sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
10c2de744ce76578eea299bf2ca10808dd43c1c01529144d4d64fc7e0c48fe2c | Python | 6,648 | 129 | """Project the motif tables into the two files ``vdjdb-web`` parses.
⚠ Both files are parsed positionally. ``app/backend/server/motifs/Motifs.scala`` hands Tablesaw a
fixed ``Array[ColumnType]`` with no header check -- 27 entries for ``motif_pwms.txt``, 19 for
``cluster_members.txt``. An inserted, removed or reordered... |
1e907699f0b5362cbbd6ee71d4dc4cdaa308f1da1b6abd8f3ce9b2c8965150fb | Python | 6,648 | 221 | import os
import sys
from pathlib import Path
import sanpy
from sanpy.interface.sanpy_window import SanPyWindow
from sanpy.sanpyLogger import get_logger
logger = get_logger(__name__)
TEST_DATA_DIR = Path(__file__).resolve().parents[1] / "data"
# @pytest.fixture
# def sanpyAppObject(qtbot):
# return SanPyWindow()... |
e543432944eb8de5168bf0dcf10e44d213265cc9c2521ab013d9388cdf5c4394 | Python | 6,649 | 198 | from PymoNNto.NetworkCore.Base_Attachable_Modules import *
import copy
class SynapseGroup(NetworkObjectBase):
def __init__(self, net, src, dst, tag=None, behavior={}):
if type(src) is str:
s=src
src = net[src, 0]
if src is None:
print(s, 'src not found... |
8c9c8ecdf87731af222a19ad17d15ff144982eb8b9e8b4f8aaac41da266d189f | Python | 6,654 | 177 | from warnings import warn
from functools import partial
from tqdm import tqdm
import torch
import numpy as np
from torch.optim import Adam
from torch.nn import MSELoss
from odl.contrib.torch import OperatorModule
from dival.reconstructors import IterativeReconstructor
from dival.reconstructors.networks.unet import U... |
f407a98f00ff5244eda324a46a281aeb85b0a1ae74d1153a66ae503763f2008d | Python | 6,654 | 209 | import numpy as np
import matplotlib.pyplot as plt
import torch
import torch.nn as nn
from torch.optim.lr_scheduler import StepLR,MultiStepLR
import math
import torch.nn.functional as F
from torch.utils import data
from sklearn.model_selection import train_test_split
from torch.utils.data import Dataset
from preproces... |
9058c5a71353b7f471c38cdf17a0264679552e9ffbe55f272577593fbc1fdb82 | Python | 6,655 | 193 | import torch
import torch.utils.data
import torchvision
import CustomDataset
import pdb
from typing import Iterator, List, Optional, Union
from collections import Counter
import logging
from operator import itemgetter
import random
import numpy as np
from torch.utils.data import DistributedSampler
from torch.utils.dat... |
8ab29c3ce99d394190c41ac499a7dd6afa4c0effe81211e1095c42472d888d8e | Python | 6,667 | 187 | """
A data logger for logging experiment events.
Author: Tal Eisenberg, 2021
"""
import multiprocessing as mp
import functools
import threading
import mqtt
import time
import json
import managed_state
from data_log import DataLogger
from json_convert import json_convert
class EventDataLogger(DataLogger):
"""
... |
4bee6488a619d6d18111aa0e81cda0735213c83a98e43513015280c9fa1caf94 | Python | 6,669 | 167 | """Reshape deposited ITRAP counts into the committed caller. No cutoff grid."""
from __future__ import annotations
import gzip
import importlib.util
from pathlib import Path
import polars as pl
import pytest
_SCRIPT = Path(__file__).resolve().parents[1] / "processing" / "itrap_reprocess.py"
_spec = importlib.util.s... |
c8ba77658b80e360c19fadfe6ff4e87f26c5c1b628ae18b30a2782cf158e9144 | Python | 6,669 | 188 | """
A data logger for logging experiment events.
Author: Tal Eisenberg, 2021
"""
import multiprocessing as mp
import functools
import threading
import mqtt
import time
import json
import managed_state
from data_log import DataLogger
from json_convert import json_convert
class EventDataLogger(DataLogger):
"""
... |
2f4808a916920dc8200828f610475ec007af0aa45989c3fce55ceff9a95d92ed | Python | 6,670 | 191 | import pickle
from pathlib import Path
import matplotlib.font_manager as fm
import matplotlib.pyplot as plt
import numpy as np
from matplotlib.offsetbox import AnchoredText
from mpl_toolkits.axes_grid1.anchored_artists import AnchoredSizeBar
from ScanImageTiffReader import ScanImageTiffReader
from skimage import expos... |
97b4374b6fc4695831d1c3a5a3d1c194dc7d7fb3ab44940937d70b41f9f2eb13 | Python | 6,672 | 169 | """The publication-year resolvers, with the network stubbed.
