sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
3915631ca2897f53be1da4b7a14478f51bcce6caeee944247d5498a15795b83a | Python | 1,564 | 57 | # coding: utf-8
# --------------------------------------------------------
# Fast R-CNN
# Copyright (c) 2015 Microsoft
# Licensed under The MIT License [see LICENSE for details]
# Written by Ross Girshick
# --------------------------------------------------------
import os
from os.path import join as pjoin
import num... |
cde8560d6b097365246f84488dcc1e17a49b05531921b486a604cf666e4a7bab | Python | 1,564 | 46 | import numpy as np
def merge_overlapping_bboxes(bboxes):
candidate_count = 0
while candidate_count < len(bboxes):
candidate_count += 1
overlap = False
candidate_box = bboxes.pop(0)
for index, compare_box in enumerate(bboxes):
overlapping, new_bbox = merge_if_overlap... |
f5d4e51716e5ce1a90f9ff67afcc671a6ab0db6e31dbd2e91c91b9889dbd1527 | Python | 1,564 | 80 | import numpy as np
import math
import matplotlib.pyplot as plt
x = np.arange(-90, 90, 0.1)
vhm = -12.8
ka = 15.8
vhw = -1.1
kiw = 28.8
aw = 0.5
bw = 0.5
vhs = -45.3
kis = 12.3
ass = 0.3
bs = 0.7
atmf = 395.3
btmf = 38.1
ctmf = 33.6
atms = 5503.0
btms = -5345.4
ctms = 0.0283
dtms = -23.9
etms = -4590
ftms = 0.0357
gtm... |
13906d8c9b757b32d90a4dede84bf695790793ac49a9041cba9a32efa0582153 | Python | 1,565 | 43 | import numpy as np
from scipy.stats import pearsonr
import h5py # 导入 h5py 库来处理 HDF5 文件
from scipy.io import savemat
# 创建示例数据
N = 266484
num_runs = 60
# 初始化奇数和偶数的beta系列数组
beta_series_odd = np.zeros((N, 0))
beta_series_even = np.zeros((N, 0))
# 加载所有run的数据
for run in range(1, num_runs + 1):
# 构造文件路径... |
2b3d0b569878cdae704bbf99dc5c8c7d4c6ed07016967929c4eccf7c2d6e2cc6 | Python | 1,565 | 58 | #!/usr/bin/env python
import os
from setuptools import setup, find_packages
def readme():
with open('README.md') as f:
return f.read()
def get_requirements_filename():
if 'READTHEDOCS' in os.environ:
return "REQUIREMENTS-RTD.txt"
elif 'DOCKER' in os.environ:
return "REQUIREMENTS-... |
be8e1e637c1c16f8519bd88a517e0ffb7cc96055673cd02a040d232fe06785d5 | Python | 1,565 | 42 | from torch import Tensor, flatten
from elasticai.creator.arithmetic import (
FxpArithmetic,
FxpParams,
)
def parse_fxp_tensor_to_bytearray(
tensor: Tensor, total_bits: int, frac_bits: int
) -> list[bytearray]:
tensor = flatten(tensor.permute([0, 2, 1]), start_dim=1)
fxp_params = FxpParams(total_b... |
13a87b93fbf1aefb7581cd939f3799d14eb4d11d45eedd63b0aae61edc965284 | Python | 1,566 | 54 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, MaiaEnvironment
import common_setup
from common_setup import IssueConfig, IssueExperiment
from relativescatter import RelativeScatterPlotReport
DIR = os.path.dirname(os.path.abspath(__file__))
BENCHMARKS_DIR = o... |
4a6cd76173d426206839dcd5a856ad20895c4e933074bbbee1e2f36a23aa0acf | Python | 1,566 | 54 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, MaiaEnvironment
import common_setup
from common_setup import IssueConfig, IssueExperiment
from relativescatter import RelativeScatterPlotReport
DIR = os.path.dirname(os.path.abspath(__file__))
BENCHMARKS_DIR = o... |
7874faece3656fde7e28c4b9ca42b1ce188fb6602a57025548a2f47b44156102 | Python | 1,566 | 57 | import time
from watchdog.observers import Observer
from watchdog.events import FileSystemEventHandler
from config import DIRECTORY_TO_WATCH
from restore_predict import predict_restored
import os
class Watcher:
def __init__(self, models):
self.observer = Observer()
self.models = models
def r... |
c1498f9eb1ec6739203da88272baa7f54d007134b7b1bcf9d59365bf40ceb858 | Python | 1,566 | 48 | from __future__ import annotations
from wikibaseintegrator.models.basemodel import BaseModel
class Sitelinks(BaseModel):
def __init__(self) -> None:
self.sitelinks: dict[str, Sitelink] = {}
def get(self, site: str | None = None) -> Sitelink | None:
if site in self.sitelinks:
... |
08d6c614ff11012aecc1132a0a49987487fcb6832ad94f0c4c08d9adaadf0e16 | Python | 1,567 | 34 | # Perform Signal Space Projection
# Mainly working from tutorial https://mne.tools/stable/auto_tutorials/preprocessing/50_artifact_correction_ssp.html
# SSP uses singular value decomposition to create the projection matrix
import os
import mne
import numpy as np
import pandas as pd
def apply_SSP(subject, task, sampl... |
edc84504af434e92e3351d341f84b056dd3dbea568faa4a05afa09db54eb6685 | Python | 1,567 | 37 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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 applicab... |
1c81d0ffd45521d2e836247c0aee1367f5ad568809a3eecb65dd46d211a012eb | Python | 1,568 | 43 | import datasets
import lightning.pytorch as pl
from hicdiffusion_model import HiCDiffusion
