sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
43b66e780e08a9732a6a6a916c45979955944b826cfa10400b1e4ea98e4149d1 | Python | 2,891 | 84 | """Live-refresh RunReport declares host-RNG nondeterminism (deephunt F2).
The loaded-sparse provider derives ``nondeterministic_sources`` from the
descriptor's RNG profile, but the live-refresh provider historically never
passed sources to the one report finalizer, so a Python-``random``/clock model
reported a determi... |
96dae5eff68165c2bd13dbc7dbfbf63aa4a83b558884c3072225bf10e4ab75a9 | Python | 2,891 | 96 | from typing import Optional, Union
from anndata import AnnData
from .._compat import Literal
from PIL import Image
from pathlib import Path
# Test progress bar
from tqdm import tqdm
import numpy as np
import os
def tiling(
adata: AnnData,
out_path: Union[Path, str] = "./tiling",
library_id: str = None,
... |
a27885e6fecc2c21026f714ca299e022a5681ff79a47c9efdf950fb260073f80 | Python | 2,892 | 87 | import numpy as np
import pandas as pd
from anndata import AnnData
from natsort import natsorted
from sklearn.cluster import DBSCAN
def localization(
adata: AnnData,
use_label: str = "leiden",
eps: float = 20.0,
min_samples: int = 1,
copy: bool = False,
) -> AnnData | None:
"""\
Perform lo... |
10a8e28c5e012a54f907f9098431ee5c3e1fe08672307c936450c5093a4b77ab | Python | 2,893 | 54 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
3242a268cb522da2e4b745515dac2949280cdd4bcea548bed2689b8da4ce3d72 | Python | 2,893 | 84 | """Typed run-door refusal for ``run(seed=<non-int>)`` (r77 nit).
Round-76 (free-roam) found ``seed`` typed ``int | None`` but unchecked: junk reached
``torch.manual_seed`` raw and escaped as torch's ``RuntimeError: manual_seed expected a
long`` instead of the typed precondition lane. Verified transactional pre-fix (gl... |
4baf80c87bf3be2ca7104b873b13bcb9890c23665c9312da2dac2c6f84e581b1 | Python | 2,893 | 97 | import json
import os
import ast
from src.utils.util import make_exp_dir
class Config(object):
def __init__(self, filename=None, kwargs=None, mkdir=True):
# Dataset parameters
self.dataset = "fewglue/BoolQ"
self.num_lbl = 2
self.max_num_lbl_tok = 10
self.max_num_lbl = 10
... |
8f7928ce9cb1390c9170de9cdd744f72720cb75ddc6386422037345029aecab7 | Python | 2,893 | 74 | import glob
import numpy as np
import random
import fnmatch
import os
from PIL import Image
from matplotlib import pyplot as plt
import PIL
from sklearn.model_selection import train_test_split
from sklearn.decomposition import PCA
#from tensorflow.keras.utils import to_categorical
from sklearn.metrics import confusion_... |
e30eb53606719822260b2dc84bf080c5fdff0c6c84b42f19b6eb7bc7dec0561b | Python | 2,893 | 87 | # --- 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 Textfont(_BaseTraceHierarchyType):
_parent_path_str = "scattergeo.selected"
... |
8b0b57e73e18a36b9bcc5ae8fb25275b1ffb74ac0be4db209769eaf18bdbb997 | Python | 2,897 | 107 | from __future__ import annotations
import argparse
import nox
nox.needs_version = ">=2024.3.2"
nox.options.sessions = ["lint", "tests", "tests_packaging"]
nox.options.default_venv_backend = "uv|virtualenv"
@nox.session(reuse_venv=True)
def lint(session: nox.Session) -> None:
"""
Lint the codebase (except f... |
c5fe235861da77169289052dd2907052c070ecdc6db0e23b57d302d5f3657757 | Python | 2,897 | 83 | import tensorflow as tf
# Local dependencies
import metrics
import rcan
import care
import srgan
import RESNET
import WUnet
import UnetRCAN
def create_strategy():
strategy = tf.distribute.MirroredStrategy()
print(f'Number of devices: {strategy.num_replicas_in_sync}')
return strategy
def compile_model(... |
d6af57ed06f7f1ed2c14183de47eaba5cba5d845221d314e71ba44e7295b140f | Python | 2,897 | 84 | import os
import subprocess
import threading
import errno
import pytest
from pysam import AlignmentFile
from TestUtils import make_data_files, BAM_DATADIR
def setUpModule():
make_data_files(BAM_DATADIR)
def alignmentfile_writer_thread(infile, outfile):
def _writer_thread(infile, outfile):
"""read ... |
fd623c139b680bf400cefb98ecd13a81219b9bfba31a13b5ceda10460909708d | Python | 2,897 | 104 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseLayoutHierarchyType as _BaseLayoutHierarchyType
import copy as _copy
class Title(_BaseLayoutHierarchyType):
_parent_path_str = "layout.polar.radialaxi... |
b6a7fd4653567923840cb566c985ae5a7de640c6d3515992468c56a03367f079 | Python | 2,898 | 105 | 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_landuse_with_defaults(test_pbf):
from pyrosm import OSM
from py... |
660bd2adf42ae5ee9163959a7c906d2ca933561fbdc813020f098ce4f71a4b6e | Python | 2,899 | 106 | """
====================================================================
One-way Manova with frequency
====================================================================
One-way Manova to compare Left vs Right for each frequency.