`summary/references.py` was 57 % covered: the offline resolvers had tests, the three that call an
API did not, so nothing checked that a PubMed, RCSB or GitHub payload is read correctly. The
dashboard stops rather than plotting an incomplete year axis, so a ... |
0bb1fdf00705d0d37e556ec4fd0983106f990a72bc671d036bcd0463dc2bc83f | Python | 6,677 | 158 | import numpy as np
from sklearn.linear_model import LinearRegression
from sklearn.metrics import mean_squared_error
sam_size = 2048
sam_size_test = 2048
X_train = - np.pi + np.multiply((np.pi + np.pi),np.random.rand(sam_size,1))
X_test = - np.pi + np.multiply((np.pi + np.pi),np.random.rand(sam_size_test,1))
y_train =... |
367c94b875de336299d5d47c048385c71c8de5e1c20ce01b2f383d155ae81d88 | Python | 6,677 | 186 | from PymoNNto.NetworkCore.Base_Tagable_Object import *
from PymoNNto.Exploration.Evolution.Interface_Functions import *
class Behavior(TaggableObjectBase):
initialize_on_init = False
initialize_last = False
attached_UI_Tabs = []
def initialize(self, neurons):
return
def iteration(self... |
1ca9aeeac57ec1fd092151ba969d720c3c2b2d115b90f2f5bf265d3f897463eb | Python | 6,679 | 175 | import argparse
from math import ceil
from typing import Optional, Sequence
import pytorch_lightning as pl
import torch
from pytorch_lightning.callbacks import LearningRateMonitor, ModelCheckpoint
from torch.utils.data import DataLoader, ConcatDataset
from data.dataset import GanBrats, GanBratsFromFolder, MrSliceDatas... |
d099412c3eb9f7c04ca6b8350a0ad6e1b0f315236a49010aac592f9b17e40ffc | Python | 6,679 | 186 | """Affine-based template matching and background-image selection."""
import warnings
from dataclasses import dataclass
import numpy as np
from nibabel.affines import voxel_sizes
from nltools.utils import ResamplingWarning, _find_stack_level
from .config import get_brainspace
from .paths import _resolve_paths
from .... |
dc418777b02ce907aab276090e9be45e54725bdeb0624775eb3ed11114979e10 | Python | 6,679 | 172 | """
Create frames showing the input data on the spatial grid for each time step.
"""
import os
import sys
import argparse
from pathlib import Path
import matplotlib.pyplot as plt
import numpy as np
from utils.io_utils import load_neo, save_plot
from utils.neo_utils import analogsignal_to_imagesequence
from utils.parse... |
e50bb7c4a9e5bee1d45dc50982b017ac02cced8e6455dd96ac62ba7029f6c81d | Python | 6,680 | 147 | """Coordinate conversions. The only module that may do this.
Four coordinate spaces meet in this codebase and three of them disagree with AIRR on two axes at
once (origin and closedness), so an ad-hoc `+1` in a call site is indistinguishable from a correct
one until a motif is plotted two residues off:
==============... |
84d450e0666da1c09f86fec5d6e1aae62e86588fb05c12607627f46fb1607646 | Python | 6,686 | 173 | """
Create frames showing the input data on the spatial grid for each time step.
"""
import os
import sys
import argparse
from pathlib import Path
import matplotlib.pyplot as plt
import numpy as np
from utils.io_utils import load_neo, save_plot
from utils.neo_utils import analogsignal_to_imagesequence
from utils.parse... |
a0beeab98f27eea46e97fa59a3dabf646f51aee5388117cb6d7f49077b27d274 | Python | 6,691 | 209 | """
Task scheduling of dynamically loaded task functions.
Author: Tal Eisenberg, 2021
The config module attribute `tasks_modules_dir` determines where tasks will be loaded from. Any
non-private function (which does not start with an underscode _) that is defined in a module inside
this directory will be added to the t... |
ea0a5e72e7961604e344cb43e9a873442893049aedf07c0d29cf34a4424cb1cd | Python | 6,693 | 126 | """
Adjacency Class
===============
Nltools has an additional data structure class for working with two-dimensional
square matrices. This can be helpful when working with similarity/distance
matrices or directed or undirected graphs. Similar to the Brain_Data class,
matrices are vectorized and can store multiple matri... |
a846bcb51a820239495cdb47b54536031624315a053945cf5a700150eb5d340a | Python | 6,695 | 186 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import logging
from pathlib import Path
from argparse import Namespace
from fairseq.data import Dictionary, encoders
from fairseq.data.audio.... |
da37ce4a00aa46cac0c33353d70a7d5718fbd11cdcbf0f11cfb3394f6e451b30 | Python | 6,696 | 234 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# QMCTorch documentation build configuration file, created by
# sphinx-quickstart on Wed Apr 22 17:16:01 2020.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# a... |
88d77aef65e303196e9509089a85a332e17185702ba5af7907da82ec1c7d85d9 | Python | 6,699 | 182 | import torch
import torch.nn as nn
import numpy as np
def get_unet_model(in_ch=1, out_ch=1, scales=5, skip=4,
channels=(32, 32, 64, 64, 128, 128), use_sigmoid=True,
use_norm=True):
assert (1 <= scales <= 6)
skip_channels = [skip] * (scales)
return UNet(in_ch=in_ch, ou... |
e17da6a84ded29b4514898575121094918f813dae59224d4fd98ed810ae9f361 | Python | 6,700 | 196 | # -*- coding: utf-8 -*-
# /usr/bin/env python3
#
# This software and supporting documentation are distributed by
# Institut Federatif de Recherche 49
# CEA/NeuroSpin, Batiment 145,
# 91191 Gif-sur-Yvette cedex
# France
#
# This software is governed by the CeCILL license version 2 under
# French law... |
9be841e76c943e748a58d73479170dfc76c7495132b65a079f893f45f1529c7c | Python | 6,701 | 162 | # Copyright 2020-2025 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""Notebook Tools module."""
import shutil
from importlib import import_module
from pathlib import Path
from shutil import copytree
from typing import Any, Dict, Tuple
from openfl.experimental.workflow.federated.plan import Plan
from openf... |
452b2d194c4de24464107330897307557567526c0dd49bab5038b7e0f6fae3c8 | Python | 6,704 | 202 | import math
import numpy as np
import torch
import torch_geometric
from torch_cluster import radius_graph
from torch_scatter import scatter
from utils import get_iso_permuted_dataset
from utils import get_scalar_density_comparisons
from e3nn.nn.models.gate_points_2101 import Network
from e3nn import o3
import wandb
imp... |
c1a7539f837aaff36e2588acc068184adbef5a14d97fd140bf711e97cc89bf51 | Python | 6,707 | 186 | """Four flags whose effect is visible in the model or in the resolved arguments.
