sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
608ececb4d09f4de1df657147e068904afe2660e3e11e4b13d0ea309a9c981e8 | Python | 36,399 | 1,023 | # SPDX-License-Identifier: LGPL-3.0-or-later
import logging
from collections import (
defaultdict,
)
from collections.abc import (
Callable,
Sequence,
)
from typing import (
Any,
)
import numpy as np
import torch
from torch.utils.data import (
DataLoader,
)
from deepmd.pt.utils import (
AtomEx... |
afafe9857c03d87d56d2e65e7718267d72a7ee9338d12bd01cdd47e4d06dd567 | Python | 36,873 | 1,023 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""Graph-route regression tests for the dpmodel DPA4 descriptor."""
import dataclasses
import numpy as np
import pytest
from deepmd.dpmodel.atomic_model import (
DPAtomicModel,
)
from deepmd.dpmodel.descriptor.dpa4 import (
DescrptDPA4,
_graph_from_padded_nlis... |
0fffadb20024a43ac894be1d6755f8c45c2cb94dfc772bf11a7d084c1ee5f8c9 | Python | 36,946 | 918 | r"""
Definition of a NeuronNode, NeuronTree and SWCForest class for representing the internal contents \
of an \*.swc file. Basic functions for manipulating, examining, validating and \
filtering \*.swc files. A function for reading \*.swc files from memory.
"""
from __future__ import annotations
import os
imp... |
45e10ae3a74683e68dc5b131dee62fd776f62242490512d9bc9003c3fc354504 | Python | 36,992 | 1,115 | # Copyright 2019-2021 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 numpy as np
import pytest
from itertools import islice
from ampligraph.... |
4d776d51df1c99d078685fdcbc386c2616ea50aa94b09367b5766495894ff74c | Python | 37,001 | 920 | r"""
Definition of a NeuronNode, NeuronTree and SWCForest class for representing the internal contents \
of an \*.swc file. Basic functions for manipulating, examining, validating and \
filtering \*.swc files. A function for reading \*.swc files from memory.
"""
from __future__ import annotations
import os
i... |
25d5b606fb2d137a01fe77dabc2c5c7c37ea80c43dd4fd6928f6dc252d720837 | Python | 37,079 | 927 | # 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
#
"""Data loader for graphs (big and small).
This module provides GraphDataLoade... |
8ba60b08040c6fd14743a49fd95deb5823c940d317fe0eb8b20c3617acee8d28 | Python | 37,124 | 766 |
"""
Script to build main file of analyzed data
Intended file information:
I Fit Neurons - only for neurons which were fit by the ann
<Neuron ID> <is lm id> <ZBrain Coords> <Barcode> <Jacobian> <Jac-cluster> <Complexity> <is vglut>
II Neuron list - where neurons come from and where they are for all neurons
<Neuron I... |
0636244b7ade574c3aa6f8dd7c37535ef094c44312b293ba3dc28333b6945985 | Python | 37,203 | 964 | # -*- coding: utf-8 -*-
""" various math utilities, notably `eig` and a collection of simple
functions in `Mh`
"""
from __future__ import absolute_import, division, print_function #, unicode_literals
# from future.builtins.disabled import * # don't use any function which could lead to different results in Python 2 vs... |
b393f0a7039a425034fd7e5d2619f4e33a948d87d6a607605f4981d868e3cfe1 | Python | 37,203 | 921 | # Copyright (c) OpenMMLab. All rights reserved.
import copy
import inspect
import random
from math import ceil
from numbers import Number
from typing import Sequence
import mmcv
import numpy as np
from ..builder import PIPELINES
from .compose import Compose
# Default hyperparameters for all Ops
_HPARAMS_DEFAULT = di... |
47ab0f2ac93d3a45d09b8d91d4a829ee7d40838651d81707e2a94c05b9e05743 | Python | 37,213 | 840 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""PyTorch ``torch.compile`` support for the deepmd backend.
The deepmd PyTorch backend traces selected compute functions with ``make_fx``
and lowers them through Inductor while preserving the second-order autograd
graph that force training requires. This module gathers the... |
2bfe62ad5f81253181137f943b18a718365c0f3920867265d788694ebd9c6454 | Python | 37,333 | 1,040 | """Plotting functions for linear models (broadly construed)."""
from __future__ import division
import copy
from textwrap import dedent
import warnings
import numpy as np
import pandas as pd
from scipy.spatial import distance
import matplotlib as mpl
import matplotlib.pyplot as plt
try:
import statsmodels
asse... |
8db36790cef36b7c36dba177a34c07fd9bcfc7c9f0fd55701b354f4109fd92fe | Python | 37,480 | 969 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""
Edge cache construction utilities for SeZM.
This module defines the shared procedures that assemble per-edge geometry,
radial features, rotation blocks, and normalization terms used by the SeZM
descriptor.
