sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
1322446a4241e23f3b49e1ba0f1173f6555e19748c6f776fafe53a4ec5595755 | Python | 1,131 | 42 | import matplotlib.pyplot as plt
import pickle
from pathlib import Path
import pandas as pd
from multiprocessing import Pool
from itertools import repeat
from tqdm import tqdm
plot_folder = Path('../../data/case1/plot')
def main(args):
trace, frames = args
out_path = plot_folder / f"{trace[0][1]}.png"
x ... |
422d75713666f5afeac9c837c6af9939d8e22762aacd01d8f4fab026fa18a6b3 | Python | 1,131 | 40 | '''
Created on 2015.5.27
@author: Liang Qian
'''
class Thalamus():
'''
This class defines the basic functions and properties of thalamus
'''
def __init__(self):
'''
Constructor
'''
self.neuronsNumber = 0
self.synapsesNumber = 0
self.neurons = []
... |
6743d1649d606c58e59cc05ac54ef1a17672b46c355b300704b4f1802c17b3aa | Python | 1,131 | 27 | # 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
from unittest.mock import patch
from anti... |
a8aae16b36005542628db7c299e65a911dc08d96c74d2072346a6b94baf28fcc | Python | 1,131 | 32 |
import sys
sys.path.append('.')
sys.path.append('..')
from plotting.utils import load_results, set_plotting_defaults, efcolor, pvscolor, ecscolor,occolor, dpi
import matplotlib.pyplot as plt
set_plotting_defaults()
if __name__ == '__main__':
sim_name = sys.argv[1]
mesh_name = sys.argv[2]
results = loa... |
d38824a27fc5a77f91495352468d98a67fab23f47ea9a5ad565ccf423794c1a4 | Python | 1,133 | 31 | import setuptools
import urllib.request, sys
with open("README.md", "r") as fh:
long_description = fh.read()
install_requires = ['numpy',
'setuptools',
'scipy']
setuptools.setup(
name="lang2vec",
version="1.1.6",
author="Patrick Littell, David Mortensen, Antonis Anastasopoul... |
783d1b66efc659fa02abefb05aa10a45ff85da1e40c284f23ba18c03dc093ebe | Python | 1,135 | 44 | # This test is ported from numpy.distutils
from numpy.f2py._src_pyf import process_str
from numpy.testing import assert_equal
pyf_src = """
python module foo
<_rd=real,double precision>
interface
subroutine <s,d>foosub(tol)
<_rd>, intent(in,out) :: tol
end subroutine <s,d>foosub
... |
f0afbb43199fa17086d0dc11d1b84880236b0e31a5ad3cd69eb475b11f1bb605 | Python | 1,135 | 35 | import subprocess
from pathlib import Path
import pytest
# PyInstaller has been very unproactive about replacing 'imp' with 'importlib'.
@pytest.mark.filterwarnings('ignore::DeprecationWarning')
# It also leaks io.BytesIO()s.
@pytest.mark.filterwarnings('ignore::ResourceWarning')
@pytest.mark.parametrize("mode", ["-... |
b5198cc667f624c647fc5f23d94604847190db65338025185a00053f3c8f1f72 | Python | 1,136 | 43 | #!/usr/bin/env python3.7
# isort: skip_file
"""Defines imports for the src.core module.
The copyrights of this software are owned by Duke University.
Please refer to the LICENSE and README.md files for licensing instructions.
The source code can be found on the following GitHub repository: https://github.com/wmglab-du... |
494db5b9dc1ad19b44b32aef5befc32cf18793e437ccb3b9d3af4583467fb29e | Python | 1,138 | 39 | from os import path
import yass
from yass import preprocess
from yass import detect
from yass import cluster
from yass import templates
from util import ReferenceTesting
def test_templates_returns_expected_results(path_to_config,
path_to_output_reference,
... |
94b563d2cca454e7815ce46f557c4ae554f4c671d166ee05386d720fa1918c4c | Python | 1,138 | 44 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from smac.env import StarCraft2Env
import numpy as np
def main():
env = StarCraft2Env(map_name="8m")
env_info = env.get_env_info()
n_actions = env_info["n_actions"]
n_agents = env_info["n_age... |
f4a1e250f51dcebf9ad1076cb0c4c751c118cd607c2f69e2abd25a4661dc0fb3 | Python | 1,138 | 44 | from PIL import Image
import sys
infilename = sys.argv[1]
numlines = int(sys.argv[2])
vae = sys.argv[3]
outfilename = sys.argv[4]
infile = open(infilename, "r")
data = infile.readlines()
infile.close()
data = data[30:]#remove seeds, and maybe a little bit more (oh well)
newinputs = []
count = 0
for line in data:
i... |
a24ede1e1be0932edb12727b7de3392580bb77948c47cde76eb64e6ba4bc2de6 | Python | 1,139 | 43 | from __future__ import annotations
import re
from ..utils._typed_cache import typed_cache
from ..utils.constants import RE_NONCONTRACTION_APOSTROPHE
@typed_cache
def remove_punctuation(
text: str,
rm_apostrophe: bool,
) -> str:
"""Get a copy of the text with punctuation removed.
If the parameter `r... |
d680efe6987815d053287bde5b19f1af893825a797a8ed5fca9ebc59fd500ea1 | Python | 1,139 | 32 | """
User-defined Python extensions that can be called from the menu.
"""
import spells
# class to create a submenu of Extensions
class Extension(object):
"""
A Python extension that can be added as a submenu in
the Extensions menu of Stimfit.
