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Importerror for scVI in tutorials #1464

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Zethson opened this issue Mar 26, 2022 · 21 comments · Fixed by #1466
Closed

Importerror for scVI in tutorials #1464

Zethson opened this issue Mar 26, 2022 · 21 comments · Fixed by #1466
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@Zethson
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Zethson commented Mar 26, 2022 •
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Describe the bug

Importerror for scVI.

To reproduce

Execute your very own tutorial: https://colab.research.google.com/github/scverse/scvi-tutorials/blob/0.15.3/api_overview.ipynb

ImportError                               Traceback (most recent call last)

[<ipython-input-4-c98868e3b7fa>](https://localhost:8080/#) in <module>()
----> 1 import scvi
      2 import scanpy as sc
      3 import matplotlib.pyplot as plt
      4 
      5 sc.set_figure_params(figsize=(4, 4))

12 frames

[/usr/local/lib/python3.7/dist-packages/torchtext/vocab/vocab_factory.py](https://localhost:8080/#) in <module>()
      2 from typing import Dict, Iterable, Optional, List
      3 from collections import Counter, OrderedDict
----> 4 from torchtext._torchtext import (
      5     Vocab as VocabPybind,
      6 )

ImportError: /usr/local/lib/python3.7/dist-packages/torchtext/_torchtext.so: undefined symbol: _ZNK3c104Type14isSubtypeOfExtERKSt10shared_ptrIS0_EPSo

Versions:

Latest stable

I suspect that this is some missmatch of incompatible versions of PyTorch and torchtext.
@Zethson Zethson added the bug label Mar 26, 2022
@Zethson Zethson mentioned this issue Mar 26, 2022
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@adamgayoso
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If I had to guess it's because the latest pyro version lower bounds torch to 1.11.0 and somehow the colab environment has an older version of torchtext, which I believe may be required by pytorch lightning

@adamgayoso
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I think our options are to either wait for this googlecolab/colabtools#2668 or to upper bound pyro. I'm inclined to wait.

@DRSEI
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DRSEI commented Mar 28, 2022

Hi @adamgayoso so are you saying that I cant use the SCVI at this stage?

@Zethson
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Zethson commented Mar 28, 2022

@adamgayoso I don't think that Google is known for solving their issues fast. IMO working tutorials (with collab) are very important and I would suggest to upper bound pyro instead of waiting.

Choice is yours ofc.

@rangan2510
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rangan2510 commented Mar 28, 2022 •
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Presently this works:

!pip install scvi-tools==0.15.1 pyro-ppl==1.8.0 umap-learn scanpy scikit-misc leidenalg --quiet

@adamgayoso
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Indeed the problem is solved if the very first thing that is done is pip install pyro-ppl==1.8.0.

@Zethson I think the solution is a scvi-colab package that is pip installed and runs the installation steps for colab...

@adamgayoso
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Done.

!pip install --quiet scvi-colab
from scvi_colab import install
install()

This will install scvi-tools for you in google colab. We will update all the tutorials in a patch release to reflect this.

@adamgayoso adamgayoso mentioned this issue Mar 28, 2022
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@DRSEI
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DRSEI commented Mar 28, 2022 •
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hi @adamgayoso I am still getting the same error even through I have follow your suggestion.

%%capture
import sys

#if branch is stable, will install via pypi, else will install from source
branch = "stable"
IN_COLAB = "google.colab" in sys.modules

if IN_COLAB and branch == "stable":
!pip install scvi-tools==0.15.1
!pip install pyro-ppl==1.8.0
!pip install --quiet git+https://github.com/theislab/scib.git
elif IN_COLAB and branch != "stable":
!pip install --quiet --upgrade jsonschema

ImportError Traceback (most recent call last)
in ()
5 import scanpy as sc
6 import scib
----> 7 import scvi
8 sc.set_figure_params(figsize=(4, 4))
9

12 frames
/usr/local/lib/python3.7/dist-packages/torchtext/vocab/vocab_factory.py in ()
2 from typing import Dict, Iterable, Optional, List
3 from collections import Counter, OrderedDict
----> 4 from torchtext._torchtext import (
5 Vocab as VocabPybind,
6 )

ImportError: /usr/local/lib/python3.7/dist-packages/torchtext/_torchtext.so: undefined symbol: _ZNK3c104Type14isSubtypeOfExtERKSt10shared_ptrIS0_EPSo

@adamgayoso
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@DRSEI please check the tutorials again in a few minutes

@DRSEI
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DRSEI commented Mar 28, 2022

Thank you @adamgayoso

@bigtimecodersean
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I am running into the exact same problem as DRSEI describes above:
Running:

