cannot setup.py install

[jianrong0520]

/home/jianrong/miniconda3/envs/py3.8/bin/python setup.py install
WARNING:root:In order to use the mouse gastrulation seqFISH datsets, please install squidpy (see https://github.com/scverse/squidpy).
/home/jianrong/miniconda3/envs/py3.8/lib/python3.8/site-packages/scvi_tools-1.0.3-py3.8.egg/scvi/_settings.py:63: UserWarning: Since v1.0.0, scvi-tools no longer uses a random seed by default. Run scvi.settings.seed = 0 to reproduce results from previous versions.
self.seed = seed
/home/jianrong/miniconda3/envs/py3.8/lib/python3.8/site-packages/scvi_tools-1.0.3-py3.8.egg/scvi/_settings.py:70: UserWarning: Setting dl_pin_memory_gpu_training is deprecated in v1.0 and will be removed in v1.1. Please pass in pin_memory to the data loaders instead.
self.dl_pin_memory_gpu_training = (
Traceback (most recent call last):
File "setup.py", line 9, in
from scarches import author, email, version
File "/home/jianrong/biosoft/scarches/scarches/init.py", line 1, in
from . import dataset, metrics, trainers, models, zenodo, plotting, utils, classifiers
File "/home/jianrong/biosoft/scarches/scarches/models/init.py", line 1, in
from .trvae.trvae import trVAE
File "/home/jianrong/biosoft/scarches/scarches/models/trvae/trvae.py", line 9, in
from .losses import mse, mmd, zinb, nb
File "/home/jianrong/biosoft/scarches/scarches/models/trvae/losses.py", line 1, in
from scvi.distributions import NegativeBinomial
File "/home/jianrong/miniconda3/envs/py3.8/lib/python3.8/site-packages/scvi_tools-1.0.3-py3.8.egg/scvi/init.py", line 11, in
from . import autotune, data, model, external, utils, criticism
File "/home/jianrong/miniconda3/envs/py3.8/lib/python3.8/site-packages/scvi_tools-1.0.3-py3.8.egg/scvi/autotune/init.py", line 1, in
from ._manager import TuneAnalysis, TunerManager
File "/home/jianrong/miniconda3/envs/py3.8/lib/python3.8/site-packages/scvi_tools-1.0.3-py3.8.egg/scvi/autotune/_manager.py", line 11, in
from chex import dataclass
File "/home/jianrong/miniconda3/envs/py3.8/lib/python3.8/site-packages/chex-0.1.8-py3.8.egg/chex/init.py", line 17, in
from chex._src.asserts import assert_axis_dimension
File "/home/jianrong/miniconda3/envs/py3.8/lib/python3.8/site-packages/chex-0.1.8-py3.8.egg/chex/_src/asserts.py", line 26, in
from chex._src import asserts_internal as _ai
File "/home/jianrong/miniconda3/envs/py3.8/lib/python3.8/site-packages/chex-0.1.8-py3.8.egg/chex/_src/asserts_internal.py", line 34, in
from chex._src import pytypes
File "/home/jianrong/miniconda3/envs/py3.8/lib/python3.8/site-packages/chex-0.1.8-py3.8.egg/chex/_src/pytypes.py", line 19, in
import jax
File "/home/jianrong/miniconda3/envs/py3.8/lib/python3.8/site-packages/jax-0.4.14-py3.8.egg/jax/init.py", line 35, in
from jax import config as _config_module
File "/home/jianrong/miniconda3/envs/py3.8/lib/python3.8/site-packages/jax-0.4.14-py3.8.egg/jax/config.py", line 17, in
from jax._src.config import config # noqa: F401
File "/home/jianrong/miniconda3/envs/py3.8/lib/python3.8/site-packages/jax-0.4.14-py3.8.egg/jax/_src/config.py", line 27, in
from jax._src import lib
File "/home/jianrong/miniconda3/envs/py3.8/lib/python3.8/site-packages/jax-0.4.14-py3.8.egg/jax/_src/lib/init.py", line 44, in
minimum_jaxlib_version: str) -> tuple[int, ...]:
TypeError: 'type' object is not subscriptable

[Koncopd]

Hi, @jianrong0520 jax probably dropped support of python 3.8, you will need to try with 3.9 at least.

[jianrong0520]

Thanks, I would like to try it.

[erzakiev]

Hi, @jianrong0520 jax probably dropped support of python 3.8, you will need to try with 3.9 at least.

the official docs suggest using 3.7 or 3.8 though... confusion