sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
2176aca03200e344d9b6df2f223661e1b178baff8201c2cf345523ad40f35d71 | Python | 31,520 | 800 | import os
import pathlib
import textwrap
from collections import defaultdict
import rdflib
import graphviz
from pyontutils.core import OntGraph, OntResIri, OntResPath
from pyontutils.namespaces import rdfs, ilxtr
from neurondm.core import Config, graphBase, log
from neurondm.core import OntTerm, OntId, RDFL
from neuron... |
269115e6a319b6018ae58c8cb1a7b615311ffc25614696143fc4b892820c13af | Python | 31,641 | 956 | # Copyright 2019 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... |
45096eb62504b767fdc2fb79a6d8c58df61aa783493501d1e6ece2a806864fc6 | Python | 31,654 | 817 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""The model that takes the coordinates, cell and atom types as input
and predicts some property. The models are automatically generated from
atomic models by the `deepmd.dpmodel.make_model` method.
The `make_model` method does the reduction, auto-differentiation and
commun... |
c9e3ab8349270be4b96a84a5bc34b8239d4e377e92fdc267e573fe8e2048f1a0 | Python | 31,756 | 882 | """LLM-driven blueprint generation forecaster for sktime.
Inspired by Karpathy's autoresearch: uses an LLM to iteratively generate,
evaluate, and refine sktime forecasting pipeline blueprints to find the best
combination of transformers and forecasters for a given dataset.
"""
import base64
import io
import json
impo... |
376fb01f4c06e8251d9a15d0df38e0c2bb0faf1823287acd22e9d382cb56a74a | Python | 31,778 | 625 |
import os
import pandas as pd
import numpy as np
import tensorflow as tf
import dask.dataframe as ddf
from dask.diagnostics import ProgressBar
from sklearn.model_selection import KFold
from sklearn.model_selection import GroupKFold
from sklearn.model_selection import train_test_split
from datetime import datetime ... |
b2d09a9f0c157d394f7ad4908a3ff90ef75a87575059e30102f32e037f2785ba | Python | 31,898 | 623 | # -*- coding: utf-8 -*-
"""
Created on Thu Jun 23 15:26:52 2016
@author: wanglab
"""
from tools.utils.io import makedir, removedir, chunkit, writer, load_kwargs
import multiprocessing as mp
import pandas as pd
import numpy as np
from math import ceil
import re, sys, os, cv2, gc, shutil, random
import pickle
import ti... |
149f3cf38b858b3b21995ff43e54d6ec500f21a31fc103e82d263ac924466441 | Python | 31,930 | 778 | import logging
import torch
import torch.nn as nn
from typing import Tuple, Optional, List, Union
from rxnebm.data.chem_utils import ATOM_FDIM, BOND_FDIM
from rxnebm.model import model_utils
def index_scatter(sub_data, all_data, index):
d0, d1 = all_data.size()
buf = torch.zeros_like(all_data).scatter_(0, inde... |
0e00a2ec85c8066815065ce4eed3169c79ca5680b9083a7a4feb26fbcd99344f | Python | 31,935 | 694 | #-------------------------------------------------------------------------------
# elftools: elf/relocation.py
#
# ELF relocations
#
# Eli Bendersky (eliben@gmail.com)
# This code is in the public domain
#-------------------------------------------------------------------------------
from __future__ import annotations
... |
73ff5f4e3cb51374247ff6a217fcc0a0e570c62af1711de52fbab028c0349a49 | Python | 31,983 | 627 | #!/usr/bin/env python
"""
This plot contains all of the functions
related to making the ribbon plots.
These functions can be called by the other
programs.
"""
# ODP-specific imports
import odp_plotting_functions as odp_plot
# Other standard python libraries
import logging
# non-standard dependencies
# Force the... |
9ae51a45df9e8a5987f20b0d39f5c8e3c76168aac0356984c6bd7668d02f1d1f | Python | 32,022 | 809 | """VD-CMA and VkD-CMA
Usage examples, VD-CMA:
>>> import cma
>>> from cma import restricted_gaussian_sampler as rgs
>>> es = cma.CMAEvolutionStrategy(20 * [1], 1,
... rgs.GaussVDSampler.extend_cma_options({
... 'seed': 6,
... 'ftarget': 1e-8,
... ... |
8a93f705da878db48abd0671850151297e120e092241b50f1d427ebf32885204 | Python | 32,130 | 626 | import random, json, os, time
import warnings
from typing import List, Dict, Any
from pathlib import Path
from copy import deepcopy
import numpy as np
import torch
import torch.nn as nn
from torch.utils.data import DataLoader
import wandb
from tqdm import tqdm
from vp_suite.defaults import SETTINGS, DEFAULT_RUN_CONFI... |
fcf66b7c599195b8733d2a67330052fe15f9b5c732abdbb2b596c2ee08fa68bd | Python | 32,134 | 835 | # copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Implements forecaster for applying different univariates on hierarchical data."""