%%capture
import sys

#if branch is stable, will install via pypi, else will install from source
branch = "stable"
IN_COLAB = "google.colab" in sys.modules

if IN_COLAB and branch == "stable":
!pip install --quiet scvi-tools[tutorials]
elif IN_COLAB and branch != "stable":
!pip install --quiet --upgrade jsonschema
!pip install --quiet git+https://github.com/yoseflab/scvi-tools@$branch#egg=scvi-tools[tutorials]

!pip install --quiet scvi-colab
from scvi_colab import install
install()

gives me the following error:

ImportError: /usr/local/lib/python3.7/dist-packages/torchtext/_torchtext.so: undefined symbol: _ZNK3c104Type14isSubtypeOfExtERKSt10shared_ptrIS0_EPSo

Any ideas?

@rangan2510
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rangan2510 commented Mar 29, 2022 via email

@bigtimecodersean
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@rangan2510 I believe I am using the proposed workaround:

!pip install --quiet scvi-colab
from scvi_colab import install
install()

But I still get the import error?

@rangan2510
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For me, this worked on Kaggle. You may try it out.
!pip install scvi-tools==0.15.1 pyro-ppl==1.8.0 umap-learn scanpy scikit-misc leidenalg --quiet

@bigtimecodersean
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Thanks, I successfully ran the above ^:
!pip install scvi-tools==0.15.1 pyro-ppl==1.8.0 umap-learn scanpy scikit-misc leidenalg --quiet

However the following:

import scvi
import scanpy as sc
import matplotlib.pyplot as plt

sc.set_figure_params(figsize=(4, 4))

for white background of figures (only for docs rendering)

%config InlineBackend.print_figure_kwargs={'facecolor' : "w"}
%config InlineBackend.figure_format='retina'

As well as:

!pip install --quiet scvi-colab
from scvi_colab import install
install()

Both give me the import error.

I am thinking it might have something to do with a PyTorch dependency?

Screenshot 2022-03-28 at 21 07 11

I am running PyTorch: '1.11.0+cu102'

@rangan2510
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@bigtimecodersean I believe it's something else. I am sharing a link to a notebook I have on Colab and it works fine. Did a !pip freeze so you can check the versions: scVI import.ipynb

@bigtimecodersean
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@rangan2510 Thanks for the help. I just ran your code line by line and got the exact same import error on the:

"import scvi" line in your second block. Bizarre

@bigtimecodersean
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Starting a new notebook solved the problem with your solution @rangan2510 Thank you so much!!!

@adamgayoso
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@bigtimecodersean

%%capture
import sys

#if branch is stable, will install via pypi, else will install from source
branch = "stable"
IN_COLAB = "google.colab" in sys.modules

if IN_COLAB and branch == "stable":
!pip install --quiet scvi-tools[tutorials]
elif IN_COLAB and branch != "stable":
!pip install --quiet --upgrade jsonschema
!pip install --quiet git+[https://github.com/yoseflab/scvi-tools@$branch#egg=scvi-tools[tutorials]](https://github.com/yoseflab/scvi-tools@$branch#egg=scvi-tools%5Btutorials%5D)

!pip install --quiet scvi-colab
from scvi_colab import install
install()

should instead only be

!pip install --quiet scvi-colab
from scvi_colab import install
install()

I don't believe this new code will work in kaggle unless you run it like

!pip install --quiet scvi-colab
from scvi_colab import install
install(run_outside_colab=True)

@rangan2510
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rangan2510 commented Oct 11, 2022 via email

@michaelmather15
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Hi. I am hoping to ask a question related to the above point please. I had scVI working fine in Colab a few months ago but when I have come back to it today, when I run

!pip install --quiet scvi-colab
from scvi_colab import install
install()

I get the following message:

INFO scvi-colab: Installing scvi-tools.
INFO scvi-colab: Install successful. Testing import.

AssertionError Traceback (most recent call last)
in <cell line: 3>()
1 get_ipython().system('pip install --quiet scvi-colab')
2 from scvi_colab import install
----> 3 install()

9 frames
/usr/local/lib/python3.10/dist-packages/pyro/distributions/torch_patch.py in
8 import torch
9
---> 10 assert torch.version.startswith("1.")
11
12

AssertionError:

If I do !pip freeze after this it looks like scvi has indeed installed. But then when I run import scvi I get the exact same error message as above. I've also tried this in a fresh notebook.

Does anyone know why this is happening please? Thanks in advance.

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Prep 0.15.4 release scverse/scvi-tools
6 participants
@adamgayoso @Zethson @rangan2510 @DRSEI @michaelmather15 @bigtimecodersean