youzhi Luo (yzluo@tamu.edu)
# Updated by: Anmol Anand (aanand@tamu.edu)
import argparse
from dig.auggraph.method.GraphAug.runner_aug_cls import RunnerAugCls
from dig.auggraph.method.GraphAug.constants import *
from examples.auggraph.GraphAug.conf.generator_conf import generator_conf
from examples.auggraph.Gr... |
9270f939204ccd028e1090b2f3f17eecae25a36ac27d4a5a25b6b83603886d6e | Python | 1,564 | 60 | import pytest
from pathlib import Path
import torch
from reinvent.runmodes.TL.run_transfer_learning import run_transfer_learning
from reinvent.runmodes.utils.helpers import set_torch_device
from reinvent.models.meta_data import check_valid_hash
@pytest.fixture
def setup(tmp_path, json_config, pytestconfig):
dev... |
ca48e09efb9a429c8e081445886cdd3157210d03c5e3a417a2cbd598dda6ee46 | Python | 1,564 | 41 | import os.path as osp
import pickle
def get_white_list():
root = '/mnt/dive/shared/kaleb/Datasets/PubChemQC/utils'
with open(osp.join(root, 'list_of_mol_dirs.pkl'), 'rb') as f:
mol_dirs = pickle.load(f)
mol_dirs = [d.decode('UTF-8') for d in mol_dirs]
mol_dirs.sort()
print('Al... |
39aeb1ed2111ff2d1c71e7c7f5dbf63177f81fc70e2229646f5e68abe1c851ad | Python | 1,565 | 52 | from pymonntorch.NetworkCore.Behavior import Behavior
from pymonntorch.NetworkBehavior.EulerEquationModules.Helper import (
eq_split,
remove_units,
)
from sympy import symbols
import torch
class Equation(Behavior):
def __init__(self, *args, eq=None, step_size="1*ms", **kwargs):
super().__init__(*a... |
862f9b28c6a76e8ee3ae52b1d8a0b2a19856c7daa2d4230ce06e6106282728ef | Python | 1,565 | 63 | #
# For licensing see accompanying LICENSE file.
# Copyright (C) 2022 Apple Inc. All Rights Reserved.
#
from torch import nn
from typing import Optional
from utils import logger
from .activation import (
ReLU,
Hardswish,
Hardsigmoid,
PReLU,
LeakyReLU,
Swish,
GELU,
Sigmoid,
ReLU6,
... |
a1f61724828833ba47567cac6a712291996d33c1aad7e3d734a04c28ad38fe24 | Python | 1,565 | 46 |
from omegaconf import DictConfig
from navidiv.reinvent.InputGenerator import InputGenerator
class model_params_rdkit_physchem:
def __init__(self, cfg, id):
self.property_name = cfg.params_list[id]
self.lower_bound = cfg.lower_bound[id]
self.upper_bound = cfg.higher_bound[id]
self... |
a6320fdb9c9307a4ac99bccbc1bb55c2a356839ede8447b96886fb83b75f03c0 | Python | 1,566 | 55 | 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 = [
('distComputation', int32)
]
@jitclass(spec)
cl... |
a715ea770982a4dba41201e4d504dfb7cdcc27b1a6a6482a4c046ab3bde2769c | Python | 1,566 | 42 | """The run-or-raise device policy: explicit GPU requests never silently degrade.
GPU execution in nltools means Himalaya ridge fitting (``_Ridge(device='gpu')``)
and the ridge bootstrap (``BrainData.bootstrap(device='gpu')``); nothing else
runs on a GPU. Both resolve their backend through ``_resolve_backend``, so an
e... |
d9637b8a039010417c92bb6e5e8c5e5af25b02e1a9adaf2efd098a3a785201b6 | Python | 1,566 | 46 | import os
import cv2
import time
import pyfftw
import multiprocessing as mp
''' This script is used to learn 2D wistom used to speed up FFT-based spatial homomorphic filtering
2D wistom is only used in SUNS online.