__author__ = ["VyomkeshVyas"]
__all__ = ["HierarchyEnsembleForecaster"]
import pandas as pd
from sktime.base._meta import flatten
from sktime.forecasting.base.... |
52719a209a14951d18399a172f6348cd1c3e9beb711fad956b39bd5c400a3d7d | Python | 32,167 | 600 | import matplotlib.pyplot as plt
import numpy as np
import pickle
import seaborn as sea
from PIL import Image
import pandas as pd
def stim2activation(stim):
"""
converts from a neural potential to a muscle activation between 0 and 1 with a clipped sigmoid curve
:param stim: MN potential in mV
:return: a... |
2191da00672f4059ead009e30433d14864549561ab38af6ec3b0fba366fbf262 | Python | 32,201 | 779 | #-------------------------------------------------------------------------------
# elftools: dwarf/callframe.py
#
# DWARF call frame information
#
# Eli Bendersky (eliben@gmail.com)
# This code is in the public domain
#-------------------------------------------------------------------------------
from __future__ impor... |
47d48513d6b0a5948a203136278f3c028e6843e3e8516aa4f8fdaa75af111a3f | Python | 32,262 | 710 | """
@file: PGN2PlanesConverter.py
Created on 09.06.18
@project: DeepCrazyhouse
@author: queensgambit
Loads the pgn-file and calls the pgn_converter functions to create a plane representation.
Multiprocessing is used for loading, computing and saving.
IMPORTANT NOTICE: This file is only compatible with python-chess v0... |
eaaf14830abf800c8b7794173d284dfb387f49b21c27a5f63c2802ba6502a121 | Python | 32,263 | 794 | # Copyright 2019-2026 The AmpliGraph Authors. All Rights Reserved.
#
# This file is Licensed under the Apache License, Version 2.0.
# A copy of the Licence is available in LICENCE, or at:
#
# http://www.apache.org/licenses/LICENSE-2.0
#
"""
Graph partitioning strategies.
This module contains several graph partitio... |
d11cd6de7ec7fea543a46c77498e6e66a191356db93c55ebc87b26924e4c3c10 | Python | 32,296 | 567 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import json
import logging
import os
import shutil
import time
import dill
import numpy as np
import ray
from ray.rllib.utils.memory import ray_get_and_free
from termcolor import colored
from mprl.utility_ser... |
6f567f3cc15bff81bc2230efa9932cc8b0252d42ae12a276f053f13587f44c35 | Python | 32,307 | 724 | # ----------------------------------------------------------------------------
# Copyright (c) 2017-2026, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------------... |
fc7110e2836b45cd5ce3cf31bd1ac42749f7c69e87387e9d0e9785d2e8fc8dd1 | Python | 32,374 | 802 | import math
import warnings
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from mmcv.cnn import (Conv2d, build_activation_layer, build_norm_layer,
constant_init, normal_init, trunc_normal_init,build_conv_layer,)
from mmcv.cnn.bricks.drop import build_dropout... |
c0b9adaa85c10e83ef1375813bf1dcf2e9f2ddc744f660742a0742ab42ce4dad | Python | 32,408 | 885 | # Copyright 2018-2025
# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
# 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/LICE... |
8f70db0e43acdeb10092f51907704d4c272b0e3885efc1aa8e6ba423b1709f0b | Python | 32,426 | 840 | """
Dirichlet-multinomial models for statistical analysis of compositional changes in single-cell data.
For further reference, see:
Büttner, Ostner et al.: scCODA: A Bayesian model for compositional single-cell data analysis
:authors: Johannes Ostner
"""
import numpy as np
import time
import warnings
import tensorfl... |
a17a9670e7771e575ba1c5c9ee08d4be49c2ff5af8d49f0813c7688441d9e23e | Python | 32,434 | 854 | from __future__ import annotations
import logging
import pathlib
import sys
import warnings
import numpy as np
import torch
from energyflow.emd import emds
from numba import njit, prange, set_num_threads
from numpy.typing import ArrayLike
from scipy import linalg
from scipy.optimize import curve_fit
from scipy.stats ... |
f0c167fd561ccb6bdd7142dd48f01d4f7a650b6dd3edb75ad220678ad351e687 | Python | 32,441 | 918 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""Bindings and model entry for the fused DPA4 / SeZM SO(2) convolution.
The CUDA operator ``deepmd::dpa4_so2_conv`` (see
``source/op/pt/dpa4/so2_conv.cu``) evaluates the whole per-edge span of one
``SO2Convolution``: the attention logits and their envelope-gated segment
so... |
73d024217aaaddf6a6697b38158df2ec90b12ddb4229dfb3427ad1c0980bdb07 | Python | 32,445 | 869 | # Copyright 2019 DeepMind Technologies Ltd. All rights reserved.
