sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
09394e54ecb3646795979086dc1e7c69c8becd316936791901954379fe1811a9 | Python | 2,271 | 67 | import numpy as np
from scipy import linalg
def getUi(P, data, d, r, dr_type):
# get Pi = UiUi' for each pi
# each column of P is a point in X1, the epsilon-net(cf18)
# data is the entire dataset
#
# xiayq @ 04/21/2022
# modify the comments
# remove 'cf1', replace 'cf2... |
963c42e611f38d0b12e4957cca634a87639ce86fbc55a940525b4fd25bac1dfc | Python | 2,271 | 58 | from __future__ import division
import unittest
import numpy as np
from wyrm.types import Data
from wyrm.processing import append_cnt
from wyrm.processing import swapaxes
class TestAppendCnt(unittest.TestCase):
def setUp(self):
ones = np.ones((10, 5))
# cnt with 1, 2, 3
cnt = np.append... |
9ad6a95c90674a7a2af390d70f5656770c578942350912178659ccf6d4105c4a | Python | 2,272 | 56 | import unittest
from CEST.src.matlab_style_functions import *
class TestInterpolateFunctions(unittest.TestCase):
def test_matlab_style_gauss2D(self):
# Test with default sigma value
kernel = matlab_style_gauss2D((5, 5))
expected_kernel = np.array(
[
[0.00296902,... |
ce3049200be7012b2988ec8801d4116cbc426a0fde6c63cc59d7092609d8e07a | Python | 2,272 | 77 | """ Task definitions for invoke command line utility for python bindings
overview article.
"""
import invoke
import pathlib
import sys
import os
import shutil
import re
import glob
def print_banner(msg):
print("==================================================")
print("= {} ".format(msg))
@invoke.task... |
e3e0b06477fe05d60210aabf29361e81b9e336e533ec752767f9b59ac81a3e10 | Python | 2,272 | 73 | import os
import joblib
import yaml
from sklearn.feature_selection import SelectKBest
from sklearn.pipeline import Pipeline
from pmsurv.models.gaussian_process import GaussianProcessModel
from skopt.space import Real, Categorical, Integer
import utils
import arviz as az
def preprocess_data(dataset, config):
X = d... |
eb9e37af02f507c5c1c8a4a15d37ef3a36de3689086c428ae6406287c2d2a02f | Python | 2,272 | 76 | import glob
import re
import sys
cdhitcluster = sys.argv[1]
cluster_seqs_stats_path = "RESULTS/*.cluster.all"
cluster_seqs_stats_files = glob.glob(cluster_seqs_stats_path)
repSeqRedSeqdict = {}
repLine = ""
count = 0
first = False
add_FullId = ""
k = 0
with open(cdhitcluster, "r+") as f:
content = f.read()
... |
04bd03cfc3064ecebe77866fe72fefcec66569e506c34c7feeabb92b42b9db84 | Python | 2,273 | 52 | # -*- coding: utf-8 -*-
"""
"""
import os
os.chdir('/Users/wang/Desktop/Research_projects/BBSC/Functional/Pre_processing/sub-1/ses_groupICA/ICA_15')
path = os.getcwd()
from nilearn import datasets, image, surface, plotting
fsaverage = datasets.fetch_surf_fsaverage()
ICA2plot = image.load_img('melodic_... |
6e82c3caae031cc46966cf2cfa4d908f9be868893dfa63581f5d819d3d78b040 | Python | 2,274 | 55 | """ Onmt NMT Model base class definition """
import torch
import torch.nn as nn
class NMTModel(nn.Module):
"""
Core trainable object in OpenNMT. Implements a trainable interface
for a simple, generic encoder + decoder model.
Args:
encoder (onmt.encoders.EncoderBase): an encoder object
deco... |
a2589194a3521716855bacd7423e47cb8fe2f16a4f2c523a7b68181a8c7e7038 | Python | 2,274 | 71 | import math
from typing import Sequence, Union
from pytorch_lightning import Callback, LightningModule, Trainer
from torch import Tensor
from torch.nn import Module
class BYOLMAWeightUpdate(Callback):
"""Weight update rule from BYOL.
Your model should have:
- ``self.online_network``
- ``sel... |
bb4671d5f72362431edfcfd784999407b87f7a64c723c2b3f449d25800e5ffa6 | Python | 2,274 | 93 | from anndata import AnnData
from typing import Optional, Union
from .weight_optimization import weight_optimizing_global, weight_optimizing_local
from .global_level import global_level
from .local_level import local_level
def pseudotimespace_global(
adata: AnnData,
use_label: str = "louvain",
use_rep: str... |
1c06370d113cae86dc06d16c4d82a3c62cad447f20e5c6048b5d2f9d69db173c | Python | 2,275 | 59 | from ptic import pmi_tfidf_classifier as ptah
import numpy as np
import pandas as pd
from sklearn import metrics
import torch
from ptic import neuro_ptic
np.random.seed(42)
path = "doc/datasets/"
# Data is taken from here
# https://raw.githubusercontent.com/susanli2016/NLP-with-Python/master/data/title_conference.csv... |
1d6b6a62ad7e72435838e83ffcf905697aa7a8d59b3937e864de563c884c329d | Python | 2,275 | 74 | # 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 app... |
8e272e60129f528e409b066a04fa12db2c7edb27fc653c32901edecdace685cb | Python | 2,275 | 63 | """3. Getting Started with Pre-trained Models on ImageNet
===========================================================
`ImageNet <http://www.image-net.org/>`__ is a
large labeled dataset of real-world images. It is one of the most
widely used dataset in latest computer vision research.
