sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
da09c77850b77ced6a00a7725332a427e0fd88d1c55a08859465736161fa79e7 | Python | 2,051 | 59 | import os
from create_embeddings import create_graphs
import os
from statistics import mean
import pandas as pd
from math import log2
from statistics import mean
import numpy as np
import networkx as nx
import matplotlib.pyplot as plt
from scipy.stats import pearsonr
from IPython.display import display
from networkx.dr... |
4c066557a25964ff61512a154cb4ea90decaf2a899527f59b959d003f27e27ba | Python | 2,053 | 79 | from rdkit import Chem
from rdkit.Chem.SaltRemover import SaltRemover
from rdkit.Chem.MolStandardize import rdMolStandardize
from rdkit import RDLogger
from rules import ATOMIC_NUMBER, METALS_LIST
lg = RDLogger.logger()
lg.setLevel(RDLogger.CRITICAL)
def remove_metals(mol):
mol = Chem.RWMol(mol)
... |
f3489f71606c5e80adcf3fb4d5628636a16d4afefac2bcdb036af4264b80e0dd | Python | 2,053 | 85 | """
Demonstration on the correctness and efficiency of parameter shift gradient implementation
"""
import numpy as np
import tensorcircuit as tc
from tensorcircuit import experimental as E
K = tc.set_backend("tensorflow")
n = 6
m = 3
def f1(param):
c = tc.Circuit(n)
for j in range(m):
for i in ra... |
002cd5b3d209638942d9241be9fac755ee1d19de982c5203e54030e01b996bb7 | Python | 2,059 | 77 | import numpy as np
import pytest
from pandas import (
NA,
Categorical,
Series,
)
import pandas._testing as tm
@pytest.mark.parametrize(
"keep, expected",
[
("first", Series([False, False, True, False, True], name="name")),
("last", Series([True, True, False, False, False], name="n... |
39b6d2517538476a566a31ffff101d8b3003ad4da404a0c30b190357ea150577 | Python | 2,059 | 93 | """ Test functions for linalg module using the matrix class."""
import numpy as np
from numpy.linalg.tests.test_linalg import (
LinalgCase, apply_tag, TestQR as _TestQR, LinalgTestCase,
_TestNorm2D, _TestNormDoubleBase, _TestNormSingleBase, _TestNormInt64Base,
SolveCases, InvCases, EigvalsCases, EigCases, ... |
2c2ce445441bdf6fa81a8cec6c0046e027032b3a4140338b7c66c0435ce2a871 | Python | 2,060 | 69 | """contains code for the generation of distances between all records in a given dataset"""
# from python
import logging
# from dependencies
import tqdm
# from other modules
import big_scape.data as bs_data
import big_scape.genbank as bs_gbk
import big_scape.comparison as bs_comparison
def calculate_distances_mix(
... |
113e0bc8d108df69e0536b8856a47d6f6fcffefc71efafb904fc99a0d762f2c4 | Python | 2,061 | 62 | import re
from pathlib import Path
from typing import List, Optional, Tuple, Union
import numpy as np
from readimc import TXTFile
from ..io.base import FileReaderBase, ImageDimensions
from ..models import IMCFileAcquisitionModel, IMCFileModel, IMCFilePanoramaModel
class TxtFileReader(FileReaderBase):
def __init... |
69f8b8075af5ba7783a5c93e14dd1a2bde3a3467cd94941fef5f5c8d406ce3c7 | Python | 2,061 | 46 | """
Code for creating a multiagent environment with one of the scenarios listed
in ./scenarios/.
Can be called by using, for example:
env = make_env('simple_speaker_listener')
After producing the env object, can be used similarly to an OpenAI gym
environment.
A policy using this environment must output actions in ... |
6ea6a6fc9745a3d6d63c822096dd11be6b3e289c46d70679ce74edac09f979a2 | Python | 2,063 | 70 | import pytest
from pandas import (
Index,
Series,
date_range,
)
import pandas._testing as tm
class TestSeriesDelItem:
def test_delitem(self):
# GH#5542
# should delete the item inplace
s = Series(range(5))
del s[0]
expected = Series(range(1, 5), index=range(1,... |
13bb24e8ed0135c3c03b78bcfa9434519e35cb9646258c3936849917a469a4bc | Python | 2,064 | 59 | # License: GNU Affero General Public License v3 or later
# A copy of GNU AGPL v3 should have been included in this software package in LICENSE.txt.
""" Signature related helpers """
from typing import List
from .path import get_full_path
class Signature:
"""Secondary metabolite signature"""
def __init__(se... |
a0b82d0c4cf4a16b17319ea8a1b139d8e46df2c5cbea59b771d435a2fa6435b1 | Python | 2,066 | 67 | # -*- coding: utf-8 -*-
