sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
0b5b88f2ee13c4cfee90dd361d669d1d620582f4445841623cb3b0664e5596ee | Python | 7,702 | 237 | """
Bonito nn modules.
"""
import torch
from torch.nn import Module
from torch.nn.init import orthogonal_
layers = {}
def register(layer):
layer.name = layer.__name__.lower()
layers[layer.name] = layer
return layer
register(torch.nn.ReLU)
register(torch.nn.Tanh)
@register
class Swish(torch.nn.SiLU)... |
6825f8f3d8116b836ed1d30a445c86855ea6689afad2e1329eee6e09b291e108 | Python | 7,702 | 246 | import errno
import itertools
import logging
import os.path
import tempfile
from contextlib import ExitStack, contextmanager
from typing import Any, Dict, Generator, Optional, TypeVar, Union
from pip._internal.utils.misc import enum, rmtree
logger = logging.getLogger(__name__)
_T = TypeVar("_T", bound="TempDirectory... |
a0dd90ca6a368f008e6cfd9590a198090c509dc05252d35584aab13ebaddd2d6 | Python | 7,703 | 262 | """Radiated flux of a lossless dielectric disc in cylindrical coordinates.
Tutorial Reference:
https://meep.readthedocs.io/en/latest/Python_Tutorials/Near_to_Far_Field_Spectra/#radiation-pattern-of-a-disc-in-cylindrical-coordinates
"""
import math
from typing import Tuple
import matplotlib.pyplot as plt
import meep... |
b78f9dac38a3fc29b014da28b8a7421bdc5a6b26df968d69e814c9240fe9999b | Python | 7,705 | 221 | # coding=utf-8
# Copyright 2026 The Google Research 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 applicab... |
aa477575b582847242d91ef6649b8a9a8bc4516a45ef1d6d9d424f183fe3f1af | Python | 7,707 | 285 | from __future__ import annotations
import pytest
dask = pytest.importorskip("dask")
pytest.importorskip("distributed")
import gzip
from shutil import which
from dask.distributed import default_client
from quacc import get_settings
settings = get_settings()
pytestmark = pytest.mark.skipif(
which(str(settings.E... |
4b8e54ec0edef336752326e07a484202d245540ea9dd0c9493769116d0db220f | Python | 7,709 | 199 | import os
import logging
import re
from utilities.Log import define_root_logger
import logging
import pickle
import torch
import utilities.Log as Log
import numpy as np
import yaml
def init(args, default_path, config):
if not os.path.exists(default_path):
os.makedirs(default_path)
exp_num=0
el... |
68cda8ba6cdabb98855e7035aa0d8e2b3f0765606dcc3c93ddb7e9a151bbb147 | Python | 7,709 | 270 | import click
import numpy as np
import pandas as pd
import tensorflow as tf
from lib.model import simplified, standard, saluki
from lib.sequence import SeqClassificationDataLoader1D, SeqRegressionDataLoader1D
model_type = {
"standard": standard,
"simplified": simplified,
"saluki": saluki
}
# options
@clic... |
f6a4fe2dfd785c67e2e7227d2912fda15b37d332f7895f14d116854647b2ec41 | Python | 7,709 | 207 | import geohash2.geohash as geoh
import shapely.geometry as geos
import numpy as np
def linecell_lons_bigger_step(p1, p2, cell_start, lons_all, lats_all, lons_center_all, lats_center_all):
reverse = False
if p2[1] < p1[1]:
tmp = p1
p1 = p2
p2 = tmp
reverse = True
lats_start... |
f39e4d647bab6ecb57be193b523a734b1e9f876d34958d0599ac08c54fa00964 | Python | 7,710 | 279 | import os
os.environ["OMP_NUM_THREADS"] = "6" # export OMP_NUM_THREADS=1
os.environ["OPENBLAS_NUM_THREADS"] = "6" # export OPENBLAS_NUM_THREADS=1
os.environ["MKL_NUM_THREADS"] = "6" # export MKL_NUM_THREADS=1
os.environ["VECLIB_MAXIMUM_THREADS"] = "6" # export VECLIB_MAXIMUM_THREADS=1
os.environ["NUMEXPR_NUM_THREA... |
fbff3f6cc11b82203547851f9548b9a76c5751eddf6728baac27f2baf33ca942 | Python | 7,710 | 224 | import torch
import torch.nn as nn
from elasticai.creator.nn.integer.addition import Addition
from elasticai.creator.nn.integer.conv1dbn import Conv1dBN
from elasticai.creator.nn.integer.design_creator_module import DesignCreatorModule
from elasticai.creator.nn.integer.quant_utils import (
AsymmetricSignedQParams,... |
3b9c22b80605a7553901d2adb64bb6990947a2dd06da9dba866a4635fffdd2ea | Python | 7,711 | 112 | # coding=utf-8
# Copyright 2026 The Google Research 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 applicab... |
7a6f2499bfa02a45e5f93b9876b41ae376c066d24b5ddd1bb059d8196bbea48f | Python | 7,716 | 192 | import SimpleITK as sitk
import pandas as pd
import numpy as np
from skmultilearn.model_selection.iterative_stratification import iterative_train_test_split
from data.constants import *
def anonIDToRadiomicsUID(anon_id, patient_key):
# Find UID from a given filename
# Look up UID in patient key -re... |
d77995a59f6c4c3162e87662d9b3f0222a519c9ff3437ce396d5683584ed401f | Python | 7,716 | 198 | """Tests for the report_figures/<kind>/*.png embed sections (Phase 2 Task 5)."""
import json
import os
import struct
import zlib
from regtools.registration.report import build_html_report
from regtools.registration.report.analysis_figures import (
_render_cell_density,
_render_checkerboard,
_re... |
25d8f643d5a90673f6bff88786d1a079a503ed925e1a96ef73c7304edf40d6d3 | Python | 7,717 | 182 | """
Prosper_nn provides implementations for specialized time series forecasting
neural networks and related utility functions.