#
# 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 appl... |
4ef3b083e5c3e7dad6c5725492dd72e20101754ded20332b2d094c9c924590ec | Python | 32,476 | 819 | # coding=utf-8
# Copyright 2018 The Google AI Language Team Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ... |
c6f5daa08280050d84e76acba87d6b0e0d901711b0723644b7cb9b388b48b0ba | Python | 32,477 | 1,021 | # coding=utf-8
# Copyright (C) 2021. Huawei Technologies Co., Ltd. All rights reserved.
#
# 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
#
# ... |
578fa62a739314e86f16eb29faad3b440b5a8c46d5cf4b055c6d3983c877f6c7 | Python | 32,573 | 757 | #-------------------------------------------------------------------------------
# elftools: dwarf/dwarfinfo.py
#
# DWARFInfo - Main class for accessing DWARF debug information
#
# Eli Bendersky (eliben@gmail.com)
# This code is in the public domain
#---------------------------------------------------------------------... |
b67efeecb8379d99b7b17c056f2ac6ab48afb6fe8a239382b218f6dff4cdf87f | Python | 32,726 | 753 | # -*- coding: utf-8 -*-
"""A collection of variable boundaries (AKA box constraints) handling classes.
"""
from __future__ import absolute_import, division, print_function #, unicode_literals
import warnings as _warnings
import numpy as np
from .utilities import utils as _utils
from .utilities.utils import rglen
from ... |
edb8a1ee3386fac68ae68d6e87cccbaf4fec2b95d2f73d429d678ca3b49b4c9c | Python | 32,755 | 1,082 | # Copyright 2026 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... |
d4cfa71f6838ba71e2dd1c114bf08a804ae3f257bece8cbca1b1edce0d32eaca | Python | 32,788 | 893 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Frozen-feature UCR evaluation with multi-layer feature fusion.
The script follows a Mantis-style evaluation protocol:
1. keep the pretrained encoder completely frozen;
2. resize each UCR series to a fixed length (512 by default; the paper run uses 1024);
3. extract re... |
511ed508286128463f9c0e150170e4ce7d217311aa9e496c0eb2a55f572d069b | Python | 32,842 | 878 | # Copyright 2019 DeepMind Technologies Ltd. All rights reserved.
#
# 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 appl... |
1ba8952323b167a016680fb74001ad76fb2e54dbf37fabf36d04175ba353bf1e | Python | 32,848 | 925 | """Tests for source/odp_functions.py.
Focuses on the small utility functions that are exercised throughout
the odp pipeline: resource estimators, file-existence guards, chrom
file legality + parsing, expand-style helpers used to build
snakemake input lists, and small text/IO helpers.
Heavier statistical functions (`c... |
600a160831d70aa300da76df3512032e11a030ceda3e3fab147a10b4910f7d3f | Python | 33,028 | 847 | # Copyright 2018-2026
# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
# 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/LICE... |
c26ca543bf3d3e21af04b94bf5f052f19a10920135f16f29109108c8422a0dee | Python | 33,031 | 858 | from aiohttp import ClientSession, TCPConnector, BasicAuth
import asyncio
from collections import defaultdict, namedtuple
from IPython import embed
import json
import pandas as pd
import random
import requests as r
import string
from sys import exit
from typing import Union, List, Dict
import ilxutils.scicrunch_client_... |
06ad39cad4cc7c3e47a8b3a6d193b5dd8f8a39cde2d4d6391398d254fe195c3c | Python | 33,117 | 877 | # SPDX-License-Identifier: LGPL-3.0-or-later
import functools
import logging
from collections.abc import (
Callable,
)
from typing import (
NoReturn,
Optional,
)
import torch
from deepmd.dpmodel.atomic_model import (
make_base_atomic_model,
)
from deepmd.dpmodel.output_def import (
FittingOutputD... |
6a60519948cf8d64f316be7a1342cb8e29db879c101e53ffc70a6aa59a825cac | Python | 33,142 | 1,300 | """Pre-calculated tags for UCR UEA datasets."""
DATASET_TAGS = {
"BirdChicken": {
"n_splits": 1,
"is_univariate": True,
"n_instances": 40,
"n_instances_train": 20,
"n_instances_test": 20,
"n_classes": 2,
},
"AllGestureWiimoteY": {
"n_splits": 1,
... |
743fe5d3dd82f74bd2387c01bc8fd323a6e21822c73d568a2f592be5c89a153d | Python | 33,216 | 821 | """Tools for (lean) experimentation and collecting data.
See also cma.optimization_tools and cma.utilities.math.test*.
TODO: write some running examples as doctests.
"""
from __future__ import division, print_function
import warnings
import os
import shutil
import time
from collections import defaultdict, namedtuple
... |
ac45355e414676f6b00d0b6eca456143aff24a0375968fb4cf8ad1699198bcad | Python | 33,251 | 1,081 | from __future__ import division
import colorsys
from itertools import cycle
import numpy as np
import matplotlib as mpl
from .external import husl
from .external.six import string_types
from .external.six.moves import range
from .utils import desaturate, set_hls_values, get_color_cycle
from .colors import xkcd_rgb, ... |
218b6852528a1940daf60b3defd924e745795da6e269563d1900006378292640 | Python | 33,322 | 857 | # SPDX-License-Identifier: LGPL-3.0-or-later
from collections.abc import (
Callable,
)
from typing import (
Any,
)
import torch
from deepmd.dpmodel import (
ModelOutputDef,
)
from deepmd.dpmodel.output_def import (
FittingOutputDef,
OutputVariableCategory,
OutputVariableOperation,
check_op... |
1a266ad45703264a346d724565245ab2b00af35a77c0128be4eeb93e63ff79a5 | Python | 33,326 | 865 | #!/usr/bin/env python2
'''Subclass of standard PsychoPy Window to perform warping and RGB60 -> Mono180 Hz'''
import sys
import os
# Ensure setting pyglet.options['debug_gl'] to False is done prior to any
# other calls to pyglet or pyglet submodules, otherwise it may not get picked
# up by the pyglet GL engine and hav... |
eae689e62fffbf468cb5e1bdbfdf71728ce94e4caa80e2c136785d9b24f7df51 | Python | 33,400 | 933 | """This module provide the necessary tools to read and write different geometry
formats including the molecule object format of pyRDPT
Attributes:
GENERIC_CELL (obj:`np.ndarray[3,3]`): Generic cell parameters used to
generate cell parameters if they are not defined in the given format.