# @Author : DevinYang(pistonyang@gmail.com)
# This file defind the HybridTransform to handle complex objects.
import abc
from PIL import Image
from torch import nn
from torchvision.transforms import Compose
from torchvision.transforms import functional as pil_functional
from . import function... |
1eb0a795c3add1d68996ce4e17d7fa33a62237f96340bdf6296fb1487762927b | Python | 2,069 | 59 | #!/usr/bin/python
import sys
import os
import commands
import time
import csv
def is_number(s):
try:
int(s)
return True
except ValueError:
return False
if len(sys.argv) != 8:
print 'Incorrect number of arguments:', len(sys.argv)
print 'Usage:', sys.argv[0], '<tf_name> <encoded_... |
8b0779dc40ec1ab8a37d2f47bf11cd41db570655f304fe98c30d18aee655c585 | Python | 2,070 | 71 | import logging
import time
import cv2
import numpy as np
from app.recording.camera_recorder.source.base_source import CameraSource
from util.trace import Trace
logger = logging.getLogger("grimace_box."+__name__)
class FileCameraSource(CameraSource):
@Trace.trace(logger)
def __init__(self, video_file: str):... |
0beaf0353bf916d52fa37a1607c5cdaae08e6bf5d01dfe91f494585fa255006d | Python | 2,071 | 65 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.core.arrays import FloatingArray
from pandas.tests.arrays.masked_shared import (
ComparisonOps,
NumericOps,
)
class TestComparisonOps(NumericOps, ComparisonOps):
@pytest.mark.parametrize("other", [True, False, p... |
a13ade26a76e2bda6e49921544958ccfa439e30bf1a66b41363ae0a0d281b137 | Python | 2,071 | 58 | import pytest
import numpy as np
from yass import geometry
from yass.geometry import (parse, find_channel_neighbors,
n_steps_neigh_channels)
from yass.threshold import detect
def test_can_load_npy(path_to_npy_geometry):
geom = geometry.parse(path_to_npy_geometry, n_channels=10)
asse... |
054d42db5e37f47468ef21f54ac37d99ee960833e93b0450dfb6693700cca82c | Python | 2,074 | 64 | """
An enhanced distutils, providing support for Fortran compilers, for BLAS,
LAPACK and other common libraries for numerical computing, and more.
Public submodules are::
misc_util
system_info
cpu_info
log
exec_command
For details, please see the *Packaging* and *NumPy Distutils User Guide*
secti... |
abb2ad970e29d15f4d167ed87bed01d8727c112badebd3712a833f3991510690 | Python | 2,074 | 57 | import pickle
from pathlib import Path
import zipfile
import tempfile
import cv2
from multiprocessing import Pool
from tqdm import tqdm
from crystal_tracer.algorithm.detection import frame_detection
flood_folder = Path('../../data/case1/flood')
flood_folder.mkdir(exist_ok=True)
detection_folder = Path('../../data/cas... |
ef21d5a7c747797348dd5a00c8d4d4d91864965f08eb0a249d95b6313e8e0e13 | Python | 2,074 | 65 | import torch
import torch.nn as nn
from torch.nn import TransformerEncoderLayer
from omegaconf import DictConfig
from .base import BaseModel
class GraphTransformer(BaseModel):
def __init__(self, cfg: DictConfig):
super().__init__()
self.attention_list = nn.ModuleList()
self.readout = cf... |
87028867c85110b2660ba9d23b70e6c1ef3dc187e62dac36d833e39c8ee9e2b5 | Python | 2,075 | 62 | import pytest
import torch
from nablaDFT import model_registry
from schnetpack.data.loader import AtomsLoader
from torch_geometric.data import Batch
from tests.decorators import withCUDA
@withCUDA
@pytest.mark.model
@pytest.mark.parametrize(
"model_name",
[
"DimeNet++",
"Equiformer-v2",
... |
cfd5755227bdf87e72c0acc27585f8171bef3aad72ec8de41befdf3696ec3574 | Python | 2,077 | 73 | # ||AUM||
import scipy.io as spio
import scipy as sp
import numpy as np
from fmri_methods_sipi import rot_sub_data
from surfproc import view_patch_vtk, patch_color_attrib
from dfsio import readdfs
import os
import glob
from brainsync import normalizeData, brainSync
from sklearn.manifold import MDS
import matplotlib.pyp... |
ffe1546257ef5dd94b63f36665af8cc275d6acbfb9b9df8200156ee333fefaea | Python | 2,078 | 55 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from rna3db.utils import read_json, to_case_insensitive
from rna3db.parser import parse_file
from pathlib import Path
from tqdm import tqdm
import argparse
def main(args):
data = read_json(args.input_json_path)
num_chains = sum(
len(i.keys()) for s in dat... |
b4456abc7e39104d74647a09cab20fa0932148a6017cda2a538d71628adfadbe | Python | 2,079 | 57 |
import numpy as np
import csv
# sklearn does things differently and pylint doesn't like that
# pylint: disable=no-name-in-module
from sklearn.model_selection import train_test_split
# pylint: enable=no-name-in-module
# CONFIGURATION OPTIONS
''' change these as desired '''
csv_filename = 'full_set.csv' # the ... |
35ebf3a3bfa0bcc8394af2f7460eba6ff5327d517a89fc3fa81f43e88327f020 | Python | 2,080 | 84 | # -*- coding: utf-8 -*-
"""
Script for randomly separate all the auditory stim of this protocol into
4 sets of 72 stimuli, with 12 of each category per set
author: Juan Jesus Torre Tresols
e-mail: juan-jesus.torre-tresols@inria.fr
"""
import os
from random import shuffle
import shutil
# %% PARAMETERS
... |
c3df007de9ee994b37c4fa0eaf2fa0a86529564e05a217bf45afc3bd95824fcd | Python | 2,083 | 121 | # Copyright (C) 2012-2014,2016-2018 Bernd Feige
