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Python
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5
from setuptools import setup if __name__ == "__main__": setup()
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from .adapterremoval import MultiqcModule __all__ = ["MultiqcModule"]
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from .damageprofiler import MultiqcModule __all__ = ["MultiqcModule"]
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from .cellranger_arc import MultiqcModule __all__ = ["MultiqcModule"]
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"""Schema Generator Agent for creating sophisticated LinkML schemas."""
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"""Aggregator Agent for combining results from multiple other agents."""
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from .fetchers import fetch_hcpl2k8 from .generators import gen_cube
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from .goleft_indexcov import MultiqcModule __all__ = ["MultiqcModule"]
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import os this_directory = os.path.dirname(os.path.realpath(__file__))
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from .prinseqplusplus import MultiqcModule __all__ = ["MultiqcModule"]
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""" Phenopackets agent module for working with phenopacket databases. """
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from .multivcfanalyzer import MultiqcModule __all__ = ["MultiqcModule"]
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from importlib.metadata import version __version__ = version("pontibus")
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import sys sys.setrecursionlimit(5000) print("Recursion limit hook active")
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from .phantompeakqualtools import MultiqcModule __all__ = ["MultiqcModule"]
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from .datasets import CustomDGLDataset __all__ = [ 'CustomDGLDataset' ]
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from .eigenstratdatabasetools import MultiqcModule __all__ = ["MultiqcModule"]
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#!/usr/bin/env python3 import sys __version__ = '1.0.1' VERSION = __version__
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from .more import * # noqa from .recipes import * # noqa __version__ = '8.8.0'
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#!/usr/bin/env python # -*- coding: utf-8 -*- if __name__ == '__main__': pass
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from pathlib import Path ROBOT_ONTOLOGY_AGENT_CONTENTS_DIR = Path(__file__).parent
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from multiqc.modules.ngsbits.ngsbits import MultiqcModule __all__ = ["MultiqcModule"]
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""" Talisman agent package for advanced gene analysis using UniProt and NCBI Entrez. """
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""" AmiGO agent module for interacting with GO KnowledgeBase via AmiGO solr endpoint. """
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from . import ( lambdaprotocol, multistate, relative, topologyhelpers, )
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from .fused_act import FusedLeakyReLU, fused_leaky_relu from .upfirdn2d import upfirdn2d
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__all__ = ['graphs', 'files', 'df_processing', 'wiki', 'plotting', 'obo_processing', 'ml']
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from . import input_validation from . import plan_rbfe_network from . import results_cleanup
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"""Hi-Compass: Cell-type-specific chromatin interaction prediction.""" __version__ = '1.0.5'
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"""Hi-Compass: Cell-type-specific chromatin interaction prediction.""" __version__ = '1.0.1'
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from pydantic import BaseModel class DatasetRow(BaseModel): prompt: str completion: str
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# Versioneer boilerplate. from . import _version __version__ = _version.get_versions()['version']
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from .plotting import plot_fc from .plotting import plot_timeseries from .plotting import plot_psd
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""" Literature agent module for working with scientific literature, publications, and references. """
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# !/usr/bin/env python # -*-coding:utf-8 -*- # @Time : 2022/05/28 21:19 # @Author : Liangdi.Ma
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# !/usr/bin/env python # -*-coding:utf-8 -*- # @Time : 2022/05/25 20:40 # @Author : Liangdi.Ma
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# !/usr/bin/env python # -*-coding:utf-8 -*- # @Time : 2022/05/25 15:47 # @Author : Liangdi.Ma
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# !/usr/bin/env python # -*-coding:utf-8 -*- # @Time : 2022/05/28 21:16 # @Author : Liangdi.Ma
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import setuptools setuptools.setup( name="my-test-package", version="1.0", zip_safe=True, )
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"""Torsion-specific models.""" from yammbs.torsion._store import TorsionStore __all__ = ("TorsionStore",)
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from manipulations import manipulations, manip_strs, default_manipulation from conditions import conditions
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from __future__ import absolute_import, division, unicode_literals from .py import Trie __all__ = ["Trie"]