|imagenet|
In this tutorial, we... |
2c40e8e830a17a66e6df143ebe37aaa998b4ba05b1ee98ae711f7f2dd0de72b2 | Python | 2,276 | 61 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Tests for embeddings metrics."""
import unittest
import numpy as np
from sknetwork.data import house, star_wars
from sknetwork.linalg.sparse_lowrank import SparseLR
class TestSparseLowRank(unittest.TestCase):
def setUp(self):
"""Simple regularized adja... |
8209e5fb75521c7d7c95b5e2129c5d02de15d59b049d63f49cb7a2407a63b389 | Python | 2,276 | 82 | from ...core.flowdataframe import FlowDataFrame
from ...utils import constants, gislib
import geopandas as gpd
from ...models import Radiation
import numpy as np
import shapely
import pytest
distfunc = gislib.getDistance
atol = 1e-12
# fix a random seed
np.random.seed(2)
def all_equal(a, b):
return np.allclose... |
e566a2565d07a09b748896139161b9a2e0af783f9ce1dc119020bfc16c3150a0 | Python | 2,276 | 70 | # Copyright (c) Microsoft Corporation.
# Licensed under the MIT License.
import torch
import numpy as np
import torch_geometric.datasets
import pyximport
from role_prediction.role_prediction_dataset import RolePredictionDataset
pyximport.install(setup_args={'include_dirs': np.get_include()})
from role_prediction.gra... |
8cad3a213ff26eac55e2be9b0e155cbd5abcc82d82e6fb898031a74b48ef792f | Python | 2,277 | 75 | import numpy as np
from permacache import permacache
from modular_splicing.legacy.hash_model import hash_model
def calibrate_sparsities(binarized_to_calibrate_to, non_binarized):
"""
Returns a version of non_binarized with the same sparsity as binarized_to_calibrate_to,
by magnitude.
"""
_, t... |
d8ee0e8b3fb37722b2dfa7c1309fb7ff7a3640fe880bdb79fc0389d0e209bf3f | Python | 2,277 | 58 | from typing import (
TYPE_CHECKING,
Union,
)
from galaxy import exceptions
from .adapters import PromoteCollectionElementToCollectionAdapter
if TYPE_CHECKING:
from galaxy.model import (
DatasetCollection,
DatasetCollectionElement,
HistoryDatasetCollectionAssociation,
)
SplitR... |
d94efbd16f0b0874322af2919b639eac933bd70e9236856cdc5fc8d43899548c | Python | 2,277 | 66 | """Tests of utils for `pynapple` package."""
import numpy as np
import pandas as pd
import pytest
import pynapple as nap
def test_get_backend():
assert nap.core.utils.get_backend() in ["numba", "jax"]
def test_is_array_like():
assert nap.core.utils.is_array_like(np.ones(3))
assert nap.core.utils.is_ar... |
40496b4597b29e0903bd26f41dec2d0a6cc0d2050a4bb6bb6c3b8f5bdc3b44cf | Python | 2,278 | 79 | #define library
!pip install tensorflow-addons==0.16.1
import tensorflow_addons as tfa
import random
import os
import numpy as np
import cv2
import glob
from sklearn.metrics import accuracy_score, precision_score, recall_score, confusion_matrix,f1_score
from keras.utils import np_utils
from keras.datasets import ... |
806740ab58a94d39003581633e4803f8b815148a37db3632a01908c721a7992c | Python | 2,278 | 69 | # Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If ex... |
0733147a42c789710e08af81fd0527a2dbe7995412d5d6df95338d89c6464f55 | Python | 2,280 | 82 | import numpy as np
import torch
def run_batched(m, x, bs, pbar=lambda x: x):
"""
Run m on x in batches of size bs, and concatenate the results.
If x is a dict, treat it as a dict of arrays, each of which is batched
together. This requires that the length of each array is the same.
If m retur... |
09092bce4f57df6bddb0bfb52da4b86f679280cb45fe035cd4949b390afae280 | Python | 2,280 | 71 | import json
class ConceptTokenizer():
def __init__(
self,
concept_set,
bos_token = "[BOS]",
eos_token = "[EOS]",
sep_token = "[SEP]",
pad_token = "[PAD]",
unk_token = "[UNK]",
):
self.concept_list = [bos_token, eos_token, sep_token, pad_token, un... |
49f22279f021a700b32a1974d5b3e53ec5e86185cbe84257e1580fe4d7972cec | Python | 2,280 | 66 | import argparse
import json
import matplotlib.pyplot as plt
import numpy as np
import scipy.stats as st
from dexterity.design.common import QUALITATIVE_COLOR_PALETTE
from utilities.plotting import plot_with_confidence
parser = argparse.ArgumentParser()
parser.add_argument("exp", nargs="*", type=str, default=["defaul... |
8871dc1c6a005432003bf404651add12180921f9af4763109f64fecb99c5eaf9 | Python | 2,280 | 77 | """
df_loader.py
Modules to import xlsx files
from a directory.
