sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
aaed2251e433e02edfd59163412a7893dbd34a00952a042c1bf26d19f500a344 | Python | 8,754 | 255 | # -*- coding: utf-8 -*-
# encodermap/misc/distances.py
################################################################################
# EncoderMap: A python library for dimensionality reduction.
#
# Copyright 2019-2024 University of Konstanz and the Authors
#
# Authors:
# Kevin Sawade, Tobias Lemke
#
# Encodermap is ... |
f955b0b6dc0e0f621b0c91637279b4acc023df4f5a49dfb2cc1027429ac6669f | Python | 8,760 | 253 | #!/usr/bin/env python
"""
MetaWIBELE: maaslin2 module
Run maaslin2 to associate features with metadata
Copyright (c) 2019 Harvard School of Public Health
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 S... |
0617dfe6f4c09b49a832c70f215dffa9ec61578cb9cd0b2f1a5f5bcfcb268068 | Python | 8,765 | 107 | UNIVARIATE_DATASET_NAMES = ['50words', 'Adiac', 'ArrowHead', 'Beef', 'BeetleFly', 'BirdChicken', 'Car', 'CBF',
'ChlorineConcentration', 'CinC_ECG_torso', 'Coffee',
'Computers', 'Cricket_X', 'Cricket_Y', 'Cricket_Z', 'DiatomSizeReduction',
... |
78755a644d7c31c1dae7a2d28aaf3330495774010504cd7593cf0c2ae5607efa | Python | 8,768 | 264 | """
Producer threads must not share feature state through a cloned feature.
``Featurizer._clone_features`` gives every producer thread its own
``copy.copy`` of each feature, because ``cache``/``query`` write
trajectory-scoped state (``selected``, ``resids``, ``cached_array``) onto the
feature. A shallow copy also copi... |
b266c1186c8feba0e38a6a0dad6a952e7108c10af6b86bad650e76dcd1622b4c | Python | 8,771 | 204 | import os
import numpy as np
import torch
import torch.nn.functional as F
from torch.optim import Adam
from SAC.utils import soft_update, hard_update
from SAC.model import GaussianPolicy_ActionGNN, Critic_GNN
class SAC_ActionGNN(object):
algo_name = "SAC ActionGNN"
def __init__(self,
action... |
8aeec15e853db6a4038b7e320b007dded1c2c47274f4f46bf49f87318d587a44 | Python | 8,778 | 195 | import torch
import torch.nn.functional as F
import torchaudio_contrib as tac
import os, math
class NCL2NLC(torch.nn.Module):
def __init__(self):
super(NCL2NLC, self).__init__()
def forward(self, input):
"""
input : Tensor of shape (batch size, T, Cin)
Outputs a T... |
dba7b2e312a7ad533649dc5bd688c761572f654869f2544fc42746ef108ef66a | Python | 8,779 | 197 | import torch
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
from rde.modules.common.geometry import global_to_local, local_to_global, normalize_vector, construct_3d_basis, angstrom_to_nm
from rde.modules.common.layers import mask_zero, LayerNorm
from rde.utils.protein.constants import BBHeavy... |
e24028465430c8001595b0953df4843631350bb3b81a46aa5b907d6fbbb3a6d5 | Python | 8,786 | 169 | import catmaid.fields
import datetime
from django.conf import settings
import django.contrib.postgres.fields.jsonb
import django.contrib.postgres.functions
from django.db import migrations, models
import django.db.models.deletion
forward = """
CREATE TABLE catmaid_deep_link (
id int GENERATED BY DEFAULT A... |
8bde0f47cc50a57b6843034577cba6781df5faaf61e709754df8c58e4c1dd4a2 | Python | 8,788 | 192 | # Standard Library Imports
import datetime
import json
import os
from math import pi
# Local Folder Imports
from .misc import run_path, search_and_replace
class ParametersFramework:
def __init__(self):
self.main_path = os.getcwd()
def save(self, path=None):
"""
Save parameters in jso... |
9f01bfd0e58f2e4c3958a2ce7c5073018f275064e7a3cb2003fd90cefe09aa86 | Python | 8,788 | 235 | # Authors: Pierre Ablin <pierre.ablin@inria.fr>
# Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Jean-Francois Cardoso <cardoso@iap.fr>
#
# License: BSD (3-clause)
import numpy as np
import warnings
from scipy import linalg
from ._core_picard import core_picard
from ._tools import check_random_s... |
c2afa2acd9685d5accbff81f67f4c333e75ba026052a7ca890daeb09037f571e | Python | 8,793 | 276 | import numpy as np
import pickle
import pandas as pd
import seaborn as sns
import time
from matplotlib import pyplot as plt
# 25 CS, 3 TR, V2G, ProfixMax, WithLoads
# data = pd.read_csv('./results/eval_25cs_3tr_V2G_ProfixMaxWithLoads_25_11_algos_3_exp_2024_07_18_418263/data.csv')
# data1 = pd.read_csv('./results/eva... |
6cf4004f2d649dd1ad6c1240bd9d66dd80d1636fe1d104c045d05f31595b47df | Python | 8,794 | 212 | # Copyright (c) OpenMMLab. All rights reserved.
import os.path as osp
from collections import OrderedDict, defaultdict
from typing import Dict, List, Optional, Sequence
import cv2
import numpy as np
import torch
from mmengine.dist import is_main_process
from mmengine.evaluator import BaseMetric
from mmengine.logging i... |
33dc8005ab69fdd1d3e89863f87c399a1a9c24bc470e55d124c23266d5af9cb0 | Python | 8,801 | 232 | # Utilities for location the file paths of import files.
from pathlib import Path
def get_encoder_model_path(isDocker: bool = False) -> str:
"""Gets the filepath of a stored DNA encoder.
