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#!/usr/bin/env python import setuptools if __name__ == "__main__": setuptools.setup(name="gsMap")
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__version__ = "0.8.2" def exitIf(doExit, Exception, msg): if doExit: raise Exception(msg)
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"""Shared utilities for linear Lactate-Pyruvate Gradient (LPG) analyses.""" __all__ = [ "notes", ]
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from GOF_ttest_AD import main if __name__ == "__main__": main(("Positive", "Intermediate"), False)
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import torch DTYPE = torch.float64 torch.set_default_dtype(DTYPE) print(f"Default tensor type: {DTYPE}")
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from fitter import Fitter import scipy.stats as stats import numpy as np import pandas as pd from .figure
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# Copyright 2023 BioMap (Beijing) Intelligence Technology Limited from .select_model import select_model
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# Written by [xxx] and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
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from ._model import SCBASSET from ._module import ScBassetModule __all__ = ["SCBASSET", "ScBassetModule"]
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"""Spatial transcriptomics risk modeling MVP package.""" __all__ = ["__version__"] __version__ = "0.1.0"
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from .fast_resnet3d import * from .resnet3d import * from .slow_fast import * from .slow_resnet3d import *
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"""semantic_design package exports core helper functions for pipelines.""" from .semantic_design import *
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from .activation import NormReLU from .conv import Conv2dTF __all__ = [ "Conv2dTF", "NormReLU", ]
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from scvi.external.mrvi._module import MRVAE as MRVAE from ._model import MRVI __all__ = ["MRVI", "MRVAE"]
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from __future__ import annotations import pytest pytest.register_assert_rewrite("tests.mixology.helpers")
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from __future__ import annotations from poetry.utils.env.python.manager import Python __all__ = ["Python"]
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from __future__ import annotations from importlib import metadata __version__ = metadata.version("poetry")
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"""Shared dynamic segmentation utilities (standalone Simulation + CID package).""" __all__: list[str] = []
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from .HPF_accel import HPF from .pca import PCA from .incremental_residuals_pca import IncrementalResidualsPCA
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from __future__ import annotations from poetry.publishing.publisher import Publisher __all__ = ["Publisher"]
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"""This module expose the main function for the tandem package.""" from .tandem import main __all__ = ["main"]
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from fitter import Fitter import scipy.stats as stats import numpy as np import pandas as pd from .figure_Tools
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# encoding: utf-8 """ @author: Jiayang Chen @contact: yjcmydkzgj@gmail.com """ from .defaults import _C as cfg
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from setuptools import setup, find_packages setup( name = 'tangle-tracer', packages = find_packages(), )
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from __future__ import annotations from poetry.installation.installer import Installer __all__ = ["Installer"]
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from GOF_ttest_AD import main if __name__ == "__main__": main(("Positive", "Intermediate"), False, 210, 246)
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from ._model import CellAssign from ._module import CellAssignModule __all__ = ["CellAssign", "CellAssignModule"]
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# Written by Kong Xiaolu and CBIG under MIT license: # https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
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from ._model import Decipher from ._module import DecipherPyroModule __all__ = ["Decipher", "DecipherPyroModule"]
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__author__ = 'Robbert Harms' __date__ = "2016-09-02" __maintainer__ = "Robbert Harms" __email__ = "robbert@xkls.nl"
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__author__ = 'Robbert Harms' __date__ = "2015-10-27" __maintainer__ = "Robbert Harms" __email__ = "robbert@xkls.nl"
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"""NPZ / spatial preprocessing pipelines for WMB and CA1 (optional tifffile/skimage; WMB may need captum/shap)."""