from lightning.pytorch.callbacks import ModelSummary
import os
import shutil
from lightning.pytorch.loggers import WandbLogger
import time
def main():
hic_filename = "4DNFIPNP9H9T.mcool"
model_ckpt= "models/hicdiffusion_... |
4577ec449e5cfa4bb1a1737953bd2e9c41b786572d7bec1c37466fad8a57b0b9 | Python | 1,568 | 44 | import numpy as np
from sklearn import metrics
from joblib import Parallel, delayed, cpu_count
def k(x, y, gamma=1.0):
#return metrics.pairwise.rbf_kernel(x.reshape(-1, 1), y.reshape(-1, 1), gamma=gamma)
return metrics.pairwise.linear_kernel(x.reshape(-1, 1), y.reshape(-1, 1))
#return metrics.pairwise.poly... |
9f1f3900bb705bb7fdf0745d9105edbe7261f7b74be7263e8c26096206ac78bf | Python | 1,568 | 39 | import warnings
import numpy as np
from ase.build import molecule
from ase.calculators.lj import LennardJones
from sella.internal import Internals
from sella.peswrapper import InternalPES
def test_get_binv_rank_deficient_fallback_matches_primary():
"""The _get_Binv cache-miss fallback must reproduce the SAME tr... |
cb5e15e9f7c6e3d2d961bccbe0498ff527815c7e03a831fc7626dea8089a0865 | Python | 1,568 | 69 | """
Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
"""
import setuptools
install_deps = [
"numpy>=1.24.0",
"scipy",
"scikit-learn",
"numba>=0.57.0",
"natsort",
"tqdm"
]
gui_deps = [
"pyqtgraph>=0.11... |
0665cc8f0ee43899b1adc5cc43aba0c91a4f118c0b4c9f1bb3b4c4a604041418 | Python | 1,569 | 45 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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 applicab... |
9df5a4687c8855641b08571d3a0e65c2680fba23549eb6ff2aa28572259e1d57 | Python | 1,570 | 50 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
import common_setup
from common_setup import IssueConfig, IssueExperiment
from relativescatter import RelativeScatterPlotReport
DIR = os.path.dirname(os.path.abspath(__file__))
BENCHMARKS_D... |
e92900c05779cd0ffca45689d80e2e2c4aa26c729faa5fa5d8816007908b667b | Python | 1,570 | 41 | import numpy as np
import nibabel as nib
from regtools.registration.gui.atlas_edit_io import atlas_edit_run_template_shape, save_atlas_edit_mask
def test_shape_whole_is_identity():
assert atlas_edit_run_template_shape(
template_path=None, ccf_index=None, is_2d=True, atlas=None, full_shape=(40, 50),... |
b6def9df49c4d96790c29382ae6585ec764906696d81df226b65d7948b9bc49b | Python | 1,571 | 76 | from invoke import task
import pandas as pd
@task
def unpack(c):
"""
Unpack downloaded `tar.gz` file
"""
c.run("tar -xzf raw_data.tar.gz --directory data")
@task
def get(c):
"""
Download the data from the online archive
"""
c.run(
"wget https://zenodo.org/record/3753498/files/... |
200b21455fdb5cf236ad172d62cf67e2d431fbc2337c230e0c5df38fe3d29fa6 | Python | 1,572 | 37 | import tensorflow as tf
from pinn.optimizers.ekf import EKF, default_ekf
from pinn.optimizers.gekf import gEKF
default_adam = {
'class_name': 'Adam',
'config': {
'learning_rate': {
'class_name': 'ExponentialDecay',
'config':{
'initial_learning_rate': 3e-4,
... |
56e73be10a391b58196ebb0e591a845b0e45b74f62e7d0854c94f8257361b2c7 | Python | 1,572 | 41 | import argparse
import github
import os
def bioimageio_upload(resource_id: str, package_url: str): #, token:str):
# Get bioimage-io/collection repodistory
g = github.Github(auth=github.Auth.Token(os.environ["PAT_GITHUB"]))
repo = g.get_repo("bioimage-io/collection")
# Get the stage.yaml workflow (CI/G... |
963bc41120c36a99a2951758989b2d21bdc885556e423754569ba9930a6f0539 | Python | 1,573 | 41 | #
# MIT License
#
# Copyright (c) 2022 GT4SD team
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge,... |
adece71a91e3e3b48a07fe4675663647bed653ddde562b62e492e4ae0e142d2b | Python | 1,573 | 16 | """posthoc_margin_finegrid_2026-10-02.py — POST HOC (after SURVIVE P3, 2 Oct late night). The pre-registered grid of P3
(excitatory local-neuron synapses scaled by g = 1.25 ... 3, no sign changed) was too coarse: g = 1.25 already broke the lobe
(34 of 50 healthy), so the test could only see the laboratory prior (g = 1)... |
5eae3b9e893269f5538322fa6e888c8ab20f7eaff6fa4a61122e723b9d92bfba | Python | 1,574 | 46 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
from downward import suites
from common_setup_no_benchmarks import IssueConfig, IssueExperiment, get_script_dir
from relativescatter import RelativeScatterPlotReport
import os
def main(revisions=None):
exp = IssueExperiment(benchmarks_dir=".", suite=[])
exp.ad... |
e268e5f6dbb5ca86466772d7786fa4862e18d9572dfb9af3d748a8fe1e08680f | Python | 1,574 | 46 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
from downward import suites
from common_setup_no_benchmarks import IssueConfig, IssueExperiment, get_script_dir
