sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
bc7f6ebc1aa2dade3aa6c78c25a603b8e42e364194b43d8e5b4b029b89ccdac0 | Python | 24,405 | 663 | """`Runnable` that can fallback to other `Runnable` objects if it fails."""
import asyncio
import inspect
import typing
from collections.abc import AsyncIterator, Iterator, Sequence
from functools import wraps
from typing import TYPE_CHECKING, Any, cast
from pydantic import ConfigDict
from typing_extensions import ov... |
9c52ab4b77d010a0acf1ed77c313bd55150301857b111674374eb47af4f5d227 | Python | 24,481 | 557 | from PyQt5.QtWidgets import (QApplication, QComboBox, QGridLayout, QGroupBox, QLabel, QPushButton,
QFileDialog, QMessageBox, QWidget, QSizePolicy, QCheckBox)
from matplotlib.backends.backend_qt5agg import FigureCanvas
from matplotlib.backends.backend_qt5agg import NavigationToolbar2QT as NavigationToolbar
impo... |
a31d01e7a20d6259087a43be39a689fc29d32e185b396a2a1ec4a1a644a477e2 | Python | 24,500 | 560 | # -*- coding: utf-8 -*-
import os
from datetime import datetime
import copy
from tqdm import trange
import numpy as np
import pandas as pd
import torch
from torch.utils.data import TensorDataset, DataLoader
from .model import ModuleUnit
from .utils import DataReader, countdown
class BTSTN:
def __init__(
... |
b9540b09810dd1f84c11f9bedc0bfdd1b4d338023691510c318cc87d066c0e6d | Python | 24,501 | 683 |
# This file helps to compute a version number in source trees obtained from
# git-archive tarball (such as those provided by githubs download-from-tag
# feature). Distribution tarballs (built by setup.py sdist) and build
# directories (produced by setup.py build) will contain a much shorter file
# that just contains t... |
69eb523d00839469d7bf314125a08f1e911a1942f70cfce5ecf7748fb9f17776 | Python | 24,502 | 673 | import os
os.environ["CUDA_VISIBLE_DEVICES"]="2"
import sys
sys.path.insert(0,"/examples")
from modulusDL.models.arch import CustomModuleArch, SumMultiplicationArch, HypernetFullyConnectedFlexiLayerSizeArch, FullyConnectedFlexiLayerSizeArch, InheritedFullyConnectedFlexiLayerSizeArch, SingleInputInheritedFullyConnectedF... |
5374b8a1ef26548d13a1e91db508d1bdda92e700f32ea5c92b7bfc2a406ef2d7 | Python | 24,520 | 690 | """Core benchmark runner: phantom → simulate → wo rec → metrics.
Each synthetic case shells out to ``wo rec`` so the benchmark proves
the exact CLI workflow. The ``cli_command.sh`` saved alongside each
case can be copy-pasted for production use.
"""
from __future__ import annotations
import json
import logging
impor... |
b0c41ac2401a2e10b34a279fe7a81f72ede1e92da0137327cdc7a92fd9d30666 | Python | 24,544 | 455 | """DDSurfer dual-stream temporal attention network."""
from __future__ import annotations
from functools import partial
from typing import Sequence
import torch
from torch.utils.checkpoint import checkpoint
import torch.nn as nn
import torch.nn.functional as F
from model.cmunext import (AttentionGate3D, CMUNeXtBloc... |
a2ca9ae1203dd6db693ad9773d51b072804c994844ea5a80a8c48353391b94b0 | Python | 24,584 | 532 | """
Module for generating a specific plot on one matplotlib axis.
Author: jonas.braun@epfl.ch
"""
import os
import sys
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
from scipy.ndimage import gaussian_filter
from scipy.stats import mannwhitneyu
from twoppp import plot as myplt
from twoppp... |
2025b6e0f1e6d27d281c25cbae0e518b157d02a315c53259d04fafd509c61e7d | Python | 24,589 | 820 | # Copyright 2021 AlQuraishi Laboratory
# Copyright 2021 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
#
# U... |
7be0036fda3c24f75db870195d4795b4b93b678faac4497bb235d99fc1750252 | Python | 24,589 | 798 | import datetime
import json
import traceback
import numpy as np
class AcqEngMetadata:
CHANNEL_GROUP = "ChannelGroup"
CORE_AUTOFOCUS_DEVICE = "Core-Autofocus"
CORE_CAMERA = "Core-Camera"
CORE_GALVO = "Core-Galvo"
CORE_IMAGE_PROCESSOR = "Core-ImageProcessor"
CORE_SLM = "Core-SLM"
CORE_SHUTTE... |
be13575f63dd9f377a7a6519c880ede68d08dec24a8839e09e0184adf96454c4 | Python | 24,611 | 521 | from typing import Optional, List
import os
import lmdb
import random
import torch
import numpy as np
import os.path as osp
from argparse import Namespace
import pickle
import gdown
from tqdm import tqdm
from apsw import Connection
import torch.nn.functional as F
from torch_geometric.utils import scatt... |
5d2127c95ac3026e05a57a0ee7640ea0e50520c115e8f487d5c8e0b4870365b7 | Python | 24,640 | 931 | #!/usr/bin/env python
# coding: utf-8
# In[1]:
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
import pingouin as pg
seed = 100
np.random.seed(seed)
get_ipython().run_line_magic('matplotlib', 'inline')