"""
from __future__ import (
annotations,
)
import math
fr... |
874ae59dd94f62ed54b2dca987678c3980b70bf87982772f7587f551d44dc1c7 | Python | 37,509 | 850 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from ray.rllib.env.multi_agent_env import MultiAgentEnv
from ray.tune.registry import register_env
from gym.spaces import Discrete, Box, Dict
import copy
import numpy as np
import time
from stratego_env.game.s... |
e2fd3f88ffbb71dfa33bc694be24a6b7d84d79dbf85a53d51c84f94c21464715 | Python | 37,527 | 743 | if __name__ == '__main__':
import os
import Path_Finder
from PyQt5 import QtCore, QtGui, QtWidgets, Qt
from PyQt5.QtWidgets import QMessageBox
from gui.CustomWidgests import BlobDetectionParameter
from ControlMainWindow import ControlMainWindow
import GuiFunctions as guif
from easysetti... |
559e2177b5ebf96d59ce1e3566a44907a2f963c1502f067a026318b3722d4dd8 | Python | 37,551 | 986 | # 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... |
cd521909522a795f75fede116bde04c9826eb1c1b4b49d1f8dff02e0bbc4a4d3 | Python | 37,565 | 773 | """
@file: trainer_agent_pytorch.py
Created on 31.05.22
@project: CrazyAra
@author: queensgambit
Definition of the main training loop done in pytorch.
Partially based on:
https://gitlab.com/jweil/PommerLearn/-/blob/master/pommerlearn/training/train_cnn.py
"""
import random
import os
import logging
import glob
from pa... |
cd538372ea3f9d6297f8a3af4f35750322b03bacd110b60ed6a0429fd5884118 | Python | 37,639 | 699 | #!/usr/bin/env python3
########################################################################
# ------CRISPRspec and CRISPRoff scores computation Pipeline----
#
# Copyright (c) 2018, 2021 by the contributors (see AUTHORS file)
#
# This file is part of CRISPRoff
#
# This program is free software: you can redistr... |
532f5aa78b7c60dbebc2b6a1cc52697e51d808a5cc9562aa087e8b7e09603a11 | Python | 37,652 | 1,033 | #!/usr/bin/env python
##Copyright (c) 2002, Fedor Baart & Hans de Wit (Stichting Farmaceutische Kengetallen)
##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 mu... |
43ce11de6a915ed4bd7a2c4c713d0d4b001bbc802376bec97d100061bd32e426 | Python | 37,682 | 868 | #!/usr/bin/env python
import os
import asyncio
import json
import logging
import websockets
import datetime
import threading
import ctypes
import pylsl
import struct
import sys
import functools
import time
import numpy as np
import mne
import matplotlib as plt
import random
import math
import suspect_selector
import r... |
4973019c0875f3e1f6611a45d32454e04dfebe8b7eccabb9f1c242dbc41618e3 | Python | 37,704 | 1,138 | # SPDX-License-Identifier: LGPL-3.0-or-later
import inspect
import logging
from abc import (
ABC,
abstractmethod,
)
from enum import (
Enum,
)
from typing import (
TYPE_CHECKING,
Any,
NoReturn,
)
if TYPE_CHECKING:
from typing_extensions import (
Self,
)
from deepmd.tf.utils... |
9f113698372364f2a661d17732d3b52ad2ce7ada331a1713810f94dd811ce5db | Python | 37,772 | 1,164 | # 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... |
d509da4cdacaca1c4581f44a5c71ea0573c88600367f35a9b7ca20d16afaf8a2 | Python | 37,822 | 916 | from src.visualization.useSansMaths import use_sans_maths
# use_sans_maths()
import matplotlib.pyplot as plt
import seaborn as sns
from matplotlib_venn import venn3
import glob
import os
import pickle as pkl
import numpy as np
import pandas as pd
import pdb # debugging
FIG_DPI = 300
import itertools
# Distribution ... |
039137ee2b1b3e9c50d7007a2ef39523b646856a6cdc66d2f647b730db6553bc | Python | 37,836 | 1,115 | # 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... |
08cf2840dee0cdf803c16d2c172c2c8885982008120922509340d64c617d8dab | Python | 38,028 | 930 | #!/usr/bin/env python3
#!/usr/bin/env pypy3
from pyontutils.config import auth
__doc__ = f"""Common commands for ontology processes.
Also old ontology refactors to run in the root ttl folder.
Usage:
ontutils set ontology-local-repo <path>
ontutils set scigraph-api-key <key>
ontutils devconfig [--write] [<f... |
4000bfaa6891f35eaeebad75e2e3e1026bea183b4f09da0652ecce4e3cb1d0ee | Python | 38,055 | 1,072 | """TDE classifiers.
Dictionary based TDE classifiers based on SFA transform. Contains a single IndividualTDE
and TDE.
"""
__author__ = ["MatthewMiddlehurst"]
__all__ = ["TemporalDictionaryEnsemble", "IndividualTDE", "histogram_intersection"]
import math
import time
from collections import defaultdict
import numpy a... |
bcfdd8b314bf34c527c86698a73c10287f40d4a5931b6442f9efcd0eacf1af13 | Python | 38,160 | 1,007 | #!/usr/bin/env python3 -u
# copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Implements meta estimator for estimators composed of other estimators."""
