sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
b579d0dadb5d1fbd1c92b0c037dc923c6bdaf6107d554952eb35a003ca0e9909 | Python | 18,690 | 561 | from typing import Any, Optional, Sequence, Tuple, Union
from ..commons.utils import JsCode
Numeric = Union[int, float]
JSFunc = Union[str, JsCode]
class BasicOpts:
__slots__ = ("opts",)
def update(self, **kwargs):
self.opts.update(kwargs)
def get(self, key: str) -> Any:
return self.op... |
ce445d47efbbf3a19fad49f01ce470343c0e3f296a5f761f7e3c66f0bbde9417 | Python | 18,694 | 467 | """Class that represent a model builit into ``vak``."""
from __future__ import annotations
import inspect
from typing import Callable, Type
import lightning
import torch
from .decorator import ModelDefinitionValidationError
from .definition import validate as validate_definition
class ModelFactory:
"""Class t... |
8c8faac6067e09756dbd6786b6742e22fb2615d4d7da8ee672f1496e3ff80980 | Python | 18,697 | 517 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
from dataclasses import dataclass, field
from typing import Optional
import logging
import math
import torch
import torch.nn as nn
import tor... |
bf9f987606a1b87ec0a92daef274eafecf20fa250a731f4c48e486ea60e80369 | Python | 18,698 | 500 | import os
import tempfile
import unittest
import warnings
import numpy as np
import numpy.testing as np_test
from skbase.utils.dependencies import _check_soft_dependencies
from pgmpy import config
from pgmpy.example_models import load_model
from pgmpy.factors.discrete import TabularCPD
from pgmpy.models i... |
5eefd7375baf9b77b5df4b3a68ac7e1610c8d5ae4fdf48d5053a7f9d66466a89 | Python | 18,699 | 611 | """Base wrapper for VTK objects."""
# Author: Oualid Benkarim <oualid.benkarim@mcgill.ca>
# License: BSD 3 clause
import numpy as np
import vtk
from vtk.numpy_interface import dataset_adapter as dsa
from vtk.util.vtkConstants import VTK_STRING
from .utils import call_vtk, get_vtk_methods, is_numpy_string, is_vtk_str... |
a152ee48e2f82bdbbf65a51a9c77b2d708b2bc3b3c6e9a750a9bd10a217b452f | Python | 18,711 | 507 | from neuron import h
import math
import time
import random
import numpy
from matplotlib import pyplot as plt
#cell that contains only 1 spine
class cell() :
def __init__(self, name="cell", gid=0):
#random.seed(1) #use the same seed to get same number in every run
random.seed(time.time())
... |
62fed99ca4c9b0bbea71686e282833a8b2acb6cd162abfd1dff0b1a471d5cf9d | Python | 18,713 | 491 | import warnings
warnings.filterwarnings('ignore')
from typing import Callable, Tuple, Union
import math
import torch
from torch import Tensor
import torch.nn as nn
import torch_geometric.nn as gnn
import torch.nn.functional as F
from torch_geometric.nn.conv import MessagePassing
from torch_geometric.nn.dense.linear im... |
8a1c16964146a8cf33f4a507c15ea1b0a5d6f0390b406f4361fc1451655010aa | Python | 18,745 | 438 | #!/usr/bin/env python3
"""
@file interpret.py
@author Simon Yu
@date 03/12/2024
@brief NPC Interpretation Utility.
"""
import header
import json
import logger
import os
os.environ["QT_LOGGING_RULES"] = "qt.gui.icc=false"
import PyQt5.QtCore
import PyQt5.QtGui
import PyQt5.QtWidgets
application = PyQt5.QtWidge... |
962a23c28d10ed9905002d2000e1b3c20ad124c95ef19665816de6e9b46c99c8 | Python | 18,751 | 451 | # Copyright (c) 2024, Shenghao Cao & Ye Yuan. Shanghai Jiao Tong University, Shanghai 200240, China
# Some classes and functions are modified from scGPT (https://github.com/bowang-lab/scGPT), copyright (c) 2022 suber
# The gene symbol and value encoding modules and initialization weights are from scFoundation (https://... |
74ea537748541302b8dc183be874ac7d75e1f307eb8c7e208554ec7036230a76 | Python | 18,758 | 329 | # -*- coding: utf-8 -*-
# Resource object code
#
# Created by: The Resource Compiler for PyQt5 (Qt v5.9.5)
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore
qt_resource_data = b"\
\x00\x00\x02\x1f\
\x89\
\x50\x4e\x47\x0d\x0a\x1a\x0a\x00\x00\x00\x0d\x49\x48\x44\x52\x00\
\x00\x00\x1e\x0... |
d2eeb4267c25146b7058e623eae21bdea972d8a33f6cac4e05c34fcc65119ed9 | Python | 18,778 | 503 | from __future__ import annotations
import dataclasses
import functools
import logging
import time
import urllib.parse
from pathlib import Path
from typing import TYPE_CHECKING
from typing import Any
import requests
import requests.adapters
import requests.auth