# %config InlineBackend.figure_format = 'retina'
from scipy import s... |
85c3969b6cadd237a4425f62f3c73eb8195ab0982f9b3bc38be9464a4dc5f750 | Python | 24,640 | 608 | import logging
import cv2
import numpy as np
import math
import os
from nowcasting.config import cfg
logger = logging.getLogger(__name__)
def load_mnist(training_num=50000):
"""Load the mnist dataset
Parameters
----------
training_num
Returns
-------
"""
data_path = os.path.join(cf... |
0b92d75285d1741f2909502a323d0bf8fb536afcd33110686728cf5db2708cb5 | Python | 24,732 | 694 | import numpy as np
import pytest
import time
from pycromanager import Acquisition, Core, multi_d_acquisition_events
from pycromanager.acquisition.acquisition_superclass import AcqAlreadyCompleteException
def check_acq_sequenced(events, expected_num_events):
return isinstance(events, list) and len(events) == expec... |
8074244b174568124591047715a01e063c5f198466b2898e205a04c42899472d | Python | 24,733 | 547 | import numpy as np
import scipy.sparse as sp
import torch as th
from sklearn.preprocessing import OneHotEncoder
def encode_onehot(labels):
labels = labels.reshape(-1, 1)
enc = OneHotEncoder()
enc.fit(labels)
labels_onehot = enc.transform(labels).toarray()
return labels_onehot
def preprocess_feat... |
8151fbf38c1e59a5d49ceb57ff34003b2600c045f6c992b73196866c749eaa9c | Python | 24,741 | 691 | """
Created by
@author Shengze Cai
"""
import os
os.environ["TF_CPP_MIN_LOG_LEVEL"] = "2"
import tensorflow as tf
if tf.__version__ >= "2.0.0":
import tensorflow.compat.v1 as tf
tf.disable_v2_behavior()
import numpy as np
import time
# ====================================================================
#... |
8f77fbf1e34f6ab246b4ce398971d00149c5e07d0160f6eff9c6a19db2b8eb94 | Python | 24,761 | 392 | import pandas as pd
import numpy as np
from sklearn.model_selection import StratifiedGroupKFold, StratifiedKFold
from bernn.utils.utils import plot_confusion_matrix, scale_data, get_unique_labels, to_csv, scale_data_per_batch
def get_harvard(args, path='data'):
"""
Args:
path: Path where the csvs can... |
ec163e4b6f3d24847c7cd256990d90d5ca474fff2bc2cc9797074ba3bcef4dcc | Python | 24,785 | 631 | """`Runnable` that manages chat message history for another `Runnable`."""
from __future__ import annotations
import inspect
from collections.abc import Callable, Sequence
from types import GenericAlias
from typing import (
TYPE_CHECKING,
Any,
)
from pydantic import BaseModel
from typing_extensions import ov... |
688dca4c8f07ef480f117b8cae1b3fa692a1d2f3b299ef1217918db5a3dc6908 | Python | 24,800 | 743 | import scipy.sparse
from rfdiffusion.chemical import *
from rfdiffusion.scoring import *
def generate_Cbeta(N, Ca, C):
# recreate Cb given N,Ca,C
b = Ca - N
c = C - Ca
a = torch.cross(b, c, dim=-1)
# These are the values used during training
Cb = -0.58273431*a + 0.56802827*b - 0.54067466*c + C... |
603c2de9c883b2c95df560fa18704b0dbae22f5b1e571e8f5033a268177a4875 | Python | 24,881 | 571 | import matplotlib
matplotlib.use('agg')
import matplotlib.pyplot as plt
from scipy import interp
from sklearn.metrics import auc
import pandas as pd
import numpy as np
import random
import sys
import os
from pathlib import Path
import pickle
import json
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '2'
import wa... |
6c5096ace8186873236483ac0f016471b184c9ed5be21917b02fb0ce781cd105 | Python | 24,891 | 579 | """Tests for motornet.environment — Environment base class and RandomTargetReach."""
import numpy as np
import pytest
import torch
from motornet.effector import ReluPointMass24, RigidTendonArm26
from motornet.environment import Environment, RandomTargetReach
from motornet.muscle import RigidTendonHillMuscleThelen
#... |
9810b0ead849a359468ec825ce7cbb67b3c8e2facbea838307c05a6ee11e6540 | Python | 24,895 | 751 | from sklearn.model_selection import RepeatedKFold
from sklearn.metrics import mean_squared_error
from SMdRQA.RQA_functions import *
from SMdRQA.RQA2 import *
import ast
import memory_profiler
from scipy.interpolate import pchip_interpolate
from functools import partial
from p_tqdm import p_map
import numpy as np
from s... |
0fa055c8c75e355449c23fa2a4c193dc4c006feb819d8ef501e6a6bac0d8ee28 | Python | 24,900 | 598 | import numpy as np
import glob
import os
import sys
BASE_DIR = os.path.dirname(os.path.abspath(__file__))
ROOT_DIR = os.path.dirname(BASE_DIR)
sys.path.append(BASE_DIR)
DATA_PATH = os.path.join(ROOT_DIR, 'data','s3dis', 'Stanford3dDataset_v1.2_Aligned_Version')
g_classes = [x.rstrip() for x in open(os.path.join(BASE_... |
ae69195d61b8e94e47aab0082cb2bf7ffae4b3f98ab55a68bc52dc4fd8bba81b | Python | 24,931 | 578 | '''
1. Normalize features of shape (N, sphere_basis, C),
with sphere_basis = (lmax + 1) ** 2.