# This file is part of avg_q and released under the GPL v3 (see avg_q/COPYING).
"""
Utility module defining global default channel sets
"""
import collections
# This is for finding EEG channels given a generic name such as 'C3'
# Note that the order is significant: The f... |
accbddd0add6ecddb8aa7ed0fed4e4bdbcfb74e7a622fdf0f3d86d85ce9ce58d | Python | 2,084 | 68 | from datetime import timezone
import numpy as np
import pytest
from pandas import (
DataFrame,
Series,
date_range,
)
import pandas._testing as tm
class TestTZLocalize:
# See also:
# test_tz_convert_and_localize in test_tz_convert
def test_tz_localize(self, frame_or_series):
rng = da... |
507d701dc607d84c05b27994b8abef26a0b52b1fef40cfbc9d1b24b6a6d2e605 | Python | 2,085 | 83 | # !/usr/bin/python
# -*- Mode: Python; tab-width: 4; py-indent-offset: 4; -*-
#
# An OpenGL movie class with buffer (buffermovie.py)
#
# 01-09-2009: sn
# A movie class with buffer
#
import sys
from string import *
import pygame
from pygame.locals import *
class buffermovie:
"""
A class to load and store movie (... |
c69f11cd08272d3f163c0388e351d6e2b06fd735aa14d8b7d94f0ea905bacd36 | Python | 2,089 | 61 | from rdkit import Chem, DataStructs
from rdkit.Chem import AllChem
import numpy as np
import os
class Molecule(object):
def __init__(self, sid, smiles):
self.sid = sid
self.smiles = smiles
mol = Chem.MolFromSmiles(smiles)
if any(a.GetSymbol() in ('B', 'Si') for a in mol.GetAtoms()):... |
302ae2df8eaaa356d8c23966df6c47472465f9b00835395f548b9b37a1c3cfaf | Python | 2,090 | 71 | import sys
from numpy.distutils.fcompiler import FCompiler, dummy_fortran_file
from sys import platform
from os.path... |
96eb6f42dd99f0f956b127e57e93d87b4c9dd6fea42e7d4626e56236f256a545 | Python | 2,090 | 41 | # License: GNU Affero General Public License v3 or later
# A copy of GNU AGPL v3 should have been included in this software package in LICENSE.txt.
# for test files, silence irrelevant and noisy pylint warnings
# pylint: disable=no-self-use,protected-access,missing-docstring
import unittest
from antismash.common.sec... |
2331e8a9d1a63fb0cccb274f74c42a24b00028be604459e2660977d0ab7bd97a | Python | 2,091 | 51 | # -*- coding: utf-8 -*-
import numpy as np
def select_probetype(nsentence_cond, cond_names, dataframe, word_present,
word_absent):
"""
Selection of type of probe, i.e., word_present or word_absent
The probe scattering is the following:
b = 0, 2, 4: for #nb_sentence_cond = [0;nb_s... |
d2f824db6504803f482460807cc2aed536e4fb6197359c1e24cfd27926e3405e | Python | 2,091 | 68 | from __future__ import annotations
import argparse # noqa: TC003
import logging
from cli.lib.common.cli_helper import register_targets, RichHelp, TargetSpec
from cli.lib.core.torchtitan.torchtitan_test import TorchtitanTestRunner
from cli.lib.core.vllm.vllm_test import VllmTestRunner
logger = logging.getLogger(__n... |
646196ab76e4564d8f6cd4443a897689b071d3a3e50c3b85c3652ab880053e3f | Python | 2,092 | 71 | # ||AUM||
import scipy.io as spio
import scipy as sp
import numpy as np
from fmri_methods_sipi import rot_sub_data
from surfproc import view_patch_vtk, patch_color_attrib
from dfsio import readdfs
import os
import glob
from brainsync import normalizeData, brainSync
from sklearn.manifold import MDS
import matplotlib.pyp... |
afc4cd685dd66d4be77b8a0951796be4093c3c53c5cf249e5dc3f4f63eda61c2 | Python | 2,092 | 65 | """Created on Wed Mar 2 17:26:43 2022.
@author: dpm42
"""
import json
import os
import numpy as np
def get_activation(
filepath,
delta_V: float = 60,
rounding_precision: int = 5,
plot: bool = False,
plot_nodes_on_find: bool = False,
plot_compiled: bool = False,
absolu... |
b66304a3e2a30eebb1a47cdb66e1b52fbc76375f504f5a0d53c5dfd8f97f7581 | Python | 2,092 | 74 | from __future__ import annotations
import click
import numpy as np
from .. import set_log_level
from ..tasks import asynchronous as asynchronous_task
from ..tasks import baseline as baseline_task
from ..tasks import isochronous as isochronous_task
from ..tasks import synchronous as synchronous_task
from ..tasks._conf... |
3ac6dabe62d1c4a34d6d5f129cf11cde654d93d10856332165e46cf67094b135 | Python | 2,093 | 40 | """
Create the numpy._core.umath namespace for backward compatibility. In v1.16
the multiarray and umath c-extension modules were merged into a single
_multiarray_umath extension module. So we replicate the old namespace
by importing from the extension module.
"""
import numpy
from . import _multiarray_umath
from ._m... |
5f8917169228c9f732995d0e4498a6e18fa470ebdb6ad7806b0b4bcff947e652 | Python | 2,093 | 68 | from ase.calculators.calculator import Calculator
from Calculators.device_strategy import DeviceStrategy
from Calculators.bonded import DLBondedCalculator
from Calculators.combiner import DipeptideCombiner
from Calculators.nonbonded import MMNonBondedCalculator
from Calculators.pme import PMENonBondedCalculator
from u... |
d2b36d96b7a43b0472899d29bd63d07066f58a959ccb848e22374f90949b4b38 | Python | 2,093 | 41 | # License: GNU Affero General Public License v3 or later
# A copy of GNU AGPL v3 should have been included in this software package in LICENSE.txt.
# for test files, silence irrelevant and noisy pylint warnings
# pylint: disable=no-self-use,protected-access,missing-docstring
import unittest
from antismash.common.sec... |
85ad4755176c4427f121f7ab33115cf3156530bac941103f9c85b132631b45d9 | Python | 2,094 | 73 |
import sys
sys.path.append('.')