"""
def __init__(self, menuEntryString, pyFunc, descri... |
1ac3536b5ef880262194a42f0d7034fb225fff3fd38c98cdc542531ee7f7593d | Python | 1,140 | 44 | '''
Following timm implementation
'''
import sys
import re
import fnmatch
from collections import defaultdict
from copy import deepcopy
__all__ = ['model_entrypoint']
_module_to_models = defaultdict(set) # dict of sets to check membership of model in module
_model_to_module = {} # mapping of model names to m... |
5f9118b313862ed0caa0a781a919df8f9c98faf114064d66febbcdd2f30e7ca7 | Python | 1,141 | 38 | from setuptools import setup
from os.path import join, dirname
try:
# obtain long description from README
readme_path = join(dirname(__file__), "README.rst")
with open(readme_path, encoding="utf-8") as f:
README = f.read()
# remove raw html not supported by PyPI
README = "\n".join(R... |
1ab7a4ae478e9bdcf7d46762e28aab66cf66724d9060f33714c1d5b1026b06d7 | Python | 1,143 | 29 | import numpy as np
from sklearn.neighbors import KDTree
import yaml
from pathlib import Path
import nrrd
import pandas as pd
from CrystalTracer3D.io import CrystalReader
from skimage.measure import regionprops
if __name__ == '__main__':
with open('config.yml', 'r') as ymlfile:
cfg = yaml.safe_load(ymlfile... |
e8d905946155739fc1c16c30bd4d9cbdfbf8291ff46981d0cf4eb61cb6db698e | Python | 1,143 | 33 | import torch
import torch.nn as nn
from ..functional import cutoff_function
"""
computes radial basis functions with exponential Gaussians
"""
class GaussianRadialBasisFunctions(nn.Module):
def __init__(self, num_basis_functions, cutoff):
super(GaussianRadialBasisFunctions, self).__init__()
self... |
ea22fe787310686debc674b912072fac2a84966f5a28bd3b0a3af51592525e5b | Python | 1,143 | 32 | """A crude *bit of everything* smoke test to verify PyInstaller compatibility.
PyInstaller typically goes wrong by forgetting to package modules, extension
modules or shared libraries. This script should aim to touch as many of those
as possible in an attempt to trip a ModuleNotFoundError or a DLL load failure
due to ... |
5e22d9d9dfed98213cb86e55014e4e2b6ce5cd06b205f798e25f0514496d6e28 | Python | 1,144 | 31 | from distutils.command.build_py import build_py as old_build_py
from numpy.distutils.misc_util import is_string
class build_py(old_build_py):
def run(self):
build_src = self.get_finalized_command('build_src')
if build_src.py_modules_dict and self.packages is None:
self.packages = list(... |
2b75d2376b16aa13200d930a67abee3b286ea01b57faf6b39cb4f7d3040a8612 | Python | 1,146 | 34 |
import sys
sys.path.append('.')
from plotting.utils import load_results, set_plotting_defaults, efcolor, pvscolor, ecscolor, dpi
import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
set_plotting_defaults()
if __name__ == '__main__':
sim_name = sys.argv[1]
mesh_name = sys.argv[2]
results ... |
5acd447905827fbbf3f06fd5b054c8654548fa180a5d41006ed429be8063047a | Python | 1,147 | 35 | import pytest
import random
from numpy._core._multiarray_tests import identityhash_tester
@pytest.mark.parametrize("key_length", [1, 3, 6])
@pytest.mark.parametrize("length", [1, 16, 2000])
def test_identity_hashtable(key_length, length):
# use a 30 object pool for everything (duplicates will happen)
pool = ... |
a417fb7a14e653b42557e83bedc40a51ed8f4173534d79054f9772200ca946be | Python | 1,147 | 30 |
import sys
sys.path.append('.')
from plotting.utils import load_results, mesh_name, sim_name, set_plotting_defaults, efcolor, pvscolor, ecscolor, occolor,dpi
import matplotlib.pyplot as plt
if __name__ == '__main__':
sim_name = sys.argv[1]
mesh_name = sys.argv[2]
results = load_results(mesh_name, sim_name)... |
1d02502d2f7e453edd7ba9c11ecc39d25068e1aac199711566154cb788ae1f28 | Python | 1,148 | 44 | import pytest
from pandas import (
IntervalIndex,
MultiIndex,
RangeIndex,
)
import pandas._testing as tm
@pytest.fixture
def range_index():
return RangeIndex(3, name="range_index")
@pytest.fixture
def interval_index():
return IntervalIndex.from_tuples(
[(0.0, 1.0), (1.0, 2.0), (1.5, 2.5... |
3dc3f1f8f2a5a8b87d48b37bcb2e44f57eb85c00068604cd943fc3abdc170765 | Python | 1,149 | 46 | from yass import util
def add(a, b, c):
return a + b + c
class Object(object):
def add(self, a, b, c):
return a + b + c
obj = Object()
expected = dict(a=0, b=1, c=2)
# TODO: test this case
# util.map_parameters_in_fn_call([0, 1], dict(b=1), add)
def test_all_kwargs_function():
assert util.... |
54729711ec1586e0c855719c8ca5e6727b02c0e3a50c2b21babe0e1c525f54b0 | Python | 1,150 | 38 | from re import L
import numpy as np
import os
from scipy.linalg import svd
from numpy_groupies import aggregate
from skimage.util.shape import view_as_windows
def vectorize(image, mask):
"""
- If the input is 1D or 2D: unpatch it to 3D or 4D using a mask.
- If the input is 3D or 4D: vectorize to 2D using ... |
66ced438884e1f709aad7b13f1059003f99071dad6b6dae7ddc848d2d6db8b93 | Python | 1,150 | 41 | # Copyright 2024 RADar-AZDelta
# SPDX-License-Identifier: gpl3+
from abc import ABC, abstractmethod
from .etl_base import EtlBase
class CreateOmopDb(EtlBase, ABC):
"""
Class that creates the CDM folder structure that holds the raw queries, Usagi CSV's and custom concept CSV's.
