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04b47956faf7178d215aa32173c00e7766d4bab71cdc428993653dc94ceb8ab2
Python
55
1
from escargot.prompter.prompter import ESCARGOTPrompter
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Python
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"""Modules relating to photogrammetry calculations."""
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Python
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from yass.deconvolve.run import run __all__ = ['run']
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Python
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"""Contains tests involving CC and family generation"""
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Python
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""" Compiled fixed-shape tensor-network algorithms. """
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Python
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from .image_loader import * from .subsample_mean import *
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Python
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""" Utilities for generating phy configuration files """
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Python
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from asap.trainer.trainer import Trainer, make_dataloader
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Python
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from flask_sqlalchemy import SQLAlchemy db = SQLAlchemy()
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Python
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"""Benchmark helpers for full CLI simulation scenarios."""
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Python
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# tzwin has moved to dateutil.tz.win from .tz.win import *
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Python
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from ._mda_viewer import MDAViewer __all__ = ["MDAViewer"]
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Python
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tencent_base_url = "https://quantum.tencent.com/cloud/quk/"
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Python
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from ._preview_viewer import Preview __all__ = ["Preview"]
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Python
60
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import cedalion.mlutils.cv import cedalion.mlutils.features
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Python
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from .ica_erbm import ICA_ERBM from .ica_ebm import ICA_EBM
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Python
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from yass.soft_assignment.run import run __all__ = ['run']
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Python
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"""A package that contains models that represent entities."""
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Python
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from ._npyio_impl import ( __doc__, DataSource, NpzFile )
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Python
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from . import mdoc, file, image, mrc, relion, transformations
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Python
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from rlign.rlign import Rlign from rlign.utils import Template
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import numpy as np arr = np.array([1]) np.nditer([arr, None])
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from .distro import main if __name__ == "__main__": main()
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# This file is protected via CODEOWNERS __version__ = "1.26.20"
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__all__ = ["eval"] from pandas.core.computation.eval import eval
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"""Contains tests involving (py)HMMer analysis and processing"""
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from .transformer_encoder import InterpretableTransformerEncoder
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__anthor__ = """DeepOmics lab""" __email__ = "yfsheng6@gmail.com"
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__all__ = ['normalization'] from . import ( normalization, )
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from .layers import * from .utils import * from .wrappers import *
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import numpy as np import sys import pylab as pl _, f = sys.argv
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""" Compute RF """ from yass.rf.run import run __all__ = ['run']
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from pandas.io.sas.sasreader import read_sas __all__ = ["read_sas"]
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# __init__.py # GUI version adapted from AIMS: __version__ = "0.9.3"
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from .task import AtomisticTaskFixed __all__ = [AtomisticTaskFixed]
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from . import acfunc, tau __all__ = ["acfunc", "tau", "spike_utils"]
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OUT_FORMAT_CONVERSION = { "t": "", "b": "b", "u": "bu", }
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""" run merge """ from yass.merge.run import run __all__ = ['run']
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from .escn import eSCN, eSCNLightning __all__ = [eSCN, eSCNLightning]
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"""Contains tests for modules that parse genbank files and load data"""
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from .train import cryoCARE_train from .predict import cryoCARE_predict
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""" Compute RF """ from yass.visual.run import run __all__ = ['run']
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from . import _version __version__ = _version.get_versions()['version']
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from .distancefrag import DistanceFragment __all__ = ["DistanceFragment"]
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from importlib.metadata import version __version__ = version(__package__)
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import importlib.metadata __version__ = importlib.metadata.version('sinto')
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from .painn import PaiNN, PaiNNLightning __all__ = [PaiNN, PaiNNLightning]
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from pkgutil import extend_path __path__ = extend_path(__path__, __name__)
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from . import evaluation, gcn_model, protein_graph, run_model, model_helpers
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""" Detecting spikes """ from yass.detect.run import run __all__ = ['run']
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__version__="2.2.3" __git_version__="0691c5cf90477d3503834d983f69350f250a6ff7"
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""" Clustering spikes """ from yass.cluster.run import run __all__ = ['run']
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"""Each script is a command callable when using the command line interface."""
