sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
58d6a50ce931de96eff657b854a1f8eb4dd165331f86a212b26edee068d5d259 | Python | 21,379 | 583 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import logging
import tempfile
from itertools import product
from string import ascii_uppercase
import numpy as np
import numpy.typing as npt
from gufe import Component, ProteinComponent, Sm... |
21938b3566b68aa3f4f2925e9f7f0a77a4425bdc13bae737696a3d1f6fb03182 | Python | 21,384 | 583 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import logging
import tempfile
from itertools import product
from string import ascii_uppercase
import numpy as np
import numpy.typing as npt
from gufe import Component, ProteinComponent, Sm... |
86babbd7c9907197e7c80bde71b53efbe709fd9876d7e6270e3d9400d996588c | Python | 21,387 | 464 | import pandas as pd
import numpy as np
import glob, os, yaml, sparse, itertools, subprocess, sys, argparse, pickle, tracemalloc
from Bio import SeqIO, Seq
import scipy.stats as st
import warnings
warnings.filterwarnings("ignore")
# load all utils functions
sys.path.append("utils")
from data_utils import *
from analys... |
b3764d2973bafeddb7650320f3396edb43cc4aaada4f8f79f92fe6118ff5f5a9 | Python | 21,396 | 602 | from __future__ import absolute_import
import email
import logging
import re
import time
import warnings
from collections import namedtuple
from itertools import takewhile
from ..exceptions import (
ConnectTimeoutError,
InvalidHeader,
MaxRetryError,
ProtocolError,
ProxyError,
ReadTimeoutError,... |
f0e10ef2acbf7fcd933649d29cce144b9f2faf5a4d789e30619e643ffd43e179 | Python | 21,409 | 566 | from configparser import ConfigParser
import json
import os
# =============================================================================
# ADAPT THE FOLLOWING VARIABLES WHICH ARE SHARED ACROSS CONFIGS
config = ConfigParser()
# ADAPT ROOT_DIR!
root_dir = "/scratch/alexandel91/mid_level_features"
# ===============... |
e706d117176fdfa753183e1ed0db4e74819fe5a904a0f61be49c90ce0589f70c | Python | 21,429 | 626 | # 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... |
bec33ef99ce9688fb73875cadea31ea6e54d4b4448593fda2f82b417cfb9ef5b | Python | 21,440 | 606 | """
Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
"""
import numpy as np
import pyqtgraph as pg
from qtpy import QtCore, QtGui, QtWidgets
from qtpy.QtWidgets import (
QAbstractItemView,
QButtonGroup,
QDialog,
QGraphicsPathItem,
QGridLayout,
QLabel,... |
d3dfe1e67ccf09681bb49ba1ed41016fad8ce98501b5c6e517b7ec1dc43fdd5d | Python | 21,456 | 540 | import logging
import os
from collections.abc import Iterable
from concurrent.futures import ThreadPoolExecutor, as_completed
from io import StringIO
from typing import Dict, List, Optional
from xml.etree import cElementTree as ET
import pandas as pd
import requests
from gseapy.utils import log_init, mkdirs, retry
... |
4c7630c95b3c7303e59c5ab1b0d5d446c4a4df72d90e5091925b579c4137f1d8 | Python | 21,459 | 568 | import json
import shlex
import pandas as pd
from queue import Queue
from collections import defaultdict
def read_lines(filename):
"""Generator to read lines of a file"""
with open(filename, 'r') as fin:
for line in fin.readlines():
yield line
def get_term_keys(obo_file):
"""
Ret... |
38ffad742da727886fbc3367cda2c686e067c3ea1d2e4686388bdb8917556310 | Python | 21,471 | 775 | #!/usr/bin/env python3
# ----------------------------------------------------------------------------
# Copyright (c) 2020--, Qiyun Zhu.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------... |
2215994aed85fd74a7afe70b199b59a69d1e6198a2cd92e53d5504aaa4cdebf9 | Python | 21,483 | 628 | # Copyright 2022 Google LLC.
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
9c12b6d48a69af99797c07714b02214020c60980db4cd72eb9b9c2330c9f35b5 | Python | 21,485 | 718 | """
Utility functions for the EEG encoding analysis.
"""
from sklearn.decomposition import PCA
from sklearn.decomposition import KernelPCA
from sklearn.preprocessing import StandardScaler
import cv2 as cv
from scipy.ndimage import convolve, gaussian_filter
from PIL import Image
import numpy as np
import torch
import o... |
de56ceb6c2f057c598a57c865e38b3581f57a07016cabfb300eeaa4c903bff05 | Python | 21,513 | 562 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Result classes for the Absolute Free Energy Protocols
=====================================================
This module implements :class:`gufe.ProtocolResult` classes for the absolute
f... |
dd69a5acb42db5ddbfda244f86ef2b6be5a4f897eee9686fc1b3f5274289b9ed | Python | 21,550 | 469 | # 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
c78e7c5cbe4f23c584a0245e7cffce96f64d14725f58902b6ed0ff5811e03ed6 | Python | 21,552 | 648 | """
Kinetic Monte Carlo (KMC) classes and functions.