'''
folder = 'train_3_test_1'
dir_wisdom = os.path.join(folder, 'wisdom')
if not os.path.exists(dir... |
1d0363fce37a38ef21bdf0412f821fb37474f8dad01834f8337c39345e38cec5 | Python | 1,567 | 59 | """
This module contains some test cases.
"""
import string
import numpy as np
import pytest
from rbo.rbo import RankingSimilarity
TESTS = [
# Sanity checks
(string.ascii_lowercase, string.ascii_lowercase, 1.0),
(string.ascii_lowercase, string.ascii_lowercase[:7], 1.0),
("abcde", "fghij", 0.0),
#... |
e9f049e3ea80d690d40543b19f562eda2baa239ce97b232afbf24d8d4eddeea9 | Python | 1,568 | 45 | from dival import get_standard_dataset
from dival.measure import PSNR
from dival.reconstructors.dip_ct_reconstructor import (
DeepImagePriorCTReconstructor)
from dival.reference_reconstructors import (
check_for_params, download_params, get_params_path)
from dival.util.plot import plot_images
import matplotlib.... |
be08ac12d6b43ed1fc3a8fa63c3597eddfe6f6c79eae839f4b188ae16ab1e26d | Python | 1,570 | 59 | """Benchmark metric distance."""
from importlib import import_module
import pandas as pd
import pytest
def read_benchmark_dist_data():
"""Read benchmark parameters from file benchmark_params.pkl."""
data = []
ids = []
df = pd.read_pickle("benchmark_params.pkl")
params = list(df.itertuples(index=... |
ceb5c08455ab30387a56e33334d62699c0d8063261924379862eca155d94013d | Python | 1,571 | 36 | import numpy as np
from torchvision.models import resnet50
from torchvision import transforms
from model_tools.activations.pytorch import PytorchWrapper, load_images
from utils import properties_to_id
def get_gcl_fig5_models():
resnet50_pt_layers = ['conv1', 'bn1', 'relu', 'maxpool'] + \
... |
f75a2d8b534f1750178992b709b513f5d130f91640838aeeffc1cb857702f76f | Python | 1,572 | 44 | def smooth_signal(x,window_len=10,window='flat'):
"""smooth the data using a window with requested size.
This method is based on the convolution of a scaled window with the signal.
The signal is prepared by introducing reflected copies of the signal
(with the window size) in both ends so that tra... |
fdc650376a985df60b0fe3dc8898e32d2f074f3bfb199e10d5ba51af24083e00 | Python | 1,572 | 46 | from abc import ABC
class PointTransformer(ABC):
def transform_point(self, point):
raise NotImplementedError("`transform_point` not implemented")
def transform_tangent_vec(self, tangent_vec, base_point):
raise NotImplementedError("`transform_tangent_vec` not implemented")
def inverse_tra... |
1578cbd6ef9337266db79ee2a81b48aadc8be4af672b2fe0998617f985933f1e | Python | 1,574 | 60 | import random
import pytest
from geomstats.information_geometry.dirichlet import DirichletDistributions
from geomstats.test.parametrizers import DataBasedParametrizer
from geomstats.test.random import RandomDataGenerator
from geomstats.test_cases.information_geometry.dirichlet import (
DirichletDistributionsTestC... |
2ed9c2be1d04aa3f80e714114cb4fcd61329fda18aafaeb5d224b9638bed0c7d | Python | 1,575 | 72 |
import sklearn.metrics as metrics
from torch.nn import BCEWithLogitsLoss, MSELoss, L1Loss
from hyper_dti.utils.metrics import mcc_score, ci_score, rm2_score, re05_score, re1_score, re2_score, re5_score
METRICS = {
'classification': {
'AUC': metrics.roc_auc_score,
'AUPRC': metrics.average_precisi... |
2b2c86f121bbb03ffa6de3d69f6b420ee199f9a572eb8579bdb38a5793605b6b | Python | 1,577 | 43 | """Apply light/dark display colours to generated documentation SVGs; no data changes.
Run after Graphviz or gnuplot. The embedding page supplies the colour scheme.