All four are MERGE rows in the inventory: they survive the rewrite in some other
form, and a MERGE promises the same behaviour under a different name, so today's
behaviour is what the merge gets judged against.
`--use_last_readout_only` ... |
b12d1d35ae23e07f79eaf22a54e8136e681309e1218823f96e2f1c592af01fa9 | Python | 6,711 | 250 | from pylab import *
import scipy.stats as st
import torch
from torch import optim
from matplotlib import animation, rc
from tqdm import tqdm
rc('animation', html='html5')
set_printoptions(precision=4)
def run_multiple(xs, ny = 9, eta_adam = 0.02, w0 = None,
mb = 100, nt = 100000, rule = 'bcm', hyk ... |
03a24ab148cc86f62b321764e02ef201ec840e2a61342dc2ddebbf7745311fdd | Python | 6,712 | 202 | """Tests for file-table column visibility."""
import shutil
from pathlib import Path
from typing import Any
from unittest.mock import Mock
import pandas as pd
import pytest
from PyQt5 import QtWidgets
import sanpy
from sanpy.interface.bFileTable import pandasModel
from sanpy.interface.bTableView import (
DEFAULT... |
736b2c8a9cfe3ef586d91a429402e02bef1c715b9eaf361553c270e49880231c | Python | 6,712 | 185 | '''
Module focused on the implementation of the Polunomial Chaos
Expansion Layer (PCE).
'''
import torch
import torch.nn as nn
import scipy.misc
from sklearn.linear_model import LinearRegression
import numpy as np
class PCEModel(nn.Module):
'''
Class that handles the implementation of the PCE layer as given
... |
b1620793515711ff265badb95ccf8681c4b38b6fcc1b682ec7a54d651a49aec5 | Python | 6,713 | 166 | # allowable multiple choice node and edge features
allowable_features = {
'possible_atomic_num_list' : list(range(1, 119)) + ['misc'],
'possible_chirality_list' : [
'CHI_UNSPECIFIED',
'CHI_TETRAHEDRAL_CW',
'CHI_TETRAHEDRAL_CCW',
'CHI_OTHER'
],
'possible_degree_list' : [0,... |
90e9470314fb8c0b47e4fd6d8ea0e208a37bee3f531293ef424b6531b9713ffb | Python | 6,714 | 145 | from plotly import graph_objs as go
import numpy as np
import json
import pickle5 as pickle
from scipy.io import savemat
#
bn_atlas_file = '/Users/zhangyuan/Desktop/Sherlock/projects/sryali/2019_DNN/scripts/features/bnatlas_tree.json'
with open(bn_atlas_file) as f:
bn_atlas=json.load(f)
def generate_radial_pl... |
c8bb3bb05675a71ef5972ea7722af0f4e194597b89f9add17e9d7f370607a47a | Python | 6,716 | 219 | # Copyright (c) 2020 PaddlePaddle 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 appli... |
599a7765b6ef5831d4dbaa184c2697399d0dcc7f4d1fcc705c58167b90974f74 | Python | 6,718 | 213 | # Copyright (c) 2021 PaddlePaddle 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 appli... |
2db908932a6db7e883a65b8863f27224660734c354af395aedb6d6c7c60f6553 | Python | 6,725 | 225 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.autograd import Variable
import math
from functools import partial
__all__ = ['ResNeXt', 'resnet50', 'resnet101']
def conv3x3x3(in_planes, out_planes, stride=1):
# 3x3x3 convolution with padding
return nn.Conv3d(
in_planes,... |
b8b65a57eaaeaf979528409fa9f4d74889b20c61210e9cd5a4369ad8a0a6f60d | Python | 6,726 | 172 | """Tests for nltools.algorithms.inference.intersubject — ISC, ISFC, ISPS."""
import numpy as np
import polars as pl
from numpy import sin, pi, arange
import pytest
from nltools.algorithms.inference.intersubject import isc, isc_group, isfc, isps
class TestISC:
"""Test intersubject correlation calculation."""
... |
4f8c186f392e879c4ca66262c3a882ab08cd99862d0f83652ff27720ad25fac1 | Python | 6,727 | 157 | import os
import glob
import json
import torch
import pickle
import numpy as np
import os.path as osp
from torch_geometric.data import Data, InMemoryDataset
import traceback
def undirected_graph(data):
"""
A pre_transform function that transfers the directed graph into undirected graph.