"""
def __init__(
... |
a0ec8ee2d717b07888fcf46c20ea06ca52dae7e291cd0f6bbf5be77887334e51 | Python | 1,151 | 30 | import numpy as np
import pyvista as pv
import sys
import yaml
def compute_lumen_centerline(mesh, lumen):
surf = mesh.extract_surface()
surf.compute_normals(non_manifold_traversal=False, inplace=True)
b = np.array(lumen.bounds).reshape(3,2)
xrng = np.linspace(*b[0], 100)
yrng = np.linspace(*b[1], 1... |
ff3784a5a70ec14bf7290eb96536a6b3327027b1241d99c197e8e03b486acded | Python | 1,151 | 28 | # 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.
""" The base Pairing class and all default promoter ranges for CASSIS """
class Pairing:
""" A common component throughout CASSIS is a range given by number of
... |
d5152559530f8845b0c7f10e80dded576ed870e75e6785e24aae651c31845695 | Python | 1,152 | 43 | import asap
# The below code is to be used for exporting predictions from a trained model using the ASAP library.
# It includes data paths, model parameters, and the creation of datasets for prediction.
def main():
# Data paths
signal_file = "../data/TCGA-A6-A567/TCGA-A6-A567.nodup.no_chrM_MT.tn5.pval.signal... |
b00f001d06fe67afcff5908e79998ad1e17bcdc5a8bda41ecc83775482b0f6b5 | Python | 1,153 | 40 | from __future__ import annotations
import os
from tempfile import NamedTemporaryFile
from typing import TYPE_CHECKING
from .utils.logs import logger
if TYPE_CHECKING:
import pytest
lsl_cfg = NamedTemporaryFile("w", prefix="lsl", suffix=".cfg", delete=False)
if "LSLAPICFG" not in os.environ:
with lsl_cfg as... |
0ac125645e0de537fb7ebdbb4c9b9dbb7243fc929beb74ae6d45cf6239792e58 | Python | 1,154 | 44 | import pytest
import numpy as np
from . import util
class TestSizeSumExample(util.F2PyTest):
sources = [util.getpath("tests", "src", "size", "foo.f90")]
@pytest.mark.slow
def test_all(self):
r = self.module.foo([[]])
assert r == [0]
r = self.module.foo([[1, 2]])
assert r... |
e87fe8e01a17a99133c9348b41bcd83161f6cfc7bbe8ddbc318c2764735b5156 | Python | 1,154 | 46 | """ Creates numpy array from a CSV file containing axial currents
Author: Drew B. Headley
"""
import numpy as np
import pandas as pd
def load_axcurrent_csv(fpath, dend_pairs, apic_pair):
"""
Loads a CSV file that contains axial currents from dendritic segments
entering the soma.
Parameters
---... |
37f057ecd6d4f0f9638b3d9ba2e58cceb3f6db187feb0ffca4778f101db2715c | Python | 1,157 | 47 | import numpy as np
import pytest
import pandas as pd
from pandas.core.arrays.floating import (
Float32Dtype,
Float64Dtype,
)
def test_dtypes(dtype):
# smoke tests on auto dtype construction
np.dtype(dtype.type).kind == "f"
assert dtype.name is not None
@pytest.mark.parametrize(
"dtype, exp... |
883ff1f46a1ca58ca4639926cbb233b031af259f95967696450150d2ea800612 | Python | 1,158 | 25 | from torch.nn import TransformerEncoderLayer
from torch import Tensor
from typing import Optional
import torch.nn.functional as F
class InterpretableTransformerEncoder(TransformerEncoderLayer):
def __init__(self, d_model, nhead, dim_feedforward=2048, dropout=0.1, activation=F.relu,
layer_norm_eps... |
31f1b0927996dc9246fd801a399b01c2308afcce072cea602155a852a53fc5f3 | Python | 1,159 | 27 | from setuptools import find_packages
from setuptools import setup
with open("./requirements.txt", "r", encoding="utf-8") as fh:
install_requires = fh.read()
with open("README.md", "r", encoding="utf-8") as fh:
long_description = fh.read()
setup(
install_requires=install_requires,
packages=find_packages... |
47721da6bf57219f02f37b32f0dbd64ac87d9272b18b8d9300e375dc7a4646ad | Python | 1,159 | 37 | import sys
from importlib.util import LazyLoader, find_spec, module_from_spec
import pytest
# Warning raised by _reload_guard() in numpy/__init__.py
@pytest.mark.filterwarnings("ignore:The NumPy module was reloaded")
def test_lazy_load():
# gh-22045. lazyload doesn't import submodule names into the namespace
... |
c2b3738687cf0c566c55dd541bb504d101514b4b73035ea82d574477ca2f293e | Python | 1,159 | 55 | """Functions for loading, saving, and displaying images, and for creating masks."""
