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theislab / scvelo

RNA Velocity generalized through dynamical modeling
https://scvelo.org
BSD 3-Clause "New" or "Revised" License
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Unable to install and use scvelo #35

Closed aditisk closed 5 years ago

aditisk commented 5 years ago

I tried to install scvelo using pip install scvelo and I got no error. But when I try to import scvelo I am getting this error:

AttributeError Traceback (most recent call last)

in () ----> 1 import scvelo as scv 2 scv.logging.print_version() /anaconda3/lib/python3.6/site-packages/scvelo/__init__.py in () 1 """scvelo - stochastic single cell RNA velocity""" 2 ----> 3 from . import preprocessing as pp 4 from . import tools as tl 5 from . import plotting as pl /anaconda3/lib/python3.6/site-packages/scvelo/preprocessing/__init__.py in () ----> 1 from .utils import show_proportions, cleanup 2 from .moments import moments 3 from .recipes import recipe_velocity /anaconda3/lib/python3.6/site-packages/scvelo/preprocessing/utils.py in () ----> 1 import numpy as np 2 3 4 def show_proportions(adata, copy=False): 5 """Fraction of spliced/unspliced/ambiguous abundances /anaconda3/lib/python3.6/site-packages/numpy/__init__.py in () 140 from . import _distributor_init 141 --> 142 from . import core 143 from .core import * 144 from . import compat /anaconda3/lib/python3.6/site-packages/numpy/core/__init__.py in () 55 from . import umath 56 from . import _internal # for freeze programs ---> 57 from . import numerictypes as nt 58 multiarray.set_typeDict(nt.sctypeDict) 59 from . import numeric /anaconda3/lib/python3.6/site-packages/numpy/core/numerictypes.py in () 109 ) 110 --> 111 from ._type_aliases import ( 112 sctypeDict, 113 sctypeNA, /anaconda3/lib/python3.6/site-packages/numpy/core/_type_aliases.py in () 61 _concrete_typeinfo[k] = v 62 ---> 63 _concrete_types = {v.type for k, v in _concrete_typeinfo.items()} 64 65 /anaconda3/lib/python3.6/site-packages/numpy/core/_type_aliases.py in (.0) 61 _concrete_typeinfo[k] = v 62 ---> 63 _concrete_types = {v.type for k, v in _concrete_typeinfo.items()} 64 65 AttributeError: 'tuple' object has no attribute 'type' Any help on how to fix this would be great. I also tried the Git clone install and that gives me a similar error.
VolkerBergen commented 5 years ago

Could you check your numpy version import numpy; print(numpy.__version__), and try upgrading via pip install --upgrade numpy?

If you have v1.16.0, there might be something broken with numpy. In that case, try downgrading to you might try downgrading to numpy v.1.15.4.

VolkerBergen commented 5 years ago

Any updates on this?

aditisk commented 5 years ago

Hi, sorry I haven't tried doing anything since the past 2 days because when I installed scvelo the last time I could not use scanpy on my computer due to version conflicts of some packages including numpy. I am afraid that this will mess up my scanpy installation and I have a deadline this Friday.

I will try what you suggested over the weekend and get back to you at the earliest. Thanks,

VolkerBergen commented 5 years ago

Sure, no worries. Good luck! :)

side note: scanpy and scvelo should not have any conflicting dependencies. scvelo's main dependencies are basically scanpy and anndata.

aditisk commented 5 years ago

Thanks a lot. I am sure I got some version conflict messages and everything stopped working after that. I will re-try the installation and post the messages/errors here and we can go from there :)

VolkerBergen commented 5 years ago

Any updates on the installation?