"""
from time import time
from mne import Epochs, pick_types, events_from_annotations... |
aa0681dad50a195511a8f78e23bec69eb68c8a5f894c1ffbe98564428f1df448 | Python | 2,899 | 91 | import networkx as nx
from stlearn.pl.utils import get_node
from stlearn.utils import _read_graph
def shortest_path_spatial_paga(
adata,
use_label,
key="dpt_pseudotime",
):
# Read original PAGA graph
G = nx.from_numpy_array(adata.uns["paga"]["connectivities"].toarray())
edge_weights = nx.get_... |
257bc3b7fcce35cb93c731eaf6464b1fb197151cf94acc3e0f75fad6d8837acf | Python | 2,900 | 85 | from pyrosm.data_manager import get_osm_data
from pyrosm.frames import prepare_geodataframe
from pyrosm.utils import validate_custom_filter, require_layer_key, warn_empty_result
# Values of ``building`` that mark a part of a building (an entrance, a window) or say
# that a feature is not a building.
NOT_BUILDINGS = fr... |
ac993e823e85fac1e0817006f7b761ca7a941c5160029c992d681a1b6c421cc1 | Python | 2,900 | 94 | from __future__ import absolute_import
import hashlib
from pip._vendor.six import iteritems, iterkeys, itervalues
from pip._internal.exceptions import (
HashMismatch, HashMissing, InstallationError,
)
from pip._internal.utils.misc import read_chunks
# The recommended hash algo of the moment. Change this wheneve... |
d42fe87a8dcd9e849d574e3b55d1aee41bcdbd167cd8204a16d4bb93593b3431 | Python | 2,900 | 78 | from __future__ import annotations
import os
import socket
import time
from contextlib import closing, suppress
from time import monotonic
from unittest.mock import Mock, patch
from pytest_celery import CeleryTestSetup
from celery import uuid
from celery.events.state import HEARTBEAT_DRIFT_MAX
from celery.utils.obje... |
33e16c3141356c844a5969f36fd0ed53430a3121b19d15a7e687de8d365bb189 | Python | 2,901 | 112 | """
Centralized ROI-to-channel mappings for mAGO-based hardware modules.
All mAGO firmware modules share the same serial protocol but use different
channel layouts depending on module type and connected hardware. This module
consolidates the scattered channel maps from individual stimulator classes.
Channel layout re... |
f35c5fda5d6e31db5a31c9e13b4032c853fda95bb2daafece7bdc4d00d7492b6 | Python | 2,901 | 94 | import warnings
class deprecated(object):
"""Mark a function or class as deprecated (decorator).
Issue a warning when the function is called/the class is instantiated and
adds a warning to the docstring.
The optional extra argument will be appended to the deprecation message
and the docstring. N... |
69d2ad68e8e0656bc797e3a1ab7f46698e1747662790f592a91530f37f6fda06 | Python | 2,902 | 73 | """
Classes for all common sequence formats
"""
from galaxy.datatypes.data import get_file_peek
from galaxy.datatypes import data
from galaxy.datatypes.metadata import MetadataElement
import logging
log = logging.getLogger(__name__)
class GenBank( data.Text ):
"""
abstract class for most of the sequence ... |
ad1f86056e8dd389951edaa78b474f52e57af8f91d1197c0656f232a29a2c6bf | Python | 2,902 | 96 | import sys
from datetime import datetime
from .DL import DelhiDB
from .GA import GoaDB
from .HR import HaryanaDB
from .KA import KarnatakaDB
from .KL import KeralaDB
from .MH import MaharashtraDB
from .MP import MadhyaPradeshDB
from .PB import PunjabDB
from .TG import TelanganaDB
from .TN import TamilNaduDB
from .UK ... |
88ccf76d184346773235cb2b850936edc26a64a38cf066b2b3d15ac6c9579fc7 | Python | 2,903 | 82 | import json
import sys
import threading
from typing import Any
def _locate_schedd(
htcondor,
schedd_cache: dict,
schedd_lock: threading.Lock,
collector: str | None,
schedd_name: str | None,
):
cache_key = (collector, schedd_name)
with schedd_lock:
cached = schedd_cache.get(cache_ke... |
f3a0ca91e95838efb6a4515b1cfe12020852de196d2deca39c6fba04e0ad98cc | Python | 2,903 | 81 | import torch
from torch import nn
from schnetpack.nn import shifted_softplus, Dense
class EndToEndModel(nn.Module):
"""
Join a representation model with nn module.