"""
import re
import sys
from pathlib import Path
STYLE = """<style id="figure-theme">
:root { fill: var(--ink); --ink: #253444; --line: #526375; --panel:... |
bc08f0ff0b3965e5377d31942b7efb4eb50a8142bc2478d36d6be7a59b042ca3 | Python | 1,577 | 51 | #!/usr/bin/env python3
__description__ = \
"""
Test that sends 10000 floats as fast as possible back and forth to the arduino.
It uses random number floats, so this should cover a wide variety of possible
characters in the binary strings that could (possibly) be mangled.
Works with arduino sketch in rapid-float direc... |
194bd1c28c445a117a515bf02d78c47b2d687424b73a9b4768b74ce5c644e656 | Python | 1,581 | 41 | # Copyright (c) 2022 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
#
# Un... |
eaad14381c716f6177759b9284c2ade4816af0034c9fe1440c47dadec6cbc38b | Python | 1,582 | 49 | import pytest
from geomstats.information_geometry.exponential import (
ExponentialDistributions,
ExponentialDistributionsRandomVariable,
ExponentialMetric,
)
from geomstats.test.parametrizers import DataBasedParametrizer
from geomstats.test_cases.geometry.riemannian_metric import RiemannianMetricTestCase
f... |
84d0ed7d79ff9068a209551153fa94233ba9c7a333bba33bd544db5c1566d0c8 | Python | 1,583 | 45 | import experiment as exp
import arena
import schedule
import video_system
class HeatImagesExperiment(exp.Experiment):
default_params = {
"image_src_ids": ["top", "thermal"],
"video_src_ids": ["thermal"],
"on_time": 30*60,
"off_time": 30*60,
"$inter_trial_interval": 5,
}... |
a9a81511d467480a90ad8db909c3ad57cc86d1a1b101b3c6913308b0adccec84 | Python | 1,583 | 56 | #
# For licensing see accompanying LICENSE file.
# Copyright (C) 2022 Apple Inc. All Rights Reserved.
#
import os
import importlib
import argparse
from .base_transforms import BaseTransformation
SUPPORTED_AUG_CATEGORIES = []
AUGMENTAION_REGISTRY = {}
def register_transformations(name, type):
def register_trans... |
665f5237346f53537f500ad094eff346636510ec45aea8c2671c6ac2a930449f | Python | 1,585 | 49 | import pytest
from geomstats.information_geometry.poisson import (
PoissonDistributions,
PoissonDistributionsRandomVariable,
PoissonMetric,
)
from geomstats.test.parametrizers import DataBasedParametrizer
from geomstats.test.random import RandomDataGenerator
from geomstats.test_cases.geometry.riemannian_me... |
fd27e448f8302caecc0c6bc328b633f5e11afe8182c32c2dc6c68ba4c7f08f85 | Python | 1,585 | 57 | import experiment as exp
import asyncio
# TODO: add async action
class AsyncPhasesExperiment(exp.Experiment):
default_params = {
"run_msg": "TestExperiment is running",
"end_msg": "TestExperiment has ended",
}
async def setup(self):
self.log.info("setup")
await asyncio.sle... |
2bc052c72c575a590094371a7aea73a641025782f12359657a685fb574d02023 | Python | 1,586 | 43 | from reinvent.models.linkinvent.link_invent_model import LinkInventModel
from reinvent.models.linkinvent.model_vocabulary.paired_model_vocabulary import (
PairedModelVocabulary,
)
from reinvent.models.linkinvent.networks import EncoderDecoder
from reinvent.models.model_mode_enum import ModelModeEnum
from reinvent.m... |
9eb0028e876385beead8b20bfbfaa9df04daa577ad031a90bdaf20bdb89814cf | Python | 1,587 | 45 | import sys
unmaskedFracsFileName, winSize = sys.argv[1:]
winSize = int(winSize)
unmaskedFracs = []
if unmaskedFracsFileName != "None":
with open(unmaskedFracsFileName) as unmaskedFracsFile:
for line in unmaskedFracsFile:
unmaskedFracs.append(float(line.strip()))
line = sys.stdin.readline()
fi... |
d6adf5d1c14d24ae23302b59c80d4e52544ed5e7e7942c2df4861d5ef25e4e35 | Python | 1,587 | 58 | """Topological polar surface area (TPSA) descriptor from RDKit
This implementation allows to include polar S and P as described in
https://www.rdkit.org/docs/RDKit_Book.html#implementation-of-the-tpsa-descriptor
"""
from __future__ import annotations
__all__ = ["TPSA"]
from typing import List, Optional
from rdkit ... |
9cb4f455483bb4202140ee8fd65d9815e7e19320c2cd210569dbb4543a90f909 | Python | 1,589 | 55 | """Declare runtime-owned mappings from analysis results to trace overlays."""