FORMATS_DIC (dic... |
c0ad5447fd305fc7f9b47fc6a937f416fcb9be827bd584c5a31b65f308713961 | Python | 33,516 | 982 | #!/usr/bin/env python3
import tempfile
from pyontutils.config import auth
__doc__ = f"""Client library generator for SciGraph REST api.
Usage:
scigraph-codegen [options] [--dynamic=<PATH>...]
Options:
-o --output-file=FILE save client library here [default: {tempfile.tempdir}/scigraph_client.py]
... |
c72050d5c35fa05e7ce50e8b3c58b36bce0a497965f7355c2e1e507109304dab | Python | 33,540 | 1,015 | # Copyright (c) ONNX Project Contributors
#
# SPDX-License-Identifier: Apache-2.0
"""Automates the generation of ONNX operators."""
from __future__ import annotations
import difflib
import importlib
import inspect
import keyword
import os
import pathlib
import re
import shutil
import sys
import textwrap
from typing i... |
459ee27f65498553ef2b2223044a0a097e57ab74981b2aacdfe115865d782e46 | Python | 33,593 | 891 | # -*- coding: utf-8 -*-
"""Collection of classes that sample from parametrized distributions and
provide an update mechanism of the distribution parameters.
All classes are supposed to follow the base class
`StatisticalModelSamplerWithZeroMeanBaseClass` interface in module
`interfaces`.
"""
from __future__ import abso... |
d01db1a30ba472aa7e5340f665ac112b5c96b6a64807cb22c13c9951dbb5b97a | Python | 33,618 | 916 | from models.se3transformer_layers.utils_profiling import * # load before other local modules
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from contextlib import nullcontext
from typing import Dict
from models.se3transformer_layers.from_se3cnn import utils_steerable
from mod... |
efe750b9ff427c09dd12b242bd29c7b2bd2c9bc187196b19440da8361776cdf9 | Python | 33,644 | 816 | # -*- coding: utf-8 -*-
"""
Created on Tue Apr 24 03:35:50 2018
@author: lyra7
"""
import logging
import os
import time
from PIL import ImageChops
from psychopy import logging as logging_psychopy
from psychopy import event, core
from psychopy.visual import ElementArrayStim
from psychopy.tools.arraytools import val2ar... |
836f9b59c33793699632709a386040acd876d0e9c716d0527a81611a7af5ff62 | Python | 33,760 | 841 | from __future__ import annotations
import argparse
import json
import math
import time
from dataclasses import dataclass
from pathlib import Path
import numpy as np
import pandas as pd
import torch
from scipy import sparse
from sklearn.decomposition import PCA
from sklearn.cluster import KMeans
from sklearn.linear_mo... |
e8fe2ee8269202a1134ad81c668494c8f807f88e000bb25e115c82d27ddf1f09 | Python | 33,796 | 575 | # get rare diseases from free-texts using Gate-BioYODIE and ontologies
import json
import sys
import urllib
# pip install requests
# https://pypi.org/project/requests/
import requests
from collections import defaultdict
import pandas as pd
import os
import re
import requests
# extracting umls from... |
ed9e3f1dc2f40de3d49268f91e690c0d2fcf3cc272e69b4d416b1d4d04a806ef | Python | 33,816 | 849 | # Copyright 2019 DeepMind Technologies Ltd. All rights reserved.
#
# 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 appl... |
ed46162d480e358d3c1f13ae8341f80aee69b6503c185acd44d44e8dcca18f27 | Python | 33,822 | 867 | # SPDX-License-Identifier: LGPL-3.0-or-later
import functools
from collections.abc import (
Callable,
)
from copy import (
deepcopy,
)
from typing import (
Any,
)
import torch
from deepmd.dpmodel import (
ModelOutputDef,
)
from deepmd.pt.model.atomic_model import (
DPAtomicModel,
)
from deepmd.pt.... |
43f808498089df664cfd8d5a85e06a7c816515e67857a1daf15632944646e8df | Python | 33,878 | 866 | from gui.CustomWidgests import BlobColor,BlobColor_,BlobColor_object,names
from gui.GUI import Ui_MainWindow
from PyQt5 import QtCore, QtGui, QtWidgets
from PyQt5.QtCore import QPoint,Qt
import pathlib
import Path_Finder
from PyQt5.QtWidgets import (QMainWindow, QTextEdit, QGraphicsScene,QFrame,
... |
2a1088b008d26928ca51af89f5cdc3a05c8f51139ac5cb78e84ee5b31d4f07a8 | Python | 33,924 | 852 | import torch.nn as nn
import torch
import torch.nn.functional as F
from torch.distributions import Bernoulli
from torch.autograd import Variable
# from scipy.special import gamma
# NOTE: This is not used!
import numpy as np
import math
import pdb
import torchvision.models as models
from torch.nn.parameter import Par... |
218091ecddf94253659030bbea1b2ad7ebfe8ab5fff903510272e8d97e46d3aa | Python | 34,058 | 1,016 | """Signature kernels from Kiraly et al, 2016."""