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import gl gl.resetdefaults() gl.meshload('AICHAhr_left') gl.atlas2node('/Users/chris/afni/pial/mynodes.node');
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from .extended_solvent_component import ExtendedSolventComponent __all__ = [ "ExtendedSolventComponent", ]
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""" Empty init file in case you choose a package besides PyTest such as Nose which may look for such a file """
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""" Empty init file in case you choose a package besides PyTest such as Nose which may look for such a file. """
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""" Utilities package for ethopy control. Contains setup, configuration, and database initialization utilities. """
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from .base import IRI from .vprofile import timeprofile, geoprofile __all__ = ["IRI", "timeprofile", "geoprofile"]
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import functools from torch.testing import assert_close assert_equal = functools.partial(assert_close, rtol=0, atol=0)
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from pathlib import Path THIS_DIR = Path(__file__).parent INPUT_DIR = THIS_DIR / "input" OUTPUT_DIR = THIS_DIR / "output"
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from .model_fitting import ModelFitting from .custom_fitting import FittingFNGFPG from .batch_fitting import FittingBatch
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from custom_time import now,now2 from logs import setup_logging from tcpip import TCPIP from notifications import email_alert
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from .paretoexp import paretoexp from .gengamma import gengamma from .lognorm import lognorm from .weibull import weibull
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#!/usr/bin/env python # -*- coding: utf-8 -*- from .surface import * from .smooth import ScalarValuedMesh, ValueSpecificSmoother
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from .sakepp import SAKEPP from .dgn import DGN, DGNLinearFusion __all__ = [ 'SAKEPP', 'DGN', 'DGNLinearFusion' ]
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from setuptools import setup setup( name="CANDO", version="2.2.1", packages=['cando'], license='BSD-3-Clause', )
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"""Wrappers to build Python packages using PEP 517 hooks """ __version__ = '0.10.0' from .wrappers import * # noqa: F401, F403
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# This code is part of kartograf and is licensed under the MIT license. # For details, see https://github.com/OpenFreeEnergy/kartograf
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"""Exceptions used within YAMMBS.""" class DatabaseExistsError(Exception): """A database with this (file) name already exists."""
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#!/usr/bin/env python3 import sys from scripts_of.__main__ import main if __name__ == "__main__": args = sys.argv[1:] main(args)
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def cluster_warning(node_iri: str | None, message: str) -> str: if node_iri: return f"{node_iri}: {message}" return message
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__all__ = ['model', 'spatial', 'arrangements', 'emissions', 'evaluation', 'full_model']
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"""Analysis components for TimeFlies.""" from .eda import EDAHandler from .visuals import Visualizer __all__ = ["EDAHandler", "Visualizer"]
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import marshall_intrinsic_units marshall_intrinsic_units.run_minimal_macro_example() marshall_intrinsic_units.summarize_minimal_macro_example()
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import marshall_intrinsic_units marshall_intrinsic_units.run_minimal_micro_example() marshall_intrinsic_units.summarize_minimal_micro_example()
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import numpy as np def receive_noise_input(n_samples, latent_dim): noise = np.random.normal(0, 1, (n_samples, latent_dim)) return noise
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import marshall_intrinsic_units marshall_intrinsic_units.run_blackbox_macro_example() marshall_intrinsic_units.summarize_blackbox_macro_example()
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import pandas as pd df = pd.read_csv(snakemake.input.sv, sep="\t") df.loc[df["chrom"] != "chrY"].to_csv(snakemake.output[0], sep="\t", index=False)
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print("This isn't the package you are looking for") print("Please install kartograf from conda-forge") print("conda install -c conda-forge kartograf")
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from openai import BaseModel from pydantic import ConfigDict class TsBaseModel(BaseModel): model_config = ConfigDict(strict=True, extra="forbid")
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import marshall_intrinsic_units marshall_intrinsic_units.run_coarsegrain_macro_example() marshall_intrinsic_units.summarize_coarsegrain_macro_example()
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import marshall_intrinsic_units marshall_intrinsic_units.run_coarsegrain_micro_example() marshall_intrinsic_units.summarize_coarsegrain_micro_example()
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from typing import Union from .batch import DGLMoleculeBatch from .molecule import DGLMolecule DGLMoleculeOrBatch = Union[DGLMolecule, DGLMoleculeBatch]
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__all__ = ["Mapping", "Sequence"] try: from collections.abc import Mapping, Sequence except ImportError: from collections import Mapping, Sequence