Parameters
----------
isDocker : bool
Whether this program is being run from a Docker container (and thus ... |
5a23a32ef4b562bf3dbcccf162241f85c96c71b645cccd53ca275e1c76111e9e | Python | 8,801 | 287 | import typer
from typing import Optional
import medperf.config as config
from medperf.decorators import clean_except
from medperf.entities.dataset import Dataset
from medperf.commands.list import EntityList
from medperf.commands.view import EntityView
from medperf.commands.dataset.submit import DataCreation
from medpe... |
79914590f9306928cff96e8883f10c96b252386a010a24c38f3550e8b416fa20 | Python | 8,804 | 373 | import pytest
from neo4j import GraphDatabase
from kgx.graph.nx_graph import NxGraph
NEO4J_CONTAINER_NAME = "kgx-neo4j-unit-test"
DEFAULT_NEO4J_URL = "neo4j://localhost:7687"
DEFAULT_NEO4J_USERNAME = "neo4j"
DEFAULT_NEO4J_PASSWORD = "test"
DEFAULT_NEO4J_DATABASE = "neo4j"
def check_neo4j_container():
"""
Ch... |
c788f50a7f7d6c8397fae639dc44838266d873332f632323354b3376dba941d4 | Python | 8,807 | 274 | # #############################
#
# Copyright (C) 2018
# Jennifer Dreiling (dreiling@gfz-potsdam.de)
#
#
# #############################
import numpy as np
import copy
class Model(object):
"""Handle interpolating methods for a single model vector."""
@staticmethod
def split_modelparams(model):
... |
cecc500bee1eca73173a9b7053a68f7f68c678e260317b2a65b2a261a2faa696 | Python | 8,808 | 246 | """Shared ndx-fiber-photometry v0.2 hardware-metadata boilerplate for the mock-NWB generators.
Imported as a sibling module by the ``create_mock_nwbfile_ndx_fiber_photometry_v0_2_*`` scripts
(the script's own directory is on ``sys.path`` when run as ``python .../create_mock_...py``), so it
must only depend on the same... |
2a571dc9b5965ca2694e3180261ae5891531c233ddbc8ec10e62d634f41bfef8 | Python | 8,809 | 255 | """Unit tests for src/datahandlers/mesh.py
Tests cover:
- write_ids() parameter validation
- write_ids() SCR filtering logic (mock-based)
- Mesh.get_scr_terms_mapped_to_trees() (inline pyoxigraph store)
"""
from unittest.mock import MagicMock, patch
import pyoxigraph
import pytest
from src.categories import C... |
d4417f6648818f2b9af2d6f1834ab35db34b0269cffcd94ed951fda3b655fe38 | Python | 8,809 | 237 | import argparse
import os
import pickle
import sys
from pathlib import Path
import pandas as pd
from tqdm.auto import tqdm
sys.path.append(".")
from easydict import EasyDict
from rdkit import RDLogger
from utils.dataset import get_dataset
from utils.evaluation import *
from utils.misc import *
from utils.reconstruc... |
6ffd208601e781066ac7c4630a3d9b29b5705d7c329b099ceaed532f373e0729 | Python | 8,816 | 235 | # -*- coding: utf-8 -*-
"""
Created on Thu Oct 24 11:56:14 2024
@author: A0067501
"""
import yaml
import torch
import os
import pydicom
import numpy as np
from skimage.measure import label
from scipy import ndimage
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
import logging
import sys
from... |
2137dc90f0c6632dd9be880d961f29ae3a607a366c7a97e8529124f0064b94ff | Python | 8,821 | 266 | import logging
import os
import shutil
from abc import ABC, abstractmethod
from pyalfe.interfaces.greedy import Greedy
try:
import ants
except ImportError:
pass
class ImageRegistration(ABC):
@abstractmethod
def register_rigid(self, fixed, moving, transform_output, init_transform=None):
"""Pe... |
96023605b824890daf0f45a6aa51e59888d494239f00b8771beb17e341b03ba7 | Python | 8,822 | 261 | import csv
import json
import torch
from transformers import BertTokenizer
class CNerTokenizer(BertTokenizer):
def __init__(self, vocab_file, do_lower_case=True):
super().__init__(vocab_file=str(vocab_file), do_lower_case=do_lower_case)
self.vocab_file = str(vocab_file)
self.do_lower_case ... |
44673cec183dc2596141854d82a8b4fc321dc2090b77e064c882edb83ac40d9d | Python | 8,824 | 255 | import math
import torch
from torch import nn as nn
from torch.nn import functional as F
from torch.nn import init as init
from torch.nn.modules.batchnorm import _BatchNorm
from basicsr.utils import get_root_logger
# try:
# from basicsr.models.ops.dcn import (ModulatedDeformConvPack,
# ... |
2482bbc6044ac1bdd65702786af46c534b1ae93722780f34b6275d81a2e35bd5 | Python | 8,825 | 273 | from typing import List, Dict, Union, Callable
from abc import ABC
import logging
import os
from medperf.utils import sanitize_path