from plotting.utils import load_results, mesh_name, sim_name, m3topl
import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
import yaml
import pandas as pd
import matplotlib.gridspec as gridspec
sns.set_theme()
sns.set_style(style='ticks')
m32fl = 1e18
m2nm = 1e9
m2... |
61bd0739179cff070457744d354e116679404d84d442d8c01cc6262f8a6f34bb | Python | 2,096 | 55 | from numpy._core import _multiarray_umath
from numpy import ufunc
for item in _multiarray_umath.__dir__():
# ufuncs appear in pickles with a path in numpy.core._multiarray_umath
# and so must import from this namespace without warning or error
attr = getattr(_multiarray_umath, item)
if isinstance(attr,... |
a99a2b00f23fa16733e5674112bd2742e4ff9ab0294e04a1aa0dc9565ce954a5 | Python | 2,096 | 77 | from datetime import (
datetime,
timedelta,
)
from pandas import (
DatetimeIndex,
NaT,
Timestamp,
)
import pandas._testing as tm
def test_unique(tz_naive_fixture):
idx = DatetimeIndex(["2017"] * 2, tz=tz_naive_fixture)
expected = idx[:1]
result = idx.unique()
tm.assert_index_equa... |
e81887c7108d5c1be2f3be9a4d8e458fc4dc65c3222818a3ce6e9bf46e372df7 | Python | 2,097 | 83 | # !/usr/bin/python
# -*- Mode: Python; tab-width: 4; py-indent-offset: 4; -*-
#
# An OpenGL movie class with buffer (buffermovie.py)
#
# 01-09-2009: sn
# A movie class with buffer
#
import sys
from string import *
import pygame
from pygame.locals import *
class buffermovie:
"""
A class to load and store movie (... |
069303ab0f99193fad1d424dee4e97a16cf61f8eac06a4b19a8ba9a5b58c1ec5 | Python | 2,098 | 80 | import numpy as np
import pandas as pd
from pandas import (
DataFrame,
Index,
)
import pandas._testing as tm
def test_pipe():
# Test the pipe method of DataFrameGroupBy.
# Issue #17871
random_state = np.random.default_rng(2)
df = DataFrame(
{
"A": ["foo", "bar", "foo", "... |
21f3ed40e2df2c9e7284e2b897c80ef567e820369efd98b30b7429e8c5528209 | Python | 2,101 | 60 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sun Aug 25 20:29:36 2019
@author: charleshen
@note: this code derived from PybioMed<https://github.com/gadsbyfly/PyBioMed>, with a major modified
This module mainly implements the calculation of MOE-type descriptors, which include LabuteASA, TPSA, slogP... |
b735870a11b6a1c3e7d862f8cd61ab376ebf777b3aae403638ce0c7240094694 | Python | 2,102 | 61 | import shutil
import zipfile
import argparse
from pathlib import Path
import deeplake
import numpy as np
import requests
from tqdm import tqdm
from src import constants
def parse_arguments():
parser = argparse.ArgumentParser()
parser.add_argument("-p", "--path", default=constants.sensorium_dir, type=Path)
... |
5b12a128142d0f69869987d8211ddb440e7b58e580004bfe42302fe2f3ac4ce3 | Python | 2,106 | 64 | """
Small PySCF -> TenCirPauli -> TensorCircuit/JAX VQE bridge example.
This is a short integration preview. For the complete chemistry workflow,
correctness checks, and benchmark study, see:
https://github.com/tensorcircuit/TenCirPauli/blob/main/examples/quantum_chemistry_pyscf.py
"""
from __future__ import annotati... |
5cdb5d2e8df74954e341b5de8a62c56b966e773a441309df241368ad56f1bb27 | Python | 2,106 | 95 | """
``numpy.linalg``
================
The NumPy linear algebra functions rely on BLAS and LAPACK to provide efficient
low level implementations of standard linear algebra algorithms. Those
libraries may be provided by NumPy itself using C versions of a subset of their
reference implementations but, when possible, high... |
6e51ae23d5742f0002b14dbf658f244b193f01e86dbcf47fc3b18a4142a64a9c | Python | 2,106 | 41 | from qcportal import PortalClient
from qcportal.singlepoint import QCSpecification, SinglepointDatasetNewEntry
from qcportal.molecules import Molecule
from qcportal.utils import chunk_iterable
from openmm.unit import nanometer, bohr
import openff.toolkit
import numpy as np
import h5py
import sys
dataset_name = sys.arg... |
b34333ddb0233eba59b272b186c9332bb9d909bbc53d26646814c17837a986a7 | Python | 2,110 | 68 | import time
def wait_for_data(tbvNetInt, wait_time):
"""
Control function
Waits for all correct initial parameters to run the thermometer.
Args:
tbvNetInt: TBVNetworkInterface instance
wait_time: float - sleep time in seconds
Returns:
n_rois: int - number of ROIs in TB... |
d6c7717222846d2b4707457eabd4f6df63fa834acfe831eb6f280fd076dd0e20 | Python | 2,112 | 64 | import numpy as np
import matplotlib.pyplot as pl
from matplotlib.ticker import MaxNLocator
# TODO: Add docstrings
def principal_curve(adata):
"""TODO."""
X_curve = adata.uns["principal_curve"]["projections"]
ixsort = adata.uns["principal_curve"]["ixsort"]
pl.plot(X_curve[ixsort, 0], X_curve[ixsort, ... |
ebbac332d64f2a20598ade62e683a59033b944ff531cf4f5985e3d2f9557a0f4 | Python | 2,112 | 70 | """
======================================================================
ShinGLMCC_fig.py
Author: Yasuhiro Tsubo (tsubo@fc.ritsumei.ac.jp)
Version 1.0: 2024.07.13
Version 2.0: 2024.08.28
* Adjusted the script's argument format to match that of ShinGLMCC_main.py.
