---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
Cell In[27], line 1
----> 1 import scarches
File /opt/homebrew/Caskroom/mambaforge/base/envs/cellcharter_v3/lib/python3.8/site-packages/scarches/__init__.py:1
----> 1 from . import dataset, metrics, trainers, models, zenodo, plotting, utils, classifiers
3 __author__ = ', '.join([
4 'Mohammad Lotfollahi',
5 'Sergei Rybakov',
6 'Marco Wagenstetter',
7 'Mohsen Naghipourfar',
8 ])
10 __email__ = ', '.join([
11 'mohammad.lotfollahi@helmholtz-muenchen.de',
12 'sergei.rybakov@helmholtz-muenchen.de'
13 ])
File /opt/homebrew/Caskroom/mambaforge/base/envs/cellcharter_v3/lib/python3.8/site-packages/scarches/models/__init__.py:1
----> 1 from .trvae.trvae import trVAE
2 from .trvae.trvae_model import TRVAE
3 from .trvae.adaptors import Adaptor, attach_adaptors
File /opt/homebrew/Caskroom/mambaforge/base/envs/cellcharter_v3/lib/python3.8/site-packages/scarches/models/trvae/trvae.py:9
6 import torch.nn.functional as F
8 from .modules import Encoder, Decoder
----> 9 from .losses import mse, mmd, zinb, nb
10 from ._utils import one_hot_encoder
11 from ..base._base import CVAELatentsModelMixin
File /opt/homebrew/Caskroom/mambaforge/base/envs/cellcharter_v3/lib/python3.8/site-packages/scarches/models/trvae/losses.py:1
----> 1 from scvi.distributions import NegativeBinomial
2 import torch
3 from torch.autograd import Variable
File /opt/homebrew/Caskroom/mambaforge/base/envs/cellcharter_v3/lib/python3.8/site-packages/scvi/__init__.py:10
7 from ._settings import settings
9 # this import needs to come after prior imports to prevent circular import
---> 10 from . import autotune, data, model, external, utils
12 from importlib.metadata import version
14 package_name = "scvi-tools"
File /opt/homebrew/Caskroom/mambaforge/base/envs/cellcharter_v3/lib/python3.8/site-packages/scvi/autotune/__init__.py:1
----> 1 from ._manager import TuneAnalysis, TunerManager
2 from ._tuner import ModelTuner
3 from ._types import Tunable, TunableMixin
File /opt/homebrew/Caskroom/mambaforge/base/envs/cellcharter_v3/lib/python3.8/site-packages/scvi/autotune/_manager.py:22
20 from scvi._types import AnnOrMuData
21 from scvi.data._constants import _SETUP_ARGS_KEY, _SETUP_METHOD_NAME
---> 22 from scvi.model.base import BaseModelClass
23 from scvi.utils import InvalidParameterError
25 from ._defaults import COLORS, COLUMN_KWARGS, DEFAULTS, TUNABLE_TYPES
File /opt/homebrew/Caskroom/mambaforge/base/envs/cellcharter_v3/lib/python3.8/site-packages/scvi/model/__init__.py:2
1 from . import utils
----> 2 from ._amortizedlda import AmortizedLDA
3 from ._autozi import AUTOZI
4 from ._condscvi import CondSCVI
File /opt/homebrew/Caskroom/mambaforge/base/envs/cellcharter_v3/lib/python3.8/site-packages/scvi/model/_amortizedlda.py:7
5 import numpy as np
6 import pandas as pd
----> 7 import pyro
8 import torch
9 from anndata import AnnData
File /opt/homebrew/Caskroom/mambaforge/base/envs/cellcharter_v3/lib/python3.8/site-packages/pyro/__init__.py:4
1 # Copyright (c) 2017-2019 Uber Technologies, Inc.
2 # SPDX-License-Identifier: Apache-2.0
----> 4 import pyro.poutine as poutine
5 from pyro.infer.inspect import render_model
6 from pyro.logger import log
File /opt/homebrew/Caskroom/mambaforge/base/envs/cellcharter_v3/lib/python3.8/site-packages/pyro/poutine/__init__.py:4
1 # Copyright (c) 2017-2019 Uber Technologies, Inc.