from __future__ import annotations
from dataclasses import dataclass
@dataclass(frozen=True)
class TraceOverlayDefinition:
"""Describe one analysis-result overlay without prescribing GUI styling.
Attributes:
id: Stable ma... |
8722188ccc56106ab39d1fa22d5c50b1caf357e5d66078647f7c8d8d8bcc8b35 | Python | 1,590 | 65 | import logging
from torchmin import minimize as torchmin_minimize
from geomstats.numerics._common import params_to_kwargs
from ._optimization import Minimizer
class TorchminMinimize(Minimizer):
"""Wrapper for torchmin.minimize.
Check out
https://pytorch-minimize.readthedocs.io/en/latest/api/index.html... |
00ae17afe4d6fce11d0d2e99c7b7efe60d22d42cb34f0c0579606e71b4e55af3 | Python | 1,592 | 59 | """Benchmark metric exponential."""
from importlib import import_module
import pandas as pd
import pytest
def read_benchmark_exp_data():
"""Read benchmark parameters from file benchmark_params.pkl."""
data = []
ids = []
df = pd.read_pickle("./benchmark_params.pkl")
params = list(df.itertuples(in... |
ca597dabe3ab36942d6a7d3c95260462ccacca4219922b0f38d3e42c1d9d7204 | Python | 1,593 | 43 | import unittest
from rdkit import Chem
from reinvent.chemistry.library_design import bond_maker, attachment_points
from reinvent.chemistry.library_design.reaction_filters import ReactionFiltersEnum
from tests.chemistry.fixtures.test_data import (
REACTION_SUZUKI,
SCAFFOLD_SUZUKI,
DECORATION_SUZUKI,
SC... |
499c96aaa00ba83db100905af77f3a2d4e636999fdcee47ac38b3f6e3378a991 | Python | 1,594 | 46 | import pandas as pd
import glob
import seaborn as sns
import matplotlib.pyplot as plt
# path_files = 'Results/inferring_dtis/'
# fileslist = glob.glob(path_files + '*_statistics_results.txt')
# fileslist[0]
# datasets = [file.replace(path_files,'').replace('_statistics_results.txt', '') for file in fileslist]
data... |
a5df3a921bdb7f8117aff9d76cad65750c0566da6ad00b317f1e9b7982e9f30c | Python | 1,594 | 46 | import os
import cv2
import time
import pyfftw
import multiprocessing as mp
''' This script is used to learn wistom used to speed up FFT-based spatial homomorphic filtering
'''
folder = 'train_3_test_1'
dir_wisdom = os.path.join(folder, 'wisdom')
if not os.path.exists(dir_wisdom):
os.makedirs(dir_wisdom)
Dimens ... |
22d8d35a1616e57f450cfddc69df3b3e71b802b7ced73ca0f5256a48268bc30b | Python | 1,595 | 44 | import rdkit
import rdkit.Chem as Chem
from scipy.sparse import csr_matrix
from scipy.sparse.csgraph import minimum_spanning_tree
from collections import defaultdict
from rdkit.Chem.EnumerateStereoisomers import EnumerateStereoisomers, StereoEnumerationOptions
import torch
def get_mol(smiles):
mol = Chem.MolFromS... |
693699fde3b14ebc02308b4b1900c20c10169ecb7c32d1817afc86cb15f4faac | Python | 1,595 | 77 | import factory
from factory.django import DjangoModelFactory
from celsus.models import Author, TissueType, Disease, Organism, OrganismPart, Instrument, \
QuantificationMethod, Keyword
from celsus.models import CellType as ct
from faker_biology.physiology import CellType, Organ
from faker_web import WebProvider
f... |
0b7fbee38b14200d80c7396de794bf8d29d657bc777be52a10484b3fb1ffb311 | Python | 1,597 | 61 | from pathlib import Path
import click
import numpy as np
import SimpleITK as sitk
from tqdm import tqdm
def _process_patient(input_files: list[Path], output_file: Path):
images = [sitk.ReadImage(f) for f in input_files]