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import urllib.request try: urllib.request.urlopen('https://www.google.com') except: # -no-cov- HAS_INTERNET = False else: HAS_INTERNET = True
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from .interface import AlchemiscaleClient from .models import Scope, ScopedKey from importlib.metadata import version __version__ = version("alchemiscale")
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""" The project is configured in pyproject.toml. This script is left for the editable installation. """ from setuptools import setup # type: ignore setup()
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#!/usr/bin/env python # -*- coding: utf-8 -*- from .ome_tiff_writer import OmeTiffWriter # noqa: F401 from .ome_zarr_writer import OmeZarrWriter # noqa: F401
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#!/usr/bin/env python from forcebalance.molecule import * M = Molecule('all.xyz') M.qm_energies = [float(l.split()[-1]) for l in M.comms] M.write('qdata.txt')
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from pathlib import Path import yaml def load_config(path: str | Path) -> dict: with open(path, "r", encoding="utf-8") as f: return yaml.safe_load(f)
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""" Data loading and preprocessing utilities """ from .loaders import DataLoader from .setup import DataSetupManager __all__ = ["DataLoader", "DataSetupManager"]
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""" Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda. """ name = "facemap" from facemap.version import version, version_str
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import pandas as pd pd.concat([pd.read_csv(e) for e in sorted(list(snakemake.input))])[["prob1", "prob2"]].reset_index().to_csv( snakemake.output[0], index=False )
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from os import listdir from os.path import dirname __all__ = [ i[:-3] for i in listdir(dirname(__file__)) if not i.startswith("__") and i.endswith(".py") ]
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import sys from pathlib import Path PROJECT_ROOT = Path(__file__).resolve().parents[1] if str(PROJECT_ROOT) not in sys.path: sys.path.insert(0, str(PROJECT_ROOT))
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""" Shared data preprocessing utilities """ from .data_processor import DataPreprocessor from .gene_filter import GeneFilter __all__ = ["DataPreprocessor", "GeneFilter"]
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from .interface import AlchemiscaleClient, ResultFormat from .models import Scope, ScopedKey from importlib.metadata import version __version__ = version("alchemiscale")
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from ProtoCloud.data import scRNAdata from ProtoCloud.data.scRNAdata import (CustomDataset, EPS, scRNAData,) __all__ = ['CustomDataset', 'EPS', 'scRNAData', 'scRNAdata']
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import importlib.resources data_directory = importlib.resources.files("openff.nagl") / "training" / "templates" JINJA_REPORT_TEMPLATE = data_directory / "jinja_report.html"
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import marshall_intrinsic_units marshall_intrinsic_units.run_something_from_nothing_micro_example() marshall_intrinsic_units.summarize_something_from_nothing_micro_example()
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#from . import models #from . import optimization #from . import run #from . import datasets #from . import datatypes #from . import functions #from . import visualization
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import marshall_intrinsic_units marshall_intrinsic_units.run_something_from_something_micro_example() marshall_intrinsic_units.summarize_something_from_something_micro_example()
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import pandas as pd df = pd.read_csv(snakemake.input.ploidy, sep="\t") df = df.groupby("#chrom")["ploidy_estimate"].describe() print(df) df.to_csv(snakemake.output.summary, sep="\t")
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"""Multiplex segmentation application. Deprecated in favor of ``deepcell.applications.Mesmer`` instead. """ from deepcell.applications.mesmer import Mesmer as MultiplexSegmentation
d2d55c3641124ca6c5b42151d9e91860ab2684c3b917c760b98cb9b5271e86f6
Python
184
5
"""A cell tracking class capable of extending labels across sequential frames.""" from deepcell_tracking import CellTracker from deepcell_tracking import CellTracker as cell_tracker
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Python
185
6
"""Shared evaluation components for TimeFlies projects.""" from .interpreter import Interpreter from .metrics import EvaluationMetrics as Metrics __all__ = ["Interpreter", "Metrics"]
cd30e928abab4bef61f8955b7aac83c7eca0b83a960424684e80e22502166215
Python
187
8
#!/usr/bin/env python from forcebalance.molecule import * M = Molecule('all.gro') M1 = M.atom_select([i for i in range(M.na) if i%4 != 3]) M1[0].write('conf.pdb') M1.write('all.mdcrd')
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Python
188
5
import gl gl.resetdefaults() gl.meshload('/Users/chris/afni/pial/lh.pial') gl.overlayload('/Users/chris/afni/pial/lh.HCP-MMP1.annot') gl.atlas2node('/Users/chris/afni/pial/mynodes.node');
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Python
189
4
import marshall_intrinsic_units marshall_intrinsic_units.run_something_from_nearly_nothing_micro_example() marshall_intrinsic_units.summarize_something_from_nearly_nothing_micro_example()
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Python
189
6
from PyInstaller.utils.hooks import collect_submodules from PyInstaller.utils.hooks import collect_data_files hiddenimports = collect_submodules("dipy") datas = collect_data_files("dipy")