Args:
data ... |
95418a50f4482477392114d7658b268b62ef3d09186eb4b4bff14c947e2fd510 | Python | 6,727 | 188 | import torch
import torchvision
import numpy as np
import skimage
import six
import copy
class Augmentor():
def __init__(self, augmentations=[]):
transform = []
for a_spec in augmentations:
t = a_spec['type']
del a_spec['type']
if t == "warp":
... |
7577d78cc8a5762eb2ea38693196a4859e2ce1d90ff36fd84b7f6f1859978c8d | Python | 6,730 | 166 | from copy import deepcopy
import logging
import torch
import torch.nn as nn
import torch.nn.functional as F
import pdb
logger = logging.getLogger(__name__)
class ModelEMA(nn.Module):
def __init__(self, model, decay=0.9999, device=None):
super().__init__()
self.module = deepcopy(model)
se... |
49ef8d77ad7df45e0c8c18c72e64b71dd47c3bddd115feafaad083609ebd4899 | Python | 6,738 | 194 | from __future__ import division
import warnings
from pycircstat import CI
from pycircstat.iterators import index_bootstrap
import numpy as np
from scipy import stats
import pandas as pd
class BaseRegressor(object):
"""
Basic regressor object. Mother class to all other regressors.
Regressors support indexi... |
9679626120f458af64fbd66cdc9cafe44d1cde553c4fa31f5834b28b5c2c643c | Python | 6,750 | 171 | # SPDX-License-Identifier: BSD-3-Clause
# Copyright (c) 2020-2026, Christian Gaser. See LICENSE.
"""
The permuted GLM.
The point of this module is one piece of algebra. A permutation test refits the
same model thousands of times, and the obvious way to do it -- build the permuted
dataset, then regress -- costs an ``n_... |
a1f6e42bd0147554f368f25bf375e242093f065be9a7fad4a78506f52f332262 | Python | 6,750 | 178 | import logging
from typing import Dict, Optional, Tuple
import pytest
from chromadb.api import AdminAPI
import chromadb.api.types as types
from chromadb.config import DEFAULT_TENANT
from chromadb.test.conftest import (
ClientFactories,
DEFAULT_MCMR_DATABASE,
MULTI_REGION_TOPOLOGY,
multi_region_test,
)
... |
4b40fb093b26e184caf1b4e7bcabf1a3b1cb038547507566edbb663bffe1bd28 | Python | 6,752 | 153 | """Two adapters that let a non-energy model reach the golden harness.
The harness accepts three shapes (``harness._evaluate``), and for an energy
model the middle one -- "an ase calculator" -- is the whole story: hand it the
calculator and it drives ``get_potential_energy`` / ``get_forces`` / (for a
periodic structure... |
40aa46522da78e14eb161bd74f64c15bc904b56deabf7338d1429bfa6e263373 | Python | 6,757 | 190 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import logging
from collections import defaultdict
from dataclasses import dataclass, field
from typing import Dict, Any, List, Optional
impo... |
d9d61cee9c7c5d3e2a22e755c0eb30401538b4505892805c5cd369b8751f3be5 | Python | 6,760 | 222 | from dataclasses import dataclass
from typing import List, Dict, Optional
import pytest
from rdkit import Chem
from rdkit.Chem import Descriptors
import numpy as np
from reinvent.scoring.compute_scores import compute_component_scores, compute_transform
from reinvent.runmodes.samplers.sampler import validate_smiles
fr... |
3e2e07e2d1a6ecbfd922ce0ee8c0903aaa788bb92307362e876c7543181fd0da | Python | 6,761 | 216 | from PymoNNto.Exploration.Network_UI.TabBase import *
from PymoNNto.Exploration.Visualization.Visualization_Helper import *
import os
from io import StringIO
from contextlib import redirect_stdout
from PymoNNto.Exploration.Network_UI.Basic_Tabs.Helper.syntax import *
class code_execution_tab(TabBase):
sample_cod... |
93a5c1273b240edb00fa094582a48ba03dfb924a05846ba36c623174e600b02b | Python | 6,762 | 227 | # execute using the same docker to have everything in the same torch version
# and pyg version
# bslins
# baseline random forest
# docker run -dt --gpus all -v /home/uveleiro/data/uveleiro/ALL_GENNIUS:/wdir/ --name bslins genniusdoc
import numpy as np
import torch
import torch_geometric.transforms as T
import seabor... |
47d3ee77c6346915bf1e37a8b973b956e43a37df13b580901345d874229b3647 | Python | 6,763 | 152 | """
Implementation of the BFGS 2nd-order optimizer.