In our system, the reaction rate r = (deterministic) reaction constant k
= stochastic reaction constant c (from gillespie 1977)
= propensity a (from Anderson 2007)
because of the fundamental premise of chemical kinetics
and because we have one reactant molecule
"""
... |
672aa93bd4d805783e4bf99e4039cb45bac640176a547806cd2f6fd756bed165 | Python | 21,576 | 646 | import sys
import string
import simplejson
import pandas as pd
import networkx as nx
from itertools import chain
from yaml.scanner import ScannerError
from collections import defaultdict, Counter
# Multiple imports depending on if command line or import from script
try:
from pathtester import PathTester, ALLOWED_C... |
422e183205e5d93d72da3f8acb49a096a20ff9f80c168060b17ac690b35b7530 | Python | 21,626 | 496 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Mar 11 02:45:20 2025
@author: saiful
"""
import random
import numpy as np
import torch
import pandas as pd
from sklearn.model_selection import train_test_split
from sklearn.preprocessing import LabelEncoder, StandardScaler
from sklearn.metrics import acc... |
3857a801e8635fad09a8d627944fd59559b43234c3f5bfdde76ea4471e712c8c | Python | 21,680 | 479 | import logging
import traceback
from PySide6.QtWidgets import QWidget, QDialog, QHBoxLayout, QVBoxLayout, QDialogButtonBox, QGroupBox, QLabel,\
QLineEdit, QListWidget, QListWidgetItem, QTableWidget, QTableWidgetItem, QSpacerItem
from PySide6.QtCore import Qt, QSize, Signal
import nibabel as nib
import numpy as np
... |
bd9f6f56c1b11981d059ddb160267a3dcfedf2b0d70a8222eaef1f12e5873131 | Python | 21,682 | 555 | import glob
import gzip
import os
import pathlib
from unittest import mock
import pandas as pd
import pooch
import pytest
from click.testing import CliRunner
from openfecli.commands.gather import (
_get_column,
_get_legs_from_result_jsons,
_load_valid_result_json,
format_estimate_uncertainty,
gath... |
13277ab447336b52bfdae4775dce90accec4fa1c496ee5af109abece56e63b75 | Python | 21,701 | 420 | """
Authors: Zheng Wang, John Griffiths, Andrew Clappison, Hussain Ather, Kevin Kadak
Neural Mass Model fitting module for model fitting using pytorch
"""
import numpy as np # for numerical operations
import torch
import torch.optim as optim
from ..datatypes import Timeseries as Recording # JG: rename this to... |
69b2423a41199b549f06d4cddb5a49f519fdd6c2d2b32bc31495229ca32752a3 | Python | 21,711 | 500 | """Tests for bases2fastq module: parsers and integration."""
import json
from pathlib import Path
from typing import Any, List
from unittest.mock import patch
import pytest
from multiqc import report, config
from multiqc.base_module import ModuleNoSamplesFound
from multiqc.types import LoadedFileDict
from multiqc.m... |
e0848ac0c21138d53bfedb2ee5fa5d6cdd61852e58ddc69b49970ee7f8d33607 | Python | 21,772 | 560 | import datetime
from uuid import UUID
import matplotlib.pyplot as plt
import pandas as pd
from truesight import plot_utils, stats_utils
from truesight.db.session import get_session
from loguru import logger
from truesight.db.models import DbEvaluation, DbLLM
from truesight.evaluation import services as evaluation_servi... |
a8612f7f65896eff041e1b8e2809eb86b140c42305a65f0bfa2dca72869a86d2 | Python | 21,797 | 504 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Mar 11 02:45:20 2025
@author: saiful
"""
import random
import numpy as np
import torch
import pandas as pd
from sklearn.model_selection import train_test_split
from sklearn.preprocessing import LabelEncoder, StandardScaler
from sklearn.metrics import acc... |
03c4c591d3d65c354f70ae401681584f596cc33a11407558c852ed5cb5944be0 | Python | 21,805 | 510 | import sys
sys.path.append('/home/tconstab1/kg98_scratch2/oldscratch/Toby/python_venv/lib/python3.9/site-packages/ptitprince/')
import PtitPrince as pt
import os
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
#Display FCI first
SE_FCI= pd.read_csv('/home/tconstab1/kg98_sc... |
18077c96d9f8ab38f093da16477ff76eab00e16b98280360ba03ae751edc6f5c | Python | 21,835 | 522 | """Interface with checkmol."""
import functools
import warnings
from enum import Enum
from openff.toolkit.utils.exceptions import AtomMappingWarning
from openff.utilities import MissingOptionalDependencyError
class MissingCheckmolError(MissingOptionalDependencyError):
"""Checkmol is not installed."""
def _... |
1966a039891039ed4deda8598f49db39539b6539020891c9166f5b002de1724a | Python | 21,835 | 522 | """Interface with checkmol."""
import functools
import warnings
from enum import Enum
from openff.toolkit.utils.exceptions import AtomMappingWarning
from openff.utilities import MissingOptionalDependencyError
class MissingCheckmolError(MissingOptionalDependencyError):
"""Checkmol is not installed."""