"""
import glob
import os
import pandas as pd
###################################################################################################
###################################################################################################
def ... |
d35572eae1a157b8950085162b0c6bd7a723accda53eafa2276180fc567969ff | Python | 2,281 | 50 | # LICENSE
#
# _This file is Copyright 2018 by the Image Processing and Analysis Group (BioImage Suite Team). Dept. of Radiology & Biomedical Imaging, Yale School of Medicine._
#
# BioImage Suite Web is licensed under the Apache License, Version 2.0 (the "License");
#
# - you may not use this software except in compl... |
e63c80c287414224e13f67484662468b78cea09fcbc6299027078394e5de0ec8 | Python | 2,281 | 48 | """
This pipeline reads the data files, computes ER and alpha amplitude envelope for target and standard stimuli.
"""
import os
import numpy as np
from scipy.stats import pearsonr
from tools_general import load_json, save_pickle, list_from_many
from tools_signal import compute_envelope, from_epoch_to_cont, filter_in_lo... |
f30f66a7d34896aeb67927748a5e7806ca47cbaf05df085bc70843a993f934db | Python | 2,281 | 66 | import larvaworld.lib.reg as reg
import larvaworld.lib.sim as sim
import larvaworld.lib.model.modules as mods
from larvaworld.lib.model import BrainModuleDB
from larvaworld.lib.model.modules.remote_brian_interface import (
RemoteBrianModelInterface,
)
from sensors import LocalOlfactor, CustomBehaviorModule
# over... |
fb058aeeebac33ed50cdc3622b7fdc7490fb1ef7861ab6d0c6cf4b4fe7c7a7a6 | Python | 2,281 | 63 |
# coding: utf-8
#flip catching/correcting script that detects strand flips and corrects them back in RFmix output
#this version fixes the RFmix output, .msp file with LAI calls for 2-way admixed individuals and outputs a file documenting the switch locations for the RFmix LAI call windows and whether that window was ... |
40e686aaa37d12004395a5acf2b4c88c63a92bfa6235ac27d53348354532332f | Python | 2,284 | 68 | """
Implementation of "Convolutional Sequence to Sequence Learning"
"""
import torch
import torch.nn as nn
import torch.nn.init as init
import bioseq2seq.modules
from torch import linalg as LA
SCALE_WEIGHT = 0.5 ** 0.5
def shape_transform(x):
""" Tranform the size of the tensors to fit for conv input. """
ret... |
47ea6241eea05185d3502cd8aac961962a3f63b347df7ec5e3d57dce4fefe45b | Python | 2,284 | 74 | # This example requires the following dependencies to be installed:
# pip install lightly
# Note: The model and training settings do not follow the reference settings
# from the paper. The settings are chosen such that the example can easily be
# run on a small dataset with a single GPU.
import pytorch_lightning as p... |
c0aec0f2838d0c8db35987f306556b5197c9449345056384950a8302d79bbde9 | Python | 2,284 | 49 | # Calculate True label per frame and predicted label. At the very end, this is simply a multiclass classification problem, which can be solved with sklearn.
# We want a score both per take, and for entire dataset.
import json
from pathlib import Path
import numpy as np
from sklearn.metrics import classification_report
... |
478104baff9934d0f406c54927f00f448355532ff3281a3df0527620caf140e8 | Python | 2,285 | 80 | from brian2 import (
NeuronGroup,
SpikeMonitor,
StateMonitor,
PopulationRateMonitor,
TimedArray,
run,
)
from brian2.units import *
def osn_params(custom_params: dict = {}):
"""
factory method for model parameters
:param custom_params:
:return:
"""
params = {
"C_... |
d543eaf3af877d9328a3023374cad0a78611edf5bb5177bde67177980c8a5323 | Python | 2,285 | 89 | # -*- coding: utf-8 -*-
"""
Spyder Editor
This is a temporary script file.
"""
#resolution of the data 2
#TR=2
import os
import numpy as np
from nilearn import datasets
#read in text files with session
os.chdir('/home/restate/Documents/BBSC/Functional/Pre_processing/sub-2/')
path='/home/restate/... |
ebb03ecef0ba74b0e7897deee3300c1602fd23f0ebd41d63474e4a1db22d89b7 | Python | 2,285 | 68 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
"""
.. _exa-trf_intro:
.. currentmodule:: eelbrain
Introduction to Temporal Response Functions (TRFs)
==================================================
A temporal response functions (TRFs) is a linear model of the stimulus-response
depency. The response is pre... |
f5ffb58cb9e46f7e89a90fbeae79e5540bdd31f19059490187dae6756bd19286 | Python | 2,285 | 82 | # Copyright 2024 The Google Research Authors
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agree... |
c962dac38c29df8139cf32d9ae8ecdbb83c321380be4b0c77ed87031d1cefb8f | Python | 2,286 | 49 | import os
import shutil
import numpy as np
from mako.template import Template
from mako.lookup import TemplateLookup
def make_simple_index(path, path_list):
lookup = TemplateLookup(directories=['templates/', '.'])
t = Template(filename=os.path.join('templates', 'simple.html'),
lookup=lookup)... |
dcd575c58b4a8457c05c46432ab85e861f763712bf0e16e70f6d6e241f1a112c | Python | 2,286 | 60 | from pyrosm.data_manager import get_osm_data
from pyrosm.frames import prepare_geodataframe
import warnings
def get_user_defined_data(nodes,
node_coordinates,
way_records,
relations,
tags_as_columns,
... |
61129938f704259be7e6a833b48004fa9d67ec43dd9b4c592786a6d5955b0f33 | Python | 2,287 | 68 | def findNodePositions(section,numNewNodes,nodeSpacing):
from neuron import h
import math
section_list = [None]*int(numNewNodes+1)
sec = h.Section()
parent_section_ref = h.SectionRef(sec = section)
section_children = parent_section_ref.child
sec.connect(parent_section_ref.parent(1))
h.disconnect(sec = section... |
2ab236eae193dfc10f0a7586bc3aa9c358f7a1424c420fe889cd7c9de48cd3ea | Python | 2,291 | 56 | from typing import Dict
from gensim.models import Word2Vec
import numpy as np
from tqdm import tqdm
class Char2VecFeature():
def __init__(self, **kwargs):
self.embedding_size = kwargs["embedding_size"]
self.window = kwargs["window"]
self.min_count = kwargs["min_count"]
self.worke... |
6f45f04c21ea6a8043a0642bc9bfebdddbcba90cf423f01e118d3ff9603393af | Python | 2,293 | 69 | """
Generate SV-supporting reads BAM file.
