No module named 'scvelo.tools.dynamical_model_utils'

[19mengyanyan33]

Hi,

I met error below when I was running the notebooks in the examples folder.

{
"name": "ModuleNotFoundError",
"message": "No module named 'scvelo.tools.dynamical_model_utils'",
"stack": "---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
Cell In[1], line 7
4 import torch
5 from scipy.stats import mannwhitneyu
----> 7 from deepvelo.utils import velocity, velocity_confidence, latent_time, update_dict, cross_boundary_correctness
8 from deepvelo.utils.preprocess import autoset_coeff_s
9 from deepvelo.utils.plot import statplot, compare_plot

File ~/Methods/DeepVelo/deepvelo/init.py:1
----> 1 from .train import *
3 from . import tool as tl
4 from . import plot as pl

File ~/Methods/DeepVelo/deepvelo/train.py:9
6 from anndata import AnnData
7 from scvelo import logging as logg
----> 9 from deepvelo.trainer import Trainer
10 import deepvelo.data_loader.data_loaders as module_data
11 import deepvelo.model.loss as module_loss

File ~/Methods/DeepVelo/deepvelo/trainer/init.py:1
----> 1 from .trainer import *

File ~/Methods/DeepVelo/deepvelo/trainer/trainer.py:8
4 import torch
5 # import dgl
6
7 # from torchvision.utils import make_grid
----> 8 from deepvelo.base import BaseTrainer
9 from deepvelo.utils import inf_loop, MetricTracker
10 from deepvelo.logger import TensorboardWriter

File ~/Methods/DeepVelo/deepvelo/base/init.py:3
1 from .base_data_loader import *
2 from .base_model import *
----> 3 from .base_trainer import *

File ~/Methods/DeepVelo/deepvelo/base/base_trainer.py:5
3 from abc import abstractmethod
4 from numpy import inf
----> 5 from deepvelo.logger import TensorboardWriter
8 class BaseTrainer:
9 """
10 Base class for all trainers
11 """

File ~/Methods/DeepVelo/deepvelo/logger/init.py:1
----> 1 from .logger import *
2 from .visualization import *

File ~/Methods/DeepVelo/deepvelo/logger/logger.py:4
2 import logging.config
3 from pathlib import Path
----> 4 from deepvelo.utils import read_json
7 def setup_logging(
8 save_dir, log_config="logger/logger_config.json", default_level=logging.INFO
9 ):
10 """
11 Setup logging configuration
12 """

File ~/Methods/DeepVelo/deepvelo/utils/init.py:17
1 from .util import (
2 ensure_dir,
3 read_json,
(...)
14 MetricTracker,
15 )
16 from .confidence import *
---> 17 from .temporal import *
19 # deprecated import velocity
20 from ..tool.velocity import *

File ~/Methods/DeepVelo/deepvelo/utils/temporal.py:5
3 from scvelo.preprocessing.moments import get_connectivities
4 from scvelo.tools.utils import make_unique_list, test_bimodality
----> 5 from scvelo.tools.dynamical_model_utils import (
6 BaseDynamics,
7 linreg,
8 convolve,
9 tau_inv,
10 unspliced,
11 )
12 from scvelo.tools.terminal_states import eigs
14 import numpy as np

ModuleNotFoundError: No module named 'scvelo.tools.dynamical_model_utils'"
}

---

I installed the scvelo==0.2.5 initailly, but it didn't work, I also tried the version 0.2.4 and 0.3.2, they also didn't work.

Which scvelo version would you recommend for deepvelo?

Thank you so much,
Mengyanyan

[hsmaan]

Hi Mengyanyan,

Currently the environment should be using scvelo==0.2.5, so you were correct in using that version.

Could you please let me know which exact notebook you were testing in examples so I can try to reproduce the error?