import yaml
from medperf.exceptions import MedperfException, InvalidArgumentError
from medperf.entities.schemas import MedperfSchema
from typing import Type, TypeVar
from medperf.account_m... |
426b329d68ae1a1485de3bb4757ef90bde3c80a33dfe920b0b8d3aec696df1cb | Python | 8,835 | 255 | from abc import ABC, abstractmethod
import ase
import numpy as np
import numpy.typing as npt
import torch
from einops import einsum, reduce
from scipy.special import softmax # type: ignore
class PriorManifold(ABC):
@abstractmethod
def initialise_positions(self, molecule: ase.Atoms, scale: float) -> ase.Atom... |
87155f92317c66028008498b00343ae878bbdb9676ce984b9ea5deed094c6072 | Python | 8,839 | 269 | from rest_framework import status
from medperf.tests import MedPerfTest
from parameterized import parameterized, parameterized_class
class CertificateTest(MedPerfTest):
def generic_setup(self):
# setup users
cert_owner = "cert_owner"
ca_owner = "ca_owner"
other_user = "other_user... |
47a4986a3d9bfb4b42c8e84281ac5fab47bbbad3fac2573440fc1778120203b0 | Python | 8,842 | 219 | import quantities
import pkg_resources
try:
import cPickle as pickle
except:
import pickle
import gzip
from hippounit import plottools
import matplotlib.pyplot as plt
import os
import numpy
from quantities import mV, nA, ms, V, s
import json
import collections
# adding the result data to dictionary
data_dict ... |
3c09ba1bd5d963f21e67b951cf4d95d45d5b19c49cbd052b6ee0e0b443c4a767 | Python | 8,844 | 249 | from rest_framework import status
from medperf.tests import MedPerfTest
from parameterized import parameterized, parameterized_class
class BenchmarkCertificatesTest(MedPerfTest):
def generic_setup(self):
# setup users
bmk_owner = "bmk_owner"
prep_mlcube_owner = "prep_mlcube_owner"
... |
a116d189257c0cf731378e1618867db91931f828d24663fcf6ea682b787f82f7 | Python | 8,845 | 158 | # 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
#
# http://w... |
8e875513f93e617abfc6a48aadf849bcc46864be2ca098c1e6a48469bcc84b14 | Python | 8,858 | 269 | """Tests for running inplace prediction."""
from concurrent.futures import ThreadPoolExecutor
from typing import List, Union
import numpy as np
import pandas as pd
import pytest
from scipy import sparse
import xgboost as xgb
from xgboost import testing as tm
from xgboost.testing.data import np_dtypes, pd_dtypes
from... |
a30a5c0b8538541f3e5aadbd2a69731fc52132d42f22362f4e2881adb1faa12f | Python | 8,860 | 199 | import numpy as np
import pytest
from guppy.analysis import control_fit
from guppy.analysis.artifact_removal import retained_chunk_indices
from guppy.analysis.control_fit import ControlFitModel, select_fit_window_indices
def _fit_and_predict(control, signal, method="OLS", photobleaching_detrend=False):
"""Fit on... |
e5d02bf8398927be65e5dc10357110af378f6baba33be739ea47a4ce698941a8 | Python | 8,862 | 295 | """
Validate a Nearl installation.
Run with ``python -m nearl.valid_installation``. The static checks need no GPU,
so a build can be verified on a GPU-less login node before spending an
allocation. Checks that have to launch a kernel are reported as skipped rather
than passed when no CUDA device is visible; ``--requir... |
4d72421645e22ffcb63ff5ad9aa7302bfc616b7633564d04d7f9c5e54360ea89 | Python | 8,864 | 238 | """
Deal with SCT dataset metadata
Copyright (c) 2018 Polytechnique Montreal <www.neuro.polymtl.ca>
License: see the file LICENSE
"""
import io
import os
import re
from operator import itemgetter
from spinalcordtoolbox.utils.shell import parse_num_list
class InfoLabel(object):
"""
Class representing data a... |
57815d12abd8e02df453338c9339cbd3e9501214b00e64b735d1b6a5d1f1f388 | Python | 8,868 | 199 | #!/usr/bin/env python
import torch
import numpy as np
import pandas as pd
import time
import os
from shutil import copyfile
from models.model import RNN
from MCMG_utils.data_structs_fragment import Vocabulary, Experience
from properties import multi_scoring_functions_one_hot_dual
from properties import get_scoring_f... |
994ec17215c648cd9ddd8d142f2926dadda7d5734bfc1bda9b2c188d05ba9059 | Python | 8,869 | 187 | """io.py Input/Output functions to aid in analyses done for (Fickling et al., 2025)
author: Logan James Fickling github.com/LoganJF
TODO: Come up with more sensible loading scheme. Perhaps have a function for the path finding stuff, and just call that?