__author__ = ["mloning", "fkiraly"]
__all__ = ["_HeterogenousMetaEstimator", "_ColumnEstimator"]
from inspect import isclass
import numpy as n... |
cd522190063d7a330fe28dba0df35747c0ccb6a15f55e724e377edac4df791c8 | Python | 38,424 | 887 | #!/usr/bin/env python
import os
import asyncio
import json
import logging
import websockets
import datetime
import threading
import ctypes
import pylsl
import struct
import sys
import functools
import time
import numpy as np
import mne
import matplotlib as plt
import random
import math
import re
import janus
import si... |
d8dff9f816470dd252fa6565e87158431467d1ad56ba5d499d32e1210cbac654 | Python | 38,465 | 851 | import re
from numpy.random import shuffle
from copy import deepcopy
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem.rdchem import ChiralType
VERBOSE = False
USE_STEREOCHEMISTRY = True
MAXIMUM_NUMBER_UNMAPPED_PRODUCT_ATOMS = 5
INCLUDE_ALL_UNMAPPED_REACTANT_ATOMS = True
def mols_from_smiles_list(... |
8fa503df947adf5e2419ccb7a567406661482f001e9d38f037d5dc1a82c6cea0 | Python | 38,518 | 1,222 | # 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... |
d832043d1ce5ea73e1d38608030d325038439872d8f56b213ce6d0a94df65631 | Python | 38,640 | 1,067 | """
Author: Junhong Shen (jhshen@g.ucla.edu) and Peidi Xu (peidi@di.ku.dk)
Description:
Implementation of GCO Forest, a modified version of Global Constructive Optimization (GCO)
algorithm with multiple root nodes.
References:
Georg, Manfred; Preusser, Tobias; and Hahn, Horst K., "Global Constructive Opti... |
fb79a26f2e1d6e48230e65e87e534fbec372ef256b8a95f1631f0f9ba18ba8aa | Python | 38,689 | 766 | import pandas as pd
import json
import os
import logging
from dendrogram_tools import dend_json_2_nodes_n_edges
from template_generation_utils import get_synonyms_from_taxonomy, read_taxonomy_config, \
get_subtrees, generate_dendrogram_tree, read_taxonomy_details_yaml, read_csv_to_dict,\
read_csv, read_gene_da... |
5b21c7a5558521e6c6edce0664b487c156ae70daf4823ce33dbbb11a7f38a55e | Python | 38,720 | 1,171 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""The entry points for DeePMD-kit.
If only printing the help message, this module does not call
the main DeePMD-kit module to avoid the slow import of TensorFlow.
"""
import argparse
import logging
import os
import textwrap
import warnings
from collections import (
de... |
6a502b61bcfb844d86e322e479eb738e69c488ad3f3651f008459e82c386e5a3 | Python | 38,720 | 881 | from __future__ import annotations
from functools import lru_cache
import json
import math
from typing import Any
from typing import cast
from typing import TYPE_CHECKING
from typing import TypeVar
import numpy as np
from optuna import _deprecated
from optuna._convert_positional_args import convert_positional_args
f... |
6b76dfdb09ad0d71b3bf51d02703fa2f8289406f4b67caff539e9a7f40ea1db1 | Python | 38,764 | 993 | # 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 abc
import glob
import logging
import os
import shelve
import shutil
imp... |
55205f32c1b15af5efe57c0949959f687bb7c88cb766d7ab860ac58e5d17f4a3 | Python | 38,784 | 1,055 | # !/usr/bin/env python3 -u
# copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Implements functionality for specifying forecast horizons in sktime."""
__author__ = ["mloning", "fkiraly", "eenticott-shell", "khrapovs"]
__all__ = ["ForecastingHorizon"]
from functools import lru_cache
import nump... |
e3039823d67d86f85e6015d7262d3712c8a66468dda837462b3c051275108671 | Python | 38,790 | 1,006 | import pytest
import flair
from flair.data import Sentence, Token, Relation
from flair.splitter import (
NewlineSentenceSplitter,
NoSentenceSplitter,
SciSpacySentenceSplitter,
SegtokSentenceSplitter,
SpacySentenceSplitter,
TagSentenceSplitter,
)
from flair.tokenization import (
JapaneseToke... |
d2cb4e5c2fa004567051db73f0244e0a5890a154a64412a325032c1a963c618c | Python | 38,804 | 807 | import logging
import numpy as np
import ase
logger = logging.getLogger('DockOnSurf')
def select_confs(conf_list: list, magns: list, num_sel: int):
"""Takes a list ase.Atoms and selects the most different magnitude-wise.
Given a list of ase.Atoms objects and a list of magnitudes, it selects a
number of ... |
5b7119dfef68c69b047c877af96a0027a4a7f2624897562afb9b5ae40b3323d5 | Python | 38,854 | 1,023 | # -*- coding: utf-8 -*-
# Written (W) 2008-2012 Christian Widmer
# Written (W) 2008-2010 Cheng Soon Ong
# Written (W) 2012-2014 Daniel Blanchard, dblanchard@ets.org
# Copyright (C) 2008-2012 Max-Planck-Society, 2012-2014 ETS
# This file is part of GridMap.
# GridMap is free software: you can redistribute it and/or m... |
deaece93e9682e08a027d922664d354044dbb6723880ccbc84e8ab152b9cf986 | Python | 38,868 | 831 | """
Networks store neuron and synapse types, and the pattern of connections between them. While not capable of being
simulated directly, they are used as a template for compilation.