def _... |
477989fefc2375d17dd1ba376ef2bb6bcadcc0047c352046a1220f5e765a8eea | Python | 21,849 | 505 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Mar 11 02:45:20 2025
@author: saiful
"""
import random
import numpy as np
import torch
import pandas as pd
from sklearn.model_selection import train_test_split
from sklearn.preprocessing import LabelEncoder, StandardScaler
from sklearn.metrics import acc... |
ba46364e435a7b998fe34d8d777ec723942690bcf73ab37449dc9fc12d0808ec | Python | 21,866 | 496 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Author: Caro Nettekoven
"""
import numpy as np
import TaskRest.paths as indiv_paths
import Functional_Fusion.atlas_map as am
import numpy as np
import scipy.ndimage as ndimage
import matplotlib.pyplot as plt
import Functional_Fusion.dataset as ds
import nibabel as nb
i... |
34cdb8d0e9b803cdc3054391db035d2ea26fd404ae198922b536905ff3438584 | Python | 21,901 | 445 | from dna_features_viewer import BiopythonTranslator, GraphicFeature, GraphicRecord
from dna_features_viewer.biotools import annotate_biopython_record
import pandas as pd
import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
import glob, os, yaml, sparse, itertools, sys
from Bio import SeqIO
from Bio.... |
b7a3ed87dbde2bd28a12ddbbc8da5871162296c36802207e66530cfebd801195 | Python | 21,907 | 504 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Mar 11 02:45:20 2025
@author: saiful
"""
import random
import numpy as np
import torch
import pandas as pd
from sklearn.model_selection import train_test_split
from sklearn.preprocessing import LabelEncoder, StandardScaler
from sklearn.metrics import acc... |
419c32d5f8fdc6d3f405c56ff2d624c2013fe3c319d98e5c3f19a639f90f81d7 | Python | 21,952 | 536 | from PySide6.QtWidgets import QWidget, QHBoxLayout, QVBoxLayout, QSpacerItem, QGridLayout, QComboBox, QPushButton,\
QStackedWidget, QGroupBox, QLabel
from PySide6.QtCore import Qt, QSize, Signal
from PySide6.QtGui import QColor, QPixmap, QIcon
import os
import logging
from utils.software_config import SoftwareConf... |
ba3fb249a977d9a8abfda2d7a8a1ecdb7212bd4efaa8fc39087bff4cc3d69c33 | Python | 21,966 | 494 | """Tests for data_utils"""
import os
import json
import tarfile
import tempfile
import numpy as np
from tensorflow.keras import backend as K
from tensorflow.python.platform import test
from deepcell.utils import data_utils
class TestDataUtils(test.TestCase):
def _write_test_trks(self, path):
img_w, im... |
e2d785417f54872bda5639cd02acb7317135080d2d9f1c05293b5edf6dfa2079 | Python | 21,987 | 568 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""OpenMM Equilibrium Binding AFE Protocol --- :mod:`openfe.protocols.openmm_afe.equil_binding_afe_method`
====================================================================================... |
184cd5bf1f930d5aa8789017c577e08dc6d8319934df1d8e55cac54b022f2437 | Python | 21,989 | 438 | from aenum import Enum, unique
import logging
import os
from os.path import expanduser
import shutil
import datetime
import dateutil
import json
import traceback
from copy import deepcopy
from typing import Union, Any, Tuple, List
class UserPreferencesStructure:
"""
"""
__instance = None
_preferences_... |
b865c3505dab456de777696f49d98fb9f8b5992105a858a64fe825d3e6791e4e | Python | 21,996 | 564 | """Functions for training convolutional neural networks"""
import datetime
import os
import numpy as np
import tensorflow as tf
from tensorflow.keras import backend as K
from tensorflow.keras.optimizers import SGD
from tensorflow.keras.losses import MSE
from tensorflow.python.data import Dataset
from deepcell impor... |
35e00ebb60d0599a2989a6daca9753a72ecad5e771eaa9dad488cd7aece73164 | Python | 22,018 | 426 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# Copyright 2014 David Emms
#
# This program (OrthoFinder) is distributed under the terms of the GNU General Public License v3
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publish... |
31b8bbd0f01dd6f987bd544a938b35bc79c6f8224aa5d2a30f9a637781477f17 | Python | 22,041 | 451 | # This script plots the analyses of sentence-loudness and instructed breath tasks during which a breath belt was worn by the participant.
# This script plots the breath belt expansion during both tasks, psths from example electrodes and decoding accuracy under different task conditions.