"""
import numpy as np
import pandas as pd
from glob import glob... |
40e411505921ba79ef7ebdf081d472ec85ba7b82ce90586c75032a96f11b16d3 | Python | 8,872 | 194 | #!/usr/bin/env python
#
# Copyright 2006, Google Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list... |
58407ec2b19541f111dbeac6eb46748b1941af50cdfb7f9d80284ba7754fb4fa | Python | 8,873 | 295 | import math
from functools import partial
import torch
import torch.nn as nn
import torch.nn.functional as F
def get_inplanes():
return [64, 128, 256, 512]
def conv1x3x3(in_planes, mid_planes, stride=1):
return nn.Conv3d(
in_planes,
mid_planes,
kernel_size=(1, 3, 3),
stride=... |
85bf51a3943235a805cce0f9f86ace2edd07f90bb5eb7689ba702519e98710ce | Python | 8,874 | 192 | # coding: utf-8
# Copyright 2019 Sinovation Ventures AI Institute
#
# 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 app... |
ba70371b0c09182b38f70834c3825d1db2490e93df14f0090f128d8e1f6c08ef | Python | 8,876 | 213 | # Copyright (c) OpenMMLab. All rights reserved.
import os
import os.path as osp
import tempfile
from unittest import TestCase
import cv2
import mmcv
import numpy as np
import torch
from mmengine.structures import PixelData
from mmseg.structures import SegDataSample
from mmseg.visualization import SegLocalVisualizer
... |
a7e7f71ac8e7d1daa86cbf7004025f2f98ec5d1e560d8071befb54709e407c03 | Python | 8,880 | 230 | # -*- coding: utf-8 -*-
# A 'tree' is a networkx.DiGraph with a single root node (a node without parents)
import networkx as nx
from collections import defaultdict
from itertools import islice
from math import sqrt
from operator import itemgetter
from typing import Any, DefaultDict, Dict, List, Optional, Set, Tuple
... |
c5f4a68cc7042cca852782fb4b796756056e15da66e986e21eee4aa487a3d06f | Python | 8,884 | 253 | #!/usr/bin/env python
#
# Copyright 2009, Google Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list... |
ef748d80dc29721e0d13cc0caf7d29057a90b9606c7125007668c6e6f8abb89e | Python | 8,884 | 193 | #!/usr/bin/env python
import argparse
import warnings
import torch
import numpy as np
import pandas as pd
import time
from models.model_rnn import RNN
from MCMG_utils.data_structs import Vocabulary, Experience
from properties import multi_scoring_functions_one_hot_dual
from properties import get_scoring_function, qe... |
e68b1f92e5625d267b81dd012216de2b70a1b44d0cb5caee852f1790d4706fdf | Python | 8,885 | 199 | #!/usr/bin/env python
import torch
import numpy as np
import pandas as pd
import time
import os
from shutil import copyfile
from models.model import RNN
from MCMG_utils.data_structs_fragment import Vocabulary, Experience
from properties import multi_scoring_functions_one_hot_dual
from properties import get_scoring_f... |
658b224371d5f7eef1792267274a3aee5aadc06f2b1fc963cc95ae8f96c4ab78 | Python | 8,889 | 216 | """This module is to handle saving results in a structured way.
This also includes testing if results are available for all
layers of the model and merging results from different runs.
Class ResultsManager:
- saves results in a structured way
- checks if results are available for all layers
- merges result... |
76be8ad0c969e557f0fd095a72b68caa81e9e012e6b7cdd84b69c857fe20fa4c | Python | 8,898 | 233 | # -*- coding: utf-8 -*-
import json
import time
from unittest import skipUnless
from django.conf import settings
from django.core.cache import cache
from django.db import connection, transaction, InternalError
from django.test import Client, TestCase, TransactionTestCase
from guardian.shortcuts import assign_perm
fro... |
0760dfcd9ca51e7b5c933ea0cd469a8f614c96c676a1e7084fed02c3923e7f51 | Python | 8,904 | 223 | ############################################################
# See https://github.com/raphael-group/GASTON/blob/main/src/gaston/segmented_fit.py
############################################################
from tqdm import trange
from sklearn import linear_model,preprocessing
import numpy as np
from scipy.stats impor... |
c86dd197929d0817d5f26d9897195a7f4dce154992cecc7eb035523bd15144c8 | Python | 8,905 | 200 | import os
import sys
import torch.nn
import pandas as pd
from tqdm import tqdm
# Dynamically append project root to sys.path
ROOT_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
if ROOT_DIR not in sys.path:
sys.path.insert(0, ROOT_DIR)
from PytorchModels.Models import RNN, LSTM, GRU
from Pyto... |
f7034ba7c4c411a3b15abe20027e1ecafd2ec91fd63149c6480469c5794cebda | Python | 8,906 | 244 | import logging
from functools import partial
from time import monotonic
from typing import Literal
import ase
import numpy as np
import torch
from hydromace.interface import HydroMaceCalculator
from mace.tools import AtomicNumberTable
from simgen.atoms_cleanup import cleanup_atoms
from simgen.calculators import MaceS... |
f54e335ae844517a59fc31f9321546004a5feab6e46a7573c68df5773df5469b | Python | 8,913 | 240 | """Tests for CLI auth commands (login, status, logout)."""
