sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
e068e22aed05593ce552b2f0001b838d4959ea5430553ef60119fc81cc59d9f6 | Python | 7,487 | 218 | """
Manager and Serializers for Visualizations.
Visualizations are saved configurations/variables used to
reproduce a specific view in a Galaxy visualization.
"""
import logging
from typing import (
TYPE_CHECKING,
)
from sqlalchemy import (
false,
func,
or_,
select,
true,
)
from sqlalchemy.or... |
45d41a24bf210972ca7aca00a30d15c6089734869f02025b8423832889a7e1df | Python | 7,488 | 215 | """
experiment launcher using tmux panes
"""
import os
import math
import GPUtil
import re
available_gpu_devices = None
class Options():
def __init__(self, *args, **kwargs):
self.args = []
self.kvs = {"gpu_ids": "0"}
self.set(*args, **kwargs)
def set(self, *args, **kwargs):
f... |
4baeefcd9ccaf0af5eb7ca133f0e524576dd91feaf15295f46215664edb7929f | Python | 7,488 | 171 | '''
@saulzhang
The implementation code of dataset loader class in the the paper
"Predicting Future Frames using Retrospective Cycle GAN" with Pytorch
data: Nov,17,2019
'''
import glob
import random
import os
import torchvision.transforms as transforms
import torch
import random
import pickle
from torch.utils.data im... |
f3cbbd5d115d86cd577e23238c545bcfe3f8edec6f1731e2672bb66f779b1de5 | Python | 7,488 | 332 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import cv2
import numpy as np
import mahotas as mh
__author__ = ['Nico Curti']
__email__ = ['nico.curti2@unibo.it']
__all__ = [
'evaluate_features'
]
def get_haralick (masked : np.ndarray) -> np.ndarray :
'''
Extract the Haralick features from the masked image
... |
358c028834362f3f9c2d213af4e14581fc38351d2599a8c4e2079cd0a92be0cd | Python | 7,489 | 180 | import os
import torch
import pandas as pd
import scanpy as sc
import numpy as np
from sklearn import metrics
import multiprocessing as mp
from sklearn.metrics.cluster import adjusted_rand_score
from sklearn.metrics.cluster import (
v_measure_score, homogeneity_score, completeness_score)
import glob2
import matplot... |
ab1486e6500fdc59d20df7ecb6da2e8b9b87980d8e1987e87ee9ab6ef9390eb3 | Python | 7,489 | 138 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'tracking_controller/tracker_control_ui.ui'
#
# Created by: PyQt5 UI code generator 5.6
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_TrackerControl(object):
def setupUi(sel... |
febd01c396faf765b8fce27644ed5cdd2ff3e705800f066e3d2051c9cb841a7a | Python | 7,489 | 174 | import logging
import os
from os.path import dirname
from galaxy.queue_worker import job_rule_modules
from galaxy.structured_app import StructuredApp
from galaxy.tool_util.toolbox.watcher import (
get_tool_conf_watcher,
get_tool_watcher,
)
from galaxy.util.watcher import get_watcher
log = logging.getLogger(__... |
e3ffec68ca2f4685655edcfe8f0bd12dff1f9fc3f4f5bcbff6b61028a887f4dd | Python | 7,490 | 156 | # Copyright (c) 2021, NVIDIA CORPORATION. All rights reserved.
#
# NVIDIA CORPORATION and its licensors retain all intellectual property
# and proprietary rights in and to this software, related documentation
# and any modifications thereto. Any use, reproduction, disclosure or
# distribution of this software and rel... |
54510b76c1508ba74a5c8b679b654ec463e69cf50ea6c0ab591160b10e2ce3f9 | Python | 7,492 | 212 | # Copyright 2022 Deepfold Team
#
# 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 applicable law or agreed to i... |
c0beb72258193a7d41f0fe14b2e33d9b0dda9f697bbc9b2f84ffa5fd8a3cce87 | Python | 7,493 | 202 | #!/usr/bin/env python
"""
download_db.py
Helper script to download databases for the knead_data.py pipeline
Requires an internet connection and Python v2.7+.
"""
import sys
# Try to load argparse to check for python v2.7+
try:
import argparse
except ImportError:
sys.exit("Please upgrade to Python versio... |
fc31062426ea602e61bd42369ba6f8f66851aa9bb8a0d7a511046b97f9bef354 | Python | 7,493 | 217 | import pickle
import numpy as np
from numpy.testing import assert_array_equal
import pytest
from conftest import get_distances, get_means, get_metrics
from pyriemann.regression import (SVR, KNearestNeighborRegressor)
from pyriemann.utils.kernel import kernel
from pyriemann.utils.mean import mean_covariance
regs = [S... |
2217595d16856a5c72857dc283f9eec2fb3bbc5c68edd59ce6f6d08ac4a358ff | Python | 7,496 | 177 | from . import InvertibleModule
import warnings
from copy import deepcopy
from typing import Sequence, Union
import torch
class Split(InvertibleModule):
"""Invertible split operation.
Splits the incoming tensor along the given dimension, and returns a list of
separate output tensors. The inverse is the ... |
5222d8d6ce8eaaf572c82afb78194307e017bb582e7420fcff0f0d550b66627f | Python | 7,498 | 211 | """Regression tests: selective save/grad selectors under orphan-removed ops.