Args:
representation (torch.nn.Module): Representation block of the model.
output_module (e.g. nn modul): Output block of the... |
94b0046ec6bc6e2d84629b04d43edfffe4e10865249f499444d4b677c4bcae0d | Python | 2,904 | 87 | # --- 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 Textfont(_BaseTraceHierarchyType):
_parent_path_str = "scatterpolar.selected"... |
a2b10323bfc3a0a776259a993903d8486953b4b253ddabf5b9c4f2897f8e0d26 | Python | 2,904 | 87 | # --- 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 Textfont(_BaseTraceHierarchyType):
_parent_path_str = "scattersmith.selected"... |
c4fc5d27bd4c2bb426b57993e67609b33d6b6b3ebfd2fbcfe607a032f7e90ba7 | Python | 2,904 | 78 | # Copyright (c) 2023 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... |
5477b3332ed385b7aa43ca35922c11898fb081a520bba1983d9f84d058cb702c | Python | 2,905 | 87 | """
Utilities for manipulating or evaluating the R language.
"""
# TODO: uuid is used to create a temporary symbol. This is a ugly
# hack to work around an issue with with calling R functions
# (language objects seem to be evaluated when doing so from rpy2
# but not when doing it from R).
import typing
imp... |
c704a60e8aa84031f1ea050bf78018ce1bffab690fb372e07031c512929ed7a7 | Python | 2,905 | 99 | import warnings
import numpy as np
import scanpy as sc
import tensorflow as tf
import sys
sys.path.append('../pkgs/scGAE/')
warnings.simplefilter(action='ignore', category=FutureWarning)
tf.compat.v1.logging.set_verbosity(tf.compat.v1.logging.ERROR)
# scGAE modules
from scgae import SCGAE
from preprocessing import *
... |
27729f1a20110389832a3e7cb0018438e3262c9c5bd5d9de4a61669db7ef4344 | Python | 2,906 | 93 | from typing import List
import plotly
import plotly.graph_objs as go
from plotly.offline import get_plotlyjs_version
def validate_coerce_fig_to_dict(fig, validate):
from plotly.basedatatypes import BaseFigure
if isinstance(fig, BaseFigure):
fig_dict = fig.to_dict()
elif isinstance(fig, dict):
... |
320002e3bff5d07d20d78e92c5e3c692dc7a1522431821f6d5138bca083b5c9f | Python | 2,906 | 73 | from abc import ABC, abstractmethod
from typing import List, Union, Optional
from config_manager import config_field
class Template:
"""Object to specify required structure of configuration file."""
def __init__(
self,
fields: List[config_field.Field],
nested_templates: Optional[Li... |
72d3c0ab65f6b276f90e0d4715d7ca4858ef51023a63ceb8ce15018a1de72e55 | Python | 2,907 | 69 | """ AvgPool2d w/ Same Padding
Hacked together by Ross Wightman
"""
import torch
import torch.nn as nn
import torch.nn.functional as F
from typing import List, Tuple, Optional
from .helpers import tup_pair
from .padding import pad_same, get_padding_value
def avg_pool2d_same(x, kernel_size: List[int], stride: List[int... |
a766a23d2fcc49d47e67ee6ece67166481c209db2cef6b7e55b54741918bd070 | Python | 2,907 | 82 | """Intervention honesty: fire records count the CURRENT value's fires
(edits memo row 0e -- the 2-edits-3-records over-count).
A replay push recomputes each site from capture truth through exactly this
push's hook fires, so the push REPLACES the site's replay-minted node-hook
records instead of extending them. Live-do... |
4c890a781aafc5c829b0a17649e4316ecdfcb66b90a07211005cca0830bc3b19 | Python | 2,908 | 108 | from typing import Literal
from anndata import AnnData
from .global_level import global_level
from .local_level import local_level
from .weight_optimization import weight_optimizing_global, weight_optimizing_local
def pseudotimespace_global(
adata: AnnData,
use_label: str = "leiden",
use_rep: str = "X_p... |
67eaac9d4ff9f39abbe8973adfe47dfc205ffc990cb65aa5c4a53d771701316c | Python | 2,908 | 75 | #!/usr/bin/env python3
"""Empirical p-value and manuscript sentence from permutation null accuracies."""
import argparse
import os
import numpy as np
OBSERVED = {"stroke": 0.5404, "healthy": 0.6232}
def load(path):
ext = os.path.splitext(path)[1].lower()
if ext == ".npy":
a = np.load(path)
elif ... |
791b359d9ce417df5c3bda92ae229fa7d8baa165df4071437af67655de00df00 | Python | 2,908 | 33 | config = {
'SERVER' : 'http://localhost:8080', # localhost, URL of your homepage e.g. 'https://biomedisa.info' or your internal IP e.g. 'http://192.168.176.30'
'SERVER_ALIAS' : 'biomedisa-001', # an alias name for your server (for email notification and logfiles)
'SECRET_KEY' : '...', # some random string
... |
0146c6c62691b9fc75fad56809b60ce563ae984bb5a9c790a569798acba1e76c | Python | 2,909 | 76 | # 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... |
1aadf3bce85fefbfc9aa51b609d68f8782bcf9c1a045cafe42c47771b29772fd | Python | 2,909 | 81 | """Generated, closed Tier-R inventory (design-of-record section 2.4).