Copyright (C) 2022 Nico Beck, Julia Schemm, Henning Frechen, Jacob Fidorra,
Denni Schmidt, Sai Kiran Srivatsav Gollapalli
This file is part of Propser_nn.
Propser_nn is free software: yo... |
5b15dac3bedd3698ce5d479f0aef882519e243430ae60fcfbd4cfcbc4e1a4446 | Python | 7,717 | 225 | # -*- coding: utf-8 -*-
# IMPORTS
import sys
from PIL import Image
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import random
import argparse
import os
import time
import glob
from tqdm import tqdm
USER = os.getenv('USER')
sys.path.append('../.')
# torch packages
import torch
import torchvisi... |
d5ae8286bdeb3f6e8438ed6c1d4ceda88d26a3decc0ebe50ca1bf199437c2095 | Python | 7,717 | 199 | # coding=utf-8
# Copyright 2026 The Google Research 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 applicab... |
38be2f46832ee1be6787cbec1b3eca23d0eca4a3d4cbe77fb41308d3d7f48c81 | Python | 7,719 | 198 | # -*- coding: utf-8 -*-
r"""
This file implements a combination of the atomic charge dipole model and the bond charge dipole
model with regularization resulting in the AC+BC(R) dipole model.
Atomic property predictions from the network are interpreted as atomic charges.
A charge neutrality constraint is applied to enf... |
7c4f790472c76daa2c43bf23fd359d9acdb0f637319627f11e33c7989dd1279f | Python | 7,719 | 209 | import torch
from torch import nn
from torch.nn.functional import normalize
from torchvision.models.resnet import Bottleneck, BasicBlock, conv1x1
class BackBoneModel(nn.Module):
def __init__(self,
input_shape: int,
output_shape: int):
super().__init__()
self.conv_... |
8075f4155000aa9c07253f0bd507418db3653e9c67760cb7d34dd0ae3e5b9482 | Python | 7,719 | 183 | """"""
"""
Prosper_nn provides implementations for specialized time series forecasting
neural networks and related utility functions.
Copyright (C) 2022 Nico Beck, Julia Schemm, Henning Frechen, Jacob Fidorra,
Denni Schmidt, Sai Kiran Srivatsav Gollapalli
This file is part of Propser_nn.
Propser_nn is free softw... |
00691541e3d289dce762af9046e3a5e18ab1d1508848fa3eddb05e719b52128b | Python | 7,723 | 204 | import torch
import torch.nn as nn
import torch.nn.functional as F
class Attention(nn.Module): # Checked
def __init__(self, dim, num_heads, attn_dropout=0.0):
super(Attention, self).__init__()
self.num_heads = num_heads
head_dim = dim // self.num_heads
self.scale = head_di... |
d9c5c8aa321b10e9dbc6c0727d33ca031558770892c1b7d07b22afd0d15df47c | Python | 7,724 | 215 | # coding=utf-8
# Copyright 2026 The Google Research 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 applicab... |
432ff1f4fd2c49b747b0fe343089a3ad15fba1bb9d869485ea232667af23886b | Python | 7,727 | 202 | import numpy as np
import pytest
from molecularnodes import framing
def random_basis(rng) -> np.ndarray:
"A random orthonormal (right, up, forward) basis."
basis, _ = np.linalg.qr(rng.normal(size=(3, 3)))
if np.linalg.det(basis) < 0:
basis[0] *= -1
return basis
def frustum_slack(points, loca... |
8980d37b794495fab32663f45208092cd10a4040c6aeb8c75615c0cabfe879c8 | Python | 7,727 | 221 | import numpy as np
import nibabel as nib
import re
import os
os.environ["OMP_NUM_THREADS"] = "15" # export OMP_NUM_THREADS=1
os.environ["OPENBLAS_NUM_THREADS"] = "15" # export OPENBLAS_NUM_THREADS=1
os.environ["MKL_NUM_THREADS"] = "15" # export MKL_NUM_THREADS=1
os.environ["VECLIB_MAXIMUM_THREADS"] = "15" # export VE... |
0cbf000e4e43f1496f7b800db00bccf5b6358ed8d31aa8366a12eda4b3abb776 | Python | 7,728 | 274 | import numpy as np
import torch
from hippo.models.hmm import HMM
from hippo.agents.memory import Memory
from hippo.free_energy.tree import construct_tree
from hippo.models.cscg_tools import add_death
from hippo.free_energy import free_energy
from pymdp.maths import softmax
from gymnasium import spaces
import netwo... |
0618e4a053f713a076d207afb69bebe6d5f514cc2cb91d9befeaab35e38674a7 | Python | 7,732 | 240 | """
(*)~---------------------------------------------------------------------------
Pupil - eye tracking platform
Copyright (C) 2012-2020 Pupil Labs
Distributed under the terms of the GNU
Lesser General Public License (LGPL v3.0).