Postprocess removes internally-sourced dead branches (orphans) from the raw
capture, which renumbers final layer ordinals, type indexes, and labels
relative to capture-time raw indexes. Integer ``layers_to_save`` ordinals,
exact final labels ... |
d2c7657e6081ad1cdf3a7b4f4451bd6cae9a3c4329831d21a90806dd1a532a16 | Python | 7,499 | 188 | """Deep chains (compo memo stratum 3; F36 waves A-D).
One invariant at every hop: honesty and provenance facts SURVIVE the chain.
Each chain crosses at least three product transitions, and every
cross-member/ragged read is exercised AFTER a save/load round trip (foldB
D18 law 2). Toy models by design -- the chain topo... |
49bdd465e66a12fb536ac08dd0cfc827e1b413549d712cf34ea846d11a349d5f | Python | 7,500 | 184 | import numpy as np
import pathlib
import sys
import shutil
import tempfile
import unittest
from asmc.asmc import *
data_dir = pathlib.Path(__file__).resolve().parent.parent / 'ASMC_data'
if not data_dir.exists():
print(f'ERROR. {data_dir} does not exist. Did you clone ASMC recursively with submodules?')
sys.... |
5cda411c354d1d088e50b6bad9cd3bd9e99052d16dfd4e0417038a35b35dc64e | Python | 7,500 | 297 | # 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.
''' Modified based on Ref: https://github.com/erikwijmans/Pointnet2_PyTorch '''
import torch
import torch.nn as nn
from typing import List, T... |
ff05ea873a3f5f9c8a302c98e34ebbb60cefefc2c9e7c9e30dcaf1ffda971716 | Python | 7,500 | 218 | import sys
import glob
import pickle
import powerlaw
from itertools import groupby
from scipy.optimize import curve_fit
from brian2 import second, np, ms
def process_data(times, nidx, M, bin_size):
si_time = sim_time/ms # ms but unitless
bins = np.arange(0, si_time, bin_size)
valids = np.zeros_like(bins... |
60555f3022836a3d7fc1d076af70e7d2fa8dd38ba9d8c00981bd5c58b0aae9f7 | Python | 7,502 | 237 | import warnings
from typing import Optional
import numpy as np
import torch
def cosine_schedule(
step: int,
max_steps: int,
start_value: float,
end_value: float,
period: Optional[int] = None,
) -> float:
"""Use cosine decay to gradually modify start_value to reach target end_value.
Args:... |
08e8dcb5ea9a599c8e34352321ac9de2765906f24bcdb2911e789670a7622c9c | Python | 7,503 | 258 | # This file was automatically generated by SWIG (https://www.swig.org).
# Version 4.2.0
#
# Do not make changes to this file unless you know what you are doing - modify
# the SWIG interface file instead.
from sys import version_info as _swig_python_version_info
# Import the low-level C/C++ module
if __package__ or "."... |
1b01dca983709747faca1b689e1d17a4dadedb3405ed0d3ad57338e98ccc16f1 | Python | 7,504 | 187 | from __future__ import absolute_import, division, print_function
import os
import sys
import tensorflow.compat.v1 as tfv1
from attrdict import AttrDict
from xdg import BaseDirectory as xdg
from ds_ctcdecoder import Alphabet, UTF8Alphabet
from .flags import FLAGS
from .gpu import get_available_gpus
from .logging impo... |
17a25b9a383e38e727e950e4ea082c8a38ab4fcc9b636a42de389a52011c9c0c | Python | 7,506 | 185 | #!/usr/bin/env python
"""BaseShadowHandEnv Environment Wrappers."""
import abc
from typing import Optional
import gymnasium as gym
import numpy as np
from gymnasium import spaces
from angorapy.common.const import N_SUBSTEPS
from angorapy.tasks.core import AnthropomorphicEnv
from angorapy.tasks.envs.dexterity.consts i... |
def13bbed3485adf8d59327b487fd66ac34cfcca866fff93e6182f3e2e7297e7 | Python | 7,506 | 156 | import numpy as np
import os.path
from data.base_dataset import BaseDataset, get_transform
from data.image_folder import make_dataset
from PIL import Image
import random
import util.util as util
class SingleImageDataset(BaseDataset):
"""
This dataset class can load unaligned/unpaired datasets.
It require... |
335633fc1d3514514d6892d3ffa910ce701c93c10ec671a1b30c3181b319a4b3 | Python | 7,507 | 210 | import argparse
import copy
import json
import pandas as pd
import numpy as np
import sys
from pathlib import Path
from survival_plus_x.models.cox_lightning import compute_cindex, compute_stratification_logrank_pvalue
def main(args):
# configure the reduction function of the ensemble
assert args.ensemble_r... |
52d89a57e46fe7bed1b34e67d8e56e4a29511f9664449706e1ef0c75134bc943 | Python | 7,508 | 167 | import sys
import os
sys.path.append("../src")
from tensorflow import keras
import modeling
import data_prep
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
from scipy.stats import spearmanr, pearsonr
import pandas as pd
from functools import reduce
from matplotlib import rcParams
rcParams['fi... |
1388c2930bacb1f4747243337d226730354c6c156c58db4e7a432bdb2811323f | Python | 7,509 | 226 | import numpy as np
from keras.src import backend
from keras.src.api_export import keras_export
from keras.src.utils import tf_utils
@keras_export("keras.utils.normalize")
def normalize(x, axis=-1, order=2):
"""Normalizes an array.
