update LossRecorder to LossOutput

[rpeys]

this makes mrVI code compatible with updated scvi-tools (see scvi-tools PR#1869 scverse/scvi-tools#1869)

[rpeys]

I was just looking back at this PR and realized that I accidentally included a second commit in the PR, [7f0b895] titled "handle no categorical_nuisance_keys." Only the first commit, efc5981, is needed to make the code compatible with the current scvi-tools.

The second commit handles the case where a user does not want to input any nuisance keys. With this update, if no nuisance keys are passed in, the code simply creates a vectors of zeros and treats those as the nuisance keys, which effectively has no impact on the learned latent space since there is only one category.

The one thing that I want to flag for update in the second commit is that you might have a more elegant way of moving this dummy vector onto the GPU. Currently, I just move it on to the same device that the gene expression data is on nuisance_oh = torch.zeros(x.shape[0], 1).to(x.device).

[SamuelCWJ]

Hi!

I'm getting this error when importing mrvi. Please may I know if I'm doing something wrong? I believe I have installed the latest version of both MrVI and scvi tools.

ImportError Traceback (most recent call last)
Cell In[2], line 1
----> 1 import mrvi

File ~/miniconda3/envs/test1/lib/python3.11/site-packages/mrvi/init.py:8
5 from rich.console import Console
6 from rich.logging import RichHandler
----> 8 from ._model import MrVI, MrVAE
10 # python-poetry/poetry#2366 (comment)
11 # python-poetry/poetry#144 (comment)
12 try:

File ~/miniconda3/envs/test1/lib/python3.11/site-packages/mrvi/_model.py:21
18 from scvi.model.base import UnsupervisedTrainingMixin
19 from scvi.model.base import BaseModelClass, VAEMixin
---> 21 from ._module import MrVAE
22 from ._constants import MRVI_REGISTRY_KEYS
24 logger = logging.getLogger(name)

File ~/miniconda3/envs/test1/lib/python3.11/site-packages/mrvi/_module.py:5
3 import torch.nn as nn
4 from scvi import REGISTRY_KEYS
----> 5 from scvi.module.base import BaseModuleClass, LossRecorder, auto_move_data
6 from scvi.nn import one_hot
7 from torch.distributions import kl_divergence as kl

ImportError: cannot import name 'LossRecorder' from 'scvi.module.base'

Any assistance would be much appreciated! Thank you!

[martinkim0]

Closing this in favor of #11.

[martinkim0]

@SamuelCWJ The PR I linked above should solve the error you're seeing. I'll be re-releasing after this merges.