* Modified the program to avoid the "SettingWithC... |
ebe95b35b6930f6a605d6676a4daf3a5b8ce8a3600d767b5643577d5c8c3d81c | Python | 2,112 | 65 | # License: GNU Affero General Public License v3 or later
# A copy of GNU AGPL v3 should have been included in this software package in LICENSE.txt.
"""Gene finding using GlimmerHMM
mostly for fungi/eukaryotes
"""
from io import StringIO
import logging
from helperlibs.bio import seqio
from helperlibs.wrappers.io ... |
3b8d3fdff44d63e1de5e0c95819030d556d053282b4c640871c9f55b70de9e19 | Python | 2,114 | 72 | import matplotlib.pyplot as plt
import pandas as pd
import numpy as np
from tqdm import tqdm
from joblib import load, dump
import time
from molmap import dataset
from molmap import loadmap
from molmap import model as molmodel
import molmap
#use GPU, if negative value, CPUs will be used
import tensorflow as tf
import... |
50a53fb79a086bf91532ff3d62cf4a37a67f172e5b7aa3c352c0c058f99ca11f | Python | 2,114 | 79 | import pytest
import subprocess
import json
import sys
from numpy.distutils import _shell_utils
from numpy.testing import IS_WASM
argv_cases = [
[r'exe'],
[r'path/exe'],
[r'path\exe'],
[r'\\server\path\exe'],
[r'path to/exe'],
[r'path to\exe'],
[r'exe', '--flag'],
[r'path/exe', '--fla... |
c97505e83ac38623ca11f11724b9dbef56d99f271ba3808a5e4975e15cafdd06 | Python | 2,114 | 78 | """
Tests that work on both the Python and C engines but do not have a
specific classification into the other test modules.
"""
from io import StringIO
import numpy as np
import pytest
from pandas import (
DataFrame,
option_context,
)
import pandas._testing as tm
pytestmark = pytest.mark.filterwarnings(
... |
b942a6a141cde51d5cf8f07406d03e8da166ec4a92511826807f27849780bf36 | Python | 2,117 | 51 | # License: GNU Affero General Public License v3 or later
# A copy of GNU AGPL v3 should have been included in this software package in LICENSE.txt.
""" A more detailed Domain feature """
from collections import OrderedDict
from typing import Dict, List
from typing import Optional # comment hints, pylint: disable=unu... |
bbbd9c3d4b17b5c7257615229e95f1295dc6612ecab823431bfa75e57dff9ff1 | Python | 2,121 | 61 | import pandas as pd
import numpy as np
import os, sys, shutil, importlib, glob
from tqdm.notebook import tqdm
import celloracle as co
from celloracle import motif_analysis as ma
from genomepy import Genome
import scanpy as sc
def decompose_chrstr(peak_str):
"""
Args:
peak_str (str): peak_str. e.g. 'chr... |
5bdcb020107d0ca5ce6e93b08477d47fe60f71b9c03ace3e0934183fec9ccacd | Python | 2,122 | 66 | # -*- coding: utf-8 -*-
"""
Created on Mon Jan 7 17:27:25 2019
@author: bxin
"""
import sys
import os
import argparse
import numpy as np
import h5py as h5
import CNN_utils_deeplift as util
datadir = "../data/SELEX_"
def main():
args = loadargs()
for tf in args.tfs:
if "train" i... |
6322e4db6fcfc8a6412aac595cbbe07646fef21dd41d07a22713601a858c2ae0 | Python | 2,122 | 64 | import os, gdown, zipfile, pickle
def download_file_from_google_drive(file_id, destination):
url = f"https://drive.google.com/uc?id={file_id}"
try:
gdown.download(url, destination, quiet=False)
print(f"File downloaded successfully to {destination}")
except Exception as e:
prin... |
aa783f82f57b3923995770a94180af9831232063f4b22e5dc321086e1898ba54 | Python | 2,124 | 60 | # License: GNU Affero General Public License v3 or later
# A copy of GNU AGPL v3 should have been included in this software package in LICENSE.txt.
"""Identify TTA codons in BGCs"""
from typing import Any, Dict, List, Optional
from antismash.common.secmet import Record
from antismash.config import ConfigType
from an... |
768c084cd5771b1abcc01dd776a8b2442b440e7f37fc690b706262427cccd660 | Python | 2,125 | 87 | __all__ = [
"dtypes",
"localize_pydatetime",
"NaT",
"NaTType",
"iNaT",
"nat_strings",
"OutOfBoundsDatetime",
"OutOfBoundsTimedelta",
"IncompatibleFrequency",
"Period",
"Resolution",
"Timedelta",
"normalize_i8_timestamps",
"is_date_array_normalized",
"dt64arr_t... |
448d3ca52ae6e6d052ccf32f9db4ea6c3f5621a95a3a837977833545398bab56 | Python | 2,128 | 76 | CONSOLE_HTML_FORMAT = """\
<!DOCTYPE html>
<html>
<head>
<meta charset="UTF-8">
<style>
{stylesheet}
body {{
color: {foreground};
background-color: {background};
}}
</style>
</head>
<body>
<pre style="font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace"><code style="font-family:inherit">{c... |
d61d671e103c04ba5bb844c4f14a70eea946dc549ff95eded4d9533dc52a94e7 | Python | 2,128 | 54 | from qcportal import PortalClient
