sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
e8478f2c843b2a2e16ecefe195e013cb1dc463865c84acb18ccc571c9ec4bc8b | Python | 1,243 | 38 | #==========================================================================
#
# 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://www.apache.org/l... |
eb33c468e1211bb3033f7a1c7bc021ca65e9df518e78eb537f6095537b8ff5dc | Python | 1,244 | 38 | import sys
from typing import TYPE_CHECKING
if TYPE_CHECKING:
from ._error_x import ErrorX
from ._error_y import ErrorY
from ._hoverlabel import Hoverlabel
from ._insidetextfont import Insidetextfont
from ._legendgrouptitle import Legendgrouptitle
from ._marker import Marker
from ._outsidet... |
1ac4658f752b23bce4315b2c20aaa72c58940c5d6140b064688f71a6aebe2cf9 | Python | 1,245 | 34 | from cvnn.montecarlo import MonteCarlo
import tensorflow as tf
import layers.__init__ as layers
import numpy as np
fashion_mnist = tf.keras.datasets.fashion_mnist
(train_images, train_labels), (test_images, test_labels) = fashion_mnist.load_data()
own_model = tf.keras.Sequential([
layers.ComplexFlatten(input_sh... |
37c9f9843cefc3f682ce4358ed3f70e47084942677191d8777a6d99316aba016 | Python | 1,245 | 40 | from rpy2.robjects.packages import (importr,
WeakPackage)
from rpy2.robjects.lib import dplyr
import warnings
with warnings.catch_warnings():
warnings.simplefilter("ignore")
tidyr = importr('tidyr', on_conflict="warn")
TARGET_VERSION = '1.3.'
if not tidyr.__version__.starts... |
58b422a4d6265fa38e95277b3ade8f51ade7ba550b8f863739cfc7fb22dc8138 | Python | 1,245 | 35 | import numpy as np
import torch
import time
class Print_Info():
def __init__(self,fout,end_lr,train_nele,val_nele,Prop_list):
self.ntrain=train_nele
self.nval=val_nele
self.fout=fout
self.end_lr=end_lr
# print the required information
self.fout.write("{:<8}{:<8}{:<6... |
42144044ea837b2085c0b5218b94faca0724ec7285f9946b4b6d7df7f83794b6 | Python | 1,246 | 41 | """
This code demonstrates how to access tags in ABF files
"""
# import the pyabf module from this development folder
import os
import sys
PATH_HERE = os.path.abspath(os.path.dirname(__file__))
PATH_SRC = os.path.abspath(PATH_HERE+"/../src/")
PATH_DATA = os.path.abspath(PATH_HERE+"/../data/abfs/")
sys.path.insert(0, P... |
6ff173d90f67c517539385ec3e7fa500250e17458302a552a2b8e7e2fd78a9b3 | Python | 1,246 | 41 | from typing import Tuple
import numpy as np
import torch
from torch import Tensor
class RandomFrequencyMaskTransform:
"""2D Random Frequency Mask Transformation.
This transformation applies a binary mask on the fourier transform,
across all channels. A proportion of k frequencies are set to 0 with this.... |
93227c48ce9d26e48eda7feef531e6a3108158677fb6b8e18a014e0f82b94f7e | Python | 1,246 | 39 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Summaries of metadata
@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.,
Oostenveld, R., Ingvar, M., Svenningsson, P., & Lundqvist, D. (2024). The
... |
60becec0eff8e3595fe7a56ff2c85d1339c4992fecd0d27034130f91da5006fa | Python | 1,247 | 38 | import numpy as np
import pandas as pd
def apply_alignment_transformation(
coordinates: pd.DataFrame,
transform_mat: np.ndarray,
pixel_size_microns: float = 0.2125,
) -> pd.DataFrame:
"""
Apply transformation matrix to convert coordinates between spaces.
From https://kb.10xgenomics.com/hc/en-... |
6bc382696e2dbdd1fcafd2b1fcb011181750465b0d7d41429d2220489dc6557f | Python | 1,247 | 35 | import unittest
from unittest.mock import MagicMock, patch
from cellxgene_gateway.dir_util import ensure_dir_exists, make_annotations, make_h5ad
class TestMakeH5ad(unittest.TestCase):
def test_GIVEN_annotation_dir_THEN_returns_h5ad(self):
self.assertEqual(make_h5ad("pbmc_annotations"), "pbmc.h5ad")
cla... |
e653f5f366259358505da60e6d70780dba514746e33d194cac73d2981d9d3c4d | Python | 1,248 | 53 | #!/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
logger = logging.getLogger(__name__)
class DP_matrix:
""... |
948073553d447915162c02b2c1ce5d2dfa1381d7e61bbcec0a841a4101a5670f | Python | 1,249 | 37 | #!/usr/bin/env python
import setuptools
__version__ = "1.0.1"
CLASSIFIERS = [
"Development Status :: 5 - Production/Stable",
"Intended Audience :: Developers",
"License :: OSI Approved :: MIT License",
"Natural Language :: English",
"Operating System :: OS Independent",
"Programming Language ... |
c7aec6efbce68c1feb8cddb3562bd1358091c41caff1c7b77c794416734250fe | Python | 1,249 | 31 | import numpy as np
import tensorflow as tf
(mnist_images, mnist_labels), _ = tf.keras.datasets.mnist.load_data()
mnist_images, mnist_labels = mnist_images[:128], mnist_labels[:128]
dataset = tf.data.Dataset.from_tensor_slices((tf.cast(mnist_images[..., tf.newaxis] / 255, tf.float32), tf.cast(mnist_labels, tf.int64)))
... |
36045ddf28ec97f3330033ab8c7abff2c81f03ada366d9f9cb429ac7c8258155 | Python | 1,250 | 44 | #!/usr/bin/env python
# painfully converted from b0rken perl from
# https://unpkg.com/browse/jbrowse-plugin-mafviewer@1.0.6/dist/
# license is Apache2_license.txt included here
import sys
id = 0
buffer = ''
start = 0
end = 0
score = 0
chrom = ''
db = "%s." % sys.argv[1]
# Read input from stdin
for line in sys.stdin:... |
a5bcc09a9ce610a5aaef4aa36dada176dbd81d277adbdf272eea494309bb50b4 | Python | 1,250 | 46 | from typing import Optional, Union
from anndata import AnnData
from matplotlib import pyplot as plt
from pathlib import Path
import os
def annotation(
adata: AnnData,
label_list: list,
use_label: str = "louvain",
copy: bool = False,
) -> Optional[AnnData]:
"""\
Adding annotation for cluster
... |
6e74635891cc6f16a4695ccd91cdd0744810345cf653159c708aa4c2196c5a9c | Python | 1,251 | 37 | from setuptools import setup
setup(name='hd_glio',
version='2.0',
packages=["hd_glio"],
description='Tool for brain tumor segmentation. This is the result of a joint project between the Department of '
'Neuroradiology at the Heidelberg University Hospital and the Division of Medica... |
80031a4f0d604b1de0ea7e327a829c1f824f60fa9204e5b542dfbee98466e8db | Python | 1,251 | 36 | """Regenerate the frozen root SURFACE table (C01 item 7).