See COPYING and COPYING.LESSER for license details.
------------------------------------... |
50efb122b61975c62a1f7829f1104d5e7cc76f6d050a8986490d8b7574e1abef | Python | 7,732 | 181 | #!/usr/bin/env python
# Copyright (c) 2019-2020 Intel Corporation
#
# This work is licensed under the terms of the MIT license.
# For a copy, see <https://opensource.org/licenses/MIT>.
"""
Change lane scenario:
The scenario realizes a driving behavior, in which the user-controlled ego vehicle
follows a fast driving ... |
eee652c65e26d8e94a794462250c2eb9dc86aeb0c5cf875a428c415cb9e60b5e | Python | 7,733 | 129 | """REAL_PN_BADEL.py 2026-10-01. Pre-registration: 04-NOTES/PREREG-2026-09-30p-BADEL-REAL-PN.md (frozen before the data).
A second real fly: Badel, Ohta, Tsuchimoto & Kazama (Neuron 2016) Table S2, projection-neuron responses of 37 glomeruli to
84 odours. Hallem & Carlson (2006) receptor responses (DoOR) drive the anten... |
f0346ffc6209ec78312e4f41f37bd25edfc247f204a9d4e9a33bacb236fde60e | Python | 7,734 | 171 | import warnings
warnings.filterwarnings("ignore")
warnings.filterwarnings("ignore", category=UserWarning,
message="A NumPy version >=1.18.5 and <1.25.0 is required for this version of SciPy*")
import sys
import os
import argparse
import pandas as pd
from glob import glob
from nilearn.glm.first_l... |
95476143407c36162f82df567364d3743c500164d15c5826f7095953b3b8332b | Python | 7,735 | 250 | # coding=utf-8
# Copyright 2026 The Google Research 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 applicab... |
7a4cdc956d7c5d278e62fcc1c259ddd595900def408effa5485128c48f4013bf | Python | 7,736 | 217 | ##
# \file run_reconstruction_parameter_study.py
# \brief Script to study reconstruction parameters and their impact on the
# volumetric reconstruction quality.
#
# \author Michael Ebner (michael.ebner.14@ucl.ac.uk)
# \date September 2017
#
import os
import numpy as np
import SimpleITK as si... |
39e8dc75e281433d08dec16c1d01a39a5f4a0de105425e2eaf6e62b717feb050 | Python | 7,737 | 211 | """Assemble the report's data payload.
The redesigned report is interactive - point-set switching, metric switching,
region search, hierarchy roll-up, threshold switching - so numbers can no
longer be baked into markup at build time. This module collects everything the
front end needs into ONE JSON-serialisable d... |
7d90ac0f987cd2ad587a16f2585396b08e8a5c0a4526d352466e90fcdf373fee | Python | 7,740 | 197 | """Estimate all possible number events starting from a base model or the maximum possible."""
import gc
from typing import Any
import numpy as np
import pandas as pd
import xarray as xr
from hmp.basedata import BaseData
from hmp.models.base import BaseModel
from hmp.models.event import EventModel
from hmp.patterndat... |
aace557756195fbc7276fd3fb0f913ed6293543ec05871b3943e39e327fa8a47 | Python | 7,740 | 172 | from torch import nn
from typing import Optional
from segmentation_models_pytorch.base import (
SegmentationModel,
SegmentationHead,
ClassificationHead,
)
from segmentation_models_pytorch.encoders import get_encoder
from .decoder import DeepLabV3Decoder, DeepLabV3PlusDecoder
class DeepLabV3(SegmentationM... |
ac7f44b548cb04213dcbb3d72676adc47131cfc844e3ed6ac48f6ce719d68aa3 | Python | 7,740 | 216 | from pathlib import Path
import numpy as np
import torch
from torch import nn
from elasticai.creator.nn.integer.design_creator_module import DesignCreatorModule
from elasticai.creator.nn.integer.matrixmulti import MatrixMulti
from elasticai.creator.nn.integer.quant_utils import (
AsymmetricSignedQParams,
Glob... |
e0b065ce594bf8e120bde9bf148d5b1b7282ea75bfcfbe132949663e5b2c5e81 | Python | 7,742 | 168 | import os.path
from collections import defaultdict
from lxml import etree
import zipfile
from ckg.graphdb_builder import mapping as mp, builder_utils
#########################
# Drug Bank #
#########################
def parser(databases_directory):
config = builder_utils.get_config(config_name="drugBan... |
6f35fd075e4be4d62880203d3547f8d451cce51402bee677eb737ee84674020b | Python | 7,744 | 225 | # Plots the individual trials and trial average of the epidural recordings
# used in Fig 1B
from os.path import join
from get_paths import *
import numpy as np
import matplotlib.pyplot as plt
from scipy.io import loadmat
from scipy import signal
from colors_paultol import colors
plt.rcParams["mathtext.default"] = "re... |
28d6ef13700ee66e43c31243b93ac97910cef30769658aa6d773799a97657f42 | Python | 7,745 | 299 | import abc
import logging
import os
import subprocess
import time
import cv2
logger = logging.getLogger(__name__)
class BaseVideoEncoder(object):
""" Base class for encoder interfaces. """
def __init__(
self,
folder,
stream_name,
resolution,
fps,
color_format... |
389af1172b8ae830dc940283a5e7197d05ab6d9ec15c673bb383c03d957f84bf | Python | 7,745 | 166 | import argparse
import cv2
import glob
import os
from basicsr.archs.rrdbnet_arch import RRDBNet
from basicsr.utils.download_util import load_file_from_url
from realesrgan import RealESRGANer
from realesrgan.archs.srvgg_arch import SRVGGNetCompact
def main():
"""Inference demo for Real-ESRGAN.