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from .cli import main if __name__ == "__main__": raise SystemExit(main())
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# prerun to hack base abstract backend from .backend_factory import get_backend
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from .test_base import get_adata, TestBase __all__ = ["get_adata", "TestBase"]
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raise ModuleNotFoundError("Sorry PyTorch, but our NumPy is in the other folder")
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from cedalion.sigdecomp.multimodal.utils import validate_time_shifts, standardize
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from ._arduino_led_widget import ArduinoLedWidget __all__ = ["ArduinoLedWidget"]
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""" code package: initialization for core models and data processing modules. """
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from ._stride_tricks_impl import ( __doc__, as_strided, sliding_window_view )
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""" Adaptive CNN for Influenza Antigen Prediction """ __version__ = '1.0.0'
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""" run post process """ from yass.postprocess.run import run __all__ = ['run']
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from ._is_difficult_word import is_difficult_word __all__ = ["is_difficult_word"]
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from numpy._core.records import __all__, __doc__ from numpy._core.records import *
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from numpy._core.strings import __all__, __doc__ from numpy._core.strings import *
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def main(): print("Hello from amr-gnn!") if __name__ == "__main__": main()
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from ._remove_punctuation import remove_punctuation __all__ = ["remove_punctuation"]
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from yass.config.config import FrozenJSON, Config __all__ = ['FrozenJSON', 'Config']
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def main(): print("Hello from preprocess!") if __name__ == "__main__": main()
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def normalize_x_sf(df, scale=1e4): sf = df.sum(axis=0) / scale return sf.values
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from . import counts from . import readout_mitigation rem = readout_mitigation # alias
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#!/usr/bin/env python3 def test(): print("Successfully installed stereoscope CLI")
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from .odeint import odeint, odeint_dense, odeint_event from .adjoint import odeint_adjoint
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from asap.snv.data_loader import make_pcawg_df from asap.snv.predict import add_predictions
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from escargot.vector_db.azure_embedding import * from escargot.vector_db.weaviate import *
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from .cli_fiducials import fiducials_cli from .cli_patch_tracking import patch_tracking_cli
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from numpy._core.defchararray import __all__, __doc__ from numpy._core.defchararray import *
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"""MDA widgets.""" from ._mda_widget import MDAWidget_ as MDAWidget __all__ = ["MDAWidget"]
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from .core import contents, where __all__ = ["contents", "where"] __version__ = "2025.10.05"
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import typer cli = typer.Typer(name='relion_tomo_align_tilt_series', add_completion=False)
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# -*- coding: utf-8 -*- """ Created on Wed May 28 15:01:28 2025 @author: jkosnoff """
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import numpy as np array = np.array([1, 2]) # The @ operator is not in python 2 array @ array
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# This allows doing relative imports from the tests directory, # e.g. `from .helpers import ...`
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from cedalion.sigdecomp.unimodal import ica_ebm from cedalion.sigdecomp.unimodal import ica_erbm
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from cedalion.sigdecomp.multimodal.mspoc import mSPoC, temporal_embedding, get_orthonormal_matrix
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raise DeprecationWarning( "Functions from cedalion.plots have been moved into cedalion.vis." )
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from .preprocessor import * from .features import * from .scaling import * from .sequence import *
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import typer CLI_NAME = 'relion_tomo_import' cli = typer.Typer(name=CLI_NAME, add_completion=False)
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import typer CLI_NAME = 'relion_tomo_denoise' cli = typer.Typer(name=CLI_NAME, add_completion=False)
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from .default_styles import DEFAULT_STYLES from .theme import Theme DEFAULT = Theme(DEFAULT_STYLES)
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# # This file is part of gunicorn released under the MIT license. # See the NOTICE for more information.
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from dp5.run.load_nmr_files import find_nmr_files from dp5.run.mol_file_preparation import prepare_inputs
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""" ZX-calculus based simulation and optimization """ from .stabilizertcircuit import StabilizerTCircuit
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"""Initialization code for the cali.gui package.""" from ._cali_gui import CaliGui __all__ = ["CaliGui"]
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from ._mda_viewer import MDAViewer from ._preview_viewer import Preview __all__ = ["MDAViewer", "Preview"]
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from typing import Dict from .tilt_series import GuiTiltSeries GuiTiltSeriesSet = Dict[str, GuiTiltSeries]
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""" Created on Aug 19, 2024 Calculate TEP regression score as index for TEP variability @author: mning """
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from diptest import dip import numpy as np def test_can_run_diptest(): assert dip(np.random.rand(1000))
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from .graphormer_3d import Graphormer3D, Graphormer3DLightning __all__ = [Graphormer3D, Graphormer3DLightning]