import numpy as np
import sys
# Look for suspect records that should be rerun.
dataset_name = sys.argv[1]
client = PortalClient.from_file()
dataset = client.get_dataset('singlepoint', dataset_name)
include_specs = [name for name in dataset.specifications if dataset.specifications[nam... |
bc69d4f72a2bde4cce84fa097aba07360d31f08fbf7fefb122e6d941d42fb493 | Python | 2,129 | 60 | from __future__ import annotations
from stimuli.time import Clock, sleep
from ..detector import _BUFSIZE
from ..utils._checks import check_type
from ..utils._docs import fill_doc
from ..utils.logs import logger
from ._config import BACKEND, SOUND_DURATION, TARGET_DELAY, TRIGGER_TASKS
from ._utils import create_sound,... |
dd30467f7a3c0d97582129cf5c6b0f22543344aa083b7b0f04c1b86d35c93697 | Python | 2,132 | 74 | """
Created on Jun 25, 2024
@author: mning
"""
from dataclasses import dataclass
from math import ceil
import numpy as np
from numpy.random import uniform
from sklearn import metrics
@dataclass
class ScoresTuple:
acc: float = 0.0
sen: float = 0.0
spc: float = 0.0
f1: float = 0.0
roc_auc: float =... |
e4362cfddbb41d93b801493753d09f8c989e277da57e70765caea6a556ba3f78 | Python | 2,132 | 75 | """ Bin a point process by the values in a series
Author: Drew B. Headley
"""
import numpy as np
def bin_ptser(val_pt, bin_ser, edges, func=np.mean):
"""
A points are binned together based on shared corresponding
values in another series and a function is applied.
Parameters
----------
val_... |
222570b26ddc0f09c976b934154161ec92c96049d1fc07d859046a58878e14d4 | Python | 2,133 | 83 | """Tools for testing implementations of __array_function__ and ufunc overrides
"""
from numpy._core.overrides import ARRAY_FUNCTIONS as _array_functions
from numpy import ufunc as _ufunc
import numpy._core.umath as _umath
def get_overridable_numpy_ufuncs():
"""List all numpy ufuncs overridable via `__array_ufun... |
684e42c818fc7aded220607412b162cbeedb78d315c88ee20054cbb2ea0beb12 | Python | 2,133 | 58 |
def train_epoch(model, dataloader, optimizer, criterion, device,epoch):
model.train()
total_loss = 0
for batch in dataloader:
src, tgt, _, _, _, tgt_lens = batch
src, tgt = src.to(device), tgt.to(device)
#print('tgt,tgt.shape',tgt,tgt.shape)
optimizer.z... |
b56ecdefe7ae95cd3e32d6e8b0178b96973075b3e341cca6440046af9a95e39c | Python | 2,133 | 74 | """Example of how to run the full CALI pipeline."""
from pathlib import Path
from sqlmodel import create_engine
from cali.runner import CaliRunner
from cali.sqlmodel import (
AnalysisSettings,
DetectionSettings,
Experiment,
ExtractionSettings,
)
from cali.sqlmodel._visualize_experiment import print_c... |
b4ebee05875c40655847191376f1ecbc5a40a886d7f67eb7ade0bad91eee6d89 | Python | 2,135 | 92 | """
DQAS for GHZ state preparation circuit, deprecated DQAS implementation
"""
import numpy as np
import tensorflow as tf
import cirq
import tensorcircuit as tc
from tensorcircuit.applications.vags import double_qubits_initial, GHZ_vag, GHZ_vag_tfq
from tensorcircuit.applications.dqas import (
set_op_pool,
ge... |
9e67da1425736d5888390dbe323817b7e6cdf148faef8842822c2be48a25fbf5 | Python | 2,136 | 55 | from numpy.testing import assert_
import numpy.distutils.fcompiler
g77_version_strings = [
('GNU Fortran 0.5.25 20010319 (prerelease)', '0.5.25'),
('GNU Fortran (GCC 3.2) 3.2 20020814 (release)', '3.2'),
('GNU Fortran (GCC) 3.3.3 20040110 (prerelease) (Debian)', '3.3.3'),
('GNU Fortran (GCC) 3.3.3 (De... |
78beaefd6108493057a67e7e625db42235ab7fe63ce71e9bfb8eb534e79381d8 | Python | 2,141 | 61 | from wordfreq import tokenize
from wordfreq.preprocess import preprocess_text
def test_transliteration():
# "Well, there's a lot of things you do not understand."
# (from somewhere in OpenSubtitles
assert tokenize("Па, има ту много ствари које не схваташ.", "sr") == [
"pa",
"ima",
... |
a6c754d0d997bda2572715b282230123f57ceb0e1b058d959e0f23f61603532b | Python | 2,142 | 60 | import numpy as np
import scanpy as sc
import decoupler as dc
import scvi
import pandas as pd
# Open the RNA merged and filtered
adata = sc.read_h5ad(snakemake.input.merged_rna_anndata)
doublet_clusters = []
for cluster in adata.obs['leiden_2'].drop_duplicates():
#print(cluster, adata[adata.obs['leiden'] == clust... |
9e2b7f913a5c9999888b2599d8161b2672a06080b9ea02c2032f9a5ddd53b8ea | Python | 2,143 | 94 | from pydantic import BaseModel
from typing import List, Optional, Dict, Any
class TripleResponse(BaseModel):
head: str
relation: str
tail: str
class NodeProperties(BaseModel):
attributes: dict
class NodeConnection(BaseModel):
relationship_type: str
target_node: NodeProperties
class Subgr... |
19d115589d3caf7d41c6ceacbb25b4073b2a12ffa76dab0f52dd89328edcef37 | Python | 2,144 | 76 | import importlib
import sys
import pandas
def test_top_level_import_exposes_lightweight_features():
sys.modules.pop("sbmlcore", None)
sbmlcore = importlib.import_module("sbmlcore")
feature = sbmlcore.AminoAcidMWChange()
df = pandas.DataFrame({"mutation": ["A1D"]})
result = feature._add_feature(... |
2db4bbabf8fb0225817e4d2d55c6043f96125971279ee6b75610a16ce515ed61 | Python | 2,145 | 46 | # License: GNU Affero General Public License v3 or later