"""
parser ... |
908973f04f48e815fd3f55f2b2b49e1f1f68c3250f111406ad1fc2034a67ba73 | Python | 7,745 | 218 | import os.path as osp
import numpy as np
import torch
import pandas as pd
from torch_geometric.data import InMemoryDataset
from torch_geometric import data as DATA
from rdkit import Chem
from rdkit.Chem import MolFromSmiles
import networkx as nx
from rdkit import Chem
from rdkit.Chem import ChemicalFeatures
from rdkit ... |
f1a5bda1f7053c13e6142f5561af8bdbfa443ddfd3547f699896a9e2589152ea | Python | 7,745 | 247 | from collections import namedtuple, Mapping
from heapq import heappop, heappush
import operator
from .utils import INF, get_pairs, merge_dicts, flatten
# TODO - Visibility-PRM, PRM*
class Vertex(object):
def __init__(self, q):
self.q = q
self.edges = {}
self._handle = None
def clea... |
c31557da01e4c4d6ecb2d9ecde63766d73e11eab477a33ca2b566799ad12bd4e | Python | 7,746 | 193 | """Preset UI in the Parameters tab (issues #114, #116).
Builds a real RegistrationApp offscreen (so the Parameters tab has its sibling
RegistrationTab combos) with the preset JSON sandboxed via redirect_to.
"""
import os
import sys
PROJECT_ROOT = os.path.abspath(os.path.join(os.path.dirname(__file__), "..")... |
a5c72e34b2d4f3a2f570dde4e0d59913b91f28ea2237451e5f4e5f72d1e11bc3 | Python | 7,748 | 229 | import numpy as np
import matplotlib.pyplot as plt
from hippo.environments.w_maze import get_wmaze
from hippo.environments.action_perception import action_perception_loop
from hippo.visualization import visualize_trajectories
from hippo.evaluation.replay import ReplayEvaluation
import logging
from copy import copy
... |
a8cad7b8423a168a3df46950b0d3e6e2d515da8c2d10d3915dcf735d938e382c | Python | 7,749 | 180 | """
Script for plotting bivariate statistical analysis of pattern pairs
Input: - Path to the input UniStat pickles for two set of patterns
- Parameters for the bivariate analysis
Output: - Plot graphs with the statistical bivariate analysis of every pair
"""
__author__ = 'Antonio Martinez-Sanche... |
2849e1e9d53de7da1fd4e994084823f3b517ad633700178cee68d5c36b8444c2 | Python | 7,750 | 220 | import torch
import torch.nn as nn
from elasticai.creator.nn.integer.addition import Addition
from elasticai.creator.nn.integer.fusedsepresidualblock.design import (
SepResidualBlock as SepResidualBlockDesign,
)
from elasticai.creator.nn.integer.quant_utils import (
AsymmetricSignedQParams,
GlobalMinMaxObs... |
4563093b5be02c9b37887b84e72df160912cbb64fb9fe3d056e8cec6ea46eff4 | Python | 7,750 | 154 | """
EFFECTOME_SIGN_PERTURBATION.py
THE POINT OF THIS SCRIPT, in one paragraph.
Pospisil's supplementary information asks, in his own words: "would our results change
if the protocol for measuring the connectome had changed, or if the connectome of a
different fly had been measured?" He answers it by adding Gaussian n... |
54a3be0cea92d5f801bdfe1c4e828bc3601a6b7fa4bcdb8f0c7481cdc578209b | Python | 7,751 | 220 | import numpy as np
import keras
#from keras.datasets import mnist
from keras.models import Sequential
from keras.layers import Dense, Dropout, Flatten, Merge
from keras.layers import Conv1D, MaxPooling1D, AveragePooling1D
from generic_tajD import calc_S_and_k_from_seqs, count_all, tajD
from random import choice
from ma... |
82ebffd1bc67896b7803636d23c62f42d2d672146c3c933562d740fd35c4c666 | Python | 7,751 | 287 | # coding=utf-8
# Copyright 2026 The Google Research 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 applicab... |
9bdd48dc67e5527bd17fab51daebb87a29c549a6a40bb54aaac8101fbbf8f939 | Python | 7,751 | 187 | from __future__ import annotations
import pytest
pytest.importorskip("tblite.ase")
from copy import deepcopy
import numpy as np
from ase.build import bulk, molecule
from numpy.testing import assert_array_equal
from quacc import change_settings
from quacc.recipes.tblite.core import freq_job, relax_job, static_job
... |
8445acded58edc11f84345f2d9c4560453442495fb57f3c94850eaedc3747edb | Python | 7,752 | 214 | #
# MIT License
#
# Copyright (c) 2022 GT4SD team
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge,... |
9ce47a358bbb485fd49bf9d632b60128ef943d4d44305f5f2998288b9bdeae31 | Python | 7,753 | 154 | from PyQt5.QtGui import QFont
from PyQt5.QtWidgets import QDialog, QGridLayout, QLabel, QHBoxLayout, QSpinBox, \
QCheckBox, QComboBox, QPushButton
from src.settings import Settings
class ImagePipelineSettingsDialog(QDialog):
def __init__(self, parent=None,apply_flag=False,process=False,progress_bar=None):
s... |
06fd182621bbfc44a3b964ea419f80bd335d296f4a3a31bd9b3cfe8eb019227e | Python | 7,755 | 216 | """Unit tests.