Walks the dataclass graph reachable from the record universe and fails on any
field the checked-in classification table does not cover — and on any table
entry whose field no longer exists. The inventory is therefore mechanically
closed in both dire... |
53a2e0e589efcc004875ac20bbe74e9e84036dd80739988a81b61899de4a50d1 | Python | 2,909 | 87 | # --- 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 Textfont(_BaseTraceHierarchyType):
_parent_path_str = "scattercarpet.selected... |
73317312940a1c7327c393f01103c0a40efdb2d0bd1c94886e8b803a080ad17b | Python | 2,909 | 88 | """FlopCounterMode differential legs (M(oracles) item 12; F36 oracle wave 1).
torch.utils.flop_counter.FlopCounterMode is the EXTERNAL oracle (I2, ships
with torch): TorchLens's analytic MAC census must satisfy the exact
convention identity ``torch_total == 2 * true_MACs`` on MAC-only models
(FlopCounterMode counts ma... |
ed8d1463e30c6144a62f1a6ae3864b73a09e64dd71243c1e3399eb4d598f2872 | Python | 2,909 | 114 | """Smoke tests tasks."""
from __future__ import annotations
import os
import sys
from signal import SIGKILL
from time import sleep
import celery.utils
from celery import Task, current_app, shared_task, signature
from celery.canvas import Signature
from t.integration.tasks import * # noqa
from t.integration.tasks im... |
071fb7b0c72f679f723bcea056e207dd5ce2baad1a3a2e3f95aa5da77722d5fe | Python | 2,910 | 88 | import torch
import torch.nn as nn
from spliceai_torch import ResidualUnit
class SplicePointIdentifier(nn.Module):
def __init__(self, cl, asymmetric_cl, hidden_size, n_layers=3, starting_channels=4):
super().__init__()
assert cl % 2 == 0
if asymmetric_cl is None:
first_layer =... |
3163d724416e5c3089c7ace8b3af8330ac5bd982cbb588a5442095b071c22a6b | Python | 2,910 | 82 | # 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 os
from typing import Any, Callable, Optional, Tuple
import PIL.Image as PImage
from timm.data import IMAGENET_DEF... |
f60b2aabdcd01c46dc8781a893d978a74b34c69d4dc8b3413c04c2927f17c4ae | Python | 2,910 | 119 | import gc
import os
import re
import time
import pytest
import gym
from gym.wrappers.monitoring.video_recorder import VideoRecorder
class BrokenRecordableEnv(gym.Env):
metadata = {"render_modes": ["rgb_array_list"]}
def __init__(self, render_mode="rgb_array_list"):
self.render_mode = render_mode
... |
1145ef90b9e3be726cfb42a53ea6644cc9ea9c1038b106270fe9d4193b3817e6 | Python | 2,911 | 104 | # --- 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 Legendgrouptitle(_BaseTraceHierarchyType):
_parent_path_str = "pie"
_path... |
3141fdeac62ecc887ef337ea40587e09b379e84d9f1d058706b4bbd6b4e47d5e | Python | 2,911 | 104 | # --- 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 Legendgrouptitle(_BaseTraceHierarchyType):
_parent_path_str = "box"
_path... |
47fb414f582653d73147adfdd6e9f1b3899b7a47f827f56891c23e0f2e2d372a | Python | 2,911 | 87 | # 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 copy
import pytorch_l... |
dfc990c19e2eb538ba0df8ac481e00e7f61e21d98865b7d81bbc778625c8ca9b | Python | 2,911 | 104 | # --- 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 Legendgrouptitle(_BaseTraceHierarchyType):
_parent_path_str = "bar"
_path... |
ac0d3bf9ba867c5a9935546ddac1ce43535eff1f129f4a779ce34344d99a2901 | Python | 2,912 | 63 | import numpy as np
import cvnn.layers as complex_layers
import tensorflow as tf
from pdb import set_trace
def get_dataset():
(train_images, train_labels), (test_images, test_labels) = tf.keras.datasets.cifar10.load_data()
train_images = train_images.astype(dtype=np.complex64) / 255.0
test_images = test_im... |
008203aa010311fc84aa1ddd25223ab14eba831889e453527a769a1d128085c4 | Python | 2,913 | 74 | from .bulletin import Bulletin
from bs4 import BeautifulSoup
class Uttarakhand(Bulletin):
def __init__(self, basedir):
statename = 'UK'
super().__init__(basedir, statename)
# NOTE: Need to update this list of URLs every 2-3 months or so
self.bulletin_urls = [
"https:... |
2f2b975798c5dc9c6f6ac732a318ae3574192602c107f44f5714670e5c99d595 | Python | 2,914 | 111 | """
Feature calculations.