2. The difference from `layer_norm.py` is that all type-L vectors have
the same number of channels and input features are of shape (N, sphere_basis, C).
'''
import torch
import torch.nn as nn
def get_... |
ee9f69176f0db4fcee6f8652f70463ba8af5cde0a56e3739a07215dbdfea98de | Python | 24,933 | 746 | """Test functionality related to prompts."""
import re
from collections import ChainMap, UserDict
from pathlib import Path
from types import MappingProxyType
from typing import Any, Literal
from unittest import mock
import pytest
from packaging import version
from syrupy.assertion import SnapshotAssertion
from langc... |
677aaefc3d4d6204ae8e52f7cca0504d6c2b9cd5c4b5fa9cdd15876adbe46af4 | Python | 24,969 | 538 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Sep 10 11:43:50 2021
@author: shni2598
"""
import frequency_analysis as fqa
import firing_rate_analysis as fra
import numpy as np
#from get_onoff_cpts import get_onoff_cpts
#%%
def get_phase_sync(spk_mat_MUA_1, spk_mat_MUA_2, dura, \
... |
68a8e77542c35ba2ffaa624b230600289e7af9446438b1964a93b68c9b91b928 | Python | 24,985 | 748 |
# todo: 1. DeprecationWarning: an integer is required (got type numpy.float64).
# Implicit conversion to integers using int is deprecated, and may be removed in
# a future version of Python. y = torch.tensor([Y], dtype=torch.long)
# todo: 2.Creating a tensor from a list of numpy.ndarrays is extremely slow.
# Plea... |
77735e35a9010be2b48503e841f8c0ed9d927c56f999d2817e7fd3d237ad689d | Python | 25,046 | 693 | import copy
from functools import partial
import json
import logging
import os
import pickle
from typing import Optional, Sequence, List, Any
import ml_collections as mlc
import numpy as np
import pytorch_lightning as pl
import torch
from torch.utils.data import RandomSampler
from openfold.data import (
data_pipe... |
e261ba021142ab1e0f08e76e4de8166f0687511928d76ad6565ff19a1f403c7d | Python | 25,049 | 569 | # Imports
import sys
import os
import argparse
import inspect
from datetime import datetime
import numpy as np
from tqdm import tqdm
from math import ceil
from time import perf_counter, process_time
import torch
import torch.optim as optim
try:
from torchdiffeq.__init__ import odeint_adjoint as odeint
except Impo... |
f56eeec55723edf4498af620b027baeb9780bb055c17cc67607280a671629ab5 | Python | 25,070 | 522 | import argparse, os
from pathlib import Path
import numpy as np
import pandas as pd
from tqdm import tqdm
import matplotlib.pyplot as plt
from matplotlib.lines import Line2D
import seaborn as sns
from matplotlib.backends.backend_pdf import PdfPages
import matplotlib.ticker as mticker
import polars as pl
import re
from... |
390b0e1ef1cf426c6fa370eec417f354b31cda80de39b1836a2d7421be9fccb3 | Python | 25,072 | 572 | import unittest
import gc
import os
import matplotlib.pyplot as plt
import numpy as np
from pensa.clusters import \
obtain_clusters, wss_over_number_of_clusters, \
obtain_combined_clusters, wss_over_number_of_combined_clusters, \
write_cluster_traj
from pensa.statesinfo import \
get_discrete_states
f... |
6a0b4ecf854487a96717280fbd8961a4f513c2c5c396abacdd1142d223e8a0d8 | Python | 25,078 | 611 | """
Analyze perses calculations for a benchmark set of ligands annotated with experimental data
"""
# SDF filename containing all ligands annotated with experimental data
# Ligands should be annotated with experimental data using the SD tags
# EXP_BINDING_AFFINITY_IN_KCAL_PER_MOL
# EXP_BINDING_AFFINITY_IN_KCAL_PER_MO... |
293a0dc6fe52203debf4136c4b113c6a295a0282d5d85ff7f893404c286e2db3 | Python | 25,089 | 610 | """Derivations of standard content blocks from Google (GenAI) content."""
import base64
import re
from collections.abc import Iterator
from typing import Any, cast
from langchain_core.messages import AIMessage, AIMessageChunk
from langchain_core.messages import content as types
from langchain_core.messages.content im... |
370d4c422a0f1e465b46354989fb18cb35f28f257b77d902e438c8d84644c796 | Python | 25,089 | 548 | import warnings
import numpy as np
import torch
import gymnasium as gym
from typing import Any
class Environment(gym.Env, torch.nn.Module):
"""Base class for environments.
Args:
effector: :class:`motornet.effector.Effector` object class or subclass. This is the effector that will evolve in
the environm... |
a7441996c0d3e687aad108f0a7409f8a72efc4f7f148b59d78cdd480355eba90 | Python | 25,103 | 665 | import multiprocessing
import re
import warnings
from abc import ABCMeta, abstractmethod
from collections import OrderedDict
from pathlib import Path
from typing import Any, Callable, Dict, List, Sequence, Tuple, Union
import arviz as az
import cmdstanpy
import matplotlib.pyplot as plt
import numpy as np
import pandas... |
a25bfa026fd03ae4a7ae55e54eaf627fced3f20f0824ac0526d79737aa962b47 | Python | 25,109 | 535 | """cohort/batch-analysis endpoints: loading an accumulated cohort
spreadsheet, running the one thing that genuinely needs a real numerical
library (inferential statistical tests, via scipy.stats - everything else
in the cohort workspace, descriptive stats and plotting, runs client-side
in JS, see frontend/src/workspace... |
52588b4b44773664fb665eabb02930e26ade3e6426952c792ec0354e1662e313 | Python | 25,112 | 715 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Interfaces to deal with the various types of fieldmap sources.