arrays = [sitk.GetArrayFromImage(i) for i in images]
output = np.zeros_like(arrays[0... |
1d831de784de0df446980e589ed07df634232f92cdb8acedf19c19915a852f67 | Python | 1,598 | 41 |
# -*- coding: utf-8 -*-
#
#
# PyRates software framework for flexible implementation of neural
# network models and simulations. See also:
# https://github.com/pyrates-neuroscience/PyRates
#
# Copyright (C) 2017-2018 the original authors (Richard Gast and
# Daniel Rose), the Max-Planck-Institute for Human Cognitiv... |
42a5083b6bd347ad4f4eb52d8b158115b2b1d1279a6f73945a9c9ca07f24c380 | Python | 1,598 | 43 | from idtrackerai import ListOfBlobs, Session
from idtrackerai.utils import create_dir
from .crossing_detector import detect_crossings
from .model_area import compute_body_length
def crossings_detection_API(session: Session, list_of_blobs: ListOfBlobs) -> None:
"""Generates the identification images and classifie... |
61c7cb70d647714afade6dd8b3507180b2ce9204f2617f9426fcc225bc89d78a | Python | 1,598 | 52 | import pytest
import numpy as np
from reinvent.runmodes.RL.intrinsic_penalty.identical_murcko_scaffold_rnd import (
IdenticalMurckoScaffoldRND,
)
from reinvent.models.model_factory.sample_batch import SmilesState, SampleBatch
from reinvent.runmodes.RL.validation import SectionIntrinsicPenalty
from tests.runmodes.... |
8c50a02bdcb1aea995188c41604abe918342a65a2f4653bda0d8cca1e231cd5b | Python | 1,598 | 48 | # 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
import contextlib
import contextvars
import torch
from e3nn import set_optimization_defaults, get_optimization_defaults
from nequip.utils.versions.torch_versions import _TORCH... |
b96eddc04961d76b17c1ad28273451fb900393b05eb11c004cd5aae988040e0e | Python | 1,598 | 40 |
# -*- coding: utf-8 -*-
#
#
# PyRates software framework for flexible implementation of neural
# network models and simulations. See also:
# https://github.com/pyrates-neuroscience/PyRates
#
# Copyright (C) 2017-2018 the original authors (Richard Gast and
# Daniel Rose), the Max-Planck-Institute for Human Cognitiv... |
b0c4eaa30c68b8af145dd44e2c8057a20584840259e3abf045421e697be3a78d | Python | 1,599 | 49 | # coding=utf-8
"""
Implementation of a SMILES dataset.
"""
import torch
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):
"""
:param smiles_list: A list with SMILES strings
... |
f100b3cb40341f3a7ff6d08e5f823fecc5f7b961c9afceaf560f56ba02e60ee0 | Python | 1,600 | 43 | import unittest
from rdkit import Chem
from reinvent.chemistry.library_design import bond_maker, attachment_points
from reinvent.chemistry.library_design.reaction_filters import ReactionFiltersEnum
from tests.chemistry.fixtures.test_data import (
REACTION_SUZUKI,
SCAFFOLD_SUZUKI,
SCAFFOLD_NO_SUZUKI,
D... |
73c1e6a4089ae5f33630b631f0eba6451673971979849981a33ff48d992dc5ff | Python | 1,603 | 65 | import pyNN.nest as sim
from pyNN.utility.plotting import Figure, Panel
from pyNN.random import RandomDistribution, NumpyRNG
import time
from globparams import *
import os
sim.setup(timestep=1, min_delay=1, max_delay=1, threads=os.cpu_count())
rng = NumpyRNG()
cell_type = sim.Izhikevich(a=A, b=B, c=C, d=D, i_offset=O... |
909d6e7e5c42cb79d90a6b3599be9ad990de2dba23a0c339c164aef340909ad7 | Python | 1,604 | 109 | configs = {}
configs['example_config'] = {
"n": 10, # Parameter in the subsequence kernel.