# A copy of GNU AGPL v3 should have been included in this software package in LICENSE.txt.
# for test files, silence irrelevant and noisy pylint warnings
# pylint: disable=no-self-use,protected-access,missing-docstring
import unittest
from antismash.common.sec... |
b35a6ddce94afc975671a1ecc65b2f4a1df89aa16c478c2b38d030141a39c95c | Python | 2,145 | 56 | from datetime import timedelta
import numpy as np
from pandas import (
DatetimeIndex,
date_range,
)
import pandas._testing as tm
class TestDatetimeIndexReindex:
def test_reindex_preserves_tz_if_target_is_empty_list_or_array(self):
# GH#7774
index = date_range("2013-01-01", periods=3, tz=... |
95368a973da105238530a1dc3a0fcc73fdefb6b1951f56f5ea38c7d1609f3433 | Python | 2,146 | 48 | #!/usr/bin/env python3
"""
Production Server Runner for iAODE
Serves the static frontend build and API backend together
"""
import uvicorn
import os
import sys
if __name__ == "__main__":
# Ensure we are running from the api directory
# This helps with relative path resolution for static files
current_dir ... |
2a3b15eedb3deb7452c8d1062c64258b2a731c9fe1b37993b2558f3176691a91 | Python | 2,151 | 66 | from __future__ import annotations
import warnings
import numpy as np
import pyarrow
from pandas.errors import PerformanceWarning
from pandas.util._exceptions import find_stack_level
def fallback_performancewarning(version: str | None = None) -> None:
"""
Raise a PerformanceWarning for falling back to Exte... |
1b5183c2602e02ac9dea2eb8c1032b192c87af146bb7a2a2b978d57ff42d7e1e | Python | 2,152 | 59 | import logging
import time
from typing import Optional
import backoff
from sqlalchemy import CursorResult, create_engine, engine, text
class Db:
"""SQLAlchemy database connection."""
def __init__(self, url: engine.URL):
logging.debug("Creating SQL Alchemy engine to database: %s", url)
self._... |
91bf92b536cf3d0fe78d25a2989de55238670a44174e0500d2264dcab5a4d40c | Python | 2,154 | 71 | """Helper functions for tests."""
import zipfile
from pathlib import Path
from nibabel import Nifti1Image
from numpy.testing import assert_allclose
def set_up_cmb_data(zipped_data_path: Path, cmb_path: Path) -> None:
"""Set up the CMB data directory by extracting the contents of a zipped file.
Parameters
... |
c22bda8033b39327665c35e6d93e80fdaed0ccbb4caa2ecf2efb01367c9b8824 | Python | 2,154 | 78 | #!/usr/bin/env python3
"""
PostToolUse hook to automatically add the bot-triaged label after any issue mutation.
This hook runs after successful GitHub issue mutations (label/comment/close/transfer)
and directly applies the `bot-triaged` label via the gh CLI.
Exit codes:
0 - Success
"""
import json
import os
impor... |
c255b699e073b2492b05830bb8b65fb83e1dce472fd78cd85c305754868d7499 | Python | 2,156 | 64 | #!/usr/bin/env python3
"""macOS arm64 build environment setup (runs once per Python before the build).
Mirrors .ci/wheel/linux/build_env_setup.py for the macOS CD wheel build. macOS
needs far less toolchain wiring than the manylinux path: there is no
CUDA/ROCm/XPU split and the heavy deps come from the runner image or... |
654eea52dcd5105806b7dc78841bab6541b268a85b63d2a29c2f89baab821dc6 | Python | 2,157 | 59 | import pandas as pd
import matplotlib.pyplot as plt
import numpy as np
import os
# Create output directory
os.makedirs('paper_graphs/Edge_Weight_Plots', exist_ok=True)
# Read the data
control_df = pd.read_csv('table/CT2_log/concise/control.csv')
deletion_df = pd.read_csv('table/CT2_log/concise/large_deletion.csv')
#... |
98dd45235c026c6a70792b16444d06c2a4c7c5ad3f7d739619ac91e7454c30ff | Python | 2,158 | 61 | import logging
import sys
from pathlib import Path
from typing import Any
from cli.lib.common.cli_helper import BaseRunner
from cli.lib.common.pip_helper import pip_install_packages
from cli.lib.common.utils import working_directory
from cli.lib.core.torchtitan.lib import (
clone_torchtitan,
load_torchtitan_te... |
b85c90c2b394951d7b2255ed4511e25ed9d9bd32778bc84e8ab39de46cd090cc | Python | 2,158 | 63 | from pytest import approx
from wordfreq import word_frequency
from wordfreq.numbers import digit_freq, smash_numbers
def test_number_smashing():
assert smash_numbers("1") == "1"
assert smash_numbers("3.14") == "0.00"
assert smash_numbers("24601") == "00000"
def test_decimals():
assert word_frequency... |
b872c57f55dabf38069d99e61520ccb79e2e86d39322ad63e66ab099d676bdfe | Python | 2,160 | 67 | """Splits data into train, validation, and test sets."""
import csv
import os
import sys
from typing import Tuple
from tap import Tap # pip install typed-argument-parser (https://github.com/swansonk14/typed-argument-parser)
from tqdm import tqdm
from typing_extensions import Literal
sys.path.append(os.path.dirname(... |
729232a5058ebc9eb63bd71675085441c197ccaaf8ae72d3545c8eb167b13921 | Python | 2,161 | 72 | # coding: utf-8
# See notebook:
# https://github.com/paninski-lab/yass-examples/blob/master/batch/multi_channel_apply_disk.ipynb
"""
Applying transformations to large files in batches:
BatchProcessor.multi_channel_apply lets you apply transformations to
batches of data where every batch has observations from every c... |
1205833f3144dcbe74b374f4edc4a96854a475fafd8c826a83c99aa178289526 | Python | 2,162 | 64 | import logging
import json
from rna3db.utils import PathLike, write_json
class Filterer:
def __init__(
self,
min_length: int = 32,
max_resolution: float = 9.0,
single_ratio_cutoff: float = 0.8,
max_unknown_ratio: float = 0.3,
):
self.min_length = min_length
... |
d3ec9a149bddba0117ec71832b193e7b706983a4eb80bcec3e74b216f183ae8b | Python | 2,163 | 80 | """
A plain QAOA optimization example with given graphs using networkx.