"""
import types
import pdb
import numpy as np
from rdkit import Chem
from rdkit.Chem import rdGeometry, rdMolTransforms
from deepchem.utils.save import log
from dcCustom.feat.proteins import Protein
__author__ = "Steven Kearnes, modified by Qingyuan Feng"
__copyright__ = "Copyright 2014, Sta... |
3d71592e9d267208f3e14aa697004e612fcc6ed234508c41fc163514af71a2af | Python | 2,914 | 87 | # --- 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 Textfont(_BaseTraceHierarchyType):
_parent_path_str = "scatterpolargl.selecte... |
54e7358c521d3c4d6cd28188711f9448fe1c0eeae2e2c484d54bc3032955128b | Python | 2,914 | 87 | # --- 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 Textfont(_BaseTraceHierarchyType):
_parent_path_str = "scatterternary.selecte... |
57071da194c476e68e307ec1f189cf4f0c664fff88a0caa9a52c7acb4d3b0066 | Python | 2,914 | 93 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Import raw (MaxFiltered) MEG data to remove metadata then save in same format for
further BIDSifying.
@author: mikkel
For information about NatMEG-PD please refer to the data descriptor:
Vinding, M. C., Eriksson, A., Comarovschii, I., Waldthaler, J., Manting, C. L.,... |
5e33ccc038b2321b2c8005a7b4c9542b42a71ab35e8edc6ba4b2fee6a13bee60 | Python | 2,914 | 89 | """Shared journal-grabbing probe for the P4 test files.
Intercepts step-0 materialization to hand tests the REAL journal entries a
tiny capture produced, without depending on postprocess internals beyond the
one compat seam every path routes through.
Since P7 there is ONE torch producer (decomposed ``OpRecord``). The... |
d409b587694de3e3a88fc4a613a760c8fe0becdc08d57f268df4ebbbabbbcd8a | Python | 2,914 | 92 | # 05/23/2023 Fengyao Yan
# Validation test on semi silico cmp data
import random
import numpy as np
import pandas as pd
from numpy import NaN
import tensorflow as tf
from sklearn.metrics import mean_squared_error
from scipy.stats import pearsonr
from gen_composition import gen_comp
from decide_organ import model_name,... |
99d16afe6e2045148f61d1ae7e0239712be372a5b8a35d30da559f83e120049a | Python | 2,915 | 85 | import json
import os
import sys
import traceback
import urllib.request
from packaging.version import parse as parse_version
from PyQt6 import QtCore
class UpdateWorker(QtCore.QObject):
finished = QtCore.pyqtSignal()
data_ready = QtCore.pyqtSignal(dict)
@QtCore.pyqtSlot(str, str)
def processUpdate(s... |
bc71edfa4b1cb7af64b78def09e790ff4c6fe64ab4fcf8e3d9699f44e8d3c0a0 | Python | 2,915 | 97 | # Copyright (c) 2025, Tri Dao.
"""Unified FlashAttention logging controlled by a single ``FA_LOG_LEVEL`` env var.
Host-side messages go through Python ``logging`` (logger name ``flash_attn``).
A default ``StreamHandler`` is attached automatically when ``FA_LOG_LEVEL >= 1``
so that standalone scripts get output withou... |
1180fe21d4efc7b26943dd62ecd9fb6b99f0ad76feb7423450a03da586e56acf | Python | 2,916 | 92 | #!/usr/bin/env python
##
# This script reads multiple alignments merged in single stockholm file
# and splits the alignment blocks according to data.names table
# The first sequence of each alignment file assumed to match to names table entries
# Author: M. Miladi
##
import re
import sys
from Bio import AlignIO
try:... |
d13ee4df2883e007e752cf46b04da3324fa60c89f9779d35d464b4925794ad5a | Python | 2,916 | 76 | """Parse ISO8601 dates.