If the input is a NumPy array, a NumPy array will be returned.
If it's a ... |
c0a7bd37dfd342053e3ca366dbc28ddef55f13e98d16c87ea4e8bbea9f4a89ec | Python | 7,510 | 185 | #!/usr/bin/env python3
"""
File: export_fim_to_excel.py
Created: 2022/06/23
Last Changed:
Author: M.Vochteloo
Copyright (C) 2020 University Medical Center Groningen.
A copy of the BSD 3-Clause "New" or "Revised" License can be found in the
LICENSE file in the root directory of this source tree.
""... |
49507daf99137a90878d8685dd39ee4f9ccac5f1b047d8de895ffbc428c431ae | Python | 7,511 | 144 | # Written by Seonwoo Min, Seoul National University (mswzeus@gmail.com)
# PLUS
import os
import sys
import argparse
import torch
import plus.config as config
from plus.data.alphabets import Protein
import plus.data.homology as homology
import plus.data.dataset as dataset
import plus.model.plus_rnn as plus_rnn
import... |
799d5bcc30f15c9a7d5ef524b094bf74c7ce3f827db779db897a007699d1f0d9 | Python | 7,511 | 187 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class YBins(_BaseTraceHierarchyType):
_parent_path_str = "histogram2dcontour"
_... |
79ac8b1f1c0ebd14db2534cd7d8d4fc62f6af1ca62d16cbf9e6c8c1f0d924cdd | Python | 7,511 | 187 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class XBins(_BaseTraceHierarchyType):
_parent_path_str = "histogram2dcontour"
_... |
6e870e29c1f6d56852a9ff222045fb63c9e0f49770ced7577f198fd77eb86d40 | Python | 7,512 | 222 | import unittest
from unittest.mock import MagicMock, patch
from codecarbon.output_methods.emissions_data import EmissionsData
from codecarbon.output_methods.http import CodeCarbonAPIOutput, HTTPOutput
class TestHTTPOutput(unittest.TestCase):
def setUp(self):
self.emissions_data = EmissionsData(
... |
381eeab98e26cf03f92880a9a6ec78e4441b811d6c51f1af5e35f394ccb22638 | Python | 7,513 | 203 | """M4 equivalent-lane parity (compo memo stratum 1; F36 wave A).
The same semantic request down different lanes (string label, Selection,
predicate, accessor) must accept/refuse IDENTICALLY -- the memo's founding
counterexamples were zero-match asymmetries (a selector lane refuses typed
while the plan lane silently wa... |
e22fcde664c4e849ae26556a72cf77e890fdaf82031b1b239ce4571b4bace39f | Python | 7,513 | 144 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
from pathlib import Path
import numpy as np
import torch
from ultralytics.utils import LOGGER, NUM_THREADS
from ultralytics.utils.checks import check_requirements
from .base import BaseBackend
class LiteRTBacke... |
c3e3cd763a39cb56ef37100cfbed7f2d95cf6a2786af359e7bad644a0bf7c4f2 | Python | 7,514 | 185 | #!/usr/bin/env python3
import numpy as np
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import glob, re, sklearn, collections, argparse, sys, os
import sklearn.metrics
import scipy
import caffe
from caffe.proto.caffe_pb2 import NetParameter
import google.protobuf.text_format as prototxt
from ... |
f4be3e6caf6f7f62d02c22aede767798a5a176f77d1b2f90df45439354e7df49 | Python | 7,517 | 141 | import torch
from .base_model import BaseModel
from . import networks
import itertools
from data import aux_dataset
class Pix2PixAttnModel(BaseModel):
""" This class implements the pix2pix model, for learning a mapping from input images to output images given paired data.
The model training requires '--datas... |
3fdfa5367bc0cf32cb0e2021eb0d6dd7690e6108a2a7610fe0812e494c706226 | Python | 7,518 | 231 | """
Braitenberg-style robot agents.
Implements the classic sensor-to-motor crossed and uncrossed wirings, used as a
minimal reference controller for the 2D robot simulation.
"""
from __future__ import annotations
from typing import Any
import random
import numpy as np
from ... import util
from ...model.modules impo... |
4cf9f4fddeff18324814db338757a0490ca9dfdf02c8ac35bdecd77f22c93dae | Python | 7,518 | 259 | #!/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 datetime
import time
logging.basicConfig(stream=sys.stderr, level=logging.INFO)
logger = logg... |
5a91481bda22ad953ccf8de863253caa1c7b973d9a22ed0e72dcb23363d4ebc1 | Python | 7,518 | 198 | import math
from typing import List, Tuple
import torch
from pytorch_lightning import LightningModule
from torch import Tensor
from torch.nn import Identity, ModuleList
from torch.nn import functional as F
from torchvision.models import resnet50
from lightly.loss.swav_loss import SwaVLoss
from lightly.models.modules ... |
d7b8ed4672c97488069554ea00cc3a7bddd7cbebd8734d267ab5ae553f46f1c9 | Python | 7,518 | 267 | import copy
import gc
import pytest
import rpy2.rinterface as rinterface
rinterface.initr()
def test_invalid_init():
with pytest.raises(ValueError):
rinterface.Sexp('a')
def test_init_from_existing():
sexp = rinterface.baseenv.find('letters')
sexp_new = rinterface.Sexp(sexp)
assert sexp_new... |
beeda41ffb5cb4d85c8fcec6710dff951f43421811ee5ec25ba08222355c1c31 | Python | 7,519 | 175 | """Implementation of a space that represents the cartesian product of `Discrete` spaces."""