@author: asmaa, cytham
# Test
wk_dir = '.'
vcf_file = 'sample.nanovar.pass.vcf'
sv_supp_tsv_file = 'sv_support_reads.tsv'
in_bam_path = 'input.bam'
input_type = 'bam'
ref_path = 'ref.fa'
vcf = os.path.join(wk_dir, vcf_file)
sv_supp_tsv = os.path.join(wk_dir, sv_supp_tsv_fil... |
297ac2775951e897cbf961b38f5488f646bb36a239a72b6ce2bd11fdf665675c | Python | 2,294 | 56 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
"""Depth estimation predictor for YOLO models."""
from __future__ import annotations
from typing import Any
import numpy as np
import torch
import torch.nn.functional as F
from ultralytics.engine.predictor import BasePredictor
from ultralytics.engi... |
ada1927131c16cc4a715e335ee931cbe389c9c162e2ee3386e5cf935776a102b | Python | 2,294 | 58 | #!/usr/bin/env python
#
# Copyright 2019, Google Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list... |
ade937d3cb815a6809f0c428de58beece33a10d945025cc8ed947147cc50899b | Python | 2,294 | 77 | #!/usr/bin/env python
"""
Input: User-defined set of filters and the database authentifications.
Output: set of compounds that pass all the selected filters.
"""
import argparse
import json
import sys
import cheminfolib
import psycopg2.extras
cheminfolib.pybel_stop_logging()
def parse_command_line(argv):
parse... |
bc8ab1db020781dcf4061151c06a9920f568897949f7cea33ace492b755d531f | Python | 2,294 | 60 | """Basic class for TreeGrower Algorithms"""
import logging
import numpy as np
from tns.generate.algorithms.abstractgrower import AbstractAlgo
from tns.generate.algorithms.common import bif_methods
from tns.generate.algorithms.common import section_data
logger = logging.getLogger(__name__)
class TrunkAlgo(AbstractAl... |
fab749d61debdec4844edee016a58ef0cb04526f239700b1ef4de1c652292ab5 | Python | 2,295 | 78 | # This example requires the following dependencies to be installed:
# pip install lightly
# Note: The model and training settings do not follow the reference settings
# from the paper. The settings are chosen such that the example can easily be
# run on a small dataset with a single GPU.
import torch
import torchvisi... |
d7e83dfcfb8e78f5cf25ea7868bca0d23681927259b765961c2f23789fedbb88 | Python | 2,296 | 70 | # -*- coding: utf-8 -*-
# Generated by the protocol buffer compiler. DO NOT EDIT!
# source: bream/hardware_check_result.proto
"""Generated protocol buffer code."""
from google.protobuf import descriptor as _descriptor
from google.protobuf import message as _message
from google.protobuf import reflection as _reflection... |
ccb3f7174c79c3f871d84ca8998e38b27ac8bdbab37863a0ed77ca96718fe720 | Python | 2,297 | 83 |
"""
Auto-generated download script for Thingi10K dataset.
Assuming the following python packages and external commands are available.
* argparse: for parse command line args.
* requests: for http communication.
* wget: for downloading files.
Usage:
python Thingi10K_download.py
or
python Thingi10K_download... |
665cfd10af7f29bbc539f9af7e75e509891fe724fda83968dd928547ef990731 | Python | 2,299 | 68 | import numpy as np
"""This implementation is courtesy of Aaron Kaplan, Lawrence Berkeley Lab."""