"""
import jax
import numpy as np
from jax import numpy as jnp
from jax.flatten_util import ravel_pytree
from deeperwin.configuration import BFGSOptimizerConfig, OptimizationConfig
from deeperwin.mcmc import MCMCState, MetropolisHastingsMonteCarlo
from deeperwin.uti... |
0f3aa4ce68946611e3b1a40604e3f80af3d259abc9fb52026ea4deb895cf7602 | Python | 6,765 | 198 | import numpy as np
# allowable multiple choice node and edge features
allowable_features = {
'possible_atomic_num_list' : list(range(1, 119)) + ['misc'],
'possible_chirality_list' : [
'CHI_UNSPECIFIED',
'CHI_TETRAHEDRAL_CW',
'CHI_TETRAHEDRAL_CCW',
'CHI_OTHER'
],
'possibl... |
505473ab24a33ad3ae914484672a5eee594db7d5d4ff0677e2d90cfcda801163 | Python | 6,766 | 180 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Dec 12 15:25:17 2018
@author: ngritti
"""
# from csbdeep.models import CARE
# from deeprest.rawDataClass import rawData
# from deeprest.modelClass import modelRest
# from deeprest.timeLapseClass import sampleTimeLapse
import time, os, glob
import shutil... |
51570b73f34d3cf96a88f6a08cd3bdfd791e97f29a8f9df23b8d3e7b1e285d13 | Python | 6,769 | 203 | import geomstats.backend as gs
from geomstats.geometry.base import ComplexMatrixVectorSpace
from geomstats.geometry.euclidean import Euclidean
from geomstats.geometry.general_linear import SquareMatrices
from geomstats.vectorization import get_n_points
def get_random_quaternion(n_points=1):
# https://stackoverflo... |
e116e60509bf41dba9145035c806d513fa4d13da611072171cc8f1378ce56801 | Python | 6,771 | 170 | import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
import analysis_utils as au
import fit_data as fd
def fit_data_and_plot(df, kind='bar'):
config_columns = [
'init_std',
'lr',
'memory_lr',
]
mean_columns = [
'seed',
]
metric_column = 'valu... |
5ca6144343f5199f22c9f7f63eb8fa60436bb43551d20cdecebb6207578a79a7 | Python | 6,776 | 236 | #!/usr/bin/env python
"""This script will run part of the movie, and will let the subject choose
the volume. It will then save the volume and use it for the experiment"""
from psychopy import prefs
prefs.general['audioLib'] = ['pygame']
from psychopy import visual, gui, event, logging
from psychopy import sound, core
i... |
9658233c27a0147dccacd0112d79c59a0f113bc6f8b989b90133e327fecf6a01 | Python | 6,779 | 234 | import flammkuchen as fl
import numpy as np
from joblib import Parallel, delayed
from skimage.measure import block_reduce
from split_dataset import Blocks, SplitDataset, EmptySplitDataset
def _time_percentile(
dataset, block, out_file, method="mean", percentile=50, time_slice=None
):
if time_slice is None:
... |
4a23b032cd71d7a47c670d85169f44cba9a5cbe5b8622c31d343d5a686d369c8 | Python | 6,783 | 204 | """Classical multi-dimensional scaling (classical MDS)."""
# Authors: The scikit-learn developers
# SPDX-License-Identifier: BSD-3-Clause
from numbers import Integral
from sklearn.base import BaseEstimator, _fit_context
from sklearn.metrics import pairwise_distances
from sklearn.utils import check_symmetric
from skl... |
ba3816edb268d39958b48341f6814a3ed75dbdf4c9ebf7c2978f5f7a4f127e2e | Python | 6,783 | 227 | import math
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
class LayerNormNoBias(nn.Module):
""" From nanoGPT:
LayerNorm but with an optional bias. PyTorch doesn't support simply bias=False
"""
def __init__(self, ndim: int):
super().__init__()
... |
6515671408ba1193c92f82b7810a4205c2aab9487a8d2c983896ce266824d9d1 | Python | 6,785 | 185 | import ase
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.nn import Embedding, Linear, ModuleList, Sequential
from dgl.nn.pytorch import GraphConv, AvgPooling
class SchNet(torch.nn.Module):
def __init__(self, sch_n_interaction, sch_hidden_dim, sch_n_gaussian,
sch_n_... |
ce7767ac12451c901b89fe75227804044fd162641e152c11681f52939a282342 | Python | 6,787 | 158 | import argparse
from sklearn import svm
from sklearn.model_selection import KFold
from sklearn.metrics import precision_recall_curve, roc_curve, auc
from sklearn.model_selection import train_test_split
import pandas as pd
import numpy as np
import joblib
# Calculate and update the best metrics, fold index and results... |
ac0764712a9f96d9d81b964d80e414eebd0710baa5b75c2e99bbaa2b6dd23e98 | Python | 6,789 | 181 | import math
import random
from PIL import Image
import blobfile as bf
from mpi4py import MPI
import numpy as np
from torch.utils.data import DataLoader, Dataset
import cv2
def load_data(
*,
data_dir,
batch_size,
image_size,
class_cond=False,
deterministic=False,
random_crop=False,
rand... |
bae7b3b5c710cc800956863c192dd279911fcccab71f62ed42c0d969a423625d | Python | 6,791 | 192 | import numpy as np
import xarray as xr
from scipy.spatial.distance import cdist
from numpy.testing import assert_raises, assert_array_almost_equal, \
assert_equal
from xarray.testing import assert_allclose as assert_xr_allclose
import gemmr.generative_model
from gemmr.data import generate_example_dataset
from ge... |
baa2db35334bbff6146224e787a98b0b2a536d8819d2ab407405a9c9886f990d | Python | 6,797 | 191 | import torch
import torch.nn as nn
import torch.nn.functional as F
import torch_geometric.transforms as T
from torch_geometric.nn.conv import MessagePassing
from torch_geometric.nn.glob import global_add_pool, global_mean_pool, global_max_pool
from typing import List, Optional, Union, Callable
from torch import Tenso... |
069a3f684660d888016bca7820e5a94340aed52d6bae4d1f3b967404e7d1ef94 | Python | 6,798 | 163 | """Build the tiny ``AtomicDipolesMACE`` anchor by direct instantiation.
Same discipline as ``build_mace_anchor.py`` and for the same reason: a seeded
untrained network exercises the readout assembly exactly as a trained one
does, so the anchor is initialised and saved rather than fitted. What it
exists to pin is the d... |
d7afb3b55f8ab420a61845c02981390cd9c55ac8b1f0d2cb1cc1c62c27d56b00 | Python | 6,798 | 143 | """Merging Fingerprinting output
The goal of the current package is to extract functional connectivity data from already scrubbed and cleaned fMRI data. The goal is simply to extract the data using specifical parcellations.