One command: ``python tools/generate_surface.py``. Rerun after any
deliberate root-facade change (e.g. rebasing over a lane that added lazy
names) and review the diff; the lockstep test
(tests/test_arch_spine_surface.py) byte-checks the table against the live
w... |
bf814ce4f6d547cb029a7eb4a69a40a19cc0695bb39a972c441ae6663ebd7805 | Python | 1,251 | 41 | # coding: utf-8
# pylint: disable=wrong-import-position
"""GluonCV: a deep learning vision toolkit powered by Gluon."""
from __future__ import absolute_import
from .check import _deprecate_python2
from .check import _require_mxnet_version, _require_pytorch_version
__version__ = '0.11.0'
_deprecate_python2()
# optio... |
3a830bec90c0602c4841205ee267d49460dfa957e491723a87189d171ec7f3b7 | Python | 1,252 | 31 | """Tests for specparam.algorthms.spectral_fit."""
from specparam.models.base import BaseModel
from specparam.data.data import Data
from specparam.results.results import Results
from specparam.sim import sim_power_spectrum
from specparam.algorithms.algorithm import Algorithm
from specparam.tests.tdata import default_s... |
a213d7175e4d2a9374b2b5e5afff8499add9d3ba7c5776c7c324741b2e03c558 | Python | 1,252 | 31 | import os
from gluoncv import data
class COCODetectionTiny(data.COCODetection):
CLASSES = ['bicycle', 'motorcycle']
def __init__(self, root=os.path.join('~', '.mxnet', 'datasets', 'tiny_coco'),
splits=('instances_val2017_tiny',), **kwargs):
super().__init__(root=root, splits=splits, *... |
ec29e2965551b141ec95a47a45c328b66ef556213f31b5297eeb03a2d9f09b22 | Python | 1,252 | 42 | from sys import argv
from msp import MSP
msp = MSP()
msp.file = __file__
msp.seed = int(argv[1])
msp.architecture["num_motifs"] = 82
msp.architecture["sparse_spec"] = dict(type="SpatiallySparseAcrossChannels")
msp.architecture["motif_model_spec"] = dict(
type="AdjustedMotifModel",
model_to_adjust_spec=dict(
... |
5590565f5eeb61a0da19b5898a395ed38a559da77399ec0a216a4c6d6f21f898 | Python | 1,255 | 32 | import numpy as np
import open3d as o3d
from pathlib import Path
from helpers.configurations import INSTANCE_LABELS_PATH, INSTANCE_LABELS_PRED_PATH, OBJECT_LABEL_MAP, OBJECT_COLOR_MAP
def main():
FROM_GT = False
print(f'Using GT {FROM_GT}')
for take_idx in range(1, 11):
pcd_paths = sorted(list(P... |
7423c98279fd4320e28ada29fc8d7a9b56d8117538f692fffae7d72e784645be | Python | 1,255 | 44 | from sys import argv
from msp import MSP
msp = MSP()
msp.file = __file__
msp.seed = int(argv[1])
msp.batch_size = 2 * msp.batch_size // 3
msp.lr = float(msp.lr) * 2 / 3
msp.architecture["num_motifs"] = 12 + 2
msp.architecture["sparse_spec"] = dict(type="SpatiallySparseAcrossChannels")
msp.architecture["motif_model_... |
aac5c2d222d414a86dc0d43e9ba173ef3f4c96cf3f110e63912ac28d7868a738 | Python | 1,255 | 37 | from __future__ import division
import unittest
import numpy as np
from wyrm.types import Data
from wyrm.processing import remove_channels
from wyrm.processing import swapaxes
class TestRemoveChannels(unittest.TestCase):
def setUp(self):
raw = np.arange(20).reshape(4, 5)
channels = ['ca1', 'ca2... |
b7ab7b55500fd0859a98b91c86fc990772fd285d96ab36f61876017739657290 | Python | 1,255 | 38 | import nibabel as nib
from skimage.util import random_noise
from PIL import Image
import numpy as np
from pathlib import Path
from Transform.src.noise import Noiser
def add_noise_and_save(output_path, sigma):
# Load the default "Lena" image using Pillow
image = Image.open("default.jpg").convert("L")
# C... |
148fc2d4f8a518edbf3e7be806663ca23c4443e7084e6884949434aa314f177f | Python | 1,256 | 45 | from typing import List, Sequence, TypeVar
_K = TypeVar("_K")
_V = TypeVar("_V")
def sort_items_by_keys(
keys: Sequence[_K], items: Sequence[_V], sorted_keys: Sequence[_K]
) -> List[_V]:
"""Sorts the items in the same order as the sorted keys.