from ._core import collage, load_image, load_mask, save_image, export_image, save_mask, show_image, smooth_gaussian
from ._edit import normalize, crop, flip_left_right, flip_up_down, pad, resize, rotate_left, rotate_right
from ._mask i... |
5c1c654164bbff0279aad29ec03b9bff3d6ff4c70dbc7dd62f8b2746959bab50 | Python | 1,160 | 32 | from crystal_tracer.visual.draw import draw_contour
import numpy as np
import cv2
from pathlib import Path
from crystal_tracer.utils import load_czi_slice, get_czi_shape
import platform
font = cv2.FONT_HERSHEY_PLAIN
color = (255, 255, 255) # white color
font_scale = 1
position = (2, 2 + int(font_scale * 10)) # posit... |
cd1ee9f33da806f314d71d1e21548bd5e2b8067036071248f00775ad2ff8284b | Python | 1,160 | 29 | # 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... |
3e400e774a03bde3c1b572fe37432798418298330fdff0f0f98c29c6035f97e9 | Python | 1,161 | 48 | import numpy as np
import pytest
import pandas as pd
from pandas.core.arrays.floating import (
Float32Dtype,
Float64Dtype,
)
@pytest.fixture(params=[Float32Dtype, Float64Dtype])
def dtype(request):
"""Parametrized fixture returning a float 'dtype'"""
return request.param()
@pytest.fixture
def data(... |
5a76476bb3bd4aa4c016c23b9851b9c710597f2cc4c538527da80b333de3236e | Python | 1,163 | 51 | import datetime
import viz
# UNIQUE names!!!
class myTimer():
def __init__(self,dateFormat = '%d.%m.%Y', timeFormat = '%H%M%S'):
self.dateFormat = dateFormat
self.timeFormat = timeFormat
self.started = False
# timer methods to calculate time differences
def start(self):
self.startTick = viz.tick()... |
7d731e74fa81e8323a8925bbc49b58975aa4f407f253572bb3dc8ae4eab0892f | Python | 1,163 | 34 | from typing import Tuple
import torch
class CropBoundingBox(torch.nn.Module):
def __init__(self):
super().__init__()
def forward(self, img: Tuple[torch.Tensor, torch.Tensor]) -> torch.Tensor:
img, bounding_box = img
width = bounding_box[2] - bounding_box[0]
height = bounding... |
4da5f4a4d92e9d276e62426e92bf53b47c049f08f7e3cd1f2ad9b7c069cc7276 | Python | 1,164 | 64 | """
Created on Apr 9, 2025
@author: mning
"""
from src.pipelines.calc_Classification_Entropy_Bands_Ratio import (
calc_Classification_Entropy_Bands_Ratio,
)
calc_Classification_Entropy_Bands_Ratio(
op_Training="V1CV",
band_name="broadband",
op_NumClass=2,
dist_Medn=0,
op_Num_Epoch=0,
op_Pe... |
babe6bb2fbccbb2ed11e114291b0d84878817892ee6248641a6ec9294270f4a1 | Python | 1,164 | 45 | """
topological fingerprint
"""
import numpy as np
from rdkit.Chem.rdmolops import RDKFingerprint
from rdkit.Chem import DataStructs
_type = 'topological-based'
def GetRDkitFPs(mol, nBits = 2048, return_bitInfo = False):
"""
#################################################################
Calculate... |
5dd3549138b43b5747e2d3e836b72d615ae73c74773b2cc960399fb4a2465a93 | Python | 1,165 | 35 | from pySOT.surrogate import RBFInterpolant, CubicKernel, TPSKernel, LinearTail, ConstantTail
class RBF:
""" Radial Basis Function """
def __init__(self, kernel='cubic', tail='linear'):
self.kernel = kernel
self.tail = tail
self.name = 'rbf'
self.model = None
def fit(self,... |
7e68fae32608e024031d44b31b3fe39806e7e77967bbfac45e60c4314c6087a2 | Python | 1,165 | 27 | from brainiak.searchlight.searchlight import Searchlight
from nilearn.image import new_img_like
import numpy as np
from .fear_rsa_core import calculate_similarity_matrix, get_item_stability, get_cue_generalization
def run_fear_searchlight(anat_mask, beta_data, metadata, radius=5):
"""
[cite_start]Runs whole-br... |
44990867758849332798d9af7846f3734bdb07224cb8800a2925fa53ba574ab0 | Python | 1,166 | 31 | # -*- coding: utf-8 -*-
import os
import csv
import dirfiles
def trial_order(order_directory):
"""
Reads a specific trial order for n blocks from n csv files and
returns n lists to be used by the object block_list.order_trials()
of Expyriment library
"""
# Define the pathway of the inputs dir... |
fb6c51ad6eb8c6673295e54b8023ba2ced6f44c49737faf78dfdea506324a668 | Python | 1,167 | 42 | import matplotlib.pyplot as plt
import pickle
from pathlib import Path
import pandas as pd
from multiprocessing import Pool
from itertools import repeat
from tqdm import tqdm
plot_folder = Path('../../data/case2/plot')
def main(args):
trace, frames = args
out_path = plot_folder / f"{trace[0][1]}.png"
x ... |
07c69d9fa3baf820b3d5d7ab52baf3ed5ac351a407e21310db29bab1630440d1 | Python | 1,168 | 43 | import pytest
import pandas
import sbmlcore
def test_stride():
a = sbmlcore.Stride('tests/3pl1.pdb')
assert len(a.results) == 185
# check that all the -180 < phi <= 180 (and also for psi)
assert all((a.results.phi > -180) & (a.results.phi <= 180))
assert (a.results.n_hbond_acceptors>=0).sum(... |
457c9c26bb6309368ace8ba5c7fc3f3ff2d1b1eb9530ec2e149ec841e9b50c89 | Python | 1,169 | 41 | import torch
import numpy as np
class Cutout(object):
"""Randomly mask out one or more patches from an image.
Args:
n_holes (int): Number of patches to cut out of each image.
length (int): The length (in pixels) of each square patch.