from relativescatter import RelativeScatterPlotReport
import os
def main(revisions=None):
exp = IssueExperiment(benchmarks_dir=".", suite=[])
exp.ad... |
0d212c57e840d026c73a0972b22a4762a6b3b759f8a97a0114e2cbf8584a32a0 | Python | 1,575 | 37 | import os
import tempfile
import unittest
from torcheeg.model_selection import Subcategory
from .test_utils import _make_dataset
class TestSubcategory(unittest.TestCase):
def test_string_numeric_and_mixed_categories_preserve_values(self):
for categories in ([0, 1, 2, 3, 4], ['001', '002', '003', '004',... |
cd2956892f41b2dbefb2d6df068c172d36eeade44387f2089f2a1fb274ea8948 | Python | 1,575 | 36 | from typing import Callable, List, Dict, Optional
import torch
from torch import nn
from .base import AtomicModule
from ..layer import EmbeddingLayer, CutoffLayer
from ..utils import _scatter_add, find_distances
class TwoBody(AtomicModule):
def __init__(self,
embedding_layer : EmbeddingLayer,
... |
21023e6be3d05d617b8c016386729c381a32d36beb01b8a72992cc13c8bb80a0 | Python | 1,576 | 44 | """
Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
"""
import numpy as np
from scipy.stats import zscore
def grid_upsampling(X, X_nodes, Y_nodes, n_X, n_neighbors=50, e_neighbor=1):
e_neighbor = min(n_neighbors - 1, e_neighbor)
xy = []
n_clusters = Y_no... |
ebeb79cc74b3860eaf0ddd57f92e1a5c0a7d5f8ecc6bed105eaafd057ebf3aea | Python | 1,577 | 62 | from . import datasets
from . import encoders
from . import decoders
from . import losses
from . import metrics
from .decoders.unet import Unet
from .decoders.unetplusplus import UnetPlusPlus
from .decoders.manet import MAnet
from .decoders.linknet import Linknet
from .decoders.fpn import FPN
from .decoders.pspnet imp... |
eee3fd752de17d25c028b05f6dd8ec7b03f397aa5fb0495f88a61e1c146edd02 | Python | 1,578 | 56 | """
Tests module pyto.util.scipy_plus.
# Author: Vladan Lucic (Max Planck Institute for Biochemistry)
# $Id$
"""
from __future__ import unicode_literals
__version__ = "$Revision$"
import unittest
import numpy
import numpy.testing as np_test
import scipy
from pyto.util.scipy_plus import *
#from ..scipy_plus impor... |
224f2ed5ed6e06613d4c7a5ed779ed14923d84a70ab60bdfd87ed6232d992fee | Python | 1,580 | 48 | #!/usr/bin/env python3
import os
import sys
def second_newest_directory(path):
dirs = []
for entry in os.scandir(path):
if (
entry.is_dir(follow_symlinks=False)
and not entry.is_symlink()
and entry.name != "GSvarServer-current"
and entry.name != "default-... |
4b188ec9797f45d082ea6f6ada21b50d92516b09c9cf1ae2fc4a5189a9e75733 | Python | 1,581 | 33 | from pyproteonet.data import Dataset
from gnn_imputation import impute_gnn
def main():
for ds_name in ['prostate_cancer']:
# Remove skip connection
# print('Imputing ' + ds_name + ' without skip connection')
# ds = Dataset.load(f'data/datasets_imputed/{ds_name}')
# impute_gnn(ds, s... |
4e03b987f51c61e9febe6e5decbbce9872e1299026bbee447a2fdf0fd41af56c | Python | 1,581 | 50 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
import common_setup
from common_setup import IssueConfig, IssueExperiment
from relativescatter import RelativeScatterPlotReport
DIR = os.path.dirname(os.path.abspath(__file__))
BENCHMARKS_D... |
6c9e518540d7849b3080b7b9c54b715667c107439b0c6f4a5f60649733f7ce5a | Python | 1,581 | 50 | import torch
import torch.nn as nn
import numpy as np
class DensityNetwork(nn.Module):
def __init__(self, encoder, bound=0.2, num_layers=8, hidden_dim=256, skips=[4], out_dim=1, last_activation="sigmoid"):
super().__init__()
self.nunm_layers = num_layers
self.hidden_dim = hidden_dim
... |
1028b6bb5080df9b5040c5fb1776b0311c683bf7e2c833b45ecf604799bc7a62 | Python | 1,582 | 50 | #!/usr/bin/env python3
import logging
import argparse
# https://stackoverflow.com/questions/2130016/splitting-a-list-into-n-parts-of-approximately-equal-length
def split(a, n):
k, m = divmod(len(a), n)
return (a[i * k + min(i, m) : (i + 1) * k + min(i + 1, m)] for i in range(n))
def parse():
"""Split zmw... |
ea84d0f16eeb0ec1b376b4b77f9722b1d3d90f1a159f28f1e3d435e0780f69d1 | Python | 1,582 | 50 | """Matching input resolution to the template leaves moving-pitch controls usable."""
import os
import sys
PROJECT_ROOT = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
if PROJECT_ROOT not in sys.path:
sys.path.insert(0, PROJECT_ROOT)
os.environ.setdefault("QT_QPA_PLATFORM", "offscreen")
... |
4bb0c087eb168791364c4aec32ca1174270a9389eee945cbbf2c40d124089165 | Python | 1,583 | 56 | import re
from typing import List, Union, Dict
from ..base_transform import LabelTransform
class StringToInt(LabelTransform):
r'''
Identify numbers in strings and convert strings to numbers. If there is no number in the string, the output corresponding to the string is 0.