Args:
keys:
Keys by which items can be i... |
14957f8ea0b852ec50446ab5c56a655141b16c824f3dd7fcc8e217d9edbce0bb | Python | 1,256 | 49 | # Configuration file for the Sphinx documentation builder.
import os
# -- Project information
project = u'SimplyFire'
copyright = u'2023, Andrew Rosko'
author = u'Megumi Mori, Andrew Rosko'
release = '0.5'
version = '0.5.1'
# -- General configuration
extensions = [
'sphinx.ext.duration',
'sphinx.ext.doctest... |
1bd62fd4ea2431c286a516e189136384f913c5f51f785288ec6fe464fac3ac82 | Python | 1,257 | 56 | """Some utilities"""
import sys
import subprocess
def find_gapped_pos(aln, ref_id=None, pos=0, nbp=1):
""" Find gapped position given a position on the reference genome
Parameters:
aln: MultipleSeqAlignment obj
ref_id: reference genome seq id
pos: (ungapped) position on the reference... |
6043885d5d2b0aa8d2b79bd5d28903c161b931f95361f1d54170d397e06b0e38 | Python | 1,257 | 28 | """Tests for specparam.modutils.functions."""
from specparam.modutils.functions import *
###################################################################################################
###################################################################################################
def test_resolve_aliases():
... |
b023875025db817b61543a5ba51ce41ad03a54b875cbe296347d1fada3fe3462 | Python | 1,257 | 41 | # This file is part of MOXελ.
# Copyright (C) 2023 Antonios P. Sarikas
# MOXελ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# This... |
020c703d1c8fb29224b443cef438fb7a4ec3e21a086a3be0ed54c5477d3b609f | Python | 1,258 | 30 | import numpy as np
import pandas as pd
import scanpy as sc
import anndata as an
import sys
DATADIR="data/tidy_data/hierarchical_deg_analyses/"
save_file = "data/tidy_data/Seurat_projects/OUD_Striatum_refined_all_SeuratObj_N22.h5ad"
striatum_ann = sc.read_h5ad(save_file)
## relabel the columns for multi-level hierarch... |
0a544a799706683b43fdeecbc92ad70ed636084a8b1deb88f2b13e7ea4209d2f | Python | 1,258 | 34 | from abc import ABCMeta, abstractmethod
from dataclasses import dataclass, field
from typing import Any, Dict, Iterable, List, Optional
class IntensityFetch():
def __init__(self,carbon_intensity : float, address : str, country : str, is_fetched : bool, is_localized : bool, is_prediction = False, time_duration : Op... |
6f33dd1adbc92ff756eb19b228c4a6dadba582f24b237c455a267d051b58beb4 | Python | 1,258 | 41 | # Get features batch-wise for PCA
import pickle
import numpy as np
from tensorflow.keras.applications.vgg19 import VGG19
from tensorflow.keras.applications.vgg19 import preprocess_input
from tensorflow.keras.preprocessing.image import smart_resize
from tensorflow.keras.models import Model
import sys
with open... |
cba1a039883a03c568af7facb125d90c896618ef997c689f72a3a19926445322 | Python | 1,258 | 38 | """Tests for specparam.modes.modes."""
from specparam.data import ModelModes
from specparam.modes.mode import Mode
from specparam.modes.definitions import AP_MODES, PE_MODES
from specparam.modes.modes import *
###################################################################################################
#######... |
0d32827eee0f40660ada689a0ec2dcb96a9827b0c99821011699834b4cac2075 | Python | 1,259 | 43 | # SPDX-License-Identifier: LGPL-2.1-or-later
from __future__ import print_function, division, absolute_import
import unittest
import os
from pyEcoHAB import single_antenna_registrations as sar
from pyEcoHAB import Loader
from pyEcoHAB import Timeline
from pyEcoHAB import data_path
class TestExecution(unittest.TestCa... |
df4ae50a169b6554c7e436887de0d6aa43fc4f3705668138af7249b72afd7e20 | Python | 1,259 | 40 | """
Gregory Way 2017
PanCancer Classifier
scripts/copy_burden_merge.py
Merge per sample classifier scores with segment based scores
Usage: Run in command line with required command argument:
python scripts/copy_burden_merge.py --classifier_folder
classifier_folder is a string pointing to the location of the... |
0c6009f75e0f05cb882a3cb86e7a1aced76af2263eec46950b7b14fb1cb67ff7 | Python | 1,260 | 57 | import unicodedata
import sys
import re
from setuptools.extern import six
# HFS Plus uses decomposed UTF-8
def decompose(path):
if isinstance(path, six.text_type):
return unicodedata.normalize('NFD', path)
try:
path = path.decode('utf-8')
path = unicodedata.normalize('NFD', path)
... |
ac06afa872c3b913948299783f9b8b0d621866e618e4116258a09bd3627d0f40 | Python | 1,260 | 17 | import os
ROOT_REPO_DIR = os.path.realpath(os.path.join(os.path.dirname(__file__), '..'))