2 # SPDX-License-Identifier: Apache-2.0
----> 4 from .handlers import (
5 block,
6 broadcast,
7 collapse,
8 condition,
9 do,
10 enum,
11 escape,
12 infer_config,
13 lift,
14 markov,
15 mask,
16 queue,
17 reparam,
18 replay,
19 scale,
20 seed,
21 substitute,
22 trace,
23 uncondition,
24 )
25 from .messenger import unwrap
26 from .runtime import NonlocalExit, get_mask
File /opt/homebrew/Caskroom/mambaforge/base/envs/cellcharter_v3/lib/python3.8/site-packages/pyro/poutine/handlers.py:71
68 from typing_extensions import ParamSpec
70 from pyro.poutine import util
---> 71 from pyro.poutine.block_messenger import BlockMessenger
72 from pyro.poutine.broadcast_messenger import BroadcastMessenger
73 from pyro.poutine.collapse_messenger import CollapseMessenger
File /opt/homebrew/Caskroom/mambaforge/base/envs/cellcharter_v3/lib/python3.8/site-packages/pyro/poutine/block_messenger.py:7
4 from functools import partial
5 from typing import TYPE_CHECKING, Callable, List, Optional
----> 7 from pyro.poutine.messenger import Messenger
9 if TYPE_CHECKING:
10 from pyro.poutine.runtime import Message
File /opt/homebrew/Caskroom/mambaforge/base/envs/cellcharter_v3/lib/python3.8/site-packages/pyro/poutine/messenger.py:19
7 from typing import (
8 Any,
9 Callable,
(...)
14 TypeVar,
15 )
17 from typing_extensions import ParamSpec, Self
---> 19 from pyro.poutine.runtime import _PYRO_STACK, Message
21 _P = ParamSpec("_P")
22 _T = TypeVar("_T")
File /opt/homebrew/Caskroom/mambaforge/base/envs/cellcharter_v3/lib/python3.8/site-packages/pyro/poutine/runtime.py:22
19 import torch
20 from typing_extensions import Literal, ParamSpec, TypedDict
---> 22 from pyro.params.param_store import ( # noqa: F401
23 _MODULE_NAMESPACE_DIVIDER,
24 ParamStoreDict,
25 )
27 _P = ParamSpec("_P")
28 _T = TypeVar("_T")
File /opt/homebrew/Caskroom/mambaforge/base/envs/cellcharter_v3/lib/python3.8/site-packages/pyro/params/__init__.py:4
1 # Copyright (c) 2017-2019 Uber Technologies, Inc.
2 # SPDX-License-Identifier: Apache-2.0
----> 4 from .param_store import (
5 module_from_param_with_module_name,
6 param_with_module_name,
7 user_param_name,
8 )
10 __all__ = [
11 "module_from_param_with_module_name",
12 "param_with_module_name",
13 "user_param_name",
14 ]
File /opt/homebrew/Caskroom/mambaforge/base/envs/cellcharter_v3/lib/python3.8/site-packages/pyro/params/param_store.py:21
19 import torch
20 from torch.distributions import constraints, transform_to
---> 21 from torch.serialization import MAP_LOCATION
22 from typing_extensions import TypedDict
25 class StateDict(TypedDict):
ImportError: cannot import name 'MAP_LOCATION' from 'torch.serialization' (/opt/homebrew/Caskroom/mambaforge/base/envs/cellcharter_v3/lib/python3.8/site-packages/torch/serialization.py)
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The installation is not working as expected, and I am not able to run tutorial imports correctly (especifically lightning).
I think that I am not able to get a stable env going, any help for a MacOS would be super appreciated :)
If I ignore that requirement, I can continue with the tutorial until:
Here I get that scarches is not installed
If i try
import scarchesthis happens:import scarches error
Here is my very long traceback of installing the environment:
https://gist.github.com/josenimo/b694b7edf7822ae0bbd9eac768ec294c
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