from __future__ import annotations
import json
from datetime import UTC, datetime
from unittest.mock import MagicMock, patch
import httpx
import pytest
from typer.testing import CliRunner
from zndraw.cli_agent import app
from zndraw.state_file import StateF... |
2cb1ba165eaf4ca9e3a5a9bc0d6e644b4fb847e7386618288981334999bd94a3 | Python | 8,914 | 164 | # 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
#
# http://w... |
f4d50c4304437a17007087d54ad43e22303196f0ca3dd188ed91c70526d28a9b | Python | 8,916 | 198 | import pytest
from pprint import pprint
from random import choice as rand_choice
from CybORG import CybORG
from CybORG.Simulator.Scenarios.EnterpriseScenarioGenerator import EnterpriseScenarioGenerator
from CybORG.Agents import SleepAgent, EnterpriseGreenAgent
from CybORG.Shared.Session import Session, VelociraptorSer... |
caaac9545c66096ed3ae33736794943fb1ef5251334db96d964bc80a24f7da73 | Python | 8,918 | 257 | # #START_LICENSE###########################################################
#
#
# This file is part of the Environment for Tree Exploration program
# (ETE). http://etetoolkit.org
#
# ETE is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the... |
7c7e4328ed47d3e221d3d838d3e534fe6e2cd7f973f823332e1a4104b9937f01 | Python | 8,919 | 235 | # coding=utf8
# Script for converting a HF Diffusers saved pipeline to a Stable Diffusion checkpoint.
# *Only* converts the UNet, VAE, and Text Encoder.
# Does not convert optimizer state or any other thing.
import argparse
import os.path as osp
import torch
# =================#
# UNet Conversion #
# ==============... |
b0bf4c99f5f90b99548faf80e2f18e103aa6816c10648529d8b0319f51223526 | Python | 8,921 | 304 | # -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
#
# This file does only contain a selection of the most common options. For a
# full list see the documentation:
# http://www.sphinx-doc.org/en/master/config
# -- Path setup ------------------------------------------------------------... |
d45eeb334c13339bfcbee4bc065d77b81b0123c602df203134c8ec8dc117058c | Python | 8,944 | 275 | import cv2
import random
import numpy as np
def mod_crop(img, scale):
"""Mod crop images, used during testing.
Args:
img (ndarray): Input image.
scale (int): Scale factor.
Returns:
ndarray: Result image.
"""
img = img.copy()
if img.ndim in (2, 3):
h, w = img.sh... |
9c65940a3f3d1d83c66a202f1bb3ecc252981050fbb9e4c7892e0421effcf421 | Python | 8,948 | 171 | import numpy as np
import math
eps = np.finfo( float ).eps
class BiasField:
def __init__(self, imageSize, smoothingKernelSize):
self.fullBasisFunctions = self.getBiasFieldBasisFunctions(imageSize, smoothingKernelSize)
self.basisFunctions = self.fullBasisFunctions.copy()
self.coefficients ... |
d08502ac5d12c2998d3f1cf894237bc438afad84814d4ca582a6007af56df101 | Python | 8,948 | 253 | #!/usr/bin/env python
"""
Module for calculations related to the contrast transfer function (CTF)
in cryo-EM single particle analysis.
"""
from typing import Tuple, Union, TypeVar, Dict
import numpy as np
import torch
Tensor = TypeVar('torch.tensor')
class ContrastTransferFunction:
def __init__(
s... |
a3593731f4fe238363825ff75966a4d60c900da974f75035f2ded9ab5ec0a5ff | Python | 8,950 | 217 | # This notebook is based on the AfDesign binder hallucination protocol in ColabDesign, which is published by Dr. Sergey Ovchinnikov on [GitHub](https://github.com/sokrypton/ColabDesign/tree/main/af)
# # AfDesign - cyclic peptide binder design
# For a given protein target and cyclic binder length, generate/hallucinate a... |
8328a0188f791ac6a00304167130e0b993d08df21558c4fade5fc5910e2981c8 | Python | 8,961 | 247 | import argparse
import os
import shutil
import sys
sys.path.append(".")
import numpy as np
import torch
import torch.utils.tensorboard
from easydict import EasyDict
from rdkit import Chem
from models.bond_predictor import BondPredictor
from models.model import MolDiff
from utils.misc import *
from utils.reconstruct ... |
7559c66ff20bf0e65e4ead75e2271aaad478e16e781e86c05d5033a98c71caf1 | Python | 8,967 | 272 | """
Checks the OBMol and per-property label caches in :mod:`nearl.chemtools`.