WORD_AND_SPEAKER_ENCODINGS_PATH = os.path.join(ROOT_REPO_DIR, 'robustness', 'audio_functions', 'word_and_speaker_encodings_jsinv3.pckl')
ASSETS_PATH = os.path.join(ROOT_REPO_DIR, 'assets')
WORDNET_ID_TO_HUMAN_PATH = os.path.join(... |
cfbb6b17cbb56bfbb6c7ffbc152f714e5a210be63b2ed8f236a57d8cd873c0c6 | Python | 1,260 | 47 | # 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 in writin... |
2bb66ee3cb11a34fb1993a4bef5d7ed344a66723bd76097457f2f155b0f4418e | Python | 1,261 | 42 | import torch
def weighted_mean(x, weights):
if weights is None:
return torch.mean(x)
else:
return torch.sum(weights * x) / torch.sum(weights)
def weighted_mad():
"""Mean absolute difference (weighted)"""
return lambda source, target, weights: weighted_mean(torch.abs(source - target),... |
8af7f02838ce78fb330fbf68f51e1554462945c92da36ed9dd48d96c80d5075b | Python | 1,262 | 42 | import os
import subprocess
from packaging.version import parse, Version
import torch
from setuptools import setup
from torch.utils.cpp_extension import BuildExtension, CUDAExtension, CUDA_HOME
def get_cuda_bare_metal_version(cuda_dir):
raw_output = subprocess.check_output([cuda_dir + "/bin/nvcc", "-V"], univers... |
4b932250e72bed511dd343663e1349e71637c107ff1317c0b89f2d8fdb3d724b | Python | 1,263 | 36 | """Version coherence: pyproject.toml and torchlens.__version__ must agree.
Releases are cut by python-semantic-release, which rewrites both declared
version strings together -- but a manual edit desyncs them and ships in every
source install until the next release. Nothing else pins them equal.
"""
from __future__ im... |
529415e8e628a88664277dba98ec59452d71809ff236341d095479dfc399dcbc | Python | 1,263 | 37 | import torch
import torch.nn.functional as F
from torch.nn.modules.module import Module
from torch.nn.parameter import Parameter
class GraphConvolution(Module):
"""
Simple GCN layer, similar to https://arxiv.org/abs/1609.02907
"""
def __init__(self, in_features, out_features, dropout=0., act=F.relu):... |
28ef1bfd76d4983829c8faa4f9f8a9c13fd9ea95d869e1bc8f9c9a7be5dcc488 | Python | 1,264 | 40 | # 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, '../'))
import prob2020.console.annotate as sm
def test_sim_summary():
opts = {'input': os.path.join(file_dir, 'data/sim_summary.fa'),
'... |
43e67e4836a55ebd0bbeb01de624a12d8dc7e697413af6025161703ef54defb7 | Python | 1,265 | 49 | """Tests for the specparam.data.stores."""
import numpy as np
from specparam.data.stores import *
###################################################################################################
###################################################################################################
def test_model_set... |
5a1333a8b3413d133ef904464011b3ed10c642410497c264d160edcdbda2dd81 | Python | 1,265 | 32 | #!/usr/bin/env python
"""Components that can be loaded into another network."""
import tensorflow as tf
def _build_fcn_component(input_dim: int, hidden_dim: int, output_dim: int, batch_size: int = None,
name: str = None):
inputs = tf.keras.Input(batch_shape=(batch_size, input_dim))
... |
265632ab9e138b477b80547e4004a26f2637ccf59a22113af547c6cf027df051 | Python | 1,266 | 33 | from setuptools import setup, find_packages
with open("README.md", "r") as fh:
long_description = fh.read()
setup(
name="kelluwen",
version="0.0.29",
description="Open AI library for research and education.",
packages=find_packages(),
url="https://github.com/felipemoser/kelluwen",
author="... |
a06b8221147daced8bf8a9c3c85950d196a7a2ff6974a2c45bf74222a4e82abd | Python | 1,266 | 47 | """
Invent a better (truly unique) GUID system
"""
import glob
import os
import sys
import matplotlib.pyplot as plt
import uuid
import datetime
import time
import hashlib
try:
PATH_HERE = os.path.abspath(os.path.dirname(__file__))
PATH_DATA = os.path.abspath(PATH_HERE+"../../../data/abfs/")
PATH_SRC = os.... |
f89c641b6f07e345a2c518b8378725ae4ccc49444da8a0cddc07b026636b1c76 | Python | 1,266 | 51 | """Run post-hooks during the original capture.
What this demonstrates
----------------------
Pass ``hooks=...`` to ``trace`` so the intervention fires live while
the model is executing.
How to run
----------
``python examples/intervention/08_live_post_hooks_during_capture.py``
Runnable by default.
"""
from __future... |
f9c36197e4d93cc335d461d481485f1f06c47b048bb412c9baf85ead0ab18732 | Python | 1,266 | 39 | """This module implements various spaces.
Spaces describe mathematical sets and are used in Gym to specify valid actions and observations.
Every Gym environment must have the attributes ``action_space`` and ``observation_space``.