Originally taken from :pypi:`pyiso8601`
(https://bitbucket.org/micktwomey/pyiso8601)
Modified to match the behavior of ``dateutil.parser``:
- raise :exc:`ValueError` instead of ``ParseError``
- return naive :class:`~datetime.datetime` by default
This is the original License:
Copyrig... |
d3ff3558de48d6c826f4daea1ad365d11edad4851ff2e6c29851be07f938c2cb | Python | 2,916 | 95 | """
#--------------------
Created on 2021.10.24
Version 1.0
__author__ = 'Xx'
#--------------------
"""
'''
Description:
Routine for determining the level of confidence of a particular clear sky test. Input single threshold value
('midpt') with associated confidence limits ('locut', 'hicut'). "Low" and... |
db45dca59c8b146f5c935bcef0659d21249a4d650779d1ee0de6bf309122a15a | Python | 2,916 | 90 | import numbers
import cv2
import numpy as np
import PIL
import torch
def _is_tensor_clip(clip):
return torch.is_tensor(clip) and clip.ndimension() == 4
def crop_clip(clip, min_h, min_w, h, w):
if isinstance(clip[0], np.ndarray):
cropped = [img[min_h:min_h + h, min_w:min_w + w, :] for img in clip]
... |
06d8b0f06ef303cb45e8af5b4e29b5e92a5ec573ffd0477406fe4cfd8e1420bf | Python | 2,918 | 104 | # --- 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 Legendgrouptitle(_BaseTraceHierarchyType):
_parent_path_str = "ohlc"
_pat... |
1049417779bc5397bb30b97302b36a340ecb0cf59f2feca9a08d6c37cb650775 | Python | 2,918 | 104 | # --- 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 Legendgrouptitle(_BaseTraceHierarchyType):
_parent_path_str = "cone"
_pat... |
61584d51e64830fdd6260ceec37c141466fdc3c84dae13b93977751a608d054b | Python | 2,918 | 80 | """
analyses.core — library functions for the cross-cohort EEG-AD methodology.
This package extracts the genuine library functions out of the
historical diagnostic_*.py development scripts and exposes them as a
stable API. New code (build_trained_model, deploy_classifier,
proper_cv, INGEST_TEMPLATE) should import from... |
01662406a4035c4f91bb81a23d5cda9c1b1b6101a82398763706e162a8337470 | Python | 2,920 | 99 | """
setup.py
========
This is the setup.py script for Eelbrain.
http://docs.python.org/distutils/index.html
https://setuptools.readthedocs.io/en/latest/setuptools.html
About MANIFEST.in:
https://docs.python.org/2/distutils/sourcedist.html#manifest-template
"""
# Setuptools bootstrap module
# http://pythonhosted.o... |
827ddb661c91fa335a0fc841a7a7a68ef2c6d915e19a3466deeff69ac291c973 | Python | 2,920 | 69 | """Input distributions"""
import logging
import neurom as nm
from neurom import load_neurons
import tmd
from tns.extract_input.from_TMD import persistent_homology_angles
from tns.extract_input.from_neurom import soma_data, trunk_neurite, number_neurites
from tns.extract_input import from_diameter
from tns.morphio_util... |
d504923f4870d66a7a266dd3bf391c5d8cc418423b6db9fcc28ad5e6c391ef47 | Python | 2,921 | 59 | from Bio import SeqIO
import unittest
import os
class TestTrinitySampleData(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.sampledata_dir = os.environ["TRINITY_SAMPLEDATA"]
def test_genome_guided(self):
seq_count = self.count_sequences('test_GenomeGuidedTrinity', 'test_GG_use_b... |
81cefeace6814f506b6437e8af5980d1cc19df67fa273134a18a080097618049 | Python | 2,922 | 83 | import sys
import unittest
from unittest.mock import patch
import logfire
from codecarbon.output_methods.emissions_data import EmissionsData
from codecarbon.output_methods.metrics.logfire import LogfireOutput
class TestLogfireOutput(unittest.TestCase):
def setUp(self):
self.emissions_data = EmissionsDat... |
991ca5cfae8a60b3c869d9c563a541037e4c4128d3b40968fad1fa2eee8c96d8 | Python | 2,922 | 72 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
import shlex
import shutil
import subprocess
import tempfile
from pathlib import Path
from ultralytics.utils import LOGGER, YAML
def _check_atc() -> None:
"""Raise if the CANN ATC compiler is not on PATH."""
... |
a197a79b4e6f3d91d8773c631a42e93789d18b7e2785cb6154eac788c166fe67 | Python | 2,922 | 69 | """Riemannian tangent-space baseline under the same leakage controls as CSP+RF."""
