ImportError: cannot import name 'config' from 'jax.config'

[namsaraeva]

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scvi-tools were installed from main branch, the environment was brand new. jax was at the latest version.

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[SamuelCWJ]

Hi! @Zethson Please may I have some assistance with this too? I note that this issue has been closed 3 weeks ago, but it is still happening for me using a fresh install of pertpy.

ImportError Traceback (most recent call last)
Cell In[1], line 9
7 import matplotlib.pyplot as plt
8 import mudata as mu
----> 9 import pertpy as pt

File /scbio4/home/samuel/miniforge3/envs/py3116-env/lib/python3.11/site-packages/pertpy/init.py:19
17 from . import plot as pl
18 from . import preprocessing as pp
---> 19 from . import tools as tl

File /scbio4/home/samuel/miniforge3/envs/py3116-env/lib/python3.11/site-packages/pertpy/tools/init.py:24
22 print("[bold yellow]To use sccoda or tasccoda please install ete3 with [green]pip install ete3")
23 else:
---> 24 raise e

File /scbio4/home/samuel/miniforge3/envs/py3116-env/lib/python3.11/site-packages/pertpy/tools/init.py:18
15 from pertpy.tools._scgen import SCGEN
17 try:
---> 18 from pertpy.tools._coda._sccoda import Sccoda
19 from pertpy.tools._coda._tasccoda import Tasccoda
20 except ImportError as e:

File /scbio4/home/samuel/miniforge3/envs/py3116-env/lib/python3.11/site-packages/pertpy/tools/_coda/_sccoda.py:12
10 from anndata import AnnData
11 from jax import random
---> 12 from jax.config import config
13 from mudata import MuData
14 from numpyro.infer import Predictive

ImportError: cannot import name 'config' from 'jax.config' (/scbio4/home/samuel/miniforge3/envs/py3116-env/lib/python3.11/site-packages/jax/config.py)

Thank you so much!

Best Regards,
Samuel

[SamuelCWJ]

Hi! @Zethson Please may I have some assistance with this too? I note that this issue has been closed 3 weeks ago, but it is still happening for me using a fresh install of pertpy.

ImportError Traceback (most recent call last) Cell In[1], line 9 7 import matplotlib.pyplot as plt 8 import mudata as mu ----> 9 import pertpy as pt

File /scbio4/home/samuel/miniforge3/envs/py3116-env/lib/python3.11/site-packages/pertpy/init.py:19 17 from . import plot as pl 18 from . import preprocessing as pp ---> 19 from . import tools as tl

File /scbio4/home/samuel/miniforge3/envs/py3116-env/lib/python3.11/site-packages/pertpy/tools/init.py:24 22 print("[bold yellow]To use sccoda or tasccoda please install ete3 with [green]pip install ete3") 23 else: ---> 24 raise e

File /scbio4/home/samuel/miniforge3/envs/py3116-env/lib/python3.11/site-packages/pertpy/tools/init.py:18 15 from pertpy.tools._scgen import SCGEN 17 try: ---> 18 from pertpy.tools._coda._sccoda import Sccoda 19 from pertpy.tools._coda._tasccoda import Tasccoda 20 except ImportError as e:

File /scbio4/home/samuel/miniforge3/envs/py3116-env/lib/python3.11/site-packages/pertpy/tools/_coda/_sccoda.py:12 10 from anndata import AnnData 11 from jax import random ---> 12 from jax.config import config 13 from mudata import MuData 14 from numpyro.infer import Predictive

ImportError: cannot import name 'config' from 'jax.config' (/scbio4/home/samuel/miniforge3/envs/py3116-env/lib/python3.11/site-packages/jax/config.py)

Thank you so much!

Best Regards, Samuel

Hi again, just to update that I managed to solve this by compiling the latest version of pertpy instead of using pip install. Thank you!

[Zethson]

Sorry about that. We ll make a release ASAP

[spatts14]

@SamuelCWJ how do you compile the latest version? I'm hitting the same error.

[SamuelCWJ]

@SamuelCWJ how do you compile the latest version? I'm hitting the same error.

Hi @spatts14 ,

I followed their instructions here: https://pertpy.readthedocs.io/en/latest/installation.html

$ curl -OJL https://github.com/theislab/pertpy/tarball/master
Extract the files from the tar.gz folder
$ cd (into the extracted folder)
$ pip install .

[Zethson]

You can also just git clone the main branch and don't have to download/extract the tar ball.

Again, sorry about this - release ASAP!

[spatts14]

Thank you both! All set now :)

[majmal7]

how to fix this "ImportError: cannot import name 'config' from 'jax.config'"

[majmal7]

@spatts14 @Zethson, how to fix this "ImportError: cannot import name 'config' from 'jax.config'"?

[Zethson]

@majmal7 please install from the main branch as outlined here. A new release will happen within the next 3-7 days.