If, for instance, three possible actions (0,1,2) can be performed in your environment and... |
3b540a1784cbd2e522883946065ef5412876e6ebf1488dcdcc0321eaf0f0b6a7 | Python | 1,267 | 65 | #!/usr/bin/env python
# coding: utf-8
# In[ ]:
from pathlib import Path
import argparse
import json
import tempfile
import subprocess
# In[ ]:
from pysster import Data, Model
from pysster import utils
# In[ ]:
parser = argparse.ArgumentParser()
parser.add_argument('-s', '--seed', type=int, default=None)
pars... |
6fc2a8b484929f92bd6644201a4498aea85502b9707a6bca8ac828d864d033a6 | Python | 1,267 | 36 | # -*- coding: utf-8 -*-
# Copyright (c) 2016-2018 Braintech Sp. z o.o. [Ltd.] <http://www.braintech.pl>
# All rights reserved.
"""Module defines a single method get_logger that returns logger with set logging level."""
import logging
LEVELS = {'debug': logging.DEBUG,
'info': logging.INFO,
'warnin... |
8afde3bd24f559ba3be8d8fa95a72d87ff3a9dd2102c3d04d574f2e821330aed | Python | 1,268 | 30 | # type: required: obj(file)/int(index)/np.array/list/np.array/np.array/np.array/np.array
# optional: force: atomic force, cell: lattice parameters
def write_format(fileobj,num,pbc,element,mass,coordinates,ef,abprop,Prop_list,cell,force=None,temperature=None):
fileobj.write("point= {} ".format(num))
... |
ee39a616a56fdc5f5a307997682c963c4c00506684e7de458384ca5474f02a1c | Python | 1,268 | 48 | #!/usr/bin/env python
"""
Connects to sites and determines which builds are available at each.
"""
import xml.etree.ElementTree as ElementTree
from galaxy.util import requests
sites = [
"http://genome.ucsc.edu/cgi-bin/",
"http://archaea.ucsc.edu/cgi-bin/",
"http://genome-test.gi.ucsc.edu/cgi-bin/",
]
nam... |
167e376ed855e62443ba5eb6bafadcfdec6dee9cb6d5034c27948c7940b2b398 | Python | 1,269 | 39 | # %%
import pandas as pd
from globals import path, sessions, subjects, folder_spots_noboth
import os
path_to_save = f"../../data/spots_locations/{folder_spots_noboth}"
# %%
# Load data
for index, subject in enumerate(subjects):
for session in sessions:
spots = {}
for key in [0, 1, 2]:
... |
3924adad34cc2cbd2f49c97b912ac1dcb80361e9f4cdc3ef290c9252ce76a153 | Python | 1,269 | 50 | from setuptools import setup, find_packages
def readme():
with open('README.md', 'r', encoding='utf-8') as f:
content = f.read()
return content
setup(
name='cefcon',
version='0.3.0',
description='Deciphering cell fate control from single-cell RNA-seq data',
long_descript... |
a18867ab926066c58ceb9403755880c3f5dc1ff0fccaf9f929d5a42353518565 | Python | 1,269 | 40 | from typing import List, Tuple
from lightly.utils.bounding_box import BoundingBox
def read_yolo_label_file(
filepath: str, padding: float, separator: str = " "
) -> Tuple[List[int], List[BoundingBox]]:
"""Reads a file in the yolo file format
Args:
filepath:
The path to the yolo file,... |
cccfa049c87a5cc58c7d73bb3d7e689a112d7ea570cfe67b8babf40f96ae0155 | Python | 1,269 | 43 | import os
import sys
from typing import List
from pathlib import Path
import itertools
import numpy as np
import snapatac2 as sa2
# get barcodes after qc and doublet removal
with open("../meta/mba.whole.sample.lst", 'r') as f:
samples = [ l.strip() for l in f.readlines()]
# * summarize doublet removal under bmat... |
e24307f44fa7c30778dfcf12eec4b501d735d8b202f6f72a1139b6da6e6c2e13 | Python | 1,269 | 38 | # -*- coding: utf-8 -*-
# Copyright (c) 2016-2018 Braintech Sp. z o.o. [Ltd.] <http://www.braintech.pl>
# All rights reserved.
"""
Module providing generic temporary data buffer.
Author:
Mateusz Kruszyński <mateusz.kruszynski@gmail.com>
"""
from .data_raw_write_proxy import DataRawWriteProxy, SamplePacket
BUF_S... |
e3bdeb2adb89089de4e79d794725855a439a65f22bcdaa44044fe609ee4ecfd7 | Python | 1,269 | 33 | import logging
from typing import Callable, Optional
class GlobalTrigger(object):
"""
Global trigger class, designed to trigger the exit of a feature manager loop when triggered
The class has a simple boolean attribute that allows you to test the defined triggers to determine which one has
triggered t... |
4d3920a98c2b945a46f4fbedadad3d58eddc7a86bbad89f08ec4a794ce30d075 | Python | 1,271 | 44 | from pl_bolts.utils import _PIL_AVAILABLE, _TORCHVISION_AVAILABLE
from pl_bolts.utils.warnings import warn_missing_pkg
if _TORCHVISION_AVAILABLE:
from torchvision.datasets import EMNIST
else: # pragma: no cover
warn_missing_pkg("torchvision")
EMNIST = object
if _PIL_AVAILABLE:
from PIL import Image
e... |
776230cdcaf8bda95a6ba2bc4162ca678e629ca9a6815769045c64f28a76422b | Python | 1,271 | 39 | """Phase 5(a): identity / pass-through ordering in EXHAUSTIVE mode."""
from __future__ import annotations
import torch
import torchlens as tl
class IdentityChild(torch.nn.Module):
"""Module with an identity child followed by a parameterized child."""
def __init__(self) -> None:
"""Initialize child... |
8d692bd490cfbd1943e25e1024902d8d0633adc8bd19acdae82538ace1228f06 | Python | 1,271 | 48 | def main():
import os
from importlib import resources
import sys
import logging
from PyQt6 import QtGui, QtWidgets
from bmicro.gui.main import BMicro
from bmicro._version import version as __version__
"""
Starts the BMicro application and handles its life cycle.