A cache is only correct if it is invisible: whatever the caller asks for, it must
get what an uncached build would have returned. So the tests come in two halves -
the cache hits (that the work really is skipped) and the cache misses (that
c... |
b6d5f890e2b09264d8428d321c618c4609cd3781884e7ed56a50f11a385d914a | Python | 8,969 | 322 | # Standard Library Imports
import os
from math import pi
# Third Party Imports
import numpy as np
import tensorflow.compat.v1 as tf
from tensorboard.backend.event_processing.event_accumulator import EventAccumulator
def add_layer_summaries(layer, debug=False):
"""
:param layer:
:return:
"""
weig... |
ffae4a179a8766ab674006c36b0cc7e1fd8ecd94389c8c34ef294f5a31c2259e | Python | 8,974 | 259 | import logging
import os
import stat
import urllib
import uuid
from collections.abc import ItemsView, Iterable, Iterator, KeysView, MutableSequence
from typing import NamedTuple, Optional, cast
from cwl_utils.types import CWLDirectoryType, CWLFileType, is_directory
from mypy_extensions import mypyc_attr
from schema_sa... |
d336e93a391e1ac869de9522b3f3598180dd832fe7c00bef95c206f6ecb7c8d6 | Python | 8,975 | 256 | """Multi Objective CMA-es class"""
"""
Copyright (c) 2016-2022, EPFL/Blue Brain Project
This file is part of BluePyOpt <https://github.com/BlueBrain/BluePyOpt>
This library is free software; you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License version 3.0 as published
... |
b1dec6844b92e6d278f70590e4e5727d0ef2a8f71a71235da81e1f9b4ea0b1d1 | Python | 8,977 | 245 | # -*- coding: utf-8 -*-
import json
from typing import Any, Dict, Iterable
from guardian.utils import get_anonymous_user
from django.conf import settings
from django.db import connection
from django.http import HttpRequest, JsonResponse
from django.contrib.auth.decorators import user_passes_test
from django.contrib.... |
9ab8845599e0581eb817812b59fc3df476d7bf25f99ff9a767ffbb2debbb183f | Python | 8,978 | 212 | import torch
import torch.nn as nn
from transformers import AutoConfig, AutoTokenizer, AutoModel, BertForNextSentencePrediction
import pickle
from tqdm import tqdm
import os
import argparse
import gc
class PackedBert(nn.Module):
def __init__(self, model_path ='bert_path', map_path='dataset/hf0812', pooling='cls'... |
8686feef1f60c50bb2c887bf2aaf18c879e0572aa68a6823484637dcb85df10f | Python | 8,980 | 231 | """
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 ase.db.sqlite
import ase.io.trajectory
import numpy as np
import torch
from torch_geometric.data import Data
from ocpmodels.common.ut... |
b51404718c0d38f381293c8e5e00a15d129651b7f09b1158002d8974a30967b5 | Python | 8,980 | 239 | # Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
import math
from typing import Any, Optional, Tuple
import numpy as np
import torch
from torch import nn
class Positio... |
d288bc9dd41ff37b9d8a3f160fcc212a7e3644014d566883d43058189d9f5d1b | Python | 8,981 | 276 | """
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 torch
from torch_geometric.nn import SchNet
from torch_scatter import scatter
from ocpmodels.common.registry import registry
from ocp... |
9ae9f76c3d60b85c47ef18df8bf2f4b072ecdf4cbfda4af470ba5793b591eddc | Python | 8,984 | 282 | """Tests for Progress REST API endpoints."""
import json
import pytest
from helpers import (
MockSioServer,
auth_header,
create_test_room,
create_test_user_in_db,
)
from httpx import AsyncClient
from redis.asyncio import Redis
from sqlalchemy.ext.asyncio import AsyncSession
from zndraw.redis import R... |
eea078583e49d54339009a6701099c61195afc3e538752af539dc9e91c8c5e76 | Python | 8,985 | 253 | # Copyright (c) OpenMMLab. All rights reserved.
from typing import Dict, List, Optional, Sequence, Union
import torch
import torch.nn as nn
import torch.nn.functional as F
from mmcv.cnn import build_conv_layer, build_norm_layer, build_upsample_layer
from mmengine.model import BaseModule
from torch import Tensor
from ... |
f3ff254919b737cd7208d88673ff330b6d5c9cf707447960c2bebe3e6e5aea2b | Python | 8,989 | 263 | import pathlib
import subprocess
import tempfile
from collections.abc import Iterable
from dataclasses import dataclass
import ase
import ase.io as aio
import fire
import numpy as np
import pandas as pd
import zntrack
from rdkit import Chem
from simgen.analysis import (
analyse_base,
analyse_calculator,
a... |
2a3f7c4baed5a7416c93bef94c02e730f0ce26e3e3640fc080ff249909a7fee6 | Python | 8,997 | 159 | #!/usr/bin/env python3
# created by Daiki Sato and updated on 2025/3/20
# python3 5_2_4_simulation_groupsinglemovediversity.py 10 0
import matplotlib.pyplot as plt
import matplotlib.animation as animation
import numpy as np
import pandas as pd
import math
import sys
import os
args = sys.argv
num_agents = 6 ... |
8d42f079561dda8aa03972889080e78b1d55c4fd5a8bb73b9ed5b2d70e8cf910 | Python | 9,008 | 270 | from typing import Tuple
import torch.nn as nn
from monai.networks.blocks.dynunet_block import UnetOutBlock
from monai.networks.blocks.unetr_block import UnetrBasicBlock, UnetrUpBlock
from typing import Union
import torch.nn.functional as F
# from lib.utils.tools.logger import Logger as Log
# from lib.models.tools.mo... |
acb92a21aef7ecd38a5a543f1498a1822262cfc8ae718fb946a0e1f1010f06e0 | Python | 9,008 | 159 | #!/usr/bin/env python3
# created by Daiki Sato and updated on 2025/3/20
# python3 5_2_5_simulation_groupsocialcontagiondiversity.py 10 0.1
import matplotlib.pyplot as plt
import matplotlib.animation as animation
import numpy as np
import pandas as pd
import math
import sys