__author__ = ["fkiraly"]
import collections
from functools import partial
import numpy as np
from scipy.sparse.linalg import svds
from sklearn.base import BaseEstimator, TransformerMixin
from sktime.dists_kernels.base import BasePairwiseTransformerPanel
# cumsum var... |
88cf937a4c21f66e35048ada4f215703780dda08f7675bbd46ded2ce7e523e30 | Python | 34,086 | 1,035 | # Copyright 2026 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... |
5746637a7635605522fcb2775fc247200f065cda85a52b7a12a5a4a8cb12c404 | Python | 34,259 | 932 | # Copyright 2019-2026 The AmpliGraph Authors. All Rights Reserved.
#
# This file is Licensed under the Apache License, Version 2.0.
# A copy of the Licence is available in LICENCE, or at:
#
# http://www.apache.org/licenses/LICENSE-2.0
#
import logging
from collections.abc import Iterable
from itertools import isli... |
f79fafe365d9caa07ed4f64f1ccbe97718905de5c8da19ea858f749e57b04a93 | Python | 34,285 | 969 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""Training entrypoint for the pt_expt backend."""
import argparse
import logging
import os
from dataclasses import (
replace,
)
from pathlib import (
Path,
)
from typing import (
Any,
)
from deepmd.dpmodel.atomic_model.inner_potential import (
InnerPotenti... |
5c036f56675ec329030fe56ed98253d037520059549e0e76848bd51f07058b68 | Python | 34,326 | 950 | """Plotting functions for linear models (broadly construed)."""
import copy
from textwrap import dedent
import warnings
import numpy as np
import pandas as pd
import matplotlib as mpl
import matplotlib.pyplot as plt
try:
import statsmodels
assert statsmodels
_has_statsmodels = True
except ImportError:
... |
41678c812847b1f8b0932053a2be6f252ff3d73538c7336dffddb345c885d2e9 | Python | 34,347 | 1,106 | #-------------------------------------------------------------------------------
# elftools: elf/descriptions.py
#
# Textual descriptions of the various enums and flags of ELF
#
# Eli Bendersky (eliben@gmail.com)
# This code is in the public domain
#----------------------------------------------------------------------... |
a2fe06a66e93c4592be784ca48df5503b55e457147326018f7f976a672b5108d | Python | 34,365 | 676 | from os.path import join
from pandas.api.types import is_numeric_dtype
# Seeds
from os import environ
from random import seed as rseed
import numpy as np
import pandas as pd
from sklearn.preprocessing import MinMaxScaler, StandardScaler
from sklearn.decomposition import PCA
import matplotlib.pyplot as ... |
9d3cd2d052e250f337c49d3c828e358cb2ceabbf6e99519a9435b218eb7c8d4e | Python | 34,410 | 929 | import types
import rdflib
from ontquery.terms import OntId
from pyontutils.utils_extra import check_value
from pyontutils.namespaces import TEMP
from pyontutils.closed_namespaces import rdf, rdfs, owl
try:
breakpoint
except NameError:
from IPython import embed as breakpoint
def flattenTriples(triples):
f... |
72f96f1bb0d9f9c79589e1ba3ae434ab2046a561e6c18b5d8afb80e220b9431c | Python | 34,456 | 869 | # copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Wrapper for easy vectorization/iteration of time series data.
Contains ``VectorizedDF`` (iteration schema) and ``prepare_VectorizedDF``
(convert once, then construct the schema).
"""
__author__ = ["fkiraly", "hoesler"]
import itertools
impo... |
d8eafd39040b41bcaba80710cd771fb16efb44d11928ba632e9b5a49505f5c9d | Python | 34,467 | 1,214 | # SPDX-License-Identifier: LGPL-3.0-or-later
# ruff: noqa: ANN001, ANN202
"""Bindings and model entry for the fused SO(2) value path, training form.
The CUDA operator ``deepmd::sezm_so2_value_fwd`` (see
``source/op/pt/dpa4/so2_conv_train.cu``) evaluates the value stream of one
``SO2Convolution`` up to the attention ag... |
db7e9d1fa38e5477fcd61052577d93fa8545c02bee6c0ee62dcb4d14aa85d001 | Python | 34,511 | 795 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""Freeze-time measurement of the fitting route of compressed DPA4C.