import requests.exceptions
from cachecontrol import Cac... |
cb31ceb6ce60c77086da3ef3cdb90552ac86ce52e783b83a8aba24d913714d10 | Python | 18,779 | 486 | import os
import re
from pathlib import Path
import numpy as np
import pandas as pd
import bombcell.extract_raw_waveforms as erw
def load_ephys_data(ephys_path):
"""
This function loads the necessary data from the spike sorting to run BombCell
Parameters
----------
ephys_path : str
The ... |
75424ace3ffb1d26f8d479f261acc456f3c4bab7b363f1b53e5a206cff3bc92f | Python | 18,799 | 512 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""methods to more reliably save random forest classifiers with ONNX
Data are stored with the following scheme
- onnx_rdf_classifier/
| - onnx_rdf_classifier_meta_data.json
| - onnx_rdf_classifier.onnx
| - onnx_rdf_classifier_training_data.csv
| - onnx_rdf_classifie... |
1d6c461e1aadff30bc4b86222c4c2890a8b7973465f05f253b4804ab430d871a | Python | 18,833 | 310 | ###主要功能：对一次实验的所有数据进行预处理
###先对视觉刺激记录的数据进行第一帧分析，紧接着做组内叠加平均（分别获得各组水平、竖直和功能柱）
###其次对电流刺激记录的数据进行第一帧分析和组内叠加平均
##1.先在第27行设置存储组内叠加平均结果的日期文件夹
##2.点击选择数据按钮，在Fileoperate目录下选择需要处理的原始数据，选到日期目录即可
###20210928 读取相机记录的数据后归一化到[-1,1]
##20210929 读取相机记录的数据后进行高斯滤波
##20211014修改视觉刺激组间平均dR/R的计算方式
##20211104视觉刺激数据处理和电流刺激数据处理各自用不同的图片数量... |
9582169ced6c1d8d4887bfd218ae6d8658ddb2cc46d690ca5f1ca36a5c17040a | Python | 18,836 | 551 | import json
import pickle
from pathlib import Path
from collections import Counter, OrderedDict
from typing import Dict, Iterable, List, Optional, Tuple, Union
from typing_extensions import Self
import numpy as np
import pandas as pd
import torch
import torchtext.vocab as torch_vocab
from torchtext.vocab import Vocab
... |
776b41af9c8d49131d103ef54c8e0bea892a8313137e9c191fd8e74a41c05b58 | Python | 18,902 | 410 | import pandas as pd
import numpy as np
import scanpy as sc
from random import shuffle
sc.settings.verbosity = 0
from tqdm import tqdm
import requests
import os, sys
import warnings
warnings.filterwarnings("ignore")
from .utils import parse_single_pert, parse_combo_pert, parse_any_pert, print_sys
def rank_genes_group... |
eafbca883d7ae086f9b025e7eccff7fc73d19d79ff8f2821d3a68814ecf563ec | Python | 18,904 | 400 | import pandas as pd
import pytest
from pgmpy.estimators import (
AIC,
BIC,
K2,
AICCondGauss,
AICGauss,
BDeu,
BDs,
BICCondGauss,
BICGauss,
LogLikelihoodCondGauss,
LogLikelihoodGauss,
)
from pgmpy.models import DiscreteBayesianNetwork
# Score values in the tests are compared ... |
47d198c274602ff9076674b7c1ad1599dc0a9b452be3e35e4af6f0f6046e8451 | Python | 18,910 | 667 | # -*- coding: utf-8 -*-
"""
Created on Mon Feb 17 23:30:30 2025
@author: hanna
"""
import os
import pickle
import numpy as np
import pandas as pd
from tqdm import tqdm
import seaborn as sb
import matplotlib as mpl
import matplotlib.pyplot as plt
from matplotlib.lines import Line2D
from scipy import stats
from sci... |
075240984d50ca3c3c7390c8a4b7c68ab9937a98a8a6aa5c635a597b379a289a | Python | 18,928 | 714 | """
Ablation Study for Garfield: Denoised-Graph Branch and Hyperparameter Analysis
This script performs comprehensive ablation studies to answer reviewer questions:
1. Quantify the contribution of the SVD-based denoised-graph branch
2. Compare performance with SVD vs dropout augmentation
3. Evaluate impact of GNN iter... |
bec5a88d652f3724fe594e2816180838166a9778bf1ab70cfd22a2d2589c6248 | Python | 18,934 | 413 | #!/usr/bin/env python
# This covers the obvious parameters, however, there are some that aren't
# being tested for absence or alternate values and combinations.
import sys
import io
# This allows us to run an individual test as it's own 'program'. Very useful
# for debugging
if "DEBUG" in sys.argv:
sys.path.inser... |
b0f4465bf6188511bbdc8c9cf41d4915630e9925fdc202758a883f8da0b67f3b | Python | 18,941 | 525 | """Section construction for the graph settings panel."""
from __future__ import annotations
from typing import TYPE_CHECKING
from PySide6.QtWidgets import (
QFrame,
QGridLayout,
QHBoxLayout,
QLabel,
QPushButton,
QScrollArea,
QVBoxLayout,
QWidget,
)
from src.gui.framework.qt_view_styl... |
a9d67ab4c1bc8bab1c036dc5355c9df4822ed2c799e9cb48afaf7626b15424fc | Python | 18,944 | 482 | # Authors: Christian O'Reilly <christian.oreilly@sc.edu>
# Scott Huberty <seh33@uw.edu>
# License: MIT
"""Python file to instantiate the graphs for the qcr app."""