.. code-block:: python
... |
9c4aeb1d3d5dc37f60625ee71f8a6a5c1771ccafeb41023338630a22621efa43 | Python | 1,583 | 67 | from __future__ import annotations
import pytest
redun = pytest.importorskip("redun")
from quacc import flow, job, subflow
@pytest.fixture
def scheduler():
return redun.Scheduler()
def test_redun_decorators(tmp_path, monkeypatch, scheduler):
monkeypatch.chdir(tmp_path)
@job
def add(a, b):
... |
60fd0447c48b921df6aeb7aac6cac967c41835eb6df99ea5933401dd6477edb4 | Python | 1,584 | 66 | # \file TestLinearImageQualityTransfer.py
# \brief Class containing unit tests for module DifferentialOperations
#
# \author Michael Ebner (michael.ebner.14@ucl.ac.uk)
# \date July 2016
import unittest
# Import libraries
import numpy as np
from scipy import ndimage
from niftymic.definitions import DIR_TEST
# ... |
8f8e29d2e502c514e2e92da8c6500cc8b3488198834e73012b35fac4351fe2ad | Python | 1,584 | 72 | from __future__ import annotations
import csv
from pathlib import Path
from typing import Iterable
def format_seconds(seconds: float | int | None) -> str:
"""
Convert elapsed seconds to HH:MM:SS using whole seconds.
Examples
--------
0 -> 00:00:00
126 -> 00:02:06
4472 -> 01:... |
f2abf6b114b2b56a3f2cc7b13f7a973113514665f0ff79ade52efc27722be6ba | Python | 1,584 | 52 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
from downward.reports.compare import ComparativeReport
import common_setup
from common_setup import IssueConfig, IssueExperiment, RelativeScatterPlotReport
DIR = os.path.dirname(os.path.ab... |
fc2f96e3b5cdbd32305f0aa2632dff447b87308a3285bd38dd399f9ae8c92185 | Python | 1,584 | 49 | import logging
from pupil_recording_interface.decorators import process
from pupil_recording_interface.process import BaseProcess
from pupil_recording_interface.device.video import VideoFileDevice
logger = logging.getLogger(__name__)
@process("video_file_syncer")
class VideoFileSyncer(BaseProcess):
""" Syncer f... |
68a6602514cc9cb5fae2916fbaa53ea24a083fac43fe24536de4dc2f46865f8f | Python | 1,585 | 67 | from __future__ import annotations
import pytest
redun = pytest.importorskip("redun")
from quacc import flow, job, subflow
@pytest.fixture()
def scheduler():
return redun.Scheduler()
def test_redun_decorators(tmp_path, monkeypatch, scheduler):
monkeypatch.chdir(tmp_path)
@job
def add(a, b):
... |
77351f4ba389f995c5291b013c9f4a6ea42961db13c64d853dcb5177d42f3b60 | Python | 1,585 | 52 | """Test functions for interface classes."""
import tempfile
from concurrent.futures import ThreadPoolExecutor
from pathlib import Path
import numpy as np
from console.interfaces.acquisition_data import AcquisitionData
def test_acquisition_data(acquisition_parameter, test_sequence, random_acquisition_data):
"""T... |
0c34159d7379f6ef394cb12ca365000b9f68f52e27e9c2940b5b4bdca82c820a | Python | 1,586 | 44 | import torch
@torch.jit.script
def gaussian(x, mean, std):
pi = 3.14159
a = (2 * pi) ** 0.5
return torch.exp(-0.5 * (((x - mean) / std) ** 2)) / (a * std)
# From Graphormer
class GaussianRadialBasisLayer(torch.nn.Module):
def __init__(self, num_basis, cutoff):
super().__init__()
self... |
1ce98dbbaa5f8c6d1a9b1f97e8374c038a40e668af554a5947da5064952ea6e9 | Python | 1,586 | 66 | #!/usr/bin/env python
from __future__ import print_function
import os, shutil, sys
#sys.args.append('build')
from distutils.core import setup, Extension
# pr2_without_sensor_ik_files
# python setup.py build
LEFT_IK = 'ikLeft'
RIGHT_IK = 'ikRight'
LIBRARY_TEMPLATE = '{}.so' # might need to be '{}.pyd' on windows
l... |
d9338c11fbcdc05e6be7d616fbb5b0287d531b48738ffff303005a79ae3a6a33 | Python | 1,586 | 45 | import pandas as pd
import pickle as pkl
from Bio import Align
utr_data = pd.read_csv('/fast/AG_Ohler/frederick/projects/mlcis/data/riboseq/calviello_te_processed.csv')
mrl50 = pd.read_csv('/fast/AG_Ohler/frederick/projects/mlcis/data/mrl25to100/GSM3130443_designed_library.csv').drop('Unnamed: 0', axis=1)
mrl50 = mrl... |
803f5ed9536986dbd8151839888fdd2902a238595832993845cee7cc380ff815 | Python | 1,587 | 48 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
import common_setup
from common_setup import IssueConfig, IssueExperiment
from relativescatter import RelativeScatterPlotReport
DIR = os.path.dirname(os.path.abspath(__file__))
BENCHMARKS_DI... |
d0caf0d13e8c69cfd6b011fcb3aad8e32eb6a83e55199e7d88b2d31ffff65d58 | Python | 1,587 | 57 | import numpy as np
import os
import torch
from .base import AtomsDataset
from typing import List, Optional
from ase import Atoms
__all__ = ["RevisedMD17"]
class RevisedMD17(AtomsDataset):
file_names = [
"aspirin",
"azobenzene",
"benzene",
"ethanol",
"malonaldehyde",
... |
f37e32c021db348eb241cb02bf5c02d2c67f0de8f43125afc0e2c7c2963b75a3 | Python | 1,587 | 47 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
import common_setup
from common_setup import IssueConfig, IssueExperiment
from relativescatter import RelativeScatterPlotReport
DIR = os.path.dirname(os.path.abspath(__file__))
BENCHMARKS_DI... |
4ff1761b2670c674c61be925f0f181b2d36839bddef5232417e7ec7cc990fb09 | Python | 1,588 | 49 | """Headless checks that the Parameters tab exposes N4 properties.