"""
import unittest
from os.path import abspath, curdir, join
import pyensembl
from agfusion import database, model, parsers
data_mouse = pyensembl.EnsemblRelease(84, "mouse")
db_mouse = database.AGFusionDB(abspath(join(curdir, "agfusion.mus_musculus.84.db")))
db_mouse.build = "mus_musculus_84"
data... |
c7a21e552968d2f3c737015834a481fa0484d21fc0f7fd0665cff7a161c25fdf | Python | 7,761 | 197 | """End-to-end integration tests against the real bundled Allen CCF.
These exercise the full pipeline the way a user would:
load real CCF + real brain backdrop
-> make a small set of edits
-> export the modified annotation
-> re-load the exported session
-> verify the export reconst... |
444d1513847c1c985529538db2dcc443a3a53fe7b659aabf361349b75eac3cc0 | Python | 7,764 | 186 | import importlib
import networkx
from merlin.core import analysistask
from merlin.core import dataset
class SnakemakeRule(object):
def __init__(self, analysisTask: analysistask.AnalysisTask,
pythonPath=None):
self._analysisTask = analysisTask
self._pythonPath = pythonPath
@s... |
defcac05f44d363d1e06b04f12bc129f20885c256adedd2fed98c69f883e0f1a | Python | 7,764 | 242 | # coding=utf-8
# Copyright 2026 The Google Research 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 applicab... |
2cd51fe7e5162155ce8f9a1a8b975e8b2862da4b85b4afeb25f2d4bf1eb09657 | Python | 7,765 | 239 | """Transition state recipes for Q-Chem."""
from __future__ import annotations
from importlib.util import find_spec
from typing import TYPE_CHECKING
from monty.dev import requires
from quacc import job
from quacc.atoms.core import perturb
from quacc.recipes.qchem._base import run_and_summarize_opt
from quacc.recipes... |
421e5aebbf1e84fd88dfcb778712107521f9d6e621eb62602c74660cd87a2530 | Python | 7,767 | 215 | import sys
import os
import schnarc
import logging
import shutil
import argparse
import numpy as np
import datetime
import copy
import time
(tc, tt) = (time.process_time(), time.time())
#import schnet
import schnetpack as spk
import torch
import torch.nn as nn
from torch.optim import Adam
from torch.utils.data.sampler ... |
4505f536d033aa12204280c8ef188de04c4f107ba5409cd09e6a65b8e79d7025 | Python | 7,767 | 194 | from neuron import h
import neuron
import math
import numpy as np
from matplotlib import pyplot as plt
class test_cell(object):
def __init__(self, channel_name, step_v, gbar, area, volumn, tstop) -> None:
# channel_name = ['shl1', 'egl2' ...], a list
# step_v = list(range(stim_start, stim_end+1, st... |
61f734dd85b68705c452e06b7ba2041665b9f98f6a7754ebac7765ca2360a13f | Python | 7,767 | 230 | ##
# \file show_evaluated_simulated_stack_similarity.py
# \brief Script to show the evaluated similarity between simulated stack
# from obtained reconstruction and original stack.
#
# This function takes the result of evaluate_simulated_stack_similarity.py as
# input.
# \author Michael Ebner (micha... |
4059b6b9de0de303b157c37428f2d531a2089c5221d8c8ac17b7e5b8e76c2ed8 | Python | 7,768 | 285 | """Methods for loading files and handling the resulting objects."""
import os
from typing import Union
from mne import read_epochs
from coh_handle_files import generate_sessionwise_fpath, load_file
from coh_signal import data_dict_to_signal, Signal
def load_preprocessed_dict(
folderpath_preprocessing: str,
d... |
7edd94cd9b7e604442d6c7206c0bdc395c7b283a8563444783b7f6f0a5cbca3a | Python | 7,768 | 209 |
""" Authored by: Neel Kanwal (neel.kanwal0@gmail.com)"""
# This file provides inference code for binary DCNN and ViT models mentioned in the paper.
# Update paths to processed datasets
if __name__ == "__main__":
import warnings
warnings.simplefilter(action='ignore', category=FutureWarning)
war... |
41a7f5bff7c25859587c4c47a1459362e5c043d4d56648c2f6b57d6ed5dea211 | Python | 7,770 | 242 | # -*- coding: utf-8 -*-
#
# Tempo documentation build configuration file, created by
# sphinx-quickstart on Mon Jan 13 15:59:22 2014.
#
# 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.
#
# All c... |
1473c6eaeff9ababce1b17c93d106920805349e3c5ce2e3bb7d8ccf81af0fb9b | Python | 7,772 | 185 | """Tests for fingerprint comparison metrics.