The fused energy-force operator of compressed DPA4C evaluates its fitting
network over runs of nodes, either through the fused kernel, in one of the
shapes compiled for the hidden width, or through the per... |
530d2f5606f33bd189bdef544242a1f7ba37dac7a243fbda0786765426b1a211 | Python | 34,630 | 982 | from functools import partial
import warnings
import numpy as np
import pandas as pd
import matplotlib as mpl
import matplotlib.pyplot as plt
from matplotlib.cbook import normalize_kwargs
from ._base import (
VectorPlotter,
)
from .utils import (
adjust_legend_subtitles,
_default_color,
_deprecate_ci,... |
411d7452a18f6d8b7a3d60a15303d5e256ae030f12249db32bec3d9e4ebe6b85 | Python | 34,682 | 782 | """
test_bushy_variation.py
Test inputs to bushy cells as we co-vary the KLT and IH conductances
Two tests: IV and spikes.
Simulation results are first written to disk (.p files); plotting is done separately
Usage:
python test_bushy_variation.py [a, b]
a runs IV curvers with variations of gKlt/gh
b runs PSTHs to AN i... |
acd28727c4bc5a91faa98cbaac6eea13f532b461dde0ec24a6032a9b292315a6 | Python | 34,703 | 669 | from __future__ import print_function
from os import mkdir
from os.path import isdir
import numpy as np
from stageLabelAndOneHot import stageLabel2oneHot
from inputAndOutputExtractor import InputAndOutputExtractor
import torch
import torch.utils.data
from torch import nn, optim, cat
from functools import reduce
from op... |
dabcd1a802acfb060439f9aabdeba5536ad7a9f19a78f9a41a33d7bd4f388f71 | Python | 34,931 | 949 | # Copyright 2019-2026 The AmpliGraph Authors. All Rights Reserved.
#
# This file is Licensed under the Apache License, Version 2.0.
# A copy of the Licence is available in LICENCE, or at:
#
# http://www.apache.org/licenses/LICENSE-2.0
#
"""SQLite backend for storing graphs.
This module provides SQLite backend for ... |
9211dbdbde4592f9aeccefd3224d4d91a6ebb2294f3551c6da9cdaf16764ed2d | Python | 35,097 | 913 | """
Core functions for running Palantir
"""
from __future__ import annotations
import numpy as np
import pandas as pd
import time
import copy
from sklearn.metrics import pairwise_distances
from sklearn import preprocessing
from sklearn.neighbors import NearestNeighbors
from joblib import Parallel, delayed, effective... |
e4ac68281aeade64c4ac52562da8c425f311ced2fe968ddbfae0f007846cb3a6 | Python | 35,137 | 883 | # Copyright 2019 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... |
24adc1406fb00943ae1f61cbe6dc8ecca8a5b6d5e17f8bac8ea939efb7cfe6f3 | Python | 35,141 | 965 | import numpy as np
import tensorflow as tf
import tensorflow_probability as tfp
from lfads_tf2.initializers import make_variance_scaling, ones_zeros, variance_scaling
from lfads_tf2.regularizers import DynamicL2
from lfads_tf2.tuples import (
DecoderInput,
DecoderOutput,
DecoderRNNInput,
DecoderState,
... |
af5086f7aeafd069caa546420f5f1aaa99ce3d2ecadc2f1d81ba680efc569506 | Python | 35,213 | 817 | #!/usr/bin/env python3 -u
# copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Interface to ARIMA and AutoARIMA models from pmdarima package."""
__author__ = ["mloning", "hyang1996", "fkiraly", "ilkersigirci"]
__all__ = ["AutoARIMA", "ARIMA"]
from sktime.forecasting.base.adapters._pmdarima impor... |
78d7ed5058853479d3e7399bc58cfe89bfeac95a486190a37cb7bb9893ae6bfe | Python | 35,303 | 717 | import logging
from math import inf
from typing import Optional, Union
import torch
from torch import nn
import flair.embeddings
import flair.nn
from flair.data import Dictionary, Sentence, Token
from flair.datasets import DataLoader, FlairDatapointDataset
from flair.training_utils import Result, store_embeddings
lo... |
0c6c3dc0a526af32166bd281c9a900b474b6f89f722d2c329d567c1507eb6940 | Python | 35,350 | 756 | import pandas as pd
import os
import time
from dotmap import DotMap
from pathlib import Path
import math
import numpy as np
from cutadapt.adapters import AdapterParser
from cutadapt.seqio import Sequence
from scripts import feature_util
#####################################################################... |
d22b45971abea64067dbf03cbfaf7243d604a2eac2f414ae2a39fe0152cfda20 | Python | 35,371 | 926 | # Copyright 2022 The TensorFlow Authors. All Rights Reserved.