from pathlib import Path
# file selection
import tkinter as tk
from tkinter import filedialog
import multiprocessing
import pandas as pd
impo... |
4b6f5e664313bc00b10ed0f6e3195d9a003218f7792febb0abe4e37289edb916 | Python | 18,962 | 339 | import argparse
import os.path
from copy import deepcopy
from typing import Union, List, Tuple
from batchgenerators.utilities.file_and_folder_operations import (
load_json, join, isdir, listdir, save_json
)
from nnunetv2.configuration import default_num_processes
from nnunetv2.ensembling.ensemble import ensemble_c... |
162ed66ff4dda5e962944a22a6d2ea87fec408c95cc8d16b6a6a7bcc093a2d36 | Python | 18,964 | 517 | from __future__ import annotations
import re
from enum import IntEnum
from io import BytesIO
from pathlib import Path
from typing import TYPE_CHECKING
from typing import Protocol
from urllib.parse import urlparse
from zipfile import ZipInfo
import pytest
import requests
import responses
from requests import codes
... |
a3057033ec394aefd424f51fe8b866f6bd868930fe06f10b213a5d846ef7d96e | Python | 18,983 | 527 | from __future__ import annotations
from typing import TYPE_CHECKING
import torch
from scvi import REGISTRY_KEYS
from scvi.module._constants import MODULE_KEYS
from scvi.module.base import BaseModuleClass, EmbeddingModuleMixin, LossOutput, auto_move_data
from ._base_components import EncoderDecoder
from ._priors imp... |
63330770e709e8f72759a98451b8a0d088ab9dab762627566550c5564b2300fc | Python | 18,988 | 462 | """Code that handles classes that represent the definition
of a neural network model; the abstraction of how models
are declared with code in vak."""
from __future__ import annotations
import dataclasses
import inspect
from typing import Type, Union
import torch
REQUIRED_MODEL_DEFINITION_CLASS_VARS = (
"network... |
e07821f94443c92a8f407795f6cdb2e0b78968987e71bf964732eb2a87bd22b4 | Python | 19,006 | 477 | # Copyright (c) 2017-present, Facebook, Inc.
# All rights reserved.
#
# This source code is licensed under the license found in the LICENSE file in
# the root directory of this source tree. An additional grant of patent rights
# can be found in the PATENTS file in the same directory.
import logging
import os
import to... |
fe3b1e943f518d265253772bb101e55171db4abf08161638fcf81aabe045ef82 | Python | 19,010 | 509 | # -*- coding: utf-8 -*-
"""
This module contains methods used for e-mailing. Currently, is used to write
notification message in a folder. Codes to send e-mail is saved as commentar.
Custom notification messages are saved in Email folder also in HelperFunctions
folder as text files. The text files can be edited accor... |
b140c624ead505099188417655e001565aa824a303741cb4216434fd798a7ea4 | Python | 19,015 | 446 | import slicer, vtk
import numpy as np
from io import StringIO
import warnings
#
# Feature
#
class Feature():
def __init__(self, projectTo):
self.projectTo = projectTo
def addSourceNode(self, sourceNodeID, property, visible):
shNode = slicer.mrmlScene.GetSubjectHierarchyNode()
id = shNode.GetItemBy... |
f4bccff3b6c2a63eb4039bb3f7cdab451b664a1db49d66052b5f8fdab65cbc29 | Python | 19,038 | 527 | from __future__ import annotations
import os
import shutil
import zipfile
from functools import cached_property
from importlib import metadata
from pathlib import Path
from typing import TYPE_CHECKING
from typing import NamedTuple
import pytest
from poetry.repositories.installed_repository import InstalledRepositor... |
8466653c231a4fa04e97375967c299c6c6fa25405dd81bf119bf2a4455982e27 | Python | 19,046 | 521 | import itertools
import xml.etree.ElementTree as etree
import numpy as np
from pgmpy.factors.discrete import TabularCPD
from pgmpy.models import DiscreteBayesianNetwork
from pgmpy.utils._warnings import _warn_external
class XBNReader:
"""
Initializer for XBNReader class.
Parameters
----------
p... |
c56c35153b02ebf2230b01f4cac2c68dc629cfed5016e921ccb5404206eb4bcc | Python | 19,051 | 456 | ## cluster statistics
#
# written by S-C. Baek
# update: 16.12.2024
#
'''
The following code is to infer the results of time-resolved RSA or mTE analysis at the group-level.
'''
import os
import pickle
import itertools
import numpy as np
from scipy import stats as stats
import mne
from utils import fisher_z_transfo... |
a984ded898506ccc608f6eb10e9ec003e0c3a812222a37216fd52c68ab433d45 | Python | 19,056 | 396 | import unittest
from pathlib import Path
from tempfile import TemporaryDirectory
from types import SimpleNamespace
from unittest.mock import patch
import parmed
from GMXMMPBSA.alamdcrd import GlyMutantMdcrd, MutantMdcrd, _getnumatms
from GMXMMPBSA.exceptions import MMPBSA_Error
from GMXMMPBSA.make_top import CheckMak... |
bd5ce6366ff8000164d14ce5287f102af5f6f86cf4d25964f10eaab4164c2fbb | Python | 19,059 | 533 | from pathlib import Path
# from plistlib import Dict
from typing import Union
import pickle as pkl
import lmdb
import numpy as np
import pandas as pd
import re
import torch
from scipy.spatial.distance import squareform, pdist
from tape.datasets import pad_sequences, dataset_factory
from torch.utils.data import Dataset... |
0e45ebc99661d565b6784db3d17f493cfee2a2d40f6aaeebd182459e512adda5 | Python | 19,061 | 505 | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
370a314d0dad44652f459db859ba763ce3466575625fe1d5ea228de6a3ff920c | Python | 19,081 | 514 | import numpy as np
import pdb
import os
# import h5py
import random
# from sklearn.model_selection import StratifiedKFold
import math
import time
from matplotlib import pyplot as plt
# import seaborn as sns
import pandas as pd
plt.switch_backend('agg')
import glob
import pdb
import argparse
import sys
i... |
032711a866ce80ab9222ffa032f082f546de5d3c7048a861f4390546c03ad341 | Python | 19,082 | 538 | # src/cluster_compare.py
# -----------------------------------------------------------------------------
# Purpose
# Direct, paired comparisons between TWO clusterings (e.g., mincut vs mincut+fp)
#
# Additions
# - boundary-matched evaluation over MULTIPLE seeds + aggregation
# - paired Wilcoxon + sign test on del... |
2be2e04cf32ba9a51f88862fe24580a76589f45f63fb53ec5c797f18c6f0ae6e | Python | 19,083 | 421 | import collections
import shutil
from contextlib import contextmanager
import logging
import os
import timeit
import time
import numpy as np
from numpy.lib.format import open_memmap
from mdt.configuration import gzip_sampling_results, get_processing_strategy
from mdt.lib.fsl_sampling_routine import FSLSamplingRoutine
f... |
44ef66654b761c10a06464a60d560203bcd404f2811a53a5c5b3f1088e313c4a | Python | 19,096 | 471 | """Helper functions for frame classification dataset prep."""