"""
def __init__(self, n_holes, length):
self... |
b6453db3656da285990dd327ef8e3b499e9098d8a5aa8580d831c51a8814eff5 | Python | 1,171 | 45 | """
Test script for an upload
"""
import os
import argparse
import requests
from requests.auth import HTTPBasicAuth
def test_upload(local_file_path, upload_url, username, password):
if not os.path.exists(local_file_path):
print(f"File does not exist: {local_file_path}")
return
filename = os.... |
833459e4303d857b49cf00cb0109f954b56afdc3fa9401bc439551b4f74d4080 | Python | 1,172 | 38 | """Generate a heatmap of activation thresholds.
The copyrights of this software are owned by Duke University.
Please refer to the LICENSE and README.md files for licensing instructions.
The source code can be found on the following GitHub repository: https://github.com/wmglab-duke/ascent.
Note: if more than one heatm... |
c8cba4830fb84b29cbc087d4f4c87d6a7b170ab88c046c4b559f01575bc4a86b | Python | 1,174 | 33 | from pathlib import Path
import typer
from .._qt.components.tilt_series_browser import TiltSeriesBrowserWidget
from .._metadata_models.relion.tilt_series_set import RlnTiltSeriesSet
from ..view._cli import cli
COMMAND_NAME = 'tilt-series'
@cli.command(name=COMMAND_NAME, no_args_is_help=True)
def view_tilt_series(
... |
d018e7380448efd36e6c5168a855b5de8821be8b2ab44dab959a9de49a2df805 | Python | 1,174 | 36 | """Configure file paths and parameters for project
"""
import os
pjoin = os.path.join
class Config(object):
# project directories
config_path = os.path.dirname(os.path.abspath(__file__))
resources = pjoin(config_path, '../resources')
fmriprep_dir = '/Raid6/raw/VMR-Learning-Complete/derivatives/2020/... |
6e608ba7da8c860c603074b348515c2ca20e258d076739094a1e62c838d65488 | Python | 1,179 | 29 | import numpy as np
from .io import get_bw_from_file
def get_coverage(bw, chrom, start, end):
chroms_in_bw = bw.chroms()
use_chr = any(c.startswith("chr") for c in chroms_in_bw)
chrom_query = f'chr{chrom}' if use_chr else f'{chrom}'
return bw.values(chrom_query, start, end, numpy=True).astype('float16'... |
3f416d24e82a8060a8614b6a6d31e04efe9aa317369fcae700f736430370147c | Python | 1,180 | 42 | """
matrix product: a new twist
rewrite matrix product in a vmap style
"""
from functools import partial
import numpy as np
import tensorcircuit as tc
for bk in ["jax", "tensorflow"]:
with tc.runtime_backend(bk) as K:
print("~~~~~~~~~~~~~~~~~~~~~")
print(f"using {K.name} backend")
@parti... |
bcb8ba124bc018c2ae75171bc5ca2cc4757bcffaba19b92766e61d122b078f2e | Python | 1,181 | 43 | from io import BytesIO
import pytest
from pandas import read_csv
def test_streaming_s3_objects():
# GH17135
# botocore gained iteration support in 1.10.47, can now be used in read_*
pytest.importorskip("botocore", minversion="1.10.47")
from botocore.response import StreamingBody
data = [b"foo,b... |
321ba044d95a2a1bf9b8c53074cc88d4f72100b9d708f0fa4ddaea3332f2f70f | Python | 1,182 | 34 |
import numpy as np
import torch
import torch.nn as nn
from .electron_configurations import *
"""
Embedding layer which takes scalar nuclear charges Z and transforms
them to vectors of size num_features
"""
class Embedding(nn.Module):
def __init__(self, num_features, Zmax=87):
super(Embedding, self).__i... |
3f1ae0a073cd6b0d8fc36a8d8e31c33c2f80cbf21a0db0aa3f777fe4df9c8f60 | Python | 1,182 | 40 | import distutils.command.bdist_rpm as orig
import warnings
from setuptools import SetuptoolsDeprecationWarning
class bdist_rpm(orig.bdist_rpm):
"""
Override the default bdist_rpm behavior to do the following:
1. Run egg_info to ensure the name and version are properly calculated.
2. Always run 'inst... |
84e9891be0f89b3236c02f15430a4b38fc0f17a04a3c3fa382d22d5d73964ebc | Python | 1,184 | 44 | """Tests the trace module.
The copyrights of this software are owned by Duke University. Please
refer to the LICENSE and README.md files for licensing instructions. The
source code can be found on the following GitHub repository:
https://github.com/wmglab-duke/ascent
"""
import numpy as np
import pytest
from src.core... |
8552cd734651f932bb9ea03ed62ac298f375867d3ff4c4e532f8e06c005be4e2 | Python | 1,185 | 51 | # type: ignore
import sys
if sys.version_info[:2] >= (3, 8):
# TODO: Import directly (no need for conditional) when `python_requires = >= 3.8`
from importlib.metadata import PackageNotFoundError, version # pragma: no cover
else:
from importlib_metadata import PackageNotFoundError, version # pragma: no c... |
c4812f4bde856d8c80b867e4ee19c7cd8044aad469287862f6f2b42044733b5e | Python | 1,185 | 45 | """Tests the trace module.
The copyrights of this software are owned by Duke University. Please
refer to the LICENSE and README.md files for licensing instructions. The
source code can be found on the following GitHub repository:
https://github.com/wmglab-duke/ascent
"""
import numpy as np
import pytest
from src.cor... |
e1d4b46822cca7d91eac32a3553cf85ceb7e65b6b9d21026a14382c1f7fa2b22 | Python | 1,185 | 37 | """Compare thresholds across models using a boxplot.
The copyrights of this software are owned by Duke University.
Please refer to the LICENSE and README.md files for licensing instructions.
The source code can be found on the following GitHub repository: https://github.com/wmglab-duke/ascent.