def cart_to_sph_d():
"""
From Table I of H. Bernhard Schlegel and M.J. Frisch,
Int. J. Quantum Chem. 54, 83-87 (1995),
doi: 10.1002/qua.560540202
Expected order is
d_20 0 ... |
337c3a128eaade994e30ee1aeb1fd7660cce6e64ea9c7f4140a7715addfa8376 | Python | 2,300 | 54 | import torch
from models.basic import DeepLearningModel
from strategies.basic import MultiSiteLearningStrategy
class SI(MultiSiteLearningStrategy):
name = 'si'
def __init__(self, model: DeepLearningModel, config: dict, c=0.5, xi=1.0, **kwargs):
super().__init__(model, config, **kwargs)
self... |
34f5a398b2c41a9ccf3c24272344e101b784d612cb6b77fa4548aa7f20227683 | Python | 2,300 | 73 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch_geometric.nn import GCNConv, global_max_pool as gmp
# GCN based model
class GCNNet(torch.nn.Module):
def __init__(self, n_output=1, n_filters=32, embed_dim=128,num_features_xd=78, num_features_xt=25, output_dim=128, dropout=0.2):
... |
7318023ce2c29c28cf8f8d4eaa52938a961f773e843d3660f4fbff67af102715 | Python | 2,300 | 78 | #!/usr/bin/env python
# encoding: utf-8
from __future__ import (absolute_import, division,
print_function, unicode_literals)
import os, sys, re
import logging
import argparse
import collections
import numpy
import time
import TNode
from GraphCycleException import GraphCycleException
logger ... |
883ff35cade6fed3b68f0c789854e7dfbdb49159dc95fb4650c531c3c224775b | Python | 2,300 | 67 | import json
import os
from typing import List
import matplotlib.pyplot as plt
import pandas as pd
import seaborn as sns
from matplotlib.axes import Axes
from matplotlib.figure import Figure
from scipy.signal import savgol_filter
from agent.ppo_agent import PPOAgent
from dexterity.design.common import QUALITATIVE_COLO... |
d6671a3f5dbeb094b44362bef95707ed4467278d7080ae1b4909e25c2fddae4e | Python | 2,300 | 78 |
#-- setup-begin
import rpy2.robjects as robjects
import rpy2.rinterface as rinterface
from rpy2.robjects.packages import importr, data
from rpy2.robjects.methods import getmethod
lme4 = importr('lme4')
utils = importr('utils')
StrVector = robjects.StrVector
#-- setup-end
#-- LmList-begin
class LmList(robjects.metho... |
24408013905bc5fb2fadb9d3ab4ea55ba5af4f8dfd481166c861618e7adefc86 | Python | 2,301 | 74 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
from os.path import join
from warnings import catch_warnings, filterwarnings
import pytest
from eelbrain import *
from eelbrain.pipeline import *
from eelbrain.testing import TempDir, path, requires_mne_sample_data
class Experiment(MneExperiment):
meg_sy... |
4fe026afadf96003cb97c019da8fcd441541f21d1efac7cf1db4eb240baab88a | Python | 2,301 | 75 | import numpy as np
def onehot(DNA_seq):
"""
:param DNA_seq:
:return: a onehot matrix
"""
singleDNAFragement = np.zeros([len(DNA_seq),4])
for i in range(len(DNA_seq)):
if DNA_seq[i]=='A':
singleDNAFragement[i,0]=1
elif DNA_seq[i]=='T':
single... |
c1ba4c010c87789fa98f24849c48d7c8ac6e08a6f3865558c00da081f0946e5a | Python | 2,301 | 67 | """Generate ``torchlens/ir/op_record_manifest.py`` from the source spec.
The manifest is the FROZEN ``CellSourceManifest`` v1: one row per op store
cell naming its step-0 ingest source class. Regenerate-and-diff is CI-gated
(``tests/producer_parity/test_p1_record_types.py``); editing the generated
file by hand is a bu... |
3ae9a420732ea127a74525b5dfcda4296235540c31344f3a1395bc883777e056 | Python | 2,302 | 74 | def __boot():
import sys
import os
PYTHONPATH = os.environ.get('PYTHONPATH')
if PYTHONPATH is None or (sys.platform == 'win32' and not PYTHONPATH):
PYTHONPATH = []
else:
PYTHONPATH = PYTHONPATH.split(os.pathsep)
pic = getattr(sys, 'path_importer_cache', {})
stdpath = sys.pat... |
5f8cd13a252f28e7b807738f56035678e7b00fcf9474d49345b4872e74799ea8 | Python | 2,302 | 52 | '''Package implementing a data model for the whole brain recordings (more
broadly, of any multichannel volumetric recording - sequence of "hyperstacks").
While there are only a few options to efficiently store an uncompressed sequence
of images, so that the issues with uncompatibility of that data with different
sof... |
694e3dc8cf8078135cac975a9973ca4ce64f41514fb0e754223bcd739a01e63d | Python | 2,302 | 63 | import sys
import csv
import utils
def WriteCSVFromDict(filename, data, interval):
fieldnames = ['old track ID',
'old time (s)', 'track ID', 'time (s)', 'x', 'y', 'z', 'TimeDiff']
with open(filename, 'w', newline='') as file:
writer = csv.writer(file)
csvwriter = ... |
ca2d0994431dd712aa9ef382e240b850944d7affc39591eb02d8af6d8271c965 | Python | 2,302 | 60 | import numpy as np
import torch
from torch_geometric.data import Data
from data_loading.loading_utils import train_scaler, scale_dataset
TARGET_ID_TO_PROPERTY = {
0: 'First excitation energy (ZINDO)',
1: 'Electron affinity (ZINDO/s)',
2: 'Excitation energy at maximal absorption (ZINDO)',
3: 'Atomizat... |
ea1d72d3bfa056ef2da2be4f0777aa944838fb480e519fc2f64681fa0376f092 | Python | 2,302 | 68 | """
Companion functions for cell-cell communication inference analyses
"""
try:
from typing import Literal
except ImportError:
from typing_extensions import Literal
import numpy as np
import pandas as pd
def fdr_correct(
pvals: pd.DataFrame,
corr_method: str,
corr_axis: Literal["interactions", "c... |
67ca195e8e3dc902c2962a13e5afd3e22d86e1a0e68bb5f82e74e20b725ee315 | Python | 2,303 | 73 | """
networkevents.py
Modules for processing network event
vectors from multi-unit activity spikes.