"""
import networkx as nx
import tensorflow as tf
import tensorcircuit as tc
K = tc.set_backend("tensorflow")
## 1. define the graph
def dict2graph(d):
g = nx.to_networkx_graph(d)
for e in g.edges:
if not g[e[0]][e[1]].get("wei... |
6edc8df7cf0b6ae20d3db31dbe188df9f816b7b22a9e5a726efaa61e4993b114 | Python | 2,164 | 55 | from scanip_api3 import *
# 2022-06-16 14:52:31 - Background to mask copy
App.GetDocument().CopyBackgroundToMask()
# 2022-06-16 14:52:34 - Background removal
App.GetDocument().RemoveBackground(App.GetDocument().GetBackgroundByName("Stack"))
# 2022-06-16 14:52:38 - Mask renaming
App.GetDocument().GetGenericMaskByName... |
eecfa7de3ca9f9ed22915c6422ac5fdf146dc64dda055e21e45b27308712b4c6 | Python | 2,166 | 86 | """
Tests for the pseudo-public API implemented in internals/api.py and exposed
in core.internals
"""
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.core import internals
from pandas.core.internals import api
def test_internals_api():
assert internals.make_block is api.make_block
d... |
58e35e8aa8cb192728e89fdc521e356cf920133810632ff037cb00bd81c25a0a | Python | 2,167 | 64 | import os
import numpy as np
from pyfaidx import Fasta
from typing import Tuple
def get_chr_seq(genome: str, chrom: int) -> np.ndarray:
genome_seq = Fasta(genome)
if f'chr{chrom}' in genome_seq.keys():
chr_seq = genome_seq[f'chr{chrom}'][:].seq
else:
chr_seq = genome_seq[f'{chrom}'][:].se... |
7e538530a8d9457c66c3aea895355f19c18dc99b3dcff540664185e86c927f43 | Python | 2,167 | 65 | # coding: utf-8
import math
import torch
import torch.nn.functional as F
"""
IMPORTANT NOTE: The cutoff and the switch function are numerically a bit tricky:
Right at the "seems" of these functions, i.e. where the piecewise definition changes,
there is formally a division by 0 (i.e. 0/0). This is of no i... |
87c10a276b741ee3e49845a19b5c60a77cc38c7c25402067d6452c7800603d58 | Python | 2,167 | 68 | import einops
import numpy as np
def Rx(angles_degrees: np.ndarray) -> np.ndarray:
"""Affine matrix for a rotation around the X-axis."""
angles_degrees = np.asarray(angles_degrees).reshape(-1)
c = np.cos(np.deg2rad(angles_degrees))
s = np.sin(np.deg2rad(angles_degrees))
matrices = einops.repeat(
... |
5390aa725685694134695c11caea9acc422e7008b5e997366151e0ac3bb1ea79 | Python | 2,168 | 70 | """Conversion utilities between VTK, PyVista, and Trimesh mesh representations."""
import vtk
from vtk.util.numpy_support import numpy_to_vtkIdTypeArray, numpy_to_vtk
import trimesh
import pyvista as pv
import numpy as np
def trimesh_to_vtk_polydata(mesh: trimesh.Trimesh):
"""Convert a Trimesh object to a VTK Po... |
135bfa1eacb3b2a6f21600afb5da973c9875399cdb41139e489fafd4a7cde03b | Python | 2,173 | 64 | from dfsio import readdfs, writedfs
import os
from surfproc import mean_curvature, view_patch_vtk, patch_color_attrib, smooth_patch
import numpy as np
from scipy.io import loadmat
# load mat file /home/ajoshi/Downloads/c.mat
cmat = loadmat("/home/ajoshi/Downloads/c.mat")
c = cmat["c"]
lsurf = readdfs("/home/ajoshi/... |
0b52ca274cf0376e399ee5b130ac989d83fae44a57bbf37206e48e43b67a7d5d | Python | 2,175 | 63 | """Script to compare two source spaces and check for equality."""
import pickle
from pathlib import Path
from numpy.testing import assert_allclose, assert_array_equal
# Set paths to the reference and new source space files here.
reference_src_path = Path(__file__).parent / "reference_src.pkl"
new_src_path = Path(__f... |
68fead3005869eca070993eedcc68664f8b1b5b0a01b1a3542f6cb3bffacb7a1 | Python | 2,175 | 105 | """
Global constants for the gridworld env.
"""
# =============================================================================
# set the value of interface
# =============================================================================
FPS = 25
WinWidth = 340 #window width
WinHeight = 260 #window width
BoxSize = 20 ... |
d13d32e2d81a052c50b1f2bc426a5bbc2398c4bfe72a7d9c16e53fb877d7d004 | Python | 2,175 | 59 | # License: GNU Affero General Public License v3 or later
# A copy of GNU AGPL v3 should have been included in this software package in LICENSE.txt.
""" Individual tools/methods for detection of gene functions """
import os
from typing import List
from antismash.common.secmet import CDSFeature, Record
from antismash.... |
8181a5f70f5476d71f376e8a531d50c98e268e1e80d26e02b24de0b0221c768b | Python | 2,176 | 72 | import pytest
from pandas import TimedeltaIndex
from pandas.tseries.offsets import (
DateOffset,
Day,
Hour,
MonthEnd,
)
class TestFreq:
@pytest.mark.parametrize("values", [["0 days", "2 days", "4 days"], []])
@pytest.mark.parametrize("freq", ["2D", Day(2), "48h", Hour(48)])
def test_freq... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.