"""
"""
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
IMPORTS
... |
639ab586911ecdc39f014ec92d94045c705a79a58c61a965769b7005ddd10f3b | Python | 38,898 | 1,075 | from timeit import default_timer as timer
import tifffile
import warnings
import sys
import numpy as np
from math import ceil
import cv2
import os
from seas.rois import get_masked_region, insert_masked_region
from seas.colormaps import DEFAULT_COLORMAP, save_colorbar
from typing import Tuple, List
def load(pathlist... |
8ea6cb12d05ccc6ab10d31d6e111eeeaecd7eb4a10dedad41b75b22b3d6d6533 | Python | 39,101 | 1,141 | """
Change detection module. Contains base classes for change
detection task.
"""
import time
import datetime
import numpy as np
import os
import sys
import ConfigParser
import io
import random
import itertools
import json
import pickle
import zipfile
import string
from collections import OrderedDict
from psycho... |
d9bee3298cc52704387fc93e8a30fde050f4a52daf85d7a23d03ae302ec030bc | Python | 39,104 | 1,019 | """
[Legacy] - This is a very old version of the simulation routine in
simulation_utilities.py.
"""
import numpy as np
import matplotlib.pyplot as plt
from extended_ring_model import *
from test_utilities import angular_difference, circ_scatter
import sys
#from scipy.stats import vonmises
import copy
class Agent():
... |
d920d0cf71f4783ea136b86d16bb0ac41da3f0a291481b042374d6bee40c8685 | Python | 39,140 | 892 | '''
This script (generate_reaction_templates) uses a MongoDB collection
with atom-mapped reaction SMILES strings and parses them into a new
collection containing the transforms.
This is intended to be used with the Reaxys database. In the database,
reagents can contribute atoms to the products. This means that those... |
4d8e38ea33cde34fa77b052b975f5752bd8b92c34125493669bb39c477d420d2 | Python | 39,180 | 833 |
"""
Module with data preparation classes and functions
"""
from __future__ import annotations
import numpy as np
import tensorflow as tf
import model
import h5py
from typing import Union, List, Any, Optional, Tuple
from scipy import signal as sig
from scipy.stats import entropy
from sklearn.neighbors import KDTree
fr... |
77dbca1e8276d3acf06378f198adbb04b50e0ce8da55d0f837447d8d040bc8f3 | Python | 39,217 | 1,216 | """
Tools for generating auditory stimuli.
"""
from __future__ import division
import numpy as np
import scipy
import scipy.io.wavfile
import resampy
def create(type, **kwds):
""" Create a Sound instance using a key returned by Sound.key().
"""
cls = globals()[type]
return cls(**kwds)
class Sound(ob... |
94403f9898d517f19bd7713172e790b6c12dd9801d0a0e2f97430cab84536f1b | Python | 39,361 | 1,275 | # 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... |
5033c2b0f3a3aa7852b59103a0feefce434382353340ae959634605409b03422 | Python | 39,371 | 946 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Jun 11 14:12:04 2021
Multi-unit clustering model
@author: robert.mok
"""
import numpy as np
import torch
import torch.nn as nn
import torch.optim as optim
import warnings
from scipy.stats import norm
class MultiUnitCluster(nn.Module):
def __ini... |
4be8d2d376a49a3c2d3e187473c97180c85478b0a2b7d82593b0dd1c51be2f4a | Python | 39,421 | 832 | import itertools
import logging
import typing
from abc import ABC, abstractmethod
from collections.abc import Iterator, Sequence
from pathlib import Path
from typing import (
Any,
NamedTuple,
Optional,
Union,
cast,
)
import torch
from torch.utils.data.dataset import Dataset
import flair
from flair... |
87de2d5d971b1960fea3ac7cc95b3ba859c7318850ce83927b74fe0adcdfeefb | Python | 39,529 | 1,111 | # 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... |
10b34181cd0615407471b7100a0d7e18054765e52d9a5d410f318ca4a7d849b7 | Python | 39,781 | 1,056 | # SPDX-License-Identifier: LGPL-3.0-or-later
import collections
import logging
import warnings
from collections.abc import (
Callable,
)
from functools import (
cached_property,
)
from types import (
SimpleNamespace,
)
from typing import (
Any,
)
import numpy as np
import deepmd.utils.random as dp_ran... |
194e4cc1883fc4f9804c9515249cc33d1eb1b7088f67e5f7bdc496c9d9b8db58 | Python | 39,842 | 970 | """Tests for the input-validation helpers added to bcblib.tools.best_overlap.
These tests cover:
- _write_diagnostic
- _check_image_space (shape / affine / orientation, error vs warn modes)
- compute_cluster_features (shape guard, empty-overlap path)
- compute_rope_classification (all three categories, edge cases)
- g... |
a2f62610dcac88ae570a588133b491ddaecce774e433bdcb72432ee1acdbcb1e | Python | 39,958 | 1,091 | # copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Tests for ForecastingHorizon object."""