.. testsetup::
>>> tmpdir = getfixture('tmpdir')
>>> tmp = tmpdir.chdir() # changing to a temporary directory
... |
69a161f814212148e3f920035621be1a6be6a8fd44be9d8e8d6ec1693c20ea0f | Python | 25,130 | 591 | ####################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for d... |
47e36f1131a351dcd014fa92e70f61e0fa7551addcc68aec191e26e86bba8ddc | Python | 25,155 | 740 | import torch, math
import torch.nn as nn
from typing import Optional, Tuple
from h3xsemble.model.primitives import Linear, ipa_point_weights_init_, LayerNorm
from h3xsemble.utils.rigid_utils import Rotation, Rigid
from h3xsemble.utils.tensor_utils import (
dict_multimap,
permute_final_dims,
flatten_final_di... |
08706ff6b29a269e40b6c1268642de8ae3f6f4fc6c0b28144a209b2ca92219cf | Python | 25,184 | 690 | from __future__ import annotations
import logging
import os
import warnings
from typing import TYPE_CHECKING
import numpy as np
import torch
from scvi import REGISTRY_KEYS, settings
from scvi.data import AnnDataManager
from scvi.data._compat import registry_from_setup_dict
from scvi.data._constants import _MODEL_NAM... |
40cec874deae943b2ac57884d0f21c1bdb26245c92c4cbc4bbdf9ec381e59246 | Python | 25,197 | 749 | ###########################################################################################
# Elementary Block for Building O(3) Equivariant Higher Order Message Passing Neural Network
# Authors: Ilyes Batatia, Gregor Simm
# This program is distributed under the MIT License (see MIT.md)
################################... |
b9d27ff4307e233d127a86fd5d5e39365ade2f3ac75264f479ff8b7e76efbab7 | Python | 25,198 | 629 | import os
import pandas as pd
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
import networkx as nx
from sklearn.metrics import confusion_matrix
from sklearn.metrics import ConfusionMatrixDisplay
import re
from iteround import saferound
from sklearn.utils import check_matplotlib_support
from... |
6c0f6a2896e78928e18a3764468fb89c3b1cab5a981665accb957f8b03c39d69 | Python | 25,246 | 693 | from builtins import print
import numpy as np
import pandas as pd
import matplotlib
matplotlib.use('agg')
import matplotlib.pyplot as plt
# matplotlib.rcParams['font.family'] = 'sans-serif'
# matplotlib.rcParams['font.sans-serif'] = 'Arial'
import os
import operator
import utils
from utils.constants import UNIVARIA... |
9a598f4fd05c60c9a571664a7ba087765982b2a830d1cc24703a0826146ff1e8 | Python | 25,254 | 538 | import os
import matplotlib.pyplot as plt
import numpy as np
import torch
from torch.utils.data import TensorDataset
from data import generate_recog_data, generate_recog_data_batch, GenRecogClassifyData
from net_utils import load_from_file
import plotting, networks
def choose_gen_data(net, chooseT=False... |
1a922fca6a77276d820df9d04ae0e8472b71e38ae424907186893f4b579dd58e | Python | 25,266 | 710 | # Copyright 2024 DeepMind Technologies Limited
#
# AlphaFold 3 source code is 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... |
983ce946009b48b98ec1261482c35f841fdbcfc97716d14f83bcea70b6680167 | Python | 25,281 | 652 | from pathlib import Path
from time import time
import random
from collections import defaultdict
import argparse
import warnings
from tqdm import tqdm
import numpy as np
import torch
from Bio.PDB import PDBParser
from Bio.PDB.Polypeptide import three_to_one, is_aa
from Bio.PDB import PDBIO, Select
from openbabel impor... |
d60279f8259dc8776afa08d9dfb067f70f8d557cc7c0348b7cfff49babc6dec9 | Python | 25,284 | 510 | # Code from: https://github.com/PDillis/stylegan3-fun
import os
import re
import json
from typing import List, Tuple, Union, Optional
from collections import OrderedDict
from locale import atof
import click
import numpy as np
import torch
import torch.nn.functional as F
import dnnlib
# ----------------------------... |
7e9392e8dc73ac9ed52b35ceb40f2ee62bc4b008d8db41e96bf659dab1362a20 | Python | 25,286 | 663 | import torch
from torch_geometric.data import Batch, Data
from typing import Tuple, List
from pdearena.pl_models.pdemodel import PDEModel
from pdearena.configs.config import CFDConfig, PretrainedCFDConfig
from pdearena.configs.registry import get_config
from pdearena.utils.metrics import ErrorStats
from pdeare... |
d0d58ba89f9c5cc0b56c4bde70a503cfdca4c5644af120d6e51632b68ad6f8e7 | Python | 25,302 | 622 | import pytest
from qupkake.xtbp import XTBP, RunXTB
from rdkit import Chem
# Mock xtb output data
xtb_output = """
-----------------------------------------------------------
| ===================== |
| x T B ... |
4e62de23bad29aa6dfab4ff870edfcac7a1a650621790e9a144c33217b03dd25 | Python | 25,325 | 863 | import mxnet as mx
from nowcasting.ops import \
conv3d, conv3d_act, conv3d_bn_act, \
conv2d, conv2d_act, conv2d_bn_act, \
deconv3d, deconv3d_act, deconv3d_bn_act, \
deconv2d, deconv2d_act, deconv2d_bn_act, \
fc_layer, fc_layer_act
from nowcasting.config import cfg
### Network structure
def encode_... |
5724ea3c0858fa44cc7e02b077f59f3b826b0cb5b266aea03e828b08776f095c | Python | 25,328 | 851 | """==============
Motif pipeline
==============
The motif pipeline runs a set of motif discovery and enrichment
analysis on a set of intervals.
