TypeError: Can't instantiate abstract class SCGEN with abstract methods setup_anndata

[GGboy-Zzz]

I have been trying to merge multiple single cell data using scgen recently, but when I tried to run the tutorial, an error occurred，as follows,

TypeError Traceback (most recent call last)
in
1 scgen.SCGEN.setup_anndata(train, batch_key="batch", labels_key="cell_type")
----> 2 model = scgen.SCGEN(train)
3 model.save("/home/zhuyong/test_scgen/saved_models/model_batch_removal.pt", overwrite=True)

TypeError: Can't instantiate abstract class SCGEN with abstract methods setup_anndata
I referred to issue #53 #54 etc and confirmed that my scvi-tools version is 0.14.0. I even reinstalled version 0.13.0, but it still doesn't work. Do you have any good suggestions? @adamgayoso @M0hammadL

[Tigerrr07]

Hello, I encountered the same issue as you. I was able to solve it by following these steps:

1. Install scgen from the repo using the following commands:

conda create -n scgen-dev python=3.8 -y
pip install torch==1.12.0+cu102 torchvision==0.13.0+cu102 torchaudio==0.12.0 --extra-index-url https://download.pytorch.org/whl/cu102  # a given version of pytorch, here I use torch1.12.0+cu102
pip install git+https://github.com/theislab/scgen.git  # or git clone the repo and run pip install .

2. Modify train_new in the python code as follows::

train_new = train[~((train.obs["cell_type"] == "CD4T") &
                    (train.obs["condition"] == "stimulated"))].copy()

This solution worked for me and the tutorial. I hope it is helpful for you too!

[JeanRadig]

Instead of scgen.SCGEN.setup_anndata(train, batch_key="batch", labels_key="cell_type") write scgen.setup_anndata(train, batch_key="batch", labels_key="cell_type"). Remove SCGEN

[tjiyyanki1]

I get the same error with scvi-tools: 0.14.6 and scgen: 2.0.0.

from scvi.data import setup_anndata
setup_anndata(train, batch_key="batch", labels_key="cell_type")
model = scgen.SCGEN(train)
model.save("../saved_models/model_batch_removal.pt", overwrite=True)

---

TypeError Traceback (most recent call last)
/tmp/ipykernel_2283/288038477.py in
1 #from scvi.external import SCGEN
2 setup_anndata(train, batch_key="batch", labels_key="cell_type")
----> 3 model = scgen.SCGEN(train)
4 model.save("../saved_models/model_batch_removal.pt", overwrite=True)

TypeError: Can't instantiate abstract class SCGEN with abstract methods setup_anndata

[jnmaciuch]

Were you able to solve the problem @tjiyyanki1 ? I am getting the same error with scvi-tools 0.14.6 and scgen 2.0.0