from __future__ import annotations
import collections
import copy
import logging
import pathlib
import shutil
import attrs
import crowsetta
import dask.bag as db
import numpy as np
import pandas as pd
from dask.diagnostics import ProgressBar
from ... imp... |
f3c660f952d5d924fb3c8ce4bcf02857f9b0cab1658ea35fe6bd510e12a710b2 | Python | 19,102 | 477 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import logging
import numpy as np
import torch
from fairseq.data import FairseqDataset, data_utils
logger = logging.getLogger(__name__)
d... |
99a604d97c6404d9df1a730e0feb27f343caf4605bb48337b88e31ec96ec1d11 | Python | 19,120 | 649 | # @license
# Copyright 2017 Google Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in... |
7218f80bb357c23d146042c9e99450acd0ca721c6662077e047c35bd96c8ce15 | Python | 19,137 | 475 | from __future__ import annotations
import hashlib
from PySide6.QtGui import QColor
from PySide6.QtWidgets import (
QColorDialog,
QDialog,
QFrame,
QLabel,
QPushButton,
QScrollArea,
QVBoxLayout,
QWidget,
)
from src.gui.framework.qt_view_styles import (
PALETTE,
panel_stylesheet,... |
b394a76854243cd33ab904634029e416a1f273409f911c88d660f52d0cffe153 | Python | 19,137 | 466 | # Source code:
# https://github.com/zbmed-semtec/doc2vec-doc-relevance-training/blob/main/code/train_model/utilities.py
# This file includes the modifications to the source codes according to this project!
import tqdm
import logging
import numpy as np
import pandas as pd
import gensim
from gensim.models import Word2V... |
1668747a0a391c447cddc3321385ee95f3ee6555e3b5ec804cf57b02ebe0d063 | Python | 19,139 | 525 | from __future__ import annotations
import logging
import warnings
from collections import defaultdict
from functools import partial
from typing import TYPE_CHECKING
from torch import nn
from torch.distributions import Binomial
from scvi.distributions import BetaBinomial
from scvi.external.methylvi._utils import METH... |
c58de32d063071eaccfb5d7ebeb65e9d2ae7ed3ee40c9c3377650c5293cab774 | Python | 19,149 | 574 | import os
import sys
import argparse
import numpy as np
import pandas as pd
# Add project root to path
project_root = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
sys.path.append(project_root)
from lib.utils.utils_data_generation import simulate_tumor_volume, simulate_single_drug_concentra... |
43d2eb49707c3a1f420776eff02a8e39bb371fa1bfbf5a7f67b8cc7ce1227bd0 | Python | 19,151 | 481 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import math
from typing import Dict, Optional, Tuple
import torch
import torch.nn.functional as F
from fairseq import utils
from fairseq.incr... |
b9a64a4f811ba5675b555a3759f2cc4c90ff4f25cf3d017eb16a2633e83cfdc7 | Python | 19,169 | 564 | import pymol2
import matplotlib.pyplot as plt
import numpy as np
import json
import pandas as pd
import seaborn as sns
import networkx as nx
from torch_geometric.utils import to_networkx
from typing import List
from itertools import groupby
from PIL import Image
from collections import Counter
from tqdm import tqdm
s... |
280a677a899e4682d69e501d7e5fb8515cd12f9eafa460cce929f98afa53d27b | Python | 19,170 | 450 | import os
import re
import tkinter as tk
from tkinter import filedialog
from tkinter import messagebox
from tkinter import simpledialog
from tkinter import ttk
import pandas as pd
from src.window_utils import center_window_on_screen
from src.app_settings_manager import AppSettingsManager
class DataSelectionFrame(ttk... |
7a1070e09de298589ca50ece81f20d1f66b988772cc7256b44f6741253b00df3 | Python | 19,194 | 521 | #!/usr/bin/env python3
from typing import Any
import matplotlib.pyplot as plt
import numpy as np
import numpy.typing as npt
import yaml
from microcircuits import model as model
from microcircuits.model import WeightsList
class Descriptor(dict):
"""Parameter container supporting both dict and attribute access.