import argparse
import os
impor... |
9c1211c922a37d1076e712022589de85cdc19b94f51c1189995bba18bb3c1174 | Python | 22,042 | 666 | "Classes for handling featurized molecule data to train GNN models"
from collections import defaultdict
import functools
import glob
import hashlib
import io
import logging
import pickle
import tempfile
import typing
import json
import tqdm
import torch
from openff.utilities import requires_package
from torch.utils.d... |
c04fb9128d10f29121dbc5a7f43f9871fea60efd00acc134e8147d50fef6f015 | Python | 22,073 | 571 | from typing import Optional, Tuple, Dict, List
import os
import pandas as pd
import random
import time
import h5py
import numpy as np
from Bio import PDB
from Bio.PDB import PDBParser, NeighborSearch
import torch
from torch.utils.data import Dataset
import warnings
from Bio import BiopythonWarning
from dataclasses impo... |
f189c58fa3efe54ee4d7e85cd0633c8e09c06cca6bb574a40eb5c8dc9b8d8330 | Python | 22,112 | 660 | import tempfile
from collections.abc import Callable, Mapping
from dataclasses import dataclass
from pathlib import Path
from typing import Any
import torch
from ptmelt.models import (
ArtificialNeuralNetwork,
BayesianNeuralNetwork,
RecurrentNeuralNetwork,
ResidualNeuralNetwork,
TemporalTransforme... |
6a1e4db8c6a352294d78138e4d85470dd1ceba363ed33b7205e7b686f763a4bd | Python | 22,171 | 460 | import os
import configparser
import platform
import traceback
from os.path import expanduser
import numpy as np
from typing import Union, Any, List, Optional
import names
from PySide6.QtCore import QSize
import logging
import json
from utils.data_structures.PatientParametersStructure import PatientParameters
from uti... |
2f4d9a993617301ebcc84df6f99604c93c17807097426a719b4bee38c024c808 | Python | 22,175 | 588 | import argparse
import os
from typing import Callable, Optional, Tuple
import numpy as np
import pandas as pd
import torch
import pickle
from sklearn.decomposition import PCA
from sklearn.neighbors import NearestNeighbors
from lifelines.utils import concordance_index
from lifelines import CoxPHFitter
from statsmodel... |
46a30f8a0baab3088188c90094a597feff562dd62cbfa4ffbd1280bfc16cf608 | Python | 22,180 | 498 | import logging
import re
from multiqc import config
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import bargraph, linegraph, violin
log = logging.getLogger(__name__)
# Log parsing regexes
regexes = {
"alignment": {
"total_reads": r"Sequence(?:s| pairs) analys... |
51632b70d0ec0f08301929bbf330a65fa7642be888a1f4619b981ff5c6ee3c35 | Python | 22,206 | 447 | #!/usr/local/bin/env python
# ==============================================================================
# MODULE DOCSTRING
# ==============================================================================
"""
ReplicaExchangeSampler
======================
Derived multi-thermodynamic state multistate class with ex... |
494e1005f128cc07a4bb64e17955080b31c997d572369b17a9ed2ac8156a558f | Python | 22,210 | 626 | import warnings
from typing import Any
import torch
import torch.nn as nn
from ptmelt.layers import MELTBatchNorm, MELTBayesianDenseFlipOut, PositionalEncoding
def _get_initializer(initializer: str):
"""Get the initializer function."""
if not initializer.endswith("_"):
initializer += "_"
if in... |
51c3b5fb6efa0c571e3cad33e873765795cd2f379a27052a7dbdf46eaf0a8995 | Python | 22,249 | 431 | #!/usr/bin/env python
#
# MIT License
#
# Copyright (c) 2018 Volker Hovestadt
#
# 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 r... |
c10662750776d5574ec972c2ffa73068d443ade0c0c23a5aaf023ecc03a65208 | Python | 22,267 | 583 | import logging
import multiprocessing as mp
import os
import time
from abc import ABC, abstractmethod
from datetime import datetime
from queue import Empty
from typing import Any, Dict, Optional, Tuple
try:
import cv2
IMPORT_CV2 = True
except ImportError:
IMPORT_CV2 = False
import numpy as np
try:
fro... |
6bf4bd76a6f9975f2f96a7b906b537d37a99e9e1686a00b93d98d8c11617fe6c | Python | 22,279 | 715 | import ast
import io
import os
import sys
import warnings
import functools
import importlib
from collections import defaultdict
from functools import partial
from functools import wraps
import contextlib
from distutils.errors import DistutilsOptionError, DistutilsFileError
from setuptools.extern.packaging.version imp... |
fe775b0710039df321adcc915b52f427ac6670de5be7754c743872689af06421 | Python | 22,350 | 437 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
from pyminc.volumes.factory import *
from numpy import *
from argparse import ArgumentParser
import tempfile
import os
import functools
import signal
import shutil
import subprocess
import sys
import math
def get_tempfile(suffix):
counter = 0
pid = os.getpid()
... |
b41e629ccd8f2a4314f6d0b9cdf7589575d007c37af1136004a3bc1baf60c678 | Python | 22,392 | 451 | #!/usr/local/bin/env python
# ==============================================================================
# MODULE DOCSTRING
# ==============================================================================
"""
ReplicaExchangeSampler
======================
Derived multi-thermodynamic state multistate class with ex... |
7fe5809073f3379e00c39933d426c0891a4d9fba32a99bf2332e2e768ad973e1 | Python | 22,401 | 638 | # Copyright 2022 Google LLC.
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
17fa8357e04dbea012191098204615faf1b484582efd59df9134e3d9cbd1462b | Python | 22,467 | 461 | # -*- coding: utf-8 -*-
"""
Created on Thu Sep 8 11:00:11 2016
@author: david
"""
import numpy as np
from scipy.special import beta
"""
T - topology of the tree
B - set of branches in the tree
D - set of all duplications, {d_i | i \in B}
d_i - the duplications on branch i = (x_i, y_i)
O_i(j), where i, j \in B if th... |
659390abf987f724b085c02dc7832f9d62aed4fc4eba97bdfb7ccfbed5831006 | Python | 22,479 | 719 | # Copyright 2022 Google LLC.