"lambda": 1, # Parameter in the subsequence kernel.
"n_iters": 3, # Iteration of WL kernel.
"norm": False, # Whether to normalize kernel.
"base_k": 'subtree' # Base kernel, choose from subtree, sp
}
delaney... |
34a57806aedf4edd9e847367aecf9dc71f1539c5a5990c2e7143bddd95620f3a | Python | 1,607 | 37 | import rdkit
import rdkit.Chem as Chem
import copy
def get_slots(smiles):
mol = Chem.MolFromSmiles(smiles)
return [(atom.GetSymbol(), atom.GetFormalCharge(), atom.GetTotalNumHs()) for atom in mol.GetAtoms()]
class Vocab(object):
benzynes = ['C1=CC=CC=C1', 'C1=CC=NC=C1', 'C1=CC=NN=C1', 'C1=CN=CC=N1',
... |
8d8508a1b37a30558fbcbc7c01e9fe0901880fed72e2abdfb2c50385d81b47b5 | Python | 1,607 | 59 | #!/usr/bin/env python3
__description__ = \
"""
Test ability to send duplex data (e.g. read args while sending them out with
an unterminated command).
"""
__author__ = "Michael J. Harms"
__date__ = "2016-06-04"
__usage__ = "./duplex.py serial_device (like /dev/ttyACM0)"
import random, sys
import PyCmdMessenger
def mai... |
4fbe45187df9d0dc22e35d818041beb4b875d748306c153951fd1bc5532bb172 | Python | 1,608 | 59 | import pytest
from pathlib import Path
import torch
from reinvent.runmodes.TL.run_transfer_learning import run_transfer_learning
from reinvent.runmodes.utils.helpers import set_torch_device
from reinvent.models.meta_data import check_valid_hash
@pytest.fixture
def setup(tmp_path, json_config, pytestconfig):
dev... |
fabc4c15e034a0c528a4bfb1be52158e892a1fe8e8cf7db8f0e4acc829cebd50 | Python | 1,608 | 52 |
import random
import glob
import matplotlib.pyplot as plt
import numpy as np
from skimage.io import imsave
from skimage.transform import radon, iradon
from sparse_ct.tool import plot_grid
from sparse_ct.data import image_to_sparse_sinogram, ellipses_to_sparse_sinogram
from sparse_ct.reconstructor_2d import IRadonRecon... |
2a1d9aae87b50de0a8b65f7ae34f851c1b20121e5cfcdda35711387d214a0788 | Python | 1,610 | 70 | import torch
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
names_drug = [
'MolLogP',
'MolWt',
'NumHAcceptors',
'NumHDonors',
'NumHeteroatoms',
'NumRotatableBonds',
'TPSA',
'RingCount',
'NHOHCount',
'NOCount',
... |
0f34994b076e9bf6da11b667afbec5a08d2d29121cad3920f5d31313a10f2b93 | Python | 1,611 | 56 | # Copyright 2020-2024 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""Logs utilities."""
import logging
from rich.console import Console
from rich.logging import RichHandler
from openfl.utilities import add_log_level
def setup_logger(log_level=logging.INFO, log_file=None):
"""Configure loggers.
