sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
023a18e4ddd702978d69f19f240260d61bc661f5e868d215b2df6ceaad9310e3 | Python | 2,675 | 47 |
import sciunit
from sciunit import Capability
import multiprocessing
class ProvidesRecordingLocationsOnTrunk(sciunit.Capability):
""" Indicates that the model provides a list of locations on the trunk (primary apical dendrite) to be tested"""
def find_trunk_locations(self,distances, tolerance, trunk_origin)... |
809e4e2c841c7ec8a7a8ff638ba926cb6c33b430057835ff76039b768bf09c64 | Python | 2,677 | 69 | import torch
import numpy as np
from torch.utils.data import Dataset, DataLoader
from torch.utils.data.sampler import WeightedRandomSampler
class DRODataset(Dataset):
def __init__(self, dataset, process_item_fn, n_groups, n_classes, group_str_fn):
self.dataset = dataset
self.process_item = ... |
ecf48c771731721fa8942fe57f5d5028363253fcd7a2ce0801ff177943667b7f | Python | 2,677 | 72 | # Generated by Django 2.1.9 on 2019-06-13 18:47
from django.db import migrations
forward = """
CREATE OR REPLACE FUNCTION on_edit_treenode_connector_update_edges() RETURNS trigger
LANGUAGE plpgsql
AS $$ BEGIN
IF OLD.treenode_id IS DISTINCT FROM NEW.treenode_id OR
OLD.connector_id IS DISTINCT FRO... |
f82d54138ebf00ec455ad539b41bffbb932a547d85a0394d88d0301f337a0c2b | Python | 2,678 | 88 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sep 1, 2023
@author: Claire Cooper
"""
from RipNetClaire import RipNetClaire
from sklearn.model_selection import train_test_split
from sklearn.metrics import classification_report
from tensorflow.keras.optimizers import Adam
from tensorflow.keras.regulari... |
c3228dd280da52a59ca6d3c2e8cbc7bcf7c0185765151098560a233c66783d8e | Python | 2,680 | 88 | import scanpy as sc
import numpy as np
import scib
import warnings
warnings.simplefilter(action='ignore', category=FutureWarning)
def get_adata_rand_batch(pca=False, neighbors=False):
"""
Download paul15 dataset and preprocess for data integration pipeline
"""
adata = sc.datasets.paul15()
adata.o... |
caae064d46596dd1fa961428f4f7ef39ee312cfdcdd928861e784af213a0685d | Python | 2,680 | 102 | import os
import pandas as pd
from utils import get_collaborator_cn
def __modify_df(df):
# gandlf convention: labels columns could be "target", "label", "mask"
# subject id column is subjectid. data columns are Channel_0.
# Others could be scalars. # TODO
labels_columns = ["target", "label", "mask"]
... |
d28162b8444f7a2b9ccff23e5ab74821f30c3d253f6fbaed771ae8ed23fb013b | Python | 2,680 | 89 | import inspect
import time
import os
from statistics import mean, stdev
from typing import Any
from rich import print
from CybORG import CybORG
from CybORG.Agents import SleepAgent, EnterpriseGreenAgent, FiniteStateRedAgent
from CybORG.Simulator.Scenarios import EnterpriseScenarioGenerator
from CybORG.Agents.Wrappers... |
78d00bcd95c8d1b3012eac7714833c38d79ce23843f33997c3541205e934600c | Python | 2,685 | 71 | """Atlas-related ("register") tasks for MagellanMapper"""
import os
import re
from typing import Optional, Sequence
from magmap.io import export_regions
from magmap.settings import config
from magmap.stats import vols
_logger = config.logger.getChild(__name__)
def build_labels_diff_images(paths: Optional[Sequence[... |
d0e59bda510469d95f2e8b45a6a9e88f771c7ac44bd1e11a59c79b2a0322ceb1 | Python | 2,686 | 57 | # 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... |
04cf0edf57ad51f6bef3af76c02afeee381de3553bae4bf5573eb14610eceb52 | Python | 2,688 | 86 | import torch
import torch.nn as nn
class GraphConvLayer(nn.Module):
def __init__(self,n_vars):
super(GraphConvLayer, self).__init__()
self.W = nn.Parameter(torch.ones((n_vars,1)),requires_grad=True)
self.b = nn.Parameter(torch.ones(n_vars,1),requires_grad=True)
nn.init.xavier_normal_(self.W.data)
nn.ini... |
ebfaf449ad02b4f0705230b6c915bb8dab8127ab4d835d6af7d3e23209138cee | Python | 2,690 | 66 | import numpy as np
import matplotlib.pyplot as plt
import os
from grid_cell.grid_cell_processor import Grid_Cell_Processor
from grid_cell.ploter import scatter_torus_ploter
from grid_cell.manifold_fitter import GP_Fitter, Avg_Fitter, label_mesh
from grid_cell.gkr import GKR_Fitter
from sklearn.decomposition import PCA
... |
7fe1c64261becbabeb48e1ef3a00c9a1a6bbdbe077e175d52e39e2979172a39e | Python | 2,691 | 58 | # 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... |
8040a72bff051155cec6f516f52f1686b5c376bfd6ff9d3c77985c9a0b891640 | Python | 2,691 | 82 | import os
import argparse
import sys
import re
import pandas as pd
def create_csv(predictions, labels):
"""A function that creates a ./data.csv file from input folders."""