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
0f8dd94bd62e5dacda4486f7d7b96d9b6ed0947ee38d61df6bceb6547da01c1c | Python | 22,536 | 749 | """
The main function to run MultiQC.
Primarily called by multiqc.__main__.py
Imported by __init__.py so available as multiqc.run()
"""
import logging
import os
import subprocess
import sys
import time
import traceback
from typing import Optional, Tuple
import rich_click as click
from multiqc import config, report, ... |
29af17e118195a13bc181b517b0ed2570ae939d8491be5abc1236aa6f2992c6d | Python | 22,576 | 550 | import json
import logging
import re
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import bargraph, linegraph, table
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
"""
The module parses the reports from an assembly run. As a bare minimu... |
f8df527ec258e39b10baa91241e421be98c00809bb084718cf16f9512e3542f5 | Python | 22,590 | 520 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Mar 11 02:45:20 2025
@author: saiful
"""
import random
import numpy as np
import torch
import pandas as pd
from sklearn.model_selection import train_test_split
from sklearn.preprocessing import LabelEncoder, StandardScaler
from sklearn.metrics import acc... |
9cfbc9dc6337a858639b0f7003750c3971b143386e0f941b938cd3d7f966c904 | Python | 22,615 | 611 | # Imports
from torch.nn.functional import normalize
import os
# import os
os.environ["CUDA_VISIBLE_DEVICES"]="7"
os.environ["DGLBACKEND"] = "pytorch"
import sys
sys.stdout = open("final_console_outputs/console_output_lr-2_all_graph_bioembed_gat_run1_no_normedge.txt", "w")
# sys.stdout = open("console_outputs/console_ou... |
e6a7883eb4368fe31a6c5e14bd5db304b61421a79e169fc24a09a619fa58b4a0 | Python | 22,636 | 568 | """MultiQC functions to plot a scatter plot"""
import copy
import json
import logging
import math
from collections import defaultdict
from typing import Any, Dict, List, Mapping, Optional, Set, Tuple, Union, cast
import numpy as np
import polars as pl
from plotly import graph_objects as go # type: ignore
from multi... |
83b6444695b7a4e22bae7da9ed8799a2d672d80c61e56c4ecb275b30dbb8dbc5 | Python | 22,638 | 463 | from PySide6.QtWidgets import QGraphicsView, QGraphicsScene, QGraphicsPixmapItem, QGraphicsOpacityEffect
from PySide6.QtGui import QPixmap, QImage, QPen, QColor, QTransform
from PySide6.QtCore import Qt, Signal, QPoint, QSize
import numpy as np
import os
import logging
from scipy.ndimage import rotate
from utils.soft... |
b5932159e62bd3e05d8c5562d44e8082205cabacd005c430418c4266ab294ae1 | Python | 22,650 | 603 | import os
import numpy as np
import torch
from scipy import sparse
from scipy.sparse import csr_matrix
from sklearn.model_selection import train_test_split
from sklearn.preprocessing import LabelEncoder
from .model.model import protoCloud
from .model.train import run_model, get_predictions, get_log_likelihood
from .m... |
4b8a0b099441596698ea7ca0e359001f9f7ffc1a82de0b6be20ec4ac89f9910c | Python | 22,679 | 675 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import click
import os
import pathlib
import pandas as pd
import sys
from typing import Literal, List
from openfecli import OFECommandPlugin
from openfecli.clicktypes import HyphenAwareChoi... |
2b3b1d8f933ab6c46aa24cdea75784fd6ff84f71be599a07c022377ee119a579 | Python | 22,717 | 636 | # Example Models - for full, closed form inference via junction tree algorithm
# Or loopy belief propagation
import numpy as np
from numpy import exp,sqrt,log
import matplotlib.pyplot as plt
import copy
import emissions as em
import arrangements as ar
import spatial as sp
from full_model import FullModel
import pandas... |
f8ba4277663418a6cf703dd1939d402506a9e866e0638ee14883af0afcb53f3a | Python | 22,728 | 745 | """
Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
"""
import os
import time
import numpy as np
import torch
from scipy.interpolate import interp1d
from scipy.linalg import eigh
from scipy.ndimage import gaussian_filter1d
from sklearn.decomposition import PCA
from torch.n... |
0fe5e3c36464f77e3297a747a64a0f4388fa5f0be53e032815b6cdc52ba90f27 | Python | 22,733 | 559 | #import os
#import cv2
#import numpy as np
#import tensorflow as tf
#from glob import glob
#from keras.utils import Sequence
#from keras.models import load_model
#from keras.models import Model
#from project import ViT, ClassToken # Ensure these are correctly imported according to your project structure
#
## Define hy... |
6fba0a59d41c5522e8226c2120b93ba9f3bf0cf8673f15ce0e863e8040a6bd6a | Python | 22,734 | 588 | #!/usr/bin/env python3
"""
Parallel MRI Registration and Brain Extraction Pipeline
======================================================
This script processes brain MRI data in parallel by:
1. Registering T1WI and T2WI images to FLAIR space using FSL FLIRT
2. Performing brain extraction on FLAIR images using FSL BET
... |
514b040210c31c0bb01b948143fac6df497ab4bc0c4c2ee9c791cf8879228e9e | Python | 22,735 | 674 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import json
import logging
import pathlib
import sys
from unittest import mock
import gufe
import numpy as np
import openmm
import pytest
from gufe import ChemicalSystem, LigandAtomMapping, ... |
cc9850eb99b2f4435a3ce83f573c81fb55b9c860005f207f59ed8b79bed862ab | Python | 22,741 | 589 | """
SFF_ELM_model.py
Sector Fruit Fly based Extreme Learning Machine (SFF-ELM) for UCS prediction
of geopolymer-stabilized clays.