Author: Seth Axen
E-mail: seth.axen@gmail.com
"""
import pytest
import numpy as np
from scipy.sparse import csr_matrix
from scipy.spatial.distance import cdist
from e3fp.fingerprint import metrics, fprint, db
from e3fp.fingerprint.metrics import array_metrics, fprint_metri... |
ebdbd321e02398a830bdf071214f56237382fc76787d49e380c4c8c5af9e6775 | Python | 7,772 | 236 | #!/usr/bin/env python3
# ******************************************
#
# SHARC Program Suite
#
# Copyright (c) 2023 University of Vienna
#
# This file is part of SHARC.
#
# SHARC is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by... |
34c272591c5d115f2b74174f223a1822a9b7e110a21378a1117cef4b4c916c96 | Python | 7,773 | 222 | """upload_docs
Implements a Distutils 'upload_docs' subcommand (upload documentation to
sites other than PyPi such as devpi).
"""
from base64 import standard_b64encode
from distutils import log
from distutils.errors import DistutilsOptionError
import os
import socket
import zipfile
import tempfile
import shutil
impor... |
d8d18901e0a2a0912f5765a84a4bcdd168a5b4d0e1a5d80abad37edba21906df | Python | 7,773 | 243 | # -*- coding: utf-8 -*-
from __future__ import annotations
import os
import pickle
import struct
from io import BytesIO
from typing import Any, Iterable, Optional
import torch
from torch.distributions.utils import lazy_property
from supar.utils.logging import get_logger, progress_bar
logger = get_logger(__name__)
... |
7ae2810832a7b1f94a53e055695dcca6e9199fe4c5e451531eb63d1b886c0a5a | Python | 7,776 | 197 | #
# Tests for memory_profiler module
#
# Copyright © 2026 Ernst Strüngmann Institute (ESI) of the Max Planck Society
#
# SPDX-License-Identifier: BSD-3-Clause
#
from unittest.mock import patch, MagicMock
from acme.memory_profiler import MemoryProfiler
from acme.argument_processor import ArgumentProcessor
class TestM... |
8fa393962188f00c3e2ad8d1dd6b2962d823016f690ee88d65a4c4b9272a55f6 | Python | 7,780 | 183 | import torch
import torch.nn as nn
import cv2
import numpy as np
from flytracking.detection.utils.process import postprocess
from flytracking.detection.utils.efficientdet import (
BBoxTransform,
ClipBoxes,
)
def calc_iou(a, b):
# a(anchor) [boxes, (y1, x1, y2, x2)]
# b(gt, coco-style) [boxes, (x1, y1... |
0844860b87463190b9c472fa62046251cc578ab515f4c6e07685c111a2865bf2 | Python | 7,782 | 253 | # coding: utf-8
"""
This code is based on the following paper:
Renner, A., Sheldon, F., Zlotnik, A., Tao, L., & Sornborger, A. T. The Backpropagation Algorithm Implemented
on Spiking Neuromorphic Hardware. arXiv:2106.07030 (2021).
This is a numpy implementation of the backpropagation algorithm for the binary neu... |
2bbebfa8d0d66f6a3bb10ede12c1eb929448a8d20e85cbfe8c51eab66e910838 | Python | 7,782 | 181 |
import os
os.environ['KMP_DUPLICATE_LIB_OK']='True'
import numpy as np
import torch
from torch_geometric.nn import GCNConv
import networkx as nx
import GNN_core
import argparse
import random
import torch.optim as optim
import copy
from sklearn.metrics import confusion_matrix, roc_curve, auc
parser = argparse.Argument... |
05ae8dccca1ef5f103bdbb9b6ae97feb11123cade1da515ef9968b19c5283f2e | Python | 7,783 | 175 | import numpy as np
import unittest
import pyntbci
FS = 120
N_TRIALS = 11
N_CHANNELS = 7
N_SAMPLES = 2 * FS
N_CLASSES = 5
CYCLE_SIZE = 1.0
class TestGenerateImpulseResponse(unittest.TestCase):
def test_default(self):
ir = pyntbci.eeg.generate_impulse_response(FS)
self.assertEqual(ir.ndim, 1)
... |
c3b436bd309a554e8bc2f6956d4bbfb4c0279356c520b7f1deb21d68b16297fd | Python | 7,783 | 200 | import torch
import torch.nn as nn
from model.backbone import get_visual_backbone
from model.encoder import get_encoder, TransformerEncoder
from model.decoder import get_decoder
from utils.utils import *
import numpy as np
class MLMTransformerPretrain(nn.Module):
def __init__(self, cfg, src_lang):
super(... |
1feeabe3a4655874b33ab77672ba3334a8f24d46ccc0c6f3aaa9188ddc0d0d2c | Python | 7,784 | 199 | """Write a copy of an input ``.h5ad`` with registered CCF coordinates and
per-cell atlas labels appended - without materializing ``X``.
The source file is copied byte-for-byte (``shutil.copy2``) so the expression
matrix and all existing metadata are preserved on disk, then the new elements
are appended in-place w... |
c4b9f0e6ec7225c60ba12790ce9784ea40a8da8b206de40a5ad383b87f172ec0 | Python | 7,784 | 200 | import gc
import multiprocessing as mp
import os
import tempfile
import unittest
from copy import copy
import numpy as np
import pandas as pd
from torcheeg.datasets import BaseDataset
from torcheeg.io import EEGSignalIO
from torcheeg.model_selection import Subcategory
from torch.utils.data import DataLoader
def _re... |
3b0bd69c6cf8e2ad946b603dbce215865f8425ad91f5b6f8efbbb8e435440be3 | Python | 7,788 | 225 | # -*- coding: utf-8 -*-
# IMPORTS
import sys
from PIL import Image
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import random
import argparse
import os
import time
import glob
from tqdm import tqdm
USER = os.getenv('USER')
sys.path.append(f'/home/{USER}/CODE/Pytorch-fingerprints/')
# torch pa... |
6c016dd7fc90c10069ec1e04725e8eaef47deee21a2bd7ecbe43377a43d6c04a | Python | 7,788 | 146 | """Language-model loading and logit comparison (the Qwen3 adapter's loader).