from typing import Iterable, List, Optional, Sequence, Tuple, Union
import numpy as np
from gym import logger
from gym.spaces.discrete import Discrete
from gym.spaces.space import Space
class MultiDiscrete(Space[np.ndarray])... |
e3834d6be645f6d829586071de9c26decb058249ae7e00ed2c5d2a8604cbcd73 | Python | 7,521 | 167 | """ Diffusion utils. """
import paddle
from helixfold.model import all_atom
from helixfold.model import r3
from helixfold.data.data_utils import generate_backbone_affine, generate_torsion_angles
from helixfold.model import quat_affine, all_atom
from helixfold.relax.amber_minimize import make_atom14_positions
import gzi... |
b7bee65760e32d9f00c0cb2ecc1eb55b72301f6744183be4872c03f54fd0f544 | Python | 7,526 | 191 | import argparse
import logging
import time
import warnings
import sys
import contextlib
import os
import utils
import numpy as np
from pqdm.processes import pqdm
import pmsurv_exponential
import pmsurv_weibull
import deepsurv
import pmsurv_common
#TODO: https://docs.pymc.io/en/v3/pymc-examples/examples/pymc3_howto/up... |
6449f3e105884aa7d9aac4ae3ae0b0782e1c4f6ff3eccbae6bc1397eab7f69ca | Python | 7,527 | 194 | """Save out reports from model objects."""
from specparam.io.utils import create_file_path
from specparam.modutils.dependencies import safe_import, check_dependency
from specparam.plts.templates import plot_text
from specparam.plts.group import (plot_group_aperiodic, plot_group_metrics,
... |
7d77a6bdbcafe43fb7f50f51c67d8afe6a1e30628ac83dc6b77fe3611372b3a0 | Python | 7,527 | 205 | import time
from pathlib import Path
from h5py import File
import torch
from tqdm import tqdm
from torch.utils.data import Dataset, DataLoader
from itertools import cycle
from rbm.potts.functions import init_chains, init_parameters
from rbm.potts.pcd import fit_batch
from rbm.potts.functions import init_chains, init_p... |
27b35218edbd61bd310266544c28c0ac8135ac19bf67d4c43f1672a8e826d765 | Python | 7,531 | 199 | """Declared episode derivation on a REAL model (lane F40b; foldA s6 F40).
The realism arms the D8 rebuild must flip from refused to supported, on the
R0 roster's REAL distilgpt2 class (vendored config, zero network): a root
returning what real ``generate()`` returns (prompt+completion); the
KV-cache last-token feed (t... |
8ca510646d350f29d3ee8d25cd525c3b8c07db41daddaaf058dd2ce7bd05686f | Python | 7,531 | 225 | # 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... |
3e282b2b96e45b2d60b6126bcc8fb1d9944e84a7c0a1c5372fd71389d7aa428f | Python | 7,534 | 241 | """Caper's HPC Wrapper based on job engine's CLI (shell command).
e.g. sbatch, squeue, qsub, qstat
"""
import logging
import os
import subprocess
from abc import ABC, abstractmethod
from pathlib import Path
from tempfile import NamedTemporaryFile
logger = logging.getLogger(__name__)
CAPER_LEADER_JOB_NAME_PREFIX = 'CA... |
6dfaeb9e97a2be08b2cb3ac01e1a8a7b8e18000ba9adbdb5b73bd51696f219a0 | Python | 7,534 | 168 | from __future__ import annotations
import logging
import os
import pprint
from typing import Optional
import grpc
import minknow_api.statistics_pb2 as mk_stats
import pandas as pd
from bream4.device_interfaces.devices.base_device import BaseDeviceInterface
from bream4.toolkit.procedure_components.grpc_streamer impor... |
e8e1163796b16c037979dc53bdd34ef649eebe321ba9afcf425e72c962ff90ca | Python | 7,534 | 231 | import logging
import os
import platform
import re
import sys
import traceback
import uuid
import sentry_sdk
from qtpy import QT_VERSION, QtCore
from sentry_sdk.integrations.logging import ignore_logger
import llspy
from llspy import schema
from llspy.cudabinwrapper import CUDAbinException, gpulist
logger = logging.... |
4f08c95e481a6578a34a6b1e62d0a540b553be8f78683011e162521895c48aa3 | Python | 7,535 | 194 | import numpy as np
from keras.src import initializers
from keras.src import layers
from keras.src import ops
from keras.src import regularizers
from keras.src import testing
from keras.src.backend.common import AutocastScope
class LayerNormalizationTest(testing.TestCase):
def test_ln_basics(self):
self.r... |
61b50829adeff40871bd43cf322493b15ab2777a2503eedae20f228c882ea3b1 | Python | 7,535 | 198 | import copy
import cv2
import numpy as np
import torch
from skimage import measure
from utils.lung_cropping_model.deeplab import DeepLab
def refine_lung_region(imgsSegResult):
imgs = np.where(imgsSegResult > 0.5, 1, 0)
region = measure.label(imgs)
props = measure.regionprops(region)
nu... |
945095641c407a6373e852a3301af89fb3e3b4252c691a575979ffea678267fe | Python | 7,536 | 203 | """