Constructing the QWidget needs a QApplication, so we introspect the class
and its source instead of instantiating it (mirrors the Qt-free style of
test_registration_cli_args.py).
"""
import inspect
import pytest
def _params_tab_cls():
... |
9ebf950d1cea007d273c4ae6919f3116dd9a291dfc7722dd605ecba1b9c2cada | Python | 1,588 | 52 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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 applicab... |
a61214ef78f6b8e4eee8abbde9f82b62d7a03e87e51c449d3f43cb81f2dd7800 | Python | 1,588 | 52 | from __future__ import annotations
import pytest
sella = pytest.importorskip("sella")
from ase.build import bulk, molecule
from ase.calculators.emt import EMT
from ase.calculators.lj import LennardJones
from ase.io import read
from sella import Sella
from quacc.runners.ase import Runner
def test_sella(tmp_path, mo... |
b4fc69ea787db65e7131f90d1f522e1facb4bd5bddca87afb47deddd5ac5028f | Python | 1,588 | 40 | """
Created on Mon Jul 17 13:14:11 2023
@author: trianaa1
"""
import os, glob
import pandas as pd
path = "/m/cs/project/networks-pm/behavioral"
savepath = "/m/cs/scratch/networks-pm/effects_externalfactors_on_functionalconnectivity/data/behavioral"
files = []
pattern = f'*device-smartphone*'
for dir,_,_ in os.wal... |
cb2ceb2123a0ba86fe318842c96e67c09db6014e64f54a7277ae8267985f8b0d | Python | 1,588 | 41 | #!/usr/bin/env python3
import os
import pandas as pd
from itertools import combinations
# ------------------------------------------------------------------
# paths
# ------------------------------------------------------------------
projpath = "/project/3011157.03/Simon/proj_2022_CABB_movie"
subjlist_path = os.path.j... |
e0c9ed29cb4621cba1341be57ddc1d9a386ec4de278e629293decbb1b171ea93 | Python | 1,588 | 40 | import torchaudio
from speechbrain.pretrained import Tacotron2
from speechbrain.pretrained import HIFIGAN
import simpleaudio
# # Intialize TTS (tacotron2) and Vocoder (HiFIGAN)
# tacotron2 = Tacotron2.from_hparams(source="speechbrain/tts-tacotron2-ljspeech",
# savedir="tmpdir_tts")
#... |
e9d39c7930c00a2b4e783039957f50505e4ac64d4f0bb7388c56f5a24ec56981 | Python | 1,588 | 54 | """Experiment to acquire a spin echo spectrum."""
# %%
import matplotlib.pyplot as plt
import numpy as np
import console
from console.interfaces.acquisition_data import AcquisitionData
from console.spcm_control.acquisition_control import AcquisitionControl
from console.utilities import sequences
# Create acquisition ... |
881c433f870edf77487d6dde77ce0d51a13f2fcf795d9cde77d399e068acccba | Python | 1,589 | 45 | from codex.configuration import RedirectHomeError
from codex.data.local_data_loader import unpickle_neuron_db, DATA_ROOT_PATH
from codex.data.versions import DEFAULT_DATA_SNAPSHOT_VERSION, DATA_SNAPSHOT_VERSIONS
from codex import logger
# Singleton
_instance = None
class NeuronDataFactory(object):
def __init__(s... |
8d20b523a85625e07809227233a8faf1c2e0cbe3dea9d86d6c0abaca8ab1b142 | Python | 1,589 | 45 | #!/usr/bin/env python3
import os
import pandas as pd
from itertools import combinations
# ------------------------------------------------------------------
# paths
# ------------------------------------------------------------------
projpath = "/project/3011157.03/Simon/proj_2022_CABB_movie"
subjlist_path = os.path.j... |
c7faf5c13b8195733454dd674b8f1f2adbe24390f88aae1fa6be75be2c96028b | Python | 1,589 | 45 | # -*- coding: utf-8 -*-
"""
"""
import scipy.stats as stats
import matplotlib.pyplot as plt
from scipy.io import loadmat, savemat
import numpy as np
import os
if __name__=='__main__':
pwd_current = '%s/' % os.getcwd()
pwd_data = '%sdata/' % pwd_current
if not(os.path.isdir('%sfigures' % pwd_cur... |
93f9605dcb097604bd1ac39d5bd66628a9e23910b3b103a73ae05fb6869b0255 | Python | 1,590 | 43 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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
#
# ht... |
dcb28b0cf90fe032f355e9266e2343c3230281d90cb3a5086be80935379a39e8 | Python | 1,590 | 48 | import os
from collections import defaultdict
from torch.utils import data as torch_data
from torchdrug import data, utils
from torchdrug.core import Registry as R
@R.register("datasets.MOSES")
@utils.copy_args(data.MoleculeDataset.load_csv, ignore=("smiles_field", "target_fields"))
class MOSES(data.MoleculeDataset... |
37ae6d922c9d1b44e9d493d6e8a28a4e83af81938d1196f6276579d5522ae19c | Python | 1,591 | 56 | """Base jobs for Psi4."""