For more controls over ... |
205c3c0db7f4c29e2cee1af0dbcd4229a2321a6416c587b2630d8c6b74feb33f | Python | 1,186 | 38 | """Compare thresholds across models using a boxplot.
The copyrights of this software are owned by Duke University.
Please refer to the LICENSE and README.md files for licensing instructions.
The source code can be found on the following GitHub repository: https://github.com/wmglab-duke/ascent.
For more controls over ... |
76e7416e6412ae00d0fe75e72b52dc43d5699410653c71ace6225726f86a1a0a | Python | 1,186 | 25 | """estimate_r: one shared initial GLM for the r grid, per-r wall time, sane JIC."""
import numpy as np
import pandas as pd
from causarray import estimate_r
def test_estimate_r_returns_time_and_finite_jic():
rng = np.random.default_rng(0)
n, p, a, r_true = 400, 150, 3, 2
U = rng.normal(0, 0.6, (n, r_true)... |
a337317d32a9d20c32259fad7beba3427380f6b1b59cd8fe752b7d6e2c14ff0b | Python | 1,186 | 45 | from __future__ import division
import viz
import vizact
import vizmat
import vizshape
import os
import random
import itertools
import sys
import math
import cPickle
## user librarys
sys.path.insert(0,os.path.realpath('..\py'))
sys.path.insert(0,os.path.realpath('..\objects'))
# File I/O
from csv_io import write_to_c... |
18a6fdf94685b334f4e39bd4815ba43ecd67f7b8b2ca3a9a86b58ac4b38a358a | Python | 1,187 | 46 | from __future__ import annotations
from abc import ABC, abstractmethod
class Backend(ABC):
def __init__(
self,
modulename,
sources,
extra_objects,
build_dir,
include_dirs,
library_dirs,
libraries,
define_macros,
undef_macros,
... |
66cc9c9bea8dcef9d037b0c2f9f7af58f47e7e6971b010e8bfb4ff224ec2e299 | Python | 1,187 | 36 | # 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,too-many-public-methods
import os
from tem... |
b55efc1109e60ce7893d620f356d9296e91de13f06c64530ac13010f0c4b4d76 | Python | 1,187 | 44 | import hashlib
REGISTRIES = {
"LIGHTNING_REGISTRY": {},
"DATASET_REGISTRY": {},
"MODEL_REGISTRY": {},
"LOSS_REGISTRY": {},
"METRIC_REGISTRY": {},
"OPTIMIZER_REGISTRY": {},
"SCHEDULER_REGISTRY": {},
"SEARCHER_REGISTRY": {},
"CALLBACK_REGISTRY": {},
"INPUT_LOADER_REGISTRY": {},
... |
daa82a6870d210a60ed61c04f4c68f4c52619789bbade8c7cae39cae6bea6818 | Python | 1,187 | 39 | import numpy as np
import pytest
from pandas import DataFrame
import pandas._testing as tm
class TestDataFrameReindexLike:
def test_reindex_like(self, float_frame):
other = float_frame.reindex(index=float_frame.index[:10], columns=["C", "B"])
tm.assert_frame_equal(other, float_frame.reindex_like... |
0a9f79c2d70c4a21a63093607586c32750364703fa7d25e0682f1ca0bebbc8fe | Python | 1,188 | 33 | from mpe.MPE_Env import MPEEnv
class MPE:
def __init__(self, args):
self.env = MPEEnv(args) # TODO args name and random seed
# scenario_name=args.scenario_name, benchmark=args.benchmark, num_agents=args.num_agents,
# num_adversaries, num_landmarks, episode_length
self.env.seed(ar... |
af0c74939eba4226483a614e3b48c3742af887499e9b6e84449fc7b7128d809e | Python | 1,188 | 36 | # Add this after your other imports
import zmq
import pickle
ZMQ_CONTROL_PUB_SOCKET = "tcp://127.0.0.1:5521"
def initialize_control_socket():
# Create command publisher (add this in main or as global)
context = zmq.Context.instance()
command_push_socket = context.socket(zmq.PUSH)
command_push_socket.c... |
ea112ba9036f2c7f73b792edb99db95b8d8afb0fc78d17cdf17cb55de243c89b | Python | 1,188 | 37 | """Compare thresholds across models using a barchart.
The copyrights of this software are owned by Duke University.
Please refer to the LICENSE and README.md files for licensing instructions.
The source code can be found on the following GitHub repository: https://github.com/wmglab-duke/ascent.
For more controls over... |
85f40c16b6f71099dfec1260d0b656c8db40050161aa9ec74d1435d6bdf68bad | Python | 1,189 | 38 | """Compare thresholds across models using a barchart.
The copyrights of this software are owned by Duke University.
Please refer to the LICENSE and README.md files for licensing instructions.
The source code can be found on the following GitHub repository: https://github.com/wmglab-duke/ascent.
For more controls over... |
ea9c5264a99d7b9287a0dde210c291780147acc95d026dd9650c1587f910f54c | Python | 1,189 | 45 | import pytest
import warnings
import numpy as np
@pytest.mark.filterwarnings("error")
def test_getattr_warning():
# issue gh-14735: make sure we clear only getattr errors, and let warnings
# through
class Wrapper:
def __init__(self, array):
self.array = array
def __len__(self)... |
f9cb29960b31cf76ac1650994f580b6841eceac5b35e06dec033edf86e25f3e8 | Python | 1,189 | 45 | import os
import tempfile
import pytest
import numpy as np
from yass.batch import BatchProcessor
@pytest.fixture
def path_to_data(request):
temp = tempfile.NamedTemporaryFile(delete=False)
path = temp.name
def delete_file():
os.unlink(path)
request.addfinalizer(delete_file)
array = (np.... |
10a60468cea084d32cfbff870c470a205556b42d844170faabb014bd04a9500f | Python | 1,192 | 42 | # Copyright (C) 2013,2015 Bernd Feige
# This file is part of avg_q and released under the GPL v3 (see avg_q/COPYING).
"""
Delphi table storage format - serialized into lines, row-fastest, with empty row separator lines.