====================================================================
Offline SSVEP-based BCI Multiclass Prediction
====================================================================
Building extended covariance matrices for SSVEP-based BCI. The
obtained matrices are shown. A Minimum Distance to Mean classifier
i... |
fa03af382f9b267153d13d92c8a20346f5bd69590c2031e667d8f5bdb2118544 | Python | 7,536 | 192 | import argparse
import csv
import pandas as pd
import numpy as np
def compute_indel_length(fs_df):
fs_df['indel len'] = 0
fs_df['indel len'][fs_df['Reference_Allele']=='-'] = fs_df['Tumor_Allele'][fs_df['Reference_Allele']=='-'].str.len()
fs_df['indel len'][fs_df['Tumor_Allele']=='-'] = fs_df['Reference_A... |
7b123b2bb0b159be1a81bdeadfa1afa360dbc44d44cad7c35434d6c006b94f9d | Python | 7,537 | 255 | from anndata import AnnData
from typing import Optional, Union
import numpy as np
import pandas as pd
import networkx as nx
from scipy.spatial.distance import cdist
import scanpy
def pseudotime(
adata: AnnData,
use_label: str = None,
eps: float = 20,
n_neighbors: int = 25,
use_rep: str = "X_pca",
... |
7d196832742861dcbcf8f1792276d403acf30322da698f639b0f2b2d00bf8fa7 | Python | 7,539 | 193 | import lifelines
import scipy.stats as st
import numpy as np
import pandas as pd
import pymc as pm
from pmsurv.exc import PyMCModelsError
from pmsurv.models.base import BayesianModel
import pmsurv.utils
class GaussianProcessModel(BayesianModel):
def __init__(self):
super(GaussianProcessModel, self).__init... |
bc6bfad440d81797b6edc33d728cec205587cdb8efe854f4a600a10e52767cdc | Python | 7,539 | 234 | """
===============================================================================
Metric comparison
===============================================================================
A comparison of the usual metrics used to process SPD matrices,
computed mainly for 2x2 matrices to display intuitive visualizations.
"""... |
3b8f9623731e0016f659f5c43767aa0da9630ee819459a98338a25e5446a3d8d | Python | 7,541 | 180 | """
Test objects and function in the package ``tfep.app``.
"""
# =============================================================================
# GLOBAL IMPORTS
# =============================================================================
from collections.abc import Sequence
from typing import List, Optional, Type,... |
95f8956a4a5ec7eda9dd2d914251aab1fa07722cdfd0eaec842f170e75678094 | Python | 7,543 | 217 | from pydantic import TypeAdapter
from galaxy.datatypes._schema import (
DatatypeConverterList,
DatatypeDetails,
DatatypesCombinedMap,
DatatypesEDAMDetailsDict,
DatatypesMap,
DatatypeVisualizationMapping,
DatatypeVisualizationMappingsList,
)
from galaxy.datatypes.data import Data
from galaxy... |
cb10bb82d0c8a0e7173a7c020443e0ebbd65a39fcc23fd18bf6e29504387eb4f | Python | 7,544 | 241 | import os
import sys
import traceback
from typing import Dict, Tuple
from pathlib import Path
import pickle
import shutil
import numpy as np
import pandas as pd
from numba.core.errors import NumbaDeprecationWarning
from numba.core.errors import NumbaPendingDeprecationWarning
import warnings
warnings.simplefilter('ig... |
f11a491d7a0493e347f76f0d45f018bd7a5f721fa4e729e578f01c2b9817fa14 | Python | 7,546 | 234 | import math
from functools import partial
import torch
import torch.nn as nn
import torch.nn.functional as F
def get_inplanes():
return [64, 128, 256, 512]
def conv3x3x3(in_planes, out_planes, stride=1):
return nn.Conv3d(in_planes,
out_planes,
kernel_size=3,
... |
c535a828fc55dd62be6746b80c6427d14f90a5f94a638112ec073c9f7ffc6ace | Python | 7,549 | 241 | """
Triple format classes
"""
import logging
import re
from galaxy.datatypes import (
binary,
data,
text,
xml,
)
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes.protocols import DatasetProtocol
from galaxy.datatypes.sniff import (
build_sniff_from_prefix,
FilePrefix... |
3d1d4f9444315f1acb1fa5454aede880eab3e2849cacddbc221b6a29d1227401 | Python | 7,552 | 214 | """``tl.validate`` hands the live model back without writing into its tensors.
Regression pin: every validate scope used to restore the model's state by
``load_state_dict`` even when the validation runs had not changed it. That
copies the snapshot into each parameter and buffer in place, so every
``_version`` counter ... |
3f00560d8324487b683bdfb06e5b10d573284d12c42351f4ee0df519fb53bf56 | Python | 7,552 | 199 | '''
this project were based the pytorch, pytorch lightning and pytorch video library,
for rapid development.