* Motif discovery using MEME
* Motif detection using MAST
* requires a set of known motifs
Usage
=====
See :ref:`PipelineSettingUp` and :ref:`PipelineRunning`... |
113f4ab0929e156a3249ac66438064add1219dbec92765ac53d447d39440474d | Python | 25,341 | 691 | import numpy as np
import torch
import torch.nn as nn
import torchvision
from torchvision import models
from torch.nn import init
import torch.nn.functional as F
# convnet without the last layer
class ContBatchNorm3d(nn.modules.batchnorm._BatchNorm):
def _check_input_dim(self, input):
if input.dim() != 5... |
c0367da54a4310ddeecf97bec53ce7378e4c738e4c3f9433d1415334612d116e | Python | 25,347 | 835 | # Copyright 2021 AlQuraishi Laboratory
# Copyright 2021 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
#
# U... |
d2407d2e485b25976c92f61bb69f83173f647765e9739a2f750943e032f69285 | Python | 25,348 | 534 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of... |
42aa009a6f283704fadaba845b6a647204ecd0b95dafd9633178b512d1c84c86 | Python | 25,365 | 651 | from re import sub
import copy
import os
from .tokenizer import Tokenizer
from .data_helper import DataHelper
from .token_merger import ClassifierChunkParser
class Normalizer():
def __init__(self,
half_space_char='\u200c',
statistical_space_correction=False,
... |
ba63880480fd31a73c6b182a4b886c6251bf8822cebe29fc96aa071c16c6bd72 | Python | 25,410 | 506 | import os
import pathlib
import time
from typing import Union, List, Literal
import equinox as eqx
import numpy as np
import torch
import torch.nn.functional as F
import wandb
from einops import rearrange, repeat, pack, unpack, reduce
from torch_scatter import scatter, scatter_std
from torchdiffeq import odeint as nn_... |
e2e0a7f1ec3e6d3086c3e748cb4b0894c1633f37bd717649a3d1a767fb98317d | Python | 25,413 | 504 | import os
import pathlib
import time
from typing import Union, List, Literal
import equinox as eqx
import numpy as np
import torch
import torch.nn.functional as F
import wandb
from einops import rearrange, repeat, pack, unpack, reduce
from torch_scatter import scatter, scatter_std
from torchdiffeq import odeint as nn_... |
40699331cbf63a3f50497692c4789cb016747bbb19a6780b92b0855486c0afb2 | Python | 25,425 | 653 | import pandas as pd
import numpy as np
import random
import sys
import os
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '2'
import warnings
warnings.filterwarnings("ignore", message="numpy.dtype size changed")
warnings.filterwarnings("ignore", message="numpy.ufunc size changed")
from multiprocessing import Process, M... |
84ff372845db72c7d406d1eaeb5ce9aa7e3733b974222db0b3cd9033ea8a3020 | Python | 25,487 | 558 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
#Version 5.5
import xml.dom.minidom as dom
import xml.dom
from decimal import *
import sys
import os
import datetime
#from Numeric import *
# Dokument erzeugen
implement = xml.dom.getDOMImplementation()
###################Globale Variablen###################
musicbrain... |
d2fbf50da1196a336f95f3f18c26c2bc2d0a02b76346a4cd63c0c70ee68f933b | Python | 25,509 | 617 | import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import pytorch_lightning as pl
from torchmetrics import R2Score
from pytorch_lightning.strategies import DDPStrategy
import seaborn as sns
import torch
from lightning_lite.utilities.seed import seed_everything
from torch.optim import SGD, Adam
fro... |
9bfc34f5d36f625671eb47f671f31538da6664d133c9b7094e44b1b09391ebb2 | Python | 25,510 | 508 | #!/usr/bin/env python3
import os
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '1'
import sys
import json
import keras
from keras import layers
from keras import backend as K
import tensorflow as tf
from talos.utils.exceptions import TalosParamsError
from time import time
import pandas as pd
import numpy as np
import logging
i... |
d93952ae338e365ed43300b83f7ee497fdaa56a1e8e98e82df79fb2b1c8cfd19 | Python | 25,529 | 728 | """
2023.08.30
author: femke.hurtak@epfl.ch
Script to compute the connectivity statistics for specific neuron sets.
"""
import os
import pandas as pd
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1.inset_locator import inset_axes
import seaborn as sns
import numpy as np
from scipy import stats, sparse
i... |
342b7a668aa3d688b413e588f9bbbd79452828726ba9d00d8adc73c742d2ae78 | Python | 25,554 | 664 | # main file for CNN classifier
# Created: 9/2/2021
# Status: in progress
# CUBLAS_WORKSPACE_CONFIG=:4096:8 python inception.py
from collections import namedtuple
import warnings
import torch
from torch import nn, Tensor
import torch.nn.functional as F
from typing import Callable, Any, Optional, Tuple, List
from sklear... |
80c3c18af1928a70e9755dd4e515897fcc78c0efa59b6fddf8a0228a14b427ab | Python | 25,555 | 615 | # Copyright (c) Microsoft Corporation.