To do:
- WARNING: Bug when running in variance data. For some reason, the index columns ar... |
8bdc34a104e071b81e7be8ce5372108a3d595c8e108dc9b0f2dd05418a27a87a | Python | 6,802 | 168 | """Tests for Adjacency core operations: init, type inference, properties,
indexing, arithmetic, copy, squareform, append, aggregation, distance."""
import numpy as np
import polars as pl
import pytest
from scipy.spatial.distance import correlation
from scipy.stats import pearsonr
from nltools.data import Adjacency
... |
0b25b56de19fea54e7ac145bb04c414b1c5616252ba7eb397a39efc01ce46445 | Python | 6,803 | 184 | import numpy as np
from scipy.spatial.distance import cosine as cosdist
from numpy.testing import assert_raises, assert_allclose, assert_equal, assert_warns, assert_array_almost_equal
from unittest.mock import patch, create_autospec
from sklearn.utils import check_random_state
import gemmr.generative_model
from gem... |
2a7e688f25ed77867818e812367cecfc6165bc69a0f2201bbf33eb46e968aaff | Python | 6,803 | 203 | import geomstats.backend as gs
from geomstats.metric_geometry.bhv_space import Split, Tree
from geomstats.test.data import TestData
from .point_set import PointSetMetricTestData
class TreeTopologyTestData(TestData):
def raises_empty_splits_test_data(self):
data = [
dict(
inval... |
a50b5ab7b6ad42a6dcb82c8fb3d78c786107ad6efd9704d642b8a3bb2cfbccc6 | Python | 6,805 | 129 | """
Quadratic Integrate-and-Fire (QIF) Neuron Mean-Field Model
==========================================================
Here, we will introduce the QIF population mean-field model, which has been derived from a population of all-to-all
coupled QIF neurons in [1]_. The model equations are given by:
.. math::
\\... |
4557635e3cf86d81bc88159d53654e1a5601dea7719b25d4f1d136ece762e83c | Python | 6,807 | 186 | # pyright: reportIncompatibleMethodOverride=false
import logging
from collections.abc import Iterable, Sequence
from dataclasses import dataclass
from math import sqrt
from qtpy.QtCore import Signal # type: ignore[reportPrivateImportUsage]
from qtpy.QtCore import QPoint, QPointF, Qt
from qtpy.QtGui import (
QColo... |
797325f0d189d8be41c1d1fd71fcdbc764134bbcb99a64d0e6b87775f22ef580 | Python | 6,808 | 181 | from chromadb.api.types import (
SparseEmbeddingFunction,
SparseVector,
SparseVectors,
Documents,
)
from typing import Dict, Any, List, Optional
from enum import Enum
from chromadb.utils.embedding_functions.schemas import validate_config_schema
from chromadb.utils.sparse_embedding_utils import normalize... |
5693186d35296cf3540a96f1977ab966486ee1eb4de7bb0f588fd2bb836d5e05 | Python | 6,812 | 215 | # -*- coding: utf-8 -*-
#
# BigFeta documentation build configuration file, created by
# sphinx-quickstart on Mon May 20 10:03:21 2019.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# A... |
5fa7205892dab0ed6d2dde9f40fe3b4df1834068dbcb43c1c4f65821f5e42513 | Python | 6,812 | 195 | from brian2 import *
def visualise_connectivity(S):
Ns = len(S.source)
Nt = len(S.target)
figure(figsize=(10, 4))
subplot(121)
plot(zeros(Ns), arange(Ns), 'ok', ms=10)
plot(ones(Nt), arange(Nt), 'ok', ms=10)
for i, j in zip(S.i, S.j):
plot([0, 1], [i, j], '-k')
xticks([0, 1], ['... |
695ea297857eef465e8d3cb1b803b733370f9592cbeeaf7493768eaea267f965 | Python | 6,825 | 178 | """`--multi_processed_test`, which is a statement about a directory layout.
Both branches read `--test_dir`, and they disagree about what is in it: without
the flag the directory holds files whose names end `_test.h5`, one dataset each;
with it the directory holds one *folder* per test set, each holding the shards a
m... |
ce22a0c1e8f08644c6c3e47499f5280daa99583d51f668fa1acea69ef469f3bf | Python | 6,828 | 134 | # 2026-09-26 Shared scoring harness for the clustering bake-off (VDJdb motif stage).
#
# Every candidate algorithm is scored through ONE code path: produce a label vector in the
# tcremp contract (-1 noise, otherwise unique across epitopes), push it through clusters() so the
# legacy length-split and the min_cluster p... |
6699c22397be045c70a4b848ee0902b3de8d878818d27bc4fbb9b3eb8dca5cc6 | Python | 6,830 | 206 | """Mixin for manifolds of probability distributions."""
import math
import geomstats.backend as gs
from geomstats.vectorization import get_batch_shape
class InformationManifoldMixin:
"""Mixin for manifolds of probability distributions."""
def __init__(self, support_shape, **kwargs):
self.support_sh... |
bb5bb27e71761a99eddc0d727c14da369e26cbdfb82c6e476d4dc0e539e94956 | Python | 6,832 | 136 | # Copyright 2020 Forschungszentrum Jülich GmbH and Aix-Marseille Université
# "Licensed to the Apache Software Foundation (ASF) under one or more contributor license agreements; and to You under the Apache License, Version 2.0. "
from mpi4py import MPI
import os
import json
import time
import numpy as np
from nest_el... |
4a39c8c99f7893c3b85eb0e8249be2cc95b99ee9725786287c6e970e80aa9355 | Python | 6,833 | 213 | """Spatial neighborhood computation for neuroimaging analyses.