# labels
labels_dict = {}
pattern = r".*(\d{5}-\d{3})$"
for folder in os.listdir(labels):
reg = re.match(pattern, fol... |
ff165b7730d9b96ecc7675a72a3a76c929bbb0042c0bb44acfb6180a0ec183b8 | Python | 2,691 | 102 | # tests/test_init.py
"""Tests for public API exports."""
def test_public_api_exports():
"""All public API should be importable from the main package."""
from zndraw_joblib import (
Category,
# Models
Job,
JobManager,
# Router
router,
)
assert router is ... |
6bd4edcaf9b92906a6b1a951af0d1d9439ed5d7986500107da59e9e9913d58a0 | Python | 2,693 | 81 | """Functions to create neuroml simulation"""
"""
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 License version 3.0 as p... |
96ac2922baf96244d8f324d18a800dadda3548e38f0a43ced05e109e3b64661b | Python | 2,693 | 74 | import h5py
import json
import numpy as np
import pandas as pd
from sklearn.mixture import GaussianMixture
from experiment import *
if __name__ == "__main__":
for species in expt.species_names:
print(species)
# Params
params = get_params(species)
n_gauss_mix = params["n_gauss_m... |
602d174228b44b9c752a36e0907db7d7b6df616092f80c33489593d26023ab4b | Python | 2,694 | 60 | import torch
from nnunet_mednext.network_architecture.generic_UNet import Generic_UNet
from nnunet_mednext.network_architecture.initialization import InitWeights_He
from nnunet_mednext.training.network_training.nnUNet_variants.data_augmentation.nnUNetTrainerV2_insaneDA import \
nnUNetTrainerV2_insaneDA
from nnunet_... |
d8b4150bba3f0d3da9ce98312a84579c4f1ea3c35141bb8c9d1fcb0ae3f05b6c | Python | 2,694 | 89 | """Tests for zndraw.io — unified file reading."""
from __future__ import annotations
from collections.abc import Iterator
from typing import TYPE_CHECKING
import ase
import pytest
if TYPE_CHECKING:
from pathlib import Path
from zndraw.io import open_frames
@pytest.fixture
def xyz_file(tmp_path: Path) -> Path... |
04eb15b4519a60a51b671742d67065b12b5b1490ca4353de66996a3bcfcffe0c | Python | 2,695 | 77 |
import torch
import numpy as np
from ..models.constants import ConsensusInitializationMode
from ..models.losses import GeometricLoss
from ..utils.utils_new import frc, fourier_loss
from tqdm import tqdm
def optimize_epoch(
encoder: torch.nn.Module,
decoder: torch.nn.Module,
inverse_model: torch.nn.Mod... |
02434a77412b4ddccfb18edd6f9ce8f88105cb5814b5a02a4ca9b0210657fe1a | Python | 2,696 | 75 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Jul 23 12:22:09 2024
@author: max
Map T1w/T2w ratio on parcels in DK atlas
"""
import numpy as np
import pandas as pd
from neuromaps.datasets import fetch_annotation
from neuromaps import transforms
import nibabel as nib
# Choose annotation ['myelin',... |
57303cf6be835e865782cb0358e5238a8666ae00607a3d31356dd8ae4b204f01 | Python | 2,696 | 81 | from django.http import Http404
from rest_framework.generics import GenericAPIView
from rest_framework.response import Response
from rest_framework import status
from drf_spectacular.utils import extend_schema
from .models import Model
from .serializers import ModelSerializer, ModelDetailSerializer
from .permissions i... |
6534f67054cb75b733e21e1b713181bb53083b5a7b5b0a5b76b9a10d18f15956 | Python | 2,700 | 77 | from django.http import Http404
from rest_framework.generics import GenericAPIView
from rest_framework.response import Response
from rest_framework import status
from .models import Aggregator
from .serializers import AggregatorSerializer
from training.serializers import ReadTrainingExperimentSerializer
from drf_spect... |
9af8b617cfff835b91f745f3b7e40715c13ef8e56232edf4cedf8ee2aa739c2d | Python | 2,701 | 67 | #!/usr/bin/env python3
"""Public-safe static regression checks for CICADA roadmap item 1B."""
from pathlib import Path
ROOT = Path(__file__).resolve().parents[2]
def main():
qc3 = (ROOT / "basescripts" / "CICADA_3_QC.m").read_text()
file_qc = (ROOT / "helper_functions" / "CICADA_fileQC.m").read_text()
g... |
b8f6ffba8a42320f83fedf7b9fafaf416a39b4f433558febec6fc3802d16f602 | Python | 2,701 | 93 | """Bundle HDF5 DLLs into an h5py wheel on Windows
This is meant to do something like auditwheel on Linux & delocate on Mac,
but h5py-specific.