# Licensed under the MIT license.
import functools
from typing import Optional
import os
import h5py
import torch
import torchdata.datapipes as dp
from torch_geometric.data import Data
from pdearena.data.datapipes_common import build_datapipes
from pdearena.configs.confi... |
cc669467195c44443c8939f11a3c464d8268e917ecab3e7468c9e884713b03f0 | Python | 25,581 | 765 | """Tracer that streams run logs to a stream."""
from __future__ import annotations
import asyncio
import contextlib
import copy
import threading
from collections import defaultdict
from pprint import pformat
from typing import (
TYPE_CHECKING,
Any,
Literal,
TypeVar,
overload,
)
import jsonpatch ... |
a52974116d7cfd2f324369504f1a923ee7e7e0176a19bf444cff924e1374a353 | Python | 25,593 | 616 | # Copyright 2020 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed... |
aad92cb520a18e4f17a8011be0c96bdd920cc13b9adb7a291341abb7e06dafde | Python | 25,676 | 587 | # Imports
import sys
import os
import argparse
import inspect
from datetime import datetime
import numpy as np
from tqdm import tqdm
from math import ceil
from time import perf_counter, process_time
import torch
import torch.optim as optim
try:
from torchdiffeq.__init__ import odeint_adjoint as odeint
except Impo... |
c88c29f306b6cb28dc30760354d6c1c6dd11568af665b60a62848bca5600f472 | Python | 25,704 | 589 | # Imports
import sys
import os
import argparse
import inspect
from datetime import datetime
import numpy as np
from tqdm import tqdm
from math import ceil
from time import perf_counter, process_time
import torch
import torch.optim as optim
try:
from torchdiffeq.__init__ import odeint_adjoint as odeint
except Impo... |
5ed48a935c071724a6dba84bd474a75b424ab8a023efac0f58b9fcdd4d288516 | Python | 25,711 | 783 | """
Tables for processing individual recordings
"""
"""
Main tables for loading individual recordings and processing responses
"""
from glob import glob
import os
import warnings
import numpy as np
import pandas as pd
import datajoint as dj
from scipy.interpolate import interp1d
from scipy.signal import savgol_filt... |
9563d1ca9e991239a1b1547f581fcc32955b74669002cdc59bb11b926ce7ac63 | Python | 25,715 | 598 | """
Defines model classes to store thumbnail data in text and/or image formats.
"""
import json
from typing import Text
import numpy as np
import pandas as pd
from io import BytesIO
from PIL import Image
import base64
import copy
from .datasets import ColumnarData
from .utils import Field, standardize_json
class Thum... |
e56a82b27a14436def0e17b6e13fe40ee5382c12c52a9c1c749bcc555bc22d39 | Python | 25,715 | 618 | #!/usr/bin/env python
import argparse
arg_parser = argparse.ArgumentParser()
arg_parser.add_argument("chain_file", help="list of PDB and chain ids and their corresponding assemblies")
arg_parser.add_argument("structures_directory", help="directory where structures are stored")
arg_parser.add_argument("output_directory... |
cda12c606eb8a83fa1a3077302a18de0ac19bf131437d3513f60793a2ccd3e9d | Python | 25,783 | 724 | # Copyright (c) Microsoft Corporation.
# Licensed under the MIT license.
from typing import List, Optional, Tuple, Union
import torch
from torch import nn
import math
from pdearena.utils.activations import (
ACTIVATION_REGISTRY,
SinusoidalEmbedding
)
from pdearena.configs.config import Config
from torch_geome... |
447b882e1a722e3d61aac98ca1a899e52461962bb0dddc8e6b81ad7828d7a178 | Python | 25,850 | 710 | import logging
import platform
import tempfile
from pathlib import Path
import dask.array as da
import h5py
import numpy as np
import pytest
import tiledb
from tifffile import tifffile
from astrocast.helper import SampleInput
from astrocast.preparation import Delta, IO, Input, MotionCorrection
class TestDelta:
... |
ddd714b9de3582b7cdae315108c98e2a2cf94de1337a6f4feeff420128f20f33 | Python | 25,855 | 735 | import ast
import glob
import logging
import traceback
from abc import ABC
from typing import Any, Tuple, Union
import numpy as np
import torch
from rdkit import Chem
from rdkit.Chem import AllChem, Descriptors3D, Lipinski
from rdkit.Chem.rdmolops import GetAdjacencyMatrix
from torch_geometric.data import Data
from .... |
283aa6c58fa9c5d0f0e935e54eb0cec683b8c4d2aacea3f1f1f18dff07402632 | Python | 25,856 | 573 | import copy
import math
import numpy as np
import torch
import torch.nn as nn
import warnings
class MLP(nn.Module):
def __init__(self, input_size, hidden_size):
super(MLP, self).__init__()
self.input_size = input_size
self.hidden_size = hidden_size
self.fc1 = torch.nn.Linear(self.i... |
cf0fcfc59cf136f7bdaa5ac83a39e2afba72ac8b711d25fb683f6ceeded6850b | Python | 25,856 | 804 | # This file is a part of the `allegro` package. Please see LICENSE and README at the root for information on using it.