import os, sys, numpy as np, pandas as pd
ROOT = os.path.dirname(os.path.abspath(__file__))
sys.path.insert(0, os.path.join(ROOT, "src"))
from sklearn.pipeline import make_pipeline
from sklearn.preprocessing import StandardScaler
from s... |
2e2695292aacea76a2dd287d5005e2c872681f7aa88c604c8c0a5bea49f77fc8 | Python | 2,925 | 93 | # 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 copy
import torch
imp... |
4f4e35d2bb8e099f327c23bb6dd338a1f4616ef963ff29c13f069d45f7a56415 | Python | 2,925 | 105 | import pandas as pd
import gc
from camelot.core import TableList, Table
def _merge_tables_samewidth(table1, table2):
# return were_tables_merged = False if either of tables is None
if table1 is None or table2 is None:
return False, None
ncols1 = table1.shape[1]
ncols2 = table2.shape[1]
... |
6c47ef3b6d321a971333052d1246d8a77d6e0c1e21185ada98a687de5499a961 | Python | 2,925 | 66 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created in April 2020
@author: Thomas Bonald <bonald@enst.fr>
@author: Nathan de Lara <nathan.delara@polytechnique.org>
"""
import unittest
from sknetwork.data.test_graphs import *
from sknetwork.linalg import Laplacian, Normalizer, CoNeighbor
from sknetwork.linalg.ba... |
c9b24d4fa431c8d93038f59dfc324460f2374f44fac8874a64492eb8191cbdfb | Python | 2,925 | 104 | # --- 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 Legendgrouptitle(_BaseTraceHierarchyType):
_parent_path_str = "image"
_pa... |
e581b65f486997df54cb10f5217b15be85806c3665b0795d35b08ee8abc1dc9e | Python | 2,925 | 104 | # --- 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 Legendgrouptitle(_BaseTraceHierarchyType):
_parent_path_str = "table"
_pa... |
fcf8d3ec19ee74e52df212285208392704f1d2e025565a7b154bd5d303141ea9 | Python | 2,925 | 104 | # --- 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 Legendgrouptitle(_BaseTraceHierarchyType):
_parent_path_str = "splom"
_pa... |
28c6c0be7e2235f18621ca5d53ab0070763481ebda81e17d867f2dc28eae0150 | Python | 2,926 | 105 | """Shared TensorFlow backend test configuration."""
from __future__ import annotations
from importlib.metadata import PackageNotFoundError, version
from typing import Any
import pytest
from packaging.version import InvalidVersion, Version
_MIN_TENSORFLOW_VERSION = Version("2.16")
_MIN_KERAS_MAJOR = 3
_TF_CPU_CONFIG... |
3692bfaed5d26cc023ba0c1edab5abf1cd025cc17e8d25ce62757e73a1c488e0 | Python | 2,926 | 110 | import pytest
from pyrosm import get_data
@pytest.fixture
def helsinki_pbf():
pbf_path = get_data("helsinki_pbf")
return pbf_path
@pytest.fixture
def helsinki_history_pbf():
pbf_path = get_data("helsinki_test_history_pbf")
return pbf_path
def test_reading_points_of_interest_with_defaults(helsinki_... |
6b9865a324591deaf8e0616128481b5fb5203f0e4e634d3c4b32c04785d3452a | Python | 2,929 | 74 | """F11 visual-token gates (collapse memo item 10 / D10, machinery wave).
The ONE ``collapse_tokens`` table in ``themes.py`` holds every kind's marks
and panel-fixed wording (the naming sprint renames in one place; a compact
mode is a table change), the K4/K3 theming bug is fixed (hardcoded grays
ignored dark themes), ... |
790d4f4f699bfa0ac0412cb66432b37bafc1692fa68c0758b4c5c22ce4360833 | Python | 2,929 | 101 | #!/usr/bin/env python
# coding: utf-8
# In[4]:
import pandas as pd
from sklearn.model_selection import train_test_split, TimeSeriesSplit
from sklearn.linear_model import LinearRegression
from sklearn.metrics import mean_squared_error, r2_score, mean_absolute_percentage_error
from sklearn import preprocessing
import... |
86abc2be8c6c2078f2b220fba251ca4ea2b6973135fe54ba2d69faf64379ab22 | Python | 2,929 | 94 | from __future__ import absolute_import
import sys
import textwrap
from pip._internal.cli.base_command import Command
from pip._internal.utils.misc import get_prog
BASE_COMPLETION = """
# pip %(shell)s completion start%(script)s# pip %(shell)s completion end
"""
COMPLETION_SCRIPTS = {
'bash': """
_pip_co... |
d5dfacec76fdfb7d12f91ed003923d0b704991adea0029ce3174402109491d03 | Python | 2,929 | 81 | """
Copyright (c) 2022 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE BLUE BRAIN PROJE... |
09c190e38e49b096bd48d9cb6904f1b01a43cb9565c3b9aefa67fa6123369d6c | Python | 2,930 | 72 | # !/usr/bin/env python
## created by Yun Hao @MooreLab 2021
## This script contains data-formatting functions used for DTox model training
## Module
import numpy as np
import pandas as pd
import torch
from torch.utils.data.dataset import Dataset
from sklearn.model_selection import train_test_split
## This function ... |
9307134202511234ca8a82404186320275dea05ada2560669fbe28d2350b4330 | Python | 2,930 | 101 | #!/usr/bin/env python
# coding: utf-8
# In[4]:
import pandas as pd
from sklearn.model_selection import train_test_split, TimeSeriesSplit
from sklearn.linear_model import LinearRegression
from sklearn.metrics import mean_squared_error, r2_score, mean_absolute_percentage_error
from sklearn import preprocessing
import... |
125aab243307c5a5e5a5ac38a7d5ceae9e7ae175e297cfd6c4b668768499a53a | Python | 2,932 | 104 | # --- 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 Legendgrouptitle(_BaseTraceHierarchyType):
_parent_path_str = "quiver"
_p... |
25b24f62f99476aa37fdc2652a8d722f4e72ad9c82dcd5ff9c41f7e7556c69f5 | Python | 2,932 | 90 | # Copyright (c) 2021. Lightly AG and its affiliates.