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__author__ = 'Robbert Harms' __date__ = "2017-03-29" __maintainer__ = "Robbert Harms" __email__ = "robbert@xkls.nl"
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__author__ = 'Robbert Harms' __date__ = "2015-11-29" __maintainer__ = "Robbert Harms" __email__ = "robbert@xkls.nl"
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__author__ = 'Robbert Harms' __date__ = "2017-02-22" __maintainer__ = "Robbert Harms" __email__ = "robbert@xkls.nl"
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__author__ = 'Robbert Harms' __date__ = "2017-01-26" __maintainer__ = "Robbert Harms" __email__ = "robbert@xkls.nl"
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__author__ = 'Robbert Harms' __date__ = "2016-09-03" __maintainer__ = "Robbert Harms" __email__ = "robbert@xkls.nl"
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from lucent.modelzoo.inceptionv1.InceptionV1 import * from lucent.modelzoo.inceptionv1.InceptionV1_avgPool import *
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__author__ = 'Robbert Harms' __date__ = "2016-06-26" __maintainer__ = "Robbert Harms" __email__ = "robbert@xkls.nl"
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__author__ = 'Robbert Harms' __date__ = "2016-06-27" __maintainer__ = "Robbert Harms" __email__ = "robbert@xkls.nl"
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__author__ = 'Robbert Harms' __date__ = "2017-02-14" __maintainer__ = "Robbert Harms" __email__ = "robbert@xkls.nl"
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from . import ( config_metadata, configs, constants, dirs, parser, prep, source_files, )
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__author__ = 'heroico' IMPUTE = "IMPUTE" PrediXcan = "PrediXcan" DatabaseFile = "DatabaseFile" FlatFile = "FlatFile"
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from .discriminative_reranking_model import DiscriminativeNMTReranker __all__ = [ "DiscriminativeNMTReranker", ]
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class EarlyStopping(Exception): """Raised when stopping training b/c no improvement in validation loss""" pass
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from . import unit_dataset from .unit_dataset import prep_unit_dataset __all__ = ["prep_unit_dataset", "unit_dataset"]
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from fitter import Fitter import scipy.stats as stats import numpy as np import pandas as pd from .figure_Tools import
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from .Garfield import Garfield from .basemodelmixin import BaseModelMixin __all__ = ["Garfield", "BaseModelMixin"]
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# Copyright 2023 BioMap (Beijing) Intelligence Technology Limited from pretrainmodels.select_model import select_model
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from importlib.metadata import version from .plotting import Plot __version__ = version('surfplot') __all__ = ['Plot']
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from .Independencies import IndependenceAssertion, Independencies __all__ = ["Independencies", "IndependenceAssertion"]
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from .math import * from .light import * from .material import * from .optical_element import * from .propagator import *
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from __future__ import annotations def main() -> None: raise SystemExit(42) if __name__ == "__main__": main()
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from .train_loop import train, validate, inference, compute_saliency, compute_saliency_img, compute_high_attention_region
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from . import spect from .files import find_fname, from_dir __all__ = [ "find_fname", "from_dir", "spect", ]
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#! /usr/bin/env python # Third-party modules - we depend on numpy for everything import numpy print numpy.get_include()
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from evo2.models import evo2_model def test_model_load(): evo2_1b_base = evo2_model('evo2_1b_base') test_model_load()
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from setuptools import setup, find_packages setup( package_dir={"": "src"}, packages=find_packages(where="src"), )
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from .PrismNet import PrismNet, PrismNet_large from .utils import param_num from .smoothgrad import GuidedBackpropSmoothGrad
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""" Package for calculating PCIst.""" __author__ = "Renzo Comolatti" __email__ = "renzo.com@gmail.com" __license__ = "GPL"
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def recursive_sorted(li): li = list(li) for i in range(len(li)): li[i] = sorted(li[i]) return sorted(li)
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from .spectralevents import (tfr, tfr_normalize, find_events, plot_events, plot_avg_spectrogram)
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from .classification import * # noqa: F401, F403 from .distance import * # noqa: F401, F403 from . import boundary_detection
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""" This module contains code related to the graphical user interface. """ from .main import main def run_gui(): main()
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from .discriminative_reranking_task import DiscriminativeRerankingNMTTask __all__ = [ "DiscriminativeRerankingNMTTask", ]
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from __future__ import annotations def main() -> int: return 42 if __name__ == "__main__": raise SystemExit(main())
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from . import functional # noqa: F401, F403 from .loss import * # noqa: F401, F403 from .modules import * # noqa: F401, F403
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# A potential monitor helper class/mixin to track the syncronization between # in-memory objects and on-disk files for DataBank.