"""
from base64 import urlsafe_b64encode
from contextlib import contextmanager
from glob import glob
import hashlib
import os
import os.path as osp
import shutil
import sys
imp... |
f5ed341b998602ba833a449cc472ce1498fedd518cbba0a0bb0f8ec9c865df21 | Python | 2,702 | 96 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Nov 3 12:48:13 2021
@author: Andrei Istudor andrei.istudor@gmail.com
"""
import numpy as np
import pandas as pd
import torch
from random import randint, random
from EthoCNN import EthoCNN
from DataReaderAV import DataReaderAV
from sklearn.metrics... |
0ecb6d73fa3e643762540546543ede4266a20fed7be1762895774a24ef4e9b38 | Python | 2,704 | 67 | #!/bin/python
# arrange
import truster
import os
import gzip
raw_path = "/Volumes/MyPassport/trusTEr/test/raw/"
lunarc = "config_files/lunarc_config.json"
modules = "config_files/software_modules.json"
test = truster.Experiment("test", lunarc, modules)
test.register_samples_from_path(raw_path)
merge_samples_outdir =... |
c95deb6a5b7ffb1e70d99dca01163e5be14e5b519ee6f733d2d298f9ce4a4abf | Python | 2,704 | 81 | '''
Date: 2022-07-20 15:36:44
LastEditors: yuhhong
LastEditTime: 2022-11-11 23:29:18
'''
import torch
import torch.nn as nn
import torch.optim as optim
import torch.nn.functional as F
import numpy as np
import random
def get_lr(optimizer):
for param_group in optimizer.param_groups:
return param_grou... |
7e102b7034df4797aab00908aa35484855c3b275ffc46da38ade792d6c0ba9cd | Python | 2,705 | 68 | # An Pytorch implementation of the pafnucy model
# The original model was in outdated TensorFlow 1.x.
import torch
import torch.nn as nn
from collections import OrderedDict
class PafnucyNetwork(nn.Module):
"""
Pytorch implementation of the Pafnucy model.
Original paper:
Stepniewska-Dziubinska, M.M., Zielenki... |
057ffa38b5dce10b146d2bd3551888b7758b7a313eedabcd591849f3e713301e | Python | 2,706 | 98 | #!/usr/bin/env python
import sys, os, signal
import string, re
signal.signal(signal.SIGPIPE, signal.SIG_DFL)
use_message = '''
'''
osx_mode = False
if sys.platform == 'darwin':
osx_mode = True
def make_cat_cmd(gzmode, read_dir_base, read_dir, fq_name, num_read):
cmd = []
if gzmode:
if osx_mode:
... |
72faa34d68c6c8a8d4fbf0c21d222e03ebc8587ae21a4e801eea0da13f9ec56c | Python | 2,706 | 67 | # -*- encoding: utf-8 -*-
'''
Copyright 2022 The International Digital Economy Academy (IDEA). CCNL 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.o... |
8c42afdbf9a444caa4fdf322111bbfd64c9efdc07262d9c3b80b6f54cc9754d5 | Python | 2,706 | 101 |
__doc__= """
This script filter the output of Kallisto, taking into account only protein
#coding RNA.
Input files: txtfile_1: name of the txt file with the all the Ensembl transcript ID passing the filters
(this file is the output of removes_3UTR_5UTR_from_GTF.py)
... |
9f9823585807b660ed4ad747c2c8c38efd161ad3d88afe194233c8b038abe460 | Python | 2,707 | 99 | from __future__ import annotations
from typing import Annotated
import typer
from zndraw.schemas import (
BookmarkCreateRequest,
BookmarkResponse,
BookmarksResponse,
StatusResponse,
)
from .connection import (
PasswordOpt,
RoomOpt,
TokenOpt,
UrlOpt,
UserOpt,
cli_error_handler... |
3bc817377139bfc2342fbdb08fe006cb7547cca3247657a43214ba9202a4c892 | Python | 2,708 | 71 | import pandas as pd
import numpy as np
import cv2
from behavior_analysis.io import TrackingInterface
from experiment import *
from skimage.transform import AffineTransform, warp
from skimage.exposure import rescale_intensity
from matplotlib import pyplot as plt
if __name__ == "__main__":
examples = {"o_latipes"... |
de84490711a935254c3f712ba65254107a80097508c9e9ba04a95fbb39c038ca | Python | 2,709 | 86 | import pytest
try:
import torch
except ImportError as exc: # absent, or installed but unusable
pytest.skip(f"torch is unavailable: {exc}", allow_module_level=True)
from nearl.models.model_atom3d import Atom3DNetwork
from nearl.models.model_deeprank import DeepRankNetwork
from nearl.models.model_gnina import ... |
aa7b3c19b0f50e37d6c0798bf65c107fc4162667f61c78ec2109ade577f68928 | Python | 2,710 | 88 | from calendar import c
import numpy as np
import pandas as pd
import scipy
from cogmodels.base import CogModel2ABT_BWQ, CogParam
from cogmodels.utils import Probswitch_2ABT
class WSLS(CogModel2ABT_BWQ):
"""
Win-stay-lose-shift model can be derived as a RLCF model with high beta,
and alpha=1. But here... |
c62502ec8dbf9d96b4c9e20218636c9f4554f9e2c4b35965c215fa90c3147c46 | Python | 2,710 | 82 | import os
import torch
os.environ['TORCH'] = torch.__version__
print(torch.__version__)
import numpy as np
import pandas as pd
from scipy import stats
import matplotlib.pyplot as plt
import seaborn as sns
import json, os, sys
import sklearn
from scipy.stats import pearsonr
from sklearn.metrics import r2_score
from to... |
4eebf2bf6d7c919335d18e1726d50a9ee09ac4ef1e70d24c8693681aa785c90d | Python | 2,714 | 92 | import os
from setuptools import setup
from setuptools import find_packages
# Function to read version from __version__.py
def get_version():
with open(os.path.join(os.path.dirname(__file__), 'tsgm/version.py')) as f:
exec(f.read())
return locals()['__version__']
name = "tsgm"
version = get_version(... |
6c801834542e5863bd26cb16d32fe45083390ecb2a580deb34d265d85912b4ac | Python | 2,714 | 88 | import shutil
baseFileName = './shellScripts/sparse099_10class_'
baseSimTag = 'sparse099_10class_'
def generateCommand(trial_num=0,
num_trials=10,
learning_rate=0.001,
sim_tag='default',
exc_hid_rat=0.5,
epochs=30,
log_file='example.log',
w1_std=-1,
w1_... |
9a39319ffbb4fda3639f1ddaa8705edcfc4b6d663494f3e72fc7fd159c732a9a | Python | 2,714 | 87 | """Core in-memory similarity scoring for tandem mass spectra."""