This file contains:
- Baseline ELM
- FOA-ELM (Fruit Fly Optimization Algorithm)
- SFF-ELM (Sector Fruit Fly Optimization)
- Training, prediction, evaluation, and visualization
Author: Moha... |
9953f5941ae114e39d025584c3dbc2c19c3b3916f818d8e0b2cc84a308cc321b | Python | 22,755 | 656 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import annotations
import os
from functools import cached_property, lru_cache
from pathlib import Path
from threading import Lock
from typing import TYPE_CHECKING, Any, Dict, NamedTuple, Optional, Tuple, Union
import dask.array as da
import numpy as np
imp... |
02c775919d61e486d76d6966267670dce86ad46d90d023420e7a1358699c2e3e | Python | 22,779 | 519 | from typing import Any, Dict, List, Optional, cast
from natsort import natsorted
from multiqc.plots import bargraph, linegraph, table
from multiqc.plots.table_object import ColumnDict
from multiqc import config
from multiqc.types import SectionAlert
def _drop_low_samples(data: Dict[str, Dict[Any, float]], threshold... |
1842704f30fa52f19ba7c4c446cba8e49c560170fa6f3dc0e4705dc4f13213ea | Python | 22,808 | 697 | """
All read_<...> and write_<...> functions.
"""
import csv
import json
import logging
import os
from datetime import datetime
from itertools import takewhile
from pathlib import Path
from typing import Optional, TypeAlias, TypedDict, Union
import numpy as np
from kimmdy.utils import get_gmx_dir
logger = logging.g... |
a039429085657f3e9a5b110710f1f34ab2fcaec02d97a00d3579057054c5b61a | Python | 22,863 | 660 | import queue
import random
import numpy as np
import numpy.ma as ma
from numpy.linalg import norm
import glm
import trimesh
import open3d as o3d
import pickle
import matplotlib.pyplot as plt # TODO: remove and plot with nemsi
from FyeldGenerator import generate_field
from scipy.spatial import cKDTree
plt.style.use("d... |
65af1a18b7223b5a3b373d25c58446d08c2f50e60a3dff1632471443972569f1 | Python | 22,877 | 818 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import xml.etree.ElementTree as ET
from pathlib import Path
from tempfile import TemporaryDirectory
from typing import Any, Dict, List, Optional, Tuple, Union
from unittest.mock import MagicMock, patch
import numpy as np
import pytest
from _aicspylibczi import PylibCZI_CD... |
25369121d174da051b0d945121a6f994f2c9e0703deec18e176111533d952606 | Python | 22,881 | 662 | """
:mod:`alchemiscale.base.client` --- base class for API clients
==============================================================
"""
import asyncio
import time
import random
from itertools import islice
import json
from urllib.parse import urljoin
from functools import wraps
import gzip
from pathlib import Path
impo... |
3b1fbf559af75548ed854a6d82f8c77179b8e3b6aefa77869a2f0ff4339c0f8b | Python | 23,003 | 565 | #!/usr/bin/env python3
"""
qc_video.py — minimal QC viewer for facial keypoints (2-D overlays + skeletons)
--------------------------------------------------------------------------------------
Focus:
1) Load 3D keypoints from pose_3d/*.csv
2) Optionally apply per-frame head->world transform (M_ij, center_k)
3) ... |
7a7da6b5c5f7bee63408b4192eca35e61b23f5a85b013672ac4a29c60ef76261 | Python | 23,013 | 587 | """
bootstrap_snn_evaluation.py #1628074
用途：
- 对每个癌种进行 B 次 bootstrap 重训练（有放回抽样）
- 每轮训练在 D_boot 上训练模型，在未抽中的 OOB 上评估
- 在 OOB 上计算 C-index（sksurv）
- 汇总每种癌症的中位数/均值/Std/95%CI 并保存结果
注意：
- 请实现 `fit_snn_on_bootstrap(train_df, seed)` 和 `predict_risk_scores(model, df_oob)` 两个函数：
- fit_snn_on_bootstrap: 接受训练 DataFrame，返回已训练模型... |
89d90e2d94c672c5d54e1bd7edc6e77d968fe76f1d4284f4bc93b5a3c878a7e7 | Python | 23,025 | 718 | # Copyright 2022 Google LLC.
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
83e0068e7889ff44589ac50ba0798de6fa52ef85e16417f9f1e29f72c40ede28 | Python | 23,036 | 437 | """
Special case MultiQC module to load multiqc.parquet
It allows rerunning MultiQC when original data is gone, as well as extend
existing reports with new data.