... |
92593a852730e1749bc5df0ac0b9ec9b0c5bd7119d49ab4ecb79788f8bbac657 | Python | 1,611 | 54 | """app-pytorch: A Flower / PyTorch app."""
import torch
from flwr.client import ClientApp, NumPyClient
from flwr.common import Context
from app_pytorch.task import Net, get_weights, load_data, set_weights, test, train
# Define Flower Client and client_fn
class FlowerClient(NumPyClient):
def __init__(self, net, ... |
c476be9d4c8ee44d4f6fd98193319830e16b5052383508e33b07fc7b11067e0b | Python | 1,611 | 54 | from PymoNNto.NetworkCore.Behavior import *
from PymoNNto.NetworkBehavior.EulerEquationModules.Helper import *
class Variable(Behavior):
def initialize(self, neurons):
n = neurons
eq_parts = eq_split(self.parameter('eq', None))
if eq_parts[1] == '=' and len(eq_parts) >= 3:
se... |
e1a69e719e09cef57b0bbaeff5f49e2d35e451da1ac3768a9c9d3d7ff796f324 | Python | 1,611 | 42 | import argparse
import os
import pandas as pd
from common import most
from common import oai
from common.oai import build_jsw
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument('--oai_meta',
default='/home/hoang/data/X-Ray_Image_Assessments_SAS')
par... |
6f1b1827e283350645ceef3257d997945972a39961f7c320fd9819828dcac97d | Python | 1,614 | 55 | # 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.
"""isort:skip_file"""
from .transformer_config import (
TransformerConfig,
DEFAULT_MAX_SOURCE_POSITIONS,
DEFAULT_MAX_TARGET_POSITIO... |
cbb504d788ccad8f5ba98eb5e9d720aeb710224c477da9b9a8c86ebe0367d4c6 | Python | 1,616 | 45 | #!/usr/bin/env python3
import sys
import json # Better to use dedicated package to write JSON
from peds import open_ped # pip install peds
from peds import get_probands
# MAIN:
families = open_ped(sys.argv[1])
# Extract 'status' of each family = casIndex, members_list, father, mother and affected_list:
status_l... |
d688c3a554a3cbfa987d309d25920ddd34bab7826ae244174db99af5ad3e0399 | Python | 1,616 | 53 | import matplotlib.pyplot as plt
import matplotlib.lines as lines
class draggable_lines:
def __init__(self, ax, xPos, yPos, hLength=5, vLength=20, linewidth=3, color='m', doPick=False):
self.ax = ax
self.c = ax.get_figure().canvas
self.hLineLength = hLength
self.vLineLength = vLength
# horz line
x = [xPo... |
ead35a472203f055bbc7be5882e71c9e81b9e67aeb6b50e6a56d053649582525 | Python | 1,616 | 52 | import pytest
from geomstats.geometry.euclidean import Euclidean
from geomstats.geometry.hyperboloid import Hyperboloid
from geomstats.geometry.hypersphere import Hypersphere
from geomstats.geometry.minkowski import Minkowski
from geomstats.geometry.spd_matrices import SPDMatrices
from geomstats.geometry.special_ortho... |
904e24f29c48c3aaeb534c321ec38cef38c1cc09a2ed3ec1e8ffe3c2ba8be5b8 | Python | 1,620 | 60 | # Copyright 2020-2025 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""
This file contains utility functions for Secure Aggregation for key operations.
"""
from Crypto.PublicKey import ECC # nosec B413
def generate_key_pair(curve: str = "ed25519") -> tuple[str, str]:
"""
Generates a public-priva... |
a8b203d28d9ea2216cdc76362185937c875be27298a20838fb29f1a7f25e5e3c | Python | 1,620 | 57 | import torch
from nequip.data import AtomicDataDict
from ._graph_mixin import GraphModuleMixin
from .model_modifier_utils import replace_submodules, model_modifier
class GhostExchangeModule(GraphModuleMixin, torch.nn.Module):
"""Base class for ghost atom exchange modules."""
def __init__(
self,
... |
f451aecb93be0574f9f9807384e0636db309a9691e6f40e82cd33b8445ccf1ad | Python | 1,621 | 66 | import random
import pytest
from geomstats.geometry.poincare_ball import PoincareBall, PoincareBallMetric
from geomstats.test.parametrizers import DataBasedParametrizer
from geomstats.test_cases.geometry.poincare_ball import (
PoincareBallMetricTestCase,
PoincareBallTestCase,
)
from .data.poincare_ball impor... |
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