"""
import numpy as np
import warnings
# DeprecationWarning: elementwise comparison failed; this will raise an error in the future
warnings.filterwarnings("ignore", category=DeprecationWarning)
######################... |
6b42fc583c31b12ff3fa5636a5ef4f3910fa79fd0776557e3a897094231975e5 | Python | 2,303 | 65 | # -*- coding: utf-8 -*-
#from galaxy.datatypes.json_datatyp import Json as JsonClass
from galaxy.datatypes.data import Text
from galaxy.datatypes.data import get_file_peek
from galaxy import util
import subprocess
import tempfile
import logging
import json
import os
log = logging.getLogger(__name__)
#c... |
781b3ee6e004cf6b3c82e90cc9f850d3b192168cafc6db2c94bb9ce95814c415 | Python | 2,303 | 53 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Tests for classification metrics"""
import unittest
from sknetwork.classification.metrics import *
class TestMetrics(unittest.TestCase):
def setUp(self) -> None:
self.labels_true = np.array([0, 1, 1, 2, 2, -1])
self.labels_pred1 = np.array([0, -... |
833bd8a303c1c77869f0639374b396345c439147d4509e3a6fab7f8010b55a6c | Python | 2,303 | 63 | import drawsvg as draw
import numpy as np
def draw_line(d,x1,y1,x2,y2,color):
d.append(draw.Lines(x1,y1,
x2,y2,
close=False,
fill="none",
stroke=color,
stroke_width=2))
def draw_nucleotide(d,x, y, nt, color):
""" Draw one nucleotide in a circle
... |
ca77cc6ad3a5d15efa91a102c721fd7ada6073cb596cbf475bc5659aeef1b1d3 | Python | 2,303 | 62 | # a simplified UI for testing/profiling of animal tracking
from PyQt5 import QtCore
from PyQt5 import QtWidgets
import logging
from score_behavior.cv_video_widget import CVVideoWidget
from score_behavior.score_controller import VideoDeviceManager
from score_behavior.ObjectSpace.analyzer import ObjectSpaceFrameAnalyze... |
1f70f7d6eecdcef11b1fcd57d5758a1dc646bf2175debe7d4f0999c898e21618 | Python | 2,304 | 62 | import pytest
pytest.importorskip('curses')
class MockWindow:
def getmaxyx(self):
return self.y, self.x
class test_CursesDisplay:
def setup_method(self):
from celery.events import cursesmon
self.monitor = cursesmon.CursesMonitor(object(), app=self.app)
self.win = MockWindo... |
3bf89bf7b32ddfcdf1ef9f7acfb3b7abdcc75cd0e9406e69fd1b32dd4743fc29 | Python | 2,304 | 76 | import os
import sys
import logging
from pathlib import Path
from typing import Dict, List
import numpy as np
import pandas as pd
import snapatac2 as sa2
import pyprojroot
proj_dir = str(pyprojroot.here())
pack_dir = f"{proj_dir}/package/python"
sys.path.insert(0, pack_dir)
from mylog import StreamToLogger, set_file... |
7f9e4d1a666a33868417590c161823cdc63c03165031bd99262891d0f56c8ffd | Python | 2,304 | 80 | """Extraction data substrates: digest primitives + artifact v2 + model identity.
The C04 substrate half of dataset extraction (extract memo items 1, 2, 6):
:mod:`digests` builds the two pinned digest primitives once (threaded Merkle
crypto fold, order-sensitive value reduction) for every consumer;
:mod:`artifact` owns... |
0e60f76b2ce9559aa77c3a960ab57365e907ce9fd2faa33d392917f31e9bc689 | Python | 2,305 | 75 | """migrate custos to psa tokens
Revision ID: 724237cc4cf0
Revises: 1d1d7bf6ac02
Create Date: 2025-11-03 15:22:13.111461
"""
import sqlalchemy as sa
from alembic import op
from galaxy.model.migrations.data_fixes.custos_to_psa import (
CUSTOS_TABLE,
migrate_custos_tokens_to_psa,
remove_migrated_psa_tokens... |
12afbb119371f317d7cc325508ed625e67062baa18b32f846260c85ef0d0ad5c | Python | 2,305 | 108 | import collections
import csv
import time
from datetime import datetime
from pathlib import Path
import yaml
ISO_FORMAT = "%Y-%m-%dT%H:%M:%S.%f"
def read_csv_to_dict(path):
columns = collections.defaultdict(list)
with open(path) as f:
reader = csv.DictReader(f)
for row in reader:
... |
7d79d9b2012ed6a168652ce104a400e0bac5a21e8bbd45445db6d46e9ec2edb8 | Python | 2,305 | 78 | import os
from logging import getLogger
from subprocess import (
PIPE,
Popen,
)
from tempfile import TemporaryFile
from time import sleep
from galaxy.util.bunch import Bunch
from . import BaseShellExec
from ....util.process_groups import (
check_pg,
kill_pg,
)
log = getLogger(__name__)
TIMEOUT_ERROR_... |
7f41950676ce2255dbdc29215382e499b05a5afc3d12b68212450e1f0a89cfcb | Python | 2,305 | 74 | # ---
# jupyter:
# jupytext:
# formats: ipynb,py:light
# text_representation:
# extension: .py
# format_name: light
# format_version: '1.5'
# jupytext_version: 1.11.3
# kernelspec:
# display_name: Python 3
# language: python
# name: python3
# ---
# # Original Alice word ... |
dfcb4d79c5b580a30b61abb201d3d9c3456f382f59c989df73aec4e604fdfcf5 | Python | 2,305 | 79 | # %%
'''
Recoded to run on lucky2. Copies (not SYMLINK) data from BIDS and fix cleaned data
'''
import subprocess
import numpy as np
import os
from time import time
from shutil import copyfile
import sys
sys.path.append("..")