__author__ = ["mloning", "khrapovs"]
from datetime import timedelta
import numpy as np
import pandas as pd
import pytest
from numpy.testing._private.utils import assert_array_equal
from pytest import ra... |
ccb3aa07e8b166c1a1462d82965f4a703d7a48bf7787bb908f603cc6786f85fd | Python | 39,987 | 943 | '''
This script (generate_reaction_templates) uses a MongoDB collection
with atom-mapped reaction SMILES strings and parses them into a new
collection containing the transforms.
This is intended to be used with the Reaxys database. In the database,
reagents can contribute atoms to the products. This means that those
a... |
9a343475596064223cf3faca7a75e35aa5a3189f8ce1dc8dcea77b50869d8089 | Python | 40,128 | 73 | from regionscode.regions_per_sections_p56 import regs_per_section, Regions_n_colors_List
def create_regs_n_colors_per_sec_list(atlasnum):
regs_per_sec_List = regs_per_section[int(atlasnum)] #list
regs_n_colors_per_sec_List = [('root', 'not detected', '000000', (0, 0, 0))]
for elem in Regions_n_colors_List... |
c20062fcd713cd355905ab5d4564271338ae5f48721891f15f1103f588c5a92f | Python | 40,130 | 1,293 | # roifile.py
# Copyright (c) 2020-2022, Christoph Gohlke
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this li... |
b34aea040881804b646208ae34df7ab6ceedce84e627e528dde9020e69f170c5 | Python | 40,572 | 1,046 | """
Make networks with all of the components, and make sure they all compile and perform the same.
"""
import numpy as np
import matplotlib.pyplot as plt
import torch
import sns_toolbox
from sns_toolbox.networks import Network
from sns_toolbox.neurons import NonSpikingNeuron, SpikingNeuron, NonSpikingNeuronWithPersis... |
e6985a1a7bcc262019856dd27e30ae443f315d5e08ee62c2b4d95ebee727134f | Python | 40,582 | 1,038 | import re
import sys
from decimal import Decimal
from datetime import datetime
from rdflib import RDF, RDFS, OWL, XSD, BNode, URIRef, Literal
from rdflib.graph import QuotedGraph
from rdflib.namespace import SKOS, DC, Namespace
from rdflib.plugins.serializers.turtle import TurtleSerializer
from ttlser.utils import subc... |
db8f66c29e54ef05a60eb093f27c6d39f94dabae58da7a1242876e9a8d58f66d | Python | 40,653 | 939 | import re
from collections import defaultdict, Counter
from ttlser import natsort
from pyontutils.core import LabelsBase, Collector, Source, resSource, ParcOnt
from pyontutils.core import makePrefixes
from pyontutils.config import auth
from pyontutils.namespaces import nsExact
from pyontutils.namespaces import NIFRID, ... |
6cdd7deac13ca3dc3b2e23b51115c9d7416011a670a92d17262710b87c22ed02 | Python | 40,753 | 1,171 | import random
import numpy as np
from copy import deepcopy
from dnnbrain.io import fileio as fio
from dnnbrain.dnn.base import dnn_mask, dnn_fe, array_statistic
from dnnbrain.dnn.base import UnivariateMapping, MultivariateMapping
from dnnbrain.brain.algo import convolve_hrf
class Stimulus:
"""
Store and hand... |
b14d8a1e462dc4d3a3246ac0a770e86de7fb71b2834928e5e6069cebfce21b6d | Python | 40,853 | 1,090 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""
Embedding layers for the SeZM descriptor.
This module defines the type embedding, geometric initial embedding, and
environment-seed embedding used to initialize SeZM node features.
"""
from __future__ import (
annotations,
)
import math
from typing import (
TY... |
6637ef01cdfdc5b5fdc40ba860bcfc1218df0245632afae639230d2d01294a7d | Python | 40,856 | 1,098 | import itertools
import tempfile
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
import pandas as pd
from scipy.spatial import distance
from scipy.cluster import hierarchy
import nose.tools as nt
import numpy.testing as npt
try:
import pandas.testing as pdt
except ImportError:
impo... |
1c00a56fab530a949ec4641d41868f62d0058e24c7a6519e20548f1c6ebeefb6 | Python | 40,904 | 941 | '''
This script (generate_reaction_templates) uses a MongoDB collection
with atom-mapped reaction SMILES strings and parses them into a new
collection containing the transforms.
This is intended to be used with the Reaxys database. In the database,
reagents can contribute atoms to the products. This means that t... |
b73f253858f4e72f4d2b174b8731495742f3288598db76ce18bfd87639b7e07f | Python | 41,072 | 1,162 | import copy
import shutil
import pytest
import flair
import flair.datasets
from flair.data import MultiCorpus, Sentence
from flair.datasets import ColumnCorpus
from flair.datasets.sequence_labeling import (
ONTONOTES,
JsonlCorpus,
JsonlDataset,
MultiFileJsonlCorpus,
)
from flair.tokenization import St... |
0e7335221620222aa377e6a19ed2185c51bf6055dc88f042e0e1c0e31646829f | Python | 41,135 | 700 | import os
import pickle
import numpy as np
import math
from typing import Tuple
import torch
from torch import nn, Tensor
import torch.nn.functional as F
from torch.nn.modules import LayerNorm
from torch.nn import TransformerEncoder, TransformerEncoderLayer, Transformer, TransformerDecoder, TransformerDecoderLayer
fro... |
4b07d050e1cdbefd71912e78ad4c0a6329a5bcb81f08452407a4b6bd0bbd1b0d | Python | 41,159 | 944 | # -*- coding: utf-8 -*-
"""Fitness surrogate model classes and handler for incremental evaluations.