# All Rights Reserved
from typing import TYPE_CHECKING, Callable, List
import numpy as np
import torch
from PIL import Image as Image
from PIL.Image import Image as PILImage
from torch import Tensor
from lightly.transforms.torchvision_v2_compatibility import torch... |
33e7a2238b458cda6857a2cce6e52c0df1db5e7932b749f06a46fa726c05ed78 | Python | 2,932 | 104 | # --- 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 Legendgrouptitle(_BaseTraceHierarchyType):
_parent_path_str = "violin"
_p... |
35aad2c93afa964594f952ca330f7629e8f900c2d636824a722cd560c50c56cb | Python | 2,932 | 104 | # --- 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 Legendgrouptitle(_BaseTraceHierarchyType):
_parent_path_str = "mesh3d"
_p... |
4c913585e2b236737317c1bc4bafd5e953601a6615ba5463bd891a3fc2ac47d9 | Python | 2,932 | 74 | # 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 typing import List
import torch
import torch.nn as nn
from timm.models.layers import trunc_normal_
from... |
57eb3a67a174dc7919a86fa201e6f27426d2e2b9cfa28d63d1cd38b73bc6e702 | Python | 2,932 | 104 | # --- 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 Legendgrouptitle(_BaseTraceHierarchyType):
_parent_path_str = "carpet"
_p... |
5b3c3367b77edd527ef6b60c8e9b86ae3dffec47f17dc78c8ee4a3271fb73dee | Python | 2,932 | 104 | # --- 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 Legendgrouptitle(_BaseTraceHierarchyType):
_parent_path_str = "funnel"
_p... |
628778482c923fe7eacf518d2c46722d6c39f78a21bc50ec7db609bce544a038 | Python | 2,932 | 87 | from typing import (
Annotated,
)
from pydantic import (
Field,
)
from galaxy.files.models import FilesSourceRuntimeContext
from galaxy.util.config_templates import TemplateExpansion
from ._fsspec import (
CacheOptionsDictType,
FsspecBaseFileSourceConfiguration,
FsspecBaseFileSourceTemplateConfigu... |
c49b21863ed43e2bcf98a9f8424232dd14143572ae2a96d512af37d179b9cc1e | Python | 2,932 | 93 | import pytorch_lightning as pl
import torch
class SurvivalModelHead(pl.LightningModule):
def __init__(self,
input_shape):
super().__init__()
self.mlp_head = self._create_network(input_shape)
def _create_network(self, input_shape):
raise NotImplementedError
def c... |
d54d2bd9e8f546a5940c031d9a3eb723fd7548d074e554508eb6031de152d839 | Python | 2,932 | 104 | # --- 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 Legendgrouptitle(_BaseTraceHierarchyType):
_parent_path_str = "volume"
_p... |
f00b86bd1c9b18956673fd1be600126a99cd9853be40f9a9439dea6095f5d287 | Python | 2,932 | 104 | # --- 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 Legendgrouptitle(_BaseTraceHierarchyType):
_parent_path_str = "icicle"
_p... |
f4ed6ae7cbf139ba13a79a3e9390791dd8d7d5064ad40388b9394c7c1a5eaf5a | Python | 2,932 | 104 | # --- 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 Legendgrouptitle(_BaseTraceHierarchyType):
_parent_path_str = "sankey"
_p... |
f5e4a42731bd8450adf7d91cd83066c1e7851f589354b8f83e4a0eca811aaef1 | Python | 2,932 | 99 | # This example requires the following dependencies to be installed:
# pip install lightly[timm]
# 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_lightnin... |
21e164bc04b5f8725a6099179654fd8b57d2cc4347dda9955c03befc8108a2c1 | Python | 2,933 | 73 | """F06 real-model rows: the DenseNet-121 divergence identity (attrib memo D13).
The kit's marketing sentence as a blocking test with no download (weights are
cached in this checkout's torch hub): restricted to module-dispatched ReLUs
our guided backprop matches the module-hook coverage class (captum parity is
pinned s... |
a171567be0cad69505278b4ec8da15f75ee59df90600478a9e154ee8d8b33f78 | Python | 2,933 | 77 | import numpy as np
from . import xpu
from .xpu import cupy_wrapper, iscupy
@cupy_wrapper(['X', 'Y'], dtype='float64')
def pdist(X, Y=None, metric='euclidean'):
if iscupy(X):
import pylibraft.distance.pairwise_distance
import cupy as cp
if Y is None:
Y = X
D = pylibraft... |
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