Coupling policies live in coupling.py and the interface mathematics in interfaces.py; they are
re-exported here for existing imports.
"""
from __future__ import annotations
import time
from typing import Any
import numpy as np
import torch
... |
99335be8f773bf5072b17f64f05bc68705be1def1c0fb01e6b2e16103649d1d9 | Python | 7,788 | 208 | #!/usr/bin/env python
#================================================================
# Copyright (C) 2022 Yufeng Liu (Braintell, Southeast University). All rights reserved.
#
# Filename : main_projection_analyzer.py
# Author : Yufeng Liu
# Date : 2022-08-03
# Description :
#
#======... |
3223516b758e0d4acd44d5235c5cf52e84649d8d2303b3a7da0ce65f69a23030 | Python | 7,789 | 227 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Written by Tong He and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
"""
import os
import time
import random
import argparse
import numpy as np
from pathlib import PurePath
import torch
import torch.utils.data
import torch.nn as ... |
a5bb824f822e10f65623ced3ccd066feb39c6a3e656f7bf4d71bb663aca6ae62 | Python | 7,792 | 257 | import os
import argparse
import numpy as np
import pandas as pd
import torch
from maldi_nn.models import SpeciesClassifier, MaldiTransformer
from maldi_nn.utils.data import SpeciesClfDataModule
from lightning.pytorch.callbacks import ModelCheckpoint, EarlyStopping
from lightning.pytorch.loggers import TensorBoardLogge... |
c1a1af13a7435329300b4a84e6baed8dbdc07d0dd0ae3722f1d5f1fae1b05a9c | Python | 7,796 | 196 | # coding=utf-8
# Copyright 2026 The Google Research 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 applicab... |
c9f46393556620726077d4cb6c67d1346000846315fa0fa5a984e7fc99c97de7 | Python | 7,800 | 228 | #!/usr/bin/env python
# requires band_deeph.json and band_dft.json created by plot_bands.py
import numpy as np
import json
import matplotlib.pyplot as plt
import matplotlib.lines as mlines
min_plot_energy = -2.5
max_plot_energy = 4
trim_gap = True
trim_min = 0.1
trim_max = 1.0
fontsize = 22
legend = False
legend_k... |
03e7e376bbdcbf38f3816440c2fb8174f7f0896aac6dc793476015624997745c | Python | 7,801 | 213 | #
# MIT License
#
# Copyright (c) 2022 GT4SD team
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge,... |
327b366893e903c64408011b98d5c1d8ebe6701f71f000cc21029c30ac3cbf90 | Python | 7,801 | 263 | # coding=utf-8
# Copyright 2026 The Google Research 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 applicab... |
15424caa574d687a497f0c07f6e4f97270d4949f04c9b09705ae1c3f186fe37a | Python | 7,803 | 204 | import tensorflow as tf
from tensorflow.keras.layers import Dense, Layer, Concatenate, AveragePooling1D
from tensorflow.keras import Model
from tensorflow.keras.activations import sigmoid, linear
from tensorflow import transpose, matmul, expand_dims
from tensorflow import keras
from tensorflow import reshape
from tenso... |
ab8053b8a794716c1751b4980655504bfe1c6304de0699adc2787b43b0b3b201 | Python | 7,803 | 190 | import configparser
import logging
import logging.config
import multiprocessing
import os
import time
import yaml
from pkg_resources import resource_filename
import NDATools
from NDATools import NDA_TOOLS_LOGGING_YML_FILE
from NDATools.upload.cli import NdaUploadCli
from NDATools.upload.submission.api import Submissi... |
fde14b849c6872b04a91029fde0c7b0ecc68296c18dd3e442093f1bcf50ee790 | Python | 7,804 | 161 | import os
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import re
from scipy import stats
def one_sample_ttest(sample_data, null_hypothesis_mean=0.0, significance_level=0.01):
# Calculate the T-test for the mean of ONE group of scores
t_statistic, p_value = stats.ttest_1samp(sample_dat... |
00c004d1c83834a34103fc23cd78253fe96452876eec11fc43c974afc63a9838 | Python | 7,809 | 236 | # coding=utf-8
# Copyright 2026 The Google Research 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 applicab... |
76b690ffd262860f3fdff731cc0f1163b5f5f6c7ca2dd6ad066a4222b8ce0d98 | Python | 7,810 | 176 | from typing import Tuple
import torch
import torch.nn as nn
class BEncoder(nn.Module):
r'''
The variational autoencoder consists of two parts, an encoder, and a decoder. The encoder compresses the input into the latent space. The decoder receives as input the information sampled from the latent space and pro... |
bf497f06915159d4363ae50eb0e7da73d398352c02c89b30d4a7a344ae4971bc | Python | 7,810 | 248 | import os
import numpy as np
from ...annotations.base import BaseAnnotation
from ...annotations.manager import BaseAnnotationManager
from ...nodes._utils import get_final_style_nodes
from ..annotations import Label2D, Label3D