'''
# %%
import os
from pytorch_lightning import Trainer, seed_everything
from pytorch_lightning import loggers as pl_loggers
# callbacks
from pytorch_lightning.callbacks import TQDMProgressBar, RichModelSumma... |
e27f8bc7d61d62330c498d100d4a5c77754553f12833a74be8546a69653c5c4f | Python | 7,552 | 184 | """W051-AGENT: closure handoff on multi-pass traces (AUD-CODE 3.11d), per-row
reduction status (3.11f), JSON-safe logged values (2.6), and the 4.8 boundary
refusals, plus realistic-fixture paging (4.9)."""
from __future__ import annotations
import json
from pathlib import Path
import pytest
import torch
from torch i... |
f54e3ee707459ff4003e8280554a6a8ec7bc7340c00a35a7a534d9c07851b5ae | Python | 7,553 | 198 | """Tests for bdpy.recon.torch.modules.generator."""
import unittest
import copy
import torch
import torch.nn as nn
import torch.optim as optim
from torchvision.models import get_model
from bdpy.recon.torch.modules import generator as generator_module
class LinearGenerator(generator_module.NNModuleGenerator):
... |
19faf76fd93c6b7b26474c4bf46f7f06f618e95c0937ffb5199773c846a79834 | Python | 7,554 | 242 | import pickle
import numpy as np
from numpy.testing import assert_array_equal
import pytest
from sklearn.model_selection import cross_val_score, KFold
from sklearn.pipeline import make_pipeline
from pyriemann.estimation import Covariances
from pyriemann.geometry.kernel import kernel
from pyriemann.geometry.mean impor... |
5a8bba9a6f38015b3216d4f187657ceb54b4d9c610fa856d4f28858b5d284587 | Python | 7,554 | 198 | #Autor: Carlos Alberto Hernández Nava
#ASVspoof2017 Spectrogram extractor an convert to csv
import sys, csv, os, time, shutil, cv2
import pydub
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import scipy.signal as signal
import soundfile as sf
from PIL import Image
from pydub import AudioSegmen... |
e86c02fc1592f37d7ba0c59f8d5bd32d6d5fc93ca92a3819b0a5366d5d7e96fa | Python | 7,555 | 177 | import io
import os, sys, glob
import shutil
import zipfile
import requests
import src.EP_Generator_utils as EP_Generator_utils
from eppy.modeleditor import IDF
from src.Signal_Generator import generate_signal_for_EP
from src.OB_GEN.OB_Generator import ob_gen
def download_epw_create_directory(epw_url, configs):
e... |
972e73df1353b3367f4159c1b2f4540a3dcd8112e2489ea09854b42994309ba0 | Python | 7,556 | 215 | from operator import concat
from typing_extensions import Self
import torch
import torch.nn as nn
import torch.nn.functional as F
import dgl
import dgl.function as fn
from dgl.utils import expand_as_pair
from graphmae.utils import create_activation
class GCN(nn.Module):
def __init__(self,
in_di... |
edf3cc84eb22bdd90b0e658b254aff0df274b24c96175ed77a71af7a810774c7 | Python | 7,556 | 204 | """Replay engine: buffer-state threading and in-place ownership.
Regression net for the 2026-08-19 buffer-replay finding: the replay engine
executed in-place funcs on tensors it did not own (captured record outs and
committed overlay tensors, resolved BY IDENTITY), and buffer version records
were excluded from overlay... |
7b316183d82b79ac50084c759ed828ba3e0823674b11b303e0d1a660ad6d7774 | Python | 7,557 | 221 | """
Base class for making forms in the system UI.
Use with plugin_controller for automated plugin-controls
SimplyFire - Customizable analysis of electrophysiology data
Copyright (C) 2022 Megumi Mori
This program comes with ABSOLUTELY NO WARRANTY
This program is free software: you can redistribute it and/or modify
it ... |
f9cf252932c23cfda1497f91fe2e55603a019952ad84554ae232681ad1a17212 | Python | 7,557 | 182 | import contextlib
import os
import random
import numpy as np
from sklearn.model_selection import KFold, StratifiedKFold
import torch
from torch.utils.data.dataloader import DataLoader
# from torchsummary import summary
from hn_cnn.cnn import MODELS
from hn_cnn.constants import *
from hn_cnn.data_augmentation import ... |
b50e2f78d727d4d35964e7a12243aeaec25e82d108b2ea7b7d617d2a432014ce | Python | 7,567 | 195 | """
Larva-shaped agents for the 2D robot simulation.
Adapts the robot control loop to the larva body model, so that sensor-driven
Braitenberg behaviour can be simulated with the same body as the larva agents.
"""
from __future__ import annotations
from typing import Any
from ... import util
from ...model.modules imp... |
2a37abecf9ba4f6f94437036a67134f05149496ed5b10ea8bb73c72214240337 | Python | 7,568 | 150 | from skmob import TrajDataFrame
from skmob.measures import collective
from skmob.utils import constants
import numpy as np
import pandas as pd
import math
class TestCollectiveMetrics:
def setup_method(self):
latitude = constants.LATITUDE
longitude = constants.LONGITUDE
date_time = constant... |
57e83827f993b8f6ad5634bbaeb2ee0e2bfe761f4da10f6ca3119ac1a32a80bc | Python | 7,568 | 205 | import os
import h5py
import numpy as np
import pandas as pd
from modiscolite.io import save_hdf5
from modiscolite.tfmodisco import TFMoDISco
from .._utils import _make_dirs, _path_to_image_html
from modiscolite.report import run_tomtom, create_modisco_logos, report_motifs
def _trim_cwm(
cwm,
trim_threshold=0.... |
8d841edd8dbf24fd63f8d1be0b53db0f3768b479403c6795ab719bc8e0307638 | Python | 7,568 | 245 | """Define object to manage algorithm implementations."""