... |
0023ac43fc4b8513e5f222e09352b71d6c9131e34fffff1322df4056db2778f2 | Python | 19,200 | 544 | from __future__ import annotations
import contextlib
import functools
import glob
import logging
import tempfile
from pathlib import Path
from tempfile import TemporaryDirectory
from typing import TYPE_CHECKING
from typing import Any
import pkginfo
from poetry.core.constraints.version import Version
from poetry.cor... |
3b40bf62ccd6d6e3db6b06c5a6c40b387f92b682336edeadc0435bbb65aefa82 | Python | 19,214 | 562 | from __future__ import annotations
import os
from typing import TYPE_CHECKING
import numpy as np
import pyro
import pyro.distributions as dist
import pytest
import torch
from pyro import clear_param_store
from pyro.infer.autoguide import AutoNormal, init_to_mean
from pyro.nn import PyroModule, PyroSample
from torch i... |
5ccf6fcfd1a5dbce32ea1228d71186ae3e70d33ffd63e5e79c5d34afca6c103b | Python | 19,224 | 609 | from __future__ import annotations
from typing import TYPE_CHECKING
from typing import Any
import pytest
from packaging.utils import canonicalize_name
from poetry.core.packages.dependency import Dependency
from poetry.core.packages.dependency_group import MAIN_GROUP
from poetry.core.packages.package import Package
f... |
9ff6dcb921ac2e42378d1fdffd83edc93ba05b84f710b8b7c61d25012071957e | Python | 19,235 | 614 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import shutil
import struct
from functools import lru_cache
import numpy as np
import torch
from fairseq.dataclass.constants import DATASET_I... |
193e4f1c60c10890887134ecde28dd55f160614d4a37203f9b04d2489421672f | Python | 19,241 | 517 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import logging
import math
from collections import OrderedDict
import torch
from fairseq import utils
from fairseq.logging import metrics
fr... |
4f3437ebfb94363d3d8d466f17e3db98c66608400c0fa1fabfaaeb1a58f3d289 | Python | 19,244 | 560 | # Illustration of the BEM Simulation
#%%
# Imports
import os.path as op
import numpy as np
import pyvista as pv
import mne
from pyvistaqt import BackgroundPlotter
from bfieldtools import sphtools as sph
import functions
#%%
import matplotlib.pyplot as plt
font = { 'size' : 20}
plt.rc('font', **font)
#%% Plot para... |
13c5086c0296b570617077c0e67844e7539bde9a937b0e73e7cf3db557edf1b3 | Python | 19,251 | 411 | """Page 11: BDP Degradation Explorer."""
import streamlit as st
import plotly.express as px
import plotly.graph_objects as go
import pandas as pd
import numpy as np
from utils import PIPE_ORDER, PIPE_COLORS, DEGRADE_COLORS, style_figure
def render(store, dataset):
st.header("BDP Degradation Explorer")
st.mar... |
1bf075b3b1eee0e9e351a32f909558161cafde58684b22f863e5014715141c32 | Python | 19,254 | 431 | import time
import RPi.GPIO as GPIO
from VariableList import var_list
from RotatryEncoderv1 import RotaryEncoder
import tkinter as tk
from tkinter import simpledialog
class threadedcontrols:
# setup GPIO
GPIO.setwarnings(False)
GPIO.setmode(GPIO.BCM)
def __init__(self, UIinstance):
self.sendtoUI... |
c7b4ff1765fdb2781c6c6074851412f137cb7c39c2f0ab2185d1ede335f097cf | Python | 19,254 | 431 | import time
import RPi.GPIO as GPIO
from VariableList import var_list
from RotatryEncoderv1 import RotaryEncoder
import tkinter as tk
from tkinter import simpledialog
class threadedcontrols:
# setup GPIO
GPIO.setwarnings(False)
GPIO.setmode(GPIO.BCM)
def __init__(self, UIinstance):
self.sendtoUI... |
223c5ac29310210dac09b4042ae72466494ea2c3c6f4bb7d6e7e0546cb1d7012 | Python | 19,258 | 389 | from distutils.archive_util import make_tarball
import os
import importlib
from pickle import TRUE
import numpy as np
import matplotlib.pyplot as plt
import time
import torchvision
import seaborn as sns
import numpy as np
import pytorch_lightning as pl
import torch.nn.functional as F
import torchvision
from torchvision... |
a1d6b98fd1816e094d1e401cef6d7ac02127fdb9f4948b5c3f60625015c4601e | Python | 19,303 | 617 | # -*- coding: utf-8 -*-
"""
Created on Tue Feb 25 17:21:36 2025
@author: hanna
"""
import os
import pickle
import numpy as np
import pandas as pd
from tqdm import tqdm
from datetime import datetime
from scipy import stats
from scipy.optimize import curve_fit
# import warnings
# warnings.filterwarnings("ignore")
f... |
774c6b4301623d64b04f3c2d8ef43d89d6bfd27c5568d26de967df69deb1b7d2 | Python | 19,318 | 499 | import collections
import os
import pathlib
import rootutils
import functools
import pandas as pd
import hydra
import lightning as L
import omegaconf
import copy
import torch
import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
from sklearn.metrics import roc_auc_score, roc_curve
from loguru import... |
18023b94c7186c23ac479c87e9183368f13a77504566cdaeb205dcd4d358c35a | Python | 19,322 | 526 | #!/usr/bin/env python