"""
from __future__ import absolute_import, division, print_function #, unicode_literals, with_statement
del absolute_import, division, print_function #, unicode_literals, with_statement
___author__ = "Nikolaus Hansen"... |
4513c5b2fe70ddcbee60acb19ff516c7c49f8f5edf9c246df1fdedd7777af1e1 | Python | 41,260 | 786 | """ Implementation of all available options """
from __future__ import print_function
import configargparse
from onmt.models.sru import CheckSRU
def config_opts(parser):
parser.add('-config', '--config', required=False,
is_config_file_arg=True, help='config file path')
parser.add('-save_config... |
9c932a14a4f92d791c95f4b3b7ae88cf2b8d5414a68f643d2f32acfce740bed4 | Python | 41,351 | 953 | import logging
import tempfile
from pathlib import Path
from typing import Any, Optional, Union, cast
import torch
import torch.nn
import torch.nn.functional as F
from torch.nn.utils.rnn import pack_padded_sequence, pad_packed_sequence
from tqdm import tqdm
import flair.nn
from flair.data import Dictionary, Label, Se... |
dd3e7adbb9de6ca996f2c183973eae28c3d7f378ba1f708d2589213762245d59 | Python | 41,444 | 1,152 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
from typing import TYPE_CHECKING
import numpy as np
import pytest
from onnx import (
FunctionProto,
GraphProto,
ModelProto,
NodeProto,
SparseTensorProto,
TensorProto,
ValueI... |
2570d3e06ff6f934ff7388b7a746b6c73358935b16406723fd9b8c82a5ad5e57 | Python | 41,692 | 1,062 | """ Compute the cross-correlation between two spike trains For all of the spikes
in st1, compute the time difference with each spike in st2, find where the
difference is within a time window we are interested in, then get and return the
indices for all of those spikes.
We define 3 data structures first: RevCorrPars ar... |
231e4c2acee3d6a202286885dfb7e409782638da06de0c215db0950c23919435 | Python | 41,737 | 984 | import logging
import typing
from abc import ABC
from collections import OrderedDict
from pathlib import Path
from typing import Any, Optional, Union
import numpy as np
import torch
from sklearn.metrics.pairwise import cosine_similarity
from sklearn.preprocessing import minmax_scale
from tqdm import tqdm
import flair... |
b95620630a4fa341896671ce28480cbfd4c072cca5029cbcd262579827009ea4 | Python | 41,739 | 1,057 | # SPDX-License-Identifier: LGPL-3.0-or-later
from collections.abc import (
Callable,
)
from typing import (
Any,
)
import array_api_compat
import numpy as np
from deepmd.dpmodel.array_api import (
Array,
)
from deepmd.dpmodel.utils.neighbor_graph import (
ALL_PAIRS,
)
from deepmd.dpmodel.utils.nlist i... |
741cf82f8c5b1390d0040de26654b07dcab5d064c89d732d9085c7293d1a11ab | Python | 41,751 | 1,074 | #!/usr/bin/env python3
# SPDX-License-Identifier: LGPL-3.0-or-later
from __future__ import (
annotations,
)
import logging
import re
import shutil
import traceback
from contextlib import (
nullcontext,
)
from dataclasses import (
dataclass,
replace,
)
from pathlib import (
Path,
)
from typing impo... |
31bb3b07d290e6b3c27505c041eebe871768ec7109711d919bb79760fd841526 | Python | 41,760 | 860 | import numpy as np
import pandas as pd
import argparse
import os
import re
import random
import multiprocessing
from rdkit import Chem
from tqdm import tqdm
from rdkit import RDLogger
RDLogger.DisableLog('rdApp.*')
# Get the mapping numbers in a SMARTS.
def get_idx(smarts_item):
item = re.findall('(?<=:)\d+', ... |
b8937722265dcc327a3c6c7d4d4860486549ebe85d8958229c01c445b4f2caa6 | Python | 41,815 | 727 | """
Main script for training, evaluation, and running inference on object detection models.