import os
args = sys.argv
num_agents = 6 ... |
126a55677f0d7bb2332861b997572af1065b902e2e07516703cfd75b8bb02446 | Python | 9,009 | 220 | from typing import List
from ipaddress import IPv4Address
from CybORG.Simulator.Actions.Action import RemoteAction
from CybORG.Simulator.State import State
from CybORG.Shared import Observation
from CybORG.Simulator.HostEvents import NetworkConnection
from CybORG.Shared.Enums import ProcessName
class GreenAccessServ... |
c3650e870a8a24e5069206a2ae345222d4964b527f67ebc206e02e0c76e488eb | Python | 9,009 | 215 | from PyQt5 import QtCore, QtWidgets, QtGui
from pystackreg import StackReg
from copy import deepcopy
from dipy.align.imwarp import SymmetricDiffeomorphicRegistration
from dipy.align.metrics import CCMetric
import numpy as np
from features.Feature import Feature
from util.conf import mc_params
from threads.Worker impor... |
372e8ad8da0243b4020f16252e67817ce2f82c26a7689b26f4079aa0ad08b567 | Python | 9,010 | 274 | """
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 torch
from torch_geometric.nn import SchNet
from torch_scatter import scatter
from ocpmodels.common.registry import registry
from ocp... |
ab11ee885458f64cb5d705f4adda9b387b10bfcc4f709c4efe244b9c745743ac | Python | 9,011 | 216 | import numpy as np
import igraph as ig
from collections import Counter
from utils import retrieve_multiple_edges
INF = float("inf")
class PatternChecker(object):
def __init__(self):
pass
@classmethod
def node_compat_fn(cls, g1, g2, v1, v2):
vertex1 = g1.vs[v1]
vertex2 = g2.vs[... |
3e8a0b7cd4fe0ed74d7f232ae8c1da9ad56e769bc87559429d33761ddedfe184 | Python | 9,013 | 201 | #!/usr/bin/env python
import torch
import numpy as np
import pandas as pd
import time
import os
from shutil import copyfile
from models.model import RNN
from MCMG_utils.data_structs_fragment import Vocabulary, Experience
from properties import multi_scoring_functions_one_hot_dual
from properties import get_scoring_f... |
670e4a621e645385a52aa03aabca063a20be0521eaa287e302354b45d231b9a3 | Python | 9,015 | 310 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Apr 14 11:52:24 2023
@author: george
"""
import os
from os.path import expanduser
import numpy as np
from qtpy import QtGui, QtWidgets, QtCore
from time import time
from distutils.version import StrictVersion
import pyqtgraph as pg
import pandas as pd... |
e3fe52d006fa93c5ff8474e6f67ecac2b2ad25b0f6d4e8ce925e52d50dd7173f | Python | 9,018 | 231 | import logging
import math
import re
from pathlib import Path
import numpy as np
import pandas as pd
from .io_utils import recording_site_from_preprocessed_label
logger = logging.getLogger(__name__)
def create_Df_for_psth(filepath: str, event: str, name: str, psth: np.ndarray, columns: list[object]) -> None:
"... |
fcb3cc78a6aa5a615da0ac8cc5c9481b8fa0bd3513c072079b1bfd294e75988e | Python | 9,019 | 252 | """Module to evaluate generic functions on rows of dataframe."""
import logging
import sys
import traceback
from functools import partial
import pandas as pd
from tqdm import tqdm
from emodel_generalisation.parallel.database import DataBase
from emodel_generalisation.parallel.parallel import DaskDataFrameFactory
from... |
72b4d97b02000d62e32c1676d6fb351f1a606c05067bb8f34571c5357814cdc0 | Python | 9,021 | 179 | # Generate events files for task-faces
# This script reads raw behavior data files from d_beh for task-faces, extracts time stamps and design information, and stores them in new *events.tsv files accompanying BOLD files.
# For more information, please see README.md and the associated paper (Jung et al., 2024)
import... |
2af85e51a0e20bdcd5334170e2c2e23b8c786c5f1bfeed0586600242fbb8ecce | Python | 9,022 | 303 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Jul 2 10:38:57 2021
Epochs helping function
@author: leupinv
"""
import pandas as pd
import numpy as np
import mne
from mne.preprocessing import ICA
import base.files_in_out as files_in_out
import feather
import epochs.epochs_constants as cs
def fi... |
066c8dafd12e1d1833eb2ba637fb397ada85444ad6c60d4aa07324ec15236c61 | Python | 9,029 | 189 | # 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
#
# http://w... |
29ad9737d969447bd5f53c408f7d67fcdfef3061752ac14ba88a1f69a0c74ec1 | Python | 9,032 | 204 | import numpy as np
import pytest
from guppy.analysis.psth_significance import (
BOOTSTRAP_SEED,
bootstrap_difference_confidence_interval,
bootstrap_mean_confidence_interval,
minimum_consecutive_samples_for,
significant_sample_mask,
)
@pytest.fixture
def rng():
return np.random.default_rng(BOO... |
c35e171ef39658f1ca69aff9de4ab16ad683094e6d2d1e8e21b33be2e306188c | Python | 9,038 | 249 | import yaml
import argparse
import csv
from pathlib import Path
from dataset import backbone_dataset
import tensorflow as tf
from models import MultiStageModel
class Inference:
def __init__(
self,
data_root,
params_file,
feature_extraction_weights_path,
mstcn_weights_path,... |
79cc47f2092e32b1e1d232d33931a52954b359650377063f49917e60b4f9f501 | Python | 9,040 | 249 | #!/usr/bin/env python
# Load a virtual environment to run MagellanMapper
"""Cross-platform environment activation and MagellanMapper launcher script.
Launches MagellanMapper within a Conda or Venv environment. Environment
activation is in this order:
* If a Conda or Venv environment is already activate, launch in curr... |
38e84c36120f66265f41fbffc8c8e97d843606e9697f652e745436cf7e666d99 | Python | 9,044 | 240 | """
Computations on the Hyperbolic space H_n
as embedded in Minkowski space R^{1,n}.