#
# 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 applica... |
f80792af1c27aed0e7f865961aef11400e759d75a01f02a65a89635501403f2a | Python | 35,379 | 949 | xkcd_rgb = {'acid green': '#8ffe09',
'adobe': '#bd6c48',
'algae': '#54ac68',
'algae green': '#21c36f',
'almost black': '#070d0d',
'amber': '#feb308',
'amethyst': '#9b5fc0',
'apple': '#6ecb3c',
'apple green': '#76cd26',
... |
92e6b2306d8683345aec7e348bfe1416dfdc004a72cda30e32ba7213ab416106 | Python | 35,426 | 579 | #!/usr/bin/env python3
import rdflib
import ontquery
#from pyontutils.core import OntId, OntTerm
from pyontutils.utils import relative_path
from pyontutils.namespaces import makePrefixes, makeNamespaces
from pyontutils.namespaces import NIFRID, ilxtr, hasRole, definition
from pyontutils.closed_namespaces import rdf, rd... |
0d3695ccefa966bc8e039fbc3eb6010e3b414db4507be597b50e77b5abf1424b | Python | 35,434 | 775 | import pandas as pd
import pickle as pkl
import numpy as np
import os
import glob
import matplotlib.pyplot as plt
import matplotlib as mpl
from tqdm import tqdm
import src.data.struct_to_dataframe as stdf
# Plotting
import sciplotlib.polish as splpolish
import sciplotlib.style as splstyle
import src.models.predict_... |
8c7e6aa760b926193a2e5f892e9a76a729c88c4db46fd965f5183df48b0ab0eb | Python | 35,434 | 579 | #!/usr/bin/env python3
import rdflib
import ontquery
#from pyontutils.core import OntId, OntTerm
from pyontutils.utils import relative_path
from pyontutils.namespaces import makePrefixes, makeNamespaces
from pyontutils.namespaces import NIFRID, ilxtr, hasRole, definition
from pyontutils.closed_namespaces import rdf, rd... |
5b79c9564f4e8660c603c9c7bf0feb2e288cc330bf0ec2f137a7963088d5c842 | Python | 35,460 | 767 | from src.utilities.DDE_Solver import ddeinttf
import quadpy
import time
import timeit
import sys
import os
from tqdm import tqdm
from IPython.core.debugger import set_trace
import numpy as np
import tensorflow as tf
import matplotlib.pyplot as plt
from scipy import integrate
import scipy.interpolate
import pickle
im... |
f398ac15f164f23f2111b43d32dcabb24d4ca131f7b7650dc64424cc20ee498b | Python | 35,522 | 1,094 | from __future__ import annotations
import re
from copy import copy
from collections.abc import Sequence
from dataclasses import dataclass
from functools import partial
from typing import Any, Callable, Tuple, Optional, ClassVar
import numpy as np
import matplotlib as mpl
from matplotlib.ticker import (
Locator,
... |
5afb9c1e0ea71edd89862ce45e698ec43fea25c07e84908e818fa25d77bdc524 | Python | 35,529 | 1,218 | """Machine type converters for Panel scitype.
Exports conversion and mtype dictionary for Panel scitype:
convert_dict: dict indexed by triples of str
1st element = convert from - str
2nd element = convert to - str
3rd element = considered as this scitype - str
elements are conversion functions of machine type (... |
b954e9d6fbd946797d0c892ce3df92b6b67cf1411f11efa2c6c86e2b9fdbbf08 | Python | 35,576 | 979 | # Copyright 2018-2025
# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
# 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/LICE... |
15a37e4762567c835632866fbd25cd7884de17c87eb67ee889e9197dc7278d25 | Python | 35,645 | 780 | """
@file: PGN2PlanesConverter.py
Created on 09.06.18
@project: DeepCrazyhouse
@author: queensgambit
Loads the pgn-file and calls the pgn_converter functions to create a plane representation.
Multiprocessing is used for loading, computing and saving.
IMPORTANT NOTICE: This file is only compatible with python-chess v0... |
5e0e642ff80c4116be093e501d616330e07a980f0b492840ae8564dca7cd2549 | Python | 35,653 | 1,158 | # Copyright (c) ONNX Project Contributors
#
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
from typing import Any
import numpy as np
import onnx
from onnx.backend.test.case.base import Base
from onnx.backend.test.case.node import expect
def softmaxcrossentropy(
x: np.ndarray,
targ... |
9a684652772d8bcc33b6bbcbc5c9206d53a84e37676ae08a2a35f8c54e083bbd | Python | 35,766 | 1,156 | """
Models for the model comparison benchmark in `scCODA: A Bayesian model for compositional single-cell data analysis`
(Büttner, Ostner et al., 2020).
These models are otherwise not part of scCODA, but make a nice addition for comparison purposes
and are thus part of the main package.
:authors: Johannes Ostner, Mare... |
a0732d2e5b7f98f4d74cfc40a039a80fd63e0dd1ba815c82dff3da83f35a40e5 | Python | 35,768 | 1,100 | # Copyright 2019-2020 The ASReview Authors. All Rights Reserved.
#
# 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 appl... |
bbceeb5107c7da4607f4a0e64ac3ba6d2ea0abb0f64a87ae1fed85bd32d6f7b5 | Python | 35,889 | 773 | # copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Extension template for forecasters.
Purpose of this implementation template:
quick implementation of new estimators following the template
NOT a concrete class to import! This is NOT a base class or concrete class!
This is to be use... |
390e466b63869cbf7a285b510329eecbd352c48bb9c525a9a5594278f23fab68 | Python | 35,929 | 837 | # -*- coding: utf-8 -*-
"""versatile container for test objective functions.