"""
import os
import numpy as np
import cv2
import math
import json
import argparse
import traceback
from tqdm import tqdm
import torch
from torch.utils.data import ConcatDataset, DataLoader
from torch.optim import SGD, Adam
... |
6042163ecf36c336f75f8a5ba6ad2f1800792ef95d18fc37a0f7bc08680872f0 | Python | 41,953 | 1,282 | # 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... |
5829b38bae2c8d637ff455e53c369e12eeaf6caabcd3f7b62cf2746cfb3126b8 | Python | 42,074 | 1,022 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""Primitives of the long-range modules: pair topology, kernels and constraint."""
import itertools
import pathlib
import numpy as np
import pytest
from scipy.integrate import (
trapezoid,
)
from scipy.special import (
erf,
)
from deepmd.dpmodel.fitting.latent_cha... |
6b68aac3fc0a269a4ca448e3c8f9f3f0ffc556d7e5397396b6fb65ba79170c4f | Python | 42,387 | 879 | from rdflib import Literal
from pyontutils.core import OntId, OntTerm
from pyontutils.core import simpleOnt
from pyontutils.namespaces import OntCuries, partOf
from pyontutils.namespaces import NIFRID, ilxtr, ilx, BFO
from pyontutils.namespaces import definition, hasPart
from pyontutils.combinators import unionOf, inte... |
9e40da6e96a48eac200e3a0a1df9cb665a107e87549bd9bbd8098b7af2365c65 | Python | 42,439 | 1,144 | from __future__ import annotations
from typing import Iterable, Generator
from warnings import warn
import pandas as pd
import numpy as np
import os
import warnings
from joblib import Parallel, delayed
import gc
from scipy.sparse import csr_matrix, find, issparse, hstack
from scipy.sparse.linalg import eigs
from nump... |
4e6089e951197e42fff40652ffefc337ea825e565a6e004009d97f3f43300f71 | Python | 42,543 | 1,053 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""dpmodel ZBL bridging as COMPOSITION (review 3638077323, redesigned).
``bridging_method: ZBL`` builds a
``LinearEnergyModel(LinearEnergyAtomicModel([dp, InnerPotentialAtomicModel],
weights="sum"))`` -- the analytical term is its own atomic model summed
with the learned on... |
107479fbdd0e4eecae65874fbf0a8bbe197c4ada62bf655a1d0bd9ffbe264e84 | Python | 42,565 | 1,017 | #!/usr/bin/env python3
import tempfile
from pyontutils.config import auth
__doc__ = f"""Use SciGraph to load an ontology from a loacal git repository.
Remote imports are replaced with local imports.
NIF -> http://ontology.neuinfo.org/NIF
Usage:
ontload graph [options] <repo> <remote_base>
ontload config [optio... |
0dd79e67126ac240764d6c39ebf65bedb3d31f70ea6a98c1925ad1251334e907 | Python | 42,806 | 1,023 | #!/usr/bin/env python3
import tempfile
from pyontutils.config import auth
__doc__ = f"""Use SciGraph to load an ontology from a loacal git repository.
Remote imports are replaced with local imports.
NIF -> http://ontology.neuinfo.org/NIF
Usage:
ontload graph [options] <repo> <remote_base>
ontload config [optio... |
a27db1e59d73b76ca8e79237bf617e4e2e2ca1d09ad1b5e622af66042b578779 | Python | 43,102 | 1,113 | # SPDX-License-Identifier: LGPL-3.0-or-later
import functools
from collections.abc import (
Callable,
)
from copy import (
deepcopy,
)
from typing import (
Any,
)
import array_api_compat
from deepmd.dpmodel.array_api import (
Array,
xp_asarray_nodetach,
)
from deepmd.dpmodel.atomic_model.dp_atomic... |
fafb4ef10bbc2c28637b5e28e32a0d545b843e57df0daf62d11f5c4ae869872c | Python | 43,171 | 1,156 | """Machine type checkers for Series scitype.
Exports checkers for Series scitype:
check_dict: dict indexed by pairs of str
1st element = mtype - str
2nd element = scitype - str
elements are checker/validation functions for mtype
Function signature of all elements
check_dict[(mtype, scitype)]
Parameters
--------... |
3058ed5ce88fa7c57ff659c4ba6bd783e5ff751bf81fe3d9d430604eac4902b5 | Python | 43,230 | 902 | # -*- coding: utf-8 -*-
"""
Created on Fri Sep 1 16:36:50 2017
@author: daniel
"""
from neuron import h
import experiment as e
import parameters as p
import time
import random as rnd
import numpy as np
import sys
import matplotlib.pyplot as plt
import seaborn as sns
class Spillover_Experiment(e.Experiment):
... |
1e43fb83d06b47e3858459f76453dd0196949e45a1529687a6880185cdfb951f | Python | 43,237 | 927 | from __future__ import print_function
import os
import subprocess
import vtk, qt, slicer
from ElastixLib.utils import *
from ElastixLib.manager import PresetManagerLogic
from ElastixLib import web_launcher
from slicer.ScriptedLoadableModule import *
from slicer.util import VTKObservationMixin
import logging
#
# Elas... |
056887706b49beb99a2baf5eb1320543b7f7eb07fdbfec9efea2b0c231634172 | Python | 43,272 | 1,415 | # -*- coding: utf-8 -*-
"""
Module: anlffr.spectral
A collection of spectral analysis functions for FFR or other kinds of M/EEG
data.