import numpy as np
from specparam.data.data import DATA_FORMATS
from specparam.utils.checks import check_input_options
from specparam.algorithms.settings import SettingsDefinition, SettingsValues
from specparam.modutils.docs import docs_get_section, replace_doc... |
e21f64d632a7f6658cf9a780ede24271a53f3b4d3be5cb453c7ad5a69ee155ad | Python | 7,571 | 204 | import torch
import torch.nn as nn
import torch.nn.functional as F
from ..base import _layers as layers
from ..base import _regularizers as regularizers
from ..base import _blocks as blocks
from ..base import _towers as towers
class DeepMEL(nn.Module):
"""DeepMEL model implementation from Minnoye et al 2020 in Py... |
efcdc34a470f65e12a4f1372256f14c9083f33459a1223fa0de6b8e42a7aba79 | Python | 7,571 | 197 | """Eelbrain GUIs"""
def run(block=False):
"""Hand over command to the GUI (quit the GUI to return to the terminal)
Parameters
----------
block : bool
Block the Terminal even if the GUI is capable of being run in parallel.
Control returns to the Terminal when the user quits the GUI app... |
f7fa9efc66ea777a44f68c2dc0fdd012205a7eb913bf511623957530cca512bf | Python | 7,571 | 218 | from unittest import mock
from uuid import UUID
import pytest
from carbonserver.api.infra.repositories.repository_emissions import (
SqlAlchemyRepository as EmissionRepository,
)
from carbonserver.api.infra.repositories.repository_experiments import (
SqlAlchemyRepository as ExperimentRepository,
)
from carbo... |
8a33ef029b0de2369c7d6e8df85417b193189ac338fc91bc5648e1c605913935 | Python | 7,575 | 198 | import time
## Panel classes
class BasePanel(object):
"""Returns a panel instance.
This class should be subclassed to define a local panel configuration.
To build a panel, do the following in the __init__() method of your local
subclass:
1. add instances of the necessary interfaces to the ... |
45def4c5282078c57b43827d7ea884e2dd160132cf2d8d75dae57a20a296c132 | Python | 7,576 | 246 | ### Prototype of Growing neural gas
import numpy as np
import random as pyrnd
from pylab import *
from .metrics import euclidean, cityblock, pearson, spearman, xcorrdist
class Edge:
def __init__(self, node1, node2):
self.nodes = (node1,node2)
self.age = 0
def length(self, distfn=euclidean):
... |
b356764b4c5a04180e5d856f68b5b92e433461dec22f17f0a8c7362096905331 | Python | 7,577 | 216 | """Brain-Score ``ActivationsExtractorHelper`` adapter tests (bridge P11).
The ``get_activations`` contract is exercised offline (no Brain-Score
install needed); the extractor wiring is verified against a stub mirroring
the real ``ActivationsExtractorHelper`` constructor read from the
brainscore-vision 2.3.22 wheel, pl... |
21e3cad7d7f74b07b5829842232fa3221c2020b8a161dc431f48292c48071a94 | Python | 7,578 | 220 | #!/usr/bin/python3
#-*-coding:utf-8-*-
# Copyright (c) 2022 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not us... |
44c527b8af0f6247baad2de65973fbaf33659c7aa0dfb2d581cc24b944f88b41 | Python | 7,579 | 206 | """
Code here relates to the from-scratch creation of data which simulates
electrical recordings of neurons. Creating data from scratch is useful
because (1) you can generate your own ABFs to analyze without requiring
access to real recordings and, (2) generating data with known events allows you
to test your event de... |
4966b295bb342979c8337aa0213668c892d2960ee3fd4c539c203e7cdee48ff0 | Python | 7,579 | 259 | # This file was automatically generated by SWIG (https://www.swig.org).
# Version 4.2.0
#
# Do not make changes to this file unless you know what you are doing - modify
# the SWIG interface file instead.
from sys import version_info as _swig_python_version_info
# Import the low-level C/C++ module
if __package__ or "."... |
732a492ae616fe07490d7831f86b1af08da3771a4ce1a6793ccef768c3e480b1 | Python | 7,580 | 190 | import os
import pandas as pd
import numpy as np
import sys
sys.path.insert(0, "/home/abraun/pymeg")
import pymeg
from pymeg.contrast_tfr import Cache, compute_contrast, augment_data
from pymeg import contrast_tfr
from pymeg import parallel
from joblib import Memory
import logging
import glob
import pdb
from optparse ... |
e9e43d24626e75f2398657d788118f944fb47a85b3e583506de5d39dd509887c | Python | 7,582 | 257 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
from typing import List
from warnings import catch_warnings, filterwarnings
import numpy as np
from scipy.linalg import norm
from scipy.stats import spearmanr, SpearmanRConstantInputWarning
from ._boosting_opt import l1, l2
from .shared import DeconvolutionData... |
8df990c645cce9a02180e12e88c2cd404ff37781a15e79a87b3fb0a2c8f94b81 | Python | 7,583 | 223 | """Evidence envelope + all-channels disclosure sweep (memo sec 5 / item 14).