"""
class delphi_table(list):
def read_file(self,filename):
with open(filename,"rb") as infile:... |
11d7873ee962490897468817b69710e249bf16ca0daafa65f874dfd191daffc8 | Python | 1,193 | 37 | """Compare thresholds across models using a boxplot.
The copyrights of this software are owned by Duke University.
Please refer to the LICENSE and README.md files for licensing instructions.
The source code can be found on the following GitHub repository: https://github.com/wmglab-duke/ascent.
For more controls over ... |
a4fecd7c79d0ec9721acf11ed1777d2cfa4900bceec44b6970cab11bb7e98c77 | Python | 1,193 | 32 | import uuid
import os
import utils
if __name__ == "__main__":
_uuid = str(uuid.uuid4())
nwires, nlayer, nitrs, timeLimit, isgpu, minus, path = utils.arg()
if isgpu == 0:
os.environ["CUDA_VISIBLE_DEVICES"] = "-1"
else:
import tensorflow as tf
gpu = tf.config.list_physical_devic... |
34d0a456b36a30ac548be6d41030a5f6d0ced6420977619cc03fc4f501ee896b | Python | 1,194 | 38 | """Compare thresholds across models using a boxplot.
The copyrights of this software are owned by Duke University.
Please refer to the LICENSE and README.md files for licensing instructions.
The source code can be found on the following GitHub repository: https://github.com/wmglab-duke/ascent.
For more controls over ... |
ab9cbb0bb49d6d037eaaa44eedcbdd1a9126929dba0761254bd994b1ccebe089 | Python | 1,195 | 41 | import logging
from pathlib import Path
from typing import Tuple
from omegaconf import DictConfig
def get_formatter() -> logging.Formatter:
return logging.Formatter('[%(asctime)s][%(filename)s][L%(lineno)d][%(levelname)s] %(message)s')
def initialize_logger() -> logging.Logger:
logger = logging.getLogger()
... |
19e21ffeb36c9881299af38f43b6d9a7ca45f4e3f2eb6f3b5636de8079514748 | Python | 1,198 | 40 | # Resume all interrupted trainings in yolov5/ dir including DDP trainings
# Usage: $ python utils/aws/resume.py
import os
import sys
from pathlib import Path
import torch
import yaml
FILE = Path(__file__).resolve()
ROOT = FILE.parents[2] # YOLOv5 root directory
if str(ROOT) not in sys.path:
sys.path.append(str(... |
5c781b2244e7ec610da933d3a6ff4bed4d5c1f5603119b6ed64cd58257b5fb4b | Python | 1,198 | 36 | import torch.nn as nn
import torch.nn.functional as F
import torch
class BCE_plus_DICE_Loss_function(nn.Module):
"""Combined Binary Cross-Entropy and DICE Loss"""
def __init__(self, smooth=1, alpha=0.5):
super(BCE_plus_DICE_Loss_function, self).__init__()
self.smooth = smooth
sel... |
cc0bc70a751ad9e27ca77093f5fba88b67d05ca3b9f603ce96711deb8adb9dfe | Python | 1,198 | 44 | import polars as pl
from tqdm import tqdm
import numpy as np
import pickle
from Functions import *
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--config_path', type=str, default="configs/pairwise.yaml")
args = parser.parse_args()
np.random.seed(0)
config = load_config_from_yaml(args.confi... |
ebd46932354b23a751e6c5f5ab2555f8f3202ef544e3d8fa6625959946761fab | Python | 1,199 | 30 | import numpy as np
from nilearn.glm import non_parametric_inference
from nilearn.image import concat_imgs
def run_group_inference(map_paths, mask_img, phase_name, n_perm=10000):
"""
Runs group-level non-parametric permutation testing with phase-specific
alpha thresholding[cite: 335, 372, 374].
"""
... |
689b31e2e9f1e0e337a442ba49b8b4cec1566d6a82eeb1ad00dbeabbc112f543 | Python | 1,200 | 49 | """
Created on Jun 13, 2024
@author: mning
Compute AUC of curve.
Likely will re-use this many times, so worth creating
even a short function
"""
import numpy as np
from numpy.typing import ArrayLike
from numpy.typing import NDArray
from scipy.integrate import simpson
def calc_AUC(X: ArrayLike, T: ArrayLike, param... |
81250a1873240e5e860b21a7fdba5b37f36dde19f0d27c24c1525936f2a938e1 | Python | 1,203 | 30 | #!/usr/bin/env python3
from pathlib import Path
import pandas as pd
import numpy as np
def cont(s):
s = pd.to_numeric(s, errors="coerce")
return f"{s.mean():.2f} ({s.std(ddof=1):.2f})"
def cat(s):
c = s.value_counts(dropna=False)
n = len(s)
return " | ".join([f"{k}: {int(v)} ({v/n*100:.1f}%)" for ... |
bceabd7eea8fa52036fb24a61617ac281e4e9a632dfa398b3acee70955c6e599 | Python | 1,204 | 41 | import setuptools
import nnap
setuptools.setup(
name="aggreprot-predictor",
version=nnap.__version__,
maintainer="Simeon Borko",
maintainer_email="simeon.borko@recetox.muni.cz",
description="NNAP: Neural Network based Amyloid Predictor",
long_description=None,
long_description_content_type=... |
03349740acc2b63d1be23bd87a583e6cdb2f72e1a2b2b8d453a43feb2a30cc45 | Python | 1,205 | 47 | # timeout_tests_working.py
import time
import multiprocessing as mp
# --- top-level worker (must NOT be nested) ---
def _wrap_fn(q, fn, a):
try:
q.put(("ok", fn(a)))
except Exception as e:
q.put(("err", repr(e)))
def run_with_timeout(fn, arg, timeout_s=5):
ctx = mp.get_context("spawn") #... |
bb35ce84297d3782cf57d855d88aa0fec92090a31b04f045d065cf53d10c7ae1 | Python | 1,205 | 64 | """Typing tests for `numpy._core._ufunc_config`."""