import torch
from torch.library import triton_op, wrap_triton
import triton
import triton.language as tl
from nequip.nn import scatter
from ._contract import Contracter
from ._lexsort import lexsort
... |
464b2cd7091564b2d4b7f27f93b0b196c8504ef511c044207f9f8e360afb7311 | Python | 25,859 | 482 | from __future__ import print_function
import numpy as np
import logging
import copy
from openmmtools.alchemy import AlchemicalState
_logger = logging.getLogger("lambda_protocol")
_logger.setLevel(logging.INFO)
class LambdaProtocol(object):
"""Protocols for perturbing each of the compent energy terms in alchemica... |
991d0638944abbde7565fcea051221679668d617351118d041b39020727f3836 | Python | 25,860 | 670 | import os
os.environ["CUDA_VISIBLE_DEVICES"]="2"
import sys
sys.path.insert(0,"/examples")
from modulusDL.models.arch import CustomModuleArch, InheritedFullyConnectedFlexiLayerSizeArch, FullyConnectedFlexiLayerSizeArch, SingleInputInheritedFullyConnectedFlexiLayerSizeArch, CaseIDtoFeatureArch
from modulusDL.eq.pde impo... |
00c8750966bb638cef68dfde3645dcaf0fce53cbb0feee1ea0c8d6d96725c7ee | Python | 25,876 | 676 | from collections import namedtuple
from functools import partial
from typing import Any
try:
from collections import Iterable
except:
from collections.abc import Iterable
import numpy as np
import torch
from skimage.transform import rescale
def transform_function(img, behavior, key):
"""
Function th... |
c89fc8b759da364891d6ec0badb20810482605be10f7a6e7ce0e1b1d6e9d242d | Python | 25,877 | 582 | #!/usr/bin/env python
import logging
import pysam
import json
import argparse, sys, os.path
import math, time
from argparse import RawTextHelpFormatter
import svtyper.version
from svtyper.parsers import Vcf, Variant, Sample, confidence_interval
from svtyper.utils import *
from svtyper.statistics import bayes_gt
# -... |
57c1ac70174b647dd7c12059681ecc8d507d882e541d363476bcf71d2e3ec521 | Python | 25,898 | 636 | import os.path
import torch
# from protein_learning.common.data.data_types.protein import safe_load_sequence
from collections import defaultdict
# from rde.utils.protein.pdb_utils import (
# extract_atom_coords_n_mask_tensors,
# extract_pdb_seq_from_pdb_file,
# )
from rde.utils.protein.helpers import disable_t... |
5194534355064af0a8b2709554be52f25e0f65319baf97d70a31ba81f38b7638 | Python | 25,901 | 678 | """
Classes for creating patient objects compatible with TWSTRS.
"""
import logging
import numpy as np
import pandas as pd
#import simdkalman
from scipy import ndimage
from scipy.signal import medfilt
from .structural_features import compute_distances
from .utils import pre_high_pass_filter, pre_low_pass_filter
from .... |
ce1fa471c584b74635cbe5545d510178b6c278b4a58b33a57a66c602648fac78 | Python | 25,901 | 483 | from __future__ import print_function
import numpy as np
import logging
import copy
from openmmtools.alchemy import AlchemicalState
logging.basicConfig(level=logging.NOTSET)
_logger = logging.getLogger("lambda_protocol")
_logger.setLevel(logging.INFO)
class LambdaProtocol(object):
"""Protocols for perturbing eac... |
b74ecb35b56b3d95cc60c973b8c29738d88bac45fe5a48ccd2be234d960ca497 | Python | 25,904 | 668 | import os
os.environ["CUDA_VISIBLE_DEVICES"]="1"
import sys
sys.path.insert(0,"/examples")
from modulusDL.models.arch import CustomModuleArch, InheritedFullyConnectedFlexiLayerSizeArch, SingleInputInheritedFullyConnectedFlexiLayerSizeArch, CaseIDtoFeatureArch
from modulusDL.eq.pde import NavierStokes_CoordTransformed
i... |
b89f733269990d0b9630cf8cff5669f1e0b112a4de6ad1ed9a6d1e8d377ef556 | Python | 25,920 | 589 | import Bio.PDB
import Bio.PDB.vectors
import torch
from torch.utils import data
import torch.nn.functional as F
import json
import numpy as np
import os
import re
import glob
import common.atoms
import seq_des.util.canonicalize as canonicalize
import seq_des.util.voxelize as voxelize
CHI_BINS = np.linspace(-np.pi,... |
27512f23140743211ca70281e779b3057a67c211682e7c3b6ba0851a7550bb84 | Python | 25,926 | 513 | import torch
import numpy as np
from typing import Any, Union
class Skeleton(torch.nn.Module):
"""Base class for `Skeleton` objects.
Args:
dof: `Integer`, number of degrees of freedom of the skeleton. Typically this is the number of joints.
space_dim: `Integer`, the dimensionality of the space in which t... |
a4f607691553dc36de9bd5619e44f5f4d7cfbfd3969820f36ce9915921c0e5cd | Python | 25,967 | 679 | # This file takes all available input data and trains the regressors
# using the prescribed preprocess methods.
# It displays time domain estimates for all data files as well as
# sensitivity plots for sensor channels and estimates
import time
import os
import numpy as np
import pandas as pd
import matplotlib.pyplot ... |
3370f52580f8cc9458420f61cd36eb6fe6abde5cdd9cffcfc130bb7258a99608 | Python | 25,994 | 508 | ''' Test module for AE trainer.