"""
app = Q... |
bbaa067c2024cdbcf5aec91a55cd4780768cbe85decd4e49ac4edb21fdb92751 | Python | 1,271 | 49 | import os
import sys
from os import system
from shutil import copyfile
def sh(script):
system("bash -c '%s'" % script)
model_tree_stk = sys.argv[1]
cmfinder_fa = sys.argv[2]
path = sys.argv[3]
gapCmd = ""
gapVal = ""
if len(sys.argv) > 4:
gapCmd = sys.argv[4]
gapVal = sys.argv[5]
cmd = " cp -f %s mod... |
c9b6646f96b62aba85aa30aca35874699ed21ff0caaab6a5a8863cf2fbc28d25 | Python | 1,271 | 41 | """
Inspect command waveform synthesis for a trouble ABF.
https://github.com/swharden/pyABF/issues/81
"""
import os
import sys
PATH_HERE = os.path.abspath(os.path.dirname(__file__))
PATH_DATA = os.path.abspath(PATH_HERE+"../../../data/abfs/")
PATH_SRC = os.path.abspath(PATH_HERE+"../../../src/")
sys.path.insert(0, PAT... |
1e3246c32d2d00ae4804ed4983109e77597102bd52d0f3c155fbf8d39189940d | Python | 1,272 | 38 | import sys
from ij import IJ
# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
input = sys.argv[-6]
equalize_histogram = sys.argv[-5] == "yes"
saturated_pixels = sys.argv[-4]
normalize = sys.argv[-3] == "yes"
tmp_output_path = sys.argv[-2]
output_datatype = sys.argv[-1]
#... |
b1594b5d0bc37ebd344c3cea04a0765d83902f26d1fa5e432571bff12467f314 | Python | 1,272 | 34 | """
This module create TransformerClassifPerProt
"""
# pylint: disable=W0223
import torch.nn as nn
from torch.nn.modules.normalization import LayerNorm
class TransformerClassifPerProtLayerNorm(nn.Module):
"""
This class define a Transformer model that classify an entire protein to ONE classe
"""
def ... |
bb3cab9c77994277b8d2399fb87130f8d58a5b121bd0df237bb2444dc6843196 | Python | 1,272 | 59 | """add workflow_invocation_completion table and on_complete column
Revision ID: 9930b68c85af
Revises: 312602e3191d
Create Date: 2026-01-03 12:00:00.000000
"""
from sqlalchemy import (
Column,
DateTime,
ForeignKey,
Integer,
JSON,
)
from galaxy.model.migrations.util import (
add_column,
cr... |
e1453db8ba887b6299d15bc3420471a99526109cc831c6de2007d070a6cc5b1b | Python | 1,272 | 40 | from torch import nn
from pl_bolts.utils.self_supervised import torchvision_ssl_encoder
class MLP(nn.Module):
def __init__(self, input_dim=2048, hidden_size=4096, output_dim=256):
super().__init__()
self.output_dim = output_dim
self.input_dim = input_dim
self.model = nn.Sequential... |
5fdc70e0fa2ec64c25c9a3fddc8fd96ef807733dfc7943abcd387fb8e8c99733 | Python | 1,273 | 34 | import sqlite3
from .db import DB
class DistrictDetailsTable(DB):
def __init__(self):
self.table_name = "TN_district_details"
self.table_desc = "Tamil Nadu district wise details, table on pages 3, 4 and 6"
self.cols = self.getcolumns()
def getcolumns(self):
cols = {
... |
63b04b30965d0b29cca6b578ce391320535e2ab4fde37bacfadd307016f270d1 | Python | 1,273 | 57 | #!/usr/bin/env python
import json
import sys
import collections
# this script takes one argument the name of a json file.
# it converts the old style "inputA", "inputB" to the new style
# "inputs[]" for the testing fields in the json. Example of the change
# below:
# "tests" : [ {
# "tag" : "2d",
# "descripti... |
796a2fa19109a29b4416b52c6250788abb43c52cde4943e2e3c86e4dbfad1525 | Python | 1,273 | 44 | # ruff: noqa: E402
from plotly import optional_imports
# Require that numpy exists for figure_factory
np = optional_imports.get_module("numpy")
if np is None:
raise ImportError(
"""\
The figure factory module requires the numpy package"""
)
from plotly.figure_factory._dendrogram import create_dendro... |
d06deadf3af5c906ef7a6eb81798a4a4ef130b8f12d8df64e7481a7c67d098f0 | Python | 1,273 | 48 | class DH_Cell(object):
def __init__(self, cell_file):
from neuron import h
h.load_file('stdrun.hoc')
self.load_cell(cell_file)
self.x = 0
self.y = 0
self.z = 0
self.all_list = []
def _xtra_(self):
for sec in self.all_list:
sec.insert('xtra')
from neuron import h
h.load_file("interpxyz.hoc") ... |
d2ffd42b07fb706de01e9c0b3c227fd4c4383baefd0189b651c0e7f060b2df84 | Python | 1,273 | 38 | from sklearn.model_selection import train_test_split
from sklearn.feature_extraction.text import CountVectorizer
import imodelsx.data
import imodelsx.augtree.utils
def convert_text_data_to_counts_array(
X_train, X_test, ngrams=2, all_ngrams=True,
tokenizer=None,
):
if tokenizer == None:
tokenizer ... |
064950da46fb80b3c9d2885d248882628e5fdb89401f564e6240929875c767c1 | Python | 1,274 | 38 | """
This module define the ensembling model class
"""
import torch
import torch.nn as nn
import logging
class EnsemblingModel(nn.Module):
"""
This class allow you to make ensembling model
"""
def __init__(self, list_of_model):
super(EnsemblingModel, self).__init__()
self.list_of_model... |
cd6ec1b9454c5c6522bf50deff7037dc8dc6af94a932d497b7d3f85ccea6cb7f | Python | 1,274 | 44 | import pandas as pd
def remove_cmp_formatting(s):
"""
Used in read_cmp() to remove formatting in .cmp file
Parameters
----------
s: str
one line in the file
Returns
-------
list of strings
"""
for r in (('\t', ' '), ('\n', ''), ('elec', '')):
s = s.replace(*r)
... |
d02ebde8c033eab361b66460f8d0289e61eff476477631e694baad5cbe1023ad | Python | 1,274 | 55 | from neuron import h, gui
import numpy as np
def test_voltage_access():
s = h.Section()
s.insert("accessors")
h.finitialize()
v = s(0.5).v
vinst = s(0.5).accessors.get_voltage()