Includes functions to estimate frequency content / phase locking of
single-channel or individual data channels, as well as functions that produce
estimates by combining across channels... |
839c788754b1c7d5191b8e3d2f0d0b69b16e722e885e5ad9a7c5ce13b9ec359b | Python | 43,445 | 1,139 | # Copyright 2026 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... |
dfdab5061bea31046360eb0d1bcf6330970ddbda7ada8e2287b501a5f5c37e4e | Python | 43,619 | 899 | # -*- coding: utf-8 -*-
"""
Created on Fri Aug 26 13:07:55 2016
@author: wanglab
"""
import os, sys, cv2, shutil
import numpy as np, pandas as pd, SimpleITK as sitk
import pickle
import subprocess as sp
from collections import Counter
import tifffile
from tools.imageprocessing.preprocessing import resample_par, color... |
fbf3f4f837fecd1dafc175c78237f067edad627eea6352c7631ffca4da95d393 | Python | 43,634 | 1,195 | # -*- coding: utf-8 -*-
'''
py-iCSD toolbox!
Translation of the core functionality of the CSDplotter MATLAB package
to python.
The methods were originally developed by Klas H. Pettersen, as described in:
Klas H. Pettersen, Anna Devor, Istvan Ulbert, Anders M. Dale, Gaute T. Einevoll,
Current-source density estimation ... |
33f572fb92b89b8eab2a1e2addcea35f8c02341275c70dc8ffafa5cbd7f21ca3 | Python | 43,663 | 1,081 | # SPDX-License-Identifier: LGPL-3.0-or-later
from collections.abc import (
Callable,
)
from typing import (
TYPE_CHECKING,
Any,
)
if TYPE_CHECKING:
from deepmd.dpmodel.utils.neighbor_graph import (
NeighborGraph,
)
import array_api_compat
from deepmd.dpmodel.array_api import (
Array,
... |
141dda6a0656a890beaba388afb638fd0b496ac5b2e88c35bdd5acec6235700c | Python | 43,801 | 1,179 | # SPDX-License-Identifier: LGPL-3.0-or-later
import copy
import dataclasses
from typing import (
Any,
)
import torch
from torch.fx.experimental.proxy_tensor import (
make_fx,
)
from deepmd.dpmodel.atomic_model import (
DPEnergyAtomicModel,
)
from deepmd.dpmodel.model.dp_model import (
DPModelCommon,
)... |
70b875c0b0fb35374f22d3904da3a696ab70e9a67873561d3f2d6064a93038d6 | Python | 43,835 | 1,121 | # Copyright [2020] Luis Alberto Pineda Cortés, Gibrán Fuentes Pineda,
# Rafael Morales Gamboa.
#
# 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.... |
babb44686eae89dcb8523b9d9b30abf29314bbaa0fb4653d31878935a4dc5267 | Python | 43,854 | 797 | from tqdm import tqdm
import re
import numpy as np
import torch
from torch.utils.data import Dataset, DataLoader
import random
import pickle
import pandas as pd
import os
from Bio import SeqIO
from sp_data.bert_tuning import ProtBertClassifier, parse_arguments_and_retrieve_logger
from sp_data.sp6_data.read_extract_sp6_... |
cff97fc7acac72315c8e1231595812b56116292110bb83178fcb9a6f92d401a0 | Python | 43,862 | 899 | """
Networks store neuron and synapse types, and the pattern of connections between them. While not capable of being
simulated directly, they are used as a template for compilation.
"""
"""
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
IMPORTS
... |
de5114de74ad4bb97a20bfcd5babaac7c32fe55df8433487cd06d38c35fa0f84 | Python | 43,874 | 1,151 | #!/usr/bin/env python3
"""Render a tree from a predicate root pair.
Normally run as a web service.
Usage:
ontree server [options]
ontree [options] <predicate-curie> <root-curie>
ontree --test
Options:
-a --api=API Full url to SciGraph api endpoint
--data-api=DAPI Full url to Sci... |
d37e858dc9351fac064ae6c9a268c41d437523e5cc3d23eac77ffbf0c1186c6f | Python | 44,108 | 1,232 | # 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... |
8ff58d87dc1b438e84c3ae572d785fb21c00eb9e45e3302945f14fd9629b4081 | Python | 44,186 | 899 | """step-size adaptation classes, currently tightly linked to CMA,
because `hsig` is computed in the base class
"""
from __future__ import absolute_import, division, print_function #, unicode_literals, with_statement
import warnings as _warnings
import numpy as np
from numpy import square as _square, sqrt as _sqrt
from... |
1008231a49d30f5e9b2b99a53e512d99a2c3a24f4e8afc9e0e7b16dafdd7780c | Python | 44,225 | 1,234 | # 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... |
e5b9329f6640f71ba29f5afff47093273297814e77c890385f59eaa7df22c825 | Python | 44,250 | 1,164 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""DPA4 / SeZM → AOTInductor ``.pt2`` freeze path for the pt backend.
SeZM relies on a nested ``autograd.grad(create_graph=True)`` inside
``fit_output_to_model_output``; TorchScript cannot represent that
graph, so DPA4 / SeZM checkpoints are routed through AOTInductor inste... |
3650f45448f61b0d192f11e6b628f74883ed8bdb4942a42deca801af892c8a6b | Python | 44,338 | 1,160 | """
This program provides a graphical interface to help access model results for
the SBEM reconstruction project. The display appears as 3 panels: One on the
left with controls, one on the top right that is tabbed, showing either the
current table, or the traces, and one on the bottom for text output.
The left panel p... |
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