For the time being this is probably best used like::
from cma.fitness_functions import ff
"""
from __future__ import (absolute_import, division, print_function,
) # unicode_literals, with_statement)
# from __fu... |
537c087d8f1c1a033af4c9b2f6272dedb576288012ec60b3d3e2903086c34bb7 | Python | 35,938 | 918 | # ----------------------------------------------------------------------------
# Copyright (c) 2017-2026, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------------... |
3fb29af293a014ebbaf64423d27e44fa1a7268869c267fd0034829bf573a579f | Python | 35,952 | 768 | """
@file: crazyara.py
Created on 18.10.18
@project: crazy_ara_refactor
@author: queensgambit
Universal chess interface (CUI) communication protocol interface for the engine.
The protocol was published by Stefan-Meyer Kahlen (ShredderChess) and can be accessed at:
http://wbec-ridderkerk.nl/html/UCIProtocol.html
"""
f... |
2dbbf4bf18b8103890cc372a637d7cb77100f67b9b3c61c029830399052e0520 | Python | 35,953 | 768 | """
@file: crazyara.py
Created on 18.10.18
@project: crazy_ara_refactor
@author: queensgambit
Universal chess interface (CUI) communication protocol interface for the engine.
The protocol was published by Stefan-Meyer Kahlen (ShredderChess) and can be accessed at:
http://wbec-ridderkerk.nl/html/UCIProtocol.html
"""
f... |
0c5a5516337bc199a692526c26981381a06cd28fa7edc02690fc4c057804ddf8 | Python | 35,961 | 1,075 | # Copyright 2023 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... |
7fe8c6d51f87282e4a0d0d3492c46689047dd6ae50ba873f3f190372cc73f952 | Python | 36,088 | 1,104 | '''
All processes that operate outside of the EVOLVE main code like simulation codes should be included in this.
.. codeauthor:: Nicholas Browning
.. codeauthor:: Simon Duerr dev@simonduerr.eu
.. codeauthor:: Justin Villard
'''
from __future__ import division
from __future__ import print_function
from builtins impor... |
00cb37bae63b970b803346e65320cb7ec8e8f0b3a2c2cd031524276751a689be | Python | 36,118 | 937 | '''
Evaluators in EVOLVE are functions that can call outprocesses and that return fitness values.
.. codeauthor:: Nicholas Browning
.. codeauthor:: Simon Duerr dev@simonduerr.eu
'''
from __future__ import print_function
from builtins import str
from builtins import range
from src.gaapi import Individual
from src.g... |
b41a51c0d4630639ae5e612c5a777f4bf284bcf34bae107fe3f58407b0035267 | Python | 36,123 | 770 | from src.utilities.DDE_Solver import ddeinttf
import quadpy
import time
import timeit
import sys
import os
from tqdm import tqdm
from IPython.core.debugger import set_trace
import numpy as np
import tensorflow as tf
import matplotlib.pyplot as plt
from scipy import integrate
import scipy.interpolate
import pickle
im... |
2b02afc1e02d10f668a9abaae6d8f712534cff974a1f538fb251efba25abf57f | Python | 36,238 | 860 | """Wrapper for objective functions like noise, rotation, gluing args
"""
from __future__ import absolute_import, division, print_function #, unicode_literals, with_statement
import warnings
from functools import partial
import numpy as np
import time
from .utilities import utils
from .utilities.math import Mh as _Mh
f... |
70e0b6cc70092bfb5c5da95987bcc801c5b155003f775f071baf49c913181faa | Python | 36,256 | 1,047 | """
Adjust areas of hoc files (mesh expansion)
This module is part of *vcnmodel*
Support::
NIH grants:
DC R01 DC015901 (Spirou, Manis, Ellisman),
DC R01 DC004551 (Manis, 2013-2019, Early development)
DC R01 DC019053 (Manis, 2020-2025, Later development)
Copyright 2019 Paul B. Manis... |
d6d8b38de563fc655064a168ec9a001b8daf82533aa59100f007744ce12ebdc8 | Python | 36,277 | 988 | """
This module provides tools that take an original HOC file and replaces the axon
sections (including the AIS, hillock, and myelinated sections) with some variant
of a "standardized" axon. The modified version of the cell is written to a new
file.
This module is part of *vcnmodel*.
Support::
NIH grants:
DC... |
6c929bf655022d6b34640b8aea7e6362f73d565e7856fa2a4456258cb3994772 | Python | 36,325 | 791 | import numpy as np
from dnnbrain.io.fileio import RoiFile
from dnnbrain.dnn.base import UnivariateMapping, MultivariateMapping
class ROI:
"""
A class used to encapsulate and manipulate ROI data of brain
"""
def __init__(self, rois=None, value=None):
"""
Parameters
----------
... |
817e1e30660ce50dd4fa26cd173d341bdd3c4582985db3f91d001ebd3e97bf81 | Python | 36,370 | 1,103 | # Copyright (c) OpenMMLab. All rights reserved.
import os
import numpy as np
from .base_dataset import BaseDataset
from .builder import DATASETS
def has_file_allowed_extension(filename, extensions):
"""Checks if a file is an allowed extension.
Args:
filename (string): path to a file
Returns:
... |
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