Comments (3)
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!
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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'
from deeptime.
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
from deeptime.
Related Issues (20)
- Cannot install deeptime. I have Python 3.10 (Windows 10) and trying to install using Visual Studio 2022 HOT 12
- Error when installing from local repo via pip HOT 4
- TICA fit-once transform-many HOT 6
- Automate generating bdist wheels HOT 1
- Allowing weights for VAMP dimensionality reduction HOT 6
- Error importing deeptime with scikit-learn 1.2.0 HOT 4
- About applying Deeptime to molecular dynamics simulation trajectories on protien HOT 3
- Handling parallel simulations HOT 1
- Implied timescales from deeptime.decomposition.TICA HOT 2
- [Bug] At least one of the given states is not contained in this model HOT 2
- VAMPnet gives highly fluctuating score results HOT 1
- Bayesian Markov models give different MFPT
- How to compute any actual quantity of the coarse-grained kinetics with employing the fuzzy memberships? HOT 7
- Which version of VAMPNets is there? HOT 1
- deeptime cannot be installed on Mac computers with Apple Silicon and Python 3.12.0. HOT 4
- Does one need identical features to compare between related systems? HOT 4
- Example/tutorial for dealing with MD trajectories HOT 1
- Applying TICA to ragged feature vectors HOT 2
- Cross Validation score for MaximumLikelihoodMSMs and BayesianMSMs HOT 2
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from deeptime.