:Version:
1.0
:Date:
08.02.2016
:Author:
Jan Melchior
:Contact:
JanMelchior@gmx.de
:License:
Copyright (C) 2016
This program is free software: you can redistribute it and/or modify
it under the terms o... |
f3653b44da2b6b44037f5d7d5df4170f81906ebcdcdbeeb64cd184cfbbd719b4 | Python | 26,076 | 739 | import logging
import os
from fcest.models.sliding_windows import SlidingWindows
from fcest.models.wishart_process import VariationalWishartProcess, SparseVariationalWishartProcess
from fcest.helpers.array_operations import to_correlation_structure
from fcest.helpers.data import to_3d_format
import gpflow
import matpl... |
f81c4458dae15a397546383197191a5956d4e245ce38e385490863ca4aed8ec9 | Python | 26,078 | 549 | #!/usr/bin/env python
# =============================================================================
# MODULE DOCSTRING
# =============================================================================
"""
Test State classes in mcmc.py.
"""
# ==========================================================================... |
a016daddf997bb56a5890f663d3e3f8b15f72378c8d4882833cd38457a9d3707 | Python | 26,099 | 545 | import chrombpnet.parsers as parsers
import os
from chrombpnet.data import DefaultDataFile, get_default_data_path
from chrombpnet.data import print_meme_motif_file
import chrombpnet.pipelines as pipelines
import copy
import pandas as pd
import logging
logging.getLogger('matplotlib.font_manager').disabled = True
# invo... |
4a5fc589a344deedbc23a48e89480a876f1ad1e6f474f16d2dd5bb40dbf1a973 | Python | 26,102 | 633 | ####################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for d... |
4a467ab87037a0fb9f6c29d1f3962e0b6560567ade57128438d95a34dd276b2f | Python | 26,107 | 858 | """ Different kind of non linear activation functions and their derivatives.
:Implemented:
# Unbounded
# Linear
- Identity
# Piecewise-linear
- Rectifier
- RestrictedRectifier (hard bounded)
- LeakyRectifier
# Soft-linear
- Ex... |
e0ecdc558c248f471d08f492816c3b28fb06bc43b567853cde91406e2b46cd22 | Python | 26,131 | 771 | from typing import Any
from unittest.mock import MagicMock, patch
from packaging import version
from pydantic import BaseModel
from syrupy.assertion import SnapshotAssertion
from typing_extensions import override
from langchain_core.language_models import FakeListLLM
from langchain_core.messages import BaseMessage
fr... |
db07c1e4fcc7bbce5b9d68c1791dc5aa4d055dd8d7116530fe3485d46abf0e46 | Python | 26,162 | 619 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
train_ae_head.py
================
Train an AE encoder with domain adaptation (DANN / inverseTriplet / normae)
**without** any neural-network classification head.
Every epoch the training loop is:
1. Forward pass: enc, rec = AE(inputs)
2. Loss: reconstruction + gam... |
235198132e756402a1b4b20dca36f12e316cb8f14ced5c0a151f02e169b84c5a | Python | 26,166 | 737 | import torch.nn.functional as F
from torch_geometric.nn import GATConv, LayerNorm
from torch_geometric.nn import TopKPooling
import torch.nn as nn
from torch.nn import Linear
import torch
"""
Appling pyG lib
"""
######################################################################################
# origi... |
ccb961c3098b8a6dfb7546af346c0e5ad9c7fff0dc657a4679b3d0e2c178d8a2 | Python | 26,184 | 785 | #!usr/bin/python
## Pairwise distance estimation for homologous and non-homologous TCR CDR3 sequences
## immuno-Similarity Measurement by Aligning Receptors of T cell (iSMART)
## Apr 14th, 2018, first version
## Ultra-fast alignment version for iSMART, based on motif finding, July 15th, 2018
## Motif-guided iSMART (Mi... |
0fc75d1482bcfc0f095afd27a7d12323a6474e0e714bdc6560a9ba5abb81cb15 | Python | 26,232 | 582 | '''
The MSN class defining the cell
'''
from neuron import h
import numpy as np
import json
# Distributions:
'''
T-type Ca: g = 1.0/( 1 +np.exp{(x-70)/-4.5} )
naf (den): (0.1 + 0.9/(1 + np.exp((x-60.0)/10.0)))
'''
def calculate_distribution(d3, dist, a4, a5, a6, a7, g8):
'''
Used for setting the maximal c... |
2d4ca8a053fe24062d6b945daf44e2cc1c65331e98fc474509a9b3b258607a9b | Python | 26,257 | 601 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import xml.dom.minidom as dom
import xml.dom
from decimal import *
import sys
import os
import datetime
#from Numeric import *
# Dokument erzeugen
implement = xml.dom.getDOMImplementation()
###################Globale Variablen###################
task=None
choosen_tag={}... |
7d1d43d607b7d8f2d34da11bc4d476594029c5eab22face67ea2a6dd1f2a2068 | Python | 26,261 | 615 | """Caduceus model for Hugging Face.
"""
import math
from functools import partial
from typing import Optional, Tuple, Union
import torch
from mamba_ssm.modules.mamba_simple import Mamba, Block
from torch import nn
from torch.nn import functional as F
from transformers import PreTrainedModel
from transformers.modelin... |
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