"""
import json
import logging
from datetime import datetime
from pathlib import Path
from typing import Any, Dict, List, Optional, Tuple, Union, cast
impor... |
cf0b8faf45a1b7fab4a3c1c521623c0762e2f9d7375b20ba9a9acd2142747342 | Python | 23,039 | 587 | import torch
import numpy as np
import torch.nn as nn
import torch.nn.functional as F
from torch import Tensor
from typing import List, Tuple
import math
from functools import partial
from torch import nn, einsum, diagonal
from math import log2, ceil
import pdb
from sympy import Poly, legendre, Symbol, chebyshevt
from ... |
46190a3664da00bcf3838582092c1c1f06f89acc729fd20a8d4bda76da7939ff | Python | 23,050 | 538 | #!/usr/local/bin/env python
#=============================================================================================
# MODULE DOCSTRING
#=============================================================================================
"""
Test all test systems on different platforms to ensure differences in potenti... |
6bf5193ac8d9ea187e8d1ac7ac94c9df09ca60ea8acadd545154a11e02935f2f | Python | 23,056 | 470 | from PySide6.QtWidgets import QWidget, QHBoxLayout, QVBoxLayout, QScrollArea, QPushButton, QLabel, QSpacerItem,\
QGridLayout, QMenu, QMessageBox
from PySide6.QtCore import QSize, Qt, Signal, QPoint
from PySide6.QtGui import QIcon, QPixmap, QAction
import os
import logging
from gui.SinglePatientComponent.PatientResu... |
51cbc6310467f3fea4448fe4ef3c8ad4223866de9bc1ca1063416e3d99f72821 | Python | 23,069 | 601 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import warnings
from typing import Any, Dict, List, Optional, Tuple, Union
import dask.array as da
import numpy as np
import xarray as xr
from dask import delayed
from fsspec.spec import AbstractFileSystem
from tifffile import TIFF, TiffFile, TiffFileError, imread
from ti... |
14729ec64f3717e52b40db1dff8e66df589cf5d06e92929847cc9a3a26c08055 | Python | 23,084 | 539 | #!/usr/local/bin/env python
#=============================================================================================
# MODULE DOCSTRING
#=============================================================================================
"""
Test all test systems on different platforms to ensure differences in potenti... |
37ad1348c6d3afbf400f347ad410ab93c62881441c0419cd68b8093d37d7b1f7 | Python | 23,086 | 715 | """Handles all VCS (version control) support"""
import logging
import os
import shutil
import sys
import urllib.parse
from typing import (
Any,
Dict,
Iterable,
Iterator,
List,
Mapping,
Optional,
Tuple,
Type,
Union,
)
from pip._internal.cli.spinners import SpinnerInterface
from ... |
c3be05662d0d49fbf33df2aac4d5eb9df6df4c4d9a515052c6a0ac585e877cd4 | Python | 23,089 | 558 | # Inital setup for stratified splitting of AnnData objects and verification of the splits. Needs to be run before training the models.
import logging
from pathlib import Path
import anndata
import numpy as np
from timeflies.core import ConfigManager
# Configure logging for better control over output
logging.basicCo... |
f7bdf1f72c23f79ff02b0fdafdeba7b48b5cde2df062ea6b87c34ee9215ab4a8 | Python | 23,121 | 546 | """
Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
"""
import os
import typing
import numpy as np
from qtpy import QtCore
from qtpy.QtCore import Qt
from qtpy.QtGui import QPixmap, QGuiApplication
from qtpy.QtWidgets import (
QDialog,
QGroupBox,
QHBoxLayout,
... |
6c91efc55bfc1f31ff6cd5c6232766d4929d86620c002ec0e45e8c4c237938b7 | Python | 23,160 | 654 | import math
import os
import time
from multiprocessing.shared_memory import SharedMemory
import datajoint as dj
import numpy as np
import panda3d.core as core
from direct.showbase.Loader import Loader
from direct.showbase.ShowBase import ShowBase
from direct.task import Task
from panda3d.core import CardMaker, ClockOb... |
1d6a95e065ea2e9feb262a5ad7dcb1f7cdd4a3dc6c8c5b223ee4eb6fb22eb1a1 | Python | 23,176 | 446 | import numpy as np
from matplotlib.figure import Figure
import matplotlib.gridspec as gridspec
from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg
import matplotlib.cm as cm
import logging, wx, threading
class RedirectText(object):
def __init__(self, text_ctrl):
self.text_ctrl = text_ctrl
d... |
6dc9c5e7a33f1427778802fa27edfafa5a931da2e0c50310535af459928c2e05 | Python | 23,223 | 629 | # Imports
from torch.nn.functional import normalize
import os
# import os
os.environ["CUDA_VISIBLE_DEVICES"]="1"
os.environ["DGLBACKEND"] = "pytorch"
import sys
# sys.stdout = open("console_outputs/inference_output", "w")
# =============================================================================
#
# ============... |
eb02c996b2e37e40a52c71d500f0075bf815105b7a17b9f698075f09452d8f64 | Python | 23,229 | 612 | import os
import logging
import time
import glob
import numpy as np
import tqdm
import torch
import torch.utils.data as data
from datasets import get_dataset, data_transform, inverse_data_transform
from functions.ckpt_util import get_ckpt_path, download
# from functions.svd_ddnm import ddnm_diffusion, ddnm_plus_diffu... |
edcb6ac96cc9ee002976ab51da28b4059ce57a7e70326824c47fa8c7840b39da | Python | 23,248 | 629 | import matplotlib.pylab as plt
import numpy as np
import pytest
from openff.units import unit
from cinnabar import FEMap, plotting
from cinnabar.measurements import ReferenceState
@pytest.fixture(scope="function")
def show_called(monkeypatch):
"""Fixture to mock plt.show() and track if it was called."""