import numpy as np
def func1(a: str, b: int) -> None:
return None
def func2(a: str, b: int, c: float = 1.0) -> None:
return None
def func3(a: str, b: int) -> int:
return 0
class Write1:
def write(self, a: str) -> None:
return None
cl... |
e6a0bb596dc7526523336b9adad5b44a792dac29dcb69d9026e51f29b353a34a | Python | 1,205 | 33 | #!/usr/bin/env python3
from setuptools import setup
import os
import sys
setup(name='stereoscope',
version='0.3.1',
description='Integration of ST and SC data',
author='Alma Andersson',
author_email='alma.andersson@scilifelab.se',
url='http://github.com/alma... |
218540412c09bbe45209d2911ee9d8494d706ead8ff2d39098e204da7efb2019 | Python | 1,207 | 37 | import logging
from functools import wraps
class Trace:
"""
Decorator for tracing function calls. If you add the trace decorator to a function,
it logs the start and end of every function call to the provided logger.
Helps debugging the program flow, especially once we deploy the program to our collab... |
a808d284dbd1464f728f8709e38e2bcf9c6aeb19d919dfa2cff9527fb06a48ca | Python | 1,207 | 34 | import pickle
import h5py
def save_pkl(filename, save_object):
writer = open(filename,'wb')
pickle.dump(save_object, writer)
writer.close()
def load_pkl(filename):
loader = open(filename,'rb')
file = pickle.load(loader)
loader.close()
return file
def save_hdf5(output_path, asset_dict, attr_dict= None, mode='... |
8d4afc76693fe8542c4cd8c3918b1acd69e2a078ace1c2e2f789e8cb8b711b9e | Python | 1,212 | 39 | import pytest
import pandas as pd
import pandas._testing as tm
from pandas.tests.arrays.masked_shared import (
ComparisonOps,
NumericOps,
)
class TestComparisonOps(NumericOps, ComparisonOps):
@pytest.mark.parametrize("other", [True, False, pd.NA, -1, 0, 1])
def test_scalar(self, other, comparison_op,... |
a6c5375914f09f36eaecffe571d4f4a7297aac8e43c11ebf00bc7f1023c0263f | Python | 1,213 | 41 | import sys
from pathlib import Path
import wandb
FILE = Path(__file__).resolve()
ROOT = FILE.parents[3] # YOLOv5 root directory
if str(ROOT) not in sys.path:
sys.path.append(str(ROOT)) # add ROOT to PATH
from train import parse_opt, train
from utils.callbacks import Callbacks
from utils.general import incremen... |
f832138c900773291c941db1b0d7eac9a4a5b37eae29a1ba430956dfa9184e17 | Python | 1,218 | 45 | from ..base_loss import *
from .tensor_models import logsigmoid
class HingeLoss(BaseHingeLoss):
def __init__(self, margin):
assert False, 'HingeLoss is not implemented'
def __call__(self, score, label):
pass
class LogisticLoss(BaseLogisticLoss):
def __init__(self):
assert False, '... |
6bcbd462fd77d023cdf1c04ec3a949ce7829a0c1c605b1bc3185410117d96daf | Python | 1,219 | 36 | import numpy as np
from shap.links import identity, logit
class LinkSuite:
params = ([1, 2], [1, 100, 10_000])
param_names = ["ndim", "element_count"]
def setup(self, ndim, element_count):
if ndim == 1:
shape = (element_count,)
else:
side_length = int(np.sqrt(elem... |
c22d514719a801d71b17394ff4e425cb510366efc50ab7f9419a64318bba06ca | Python | 1,219 | 34 | import os
import sys
sys.path.append(r'D:\ASCENT\fresh')
os.chdir(r'D:\ASCENT\fresh')
import pickle
import shutil
new_nsim = 1
dest_samples, dest_model, dest_sim = [3070, 3150, 3230], 0, 3000
source_sample, source_model, source_sim = 3000, 0, 3000
for dest_sample in dest_samples:
with open(fr'samples\{dest_sample... |
e165143d80053d093fc72e1ab1d9e21b3f8114bb6b18adf5c6c29063ef21cb79 | Python | 1,220 | 54 | """
"""
import sys, time, logging, warnings
import numpy as np
import matplotlib as mpl
warnings.filterwarnings("ignore")
mpl.use('Qt5Agg') # ignore qtapp warning...
import matplotlib.pyplot as plt
def DrawFigure(num):
mpl.rcParams['toolbar'] = 'None'
figure = plt.figure(num)
ax = plt.axes([0,0,1,1], frameon=Fa... |
03c91d0876845ae9af23989d8f316d832ecdf046d057ca7c13feb397d26160c8 | Python | 1,225 | 33 | from setuptools import setup, find_packages
from io import open
setup(
name="textstat",
packages=find_packages(),
version="0.7.12",
description="Calculate statistical features from text",
author="Shivam Bansal, Chaitanya Aggarwal",
author_email="shivam5992@gmail.com",
url="https://github.co... |
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