from __future__ import annotations
from typing import Optional
import numpy as np
from .utils import _as_spectrum, align_fragments
def dot_product_similarity(
query_spectrum: np.ndarray,
library_spectrum: np.ndarray,
mz_tol: float,
q... |
39683f6341f08866084dece63faf9d10ab520eb4539b867d1c514d3b9131bae4 | Python | 2,715 | 66 | import numpy as np
from grid_cell.persistent_homology import Is_Torus
from grid_cell.manifold_fitter import GP_Fitter, Avg_Fitter
import matplotlib.pyplot as plt
import os
from sklearn import datasets
from global_setting import *
#################### Hyperparameters ####################
mouse_name = 'R'
day = 'day1'
m... |
f19e4544f59ff2a5cb5ac12ad09beb3a68f7b13ded678f9951ca1303caadba95 | Python | 2,717 | 77 | # coding=utf-8
# Copyright 2021 The IDEA 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 a... |
280a68c2ae61863e93458aac802cbb550de79c7cd7bd8ed80db5876b1f1f7aee | Python | 2,718 | 105 | import pytest
import numpy as np
from keras import layers
import sklearn.metrics.pairwise
import tsgm
@pytest.mark.parametrize("model_type", [
tsgm.models.architectures.zoo["cvae_conv5"],
])
def test_zoo_cvae(model_type):
seq_len = 10
feat_dim = 2
latent_dim = 1
output_dim = 1
arch = m... |
e534553becef8b53037d94f88c3d4ba4094b18c6454f92cd08a6c58e4b94e08d | Python | 2,721 | 53 | import pandas as pd
from functools import reduce
embedding = 'ESM' # Specify the embedding type 'ESM' or 'ProtTrans'
# Original sequence for comparison
original_sequence = "MGLSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGATVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKHPGDFGADAQGAMNKALELFRKDMAS... |
35ae39ee4761fbb65884f38d7d694e9959249c879c5224b4dc8cafc4fa14de94 | Python | 2,723 | 78 | # Generated by Django 2.1.9 on 2019-06-26 00:42
from django.db import migrations
forward = """
CREATE FUNCTION refresh_skeleton_summary_table_selectively(skeleton_ids bigint[]) RETURNS void
LANGUAGE plpgsql AS
$$
BEGIN
-- Cable length, nodes, creation info, edition info
WITH filtered_... |
3dc2b121b4826232ff42b6de087c3cf8c1d60c1c4e9440c6fd41ef3f8681b8a6 | Python | 2,723 | 103 | # 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 a portion of the selection operat... |
b60a3ff75d34be12ae44adce3b27214a4e38c291a7061ed300a9c78379e50bf3 | Python | 2,723 | 50 | # 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... |
e180e712eb3aec8c9258ee742b36ddef7a77a85bec91187334a2214045259233 | Python | 2,723 | 50 | # pytest unit tests for sct_extract_metric
import numpy as np
import pytest
import logging
from spinalcordtoolbox.scripts import sct_extract_metric
from spinalcordtoolbox.utils.sys import sct_test_path
logger = logging.getLogger(__name__)
@pytest.mark.sct_testing
def test_sct_extract_metric_against_groundtruth():... |
2473690c928edaee5a2f92c05083caf1022003252f6ab18b15d26a8458a57830 | Python | 2,725 | 92 | import numpy as np
import pandas as pd
import cupy as cp
from .conv import *
from .core import iSeq
from .sig import *
from .wtx import *
def open_csv(filepath, n_null=100, random_seed=None):
np.random.seed(random_seed)
x = pd.read_csv(filepath, header=None).values[:, :-100]
t, n_cell = x.shape
x /= ... |
30945f83fab5246bf71b997a679ba7a97c4292adb0fae580abff4fbb010885d9 | Python | 2,725 | 102 | import numpy as np
import pathlib
import pytest
import jax
import jax.numpy as jnp
from ase.io import read
from jax_md import space
from jax_md import quantity
from so3lr import to_jax_md
from so3lr import So3lrPotential
from so3lr import So3lrCalculator
@pytest.mark.parametrize('name', ['atat', 'dha', 'bb'])
def te... |
b60600f2c75c3c3011ce7d8da2fbe7a9a270888e4ee0e412301549bd1ea8af9e | Python | 2,726 | 64 | from ipaddress import IPv4Network
from CybORG.Shared import Observation
from CybORG.Simulator.Actions.Action import RemoteAction
from CybORG.Simulator.Actions.Action import lo_subnet, lo
from CybORG.Simulator.State import State
class Pingsweep(RemoteAction):
"""
Concrete action that simulates a pingsweep, re... |
2a0459237eec8a3f5c394e51f70294c19f186aa2081b687d7d13cf83107a80ed | Python | 2,727 | 82 | import os