call... |
6cc0f97e0dcfd45d66460caa8a808974e28d1fc9676146525b65f6498534ec12 | Python | 23,260 | 390 | #!/usr/bin/env python3
# https://neurostars.org/t/extract-voxel-coordinates/7282
# http://blog.chrisgorgolewski.org/2014/12/how-to-convert-between-voxel-and-mm.html
# https://stackoverflow.com/questions/6967463/iterating-over-a-numpy-array
# https://stackabuse.com/calculating-euclidean-distance-with-numpy/
# https://n... |
71632b460b040971ada5d1458ba5be5140177fe3b3a1a18ab1436968d81b914e | Python | 23,268 | 599 | import numpy as np
import pandas as pd
from scipy.spatial import ConvexHull
def compute_euclidean_dist(a, b):
"""Compute the Euclidean distance between two 3D points.
### Arguments
- `a`, `b`: the 3D vectors as arrays of shape `(batch..., 3)`
### Returns
The distance as an array of shape `(batch.... |
ff485ed293dff76f315d707a7c52c600f02767ec6a9a8342a3469c2e92246295 | Python | 23,269 | 552 | import numpy as np
import pandas as pd
import seaborn as sns
import networkx as nx
import matplotlib.pyplot as plt
import matplotlib.patheffects as pe
from collections import defaultdict
from scipy.spatial import distance
__all__ = ['shift_centers_to_min_distance', 'darken_hex_color', 'determine_text_color',
'pre... |
3866312f50ae2700f582cf553e22ed41016ee72c372006bfb4df5266a5a246a5 | Python | 23,299 | 563 | """MultiQC functions to plot a box plot"""
import copy
import json
import logging
from typing import Any, Dict, List, Mapping, Optional, OrderedDict, Tuple, Union, cast
import plotly.graph_objects as go # type: ignore
import polars as pl
from natsort import natsorted
from multiqc import config, report
from multiqc.... |
ffe78503a16d55d27a94a33aa4b0201a469b49ae7a9a5ed822e90e6153030aae | Python | 23,308 | 486 | from config import TESTING_MODE
from ctypes import c_int, c_void_p, c_char_p, c_float, c_uint16, c_uint32, c_uint8
from ctypes import Structure, byref
import os, time, json, sys, warnings, ctypes, logging, threading, h5py, Queue
import numpy as np
import multiprocessing as mp
from util import now,now2
if TESTING_MODE:... |
17b2c36fa3d02309e26302dcce1536a520321d9f5b9d3553d7223f39db98877c | Python | 23,315 | 821 | # The following comment should be removed at some point in the future.
# mypy: strict-optional=False
import contextlib
import errno
import getpass
import hashlib
import io
import logging
import os
import posixpath
import shutil
import stat
import sys
import urllib.parse
from io import StringIO
from itertools import fi... |
41b0697290ea802fdbd8205294dded94a85d3fd035db47770b80b0d6bd8d4ca2 | Python | 23,319 | 542 | import pandas as pd
import numpy as np
import glob, os, yaml, sparse, itertools, subprocess, sys, argparse, pickle, tracemalloc
from Bio import SeqIO, Seq
import scipy.stats as st
import warnings
warnings.filterwarnings("ignore")
# load all utils functions
# sys.path.append(os.path.join(os.path.dirname(os.getcwd()), ... |
56e429931099230da72ee16385beb27fe6f102c8528a5badaeb7d4e8e8b219e8 | Python | 23,319 | 537 | import yaml
import random
from datasets import load_dataset
from sqlalchemy import select
from refs import llm_base_refs
from truesight.db.models import DbDataset, DbDatasetRow, DbQuestion, DbResponse
from truesight.db.session import get_session
from truesight.experiment.services import EvaluationRef, JudgmentRef
from ... |
6ca400c7a7438a4264dcf3151cc9c7affdc29deaad3d5f25a0e1ba2968d03ad4 | Python | 23,343 | 771 | """See test_creation_indices.py for tests with 'indices' parameter."""
import numpy as np
import pytest
from numpy.testing import assert_array_equal
import shapely
# Note: Point is not imported because it is overridden for testing
from shapely import (
GeometryCollection,
GeometryType,
LinearRing,
Li... |
c0509f645ae4d94198c2f25d490790d5dc70b871288fe30f776d6ad3b1a62657 | Python | 23,349 | 532 |
'''
Custom Blue Orange Color Map
set cmap = blueOrangeCmap()
'''
import numpy as np; np.random.seed(0)
import seaborn as sns; sns.set()
import matplotlib.pyplot as plt
from matplotlib.colors import ListedColormap, LinearSegmentedColormap
import matplotlib.colors as colors
import numpy as np
import warn... |
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