# @license
# Copyright 2018 Google Inc.
# 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... |
9ca58b466f7b487860dbf50fc017d52e68852d9cee04c8cd3f55c4d52877d89d | Python | 19,336 | 514 | # utils/movefuncs_utils.py
import datetime
import numpy as np
import os
import re
import scipy.io.wavfile as wav
import threading
from jinja2 import Template
from pathlib import Path
from scipy.io import savemat
from PyQt6.QtWidgets import QMessageBox
from moove.qt_helpers import invoke_in_main_thread, set_combo_item... |
3116d57c22bae9528a598a1fdfd20f4f93fdeb2abd4d2f067fccde6c821102df | Python | 19,376 | 443 | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
d5a6b726fa8b1e3e07fd2c3f4c4e1e7b70f0a7718b2d577a048c8a97d4fa592c | Python | 19,384 | 407 | import torch
from dataclasses import dataclass
from torch._C import dtype
from transformers import PreTrainedTokenizerBase
from typing import List, Dict, Optional, Tuple
from src.dataset import ProteinGoInputFeatures, GoGoInputFeatures, ProteinSeqInputFeatures
def _collate_batch_for_protein_seq(
examples: List[D... |
1783a08a4eabec68723f4544ba93c1cb1fa92809a59e1ae91a90bd4c43ec90c3 | Python | 19,408 | 536 | import argparse
import gzip
import os
import re
from pathlib import Path
import numpy as np
import pandas as pd
TARGETS_PATH = "__MS_GEO_ROOT__/Methylation_Target_Datasets.csv"
BASE_DIR = "__MS_GEO_ROOT__/Methylation_Data"
MIN_FEATURE_OVERLAP = 5000
def sanitize_label(value: str) -> str:
clean = re.sub(r"[^A-Z... |
901b08c0d0cf2261f2d25e73484993f207f160b4fe0a81bbdf2dd772f957b516 | Python | 19,408 | 510 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import ast
import inspect
import logging
import os
import re
from argparse import ArgumentError, ArgumentParser, Namespace
from dataclasses im... |
ad2c2eba5406d4225557e92654bc5d2a912b47134b4f9e7de2c07196c4ff9594 | Python | 19,422 | 602 | """Shared execution and resumability for maintained inference families."""
from __future__ import annotations
import hashlib
import importlib.metadata
import json
import os
import tempfile
from collections.abc import Callable
from dataclasses import dataclass, replace
from pathlib import Path
from typing import Any, ... |
dd9e8b28d098dfa7eca0ed27adb3d5b7b8e8516bc0d131961d676abda035f64f | Python | 19,449 | 327 | """InferRef3D v1.0: trusted TrainRef3D state_dict + canonical request -> reviewable labelmap.
Archives are validated before extraction. The source is never uploaded by this
module itself, model checkpoints are loaded with weights_only=True, and the
prediction is resampled back to the request's exact original NIfTI gri... |
739f2d5976b22ce9d4a30c905474890abfcd26dff2c1605e3e8e9b275ed570ad | Python | 19,469 | 557 | #!/usr/bin/env python3
import argparse
import os
import unittest
from inspect import currentframe, getframeinfo
import numpy as np
import torch
from examples.speech_recognition.data.data_utils import lengths_to_encoder_padding_mask
from fairseq.data import data_utils as fairseq_data_utils
from fairseq.data.dictionary... |
412eab9ddb0087df073ea62386a1f56ac1c5dac5ecfff870c3a9d5ab7a7a6789 | Python | 19,481 | 1,119 | """
CGCNN-like embeddings using continuous values instead of original k-hot.
Properties:
Group number
Period number
Electronegativity
Covalent radius
Valence electrons
First ionization energy
Electron affinity
Block
Atomic Volume
NaN stored for unavaialable parameters.
"""
CONTINUO... |
3b4e23f0b37b76566001397ea459acb786825b44caa1b14c8cc56457a58b0fd1 | Python | 19,482 | 489 | """`compile_trunk` compiles the trainable top encoder layers, not the model.
A real, tiny 4-layer `BertModel` (`patch_base_model` only injects 2, so this
builds its own), top 2 layers trainable: a frozen prefix and a trainable
top both exist, the shape that makes `BertLayer.forward`'s one code object
guard on `require... |
11ac2ea8febb952ef39baccdf52abcdcd60c93b956e58eeb62db9353e7f26eed | Python | 19,505 | 463 | # Source code:
# https://github.com/zbmed-semtec/doc2vec-doc-relevance-training/blob/main/code/train_model/utilities.py
# This file includes the modifications to the source codes according to this project!
import tqdm
import logging
import gensim
import numpy as np
import pandas as pd
from scipy.spatial.distance impo... |
7259d043f828f980d97fff9a8ac49cc052c70754f8fd18b9cdae574fedcc5636 | Python | 19,516 | 412 | """Shared SegRef3D <-> SegAnything segmentation job archive support."""
from __future__ import annotations
import copy
import io
import json
import os
from pathlib import Path, PurePosixPath
import shutil
import zipfile
from PIL import Image
FORMAT_VERSION = "segref3d-segjob-1.0"
MANIFEST_NAME = "manifest.json"
JO... |
d2fa971962b70948204085131b186b8f36d6262944e7e921da972a3449c2839e | Python | 19,522 | 548 | """The mention spans: the boundaries the per-token codes cannot carry."""