from functions.data_helpers import get_computer
# tasks
task_list = ['fearRev', 'rest']
# ... |
3af41ff232902944aa9a504c48f8a7c6bb0fdedf61ce34aab0fc3f4b260b0095 | Python | 2,306 | 55 | """A passive environment checker wrapper for an environment's observation and action space along with the reset, step and render functions."""
import gym
from gym.core import ActType
from gym.utils.passive_env_checker import (
check_action_space,
check_observation_space,
env_render_passive_checker,
env_... |
482ee185c750754c975fb27311e6969119512723d46cb90e86457981c142fe88 | Python | 2,306 | 84 | import os
import yaml
import torch
import argparse
from model.model_training import ModelTraining
from training_strategy.query_false_positive import QueryFalsePositives
from training_strategy.hard_nagative_mining import HardNegativeMining
import warnings
warnings.filterwarnings(action="ignore")
def load_config(con... |
bd2b0842a37c7e62e5dd6eafe9994f7741f2fa57eae6211ffe8110ef2318fb79 | Python | 2,307 | 90 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on April 2022
@author: Simon Delarue <sdelarue@enst.fr>
"""
import numpy as np
class BaseActivation:
"""Base class for activation functions.
Parameters
----------
name : str
Name of the activation function.
"""
def __init__(se... |
533a33eadec3762fff3709f5dea250dcad514c60a7ffd2bf6280988e6b4edb3e | Python | 2,308 | 75 | import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
# %%
class torch_grid_augmentation(nn.Module):
def __init__(self,
p_rot=0.2,
p_zoom=0.2,
p_transl=0,
p_shear=0,
mm_zoom=[0.7, 1.4],
... |
827c3e34b1956928a3004e8c2bef023a9a0d98dd899f38a89fef40802426c5e4 | Python | 2,308 | 55 | # -*- coding: utf-8 -*-
import logging
from controller_validation.data.preprocessing import build_FD_dataframe, get_confounds_list
from controller_validation import DATA_PATH
import os.path as op
import mne
import pickle
import os
from mne import compute_raw_covariance, pick_types, write_cov
from scipy.stats import ks_... |
18d700534377aafdb276eb50207b9a4a85b6bccdf3f5abde692bff10661bb7cd | Python | 2,309 | 93 | '''Tests for bdpy.util'''
import unittest
import numpy as np
from bdpy.util import utils
class TestCreateGroupVector(unittest.TestCase):
'''Tests for 'utils.create_groupvector'''
def test_create_groupvector_pass0001(self):
'''Test for create_groupvector (list and scalar inputs).'''
x = [... |
262d7bc8ae40bd9c3521974c0ee5f3673f0f9e08b0275979fc4dcbabd8d62c1a | Python | 2,309 | 60 | #!/usr/bin/env python
#=========================================================================
#
# Copyright NumFOCUS
#
# 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://... |
3c399726cc0e3a6be905d5b77f04b62d4b16be33c84c33cf36a6a3beb2900249 | Python | 2,309 | 77 | from typing import List
from dependency_injector.wiring import Provide, inject
from fastapi import APIRouter, Depends
from starlette import status
from carbonserver.api.schemas import ProjectToken, ProjectTokenCreate
from carbonserver.api.services.auth_service import (
MandatoryUserWithAuthDependency,
UserWit... |
fb9d0f4d241a08a3042f70c67cf1b8cddad3ed8cf52dbed94a1f5b7d7a08cec2 | Python | 2,309 | 77 | import pytest
import operator
from . import utils
import rpy2.rinterface as ri
ri.initr()
def test_init_from_seq():
seq = (ri.FloatSexpVector([1.0]),
ri.IntSexpVector([2, 3]),
ri.StrSexpVector(['foo', 'bar']))
v = ri.ListSexpVector(seq)
assert len(v) == 3
for x, y in zip(seq, v)... |
779cfec7e5b2d6af2c83da9dd566fa1c5e8a6ed2991a74ec619ef4f971b80829 | Python | 2,310 | 54 | """YOLO Demo script."""
import os
import argparse
import mxnet as mx
import gluoncv as gcv
gcv.utils.check_version('0.6.0')
from gluoncv.data.transforms import presets
from matplotlib import pyplot as plt
def parse_args():
parser = argparse.ArgumentParser(description='Test with YOLO networks.')
parser.add_argu... |
e97feccf1560638fb03e267eb31036f140ca2b46257c857d39a889680b61803c | Python | 2,311 | 62 | # fix problems with pythons terrible import system
import os
import sys
file_dir = os.path.dirname(os.path.realpath(__file__))
sys.path.append(os.path.join(file_dir, '../bin/'))
sys.path.append(os.path.join(file_dir, '../prob2020/python/'))
sys.path.append(os.path.join(file_dir, '../prob2020/cython/'))
# useful import... |
c55b253b3bcf28e0a2ff1669ceaf398d4fc66b9f66df8b4b7fe195dc394a5744 | Python | 2,312 | 55 | """Barcode RNG must track ``set_random_seed`` yet stay off the global host stream.