from __future__ import annotations
from typing import TYPE_CHECKING
from ase.calculators.psi4 import Psi4
from quacc.runners.ase import Runner
from quacc.schemas.ase import Summarize
from quacc.utils.dicts import recursive_dict_merge
if TYPE_CHECKING:
from typing import Any
from ... |
59970564b80ceb348c7315b0bcf493026a767a741e9c16cc88e5d9db63fcef7c | Python | 1,591 | 45 |
import pandas as pd
import numpy as np
import rpy2.robjects as robjects
import os
fitdistPath=os.path.join(os.path.dirname(__file__), "fitdistrplus/fitdist.R")
quantilePath=os.path.join(os.path.dirname(__file__), "fitdistrplus/quantile.R")
def main__DBLsMark_wEmpty(DBLmetricsDF, FullDrops):
'''
Iterating over ra... |
b100149f2dd33550f3831ab88063ae1bb4b96f2d39b4ffd382fab629cd0bdc6f | Python | 1,591 | 37 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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
#
# ht... |
e64ec5f55838789203e6727d9e5693576d72f7b0801a252bb9a2484ec4e72727 | Python | 1,591 | 57 | import argparse
def add_subparser_args(subparsers: argparse) -> argparse:
'''Add tool-specific arguments.
Args:
subparsers: Parser object before addition of arguments specific to
`preprocess`.
Returns:
parser: Parser object with additional parameters.
'''
subparser = s... |
fc2185713cb24d82009f758fa144e610859f79402cb8a1e1f5cf5b593c3a00f3 | Python | 1,591 | 44 | #!/usr/bin/env python3
import pandas as pd
from pathlib import Path
# ------------------------------------------------------------------
# Paths
# ------------------------------------------------------------------
base_dir = Path("/project/3011157.03/Simon/proj_2022_CABB_movie/MRI")
subjectlist_file = base_dir / "su... |
8e18ed69e9df84db66f1a658960400f576fe1bbf1755d4d23c4c32fed4f2ac53 | Python | 1,593 | 60 | import pdb
from typing import Dict, List, Callable
from ..base_transform import BaseTransform
class PDB(BaseTransform):
r'''
For debugging, insert breakpoints in transforms. The transformation itself does not change the input data.
.. code-block:: python
from torcheeg import transforms
... |
2f8f383ea67b54a7f9a0bfee149cc94cea524a8e6cc67bc9a4e4a5ba8ba3b4c1 | Python | 1,594 | 43 | """Re order the empatica files and name it using the pre-established convention.
This script will unify the different measurements splitted in several files
into one dataframe per day. The dataframe is stored as a csv file.
The input should be done in the following order:
Parameters
--------... |
660b604eab1c21364588590988ee99da83f739bde71738f0dc4a4542dad354a8 | Python | 1,594 | 52 | """
This script visually test the deconv layer.
Construct an MLP with conv ,and deconv layer,
set their W to same values and show the original
input and the output of the mlp side by side.
They are supposed to look same.
"""
import theano
from adversarial.deconv import Deconv
from pylearn2.datasets.mnist import MNIST... |
dacf9531092d9728e3f3858e4ca144af41218536c585c447d68057639afe18a7 | Python | 1,594 | 57 | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
"""Logging."""
import time
import os
import logging
import functools
import sys
from fvcore.common.file_io import PathManager
@functools.lru_cache(maxsize=None)
def _cached_log_stream(filename):
return PathManager.ope... |
1d7b396793719edd5862ca8a84b280bde3b4bcb55f62fdecb1a85be83e93ffb6 | Python | 1,595 | 49 | # This script runs the pipeline on all folders in a directory
import warnings
import os
warnings.filterwarnings("ignore")
os.environ["TF_CPP_MIN_LOG_LEVEL"]="2"
# Here you can choose which GPU to use
os.environ["CUDA_VISIBLE_DEVICES"]="0"
import cryovesnet
dataset_directory = "/mnt/data/amin/Handpicked/"
dataset_dir... |
f71d6068af37cd57d68ee5d9443aed9424811a7a5493ce943e246b5ee7c3d9d0 | Python | 1,595 | 66 | #!/usr/bin/env python
from __future__ import print_function
import os, shutil, sys
#sys.args.append('build')
from distutils.core import setup, Extension
# pr2_without_sensor_ik_files
# python setup.py build
LEFT_IK = 'ikLeft'
RIGHT_IK = 'ikRight'
LIBRARY_TEMPLATE = '{}.pyd'#'{}.so' # might need to be '{}.pyd' on w... |
4810ba22f5c7acc2709cc0f08d8e97d5cd8bcf70c72ac2ab0e9ab2a82ce6d09f | Python | 1,596 | 57 | from ray import tune
def _tune_config(params, cli_report_columns=[]):
result = {}
for key, val in params.items():
if isinstance(val, dict): # not an end-point
val, _ = _tune_config(val, cli_report_columns)
if not val: #
continue
if ... |
8340dc0fe5f054febce468e9601b14a469aad06582a3679a1cf9acd40e8189b9 | Python | 1,596 | 57 | import os
import re
from setuptools import setup, find_packages
from setuptools.command.install import install
__pkg_name__ = 'bonito'
verstrline = open(os.path.join(__pkg_name__, '__init__.py'), 'r').read()
vsre = r"^__version__ = ['\"]([^'\"]*)['\"]"
mo = re.search(vsre, verstrline, re.M)
if mo:
__version__ = ... |
eff02b81abf05aaa4b3e182b42028a64c39ba62f79f70c575add660521d11202 | Python | 1,596 | 46 | """Progress-queue engine tests for installer.wizard: run_steps() is a pure,
module-level function driven with a real queue.Queue and fake Steps - NO
threads, NO tkinter mainloop. Kept in its own module per the smoke-test
isolation convention (see test_wizard_smoke.py)."""