import django
import kombu
import logging
from celery import Celery
from celery.signals import setup_logging, worker_process_init
from django.conf import settings
# Set the default Django settings module for the 'celery' program.
os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'mysite.settings')
logger = lo... |
751a0b5aa33c4a96578297b5a4ca0839eff7c6d17d2ea40f1f6880ff147dde9b | Python | 2,728 | 71 | import requests
import langid
import streamlit as st
from translate import baiduTranslatorMedical
from translate import baiduTranslator
langid.set_languages(['en', 'zh'])
lang_dic = {'zh': 'en', 'en': 'zh'}
st.set_page_config(
page_title="余元医疗问答",
page_icon=":shark:",
# layout="wide",
initial_sidebar... |
2b7f1cf09410297ca6deadbf2646440aa3ec37860ee06bc5a38f44afd8818aff | Python | 2,729 | 90 | import tempfile
import numpy as np
import pytest
from keras.datasets import boston_housing
from keras.datasets import imdb
from keras.datasets import reuters
@pytest.fixture
def fake_downloaded_boston_path(monkeypatch):
num_rows = 100
num_cols = 10
rng = np.random.RandomState(123)
x = rng.randint(1... |
65182eb322f74b6c824d9372a1cf6d0a36ae328bf0a5b92d7a1fe57c203f7187 | Python | 2,731 | 73 |
baseFileName = './shellScripts/sparse100_10class_'
baseSimTag = 'sparse100_10class_'
def generateCommand(trial_num=0,
num_trials=10,
learning_rate=0.001,
sim_tag='default',
exc_hid_rat=0.5,
epochs=30,
log_file='example.log',
w1_std=-1,
w1_sparse=-1,
... |
8d4002b5f332f8d58a6f6f1a47a9c0362ecf7edb1738b691360da60e0d11e040 | Python | 2,731 | 73 |
baseFileName = './shellScripts/sparse050_10class_'
baseSimTag = 'sparse050_10class_'
def generateCommand(trial_num=0,
num_trials=10,
learning_rate=0.001,
sim_tag='default',
exc_hid_rat=0.5,
epochs=30,
log_file='example.log',
w1_std=-1,
w1_sparse=-1,
... |
d5f8e9273fc5cb9f0be4f541bea6b0d49d10bb396d6e7d68cdd3a67438af694f | Python | 2,731 | 73 |
baseFileName = './shellScripts/sparse080_10class_'
baseSimTag = 'sparse080_10class_'
def generateCommand(trial_num=0,
num_trials=10,
learning_rate=0.001,
sim_tag='default',
exc_hid_rat=0.5,
epochs=30,
log_file='example.log',
w1_std=-1,
w1_sparse=-1,
... |
da614090820082770a4f85c6d4efcd803eee946e770bedfc80e7e1a107af6c1f | Python | 2,731 | 71 | from medperf.utils import (
generate_tmp_path,
tmp_path_for_cc_asset_key,
secure_write_to_file,
get_file_hash,
remove_path,
)
from medperf.encryption import SymmetricEncryption
from medperf.asset_management.gcp_utils import (
GCPAssetConfig,
upload_from_file_object_to_gcs,
)
from medperf.ass... |
4a727a416d35686964c88126dc0395bc029ce35d07d49bd955226ea2bfe053f2 | Python | 2,732 | 73 |
baseFileName = './shellScripts/sparse095_10class_'
baseSimTag = 'sparse095_10class_'
def generateCommand(trial_num=0,
num_trials=10,
learning_rate=0.001,
sim_tag='default',
exc_hid_rat=0.5,
epochs=30,
log_file='example.log',
w1_std=-1,
w1_sparse=-1,
... |
8316234d0adb90665af03affd40ca45824a020c2947c69fbd215ddfe2f08744f | Python | 2,733 | 89 | from pathlib import Path
import yaml
yml_path = 'config.yml'
class Conf:
def __init__(self):
self.bm_values = BmValues()
self.gf_values = GfValues()
self.peak = PeakSettings()
self.heatmap = HeatmapSettings()
self.quiver = QuiverSettings()
self.session = SessionSe... |
07690c0903a5ce6457f006ec5a72dba9b33476d5ca52e43ac3f2ba4134fd9143 | Python | 2,735 | 91 | import os
import sys
import platform
import subprocess as sp
def run(command, silent=False, background=False, executable='/bin/bash', logfile=None):
'''Runs a shell command and returns the exit code.
Note:
A command run in the background will always return `None`.