Regression guard for the facet-rerun ``[param_xrefs]`` breakage: internal tensor
barcodes draw from a process-private ``random.Random`` (so they never masquerade as
user Python/NumPy RNG consumption during a forward), but a fixed captur... |
f7da6cf4ef3f8c2e8e38f1f53a8b5de5a67da5658b07f17b1e8c9ff2646cec07 | Python | 2,312 | 54 | """SSD Demo script."""
import os
import argparse
import mxnet as mx
import gluoncv as gcv
gcv.utils.check_version('0.6.0')
from gluoncv.data.transforms import presets
from matplotlib import pyplot as plt
def parse_args():
parser = argparse.ArgumentParser(description='Test with SSD networks.')
parser.add_argume... |
39422b0febb7c98bb8694bce67539e638eac3dca249d616bab78926e77e41a76 | Python | 2,313 | 73 | #!/usr/bin/env python
# Dan Blankenberg
import sys
import bx.intervals.io
def __main__():
output_name = sys.argv[1]
input_name = sys.argv[2]
try:
chromCol = int(sys.argv[3]) - 1
except Exception:
sys.exit(
f"'{str(sys.argv[3])}' is an invalid chrom column, correct the col... |
47d21326d5e3b3ef1549d366e4e8f618990649c5f87420cee787829aeba04963 | Python | 2,313 | 56 | from setuptools import setup
from setuptools import find_packages
with open("docs/README.PyPI.md", "r") as fh:
long_description = fh.read()
setup(
name='aucmedi',
version='0.11.0',
description='AUCMEDI - a framework for Automated Classification of Medical Images',
author='Dominik Müller',
aut... |
8291bc652af0567086db4829a88c4ddefedb463d2c0f518bb3dc2f27ab8babea | Python | 2,315 | 86 | """OpenAI Shap-E transmitter: asset encoder to implicit-function parameters.
Paper: Jun and Nichol 2023, "Shap-E: Generating Conditional 3D Implicit
Functions".
Shap-E first trains an encoder that maps 3D assets to the parameters of an
implicit function renderable as textured meshes and NeRFs. This compact
transmitt... |
be8db9d840224447ef760f61c1d655545c7c3d73362efa3ea4b860d95233b6e6 | Python | 2,315 | 84 | from . import utils
import numpy as np
@utils.copy_td
def backshift_idx_fields(trial_data):
"""
Adjust index fields from 1-based to 0-based indexing
Parameters
----------
trial_data : pd.DataFrame
data in trial_data format
Returns
-------
trial_data with the 'idx_' fields adj... |
04f38291a9c9070087e7bf6829f472980c7a38cb6c56a7971a32220ec611d315 | Python | 2,316 | 68 | """MLflow tracker export against the real mlflow package (sqlite backend).
``tl.export.mlflow`` must work with both MLflow client shapes: the fluent
``mlflow`` module (active run) and an ``MlflowClient`` (``run_id=``), and log
exactly what logging the same metrics with MLflow directly records.
"""
from __future__ imp... |
858c227871e702e92a885b4545580cf42af195ceaf0000651fd14f0ff1297519 | Python | 2,316 | 80 | # 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
project = "larvaworld"
author = "Panagiotis Sakagiannis"
copyright = "2024, Panagiotis Sakagian... |
3280aa0f42fcfc6fde5af2ce43c7a80b512e9331c33e1293bd41076784a2101f | Python | 2,317 | 49 | """Out-of-core PBF reading engine (the ``engine="out_of_core"`` backend).
The file is read in one pass: data blobs are decoded in parallel with the raw Cython
``primitive_block_decoder`` (protobuf is used only for the small ``BlobHeader`` / ``Blob``
framing), each decode task spills the node coordinates and the featur... |
8f4b76d044103c2cb5f9220943a4f257fd8ebd957c68f63e2851896fe4221ab1 | Python | 2,317 | 66 | """Defines the :class:`ErrorCode` class and instantiates concrete objects from JSON.
See the file error_codes.json for actual error code descriptions.
"""
from json import loads
from galaxy.util.resources import resource_string
# Error codes are provided as a convience to Galaxy API clients, but at this
# time they... |
336cf1d35d4bb5e4eac6e6df99f375a7c701cbd15643c204429d88c1ca4dd0be | Python | 2,318 | 53 | # Copyright (c) ByteDance, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
import math
from pprint import pformat
def lr_wd_annealing(optimizer, peak_lr, wd, wd_end, cur_it, wp_it, max_it):
w... |
4bcc84f674ac6c9e876050c37472ae69139cfbfc974ae19b28f11fcbae2670d2 | Python | 2,318 | 63 | #!/usr/bin/env python
"""
Does naive decoding of Hadamard time-encoded data
Assumes that the Hadamard blocks are in adjacent volumes in the data
and simply decodes each block, outputting the same order
"""
import sys
import argparse
from fsl.data.image import Image
import numpy as np
import scipy.linalg
class Argum... |
92342c3afcae79fbd4df0216c281c8b3fbc9b85bf869cd517a2db761dd568f65 | Python | 2,318 | 87 | import pytest
from pyrosm import get_data
@pytest.fixture
def test_pbf():
pbf_path = get_data("test_pbf")
return pbf_path
@pytest.fixture
def helsinki_pbf():
pbf_path = get_data("helsinki_pbf")
return pbf_path
def test_parsing_natural_with_defaults(test_pbf):
from pyrosm import OSM
from ge... |
8032171a85d2a7e787a36743d9a320126e422eb0c69cfe798e57637da3ffda4e | Python | 2,319 | 60 | from numpy.testing import assert_allclose
from ..permutation import permutation_test
import numpy as np
N_PERM = 500
def _test_one_sample(sample_shape, n_obs = 50):
'''
note that even when setting the seed, the permutation p-vals will never be
exactly equal to their opposite tailed p-vals because of how they... |
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