deeptime

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Hi, I'm currently trying to install the deeptime for the project of investigating conformation kinetics of an ion channel. But I encounter problems when trying to install it. Since I am use the latest python version and that version is not recommended to use pip to install python packages any more for security reasons. So I wonder if there are other ways to install deeptime. It may be great if there is a way to install it using just shell scripts. Thank you all.

Hi, currently only pip and conda are supported really - could you provide a source to the security concerns with the newest Python? Are these security concerns also regarding conda? The closest you can come to a shell script installation right now is downloading the pypi binaries and putting them in place. But that probably defeats the purpose a bit. Thanks!

Hi, when I am trying to run the "vamp.ipynb" notebook under example folder the deeptime project after unpacking the binary distribution file I got from "https://pypi.org/project/deeptime/#files" to path "/usr/lib64/python3.11/site-packages". I got these errors when running the first section of the code :

Code that I ran: from deeptime.decomposition import VAMP

vamp_estimator = VAMP( dim=1 # projection dimension )

Errors I got

ModuleNotFoundError Traceback (most recent call last) Cell In[1], line 1 ----> 1 from deeptime.decomposition import VAMP 3 vamp_estimator = VAMP( 4 dim=1 # projection dimension 5 )

File /usr/lib/python3.11/site-packages/deeptime/init.py:6 4 from . import util 5 from . import numeric ----> 6 from . import data 7 from . import basis 8 from . import kernels

File /usr/lib/python3.11/site-packages/deeptime/data/init.py:76 1 r""" 2 .. currentmodule: deeptime.data 3 (...) 72 CustomSystem 73 """ 75 from ._systems import CustomSystem, TimeIndependentSystem, TimeDependentSystem ---> 76 from ._datasets import double_well_discrete, ellipsoids, position_based_fluids, drunkards_walk, bickley_jet,
77 birth_death_chain, tmatrix_metropolis1d, sqrt_model, quadruple_well, triple_well_2d, abc_flow, ornstein_uhlenbeck,
78 triple_well_1d, quadruple_well_asymmetric, double_well_2d, swissroll_model, prinz_potential,
79 time_dependent_quintuple_well, lorenz_system, thomas_attractor 80 from ._datasets import custom_sde, custom_ode 81 from ._double_well import DoubleWellDiscrete

File /usr/lib/python3.11/site-packages/deeptime/data/_datasets.py:8 6 from ._double_well import DoubleWellDiscrete 7 from ._ellipsoids import Ellipsoids ----> 8 from ._pbf_simulator import PBFSimulator 9 from ._drunkards_walk_simulator import DrunkardsWalk 10 from ._bickley_simulator import BickleyJet, BickleyJetDataset

File /usr/lib/python3.11/site-packages/deeptime/data/_pbf_simulator.py:3 1 import numpy as np ----> 3 from threadpoolctl import threadpool_limits 5 from . import _data_bindings as bd 6 from ..util.decorators import plotting_function

ModuleNotFoundError: No module named 'threadpoolctl'

that is because you are simply unpacking, opposed to using pip as it is intended. deeptime is not self-contained as a package but has dependencies which again can have dependencies of their own etc. That is something that pip and conda resolve. If you do not want to use them, you have to install these dependencies manually. This file defines the list of requirements: https://github.com/deeptime-ml/deeptime/blob/main/pyproject.toml