ONE immutable envelope, computed once at settlement, consumed by every
surface; the banner ladder is HYPOTHESIS -> CORROBORATED -> REFUTED and no
channel may launder it. The parametrized all-channels test enumerates every
banner-bearing surfa... |
01c152ac5bc98fc49080531d66da8fd8db4e6111503def5f47c636b57402ae8d | Python | 7,586 | 209 | from __future__ import annotations
from typing import (
Annotated,
Literal,
)
from urllib.parse import quote
from pydantic import (
AliasChoices,
Field,
)
from galaxy.exceptions import (
AuthenticationRequired,
MessageException,
RequestParameterInvalidException,
)
from galaxy.files.models... |
37beebc5b253a608e73a64ea6699809ea2cb6c9187e37722cd2b08b373c39ca5 | Python | 7,590 | 203 | import argparse
import os
import numpy as np
import torch
import pytorch_lightning as pl
from pytorch_lightning.callbacks import ModelCheckpoint, EarlyStopping
from pytorch_lightning.loggers import WandbLogger
from torch_geometric.loader import DataLoader as GeometricDataLoader
from pathlib import Path
# Imports from ... |
3cfa7712575fafd3dcf894275b5b81a51c2a889c292a1a982f7cafdc254d3b51 | Python | 7,591 | 225 | from unittest import mock
import pytest
from api.mocks import FakeAuthContext, FakeUserWithAuthDependency
from dependency_injector import providers
from fastapi import FastAPI, status
from fastapi.testclient import TestClient
from carbonserver.api.infra.repositories.repository_organizations import (
SqlAlchemyRep... |
4b1b613064fad8589407e1eddcad0b198b7bc0adb974642a0b8223403d13ff9d | Python | 7,591 | 232 | """
plot_from_dicts_tool.py
This script contains functions to plot from dictionaries.
Authors: Colleen Gillon
Date: October, 2019
Note: this code uses python 3.7.
"""
import argparse
import glob
import inspect
from pathlib import Path
# try to set cache/config as early as possible (for clusters)
from util import... |
c6bd34bc8d22b4c46eafd6922ed65abcc453528989dc3e9a59e151ae2079d56e | Python | 7,591 | 174 | #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Written by Yuichiro Yada
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
################################################
# A code for Fig. 3. This code uses an output .pkl file from "prediction_realdata.py".
################################################
import... |
317c95fcae4bd662d4e9a4d57aea87ba39c147cd64f048cd500f0f1bceab8851 | Python | 7,592 | 216 | import os
import sys
import time
import heapq
import semver
import random
from multiprocessing import Pool
from collections import namedtuple
KILO = 1024
KILOBYTE = 1 * KILO
MEGABYTE = KILO * KILOBYTE
GIGABYTE = KILO * MEGABYTE
TERABYTE = KILO * GIGABYTE
SIZE_PREFIX_LOOKUP = {'k': KILOBYTE, 'm': MEGABYTE, 'g': GIGABY... |
c38a36643695ad847f45bf112ef682e9de7d558bb40f2a59d7227e2407e05981 | Python | 7,592 | 215 | from typing import Optional
import numpy as np
import pytest
import gym
from gym.envs.box2d import BipedalWalker
from gym.envs.box2d.lunar_lander import demo_heuristic_lander
from gym.envs.toy_text import TaxiEnv
from gym.envs.toy_text.frozen_lake import generate_random_map
def test_lunar_lander_heuristics():
"... |
51a2312e73b0f6d6cd560afcf17a1835bb26591f31504165618cebecdcf9d01b | Python | 7,593 | 205 |
import os
import json
import random
import torch
import numpy as np
from collections import defaultdict
from src.utils.util import device
from src.data.tokenize import tokenize_pet_txt, tokenize_pet_mlm_txt
class WiCReader(object):
'''
WiCReaer reads WiC dataset
'''
def __init__(self, config, tokeni... |
71afe82da8b72fb5eb6336ba0330959ac2a1a098934be2d6c275a7529db0232a | Python | 7,594 | 163 | """
Created on 13/07/2015
Author Peter van Heusden (pvh@sanbi.ac.za)
"""
import logging
import shlex
from galaxy.util import (
commands,
string_as_bool,
)
from . import AuthProvider
log = logging.getLogger(__name__)
"""
This module provides an AuthProvider for PAM (pluggable authentication module) authenti... |
eee255c6e56393b925ee0d4f44036b1650a84f30661d60a13e61eabfa7801763 | Python | 7,594 | 173 | # 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 applic... |
c0451e202b4b3996e97e876423e1cdd4864cbc71f6853594601fef75e211803f | Python | 7,595 | 171 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Feb 9 17:53:00 2022
@author: fcheng
"""
import os
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
def change_width(ax, new_value) :
"""
Change bar width
"""
for patch in ax.patches :
current_width = pa... |
ce0611752a941b2bd3051b06e220e7bc6e062e58824fd4bb9335edc5d516dedf | Python | 7,595 | 171 | #! /usr/bin/env python3
# -*- coding: utf-8 -*-
import math
#import copy
import numpy as np
# ROS libraries
import rospy
# ROS messages
from std_msgs.msg import String
from geometry_msgs.msg import Twist
#from nav_msgs.msg import Odometry
class MoveRobot(object):
def __init__(self, hz = 10.0):
... |
7cc64c33347344faf8f0e183adfdaafb515936110750cd94299e17f9d3d91745 | Python | 7,596 | 241 | from pyoperant import hwio, components, panels, utils
from pyoperant.interfaces import comedi_, pyaudio_
from pyoperant import InterfaceError
import socket
import time
_ZOG_MAP = {
1: ('/dev/comedi0', 2, 0, 2, 8), # box_id:(subdevice,in_dev,in_chan,out_dev,out_chan)
2: ('/dev/comedi0', 2, 4, 2, 16),
3: ('/... |
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