This module computes spatial neighborhoods (spheres) around brain voxels. It is
designed to support searchlight analyses, ISC, and other operations that require
iterating over local brain regions.
Examples:
```python
import nibabel as nib
from... |
74073ce98188953528f64d4943871bbb4ac475bfc790125c828c7de81ba2fbd0 | Python | 6,835 | 208 | # -*- coding: utf-8 -*-
import argparse
import sys
import math
import csv
import copy
import scipy
import numpy as np
import scipy.stats as sp
import sklearn.cluster
import sklearn.metrics.pairwise
import warnings
warnings.filterwarnings("ignore")
def min_dist_ref(genotypes, ref_genotypes, focal_idx):
f = np.ar... |
22d01d7894ecd0c0622d55be5f4611005a3d8141a8beec782d93417105f93bf1 | Python | 6,837 | 194 | # Copyright (c) 2021 PaddlePaddle 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 appli... |
38cb98d683f9d173576a74c0d640a8a16af9ac90af39bff15e8ad0501f8b4ee2 | Python | 6,838 | 166 | import numpy as np
from rdkit.Chem import Descriptors
from reinvent_plugins.components.RDKit.comp_linkinvent import FragmentQed
from reinvent_plugins.components.RDKit.comp_linkinvent import FragmentMolecularWeight
from reinvent_plugins.components.RDKit.comp_linkinvent import FragmentTPSA
from reinvent_plugins.compone... |
8b9ebfbbb590cf1d10960234edc8e6189551c58087a98891cb55643eb24ed354 | Python | 6,840 | 248 | import json
import six
import copy
import cachetools
import cloudvolume
from cloudvolume import CloudVolume, Storage
from corgie.log import logger as corgie_logger
def jsonize_key(*kargs, **kwargs):
result = ""
for k in kargs[1:]:
result += json.dumps(k)
result += "_"
result += json.dum... |
54395c6627fa190b2892bea7adac43791d6849bf6d02a3b99fdbf4404d4577ed | Python | 6,843 | 193 | """Visualization for Geometric Statistics."""
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D # NOQA
import geomstats.backend as gs
from geomstats.geometry.hyperboloid import Hyperboloid
from geomstats.geometry.poincare_half_space import PoincareHalfSpace
H2 = Hyperboloid(dim=2)
POINCARE_HAL... |
3bdb39faacd34ac4ea6d0f2ae7c3bd62dc0ce896ee9ddcf255e4530c32eb7265 | Python | 6,848 | 194 | import numpy as np
import torch
import torch.nn as nn
class ST_Net_Sigmoid(nn.Module):
def __init__(self, input_dim, output_dim, hid_dim=64, num_layers=2, bias=True, scale_weight_norm=False, sigmoid_shift=2., apply_batch_norm=False):
super(ST_Net_Sigmoid, self).__init__()
self.num_layers = num_laye... |
bbabc374e723d7cb3410f223a2636fca786b8d1c1e4a54f3aa8f888ee1225da1 | Python | 6,848 | 134 | import torch
import numpy as np
from dig.ggraph3D.utils import xyz2mol, collect_bond_dists, compute_mmd, compute_prop
class RandGenEvaluator:
r"""
Evaluator for random generation task. Metric is the chemical validity ratio (represented in percentage) and the MMD distances of bond length distribution between ... |
dec71bd774264423e8f0ce6533435b37d4ae70d93d7d83480faa1615b1c45f07 | Python | 6,848 | 158 | import argparse
from sklearn.ensemble import RandomForestClassifier
from sklearn.model_selection import KFold
from sklearn.metrics import precision_recall_curve, roc_curve, auc
from sklearn.model_selection import train_test_split
import pandas as pd
import numpy as np
import joblib
# Calculate and update the best met... |
12a234fa7a7a0c702eb98b44f24c45aec73fbe05917677c44a9c5c0b0033343b | Python | 6,855 | 196 | """
original author :
__author__ = https://wiki.python.org/moin/PyQt/Python%20syntax%20highlighting
"""
__author__ = "Seounghun, Chung <4uwingnet@naver.com>"
__license__ = "License:BSD 3Clause"
import sys
from PyQt5.QtCore import QRegExp
from PyQt5.QtGui import QColor, QTextCharFormat, QFont, QSyntaxHighlighter
from... |
27805765b98abd215e57cce465fe0b68f98859f6ebd504321c7bd063894f9aae | Python | 6,855 | 166 | """References for the two published non-energy models. Needs a download.