from ..base import EntityType
class DensityAnnotation(BaseAnnotation):
"""
Base clas... |
d13237bc2e4772f30d636edf23f6e2da8513e78b1f48c07356e62c4f86921c36 | Python | 7,811 | 120 | """SFF_SEARCH.py 2026-09-28. Pre-registration: 04-NOTES/PREREG-2026-09-28-SFF-SEARCH.md
Test 2 of SIGN_FROM_FUNCTION got stuck far above the truth's loss. Can a search that does not know the truth find it,
and does the lowest loss pick it? Four searches (literature start, steepest from the classifier, two random starts... |
04aa3bc4469c1f0577ba5080d588821b62c47c1cb42e7eff19e71fc14f70113d | Python | 7,812 | 193 | from __future__ import annotations
from shutil import which
import pytest
DFTBPLUS_EXISTS = bool(which("dftb+"))
pytestmark = pytest.mark.skipif(not DFTBPLUS_EXISTS, reason="Needs DFTB+")
import logging
import os
import numpy as np
from ase.build import bulk, molecule
from quacc import change_settings
from quacc.... |
61434df00ae5eef7f6295295ad002cfecef9517bf17dc3b04d409407bdd62de6 | Python | 7,813 | 163 | # SPDX-FileCopyrightText: 2024 Blue Brain Project / EPFL
#
# SPDX-License-Identifier: AGPL-3.0-or-later
'''Description: Functions to extract (and cut) spike trains in topo-sample format
using bluepysnap and SONATA circuit configs
Author: C. Pokorny
Date: 09/2023
'''
import json
import numpy as n... |
544e538a2f22364436aea00226230b656f7d81e219e2be8b046a192e23f3f593 | Python | 7,815 | 240 | # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, ... |
a25dd659be49ebc01c8adc373da01d1b9ceaf05c29fcfba24ee407ac6896db11 | Python | 7,815 | 260 | import cocotb
import pytest
from cocotb.clock import Clock
from cocotb.triggers import RisingEdge, Timer
from cocotb.types import LogicArray
from cocotb.utils import get_sim_time
import elasticai.creator_plugins.mac_delta as mac_delta
import elasticai.creator_plugins.multipliers as multipliers
from elasticai.creator.a... |
3f5df0a23d9294bb8897dc88930e729f18487695c897c2f8ef348e1c34196b7f | Python | 7,816 | 209 | import os
from multiprocessing import Process, Queue
from queue import Empty
import numpy as np
import open3d as o3d
import torch
def normalize(x):
return x / np.linalg.norm(x)
def create_camera_actor(i, is_gt=False, scale=0.005):
cam_points = scale * np.array([
[0, 0, 0],
[-1, -1, 1.5... |
291ba0d8dddbf9898d193f880434436b9a7357fdcd330417bf32b51747e117dd | Python | 7,817 | 249 | #!/usr/bin/env python3
import pysam
import sys
import numpy as np
import pandas as pd
import numpy as np
from sklearn.mixture import GaussianMixture
import argparse
import logging
import tqdm
import pickle
def coordinateConversion_MMTag(sequence, base, modification_coords):
"""Sequence is array of bases. Base is ... |
dc0be37cf1dedeaddba70ddf35ff40de07418109a6f35093b50085effc1f526f | Python | 7,817 | 234 | import torch
import torch.nn as nn
import torch.nn.functional as F
import argparse
import os
#import wandb
import tqdm
import numpy as np
import pandas as pd
import data
import util
import net as networks
from sklearn.model_selection import KFold
from torch.utils.data import DataLoader
"""
Optimized Hyperparameter
... |
123f973de307e76764d56d5f1f8eac1d8145e742826ce674ffdda9572267c856 | Python | 7,819 | 175 | '''
Description:
Test scNODE when using different number of pre-training timepoints and fixing the latent space.
Author:
Jiaqi Zhang <jiaqi_zhang2@brown.edu>
'''
import os.path
import sys
import matplotlib.pyplot as plt
import torch
import torch.distributions as dist
import numpy as np
import pandas as pd
fro... |
10edf4bf262dad2ee1ab5f746d6c9262605bb1ec182e2d8ee03b2ae58cdd6274 | Python | 7,820 | 233 | # -*- coding: utf-8 -*-
import tensorflow as tf
from tensorflow.python.util.deprecation import deprecated
from .. import _logging as logging
from .core import *
__all__ = [
'LambdaLayer',
'SlimNetsLayer',
'KerasLayer',
'EstimatorLayer',
]
class LambdaLayer(Layer):
"""A layer that takes a user-d... |
fccb2c3b072d8567d49d134c06bffb657927a89b1dddda4a8d1c16d103f25d4f | Python | 7,821 | 184 | # coding=utf-8
# Copyright 2018 Google AI, Google Brain and Carnegie Mellon University Authors and the HuggingFace Inc. team.
# Copyright (c) 2018, NVIDIA CORPORATION. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the Lice... |
8b0929629350557a12c312bddf59887191d7ee0a1b28affd0239d74aece9f203 | Python | 7,824 | 169 | import numpy as np
import torch
from transcal.utils import get_weight, ECELoss, VectorOrMatrixScaling, TempScaling, CPCS, TransCal, Oracle
from transcal.TransCal import cal_acc_error
class ECE:
def __init__(self, n_bins=10):
self.n_bins = n_bins
self.n_samples = 0
self.correct = [[] for ... |
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