import os
import queue
import sys
_R... |
78db3093469f68af5a00f1f6279cd2595e805101f82ef643a2fc126edce2f47e | Python | 1,597 | 50 | # -*- coding: utf-8 -*-
from __future__ import print_function
import logging
import sys
from . import aliases
from . import arguments
from . import cleanup
from . import run_components
def main():
args = arguments.parse_args()
logging.basicConfig(level=getattr(logging, args.log_level.upper()),
... |
c8b73d3e93a2770d079e1ef466a5076767de0acf2d57e1dbbbd3c206b8fc47f5 | Python | 1,597 | 50 | import sys
from cuppa.runners.args import RunnerArgParser
from cuppa.runners.prediction_runner import PredictionRunner
from cuppa.runners.training_runner import TrainingRunner
class TestRunnerArgParser:
def test_can_add_and_parse_one_arg(self):
sys.argv = [
"example_module.py",
"... |
49b959a0f9b929e47ff36a89e4738df63f16f8d8f0902b8e2d85c944262ac6ce | Python | 1,598 | 42 | """Regression guard for the gain-compensation name-shadowing bug.
The module does ``from . import gain_compensation`` (the module). The
standalone ``__main__`` block used to also do ``gain_compensation =
args.gain_compensation`` (a bool) at module/global scope, which rebound that
global. ``compute_gain_field`` ... |
661241694b2dcf8547ca9c7ce6249bfc7a34ccfeb3fc81bb505a1723100cca8f | Python | 1,598 | 59 | import os
from flask import Flask, request, redirect, url_for
from codex.blueprints.app import app
from codex.blueprints.base import base
from codex.data.neuron_data_factory import NeuronDataFactory
from codex.configuration import RedirectHomeError
from codex import logger
import logging
# Set logger level
logger.se... |
9dc37d07f6866140d54075aff8425518224d4b55f7b8420e43b73f283fc93ca4 | Python | 1,598 | 60 | """Module with helper functions for plotting
"""
from vispy.app import Application
from PyQt5.QtWidgets import QApplication
app = Application('pyqt5')
from vispy.scene import SceneCanvas, TurntableCamera
from vispy.visuals import Visual
from vispy.scene.visuals import create_visual_node
from vispy.geometry import cre... |
1c6ff43ce25b4fac78517c9dad275171c73672e877f4e4a2512187484228823d | Python | 1,600 | 51 | import os
from torch.utils import data as torch_data
from torchdrug import data, utils
from torchdrug.core import Registry as R
@R.register("datasets.Stability")
@utils.copy_args(data.ProteinDataset.load_lmdbs, ignore=("target_fields",))
class Stability(data.ProteinDataset):
"""
The stability values of prot... |
f6e8938f5d927d93e38bc7c4843e63e4876512a1f127d6847b4f986dc7d3c4e1 | Python | 1,600 | 60 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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 applicab... |
4d26d1996cd3736eb0d2082c5756f15697960c1f10348adeeadc1897b1886411 | Python | 1,601 | 43 | class BaseReporter(object):
"""Delegate class to provider progress reporting for the resolver."""
def starting(self):
"""Called before the resolution actually starts."""
def starting_round(self, index):
"""Called before each round of resolution starts.
The index is zero-based.
... |
9ea79041785a10b9d4e463f45046fb0baec2bbbe27d95608ad485e1da7e10629 | Python | 1,601 | 44 | #!/bin/env python3
'''
Define a Feynman diagram
'''
import pdlfeynman as fy
import yaml
diagram = fy.diagram.Diagram()
x = 1
n00 = fy.diagram.Node.Reaction(time=x, reaction=fy.particle.growth.pair_production)
diagram.add_node(n00, x=x, y=0)
x += 1
n10 = fy.diagram.Node.Reaction(time=x, reaction=fy.reaction.growth_de... |
cc91f0c0487ae44b508e57f43ab3cc00d658a4e79e2f1ceda95e2ea631bd7709 | Python | 1,601 | 68 | """raw.py - read and write .raw files
"""
import numpy as np
def raw_imread(path):
"""Read a .raw file
:param path: path to the file
:returns: a Numpy read-only array mapping the file as an image
"""
as_uint32 = np.memmap(
path,
dtype=">u4",
mode="r", shape=(2,))
wid... |
2759cb98c7da06ce46991a51eebc125b46c66a09cd02502803f57a59adfa6aa9 | Python | 1,603 | 50 | """Atlas segmentation - port of utils/atlas_segmentation.m."""