Args:
command: Command t... |
9b95ee5502e79486241e319a627e85975a56ed93f63cdc581219417625bb908c | Python | 2,735 | 74 |
from CybORG.Shared import Observation
from .Monitor import Monitor
from CybORG.Simulator.Actions import Action
from CybORG.Simulator.Actions.ConcreteActions.StopProcess import StopProcess
from CybORG.Shared.Session import VelociraptorServer
from CybORG.Simulator.State import State
class Remove(Action):
""" Remo... |
b21883ec5fc80da97df1c2d6ccb3e7e432daaedd48950ea3fcc9958206c81208 | Python | 2,735 | 79 | from provdbconnector import ProvDb
from provdbconnector import Neo4jAdapter
from prov.tests.examples import primer_example
import os
# create the api
NEO4J_USER = os.environ.get('NEO4J_USERNAME', 'neo4j')
NEO4J_PASS = os.environ.get('NEO4J_PASSWORD', 'neo4jneo4j')
NEO4J_HOST = os.environ.get('NEO4J_HOST', 'localhost'... |
a20785a1732f1dd9eace7b04462da5021366599d00e6f8fb781eb6cad1d8b8a0 | Python | 2,736 | 63 | """Convert ALBERT checkpoint."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import argparse
import torch
from transformers import BertConfig, BertForPreTraining, load_tf_weights_in_bert
# from models.transformers.modeling_albert_bright import AlbertCon... |
8e77dd8e9d804309fe92205979bb91eceb8530f43d8e4c2e0fb10ad3281f158c | Python | 2,737 | 70 | from dfa_lib_python.transformation import Transformation
from dfa_lib_python.set import Set
from dfa_lib_python.set_type import SetType
from dfa_lib_python.attribute import Attribute
from dfa_lib_python.attribute_type import AttributeType
def test_get_sets_pass():
attributes = [Attribute("att1", AttributeType.TEX... |
fde4a88feeb5f4dbe6321c8085b96c2cc65bcbdc7b664d1f5fb3c6391e7b2ff3 | Python | 2,737 | 75 | import torch
import torch.nn as nn
import torch.nn.functional as F
from utils import extend_dimensions
class NormalEmbedding(nn.Module):
def __init__(self, input_dim, emb_dim):
super(NormalEmbedding, self).__init__()
self.input_dim = input_dim
self.emb_dim = emb_dim
self... |
6a140de3801ba7fee0ece4abf1522e3c34fe3bb7a665296ec26ebb1506feabd1 | Python | 2,738 | 80 | from typing import List, Type
from medperf.entities.interface import Entity
from medperf.exceptions import InvalidArgumentError
from tabulate import tabulate
from medperf import config
from medperf.account_management import get_medperf_user_data
class EntityList:
@staticmethod
def run(
entity_class: ... |
539622f05d2d96ffc34010ba9c0c734c1888c3347e8b993cf406f60886fffcbe | Python | 2,739 | 74 | #!/usr/bin/env python
# -*- encoding: utf-8 -*-
from langchain.llms.base import LLM
from typing import Any, List, Mapping, Optional, Dict, Union, Tuple
from pydantic import Field
from llm.self_llm import Self_LLM
import json
import requests
from langchain.callbacks.manager import CallbackManagerForLLMRun
# 调用文心 API 的工具... |
b071a9c9747f5864f1f8de0e508aa5eeecb5735d1cb1d5d792cb3a63b9412c49 | Python | 2,739 | 79 | # Copyright (c) OpenMMLab. All rights reserved.
import torch.nn as nn
from mmcv.cnn import ConvModule
from mmengine.model.weight_init import xavier_init
from mmseg.registry import MODELS
from ..utils import resize
@MODELS.register_module()
class MultiLevelNeck(nn.Module):
"""MultiLevelNeck.
A neck structure... |
14f58160f8fe720a59c0c567db5512559aa81351457f6e8e6dd7fcca7eee1e0d | Python | 2,740 | 102 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# If you have a terminal that is not part_of any skeleton, this script
# will try to find the right skeleton via its treenode and update with
# that.
# You may need to install psycopg2, e.g. with:
# sudo apt-get install python-psycopg2
# Requires the file .catmaid-db t... |
e5786fa4747fb0174e44b96fb5acbbd179ea073e71f39b4d895c5ec3c9b9b617 | Python | 2,740 | 87 | # Copyright (c) OpenMMLab. All rights reserved.
import argparse
import os.path as osp
from collections import OrderedDict
import mmengine
import torch
from mmengine.runner import CheckpointLoader
def convert_swin(ckpt):
new_ckpt = OrderedDict()
def correct_unfold_reduction_order(x):
out_channel, in_... |
58e3cdca4fd35b19bc725a09b8c87ca5b16c26f3b8cac8cd415eef536f1e8208 | Python | 2,745 | 90 | from pysisyphus.constants import AU2EV, BOHR2ANG
from ReactBench.Calculators._utils import compute_hessian
from ReactBench.MLIP.leftnet.oa_reactdiff.trainer.calculator import LeftNetCalculator, mols_to_batch
# get leftnet calculator for run_pygsm.py
def get_leftnet_calculator(device="cpu", use_autograd=True):
... |
5e16aebbcaf14a19cc5cbc6a0f96f95362c6800da4232958f7633906ee26500d | Python | 2,745 | 97 | """
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 logging
import os
import random
import numpy as np
import pytest
import torch
from ase.io import read
from ocpmodels.common.registry... |
1d5f59b5b819bfa5ce94c038d641652d2e436eb00f4d3eecb6a1952ca9993d30 | Python | 2,748 | 82 | # -*- coding: utf-8 -*-
# Generated by Django 1.11.8 on 2017-12-16 00:24
import django.core.validators
from django.db import migrations, models
forward_history = """
SELECT disable_history_tracking_for_table('catmaid_sampler'::regclass,
get_history_table_name('catmaid_sampler'::regclass));
SELECT ... |
3cd5a1e8db8c7eeaab760ebb8999021c644da2a5918445f7359d0b0fd2e6aac1 | Python | 2,748 | 70 | import os
import shutil
import subprocess
import warnings
from typing import ClassVar
from setuptools import Extension, find_packages, setup
from setuptools.command.build_ext import build_ext as _build_ext
SRC_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), "src")
# build_ext (unlike the old "install... |
41b6c214b05884e70cef9655260d5f9d5aee45fb9bb88520228bd3b13f54190b | Python | 2,751 | 88 | import json
from tqdm import tqdm
import os
import jieba.analyse
import argparse
label2desc={'1':'可以','0':'不能'}
def load_data(file_path,is_training=False):
with open(file_path, 'r', encoding='utf8') as f:
lines = f.readlines()
result=[]
for line in tqdm(lines):
data = json.lo... |
e440a427a6ebb9682a47dc1c4376adcd3b4f81f6f50ab7438fc8826c2eb3d64a | Python | 2,751 | 67 | import numpy as np
import pandas as pd
import re
def retrieve_convergence_results(results_dir, file_list):
# file_list
loss_dfs = {}
params_dfs = {}
norms_dfs = {}
for file in file_list:
if "losses" in file:
loss_data = pd.read_csv(results_dir + file, index_col=0)
... |
061bed2fa555f0191cb121be01b89844a6efd987fd13ca47a02bf423b8b6f15d | Python | 2,752 | 74 | # Copyright (c) 2016 Salle, Alexandre <atsalle@inf.ufrgs.br>
# Author: Salle, Alexandre <atsalle@inf.ufrgs.br>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy of
# this software and associated documentation files (the "Software"), to deal in
# the Software without restriction, including... |
298aa6ae9df6026d59706e5f001191554f434c57f51b205993c77f7dc1edc45d | Python | 2,752 | 72 | import numpy as np
import matplotlib.pyplot as plt
import os
import hickle as hkl
from grid_cell.speed_partition_processor import Speed_Partition_Processor
from sklearn.linear_model import MultiTaskLassoCV, RidgeCV
from sklearn.model_selection import train_test_split, GridSearchCV, RandomizedSearchCV
from sklearn.neigh... |
479008f9e42d84c4cff0f03353a055d661974b144125511e1989f01921e6f5e6 | Python | 2,752 | 86 | """Tests for FrameStorage provider metadata (frame count, mount, room isolation)."""