import collections
import dataclasses
import h5py
import numpy
import pytest
from conftest import (
_BACTERIUM,
_ENZYME,
_STAMP,
_TOKENIZER,
_empty_labels,
_encode,
_labels_over,
_rows,
)
from d3text import surfa... |
1233f42daa681360294f46c512b9df0381fff5b695e4b05eb547f17314145bbb | Python | 19,551 | 522 | #!/usr/bin/env python3
import itertools
from collections import defaultdict
import numpy as np
from networkx.algorithms import bipartite
from pgmpy.base import UndirectedGraph
from pgmpy.factors import factor_product
from pgmpy.factors.discrete import DiscreteFactor
from pgmpy.models.DiscreteMarkovNetwork import Dis... |
6934c82eb55c522e1116da944917193b8d850c08306cd35f4a80e07d8c200142 | Python | 19,565 | 517 | import os
import numpy as np
import pandas as pd
import pytest
from mudata import MuData
from scvi.data import synthetic_iid
from scvi.external import TOTALANVI
from scvi.model import TOTALVI
def test_totalanvi():
# test transfer_anndata_setup + view
adata = synthetic_iid()
TOTALANVI.setup_anndata(
... |
a6dff3fff64f49f061847b91ec67041586d59720426ec360e78c15a24fb59d2f | Python | 19,594 | 546 | import os
import math
import warnings
from typing import Mapping, Optional, Tuple, Any, Union
import torch
from torch import nn, Tensor
import torch.distributed as dist
import torch.nn.functional as F
from torch.nn import TransformerEncoder, TransformerEncoderLayer
from torch.distributions import Bernoulli
from torch.... |
1bea7d6fbf6a57759105eb4880634b710a4d2d26f42a4899cc2ef65287300078 | Python | 19,615 | 541 | """Training program and ancillary functions."""
import csv
import functools
import os
import numpy as np
import toml
import torch
import medaka.common
import medaka.datastore
import medaka.labels
import medaka.models
import medaka.torch_ext
def train(args):
"""Training program."""
train_name = args.train_na... |
052d750f8ef54dc688f9f7d7bc8c96bfcfc4f5f7e676618a9c35a067cd932a16 | Python | 19,625 | 486 | import numpy as np
import pdb
import os
import h5py
import random
from sklearn.model_selection import StratifiedKFold
import math
import time
from matplotlib import pyplot as plt
# import seaborn as sns
import pandas as pd
plt.switch_backend('agg')
import glob
import pdb
import argparse
import sys
d... |
ef3485b58e1f9d7e313ebab910ea618db90de11c06c82c7104c9045491c4170e | Python | 19,636 | 624 | # Copyright (c) 2017-present, Facebook, Inc.
# All rights reserved.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ ... |
b6ec24f9757db6cd2fc87bd25df971d5d9435f66261097815d0743aaeb404e9c | Python | 19,666 | 449 | # Copyright (c) 2017-present, Facebook, Inc.
# All rights reserved.
#
# This source code is licensed under the license found in the LICENSE file in
# the root directory of this source tree. An additional grant of patent rights
# can be found in the PATENTS file in the same directory.
import math
from tqdm import tqdm
... |
088f96298e268a241007c37d6ac02e9a6bb9d5c6fd47dcd84858adea5d22691b | Python | 19,680 | 439 | """Read a GO Annotation File (GAF) and store the data in a Python object.
Annotations available from the Gene Ontology Consortium:
http://current.geneontology.org/annotations/
"""
import sys
import os
import re
import collections as cx
import datetime
import logging
from goatools.anno.annoreader_base imp... |
ff7ebd57c280c24a6e560d90a591209c52606f7814688ec9e5e0f1ca2892bdff | Python | 19,691 | 466 | import os
from posixpath import join
from sys import path
import time
import lmdb
import torch
import json
import numpy as np
import pickle as pkl
import dataclasses
from dataclasses import dataclass
from typing import Dict, List, Optional, Tuple, Union
from torch.utils.data import Dataset
from transformers import PreT... |
595f77c86381003912b1a54423fa29fe7f8c4ccce9be818cdb816fe91231a991 | Python | 19,697 | 526 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
from typing import Dict, Optional
import torch
import torch.nn as nn
import torch.nn.functional as F
from fairseq import utils
from fairseq.i... |
cc311f837dce792adcb27d9b51e76189d90c7062be77131a0e6546942c8dd9df | Python | 19,725 | 744 | """Functions on surface mesh elements."""
# Author: Oualid Benkarim <oualid.benkarim@mcgill.ca>
# License: BSD 3 clause
import numpy as np
import scipy.sparse as ssp
from scipy.spatial.distance import cdist
from scipy.sparse.csgraph import dijkstra
import vtk
from ..vtk_interface import wrap_vtk, serial_connect
fr... |
9aa2ac798cb999ad94f8c14a57b49e1eff7af04b00d6d6dac5edc19df1009649 | Python | 19,732 | 433 | import os
import torch
import numpy as np
import skimage.io as skio
import torch.nn.functional as F
import argparse
# from tqdm import tqdm
import tqdm
from scipy.io import savemat
import matplotlib.pyplot as plt
import matplotlib.cm as cm
import time
from utils import *
import csv
from torch.fft import fftshift, ifft... |
1ffad8ed098fcba2b8f9f6f1d893399cd275d212ab190fb0fe154733a60d68c4 | Python | 19,744 | 617 | """Maintained GPN single-species inference operations."""