Elements of the Hyperbolic space are the elements
of Minkowski space of squared norm -1.
NB: we use "riemannian" to refer to "pseudo-riemannian".
"""
import logging
import numpy as np
import math
from geomstats.minkowski_space impo... |
0432f6aa1f5e636d766c5502f9a2b2332147b6f37656058d3002629843beb19a | Python | 9,045 | 227 | # Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
# Borrowed from https://github.com/facebookresearch/segment-anything
from typing import Any, Optional, Tuple, Type
impor... |
a476339ddd3074aa1bcb42dd9d737e1fa518af78b4376473945ea33ad2113c69 | Python | 9,048 | 168 | # pytest unit tests for sct_register_multimodal
import os
import pytest
import logging
import numpy as np
from spinalcordtoolbox.image import Image
from spinalcordtoolbox.utils.sys import sct_dir_local_path, sct_test_path
from spinalcordtoolbox.scripts import sct_register_multimodal, sct_create_mask
logger = loggin... |
4209db2f72e253e7d751cdd39b6f6f5999d3ff1721dd2f91df5e8f136589eeb4 | Python | 9,051 | 232 | """Panel component that renders what one DANDI NWB asset holds.
Given an :class:`~guppy.utils.dandi_preview.AssetPreview`, it shows the file's channels, the
recording sites and indicators behind them, the store names Step 1 will ask for labels against,
and the first seconds of every trace. A file holding several respo... |
0baba9b1ede9c8f812a0e9fe1f8a361f9d8c49b3103a8fa4e6bb6e477353749b | Python | 9,061 | 298 | from medperf.exceptions import (
CommunicationError,
InvalidArgumentError,
ExecutionError,
CleanExit,
)
import pytest
from medperf.tests.mocks.dataset import TestDataset
from medperf.tests.mocks.cube import TestCube
from medperf.commands.dataset.prepare import DataPreparation, Observer
PATCH_REGISTER ... |
b116608e3d642ff3672c83c8aabeb1111d27c8b415ac45a8c7c217760d25b8a0 | Python | 9,062 | 245 | from scipy.stats import zscore
import numpy as np
from math import ceil
import torch
from run_moe_script import *
from isodepth_scaling import adjust_isodepth
# outlier threshold doesnt show points that are far away
# set to np.inf if you want to show all points
def plot_all_isodepths(output_folder,seed,model='final_... |
da30ccc13f0832deaed82903efa1d33db7673e8fa454ee227b53471e343c03eb | Python | 9,066 | 295 | """Contains classes and functions for logging."""
from __future__ import annotations
from collections.abc import Mapping
from typing import TYPE_CHECKING, Any
from colorama import Fore, just_fix_windows_console
if TYPE_CHECKING:
from bayes_opt_dnn.parameter import ParameterConfig
just_fix_windows_console()
c... |
779318ff01a700ffec6440d0f9eff373958c80f631b2da3c1891dfd0c44e782b | Python | 9,069 | 233 | ###########################################################################################
# Implementation of the symmetric contraction algorithm presented in the MACE paper
# (Batatia et al, MACE: Higher Order Equivariant Message Passing Neural Networks for Fast and Accurate Force Fields , Eq.10 and 11)
# Authors: I... |
ce03739b64d13e29087dbe1f541e08533a36ae07bb2fe15c0d6ca948af6de783 | Python | 9,072 | 245 | """
Computations on the n-dimensional sphere
embedded in the (n+1)-dimensional Euclidean space.
"""
import logging
import math
import numpy as np
from geomstats.euclidean_space import EuclideanMetric
from geomstats.manifold import Manifold
from geomstats.riemannian_metric import RiemannianMetric
import geomstats.vect... |
47dd3a0be18e76d1decb27423dbd1c7afe62a12fcbf8247d9e0ecdb7a306c0c3 | Python | 9,073 | 288 | from typing import List, Union, Any
from neo4j import GraphDatabase, Neo4jDriver, Session
from kgx.config import get_logger
from kgx.error_detection import ErrorType
from kgx.sink.sink import Sink
from kgx.source.source import DEFAULT_NODE_CATEGORY
log = get_logger()
class NeoSink(Sink):
"""
NeoSink is respo... |
d37a94cfacac07989e9027076e8bc451f26421b9cade69aea7b3c9210f96cc98 | Python | 9,078 | 179 | import numpy as np
import pyqtgraph as pg
from PyQt5.QtCore import Qt
# Enable antialiasing for prettier plots
pg.setConfigOptions(antialias=True)
class PlotWindow(pg.PlotItem):
def __init__(self):
pg.PlotItem.__init__(self)
# Initialize the class instance variables.
self.x = None
... |
3aa01147067001b1282659239bfefb0e8a4be7c0dfb0ad4c29a7fc9566ff6d9e | Python | 9,080 | 265 | import numpy as np
import math
import os
import sys
import gmsh
# gmsh.model.occ.addBox(x, y, z, dx, dy, dz, tag = -1)
# gmsh.model.occ.addBox(x, y, z, dx, dy, dz, tag = -1)
# gmsh.model.occ.addCone(x, y, z, dx, dy, dz, r1, r2, tag = -1, angle = 2*pi)
# gmsh.model.occ.addCylinder(x, y, z, dx, dy, dz, r, tag =... |
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