import uuid
import pytest
from zndraw.storage import FrameStorage
@pytest.fixture
def room() -> str:
"""Unique room ID per test."""
return uuid.uuid4().hex
@pytest.mark.asyncio
async def test_has_mount_false_by_default(
... |
3ab21113c5ab720410a61406b0c0e58d3d6f02e671a3b9fabed35710e84fb6bb | Python | 2,754 | 91 | """Box geometry for ZnDraw."""
from pydantic import Field
from .base import (
BaseGeometry,
ColorProp,
InteractionSettings,
PositionProp,
RotationProp,
ScaleProp,
Size3DProp,
)
class Box(BaseGeometry):
"""Box/cuboid geometry with customizable dimensions.
Boxes are defined by a c... |
707c8340b25900cd48d1b689849101589e92bee6d2b0aaff1074864137fa89cf | Python | 2,754 | 59 | """One-off script: stub the PhAT Sample2 Neurophotometrics session.
Unlike create_stubbed_testing_data.py, this does NOT read from testing_data/ —
the source is third-party sample data from the Donaldson Lab's PhAT toolkit
(MIT licensed), cloned locally, and this script is intended to be run once to
produce the commit... |
92ab728504842452db100476b74f44e336b27aca581d7e0e9472c11d99284d5b | Python | 2,754 | 71 | import torch
from torch.utils.data import Dataset
import numpy as np
class NoisyDataset(Dataset):
def __init__(self, x1, x2, td, noise = 0.0):
self.x1 = x1
self.x2 = x2
self.td = td
self.noise = noise
self.indexer = len(x1)
def __getitem__(self, idx):
return se... |
834f1dbf01f0317c238142ee797acce21a0c482610e2fb3fd307b7a3c60f20ca | Python | 2,755 | 91 | import torch
import torch.nn as nn
class Fire_Block(nn.Module):
def __init__(self, in_channels, sequeeze_channels):
super(Fire_Block, self).__init__()
self.squeeze = nn.Sequential(
nn.Conv3d(in_channels, sequeeze_channels, kernel_size=1),
nn.ReLU(inplace=True),
)
self.expand1 = nn.Sequent... |
5ad9fd0e4e228ab1fb41c98b5ed40d1d6d4fa2ddb94571b2507a2b0605824bb6 | Python | 2,758 | 91 | import json
from dataclasses import dataclass
import ase
import numpy as np
from znframe import Frame
def atoms_from_json(atoms_json: dict) -> ase.Atoms:
try:
return Frame.from_dict(atoms_json).to_atoms()
except Exception as e:
print(f"Failed to convert atoms from json: {e}. Returning empty a... |
94feb27c5630df6f4d2f0cf62925a4214ba72618fbf8bb39f73939507f0cfcad | Python | 2,758 | 67 | # ###### run DeepST
# cd ~/DATA/luomeng/STEREO/DeepST
# ls data | grep 200.h5ad | xargs -I {} -P 5 ~/miniconda3/envs/deepst/bin/python DeepST.py {}
import os
import sys
import datetime
print(f"{sys.argv[1]} start at {datetime.datetime.now()}", flush=True)
fileName = '/media/desk16/lwx/Epilepsy/upload/A01895D1/h5ad/A... |
28248b40b6f7ca6a261de5fcf36dfa569b04b660b58a0628ccfcff8d5b4b8a56 | Python | 2,759 | 97 | """
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 os
import random
import numpy as np
import pytest
import torch
from ase.io import read
from ocpmodels.common.registry import registr... |
f6c10d88e30c5594c1d10447030eacaad61a09151ca4eb8353c5c836028b6675 | Python | 2,759 | 60 | # 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... |
1a4a2b4ec010d6f1b44e91e450cb8a01e4bf13f610644681dd2110662b3310d3 | Python | 2,761 | 110 | """Unit tests for the Room namespace data model."""