from __future__ import annotations
import numpy as np
from skimage import feature
from .edges import largest_connected_component, canny_edge
def atlas_segmentation(image: np.ndarray) -> np.ndarray:
"""Extract registration contours from a... |
02af20d5d715f9aa85bdc2c7ce33cc1600446bedffcd3ced0a59e6f89e431c6a | Python | 1,604 | 58 | from dreamcoder.program import *
from dreamcoder.type import *
def _addition(x): return lambda y: x + y
def _subtraction(x): return lambda y: x - y
def _division(x): return lambda y: x / y
subtraction = Primitive("-",
arrow(tint, arrow(tint, tint)),
_subtraction)
... |
afdc4c15e52f46690371797fefd532cd847a2d9417178ebed16f68b2b8d20330 | Python | 1,604 | 60 | from __future__ import annotations
import pytest
from quacc import job
from quacc.wflow_tools.customizers import customize_funcs
def test_basic_customizers():
def add(a, b=1, c=2):
return a + b + c
def mult(a, b=1, c=2, d=2):
return a * b * c * d
add_, mult_ = customize_funcs(
... |
b449089fbb1965244159aa76e477ff50fa36e93cec8576b465fae4459bbf2a2b | Python | 1,604 | 48 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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 applicab... |
57c9ad3962d3349b582d6fb3f248e20b517474f50dd39a284288af3758d8a0f5 | Python | 1,605 | 48 | # ----------------------------------------------------------------------------
# Contributors: Thiago O. Bezerra
# Antonio C. Roque
# ----------------------------------------------------------------------------
# File description:
#
# Run all simulations specified in text files from the Input direct... |
ae9a809a9bd82665799b95e32df5e47af6627438910217807bb39639997815d9 | Python | 1,605 | 55 | # -*- coding: utf-8 -*-
from setuptools import find_packages, setup
setup(
name='supar',
version='1.1.4',
author='Yu Zhang',
author_email='yzhang.cs@outlook.com',
license='MIT',
description='State-of-the-art parsers for natural language',
long_description=open('README.md', 'r').read(),
... |
69f011e21be7b8355f5dfb889846102479d4802e162e5700d16b31d0e32fb87f | Python | 1,606 | 45 | import pandas as pd
import pickle as pkl
from Bio import Align
utr_data = pd.read_csv('/fast/AG_Ohler/frederick/projects/mlcis/data/riboseq/calviello_te_processed.csv')
mrl50 = pd.read_csv('/fast/AG_Ohler/frederick/projects/mlcis/data/mrl25to100/GSM3130443_designed_library.csv').drop('Unnamed: 0', axis=1)
mrl50 = mrl... |
acee1b177ffb039c56e0f15891b2899a89c5ca73907baa73d85f44515f419f7a | Python | 1,606 | 46 | """Unit tests for the SSC (Self-Similarity Context) descriptor generator."""
import os
import sys
PROJECT_ROOT = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
if PROJECT_ROOT not in sys.path:
sys.path.insert(0, PROJECT_ROOT)
import numpy as np
import pytest
from regtools.registration.... |
54d92bbc65e365d19ad4da34dc0e5cf9d025fa809865771ebae5fd1ec23c16eb | Python | 1,607 | 70 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Author:
Maximilia F. S. Degenhardt <frazaodesouzam2@nih.gov>
Hermann F. Degenhardt <degenhardthf@nih.gov>
"""
import os, sys, math
sys.path.append("../src")
from hornet.uml import uml_analysis
def help():
return """
uml.py: Run the UML approach f... |
696b4092631b9b8e081dc7d03960355f6a2182f110b40880088c24c2154d908b | Python | 1,607 | 46 | # Defining color-blind friendly color palettes
import tol_colors as tc
cmap_iridescent = tc.tol_cmap("iridescent")
cset_bright = list(tc.tol_cset("bright"))
cset_light = list(tc.tol_cset("light"))
cset_vibrant = list(tc.tol_cset("vibrant"))
cset_high_contrast = list(tc.tol_cset("high-contrast"))
cset_muted... |
a50a253766ae2b47c408f49efb588ca793877d51bc1711c3bcb085d13c747944 | Python | 1,607 | 47 | import numpy as np
from pandas import read_json
from .deprecation import deprecated
from .model_assembly import (
CompartmentContainer,
ParameterContainer,
ReactionContainer,
SpeciesContainer,
)
from typing import Union
from pathlib import Path
__all__ = ["json_to_ObjectContainer"]
@deprecated
def js... |
bbdb704ca0b961ef47ee960e2be77779ee0d99eaf262e585fbd52b6313015cb8 | Python | 1,607 | 34 | # -*- coding: utf-8 -*-
import os
import supar
from supar import Parser
def test_parse():
sents = {'en': ['She enjoys playing tennis.', 'Too young too simple!'],
'zh': '她喜欢打网球.',
'de': 'Sie spielt gerne Tennis.',
'fr': 'Elle aime jouer au tennis.',
'ru': 'Она ... |
21f56622a01f6bdd78f306c11b73644d92c00d166147190d44ae9a2c130eb56d | Python | 1,608 | 65 | import pandas as pd
from sklearn.compose import make_column_selector
from tests.mock_data import MockTrainingData
from cuppa.components.feature_selection import Chi2FeatureSelector
class TestChi2FeatureSelector:
X = pd.DataFrame([
[10, 0, 0, 0],
[10, 1, 0, 0],
[10, 0, 0, 0],
[0,... |
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