Not part of ``--target all``: regenerating these fetches published releases,
and MACE-Polar additionally needs the ``graph_longrange`` extra. Folding it
into the default sequence would mean ``--target all`` fails on a plain
development box that c... |
2d20bbd9131fafba2131cc626e4be29afec65027dbba66b6c60d5e84bfa49195 | Python | 6,859 | 196 | """Plot every analyzed file in the open folder with NicePool."""
from __future__ import annotations
from functools import partial
from typing import Any
import pandas as pd
from PyQt5 import QtCore, QtGui
from sanpy.interface.plugins.nicepool_plugin import NicePoolPlugin
from sanpy.interface.window_state import Win... |
6d051f01969bdb95353fcd04884c972675c6eadf6780275a88f94fdc0e605531 | Python | 6,862 | 117 | #*----------------------------------------------------------------------------*
#* Copyright (C) 2024 ETH Zurich, Switzerland *
#* SPDX-License-Identifier: Apache-2.0 *
#* *
... |
819afb45caf24dedabc03f53b04d2cdeed9866574a8a9de704a97249dabae249 | Python | 6,862 | 235 | import time, h5py, logging, itertools
from tqdm.auto import tqdm, trange
from typing import Union, List, Tuple
import numpy as np, pandas as pd
from sklearn.neighbors import RadiusNeighborsClassifier, RadiusNeighborsRegressor
from anndata import AnnData
import scanpy as sc
import torch
def config_logger(logger, le... |
47f7ba15a81b6ea9ebc3d4a6c7bce70b7983f730e9fb08e0362296cb02389dc8 | Python | 6,866 | 210 | import numpy as np
class coupled_oscillators:
"""
Simulate coupled oscillators, with parameters extracted from trained LRRNNs
"""
def __init__(self, tau, freq, m, n, I_orth, alphas, rad, amp,n_osc=1):
"""
Initialise coupled oscillators
Args:
tau: time constant of ... |
98a75eb5ff8b0deec74b63bec88628e2b1e61951ea10b6339f3ae450fd5ca26e | Python | 6,866 | 174 | # Copyright 2025 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
import logging
from azure.storage.blob import BlobServiceClient
from pathlib import Path
import tests.end_to_end.utils.defaults as defaults
import tests.end_to_end.utils.docker_helper as docker_helper
import tests.end_to_end.utils.exceptions as ... |
3dd15ac2e73d8fb15491bb338b8251a509b30b433a7d7431383170a000dd3037 | Python | 6,867 | 168 | import os, glob, tqdm
from skimage.io import imread, imsave
import numpy as np
import matplotlib.pyplot as plt
from matplotlib import rc
import matplotlib as mpl
import pandas as pd
import seaborn as sns
import scipy.ndimage as ndi
from skimage.metrics import structural_similarity as ssimi
from skimage.metrics import n... |
261c1e02c68beb675f17e59ac719c31c3dea83ea0a5b62cc0d8e3e93cf74a486 | Python | 6,870 | 160 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
from typing import Union, Callable, Dict, List
import torch
from ase import Atoms
from ase.calculators.calculator import Calculator, all_changes
from ase.stress import full_3x3_to_voigt_6_stress
from ... |
5b6c1e4f8921ef15ef7cccc2768bf58151b6ea9c92596b860a966fc4fc16c60b | Python | 6,875 | 223 | # ruff: noqa: PLR2004
from __future__ import annotations
import argparse
from typing import Any
import pytest
from pytest_mock import MockerFixture
from snakebids import bidsapp, plugins
from snakebids.bidsapp.args import ArgumentGroups
class TestRunner:
def setup_method(self):
self.hooks_run = 0
... |
fd5ea40acd57149c6512d75406094fdb40da06ce6c003891e170c7af343d6941 | Python | 6,875 | 259 | import click
import procspec
import math
from corgie import scheduling, helpers
from corgie.log import logger as corgie_logger
from corgie.boundingcube import get_bcube_from_coords
from corgie.argparsers import (
LAYER_HELP_STR,
create_layer_from_spec,
corgie_optgroup,
corgie_option,
create_stack_... |
070b7a94c3700612fb12a1d9e06ac918f556f7f7c9db1e11dd17939c72167276 | Python | 6,876 | 205 | from __future__ import annotations
import argparse
import sys
from collections import defaultdict
from typing import TYPE_CHECKING, Any, Iterable, Protocol, Sequence, TypedDict
import attrs
import pluggy
from attrs.converters import default_if_none
from typing_extensions import TypeAlias, Unpack
from snakebids.bidsa... |
f8da2e16654116392f7ddb90bda194324e61aa544103d4628a8c535830e6615f | Python | 6,886 | 230 | # /// script
# requires-python = ">=3.11"
# dependencies = [
# "marimo",
# "nltools>=0.6.0",
# ]
# ///
# Decomposition — marimo notebook. Source of truth for the docs page; rendered to the docs page by scripts/marimo_to_zensical.py.
import marimo
__generated_with = "0.24.0"
app = marimo.App(width="medium")
... |
538802f12ac99f5f0674cb5b8c39f92deab1b0ec1ec291606067aa2156e00b8a | Python | 6,889 | 173 | """
A script to run many motion estimation method.
The run many combinaisons of peak localization x estimation from spikeinterface.
This done using the BenchmarkMotionEstimationMearec class from
spikeinterface.sortingcomponents.benchmark.benchmark_motion_estimation
"""
from configuration import *
from spikeinterface... |
f3ac28230ae9e20aa47b10e6c4cca614becdaad819e9c6a7a21f90b6e748cde4 | Python | 6,890 | 170 | """Tests for the file-path / events-DataFrame paths in DesignMatrix.
The old standalone `nltools.io.onsets_to_dm` was folded into
`DesignMatrix.__init__` (file path) and `nltools.io.events_to_dm`
(in-memory events DataFrame).
"""
import os
import numpy as np
import pandas as pd
import polars as pl
import pytest
fro... |
7f7b4b96956ed65680eb8d643f80ec5d6b0965ed10ce390ad9ff67737add060b | Python | 6,891 | 203 | # 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
import torch.nn as nn
import torch.nn.functional as F
class GumbelVectorQuantizer(nn.Module):
def __init__(
self,
... |
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