from __future__ import annotations
from typing import TYPE_CHECKING
import pytest
import pytest_asyncio
from sqlalchemy.exc import IntegrityError
from zndraw.access import Visibility
from zndraw.models import Group, Room
from zndraw_auth import User
if TYPE_CHECK... |
47747c4ca59e00c022fc1686a5a26768a09096f0acbbaf56c7aad0365552e9d1 | Python | 2,761 | 60 | # 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... |
e4bb07c0682797ca7e6d74713ec43cbe344b52a0a34fdb391c6ee3f17cd0bc35 | Python | 2,762 | 84 | import pytest
import random
from CybORG import CybORG
from CybORG.Agents.Wrappers import BlueEnterpriseWrapper
from CybORG.Simulator.Scenarios import EnterpriseScenarioGenerator
from CybORG.Agents import SleepAgent, RandomSelectRedAgent, EnterpriseGreenAgent, FiniteStateRedAgent, cc4BlueRandomAgent
@pytest.fixture(p... |
2f1e105ecbbc5ff3f357458f7c34f9d7a01e25c91ff949da31bd22819ae4994f | Python | 2,763 | 76 | from typing import Union
from pandas._typing import FilePath, WriteBuffer
class SoccerTrackMixin(object):
def save_dataframe(
self,
path_or_buf: Union[FilePath, WriteBuffer[bytes], WriteBuffer[str]],
) -> None:
"""Save a dataframe to a file.
Args:
df (pd.DataFrame... |
82840b23b9c2ffd54d93eb6fd17ee94275fd69499cdb2d22183afc698d49c467 | Python | 2,763 | 94 | """Regression: pyclient ZnDraw refreshes cached_length on FramesInvalidate (finding #3).
Stand up a real server via ``server_factory``, register an admin user, create
a room, and spawn a ``ZnDraw`` client pointed at that room's composed address.
A second authenticated HTTP request appends a frame. The first client's
`... |
0d2daf75a2955fac270164b82ca86facd1e5a3c7029163139859e055b2900c59 | Python | 2,764 | 96 | from tests.common import *
import pathlib
import json
METHODS = {
"mnn": {"output_type": "full"},
"scanorama": {"output_type": ["embed", "full"]},
"seurat": {"output_type": ["embed", "full"], "R": True},
"trvae": {"output_type": ["embed", "full"], "no_scale": True},
"scgen": {"output_type": ["full"... |
6b0e412536c74df68f7a6768a62c5763473f9726eaf1dc1206ab712502133834 | Python | 2,764 | 87 | # Copyright (c) OpenMMLab. All rights reserved.
import argparse
import os.path as osp
from collections import OrderedDict
import mmengine
import torch
from mmengine.runner import CheckpointLoader
def convert_twins(args, ckpt):
new_ckpt = OrderedDict()
for k, v in list(ckpt.items()):
new_v = v
... |
c4f2f8f9ef80fd15fedc72b421e10bc3cb83aa07202eac7dac41faaeae945333 | Python | 2,767 | 67 | import torch
import torch.nn as nn
import torch.nn.functional as F
class FeedForwardNetwork(nn.Module):
def __init__(self, input_size, hidden_size, output_size, dropout_rate=0):
super(FeedForwardNetwork, self).__init__()
self.dropout_rate = dropout_rate
self.linear1 = nn.Linear(inpu... |
f86d98da8239b04e44044db08d3c399d1158be27cb9739695e9ca252ea765407 | Python | 2,769 | 74 |
baseFileName = './shellScripts/sparse099_10class_'
baseSimTag = 'sparse099_10class_'
def generateCommand(trial_num=0,
num_trials=10,
learning_rate=0.001,
sim_tag='default',
exc_hid_rat=0.5,
epochs=30,
log_file='example.log',
w1_std=-1,
w1_sparse=-1,
... |
5d729dd33573c0768db774eeb517635f122576d330a34801a0ef74b3e6ac6a68 | Python | 2,770 | 98 | """Tests for CLI admin commands (users list, users login)."""
from __future__ import annotations
import json
from unittest.mock import MagicMock, patch
import pytest
from typer.testing import CliRunner
from zndraw.cli_agent import app
from zndraw.cli_agent.connection import Connection
from zndraw.state_file import ... |
8453a1659f1130f00fe33f20d49bdebaefca80407ac9c9ddb4f9eba76740705e | Python | 2,772 | 98 | import operator
def _acgt_table():
"""
Return a translation table that maps A, C, G, T characters to the lower
four bits of a byte. Other characters (including possibly IUPAC characters)
are mapped to the most significant bit (0x80).
Lowercase versions are also translated, and U is treated the sa... |
0bbde2addac9ab66d7c8d06c9819c1be1a7e5da54709c40d52b5071ecbc6a33d | Python | 2,773 | 71 | # import cProfile, pstats
# pr = cProfile.Profile()
# pr.enable()
# test the performance of methods depending on the number of datapoints
import numpy as np
import matplotlib.pyplot as plt
import hickle as hkl
import os
from grid_cell.sphere_manifold import Circle_Manifold, get_circle_mesh
from grid_cell.ori_tuning_ma... |
1963970111c4594ad2a0acc2c26718cb209ff45b8dee9f24754f29df049474f5 | Python | 2,774 | 69 | """Context-Aware Implicit Neural Representations to Compress Earth Systems Model Data
DEVELOPED AT:
Department of Chemical Engineering
University of Utah, Salt Lake City,
Utah 84112, USA
DIRECTOR: Prof. Salah A Faroughi
DEVELOPED BY:
... |
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