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"""Run the GOATOOLS CLI with `python -m goatools`.""" from goatools.cli.main import main if __name__ == "__main__": main()
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from .balanced_knn import BalancedKNN from .graph_skeletonizer import GraphSkeletonizer from .poisson_pooling import PoissonPooling
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import pandas as pd import numpy as np import logging from mentor import _metrics as metrics LOGGER = logging.getLogger(__name__)
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from ._model import JointEmbeddingSCVI from ._module import JointEmbeddingVAE __all__ = ["JointEmbeddingSCVI", "JointEmbeddingVAE"]
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from .discriminative_reranking_criterion import KLDivergenceRerankingCriterion __all__ = [ "KLDivergenceRerankingCriterion", ]
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from st_risk.paths import project_root def test_project_root_contains_readme(): assert (project_root() / "README.md").exists()
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from .normalizer import Normalizer from .utils import div0 from .doublet_finder import doublet_finder from .genotyping import genotype
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"""The GPN family of genomic language models.""" from ._registration import register_auto_classes __all__ = ["register_auto_classes"]
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from .hf import load_dataset from .toy import toy_dataset from ._wandb import _load_wandb_artifact from .local import load_local_dataset
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from .metadata import Metadata from .parametric_umap import Datapipe __all__ = [ "InferDatapipe", "Metadata", "Datapipe", ]
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from ._base import BaseExampleModel, list_models, load_model __all__ = [ "BaseExampleModel", "load_model", "list_models", ]
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""" This module contains various utility functions. \ This module is used mainly by other modules, and is meant for internal use only. """
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__author__ = 'Robbert Harms' __date__ = '2019-11-18' __maintainer__ = 'Robbert Harms' __email__ = 'robbert@xkls.nl' __licence__ = 'LGPL v3'
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from ._rotate import rotate_decipher_components from ._trajectory import Trajectory __all__ = ["rotate_decipher_components", "Trajectory"]
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__author__ = 'Robbert Harms' __date__ = '2018-08-14' __maintainer__ = 'Robbert Harms' __email__ = 'robbert@xkls.nl' __licence__ = 'LGPL v3'
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__author__ = 'Robbert Harms' __date__ = "2014-11-27" __license__ = "LGPL v3" __maintainer__ = "Robbert Harms" __email__ = "robbert@xkls.nl"
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import pytest pytestmark = pytest.mark.skip( reason="Telemetry startup coverage will be restored once the full Qt port is complete." )
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__author__ = 'Robbert Harms' __date__ = "2014-05-21" __license__ = "LGPL v3" __maintainer__ = "Robbert Harms" __email__ = "robbert@xkls.nl"
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import sys import os module_path = os.path.abspath(os.path.join(os.pardir)) if module_path not in sys.path: sys.path.append(module_path)
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from pyecharts import charts, commons, components, datasets, options, render, scaffold from pyecharts._version import __author__, __version__
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# -*- coding: UTF-8 -*- """ @Project: iDCF @File : __init__.py.py @IDE : PyCharm @Author : staryu @Date : 2025/7/9 11:35 @Doc : """
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from importlib.metadata import version from .global_vars import config, logger __all__ = ["config", "logger"] __version__ = version("pgmpy")
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from .celltype_specific_genes import * from .highly_variable_genes import * from .spapros_genes import * from .spatially_variable_genes import *
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from fitter import Fitter import scipy.stats as stats import numpy as np import pandas as pd from .figure_Tools import Subtypes, Subtype_colours
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from fitter import Fitter import scipy.stats as stats import numpy as np import pandas as pd from .figure_Tools import Subtypes, Subtype_colours
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Python
146
9
from __future__ import annotations import sys if __name__ == "__main__": from poetry.console.application import main sys.exit(main())
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Python
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from .auto_annotator import AutoAnnotator from .auto_auto_annotator import AutoAutoAnnotator from .cell_cycle_annotator import CellCycleAnnotator
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Python
148
4
from . import pipeline, bids, config, datasets, flagging, utils from .pipeline import LosslessPipeline from .config import Config, RejectionPolicy
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Python
149
8
# -*- coding: utf-8 -*- """Setup module for :mod:`compositionality-study`.""" import setuptools if __name__ == "__main__": setuptools.setup()
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Python
149
7
# -*- coding: utf-8 -*- """ Package for calculating PCIst.""" __author__ = "Renzo Comolatti" __email__ = "renzo.com@gmail.com" __license__ = "GPL"
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Python
151
4
try: from torch.hub import load_state_dict_from_url except ImportError: from torch.utils.model_zoo import load_url as load_state_dict_from_url
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Python
156
9
class test_vary: eventime = None eventdelay = 175 backwardrotdelay = 400 lastdirection = 0 #3 = counterclock, 1 = clock thecount = 0