# The voltage will be consistent right after
# finitialize.
assert vinst == v
for _ in range(4):
... |
d23215f0b094a74a33dc352943915aeec322bd1dca167ceac91f39cdc6a2d407 | Python | 1,274 | 38 | import shutil
import tempfile
import time
from PyQt6 import QtCore
TMPDIR = tempfile.mkdtemp(prefix=time.strftime(
"pyjibe_test_%H.%M_"))
def pytest_configure(config):
"""
Allows plugins and conftest files to perform initial configuration.
This hook is called for every plugin and initial conftest
... |
26365cd30b4bdbbfff5323e0704b55cfd086d934b3d4b42345bd45689cc9aa0d | Python | 1,275 | 43 | from prodict import Prodict
import matplotlib.pyplot as plt
from sklearn import metrics
import utils
import pandas as pd
import numpy as np
def plot_loss_curves(cfg: Prodict) -> None:
"""Plots Loss and R2 curves during model training.
Parameters
----------
cfg : Prodict
A configuration file d... |
4a3a874bff7012df3e2f75431844f72e0e354f87d316c1e8de6b322b637e2ffd | Python | 1,275 | 49 | import numpy as np
def ar1(alpha=0.74):
"Simple auto-regression model"
randn = np.random.randn
prev = randn()
while True:
res = prev * alpha + randn()
prev = res
yield res
from collections import deque
def ar_process(noise, p):
buff = deque()
memlen = len(p)
for... |
4f4682901947283410938231b3cb9bfcdac4aa75357b740645ed86c97459eb83 | Python | 1,275 | 40 | import sys
from typing import TYPE_CHECKING
if TYPE_CHECKING:
from ._error_x import ErrorX
from ._error_y import ErrorY
from ._fillgradient import Fillgradient
from ._fillpattern import Fillpattern
from ._hoverlabel import Hoverlabel
from ._legendgrouptitle import Legendgrouptitle
from ._li... |
a5d6c62cfcb8e2daf1c4e363e4ec6a39f5a08618160ff58918c961de56ccad67 | Python | 1,275 | 42 | import numpy as np
from fun_h import fun_h
from fun_dh import fun_dh
from fun_ddh import fun_ddh
# import random
# from fun_dtheta import fun_dtheta
def fun_ddtheta(x):
# the second order deriative of the bump function
# theta(x) = h(1-x)./(h(1-x)+h(x-1/4))
# that is
# thet... |
f60de79a5dd334e8881472c90e28793d3c56ba70c97a69a92d0cb6b66a10c386 | Python | 1,275 | 38 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Tests for triangle counting"""
import unittest
from scipy.special import comb
from sknetwork.data import karate_club
from sknetwork.data.parse import from_edge_list
from sknetwork.data.test_graphs import *
from sknetwork.topology.triangles import count_triangles, get... |
92cbc017078864ca74adad9edeb40364accd09b4bf52c9b7c96c5fe76fc9114b | Python | 1,276 | 39 | # 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 in writin... |
29d7c436848c0fcf1cf2123669d7995d86461e77f9882fe12a9406aed13459d9 | Python | 1,277 | 41 | from .hsmm_model import HSMM
def flatten_hsmm(hsmm):
assert all(v[-1] == 1 for v in hsmm.distance_distributions.values())
to_split = {
k: len(hsmm.distance_distributions[k])
for k in hsmm.states
if len(hsmm.distance_distributions[k]) > 1
}
new_initial = modify_flattened_inflo... |
2a2abe731d9850cf85174a3c5e4aac27fa9c4fc5e2ed506b5fca2209cc2cf61b | Python | 1,277 | 36 | from pathlib import Path
from setuptools import setup, find_packages
import sys
lines = (Path(__file__).parent / "mne_ari" / "__init__.py").read_text().splitlines()
for line in lines:
if line.startswith("__version__"):
version = line.split("=")[1].strip().strip("\"")
break
else:
raise RuntimeEr... |
e5ccd89b9a3d8cb7e6ce7a951d79811943411294c6946c0071f7a0138b571b3e | Python | 1,277 | 36 | import pytest
import gym
from gym import spaces
from gym.wrappers import TimeAwareObservation
@pytest.mark.parametrize("env_id", ["CartPole-v1", "Pendulum-v1"])
def test_time_aware_observation(env_id):
env = gym.make(env_id, disable_env_checker=True)
wrapped_env = TimeAwareObservation(env)
assert isinst... |
b09c7aa76469e8822aae7236d3f28af8ba79ed359ab80d9e6f5fd3aed5660367 | Python | 1,279 | 38 | import io
class KerasSaveable:
# Note: renaming this function will cause old pickles to be broken.
# This is probably not a huge deal, as pickle should not be a recommended
# saving format -- it should only be supported for use with distributed
# computing frameworks.
def _obj_type(self):
... |
644c92f3eb7ff5f82e2e7d9d193787a895d3c2f24eeb4608a49536ec5df3274f | Python | 1,280 | 42 | #!/usr/bin/env python
"""
Uses the python csv library to convert to and from tabular
usage: %prog [--from-tabular] -i in_file -o out_file
"""
import argparse
import csv
def main():
usage = "Usage: %prog [options]"
parser = argparse.ArgumentParser(usage=usage)
parser.add_argument("-f", "--from-tabular", ... |
b46b3975ce7c9e43d94fb6a84f0e0c87ea0c271131f9f24d5b9bc984e3703f96 | Python | 1,280 | 35 | import tensorflow as tf
import numpy as np
import cvnn.layers as complex_layers
from pdb import set_trace
def all_layers_model():
"""
Creates a model using all possible layers to assert no layer changes the dtype to real.
"""
input_shape = (4, 28, 28, 3)
x = tf.cast(tf.random.normal(input_shape), ... |
5729e75e91ae56615b6d5ec194aadbe19a026440532778d9a4e976e633ab7627 | Python | 1,281 | 44 | """
.. _exa-dataset:
Dataset basics
==============
"""
# Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
from eelbrain import *
import numpy as np
###############################################################################
# A dataset can be constructed column by column, by adding one variable after
# anot... |
71711304736fecfdd1a084242943677a233ff3800521ac837e965cbbb859beb4 | Python | 1,281 | 47 | import numpy as np
import torch
from torch_geometric.data import Data
from data_loading.loading_utils import train_scaler, scale_dataset, select_target_id
TARGET_ID_TO_PROPERTY = {
0: 'E1-CC2',
1: 'E2-CC2',
2: 'f1-CC2',
3: 'f2-CC2',
4: 'E1-PBE0/def2SVP',
5: 'E2-PBE0/def2SVP',
6: 'f1-PBE0/... |
7ee48c3f1f71a7b7c21cc833bfff58f0eedf35cc66f6a963e44e76176eb8b7fd | Python | 1,281 | 41 | #!/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://... |
97d97cd093a9c1d9e4de3a7995e148b8e9a4d4426927e79169d9a0e9233f76fb | Python | 1,281 | 52 | import pytest
import rpy2.robjects as robjects
import rpy2.robjects.language as lg
from rpy2 import rinterface
from rpy2.rinterface_lib import embedded
@pytest.fixture(scope='module')
def clean_globalenv():
yield
for name in robjects.globalenv.keys():
del robjects.globalenv[name]
def test_eval(clean... |
a51c145334e329ba70a11b544bd8a41ccefa878ad068a8673f8577ab791eed83 | Python | 1,281 | 45 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
"""
A copy of sample_experiment.py with multiple sessions.
To produce the data directory for this experiment use (make sure
that the directory you specify exists)::
>>> from eelbrain import datasets
>>> datasets.setup_samples_experiment('~/Data', n_segme... |
f5bad1bc76cce3908d1ba222a4b5943855bccf502fbc53d4efe8b947b604aec7 | Python | 1,281 | 50 | from sys import argv
from msp import MSP
msp = MSP()
msp.file = __file__
msp.seed = int(argv[1])
msp.architecture["splicepoint_model_spec"] = dict(
type="BothLSSIModels",
acceptor="model/splicepoint-model-acceptor-1",
donor="model/splicepoint-model-donor-1",
)
density = 0.75**22
msp.architecture["num_mo... |
11ebf193f397590e319d151fa7cfad98769420bf5d83378933341fe85042b10a | Python | 1,282 | 39 | #!/usr/bin/env python
"""Export Parquet as CSV."""
import argparse
import sys
try:
import pyarrow as pa
import pyarrow.csv as csv
import pyarrow.parquet as parquet
except ImportError as exc:
if __name__ == "__main__":
sys.exit("Cannot run conversion: pyarrow is not installed. Install the conve... |
2caf33efcbc0a7b920648c0cba466d5b8c02dbc2742fdedc9e8d71a4e2818353 | Python | 1,282 | 47 | import re
import numpy as np
from matplotlib import pyplot as plt
with open("results/predictability_10000.txt", "r") as f:
results = [re.match("(.*) from (.*) has an R2 of (.*)", line) for line in f.readlines()]
results = [r.groups() for r in results if r is not None]
result_dict = {}
included_regions = ["M1_ac... |
49137bc1863963277862fb4f25198d4e5ee9ae280e9591fd110a973c545568a4 | Python | 1,282 | 42 | """There are lots of UserDict-based classesi n caper/cromwell_backend.py
In this test, only the followings classes with public methods
will be tested.
- CromwellBackendBase
"""
from caper.cromwell_backend import CromwellBackendBase
def test_cromwell_backend_base_backend():
"""Test a property backend's getter... |
df482a05feec97a4dc67c8a19cce398afe0eff93f3825fe96d79a9ffba37bc00 | Python | 1,282 | 44 | """
Similar to logging_to_file.py, but with the `allow_multiple_runs` parameter set to False (which is the default).
This will prevent multiple instances of codecarbon from running at the same time.
We run 5 instances of codecarbon. 4 wil fail and only one will succeed
"""
import multiprocessing
import time
from cod... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.