from __future__ import annotations
from pathlib import Path
from typing import Any
import numpy as np
import pandas as pd
import torch
from Bio.Seq import Seq
from datasets import Dataset, disable_caching
from jaxtyping import Float, Int
from torch import Ten... |
47b163abb7a2575e21bab1f1204177515ac7d37590e1cc3f7911ad0f6832ef9c | Python | 19,745 | 512 | import os.path
import numpy as np
import pytest
from rnalysis.gui.gui_windows import *
LEFT_CLICK = QtCore.Qt.MouseButton.LeftButton
RIGHT_CLICK = QtCore.Qt.MouseButton.RightButton
@pytest.fixture
def use_temp_settings_file(request):
settings.make_temp_copy_of_settings_file()
request.addfinalizer(settings.... |
9a82e9d4da0506fa89413eb2f33af653b8379d97a2515b654e94636170c8711e | Python | 19,747 | 512 | import numpy as np
import pytest
from mudata import MuData
import scvi
from scvi.data import synthetic_iid
from scvi.data._constants import ADATA_MINIFY_TYPE
from scvi.data._utils import _is_minified
from scvi.external import TOTALANVI
from scvi.model import MULTIVI, TOTALVI
OBSERVED_LIB_SIZE = "observed_lib_size"
... |
8758c66b6170014fa824df5963fb39f1d33f46ee69e3ea465dd860677706f7c6 | Python | 19,811 | 449 | import os
import importlib
import matplotlib.pyplot as plt
import torchvision
from torch import nn, optim
from datetime import datetime
import ambiguous.models.cvae
from torchvision.utils import save_image
import torch
from torchvision import datasets, transforms
import numpy as np
from tqdm import tqdm
import yaml
imp... |
f7a6ee9551127d76729b92716db1ca247d90fd0f27b2a83c7aa59ae3ab4fea8c | Python | 19,813 | 556 | """Models for Plat et al. probabilistic reversal learning task.
Three model families:
simulate_rl_kernel : RL + choice kernel, fixed learning rate (4 params)
simulate_metarl : Meta-RL (Plat et al.) + choice kernel; latent lambda, epsilon
simulate_rbpf : Piray & Daw (2021) RBPF; latent v_t, s_t
... |
58b51f9331a98b6c9e0e8c02ee060f6d6f551646870e86a6577843eefbed5765 | Python | 19,814 | 531 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import unittest
from typing import Dict, List
import torch
import tests.utils as test_utils
from fairseq import utils
from fairseq.data impo... |
8cdff0aae1e35a4a729f12bd95159881fe972c3a188b483a288880696d84eff7 | Python | 19,815 | 481 | from __future__ import annotations
import json
import warnings
from typing import TYPE_CHECKING, Literal
import numpy as np
import pandas as pd
from anndata import AnnData
from mudata import MuData
from scipy.sparse import csr_matrix, issparse
from scipy.stats import pearsonr, spearmanr
from sklearn.metrics import (
... |
482fed404846e25f11a1543a68001371c7ccd55f9b22f6efd9da3987cb09fcf7 | Python | 19,835 | 632 | import stat
from pathlib import Path
from types import SimpleNamespace
import numpy as np
import pandas as pd
import pytest
from transformers import TrainingArguments
import gpn.checkpoint as checkpoint_module
import gpn.inference as inference_module
import gpn.ss.inference as ss_inference
import gpn.star.inference a... |
a375d0e468fc1071b728327d999b38617fbd9d72cd949383f05c8f985f446254 | Python | 19,846 | 520 | import torch
import torch.nn.functional as F
import math
class KANLinear(torch.nn.Module):
def __init__(
self,
in_features,
out_features,
grid_size=5,
spline_order=3,
scale_noise=0.1,
scale_base=1.0,
scale_spline=1.0,
enable_standalone_scale_... |
d66e53273a4ecb1161e48efbf6b4ca8ca4e37e8df4d3d5dd41d1bded4a00acb0 | Python | 19,850 | 611 | """Plot Ramachandran-style backbone mirror QC for paired L/D peptide poses."""
from __future__ import annotations
from pathlib import Path
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from Bio.PDB import PDBParser
from Bio.PDB.vectors import calc_dihedral
from scipy.ndimage import gaussian_f... |
4c529a455c4387973d0d0e99c4143ba2c68822cdd4c0da7de94e60721e274ea7 | Python | 19,873 | 612 | """
Tests for the sklearn-compatible ExpertInLoop class in pgmpy.causal_discovery
"""
import networkx as nx
import numpy as np
import pandas as pd
import pytest
from sklearn.utils.estimator_checks import parametrize_with_checks
from pgmpy.base import DAG
from pgmpy.causal_discovery import ExpertInLoop, ExpertKnowledg... |
633f97019ae17ae5687faa194fe3885a0f2984eaac31d5c67f3d172fe9a3aaae | Python | 19,876 | 526 | from dataclasses import dataclass
from typing import Callable, Dict, List, Optional, Tuple
import haiku as hk
import jax.numpy as jnp
import numpy as np
from jax import numpy as jnp
from nucleotide_transformer.layers import MultiHeadAttention
from nucleotide_transformer.types import (
AttentionMask,
Embedding... |
4659ae6bf082c261ac0b03b7e1aa1e52b062f8bb681d7915fe6b4297890cfdc6 | Python | 19,886 | 559 | import os
import unittest
import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
import logging
import glob
import sys
import numpy as np
#
# ImportAtlas
#
class ImportAtlas(ScriptedLoadableModule):
"""Uses ScriptedLoadableModule base class, available at:
https://github.com/Slicer/Slicer/blob/ma... |
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